SimParameters.C

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/*****************************************************************************
 * $Source: /home/cvs/namd/cvsroot/namd2/src/SimParameters.C,v $
 * $Author: jim $
 * $Date: 2017/03/30 20:06:17 $
 * $Revision: 1.1478 $
 *****************************************************************************/

#include "InfoStream.h"
#include "ComputeNonbondedUtil.h"
#include "LJTable.h"
#include "ComputePme.h"
#include "ComputeCUDAMgr.h"
#include "ConfigList.h"
#include "SimParameters.h"
#include "ParseOptions.h"
#include "common.h"
#include "structures.h"
#include "Communicate.h"
#include "MStream.h"
#include "Output.h"
#include "PatchData.h"
#include <stdio.h>
#include <time.h>
#ifdef NAMD_TCL
#include <tcl.h> // needed to test version
#endif
#ifdef NAMD_FFTW
#ifdef NAMD_FFTW_3
#include <fftw3.h>
#else
// fftw2 doesn't have these defined
#define fftwf_malloc fftw_malloc
#define fftwf_free fftw_free
#ifdef NAMD_FFTW_NO_TYPE_PREFIX
#include <fftw.h>
#include <rfftw.h>
#else
#include <sfftw.h>
#include <srfftw.h>
#endif
#endif
#endif
#if defined(WIN32) && !defined(__CYGWIN__)
#include <direct.h>
#define CHDIR _chdir
#define MKDIR(X) mkdir(X)
#define PATHSEP '\\'
#define PATHSEPSTR "\\"
#else
#include <unistd.h>
#define CHDIR chdir
#define MKDIR(X) mkdir(X,0777)
#define PATHSEP '/'
#define PATHSEPSTR "/"
#endif
#include <fcntl.h>
#include <sys/stat.h>
#if defined(WIN32) && !defined(__CYGWIN__)
#include <io.h>
#define access(PATH,MODE) _access(PATH,00)
#endif
#include <fstream>
using namespace std;

#if defined(WIN32) && !defined(__CYGWIN__)
extern "C" {
  double erfc(double);
}
#endif

#include "strlib.h"    //  For strcasecmp and strncasecmp

//#ifdef NAMD_CUDA
//bool one_cuda_device_per_node();
//#endif
#include "DeviceCUDA.h"
#if defined(NAMD_CUDA) || defined(NAMD_HIP)
#if defined(WIN32) && !defined(__CYGWIN__)
#define __thread __declspec(thread)
#endif
extern __thread DeviceCUDA *deviceCUDA;
#endif

#ifdef NAMD_AVXTILES
// For "+notiles" commandline option to disable "Tiles" algorithm (BackEnd.C)
extern int avxTilesCommandLineDisable;
#endif

//#define DEBUGM
#include "Debug.h"

#define XXXBIGREAL 1.0e32


char* SimParameters::getfromparseopts(const char* name, char *outbuf) {
  if ( parseopts ) return parseopts->getfromptr(name,outbuf);
  else return 0;
}

int SimParameters::istrueinparseopts(const char* name) {
  if ( parseopts ) return parseopts->istruefromptr(name);
  else return -1;
}

int SimParameters::issetinparseopts(const char* name) {
  if ( parseopts ) return parseopts->issetfromptr(name);
  else return -1;
}


/************************************************************************/
/*                  */
/*      FUNCTION initialize_config_data      */
/*                  */
/*  This function is used by the master process to populate the     */
/*   simulation parameters from a ConfigList object that is passed to   */
/*   it.  Each parameter is checked to make sure that it has a value    */
/*   that makes sense, and that it doesn't conflict with any other      */
/*   values that have been given.          */
/*                  */
/************************************************************************/

void SimParameters::initialize_config_data(ConfigList *config, char *&cwd)

{

   parseopts = new ParseOptions;   //  Object to check consistency of config file
   ParseOptions &opts = *parseopts;

   config_parser(opts);

   if (!opts.check_consistency()) 
   {
      NAMD_die("Internal error in configuration file parser");
   }

   // Now, feed the object with the actual configuration options through the
   // ParseOptions file and make sure everything is OK
   if (!opts.set(*config)) 
   {
      NAMD_die("ERROR(S) IN THE CONFIGURATION FILE");
   }


   check_config(opts,config,cwd);

   print_config(opts,config,cwd);

}

/************************************************************************/
/*                                                                      */
/*      FUNCTION scriptSet                                              */
/*                                                                      */
/************************************************************************/

int atobool(const char *s) {
  return ( (! strncasecmp(s,"yes",8)) ||
           (! strncasecmp(s,"on",8)) || 
           (! strncasecmp(s,"true",8)) );
};
                         
void SimParameters::scriptSet(const char *param, const char *value) {

  if ( CkMyRank() ) return;

#define MAX_SCRIPT_PARAM_SIZE 128
#define SCRIPT_PARSE_BOOL(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atobool(value); return; } }
#define SCRIPT_PARSE_INT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atoi(value); return; } }
#define SCRIPT_PARSE_FLOAT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value); return; } }
#define SCRIPT_PARSE_MOD_FLOAT(NAME,VAR,MOD) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value) MOD; return; } }
#define SCRIPT_PARSE_VECTOR(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR).set(value); return; } }
#define SCRIPT_PARSE_STRING(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { strcpy(VAR,value); return; } }

  SCRIPT_PARSE_FLOAT("scriptArg1",scriptArg1)
  SCRIPT_PARSE_FLOAT("scriptArg2",scriptArg2)
  SCRIPT_PARSE_FLOAT("scriptArg3",scriptArg3)
  SCRIPT_PARSE_FLOAT("scriptArg4",scriptArg4)
  SCRIPT_PARSE_FLOAT("scriptArg5",scriptArg5)
  SCRIPT_PARSE_INT("scriptIntArg1",scriptIntArg1)
  SCRIPT_PARSE_INT("scriptIntArg2",scriptIntArg2)
  SCRIPT_PARSE_STRING("scriptStringArg1",scriptStringArg1)
  SCRIPT_PARSE_STRING("scriptStringArg2",scriptStringArg2)
  SCRIPT_PARSE_INT("numsteps",N)
  if ( ! strncasecmp(param,"firsttimestep",MAX_SCRIPT_PARAM_SIZE) ) {
    N = firstTimestep = atoi(value); return;
  }
  SCRIPT_PARSE_FLOAT("reassignTemp",reassignTemp)
  SCRIPT_PARSE_FLOAT("rescaleTemp",rescaleTemp)
  SCRIPT_PARSE_BOOL("velocityQuenching",minimizeOn)
  SCRIPT_PARSE_BOOL("maximumMove",maximumMove)
  // SCRIPT_PARSE_BOOL("Langevin",langevinOn)
  if ( ! strncasecmp(param,"Langevin",MAX_SCRIPT_PARAM_SIZE) ) {
    langevinOn = atobool(value);
    if ( langevinOn && ! langevinOnAtStartup ) {
      NAMD_die("Langevin must be enabled at startup to disable and re-enable in script.");
    }
    return;
  }
  SCRIPT_PARSE_FLOAT("langevinTemp",langevinTemp)
  SCRIPT_PARSE_BOOL("langevinBAOAB",langevin_useBAOAB) // [!!] Use the BAOAB integrator or not
  SCRIPT_PARSE_FLOAT("loweAndersenTemp",loweAndersenTemp) // BEGIN LA, END LA
  SCRIPT_PARSE_BOOL("stochRescale",stochRescaleOn)
  SCRIPT_PARSE_FLOAT("stochRescaleTemp",stochRescaleTemp)
  SCRIPT_PARSE_FLOAT("initialTemp",initialTemp)
  SCRIPT_PARSE_BOOL("useGroupPressure",useGroupPressure)
  SCRIPT_PARSE_BOOL("useFlexibleCell",useFlexibleCell)
  SCRIPT_PARSE_BOOL("useConstantArea",useConstantArea)
  SCRIPT_PARSE_BOOL("fixCellDims",fixCellDims)
  SCRIPT_PARSE_BOOL("fixCellDimX",fixCellDimX)
  SCRIPT_PARSE_BOOL("fixCellDimY",fixCellDimY)
  SCRIPT_PARSE_BOOL("fixCellDimZ",fixCellDimZ)
  SCRIPT_PARSE_BOOL("useConstantRatio",useConstantRatio)
  SCRIPT_PARSE_BOOL("LangevinPiston",langevinPistonOn)
  SCRIPT_PARSE_MOD_FLOAT("LangevinPistonTarget",
                        langevinPistonTarget,/PRESSUREFACTOR)
  SCRIPT_PARSE_FLOAT("LangevinPistonPeriod",langevinPistonPeriod)
  SCRIPT_PARSE_FLOAT("LangevinPistonDecay",langevinPistonDecay)
  SCRIPT_PARSE_FLOAT("LangevinPistonTemp",langevinPistonTemp)
  SCRIPT_PARSE_MOD_FLOAT("SurfaceTensionTarget",
                        surfaceTensionTarget,*(100.0/PRESSUREFACTOR))
  SCRIPT_PARSE_BOOL("BerendsenPressure",berendsenPressureOn)
  SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureTarget",
                        berendsenPressureTarget,/PRESSUREFACTOR)
  SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureCompressibility",
                        berendsenPressureCompressibility,*PRESSUREFACTOR)
  SCRIPT_PARSE_FLOAT("BerendsenPressureRelaxationTime",
                                berendsenPressureRelaxationTime)
  //MC pressure control
  if ( ! strncasecmp(param,"monteCarloPressureOn",MAX_SCRIPT_PARAM_SIZE) ) {
    monteCarloPressureOn = atobool(value);
    if ( monteCarloPressureOn && ! monteCarloPressureOnAtStartup ) {
      NAMD_die("Monte Carlo pressure control must be enabled at startup to disable and re-enable in script.");
    }
    return;
  }
  SCRIPT_PARSE_MOD_FLOAT("monteCarloPressureTarget",
                        monteCarloPressureTarget,/PRESSUREFACTOR)
  SCRIPT_PARSE_FLOAT("monteCarloTemp",monteCarloTemp)
  SCRIPT_PARSE_FLOAT("monteCarloAcceptanceRate",monteCarloAcceptanceRate)
  SCRIPT_PARSE_INT("monteCarloPressureFreq",monteCarloPressureFreq)
  SCRIPT_PARSE_INT("monteCarloAdjustmentFreq",monteCarloAdjustmentFreq)
  //
  SCRIPT_PARSE_FLOAT("constraintScaling",constraintScaling)
  SCRIPT_PARSE_FLOAT("consForceScaling",consForceScaling)
  SCRIPT_PARSE_BOOL("drudeHardWall",drudeHardWallOn)
  SCRIPT_PARSE_FLOAT("drudeBondConst",drudeBondConst)
  SCRIPT_PARSE_FLOAT("drudeBondLen",drudeBondLen)
  SCRIPT_PARSE_STRING("outputname",outputFilename)
  SCRIPT_PARSE_INT("computeEnergies", computeEnergies)
  SCRIPT_PARSE_INT("outputEnergies",outputEnergies)
  SCRIPT_PARSE_INT("outputEnergiesPrecision",outputEnergiesPrecision)
  SCRIPT_PARSE_STRING("restartname",restartFilename)
  SCRIPT_PARSE_INT("DCDfreq",dcdFrequency)
  if ( ! strncasecmp(param,"DCDfile",MAX_SCRIPT_PARAM_SIZE) ) { 
    close_dcdfile();  // *** implemented in Output.C ***
    strcpy(dcdFilename,value);
    return;
  }
  if ( ! strncasecmp(param,"velDCDfile",MAX_SCRIPT_PARAM_SIZE) ) { 
    close_veldcdfile();  // *** implemented in Output.C ***
    strcpy(velDcdFilename,value);
    return;
  }
  SCRIPT_PARSE_INT("globalMasterFrequency",globalMasterFrequency)
  SCRIPT_PARSE_BOOL("globalMasterScaleByFrequency",globalMasterScaleByFrequency)
  SCRIPT_PARSE_BOOL("globalMasterStaleForces",globalMasterStaleForces)
  SCRIPT_PARSE_STRING("tclBCArgs",tclBCArgs)
  SCRIPT_PARSE_VECTOR("eField",eField)
  SCRIPT_PARSE_FLOAT("eFieldFreq",eFieldFreq)
  SCRIPT_PARSE_FLOAT("eFieldPhase",eFieldPhase) 
  SCRIPT_PARSE_FLOAT("accelMDE",accelMDE) 
  SCRIPT_PARSE_FLOAT("accelMDalpha",accelMDalpha) 
  SCRIPT_PARSE_FLOAT("accelMDTE",accelMDTE) 
  SCRIPT_PARSE_FLOAT("accelMDTalpha",accelMDTalpha) 
  SCRIPT_PARSE_FLOAT("accelMDGSigma0P",accelMDGSigma0P) 
  SCRIPT_PARSE_FLOAT("accelMDGSigma0D",accelMDGSigma0D) 
  SCRIPT_PARSE_STRING("accelMDGRestartFile",accelMDGRestartFile)
  SCRIPT_PARSE_VECTOR("stirAxis",stirAxis)
  SCRIPT_PARSE_VECTOR("stirPivot",stirPivot)

  if ( ! strncasecmp(param,"CUDASOAintegrate",MAX_SCRIPT_PARAM_SIZE) || 
       ! strncasecmp(param,"GPUresident",MAX_SCRIPT_PARAM_SIZE) ) {
    if ( ! CUDASOAintegrateMode ) {
      NAMD_die("Can't modify CUDASOAintegrate when that mode was never enabled");
    }
    CUDASOAintegrate = atobool(value);
    return;
  }

  if ( ! strncasecmp(param,"mgridforcescale",MAX_SCRIPT_PARAM_SIZE) ) {
    NAMD_die("Can't yet modify mgridforcescale in a script");
    return;
  }
  if ( ! strncasecmp(param,"mgridforcevoff",MAX_SCRIPT_PARAM_SIZE) ) {
    NAMD_die("Can't yet modify mgridforcevoff in a script");
    return;
  }
   
  if ( ! strncasecmp(param,"fixedatoms",MAX_SCRIPT_PARAM_SIZE) ) {
    if ( ! fixedAtomsOn )
      NAMD_die("FixedAtoms may not be enabled in a script.");
    if ( ! fixedAtomsForces )
      NAMD_die("To use fixedAtoms in script first use fixedAtomsForces yes.");
    fixedAtomsOn = atobool(value);
    return;
  }

//fepb
  if ( ! strncasecmp(param,"alch",MAX_SCRIPT_PARAM_SIZE) ) {
    alchOn = atobool(value);
    if ( alchOn && ! alchOnAtStartup ) {
       NAMD_die("Alchemy must be enabled at startup to disable and re-enable in script.");
    }
    alchFepOn = alchOn && alchFepOnAtStartup;
    alchThermIntOn = alchOn && alchThermIntOnAtStartup;
    ComputeNonbondedUtil::select();
    if ( PMEOn ) ComputePmeUtil::select();
#if defined(NAMD_CUDA) || defined(NAMD_HIP)
#ifdef BONDED_CUDA
    if (bondedCUDA > 0) {
      ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateHostCudaAlchFlags();
      ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateKernelCudaAlchFlags();
    }
#endif // BONDED_CUDA
#endif // NAMD_CUDA
    return;
  }
  SCRIPT_PARSE_INT("alchEquilSteps",alchEquilSteps)

  if ( ! strncasecmp(param,"alchLambda",MAX_SCRIPT_PARAM_SIZE) ) {
    alchLambda = atof(value);
    if ( alchLambda < 0.0 || 1.0 < alchLambda ) {
      NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n");
    }
    ComputeNonbondedUtil::select();
#if defined(NAMD_CUDA) || defined(NAMD_HIP)
#ifdef BONDED_CUDA
    if (bondedCUDA > 0) {
      ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateHostCudaAlchLambdas();
      ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateKernelCudaAlchLambdas();
    }
#endif // BONDED_CUDA
#endif // NAMD_CUDA
    return;
  }

  if ( ! strncasecmp(param,"alchLambda2",MAX_SCRIPT_PARAM_SIZE) ) {
    alchLambda2 = atof(value);
    if ( alchLambda2 < 0.0 || 1.0 < alchLambda2 ) {
      NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n");
    }
    ComputeNonbondedUtil::select();
#if defined(NAMD_CUDA) || defined(NAMD_HIP)
#ifdef BONDED_CUDA
    if (bondedCUDA > 0) {
      ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateHostCudaAlchLambdas();
      ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateKernelCudaAlchLambdas();
    }
#endif // BONDED_CUDA
#endif // NAMD_CUDA
    return;
  }

  if ( ! strncasecmp(param,"alchLambdaIDWS",MAX_SCRIPT_PARAM_SIZE) ) {
    alchLambdaIDWS = atof(value);
    setupIDWS();
    ComputeNonbondedUtil::select();
#ifdef NAMD_CUDA
#ifdef BONDED_CUDA
    if (bondedCUDA > 0) {
      ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateHostCudaAlchLambdas();
      ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateKernelCudaAlchLambdas();
    }
#endif // BONDED_CUDA
#endif // NAMD_CUDA
    return;
  }

  if ( ! strncasecmp(param,"alchLambdaFreq",MAX_SCRIPT_PARAM_SIZE) ) {
    alchLambdaFreq = atoi(value);
    if ( alchLambdaIDWS >= 0 ) {
      NAMD_die("alchLambdaIDWS and alchLambdaFreq are not compatible.\n");
    }
    ComputeNonbondedUtil::select();
#ifdef NAMD_CUDA
#ifdef BONDED_CUDA
    if (bondedCUDA > 0) {
      ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateHostCudaAlchLambdas();
      ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateKernelCudaAlchLambdas();
    }
#endif // BONDED_CUDA
#endif // NAMD_CUDA
    return;
  }
//fepe

  if ( ! strncasecmp(param,"nonbondedScaling",MAX_SCRIPT_PARAM_SIZE) ) {
    nonbondedScaling = atof(value);
    ComputeNonbondedUtil::select();
    return;
  }

  if ( ! strncasecmp(param,"commOnly",MAX_SCRIPT_PARAM_SIZE) ) {
    commOnly = atobool(value);
    ComputeNonbondedUtil::select();
    return;
  }

  // REST2 - We don't have to make any changes to ComputeNonbondedUtil
  // other than recalculating the LJTable.  Skip doing the other stuff.
  if ( ! strncasecmp(param,"soluteScalingFactor",MAX_SCRIPT_PARAM_SIZE)) {
    if (!soluteScalingOn) {
      NAMD_die("Cannot set solute scaling factor when soluteScaling is off\n");
    }
    soluteScalingFactor = atof(value);
    if (soluteScalingFactor < 0.0) {
      NAMD_die("Solute scaling factor should be non-negative\n");
    }
    soluteScalingFactorCharge = soluteScalingFactor;
    soluteScalingFactorVdw = soluteScalingFactor;
    // update LJTable for CPU
    ComputeNonbondedUtil::select();
#if defined(NAMD_CUDA) || defined(NAMD_HIP)
    // update LJTable for GPU, needs CPU update first
    ComputeCUDAMgr::getComputeCUDAMgr()->update();
#endif
    return;
  }
  if ( ! strncasecmp(param,"soluteScalingFactorVdw",MAX_SCRIPT_PARAM_SIZE)) {
    soluteScalingFactorVdw = atof(value);
    if (soluteScalingFactorVdw < 0.0) {
      NAMD_die("Solute scaling factor for van der Waals "
          "should be non-negative\n");
    }
    // update LJTable for CPU
    ComputeNonbondedUtil::select();
#if defined(NAMD_CUDA) || defined(NAMD_HIP)
    // update LJTable for GPU, needs CPU update first
    ComputeCUDAMgr::getComputeCUDAMgr()->update();
#endif
    return;
  }
  if ( ! strncasecmp(param,"soluteScalingFactorCharge",MAX_SCRIPT_PARAM_SIZE)) {
    soluteScalingFactorCharge = atof(value);
    if (soluteScalingFactorCharge < 0.0) {
      NAMD_die("Solute scaling factor for electrostatics "
          "should be non-negative\n");
    }
    return;
  }

  char *error = new char[2 * MAX_SCRIPT_PARAM_SIZE + 100];
  sprintf(error,"Setting parameter %s from script failed!\n",param);
  NAMD_die(error);

}

void SimParameters::nonbonded_select() {
    ComputeNonbondedUtil::select();
}

void SimParameters::pme_select() {
  ComputePmeUtil::select();
}

/************************************************************************/
/*                                                                      */
/*      FUNCTION config_parser                                          */
/*                                                                      */
/************************************************************************/
                         
void SimParameters::config_parser(ParseOptions &opts) {

   //  Set all variable to fallback default values.  This is not really
   //  necessary, as we give default values when we set up the ParseOptions
   //  object, but it helps the debuggers figure out we've initialized the
   //  variables.
   HydrogenBonds = FALSE;
   useAntecedent = TRUE;
   aaAngleExp = 2;
   haAngleExp = 4;
   distAttExp = 4;
   distRepExp = 6;
   dhaCutoffAngle = 100.0;
   dhaOnAngle = 60.0;
   dhaOffAngle = 80.0;
   daCutoffDist = 7.5;
   daOnDist = 5.5;
   daOffDist = 6.5;

   config_parser_basic(opts);
   config_parser_fileio(opts);
   config_parser_fullelect(opts);
   config_parser_methods(opts);
   config_parser_constraints(opts);
   #ifdef OPENATOM_VERSION
   config_parser_openatom(opts);
   #endif // OPENATOM_VERSION

   config_parser_gridforce(opts);
   config_parser_mgridforce(opts);
   config_parser_group_restraints(opts);
   config_parser_dcd_selections(opts);
   config_parser_movdrag(opts);
   config_parser_rotdrag(opts);
   config_parser_constorque(opts);
   config_parser_boundary(opts);
   config_parser_misc(opts);

}

void SimParameters::config_parser_basic(ParseOptions &opts) {
   
   //  So first we set up the ParseOptions objects so that it will check
   //  all of the logical rules that the configuration file must follow.

   opts.optional("main", "obsolete", "used to flag obsolete options",
    PARSE_STRING);

   opts.require("main", "timestep", "size of the timestep, in fs",
    &dt, 1.0);
   opts.range("timestep", NOT_NEGATIVE);
   opts.units("timestep", N_FSEC);

   opts.optional("main", "numsteps", "number of timesteps to perform",
    &N,0);
   opts.range("numsteps", NOT_NEGATIVE);

   opts.optional("main", "stepspercycle",
      "Number of steps between atom migrations", 
      &stepsPerCycle, 20);
   opts.range("stepspercycle", POSITIVE);

   opts.require("main", "cutoff", "local electrostatic and Vdw distance", 
      &cutoff);
   opts.range("cutoff", POSITIVE);
   opts.units("cutoff", N_ANGSTROM);
   
   opts.optional("main", "nonbondedScaling", "nonbonded scaling factor",
     &nonbondedScaling, 1.0);
   opts.range("nonbondedScaling", NOT_NEGATIVE);

   opts.optional("main", "limitDist", "limit nonbonded below this distance",
     &limitDist, 0.0);
   opts.range("limitDist", NOT_NEGATIVE);

   opts.require("main", "exclude", "Electrostatic and VDW exclusion policy",
    PARSE_STRING);

   opts.optional("exclude", "1-4scaling", "1-4 electrostatic scaling factor",
     &scale14, 1.0);
   opts.range("1-4scaling", POSITIVE);

   opts.optional("exclude", "oneFourScaling", "1-4 electrostatic scaling factor",
     &scale14alt);
   opts.range("oneFourScaling", POSITIVE);

   opts.optionalB("main", "switching",
     "Should a smoothing function be used?", &switchingActive, TRUE);
   
   opts.optionalB("switching", "vdwForceSwitching",
     "Use force switching for vdw?", &vdwForceSwitching, FALSE);
   
   opts.optional("switching", "switchdist",
     "Distance for switching function activation",
     &switchingDist);
   opts.range("switchdist", POSITIVE);
   opts.units("switchdist", N_ANGSTROM);
   
   opts.optionalB("main", "martiniSwitching",
     "Use Martini residue-based coarse-grain switching?", &martiniSwitching, FALSE);
   opts.optionalB("main", "martiniDielAllow",
     "Allow use of dielectric != 15.0 when using Martini", &martiniDielAllow, FALSE);

   opts.optional("main", "pairlistdist",  "Pairlist inclusion distance",
     &pairlistDist);
   opts.range("pairlistdist", POSITIVE);
   opts.units("pairlistdist", N_ANGSTROM);

   opts.optional("main", "pairlistMinProcs",  "Min procs for pairlists",
     &pairlistMinProcs,1);
   opts.range("pairlistMinProcs", POSITIVE);

   opts.optional("main", "pairlistsPerCycle",  "regenerate x times per cycle",
     &pairlistsPerCycle,2);
   opts.range("pairlistsPerCycle", POSITIVE);

   opts.optional("main", "outputPairlists", "how often to print warnings",
     &outputPairlists, 0);
   opts.range("outputPairlists", NOT_NEGATIVE);

   opts.optional("main", "pairlistShrink",  "tol *= (1 - x) on regeneration",
     &pairlistShrink,0.01);
   opts.range("pairlistShrink", NOT_NEGATIVE);

   opts.optional("main", "pairlistGrow",  "tol *= (1 + x) on trigger",
     &pairlistGrow, 0.01);
   opts.range("pairlistGrow", NOT_NEGATIVE);

   opts.optional("main", "pairlistTrigger",  "trigger is atom > (1 - x) * tol",
     &pairlistTrigger, 0.3);
   opts.range("pairlistTrigger", NOT_NEGATIVE);

   opts.optional("main", "temperature", "initial temperature",
     &initialTemp);
   opts.range("temperature", NOT_NEGATIVE);
   opts.units("temperature", N_KELVIN);

   opts.optionalB("main", "COMmotion", "allow initial center of mass movement",
      &comMove, FALSE);

   opts.optionalB("main", "zeroMomentum", "constrain center of mass",
      &zeroMomentum, FALSE);
   opts.optionalB("zeroMomentum", "zeroMomentumAlt", "constrain center of mass",
      &zeroMomentumAlt, FALSE);

   opts.optionalB("main", "wrapWater", "wrap waters around periodic boundaries on output",
      &wrapWater, FALSE);
   opts.optionalB("main", "wrapAll", "wrap all clusters around periodic boundaries on output",
      &wrapAll, FALSE);
   opts.optionalB("main", "wrapNearest", "wrap to nearest image to cell origin",
      &wrapNearest, FALSE);

   opts.optional("main", "dielectric", "dielectric constant",
     &dielectric, 1.0);
   opts.range("dielectric", POSITIVE); // Hmmm, dielectric < 1 ...

   opts.optional("main", "margin", "Patch width margin", &margin, XXXBIGREAL);
   opts.range("margin", NOT_NEGATIVE);
   opts.units("margin", N_ANGSTROM);

   opts.optional("main", "seed", "Initial random number seed", &randomSeed);
   opts.range("seed", POSITIVE);

   opts.optional("main", "outputEnergies", "How often to print energies in timesteps",
     &outputEnergies, 1);
   opts.range("outputEnergies", POSITIVE);

   opts.optional("main", "outputEnergiesPrecision", "Output energy precision",
     &outputEnergiesPrecision, 4);
   opts.range("outputEnergiesPrecision", POSITIVE);

   opts.optional("main", "computeEnergies", "How often to evaluate energies in timesteps",
     &computeEnergies);
   opts.range("computeEnergies", POSITIVE);

   opts.optional("main", "outputMomenta", "How often to print linear and angular momenta in timesteps",
     &outputMomenta, 0);
   opts.range("outputMomenta", NOT_NEGATIVE);
     
   opts.optional("main", "outputTiming", "How often to print timing data in timesteps",
     &outputTiming);
   opts.range("outputTiming", NOT_NEGATIVE);

   opts.optionalB("main", "outputPerformance",
       "Print performance statistics on \"outputTiming\" steps",
       &outputPerformance, TRUE);
   opts.optional("main", "benchmarkTime",
       "Perform benchmark simulation stopping after some number of seconds",
       &benchmarkTime, 0);

   opts.optional("main", "outputCudaTiming", "How often to print CUDA timing data in timesteps",
     &outputCudaTiming, 0);
   opts.range("outputCudaTiming", NOT_NEGATIVE);
     
   opts.optional("main", "outputPressure", "How often to print pressure data in timesteps",
     &outputPressure, 0);
   opts.range("outputPressure", NOT_NEGATIVE);
     
   opts.optionalB("main", "mergeCrossterms", "merge crossterm energy with dihedral when printing?",
      &mergeCrossterms, TRUE);

   opts.optional("main", "MTSAlgorithm", "Multiple timestep algorithm",
    PARSE_STRING);

   opts.optional("main", "longSplitting", "Long range force splitting option",
    PARSE_STRING);

   opts.optionalB("main", "ignoreMass", "Do not use masses to find hydrogen atoms",
    &ignoreMass, FALSE);

   opts.optional("main", "splitPatch", "Atom into patch splitting option",
    PARSE_STRING);
   opts.optional("main", "hgroupCutoff", "Hydrogen margin", &hgroupCutoff, 2.5);

   opts.optional("main", "extendedSystem",
    "Initial configuration of extended system variables and periodic cell",
    PARSE_STRING);

   opts.optional("main", "cellBasisVector1", "Basis vector for periodic cell",
    &cellBasisVector1);
   opts.optional("main", "cellBasisVector2", "Basis vector for periodic cell",
    &cellBasisVector2);
   opts.optional("main", "cellBasisVector3", "Basis vector for periodic cell",
    &cellBasisVector3);
   opts.optional("main", "cellOrigin", "Fixed center of periodic cell",
    &cellOrigin);

   opts.optionalB("main", "molly", "Rigid bonds to hydrogen",&mollyOn,FALSE);
   opts.optional("main", "mollyTolerance", "Error tolerance for MOLLY",
                 &mollyTol, 0.00001);
   opts.optional("main", "mollyIterations", 
                 "Max number of iterations for MOLLY", &mollyIter, 100);

   opts.optional("main", "rigidBonds", "Rigid bonds to hydrogen",PARSE_STRING);
   opts.optional("main", "rigidTolerance", 
                 "Error tolerance for rigid bonds to hydrogen",
                 &rigidTol, 1.0e-8);
   opts.optional("main", "rigidIterations", 
                 "Max number of SHAKE iterations for rigid bonds to hydrogen",
                 &rigidIter, 100);
   opts.optionalB("main", "rigidDieOnError", 
                 "Die if rigidTolerance is not achieved after rigidIterations",
                 &rigidDie, TRUE);
   opts.optionalB("main", "useSettle",
                  "Use the SETTLE algorithm for rigid waters",
                 &useSettle, TRUE);

   opts.optional("main", "nonbondedFreq", "Nonbonded evaluation frequency",
    &nonbondedFrequency, 1);
   opts.range("nonbondedFreq", POSITIVE);

   opts.optionalB("main", "outputPatchDetails", "print number of atoms in each patch",
      &outputPatchDetails, FALSE);
   opts.optionalB("main", "staticAtomAssignment", "never migrate atoms",
      &staticAtomAssignment, FALSE);
   opts.optionalB("main", "replicaUniformPatchGrids", "same patch grid size on all replicas",
      &replicaUniformPatchGrids, FALSE);
#ifndef MEM_OPT_VERSION
   // in standard (non-mem-opt) version, enable lone pairs by default
   // for compatibility with recent force fields
   opts.optionalB("main", "lonePairs", "Enable lone pairs", &lonepairs, TRUE);
#else
   // in mem-opt version, disable lone pairs by default
   // because they are not supported
   opts.optionalB("main", "lonePairs", "Enable lone pairs", &lonepairs, FALSE);
#endif
   opts.optional("main", "waterModel", "Water model to use", PARSE_STRING);

   // experimental feature to disable exclusion checksum mismatch
   opts.optionalB("main", "ignoreExclusionChecksum",
       "Ignore exclusion checksum mismatch for explicitly defined "
       "exclusions between atoms that might exceed the cutoff distance",
       &ignoreExclusionChecksum, FALSE);

   opts.optionalB("main", "LJcorrection", "Apply analytical tail corrections for energy and virial", &LJcorrection, FALSE);
   opts.optionalB("main", "LJcorrectionAlt", "Apply alternative analytical tail corrections for energy and virial", &LJcorrectionAlt, FALSE);
   // XXX label "SOAintegrate" as experimental
   // SOA integration routine for higher performance
   opts.optionalB("main", "SOAintegrate", "Use SOA integration routine",
       &SOAintegrateOn, FALSE);
   // CUDA SOA integration routine for higher performance
   opts.optionalB("main", "CUDASOAintegrate", "Use CUDA SOA integration routine",
       &CUDASOAintegrateMode, FALSE);
   // New user parameter to replace CUDASOAintegrate
   opts.optionalB("main", "GPUresident", "Use GPU-resident mode",
       &GPUresidentMode);
   opts.optionalB("main", "GPUresidentSingleProcess", "Use GPU-resident single-process mode",
       &GPUresidentSingleProcessMode, TRUE);
   // Expected to have GPU-resident mode enabled
   opts.optional("main", "movingAverageWindowSize", 
       "Window size for moving averages of reductions for GPUresident",
       &movingAverageWindowSize, 20);
   opts.optionalB("main", "nsPerDay", "Prints sampling rate in ns/day instead of days/ns",
       &nsPerDayOn, FALSE);
#ifdef TIMER_COLLECTION
   opts.optional("main", "TimerBinWidth",
       "Bin width of timer histogram collection in microseconds",
       &timerBinWidth, 1.0);
#endif
#if defined(NAMD_NVTX_ENABLED) || defined(NAMD_CMK_TRACE_ENABLED) || defined(NAMD_ROCTX_ENABLED)
   // default NVTX or Projections profiling is up to the first 1000 patches
   opts.optional("main", "beginEventPatchID","Beginning patch ID for profiling",
       &beginEventPatchID, 0);
   opts.optional("main", "endEventPatchID", "Ending patch ID for profiling",
       &endEventPatchID, 5000);
   // default NVTX or Projections profiling is up to the first 1000 time steps
   opts.optional("main", "beginEventStep", "Beginning time step for profiling",
       &beginEventStep, 0);
   opts.optional("main", "endEventStep", "Ending time step for profiling",
       &endEventStep, 1000);
#endif
   opts.optionalB("main", "mshake", "Using MSHAKE for rigid bond constraints",
       &mshakeOn, FALSE);
   opts.optionalB("main", "lincs", "Using LINCS for rigid bond constrainsts", 
       &lincsOn, FALSE);

   opts.optionalB("main", "CUDAForceTable", "Always use force table interpolation for nonbonded CUDA kernel",
       &useCUDANonbondedForceTable, TRUE);
   opts.optionalB("main", "GPUForceTable", "Always use force table interpolation for nonbonded GPU kernel",
       &useGPUNonbondedForceTable);

   opts.optionalB("main", "DeviceMigration", "Perform migration on the device",
       &useDeviceMigration, FALSE);
   opts.optionalB("main", "GPUAtomMigration", "Perform atom migration on GPU",
       &useGPUAtomMigration);
   opts.optionalB("main", "UpdateAtomMap", "Update the atom map when using GPU migration",
       &updateAtomMap, FALSE);
}

void SimParameters::config_parser_fileio(ParseOptions &opts) {
   

   opts.optional("main", "cwd", "current working directory", PARSE_STRING);

// In order to include AMBER options, "coordinates", "structure"
// and "parameters" are now optional, not required. The presence
// of them will be checked later in check_config()

//   opts.require("main", "coordinates", "initial PDB coordinate file",
//    PARSE_STRING);
   opts.optional("main", "coordinates", "initial PDB coordinate file",
    PARSE_STRING);

   opts.optional("main", "velocities",
     "initial velocities, given as a PDB file", PARSE_STRING);
   opts.optional("main", "binvelocities",
     "initial velocities, given as a binary restart", PARSE_STRING);
   opts.optional("main", "bincoordinates",
     "initial coordinates in a binary restart file", PARSE_STRING);
#ifdef MEM_OPT_VERSION
   opts.optional("main", "binrefcoords",
     "reference coordinates in a binary restart file", PARSE_STRING);
#endif

//   opts.require("main", "structure", "initial PSF structure file",
//    PARSE_STRING);
   opts.optional("main", "structure", "initial PSF structure file",
    PARSE_STRING);   

//   opts.require("main", "parameters",
//"CHARMm 19 or CHARMm 22 compatable force field file (multiple "
//"inputs allowed)", PARSE_MULTIPLES);
   opts.optional("main", "parameters",
"CHARMm 19 or CHARMm 22 compatable force field file (multiple "
"inputs allowed)", PARSE_MULTIPLES);


   //****** BEGIN CHARMM/XPLOR type changes
   opts.optionalB("parameters", "paraTypeXplor", "Parameter file in Xplor format?", &paraTypeXplorOn, FALSE);
   opts.optionalB("parameters", "paraTypeCharmm", "Parameter file in Charmm format?", &paraTypeCharmmOn, FALSE); 
   //****** END CHARMM/XPLOR type changes

   // Ported by JLai -- JE - Go parameters
   opts.optionalB("main", "GromacsPair", "Separately calculate pair interactions", &goGroPair, FALSE);
   opts.optionalB("main", "GoForcesOn", "Go forces will be calculated", &goForcesOn, FALSE);
   opts.require("GoForcesOn", "GoParameters", "Go parameter file", goParameters);
   opts.require("GoForcesOn", "GoCoordinates", "target coordinates for Go forces", goCoordinates);
   // Added by JLai -- Go-method parameter -- switches between using the matrix and sparse matrix representations [6.3.11] 
   //   opts.optional("GoForcesOn", "GoMethod", "Which type of matrix should be used to store Go contacts?", &goMethod);
   // Added by JLai -- Go-method parameter [8.2.11]
   //opts.optional("GoForcesOn", "GoMethod", "Which type of matrix should be used to store Go contacts?", PARSE_STRING); 
   opts.require("GoForcesOn", "GoMethod", "Which type of matrix should be used to store Go contacts?", PARSE_STRING); 
  // End of Port -- JL
   
   opts.require("main", "outputname",
    "prefix for the final PDB position and velocity filenames", 
    outputFilename);

   opts.optional("main", "auxFile", "Filename for data stream output",
     auxFilename);

   opts.optional("main", "numinputprocs", "Number of pes to use for parallel input", 
                 &numinputprocs, 0);
   opts.range("numinputprocs", NOT_NEGATIVE);

   opts.optional("main", "numoutputprocs", "Number of pes to use for parallel output", 
                 &numoutputprocs, 0);
   opts.range("numoutputprocs", NOT_NEGATIVE);
   opts.optional("main", "numoutputwriters", "Number of output processors that simultaneously write to an output file", 
                 &numoutputwrts, 1);
   opts.range("numoutputwriters", NOT_NEGATIVE);

   opts.optional("main", "DCDfreq", "Frequency of DCD trajectory output, in "
    "timesteps", &dcdFrequency, 0);
   opts.range("DCDfreq", NOT_NEGATIVE);
   opts.optional("DCDfreq", "DCDfile", "DCD trajectory output file name",
     dcdFilename);
   opts.optionalB("DCDfreq", "DCDunitcell", "Store unit cell in dcd timesteps?",
       &dcdUnitCell);

   opts.optional("main", "velDCDfreq", "Frequency of velocity "
    "DCD output, in timesteps", &velDcdFrequency, 0);
   opts.range("velDCDfreq", NOT_NEGATIVE);
   opts.optional("velDCDfreq", "velDCDfile", "velocity DCD output file name",
     velDcdFilename);
   
   opts.optional("main", "forceDCDfreq", "Frequency of force"
    "DCD output, in timesteps", &forceDcdFrequency, 0);
   opts.range("forceDCDfreq", NOT_NEGATIVE);
   opts.optional("forceDCDfreq", "forceDCDfile", "force DCD output file name",
     forceDcdFilename);
   
   opts.optional("main", "XSTfreq", "Frequency of XST trajectory output, in "
    "timesteps", &xstFrequency, 0);
   opts.range("XSTfreq", NOT_NEGATIVE);
   opts.optional("XSTfreq", "XSTfile", "Extended sytem trajectory output "
    "file name", xstFilename);

   opts.optional("main", "restartfreq", "Frequency of restart file "
    "generation", &restartFrequency, 0);
   opts.range("restartfreq", NOT_NEGATIVE);
   opts.optional("restartfreq", "restartname", "Prefix for the position and "
     "velocity PDB files used for restarting", restartFilename);
   opts.optionalB("restartfreq", "restartsave", "Save restart files with "
     "unique filenames rather than overwriting", &restartSave, FALSE);
   opts.optionalB("restartfreq", "restartsavedcd", "Save DCD files with "
     "unique filenames at each restart", &restartSaveDcd, FALSE);

   opts.optionalB("restartfreq", "binaryrestart", "Specify use of binary restart files ", 
       &binaryRestart, TRUE);

   opts.optional("main", "crashOutputFlag",
                 "Flag of saving atom positions and velocities in case of crashing", &crashOutputFlag, NAMD_CRASH_ALL);
   opts.optional("crashOutputFlag", "crashFile",
                 "Positions and velocities output file when crashing", crashFilename);

   opts.optionalB("outputname", "binaryoutput", "Specify use of binary output files ", 
       &binaryOutput, TRUE);

   opts.optionalB("main", "amber", "Is it AMBER force field?",
       &amberOn, FALSE);
   opts.optionalB("amber", "oldParmReader", "Use the old AMBER parm/parm7 reader?", &oldParmReader, FALSE);
   opts.optionalB("amber", "readexclusions", "Read exclusions from parm file?",
       &readExclusions, TRUE);
   opts.require("amber", "scnb", "1-4 VDW interactions are divided by scnb",
       &vdwscale14, 2.0);
   opts.require("amber", "parmfile", "AMBER parm file", PARSE_STRING);
   opts.optional("amber", "ambercoor", "AMBER coordinate file", PARSE_STRING);

   /* GROMACS options */
   opts.optionalB("main", "gromacs", "Use GROMACS-like force field?",
       &gromacsOn, FALSE);
   opts.require("gromacs", "grotopfile", "GROMACS topology file",
                PARSE_STRING);
   opts.optional("gromacs", "grocoorfile","GROMACS coordinate file",
                 PARSE_STRING);

  // OPLS options
   opts.optionalB("main", "vdwGeometricSigma",
       "Use geometric mean to combine L-J sigmas, as for OPLS",
       &vdwGeometricSigma, FALSE);

   // load/store computeMap
   opts.optional("main", "computeMapFile", "Filename for computeMap",
     computeMapFilename);
   opts.optionalB("main", "storeComputeMap", "store computeMap?",
       &storeComputeMap, FALSE);
   opts.optionalB("main", "loadComputeMap", "load computeMap?",
       &loadComputeMap, FALSE);
}

void SimParameters::config_parser_fullelect(ParseOptions &opts) {
   
#ifdef DPMTA
   DebugM(1,"DPMTA setup start\n");
   //  PMTA is included, so really get these values
   opts.optionalB("main", "FMA", "Should FMA be used?", &FMAOn, FALSE);
   opts.optional("FMA", "FMALevels", "Tree levels to use in FMA", &FMALevels,
     5);
   opts.range("FMALevels", POSITIVE);
   opts.optional("FMA", "FMAMp", "Number of FMA multipoles", &FMAMp, 8);
   opts.range("FMAMp", POSITIVE);
   opts.optionalB("FMA", "FMAFFT", "Use FFT enhancement in FMA?", &FMAFFTOn, TRUE);
   opts.optional("FMAFFT", "FMAFFTBlock", "FFT blocking factor",
    &FMAFFTBlock, 4);
   opts.range("FMAFFTBlock", POSITIVE);
   DebugM(1,"DPMTA setup end\n");
#else
   //  PMTA is NOT included.  So just set all the values to 0.
   FMAOn = FALSE;
   FMALevels = 0;
   FMAMp = 0;
   FMAFFTOn = FALSE;
   FMAFFTBlock = 0;
#endif

   opts.optional("main", "fullElectFrequency",
      "Number of steps between full electrostatic executions", 
      &fullElectFrequency);
   opts.range("fullElectFrequency", POSITIVE);

   opts.optional("main", "fullDispersionFrequency",
      "Number of steps between full LJ dispersion executions", 
      &fullDispersionFrequency, 1); // Default is every steps
   opts.range("fullDispersionFrequency", POSITIVE);

   //  USE OF THIS PARAMETER DISCOURAGED
   opts.optional("main", "fmaFrequency",
      "Number of steps between full electrostatic executions", 
      &fmaFrequency);
   opts.range("fmaFrequency", POSITIVE);

   opts.optional("main", "fmaTheta",
      "FMA theta parameter value", 
      &fmaTheta,0.715);
   opts.range("fmaTheta", POSITIVE);

   opts.optionalB("main", "FullDirect", "Should direct calculations of full electrostatics be performed?",
      &fullDirectOn, FALSE);



   opts.optionalB("main", "MSM",
       "Use multilevel summation method for electrostatics?",
       &MSMOn, FALSE);
   opts.optional("MSM", "MSMQuality", "MSM quality",
       &MSMQuality, 0);
   opts.optional("MSM", "MSMApprox", "MSM approximation",
       &MSMApprox, 0);
   opts.optional("MSM", "MSMSplit", "MSM splitting",
       &MSMSplit, 0);
   opts.optional("MSM", "MSMLevels", "MSM maximum number of levels",
       &MSMLevels, 0);  // set to 0 adapts to as many as needed
   opts.optional("MSM", "MSMGridSpacing", "MSM grid spacing (Angstroms)",
       &MSMGridSpacing, 2.5);
   opts.optional("MSM", "MSMPadding", "MSM padding (Angstroms)",
       &MSMPadding, 2.5);
   opts.optional("MSM", "MSMxmin", "MSM x minimum (Angstroms)", &MSMxmin, 0);
   opts.optional("MSM", "MSMxmax", "MSM x maximum (Angstroms)", &MSMxmax, 0);
   opts.optional("MSM", "MSMymin", "MSM y minimum (Angstroms)", &MSMymin, 0);
   opts.optional("MSM", "MSMymax", "MSM y maximum (Angstroms)", &MSMymax, 0);
   opts.optional("MSM", "MSMzmin", "MSM z minimum (Angstroms)", &MSMzmin, 0);
   opts.optional("MSM", "MSMzmax", "MSM z maximum (Angstroms)", &MSMzmax, 0);
   opts.optional("MSM", "MSMBlockSizeX",
       "MSM grid block size along X direction (for decomposing parallel work)",
       &MSMBlockSizeX, 8);
   opts.optional("MSM", "MSMBlockSizeY",
       "MSM grid block size along Y direction (for decomposing parallel work)",
       &MSMBlockSizeY, 8);
   opts.optional("MSM", "MSMBlockSizeZ",
       "MSM grid block size along Z direction (for decomposing parallel work)",
       &MSMBlockSizeZ, 8);

   opts.optionalB("MSM", "MsmSerial",
       "Use MSM serial version for long-range calculation?",
       &MsmSerialOn, FALSE);



   opts.optionalB("main", "FMM",
       "Use fast multipole method for electrostatics?",
       &FMMOn, FALSE);
   opts.optional("FMM", "FMMLevels", "FMM number of levels",
       &FMMLevels, 0);
   opts.optional("FMM", "FMMPadding", "FMM padding margin (Angstroms)",
       &FMMPadding, 0);


   opts.optionalB("main", "LJPME", "Use particle mesh Ewald for LJ dispersion?",
        &LJPMEOn, FALSE);
   opts.optional("LJPME", "LJPMETolerance", "LJ-PME direct space tolerance",
        &LJPMETolerance, 1.e-6);
   opts.optional("LJPME", "LJPMEInterpOrder", "LJ-PME interpolation order",
        &LJPMEInterpOrder, 4);  // cubic interpolation is default
   opts.optional("LJPME", "LJPMEGridSizeX", "LJ-PME grid in x dimension",
        &LJPMEGridSizeX, 0);
   opts.optional("LJPME", "LJPMEGridSizeY", "LJ-PME grid in y dimension",
        &LJPMEGridSizeY, 0);
   opts.optional("LJPME", "LJPMEGridSizeZ", "LJ-PME grid in z dimension",
        &LJPMEGridSizeZ, 0);
   opts.optional("LJPME", "LJPMEGridSpacing", "Maximum LJ-PME grid spacing (Angstroms)",
        &LJPMEGridSpacing, 0.);
   opts.range("LJPMEGridSpacing", NOT_NEGATIVE);

   // For "LJPMESerial" option below:
   // TRUE uses the full serial reference version that include O(N^2) loop
   // for calculating short-range contribution.
   // FALSE (default) uses the CPU compute kernels for short-range part
   // and, for now, the serial reference version for the gridded part.
   opts.optionalB("LJPME", "LJPMESerial", "LJ-PME use serial implementation",
        &LJPMESerialOn, FALSE);
   opts.optionalB("LJPME", "LJPMESerialRealSpace", "LJ-PME use serial test code for real space part",
        &LJPMESerialRealSpaceOn, FALSE);


   opts.optionalB("main", "PME", "Use particle mesh Ewald for electrostatics?",
        &PMEOn, FALSE);
   opts.optional("PME", "PMETolerance", "PME direct space tolerance",
        &PMETolerance, 1.e-6);
   opts.optional("PME", "PMEInterpOrder", "PME interpolation order",
        &PMEInterpOrder, 4);  // cubic interpolation is default
   opts.optional("PME", "PMEGridSizeX", "PME grid in x dimension",
        &PMEGridSizeX, 0);
   opts.optional("PME", "PMEGridSizeY", "PME grid in y dimension",
        &PMEGridSizeY, 0);
   opts.optional("PME", "PMEGridSizeZ", "PME grid in z dimension",
        &PMEGridSizeZ, 0);
   opts.optional("PME", "PMEGridSpacing", "Maximum PME grid spacing (Angstroms)",
        &PMEGridSpacing, 0.);
   opts.range("PMEGridSpacing", NOT_NEGATIVE);
   opts.optional("PME", "PMEProcessors",
        "PME FFT and reciprocal sum processor count", &PMEProcessors, 0);
   opts.optional("PME", "PMEMinSlices",
        "minimum thickness of PME reciprocal sum slab", &PMEMinSlices, 2);
   opts.range("PMEMinSlices", NOT_NEGATIVE);
   opts.optional("PME", "PMEPencils",
        "PME FFT and reciprocal sum pencil grid size", &PMEPencils, -1);
   opts.optional("PME", "PMEPencilsX",
        "PME FFT and reciprocal sum pencil grid size X", &PMEPencilsX, 0);
   opts.optional("PME", "PMEPencilsY",
        "PME FFT and reciprocal sum pencil grid size Y", &PMEPencilsY, 0);
   opts.optional("PME", "PMEPencilsZ",
        "PME FFT and reciprocal sum pencil grid size Z", &PMEPencilsZ, 0);
   opts.range("PMEPencilsX", NOT_NEGATIVE);
   opts.range("PMEPencilsY", NOT_NEGATIVE);
   opts.range("PMEPencilsZ", NOT_NEGATIVE);
   opts.optional("PME", "PMEPencilsYLayout",
        "PME FFT and reciprocal sum Y pencil layout strategy", &PMEPencilsYLayout, 0);
   opts.optional("PME", "PMEPencilsXLayout",
        "PME FFT and reciprocal sum X pencil layout strategy", &PMEPencilsXLayout, 1);
   opts.range("PMEPencilsYLayout", NOT_NEGATIVE);
   opts.range("PMEPencilsXLayout", NOT_NEGATIVE);
   opts.optional("PME", "PMESendOrder",
        "PME message ordering control", &PMESendOrder, 0);
   opts.range("PMESendOrder", NOT_NEGATIVE);
   opts.optional("PME", "PMEMinPoints",
        "minimum points per PME reciprocal sum pencil", &PMEMinPoints, 10000);
   opts.range("PMEMinPoints", NOT_NEGATIVE);
   opts.optionalB("main", "PMEBarrier", "Use barrier in PME?",
        &PMEBarrier, FALSE);
   opts.optionalB("main", "PMEOffload", "Offload PME to accelerator?",
        &PMEOffload);

   opts.optionalB("PME", "usePMECUDA", "Use the PME CUDA version", &usePMECUDA, CmiNumPhysicalNodes() == 1);
   opts.optionalB("PME", "usePMEGPU", "Use the PME GPU version", &usePMEGPU);

#ifdef DPME
   opts.optionalB("PME", "useDPME", "Use old DPME code?", &useDPME, FALSE);
#else
   useDPME = 0;
#endif
   opts.optionalB("main", "FFTWPatient", "Use intensive plan creation to optimize FFTW?",
#ifdef WIN32
        &FFTWPatient, TRUE);
#else
        &FFTWPatient, FALSE);
#endif

   opts.optionalB("main", "FFTWEstimate", "Use estimates to optimize FFTW?",
#ifdef WIN32
        &FFTWEstimate, TRUE);
#else
        &FFTWEstimate, FALSE);
#endif
   opts.optionalB("main", "FFTWUseWisdom", "Read/save wisdom file for FFTW?",
#ifdef WIN32
        &FFTWUseWisdom, FALSE);
#else
        &FFTWUseWisdom, TRUE);
#endif
   opts.optional("FFTWUseWisdom", "FFTWWisdomFile", "File for FFTW wisdom",
        FFTWWisdomFile);

  // LJ-PME
//    opts.optionalB("main", "LJFFTWUseWisdom", "Read/save wisdom file for LJ FFTW?",
// #ifdef WIN32
//      &LJFFTWUseWisdom, FALSE);
// #else
//      &LJFFTWUseWisdom, TRUE);
// #endif
//    opts.optional("LJFFTWUseWisdom", "LJFFTWWisdomFile", "File for LJ FFTW wisdom",
//      LJFFTWWisdomFile);

   opts.optionalB("main", "useAVXTiles",
                  "Use \"Tiles\" mode for AVX-512 optimized calculations",
                  &useAVXTiles, TRUE);
#if defined(NAMD_CUDA) || defined(NAMD_HIP)
  opts.optionalB("main", "gpuGlobal", "use GPU global (external) force",
                 &useCudaGlobal, FALSE);
  // opts.optional("gpuGlobal", "gpuGlobalLibrary", "gpuGlobal library (.so or .dll file) location", PARSE_STRING);
  opts.optional("gpuGlobal", "gpuGlobalProfilingFreq", "Frequency of printing GPU global profiling information", &cudaGlobalProfilingFreq, -1);
#else
  useCudaGlobal = false;
#endif
}

void SimParameters::config_parser_methods(ParseOptions &opts) {
   
   opts.optionalB("main", "minimization", "Should minimization be performed?",
      &minimizeCGOn, FALSE);
   opts.optionalB("main", "minVerbose", "Print extra minimization diagnostics?",
      &minVerbose, FALSE);
   opts.optional("main", "minTinyStep", "very first minimization steps",
      &minTinyStep, 1.0e-6);
   opts.range("minTinyStep", POSITIVE);
   opts.optional("main", "minBabyStep", "initial minimization steps",
      &minBabyStep, 1.0e-2);
   opts.range("minBabyStep", POSITIVE);
   opts.optional("main", "minLineGoal", "line minimization gradient reduction",
      &minLineGoal, 1.0e-3);
   opts.range("minLineGoal", POSITIVE);

   opts.optionalB("main", "velocityQuenching",
      "Should old-style minimization be performed?", &minimizeOn, FALSE);

   opts.optional("main", "maximumMove", "Maximum atom movement per step", &maximumMove, 0.0);
   opts.range("maximumMove", NOT_NEGATIVE);
   opts.units("maximumMove", N_ANGSTROM);

   opts.optionalB("main", "Langevin", "Should Langevin dynamics be performed?",
      &langevinOn, FALSE);
   opts.require("Langevin", "langevinTemp", "Temperature for heat bath in Langevin "
     "dynamics", &langevinTemp);
   opts.range("langevinTemp", NOT_NEGATIVE);
   opts.units("langevinTemp", N_KELVIN);
   opts.optional("Langevin", "langevinDamping", "Damping coefficient (1/ps)",
      &langevinDamping);
   opts.range("langevinDamping", POSITIVE);
   opts.optionalB("Langevin", "langevinHydrogen", "Should Langevin dynamics be applied to hydrogen atoms?",
      &langevinHydrogen);
   opts.optional("Langevin", "langevinFile", "PDB file with temperature "
     "coupling terms (B(i)) (default is the PDB input file)",
     PARSE_STRING);
   opts.optional("Langevin", "langevinCol", "Column in the langevinFile "
     "containing the temperature coupling term B(i);\n"
     "default is 'O'", PARSE_STRING);

   // use BAOAB integration instead of BBK
   opts.optionalB("Langevin", "langevinBAOAB",
       "Should Langevin dynamics be performed using BAOAB integration?",
       &langevin_useBAOAB, FALSE);

// BEGIN LA
   opts.optionalB("main", "LoweAndersen", "Should Lowe-Andersen dynamics be performed?",
                  &loweAndersenOn, FALSE);
   opts.require("LoweAndersen", "loweAndersenTemp", "Temperature for heat bath in Lowe-Andersen "
                "dynamics", &loweAndersenTemp);
   opts.range("loweAndersenTemp", NOT_NEGATIVE);
   opts.units("loweAndersenTemp", N_KELVIN);
   opts.optional("LoweAndersen", "loweAndersenRate", "Collision rate (1/ps)",
                 &loweAndersenRate, 50);
   opts.range("loweAndersenRate", POSITIVE);
   opts.optional("LoweAndersen", "loweAndersenCutoff", "Cutoff radius",
                 &loweAndersenCutoff, 2.7);
   opts.range("loweAndersenCutoff", POSITIVE);
   opts.units("loweAndersenCutoff", N_ANGSTROM);
// END LA

//fepb
   opts.optionalB("main", "alch", "Is achemical simulation being performed?",
     &alchOn, FALSE);
   opts.require("alch", "alchLambda", "Alchemical coupling parameter value",
     &alchLambda);
   opts.range("alchLambda", NOT_NEGATIVE);

   opts.optionalB("alch", "singleTopology",
     "Is single topology used for relative free energy?", &singleTopology, FALSE);

   opts.optionalB("alch", "sdBondScaling",
     "Is S-D bonded terms scaling for relative free energy?", &sdScaling, FALSE);
   
   opts.optional("alch", "alchFile", "PDB file with perturbation flags "
     "default is the input PDB file", PARSE_STRING);
   opts.optional("alch", "alchCol", "Column in the alchFile with the "
     "perturbation flag", PARSE_STRING);

   opts.optional("alch", "unperturbedBondFile", "mini psf file with unperturbed bond info"
     " ", PARSE_STRING);
   opts.optional("alch", "alchOutFreq", "Frequency of alchemical energy"
     "output in timesteps", &alchOutFreq, 5);
   opts.range("alchoutfreq", NOT_NEGATIVE);
   opts.optional("alch", "alchOutFile", "Alchemical energy output filename",
     alchOutFile);

   // soft-core parameters
   opts.optional("alch", "alchVdwShiftCoeff", "Coeff used for generating"
     "the altered alchemical vDW interactions", &alchVdwShiftCoeff, 5.);
   opts.range("alchVdwShiftCoeff", NOT_NEGATIVE);

   opts.optionalB("alch", "alchWCA", "Is WCA decomposition being performed?",
     &alchWCAOn, FALSE);

   // scheduling options for different interaction types
   opts.optional("alch", "alchElecLambdaStart", "Lambda at which electrostatic"
      "scaling of exnihilated particles begins", &alchElecLambdaStart, 0.5);
   opts.range("alchElecLambdaStart", NOT_NEGATIVE);

   opts.optional("alch", "alchVdwLambdaEnd", "Lambda at which vdW"
      "scaling of exnihilated particles ends", &alchVdwLambdaEnd, 1.0);
   opts.range("alchVdwLambdaEnd", NOT_NEGATIVE);

   opts.optional("alch", "alchRepLambdaEnd", "Lambda at which repulsive vdW"
      "scaling of exnihilated particles ends and attractive vdW scaling"
      "begins", &alchRepLambdaEnd, 0.5);
   opts.range("alchRepLambdaEnd", NOT_NEGATIVE);

   opts.optional("alch", "alchBondLambdaEnd", "Lambda at which bonded"
      "scaling of exnihilated particles begins", &alchBondLambdaEnd, 0.0);
   opts.range("alchBondLambdaEnd", NOT_NEGATIVE);
   
   opts.optionalB("alch", "alchDecouple", "Enable alchemical decoupling?",
     &alchDecouple, FALSE);
   opts.optionalB("alch", "alchBondDecouple", "Enable decoupling of purely "
     "alchemical bonds?", &alchBondDecouple, FALSE);

   // parameters for alchemical analysis options
   opts.optional("alch", "alchType", "Which alchemical method to use?",
     PARSE_STRING);
   opts.optional("alch", "alchLambda2", "Alchemical coupling comparison value",
     &alchLambda2, -1);
   opts.optional("alch", "alchLambdaIDWS", "Alchemical coupling comparison value for interleaved double-wide sampling",
     &alchLambdaIDWS, -1);
   opts.optional("alch", "alchLambdaFreq",
     "Frequency of increasing coupling parameter value", &alchLambdaFreq, 0);
   opts.range("alchLambdaFreq", NOT_NEGATIVE);
   opts.optional("alch", "alchSwitchType", "Switching type flag",
     PARSE_STRING);
   opts.optional("alch", "alchEquilSteps", "Equilibration steps, before "
     "data collection in the alchemical window", &alchEquilSteps, 0);
   opts.range("alchEquilSteps", NOT_NEGATIVE);

   opts.optionalB("alch", "alchEnsembleAvg", "Ensemble Average in use?",
     &alchEnsembleAvg, TRUE);
//fepe

   opts.optionalB("main", "les", "Is locally enhanced sampling enabled?",
     &lesOn, FALSE);
   opts.require("les", "lesFactor", "Local enhancement factor", &lesFactor);
   opts.optional("les", "lesFile", "PDB file with enhancement flags "
     "default is the input PDB file", PARSE_STRING); 
   opts.optional("les", "lesCol", "Column in the lesFile with the "
     "enhancement flag", PARSE_STRING);
   opts.optionalB("les", "lesReduceTemp", "Reduce enhanced atom temperature?",
     &lesReduceTemp, FALSE);
   opts.optionalB("les", "lesReduceMass", "Reduce enhanced atom mass?",
     &lesReduceMass, FALSE);

   // REST2 (replica exchange solute tempering) parameters
   opts.optionalB("main", "soluteScaling",
       "Is replica exchange solute tempering enabled?",
       &soluteScalingOn, FALSE);
   opts.optional("soluteScaling", "soluteScalingFactor",
       "Solute scaling factor",
       &soluteScalingFactor, 1.0);
   opts.range("soluteScalingFactor", NOT_NEGATIVE);
   opts.optional("soluteScaling", "soluteScalingFactorCharge",
       "Solute scaling factor for electrostatic interactions",
       &soluteScalingFactorCharge);
   opts.range("soluteScalingFactorCharge", NOT_NEGATIVE);
   opts.optional("soluteScaling", "soluteScalingFactorVdw",
       "Solute scaling factor for van der Waals interactions",
       &soluteScalingFactorVdw);
   opts.range("soluteScalingFactorVdw", NOT_NEGATIVE);
   opts.optional("soluteScaling", "soluteScalingFile",
       "PDB file with scaling flags; if undefined, defaults to main PDB file",
       PARSE_STRING);
   opts.optional("soluteScaling", "soluteScalingCol",
       "Column in the soluteScalingFile providing the scaling flag",
       PARSE_STRING);
   opts.optionalB("main", "soluteScalingAll",
       "Apply scaling also to bond and angle interactions?",
       &soluteScalingAll, FALSE);

   // Drude oscillators
   opts.optionalB("main", "drude", "Perform integration of Drude oscillators?",
       &drudeOn, FALSE);
   opts.require("drude", "drudeTemp", "Temperature for freezing "
       "Drude oscillators", &drudeTemp);
   opts.range("drudeTemp", NOT_NEGATIVE);
   opts.units("drudeTemp", N_KELVIN);
   opts.optional("drude", "drudeDamping", "Damping coefficient (1/ps) for "
       "Drude oscillators", &drudeDamping);
   opts.range("drudeDamping", POSITIVE);
   opts.optional("drude", "drudeNbtholeCut", "Nonbonded Thole interactions "
       "interaction radius", &drudeNbtholeCut, 5.0);
   opts.range("drudeNbtholeCut", POSITIVE);
   opts.optionalB("drude", "drudeHardWall", "Apply maximum Drude bond length "
       "restriction?", &drudeHardWallOn, TRUE);
   opts.optional("drude", "drudeBondLen", "Drude oscillator bond length "
       "beyond which to apply restraint", &drudeBondLen, 0.25);
   opts.range("drudeBondLen", POSITIVE);
   opts.optional("drude", "drudeBondConst", "Drude oscillator restraining "
       "force constant", &drudeBondConst, 40000.0);
   opts.range("drudeBondConst", POSITIVE);

   // Pair interaction calculations
    opts.optionalB("main", "pairInteraction", 
        "Are pair interactions calculated?", &pairInteractionOn, FALSE);
    opts.optional("pairInteraction", "pairInteractionFile", 
        "PDB files with interaction flags " "default is the input PDB file", 
        PARSE_STRING);
    opts.optional("pairInteraction", "pairInteractionCol", 
        "Column in the pairInteractionFile with the interaction flags",
        PARSE_STRING);
    opts.require("pairInteraction", "pairInteractionGroup1",
        "Flag for interaction group 1", &pairInteractionGroup1);
    opts.optional("pairInteraction", "pairInteractionGroup2",
        "Flag for interaction group 2", &pairInteractionGroup2, -1);
    opts.optionalB("pairInteraction", "pairInteractionSelf",
        "Compute only within-group interactions?", &pairInteractionSelf, 
        FALSE);
   // Options for CG simulations
   opts.optionalB("main", "cosAngles", "Are some angles cosine-based?", &cosAngles, FALSE);


   //  Dihedral angle dynamics
   opts.optionalB("main", "globalTest", "Should global integration (for development) be used?",
    &globalOn, FALSE);
   opts.optionalB("main", "dihedral", "Should dihedral angle dynamics be performed?",
    &dihedralOn, FALSE);
   COLDOn = FALSE;
   opts.optionalB("dihedral", "COLD", "Should overdamped Langevin dynamics be performed?",
    &COLDOn, FALSE);
   opts.require("COLD", "COLDTemp", "Temperature for heat bath in COLD",
    &COLDTemp);
   opts.range("COLDTemp", NOT_NEGATIVE);
   opts.units("COLDTemp", N_KELVIN);
   opts.require("COLD", "COLDRate", "Damping rate for COLD",
    &COLDRate, 3000.0);
   opts.range("COLDRate", NOT_NEGATIVE);

   //  Get the parameters for temperature coupling
   opts.optionalB("main", "tcouple", 
      "Should temperature coupling be performed?",
      &tCoupleOn, FALSE);
   opts.require("tcouple", "tCoupleTemp", 
    "Temperature for temperature coupling", &tCoupleTemp);
   opts.range("tCoupleTemp", NOT_NEGATIVE);
   opts.units("tCoupleTemp", N_KELVIN);
   opts.optional("tCouple", "tCoupleFile", "PDB file with temperature "
     "coupling terms (B(i)) (default is the PDB input file)",
     PARSE_STRING);
   opts.optional("tCouple", "tCoupleCol", "Column in the tCoupleFile "
     "containing the temperature coupling term B(i);\n"
     "default is 'O'", PARSE_STRING);

   opts.optionalB("main", "stochRescale",
      "Should stochastic velocity rescaling be performed?",
      &stochRescaleOn, FALSE);
   opts.require("stochRescale", "stochRescaleTemp",
      "Temperature for stochastic velocity rescaling",
       &stochRescaleTemp);
   opts.range("stochRescaleTemp", NOT_NEGATIVE);
   opts.units("stochRescaleTemp", N_KELVIN);
   opts.require("stochRescale", "stochRescalePeriod",
      "Time scale for stochastic velocity rescaling (ps)",
       &stochRescalePeriod);
   opts.range("stochRescalePeriod", POSITIVE);
   opts.optional("stochRescale", "stochRescaleFreq",
       "Number of steps between stochastic rescalings",
        &stochRescaleFreq);
   opts.range("stochRescaleFreq", POSITIVE);
   opts.optionalB("stochRescale", "stochRescaleHeat",
       "Should heat transfer and work be computed?", &stochRescaleHeat, FALSE);

   opts.optional("main", "rescaleFreq", "Number of steps between "
    "velocity rescaling", &rescaleFreq);
   opts.range("rescaleFreq", POSITIVE);
   opts.optional("main", "rescaleTemp", "Target temperature for velocity rescaling",
    &rescaleTemp);
   opts.range("rescaleTemp", NOT_NEGATIVE);
   opts.units("rescaleTemp", N_KELVIN);

   opts.optional("main", "reassignFreq", "Number of steps between "
    "velocity reassignment", &reassignFreq);
   opts.range("reassignFreq", POSITIVE);
   opts.optional("main", "reassignTemp", "Target temperature for velocity reassignment",
    &reassignTemp);
   opts.range("reassignTemp", NOT_NEGATIVE);
   opts.units("reassignTemp", N_KELVIN);
   opts.optional("main", "reassignIncr", "Temperature increment for velocity reassignment",
    &reassignIncr);
   opts.units("reassignIncr", N_KELVIN);
   opts.optional("main", "reassignHold", "Final holding temperature for velocity reassignment",
    &reassignHold);
   opts.range("reassignHold", NOT_NEGATIVE);
   opts.units("reassignHold", N_KELVIN);

   opts.optionalB("main", "useGroupPressure", 
      "Use group rather than atomic quantities for pressure control?",
      &useGroupPressure, FALSE);

   opts.optionalB("main", "useFlexibleCell",
      "Use anisotropic cell fluctuation for pressure control?",
      &useFlexibleCell, FALSE);

   // Fix specific cell dimensions
   opts.optionalB("main", "fixCellDims",
      "Fix some cell dimensions?",
      &fixCellDims, FALSE);

   opts.optionalB("fixCellDims", "fixCellDimX",
      "Fix the X dimension?",
      &fixCellDimX, FALSE);
   opts.optionalB("fixCellDims", "fixCellDimY",
      "Fix the Y dimension?",
      &fixCellDimY, FALSE);
   opts.optionalB("fixCellDims", "fixCellDimZ",
      "Fix the Z dimension?",
      &fixCellDimZ, FALSE);

   opts.optionalB("main", "useConstantRatio",
      "Use constant X-Y ratio for pressure control?",
      &useConstantRatio, FALSE);

   opts.optionalB("main", "useConstantArea",
      "Use constant area for pressure control?",
      &useConstantArea, FALSE);

   opts.optionalB("main", "excludeFromPressure",
        "Should some atoms be excluded from pressure rescaling?",
        &excludeFromPressure, FALSE);
   opts.optional("excludeFromPressure", "excludeFromPressureFile",
        "PDB file for atoms to be excluded from pressure",
        PARSE_STRING);
   opts.optional("excludeFromPressure", "excludeFromPressureCol", 
        "Column in the excludeFromPressureFile"
        "containing the flags (nonzero means excluded);\n"
        "default is 'O'", PARSE_STRING);

   opts.optionalB("main", "MonteCarloPressure", 
      "Should Monte Carlo pressure control be used?",
      &monteCarloPressureOn, FALSE);
   opts.require("MonteCarloPressure", "MonteCarloPressureTarget",
    "Target pressure for Monte Carlo pressure control",
    &monteCarloPressureTarget);
   opts.require("MonteCarloPressure", "MonteCarloTemp",
    "Temperature for Monte Carlo pressure control",
    &monteCarloTemp);
   opts.range("MonteCarloTemp", POSITIVE);
   opts.units("MonteCarloTemp", N_KELVIN);
   opts.optional("MonteCarloPressure", "MonteCarloAcceptanceRate",
    "Acceptance rate for Monte Carlo pressure control",
    &monteCarloAcceptanceRate);
   opts.range("MonteCarloAcceptanceRate", POSITIVE);
   opts.optional("MonteCarloPressure", "MonteCarloMaxVolume",
    "Maximum Volume change vector for Monte Carlo pressure control",
    &monteCarloMaxVolume);
   opts.optional("MonteCarloPressure", "MonteCarloAdjustmentFreq",
    "Number of steps between volume rescaling",
    &monteCarloAdjustmentFreq, 30);
   opts.range("MonteCarloAdjustmentFreq", POSITIVE);
   opts.optional("MonteCarloPressure", "MonteCarloPressureFreq",
    "Number of steps between volume rescaling",
    &monteCarloPressureFreq, 50);
   opts.range("MonteCarloPressureFreq", POSITIVE);

   opts.optionalB("main", "BerendsenPressure", 
      "Should Berendsen pressure bath coupling be performed?",
      &berendsenPressureOn, FALSE);
   opts.require("BerendsenPressure", "BerendsenPressureTarget",
    "Target pressure for pressure coupling",
    &berendsenPressureTarget);
   // opts.units("BerendsenPressureTarget",);
   opts.require("BerendsenPressure", "BerendsenPressureCompressibility",
    "Isothermal compressibility for pressure coupling",
    &berendsenPressureCompressibility);
   // opts.units("BerendsenPressureCompressibility",);
   opts.require("BerendsenPressure", "BerendsenPressureRelaxationTime",
    "Relaxation time for pressure coupling",
    &berendsenPressureRelaxationTime);
   opts.range("BerendsenPressureRelaxationTime", POSITIVE);
   opts.units("BerendsenPressureRelaxationTime", N_FSEC);
   opts.optional("BerendsenPressure", "BerendsenPressureFreq",
    "Number of steps between volume rescaling",
    &berendsenPressureFreq, 1);
   opts.range("BerendsenPressureFreq", POSITIVE);

   opts.optionalB("main", "LangevinPiston",
      "Should Langevin piston pressure control be used?",
      &langevinPistonOn, FALSE);
   opts.optionalB("LangevinPiston", "LangevinPistonBarrier",
      "Should Langevin piston barrier be used?",
      &langevinPistonBarrier, TRUE);
   opts.require("LangevinPiston", "LangevinPistonTarget",
      "Target pressure for pressure control",
      &langevinPistonTarget);
   opts.require("LangevinPiston", "LangevinPistonPeriod",
      "Oscillation period for pressure control",
      &langevinPistonPeriod);
   opts.range("LangevinPistonPeriod", POSITIVE);
   opts.units("LangevinPistonPeriod", N_FSEC);
   opts.require("LangevinPiston", "LangevinPistonDecay",
      "Decay time for pressure control",
      &langevinPistonDecay);
   opts.range("LangevinPistonDecay", POSITIVE);
   opts.units("LangevinPistonDecay", N_FSEC);
   opts.require("LangevinPiston", "LangevinPistonTemp",
      "Temperature for pressure control piston",
      &langevinPistonTemp);
   opts.range("LangevinPistonTemp", POSITIVE);
   opts.units("LangevinPistonTemp", N_KELVIN);
   opts.optional("LangevinPiston", "StrainRate",
      "Initial strain rate for pressure control (x y z)",
      &strainRate);

   // Multigrator temperature and/or pressure control
   opts.optionalB("main", "Multigrator", 
      "Should multigrator temperature and/or pressure control be used?",
      &multigratorOn, FALSE);
   opts.require("Multigrator", "MultigratorPressureTarget",
    "Target pressure for pressure coupling",
    &multigratorPressureTarget);
   opts.require("Multigrator", "MultigratorTemperatureTarget",
    "Target temperature for temperature coupling",
    &multigratorTemperatureTarget);
   opts.require("Multigrator", "MultigratorPressureFreq",
    "Number of steps between pressure control moves",
    &multigratorPressureFreq);
   opts.range("MultigratorPressureFreq", POSITIVE);
   opts.optional("Multigrator", "MultigratorPressureRelaxationTime",
    "Relaxation time for pressure coupling is fs",
    &multigratorPressureRelaxationTime, 30000);
   opts.range("MultigratorPressureRelaxationTime", POSITIVE);
   opts.units("MultigratorPressureRelaxationTime", N_FSEC);
   opts.optional("Multigrator", "MultigratorTemperatureRelaxationTime",
    "Relaxation time for temperature coupling is fs",
    &multigratorTemperatureRelaxationTime, 1000);
   opts.range("MultigratorTemperatureRelaxationTime", POSITIVE);
   opts.units("MultigratorTemperatureRelaxationTime", N_FSEC);
   opts.require("Multigrator", "MultigratorTemperatureFreq",
    "Number of steps between temperature control moves",
    &multigratorTemperatureFreq);
   opts.range("MultigratorTemperatureFreq", POSITIVE);
   opts.optional("Multigrator", "MultigratorNoseHooverChainLength",
    "Nose-Hoover chain length",
    &multigratorNoseHooverChainLength, 4);
   opts.range("MultigratorNoseHooverChainLength", POSITIVE);

   opts.optional("main", "SurfaceTensionTarget",
      "Surface tension in the x-y plane",
      &surfaceTensionTarget, 0);

   opts.optionalB("main", "pressureprofile", "Compute pressure profile?",
     &pressureProfileOn, FALSE);
   opts.require("pressureprofile", "pressureprofileslabs", 
     "Number of pressure profile slabs", &pressureProfileSlabs, 10);
   opts.optional("pressureprofile", "pressureprofilefreq",
     "How often to store profile data", &pressureProfileFreq, 1);
   opts.optional("pressureprofile", "pressureProfileAtomTypes", 
     "Number of pressure profile atom types", &pressureProfileAtomTypes, 1);
   opts.range("pressureProfileAtomTypes", POSITIVE);
   opts.optional("pressureProfile", "pressureProfileAtomTypesFile", 
        "PDB files with pressure profile atom types" "default is the input PDB file", 
        PARSE_STRING);
   opts.optional("pressureProfile", "pressureProfileAtomTypesCol", 
        "Column in the pressureProfileAtomTypesFile with the atom types ",
        PARSE_STRING);
   opts.optionalB("pressureProfile", "pressureProfileEwald", 
       "Compute Ewald contribution to pressure profile",
       &pressureProfileEwaldOn, FALSE);
   opts.optional("pressureProfile", "pressureProfileEwaldX",
       "Ewald grid size X", &pressureProfileEwaldX, 10);
   opts.range("pressureProfileEwaldX", POSITIVE);
   opts.optional("pressureProfile", "pressureProfileEwaldY",
       "Ewald grid size Y", &pressureProfileEwaldY, 10);
   opts.range("pressureProfileEwaldY", POSITIVE);
   opts.optional("pressureProfile", "pressureProfileEwaldZ",
       "Ewald grid size Z", &pressureProfileEwaldZ, 10);
   opts.range("pressureProfileEwaldZ", POSITIVE);

   opts.optionalB("main", "accelMD", "Perform acclerated MD?", &accelMDOn, FALSE);
   opts.optional("accelMD", "accelMDFirstStep", "First accelMD step", &accelMDFirstStep, 0);
   opts.range("accelMDFirstStep", NOT_NEGATIVE);
   opts.optional("accelMD", "accelMDLastStep", "Last accelMD step", &accelMDLastStep, 0);
   opts.range("accelMDLastStep", NOT_NEGATIVE);
   opts.optional("accelMD", "accelMDOutFreq", "Frequency of accelMD output", &accelMDOutFreq, 1);
   opts.range("accelMDOutFreq", POSITIVE);
   opts.optionalB("accelMD", "accelMDdihe", "Apply boost to dihedral potential", &accelMDdihe, TRUE);
   opts.optionalB("accelMD", "accelMDDebugOn", "Debugging accelMD", &accelMDDebugOn, FALSE);
   opts.optional("accelMD", "accelMDE","E for AMD", &accelMDE);
   opts.units("accelMDE", N_KCAL);
   opts.optional("accelMD", "accelMDalpha","alpha for AMD", &accelMDalpha);
   opts.units("accelMDalpha", N_KCAL);
   opts.range("accelMDalpha", POSITIVE);
   opts.optionalB("accelMD", "accelMDdual", "Apply dual boost", &accelMDdual, FALSE);
   opts.optional("accelMDdual", "accelMDTE","E for total potential under accelMDdual mode", &accelMDTE);
   opts.units("accelMDTE", N_KCAL);
   opts.optional("accelMDdual", "accelMDTalpha","alpha for total potential under accelMDdual mode", &accelMDTalpha);
   opts.units("accelMDTalpha", N_KCAL);
   opts.range("accelMDTalpha", POSITIVE);
   // GaMD parameters
   opts.optionalB("accelMD", "accelMDG", "Perform Gaussian accelMD calculation?", &accelMDG, FALSE);
   opts.optional("accelMDG", "accelMDGiE", "Flag to set the mode iE in Gaussian accelMD", &accelMDGiE, 1);
   opts.optional("accelMDG", "accelMDGcMDSteps", "Number of cMD steps", &accelMDGcMDSteps, 1000000);
   opts.range("accelMDGcMDSteps", NOT_NEGATIVE);
   opts.optional("accelMDG", "accelMDGEquiSteps", "Number of equilibration steps after adding boost potential", &accelMDGEquiSteps, 1000000);
   opts.range("accelMDGEquiSteps", NOT_NEGATIVE);
   opts.require("accelMDG", "accelMDGcMDPrepSteps", "Number of preparation cMD steps", &accelMDGcMDPrepSteps, 200000);
   opts.range("accelMDGcMDPrepSteps", NOT_NEGATIVE);
   opts.require("accelMDG", "accelMDGEquiPrepSteps", "Number of preparation equilibration steps", &accelMDGEquiPrepSteps, 200000);
   opts.range("accelMDGEquiPrepSteps", NOT_NEGATIVE);
   opts.optional("accelMDG", "accelMDGStatWindow", "Number of steps to calculate avg and std", &accelMDGStatWindow, -1);
   opts.optional("accelMDG", "accelMDGSigma0P", "Upper limit of std of total potential", &accelMDGSigma0P, 6.0);
   opts.units("accelMDGSigma0P", N_KCAL);
   opts.range("accelMDGSigma0P", NOT_NEGATIVE);
   opts.optional("accelMDG", "accelMDGSigma0D", "Upper limit of std of dihedral potential", &accelMDGSigma0D, 6.0);
   opts.units("accelMDGSigma0D", N_KCAL);
   opts.range("accelMDGSigma0D", NOT_NEGATIVE);
   opts.optionalB("accelMDG", "accelMDGRestart", "Flag to set use restart file in Gaussian accelMD", &accelMDGRestart, FALSE);
   opts.require("accelMDGRestart", "accelMDGRestartFile", "Restart file name for Gaussian accelMD", accelMDGRestartFile);
   opts.optionalB("accelMDG", "accelMDGresetVaftercmd", "Flag to reset potential after accelMDGcMDSteps steps", 
           &accelMDGresetVaftercmd, FALSE);

   // Adaptive Temperature Sampling (adaptTemp) parameters
   opts.optionalB("main", "adaptTempMD", "Perform adaptive temperature sampling", &adaptTempOn, FALSE);
   opts.optional("adaptTempMD", "adaptTempFirstStep", "First adaptTemp step", &adaptTempFirstStep, 0);
   opts.range("adaptTempFirstStep", NOT_NEGATIVE);
   opts.optional("adaptTempMD", "adaptTempLastStep", "Last adaptTemp step", &adaptTempLastStep, 0);
   opts.range("adaptTempLastStep", NOT_NEGATIVE);
   opts.optional("adaptTempMD", "adaptTempOutFreq", "Frequency of adaptTemp output", &adaptTempOutFreq, 10);
   opts.range("adaptTempOutFreq", POSITIVE);
   opts.optional("adaptTempMD", "adaptTempFreq", "Frequency of writing average energies to adaptTempOutFile", &adaptTempFreq, 10);
   opts.range("adaptTempFreq", POSITIVE);
   opts.optionalB("adaptTempMD", "adaptTempDebug", "Print debug output for adaptTemp", &adaptTempDebug, FALSE);
   opts.optional("adaptTempMD", "adaptTempTmin","Minimun temperature for adaptTemp", &adaptTempTmin);
   opts.units("adaptTempTmin", N_KELVIN);
   opts.range("adaptTempTmin", POSITIVE);
   opts.optional("adaptTempMD", "adaptTempTmax","Maximum temperature for adaptTemp", &adaptTempTmax);
   opts.units("adaptTempTmax", N_KELVIN);
   opts.range("adaptTempTmax", POSITIVE);
   opts.optional("adaptTempMD", "adaptTempBins","Number of bins to store average energies", &adaptTempBins,0);
   opts.range("adaptTempBins", NOT_NEGATIVE);
   opts.optional("adaptTempMD", "adaptTempDt", "Integration timestep for Temp. updates", &adaptTempDt, 0.0001);
   opts.units("adaptTempDt", N_FSEC);
   opts.range("adaptTempDt", NOT_NEGATIVE);
   opts.optional("adaptTempMD", "adaptTempAutoDt", "Average temperature update in percent of temperature range", &adaptTempAutoDt, 0.0);
   opts.range("adaptTempAutoDt", NOT_NEGATIVE);
   opts.optional("adaptTempMD", "adaptTempCgamma", "Adaptive bin averaging constant", &adaptTempCgamma, 0.1);
   opts.range("adaptTempCgamma", NOT_NEGATIVE);
   opts.optionalB("adaptTempMD","adaptTempLangevin","Send adaptTemp temperature to langevin thermostat",&adaptTempLangevin,TRUE);
   opts.optionalB("adaptTempMD","adaptTempRescaling","Send adaptTemp temperature to velocity rescaling thermostat", &adaptTempRescale,TRUE);
   opts.optional("adaptTempMD", "adaptTempInFile", "File containing restart information for adaptTemp", adaptTempInFile);
   opts.optional("adaptTempMD", "adaptTempRestartFile", "File for writing adaptTemp restart information", adaptTempRestartFile);
   opts.require("adaptTempRestartFile","adaptTempRestartFreq", "Frequency of writing restart file", &adaptTempRestartFreq,0);
   opts.range("adaptTempRestartFreq",NOT_NEGATIVE);
   opts.optionalB("adaptTempMD", "adaptTempRandom", "Randomly assign a temperature if we step out of range", &adaptTempRandom, FALSE);
}

void SimParameters::config_parser_constraints(ParseOptions &opts) {
   
   opts.optionalB("main", "fixedatoms", "Are there fixed atoms?",
    &fixedAtomsOn, FALSE);
   opts.optionalB("fixedatoms", "fixedAtomsForces",
     "Calculate forces between fixed atoms?  (Required to unfix during run.)",
     &fixedAtomsForces, FALSE);
   opts.optional("fixedatoms", "fixedAtomsFile", "PDB file with flags for "
     "fixed atoms (default is the PDB input file)",
     PARSE_STRING);
   opts.optional("fixedatoms", "fixedAtomsCol", "Column in the fixedAtomsFile "
     "containing the flags (nonzero means fixed);\n"
     "default is 'O'", PARSE_STRING);
   opts.optional("fixedatoms", "fixedAtomListFile", "the text input file for fixed atoms "
                 "used for parallel input IO", PARSE_STRING);
   opts.optionalB("fixedatoms", "fixedAtomsForceOutput",
     "Do we write out forces acting on fixed atoms?",
     &fixedAtomsForceOutput, FALSE);

   opts.optionalB("main", "constraints", "Are harmonic constraints active?",
     &constraintsOn, FALSE);
   opts.require("constraints", "consexp", "Exponent for harmonic potential",
    &constraintExp, 2);
   opts.range("consexp", POSITIVE);
#ifndef MEM_OPT_VERSION
   opts.require("constraints", "consref", "PDB file containing reference "
    "positions",
    PARSE_STRING);
   opts.require("constraints", "conskfile", "PDB file containing force "
    "constaints in one of the columns", PARSE_STRING);
   opts.require("constraints", "conskcol", "Column of conskfile to use "
    "for the force constants", PARSE_STRING);
#else
   opts.require("constraints", "consAtomListFile", "the text input file for constrained atoms "
                 "used for parallel input IO", PARSE_STRING);
#endif
   opts.require("constraints", "constraintScaling", "constraint scaling factor",
     &constraintScaling, 1.0);
   opts.range("constraintScaling", NOT_NEGATIVE);



   //****** BEGIN selective restraints (X,Y,Z) changes

   opts.optionalB("constraints", "selectConstraints", 
   "Restrain only selected Cartesian components of the coordinates?",
     &selectConstraintsOn, FALSE);
   opts.optionalB("selectConstraints", "selectConstrX",  
   "Restrain X components of coordinates ", &constrXOn, FALSE);
   opts.optionalB("selectConstraints", "selectConstrY",  
   "Restrain Y components of coordinates ", &constrYOn, FALSE);
   opts.optionalB("selectConstraints", "selectConstrZ",  
   "Restrain Z components of coordinates ", &constrZOn, FALSE);
   //****** END selective restraints (X,Y,Z) changes

   // spherical constraints
   opts.optionalB("constraints", "sphericalConstraints", 
   "Restrain only radial spherical component of the coordinates?",
     &sphericalConstraintsOn, FALSE);
   opts.optional("sphericalConstraints", "sphericalConstrCenter",
   "Center of spherical constraints", &sphericalConstrCenter);
 
   //****** BEGIN moving constraints changes 

   opts.optionalB("constraints", "movingConstraints",
      "Are some of the constraints moving?", 
      &movingConstraintsOn, FALSE);
   opts.require("movingConstraints", "movingConsVel",
    "Velocity of the movement, A/timestep", &movingConsVel);
   //****** END moving constraints changes 

   // BEGIN rotating constraints changes
   opts.optionalB("constraints", "rotConstraints",
      "Are the constraints rotating?", 
      &rotConstraintsOn, FALSE);
   opts.require("rotConstraints", "rotConsAxis",
    "Axis of rotation", &rotConsAxis);
   opts.require("rotConstraints", "rotConsPivot",
    "Pivot point of rotation", 
    &rotConsPivot);
   opts.require("rotConstraints", "rotConsVel",
    "Velocity of rotation, deg/timestep", &rotConsVel);

   // END rotating constraints changes

   // external command forces
   opts.optionalB("main", "extForces", "External command forces?",
      &extForcesOn, FALSE);
   opts.require("extForces", "extForcesCommand",
      "External forces command", extForcesCommand);
   opts.require("extForces", "extCoordFilename",
      "External forces coordinate filename", extCoordFilename);
   opts.require("extForces", "extForceFilename",
      "External forces force filename", extForceFilename);

   
  // QM/MM forces
   opts.optionalB("main", "QMForces", "Apply QM forces?",
      &qmForcesOn, FALSE);
   opts.require("QMForces", "QMSoftware",
      "software whose format will be used for input/output", qmSoftware);
   opts.require("QMForces", "QMExecPath",
      "path to executable", qmExecPath);
   opts.optional("QMForces", "QMChargeMode",
      "type of QM atom charges gathered from the QM software", qmChrgModeS);
   opts.require("QMForces", "QMColumn",
      "column defining QM and MM regions", qmColumn);
   opts.require("QMForces", "QMBaseDir",
      "base path and name for QM input and output (preferably in memory)", qmBaseDir);
   opts.optional("QMForces", "QMConfigLine",
      "Configuration line for QM (multiple inputs allowed)", PARSE_MULTIPLES);
   opts.optional("QMForces", "QMParamPDB",
      "PDB with QM parameters", qmParamPDB);
   opts.optional("QMForces", "QMPrepProc",
      "initial preparation executable", qmPrepProc);
   opts.optional("QMForces", "QMSecProc",
      "secondary executable", qmSecProc);
   opts.optional("QMForces", "QMCharge",
      "charge of the QM group", PARSE_MULTIPLES);
   opts.optionalB("QMForces", "QMChargeFromPSF",
      "gets charge of the QM group form PSF values", &qmChrgFromPSF, FALSE);
   opts.optional("QMForces", "QMMult",
      "multiplicity of the QM group", PARSE_MULTIPLES);
   opts.optional("QMForces", "QMLinkElement",
      "element of link atom", PARSE_MULTIPLES);
   opts.optionalB("QMForces", "QMReplaceAll",
      "replace all NAMD forces with QM forces", &qmReplaceAll, FALSE);
   opts.optional("QMForces", "QMPCStride",
      "frequency of selection of point charges", &qmPCSelFreq, 1);
   opts.range("QMPCStride", POSITIVE);
   opts.optionalB("QMForces", "QMNoPntChrg",
      "no point charges will be passed to the QM system(s)", &qmNoPC, FALSE);
   opts.optionalB("QMForces", "QMElecEmbed",
      "activates electrostatic embedding", &qmElecEmbed, TRUE);
   opts.optionalB("QMForces", "QMVdWParams",
      "use special VdW parameters for QM atoms", &qmVDW, FALSE);
   opts.optionalB("QMForces", "QMBondGuess",
      "Guess QM-MM bonds from topology and QM atom definitions", &qmBondGuess, FALSE);
   opts.optional("QMForces", "QMBondColumn",
      "column defining QM-MM bonds", qmBondColumn);
   opts.optionalB("QMForces", "QMBondDist",
      "values in QMBondColumn defines the distance of new link atom", &qmBondDist, FALSE);
   opts.optional("QMForces", "QMBondValueType",
      "type of value in bond column: len or ratio", qmBondValueTypeS);
   opts.optional("QMForces", "QMBondScheme",
      "type of treatment given to QM-MM bonds.", qmBondSchemeS);
   opts.optional("QMForces", "QMenergyStride",
      "frequency of QM specific energy output (every x steps)", &qmEnergyOutFreq, 1);
   opts.optional("QMForces", "QMOutStride",
      "frequency of QM specific charge output (every x steps)", &qmOutFreq, 0);
   opts.range("QMOutStride", NOT_NEGATIVE);
   opts.optional("QMForces", "QMPositionOutStride",
      "frequency of QM specific position output (every x steps)", &qmPosOutFreq, 0);
   opts.range("QMPositionOutStride", NOT_NEGATIVE);
   opts.optional("QMForces", "QMSimsPerNode",
      "QM executions per node", &qmSimsPerNode, 1);
   opts.range("QMSimsPerNode", POSITIVE);
   opts.optionalB("QMForces", "QMSwitching",
      "apply switching to point charges.", &qmPCSwitchOn, FALSE);
   opts.optional("QMForces", "QMSwitchingType",
      "How are charges scaled down to be presented to QM groups.", qmPCSwitchTypeS);
   opts.optional("QMForces", "QMPointChargeScheme",
      "type of treatment given to the total sum of point charges.", qmPCSchemeS);
   opts.optionalB("QMForces", "QMCustomPCSelection",
      "custom and fixed selection of point charges per QM group.", &qmCustomPCSel, FALSE);
   opts.optional("QMForces", "QMCustomPCFile",
      "file with a selection of point charges for a single QM group", PARSE_MULTIPLES);
   opts.optionalB("QMForces", "QMLiveSolventSel",
      "Continuously update the selection of solvent molecules in QM groups", &qmLSSOn, FALSE);
   opts.optional("QMForces", "QMLSSFreq",
      "frequency of QM water selection update", &qmLSSFreq, 100);
   opts.range("QMLSSFreq", POSITIVE);
   opts.optional("QMForces", "QMLSSResname",
      "residue name for the solvent molecules (TIP3).", qmLSSResname);
   opts.optional("QMForces", "QMLSSMode",
      "mode of selection of point solvent molecules", qmLSSModeS);
   opts.optional("QMForces", "QMLSSRef",
      "for COM mode, defines reference for COM distance calculation", PARSE_MULTIPLES);
   opts.optionalB("QMForces", "QMCSMD",
      "Do we use Conditional SMD option?", &qmCSMD, FALSE);
   opts.optional("QMForces", "QMCSMDFile",
                "File for Conditional SMD information",qmCSMDFile);
   
   //print which bad contacts are being moved downhill
   opts.optionalB("main", "printBadContacts", "Print atoms with huge forces?",
      &printBadContacts, FALSE);

   /* GBIS generalized born implicit solvent*/

   opts.optionalB("main", "GBIS", "Use GB implicit solvent?",
      &GBISOn, FALSE);
   opts.optionalB("main", "GBISSer", "Use GB implicit solvent?",
      &GBISserOn, FALSE);

   opts.optional("GBIS", "solventDielectric",
      "Solvent Dielectric", &solvent_dielectric, 78.5);
   opts.optional("GBIS", "intrinsicRadiusOffset",
      "Coulomb Radius Offset", &coulomb_radius_offset, 0.09);
   opts.optional("GBIS", "ionConcentration",
      "Ion Concentration", &ion_concentration, 0.2); //0.2 mol/L
   opts.optional("GBIS", "GBISDelta",
      "delta from GBOBC", &gbis_delta, 1.0); //0.8 or 1.0
   opts.optional("GBIS", "GBISBeta",
      "beta from GBOBC", &gbis_beta, 0.8);   //0.0 or 0.8
   opts.optional("GBIS", "GBISGamma",
      "gamma from GBOBC", &gbis_gamma, 4.85);//2.290912 or 4.85
   opts.optional("GBIS", "alphaCutoff",
      "cutoff for calculating effective born radius", &alpha_cutoff, 15);
   opts.optional("GBIS", "alphaMax",
      "maximum allowable born radius", &alpha_max, 30);
   opts.optional("GBIS", "fsMax",
      "maximum screened intrinsic radius", &fsMax, 1.728);

   opts.optionalB("main", "SASA", "Use Linear Combination of Pairwise Overlaps (LCPO) for calculating SASA",
      &LCPOOn, FALSE);
   opts.optional("SASA", "surfaceTension",
      "Surfce Tension for SASA (kcal/mol/Ang^2)", &surface_tension, 0.005);

   //****** BEGIN SMD constraints changes 

   // SMD constraints
   opts.optionalB("main", "SMD",
      "Do we use SMD option?", 
      &SMDOn, FALSE);
   opts.require("SMD", "SMDVel",
                "Velocity of the movement, A/timestep", &SMDVel);
   opts.range("SMDVel", NOT_NEGATIVE);
   opts.require("SMD", "SMDDir",
                "Direction of movement", &SMDDir);
   opts.require("SMD", "SMDk",
                "Elastic constant for SMD", &SMDk);
   opts.optional("SMD", "SMDk2",
                "Transverse elastic constant for SMD", &SMDk2, 0);
   opts.range("SMDk", NOT_NEGATIVE);
   opts.range("SMDk2", NOT_NEGATIVE);
   opts.require("SMD", "SMDFile",
                "File for SMD information",
                 SMDFile);
   opts.optional("SMD", "SMDOutputFreq",
                 "Frequency of output",
                 &SMDOutputFreq, 1);
   opts.range("SMDOutputFreq", POSITIVE);
   
   //****** END SMD constraints changes 

   //****** BEGIN tabulated energies section
   opts.optionalB("main", "tabulatedEnergies", "Do we get energies from a table?", &tabulatedEnergies, FALSE);
//   opts.require("tabulatedEnergies", "tableNumTypes","Number of types for energy tabulation", &tableNumTypes);
   opts.require("tabulatedEnergies", "tabulatedEnergiesFile", "File containing energy table", tabulatedEnergiesFile);
   opts.require("tabulatedEnergies", "tableInterpType", "Cubic or linear interpolation", tableInterpType);

   // TMD parameters
   opts.optionalB("main", "TMD", "Perform Targeted MD?", &TMDOn, FALSE);
   opts.optional("TMD", "TMDk", "Elastic constant for TMD", &TMDk, 0); 
   opts.range("TMDk", NOT_NEGATIVE);
   opts.require("TMD", "TMDFile", "File for TMD information", TMDFile);
   opts.optionalB("TMD", "TMDDiffRMSD", "Restrain Difference between the RMSD from two structures", &TMDDiffRMSD, FALSE);
   opts.require("TMDDiffRMSD", "TMDFile2",  "Second file for TMD information", TMDFile2); 
    
   opts.optional("TMD", "TMDOutputFreq", "Frequency of TMD output", 
       &TMDOutputFreq, 1);
   opts.range("TMDOutputFreq", POSITIVE);
   opts.require("TMD", "TMDLastStep", "Last TMD timestep", &TMDLastStep);
   opts.range("TMDLastStep", POSITIVE);
   opts.optional("TMD", "TMDFirstStep", "First TMD step (default 0)", &TMDFirstStep, 0);
   opts.optional("TMD", "TMDInitialRMSD", "Target RMSD at first TMD step (default -1 to use initial coordinates)", &TMDInitialRMSD);
   TMDInitialRMSD = -1;
   opts.optional("TMD", "TMDFinalRMSD", "Target RMSD at last TMD step (default 0 )", &TMDFinalRMSD, 0);
   opts.range("TMDInitialRMSD", NOT_NEGATIVE);
   // End of TMD parameters

   // Symmetry restraint parameters
   opts.optionalB("main", "symmetryRestraints", "Enable symmetry restraints?", &symmetryOn, FALSE); 
   opts.optional("symmetryRestraints", "symmetryk", "Elastic constant for symmetry restraints", &symmetryk, 0);
   opts.range("symmetryk", NOT_NEGATIVE);
   opts.optional("symmetryRestraints", "symmetrykfile", "PDB file specifying force contants on a per-atom basis", PARSE_MULTIPLES);
   opts.optionalB("symmetryRestraints", "symmetryScaleForces", "Scale applied forces over time?", &symmetryScaleForces, FALSE);
   opts.require("symmetryRestraints", "symmetryFile", "File for symmetry information", PARSE_MULTIPLES);
   opts.optional("symmetryRestraints", "symmetryMatrixFile", "File(s) for transfromation matrices", PARSE_MULTIPLES);
   opts.optional("symmetryRestraints", "symmetryLastStep", "Last symmetry timestep", &symmetryLastStep, -1);
   opts.optional("symmetryRestraints", "symmetryFirstStep", "First symmetry step (default 0)", &symmetryFirstStep, 0);
   opts.optional("symmetryRestraints", "symmetryLastFullStep", "Last full force symmetry timestep (default symmetryLastStep)", &symmetryLastFullStep, symmetryLastStep);
   opts.optional("symmetryRestraints", "symmetryFirstFullStep", "First full force symmetry step (default symmetryFirstStep)", &symmetryFirstFullStep, symmetryFirstStep);
  //End of symmetry restraint parameters.

   opts.optionalB("main", "tclForces", "Are Tcl global forces active?",
     &tclForcesOn, FALSE);
   opts.require("tclForces", "tclForcesScript",
     "Tcl script for global forces", PARSE_MULTIPLES);

   opts.optionalB("main", "tclBC", "Are Tcl boundary forces active?",
     &tclBCOn, FALSE);
   opts.require("tclBC", "tclBCScript",
     "Tcl script defining calcforces for boundary forces", PARSE_STRING);
   tclBCScript = 0;
   opts.optional("tclBC", "tclBCArgs", "Extra args for calcforces command",
     tclBCArgs);
   tclBCArgs[0] = 0;

   opts.optionalB("main", "miscForces", "Are misc global forces active?",
     &miscForcesOn, FALSE);
   opts.optional("miscForces", "miscForcesScript",
     "script for misc forces", PARSE_MULTIPLES);

   opts.optionalB("main", "freeEnergy", "Perform free energy perturbation?",
     &freeEnergyOn, FALSE);
   opts.require("freeEnergy", "freeEnergyConfig",
     "Configuration file for free energy perturbation", PARSE_MULTIPLES);

   opts.optionalB("main", "constantforce", "Apply constant force?",
     &consForceOn, FALSE);
   opts.optional("constantforce", "consForceFile",
       "Configuration file for constant forces", PARSE_STRING);
   opts.require("constantforce", "consForceScaling",
       "Scaling factor for constant forces", &consForceScaling, 1.0);
 
    opts.optionalB("main", "colvars", "Is the colvars module enabled?",
      &colvarsOn, FALSE);
    opts.optional("colvars", "colvarsConfig",
      "configuration for the collective variables", PARSE_MULTIPLES);
    opts.optional("colvars", "colvarsInput",
      "input restart file for the collective variables", PARSE_STRING);

    opts.optional("main", "globalMasterFrequency", "Number of steps between globalMaster client calls", &globalMasterFrequency, 1);
    opts.range("globalMasterFrequency", POSITIVE);
    opts.optionalB("main", "globalMasterScaleByFrequency", "Scale globalmaster forces by frequency?",
      &globalMasterScaleByFrequency, FALSE);
    opts.optionalB("main", "globalMasterStaleForces", "Use stale forces MTS for globalmaster forces by frequency?",
      &globalMasterStaleForces, FALSE);


}

#ifdef OPENATOM_VERSION
void SimParameters::config_parser_openatom(ParseOptions &opts) {
  opts.optionalB("main", "openatom", "OpenAtom active?", &openatomOn, FALSE);
  opts.require("openatom", "openatomDriverFile", "What config file specifies openatom input parameters", PARSE_STRING);
  opts.require("openatom", "openatomPhysicsFile", "What structure file specifies openatom input system", PARSE_STRING);
  opts.require("openatom", "openatomPdbFile", "NAMD input file defining QM and MM regions", PARSE_STRING);
   opts.optional("openatom", "openatomCol", "Column in the openatomPdb with the QM/MM flag", PARSE_STRING);
}
#endif // OPENATOM_VERSION

/* BEGIN gf */
void SimParameters::config_parser_mgridforce(ParseOptions &opts) {
    opts.optionalB("main", "mgridforce", "Is Multiple gridforce active?", 
                   &mgridforceOn, FALSE);
    opts.optional("mgridforce", "mgridforcevolts", "Is Gridforce using Volts/eV as units?",
                  PARSE_MULTIPLES);
    opts.require("mgridforce", "mgridforcescale", "Scale factor by which to multiply "
                 "grid forces", PARSE_MULTIPLES);
    opts.require("mgridforce", "mgridforcefile", "PDB file containing force "
                 "multipliers in one of the columns", PARSE_MULTIPLES);
    opts.require("mgridforce", "mgridforcecol", "Column of gridforcefile to "
                 "use for force multiplier", PARSE_MULTIPLES);
    opts.optional("mgridforce", "mgridforcechargecol", "Column of gridforcefile to "
                  "use for charge", PARSE_MULTIPLES);
    opts.require("mgridforce", "mgridforcepotfile", "Gridforce potential file",
                 PARSE_MULTIPLES);
    opts.optional("mgridforce", "mgridforcecont1", "Use continuous grid "
                   "in K1 direction?", PARSE_MULTIPLES);
    opts.optional("mgridforce", "mgridforcecont2", "Use continuous grid "
                   "in K2 direction?", PARSE_MULTIPLES);
    opts.optional("mgridforce", "mgridforcecont3", "Use continuous grid "
                   "in K3 direction?", PARSE_MULTIPLES);
    opts.optional("mgridforce", "mgridforcevoff", "Gridforce potential offsets",
                  PARSE_MULTIPLES);
    opts.optional("mgridforce", "mgridforcechecksize", "Check if grid exceeds PBC cell dimensions?", PARSE_MULTIPLES);
}

void SimParameters::config_parser_gridforce(ParseOptions &opts) {
    opts.optionalB("main", "gridforce", "Is Gridforce active?", 
                   &gridforceOn, FALSE);
    opts.optionalB("gridforce", "gridforcevolts", "Is Gridforce using Volts/eV as units?",
                   &gridforceVolts, FALSE);
    opts.require("gridforce", "gridforcescale", "Scale factor by which to multiply "
                 "grid forces", &gridforceScale);
    opts.require("gridforce", "gridforcefile", "PDB file containing force "
                 "multipliers in one of the columns", PARSE_STRING);
    opts.require("gridforce", "gridforcecol", "Column of gridforcefile to "
                 "use for force multiplier", PARSE_STRING);
    opts.optional("gridforce", "gridforcechargecol", "Column of gridforcefile to "
                  "use for charge", PARSE_STRING);
    opts.require("gridforce", "gridforcepotfile", "Gridforce potential file",
                 PARSE_STRING);
    opts.optionalB("gridforce", "gridforcecont1", "Use continuous grid "
                   "in A1 direction?", &gridforceContA1, FALSE);
    opts.optionalB("gridforce", "gridforcecont2", "Use continuous grid "
                   "in A2 direction?", &gridforceContA2, FALSE);
    opts.optionalB("gridforce", "gridforcecont3", "Use continuous grid "
                   "in A3 direction?", &gridforceContA3, FALSE);
    opts.optional("gridforce", "gridforcevoff", "Gridforce potential offsets",
                  &gridforceVOffset);
    opts.optionalB("gridforce", "gridforcechecksize", "Check if grid exceeds PBC cell dimensions?",
                   &gridforcechecksize, TRUE);
}
/* END gf */
void SimParameters::config_parser_dcd_selections(ParseOptions &opts) {

  opts.optionalB("main", "DcdSelection", "Selection list DCD trajectory output",
                 &dcdSelectionOn, FALSE);

  opts.require("DcdSelection", "DcdSelectionInputFile",
       "Configuration file for selection DCD definition", PARSE_MULTIPLES);

  opts.require("DcdSelection", "DCDSelectionFreq",
               "Frequency of selection list DCD trajectory output, in timesteps",
               PARSE_MULTIPLES);
  opts.optional("DcdSelection", "DCDSelectionFile",
               "Selection list DCD trajectory output file name",
               PARSE_MULTIPLES);
}

void SimParameters::config_parser_group_restraints(ParseOptions &opts) {
    opts.optionalB("main", "groupRestraints", "Is Group restraints active?", 
                   &groupRestraintsOn, FALSE);
    opts.require("groupRestraints", "groupResCenter", "The center or equilibrium "
    "vector value for restraints", PARSE_MULTIPLES);
    opts.require("groupRestraints", "groupResK", "Restraints force constant",
                 PARSE_MULTIPLES);
    opts.optional("groupRestraints", "groupResExp", "Restraints exponent",
                 PARSE_MULTIPLES);
    opts.optional("groupRestraints", "groupResUseMagnitude", "Should magnitude of "
                 "distance be used for applying restraint?", PARSE_MULTIPLES);
    opts.optional("groupRestraints", "group1File", "Text file containing atom indices " 
      "for group 1", PARSE_MULTIPLES);
    opts.optional("groupRestraints", "group1List", "List of atom indices for group 1"
                 , PARSE_MULTIPLES);
    opts.optional("groupRestraints", "group1RefPos", "Reference COM position for group 1",
                 PARSE_MULTIPLES);
    opts.optional("groupRestraints", "group2File", "Text file containing atom indices "
                 "for group 2", PARSE_MULTIPLES);
    opts.optional("groupRestraints", "group2List", "List of atom indices for group 2",
                 PARSE_MULTIPLES);
    opts.optional("groupRestraints", "groupResX", "Apply restraints in x direction",
                 PARSE_MULTIPLES);
    opts.optional("groupRestraints", "groupResY", "Apply restraints in y direction",
                 PARSE_MULTIPLES);
    opts.optional("groupRestraints", "groupResZ", "Apply restraints in z direction",
                 PARSE_MULTIPLES);
}

void SimParameters::config_parser_movdrag(ParseOptions &opts) {
   opts.optionalB("main", "movDragOn", "Do we apply moving drag?",
      &movDragOn, FALSE);
   opts.require("movDragOn", "movDragFile",
      "Main moving drag PDB file", movDragFile);
   opts.require("movDragOn", "movDragCol",
      "Main moving drag PDB column", PARSE_STRING);
   opts.require("movDragOn", "movDragGlobVel",
      "Global moving drag velocity (A/step)", &movDragGlobVel);
   opts.require("movDragOn", "movDragVelFile",
      "Moving drag linear velocity file", movDragVelFile);
}

void SimParameters::config_parser_rotdrag(ParseOptions &opts) {
   opts.optionalB("main", "rotDragOn", "Do we apply rotating drag?",
      &rotDragOn, FALSE);
   opts.require("rotDragOn", "rotDragFile",
      "Main rotating drag PDB file", rotDragFile);
   opts.require("rotDragOn", "rotDragCol",
      "Main rotating drag PDB column", PARSE_STRING);
   opts.require("rotDragOn", "rotDragAxisFile",
      "Rotating drag axis file", rotDragAxisFile);
   opts.require("rotDragOn", "rotDragPivotFile",
      "Rotating drag pivot point file", rotDragPivotFile);
   opts.require("rotDragOn", "rotDragGlobVel",
      "Global rotating drag angular velocity (deg/step)", &rotDragGlobVel);
   opts.require("rotDragOn", "rotDragVelFile",
      "Rotating drag angular velocity file", rotDragVelFile);
   opts.require("rotDragOn", "rotDragVelCol",
      "Rotating drag angular velocity column", PARSE_STRING);
}

void SimParameters::config_parser_constorque(ParseOptions &opts) {
   opts.optionalB("main", "consTorqueOn", "Do we apply \"constant\" torque?",
      &consTorqueOn, FALSE);
   opts.require("consTorqueOn", "consTorqueFile",
      "Main \"constant\" torque PDB file", consTorqueFile);
   opts.require("consTorqueOn", "consTorqueCol",
      "Main \"constant\" torque PDB column", PARSE_STRING);
   opts.require("consTorqueOn", "consTorqueAxisFile",
      "\"Constant\" torque axis file", consTorqueAxisFile);
   opts.require("consTorqueOn", "consTorquePivotFile",
      "\"Constant\" torque pivot point file", consTorquePivotFile);
   opts.require("consTorqueOn", "consTorqueGlobVal",
      "Global \"constant\" torque value (Kcal/(mol*A^2))", &consTorqueGlobVal);
   opts.require("consTorqueOn", "consTorqueValFile",
      "\"constant\" torque factors file", consTorqueValFile);
   opts.require("consTorqueOn", "consTorqueValCol",
      "\"constant\" torque factors column", PARSE_STRING);
}

void SimParameters::config_parser_boundary(ParseOptions &opts) {
    
   opts.optionalB("main", "sphericalBC", "Are spherical boundary counditions "
      "active?", &sphericalBCOn, FALSE);
   opts.require("sphericalBC", "sphericalBCCenter",
     "Center of spherical boundaries", &sphericalCenter);
   opts.require("sphericalBC", "sphericalBCr1", "Radius for first sphere "
     "potential", &sphericalBCr1);
   opts.range("sphericalBCr1", POSITIVE);
   opts.units("sphericalBCr1", N_ANGSTROM);
   opts.require("sphericalBC", "sphericalBCk1", "Force constant for first "
    "sphere potential (+ is an inward force, - outward)",
    &sphericalBCk1);
   opts.units("sphericalBCk1", N_KCAL);
   opts.optional("sphericalBC", "sphericalBCexp1", "Exponent for first "
    "sphere potential", &sphericalBCexp1, 2);
   opts.range("sphericalBCexp1", POSITIVE);
   
   opts.optional("sphericalBCr1", "sphericalBCr2", "Radius for second sphere "
     "potential", &sphericalBCr2);
   opts.range("sphericalBCr2", POSITIVE);
   opts.units("sphericalBCr2", N_ANGSTROM);
   opts.require("sphericalBCr2", "sphericalBCk2", "Force constant for second "
    "sphere potential (+ is an inward force, - outward)",
    &sphericalBCk2);
   opts.units("sphericalBCk2", N_KCAL);
   opts.optional("sphericalBCr2", "sphericalBCexp2", "Exponent for second "
    "sphere potential", &sphericalBCexp2, 2);
   opts.range("sphericalBCexp2", POSITIVE);

   opts.optionalB("main", "cylindricalBC", "Are cylindrical boundary counditions "
                  "active?", &cylindricalBCOn, FALSE);
   opts.require("cylindricalBC", "cylindricalBCr1", "Radius for first cylinder "
                 "potential", &cylindricalBCr1);
   opts.range("cylindricalBCr1", POSITIVE);
   opts.units("cylindricalBCr1", N_ANGSTROM);
   opts.require("cylindricalBC", "cylindricalBCk1", "Force constant for first "
                "cylinder potential (+ is an inward force, - outward)",
                &cylindricalBCk1);
   opts.units("cylindricalBCk1", N_KCAL);
   opts.optional("cylindricalBC", "cylindricalBCexp1", "Exponent for first "
                "cylinder potential", &cylindricalBCexp1, 2);
   opts.range("cylindricalBCexp1", POSITIVE);


// additions beyond those already found in spherical parameters    JJU
   opts.optional("cylindricalBC", "cylindricalBCAxis", "Cylinder axis (defaults to x)",
    PARSE_STRING);
   opts.require("cylindricalBC", "cylindricalBCCenter",
     "Center of cylindrical boundaries", &cylindricalCenter);
   opts.require ("cylindricalBC", "cylindricalBCl1", "Length of first cylinder",
                 &cylindricalBCl1);
   opts.range("cylindricalBCl1", POSITIVE);
   opts.units("cylindricalBCl1", N_ANGSTROM);
   opts.optional ("cylindricalBCl1", "cylindricalBCl2", "Length of second cylinder",
                  &cylindricalBCl2);
   opts.range ("cylindricalBCl2", POSITIVE);
   opts.units ("cylindricalBCl2", N_ANGSTROM);
// end  additions

   opts.optional("cylindricalBCr1", "cylindricalBCr2", "Radius for second cylinder "
                 "potential", &cylindricalBCr2);
   opts.range("cylindricalBCr2", POSITIVE);
   opts.units("cylindricalBCr2", N_ANGSTROM);
   opts.require("cylindricalBCr2", "cylindricalBCk2", "Force constant for second "
                "cylinder potential (+ is an inward force, - outward)",
                &cylindricalBCk2);
   opts.units("cylindricalBCk2", N_KCAL);
   opts.optional("cylindricalBCr2", "cylindricalBCexp2", "Exponent for second "
                "cylinder potential", &cylindricalBCexp2, 2);
   opts.range("cylindricalBCexp2", POSITIVE);

   opts.optionalB("main", "eFieldOn", "Should an electric field be applied",
                 &eFieldOn, FALSE);
   opts.optionalB("eFieldOn", "eFieldNormalized", "Is eField vector scaled by cell basis vectors?",
                 &eFieldNormalized, FALSE);
   opts.require("eFieldOn", "eField", "Electric field vector", &eField);
   opts.optional("eFieldOn", "eFieldFreq", "Electric field frequency", &eFieldFreq);
   opts.optional("eFieldOn", "eFieldPhase", "Electric field phase", &eFieldPhase);

   opts.optionalB("main", "stirOn", "Should stirring torque be applied",
                 &stirOn, FALSE);
   opts.optional("stirOn", "stirFilename", "PDB file with flags for "
     "stirred atoms (default is the PDB input file)",
                 PARSE_STRING);
   opts.optional("stirOn", "stirredAtomsCol", "Column in the stirredAtomsFile "
                 "containing the flags (nonzero means fixed);\n"
                 "default is 'O'", PARSE_STRING);
   opts.require("stirOn", "stirStartingTheta", "Stir starting theta offset", &stirStartingTheta);
   opts.require("stirOn", "stirK", "Stir force harmonic spring constant", &stirK);
   //should make this optional, compute from firsttimestep * stirVel
   opts.require("stirOn", "stirVel", "Stir angular velocity (deg/timestep)", &stirVel);
   opts.require("stirOn", "stirAxis", "Stir axis (direction vector)", &stirAxis);
   opts.require("stirOn", "stirPivot", "Stir pivot point (coordinate)", &stirPivot);

   opts.optionalB("main", "extraBonds",
                "Should extra bonded forces be applied",
                 &extraBondsOn, FALSE);
   opts.optional("extraBonds", "extraBondsFile",
                "file with list of extra bonds",
                 PARSE_MULTIPLES);
   opts.optionalB("extraBonds", "extraBondsCosAngles",
                "Should extra angles be cosine-based to match ancient bug",
                &extraBondsCosAngles, TRUE);

}

void SimParameters::config_parser_misc(ParseOptions &opts) {
   
   opts.optional("main", "ldBalancer", "Load balancer",
     loadBalancer);
   opts.optional("main", "ldbStrategy", "Load balancing strategy",
     loadStrategy);
   opts.optional("main", "ldbPeriod", "steps between load balancing", 
     &ldbPeriod);
   opts.range("ldbPeriod", POSITIVE);
   opts.optional("main", "firstLdbStep", "when to start load balancing",
     &firstLdbStep);
   opts.range("firstLdbStep", POSITIVE);
   opts.optional("main", "lastLdbStep", "when to stop load balancing",
     &lastLdbStep);
   opts.range("lastLdbStep", POSITIVE);
   opts.optional("main", "hybridGroupSize", "Hybrid load balancing group size",
     &hybridGroupSize);
   opts.optional("main", "ldbBackgroundScaling",
     "background load scaling", &ldbBackgroundScaling);
   opts.range("ldbBackgroundScaling", NOT_NEGATIVE);
   opts.optional("main", "ldbPMEBackgroundScaling",
     "PME node background load scaling", &ldbPMEBackgroundScaling);
   opts.range("ldbPMEBackgroundScaling", NOT_NEGATIVE);
   opts.optional("main", "ldbHomeBackgroundScaling",
     "home node background load scaling", &ldbHomeBackgroundScaling);
   opts.range("ldbHomeBackgroundScaling", NOT_NEGATIVE);
   opts.optional("main", "ldbRelativeGrainsize",
     "fraction of average load per compute", &ldbRelativeGrainsize, 0.);
   opts.range("ldbRelativeGrainsize", NOT_NEGATIVE);
   
   opts.optional("main", "traceStartStep", "when to start tracing", &traceStartStep);
   opts.range("traceStartStep", POSITIVE);
   opts.optional("main", "numTraceSteps", "the number of timesteps to be traced", &numTraceSteps);
   opts.range("numTraceSteps", POSITIVE);
 
#ifdef MEASURE_NAMD_WITH_PAPI
   opts.optionalB("main", "papiMeasure", "whether use PAPI to measure performacne", &papiMeasure, FALSE);
   opts.optional("main", "papiMeasureStartStep", "when to measure performacne using PAPI", &papiMeasureStartStep);
   opts.range("papiMeasureStartStep", POSITIVE);
   opts.optional("main", "numPapiMeasureSteps", "the number of timesteps to be measured using PAPI", &numPapiMeasureSteps);
   opts.range("numPapiMeasureSteps", POSITIVE);
#endif

   opts.optionalB("main", "outputMaps", "whether to dump compute map and patch map for analysis just before load balancing", &outputMaps, FALSE);
   opts.optionalB("main", "benchTimestep", "whether to do benchmarking timestep in which case final file output is disabled", &benchTimestep, FALSE);
   opts.optional("main", "useCkLoop", "whether to use CkLoop library to parallelize a loop in a function like OpenMP", &useCkLoop,
    #if CMK_SMP && USE_CKLOOP
     ( CkNumPes() < 2 * CkNumNodes() ? 0 : CKLOOP_CTRL_PME_FORWARDFFT ) );
    #else
     0);
    #endif
   opts.range("useCkLoop", NOT_NEGATIVE);

   opts.optionalB("main", "simulateInitialMapping", "whether to study the initial mapping scheme", &simulateInitialMapping, FALSE);
   opts.optional("main", "simulatedPEs", "the number of PEs to be used for studying initial mapping", &simulatedPEs);
   opts.range("simulatedPEs", POSITIVE);
   opts.optional("main", "simulatedNodeSize", "the node size to be used for studying initial mapping", &simulatedNodeSize);
   opts.range("simulatedNodeSize", POSITIVE);
   opts.optionalB("main", "disableTopology", "ignore torus information during patch placement", &disableTopology, FALSE);
   opts.optionalB("main", "verboseTopology", "print torus information during patch placement", &verboseTopology, FALSE);

   opts.optionalB("main", "ldbUnloadPME", "no load on PME nodes",
     &ldbUnloadPME, FALSE);
   opts.optionalB("main", "ldbUnloadZero", "no load on pe zero",
     &ldbUnloadZero, FALSE);
   opts.optionalB("main", "ldbUnloadOne", "no load on pe one",
     &ldbUnloadOne, FALSE);
   opts.optionalB("main", "ldbUnloadOutputPEs", "no load on output PEs",
     &ldbUnloadOutputPEs, FALSE);
   opts.optionalB("main", "noPatchesOnZero", "no patches on pe zero",
     &noPatchesOnZero, FALSE);
   opts.optionalB("main", "noPatchesOnOutputPEs", "no patches on Output PEs",
     &noPatchesOnOutputPEs, FALSE);
   opts.optionalB("main", "noPatchesOnOne", "no patches on pe one",
     &noPatchesOnOne, FALSE);
   opts.optionalB("main", "useCompressedPsf", "The structure file psf is in the compressed format",
                  &useCompressedPsf, FALSE);
   opts.optionalB("main", "genCompressedPsf", "Generate the compressed version of the psf file",
                  &genCompressedPsf, FALSE);
   opts.optionalB("main", "usePluginIO", "Use the plugin I/O to load the molecule system", 
                  &usePluginIO, FALSE);   
   opts.optionalB("main", "mallocTest", "test how much memory all PEs can allocate", 
                  &mallocTest, FALSE);   
   opts.optionalB("main", "printExclusions", "print exclusion lists to stdout", 
                  &printExclusions, FALSE);   
   opts.optional("main", "proxySendSpanningTree", "using spanning tree to send proxies",
                  &proxySendSpanningTree, -1);
   opts.optional("main", "proxyRecvSpanningTree", "using spanning tree to receive proxies",
                  &proxyRecvSpanningTree, 0);  // default off due to memory leak -1);
   opts.optional("main", "proxyTreeBranchFactor", "the branch factor when building a spanning tree",
                  &proxyTreeBranchFactor, 0);  // actual default in ProxyMgr.C
   opts.optionalB("main", "twoAwayX", "half-size patches in 1st dimension",
     &twoAwayX, -1);
   opts.optionalB("main", "twoAwayY", "half-size patches in 2nd dimension",
     &twoAwayY, -1);
   opts.optionalB("main", "twoAwayZ", "half-size patches in 3rd dimension",
     &twoAwayZ, -1);
   opts.optional("main", "maxPatches", "maximum patch count", &maxPatches, -1);

   opts.optional("main", "firsttimestep", "Timestep to start simulation at",
     &firstTimestep, 0);
   opts.range("firsttimestep", NOT_NEGATIVE);
 
   opts.optionalB("main", "test", "Perform self-tests rather than simulation",
                &testOn, FALSE);
   opts.optionalB("main", "commOnly", "Do not evaluate forces or integrate",
                &commOnly, FALSE);

   opts.optionalB("main", "statsOn", "counters in machine layer",
                &statsOn, FALSE);
   opts.optionalB("main", "hbonds", "Use explicit hydrogen bond term",
                 &HydrogenBonds, FALSE);
   opts.optionalB("hbonds","hbAntecedents","Include Antecedent in hbond term",
                 &useAntecedent, TRUE);
   opts.optional("hbonds","hbAAexp","Hbond AA-A-H angle cos exponential",
                 &aaAngleExp, 2);
   opts.optional("hbonds","hbHAexp","Hbond D-H-A angle cos exponential",
                 &haAngleExp, 4);
   opts.optional("hbonds","hbDistAexp","Hbond A-D dist attractive exponential",
                 &distAttExp, 4);
   opts.optional("hbonds","hbDistRexp","Hbond A-D dist repulstive exponential",
                 &distRepExp, 6);
   opts.optional("hbonds","hbCutoffAngle","Hbond D-H-A cutoff angle",
                 &dhaCutoffAngle, 100.0);
   opts.range("hbCutoffAngle", NOT_NEGATIVE);
   opts.optional("hbonds","hbOnAngle","Hbond D-H-A switch function on angle",
                 &dhaOnAngle, 60.0);
   opts.range("hbOnAngle", NOT_NEGATIVE);
   opts.optional("hbonds","hbOffAngle","Hbond D-H-A switch function off angle",
                 &dhaOffAngle, 80.0);
   opts.range("hbOffAngle", NOT_NEGATIVE);
   opts.optional("hbonds","hbCutoffDist","Hbond A-D cutoff distance",
                 &daCutoffDist, 7.5);
   opts.range("hbCutoffDist", POSITIVE);
   opts.units("hbCutoffDist", N_ANGSTROM);
   opts.optional("hbonds","hbOnDist","Hbond A-D switch function on distance",
                 &daOnDist, 5.5);
   opts.range("hbOnDist", POSITIVE);
   opts.units("hbOnDist", N_ANGSTROM);
   opts.optional("hbonds","hbOffDist","Hbond A-D switch function off distance",
                 &daOffDist, 6.5);
   opts.range("hbOffDist", POSITIVE);
   opts.units("hbOffDist", N_ANGSTROM);

   // IMD options
   opts.optionalB("main","IMDon","Connect using IMD?",&IMDon, FALSE);
   opts.optional("IMDon","IMDversion","IMD protocol version number",&IMDversion,2);
   opts.range("IMDversion",POSITIVE);
   opts.require("IMDon","IMDport", "Port to which to bind", &IMDport);
   opts.range("IMDport",POSITIVE);
   opts.require("IMDon","IMDfreq", "Frequency at which to report", &IMDfreq);
   opts.range("IMDfreq",POSITIVE);
   opts.optionalB("IMDon","IMDwait","Pause until IMD connection?",&IMDwait,
     FALSE);
   opts.optionalB("IMDon","IMDignore","Ignore any user input?",&IMDignore,
     FALSE);
   opts.optionalB("IMDon","IMDignoreForces","Ignore forces ONLY?",&IMDignoreForces,
     FALSE);
   opts.optionalB("IMDon","IMDsendTime","Send time information",&IMDsendsettings.time_switch,
     FALSE);
   opts.optionalB("IMDon","IMDsendEnergies","Send energies via IMD:",&IMDsendsettings.energies_switch,
     TRUE);
   opts.optionalB("IMDon","IMDsendBoxDimensions","Send box dimensions via IMD:",&IMDsendsettings.box_switch,
     FALSE);
   opts.optionalB("IMDon","IMDsendPositions","Send positions via IMD:",&IMDsendsettings.fcoords_switch,
     TRUE);
   opts.optionalB("IMDon","IMDwrapPositions","Send positions as wrapped:",&IMDsendsettings.wrap_switch,
     TRUE);
   opts.optionalB("IMDon","IMDsendVelocities","Send velocities via IMD:",&IMDsendsettings.velocities_switch,
     FALSE);
   opts.optionalB("IMDon","IMDsendForces","Send forces via IMD:",&IMDsendsettings.forces_switch,
     FALSE);
   // Maximum Partition options
   opts.optional("ldBalancer", "maxSelfPart", 
     "maximum number of self partitions in one patch", &maxSelfPart, 20);
   opts.range("maxSelfPart",POSITIVE);
   opts.optional("ldBalancer", "maxPairPart", 
     "maximum number of pair partitions in one patch", &maxPairPart, 8);
   opts.range("maxPairPart",POSITIVE);
   opts.optional("ldBalancer", "numAtomsSelf", 
                 "maximum number of atoms in one self compute distribution", 
                 &numAtomsSelf, 154);
   opts.range("numAtomsSelf",NOT_NEGATIVE);

   opts.optional("ldBalancer", "numAtomsSelf2", 
                 "maximum number of atoms in one self compute distribution", 
                 &numAtomsSelf2, 154);
   opts.range("numAtomsSelf2",NOT_NEGATIVE);

   opts.optional("ldBalancer", "numAtomsPair", 
                 "maximum number of atoms in one pair compute distribution", 
                 &numAtomsPair, 318);
   opts.range("numAtomsPair",NOT_NEGATIVE);
   opts.optional("ldBalancer", "numAtomsPair2", 
               "maximum number of atoms in one pair compute distribution", 
               &numAtomsPair2, 637);
   opts.range("numAtomsPair2",NOT_NEGATIVE);
   opts.optional("main", "minAtomsPerPatch", 
               "minimum average atoms per patch", 
               &minAtomsPerPatch, 40);
   opts.range("minAtomsPerPatch",NOT_NEGATIVE);

   // Set number added to patch atom count during initial node assignment
   opts.optional("main", "emptyPatchLoad",
               "load generated by empty patch, in atoms",
               &emptyPatchLoad, 40);
   opts.range("emptyPatchLoad",POSITIVE);

   // Maximum exclusion flags per atom
   opts.optional("main", "maxExclusionFlags", 
     "maximum number of exclusion flags per atom", &maxExclusionFlags, 256);
   opts.range("maxExclusionFlags",POSITIVE);

   // Bonded interactions on GPU
   opts.optional("main", "bondedCUDA", "Bitmask for calculating bonded interactions on GPU", &bondedCUDA, NAMD_BONDEDGPU_ALL);
   opts.optional("main", "bondedGPU", "Bitmask for calculating bonded interactions on GPU", &bondedGPU);

   // Automatically disable individual CUDA kernels that are
   // incompatible with simulation options.
   // Set FALSE to manually control kernel use for development.
   opts.optionalB("main", "useCUDAdisable", "Disable kernels to maintain feature compatibility with CUDA", &useCUDAdisable, TRUE);

   // MIC specific parameters
   opts.optional("main", "mic_unloadMICPEs", "Indicates whether or not the load balancer should unload PEs driving Xeon Phi cards", &mic_unloadMICPEs, 1);
   opts.optional("main", "mic_singleKernel", "Set to non-zero to have all MIC work to be placed in a single kernel", &mic_singleKernel, 1);
   opts.optional("main", "mic_deviceThreshold", "Threshold to use for directing computes to Xeon Phi devices", &mic_deviceThreshold, -1);
   opts.optional("main", "mic_hostSplit", "DMK - reserved", &mic_hostSplit, -1);
   opts.optional("main", "mic_numParts_self_p1", "MIC-Specific NumParts SELF Parameter 1", &mic_numParts_self_p1, -1);
   opts.optional("main", "mic_numParts_pair_p1", "MIC-Specific NumParts PAIR Parameter 1", &mic_numParts_pair_p1, -1);
   opts.optional("main", "mic_numParts_pair_p2", "MIC-Specific NumParts PAIR Parameter 2", &mic_numParts_pair_p2, -1);
   opts.range("mic_unloadMICPEs", NOT_NEGATIVE);
   opts.range("mic_singleKernel", NOT_NEGATIVE);
}

void SimParameters::readExtendedSystem(const char *filename, Lattice *latptr) {

     if ( ! latptr ) {
       iout << iINFO << "EXTENDED SYSTEM FILE   " << filename << "\n" << endi;
     }

     ifstream xscFile(filename);
     if ( ! xscFile ) NAMD_die("Unable to open extended system file.\n");

     char labels[1024];
     do {
       if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
       xscFile.getline(labels,1023);
     } while ( strncmp(labels,"#$LABELS ",9) );

     int a_x, a_y, a_z, b_x, b_y, b_z, c_x, c_y, c_z;
     a_x = a_y = a_z = b_x = b_y = b_z = c_x = c_y = c_z = -1;
     int o_x, o_y, o_z, s_u, s_v, s_w, s_x, s_y, s_z;
     o_x = o_y = o_z = s_u = s_v = s_w = s_x = s_y = s_z = -1;
     int v_x = -1, v_y = -1 , v_z = -1;

     int pos = 0;
     char *l_i = labels + 8;
     while ( *l_i ) {
       if ( *l_i == ' ' ) { ++l_i; continue; }
       char *l_i2;
       for ( l_i2 = l_i; *l_i2 && *l_i2 != ' '; ++l_i2 );
       if ( (l_i2 - l_i) == 3 && (l_i[1] == '_') ) {
         if (l_i[0] == 'a' && l_i[2] == 'x') a_x = pos;
         if (l_i[0] == 'a' && l_i[2] == 'y') a_y = pos;
         if (l_i[0] == 'a' && l_i[2] == 'z') a_z = pos;
         if (l_i[0] == 'b' && l_i[2] == 'x') b_x = pos;
         if (l_i[0] == 'b' && l_i[2] == 'y') b_y = pos;
         if (l_i[0] == 'b' && l_i[2] == 'z') b_z = pos;
         if (l_i[0] == 'c' && l_i[2] == 'x') c_x = pos;
         if (l_i[0] == 'c' && l_i[2] == 'y') c_y = pos;
         if (l_i[0] == 'c' && l_i[2] == 'z') c_z = pos;
         if (l_i[0] == 'o' && l_i[2] == 'x') o_x = pos;
         if (l_i[0] == 'o' && l_i[2] == 'y') o_y = pos;
         if (l_i[0] == 'o' && l_i[2] == 'z') o_z = pos;
         if (l_i[0] == 's' && l_i[2] == 'u') s_u = pos;
         if (l_i[0] == 's' && l_i[2] == 'v') s_v = pos;
         if (l_i[0] == 's' && l_i[2] == 'w') s_w = pos;
         if (l_i[0] == 's' && l_i[2] == 'x') s_x = pos;
         if (l_i[0] == 's' && l_i[2] == 'y') s_y = pos;
         if (l_i[0] == 's' && l_i[2] == 'z') s_z = pos;
         if (l_i[0] == 'v' && l_i[2] == 'x') v_x = pos;
         if (l_i[0] == 'v' && l_i[2] == 'y') v_y = pos;
         if (l_i[0] == 'v' && l_i[2] == 'z') v_z = pos;
       }
       ++pos;
       l_i = l_i2;
     }
     int numpos = pos;

     for ( pos = 0; pos < numpos; ++pos ) {
       double tmp;
       xscFile >> tmp;
       if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
       if ( pos == a_x ) cellBasisVector1.x = tmp;
       if ( pos == a_y ) cellBasisVector1.y = tmp;
       if ( pos == a_z ) cellBasisVector1.z = tmp;
       if ( pos == b_x ) cellBasisVector2.x = tmp;
       if ( pos == b_y ) cellBasisVector2.y = tmp;
       if ( pos == b_z ) cellBasisVector2.z = tmp;
       if ( pos == c_x ) cellBasisVector3.x = tmp;
       if ( pos == c_y ) cellBasisVector3.y = tmp;
       if ( pos == c_z ) cellBasisVector3.z = tmp;
       if ( pos == o_x ) cellOrigin.x = tmp;
       if ( pos == o_y ) cellOrigin.y = tmp;
       if ( pos == o_z ) cellOrigin.z = tmp;
       if ( pos == s_u ) strainRate2.x = tmp;
       if ( pos == s_v ) strainRate2.y = tmp;
       if ( pos == s_w ) strainRate2.z = tmp;
       if ( pos == s_x ) strainRate.x = tmp;
       if ( pos == s_y ) strainRate.y = tmp;
       if ( pos == s_z ) strainRate.z = tmp;
       if ( pos == v_x ) monteCarloMaxVolume.x = tmp;
       if ( pos == v_y ) monteCarloMaxVolume.y = tmp;
       if ( pos == v_z ) monteCarloMaxVolume.z = tmp;
     }

   if ( latptr ) {
     Lattice test;
     test.set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
    
     if ( test.a_p() && ! lattice.a_p() ) {
       NAMD_die("cellBasisVector1 added during atom reinitialization");
     }
     if ( lattice.a_p() && ! test.a_p() ) {
       NAMD_die("cellBasisVector1 dropped during atom reinitialization");
     }
     if ( test.b_p() && ! lattice.b_p() ) {
       NAMD_die("cellBasisVector2 added during atom reinitialization");
     }
     if ( lattice.b_p() && ! test.b_p() ) {
       NAMD_die("cellBasisVector2 dropped during atom reinitialization");
     }
     if ( test.c_p() && ! lattice.c_p() ) {
       NAMD_die("cellBasisVector3 added during atom reinitialization");
     }
     if ( lattice.c_p() && ! test.c_p() ) {
       NAMD_die("cellBasisVector3 dropped during atom reinitialization");
     }

     latptr->set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
   }

}

#ifdef MEM_OPT_VERSION
//This global var is defined in mainfunc.C
extern char *gWorkDir;
#endif

void SimParameters::check_config(ParseOptions &opts, ConfigList *config, char *&cwd) {
   
   int len;    //  String length
   StringList *current; //  Pointer to config option list

#ifdef MEM_OPT_VERSION
   char *namdWorkDir = NULL;
#endif

  if ( opts.defined("obsolete") ) {
    iout << iWARN <<
      "\"obsolete\" defined, silently ignoring obsolete options\n" << endi;
  }

   //  Take care of cwd processing
   if (opts.defined("cwd"))
   {
    //  First allocate and get the cwd value
    current = config->find("cwd");

    len = strlen(current->data);

    if ( CHDIR(current->data) )
    {
      NAMD_die("chdir() to given cwd failed!");
    } else {
      iout << iINFO << "Changed directory to " << current->data << "\n" << endi;
    }

    if (current->data[len-1] != PATHSEP)
      len++;

    cwd = new char[len+1];

    strcpy(cwd, current->data);

    if (current->data[strlen(current->data)-1] != PATHSEP)
      strcat(cwd, PATHSEPSTR);
   }

#ifdef MEM_OPT_VERSION
   if(cwd!=NULL)namdWorkDir = cwd;     
   else namdWorkDir = gWorkDir;
   int dirlen = strlen(namdWorkDir);
   //only support the path representation on UNIX-like platforms
   char *tmpDir;
   if(namdWorkDir[dirlen-1]=='/'){
     tmpDir = new char[dirlen+1];
     tmpDir[dirlen] = 0;
   }else{
     tmpDir = new char[dirlen+2];
     tmpDir[dirlen]='/';
     tmpDir[dirlen+1]=0;
   } 
   memcpy(tmpDir, namdWorkDir, dirlen);
   namdWorkDir = tmpDir;
 //finished recording the per atom files, free the space for gWorkDir
   delete [] gWorkDir;
#endif

   // XXX Deal with deprecated parameters here!
   //
   // Checking for deprecated parameters and multiple definitions when using 
   // different keywords below, keep in mind some quirks:
   //
   // opts.defined("keyword") is true if "keyword" defined with initial value,
   // whether or not it is set in the config file
   //
   // config->find("keyword") is true only if "keyword" set in config file;
   // however, the find() function requires searching through a linked list,
   // so is best avoided
   //
   // The conditional block checking to overwrite existing parameter with 
   // new one (e.g. scale14 = scale14alt) works by NOT giving the 
   // config parameter name (e.g. "oneFourScaling") an initial value.

   // Overwrite scale14?
   if (opts.defined("oneFourScaling")) {
     // check if "1-4scaling" was also defined and bail if it did
     if (config->find("1-4scaling")) {
      NAMD_die("Multiple definitions of 1-4scaling using \"1-4scaling\" and \"oneFourScaling\".");
     }
     scale14 = scale14alt;
   }
   else if (config->find("1-4scaling")) {
     iout << iWARN << "Option \"1-4scaling\" has been deprecated. Instead use \"oneFourScaling\".\n" << endi;
   }

   // Overwrite CUDASOAintegrateMode with value from GPUresidentMode?
   if (opts.defined("GPUresident")) {
     // make sure not both "GPUresident" and "CUDASOAintegrate" defined
     if (config->find("CUDASOAintegrate")) {
       NAMD_die("Multiple definitions of GPUresident using \"CUDASOAintegrate\" and \"GPUresident\".");
     }
     CUDASOAintegrateMode = GPUresidentMode;
   }
   else if (config->find("CUDASOAintegrate")) {
     iout << iWARN << "Option \"CUDASOAintegrate\" has been deprecated. Instead use \"GPUresident\".\n" << endi;
   }

   // Overwrite CUDAForceTable with value from GPUForceTable?
   if (opts.defined("GPUForceTable")) {
     // make sure not both "GPUForceTable" and "CUDAForceTable" are defined
     if (config->find("CUDAForceTable")) {
       NAMD_die("Multiple definitions of GPUForceTable using \"CUDAForceTable\" and \"GPUForceTable\".");
     }
     useCUDANonbondedForceTable = useGPUNonbondedForceTable;
   }
   else if (config->find("CUDAForceTable")) {
     iout << iWARN << "Option \"CUDAForceTable\" has been deprecated. Instead use \"GPUForceTable\".\n" << endi;
   }
   if ( ! useCUDANonbondedForceTable) {
     iout << iWARN << "Setting \"GPUForceTable off\" is considered experimental.\n" << endi;
   }

   // Overwrite DeviceMigration with value from GPUAtomMigration?
   if (opts.defined("GPUAtomMigration")) {
     // make sure not both "GPUAtomMigration" and "DeviceMigration" are defined
     if (config->find("DeviceMigration")) {
       NAMD_die("Multiple definitions of GPUAtomMigration using \"DeviceMigration\" and \"GPUAtomMigration\".");
     }
     useDeviceMigration = useGPUAtomMigration;
   }
   else if (config->find("DeviceMigration")) {
     iout << iWARN << "Option \"DeviceMigration\" has been deprecated. Instead use \"GPUAtomMigration\".\n" << endi;
   }
   if (useDeviceMigration) {
     iout << iWARN << "Setting \"GPUAtomMigration on\" is considered experimental.\n" << endi;
   }

   // Overwrite usePMECUDA with value from usePMEGPU?
   if (opts.defined("usePMEGPU")) {
     // make sure not both "usePMEGPU" and "usePMECUDA" are defined
     if (config->find("usePMECUDA")) {
       NAMD_die("Multiple definitions of usePMEGPU using \"usePMECUDA\" and \"usePMEGPU\".");
     }
     usePMECUDA = usePMEGPU;
   }
   else if (config->find("usePMECUDA")) {
     iout << iWARN << "Option \"usePMECUDA\" has been deprecated. Instead use \"usePMEGPU\".\n" << endi;
   }

   // Overwrite bondedCUDA with value from bondedGPU?
   if (opts.defined("bondedGPU")) {
     // make sure not both "bondedGPU" and "bondedCUDA" are defined
     if (config->find("bondedCUDA")) {
       NAMD_die("Multiple definitions of bondedGPU using \"bondedCUDA\" and \"bondedGPU\".");
     }
     bondedCUDA = bondedGPU;
   }
   else if (config->find("bondedCUDA")) {
     iout << iWARN << "Option \"bondedCUDA\" has been deprecated. Instead use \"bondedGPU\".\n" << endi;
   }


   // Don't try to specify coordinates with pluginIO
   if ( usePluginIO && opts.defined("coordinates") ) {
     NAMD_die("Separate coordinates file not allowed with plugin IO, coordinates will be taken from structure file.");
   }

   // If it's not AMBER||GROMACS, then "coordinates", "structure"
   // and "parameters" must be specified.
   if (!amberOn && !gromacsOn) {
#ifndef MEM_OPT_VERSION
     if (useCompressedPsf)
       NAMD_die("useCompressedPsf requires memory-optimized build!");
     if (!usePluginIO && !genCompressedPsf && !opts.defined("coordinates"))
       NAMD_die("coordinates not found in the configuration file!");
#else
     if(!usePluginIO && !opts.defined("bincoordinates")) {
       NAMD_die("bincoordinates not found in the configuration file for the memory optimized version!");
     }
     if(!usePluginIO && opts.defined("coordinates")) {
       NAMD_die("coordinates not allowed in the configuration file for the memory optimized version!");
     }
#endif
     if (!opts.defined("structure"))
       NAMD_die("structure not found in the configuration file!");
     if (!opts.defined("parameters"))
       NAMD_die("parameters not found in the configuration file!");
   }
   
   // In any case, there should be either "coordinates" or
   // "ambercoor", but not both
   if (opts.defined("coordinates") && opts.defined("ambercoor"))
     NAMD_die("Cannot specify both coordinates and ambercoor!");
#ifndef MEM_OPT_VERSION
   if (!genCompressedPsf && !opts.defined("coordinates") && !opts.defined("ambercoor")
       && !opts.defined("grocoorfile") && !usePluginIO)
     NAMD_die("Coordinate file not found!");
#endif

   //  Make sure that both a temperature and a velocity PDB were
   //  specified
   if (opts.defined("temperature") &&
       (opts.defined("velocities") || opts.defined("binvelocities")) ) 
   {
      NAMD_die("Cannot specify both an initial temperature and a velocity file");
   }

#ifdef MEM_OPT_VERSION
//record the absolute file name for binAtomFile, binCoorFile and binVelFile etc.
   binAtomFile = NULL;
   binCoorFile = NULL;
   binVelFile = NULL;   
   binRefFile = NULL;

   char *curfile = NULL;
   dirlen = strlen(namdWorkDir);
   current = config->find("structure");;
   curfile = current->data;
   int filelen = strlen(curfile);
   if(*curfile == '/' || *curfile=='~') {
     //check whether it is an absolute path
     //WARNING: Only works on Unix-like platforms!
     //Needs to fix on Windows platform.
     //-Chao Mei     
     //adding 5 because of ".bin"+"\0"
     binAtomFile = new char[filelen+5];
     memcpy(binAtomFile, curfile, filelen);
     memcpy(binAtomFile+filelen, ".bin", 4);
     binAtomFile[filelen+4] = 0;
   }else{
     binAtomFile = new char[dirlen+filelen+5];
     memcpy(binAtomFile, namdWorkDir, dirlen);
     memcpy(binAtomFile+dirlen, curfile, filelen);
     memcpy(binAtomFile+dirlen+filelen, ".bin", 4);
     binAtomFile[dirlen+filelen+4] = 0;
   }

   current = config->find("bincoordinates");
   curfile = current->data;
   filelen = strlen(curfile);
   if(*curfile == '/' || *curfile=='~') {
     binCoorFile = new char[filelen+1];
     memcpy(binCoorFile, curfile, filelen);
     binCoorFile[filelen] = 0;
   }else{
     binCoorFile = new char[dirlen+filelen+1];
     memcpy(binCoorFile, namdWorkDir, dirlen);
     memcpy(binCoorFile+dirlen, curfile, filelen);
     binCoorFile[dirlen+filelen] = 0;
   }

   if(opts.defined("binvelocities")){
     current = config->find("binvelocities");
     curfile = current->data;
     filelen = strlen(curfile);
     if(*curfile == '/' || *curfile=='~') {
       binVelFile = new char[filelen+1];
       memcpy(binVelFile, curfile, filelen);
       binVelFile[filelen] = 0;
     }else{
       binVelFile = new char[dirlen+filelen+1];
       memcpy(binVelFile, namdWorkDir, dirlen);
       memcpy(binVelFile+dirlen, curfile, filelen);
       binVelFile[dirlen+filelen] = 0;
     }
   }

   if(opts.defined("binrefcoords")){
     current = config->find("binrefcoords");
     curfile = current->data;
     filelen = strlen(curfile);
     if(*curfile == '/' || *curfile=='~') {
       binRefFile = new char[filelen+1];
       memcpy(binRefFile, curfile, filelen);
       binRefFile[filelen] = 0;
     }else{
       binRefFile = new char[dirlen+filelen+1];
       memcpy(binRefFile, namdWorkDir, dirlen);
       memcpy(binRefFile+dirlen, curfile, filelen);
       binRefFile[dirlen+filelen] = 0;
     }
   }

   //deal with output file name to make it absolute path for parallel output
   if(outputFilename[0] != '/' && outputFilename[0]!='~') {
     filelen = strlen(outputFilename);
     char *tmpout = new char[filelen];
     memcpy(tmpout, outputFilename, filelen);
     CmiAssert(filelen+dirlen <= 120); //leave 8 chars for file suffix
     memcpy(outputFilename, namdWorkDir, dirlen);
     memcpy(outputFilename+dirlen, tmpout, filelen);
     outputFilename[filelen+dirlen] = 0;     
     delete [] tmpout;
   }

   if ( dcdFrequency && opts.defined("dcdfile") &&
        dcdFilename[0] != '/' && dcdFilename[0]!='~' ) {
     filelen = strlen(dcdFilename);
     char *tmpout = new char[filelen];
     memcpy(tmpout, dcdFilename, filelen);
     CmiAssert(filelen+dirlen <= 120); //leave 8 chars for file suffix
     memcpy(dcdFilename, namdWorkDir, dirlen);
     memcpy(dcdFilename+dirlen, tmpout, filelen);
     dcdFilename[filelen+dirlen] = 0;     
     delete [] tmpout;
   }

   if ( velDcdFrequency && opts.defined("veldcdfile") &&
        velDcdFilename[0] != '/' && velDcdFilename[0]!='~' ) {
     filelen = strlen(velDcdFilename);
     char *tmpout = new char[filelen];
     memcpy(tmpout, velDcdFilename, filelen);
     CmiAssert(filelen+dirlen <= 120); //leave 8 chars for file suffix
     memcpy(velDcdFilename, namdWorkDir, dirlen);
     memcpy(velDcdFilename+dirlen, tmpout, filelen);
     velDcdFilename[filelen+dirlen] = 0;     
     delete [] tmpout;
   }

   if ( forceDcdFrequency && opts.defined("forcedcdfile") &&
        forceDcdFilename[0] != '/' && forceDcdFilename[0]!='~' ) {
     filelen = strlen(forceDcdFilename);
     char *tmpout = new char[filelen];
     memcpy(tmpout, forceDcdFilename, filelen);
     CmiAssert(filelen+dirlen <= 120); //leave 8 chars for file suffix
     memcpy(forceDcdFilename, namdWorkDir, dirlen);
     memcpy(forceDcdFilename+dirlen, tmpout, filelen);
     forceDcdFilename[filelen+dirlen] = 0;     
     delete [] tmpout;
   }

   if ( restartFrequency && opts.defined("restartname") &&
        restartFilename[0] != '/' && restartFilename[0]!='~' ) {
     filelen = strlen(restartFilename);
     char *tmpout = new char[filelen];
     memcpy(tmpout, restartFilename, filelen);
     CmiAssert(filelen+dirlen <= 120); //leave 8 chars for file suffix
     memcpy(restartFilename, namdWorkDir, dirlen);
     memcpy(restartFilename+dirlen, tmpout, filelen);
     restartFilename[filelen+dirlen] = 0;     
     delete [] tmpout;
   }

   if ( (crashOutputFlag & NAMD_CRASH_ALL) && opts.defined("crashFile") &&
        crashFilename[0] != '/' && crashFilename[0] != '~') {
     filelen = strlen(crashFilename);
     char *tmpout = new char[filelen];
     memcpy(tmpout, crashFilename, filelen);
     CmiAssert(filelen+dirlen <= 120); //leave 8 chars for file suffix
     memcpy(crashFilename, namdWorkDir, dirlen);
     memcpy(crashFilename+dirlen, tmpout, filelen);
     crashFilename[filelen+dirlen] = 0;
     delete [] tmpout;
   }

   delete [] namdWorkDir;

   if (opts.defined("numinputprocs")) { 
     if(numinputprocs > CkNumPes()) {
       iout << iWARN << "The number of input processors exceeds the total number of processors. Resetting to half of the number of total processors.\n" << endi;
       numinputprocs = (CkNumPes()>>1)+(CkNumPes()&1);
     }
   }

   if (opts.defined("numoutputprocs")) {        
     if(numoutputprocs > CkNumPes()) {
       iout << iWARN << "The number of output processors exceeds the total number of processors. Resetting to half of the number of total processors.\n" << endi;
       numoutputprocs = (CkNumPes()>>1)+(CkNumPes()&1);
     }
   }

#ifndef OUTPUT_SINGLE_FILE
#error OUTPUT_SINGLE_FILE not defined!
#endif

   #if !OUTPUT_SINGLE_FILE
   //create directories for multi-file output scheme   
   create_output_directories("coor");
   create_output_directories("vel");
   if(dcdFrequency) {
           create_output_directories("dcd");
           if(opts.defined("dcdfile")){
                   iout << iWARN << "The dcd file output has been changed to directory: " << outputFilename << ".\n" << endi; 
           }
   }
   if (velDcdFrequency) {
           create_output_directories("veldcd");
           if(opts.defined("veldcdfile")){       
                   iout << iWARN << "The veldcd file output has been changed to directory: " << outputFilename << ".\n" << endi;
           }
   }
   if (forceDcdFrequency) {
           create_output_directories("forcedcd");
           if(opts.defined("forcedcdfile")){       
                   iout << iWARN << "The forcedcd file output has been changed to directory: " << outputFilename << ".\n" << endi;
           }
   }
   #endif
#endif

   if (! opts.defined("auxFile")) {
     strcpy(auxFilename,outputFilename);
     strcat(auxFilename,".aux");
   }

   //  Check for frequencies
   if (dcdFrequency) {
     if (! opts.defined("dcdfile")) {
       strcpy(dcdFilename,outputFilename);
       strcat(dcdFilename,".dcd");
     }
   } else {
     dcdFilename[0] = STRINGNULL;
   }

   if (velDcdFrequency) {
     if (! opts.defined("veldcdfile")) {
       strcpy(velDcdFilename,outputFilename);
       strcat(velDcdFilename,".veldcd");
     }
   } else {
     velDcdFilename[0] = STRINGNULL;
   }
   
   if (forceDcdFrequency) {
     if (! opts.defined("forcedcdfile")) {
       strcpy(forceDcdFilename,outputFilename);
       strcat(forceDcdFilename,".forcedcd");
     }
   } else {
     forceDcdFilename[0] = STRINGNULL;
   }
   
   if (xstFrequency) {
     if (! opts.defined("xstfile")) {
       strcpy(xstFilename,outputFilename);
       strcat(xstFilename,".xst");
     }
   } else {
     xstFilename[0] = STRINGNULL;
   }

   if (restartFrequency) {
     if (! opts.defined("restartname")) {
       strcpy(restartFilename,outputFilename);
       if ( ! restartSave ) strcat(restartFilename,".restart");
     }
   } else {
     restartFilename[0] = STRINGNULL;
     restartSave = FALSE;
     binaryRestart = FALSE;
   }

   if (crashOutputFlag & NAMD_CRASH_ALL) {
     if (!opts.defined("crashFile")) {
       strcpy(crashFilename, outputFilename);
       strcat(crashFilename, ".crash.csv");
     }
   } else {
     crashFilename[0] = STRINGNULL;
   }

   if (storeComputeMap || loadComputeMap) {
     if (! opts.defined("computeMapFile")) {
       strcpy(computeMapFilename,"computeMapFile");
       strcat(computeMapFilename,".txt");
     }
   }


   if (!amberOn)
   { //****** BEGIN CHARMM/XPLOR type changes
     if (!paraTypeXplorOn && !paraTypeCharmmOn) 
     {
       paraTypeXplorOn = TRUE;
     }
     if (paraTypeXplorOn && paraTypeCharmmOn) 
     {
       NAMD_die("Please specify either XPLOR or CHARMM format for parameters!");
     }
     //****** END CHARMM/XPLOR type changes
   }

   
   //  If minimization isn't on, must have a temp or velocity
   if (!(minimizeOn||minimizeCGOn) && !opts.defined("temperature") && 
       !opts.defined("velocities") && !opts.defined("binvelocities") ) 
   {
      NAMD_die("Must have either an initial temperature or a velocity file");
   }

   if (minimizeOn||minimizeCGOn) { initialTemp = 0.0; }
   if (opts.defined("velocities") || opts.defined("binvelocities") )
   {
  initialTemp = -1.0;
   }

  if (LJcorrection && LJcorrectionAlt) {
    NAMD_die("Only one method for LJ tail correction must be used.");
  }

   if ( opts.defined("extendedSystem") ) readExtendedSystem(config->find("extendedSystem")->data);

#ifdef MEM_OPT_VERSION
   if ( LJcorrection ) {
      NAMD_die("LJ tail corrections not yet available for memory optimized builds");
   }
   if ( LJcorrectionAlt ) {
      NAMD_die("Alternative LJ tail corrections not yet available for memory optimized builds");
   }
#endif

   if ( LJcorrection && ! cellBasisVector3.length2() ) {
     NAMD_die("Can't use LJ tail corrections without periodic boundary conditions!");
   }

   if ( LJcorrectionAlt && ! cellBasisVector3.length2() ) {
     NAMD_die("Can't use alternative LJ tail corrections without periodic boundary conditions!");
   }

   if ( cellBasisVector3.length2() && ! cellBasisVector2.length2() ) {
     NAMD_die("Used cellBasisVector3 without cellBasisVector2!");
   }

   if ( cellBasisVector2.length2() && ! cellBasisVector1.length2() ) {
     NAMD_die("Used cellBasisVector2 without cellBasisVector1!");
   }

   if ( cellOrigin.length2() && ! cellBasisVector1.length2() ) {
     NAMD_die("Used cellOrigin without cellBasisVector1!");
   }

   lattice.set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);

   if (! opts.defined("DCDunitcell")) {
      dcdUnitCell = lattice.a_p() && lattice.b_p() && lattice.c_p();
   }

   char s[129];

   if ( ! opts.defined("cylindricalBCAxis") )
   {
      cylindricalBCAxis = 'x';
   }
   else
   {
     opts.get("cylindricalBCAxis", s);

     if (!strcasecmp(s, "x"))
     {
      cylindricalBCAxis = 'x';
     }
     else if (!strcasecmp(s, "y"))
     {
      cylindricalBCAxis = 'y';
     }
     else if (!strcasecmp(s, "z"))
     {
      cylindricalBCAxis = 'z';
     }
   else
     {
      char err_msg[128];

      sprintf(err_msg, "Illegal value '%s' for 'cylindricalBCAxis' in configuration file", s);
      NAMD_die(err_msg);
     }
   }

   if (!opts.defined("splitPatch"))
   {
     splitPatch = SPLIT_PATCH_HYDROGEN;
   }
   else
   {
     opts.get("splitPatch", s);
     if (!strcasecmp(s, "position"))
       splitPatch = SPLIT_PATCH_POSITION;
     else if (!strcasecmp(s,"hydrogen"))
       splitPatch = SPLIT_PATCH_HYDROGEN;
     else
     {
       char err_msg[129];
       sprintf(err_msg, 
          "Illegal value '%s' for 'splitPatch' in configuration file", 
       s);
       NAMD_die(err_msg);
     }
   }

   opts.get("exclude", s);

   if (!strcasecmp(s, "none"))
   {
      exclude = NONE;
      splitPatch = SPLIT_PATCH_POSITION;
   }
   else if (!strcasecmp(s, "1-2"))
   {
      exclude = ONETWO;
      splitPatch = SPLIT_PATCH_POSITION;
   }
   else if (!strcasecmp(s, "1-3"))
   {
      exclude = ONETHREE;
   }
   else if (!strcasecmp(s, "1-4"))
   {
      exclude = ONEFOUR;
   }
   else if (!strcasecmp(s, "scaled1-4"))
   {
      exclude = SCALED14;
   }
   else
   {
      char err_msg[128];

      sprintf(err_msg, "Illegal value '%s' for 'exclude' in configuration file",
   s);
      NAMD_die(err_msg);
   }

   if (scale14 != 1.0 && exclude != SCALED14)
   {
      iout << iWARN << "Exclude is not scaled1-4; 1-4scaling ignored.\n" << endi;
   }

   // water model stuff
   if (!opts.defined("waterModel")) {
     watmodel = WaterModel::TIP3;
   } else {
     opts.get("waterModel", s);
     if (!strncasecmp(s, "tip4", 4)) {
       iout << iINFO << "Using TIP4P water model.\n" << endi;
       watmodel = WaterModel::TIP4;
     } else if (!strncasecmp(s, "tip3", 4)) {
       iout << iINFO << "Using TIP3P water model.\n" << endi;
       watmodel = WaterModel::TIP3;
     } else if (!strncasecmp(s, "swm4", 4)) {
       iout << iINFO << "Using SWM4-DP water model.\n" << endi;
       watmodel = WaterModel::SWM4;
     } else {
       char err_msg[128];
       sprintf(err_msg,
           "Illegal value %s for 'waterModel' in configuration file", s);
       NAMD_die(err_msg);
     }
   }
   if (watmodel == WaterModel::SWM4 && !drudeOn) {
     NAMD_die("Must have 'drudeOn' enabled to use SWM4-DP water model.");
   }
   if (drudeOn && watmodel != WaterModel::SWM4) {
     watmodel = WaterModel::SWM4;
     iout << iWARN
       << "Setting water model to 'swm4' (SWM4-DP) for Drude polarization.\n"
       << endi;
   }

   // Drude water model uses "lonepairs"
   if (watmodel == WaterModel::SWM4) {
     lonepairs = TRUE;
   }

   // Added by JLai -- 8.2.11 -- Checks if Go method is defined
   if (goForcesOn) {
     iout << iINFO << "Go forces are on\n" << endi;
   // Added by JLai -- 6.3.11 -- Checks if Go method is defined
     int * gomethod = &goMethod;
     if (!opts.defined("GoMethod")) {
       *gomethod = 0;
       //     printf("GO METHOD IS NOT DEFINED SO WE'LL SET IT TO SOME WEIRD VALUE\n");
     } else {
       opts.get("GoMethod",s);
       // printf("GO METHOD IS DEFINED SO WE'LL PRINT IT OUT: %s\n",s);
       *gomethod = atoi(s);
     }
     if (!strcasecmp(s, "matrix")) {
       goMethod = 1;
       //GoMethod = GO_MATRIX;
     } else if (!strcasecmp(s, "faster")) {
       goMethod = 2;
       //GoMethod = GO_FASTER;
     } else if (!strcasecmp(s, "lowmem")) {
       goMethod = 3;
       //GoMethod = GO_LOWMEM;
     }
     else {
       char err_msg[129];     
       sprintf(err_msg,
               "Illegal value '%s' for 'GoMethod' in configuration file",
               s);
       NAMD_die(err_msg);
     }
   }  // End of NAMD code to check goMethod
   // End of Port -- JL

   //  Get multiple timestep integration scheme
   if (!opts.defined("MTSAlgorithm"))
   {
  MTSAlgorithm = VERLETI;
   }
   else
   {
  opts.get("MTSAlgorithm", s);

  if (!strcasecmp(s, "naive"))
  {
    MTSAlgorithm = NAIVE;
  }
  else if (!strcasecmp(s, "constant"))
  {
    MTSAlgorithm = NAIVE;
  }
  else if (!strcasecmp(s, "impulse"))
  {
    MTSAlgorithm = VERLETI;
  }
  else if (!strcasecmp(s, "verleti"))
  {
    MTSAlgorithm = VERLETI;
  }
  else
  {
    char err_msg[129];

    sprintf(err_msg, 
       "Illegal value '%s' for 'MTSAlgorithm' in configuration file", 
       s);
    NAMD_die(err_msg);
  }
   }

   //  Get the long range force splitting specification
   if (!opts.defined("longSplitting"))
   {
  longSplitting = C1;
   }
   else
   {
  opts.get("longSplitting", s);
  if (!strcasecmp(s, "sharp"))
    longSplitting = SHARP;
  else if (!strcasecmp(s, "xplor"))
    longSplitting = XPLOR;
  else if (!strcasecmp(s, "c1"))
    longSplitting = C1;
  else if (!strcasecmp(s, "c2"))
    longSplitting = C2;
  else
  {
    char err_msg[129];

    sprintf(err_msg, 
       "Illegal value '%s' for 'longSplitting' in configuration file", 
       s);
    NAMD_die(err_msg);
  }
   }

   // take care of rigid bond options
   if (!opts.defined("rigidBonds"))
   {
      rigidBonds = RIGID_NONE;
   }
   else
   {
      opts.get("rigidBonds", s); 
      if (!strcasecmp(s, "all"))
      {
          rigidBonds = RIGID_ALL;
      }
      else if (!strcasecmp(s, "water"))
      {
           rigidBonds = RIGID_WATER;
      } 
      else if (!strcasecmp(s, "none"))
      {
           rigidBonds = RIGID_NONE;
      } 
      else
      {
        char err_msg[256];
        sprintf(err_msg, 
          "Illegal value '%s' for 'rigidBonds' in configuration file", s);
        NAMD_die(err_msg);
      }
   }

   // TIP4P and SWM4-DP water models require rigid water
   if ((watmodel == WaterModel::TIP4 || watmodel == WaterModel::SWM4)
       && rigidBonds == RIGID_NONE) {
     char err_msg[256];
     sprintf(err_msg,
         "Water model %s requires rigidBonds set to \"all\" or \"water\"",
         (watmodel == WaterModel::TIP4 ? "TIP4P" : "SWM4-DP"));
     NAMD_die(err_msg);
   }

   //  Take care of switching stuff
   if (switchingActive)
   {

     if (!opts.defined("switchDist")) {
       NAMD_die("switchDist must be defined when switching is enabled");
     }

     if ( (switchingDist>cutoff) || (switchingDist<0) )
     {
       char err_msg[129];

       sprintf(err_msg, 
         "switchDist muct be between 0 and cutoff, which is %f", cutoff);
       NAMD_die(err_msg);
     }

   }

   if ( martiniSwitching )
   {
     if ( ! switchingActive && ! LJPMEOn) 
     { 
       NAMD_die("martiniSwitching requires switching");
     }
     if ( vdwForceSwitching ) 
     { 
       NAMD_die("martiniSwitching and vdwForceSwitching are exclusive to one another. Select only one."); 
     }
     if ( dielectric != 15.0 && ! martiniDielAllow ) 
     {
       iout << iWARN << "USE DIELECTRIC OF 15.0 WITH MARTINI.\n";
       iout << iWARN << "SETTING dielectric 15.0\n";
       iout << iWARN << "FOR NON-STANDARD DIELECTRIC WITH MARTINI, SET: martiniDielAllow on\n";
       dielectric = 15.0;
     }
     if ( ! cosAngles )
     {
       iout << iWARN << "USE COSINE BASED ANGLES WITH MARTINI.\n";
       iout << iWARN << "SETTING cosAngles on\n";
       cosAngles = TRUE;
     }
     if ( PMEOn )
     {
       NAMD_die("Do not use Particle Mesh Ewald with Martini.  Set: PME off");
     }
     if ( MSMOn )
     {
       NAMD_die("Do not use Multilevel Summation Method with Martini.  Set: MSM off");
     }
     if ( FMMOn )
     {
       NAMD_die("Do not use Fast Multipole Method with Martini.  Set: FMM off");
     }

   }


   if (!opts.defined("pairlistDist"))
   {
  pairlistDist = cutoff;
   }
   else if (pairlistDist < cutoff)
   {
  NAMD_die("pairlistDist must be >= cutoff distance");
   }

   patchDimension = pairlistDist;

   if ( splitPatch == SPLIT_PATCH_HYDROGEN ) {
     patchDimension += hgroupCutoff;
   }

   BigReal defaultMargin = 0.0;
   if (berendsenPressureOn || langevinPistonOn || monteCarloPressureOn) {
      defaultMargin = ( useFlexibleCell ? 0.06 : 0.03 ) * patchDimension;
   }
   if ( margin == XXXBIGREAL ) {
     margin = defaultMargin;
   }

   if (CUDASOAintegrateMode) {
    iout << iINFO
     << "Tuning parameters to improve GPU-resident performance\n"
     << endi;
      
    // JM: Margin 8 might be a bit large for small systems (20k or such)
    //     which might starve the GPU of work
    //     Let's set it to 4 for now and later we can write a 
    //     tuning scheme to optimize it on-the-fly
    const double CUDASOA_defaultMargin = 4;
    const int CUDASOA_defaultOutputEnergies = 100;

    if (! config->find("margin")) {
      margin = CUDASOA_defaultMargin;
      iout << iINFO
        << "Setting margin to " << margin << "\n"
        << endi;
    }
    else if (margin < CUDASOA_defaultMargin) {
      iout << iWARN
        << "Keeping margin at user-specified value " << margin << "\n"
        << iWARN
        << "Performance might be improved by increasing margin size to >= "
        << CUDASOA_defaultMargin << "\n"
        << endi;
    }

    if (! config->find("outputEnergies")) {
      outputEnergies = CUDASOA_defaultOutputEnergies;;
      iout << iINFO
        << "Setting outputEnergies to " << outputEnergies << "\n"
        << endi;
    }
    else if (outputEnergies < CUDASOA_defaultOutputEnergies) {
      iout << iWARN
        << "Keeping outputEnergies at user-specified value " 
        << outputEnergies << "\n"
        << iWARN
        << "Performance might be improved by increasing outputEnergies to >= "
        << CUDASOA_defaultOutputEnergies << "\n"
        << endi;
    }
   } // end tuning CUDASOA parameters

   if ( defaultMargin != 0.0 && margin == 0.0 ) {
     margin = defaultMargin;
     iout << iWARN << "ALWAYS USE NON-ZERO MARGIN WITH CONSTANT PRESSURE!\n";
     iout << iWARN << "CHANGING MARGIN FROM 0 to " << margin << "\n" << endi;
   }

    patchDimension += margin;

    //ensure patch can handle alpha_cutoff for gbis
    if (GBISOn) {
      //Check compatibility
      if (fullDirectOn) {
        NAMD_die("GBIS not compatible with FullDirect");
      }
      if (PMEOn) {
        NAMD_die("GBIS not compatible with PME");
      }
      if (MSMOn) {
        NAMD_die("GBIS not compatible with MSM");
      }
      if (FMMOn) {
        NAMD_die("GBIS not compatible with FMM");
      }
      if (alchOn) {
        NAMD_die("GBIS not compatible with Alchemical Transformations");
      }
      if (lesOn) {
        NAMD_die("GBIS not compatible with Locally Enhanced Sampling");
      }
      if (FMAOn) {
        NAMD_die("GBIS not compatible with FMA");
      }
      if (drudeOn) {
        NAMD_die("GBIS not compatible with Drude Polarization");
      }

      if (alpha_cutoff > patchDimension) {
        patchDimension = alpha_cutoff; 
      }
      //calculate kappa
      BigReal tmp = (initialTemp > 0) ? initialTemp : 300;
      kappa = 50.29216*sqrt(ion_concentration/solvent_dielectric/tmp);
      /*magic number = 1/sqrt(eps0*kB/(2*nA*e^2*1000))*/
    } // GBISOn

    if (LCPOOn) {
#ifdef MEM_OPT_VERSION
      NAMD_die("SASA not yet available for memory optimized builds");
#endif
      if ( lattice.volume() > 0 ) {
        NAMD_die("SASA does not yet support periodic boundary conditions.");
      }
      //LCPO requires patches to be at least 16.2Ang in each dimension
      // twoAway[XYZ} is ignored for now
    }

   //  Turn on global integration if not explicitly specified

   if ( dihedralOn ) globalOn = TRUE;

#if defined(NAMD_CUDA) || defined(NAMD_HIP)
   if (loweAndersenOn) {
       NAMD_die("Lowe-Andersen dynamics not compatible with CUDA at this time");
   }
#endif
   // END LA

   // BEGIN LA
   if (loweAndersenOn && (langevinOn || tCoupleOn))
   {
      NAMD_die("Lowe-Andersen dynamics, Langevin dynamics and temperature coupling are mutually exclusive dynamics modes");
   }
   // END LA

   if (tCoupleOn && opts.defined("rescaleFreq") )
   {
      NAMD_die("Temperature coupling and temperature rescaling are mutually exclusive");
   }

   if (globalOn && CkNumPes() > 1)
   {
      NAMD_die("Global integration does not run in parallel (yet).");
   }

   if (COLDOn && langevinOn)
   {
      NAMD_die("COLD and Langevin dynamics are mutually exclusive dynamics modes");
   }
   if (COLDOn && minimizeOn)
   {
      NAMD_die("COLD and minimization are mutually exclusive dynamics modes");
   }
   if (COLDOn && tCoupleOn)
   {
      NAMD_die("COLD and temperature coupling are mutually exclusive dynamics modes");
   }
   if (COLDOn && opts.defined("rescaleFreq"))
   {
      NAMD_die("COLD and velocity rescaling are mutually exclusive dynamics modes");
   }

   if (splitPatch == SPLIT_PATCH_POSITION && mollyOn )
   {
      NAMD_die("splitPatch hydrogen is required for MOLLY");
   }

   if (splitPatch == SPLIT_PATCH_POSITION && rigidBonds != RIGID_NONE)
   {
      NAMD_die("splitPatch hydrogen is required for rigidBonds");
   }

   if (accelMDOn) {
       if(accelMDG){
           char msg[128];
           if(accelMDGiE < 1 || accelMDGiE > 2){
               sprintf(msg, "accelMDGiE was set to %d but it should be 1 or 2", accelMDGiE);
               NAMD_die(msg);
           }
           if(accelMDGStatWindow > 0){
               if(accelMDGcMDPrepSteps % accelMDGStatWindow != 0)
                   NAMD_die("'accelMDGcMDPrepSteps' has to be a multiple of 'accelMDGStatWindow'");
               if(accelMDGcMDSteps % accelMDGStatWindow != 0)
                   NAMD_die("'accelMDGcMDSteps' has to be a multiple of 'accelMDGStatWindow'");
               if(accelMDGEquiPrepSteps % accelMDGStatWindow != 0)
                   NAMD_die("'accelMDGEquiPrepSteps' has to be a multiple of 'accelMDGStatWindow'");
               if(accelMDGEquiSteps % accelMDGStatWindow != 0)
                   NAMD_die("'accelMDGEquiSteps' has to be a multiple of 'accelMDGStatWindow'");
           }
           if(accelMDGRestart && accelMDGcMDSteps == 0)
               accelMDGcMDPrepSteps = 0;
           else if(accelMDGcMDSteps - accelMDGcMDPrepSteps < 2)
               NAMD_die("'accelMDGcMDSteps' should be larger than 'accelMDGcMDPrepSteps'");

           if(accelMDGEquiSteps == 0)
               accelMDGEquiPrepSteps = 0;
           else if(accelMDGresetVaftercmd){
               if(accelMDGEquiPrepSteps <= 0)
                   NAMD_die("'accelMDGEquiPrepSteps' should be non-zero");
               if(accelMDGEquiSteps - accelMDGEquiPrepSteps < 1)
                   NAMD_die("'accelMDGEquiSteps' should be larger than 'accelMDGEquiPrepSteps'");
           }

           //warn user that accelMD params will be ignored
           if(opts.defined("accelMDE"))
               iout << iWARN << "accelMDE will be ignored with accelMDG on.\n" << endi;
           if(opts.defined("accelMDalpha"))
               iout << iWARN << "accelMDalpha will be ignored with accelMDG on.\n" << endi;
           if(opts.defined("accelMDTE"))
               iout << iWARN << "accelMDTE will be ignored with accelMDG on.\n" << endi;
           if(opts.defined("accelMDTalpha"))
               iout << iWARN << "accelMDTalpha will be ignored with accelMDG on.\n" << endi;
       }
       else{
           if(!opts.defined("accelMDE") || !opts.defined("accelMDalpha"))
               NAMD_die("accelMDE and accelMDalpha are required for accelMD with accelMDG off");

           if(accelMDdual && (!opts.defined("accelMDTE") || !opts.defined("accelMDTalpha"))){
               NAMD_die("accelMDTE and accelMDTalpha are required for accelMDdual with accelMDG off");
           }
       }
   }

   //  Set the default value for the maximum movement parameter
   //  for minimization
   if (minimizeOn && (maximumMove == 0.0)) 
   {
      maximumMove = 0.75 * pairlistDist/stepsPerCycle;
   }
   if (adaptTempOn) {
     if (!adaptTempRescale && !adaptTempLangevin) 
        NAMD_die("Adaptive tempering needs to be coupled to either the Langevin thermostat or velocity rescaling.");
     if (opts.defined("adaptTempInFile") && (opts.defined("adaptTempTmin") ||
                                             opts.defined("adaptTempTmax") ||
                                             adaptTempBins != 0)) 
        NAMD_die("cannot simultaneously specify adaptTempInFile and any of {adaptTempTmin, adaptTempTmax,adaptTempBins} as these are read from the input file");
     if (!opts.defined("adaptTempInFile") && !(opts.defined("adaptTempTmin") &&
                                             opts.defined("adaptTempTmax") &&
                                             adaptTempBins != 0 ))  
        NAMD_die("Need to specify either adaptTempInFile or all of {adaptTempTmin, adaptTempTmax,adaptTempBins} if adaptTempMD is on.");
   }

   // to check if MC pressure was activated at start
   monteCarloPressureOnAtStartup = monteCarloPressureOn;

   langevinOnAtStartup = langevinOn;
   if (langevinOn) {
     if ( ! opts.defined("langevinDamping") ) langevinDamping = 0.0;
     if ( ! opts.defined("langevinHydrogen") ) langevinHydrogen = TRUE;
     if ( (opts.defined("langevinDamping") || opts.defined("langevinHydrogen"))
       && (opts.defined("langevinFile") || opts.defined("langevinCol")) )
       NAMD_die("To specify Langevin dynamics parameters, use either langevinDamping and langevinHydrogen or langevinFile and langevinCol.  Do not combine them.");
     if ( opts.defined("langevinHydrogen") && langevinDamping == 0.0 )
       NAMD_die("langevinHydrogen requires langevinDamping to be set.");
     // Assume Langevin gammas differ when parameters are read from file.
     // Note that if Drude is on but drudeDamping is not defined,
     // then drudeDamping will be set to langevinDamping.
     langevinGammasDiffer = ( ! langevinHydrogen ) ||
       opts.defined("langevinFile") ||
       ( opts.defined("drudeDamping") && drudeDamping != langevinDamping );
     if (langevinGammasDiffer) {
       iout
         << iWARN
         << "The Langevin gamma parameters differ over the particles,\n"
         << iWARN
         << "requiring extra work per step to constrain rigid bonds.\n"
         << endi;
     }
   }
   
   // BEGIN LA
   if (loweAndersenOn) {
       if (!opts.defined("loweAndersenRate")) loweAndersenRate = 100;
       if (!opts.defined("loweAndersenCutoff")) loweAndersenCutoff = 2.7;
   }
   // END LA

   // BKR - stochastic velocity rescaling
   if (stochRescaleOn) {
     if (langevinOn || loweAndersenOn || tCoupleOn ||
         opts.defined("rescaleFreq") || opts.defined("reassignFreq"))
       NAMD_die("Stochastic velocity rescaling is incompatible with other temperature control methods");
     // This is largely the same default used in GROMACS.
     if (!opts.defined("stochRescaleFreq")) stochRescaleFreq = stepsPerCycle;
   }

   if (opts.defined("rescaleFreq"))
   {
  if (!opts.defined("rescaleTemp"))
  {
    if (opts.defined("temperature"))
    {
      rescaleTemp = initialTemp;
    }
    else
    {
      NAMD_die("Must give a rescale temperature if rescaleFreq is defined");
    }
  }
   }
   else
   {
  rescaleFreq = -1;
  rescaleTemp = 0.0;
   }

   if (opts.defined("rescaleTemp"))
   {
  if (!opts.defined("rescaleFreq"))
  {
    NAMD_die("Must give a rescale freqency if rescaleTemp is given");
  }
   }

   if (opts.defined("reassignFreq"))
   {
  if (!opts.defined("reassignTemp"))
  {
    if (opts.defined("temperature"))
    {
      reassignTemp = initialTemp;
    }
    else
    {
      NAMD_die("Must give a reassign temperature if reassignFreq is defined");
    }
  }
   }
   else
   {
  reassignFreq = -1;
  reassignTemp = 0.0;
   }

   if (opts.defined("reassignTemp"))
   {
  if (!opts.defined("reassignFreq"))
  {
    NAMD_die("Must give a reassignment freqency if reassignTemp is given");
  }
   }

   if (opts.defined("reassignIncr"))
   {
  if (!opts.defined("reassignFreq"))
  {
    NAMD_die("Must give a reassignment freqency if reassignIncr is given");
  }
   }
   else
   {
  reassignIncr = 0.0;
   }

   if (opts.defined("reassignHold"))
   {
  if (!opts.defined("reassignIncr"))
  {
    NAMD_die("Must give a reassignment increment if reassignHold is given");
  }
   }
   else
   {
  reassignHold = 0.0;
   }

   if (!opts.defined("seed")) 
   {
      randomSeed = (unsigned int) time(NULL) + 31530001 * CmiMyPartition();
   }

   // REST2
   if (opts.defined("soluteScaling")) {
     // Parameters soluteScalingFactorCharge and soluteScalingFactorVdw
     // allow independent scaling of electrostatics and van der Waals.
     // Initialize with soluteScalingFactor if either is not already set.
     if ( ! opts.defined("soluteScalingFactorCharge") ) {
       soluteScalingFactorCharge = soluteScalingFactor;
     }
     if ( ! opts.defined("soluteScalingFactorVdw") ) {
       soluteScalingFactorVdw = soluteScalingFactor;
     }
   }

//fepb
   alchFepOnAtStartup = alchFepOn = FALSE;
   alchThermIntOnAtStartup = alchThermIntOn = FALSE;
   alchOnAtStartup = alchOn;

   if (alchOn) {
#if !defined(NAMD_CUDA) && !defined(NAMD_HIP)
     usePMECUDA  = false;
#endif
     if (martiniSwitching) {
       iout << iWARN << "Martini switching disabled for alchemical "
         "interactions.\n" << endi;
     }

     if (!opts.defined("alchType")) {
       NAMD_die("Must define type of alchemical simulation: fep or ti\n");
     }
     else {
       opts.get("alchType",s);
       if (!strcasecmp(s, "fep")) {
         alchFepOnAtStartup = alchFepOn = TRUE;
       }
       else if (!strcasecmp(s, "ti")) {
         alchThermIntOnAtStartup = alchThermIntOn = TRUE;
       }
       else {
         NAMD_die("Unknown type of alchemical simulation; choices are fep or ti\n");
       }
     }

     if      (rescaleFreq > 0)  alchTemp = rescaleTemp;
     else if (reassignFreq > 0) alchTemp = reassignTemp;
     else if (langevinOn)       alchTemp = langevinTemp;
     else if (stochRescaleOn)   alchTemp = stochRescaleTemp;
     else if (tCoupleOn)        alchTemp = tCoupleTemp;
     else NAMD_die("Alchemical FEP can be performed only in constant temperature simulations\n");

     if (reassignFreq > 0 && reassignIncr != 0)
       NAMD_die("reassignIncr cannot be used in alchemical simulations\n");

     if (alchLambda < 0.0 || alchLambda > 1.0)
       NAMD_die("alchLambda values should be in the range [0.0, 1.0]\n");
     
     if (alchVdwLambdaEnd > 1.0) 
       NAMD_die("Gosh tiny Elvis, you kicked soft-core in the van der Waals! alchVdwLambdaEnd should be in the range [0.0, 1.0]\n");

     if (alchBondLambdaEnd > 1.0)
       NAMD_die("alchBondLambdaEnd should be in the range [0.0, 1.0]\n");

     if (alchElecLambdaStart > 1.0) 
       NAMD_die("alchElecLambdaStart should be in the range [0.0, 1.0]\n");

     if (alchWCAOn) {
       if (alchRepLambdaEnd > 1.0)
         NAMD_die("alchRepLambdaEnd should be in the range [0.0, 1.0]\n");
       if (alchVdwLambdaEnd < alchRepLambdaEnd)
         NAMD_die("alchVdwLambdaEnd should be greater than alchRepLambdaEnd\n");
       if (alchVdwShiftCoeff > 0.0) {
         iout << iWARN << "alchVdwShiftCoeff is non-zero but not used when WCA"
              << " is active. Setting it to zero now.\n" << endi;
         alchVdwShiftCoeff = 0.0;
       }
       if (alchThermIntOn) {
         NAMD_die("alchWCA is not currently compatible with TI");
       }
#if defined(NAMD_CUDA) || defined(NAMD_HIP)
       NAMD_die("alchWCA is not currently available with CUDA");
#endif
     }
     
     if (alchFepOn) {
       if (alchLambda2 < 0.0 || alchLambda2 > 1.0)
         NAMD_die("alchLambda2 values should be in the range [0.0, 1.0]\n");

       setupIDWS(); // setup IDWS if it was activated.
       
       if (!opts.defined("alchoutfile")) {
         strcpy(alchOutFile, outputFilename);
         strcat(alchOutFile, ".fep");
       }

       if (!opts.defined("alchLambda") || !opts.defined("alchLambda2")) {
         NAMD_die("alchFepOn is on, but alchLambda or alchLambda2 is not set.");
       }
     }
     else if (alchThermIntOn) {
       // alchLambda2 is only needed for nonequilibrium switching
       if (alchLambdaFreq && (alchLambda2 < 0.0 || alchLambda2 > 1.0))
         NAMD_die("alchLambda2 values should be in the range [0.0, 1.0]\n");

       if (!opts.defined("alchoutfile")) { 
         strcpy(alchOutFile, outputFilename); 
         strcat(alchOutFile, ".ti"); 
       } 
     }
   }
        
//fepe

   if ( alchOn && alchFepOn && alchThermIntOn )
     NAMD_die("Sorry, combined TI and FEP is not implemented.\n");
   if ( alchOn && lesOn )
     NAMD_die("Sorry, combined LES with FEP or TI is not implemented.\n");
   if ( alchOn && alchThermIntOn && lesOn )
     NAMD_die("Sorry, combined LES and TI is not implemented.\n");
   if ( alchWCAOn && !alchOn ) {
     iout << iWARN << "Alchemical WCA decomposition was requested but \
       alchemical free energy calculation is not active. Setting \
       alchWCA to off.\n" << endi;
     alchWCAOn = FALSE;
   }
   if ( alchDecouple && !alchOn ) {
         iout << iWARN << "Alchemical decoupling was requested but \
           alchemical free energy calculation is not active. Setting \
           alchDecouple to off.\n" << endi;
         alchDecouple = FALSE;
   }
   if ( alchBondDecouple && !alchOn ) {
         iout << iWARN << "Alchemical bond decoupling was requested but \
           alchemical free energy calculation is not active. Setting \
           alchBondDecouple to off.\n" << endi;
         alchBondDecouple = FALSE;
   }

   if ( lesOn && ( lesFactor < 1 || lesFactor > 255 ) ) {
     NAMD_die("lesFactor must be positive and less than 256");
   }
   if ((pairInteractionOn && alchOn) || (pairInteractionOn && lesOn)) 
     NAMD_die("Sorry, pair interactions may not be calculated when LES, FEP or TI is enabled.");

   // Drude model
   if (drudeOn) {
     if ( ! langevinOn ) {
       NAMD_die("Drude model requires use of Langevin thermostat.");
     }
     if ( ! opts.defined("drudeDamping")) {
       drudeDamping = langevinDamping;
       iout << iWARN << "Undefined 'drudeDamping' will be set to "
         "value of 'langevinDamping'\n" << endi;
     }
     if ( alchOn ) {
       NAMD_die("Drude implementation is incompatible with alchemical "
           "free energy calculation.");
     }
   }

   //  Set up load balancing variables
   if (opts.defined("ldBalancer")) {
     if (strcasecmp(loadBalancer, "none") == 0)
       ldBalancer = LDBAL_NONE;
     else if (strcasecmp(loadBalancer, "hybrid") == 0)
       ldBalancer = LDBAL_HYBRID;
     else
       NAMD_die("Unknown ldBalancer selected");
   } else {
     ldBalancer = LDBAL_CENTRALIZED;
#ifdef MEM_OPT_VERSION
     if ( CkNumPes() > 1400 ) ldBalancer = LDBAL_HYBRID;
#endif
   }

   if (opts.defined("ldbStrategy")) {
     //  Assign the load balancing strategy
     if (strcasecmp(loadStrategy, "comprehensive") == 0)
       ldbStrategy = LDBSTRAT_COMPREHENSIVE;
     else if (strcasecmp(loadStrategy, "refineonly") == 0)
       ldbStrategy = LDBSTRAT_REFINEONLY;
     else if (strcasecmp(loadStrategy, "old") == 0)
       ldbStrategy = LDBSTRAT_OLD;
     else
       NAMD_die("Unknown ldbStrategy selected");
   } else {
     ldbStrategy = LDBSTRAT_DEFAULT;
   }

  if (!opts.defined("ldbPeriod")) {
    ldbPeriod=200*stepsPerCycle;
  }

  //  Set default values
  if (!opts.defined("firstLdbStep")) {
    firstLdbStep=5*stepsPerCycle;
  }

  if (ldbPeriod <= firstLdbStep) {
    NAMD_die("ldbPeriod must greater than firstLdbStep.");
  }

  if (!opts.defined("lastLdbStep")) {
    lastLdbStep = -1;
  }

  if (!opts.defined("hybridGroupSize")) {
    hybridGroupSize = 512;
  }
  if ( hybridGroupSize < CkNumPes() ) {
    // match load balancer boundaries to physical nodes if possible
    int groupsize = hybridGroupSize;
    int *rpelist;
    int nodesize;
    CmiGetPesOnPhysicalNode(CmiPhysicalNodeID(0), &rpelist, &nodesize);
    if ( CkNumPes() % nodesize ) nodesize = CmiNodeSize(CmiNodeOf(0));
    if ( CkNumPes() % nodesize ) nodesize = 1;
    groupsize += nodesize - 1;
    while ( 2 * groupsize > CkNumPes() ) --groupsize;
    if ( groupsize < nodesize ) groupsize = nodesize;
    while ( groupsize % nodesize ) --groupsize;
    while ( groupsize && CkNumPes() % groupsize ) groupsize -= nodesize;
    if ( 2 * groupsize < hybridGroupSize ) {
      groupsize += nodesize;
      while ( CkNumPes() % groupsize ) groupsize += nodesize;
    }
    if ( 2 * groupsize <= CkNumPes() ) hybridGroupSize = groupsize;
  }

  // tracing will be done if trace is available and user says +traceOff
  // in that case we set nice values for some functions
  bool specialTracing = traceAvailable() && (traceIsOn() == 0);

  if(!opts.defined("traceStartStep")) {
    traceStartStep = 4 * firstLdbStep + 2 * ldbPeriod;
  }
  if(!opts.defined("numTraceSteps")) {
    numTraceSteps = 100;
  }

  if(specialTracing) {
    if (!opts.defined("firstLdbStep")) firstLdbStep = 20;
    if (!opts.defined("ldbPeriod")) ldbPeriod = 100;

    if(!opts.defined("traceStartStep")) {
      traceStartStep = 4 * firstLdbStep + 2 * ldbPeriod; // 380
    }

    if(!opts.defined("numTraceSteps")) {
      numTraceSteps = 80;
    }
  }

#ifdef MEASURE_NAMD_WITH_PAPI
  if(papiMeasure){
          if(!opts.defined("papiMeasureStartStep")) {
                  papiMeasureStartStep = 3 * firstLdbStep;
          }
          if(!opts.defined("numPapiMeasureSteps")) {
                  numPapiMeasureSteps = 8; //including two pme steps
          }
  }
#endif

  if(simulateInitialMapping) {
          if(!opts.defined("simulatedPEs")){
                  simulatedPEs = CkNumPes();
          }
          if(!opts.defined("simulatedNodeSize")){
                  simulatedNodeSize = CkMyNodeSize();
          }
  }

#ifdef MEM_OPT_VERSION
  //Some constraints on the values of load balancing parameters.
  //The reason is related to communication schemes used in sending proxy
  //data. If the step immediately after the load balancing is not a step
  //for atom migration, then it's possible there are some necessary information 
  // missing inside the ProxyPatch which will crash the program. Therefore,
  // It's better that the step immediately after the load balancing be a step
  // for atom migration so that the some overhead in Proxy msgs are removed. 
  // --Chao Mei
  if(ldbPeriod%stepsPerCycle!=0 || firstLdbStep%stepsPerCycle!=0) {
      iout << iWARN << "In memory optimized version, the ldbPeriod parameter or firstLdbStep parameter is better set to be a multiple of stepsPerCycle parameter!\n";
  }
#endif

   if (N < firstTimestep) { N = firstTimestep; }

   if ( (firstTimestep%stepsPerCycle) != 0)
   {
  NAMD_die("First timestep must be a multiple of stepsPerCycle!!");
   }

   //  Make sure only one full electrostatics algorithm is selected
   {
     int i = 0;
     if ( FMAOn ) ++i;
     if ( PMEOn ) ++i;
     if ( MSMOn ) ++i;
     if ( FMMOn ) ++i;
     if ( fullDirectOn ) ++i;
     if ( i > 1 )
        NAMD_die("More than one full electrostatics algorithm selected!!!");
   }

   if (!opts.defined("ldbBackgroundScaling")) {
     ldbBackgroundScaling = 1.0;
   }
   if (!opts.defined("ldbPMEBackgroundScaling")) {
     ldbPMEBackgroundScaling = ldbBackgroundScaling;
   }
   if (!opts.defined("ldbHomeBackgroundScaling")) {
     ldbHomeBackgroundScaling = ldbBackgroundScaling;
   }

   //  Check on PME parameters
   if (PMEOn) {  // idiot checking
     if ( lattice.volume() == 0. ) {
        NAMD_die("PME requires periodic boundary conditions.");
     }
     if ( PMEGridSpacing == 0. ) {
       if ( PMEGridSizeX * PMEGridSizeY * PMEGridSizeZ == 0 )
         NAMD_die("Either PMEGridSpacing or PMEGridSizeX, PMEGridSizeY, and PMEGridSizeZ must be specified.");
       else PMEGridSpacing = 1.5;  // only exit in very bad cases
     }
#ifndef TEST_PME_GRID
     for ( int idim = 0; idim < 3; ++idim ) {
        int *gridSize;
        BigReal cellLength;
        const char *direction;
        switch ( idim ) {
        case 0:  direction = "X";
           gridSize = &PMEGridSizeX;  cellLength = lattice.a().length();
           break;
        case 1:  direction = "Y";
           gridSize = &PMEGridSizeY;  cellLength = lattice.b().length();
           break;
        case 2:  direction = "Z";
           gridSize = &PMEGridSizeZ;  cellLength = lattice.c().length();
           break;
        }
        int minSize = (int) ceil(cellLength/PMEGridSpacing);
#else
  for ( int minSize = 1; minSize < 300; ++minSize ) {
#endif
        int bestSize = 10 * (minSize + 10);  // make sure it's big
        int max2, max3, ts;
        for ( max2=2, ts=1; ts < minSize; ++max2 ) ts *= 2;
        for ( max3=2, ts=1; ts < minSize; ++max3 ) ts *= 3;
        int max5 = 2;
        int max7 = 1;
        int max11 = 1;
        for ( int i2 = 0; i2 <= max2; ++i2 ) {
        for ( int i3 = 0; i3 <= max3; ++i3 ) {
        for ( int i5 = 0; i5 <= max5; ++i5 ) {
        for ( int i7 = 0; i7 <= max7; ++i7 ) {
        for ( int i11 = 0; i11 <= max11; ++i11 ) {
           if ( i5 + i7 + i11 > i2 ) continue;
           int testSize = 2;  // must be even
           for ( int j2 = 0; j2 < i2; ++j2 ) testSize *= 2;
           if ( testSize > bestSize ) continue;
           for ( int j3 = 0; j3 < i3; ++j3 ) testSize *= 3;
           if ( testSize > bestSize ) continue;
           for ( int j5 = 0; j5 < i5; ++j5 ) testSize *= 5;
           if ( testSize > bestSize ) continue;
           for ( int j7 = 0; j7 < i7; ++j7 ) testSize *= 7;
           if ( testSize > bestSize ) continue;
           for ( int j11 = 0; j11 < i11; ++j11 ) testSize *= 11;
           if ( testSize > bestSize ) continue;
           if ( testSize >= minSize ) bestSize = testSize;
        } } } } }
#ifdef TEST_PME_GRID
  iout << minSize << " " << bestSize << "\n" << endi;
#else
        if ( ! *gridSize ) {   // set it
           *gridSize = bestSize;
        }
        if ( *gridSize * PMEGridSpacing < cellLength ) {
           char errmsg[512];
           sprintf(errmsg, "PMEGridSize%s %d is too small for cell length %f and PMEGridSpacing %f\n",
                direction, *gridSize, cellLength, PMEGridSpacing);
           NAMD_die(errmsg);
        }
#endif
     }
     if ( PMEGridSizeX < 5 ) {
        NAMD_die("PMEGridSizeX (number of grid points) is very small.");
     }
     if ( PMEGridSizeY < 5 ) {
        NAMD_die("PMEGridSizeY (number of grid points) is very small.");
     }
     if ( PMEGridSizeZ < 5 ) {
        NAMD_die("PMEGridSizeZ (number of grid points) is very small.");
     }
     BigReal tolerance = PMETolerance;
     BigReal ewaldcof = 1.0;
     while ( erfc(ewaldcof*cutoff)/cutoff >= tolerance ) ewaldcof *= 2.0;
     BigReal ewaldcof_lo = 0.;
     BigReal ewaldcof_hi = ewaldcof;
     for ( int i = 0; i < 100; ++i ) {
       ewaldcof = 0.5 * ( ewaldcof_lo + ewaldcof_hi );
       if ( erfc(ewaldcof*cutoff)/cutoff >= tolerance ) {
         ewaldcof_lo = ewaldcof;
       } else {
         ewaldcof_hi = ewaldcof;
       }
     }
     PMEEwaldCoefficient = ewaldcof;

#if defined(NAMD_CUDA) || defined(NAMD_HIP)
     bool one_device_per_node = deviceCUDA->one_device_per_node();  // only checks node 0
     if ( ! opts.defined("PMEOffload") ) {
       PMEOffload = ( (PMEInterpOrder > 4) && one_device_per_node );
       if ( PMEOffload ) iout << iINFO << "Enabling PMEOffload because PMEInterpOrder > 4.\n" << endi;
     } else if ( PMEOffload && ! one_device_per_node ) {
       PMEOffload = 0;
       iout << iWARN << "Disabling PMEOffload because multiple CUDA devices per process are not supported.\n" << endi;
     }
#else
     PMEOffload = 0;
#endif
   } else {  // initialize anyway
     useDPME = 0;
     PMEGridSizeX = 0;
     PMEGridSizeY = 0;
     PMEGridSizeZ = 0;
     PMEGridSpacing = 1000.;
     PMEEwaldCoefficient = 0;
     PMEOffload = 0;
   }

   // Check on LJ-PME parameters
   if (LJPMESerialRealSpaceOn && ! LJPMESerialOn) {
     NAMD_die("LJPMESerial must be enabled to use LJPMESerialRealSpace.\n");
   }
   else if (LJPMESerialOn && ! LJPMEOn) {
     NAMD_die("LJPME must be enabled to use LJPMESerial.\n");
   }
   if (LJPMEOn) {
#if defined(NAMD_CUDA) || defined(NAMD_HIP) || defined(NAMD_MIC)
     NAMD_die("LJ-PME does not yet support special GPU-accelerated NAMD builds.");
#endif
     if ( lattice.volume() == 0. ) {
        NAMD_die("LJ-PME requires periodic boundary conditions.");
     }
     // XXX Make sure that LJ-PME grid is configured identically to PME.
     // Permits simplified config for LJ-PME, just set "LJPME on" to enable.
     if ( ! PMEOn ) {
       NAMD_die("LJ-PME requires also using PME.");
     }
     if (config->find("LJPMEGridSpacing")
         && LJPMEGridSpacing != PMEGridSpacing) {
       NAMD_die("LJ-PME must use same grid spacing as PME.");
     }
     else {
       LJPMEGridSpacing = PMEGridSpacing;
     }
     if ((config->find("LJPMEGridSizeX")
           && LJPMEGridSizeX != PMEGridSizeX)
         || (config->find("LJPMEGridSizeY")
           && LJPMEGridSizeY != PMEGridSizeY)
         || (config->find("LJPMEGridSizeZ")
           && LJPMEGridSizeZ != PMEGridSizeZ)) {
       NAMD_die("LJ-PME must use same grid sizes as PME.");
     }
     else {
       LJPMEGridSizeX = PMEGridSizeX;
       LJPMEGridSizeY = PMEGridSizeY;
       LJPMEGridSizeZ = PMEGridSizeZ;
     }
     if (config->find("LJPMEInterpOrder")
         && LJPMEInterpOrder != PMEInterpOrder) {
       NAMD_die("LJ-PME must use same interpolation order as PME.");
     }
     else {
       LJPMEInterpOrder = PMEInterpOrder;
     }
     // END set LJ-PME grid identical to PME.
     if ( LJPMEGridSpacing == 0. ) {
       if ( LJPMEGridSizeX * LJPMEGridSizeY * LJPMEGridSizeZ == 0 )
         NAMD_die("Either LJPMEGridSpacing or LJPMEGridSizeX, LJPMEGridSizeY, and LJPMEGridSizeZ must be specified.");
       else LJPMEGridSpacing = 1.5;  // only exit in very bad cases
     }
#ifndef TEST_PME_GRID
     for ( int idim = 0; idim < 3; ++idim ) {
        int *gridSize;
        BigReal cellLength;
        const char *direction;
        switch ( idim ) {
        case 0:  direction = "X";
           gridSize = &LJPMEGridSizeX;  cellLength = lattice.a().length();
           break;
        case 1:  direction = "Y";
           gridSize = &LJPMEGridSizeY;  cellLength = lattice.b().length();
           break;
        case 2:  direction = "Z";
           gridSize = &LJPMEGridSizeZ;  cellLength = lattice.c().length();
           break;
        }
        int minSize = (int) ceil(cellLength/LJPMEGridSpacing);
#else
  for ( int minSize = 1; minSize < 300; ++minSize ) {
#endif
        int bestSize = 10 * (minSize + 10);  // make sure it's big
        int max2, max3, ts;
        for ( max2=2, ts=1; ts < minSize; ++max2 ) ts *= 2;
        for ( max3=2, ts=1; ts < minSize; ++max3 ) ts *= 3;
        int max5 = 2;
        int max7 = 1;
        int max11 = 1;
        for ( int i2 = 0; i2 <= max2; ++i2 ) {
        for ( int i3 = 0; i3 <= max3; ++i3 ) {
        for ( int i5 = 0; i5 <= max5; ++i5 ) {
        for ( int i7 = 0; i7 <= max7; ++i7 ) {
        for ( int i11 = 0; i11 <= max11; ++i11 ) {
           if ( i5 + i7 + i11 > i2 ) continue;
           int testSize = 2;  // must be even
           for ( int j2 = 0; j2 < i2; ++j2 ) testSize *= 2;
           if ( testSize > bestSize ) continue;
           for ( int j3 = 0; j3 < i3; ++j3 ) testSize *= 3;
           if ( testSize > bestSize ) continue;
           for ( int j5 = 0; j5 < i5; ++j5 ) testSize *= 5;
           if ( testSize > bestSize ) continue;
           for ( int j7 = 0; j7 < i7; ++j7 ) testSize *= 7;
           if ( testSize > bestSize ) continue;
           for ( int j11 = 0; j11 < i11; ++j11 ) testSize *= 11;
           if ( testSize > bestSize ) continue;
           if ( testSize >= minSize ) bestSize = testSize;
        } } } } }
#ifdef TEST_PME_GRID
  iout << "LJ-PME: " << minSize << " " << bestSize << "\n" << endi;
#else
        if ( ! *gridSize ) {   // set it
           *gridSize = bestSize;
        }
        if ( *gridSize * LJPMEGridSpacing < cellLength ) {
           char errmsg[512];
           sprintf(errmsg, "LJPMEGridSize%s %d is too small for cell length %f and LJPMEGridSpacing %f\n",
                direction, *gridSize, cellLength, LJPMEGridSpacing);
           NAMD_die(errmsg);
        }
#endif
     }
     if ( LJPMEGridSizeX < 5 ) {
        NAMD_die("LJPMEGridSizeX (number of grid points) is very small.");
     }
     if ( LJPMEGridSizeY < 5 ) {
        NAMD_die("LJPMEGridSizeY (number of grid points) is very small.");
     }
     if ( LJPMEGridSizeZ < 5 ) {
        NAMD_die("LJPMEGridSizeZ (number of grid points) is very small.");
     }
     BigReal tolerance = LJPMETolerance;
     BigReal ewaldcof = 1.0;
     BigReal aRc = ewaldcof*cutoff;
     BigReal denom = 1.0; //cutoff;
     // LJ dispersion screening function
     BigReal damping = (1 + (aRc*aRc) + 0.5*(aRc*aRc*aRc*aRc))*exp(-aRc*aRc)/denom;
     while ( damping >= tolerance ) { 
       ewaldcof *= 2.0;
       aRc = ewaldcof*cutoff;
       damping = (1 + (aRc*aRc) + 0.5*(aRc*aRc*aRc*aRc))*exp(-aRc*aRc)/denom;
     }
     BigReal ewaldcof_lo = 0.;
     BigReal ewaldcof_hi = ewaldcof;
     for ( int i = 0; i < 100; ++i ) {
       ewaldcof = 0.5 * ( ewaldcof_lo + ewaldcof_hi );
       aRc = ewaldcof*cutoff;
       if ( (1 + (aRc*aRc) + 0.5*(aRc*aRc*aRc*aRc))*exp(-aRc*aRc)/denom >= tolerance ) {
         ewaldcof_lo = ewaldcof;
       } else {
         ewaldcof_hi = ewaldcof;
       }
     }
     LJPMEEwaldCoefficient = ewaldcof;
   } else {  // initialize anyway
     LJPMEGridSizeX = 0;
     LJPMEGridSizeY = 0;
     LJPMEGridSizeZ = 0;
     LJPMEGridSpacing = 1000.;
     LJPMEEwaldCoefficient = 0;
   }

   //  Take care of initializing FMA values to something if FMA is not
   //  active
   if (!FMAOn)
   {
     FMALevels = 0;
     FMAMp = 0;
     FMAFFTOn = FALSE;
     FMAFFTBlock = 0;
   }
   else
   {
  // idiot checking: frm bug reported by Tom Bishop.
  // DPMTA requires: (#terms in fma)/(fft blocking factor) = integer.
  if (FMAFFTBlock != 4)
    NAMD_die("FMAFFTBlock: Block length must be 4 for short FFT's");
  if (FMAMp % FMAFFTBlock != 0)
    NAMD_die("FMAMp: multipole term must be multiple of block length (FMAFFTBlock)");
    }

   if ( (nonbondedFrequency > stepsPerCycle) || ( (stepsPerCycle % nonbondedFrequency) != 0) )
   {
     NAMD_die("stepsPerCycle must be a multiple of nonbondedFreq");
   }

   if (!LCPOOn && !GBISOn && !GBISserOn && !FMAOn && !PMEOn && !MSMOn && !fullDirectOn && !FMMOn)
   {
     fullElectFrequency = 0;
   }
   else
   {
     if (!opts.defined("fullElectFrequency"))
     {
       if (opts.defined("fmaFrequency")) {
         iout << iWARN << "The parameter fmaFrequency has been renamed fullElectFrequency.\n" << endi;
         fullElectFrequency = fmaFrequency;
       } else {
         iout << iWARN << "The parameter fullElectFrequency now defaults to nonbondedFreq (" << nonbondedFrequency << ") rather than stepsPerCycle.\n" << endi;
         fullElectFrequency = nonbondedFrequency;
       }
     }
     else
     {
       if (opts.defined("fmaFrequency")) {
         iout << iWARN << "Ignoring redundant parameter fmaFrequency in favor of fullElectFrequency.\n" << endi;
       }
       if ( (fullElectFrequency > stepsPerCycle) || ( (stepsPerCycle % fullElectFrequency) != 0) )
       {
         NAMD_die("stepsPerCycle must be a multiple of fullElectFrequency");
       }
     }

     if ( (nonbondedFrequency > fullElectFrequency) || ( (fullElectFrequency % nonbondedFrequency) != 0) )
     {
       NAMD_die("fullElectFrequency must be a multiple of nonbondedFreq");
     }

     if (singleTopology && fullElectFrequency > 1) NAMD_die("Single topology free energy calculation discourages multiple timesteps to assure accuracy!");
     if (singleTopology && alchDecouple) NAMD_die("Single topology free energy calculation can NOT work with alchDecouple on");

      if (multigratorOn) {
        if ( (multigratorTemperatureFreq > multigratorPressureFreq) || ( (multigratorPressureFreq % multigratorTemperatureFreq) != 0) )
        {
          NAMD_die("multigratorTemperatureFreq must be a multiple of multigratorPressureFreq");
        }
        if ( (fullElectFrequency > multigratorTemperatureFreq) || ( (multigratorTemperatureFreq % fullElectFrequency) != 0) )
        {
          NAMD_die("fullElectFrequency must be a multiple of multigratorTemperatureFreq");
        }
        if (multigratorNoseHooverChainLength <= 2) {
          NAMD_die("multigratorNoseHooverChainLength must be greater than 2");
        }
      }

     if (!opts.defined("fmaTheta"))
     fmaTheta=0.715;  /* Suggested by Duke developers */
   }

   if ( lesOn && ( FMAOn || useDPME || fullDirectOn ) ) {
     NAMD_die("Sorry, LES is only implemented for PME full electrostatics.");
   }
   if ( alchFepOn && ( FMAOn || useDPME || fullDirectOn ) ) {
     NAMD_die("Sorry, FEP is only implemented for PME full electrostatics.");
   }
   if ( alchThermIntOn && ( FMAOn || useDPME || fullDirectOn ) ) {
     NAMD_die("Sorry, TI is only implemented for PME full electrostatics.");
   }
   if ( pairInteractionOn && FMAOn ) {
     NAMD_die("Sorry, pairInteraction not implemented for FMA.");
   }
   if ( pairInteractionOn && useDPME ) {
     NAMD_die("Sorry, pairInteraction not implemented for DPME.");
   }
   if ( pairInteractionOn && fullDirectOn ) {
     NAMD_die("Sorry, pairInteraction not implemented for full direct electrostatics.");
   }
   if ( ! pairInteractionOn ) {
     pairInteractionSelf = 0;
   }
   if ( pairInteractionOn && !pairInteractionSelf && !config->find("pairInteractionGroup2")) 
     NAMD_die("pairInteractionGroup2 must be specified");

   if ( ! fixedAtomsOn ) {
     fixedAtomsForces = 0;
   }

   if ( gridforceOn || mgridforceOn ) {
     parse_mgrid_params(config);
   }

   if (groupRestraintsOn) {
#ifdef NODEGROUP_FORCE_REGISTER     
     if (CUDASOAintegrateMode) {
       // Parse the group restraint field
       parse_group_restraints_params(config);
       // make sure all necessary parameters are provided.
       groupRestraints.CheckGroupRestraints();
     } else {
        char msg[1024];
        sprintf(msg, "GroupRestraints requires GPUresident.\n" 
        "             Otherwise, use Colvars for similar functionality.");
        NAMD_die(msg);
     }
#else
    char msg[1024];
    sprintf(msg, "GroupRestraints is not supported on regular multicore builds.\n" 
    "             Please use single-node GPU build with GPUresident on\n"
    "             or use Colvars for similar functionality.");
    NAMD_die(msg);
#endif
   }   

   if ( extraBondsOn ) {
     extraBondsCosAnglesSetByUser = ! ! config->find("extraBondsCosAngles");
   } else {
     extraBondsCosAnglesSetByUser = false;
   }
      
   if (!opts.defined("constraints"))
   {
     constraintExp = 0;     
     constraintScaling = 1.0;     

     //****** BEGIN selective restraints (X,Y,Z) changes
     selectConstraintsOn = FALSE;
     //****** END selective restraints (X,Y,Z) changes
 
     //****** BEGIN moving constraints changes 
     movingConstraintsOn = FALSE;
     //****** END moving constraints changes 
     //****** BEGIN rotating constraints changes 
     rotConstraintsOn = FALSE;
    //****** END rotating constraints changes 
   } 
   //****** BEGIN rotating constraints changes 
   else {
     if (rotConstraintsOn) {
       rotConsAxis = rotConsAxis.unit();
     }
   }
   if(opts.defined("rotConstraints") 
      && opts.defined("movingConstraints")) {
     NAMD_die("Rotating and moving constraints are mutually exclusive!");
   }
   //****** END rotating constraints changes 

   //****** BEGIN selective restraints (X,Y,Z) changes
   if(opts.defined("selectConstraints") && !opts.defined("selectConstrX")
      && !opts.defined("selectConstrY") && !opts.defined("selectConstrZ")) {
     NAMD_die("selectConstraints was specified, but no Cartesian components were defined!");
   }
   if (!opts.defined("selectConstraints")) {
       constrXOn = FALSE;
       constrYOn = FALSE;
       constrZOn = FALSE;
   }
   //****** END selective restraints (X,Y,Z) changes


   //****** BEGIN SMD constraints changes 
   
   if (!opts.defined("SMD")) {     
     SMDOn = FALSE;
   }

   if (SMDOn) {
     // normalize direction
     if (SMDDir.length2() == 0) {
       NAMD_die("SMD direction vector must be non-zero");
     }
     else {
       SMDDir = SMDDir.unit();
     }

     if (SMDOutputFreq > 0 && SMDOutputFreq < stepsPerCycle
         || SMDOutputFreq % stepsPerCycle != 0) {
       NAMD_die("SMDOutputFreq must be a multiple of stepsPerCycle");
     }
   }
     
   //****** END SMD constraints changes 
   
   if (!sphericalBCOn)
     {
  sphericalBCr1 = 0.0;
  sphericalBCk1 = 0.0;
  sphericalBCexp1 = 0;
  sphericalBCr2 = 0.0;
  sphericalBCk2 = 0.0;
  sphericalBCexp2 = 0;
   }
   else if (!opts.defined("sphericalBCr2"))
   {
      sphericalBCr2 = -1.0;
      sphericalBCk2 = 0.0;
      sphericalBCexp2 = 0;
   }

   if (!cylindricalBCOn)
   {
    cylindricalBCr1 = 0.0;
    cylindricalBCk1 = 0.0;
    cylindricalBCexp1 = 0;
    cylindricalBCr2 = 0.0;
    cylindricalBCk2 = 0.0;
    cylindricalBCexp2 = 0;
    cylindricalBCl1 = 0.0;
    cylindricalBCl2 = 0.0;
   }
   else if (!opts.defined("cylindricalBCr2"))
   {
    cylindricalBCr2 = -1.0;
    cylindricalBCk2 = 0.0;
    cylindricalBCexp2 = 0;
    cylindricalBCl2 = 0.0;
   }

   if (!eFieldOn)
   {
        eField.x = 0.0;
        eField.y = 0.0;
        eField.z = 0.0;
        eFieldFreq = 0.0;
        eFieldPhase = 0.0;
   }
   else
   {
        if (!opts.defined("eFieldFreq")) eFieldFreq = 0.0;
        if (!opts.defined("eFieldPhase")) eFieldPhase = 0.0;
   }

   if (!stirOn)
   { 
     stirFilename[0] = STRINGNULL;
     stirStartingTheta = 0.0;
     stirVel = 0.0;
     stirK = 0.0;
     stirAxis.x = 0.0;
     stirAxis.y = 0.0;
     stirAxis.z = 0.0;
     stirPivot.x = 0.0;
     stirPivot.y = 0.0;
     stirPivot.z = 0.0;
   }
  
   if (!opts.defined("langevin"))
   {
  langevinTemp = 0.0;
   }
   
   // BEGIN LA
   if (!opts.defined("loweAndersen"))
   {
       loweAndersenTemp = 0.0;
   }
   // END LA

   if (!opts.defined("tcouple"))
   {
  tCoupleTemp = 0.0;
   }

   if (HydrogenBonds)
   {
     if (daCutoffDist > pairlistDist)
       NAMD_die("Hydrogen bond cutoff distance must be <= pairlist distance");
   }

   // If we're doing pair interaction, set 
   // outputEnergies to 1 to make NAMD not die (the other nonbonded code paths 
   // aren't defined when these options are enabled), and set nonbondedFreq to 
   // 1 to avoid getting erroneous output.  Warn the user of what we're doing.
   if (pairInteractionOn) {
           if (outputEnergies != 1) {
                   iout << iWARN << "Setting outputEnergies to 1 due to\n";
                   iout << iWARN << "pairInteraction calculations\n" << endi;
                   outputEnergies  = 1;
           }
   }
   if (pairInteractionOn || pressureProfileOn) {
           if (nonbondedFrequency != 1) {
                   iout << iWARN << "Setting nonbondedFreq to 1 due to\n";
                   iout << iWARN << "pairInteraction or pressure profile calculations\n" << endi;
           }
   }

   // print timing at a reasonable interval by default
   if (!opts.defined("outputTiming"))
   {
      outputTiming = firstLdbStep;
      int ot2 = 10 * outputEnergies;
      if ( outputTiming < ot2 ) outputTiming = ot2;
   }

    // Checks if a secondary process was added in the configuration, and sets
    // the appropriated variable
    if(qmForcesOn){
        
        // Check added to ensure that PME is executed at every step during QM/MM.
        // Prevents a conflict in PME code when QM/MM updates partial charges.
        if (fullElectFrequency > 1) NAMD_die("QM/MM discourages multiple timesteps to assure accuracy!");

        if (opts.defined("QMSecProc")){
            qmSecProcOn = true;
        }
        else {
            qmSecProcOn = false;
        }
        
        if (opts.defined("qmPrepProc")){
            qmPrepProcOn = true;
        }
        else {
            qmPrepProcOn = false;
        }
        
        if (opts.defined("QMParamPDB")){
            qmParamPDBDefined = true;
        }
        else {
            qmParamPDBDefined = false;
        }
        
        if (opts.defined("QMBondColumn")){
            qmBondColumnDefined = true;
        }
        else {
            qmBondColumnDefined = false;
        }

        if (qmBondColumnDefined || qmBondGuess){
            qmBondOn = true;
        }
        else {
            qmBondOn = false;
        }
        
        if ( strcasecmp(qmSoftware,"orca") != 0 &&
             strcasecmp(qmSoftware,"mopac") != 0 &&
             strcasecmp(qmSoftware,"custom") != 0 ) {
            NAMD_die("Available QM software options are \'mopac\', \'orca\', or \'custom\'.");
        }
        else {
            if ( strcasecmp(qmSoftware,"orca") == 0 ) 
                qmFormat = QMFormatORCA;
            if ( strcasecmp(qmSoftware,"mopac") == 0 ) 
                qmFormat = QMFormatMOPAC;
            if ( strcasecmp(qmSoftware,"custom") == 0 ) 
                qmFormat = QMFormatUSR;
            
            if (qmFormat == QMFormatORCA || qmFormat == QMFormatMOPAC) {
                
                if (! opts.defined("QMConfigLine"))
                    NAMD_die("If the selected QM software is \'mopac\' or \'orca\'\
, QMConfigLine needs to be defined.");
                
            }
        }
        
        qmChrgMode = QMCHRGMULLIKEN;
        if (opts.defined("QMChargeMode")) {
            if ( strcasecmp(qmChrgModeS,"none") != 0 &&
                 strcasecmp(qmChrgModeS,"mulliken") != 0 &&
                 strcasecmp(qmChrgModeS,"chelpg") != 0) {
                NAMD_die("Available charge options are \'none\', \'mulliken\' or \'chelpg\'.");
            }
            else {
                if ( strcasecmp(qmChrgModeS,"none") == 0 ) 
                    qmChrgMode = QMCHRGNONE;
                if ( strcasecmp(qmChrgModeS,"mulliken") == 0 ) 
                    qmChrgMode = QMCHRGMULLIKEN;
                if ( strcasecmp(qmChrgModeS,"chelpg") == 0 ) 
                    qmChrgMode = QMCHRGCHELPG;
            }
        }
        
        if (qmFormat == QMFormatMOPAC && qmChrgMode == QMCHRGCHELPG)
            NAMD_die("Available charge options for MOPAC are \'none\' and \'mulliken\'.");
        
        if (qmFormat == QMFormatUSR && qmChrgMode == QMCHRGCHELPG)
            NAMD_die("Available charge options for MOPAC are \'none\' and \'mulliken\'.");
        
        if (qmBondOn && (opts.defined("QMBondValueType"))) {
            if ( strcasecmp(qmBondValueTypeS,"len") != 0 &&
                strcasecmp(qmBondValueTypeS,"ratio") != 0 ) {
                NAMD_die("Available QM bond value type options are \'len\' or \'ratio\'.");
            }
            else {
    //         #define QMLENTYPE 1
    //         #define QMRATIOTYPE 2
                if ( strcasecmp(qmBondValueTypeS,"len") == 0 ) 
                    qmBondValType = 1;
                if ( strcasecmp(qmBondValueTypeS,"ratio") == 0 ) 
                    qmBondValType = 2;
            }
        }
        else if (qmBondOn && ! (opts.defined("QMBondValueType")))
            qmBondValType = 1;
        
        if ( strcmp(qmColumn,"beta") != 0 &&
             strcmp(qmColumn,"occ") != 0 ) {
            NAMD_die("Available column options are \'beta\' and \'occ\'.");
        }
        
        if (qmBondColumnDefined) {
            if ( strcmp(qmBondColumn,"beta") != 0 &&
                 strcmp(qmBondColumn,"occ") != 0 ) {
                NAMD_die("Available column options are \'beta\' and \'occ\'.");
            }
            
            if (strcmp(qmBondColumn,qmColumn) == 0)
                NAMD_die("QM column and bond-column must be different!");
        }
        
        qmBondScheme = 1;
        if (opts.defined("QMBondScheme")) {
            if ( strcasecmp(qmBondSchemeS,"CS") == 0 )
                qmBondScheme = QMSCHEMECS;
            if ( strcasecmp(qmBondSchemeS,"RCD") == 0 )
                qmBondScheme = QMSCHEMERCD;
            if ( strcasecmp(qmBondSchemeS,"Z1") == 0 )
                qmBondScheme = QMSCHEMEZ1;
            if ( strcasecmp(qmBondSchemeS,"Z2") == 0 )
                qmBondScheme = QMSCHEMEZ2;
            if ( strcasecmp(qmBondSchemeS,"Z3") == 0 )
                qmBondScheme = QMSCHEMEZ3;
        }
        
//         #define QMPCSCHEMENONE 1
//         #define QMPCSCHEMEROUND 2
//         #define QMPCSCHEMEZERO 3
        qmPCScheme = 1;
        if (opts.defined("QMPointChargeScheme") && qmPCSwitchOn) {
            if ( strcasecmp(qmPCSchemeS,"none") == 0 )
                qmPCScheme = 1;
            
            if ( strcasecmp(qmPCSchemeS,"round") == 0 )
                qmPCScheme = 2;
            if ( strcasecmp(qmPCSchemeS,"zero") == 0 )
                qmPCScheme = 3;
            
            if ( qmPCScheme > 1 && ! qmPCSwitchOn)
                NAMD_die("QM Charge Schemes \'round\' or \'zero\' can only be applied with QMswitching set to \'on\'!");
        }
        
        // Redundant option to deprecate "qmNoPC" option.
        if (qmElecEmbed)
            qmNoPC = FALSE;
        
//         #define QMLSSMODEDIST 1
//         #define QMLSSMODECOM 2
        if (qmLSSOn) {
            
            if (qmNoPC)
                NAMD_die("QM Live Solvent Selection cannot be done with QMNoPntChrg set to \'on\'!") ;
            
            if (rigidBonds != RIGID_NONE)
                NAMD_die("QM Live Solvent Selection cannot be done with fixed bonds!") ;
            
            if (qmLSSFreq % qmPCSelFreq != 0)
                NAMD_die("Frequency of QM solvent update must be a multiple of frequency of point charge selection.");
            
            if (qmLSSFreq % stepsPerCycle != 0)
                NAMD_die("Frequency of QM solvent update must be a multiple of steps per cycle.");
            
            if (opts.defined("QMLSSMode") ) {
                if ( strcasecmp(qmLSSModeS,"dist") != 0 &&
                     strcasecmp(qmLSSModeS,"COM") != 0 ) {
                    NAMD_die("Available LSS mode options are \'dist\' and \'COM\'.");
                }
                if ( strcasecmp(qmLSSModeS,"dist") == 0 )
                    qmLSSMode = 1;
                else if ( strcasecmp(qmLSSModeS,"COM") == 0 )
                    qmLSSMode = 2;
            }
            else
                qmLSSMode = 1;
        }
        
//         #define QMPCSCALESHIFT 1
//         #define QMPCSCALESWITCH 2
        if (qmPCSwitchOn) {
            
            if (opts.defined("QMSwitchingType") ) {
                if ( strcasecmp(qmPCSwitchTypeS,"shift") != 0 &&
                     strcasecmp(qmPCSwitchTypeS,"switch") != 0 ) {
                    NAMD_die("Available scaling options are \'shift\' and \'switch\'.");
                }
                if ( strcasecmp(qmPCSwitchTypeS,"shift") == 0 )
                    qmPCSwitchType = 1;
                else if ( strcasecmp(qmPCSwitchTypeS,"switch") == 0 )
                    qmPCSwitchType = 2;
            }
            else
                qmPCSwitchType = 1;
        }
        
        if (qmNoPC && qmPCSelFreq > 1) {
            iout << iWARN << "QMPCStride being IGNORED since QMNoPntChrg is set to \'on\'!\n" << endi;
            qmPCSelFreq = 1;
        }
        
        if (qmNoPC && qmPCSwitchOn)
            NAMD_die("QM PC switching can only be applied with QMNoPntChrg set to \'off\'!");
        
//         if (qmNoPC && qmBondOn)
//             NAMD_die("QM-MM bonds can only be applied with QMNoPntChrg set to \'off\'!");
        
        if (qmPCSelFreq <= 0)
            NAMD_die("QMPCFreq can only be a positive number! For static point charge selection, see QMCutomPC.");
        
        if (qmCustomPCSel && qmNoPC)
            NAMD_die("QM Custom PC Selection is incompatible with QMNoPntChrg!");
        
//         if (qmCustomPCSel && qmPCSwitchOn)
//             NAMD_die("QM Custom PC Selection is incompatible with QMSwitching!");
        
        if (qmCustomPCSel && qmPCSelFreq > 1)
            NAMD_die("QM Custom PC Selection is incompatible with QMPCStride > 1!");
        
        if (qmCSMD && (! opts.defined("QMCSMDFile") ))
            NAMD_die("QM Conditional SMD is ON, but no CSMD configuration file was profided!");
    }

    // CUDASOAintegrateMode implies CUDASOAintegrate and SOAintegrate
    if (CUDASOAintegrateMode) {
      nsPerDayOn = TRUE; // We want to measure sampling in ns/day here.
      CUDASOAintegrate = TRUE; // Assume we will start dynamics
      SOAintegrateOn = TRUE;
      if (!GPUresidentSingleProcessMode && CkNumNodes() > 0) {
        // Disable running multi-process mode for now.
        NAMD_die("GPU Resident mode must be run in single process mode");
      }
    }
    else {
      CUDASOAintegrate = FALSE; // Don't leave uninitialized
      GPUresidentSingleProcessMode = FALSE; // This flag should be false when not using GPU-resident
    }

    if (CUDASOAintegrateMode && (minimizeOn || minimizeCGOn)) {
      NAMD_die(
          "GPUresident does not support \"minimization\" keyword.\n"
          "Instead use \"minimize\" available through Tcl scripting interface."
          );
    }

    if (SOAintegrateOn) {
      // Can we use SOA integration?

      // We need to explicitly turn off lonepairs because now it defaults TRUE.
      // if (lonepairs) {
      //   iout << iWARN
      //     << "Disabling lonepair support due to incompatability with "
      //     << (CUDASOAintegrateMode ? "GPU-resident" : "SOA") << ".\n"
      //     << endi;
      //   lonepairs = false;
      // }

      // Not compatible with the following options...
      if (testOn || commOnly || statsOn ||
          minimizeOn || minimizeCGOn ||
          maximumMove != 0 ||
          pressureProfileOn ||
          accelMDOn ||
          adaptTempOn ||
          mollyOn ||
          multigratorOn ||
          loweAndersenOn ||
          langevin_useBAOAB ||
          GBISOn ||
          LCPOOn ||
          zeroMomentum || zeroMomentumAlt ||
          (constraintsOn && ! CUDASOAintegrateMode) ||
          (monteCarloPressureOn && ! CUDASOAintegrateMode) ||
#ifdef NAMD_TCL
          (tclForcesOn && (TCL_MAJOR_VERSION<=8 && TCL_MINOR_VERSION <6)) ||
#endif    
          FMAOn ||
          fullDirectOn ||
          MSMOn ||
          FMMOn ||
          globalOn ||
          dihedralOn ||
          berendsenPressureOn ||
          printBadContacts ||
          freeEnergyOn ||
          miscForcesOn ||
          TMDOn ||
          symmetryOn ||
          qmForcesOn ||
          sphericalBCOn ||
          cylindricalBCOn ||
          extForcesOn ||
          tabulatedEnergies ||
          tclBCOn ||
          lesOn ||
          goForcesOn ||
          pairInteractionOn ||
#ifdef OPENATOM_VERSION
          openatomOn ||
#endif
          movDragOn ||
          rotDragOn ||
          consTorqueOn ||
          stirOn ||
          HydrogenBonds ||
          tCoupleOn ||
          rescaleFreq > 0 ||
          watmodel == WaterModel::SWM4 ||
          // lonepairs ||
          drudeOn
          ) {
        char msg[2048];
        sprintf(msg,
            "%s is incompatible with the following options:\n"
            "   minimization; pressure profiling; multigrator; Lowe-Andersen;\n"
            "   fixed atoms; GBIS; LCPO; zero momentum;%s\n"
            "   temperature coupling, rescaling, or reassignment;\n"
            "   water models other than TIP3 and TIP4; Drude.\n"
            "\n" 
            "( Bribe us with coffee to get your feature GPU-Resident! :)",
                (CUDASOAintegrateMode ? "GPUresident" : "SOAintegrate"),
                (CUDASOAintegrateMode ? "" : " Monte Carlo pressure control;"),
                (CUDASOAintegrateMode ? "" : " harmonic restraints;")
            );
        char featuremsg[1024];
        snprintf(featuremsg,1024,"\nConfiguration could amend the following options to proceeed :\n");
        if(testOn) strncat(featuremsg,"  test\n",1023);
        if(commOnly) strncat(featuremsg,"  commOnly\n",1023);
        if(statsOn) strncat(featuremsg,"  stats\n",1023);
        if(minimizeOn) strncat(featuremsg,"  minimize\n",1023);
        if(minimizeCGOn) strncat(featuremsg,"  minimizeCG\n",1023);
        if(maximumMove != 0) strncat(featuremsg,"  maximumMove\n",1023);
        if(pressureProfileOn) strncat(featuremsg,"  pressureProfile\n",1023);
        if(accelMDOn) strncat(featuremsg,"  accelMD\n",1023);
        if(adaptTempOn) strncat(featuremsg,"  adaptTemp\n",1023);
        if(mollyOn) strncat(featuremsg,"  molly\n",1023);
        if(multigratorOn) strncat(featuremsg,"  multigrator\n",1023);
        if(loweAndersenOn) strncat(featuremsg,"  loweAndersen\n",1023);
        if(langevin_useBAOAB) strncat(featuremsg,"  langevin_useBAOAB\n",1023);
        if(fixedAtomsOn) strncat(featuremsg,"  fixedAtoms\n",1023);
        if(GBISOn) strncat(featuremsg,"  GBIS\n",1023);
        if(LCPOOn) strncat(featuremsg,"  LCPO\n",1023);
        if(zeroMomentum) strncat(featuremsg,"  zeroMomentum\n",1023);
        if(zeroMomentumAlt) strncat(featuremsg,"  zeroMomentumAlt\n",1023);
        if(constraintsOn && ! CUDASOAintegrateMode) strncat(featuremsg,"  constraints\n",1023);
        if(monteCarloPressureOn && ! CUDASOAintegrateMode) strncat(featuremsg,"  monteCarloPressure\n",1023);
        if(tCoupleOn) strncat(featuremsg,"  tCouple\n",1023);
        if(rescaleFreq > 0) strncat(featuremsg,"  rescaleFreq\n",1023);
        if(watmodel == WaterModel::SWM4) strncat(featuremsg,"  watmodel != SWM4\n",1023);
        if(lonepairs) strncat(featuremsg,"  lonepairs\n",1023);
        if(drudeOn) strncat(featuremsg,"  drude\n",1023);
#ifdef NAMD_TCL 
        if(tclForcesOn && (TCL_MAJOR_VERSION<=8 && TCL_MINOR_VERSION <6))
          {
            strncat(featuremsg, " tclForces supported in GPU resident mode only with TCL newer than 8.6, we recommended 8.6.13, your build has ",1023);
            strncat(featuremsg, TCL_PATCH_LEVEL,1023);
          }
#endif
        if(FMAOn)  strncat(featuremsg,"  FMAOn\n",1023);
        if(fullDirectOn)  strncat(featuremsg,"  fullDirectOn\n",1023);
        if(MSMOn) strncat(featuremsg,"  MSMon\n",1023);
        if(FMMOn) strncat(featuremsg,"  FMMon\n",1023);
        if(globalOn) strncat(featuremsg,"  globalOn\n",1023);
        if(dihedralOn) strncat(featuremsg,"  dihedralOn\n",1023);
        if(berendsenPressureOn) strncat(featuremsg,"  berendsenPressureOn\n",1023);
        if(printBadContacts) strncat(featuremsg,"  printBadContacts\n",1023);
        if(freeEnergyOn) strncat(featuremsg,"  freeEnergyOn\n",1023);
        if(miscForcesOn) strncat(featuremsg,"  miscForcesOn\n",1023);
        if(IMDon) strncat(featuremsg,"  IMDOn\n",1023);
        if(TMDOn) strncat(featuremsg,"  TMDOn\n",1023);
        if(symmetryOn) strncat(featuremsg,"  symmetryOn\n",1023);
        if(qmForcesOn) strncat(featuremsg,"  qmForcesOn\n",1023);
        if(sphericalBCOn) strncat(featuremsg,"  sphericalBCOn\n",1023);
        if(cylindricalBCOn) strncat(featuremsg,"  cylindricalBCOn\n",1023);
        if(extForcesOn) strncat(featuremsg,"  extForcesOn\n",1023);
        if(tabulatedEnergies) strncat(featuremsg,"  tabulatedEnergies\n",1023);
        if(tclBCOn) strncat(featuremsg,"  tclBCOn\n",1023);
        if(lesOn) strncat(featuremsg,"  lesOn\n",1023);
        if(goForcesOn) strncat(featuremsg,"  goForcesOn\n",1023);
        if(pairInteractionOn) strncat(featuremsg,"  pairInteractionOn\n",1023);
#ifdef OPENATOM_VERSION
        if(openatomOn) strncat(featuremsg,"  openatomOn\n",1023);
#endif
        if(movDragOn) strncat(featuremsg,"  movDragOn\n",1023);
        if(rotDragOn) strncat(featuremsg,"  rotDragOn\n",1023);
        if(consTorqueOn) strncat(featuremsg,"  consTorqueOn\n",1023);
        if(stirOn) strncat(featuremsg,"  stirOn\n",1023);
        if(HydrogenBonds) strncat(featuremsg,"  HydrogenBonds\n",1023);
        strncat(msg,featuremsg,2047);
        if (CUDASOAintegrateMode) {
          NAMD_die(msg);
        }
        else {
          iout << iWARN << msg << "\n" << endi;
          iout << iWARN
            << "Falling back on standard integration code path\n" << endi;
        }
        SOAintegrateOn = FALSE;
      }
      else {
        if (CUDASOAintegrateMode) {
#ifndef NODEGROUP_FORCE_REGISTER
          NAMD_die("GPUresident not supported on regular multicore builds");
#endif
          if (monteCarloPressureOn && fixedAtomsOn) {
            NAMD_die("Monte Carlo barostat is not compatible with fixed atoms in GPU-resident mode.\n");
          }
          if (qmForcesOn) {
            NAMD_die("GPUresident does not support QM forces");
          }
          if (lesOn) {
            NAMD_die("GPUresident does not support "
                "locally enhanced sampling");
          }
          // Check other funny values, such as Node count > 1 or ndevices > 1
          if(CkNumNodes() > 1){
            // safety check for multiple-node run
            NAMD_die(
              "GPUresident is a shared-memory, single-process mode of execution.\n"
              "You're probably not setting the '++ppn' flags accordingly or\n"
              "the Charm++ build is not a multicore build and you're spawning\n"
              "multiple processes, which is not cool."
              );
          }
#if defined(NAMD_CUDA) || defined(NAMD_HIP)
          else if (deviceCUDA->getNumDevice() > 1) {
            // MGPU with CUDASOA is still not compatible with this

            if(monteCarloPressureOn){
              NAMD_die("Monte Carlo barostat is not compatible with multi-GPU GPUresident");
            }
          }
#endif
          else {
            iout << iINFO
              << "Running with GPU-resident mode\n"
              << endi;
          }
        }
        else { //  ! CUDASOAintegrateMode
          // XXX SOA integrate for host-side-only is not fully working
          NAMD_die("SOAintegrate is not fully supported. Please use GPUresident instead.");
        }
      }
    }

    if (!CUDASOAintegrateMode && monteCarloPressureOn) {
      NAMD_die("GPUresident is required for Monte Carlo pressure control. \n");
    }

#if defined(NAMD_CUDA) || defined(NAMD_HIP)
    if (CUDASOAintegrateMode) {
      if (bondedCUDA != NAMD_BONDEDGPU_ALL) {
        iout << iWARN << "GPUresident cannot delegate the bonded calculations to CPU (bondedGPU != " << NAMD_BONDEDGPU_ALL << ").\n";
        iout << iWARN << "Will reset bondedGPU to "<< NAMD_BONDEDGPU_ALL << ".\n";
        bondedCUDA = NAMD_BONDEDGPU_ALL;
      }
    }
    // Disable various CUDA kernels if they do not fully support
    // or are otherwise incompatible with simulation options.
    if ( useCUDAdisable ) {
      if ( drudeOn && (bondedCUDA & NAMD_BONDEDGPU_BONDS) ) {
        // disable CUDA kernels for spring bonds
        bondedCUDA &= ~NAMD_BONDEDGPU_BONDS;
        iout << iWARN << "Disabling GPU kernel for bonds due to incompatibility with Drude oscillators.\n";
      }
      if ( accelMDOn && (accelMDdihe || accelMDdual) && (bondedCUDA & (NAMD_BONDEDGPU_DIHEDRALS | NAMD_BONDEDGPU_CROSSTERMS)) ) {
        // disable CUDA kernels for dihedrals and crossterms
        bondedCUDA &= ~(NAMD_BONDEDGPU_DIHEDRALS | NAMD_BONDEDGPU_CROSSTERMS);
        iout << iWARN << "Disabling GPU kernels for dihedrals and crossterms due to incompatibility with accelerated MD options.\n";
      }
    }

    if ( alchOn || !switchingActive || vdwForceSwitching || martiniSwitching || !PMEOn || 
         longSplitting!=C1 || scale14!=1.0 || limitDist > 0.0) {
      useCUDANonbondedForceTable = TRUE;
      iout << iWARN << "Always using force tables for GPU nonbonded kernel due to unsupported config parameters.\n";
    }

    if (useDeviceMigration && !CUDASOAintegrateMode) {
      useDeviceMigration = FALSE;
      iout << iWARN << "GPUAtomMigration is only supported for GPUresident. Disabling GPUAtomMigration.\n";
    }

    if ( useDeviceMigration ) { 
      if (constraintsOn || SMDOn || groupRestraintsOn || eFieldOn || fixedAtomsOn || monteCarloPressureOn ||
          tclForcesOn || colvarsOn || gridforceOn || mgridforceOn || consForceOn || useCudaGlobal || IMDon) {
        updateAtomMap = TRUE;
      }
      if (fixedAtomsOn) {
        // TODO: In the device migration code path, we have to partition the
        //       fixed atoms at the end of patches. We are not done yet.
        NAMD_die("Fixed atoms are not supported in GPUAtomMigration.\n");
      }
    }
    if ( useDeviceMigration ) { 
      iout << iWARN << "GPUAtomMigration is experimental\n"; 
    }
    if ( !GPUresidentSingleProcessMode ) {
      if (monteCarloPressureOn) {
        NAMD_die("MC Pressure is not supported with GPU resident multi-process mode\n");
      }
    }
    if (drudeOn) {
      if (drudeNbtholeCut * drudeNbtholeCut > cutoff * cutoff) {
        NAMD_die("The GPU implementation of NbThole expects drudeNbtholeCut to be greater than cutoff!\n");
      }
    }
#endif

#ifdef NAMD_AVXTILES
    if (avxTilesCommandLineDisable) useAVXTiles = FALSE;
    if (useAVXTiles) {
      if (alchOn || lesOn || tabulatedEnergies || drudeOn || goForcesOn ||
          pressureProfileOn || qmForcesOn || LJPMEOn) {
        useAVXTiles = FALSE;
        iout << iWARN << "Disabling AVX tiles optimizations due to "
             << "incompatible simulation params.\n";
      }
    }
#else
    useAVXTiles = FALSE;
#endif

    if (ignoreExclusionChecksum) {
      iout << iWARN << "Error checking will ignore exclusion checksum\n";
    }
    
} // check_config()


void SimParameters::print_config(ParseOptions &opts, ConfigList *config, char *&cwd) {

   StringList *current; //  Pointer to config option list

   //  Now that we have read everything, print it out so that
   //  the user knows what is going on
   iout << iINFO << "SIMULATION PARAMETERS:\n";
   iout << iINFO << "TIMESTEP               " << dt << "\n" << endi;
   iout << iINFO << "NUMBER OF STEPS        " << N << "\n";
   iout << iINFO << "STEPS PER CYCLE        " << stepsPerCycle << "\n";
   iout << endi;

   if ( lattice.a_p() || lattice.b_p() || lattice.c_p() ) {
     if ( lattice.a_p() )
       iout << iINFO << "PERIODIC CELL BASIS 1  " << lattice.a() << "\n";
     if ( lattice.b_p() )
       iout << iINFO << "PERIODIC CELL BASIS 2  " << lattice.b() << "\n";
     if ( lattice.c_p() )
       iout << iINFO << "PERIODIC CELL BASIS 3  " << lattice.c() << "\n";
     iout << iINFO << "PERIODIC CELL CENTER   " << lattice.origin() << "\n";
     if (wrapWater) {
       iout << iINFO << "WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.\n";
     }
     if (wrapAll) {
       iout << iINFO << "WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.\n";
     }
     if (wrapNearest) {
       iout << iINFO << "WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER.\n";
     }
     iout << endi;
   }

   if ( CkNumPes() > 512 ) ldbUnloadOne = TRUE;
   if ( ldbUnloadOne || CkNumPes() > 128 ) ldbUnloadZero = TRUE;

   if (ldBalancer == LDBAL_NONE) {
     iout << iINFO << "LOAD BALANCER  None\n" << endi;
   } else {
     if (ldBalancer == LDBAL_CENTRALIZED) {
       iout << iINFO << "LOAD BALANCER  Centralized\n" << endi;
     } else if (ldBalancer == LDBAL_HYBRID) {
       iout << iINFO << "LOAD BALANCER  Hybrid\n" << endi;
     }

     if (ldbStrategy == LDBSTRAT_DEFAULT) {
       iout << iINFO << "LOAD BALANCING STRATEGY  New Load Balancers -- DEFAULT\n";
     } else if (ldbStrategy == LDBSTRAT_REFINEONLY) {
       iout << iINFO << "LOAD BALANCING STRATEGY  Refinement Only\n";
     } else if (ldbStrategy == LDBSTRAT_COMPREHENSIVE) {
       iout << iINFO << "LOAD BALANCING STRATEGY  Comprehensive\n";
     } else if (ldbStrategy == LDBSTRAT_OLD) {
       iout << iINFO << "LOAD BALANCING STRATEGY  Old Load Balancers\n";
     }

     iout << iINFO << "LDB PERIOD             " << ldbPeriod << " steps\n";
     iout << iINFO << "FIRST LDB TIMESTEP     " << firstLdbStep << "\n";
     if (ldBalancer == LDBAL_HYBRID)
       iout << iINFO << "HYBRIDLB GROUP SIZE     " << hybridGroupSize << "\n";
     iout << iINFO << "LAST LDB TIMESTEP     " << lastLdbStep << "\n";
     if ( ldbRelativeGrainsize > 0. )
       iout << iINFO << "LDB RELATIVE GRAINSIZE " << ldbRelativeGrainsize << "\n";
     iout << iINFO << "LDB BACKGROUND SCALING " << ldbBackgroundScaling << "\n";
     iout << iINFO << "HOM BACKGROUND SCALING " << ldbHomeBackgroundScaling << "\n";
     if ( PMEOn ) {
       iout << iINFO << "PME BACKGROUND SCALING "
                                << ldbPMEBackgroundScaling << "\n";
     if ( ldbUnloadPME )
     iout << iINFO << "REMOVING LOAD FROM PME NODES" << "\n";
     }
     if ( ldbUnloadZero ) iout << iINFO << "REMOVING LOAD FROM NODE 0\n";
     if ( ldbUnloadOne ) iout << iINFO << "REMOVING LOAD FROM NODE 1\n";
     if ( ldbUnloadOutputPEs ) iout << iINFO << "REMOVING LOAD FROM OUTPUT PES\n";
     iout << endi;
   }

   if ( ldbUnloadOne || CkNumPes() > 256 ) noPatchesOnOne = TRUE;
   if ( ldbUnloadZero || noPatchesOnOne ||
          CkNumPes() > 64 || ( IMDon && CkNumPes() > 8 ) ) {
     noPatchesOnZero = TRUE;
   }
   if ( (noPatchesOnZero || noPatchesOnOne) && CUDASOAintegrateMode ) {
     noPatchesOnZero = FALSE;
     noPatchesOnOne = FALSE;
     iout << iWARN << "OVERRIDING NOPATCH SETTING. Not supported with GPUresident on\n";
   }
   if ( noPatchesOnZero ) iout << iINFO << "REMOVING PATCHES FROM PROCESSOR 0\n";
   if ( noPatchesOnOne ) iout << iINFO << "REMOVING PATCHES FROM PROCESSOR 1\n";     
   iout << endi;

#if defined(NAMD_CUDA) || defined(NAMD_HIP) || defined(NAMD_MIC)
    maxSelfPart = maxPairPart = 1;
#endif

   if (ldBalancer == LDBAL_HYBRID) {
     iout << iINFO << "MAX SELF PARTITIONS    " << maxSelfPart << "\n"
          << iINFO << "MAX PAIR PARTITIONS    " << maxPairPart << "\n"
          << iINFO << "SELF PARTITION ATOMS   " << numAtomsSelf << "\n"
          << iINFO << "SELF2 PARTITION ATOMS   " << numAtomsSelf2 << "\n"
          << iINFO << "PAIR PARTITION ATOMS   " << numAtomsPair << "\n"
          << iINFO << "PAIR2 PARTITION ATOMS  " << numAtomsPair2 << "\n";
   }
   iout << iINFO << "MIN ATOMS PER PATCH    " << minAtomsPerPatch << "\n"
        << iINFO << "EMPTY PATCH LOAD       " << emptyPatchLoad << " ATOMS\n"
        << endi;
   
   if (initialTemp < 0)
   {
  current = config->find("velocities");

  if (current == NULL)
  {
    current = config->find("binvelocities");
  }

  iout << iINFO << "VELOCITY FILE          " << current->data << "\n";
   }
   else
   {
  iout << iINFO << "INITIAL TEMPERATURE    " 
     << initialTemp << "\n";
   }
   iout << endi;

   iout << iINFO << "CENTER OF MASS MOVING INITIALLY? ";

   if (comMove)
   {
     iout << "YES\n";
   }
   else
   {
     iout << "NO\n";
   }
   iout << endi;

   if ( zeroMomentum ) {
     iout << iINFO << "REMOVING CENTER OF MASS DRIFT DURING SIMULATION";
     if ( zeroMomentumAlt ) iout << " (ALT METHOD)";
     iout << "\n" << endi;
   }

   iout << iINFO << "DIELECTRIC             " 
      << dielectric << "\n";

   if ( nonbondedScaling != 1.0 )
   {
     iout << iINFO << "NONBONDED SCALING    " << nonbondedScaling << "\n" << endi;
   }
   iout << iINFO << "EXCLUDE                ";

   switch (exclude)
   {
     case NONE:
       iout << "NONE\n";
       break;
     case ONETWO:
       iout << "ONETWO\n";
       break;
     case ONETHREE:
       iout << "ONETHREE\n";
       break;
     case ONEFOUR:
       iout << "ONE-FOUR\n";
       break;
     default:
       iout << "SCALED ONE-FOUR\n";
       break;
   }
   iout << endi;

   if (exclude == SCALED14)
   {
     iout << iINFO << "1-4 ELECTROSTATICS SCALED BY " << scale14 << "\n";
     iout << iINFO << "MODIFIED 1-4 VDW PARAMETERS WILL BE USED\n" << endi;
   } else {
     iout << iWARN << "MODIFIED 1-4 VDW PARAMETERS WILL BE IGNORED\n" << endi;
   }

#ifdef SPEC_DISABLED_VERSION
   if (dcdFrequency > 0) {
     dcdFrequency = 0;
     iout << iWARN << "DCD TRAJECTORY OUTPUT IS DISABLED IN SPEC RELEASE\n";
   }
#endif

   if (dcdFrequency > 0)
   {
     iout << iINFO << "DCD FILENAME           " 
        << dcdFilename << "\n";
     iout << iINFO << "DCD FREQUENCY          " 
        << dcdFrequency << "\n";
     iout << iINFO << "DCD FIRST STEP         " 
        << ( ((firstTimestep + dcdFrequency)/dcdFrequency)*dcdFrequency ) << "\n";
     if ( dcdUnitCell ) {
       iout << iINFO << "DCD FILE WILL CONTAIN UNIT CELL DATA\n";
     }
   }
   else
   {
     iout << iINFO << "NO DCD TRAJECTORY OUTPUT\n";
   }
   iout << endi;
   
   if (xstFrequency > 0)
   {
     iout << iINFO << "XST FILENAME           " 
        << xstFilename << "\n";
     iout << iINFO << "XST FREQUENCY          " 
        << xstFrequency << "\n";
   }
   else
   {
     iout << iINFO << "NO EXTENDED SYSTEM TRAJECTORY OUTPUT\n";
   }
   iout << endi;
   
   if (velDcdFrequency > 0)
   {
     iout << iINFO << "VELOCITY DCD FILENAME    " 
        << velDcdFilename << "\n";
     iout << iINFO << "VELOCITY DCD FREQUENCY   " 
        << velDcdFrequency << "\n";
     iout << iINFO << "VELOCITY DCD FIRST STEP  " 
        << ( ((firstTimestep + velDcdFrequency)/velDcdFrequency)*velDcdFrequency ) << "\n";
   }
   else
   {
     iout << iINFO << "NO VELOCITY DCD OUTPUT\n";
   }
   iout << endi;
   
   if (forceDcdFrequency > 0)
   {
     iout << iINFO << "FORCE DCD FILENAME     " 
        << forceDcdFilename << "\n";
     iout << iINFO << "FORCE DCD FREQUENCY    " 
        << forceDcdFrequency << "\n";
     iout << iINFO << "FORCE DCD FIRST STEP   " 
        << ( ((firstTimestep + forceDcdFrequency)/forceDcdFrequency)*forceDcdFrequency ) << "\n";
   }
   else
   {
     iout << iINFO << "NO FORCE DCD OUTPUT\n";
   }
   iout << endi;
   
   iout << iINFO << "OUTPUT FILENAME        " 
      << outputFilename << "\n" << endi;
   if (binaryOutput)
   {
     iout << iINFO << "BINARY OUTPUT FILES WILL BE USED\n" << endi;
   }
#ifdef MEM_OPT_VERSION
    if(!binaryOutput){
        iout << iWARN <<"SINCE MEMORY OPTIMIZED VERSION IS USED, OUTPUT IN TEXT FORMAT IS DISABLED!\n" << endi;
        binaryOutput = TRUE;
    }
#endif

   if (! restartFrequency)
   {
     iout << iINFO << "NO RESTART FILE\n";
   }
   else
   {
     iout << iINFO << "RESTART FILENAME       "
        << restartFilename << "\n";
     iout << iINFO << "RESTART FREQUENCY      " 
        << restartFrequency << "\n";
  if (restartSave) {
    iout << iINFO << "RESTART FILES WILL NOT BE OVERWRITTEN\n";
  }
  if (restartSaveDcd) {
    iout << iINFO << "DCD FILE WILL BE SPLIT WHEN RESTART FILES ARE WRITTEN\n";
  }

  if (binaryRestart)
  {
    iout << iINFO << "BINARY RESTART FILES WILL BE USED\n";
  }
   }
   iout << endi;

   if (crashOutputFlag & NAMD_CRASH_ALL) {
     iout << iINFO << "NAMD will save positions and velocities to " << crashFilename << " when ";
     if (crashOutputFlag & NAMD_CRASH_ATOM_TOO_FAST) iout << " atoms are moving too fast.";
     iout << '\n';
   }
   iout << endi;
   
   if (switchingActive)
   {
      iout << iINFO << "SWITCHING ACTIVE\n";
      if ( vdwForceSwitching ) {
        iout << iINFO << "VDW FORCE SWITCHING ACTIVE\n";
      }
      if ( martiniSwitching ) { 
        iout << iINFO << "MARTINI RESIDUE-BASED COARSE-GRAIN SWITCHING ACTIVE\n";
      }
      iout << iINFO << "SWITCHING ON           "
               << switchingDist << "\n";
      iout << iINFO << "SWITCHING OFF          "
               << cutoff << "\n";
   }
   else
   {
      iout << iINFO << "CUTOFF                 " 
         << cutoff << "\n";
   }

   iout << iINFO << "PAIRLIST DISTANCE      " << pairlistDist << "\n";
   iout << iINFO << "PAIRLIST SHRINK RATE   " << pairlistShrink << "\n";
   iout << iINFO << "PAIRLIST GROW RATE     " << pairlistGrow << "\n";
   iout << iINFO << "PAIRLIST TRIGGER       " << pairlistTrigger << "\n";
   iout << iINFO << "PAIRLISTS PER CYCLE    " << pairlistsPerCycle << "\n";
   if ( outputPairlists )
     iout << iINFO << "PAIRLIST OUTPUT STEPS  " << outputPairlists << "\n";
   iout << endi;

   if ( pairlistMinProcs > 1 )
     iout << iINFO << "REQUIRING " << pairlistMinProcs << " PROCESSORS FOR PAIRLISTS\n";
   usePairlists = ( CkNumPes() >= pairlistMinProcs );

#ifdef OPENATOM_VERSION
if ( openatomOn ) 
{
  iout << iINFO << "OPENATOM QM/MM CAR-PARINELLO ACTIVE\n";
  iout << iINFO << "OPENATOM CONFIG FILE:  " << openatomConfig << "\n";
  iout << iINFO << "OPENATOM STRUCT FILE:  " << openatomStruct << "\n";
  iout << iINFO << "OPENATOM PDB FILE:     " << openatomPDB << "\n";
}
#endif // OPENATOM_VERSION

   // FB - FEP and TI are now dependent on pairlists - disallow usePairlists=0
   if ( (alchOn) && (!usePairlists)) {
     NAMD_die("Sorry, Alchemical simulations require pairlists to be enabled\n");
   }
#if defined(NAMD_CUDA) || defined(NAMD_HIP)
   if ( ! usePairlists ) {
     usePairlists = 1;
     iout << iINFO << "GPU ACCELERATION REQUIRES PAIRLISTS\n";
   }
#endif
     
   iout << iINFO << "PAIRLISTS " << ( usePairlists ? "ENABLED" : "DISABLED" )
                                                        << "\n" << endi;

   iout << iINFO << "MARGIN                 " << margin << "\n";
   if ( margin > 4.0 ) {
      iout << iWARN << "MARGIN IS UNUSUALLY LARGE AND WILL LOWER PERFORMANCE\n";
      BigReal f = patchDimension/(patchDimension-margin);
      f *= f*f;
      iout << iWARN << "MARGIN INCREASED PATCH VOLUME BY A FACTOR OF " << f << "\n";
   }

   if ( splitPatch == SPLIT_PATCH_HYDROGEN ) {
      iout << iINFO << "HYDROGEN GROUP CUTOFF  " << hgroupCutoff << "\n";
   }
   
   iout << iINFO << "PATCH DIMENSION        "
            << patchDimension << "\n";

   iout << endi;

   if (outputEnergies != 1)
   {
      iout << iINFO << "ENERGY OUTPUT STEPS    "
         << outputEnergies << "\n";
      iout << endi;
   }
   
   if (!opts.defined("computeEnergies")) {
       computeEnergies = outputEnergies;
   }

   if (computeEnergies != 1)
   {
     // in the CUDA version, energies are only evaluated at specified steps
     // check if outputEnergies is a multiple of computeEnergies
     if (outputEnergies % computeEnergies != 0) {
       const std::string err_msg = std::string{"The period of outputting energies (outputEnergies = "}
                                 + std::to_string(outputEnergies)
                                 + std::string{") is not a multiple of the period of computing energies (computeEnergies = "}
                                 + std::to_string(computeEnergies)
                                 + std::string{").\n"};
       NAMD_die(err_msg.c_str());
     }
     if (alchOn && (alchOutFreq % computeEnergies != 0)) {
       // will use NAMD_gcd(alchOutFreq, computeEnergies) to determine the period of updating energies in Sequencer.C
       const std::string err_msg = std::string{"The period of outputting energies relating to alchemical transformations (alchOutFreq = "}
                                 + std::to_string(alchOutFreq)
                                 + std::string{") is not a multiple of the period of computing energies (computeEnergies = "}
                                 + std::to_string(computeEnergies)
                                 + std::string{"). If alchOutFreq is smaller than outputEnergies and computeEnergies is not defined, a better solution is to set computeEnergies explicitly and keep it the same as alchOutFreq. The simulation will use the greatest common divisor of computeEnergies and alchOutFreq as the period of energy evaluation.\n"};
       iout << iWARN << err_msg.c_str();
     }
     // Do we need to check other settings?
     iout << iINFO << "ENERGY EVALUATION STEPS    "
          << computeEnergies << "\n";
     iout << endi;
   }

   iout << iINFO << "OUTPUT ENERGY PRECISION " << outputEnergiesPrecision << "\n";

   if (mergeCrossterms) {
      iout << iINFO << "CROSSTERM ENERGY INCLUDED IN DIHEDRAL\n" << endi;
   }
   
   if (outputMomenta != 0)
   {
      iout << iINFO << "MOMENTUM OUTPUT STEPS  "
         << outputMomenta << "\n";
      iout << endi;
   }
   
   if (outputTiming != 0)
   {
      iout << iINFO << "TIMING OUTPUT STEPS    "
         << outputTiming << "\n";
      iout << endi;
   }
   
   if (outputCudaTiming != 0)
   {
      iout << iINFO << "GPU TIMING OUTPUT STEPS    "
         << outputCudaTiming << "\n";
      iout << endi;
   }
   
   if (outputPressure != 0)
   {
      iout << iINFO << "PRESSURE OUTPUT STEPS  "
         << outputPressure << "\n";
      iout << endi;
   }
   
   if (fixedAtomsOn)
   {
      iout << iINFO << "FIXED ATOMS ACTIVE\n";
      if ( fixedAtomsForces )
        iout << iINFO << "FORCES BETWEEN FIXED ATOMS ARE CALCULATED\n";
      iout << endi;
   }

   if (constraintsOn)
   {
      iout << iINFO << "HARMONIC CONSTRAINTS ACTIVE\n";

      iout << iINFO << "HARMONIC CONS EXP      "
         << constraintExp << "\n";

      if (constraintScaling != 1.0) {
        iout << iINFO << "HARMONIC CONS SCALING  "
         << constraintScaling << "\n";
      }

      //****** BEGIN selective restraints (X,Y,Z) changes 

      if (selectConstraintsOn) {
        iout << iINFO << "SELECTED CARTESIAN COMPONENTS OF HARMONIC RESTRAINTS ACTIVE\n";

        if (constrXOn)
        iout << iINFO << "RESTRAINING X-COMPONENTS OF CARTESIAN COORDINATES!\n";

        if (constrYOn)
        iout << iINFO << "RESTRAINING Y-COMPONENTS OF CARTESIAN COORDINATES!\n";

        if (constrZOn)
        iout << iINFO << "RESTRAINING Z-COMPONENTS OF CARTESIAN COORDINATES!\n";
      }
      //****** END selective restraints (X,Y,Z) changes 

      if (sphericalConstraintsOn) {
        iout << iINFO << "SPHERICAL HARMONIC CONSTRAINTS ACTIVE\n";
        iout << iINFO << "RESTRAINING DISTANCE TO " << sphericalConstrCenter <<"\n";
      }
      iout << endi;

      //****** BEGIN moving constraints changes 

      if (movingConstraintsOn) {
        iout << iINFO << "MOVING HARMONIC CONSTRAINTS ACTIVE\n";

        iout << iINFO << "MOVING CONSTRAINT VELOCITY    "
             << movingConsVel << " ANGSTROM/TIMESTEP\n";
        
        iout << iINFO << "ALL CONSTRAINED ATOMS WILL MOVE\n";
      }
      //****** END moving constraints changes 
      iout << endi;

      //****** BEGIN rotating constraints changes 

      if (rotConstraintsOn) {
        iout << iINFO << "ROTATING HARMONIC CONSTRAINTS ACTIVE\n";

        iout << iINFO << "AXIS OF ROTATION    "
             << rotConsAxis << "\n";
        
        iout << iINFO << "PIVOT OF ROTATION   "
             << rotConsPivot << "\n";

        iout << iINFO << "ROTATING CONSTRAINT VELOCITY    "
             << rotConsVel << " DEGREES/TIMESTEP\n";
      }
      iout << endi;
      //****** END rotating constraints changes 
   }

   // moving drag
   if (movDragOn) {
     iout << iINFO << "MOVING DRAG ACTIVE.\n";
     
     iout << iINFO << "MOVING DRAG MAIN PDB FILE "
          << movDragFile << "\n";
     
     iout << iINFO << "MOVING DRAG GLOBAL VELOCITY (A/step) "
          << movDragGlobVel << "\n";
     
     iout << iINFO << "MOVING DRAG LINEAR VELOCITY FILE " 
          << movDragVelFile << "\n";
     
     iout << endi;
   }
   
   // rotating drag
   if (rotDragOn) {
     iout << iINFO << "ROTATING DRAG ACTIVE.\n";
     
     iout << iINFO << "ROTATING DRAG MAIN PDB FILE "
          << rotDragFile << "\n";
     
     iout << iINFO << "ROTATING DRAG AXIS FILE " 
          << rotDragAxisFile << "\n";
     
     iout << iINFO << "ROTATING DRAG PIVOT POINT FILE " 
          << rotDragPivotFile << "\n";
     
     iout << iINFO << "ROTATING DRAG GLOBAL ANGULAR VELOCITY (deg/step) "
          << rotDragGlobVel << "\n";
     
     iout << iINFO << "ROTATING DRAG ANGULAR VELOCITY FILE " 
          << rotDragVelFile << "\n";
     
     iout << endi;
   }
   

   // "constant" torque
   if (consTorqueOn) {
     iout << iINFO << "\"CONSTANT\" TORQUE ACTIVE.\n";
     
     iout << iINFO << "\"CONSTANT\" TORQUE MAIN PDB FILE "
          << consTorqueFile << "\n";
     
     iout << iINFO << "\"CONSTANT\" TORQUE AXIS FILE " 
          << consTorqueAxisFile << "\n";
     
     iout << iINFO << "\"CONSTANT\" TORQUE PIVOT POINT FILE " 
          << consTorquePivotFile << "\n";
     
     iout << iINFO << "\"CONSTANT\" TORQUE GLOBAL VALUE (Kcal/(mol*A^2)) "
          << consTorqueGlobVal << "\n";
     
     iout << iINFO << "\"CONSTANT\" TORQUE DACTORS FILE " 
          << consTorqueValFile << "\n";
     
     iout << endi;
   }

   if (mgridforceOn) {
     iout << iINFO << "GRID FORCE ACTIVE\n";
     iout << iINFO << " Please include this reference in published work using\n";
     iout << iINFO << " the Gridforce module of NAMD: David Wells, Volha Abramkina,\n";
     iout << iINFO << " and Aleksei Aksimentiev, J. Chem. Phys. 127:125101-10 (2007).\n";
     print_mgrid_params();
   }

   if (groupRestraintsOn) {
     iout << iINFO << "GROUP RESTRAINTS ACTIVE\n";
     groupRestraints.PrintGroupRestraints();
   }
   
   //****** BEGIN SMD constraints changes 
   
   if (SMDOn) {
     iout << iINFO << "SMD ACTIVE\n";
     
     iout << iINFO << "SMD VELOCITY    "
          << SMDVel << " ANGSTROM/TIMESTEP\n";
        
     iout << iINFO << "SMD DIRECTION   "
          << SMDDir << "\n";
 
     iout << iINFO << "SMD K   " 
          << SMDk << "\n";

     iout << iINFO << "SMD K2  " 
          << SMDk2 << "\n";

     iout << iINFO << "SMD OUTPUT FREQUENCY   "
          << SMDOutputFreq << " TIMESTEPS\n";
    
     iout << iINFO << "SMD FILE " << SMDFile << "\n"; 

     iout << endi;
   }
   
   //****** END SMD constraints changes 

   if (TMDOn) {
     iout << iINFO << "TMD ACTIVE BETWEEN STEPS " << TMDFirstStep 
          << " and " << TMDLastStep << "\n";
     iout << iINFO << "TMD K  " << TMDk << "\n";
     iout << iINFO << "TMD FILE  " << TMDFile << "\n";
     iout << iINFO << "TMD OUTPUT FREQUENCY  " << TMDOutputFreq << "\n";
     if (TMDInitialRMSD) {
       iout << iINFO << "TMD TARGET RMSD AT FIRST STEP  " << TMDInitialRMSD << "\n";
     } else {
       iout << iINFO << "TMD TARGET RMSD AT FIRST STEP COMPUTED FROM INITIAL COORDINATES\n";
     }
     iout << iINFO << "TMD TARGET RMSD AT FINAL STEP  " << TMDFinalRMSD << "\n";
     iout << endi;
   }

   if (symmetryOn) {
     if (symmetryLastStep == -1){
       iout << iINFO << "SYMMETRY RESTRAINTS ACTIVE BETWEEN STEPS " << symmetryFirstStep << " and " << "INFINITY" << "\n";
     }
     else{
       iout << iINFO << "SYMMETRY RESTRAINTS ACTIVE BETWEEN STEPS " << symmetryFirstStep << " and " << symmetryLastStep << "\n";
     }
    // iout << iINFO << "SYMMETRY FILE " << symmetryFile << "\n";

     current = config->find("symmetryFile");
     for ( ; current; current = current->next ) {
       iout << iINFO << "SYMMETRY FILE  " << current->data << "\n";
     }

     current = config->find("symmetryMatrixFile");
     for ( ; current; current = current->next ) {
      iout << iINFO << "SYMMETRY MATRIX FILE " << current->data << "\n";
     }
     iout << iINFO << "SYMMETRY FORCE CONSTANT " << symmetryk << "\n";
     if (symmetryScaleForces){
      iout << iINFO << "SYMMETRY SCALE FORCES ON\n";
     }
     iout << iINFO << "SYMMETRY FIRST FULL STEP " << symmetryFirstFullStep << "\n";
     if (symmetryLastFullStep == -1){
      iout << iINFO << "SYMMETRY LAST FULL STEP " << "INFINITY" << "\n"; 
      //iout << iINFO << "FULL SYMMETRY FORCE BETWEEN STEPS " << symmetryFirstFullStep << " and " << "INFINITY" << "\n";
     }
     else {
      iout << iINFO << "SYMMETRY LAST FULL STEP " << symmetryLastFullStep << "\n"; 
     // iout << iINFO << "FULL SYMMETRY FORCE BETWEEN STEPS " << symmetryFirstFullStep << " and " << symmetryLastFullStep << "\n";
     }

     iout << endi;
   }
//Modifications for alchemical fep
//  Alchemical FEP status

//   current = config->find("alchOutFile");
   if (alchFepOn)
   {
     iout << iINFO << "ALCHEMICAL FEP ON\n";
     iout << iINFO << "FEP CURRENT LAMBDA VALUE     "
          << alchLambda << "\n";
     iout << iINFO << "FEP COMPARISON LAMBDA VALUE  "
          << alchLambda2 << "\n";
     if (alchLambdaIDWS >= 0.) {
        iout << iINFO << "FEP ALTERNATE COMPARISON LAMBDA VALUE  "
          << alchLambdaIDWS << "\n";
     }
     if (alchLambdaFreq > 0) {
       iout << iINFO << "FEP CURRENT LAMBDA VALUE SET TO INCREASE IN EVERY  "
            << alchLambdaFreq << " STEPS\n";
     }
     if (!alchDecouple) {
       iout << iINFO << "FEP INTRA-ALCHEMICAL NON-BONDED INTERACTIONS WILL BE "
            << "DECOUPLED\n";
     }else{
       iout << iINFO << "FEP INTRA-ALCHEMICAL NON-BONDED INTERACTIONS WILL BE "
            << "RETAINED\n";
     }
     if (alchBondDecouple) {
       iout << iINFO << "FEP INTRA-ALCHEMICAL BONDED INTERACTIONS WILL BE "
            << "DECOUPLED\n";
     }else{
       iout << iINFO << "FEP INTRA-ALCHEMICAL BONDED INTERACTIONS WILL BE "
            << "RETAINED\n";
     }
     if (alchWCAOn) {
       iout << iINFO << "FEP WEEKS-CHANDLER-ANDERSEN (WCA) VDW DECOUPLING "
            << "ACTIVE\n";
     } else {
       iout << iINFO << "FEP VDW SHIFTING COEFFICIENT "
            << alchVdwShiftCoeff << "\n";
     }
     iout << iINFO << "FEP ELEC. ACTIVE FOR ANNIHILATED "
          << "PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = "
          << (1 - alchElecLambdaStart) << "\n";
     iout << iINFO << "FEP ELEC. ACTIVE FOR EXNIHILATED "
          << "PARTICLES BETWEEN LAMBDA = "
          << alchElecLambdaStart << " AND LAMBDA = 1\n";
     if (alchWCAOn) {
       iout << iINFO << "FEP VDW-REPU. ACTIVE FOR ANNIHILATED PARTICLES "
            << "BETWEEN LAMBDA = " << (1 - alchRepLambdaEnd) << " AND LAMBDA "
            << "= 1\n";
       iout << iINFO << "FEP VDW-REPU. ACTIVE FOR EXNIHILATED PARTICLES "
            << "BETWEEN LAMBDA = 0 AND LAMBDA " << alchRepLambdaEnd << "\n";
       iout << iINFO << "FEP VDW-ATTR. ACTIVE FOR ANNIHILATED PARTICLES "
            << "BETWEEN LAMBDA = " << (1 - alchVdwLambdaEnd) << " AND LAMBDA = "
            << (1 - alchRepLambdaEnd) << "\n";
       iout << iINFO << "FEP VDW-ATTR. ACTIVE FOR EXNIHILATED PARTICLES "
            << "BETWEEN LAMBDA = " << alchRepLambdaEnd << " AND LAMBDA = "
            << alchVdwLambdaEnd << "\n";
     } else {
       iout << iINFO << "FEP VDW ACTIVE FOR ANNIHILATED "
            << "PARTICLES BETWEEN LAMBDA = "
            << (1 - alchVdwLambdaEnd) << " AND LAMBDA = 1\n";
       iout << iINFO << "FEP VDW ACTIVE FOR EXNIHILATED "
            << "PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = "
            << alchVdwLambdaEnd << "\n";
     }
     iout << iINFO << "FEP BOND ACTIVE FOR ANNIHILATED "
          << "PARTICLES BETWEEN LAMBDA = "
          << (1 - alchBondLambdaEnd) << " AND LAMBDA = 1\n";
     iout << iINFO << "FEP BOND ACTIVE FOR EXNIHILATED "
          << "PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = "
          << alchBondLambdaEnd << "\n";
   }
//fepe

   if (alchThermIntOn)
   {
     iout << iINFO << "THERMODYNAMIC INTEGRATION (TI) ON\n";
     iout << iINFO << "TI LAMBDA VALUE     "
          << alchLambda << "\n";
     if (alchLambdaFreq > 0) {
       iout << iINFO << "TI COMPARISON LAMBDA VALUE  "
            << alchLambda2 << "\n";
       iout << iINFO << "TI CURRENT LAMBDA VALUE SET TO INCREASE IN EVERY  "
            << alchLambdaFreq << " STEPS\n";
     }
     if (!alchDecouple) {
       iout << iINFO << "TI INTRA-ALCHEMICAL NON-BONDED INTERACTIONS WILL BE "
            << "DECOUPLED\n";
     }else{
       iout << iINFO << "TI INTRA-ALCHEMICAL NON-BONDED INTERACTIONS WILL BE "
            << "RETAINED\n";
     }
     if (alchBondDecouple) {
       iout << iINFO << "TI INTRA-ALCHEMICAL BONDED INTERACTIONS WILL BE "
            << "DECOUPLED\n";
     }else{
       iout << iINFO << "TI INTRA-ALCHEMICAL BONDED INTERACTIONS WILL BE "
            << "RETAINED\n";
     }
     iout << iINFO << "TI VDW SHIFTING COEFFICIENT "
          << alchVdwShiftCoeff << "\n";
     iout << iINFO << "TI ELEC. ACTIVE FOR ANNIHILATED "
          << "PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = "
          << (1 - alchElecLambdaStart) << "\n";
     iout << iINFO << "TI ELEC. ACTIVE FOR EXNIHILATED "
          << "PARTICLES BETWEEN LAMBDA = "
          << alchElecLambdaStart << " AND LAMBDA = 1\n";
     iout << iINFO << "TI VDW ACTIVE FOR ANNIHILATED "
          << "PARTICLES BETWEEN LAMBDA = "
          << (1 - alchVdwLambdaEnd) << " AND LAMBDA = 1\n";
     iout << iINFO << "TI VDW ACTIVE FOR EXNIHILATED "
          << "PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = "
          << alchVdwLambdaEnd << "\n";
     iout << iINFO << "TI BOND ACTIVE FOR ANNIHILATED "
          << "PARTICLES BETWEEN LAMBDA = "
          << (1 - alchBondLambdaEnd) << " AND LAMBDA = 1\n";
     iout << iINFO << "TI BOND ACTIVE FOR EXNIHILATED "
          << "PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = "
          << alchBondLambdaEnd << "\n";
   }


   if ( lesOn ) {
     iout << iINFO << "LOCALLY ENHANCED SAMPLING ACTIVE\n";
     iout << iINFO << "LOCAL ENHANCEMENT FACTOR IS "
          << lesFactor << "\n";
     if ( lesReduceTemp ) iout << iINFO
       << "SCALING ENHANCED ATOM TEMPERATURE BY 1/" << lesFactor << "\n";
     if ( lesReduceMass ) iout << iINFO
       << "SCALING ENHANCED ATOM MASS BY 1/" << lesFactor << "\n";
   }

   if ( singleTopology ) {
     iout << iINFO << "SINGLE TOPOLOGY IS ON FOR RELATIVE FREE ENERGY CALCULATION\n";
       }

   // REST2
   if ( soluteScalingOn ) {
     iout << iINFO << "SOLUTE SCALING IS ACTIVE\n";
     if (soluteScalingFactorCharge != soluteScalingFactorVdw) {
       iout << iINFO << "SCALING FOR ELECTROSTATIC INTERACTIONS IS "
            << soluteScalingFactorCharge << "\n";
       iout << iINFO << "SCALING FOR VAN DER WAALS INTERACTIONS IS "
            << soluteScalingFactorVdw << "\n";
       iout << iINFO << "SCALING FOR BONDED INTERACTIONS IS "
            << soluteScalingFactor << "\n";
     }
     else {
       iout << iINFO << "SOLUTE SCALING FACTOR IS "
            << soluteScalingFactor << "\n";
     }
     if ( ! soluteScalingAll ) {
       iout << iINFO << "SOLUTE SCALING DISABLED FOR BONDS AND ANGLES\n";
     }
   }
   
   if ( pairInteractionOn ) {
     iout << iINFO << "PAIR INTERACTION CALCULATIONS ACTIVE\n";
     iout << iINFO << "USING FLAG " << pairInteractionGroup1 
          << " FOR GROUP 1\n";
     if (pairInteractionSelf) {
       iout << iINFO << "COMPUTING ONLY SELF INTERACTIONS FOR GROUP 1 ATOMS\n";
     } else {
       iout << iINFO << "USING FLAG " << pairInteractionGroup2 
            << " FOR GROUP 2\n";
     }
   }

   if (consForceOn) {
     iout << iINFO << "CONSTANT FORCE ACTIVE\n";
     if ( consForceScaling != 1.0 ) {
       iout << iINFO << "CONSTANT FORCE SCALING   "
                                << consForceScaling << "\n" << endi;
     }
   }


   // external command forces

   if (extForcesOn) {
     iout << iINFO << "EXTERNAL COMMAND FORCES ACTIVE\n";
     iout << iINFO << "EXT FORCES COMMAND: " << extForcesCommand << "\n";
     iout << iINFO << "EXT COORD FILENAME: " << extCoordFilename << "\n";
     iout << iINFO << "EXT FORCE FILENAME: " << extForceFilename << "\n";
     iout << endi;
   }

    // QM command forces

    if (qmForcesOn) {
        iout << iINFO << "QM FORCES ACTIVE\n";
        if (qmParamPDBDefined){
            iout << iINFO << "QM PDB PARAMETER FILE: " << qmParamPDB << "\n";
        }
        iout << iINFO << "QM SOFTWARE: " << qmSoftware << "\n";
        
        if ( qmChrgMode == QMCHRGNONE ) 
            iout << iINFO << "QM ATOM CHARGES FROM QM SOFTWARE: NONE\n";
        if ( qmChrgMode == QMCHRGMULLIKEN ) 
            iout << iINFO << "QM ATOM CHARGES FROM QM SOFTWARE: MULLIKEN\n";
        if ( qmChrgMode == QMCHRGCHELPG ) 
            iout << iINFO << "QM ATOM CHARGES FROM QM SOFTWARE: CHELPG\n";
        
        iout << iINFO << "QM EXECUTABLE PATH: " << qmExecPath << "\n";
        iout << iINFO << "QM COLUMN: " << qmColumn << "\n";
        if (qmBondOn) {
            iout << iINFO << "QM WILL DETECT BONDS BETWEEN QM AND MM ATOMS.\n";

            if (qmBondGuess) {
                iout << iINFO << "QM BONDS WILL BE GUESSED FROM TOPOLOGY AND QM REGIONS.\n";
            }
            if (qmBondColumnDefined) {
                iout << iINFO << "QM BOND COLUMN: " << qmBondColumn << "\n";
            }
            if (qmBondDist) {
                iout << iINFO << "QM BOND COLUMN WILL DEFINE LINK AOTM DISTANCE.\n";
                if (qmBondValType == 1)
                    iout << iINFO << "QM BOND COLUMN HAS LENGTH INFORMATION.\n";
                else if (qmBondValType == 2)
                    iout << iINFO << "QM BOND COLUMN HAS RATIO INFORMATION.\n";
            }
            if (qmNoPC) {
                iout << iINFO << "MECHANICHAL EMBEDDING SELECTED."
                " BOND SCHEME WILL BE IGNORED!\n" << endi;
                qmBondScheme = QMSCHEMEZ1;
            }
            else {
                if (qmBondScheme == QMSCHEMECS)
                    iout << iINFO << "QM-MM BOND SCHEME: Charge Shift.\n";
                else if (qmBondScheme == QMSCHEMERCD)
                    iout << iINFO << "QM-MM BOND SCHEME: Redistributed Charge and Dipole.\n";
                else if (qmBondScheme == QMSCHEMEZ1)
                    iout << iINFO << "QM-MM BOND SCHEME: Z1.\n";
                else if (qmBondScheme == QMSCHEMEZ2)
                    iout << iINFO << "QM-MM BOND SCHEME: Z2.\n";
                else if (qmBondScheme == QMSCHEMEZ3)
                    iout << iINFO << "QM-MM BOND SCHEME: Z3.\n";
            }
            
        }
        
        if (qmChrgFromPSF) {
            iout << iINFO << "QM Will use PSF charges.\n";
        }
        
        iout << iINFO << "QM BASE DIRECTORY: " << qmBaseDir << "\n";
        
        if (qmPrepProcOn) {
            iout << iINFO << "QM PREPARATION PROCESS: " << qmPrepProc << "\n";
        }
        if (qmSecProcOn) {
            iout << iINFO << "QM SECONDARY PROCESS: " << qmSecProc << "\n";
        }
        
        current = config->find("QMConfigLine");
        for ( ; current; current = current->next ) {
            
            if ( strstr(current->data,"\n") ) {
                iout << iINFO << "QM configuration lines from NADM config file\n";
                continue;
            }
            
            iout << iINFO << "QM CONFIG LINE: " << current->data << "\n";
            
        }
        
        if (qmReplaceAll) {
            iout << iINFO << "QM FORCES WILL REPLACE ALL NAMD FORCES!\n";
        }
        
        if (qmNoPC)
            iout << iINFO << "QM NO POINT CHARGE: ON.\n";
        
        if (qmCustomPCSel)
            iout << iINFO << "QM CUSTOM POINT CHARGE SELECTION IS ACTIVATED\n";
        
        if (! qmNoPC && ! qmCustomPCSel)
            iout << iINFO << "QM POINT CHARGES WILL BE SELECTED EVERY " 
            << qmPCSelFreq << " STEPS.\n";
        
        if (qmPCSwitchOn) {
            iout << iINFO << "QM Point Charge Switching: ON.\n";
        
            if (qmPCScheme == 1)
                iout << iINFO << "QM Point Charge SCHEME: none.\n";
            else if (qmPCScheme == 2)
                iout << iINFO << "QM Point Charge SCHEME: round.\n";
            else if (qmPCScheme == 3)
                iout << iINFO << "QM Point Charge SCHEME: zero.\n";
        }
        
        if (qmLSSOn) {
            iout << iINFO << "QM LIVE SOLVENT SELECTION IS ACTIVE.\n" ;
            iout << iINFO << "QM LIVE SOLVENT SELECTION FREQUENCY: " 
            << qmLSSFreq << "\n" << endi;
            
            current = config->find("QMLSSSize");
            for ( ; current; current = current->next ) {
                iout << iINFO << "QM LIVE SOLVENT SELECTION SIZE (\"qmGrpID numMolecules\"): " << current->data << "\n";
            }
            
            if (! opts.defined("QMLWSResname"))
                strcpy(qmLSSResname,"TIP3");
            iout << iINFO << "QM LIVE SOLVENT SELECTION WILL USE RESIDUE TYPE: " << qmLSSResname << "\n" << endi;
        }
        
        iout << iINFO << "QM executions per node: " << qmSimsPerNode << "\n";
        
        iout << endi;
    }
    
    
   // gbis gbobc implicit solvent parameters

  if (GBISserOn) {
      GBISOn = 0;//turning gbis-ser on turns gbis-parallel off
     iout << iINFO<< "GBIS GENERALIZED BORN IMPLICIT SOLVENT ACTIVE (SERIAL)\n";
  }
  if (GBISOn) {
     iout << iINFO << "GBIS GENERALIZED BORN IMPLICIT SOLVENT ACTIVE\n";
  }
  if (GBISOn || GBISserOn) {
     iout << iINFO << "GBIS SOLVENT DIELECTRIC: " << solvent_dielectric<< "\n";
     iout << iINFO << "GBIS PROTEIN DIELECTRIC: " << dielectric<< "\n";
     iout <<iINFO<<"GBIS COULOMB RADIUS OFFSET: "<< coulomb_radius_offset<<" Ang\n";
     iout << iINFO << "GBIS ION CONCENTRATION: " << ion_concentration << " M\n";
     iout << iINFO << "GBIS DEBYE SCREENING LENGTH: " << 1.0/kappa << " Ang\n";
     iout << iINFO << "GBIS DELTA: " << gbis_delta << "\n";
     iout << iINFO << "GBIS BETA: " << gbis_beta << "\n";
     iout << iINFO << "GBIS GAMMA: " << gbis_gamma << "\n";
     iout << iINFO << "GBIS BORN RADIUS CUTOFF: " << alpha_cutoff << " Ang\n";
     iout << iINFO << "GBIS MAX BORN RADIUS: " << alpha_max << " Ang\n";
     iout << endi;
  }

  if (LCPOOn) {
    iout << iINFO << "SASA SURFACE TENSION: " << surface_tension<< " kcal/mol/Ang^2\n";
  }

   tclBCScript = 0;
   if (tclBCOn) {
     iout << iINFO << "TCL BOUNDARY FORCES ACTIVE\n";
     current = config->find("tclBCScript");
     if ( current ) {
       tclBCScript = current->data;
       iout << iINFO << "TCL BOUNDARY FORCES SCRIPT   " << current->data << "\n";
     }
       iout << iINFO << "TCL BOUNDARY FORCES ARGS     " << tclBCArgs << "\n";
     iout << endi;
   }
   
   // Global forces configuration

   globalForcesOn = ( tclForcesOn || freeEnergyOn || miscForcesOn ||
                      (IMDon && ! (IMDignore || IMDignoreForces)) || (SMDOn && !CUDASOAintegrateMode) || TMDOn || 
                      colvarsOn || symmetryOn || qmForcesOn );

   if (globalForcesOn && monteCarloPressureOn) {
     NAMD_die("Monte Carlo pressure control is not compatible with "
         "global forces computations (Colvars, TclForces, TMD, IMD, "
         "symmetryRestraints, and similar features)");
   }
   if(globalForcesOn && globalMasterFrequency >1 && !CUDASOAintegrateMode)
     {
       NAMD_die("GlobalMaster multiple time-stepping is not available in non GPU-resident mode!\n");
     }
   if(globalForcesOn && globalMasterFrequency >1 )
     {
       iout << iINFO << "GLOBAL FORCES FREQENCY " << globalMasterFrequency<< "\n";
       iout << iINFO << "GLOBAL FORCES SCALING " << globalMasterScaleByFrequency<< "\n";
       iout << iINFO << "GLOBAL FORCES STALE FORCES MTS " << globalMasterStaleForces<< "\n";
     }
   if (tclForcesOn)
   {
     iout << iINFO << "TCL GLOBAL FORCES ACTIVE\n";

     current = config->find("tclForcesScript");

     for ( ; current; current = current->next ) {

     if ( strstr(current->data,"\n") ) {
       iout << iINFO << "TCL GLOBAL FORCES SCRIPT INLINED IN CONFIG FILE\n";
       continue;
     }

     iout << iINFO << "TCL GLOBAL FORCES SCRIPT   " << current->data << "\n";

     }
     iout << endi;
   }

   if (miscForcesOn)
   {
     iout << iINFO << "MISC FORCES ACTIVE\n";

     current = config->find("miscForcesScript");

     for ( ; current; current = current->next ) {

     if ( strstr(current->data,"\n") ) {
       iout << iINFO << "MISC FORCES SCRIPT INLINED IN CONFIG FILE\n";
       continue;
     }

     iout << iINFO << "MISC FORCES SCRIPT   " << current->data << "\n";

     }
     iout << endi;
   }

   if (freeEnergyOn)
   {
     iout << iINFO << "FREE ENERGY PERTURBATION ACTIVE\n";

     current = config->find("freeEnergyConfig");

     for ( ; current; current = current->next ) {

     if ( strstr(current->data,"\n") ) {
       iout << iINFO << "FREE ENERGY PERTURBATION SCRIPT INLINED IN CONFIG FILE\n";
       continue;
     }

     iout << iINFO << "FREE ENERGY PERTURBATION SCRIPT   " << current->data << "\n";

     }
     iout << endi;
   }

   if (colvarsOn)
   {
     iout << iINFO << "COLLECTIVE VARIABLES CALCULATION REQUESTED\n";

     current = config->find ("colvarsConfig");
     for ( ; current; current = current->next ) {
       if ( strstr(current->data,"\n") ) {
         iout << iINFO << "COLLECTIVE VARIABLES CONFIGURATION INLINED IN CONFIG FILE\n";
         continue;
       }
       iout << iINFO << "COLLECTIVE VARIABLES CONFIGURATION   " << current->data << "\n";
     }

     current = config->find ("colvarsInput");
     for ( ; current; current = current->next ) {
       if ( strstr(current->data,"\n") ) {
         iout << iINFO << "COLLECTIVE VARIABLES RESTART INFORMATION INLINED IN CONFIG FILE\n";
         continue;
       }
       iout << iINFO << "COLLECTIVE VARIABLES RESTART INFORMATION   " << current->data << "\n";
     }

     iout << endi;
   }

   if (IMDon)
   {
     iout << iINFO << "INTERACTIVE MD ACTIVE\n";
     iout << iINFO << "INTERACTIVE MD VERSION    " << static_cast<int>(IMDversion) << "\n";
     iout << iINFO << "INTERACTIVE MD PORT    " << IMDport << "\n";
     iout << iINFO << "INTERACTIVE MD FREQ    " << IMDfreq << "\n";
     if (IMDignore) {
        iout << iINFO << "INTERACTIVE MD WILL NOT INFLUENCE SIMULATION\n";
     } else {
       if (IMDignoreForces) 
         {
            iout << iINFO << "INTERACTIVE FORCES ARE DISABLED\n";
            iout << iINFO << "PAUSE, RESUME, DETACH AND FINISH INTERACTIVE MD ARE ENABLED\n";
         }
       if (IMDwait) iout << iINFO << "WILL AWAIT INTERACTIVE MD CONNECTION\n";
     }
     if (IMDversion == IMDversion_t::IMDv3) {
        iout << iINFO << "INTERACTIVE MD WILL SEND THE FOLLOWING:\n";
        if (IMDsendsettings.time_switch == 1) {
            iout << iINFO << "TIME\n";
        }
        if (IMDsendsettings.energies_switch == 1) {
            iout << iINFO << "ENERGIES\n";
            if (CUDASOAintegrate && (IMDfreq % computeEnergies != 0)) {
                iout << iWARN << "IMDfreq is not a multiple of computeEnergies in GPU-resident mode.\n" << endi;
                iout << iWARN << "Energies sent to the IMD client might be incorrect.\n" << endi;
            }
        }
        if (IMDsendsettings.box_switch == 1) {
            iout << iINFO << "BOX DIMENSIONS\n";
        }
        if (IMDsendsettings.fcoords_switch == 1) {
          if (IMDsendsettings.wrap_switch == 1) {
            iout << iINFO << "WRAPPED COORDINATES\n";
          } else {
            iout << iINFO << "UNWRAPPED COORDINATES\n";
          }
        }
        if (IMDsendsettings.velocities_switch == 1) {
            iout << iINFO << "VELOCITIES\n";
        }
        if (IMDsendsettings.forces_switch == 1) {
            iout << iINFO << "FORCES\n";
        }
     }
     iout << endi;
   }

   if (globalOn && !dihedralOn)
   {
      iout << iINFO << "GLOBAL INTEGRATION TEST MODE ACTIVE\n";
   }


   if (dihedralOn)
   {
      iout << iINFO << "DIHEDRAL ANGLE DYNAMICS ACTIVE\n";
      if (!COLDOn)
      {
         iout << iINFO << "*** DIHEDRAL ANGLE DYNAMICS IS HIGHLY EXPERIMENTAL ***\n";
         iout << iINFO << "PLEASE CONSIDER USING THE COLD OPTION AS WELL\n";
      }
   }

   // This function is so long that it exceeds the emacs brace
   // matching default max length of 25600 (a bit before this comment). We
   // should take this is a not too subtle hint about scale of this
   // violation of good coding practices.  Especially considering the
   // fact that this function still has about a thousand lines to go
   // before its done, and is doomed to grow with new features. 

   if (COLDOn)
   {
      iout << iINFO << "COLD (CONSTRAINED OVERDAMPED LANGEVIN DYNAMICS) ACTIVE\n";

      iout << iINFO << "COLD TARGET TEMP       "
         << COLDTemp << "\n";

      iout << iINFO << "COLD COLLISION RATE    "
         << COLDRate << "\n";
   }

   if (cylindricalBCOn)
   {
    iout << iINFO << "CYLINDRICAL BOUNDARY CONDITIONS ACTIVE\n";
    iout << iINFO << "AXIS                     " << cylindricalBCAxis << "\n";
    iout << iINFO << "RADIUS #1                " << cylindricalBCr1 << "\n";
    iout << iINFO << "FORCE CONSTANT #1        " << cylindricalBCk1 << "\n";
    iout << iINFO << "EXPONENT #1              " << cylindricalBCexp1 << "\n";
    iout << iINFO << "LENGTH #1                " << cylindricalBCl1 << "\n";
    if (cylindricalBCr2 > 0.0)
    {
     iout << iINFO << "RADIUS #2               " << cylindricalBCr2 << "\n";
     iout << iINFO << "FORCE CONSTANT #2       " << cylindricalBCk2 << "\n";
     iout << iINFO << "EXPONENT #2             " << cylindricalBCexp2 << "\n";
     iout << iINFO << "LENGTH #2               " << cylindricalBCl2 << "\n";
    }
    iout << iINFO << "CYLINDER BOUNDARY CENTER(" << cylindricalCenter.x << ", "
             << cylindricalCenter.y << ", " << cylindricalCenter.z << ")\n";
    iout << endi;
  }

   if (sphericalBCOn)
   {
      iout << iINFO << "SPHERICAL BOUNDARY CONDITIONS ACTIVE\n";

      iout << iINFO << "RADIUS #1              "
         << sphericalBCr1 << "\n";
      iout << iINFO << "FORCE CONSTANT #1      "
         << sphericalBCk1 << "\n";
      iout << iINFO << "EXPONENT #1            "
         << sphericalBCexp1 << "\n";

      if (sphericalBCr2 > 0)
      {
        iout << iINFO << "RADIUS #2              "
              << sphericalBCr2 << "\n";
        iout << iINFO << "FORCE CONSTANT #2      "
            << sphericalBCk2 << "\n";
        iout << iINFO << "EXPONENT #2            "
        << sphericalBCexp2 << "\n";
      }

      iout << iINFO << "SPHERE BOUNDARY CENTER(" << sphericalCenter.x << ", "
               << sphericalCenter.y << ", " << sphericalCenter.z << ")\n";
      iout << endi;
   }

   if (eFieldOn)
   {
      iout << iINFO << "ELECTRIC FIELD ACTIVE\n";
      
      iout << iINFO << "E-FIELD VECTOR         ("
         << eField.x << ", " << eField.y
         << ", " << eField.z << ")\n";
      if ( eFieldNormalized ) iout << iINFO << "E-FIELD VECTOR IS SCALED BY CELL BASIS VECTORS\n";
      iout << iINFO << "E-FIELD FREQUENCY IS (1/ps) " << eFieldFreq << "\n";
      iout << iINFO << "E-FIELD PHASE IS     (deg)  " << eFieldPhase << "\n";

      iout << endi;
   }

      if (stirOn)
   {
      iout << iINFO << "STIRRING TORQUES ACTIVE\n";
      
      iout << iINFO << "STIR STARTING THETA   (deg)  "<< stirStartingTheta << "\n";
      iout << iINFO << "STIR ANGULAR VELOCITY (deg/ts)   " << stirVel <<"\n";
      iout << iINFO << "STIR FORCE HARMONIC SPRING CONSTANT "<< stirK << "\n";
      iout << iINFO << "STIR AXIS OF ROTATION (DIRECTION)      ("
         << stirAxis.x << ", " << stirAxis.y
         << ", " << stirAxis.z << ")\n";
                  iout << iINFO << "STIR PIVOT POINT (COORDINATE)           ("
         << stirPivot.x << ", " << stirPivot.y
         << ", " << stirPivot.z << ")\n";
      current = config->find("stirFilename");
                  
      iout << iINFO << "STIR ATOMS AND ORIGINAL POSITIONS FROM FILE    " <<current ->data << '\n';
      current = config->find("stirredAtomsCol");
      iout << iINFO <<"STIR FILE COLUMN " << current ->data << '\n';
      iout << endi;
   }

   if (drudeOn)
   {
      iout << iINFO << "DRUDE MODEL DUAL THERMOSTAT IS ACTIVE\n";
      iout << iINFO << "DRUDE BOND TEMPERATURE " << drudeTemp << "\n";
      if (drudeDamping > 0.0) {
        iout << iINFO << "DRUDE DAMPING COEFFICIENT IS "
             << drudeDamping << " INVERSE PS\n";
      }
      if (drudeHardWallOn) {
        iout << iINFO << "DRUDE HARD WALL RESTRAINT IS ACTIVE FOR DRUDE BONDS\n";
        iout << iINFO << "DRUDE MAXIMUM BOND LENGTH BEFORE RESTRAINT IS   "
             << drudeBondLen << "\n";
      } else if (drudeBondConst > 0.0) {
        iout << iINFO << "DRUDE QUARTIC RESTRAINT IS ACTIVE FOR DRUDE BONDS\n";
        iout << iINFO << "DRUDE MAXIMUM BOND LENGTH BEFORE RESTRAINT IS   "
             << drudeBondLen << "\n";
        iout << iINFO << "DRUDE BOND RESTRAINT CONSTANT IS                "
             << drudeBondConst << "\n";
      }
      if (drudeNbtholeCut > 0.0) {
        iout << iINFO << "DRUDE NBTHOLE IS ACTIVE\n";
        iout << iINFO << "DRUDE NBTHOLE RADIUS IS   "
             << drudeNbtholeCut << "\n";
      }
   }

   if (langevinOn)
   {
      iout << iINFO << "LANGEVIN DYNAMICS ACTIVE\n";
      iout << iINFO << "LANGEVIN TEMPERATURE   "
         << langevinTemp << "\n";
      if (! langevin_useBAOAB) iout << iINFO << "LANGEVIN USING BBK INTEGRATOR\n";
      else  iout << iINFO << "LANGEVIN USING BAOAB INTEGRATOR\n"; // [!!] Info file
      if (langevinDamping > 0.0) {
        iout << iINFO << "LANGEVIN DAMPING COEFFICIENT IS "
                << langevinDamping << " INVERSE PS\n";
        if (langevinHydrogen)
                iout << iINFO << "LANGEVIN DYNAMICS APPLIED TO HYDROGENS\n";
        else
                iout << iINFO << "LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS\n";
      } else {
        iout << iINFO << "LANGEVIN DAMPING COEFFICIENTS DETERMINED FROM FILES\n";
        current = config->find("langevinFile");
        if ( current ) iout << iINFO << "LANGEVIN DAMPING FILE:  " <<
          current->data << "\n";
        else iout << iINFO << "LANGEVIN DAMPING FILE IS COORDINATE PDB\n";
        current = config->find("langevinCol");
        if ( current ) iout << iINFO << "LANGEVIN DAMPING COLUMN:  " <<
          current->data << "\n";
        else iout << iINFO << "LANGEVIN DAMPING COLUMN:  DEFAULT (4TH, O)\n";
      }
      iout << endi;
   }
   
   // BEGIN LA
   if (loweAndersenOn)
   {
      iout << iINFO << "LOWE-ANDERSEN DYNAMICS ACTIVE\n";
      iout << iINFO << "LOWE-ANDERSEN TEMPERATURE     "
         << loweAndersenTemp << " K\n";
      iout << iINFO << "LOWE-ANDERSEN RATE            "
         << loweAndersenRate << " INVERSE PS\n";
      iout << iINFO << "LOWE-ANDERSEN CUTOFF          "
         << loweAndersenCutoff << " ANGSTROMS\n";
      iout << endi;
   }
   // END LA

   if (tCoupleOn)
   {
      iout << iINFO << "TEMPERATURE COUPLING ACTIVE\n";
      iout << iINFO << "COUPLING TEMPERATURE   "
         << tCoupleTemp << "\n";
      iout << endi;
   }

   if (stochRescaleOn)
   {
      iout << iINFO << "STOCHASTIC RESCALING ACTIVE\n";
      iout << iINFO << "STOCHASTIC RESCALING TEMPERATURE "
           << stochRescaleTemp << " K\n";
      iout << iINFO << "STOCHASTIC RESCALING PERIOD " 
           << stochRescalePeriod << " PS\n";
      iout << iINFO << "STOCHASTIC RESCALING WILL OCCUR EVERY "
           << stochRescaleFreq << " STEPS\n";
      iout << endi;
   }

   if (minimizeOn)
   {
      iout << iINFO << "OLD STYLE MINIMIZATION ACTIVE\n";
      iout << endi;
   }

   if (minimizeCGOn)
   {
      iout << iINFO << "CONJUGATE GRADIENT MINIMIZATION ACTIVE\n";
      iout << iINFO << "LINE MINIMIZATION GOAL = " << minLineGoal << "\n";
      iout << iINFO << "BABY STEP SIZE = " << minBabyStep << "\n";
      iout << iINFO << "TINY STEP SIZE = " << minTinyStep << "\n";
      iout << endi;
   }

   if (maximumMove)
   {
      iout << iINFO << "MAXIMUM MOVEMENT       "
         << maximumMove << "\n";
      iout << endi;
   }

   if (rescaleFreq > 0)
   {
     iout << iINFO << "VELOCITY RESCALE FREQ  "
        << rescaleFreq << "\n";
     iout << iINFO << "VELOCITY RESCALE TEMP  "
        << rescaleTemp << "\n";
     iout << endi;
   }

   if (reassignFreq > 0)
   {
     iout << iINFO << "VELOCITY REASSIGNMENT FREQ  "
        << reassignFreq << "\n";
     iout << iINFO << "VELOCITY REASSIGNMENT TEMP  "
        << reassignTemp << "\n";
     if ( reassignIncr != 0. )
       iout << iINFO << "VELOCITY REASSIGNMENT INCR  "
        << reassignIncr << "\n";
     if ( reassignHold != 0. )
       iout << iINFO << "VELOCITY REASSIGNMENT HOLD  "
        << reassignHold << "\n";
     iout << endi;
   }

   if ((int)berendsenPressureOn + (int)langevinPistonOn + (int)monteCarloPressureOn + (int)multigratorOn > 1)
   {
      NAMD_die("Multiple pressure control algorithms selected!\n");
   }

   if (excludeFromPressure) {
     iout << iINFO << "EXCLUDE FROM PRESSURE ACTIVE\n";
   }
   if (useConstantArea && useConstantRatio) {
     NAMD_die("useConstantArea and useConstantRatio are mutually exclusive.\n");
   }
   if (useConstantRatio && !useFlexibleCell) {
     NAMD_die("useConstantRatio requires useFlexibleCell.\n");
   }
   if (useConstantArea && surfaceTensionTarget) {
     NAMD_die("surfaceTensionTarget and useConstantArea are mutually exclusive.\n");
   }
   if (useConstantArea && !useFlexibleCell) {
     NAMD_die("useConstantArea requires useFlexibleCell.\n");
   }

   if (fixCellDims) {
     if (!useFlexibleCell) {
       if (fixCellDimX || fixCellDimY || fixCellDimZ) {
         NAMD_die("fixCellDims requires useFlexibleCell.\n");
       }
     } else {
       if(useConstantArea && fixCellDimZ) {
         NAMD_die("fixCellDimZ can not be used with useConstantArea.\n");
       } else if (useConstantRatio && fixCellDimX) {
         NAMD_die("fixCellDimX can not be used with useConstantRatio.\n");
       } else if (useConstantRatio && fixCellDimY) {
         NAMD_die("fixCellDimY can not be used with useConstantRatio.\n");
       }
     }

     if (fixCellDimX && fixCellDimY && fixCellDimZ) {
       NAMD_die("Cell dimension can not be fixed in X, Y, and Z axis, simultaneously.\n");
     }
   }

   if (berendsenPressureOn || langevinPistonOn) {
     if (rigidBonds != RIGID_NONE && useGroupPressure == FALSE) {
       useGroupPressure = TRUE;
       iout << iWARN << "Option useGroupPressure is being enabled "
            << "due to pressure control with rigidBonds.\n" << endi;
     }
   }

   if (monteCarloPressureOn) {
     if (!opts.defined("MonteCarloAcceptanceRate")) {
       monteCarloAcceptanceRate = 0.5;
     } else if (monteCarloAcceptanceRate > 0.8 || monteCarloAcceptanceRate < 0.2) {
       NAMD_die("Acceptance rate in Monte Carlo pressure control must be between 0.2 and 0.8!\n");
     }
 
     if ( monteCarloAdjustmentFreq < 10 ) {
       iout << iWARN << "Modifying the frequency of adjusting the maximum volume change.\n" << endi;
       monteCarloAdjustmentFreq = 30;
     }
     
     if (!opts.defined("MonteCarloMaxVolume")) {
       // Default max volume change is 0.01 of system volume
       monteCarloMaxVolume.x = 0.01 * lattice.volume();
       monteCarloMaxVolume.y = 0.01 * lattice.volume();
       monteCarloMaxVolume.z = 0.01 * lattice.volume();
     } else {
       // Make sure max Volume change is not too small or large
      if (0.3 < (monteCarloMaxVolume.x / lattice.volume())) {
       iout << iWARN << "Modifying the maximum volume change for x-axis.\n" << endi;
       monteCarloMaxVolume.x = 0.01 * lattice.volume();
      }
      if (0.3 < (monteCarloMaxVolume.y / lattice.volume())) {
       iout << iWARN << "Modifying the maximum volume change for y-axis.\n" << endi;
       monteCarloMaxVolume.y = 0.01 * lattice.volume();
      }
      if (0.3 < (monteCarloMaxVolume.z / lattice.volume())) {
       iout << iWARN << "Modifying the maximum volume change for z-axis.\n" << endi;
       monteCarloMaxVolume.z = 0.01 * lattice.volume();
      }
      if (monteCarloMaxVolume.x < 1.0) {
       iout << iWARN << "Maximum volume change is negative or too small for x-axis.\n" <<
        "         Modifying the maximum volume change for x-axis.\n" << endi;
       monteCarloMaxVolume.x = 0.01 * lattice.volume();
      }
      if (monteCarloMaxVolume.y < 1.0) {
       iout << iWARN << "Maximum volume change is negative or too small for y-axis.\n" <<
        "         Modifying the maximum volume change for y-axis.\n" << endi;
       monteCarloMaxVolume.y = 0.01 * lattice.volume();
      }
      if (monteCarloMaxVolume.z < 1.0) {
       iout << iWARN << "Maximum volume change is negative or too small for z-axis.\n" <<
        "         Modifying the maximum volume change for z-axis.\n" << endi;
       monteCarloMaxVolume.z = 0.01 * lattice.volume();
      }
     }
     
     if (!opts.defined("MonteCarloPressureFreq")) {
       monteCarloPressureFreq = 50 * nonbondedFrequency;
            if ( fullElectFrequency ) {
                    monteCarloPressureFreq = 50 * fullElectFrequency;
      }
     } else if ((monteCarloPressureFreq % nonbondedFrequency) || ( fullElectFrequency
                          && (monteCarloPressureFreq % fullElectFrequency) )) {
              NAMD_die("monteCarloPressureFreq must be a multiple of both fullElectFrequency and nonbondedFrequency\n");
     }
 
     iout << iINFO << "MONTE CARLO PRESSURE CONTROL ACTIVE\n";
     iout << iINFO << "      TARGET PRESSURE IS "
       << monteCarloPressureTarget << " BAR\n";
     iout << iINFO << "      TARGET ACCEPTANCE RATE IS "
       << monteCarloAcceptanceRate << "\n";
     iout << iINFO << "      IMPOSED TEMPERATURE IS "
         << monteCarloTemp << " K\n";
     iout << iINFO << "      MAXIMUM VOLUME CHANGE IS ("
       << monteCarloMaxVolume.x << ", " << monteCarloMaxVolume.y << ", "
       << monteCarloMaxVolume.z << ") A^3 \n";
     iout << iINFO << "      ADJUST MAXIMUM VOLUME CHANGE EVERY "
       << monteCarloAdjustmentFreq << " TRIALS\n";
     iout << iINFO << "      APPLIED EVERY "
       << monteCarloPressureFreq << " STEPS\n";
     iout << iINFO << "      PRESSURE CONTROL IS "
       << (useGroupPressure?"GROUP":"ATOM") << "-BASED\n";
     iout << endi;
     monteCarloPressureTarget /= PRESSUREFACTOR;
   }

   if (berendsenPressureOn) 
   {
     if ( ! opts.defined("BerendsenPressureFreq") ) {
            berendsenPressureFreq = nonbondedFrequency;
            if ( fullElectFrequency )
                    berendsenPressureFreq = fullElectFrequency;
     }
     if ( (berendsenPressureFreq % nonbondedFrequency) || ( fullElectFrequency
                    && (berendsenPressureFreq % fullElectFrequency) ) ) {
              NAMD_die("berendsenPressureFreq must be a multiple of both fullElectFrequency and nonbondedFrequency\n");
    }
     iout << iINFO << "BERENDSEN PRESSURE COUPLING ACTIVE\n";
     iout << iINFO << "    TARGET PRESSURE IS "
        << berendsenPressureTarget << " BAR\n";
     iout << iINFO << "    COMPRESSIBILITY ESTIMATE IS "
        << berendsenPressureCompressibility << " BAR^(-1)\n";
     iout << iINFO << "    RELAXATION TIME IS "
        << berendsenPressureRelaxationTime << " FS\n";
     iout << iINFO << "    APPLIED EVERY "
        << berendsenPressureFreq << " STEPS\n";
     iout << iINFO << "    PRESSURE CONTROL IS "
              << (useGroupPressure?"GROUP":"ATOM") << "-BASED\n";
     iout << endi;
     berendsenPressureTarget /= PRESSUREFACTOR;
     berendsenPressureCompressibility *= PRESSUREFACTOR;
   }

   if (langevinPistonOn)
   {
     iout << iINFO << "LANGEVIN PISTON PRESSURE CONTROL ACTIVE\n";
     iout << iINFO << "       TARGET PRESSURE IS "
        << langevinPistonTarget << " BAR\n";
     iout << iINFO << "    OSCILLATION PERIOD IS "
        << langevinPistonPeriod << " FS\n";
     iout << iINFO << "            DECAY TIME IS "
        << langevinPistonDecay << " FS\n";
     iout << iINFO << "    PISTON TEMPERATURE IS "
        << langevinPistonTemp << " K\n";
     iout << iINFO << "      PRESSURE CONTROL IS "
              << (useGroupPressure?"GROUP":"ATOM") << "-BASED\n";
     iout << iINFO << "   INITIAL STRAIN RATE IS "
        << strainRate << "\n";
     iout << endi;
     langevinPistonTarget /= PRESSUREFACTOR;
   }

    if (multigratorOn) {
      multigratorPressureTarget /= PRESSUREFACTOR;
    }

   if (berendsenPressureOn || langevinPistonOn || monteCarloPressureOn) {
     iout << iINFO << "      CELL FLUCTUATION IS "
            << (useFlexibleCell?"AN":"") << "ISOTROPIC\n";
     if (useConstantRatio) 
       iout << iINFO << "    SHAPE OF CELL IS CONSTRAINED IN X-Y PLANE\n";
     if (useConstantArea) 
       iout << iINFO << "    CONSTANT AREA PRESSURE CONTROL ACTIVE\n";
   }

   if (surfaceTensionTarget != 0)
   {
     iout << iINFO << "SURFACE TENSION CONTROL ACTIVE\n";
     iout << iINFO << "      TARGET SURFACE TENSION IS "
          << surfaceTensionTarget << " DYN/CM\n";
     iout << endi;
     // multiply by 100 to convert from dyn/cm to bar-Angstroms, then divide
     // by PRESSURE factor to convert bar to NAMD internal pressure units. 
     surfaceTensionTarget *= 100.0 / PRESSUREFACTOR;
   }

   if (pressureProfileOn) {
     if ((berendsenPressureOn || langevinPistonOn || monteCarloPressureOn) && !dcdUnitCell) {
#if 1
       iout << iWARN << "Turning on dcdUnitCell so that trajectory files contain unit cell data.\n" << endi;
       dcdUnitCell = 1;
#else
       NAMD_die("Sorry, pressure profile not implemented for constant pressure.");
#endif
     }
     // if Ewald is on, only calculate Ewald
     if (pressureProfileEwaldOn)
       pressureProfileOn = 0;

     if (pressureProfileSlabs < 1) 
       NAMD_die("pressureProfileSlabs must be positive.");
     iout << iINFO << "PRESSURE PROFILE CALCULATIONS ACTIVE\n";
     iout << iINFO << "      NUMBER OF SLABS: " << pressureProfileSlabs << "\n";
     iout << iINFO << "      SLAB THICKNESS: " << cellBasisVector3.z / pressureProfileSlabs
                   << "\n";
     iout << iINFO << "      TIMESTEPS BETWEEN DATA OUTPUT: " 
                   << pressureProfileFreq << "\n";
     iout << iINFO << "      NUMBER OF ATOM TYPES: " << pressureProfileAtomTypes << "\n";
     iout << endi;
   } else {
     pressureProfileEwaldOn = 0;
     pressureProfileAtomTypes = 1;
   }

   if (accelMDOn) {
     iout << iINFO << "ACCELERATED MD ACTIVE\n";

     if ( accelMDdual) {
        accelMDdihe = FALSE;
        iout << iINFO << "APPLYING DUAL BOOST\n";
     }
     else if ( accelMDdihe ) {
        iout << iINFO << "BOOSTING DIHEDRAL POTENTIAL\n";
     } else {
        iout << iINFO << "BOOSTING TOTAL POTENTIAL\n";
     }

     if(accelMDG){
         switch(accelMDGiE) {
             case 1:
                 iout << iINFO << "accelMDG THRESHOLD ENERGY SET TO LOWER BOUND Vmax\n";
                 break;
             case 2:
                 iout << iINFO << "accelMDG THRESHOLD ENERGY SET TO UPPER BOUND Vmin+(Vmax-Vmin)/k0\n";
                 break;
         }
         if(accelMDGRestart)
             iout << iINFO << "accelMDG USING RESTART FILE " << accelMDGRestartFile << "\n";
         if(accelMDGresetVaftercmd)
             iout << iINFO << "accelMDG WILL RESET STATISTICS AFTER FIRST CMD STEPS\n";

         iout << iINFO << "accelMDG " << accelMDGcMDSteps << " CONVENTIONAL MD STEPS "
             << "(WITH " << accelMDGcMDPrepSteps << " PREPARATION STEPS)\n";
         if(accelMDGcMDSteps == 0)
                 iout << iINFO << "(accelMDGcMDPrepSteps is set to zero automatically)\n";

         iout << iINFO << "accelMDG " << accelMDGEquiSteps << " EQUILIBRATION STEPS "
             << "(WITH " << accelMDGEquiPrepSteps << " PREPARATION STEPS)\n";
         if(accelMDGEquiSteps == 0)
                 iout << iINFO << "(accelMDGEquiPrepSteps is set to zero automatically)\n";

         if(accelMDGStatWindow > 0)
             iout << iINFO << "accelMDG WILL RESET AVERAGE AND STANDARD DEVIATION EVERY " << accelMDGEquiSteps << " STEPS\n";
         else
             iout << iINFO << "accelMDG WILL NOT RESET AVERAGE AND STANDARD DEVIATION\n";

         if(accelMDdihe)
             iout << iINFO << "accelMDGSigma0D: " << accelMDGSigma0D << " KCAL/MOL\n";
         else if(accelMDdual)
             iout << iINFO << "accelMDGSigma0P: " << accelMDGSigma0P << " KCAL/MOL, "
                 << "accelMDGSigma0D: " << accelMDGSigma0D << " KCAL/MOL\n";
         else
             iout << iINFO << "accelMDGSigma0P: " << accelMDGSigma0P << " KCAL/MOL\n";
     }
     else{
         iout << iINFO << "accelMDE: " << accelMDE << " KCAL/MOL, accelMDalpha: " << accelMDalpha << " KCAL/MOL\n";
         if (accelMDdual) {
             iout << iINFO << "accelMDTE: " << accelMDTE << " KCAL/MOL, "
                 << "accelMDTalpha: " << accelMDTalpha << " KCAL/MOL\n";
         }
     }
     if ( accelMDLastStep > 0) {
        iout << iINFO << "accelMD WILL BE DONE FROM STEP " << accelMDFirstStep << " TO STEP " << accelMDLastStep << "\n";
     } else {
        iout << iINFO << "accelMD WILL BE DONE FROM STEP " << accelMDFirstStep << " TO THE END OF THE SIMULATION \n";
     }        
     iout << iINFO << "accelMD OUTPUT FREQUENCY " << accelMDOutFreq << "\n";
     iout << endi;
   }

   if (adaptTempOn) {
     iout << iINFO << "ADAPTIVE TEMPERING ACTIVE:\n";
     iout << iINFO << "      OUTPUT FREQUENCY: " << adaptTempOutFreq << "\n";
     iout << iINFO << "      TEMPERATURE UPDATE FREQUENCY: " << adaptTempFreq << "\n";
     if ( adaptTempLastStep > 0 )
        iout << iINFO << "      ADAPTIVE TEMPERING WILL BE DONE FROM STEP " << adaptTempFirstStep  << " TO " << adaptTempLastStep << "\n";
     else
        iout << iINFO << "      ADAPTIVE TEMPERING WILL BE DONE FROM STEP " << adaptTempFirstStep << "\n";
     if ( adaptTempLangevin )
        iout << iINFO << "      ADAPTIVE TEMPERING COUPLED TO LANGEVIN THERMOSTAT\n";
     if ( adaptTempRescale )
        iout << iINFO << "      ADAPTIVE TEMPERING COUPLED TO VELOCITY RESCALING\n";
     if (adaptTempRestartFreq > 0) {
        iout << iINFO << "      WRITING RESTART INFORMATION TO " << adaptTempRestartFile << " EVERY " << adaptTempRestartFreq << " STEPS\n";
     }
        
   }

   if (FMAOn)
   {
     iout << iINFO << "FMA ACTIVE\n";
     iout << iINFO << "FMA THETA              "
        << fmaTheta << "\n";
     iout << endi;
   }

  // PME
   FFTWWisdomString = 0;
   if (PMEOn)
   {
     iout << iINFO << "PARTICLE MESH EWALD (PME) ACTIVE\n";
     iout << iINFO << "PME TOLERANCE               "
        << PMETolerance << "\n";
     iout << iINFO << "PME EWALD COEFFICIENT       "
        << PMEEwaldCoefficient << "\n";
     iout << iINFO << "PME INTERPOLATION ORDER     "
        << PMEInterpOrder << "\n";
     iout << iINFO << "PME GRID DIMENSIONS         "
        << PMEGridSizeX << " "
        << PMEGridSizeY << " "
        << PMEGridSizeZ << "\n";
     iout << iINFO << "PME MAXIMUM GRID SPACING    "
        << PMEGridSpacing << "\n";
     if ( PMEBarrier ) {
       iout << iINFO << "PME BARRIER ENABLED\n";
     }
     if ( PMEOffload ) {
       iout << iINFO << "PME RECIPROCAL SUM OFFLOADED TO GPU\n";
     }
     iout << endi;
     if ( useDPME ) iout << iINFO << "USING OLD DPME CODE\n";
#if defined(NAMD_CUDA) || defined(NAMD_HIP)
     else if ( usePMECUDA ) {
       iout << iINFO << "PME CALCULATION WILL BE PERFORMED ON GPU" << "\n" 
         << endi;
     }
#endif
#ifdef NAMD_FFTW
     else if ( FFTWUseWisdom ) {  // handle FFTW wisdom
#ifdef NAMD_FFTW_3
       iout << iINFO << "Attempting to read FFTW data from system" <<"\n" <<endi;
       fftwf_import_system_wisdom();
#endif
       if (! opts.defined("FFTWWisdomFile")) {
         strcpy(FFTWWisdomFile,"FFTW_NAMD_");
         strcat(FFTWWisdomFile,NAMD_VERSION);
         strcat(FFTWWisdomFile,"_");
         strcat(FFTWWisdomFile,NAMD_PLATFORM);
#ifdef NAMD_FFTW_3
         strcat(FFTWWisdomFile,"_FFTW3");
#endif
         strcat(FFTWWisdomFile,".txt");
       }

       iout << iINFO << "Attempting to read FFTW data from "
                << FFTWWisdomFile << "\n" << endi;
       FILE *wisdom_file = fopen(FFTWWisdomFile,"r");
       if ( wisdom_file ) {
#ifdef NAMD_FFTW_3
         fftwf_import_wisdom_from_file(wisdom_file);
#else
         fftw_import_wisdom_from_file(wisdom_file);
#endif
         fclose(wisdom_file);
       }
       int nrp = 1;

       // rules based on work available
       int minslices = PMEMinSlices;
       int dimx = PMEGridSizeX;
       int nrpx = ( dimx + minslices - 1 ) / minslices;
       if ( nrpx > nrp ) nrp = nrpx;
       int dimy = PMEGridSizeY;
       int nrpy = ( dimy + minslices - 1 ) / minslices;
       if ( nrpy > nrp ) nrp = nrpy;

       // rules based on processors available
       int nrpp = CkNumPes();
       // if ( nrpp > 32 ) nrpp = 32;  // cap to limit messages
       if ( nrpp < nrp ) nrp = nrpp;

       // user override
       int nrps = PMEProcessors;
       if ( nrps > CkNumPes() ) nrps = CkNumPes();
       if ( nrps > 0 ) nrp = nrps;

       // make sure there aren't any totally empty processors
       int bx = ( dimx + nrp - 1 ) / nrp;
       int nrpbx = ( dimx + bx - 1 ) / bx;
       int by = ( dimy + nrp - 1 ) / nrp;
       int nrpby = ( dimy + by - 1 ) / by;
       nrp = ( nrpby > nrpbx ? nrpby : nrpbx );
       if ( bx != ( dimx + nrp - 1 ) / nrp )
         NAMD_bug("Error in selecting number of PME processors.");
       if ( by != ( dimy + nrp - 1 ) / nrp )
         NAMD_bug("Error in selecting number of PME processors.");

       // numGridPes = nrpbx;
       // numTransPes = nrpby;
       // numRecipPes = nrp;
       int block2 = (PMEGridSizeY + nrp - 1) / nrp;
       int block2_min = PMEGridSizeY % block2;
       if ( ! block2_min ) block2_min = block2;
       int dim3 = 2 * (PMEGridSizeZ/2 + 1);

       int n[3]; n[0] = PMEGridSizeX; n[1] = PMEGridSizeY; n[2] = PMEGridSizeZ;
       fftw_complex *work = new fftw_complex[n[0]];
       float *grid1 = (float *) fftwf_malloc(sizeof(float) *n[1]*dim3);
       float *grid2 = (float *) fftwf_malloc(sizeof(float) *n[0]*block2*dim3*2);
       iout << iINFO << "Optimizing 6 FFT steps.  1..." << endi;
#ifdef NAMD_FFTW_3
       int fftwFlags = FFTWPatient ? FFTW_PATIENT  : FFTWEstimate ? FFTW_ESTIMATE  : FFTW_MEASURE ;
       int planLineSizes[1];
       planLineSizes[0]=n[2];
       int nx= n[0];
       int ny=block2;
       int sizeLines=nx*ny;
       int zdim = dim3;
       int nz=zdim;
       int xStride=block2 * dim3 / 2;
       fftwf_destroy_plan(
                         fftwf_plan_many_dft_r2c(1, planLineSizes, sizeLines,
                                                 (float *) grid2, NULL, 1, 
                                                 dim3,
                                                 (fftwf_complex *) grid2, 
                                                 NULL, 1,
                                                 dim3/2,
                                                 fftwFlags));

       iout << " 2..." << endi;
       fftwf_destroy_plan(
                         fftwf_plan_many_dft_c2r(1, planLineSizes, sizeLines,
                                                 (fftwf_complex *) grid2,
                                                 NULL, 1, 
                                                 dim3/2,
                                                 (float *) grid2, NULL, 1,
                                                 dim3,
                                                 fftwFlags));
       iout << " 3..." << endi;
       sizeLines=nz;
       planLineSizes[0]=block2;
       fftwf_destroy_plan(fftwf_plan_many_dft(1, planLineSizes, sizeLines, 
                                              (fftwf_complex *) grid2, NULL, 
                                              sizeLines, 1,
                                              (fftwf_complex *) grid2, NULL, 
                                              sizeLines, 1,
                                              FFTW_FORWARD, 
                                              fftwFlags));
       iout << " 4..." << endi;
       fftwf_destroy_plan(fftwf_plan_many_dft(1, planLineSizes, sizeLines, 
                                              (fftwf_complex *) grid2, NULL, 
                                              sizeLines, 1,
                                              (fftwf_complex *) grid2, NULL, 
                                              sizeLines, 1,
                                              FFTW_FORWARD, 
                                              fftwFlags));
       iout << " 5..." << endi;
       sizeLines=ny*nz;
       planLineSizes[0]=n[0];
       fftwf_destroy_plan(fftwf_plan_many_dft(1, planLineSizes, sizeLines,
                                              (fftwf_complex *) grid2, NULL,
                                              sizeLines, 1,
                                              (fftwf_complex *) grid2, NULL, 
                                              sizeLines, 1,
                                              FFTW_FORWARD,
                                              fftwFlags));
       iout << " 6..." << endi;
       fftwf_destroy_plan(fftwf_plan_many_dft(1, planLineSizes, sizeLines,
                                              (fftwf_complex *) grid2, NULL, 
                                              sizeLines, 1,
                                              (fftwf_complex *) grid2, NULL, 
                                              sizeLines, 1,
                                              FFTW_BACKWARD,
                                              fftwFlags));

#else
       rfftwnd_destroy_plan( rfftwnd_create_plan_specific(
         2, n+1, FFTW_REAL_TO_COMPLEX,
         ( FFTWEstimate ? FFTW_ESTIMATE : FFTW_MEASURE )
         | FFTW_IN_PLACE | FFTW_USE_WISDOM, grid1, 1, 0, 0) );
       iout << " 2..." << endi;
       fftw_destroy_plan( fftw_create_plan_specific(n[0], FFTW_REAL_TO_COMPLEX,
         ( FFTWEstimate ? FFTW_ESTIMATE : FFTW_MEASURE )
         | FFTW_IN_PLACE | FFTW_USE_WISDOM, (fftw_complex *) grid2,
         block2*dim3/2, work, 1) );
       iout << " 3..." << endi;
       fftw_destroy_plan( fftw_create_plan_specific(n[0], FFTW_REAL_TO_COMPLEX,
         ( FFTWEstimate ? FFTW_ESTIMATE : FFTW_MEASURE )
         | FFTW_IN_PLACE | FFTW_USE_WISDOM, (fftw_complex *) grid2,
         block2_min*dim3/2, work, 1) );
       iout << " 4..." << endi;
       fftw_destroy_plan( fftw_create_plan_specific(n[0], FFTW_COMPLEX_TO_REAL,
         ( FFTWEstimate ? FFTW_ESTIMATE : FFTW_MEASURE )
         | FFTW_IN_PLACE | FFTW_USE_WISDOM, (fftw_complex *) grid2,
         block2*dim3/2, work, 1) );
       iout << " 5..." << endi;
       fftw_destroy_plan( fftw_create_plan_specific(n[0], FFTW_COMPLEX_TO_REAL,
         ( FFTWEstimate ? FFTW_ESTIMATE : FFTW_MEASURE )
         | FFTW_IN_PLACE | FFTW_USE_WISDOM, (fftw_complex *) grid2,
         block2_min*dim3/2, work, 1) );
       iout << " 6..." << endi;
       rfftwnd_destroy_plan( rfftwnd_create_plan_specific(
         2, n+1, FFTW_COMPLEX_TO_REAL,
         ( FFTWEstimate ? FFTW_ESTIMATE : FFTW_MEASURE )
         | FFTW_IN_PLACE | FFTW_USE_WISDOM, grid1, 1, 0, 0) );
#endif
       iout << "   Done.\n" << endi;
       delete [] work;
       fftwf_free(grid1);
       fftwf_free(grid2);

#ifdef NAMD_FFTW_3 
       FFTWWisdomString = fftwf_export_wisdom_to_string();
#else
       FFTWWisdomString = fftw_export_wisdom_to_string();
#endif

      if ( FFTWWisdomString && (CmiNumPartitions() == 1) ) {
       iout << iINFO << "Writing FFTW data to "
                << FFTWWisdomFile << "\n" << endi;
       wisdom_file = fopen(FFTWWisdomFile,"w");
       if ( wisdom_file ) {
#ifdef NAMD_FFTW_3 
         fftwf_export_wisdom_to_file(wisdom_file);
#else
         fftw_export_wisdom_to_file(wisdom_file);
#endif
         fclose(wisdom_file);
       }
      }
     }
#endif
     iout << endi;
   }

  // LJ-PME
   if (LJPMEOn)
   {
      // Check LJ-PME compatibility with other NAMD features.
      if (switchingActive || vdwForceSwitching) {
        if (LJPMESerialOn) {
          NAMD_die("The serial version of LJ-PME does not support LJ switching functions.");
        } else {
          iout << iWARN << "LJ switching function is not intended for use with LJ-PME\n";
        }
      }
      if (LJcorrection) {
        NAMD_die("Cannot use LJ-PME with LJ tail corrections. Select only one.");
      }
      if (alchOn) {
        NAMD_die("Sorry, alchemical transformation is not supported with LJ-PME.");
      }
      #ifdef OPENATOM_VERSION
      if (openatomOn) {
        NAMD_die("Sorry, open-atom simulation is not supported with LJ-PME.");
      }
      #endif

      #ifdef MEM_OPT_VERSION
        NAMD_die("Sorry, memory-optimized version of NAMD does not support LJ-PME.");
      #endif
      if(LJPMESerialOn && (fullElectFrequency > 1 || nonbondedFrequency > 1 || fullDispersionFrequency > 1)) {
        NAMD_die("The serial version of LJ-PME does not support multiple time stepping.");
      }
      if (fullDispersionFrequency != fullElectFrequency) {
        if ( ! config->find("fullDispersionFrequency") ) {
          iout << iWARN << "Setting fullDispersionFrequency to match fullElectFrequency\n";
          fullDispersionFrequency = fullElectFrequency;
        }
        else {
          NAMD_die("For LJ-PME, fullDispersionFrequency must equal fullElectFrequency.");
        }
      }
  
     iout << iINFO << "LJ PARTICLE MESH EWALD (LJ-PME) ACTIVE\n";
     iout << iINFO << "LJ-PME TOLERANCE               "
                << LJPMETolerance << "\n";
     iout << iINFO << "LJ-PME EWALD COEFFICIENT       "
                << LJPMEEwaldCoefficient << "\n";
     iout << iINFO << "LJ-PME INTERPOLATION ORDER     "
                << LJPMEInterpOrder << "\n";
     iout << iINFO << "LJ-PME GRID DIMENSIONS         "
          << LJPMEGridSizeX << " "
          << LJPMEGridSizeY << " "
          << LJPMEGridSizeZ << "\n";
     iout << iINFO << "LJ-PME MAXIMUM GRID SPACING    "
                << LJPMEGridSpacing << "\n";
     iout << iINFO << "FULL LJ DISPERSION EVALUATION FREQUENCY      "
                << fullDispersionFrequency << "\n";
   }

   if (fullDirectOn)
   {
     iout << iINFO << "DIRECT FULL ELECTROSTATIC CALCULATIONS ACTIVE\n";
     iout << endi;
   }

   // MSM configure
   if (MSMOn)
   {
     // check MSMQuality
     enum { LO=0, MEDLO, MED, MEDHI, HI };

     // MSMApprox
     enum { CUBIC=0, QUINTIC, QUINTIC2,
       SEPTIC, SEPTIC3, NONIC, NONIC4, C1HERMITE, NUM_APPROX };

     // MSMSplit
     enum { TAYLOR2=0, TAYLOR3, TAYLOR4,
       TAYLOR5, TAYLOR6, TAYLOR7, TAYLOR8, NUM_SPLIT };

     if (MSMApprox || MSMSplit) {  // take these definitions
       if (MSMApprox < 0 || MSMApprox >= NUM_APPROX) {
         NAMD_die("MSM: unknown approximation requested (MSMApprox)");
       }
       if (MSMSplit < 0 || MSMSplit >= NUM_SPLIT) {
         NAMD_die("MSM: unknown splitting requested (MSMSplit)");
       }
     }
     else {  // otherwise use MSMQuality to set MSMApprox and MSMSplit
       switch (MSMQuality) {
         case LO:
           MSMApprox = CUBIC;
           MSMSplit = TAYLOR2;
           break;
         case MEDLO:
           MSMApprox = C1HERMITE;
           MSMSplit = TAYLOR3;
           break;
         case MED:
           MSMApprox = QUINTIC;
           MSMSplit = TAYLOR3;
           break;
         case MEDHI:
           MSMApprox = SEPTIC;
           MSMSplit = TAYLOR4;
           break;
         case HI:
           MSMApprox = NONIC;
           MSMSplit = TAYLOR5;
           break;
         default:
           NAMD_die("MSM: unknown quality requested (MSMQuality)");
       }
     }

     iout << iINFO
       << "MULTILEVEL SUMMATION METHOD (MSM) FOR ELECTROSTATICS ACTIVE\n";
     if (MsmSerialOn) {
       iout << iINFO
         << "PERFORMING SERIAL MSM CALCULATION FOR LONG-RANGE PART\n";
     }
     const char *approx_str, *split_str;
     switch (MSMApprox) {
       case CUBIC:    approx_str = "C1 CUBIC";   break;
       case QUINTIC:  approx_str = "C1 QUINTIC"; break;
       case QUINTIC2: approx_str = "C2 QUINTIC"; break;
       case SEPTIC:   approx_str = "C1 SEPTIC";  break;
       case SEPTIC3:  approx_str = "C3 SEPTIC";  break;
       case NONIC:    approx_str = "C1 NONIC";   break;
       case NONIC4:   approx_str = "C4 NONIC";   break;
       case C1HERMITE:approx_str = "C1 HERMITE"; break;
       default:       approx_str = "UNKNOWN";    break;
     }
     switch (MSMSplit) {
       case TAYLOR2:  split_str = "C2 TAYLOR";   break;
       case TAYLOR3:  split_str = "C3 TAYLOR";   break;
       case TAYLOR4:  split_str = "C4 TAYLOR";   break;
       case TAYLOR5:  split_str = "C5 TAYLOR";   break;
       case TAYLOR6:  split_str = "C6 TAYLOR";   break;
       case TAYLOR7:  split_str = "C7 TAYLOR";   break;
       case TAYLOR8:  split_str = "C8 TAYLOR";   break;
       default:       split_str = "UNKNOWN";     break;
     }
     iout << iINFO
       << "MSM WITH " << approx_str << " INTERPOLATION "
       << "AND " << split_str << " SPLITTING\n"
       << endi;

   } // end MSM configure
   if (FMMOn)
   {
#ifdef FMM_SOLVER
     iout << iINFO << "FAST MULTIPOLE METHOD (FMM) FOR ELECTROSTATICS ACTIVE\n";
     iout << iINFO << "PERFORMING SERIAL FMM CALCULATION\n";
     iout << iINFO << "FMM LEVELS = " << FMMLevels << "\n";
     iout << iINFO << "FMM PADDING = " << FMMPadding << " ANGSTROMS\n";
     iout << endi;
#else
     NAMD_die("Must link to FMM library to use FMM\n");
#endif
   }

   if ( FMAOn || PMEOn || MSMOn || fullDirectOn || GBISOn || FMMOn )
   {
     iout << iINFO << "FULL ELECTROSTATIC EVALUATION FREQUENCY      "
        << fullElectFrequency << "\n";
     iout << endi;

     if ( ( computeEnergies % fullElectFrequency ) &&
          ( fullElectFrequency % computeEnergies ) )
        NAMD_die("Either computeEnergies must be a multiple of fullElectFrequency or vice versa.\n");
   }

  if (LJPMEOn) {
    if ( ( outputEnergies % fullDispersionFrequency ) &&
        ( fullDispersionFrequency % outputEnergies ) ) {
      NAMD_die("Either outputEnergies must be a multiple of fullDispersionFrequency or vice versa.\n");
    }
  }

  if (MTSAlgorithm == NAIVE)
  {
    iout << iINFO << "USING NAIVE (CONSTANT FORCE) MTS SCHEME.\n" << endi;
  }
  if (MTSAlgorithm == VERLETI )
  {
    iout << iINFO << "USING VERLET I (r-RESPA) MTS SCHEME.\n" << endi;
  }

   if (longSplitting == SHARP)
  iout << iINFO << "SHARP SPLITTING OF LONG RANGE ELECTROSTATICS\n";
   else if (longSplitting == XPLOR)
  iout << iINFO << "XPLOR SPLITTING OF LONG RANGE ELECTROSTATICS\n";
   else if (longSplitting == C1)
  iout << iINFO << "C1 SPLITTING OF LONG RANGE ELECTROSTATICS\n";
   else if (longSplitting == C2)
  iout << iINFO << "C2 SPLITTING OF LONG RANGE ELECTROSTATICS\n";

   if (splitPatch == SPLIT_PATCH_POSITION)
  iout << iINFO << "PLACING ATOMS IN PATCHES BY POSITION\n";
   else if (splitPatch == SPLIT_PATCH_HYDROGEN)
  iout << iINFO << "PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS\n";

   iout << endi;

   if (mollyOn)
   {
     iout << iINFO << "SLOW FORCE MOLLIFICATION : \n";
     iout << iINFO << "         ERROR TOLERANCE : " << mollyTol << "\n";
     iout << iINFO << "          MAX ITERATIONS : " << mollyIter << "\n";
     iout << endi;
   }

   if (rigidBonds != RIGID_NONE)
   {
     iout << iINFO << "RIGID BONDS TO HYDROGEN : ";
     if (rigidBonds == RIGID_ALL)    iout << "ALL\n";
     if (rigidBonds == RIGID_WATER)  iout << "WATER\n";
     iout << iINFO << "        ERROR TOLERANCE : " << rigidTol << "\n";
     iout << iINFO << "         MAX ITERATIONS : " << rigidIter << "\n";
     if (useSettle) iout << iINFO << "RIGID WATER USING SETTLE ALGORITHM\n";
     iout << endi;
   }
   

   if (nonbondedFrequency != 1)
   {
     iout << iINFO << "NONBONDED FORCES EVALUATED EVERY " << nonbondedFrequency << " STEPS\n";
   }

   iout << iINFO << "RANDOM NUMBER SEED     "
      << randomSeed << "\n";

   iout << endi;

   iout << iINFO << "USE HYDROGEN BONDS?    ";
   if (HydrogenBonds)
   {
  iout << "YES\n" << endi;
  iout << iINFO << "USE ANTECEDENT ATOMS?  ";
  iout << (useAntecedent ? "YES" : "NO");
        iout << "\nHB DIST CUT, ON, OFF   ";
  iout << daCutoffDist << " , " << daOnDist << " , " << daOffDist;
        iout << "\nHB ANGLE CUT, ON, OFF  ";
  iout << dhaCutoffAngle << " , " << dhaOnAngle << " , ";
  iout << dhaOffAngle;
        iout << "\nHB ATT, REP exponents  ";
  iout << distAttExp << " , " << distRepExp;
        iout << "\nHB AA, HA exponents    ";
  iout << aaAngleExp << " , " << haAngleExp;
  iout << "\n" << endi;
   }
   else
   {
  iout << "NO\n" << endi;
   }

// If this is AMBER, then print AMBER options

   if (amberOn)
   { iout << iINFO << "Using AMBER format force field!\n";
     current = config->find("parmfile");
     iout << iINFO << "AMBER PARM FILE        " << current->data << '\n';
     if (opts.defined("coordinates"))
     { current = config->find("coordinates");
       iout << iINFO << "COORDINATE PDB         " << current->data << '\n';
     }
     else
     { current = config->find("ambercoor");
       iout << iINFO << "AMBER COORDINATE FILE  " << current->data << '\n';
     }
     if (readExclusions)
       iout << iINFO << "Exclusions will be read from PARM file!\n";
     else
       iout << iINFO << "Exclusions in PARM file will be ignored!\n";
     iout << iINFO << "SCNB (VDW SCALING)     " << vdwscale14 << "\n" << endi;
   }
   else if(gromacsOn)
   {
     iout << iINFO << "Using GROMACS format force field!\n";

     current = config->find("grotopfile");
     // it should be defined, but, just in case...
     if (current == NULL)
       NAMD_die("no GROMACS topology file defined!?");
     iout << iINFO << "GROMACS TOPO FILE        " << current->data << '\n';

     // XXX handle the two types of coordinates more gracefully
     current = config->find("grocoorfile");
     if (current == NULL) {
       current = config->find("coordinates");
       if (current == NULL) {
         NAMD_die("no coordinate file defined!?");
       }
     }
     iout << iINFO << "GROMACS COOR FILE        " << current->data << '\n' 
          << endi;

   }
   else {
     if ( !usePluginIO ) {
       if ( current = config->find("coordinates") )
       iout << iINFO << "COORDINATE PDB         " << current->data << '\n' << endi;
     }

     current = config->find("structure");

     iout << iINFO << "STRUCTURE FILE         " 
        << current->data << "\n" << endi;

     if (cosAngles) 
     {
       iout << iINFO << "COSANGLES ON. SOME ANGLES WILL BE COSINE-BASED\n" << endi;
     }

     //****** BEGIN CHARMM/XPLOR type changes
     if (paraTypeXplorOn)
     {
       iout << iINFO << "PARAMETER file: XPLOR format! (default) \n" << endi;
     }
     else if (paraTypeCharmmOn)
     {
       iout << iINFO << "PARAMETER file: CHARMM format! \n" << endi;
     }
     //****** END CHARMM/XPLOR type changes

     current = config->find("parameters");

     while (current != NULL)
     {
       iout << iINFO << "PARAMETERS             " 
          << current->data << "\n" << endi;
       current = current->next;
     }
   }

     iout << iINFO << "USING " <<
        ( vdwGeometricSigma ? "GEOMETRIC" : "ARITHMETIC" ) <<
        " MEAN TO COMBINE L-J SIGMA PARAMETERS\n" << endi;

   if (opts.defined("bincoordinates"))
   {
     current = config->find("bincoordinates");

     iout << iINFO << "BINARY COORDINATES     " 
              << current->data << "\n";
   }

#ifdef NAMD_AVXTILES
   iout << iINFO << "MIXED PRECISION AVX-512 TILES OPTIMIZATIONS: ";
   if (useAVXTiles) iout << "ENABLED\n";
   else iout << "DISABLED\n";
#endif

#ifdef MEM_OPT_VERSION
   if (opts.defined("binrefcoords"))
   {
     current = config->find("binrefcoords");

     iout << iINFO << "BINARY REF COORDS      " 
              << current->data << "\n";
   }
#endif

   if (firstTimestep)
   {
  iout << iINFO << "FIRST TIMESTEP         "
     << firstTimestep << "\n" << endi;
   }
}
/*    END OF FUNCTION initialize_config_data    */
   
   
/****************************************************************/
/*                                                              */
/*      FUNCTION parse_mgrid_params                             */
/*                                                              */
/*                                                              */
/****************************************************************/
void SimParameters::parse_mgrid_params(ConfigList *config)
{
  StringList *current;

  mgridforcelist.clear();
  char *key = new char[81];
  char *valstr = new char[256];
  // If the old gridforce commands are still in use, parse them too.
  if (gridforceOn) {
    mgridforceOn = TRUE;
    const char *default_key = MGRIDFORCEPARAMS_DEFAULTKEY;
    MGridforceParams* mgfp = NULL;
    mgfp = mgridforcelist.find_key(default_key);
    if (mgfp != NULL) {
      iout << iINFO << "MGRIDFORCEPOTFILE key " 
        << key << " redefined for file " << valstr << "\n" << endi;
    } else {
      mgfp = mgridforcelist.add(default_key);
    }
    mgfp->gridforceVolts = gridforceVolts;
    mgfp->gridforceScale = gridforceScale;

    parse_mgrid_string_param(config,"gridforcefile",&(mgfp->gridforceFile));
    parse_mgrid_string_param(config,"gridforcecol",&(mgfp->gridforceCol));
    parse_mgrid_string_param(config,"gridforcechargecol",&(mgfp->gridforceQcol));
    parse_mgrid_string_param(config,"gridforcepotfile",&(mgfp->gridforceVfile));
    
    mgfp->gridforceCont[0] = gridforceContA1;
    mgfp->gridforceCont[1] = gridforceContA2;
    mgfp->gridforceCont[2] = gridforceContA3;
    mgfp->gridforceVOffset = gridforceVOffset;
    
    mgfp->gridforceCheckSize = gridforcechecksize;
  }
  
  // Create multigrid parameter structures
  current = config->find("mgridforcepotfile");
  while (current != NULL) {
    int curlen = strlen(current->data);
    //    iout << iINFO << "MGRIDFORCEPOTFILE " << current->data 
    //         << " " << curlen << "\n"  << endi;
    sscanf(current->data,"%80s%255s",key,valstr);
    
    MGridforceParams* mgfp = NULL;
    mgfp = mgridforcelist.find_key(key);
    if ( mgfp != NULL) {
      iout << iINFO << "MGRIDFORCEPOTFILE key " 
        << key << " redefined for file " << valstr << "\n" << endi;
    } else {
      mgfp = mgridforcelist.add(key);
    }
    int fnamelen = strlen(valstr);
    mgfp->gridforceVfile = new char[fnamelen+1];
    strncpy(mgfp->gridforceVfile,valstr,fnamelen+1);
    mgfp->gridforceScale.x = 
      mgfp->gridforceScale.y = 
        mgfp->gridforceScale.z = 1.;
    mgfp->gridforceVOffset.x = 
      mgfp->gridforceVOffset.y = 
        mgfp->gridforceVOffset.z = 0.;
    
    current = current->next;
  }

  current = config->find("mgridforcefile");
  while (current != NULL) {
    int curlen = strlen(current->data);
    //    iout << iINFO << "MGRIDFORCEFILE " << current->data          
    //         << " " << curlen << "\n"  << endi;
    sscanf(current->data,"%80s%255s",key,valstr);
    
    MGridforceParams* mgfp = NULL;
    mgfp = mgridforcelist.find_key(key);
    if ( mgfp == NULL) {
      iout << iINFO << "MGRIDFORCEFILE no key " 
      << key << " defined for file " << valstr << "\n" << endi;
    } else {
      int fnamelen = strlen(valstr);
      if (mgfp->gridforceFile != NULL) {
        delete [] mgfp->gridforceFile;
      }
      mgfp->gridforceFile = new char[fnamelen+1];
      strncpy(mgfp->gridforceFile,valstr,fnamelen+1);
    }

    current = current->next;
  }
  
  current = config->find("mgridforcevolts");
  while (current != NULL) {
    //    iout << iINFO << "MGRIDFORCEVOLTS " << current->data << "\n"  
    //         << endi;
    int curlen = strlen(current->data);
    sscanf(current->data,"%80s%255s",key,valstr);
    
    MGridforceParams* mgfp = NULL;
    mgfp = mgridforcelist.find_key(key);
    if ( mgfp == NULL) {
      iout << iINFO << "MGRIDFORCEVOLTS no key " 
      << key << " defined for file " << valstr << "\n" << endi;
    } else {
      int boolval = MGridforceParamsList::atoBool(valstr);
      if (boolval == -1) {
        iout << iINFO << "MGRIDFORCEVOLTS  key " 
          << key << " boolval " << valstr << " badly defined" << endi;
      } else {
        mgfp->gridforceVolts = (boolval == 1);
      }
    }

    current = current->next;
  }
  
  current = config->find("mgridforcescale");
  while (current != NULL) {
    //    iout << iINFO << "MGRIDFORCESCALE " << current->data 
    //         << "\n"  << endi;
    int curlen = strlen(current->data);
    int nread;
    sscanf(current->data,"%80s%n",key,&nread);
    char *val = current->data + nread + 1;
    
    MGridforceParams* mgfp = NULL;
    mgfp = mgridforcelist.find_key(key);
    if ( mgfp == NULL) {
      iout << iINFO << "MGRIDFORCESCALE no key " 
      << key << " defined for vector " << val << "\n" << endi;
    } else {
      mgfp->gridforceScale.set(val);
    }
    
    current = current->next;
  }
  
  current = config->find("mgridforcevoff");
  while (current != NULL) {
    //    iout << iINFO << "MGRIDFORCEVOFF " << current->data 
    //         << "\n"  << endi;
    int curlen = strlen(current->data);
    int nread;
    sscanf(current->data,"%80s%n",key,&nread);
    char *val = current->data + nread + 1;
    
    MGridforceParams* mgfp = NULL;
    mgfp = mgridforcelist.find_key(key);
    if ( mgfp == NULL) {
      iout << iINFO << "MGRIDFORCEVOFF no key " 
      << key << " defined for vector " << val << "\n" << endi;
    } else {
      mgfp->gridforceVOffset.set(val);
    }
    
    current = current->next;
  }
  
  current = config->find("mgridforcecol");
  while (current != NULL) {
    //    iout << iINFO << "MGRIDFORCECOL " << current->data 
    //         << "\n"  << endi;
    int curlen = strlen(current->data);
    sscanf(current->data,"%80s%255s",key,valstr);
    
    MGridforceParams* mgfp = NULL;
    mgfp = mgridforcelist.find_key(key);
    if ( mgfp == NULL) {
      iout << iINFO << "MGRIDFORCECOL no key " 
      << key << " defined for file " << valstr << "\n" << endi;
    } else {
      int collen = strlen(valstr);
      if (mgfp->gridforceCol != NULL) {
        delete [] mgfp->gridforceCol;
      }
      mgfp->gridforceCol = new char[collen+1];
      strncpy(mgfp->gridforceCol,valstr,collen+1);
     }
    
    current = current->next;
  }
  
  current = config->find("mgridforcechargecol");
  while (current != NULL) {
    //    iout << iINFO << "MGRIDFORCECHARGECOL " << current->data << "\n"  
    //         << endi;
    int curlen = strlen(current->data);
    sscanf(current->data,"%80s%255s",key,valstr);
    
    MGridforceParams* mgfp = NULL;
    mgfp = mgridforcelist.find_key(key);
    if ( mgfp == NULL) {
      iout << iINFO << "MGRIDFORCECHARGECOL no key " 
      << key << " defined for file " << valstr << "\n" << endi;
    } else {
      int collen = strlen(valstr);
      if (mgfp->gridforceQcol != NULL) {
        delete [] mgfp->gridforceQcol;
      }
      mgfp->gridforceQcol = new char[collen+1];
      strncpy(mgfp->gridforceQcol,valstr,collen+1);
    }
    
    current = current->next;
  }
  
  current = config->find("mgridforcecont1");
  while (current != NULL) {
    //    iout << iINFO << "MGRIDFORCECONT1 " << current->data 
    //         << "\n"  << endi;
    int curlen = strlen(current->data);
    sscanf(current->data,"%80s%255s",key,valstr);
    
    MGridforceParams* mgfp = NULL;
    mgfp = mgridforcelist.find_key(key);
    if ( mgfp == NULL) {
      iout << iINFO << "MGRIDFORCECONT1 no key " 
      << key << " defined for file " << valstr << "\n" << endi;
    } else {
      int boolval = MGridforceParamsList::atoBool(valstr);
      if (boolval == -1) {
        iout << iINFO << "MGRIDFORCECONT1  key " 
        << key << " boolval " << valstr << " badly defined" << endi;
      } else {
        mgfp->gridforceCont[0] = (boolval == 1);
      }
    }
    
    current = current->next;
  }
  
  current = config->find("mgridforcecont2");
  while (current != NULL) {
    //    iout << iINFO << "MGRIDFORCECONT2 " << current->data 
    //         << "\n"  << endi;
    int curlen = strlen(current->data);
    sscanf(current->data,"%80s%255s",key,valstr);
    
    MGridforceParams* mgfp = NULL;
    mgfp = mgridforcelist.find_key(key);
    if ( mgfp == NULL) {
      iout << iINFO << "MGRIDFORCECONT2 no key " 
      << key << " defined for file " << valstr << "\n" << endi;
    } else {
      int boolval = MGridforceParamsList::atoBool(valstr);
      if (boolval == -1) {
        iout << iINFO << "MGRIDFORCECONT2  key " 
        << key << " boolval " << valstr << " badly defined" << endi;
      } else {
        mgfp->gridforceCont[1] = (boolval == 1);
      }
    }
    
    current = current->next;
  }
  current = config->find("mgridforcecont3");
  while (current != NULL) {
    //    iout << iINFO << "MGRIDFORCECONT3 " << current->data 
    //         << "\n"  << endi;
    int curlen = strlen(current->data);
    sscanf(current->data,"%80s%255s",key,valstr);
    
    MGridforceParams* mgfp = NULL;
    mgfp = mgridforcelist.find_key(key);
    if ( mgfp == NULL) {
      iout << iINFO << "MGRIDFORCECONT3 no key " 
      << key << " defined for file " << valstr << "\n" << endi;
      NAMD_die("MGRIDFORCE error");
    } else {
      int boolval = MGridforceParamsList::atoBool(valstr);
      if (boolval == -1) {
        iout << iINFO << "MGRIDFORCECONT3  key " 
        << key << " boolval " << valstr << " badly defined" << endi;
      } else {
        mgfp->gridforceCont[2] = (boolval == 1);
      }
    }
    
    current = current->next;
  }
  
  
  current = config->find("mgridforcechecksize");
  while (current != NULL) {
    //    iout << iINFO << "MGRIDFORCELITE " << current->data << "\n"  
    //         << endi;
    int curlen = strlen(current->data);
    sscanf(current->data,"%80s%255s",key,valstr);
    
    MGridforceParams* mgfp = NULL;
    mgfp = mgridforcelist.find_key(key);
    if ( mgfp == NULL) {
      iout << iINFO << "MGRIDFORCECHECKSIZE no key " 
      << key << " defined for file " << valstr << "\n" << endi;
    } else {
      int boolval = MGridforceParamsList::atoBool(valstr);
      if (boolval == -1) {
        iout << iINFO << "MGRIDFORCECHECKSIZE  key " 
          << key << " boolval " << valstr << " badly defined" << endi;
      } else {
        mgfp->gridforceCheckSize = (boolval == 1);
      }
    }

    current = current->next;
  }
  
  delete [] valstr;
  delete [] key;

  // Fill in default values for optional items
  
  MGridforceParams* params = mgridforcelist.get_first();
  
  while (params != NULL) {
    if (params->gridforceFile == NULL) {
      char errmsg[255];
      sprintf(errmsg,"Value undefined for gridforceFile for key %s\n",
              params->gridforceKey);
         NAMD_die(errmsg);
    }
    if (params->gridforceCol == NULL) {
      char errmsg[255];
      sprintf(errmsg,"Value undefined for gridforceCol for key %s\n",
              params->gridforceKey);
         NAMD_die(errmsg);
    }
    params = params->next;
  }
  
}

void SimParameters::parse_mgrid_string_param(ConfigList *cl,
                                             const char *fieldname,
                                             char **dest) 
{
  StringList *vallist = cl->find(fieldname);
  char *val = NULL;
  
  if (vallist != NULL) {
    val = vallist->data;
  } else {
    return;
  }
  
  int len = 0;
  if (val == NULL) {
    *dest = NULL;
  } else {
    len = strlen(val);
    if (len == 0) {
      *dest = NULL;
    } else {
      *dest = new char[len+1];
      strncpy(*dest,val,len+1);
    }
  }
}


void SimParameters::parse_group_restraints_params(ConfigList *config)
{
  StringList *arguments;
  char key[128];
  char strValue[512];
  char err_msg[512];

  if (groupRestraintsOn) {

    arguments = config->find("group1File");
    for ( ; arguments != NULL; arguments = arguments->next) {
      if (sscanf(arguments->data,"%127s%511s", key, strValue) == 2) {
        groupRestraints.SetGroup1AtomFileIndices(key, strValue);
      } else {
        sprintf(err_msg, "For group1File, expected a tag and file name, but recieved: %s\n", arguments->data);
        NAMD_die(err_msg);
      }
    }

    arguments = config->find("group1List");
    for ( ; arguments != NULL; arguments = arguments->next) {
      int nread = 0;
      sscanf(arguments->data,"%127s%n", key, &nread);
      char *val = arguments->data + nread + 1;
      groupRestraints.SetGroup1AtomListIndices(key, val);
    }

    arguments = config->find("group1RefPos");
    for ( ; arguments != NULL; arguments = arguments->next) {
      int nread = 0;
      sscanf(arguments->data,"%127s%n", key, &nread);
      char *val = arguments->data + nread + 1;
      groupRestraints.SetGroup1RefPosition(key, val);
    }

    arguments = config->find("group2File");
    for ( ; arguments != NULL; arguments = arguments->next) {
      if (sscanf(arguments->data,"%127s%511s", key, strValue) == 2) {
        groupRestraints.SetGroup2AtomFileIndices(key, strValue);
      } else {
        sprintf(err_msg, "For group2File, expected a tag and file name, but recieved: %s\n", arguments->data);
        NAMD_die(err_msg);
      }
    }

    arguments = config->find("group2List");
    for ( ; arguments != NULL; arguments = arguments->next) {
      int nread = 0;
      sscanf(arguments->data,"%127s%n", key, &nread);
      char *val = arguments->data + nread + 1;
      groupRestraints.SetGroup2AtomListIndices(key, val);
    }

    arguments = config->find("groupResK");
    for ( ; arguments != NULL; arguments = arguments->next) {
      BigReal kForce = 0.0;
      if (sscanf(arguments->data,"%127s%lf", key, &kForce) == 2) {
        groupRestraints.SetForce(key, kForce);
      } else {
        sprintf(err_msg, "For groupResK, expected a tag and force value, but recieved: %s\n", arguments->data);
        NAMD_die(err_msg);
      }
    }

    arguments = config->find("groupResExp");
    for ( ; arguments != NULL; arguments = arguments->next) {
      int exponent = 0.0;
      if (sscanf(arguments->data,"%127s%d", key, &exponent) == 2) {
        groupRestraints.SetExponent(key, exponent);
      } else {
        sprintf(err_msg, "For groupResExp, expected a tag and exponent but recieved: %s\n", arguments->data);
        NAMD_die(err_msg);
      }
    }

    arguments = config->find("groupResCenter");
    for ( ; arguments != NULL; arguments = arguments->next) {
      int nread = 0;
      sscanf(arguments->data,"%127s%n", key, &nread);
      char *val = arguments->data + nread + 1;
      groupRestraints.SetResCenter(key, val);
    }

    arguments = config->find("groupResX");
    for ( ; arguments != NULL; arguments = arguments->next) {
      if (sscanf(arguments->data,"%127s%511s", key, strValue) == 2) {
        groupRestraints.SetResDirectionX(key, strValue);
      } else {
        sprintf(err_msg, "For groupResX, expected a tag and status (true/false), but recieved: %s\n", arguments->data);
        NAMD_die(err_msg);
      }
    }

    arguments = config->find("groupResY");
    for ( ; arguments != NULL; arguments = arguments->next) {
      if (sscanf(arguments->data,"%127s%511s", key, strValue) == 2) {
        groupRestraints.SetResDirectionY(key, strValue);
      } else {
        sprintf(err_msg, "For groupResY, expected a tag and status (true/false), but recieved: %s\n", arguments->data);
        NAMD_die(err_msg);
      }
    }

    arguments = config->find("groupResZ");
    for ( ; arguments != NULL; arguments = arguments->next) {
      if (sscanf(arguments->data,"%127s%511s", key, strValue) == 2) {
        groupRestraints.SetResDirectionZ(key, strValue);
      } else {
        sprintf(err_msg, "For groupResZ, expected a tag and status (true/false), but recieved: %s\n", arguments->data);
        NAMD_die(err_msg);
      }
    }

    arguments = config->find("groupResUseMagnitude");
    for ( ; arguments != NULL; arguments = arguments->next) {
      if (sscanf(arguments->data,"%127s%511s", key, strValue) == 2) {
        groupRestraints.SetUseDistMagnitude(key, strValue);
      } else {
        sprintf(err_msg, "For groupResUseMagnitude, expected a tag and status (true/false), but recieved: %s\n", arguments->data);
        NAMD_die(err_msg);
      }
    }
    auto grps = groupRestraints.GetGroupResMap();
    groupRestraintsCount = grps.size();
  }
}


//This function is used to create directories when outputing into
//multiple files, i.e. used for Parallel IO. -Chao Mei
void SimParameters::create_output_directories(const char *dirname){
        //output files organization:
        //$outputFilename/$dirname/$outputproc_rank
        
        //Step 1: create $outputFilename if necessary
        int baselen = strlen(outputFilename);
        char *filename = new char[baselen+32];
        memset(filename, 0, baselen+32);
        strcpy(filename, outputFilename);
        if(access(filename, F_OK)!=0) {
                int ret = MKDIR(filename);
                if(ret!=0) {
                        char errmsg[512];
                        sprintf(errmsg, "Error in creating top-level directory %s!", filename);
                        NAMD_die(errmsg);
                }
        }

        //Step 2: create $dirname if necessary
        strcat(filename, PATHSEPSTR);
        strcat(filename, dirname);
        //check if the directory exists or not  
        if(access(filename, F_OK)!=0) {
                int ret = MKDIR(filename);
                if(ret!=0) {
                        char errmsg[512];
                        sprintf(errmsg, "Error in creating middle-level directory %s!", filename);
                        NAMD_die(errmsg);
                }
        }

        //step 3: create $outputproc_rank if necessary
        char tmpstr[256];
        for(int i=0; i<numoutputprocs; i++) {
                memset(tmpstr, 0, 256);
                sprintf(tmpstr, "%s%s%d", filename, PATHSEPSTR, i);
                if(access(tmpstr, F_OK)!=0) {
                        int ret = MKDIR(tmpstr);
                        if(ret!=0) {
                                char errmsg[512];
                                sprintf(errmsg, "Error in creating last-level directory %s!", tmpstr);
                                NAMD_die(errmsg);
                        }
                }
        }
}
   
/****************************************************************/
/*                                                              */
/*      FUNCTION print_mgrid_params                             */
/*                                                              */
/*                                                              */
/****************************************************************/
#define BoolToString(b) ((b) ? "TRUE" : "FALSE")
  
void SimParameters::print_mgrid_params()
{
  const MGridforceParams* params = mgridforcelist.get_first();
  
  while (params != NULL) {
    iout << iINFO << "MGRIDFORCE key " << params->gridforceKey << "\n" << endi;
    iout << iINFO << "           Potfile " << params->gridforceVfile 
      << "\n" << endi;
    iout << iINFO << "           Scale " << params->gridforceScale 
      << "\n" << endi;
    iout << iINFO << "           File " << params->gridforceFile 
      << "\n" << endi;
    iout << iINFO << "           Col " << params->gridforceCol 
      << "\n" << endi;
    
    const char *qcol_msg = "Use atom charge";
    if (params->gridforceQcol != NULL) {
      qcol_msg = params->gridforceQcol;
    }
    iout << iINFO << "           ChargeCol " << qcol_msg
      << "\n" << endi;
    iout << iINFO << "           VOffset " << params->gridforceVOffset 
      << "\n" << endi;
    iout << iINFO << "           Continuous K1 " 
      << BoolToString(params->gridforceCont[0]) 
      << "\n" << endi;
    iout << iINFO << "           Continuous K2 " 
      << BoolToString(params->gridforceCont[1]) 
    << "\n" << endi;
    iout << iINFO << "           Continuous K3 " 
      << BoolToString(params->gridforceCont[2]) 
      << "\n" << endi;
    iout << iINFO << "           Volts " 
      << BoolToString(params->gridforceVolts)
      << "\n" << endi;
    iout << iINFO << "           Gridforce-CheckSize " 
      << BoolToString(params->gridforceCheckSize)
      << "\n" << endi;
    params = params->next;
  }
}
   
   
/****************************************************************/
/*                */
/*    FUNCTION send_SimParameters      */
/*                */
/*  This function is used by the master process to broadcast*/
/*  the parameter data to all the other nodes.  It just builds  */
/*  a message with all the relevant data and broadcasts it to   */
/*  the other nodes.  The routine receive_SimParameters is used */
/*  by all the other nodes to receive this message.    */
/*                */
/****************************************************************/

void SimParameters::send_SimParameters(MOStream *msg)

{
  /*MOStream *msg = com_obj->newOutputStream(ALLBUTME, SIMPARAMSTAG, BUFSIZE);
  if ( msg == NULL )
  {
    NAMD_die("memory allocation failed in SimParameters::send_SimParameters");
  }*/

  msg->put(sizeof(SimParameters),(char*)this);
  if ( FFTWWisdomString ) {
    int fftwlen = strlen(FFTWWisdomString) + 1;
    msg->put(fftwlen);
    msg->put(fftwlen,FFTWWisdomString);
  }
  if ( tclBCScript ) {
    int tcllen = strlen(tclBCScript) + 1;
    msg->put(tcllen);
    msg->put(tcllen,tclBCScript);
  }

#ifdef MEM_OPT_VERSION
  int filelen = strlen(binAtomFile)+1;
  msg->put(filelen);
  msg->put(filelen, binAtomFile);

  filelen = strlen(binCoorFile)+1;
  msg->put(filelen);
  msg->put(filelen, binCoorFile);

  if(binVelFile) {
    filelen = strlen(binVelFile)+1;
    msg->put(filelen);
    msg->put(filelen, binVelFile);
  }

  if(binRefFile) {
    filelen = strlen(binRefFile)+1;
    msg->put(filelen);
    msg->put(filelen, binRefFile);
  }
#endif

  mgridforcelist.pack_data(msg);
  
  msg->end();
}
/*    END OF FUNCITON send_SimParameters    */

/****************************************************************/
/*                */
/*      FUNCTION receive_SimParameters    */
/*                */
/*  This function is used by all the child nodes to   */
/*  receive the simulation parameters from the master node.  */
/*                */
/****************************************************************/

void SimParameters::receive_SimParameters(MIStream *msg)

{
  msg->get(sizeof(SimParameters),(char*)this);
  if ( FFTWWisdomString ) {
    int fftwlen;
    msg->get(fftwlen);
    FFTWWisdomString = new char[fftwlen];
    msg->get(fftwlen,FFTWWisdomString);
#ifdef NAMD_FFTW
#ifdef NAMD_FFTW_3
    fftwf_import_wisdom_from_string(FFTWWisdomString);
#else
    fftw_import_wisdom_from_string(FFTWWisdomString);
#endif
#endif
  }
  if ( tclBCScript ) {
    int tcllen;
    msg->get(tcllen);
    tclBCScript = new char[tcllen];
    msg->get(tcllen,tclBCScript);
  }

#ifdef MEM_OPT_VERSION
  int filelen;
  msg->get(filelen);
  binAtomFile = new char[filelen];
  msg->get(filelen, binAtomFile);
  
  msg->get(filelen);
  binCoorFile = new char[filelen];
  msg->get(filelen, binCoorFile);

  if(binVelFile) {    
    msg->get(filelen);
    binVelFile = new char[filelen];
    msg->get(filelen, binVelFile);
  }

  if(binRefFile) {    
    msg->get(filelen);
    binRefFile = new char[filelen];
    msg->get(filelen, binRefFile);
  }
#endif


  // The simParameters bit copy above put illegal values in the list pointers
  // So this resets everything so that unpacking will work.
  mgridforcelist.clear();
  mgridforcelist.unpack_data(msg);
  
  delete msg;
}
/*      END OF FUNCTION receive_SimParameters  */


//fepb IDWS
BigReal SimParameters::getCurrentLambda2(const int step) const {
  if ( alchLambdaIDWS >= 0. ) {
    const BigReal lambda2 = ( (step / alchIDWSFreq) % 2 == 1 ) ? alchLambda2 : alchLambdaIDWS;
    return lambda2;
  } else {
    return alchLambda2;
  }
}

/* Return true if IDWS is active, else return false. */
int SimParameters::setupIDWS() {
  if (alchLambdaIDWS < 0.) return 0;
  if (alchLambdaIDWS > 1.) {
    NAMD_die("alchLambdaIDWS should be either in the range [0.0, 1.0], or negative (disabled).\n");
  }
 /* 
  * The internal parameter alchIDWSFreq determines the number of steps of MD
  * before each switch of the value of alchLambda2. At most this occurs every
  * time the energy is evaluated and thus the default is the greater of
  * fullElectFrequency and nonbondedFrequency. However, this choice fails to
  * report alternating values if output is printed less often than every step
  * (which is almost certainly true). Thus the frequency is reset to match
  * alchOutFreq or, if that is zero, outputEnergies. Note that, if 
  * alchOutFreq > 0 but != outputEnergies, then the data going to stdout
  * are likely not useful since the comparison value is difficult to infer.
  */
  if ( alchOutFreq % nonbondedFrequency != 0 ) {
    NAMD_die("For IDWS, alchOutFreq must be a multiple of nonBondedFrequency.\n");
  }
  if ( fullElectFrequency > 0 ) {
    if ( alchOutFreq % fullElectFrequency != 0 ) {
      NAMD_die("For IDWS, alchOutFreq must be a multiple of fullElectFrequency.\n");
    }
  }
  if ( alchOutFreq ) {
    alchIDWSFreq = alchOutFreq;
  } else if ( outputEnergies ) {
    alchIDWSFreq = outputEnergies;
  } else {
    NAMD_die("Either alchOutFreq or outputEnergies should be non-zero.\n");
  }
  if ( alchOutFreq && alchOutFreq != outputEnergies) {
    iout << iWARN << "alchOutFreq and outputEnergies do not match. IDWS output"
         << " to stdout may not be useful!\n" << endi;
  }
  return 1;
}
//fepe IDWS

//fepb BKR
BigReal SimParameters::getCurrentLambda(const int step) const {
  /*Get lambda at the current step. 

   If alchLambdaFreq = 0, return alchLambda. For positive values of 
   alchLambdaFreq, apply a linear stepwise schedule from alchLambda to 
   alchLambda2:

   l(t) = l + (l2 - l)*[dn / (N - n0)]*{floor[(n - n0)/dn] + 1}

   n - the current time step
   n0 - step at which switching begins (default = 0)
   N - total steps in the simulation
   dn - alchLambdaFreq (increment frequency, in steps)
   l/l2 - alchLambda/alchLambda2
 
   Note that each step _begins_ by incrementing alchLambda and then integrates
   in time. This means that the first and last switch steps may not behave as
   immediately expected - at step 0, alchLambda is NOT evaluated and at step N
   no step occurs because alchLambda2 has already been reached.
  */
  if ( alchLambdaFreq > 0 && step >= alchEquilSteps ) {
    if ( step == N ) {
      return alchLambda2;
    }
    else {
      const int timeOrigin = firstTimestep + alchEquilSteps;
      const BigReal alchLambdaDelta = getLambdaDelta();
      const BigReal increment = (step - timeOrigin) / BigReal(alchLambdaFreq);
      return alchLambda + alchLambdaDelta*(floor(increment) + 1);
    }
  }
  else {
    return alchLambda;
  }
}

BigReal SimParameters::getLambdaDelta(void) const {
  // Increment by which Lambda changes.
  return ((alchLambda2 - alchLambda)*alchLambdaFreq
          / BigReal(N - firstTimestep - alchEquilSteps));
}

BigReal SimParameters::getElecLambda(const BigReal lambda) const {
  // Convenience function for staggered lambda scaling
  return (lambda <= alchElecLambdaStart ? 0.
          : (lambda - alchElecLambdaStart) / (1. - alchElecLambdaStart));
}

/*
 * Modifications for WCA decomposition of van der Waal interactions.
 *
 * WCA requires that repulsive and attractive components of the vdW 
 * forces be treated separately. To keep the code clean, the same scaling
 * function is always used and simply has its behavior modified. However,
 * the new repluslive scaling only ever gets used when alchWCAOn.
 */
BigReal SimParameters::getVdwLambda(const BigReal lambda) const {
  // Convenience function for staggered lambda scaling
  if ( alchWCAOn ) {
    // Read this with the alias alchRepLambdaEnd --> alchAttLambdaStart.
    // The second condition is needed when attractive interactions are inactive
    // for the whole range, otherwise lambda = 0/1 are incorrect.
    if ( lambda < alchRepLambdaEnd || alchRepLambdaEnd == 1.0 ) {
      return 0.0;
    } else if ( lambda >= alchVdwLambdaEnd ) {
      return 1.0;
    } else {
      return (lambda - alchRepLambdaEnd) / (alchVdwLambdaEnd - alchRepLambdaEnd);
    }
  } else {
    return (lambda >= alchVdwLambdaEnd ? 1. : lambda / alchVdwLambdaEnd);
  }
}

BigReal SimParameters::getRepLambda(const BigReal lambda) const {
  // Convenience function for staggered lambda scaling
  return (lambda >= alchRepLambdaEnd ? 1. : lambda / alchRepLambdaEnd);
}

BigReal SimParameters::getBondLambda(const BigReal lambda) const {
  // Convenience function for staggered lambda scaling
  return (lambda >= alchBondLambdaEnd ? 1. : lambda / alchBondLambdaEnd);
}

size_t SimParameters::alchGetNumOfPMEGrids() const {
  size_t num_max_grids = 1;
  if (!alchOn) return num_max_grids;
  if (alchFepOn && !alchThermIntOn) {
    num_max_grids += 1;
    if (alchDecouple) {
      num_max_grids += 2;
    }
    if (alchElecLambdaStart > 0) {
      num_max_grids += 1;
    }
  }
  if (!alchFepOn && alchThermIntOn) {
    num_max_grids += 2;
    if (alchDecouple) {
      num_max_grids += 2;
    }
  }
  return num_max_grids;
    
}
//fepe