Output.C File Reference

#include "largefiles.h"
#include <string.h>
#include <stdlib.h>
#include "InfoStream.h"
#include "IMDOutput.h"
#include "Output.h"
#include "dcdlib.h"
#include "strlib.h"
#include "Molecule.h"
#include "Node.h"
#include "Parameters.h"
#include "PDB.h"
#include "SimParameters.h"
#include "Vector.h"
#include "structures.h"
#include "MStream.h"
#include "Communicate.h"
#include "PatchMap.h"
#include "PatchMap.inl"
#include "ScriptTcl.h"
#include "Lattice.h"
#include "DataExchanger.h"
#include <fcntl.h>
#include <sys/stat.h>
#include "PatchData.h"
#include "Debug.h"

Go to the source code of this file.

Macros
#define	PATHSEPSTR   "/"
#define	MKDIR(X)   mkdir(X,0777)
#define	NAMD_open   NAMD_open64
#define	NAMD_write   NAMD_write64
#define	NAMD_close   NAMD_close64
#define	O_LARGEFILE   0x0
#define	MIN_DEBUG_LEVEL   3
#define	seek_dcdfile   NAMD_seek
#define	namdMyNode   Node::Object()
#define	simParams   simParameters
#define	pdbData   pdb
#define	RAD2DEG   180.0/3.14159265359

Functions
int	NAMD_open (const char *fname)
void	NAMD_write (int fd, const char *buf, size_t count, const char *errmsg="NAMD_write64")
void	NAMD_close (int fd, const char *fname)
static void	lattice_to_unitcell (const Lattice *lattice, double *unitcell)
template<class xVector , class xDone >
void	wrap_coor_int (xVector *coor, Lattice &lattice, xDone *done)
template<class xVector , class xDone >
void	wrap_coor_int_dcd_selection (xVector *coor, Lattice &lattice, xDone *done, int index)
void	wrap_coor_dcd_selection (Vector *coor, Lattice &lattice, double *done, int index)
void	wrap_coor_dcd_selection (FloatVector *coor, Lattice &lattice, float *done, int index)
void	wrap_coor (Vector *coor, Lattice &lattice, double *done)
void	wrap_coor (FloatVector *coor, Lattice &lattice, float *done)

Variables
static const short	maxDCD =257

Macro Definition Documentation

MIN_DEBUG_LEVEL

#define MIN_DEBUG_LEVEL   3

Definition at line 58 of file Output.C.

MKDIR

#define MKDIR

(

X

)

mkdir(X,0777)

Definition at line 48 of file Output.C.

NAMD_close

#define NAMD_close   NAMD_close64

Definition at line 53 of file Output.C.

Referenced by ofstream_namd::close().

NAMD_open

#define NAMD_open   NAMD_open64

Definition at line 51 of file Output.C.

NAMD_write

#define NAMD_write   NAMD_write64

Definition at line 52 of file Output.C.

namdMyNode

#define namdMyNode   Node::Object()

Definition at line 130 of file Output.C.

Referenced by Output::recvReplicaDcdData(), and Output::replicaDcdSelectInit().

O_LARGEFILE

#define O_LARGEFILE   0x0

Definition at line 56 of file Output.C.

Referenced by NAMD_open().

PATHSEPSTR

#define PATHSEPSTR   "/"

Definition at line 47 of file Output.C.

pdbData

#define pdbData   pdb

Definition at line 132 of file Output.C.

RAD2DEG

#define RAD2DEG   180.0/3.14159265359

Definition at line 1000 of file Output.C.

seek_dcdfile

#define seek_dcdfile   NAMD_seek

Definition at line 127 of file Output.C.

simParams

#define simParams   simParameters

Definition at line 131 of file Output.C.

Referenced by HomePatch::addForceToMomentum(), HomePatch::addForceToMomentum3(), HomePatch::addVelocityToPosition(), LdbCoordinator::barrier(), HomePatch::boxClosed(), Molecule::build_gridforce_params(), HomePatch::buildRattleList(), HomePatch::buildRattleList_SOA(), ComputePmeMgr::chargeGridSubmitted(), CudaPmeOneDevice::checkPatchLevelLatticeCompatibilityAndComputeOffsets(), ComputeCylindricalBC::ComputeCylindricalBC(), OneFourNbTholeElem::computeForce(), AngleElem::computeForce(), ImproperElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), TholeElem::computeForce(), AnisoElem::computeForce(), ExclElem::computeForce(), BondElem::computeForce(), GromacsPairElem::computeForce(), ComputeFullDirect::ComputeFullDirect(), ComputeLCPO::ComputeLCPO(), ComputeMsm::ComputeMsm(), ComputePme::ComputePme(), ComputeRestraints::ComputeRestraints(), ComputeSphericalBC::ComputeSphericalBC(), ComputeStir::ComputeStir(), ComputeTclBC::ComputeTclBC(), Output::coordinate(), Output::coordinateNeeded(), ComputeMgr::createComputes(), ComputeCUDAMgr::createCudaGlobalMaster(), ComputeCUDAMgr::createCudaPmeOneDevice(), LdbCoordinator::createLoadBalancer(), CudaComputeNonbonded::CudaComputeNonbonded(), HomePatch::depositMigration(), CollectionMaster::disposePositions(), ComputeEField::doForce(), ComputeConsTorque::doForce(), ComputeStir::doForce(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), ComputeGridForce::doForce(), ComputeRestraints::doForce(), HomePatch::doGroupSizeCheck(), HomePatch::doGroupSizeCheck_SOA(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), HomePatch::doPairlistCheck(), ComputeTclBC::doWork(), ComputeGBISser::doWork(), CudaComputeNonbonded::doWork(), dumpbench(), HomePatch::exchangeAtoms(), HomePatch::exchangeCheckpoint(), PmeZPencil::fft_init(), PmeYPencil::fft_init(), PmeXPencil::fft_init(), Output::force(), Output::forceNeeded(), ComputePmeCUDADevice::gatherForce(), HomePatch::gbisComputeAfterP1(), HomePatch::gbisComputeAfterP2(), Molecule::get_fep_bonded_type(), CudaComputeNonbonded::getCurrentReduction(), CudaComputeNonbonded::getDoTable(), ComputeLjPmeSerialMgr::getLJparameters(), CudaComputeNonbonded::getNonbondedCoef(), ComputePmeMgr::gridCalc2(), HomePatch::hardWallDrude(), ComputeCUDAMgr::initialize(), ComputePmeCUDA::initialize(), LjPmeMgr::initialize(), LdbCoordinator::initialize(), GridforceFullMainGrid::initialize(), GridforceFullSubGrid::initialize(), GridforceLiteGrid::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize(), ComputePmeCUDADevice::initialize(), ComputePmeMgr::initialize_computes(), ComputePmeMgr::initialize_pencils(), isPmeProcessor(), CudaComputeNonbonded::launchWork(), HomePatch::loweAndersenVelocities(), WorkDistrib::mapComputes(), ComputePmeCUDADevice::mergeForcesOnPatch(), HomePatch::minimize_rattle2(), Molecule::Molecule(), HomePatch::mollyAverage(), HomePatch::mollyMollify(), NamdHybridLB::NamdHybridLB(), GridforceGrid::new_grid(), Molecule::num_deg_freedom(), Molecule::num_fixed_atoms(), Molecule::num_group_deg_freedom(), Parameters::Parameters(), PatchDataSOA_set_buffer(), PatchDataSOA_set_size(), Compute::patchReady(), Patch::positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), Molecule::print_atoms(), HomePatch::qmSwapAtoms(), HomePatch::rattle1(), HomePatch::rattle1_SOA(), HomePatch::rattle1old(), HomePatch::rattle2(), Parameters::read_ener_table(), Molecule::receive_Molecule(), recursive_bisect_with_curve(), ComputePmeCUDADevice::recvAtoms(), ComputePmeCUDADevice::recvAtomsFromNeighbor(), HomePatch::recvCheckpointLoad(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), ComputeLjPmeSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeMgr::recvCudaGlobalMasterCreateMsg(), ComputeMgr::recvCudaGlobalMasterRemoveMsg(), ComputeMgr::recvCudaGlobalMasterUpdateMsg(), HomePatch::recvExchangeMsg(), GridforceFullMainGrid::reinitialize(), GridforceLiteGrid::reinitialize(), CudaComputeNonbonded::reSortTileLists(), HomePatch::revert(), ScriptTcl::run(), ComputePmeUtil::select(), ComputeNonbondedUtil::select(), Molecule::send_Molecule(), ComputePmeCUDADevice::sendAtomsToNeighbor(), ComputePmeCUDADevice::sendForcesToNeighbors(), HomePatch::setGBISIntrinsicRadii(), ComputeLjPmeSerialMgr::setLJparameters(), PmeAtomStorage::setupAlch(), ComputePmeCUDAMgr::setupPencils(), NamdHybridLB::splitComputes(), ComputePmeCUDADevice::spreadCharge(), NamdCentLB::Strategy(), CollectionMgr::submitPositions(), ExclElem::submitReductionData(), PmePencilXYZ::submitReductions(), PmePencilZ::submitReductions(), ComputePmeMgr::submitReductions(), CollectionMgr::submitVelocities(), ComputePme::ungridForces(), ComputeMgr::updateLocalComputes4(), Output::velocity(), Output::velocityNeeded(), ReductionMgr::willRequire(), ReductionMgr::willSubmit(), wrap_coor_int(), wrap_coor_int_dcd_selection(), and Controller::write_accelMDG_rest_file().

Function Documentation

lattice_to_unitcell()

static void lattice_to_unitcell ( const Lattice *  lattice, double *  unitcell  )

static

Definition at line 134 of file Output.C.

References Lattice::a(), Lattice::a_p(), Lattice::b(), Lattice::b_p(), Lattice::c(), Lattice::c_p(), and Vector::length().

                                                                          {

  unitcell[0] = unitcell[2] = unitcell[5] = 0.0;
  unitcell[1] = unitcell[3] = unitcell[4] = 0.0;

  if (lattice) {
    const Vector &a=lattice->a();
    const Vector &b=lattice->b();
    const Vector &c=lattice->c();
    unitcell[0] = (lattice->a_p()) ? a.length() : 0.0;
    unitcell[2] = (lattice->b_p()) ? b.length() : 0.0;
    unitcell[5] = (lattice->c_p()) ? c.length() : 0.0;
    double cosAB = (lattice->a_p() && lattice->b_p() ) ?
      (a*b)/(unitcell[0]*unitcell[2]) : 0.0;
    double cosAC = (lattice->a_p() && lattice->c_p() ) ?
      (a*c)/(unitcell[0]*unitcell[5]) : 0.0;
    double cosBC = (lattice->b_p() && lattice->c_p() ) ?
      (b*c)/(unitcell[2]*unitcell[5]) : 0.0;
    if (cosAB > 1.0) cosAB = 1.0; else if (cosAB < -1.0) cosAB = -1.0;
    if (cosAC > 1.0) cosAC = 1.0; else if (cosAC < -1.0) cosAC = -1.0;
    if (cosBC > 1.0) cosBC = 1.0; else if (cosBC < -1.0) cosBC = -1.0;
    unitcell[1] = cosAB;
    unitcell[3] = cosAC;
    unitcell[4] = cosBC;
  }
}

NAMD_close()

void NAMD_close	(	int	fd,
		const char *	fname
	)

Definition at line 112 of file Output.C.

References NAMD_err().

                                           {
#ifdef WIN32
  while ( _close(fd) ) {
#else
  while ( close(fd) ) {
#endif
    if ( errno != EINTR ) {
      char errmsg[1024];
      sprintf(errmsg, "Error on closing file %s", fname);
      NAMD_err(errmsg);
    }
  }
}

NAMD_open()

int NAMD_open

(

const char *

fname

)

Definition at line 63 of file Output.C.

References NAMD_err(), and O_LARGEFILE.

                                 {
  int fd;

  //  open the file and die if the open fails
#ifdef WIN32
  while ( (fd = _open(fname, O_WRONLY|O_CREAT|O_EXCL|O_BINARY|O_LARGEFILE,_S_IREAD|_S_IWRITE)) < 0) {
#else
#ifdef NAMD_NO_O_EXCL
  while ( (fd = open(fname, O_WRONLY|O_CREAT|O_TRUNC|O_LARGEFILE,
#else
  while ( (fd = open(fname, O_WRONLY|O_CREAT|O_EXCL|O_LARGEFILE,
#endif
                           S_IRUSR|S_IWUSR|S_IRGRP|S_IROTH)) < 0) {
#endif
    if ( errno != EINTR ) {
      char errmsg[1024];
      sprintf(errmsg, "Unable to open binary file %s", fname);
      NAMD_err(errmsg);
    }
  }

  return fd;
}

NAMD_write()

void NAMD_write	(	int	fd,
		const char *	buf,
		size_t	count,
		const char *	errmsg = "NAMD_write64"
	)

Definition at line 88 of file Output.C.

References endi(), iout, iWARN(), NAMD_bug(), and NAMD_err().

                                                                                          {
  double firsttime = 0.;
  while ( count ) {
#if defined(WIN32) && !defined(__CYGWIN__)
    long retval = _write(fd,buf,count);
#else
    ssize_t retval = write(fd,buf,count);
#endif
    if ( retval < 0 && errno == EINTR ) retval = 0;
    if ( retval < 0 && errno == ENOMEM ) {
      if ( firsttime == 0. ) firsttime = CmiWallTimer();
      if ( (CmiWallTimer() - firsttime) < 300. ) retval = 0;
    }
    if ( retval < 0 ) NAMD_err(errmsg);
    if ( retval > count ) NAMD_bug("extra bytes written in NAMD_write64()");
    buf += retval;
    count -= retval;
  }
  if ( firsttime != 0. ) {
    iout << iWARN << errmsg << ": NAMD_write64() retried for " << (CmiWallTimer() - firsttime) << " seconds.\n" << endi;
  }
}

wrap_coor() [1/2]

void wrap_coor	(	Vector *	coor,
		Lattice &	lattice,
		double *	done
	)

Definition at line 342 of file Output.C.

References wrap_coor_int().

Referenced by Output::coordinate().

                                                             {
  wrap_coor_int(coor,lattice,done);
};

wrap_coor() [2/2]

void wrap_coor	(	FloatVector *	coor,
		Lattice &	lattice,
		float *	done
	)

Definition at line 346 of file Output.C.

References wrap_coor_int().

                                                                 {
  wrap_coor_int(coor,lattice,done);
};

wrap_coor_dcd_selection() [1/2]

void wrap_coor_dcd_selection	(	Vector *	coor,
		Lattice &	lattice,
		double *	done,
		int	index
	)

Definition at line 334 of file Output.C.

References wrap_coor_int_dcd_selection().

Referenced by Output::coordinate().

                                                                                       {
   wrap_coor_int_dcd_selection(coor,lattice,done, index);
};

wrap_coor_dcd_selection() [2/2]

void wrap_coor_dcd_selection	(	FloatVector *	coor,
		Lattice &	lattice,
		float *	done,
		int	index
	)

Definition at line 338 of file Output.C.

References wrap_coor_int_dcd_selection().

                                                                                           {
   wrap_coor_int_dcd_selection(coor,lattice,done, index);
};

wrap_coor_int()

template<class xVector , class xDone >

void wrap_coor_int	(	xVector *	coor,
		Lattice &	lattice,
		xDone *	done
	)

Definition at line 259 of file Output.C.

References Molecule::get_cluster(), Molecule::get_clusterSize(), Molecule::is_water(), Node::molecule, Molecule::numAtoms, Node::Object(), Node::simParameters, simParams, Lattice::wrap_delta(), and Lattice::wrap_nearest_delta().

Referenced by wrap_coor().

                                                                 {
  SimParameters *simParams = Node::Object()->simParameters;
  if ( *done ) return;
  *done = 1;
  if ( ! ( simParams->wrapAll || simParams->wrapWater ) ) return;
  const int wrapNearest = simParams->wrapNearest;
  const int wrapAll = simParams->wrapAll;
  Molecule *molecule = Node::Object()->molecule;
  int n = molecule->numAtoms;
  int i;
#ifndef MEM_OPT_VERSION
  Position *con = new Position[n];
  for ( i = 0; i < n; ++i ) {
    con[i] = 0;
    int ci = molecule->get_cluster(i);
    con[ci] += coor[i];
  }
  for ( i = 0; i < n; ++i ) {
    if ( ! wrapAll && ! molecule->is_water(i) ) continue;
    int ci = molecule->get_cluster(i);
    if ( ci == i ) {
      Vector coni = con[i] / molecule->get_clusterSize(i);
      Vector trans = ( wrapNearest ?
        lattice.wrap_nearest_delta(coni) : lattice.wrap_delta(coni) );
      con[i] = trans;
    }
    coor[i] = coor[i] + con[ci];
  }
  delete [] con;
#endif
}

wrap_coor_int_dcd_selection()

template<class xVector , class xDone >

void wrap_coor_int_dcd_selection	(	xVector *	coor,
		Lattice &	lattice,
		xDone *	done,
		int	index
	)

Definition at line 293 of file Output.C.

References Molecule::get_atom_index_from_dcd_selection(), Molecule::get_cluster(), Molecule::get_clusterSize(), Molecule::get_dcd_selection_index_from_atom_id(), Molecule::get_dcd_selection_size(), Molecule::is_water(), Node::molecule, Node::Object(), Node::simParameters, simParams, Lattice::wrap_delta(), and Lattice::wrap_nearest_delta().

Referenced by wrap_coor_dcd_selection().

                                                                                            {
  SimParameters *simParams = Node::Object()->simParameters;
  if ( *done ) return;
  *done = 1;
  if ( ! ( simParams->wrapAll || simParams->wrapWater ) ) return;
  const int wrapNearest = simParams->wrapNearest;
  const int wrapAll = simParams->wrapAll;
  Molecule *molecule = Node::Object()->molecule;
  const int n = molecule->get_dcd_selection_size(index);
  int i;
#ifndef MEM_OPT_VERSION
  Position *con = new Position[n];
  for ( i = 0; i < n; ++i ) {
    int molIndex = molecule->get_atom_index_from_dcd_selection(index, i);
    con[i] = 0;
    int ci = molecule->get_cluster(molIndex);
    int dcdci = molecule->get_dcd_selection_index_from_atom_id(index, ci);
    // the cluster index might not be in the selection
    if(dcdci>=0)
      con[dcdci] += coor[i];
  }
  for ( i = 0; i < n; ++i ) {
    int molIndex = molecule->get_atom_index_from_dcd_selection(index, i);
    if ( ! wrapAll && ! molecule->is_water(molIndex) ) continue;
    int ci = molecule->get_cluster(molIndex);
    int dcdci = molecule->get_dcd_selection_index_from_atom_id(index, ci);
    if ( ci == molIndex ) {
      Vector coni = con[i] / molecule->get_clusterSize(molIndex);
      Vector trans = ( wrapNearest ?
        lattice.wrap_nearest_delta(coni) : lattice.wrap_delta(coni) );
      con[i] = trans;
    }
    if(dcdci>0)
      coor[i] = coor[i] + con[dcdci];
    else
      coor[i] = coor[i];
  }
  delete [] con;
#endif
}

Variable Documentation

maxDCD

const short maxDCD =257

static

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 42 of file Output.C.