Parameters.C File Reference

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <vector>
#include <strings.h>
#include "InfoStream.h"
#include <charm++.h>
#include "Parameters.h"
#include "Communicate.h"
#include "ConfigList.h"
#include "SimParameters.h"
#include "Debug.h"

Go to the source code of this file.

Classes
struct	bond_params
struct	angle_params
struct	dihedral_params
struct	improper_params
struct	crossterm_params
struct	vdw_params
struct	vdw_pair_params
struct	table_pair_params
struct	nbthole_pair_params

Macros
#define	MIN_DEBUG_LEVEL   3
#define	INDEX(ncols, i, j)   ((i)*ncols + (j))
#define	ENABLETABLES

Functions
void	crossterm_setup (CrosstermData *)

Variables
static char **	table_types

Macro Definition Documentation

ENABLETABLES

#define ENABLETABLES

Definition at line 37 of file Parameters.C.

INDEX

#define INDEX	(		ncols,
			i,
			j
	)		((i)*ncols + (j))

Definition at line 35 of file Parameters.C.

Referenced by Parameters::read_energy_type_bothcubspline(), and Parameters::read_energy_type_cubspline().

MIN_DEBUG_LEVEL

#define MIN_DEBUG_LEVEL   3

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

Definition at line 31 of file Parameters.C.

Function Documentation

crossterm_setup()

void crossterm_setup

(

CrosstermData *

)

Definition at line 589 of file ComputeCrossterms.C.

References CMAP_SETUP_DIM, CMAP_SPACING, CMAP_TABLE_DIM, CrosstermData::d00, CrosstermData::d01, CrosstermData::d10, CrosstermData::d11, forward_back_sub(), INDEX, lu_decomp_nopivot(), and PI.

Referenced by Parameters::read_parm().

{
  enum { D = CMAP_TABLE_DIM };
  enum { N = CMAP_SETUP_DIM };
  const double h_1 = 1.0 / ( CMAP_SPACING * PI / 180.0) ;
  const double h_2 = h_1 * h_1;
  const double tr_h = 3.0 * h_1;
  int i, j;
  int ij;
  int ijp1p1, ijm1m1, ijp1m1, ijm1p1;
  int ijp2p2, ijm2m2, ijp2m2, ijm2p2;

  /* allocate spline coefficient matrix */
  double* const m = new double[N*N];
  memset(m,0,N*N*sizeof(double));

  /* initialize spline coefficient matrix */
  m[0] = 4;
  for (i = 1;  i < N;  i++) {
    m[INDEX(N,i-1,i)] = 1;
    m[INDEX(N,i,i-1)] = 1;
    m[INDEX(N,i,i)] = 4;
  }
  /* periodic boundary conditions for spline */
  m[INDEX(N,0,N-1)] = 1;
  m[INDEX(N,N-1,0)] = 1;

  /* compute LU-decomposition for this matrix */
  lu_decomp_nopivot(m, N);

  /* allocate vector for solving spline derivatives */
  double* const v = new double[N];
  memset(v,0,N*sizeof(double));

    /* march through rows of table */
    for (i = 0;  i < N;  i++) {

      /* setup RHS vector for solving spline derivatives */
      v[0] = tr_h * (table[INDEX(D,i,1)].d00 - table[INDEX(D,i,N-1)].d00);
      for (j = 1;  j < N;  j++) {
        v[j] = tr_h * (table[INDEX(D,i,j+1)].d00 - table[INDEX(D,i,j-1)].d00);
      }

      /* solve system, returned into vector */
      forward_back_sub(v, m, N);

      /* store values as derivatives wrt differenced table values */
      for (j = 0;  j < N;  j++) {
        table[INDEX(D,i,j)].d01 = v[j];
      }
      table[INDEX(D,i,N)].d01 = v[0];
    }
    for (j = 0;  j <= N;  j++) {
      table[INDEX(D,N,j)].d01 = table[INDEX(D,0,j)].d01;
    }

    /* march through columns of table */
    for (j = 0;  j < N;  j++) {

      /* setup RHS vector for solving spline derivatives */
      v[0] = tr_h * (table[INDEX(D,1,j)].d00 - table[INDEX(D,N-1,j)].d00);
      for (i = 1;  i < N;  i++) {
        v[i] = tr_h * (table[INDEX(D,i+1,j)].d00 - table[INDEX(D,i-1,j)].d00);
      }

      /* solve system, returned into vector */
      forward_back_sub(v, m, N);

      /* store values as derivatives wrt differenced table values */
      for (i = 0;  i < N;  i++) {
        table[INDEX(D,i,j)].d10 = v[i];
      }
      table[INDEX(D,N,j)].d10 = v[0];
    }
    for (i = 0;  i <= N;  i++) {
      table[INDEX(D,i,N)].d10 = table[INDEX(D,i,0)].d10;
    }

    /* march back through rows of table
     *
     * This is CHARMM's approach for calculating mixed partial derivatives,
     * by splining the first derivative values.
     *
     * Here we spline the dx values along y to calculate dxdy derivatives.
     *
     * Test cases show error with CHARMM is within 1e-5 roundoff error.
     */
    for (i = 0;  i < N;  i++) {

      /* setup RHS vector for solving dxy derivatives from dx */
      v[0] = tr_h * (table[INDEX(D,i,1)].d10 - table[INDEX(D,i,N-1)].d10);
      for (j = 1;  j < N;  j++) {
        v[j] = tr_h * (table[INDEX(D,i,j+1)].d10 - table[INDEX(D,i,j-1)].d10);
      }

      /* solve system, returned into vector */
      forward_back_sub(v, m, N);

      /* store values as dxy derivatives wrt differenced table values */
      for (j = 0;  j < N;  j++) {
        table[INDEX(D,i,j)].d11 = v[j];
      }
      table[INDEX(D,i,N)].d11 = v[0];
    }
    for (j = 0;  j <= N;  j++) {
      table[INDEX(D,N,j)].d11 = table[INDEX(D,0,j)].d11;
    }

  /* done with temp storage */
  delete [] m;
  delete [] v;

}

Variable Documentation

table_types

char** table_types

static

Definition at line 39 of file Parameters.C.

Referenced by Parameters::get_int_table_type(), and Parameters::read_ener_table().