Merge pull request #186 from akohlmey/small-bugfixes

# Title: charmm correction map

# DATE: 2016-09-26 CONTRIBUTOR: Robert Latour, latourr@clemson.edu  CITATION: TBA

# Title: charmm22/charmm27 dihedral correction map

#  alanine map, type 1

/* ----------------------------------------------------------------------

   Implementation of the CHARMM CMAP; adds an extra energy term for the

   peptide backbone dihedrals.  The tools/ch2lmp.pl conversion script, which

   generates an extra section in the LAMMPS data file, is needed in order to

   generate the info used by this fix style.

   peptide backbone dihedrals.  The tools/ch2lmp/charmm2lammps.pl

   conversion script, which generates an extra section in the LAMMPS data

   file, is needed in order to generate the info used by this fix style.

   Contributing authors:

   Xiaohu Hu, CMB/ORNL (hux2@ornl.gov)

   - MacKerell et al., J. Comput. Chem. 25(2004):1400-1415.

 -------------------------------------------------------------------------*/

#include "mpi.h"

#include "math.h"

#include "stdlib.h"

#include "string.h"

#include "stdio.h"

#include <mpi.h>

#include <math.h>

#include <stdlib.h>

#include <string.h>

#include <stdio.h>

#include "fix_cmap.h"

#include "atom.h"

#include "atom_vec.h"

void FixCMAP::read_grid_map(char *cmapfile)

{

  char line[MAXLINE];

  char *chunk;

  char linebuf[MAXLINE];

  char *chunk,*line;

  int i1, i2, i3, i4, i5, i6, j1, j2, j3, j4, j5, j6, counter;

  FILE *fp = fopen(cmapfile,"r");

  FILE *fp = NULL;

  if (comm->me == 0) {

    fp = force->open_potential(cmapfile);

    if (fp == NULL) {

      char str[128];

      sprintf(str,"Cannot open fix cmap file %s",cmapfile);

      error->one(FLERR,str);

    }

  }

  for (int ix1 = 0; ix1 < 6; ix1++)

    for (int ix2 = 0; ix2 < CMAPDIM; ix2++)

  i1 = i2 = i3 = i4 = i5 = i6 = 0;

  j1 = j2 = j3 = j4 = j5 = j6 = 0;

  while (fgets(line,MAXLINE,fp) != NULL) {

    if (line == "" || line[0] == '#') { ;; }

  int done = 0;

  while (!done) {

    // only read on rank 0 and broadcast to all other ranks

    if (comm->me == 0)

      done = (fgets(linebuf,MAXLINE,fp) == NULL);

    MPI_Bcast(&done,1,MPI_INT,0,world);

    if (done) continue;

    MPI_Bcast(linebuf,MAXLINE,MPI_CHAR,0,world);

    // remove leading whitespace

    line = linebuf;

    while (line && (*line == ' ' || *line == '\t' || *line == '\r')) ++line;

    // skip if empty line or comment

    if (!line || *line =='\n' || *line == '\0' || *line == '#') continue;

    // read in the cmap grid point values

    // NOTE: The order to read the 6 grid maps is HARD-CODED, thus errors

    // 5. Glycine map

    // 6. Glycine before proline map

    else {

    chunk = strtok(line, " \r\n");

    while (chunk != NULL) {

      else break;

    }

  }

  }

  fclose(fp);

  if (comm->me == 0) fclose(fp);

}

/* ---------------------------------------------------------------------- */

      4,-4, 4,-4, 2, 2,-2,-2, 2,-2,-2, 2, 1, 1, 1, 1

    };

  int i, j, k, l, in;

  int i, j, k, in;

  double xx, x[16];

  for (i = 0; i < 4; i++) {

/* ----------------------------------------------------------------------

/* -*- c++ -*- ----------------------------------------------------------

   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator

   http://lammps.sandia.gov, Sandia National Laboratories

   Steve Plimpton, sjplimp@sandia.gov