lammps-sys 0.6.0

/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   http://lammps.sandia.gov, Sandia National Laboratories
   Steve Plimpton, sjplimp@sandia.gov

   Copyright (2003) Sandia Corporation.  Under the terms of Contract
   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
   certain rights in this software.  This software is distributed under
   the GNU General Public License.

   See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */

#include "write_coeff.h"
#include <cstring>
#include <cstdlib>
#include <cctype>
#include <unistd.h>
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "comm.h"
#include "force.h"
#include "universe.h"
#include "error.h"
#include "domain.h"
#include "utils.h"

using namespace LAMMPS_NS;

enum {REGULAR_MODE, CLASS2_MODE};

/* ----------------------------------------------------------------------
   called as write_coeff command in input script
------------------------------------------------------------------------- */

void WriteCoeff::command(int narg, char **arg)
{
  if (domain->box_exist == 0)
    error->all(FLERR,"Write_coeff command before simulation box is defined");

  if (narg != 1) error->all(FLERR,"Illegal write_coeff command");

  int n = strlen(arg[0]) + 5;
  char *file = new char[n];

  strcpy(file,"tmp.");
  strcat(file,arg[0]);

  // initialize relevant styles
  force->init();

  if (comm->me == 0) {
    char str[256], coeff[256];
    FILE *one = fopen(file,"wb+");

    if (one == NULL) {
      snprintf(str,256,"Cannot open coeff file %s",file);
      error->one(FLERR,str);
    }

    if (force->pair && force->pair->writedata) {
      fprintf(one,"# pair_style %s\npair_coeff\n",force->pair_style);
      force->pair->write_data_all(one);
      fprintf(one,"end\n");
    }
    if (force->bond && force->bond->writedata) {
      fprintf(one,"# bond_style %s\nbond_coeff\n",force->bond_style);
      force->bond->write_data(one);
      fprintf(one,"end\n");
    }
    if (force->angle && force->angle->writedata) {
      fprintf(one,"# angle_style %s\nangle_coeff\n",force->angle_style);
      force->angle->write_data(one);
      fprintf(one,"end\n");
    }
    if (force->dihedral && force->dihedral->writedata) {
      fprintf(one,"# dihedral_style %s\ndihedral_coeff\n",
              force->dihedral_style);
      force->dihedral->write_data(one);
      fprintf(one,"end\n");
    }
    if (force->improper && force->improper->writedata) {
      fprintf(one,"# improper_style %s\nimproper_coeff\n",
              force->improper_style);
      force->improper->write_data(one);
      fprintf(one,"end\n");
    }
    rewind(one);

    FILE *two = fopen(file+4,"w");
    if (two == NULL) {
      snprintf(str,256,"Cannot open coeff file %s",file+4);
      error->one(FLERR,str);
    }
    fprintf(two,"# LAMMPS coeff file via write_coeff, version %s\n",
            universe->version);

    while(1) {
      int coeff_mode = REGULAR_MODE;
      if (fgets(str,256,one) == NULL) break;

      // some coeffs need special treatment
      if (strstr(str,"class2") != NULL) {
        if (strstr(str,"angle_style") != NULL)
          coeff_mode = CLASS2_MODE;
        else if (strstr(str,"dihedral_style") != NULL)
          coeff_mode = CLASS2_MODE;
        else if (strstr(str,"improper_style") != NULL)
          coeff_mode = CLASS2_MODE;
      }

      const char *section = (const char *)"";
      fputs(str,two);      // style
      utils::sfgets(FLERR,str,256,one,file,error);  // coeff
      n = strlen(str);
      strcpy(coeff,str);
      coeff[n-1] = '\0';
      utils::sfgets(FLERR,str,256,one,file,error);

      while (strcmp(str,"end\n") != 0) {

        if (coeff_mode == REGULAR_MODE) {

          fprintf(two,"%s %s",coeff,str);
          utils::sfgets(FLERR,str,256,one,file,error);

        } else if (coeff_mode == CLASS2_MODE) {

          // class2 angles, dihedrals, and impropers can have
          // multiple sections and thus need special treatment

          if (strcmp(str,"\n") == 0) {

            // all but the the last section end with an empty line.
            // skip it and read and parse the next section title

            utils::sfgets(FLERR,str,256,one,file,error);

            if (strcmp(str,"BondBond Coeffs\n") == 0)
              section = (const char *)"bb";
            else if (strcmp(str,"BondAngle Coeffs\n") ==0)
              section = (const char *)"ba";
            else if (strcmp(str,"MiddleBondTorsion Coeffs\n") == 0)
              section = (const char *)"mbt";
            else if (strcmp(str,"EndBondTorsion Coeffs\n") == 0)
              section = (const char *)"ebt";
            else if (strcmp(str,"AngleTorsion Coeffs\n") == 0)
              section = (const char *)"at";
            else if (strcmp(str,"AngleAngleTorsion Coeffs\n") == 0)
              section = (const char *)"aat";
            else if (strcmp(str,"BondBond13 Coeffs\n") == 0)
              section = (const char *)"bb13";
            else if (strcmp(str,"AngleAngle Coeffs\n") == 0)
              section = (const char *)"aa";

            // gobble up one more empty line
            utils::sfgets(FLERR,str,256,one,file,error);
            utils::sfgets(FLERR,str,256,one,file,error);
          }

          // parse type number and skip over it
          int type = atoi(str);
          char *p = str;
          while ((*p != '\0') && (*p == ' ')) ++p;
          while ((*p != '\0') && isdigit(*p)) ++p;

          fprintf(two,"%s %d %s %s",coeff,type,section,p);
          utils::sfgets(FLERR,str,256,one,file,error);
        }
      }
      fputc('\n',two);
    }
    fclose(one);
    fclose(two);
    unlink(file);
  }

  delete [] file;
}