lammps/src/dump_cfg.cpp

/* ----------------------------------------------------------------------
   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.
------------------------------------------------------------------------- */

/* ----------------------------------------------------------------------
   Contributing author: Liang Wan (Chinese Academy of Sciences)
------------------------------------------------------------------------- */

#include "math.h" 
#include "stdlib.h"
#include "string.h"
#include "dump_cfg.h"
#include "atom.h"
#include "domain.h"
#include "comm.h"
#include "modify.h"
#include "compute.h"
#include "input.h"
#include "fix.h"
#include "variable.h"
#include "memory.h"
#include "error.h"

#define UNWRAPEXPAND 10.0

using namespace LAMMPS_NS;

enum{INT,DOUBLE};  // same as in dump_custom.cpp

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

DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
  DumpCustom(lmp, narg, arg)
{
  if (narg < 10 ||
      strcmp(arg[5],"id") != 0 || strcmp(arg[6],"type") != 0 ||
      (strcmp(arg[7],"xs") != 0 && strcmp(arg[7],"xsu") != 0) || 
      (strcmp(arg[8],"ys") != 0 && strcmp(arg[8],"ysu") != 0) ||
      (strcmp(arg[9],"zs") != 0 && strcmp(arg[9],"zsu") != 0)
      )
    error->all("Dump cfg arguments must start with 'id type xs ys zs' or 'id type xsu ysu zsu'");

  if (strcmp(arg[7],"xs") == 0)
    if (strcmp(arg[8],"ysu") == 0 || strcmp(arg[9],"zsu") == 0)
      error->all("Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
    else unwrapflag = 0;
  else if (strcmp(arg[8],"ys") == 0 || strcmp(arg[9],"zs") == 0)
    error->all("Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
  else unwrapflag = 1;
    
  ntypes = atom->ntypes;
  typenames = NULL;

  // arrays for data rearrangement

  rbuf = NULL;
  nchosen = nlines = 0;

  // setup auxiliary property name strings
  // convert 'X_ID[m]' (X=c,f,v) to 'ID_m'

  if (narg > 10) auxname = new char*[narg-10];
  else auxname = NULL;

  int i = 0;
  for (int iarg = 10; iarg < narg; iarg++, i++) {
    if (strncmp(arg[iarg],"c_",2) == 0 ||
	strncmp(arg[iarg],"f_",2) == 0 ||
	strncmp(arg[iarg],"v_",2) == 0) {
      int n = strlen(arg[iarg]);
      char *suffix = new char[n];
      strcpy(suffix,&arg[iarg][2]);

      char *ptr = strchr(suffix,'[');
      if (ptr) {
	if (suffix[strlen(suffix)-1] != ']')
	  error->all("Invalid keyword in dump cfg command");
	*ptr = '\0';
	*(ptr+2) = '\0';
	auxname[i] = new char[strlen(suffix) + 3];
	strcpy(auxname[i],suffix);
	strcat(auxname[i],"_");
	strcat(auxname[i],ptr+1);
      } else {
	auxname[i] = new char[strlen(suffix) + 1];
	strcpy(auxname[i],suffix);
      }

      delete [] suffix;

    } else {
      auxname[i] = new char[strlen(arg[iarg]) + 1];
      strcpy(auxname[i],arg[iarg]);
    }
  }
}

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

DumpCFG::~DumpCFG()
{
  if (typenames) {
    for (int i = 1; i <= ntypes; i++) delete [] typenames[i];
    delete [] typenames;
  }

  if (rbuf) memory->destroy(rbuf);

  if (auxname) {
    for (int i = 0; i < nfield-5; i++) delete [] auxname[i];
    delete [] auxname;
  }
}

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

void DumpCFG::init_style()
{
  if (multifile == 0) error->all("Dump cfg requires one snapshot per file");

  if (typenames == NULL) {
    typenames = new char*[ntypes+1];
    for (int itype = 1; itype <= ntypes; itype++) {
      typenames[itype] = new char[3];
      strcpy(typenames[itype],"C");
    }
    if (comm->me == 0)
      error->warning("All element names have been set to 'C' for dump cfg");
  }

  // setup format strings

  delete [] format;
  char *str;
  if (format_user) str = format_user;
  else str = format_default;

  int n = strlen(str) + 1;
  format = new char[n];
  strcpy(format,str);

  // tokenize the format string and add space at end of each format element

  char *ptr;
  for (int i = 0; i < size_one; i++) {
    if (i == 0) ptr = strtok(format," \0");
    else ptr = strtok(NULL," \0");
    delete [] vformat[i];
    vformat[i] = new char[strlen(ptr) + 2];
    strcpy(vformat[i],ptr);
    vformat[i] = strcat(vformat[i]," ");
  }

  // find current ptr for each compute,fix,variable
  // check that fix frequency is acceptable

  int icompute;
  for (int i = 0; i < ncompute; i++) {
    icompute = modify->find_compute(id_compute[i]);
    if (icompute < 0) error->all("Could not find dump cfg compute ID");
    compute[i] = modify->compute[icompute];
  }

  int ifix;
  for (int i = 0; i < nfix; i++) {
    ifix = modify->find_fix(id_fix[i]);
    if (ifix < 0) error->all("Could not find dump cfg fix ID");
    fix[i] = modify->fix[ifix];
    if (nevery % modify->fix[ifix]->peratom_freq)
      error->all("Dump cfg and fix not computed at compatible times");
  }

  int ivariable;
  for (int i = 0; i < nvariable; i++) {
    ivariable = input->variable->find(id_variable[i]);
    if (ivariable < 0) error->all("Could not find dump cfg variable name");
    variable[i] = ivariable;
  }

  // set index and check validity of region

  if (iregion >= 0) {
    iregion = domain->find_region(idregion);
    if (iregion == -1) error->all("Region ID for dump cfg does not exist");
  }
}

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

void DumpCFG::write_header(bigint n)
{
  // special handling for atom style peri
  // use average volume of particles to scale particles to mimic C atoms
  // scale box dimension to sc lattice for C with sigma = 1.44 Angstroms  

  // Special handling for unwrapped coordinates

  double scale;
  if (atom->peri_flag) {
    int nlocal = atom->nlocal;
    double vone = 0.0;
    for (int i = 0; i < nlocal; i++) vone += atom->vfrac[i];
    double vave;
    MPI_Allreduce(&vone,&vave,1,MPI_DOUBLE,MPI_SUM,world); 
    if (atom->natoms) vave /= atom->natoms; 
    if (vave > 0.0) scale = 1.44 / pow(vave,1.0/3.0); 
  } else if (unwrapflag == 1) scale = UNWRAPEXPAND;
  else scale = 1.0;
    
  if (me == 0 || multiproc) {
    char str[64];
    sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT);
    fprintf(fp,str,n);
    fprintf(fp,"A = %g Angstrom (basic length-scale)\n",scale);
    fprintf(fp,"H0(1,1) = %g A\n",domain->xprd);
    fprintf(fp,"H0(1,2) = 0 A \n");
    fprintf(fp,"H0(1,3) = 0 A \n");
    fprintf(fp,"H0(2,1) = %g A \n",domain->xy);
    fprintf(fp,"H0(2,2) = %g A\n",domain->yprd);
    fprintf(fp,"H0(2,3) = 0 A \n");
    fprintf(fp,"H0(3,1) = %g A \n",domain->xz);
    fprintf(fp,"H0(3,2) = %g A \n",domain->yz);
    fprintf(fp,"H0(3,3) = %g A\n",domain->zprd);
    fprintf(fp,".NO_VELOCITY.\n");
    fprintf(fp,"entry_count = %d\n",nfield-2);
    for (int i = 0; i < nfield-5; i++)
      fprintf(fp,"auxiliary[%d] = %s\n",i,auxname[i]);
  }

  // calculate total # of data lines to be written on a writing proc

  if (multiproc) nchosen = nmine;
  else MPI_Reduce(&nmine,&nchosen,1,MPI_INT,MPI_SUM,0,world);

  // allocate memory needed for data rearrangement on writing proc(s)

  if (multiproc || me == 0) {
    if (rbuf) memory->destroy(rbuf);
    memory->create(rbuf,nchosen,size_one,"dump:rbuf");
  }
}

/* ----------------------------------------------------------------------
   write data lines to file in a block-by-block style
   write head of block (mass & element name) only if has atoms of the type
------------------------------------------------------------------------- */

void DumpCFG::write_data(int n, double *mybuf)
{
  int i,j,m,itype;
  int tag_i,index;

  double *rmass = atom->rmass;
  double *mass = atom->mass;
  int *type = atom->type;
  int nlocal = atom->nlocal;

  // transfer data from buf to rbuf
  // if write by proc 0, transfer chunk by chunk

  for (i = 0, m = 0; i < n; i++) {
    for (j = 0; j < size_one; j++)
      rbuf[nlines][j] = mybuf[m++];
    nlines++;
  }

  //  write data lines in rbuf to file after transfer is done
  
  double unwrap_coord;

  if (nlines == nchosen) {
    for (itype = 1; itype <= ntypes; itype++) {
      for (i = 0; i < nchosen; i++)
	if (rbuf[i][1] == itype) break;
      if (i < nchosen) {
	if (rmass) fprintf(fp,"%g\n",rmass[i]);
	else fprintf(fp,"%g\n",mass[itype]);
	fprintf(fp,"%s\n",typenames[itype]);
	for (; i < nchosen; i++) {
	  if (rbuf[i][1] == itype) {
	    if (unwrapflag == 0)
	      for (j = 2; j < size_one; j++) {
		if (vtype[j] == INT)
		  fprintf(fp,vformat[j],static_cast<int> (rbuf[i][j]));
		else fprintf(fp,vformat[j],rbuf[i][j]);
	      }
	    else

	      // Unwrapped scaled coordinates are shifted to
	      // center of expanded box, to prevent
	      // rewrapping by AtomEye. Dividing by 
	      // expansion factor restores correct
	      // interatomic distances.

	      for (j = 2; j < 5; j++) {
		unwrap_coord = (rbuf[i][j] - 0.5)/UNWRAPEXPAND + 0.5;
		fprintf(fp,vformat[j],unwrap_coord);
	      }
	      for (j = 5; j < size_one; j++) {
		if (vtype[j] == INT)
		  fprintf(fp,vformat[j],static_cast<int> (rbuf[i][j]));
		else fprintf(fp,vformat[j],rbuf[i][j]);
	      }

	    fprintf(fp,"\n");
	  }
	}
      }
    }
    nlines = 0;
  }
}

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

int DumpCFG::modify_param2(int narg, char **arg)
{
  if (strcmp(arg[0],"element") == 0) {
    if (narg != ntypes+1)
      error->all("Dump modify element names do not match atom types");

    if (typenames) {
      for (int i = 1; i <= ntypes; i++) delete [] typenames[i];
      delete [] typenames;
      typenames = NULL;
    }

    typenames = new char*[ntypes+1];
    for (int itype = 1; itype <= ntypes; itype++) {
      typenames[itype] = new char[3];
      if (strlen(arg[itype]) >= 3)
	error->all("Illegal chemical element names");
      strcpy(typenames[itype],arg[itype]);
    }
    return ntypes+1;

  } else return 0;
}