/* ----------------------------------------------------------------------
   LIGGGHTS - LAMMPS Improved for General Granular and Granular Heat
   Transfer Simulations

   LIGGGHTS is part of the CFDEMproject
   www.liggghts.com | www.cfdem.com

   This file was modified with respect to the release in LAMMPS
   Modifications are Copyright 2009-2012 JKU Linz
                     Copyright 2012-     DCS Computing GmbH, Linz

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

#include "mpi.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "ctype.h"
#include "unistd.h"
#include "sys/stat.h"
#include "input.h"
#include "style_command.h"
#include "universe.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "group.h"
#include "domain.h"
#include "output.h"
#include "thermo.h"
#include "force.h"
#include "pair.h"
#include "min.h"
#include "modify.h"
#include "compute.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "update.h"
#include "neighbor.h"
#include "special.h"
#include "variable.h"
#include "accelerator_cuda.h"
#include "error.h"
#include "memory.h"

#ifdef _OPENMP
#include "omp.h"
#endif

using namespace LAMMPS_NS;

#define DELTALINE 256
#define DELTA 4

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

Input::Input(LAMMPS *lmp, int argc, char **argv) : Pointers(lmp)
{
  MPI_Comm_rank(world,&me);

  maxline = maxcopy = maxwork = 0;
  line = copy = work = NULL;
  narg = maxarg = 0;
  arg = NULL;

  echo_screen = 0;
  echo_log = 1;

  label_active = 0;
  labelstr = NULL;
  jump_skip = 0;
  ifthenelse_flag = 0;

  if (me == 0) {
    nfile = maxfile = 1;
    infiles = (FILE **) memory->smalloc(sizeof(FILE *),"input:infiles");
    infiles[0] = infile;
  } else infiles = NULL;

  variable = new Variable(lmp);

  // fill map with commands listed in style_command.h

  command_map = new std::map<std::string,CommandCreator>();

#define COMMAND_CLASS
#define CommandStyle(key,Class) \
  (*command_map)[#key] = &command_creator<Class>;
#include "style_command.h"
#undef CommandStyle
#undef COMMAND_CLASS

  // process command-line args
  // check for args "-var" and "-echo"
  // caller has already checked that sufficient arguments exist

  int iarg = 0;
  while (iarg < argc) {
    if (strcmp(argv[iarg],"-var") == 0 || strcmp(argv[iarg],"-v") == 0) {
      int jarg = iarg+3;
      while (jarg < argc && argv[jarg][0] != '-') jarg++;
      variable->set(argv[iarg+1],jarg-iarg-2,&argv[iarg+2]);
      iarg = jarg;
    } else if (strcmp(argv[iarg],"-echo") == 0 ||
               strcmp(argv[iarg],"-e") == 0) {
      narg = 1;
      char **tmp = arg;        // trick echo() into using argv instead of arg
      arg = &argv[iarg+1];
      echo();
      arg = tmp;
      iarg += 2;
    } else iarg++;
  }
}

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

Input::~Input()
{
  // don't free command and arg strings
  // they just point to other allocated memory

  memory->sfree(line);
  memory->sfree(copy);
  memory->sfree(work);
  if (labelstr) delete [] labelstr;
  memory->sfree(arg);
  memory->sfree(infiles);
  delete variable;

  delete command_map;
}

/* ----------------------------------------------------------------------
   process all input from infile
   infile = stdin or file if command-line arg "-in" was used
------------------------------------------------------------------------- */

void Input::file()
{
  int m,n;

  while (1) {

    // read a line from input script
    // n = length of line including str terminator, 0 if end of file
    // if line ends in continuation char '&', concatenate next line

    if (me == 0) {
      m = 0;
      while (1) {
        if (maxline-m < 2) reallocate(line,maxline,0);
        if (fgets(&line[m],maxline-m,infile) == NULL) {
          if (m) n = strlen(line) + 1;
          else n = 0;
          break;
        }
        m = strlen(line);
        if (line[m-1] != '\n') continue;

        m--;
        while (m >= 0 && isspace(line[m])) m--;
        if (m < 0 || line[m] != '&') {
          line[m+1] = '\0';
          n = m+2;
          break;
        }
      }
    }

    // bcast the line
    // if n = 0, end-of-file
    // error if label_active is set, since label wasn't encountered
    // if original input file, code is done
    // else go back to previous input file

    MPI_Bcast(&n,1,MPI_INT,0,world);
    if (n == 0) {
      if (label_active) error->all(FLERR,"Label wasn't found in input script");
      if (me == 0) {
        if (infile != stdin) fclose(infile);
        nfile--;
      }
      MPI_Bcast(&nfile,1,MPI_INT,0,world);
      if (nfile == 0) break;
      if (me == 0) infile = infiles[nfile-1];
      continue;
    }

    if (n > maxline) reallocate(line,maxline,n);
    MPI_Bcast(line,n,MPI_CHAR,0,world);

    // echo the command unless scanning for label

    if (me == 0 && label_active == 0) {
      if (echo_screen && screen) fprintf(screen,"%s\n",line);
      if (echo_log && logfile) fprintf(logfile,"%s\n",line);
    }

    // parse the line
    // if no command, skip to next line in input script

    parse();
    if (command == NULL) continue;

    // if scanning for label, skip command unless it's a label command

    if (label_active && strcmp(command,"label") != 0) continue;

    // execute the command

    if (execute_command()) {
      char *str = new char[maxline+32];
      sprintf(str,"Unknown command: %s",line);
      error->all(FLERR,str);
    }
  }
}

/* ----------------------------------------------------------------------
   process all input from filename
   called from library interface
------------------------------------------------------------------------- */

void Input::file(const char *filename)
{
  // error if another nested file still open, should not be possible
  // open new filename and set infile, infiles[0], nfile
  // call to file() will close filename and decrement nfile

  if (me == 0) {
    if (nfile > 1)
      error->one(FLERR,"Invalid use of library file() function");
    infile = fopen(filename,"r");
    if (infile == NULL) {
      char str[128];
      sprintf(str,"Cannot open input script %s",filename);
      error->one(FLERR,str);
    }
    infiles[0] = infile;
    nfile = 1;
  }

  file();
}

/* ----------------------------------------------------------------------
   copy command in single to line, parse and execute it
   return command name to caller
------------------------------------------------------------------------- */

char *Input::one(const char *single)
{
  int n = strlen(single) + 1;
  if (n > maxline) reallocate(line,maxline,n);
  strcpy(line,single);

  // echo the command unless scanning for label

  if (me == 0 && label_active == 0) {
    if (echo_screen && screen) fprintf(screen,"%s\n",line);
    if (echo_log && logfile) fprintf(logfile,"%s\n",line);
  }

  // parse the line
  // if no command, just return NULL

  parse();
  if (command == NULL) return NULL;

  // if scanning for label, skip command unless it's a label command

  if (label_active && strcmp(command,"label") != 0) return NULL;

  // execute the command and return its name

  if (execute_command()) {
    char *str = new char[maxline+32];
    sprintf(str,"Unknown command: %s",line);
    error->all(FLERR,str);
  }

  return command;
}

/* ----------------------------------------------------------------------
   parse copy of command line by inserting string terminators
   strip comment = all chars from # on
   replace all $ via variable substitution
   command = first word
   narg = # of args
   arg[] = individual args
   treat text between single/double quotes as one arg
------------------------------------------------------------------------- */

void Input::parse()
{
  // duplicate line into copy string to break into words

  int n = strlen(line) + 1;
  if (n > maxcopy) reallocate(copy,maxcopy,n);
  strcpy(copy,line);

  // strip any # comment by replacing it with 0
  // do not strip # inside single/double quotes

  char quote = '\0';
  char *ptr = copy;
  while (*ptr) {
    if (*ptr == '#' && !quote) {
      *ptr = '\0';
      break;
    }
    if (*ptr == quote) quote = '\0';
    else if (*ptr == '"' || *ptr == '\'') quote = *ptr;
    ptr++;
  }

  // perform $ variable substitution (print changes)
  // except if searching for a label since earlier variable may not be defined

  if (!label_active) substitute(copy,work,maxcopy,maxwork,1);

  // command = 1st arg in copy string

  char *next;
  command = nextword(copy,&next);
  if (command == NULL) return;

  // point arg[] at each subsequent arg in copy string
  // nextword() inserts string terminators into copy string to delimit args
  // nextword() treats text between single/double quotes as one arg

  narg = 0;
  ptr = next;
  while (ptr) {
    if (narg == maxarg) {
      maxarg += DELTA;
      arg = (char **) memory->srealloc(arg,maxarg*sizeof(char *),"input:arg");
    }
    arg[narg] = nextword(ptr,&next);
    if (!arg[narg]) break;
    narg++;
    ptr = next;
  }
}

/* ----------------------------------------------------------------------
   find next word in str
   insert 0 at end of word
   ignore leading whitespace
   treat text between single/double quotes as one arg
     matching quote must be followed by whitespace char if not end of string
     strip quotes from returned word
   return ptr to start of word
   return next = ptr after word or NULL if word ended with 0
   return NULL if no word in string
------------------------------------------------------------------------- */

char *Input::nextword(char *str, char **next)
{
  char *start,*stop;

  start = &str[strspn(str," \t\n\v\f\r")];
  if (*start == '\0') return NULL;

  if (*start == '"' || *start == '\'') {
    stop = strchr(&start[1],*start);
    if (!stop) error->all(FLERR,"Unbalanced quotes in input line");
    if (stop[1] && !isspace(stop[1]))
      error->all(FLERR,"Input line quote not followed by whitespace");
    start++;
  } else stop = &start[strcspn(start," \t\n\v\f\r")];

  if (*stop == '\0') *next = NULL;
  else *next = stop+1;
  *stop = '\0';
  return start;
}

/* ----------------------------------------------------------------------
   substitute for $ variables in str using work str2 and return it
   reallocate str/str2 to hold expanded version if necessary & reset max/max2
   print updated string if flag is set and not searching for label
   label_active will be 0 if called from external class
------------------------------------------------------------------------- */

void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
{
  // use str2 as scratch space to expand str, then copy back to str
  // reallocate str and str2 as necessary
  // do not replace $ inside single/double quotes
  // var = pts at variable name, ended by NULL
  //   if $ is followed by '{', trailing '}' becomes NULL
  //   else $x becomes x followed by NULL
  // beyond = points to text following variable

  int i,n,paren_count;
  char immediate[256];
  char *var,*value,*beyond;
  char quote = '\0';
  char *ptr = str;

  n = strlen(str) + 1;
  if (n > max2) reallocate(str2,max2,n);
  *str2 = '\0';
  char *ptr2 = str2;

  while (*ptr) {
    // variable substitution
    if (*ptr == '$' && !quote) {

      // value = ptr to expanded variable
      // variable name between curly braces, e.g. ${a}

      if (*(ptr+1) == '{') {
        var = ptr+2;
        i = 0;
        while (var[i] != '\0' && var[i] != '}') i++;
        if (var[i] == '\0') error->one(FLERR,"Invalid variable name");
        var[i] = '\0';
        beyond = ptr + strlen(var) + 3;
        value = variable->retrieve(var);

        // immediate variable between parenthesis, e.g. $(1/2)

      } else if (*(ptr+1) == '(') {
        var = ptr+2;
        paren_count = 0;
        i = 0;

        while (var[i] != '\0' && !(var[i] == ')' && paren_count == 0)) {
          switch (var[i]) {
          case '(': paren_count++; break;
          case ')': paren_count--; break;
          default: ;
          }
          i++;
        }

        if (var[i] == '\0') error->one(FLERR,"Invalid immediate variable");
        var[i] = '\0';
        beyond = ptr + strlen(var) + 3;
        sprintf(immediate,"%.20g",variable->compute_equal(var));
        value = immediate;

        // single character variable name, e.g. $a
      } else {
        var = ptr;
        var[0] = var[1];
        var[1] = '\0';
        beyond = ptr + 2;
        value = variable->retrieve(var);
      }
      if (value == NULL) error->one(FLERR,"Substitution for illegal variable");

      // check if storage in str2 needs to be expanded
      // re-initialize ptr and ptr2 to the point beyond the variable.

      n = strlen(str2) + strlen(value) + strlen(beyond) + 1;
      if (n > max2) reallocate(str2,max2,n);
      strcat(str2,value);
      ptr2 = str2 + strlen(str2);
      ptr = beyond;

      // output substitution progress if requested
      if (flag && me == 0 && label_active == 0) {
        if (echo_screen && screen) fprintf(screen,"%s%s\n",str2,beyond);
        if (echo_log && logfile) fprintf(logfile,"%s%s\n",str2,beyond);
      }
      continue;
    }
    if (*ptr == quote) quote = '\0';
    else if (*ptr == '"' || *ptr == '\'') quote = *ptr;
    // copy current character into str2

    *ptr2++ = *ptr++;
    *ptr2 = '\0';
  }
  // set length of input str to length of work str2
  // copy work string back to input str

  if (max2 > max) reallocate(str,max,max2);
  strcpy(str,str2);
}

/* ----------------------------------------------------------------------
   rellocate a string
   if n > 0: set max >= n in increments of DELTALINE
   if n = 0: just increment max by DELTALINE
------------------------------------------------------------------------- */

void Input::reallocate(char *&str, int &max, int n)
{
  if (n) {
    while (n > max) max += DELTALINE;
  } else max += DELTALINE;

  str = (char *) memory->srealloc(str,max*sizeof(char),"input:str");
}

/* ----------------------------------------------------------------------
   process a single parsed command
   return 0 if successful, -1 if did not recognize command
------------------------------------------------------------------------- */

int Input::execute_command()
{
  int flag = 1;

  if (!strcmp(command,"clear")) clear();
  else if (!strcmp(command,"echo")) echo();
  else if (!strcmp(command,"if")) ifthenelse();
  else if (!strcmp(command,"include")) include();
  else if (!strcmp(command,"jump")) jump();
  else if (!strcmp(command,"label")) label();
  else if (!strcmp(command,"log")) log();
  else if (!strcmp(command,"next")) next_command();
  else if (!strcmp(command,"partition")) partition();
  else if (!strcmp(command,"print")) print();
  else if (!strcmp(command,"quit")) quit();
  else if (!strcmp(command,"shell")) shell();
  else if (!strcmp(command,"variable")) variable_command();

  else if (!strcmp(command,"angle_coeff")) angle_coeff();
  else if (!strcmp(command,"angle_style")) angle_style();
  else if (!strcmp(command,"atom_modify")) atom_modify();
  else if (!strcmp(command,"atom_style")) atom_style();
  else if (!strcmp(command,"bond_coeff")) bond_coeff();
  else if (!strcmp(command,"bond_style")) bond_style();
  else if (!strcmp(command,"boundary")) boundary();
  else if (!strcmp(command,"box")) box();
  else if (!strcmp(command,"communicate")) communicate();
  else if (!strcmp(command,"compute")) compute();
  else if (!strcmp(command,"compute_modify")) compute_modify();
  else if (!strcmp(command,"dielectric")) dielectric();
  else if (!strcmp(command,"dihedral_coeff")) dihedral_coeff();
  else if (!strcmp(command,"dihedral_style")) dihedral_style();
  else if (!strcmp(command,"dimension")) dimension();
  else if (!strcmp(command,"dump")) dump();
  else if (!strcmp(command,"dump_modify")) dump_modify();
  else if (!strcmp(command,"fix")) fix();
  else if (!strcmp(command,"fix_modify")) fix_modify();
  else if (!strcmp(command,"group")) group_command();
  else if (!strcmp(command,"improper_coeff")) improper_coeff();
  else if (!strcmp(command,"improper_style")) improper_style();
  else if (!strcmp(command,"kspace_modify")) kspace_modify();
  else if (!strcmp(command,"kspace_style")) kspace_style();
  else if (!strcmp(command,"lattice")) lattice();
  else if (!strcmp(command,"mass")) mass();
  else if (!strcmp(command,"min_modify")) min_modify();
  else if (!strcmp(command,"min_style")) min_style();
  else if (!strcmp(command,"neigh_modify")) neigh_modify();
  else if (!strcmp(command,"neighbor")) neighbor_command();
  else if (!strcmp(command,"newton")) newton();
  else if (!strcmp(command,"package")) package();
  else if (!strcmp(command,"pair_coeff")) pair_coeff();
  else if (!strcmp(command,"pair_modify")) pair_modify();
  else if (!strcmp(command,"pair_style")) pair_style();
  else if (!strcmp(command,"pair_write")) pair_write();
  else if (!strcmp(command,"processors")) processors();
  else if (!strcmp(command,"region")) region();
  else if (!strcmp(command,"reset_timestep")) reset_timestep();
  else if (!strcmp(command,"restart")) restart();
  else if (!strcmp(command,"run_style")) run_style();
  else if (!strcmp(command,"special_bonds")) special_bonds();
  else if (!strcmp(command,"suffix")) suffix();
  else if (!strcmp(command,"thermo")) thermo();
  else if (!strcmp(command,"thermo_modify")) thermo_modify();
  else if (!strcmp(command,"thermo_style")) thermo_style();
  else if (!strcmp(command,"timestep")) timestep();
  else if (!strcmp(command,"uncompute")) uncompute();
  else if (!strcmp(command,"undump")) undump();
  else if (!strcmp(command,"unfix")) unfix();
  else if (!strcmp(command,"units")) units();
  else if (!strcmp(command,"modify_timing")) modify_timing();

  else flag = 0;

  // return if command was listed above

  if (flag) return 0;

  // invoke commands added via style_command.h

  if (command_map->find(command) != command_map->end()) {
    CommandCreator command_creator = (*command_map)[command];
    command_creator(lmp,narg,arg);
    return 0;
  }

  // unrecognized command

  return -1;
}

/* ----------------------------------------------------------------------
   one instance per command in style_command.h
------------------------------------------------------------------------- */

template <typename T>
void Input::command_creator(LAMMPS *lmp, int narg, char **arg)
{
  T cmd(lmp);
  cmd.command(narg,arg);
}

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

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

void Input::clear()
{
  if (narg > 0) error->all(FLERR,"Illegal clear command");
  lmp->destroy();
  lmp->create();
  lmp->post_create();
}

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

void Input::echo()
{
  if (narg != 1) error->all(FLERR,"Illegal echo command");

  if (strcmp(arg[0],"none") == 0) {
    echo_screen = 0;
    echo_log = 0;
  } else if (strcmp(arg[0],"screen") == 0) {
    echo_screen = 1;
    echo_log = 0;
  } else if (strcmp(arg[0],"log") == 0) {
    echo_screen = 0;
    echo_log = 1;
  } else if (strcmp(arg[0],"both") == 0) {
    echo_screen = 1;
    echo_log = 1;
  } else error->all(FLERR,"Illegal echo command");
}

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

void Input::ifthenelse()
{
  if (narg < 3) error->all(FLERR,"Illegal if command");

  // substitute for variables in Boolean expression for "if"
  // in case expression was enclosed in quotes
  // must substitute on copy of arg else will step on subsequent args

  int n = strlen(arg[0]) + 1;
  if (n > maxline) reallocate(line,maxline,n);
  strcpy(line,arg[0]);
  substitute(line,work,maxline,maxwork,0);

  // evaluate Boolean expression for "if"
  
  double btest;

  if(strncmp(line,"property_",9) == 0)
  {
      if(strlen(line) < 11)
        error->all(FLERR,"Illegal if command, length of argument too short");
      if(modify->find_fix_property(&(line[9]),"property/global","any",0,0,"if",false))
        btest = 1.0;
      else
        btest = 0.0;
  }
  
  else
    btest = variable->evaluate_boolean(line);

  // bound "then" commands

  if (strcmp(arg[1],"then") != 0) error->all(FLERR,"Illegal if command");

  int first = 2;
  int iarg = first;
  while (iarg < narg &&
         (strcmp(arg[iarg],"elif") != 0 && strcmp(arg[iarg],"else") != 0))
    iarg++;
  int last = iarg-1;

  // execute "then" commands
  // make copies of all arg string commands
  // required because re-parsing a command via one() will wipe out args

  if (btest != 0.0) {
    int ncommands = last-first + 1;
    if (ncommands <= 0) error->all(FLERR,"Illegal if command");

    char **commands = new char*[ncommands];
    ncommands = 0;
    for (int i = first; i <= last; i++) {
      int n = strlen(arg[i]) + 1;
      if (n == 1) error->all(FLERR,"Illegal if command");
      commands[ncommands] = new char[n];
      strcpy(commands[ncommands],arg[i]);
      ncommands++;
    }

    ifthenelse_flag = 1;
    for (int i = 0; i < ncommands; i++) one(commands[i]);
    ifthenelse_flag = 0;

    for (int i = 0; i < ncommands; i++) delete [] commands[i];
    delete [] commands;

    return;
  }

  // done if no "elif" or "else"

  if (iarg == narg) return;

  // check "elif" or "else" until find commands to execute
  // substitute for variables and evaluate Boolean expression for "elif"
  // must substitute on copy of arg else will step on subsequent args
  // bound and execute "elif" or "else" commands

  while (1) {
    if (iarg+2 > narg) error->all(FLERR,"Illegal if command");
    if (strcmp(arg[iarg],"elif") == 0) {
      n = strlen(arg[iarg+1]) + 1;
      if (n > maxline) reallocate(line,maxline,n);
      strcpy(line,arg[iarg+1]);
      substitute(line,work,maxline,maxwork,0);
      btest = variable->evaluate_boolean(line);
      first = iarg+2;
    } else {
      btest = 1.0;
      first = iarg+1;
    }

    iarg = first;
    while (iarg < narg &&
           (strcmp(arg[iarg],"elif") != 0 && strcmp(arg[iarg],"else") != 0))
      iarg++;
    last = iarg-1;

    if (btest == 0.0) continue;

    int ncommands = last-first + 1;
    if (ncommands <= 0) error->all(FLERR,"Illegal if command");

    char **commands = new char*[ncommands];
    ncommands = 0;
    for (int i = first; i <= last; i++) {
      int n = strlen(arg[i]) + 1;
      if (n == 1) error->all(FLERR,"Illegal if command");
      commands[ncommands] = new char[n];
      strcpy(commands[ncommands],arg[i]);
      ncommands++;
    }

    // execute the list of commands

    ifthenelse_flag = 1;
    for (int i = 0; i < ncommands; i++) one(commands[i]);
    ifthenelse_flag = 0;

    // clean up

    for (int i = 0; i < ncommands; i++) delete [] commands[i];
    delete [] commands;

    return;
  }
}

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

void Input::include()
{
  if (narg != 1) error->all(FLERR,"Illegal include command");

  // do not allow include inside an if command
  // NOTE: this check will fail if a 2nd if command was inside the if command
  //       and came before the include

  if (ifthenelse_flag)
    error->all(FLERR,"Cannot use include command within an if command");
  if (me == 0) {
    if (nfile == maxfile) {
      maxfile++;
      infiles = (FILE **)
        memory->srealloc(infiles,maxfile*sizeof(FILE *),"input:infiles");
    }
    infile = fopen(arg[0],"r");
    if (infile == NULL) {
      char str[128];
      sprintf(str,"Cannot open input script %s",arg[0]);
      error->one(FLERR,str);
    }
    infiles[nfile++] = infile;
  }
}

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

void Input::jump()
{
  if (narg < 1 || narg > 2) error->all(FLERR,"Illegal jump command");

  if (jump_skip) {
    jump_skip = 0;
    return;
  }

  if (me == 0) {
    if (strcmp(arg[0],"SELF") == 0) rewind(infile);
    else {
      if (infile != stdin) fclose(infile);
      infile = fopen(arg[0],"r");
      if (infile == NULL) {
        char str[128];
        sprintf(str,"Cannot open input script %s",arg[0]);
        error->one(FLERR,str);
      }
      infiles[nfile-1] = infile;
    }
  }

  if (narg == 2) {
    label_active = 1;
    if (labelstr) delete [] labelstr;
    int n = strlen(arg[1]) + 1;
    labelstr = new char[n];
    strcpy(labelstr,arg[1]);
  }
}

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

void Input::label()
{
  if (narg != 1) error->all(FLERR,"Illegal label command");
  if (label_active && strcmp(labelstr,arg[0]) == 0) label_active = 0;
}

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

void Input::log()
{
  if (narg > 2) error->all(FLERR,"Illegal log command");

  int appendflag = 0;
  if (narg == 2) {
    if (strcmp(arg[1],"append") == 0) appendflag = 1;
    else error->all(FLERR,"Illegal log command");
  }

  if (me == 0) {
    if (logfile) fclose(logfile);
    if (strcmp(arg[0],"none") == 0) logfile = NULL;
    else {
      if (appendflag) logfile = fopen(arg[0],"a");
      else logfile = fopen(arg[0],"w");
      if (logfile == NULL) {
        char str[128];
        sprintf(str,"Cannot open logfile %s",arg[0]);
        error->one(FLERR,str);
      }
    }
    if (universe->nworlds == 1) universe->ulogfile = logfile;
  }
}

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

void Input::next_command()
{
  if (variable->next(narg,arg)) jump_skip = 1;
}

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

void Input::partition()
{
  if (narg < 3) error->all(FLERR,"Illegal partition command");

  int yesflag;
  if (strcmp(arg[0],"yes") == 0) yesflag = 1;
  else if (strcmp(arg[0],"no") == 0) yesflag = 0;
  else error->all(FLERR,"Illegal partition command");

  int ilo,ihi;
  force->bounds(arg[1],universe->nworlds,ilo,ihi);

  // copy original line to copy, since will use strtok() on it
  // ptr = start of 4th word

  strcpy(copy,line);
  char *ptr = strtok(copy," \t\n\r\f");
  ptr = strtok(NULL," \t\n\r\f");
  ptr = strtok(NULL," \t\n\r\f");
  ptr += strlen(ptr) + 1;
  ptr += strspn(ptr," \t\n\r\f");

  // execute the remaining command line on requested partitions

  if (yesflag) {
    if (universe->iworld+1 >= ilo && universe->iworld+1 <= ihi) one(ptr);
  } else {
    if (universe->iworld+1 < ilo || universe->iworld+1 > ihi) one(ptr);
  }
}

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

void Input::print()
{
  if (narg < 1) error->all(FLERR,"Illegal print command");

  // copy 1st arg back into line (copy is being used)
  // check maxline since arg[0] could have been exanded by variables
  // substitute for $ variables (no printing) and print arg

  int n = strlen(arg[0]) + 1;
  if (n > maxline) reallocate(line,maxline,n);
  strcpy(line,arg[0]);
  substitute(line,work,maxline,maxwork,0);

  // parse optional args

  FILE *fp = NULL;
  int screenflag = 1;

  int iarg = 1;
  while (iarg < narg) {
    if (strcmp(arg[iarg],"file") == 0 || strcmp(arg[iarg],"append") == 0) {
      if (iarg+2 > narg) error->all(FLERR,"Illegal print command");
  if (me == 0) {
        if (strcmp(arg[iarg],"file") == 0) fp = fopen(arg[iarg+1],"w");
        else fp = fopen(arg[iarg+1],"a");
        if (fp == NULL) {
          char str[128];
          sprintf(str,"Cannot open print file %s",arg[iarg+1]);
          error->one(FLERR,str);
        }
      }
      iarg += 2;
    } else if (strcmp(arg[iarg],"screen") == 0) {
      if (iarg+2 > narg) error->all(FLERR,"Illegal print command");
      if (strcmp(arg[iarg+1],"yes") == 0) screenflag = 1;
      else if (strcmp(arg[iarg+1],"no") == 0) screenflag = 0;
      else error->all(FLERR,"Illegal print command");
      iarg += 2;
    } else error->all(FLERR,"Illegal print command");
  }

  if (me == 0) {
    if (screenflag && screen) fprintf(screen,"%s\n",line);
    if (screenflag && logfile) fprintf(logfile,"%s\n",line);
    if (fp) {
      fprintf(fp,"%s\n",line);
      fclose(fp);
    }
  }
}

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

void Input::quit()
{
  if (narg) error->all(FLERR,"Illegal quit command");
  error->done();
}

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

void Input::shell()
{
  if (narg < 1) error->all(FLERR,"Illegal shell command");

  if (strcmp(arg[0],"cd") == 0) {
    if (narg != 2) error->all(FLERR,"Illegal shell cd command");
    chdir(arg[1]);

  } else if (strcmp(arg[0],"mkdir") == 0) {
    if (narg < 2) error->all(FLERR,"Illegal shell mkdir command");
#if !defined(WINDOWS) && !defined(__MINGW32__)
    if (me == 0)
      for (int i = 1; i < narg; i++)
        mkdir(arg[i], S_IRWXU | S_IRGRP | S_IXGRP);
#endif

  } else if (strcmp(arg[0],"mv") == 0) {
    if (narg != 3) error->all(FLERR,"Illegal shell mv command");
    if (me == 0) rename(arg[1],arg[2]);

  } else if (strcmp(arg[0],"rm") == 0) {
    if (narg < 2) error->all(FLERR,"Illegal shell rm command");
    if (me == 0)
      for (int i = 1; i < narg; i++) unlink(arg[i]);

  } else if (strcmp(arg[0],"rmdir") == 0) {
    if (narg < 2) error->all(FLERR,"Illegal shell rmdir command");
    if (me == 0)
      for (int i = 1; i < narg; i++) rmdir(arg[i]);
  } else if (strcmp(arg[0],"putenv") == 0) {
    if (narg < 2) error->all(FLERR,"Illegal shell putenv command");
    for (int i = 1; i < narg; i++) {
      char *ptr = strdup(arg[i]);
#ifdef _WIN32
      if (ptr != NULL) _putenv(ptr);
#else
      if (ptr != NULL) putenv(ptr);
#endif
    }

  // use work string to concat args back into one string separated by spaces
  // invoke string in shell via system()

  } else {
    int n = 0;
    for (int i = 0; i < narg; i++) n += strlen(arg[i]) + 1;
    if (n > maxwork) reallocate(work,maxwork,n);
    strcpy(work,arg[0]);
    for (int i = 1; i < narg; i++) {
      strcat(work," ");
      strcat(work,arg[i]);
    }
    if (me == 0) system(work);
  }
}

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

void Input::variable_command()
{
  variable->set(narg,arg);
}

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

/* ----------------------------------------------------------------------
   one function for each LAMMPS-specific input script command
------------------------------------------------------------------------- */

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

void Input::angle_coeff()
{
  if (domain->box_exist == 0)
    error->all(FLERR,"Angle_coeff command before simulation box is defined");
  if (force->angle == NULL)
    error->all(FLERR,"Angle_coeff command before angle_style is defined");
  if (atom->avec->angles_allow == 0)
    error->all(FLERR,"Angle_coeff command when no angles allowed");
  force->angle->coeff(narg,arg);
}

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

void Input::angle_style()
{
  if (narg < 1) error->all(FLERR,"Illegal angle_style command");
  if (atom->avec->angles_allow == 0)
    error->all(FLERR,"Angle_style command when no angles allowed");
  force->create_angle(arg[0],lmp->suffix);
  if (force->angle) force->angle->settings(narg-1,&arg[1]);
}

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

void Input::atom_modify()
{
  atom->modify_params(narg,arg);
}

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

void Input::atom_style()
{
  if (narg < 1) error->all(FLERR,"Illegal atom_style command");
  if (domain->box_exist)
    error->all(FLERR,"Atom_style command after simulation box is defined");
  atom->create_avec(arg[0],narg-1,&arg[1],lmp->suffix);
}

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

void Input::bond_coeff()
{
  if (domain->box_exist == 0)
    error->all(FLERR,"Bond_coeff command before simulation box is defined");
  if (force->bond == NULL)
    error->all(FLERR,"Bond_coeff command before bond_style is defined");
  if (atom->avec->bonds_allow == 0)
    error->all(FLERR,"Bond_coeff command when no bonds allowed");
  force->bond->coeff(narg,arg);
}

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

void Input::bond_style()
{
  if (narg < 1) error->all(FLERR,"Illegal bond_style command");
  if (atom->avec->bonds_allow == 0)
    error->all(FLERR,"Bond_style command when no bonds allowed");
  force->create_bond(arg[0],lmp->suffix);
  if (force->bond) force->bond->settings(narg-1,&arg[1]);
}

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

void Input::boundary()
{
  if (domain->box_exist)
    error->all(FLERR,"Boundary command after simulation box is defined");
  domain->set_boundary(narg,arg,0);
}

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

void Input::box()
{
  if (domain->box_exist)
    error->all(FLERR,"Box command after simulation box is defined");
  domain->set_box(narg,arg);
}

/* ---------------------------------------------------------------------- */
void Input::communicate()
{
  comm->set(narg,arg);
}

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

void Input::compute()
{
  modify->add_compute(narg,arg,lmp->suffix);
}

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

void Input::compute_modify()
{
  modify->modify_compute(narg,arg);
}

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

void Input::dielectric()
{
  if (narg != 1) error->all(FLERR,"Illegal dielectric command");
  force->dielectric = force->numeric(FLERR,arg[0]);
}

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

void Input::dihedral_coeff()
{
  if (domain->box_exist == 0)
    error->all(FLERR,"Dihedral_coeff command before simulation box is defined");
  if (force->dihedral == NULL)
    error->all(FLERR,"Dihedral_coeff command before dihedral_style is defined");
  if (atom->avec->dihedrals_allow == 0)
    error->all(FLERR,"Dihedral_coeff command when no dihedrals allowed");
  force->dihedral->coeff(narg,arg);
}

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

void Input::dihedral_style()
{
  if (narg < 1) error->all(FLERR,"Illegal dihedral_style command");
  if (atom->avec->dihedrals_allow == 0)
    error->all(FLERR,"Dihedral_style command when no dihedrals allowed");
  force->create_dihedral(arg[0],lmp->suffix);
  if (force->dihedral) force->dihedral->settings(narg-1,&arg[1]);
}

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

void Input::dimension()
{
  if (narg != 1) error->all(FLERR,"Illegal dimension command");
  if (domain->box_exist)
    error->all(FLERR,"Dimension command after simulation box is defined");
  domain->dimension = force->inumeric(FLERR,arg[0]);
  if (domain->dimension != 2 && domain->dimension != 3)
    error->all(FLERR,"Illegal dimension command");

  // must reset default extra_dof of all computes
  // since some were created before dimension command is encountered

  for (int i = 0; i < modify->ncompute; i++)
    modify->compute[i]->reset_extra_dof();
}

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

void Input::dump()
{
  output->add_dump(narg,arg);
}

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

void Input::dump_modify()
{
  output->modify_dump(narg,arg);
}

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

void Input::fix()
{
  modify->add_fix(narg,arg,lmp->suffix);
}

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

void Input::fix_modify()
{
  modify->modify_fix(narg,arg);
}

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

void Input::group_command()
{
  group->assign(narg,arg);
}

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

void Input::improper_coeff()
{
  if (domain->box_exist == 0)
    error->all(FLERR,"Improper_coeff command before simulation box is defined");
  if (force->improper == NULL)
    error->all(FLERR,"Improper_coeff command before improper_style is defined");
  if (atom->avec->impropers_allow == 0)
    error->all(FLERR,"Improper_coeff command when no impropers allowed");
  force->improper->coeff(narg,arg);
}

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

void Input::improper_style()
{
  if (narg < 1) error->all(FLERR,"Illegal improper_style command");
  if (atom->avec->impropers_allow == 0)
    error->all(FLERR,"Improper_style command when no impropers allowed");
  force->create_improper(arg[0],lmp->suffix);
  if (force->improper) force->improper->settings(narg-1,&arg[1]);
}

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

void Input::kspace_modify()
{
  if (force->kspace == NULL)
    error->all(FLERR,"KSpace style has not yet been set");
  force->kspace->modify_params(narg,arg);
}

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

void Input::kspace_style()
{
  force->create_kspace(narg,arg,lmp->suffix);
}

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

void Input::lattice()
{
  domain->set_lattice(narg,arg);
}

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

void Input::mass()
{
  if (narg != 2) error->all(FLERR,"Illegal mass command");
  if (domain->box_exist == 0)
    error->all(FLERR,"Mass command before simulation box is defined");
  atom->set_mass(narg,arg);
}

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

void Input::min_modify()
{
  update->minimize->modify_params(narg,arg);
}

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

void Input::min_style()
{
  if (domain->box_exist == 0)
    error->all(FLERR,"Min_style command before simulation box is defined");
  update->create_minimize(narg,arg);
}

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

void Input::neigh_modify()
{
  neighbor->modify_params(narg,arg);
}

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

void Input::neighbor_command()
{
  neighbor->set(narg,arg);
}

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

void Input::newton()
{
  int newton_pair,newton_bond;

  if (narg == 1) {
    if (strcmp(arg[0],"off") == 0) newton_pair = newton_bond = 0;
    else if (strcmp(arg[0],"on") == 0) newton_pair = newton_bond = 1;
    else error->all(FLERR,"Illegal newton command");
  } else if (narg == 2) {
    if (strcmp(arg[0],"off") == 0) newton_pair = 0;
    else if (strcmp(arg[0],"on") == 0) newton_pair= 1;
    else error->all(FLERR,"Illegal newton command");
    if (strcmp(arg[1],"off") == 0) newton_bond = 0;
    else if (strcmp(arg[1],"on") == 0) newton_bond = 1;
    else error->all(FLERR,"Illegal newton command");
  } else error->all(FLERR,"Illegal newton command");

  force->newton_pair = newton_pair;

  if (newton_bond == 0) {
    if (domain->box_exist && force->newton_bond == 1)
      error->all(FLERR,"Newton bond change after simulation box is defined");
    force->newton_bond = 0;
  } else {
    if (domain->box_exist && force->newton_bond == 0)
      error->all(FLERR,"Newton bond change after simulation box is defined");
    force->newton_bond = 1;
  }

  if (newton_pair || newton_bond) force->newton = 1;
  else force->newton = 0;
}

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

void Input::modify_timing()
{
  int timing = 0;

  if (narg == 1) {
    if (strcmp(arg[0],"off") == 0) timing = 0;
    else if (strcmp(arg[0],"on") == 0) timing = 1;
    else error->all(FLERR,"Illegal modify_timing command");
  } else error->all(FLERR,"Illegal modify_timing command");

  modify->timing = timing;
}

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

void Input::package()
{
  if (domain->box_exist)
    error->all(FLERR,"Package command after simulation box is defined");
  if (narg < 1) error->all(FLERR,"Illegal package command");

  if (strcmp(arg[0],"cuda") == 0) {
    if (!lmp->cuda)
      error->all(FLERR,"Package cuda command without USER-CUDA installed");
    lmp->cuda->accelerator(narg-1,&arg[1]);

  } else if (strcmp(arg[0],"gpu") == 0) {
    char **fixarg = new char*[2+narg];
    fixarg[0] = (char *) "package_gpu";
    fixarg[1] = (char *) "all";
    fixarg[2] = (char *) "GPU";
    for (int i = 1; i < narg; i++) fixarg[i+2] = arg[i];
    modify->add_fix(2+narg,fixarg,NULL);
    delete [] fixarg;
    force->newton_pair = 0;

  } else if (strcmp(arg[0],"omp") == 0) {
    char **fixarg = new char*[2+narg];
    fixarg[0] = (char *) "package_omp";
    fixarg[1] = (char *) "all";
    fixarg[2] = (char *) "OMP";
    for (int i = 1; i < narg; i++) fixarg[i+2] = arg[i];
    modify->add_fix(2+narg,fixarg,NULL);
    delete [] fixarg;

  } else error->all(FLERR,"Illegal package command");
}

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

void Input::pair_coeff()
{
  if (domain->box_exist == 0)
    error->all(FLERR,"Pair_coeff command before simulation box is defined");
  if (force->pair == NULL)
    error->all(FLERR,"Pair_coeff command before pair_style is defined");
  force->pair->coeff(narg,arg);
}

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

void Input::pair_modify()
{
  if (force->pair == NULL)
    error->all(FLERR,"Pair_modify command before pair_style is defined");
  force->pair->modify_params(narg,arg);
}

/* ----------------------------------------------------------------------
   if old pair style exists and new style is same, just change settings
   else create new pair class
------------------------------------------------------------------------- */

void Input::pair_style()
{
  if (narg < 1) error->all(FLERR,"Illegal pair_style command");
  
  /*
  if (force->pair && strcmp(arg[0],force->pair_style) == 0) {
    force->pair->settings(narg-1,&arg[1]);
    return;
  }*/
  int num_remaining_arg = narg - 1;
  char ** remaining_args = &arg[1];
  force->create_pair(arg[0], num_remaining_arg, remaining_args, lmp->suffix);
  if (force->pair) force->pair->settings(num_remaining_arg,remaining_args);
}

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

void Input::pair_write()
{
  if (force->pair == NULL)
    error->all(FLERR,"Pair_write command before pair_style is defined");
  force->pair->write_file(narg,arg);
}

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

void Input::processors()
{
  if (domain->box_exist)
    error->all(FLERR,"Processors command after simulation box is defined");
  comm->set_processors(narg,arg);
}

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

void Input::region()
{
  domain->add_region(narg,arg);
}

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

void Input::reset_timestep()
{
  update->reset_timestep(narg,arg);
}

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

void Input::restart()
{
  output->create_restart(narg,arg);
}

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

void Input::run_style()
{
  if (domain->box_exist == 0)
    error->all(FLERR,"Run_style command before simulation box is defined");
  update->create_integrate(narg,arg,lmp->suffix);
}

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

void Input::special_bonds()
{
  // store 1-3,1-4 and dihedral/extra flag values before change
  // change in 1-2 coeffs will not change the special list

  double lj2 = force->special_lj[2];
  double lj3 = force->special_lj[3];
  double coul2 = force->special_coul[2];
  double coul3 = force->special_coul[3];
  int angle = force->special_angle;
  int dihedral = force->special_dihedral;
  int extra = force->special_extra;

  force->set_special(narg,arg);

  // if simulation box defined and saved values changed, redo special list

  if (domain->box_exist && atom->molecular) {
    if (lj2 != force->special_lj[2] || lj3 != force->special_lj[3] ||
        coul2 != force->special_coul[2] || coul3 != force->special_coul[3] ||
        angle != force->special_angle ||
        dihedral != force->special_dihedral ||
        extra != force->special_extra) {
      Special special(lmp);
      special.build();
    }
  }
}

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

void Input::suffix()
{
  if (narg != 1) error->all(FLERR,"Illegal suffix command");

  if (strcmp(arg[0],"off") == 0) lmp->suffix_enable = 0;
  else if (strcmp(arg[0],"on") == 0) lmp->suffix_enable = 1;
  else {
    delete [] lmp->suffix;
    int n = strlen(arg[0]) + 1;
    lmp->suffix = new char[n];
    strcpy(lmp->suffix,arg[0]);
    lmp->suffix_enable = 1;
  }
}

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

void Input::thermo()
{
  output->set_thermo(narg,arg);
}

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

void Input::thermo_modify()
{
  output->thermo->modify_params(narg,arg);
}

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

void Input::thermo_style()
{
  output->create_thermo(narg,arg);
}

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

void Input::timestep()
{
  if (narg != 1) error->all(FLERR,"Illegal timestep command");
  update->dt = force->numeric(FLERR,arg[0]);
}

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

void Input::uncompute()
{
  if (narg != 1) error->all(FLERR,"Illegal uncompute command");
  modify->delete_compute(arg[0],true); 
}

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

void Input::undump()
{
  if (narg != 1) error->all(FLERR,"Illegal undump command");
  output->delete_dump(arg[0]);
}

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

void Input::unfix()
{
  if (narg != 1) error->all(FLERR,"Illegal unfix command");
  modify->delete_fix(arg[0],true); 
}

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

void Input::units()
{
  if (narg != 1) error->all(FLERR,"Illegal units command");
  if (domain->box_exist)
    error->all(FLERR,"Units command after simulation box is defined");
  update->set_units(arg[0]);
}

/* ----------------------------------------------------------------------
   parse line of non-LAMMPS origin
------------------------------------------------------------------------- */

void Input::parse_nonlammps()
{
  // duplicate line into copy string to break into words

  int n = strlen(line) + 1;
  if (n > maxcopy) reallocate(copy,maxcopy,n);
  strcpy(copy,line);

  // strip any # comment by replacing it with 0
  // do not strip # inside single/double quotes

  char quote = '\0';
  char *ptr = copy;
  while (*ptr) {
    if (*ptr == '#' && !quote) {
      *ptr = '\0';
      break;
    }
    if (*ptr == quote) quote = '\0';
    else if (*ptr == '"' || *ptr == '\'') quote = *ptr;
    ptr++;
  }

  // point arg[] at each subsequent arg in copy string
  // nextword() inserts string terminators into copy string to delimit args
  // nextword() treats text between single/double quotes as one arg

  narg = 0;
  ptr = copy;
  char *next;

  while (ptr) {
    if (narg == maxarg) {
      maxarg += DELTA;
      arg = (char **) memory->srealloc(arg,maxarg*sizeof(char *),"input:arg");
    }
    arg[narg] = nextword(ptr,&next);
    if (!arg[narg]) break;
    narg++;
    ptr = next;
  }
}

