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0628bb89ce19abe622f58144801d4b8810acb96d
lammps/src/input.cpp

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://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 "input.h"
#include "accelerator_kokkos.h"
#include "angle.h"
#include "atom.h"
#include "atom_vec.h"
#include "bond.h"
#include "comm.h"
#include "comm_brick.h"
#include "comm_tiled.h"
#include "compute.h"
#include "dihedral.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "group.h"
#include "improper.h"
#include "kspace.h"
#include "memory.h"
#include "min.h"
#include "modify.h"
#include "neighbor.h"
#include "output.h"
#include "pair.h"
#include "special.h"
#include "style_command.h"
#include "thermo.h"
#include "timer.h"
#include "universe.h"
#include "update.h"
#include "variable.h"
#include <cstring>
#include <errno.h>
#include <cctype>
#include <sys/stat.h>
#include <unistd.h>
#ifdef _WIN32
#include <direct.h>
#endif
using namespace LAMMPS_NS;
#define DELTALINE 256
#define DELTA 4
/* ---------------------------------------------------------------------- */
/** \class LAMMPS_NS::Input
* \brief Class for processing commands and input files
*
\verbatim embed:rst
The Input class contains methods for reading, pre-processing and
parsing LAMMPS commands and input files and will dispatch commands
to the respective class instances or contains the code to execute
the commands directly. It also contains the instance of the
Variable class which performs computations and text substitutions.
\endverbatim */
/** Input class constructor
*
\verbatim embed:rst
This sets up the input processing, processes the *-var* and *-echo*
command line flags, holds the factory of commands and creates and
initializes an instance of the Variable class.
To execute a command, a specific class instance, derived from
:cpp:class:`Pointers`, is created, then its ``command()`` member
function executed, and finally the class instance is deleted.
\endverbatim
*
* \param lmp pointer to the base LAMMPS class
* \param argc number of entries in *argv*
* \param argv argument vector */
Input::Input(LAMMPS *lmp, int argc, char **argv) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
maxline = maxcopy = maxwork = 0;
line = copy = work = nullptr;
narg = maxarg = 0;
arg = nullptr;
echo_screen = 0;
echo_log = 1;
label_active = 0;
labelstr = nullptr;
jump_skip = 0;
utf8_warn = true;
if (me == 0) {
nfile = 1;
maxfile = 16;
infiles = new FILE *[maxfile];
infiles[0] = infile;
} else infiles = nullptr;
variable = new Variable(lmp);
// fill map with commands listed in style_command.h
command_map = new CommandCreatorMap();
#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 = 1;
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);
delete [] infiles;
delete variable;
delete command_map;
}
/** Process all input from the ``FILE *`` pointer *infile*
*
\verbatim embed:rst
This will read lines from *infile*, parse and execute them until the end
of the file is reached. The *infile* pointer will usually point to
``stdin`` or the input file given with the ``-in`` command line flag.
\endverbatim */
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 (infile == nullptr) {
n = 0;
break;
}
if (maxline-m < 2) reallocate(line,maxline,0);
// end of file reached, so break
// n == 0 if nothing read, else n = line with str terminator
if (fgets(&line[m],maxline-m,infile) == nullptr) {
if (m) n = strlen(line) + 1;
else n = 0;
break;
}
// continue if last char read was not a newline
// could happen if line is very long
m = strlen(line);
if (line[m-1] != '\n') continue;
// continue reading if final printable char is & char
// or if odd number of triple quotes
// else break with n = line with str terminator
m--;
while (m >= 0 && isspace(line[m])) m--;
if (m < 0 || line[m] != '&') {
if (numtriple(line) % 2) {
m += 2;
continue;
}
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");
break;
}
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 == nullptr) 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() && line)
error->all(FLERR,fmt::format("Unknown command: {}",line));
}
}
/** Process all input from the file *filename*
*
\verbatim embed:rst
This function opens the file at the path *filename*, put the current
file pointer stored in *infile* on a stack and instead assign *infile*
with the newly opened file pointer. Then it will call the
:cpp:func:`Input::file() <LAMMPS_NS::Input::file()>` function to read,
parse and execute the contents of that file. When the end of the file
is reached, it is closed and the previous file pointer from the infile
file pointer stack restored to *infile*.
\endverbatim
*
* \param filename name of file with LAMMPS commands */
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 == maxfile)
error->one(FLERR,"Too many nested levels of input scripts");
infile = fopen(filename,"r");
if (infile == nullptr)
error->one(FLERR,fmt::format("Cannot open input script {}: {}",
filename, utils::getsyserror()));
infiles[nfile++] = infile;
}
// process contents of file
file();
if (me == 0) {
fclose(infile);
nfile--;
infile = infiles[nfile-1];
}
}
/** Process a single command from a string in *single*
*
\verbatim embed:rst
This function takes the text in *single*, makes a copy, parses that,
executes the command and returns the name of the command (without the
arguments). If there was no command in *single* it will return
``nullptr``.
\endverbatim
*
* \param single string with LAMMPS command
* \return string with name of the parsed command w/o arguments */
char *Input::one(const std::string &single)
{
int n = single.size() + 1;
if (n > maxline) reallocate(line,maxline,n);
strcpy(line,single.c_str());
// 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 a null pointer
parse();
if (command == nullptr) return nullptr;
// if scanning for label, skip command unless it's a label command
if (label_active && strcmp(command,"label") != 0) return nullptr;
// execute the command and return its name
if (execute_command())
error->all(FLERR,fmt::format("Unknown command: {}",line));
return command;
}
/* ----------------------------------------------------------------------
Send text to active echo file pointers
------------------------------------------------------------------------- */
void Input::write_echo(const std::string &txt)
{
if (me == 0) {
if (echo_screen && screen) fputs(txt.c_str(),screen);
if (echo_log && logfile) fputs(txt.c_str(),logfile);
}
}
/* ----------------------------------------------------------------------
parse copy of command line by inserting string terminators
strip comment = all chars from # on
replace all $ via variable substitution except within quotes
command = first word
narg = # of args
arg[] = individual args
treat text between single/double/triple quotes as one arg via nextword()
------------------------------------------------------------------------- */
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 from a # inside single/double/triple quotes
// quoteflag = 1,2,3 when encounter first single/double,triple quote
// quoteflag = 0 when encounter matching single/double,triple quote
int quoteflag = 0;
char *ptr = copy;
while (*ptr) {
if (*ptr == '#' && !quoteflag) {
*ptr = '\0';
break;
}
if (quoteflag == 0) {
if (strstr(ptr,"\"\"\"") == ptr) {
quoteflag = 3;
ptr += 2;
}
else if (*ptr == '"') quoteflag = 2;
else if (*ptr == '\'') quoteflag = 1;
} else {
if (quoteflag == 3 && strstr(ptr,"\"\"\"") == ptr) {
quoteflag = 0;
ptr += 2;
}
else if (quoteflag == 2 && *ptr == '"') quoteflag = 0;
else if (quoteflag == 1 && *ptr == '\'') quoteflag = 0;
}
ptr++;
}
if (utils::has_utf8(copy)) {
std::string buf = utils::utf8_subst(copy);
strcpy(copy,buf.c_str());
if (utf8_warn && (comm->me == 0))
error->warning(FLERR,"Detected non-ASCII characters in input. "
"Will try to continue by replacing with ASCII "
"equivalents where known.");
utf8_warn = false;
}
// 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 == nullptr) 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/triple 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/triple 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 or null pointer if no word in string
also return next = ptr after word
------------------------------------------------------------------------- */
char *Input::nextword(char *str, char **next)
{
char *start,*stop;
// start = first non-whitespace char
start = &str[strspn(str," \t\n\v\f\r")];
if (*start == '\0') return nullptr;
// if start is single/double/triple quote:
// start = first char beyond quote
// stop = first char of matching quote
// next = first char beyond matching quote
// next must be null char or whitespace
// if start is not single/double/triple quote:
// stop = first whitespace char after start
// next = char after stop, or stop itself if stop is null char
if (strstr(start,"\"\"\"") == start) {
stop = strstr(&start[3],"\"\"\"");
if (!stop) error->all(FLERR,"Unbalanced quotes in input line");
start += 3;
*next = stop+3;
if (**next && !isspace(**next))
error->all(FLERR,"Input line quote not followed by white-space");
} else if (*start == '"' || *start == '\'') {
stop = strchr(&start[1],*start);
if (!stop) error->all(FLERR,"Unbalanced quotes in input line");
start++;
*next = stop+1;
if (**next && !isspace(**next))
error->all(FLERR,"Input line quote not followed by white-space");
} else {
stop = &start[strcspn(start," \t\n\v\f\r")];
if (*stop == '\0') *next = stop;
else *next = stop+1;
}
// set stop to null char to terminate word
*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/triple quotes
// var = pts at variable name, ended by null char
// if $ is followed by '{', trailing '}' becomes null char
// else $x becomes x followed by null char
// beyond = points to text following variable
int i,n,paren_count;
char immediate[256];
char *var,*value,*beyond;
int quoteflag = 0;
char *ptr = str;
n = strlen(str) + 1;
if (n > max2) reallocate(str2,max2,n);
*str2 = '\0';
char *ptr2 = str2;
while (*ptr) {
// variable substitution
if (*ptr == '$' && !quoteflag) {
// 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. $(1/3) or $(1/3:%.6g)
} 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;
// check if an inline format specifier was appended with a colon
char fmtstr[64] = "%.20g";
char *fmtflag;
if ((fmtflag=strrchr(var, ':')) && (fmtflag[1]=='%')) {
strncpy(fmtstr,&fmtflag[1],sizeof(fmtstr)-1);
*fmtflag='\0';
}
// quick check for proper format string
if (!utils::strmatch(fmtstr,"%[0-9 ]*\\.[0-9]+[efgEFG]"))
error->all(FLERR,"Incorrect conversion in format string");
snprintf(immediate,256,fmtstr,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 == nullptr)
error->one(FLERR,fmt::format("Substitution for illegal "
"variable {}",var));
// 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;
}
// quoteflag = 1,2,3 when encounter first single/double,triple quote
// quoteflag = 0 when encounter matching single/double,triple quote
// copy 2 extra triple quote chars into str2
if (quoteflag == 0) {
if (strstr(ptr,"\"\"\"") == ptr) {
quoteflag = 3;
*ptr2++ = *ptr++;
*ptr2++ = *ptr++;
}
else if (*ptr == '"') quoteflag = 2;
else if (*ptr == '\'') quoteflag = 1;
} else {
if (quoteflag == 3 && strstr(ptr,"\"\"\"") == ptr) {
quoteflag = 0;
*ptr2++ = *ptr++;
*ptr2++ = *ptr++;
}
else if (quoteflag == 2 && *ptr == '"') quoteflag = 0;
else if (quoteflag == 1 && *ptr == '\'') quoteflag = 0;
}
// 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);
}
/* ----------------------------------------------------------------------
return number of triple quotes in line
------------------------------------------------------------------------- */
int Input::numtriple(char *line)
{
int count = 0;
char *ptr = line;
while ((ptr = strstr(ptr,"\"\"\""))) {
ptr += 3;
count++;
}
return count;
}
/* ----------------------------------------------------------------------
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,"python")) python();
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,"bond_write")) bond_write();
else if (!strcmp(command,"boundary")) boundary();
else if (!strcmp(command,"box")) box();
else if (!strcmp(command,"comm_modify")) comm_modify();
else if (!strcmp(command,"comm_style")) comm_style();
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,"molecule")) molecule();
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,"timer")) timer_command();
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 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 = 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++;
}
for (int i = 0; i < ncommands; i++) {
one(commands[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 (iarg != narg) {
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
for (int i = 0; i < ncommands; i++) {
one(commands[i]);
delete [] commands[i];
}
delete [] commands;
return;
}
}
/* ---------------------------------------------------------------------- */
void Input::include()
{
if (narg != 1) error->all(FLERR,"Illegal include command");
if (me == 0) {
if (nfile == maxfile)
error->one(FLERR,"Too many nested levels of input scripts");
infile = fopen(arg[0],"r");
if (infile == nullptr)
error->one(FLERR,fmt::format("Cannot open input script {}: {}",
arg[0], utils::getsyserror()));
infiles[nfile++] = infile;
}
// process contents of file
file();
if (me == 0) {
fclose(infile);
nfile--;
infile = infiles[nfile-1];
}
}
/* ---------------------------------------------------------------------- */
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 && infile != stdin) fclose(infile);
infile = fopen(arg[0],"r");
if (infile == nullptr)
error->one(FLERR,fmt::format("Cannot open input script {}: {}",
arg[0], utils::getsyserror()));
infiles[nfile-1] = infile;
}
}
if (narg == 2) {
label_active = 1;
if (labelstr) delete [] labelstr;
labelstr = utils::strdup(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 < 1) || (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 = nullptr;
else {
if (appendflag) logfile = fopen(arg[0],"a");
else logfile = fopen(arg[0],"w");
if (logfile == nullptr)
error->one(FLERR,fmt::format("Cannot open logfile {}: {}",
arg[0], utils::getsyserror()));
}
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 = 0;
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;
utils::bounds(FLERR,arg[1],1,universe->nworlds,ilo,ihi,error);
// new command starts at the 3rd argument,
// which must not be another partition command
if (strcmp(arg[2],"partition") == 0)
error->all(FLERR,"Illegal partition command");
char *cmd = strstr(line,arg[2]);
// execute the remaining command line on requested partitions
if (yesflag) {
if (universe->iworld+1 >= ilo && universe->iworld+1 <= ihi) one(cmd);
} else {
if (universe->iworld+1 < ilo || universe->iworld+1 > ihi) one(cmd);
}
}
/* ---------------------------------------------------------------------- */
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 expanded 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 = nullptr;
int screenflag = 1;
int universeflag = 0;
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 (fp != nullptr) fclose(fp);
if (strcmp(arg[iarg],"file") == 0) fp = fopen(arg[iarg+1],"w");
else fp = fopen(arg[iarg+1],"a");
if (fp == nullptr)
error->one(FLERR,fmt::format("Cannot open print file {}: {}",
arg[iarg+1], utils::getsyserror()));
}
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 if (strcmp(arg[iarg],"universe") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal print command");
if (strcmp(arg[iarg+1],"yes") == 0) universeflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) universeflag = 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);
}
}
if (universeflag && (universe->me == 0)) {
if (universe->uscreen) fprintf(universe->uscreen, "%s\n",line);
if (universe->ulogfile) fprintf(universe->ulogfile,"%s\n",line);
}
}
/* ---------------------------------------------------------------------- */
void Input::python()
{
variable->python_command(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::quit()
{
if (narg == 0) error->done(0); // 1 would be fully backwards compatible
if (narg == 1) error->done(utils::inumeric(FLERR,arg[0],false,lmp));
error->all(FLERR,"Illegal quit command");
}
/* ---------------------------------------------------------------------- */
char *shell_failed_message(const char* cmd, int errnum)
{
std::string errmsg = fmt::format("Shell command '{}' failed with error '{}'",
cmd, strerror(errnum));
char *msg = new char[errmsg.size()+1];
strcpy(msg, errmsg.c_str());
return msg;
}
void Input::shell()
{
int rv,err;
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");
rv = (chdir(arg[1]) < 0) ? errno : 0;
MPI_Reduce(&rv,&err,1,MPI_INT,MPI_MAX,0,world);
if (me == 0 && err != 0) {
char *message = shell_failed_message("cd",err);
error->warning(FLERR,message);
delete [] message;
}
} else if (strcmp(arg[0],"mkdir") == 0) {
if (narg < 2) error->all(FLERR,"Illegal shell mkdir command");
if (me == 0)
for (int i = 1; i < narg; i++) {
#if defined(_WIN32)
rv = _mkdir(arg[i]);
#else
rv = mkdir(arg[i], S_IRWXU | S_IRGRP | S_IXGRP);
#endif
if (rv < 0) {
char *message = shell_failed_message("mkdir",errno);
error->warning(FLERR,message);
delete [] message;
}
}
} else if (strcmp(arg[0],"mv") == 0) {
if (narg != 3) error->all(FLERR,"Illegal shell mv command");
rv = (rename(arg[1],arg[2]) < 0) ? errno : 0;
MPI_Reduce(&rv,&err,1,MPI_INT,MPI_MAX,0,world);
if (me == 0 && err != 0) {
char *message = shell_failed_message("mv",err);
error->warning(FLERR,message);
delete [] message;
}
} 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++) {
if (unlink(arg[i]) < 0) {
char *message = shell_failed_message("rm",errno);
error->warning(FLERR,message);
delete [] message;
}
}
} 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++) {
if (rmdir(arg[i]) < 0) {
char *message = shell_failed_message("rmdir",errno);
error->warning(FLERR,message);
delete [] message;
}
}
} else if (strcmp(arg[0],"putenv") == 0) {
if (narg < 2) error->all(FLERR,"Illegal shell putenv command");
for (int i = 1; i < narg; i++) {
rv = 0;
#ifdef _WIN32
if (arg[i]) rv = _putenv(utils::strdup(arg[i]));
#else
if (arg[i]) {
std::string vardef(arg[i]);
auto found = vardef.find_first_of("=");
if (found == std::string::npos) {
rv = setenv(vardef.c_str(),"",1);
} else {
rv = setenv(vardef.substr(0,found).c_str(),
vardef.substr(found+1).c_str(),1);
}
}
#endif
rv = (rv < 0) ? errno : 0;
MPI_Reduce(&rv,&err,1,MPI_INT,MPI_MAX,0,world);
if (me == 0 && err != 0) {
char *message = shell_failed_message("putenv",err);
error->warning(FLERR,message);
delete [] message;
}
}
// 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)
if (system(work) != 0)
error->warning(FLERR,"Shell command returned with non-zero status");
}
}
/* ---------------------------------------------------------------------- */
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 == nullptr)
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],1);
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],1);
}
/* ---------------------------------------------------------------------- */
void Input::bond_coeff()
{
if (domain->box_exist == 0)
error->all(FLERR,"Bond_coeff command before simulation box is defined");
if (force->bond == nullptr)
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],1);
if (force->bond) force->bond->settings(narg-1,&arg[1]);
}
/* ---------------------------------------------------------------------- */
void Input::bond_write()
{
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Bond_write command when no bonds allowed");
if (force->bond == nullptr)
error->all(FLERR,"Bond_write command before bond_style is defined");
else force->bond->write_file(narg,arg);
}
/* ---------------------------------------------------------------------- */
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::comm_modify()
{
comm->modify_params(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::comm_style()
{
if (narg < 1) error->all(FLERR,"Illegal comm_style command");
if (strcmp(arg[0],"brick") == 0) {
if (comm->style == 0) return;
Comm *oldcomm = comm;
comm = new CommBrick(lmp,oldcomm);
delete oldcomm;
} else if (strcmp(arg[0],"tiled") == 0) {
if (comm->style == 1) return;
Comm *oldcomm = comm;
if (lmp->kokkos) comm = new CommTiledKokkos(lmp,oldcomm);
else comm = new CommTiled(lmp,oldcomm);
delete oldcomm;
} else error->all(FLERR,"Illegal comm_style command");
}
/* ---------------------------------------------------------------------- */
void Input::compute()
{
modify->add_compute(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::compute_modify()
{
modify->modify_compute(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::dielectric()
{
if (narg != 1) error->all(FLERR,"Illegal dielectric command");
force->dielectric = utils::numeric(FLERR,arg[0],false,lmp);
}
/* ---------------------------------------------------------------------- */
void Input::dihedral_coeff()
{
if (domain->box_exist == 0)
error->all(FLERR,"Dihedral_coeff command before simulation box is defined");
if (force->dihedral == nullptr)
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],1);
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 = utils::inumeric(FLERR,arg[0],false,lmp);
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);
}
/* ---------------------------------------------------------------------- */
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 == nullptr)
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],1);
if (force->improper) force->improper->settings(narg-1,&arg[1]);
}
/* ---------------------------------------------------------------------- */
void Input::kspace_modify()
{
if (force->kspace == nullptr)
error->all(FLERR,"KSpace style has not yet been set");
force->kspace->modify_params(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::kspace_style()
{
force->create_kspace(arg[0],1);
if (force->kspace) force->kspace->settings(narg-1,&arg[1]);
}
/* ---------------------------------------------------------------------- */
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(FLERR,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,1);
}
/* ---------------------------------------------------------------------- */
void Input::molecule()
{
atom->add_molecule(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=1,newton_bond=1;
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 (domain->box_exist && (newton_bond != force->newton_bond))
error->all(FLERR,"Newton bond change after simulation box is defined");
force->newton_bond = newton_bond;
if (newton_pair || newton_bond) force->newton = 1;
else force->newton = 0;
}
/* ---------------------------------------------------------------------- */
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");
// same checks for packages existing as in LAMMPS::post_create()
// since can be invoked here by package command in input script
if (strcmp(arg[0],"gpu") == 0) {
if (!modify->check_package("GPU"))
error->all(FLERR,"Package gpu command without GPU package installed");
std::string fixcmd = "package_gpu all GPU";
for (int i = 1; i < narg; i++) fixcmd += std::string(" ") + arg[i];
modify->add_fix(fixcmd);
} else if (strcmp(arg[0],"kokkos") == 0) {
if (lmp->kokkos == nullptr || lmp->kokkos->kokkos_exists == 0)
error->all(FLERR,
"Package kokkos command without KOKKOS package enabled");
lmp->kokkos->accelerator(narg-1,&arg[1]);
} else if (strcmp(arg[0],"omp") == 0) {
if (!modify->check_package("OMP"))
error->all(FLERR,
"Package omp command without USER-OMP package installed");
std::string fixcmd = "package_omp all OMP";
for (int i = 1; i < narg; i++) fixcmd += std::string(" ") + arg[i];
modify->add_fix(fixcmd);
} else if (strcmp(arg[0],"intel") == 0) {
if (!modify->check_package("INTEL"))
error->all(FLERR,
"Package intel command without USER-INTEL package installed");
std::string fixcmd = "package_intel all INTEL";
for (int i = 1; i < narg; i++) fixcmd += std::string(" ") + arg[i];
modify->add_fix(fixcmd);
} 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 == nullptr)
error->all(FLERR,"Pair_coeff command before pair_style is defined");
if ((narg < 2) || (force->pair->one_coeff && ((strcmp(arg[0],"*") != 0)
|| (strcmp(arg[1],"*") != 0))))
error->all(FLERR,"Incorrect args for pair coefficients");
force->pair->coeff(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::pair_modify()
{
if (force->pair == nullptr)
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) {
std::string style = arg[0];
int match = 0;
if (style == force->pair_style) match = 1;
if (!match && lmp->suffix_enable) {
if (lmp->suffixp)
if (style + "/" + lmp->suffixp == force->pair_style) match = 1;
if (lmp->suffix && !lmp->suffixp)
if (style + "/" + lmp->suffix == force->pair_style) match = 1;
if (lmp->suffix2)
if (style + "/" + lmp->suffix2 == force->pair_style) match = 1;
}
if (match) {
force->pair->settings(narg-1,&arg[1]);
return;
}
}
force->create_pair(arg[0],1);
if (force->pair) force->pair->settings(narg-1,&arg[1]);
}
/* ---------------------------------------------------------------------- */
void Input::pair_write()
{
if (force->pair == nullptr)
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,1);
}
/* ---------------------------------------------------------------------- */
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;
force->set_special(narg,arg);
// if simulation box defined and saved values changed, redo special list
if (domain->box_exist && atom->molecular == 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) {
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) {
if (!lmp->suffix)
error->all(FLERR,"May only enable suffixes after defining one");
lmp->suffix_enable = 1;
} else {
lmp->suffix_enable = 1;
delete [] lmp->suffix;
delete [] lmp->suffix2;
lmp->suffix = lmp->suffix2 = nullptr;
if (strcmp(arg[0],"hybrid") == 0) {
if (narg != 3) error->all(FLERR,"Illegal suffix command");
lmp->suffix = utils::strdup(arg[1]);
lmp->suffix2 = utils::strdup(arg[2]);
} else {
if (narg != 1) error->all(FLERR,"Illegal suffix command");
lmp->suffix = utils::strdup(arg[0]);
}
}
}
/* ---------------------------------------------------------------------- */
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::timer_command()
{
timer->modify_params(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::timestep()
{
if (narg != 1) error->all(FLERR,"Illegal timestep command");
update->dt = utils::numeric(FLERR,arg[0],false,lmp);
update->dt_default = 0;
}
/* ---------------------------------------------------------------------- */
void Input::uncompute()
{
if (narg != 1) error->all(FLERR,"Illegal uncompute command");
modify->delete_compute(arg[0]);
}
/* ---------------------------------------------------------------------- */
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]);
}
/* ---------------------------------------------------------------------- */
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]);
}
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