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Merge branch 'master' of https://github.com/lammps/lammps into lammps-master

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This commit is contained in:
Jacob Gissinger
2021-04-27 14:46:33 -04:00
parent e21c63192a 3455172f7d
commit 1e294111e7
4905 changed files with 257534 additions and 191333 deletions
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83
src/input.cpp
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@ -21,6 +21,7 @@
#include "comm.h"
#include "comm_brick.h"
#include "comm_tiled.h"
#include "command.h"
#include "compute.h"
#include "dihedral.h"
#include "domain.h"
@ -83,7 +84,7 @@ 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
:cpp:class:`Command`, is created, then its ``command()`` member
function executed, and finally the class instance is deleted.
\endverbatim
@ -107,6 +108,7 @@ Input::Input(LAMMPS *lmp, int argc, char **argv) : Pointers(lmp)
label_active = 0;
labelstr = nullptr;
jump_skip = 0;
utf8_warn = true;
if (me == 0) {
nfile = 1;
@ -422,6 +424,16 @@ void Input::parse()
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
@ -816,7 +828,9 @@ int Input::execute_command()
if (command_map->find(command) != command_map->end()) {
CommandCreator &command_creator = (*command_map)[command];
command_creator(lmp,narg,arg);
Command *cmd = command_creator(lmp);
cmd->command(narg,arg);
delete cmd;
return 0;
}
@ -830,10 +844,9 @@ int Input::execute_command()
------------------------------------------------------------------------- */
template <typename T>
void Input::command_creator(LAMMPS *lmp, int narg, char **arg)
Command *Input::command_creator(LAMMPS *lmp)
{
T cmd(lmp);
cmd.command(narg,arg);
return new T(lmp);
}
/* ---------------------------------------------------------------------- */
@ -912,7 +925,7 @@ void Input::ifthenelse()
char **commands = new char*[ncommands];
ncommands = 0;
for (int i = first; i <= last; i++) {
int n = strlen(arg[i]) + 1;
n = strlen(arg[i]) + 1;
if (n == 1) error->all(FLERR,"Illegal if command");
commands[ncommands] = new char[n];
strcpy(commands[ncommands],arg[i]);
@ -965,7 +978,7 @@ void Input::ifthenelse()
char **commands = new char*[ncommands];
ncommands = 0;
for (int i = first; i <= last; i++) {
int n = strlen(arg[i]) + 1;
n = strlen(arg[i]) + 1;
if (n == 1) error->all(FLERR,"Illegal if command");
commands[ncommands] = new char[n];
strcpy(commands[ncommands],arg[i]);
@ -1040,9 +1053,7 @@ void Input::jump()
if (narg == 2) {
label_active = 1;
if (labelstr) delete [] labelstr;
int n = strlen(arg[1]) + 1;
labelstr = new char[n];
strcpy(labelstr,arg[1]);
labelstr = utils::strdup(arg[1]);
}
}
@ -1103,22 +1114,20 @@ void Input::partition()
int ilo,ihi;
utils::bounds(FLERR,arg[1],1,universe->nworlds,ilo,ihi,error);
// copy original line to copy, since will use strtok() on it
// ptr = start of 4th word
// new command starts at the 3rd argument,
// which must not be another partition command
strcpy(copy,line);
char *ptr = strtok(copy," \t\n\r\f");
ptr = strtok(nullptr," \t\n\r\f");
ptr = strtok(nullptr," \t\n\r\f");
ptr += strlen(ptr) + 1;
ptr += strspn(ptr," \t\n\r\f");
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(ptr);
if (universe->iworld+1 >= ilo && universe->iworld+1 <= ihi) one(cmd);
} else {
if (universe->iworld+1 < ilo || universe->iworld+1 > ihi) one(ptr);
if (universe->iworld+1 < ilo || universe->iworld+1 > ihi) one(cmd);
}
}
@ -1281,9 +1290,18 @@ void Input::shell()
for (int i = 1; i < narg; i++) {
rv = 0;
#ifdef _WIN32
if (arg[i]) rv = _putenv(arg[i]);
if (arg[i]) rv = _putenv(utils::strdup(arg[i]));
#else
if (arg[i]) rv = putenv(arg[i]);
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);
@ -1761,6 +1779,10 @@ void Input::pair_coeff()
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");
int newflag0 = readtype(arg[0],Atom::ATOM);
int newflag1 = readtype(arg[1],Atom::ATOM);
@ -1808,7 +1830,10 @@ void Input::pair_style()
int match = 0;
if (style == force->pair_style) match = 1;
if (!match && lmp->suffix_enable) {
if (lmp->suffix)
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)
@ -1921,17 +1946,11 @@ void Input::suffix()
if (strcmp(arg[0],"hybrid") == 0) {
if (narg != 3) error->all(FLERR,"Illegal suffix command");
int n = strlen(arg[1]) + 1;
lmp->suffix = new char[n];
strcpy(lmp->suffix,arg[1]);
n = strlen(arg[2]) + 1;
lmp->suffix2 = new char[n];
strcpy(lmp->suffix2,arg[2]);
lmp->suffix = utils::strdup(arg[1]);
lmp->suffix2 = utils::strdup(arg[2]);
} else {
if (narg != 1) error->all(FLERR,"Illegal suffix command");
int n = strlen(arg[0]) + 1;
lmp->suffix = new char[n];
strcpy(lmp->suffix,arg[0]);
lmp->suffix = utils::strdup(arg[0]);
}
}
}