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Merge branch 'develop' into type-labels

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This commit is contained in:
Jacob Gissinger
2022-03-23 01:08:35 -04:00
committed by GitHub
parent 44522221ad 3e7de83e6e
commit e13a70ad2f
3143 changed files with 258487 additions and 425132 deletions
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118
src/input.cpp
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@ -27,9 +27,11 @@
#include "dihedral.h"
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "force.h"
#include "group.h"
#include "improper.h"
#include "integrate.h"
#include "kspace.h"
#include "label_map.h"
#include "memory.h"
@ -49,13 +51,21 @@
#include <cstring>
#include <cerrno>
#include <cctype>
#include <sys/stat.h>
using namespace LAMMPS_NS;
#define DELTALINE 256
#define DELTA 4
/* ----------------------------------------------------------------------
one instance per command in style_command.h
------------------------------------------------------------------------- */
template <typename T> static Command *command_creator(LAMMPS *lmp)
{
return new T(lmp);
}
/* ---------------------------------------------------------------------- */
/** \class LAMMPS_NS::Input
@ -819,9 +829,21 @@ int Input::execute_command()
if (flag) return 0;
// invoke commands added via style_command.h
// try suffixed version first
if (command_map->find(command) != command_map->end()) {
CommandCreator &command_creator = (*command_map)[command];
std::string mycmd = command;
if (lmp->suffix_enable) {
mycmd = command + std::string("/") + lmp->suffix;
if (command_map->find(mycmd) == command_map->end()) {
if (lmp->suffix2) {
mycmd = command + std::string("/") + lmp->suffix2;
if (command_map->find(mycmd) == command_map->end())
mycmd = command;
} else mycmd = command;
}
}
if (command_map->find(mycmd) != command_map->end()) {
CommandCreator &command_creator = (*command_map)[mycmd];
Command *cmd = command_creator(lmp);
cmd->command(narg,arg);
delete cmd;
@ -833,16 +855,6 @@ int Input::execute_command()
return -1;
}
/* ----------------------------------------------------------------------
one instance per command in style_command.h
------------------------------------------------------------------------- */
template <typename T>
Command *Input::command_creator(LAMMPS *lmp)
{
return new T(lmp);
}
/* ---------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
@ -1001,10 +1013,15 @@ void Input::include()
if (nfile == maxfile)
error->one(FLERR,"Too many nested levels of input scripts");
infile = fopen(arg[0],"r");
// expand variables
int n = strlen(arg[0]) + 1;
if (n > maxline) reallocate(line,maxline,n);
strcpy(line,arg[0]);
substitute(line,work,maxline,maxwork,0);
infile = fopen(line,"r");
if (infile == nullptr)
error->one(FLERR,"Cannot open input script {}: {}",
arg[0], utils::getsyserror());
error->one(FLERR,"Cannot open input script {}: {}", line, utils::getsyserror());
infiles[nfile++] = infile;
}
@ -1214,7 +1231,10 @@ void Input::shell()
if (narg < 2) error->all(FLERR,"Illegal shell mkdir command");
if (me == 0) {
for (int i = 1; i < narg; i++) {
if (platform::mkdir(arg[i]) < 0)
rv = (platform::mkdir(arg[i]) < 0) ? errno : 0;
MPI_Reduce(&rv,&err,1,MPI_INT,MPI_MAX,0,world);
errno = err;
if (err != 0)
error->warning(FLERR, "Shell command 'mkdir {}' failed with error '{}'",
arg[i],utils::getsyserror());
}
@ -1222,18 +1242,30 @@ void Input::shell()
} else if (strcmp(arg[0],"mv") == 0) {
if (narg != 3) error->all(FLERR,"Illegal shell mv command");
if (me == 0) {
if (rename(arg[1],arg[2]) < 0) {
error->warning(FLERR, "Shell command 'mv {} {}' failed with error '{}'",
arg[1],arg[2],utils::getsyserror());
if (platform::path_is_directory(arg[2])) {
if (system(fmt::format("mv {} {}", arg[1], arg[2]).c_str()))
error->warning(FLERR,"Shell command 'mv {} {}' returned with non-zero status", arg[1], arg[2]);
} else {
if (rename(arg[1],arg[2]) < 0) {
error->warning(FLERR, "Shell command 'mv {} {}' failed with error '{}'",
arg[1],arg[2],utils::getsyserror());
}
}
}
} 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++) {
int i = 1;
bool warn = true;
if (strcmp(arg[i], "-f") == 0) {
warn = false;
++i;
}
for (;i < narg; i++) {
if (platform::unlink(arg[i]) < 0)
error->warning(FLERR, "Shell command 'rm {}' failed with error '{}'",
arg[i], utils::getsyserror());
if (warn)
error->warning(FLERR, "Shell command 'rm {}' failed with error '{}'",
arg[i], utils::getsyserror());
}
}
} else if (strcmp(arg[0],"rmdir") == 0) {
@ -1257,23 +1289,20 @@ void Input::shell()
error->warning(FLERR, "Shell command 'putenv {}' failed with error '{}'",
arg[i], utils::getsyserror());
}
// use work string to concat args back into one string separated by spaces
// invoke string in shell via system()
// concat arguments and 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);
if (me == 0) {
std::string cmd = arg[0];
for (int i = 1; i < narg; i++) {
cmd += " ";
cmd += arg[i];
}
strcpy(work,arg[0]);
for (int i = 1; i < narg; i++) {
strcat(work," ");
strcat(work,arg[i]);
if (system(cmd.c_str()) != 0)
error->warning(FLERR,"Shell command {} returned with non-zero status", cmd);
}
if (me == 0)
if (system(work) != 0)
error->warning(FLERR,"Shell command returned with non-zero status");
}
}
@ -1929,8 +1958,25 @@ void Input::timer_command()
void Input::timestep()
{
if (narg != 1) error->all(FLERR,"Illegal timestep command");
update->update_time();
update->dt = utils::numeric(FLERR,arg[0],false,lmp);
update->dt_default = 0;
// timestep command can be invoked between runs or by run every
// calls to other classes that need to know timestep size changed
// similar logic is in FixDtReset::end_of_step()
// only need to do this if a run has already occurred
if (update->first_update == 0) return;
int respaflag = 0;
if (utils::strmatch(update->integrate_style, "^respa")) respaflag = 1;
if (respaflag) update->integrate->reset_dt();
if (force->pair) force->pair->reset_dt();
for (auto &ifix : modify->get_fix_list()) ifix->reset_dt();
output->reset_dt();
}
/* ---------------------------------------------------------------------- */