ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

add dump skip option

Browse Source
This commit is contained in:
Steve Plimpton
2022-07-27 17:13:46 -06:00
parent 48aa9cf7ba
commit f039c00442
6 changed files with 417 additions and 31 deletions
Download Patch File Download Diff File Expand all files Collapse all files

98
src/dump.cpp
View File

@ -20,11 +20,13 @@
#include "error.h"
#include "fix.h"
#include "group.h"
#include "input.h"
#include "irregular.h"
#include "memory.h"
#include "modify.h"
#include "output.h"
#include "update.h"
#include "variable.h"
#include <cstring>
@ -87,6 +89,9 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
delay_flag = 0;
write_header_flag = 1;
skipflag = 0;
skipvar = nullptr;
maxfiles = -1;
numfiles = 0;
fileidx = 0;
@ -165,6 +170,8 @@ Dump::~Dump()
delete[] refresh;
delete[] skipvar;
// format_column_user is deallocated by child classes that use it
memory->destroy(buf);
@ -298,6 +305,15 @@ void Dump::init()
else error->all(FLERR,"Dump could not find refresh compute ID");
}
// if skipflag, check skip variable
if (skipflag) {
skipindex = input->variable->find(skipvar);
if (skipindex < 0) error->all(FLERR,"Dump skip variable not found");
if (!input->variable->equalstyle(skipindex))
error->all(FLERR,"Variable for dump skip is invalid style");
}
// preallocation for PBC copies if requested
if (pbcflag && atom->nlocal > maxpbc) pbc_allocate();
@ -359,6 +375,15 @@ void Dump::write()
nme = count();
// if skip condition is defined and met, just return
// do it after count() b/c that invoked computes
// NOTE: for multifile, will have already opened file
if (skipflag) {
double value = input->variable->compute_equal(skipindex);
if (value != 0.0) return;
}
// ntotal = total # of dump lines in snapshot
// nmax = max # of dump lines on any proc
@ -1044,6 +1069,12 @@ void Dump::modify_params(int narg, char **arg)
append_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"balance") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (nprocs > 1)
balance_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"buffer") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
buffer_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
@ -1051,6 +1082,32 @@ void Dump::modify_params(int narg, char **arg)
error->all(FLERR,"Dump_modify buffer yes not allowed for this style");
iarg += 2;
} else if (strcmp(arg[iarg],"colname") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"default") == 0) {
for (auto item : keyword_user) item.clear();
iarg += 2;
} else {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump_modify command");
int icol = -1;
if (utils::is_integer(arg[iarg + 1])) {
icol = utils::inumeric(FLERR,arg[iarg + 1],false,lmp);
if (icol < 0) icol = keyword_user.size() + icol + 1;
icol--;
} else {
try {
icol = key2col.at(arg[iarg + 1]);
} catch (std::out_of_range &) {
icol = -1;
}
}
if ((icol < 0) || (icol >= (int)keyword_user.size()))
error->all(FLERR, "Incorrect dump_modify arguments: {} {} {}",
arg[iarg], arg[iarg+1], arg[iarg+2]);
keyword_user[icol] = arg[iarg+2];
iarg += 3;
}
} else if (strcmp(arg[iarg],"delay") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
delaystep = utils::bnumeric(FLERR,arg[iarg+1],false,lmp);
@ -1131,31 +1188,6 @@ void Dump::modify_params(int narg, char **arg)
flush_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"colname") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"default") == 0) {
for (auto item : keyword_user) item.clear();
iarg += 2;
} else {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump_modify command");
int icol = -1;
if (utils::is_integer(arg[iarg + 1])) {
icol = utils::inumeric(FLERR,arg[iarg + 1],false,lmp);
if (icol < 0) icol = keyword_user.size() + icol + 1;
icol--;
} else {
try {
icol = key2col.at(arg[iarg + 1]);
} catch (std::out_of_range &) {
icol = -1;
}
}
if ((icol < 0) || (icol >= (int)keyword_user.size()))
error->all(FLERR, "Incorrect dump_modify arguments: {} {} {}",
arg[iarg], arg[iarg+1], arg[iarg+2]);
keyword_user[icol] = arg[iarg+2];
iarg += 3;
}
} else if (strcmp(arg[iarg],"format") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
@ -1212,6 +1244,7 @@ void Dump::modify_params(int narg, char **arg)
fileidx = 0;
}
iarg += 2;
} else if (strcmp(arg[iarg],"nfile") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (!multiproc)
@ -1254,6 +1287,15 @@ void Dump::modify_params(int narg, char **arg)
pbcflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"skip") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
skipflag = 1;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
delete[] skipvar;
skipvar = utils::strdup(&arg[iarg+1][2]);
} else error->all(FLERR,"Illegal dump_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"sort") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"off") == 0) sort_flag = 0;
@ -1274,12 +1316,6 @@ void Dump::modify_params(int narg, char **arg)
}
iarg += 2;
} else if (strcmp(arg[iarg],"balance") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (nprocs > 1)
balance_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"time") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
time_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);