tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

have internal fix/compute ids include the fix id for fix reaxff/species

Browse Source 
this allows using the fix multiple times
also remove code and warning that checks for multiple fix instances

# Conflicts:
#	src/REAXFF/fix_reaxff_species.cpp
This commit is contained in:
Axel Kohlmeyer
2021-12-23 11:36:28 -05:00
parent a85b310e1f
commit 5a2548a83d
1 changed files with 20 additions and 35 deletions
Download Patch File Download Diff File Expand all files Collapse all files

55
src/REAXFF/fix_reaxff_species.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -62,9 +61,9 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
MPI_Comm_size(world,&nprocs);
ntypes = atom->ntypes;
nevery = atoi(arg[3]);
nrepeat = atoi(arg[4]);
global_freq = nfreq = atoi(arg[5]);
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
nrepeat = utils::inumeric(FLERR,arg[4],false,lmp);
global_freq = nfreq = utils::inumeric(FLERR,arg[5],false,lmp);
comm_forward = 4;
@ -95,15 +94,9 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
rene_flag = 1;
}
if (me == 0 && rene_flag) {
error->warning(FLERR,"Resetting reneighboring criteria for fix reaxff/species");
}
tmparg = nullptr;
memory->create(tmparg,4,4,"reaxff/species:tmparg");
strcpy(tmparg[0],arg[3]);
strcpy(tmparg[1],arg[4]);
strcpy(tmparg[2],arg[5]);
if (me == 0 && rene_flag)
error->warning(FLERR,"Resetting reneighboring criteria to 'delay {} every {} check no' "
"for fix reaxff/species",neighbor->delay, neighbor->every);
if (me == 0) {
char *suffix = strrchr(arg[6],'.');
@ -121,8 +114,7 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
} else fp = fopen(arg[6],"w");
if (!fp)
error->one(FLERR,fmt::format("Cannot open fix reaxff/species file {}: "
"{}",arg[6],utils::getsyserror()));
error->one(FLERR,"Cannot open fix reaxff/species file {}: {}",arg[6],utils::getsyserror());
}
x0 = nullptr;
@ -169,9 +161,9 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
// set BO cutoff
if (strcmp(arg[iarg],"cutoff") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix reaxff/species command");
itype = atoi(arg[iarg+1]);
jtype = atoi(arg[iarg+2]);
bo_cut = atof(arg[iarg+3]);
itype = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
jtype = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
bo_cut = utils::numeric(FLERR,arg[iarg+3],false,lmp);
if (itype > ntypes || jtype > ntypes)
error->all(FLERR,"Illegal fix reaxff/species command");
if (itype <= 0 || jtype <= 0)
@ -201,7 +193,7 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"position") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix reaxff/species command");
posflag = 1;
posfreq = atoi(arg[iarg+1]);
posfreq = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (posfreq < nfreq || (posfreq%nfreq != 0))
error->all(FLERR,"Illegal fix reaxff/species command");
@ -259,8 +251,8 @@ FixReaxFFSpecies::~FixReaxFFSpecies()
if (me == 0) fclose(fp);
if (me == 0 && posflag && multipos_opened) fclose(pos);
modify->delete_compute("SPECATOM");
modify->delete_fix("SPECBOND");
modify->delete_compute(fmt::format("SPECATOM_{}",id));
modify->delete_fix(fmt::format("SPECBOND_{}",id));
}
/* ---------------------------------------------------------------------- */
@ -300,22 +292,16 @@ void FixReaxFFSpecies::init()
if (nvalid != update->ntimestep)
nvalid = update->ntimestep+nfreq;
// check if this fix has been called twice
int count = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"reaxff/species") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one fix reaxff/species");
if (!setupflag) {
// create a compute to store properties
modify->add_compute("SPECATOM all SPEC/ATOM q x y z vx vy vz abo01 abo02 abo03 abo04 "
"abo05 abo06 abo07 abo08 abo09 abo10 abo11 abo12 abo13 abo14 "
"abo15 abo16 abo17 abo18 abo19 abo20 abo21 abo22 abo23 abo24");
modify->add_compute(fmt::format("SPECATOM_{} all SPEC/ATOM q x y z vx vy vz abo01 abo02 "
"abo03 abo04 abo05 abo06 abo07 abo08 abo09 abo10 abo11 "
"abo12 abo13 abo14 abo15 abo16 abo17 abo18 abo19 abo20 "
"abo21 abo22 abo23 abo24",id));
// create a fix to point to fix_ave_atom for averaging stored properties
auto fixcmd = fmt::format("SPECBOND all ave/atom {} {} {}",tmparg[0],tmparg[1],tmparg[2]);
for (int i = 1; i < 32; ++i) fixcmd += " c_SPECATOM[" + std::to_string(i) + "]";
auto fixcmd = fmt::format("SPECBOND_{} all ave/atom {} {} {}",id,nevery,nrepeat,nfreq);
for (int i = 1; i < 32; ++i) fixcmd += fmt::format(" c_SPECATOM_{}[{}]",id,i);
f_SPECBOND = (FixAveAtom *) modify->add_fix(fixcmd);
setupflag = 1;
}
@ -683,8 +669,7 @@ void FixReaxFFSpecies::OpenPos()
char *ptr = strchr(filepos,'*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filepos,ntimestep,ptr+1);
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",filepos,ntimestep,ptr+1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);