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modify fix STORE/PERATOM and callers to allow ghost comm

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This commit is contained in:
Steve Plimpton
2023-03-13 17:00:54 -06:00
parent b6756c0319
commit 3815c0ef76
18 changed files with 140 additions and 69 deletions
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6
src/AMOEBA/pair_amoeba.cpp
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@ -861,7 +861,7 @@ void PairAmoeba::init_style()
Fix *myfix;
if (first_flag) {
id_pole = utils::strdup("AMOEBA_pole");
myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 13",id_pole,group->names[0]));
myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM 13 0 0 1",id_pole,group->names[0]));
fixpole = dynamic_cast<FixStorePeratom *>(myfix);
}
@ -873,12 +873,12 @@ void PairAmoeba::init_style()
if (first_flag && use_pred) {
id_udalt = utils::strdup("AMOEBA_udalt");
myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 {} 3",
myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM {} 3 0 1",
id_udalt, group->names[0], maxualt));
fixudalt = dynamic_cast<FixStorePeratom *>(myfix);
id_upalt = utils::strdup("AMOEBA_upalt");
myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 {} 3",
myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM {} 3 0 1",
id_upalt, group->names[0], maxualt));
fixupalt = dynamic_cast<FixStorePeratom *>(myfix);
}

2
src/CORESHELL/compute_temp_cs.cpp
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@ -68,7 +68,7 @@ ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) :
id_fix = utils::strdup(id + std::string("_COMPUTE_STORE"));
fix = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 0 1", id_fix, group->names[igroup])));
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 0", id_fix, group->names[igroup])));
// set fix store values = 0 for now
// fill them in via setup() once Comm::borders() has been called

2
src/EXTRA-COMPUTE/compute_hma.cpp
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@ -91,7 +91,7 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) :
id_fix = utils::strdup(std::string(id)+"_COMPUTE_STORE");
fix = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 3", id_fix, group->names[igroup])));
modify->add_fix(fmt::format("{} {} STORE/PERATOM 3 0 0 1", id_fix, group->names[igroup])));
// calculate xu,yu,zu for fix store array
// skip if reset from restart file

18
src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp
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@ -17,7 +17,7 @@
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix_property_atom.h"
#include "fix_store_peratom.h"
#include "force.h"
#include "memory.h"
#include "modify.h"
@ -59,7 +59,7 @@ void BondHarmonicRestrain::compute(int eflag, int vflag)
ev_init(eflag, vflag);
double **x = atom->x;
double **x0 = (double **) atom->extract("d2_BOND_RESTRAIN_X0");
double **x0 = initial->astore;
double **f = atom->f;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
@ -162,12 +162,12 @@ void BondHarmonicRestrain::init_style()
if (natoms < 0) {
// create internal fix to store initial positions
initial = dynamic_cast<FixPropertyAtom *>(
modify->add_fix("BOND_RESTRAIN_X0 all property/atom d2_BOND_RESTRAIN_X0 3 ghost yes"));
initial = dynamic_cast<FixStorePeratom *>(
modify->add_fix("BOND_RESTRAIN_X0 all STORE/PERATOM 3 0 1 1"));
if (!initial) error->all(FLERR, "Failure to create internal per-atom storage");
natoms = atom->natoms;
double *const *const x0 = (double **) atom->extract("d2_BOND_RESTRAIN_X0");
double **x0 = initial->astore;
const double *const *const x = atom->x;
for (int i = 0; i < atom->nlocal; ++i)
for (int j = 0; j < 3; ++j) x0[i][j] = x[i][j];
@ -176,10 +176,10 @@ void BondHarmonicRestrain::init_style()
// after a restart, natoms is set but initial is a null pointer.
// we add the fix, but do not initialize it. It will pull the data from the restart.
if (!initial) {
initial = dynamic_cast<FixPropertyAtom *>(
modify->add_fix("BOND_RESTRAIN_X0 all property/atom d2_BOND_RESTRAIN_X0 3 ghost yes"));
initial = dynamic_cast<FixStorePeratom *>(
modify->add_fix("BOND_RESTRAIN_X0 all STORE/PERATOM 3 0 1 1"));
if (!initial) error->all(FLERR, "Failure to create internal per-atom storage");
}
}
@ -230,7 +230,7 @@ void BondHarmonicRestrain::write_data(FILE *fp)
double BondHarmonicRestrain::single(int type, double rsq, int i, int j, double &fforce)
{
double **x0 = (double **) atom->extract("d2_BOND_RESTRAIN_X0");
double **x0 = initial->astore;
double delx = x0[i][0] - x0[j][0];
double dely = x0[i][1] - x0[j][1];

2
src/EXTRA-MOLECULE/bond_harmonic_restrain.h
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@ -41,7 +41,7 @@ class BondHarmonicRestrain : public Bond {
protected:
double *k;
bigint natoms;
class FixPropertyAtom *initial;
class FixStorePeratom *initial;
virtual void allocate();
};

4
src/FEP/fix_adapt_fep.cpp
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@ -212,7 +212,7 @@ void FixAdaptFEP::post_constructor()
if (diamflag) {
id_fix_diam = utils::strdup(id + std::string("_FIX_STORE_DIAM"));
fix_diam = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 1", id_fix_diam,group->names[igroup])));
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 1", id_fix_diam,group->names[igroup])));
if (fix_diam->restart_reset) fix_diam->restart_reset = 0;
else {
double *vec = fix_diam->vstore;
@ -230,7 +230,7 @@ void FixAdaptFEP::post_constructor()
if (chgflag) {
id_fix_chg = utils::strdup(id + std::string("_FIX_STORE_CHG"));
fix_chg = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 1",id_fix_chg,group->names[igroup])));
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 1",id_fix_chg,group->names[igroup])));
if (fix_chg->restart_reset) fix_chg->restart_reset = 0;
else {
double *vec = fix_chg->vstore;

2
src/REPLICA/tad.cpp
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@ -135,7 +135,7 @@ void TAD::command(int narg, char **arg)
// create FixStorePeratom object to store revert state
fix_revert = dynamic_cast<FixStorePeratom *>(modify->add_fix("tad_revert all STORE/PERATOM 0 7"));
fix_revert = dynamic_cast<FixStorePeratom *>(modify->add_fix("tad_revert all STORE/PERATOM 7 0 0 0"));
// create Finish for timing output

2
src/VTK/dump_vtk.cpp
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@ -2365,7 +2365,7 @@ int DumpVTK::modify_param(int narg, char **arg)
std::string threshid = fmt::format("{}{}_DUMP_STORE",id,nthreshlast);
thresh_fixID[nthreshlast] = utils::strdup(threshid);
threshid += fmt::format(" {} STORE/PERATOM 1 1", group->names[igroup]);
threshid += fmt::format(" {} STORE/PERATOM 1 0 0 1", group->names[igroup]);
thresh_fix[nthreshlast] = dynamic_cast<FixStorePeratom *>(modify->add_fix(threshid));
thresh_last[nthreshlast] = nthreshlast;

2
src/balance.cpp
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@ -515,7 +515,7 @@ void Balance::weight_storage(char *prefix)
fixstore = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(cmd));
if (!fixstore)
fixstore = dynamic_cast<FixStorePeratom *>(modify->add_fix(cmd + " all STORE/PERATOM 0 1"));
fixstore = dynamic_cast<FixStorePeratom *>(modify->add_fix(cmd + " all STORE/PERATOM 1 0 0 0"));
// do not carry weights with atoms during normal atom migration

2
src/compute_chunk_atom.cpp
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@ -572,7 +572,7 @@ void ComputeChunkAtom::init()
if ((idsflag == ONCE || lockcount) && !fixstore) {
id_fix = utils::strdup(id + std::string("_COMPUTE_STORE"));
fixstore = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 1", id_fix, group->names[igroup])));
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 1", id_fix, group->names[igroup])));
}
if ((idsflag != ONCE && !lockcount) && fixstore) {

2
src/compute_displace_atom.cpp
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@ -75,7 +75,7 @@ ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) :
id_fix = utils::strdup(std::string(id) + "_COMPUTE_STORE");
fix = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 3", id_fix, group->names[igroup])));
modify->add_fix(fmt::format("{} {} STORE/PERATOM 3 0 0 1", id_fix, group->names[igroup])));
// calculate xu,yu,zu for fix store array
// skip if reset from restart file

2
src/compute_msd.cpp
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@ -64,7 +64,7 @@ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, a
id_fix = utils::strdup(id + std::string("_COMPUTE_STORE"));
fix = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 3", id_fix, group->names[igroup])));
modify->add_fix(fmt::format("{} {} STORE/PERATOM 3 0 0 1", id_fix, group->names[igroup])));
// calculate xu,yu,zu for fix store array
// skip if reset from restart file

2
src/compute_vacf.cpp
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@ -40,7 +40,7 @@ ComputeVACF::ComputeVACF(LAMMPS *lmp, int narg, char **arg) :
id_fix = utils::strdup(id + std::string("_COMPUTE_STORE"));
fix = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 3", id_fix, group->names[igroup])));
modify->add_fix(fmt::format("{} {} STORE/PERATOM 3 0 0 1", id_fix, group->names[igroup])));
// store current velocities in fix store array
// skip if reset from restart file

2
src/dump_custom.cpp
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@ -2013,7 +2013,7 @@ int DumpCustom::modify_param(int narg, char **arg)
std::string threshid = fmt::format("{}{}_DUMP_STORE",id,nthreshlast);
thresh_fixID[nthreshlast] = utils::strdup(threshid);
threshid += fmt::format(" {} STORE/PERATOM 1 1", group->names[igroup]);
threshid += fmt::format(" {} STORE/PERATOM 1 0 0 1", group->names[igroup]);
thresh_fix[nthreshlast] = dynamic_cast<FixStorePeratom *>(modify->add_fix(threshid));
thresh_last[nthreshlast] = nthreshlast;

4
src/fix_adapt.cpp
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@ -279,7 +279,7 @@ void FixAdapt::post_constructor()
if (diamflag && atom->radius_flag) {
id_fix_diam = utils::strdup(id + std::string("_FIX_STORE_DIAM"));
fix_diam = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 1", id_fix_diam,group->names[igroup])));
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 1", id_fix_diam,group->names[igroup])));
if (fix_diam->restart_reset) fix_diam->restart_reset = 0;
else {
double *vec = fix_diam->vstore;
@ -297,7 +297,7 @@ void FixAdapt::post_constructor()
if (chgflag && atom->q_flag) {
id_fix_chg = utils::strdup(id + std::string("_FIX_STORE_CHG"));
fix_chg = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 1",id_fix_chg,group->names[igroup])));
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 1",id_fix_chg,group->names[igroup])));
if (fix_chg->restart_reset) fix_chg->restart_reset = 0;
else {
double *vec = fix_chg->vstore;

145
src/fix_store_peratom.cpp
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@ -22,50 +22,57 @@
using namespace LAMMPS_NS;
using namespace FixConst;
// INTERNAL fix for storing/communicating per-atom values
// syntax: id group style n1 n2 gflag rflag
// N1 = 1, N2 = 0 is per-atom vector, single value per atom
// N1 > 1, N2 = 0 is per-atom array, N1 values per atom
// N1 > 0, N2 > 0 is per-atom tensor, N1xN2 array per atom
// gflag = 0/1, no/yes communicate per-atom values with ghost atoms
// rflag = 0/1, no/yes store per-atom values in restart file
/* ---------------------------------------------------------------------- */
FixStorePeratom::FixStorePeratom(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), vstore(nullptr), astore(nullptr)
{
if (narg != 5 && narg != 6)
if (narg != 8)
error->all(FLERR, "Illegal fix STORE/PERATOM command: number of args");
// syntax: id group style 0/1 n1 n2 (n3), last arg optional
// 0/1 flag = not-store or store peratom values in restart file
// N2 = 1 and no n3 is vector, N2 > 1 and no n3 is array, N3 = tensor
// nvalues = # of peratom values, N = 1 is vector, N > 1 is array
disable = 0;
vecflag = arrayflag = tensorflag = 0;
restart_peratom = utils::inumeric(FLERR, arg[3], false, lmp);
n2 = utils::inumeric(FLERR, arg[4], false, lmp);
if (narg == 6)
n3 = utils::inumeric(FLERR, arg[5], false, lmp);
else
n3 = 1;
if (restart_peratom < 0 || restart_peratom > 1)
error->all(FLERR, "Illegal fix STORE/PERATOM restart flag: {}", restart_peratom);
if (n2 <= 0 || n3 <= 0)
error->all(FLERR, "Illegal fix STORE/PERATOM dimension args: must be >0: {} {}", n2, n3);
if (n2 == 1 && narg == 5)
vecflag = 1;
else if (narg == 5)
arrayflag = 1;
else
tensorflag = 1;
nvalues = n2 * n3;
n1 = utils::inumeric(FLERR, arg[4], false, lmp);
n2 = utils::inumeric(FLERR, arg[5], false, lmp);
ghostflag = utils::inumeric(FLERR, arg[6], false, lmp);
restartflag = utils::inumeric(FLERR, arg[7], false, lmp);
vecflag = arrayflag = tensorflag = 0;
if (n1 == 1 && n2 == 0) vecflag = 1;
else if (n1 > 1 && n2 == 0) arrayflag = 1;
else if (n1 > 0 && n2 > 0) tensorflag = 1;
else error->all(FLERR, "Illegal fix STORE/PERATOM dimension args: {} {}", n1, n2);
if (restartflag < 0 || restartflag > 1)
error->all(FLERR, "Illegal fix STORE/PERATOM restart flag: {}", restartflag);
if (ghostflag < 0 || ghostflag > 1)
error->all(FLERR, "Illegal fix STORE/PERATOM ghost flag: {}", ghostflag);
if (vecflag || arrayflag) nvalues = n1;
else nvalues = n1 * n2;
nbytes = nvalues * sizeof(double);
if (ghostflag) comm_border = nvalues;
maxexchange = nvalues;
// allocate data structs and register with Atom class
vstore = nullptr;
astore = nullptr;
tstore = nullptr;
// allocate data structs and register with Atom class
FixStorePeratom::grow_arrays(atom->nmax);
atom->add_callback(Atom::GROW);
if (restart_peratom) atom->add_callback(Atom::RESTART);
if (restartflag) atom->add_callback(Atom::RESTART);
if (ghostflag) atom->add_callback(Atom::BORDER);
// zero the storage
@ -74,13 +81,12 @@ FixStorePeratom::FixStorePeratom(LAMMPS *lmp, int narg, char **arg) :
for (int i = 0; i < nlocal; i++) vstore[i] = 0.0;
} else if (arrayflag) {
for (int i = 0; i < nlocal; i++)
for (int j = 0; j < n2; j++) astore[i][j] = 0.0;
for (int j = 0; j < n1; j++) astore[i][j] = 0.0;
} else if (tensorflag) {
for (int i = 0; i < nlocal; i++)
for (int j = 0; j < n2; j++)
for (int k = 0; k < n3; k++) tstore[i][j][k] = 0.0;
for (int j = 0; j < n1; j++)
for (int k = 0; k < n2; k++) tstore[i][j][k] = 0.0;
}
maxexchange = nvalues;
}
/* ---------------------------------------------------------------------- */
@ -90,7 +96,8 @@ FixStorePeratom::~FixStorePeratom()
// unregister callbacks to this fix from Atom class
atom->delete_callback(id, Atom::GROW);
if (restart_peratom) atom->delete_callback(id, Atom::RESTART);
if (restartflag) atom->delete_callback(id, Atom::RESTART);
if (ghostflag) atom->delete_callback(id, Atom::BORDER);
memory->destroy(vstore);
memory->destroy(astore);
@ -114,9 +121,9 @@ void FixStorePeratom::grow_arrays(int nmax)
if (vecflag)
memory->grow(vstore, nmax, "store:vstore");
else if (arrayflag)
memory->grow(astore, nmax, n2, "store:astore");
memory->grow(astore, nmax, n1, "store:astore");
else if (tensorflag)
memory->grow(tstore, nmax, n2, n3, "store:tstore");
memory->grow(tstore, nmax, n1, n2, "store:tstore");
}
/* ----------------------------------------------------------------------
@ -136,6 +143,62 @@ void FixStorePeratom::copy_arrays(int i, int j, int /*delflag*/)
}
}
/* ----------------------------------------------------------------------
pack values for border communication at re-neighboring
------------------------------------------------------------------------- */
int FixStorePeratom::pack_border(int n, int *list, double *buf)
{
int i, j, k, ncol;
int m = 0;
if (vecflag) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = vstore[j];
}
} else if (arrayflag) {
for (i = 0; i < n; i++) {
j = list[i];
for (k = 0; k < nvalues; k++)
buf[m++] = astore[j][k];
}
} else if (tensorflag) {
for (i = 0; i < n; i++) {
j = list[i];
memcpy(&buf[m], &tstore[j][0][0], nbytes);
m += nvalues;
}
}
return m;
}
/* ----------------------------------------------------------------------
unpack values for border communication at re-neighboring
------------------------------------------------------------------------- */
int FixStorePeratom::unpack_border(int n, int first, double *buf)
{
int i, k, last, ncol;
int m = 0;
last = first + n;
if (vecflag) {
for (i = first; i < last; i++)
vstore[i] = buf[m++];
} else if (arrayflag) {
for (i = first; i < last; i++)
for (k = 0; k < nvalues; k++)
astore[i][k] = buf[m++];
} else if (tensorflag) {
for (i = first; i < last; i++) {
memcpy(&tstore[i][0][0], &buf[m], nbytes);
m += nvalues;
}
}
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
@ -147,7 +210,8 @@ int FixStorePeratom::pack_exchange(int i, double *buf)
if (vecflag) {
buf[0] = vstore[i];
} else if (arrayflag) {
for (int m = 0; m < nvalues; m++) buf[m] = astore[i][m];
for (int m = 0; m < nvalues; m++)
buf[m] = astore[i][m];
} else if (tensorflag) {
memcpy(buf, &tstore[i][0][0], nbytes);
}
@ -166,7 +230,8 @@ int FixStorePeratom::unpack_exchange(int nlocal, double *buf)
if (vecflag) {
vstore[nlocal] = buf[0];
} else if (arrayflag) {
for (int m = 0; m < nvalues; m++) astore[nlocal][m] = buf[m];
for (int m = 0; m < nvalues; m++)
astore[nlocal][m] = buf[m];
} else if (tensorflag) {
memcpy(&tstore[nlocal][0][0], buf, nbytes);
}
@ -191,7 +256,8 @@ int FixStorePeratom::pack_restart(int i, double *buf)
if (vecflag) {
buf[1] = vstore[i];
} else if (arrayflag) {
for (int m = 0; m < nvalues; m++) buf[m + 1] = astore[i][m];
for (int m = 0; m < nvalues; m++)
buf[m + 1] = astore[i][m];
} else if (tensorflag) {
memcpy(&buf[1], &tstore[i][0][0], nbytes);
}
@ -219,7 +285,8 @@ void FixStorePeratom::unpack_restart(int nlocal, int nth)
if (vecflag) {
vstore[nlocal] = extra[nlocal][m];
} else if (arrayflag) {
for (int i = 0; i < nvalues; i++) astore[nlocal][i] = extra[nlocal][m++];
for (int i = 0; i < nvalues; i++)
astore[nlocal][i] = extra[nlocal][m++];
} else if (tensorflag) {
memcpy(&tstore[nlocal][0][0], &extra[nlocal][m], nbytes);
}
@ -251,5 +318,5 @@ int FixStorePeratom::size_restart(int /*nlocal*/)
double FixStorePeratom::memory_usage()
{
return (double) atom->nmax * n2 * n3 * sizeof(double);
return (double) atom->nmax * nvalues * sizeof(double);
}

8
src/fix_store_peratom.h
View File

@ -37,6 +37,8 @@ class FixStorePeratom : public Fix {
void grow_arrays(int) override;
void copy_arrays(int, int, int) override;
int pack_border(int, int *, double *) override;
int unpack_border(int, int, double *) override;
int pack_exchange(int, double *) override;
int unpack_exchange(int, double *) override;
int pack_restart(int, double *) override;
@ -50,8 +52,10 @@ class FixStorePeratom : public Fix {
int vecflag; // 1 if ncol=1
int arrayflag; // 1 if a 2d array (vector per atom)
int tensorflag; // 1 if a 3d array (array per atom)
int n2, n3; // size of 3d dims of per-atom data struct
int ghostflag; // 0/1 to communicate values with ghost atoms
int restartflag; // 0/1 to store values in restart files
int n1, n2; // size of 3d dims of per-atom data struct
int nvalues; // number of per-atom values
int nbytes; // number of per-atom bytes
};

2
src/variable.cpp
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@ -5028,7 +5028,7 @@ VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) :
id_fix = utils::strdup(std::string(name) + "_VARIABLE_STORE");
fixstore = dynamic_cast<FixStorePeratom *>(
modify->add_fix(std::string(id_fix) + " all STORE/PERATOM 0 1"));
modify->add_fix(std::string(id_fix) + " all STORE/PERATOM 1 0 0 0"));
buffer = new char[CHUNK*MAXLINE];
}
}