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incorporate changes to fix alchemy from @sjplimp

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This commit is contained in:
Axel Kohlmeyer
2023-03-06 12:14:57 -05:00
parent 646ef15d83
commit 4f420f8454
2 changed files with 62 additions and 33 deletions
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93
src/REPLICA/fix_alchemy.cpp
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@ -109,7 +109,51 @@ int FixAlchemy::setmask()
return mask;
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
check consistency of owned atom count and ordering
compare each pair of replica procs
checked before each exchange of atom coords or forces
to ensure the replicas have not become out of sync
---------------------------------------------------------------------- */
void FixAlchemy::check_consistency_atoms()
{
// check that owned atom count is same for each pair of replica procs
const int nlocal = atom->nlocal;
int my_nlocal[2] = {0, 0};
int all_nlocal[2] = {0, 0};
my_nlocal[universe->iworld] = nlocal;
MPI_Allreduce(my_nlocal, all_nlocal, 2, MPI_INT, MPI_SUM, samerank);
int fail = (all_nlocal[0] == all_nlocal[1]) ? 0 : 1;
int allfail = 0;
MPI_Allreduce(&fail, &allfail, 1, MPI_INT, MPI_MAX, universe->uworld);
if (allfail) error->universe_all(FLERR, "Fix alchemy local atom count is inconsistent");
// check that owned atom ordering is same for each pair of replica procs
// re-use communication buffer for positions and forces
tagint *tagbuf = (tagint *) commbuf;
tagint *tag = atom->tag;
if (universe->iworld == 0) {
for (int i = 0; i < nlocal; ++i) tagbuf[i] = tag[i];
}
MPI_Bcast(tagbuf, nlocal, MPI_LMP_TAGINT, 0, samerank);
fail = allfail = 0;
if (universe->iworld > 0) {
for (int i = 0; i < nlocal; ++i)
if (tag[i] != tagbuf[i]) fail = 1;
}
MPI_Allreduce(&fail, &allfail, 1, MPI_INT, MPI_MAX, universe->uworld);
if (allfail) error->universe_all(FLERR, "Fix alchemy local atom ordering is inconsistent");
}
/* ----------------------------------------------------------------------
force simulation box size and shape to be identical for 2 replicas
invoked by post_integrate() after integration may have changed box
---------------------------------------------------------------------- */
static void synchronize_box(Domain *domain, MPI_Comm samerank)
{
@ -180,36 +224,9 @@ void FixAlchemy::setup(int vflag)
void FixAlchemy::post_integrate()
{
// re-check that we have the same domain decomposition on all ranks
const int nlocal = atom->nlocal;
int my_nlocal[2] = {0, 0};
int all_nlocal[2] = {0, 0};
my_nlocal[universe->iworld] = nlocal;
MPI_Allreduce(my_nlocal, all_nlocal, 2, MPI_INT, MPI_SUM, samerank);
int fail = (all_nlocal[0] == all_nlocal[1]) ? 0 : 1;
int allfail = 0;
MPI_Allreduce(&fail, &allfail, 1, MPI_INT, MPI_MAX, universe->uworld);
if (allfail)
error->universe_all(FLERR,
"Number of atoms and domain decomposition must be the same on "
"all partitions");
// check owned atom count and ordering between replicas
// check that we have the same atom order on all ranks
// re-use communication buffer for positions and forces
tagint *tagbuf = (tagint *) commbuf;
tagint *tag = atom->tag;
if (universe->iworld == 0) {
for (int i = 0; i < nlocal; ++i) tagbuf[i] = tag[i];
}
MPI_Bcast(tagbuf, nlocal, MPI_LMP_TAGINT, 0, samerank);
fail = allfail = 0;
if (universe->iworld > 0) {
for (int i = 0; i < nlocal; ++i)
if (tag[i] != tagbuf[i]) fail = 1;
}
MPI_Allreduce(&fail, &allfail, 1, MPI_INT, MPI_MAX, universe->uworld);
if (allfail) error->universe_all(FLERR, "Atoms must have the same order on all partitions");
check_consistency_atoms();
// synchronize atom positions
@ -225,15 +242,25 @@ void FixAlchemy::post_integrate()
void FixAlchemy::post_force(int /*vflag*/)
{
// grow commbuf if necessary
if (3 * atom->nmax > nmax) {
nmax = 3 * atom->nmax;
memory->grow(commbuf, sizeof(double) * atom->nmax, "alchemy:commbuf");
}
const int nall = 3 * atom->nlocal;
double *f = &atom->f[0][0];
// check owned atom count and ordering between replicas
check_consistency_atoms();
// evaluate lambda variable
lambda = input->variable->compute_equal(ivar);
// sum forces multiplied by lambda across 2 replicas
const int nall = 3 * atom->nlocal;
double *f = &atom->f[0][0];
for (int i = 0; i < nall; ++i) commbuf[i] = f[i] * lambda;
MPI_Allreduce(commbuf, f, nall, MPI_DOUBLE, MPI_SUM, samerank);
@ -253,7 +280,7 @@ void FixAlchemy::post_force(int /*vflag*/)
MPI_Allreduce(commbuf, pressure, 6, MPI_DOUBLE, MPI_SUM, universe->uworld);
press->addstep(update->ntimestep + 1);
// print progress info
// print progress info to universe screen/logfile
if (universe->me == 0) {
double delta = update->ntimestep - update->beginstep;