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This commit is contained in:
Axel Kohlmeyer
2023-05-17 17:38:16 -04:00
parent 79f3eb6a4d
commit 5d66dc6659
1 changed files with 58 additions and 65 deletions
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123
src/REPLICA/fix_pimd_langevin.cpp
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@ -47,7 +47,8 @@
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
using MathConst::MY_PI;
using MathConst::THIRD;
enum { NMPIMD };
enum { PHYSICAL, NORMAL };
@ -63,7 +64,7 @@ enum { SINGLE_PROC, MULTI_PROC };
/* ---------------------------------------------------------------------- */
FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), random(nullptr), c_pe(nullptr), c_press(nullptr)
Fix(lmp, narg, arg), random(nullptr), c_pe(nullptr), c_press(nullptr)
{
restart_global = 1;
time_integrate = 1;
@ -114,18 +115,18 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
int seed = -1;
for (int i = 0; i < 6; i++)
{
for (int i = 0; i < 6; i++) {
p_flag[i] = 0;
p_target[i] = 0.0;
}
for (int i = 3; i < narg - 1; i += 2) {
if (strcmp(arg[i], "method") == 0) {
if (strcmp(arg[i + 1], "nmpimd") == 0)method = NMPIMD;
else error->universe_all(FLERR, "Unknown method parameter for fix pimd/langevin");
}
else if (strcmp(arg[i], "integrator") == 0) {
if (strcmp(arg[i + 1], "nmpimd") == 0)
method = NMPIMD;
else
error->universe_all(FLERR, "Unknown method parameter for fix pimd/langevin");
} else if (strcmp(arg[i], "integrator") == 0) {
if (strcmp(arg[i + 1], "obabo") == 0)
integrator = OBABO;
else if (strcmp(arg[i + 1], "baoab") == 0)
@ -157,11 +158,11 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
"Unknown ensemble parameter for fix pimd/langevin. Only nve and nvt "
"ensembles are supported!");
} else if (strcmp(arg[i], "fmass") == 0) {
fmass = utils::numeric(FLERR, arg[i+1], false, lmp);
fmass = utils::numeric(FLERR, arg[i + 1], false, lmp);
if (fmass < 0.0 || fmass > np)
error->universe_all(FLERR, "Invalid fmass value for fix pimd/langevin");
} else if (strcmp(arg[i], "sp") == 0) {
sp = utils::numeric(FLERR, arg[i+1], false, lmp);
sp = utils::numeric(FLERR, arg[i + 1], false, lmp);
if (sp < 0.0) error->universe_all(FLERR, "Invalid sp value for fix pimd/nvt");
} else if (strcmp(arg[i], "fmmode") == 0) {
if (strcmp(arg[i + 1], "physical") == 0)
@ -204,29 +205,29 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
error->universe_all(FLERR, "Unknown barostat parameter for fix pimd/langevin");
} else if (strcmp(arg[i], "iso") == 0) {
pstyle = ISO;
Pext = utils::numeric(FLERR, arg[i+1], false, lmp);
Pext = utils::numeric(FLERR, arg[i + 1], false, lmp);
p_target[0] = p_target[1] = p_target[2] = Pext;
pdim = 3;
} else if (strcmp(arg[i], "aniso") == 0) {
pstyle = ANISO;
p_flag[0] = p_flag[1] = p_flag[2] = 1;
Pext = utils::numeric(FLERR, arg[i+1], false, lmp);
Pext = utils::numeric(FLERR, arg[i + 1], false, lmp);
p_target[0] = p_target[1] = p_target[2] = Pext;
pdim = 3;
} else if (strcmp(arg[i], "x") == 0) {
pstyle = ANISO;
p_flag[0] = 1;
p_target[0] = utils::numeric(FLERR, arg[i+1], false, lmp);
p_target[0] = utils::numeric(FLERR, arg[i + 1], false, lmp);
pdim++;
} else if (strcmp(arg[i], "y") == 0) {
pstyle = ANISO;
p_flag[1] = 1;
p_target[1] = utils::numeric(FLERR, arg[i+1], false, lmp);
p_target[1] = utils::numeric(FLERR, arg[i + 1], false, lmp);
pdim++;
} else if (strcmp(arg[i], "z") == 0) {
pstyle = ANISO;
p_flag[2] = 1;
p_target[2] = utils::numeric(FLERR, arg[i+1], false, lmp);
p_target[2] = utils::numeric(FLERR, arg[i + 1], false, lmp);
pdim++;
} else if (strcmp(arg[i], "taup") == 0) {
tau_p = utils::numeric(FLERR, arg[i + 1], false, lmp);
@ -245,12 +246,12 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
global_freq = 1;
vector_flag = 1;
if (!pstat_flag) size_vector = 10;
if (!pstat_flag)
size_vector = 10;
else if (pstat_flag) {
if (pstyle == ISO){
size_vector = 15;
}
else if (pstyle == ANISO){
if (pstyle == ISO) {
size_vector = 15;
} else if (pstyle == ANISO) {
size_vector = 17;
}
}
@ -271,7 +272,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
fixedpoint[0] = 0.5 * (domain->boxlo[0] + domain->boxhi[0]);
fixedpoint[1] = 0.5 * (domain->boxlo[1] + domain->boxhi[1]);
fixedpoint[2] = 0.5 * (domain->boxlo[2] + domain->boxhi[2]);
if (pstat_flag) { p_hydro = (p_target[0]+p_target[1]+p_target[2])/pdim; }
if (pstat_flag) { p_hydro = (p_target[0] + p_target[1] + p_target[2]) / pdim; }
// initialize Marsaglia RNG with processor-unique seed
@ -293,8 +294,10 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
nreplica = universe->nworlds;
ireplica = universe->iworld;
if (nreplica == 1) mapflag = 0;
else mapflag = 1;
if (nreplica == 1)
mapflag = 0;
else
mapflag = 1;
int *iroots = new int[nreplica];
MPI_Group uworldgroup, rootgroup;
@ -426,7 +429,8 @@ void FixPIMDLangevin::init()
fbond = _fbond * force->mvv2e;
if ((universe->me == 0) && (universe->uscreen))
fprintf(universe->uscreen, "fix pimd/langevin -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
fprintf(universe->uscreen,
"fix pimd/langevin -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
if (integrator == OBABO) {
dtf = 0.5 * update->dt * force->ftm2v;
@ -724,13 +728,10 @@ void FixPIMDLangevin::qc_step()
if (barostat == BZP) {
for (int i = 0; i < nlocal; i++) {
for (int j = 0; j < 3; j++) {
if (p_flag[j])
{
if (p_flag[j]) {
x[i][j] = expq[j] * x[i][j] + (expq[j] - expp[j]) / 2. / vw[j] * v[i][j];
v[i][j] = expp[j] * v[i][j];
}
else
{
} else {
x[i][j] += dtv * v[i][j];
}
}
@ -844,10 +845,9 @@ void FixPIMDLangevin::press_v_step()
} else if (pstyle == ANISO) {
compute_stress_tensor();
for (int ii = 0; ii < 3; ii++) {
if (p_flag[ii])
{
vw[ii] +=
dtv * (volume * np * (stress_tensor[ii] - p_hydro) / force->nktv2p + Vcoeff / beta_np) / W;
if (p_flag[ii]) {
vw[ii] += dtv *
(volume * np * (stress_tensor[ii] - p_hydro) / force->nktv2p + Vcoeff / beta_np) / W;
if (universe->iworld == 0) {
double dvw_proc = 0.0, dvw = 0.0;
for (int i = 0; i < nlocal; i++) {
@ -875,10 +875,8 @@ void FixPIMDLangevin::press_o_step()
MPI_Bcast(&vw[0], 1, MPI_DOUBLE, 0, universe->uworld);
} else if (pstyle == ANISO) {
if (universe->me == 0) {
for (int ii=0; ii<3; ii++)
{
if (p_flag[ii])
{
for (int ii = 0; ii < 3; ii++) {
if (p_flag[ii]) {
r1 = random->gaussian();
vw[ii] = c1 * vw[ii] + c2 * sqrt(1.0 / W / beta_np) * r1;
}
@ -1155,9 +1153,9 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr)
m++;
}
MPI_Allgather(&m, 1, MPI_INT, counts, 1, MPI_INT, universe->uworld);
for (i = 0; i < nreplica; i++) { counts[i] *= 3; }
for (i = 0; i < nreplica; i++) counts[i] *= 3;
displacements[0] = 0;
for (i = 0; i < nreplica - 1; i++) { displacements[i + 1] = displacements[i] + counts[i]; }
for (i = 0; i < nreplica - 1; i++) displacements[i + 1] = displacements[i] + counts[i];
MPI_Allgatherv(bufsorted[0], 3 * m, MPI_DOUBLE, bufsortedall[0], counts, displacements,
MPI_DOUBLE, universe->uworld);
} else if (cmode == MULTI_PROC) {
@ -1171,11 +1169,11 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr)
}
MPI_Gather(&m, 1, MPI_INT, counts, 1, MPI_INT, 0, world);
displacements[0] = 0;
for (i = 0; i < nprocs - 1; i++) { displacements[i + 1] = displacements[i] + counts[i]; }
for (i = 0; i < nprocs - 1; i++) displacements[i + 1] = displacements[i] + counts[i];
MPI_Gatherv(tagsend, m, MPI_LMP_TAGINT, tagsendall, counts, displacements, MPI_LMP_TAGINT, 0,
world);
for (i = 0; i < nprocs; i++) { counts[i] *= 3; }
for (i = 0; i < nprocs - 1; i++) { displacements[i + 1] = displacements[i] + counts[i]; }
for (i = 0; i < nprocs; i++) counts[i] *= 3;
for (i = 0; i < nprocs - 1; i++) displacements[i + 1] = displacements[i] + counts[i];
MPI_Gatherv(bufsend[0], 3 * m, MPI_DOUBLE, bufsendall[0], counts, displacements, MPI_DOUBLE, 0,
world);
for (int iplan = 0; iplan < sizeplan; iplan++) {
@ -1203,15 +1201,15 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr)
/* ---------------------------------------------------------------------- */
void FixPIMDLangevin::remove_com_motion(){
if(universe->iworld == 0)
{
double **v = atom->v;
int *mask = atom->mask;
void FixPIMDLangevin::remove_com_motion()
{
if (universe->iworld == 0) {
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (dynamic) masstotal = group->mass(igroup);
if (dynamic) masstotal = group->mass(igroup);
double vcm[3];
group->vcm(igroup,masstotal,vcm);
group->vcm(igroup, masstotal, vcm);
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
v[i][0] -= vcm[0];
@ -1372,7 +1370,8 @@ void FixPIMDLangevin::compute_t_vir()
void FixPIMDLangevin::compute_p_prim()
{
double inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
p_prim = atom->natoms * np * force->boltz * temp * inv_volume - 1.0 / 1.5 * inv_volume * total_spring_energy;
p_prim = atom->natoms * np * force->boltz * temp * inv_volume -
1.0 / 1.5 * inv_volume * total_spring_energy;
p_prim *= force->nktv2p;
}
@ -1415,14 +1414,14 @@ void FixPIMDLangevin::write_restart(FILE *fp)
int nsize = size_restart_global();
double *list;
memory->create(list,nsize,"FixPIMDLangevin:list");
memory->create(list, nsize, "FixPIMDLangevin:list");
pack_restart_data(list);
if (comm->me == 0) {
int size = nsize * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),nsize,fp);
fwrite(&size, sizeof(int), 1, fp);
fwrite(list, sizeof(double), nsize, fp);
}
memory->destroy(list);
@ -1441,7 +1440,7 @@ int FixPIMDLangevin::size_restart_global()
int FixPIMDLangevin::pack_restart_data(double *list)
{
int n = 0;
for (int i=0; i<6; i++) { list[n++] = vw[i]; }
for (int i = 0; i < 6; i++) list[n++] = vw[i];
return n;
}
@ -1451,7 +1450,7 @@ void FixPIMDLangevin::restart(char *buf)
{
int n = 0;
auto list = (double *) buf;
for (int i=0; i<6; i++) { vw[i] = list[n++]; }
for (int i = 0; i < 6; i++) vw[i] = list[n++];
}
/* ---------------------------------------------------------------------- */
@ -1470,7 +1469,7 @@ double FixPIMDLangevin::compute_vector(int n)
if (n == 9) return p_cv;
if (pstat_flag) {
volume = domain->xprd * domain->yprd * domain->zprd;
volume = domain->xprd * domain->yprd * domain->zprd;
if (pstyle == ISO) {
if (n == 10) return vw[0];
if (barostat == BZP) {
@ -1478,21 +1477,15 @@ double FixPIMDLangevin::compute_vector(int n)
} else if (barostat == MTTK) {
if (n == 11) return 1.5 * W * vw[0] * vw[0];
}
if (n == 12) {
return np * Pext * volume / force->nktv2p;
}
if (n == 13) {
return -Vcoeff * np * kBT * log(volume);
}
if (n == 12) { return np * Pext * volume / force->nktv2p; }
if (n == 13) { return -Vcoeff * np * kBT * log(volume); }
if (n == 14) return totenthalpy;
} else if (pstyle == ANISO) {
if (n == 10) return vw[0];
if (n == 11) return vw[1];
if (n == 12) return vw[2];
if (n == 13) return 0.5 * W * (vw[0] * vw[0] + vw[1] * vw[1] + vw[2] * vw[2]);
if (n == 14) {
return np * Pext * volume / force->nktv2p;
}
if (n == 14) { return np * Pext * volume / force->nktv2p; }
if (n == 15) {
volume = domain->xprd * domain->yprd * domain->zprd;
return -Vcoeff * np * kBT * log(volume);