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

T_initial_set array is only required during reading of the mesh

Browse Source
This commit is contained in:
Axel Kohlmeyer
2020-07-30 10:36:03 -04:00
parent 6a90a2affe
commit 4a28a708b9
4 changed files with 70 additions and 21 deletions
Download Patch File Download Diff File Expand all files Collapse all files

16
src/MISC/fix_ttm.cpp
View File

@ -42,7 +42,7 @@ using namespace FixConst;
FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
random(NULL), fp(NULL), T_initial_set(NULL), nsum(NULL), nsum_all(NULL),
random(NULL), fp(NULL), nsum(NULL), nsum_all(NULL),
gfactor1(NULL), gfactor2(NULL), ratio(NULL), flangevin(NULL),
T_electron(NULL), T_electron_old(NULL), sum_vsq(NULL), sum_mass_vsq(NULL),
sum_vsq_all(NULL), sum_mass_vsq_all(NULL), net_energy_transfer(NULL),
@ -116,7 +116,6 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
memory->create(nsum,nxnodes,nynodes,nznodes,"ttm:nsum");
memory->create(nsum_all,nxnodes,nynodes,nznodes,"ttm:nsum_all");
memory->create(T_initial_set,nxnodes,nynodes,nznodes,"ttm:T_initial_set");
memory->create(sum_vsq,nxnodes,nynodes,nznodes,"ttm:sum_vsq");
memory->create(sum_mass_vsq,nxnodes,nynodes,nznodes,"ttm:sum_mass_vsq");
memory->create(sum_vsq_all,nxnodes,nynodes,nznodes,"ttm:sum_vsq_all");
@ -162,7 +161,6 @@ FixTTM::~FixTTM()
memory->destroy(nsum);
memory->destroy(nsum_all);
memory->destroy(T_initial_set);
memory->destroy(sum_vsq);
memory->destroy(sum_mass_vsq);
memory->destroy(sum_vsq_all);
@ -217,9 +215,9 @@ void FixTTM::init()
void FixTTM::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
if (utils::strmatch(update->integrate_style,"^verlet")) {
post_force_setup(vflag);
else {
} else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa_setup(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
@ -327,6 +325,8 @@ void FixTTM::reset_dt()
void FixTTM::read_initial_electron_temperatures(const char *filename)
{
int ***T_initial_set;
memory->create(T_initial_set,nxnodes,nynodes,nznodes,"ttm:T_initial_set");
memset(&T_initial_set[0][0][0],0,total_nnodes*sizeof(int));
std::string name = utils::get_potential_file_path(filename);
@ -371,6 +371,8 @@ void FixTTM::read_initial_electron_temperatures(const char *filename)
for (int iznode = 0; iznode < nznodes; iznode++)
if (T_initial_set[ixnode][iynode][iznode] == 0)
error->one(FLERR,"Initial temperatures not all set in fix ttm");
memory->destroy(T_initial_set);
}
/* ---------------------------------------------------------------------- */
@ -571,7 +573,7 @@ void FixTTM::grow_arrays(int ngrow)
}
/* ----------------------------------------------------------------------
return the energy of the electronic subsystem or the net_energy transfer
return the energy of the electronic subsystem or the net_energy transfer
between the subsystems
------------------------------------------------------------------------- */
@ -593,7 +595,7 @@ double FixTTM::compute_vector(int n)
electronic_density*del_vol;
transfer_energy +=
net_energy_transfer_all[ixnode][iynode][iznode]*update->dt;
}
}
if (n == 0) return e_energy;
if (n == 1) return transfer_energy;

1
src/MISC/fix_ttm.h
View File

@ -55,7 +55,6 @@ class FixTTM : public Fix {
FILE *fp;
int nxnodes,nynodes,nznodes;
bigint total_nnodes;
int ***T_initial_set;
int ***nsum, ***nsum_all;
double *gfactor1,*gfactor2,*ratio,**flangevin;
double ***T_electron,***T_electron_old;

73
src/USER-MISC/fix_ttm_mod.cpp
View File

@ -67,7 +67,7 @@ static const char cite_fix_ttm_mod[] =
FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
random(NULL), fp(NULL), T_initial_set(NULL), nsum(NULL), nsum_all(NULL),
random(NULL), fp(NULL), nsum(NULL), nsum_all(NULL),
gfactor1(NULL), gfactor2(NULL), ratio(NULL), flangevin(NULL),
T_electron(NULL), T_electron_old(NULL), sum_vsq(NULL), sum_mass_vsq(NULL),
sum_vsq_all(NULL), sum_mass_vsq_all(NULL), net_energy_transfer(NULL),
@ -139,7 +139,6 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
total_nnodes = nxnodes*nynodes*nznodes;
memory->create(nsum,nxnodes,nynodes,nznodes,"ttm/mod:nsum");
memory->create(nsum_all,nxnodes,nynodes,nznodes,"ttm/mod:nsum_all");
memory->create(T_initial_set,nxnodes,nynodes,nznodes,"ttm/mod:T_initial_set");
memory->create(sum_vsq,nxnodes,nynodes,nznodes,"ttm/mod:sum_vsq");
memory->create(sum_mass_vsq,nxnodes,nynodes,nznodes,"ttm/mod:sum_mass_vsq");
memory->create(sum_vsq_all,nxnodes,nynodes,nznodes,"ttm/mod:sum_vsq_all");
@ -154,15 +153,20 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
"ttm/mod:net_energy_transfer_all");
flangevin = NULL;
grow_arrays(atom->nmax);
// zero out the flangevin array
for (int i = 0; i < atom->nmax; i++) {
flangevin[i][0] = 0;
flangevin[i][1] = 0;
flangevin[i][2] = 0;
}
atom->add_callback(0);
atom->add_callback(1);
// set initial electron temperatures from user input file
if (comm->me == 0) read_initial_electron_temperatures(arg[13]);
MPI_Bcast(&T_electron[0][0][0],total_nnodes,MPI_DOUBLE,0,world);
}
@ -173,11 +177,12 @@ FixTTMMod::~FixTTMMod()
{
if (fp) fclose(fp);
delete random;
delete [] gfactor1;
delete [] gfactor2;
memory->destroy(nsum);
memory->destroy(nsum_all);
memory->destroy(T_initial_set);
memory->destroy(sum_vsq);
memory->destroy(sum_mass_vsq);
memory->destroy(sum_vsq_all);
@ -211,16 +216,20 @@ void FixTTMMod::init()
error->all(FLERR,"Cannot use non-periodic boundares with fix ttm/mod");
if (domain->triclinic)
error->all(FLERR,"Cannot use fix ttm/mod with triclinic box");
// set force prefactors
for (int i = 1; i <= atom->ntypes; i++) {
gfactor1[i] = - gamma_p / force->ftm2v;
gfactor2[i] =
sqrt(24.0*force->boltz*gamma_p/update->dt/force->mvv2e) / force->ftm2v;
}
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
net_energy_transfer_all[ixnode][iynode][iznode] = 0;
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
@ -229,7 +238,7 @@ void FixTTMMod::init()
void FixTTMMod::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet")) {
if (utils::strmatch(update->integrate_style,"^verlet")) {
post_force_setup(vflag);
} else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
@ -248,13 +257,17 @@ void FixTTMMod::post_force(int /*vflag*/)
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double dx = domain->xprd/nxnodes;
double dy = domain->yprd/nynodes;
double dz = domain->zprd/nynodes;
double gamma1,gamma2;
// apply damping and thermostat to all atoms in fix group
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
double xscale = (x[i][0] - domain->boxlo[0])/domain->xprd;
double yscale = (x[i][1] - domain->boxlo[1])/domain->yprd;
double zscale = (x[i][2] - domain->boxlo[2])/domain->zprd;
@ -267,9 +280,12 @@ void FixTTMMod::post_force(int /*vflag*/)
while (ixnode < 0) ixnode += nxnodes;
while (iynode < 0) iynode += nynodes;
while (iznode < 0) iznode += nznodes;
if (T_electron[ixnode][iynode][iznode] < 0)
error->all(FLERR,"Electronic temperature dropped below zero");
double tsqrt = sqrt(T_electron[ixnode][iynode][iznode]);
gamma1 = gfactor1[type[i]];
double vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (vsq > v_0_sq) gamma1 *= (gamma_p + gamma_s)/gamma_p;
@ -338,7 +354,9 @@ void FixTTMMod::post_force_setup(int /*vflag*/)
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// apply langevin forces that have been stored from previous run
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
f[i][0] += flangevin[i][0];
@ -526,6 +544,8 @@ void FixTTMMod::read_parameters(const char *filename)
void FixTTMMod::read_initial_electron_temperatures(const char *filename)
{
int ***T_initial_set;
memory->create(T_initial_set,nxnodes,nynodes,nznodes,"ttm/mod:T_initial_set");
memset(&T_initial_set[0][0][0],0,total_nnodes*sizeof(int));
std::string name = utils::get_potential_file_path(filename);
@ -570,6 +590,8 @@ void FixTTMMod::read_initial_electron_temperatures(const char *filename)
for (int iznode = 0; iznode < nznodes; iznode++)
if (T_initial_set[ixnode][iynode][iznode] == 0)
error->one(FLERR,"Initial temperatures not all set in fix ttm");
memory->destroy(T_initial_set);
}
/* ---------------------------------------------------------------------- */
@ -606,6 +628,7 @@ void FixTTMMod::end_of_step()
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (movsur == 1){
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
@ -621,6 +644,7 @@ void FixTTMMod::end_of_step()
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
net_energy_transfer[ixnode][iynode][iznode] = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
double xscale = (x[i][0] - domain->boxlo[0])/domain->xprd;
@ -642,9 +666,11 @@ void FixTTMMod::end_of_step()
flangevin[i][2]*v[i][2]);
}
}
MPI_Allreduce(&net_energy_transfer[0][0][0],
&net_energy_transfer_all[0][0][0],
total_nnodes,MPI_DOUBLE,MPI_SUM,world);
double dx = domain->xprd/nxnodes;
double dy = domain->yprd/nynodes;
double dz = domain->zprd/nznodes;
@ -666,6 +692,7 @@ void FixTTMMod::end_of_step()
}
// num_inner_timesteps = # of inner steps (thermal solves)
// required this MD step to maintain a stable explicit solve
int num_inner_timesteps = 1;
double inner_dt = update->dt;
double stability_criterion = 0.0;
@ -775,9 +802,13 @@ void FixTTMMod::end_of_step()
(el_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz));
} while (stability_criterion < 0.0);
// output nodal temperatures for current timestep
if ((nfileevery) && !(update->ntimestep % nfileevery)) {
// compute atomic Ta for each grid point
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++) {
@ -788,6 +819,7 @@ void FixTTMMod::end_of_step()
sum_vsq_all[ixnode][iynode][iznode] = 0.0;
sum_mass_vsq_all[ixnode][iynode][iznode] = 0.0;
}
double massone;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
@ -810,36 +842,39 @@ void FixTTMMod::end_of_step()
sum_vsq[ixnode][iynode][iznode] += vsq;
sum_mass_vsq[ixnode][iynode][iznode] += massone*vsq;
}
MPI_Allreduce(&nsum[0][0][0],&nsum_all[0][0][0],total_nnodes,
MPI_INT,MPI_SUM,world);
MPI_Allreduce(&sum_vsq[0][0][0],&sum_vsq_all[0][0][0],total_nnodes,
MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&sum_mass_vsq[0][0][0],&sum_mass_vsq_all[0][0][0],
total_nnodes,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&t_surface_l,&surface_l,
1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&t_surface_l,&surface_l,1,MPI_INT,MPI_MIN,world);
if (comm->me == 0) {
fmt::print(fp,"{}",update->ntimestep);
double T_a;
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++) {
T_a = 0;
if (nsum_all[ixnode][iynode][iznode] > 0){
if (nsum_all[ixnode][iynode][iznode] > 0) {
T_a = sum_mass_vsq_all[ixnode][iynode][iznode]/
(3.0*force->boltz*nsum_all[ixnode][iynode][iznode]/force->mvv2e);
if (movsur == 1){
if (T_electron[ixnode][iynode][iznode]==0.0) T_electron[ixnode][iynode][iznode] = electron_temperature_min;
}
}
fprintf(fp," %f",T_a);
fmt::print(fp," {}",T_a);
}
fprintf(fp,"\t");
fputs("\t",fp);
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
fprintf(fp,"%f ",T_electron[ixnode][iynode][iznode]);
fprintf(fp,"\n");
fmt::print(fp," {}",T_electron[ixnode][iynode][iznode]);
fputs("\n",fp);
}
}
}
@ -872,10 +907,12 @@ double FixTTMMod::compute_vector(int n)
{
double e_energy = 0.0;
double transfer_energy = 0.0;
double dx = domain->xprd/nxnodes;
double dy = domain->yprd/nynodes;
double dz = domain->zprd/nznodes;
double del_vol = dx*dy*dz;
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++) {
@ -883,6 +920,7 @@ double FixTTMMod::compute_vector(int n)
transfer_energy +=
net_energy_transfer_all[ixnode][iynode][iznode]*update->dt;
}
if (n == 0) return e_energy;
if (n == 1) return transfer_energy;
return 0.0;
@ -896,17 +934,21 @@ void FixTTMMod::write_restart(FILE *fp)
{
double *rlist;
memory->create(rlist,nxnodes*nynodes*nznodes+1,"ttm/mod:rlist");
int n = 0;
rlist[n++] = seed;
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
rlist[n++] = T_electron[ixnode][iynode][iznode];
rlist[n++] = T_electron[ixnode][iynode][iznode];
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(rlist,sizeof(double),n,fp);
}
memory->destroy(rlist);
}
@ -918,12 +960,16 @@ void FixTTMMod::restart(char *buf)
{
int n = 0;
double *rlist = (double *) buf;
// the seed must be changed from the initial seed
seed = static_cast<int> (0.5*rlist[n++]);
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
T_electron[ixnode][iynode][iznode] = rlist[n++];
delete random;
random = new RanMars(lmp,seed+comm->me);
}
@ -948,10 +994,13 @@ int FixTTMMod::pack_restart(int i, double *buf)
void FixTTMMod::unpack_restart(int nlocal, int nth)
{
double **extra = atom->extra;
// skip to Nth set of extra values
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
flangevin[nlocal][0] = extra[nlocal][m++];
flangevin[nlocal][1] = extra[nlocal][m++];
flangevin[nlocal][2] = extra[nlocal][m++];

1
src/USER-MISC/fix_ttm_mod.h
View File

@ -60,7 +60,6 @@ class FixTTMMod : public Fix {
FILE *fp;
int nxnodes,nynodes,nznodes;
bigint total_nnodes;
int ***T_initial_set;
int ***nsum, ***nsum_all;
double *gfactor1,*gfactor2,*ratio,**flangevin;
double ***T_electron,***T_electron_old,***T_electron_first;