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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2844 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2009-06-03 20:33:16 +00:00
parent 482c0912d6
commit aef437dc39
2 changed files with 175 additions and 151 deletions
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307
src/fix_ttm.cpp
View File

@ -12,7 +12,8 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Paul Crozier (SNL)
Contributing authors: Paul Crozier (SNL)
Carolyn Phillips (University of Michigan)
------------------------------------------------------------------------- */
#include "mpi.h"
@ -45,6 +46,12 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
{
if (narg < 15) error->all("Illegal fix ttm command");
vector_flag = 1;
size_vector = 2;
scalar_vector_freq = 1;
extvector = 1;
nevery = 1;
int seed = atoi(arg[3]);
electronic_specific_heat = atof(arg[4]);
electronic_density = atof(arg[5]);
@ -109,45 +116,35 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
total_nnodes = nxnodes*nynodes*nznodes;
nsum = memory->create_3d_int_array(nxnodes,nynodes,nznodes,"ttm:nsum");
nsum_prime = memory->create_3d_int_array(nxnodes,nynodes,nznodes,
"ttm:nsum_prime");
nsum_all = memory->create_3d_int_array(nxnodes,nynodes,nznodes,
"ttm:nsum_all");
nsum_prime_all = memory->create_3d_int_array(nxnodes,nynodes,nznodes,
"ttm:nsum_prime_all");
"ttm:nsum_all");
T_initial_set = memory->create_3d_int_array(nxnodes,nynodes,nznodes,
"ttm:T_initial_set");
"ttm:T_initial_set");
sum_vsq = memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"ttm:sum_vsq");
sum_vsq_prime = memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"ttm:sum_vsq_prime");
"ttm:sum_vsq");
sum_mass_vsq =
memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"ttm:sum_mass_vsq");
sum_mass_vsq_prime =
memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"ttm:sum_mass_vsq_prime");
"ttm:sum_mass_vsq");
sum_vsq_all = memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"ttm:sum_vsq_all");
sum_vsq_prime_all =
memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"ttm:sum_vsq_prime_all");
"ttm:sum_vsq_all");
sum_mass_vsq_all =
memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"ttm:sum_mass_vsq_all");
sum_mass_vsq_prime_all =
memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"ttm:sum_mass_vsq_prime_all");
"ttm:sum_mass_vsq_all");
T_electron_old =
memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"ttm:T_electron_old");
"ttm:T_electron_old");
T_electron =
memory->create_3d_double_array(nxnodes,nynodes,nznodes,"ttm:T_electron");
T_a = memory->create_3d_double_array(nxnodes,nynodes,nznodes,"ttm:T_a");
T_a_prime = memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"ttm:T_a_prime");
g_s = memory->create_3d_double_array(nxnodes,nynodes,nznodes,"ttm:g_s");
g_p = memory->create_3d_double_array(nxnodes,nynodes,nznodes,"ttm:g_p");
net_energy_transfer =
memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"TTM:net_energy_transfer");
net_energy_transfer_all =
memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"TTM:net_energy_transfer_all");
flangevin = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
// set initial electron temperatures from user input file
@ -167,24 +164,17 @@ FixTTM::~FixTTM()
delete [] gfactor2;
memory->destroy_3d_int_array(nsum);
memory->destroy_3d_int_array(nsum_prime);
memory->destroy_3d_int_array(nsum_all);
memory->destroy_3d_int_array(nsum_prime_all);
memory->destroy_3d_int_array(T_initial_set);
memory->destroy_3d_double_array(sum_vsq);
memory->destroy_3d_double_array(sum_vsq_prime);
memory->destroy_3d_double_array(sum_mass_vsq);
memory->destroy_3d_double_array(sum_mass_vsq_prime);
memory->destroy_3d_double_array(sum_vsq_all);
memory->destroy_3d_double_array(sum_vsq_prime_all);
memory->destroy_3d_double_array(sum_mass_vsq_all);
memory->destroy_3d_double_array(sum_mass_vsq_prime_all);
memory->destroy_3d_double_array(T_electron_old);
memory->destroy_3d_double_array(T_electron);
memory->destroy_3d_double_array(T_a);
memory->destroy_3d_double_array(T_a_prime);
memory->destroy_3d_double_array(g_s);
memory->destroy_3d_double_array(g_p);
memory->destroy_2d_double_array(flangevin);
memory->destroy_3d_double_array(net_energy_transfer);
memory->destroy_3d_double_array(net_energy_transfer_all);
}
/* ---------------------------------------------------------------------- */
@ -194,6 +184,7 @@ int FixTTM::setmask()
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= END_OF_STEP;
return mask;
}
@ -216,6 +207,11 @@ void FixTTM::init()
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 (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
@ -237,8 +233,6 @@ void FixTTM::setup(int vflag)
void FixTTM::post_force(int vflag)
{
update_electron_temperatures();
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
@ -266,6 +260,9 @@ void FixTTM::post_force(int vflag)
while (iynode < 0) iynode += nynodes;
while (iznode < 0) iznode += nznodes;
if (T_electron[ixnode][iynode][iznode] < 0)
error->all("Electronic temperature dropped to below zero");
double tsqrt = sqrt(T_electron[ixnode][iynode][iznode]);
gamma1 = gfactor1[type[i]];
@ -273,9 +270,13 @@ void FixTTM::post_force(int vflag)
if (vsq > v_0_sq) gamma1 *= (gamma_p + gamma_s)/gamma_p;
gamma2 = gfactor2[type[i]] * tsqrt;
f[i][0] += gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
f[i][1] += gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
f[i][2] += gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
f[i][0] += flangevin[i][0];
f[i][1] += flangevin[i][1];
f[i][2] += flangevin[i][2];
}
}
}
@ -335,7 +336,7 @@ void FixTTM::read_initial_electron_temperatures()
/* ---------------------------------------------------------------------- */
void FixTTM::update_electron_temperatures()
void FixTTM::end_of_step()
{
double **x = atom->x;
double **v = atom->v;
@ -344,32 +345,14 @@ void FixTTM::update_electron_temperatures()
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double massone;
// compute atomic Ta, and Ta' (for high v atoms) 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++) {
nsum[ixnode][iynode][iznode] = 0;
nsum_prime[ixnode][iynode][iznode] = 0;
nsum_all[ixnode][iynode][iznode] = 0;
nsum_prime_all[ixnode][iynode][iznode] = 0;
sum_vsq[ixnode][iynode][iznode] = 0.0;
sum_vsq_prime[ixnode][iynode][iznode] = 0.0;
sum_mass_vsq[ixnode][iynode][iznode] = 0.0;
sum_mass_vsq_prime[ixnode][iynode][iznode] = 0.0;
sum_vsq_all[ixnode][iynode][iznode] = 0.0;
sum_vsq_prime_all[ixnode][iynode][iznode] = 0.0;
sum_mass_vsq_all[ixnode][iynode][iznode] = 0.0;
sum_mass_vsq_prime_all[ixnode][iynode][iznode] = 0.0;
}
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) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
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;
@ -382,65 +365,20 @@ void FixTTM::update_electron_temperatures()
while (ixnode < 0) ixnode += nxnodes;
while (iynode < 0) iynode += nynodes;
while (iznode < 0) iznode += nznodes;
double vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
nsum[ixnode][iynode][iznode] += 1;
sum_vsq[ixnode][iynode][iznode] += vsq;
sum_mass_vsq[ixnode][iynode][iznode] += massone*vsq;
if (vsq > v_0_sq) {
nsum_prime[ixnode][iynode][iznode] += 1;
sum_vsq_prime[ixnode][iynode][iznode] += vsq;
sum_mass_vsq_prime[ixnode][iynode][iznode] += massone*vsq;
}
net_energy_transfer[ixnode][iynode][iznode] +=
(flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
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;
double del_vol = dx*dy*dz;
MPI_Allreduce(&nsum[0][0][0],&nsum_all[0][0][0],total_nnodes,
MPI_INT,MPI_SUM,world);
MPI_Allreduce(&nsum_prime[0][0][0],&nsum_prime_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_vsq_prime[0][0][0],&sum_vsq_prime_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(&sum_mass_vsq_prime[0][0][0],&sum_mass_vsq_prime_all[0][0][0],
total_nnodes,MPI_DOUBLE,MPI_SUM,world);
double max_g_p = 0.0;
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++) {
if (nsum_all[ixnode][iynode][iznode] > 0) {
T_a[ixnode][iynode][iznode] =
sum_mass_vsq_all[ixnode][iynode][iznode]/
(3.0*force->boltz*nsum_all[ixnode][iynode][iznode]/force->mvv2e);
double g_p_tmp = force->mvv2e*gamma_p*sum_vsq_all[ixnode][iynode][iznode]/
T_a[ixnode][iynode][iznode]/del_vol;
max_g_p = MAX(max_g_p,g_p_tmp);
g_p[ixnode][iynode][iznode] = g_p_tmp;
} else {
T_a[ixnode][iynode][iznode] = 0;
g_p[ixnode][iynode][iznode] = 0;
}
if (nsum_prime_all[ixnode][iynode][iznode] > 0) {
T_a_prime[ixnode][iynode][iznode] =
sum_mass_vsq_prime_all[ixnode][iynode][iznode]/
(3.0*force->boltz*nsum_prime_all[ixnode][iynode][iznode] /
force->mvv2e);
g_s[ixnode][iynode][iznode] =
force->mvv2e*gamma_s*sum_vsq_prime_all[ixnode][iynode][iznode]/
T_a_prime[ixnode][iynode][iznode]/del_vol;
} else {
T_a_prime[ixnode][iynode][iznode] = 0;
g_s[ixnode][iynode][iznode] = 0;
}
}
// num_inner_timesteps = # of inner steps (thermal solves)
// required this MD step to maintain a stable explicit solve
@ -448,12 +386,10 @@ void FixTTM::update_electron_temperatures()
double inner_dt = update->dt;
double stability_criterion = 1.0 -
2.0*inner_dt/(electronic_specific_heat*electronic_density) *
(electronic_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz) +
0.5*max_g_p);
(electronic_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz));
if (stability_criterion < 0.0) {
inner_dt = 0.5*(electronic_specific_heat*electronic_density) /
(electronic_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz) +
0.5*max_g_p);
(electronic_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz));
num_inner_timesteps = static_cast<int>(update->dt/inner_dt) + 1;
inner_dt = update->dt/double(num_inner_timesteps);
if (num_inner_timesteps > 1000000)
@ -467,7 +403,7 @@ void FixTTM::update_electron_temperatures()
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
T_electron_old[ixnode][iynode][iznode] =
T_electron[ixnode][iynode][iznode];
T_electron[ixnode][iynode][iznode];
// compute new electron T profile
@ -487,33 +423,81 @@ void FixTTM::update_electron_temperatures()
if (left_ynode == -1) left_ynode = nynodes - 1;
if (left_znode == -1) left_znode = nznodes - 1;
T_electron[ixnode][iynode][iznode] =
T_electron_old[ixnode][iynode][iznode] +
inner_dt/(electronic_specific_heat*electronic_density) *
(electronic_thermal_conductivity *
((T_electron_old[right_xnode][iynode][iznode] +
T_electron_old[left_xnode][iynode][iznode] -
2*T_electron_old[ixnode][iynode][iznode])/dx/dx +
(T_electron_old[ixnode][right_ynode][iznode] +
T_electron_old[ixnode][left_ynode][iznode] -
2*T_electron_old[ixnode][iynode][iznode])/dy/dy +
(T_electron_old[ixnode][iynode][right_znode] +
T_electron_old[ixnode][iynode][left_znode] -
2*T_electron_old[ixnode][iynode][iznode])/dz/dz) +
g_p[ixnode][iynode][iznode] *
(T_a[ixnode][iynode][iznode] -
T_electron_old[ixnode][iynode][iznode]) +
g_s[ixnode][iynode][iznode]*T_a_prime[ixnode][iynode][iznode]);
T_electron_old[ixnode][iynode][iznode] +
inner_dt/(electronic_specific_heat*electronic_density) *
(electronic_thermal_conductivity *
((T_electron_old[right_xnode][iynode][iznode] +
T_electron_old[left_xnode][iynode][iznode] -
2*T_electron_old[ixnode][iynode][iznode])/dx/dx +
(T_electron_old[ixnode][right_ynode][iznode] +
T_electron_old[ixnode][left_ynode][iznode] -
2*T_electron_old[ixnode][iynode][iznode])/dy/dy +
(T_electron_old[ixnode][iynode][right_znode] +
T_electron_old[ixnode][iynode][left_znode] -
2*T_electron_old[ixnode][iynode][iznode])/dz/dz) -
(net_energy_transfer_all[ixnode][iynode][iznode])/del_vol);
}
}
// output nodal temperatures for current timestep
if (!(update->ntimestep % nfileevery) && (me == 0)) {
if ((nfileevery) && !(update->ntimestep % nfileevery) && (me == 0)) {
fprintf(fp,"%d ",update->ntimestep);
// 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++)
fprintf(fp,"%f ",T_a[ixnode][iynode][iznode]);
for (int iznode = 0; iznode < nznodes; iznode++) {
nsum[ixnode][iynode][iznode] = 0;
nsum_all[ixnode][iynode][iznode] = 0;
sum_vsq[ixnode][iynode][iznode] = 0.0;
sum_mass_vsq[ixnode][iynode][iznode] = 0.0;
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) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
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;
int ixnode = static_cast<int>(xscale*nxnodes);
int iynode = static_cast<int>(yscale*nynodes);
int iznode = static_cast<int>(zscale*nznodes);
while (ixnode > nxnodes-1) ixnode -= nxnodes;
while (iynode > nynodes-1) iynode -= nynodes;
while (iznode > nznodes-1) iznode -= nznodes;
while (ixnode < 0) ixnode += nxnodes;
while (iynode < 0) iynode += nynodes;
while (iznode < 0) iznode += nznodes;
double vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
nsum[ixnode][iynode][iznode] += 1;
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);
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)
T_a = sum_mass_vsq_all[ixnode][iynode][iznode]/
(3.0*force->boltz*nsum_all[ixnode][iynode][iznode]/force->mvv2e);
fprintf(fp,"%f ",T_a);
}
fprintf(fp,"\t");
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
@ -534,3 +518,42 @@ double FixTTM::memory_usage()
bytes += 14*total_nnodes * sizeof(double);
return bytes;
}
/* ---------------------------------------------------------------------- */
void FixTTM::grow_arrays(int ngrow)
{
flangevin = memory->grow_2d_double_array(flangevin,ngrow,3,"TTM:flangevin");
}
/* ----------------------------------------------------------------------
return the energy of the electronic subsystem or the net_energy transfer
between the subsystems
------------------------------------------------------------------------- */
double FixTTM::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++) {
e_energy +=
T_electron[ixnode][iynode][iznode]*electronic_specific_heat*
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;
return 0.0;
}

19
src/fix_ttm.h
View File

@ -27,8 +27,11 @@ class FixTTM : public Fix {
void setup(int);
void post_force(int);
void post_force_respa(int, int, int);
void end_of_step();
void reset_dt();
double memory_usage();
void grow_arrays(int);
double compute_vector(int);
private:
int me;
@ -37,21 +40,19 @@ class FixTTM : public Fix {
class RanMars *random;
FILE *fp,*fpr;
int nxnodes,nynodes,nznodes,total_nnodes;
int ***nsum,***nsum_prime;
int ***nsum_all,***nsum_prime_all,***T_initial_set;
int ***nsum;
int ***nsum_all,***T_initial_set;
double *gfactor1,*gfactor2,*ratio;
double ***T_electron,***T_a,***T_a_prime,***g_p,***g_s;
double ***sum_vsq,***sum_vsq_prime;
double ***sum_mass_vsq,***sum_mass_vsq_prime;
double ***sum_vsq_all,***sum_vsq_prime_all;
double ***sum_mass_vsq_all,***sum_mass_vsq_prime_all;
double ***T_electron_old;
double **flangevin;
double ***T_electron,***T_electron_old;
double ***sum_vsq,***sum_mass_vsq;
double ***sum_vsq_all,***sum_mass_vsq_all;
double ***net_energy_transfer,***net_energy_transfer_all;
double electronic_specific_heat,electronic_density;
double electronic_thermal_conductivity;
double gamma_p,gamma_s,v_0,v_0_sq;
void read_initial_electron_temperatures();
void update_electron_temperatures();
};
}