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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2729 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-04-06 20:13:53 +00:00
parent 0d895e0844
commit a570406482
3 changed files with 226 additions and 158 deletions
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2
src/fix_msd.cpp
View File

@ -266,7 +266,7 @@ double FixMSD::memory_usage()
void FixMSD::grow_arrays(int nmax)
{
xoriginal =
memory->grow_2d_double_array(xoriginal,nmax,3,"fix_msd:xoriginal");
memory->grow_2d_double_array(xoriginal,nmax,3,"msd:xoriginal");
}
/* ----------------------------------------------------------------------

360
src/fix_ttm.cpp
View File

@ -11,6 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "string.h"
@ -27,18 +31,19 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define MAXLINE 1024
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 15) error->all("Illegal fix TTM command");
if (narg < 15) error->all("Illegal fix ttm command");
int seed = atoi(arg[3]);
electronic_specific_heat = atof(arg[4]);
@ -73,19 +78,22 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
}
}
if (seed <= 0) error->all("Fix TTM seed must be >= 0");
if (electronic_specific_heat <= 0.0) error->all("Fix TTM electronic_specific_heat must be > 0.0");
if (electronic_density <= 0.0) error->all("Fix TTM electronic_density must be > 0.0");
if (electronic_thermal_conductivity < 0.0) error->all("Fix TTM electronic_thermal_conductivity must be >= 0.0");
if (gamma_p <= 0.0) error->all("Fix TTM gamma_p must be > 0.0");
if (gamma_s < 0.0) error->all("Fix TTM gamma_s must be >= 0.0");
if (v_0 < 0.0) error->all("Fix TTM v_0 must be >= 0.0");
v_0_sq = v_0*v_0;
if ((nxnodes <= 0) or (nynodes <= 0) or (nznodes <= 0)) error->all("Fix TTM nnodes must be > 0");
// error check
nsum = nsum_prime = nsum_all = nsum_prime_all = T_initial_set = NULL;
sum_vsq = sum_vsq_prime = sum_mass_vsq = sum_mass_vsq_prime = sum_vsq_all = sum_vsq_prime_all = NULL;
sum_mass_vsq_all = sum_mass_vsq_prime_all = T_electron_old = T_electron = T_a = T_a_prime = g_s = g_p = NULL;
if (seed <= 0) error->all("Fix ttm seed must be >= 0");
if (electronic_specific_heat <= 0.0)
error->all("Fix ttm electronic_specific_heat must be > 0.0");
if (electronic_density <= 0.0)
error->all("Fix ttm electronic_density must be > 0.0");
if (electronic_thermal_conductivity < 0.0)
error->all("Fix ttm electronic_thermal_conductivity must be >= 0.0");
if (gamma_p <= 0.0) error->all("Fix ttm gamma_p must be > 0.0");
if (gamma_s < 0.0) error->all("Fix ttm gamma_s must be >= 0.0");
if (v_0 < 0.0) error->all("Fix ttm v_0 must be >= 0.0");
if (nxnodes <= 0 or nynodes <= 0 or nznodes <= 0)
error->all("Fix ttm number of nodes must be > 0");
v_0_sq = v_0*v_0;
// initialize Marsaglia RNG with processor-unique seed
@ -96,30 +104,52 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
gfactor1 = new double[atom->ntypes+1];
gfactor2 = new double[atom->ntypes+1];
// allocate 3d grid variables
total_nnodes = nxnodes*nynodes*nznodes;
// allocate memory for 3d vectors
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");
T_initial_set = memory->create_3d_int_array(nxnodes,nynodes,nznodes,"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");
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");
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");
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");
T_electron_old = memory->create_3d_double_array(nxnodes,nynodes,nznodes,"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");
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");
T_initial_set = memory->create_3d_int_array(nxnodes,nynodes,nznodes,
"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");
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");
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");
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");
T_electron_old =
memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"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");
// set initial electron temperatures from user-supplied file
// set initial electron temperatures from user input file
if (me == 0) read_initial_electron_temperatures();
MPI_Bcast(&T_electron[0][0][0],total_nnodes,MPI_DOUBLE,0,world);
@ -132,6 +162,7 @@ FixTTM::~FixTTM()
if (nfileevery && me == 0) fclose(fp);
delete random;
delete [] gfactor1;
delete [] gfactor2;
@ -170,63 +201,25 @@ int FixTTM::setmask()
void FixTTM::init()
{
if (atom->mass == NULL)
error->all("Cannot use fix TTM without per-type mass defined");
if (domain->dimension == 2)
error->all("Cannot use fix ttm with 2d simulation");
if (domain->nonperiodic != 0)
error->all("Cannot use nonperiodic boundares with fix ttm");
if (domain->triclinic)
error->all("Cannot use fix ttm 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;
gfactor2[i] =
sqrt(24.0*force->boltz*gamma_p/update->dt/force->mvv2e) / force->ftm2v;
}
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ----------------------------------------------------------------------
read in initial electron temperatures from a user-specified file
only called by proc 0
------------------------------------------------------------------------- */
void FixTTM::read_initial_electron_temperatures()
{
char line[MAXLINE];
for (int ixnode = 0; ixnode < nxnodes; ixnode++) {
for (int iynode = 0; iynode < nynodes; iynode++) {
for (int iznode = 0; iznode < nznodes; iznode++) {
T_initial_set[ixnode][iynode][iznode] = 0;
}
}
}
// read initial electron temperature values from file
int ixnode,iynode,iznode;
double T_tmp;
while (1) {
if (fgets(line,MAXLINE,fpr) == NULL) break;
sscanf(line,"%d %d %d %lg",&ixnode,&iynode,&iznode,&T_tmp);
if (T_tmp < 0.0) error->all("Fix TTM electron temperatures must be > 0.0");
T_electron[ixnode][iynode][iznode] = T_tmp;
T_initial_set[ixnode][iynode][iznode] = 1;
}
for (int ixnode = 0; ixnode < nxnodes; ixnode++) {
for (int iynode = 0; iynode < nynodes; iynode++) {
for (int iznode = 0; iznode < nznodes; iznode++) {
if (T_initial_set[ixnode][iynode][iznode] == 0)
error->all("All initial temperatures have not been set in the TTM fix.");
}
}
}
// close file
fclose(fpr);
}
/* ---------------------------------------------------------------------- */
void FixTTM::setup(int vflag)
@ -298,9 +291,46 @@ void FixTTM::post_force_respa(int vflag, int ilevel, int iloop)
void FixTTM::reset_dt()
{
for (int i = 1; i <= atom->ntypes; i++) {
gfactor2[i] = sqrt(24.0*force->boltz*gamma_p/update->dt/force->mvv2e) / force->ftm2v;
for (int i = 1; i <= atom->ntypes; i++)
gfactor2[i] =
sqrt(24.0*force->boltz*gamma_p/update->dt/force->mvv2e) / force->ftm2v;
}
/* ----------------------------------------------------------------------
read in initial electron temperatures from a user-specified file
only called by proc 0
------------------------------------------------------------------------- */
void FixTTM::read_initial_electron_temperatures()
{
char line[MAXLINE];
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
T_initial_set[ixnode][iynode][iznode] = 0;
// read initial electron temperature values from file
int ixnode,iynode,iznode;
double T_tmp;
while (1) {
if (fgets(line,MAXLINE,fpr) == NULL) break;
sscanf(line,"%d %d %d %lg",&ixnode,&iynode,&iznode,&T_tmp);
if (T_tmp < 0.0) error->one("Fix ttm electron temperatures must be > 0.0");
T_electron[ixnode][iynode][iznode] = T_tmp;
T_initial_set[ixnode][iynode][iznode] = 1;
}
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
if (T_initial_set[ixnode][iynode][iznode] == 0)
error->one("Initial temperatures not all set in fix ttm");
// close file
fclose(fpr);
}
/* ---------------------------------------------------------------------- */
@ -309,14 +339,18 @@ void FixTTM::update_electron_temperatures()
{
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// compute atomic Ta, and Ta' (for high v atoms) for each node
double massone;
for (int ixnode = 0; ixnode < nxnodes; ixnode++) {
for (int iynode = 0; iynode < nynodes; iynode++) {
// 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;
@ -331,12 +365,11 @@ void FixTTM::update_electron_temperatures()
sum_mass_vsq_all[ixnode][iynode][iznode] = 0.0;
sum_mass_vsq_prime_all[ixnode][iynode][iznode] = 0.0;
}
}
}
for (int i = 0; i < nlocal; i++) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
double mass = atom->mass[type[i]];
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;
@ -352,36 +385,42 @@ void FixTTM::update_electron_temperatures()
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] += mass*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] += mass*vsq;
sum_mass_vsq_prime[ixnode][iynode][iznode] += massone*vsq;
}
}
}
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);
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 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*force->boltz*nsum_all[ixnode][iynode][iznode]/force->mvv2e);
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 = gamma_p*sum_vsq_all[ixnode][iynode][iznode]/
T_a[ixnode][iynode][iznode]/del_vol;
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 {
@ -389,43 +428,51 @@ void FixTTM::update_electron_temperatures()
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*force->boltz*nsum_prime_all[ixnode][iynode][iznode]/force->mvv2e);
g_s[ixnode][iynode][iznode] = gamma_s*sum_vsq_prime_all[ixnode][iynode][iznode]/
T_a_prime[ixnode][iynode][iznode]/del_vol;
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] =
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;
}
}
}
}
// figure out how many inner steps (thermal solves) are required this MD timestep in order to maintain a stable explicit solve
// 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 = 1.0 - 2.0*inner_dt/(electronic_specific_heat*electronic_density)*
(electronic_thermal_conductivity*(1/dx/dx + 1/dy/dy + 1/dz/dz) + 0.5*max_g_p);
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);
if (stability_criterion < 0.0) {
inner_dt = 0.5*(electronic_specific_heat*electronic_density)/(electronic_thermal_conductivity*(1/dx/dx + 1/dy/dy + 1/dz/dz) + 0.5*max_g_p);
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);
num_inner_timesteps = static_cast<int>(update->dt/inner_dt) + 1;
inner_dt = update->dt/double(num_inner_timesteps);
if (num_inner_timesteps > 1e6) error->warning("In the TTM fix, trying to do more than a million inner timesteps!");
if (num_inner_timesteps > 1000000)
error->warning("Too many inner timesteps in fix ttm");
}
for (int ith_inner_timestep = 0; ith_inner_timestep < num_inner_timesteps; ith_inner_timestep++) {
for (int ixnode = 0; ixnode < nxnodes; ixnode++) {
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];
}
}
}
for (int ith_inner_timestep = 0; ith_inner_timestep < num_inner_timesteps;
ith_inner_timestep++) {
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
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];
// compute new electron T profile
for (int ixnode = 0; ixnode < nxnodes; ixnode++) {
for (int iynode = 0; iynode < nynodes; iynode++) {
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++) {
int right_xnode = ixnode + 1;
int right_ynode = iynode + 1;
@ -439,36 +486,51 @@ void FixTTM::update_electron_temperatures()
if (left_xnode == -1) left_xnode = nxnodes - 1;
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[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]);
}
}
}
}
// output nodal temperatures for current timestep
if (!(update->ntimestep % nfileevery) && (me == 0)) {
fprintf(fp,"%d ",update->ntimestep);
// print nodal temperatures for current timestep
for (int ixnode = 0; ixnode < nxnodes; ixnode++) {
for (int iynode = 0; iynode < nynodes; iynode++) {
for (int iznode = 0; iznode < nznodes; iznode++) {
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]);
}
}
}
fprintf(fp,"\t");
for (int ixnode = 0; ixnode < nxnodes; ixnode++) {
for (int iynode = 0; iynode < nynodes; iynode++) {
for (int iznode = 0; iznode < nznodes; iznode++) {
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");
}
}
/* ----------------------------------------------------------------------
memory usage of 3d grid
------------------------------------------------------------------------- */
double FixTTM::memory_usage()
{
double bytes = 0.0;
bytes += 5*total_nnodes * sizeof(int);
bytes += 14*total_nnodes * sizeof(double);
return bytes;
}

22
src/fix_ttm.h
View File

@ -24,28 +24,34 @@ class FixTTM : public Fix {
~FixTTM();
int setmask();
void init();
void read_initial_electron_temperatures();
void setup(int);
void post_force(int);
void post_force_respa(int, int, int);
void reset_dt();
void update_electron_temperatures();
double memory_usage();
private:
int me;
int nfileevery;
int nlevels_respa;
class RanMars *random;
FILE *fp, *fpr;
FILE *fp,*fpr;
int nxnodes,nynodes,nznodes,total_nnodes;
int ***nsum, ***nsum_prime, ***nsum_all, ***nsum_prime_all, ***T_initial_set;
int ***nsum,***nsum_prime;
int ***nsum_all,***nsum_prime_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, ***sum_mass_vsq, ***sum_mass_vsq_prime;
double ***sum_vsq_all, ***sum_vsq_prime_all, ***sum_mass_vsq_all, ***sum_mass_vsq_prime_all;
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 electronic_specific_heat,electronic_density,electronic_thermal_conductivity;
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();
};
}