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fix_ttm_mod.cpp
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Fri, Nov 1, 22:31

fix_ttm_mod.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: (in addition to authors of original fix ttm)
Sergey Starikov (Joint Institute for High Temperatures of RAS)
Vasily Pisarev (Joint Institute for High Temperatures of RAS)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include <mpi.h>
#include <math.h>
#include <string.h>
#include <stdlib.h>
#include "fix_ttm_mod.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "domain.h"
#include "region.h"
#include "respa.h"
#include "comm.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
#include "citeme.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
#define MAXLINE 1024
static const char cite_fix_ttm_mod[] =
"fix ttm/mod command:\n\n"
"@article{Pisarev2014,\n"
"author = {Pisarev, V. V. and Starikov, S. V.},\n"
"title = {{Atomistic simulation of ion track formation in UO2.}},\n"
"journal = {J.~Phys.:~Condens.~Matter},\n"
"volume = {26},\n"
"number = {47},\n"
"pages = {475401},\n"
"year = {2014}\n"
"}\n\n"
"@article{Norman2013,\n"
"author = {Norman, G. E. and Starikov, S. V. and Stegailov, V. V. and Saitov, I. M. and Zhilyaev, P. A.},\n"
"title = {{Atomistic Modeling of Warm Dense Matter in the Two-Temperature State}},\n"
"journal = {Contrib.~Plasm.~Phys.},\n"
"number = {2},\n"
"volume = {53},\n"
"pages = {129--139},\n"
"year = {2013}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_ttm_mod);
if (narg < 9) error->all(FLERR,"Illegal fix ttm/mod command");
vector_flag = 1;
size_vector = 2;
global_freq = 1;
extvector = 1;
nevery = 1;
restart_peratom = 1;
restart_global = 1;
seed = force->inumeric(FLERR,arg[3]);
if (seed <= 0)
error->all(FLERR,"Invalid random number seed in fix ttm/mod command");
FILE *fpr_2 = force->open_potential(arg[4]);
if (fpr_2 == NULL) {
char str[128];
sprintf(str,"Cannot open file %s",arg[4]);
error->all(FLERR,str);
}
nxnodes = force->inumeric(FLERR,arg[5]);
nynodes = force->inumeric(FLERR,arg[6]);
nznodes = force->inumeric(FLERR,arg[7]);
if (nxnodes <= 0 || nynodes <= 0 || nznodes <= 0)
error->all(FLERR,"Fix ttm/mod number of nodes must be > 0");
FILE *fpr = force->open_potential(arg[8]);
if (fpr == NULL) {
char str[128];
sprintf(str,"Cannot open file %s",arg[8]);
error->all(FLERR,str);
}
nfileevery = force->inumeric(FLERR,arg[9]);
if (nfileevery > 0) {
if (narg != 11) error->all(FLERR,"Illegal fix ttm/mod command");
MPI_Comm_rank(world,&me);
if (me == 0) {
fp = fopen(arg[10],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix ttm/mod file %s",arg[10]);
error->one(FLERR,str);
}
}
}
char linee[MAXLINE];
double tresh_d;
int tresh_i;
// C0 (metal)
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
esheat_0 = tresh_d;
// C1 (metal*10^3)
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
esheat_1 = tresh_d;
// C2 (metal*10^6)
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
esheat_2 = tresh_d;
// C3 (metal*10^9)
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
esheat_3 = tresh_d;
// C4 (metal*10^12)
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
esheat_4 = tresh_d;
// C_limit
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
C_limit = tresh_d;
//Temperature damping factor
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
T_damp = tresh_d;
// rho_e
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
electronic_density = tresh_d;
//thermal_diffusion
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
el_th_diff = tresh_d;
// gamma_p
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
gamma_p = tresh_d;
// gamma_s
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
gamma_s = tresh_d;
// v0
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
v_0 = tresh_d;
// average intensity of pulse (source of energy) (metal units)
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
intensity = tresh_d;
// coordinate of 1st surface in x-direction (in box units) - constant
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%d",&tresh_i);
surface_l = tresh_i;
// coordinate of 2nd surface in x-direction (in box units) - constant
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%d",&tresh_i);
surface_r = tresh_i;
// skin_layer = intensity is reduced (I=I0*exp[-x/skin_layer])
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%d",&tresh_i);
skin_layer = tresh_i;
// width of pulse (picoseconds)
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
width = tresh_d;
// factor of electronic pressure (PF) Pe = PF*Ce*Te
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
pres_factor = tresh_d;
// effective free path of electrons (angstrom)
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
free_path = tresh_d;
// ionic density (ions*angstrom^{-3})
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
ionic_density = tresh_d;
// if movsur = 0: surface is freezed
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%d",&tresh_i);
movsur = tresh_i;
// electron_temperature_min
fgets(linee,MAXLINE,fpr_2);
fgets(linee,MAXLINE,fpr_2);
sscanf(linee,"%lg",&tresh_d);
electron_temperature_min = tresh_d;
fclose(fpr_2);
//t_surface is determined by electronic temperature (not constant)
t_surface_l = surface_l;
mult_factor = intensity;
duration = 0.0;
v_0_sq = v_0*v_0;
surface_double = double(t_surface_l)*(domain->xprd/nxnodes);
if ((C_limit+esheat_0) < 0.0)
error->all(FLERR,"Fix ttm/mod electronic_specific_heat must be >= 0.0");
if (electronic_density <= 0.0)
error->all(FLERR,"Fix ttm/mod electronic_density must be > 0.0");
if (gamma_p < 0.0) error->all(FLERR,"Fix ttm/mod gamma_p must be >= 0.0");
if (gamma_s < 0.0) error->all(FLERR,"Fix ttm/mod gamma_s must be >= 0.0");
if (v_0 < 0.0) error->all(FLERR,"Fix ttm/mod v_0 must be >= 0.0");
if (ionic_density <= 0.0) error->all(FLERR,"Fix ttm/mod ionic_density must be > 0.0");
if (surface_l < 0) error->all(FLERR,"Surface coordinates must be >= 0");
if (surface_l >= surface_r) error->all(FLERR, "Left surface coordinate must be less than right surface coordinate");
// initialize Marsaglia RNG with processor-unique seed
random = new RanMars(lmp,seed + comm->me);
// allocate per-type arrays for force prefactors
gfactor1 = new double[atom->ntypes+1];
gfactor2 = new double[atom->ntypes+1];
// allocate 3d grid variables
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");
memory->create(sum_mass_vsq_all,nxnodes,nynodes,nznodes,
"ttm/mod:sum_mass_vsq_all");
memory->create(T_electron_old,nxnodes,nynodes,nznodes,"ttm/mod:T_electron_old");
memory->create(T_electron_first,nxnodes,nynodes,nznodes,"ttm/mod:T_electron_first");
memory->create(T_electron,nxnodes,nynodes,nznodes,"ttm/mod:T_electron");
memory->create(net_energy_transfer,nxnodes,nynodes,nznodes,
"ttm/mod:net_energy_transfer");
memory->create(net_energy_transfer_all,nxnodes,nynodes,nznodes,
"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 (me == 0) read_initial_electron_temperatures(fpr);
MPI_Bcast(&T_electron[0][0][0],total_nnodes,MPI_DOUBLE,0,world);
fclose(fpr);
}
/* ---------------------------------------------------------------------- */
FixTTMMod::~FixTTMMod()
{
if (nfileevery && me == 0) 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);
memory->destroy(sum_mass_vsq_all);
memory->destroy(T_electron_first);
memory->destroy(T_electron_old);
memory->destroy(T_electron);
memory->destroy(flangevin);
memory->destroy(net_energy_transfer);
memory->destroy(net_energy_transfer_all);
}
/* ---------------------------------------------------------------------- */
int FixTTMMod::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixTTMMod::init()
{
if (domain->dimension == 2)
error->all(FLERR,"Cannot use fix ttm/mod with 2d simulation");
if (domain->nonperiodic != 0)
error->all(FLERR,"Cannot use nonperiodic 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;
}
/* ---------------------------------------------------------------------- */
void FixTTMMod::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force_setup(vflag);
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);
}
}
/* ---------------------------------------------------------------------- */
void FixTTMMod::post_force(int vflag)
{
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
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;
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;
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;
gamma2 = gfactor2[type[i]] * tsqrt;
if (ixnode >= surface_l){
if (ixnode < surface_r){
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);
double x_surf = dx*double(surface_l)+dx;
double x_at = x[i][0] - domain->boxlo[0];
int right_xnode = ixnode + 1;
int right_ynode = iynode + 1;
int right_znode = iznode + 1;
if (right_xnode == nxnodes) right_xnode = 0;
if (right_ynode == nynodes) right_ynode = 0;
if (right_znode == nznodes) right_znode = 0;
int left_xnode = ixnode - 1;
int left_ynode = iynode - 1;
int left_znode = iznode - 1;
if (left_xnode == -1) left_xnode = nxnodes - 1;
if (left_ynode == -1) left_ynode = nynodes - 1;
if (left_znode == -1) left_znode = nznodes - 1;
double T_i = T_electron[ixnode][iynode][iznode];
double T_ir = T_electron[right_xnode][iynode][iznode];
double T_iu = T_electron[ixnode][right_ynode][iznode];
double T_if = T_electron[ixnode][iynode][right_znode];
double C_i = el_properties(T_electron[ixnode][iynode][iznode]).el_heat_capacity;
double C_ir = el_properties(T_electron[right_xnode][iynode][iznode]).el_heat_capacity;
double C_iu = el_properties(T_electron[ixnode][right_ynode][iznode]).el_heat_capacity;
double C_if = el_properties(T_electron[ixnode][iynode][right_znode]).el_heat_capacity;
double diff_x = (x_at - x_surf)*(x_at - x_surf);
diff_x = pow(diff_x,0.5);
double len_factor = diff_x/(diff_x+free_path);
if (movsur == 1){
if (x_at >= x_surf){
flangevin[i][0] -= pres_factor/ionic_density*((C_ir*T_ir*free_path/(diff_x+free_path)/(diff_x+free_path)) +
(len_factor/dx)*(C_ir*T_ir-C_i*T_i));
flangevin[i][1] -= pres_factor/ionic_density/dy*(C_iu*T_iu-C_i*T_i);
flangevin[i][2] -= pres_factor/ionic_density/dz*(C_if*T_if-C_i*T_i);
}
}
else{
flangevin[i][0] -= pres_factor/ionic_density/dx*(C_ir*T_ir-C_i*T_i);
flangevin[i][1] -= pres_factor/ionic_density/dy*(C_iu*T_iu-C_i*T_i);
flangevin[i][2] -= pres_factor/ionic_density/dz*(C_if*T_if-C_i*T_i);
}
f[i][0] += flangevin[i][0];
f[i][1] += flangevin[i][1];
f[i][2] += flangevin[i][2];
}
}
if (movsur == 1){
if (ixnode < surface_l){
t_surface_l = ixnode;
}
}
}
}
MPI_Allreduce(&t_surface_l,&surface_l,1,MPI_INT,MPI_MIN,world);
}
/* ---------------------------------------------------------------------- */
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];
f[i][1] += flangevin[i][1];
f[i][2] += flangevin[i][2];
}
}
}
/* ---------------------------------------------------------------------- */
void FixTTMMod::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixTTMMod::post_force_respa_setup(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force_setup(vflag);
}
/* ---------------------------------------------------------------------- */
void FixTTMMod::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;
}
/* ----------------------------------------------------------------------
read in initial electron temperatures from a user-specified file
only called by proc 0
------------------------------------------------------------------------- */
void FixTTMMod::read_initial_electron_temperatures(FILE *fpr)
{
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(FLERR,"Fix ttm/mod 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(FLERR,"Initial temperatures not all set in fix ttm/mod");
}
/* ---------------------------------------------------------------------- */
el_heat_capacity_thermal_conductivity FixTTMMod::el_properties(double T_e)
{
el_heat_capacity_thermal_conductivity properties;
double T_temp = T_e/1000.0, T_reduced = T_damp*T_temp;
double T2 = T_temp*T_temp;
double T3 = T2*T_temp;
double T4 = T3*T_temp;
double poly = esheat_0 + esheat_1*T_temp + esheat_2*T2 + esheat_3*T3 + esheat_4*T4;
properties.el_heat_capacity = electronic_density*(poly*exp(-T_reduced*T_reduced) + C_limit); // heat capacity
properties.el_thermal_conductivity = el_th_diff*properties.el_heat_capacity; // thermal conductivity
return properties;
}
double FixTTMMod::el_sp_heat_integral(double T_e)
{
double T_temp = T_e/1000.0, T_reduced = T_damp*T_temp;
if (T_damp != 0)
return electronic_density*(MY_PIS*(3*esheat_4/pow(T_damp,5)+2*esheat_2/pow(T_damp,3)+4*esheat_0/T_damp)*erf(T_reduced)+
4*esheat_3/pow(T_damp,4)+4*esheat_1/T_damp/T_damp-
((6*esheat_4*T_temp+4*esheat_3)/pow(T_damp,4)+
(4*esheat_1+4*esheat_4*pow(T_temp,3)+4*esheat_3*T_temp*T_temp+4*esheat_2*T_temp)/T_damp/T_damp)*exp(-T_reduced*T_reduced))*125.0+electronic_density*C_limit*T_e;
else
return electronic_density*((esheat_0 + C_limit)*T_e + esheat_1*T_temp*T_e/2.0 + esheat_2*T_temp*T_temp*T_e/3.0 + esheat_3*pow(T_temp,3)*T_e/4.0 + esheat_4*pow(T_temp,4)*T_e/5.0);
}
void FixTTMMod::end_of_step()
{
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;
if (movsur == 1){
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++){
double TTT = T_electron[ixnode][iynode][iznode];
if (TTT > 0){
if (ixnode < t_surface_l)
t_surface_l = ixnode;
}
}
}
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
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;
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;
if (ixnode >= t_surface_l){
if (ixnode < surface_r)
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;
double el_specific_heat = 0.0;
double el_thermal_conductivity = el_properties(electron_temperature_min).el_thermal_conductivity;
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
{
if (el_properties(T_electron[ixnode][iynode][iznode]).el_thermal_conductivity > el_thermal_conductivity)
el_thermal_conductivity = el_properties(T_electron[ixnode][iynode][iznode]).el_thermal_conductivity;
if (el_specific_heat > 0.0)
{
if ((T_electron[ixnode][iynode][iznode] > 0.0) && (el_properties(T_electron[ixnode][iynode][iznode]).el_heat_capacity < el_specific_heat))
el_specific_heat = el_properties(T_electron[ixnode][iynode][iznode]).el_heat_capacity;
}
else if (T_electron[ixnode][iynode][iznode] > 0.0) el_specific_heat = el_properties(T_electron[ixnode][iynode][iznode]).el_heat_capacity;
}
// 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;
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
T_electron_first[ixnode][iynode][iznode] =
T_electron[ixnode][iynode][iznode];
do {
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] =
T_electron_first[ixnode][iynode][iznode];
stability_criterion = 1.0 -
2.0*inner_dt/el_specific_heat *
(el_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz));
if (stability_criterion < 0.0) {
inner_dt = 0.25*el_specific_heat /
(el_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz));
}
num_inner_timesteps = static_cast<unsigned int>(update->dt/inner_dt) + 1;
inner_dt = update->dt/double(num_inner_timesteps);
if (num_inner_timesteps > 1000000)
error->warning(FLERR,"Too many inner timesteps in fix ttm/mod",0);
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
duration = duration + inner_dt;
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;
int right_znode = iznode + 1;
if (right_xnode == nxnodes) right_xnode = 0;
if (right_ynode == nynodes) right_ynode = 0;
if (right_znode == nznodes) right_znode = 0;
int left_xnode = ixnode - 1;
int left_ynode = iynode - 1;
int left_znode = iznode - 1;
if (left_xnode == -1) left_xnode = nxnodes - 1;
if (left_ynode == -1) left_ynode = nynodes - 1;
if (left_znode == -1) left_znode = nznodes - 1;
double skin_layer_d = double(skin_layer);
double ixnode_d = double(ixnode);
double surface_d = double(t_surface_l);
mult_factor = 0.0;
if (duration < width){
if (ixnode >= t_surface_l) mult_factor = (intensity/(dx*skin_layer_d))*exp((-1.0)*(ixnode_d - surface_d)/skin_layer_d);
}
if (ixnode < t_surface_l) net_energy_transfer_all[ixnode][iynode][iznode] = 0.0;
double cr_vac = 1;
if (T_electron_old[ixnode][iynode][iznode] == 0) cr_vac = 0;
double cr_v_l_x = 1;
if (T_electron_old[left_xnode][iynode][iznode] == 0) cr_v_l_x = 0;
double cr_v_r_x = 1;
if (T_electron_old[right_xnode][iynode][iznode] == 0) cr_v_r_x = 0;
double cr_v_l_y = 1;
if (T_electron_old[ixnode][left_ynode][iznode] == 0) cr_v_l_y = 0;
double cr_v_r_y = 1;
if (T_electron_old[ixnode][right_ynode][iznode] == 0) cr_v_r_y = 0;
double cr_v_l_z = 1;
if (T_electron_old[ixnode][iynode][left_znode] == 0) cr_v_l_z = 0;
double cr_v_r_z = 1;
if (T_electron_old[ixnode][iynode][right_znode] == 0) cr_v_r_z = 0;
if (cr_vac != 0) {
T_electron[ixnode][iynode][iznode] =
T_electron_old[ixnode][iynode][iznode] +
inner_dt/el_properties(T_electron_old[ixnode][iynode][iznode]).el_heat_capacity *
((cr_v_r_x*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[right_xnode][iynode][iznode]/2.0).el_thermal_conductivity*
(T_electron_old[right_xnode][iynode][iznode]-T_electron_old[ixnode][iynode][iznode])/dx -
cr_v_l_x*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[left_xnode][iynode][iznode]/2.0).el_thermal_conductivity*
(T_electron_old[ixnode][iynode][iznode]-T_electron_old[left_xnode][iynode][iznode])/dx)/dx +
(cr_v_r_y*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[ixnode][right_ynode][iznode]/2.0).el_thermal_conductivity*
(T_electron_old[ixnode][right_ynode][iznode]-T_electron_old[ixnode][iynode][iznode])/dy -
cr_v_l_y*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[ixnode][left_ynode][iznode]/2.0).el_thermal_conductivity*
(T_electron_old[ixnode][iynode][iznode]-T_electron_old[ixnode][left_ynode][iznode])/dy)/dy +
(cr_v_r_z*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[ixnode][iynode][right_znode]/2.0).el_thermal_conductivity*
(T_electron_old[ixnode][iynode][right_znode]-T_electron_old[ixnode][iynode][iznode])/dz -
cr_v_l_z*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[ixnode][iynode][left_znode]/2.0).el_thermal_conductivity*
(T_electron_old[ixnode][iynode][iznode]-T_electron_old[ixnode][iynode][left_znode])/dz)/dz);
T_electron[ixnode][iynode][iznode]+=inner_dt/el_properties(T_electron[ixnode][iynode][iznode]).el_heat_capacity*
(mult_factor -
net_energy_transfer_all[ixnode][iynode][iznode]/del_vol);
}
else T_electron[ixnode][iynode][iznode] =
T_electron_old[ixnode][iynode][iznode];
if ((T_electron[ixnode][iynode][iznode] > 0.0) && (T_electron[ixnode][iynode][iznode] < electron_temperature_min))
T_electron[ixnode][iynode][iznode] = T_electron[ixnode][iynode][iznode] + 0.5*(electron_temperature_min - T_electron[ixnode][iynode][iznode]);
if (el_properties(T_electron[ixnode][iynode][iznode]).el_thermal_conductivity > el_thermal_conductivity)
el_thermal_conductivity = el_properties(T_electron[ixnode][iynode][iznode]).el_thermal_conductivity;
if ((T_electron[ixnode][iynode][iznode] > 0.0) && (el_properties(T_electron[ixnode][iynode][iznode]).el_heat_capacity < el_specific_heat))
el_specific_heat = el_properties(T_electron[ixnode][iynode][iznode]).el_heat_capacity;
}
}
stability_criterion = 1.0 -
2.0*inner_dt/el_specific_heat *
(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++) {
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);
MPI_Allreduce(&t_surface_l,&surface_l,
1,MPI_INT,MPI_MIN,world);
if (me == 0) {
fprintf(fp,BIGINT_FORMAT,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){
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);
}
fprintf(fp,"\t");
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 FixTTMMod::memory_usage()
{
double bytes = 0.0;
bytes += 5*total_nnodes * sizeof(int);
bytes += 14*total_nnodes * sizeof(double);
return bytes;
}
/* ---------------------------------------------------------------------- */
void FixTTMMod::grow_arrays(int ngrow)
{
memory->grow(flangevin,ngrow,3,"ttm/mod:flangevin");
}
/* ----------------------------------------------------------------------
return the energy of the electronic subsystem or the net_energy transfer
between the subsystems
------------------------------------------------------------------------- */
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++) {
e_energy += el_sp_heat_integral(T_electron[ixnode][iynode][iznode])*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;
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
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];
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(rlist,sizeof(double),n,fp);
}
memory->destroy(rlist);
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
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);
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixTTMMod::pack_restart(int i, double *buf)
{
buf[0] = 4;
buf[1] = flangevin[i][0];
buf[2] = flangevin[i][1];
buf[3] = flangevin[i][2];
return 4;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
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++];
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixTTMMod::maxsize_restart()
{
return 4;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixTTMMod::size_restart(int nlocal)
{
return 4;
}

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