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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13170 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-03-04 16:33:18 +00:00
parent ee00c0f654
commit b33a0164de
2 changed files with 136 additions and 87 deletions
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2
src/Makefile
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@ -13,7 +13,7 @@ OBJ = $(SRC:.cpp=.o)
# Package variables # Package variables
PACKAGE = asphere body class2 colloid coreshell dipole fld gpu granular kim \ PACKAGE = asphere body class2 colloid dipole fld gpu granular kim \
kokkos kspace manybody mc meam misc molecule mpiio opt peri poems \ kokkos kspace manybody mc meam misc molecule mpiio opt peri poems \
qeq reax replica rigid shock snap srd voronoi xtc qeq reax replica rigid shock snap srd voronoi xtc

221
src/USER-MISC/fix_ttm_mod.cpp
View File

@ -33,6 +33,7 @@
#include "random_mars.h" #include "random_mars.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "citeme.h"
#include "math_const.h" #include "math_const.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -41,11 +42,34 @@ using namespace MathConst;
#define MAXLINE 1024 #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) : FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, 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"); if (narg < 9) error->all(FLERR,"Illegal fix ttm/mod command");
vector_flag = 1; vector_flag = 1;
size_vector = 2; size_vector = 2;
@ -55,16 +79,16 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
restart_peratom = 1; restart_peratom = 1;
restart_global = 1; restart_global = 1;
seed = atoi(arg[3]); seed = atoi(arg[3]);
nxnodes = atoi(arg[4]); fpr_2 = fopen(arg[4],"r");
nynodes = atoi(arg[5]); nxnodes = atoi(arg[5]);
nznodes = atoi(arg[6]); nynodes = atoi(arg[6]);
fpr = fopen(arg[7],"r"); nznodes = atoi(arg[7]);
fpr = fopen(arg[8],"r");
if (fpr == NULL) { if (fpr == NULL) {
char str[128]; char str[128];
sprintf(str,"Cannot open file %s",arg[7]); sprintf(str,"Cannot open file %s",arg[7]);
error->one(FLERR,str); error->one(FLERR,str);
} }
fpr_2 = fopen(arg[8],"r");
if (fpr == NULL) { if (fpr == NULL) {
char str[128]; char str[128];
sprintf(str,"Cannot open file %s",arg[8]); sprintf(str,"Cannot open file %s",arg[8]);
@ -233,6 +257,7 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
memory->create(sum_mass_vsq_all,nxnodes,nynodes,nznodes, memory->create(sum_mass_vsq_all,nxnodes,nynodes,nznodes,
"ttm/mod:sum_mass_vsq_all"); "ttm/mod:sum_mass_vsq_all");
memory->create(T_electron_old,nxnodes,nynodes,nznodes,"ttm/mod:T_electron_old"); 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(T_electron,nxnodes,nynodes,nznodes,"ttm/mod:T_electron");
memory->create(net_energy_transfer,nxnodes,nynodes,nznodes, memory->create(net_energy_transfer,nxnodes,nynodes,nznodes,
"ttm/mod:net_energy_transfer"); "ttm/mod:net_energy_transfer");
@ -585,89 +610,113 @@ void FixTTMMod::end_of_step()
// required this MD step to maintain a stable explicit solve // required this MD step to maintain a stable explicit solve
int num_inner_timesteps = 1; int num_inner_timesteps = 1;
double inner_dt = update->dt; double inner_dt = update->dt;
double stability_criterion = 1.0 - double stability_criterion = 0.0;
2.0*inner_dt/el_specific_heat *
(el_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz)); for (int ixnode = 0; ixnode < nxnodes; ixnode++)
if (stability_criterion < 0.0) { for (int iynode = 0; iynode < nynodes; iynode++)
inner_dt = 0.25*el_specific_heat / for (int iznode = 0; iznode < nznodes; iznode++)
(el_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz)); T_electron_first[ixnode][iynode][iznode] =
} T_electron[ixnode][iynode][iznode];
num_inner_timesteps = static_cast<unsigned int>(update->dt/inner_dt) + 1; do {
inner_dt = update->dt/double(num_inner_timesteps); for (int ixnode = 0; ixnode < nxnodes; ixnode++)
if (num_inner_timesteps > 1000000)
error->warning(FLERR,"Too many inner timesteps in fix ttm",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 iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++) for (int iznode = 0; iznode < nznodes; iznode++)
T_electron_old[ixnode][iynode][iznode] = T_electron[ixnode][iynode][iznode] =
T_electron[ixnode][iynode][iznode]; T_electron_first[ixnode][iynode][iznode];
// compute new electron T profile
duration = duration + inner_dt; stability_criterion = 1.0 -
for (int ixnode = 0; ixnode < nxnodes; ixnode++) 2.0*inner_dt/el_specific_heat *
for (int iynode = 0; iynode < nynodes; iynode++) (el_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz));
for (int iznode = 0; iznode < nznodes; iznode++) { if (stability_criterion < 0.0) {
int right_xnode = ixnode + 1; inner_dt = 0.25*el_specific_heat /
int right_ynode = iynode + 1; (el_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz));
int right_znode = iznode + 1; }
if (right_xnode == nxnodes) right_xnode = 0; num_inner_timesteps = static_cast<unsigned int>(update->dt/inner_dt) + 1;
if (right_ynode == nynodes) right_ynode = 0; inner_dt = update->dt/double(num_inner_timesteps);
if (right_znode == nznodes) right_znode = 0; if (num_inner_timesteps > 1000000)
int left_xnode = ixnode - 1; error->warning(FLERR,"Too many inner timesteps in fix ttm",0);
int left_ynode = iynode - 1; for (int ith_inner_timestep = 0; ith_inner_timestep < num_inner_timesteps;
int left_znode = iznode - 1; ith_inner_timestep++) {
if (left_xnode == -1) left_xnode = nxnodes - 1; for (int ixnode = 0; ixnode < nxnodes; ixnode++)
if (left_ynode == -1) left_ynode = nynodes - 1; for (int iynode = 0; iynode < nynodes; iynode++)
if (left_znode == -1) left_znode = nznodes - 1; for (int iznode = 0; iznode < nznodes; iznode++)
double skin_layer_d = double(skin_layer); T_electron_old[ixnode][iynode][iznode] =
double ixnode_d = double(ixnode); T_electron[ixnode][iynode][iznode];
double surface_d = double(t_surface_l); // compute new electron T profile
mult_factor = 0.0; duration = duration + inner_dt;
if (duration < width){ for (int ixnode = 0; ixnode < nxnodes; ixnode++)
if (ixnode >= t_surface_l) mult_factor = (intensity/(dx*skin_layer_d))*exp((-1.0)*(ixnode_d - surface_d)/skin_layer_d); for (int iynode = 0; iynode < nynodes; iynode++)
} for (int iznode = 0; iznode < nznodes; iznode++) {
if (ixnode < t_surface_l) net_energy_transfer_all[ixnode][iynode][iznode] = 0.0; int right_xnode = ixnode + 1;
double cr_vac = 1; int right_ynode = iynode + 1;
if (T_electron_old[ixnode][iynode][iznode] == 0) cr_vac = 0; int right_znode = iznode + 1;
double cr_v_l_x = 1; if (right_xnode == nxnodes) right_xnode = 0;
if (T_electron_old[left_xnode][iynode][iznode] == 0) cr_v_l_x = 0; if (right_ynode == nynodes) right_ynode = 0;
double cr_v_r_x = 1; if (right_znode == nznodes) right_znode = 0;
if (T_electron_old[right_xnode][iynode][iznode] == 0) cr_v_r_x = 0; int left_xnode = ixnode - 1;
double cr_v_l_y = 1; int left_ynode = iynode - 1;
if (T_electron_old[ixnode][left_ynode][iznode] == 0) cr_v_l_y = 0; int left_znode = iznode - 1;
double cr_v_r_y = 1; if (left_xnode == -1) left_xnode = nxnodes - 1;
if (T_electron_old[ixnode][right_ynode][iznode] == 0) cr_v_r_y = 0; if (left_ynode == -1) left_ynode = nynodes - 1;
double cr_v_l_z = 1; if (left_znode == -1) left_znode = nznodes - 1;
if (T_electron_old[ixnode][iynode][left_znode] == 0) cr_v_l_z = 0; double skin_layer_d = double(skin_layer);
double cr_v_r_z = 1; double ixnode_d = double(ixnode);
if (T_electron_old[ixnode][iynode][right_znode] == 0) cr_v_r_z = 0; double surface_d = double(t_surface_l);
if (cr_vac != 0) { mult_factor = 0.0;
T_electron[ixnode][iynode][iznode] = if (duration < width){
T_electron_old[ixnode][iynode][iznode] + if (ixnode >= t_surface_l) mult_factor = (intensity/(dx*skin_layer_d))*exp((-1.0)*(ixnode_d - surface_d)/skin_layer_d);
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* if (ixnode < t_surface_l) net_energy_transfer_all[ixnode][iynode][iznode] = 0.0;
(T_electron_old[right_xnode][iynode][iznode]-T_electron_old[ixnode][iynode][iznode])/dx - double cr_vac = 1;
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* if (T_electron_old[ixnode][iynode][iznode] == 0) cr_vac = 0;
(T_electron_old[ixnode][iynode][iznode]-T_electron_old[left_xnode][iynode][iznode])/dx)/dx + double cr_v_l_x = 1;
(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* if (T_electron_old[left_xnode][iynode][iznode] == 0) cr_v_l_x = 0;
(T_electron_old[ixnode][right_ynode][iznode]-T_electron_old[ixnode][iynode][iznode])/dy - double cr_v_r_x = 1;
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* if (T_electron_old[right_xnode][iynode][iznode] == 0) cr_v_r_x = 0;
(T_electron_old[ixnode][iynode][iznode]-T_electron_old[ixnode][left_ynode][iznode])/dy)/dy + double cr_v_l_y = 1;
(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* if (T_electron_old[ixnode][left_ynode][iznode] == 0) cr_v_l_y = 0;
(T_electron_old[ixnode][iynode][right_znode]-T_electron_old[ixnode][iynode][iznode])/dz - double cr_v_r_y = 1;
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* if (T_electron_old[ixnode][right_ynode][iznode] == 0) cr_v_r_y = 0;
(T_electron_old[ixnode][iynode][iznode]-T_electron_old[ixnode][iynode][left_znode])/dz)/dz); double cr_v_l_z = 1;
T_electron[ixnode][iynode][iznode]+=inner_dt/el_properties(T_electron[ixnode][iynode][iznode]).el_heat_capacity* if (T_electron_old[ixnode][iynode][left_znode] == 0) cr_v_l_z = 0;
(mult_factor - double cr_v_r_z = 1;
net_energy_transfer_all[ixnode][iynode][iznode]/del_vol); if (T_electron_old[ixnode][iynode][right_znode] == 0) cr_v_r_z = 0;
} if (cr_vac != 0) {
else T_electron[ixnode][iynode][iznode] = T_electron[ixnode][iynode][iznode] =
T_electron_old[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)) inner_dt/el_properties(T_electron_old[ixnode][iynode][iznode]).el_heat_capacity *
T_electron[ixnode][iynode][iznode] = T_electron[ixnode][iynode][iznode] + 0.5*(electron_temperature_min - T_electron[ixnode][iynode][iznode]); ((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 // output nodal temperatures for current timestep
if ((nfileevery) && !(update->ntimestep % nfileevery)) { if ((nfileevery) && !(update->ntimestep % nfileevery)) {
// compute atomic Ta for each grid point // compute atomic Ta for each grid point