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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2016-06-17 23:48:15 +00:00
parent b161fbb52a
commit d55f968432
112 changed files with 1525 additions and 1350 deletions
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69
src/USER-MISC/fix_ttm_mod.cpp
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@ -78,24 +78,33 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
nevery = 1;
restart_peratom = 1;
restart_global = 1;
seed = atoi(arg[3]);
fpr_2 = fopen(arg[4],"r");
nxnodes = atoi(arg[5]);
nynodes = atoi(arg[6]);
nznodes = atoi(arg[7]);
fpr = fopen(arg[8],"r");
if (fpr == NULL) {
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[7]);
error->one(FLERR,str);
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->one(FLERR,str);
error->all(FLERR,str);
}
nfileevery = atoi(arg[9]);
if (nfileevery) {
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) {
@ -226,19 +235,15 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
mult_factor = intensity;
duration = 0.0;
v_0_sq = v_0*v_0;
// error checks
if (nxnodes <= 0 || nynodes <= 0 || nznodes <= 0)
error->all(FLERR,"Fix ttm number of nodes must be > 0");
surface_double = double(t_surface_l)*(domain->xprd/nxnodes);
if ((C_limit+esheat_0) < 0.0)
error->all(FLERR,"Fix ttm electronic_specific_heat must be >= 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 electronic_density must be > 0.0");
if (gamma_p < 0.0) error->all(FLERR,"Fix ttm gamma_p must be >= 0.0");
if (gamma_s < 0.0) error->all(FLERR,"Fix ttm gamma_s must be >= 0.0");
if (v_0 < 0.0) error->all(FLERR,"Fix ttm v_0 must be >= 0.0");
if (ionic_density <= 0.0) error->all(FLERR,"Fix ttm ionic_density must be > 0.0");
if (seed <= 0) error->all(FLERR,"Invalid random number seed in fix ttm command");
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
@ -274,8 +279,10 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
atom->add_callback(0);
atom->add_callback(1);
// set initial electron temperatures from user input file
if (me == 0) read_initial_electron_temperatures();
if (me == 0) read_initial_electron_temperatures(fpr);
MPI_Bcast(&T_electron[0][0][0],total_nnodes,MPI_DOUBLE,0,world);
fclose(fpr);
fclose(fpr_2);
}
/* ---------------------------------------------------------------------- */
@ -317,11 +324,11 @@ int FixTTMMod::setmask()
void FixTTMMod::init()
{
if (domain->dimension == 2)
error->all(FLERR,"Cannot use fix ttm with 2d simulation");
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");
error->all(FLERR,"Cannot use nonperiodic boundares with fix ttm/mod");
if (domain->triclinic)
error->all(FLERR,"Cannot use fix ttm with triclinic box");
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;
@ -488,7 +495,7 @@ void FixTTMMod::reset_dt()
only called by proc 0
------------------------------------------------------------------------- */
void FixTTMMod::read_initial_electron_temperatures()
void FixTTMMod::read_initial_electron_temperatures(FILE *fpr)
{
char line[MAXLINE];
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
@ -501,7 +508,7 @@ void FixTTMMod::read_initial_electron_temperatures()
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 electron temperatures must be >= 0.0");
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;
}
@ -509,9 +516,7 @@ void FixTTMMod::read_initial_electron_temperatures()
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");
// close file
fclose(fpr);
error->one(FLERR,"Initial temperatures not all set in fix ttm/mod");
}
/* ---------------------------------------------------------------------- */
@ -634,7 +639,7 @@ void FixTTMMod::end_of_step()
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",0);
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++)