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convert fix ttm and fix ttm/mod to use tokenizer class for parsing files

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This commit is contained in:
Axel Kohlmeyer
2020-07-25 18:03:18 -04:00
parent 783b28906e
commit 5452f72bd9
4 changed files with 229 additions and 172 deletions
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60
src/MISC/fix_ttm.cpp
View File

@ -31,6 +31,7 @@
#include "error.h"
#include "utils.h"
#include "fmt/format.h"
#include "tokenizer.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -41,7 +42,7 @@ using namespace FixConst;
FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
random(NULL), fp(NULL), fpr(NULL), nsum(NULL), nsum_all(NULL),
random(NULL), fp(NULL), nsum(NULL), nsum_all(NULL),
T_initial_set(NULL), gfactor1(NULL), gfactor2(NULL), ratio(NULL),
flangevin(NULL), T_electron(NULL), T_electron_old(NULL), sum_vsq(NULL),
sum_mass_vsq(NULL), sum_vsq_all(NULL), sum_mass_vsq_all(NULL),
@ -67,14 +68,6 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
nxnodes = force->inumeric(FLERR,arg[10]);
nynodes = force->inumeric(FLERR,arg[11]);
nznodes = force->inumeric(FLERR,arg[12]);
if (comm->me == 0) {
fpr = fopen(arg[13],"r");
if (fpr == NULL)
error->all(FLERR,fmt::format("Cannot open input file {}: {}",
arg[13], utils::getsyserror()));
}
nfileevery = force->inumeric(FLERR,arg[14]);
if (nfileevery) {
@ -115,8 +108,11 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
gfactor2 = new double[atom->ntypes+1];
// allocate 3d grid variables
// check for allowed maxium number of total grid nodes
total_nnodes = nxnodes*nynodes*nznodes;
total_nnodes = (bigint)nxnodes * (bigint)nynodes * (bigint)nznodes;
if (total_nnodes > MAXSMALLINT)
error->all(FLERR,"Too many nodes in fix ttm");
memory->create(nsum,nxnodes,nynodes,nznodes,"ttm:nsum");
memory->create(nsum_all,nxnodes,nynodes,nznodes,"ttm:nsum_all");
@ -149,7 +145,7 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
// set initial electron temperatures from user input file
if (me == 0) read_initial_electron_temperatures();
if (me == 0) read_initial_electron_temperatures(arg[13]);
MPI_Bcast(&T_electron[0][0][0],total_nnodes,MPI_DOUBLE,0,world);
}
@ -329,36 +325,52 @@ void FixTTM::reset_dt()
only called by proc 0
------------------------------------------------------------------------- */
void FixTTM::read_initial_electron_temperatures()
void FixTTM::read_initial_electron_temperatures(const char *filename)
{
char line[MAXLINE];
memset(&T_initial_set[0][0][0],0,total_nnodes*sizeof(double));
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;
std::string name = utils::get_potential_file_path(filename);
if (name.empty())
error->one(FLERR,fmt::format("Cannot open input file: {}",
filename));
FILE *fpr = fopen(name.c_str(),"r");
// read initial electron temperature values from file
char line[MAXLINE];
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);
ValueTokenizer values(line);
if (values.has_next()) ixnode = values.next_int();
if (values.has_next()) iynode = values.next_int();
if (values.has_next()) iznode = values.next_int();
if (values.has_next()) T_tmp = values.next_double();
else error->one(FLERR,"Incorrect format in fix ttm input file");
// check correctness of input data
if ((ixnode < 0) || (ixnode >= nxnodes)
|| (iynode < 0) || (iynode >= nynodes)
|| (iznode < 0) || (iznode >= nznodes))
error->one(FLERR,"Fix ttm invalide node index in fix ttm input");
if (T_tmp < 0.0)
error->one(FLERR,"Fix ttm electron temperatures must be > 0.0");
T_electron[ixnode][iynode][iznode] = T_tmp;
T_initial_set[ixnode][iynode][iznode] = 1;
}
// check completeness of input data
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");
// close file
fclose(fpr);
}
@ -525,15 +537,15 @@ void FixTTM::end_of_step()
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);
fmt::print(fp," {}",T_a);
}
fprintf(fp,"\t");
fputs("\t",fp);
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");
fmt::print(fp," {}",T_electron[ixnode][iynode][iznode]);
fputs("\n",fp);
}
}
}

7
src/MISC/fix_ttm.h
View File

@ -53,8 +53,9 @@ class FixTTM : public Fix {
int nlevels_respa;
int seed;
class RanMars *random;
FILE *fp,*fpr;
int nxnodes,nynodes,nznodes,total_nnodes;
FILE *fp;
int nxnodes,nynodes,nznodes;
bigint total_nnodes;
int ***nsum;
int ***nsum_all,***T_initial_set;
double *gfactor1,*gfactor2,*ratio;
@ -67,7 +68,7 @@ class FixTTM : public Fix {
double electronic_thermal_conductivity;
double gamma_p,gamma_s,v_0,v_0_sq;
void read_initial_electron_temperatures();
void read_initial_electron_temperatures(const char *);
};
}

329
src/USER-MISC/fix_ttm_mod.cpp
View File

@ -34,6 +34,7 @@
#include "math_const.h"
#include "utils.h"
#include "fmt/format.h"
#include "tokenizer.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -82,26 +83,15 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
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];
snprintf(str,128,"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");
const char *filename = arg[8];
FILE *fpr = force->open_potential(filename);
if (fpr == NULL) {
char str[128];
snprintf(str,128,"Cannot open file %s",filename);
error->all(FLERR,str);
}
total_nnodes = (bigint)nxnodes * (bigint)nynodes * (bigint)nznodes;
if (total_nnodes > MAXSMALLINT)
error->all(FLERR,"Too many nodes in fix ttm/mod");
nfileevery = force->inumeric(FLERR,arg[9]);
if (nfileevery > 0) {
@ -116,121 +106,11 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
}
}
}
char linee[MAXLINE];
double tresh_d;
int tresh_i;
// C0 (metal)
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
esheat_0 = tresh_d;
// C1 (metal*10^3)
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
esheat_1 = tresh_d;
// C2 (metal*10^6)
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
esheat_2 = tresh_d;
// C3 (metal*10^9)
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
esheat_3 = tresh_d;
// C4 (metal*10^12)
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
esheat_4 = tresh_d;
// C_limit
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
C_limit = tresh_d;
//Temperature damping factor
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
T_damp = tresh_d;
// rho_e
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
electronic_density = tresh_d;
//thermal_diffusion
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
el_th_diff = tresh_d;
// gamma_p
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
gamma_p = tresh_d;
// gamma_s
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
gamma_s = tresh_d;
// v0
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
v_0 = tresh_d;
// average intensity of pulse (source of energy) (metal units)
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
intensity = tresh_d;
// coordinate of 1st surface in x-direction (in box units) - constant
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%d",&tresh_i);
surface_l = tresh_i;
// coordinate of 2nd surface in x-direction (in box units) - constant
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%d",&tresh_i);
surface_r = tresh_i;
// skin_layer = intensity is reduced (I=I0*exp[-x/skin_layer])
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%d",&tresh_i);
skin_layer = tresh_i;
// width of pulse (picoseconds)
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
width = tresh_d;
// factor of electronic pressure (PF) Pe = PF*Ce*Te
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
pres_factor = tresh_d;
// effective free path of electrons (angstrom)
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
free_path = tresh_d;
// ionic density (ions*angstrom^{-3})
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
ionic_density = tresh_d;
// if movsur = 0: surface is freezed
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%d",&tresh_i);
movsur = tresh_i;
// electron_temperature_min
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d);
electron_temperature_min = tresh_d;
fclose(fpr_2);
read_parameters(arg[4]);
// t_surface is determined by electronic temperature (not constant)
t_surface_l = surface_l;
mult_factor = intensity;
duration = 0.0;
@ -279,9 +159,8 @@ 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(fpr);
if (me == 0) read_initial_electron_temperatures(arg[13]);
MPI_Bcast(&T_electron[0][0][0],total_nnodes,MPI_DOUBLE,0,world);
fclose(fpr);
}
/* ---------------------------------------------------------------------- */
@ -488,33 +367,197 @@ void FixTTMMod::reset_dt()
sqrt(24.0*force->boltz*gamma_p/update->dt/force->mvv2e) / force->ftm2v;
}
/* ----------------------------------------------------------------------
read in ttm/mod parameters from a user-specified file
only called by proc 0
------------------------------------------------------------------------- */
void FixTTMMod::read_parameters(const char *filename)
{
char line[MAXLINE];
std::string name = utils::get_potential_file_path(filename);
if (name.empty())
error->one(FLERR,fmt::format("Cannot open input file: {}",
filename));
FILE *fpr = fopen(name.c_str(),"r");
// C0 (metal)
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
esheat_0 = utils::numeric(FLERR,line,true,lmp);
// C1 (metal*10^3)
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
esheat_1 = utils::numeric(FLERR,line,true,lmp);
// C2 (metal*10^6)
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
esheat_2 = utils::numeric(FLERR,line,true,lmp);
// C3 (metal*10^9)
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
esheat_3 = utils::numeric(FLERR,line,true,lmp);
// C4 (metal*10^12)
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
esheat_4 = utils::numeric(FLERR,line,true,lmp);
// C_limit
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
C_limit = utils::numeric(FLERR,line,true,lmp);
// Temperature damping factor
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
T_damp = utils::numeric(FLERR,line,true,lmp);
// rho_e
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
electronic_density = utils::numeric(FLERR,line,true,lmp);
// thermal_diffusion
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
el_th_diff = utils::numeric(FLERR,line,true,lmp);
// gamma_p
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
gamma_p = utils::numeric(FLERR,line,true,lmp);
// gamma_s
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
gamma_s = utils::numeric(FLERR,line,true,lmp);
// v0
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
v_0 = utils::numeric(FLERR,line,true,lmp);
// average intensity of pulse (source of energy) (metal units)
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
intensity = utils::numeric(FLERR,line,true,lmp);
// coordinate of 1st surface in x-direction (in box units) - constant
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
surface_l = utils::inumeric(FLERR,line,true,lmp);
// coordinate of 2nd surface in x-direction (in box units) - constant
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
surface_r = utils::inumeric(FLERR,line,true,lmp);
// skin_layer = intensity is reduced (I=I0*exp[-x/skin_layer])
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
skin_layer = utils::inumeric(FLERR,line,true,lmp);
// width of pulse (picoseconds)
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
width = utils::numeric(FLERR,line,true,lmp);
// factor of electronic pressure (PF) Pe = PF*Ce*Te
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
pres_factor = utils::numeric(FLERR,line,true,lmp);
// effective free path of electrons (angstrom)
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
free_path = utils::numeric(FLERR,line,true,lmp);
// ionic density (ions*angstrom^{-3})
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
ionic_density = utils::numeric(FLERR,line,true,lmp);
// if movsur = 0: surface is frozen
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
movsur = utils::inumeric(FLERR,line,true,lmp);
// electron_temperature_min
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
electron_temperature_min = utils::numeric(FLERR,line,true,lmp);
fclose(fpr);
}
/* ----------------------------------------------------------------------
read in initial electron temperatures from a user-specified file
only called by proc 0
------------------------------------------------------------------------- */
void FixTTMMod::read_initial_electron_temperatures(FILE *fpr)
void FixTTMMod::read_initial_electron_temperatures(const char *filename)
{
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;
memset(&T_initial_set[0][0][0],0,total_nnodes*sizeof(double));
std::string name = utils::get_potential_file_path(filename);
if (name.empty())
error->one(FLERR,fmt::format("Cannot open input file: {}",
filename));
FILE *fpr = fopen(name.c_str(),"r");
// read initial electron temperature values from file
char line[MAXLINE];
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");
ValueTokenizer values(line);
if (values.has_next()) ixnode = values.next_int();
if (values.has_next()) iynode = values.next_int();
if (values.has_next()) iznode = values.next_int();
if (values.has_next()) T_tmp = values.next_double();
else error->one(FLERR,"Incorrect format in fix ttm input file");
// check correctness of input data
if ((ixnode < 0) || (ixnode >= nxnodes)
|| (iynode < 0) || (iynode >= nynodes)
|| (iznode < 0) || (iznode >= nznodes))
error->one(FLERR,"Fix ttm invalide node index in fix ttm input");
if (T_tmp < 0.0)
error->one(FLERR,"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(FLERR,"Initial temperatures not all set in fix ttm/mod");
fclose(fpr);
}
/* ---------------------------------------------------------------------- */

3
src/USER-MISC/fix_ttm_mod.h
View File

@ -79,7 +79,8 @@ class FixTTMMod : public Fix {
double electron_temperature_min;
el_heat_capacity_thermal_conductivity el_properties(double);
double el_sp_heat_integral(double);
void read_initial_electron_temperatures(FILE *);
void read_parameters(const char *);
void read_initial_electron_temperatures(const char *);
};
}