convert fix ttm and fix ttm/mod to use tokenizer class for parsing files
This commit is contained in:
Axel Kohlmeyer
@ -34,6 +34,7 @@
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#include "math_const.h"
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#include "utils.h"
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#include "fmt/format.h"
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#include "tokenizer.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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@ -82,26 +83,15 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
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if (seed <= 0)
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error->all(FLERR,"Invalid random number seed in fix ttm/mod command");
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FILE *fpr_2 = force->open_potential(arg[4]);
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if (fpr_2 == NULL) {
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char str[128];
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snprintf(str,128,"Cannot open file %s",arg[4]);
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error->all(FLERR,str);
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}
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nxnodes = force->inumeric(FLERR,arg[5]);
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nynodes = force->inumeric(FLERR,arg[6]);
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nznodes = force->inumeric(FLERR,arg[7]);
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if (nxnodes <= 0 || nynodes <= 0 || nznodes <= 0)
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error->all(FLERR,"Fix ttm/mod number of nodes must be > 0");
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const char *filename = arg[8];
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FILE *fpr = force->open_potential(filename);
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if (fpr == NULL) {
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char str[128];
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snprintf(str,128,"Cannot open file %s",filename);
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error->all(FLERR,str);
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}
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total_nnodes = (bigint)nxnodes * (bigint)nynodes * (bigint)nznodes;
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if (total_nnodes > MAXSMALLINT)
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error->all(FLERR,"Too many nodes in fix ttm/mod");
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nfileevery = force->inumeric(FLERR,arg[9]);
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if (nfileevery > 0) {
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@ -116,121 +106,11 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
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}
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}
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}
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char linee[MAXLINE];
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double tresh_d;
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int tresh_i;
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// C0 (metal)
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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esheat_0 = tresh_d;
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// C1 (metal*10^3)
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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esheat_1 = tresh_d;
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// C2 (metal*10^6)
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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esheat_2 = tresh_d;
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// C3 (metal*10^9)
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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esheat_3 = tresh_d;
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// C4 (metal*10^12)
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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esheat_4 = tresh_d;
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// C_limit
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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C_limit = tresh_d;
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//Temperature damping factor
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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T_damp = tresh_d;
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// rho_e
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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electronic_density = tresh_d;
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//thermal_diffusion
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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el_th_diff = tresh_d;
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// gamma_p
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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gamma_p = tresh_d;
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// gamma_s
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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gamma_s = tresh_d;
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// v0
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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v_0 = tresh_d;
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// average intensity of pulse (source of energy) (metal units)
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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intensity = tresh_d;
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// coordinate of 1st surface in x-direction (in box units) - constant
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%d",&tresh_i);
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surface_l = tresh_i;
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// coordinate of 2nd surface in x-direction (in box units) - constant
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%d",&tresh_i);
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surface_r = tresh_i;
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// skin_layer = intensity is reduced (I=I0*exp[-x/skin_layer])
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%d",&tresh_i);
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skin_layer = tresh_i;
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// width of pulse (picoseconds)
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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width = tresh_d;
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// factor of electronic pressure (PF) Pe = PF*Ce*Te
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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pres_factor = tresh_d;
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// effective free path of electrons (angstrom)
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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free_path = tresh_d;
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// ionic density (ions*angstrom^{-3})
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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ionic_density = tresh_d;
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// if movsur = 0: surface is freezed
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%d",&tresh_i);
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movsur = tresh_i;
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// electron_temperature_min
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
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sscanf(linee,"%lg",&tresh_d);
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electron_temperature_min = tresh_d;
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fclose(fpr_2);
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//t_surface is determined by electronic temperature (not constant)
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read_parameters(arg[4]);
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// t_surface is determined by electronic temperature (not constant)
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t_surface_l = surface_l;
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mult_factor = intensity;
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duration = 0.0;
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@ -279,9 +159,8 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
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atom->add_callback(0);
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atom->add_callback(1);
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// set initial electron temperatures from user input file
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if (me == 0) read_initial_electron_temperatures(fpr);
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if (me == 0) read_initial_electron_temperatures(arg[13]);
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MPI_Bcast(&T_electron[0][0][0],total_nnodes,MPI_DOUBLE,0,world);
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fclose(fpr);
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}
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/* ---------------------------------------------------------------------- */
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@ -488,33 +367,197 @@ void FixTTMMod::reset_dt()
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sqrt(24.0*force->boltz*gamma_p/update->dt/force->mvv2e) / force->ftm2v;
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}
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/* ----------------------------------------------------------------------
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read in ttm/mod parameters from a user-specified file
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only called by proc 0
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------------------------------------------------------------------------- */
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void FixTTMMod::read_parameters(const char *filename)
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{
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char line[MAXLINE];
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std::string name = utils::get_potential_file_path(filename);
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if (name.empty())
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error->one(FLERR,fmt::format("Cannot open input file: {}",
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filename));
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FILE *fpr = fopen(name.c_str(),"r");
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// C0 (metal)
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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esheat_0 = utils::numeric(FLERR,line,true,lmp);
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// C1 (metal*10^3)
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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esheat_1 = utils::numeric(FLERR,line,true,lmp);
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// C2 (metal*10^6)
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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esheat_2 = utils::numeric(FLERR,line,true,lmp);
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// C3 (metal*10^9)
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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esheat_3 = utils::numeric(FLERR,line,true,lmp);
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// C4 (metal*10^12)
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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esheat_4 = utils::numeric(FLERR,line,true,lmp);
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// C_limit
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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C_limit = utils::numeric(FLERR,line,true,lmp);
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// Temperature damping factor
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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T_damp = utils::numeric(FLERR,line,true,lmp);
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// rho_e
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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electronic_density = utils::numeric(FLERR,line,true,lmp);
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// thermal_diffusion
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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el_th_diff = utils::numeric(FLERR,line,true,lmp);
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// gamma_p
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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gamma_p = utils::numeric(FLERR,line,true,lmp);
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// gamma_s
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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gamma_s = utils::numeric(FLERR,line,true,lmp);
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// v0
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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v_0 = utils::numeric(FLERR,line,true,lmp);
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// average intensity of pulse (source of energy) (metal units)
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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intensity = utils::numeric(FLERR,line,true,lmp);
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// coordinate of 1st surface in x-direction (in box units) - constant
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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surface_l = utils::inumeric(FLERR,line,true,lmp);
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// coordinate of 2nd surface in x-direction (in box units) - constant
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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surface_r = utils::inumeric(FLERR,line,true,lmp);
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// skin_layer = intensity is reduced (I=I0*exp[-x/skin_layer])
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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skin_layer = utils::inumeric(FLERR,line,true,lmp);
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// width of pulse (picoseconds)
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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width = utils::numeric(FLERR,line,true,lmp);
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// factor of electronic pressure (PF) Pe = PF*Ce*Te
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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pres_factor = utils::numeric(FLERR,line,true,lmp);
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// effective free path of electrons (angstrom)
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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free_path = utils::numeric(FLERR,line,true,lmp);
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// ionic density (ions*angstrom^{-3})
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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ionic_density = utils::numeric(FLERR,line,true,lmp);
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// if movsur = 0: surface is frozen
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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movsur = utils::inumeric(FLERR,line,true,lmp);
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// electron_temperature_min
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fpr,filename,error);
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electron_temperature_min = utils::numeric(FLERR,line,true,lmp);
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fclose(fpr);
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}
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/* ----------------------------------------------------------------------
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read in initial electron temperatures from a user-specified file
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only called by proc 0
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------------------------------------------------------------------------- */
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void FixTTMMod::read_initial_electron_temperatures(FILE *fpr)
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void FixTTMMod::read_initial_electron_temperatures(const char *filename)
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{
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char line[MAXLINE];
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for (int ixnode = 0; ixnode < nxnodes; ixnode++)
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for (int iynode = 0; iynode < nynodes; iynode++)
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for (int iznode = 0; iznode < nznodes; iznode++)
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T_initial_set[ixnode][iynode][iznode] = 0;
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memset(&T_initial_set[0][0][0],0,total_nnodes*sizeof(double));
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std::string name = utils::get_potential_file_path(filename);
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if (name.empty())
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error->one(FLERR,fmt::format("Cannot open input file: {}",
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filename));
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FILE *fpr = fopen(name.c_str(),"r");
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// read initial electron temperature values from file
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char line[MAXLINE];
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int ixnode,iynode,iznode;
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double T_tmp;
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while (1) {
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if (fgets(line,MAXLINE,fpr) == NULL) break;
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sscanf(line,"%d %d %d %lg",&ixnode,&iynode,&iznode,&T_tmp);
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if (T_tmp < 0.0) error->one(FLERR,"Fix ttm/mod electron temperatures must be >= 0.0");
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ValueTokenizer values(line);
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if (values.has_next()) ixnode = values.next_int();
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if (values.has_next()) iynode = values.next_int();
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if (values.has_next()) iznode = values.next_int();
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if (values.has_next()) T_tmp = values.next_double();
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else error->one(FLERR,"Incorrect format in fix ttm input file");
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// check correctness of input data
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if ((ixnode < 0) || (ixnode >= nxnodes)
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|| (iynode < 0) || (iynode >= nynodes)
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|| (iznode < 0) || (iznode >= nznodes))
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error->one(FLERR,"Fix ttm invalide node index in fix ttm input");
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if (T_tmp < 0.0)
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error->one(FLERR,"Fix ttm electron temperatures must be > 0.0");
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T_electron[ixnode][iynode][iznode] = T_tmp;
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T_initial_set[ixnode][iynode][iznode] = 1;
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}
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for (int ixnode = 0; ixnode < nxnodes; ixnode++)
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for (int iynode = 0; iynode < nynodes; iynode++)
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for (int iznode = 0; iznode < nznodes; iznode++)
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if (T_initial_set[ixnode][iynode][iznode] == 0)
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error->one(FLERR,"Initial temperatures not all set in fix ttm/mod");
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fclose(fpr);
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}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Reference in New Issue
Block a user