Merge pull request #2264 from akohlmey/fix_ttm_parser_update (59b5c7c1) · Commits · 郑智淋 / lammps

src/MISC/fix_ttm.cpp

+51 −38

Original line number	Diff line number	Diff line
		@@ -31,6 +31,7 @@
		#include "error.h"
		#include "utils.h"
		#include "fmt/format.h"
		#include "tokenizer.h"

		using namespace LAMMPS_NS;
		using namespace FixConst;
		@@ -41,11 +42,11 @@ 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),
		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),
		net_energy_transfer(NULL), net_energy_transfer_all(NULL)
		random(NULL), fp(NULL), nsum(NULL), nsum_all(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), net_energy_transfer(NULL),
		net_energy_transfer_all(NULL)
		{
		if (narg < 15) error->all(FLERR,"Illegal fix ttm command");

		@@ -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) {
		@@ -115,12 +108,14 @@ 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 = nxnodesnynodesnznodes;
		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");
		memory->create(T_initial_set,nxnodes,nynodes,nznodes,"ttm:T_initial_set");
		memory->create(sum_vsq,nxnodes,nynodes,nznodes,"ttm:sum_vsq");
		memory->create(sum_mass_vsq,nxnodes,nynodes,nznodes,"ttm:sum_mass_vsq");
		memory->create(sum_vsq_all,nxnodes,nynodes,nznodes,"ttm:sum_vsq_all");
		@@ -149,7 +144,7 @@ FixTTM::FixTTM(LAMMPS lmp, int narg, char *arg) :

		// set initial electron temperatures from user input file

		if (me == 0) read_initial_electron_temperatures();
		if (comm->me == 0) read_initial_electron_temperatures(arg[13]);
		MPI_Bcast(&T_electron[0][0][0],total_nnodes,MPI_DOUBLE,0,world);
		}

		@@ -157,7 +152,7 @@ FixTTM::FixTTM(LAMMPS lmp, int narg, char *arg) :

		FixTTM::~FixTTM()
		{
		if (nfileevery && me == 0) fclose(fp);
		if (fp) fclose(fp);

		delete random;

		@@ -166,7 +161,6 @@ FixTTM::~FixTTM()

		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);
		@@ -221,9 +215,9 @@ void FixTTM::init()

		void FixTTM::setup(int vflag)
		{
		if (strstr(update->integrate_style,"verlet"))
		if (utils::strmatch(update->integrate_style,"^verlet")) {
		post_force_setup(vflag);
		else {
		} 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);
		@@ -329,27 +323,48 @@ 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];
		int ***T_initial_set;
		memory->create(T_initial_set,nxnodes,nynodes,nznodes,"ttm:T_initial_set");
		memset(&T_initial_set[0][0][0],0,total_nnodes*sizeof(int));

		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;
		}
		fclose(fpr);

		// check completeness of input data

		for (int ixnode = 0; ixnode < nxnodes; ixnode++)
		for (int iynode = 0; iynode < nynodes; iynode++)
		@@ -357,9 +372,7 @@ void FixTTM::read_initial_electron_temperatures()
		if (T_initial_set[ixnode][iynode][iznode] == 0)
		error->one(FLERR,"Initial temperatures not all set in fix ttm");

		// close file

		fclose(fpr);
		memory->destroy(T_initial_set);
		}

		/* ---------------------------------------------------------------------- */
		@@ -514,7 +527,7 @@ void FixTTM::end_of_step()
		MPI_Allreduce(&sum_mass_vsq[0][0][0],&sum_mass_vsq_all[0][0][0],
		total_nnodes,MPI_DOUBLE,MPI_SUM,world);

		if (me == 0) {
		if (comm->me == 0) {
		fmt::print(fp,"{}",update->ntimestep);

		double T_a;
		@@ -525,15 +538,15 @@ void FixTTM::end_of_step()
		if (nsum_all[ixnode][iynode][iznode] > 0)
		T_a = sum_mass_vsq_all[ixnode][iynode][iznode]/
		(3.0force->boltznsum_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);
		}
		}
		}

src/MISC/fix_ttm.h

+6 −8

Original line number	Diff line number	Diff line
		@@ -48,17 +48,15 @@ class FixTTM : public Fix {
		double compute_vector(int);

		private:
		int me;
		int nfileevery;
		int nlevels_respa;
		int seed;
		class RanMars *random;
		FILE fp,fpr;
		int nxnodes,nynodes,nznodes,total_nnodes;
		int ***nsum;
		int *nsum_all,*T_initial_set;
		double gfactor1,gfactor2,*ratio;
		double **flangevin;
		FILE *fp;
		int nxnodes,nynodes,nznodes;
		bigint total_nnodes;
		int *nsum, *nsum_all;
		double gfactor1,gfactor2,ratio,*flangevin;
		double *T_electron,*T_electron_old;
		double *sum_vsq,*sum_mass_vsq;
		double *sum_vsq_all,*sum_mass_vsq_all;
		@@ -67,7 +65,7 @@ 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 *);
		};

		}

src/USER-MISC/fix_ttm_mod.cpp

+260 −156

File changed.

Preview size limit exceeded, changes collapsed.

src/USER-MISC/fix_ttm_mod.h

+6 −7

Original line number	Diff line number	Diff line
		@@ -53,17 +53,15 @@ class FixTTMMod : public Fix {
		double compute_vector(int);

		private:
		int me;
		int nfileevery;
		int nlevels_respa;
		int seed;
		class RanMars *random;
		FILE *fp;
		int nxnodes,nynodes,nznodes,total_nnodes;
		int ***nsum;
		int *nsum_all,*T_initial_set;
		double gfactor1,gfactor2,*ratio;
		double **flangevin;
		int nxnodes,nynodes,nznodes;
		bigint total_nnodes;
		int *nsum, *nsum_all;
		double gfactor1,gfactor2,ratio,*flangevin;
		double *T_electron,T_electron_old,**T_electron_first;
		double *sum_vsq,*sum_mass_vsq;
		double *sum_vsq_all,*sum_mass_vsq_all;
		@@ -79,7 +77,8 @@ 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 *);
		};

		}

src/utils.cpp

+13 −0

Original line number	Diff line number	Diff line
		@@ -348,6 +348,19 @@ tagint utils::tnumeric(const char file, int line, const char str,
		return ATOTAGINT(str);
		}

		/* ----------------------------------------------------------------------
		Return string without leading or trailing whitespace
		------------------------------------------------------------------------- */

		std::string utils::trim(const std::string & line) {
		int beg = re_match(line.c_str(),"\\S+");
		int end = re_match(line.c_str(),"\\s+$");
		if (beg < 0) beg = 0;
		if (end < 0) end = line.size();

		return line.substr(beg,end-beg);
		}

		/* ----------------------------------------------------------------------
		Return string without trailing # comment
		------------------------------------------------------------------------- */

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