T_initial_set array is only required during reading of the mesh (4a28a708) · Commits · 郑智淋 / lammps

src/MISC/fix_ttm.cpp

+9 −7

Original line number	Diff line number	Diff line
		@@ -42,7 +42,7 @@ using namespace FixConst;

		FixTTM::FixTTM(LAMMPS lmp, int narg, char *arg) :
		Fix(lmp, narg, arg),
		random(NULL), fp(NULL), T_initial_set(NULL), nsum(NULL), nsum_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),
		@@ -116,7 +116,6 @@ FixTTM::FixTTM(LAMMPS lmp, int narg, char *arg) :

		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");
		@@ -162,7 +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);
		@@ -217,9 +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);
		@@ -327,6 +325,8 @@ void FixTTM::reset_dt()

		void FixTTM::read_initial_electron_temperatures(const char *filename)
		{
		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));

		std::string name = utils::get_potential_file_path(filename);
		@@ -371,6 +371,8 @@ void FixTTM::read_initial_electron_temperatures(const char *filename)
		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");

		memory->destroy(T_initial_set);
		}

		/* ---------------------------------------------------------------------- */

src/MISC/fix_ttm.h

+0 −1

Original line number	Diff line number	Diff line
		@@ -55,7 +55,6 @@ class FixTTM : public Fix {
		FILE *fp;
		int nxnodes,nynodes,nznodes;
		bigint total_nnodes;
		int ***T_initial_set;
		int *nsum, *nsum_all;
		double gfactor1,gfactor2,ratio,*flangevin;
		double *T_electron,*T_electron_old;

src/USER-MISC/fix_ttm_mod.cpp

+61 −12

Original line number	Diff line number	Diff line
		@@ -67,7 +67,7 @@ static const char cite_fix_ttm_mod[] =

		FixTTMMod::FixTTMMod(LAMMPS lmp, int narg, char *arg) :
		Fix(lmp, narg, arg),
		random(NULL), fp(NULL), T_initial_set(NULL), nsum(NULL), nsum_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),
		@@ -139,7 +139,6 @@ FixTTMMod::FixTTMMod(LAMMPS lmp, int narg, char *arg) :
		total_nnodes = nxnodesnynodesnznodes;
		memory->create(nsum,nxnodes,nynodes,nznodes,"ttm/mod:nsum");
		memory->create(nsum_all,nxnodes,nynodes,nznodes,"ttm/mod:nsum_all");
		memory->create(T_initial_set,nxnodes,nynodes,nznodes,"ttm/mod:T_initial_set");
		memory->create(sum_vsq,nxnodes,nynodes,nznodes,"ttm/mod:sum_vsq");
		memory->create(sum_mass_vsq,nxnodes,nynodes,nznodes,"ttm/mod:sum_mass_vsq");
		memory->create(sum_vsq_all,nxnodes,nynodes,nznodes,"ttm/mod:sum_vsq_all");
		@@ -154,15 +153,20 @@ FixTTMMod::FixTTMMod(LAMMPS lmp, int narg, char *arg) :
		"ttm/mod:net_energy_transfer_all");
		flangevin = NULL;
		grow_arrays(atom->nmax);

		// zero out the flangevin array

		for (int i = 0; i < atom->nmax; i++) {
		flangevin[i][0] = 0;
		flangevin[i][1] = 0;
		flangevin[i][2] = 0;
		}

		atom->add_callback(0);
		atom->add_callback(1);

		// set initial electron temperatures from user input file

		if (comm->me == 0) read_initial_electron_temperatures(arg[13]);
		MPI_Bcast(&T_electron[0][0][0],total_nnodes,MPI_DOUBLE,0,world);
		}
		@@ -173,11 +177,12 @@ FixTTMMod::~FixTTMMod()
		{
		if (fp) fclose(fp);
		delete random;

		delete [] gfactor1;
		delete [] gfactor2;

		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);
		@@ -211,16 +216,20 @@ void FixTTMMod::init()
		error->all(FLERR,"Cannot use non-periodic boundares with fix ttm/mod");
		if (domain->triclinic)
		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;
		gfactor2[i] =
		sqrt(24.0force->boltzgamma_p/update->dt/force->mvv2e) / force->ftm2v;
		}

		for (int ixnode = 0; ixnode < nxnodes; ixnode++)
		for (int iynode = 0; iynode < nynodes; iynode++)
		for (int iznode = 0; iznode < nznodes; iznode++)
		net_energy_transfer_all[ixnode][iynode][iznode] = 0;

		if (strstr(update->integrate_style,"respa"))
		nlevels_respa = ((Respa *) update->integrate)->nlevels;
		}
		@@ -229,7 +238,7 @@ void FixTTMMod::init()

		void FixTTMMod::setup(int vflag)
		{
		if (strstr(update->integrate_style,"verlet")) {
		if (utils::strmatch(update->integrate_style,"^verlet")) {
		post_force_setup(vflag);
		} else {
		((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
		@@ -248,13 +257,17 @@ void FixTTMMod::post_force(int /vflag/)
		int *type = atom->type;
		int *mask = atom->mask;
		int nlocal = atom->nlocal;

		double dx = domain->xprd/nxnodes;
		double dy = domain->yprd/nynodes;
		double dz = domain->zprd/nynodes;
		double gamma1,gamma2;

		// apply damping and thermostat to all atoms in fix group

		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {

		double xscale = (x[i][0] - domain->boxlo[0])/domain->xprd;
		double yscale = (x[i][1] - domain->boxlo[1])/domain->yprd;
		double zscale = (x[i][2] - domain->boxlo[2])/domain->zprd;
		@@ -267,9 +280,12 @@ void FixTTMMod::post_force(int /vflag/)
		while (ixnode < 0) ixnode += nxnodes;
		while (iynode < 0) iynode += nynodes;
		while (iznode < 0) iznode += nznodes;

		if (T_electron[ixnode][iynode][iznode] < 0)
		error->all(FLERR,"Electronic temperature dropped below zero");

		double tsqrt = sqrt(T_electron[ixnode][iynode][iznode]);

		gamma1 = gfactor1[type[i]];
		double vsq = v[i][0]v[i][0] + v[i][1]v[i][1] + v[i][2]*v[i][2];
		if (vsq > v_0_sq) gamma1 *= (gamma_p + gamma_s)/gamma_p;
		@@ -338,7 +354,9 @@ void FixTTMMod::post_force_setup(int /vflag/)
		double **f = atom->f;
		int *mask = atom->mask;
		int nlocal = atom->nlocal;

		// apply langevin forces that have been stored from previous run

		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		f[i][0] += flangevin[i][0];
		@@ -526,6 +544,8 @@ void FixTTMMod::read_parameters(const char *filename)

		void FixTTMMod::read_initial_electron_temperatures(const char *filename)
		{
		int ***T_initial_set;
		memory->create(T_initial_set,nxnodes,nynodes,nznodes,"ttm/mod:T_initial_set");
		memset(&T_initial_set[0][0][0],0,total_nnodes*sizeof(int));

		std::string name = utils::get_potential_file_path(filename);
		@@ -570,6 +590,8 @@ void FixTTMMod::read_initial_electron_temperatures(const char *filename)
		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");

		memory->destroy(T_initial_set);
		}

		/* ---------------------------------------------------------------------- */
		@@ -606,6 +628,7 @@ void FixTTMMod::end_of_step()
		int *type = atom->type;
		int *mask = atom->mask;
		int nlocal = atom->nlocal;

		if (movsur == 1){
		for (int ixnode = 0; ixnode < nxnodes; ixnode++)
		for (int iynode = 0; iynode < nynodes; iynode++)
		@@ -621,6 +644,7 @@ void FixTTMMod::end_of_step()
		for (int iynode = 0; iynode < nynodes; iynode++)
		for (int iznode = 0; iznode < nznodes; iznode++)
		net_energy_transfer[ixnode][iynode][iznode] = 0;

		for (int i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		double xscale = (x[i][0] - domain->boxlo[0])/domain->xprd;
		@@ -642,9 +666,11 @@ void FixTTMMod::end_of_step()
		flangevin[i][2]*v[i][2]);
		}
		}

		MPI_Allreduce(&net_energy_transfer[0][0][0],
		&net_energy_transfer_all[0][0][0],
		total_nnodes,MPI_DOUBLE,MPI_SUM,world);

		double dx = domain->xprd/nxnodes;
		double dy = domain->yprd/nynodes;
		double dz = domain->zprd/nznodes;
		@@ -666,6 +692,7 @@ void FixTTMMod::end_of_step()
		}
		// num_inner_timesteps = # of inner steps (thermal solves)
		// required this MD step to maintain a stable explicit solve

		int num_inner_timesteps = 1;
		double inner_dt = update->dt;
		double stability_criterion = 0.0;
		@@ -775,9 +802,13 @@ void FixTTMMod::end_of_step()
		(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

		if ((nfileevery) && !(update->ntimestep % nfileevery)) {

		// compute atomic Ta for each grid point

		for (int ixnode = 0; ixnode < nxnodes; ixnode++)
		for (int iynode = 0; iynode < nynodes; iynode++)
		for (int iznode = 0; iznode < nznodes; iznode++) {
		@@ -788,6 +819,7 @@ void FixTTMMod::end_of_step()
		sum_vsq_all[ixnode][iynode][iznode] = 0.0;
		sum_mass_vsq_all[ixnode][iynode][iznode] = 0.0;
		}

		double massone;
		for (int i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		@@ -810,16 +842,18 @@ void FixTTMMod::end_of_step()
		sum_vsq[ixnode][iynode][iznode] += vsq;
		sum_mass_vsq[ixnode][iynode][iznode] += massone*vsq;
		}

		MPI_Allreduce(&nsum[0][0][0],&nsum_all[0][0][0],total_nnodes,
		MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&sum_vsq[0][0][0],&sum_vsq_all[0][0][0],total_nnodes,
		MPI_DOUBLE,MPI_SUM,world);
		MPI_Allreduce(&sum_mass_vsq[0][0][0],&sum_mass_vsq_all[0][0][0],
		total_nnodes,MPI_DOUBLE,MPI_SUM,world);
		MPI_Allreduce(&t_surface_l,&surface_l,
		1,MPI_INT,MPI_MIN,world);
		MPI_Allreduce(&t_surface_l,&surface_l,1,MPI_INT,MPI_MIN,world);

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

		double T_a;
		for (int ixnode = 0; ixnode < nxnodes; ixnode++)
		for (int iynode = 0; iynode < nynodes; iynode++)
		@@ -832,14 +866,15 @@ void FixTTMMod::end_of_step()
		if (T_electron[ixnode][iynode][iznode]==0.0) T_electron[ixnode][iynode][iznode] = electron_temperature_min;
		}
		}
		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);
		}
		}
		}
		@@ -872,10 +907,12 @@ double FixTTMMod::compute_vector(int n)
		{
		double e_energy = 0.0;
		double transfer_energy = 0.0;

		double dx = domain->xprd/nxnodes;
		double dy = domain->yprd/nynodes;
		double dz = domain->zprd/nznodes;
		double del_vol = dxdydz;

		for (int ixnode = 0; ixnode < nxnodes; ixnode++)
		for (int iynode = 0; iynode < nynodes; iynode++)
		for (int iznode = 0; iznode < nznodes; iznode++) {
		@@ -883,6 +920,7 @@ double FixTTMMod::compute_vector(int n)
		transfer_energy +=
		net_energy_transfer_all[ixnode][iynode][iznode]*update->dt;
		}

		if (n == 0) return e_energy;
		if (n == 1) return transfer_energy;
		return 0.0;
		@@ -896,17 +934,21 @@ void FixTTMMod::write_restart(FILE *fp)
		{
		double *rlist;
		memory->create(rlist,nxnodesnynodesnznodes+1,"ttm/mod:rlist");

		int n = 0;
		rlist[n++] = seed;

		for (int ixnode = 0; ixnode < nxnodes; ixnode++)
		for (int iynode = 0; iynode < nynodes; iynode++)
		for (int iznode = 0; iznode < nznodes; iznode++)
		rlist[n++] = T_electron[ixnode][iynode][iznode];

		if (comm->me == 0) {
		int size = n * sizeof(double);
		fwrite(&size,sizeof(int),1,fp);
		fwrite(rlist,sizeof(double),n,fp);
		}

		memory->destroy(rlist);
		}

		@@ -918,12 +960,16 @@ void FixTTMMod::restart(char *buf)
		{
		int n = 0;
		double rlist = (double ) buf;

		// the seed must be changed from the initial seed

		seed = static_cast<int> (0.5*rlist[n++]);

		for (int ixnode = 0; ixnode < nxnodes; ixnode++)
		for (int iynode = 0; iynode < nynodes; iynode++)
		for (int iznode = 0; iznode < nznodes; iznode++)
		T_electron[ixnode][iynode][iznode] = rlist[n++];

		delete random;
		random = new RanMars(lmp,seed+comm->me);
		}
		@@ -948,10 +994,13 @@ int FixTTMMod::pack_restart(int i, double *buf)
		void FixTTMMod::unpack_restart(int nlocal, int nth)
		{
		double **extra = atom->extra;

		// skip to Nth set of extra values

		int m = 0;
		for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
		m++;

		flangevin[nlocal][0] = extra[nlocal][m++];
		flangevin[nlocal][1] = extra[nlocal][m++];
		flangevin[nlocal][2] = extra[nlocal][m++];

src/USER-MISC/fix_ttm_mod.h

+0 −1

Original line number	Diff line number	Diff line
		@@ -60,7 +60,6 @@ class FixTTMMod : public Fix {
		FILE *fp;
		int nxnodes,nynodes,nznodes;
		bigint total_nnodes;
		int ***T_initial_set;
		int *nsum, *nsum_all;
		double gfactor1,gfactor2,ratio,*flangevin;
		double *T_electron,T_electron_old,**T_electron_first;

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