Merge branch 'master' into collected-small-changes (95433356) · Commits · 郑智淋 / lammps

src/KOKKOS/pair_reaxc_kokkos.cpp

+33 −41

Original line number	Diff line number	Diff line
		@@ -447,23 +447,23 @@ int PairReaxCKokkos<DeviceType>::Init_Lookup_Tables()
		num_atom_types = atom->ntypes;
		dr = control->nonb_cut / control->tabulate;
		h = (double*)
		smalloc( (control->tabulate+2) * sizeof(double), "lookup:h", world );
		smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:h");
		fh = (double*)
		smalloc( (control->tabulate+2) * sizeof(double), "lookup:fh", world );
		smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fh");
		fvdw = (double*)
		smalloc( (control->tabulate+2) * sizeof(double), "lookup:fvdw", world );
		smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fvdw");
		fCEvd = (double*)
		smalloc( (control->tabulate+2) * sizeof(double), "lookup:fCEvd", world );
		smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fCEvd");
		fele = (double*)
		smalloc( (control->tabulate+2) * sizeof(double), "lookup:fele", world );
		smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fele");
		fCEclmb = (double*)
		smalloc( (control->tabulate+2) * sizeof(double), "lookup:fCEclmb", world );
		smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fCEclmb");

		LR = (LR_lookup_table**)
		scalloc( num_atom_types+1, sizeof(LR_lookup_table*), "lookup:LR", world );
		scalloc( control->error_ptr, num_atom_types+1, sizeof(LR_lookup_table*), "lookup:LR");
		for( i = 0; i < num_atom_types+1; ++i )
		LR[i] = (LR_lookup_table*)
		scalloc( num_atom_types+1, sizeof(LR_lookup_table), "lookup:LR[i]", world );
		scalloc( control->error_ptr, num_atom_types+1, sizeof(LR_lookup_table), "lookup:LR[i]");

		for( i = 1; i <= num_atom_types; ++i ) {
		for( j = i; j <= num_atom_types; ++j ) {
		@@ -473,22 +473,18 @@ int PairReaxCKokkos<DeviceType>::Init_Lookup_Tables()
		LR[i][j].dx = dr;
		LR[i][j].inv_dx = control->tabulate / control->nonb_cut;
		LR[i][j].y = (LR_data*)
		smalloc( LR[i][j].n * sizeof(LR_data), "lookup:LR[i,j].y", world );
		smalloc( control->error_ptr, LR[i][j].n * sizeof(LR_data), "lookup:LR[i,j].y");
		LR[i][j].H = (cubic_spline_coef*)
		smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].H" ,
		world );
		smalloc( control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].H");
		LR[i][j].vdW = (cubic_spline_coef*)
		smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].vdW",
		world);
		smalloc( control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].vdW");
		LR[i][j].CEvd = (cubic_spline_coef*)
		smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].CEvd",
		world);
		smalloc( control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].CEvd");
		LR[i][j].ele = (cubic_spline_coef*)
		smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].ele",
		world );
		smalloc( control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].ele");
		LR[i][j].CEclmb = (cubic_spline_coef*)
		smalloc( LR[i][j].n*sizeof(cubic_spline_coef),
		"lookup:LR[i,j].CEclmb", world );
		smalloc( control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),
		"lookup:LR[i,j].CEclmb");

		for( r = 1; r <= control->tabulate; ++r ) {
		LR_vdW_Coulomb(i, j, r * dr, &(LR[i][j].y[r]) );
		@@ -512,24 +508,20 @@ int PairReaxCKokkos<DeviceType>::Init_Lookup_Tables()
		vlast_vdw = fCEvd[r-1];
		vlast_ele = fele[r-1];

		Natural_Cubic_Spline( &h[1], &fh[1],
		&(LR[i][j].H[1]), control->tabulate+1, world );
		Natural_Cubic_Spline( control->error_ptr, &h[1], &fh[1],
		&(LR[i][j].H[1]), control->tabulate+1 );

		Complete_Cubic_Spline( &h[1], &fvdw[1], v0_vdw, vlast_vdw,
		&(LR[i][j].vdW[1]), control->tabulate+1,
		world );
		Complete_Cubic_Spline( control->error_ptr, &h[1], &fvdw[1], v0_vdw, vlast_vdw,
		&(LR[i][j].vdW[1]), control->tabulate+1 );

		Natural_Cubic_Spline( &h[1], &fCEvd[1],
		&(LR[i][j].CEvd[1]), control->tabulate+1,
		world );
		Natural_Cubic_Spline( control->error_ptr, &h[1], &fCEvd[1],
		&(LR[i][j].CEvd[1]), control->tabulate+1 );

		Complete_Cubic_Spline( &h[1], &fele[1], v0_ele, vlast_ele,
		&(LR[i][j].ele[1]), control->tabulate+1,
		world );
		Complete_Cubic_Spline( control->error_ptr, &h[1], &fele[1], v0_ele, vlast_ele,
		&(LR[i][j].ele[1]), control->tabulate+1 );

		Natural_Cubic_Spline( &h[1], &fCEclmb[1],
		&(LR[i][j].CEclmb[1]), control->tabulate+1,
		world );
		Natural_Cubic_Spline( control->error_ptr, &h[1], &fCEclmb[1],
		&(LR[i][j].CEclmb[1]), control->tabulate+1 );
		}
		}
		free(h);
		@@ -555,16 +547,16 @@ void PairReaxCKokkos<DeviceType>::Deallocate_Lookup_Tables()
		for( i = 0; i <= ntypes; ++i ) {
		for( j = i; j <= ntypes; ++j )
		if (LR[i][j].n) {
		sfree( LR[i][j].y, "LR[i,j].y" );
		sfree( LR[i][j].H, "LR[i,j].H" );
		sfree( LR[i][j].vdW, "LR[i,j].vdW" );
		sfree( LR[i][j].CEvd, "LR[i,j].CEvd" );
		sfree( LR[i][j].ele, "LR[i,j].ele" );
		sfree( LR[i][j].CEclmb, "LR[i,j].CEclmb" );
		sfree( control->error_ptr, LR[i][j].y, "LR[i,j].y" );
		sfree( control->error_ptr, LR[i][j].H, "LR[i,j].H" );
		sfree( control->error_ptr, LR[i][j].vdW, "LR[i,j].vdW" );
		sfree( control->error_ptr, LR[i][j].CEvd, "LR[i,j].CEvd" );
		sfree( control->error_ptr, LR[i][j].ele, "LR[i,j].ele" );
		sfree( control->error_ptr, LR[i][j].CEclmb, "LR[i,j].CEclmb" );
		}
		sfree( LR[i], "LR[i]" );
		sfree( control->error_ptr, LR[i], "LR[i]" );
		}
		sfree( LR, "LR" );
		sfree( control->error_ptr, LR, "LR" );
		}

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

src/USER-MISC/fix_pimd.cpp

+4 −4

Original line number	Diff line number	Diff line
		@@ -637,14 +637,14 @@ void FixPIMD::comm_exec(double **ptr)
		if(nsend > max_nsend)
		{
		max_nsend = nsend+200;
		tag_send = (int) memory->srealloc(tag_send, sizeof(int)max_nsend, "FixPIMD:tag_send");
		tag_send = (tagint) memory->srealloc(tag_send, sizeof(tagint)max_nsend, "FixPIMD:tag_send");
		buf_send = (double) memory->srealloc(buf_send, sizeof(double)max_nsend*3, "FixPIMD:x_send");
		}

		// send tags

		MPI_Sendrecv( atom->tag, nlocal, MPI_INT, plan_send[iplan], 0,
		tag_send, nsend, MPI_INT, plan_recv[iplan], 0, universe->uworld, MPI_STATUS_IGNORE);
		MPI_Sendrecv( atom->tag, nlocal, MPI_LMP_TAGINT, plan_send[iplan], 0,
		tag_send, nsend, MPI_LMP_TAGINT, plan_recv[iplan], 0, universe->uworld, MPI_STATUS_IGNORE);

		// wrap positions

src/USER-MISC/fix_pimd.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -68,7 +68,7 @@ class FixPIMD : public Fix {
		/* inter-partition communication */

		int max_nsend;
		int* tag_send;
		tagint* tag_send;
		double *buf_send;

		int max_nlocal;

src/USER-OMP/pair_reaxc_omp.cpp

+5 −5

Original line number	Diff line number	Diff line
		@@ -113,7 +113,7 @@ PairReaxCOMP::~PairReaxCOMP()
		if (setup_flag) {
		reax_list * bonds = lists+BONDS;
		for (int i=0; i<bonds->num_intrs; ++i)
		sfree(bonds->select.bond_list[i].bo_data.CdboReduction, "CdboReduction");
		sfree(error, bonds->select.bond_list[i].bo_data.CdboReduction, "CdboReduction");
		}
		memory->destroy(num_nbrs_offset);

		@@ -209,7 +209,7 @@ void PairReaxCOMP::compute(int eflag, int vflag)

		setup();

		Reset( system, control, data, workspace, &lists, world );
		Reset( system, control, data, workspace, &lists );

		// Why not update workspace like in MPI-only code?
		// Using the MPI-only way messes up the hb energy
		@@ -410,12 +410,12 @@ void PairReaxCOMP::setup( )

		// initialize my data structures

		PreAllocate_Space( system, control, workspace, world );
		PreAllocate_Space( system, control, workspace );
		write_reax_atoms();

		int num_nbrs = estimate_reax_lists();
		if(!Make_List(system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR,
		lists+FAR_NBRS, world))
		lists+FAR_NBRS))
		error->all(FLERR,"Pair reax/c problem in far neighbor list");

		write_reax_lists();
		@@ -445,7 +445,7 @@ void PairReaxCOMP::setup( )

		// check if I need to shrink/extend my data-structs

		ReAllocate( system, control, data, workspace, &lists, mpi_data );
		ReAllocate( system, control, data, workspace, &lists );
		}
		}

src/USER-OMP/reaxc_forces_omp.cpp

+7 −5

Original line number	Diff line number	Diff line
		@@ -289,9 +289,10 @@ void Validate_ListsOMP( reax_system system, storage /workspace /, reax_list
		else comp = bonds->num_intrs;

		if (End_Index(i, bonds) > comp) {
		fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
		char errmsg[256];
		snprintf(errmsg, 256, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
		step, i, End_Index(i,bonds), comp );
		MPI_Abort( comm, INSUFFICIENT_MEMORY );
		system->error_ptr->one(FLERR,errmsg);
		}
		}
		}
		@@ -315,9 +316,10 @@ void Validate_ListsOMP( reax_system system, storage /workspace /, reax_list
		else comp = hbonds->num_intrs;

		if (End_Index(Hindex, hbonds) > comp) {
		fprintf(stderr,"step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n",
		char errmsg[256];
		snprintf(errmsg, 256, "step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n",
		step, Hindex, End_Index(Hindex,hbonds), comp );
		MPI_Abort( comm, INSUFFICIENT_MEMORY );
		system->error_ptr->one(FLERR, errmsg);
		}
		}
		}

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