Better error handling in reaxc_forces (146e2f28) · Commits · 郑智淋 / lammps

src/USER-REAXC/pair_reaxc.cpp

+6 −5

Original line number	Diff line number	Diff line
		@@ -394,6 +394,7 @@ void PairReaxC::init_style( )
		"increased neighbor list skin.");

		for( int i = 0; i < LIST_N; ++i )
		if (lists[i].allacated != 1)
		lists[i].allocated = 0;

		if (fix_reax == NULL) {
		@@ -445,7 +446,7 @@ void PairReaxC::setup( )
		error->all(FLERR,"Pair reax/c problem in far neighbor list");

		write_reax_lists();
		Initialize( system, control, data, workspace, &lists, out_control,
		Initialize( lmp, system, control, data, workspace, &lists, out_control,
		mpi_data, world );
		for( int k = 0; k < system->N; ++k ) {
		num_bonds[k] = system->my_atoms[k].num_bonds;
		@@ -465,7 +466,7 @@ void PairReaxC::setup( )

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

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

		bigint local_ngroup = list->inum;
		@@ -517,7 +518,7 @@ void PairReaxC::compute(int eflag, int vflag)

		setup();

		Reset( system, control, data, workspace, &lists, world );
		Reset( lmp, system, control, data, workspace, &lists, world );
		workspace->realloc.num_far = write_reax_lists();
		// timing for filling in the reax lists
		if (comm->me == 0) {
		@@ -527,7 +528,7 @@ void PairReaxC::compute(int eflag, int vflag)

		// forces

		Compute_Forces(system,control,data,workspace,&lists,out_control,mpi_data);
		Compute_Forces(lmp, system,control,data,workspace,&lists,out_control,mpi_data);
		read_reax_forces(vflag);

		for(int k = 0; k < system->N; ++k) {

src/USER-REAXC/reaxc_allocate.cpp

+8 −4

Original line number	Diff line number	Diff line
		@@ -35,6 +35,10 @@
		#include <omp.h>
		#endif

		#include "lammps.h"
		#include "error.h"
		using namespace LAMMPS_NS;

		/* allocate space for my_atoms
		important: we cannot know the exact number of atoms that will fall into a
		process's box throughout the whole simulation. therefore
		@@ -353,7 +357,7 @@ static int Reallocate_HBonds_List( reax_system system, reax_list hbonds,
		}


		static int Reallocate_Bonds_List( reax_system system, reax_list bonds,
		static int Reallocate_Bonds_List( LAMMPS lmp, reax_system system, reax_list *bonds,
		int total_bonds, int est_3body,
		MPI_Comm comm )
		{
		@@ -379,7 +383,7 @@ static int Reallocate_Bonds_List( reax_system system, reax_list bonds,
		Delete_List( bonds, comm );
		if(!Make_List(system->total_cap, *total_bonds, TYP_BOND, bonds, comm)) {
		fprintf( stderr, "not enough space for bonds list. terminating!\n" );
		MPI_Abort( comm, INSUFFICIENT_MEMORY );
		lmp->error->all(FLERR, "Can't allocate space for hbonds.");
		}

		#ifdef LMP_USER_OMP
		@@ -399,7 +403,7 @@ static int Reallocate_Bonds_List( reax_system system, reax_list bonds,
		}


		void ReAllocate( reax_system system, control_params control,
		void ReAllocate( LAMMPS lmp, reax_system system, control_params *control,
		simulation_data data, storage workspace, reax_list **lists,
		mpi_datatypes *mpi_data )
		{
		@@ -490,7 +494,7 @@ void ReAllocate( reax_system system, control_params control,
		/* bonds list */
		num_bonds = est_3body = -1;
		if (Nflag \|\| realloc->bonds) {
		Reallocate_Bonds_List( system, (*lists)+BONDS, &num_bonds,
		Reallocate_Bonds_List( lmp, system, (*lists)+BONDS, &num_bonds,
		&est_3body, comm );
		realloc->bonds = 0;
		realloc->num_3body = MAX( realloc->num_3body, est_3body ) * 2;

src/USER-REAXC/reaxc_allocate.h

+6 −1

Original line number	Diff line number	Diff line
		@@ -28,6 +28,11 @@
		#define __ALLOCATE_H_

		#include "reaxc_types.h"

		#include "lammps.h"
		#include "error.h"
		using namespace LAMMPS_NS;

		int PreAllocate_Space( reax_system, control_params, storage*, MPI_Comm );

		int Allocate_System( reax_system, int, int, char );
		@@ -37,6 +42,6 @@ int Allocate_Workspace( reax_system, control_params, storage*,
		int, int, MPI_Comm, char* );
		void DeAllocate_Workspace( control_params, storage );

		void ReAllocate( reax_system, control_params, simulation_data, storage,
		void ReAllocate( LAMMPS lmp, reax_system, control_params, simulation_data, storage*,
		reax_list*, mpi_datatypes );
		#endif

src/USER-REAXC/reaxc_forces.cpp

+11 −7

Original line number	Diff line number	Diff line
		@@ -39,7 +39,11 @@
		#include "reaxc_valence_angles.h"
		#include "reaxc_vector.h"

		#include "lammps.h"
		#include "error.h"

		interaction_function Interaction_Functions[NUM_INTRS];
		using namespace LAMMPS_NS;

		void Dummy_Interaction( reax_system * /system/, control_params * /control/,
		simulation_data * /data/, storage * /workspace/,
		@@ -114,7 +118,7 @@ void Compute_Total_Force( reax_system system, control_params control,

		}

		void Validate_Lists( reax_system system, storage /workspace/, reax_list **lists,
		void Validate_Lists( LAMMPS lmp, reax_system system, storage * /workspace/, reax_list **lists,
		int step, int /n/, int N, int numH, MPI_Comm comm )
		{
		int i, comp, Hindex;
		@@ -136,7 +140,7 @@ void Validate_Lists( reax_system system, storage /workspace/, reax_list **l
		if (End_Index(i, bonds) > comp) {
		fprintf( stderr, "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 );
		lmp->error->all(FLERR,"Failure in bond list.");
		}
		}
		}
		@@ -163,7 +167,7 @@ void Validate_Lists( reax_system system, storage /workspace/, reax_list **l
		if (End_Index(Hindex, hbonds) > comp) {
		fprintf(stderr,"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 );
		lmp->error->all(FLERR, "Failure in hydrogen bonds.");
		}
		}
		}
		@@ -171,7 +175,7 @@ void Validate_Lists( reax_system system, storage /workspace/, reax_list **l
		}


		void Init_Forces_noQEq( reax_system system, control_params control,
		void Init_Forces_noQEq( LAMMPS lmp, reax_system system, control_params *control,
		simulation_data data, storage workspace,
		reax_list *lists, output_controls /out_control/,
		MPI_Comm comm ) {
		@@ -307,7 +311,7 @@ void Init_Forces_noQEq( reax_system system, control_params control,
		workspace->realloc.num_bonds = num_bonds;
		workspace->realloc.num_hbonds = num_hbonds;

		Validate_Lists( system, workspace, lists, data->step,
		Validate_Lists( lmp, system, workspace, lists, data->step,
		system->n, system->N, system->numH, comm );
		}

		@@ -431,14 +435,14 @@ void Estimate_Storages( reax_system system, control_params control,
		}


		void Compute_Forces( reax_system system, control_params control,
		void Compute_Forces( LAMMPS lmp, reax_system system, control_params *control,
		simulation_data data, storage workspace,
		reax_list *lists, output_controls out_control,
		mpi_datatypes *mpi_data )
		{
		MPI_Comm comm = mpi_data->world;

		Init_Forces_noQEq( system, control, data, workspace,
		Init_Forces_noQEq( lmp, system, control, data, workspace,
		lists, out_control, comm );

		/******* bonded interactions **********/

src/USER-REAXC/reaxc_forces.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -33,7 +33,7 @@
		extern interaction_function Interaction_Functions[NUM_INTRS];

		void Init_Force_Functions( control_params* );
		void Compute_Forces( reax_system, control_params, simulation_data*,
		void Compute_Forces( LAMMPS_NS::LAMMPS lmp, reax_system, control_params, simulation_data,
		storage, reax_list, output_controls, mpi_datatypes* );
		void Estimate_Storages( reax_system, control_params, reax_list**,
		int, int, int, int, MPI_Comm );

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