Pointer moved to reax lists (111ff447) · Commits · 郑智淋 / lammps

src/USER-REAXC/pair_reaxc.cpp

+12 −9

Original line number	Diff line number	Diff line
		@@ -108,6 +108,8 @@ PairReaxC::PairReaxC(LAMMPS *lmp) : Pair(lmp)
		system->bndry_cuts.ghost_cutoff = 0;
		system->my_atoms = NULL;
		system->pair_ptr = this;
		system->error_ptr = this->lmp->error;
		control->error_ptr = this->lmp->error;

		system->omp_active = 0;

		@@ -139,13 +141,13 @@ PairReaxC::~PairReaxC()

		if (control->tabulate ) Deallocate_Lookup_Tables( lmp, system);

		if (control->hbond_cut > 0 ) Delete_List( lmp, lists+HBONDS, world);
		Delete_List( lmp, lists+BONDS, world );
		Delete_List( lmp, lists+THREE_BODIES, world );
		Delete_List( lmp, lists+FAR_NBRS, world );
		if (control->hbond_cut > 0 ) Delete_List( lists+HBONDS, world);
		Delete_List( lists+BONDS, world );
		Delete_List( lists+THREE_BODIES, world );
		Delete_List( lists+FAR_NBRS, world );

		DeAllocate_Workspace( lmp, control, workspace );
		DeAllocate_System( lmp, system );
		DeAllocate_Workspace( control, workspace );
		DeAllocate_System( system );
		}

		memory->destroy( system );
		@@ -437,13 +439,14 @@ void PairReaxC::setup( )

		// initialize my data structures

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

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

		write_reax_lists();
		Initialize( lmp, system, control, data, workspace, &lists, out_control,
		@@ -466,7 +469,7 @@ void PairReaxC::setup( )

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

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

		bigint local_ngroup = list->inum;

src/USER-REAXC/reaxc_allocate.cpp

+158 −158

File changed.

Preview size limit exceeded, changes collapsed.

src/USER-REAXC/reaxc_allocate.h

+5 −5

Original line number	Diff line number	Diff line
		@@ -33,15 +33,15 @@
		#include "error.h"
		using namespace LAMMPS_NS;

		int PreAllocate_Space( LAMMPS_NS::LAMMPS, reax_system, control_params, storage, MPI_Comm );
		int PreAllocate_Space( reax_system, control_params, storage*, MPI_Comm );

		int Allocate_System( reax_system, int, int, char );
		void DeAllocate_System( LAMMPS_NS::LAMMPS, reax_system );
		void DeAllocate_System( reax_system* );

		int Allocate_Workspace( LAMMPS_NS::LAMMPS, reax_system, control_params, storage,
		int Allocate_Workspace( reax_system, control_params, storage*,
		int, int, MPI_Comm, char* );
		void DeAllocate_Workspace( LAMMPS_NS::LAMMPS, control_params, storage* );
		void DeAllocate_Workspace( control_params, storage );

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

src/USER-REAXC/reaxc_ffield.cpp

+17 −17

Original line number	Diff line number	Diff line
		@@ -99,54 +99,54 @@ char Read_Force_Field( LAMMPS_NS::LAMMPS* lmp, FILE fp, reax_interaction reax,

		/* Allocating structures in reax_interaction */
		reax->sbp = (single_body_parameters*)
		scalloc(lmp, reax->num_atom_types, sizeof(single_body_parameters), "sbp",
		scalloc(lmp->error, reax->num_atom_types, sizeof(single_body_parameters), "sbp",
		comm );
		reax->tbp = (two_body_parameters**)
		scalloc(lmp, reax->num_atom_types, sizeof(two_body_parameters*), "tbp", comm );
		scalloc(lmp->error, reax->num_atom_types, sizeof(two_body_parameters*), "tbp", comm );
		reax->thbp= (three_body_header***)
		scalloc(lmp, reax->num_atom_types, sizeof(three_body_header**), "thbp", comm );
		scalloc(lmp->error, reax->num_atom_types, sizeof(three_body_header**), "thbp", comm );
		reax->hbp = (hbond_parameters***)
		scalloc(lmp, reax->num_atom_types, sizeof(hbond_parameters**), "hbp", comm );
		scalloc(lmp->error, reax->num_atom_types, sizeof(hbond_parameters**), "hbp", comm );
		reax->fbp = (four_body_header****)
		scalloc(lmp, reax->num_atom_types, sizeof(four_body_header***), "fbp", comm );
		scalloc(lmp->error, reax->num_atom_types, sizeof(four_body_header***), "fbp", comm );
		tor_flag = (char****)
		scalloc(lmp, reax->num_atom_types, sizeof(char***), "tor_flag", comm );
		scalloc(lmp->error, reax->num_atom_types, sizeof(char***), "tor_flag", comm );

		for( i = 0; i < reax->num_atom_types; i++ ) {
		reax->tbp[i] = (two_body_parameters*)
		scalloc(lmp, reax->num_atom_types, sizeof(two_body_parameters), "tbp[i]",
		scalloc(lmp->error, reax->num_atom_types, sizeof(two_body_parameters), "tbp[i]",
		comm );
		reax->thbp[i]= (three_body_header**)
		scalloc(lmp, reax->num_atom_types, sizeof(three_body_header*), "thbp[i]",
		scalloc(lmp->error, reax->num_atom_types, sizeof(three_body_header*), "thbp[i]",
		comm );
		reax->hbp[i] = (hbond_parameters**)
		scalloc(lmp, reax->num_atom_types, sizeof(hbond_parameters*), "hbp[i]",
		scalloc(lmp->error, reax->num_atom_types, sizeof(hbond_parameters*), "hbp[i]",
		comm );
		reax->fbp[i] = (four_body_header***)
		scalloc(lmp, reax->num_atom_types, sizeof(four_body_header**), "fbp[i]",
		scalloc(lmp->error, reax->num_atom_types, sizeof(four_body_header**), "fbp[i]",
		comm );
		tor_flag[i] = (char***)
		scalloc(lmp, reax->num_atom_types, sizeof(char**), "tor_flag[i]", comm );
		scalloc(lmp->error, reax->num_atom_types, sizeof(char**), "tor_flag[i]", comm );

		for( j = 0; j < reax->num_atom_types; j++ ) {
		reax->thbp[i][j]= (three_body_header*)
		scalloc(lmp, reax->num_atom_types, sizeof(three_body_header), "thbp[i,j]",
		scalloc(lmp->error, reax->num_atom_types, sizeof(three_body_header), "thbp[i,j]",
		comm );
		reax->hbp[i][j] = (hbond_parameters*)
		scalloc(lmp, reax->num_atom_types, sizeof(hbond_parameters), "hbp[i,j]",
		scalloc(lmp->error, reax->num_atom_types, sizeof(hbond_parameters), "hbp[i,j]",
		comm );
		reax->fbp[i][j] = (four_body_header**)
		scalloc(lmp, reax->num_atom_types, sizeof(four_body_header*), "fbp[i,j]",
		scalloc(lmp->error, reax->num_atom_types, sizeof(four_body_header*), "fbp[i,j]",
		comm );
		tor_flag[i][j] = (char**)
		scalloc(lmp, reax->num_atom_types, sizeof(char*), "tor_flag[i,j]", comm );
		scalloc(lmp->error, reax->num_atom_types, sizeof(char*), "tor_flag[i,j]", comm );

		for (k=0; k < reax->num_atom_types; k++) {
		reax->fbp[i][j][k] = (four_body_header*)
		scalloc(lmp, reax->num_atom_types, sizeof(four_body_header), "fbp[i,j,k]",
		scalloc(lmp->error, reax->num_atom_types, sizeof(four_body_header), "fbp[i,j,k]",
		comm );
		tor_flag[i][j][k] = (char*)
		scalloc(lmp, reax->num_atom_types, sizeof(char), "tor_flag[i,j,k]",
		scalloc(lmp->error, reax->num_atom_types, sizeof(char), "tor_flag[i,j,k]",
		comm );
		}
		}

src/USER-REAXC/reaxc_init_md.cpp

+7 −4

Original line number	Diff line number	Diff line
		@@ -127,7 +127,7 @@ int Init_Workspace( LAMMPS_NS::LAMMPS* lmp, reax_system *system, control_params
		{
		int ret;

		ret = Allocate_Workspace( lmp, system, control, workspace,
		ret = Allocate_Workspace( system, control, workspace,
		system->local_cap, system->total_cap, comm, msg );
		if (ret != SUCCESS)
		return ret;
		@@ -181,10 +181,11 @@ int Init_Lists( LAMMPS lmp, reax_system system, control_params *control,
		}
		total_hbonds = (int)(MAX( total_hbondssaferzone, mincapMIN_HBONDS ));

		if( !Make_List( lmp, system->Hcap, total_hbonds, TYP_HBOND,
		if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
		*lists+HBONDS, comm ) ) {
		lmp->error->one(FLERR, "Not enough space for hbonds list.");
		}
		(*lists+HBONDS)->error_ptr = system->error_ptr;
		}

		total_bonds = 0;
		@@ -194,17 +195,19 @@ int Init_Lists( LAMMPS lmp, reax_system system, control_params *control,
		}
		bond_cap = (int)(MAX( total_bondssafezone, mincapMIN_BONDS ));

		if( !Make_List( lmp, system->total_cap, bond_cap, TYP_BOND,
		if( !Make_List( system->total_cap, bond_cap, TYP_BOND,
		*lists+BONDS, comm ) ) {
		lmp->error->one(FLERR, "Not enough space for bonds list.");
		}
		(*lists+BONDS)->error_ptr = system->error_ptr;

		/* 3bodies list */
		cap_3body = (int)(MAX( num_3body*safezone, MIN_3BODIES ));
		if( !Make_List( lmp, bond_cap, cap_3body, TYP_THREE_BODY,
		if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
		*lists+THREE_BODIES, comm ) ){
		lmp->error->one(FLERR,"Problem in initializing angles list.");
		}
		(*lists+THREE_BODIES)->error_ptr = system->error_ptr;

		free( hb_top );
		free( bond_top );

Original line number	Diff line number	Diff line
		@@ -33,15 +33,15 @@
		#include "error.h"
		using namespace LAMMPS_NS;

		int PreAllocate_Space( LAMMPS_NS::LAMMPS, reax_system, control_params, storage, MPI_Comm );
		int PreAllocate_Space( reax_system, control_params, storage*, MPI_Comm );

		int Allocate_System( reax_system, int, int, char );
		void DeAllocate_System( LAMMPS_NS::LAMMPS, reax_system );
		void DeAllocate_System( reax_system* );

		int Allocate_Workspace( LAMMPS_NS::LAMMPS, reax_system, control_params, storage,
		int Allocate_Workspace( reax_system, control_params, storage*,
		int, int, MPI_Comm, char* );
		void DeAllocate_Workspace( LAMMPS_NS::LAMMPS, control_params, storage* );
		void DeAllocate_Workspace( control_params, storage );

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

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