Cleaning changes 1 (99acb4ac) · Commits · 郑智淋 / lammps

src/USER-REAXC/pair_reaxc.cpp

+5 −5

Original line number	Diff line number	Diff line
		@@ -139,7 +139,7 @@ PairReaxC::~PairReaxC()

		// deallocate reax data-structures

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

		if (control->hbond_cut > 0 ) Delete_List( lists+HBONDS, world);
		Delete_List( lists+BONDS, world );
		@@ -225,7 +225,7 @@ void PairReaxC::settings(int narg, char **arg)
		out_control->atom_info = 0;
		out_control->bond_info = 0;
		out_control->angle_info = 0;
		} else Read_Control_File(lmp, arg[0], control, out_control);
		} else Read_Control_File(arg[0], control, out_control);

		// default values

		@@ -300,7 +300,7 @@ void PairReaxC::coeff( int nargs, char **args )
		FILE *fp;
		fp = force->open_potential(file);
		if (fp != NULL)
		Read_Force_Field(lmp, fp, &(system->reax_param), control);
		Read_Force_Field(fp, &(system->reax_param), control);
		else {
		char str[128];
		snprintf(str,128,"Cannot open ReaxFF potential file %s",file);
		@@ -449,7 +449,7 @@ void PairReaxC::setup( )
		(lists+FAR_NBRS)->error_ptr=lmp->error;

		write_reax_lists();
		Initialize( lmp, system, control, data, workspace, &lists, out_control,
		Initialize( 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;
		@@ -585,7 +585,7 @@ void PairReaxC::compute(int eflag, int vflag)

		data->step = update->ntimestep;

		Output_Results( lmp, system, control, data, &lists, out_control, mpi_data );
		Output_Results( system, control, data, &lists, out_control, mpi_data );

		// populate tmpid and tmpbo arrays for fix reax/c/species
		int i, j;

src/USER-REAXC/reaxc_control.cpp

+3 −4

Original line number	Diff line number	Diff line
		@@ -28,9 +28,8 @@
		#include "reaxc_control.h"
		#include "reaxc_tool_box.h"

		using namespace LAMMPS_NS;

		char Read_Control_File( LAMMPS lmp, char control_file, control_params* control,
		char Read_Control_File( char control_file, control_params control,
		output_controls *out_control )
		{
		FILE *fp;
		@@ -40,7 +39,7 @@ char Read_Control_File( LAMMPS lmp, char control_file, control_params* control

		/* open control file */
		if ( (fp = fopen( control_file, "r" ) ) == NULL ) {
		lmp->error->all(FLERR, "The control file cannot be opened");
		control->error_ptr->all(FLERR, "The control file cannot be opened");
		}

		/* assign default values */
		@@ -367,7 +366,7 @@ char Read_Control_File( LAMMPS lmp, char control_file, control_params* control
		else {
		char errmsg[128];
		snprintf(errmsg,128,"Unknown parameter %s in the control file", tmp[0]);
		lmp->error->all(FLERR, errmsg);
		control->error_ptr->all(FLERR, errmsg);
		}
		}

src/USER-REAXC/reaxc_control.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -32,6 +32,6 @@
		#include "lammps.h"
		#include "error.h"

		char Read_Control_File( LAMMPS_NS::LAMMPS lmp, char, control_params, output_controls );
		char Read_Control_File( char, control_params, output_controls* );

		#endif

src/USER-REAXC/reaxc_ffield.cpp

+30 −30

Original line number	Diff line number	Diff line
		@@ -32,7 +32,7 @@
		#include "lammps.h"
		#include "error.h"

		char Read_Force_Field( LAMMPS_NS::LAMMPS* lmp, FILE fp, reax_interaction reax,
		char Read_Force_Field( FILE fp, reax_interaction reax,
		control_params *control )
		{
		char *s;
		@@ -64,7 +64,7 @@ char Read_Force_Field( LAMMPS_NS::LAMMPS* lmp, FILE fp, reax_interaction reax,
		n = atoi(tmp[0]);
		if (n < 1) {
		if (me == 0)
		lmp->error->warning( FLERR, "Number of globals in ffield file is 0" );
		control->error_ptr->warning( FLERR, "Number of globals in ffield file is 0" );
		fclose(fp);
		free(s);
		free(tmp);
		@@ -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->error, reax->num_atom_types, sizeof(single_body_parameters), "sbp",
		scalloc(control->error_ptr, reax->num_atom_types, sizeof(single_body_parameters), "sbp",
		comm );
		reax->tbp = (two_body_parameters**)
		scalloc(lmp->error, reax->num_atom_types, sizeof(two_body_parameters*), "tbp", comm );
		scalloc(control->error_ptr, reax->num_atom_types, sizeof(two_body_parameters*), "tbp", comm );
		reax->thbp= (three_body_header***)
		scalloc(lmp->error, reax->num_atom_types, sizeof(three_body_header**), "thbp", comm );
		scalloc(control->error_ptr, reax->num_atom_types, sizeof(three_body_header**), "thbp", comm );
		reax->hbp = (hbond_parameters***)
		scalloc(lmp->error, reax->num_atom_types, sizeof(hbond_parameters**), "hbp", comm );
		scalloc(control->error_ptr, reax->num_atom_types, sizeof(hbond_parameters**), "hbp", comm );
		reax->fbp = (four_body_header****)
		scalloc(lmp->error, reax->num_atom_types, sizeof(four_body_header***), "fbp", comm );
		scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header***), "fbp", comm );
		tor_flag = (char****)
		scalloc(lmp->error, reax->num_atom_types, sizeof(char***), "tor_flag", comm );
		scalloc(control->error_ptr, 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->error, reax->num_atom_types, sizeof(two_body_parameters), "tbp[i]",
		scalloc(control->error_ptr, reax->num_atom_types, sizeof(two_body_parameters), "tbp[i]",
		comm );
		reax->thbp[i]= (three_body_header**)
		scalloc(lmp->error, reax->num_atom_types, sizeof(three_body_header*), "thbp[i]",
		scalloc(control->error_ptr, reax->num_atom_types, sizeof(three_body_header*), "thbp[i]",
		comm );
		reax->hbp[i] = (hbond_parameters**)
		scalloc(lmp->error, reax->num_atom_types, sizeof(hbond_parameters*), "hbp[i]",
		scalloc(control->error_ptr, reax->num_atom_types, sizeof(hbond_parameters*), "hbp[i]",
		comm );
		reax->fbp[i] = (four_body_header***)
		scalloc(lmp->error, reax->num_atom_types, sizeof(four_body_header**), "fbp[i]",
		scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header**), "fbp[i]",
		comm );
		tor_flag[i] = (char***)
		scalloc(lmp->error, reax->num_atom_types, sizeof(char**), "tor_flag[i]", comm );
		scalloc(control->error_ptr, 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->error, reax->num_atom_types, sizeof(three_body_header), "thbp[i,j]",
		scalloc(control->error_ptr, reax->num_atom_types, sizeof(three_body_header), "thbp[i,j]",
		comm );
		reax->hbp[i][j] = (hbond_parameters*)
		scalloc(lmp->error, reax->num_atom_types, sizeof(hbond_parameters), "hbp[i,j]",
		scalloc(control->error_ptr, reax->num_atom_types, sizeof(hbond_parameters), "hbp[i,j]",
		comm );
		reax->fbp[i][j] = (four_body_header**)
		scalloc(lmp->error, reax->num_atom_types, sizeof(four_body_header*), "fbp[i,j]",
		scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header*), "fbp[i,j]",
		comm );
		tor_flag[i][j] = (char**)
		scalloc(lmp->error, reax->num_atom_types, sizeof(char*), "tor_flag[i,j]", comm );
		scalloc(control->error_ptr, 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->error, reax->num_atom_types, sizeof(four_body_header), "fbp[i,j,k]",
		scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header), "fbp[i,j,k]",
		comm );
		tor_flag[i][j][k] = (char*)
		scalloc(lmp->error, reax->num_atom_types, sizeof(char), "tor_flag[i,j,k]",
		scalloc(control->error_ptr, reax->num_atom_types, sizeof(char), "tor_flag[i,j,k]",
		comm );
		}
		}
		@@ -163,7 +163,7 @@ char Read_Force_Field( LAMMPS_NS::LAMMPS* lmp, FILE fp, reax_interaction reax,
		/* Sanity checks */

		if (c < 9) {
		lmp->error->one(FLERR,"Inconsistent ffield file");
		control->error_ptr->one(FLERR,"Inconsistent ffield file");
		}

		for( j = 0; j < (int)(strlen(tmp[0])); ++j )
		@@ -185,7 +185,7 @@ char Read_Force_Field( LAMMPS_NS::LAMMPS* lmp, FILE fp, reax_interaction reax,

		/* Sanity check */
		if (c < 8) {
		lmp->error->one(FLERR,"Inconsistent ffield file");
		control->error_ptr->one(FLERR,"Inconsistent ffield file");
		}

		val = atof(tmp[0]); reax->sbp[i].alpha = val;
		@@ -203,7 +203,7 @@ char Read_Force_Field( LAMMPS_NS::LAMMPS* lmp, FILE fp, reax_interaction reax,

		/* Sanity check */
		if (c < 8) {
		lmp->error->one(FLERR,"Inconsistent ffield file");
		control->error_ptr->one(FLERR,"Inconsistent ffield file");
		}

		val = atof(tmp[0]); reax->sbp[i].r_pi_pi = val;
		@@ -221,7 +221,7 @@ char Read_Force_Field( LAMMPS_NS::LAMMPS* lmp, FILE fp, reax_interaction reax,

		/* Sanity check */
		if (c < 8) {
		lmp->error->one(FLERR,"Inconsistent ffield file");
		control->error_ptr->one(FLERR,"Inconsistent ffield file");
		}

		val = atof(tmp[0]); reax->sbp[i].p_ovun2 = val;
		@@ -240,7 +240,7 @@ char Read_Force_Field( LAMMPS_NS::LAMMPS* lmp, FILE fp, reax_interaction reax,

		/* Sanity check */
		if (c > 2) {
		lmp->error->one(FLERR,"Force field file incompatible with 'lgvdw yes'");
		control->error_ptr->one(FLERR,"Force field file incompatible with 'lgvdw yes'");
		}

		val = atof(tmp[0]); reax->sbp[i].lgcij = val;
		@@ -258,7 +258,7 @@ char Read_Force_Field( LAMMPS_NS::LAMMPS* lmp, FILE fp, reax_interaction reax,
		"This may cause division-by-zero errors. "
		"Keeping vdWaals-setting for earlier atoms.",
		reax->sbp[i].name);
		lmp->error->warning(FLERR,errmsg);
		control->error_ptr->warning(FLERR,errmsg);
		}
		errorflag = 0;
		} else {
		@@ -274,7 +274,7 @@ char Read_Force_Field( LAMMPS_NS::LAMMPS* lmp, FILE fp, reax_interaction reax,
		"This may cause division-by-zero errors. "
		"Keeping vdWaals-setting for earlier atoms.",
		reax->sbp[i].name);
		lmp->error->warning(FLERR,errmsg);
		control->error_ptr->warning(FLERR,errmsg);
		}
		} else {
		reax->gp.vdw_type = 2;
		@@ -291,7 +291,7 @@ char Read_Force_Field( LAMMPS_NS::LAMMPS* lmp, FILE fp, reax_interaction reax,
		"This may cause division-by-zero errors. "
		"Keeping vdWaals-setting for earlier atoms.",
		reax->sbp[i].name);
		lmp->error->warning(FLERR,errmsg);
		control->error_ptr->warning(FLERR,errmsg);
		}
		} else {
		reax->gp.vdw_type = 1;
		@@ -301,7 +301,7 @@ char Read_Force_Field( LAMMPS_NS::LAMMPS* lmp, FILE fp, reax_interaction reax,
		snprintf(errmsg, 256, "Inconsistent vdWaals-parameters "
		"No shielding or inner-wall set for element %s",
		reax->sbp[i].name);
		lmp->error->all(FLERR, errmsg);
		control->error_ptr->all(FLERR, errmsg);
		}
		}
		}
		@@ -314,7 +314,7 @@ char Read_Force_Field( LAMMPS_NS::LAMMPS* lmp, FILE fp, reax_interaction reax,
		char errmsg[256];
		snprintf(errmsg, 256, "Changed valency_val to valency_boc for %s",
		reax->sbp[i].name);
		lmp->error->warning(FLERR,errmsg);
		control->error_ptr->warning(FLERR,errmsg);
		}
		reax->sbp[i].valency_val = reax->sbp[i].valency_boc;
		}
		@@ -324,7 +324,7 @@ char Read_Force_Field( LAMMPS_NS::LAMMPS* lmp, FILE fp, reax_interaction reax,
		c=Tokenize(s,&tmp);

		if (c == 2 && !lgflag) {
		lmp->error->all(FLERR, "Force field file requires using 'lgvdw yes'");
		control->error_ptr->all(FLERR, "Force field file requires using 'lgvdw yes'");
		}

		l = atoi(tmp[0]);

src/USER-REAXC/reaxc_ffield.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -29,6 +29,6 @@

		#include "reaxc_types.h"

		char Read_Force_Field( LAMMPS_NS::LAMMPS, FILE, reax_interaction, control_params );
		char Read_Force_Field( FILE, reax_interaction, control_params* );

		#endif

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