Merge pull request #1731 from akohlmey/safe-fread-calls (6282f9aa) · Commits · 郑智淋 / lammps

src/ASPHERE/pair_gayberne.cpp

+13 −12

Original line number	Diff line number	Diff line
		@@ -28,6 +28,7 @@
		#include "citeme.h"
		#include "memory.h"
		#include "error.h"
		#include "utils.h"

		using namespace LAMMPS_NS;

		@@ -460,20 +461,20 @@ void PairGayBerne::read_restart(FILE *fp)
		int i,j;
		int me = comm->me;
		for (i = 1; i <= atom->ntypes; i++) {
		if (me == 0) fread(&setwell[i],sizeof(int),1,fp);
		if (me == 0) utils::sfread(FLERR,&setwell[i],sizeof(int),1,fp,NULL,error);
		MPI_Bcast(&setwell[i],1,MPI_INT,0,world);
		if (setwell[i]) {
		if (me == 0) fread(&well[i][0],sizeof(double),3,fp);
		if (me == 0) utils::sfread(FLERR,&well[i][0],sizeof(double),3,fp,NULL,error);
		MPI_Bcast(&well[i][0],3,MPI_DOUBLE,0,world);
		}
		for (j = i; j <= atom->ntypes; j++) {
		if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
		if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
		MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
		if (setflag[i][j]) {
		if (me == 0) {
		fread(&epsilon[i][j],sizeof(double),1,fp);
		fread(&sigma[i][j],sizeof(double),1,fp);
		fread(&cut[i][j],sizeof(double),1,fp);
		utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
		}
		MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
		MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
		@@ -505,12 +506,12 @@ void PairGayBerne::read_restart_settings(FILE *fp)
		{
		int me = comm->me;
		if (me == 0) {
		fread(&gamma,sizeof(double),1,fp);
		fread(&upsilon,sizeof(double),1,fp);
		fread(&mu,sizeof(double),1,fp);
		fread(&cut_global,sizeof(double),1,fp);
		fread(&offset_flag,sizeof(int),1,fp);
		fread(&mix_flag,sizeof(int),1,fp);
		utils::sfread(FLERR,&gamma,sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&upsilon,sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&mu,sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
		utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
		}
		MPI_Bcast(&gamma,1,MPI_DOUBLE,0,world);
		MPI_Bcast(&upsilon,1,MPI_DOUBLE,0,world);

src/ASPHERE/pair_resquared.cpp

+9 −8

Original line number	Diff line number	Diff line
		@@ -27,6 +27,7 @@
		#include "neigh_list.h"
		#include "memory.h"
		#include "error.h"
		#include "utils.h"

		using namespace LAMMPS_NS;

		@@ -438,20 +439,20 @@ void PairRESquared::read_restart(FILE *fp)
		int i,j;
		int me = comm->me;
		for (i = 1; i <= atom->ntypes; i++) {
		if (me == 0) fread(&setwell[i],sizeof(int),1,fp);
		if (me == 0) utils::sfread(FLERR,&setwell[i],sizeof(int),1,fp,NULL,error);
		MPI_Bcast(&setwell[i],1,MPI_INT,0,world);
		if (setwell[i]) {
		if (me == 0) fread(&well[i][0],sizeof(double),3,fp);
		if (me == 0) utils::sfread(FLERR,&well[i][0],sizeof(double),3,fp,NULL,error);
		MPI_Bcast(&well[i][0],3,MPI_DOUBLE,0,world);
		}
		for (j = i; j <= atom->ntypes; j++) {
		if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
		if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
		MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
		if (setflag[i][j]) {
		if (me == 0) {
		fread(&epsilon[i][j],sizeof(double),1,fp);
		fread(&sigma[i][j],sizeof(double),1,fp);
		fread(&cut[i][j],sizeof(double),1,fp);
		utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
		}
		MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
		MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
		@@ -479,8 +480,8 @@ void PairRESquared::read_restart_settings(FILE *fp)
		{
		int me = comm->me;
		if (me == 0) {
		fread(&cut_global,sizeof(double),1,fp);
		fread(&mix_flag,sizeof(int),1,fp);
		utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
		}
		MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
		MPI_Bcast(&mix_flag,1,MPI_INT,0,world);

src/CLASS2/angle_class2.cpp

+14 −13

Original line number	Diff line number	Diff line
		@@ -27,6 +27,7 @@
		#include "math_const.h"
		#include "memory.h"
		#include "error.h"
		#include "utils.h"

		using namespace LAMMPS_NS;
		using namespace MathConst;
		@@ -372,19 +373,19 @@ void AngleClass2::read_restart(FILE *fp)
		allocate();

		if (comm->me == 0) {
		fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
		fread(&k2[1],sizeof(double),atom->nangletypes,fp);
		fread(&k3[1],sizeof(double),atom->nangletypes,fp);
		fread(&k4[1],sizeof(double),atom->nangletypes,fp);

		fread(&bb_k[1],sizeof(double),atom->nangletypes,fp);
		fread(&bb_r1[1],sizeof(double),atom->nangletypes,fp);
		fread(&bb_r2[1],sizeof(double),atom->nangletypes,fp);

		fread(&ba_k1[1],sizeof(double),atom->nangletypes,fp);
		fread(&ba_k2[1],sizeof(double),atom->nangletypes,fp);
		fread(&ba_r1[1],sizeof(double),atom->nangletypes,fp);
		fread(&ba_r2[1],sizeof(double),atom->nangletypes,fp);
		utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
		utils::sfread(FLERR,&k2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
		utils::sfread(FLERR,&k3[1],sizeof(double),atom->nangletypes,fp,NULL,error);
		utils::sfread(FLERR,&k4[1],sizeof(double),atom->nangletypes,fp,NULL,error);

		utils::sfread(FLERR,&bb_k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
		utils::sfread(FLERR,&bb_r1[1],sizeof(double),atom->nangletypes,fp,NULL,error);
		utils::sfread(FLERR,&bb_r2[1],sizeof(double),atom->nangletypes,fp,NULL,error);

		utils::sfread(FLERR,&ba_k1[1],sizeof(double),atom->nangletypes,fp,NULL,error);
		utils::sfread(FLERR,&ba_k2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
		utils::sfread(FLERR,&ba_r1[1],sizeof(double),atom->nangletypes,fp,NULL,error);
		utils::sfread(FLERR,&ba_r2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
		}

		MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);

src/CLASS2/bond_class2.cpp

+5 −4

Original line number	Diff line number	Diff line
		@@ -24,6 +24,7 @@
		#include "force.h"
		#include "memory.h"
		#include "error.h"
		#include "utils.h"

		using namespace LAMMPS_NS;

		@@ -182,10 +183,10 @@ void BondClass2::read_restart(FILE *fp)
		allocate();

		if (comm->me == 0) {
		fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
		fread(&k2[1],sizeof(double),atom->nbondtypes,fp);
		fread(&k3[1],sizeof(double),atom->nbondtypes,fp);
		fread(&k4[1],sizeof(double),atom->nbondtypes,fp);
		utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
		utils::sfread(FLERR,&k2[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
		utils::sfread(FLERR,&k3[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
		utils::sfread(FLERR,&k4[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
		}
		MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
		MPI_Bcast(&k2[1],atom->nbondtypes,MPI_DOUBLE,0,world);

src/CLASS2/dihedral_class2.cpp

+40 −39

Original line number	Diff line number	Diff line
		@@ -27,6 +27,7 @@
		#include "math_const.h"
		#include "memory.h"
		#include "error.h"
		#include "utils.h"

		using namespace LAMMPS_NS;
		using namespace MathConst;
		@@ -835,45 +836,45 @@ void DihedralClass2::read_restart(FILE *fp)
		allocate();

		if (comm->me == 0) {
		fread(&k1[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&k2[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&k3[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&phi1[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&phi2[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&phi3[1],sizeof(double),atom->ndihedraltypes,fp);

		fread(&mbt_f1[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&mbt_f2[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&mbt_f3[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&mbt_r0[1],sizeof(double),atom->ndihedraltypes,fp);

		fread(&ebt_f1_1[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&ebt_f2_1[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&ebt_f3_1[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&ebt_r0_1[1],sizeof(double),atom->ndihedraltypes,fp);

		fread(&ebt_f1_2[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&ebt_f2_2[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&ebt_f3_2[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&ebt_r0_2[1],sizeof(double),atom->ndihedraltypes,fp);

		fread(&at_f1_1[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&at_f2_1[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&at_f3_1[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&at_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);

		fread(&at_f1_2[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&at_f2_2[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&at_f3_2[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&at_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);

		fread(&aat_k[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);

		fread(&bb13t_k[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&bb13t_r10[1],sizeof(double),atom->ndihedraltypes,fp);
		fread(&bb13t_r30[1],sizeof(double),atom->ndihedraltypes,fp);
		utils::sfread(FLERR,&k1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&k2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&k3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&phi1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&phi2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&phi3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);

		utils::sfread(FLERR,&mbt_f1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&mbt_f2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&mbt_f3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&mbt_r0[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);

		utils::sfread(FLERR,&ebt_f1_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&ebt_f2_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&ebt_f3_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&ebt_r0_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);

		utils::sfread(FLERR,&ebt_f1_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&ebt_f2_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&ebt_f3_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&ebt_r0_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);

		utils::sfread(FLERR,&at_f1_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&at_f2_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&at_f3_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&at_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);

		utils::sfread(FLERR,&at_f1_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&at_f2_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&at_f3_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&at_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);

		utils::sfread(FLERR,&aat_k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);

		utils::sfread(FLERR,&bb13t_k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&bb13t_r10[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		utils::sfread(FLERR,&bb13t_r30[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
		}

		MPI_Bcast(&k1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);

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