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make use of utils::sfgets() in a few more places

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This commit is contained in:
Axel Kohlmeyer
2019-10-19 13:26:55 -04:00
parent d8c86d9abc
commit fd9da6f934
21 changed files with 247 additions and 223 deletions
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73
src/MANYBODY/pair_bop.cpp
View File

@ -45,6 +45,7 @@
#include "neigh_list.h" #include "neigh_list.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -4982,13 +4983,13 @@ void PairBOP::read_table(char *filename)
snprintf(str,128,"Cannot open BOP potential file %s",filename); snprintf(str,128,"Cannot open BOP potential file %s",filename);
error->one(FLERR,str); error->one(FLERR,str);
} }
fgets(s,MAXLINE,fp); // skip first comment line utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); // skip first comment line
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%d",&bop_types); sscanf(s,"%d",&bop_types);
elements = new char*[bop_types]; elements = new char*[bop_types];
for(i=0;i<bop_types;i++) elements[i]=NULL; for(i=0;i<bop_types;i++) elements[i]=NULL;
for(i=0;i<bop_types;i++) { for(i=0;i<bop_types;i++) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
nws=0; nws=0;
ws=1; ws=1;
for(j=0;j<(int)strlen(s);j++) { for(j=0;j<(int)strlen(s);j++) {
@ -5017,7 +5018,7 @@ void PairBOP::read_table(char *filename)
} }
nws=0; nws=0;
ws=1; ws=1;
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
for(j=0;j<(int)strlen(s);j++) { for(j=0;j<(int)strlen(s);j++) {
if(ws==1) { if(ws==1) {
if(isspace(s[j])) { if(isspace(s[j])) {
@ -5085,28 +5086,28 @@ void PairBOP::read_table(char *filename)
snprintf(str,128,"Cannot open BOP potential file %s",filename); snprintf(str,128,"Cannot open BOP potential file %s",filename);
error->one(FLERR,str); error->one(FLERR,str);
} }
fgets(s,MAXLINE,fp); // skip first comment line utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); // skip first comment line
for(i=0;i<bop_types+2;i++) { for(i=0;i<bop_types+2;i++) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
} }
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf%lf%lf",&small1,&small2,&small3g sscanf(s,"%lf%lf%lf%lf%lf%lf%lf",&small1,&small2,&small3g
,&small4,&small5,&small6,&small7); ,&small4,&small5,&small6,&small7);
for(i=0;i<bop_types;i++) { for(i=0;i<bop_types;i++) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf",&pi_p[i]); sscanf(s,"%lf",&pi_p[i]);
} }
cutmax=0; cutmax=0;
for(i=0;i<npairs;i++) { for(i=0;i<npairs;i++) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf",&rcut[i]); sscanf(s,"%lf",&rcut[i]);
if(rcut[i]>cutmax) if(rcut[i]>cutmax)
cutmax=rcut[i]; cutmax=rcut[i];
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf",&sigma_c[i],&sigma_a[i],&pi_c[i],&pi_a[i]); sscanf(s,"%lf%lf%lf%lf",&sigma_c[i],&sigma_a[i],&pi_c[i],&pi_a[i]);
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf",&sigma_delta[i],&pi_delta[i]); sscanf(s,"%lf%lf",&sigma_delta[i],&pi_delta[i]);
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf",&sigma_f[i],&sigma_k[i],&small3[i]); sscanf(s,"%lf%lf%lf",&sigma_f[i],&sigma_k[i],&small3[i]);
} }
if(nws==3) { if(nws==3) {
@ -5115,56 +5116,56 @@ void PairBOP::read_table(char *filename)
for(k=j;k<bop_types;k++) { for(k=j;k<bop_types;k++) {
if(npower<=2) { if(npower<=2) {
for(m=0;m<ntheta;m++) { for(m=0;m<ntheta;m++) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gfunc[j][i][k][n],&gfunc[j][i][k][n+1] sscanf(s,"%lf%lf%lf%lf%lf",&gfunc[j][i][k][n],&gfunc[j][i][k][n+1]
,&gfunc[j][i][k][n+2],&gfunc[j][i][k][n+3],&gfunc[j][i][k][n+4]); ,&gfunc[j][i][k][n+2],&gfunc[j][i][k][n+3],&gfunc[j][i][k][n+4]);
n+=4; n+=4;
} }
} else { } else {
if(npower==3) { if(npower==3) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3]); sscanf(s,"%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3]);
} }
else if(npower==4) { else if(npower==4) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]); sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
} }
else if(npower==5) { else if(npower==5) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]); sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf",&gpara[j][i][k][5]); sscanf(s,"%lf",&gpara[j][i][k][5]);
} }
else if(npower==6) { else if(npower==6) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]); sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6]); sscanf(s,"%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6]);
} }
else if(npower==7) { else if(npower==7) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]); sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7]); sscanf(s,"%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7]);
} }
else if(npower==8) { else if(npower==8) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]); sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8]); sscanf(s,"%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8]);
} }
else if(npower==9) { else if(npower==9) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]); sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8],&gpara[j][i][k][9]); sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8],&gpara[j][i][k][9]);
} }
else if(npower==10) { else if(npower==10) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]); sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8],&gpara[j][i][k][9]); sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8],&gpara[j][i][k][9]);
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf",&gpara[j][i][k][10]); sscanf(s,"%lf",&gpara[j][i][k][10]);
} }
} }
@ -5173,14 +5174,14 @@ void PairBOP::read_table(char *filename)
for(i=0;i<bop_types;i++) for(i=0;i<bop_types;i++)
for(j=0;j<bop_types;j++) for(j=0;j<bop_types;j++)
for(k=0;k<bop_types;k++) { for(k=0;k<bop_types;k++) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf",&gpara[i][j][k][0],&gpara[i][j][k][1],&gpara[i][j][k][2]); sscanf(s,"%lf%lf%lf",&gpara[i][j][k][0],&gpara[i][j][k][1],&gpara[i][j][k][2]);
gpara[j][i][k][3]=0; gpara[j][i][k][3]=0;
} }
} }
for(i=0;i<npairs;i++) { for(i=0;i<npairs;i++) {
for(j=0;j<nr;j++) { for(j=0;j<nr;j++) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&pRepul[i][j],&pRepul[i][j+1] sscanf(s,"%lf%lf%lf%lf%lf",&pRepul[i][j],&pRepul[i][j+1]
,&pRepul[i][j+2],&pRepul[i][j+3],&pRepul[i][j+4]); ,&pRepul[i][j+2],&pRepul[i][j+3],&pRepul[i][j+4]);
j+=4; j+=4;
@ -5188,7 +5189,7 @@ void PairBOP::read_table(char *filename)
} }
for(i=0;i<npairs;i++) { for(i=0;i<npairs;i++) {
for(j=0;j<nr;j++) { for(j=0;j<nr;j++) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&pBetaS[i][j],&pBetaS[i][j+1] sscanf(s,"%lf%lf%lf%lf%lf",&pBetaS[i][j],&pBetaS[i][j+1]
,&pBetaS[i][j+2],&pBetaS[i][j+3],&pBetaS[i][j+4]); ,&pBetaS[i][j+2],&pBetaS[i][j+3],&pBetaS[i][j+4]);
j+=4; j+=4;
@ -5196,7 +5197,7 @@ void PairBOP::read_table(char *filename)
} }
for(i=0;i<npairs;i++) { for(i=0;i<npairs;i++) {
for(j=0;j<nr;j++) { for(j=0;j<nr;j++) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&pBetaP[i][j],&pBetaP[i][j+1] sscanf(s,"%lf%lf%lf%lf%lf",&pBetaP[i][j],&pBetaP[i][j+1]
,&pBetaP[i][j+2],&pBetaP[i][j+3],&pBetaP[i][j+4]); ,&pBetaP[i][j+2],&pBetaP[i][j+3],&pBetaP[i][j+4]);
j+=4; j+=4;
@ -5204,18 +5205,18 @@ void PairBOP::read_table(char *filename)
} }
for(i=0;i<npairs;i++) { for(i=0;i<npairs;i++) {
for(j=0;j<nBOt;j++) { for(j=0;j<nBOt;j++) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&FsigBO[i][j],&FsigBO[i][j+1] sscanf(s,"%lf%lf%lf%lf%lf",&FsigBO[i][j],&FsigBO[i][j+1]
,&FsigBO[i][j+2],&FsigBO[i][j+3],&FsigBO[i][j+4]); ,&FsigBO[i][j+2],&FsigBO[i][j+3],&FsigBO[i][j+4]);
j+=4; j+=4;
} }
} }
for(i=0;i<bop_types;i++) { for(i=0;i<bop_types;i++) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf",&pro_delta[i]); sscanf(s,"%lf",&pro_delta[i]);
} }
for(i=0;i<bop_types;i++) { for(i=0;i<bop_types;i++) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf",&pro[i]); sscanf(s,"%lf",&pro[i]);
} }
for(i=0;i<npairs;i++) { for(i=0;i<npairs;i++) {
@ -5232,7 +5233,7 @@ void PairBOP::read_table(char *filename)
if(pass==1) { if(pass==1) {
for(i=0;i<npairs;i++) { for(i=0;i<npairs;i++) {
for(j=0;j<nr;j++) { for(j=0;j<nr;j++) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&pLong[i][j],&pLong[i][j+1] sscanf(s,"%lf%lf%lf%lf%lf",&pLong[i][j],&pLong[i][j+1]
,&pLong[i][j+2],&pLong[i][j+3],&pLong[i][j+4]); ,&pLong[i][j+2],&pLong[i][j+3],&pLong[i][j+4]);
j+=4; j+=4;

40
src/MANYBODY/pair_comb3.cpp
View File

@ -33,6 +33,7 @@
#include "math_const.h" #include "math_const.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace MathConst; using namespace MathConst;
@ -319,12 +320,13 @@ void PairComb3::read_lib()
// open libraray file on proc 0 // open libraray file on proc 0
if (comm->me == 0) { if (comm->me == 0) {
FILE *fp = force->open_potential("lib.comb3"); const char filename[] = "lib.comb3";
FILE *fp = force->open_potential(filename);
if (fp == NULL) error->one(FLERR,"Cannot open COMB3 lib.comb3 file"); if (fp == NULL) error->one(FLERR,"Cannot open COMB3 lib.comb3 file");
// read and store at the same time // read and store at the same time
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@ -335,7 +337,7 @@ void PairComb3::read_lib()
ccutoff[4] = atof(words[4]); ccutoff[4] = atof(words[4]);
ccutoff[5] = atof(words[5]); ccutoff[5] = atof(words[5]);
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@ -347,7 +349,7 @@ void PairComb3::read_lib()
ch_a[5] = atof(words[5]); ch_a[5] = atof(words[5]);
ch_a[6] = atof(words[6]); ch_a[6] = atof(words[6]);
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@ -355,7 +357,7 @@ void PairComb3::read_lib()
nsplrad = atoi(words[1]); nsplrad = atoi(words[1]);
nspltor = atoi(words[2]); nspltor = atoi(words[2]);
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@ -363,7 +365,7 @@ void PairComb3::read_lib()
maxy = atoi(words[1]); maxy = atoi(words[1]);
maxz = atoi(words[2]); maxz = atoi(words[2]);
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@ -372,7 +374,7 @@ void PairComb3::read_lib()
maxconj = atoi(words[2]); maxconj = atoi(words[2]);
for (l=0; l<nsplpcn; l++) { for (l=0; l<nsplpcn; l++) {
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@ -381,14 +383,14 @@ void PairComb3::read_lib()
dvmaxxcn[l] = atof(words[3]); dvmaxxcn[l] = atof(words[3]);
} }
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
ntab = atoi(words[0]); ntab = atoi(words[0]);
for (i=0; i<ntab+1; i++){ for (i=0; i<ntab+1; i++){
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@ -401,7 +403,7 @@ void PairComb3::read_lib()
for (i=0; i<maxx+1; i++) for (i=0; i<maxx+1; i++)
for (j=0; j<maxy+1; j++) for (j=0; j<maxy+1; j++)
for (k=0; k<maxz+1; k++) { for (k=0; k<maxz+1; k++) {
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@ -419,7 +421,7 @@ void PairComb3::read_lib()
for (i=0; i<maxx; i++) for (i=0; i<maxx; i++)
for (j=0; j<maxy; j++) for (j=0; j<maxy; j++)
for (k=0; k<maxz; k++) { for (k=0; k<maxz; k++) {
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@ -428,7 +430,7 @@ void PairComb3::read_lib()
jj = atoi(words[2]); jj = atoi(words[2]);
kk = atoi(words[3]); kk = atoi(words[3]);
for(iii=0; iii<2; iii++) { for(iii=0; iii<2; iii++) {
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@ -443,7 +445,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc+1; i++) for (i=0; i<maxxc+1; i++)
for (j=0; j<maxyc+1; j++) for (j=0; j<maxyc+1; j++)
for (k=0; k<maxconj; k++) { for (k=0; k<maxconj; k++) {
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@ -461,7 +463,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc; i++) for (i=0; i<maxxc; i++)
for (j=0; j<maxyc; j++) for (j=0; j<maxyc; j++)
for (k=0; k<maxconj-1; k++) { for (k=0; k<maxconj-1; k++) {
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@ -470,7 +472,7 @@ void PairComb3::read_lib()
jj = atoi(words[2]); jj = atoi(words[2]);
kk = atoi(words[3])-1; kk = atoi(words[3])-1;
for (iii=0; iii<2; iii++) { for (iii=0; iii<2; iii++) {
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@ -485,7 +487,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc+1; i++) for (i=0; i<maxxc+1; i++)
for (j=0; j<maxyc+1; j++) for (j=0; j<maxyc+1; j++)
for (k=0; k<maxconj; k++) { for (k=0; k<maxconj; k++) {
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@ -503,7 +505,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc; i++) for (i=0; i<maxxc; i++)
for (j=0; j<maxyc; j++) for (j=0; j<maxyc; j++)
for (k=0; k<maxconj-1; k++) { for (k=0; k<maxconj-1; k++) {
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@ -512,7 +514,7 @@ void PairComb3::read_lib()
jj = atoi(words[2]); jj = atoi(words[2]);
kk = atoi(words[3])-1; kk = atoi(words[3])-1;
for(iii=0; iii<2; iii++) { for(iii=0; iii<2; iii++) {
fgets(s,MAXLIB,fp); utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
nwords = 0; nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f"); words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;

9
src/MANYBODY/pair_eam.cpp
View File

@ -27,6 +27,7 @@
#include "neigh_list.h" #include "neigh_list.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -466,10 +467,10 @@ void PairEAM::read_file(char *filename)
int tmp,nwords; int tmp,nwords;
if (me == 0) { if (me == 0) {
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
sscanf(line,"%d %lg",&tmp,&file->mass); sscanf(line,"%d %lg",&tmp,&file->mass);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
nwords = sscanf(line,"%d %lg %d %lg %lg", nwords = sscanf(line,"%d %lg %d %lg %lg",
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut); &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
} }
@ -784,7 +785,7 @@ void PairEAM::grab(FILE *fptr, int n, double *list)
int i = 0; int i = 0;
while (i < n) { while (i < n) {
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,NULL,error);
ptr = strtok(line," \t\n\r\f"); ptr = strtok(line," \t\n\r\f");
list[i++] = atof(ptr); list[i++] = atof(ptr);
while ((ptr = strtok(NULL," \t\n\r\f"))) list[i++] = atof(ptr); while ((ptr = strtok(NULL," \t\n\r\f"))) list[i++] = atof(ptr);

13
src/MANYBODY/pair_eam_alloy.cpp
View File

@ -23,6 +23,7 @@
#include "force.h" #include "force.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -136,10 +137,10 @@ void PairEAMAlloy::read_file(char *filename)
int n; int n;
if (me == 0) { if (me == 0) {
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
n = strlen(line) + 1; n = strlen(line) + 1;
} }
MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(&n,1,MPI_INT,0,world);
@ -164,7 +165,7 @@ void PairEAMAlloy::read_file(char *filename)
delete [] words; delete [] words;
if (me == 0) { if (me == 0) {
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
nwords = sscanf(line,"%d %lg %d %lg %lg", nwords = sscanf(line,"%d %lg %d %lg %lg",
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut); &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
} }
@ -188,7 +189,7 @@ void PairEAMAlloy::read_file(char *filename)
int i,j,tmp; int i,j,tmp;
for (i = 0; i < file->nelements; i++) { for (i = 0; i < file->nelements; i++) {
if (me == 0) { if (me == 0) {
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
sscanf(line,"%d %lg",&tmp,&file->mass[i]); sscanf(line,"%d %lg",&tmp,&file->mass[i]);
} }
MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world); MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);

13
src/MANYBODY/pair_eam_fs.cpp
View File

@ -23,6 +23,7 @@
#include "force.h" #include "force.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -136,10 +137,10 @@ void PairEAMFS::read_file(char *filename)
int n; int n;
if (me == 0) { if (me == 0) {
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
n = strlen(line) + 1; n = strlen(line) + 1;
} }
MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(&n,1,MPI_INT,0,world);
@ -164,7 +165,7 @@ void PairEAMFS::read_file(char *filename)
delete [] words; delete [] words;
if (me == 0) { if (me == 0) {
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
nwords = sscanf(line,"%d %lg %d %lg %lg", nwords = sscanf(line,"%d %lg %d %lg %lg",
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut); &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
} }
@ -190,7 +191,7 @@ void PairEAMFS::read_file(char *filename)
int i,j,tmp; int i,j,tmp;
for (i = 0; i < file->nelements; i++) { for (i = 0; i < file->nelements; i++) {
if (me == 0) { if (me == 0) {
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
sscanf(line,"%d %lg",&tmp,&file->mass[i]); sscanf(line,"%d %lg",&tmp,&file->mass[i]);
} }
MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world); MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);

5
src/MANYBODY/pair_eim.cpp
View File

@ -26,6 +26,7 @@
#include "neigh_list.h" #include "neigh_list.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -966,11 +967,11 @@ int PairEIM::grabpair(FILE *fptr, int i, int j)
sscanf(data,"%lg %lg %lg %lg %lg", sscanf(data,"%lg %lg %lg %lg %lg",
&setfl->rcutphiA[ij],&setfl->rcutphiR[ij], &setfl->rcutphiA[ij],&setfl->rcutphiR[ij],
&setfl->Eb[ij],&setfl->r0[ij],&setfl->alpha[ij]); &setfl->Eb[ij],&setfl->r0[ij],&setfl->alpha[ij]);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,NULL,error);
sscanf(line,"%lg %lg %lg %lg %lg", sscanf(line,"%lg %lg %lg %lg %lg",
&setfl->beta[ij],&setfl->rcutq[ij],&setfl->Asigma[ij], &setfl->beta[ij],&setfl->rcutq[ij],&setfl->Asigma[ij],
&setfl->rq[ij],&setfl->rcutsigma[ij]); &setfl->rq[ij],&setfl->rcutsigma[ij]);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,NULL,error);
sscanf(line,"%lg %lg %lg %d", sscanf(line,"%lg %lg %lg %d",
&setfl->Ac[ij],&setfl->zeta[ij],&setfl->rs[ij], &setfl->Ac[ij],&setfl->zeta[ij],&setfl->rs[ij],
&setfl->tp[ij]); &setfl->tp[ij]);

69
src/MANYBODY/pair_lcbop.cpp
View File

@ -29,6 +29,7 @@
#include "my_page.h" #include "my_page.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -978,43 +979,43 @@ void PairLCBOP::read_file(char *filename)
// skip initial comment lines // skip initial comment lines
while (1) { while (1) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (s[0] != '#') break; if (s[0] != '#') break;
} }
// read parameters // read parameters
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&r_1); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&r_1);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&r_2); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&r_2);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&gamma_1); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&gamma_1);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&A); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&A);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&B_1); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&B_1);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&B_2); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&B_2);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&alpha); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&alpha);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&beta_1); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&beta_1);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&beta_2); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&beta_2);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&d); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&d);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&C_1); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&C_1);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&C_4); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&C_4);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&C_6); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&C_6);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&L); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&L);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&kappa); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&kappa);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&R_0); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&R_0);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&R_1); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&R_1);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&r_0); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&r_0);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&r_1_LR); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&r_1_LR);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&r_2_LR); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&r_2_LR);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&v_1); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&v_1);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&v_2); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&v_2);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&eps_1); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&eps_1);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&eps_2); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&eps_2);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&lambda_1); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&lambda_1);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&lambda_2); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&lambda_2);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&eps); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&eps);
fgets(s,MAXLINE,fp); sscanf(s,"%lg",&delta); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&delta);
while (1) { while (1) {
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (s[0] != '#') break; if (s[0] != '#') break;
} }
@ -1023,27 +1024,27 @@ void PairLCBOP::read_file(char *filename)
for (k = 0; k < 2; k++) { // 2 values of N_ij_conj for (k = 0; k < 2; k++) { // 2 values of N_ij_conj
for (l = 0; l < 3; l++) { // 3 types of data: f, dfdx, dfdy for (l = 0; l < 3; l++) { // 3 types of data: f, dfdx, dfdy
for (i = 0; i < 4; i++) { // 4x4 matrix for (i = 0; i < 4; i++) { // 4x4 matrix
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lg %lg %lg %lg", sscanf(s,"%lg %lg %lg %lg",
&F_conj_data[i][0][k][l], &F_conj_data[i][0][k][l],
&F_conj_data[i][1][k][l], &F_conj_data[i][1][k][l],
&F_conj_data[i][2][k][l], &F_conj_data[i][2][k][l],
&F_conj_data[i][3][k][l]); &F_conj_data[i][3][k][l]);
} }
while (1) { fgets(s,MAXLINE,fp); if (s[0] != '#') break; } while (1) { utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); if (s[0] != '#') break; }
} }
} }
// G spline // G spline
// x coordinates of mesh points // x coordinates of mesh points
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf( s,"%lg %lg %lg %lg %lg %lg", sscanf( s,"%lg %lg %lg %lg %lg %lg",
&gX[0], &gX[1], &gX[2], &gX[0], &gX[1], &gX[2],
&gX[3], &gX[4], &gX[5] ); &gX[3], &gX[4], &gX[5] );
for (i = 0; i < 6; i++) { // for each power in polynomial for (i = 0; i < 6; i++) { // for each power in polynomial
fgets(s,MAXLINE,fp); utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf( s,"%lg %lg %lg %lg %lg", sscanf( s,"%lg %lg %lg %lg %lg",
&gC[i][0], &gC[i][1], &gC[i][2], &gC[i][0], &gC[i][1], &gC[i][2],
&gC[i][3], &gC[i][4] ); &gC[i][3], &gC[i][4] );

13
src/MANYBODY/pair_polymorphic.cpp
View File

@ -29,6 +29,7 @@
#include "comm.h" #include "comm.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -573,8 +574,8 @@ void PairPolymorphic::read_file(char *file)
error->one(FLERR,str); error->one(FLERR,str);
} }
// move past comments to first data line // move past comments to first data line
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
while (line == strchr(line,'#')) fgets(line,MAXLINE,fp); while (line == strchr(line,'#')) utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
n = strlen(line) + 1; n = strlen(line) + 1;
} }
MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(&n,1,MPI_INT,0,world);
@ -590,7 +591,7 @@ void PairPolymorphic::read_file(char *file)
// map the elements in the potential file to LAMMPS atom types // map the elements in the potential file to LAMMPS atom types
for (int i = 0; i < nelements; i++) { for (int i = 0; i < nelements; i++) {
if (comm->me == 0) { if (comm->me == 0) {
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
n = strlen(line) + 1; n = strlen(line) + 1;
} }
MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(&n,1,MPI_INT,0,world);
@ -608,7 +609,7 @@ void PairPolymorphic::read_file(char *file)
} }
// sizes // sizes
if (comm->me == 0) { if (comm->me == 0) {
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
n = strlen(line) + 1; n = strlen(line) + 1;
} }
@ -644,7 +645,7 @@ void PairPolymorphic::read_file(char *file)
for (int i = 0; i < npair; i++) { for (int i = 0; i < npair; i++) {
PairParameters & p = pairParameters[i]; PairParameters & p = pairParameters[i];
if (comm->me == 0) { if (comm->me == 0) {
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
n = strlen(line) + 1; n = strlen(line) + 1;
} }
MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(&n,1,MPI_INT,0,world);
@ -875,7 +876,7 @@ void PairPolymorphic::grab(FILE *fp, int n, double *list)
int i = 0; int i = 0;
while (i < n) { while (i < n) {
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
ptr = strtok(line," \t\n\r\f"); ptr = strtok(line," \t\n\r\f");
list[i++] = atof(ptr); list[i++] = atof(ptr);
while ((ptr = strtok(NULL," \t\n\r\f"))) while ((ptr = strtok(NULL," \t\n\r\f")))

2
src/MESSAGE/message.cpp
View File

@ -28,7 +28,7 @@ void Message::command(int narg, char **arg)
{ {
if (narg < 3) error->all(FLERR,"Illegal message command"); if (narg < 3) error->all(FLERR,"Illegal message command");
int clientserver; int clientserver=0;
if (strcmp(arg[0],"client") == 0) clientserver = 1; if (strcmp(arg[0],"client") == 0) clientserver = 1;
else if (strcmp(arg[0],"server") == 0) clientserver = 2; else if (strcmp(arg[0],"server") == 0) clientserver = 2;
else error->all(FLERR,"Illegal message command"); else error->all(FLERR,"Illegal message command");

13
src/USER-DPD/fix_eos_table.cpp
View File

@ -23,6 +23,7 @@
#include "error.h" #include "error.h"
#include "force.h" #include "force.h"
#include "memory.h" #include "memory.h"
#include "utils.h"
#define MAXLINE 1024 #define MAXLINE 1024
@ -214,16 +215,16 @@ void FixEOStable::read_table(Table *tb, Table *tb2, char *file, char *keyword)
if (line[0] == '#') continue; // comment if (line[0] == '#') continue; // comment
char *word = strtok(line," \t\n\r"); char *word = strtok(line," \t\n\r");
if (strcmp(word,keyword) == 0) break; // matching keyword if (strcmp(word,keyword) == 0) break; // matching keyword
fgets(line,MAXLINE,fp); // no match, skip section utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section
param_extract(tb,tb2,line); param_extract(tb,tb2,line);
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); for (int i = 0; i < tb->ninput; i++) utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
} }
// read args on 2nd line of section // read args on 2nd line of section
// allocate table arrays for file values // allocate table arrays for file values
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
param_extract(tb,tb2,line); param_extract(tb,tb2,line);
memory->create(tb->rfile,tb->ninput,"eos:rfile"); memory->create(tb->rfile,tb->ninput,"eos:rfile");
memory->create(tb->efile,tb->ninput,"eos:efile"); memory->create(tb->efile,tb->ninput,"eos:efile");
@ -233,9 +234,9 @@ void FixEOStable::read_table(Table *tb, Table *tb2, char *file, char *keyword)
// read r,e table values from file // read r,e table values from file
int itmp; int itmp;
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
for (int i = 0; i < tb->ninput; i++) { for (int i = 0; i < tb->ninput; i++) {
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
sscanf(line,"%d %lg %lg",&itmp,&tb->rfile[i],&tb->efile[i]); sscanf(line,"%d %lg %lg",&itmp,&tb->rfile[i],&tb->efile[i]);
sscanf(line,"%d %lg %lg",&itmp,&tb2->efile[i],&tb2->rfile[i]); sscanf(line,"%d %lg %lg",&itmp,&tb2->efile[i],&tb2->rfile[i]);
} }

13
src/USER-DPD/fix_eos_table_rx.cpp
View File

@ -26,6 +26,7 @@
#include "memory.h" #include "memory.h"
#include "comm.h" #include "comm.h"
#include "modify.h" #include "modify.h"
#include "utils.h"
#define MAXLINE 1024 #define MAXLINE 1024
@ -433,16 +434,16 @@ void FixEOStableRX::read_table(Table *tb, Table *tb2, char *file, char *keyword)
if (line[0] == '#') continue; // comment if (line[0] == '#') continue; // comment
char *word = strtok(line," \t\n\r"); char *word = strtok(line," \t\n\r");
if (strcmp(word,keyword) == 0) break; // matching keyword if (strcmp(word,keyword) == 0) break; // matching keyword
fgets(line,MAXLINE,fp); // no match, skip section utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section
param_extract(tb,line); param_extract(tb,line);
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); for (int i = 0; i < tb->ninput; i++) utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
} }
// read args on 2nd line of section // read args on 2nd line of section
// allocate table arrays for file values // allocate table arrays for file values
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
param_extract(tb,line); param_extract(tb,line);
tb2->ninput = tb->ninput; tb2->ninput = tb->ninput;
memory->create(tb->rfile,tb->ninput,"eos:rfile"); memory->create(tb->rfile,tb->ninput,"eos:rfile");
@ -470,9 +471,9 @@ void FixEOStableRX::read_table(Table *tb, Table *tb2, char *file, char *keyword)
int ispecies; int ispecies;
int ninputs = tb->ninput; int ninputs = tb->ninput;
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
for (int i = 0; i < ninputs; i++) { for (int i = 0; i < ninputs; i++) {
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
nwords = atom->count_words(line); nwords = atom->count_words(line);
if(nwords != nspecies+2){ if(nwords != nspecies+2){

13
src/USER-DPD/pair_multi_lucy.cpp
View File

@ -34,6 +34,7 @@
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "citeme.h" #include "citeme.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -362,16 +363,16 @@ void PairMultiLucy::read_table(Table *tb, char *file, char *keyword)
if (line[0] == '#') continue; // comment if (line[0] == '#') continue; // comment
char *word = strtok(line," \t\n\r"); char *word = strtok(line," \t\n\r");
if (strcmp(word,keyword) == 0) break; // matching keyword if (strcmp(word,keyword) == 0) break; // matching keyword
fgets(line,MAXLINE,fp); // no match, skip section utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section
param_extract(tb,line); param_extract(tb,line);
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp);
} }
// read args on 2nd line of section // read args on 2nd line of section
// allocate table arrays for file values // allocate table arrays for file valuesutils::s
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
param_extract(tb,line); param_extract(tb,line);
memory->create(tb->rfile,tb->ninput,"pair:rfile"); memory->create(tb->rfile,tb->ninput,"pair:rfile");
memory->create(tb->efile,tb->ninput,"pair:efile"); memory->create(tb->efile,tb->ninput,"pair:efile");
@ -384,9 +385,9 @@ void PairMultiLucy::read_table(Table *tb, char *file, char *keyword)
int itmp; int itmp;
double rtmp; double rtmp;
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
for (int i = 0; i < tb->ninput; i++) { for (int i = 0; i < tb->ninput; i++) {
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
sscanf(line,"%d %lg %lg %lg",&itmp,&rtmp,&tb->efile[i],&tb->ffile[i]); sscanf(line,"%d %lg %lg %lg",&itmp,&rtmp,&tb->efile[i],&tb->ffile[i]);
if (tb->rflag == RLINEAR) if (tb->rflag == RLINEAR)

13
src/USER-DPD/pair_multi_lucy_rx.cpp
View File

@ -36,6 +36,7 @@
#include "citeme.h" #include "citeme.h"
#include "modify.h" #include "modify.h"
#include "fix.h" #include "fix.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -507,16 +508,16 @@ void PairMultiLucyRX::read_table(Table *tb, char *file, char *keyword)
if (line[0] == '#') continue; // comment if (line[0] == '#') continue; // comment
char *word = strtok(line," \t\n\r"); char *word = strtok(line," \t\n\r");
if (strcmp(word,keyword) == 0) break; // matching keyword if (strcmp(word,keyword) == 0) break; // matching keyword
fgets(line,MAXLINE,fp); // no match, skip section utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section
param_extract(tb,line); param_extract(tb,line);
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); for (int i = 0; i < tb->ninput; i++) utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
} }
// read args on 2nd line of section // read args on 2nd line of section
// allocate table arrays for file values // allocate table arrays for file values
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
param_extract(tb,line); param_extract(tb,line);
memory->create(tb->rfile,tb->ninput,"pair:rfile"); memory->create(tb->rfile,tb->ninput,"pair:rfile");
memory->create(tb->efile,tb->ninput,"pair:efile"); memory->create(tb->efile,tb->ninput,"pair:efile");
@ -529,9 +530,9 @@ void PairMultiLucyRX::read_table(Table *tb, char *file, char *keyword)
int itmp; int itmp;
double rtmp; double rtmp;
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
for (int i = 0; i < tb->ninput; i++) { for (int i = 0; i < tb->ninput; i++) {
fgets(line,MAXLINE,fp); utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
sscanf(line,"%d %lg %lg %lg",&itmp,&rtmp,&tb->efile[i],&tb->ffile[i]); sscanf(line,"%d %lg %lg %lg",&itmp,&rtmp,&tb->efile[i],&tb->ffile[i]);
if (tb->rflag == RLINEAR) if (tb->rflag == RLINEAR)

94
src/USER-MISC/fix_ttm_mod.cpp
View File

@ -32,6 +32,7 @@
#include "error.h" #include "error.h"
#include "citeme.h" #include "citeme.h"
#include "math_const.h" #include "math_const.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;
@ -93,10 +94,11 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
if (nxnodes <= 0 || nynodes <= 0 || nznodes <= 0) if (nxnodes <= 0 || nynodes <= 0 || nznodes <= 0)
error->all(FLERR,"Fix ttm/mod number of nodes must be > 0"); error->all(FLERR,"Fix ttm/mod number of nodes must be > 0");
FILE *fpr = force->open_potential(arg[8]); const char *filename = arg[8];
FILE *fpr = force->open_potential(filename);
if (fpr == NULL) { if (fpr == NULL) {
char str[128]; char str[128];
snprintf(str,128,"Cannot open file %s",arg[8]); snprintf(str,128,"Cannot open file %s",filename);
error->all(FLERR,str); error->all(FLERR,str);
} }
@ -117,113 +119,113 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
double tresh_d; double tresh_d;
int tresh_i; int tresh_i;
// C0 (metal) // C0 (metal)
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
esheat_0 = tresh_d; esheat_0 = tresh_d;
// C1 (metal*10^3) // C1 (metal*10^3)
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
esheat_1 = tresh_d; esheat_1 = tresh_d;
// C2 (metal*10^6) // C2 (metal*10^6)
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
esheat_2 = tresh_d; esheat_2 = tresh_d;
// C3 (metal*10^9) // C3 (metal*10^9)
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
esheat_3 = tresh_d; esheat_3 = tresh_d;
// C4 (metal*10^12) // C4 (metal*10^12)
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
esheat_4 = tresh_d; esheat_4 = tresh_d;
// C_limit // C_limit
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
C_limit = tresh_d; C_limit = tresh_d;
//Temperature damping factor //Temperature damping factor
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
T_damp = tresh_d; T_damp = tresh_d;
// rho_e // rho_e
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
electronic_density = tresh_d; electronic_density = tresh_d;
//thermal_diffusion //thermal_diffusion
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
el_th_diff = tresh_d; el_th_diff = tresh_d;
// gamma_p // gamma_p
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
gamma_p = tresh_d; gamma_p = tresh_d;
// gamma_s // gamma_s
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
gamma_s = tresh_d; gamma_s = tresh_d;
// v0 // v0
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
v_0 = tresh_d; v_0 = tresh_d;
// average intensity of pulse (source of energy) (metal units) // average intensity of pulse (source of energy) (metal units)
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
intensity = tresh_d; intensity = tresh_d;
// coordinate of 1st surface in x-direction (in box units) - constant // coordinate of 1st surface in x-direction (in box units) - constant
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%d",&tresh_i); sscanf(linee,"%d",&tresh_i);
surface_l = tresh_i; surface_l = tresh_i;
// coordinate of 2nd surface in x-direction (in box units) - constant // coordinate of 2nd surface in x-direction (in box units) - constant
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%d",&tresh_i); sscanf(linee,"%d",&tresh_i);
surface_r = tresh_i; surface_r = tresh_i;
// skin_layer = intensity is reduced (I=I0*exp[-x/skin_layer]) // skin_layer = intensity is reduced (I=I0*exp[-x/skin_layer])
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%d",&tresh_i); sscanf(linee,"%d",&tresh_i);
skin_layer = tresh_i; skin_layer = tresh_i;
// width of pulse (picoseconds) // width of pulse (picoseconds)
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
width = tresh_d; width = tresh_d;
// factor of electronic pressure (PF) Pe = PF*Ce*Te // factor of electronic pressure (PF) Pe = PF*Ce*Te
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
pres_factor = tresh_d; pres_factor = tresh_d;
// effective free path of electrons (angstrom) // effective free path of electrons (angstrom)
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
free_path = tresh_d; free_path = tresh_d;
// ionic density (ions*angstrom^{-3}) // ionic density (ions*angstrom^{-3})
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
ionic_density = tresh_d; ionic_density = tresh_d;
// if movsur = 0: surface is freezed // if movsur = 0: surface is freezed
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%d",&tresh_i); sscanf(linee,"%d",&tresh_i);
movsur = tresh_i; movsur = tresh_i;
// electron_temperature_min // electron_temperature_min
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
fgets(linee,MAXLINE,fpr_2); utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
sscanf(linee,"%lg",&tresh_d); sscanf(linee,"%lg",&tresh_d);
electron_temperature_min = tresh_d; electron_temperature_min = tresh_d;
fclose(fpr_2); fclose(fpr_2);

25
src/USER-MISC/pair_local_density.cpp
View File

@ -33,6 +33,7 @@
#include "error.h" #include "error.h"
#include "domain.h" #include "domain.h"
#include "citeme.h" #include "citeme.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -683,14 +684,14 @@ void PairLocalDensity::parse_file(char *filename) {
// broadcast number of LD potentials and number of (rho,frho) pairs // broadcast number of LD potentials and number of (rho,frho) pairs
if (me == 0) { if (me == 0) {
// first 2 comment lines ignored // first 2 comment lines ignored
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
// extract number of potentials and number of (frho, rho) points // extract number of potentials and number of (frho, rho) points
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
sscanf(line, "%d %d", &nLD, &nrho); sscanf(line, "%d %d", &nLD, &nrho);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
} }
MPI_Bcast(&nLD,1,MPI_INT,0,world); MPI_Bcast(&nLD,1,MPI_INT,0,world);
@ -732,7 +733,7 @@ void PairLocalDensity::parse_file(char *filename) {
sscanf(line, "%lf %lf", &lowercut[k], &uppercut[k]); sscanf(line, "%lf %lf", &lowercut[k], &uppercut[k]);
// parse and broadcast central atom filter // parse and broadcast central atom filter
fgets(line, MAXLINE, fptr); utils::sfgets(FLERR,line, MAXLINE, fptr,filename,error);
char *tmp = strtok(line, " /t/n/r/f"); char *tmp = strtok(line, " /t/n/r/f");
while (tmp != NULL) { while (tmp != NULL) {
a[k][atoi(tmp)] = 1; a[k][atoi(tmp)] = 1;
@ -740,7 +741,7 @@ void PairLocalDensity::parse_file(char *filename) {
} }
// parse neighbor atom filter // parse neighbor atom filter
fgets(line, MAXLINE, fptr); utils::sfgets(FLERR,line, MAXLINE, fptr,filename,error);
tmp = strtok(line, " /t/n/r/f"); tmp = strtok(line, " /t/n/r/f");
while (tmp != NULL) { while (tmp != NULL) {
b[k][atoi(tmp)] = 1; b[k][atoi(tmp)] = 1;
@ -748,19 +749,19 @@ void PairLocalDensity::parse_file(char *filename) {
} }
// parse min, max and delta rho values // parse min, max and delta rho values
fgets(line, MAXLINE, fptr); utils::sfgets(FLERR,line, MAXLINE, fptr,filename,error);
sscanf(line, "%lf %lf %lf", &rho_min[k], &rho_max[k], &delta_rho[k]); sscanf(line, "%lf %lf %lf", &rho_min[k], &rho_max[k], &delta_rho[k]);
// recompute delta_rho from scratch for precision // recompute delta_rho from scratch for precision
delta_rho[k] = (rho_max[k] - rho_min[k]) / (nrho - 1); delta_rho[k] = (rho_max[k] - rho_min[k]) / (nrho - 1);
// parse tabulated frho values from each line into temporary array // parse tabulated frho values from each line into temporary array
for (n = 0; n < nrho; n++) { for (n = 0; n < nrho; n++) {
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
sscanf(line, "%lf", &ftmp[k*nrho + n]); sscanf(line, "%lf", &ftmp[k*nrho + n]);
} }
// ignore blank line at the end of every block // ignore blank line at the end of every block
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
// set coefficients for local density indicator function // set coefficients for local density indicator function
uc2 = uppercut[k] * uppercut[k]; uc2 = uppercut[k] * uppercut[k];

17
src/USER-MISC/pair_meam_spline.cpp
View File

@ -43,6 +43,7 @@
#include "neigh_request.h" #include "neigh_request.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -439,13 +440,13 @@ void PairMEAMSpline::read_file(const char* filename)
// Skip first line of file. It's a comment. // Skip first line of file. It's a comment.
char line[MAXLINE]; char line[MAXLINE];
char *ptr; char *ptr;
fgets(line, MAXLINE, fp); utils::sfgets(FLERR,line,MAXLINE,fp,filename,error);
// Second line holds potential type ("meam/spline") // Second line holds potential type ("meam/spline")
// in new potential format. // in new potential format.
bool isNewFormat = false; bool isNewFormat = false;
fgets(line, MAXLINE, fp); utils::sfgets(FLERR,line,MAXLINE,fp,filename,error);
ptr = strtok(line, " \t\n\r\f"); ptr = strtok(line, " \t\n\r\f");
if (strcmp(ptr, "meam/spline") == 0) { if (strcmp(ptr, "meam/spline") == 0) {
@ -475,7 +476,7 @@ void PairMEAMSpline::read_file(const char* filename)
elements[0] = new char[1]; elements[0] = new char[1];
strcpy(elements[0], ""); strcpy(elements[0], "");
rewind(fp); rewind(fp);
fgets(line, MAXLINE, fp); utils::sfgets(FLERR,line,MAXLINE,fp,filename,error);
} }
nmultichoose2 = ((nelements+1)*nelements)/2; nmultichoose2 = ((nelements+1)*nelements)/2;
@ -639,27 +640,27 @@ void PairMEAMSpline::SplineFunction::parse(FILE* fp, Error* error,
// If new format, read the spline format. Should always be "spline3eq" for now. // If new format, read the spline format. Should always be "spline3eq" for now.
if (isNewFormat) if (isNewFormat)
fgets(line, MAXLINE, fp); utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
// Parse number of spline knots. // Parse number of spline knots.
fgets(line, MAXLINE, fp); utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
int n = atoi(line); int n = atoi(line);
if(n < 2) if(n < 2)
error->one(FLERR,"Invalid number of spline knots in MEAM potential file"); error->one(FLERR,"Invalid number of spline knots in MEAM potential file");
// Parse first derivatives at beginning and end of spline. // Parse first derivatives at beginning and end of spline.
fgets(line, MAXLINE, fp); utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
double d0 = atof(strtok(line, " \t\n\r\f")); double d0 = atof(strtok(line, " \t\n\r\f"));
double dN = atof(strtok(NULL, " \t\n\r\f")); double dN = atof(strtok(NULL, " \t\n\r\f"));
init(n, d0, dN); init(n, d0, dN);
// Skip line in old format // Skip line in old format
if (!isNewFormat) if (!isNewFormat)
fgets(line, MAXLINE, fp); utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
// Parse knot coordinates. // Parse knot coordinates.
for(int i=0; i<n; i++) { for(int i=0; i<n; i++) {
fgets(line, MAXLINE, fp); utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
double x, y, y2; double x, y, y2;
if(sscanf(line, "%lg %lg %lg", &x, &y, &y2) != 3) { if(sscanf(line, "%lg %lg %lg", &x, &y, &y2) != 3) {
error->one(FLERR,"Invalid knot line in MEAM potential file"); error->one(FLERR,"Invalid knot line in MEAM potential file");

11
src/USER-MISC/pair_meam_sw_spline.cpp
View File

@ -35,6 +35,7 @@
#include "neigh_request.h" #include "neigh_request.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -468,7 +469,7 @@ void PairMEAMSWSpline::read_file(const char* filename)
// Skip first line of file. // Skip first line of file.
char line[MAXLINE]; char line[MAXLINE];
fgets(line, MAXLINE, fp); utils::sfgets(FLERR,line,MAXLINE,fp,filename,error);
// Parse spline functions. // Parse spline functions.
phi.parse(fp, error); phi.parse(fp, error);
@ -600,23 +601,23 @@ void PairMEAMSWSpline::SplineFunction::parse(FILE* fp, Error* error)
char line[MAXLINE]; char line[MAXLINE];
// Parse number of spline knots. // Parse number of spline knots.
fgets(line, MAXLINE, fp); utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
int n = atoi(line); int n = atoi(line);
if(n < 2) if(n < 2)
error->one(FLERR,"Invalid number of spline knots in MEAM potential file"); error->one(FLERR,"Invalid number of spline knots in MEAM potential file");
// Parse first derivatives at beginning and end of spline. // Parse first derivatives at beginning and end of spline.
fgets(line, MAXLINE, fp); utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
double d0 = atof(strtok(line, " \t\n\r\f")); double d0 = atof(strtok(line, " \t\n\r\f"));
double dN = atof(strtok(NULL, " \t\n\r\f")); double dN = atof(strtok(NULL, " \t\n\r\f"));
init(n, d0, dN); init(n, d0, dN);
// Skip line. // Skip line.
fgets(line, MAXLINE, fp); utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
// Parse knot coordinates. // Parse knot coordinates.
for(int i=0; i<n; i++) { for(int i=0; i<n; i++) {
fgets(line, MAXLINE, fp); utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
double x, y, y2; double x, y, y2;
if(sscanf(line, "%lg %lg %lg", &x, &y, &y2) != 3) { if(sscanf(line, "%lg %lg %lg", &x, &y, &y2) != 3) {
error->one(FLERR,"Invalid knot line in MEAM potential file"); error->one(FLERR,"Invalid knot line in MEAM potential file");

13
src/USER-OMP/pair_eam_alloy_omp.cpp
View File

@ -24,6 +24,7 @@
#include "force.h" #include "force.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -136,10 +137,10 @@ void PairEAMAlloyOMP::read_file(char *filename)
int n; int n;
if (me == 0) { if (me == 0) {
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
n = strlen(line) + 1; n = strlen(line) + 1;
} }
MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(&n,1,MPI_INT,0,world);
@ -164,7 +165,7 @@ void PairEAMAlloyOMP::read_file(char *filename)
delete [] words; delete [] words;
if (me == 0) { if (me == 0) {
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
sscanf(line,"%d %lg %d %lg %lg", sscanf(line,"%d %lg %d %lg %lg",
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut); &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
} }
@ -184,7 +185,7 @@ void PairEAMAlloyOMP::read_file(char *filename)
int i,j,tmp; int i,j,tmp;
for (i = 0; i < file->nelements; i++) { for (i = 0; i < file->nelements; i++) {
if (me == 0) { if (me == 0) {
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
sscanf(line,"%d %lg",&tmp,&file->mass[i]); sscanf(line,"%d %lg",&tmp,&file->mass[i]);
} }
MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world); MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);

13
src/USER-OMP/pair_eam_fs_omp.cpp
View File

@ -24,6 +24,7 @@
#include "force.h" #include "force.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -136,10 +137,10 @@ void PairEAMFSOMP::read_file(char *filename)
int n; int n;
if (me == 0) { if (me == 0) {
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
n = strlen(line) + 1; n = strlen(line) + 1;
} }
MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(&n,1,MPI_INT,0,world);
@ -164,7 +165,7 @@ void PairEAMFSOMP::read_file(char *filename)
delete [] words; delete [] words;
if (me == 0) { if (me == 0) {
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
sscanf(line,"%d %lg %d %lg %lg", sscanf(line,"%d %lg %d %lg %lg",
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut); &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
} }
@ -186,7 +187,7 @@ void PairEAMFSOMP::read_file(char *filename)
int i,j,tmp; int i,j,tmp;
for (i = 0; i < file->nelements; i++) { for (i = 0; i < file->nelements; i++) {
if (me == 0) { if (me == 0) {
fgets(line,MAXLINE,fptr); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
sscanf(line,"%d %lg",&tmp,&file->mass[i]); sscanf(line,"%d %lg",&tmp,&file->mass[i]);
} }
MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world); MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);

4
src/USER-OMP/reaxc_forces_omp.cpp
View File

@ -368,7 +368,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
#if defined(_OPENMP) #if defined(_OPENMP)
#pragma omp parallel default(shared) \ #pragma omp parallel default(shared) \
private(atom_i, type_i, start_i, end_i, sbp_i, btop_i, ihb, ihb_top, \ private(atom_i, type_i, start_i, end_i, sbp_i, btop_i, ihb, ihb_top, \
j, atom_j, type_j, pj, sbp_j, nbr_pj, jhb, twbp) atom_j, type_j, pj, sbp_j, nbr_pj, jhb, twbp)
#endif #endif
{ {
@ -395,7 +395,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
for( pj = start_i; pj < end_i; ++pj ) { for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] ); nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
if (nbr_pj->d <= cutoff) { if (nbr_pj->d <= cutoff) {
j = nbr_pj->nbr; int j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]); atom_j = &(system->my_atoms[j]);
type_j = atom_j->type; type_j = atom_j->type;
sbp_j = &(system->reax_param.sbp[type_j]); sbp_j = &(system->reax_param.sbp[type_j]);

4
src/USER-PTM/compute_ptm_atom.cpp
View File

@ -23,6 +23,7 @@ under
#include <vector> #include <vector>
#include "atom.h" #include "atom.h"
#include "citeme.h"
#include "comm.h" #include "comm.h"
#include "error.h" #include "error.h"
#include "force.h" #include "force.h"
@ -82,6 +83,9 @@ ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg)
PTM_CHECK_ALL, PTM_CHECK_ALL,
PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_BCC | PTM_CHECK_ICO}; PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_BCC | PTM_CHECK_ICO};
if (lmp->citeme)
lmp->citeme->add(cite_user_ptm_package);
input_flags = 0; input_flags = 0;
while (*ptr != '\0') { while (*ptr != '\0') {