diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index 05ec27a9b4..1b08e4b88d 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -45,6 +45,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -4982,13 +4983,13 @@ void PairBOP::read_table(char *filename) snprintf(str,128,"Cannot open BOP potential file %s",filename); error->one(FLERR,str); } - fgets(s,MAXLINE,fp); // skip first comment line - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); // skip first comment line + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%d",&bop_types); elements = new char*[bop_types]; for(i=0;ione(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;icutmax) 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]); - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); 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]); } if(nws==3) { @@ -5115,56 +5116,56 @@ void PairBOP::read_table(char *filename) for(k=j;kme == 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"); // read and store at the same time - fgets(s,MAXLIB,fp); - fgets(s,MAXLIB,fp); + utils::sfgets(FLERR,s,MAXLIB,fp,filename,error); + utils::sfgets(FLERR,s,MAXLIB,fp,filename,error); nwords = 0; words[nwords++] = strtok(s," \t\n\r\f"); while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; @@ -335,7 +337,7 @@ void PairComb3::read_lib() ccutoff[4] = atof(words[4]); ccutoff[5] = atof(words[5]); - fgets(s,MAXLIB,fp); + utils::sfgets(FLERR,s,MAXLIB,fp,filename,error); nwords = 0; words[nwords++] = strtok(s," \t\n\r\f"); 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[6] = atof(words[6]); - fgets(s,MAXLIB,fp); + utils::sfgets(FLERR,s,MAXLIB,fp,filename,error); nwords = 0; words[nwords++] = strtok(s," \t\n\r\f"); while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; @@ -355,7 +357,7 @@ void PairComb3::read_lib() nsplrad = atoi(words[1]); nspltor = atoi(words[2]); - fgets(s,MAXLIB,fp); + utils::sfgets(FLERR,s,MAXLIB,fp,filename,error); nwords = 0; words[nwords++] = strtok(s," \t\n\r\f"); while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; @@ -363,7 +365,7 @@ void PairComb3::read_lib() maxy = atoi(words[1]); maxz = atoi(words[2]); - fgets(s,MAXLIB,fp); + utils::sfgets(FLERR,s,MAXLIB,fp,filename,error); nwords = 0; words[nwords++] = strtok(s," \t\n\r\f"); while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; @@ -372,7 +374,7 @@ void PairComb3::read_lib() maxconj = atoi(words[2]); for (l=0; lmass); - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); nwords = sscanf(line,"%d %lg %d %lg %lg", &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; while (i < n) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,NULL,error); ptr = strtok(line," \t\n\r\f"); list[i++] = atof(ptr); while ((ptr = strtok(NULL," \t\n\r\f"))) list[i++] = atof(ptr); diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index 5b7f9877d7..a9622f9e07 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -23,6 +23,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -136,10 +137,10 @@ void PairEAMAlloy::read_file(char *filename) int n; if (me == 0) { - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); @@ -164,7 +165,7 @@ void PairEAMAlloy::read_file(char *filename) delete [] words; if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); nwords = sscanf(line,"%d %lg %d %lg %lg", &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut); } @@ -188,7 +189,7 @@ void PairEAMAlloy::read_file(char *filename) int i,j,tmp; for (i = 0; i < file->nelements; i++) { if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line,"%d %lg",&tmp,&file->mass[i]); } MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world); diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index 7e00783922..c91e7b5298 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -23,6 +23,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -136,10 +137,10 @@ void PairEAMFS::read_file(char *filename) int n; if (me == 0) { - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); @@ -164,7 +165,7 @@ void PairEAMFS::read_file(char *filename) delete [] words; if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); nwords = sscanf(line,"%d %lg %d %lg %lg", &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut); } @@ -190,7 +191,7 @@ void PairEAMFS::read_file(char *filename) int i,j,tmp; for (i = 0; i < file->nelements; i++) { if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line,"%d %lg",&tmp,&file->mass[i]); } MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world); diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index dd65d92cdd..dc1c7fa019 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -26,6 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -966,11 +967,11 @@ int PairEIM::grabpair(FILE *fptr, int i, int j) sscanf(data,"%lg %lg %lg %lg %lg", &setfl->rcutphiA[ij],&setfl->rcutphiR[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", &setfl->beta[ij],&setfl->rcutq[ij],&setfl->Asigma[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", &setfl->Ac[ij],&setfl->zeta[ij],&setfl->rs[ij], &setfl->tp[ij]); diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index 873a675cd9..cc97fd9e9b 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -29,6 +29,7 @@ #include "my_page.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -978,43 +979,43 @@ void PairLCBOP::read_file(char *filename) // skip initial comment lines while (1) { - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); if (s[0] != '#') break; } // read parameters - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&r_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&r_2); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&gamma_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&A); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&B_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&B_2); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&alpha); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&beta_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&beta_2); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&d); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&C_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&C_4); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&C_6); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&L); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&kappa); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&R_0); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&R_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&r_0); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&r_1_LR); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&r_2_LR); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&v_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&v_2); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&eps_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&eps_2); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&lambda_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&lambda_2); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&eps); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&delta); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&r_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&r_2); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&gamma_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&A); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&B_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&B_2); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&alpha); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&beta_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&beta_2); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&d); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&C_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&C_4); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&C_6); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&L); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&kappa); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&R_0); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&R_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&r_0); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&r_1_LR); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&r_2_LR); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&v_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&v_2); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&eps_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&eps_2); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&lambda_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&lambda_2); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&eps); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&delta); while (1) { - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); 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 (l = 0; l < 3; l++) { // 3 types of data: f, dfdx, dfdy 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", &F_conj_data[i][0][k][l], &F_conj_data[i][1][k][l], &F_conj_data[i][2][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 // 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", &gX[0], &gX[1], &gX[2], &gX[3], &gX[4], &gX[5] ); 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", &gC[i][0], &gC[i][1], &gC[i][2], &gC[i][3], &gC[i][4] ); diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index d3964b292c..8db4d63d4c 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -29,6 +29,7 @@ #include "comm.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -573,8 +574,8 @@ void PairPolymorphic::read_file(char *file) error->one(FLERR,str); } // move past comments to first data line - fgets(line,MAXLINE,fp); - while (line == strchr(line,'#')) fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + while (line == strchr(line,'#')) utils::sfgets(FLERR,line,MAXLINE,fp,file,error); n = strlen(line) + 1; } 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 for (int i = 0; i < nelements; i++) { if (comm->me == 0) { - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); @@ -608,7 +609,7 @@ void PairPolymorphic::read_file(char *file) } // sizes if (comm->me == 0) { - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); n = strlen(line) + 1; } @@ -644,7 +645,7 @@ void PairPolymorphic::read_file(char *file) for (int i = 0; i < npair; i++) { PairParameters & p = pairParameters[i]; if (comm->me == 0) { - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); @@ -875,7 +876,7 @@ void PairPolymorphic::grab(FILE *fp, int n, double *list) int i = 0; while (i < n) { - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error); ptr = strtok(line," \t\n\r\f"); list[i++] = atof(ptr); while ((ptr = strtok(NULL," \t\n\r\f"))) diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp index f8fc349746..214025be63 100644 --- a/src/MESSAGE/message.cpp +++ b/src/MESSAGE/message.cpp @@ -28,7 +28,7 @@ void Message::command(int narg, char **arg) { if (narg < 3) error->all(FLERR,"Illegal message command"); - int clientserver; + int clientserver=0; if (strcmp(arg[0],"client") == 0) clientserver = 1; else if (strcmp(arg[0],"server") == 0) clientserver = 2; else error->all(FLERR,"Illegal message command"); diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp index ff9a186c47..dc6310ae42 100644 --- a/src/USER-DPD/fix_eos_table.cpp +++ b/src/USER-DPD/fix_eos_table.cpp @@ -23,6 +23,7 @@ #include "error.h" #include "force.h" #include "memory.h" +#include "utils.h" #define MAXLINE 1024 @@ -214,16 +215,16 @@ void FixEOStable::read_table(Table *tb, Table *tb2, char *file, char *keyword) if (line[0] == '#') continue; // comment char *word = strtok(line," \t\n\r"); 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); - fgets(line,MAXLINE,fp); - for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + for (int i = 0; i < tb->ninput; i++) utils::sfgets(FLERR,line,MAXLINE,fp,file,error); } // read args on 2nd line of section // allocate table arrays for file values - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); param_extract(tb,tb2,line); memory->create(tb->rfile,tb->ninput,"eos:rfile"); 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 int itmp; - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); 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,&tb2->efile[i],&tb2->rfile[i]); } diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp index 9f1bd6a3bb..152b58dbb7 100644 --- a/src/USER-DPD/fix_eos_table_rx.cpp +++ b/src/USER-DPD/fix_eos_table_rx.cpp @@ -26,6 +26,7 @@ #include "memory.h" #include "comm.h" #include "modify.h" +#include "utils.h" #define MAXLINE 1024 @@ -433,16 +434,16 @@ void FixEOStableRX::read_table(Table *tb, Table *tb2, char *file, char *keyword) if (line[0] == '#') continue; // comment char *word = strtok(line," \t\n\r"); 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); - fgets(line,MAXLINE,fp); - for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + for (int i = 0; i < tb->ninput; i++) utils::sfgets(FLERR,line,MAXLINE,fp,file,error); } // read args on 2nd line of section // allocate table arrays for file values - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); param_extract(tb,line); tb2->ninput = tb->ninput; 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 ninputs = tb->ninput; - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); for (int i = 0; i < ninputs; i++) { - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); nwords = atom->count_words(line); if(nwords != nspecies+2){ diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp index ffc1562f88..d82216d5b2 100644 --- a/src/USER-DPD/pair_multi_lucy.cpp +++ b/src/USER-DPD/pair_multi_lucy.cpp @@ -34,6 +34,7 @@ #include "memory.h" #include "error.h" #include "citeme.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -362,16 +363,16 @@ void PairMultiLucy::read_table(Table *tb, char *file, char *keyword) if (line[0] == '#') continue; // comment char *word = strtok(line," \t\n\r"); 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); - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); } // 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); memory->create(tb->rfile,tb->ninput,"pair:rfile"); memory->create(tb->efile,tb->ninput,"pair:efile"); @@ -384,9 +385,9 @@ void PairMultiLucy::read_table(Table *tb, char *file, char *keyword) int itmp; double rtmp; - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); 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]); if (tb->rflag == RLINEAR) diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp index 801e8ff039..4b08261474 100644 --- a/src/USER-DPD/pair_multi_lucy_rx.cpp +++ b/src/USER-DPD/pair_multi_lucy_rx.cpp @@ -36,6 +36,7 @@ #include "citeme.h" #include "modify.h" #include "fix.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -507,16 +508,16 @@ void PairMultiLucyRX::read_table(Table *tb, char *file, char *keyword) if (line[0] == '#') continue; // comment char *word = strtok(line," \t\n\r"); 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); - fgets(line,MAXLINE,fp); - for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + for (int i = 0; i < tb->ninput; i++) utils::sfgets(FLERR,line,MAXLINE,fp,file,error); } // read args on 2nd line of section // allocate table arrays for file values - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); param_extract(tb,line); memory->create(tb->rfile,tb->ninput,"pair:rfile"); memory->create(tb->efile,tb->ninput,"pair:efile"); @@ -529,9 +530,9 @@ void PairMultiLucyRX::read_table(Table *tb, char *file, char *keyword) int itmp; double rtmp; - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); 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]); if (tb->rflag == RLINEAR) diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp index 55526a9149..49e9cc02a6 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/USER-MISC/fix_ttm_mod.cpp @@ -32,6 +32,7 @@ #include "error.h" #include "citeme.h" #include "math_const.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -93,10 +94,11 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) : if (nxnodes <= 0 || nynodes <= 0 || nznodes <= 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) { char str[128]; - snprintf(str,128,"Cannot open file %s",arg[8]); + snprintf(str,128,"Cannot open file %s",filename); error->all(FLERR,str); } @@ -117,113 +119,113 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) : double tresh_d; int tresh_i; // C0 (metal) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); esheat_0 = tresh_d; // C1 (metal*10^3) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); esheat_1 = tresh_d; // C2 (metal*10^6) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); esheat_2 = tresh_d; // C3 (metal*10^9) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); esheat_3 = tresh_d; // C4 (metal*10^12) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); esheat_4 = tresh_d; // C_limit - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); C_limit = tresh_d; //Temperature damping factor - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); T_damp = tresh_d; // rho_e - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); electronic_density = tresh_d; //thermal_diffusion - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); el_th_diff = tresh_d; // gamma_p - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); gamma_p = tresh_d; // gamma_s - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); gamma_s = tresh_d; // v0 - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); v_0 = tresh_d; // average intensity of pulse (source of energy) (metal units) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); intensity = tresh_d; // coordinate of 1st surface in x-direction (in box units) - constant - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%d",&tresh_i); surface_l = tresh_i; // coordinate of 2nd surface in x-direction (in box units) - constant - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%d",&tresh_i); surface_r = tresh_i; // skin_layer = intensity is reduced (I=I0*exp[-x/skin_layer]) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%d",&tresh_i); skin_layer = tresh_i; // width of pulse (picoseconds) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); width = tresh_d; // factor of electronic pressure (PF) Pe = PF*Ce*Te - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); pres_factor = tresh_d; // effective free path of electrons (angstrom) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); free_path = tresh_d; // ionic density (ions*angstrom^{-3}) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); ionic_density = tresh_d; // if movsur = 0: surface is freezed - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%d",&tresh_i); movsur = tresh_i; // electron_temperature_min - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); electron_temperature_min = tresh_d; fclose(fpr_2); diff --git a/src/USER-MISC/pair_local_density.cpp b/src/USER-MISC/pair_local_density.cpp index 950b07945d..97aa3dcaca 100644 --- a/src/USER-MISC/pair_local_density.cpp +++ b/src/USER-MISC/pair_local_density.cpp @@ -33,6 +33,7 @@ #include "error.h" #include "domain.h" #include "citeme.h" +#include "utils.h" 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 if (me == 0) { - // first 2 comment lines ignored - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); + // first 2 comment lines ignored + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); - // extract number of potentials and number of (frho, rho) points - fgets(line,MAXLINE,fptr); - sscanf(line, "%d %d", &nLD, &nrho); - fgets(line,MAXLINE,fptr); + // extract number of potentials and number of (frho, rho) points + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + sscanf(line, "%d %d", &nLD, &nrho); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); } 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]); // 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"); while (tmp != NULL) { a[k][atoi(tmp)] = 1; @@ -740,7 +741,7 @@ void PairLocalDensity::parse_file(char *filename) { } // parse neighbor atom filter - fgets(line, MAXLINE, fptr); + utils::sfgets(FLERR,line, MAXLINE, fptr,filename,error); tmp = strtok(line, " /t/n/r/f"); while (tmp != NULL) { b[k][atoi(tmp)] = 1; @@ -748,19 +749,19 @@ void PairLocalDensity::parse_file(char *filename) { } // 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]); // recompute delta_rho from scratch for precision delta_rho[k] = (rho_max[k] - rho_min[k]) / (nrho - 1); // parse tabulated frho values from each line into temporary array 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]); } // 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 uc2 = uppercut[k] * uppercut[k]; diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp index 79e7ac7e09..27deff9a6e 100644 --- a/src/USER-MISC/pair_meam_spline.cpp +++ b/src/USER-MISC/pair_meam_spline.cpp @@ -43,6 +43,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -439,13 +440,13 @@ void PairMEAMSpline::read_file(const char* filename) // Skip first line of file. It's a comment. char line[MAXLINE]; char *ptr; - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,filename,error); // Second line holds potential type ("meam/spline") // in new potential format. bool isNewFormat = false; - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,filename,error); ptr = strtok(line, " \t\n\r\f"); if (strcmp(ptr, "meam/spline") == 0) { @@ -475,7 +476,7 @@ void PairMEAMSpline::read_file(const char* filename) elements[0] = new char[1]; strcpy(elements[0], ""); rewind(fp); - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,filename,error); } 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 (isNewFormat) - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error); // Parse number of spline knots. - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error); int n = atoi(line); if(n < 2) error->one(FLERR,"Invalid number of spline knots in MEAM potential file"); // 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 dN = atof(strtok(NULL, " \t\n\r\f")); init(n, d0, dN); // Skip line in old format if (!isNewFormat) - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error); // Parse knot coordinates. for(int i=0; ione(FLERR,"Invalid knot line in MEAM potential file"); diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp index eeadacf33a..73d6c81004 100644 --- a/src/USER-MISC/pair_meam_sw_spline.cpp +++ b/src/USER-MISC/pair_meam_sw_spline.cpp @@ -35,6 +35,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -468,7 +469,7 @@ void PairMEAMSWSpline::read_file(const char* filename) // Skip first line of file. char line[MAXLINE]; - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,filename,error); // Parse spline functions. phi.parse(fp, error); @@ -600,23 +601,23 @@ void PairMEAMSWSpline::SplineFunction::parse(FILE* fp, Error* error) char line[MAXLINE]; // Parse number of spline knots. - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error); int n = atoi(line); if(n < 2) error->one(FLERR,"Invalid number of spline knots in MEAM potential file"); // 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 dN = atof(strtok(NULL, " \t\n\r\f")); init(n, d0, dN); // Skip line. - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error); // Parse knot coordinates. for(int i=0; ione(FLERR,"Invalid knot line in MEAM potential file"); diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/USER-OMP/pair_eam_alloy_omp.cpp index 78b4735863..d36574713f 100644 --- a/src/USER-OMP/pair_eam_alloy_omp.cpp +++ b/src/USER-OMP/pair_eam_alloy_omp.cpp @@ -24,6 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -136,10 +137,10 @@ void PairEAMAlloyOMP::read_file(char *filename) int n; if (me == 0) { - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); @@ -164,7 +165,7 @@ void PairEAMAlloyOMP::read_file(char *filename) delete [] words; if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line,"%d %lg %d %lg %lg", &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut); } @@ -184,7 +185,7 @@ void PairEAMAlloyOMP::read_file(char *filename) int i,j,tmp; for (i = 0; i < file->nelements; i++) { if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line,"%d %lg",&tmp,&file->mass[i]); } MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world); diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/USER-OMP/pair_eam_fs_omp.cpp index 17fecf9b4f..d1014c5a14 100644 --- a/src/USER-OMP/pair_eam_fs_omp.cpp +++ b/src/USER-OMP/pair_eam_fs_omp.cpp @@ -24,6 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -136,10 +137,10 @@ void PairEAMFSOMP::read_file(char *filename) int n; if (me == 0) { - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); @@ -164,7 +165,7 @@ void PairEAMFSOMP::read_file(char *filename) delete [] words; if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line,"%d %lg %d %lg %lg", &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut); } @@ -186,7 +187,7 @@ void PairEAMFSOMP::read_file(char *filename) int i,j,tmp; for (i = 0; i < file->nelements; i++) { if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line,"%d %lg",&tmp,&file->mass[i]); } MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world); diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp index 1bde0fb970..2ebfcea1e0 100644 --- a/src/USER-OMP/reaxc_forces_omp.cpp +++ b/src/USER-OMP/reaxc_forces_omp.cpp @@ -368,7 +368,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control, #if defined(_OPENMP) #pragma omp parallel default(shared) \ 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 { @@ -395,7 +395,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control, for( pj = start_i; pj < end_i; ++pj ) { nbr_pj = &( far_nbrs->select.far_nbr_list[pj] ); if (nbr_pj->d <= cutoff) { - j = nbr_pj->nbr; + int j = nbr_pj->nbr; atom_j = &(system->my_atoms[j]); type_j = atom_j->type; sbp_j = &(system->reax_param.sbp[type_j]); diff --git a/src/USER-PTM/compute_ptm_atom.cpp b/src/USER-PTM/compute_ptm_atom.cpp index ad3d3facdb..3a2c8daac4 100644 --- a/src/USER-PTM/compute_ptm_atom.cpp +++ b/src/USER-PTM/compute_ptm_atom.cpp @@ -23,6 +23,7 @@ under #include #include "atom.h" +#include "citeme.h" #include "comm.h" #include "error.h" #include "force.h" @@ -82,6 +83,9 @@ ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg) PTM_CHECK_ALL, 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; while (*ptr != '\0') {