Loading doc/src/fix_reax_bonds.txt +7 −0 Original line number Diff line number Diff line Loading @@ -36,6 +36,10 @@ please see the "fix reaxc/c/species"_fix_reaxc_species.html command. The format of the output file should be self-explanatory. If the filename ends with ".gz", the output file is written in gzipped format. A gzipped dump file will be about 3x smaller than the text version, but will also take longer to write. :line [Restart, fix_modify, output, run start/stop, minimize info:] Loading Loading @@ -85,6 +89,9 @@ USER-REAXC package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. To write gzipped bond files, you must compile LAMMPS with the -DLAMMPS_GZIP option. [Related commands:] "pair_style reax"_pair_reax.html, "pair_style Loading doc/src/fix_reaxc_species.txt +7 −0 Original line number Diff line number Diff line Loading @@ -52,6 +52,10 @@ number of molecules of each species. In this context, "species" means a unique molecule. The chemical formula of each species is given in the first line. If the filename ends with ".gz", the output file is written in gzipped format. A gzipped dump file will be about 3x smaller than the text version, but will also take longer to write. Optional keyword {cutoff} can be assigned to change the minimum bond-order values used in identifying chemical bonds between pairs of atoms. Bond-order cutoffs should be carefully chosen, as bond-order Loading Loading @@ -164,6 +168,9 @@ USER-REAXC package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. To write gzipped species files, you must compile LAMMPS with the -DLAMMPS_GZIP option. It should be possible to extend it to other reactive pair_styles (such as "rebo"_pair_airebo.html, "airebo"_pair_airebo.html, "comb"_pair_comb.html, and "bop"_pair_bop.html), but this has not yet been done. Loading src/REAX/fix_reax_bonds.cpp +15 −1 Original line number Diff line number Diff line Loading @@ -49,7 +49,21 @@ FixReaxBonds::FixReaxBonds(LAMMPS *lmp, int narg, char **arg) : if (nevery < 1) error->all(FLERR,"Illegal fix reax/bonds command"); if (me == 0) { fp = fopen(arg[4],"w"); char *suffix = strrchr(arg[4],'.'); if (suffix && strcmp(suffix,".gz") == 0) { #ifdef LAMMPS_GZIP char gzip[128]; sprintf(gzip,"gzip -6 > %s",arg[4]); #ifdef _WIN32 fp = _popen(gzip,"wb"); #else fp = popen(gzip,"w"); #endif #else error->one(FLERR,"Cannot open gzipped file"); #endif } else fp = fopen(arg[4],"w"); if (fp == NULL) { char str[128]; sprintf(str,"Cannot open fix reax/bonds file %s",arg[4]); Loading src/USER-REAXC/fix_reaxc_bonds.cpp +15 −1 Original line number Diff line number Diff line Loading @@ -58,7 +58,21 @@ FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Illegal fix reax/c/bonds command"); if (me == 0) { fp = fopen(arg[4],"w"); char *suffix = strrchr(arg[4],'.'); if (suffix && strcmp(suffix,".gz") == 0) { #ifdef LAMMPS_GZIP char gzip[128]; sprintf(gzip,"gzip -6 > %s",arg[4]); #ifdef _WIN32 fp = _popen(gzip,"wb"); #else fp = popen(gzip,"w"); #endif #else error->one(FLERR,"Cannot open gzipped file"); #endif } else fp = fopen(arg[4],"w"); if (fp == NULL) { char str[128]; sprintf(str,"Cannot open fix reax/c/bonds file %s",arg[4]); Loading src/USER-REAXC/fix_reaxc_species.cpp +15 −1 Original line number Diff line number Diff line Loading @@ -110,7 +110,21 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) : strcpy(tmparg[2],arg[5]); if (me == 0) { fp = fopen(arg[6],"w"); char *suffix = strrchr(arg[6],'.'); if (suffix && strcmp(suffix,".gz") == 0) { #ifdef LAMMPS_GZIP char gzip[128]; sprintf(gzip,"gzip -6 > %s",arg[6]); #ifdef _WIN32 fp = _popen(gzip,"wb"); #else fp = popen(gzip,"w"); #endif #else error->one(FLERR,"Cannot open gzipped file"); #endif } else fp = fopen(arg[6],"w"); if (fp == NULL) { char str[128]; sprintf(str,"Cannot open fix reax/c/species file %s",arg[6]); Loading Loading
doc/src/fix_reax_bonds.txt +7 −0 Original line number Diff line number Diff line Loading @@ -36,6 +36,10 @@ please see the "fix reaxc/c/species"_fix_reaxc_species.html command. The format of the output file should be self-explanatory. If the filename ends with ".gz", the output file is written in gzipped format. A gzipped dump file will be about 3x smaller than the text version, but will also take longer to write. :line [Restart, fix_modify, output, run start/stop, minimize info:] Loading Loading @@ -85,6 +89,9 @@ USER-REAXC package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. To write gzipped bond files, you must compile LAMMPS with the -DLAMMPS_GZIP option. [Related commands:] "pair_style reax"_pair_reax.html, "pair_style Loading
doc/src/fix_reaxc_species.txt +7 −0 Original line number Diff line number Diff line Loading @@ -52,6 +52,10 @@ number of molecules of each species. In this context, "species" means a unique molecule. The chemical formula of each species is given in the first line. If the filename ends with ".gz", the output file is written in gzipped format. A gzipped dump file will be about 3x smaller than the text version, but will also take longer to write. Optional keyword {cutoff} can be assigned to change the minimum bond-order values used in identifying chemical bonds between pairs of atoms. Bond-order cutoffs should be carefully chosen, as bond-order Loading Loading @@ -164,6 +168,9 @@ USER-REAXC package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. To write gzipped species files, you must compile LAMMPS with the -DLAMMPS_GZIP option. It should be possible to extend it to other reactive pair_styles (such as "rebo"_pair_airebo.html, "airebo"_pair_airebo.html, "comb"_pair_comb.html, and "bop"_pair_bop.html), but this has not yet been done. Loading
src/REAX/fix_reax_bonds.cpp +15 −1 Original line number Diff line number Diff line Loading @@ -49,7 +49,21 @@ FixReaxBonds::FixReaxBonds(LAMMPS *lmp, int narg, char **arg) : if (nevery < 1) error->all(FLERR,"Illegal fix reax/bonds command"); if (me == 0) { fp = fopen(arg[4],"w"); char *suffix = strrchr(arg[4],'.'); if (suffix && strcmp(suffix,".gz") == 0) { #ifdef LAMMPS_GZIP char gzip[128]; sprintf(gzip,"gzip -6 > %s",arg[4]); #ifdef _WIN32 fp = _popen(gzip,"wb"); #else fp = popen(gzip,"w"); #endif #else error->one(FLERR,"Cannot open gzipped file"); #endif } else fp = fopen(arg[4],"w"); if (fp == NULL) { char str[128]; sprintf(str,"Cannot open fix reax/bonds file %s",arg[4]); Loading
src/USER-REAXC/fix_reaxc_bonds.cpp +15 −1 Original line number Diff line number Diff line Loading @@ -58,7 +58,21 @@ FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Illegal fix reax/c/bonds command"); if (me == 0) { fp = fopen(arg[4],"w"); char *suffix = strrchr(arg[4],'.'); if (suffix && strcmp(suffix,".gz") == 0) { #ifdef LAMMPS_GZIP char gzip[128]; sprintf(gzip,"gzip -6 > %s",arg[4]); #ifdef _WIN32 fp = _popen(gzip,"wb"); #else fp = popen(gzip,"w"); #endif #else error->one(FLERR,"Cannot open gzipped file"); #endif } else fp = fopen(arg[4],"w"); if (fp == NULL) { char str[128]; sprintf(str,"Cannot open fix reax/c/bonds file %s",arg[4]); Loading
src/USER-REAXC/fix_reaxc_species.cpp +15 −1 Original line number Diff line number Diff line Loading @@ -110,7 +110,21 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) : strcpy(tmparg[2],arg[5]); if (me == 0) { fp = fopen(arg[6],"w"); char *suffix = strrchr(arg[6],'.'); if (suffix && strcmp(suffix,".gz") == 0) { #ifdef LAMMPS_GZIP char gzip[128]; sprintf(gzip,"gzip -6 > %s",arg[6]); #ifdef _WIN32 fp = _popen(gzip,"wb"); #else fp = popen(gzip,"w"); #endif #else error->one(FLERR,"Cannot open gzipped file"); #endif } else fp = fopen(arg[6],"w"); if (fp == NULL) { char str[128]; sprintf(str,"Cannot open fix reax/c/species file %s",arg[6]); Loading
