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fix bug where it was not possible to use an absolute path for write_coeff

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This commit is contained in:
Axel Kohlmeyer
2022-03-16 09:00:56 -04:00
parent 4948438265
commit 92bfaeda10
1 changed files with 56 additions and 62 deletions
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118
src/write_coeff.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -29,7 +28,7 @@
using namespace LAMMPS_NS;
enum {REGULAR_MODE, CLASS2_MODE};
enum { REGULAR_MODE, CLASS2_MODE };
/* ----------------------------------------------------------------------
called as write_coeff command in input script
@ -38,121 +37,116 @@ enum {REGULAR_MODE, CLASS2_MODE};
void WriteCoeff::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all(FLERR,"Write_coeff command before simulation box is defined");
error->all(FLERR, "Write_coeff command before simulation box is defined");
if (narg != 1) error->all(FLERR,"Illegal write_coeff command");
if (narg != 1) error->all(FLERR, "Illegal write_coeff command");
char *file = utils::strdup(fmt::format("tmp.{}",arg[0]));
char *file = utils::strdup(fmt::format("{}.tmp", arg[0]));
// initialize relevant styles
lmp->init();
if (comm->me == 0) {
char str[256], coeff[256];
FILE *one = fopen(file,"wb+");
FILE *one = fopen(file, "wb+");
if (one == nullptr)
error->one(FLERR,"Cannot open coeff file {}: {}",
file, utils::getsyserror());
error->one(FLERR, "Cannot open coeff file {}: {}", file, utils::getsyserror());
if (force->pair && force->pair->writedata) {
fprintf(one,"# pair_style %s\npair_coeff\n",force->pair_style);
fprintf(one, "# pair_style %s\npair_coeff\n", force->pair_style);
force->pair->write_data_all(one);
fprintf(one,"end\n");
fprintf(one, "end\n");
}
if (force->bond && force->bond->writedata) {
fprintf(one,"# bond_style %s\nbond_coeff\n",force->bond_style);
fprintf(one, "# bond_style %s\nbond_coeff\n", force->bond_style);
force->bond->write_data(one);
fprintf(one,"end\n");
fprintf(one, "end\n");
}
if (force->angle && force->angle->writedata) {
fprintf(one,"# angle_style %s\nangle_coeff\n",force->angle_style);
fprintf(one, "# angle_style %s\nangle_coeff\n", force->angle_style);
force->angle->write_data(one);
fprintf(one,"end\n");
fprintf(one, "end\n");
}
if (force->dihedral && force->dihedral->writedata) {
fprintf(one,"# dihedral_style %s\ndihedral_coeff\n",
force->dihedral_style);
fprintf(one, "# dihedral_style %s\ndihedral_coeff\n", force->dihedral_style);
force->dihedral->write_data(one);
fprintf(one,"end\n");
fprintf(one, "end\n");
}
if (force->improper && force->improper->writedata) {
fprintf(one,"# improper_style %s\nimproper_coeff\n",
force->improper_style);
fprintf(one, "# improper_style %s\nimproper_coeff\n", force->improper_style);
force->improper->write_data(one);
fprintf(one,"end\n");
fprintf(one, "end\n");
}
rewind(one);
FILE *two = fopen(file+4,"w");
FILE *two = fopen(arg[0], "w");
if (two == nullptr)
error->one(FLERR,"Cannot open coeff file {}: {}",
file+4, utils::getsyserror());
error->one(FLERR, "Cannot open coeff file {}: {}", arg[0], utils::getsyserror());
fprintf(two,"# LAMMPS coeff file via write_coeff, version %s\n",
lmp->version);
fprintf(two, "# LAMMPS coeff file via write_coeff, version %s\n", lmp->version);
while (true) {
int coeff_mode = REGULAR_MODE;
if (fgets(str,256,one) == nullptr) break;
if (fgets(str, 256, one) == nullptr) break;
// some coeffs need special treatment
if (strstr(str,"class2") != nullptr) {
if (strstr(str,"angle_style") != nullptr)
if (strstr(str, "class2") != nullptr) {
if (strstr(str, "angle_style") != nullptr)
coeff_mode = CLASS2_MODE;
else if (strstr(str,"dihedral_style") != nullptr)
else if (strstr(str, "dihedral_style") != nullptr)
coeff_mode = CLASS2_MODE;
else if (strstr(str,"improper_style") != nullptr)
else if (strstr(str, "improper_style") != nullptr)
coeff_mode = CLASS2_MODE;
}
const char *section = (const char *)"";
fputs(str,two); // style
utils::sfgets(FLERR,str,256,one,file,error); // coeff
const char *section = (const char *) "";
fputs(str, two); // style
utils::sfgets(FLERR, str, 256, one, file, error); // coeff
int n = strlen(str);
strcpy(coeff,str);
coeff[n-1] = '\0';
utils::sfgets(FLERR,str,256,one,file,error);
strcpy(coeff, str);
coeff[n - 1] = '\0';
utils::sfgets(FLERR, str, 256, one, file, error);
while (strcmp(str,"end\n") != 0) {
while (strcmp(str, "end\n") != 0) {
if (coeff_mode == REGULAR_MODE) {
fprintf(two,"%s %s",coeff,str);
utils::sfgets(FLERR,str,256,one,file,error);
fprintf(two, "%s %s", coeff, str);
utils::sfgets(FLERR, str, 256, one, file, error);
} else if (coeff_mode == CLASS2_MODE) {
// class2 angles, dihedrals, and impropers can have
// multiple sections and thus need special treatment
if (strcmp(str,"\n") == 0) {
if (strcmp(str, "\n") == 0) {
// all but the the last section end with an empty line.
// skip it and read and parse the next section title
utils::sfgets(FLERR,str,256,one,file,error);
utils::sfgets(FLERR, str, 256, one, file, error);
if (strcmp(str,"BondBond Coeffs\n") == 0)
section = (const char *)"bb";
else if (strcmp(str,"BondAngle Coeffs\n") ==0)
section = (const char *)"ba";
else if (strcmp(str,"MiddleBondTorsion Coeffs\n") == 0)
section = (const char *)"mbt";
else if (strcmp(str,"EndBondTorsion Coeffs\n") == 0)
section = (const char *)"ebt";
else if (strcmp(str,"AngleTorsion Coeffs\n") == 0)
section = (const char *)"at";
else if (strcmp(str,"AngleAngleTorsion Coeffs\n") == 0)
section = (const char *)"aat";
else if (strcmp(str,"BondBond13 Coeffs\n") == 0)
section = (const char *)"bb13";
else if (strcmp(str,"AngleAngle Coeffs\n") == 0)
section = (const char *)"aa";
if (strcmp(str, "BondBond Coeffs\n") == 0)
section = (const char *) "bb";
else if (strcmp(str, "BondAngle Coeffs\n") == 0)
section = (const char *) "ba";
else if (strcmp(str, "MiddleBondTorsion Coeffs\n") == 0)
section = (const char *) "mbt";
else if (strcmp(str, "EndBondTorsion Coeffs\n") == 0)
section = (const char *) "ebt";
else if (strcmp(str, "AngleTorsion Coeffs\n") == 0)
section = (const char *) "at";
else if (strcmp(str, "AngleAngleTorsion Coeffs\n") == 0)
section = (const char *) "aat";
else if (strcmp(str, "BondBond13 Coeffs\n") == 0)
section = (const char *) "bb13";
else if (strcmp(str, "AngleAngle Coeffs\n") == 0)
section = (const char *) "aa";
// gobble up one more empty line
utils::sfgets(FLERR,str,256,one,file,error);
utils::sfgets(FLERR,str,256,one,file,error);
utils::sfgets(FLERR, str, 256, one, file, error);
utils::sfgets(FLERR, str, 256, one, file, error);
}
// parse type number and skip over it
@ -161,11 +155,11 @@ void WriteCoeff::command(int narg, char **arg)
while ((*p != '\0') && (*p == ' ')) ++p;
while ((*p != '\0') && isdigit(*p)) ++p;
fprintf(two,"%s %d %s %s",coeff,type,section,p);
utils::sfgets(FLERR,str,256,one,file,error);
fprintf(two, "%s %d %s %s", coeff, type, section, p);
utils::sfgets(FLERR, str, 256, one, file, error);
}
}
fputc('\n',two);
fputc('\n', two);
}
fclose(one);
fclose(two);