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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2330 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2009-01-05 22:26:08 +00:00
parent e1f72f6d3a
commit 0cc1d090f4
90 changed files with 1129 additions and 779 deletions
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109
src/force.cpp
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@ -56,6 +56,7 @@ Force::Force(LAMMPS *lmp) : Pointers(lmp)
special_lj[1] = special_lj[2] = special_lj[3] = 0.0;
special_coul[1] = special_coul[2] = special_coul[3] = 0.0;
special_dihedral = 0;
special_extra = 0;
dielectric = 1.0;
@ -353,54 +354,72 @@ void Force::set_special(int narg, char **arg)
{
if (narg == 0) error->all("Illegal special_bonds command");
if (strcmp(arg[0],"charmm") == 0) {
if (narg != 1) error->all("Illegal special_bonds command");
special_lj[1] = 0.0;
special_lj[2] = 0.0;
special_lj[3] = 0.0;
special_coul[1] = 0.0;
special_coul[2] = 0.0;
special_coul[3] = 0.0;
special_dihedral = 0;
return;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"amber") == 0) {
if (iarg+1 > narg) error->all("Illegal special_bonds command");
special_lj[1] = 0.0;
special_lj[2] = 0.0;
special_lj[3] = 0.5;
special_coul[1] = 0.0;
special_coul[2] = 0.0;
special_coul[3] = 5.0/6.0;
iarg += 1;
} else if (strcmp(arg[iarg],"charmm") == 0) {
if (iarg+1 > narg) error->all("Illegal special_bonds command");
special_lj[1] = 0.0;
special_lj[2] = 0.0;
special_lj[3] = 0.0;
special_coul[1] = 0.0;
special_coul[2] = 0.0;
special_coul[3] = 0.0;
iarg += 1;
} else if (strcmp(arg[iarg],"fene") == 0) {
if (iarg+1 > narg) error->all("Illegal special_bonds command");
special_lj[1] = 0.0;
special_lj[2] = 1.0;
special_lj[3] = 1.0;
special_coul[1] = 0.0;
special_coul[2] = 1.0;
special_coul[3] = 1.0;
iarg += 1;
} else if (strcmp(arg[iarg],"lj/coul") == 0) {
if (iarg+4 > narg) error->all("Illegal special_bonds command");
special_lj[1] = special_coul[1] = atof(arg[iarg+1]);
special_lj[2] = special_coul[2] = atof(arg[iarg+2]);
special_lj[3] = special_coul[3] = atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"lj") == 0) {
if (iarg+4 > narg) error->all("Illegal special_bonds command");
special_lj[1] = atof(arg[iarg+1]);
special_lj[2] = atof(arg[iarg+2]);
special_lj[3] = atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"coul") == 0) {
if (iarg+4 > narg) error->all("Illegal special_bonds command");
special_coul[1] = atof(arg[iarg+1]);
special_coul[2] = atof(arg[iarg+2]);
special_coul[3] = atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"dihedral") == 0) {
if (iarg+2 > narg) error->all("Illegal special_bonds command");
if (strcmp(arg[iarg+1],"no") == 0) special_dihedral = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) special_dihedral = 1;
else error->all("Illegal special_bonds command");
iarg += 2;
} else if (strcmp(arg[iarg],"extra") == 0) {
if (iarg+2 > narg) error->all("Illegal special_bonds command");
special_extra = atoi(arg[iarg+1]);
iarg += 2;
} else error->all("Illegal special_bonds command");
}
if (strcmp(arg[0],"amber") == 0) {
if (narg != 1) error->all("Illegal special_bonds command");
special_lj[1] = 0.0;
special_lj[2] = 0.0;
special_lj[3] = 0.5;
special_coul[1] = 0.0;
special_coul[2] = 0.0;
special_coul[3] = 5.0/6.0;
special_dihedral = 0;
return;
}
for (int i = 1; i <= 3; i++)
if (special_lj[i] < 0.0 || special_lj[i] > 1.0 ||
special_coul[i] < 0.0 || special_coul[i] > 1.0)
error->all("Illegal special_bonds command");
int iarg;
if (strcmp(arg[0],"dihedral") == 0) {
special_dihedral = 1;
iarg = 1;
} else if (strcmp(arg[0],"explicit") == 0) {
special_dihedral = 0;
iarg = 1;
} else {
special_dihedral = 0;
iarg = 0;
}
if (narg-iarg == 3) {
special_lj[1] = special_coul[1] = atof(arg[iarg+0]);
special_lj[2] = special_coul[2] = atof(arg[iarg+1]);
special_lj[3] = special_coul[3] = atof(arg[iarg+2]);
} else if (narg-iarg == 6) {
special_lj[1] = atof(arg[iarg+0]);
special_lj[2] = atof(arg[iarg+1]);
special_lj[3] = atof(arg[iarg+2]);
special_coul[1] = atof(arg[iarg+3]);
special_coul[2] = atof(arg[iarg+4]);
special_coul[3] = atof(arg[iarg+5]);
} else error->all("Illegal special_bonds command");
if (special_extra < 0) error->all("Illegal special_bonds command");
}
/* ----------------------------------------------------------------------