static void add_lj_interaction(PdbParser::PdbParser &parser, std::vector<PdbLJInteraction> interactions, const double rel_cutoff, const int first_type) {
for(std::vector<PdbLJInteraction>::const_iterator it = interactions.begin(); it != interactions.end(); ++it) {
for(std::map<std::string, PdbParser::itp_atomtype>::const_iterator jt = parser.itp_atomtypes.begin(); jt != parser.itp_atomtypes.end(); ++jt) {
const double epsilon_ij = sqrt(it->epsilon * jt->second.epsilon);
const double sigma_ij = 0.5*(it->sigma+jt->second.epsilon);
const double cutoff_ij = rel_cutoff*sigma_ij;
const double shift_ij = -pow(sigma_ij/cutoff_ij,12) - pow(sigma_ij/cutoff_ij,6);
READPDB_TRACE(printf("adding lj interaction types %d %d eps %e sig %e cut %e shift %e\n", it->other_type, first_type + jt->second.id, epsilon_ij, sigma_ij,
cutoff_ij, shift_ij););
lennard_jones_set_params(it->other_type, first_type + jt->second.id, epsilon_ij, sigma_ij,
cutoff_ij, shift_ij, 0.0, -1.0, 0.0);
}
}
int tclcommand_inter_parse_lj(Tcl_Interp * interp,
int part_type_a, int part_type_b,
int argc, char ** argv)
{
/* parameters needed for LJ */
double eps, sig, cut, shift, offset, cap_radius, min;
int compute_auto_shift, change;
/* get lennard-jones interaction type */
if (argc < 4) {
Tcl_AppendResult(interp, "lennard-jones needs at least 3 parameters: "
"<lj_eps> <lj_sig> <lj_cut> [<lj_shift> [<lj_offset> [<lj_cap> [<lj_min>]]]]",
(char *) NULL);
return 0;
}
change = 1;
/* PARSE LENNARD-JONES COMMAND LINE */
/* epsilon */
if (! ARG_IS_D(1, eps)) {
Tcl_AppendResult(interp, "<lj_eps> should be a double",
(char *) NULL);
return 0;
}
change++;
/* sigma */
if (! ARG_IS_D(2, sig)) {
Tcl_AppendResult(interp, "<lj_sig> should be a double",
(char *) NULL);
return 0;
}
change++;
/* cutoff */
if (! ARG_IS_D(3, cut)) {
Tcl_AppendResult(interp, "<lj_cut> should be a double",
(char *) NULL);
return 0;
}
change++;
/* shift */
if (argc > 4) {
if (ARG_IS_D(4, shift)) {
/* if a shift is given, use that one */
compute_auto_shift = 0;
change++;
} else if (ARG_IS_S(4, "auto")) {
Tcl_ResetResult(interp);
compute_auto_shift = 1;
/* if shift is "auto", autocompute the shift */
change++;
} else {
Tcl_AppendResult(interp, "<lj_shift> should be a double or \"auto\"",
(char *) NULL);
return 0;
}
} else {
/* by default, compute the shift automatically */
compute_auto_shift = 1;
}
/* the shift can be computed automatically only when the other
parameters have been determined, see below */
/* offset */
if (argc > 5) {
if (!ARG_IS_D(5, offset)) {
Tcl_AppendResult(interp, "<lj_off> should be a double",
(char *) NULL);
return 0;
}
change++;
} else {
offset = 0.0;
}
/* cap_radius */
if (argc > 6) {
if (!ARG_IS_D(6, cap_radius)) {
Tcl_AppendResult(interp, "<lj_cap> should be a double",
(char *) NULL);
return 0;
}
change++;
} else {
cap_radius = -1.0;
}
/* minimal radius */
if (argc > 7) {
if (!ARG_IS_D(7, min)) {
Tcl_AppendResult(interp, "<lj_rmin> should be a double",
(char *) NULL);
return 0;
}
change ++;
} else {
min = 0.0;
}
/* automatically compute the shift */
if (compute_auto_shift)
shift = -(pow(sig/cut, 12) - pow(sig/cut, 6));
/* now set the parameters */
if (lennard_jones_set_params(part_type_a, part_type_b,
eps, sig, cut, shift, offset,
cap_radius, min) == ES_ERROR) {
Tcl_AppendResult(interp, "particle types must be non-negative",
(char *) NULL);
return 0;
}
return change;
}
