public OBMol quickMinimization(OBMol mol, string coeff, string lmpdat, bool periodic)
{
double etol = 0.0;
double ftol = 1.0e-6;
int maxiter = 40000;
int maxeval = 20000;
double padding = 50;
lammps.LAMMPSsettings minSettings = new lammps.LAMMPSsettings();
if (periodic)
{
minSettings.boundary = "p p p";
padding = 0;
}
moltoUFF(mol, coeff, lmpdat, false, padding);
///graphconverter.designgraphtoUFF(child, iodir + coeff, iodir + lmpdat, false);
//LAMMPSinstance lammps = new LAMMPSinstance(iodir + data, lmpSettings);//, &lmpptr);
lammps lmps = new lammps(minSettings);
lmps.runCommand("read_data " + lmpdat);
lmps.openFile(coeff);
lmps.minimize(etol, ftol, maxiter, maxeval, "cg");
double[,] pos = lmps.getAtomPos();
OBFunctions.updatexyz(mol, pos);
return(mol);
}
private OBMol QuickMinimization(OBMol mol, string coeff, string lmpdat, bool periodic, int rankMe)
{
double padding = 50;
const double etol = 0.0;
const double ftol = 1.0e-6;
const int maxiter = 40000;
const int maxeval = 20000;
var minSettings = new lammps.LAMMPSsettings();
if (periodic)
{
minSettings.boundary = "p p p";
padding = 0;
}
if (File.Exists(coeff))
{
File.Delete(coeff);
}
if (File.Exists(lmpdat))
{
File.Delete(lmpdat);
}
Converter.moltoUFF(mol, coeff, lmpdat, false, padding);
string[] lmparg = { "", "-screen", "none", "-log", "log.lammps." + rankMe };
using (var lmps = new lammps(minSettings, lmparg)) {
lmps.runCommand("read_data " + lmpdat);
lmps.openFile(coeff);
lmps.minimize(etol, ftol, maxiter, maxeval, "cg");
OBFunctions.updatexyz(mol, lmps.getAtomPos());
}
return(mol);
}