public List <int> moltoUFF_azo(OBMol mol, string coefficientfilename, string datafilename, double padding)
{
LAMMPSNow lammpssetup = new LAMMPSNow(parameters, atomtypes, periodictable);
lammpssetup.setupUFF(mol, padding);
lammpssetup.setupcalculationsUFF_azobenzene(mol, coefficientfilename, datafilename);
List <int> esequence = lammpssetup.getesequence();
return(esequence);
}
public List <int> moltoUFFPeriodic(OBMol mol, string coefficientfilename, string datafilename, int x_rep, int y_rep, int z_rep)
{
LAMMPSNow lammpssetup = new LAMMPSNow(parameters, atomtypes, periodictable);
lammpssetup.setupUFFPeriodic(mol, coefficientfilename, datafilename, x_rep, y_rep, z_rep);
List <int> esequence = lammpssetup.getesequence();
return(esequence);
}
public List <int> moltoUFF(OBMol mol, string coefficientfilename, string datafilename, bool contingency, double padding)
{
LAMMPSNow lammpssetup = new LAMMPSNow(parameters, atomtypes, periodictable);
if (contingency)
{
//if lammps fails to minimize, try minimization using openbabel as a starting point
OBForceField uff = OBForceField.FindForceField("UFF");
mol = lammpssetup.perturbator(mol, 2); //lammps crashes when atoms are on top of each other
OBConversion obconv = new OBConversion();
obconv.SetOutFormat("cml");
obconv.WriteFile(mol, "badrun.cml");
uff.Setup(mol);
uff.SteepestDescent(1000);
}
lammpssetup.setupUFF(mol, coefficientfilename, datafilename, padding);
List <int> esequence = lammpssetup.getesequence();
return(esequence);
}
public void designgraphtoUFF(designGraph host, string coefficientfilename, string datafilename, bool contingency)
{
OBMol mol = new OBMol();
OBFunctions.designgraphtomol(host, ref mol);
LAMMPSNow lammpssetup = new LAMMPSNow(parameters, atomtypes, periodictable);
if (contingency)
{
//if lammps fails to minimize, try minimization using openbabel as a starting point
OBForceField uff = OBForceField.FindForceField("UFF");
mol = lammpssetup.perturbator(mol, 2); //lammps crashes when atoms are on top of each other
OBConversion obconv = new OBConversion();
obconv.SetOutFormat("cml");
obconv.WriteFile(mol, "badrun.cml");
uff.Setup(mol);
uff.SteepestDescent(1000);
}
lammpssetup.setupUFF(mol, coefficientfilename, datafilename, 50);
//lammpssetup.setupUFFtest(mol);
//lammpssetup.reset();
}
public void moltoReaxFF(OBMol mol, string datafilename)
{
LAMMPSNow lammpssetup = new LAMMPSNow(parameters, atomtypes, periodictable);
lammpssetup.setupReax(mol, datafilename);
}