public IEnumerator GetAmberEGH(bool suppressStretches = false, bool suppressBends = false, bool suppressTorsions = true, bool suppressNonBonding = false)
{
_busy++;
rmsForces = 0f;
int c;
for (int atomNum = 0; atomNum < atoms.size; atomNum++)
{
for (c = 0; c < 3; c++)
{
positions[atomNum * 3 + c] = atoms[atomNum].p[c];
}
}
int numAtoms = size;
forces = new double[numAtoms * 3];
Fortran.allocate_atom_arrays(ref numAtoms);
int status = 0;
double[] stretchesEnergy = new double[2];
double[] bendsEnergy = new double[2];
double[] torsionsEnergy = new double[2];
double[] vdwsEnergy = new double[2];
double[] coulombicEnergy = new double[2];
Fortran.e_amber(positions, forces,
stretchesEnergy, bendsEnergy, torsionsEnergy, vdwsEnergy,
coulombicEnergy, ref rmsForces, ref status
);
Fortran.CheckStatus(status);
//GetStretchesEGH();
//yield return null;
//GetBendsEGH();
//yield return null;
//GetTorsionEGH();
///yield return null;
//GetNonBondingEGH();
//yield return null;
allStretchesEnergy = stretchesEnergy[0];
allBendsEnergy = bendsEnergy[0];
allTorsionsEnergy = torsionsEnergy[0];
allVdwsEnergy = vdwsEnergy[0];
allCoulombicEnergy = coulombicEnergy[0];
amberEnergy = allStretchesEnergy + allBendsEnergy + allTorsionsEnergy + allVdwsEnergy + allCoulombicEnergy;
totalEnergy = amberEnergy + kineticEnergy;
for (int atomNum = 0; atomNum < atoms.size; atomNum++)
{
for (c = 0; c < 3; c++)
{
atoms[atomNum].force[c] = (float)forces[3 * atomNum + c];
}
}
_busy--;
yield return(null);
}
public void InitialiseMasses()
{
int status = 0;
Fortran.set_masses(atoms.masses, ref status);
Fortran.CheckStatus(status);
}
public IEnumerator AMBEROpt(int steps, int updateAfterSteps = 5)
{
_busy++;
int status = 0;
int c = 0;
int numAtoms = size;
positions = new double[numAtoms * 3];
for (int atomNum = 0; atomNum < numAtoms; atomNum++)
{
for (c = 0; c < 3; c++)
{
positions[3 * atomNum + c] = atoms[atomNum].p[c];
}
}
Fortran.allocate_atom_arrays(ref numAtoms);
IEnumerator iEnumerator;
iEnumerator = InitialiseParameters();
while (iEnumerator.MoveNext())
{
}
yield return(null);
double[] stretchesEnergy = new double[2];
double[] bendsEnergy = new double[2];
double[] torsionsEnergy = new double[2];
double[] vdwsEnergy = new double[2];
double[] coulombicEnergy = new double[2];
string logPath = "/Users/tristanmackenzie/Unity/ONIOM/Assets/Plugins/out.log";
System.IO.File.Delete(logPath);
double convergence_threshold = 0.00001;
int precision = 3;
int iprint = 0;
int matrix_corrections = 17;
int stepNum = 0;
Vector3 vPosition = new Vector3();
while (stepNum < steps)
{
writeArray(positions, logPath);
Fortran.lbfgs_optimise(positions, ref updateAfterSteps,
stretchesEnergy, bendsEnergy, torsionsEnergy,
vdwsEnergy, coulombicEnergy, ref convergence_threshold,
ref precision, ref iprint, ref matrix_corrections, ref status
);
writeArray(positions, logPath);
Fortran.CheckStatus(status);
allStretchesEnergy = stretchesEnergy[0];
allBendsEnergy = bendsEnergy[0];
allTorsionsEnergy = torsionsEnergy[0];
allVdwsEnergy = vdwsEnergy[0];
allCoulombicEnergy = coulombicEnergy[0];
amberEnergy = allStretchesEnergy + allBendsEnergy + allTorsionsEnergy + allVdwsEnergy + allCoulombicEnergy;
totalEnergy = amberEnergy + kineticEnergy;
stepNum += updateAfterSteps;
for (int atomNum = 0; atomNum < numAtoms; atomNum++)
{
for (c = 0; c < 3; c++)
{
vPosition[c] = (float)positions[3 * atomNum + c];
}
atoms[atomNum].transform.localPosition = vPosition;
}
yield return(null);
}
_busy--;
yield return(null);
}
public IEnumerator MDVerlet(int steps, int updateAfterSteps = 5)
{
_busy++;
int status = 0;
int c = 0;
int numAtoms = size;
positions = new double[numAtoms * 3];
for (int atomNum = 0; atomNum < numAtoms; atomNum++)
{
for (c = 0; c < 3; c++)
{
positions[3 * atomNum + c] = atoms[atomNum].p[c];
}
}
Fortran.allocate_atom_arrays(ref numAtoms);
IEnumerator iEnumerator;
iEnumerator = InitialiseParameters();
while (iEnumerator.MoveNext())
{
}
yield return(null);
double[] stretchesEnergy = new double[2];
double[] bendsEnergy = new double[2];
double[] torsionsEnergy = new double[2];
double[] vdwsEnergy = new double[2];
double[] coulombicEnergy = new double[2];
double mdTimeStep = atoms.globalSettings.mdTimeStep;
double mdDampingFactor = atoms.globalSettings.mdDampingFactor;
string logPath = "/Users/tristanmackenzie/Unity/ONIOM/Assets/Plugins/out.log";
System.IO.File.Delete(logPath);
//Run MD
int stepNum = 0;
Vector3 vPosition = new Vector3();
while (stepNum < steps)
{
writeArray(positions, logPath);
Fortran.md_verlet(positions, ref updateAfterSteps,
ref mdTimeStep, ref mdDampingFactor,
stretchesEnergy, bendsEnergy, torsionsEnergy, vdwsEnergy, coulombicEnergy,
ref kineticEnergy, ref rmsForces, ref status);
writeArray(positions, logPath);
Fortran.CheckStatus(status);
allStretchesEnergy = stretchesEnergy[0];
allBendsEnergy = bendsEnergy[0];
allTorsionsEnergy = torsionsEnergy[0];
allVdwsEnergy = vdwsEnergy[0];
allCoulombicEnergy = coulombicEnergy[0];
amberEnergy = allStretchesEnergy + allBendsEnergy + allTorsionsEnergy + allVdwsEnergy + allCoulombicEnergy;
totalEnergy = amberEnergy + kineticEnergy;
stepNum += updateAfterSteps;
for (int atomNum = 0; atomNum < numAtoms; atomNum++)
{
for (c = 0; c < 3; c++)
{
vPosition[c] = (float)positions[3 * atomNum + c];
}
atoms[atomNum].transform.localPosition = vPosition;
}
yield return(null);
}
_busy--;
yield return(null);
}