Example 1 with DYNFilter
use of ffx.potential.parsers.DYNFilter in project ffx by mjschnie.
the class MolecularDynamics method init.
/**
* <p>
* init</p>
*
* @param nSteps a int.
* @param timeStep a double.
* @param printInterval a double.
* @param saveInterval a double.
* @param fileType a String.
* @param restartFrequency the number of steps between writing restart
* files.
* @param temperature a double.
* @param initVelocities a boolean.
* @param dyn a {@link java.io.File} object.
*/
public void init(final int nSteps, final double timeStep, final double printInterval, final double saveInterval, final String fileType, final double restartFrequency, final double temperature, final boolean initVelocities, final File dyn) {
/**
* Return if already running.
*/
if (!done) {
logger.warning(" Programming error - attempt to modify parameters of a running MolecularDynamics instance.");
return;
}
this.nSteps = nSteps;
totalSimTime = 0.0;
/**
* Convert the time step from femtoseconds to picoseconds.
*/
dt = timeStep * 1.0e-3;
/**
* Convert the print interval to a print frequency.
*/
printFrequency = 100;
if (printInterval >= this.dt) {
printFrequency = (int) (printInterval / this.dt);
}
/**
* Convert the save interval to a save frequency.
*/
saveSnapshotFrequency = 1000;
if (saveInterval >= this.dt) {
saveSnapshotFrequency = (int) (saveInterval / this.dt);
}
/**
* Set snapshot file type.
*/
saveSnapshotAsPDB = true;
if (fileType.equalsIgnoreCase("XYZ")) {
saveSnapshotAsPDB = false;
} else if (!fileType.equalsIgnoreCase("PDB")) {
logger.warning("Snapshot file type unrecognized; saving snaphshots as PDB.\n");
}
/**
* Convert restart frequency to steps.
*/
saveRestartFileFrequency = 1000;
if (restartFrequency >= this.dt) {
saveRestartFileFrequency = (int) (restartFrequency / this.dt);
}
assemblyInfo();
String firstFileName = FilenameUtils.removeExtension(molecularAssembly.getFile().getAbsolutePath());
if (dyn == null) {
this.restartFile = new File(firstFileName + ".dyn");
loadRestart = false;
} else {
this.restartFile = dyn;
loadRestart = true;
}
if (dynFilter == null) {
dynFilter = new DYNFilter(molecularAssembly.getName());
}
this.targetTemperature = temperature;
this.initVelocities = initVelocities;
}Example 2 with DYNFilter
use of ffx.potential.parsers.DYNFilter in project ffx by mjschnie.
the class MolecularDynamicsOpenMM method init.
@Override
public void init(int numSteps, double timeStep, double printInterval, double saveInterval, String fileType, double restartFrequency, double temperature, boolean initVelocities, File dyn) {
this.targetTemperature = temperature;
this.dt = timeStep;
this.printFrequency = (int) printInterval;
this.restartFile = dyn;
this.initVelocities = initVelocities;
switch(thermostatType) {
case BUSSI:
case BERENDSEN:
logger.info(String.format(" Replacing thermostat %s with OpenMM's Andersen thermostat", thermostatType));
forceFieldEnergyOpenMM.addAndersenThermostat(temperature);
break;
default:
}
/**
* Convert the print interval to a print frequency.
*/
printFrequency = 100;
// Time step is in fsec, so convert printInterval to fsec.
printInterval *= 1000;
if (printInterval >= dt) {
printFrequency = (int) (printInterval / dt);
}
/**
* Convert save interval to a save frequency.
*/
saveSnapshotFrequency = 1000;
if (saveInterval >= this.dt) {
saveSnapshotFrequency = (int) (saveInterval / this.dt);
}
done = false;
assemblyInfo();
String firstFileName = FilenameUtils.removeExtension(molecularAssembly.getFile().getAbsolutePath());
if (dyn == null) {
restartFile = new File(firstFileName + ".dyn");
loadRestart = false;
} else {
restartFile = dyn;
loadRestart = true;
}
if (dynFilter == null) {
dynFilter = new DYNFilter(molecularAssembly.getName());
}
dof = forceFieldEnergyOpenMM.calculateDegreesOfFreedom();
if (!initialized) {
if (loadRestart) {
Crystal crystal = molecularAssembly.getCrystal();
// possibly add check to see if OpenMM supports this space group.
if (!dynFilter.readDYN(restartFile, crystal, x, v, a, aPrevious)) {
String message = " Could not load the restart file - dynamics terminated.";
logger.log(Level.WARNING, message);
done = true;
} else {
forceFieldEnergyOpenMM.setCrystal(crystal);
// Load positions into the main FFX data structure, move into primary unit cell, then load to OpenMM.
Atom[] atoms = molecularAssembly.getAtomArray();
double[] xyz = new double[3];
double[] vel = new double[3];
double[] acc = new double[3];
double[] accPrev = new double[3];
for (int i = 0; i < atoms.length; i++) {
Atom atom = atoms[i];
int i3 = i * 3;
for (int j = 0; j < 3; j++) {
xyz[j] = x[i3 + j];
vel[j] = v[i3 + j];
acc[j] = a[i3 + j];
accPrev[j] = aPrevious[i3 + j];
}
atom.setXYZ(xyz);
atom.setVelocity(vel);
atom.setAcceleration(acc);
atom.setPreviousAcceleration(accPrev);
}
molecularAssembly.moveAllIntoUnitCell();
}
} else {
if (initVelocities) {
getThermostat().setQuiet(true);
getThermostat().maxwell(targetTemperature);
forceFieldEnergyOpenMM.setOpenMMVelocities(v, numberOfVariables);
Atom[] atoms = molecularAssembly.getAtomArray();
double[] vel = new double[3];
for (int i = 0; i < atoms.length; i++) {
Atom atom = atoms[i];
int i3 = i * 3;
for (int j = 0; j < 3; j++) {
vel[j] = v[i3 + j];
}
atom.setVelocity(vel);
}
}
}
setOpenMMState();
}
saveSnapshotAsPDB = true;
if (fileType.equalsIgnoreCase("XYZ")) {
saveSnapshotAsPDB = false;
logger.info("Snapshots will be saved as XYZ");
} else if (!fileType.equalsIgnoreCase("PDB")) {
logger.warning("Snapshot file type unrecognized; saving snaphshots as PDB.\n");
}
Atom[] atoms = molecularAssembly.getAtomArray();
natoms = atoms.length;
int i = 0;
running = false;
// logger.info(" Calling OpenMM Update from MD Init.");
updateFromOpenMM(i, running);
}