Package ffx.algorithms.cli

Class ThermodynamicsOptions

java.lang.Object

ffx.algorithms.cli.ThermodynamicsOptions

public class ThermodynamicsOptions
extends Object

Represents command line options for scripts that calculate thermodynamics.

Since:

1.0

Author:

Michael J. Schnieders, Jacob M. Litman

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	ThermodynamicsOptions.ThermodynamicsAlgorithm	Represents categories of thermodynamics algorithms that must be handled differently.

Constructor Summary

Constructors

Constructor	Description
ThermodynamicsOptions()

Method Summary

Modifier and Type	Method	Description
ThermodynamicsOptions.ThermodynamicsAlgorithm	getAlgorithm()	Return the selected Thermodynamics algorithm as an enumerated type.
long	getEquilibrationSteps()	The number of equilibration steps prior to production OST counts begin.
long	getEquilSteps()	getEquilSteps.
boolean	getResetNumSteps()	Getter for the field resetNumSteps.
String	getThermoAlgoString()	The algorithm to be used (e.g.
boolean	isResetNumSteps()	Ignores steps detected in .lam lambda-restart files.
MolecularDynamics	runFixedAlchemy(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, WriteoutOptions writeoutOptions, File dyn, AlgorithmListener algorithmListener)	Run an alchemical free energy window.
MolecularDynamics	runNEQ(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, WriteoutOptions writeoutOptions, File dyn, AlgorithmListener algorithmListener)	Run a non-equilibrium alchemical free energy simulation.
void	setEquilibrationSteps(long equilibrationSteps)
void	setResetNumSteps(boolean resetNumSteps)
void	setThermoAlgoString(String thermoAlgoString)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

ThermodynamicsOptions

public ThermodynamicsOptions()

Method Details

getAlgorithm

public ThermodynamicsOptions.ThermodynamicsAlgorithm getAlgorithm()

Return the selected Thermodynamics algorithm as an enumerated type.

Returns:

Corresponding thermodynamics algorithm

getEquilSteps

public long getEquilSteps()

getEquilSteps.

Returns:

The number of equilibration steps.

getResetNumSteps

public boolean getResetNumSteps()

Getter for the field resetNumSteps.

Returns:

a boolean.

runFixedAlchemy

public MolecularDynamics runFixedAlchemy(MolecularAssembly[] molecularAssemblies,
 CrystalPotential crystalPotential,
 DynamicsOptions dynamicsOptions,
 WriteoutOptions writeoutOptions,
 File dyn,
 AlgorithmListener algorithmListener)

Run an alchemical free energy window.

Parameters:

molecularAssemblies - All involved MolecularAssemblies.

crystalPotential - The Potential to be sampled.

dynamicsOptions - DynamicsOptions.

writeoutOptions - WriteoutOptions

dyn - MD restart file

algorithmListener - AlgorithmListener

Returns:

The MolecularDynamics object constructed.

runNEQ

public MolecularDynamics runNEQ(MolecularAssembly[] molecularAssemblies,
 CrystalPotential crystalPotential,
 DynamicsOptions dynamicsOptions,
 WriteoutOptions writeoutOptions,
 File dyn,
 AlgorithmListener algorithmListener)

Run a non-equilibrium alchemical free energy simulation.

Parameters:

molecularAssemblies - All involved MolecularAssemblies.

crystalPotential - The Potential to be sampled.

dynamicsOptions - DynamicsOptions.

writeoutOptions - WriteoutOptions

dyn - MD restart file

algorithmListener - AlgorithmListener

Returns:

The MolecularDynamics object constructed.

getEquilibrationSteps

public long getEquilibrationSteps()

The number of equilibration steps prior to production OST counts begin.

Returns:

Returns the number of equilibration steps.

setEquilibrationSteps

public void setEquilibrationSteps(long equilibrationSteps)

isResetNumSteps

public boolean isResetNumSteps()

Ignores steps detected in .lam lambda-restart files.

Returns:

Returns true if the number of steps is being reset.

setResetNumSteps

public void setResetNumSteps(boolean resetNumSteps)

getThermoAlgoString

public String getThermoAlgoString()

The algorithm to be used (e.g. OST, window-based methods, etc.).

Returns:

Returns a String for requested algorithm.

setThermoAlgoString

public void setThermoAlgoString(String thermoAlgoString)