Uses of Interface
ffx.crystal.CrystalPotential

Packages that use CrystalPotential

Package	Description
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.
ffx.algorithms.dynamics	The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and via OpenMM.
ffx.algorithms.thermodynamics	The Thermodynamics package computes free energy differences using Orthogonal Space Tempering (OST) sampling via pure Java or OpenMM (via Monte Carlo OST).
ffx.potential	The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
ffx.potential.openmm
ffx.realspace	The Real Space package implements real space structure refinement.
ffx.xray	The X-ray package implements support for X-ray and Neutron refinement.

Uses of CrystalPotential in ffx.algorithms.cli

Methods in ffx.algorithms.cli that return CrystalPotential

Modifier and Type	Method	Description
CrystalPotential	OSTOptions.applyAllOSTOptions(OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularAssembly firstAssembly, DynamicsOptions dynamicsOptions, BarostatOptions barostatOptions)	Applies relevant options to an OST, and returns either the OST object or something that wraps the OST (such as a Barostat).
CrystalPotential	BarostatOptions.checkNPT(MolecularAssembly molecularAssembly, CrystalPotential crystalPotential)	If pressure has been set > 0, creates a Barostat around a CrystalPotential, else returns the original, unmodified CrystalPotential.

Methods in ffx.algorithms.cli with parameters of type CrystalPotential

Modifier and Type	Method	Description
MolecularDynamics	OSTOptions.assembleMolecularDynamics(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, AlgorithmListener algorithmListener)	Assembles a MolecularDynamics wrapped around a Potential.
void	OSTOptions.beginMDOST(OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, WriteoutOptions writeoutOptions, ThermodynamicsOptions thermodynamicsOptions, File dynFile, AlgorithmListener algorithmListener)	Begins MD-OST sampling from an assembled OST.
CrystalPotential	BarostatOptions.checkNPT(MolecularAssembly molecularAssembly, CrystalPotential crystalPotential)	If pressure has been set > 0, creates a Barostat around a CrystalPotential, else returns the original, unmodified CrystalPotential.
OrthogonalSpaceTempering	OSTOptions.constructOST(CrystalPotential crystalPotential, File lambdaRestartFile, File histogramRestartFile, MolecularAssembly firstAssembly, org.apache.commons.configuration2.Configuration addedProperties, DynamicsOptions dynamicsOptions, ThermodynamicsOptions thermodynamicsOptions, LambdaParticleOptions lambdaParticleOptions, AlgorithmListener algorithmListener, boolean async)	constructOST.
Barostat	BarostatOptions.createBarostat(MolecularAssembly assembly, CrystalPotential crystalPotential)	Creates a Barostat around a CrystalPotential.
void	MultiDynamicsOptions.distribute(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, AlgorithmFunctions algorithmFunctions, int rank, int worldSize)	If residues selected for distributing initial configurations, performs many-body optimization for this distribution.
void	MultiDynamicsOptions.distribute(MolecularAssembly[] molecularAssemblies, Potential[] potentials, CrystalPotential crystalPotential, AlgorithmFunctions algorithmFunctions, int rank, int worldSize)	If residues selected for distributing initial configurations, performs many-body optimization for this distribution.
MolecularDynamics	ThermodynamicsOptions.runFixedAlchemy(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, WriteoutOptions writeoutOptions, File dyn, AlgorithmListener algorithmListener)	Run an alchemical free energy window.
MolecularDynamics	ThermodynamicsOptions.runNEQ(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, WriteoutOptions writeoutOptions, File dyn, AlgorithmListener algorithmListener)	Run a non-equilibrium alchemical free energy simulation.

Uses of CrystalPotential in ffx.algorithms.dynamics

Classes in ffx.algorithms.dynamics that implement CrystalPotential

Modifier and Type	Class	Description
class	Barostat	The Barostat class maintains constant pressure using random trial moves in lattice parameters, which are consistent with the space group.

Constructors in ffx.algorithms.dynamics with parameters of type CrystalPotential

Modifier	Constructor	Description
	Barostat(MolecularAssembly molecularAssembly, CrystalPotential potential)	Initialize the Barostat.
	Barostat(MolecularAssembly molecularAssembly, CrystalPotential potential, double temperature)	Initialize the Barostat.

Uses of CrystalPotential in ffx.algorithms.thermodynamics

Classes in ffx.algorithms.thermodynamics that implement CrystalPotential

Modifier and Type	Class	Description
class	OrthogonalSpaceTempering	An implementation of the Orthogonal Space Tempering algorithm.

Fields in ffx.algorithms.thermodynamics declared as CrystalPotential

Modifier and Type	Field	Description
protected final CrystalPotential	OrthogonalSpaceTempering.potential	The potential energy of the system.

Constructors in ffx.algorithms.thermodynamics with parameters of type CrystalPotential

Modifier	Constructor	Description
	OrthogonalSpaceTempering(LambdaInterface lambdaInterface, CrystalPotential potential, HistogramData histogramData, LambdaData lambdaData, org.apache.commons.configuration2.CompositeConfiguration properties, DynamicsOptions dynamicsOptions, LambdaParticleOptions lambdaParticleOptions, AlgorithmListener algorithmListener)	OST Constructor.

Uses of CrystalPotential in ffx.potential

Classes in ffx.potential that implement CrystalPotential

Modifier and Type	Class	Description
class	DualTopologyEnergy	Compute the potential energy and derivatives for a dual-topology system.
class	ForceFieldEnergy	Compute the potential energy and derivatives of a molecular system described by a force field.
class	QuadTopologyEnergy	Implements an error-canceling quad topology, where two large dual-topology simulation legs are run simultaneously to arrive at a small sum.

Uses of CrystalPotential in ffx.potential.openmm

Classes in ffx.potential.openmm that implement CrystalPotential

Modifier and Type	Class	Description
class	OpenMMEnergy	Compute the potential energy and derivatives using OpenMM.

Uses of CrystalPotential in ffx.realspace

Classes in ffx.realspace that implement CrystalPotential

Modifier and Type	Class	Description
class	RealSpaceEnergy	Combine the Real Space target and chemical potential energy.

Uses of CrystalPotential in ffx.xray

Classes in ffx.xray that implement CrystalPotential

Modifier and Type	Class	Description
class	RefinementEnergy	Combine the X-ray target and chemical potential energy using the CrystalPotential interface
class	XRayEnergy	Combine the X-ray target and chemical potential energy.

Methods in ffx.xray that return CrystalPotential

Modifier and Type	Method	Description
CrystalPotential	RefinementEnergy.getDataEnergy()	Getter for the field dataEnergy.