Package ffx.potential.openmm
Class OpenMMState
java.lang.Object
ffx.openmm.State
ffx.potential.openmm.OpenMMState
Retrieve state information from an OpenMM Simulation.
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Field Summary
FieldsModifier and TypeFieldDescriptionfinal double
Kinetic energy (kcal/mol).final double
Potential energy (kcal/mol).final double
Total energy (kcal/mol). -
Constructor Summary
ConstructorsModifierConstructorDescriptionprotected
OpenMMState
(com.sun.jna.ptr.PointerByReference pointer) Construct an OpenMM State with the requested information. -
Method Summary
Modifier and TypeMethodDescriptiondouble[]
getAccelerations
(double[] a, Atom[] atoms) The acceleration array will contain the acceleration information for all atoms.double[]
getActiveAccelerations
(double[] a, Atom[] atoms) The acceleration array will contain the acceleration information for all atoms.double[]
getActiveGradient
(double[] g, Atom[] atoms) The force array contains the OpenMM force information for active atoms.double[]
getActivePositions
(double[] x, Atom[] atoms) The position array contains the OpenMM atomic position information for active atoms.double[]
getActiveVelocities
(double[] v, Atom[] atoms) The velocity array contains the OpenMM atomic position information for active atoms.int
Get the mask of information contained in the state.double[]
getGradient
(double[] g) The force array contains the OpenMM force information for all atoms.double
Get the kinetic energy.double[][]
Read the periodic lattice vectors from a state.double
Get the periodic box volume.double[]
getPositions
(double[] x) The position array contains the OpenMM atomic position information for all atoms.double
Get the potential energy.double
Get the total energy.double[]
getVelocities
(double[] v) The velocity array contains the OpenMM atomic position information for all atoms.Methods inherited from class ffx.openmm.State
destroy, getEnergyParameterDerivatives, getForces, getParameters, getPointer, getPositions, getStepCount, getTime, getVelocities
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Field Details
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potentialEnergy
public final double potentialEnergyPotential energy (kcal/mol). -
kineticEnergy
public final double kineticEnergyKinetic energy (kcal/mol). -
totalEnergy
public final double totalEnergyTotal energy (kcal/mol).
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Constructor Details
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OpenMMState
protected OpenMMState(com.sun.jna.ptr.PointerByReference pointer) Construct an OpenMM State with the requested information.- Parameters:
pointer
- Pointer to an OpenMM state.
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Method Details
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getAccelerations
The acceleration array will contain the acceleration information for all atoms. This method will convert the OpenMM forces to accelerations using the atom masses.- Parameters:
a
- Acceleration components for all atoms.atoms
- The array of atoms, which is needed to convert from force to acceleration.- Returns:
- The acceleration for each atom in units of Angstroms per picosecond squared.
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getActiveAccelerations
The acceleration array will contain the acceleration information for all atoms. This method will convert the OpenMM forces to accelerations using the atom masses.- Parameters:
a
- Acceleration components for all atoms.atoms
- The array of atoms, which is needed to convert from force to acceleration.- Returns:
- The acceleration for each atom in units of Angstroms per picosecond squared.
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getGradient
public double[] getGradient(@Nullable double[] g) The force array contains the OpenMM force information for all atoms.- Parameters:
g
- Gradient array to use.- Returns:
- The gradient for all atoms in units of kcal/mol/Angstrom (in a new array if g is null or the wrong size).
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getActiveGradient
The force array contains the OpenMM force information for active atoms.- Parameters:
g
- Gradient array to use.- Returns:
- The gradient for all atoms in units of kcal/mol/Angstrom (in a new array if g is null or the wrong size).
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getPeriodicBoxVectors
public double[][] getPeriodicBoxVectors()Read the periodic lattice vectors from a state.The crystal instance will be updated, and passed to the ForceFieldEnergy instance.
- Overrides:
getPeriodicBoxVectors
in classState
- Returns:
- The periodic box vectors.
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getPositions
public double[] getPositions(@Nullable double[] x) The position array contains the OpenMM atomic position information for all atoms. The returned array x is in units of Angstroms.- Parameters:
x
- Atomic coordinates array to use.- Returns:
- The atomic coordinates (in a new array if x is null or the wrong size).
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getActivePositions
The position array contains the OpenMM atomic position information for active atoms. The returned array x is in units of Angstroms.- Parameters:
x
- Atomic coordinates array to use.- Returns:
- The atomic coordinates (in a new array if x is null or the wrong size).
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getVelocities
public double[] getVelocities(@Nullable double[] v) The velocity array contains the OpenMM atomic position information for all atoms. The returned array v is in units of Angstroms per picosecond.- Parameters:
v
- Atomic velocity array to use.- Returns:
- The atomic velocities (in a new array if v is null or the wrong size).
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getActiveVelocities
The velocity array contains the OpenMM atomic position information for active atoms. The returned array v is in units of Angstroms per picosecond.- Parameters:
v
- Atomic velocity array to use.- Returns:
- The atomic velocities (in a new array if v is null or the wrong size).
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getPeriodicBoxVolume
public double getPeriodicBoxVolume()Get the periodic box volume.- Overrides:
getPeriodicBoxVolume
in classState
- Returns:
- The periodic box volume.
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getPotentialEnergy
public double getPotentialEnergy()Get the potential energy. This field will be zero if the dataTypes mask did not include the energy.- Overrides:
getPotentialEnergy
in classState
- Returns:
- The potential energy.
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getKineticEnergy
public double getKineticEnergy()Get the kinetic energy. This field will be zero if the dataTypes mask did not include the energy.- Overrides:
getKineticEnergy
in classState
- Returns:
- The kinetic energy.
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getTotalEnergy
public double getTotalEnergy()Get the total energy. This field will be zero if the dataTypes mask did not include the energy.- Returns:
- The total energy.
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getDataTypes
public int getDataTypes()Get the mask of information contained in the state.- Overrides:
getDataTypes
in classState
- Returns:
- The mask of information contained in the state.
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