apocharmm.charmm_context.CharmmContext Class Reference

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Inherits _ApoObject.

Public Member Functions
None	__init__ (self, ForceManager|CharmmPsf force_manager_or_psf, CharmmParameters|None parameters=None)
	Constructs a Python CharmmContext wrapper.
None	setPrm (self, CharmmParameters parameters)
	Sets the CHARMM parameter set.
None	setPsf (self, CharmmPsf psf)
	Sets the PSF and imports its atom charges and masses.
None	setForceManager (self, ForceManager force_manager)
	Sets the ForceManager associated with the context.
None	setCoordinatesCharges (self, Sequence[Sequence[float]] coordinates_charges)
	Sets coordinates and charges from nested Python rows.
None	setCoordinates (self, CharmmCrd|Sequence[Sequence[float]] coordinates)
	Sets coordinates from a CharmmCrd or nested Python rows.
None	setCharges (self, Sequence[float] charges)
	Sets per-atom charges while preserving coordinates.
None	setVelocitiesInverseMasses (self, Sequence[Sequence[float]] velocities_inverse_masses)
	Sets velocities and inverse masses from nested rows.
None	setVelocities (self, Sequence[Sequence[float]] velocities)
	Sets velocity components while preserving inverse masses.
None	setVelocitiesFromCHARMMVelocityFile (self, FilePath path)
	Loads velocities from a CHARMM velocity file.
None	setMasses (self, Sequence[float] masses)
	Sets masses and stores native inverse masses.
None	setTemperature (self, float temperature)
	Sets the stored target temperature.
None	setPeriodicBoundaryCondition (self, PeriodicBoundaryCondition|int pbc)
	Sets the periodic boundary condition.
None	setBoxDimensions (self, Sequence[float] box_dimensions)
	Sets orthorhombic box dimensions.
None	setRandomSeed (self, int seed)
	Sets the random seed used for velocity assignment.
None	useHolonomicConstraints (self, bool flag)
	Selects constrained degree-of-freedom accounting.
None	setKappa (self, float kappa)
	Sets the Ewald splitting parameter.
None	setCutoff (self, float cutoff)
	Sets the direct-space cutoff.
None	setCtonnb (self, float ctonnb)
	Sets the nonbonded distance exposed as ctonnb.
None	setCtofnb (self, float ctofnb)
	Sets the nonbonded distance exposed as ctofnb.
None	setFFTGrid (self, Sequence[int] grid)
	Sets the three-dimensional PME FFT grid.
None	setPmeSplineOrder (self, int order)
	Sets the PME interpolation spline order.
None	setVdwType (self, VdwType|int vdw_type)
	Sets the van der Waals model identifier.
int	getNumAtoms (self)
	Returns the context atom count.
int	getNumDegreesOfFreedom (self)
	Returns the current degree-of-freedom count.
list[list[float]]	getCoordinatesCharges (self)
	Returns a Python copy of coordinates and charges.
list[list[float]]	getVelocityMass (self)
	Returns a Python copy of velocities and inverse masses.
PeriodicBoundaryCondition	getPeriodicBoundaryCondition (self)
	Returns the periodic boundary condition.
tuple[float, float, float]	getBoxDimensions (self)
	Returns the three stored box dimensions.
int	getRandomSeed (self)
	Returns the stored random seed.
float	getVolume (self)
	Returns the orthorhombic box volume.
float	getKappa (self)
	Returns the stored Ewald splitting parameter.
float	getCutoff (self)
	Returns the stored direct-space cutoff.
float	getCtonnb (self)
	Returns the distance exposed as ctonnb.
float	getCtofnb (self)
	Returns the distance exposed as ctofnb.
tuple[int, int, int]	getFFTGrid (self)
	Returns the stored PME FFT grid.
int	getPmeSplineOrder (self)
	Returns the stored PME interpolation spline order.
VdwType	getVdwType (self)
	Returns the stored van der Waals model identifier.
ForceManager	getForceManager (self)
	Returns a Python wrapper for the associated ForceManager.
None	assignVelocitiesAtTemperature (self, float temperature)
	Assigns sampled velocities at a temperature.
float	computeTemperature (self)
	Computes the instantaneous kinetic temperature.
None	calculatePotentialEnergy (self, bool print_energy=False)
	Computes forces, potential energy, and virial.

Detailed Description

Represents mutable molecular state for apoCHARMM calculations.

Construct the wrapper from a ForceManager, or from a CharmmPsf together with CharmmParameters. The wrapper owns its C handle and retains Python references to collaborators whose native objects participate in the context.

Array setters copy Python values into temporary C buffers. Array getters return new Python lists or tuples; they do not expose native storage.

close() releases the owned context handle and is idempotent. The wrapper supports the context-manager protocol. Using a method that accesses self.handle after closure raises RuntimeError. Native nonzero statuses are raised as ApoCharmmError.

The wrapper and its native object provide no internal thread synchronization.

See also

charmm_context

Constructor & Destructor Documentation

__init__()

None apocharmm.charmm_context.CharmmContext.__init__	(		self,
		ForceManager | CharmmPsf	force_manager_or_psf,
		CharmmParameters | None	parameters = None
	)

Constructs a Python CharmmContext wrapper.

Pass either a live ForceManager and leave parameters as None, or pass a live CharmmPsf together with a live CharmmParameters. Collaborator wrappers are retained to preserve their Python and native lifetimes.

Parameters

[in]	force_manager_or_psf	ForceManager or CharmmPsf selecting the construction path.
[in]	parameters	CharmmParameters required with CharmmPsf, or None with ForceManager.

Exceptions

TypeError	If the argument combination does not match either supported construction path.
RuntimeError	If a supplied wrapper is closed, or native construction reports success but produces a NULL handle.
ApoCharmmError	If native validation, GPU setup, allocation, or force-manager initialization fails.

Member Function Documentation

assignVelocitiesAtTemperature()

None apocharmm.charmm_context.CharmmContext.assignVelocitiesAtTemperature	(		self,
		float	temperature
	)

Assigns sampled velocities at a temperature.

The native context samples independent Cartesian Gaussian components using its stored seed. It does not remove center-of-mass motion or rescale the sampled result.

Parameters

[in]

temperature

Python int or float accepted by ctypes.c_double, in kelvin. The value must be finite and non-negative.

Exceptions

TypeError	If temperature cannot initialize ctypes.c_double.
RuntimeError	If this context is closed.
ApoCharmmError	If the atom count is unset, native temperature validation fails, or the velocity transfer fails.

calculatePotentialEnergy()

None apocharmm.charmm_context.CharmmContext.calculatePotentialEnergy	(		self,
		bool	print_energy = False
	)

Computes forces, potential energy, and virial.

The Python wrapper always passes reset=False. When print_energy is truthy, the native context writes a CHARMM-style energy table to standard output.

Parameters

[in]

print_energy

Boolean selecting native energy-table output.

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If the force manager is not initialized, composite-manager printing is unsupported, or native force or CUDA work fails.

computeTemperature()

float apocharmm.charmm_context.CharmmContext.computeTemperature

(

self

)

Computes the instantaneous kinetic temperature.

The native calculation evaluates kinetic energy on the GPU and divides by 0.5 * ndegf * k_B.

Returns

Python float in kelvin.

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If atom, velocity, or degree-of-freedom state is incomplete, or native CUDA work fails.

getBoxDimensions()

tuple[float, float, float] apocharmm.charmm_context.CharmmContext.getBoxDimensions

(

self

)

Returns the three stored box dimensions.

Returns

New (x, y, z) tuple of lengths in angstroms.

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If native output validation fails.

getCoordinatesCharges()

list[list[float]] apocharmm.charmm_context.CharmmContext.getCoordinatesCharges

(

self

)

Returns a Python copy of coordinates and charges.

Native device storage is transferred to host before copying. The result contains one [x, y, z, charge] list per atom. Coordinates use angstroms and charges use elementary-charge units.

Returns

Newly allocated list[list[float]] with shape (N, 4).

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If atom-count retrieval, output validation, or the native device-to-host transfer fails.

getCtofnb()

float apocharmm.charmm_context.CharmmContext.getCtofnb

(

self

)

Returns the distance exposed as ctofnb.

Returns

Python float in angstroms.

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If no force manager is attached or the native getter fails.

getCtonnb()

float apocharmm.charmm_context.CharmmContext.getCtonnb

(

self

)

Returns the distance exposed as ctonnb.

Returns

Python float in angstroms.

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If no force manager is attached or the native getter fails.

getCutoff()

float apocharmm.charmm_context.CharmmContext.getCutoff

(

self

)

Returns the stored direct-space cutoff.

Returns

Python float in angstroms.

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If no force manager is attached or the native getter fails.

getFFTGrid()

tuple[int, int, int] apocharmm.charmm_context.CharmmContext.getFFTGrid

(

self

)

Returns the stored PME FFT grid.

Returns

New (nfftx, nffty, nfftz) tuple of dimensionless grid sizes.

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If no force manager is attached, the native grid does not contain exactly three values, or output validation fails.

getForceManager()

ForceManager apocharmm.charmm_context.CharmmContext.getForceManager

(

self

)

Returns a Python wrapper for the associated ForceManager.

When construction or setForceManager() retained a wrapper, that same Python object is returned. Otherwise, the C ABI creates a newly owned force-manager handle sharing the native manager; the wrapper takes ownership of that handle and is cached by this context.

Closing the returned ForceManager releases only its C handle. The native context continues to retain its native manager.

Returns

Cached or newly created ForceManager wrapper.

Exceptions

RuntimeError	If the context must access its native handle after closure.
ApoCharmmError	If the native context has no force manager or C handle creation fails.

getKappa()

float apocharmm.charmm_context.CharmmContext.getKappa

(

self

)

Returns the stored Ewald splitting parameter.

Returns

Python float in inverse angstroms.

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If no force manager is attached or the native getter fails.

getNumAtoms()

int apocharmm.charmm_context.CharmmContext.getNumAtoms

(

self

)

Returns the context atom count.

Returns

Python int containing the dimensionless atom count.

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If the native getter fails.

getNumDegreesOfFreedom()

int apocharmm.charmm_context.CharmmContext.getNumDegreesOfFreedom

(

self

)

Returns the current degree-of-freedom count.

Returns

Python int containing the dimensionless count.

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If the native getter fails.

getPeriodicBoundaryCondition()

PeriodicBoundaryCondition apocharmm.charmm_context.CharmmContext.getPeriodicBoundaryCondition

(

self

)

Returns the periodic boundary condition.

Returns

PeriodicBoundaryCondition mapped from the native value.

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If the C ABI getter fails.
ValueError	If a successful C ABI call returns an integer not represented by PeriodicBoundaryCondition.

getPmeSplineOrder()

int apocharmm.charmm_context.CharmmContext.getPmeSplineOrder

(

self

)

Returns the stored PME interpolation spline order.

Returns

Python int containing the dimensionless order.

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If no force manager is attached or the native getter fails.

getRandomSeed()

int apocharmm.charmm_context.CharmmContext.getRandomSeed

(

self

)

Returns the stored random seed.

Returns

Python int in the unsigned 64-bit range.

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If the native getter fails.

getVdwType()

VdwType apocharmm.charmm_context.CharmmContext.getVdwType

(

self

)

Returns the stored van der Waals model identifier.

Returns

VdwType mapped from the native model code.

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If no force manager is attached or the native getter fails.
ValueError	If a successful native call returns an integer not represented by VdwType.

getVelocityMass()

list[list[float]] apocharmm.charmm_context.CharmmContext.getVelocityMass

(

self

)

Returns a Python copy of velocities and inverse masses.

Despite the method name, each fourth component is inverse mass, not mass. Rows are [vx, vy, vz, inverse_mass]; velocity uses angstroms per AKMA time unit and inverse mass uses reciprocal atomic mass units.

Returns

Newly allocated list[list[float]] with shape (N, 4).

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If atom-count retrieval, output validation, or the native device-to-host transfer fails.

getVolume()

float apocharmm.charmm_context.CharmmContext.getVolume

(

self

)

Returns the orthorhombic box volume.

Returns

Python float in cubic angstroms.

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If valid positive box dimensions have not been set or the native getter otherwise fails.

setBoxDimensions()

None apocharmm.charmm_context.CharmmContext.setBoxDimensions	(		self,
		Sequence[float]	box_dimensions
	)

Sets orthorhombic box dimensions.

box_dimensions is converted to a temporary contiguous double buffer. It must contain exactly [x, y, z] lengths in angstroms.

Parameters

[in]

box_dimensions

Sequence of exactly three numeric values.

Exceptions

TypeError	If the input is not iterable or a value cannot be converted with float().
ValueError	If scalar conversion raises ValueError.
RuntimeError	If this context is closed.
ApoCharmmError	If the length is not three, a dimension is not positive, attached force configuration is invalid, or native initialization or neighbor-list work fails.

setCharges()

None apocharmm.charmm_context.CharmmContext.setCharges	(		self,
		Sequence[float]	charges
	)

Sets per-atom charges while preserving coordinates.

Each scalar is converted with float(), copied to a temporary C buffer, and then copied by the native context. Charges use elementary-charge units.

Parameters

[in]

charges

Sequence containing exactly one value per atom.

Exceptions

TypeError	If charges is not iterable or a value cannot be converted with float().
ValueError	If scalar conversion raises ValueError.
RuntimeError	If this context is closed.
ApoCharmmError	If the atom count is unset, the sequence length is wrong, or native transfer fails.

setCoordinates()

None apocharmm.charmm_context.CharmmContext.setCoordinates	(		self,
		CharmmCrd | Sequence[Sequence[float]]	coordinates
	)

Sets coordinates from a CharmmCrd or nested Python rows.

A CharmmCrd is borrowed for the native call and is not retained. Otherwise, coordinates must contain one [x, y, z] row per atom. Scalars are converted with float() and copied through a temporary C buffer. Coordinates use angstroms and existing charges are preserved.

Parameters

[in]

coordinates

Live CharmmCrd wrapper or sequence of three-value row sequences.

Exceptions

TypeError	If a row is not iterable, a scalar cannot be converted, or a closed CharmmCrd is accessed.
ValueError	If scalar conversion fails or a row does not contain exactly three values.
RuntimeError	If this context or a supplied CharmmCrd is closed.
ApoCharmmError	If the atom count is unset, the coordinate count is wrong, or native transfer or neighbor-list work fails.

setCoordinatesCharges()

None apocharmm.charmm_context.CharmmContext.setCoordinatesCharges	(		self,
		Sequence[Sequence[float]]	coordinates_charges
	)

Sets coordinates and charges from nested Python rows.

coordinates_charges must contain one row per atom and exactly four values per row in [x, y, z, charge] order. Coordinates use angstroms and charges use elementary-charge units. Every scalar is converted with float(), flattened into a temporary ctypes buffer, and copied by the native context.

Parameters

[in]

coordinates_charges

Sequence of fixed-width row sequences.

Exceptions

TypeError	If a row is not iterable or a scalar cannot be converted to float.
ValueError	If scalar conversion fails or a row does not contain exactly four values.
RuntimeError	If this context is closed.
ApoCharmmError	If the atom count is unset, the row count is wrong, or native transfer or neighbor-list work fails.

setCtofnb()

None apocharmm.charmm_context.CharmmContext.setCtofnb	(		self,
		float	ctofnb
	)

Sets the nonbonded distance exposed as ctofnb.

Parameters

[in]

ctofnb

Python int or float accepted by ctypes.c_double, in angstroms. The native float-converted value must be finite and positive.

Exceptions

TypeError	If ctofnb cannot initialize ctypes.c_double.
RuntimeError	If this context is closed.
ApoCharmmError	If no force manager is attached or native validation fails.

Warning

The current backend forwards this value as ron. Configure it before force-manager initialization.

setCtonnb()

None apocharmm.charmm_context.CharmmContext.setCtonnb	(		self,
		float	ctonnb
	)

Sets the nonbonded distance exposed as ctonnb.

Parameters

[in]

ctonnb

Python int or float accepted by ctypes.c_double, in angstroms. The native float-converted value must be finite and positive.

Exceptions

TypeError	If ctonnb cannot initialize ctypes.c_double.
RuntimeError	If this context is closed.
ApoCharmmError	If no force manager is attached or native validation fails.

Warning

The current backend forwards this value as roff. Configure it before force-manager initialization.

setCutoff()

None apocharmm.charmm_context.CharmmContext.setCutoff	(		self,
		float	cutoff
	)

Sets the direct-space cutoff.

Parameters

[in]

cutoff

Python int or float accepted by ctypes.c_double, in angstroms. The native float-converted value must be finite and positive.

Exceptions

TypeError	If cutoff cannot initialize ctypes.c_double.
RuntimeError	If this context is closed.
ApoCharmmError	If no force manager is attached or native validation fails.

Warning

Configure this value before force-manager initialization.

setFFTGrid()

None apocharmm.charmm_context.CharmmContext.setFFTGrid	(		self,
		Sequence[int]	grid
	)

Sets the three-dimensional PME FFT grid.

Each element is converted with int() and copied to a temporary C buffer. The sequence must contain exactly three positive dimensions in X, Y, Z order.

Parameters

[in]

grid

Sequence of three integer-convertible values.

Exceptions

TypeError	If grid is not iterable or an element cannot be converted with int().
ValueError	If integer conversion fails.
RuntimeError	If this context is closed.
ApoCharmmError	If the length is not three, a dimension is not positive, or no force manager is attached.

Warning

Configure the grid before force-manager initialization.

setForceManager()

None apocharmm.charmm_context.CharmmContext.setForceManager	(		self,
		ForceManager	force_manager
	)

Sets the ForceManager associated with the context.

The wrapper retains force_manager after a successful native state reconciliation and clears retained PSF and parameter wrappers because the new manager becomes their native source.

Parameters

[in]

force_manager

Live ForceManager wrapper.

Exceptions

TypeError	If force_manager is not a ForceManager.
RuntimeError	If this context or force_manager is closed.
ApoCharmmError	If native state reconciliation or initialization fails.

setKappa()

None apocharmm.charmm_context.CharmmContext.setKappa	(		self,
		float	kappa
	)

Sets the Ewald splitting parameter.

Parameters

[in]

kappa

Python int or float accepted by ctypes.c_double, in inverse angstroms. The native float-converted value must be finite and non-negative.

Exceptions

TypeError	If kappa cannot initialize ctypes.c_double.
RuntimeError	If this context is closed.
ApoCharmmError	If no force manager is attached or native validation fails.

Warning

Configure this value before force-manager initialization.

setMasses()

None apocharmm.charmm_context.CharmmContext.setMasses	(		self,
		Sequence[float]	masses
	)

Sets masses and stores native inverse masses.

Each scalar is converted with float() and interpreted as an atomic mass-unit value. The native context stores its reciprocal and preserves existing velocity components.

Parameters

[in]

masses

Sequence containing exactly one mass per atom.

Exceptions

TypeError	If masses is not iterable or a value cannot be converted to float.
ValueError	If scalar conversion raises ValueError.
RuntimeError	If this context is closed.
ApoCharmmError	If the atom count is unset, the sequence length is wrong, or native transfer fails.

Warning

The current native implementation does not reject zero, negative, infinite, or NaN masses before division.

setPeriodicBoundaryCondition()

None apocharmm.charmm_context.CharmmContext.setPeriodicBoundaryCondition	(		self,
		PeriodicBoundaryCondition | int	pbc
	)

Sets the periodic boundary condition.

pbc is normalized through PeriodicBoundaryCondition before its integer value is passed to the C ABI.

Parameters

[in]

pbc

PeriodicBoundaryCondition or matching integer value 0, 1, or 2.

Exceptions

TypeError	If pbc cannot be interpreted by the enumeration.
ValueError	If the integer is not a declared enum value.
RuntimeError	If this context is closed.
ApoCharmmError	If native propagation, initialization, imaging, or neighbor-list rebuilding fails.

setPmeSplineOrder()

None apocharmm.charmm_context.CharmmContext.setPmeSplineOrder	(		self,
		int	order
	)

Sets the PME interpolation spline order.

Parameters

[in]

order

Python integer accepted by ctypes.c_int. The native value must be positive.

Exceptions

TypeError	If order cannot initialize ctypes.c_int.
RuntimeError	If this context is closed.
ApoCharmmError	If order is not positive or no force manager is attached.

Warning

Configure the order before force-manager initialization.

setPrm()

None apocharmm.charmm_context.CharmmContext.setPrm	(		self,
		CharmmParameters	parameters
	)

Sets the CHARMM parameter set.

The wrapper requires a CharmmParameters, passes its borrowed handle to the C ABI, and retains the Python object after success.

Parameters

[in]

parameters

Live CharmmParameters wrapper.

Exceptions

TypeError	If parameters is not a CharmmParameters.
RuntimeError	If this context or parameters is closed.
ApoCharmmError	If native synchronization or initialization fails.

setPsf()

None apocharmm.charmm_context.CharmmContext.setPsf	(		self,
		CharmmPsf	psf
	)

Sets the PSF and imports its atom charges and masses.

The wrapper requires a CharmmPsf, passes its borrowed handle to the C ABI, and retains the Python object after success.

Parameters

[in]

psf

Live CharmmPsf wrapper.

Exceptions

TypeError	If psf is not a CharmmPsf.
RuntimeError	If this context or psf is closed.
ApoCharmmError	If the atom count conflicts, storage or transfer fails, or force-manager initialization fails.

setRandomSeed()

None apocharmm.charmm_context.CharmmContext.setRandomSeed	(		self,
		int	seed
	)

Sets the random seed used for velocity assignment.

Parameters

[in]

seed

Python int in the inclusive range [0, 2**64 - 1].

Exceptions

TypeError	If seed is not comparable with integers or cannot initialize ctypes.c_uint64.
ValueError	If seed is outside the unsigned 64-bit range.
RuntimeError	If this context is closed.
ApoCharmmError	If the native context rejects the update.

setTemperature()

None apocharmm.charmm_context.CharmmContext.setTemperature	(		self,
		float	temperature
	)

Sets the stored target temperature.

This method does not generate or rescale velocities.

Parameters

[in]

temperature

Python int or float accepted by ctypes.c_double, in kelvin. The native value must be finite and non-negative.

Exceptions

TypeError	If temperature cannot initialize ctypes.c_double.
RuntimeError	If this context is closed.
ApoCharmmError	If the native value is non-finite or negative.

setVdwType()

None apocharmm.charmm_context.CharmmContext.setVdwType	(		self,
		VdwType | int	vdw_type
	)

Sets the van der Waals model identifier.

The argument is normalized through VdwType. Native CharmmContext accepts values VdwType.VSH through VdwType.DBEXP.

Parameters

[in]

vdw_type

VdwType or matching integer value.

Exceptions

TypeError	If vdw_type cannot be interpreted by the enum.
ValueError	If it is not a declared Python enum value.
RuntimeError	If this context is closed.
ApoCharmmError	If the normalized value is VdwType.NONE, no force manager is attached, or native validation fails.

Warning

Configure the model before force-manager initialization.

setVelocities()

None apocharmm.charmm_context.CharmmContext.setVelocities	(		self,
		Sequence[Sequence[float]]	velocities
	)

Sets velocity components while preserving inverse masses.

Every row must be [vx, vy, vz] in angstroms per AKMA time unit. Scalars are converted with float() and copied through a temporary C buffer.

Parameters

[in]

velocities

Sequence containing one three-value row per atom.

Exceptions

TypeError	If a row is not iterable or a scalar cannot be converted to float.
ValueError	If scalar conversion fails or a row does not contain exactly three values.
RuntimeError	If this context is closed.
ApoCharmmError	If the atom count is unset, the row count is wrong, or native transfer fails.

setVelocitiesFromCHARMMVelocityFile()

None apocharmm.charmm_context.CharmmContext.setVelocitiesFromCHARMMVelocityFile	(		self,
		FilePath	path
	)

Loads velocities from a CHARMM velocity file.

path is encoded with os.fsencode() through encode_path() and is borrowed by the C ABI for the duration of the call. The native parser requires a matching atom count and one parseable velocity record per atom.

Parameters

[in]

path

str, bytes, or os.PathLike path accepted by os.fsencode().

Exceptions

TypeError	If path cannot be encoded as a filesystem path.
RuntimeError	If this context is closed.
ApoCharmmError	If the atom count is unset, the path is empty, the file cannot be opened or parsed, the atom count differs, or native transfer fails.

setVelocitiesInverseMasses()

None apocharmm.charmm_context.CharmmContext.setVelocitiesInverseMasses	(		self,
		Sequence[Sequence[float]]	velocities_inverse_masses
	)

Sets velocities and inverse masses from nested rows.

Every row must be [vx, vy, vz, inverse_mass]. Velocity components use angstroms per AKMA time unit and inverse mass uses reciprocal atomic mass units. Scalars are converted with float() and copied through a temporary C buffer.

Parameters

[in]

velocities_inverse_masses

Sequence of four-value rows.

Exceptions

TypeError	If a row is not iterable or a scalar cannot be converted to float.
ValueError	If scalar conversion fails or a row does not contain exactly four values.
RuntimeError	If this context is closed.
ApoCharmmError	If the atom count is unset, the row count is wrong, or native transfer fails.

useHolonomicConstraints()

None apocharmm.charmm_context.CharmmContext.useHolonomicConstraints	(		self,
		bool	flag
	)

Selects constrained degree-of-freedom accounting.

The value is converted with ctypes.c_bool. The native context recomputes its degree-of-freedom count but does not execute a constraint solver.

Parameters

[in]

flag

Boolean selection.

Exceptions

RuntimeError	If this context is closed.
ApoCharmmError	If the native context has no PSF or no force manager.