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apoCHARMM 1.0.0
High-performance molecular dynamics simulations on GPUs
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apoCHARMM 1.0.0
High-performance molecular dynamics simulations on GPUs
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Provides deterministic Nose-Hoover temperature control. More...
Public Member Functions | |
| None | __init__ (self, float time_step) |
| Constructs a Python-owned Nose-Hoover integrator. | |
| None | setReferenceTemperature (self, float temperature) |
| Sets the Nose-Hoover reference temperature. | |
| None | setNoseHooverPistonMass (self, float mass) |
| Sets the scalar Nose-Hoover coupling mass. | |
| None | useOldTemperature (self, bool flag=True) |
| Selects the native on-step temperature estimator. | |
| None | resetAverageTemperature (self) |
| Resets both running-temperature values and their sample count. | |
| float | getReferenceTemperature (self) |
| Returns the reference temperature. | |
| float | getNoseHooverPistonMass (self) |
| Returns the scalar Nose-Hoover coupling mass. | |
| float | getAverageTemperature (self) |
| Returns one native running-average temperature. | |
| float | getInstantaneousTemperature (self) |
| Returns the native selected instantaneous temperature. | |
 Public Member Functions inherited from apocharmm.cuda_integrator.CudaIntegrator | |
| ctypes.c_void_p | integrator_handle (self) |
| Returns the borrowed C base-integrator pointer. | |
| None | close (self) |
| Closes the concrete handle and invalidates the base view. | |
| None | setTimeStep (self, float time_step) |
| Sets the public integrator time step. | |
| None | setCharmmContext (self, CharmmContext context) |
| Attaches a context and initializes concrete native state. | |
| None | subscribe (self, Subscriber subscriber) |
| Subscribes one output wrapper. | |
| None | unsubscribe (self, Subscriber subscriber) |
| Removes one subscriber from native and Python scheduling state. | |
| None | propagate (self, int num_steps) |
| Propagates dynamics and scheduled subscribers. | |
| None | initializeFromRestartFile (self, FilePath path) |
| Initializes concrete state from a restart file. | |
Provides deterministic Nose-Hoover temperature control.
The wrapper owns a concrete Nose-Hoover C handle and inherits context, restart, subscription, propagation, and closure behavior from CudaIntegrator.
| None apocharmm.cuda_nose_hoover_integrator.CudaNoseHooverIntegrator.__init__ | ( | self, | |
| float | time_step | ||
| ) |
Constructs a Python-owned Nose-Hoover integrator.
| [in] | time_step | Value accepted by ctypes.c_double, interpreted as a finite positive time step in picoseconds. |
| TypeError | If conversion to a C double fails. |
| ApoCharmmError | With native status APO_STATUS_INVALID_ARGUMENT, APO_STATUS_CUDA_ERROR, or APO_STATUS_RUNTIME_ERROR if construction fails. |
| RuntimeError | If native construction or base-view conversion reports success but produces a NULL handle. |
Reimplemented from apocharmm.cuda_integrator.CudaIntegrator.
| float apocharmm.cuda_nose_hoover_integrator.CudaNoseHooverIntegrator.getAverageTemperature | ( | self | ) |
Returns one native running-average temperature.
float in kelvin. | RuntimeError | If the wrapper has been closed. |
| ApoCharmmError | With native status APO_STATUS_INVALID_ARGUMENT, APO_STATUS_CUDA_ERROR, or APO_STATUS_RUNTIME_ERROR. |
| float apocharmm.cuda_nose_hoover_integrator.CudaNoseHooverIntegrator.getInstantaneousTemperature | ( | self | ) |
Returns the native selected instantaneous temperature.
float in kelvin. Native selection uses element 1 when old-temperature mode is enabled and element 0 otherwise. | RuntimeError | If the wrapper has been closed. |
| ApoCharmmError | With native status APO_STATUS_NOT_INITIALIZED before context attachment, APO_STATUS_CUDA_ERROR for transfer failure, or another documented native status. |
| float apocharmm.cuda_nose_hoover_integrator.CudaNoseHooverIntegrator.getNoseHooverPistonMass | ( | self | ) |
Returns the scalar Nose-Hoover coupling mass.
float in the native coupling-mass convention. | RuntimeError | If the wrapper has been closed. |
| ApoCharmmError | If the native handle or output operation fails. |
| float apocharmm.cuda_nose_hoover_integrator.CudaNoseHooverIntegrator.getReferenceTemperature | ( | self | ) |
Returns the reference temperature.
float in kelvin. | RuntimeError | If the wrapper has been closed. |
| ApoCharmmError | If the native handle or output operation fails. |
| None apocharmm.cuda_nose_hoover_integrator.CudaNoseHooverIntegrator.resetAverageTemperature | ( | self | ) |
Resets both running-temperature values and their sample count.
None. | RuntimeError | If the wrapper has been closed. |
| ApoCharmmError | With native status APO_STATUS_INVALID_ARGUMENT, APO_STATUS_CUDA_ERROR, or APO_STATUS_RUNTIME_ERROR. |
| None apocharmm.cuda_nose_hoover_integrator.CudaNoseHooverIntegrator.setNoseHooverPistonMass | ( | self, | |
| float | mass | ||
| ) |
Sets the scalar Nose-Hoover coupling mass.
| [in] | mass | Value converted to C double. It must be finite and non-negative. The exact dimensional convention is not established by the repository. |
None. | TypeError | If C scalar conversion fails. |
| RuntimeError | If the wrapper has been closed. |
| ApoCharmmError | With native status APO_STATUS_INVALID_ARGUMENT, APO_STATUS_CUDA_ERROR, or APO_STATUS_RUNTIME_ERROR. |
| None apocharmm.cuda_nose_hoover_integrator.CudaNoseHooverIntegrator.setReferenceTemperature | ( | self, | |
| float | temperature | ||
| ) |
Sets the Nose-Hoover reference temperature.
| [in] | temperature | Value converted to C double, in kelvin. It must be finite and non-negative. |
None. | TypeError | If C scalar conversion fails. |
| RuntimeError | If the wrapper has been closed. |
| ApoCharmmError | With native status APO_STATUS_INVALID_ARGUMENT for an invalid value or APO_STATUS_RUNTIME_ERROR for another native failure. |
| None apocharmm.cuda_nose_hoover_integrator.CudaNoseHooverIntegrator.useOldTemperature | ( | self, | |
| bool | flag = True |
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| ) |
Selects the native on-step temperature estimator.
| [in] | flag | Value converted with ctypes.c_bool. A truthy value selects kinetic-energy element 1 for native feedback and instantaneous temperature. |
None. | TypeError | If C boolean conversion rejects the value. |
| RuntimeError | If the wrapper has been closed. |
| ApoCharmmError | If the native handle is rejected. |
1.9.8