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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 stochastic Langevin temperature control. More...
Public Member Functions | |
| None | __init__ (self, float time_step) |
| Constructs a Python-owned Langevin thermostat integrator. | |
| None | setReferenceTemperature (self, float temperature) |
| Sets the thermostat reference temperature. | |
| None | setThermostatFriction (self, float friction) |
| Sets the thermostat friction coefficient. | |
| None | setThermostatRngSeed (self, int seed) |
| Sets the thermostat RNG seed. | |
| None | resetAverageTemperature (self) |
| Resets both running-temperature values and their sample count. | |
| float | getReferenceTemperature (self) |
| Returns the reference temperature. | |
| float | getThermostatFriction (self) |
| Returns the thermostat friction coefficient. | |
| int | getThermostatRngSeed (self) |
| Returns the thermostat RNG seed. | |
| float | getAverageTemperature (self) |
| Returns the three-point running-average temperature. | |
| float | getInstantaneousTemperature (self) |
| Returns the instantaneous three-point 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 stochastic Langevin temperature control.
The wrapper owns a concrete thermostat C handle. Native state includes one Philox generator per context atom and two kinetic and temperature estimators.
| None apocharmm.cuda_langevin_thermostat_integrator.CudaLangevinThermostatIntegrator.__init__ | ( | self, | |
| float | time_step | ||
| ) |
Constructs a Python-owned Langevin thermostat integrator.
| [in] | time_step | Value converted to C double, interpreted as a finite positive time step in picoseconds. |
| TypeError | If C scalar conversion fails. |
| ApoCharmmError | With native status APO_STATUS_INVALID_ARGUMENT, APO_STATUS_CUDA_ERROR, or APO_STATUS_RUNTIME_ERROR. |
| RuntimeError | If a successful native call produces a NULL concrete or base-view handle. |
Reimplemented from apocharmm.cuda_integrator.CudaIntegrator.
| float apocharmm.cuda_langevin_thermostat_integrator.CudaLangevinThermostatIntegrator.getAverageTemperature | ( | self | ) |
Returns the three-point running-average temperature.
float containing native estimator element 0 in kelvin. | RuntimeError | If the wrapper is closed. |
| ApoCharmmError | With native status APO_STATUS_CUDA_ERROR for transfer failure, APO_STATUS_RUNTIME_ERROR for an invalid native array shape, or another documented native status. |
| float apocharmm.cuda_langevin_thermostat_integrator.CudaLangevinThermostatIntegrator.getInstantaneousTemperature | ( | self | ) |
Returns the instantaneous three-point temperature.
float in kelvin, derived from kinetic-energy element 0. | RuntimeError | If the wrapper is closed. |
| ApoCharmmError | With native status APO_STATUS_NOT_INITIALIZED before context attachment, APO_STATUS_CUDA_ERROR for transfer failure, or APO_STATUS_RUNTIME_ERROR for an invalid native array shape. |
| float apocharmm.cuda_langevin_thermostat_integrator.CudaLangevinThermostatIntegrator.getReferenceTemperature | ( | self | ) |
Returns the reference temperature.
float in kelvin. | RuntimeError | If the wrapper is closed. |
| ApoCharmmError | If native validation or output fails. |
| float apocharmm.cuda_langevin_thermostat_integrator.CudaLangevinThermostatIntegrator.getThermostatFriction | ( | self | ) |
Returns the thermostat friction coefficient.
float in inverse picoseconds. | RuntimeError | If the wrapper is closed. |
| ApoCharmmError | If native validation or output fails. |
| int apocharmm.cuda_langevin_thermostat_integrator.CudaLangevinThermostatIntegrator.getThermostatRngSeed | ( | self | ) |
Returns the thermostat RNG seed.
int in the uint64 range. | RuntimeError | If the wrapper is closed. |
| ApoCharmmError | If native validation or output fails. |
| None apocharmm.cuda_langevin_thermostat_integrator.CudaLangevinThermostatIntegrator.resetAverageTemperature | ( | self | ) |
Resets both running-temperature values and their sample count.
None. | RuntimeError | If the wrapper is closed. |
| ApoCharmmError | If native validation or device reset fails. |
| None apocharmm.cuda_langevin_thermostat_integrator.CudaLangevinThermostatIntegrator.setReferenceTemperature | ( | self, | |
| float | temperature | ||
| ) |
Sets the thermostat reference temperature.
| [in] | temperature | Value converted to C double, in kelvin. It must be finite and non-negative. |
None. | TypeError | If conversion fails. |
| RuntimeError | If the wrapper is closed. |
| ApoCharmmError | If native validation or execution fails. |
| None apocharmm.cuda_langevin_thermostat_integrator.CudaLangevinThermostatIntegrator.setThermostatFriction | ( | self, | |
| float | friction | ||
| ) |
Sets the thermostat friction coefficient.
| [in] | friction | Value converted to C double, in inverse picoseconds. It must be finite and non-negative. |
None. | TypeError | If conversion fails. |
| RuntimeError | If the wrapper is closed. |
| ApoCharmmError | With native status APO_STATUS_INVALID_ARGUMENT, APO_STATUS_CUDA_ERROR, or APO_STATUS_RUNTIME_ERROR. |
| None apocharmm.cuda_langevin_thermostat_integrator.CudaLangevinThermostatIntegrator.setThermostatRngSeed | ( | self, | |
| int | seed | ||
| ) |
Sets the thermostat RNG seed.
| [in] | seed | Python integer in [0, 2**64 - 1]. The value is converted to ctypes.c_uint64. |
None. | TypeError | If comparison or unsigned conversion rejects the object. |
| ValueError | If the integer is outside the uint64 range. |
| RuntimeError | If the wrapper is closed. |
| ApoCharmmError | If attached-context RNG allocation or initialization fails. |
1.9.8