doxygen/thermostat_8h_source.html

// -*-c++-*-

#ifndef STORMM_THERMOSTAT_H

#define STORMM_THERMOSTAT_H


#include <string>

#include <vector>

#include "copyright.h"

#include "Accelerator/gpu_details.h"

#include "Accelerator/hybrid.h"

#include "Constants/behavior.h"

#include "Constants/scaling.h"

#include "Constants/symbol_values.h"

#include "DataTypes/common_types.h"

#include "Math/vector_ops.h"

#include "Namelists/nml_dynamics.h"

#include "Reporting/error_format.h"

#include "Structure/structure_enumerators.h"

#include "Synthesis/atomgraph_synthesis.h"

#include "Synthesis/synthesis_cache_map.h"

#include "Topology/atomgraph.h"

#include "Topology/atomgraph_abstracts.h"

#include "trajectory_enumerators.h"


namespace stormm {

namespace trajectory {


using card::GpuDetails;

using card::Hybrid;

using card::HybridTargetLevel;

using constants::PrecisionModel;

using data_types::isSignedIntegralScalarType;

using namelist::default_andersen_frequency;

using namelist::default_langevin_frequency;

using namelist::default_rattle_tolerance;

using namelist::default_simulation_temperature;

using namelist::default_thermostat_cache_depth;

using namelist::default_thermostat_random_seed;

using namelist::default_tstat_evo_window_start;

using namelist::default_tstat_evo_window_end;

using namelist::DynamicsControls;

using namelist::maximum_thermostat_cache_depth;

using stmath::findBin;

using structure::ApplyConstraints;

using symbols::boltzmann_constant_gafs;

using symbols::boltzmann_constant_gafs_f;

using synthesis::AtomGraphSynthesis;

using synthesis::PhaseSpaceSynthesis;

using synthesis::PsSynthesisWriter;

using synthesis::SyAtomUpdateKit;

using synthesis::SynthesisCacheMap;

using synthesis::SystemCache;

using topology::ChemicalDetailsKit;


template <typename T> struct ThermostatWriter {


  ThermostatWriter(ThermostatKind kind_in, ThermostatPartition layout_in, int natom_in,

                   size_t padded_natom_in, int npart_in, int step_in, int depth_in,

                   int init_evolution_in, int end_evolution_in, T init_temperature_in,

                   T final_temperature_in, T dt_in, bool csnt_geom_in, T rattle_tol_in,

                   int rattle_iter_in, int andr_cyc_in, T gamma_ln_in, T ln_implicit_in,

                   T ln_explicit_in, bool load_synthesis_forces_in,

                   const int4* partition_bounds_in, const T* init_temperatures_in,

                   const T* final_temperatures_in, ullint2* state_xy_in, ullint2* state_zw_in,

                   PrecisionModel rng_mode_in, double* cache_in, float* sp_cache_in);


  ThermostatWriter(const ThermostatWriter &original) = default;

  ThermostatWriter(ThermostatWriter &&original) = default;


  const ThermostatKind kind;

  const ThermostatPartition layout;

  const int natom;

  const size_t padded_natom;

  const int npart;

  int step;

  const int depth;

  const int init_evolution;

  const int end_evolution;

  const T init_temperature;

  const T final_temperature;

  const T dt;

  const bool cnst_geom;

  const T rattle_tol;

  const int rattle_iter;

  const int andr_cyc;

  const T gamma_ln;

  const T ln_implicit;

  const T ln_explicit;

  const bool load_synthesis_forces;

  const int4* partition_bounds;

  const T* init_temperatures;

  const T* final_temperatures;

  ullint2* state_xy;

  ullint2* state_zw;

  const PrecisionModel rng_mode;

  double* cache;

  float* sp_cache;

};


template <typename T> struct ThermostatReader {


  ThermostatReader(ThermostatKind kind_in, ThermostatPartition layout_in, int natom_in,

                   size_t padded_natom_in, int npart_in, int step_in, int depth_in,

                   int init_evolution_in, int end_evolution_in, T init_temperature_in,

                   T final_temperature_in, T dt_in, bool csnt_geom_in, T rattle_tol_in,

                   int rattle_iter_in, int andr_cyc_in, T gamma_ln_in, T ln_implicit_in,

                   T ln_explicit_in, bool load_synthesis_forces_in,

                   const int4* partition_bounds_in, const T* init_temperatures_in,

                   const T* final_temperatures_in, const ullint2* state_xy_in,

                   const ullint2* state_zw_in, PrecisionModel rng_mode_in, const double* cache_in,

                   const float* sp_cache_in);


  ThermostatReader(const ThermostatWriter<T> *w);


  ThermostatReader(const ThermostatWriter<T> &w);


  ThermostatReader(const ThermostatReader &original) = default;

  ThermostatReader(ThermostatReader &&original) = default;


  const ThermostatKind kind;

  const ThermostatPartition layout;

  const int natom;

  const size_t padded_natom;

  const int npart;

  const int step;

  const int depth;

  const int init_evolution;

  const int end_evolution;

  const T init_temperature;

  const T final_temperature;

  const T dt;

  const bool cnst_geom;

  const T rattle_tol;

  const int rattle_iter;

  const int andr_cyc;

  const T gamma_ln;

  const T ln_implicit;

  const T ln_explicit;

  const bool load_synthesis_forces;

  const int4* partition_bounds;

  const T* init_temperatures;

  const T* final_temperatures;

  const ullint2* state_xy;

  const ullint2* state_zw;

  const PrecisionModel rng_mode;

  const double* cache;

  const float* sp_cache;

};


class Thermostat {

public:


  Thermostat(ThermostatKind kind_in = ThermostatKind::NONE,

             PrecisionModel cache_config_in = PrecisionModel::SINGLE,

             int random_seed_in = default_thermostat_random_seed,

             const GpuDetails &gpu = null_gpu);


  Thermostat(int atom_count_in, ThermostatKind kind_in, double temperature_in,

             PrecisionModel cache_config_in = PrecisionModel::SINGLE,

             int random_seed_in = default_thermostat_random_seed,

             const GpuDetails &gpu = null_gpu);


  Thermostat(int atom_count_in, ThermostatKind kind_in, double init_temperature_in,

             double final_temperature_in, int initial_evolution_step_in,

             int final_evolution_step_in, PrecisionModel cache_config_in = PrecisionModel::SINGLE,

             int random_seed_in = default_thermostat_random_seed,

             const GpuDetails &gpu = null_gpu);


  Thermostat(int atom_count_in, ThermostatKind kind_in,

             const std::vector<double> &initial_temperatures_in,

             const std::vector<double> &final_temperatures_in,

             const std::vector<int2> &paritions_in,

             int initial_evolution_step_in = default_tstat_evo_window_start,

             int final_evolution_step_in = default_tstat_evo_window_end,

             PrecisionModel cache_config_in = PrecisionModel::SINGLE,

             int random_seed_in = default_thermostat_random_seed,

             const GpuDetails &gpu = null_gpu);


  Thermostat(const AtomGraph *ag, ThermostatKind kind_in,

             double initial_temperature_in, double final_temperature_in,

             int initial_evolution_step_in, int final_evolution_step_in,

             PrecisionModel cache_config_in = PrecisionModel::SINGLE,

             int random_seed_in = default_thermostat_random_seed,

             const GpuDetails &gpu = null_gpu);


  Thermostat(const AtomGraph &ag, ThermostatKind kind_in,

             double initial_temperature_in,

             double final_temperature_in,

             int initial_evolution_step_in, int final_evolution_step_in,

             PrecisionModel cache_config_in = PrecisionModel::SINGLE,

             int random_seed_in = default_thermostat_random_seed,

             const GpuDetails &gpu = null_gpu);


  Thermostat(const AtomGraph *ag, ThermostatKind kind_in,

             double temperature_in = default_simulation_temperature,

             PrecisionModel cache_config_in = PrecisionModel::SINGLE,

             int random_seed_in = default_thermostat_random_seed,

             const GpuDetails &gpu = null_gpu);


  Thermostat(const AtomGraph &ag, ThermostatKind kind_in,

             double temperature_in = default_simulation_temperature,

             PrecisionModel cache_config_in = PrecisionModel::SINGLE,

             int random_seed_in = default_thermostat_random_seed,

             const GpuDetails &gpu = null_gpu);


  Thermostat(const AtomGraph *ag, ThermostatKind kind_in,

             const std::vector<double> &initial_temperatures_in,

             const std::vector<double> &final_temperatures_in,

             const std::vector<int2> &paritions_in,

             int initial_evolution_step_in = default_tstat_evo_window_start,

             int final_evolution_step_in = default_tstat_evo_window_end,

             PrecisionModel cache_config_in = PrecisionModel::SINGLE,

             int random_seed_in = default_thermostat_random_seed,

             const GpuDetails &gpu = null_gpu);


  Thermostat(const AtomGraph &ag, ThermostatKind kind_in,

             const std::vector<double> &initial_temperatures_in,

             const std::vector<double> &final_temperatures_in,

             const std::vector<int2> &paritions_in,

             int initial_evolution_step_in = default_tstat_evo_window_start,

             int final_evolution_step_in = default_tstat_evo_window_end,

             PrecisionModel cache_config_in = PrecisionModel::SINGLE,

             int random_seed_in = default_thermostat_random_seed,

             const GpuDetails &gpu = null_gpu);


  Thermostat(const AtomGraphSynthesis *poly_ag, ThermostatKind kind_in,

             double initial_temperature_in, double final_temperature_in,

             int initial_evolution_step_in, int final_evolution_step_in,

             PrecisionModel cache_config_in = PrecisionModel::SINGLE,

             int random_seed_in = default_thermostat_random_seed,

             const GpuDetails &gpu = null_gpu);


  Thermostat(const AtomGraphSynthesis &poly_ag, ThermostatKind kind_in,

             double initial_temperature_in, double final_temperature_in,

             int initial_evolution_step_in, int final_evolution_step_in,

             PrecisionModel cache_config_in = PrecisionModel::SINGLE,

             int random_seed_in = default_thermostat_random_seed,

             const GpuDetails &gpu = null_gpu);


  Thermostat(const AtomGraphSynthesis *poly_ag, ThermostatKind kind_in,

             double temperature_in = default_simulation_temperature,

             PrecisionModel cache_config_in = PrecisionModel::SINGLE,

             int random_seed_in = default_thermostat_random_seed,

             const GpuDetails &gpu = null_gpu);


  Thermostat(const AtomGraphSynthesis &poly_ag, ThermostatKind kind_in,

             double temperature_in = default_simulation_temperature,

             PrecisionModel cache_config_in = PrecisionModel::SINGLE,

             int random_seed_in = default_thermostat_random_seed,

             const GpuDetails &gpu = null_gpu);


  Thermostat(const AtomGraphSynthesis *poly_ag, ThermostatKind kind_in,

             const std::vector<double> &initial_temperatures_in,

             const std::vector<double> &final_temperatures_in,

             const std::vector<int2> &paritions_in,

             int initial_evolution_step_in = default_tstat_evo_window_start,

             int final_evolution_step_in = default_tstat_evo_window_end,

             PrecisionModel cache_config_in = PrecisionModel::SINGLE,

             int random_seed_in = default_thermostat_random_seed,

             const GpuDetails &gpu = null_gpu);


  Thermostat(const AtomGraphSynthesis &poly_ag, ThermostatKind kind_in,

             const std::vector<double> &initial_temperatures_in,

             const std::vector<double> &final_temperatures_in,

             const std::vector<int2> &paritions_in,

             int initial_evolution_step_in = default_tstat_evo_window_start,

             int final_evolution_step_in = default_tstat_evo_window_end,

             PrecisionModel cache_config_in = PrecisionModel::SINGLE,

             int random_seed_in = default_thermostat_random_seed,

             const GpuDetails &gpu = null_gpu);


  Thermostat(const AtomGraphSynthesis *poly_ag, const DynamicsControls &dyncon,

             const SystemCache &sc, const std::vector<int> &sc_origins,

             const GpuDetails &gpu = null_gpu);


  Thermostat(const AtomGraphSynthesis &poly_ag, const DynamicsControls &dyncon,

             const SystemCache &sc, const std::vector<int> &sc_origins,

             const GpuDetails &gpu = null_gpu);


  Thermostat(const Thermostat& original) = default;

  Thermostat(Thermostat&& original) = default;

  Thermostat& operator=(const Thermostat& original) = default;

  Thermostat& operator=(Thermostat&& original) = default;


  ThermostatKind getKind() const;


  ThermostatPartition getBathPartitions() const;


  PrecisionModel getCacheConfiguration() const;


  int getAtomCount() const;


  int getStepNumber() const;


  int getRandomSeed() const;


  int getRandomCacheDepth() const;


  int getInitialEvolutionStep() const;


  int getFinalEvolutionStep() const;


  ullint4 getGeneratorState(int atom_index,

                            HybridTargetLevel tier = HybridTargetLevel::HOST) const;


  double getCachedRandomResult(int atom_index, int cache_row,

                               HybridTargetLevel tier = HybridTargetLevel::HOST) const;


  double getInitialTemperature(int atom_index = 0) const;


  double getFinalTemperature(int atom_index = 0) const;


  template <typename T> std::vector<T> getTemperatureSpread(int step_number = 0) const;


  std::vector<int4> getPartitionMap() const;


  template <typename Tcalc> Tcalc getAtomTarget(int atom_index = 0) const;


  template <typename Tcalc>

  Tcalc getPartitionTarget(int index = 0) const;


  int getPartitionConstrainedDoF(int index = 0) const;


  int getPartitionFreeDoF(int index = 0) const;


  int getAndersenResetFrequency() const;


  double getLangevinCollisionFrequency() const;


  double getLangevinImplicitFactor() const;


  double getLangevinExplicitFactor() const;


  double getTimeStep() const;


  ApplyConstraints constrainGeometry() const;


  double getRattleTolerance() const;


  int getRattleIterations() const;


  bool loadSynthesisForces() const;


  //         const reference.

  const Thermostat* getSelfPointer() const;


  const ThermostatReader<double> dpData(HybridTargetLevel tier = HybridTargetLevel::HOST) const;

  ThermostatWriter<double> dpData(HybridTargetLevel tier = HybridTargetLevel::HOST);

  const ThermostatReader<float> spData(HybridTargetLevel tier = HybridTargetLevel::HOST) const;

  ThermostatWriter<float> spData(HybridTargetLevel tier = HybridTargetLevel::HOST);


  void setAtomCount(int atom_count_in, int new_seed = -1, const GpuDetails &gpu = null_gpu);


  void setTemperature(double initial_temperature_in, double final_temperature_in = -1.0);

  void setTemperature(const std::vector<double> &initial_temperatures_in,

                      const std::vector<double> &final_temperatures_in,

                      const std::vector<int2> &partitions_in);


  void checkCompartments(const AtomGraphSynthesis *poly_ag);


  void setEvolutionWindow(int init_step_in, int final_step_in);


  void setCacheConfiguration(PrecisionModel cache_config_in, const GpuDetails &gpu = null_gpu);


  void setRandomCacheDepth(int depth_in, const GpuDetails &gpu = null_gpu);


  void setLangevinCollisionFrequency(double langevin_frequency_in);


  void setAndersenResetFrequency(int andersen_frequency_in);


  void setTimeStep(double time_step_in);


  void incrementStep();


  void decrementStep();


  void setGeometryConstraints(ApplyConstraints cnst_geometry_in);


  void setRattleTolerance(double rattle_tolerance_in);


  void setRattleIterations(int rattle_iterations_in);


  void setSynthesisForceLoading(bool load_synthesis_forces_in = true);


  void validateTemperature(double temperature_in);


  void validateEvolutionWindow();


  void validateRandomCacheDepth();


  void initializeRandomStates(int new_seed = default_thermostat_random_seed,

                              int scrub_cycles = 25,

                              HybridTargetLevel tier = HybridTargetLevel::HOST,

                              const GpuDetails &gpu = null_gpu);


  void refresh(size_t index_start, size_t index_end, int refresh_depth = 0);


#ifdef STORMM_USE_HPC

  void upload();


  void download();


  void uploadPartitions();


  void downloadPartitions();

#endif


private:

  ThermostatKind kind;

  ThermostatPartition bath_layout;

  PrecisionModel cache_config;

  int atom_count;

  size_t padded_atom_count;

  int partition_count;

  int step_number;

  int random_seed;

  int random_cache_depth;

  int initial_evolution_step;

  int final_evolution_step;

  double initial_temperature;

  double final_temperature;

  int andersen_frequency;

  double langevin_frequency;

  double time_step;

  ApplyConstraints cnst_geometry;

  double rattle_tolerance;

  int rattle_iterations;

  bool load_synthesis_forces;


  Hybrid<double> initial_temperatures;

  Hybrid<float> sp_initial_temperatures;


  Hybrid<double> final_temperatures;

  Hybrid<float> sp_final_temperatures;


  Hybrid<int4> partitions;


  Hybrid<ullint2> random_state_vector_xy;

  Hybrid<ullint2> random_state_vector_zw;


  Hybrid<double> random_cache;

  Hybrid<float> sp_random_cache;


  AtomGraph *ag_pointer;

  AtomGraphSynthesis *poly_ag_pointer;


  void allocateRandomStorage(int new_seed = -1, const GpuDetails &gpu = null_gpu);


  void resizeTemperatureArrays();

};


std::string getThermostatName(ThermostatKind kind);


template <typename Tcalc>

Tcalc getAtomTemperatureTarget(const ThermostatReader<Tcalc> &tstr, int atom_index = 0);


template <typename Tcalc>

Tcalc getAtomTemperatureTarget(const ThermostatWriter<Tcalc> &tstw, int atom_index = 0);


double getAtomTemperatureTarget(const Thermostat &tst, int atom_index = 0);


template <typename Tcalc>

Tcalc getPartitionTemperatureTarget(const ThermostatReader<Tcalc> &tstr, int index = 0);


template <typename Tcalc>

Tcalc getPartitionTemperatureTarget(const ThermostatWriter<Tcalc> &tstw, int index = 0);


double getPartitionTemperatureTarget(const Thermostat &tst, int index = 0);


template <typename Tcoord, typename Tcalc>

void andersenVelocityReset(Tcoord* xvel, Tcoord* yvel, Tcoord* zvel, int* xvel_ovrf,

                           int* yvel_ovrf, int* zvel_ovrf, const Tcalc* inv_masses,

                           const ThermostatReader<Tcalc> &tstr, Tcalc vel_scale_factor = 1.0);


template <typename Tcoord, typename Tcalc>

void andersenVelocityReset(Tcoord* xvel, Tcoord* yvel, Tcoord* zvel, const Tcalc* masses,

                           const ThermostatReader<Tcalc> &tstr, Tcalc vel_scale_factor = 1.0);


void andersenVelocityReset(PhaseSpaceWriter *psw, const ChemicalDetailsKit &cdk,

                           const ThermostatReader<double> &tstr);


void andersenVelocityReset(PhaseSpace *ps, const AtomGraph &ag, const Thermostat &tst);


template <typename Tcalc, typename Tcalc2, typename Tcalc4>

void andersenVelocityReset(PsSynthesisWriter *poly_psw,

                           const SyAtomUpdateKit<Tcalc, Tcalc2, Tcalc4> &poly_auk,

                           const ThermostatReader<Tcalc> &tstr);


#ifdef STORMM_USE_HPC

void andersenVelocityReset(PsSynthesisWriter *poly_psw,

                           const SyAtomUpdateKit<void, void, void> &poly_auk,

                           const ThermostatReader<void> &tstr,

                           PrecisionModel prec = PrecisionModel::SINGLE,

                           const GpuDetails &gpu = null_gpu);

#endif


void andersenVelocityReset(PhaseSpaceSynthesis *poly_ps, const AtomGraphSynthesis *poly_ag,

                           const Thermostat *tst, PrecisionModel prec = PrecisionModel::SINGLE);


void andersenVelocityReset(PhaseSpaceSynthesis *poly_ps, const AtomGraphSynthesis &poly_ag,

                           const Thermostat &tst, PrecisionModel prec = PrecisionModel::SINGLE);


void velocityKickStart(PhaseSpace *ps, const AtomGraph *ag, Thermostat *tst,

                       const DynamicsControls &dyncon,

                       EnforceExactTemperature scale_temp = EnforceExactTemperature::YES);


void velocityKickStart(PhaseSpace *ps, const AtomGraph &ag, Thermostat *tst,

                       const DynamicsControls &dyncon,

                       EnforceExactTemperature scale_temp = EnforceExactTemperature::YES);


void velocityKickStart(PhaseSpaceSynthesis *poly_ps, const AtomGraphSynthesis *poly_ag,

                       Thermostat *tst, const DynamicsControls &dyncon,

                       PrecisionModel prec = PrecisionModel::SINGLE,

                       EnforceExactTemperature scale_temp = EnforceExactTemperature::YES,

                       const GpuDetails &gpu = null_gpu);


void velocityKickStart(PhaseSpaceSynthesis *poly_ps, const AtomGraphSynthesis &poly_ag,

                       Thermostat *tst, const DynamicsControls &dyncon,

                       PrecisionModel prec = PrecisionModel::SINGLE,

                       EnforceExactTemperature scale_temp = EnforceExactTemperature::YES,

                       const GpuDetails &gpu = null_gpu);


} // namespace trajectory

} // namespace stormm


#include "thermostat.tpp"


#endif

stormm::card::GpuDetails
Pertinent aspects of one particular GPU. Condensing the data for each GPU in this manner helps to ens...
Definition gpu_details.h:27

stormm::card::Hybrid
An evolution of GpuBuffer in pmemd.cuda, the Composite array has elements that are accessible from ei...
Definition hybrid.h:202

stormm::energy::Thermostat::Thermostat
Thermostat(ThermostatKind kind_in=ThermostatKind::NONE, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)
Constructors for the Thermostat object. Any information can be added via setter functions after const...
Definition thermostat.cpp:50

stormm::namelist::DynamicsControls
Object to encapsulate molecular dynamics control information. Like other namelist encapsualtors,...
Definition nml_dynamics.h:123

stormm::synthesis::AtomGraphSynthesis
A collection of one or more AtomGraph objects, with similar components arranged in contiguous arrays ...
Definition atomgraph_synthesis.h:55

stormm::synthesis::PhaseSpaceSynthesis
A fixed-precision representation of coordinates, velocities, and forces to manage a set of simulation...
Definition phasespace_synthesis.h:325

stormm::topology::AtomGraph
A struct to hold information relating to an Amber topology. This struct's member functions are limite...
Definition atomgraph.h:50

stormm::trajectory::DynamicsControls
Object to encapsulate molecular dynamics control information. Like other namelist encapsualtors,...
Definition nml_dynamics.h:123

stormm::trajectory::PhaseSpace
An object to complement a topology and hold positions, velocities, and forces of all particles in a s...
Definition phasespace.h:141

stormm::trajectory::SystemCache
Simple but central struct to store the primitive form of the collection of systems that most STORMM a...
Definition systemcache.h:63

stormm::trajectory::Thermostat
Store the parameters for a simulation thermostat. Includes Berendsen, Andersen, and Langevin methods....
Definition thermostat.h:221

stormm::trajectory::Thermostat::setRattleTolerance
void setRattleTolerance(double rattle_tolerance_in)
Set the convergence criterion for RATTLE.
Definition thermostat.cpp:994

stormm::trajectory::Thermostat::getRandomCacheDepth
int getRandomCacheDepth() const
Get the random number cache depth. The quantity of random numbers that will be produced and cached fo...
Definition thermostat.cpp:490

stormm::trajectory::Thermostat::setRattleIterations
void setRattleIterations(int rattle_iterations_in)
Set the maximum number of iterations to take when attempting to converge RATTLE bond length constrain...
Definition thermostat.cpp:999

stormm::trajectory::Thermostat::setLangevinCollisionFrequency
void setLangevinCollisionFrequency(double langevin_frequency_in)
Set the collision frequency for the Langevin thermostat. This will also set the scaled form of the va...
Definition thermostat.cpp:958

stormm::trajectory::Thermostat::getFinalEvolutionStep
int getFinalEvolutionStep() const
Get the step at which the temperature evolution is expected to be complete. This is the step when the...
Definition thermostat.cpp:500

stormm::trajectory::Thermostat::getInitialTemperature
double getInitialTemperature(int atom_index=0) const
Get the initial target temperature for this thermostat, in units of Kelvin.
Definition thermostat.cpp:556

stormm::trajectory::Thermostat::getRandomSeed
int getRandomSeed() const
Get the random seed used to initialize Xoshiro256++ state vectors.
Definition thermostat.cpp:485

stormm::trajectory::Thermostat::constrainGeometry
ApplyConstraints constrainGeometry() const
Get the order whether to apply geometric constraints.
Definition thermostat.cpp:622

stormm::trajectory::Thermostat::decrementStep
void decrementStep()
Decrease the step count by one. This will cause the simulation's official step counter to backtrack.
Definition thermostat.cpp:984

stormm::trajectory::Thermostat::incrementStep
void incrementStep()
Increase the step count by one. This will advance the simulation's official step counter.
Definition thermostat.cpp:979

stormm::trajectory::Thermostat::setTemperature
void setTemperature(double initial_temperature_in, double final_temperature_in=-1.0)
Set the initial target temperature.
Definition thermostat.cpp:720

stormm::trajectory::Thermostat::getPartitionConstrainedDoF
int getPartitionConstrainedDoF(int index=0) const
Get the number of constrained degrees of freedom for a particular partition of this thermostat.
Definition thermostat.cpp:585

stormm::trajectory::Thermostat::getFinalTemperature
double getFinalTemperature(int atom_index=0) const
Get the end-point target temperature for this thermostat, in units of Kelvin.
Definition thermostat.cpp:568

stormm::trajectory::Thermostat::getBathPartitions
ThermostatPartition getBathPartitions() const
Indicate whether this thermostat applies a common target temperature to all atoms,...
Definition thermostat.cpp:465

stormm::trajectory::Thermostat::setCacheConfiguration
void setCacheConfiguration(PrecisionModel cache_config_in, const GpuDetails &gpu=null_gpu)
Set the random number cache configuration.
Definition thermostat.cpp:939

stormm::trajectory::Thermostat::setAtomCount
void setAtomCount(int atom_count_in, int new_seed=-1, const GpuDetails &gpu=null_gpu)
Set the number of atoms for which the thermostat is responsible.
Definition thermostat.cpp:713

stormm::trajectory::Thermostat::setTimeStep
void setTimeStep(double time_step_in)
Set the time step. This will also set the scaled form of the value.
Definition thermostat.cpp:974

stormm::trajectory::Thermostat::getAtomCount
int getAtomCount() const
Get the total number of atoms that this thermostat can serve.
Definition thermostat.cpp:475

stormm::trajectory::Thermostat::getAtomTarget
Tcalc getAtomTarget(int atom_index=0) const
Get the current target temperature for this thermostat, in units of Kelvin, for a specific atom.

stormm::trajectory::Thermostat::validateTemperature
void validateTemperature(double temperature_in)
Validate the initial or final target temperature.
Definition thermostat.cpp:1009

stormm::trajectory::Thermostat::dpData
const ThermostatReader< double > dpData(HybridTargetLevel tier=HybridTargetLevel::HOST) const
Get the abstract.
Definition thermostat.cpp:647

stormm::trajectory::Thermostat::setRandomCacheDepth
void setRandomCacheDepth(int depth_in, const GpuDetails &gpu=null_gpu)
Set the random number cache depth. This value is kept on a tight leash, as it can easily lead to allo...
Definition thermostat.cpp:946

stormm::trajectory::Thermostat::getAndersenResetFrequency
int getAndersenResetFrequency() const
Get the Andersen reset frequency.
Definition thermostat.cpp:597

stormm::trajectory::Thermostat::getPartitionMap
std::vector< int4 > getPartitionMap() const
Get the partition boundaries between different segments of the thermostat as a vector of integer tupl...
Definition thermostat.cpp:580

stormm::trajectory::Thermostat::getRattleTolerance
double getRattleTolerance() const
Get the convergence criterion for RATTLE bond length constraints.
Definition thermostat.cpp:627

stormm::trajectory::Thermostat::refresh
void refresh(size_t index_start, size_t index_end, int refresh_depth=0)
Fill or refill the random number cache for a subset of the atoms, advancing the thermostat's random n...
Definition thermostat.cpp:1101

stormm::trajectory::Thermostat::getKind
ThermostatKind getKind() const
Get the kind of thermostat.
Definition thermostat.cpp:460

stormm::trajectory::Thermostat::getGeneratorState
ullint4 getGeneratorState(int atom_index, HybridTargetLevel tier=HybridTargetLevel::HOST) const
Get the generator state for a particular atom. For retrieving large numbers of states,...
Definition thermostat.cpp:505

stormm::trajectory::Thermostat::initializeRandomStates
void initializeRandomStates(int new_seed=default_thermostat_random_seed, int scrub_cycles=25, HybridTargetLevel tier=HybridTargetLevel::HOST, const GpuDetails &gpu=null_gpu)
Initialize the random state vectors of a thermostat, whether for Langevin or Andersen thermostating....
Definition thermostat.cpp:1046

stormm::trajectory::Thermostat::setSynthesisForceLoading
void setSynthesisForceLoading(bool load_synthesis_forces_in=true)
Set the integrator to take prior force computations residing in the PhaseSpaceSynthesis into account....
Definition thermostat.cpp:1004

stormm::trajectory::Thermostat::getLangevinCollisionFrequency
double getLangevinCollisionFrequency() const
Get the collision frequency for the Langevin thermostat (in units of femtoseconds).
Definition thermostat.cpp:602

stormm::trajectory::Thermostat::getPartitionFreeDoF
int getPartitionFreeDoF(int index=0) const
Get the number of degrees of freedom for a particular partition of this thermostat,...
Definition thermostat.cpp:591

stormm::trajectory::Thermostat::Thermostat
Thermostat(const Thermostat &original)=default
The default copy and move constructors and assignment operators are best for this object with no POIN...

stormm::trajectory::Thermostat::validateEvolutionWindow
void validateEvolutionWindow()
Validate the initial and final steps for applying the temperature evolution.
Definition thermostat.cpp:1017

stormm::trajectory::Thermostat::getTemperatureSpread
std::vector< T > getTemperatureSpread(int step_number=0) const
Get the spread of temperature targets for all segments of the thermostat at a specific time step.

stormm::trajectory::Thermostat::getCachedRandomResult
double getCachedRandomResult(int atom_index, int cache_row, HybridTargetLevel tier=HybridTargetLevel::HOST) const
Get one of the cached random numbers. This function returns the result as a double-precision real,...
Definition thermostat.cpp:528

stormm::trajectory::Thermostat::validateRandomCacheDepth
void validateRandomCacheDepth()
Validate the random number cache depth. A maxmimum cache depth of 15 (45 total random numbers per ato...
Definition thermostat.cpp:1027

stormm::trajectory::Thermostat::getLangevinExplicitFactor
double getLangevinExplicitFactor() const
Get the "explicit" Langevin factor, the portion of the velocity update to apply on the second half of...
Definition thermostat.cpp:612

stormm::trajectory::Thermostat::getStepNumber
int getStepNumber() const
Get the step number according to this thermostat. The thermostat will serve as an official reference ...
Definition thermostat.cpp:480

stormm::trajectory::Thermostat::setAndersenResetFrequency
void setAndersenResetFrequency(int andersen_frequency_in)
Set the Andersen velocity reassignment frequency. This will be taken from user input.
Definition thermostat.cpp:953

stormm::trajectory::Thermostat::Thermostat
Thermostat(ThermostatKind kind_in=ThermostatKind::NONE, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)
Constructors for the Thermostat object. Any information can be added via setter functions after const...
Definition thermostat.cpp:50

stormm::trajectory::Thermostat::getInitialEvolutionStep
int getInitialEvolutionStep() const
Get the step at which to begin changing the temperature from its initial value T(init) to its final v...
Definition thermostat.cpp:495

stormm::trajectory::Thermostat::getTimeStep
double getTimeStep() const
Get the time step, in units of femtoseconds.
Definition thermostat.cpp:617

stormm::trajectory::Thermostat::getPartitionTarget
Tcalc getPartitionTarget(int index=0) const
Get the current target temperature for a specific partition within this thermostat,...

stormm::trajectory::Thermostat::getLangevinImplicitFactor
double getLangevinImplicitFactor() const
Get the "implicit" Langevin factor, the portion of the velocity update to apply immediately after for...
Definition thermostat.cpp:607

stormm::trajectory::Thermostat::getCacheConfiguration
PrecisionModel getCacheConfiguration() const
Get the random number caching precision.
Definition thermostat.cpp:470

stormm::trajectory::Thermostat::checkCompartments
void checkCompartments(const AtomGraphSynthesis *poly_ag)
Check the compartmentalization if the thermostat regulates a synthesis of systems.

stormm::trajectory::Thermostat::loadSynthesisForces
bool loadSynthesisForces() const
Get an indication of whether extra forces should be loaded from the synthesis in periodic systems.
Definition thermostat.cpp:637

stormm::trajectory::Thermostat::setEvolutionWindow
void setEvolutionWindow(int init_step_in, int final_step_in)
Set the step at which temperature evolution, away from T(init), shall begin.
Definition thermostat.cpp:932

stormm::trajectory::Thermostat::getRattleIterations
int getRattleIterations() const
Get the number of RATTLE iterations to attempt.
Definition thermostat.cpp:632

stormm::trajectory::Thermostat::setGeometryConstraints
void setGeometryConstraints(ApplyConstraints cnst_geometry_in)
Set the instruction for carrying out geometric constraints during dynamics.
Definition thermostat.cpp:989

stormm::trajectory::Thermostat::getSelfPointer
const Thermostat * getSelfPointer() const
Get a pointer to the object itself, useful if it has been passed to a function by.
Definition thermostat.cpp:642

stormm::data_types::int4
Definition stormm_vector_types.h:33

stormm::energy::ThermostatWriter::ThermostatWriter
ThermostatWriter(ThermostatKind kind_in, ThermostatPartition layout_in, int natom_in, size_t padded_natom_in, int npart_in, int step_in, int depth_in, int init_evolution_in, int end_evolution_in, T init_temperature_in, T final_temperature_in, T dt_in, bool csnt_geom_in, T rattle_tol_in, int rattle_iter_in, int andr_cyc_in, T gamma_ln_in, T ln_implicit_in, T ln_explicit_in, bool load_synthesis_forces_in, const int4 *partition_bounds_in, const T *init_temperatures_in, const T *final_temperatures_in, ullint2 *state_xy_in, ullint2 *state_zw_in, PrecisionModel rng_mode_in, double *cache_in, float *sp_cache_in)
The constructor takes the usual list of parent object attributes with pointers applicable on either t...

stormm::mm::ThermostatReader::ThermostatReader
ThermostatReader(ThermostatKind kind_in, ThermostatPartition layout_in, int natom_in, size_t padded_natom_in, int npart_in, int step_in, int depth_in, int init_evolution_in, int end_evolution_in, T init_temperature_in, T final_temperature_in, T dt_in, bool csnt_geom_in, T rattle_tol_in, int rattle_iter_in, int andr_cyc_in, T gamma_ln_in, T ln_implicit_in, T ln_explicit_in, bool load_synthesis_forces_in, const int4 *partition_bounds_in, const T *init_temperatures_in, const T *final_temperatures_in, const ullint2 *state_xy_in, const ullint2 *state_zw_in, PrecisionModel rng_mode_in, const double *cache_in, const float *sp_cache_in)
The constructor takes the usual list of parent object attributes with pointers applicable on either t...

stormm::synthesis::PsSynthesisWriter
The writer for a PhaseSpaceSynthesis object, containing all of the data relevant for propagating dyna...
Definition phasespace_synthesis.h:87

stormm::synthesis::SyAtomUpdateKit
Collect the virtual site details and constraint parameters of the topology synthesis into a single ab...
Definition synthesis_abstracts.h:257

stormm::topology::ChemicalDetailsKit
Information on atoms and residues which may be useful for applying atom masks or identifying specific...
Definition atomgraph_abstracts.h:382

stormm::trajectory::PhaseSpaceWriter
Collect constants and pointers to the components of a modifiable PhaseSpace object.
Definition phasespace.h:31

stormm::trajectory::ThermostatReader
Read-only abstract for the Thermostat object.
Definition thermostat.h:135

stormm::trajectory::ThermostatReader::npart
const int npart
Definition thermostat.h:169

stormm::trajectory::ThermostatReader::gamma_ln
const T gamma_ln
Definition thermostat.h:194

stormm::trajectory::ThermostatReader::rattle_tol
const T rattle_tol
Convergence criterion for RATTLE bond length constraints.
Definition thermostat.h:188

stormm::trajectory::ThermostatReader::load_synthesis_forces
const bool load_synthesis_forces
Definition thermostat.h:200

stormm::trajectory::ThermostatReader::natom
const int natom
Number of atoms controlled by this thermostat.
Definition thermostat.h:167

stormm::trajectory::ThermostatReader::rattle_iter
const int rattle_iter
Definition thermostat.h:189

stormm::trajectory::ThermostatReader::kind
const ThermostatKind kind
The type of this thermostat, i.e. Andersen.
Definition thermostat.h:164

stormm::trajectory::ThermostatReader::init_evolution
const int init_evolution
Definition thermostat.h:176

stormm::trajectory::ThermostatReader::final_temperatures
const T * final_temperatures
Array of final target gemperatures for each atom.
Definition thermostat.h:206

stormm::trajectory::ThermostatReader::state_zw
const ullint2 * state_zw
Second 128 bits of each 256-bit state vector.
Definition thermostat.h:208

stormm::trajectory::ThermostatReader::depth
const int depth
Definition thermostat.h:173

stormm::trajectory::ThermostatReader::step
const int step
Current step number of the simulation.
Definition thermostat.h:172

stormm::trajectory::ThermostatReader::cache
const double * cache
Definition thermostat.h:212

stormm::trajectory::ThermostatReader::init_temperature
const T init_temperature
Definition thermostat.h:182

stormm::trajectory::ThermostatReader::ThermostatReader
ThermostatReader(ThermostatKind kind_in, ThermostatPartition layout_in, int natom_in, size_t padded_natom_in, int npart_in, int step_in, int depth_in, int init_evolution_in, int end_evolution_in, T init_temperature_in, T final_temperature_in, T dt_in, bool csnt_geom_in, T rattle_tol_in, int rattle_iter_in, int andr_cyc_in, T gamma_ln_in, T ln_implicit_in, T ln_explicit_in, bool load_synthesis_forces_in, const int4 *partition_bounds_in, const T *init_temperatures_in, const T *final_temperatures_in, const ullint2 *state_xy_in, const ullint2 *state_zw_in, PrecisionModel rng_mode_in, const double *cache_in, const float *sp_cache_in)
The constructor takes the usual list of parent object attributes with pointers applicable on either t...

stormm::trajectory::ThermostatReader::ln_implicit
const T ln_implicit
Definition thermostat.h:196

stormm::trajectory::ThermostatReader::dt
const T dt
The time step, in units of femtoseconds.
Definition thermostat.h:186

stormm::trajectory::ThermostatReader::ThermostatReader
ThermostatReader(const ThermostatReader &original)=default
The copy and move assignment operators will be implicitly deleted due to the presence of const member...

stormm::trajectory::ThermostatReader::init_temperatures
const T * init_temperatures
Array of initial target temperatures for each atom.
Definition thermostat.h:205

stormm::trajectory::ThermostatReader::andr_cyc
const int andr_cyc
Definition thermostat.h:191

stormm::trajectory::ThermostatReader::end_evolution
const int end_evolution
Definition thermostat.h:180

stormm::trajectory::ThermostatReader::padded_natom
const size_t padded_natom
The number of atoms padded by the warp size.
Definition thermostat.h:168

stormm::trajectory::ThermostatReader::ln_explicit
const T ln_explicit
Definition thermostat.h:198

stormm::trajectory::ThermostatReader::rng_mode
const PrecisionModel rng_mode
Definition thermostat.h:209

stormm::trajectory::ThermostatReader::final_temperature
const T final_temperature
Definition thermostat.h:184

stormm::trajectory::ThermostatReader::sp_cache
const float * sp_cache
Definition thermostat.h:214

stormm::trajectory::ThermostatReader::partition_bounds
const int4 * partition_bounds
Definition thermostat.h:202

stormm::trajectory::ThermostatReader::cnst_geom
const bool cnst_geom
Indicate whether to apply geometry constraints.
Definition thermostat.h:187

stormm::trajectory::ThermostatReader::layout
const ThermostatPartition layout
Definition thermostat.h:165

stormm::trajectory::ThermostatReader::state_xy
const ullint2 * state_xy
First 128 bits of each 256-bit state vector.
Definition thermostat.h:207

stormm::trajectory::ThermostatWriter
Partially writeable abstract for the Thermostat object. As with the MMControlKit struct (see the libr...
Definition thermostat.h:58

stormm::trajectory::ThermostatWriter::cnst_geom
const bool cnst_geom
Indicate whether to apply geometry constraints.
Definition thermostat.h:101

stormm::trajectory::ThermostatWriter::padded_natom
const size_t padded_natom
The number of atoms padded by the warp size.
Definition thermostat.h:83

stormm::trajectory::ThermostatWriter::depth
const int depth
Definition thermostat.h:88

stormm::trajectory::ThermostatWriter::dt
const T dt
The time step, in units of femtoseconds.
Definition thermostat.h:100

stormm::trajectory::ThermostatWriter::cache
double * cache
Definition thermostat.h:128

stormm::trajectory::ThermostatWriter::step
int step
Current step number of the simulation.
Definition thermostat.h:87

stormm::trajectory::ThermostatWriter::gamma_ln
const T gamma_ln
Definition thermostat.h:108

stormm::trajectory::ThermostatWriter::load_synthesis_forces
const bool load_synthesis_forces
Definition thermostat.h:116

stormm::trajectory::ThermostatWriter::final_temperatures
const T * final_temperatures
Array of final target gemperatures for each atom.
Definition thermostat.h:122

stormm::trajectory::ThermostatWriter::rattle_iter
const int rattle_iter
Definition thermostat.h:103

stormm::trajectory::ThermostatWriter::final_temperature
const T final_temperature
Final target temperature, common to all atoms.
Definition thermostat.h:99

stormm::trajectory::ThermostatWriter::partition_bounds
const int4 * partition_bounds
Definition thermostat.h:118

stormm::trajectory::ThermostatWriter::rattle_tol
const T rattle_tol
Convergence criterion for RATTLE bond length constraints.
Definition thermostat.h:102

stormm::trajectory::ThermostatWriter::ThermostatWriter
ThermostatWriter(const ThermostatWriter &original)=default
The copy and move assignment operators will be implicitly deleted due to the presence of const member...

stormm::trajectory::ThermostatWriter::ThermostatWriter
ThermostatWriter(ThermostatKind kind_in, ThermostatPartition layout_in, int natom_in, size_t padded_natom_in, int npart_in, int step_in, int depth_in, int init_evolution_in, int end_evolution_in, T init_temperature_in, T final_temperature_in, T dt_in, bool csnt_geom_in, T rattle_tol_in, int rattle_iter_in, int andr_cyc_in, T gamma_ln_in, T ln_implicit_in, T ln_explicit_in, bool load_synthesis_forces_in, const int4 *partition_bounds_in, const T *init_temperatures_in, const T *final_temperatures_in, ullint2 *state_xy_in, ullint2 *state_zw_in, PrecisionModel rng_mode_in, double *cache_in, float *sp_cache_in)
The constructor takes the usual list of parent object attributes with pointers applicable on either t...

stormm::trajectory::ThermostatWriter::state_xy
ullint2 * state_xy
First 128 bits of each 256-bit state vector.
Definition thermostat.h:123

stormm::trajectory::ThermostatWriter::sp_cache
float * sp_cache
Definition thermostat.h:130

stormm::trajectory::ThermostatWriter::ln_explicit
const T ln_explicit
Definition thermostat.h:114

stormm::trajectory::ThermostatWriter::layout
const ThermostatPartition layout
Definition thermostat.h:80

stormm::trajectory::ThermostatWriter::kind
const ThermostatKind kind
The type of this thermostat, i.e. Andersen.
Definition thermostat.h:79

stormm::trajectory::ThermostatWriter::end_evolution
const int end_evolution
Definition thermostat.h:95

stormm::trajectory::ThermostatWriter::natom
const int natom
Number of atoms controlled by this thermostat.
Definition thermostat.h:82

stormm::trajectory::ThermostatWriter::state_zw
ullint2 * state_zw
Second 128 bits of each 256-bit state vector.
Definition thermostat.h:124

stormm::trajectory::ThermostatWriter::init_temperatures
const T * init_temperatures
Array of initial target temperatures for each atom.
Definition thermostat.h:121

stormm::trajectory::ThermostatWriter::ln_implicit
const T ln_implicit
Definition thermostat.h:112

stormm::trajectory::ThermostatWriter::init_evolution
const int init_evolution
Definition thermostat.h:91

stormm::trajectory::ThermostatWriter::rng_mode
const PrecisionModel rng_mode
Definition thermostat.h:125

stormm::trajectory::ThermostatWriter::init_temperature
const T init_temperature
Definition thermostat.h:97

stormm::trajectory::ThermostatWriter::npart
const int npart
Definition thermostat.h:84

stormm::trajectory::ThermostatWriter::andr_cyc
const int andr_cyc
Definition thermostat.h:105