doxygen/phasespace__synthesis_8h_source.html

// -*-c++-*-

#ifndef STORMM_PHASESPACE_SYNTHESIS_H

#define STORMM_PHASESPACE_SYNTHESIS_H


#include <typeinfo>

#include <typeindex>

#include <sys/types.h>

#include "copyright.h"

#include "Accelerator/gpu_details.h"

#include "Accelerator/hybrid.h"

#include "Accelerator/hybrid_util.h"

#include "Constants/behavior.h"

#include "Constants/fixed_precision.h"

#include "DataTypes/common_types.h"

#include "DataTypes/stormm_vector_types.h"

#include "FileManagement/file_util.h"

#include "Math/rounding.h"

#include "Numerics/split_fixed_precision.h"

#include "Topology/atomgraph.h"

#include "Trajectory/coordinateframe.h"

#include "Trajectory/coordinate_series.h"

#include "Trajectory/phasespace.h"

#include "Trajectory/trajectory_enumerators.h"


namespace stormm {

namespace synthesis {


using card::default_hpc_format;

using card::GpuDetails;

using card::Hybrid;

using card::HybridFormat;

using card::HybridTargetLevel;

using constants::CartesianDimension;

using diskutil::PrintSituation;

using stmath::roundUp;

using numerics::default_globalpos_scale_bits;

using numerics::default_localpos_scale_bits;

using numerics::default_velocity_scale_bits;

using numerics::default_force_scale_bits;

using numerics::force_scale_nonoverflow_bits;

using numerics::globalpos_scale_nonoverflow_bits;

using numerics::velocity_scale_nonoverflow_bits;

using topology::AtomGraph;

using topology::UnitCellType;

using trajectory::CoordinateCycle;

using trajectory::CoordinateFileKind;

using trajectory::CoordinateFrame;

using trajectory::CoordinateFrameReader;

using trajectory::CoordinateFrameWriter;

using trajectory::CoordinateSeries;

using trajectory::CoordinateSeriesReader;

using trajectory::CoordinateSeriesWriter;

using trajectory::PhaseSpace;

using trajectory::PhaseSpaceReader;

using trajectory::PhaseSpaceWriter;

using trajectory::TrajectoryKind;


struct PsSynthesisBorders {


  PsSynthesisBorders(int system_count_in, const int* atom_starts_in, const int* atom_counts_in,

                     const double* umat_in, const double* invu_in);


  PsSynthesisBorders(const PsSynthesisBorders &original) = default;

  PsSynthesisBorders(PsSynthesisBorders &&other) = default;


  const int system_count;

  const int* atom_starts;

  const int* atom_counts;

  const double* umat;

  const double* invu;

};


struct PsSynthesisWriter {


  PsSynthesisWriter(int system_count_in, int unique_topology_count_in, UnitCellType unit_cell_in,

                    const int* atom_starts_in, const int* atom_counts_in,

                    const int* common_ag_list_in, const int* common_ag_bounds_in,

                    const int* unique_ag_idx_in, const int* replica_idx_in, float gpos_scale_in,

                    float vel_scale_in, float frc_scale_in, int gpos_bits_in, int vel_bits_in,

                    int frc_bits_in, llint* boxvecs_in, int* boxvec_ovrf_in, double* umat_in,

                    double* invu_in, double* boxdims_in, llint* alt_boxvecs_in,

                    int* alt_boxvec_ovrf_in, double* umat_alt_in, double* invu_alt_in,

                    double* alt_boxdims_in, llint* xcrd_in, llint* ycrd_in, llint* zcrd_in,

                    int* xcrd_ovrf_in, int* ycrd_ovrf_in, int* zcrd_ovrf_in, llint* xvel_in,

                    llint* yvel_in, llint* zvel_in, int* xvel_ovrf_in, int* yvel_ovrf_in,

                    int* zvel_ovrf_in, llint* xfrc_in, llint* yfrc_in, llint* zfrc_in,

                    int* xfrc_ovrf_in, int* yfrc_ovrf_in, int* zfrc_ovrf_in, llint* xalt_in,

                    llint* yalt_in, llint* zalt_in, int* xalt_ovrf_in, int* yalt_ovrf_in,

                    int* zalt_ovrf_in, llint* vxalt_in, llint* vyalt_in, llint* vzalt_in,

                    int* vxalt_ovrf_in, int* vyalt_ovrf_in, int* vzalt_ovrf_in, llint* fxalt_in,

                    llint* fyalt_in, llint* fzalt_in, int* fxalt_ovrf_in, int* fyalt_ovrf_in,

                    int* fzalt_ovrf_in);


  PsSynthesisWriter(const PsSynthesisWriter &original) = default;

  PsSynthesisWriter(PsSynthesisWriter &&other) = default;


  // Even in the writer, some information may not be altered.  This includes the simulation

  // conditions, the number of systems, and the number of atoms in each system.  The layout

  // of the data must not be corrupted.

  const int system_count;

  const int unique_topology_count;

  const UnitCellType unit_cell;

  const int* atom_starts;

  const int* atom_counts;

  const int* common_ag_list;

  const int* common_ag_bounds;

  const int* unique_ag_idx;

  const int* replica_idx;


  // Scaling factors: the PhaseSpaceSynthesis permits a customizable discretization of fixed-point

  // arithmetic.

  const float gpos_scale;

  const float vel_scale;

  const float frc_scale;

  const float inv_gpos_scale;

  const float inv_vel_scale;

  const float inv_frc_scale;

  const int gpos_bits;

  const int vel_bits;

  const int frc_bits;


  // Pointers to the transformations and box vectors are mutable if the systems change volume.

  llint* boxvecs;

  int* boxvec_ovrf;

  double* umat;

  double* invu;

  double* boxdims;

  llint* alt_boxvecs;

  int* alt_boxvec_ovrf;

  double* umat_alt;

  double* invu_alt;

  double* alt_boxdims;


  // Pointers to the coordinate, velocity, and force data--these are mutable for accumulating

  // forces and letting a trajectory evolve.

  llint* xcrd;

  llint* ycrd;

  llint* zcrd;

  int* xcrd_ovrf;

  int* ycrd_ovrf;

  int* zcrd_ovrf;

  llint* xvel;

  llint* yvel;

  llint* zvel;

  int* xvel_ovrf;

  int* yvel_ovrf;

  int* zvel_ovrf;

  llint* xfrc;

  llint* yfrc;

  llint* zfrc;

  int* xfrc_ovrf;

  int* yfrc_ovrf;

  int* zfrc_ovrf;

  llint* xalt;

  llint* yalt;

  llint* zalt;

  int* xalt_ovrf;

  int* yalt_ovrf;

  int* zalt_ovrf;

  llint* vxalt;

  llint* vyalt;

  llint* vzalt;

  int* vxalt_ovrf;

  int* vyalt_ovrf;

  int* vzalt_ovrf;

  llint* fxalt;

  llint* fyalt;

  llint* fzalt;

  int* fxalt_ovrf;

  int* fyalt_ovrf;

  int* fzalt_ovrf;

};


struct PsSynthesisReader {


  PsSynthesisReader(int system_count_in, int unique_topology_count_in, UnitCellType unit_cell_in,

                    const int* atom_starts_in, const int* atom_counts_in,

                    const int* common_ag_list_in, const int* common_ag_bounds_in,

                    const int* unique_ag_idx_in, const int* replica_idx_in, float gpos_scale_in,

                    float vel_scale_in, float frc_scale_in, int gpos_bits_in, int vel_bits_in,

                    int frc_bits_in, const llint* boxvecs_in, const int* boxvec_ovrf_in,

                    const double* umat_in, const double* invu_in, const double* boxdims_in,

                    const llint* alt_boxvecs_in, const int* alt_boxvec_ovrf_in,

                    const double* umat_alt_in, const double* invu_alt_in,

                    const double* alt_boxdims_in, const llint* xcrd_in, const llint* ycrd_in,

                    const llint* zcrd_in, const int* xcrd_ovrf_in, const int* ycrd_ovrf_in,

                    const int* zcrd_ovrf_in, const llint* xvel_in, const llint* yvel_in,

                    const llint* zvel_in, const int* xvel_ovrf_in, const int* yvel_ovrf_in,

                    const int* zvel_ovrf_in, const llint* xfrc_in, const llint* yfrc_in,

                    const llint* zfrc_in, const int* xfrc_ovrf_in, const int* yfrc_ovrf_in,

                    const int* zfrc_ovrf_in, const llint* xalt_in, const llint* yalt_in,

                    const llint* zalt_in, const int* xalt_ovrf_in, const int* yalt_ovrf_in,

                    const int* zalt_ovrf_in, const llint* vxalt_in, const llint* vyalt_in,

                    const llint* vzalt_in, const int* vxalt_ovrf_in, const int* vyalt_ovrf_in,

                    const int* vzalt_ovrf_in, const llint* fxalt_in, const llint* fyalt_in,

                    const llint* fzalt_in, const int* fxalt_ovrf_in, const int* fyalt_ovrf_in,

                    const int* fzalt_ovrf_in);


  PsSynthesisReader(const PsSynthesisWriter *psyw);


  PsSynthesisReader(const PsSynthesisWriter &psyw);


  PsSynthesisReader(const PsSynthesisReader &original) = default;

  PsSynthesisReader(PsSynthesisReader &&other) = default;


  // System sizing information

  const int system_count;

  const int unique_topology_count;

  const UnitCellType unit_cell;

  const int* atom_starts;

  const int* atom_counts;

  const int* common_ag_list;

  const int* common_ag_bounds;

  const int* unique_ag_idx;

  const int* replica_idx;


  // Scaling factors: the PhaseSpaceSynthesis permits a customizable discretization of fixed-point

  // arithmetic.

  const float gpos_scale;

  const float vel_scale;

  const float frc_scale;

  const float inv_gpos_scale;

  const float inv_vel_scale;

  const float inv_frc_scale;

  const int gpos_bits;

  const int vel_bits;

  const int frc_bits;


  // Pointers to the transformations and box vectors are likewise const--once created, this

  // object is valid for a system held in constant volume.

  const llint* boxvecs;

  const int* boxvec_ovrf;

  const double* umat;

  const double* invu;

  const double* boxdims;

  const llint* alt_boxvecs;

  const int* alt_boxvec_ovrf;

  const double* umat_alt;

  const double* invu_alt;

  const double* alt_boxdims;


  // Pointers to the coordinate, velocity, and force data--these are mutable for accumulating

  // forces and letting a trajectory evolve.

  const llint* xcrd;

  const llint* ycrd;

  const llint* zcrd;

  const int* xcrd_ovrf;

  const int* ycrd_ovrf;

  const int* zcrd_ovrf;

  const llint* xvel;

  const llint* yvel;

  const llint* zvel;

  const int* xvel_ovrf;

  const int* yvel_ovrf;

  const int* zvel_ovrf;

  const llint* xfrc;

  const llint* yfrc;

  const llint* zfrc;

  const int* xfrc_ovrf;

  const int* yfrc_ovrf;

  const int* zfrc_ovrf;

  const llint* xalt;

  const llint* yalt;

  const llint* zalt;

  const int* xalt_ovrf;

  const int* yalt_ovrf;

  const int* zalt_ovrf;

  const llint* vxalt;

  const llint* vyalt;

  const llint* vzalt;

  const int* vxalt_ovrf;

  const int* vyalt_ovrf;

  const int* vzalt_ovrf;

  const llint* fxalt;

  const llint* fyalt;

  const llint* fzalt;

  const int* fxalt_ovrf;

  const int* fyalt_ovrf;

  const int* fzalt_ovrf;

};


class PhaseSpaceSynthesis {

public:


  PhaseSpaceSynthesis(const std::vector<PhaseSpace> &ps_list,

                      const std::vector<AtomGraph*> &ag_list,

                      int globalpos_scale_bits_in = default_globalpos_scale_bits,

                      int localpos_scale_bits_in = default_localpos_scale_bits,

                      int velocity_scale_bits_in = default_velocity_scale_bits,

                      int force_scale_bits_in = default_force_scale_bits,

                      HybridFormat format_in = default_hpc_format,

                      const GpuDetails &gpu = null_gpu);


  PhaseSpaceSynthesis(const std::vector<PhaseSpace> &ps_list,

                      const std::vector<AtomGraph*> &ag_list,

                      const std::vector<int> &index_key,

                      int globalpos_scale_bits_in = default_globalpos_scale_bits,

                      int localpos_scale_bits_in = default_localpos_scale_bits,

                      int velocity_scale_bits_in = default_velocity_scale_bits,

                      int force_scale_bits_in = default_force_scale_bits,

                      HybridFormat format_in = default_hpc_format,

                      const GpuDetails &gpu = null_gpu);


  PhaseSpaceSynthesis(const std::vector<PhaseSpace> &ps_list, const std::vector<int> &ps_index_key,

                      const std::vector<AtomGraph*> &ag_list, const std::vector<int> &ag_index_key,

                      int globalpos_scale_bits_in = default_globalpos_scale_bits,

                      int localpos_scale_bits_in = default_localpos_scale_bits,

                      int velocity_scale_bits_in = default_velocity_scale_bits,

                      int force_scale_bits_in = default_force_scale_bits,

                      HybridFormat format_in = default_hpc_format,

                      const GpuDetails &gpu = null_gpu);


  PhaseSpaceSynthesis(const PhaseSpaceSynthesis &original);

  PhaseSpaceSynthesis(const PhaseSpaceSynthesis &original, HybridFormat format_in);

  PhaseSpaceSynthesis(PhaseSpaceSynthesis &&original);


  PhaseSpaceSynthesis& operator=(const PhaseSpaceSynthesis &other);

  PhaseSpaceSynthesis& operator=(PhaseSpaceSynthesis &&other);


  HybridFormat getFormat() const;


  int getSystemCount() const;


  int getUniqueTopologyCount() const;


  UnitCellType getUnitCellType() const;


  CoordinateCycle getCyclePosition() const;


  int getGlobalPositionBits() const;


  int getLocalPositionBits() const;


  int getVelocityBits() const;


  int getForceAccumulationBits() const;


  float getForceScalingFactor() const;


  float getInverseForceScalingFactor() const;


  const AtomGraph* getSystemTopologyPointer(int system_index) const;

  const std::vector<AtomGraph*>& getSystemTopologyPointer() const;


  const std::vector<AtomGraph*>& getUniqueTopologies() const;


  int getAtomOffset(int system_index) const;


  int getAtomCount(int system_index) const;


  int getPaddedAtomCount() const;


  int getUniqueTopologyIndex(int system_index) const;


  std::vector<int> getUniqueTopologyIndices() const;


  std::vector<int> getUniqueTopologyExampleIndices() const;


  int getTopologyInstanceCount(int topology_index) const;


  std::vector<int> getSystemIndicesByTopology(int topology_index) const;


  const Hybrid<llint>* getCoordinateHandle(CartesianDimension dim, TrajectoryKind kind,

                                           CoordinateCycle orientation) const;


  const Hybrid<llint>* getCoordinateHandle(CartesianDimension dim,

                                           TrajectoryKind kind = TrajectoryKind::POSITIONS) const;


  Hybrid<llint>* getCoordinateHandle(CartesianDimension dim, TrajectoryKind kind,

                                     CoordinateCycle orientation);


  Hybrid<llint>* getCoordinateHandle(CartesianDimension dim,

                                     TrajectoryKind kind = TrajectoryKind::POSITIONS);


  const Hybrid<int>* getCoordinateOverflowHandle(CartesianDimension dim, TrajectoryKind kind,

                                                CoordinateCycle orientation) const;


  const Hybrid<int>*

  getCoordinateOverflowHandle(CartesianDimension dim,

                              TrajectoryKind kind = TrajectoryKind::POSITIONS) const;


  Hybrid<int>* getCoordinateOverflowHandle(CartesianDimension dim, TrajectoryKind kind,

                                           CoordinateCycle orientation);


  Hybrid<int>* getCoordinateOverflowHandle(CartesianDimension dim,

                                           TrajectoryKind kind = TrajectoryKind::POSITIONS);


  const Hybrid<double>* getBoxTransformsHandle(CoordinateCycle orientation) const;

  const Hybrid<double>* getBoxTransformsHandle() const;

  Hybrid<double>* getBoxTransformsHandle(CoordinateCycle orientation);

  Hybrid<double>* getBoxTransformsHandle();


  const Hybrid<double>* getInverseTransformsHandle(CoordinateCycle orientation) const;

  const Hybrid<double>* getInverseTransformsHandle() const;

  Hybrid<double>* getInverseTransformsHandle(CoordinateCycle orientation);

  Hybrid<double>* getInverseTransformsHandle();


  const Hybrid<double>* getBoxDimensionsHandle(CoordinateCycle orientation) const;

  const Hybrid<double>* getBoxDimensionsHandle() const;

  Hybrid<double>* getBoxDimensionsHandle(CoordinateCycle orientation);

  Hybrid<double>* getBoxDimensionsHandle();


  const Hybrid<llint>* getBoxVectorsHandle(CoordinateCycle orientation) const;

  const Hybrid<llint>* getBoxVectorsHandle() const;

  Hybrid<llint>* getBoxVectorsHandle(CoordinateCycle orientation);

  Hybrid<llint>* getBoxVectorsHandle();


  const Hybrid<int>* getBoxVectorsOverflowHandle(CoordinateCycle orientation) const;

  const Hybrid<int>* getBoxVectorsOverflowHandle() const;

  Hybrid<int>* getBoxVectorsOverflowHandle(CoordinateCycle orientation);

  Hybrid<int>* getBoxVectorsOverflowHandle();


  const PhaseSpaceSynthesis* getSelfPointer() const;


  const PsSynthesisReader data(HybridTargetLevel tier = HybridTargetLevel::HOST) const;

  const PsSynthesisReader data(CoordinateCycle orientation,

                               HybridTargetLevel tier = HybridTargetLevel::HOST) const;

  PsSynthesisWriter data(HybridTargetLevel tier = HybridTargetLevel::HOST);

  PsSynthesisWriter data(CoordinateCycle orientation,

                         HybridTargetLevel tier = HybridTargetLevel::HOST);


  const PsSynthesisBorders borders(CoordinateCycle orientation,

                                   HybridTargetLevel tier = HybridTargetLevel::HOST) const;

  const PsSynthesisBorders borders(HybridTargetLevel tier = HybridTargetLevel::HOST) const;


#ifdef STORMM_USE_HPC

  const PsSynthesisReader deviceViewToHostData(CoordinateCycle orientation) const;

  const PsSynthesisReader deviceViewToHostData() const;

  PsSynthesisWriter deviceViewToHostData(CoordinateCycle orientation);

  PsSynthesisWriter deviceViewToHostData();


  void upload();

  void upload(TrajectoryKind kind);

  void upload(TrajectoryKind kind, int system_index, const GpuDetails &gpu);

  void upload(TrajectoryKind kind, int system_lower_bound, int system_upper_bound,

              const GpuDetails &gpu);


  void download();

  void download(TrajectoryKind kind);

  void download(TrajectoryKind kind, int system_index, const GpuDetails &gpu);

  void download(TrajectoryKind kind, int system_lower_bound, int system_upper_bound,

                const GpuDetails &gpu);

#endif


  void extractSystem(PhaseSpace *ps, int index,

                     HybridTargetLevel origin = HybridTargetLevel::HOST,

                     HybridTargetLevel destination = HybridTargetLevel::HOST,

                     const GpuDetails &gpu = null_gpu) const;


  PhaseSpace exportSystem(int index, HybridTargetLevel tier = HybridTargetLevel::HOST) const;


  CoordinateFrame exportCoordinates(int index, CoordinateCycle orientation,

                                    HybridFormat format_out,

                                    TrajectoryKind trajkind = TrajectoryKind::POSITIONS,

                                    HybridTargetLevel tier = HybridTargetLevel::HOST) const;


  CoordinateFrame exportCoordinates(int index, CoordinateCycle orientation,

                                    TrajectoryKind trajkind = TrajectoryKind::POSITIONS,

                                    HybridTargetLevel tier = HybridTargetLevel::HOST) const;


  CoordinateFrame exportCoordinates(int index, HybridFormat format_out,

                                    TrajectoryKind trajkind = TrajectoryKind::POSITIONS,

                                    HybridTargetLevel tier = HybridTargetLevel::HOST) const;


  CoordinateFrame exportCoordinates(int index, TrajectoryKind trajkind = TrajectoryKind::POSITIONS,

                                    HybridTargetLevel tier = HybridTargetLevel::HOST) const;


  std::vector<double>

  getInterlacedCoordinates(int index, CoordinateCycle orientation,

                           TrajectoryKind trajkind = TrajectoryKind::POSITIONS,

                           HybridTargetLevel tier = HybridTargetLevel::HOST) const;


  std::vector<double>

  getInterlacedCoordinates(int index, TrajectoryKind trajkind = TrajectoryKind::POSITIONS,

                           HybridTargetLevel tier = HybridTargetLevel::HOST) const;


  void updateCyclePosition();

  void updateCyclePosition(CoordinateCycle time_point);


#ifdef STORMM_USE_HPC

  void initializeForces(CoordinateCycle orientation, const GpuDetails &gpu = null_gpu,

                        HybridTargetLevel tier = HybridTargetLevel::HOST, int index = -1);

  void initializeForces(const GpuDetails &gpu = null_gpu,

                        HybridTargetLevel tier = HybridTargetLevel::HOST, int index = -1);

#else

  void initializeForces(CoordinateCycle orientation, int index = -1);

  void initializeForces(int index = -1);

#endif


#ifdef STORMM_USE_HPC

  void primeConjugateGradientCalculation(const GpuDetails &gpu,

                                         HybridTargetLevel tier = HybridTargetLevel::HOST);

#else

  void primeConjugateGradientCalculation();

#endif


  void printTrajectory(const std::vector<int> &system_indices, const std::string &file_name,

                       double current_time, CoordinateFileKind output_kind,

                       PrintSituation expectation) const;


  void importSystem(const PhaseSpaceReader &psr, int system_index, CoordinateCycle orientation,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  void importSystem(const PhaseSpaceReader &psr, int system_index,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  void importSystem(const PhaseSpaceWriter &psw, int system_index, CoordinateCycle orientation,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  void importSystem(const PhaseSpaceWriter &psw, int system_index,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  void importSystem(const PhaseSpace &ps, int system_index, CoordinateCycle orientation,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  void importSystem(const PhaseSpace &ps, int system_index,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  void importSystem(const CoordinateFrameReader &cfr, int system_index,

                    CoordinateCycle orientation, TrajectoryKind kind = TrajectoryKind::POSITIONS,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  void importSystem(const CoordinateFrameReader &cfr, int system_index,

                    TrajectoryKind kind = TrajectoryKind::POSITIONS,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  void importSystem(const CoordinateFrameWriter &cfw, int system_index,

                    CoordinateCycle orientation, TrajectoryKind kind = TrajectoryKind::POSITIONS,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  void importSystem(const CoordinateFrameWriter &cfw, int system_index,

                    TrajectoryKind kind = TrajectoryKind::POSITIONS,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  void importSystem(const CoordinateFrame &cf, int system_index, CoordinateCycle orientation,

                    TrajectoryKind kind = TrajectoryKind::POSITIONS,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  void importSystem(const CoordinateFrame &cf, int system_index,

                    TrajectoryKind kind = TrajectoryKind::POSITIONS,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  template <typename T>

  void importSystem(const T* x_import, const T* y_import, const T* z_import,

                    const double* box_xform_in, const double* inverse_xform_in,

                    const double* box_dimensions_in, int system_index,

                    CoordinateCycle orientation, double inverse_scaling_factor = 1.0,

                    TrajectoryKind kind = TrajectoryKind::POSITIONS,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  template <typename T>

  void importSystem(const CoordinateSeriesReader<T> &csr, int frame_index, int system_index,

              CoordinateCycle orientation, TrajectoryKind kind = TrajectoryKind::POSITIONS,

              HybridTargetLevel tier = HybridTargetLevel::HOST);


  template <typename T>

  void importSystem(const CoordinateSeriesReader<T> &csr, int frame_index, int system_index,

                    TrajectoryKind kind = TrajectoryKind::POSITIONS,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  template <typename T>

  void importSystem(const CoordinateSeriesWriter<T> &csw, int frame_index, int system_index,

                    CoordinateCycle orientation, TrajectoryKind kind = TrajectoryKind::POSITIONS,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  template <typename T>

  void importSystem(const CoordinateSeriesWriter<T> &csw, int frame_index, int system_index,

                    TrajectoryKind kind = TrajectoryKind::POSITIONS,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  template <typename T>

  void importSystem(const CoordinateSeries<T> &cs, int frame_index, int system_index,

                    CoordinateCycle orientation, TrajectoryKind kind = TrajectoryKind::POSITIONS,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


  template <typename T>

  void importSystem(const CoordinateSeries<T> &cs, int frame_index, int system_index,

                    TrajectoryKind kind = TrajectoryKind::POSITIONS,

                    HybridTargetLevel tier = HybridTargetLevel::HOST);


private:

  HybridFormat format;

  int system_count;

  int unique_topology_count;

  UnitCellType unit_cell;

  CoordinateCycle cycle_position;


  // Scaling constants for fixed-precision coordinates (position, velocity) and also forces

  // in this PhaseSpaceSynthesis apply identically to all systems

  double globalpos_scale;

  double localpos_scale;

  double velocity_scale;

  double force_scale;

  double inverse_globalpos_scale;

  double inverse_localpos_scale;

  double inverse_velocity_scale;

  double inverse_force_scale;

  int globalpos_scale_bits;

  int localpos_scale_bits;

  int velocity_scale_bits;

  int force_scale_bits;


  Hybrid<int> atom_starts;


  Hybrid<int> atom_counts;


  Hybrid<int> shared_topology_instances;


  Hybrid<int> shared_topology_instance_bounds;


  Hybrid<int> unique_topology_reference;


  Hybrid<int> shared_topology_instance_index;


  // These variables are POINTER-kind Hybrid objects targeting the llint_data and int_data arrays

  Hybrid<llint> x_coordinates;

  Hybrid<llint> y_coordinates;

  Hybrid<llint> z_coordinates;

  Hybrid<int> x_coordinate_overflow;

  Hybrid<int> y_coordinate_overflow;

  Hybrid<int> z_coordinate_overflow;

  Hybrid<llint> x_alt_coordinates;

  Hybrid<llint> y_alt_coordinates;

  Hybrid<llint> z_alt_coordinates;

  Hybrid<int> x_alt_coord_overflow;

  Hybrid<int> y_alt_coord_overflow;

  Hybrid<int> z_alt_coord_overflow;

  Hybrid<llint> x_velocities;

  Hybrid<llint> y_velocities;

  Hybrid<llint> z_velocities;

  Hybrid<int> x_velocity_overflow;

  Hybrid<int> y_velocity_overflow;

  Hybrid<int> z_velocity_overflow;

  Hybrid<llint> x_alt_velocities;

  Hybrid<llint> y_alt_velocities;

  Hybrid<llint> z_alt_velocities;

  Hybrid<int> x_alt_velocity_overflow;

  Hybrid<int> y_alt_velocity_overflow;

  Hybrid<int> z_alt_velocity_overflow;

  Hybrid<llint> x_forces;

  Hybrid<llint> y_forces;

  Hybrid<llint> z_forces;

  Hybrid<int> x_force_overflow;

  Hybrid<int> y_force_overflow;

  Hybrid<int> z_force_overflow;

  Hybrid<llint> x_alt_forces;

  Hybrid<llint> y_alt_forces;

  Hybrid<llint> z_alt_forces;

  Hybrid<int> x_alt_force_overflow;

  Hybrid<int> y_alt_force_overflow;

  Hybrid<int> z_alt_force_overflow;

  Hybrid<llint> box_vectors;

  Hybrid<int> box_vector_overflow;

  Hybrid<llint> alt_box_vectors;

  Hybrid<int> alt_box_vector_overflow;


  // The following are POINTER-kind Hybrid objects targeting the floating point data arrays

  Hybrid<double> box_space_transforms;

  Hybrid<double> inverse_transforms;

  Hybrid<double> box_dimensions;

  Hybrid<double> alt_box_transforms;

  Hybrid<double> alt_inverse_transforms;

  Hybrid<double> alt_box_dimensions;


  // Data arrays

  Hybrid<int> int_data;

  Hybrid<llint> llint_data;

  Hybrid<double> double_data;


  std::vector<AtomGraph*> topologies;


  std::vector<AtomGraph*> unique_topologies;


  void allocate(size_t atom_stride);


  void loadHostCoordinates(const PhaseSpace &input_ps, int sysno);


#ifdef STORMM_USE_HPC

  void loadXPciCoordinates(PsSynthesisWriter *poly_psw, int sys_idx, const PhaseSpaceReader &psr,

                           const GpuDetails &gpu);


  void extractSystem(PhaseSpaceWriter *psw, int index, const GpuDetails &gpu,

                     HybridTargetLevel origin = HybridTargetLevel::DEVICE) const;

#endif


  void validateSystemIndex(int index, const char* caller = nullptr) const;

};


static const size_t phasespace_synthesis_type_index =

  std::type_index(typeid(PhaseSpaceSynthesis)).hash_code();


} // namespace trajectory

} // namespace stormm


#include "phasespace_synthesis.tpp"


// As with common types and STORMM vector types, define the type indices for general use in the

// STORMM namespace.

namespace stormm {

using synthesis::phasespace_synthesis_type_index;

} // namespace stormm


#endif

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::chemistry::PhaseSpaceSynthesis::getBoxVectorsOverflowHandle
const Hybrid< int > * getBoxVectorsOverflowHandle(CoordinateCycle orientation) const
Get a pointer to the box space transforms. Overloading and description of the optional input paramete...
Definition phasespace_synthesis.cpp:1827

stormm::chemistry::PhaseSpaceSynthesis::getBoxTransformsHandle
const Hybrid< double > * getBoxTransformsHandle(CoordinateCycle orientation) const
Get a pointer to the box space transforms. Overloading and description of the optional input paramete...
Definition phasespace_synthesis.cpp:1694

stormm::chemistry::PhaseSpaceSynthesis::getBoxVectorsHandle
const Hybrid< llint > * getBoxVectorsHandle(CoordinateCycle orientation) const
Get a pointer to the box space transforms. Overloading and description of the optional input paramete...
Definition phasespace_synthesis.cpp:1794

stormm::chemistry::PhaseSpaceSynthesis::getInverseTransformsHandle
const Hybrid< double > * getInverseTransformsHandle(CoordinateCycle orientation) const
Get a pointer to the inverse transform that takes coordinates back into real space....
Definition phasespace_synthesis.cpp:1727

stormm::chemistry::PhaseSpaceSynthesis::PhaseSpaceSynthesis
PhaseSpaceSynthesis(const std::vector< PhaseSpace > &ps_list, const std::vector< AtomGraph * > &ag_list, int globalpos_scale_bits_in=default_globalpos_scale_bits, int localpos_scale_bits_in=default_localpos_scale_bits, int velocity_scale_bits_in=default_velocity_scale_bits, int force_scale_bits_in=default_force_scale_bits, HybridFormat format_in=default_hpc_format, const GpuDetails &gpu=null_gpu)
The constructor works from a series PhaseSpace object, importing The LabFrame is not a POINTER-kind o...
Definition phasespace_synthesis.cpp:249

stormm::chemistry::PhaseSpaceSynthesis::getBoxDimensionsHandle
const Hybrid< double > * getBoxDimensionsHandle(CoordinateCycle orientation) const
Get a pointer to the transform that takes coordinates back into real space. Overloading and descripti...
Definition phasespace_synthesis.cpp:1761

stormm::chemistry::PhaseSpaceSynthesis::getSystemTopologyPointer
const AtomGraph * getSystemTopologyPointer(int system_index) const
Get the topology pointer for a particular system within the synthesis.
Definition phasespace_synthesis.cpp:1212

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

stormm::synthesis::PhaseSpaceSynthesis::importSystem
void importSystem(const PhaseSpaceReader &psr, int system_index, CoordinateCycle orientation, HybridTargetLevel tier=HybridTargetLevel::HOST)
Import a system from one of the other coordinate objects, or from a series of C-style arrays with tru...
Definition phasespace_synthesis.cpp:3410

stormm::synthesis::PhaseSpaceSynthesis::exportSystem
PhaseSpace exportSystem(int index, HybridTargetLevel tier=HybridTargetLevel::HOST) const
Export a system's coordinates, velocities, and forces to a PhaseSpace object.
Definition phasespace_synthesis.cpp:2472

stormm::synthesis::PhaseSpaceSynthesis::getForceScalingFactor
float getForceScalingFactor() const
Get the force scaling factor used in fixed-precision accumulation.
Definition phasespace_synthesis.cpp:1202

stormm::synthesis::PhaseSpaceSynthesis::exportCoordinates
CoordinateFrame exportCoordinates(int index, CoordinateCycle orientation, HybridFormat format_out, TrajectoryKind trajkind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST) const
Export a system's coordinates, velocities, or forces to a compact CoordinateFrame object.
Definition phasespace_synthesis.cpp:2483

stormm::synthesis::PhaseSpaceSynthesis::getAtomCount
int getAtomCount(int system_index) const
Get the number of atoms in one of the systems, using its index.
Definition phasespace_synthesis.cpp:1233

stormm::synthesis::PhaseSpaceSynthesis::primeConjugateGradientCalculation
void primeConjugateGradientCalculation()
Set the alternate positions to the current forces, and initialize velocities to zero,...
Definition phasespace_synthesis.cpp:3139

stormm::synthesis::PhaseSpaceSynthesis::operator=
PhaseSpaceSynthesis & operator=(const PhaseSpaceSynthesis &other)
Copy and move assignment operators must also be explicitly written out.
Definition phasespace_synthesis.cpp:976

stormm::synthesis::PhaseSpaceSynthesis::getUniqueTopologyIndices
std::vector< int > getUniqueTopologyIndices() const
Get the unique topology index of all systems in the synthesis.
Definition phasespace_synthesis.cpp:1250

stormm::synthesis::PhaseSpaceSynthesis::getForceAccumulationBits
int getForceAccumulationBits() const
Get the force accumulation bit count.
Definition phasespace_synthesis.cpp:1197

stormm::synthesis::PhaseSpaceSynthesis::getInverseForceScalingFactor
float getInverseForceScalingFactor() const
Get the inverse of the force scaling factor used in fixed-precision accumulation.
Definition phasespace_synthesis.cpp:1207

stormm::synthesis::PhaseSpaceSynthesis::getFormat
HybridFormat getFormat() const
Get the memory format of the object.
Definition phasespace_synthesis.cpp:1157

stormm::synthesis::PhaseSpaceSynthesis::getCyclePosition
CoordinateCycle getCyclePosition() const
Get the current position in the coordinate cycle.
Definition phasespace_synthesis.cpp:1177

stormm::synthesis::PhaseSpaceSynthesis::getUniqueTopologies
const std::vector< AtomGraph * > & getUniqueTopologies() const
Get a list of unique topology pointers from this coordinate synthesis, const-casted for accessibility...
Definition phasespace_synthesis.cpp:1223

stormm::synthesis::PhaseSpaceSynthesis::getSystemCount
int getSystemCount() const
Get the number of systems in the object.
Definition phasespace_synthesis.cpp:1162

stormm::synthesis::PhaseSpaceSynthesis::getCoordinateHandle
const Hybrid< llint > * getCoordinateHandle(CartesianDimension dim, TrajectoryKind kind, CoordinateCycle orientation) const
Get a pointer to one of the Hybrid objects holding system coordinates. If the synthesis uses extended...
Definition phasespace_synthesis.cpp:1294

stormm::synthesis::PhaseSpaceSynthesis::getGlobalPositionBits
int getGlobalPositionBits() const
Get the global position scaling bit count.
Definition phasespace_synthesis.cpp:1182

stormm::synthesis::PhaseSpaceSynthesis::getUnitCellType
UnitCellType getUnitCellType() const
Get the unit cell type.
Definition phasespace_synthesis.cpp:1172

stormm::synthesis::PhaseSpaceSynthesis::borders
const PsSynthesisBorders borders(CoordinateCycle orientation, HybridTargetLevel tier=HybridTargetLevel::HOST) const
Get the read-only summary of the system sizes. The data is never needed in as a collection of device ...
Definition phasespace_synthesis.cpp:2022

stormm::synthesis::PhaseSpaceSynthesis::getSystemIndicesByTopology
std::vector< int > getSystemIndicesByTopology(int topology_index) const
Get a list of system indices which all reference the same unique topology (the unique topology index ...
Definition phasespace_synthesis.cpp:1276

stormm::synthesis::PhaseSpaceSynthesis::getAtomOffset
int getAtomOffset(int system_index) const
Get the starting index of atoms for one of the systems, using its index.
Definition phasespace_synthesis.cpp:1228

stormm::synthesis::PhaseSpaceSynthesis::getPaddedAtomCount
int getPaddedAtomCount() const
Get the total number of atoms across all systems in the synthesis, including padding between systems ...
Definition phasespace_synthesis.cpp:1238

stormm::synthesis::PhaseSpaceSynthesis::updateCyclePosition
void updateCyclePosition()
Modify the object's cycle position, as in the course of propagating dynamics.
Definition phasespace_synthesis.cpp:3020

stormm::synthesis::PhaseSpaceSynthesis::getInterlacedCoordinates
std::vector< double > getInterlacedCoordinates(int index, CoordinateCycle orientation, TrajectoryKind trajkind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST) const
Get the interlaced X, Y, and Z coordinates of one system in particular. The result is comparable to t...
Definition phasespace_synthesis.cpp:2786

stormm::synthesis::PhaseSpaceSynthesis::getTopologyInstanceCount
int getTopologyInstanceCount(int topology_index) const
Get the number of systems that make use of a particular topology.
Definition phasespace_synthesis.cpp:1265

stormm::synthesis::PhaseSpaceSynthesis::data
const PsSynthesisReader data(HybridTargetLevel tier=HybridTargetLevel::HOST) const
Get the reader or writer, as appropriate based on the const-ness of this object.
Definition phasespace_synthesis.cpp:1864

stormm::synthesis::PhaseSpaceSynthesis::initializeForces
void initializeForces(CoordinateCycle orientation, int index=-1)
Initialize the forces within a PhaseSpaceSynthesis object. This is the analog of the eponymous functi...
Definition phasespace_synthesis.cpp:3042

stormm::synthesis::PhaseSpaceSynthesis::getCoordinateOverflowHandle
const Hybrid< int > * getCoordinateOverflowHandle(CartesianDimension dim, TrajectoryKind kind, CoordinateCycle orientation) const
Get a pointer to one of the Hybrid objects holding system coordinates. Overloading and descriptions o...
Definition phasespace_synthesis.cpp:1494

stormm::synthesis::PhaseSpaceSynthesis::PhaseSpaceSynthesis
PhaseSpaceSynthesis(const std::vector< PhaseSpace > &ps_list, const std::vector< AtomGraph * > &ag_list, int globalpos_scale_bits_in=default_globalpos_scale_bits, int localpos_scale_bits_in=default_localpos_scale_bits, int velocity_scale_bits_in=default_velocity_scale_bits, int force_scale_bits_in=default_force_scale_bits, HybridFormat format_in=default_hpc_format, const GpuDetails &gpu=null_gpu)
The constructor works from a series PhaseSpace object, importing The LabFrame is not a POINTER-kind o...
Definition phasespace_synthesis.cpp:249

stormm::synthesis::PhaseSpaceSynthesis::getUniqueTopologyExampleIndices
std::vector< int > getUniqueTopologyExampleIndices() const
Get a list of system indices from within this coordinate synthesis, providing examples of each unique...
Definition phasespace_synthesis.cpp:1255

stormm::synthesis::PhaseSpaceSynthesis::getUniqueTopologyIndex
int getUniqueTopologyIndex(int system_index) const
Get the index of the unique topology used by a particular system in the synthesis.
Definition phasespace_synthesis.cpp:1245

stormm::synthesis::PhaseSpaceSynthesis::getVelocityBits
int getVelocityBits() const
Get the velocity scaling bit count.
Definition phasespace_synthesis.cpp:1192

stormm::synthesis::PhaseSpaceSynthesis::extractSystem
void extractSystem(PhaseSpace *ps, int index, HybridTargetLevel origin=HybridTargetLevel::HOST, HybridTargetLevel destination=HybridTargetLevel::HOST, const GpuDetails &gpu=null_gpu) const
Extract the phase space (plus forces) of a specific system within the synthesis.
Definition phasespace_synthesis.cpp:2388

stormm::synthesis::PhaseSpaceSynthesis::getLocalPositionBits
int getLocalPositionBits() const
Get the local position scaling bit count.
Definition phasespace_synthesis.cpp:1187

stormm::synthesis::PhaseSpaceSynthesis::printTrajectory
void printTrajectory(const std::vector< int > &system_indices, const std::string &file_name, double current_time, CoordinateFileKind output_kind, PrintSituation expectation) const
Print a list of structures to a trajectory file. Download will be performed when calling this functio...
Definition phasespace_synthesis.cpp:3201

stormm::synthesis::PhaseSpaceSynthesis::getSelfPointer
const PhaseSpaceSynthesis * getSelfPointer() const
Get a const pointer to the object itself.
Definition phasespace_synthesis.cpp:1859

stormm::synthesis::PhaseSpaceSynthesis::getUniqueTopologyCount
int getUniqueTopologyCount() const
Get the number of unique topologies in the object.
Definition phasespace_synthesis.cpp:1167

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::CoordinateFrame
Store the coordinates and box information for a frame, only. This abridged struct can serve when the ...
Definition coordinateframe.h:111

stormm::trajectory::CoordinateSeries
Store the coordinates and box information for a series of frames, in one of several levels of precisi...
Definition coordinate_series.h:137

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::chemistry::PsSynthesisReader::PsSynthesisReader
PsSynthesisReader(int system_count_in, int unique_topology_count_in, UnitCellType unit_cell_in, const int *atom_starts_in, const int *atom_counts_in, const int *common_ag_list_in, const int *common_ag_bounds_in, const int *unique_ag_idx_in, const int *replica_idx_in, float gpos_scale_in, float vel_scale_in, float frc_scale_in, int gpos_bits_in, int vel_bits_in, int frc_bits_in, const llint *boxvecs_in, const int *boxvec_ovrf_in, const double *umat_in, const double *invu_in, const double *boxdims_in, const llint *alt_boxvecs_in, const int *alt_boxvec_ovrf_in, const double *umat_alt_in, const double *invu_alt_in, const double *alt_boxdims_in, const llint *xcrd_in, const llint *ycrd_in, const llint *zcrd_in, const int *xcrd_ovrf_in, const int *ycrd_ovrf_in, const int *zcrd_ovrf_in, const llint *xvel_in, const llint *yvel_in, const llint *zvel_in, const int *xvel_ovrf_in, const int *yvel_ovrf_in, const int *zvel_ovrf_in, const llint *xfrc_in, const llint *yfrc_in, const llint *zfrc_in, const int *xfrc_ovrf_in, const int *yfrc_ovrf_in, const int *zfrc_ovrf_in, const llint *xalt_in, const llint *yalt_in, const llint *zalt_in, const int *xalt_ovrf_in, const int *yalt_ovrf_in, const int *zalt_ovrf_in, const llint *vxalt_in, const llint *vyalt_in, const llint *vzalt_in, const int *vxalt_ovrf_in, const int *vyalt_ovrf_in, const int *vzalt_ovrf_in, const llint *fxalt_in, const llint *fyalt_in, const llint *fzalt_in, const int *fxalt_ovrf_in, const int *fyalt_ovrf_in, const int *fzalt_ovrf_in)
The constructor can take lists of pointers and constants from the parent object (in this case,...
Definition phasespace_synthesis.cpp:107

stormm::energy::PsSynthesisBorders::PsSynthesisBorders
PsSynthesisBorders(int system_count_in, const int *atom_starts_in, const int *atom_counts_in, const double *umat_in, const double *invu_in)
The constructor accepts the total number of systems as well as pointers to the number of atoms and st...
Definition phasespace_synthesis.cpp:52

stormm::energy::PsSynthesisWriter::PsSynthesisWriter
PsSynthesisWriter(int system_count_in, int unique_topology_count_in, UnitCellType unit_cell_in, const int *atom_starts_in, const int *atom_counts_in, const int *common_ag_list_in, const int *common_ag_bounds_in, const int *unique_ag_idx_in, const int *replica_idx_in, float gpos_scale_in, float vel_scale_in, float frc_scale_in, int gpos_bits_in, int vel_bits_in, int frc_bits_in, llint *boxvecs_in, int *boxvec_ovrf_in, double *umat_in, double *invu_in, double *boxdims_in, llint *alt_boxvecs_in, int *alt_boxvec_ovrf_in, double *umat_alt_in, double *invu_alt_in, double *alt_boxdims_in, llint *xcrd_in, llint *ycrd_in, llint *zcrd_in, int *xcrd_ovrf_in, int *ycrd_ovrf_in, int *zcrd_ovrf_in, llint *xvel_in, llint *yvel_in, llint *zvel_in, int *xvel_ovrf_in, int *yvel_ovrf_in, int *zvel_ovrf_in, llint *xfrc_in, llint *yfrc_in, llint *zfrc_in, int *xfrc_ovrf_in, int *yfrc_ovrf_in, int *zfrc_ovrf_in, llint *xalt_in, llint *yalt_in, llint *zalt_in, int *xalt_ovrf_in, int *yalt_ovrf_in, int *zalt_ovrf_in, llint *vxalt_in, llint *vyalt_in, llint *vzalt_in, int *vxalt_ovrf_in, int *vyalt_ovrf_in, int *vzalt_ovrf_in, llint *fxalt_in, llint *fyalt_in, llint *fzalt_in, int *fxalt_ovrf_in, int *fyalt_ovrf_in, int *fzalt_ovrf_in)
Constructor takes a straight list of pointers and constants from the parent object (in this case,...
Definition phasespace_synthesis.cpp:60

stormm::synthesis::CoordinateFrameWriter
Collect C-style pointers for the elements of a writable CoordinateFrame object.
Definition coordinateframe.h:30

stormm::synthesis::CoordinateSeriesWriter
Collect C-style pointers and critical constants for a writeable CoordinateSeries object.
Definition coordinate_series.h:66

stormm::synthesis::PsSynthesisBorders::invu
const double * invu
Definition phasespace_synthesis.h:81

stormm::synthesis::PsSynthesisBorders::system_count
const int system_count
Definition phasespace_synthesis.h:75

stormm::synthesis::PsSynthesisBorders::umat
const double * umat
Definition phasespace_synthesis.h:79

stormm::synthesis::PsSynthesisBorders::PsSynthesisBorders
PsSynthesisBorders(const PsSynthesisBorders &original)=default
Copy and move constructors–as with any object containing const members, the move assignment operator ...

stormm::synthesis::PsSynthesisBorders::atom_counts
const int * atom_counts
Atom counts for each system.
Definition phasespace_synthesis.h:78

stormm::synthesis::PsSynthesisBorders::PsSynthesisBorders
PsSynthesisBorders(int system_count_in, const int *atom_starts_in, const int *atom_counts_in, const double *umat_in, const double *invu_in)
The constructor accepts the total number of systems as well as pointers to the number of atoms and st...
Definition phasespace_synthesis.cpp:52

stormm::synthesis::PsSynthesisBorders::atom_starts
const int * atom_starts
Starting indices for the atoms of each system.
Definition phasespace_synthesis.h:77

stormm::synthesis::PsSynthesisReader
The reader for a PhaseSpaceSynthesis object, containing all of the data relevant for propagating dyna...
Definition phasespace_synthesis.h:199

stormm::synthesis::PsSynthesisReader::yalt_ovrf
const int * yalt_ovrf
Overflow buffers for particles' alternate Cartesian Y locations.
Definition phasespace_synthesis.h:304

stormm::synthesis::PsSynthesisReader::vel_scale
const float vel_scale
Velocity coordinate scaling factor.
Definition phasespace_synthesis.h:258

stormm::synthesis::PsSynthesisReader::alt_boxvec_ovrf
const int * alt_boxvec_ovrf
Overflow arrays for the discretized box vectors.
Definition phasespace_synthesis.h:275

stormm::synthesis::PsSynthesisReader::replica_idx
const int * replica_idx
Definition phasespace_synthesis.h:252

stormm::synthesis::PsSynthesisReader::fyalt_ovrf
const int * fyalt_ovrf
Overflow buffers for particles' alternate Cartesian Y forces.
Definition phasespace_synthesis.h:316

stormm::synthesis::PsSynthesisReader::zfrc_ovrf
const int * zfrc_ovrf
Discretized Cartesian Z force overflow buffers.
Definition phasespace_synthesis.h:299

stormm::synthesis::PsSynthesisReader::frc_scale
const float frc_scale
Scaling factor for fixed-precision force accumulation.
Definition phasespace_synthesis.h:259

stormm::synthesis::PsSynthesisReader::gpos_scale
const float gpos_scale
Global position coordinate scaling factor.
Definition phasespace_synthesis.h:257

stormm::synthesis::PsSynthesisReader::zfrc
const llint * zfrc
Discretized Cartesian Z forces.
Definition phasespace_synthesis.h:296

stormm::synthesis::PsSynthesisReader::vyalt
const llint * vyalt
Alternate Cartesian Y velocities of particles.
Definition phasespace_synthesis.h:307

stormm::synthesis::PsSynthesisReader::fzalt
const llint * fzalt
Alternate Cartesian Z forces acting on all particles.
Definition phasespace_synthesis.h:314

stormm::synthesis::PsSynthesisReader::xvel
const llint * xvel
Cartesian X velocities.
Definition phasespace_synthesis.h:288

stormm::synthesis::PsSynthesisReader::fyalt
const llint * fyalt
Alternate Cartesian Y forces acting on all particles.
Definition phasespace_synthesis.h:313

stormm::synthesis::PsSynthesisReader::PsSynthesisReader
PsSynthesisReader(int system_count_in, int unique_topology_count_in, UnitCellType unit_cell_in, const int *atom_starts_in, const int *atom_counts_in, const int *common_ag_list_in, const int *common_ag_bounds_in, const int *unique_ag_idx_in, const int *replica_idx_in, float gpos_scale_in, float vel_scale_in, float frc_scale_in, int gpos_bits_in, int vel_bits_in, int frc_bits_in, const llint *boxvecs_in, const int *boxvec_ovrf_in, const double *umat_in, const double *invu_in, const double *boxdims_in, const llint *alt_boxvecs_in, const int *alt_boxvec_ovrf_in, const double *umat_alt_in, const double *invu_alt_in, const double *alt_boxdims_in, const llint *xcrd_in, const llint *ycrd_in, const llint *zcrd_in, const int *xcrd_ovrf_in, const int *ycrd_ovrf_in, const int *zcrd_ovrf_in, const llint *xvel_in, const llint *yvel_in, const llint *zvel_in, const int *xvel_ovrf_in, const int *yvel_ovrf_in, const int *zvel_ovrf_in, const llint *xfrc_in, const llint *yfrc_in, const llint *zfrc_in, const int *xfrc_ovrf_in, const int *yfrc_ovrf_in, const int *zfrc_ovrf_in, const llint *xalt_in, const llint *yalt_in, const llint *zalt_in, const int *xalt_ovrf_in, const int *yalt_ovrf_in, const int *zalt_ovrf_in, const llint *vxalt_in, const llint *vyalt_in, const llint *vzalt_in, const int *vxalt_ovrf_in, const int *vyalt_ovrf_in, const int *vzalt_ovrf_in, const llint *fxalt_in, const llint *fyalt_in, const llint *fzalt_in, const int *fxalt_ovrf_in, const int *fyalt_ovrf_in, const int *fzalt_ovrf_in)
The constructor can take lists of pointers and constants from the parent object (in this case,...
Definition phasespace_synthesis.cpp:107

stormm::synthesis::PsSynthesisReader::gpos_bits
const int gpos_bits
Global position coordinate bits after the decimal.
Definition phasespace_synthesis.h:263

stormm::synthesis::PsSynthesisReader::yfrc_ovrf
const int * yfrc_ovrf
Discretized Cartesian Y force overflow buffers.
Definition phasespace_synthesis.h:298

stormm::synthesis::PsSynthesisReader::umat_alt
const double * umat_alt
Box (fractional) space transformation matrices, one per warp.
Definition phasespace_synthesis.h:276

stormm::synthesis::PsSynthesisReader::vxalt_ovrf
const int * vxalt_ovrf
Overflow buffers for particles' alternate Cartesian X velocities.
Definition phasespace_synthesis.h:309

stormm::synthesis::PsSynthesisReader::fzalt_ovrf
const int * fzalt_ovrf
Overflow buffers for particles' alternate Cartesian Z forces.
Definition phasespace_synthesis.h:317

stormm::synthesis::PsSynthesisReader::boxvec_ovrf
const int * boxvec_ovrf
Overflow arrays for the discretized box vectors.
Definition phasespace_synthesis.h:270

stormm::synthesis::PsSynthesisReader::vyalt_ovrf
const int * vyalt_ovrf
Overflow buffers for particles' alternate Cartesian Y velocities.
Definition phasespace_synthesis.h:310

stormm::synthesis::PsSynthesisReader::invu
const double * invu
Inverse transformation matrices, one per warp.
Definition phasespace_synthesis.h:272

stormm::synthesis::PsSynthesisReader::xfrc_ovrf
const int * xfrc_ovrf
Discretized Cartesian X force overflow buffers.
Definition phasespace_synthesis.h:297

stormm::synthesis::PsSynthesisReader::xvel_ovrf
const int * xvel_ovrf
Cartesian X velocity overflow buffers.
Definition phasespace_synthesis.h:291

stormm::synthesis::PsSynthesisReader::yalt
const llint * yalt
Alternate Cartesian Y positions of particles.
Definition phasespace_synthesis.h:301

stormm::synthesis::PsSynthesisReader::xalt
const llint * xalt
Alternate Cartesian X positions of particles.
Definition phasespace_synthesis.h:300

stormm::synthesis::PsSynthesisReader::ycrd
const llint * ycrd
Non-wrapped Cartesian Y coordinates of all particles.
Definition phasespace_synthesis.h:283

stormm::synthesis::PsSynthesisReader::zalt
const llint * zalt
Alternate Cartesian Z positions of particles.
Definition phasespace_synthesis.h:302

stormm::synthesis::PsSynthesisReader::fxalt
const llint * fxalt
Alternate Cartesian X forces acting on all particles.
Definition phasespace_synthesis.h:312

stormm::synthesis::PsSynthesisReader::zvel_ovrf
const int * zvel_ovrf
Cartesian Z velocity overflow buffers.
Definition phasespace_synthesis.h:293

stormm::synthesis::PsSynthesisReader::xalt_ovrf
const int * xalt_ovrf
Overflow buffers for particles' alternate Cartesian X locations.
Definition phasespace_synthesis.h:303

stormm::synthesis::PsSynthesisReader::inv_gpos_scale
const float inv_gpos_scale
Inverse global coordinate scaling factor.
Definition phasespace_synthesis.h:260

stormm::synthesis::PsSynthesisReader::common_ag_list
const int * common_ag_list
Definition phasespace_synthesis.h:247

stormm::synthesis::PsSynthesisReader::frc_bits
const int frc_bits
Force component bits after the decimal.
Definition phasespace_synthesis.h:265

stormm::synthesis::PsSynthesisReader::unique_topology_count
const int unique_topology_count
The number of unique topologies.
Definition phasespace_synthesis.h:243

stormm::synthesis::PsSynthesisReader::ycrd_ovrf
const int * ycrd_ovrf
Non-wrapped Cartesian Y coordinate overflow buffers.
Definition phasespace_synthesis.h:286

stormm::synthesis::PsSynthesisReader::system_count
const int system_count
The number of independent systems.
Definition phasespace_synthesis.h:242

stormm::synthesis::PsSynthesisReader::xcrd
const llint * xcrd
Non-wrapped Cartesian X coordinates of all particles.
Definition phasespace_synthesis.h:282

stormm::synthesis::PsSynthesisReader::invu_alt
const double * invu_alt
Inverse transformation matrices, one per warp.
Definition phasespace_synthesis.h:277

stormm::synthesis::PsSynthesisReader::zcrd_ovrf
const int * zcrd_ovrf
Non-wrapped Cartesian Z coordinate overflow buffers.
Definition phasespace_synthesis.h:287

stormm::synthesis::PsSynthesisReader::inv_frc_scale
const float inv_frc_scale
Inverse force scaling factor.
Definition phasespace_synthesis.h:262

stormm::synthesis::PsSynthesisReader::yvel_ovrf
const int * yvel_ovrf
Cartesian Y velocity overflow buffers.
Definition phasespace_synthesis.h:292

stormm::synthesis::PsSynthesisReader::vzalt
const llint * vzalt
Alternate Cartesian Z velocities of particles.
Definition phasespace_synthesis.h:308

stormm::synthesis::PsSynthesisReader::common_ag_bounds
const int * common_ag_bounds
Bounds array for common_ag_list.
Definition phasespace_synthesis.h:249

stormm::synthesis::PsSynthesisReader::boxdims
const double * boxdims
Box dimensions (a, b, c, alpha, beta, gamma)
Definition phasespace_synthesis.h:273

stormm::synthesis::PsSynthesisReader::zvel
const llint * zvel
Cartesian Z velocities.
Definition phasespace_synthesis.h:290

stormm::synthesis::PsSynthesisReader::zcrd
const llint * zcrd
Non-wrapped Cartesian Z coordinates of all particles.
Definition phasespace_synthesis.h:284

stormm::synthesis::PsSynthesisReader::boxvecs
const llint * boxvecs
Discretized box vectors.
Definition phasespace_synthesis.h:269

stormm::synthesis::PsSynthesisReader::atom_starts
const int * atom_starts
Points at which each system starts in the atom list.
Definition phasespace_synthesis.h:245

stormm::synthesis::PsSynthesisReader::yfrc
const llint * yfrc
Discretized Cartesian Y forces.
Definition phasespace_synthesis.h:295

stormm::synthesis::PsSynthesisReader::unique_ag_idx
const int * unique_ag_idx
Definition phasespace_synthesis.h:250

stormm::synthesis::PsSynthesisReader::vzalt_ovrf
const int * vzalt_ovrf
Overflow buffers for particles' alternate Cartesian Z velocities.
Definition phasespace_synthesis.h:311

stormm::synthesis::PsSynthesisReader::xcrd_ovrf
const int * xcrd_ovrf
Non-wrapped Cartesian X coordinate overflow buffers.
Definition phasespace_synthesis.h:285

stormm::synthesis::PsSynthesisReader::alt_boxvecs
const llint * alt_boxvecs
Discretized box vectors.
Definition phasespace_synthesis.h:274

stormm::synthesis::PsSynthesisReader::zalt_ovrf
const int * zalt_ovrf
Overflow buffers for particles' alternate Cartesian Z locations.
Definition phasespace_synthesis.h:305

stormm::synthesis::PsSynthesisReader::umat
const double * umat
Box (fractional) space transformation matrices, one per warp.
Definition phasespace_synthesis.h:271

stormm::synthesis::PsSynthesisReader::inv_vel_scale
const float inv_vel_scale
Inverse velocity scaling factor.
Definition phasespace_synthesis.h:261

stormm::synthesis::PsSynthesisReader::alt_boxdims
const double * alt_boxdims
Box dimensions (a, b, c, alpha, beta, gamma)
Definition phasespace_synthesis.h:278

stormm::synthesis::PsSynthesisReader::vel_bits
const int vel_bits
Velocity coordinate bits after the decimal.
Definition phasespace_synthesis.h:264

stormm::synthesis::PsSynthesisReader::PsSynthesisReader
PsSynthesisReader(const PsSynthesisReader &original)=default
Copy and move constructors–as with any object containing const members, the move assignment operator ...

stormm::synthesis::PsSynthesisReader::xfrc
const llint * xfrc
Discretized Cartesian X forces.
Definition phasespace_synthesis.h:294

stormm::synthesis::PsSynthesisReader::yvel
const llint * yvel
Cartesian Y velocities.
Definition phasespace_synthesis.h:289

stormm::synthesis::PsSynthesisReader::atom_counts
const int * atom_counts
Atom counts for all systems.
Definition phasespace_synthesis.h:246

stormm::synthesis::PsSynthesisReader::vxalt
const llint * vxalt
Alternate Cartesian X velocities of particles.
Definition phasespace_synthesis.h:306

stormm::synthesis::PsSynthesisReader::fxalt_ovrf
const int * fxalt_ovrf
Overflow buffers for particles' alternate Cartesian X forces.
Definition phasespace_synthesis.h:315

stormm::synthesis::PsSynthesisReader::unit_cell
const UnitCellType unit_cell
Type of unit cells (or none) each system resides in.
Definition phasespace_synthesis.h:244

stormm::synthesis::PsSynthesisWriter::fzalt_ovrf
int * fzalt_ovrf
Overflow buffers for particles' alternate Cartesian Z force.
Definition phasespace_synthesis.h:194

stormm::synthesis::PsSynthesisWriter::fxalt
llint * fxalt
Alternate Cartesian X forces acting on particles.
Definition phasespace_synthesis.h:189

stormm::synthesis::PsSynthesisWriter::inv_vel_scale
const float inv_vel_scale
Inverse velocity scaling factor.
Definition phasespace_synthesis.h:139

stormm::synthesis::PsSynthesisWriter::vxalt
llint * vxalt
Alternate Cartesian X velocities of particles.
Definition phasespace_synthesis.h:183

stormm::synthesis::PsSynthesisWriter::umat
double * umat
Box (fractional) space transformation matrices, one per warp.
Definition phasespace_synthesis.h:148

stormm::synthesis::PsSynthesisWriter::xcrd
llint * xcrd
Non-wrapped Cartesian X coordinates of all particles.
Definition phasespace_synthesis.h:159

stormm::synthesis::PsSynthesisWriter::vyalt
llint * vyalt
Alternate Cartesian Y velocities of particles.
Definition phasespace_synthesis.h:184

stormm::synthesis::PsSynthesisWriter::alt_boxvec_ovrf
int * alt_boxvec_ovrf
Overflow arrays for the discretized box vectors.
Definition phasespace_synthesis.h:152

stormm::synthesis::PsSynthesisWriter::PsSynthesisWriter
PsSynthesisWriter(int system_count_in, int unique_topology_count_in, UnitCellType unit_cell_in, const int *atom_starts_in, const int *atom_counts_in, const int *common_ag_list_in, const int *common_ag_bounds_in, const int *unique_ag_idx_in, const int *replica_idx_in, float gpos_scale_in, float vel_scale_in, float frc_scale_in, int gpos_bits_in, int vel_bits_in, int frc_bits_in, llint *boxvecs_in, int *boxvec_ovrf_in, double *umat_in, double *invu_in, double *boxdims_in, llint *alt_boxvecs_in, int *alt_boxvec_ovrf_in, double *umat_alt_in, double *invu_alt_in, double *alt_boxdims_in, llint *xcrd_in, llint *ycrd_in, llint *zcrd_in, int *xcrd_ovrf_in, int *ycrd_ovrf_in, int *zcrd_ovrf_in, llint *xvel_in, llint *yvel_in, llint *zvel_in, int *xvel_ovrf_in, int *yvel_ovrf_in, int *zvel_ovrf_in, llint *xfrc_in, llint *yfrc_in, llint *zfrc_in, int *xfrc_ovrf_in, int *yfrc_ovrf_in, int *zfrc_ovrf_in, llint *xalt_in, llint *yalt_in, llint *zalt_in, int *xalt_ovrf_in, int *yalt_ovrf_in, int *zalt_ovrf_in, llint *vxalt_in, llint *vyalt_in, llint *vzalt_in, int *vxalt_ovrf_in, int *vyalt_ovrf_in, int *vzalt_ovrf_in, llint *fxalt_in, llint *fyalt_in, llint *fzalt_in, int *fxalt_ovrf_in, int *fyalt_ovrf_in, int *fzalt_ovrf_in)
Constructor takes a straight list of pointers and constants from the parent object (in this case,...
Definition phasespace_synthesis.cpp:60

stormm::synthesis::PsSynthesisWriter::xalt_ovrf
int * xalt_ovrf
Overflow buffers for particles' alternate Cartesian X locations.
Definition phasespace_synthesis.h:180

stormm::synthesis::PsSynthesisWriter::xvel_ovrf
int * xvel_ovrf
Cartesian X velocity overflow buffers.
Definition phasespace_synthesis.h:168

stormm::synthesis::PsSynthesisWriter::frc_bits
const int frc_bits
Force component bits after the decimal.
Definition phasespace_synthesis.h:143

stormm::synthesis::PsSynthesisWriter::atom_starts
const int * atom_starts
Points at which each system starts in the atom list.
Definition phasespace_synthesis.h:123

stormm::synthesis::PsSynthesisWriter::ycrd
llint * ycrd
Non-wrapped Cartesian Y coordinates of all particles.
Definition phasespace_synthesis.h:160

stormm::synthesis::PsSynthesisWriter::alt_boxdims
double * alt_boxdims
Box dimensions (a, b, c, alpha, beta, gamma)
Definition phasespace_synthesis.h:155

stormm::synthesis::PsSynthesisWriter::boxvec_ovrf
int * boxvec_ovrf
Overflow arrays for the discretized box vectors.
Definition phasespace_synthesis.h:147

stormm::synthesis::PsSynthesisWriter::zvel
llint * zvel
Cartesian Z velocities.
Definition phasespace_synthesis.h:167

stormm::synthesis::PsSynthesisWriter::frc_scale
const float frc_scale
Scaling factor for fixed-precision force accumulation.
Definition phasespace_synthesis.h:137

stormm::synthesis::PsSynthesisWriter::unique_ag_idx
const int * unique_ag_idx
Definition phasespace_synthesis.h:128

stormm::synthesis::PsSynthesisWriter::gpos_scale
const float gpos_scale
Global position coordinate scaling factor.
Definition phasespace_synthesis.h:135

stormm::synthesis::PsSynthesisWriter::inv_gpos_scale
const float inv_gpos_scale
Inverse global coordinate scaling factor.
Definition phasespace_synthesis.h:138

stormm::synthesis::PsSynthesisWriter::xfrc
llint * xfrc
Discretized Cartesian X forces.
Definition phasespace_synthesis.h:171

stormm::synthesis::PsSynthesisWriter::umat_alt
double * umat_alt
Box (fractional) space transformation matrices, one per warp.
Definition phasespace_synthesis.h:153

stormm::synthesis::PsSynthesisWriter::gpos_bits
const int gpos_bits
Global position coordinate bits after the decimal.
Definition phasespace_synthesis.h:141

stormm::synthesis::PsSynthesisWriter::yvel_ovrf
int * yvel_ovrf
Cartesian Y velocity overflow buffers.
Definition phasespace_synthesis.h:169

stormm::synthesis::PsSynthesisWriter::PsSynthesisWriter
PsSynthesisWriter(const PsSynthesisWriter &original)=default
Copy and move constructors–as with any object containing const members, the move assignment operator ...

stormm::synthesis::PsSynthesisWriter::vxalt_ovrf
int * vxalt_ovrf
Overflow buffers for particles' alternate Cartesian X velocities.
Definition phasespace_synthesis.h:186

stormm::synthesis::PsSynthesisWriter::inv_frc_scale
const float inv_frc_scale
Inverse force scaling factor.
Definition phasespace_synthesis.h:140

stormm::synthesis::PsSynthesisWriter::ycrd_ovrf
int * ycrd_ovrf
Non-wrapped Cartesian Y coordinate overflow buffers.
Definition phasespace_synthesis.h:163

stormm::synthesis::PsSynthesisWriter::common_ag_list
const int * common_ag_list
Definition phasespace_synthesis.h:125

stormm::synthesis::PsSynthesisWriter::fzalt
llint * fzalt
Alternate Cartesian Z forces acting on particles.
Definition phasespace_synthesis.h:191

stormm::synthesis::PsSynthesisWriter::xalt
llint * xalt
Alternate Cartesian X positions of particles.
Definition phasespace_synthesis.h:177

stormm::synthesis::PsSynthesisWriter::zvel_ovrf
int * zvel_ovrf
Cartesian Z velocity overflow buffers.
Definition phasespace_synthesis.h:170

stormm::synthesis::PsSynthesisWriter::zalt
llint * zalt
Alternate Cartesian Z positions of particles.
Definition phasespace_synthesis.h:179

stormm::synthesis::PsSynthesisWriter::vel_bits
const int vel_bits
Velocity coordinate bits after the decimal.
Definition phasespace_synthesis.h:142

stormm::synthesis::PsSynthesisWriter::xvel
llint * xvel
Cartesian X velocities.
Definition phasespace_synthesis.h:165

stormm::synthesis::PsSynthesisWriter::system_count
const int system_count
The number of independent systems.
Definition phasespace_synthesis.h:120

stormm::synthesis::PsSynthesisWriter::zfrc_ovrf
int * zfrc_ovrf
Discretized Cartesian Z force overflow buffers.
Definition phasespace_synthesis.h:176

stormm::synthesis::PsSynthesisWriter::yvel
llint * yvel
Cartesian Y velocities.
Definition phasespace_synthesis.h:166

stormm::synthesis::PsSynthesisWriter::common_ag_bounds
const int * common_ag_bounds
Bounds array for common_ag_list.
Definition phasespace_synthesis.h:127

stormm::synthesis::PsSynthesisWriter::zcrd
llint * zcrd
Non-wrapped Cartesian Z coordinates of all particles.
Definition phasespace_synthesis.h:161

stormm::synthesis::PsSynthesisWriter::yalt_ovrf
int * yalt_ovrf
Overflow buffers for particles' alternate Cartesian Y locations.
Definition phasespace_synthesis.h:181

stormm::synthesis::PsSynthesisWriter::zfrc
llint * zfrc
Discretized Cartesian Z forces.
Definition phasespace_synthesis.h:173

stormm::synthesis::PsSynthesisWriter::unique_topology_count
const int unique_topology_count
The number of unique topologies.
Definition phasespace_synthesis.h:121

stormm::synthesis::PsSynthesisWriter::alt_boxvecs
llint * alt_boxvecs
Discretized box vectors.
Definition phasespace_synthesis.h:151

stormm::synthesis::PsSynthesisWriter::invu
double * invu
Inverse transformation matrices, one per warp.
Definition phasespace_synthesis.h:149

stormm::synthesis::PsSynthesisWriter::yfrc
llint * yfrc
Discretized Cartesian Y forces.
Definition phasespace_synthesis.h:172

stormm::synthesis::PsSynthesisWriter::vzalt_ovrf
int * vzalt_ovrf
Overflow buffers for particles' alternate Cartesian Z velocities.
Definition phasespace_synthesis.h:188

stormm::synthesis::PsSynthesisWriter::invu_alt
double * invu_alt
Inverse transformation matrices, one per warp.
Definition phasespace_synthesis.h:154

stormm::synthesis::PsSynthesisWriter::vyalt_ovrf
int * vyalt_ovrf
Overflow buffers for particles' alternate Cartesian Y velocities.
Definition phasespace_synthesis.h:187

stormm::synthesis::PsSynthesisWriter::vel_scale
const float vel_scale
Velocity coordinate scaling factor.
Definition phasespace_synthesis.h:136

stormm::synthesis::PsSynthesisWriter::fyalt_ovrf
int * fyalt_ovrf
Overflow buffers for particles' alternate Cartesian Y forces.
Definition phasespace_synthesis.h:193

stormm::synthesis::PsSynthesisWriter::fyalt
llint * fyalt
Alternate Cartesian Y forces acting on particles.
Definition phasespace_synthesis.h:190

stormm::synthesis::PsSynthesisWriter::vzalt
llint * vzalt
Alternate Cartesian Z velocities of particles.
Definition phasespace_synthesis.h:185

stormm::synthesis::PsSynthesisWriter::fxalt_ovrf
int * fxalt_ovrf
Overflow buffers for particles' alternate Cartesian X forces.
Definition phasespace_synthesis.h:192

stormm::synthesis::PsSynthesisWriter::zcrd_ovrf
int * zcrd_ovrf
Non-wrapped Cartesian Z coordinate overflow buffers.
Definition phasespace_synthesis.h:164

stormm::synthesis::PsSynthesisWriter::boxvecs
llint * boxvecs
Discretized box vectors.
Definition phasespace_synthesis.h:146

stormm::synthesis::PsSynthesisWriter::unit_cell
const UnitCellType unit_cell
Type of unit cells (or none) each system resides in.
Definition phasespace_synthesis.h:122

stormm::synthesis::PsSynthesisWriter::yalt
llint * yalt
Alternate Cartesian Y positions of particles.
Definition phasespace_synthesis.h:178

stormm::synthesis::PsSynthesisWriter::xcrd_ovrf
int * xcrd_ovrf
Non-wrapped Cartesian X coordinate overflow buffers.
Definition phasespace_synthesis.h:162

stormm::synthesis::PsSynthesisWriter::atom_counts
const int * atom_counts
Atom counts for all systems.
Definition phasespace_synthesis.h:124

stormm::synthesis::PsSynthesisWriter::zalt_ovrf
int * zalt_ovrf
Overflow buffers for particles' alternate Cartesian Z locations.
Definition phasespace_synthesis.h:182

stormm::synthesis::PsSynthesisWriter::yfrc_ovrf
int * yfrc_ovrf
Discretized Cartesian Y force overflow buffers.
Definition phasespace_synthesis.h:175

stormm::synthesis::PsSynthesisWriter::xfrc_ovrf
int * xfrc_ovrf
Discretized Cartesian X force overflow buffers.
Definition phasespace_synthesis.h:174

stormm::synthesis::PsSynthesisWriter::replica_idx
const int * replica_idx
Definition phasespace_synthesis.h:130

stormm::synthesis::PsSynthesisWriter::boxdims
double * boxdims
Box dimensions (a, b, c, alpha, beta, gamma)
Definition phasespace_synthesis.h:150

stormm::trajectory::CoordinateFrameReader
Collect C-style pointers for the elements of a read-only CoordinateFrame object.
Definition coordinateframe.h:65

stormm::trajectory::CoordinateSeriesReader
Collect C-style pointers and critical constants for a read-only CoordinateSeries object.
Definition coordinate_series.h:96

stormm::trajectory::PhaseSpaceReader
Collect constants and pointers to the components of a read-only PhaseSpace object.
Definition phasespace.h:81