doxygen/trim_8h_source.html

// -*-c++-*-

#ifndef STORMM_TRAJECTORY_TRIM_H

#define STORMM_TRAJECTORY_TRIM_H


#include "copyright.h"

#include "Accelerator/gpu_details.h"

#include "Constants/behavior.h"

#include "DataTypes/common_types.h"

#include "Math/formulas.h"

#include "Math/matrix_ops.h"

#include "Math/vector_ops.h"

#include "Numerics/split_fixed_precision.h"

#include "Parsing/parsing_enumerators.h"

#include "Parsing/parse.h"

#include "Synthesis/atomgraph_synthesis.h"

#include "Synthesis/phasespace_synthesis.h"

#include "Synthesis/synthesis_abstracts.h"

#include "Topology/atomgraph.h"

#include "Topology/atomgraph_enumerators.h"

#include "motion_sweeper.h"

#include "phasespace.h"


namespace stormm {

namespace trajectory {


using card::GpuDetails;

using constants::ExceptionResponse;

using constants::PrecisionModel;

using data_types::isSignedIntegralScalarType;

using parse::NumberFormat;

using parse::realToString;

using stmath::angleOnAxes;

using stmath::angleOnAxesf;

using stmath::crossProduct;

using stmath::invertSquareMatrix;

using stmath::leibnizDeterminant;

using synthesis::AtomGraphSynthesis;

using synthesis::PhaseSpaceSynthesis;

using synthesis::PsSynthesisReader;

using synthesis::PsSynthesisWriter;

using synthesis::SyAtomUpdateKit;

using topology::AtomGraph;


template <typename T>

bool checkInertialTensor(const std::vector<T> &inrt, int natom,

                         ExceptionResponse policy = ExceptionResponse::WARN);


template <typename Tcoord, typename Tmass, typename Tcalc>

void removeMomentum(Tcoord* xcrd, Tcoord* ycrd, Tcoord* zcrd, int* xcrd_ovrf, int* ycrd_ovrf,

                    int* zcrd_ovrf, Tcoord* xvel, Tcoord* yvel, Tcoord* zvel, int* xvel_ovrf,

                    int* yvel_ovrf, int* zvel_ovrf, const Tmass* masses, UnitCellType unit_cell,

                    int natom, Tcalc gpos_scale = 1.0, Tcalc vel_scale = 1.0,

                    ExceptionResponse policy = ExceptionResponse::WARN);


void removeMomentum(PhaseSpace *ps, const AtomGraph *ag,

                    ExceptionResponse policy = ExceptionResponse::WARN);


void removeMomentum(PhaseSpace *ps, const AtomGraph &ag,

                    ExceptionResponse policy = ExceptionResponse::WARN);


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

                    const PrecisionModel prec, ExceptionResponse policy = ExceptionResponse::WARN);


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

                    const PrecisionModel prec, ExceptionResponse policy = ExceptionResponse::WARN);


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

                    MotionSweeper *mos, const GpuDetails &gpu = null_gpu,

                    ExceptionResponse policy = ExceptionResponse::WARN);


void accumulateCenterOfMassMotion(MotionSweepWriter *mosw,

                                  const SyAtomUpdateKit<double, double2, double4> &poly_auk,

                                  const PsSynthesisReader &poly_psr,

                                  const GpuDetails &gpu = null_gpu);


void removeCenterOfMassMotion(PsSynthesisWriter *poly_psw, const MotionSweepReader &mosr,

                              const GpuDetails &gpu = null_gpu);


void accumulateAngularMomentum(MotionSweepWriter *mosw,

                               const SyAtomUpdateKit<double, double2, double4> &poly_auk,

                               const PsSynthesisReader &poly_psr,

                               const GpuDetails &gpu = null_gpu);


void removeAngularMomentum(PsSynthesisWriter *poly_psw, const MotionSweepReader &mosr,

                           const GpuDetails &gpu = null_gpu,

                           ExceptionResponse policy = ExceptionResponse::WARN);


} // namespace trajectory

} // namespace stormm


#include "trim.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::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::MotionSweeper
Object to manage and stage recentering and momentum removal for a coordinate synthesis....
Definition motion_sweeper.h:226

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

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::trajectory::MotionSweepReader
Read-only abstract of the MotionSweeper class, below, with const pointers to non-modifiable data.
Definition motion_sweeper.h:117

stormm::trajectory::MotionSweepWriter
Abstract of the MotionSweeper class, below, with non-const pointers to modifiable data.
Definition motion_sweeper.h:21