stormm::trajectory::PsSynthesisWriter Struct Reference

The writer for a PhaseSpaceSynthesis object, containing all of the data relevant for propagating dynamics in a collection of systems. More...

#include <phasespace_synthesis.h>

Public Member Functions
	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, a PhaseSpaceSynthesis), like other abstracts.
	PsSynthesisWriter (const PsSynthesisWriter &original)=default
	Copy and move constructors–as with any object containing const members, the move assignment operator is implicitly deleted.
	PsSynthesisWriter (PsSynthesisWriter &&other)=default

Public Attributes
const int	system_count
	The number of independent systems.
const int	unique_topology_count
	The number of unique topologies.
const UnitCellType	unit_cell
	Type of unit cells (or none) each system resides in.
const int *	atom_starts
	Points at which each system starts in the atom list.
const int *	atom_counts
	Atom counts for all systems.
const int *	common_ag_list
const int *	common_ag_bounds
	Bounds array for common_ag_list.
const int *	unique_ag_idx
const int *	replica_idx
const float	gpos_scale
	Global position coordinate scaling factor.
const float	vel_scale
	Velocity coordinate scaling factor.
const float	frc_scale
	Scaling factor for fixed-precision force accumulation.
const float	inv_gpos_scale
	Inverse global coordinate scaling factor.
const float	inv_vel_scale
	Inverse velocity scaling factor.
const float	inv_frc_scale
	Inverse force scaling factor.
const int	gpos_bits
	Global position coordinate bits after the decimal.
const int	vel_bits
	Velocity coordinate bits after the decimal.
const int	frc_bits
	Force component bits after the decimal.
llint *	boxvecs
	Discretized box vectors.
int *	boxvec_ovrf
	Overflow arrays for the discretized box vectors.
double *	umat
	Box (fractional) space transformation matrices, one per warp.
double *	invu
	Inverse transformation matrices, one per warp.
double *	boxdims
	Box dimensions (a, b, c, alpha, beta, gamma)
llint *	alt_boxvecs
	Discretized box vectors.
int *	alt_boxvec_ovrf
	Overflow arrays for the discretized box vectors.
double *	umat_alt
	Box (fractional) space transformation matrices, one per warp.
double *	invu_alt
	Inverse transformation matrices, one per warp.
double *	alt_boxdims
	Box dimensions (a, b, c, alpha, beta, gamma)
llint *	xcrd
	Non-wrapped Cartesian X coordinates of all particles.
llint *	ycrd
	Non-wrapped Cartesian Y coordinates of all particles.
llint *	zcrd
	Non-wrapped Cartesian Z coordinates of all particles.
int *	xcrd_ovrf
	Non-wrapped Cartesian X coordinate overflow buffers.
int *	ycrd_ovrf
	Non-wrapped Cartesian Y coordinate overflow buffers.
int *	zcrd_ovrf
	Non-wrapped Cartesian Z coordinate overflow buffers.
llint *	xvel
	Cartesian X velocities.
llint *	yvel
	Cartesian Y velocities.
llint *	zvel
	Cartesian Z velocities.
int *	xvel_ovrf
	Cartesian X velocity overflow buffers.
int *	yvel_ovrf
	Cartesian Y velocity overflow buffers.
int *	zvel_ovrf
	Cartesian Z velocity overflow buffers.
llint *	xfrc
	Discretized Cartesian X forces.
llint *	yfrc
	Discretized Cartesian Y forces.
llint *	zfrc
	Discretized Cartesian Z forces.
int *	xfrc_ovrf
	Discretized Cartesian X force overflow buffers.
int *	yfrc_ovrf
	Discretized Cartesian Y force overflow buffers.
int *	zfrc_ovrf
	Discretized Cartesian Z force overflow buffers.
llint *	xalt
	Alternate Cartesian X positions of particles.
llint *	yalt
	Alternate Cartesian Y positions of particles.
llint *	zalt
	Alternate Cartesian Z positions of particles.
int *	xalt_ovrf
	Overflow buffers for particles' alternate Cartesian X locations.
int *	yalt_ovrf
	Overflow buffers for particles' alternate Cartesian Y locations.
int *	zalt_ovrf
	Overflow buffers for particles' alternate Cartesian Z locations.
llint *	vxalt
	Alternate Cartesian X velocities of particles.
llint *	vyalt
	Alternate Cartesian Y velocities of particles.
llint *	vzalt
	Alternate Cartesian Z velocities of particles.
int *	vxalt_ovrf
	Overflow buffers for particles' alternate Cartesian X velocities.
int *	vyalt_ovrf
	Overflow buffers for particles' alternate Cartesian Y velocities.
int *	vzalt_ovrf
	Overflow buffers for particles' alternate Cartesian Z velocities.
llint *	fxalt
	Alternate Cartesian X forces acting on particles.
llint *	fyalt
	Alternate Cartesian Y forces acting on particles.
llint *	fzalt
	Alternate Cartesian Z forces acting on particles.
int *	fxalt_ovrf
	Overflow buffers for particles' alternate Cartesian X forces.
int *	fyalt_ovrf
	Overflow buffers for particles' alternate Cartesian Y forces.
int *	fzalt_ovrf
	Overflow buffers for particles' alternate Cartesian Z force.

Detailed Description

The writer for a PhaseSpaceSynthesis object, containing all of the data relevant for propagating dynamics in a collection of systems.

Member Data Documentation

common_ag_list

const int* stormm::synthesis::PsSynthesisWriter::common_ag_list

Concatenated lists of systems in the synthesis sharing the same topology

replica_idx

const int* stormm::synthesis::PsSynthesisWriter::replica_idx

The instance number of each system in the list of all systems sharing its topology.

unique_ag_idx

const int* stormm::synthesis::PsSynthesisWriter::unique_ag_idx

Indices of the unique topologies referenced by each set of coordinates

---

The documentation for this struct was generated from the following files:

• src/Synthesis/phasespace_synthesis.h
• src/Synthesis/phasespace_synthesis.cpp