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VolMapCreateILS.C File Reference

#include <math.h>
#include <stdio.h>
#include "VolMapCreate.h"
#include "MoleculeList.h"
#include "VolumetricData.h"
#include "utilities.h"
#include "WKFUtils.h"
#include "VMDApp.h"
#include "Measure.h"
#include "Inform.h"

Go to the source code of this file.

Compounds

struct AtomPosType

struct BinOfAtoms

struct ComputeOccupancyMap_t

union flint_t

Defines

#define TIMING

#define BIN_DEPTH 8

#define BIN_SLOTSIZE 4

#define BIN_SIZE (BIN_DEPTH * BIN_SLOTSIZE)

#define BIN_DEPTH 8

#define DEFAULT_EXCL_DIST 1.f

#define DEFAULT_EXCL_ENERGY 87.f

#define DEFAULT_BIN_LENGTH 3.f

#define MAX_BIN_VOLUME 27.f

#define MIN_BIN_VOLUME 8.f

#define MAX_UNIQUE_TYPES 200

#define MAX_EXTRA_ATOMS 50

Typedefs

typedef flint_t flint

typedef ComputeOccupancyMap_t ComputeOccupancyMap

Functions

int ComputeOccupancyMap_setup (ComputeOccupancyMap *)

int ComputeOccupancyMap_calculate_slab (ComputeOccupancyMap *)

void ComputeOccupancyMap_cleanup (ComputeOccupancyMap *)

void write_bin_histogram_map (const ComputeOccupancyMap *, const char *filename)

void atom_bin_stats (const ComputeOccupancyMap *)

void compute_allatoms (float *map, int mx, int my, int mz, float lx, float ly, float lz, const float origin[3], const float axes[9], const float alignmat[16], int num_coords, const float *coords, const int *vdw_type, const float *vdw_params, float cutoff, const float *probe_vdw_params, int num_probe_atoms, int num_conformers, const float *conformers, float excl_energy)

bool collinear (const float *axis1, const float *axis2, float tol)

int triangulate (const float *pole, const float *eq1, const float *eq2, int freq, float *v)

void octahedron (float *vertices, int C2symm)

void hexahedron (float *vertices, int C2symm)

void dodecahedron (float *faces, float *vertices, int C2symm)

int icosahedron_geodesic (float *(&orientations), int C2symm, int freq)

float signed_angle (const float *axis, const float *v1, const float *v2)

int fill_atom_bins (ComputeOccupancyMap *p)

void tighten_bin_neighborhood (ComputeOccupancyMap *p)

void find_distance_exclusions (ComputeOccupancyMap *p)

void find_energy_exclusions (ComputeOccupancyMap *p)

void compute_occupancy_monoatom (ComputeOccupancyMap *p)

void compute_occupancy_multiatom (ComputeOccupancyMap *p)

Define Documentation

#define BIN_DEPTH 8

Definition at line 54 of file VolMapCreateILS.C.

#define BIN_DEPTH 8

Definition at line 54 of file VolMapCreateILS.C.

Referenced by compute_occupancy_monoatom, compute_occupancy_multiatom, fill_atom_bins, find_distance_exclusions, and find_energy_exclusions.

#define BIN_SIZE (BIN_DEPTH * BIN_SLOTSIZE)

Definition at line 51 of file VolMapCreateILS.C.

#define BIN_SLOTSIZE 4

Definition at line 50 of file VolMapCreateILS.C.

#define DEFAULT_BIN_LENGTH 3.f

Definition at line 140 of file VolMapCreateILS.C.

Referenced by ComputeOccupancyMap_setup.

#define DEFAULT_EXCL_DIST 1.f

Definition at line 137 of file VolMapCreateILS.C.

#define DEFAULT_EXCL_ENERGY 87.f

Definition at line 138 of file VolMapCreateILS.C.

Referenced by VolMapCreateILS::set_maxenergy, and VolMapCreateILS::VolMapCreateILS.

#define MAX_BIN_VOLUME 27.f

Definition at line 141 of file VolMapCreateILS.C.

Referenced by ComputeOccupancyMap_setup.

#define MAX_EXTRA_ATOMS 50

Definition at line 2734 of file VolMapCreateILS.C.

Referenced by fill_atom_bins.

#define MAX_UNIQUE_TYPES 200

#define MIN_BIN_VOLUME 8.f

Definition at line 142 of file VolMapCreateILS.C.

Referenced by ComputeOccupancyMap_setup.

#define TIMING

Definition at line 41 of file VolMapCreateILS.C.

Typedef Documentation

typedef struct ComputeOccupancyMap_t ComputeOccupancyMap

typedef union flint_t flint

Function Documentation

void atom_bin_stats ( const ComputeOccupancyMap * ) [static]

bool collinear ( const float * axis1,

const float * axis2,

float tol

) [static]

Definition at line 883 of file VolMapCreateILS.C.

References DEGTORAD, and dot_prod.

void compute_allatoms ( float * map,

int mx,

int my,

int mz,

float lx,

float ly,

float lz,

const float origin[3],

const float axes[9],

const float alignmat[16],

int num_coords,

const float * coords,

const int * vdw_type,

const float * vdw_params,

float cutoff,

const float * probe_vdw_params,

int num_probe_atoms,

int num_conformers,

const float * conformers,

float excl_energy

) [static]

Definition at line 3432 of file VolMapCreateILS.C.

References n, and z.

void compute_occupancy_monoatom ( ComputeOccupancyMap * p ) [static]

Definition at line 3093 of file VolMapCreateILS.C.

References BinOfAtoms::atom, BIN_DEPTH, ComputeOccupancyMap_t::bin_offsets, ComputeOccupancyMap_t::bin_zero, ComputeOccupancyMap_t::bx_1, ComputeOccupancyMap_t::by_1, ComputeOccupancyMap_t::bz_1, ComputeOccupancyMap_t::cutoff, ComputeOccupancyMap_t::excl_energy, ComputeOccupancyMap_t::exclusions, ComputeOccupancyMap_t::extra, ComputeOccupancyMap_t::hx, ComputeOccupancyMap_t::hy, ComputeOccupancyMap_t::hz, ComputeOccupancyMap_t::kstart, ComputeOccupancyMap_t::kstop, ComputeOccupancyMap_t::map, ComputeOccupancyMap_t::mx, ComputeOccupancyMap_t::my, n, ComputeOccupancyMap_t::nbx, ComputeOccupancyMap_t::nby, ComputeOccupancyMap_t::num_bin_offsets, ComputeOccupancyMap_t::num_extras, ComputeOccupancyMap_t::probe_vdw_params, ComputeOccupancyMap_t::vdw_params, ComputeOccupancyMap_t::x0, ComputeOccupancyMap_t::y0, and ComputeOccupancyMap_t::z0.

Referenced by ComputeOccupancyMap_calculate_slab.

void compute_occupancy_multiatom ( ComputeOccupancyMap * p ) [static]

Definition at line 3211 of file VolMapCreateILS.C.

References BinOfAtoms::atom, BIN_DEPTH, ComputeOccupancyMap_t::bin_offsets, ComputeOccupancyMap_t::bin_zero, ComputeOccupancyMap_t::bx_1, ComputeOccupancyMap_t::by_1, ComputeOccupancyMap_t::bz_1, ComputeOccupancyMap_t::conformers, ComputeOccupancyMap_t::cutoff, ComputeOccupancyMap_t::excl_energy, ComputeOccupancyMap_t::exclusions, ComputeOccupancyMap_t::extra, ComputeOccupancyMap_t::hx, ComputeOccupancyMap_t::hy, ComputeOccupancyMap_t::hz, ComputeOccupancyMap_t::kstart, ComputeOccupancyMap_t::kstop, ComputeOccupancyMap_t::map, ComputeOccupancyMap_t::mx, ComputeOccupancyMap_t::my, n, ComputeOccupancyMap_t::nbx, ComputeOccupancyMap_t::nby, ComputeOccupancyMap_t::num_bin_offsets, ComputeOccupancyMap_t::num_conformers, ComputeOccupancyMap_t::num_extras, ComputeOccupancyMap_t::num_probes, ComputeOccupancyMap_t::probe_vdw_params, ComputeOccupancyMap_t::vdw_params, ComputeOccupancyMap_t::x0, ComputeOccupancyMap_t::y0, z, and ComputeOccupancyMap_t::z0.

Referenced by ComputeOccupancyMap_calculate_slab.

int ComputeOccupancyMap_calculate_slab ( ComputeOccupancyMap * ) [static]

Definition at line 2646 of file VolMapCreateILS.C.

References compute_occupancy_monoatom, compute_occupancy_multiatom, ComputeOccupancyMap_t::exclusions, find_distance_exclusions, find_energy_exclusions, ComputeOccupancyMap_t::mx, ComputeOccupancyMap_t::my, ComputeOccupancyMap_t::mz, ComputeOccupancyMap_t::num_probes, wkf_timer_create, wkf_timer_destroy, wkf_timer_start, wkf_timer_timenow, and wkf_timerhandle.

void ComputeOccupancyMap_cleanup ( ComputeOccupancyMap * ) [static]

Definition at line 2723 of file VolMapCreateILS.C.

References ComputeOccupancyMap_t::bin, ComputeOccupancyMap_t::bin_offsets, ComputeOccupancyMap_t::bincnt, ComputeOccupancyMap_t::exclusions, and ComputeOccupancyMap_t::extra.

int ComputeOccupancyMap_setup ( ComputeOccupancyMap * ) [static]

Definition at line 2564 of file VolMapCreateILS.C.

References ComputeOccupancyMap_t::bin, ComputeOccupancyMap_t::bin_offsets, ComputeOccupancyMap_t::bin_zero, ComputeOccupancyMap_t::bincnt, ComputeOccupancyMap_t::bincnt_zero, ComputeOccupancyMap_t::bx, ComputeOccupancyMap_t::bx_1, ComputeOccupancyMap_t::by, ComputeOccupancyMap_t::by_1, ComputeOccupancyMap_t::bz, ComputeOccupancyMap_t::bz_1, ComputeOccupancyMap_t::cpu_only, DEFAULT_BIN_LENGTH, ComputeOccupancyMap_t::exclusions, ComputeOccupancyMap_t::extra, fill_atom_bins, ComputeOccupancyMap_t::hx, ComputeOccupancyMap_t::hy, ComputeOccupancyMap_t::hz, ComputeOccupancyMap_t::lx, ComputeOccupancyMap_t::ly, ComputeOccupancyMap_t::lz, ComputeOccupancyMap_t::map, MAX_BIN_VOLUME, MIN_BIN_VOLUME, ComputeOccupancyMap_t::mpblx, ComputeOccupancyMap_t::mpbly, ComputeOccupancyMap_t::mpblz, ComputeOccupancyMap_t::mx, ComputeOccupancyMap_t::my, ComputeOccupancyMap_t::mz, NULL, and tighten_bin_neighborhood.

void dodecahedron ( float * faces,

float * vertices,

int C2symm

) [static]

Definition at line 989 of file VolMapCreateILS.C.

References angle, cross_prod, DEGTORAD, Matrix4::identity, Matrix4::multpoint3d, RADTODEG, Matrix4::rot, Matrix4::rotate_axis, vec_add, vec_copy, vec_negate, vec_normalize, and vec_zero.

Referenced by icosahedron_geodesic.

int fill_atom_bins ( ComputeOccupancyMap * p ) [static]

Definition at line 2736 of file VolMapCreateILS.C.

References BinOfAtoms::atom, ComputeOccupancyMap_t::bin, bin, BIN_DEPTH, ComputeOccupancyMap_t::bin_zero, ComputeOccupancyMap_t::bincnt, ComputeOccupancyMap_t::bincnt_zero, ComputeOccupancyMap_t::bx_1, ComputeOccupancyMap_t::by_1, ComputeOccupancyMap_t::bz_1, ComputeOccupancyMap_t::coords, ComputeOccupancyMap_t::extcutoff, ComputeOccupancyMap_t::extra, ComputeOccupancyMap_t::lx, ComputeOccupancyMap_t::ly, ComputeOccupancyMap_t::lz, MAX_EXTRA_ATOMS, n, ComputeOccupancyMap_t::nbx, ComputeOccupancyMap_t::nby, ComputeOccupancyMap_t::nbz, ComputeOccupancyMap_t::num_coords, ComputeOccupancyMap_t::num_extras, ComputeOccupancyMap_t::padx, ComputeOccupancyMap_t::pady, ComputeOccupancyMap_t::padz, ComputeOccupancyMap_t::vdw_type, AtomPosType::vdwtype, AtomPosType::x, ComputeOccupancyMap_t::x0, AtomPosType::y, ComputeOccupancyMap_t::y0, AtomPosType::z, z, and ComputeOccupancyMap_t::z0.

Referenced by ComputeOccupancyMap_setup.

void find_distance_exclusions ( ComputeOccupancyMap * p ) [static]

void find_energy_exclusions ( ComputeOccupancyMap * p ) [static]

Definition at line 2982 of file VolMapCreateILS.C.

References BinOfAtoms::atom, BIN_DEPTH, ComputeOccupancyMap_t::bin_offsets, ComputeOccupancyMap_t::bin_zero, ComputeOccupancyMap_t::bx_1, ComputeOccupancyMap_t::by_1, ComputeOccupancyMap_t::bz_1, ComputeOccupancyMap_t::cutoff, ComputeOccupancyMap_t::excl_energy, ComputeOccupancyMap_t::exclusions, ComputeOccupancyMap_t::extra, ComputeOccupancyMap_t::hx, ComputeOccupancyMap_t::hy, ComputeOccupancyMap_t::hz, ComputeOccupancyMap_t::kstart, ComputeOccupancyMap_t::kstop, ComputeOccupancyMap_t::mx, ComputeOccupancyMap_t::my, n, ComputeOccupancyMap_t::nbx, ComputeOccupancyMap_t::nby, ComputeOccupancyMap_t::num_bin_offsets, ComputeOccupancyMap_t::num_extras, ComputeOccupancyMap_t::probe_vdw_params, ComputeOccupancyMap_t::vdw_params, ComputeOccupancyMap_t::x0, ComputeOccupancyMap_t::y0, and ComputeOccupancyMap_t::z0.

Referenced by ComputeOccupancyMap_calculate_slab.

void hexahedron ( float * vertices,

int C2symm

) [static]

Definition at line 968 of file VolMapCreateILS.C.

References vec_negate.

int icosahedron_geodesic ( float *& orientations,

int C2symm,

int freq

) [static]

Definition at line 1054 of file VolMapCreateILS.C.

References dodecahedron, norm, triangulate, vec_copy, vec_negate, vec_normalize, vec_scaled_add, and vec_sub.

void octahedron ( float * vertices,

int C2symm

) [static]

Definition at line 953 of file VolMapCreateILS.C.

References vec_negate.

float signed_angle ( const float * axis,

const float * v1,

const float * v2

) [static]

Definition at line 1292 of file VolMapCreateILS.C.

References angle, cross_prod, dot_prod, vec_copy, and vec_normalize.

void tighten_bin_neighborhood ( ComputeOccupancyMap * p ) [static]

Definition at line 2851 of file VolMapCreateILS.C.

References ComputeOccupancyMap_t::bin_offsets, ComputeOccupancyMap_t::bx, ComputeOccupancyMap_t::by, ComputeOccupancyMap_t::bz, ComputeOccupancyMap_t::extcutoff, n, ComputeOccupancyMap_t::num_bin_offsets, ComputeOccupancyMap_t::padx, ComputeOccupancyMap_t::pady, and ComputeOccupancyMap_t::padz.

Referenced by ComputeOccupancyMap_setup.

int triangulate ( const float * pole,

const float * eq1,

const float * eq2,

int freq,

float * v

) [static]

Definition at line 918 of file VolMapCreateILS.C.

References norm, vec_copy, vec_normalize, vec_scaled_add, and vec_sub.

Referenced by icosahedron_geodesic.

void write_bin_histogram_map ( const ComputeOccupancyMap * ,

const char * filename

) [static]

Definition at line 3351 of file VolMapCreateILS.C.

References ComputeOccupancyMap_t::bincnt, ComputeOccupancyMap_t::bx, ComputeOccupancyMap_t::by, ComputeOccupancyMap_t::bz, data, ComputeOccupancyMap_t::nbx, ComputeOccupancyMap_t::nby, ComputeOccupancyMap_t::nbz, ComputeOccupancyMap_t::padx, ComputeOccupancyMap_t::pady, ComputeOccupancyMap_t::padz, volmap_write_dx_file, ComputeOccupancyMap_t::x0, ComputeOccupancyMap_t::y0, and ComputeOccupancyMap_t::z0.

Referenced by atom_bin_stats.

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