Gromacs
2022.2
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#include "gmxpre.h"
#include <cmath>
#include <algorithm>
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/indexutil.h"
#include "gromacs/selection/selection.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/smalloc.h"
#include "position.h"
#include "selelem.h"
#include "selmethod.h"
#include "selmethod_impl.h"
Implements the insolidangle selection method.
Classes | |
struct | t_partition_item |
Internal data structure for the insolidangle selection method. More... | |
struct | partition |
Internal data structure for the insolidangle selection method. More... | |
struct | spheresurfacebin |
Internal data structure for the insolidangle selection method. More... | |
struct | methoddata_insolidangle |
Data structure for the insolidangle selection method. More... | |
Typedefs | |
typedef struct partition | t_partition |
Internal data structure for the insolidangle selection method. More... | |
typedef struct spheresurfacebin | t_spheresurfacebin |
Internal data structure for the insolidangle selection method. More... | |
typedef struct methoddata_insolidangle | t_methoddata_insolidangle |
Data structure for the insolidangle selection method. More... | |
Functions | |
static void * | init_data_insolidangle (int npar, gmx_ana_selparam_t *param) |
Allocates data for the insolidangle selection method. More... | |
static void | init_insolidangle (const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data) |
Initializes the insolidangle selection method. More... | |
static void | free_data_insolidangle (void *data) |
Frees the data allocated for the insolidangle selection method. More... | |
static void | init_frame_insolidangle (const gmx::SelMethodEvalContext &context, void *data) |
Initializes the evaluation of the insolidangle selection method for a frame. More... | |
static bool | accept_insolidangle (rvec x, const t_pbc *pbc, void *data) |
Internal helper function for evaluate_insolidangle(). More... | |
static void | evaluate_insolidangle (const gmx::SelMethodEvalContext &context, gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data) |
Evaluates the insolidangle selection method. More... | |
static real | sph_distc (rvec x1, rvec x2) |
Calculates the distance between unit vectors. More... | |
static int | find_partition_bin (t_partition *p, real value) |
Does a binary search on a t_partition to find a bin for a value. More... | |
static int | find_surface_bin (t_methoddata_insolidangle *surf, rvec x) |
Finds a bin that corresponds to a location on the unit sphere surface. More... | |
static void | clear_surface_points (t_methoddata_insolidangle *surf) |
Clears/initializes the bins on the unit sphere surface. More... | |
static void | free_surface_points (t_methoddata_insolidangle *surf) |
Frees memory allocated for storing the reference points in the surface bins. More... | |
static void | add_surface_point (t_methoddata_insolidangle *surf, int tbin, int pbin, rvec x) |
Adds a reference point to a given bin. More... | |
static void | mark_surface_covered (t_methoddata_insolidangle *surf, int tbin, int pbin) |
Marks a bin as completely covered. More... | |
static void | update_surface_bin (t_methoddata_insolidangle *surf, int tbin, real phi, real pdelta1, real pdelta2, real pdeltamax, rvec x) |
Helper function for store_surface_point() to update a single zenith angle bin. More... | |
static void | store_surface_point (t_methoddata_insolidangle *surf, rvec x) |
Adds a single reference point and updates the surface bins. More... | |
static void | optimize_surface_points (t_methoddata_insolidangle *surf) |
Optimizes the surface bins for faster searching. More... | |
static real | estimate_covered_fraction (t_methoddata_insolidangle *surf) |
Estimates the area covered by the reference cones. More... | |
static bool | is_surface_covered (t_methoddata_insolidangle *surf, rvec x) |
Checks whether a point lies within a solid angle. More... | |
bool | _gmx_selelem_can_estimate_cover (const gmx::SelectionTreeElement &sel) |
Returns true if the covered fraction of the selection can be calculated. More... | |
real | _gmx_selelem_estimate_coverfrac (const gmx::SelectionTreeElement &sel) |
Returns the covered fraction of the selection for the current frame. More... | |
Variables | |
static gmx_ana_selparam_t | smparams_insolidangle [] |
Parameters for the insolidangle selection method. More... | |
static const char *const | help_insolidangle [] |
Help text for the insolidangle selection method. More... | |
gmx_ana_selmethod_t | sm_insolidangle |
Selection method data for the insolidangle method. More... | |
bool _gmx_selelem_can_estimate_cover | ( | const gmx::SelectionTreeElement & | sel | ) |
Returns true if the covered fraction of the selection can be calculated.
[in] | sel | Selection element to query. |
sel
with _gmx_selelem_estimate_coverfrac(), false otherwise. real _gmx_selelem_estimate_coverfrac | ( | const gmx::SelectionTreeElement & | sel | ) |
Returns the covered fraction of the selection for the current frame.
[in] | sel | Selection for which the fraction should be calculated. |
The return value is undefined if _gmx_selelem_can_estimate_cover() returns false. Should be called after gmx_ana_evaluate_selections() has been called for the frame.
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static |
Internal helper function for evaluate_insolidangle().
[in] | x | Test point. |
[in] | pbc | PBC data (if NULL, no PBC are used). |
[in] | data | Pointer to a t_methoddata_insolidangle data structure. |
x
is within the solid angle, false otherwise.
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static |
Adds a reference point to a given bin.
[in,out] | surf | Surface data structure. |
[in] | tbin | Bin number in the zenith angle direction. |
[in] | pbin | Bin number in the azimuthal angle direction. |
[in] | x | Point to store. |
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static |
Clears/initializes the bins on the unit sphere surface.
[in,out] | surf | Surface data structure. |
Clears the reference points from the bins and (re)initializes the edges of the azimuthal bins.
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Estimates the area covered by the reference cones.
[in] | surf | Surface data structure. |
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Evaluates the insolidangle
selection method.
See sel_updatefunc() for description of the parameters. data
should point to a t_methoddata_insolidangle
.
Calculates which atoms in g
are within the solid angle spanned by t_methoddata_insolidangle::span
and centered at t_methoddata_insolidangle::center
, and stores the result in out->u.g
.
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static |
Does a binary search on a t_partition
to find a bin for a value.
[in] | p | Partition to search. |
[in] | value | Value to search for. |
p
that contains value
.If value
is outside the range of p
, the first/last index is returned. Otherwise, the return value i
satisfies p->p
[i].left<=value and p->p
[i+1].left>value
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Finds a bin that corresponds to a location on the unit sphere surface.
[in] | surf | Surface data structure to search. |
[in] | x | Unit vector to find. |
x
.The return value is an index to the surf->bin
array.
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Frees the data allocated for the insolidangle
selection method.
data | Data to free (should point to a t_methoddata_insolidangle). |
Frees the memory allocated for t_methoddata_insolidangle::center
and t_methoddata_insolidangle::span
, as well as the memory for the internal bin structure.
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static |
Frees memory allocated for storing the reference points in the surface bins.
[in,out] | surf | Surface data structure. |
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Allocates data for the insolidangle
selection method.
[in] | npar | Not used (should be 3). |
[in,out] | param | Method parameters (should point to smparams_insolidangle). |
Allocates memory for a t_methoddata_insolidangle structure and initializes the parameter as follows:
center
defines the value for t_methoddata_insolidangle::center.span
defines the value for t_methoddata_insolidangle::span.cutoff
defines the value for t_methoddata_insolidangle::angcut.
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static |
Initializes the evaluation of the insolidangle
selection method for a frame.
[in] | context | Evaluation context. |
data | Should point to a t_methoddata_insolidangle. |
Creates a lookup structure that enables fast queries of whether a point is within the solid angle or not.
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Initializes the insolidangle
selection method.
top | Not used. |
npar | Not used. |
param | Not used. |
data | Pointer to t_methoddata_insolidangle to initialize. |
Converts t_methoddata_insolidangle::angcut to radians and allocates and allocates memory for the bins used during the evaluation.
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static |
Checks whether a point lies within a solid angle.
[in] | surf | Surface data structure to search. |
[in] | x | Unit vector to check. |
x
is within the solid angle, false otherwise.
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Marks a bin as completely covered.
[in,out] | surf | Surface data structure. |
[in] | tbin | Bin number in the zenith angle direction. |
[in] | pbin | Bin number in the azimuthal angle direction. |
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Optimizes the surface bins for faster searching.
[in,out] | surf | Surface data structure. |
Currently, this function does nothing.
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Calculates the distance between unit vectors.
[in] | x1 | Unit vector 1. |
[in] | x2 | Unit vector 2. |
x1
and x2
.This function is used internally to calculate the distance between the unit vectors x1
and x2
to find out whether x2
is within the cone centered at x1
. Currently, the cosine of the angle is used for efficiency, and the minus is there to make it behave like a normal distance (larger values mean longer distances).
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static |
Adds a single reference point and updates the surface bins.
[in,out] | surf | Surface data structure. |
[in] | x | Point to store (should have unit length). |
Finds all the bins covered by the cone centered at x
and calls update_surface_bin() to update them.
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Helper function for store_surface_point() to update a single zenith angle bin.
[in,out] | surf | Surface data structure. |
[in] | tbin | Bin number in the zenith angle direction. |
[in] | phi | Azimuthal angle of x . |
[in] | pdelta1 | Width of the cone at the lower edge of tbin . |
[in] | pdelta2 | Width of the cone at the uppper edge of tbin . |
[in] | pdeltamax | Max. width of the cone inside tbin . |
[in] | x | Point to store (should have unit length). |
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static |
Help text for the insolidangle
selection method.
gmx_ana_selmethod_t sm_insolidangle |
Selection method data for the insolidangle
method.
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static |
Parameters for the insolidangle
selection method.