Gromacs
2024.4
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#include "gmxpre.h"
#include "biasgrid.h"
#include <cassert>
#include <cmath>
#include <cstring>
#include <algorithm>
#include <optional>
#include "gromacs/math/functions.h"
#include "gromacs/math/utilities.h"
#include "gromacs/mdtypes/awh_params.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/stringutil.h"
Implements functions in grid.h.
Functions | |
double | gmx::anonymous_namespace{biasgrid.cpp}::centerPeriodicValueAroundZero (const double x, double period) |
Return x so that it is periodic in [-period/2, +period/2). More... | |
int | gmx::anonymous_namespace{biasgrid.cpp}::indexWithinPeriod (int x, int period) |
If period>0, return x so that it is periodic in [0, period), else return x. More... | |
double | gmx::anonymous_namespace{biasgrid.cpp}::getIntervalLengthPeriodic (double origin, double end, double period) |
Get the length of the interval (origin, end). More... | |
double | gmx::anonymous_namespace{biasgrid.cpp}::getDeviationPeriodic (double x, double x0, double period) |
Get the deviation x - x0. More... | |
double | gmx::getDeviationFromPointAlongGridAxis (const BiasGrid &grid, int dimIndex, int pointIndex, double value) |
Get the deviation along one dimension from the given value to a point in the grid. More... | |
double | gmx::getDeviationFromPointAlongGridAxis (const BiasGrid &grid, int dimIndex, int pointIndex1, int pointIndex2) |
Get the deviation from one point to another along one dimension in the grid. More... | |
bool | gmx::pointsAlongLambdaAxis (const BiasGrid &grid, int pointIndex1, int pointIndex2) |
Checks whether two points are along a free energy lambda state axis. More... | |
bool | gmx::pointsHaveDifferentLambda (const BiasGrid &grid, int pointIndex1, int pointIndex2) |
Checks whether two points are different in the free energy lambda state dimension (if any). More... | |
void | gmx::linearArrayIndexToMultiDim (int indexLinear, int ndim, const awh_ivec numPointsDim, awh_ivec indexMulti) |
Convert a linear array index to a multidimensional one. More... | |
void | gmx::linearGridindexToMultiDim (const BiasGrid &grid, int indexLinear, awh_ivec indexMulti) |
Convert a linear grid point index to a multidimensional one. More... | |
int | gmx::multiDimArrayIndexToLinear (const awh_ivec indexMulti, int numDim, const awh_ivec numPointsDim) |
Convert multidimensional array index to a linear one. More... | |
int | gmx::anonymous_namespace{biasgrid.cpp}::multiDimGridIndexToLinear (ArrayRef< const GridAxis > axis, const awh_ivec indexMulti) |
Convert a multidimensional grid point index to a linear one. More... | |
int | gmx::multiDimGridIndexToLinear (const BiasGrid &grid, const awh_ivec indexMulti) |
Convert a multidimensional grid point index to a linear one. More... | |
bool | gmx::anonymous_namespace{biasgrid.cpp}::stepInMultiDimArray (int numDim, const awh_ivec numPoints, awh_ivec indexDim) |
Take a step in a multidimensional array. More... | |
void | gmx::anonymous_namespace{biasgrid.cpp}::gridToSubgridIndex (const BiasGrid &grid, const awh_ivec subgridOrigin, const awh_ivec subgridNpoints, int point, awh_ivec subgridIndex) |
Transforms a grid point index to to the multidimensional index of a subgrid. More... | |
bool | gmx::anonymous_namespace{biasgrid.cpp}::subgridToGridIndex (const BiasGrid &grid, const awh_ivec subgridOrigin, const awh_ivec subgridIndex, int *gridIndex) |
Transform a multidimensional subgrid index to a grid point index. More... | |
bool | gmx::advancePointInSubgrid (const BiasGrid &grid, const awh_ivec subgridOrigin, const awh_ivec subgridNpoints, int *gridPointIndex) |
Find the next grid point in the sub-part of the grid given a starting point. More... | |
static int | gmx::pointDistanceAlongAxis (const GridAxis &axis, double x, double x0) |
Returns the point distance between from value x to value x0 along the given axis. More... | |
static bool | gmx::valueIsInGrid (const awh_dvec value, ArrayRef< const GridAxis > axis) |
Query if a value is in range of the grid. More... | |
static int | gmx::getNearestIndexInGrid (const awh_dvec value, ArrayRef< const GridAxis > axis) |
Map a value to the nearest point in the grid. More... | |
void | gmx::anonymous_namespace{biasgrid.cpp}::setNeighborsOfGridPoint (int pointIndex, const BiasGrid &grid, std::vector< int > *neighborIndexArray) |
Find and set the neighbors of a grid point. More... | |
void | gmx::mapGridToDataGrid (std::vector< int > *gridpointToDatapoint, const MultiDimArray< std::vector< double >, dynamicExtents2D > &data, int numDataPoints, const std::string &dataFilename, const BiasGrid &grid, const std::string &correctFormatMessage) |
Maps each point in the grid to a point in the data grid. More... | |