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Gromacs
2024.3
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Gromacs
2024.3
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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"
Include dependency graph for biasgrid.cpp: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... | |
1.8.5