com.cpp File Reference

#include "gmxpre.h"
#include "gromacs/pbcutil/com.h"
#include <algorithm>
#include <iterator>
#include <vector>
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pbcutil/pbcenums.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/range.h"
#include "gromacs/utility/real.h"

Include dependency graph for com.cpp:

Description

Implements helper methods to place particle COM in boxes.

Author

Paul Bauer paul..nosp@m.baue.nosp@m.r.q@g.nosp@m.mail.nosp@m..com

Functions
RVec	gmx::anonymous_namespace{com.cpp}::evaluateShiftToBox (const RVec &position, const matrix box, const PbcType &pbcType, const UnitCellType &unitCellType, const CenteringType &centerType)
	Calculates shift to place COM into a box. More...
RVec	gmx::anonymous_namespace{com.cpp}::calculateCOM (ArrayRef< const RVec > x, const gmx_moltype_t &moltype, const int atomOffset=0)
	Calculates the COM for each collection of atoms. More...
void	gmx::shiftAtoms (const RVec &shift, ArrayRef< RVec > x)
	Shift all coordinates. More...
void	gmx::placeCoordinatesWithCOMInBox (const PbcType &pbcType, UnitCellType unitCellType, CenteringType centerType, const matrix box, ArrayRef< RVec > x, const gmx_mtop_t &mtop, COMShiftType comShiftType)
	Moves collection of atoms along the center of mass into a box. More...