gmx::test::anonymous_namespace{mshift.cpp} Namespace Reference

Functions
gmx_moltype_t	moleculeType ()
	Returns a molectype for generate a graph. More...
std::vector< RVec >	coordinates ()
	Coordinates for moleculeType() broken over PBC. More...
std::vector< RVec >	coordinatesWhole ()
	Coordinates for moleculeType() made whole. More...

Variables
constexpr matrix	c_box = { { 3, 0, 0 }, { 0, 3, 0 }, { 0, 0, 3 } }
	Box to go with coordinates()

Function Documentation

std::vector<RVec> gmx::test::anonymous_namespace{mshift.cpp}::coordinates

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Coordinates for moleculeType() broken over PBC.

The middle 3 atoms all need to be shifted with respect to each other to make the molecule whole. The first and last atom are not connected, so their coordinates are irrelevant for this test.

std::vector<RVec> gmx::test::anonymous_namespace{mshift.cpp}::coordinatesWhole

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Coordinates for moleculeType() made whole.

These coordinates assume the the periodic image for the molecule is chosen the same as the first connected atom.

gmx_moltype_t gmx::test::anonymous_namespace{mshift.cpp}::moleculeType

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Returns a molectype for generate a graph.

This moleculetype has the first and last atom not connected to the other atoms so we test optimizations in the shift code that generates the actual graph only for the atom range from the first to the last connected atoms.