def jumpfix(sel, **kwargs):
'''
Function passed to the Fasu object that provides the possibility
to fix PBC box jumps. The method is not foolproof, but often works.
'''
from MDAnalysis.coordinates.core import triclinic_vectors
all = sel.selectAtoms('name *')
cen = sel.selectAtoms(kwargs['centre'])
shift = triclinic_vectors(cen.dimensions).diagonal()/2 - cen.centerOfGeometry()
# shift = all.bbox(pbc=True)[1]/2 - cen.centerOfGeometry()
all.translate(shift)
all.packIntoBox()
return all
def dimensions(self, box):
x, y, z = triclinic_vectors(box)
cell = {'x': x, 'y': y, 'z': z}
self._unitcell = cell
def convert_dimensions_to_unitcell(self, ts):
"""Read dimensions from timestep *ts* and return Gromacs box vectors"""
return self.convert_pos_to_native(triclinic_vectors(ts.dimensions))
def dimensions(self, box):
self._unitcell = triclinic_vectors(box)
def dimensions(self, box):
self._unitcell = triclinic_vectors(box)
def dimensions(self, box):
x, y, z = triclinic_vectors(box)
cell = {'x': x, 'y': y, 'z': z}
self._unitcell = cell
def dimensions(self, box):
x, y, z = triclinic_vectors(box)
numpy.put(self._unitcell, self._ts_order_x, x)
numpy.put(self._unitcell, self._ts_order_y, y)
numpy.put(self._unitcell, self._ts_order_z, z)