def fn():
context.application.model.file_open("test/input/silica_layer.zml")
parameters = Parameters()
parameters.interval_a = numpy.array([0.0, 3.0], float)
parameters.interval_b = numpy.array([0.0, 3.0], float)
UnitCellToCluster = context.application.plugins.get_action("UnitCellToCluster")
assert UnitCellToCluster.analyze_selection(parameters)
UnitCellToCluster(parameters)
crd_cluster = [node.transformation.t for node in context.application.model.universe.children]
context.application.model.file_open("test/input/silica_layer.zml")
parameters = Parameters()
parameters.repetitions_a = 3
parameters.repetitions_b = 3
SuperCell = context.application.plugins.get_action("SuperCell")
assert SuperCell.analyze_selection(parameters)
SuperCell(parameters)
crd_super = [node.transformation.t for node in context.application.model.universe.children]
# check that the number of atoms is the same
assert len(crd_super) == len(crd_cluster)
# check if the coordinates match
for c_super in crd_super:
for i in xrange(len(crd_cluster)):
c_cluster = crd_cluster[i]
delta = c_cluster - c_super
delta = context.application.model.universe.shortest_vector(delta)
if numpy.linalg.norm(delta) < 1e-3:
del crd_cluster[i]
break
assert len(crd_cluster) == 0
def default_parameters(cls):
result = Parameters()
universe = context.application.model.universe
if universe.cell.active[0]:
result.repetitions_a = universe.repetitions[0]
if universe.cell.active[1]:
result.repetitions_b = universe.repetitions[1]
if universe.cell.active[2]:
result.repetitions_c = universe.repetitions[2]
return result
def default_parameters(cls):
result = Parameters()
universe = context.application.model.universe
if universe.cell.active[0]:
result.repetitions_a = universe.repetitions[0]
if universe.cell.active[1]:
result.repetitions_b = universe.repetitions[1]
if universe.cell.active[2]:
result.repetitions_c = universe.repetitions[2]
return result
def fn():
context.application.model.file_open("test/input/silica_layer.zml")
AutoConnectPhysical = context.application.plugins.get_action("AutoConnectPhysical")
assert AutoConnectPhysical.analyze_selection()
AutoConnectPhysical()
parameters = Parameters()
parameters.repetitions_a = 2
parameters.repetitions_b = 3
SuperCell = context.application.plugins.get_action("SuperCell")
assert SuperCell.analyze_selection(parameters)
SuperCell(parameters)
Bond = context.application.plugins.get_node("Bond")
for node in context.application.model.universe.children:
if isinstance(node, Bond):
node.calc_vector_dimensions()
assert node.length < 4.0
def fn():
context.application.model.file_open("test/input/silica_layer.zml")
parameters = Parameters()
parameters.repetitions_a = 2
parameters.repetitions_b = 3
SuperCell = context.application.plugins.get_action("SuperCell")
assert SuperCell.analyze_selection(parameters)
SuperCell(parameters)
crd_before = [node.transformation.t for node in context.application.model.universe.children]
WrapCellContents = context.application.plugins.get_action("WrapCellContents")
assert WrapCellContents.analyze_selection()
WrapCellContents()
# coordinates should not be changed
crd_after = [node.transformation.t for node in context.application.model.universe.children]
for i in xrange(len(crd_after)):
assert abs(crd_before[i][0] - crd_after[i][0]) < 1e-5
assert abs(crd_before[i][1] - crd_after[i][1]) < 1e-5
assert abs(crd_before[i][2] - crd_after[i][2]) < 1e-5
