def default_parameters(cls):
result = Parameters()
result.number1 = 6
result.number2 = 6
result.distance = 0.5
result.bond_type = BOND_SINGLE
return result
def fn():
context.application.model.file_open("test/input/core_objects.zml")
context.application.main.toggle_selection(context.application.model.universe.children[3], on=True)
parameters = Parameters()
parameters.translation = Translation([2.0, 4.1, -1.0])
TranslateDialog = context.application.plugins.get_action("TranslateDialog")
assert TranslateDialog.analyze_selection(parameters)
TranslateDialog(parameters)
def fn():
context.application.model.file_open("test/input/core_objects.zml")
context.application.main.toggle_selection(context.application.model.universe.children[3], on=True)
parameters = Parameters()
parameters.rotation = Rotation.from_properties(1.0, numpy.array([0.1, 1.4, 0.3]), False)
RotateDialog = context.application.plugins.get_action("RotateDialog")
assert RotateDialog.analyze_selection(parameters)
RotateDialog(parameters)
def free_optimize(self, springs):
context.application.main.select_nodes(springs)
OptimizeSprings = context.application.plugins.get_action("OptimizeSprings")
parameters = Parameters()
parameters.allow_rotation = True
parameters.update_interval = 0.4
parameters.update_steps = 1
OptimizeSprings(parameters)
def fn():
context.application.model.file_open("test/input/periodic.zml")
parameters = Parameters()
parameters.repetitions_b = 2
parameters.repetitions_c = 3
SuperCell = context.application.plugins.get_action("SuperCell")
assert SuperCell.analyze_selection(parameters)
SuperCell(parameters)
def free_optimize(self, springs):
context.application.main.select_nodes(springs)
OptimizeSprings = context.application.plugins.get_action(
"OptimizeSprings")
parameters = Parameters()
parameters.allow_rotation = True
parameters.update_interval = 0.4
parameters.update_steps = 1
OptimizeSprings(parameters)
def fn():
context.application.model.file_open("test/input/core_objects.zml")
context.application.main.toggle_selection(context.application.model.universe.children[3], on=True)
parameters = Parameters()
parameters.center = numpy.array([1.0, 0.2, -0.9], float)
parameters.normal = numpy.array([2.0, 4.1, -1.0], float)
ReflectionDialog = context.application.plugins.get_action("ReflectionDialog")
assert ReflectionDialog.analyze_selection(parameters)
ReflectionDialog(parameters)
def fn():
context.application.model.file_open("test/input/core_objects.zml")
context.application.main.toggle_selection(context.application.model.universe.children[3], on=True)
context.application.cache.drag_destination = context.application.model.universe.children[2].children[0]
DropTarget = context.application.plugins.get_action("DropTarget")
parameters = Parameters()
parameters.child_index = -1
assert DropTarget.analyze_selection(parameters)
DropTarget(parameters)
def fn():
context.application.model.file_open("test/input/core_objects.zml")
context.application.main.toggle_selection(context.application.model.folder.children[0], on=True)
context.application.cache.drag_destination = context.application.model.folder
parameters = Parameters()
parameters.child_index = 2
MoveNon3DObjects = context.application.plugins.get_action("MoveNon3DObjects")
assert MoveNon3DObjects.analyze_selection(parameters)
MoveNon3DObjects(parameters)
def execute_drag(self, destination, child_index):
parameters = Parameters()
context.application.cache.drag_destination = destination
parameters.child_index = child_index
for drag_action in self.drag_actions:
if drag_action.cached_analyze_selection(parameters=parameters):
drag_action(parameters=parameters)
return True
return False
def default_parameters(cls):
result = Parameters()
universe = context.application.model.universe
if universe.cell.active[0]:
result.interval_a = numpy.array([0.0, universe.repetitions[0]], float)
if universe.cell.active[1]:
result.interval_b = numpy.array([0.0, universe.repetitions[1]], float)
if universe.cell.active[2]:
result.interval_c = numpy.array([0.0, universe.repetitions[2]], float)
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 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/lau.zml")
context.application.main.select_nodes([context.application.model.universe])
parameters = Parameters()
parameters.number1 = 14
parameters.number2 = 14
parameters.distance = 6.0
parameters.bond_type = BOND_SINGLE
AutoConnectParameters = context.application.plugins.get_action("AutoConnectParameters")
assert AutoConnectParameters.analyze_selection(parameters)
AutoConnectParameters(parameters)
def fn():
context.application.model.file_open("test/input/core_objects.zml")
context.application.main.toggle_selection(context.application.model.universe, on=True)
ScaleUnitCell = context.application.plugins.get_action("ScaleUnitCell")
assert ScaleUnitCell.analyze_selection()
parameters = Parameters()
parameters.matrix = numpy.array([
[1.0, 0.0, 0.0],
[0.0, 2.0, 0.0],
[0.0, 0.0, 3.0],
])
ScaleUnitCell(parameters)
def fn():
context.application.model.file_open("test/input/precursor.zml")
context.application.main.select_nodes([context.application.model.universe])
parameters = Parameters()
parameters.filter_atom1 = Expression()
parameters.filter_bond12 = Expression()
parameters.filter_atom2 = Expression()
DistributionBondLengths = context.application.plugins.get_action("DistributionBondLengths")
assert DistributionBondLengths.analyze_selection(parameters)
DistributionBondLengths(parameters)
def default_parameters(cls):
result = Parameters()
universe = context.application.model.universe
if universe.cell.active[0]:
result.interval_a = numpy.array([0.0, universe.repetitions[0]],
float)
if universe.cell.active[1]:
result.interval_b = numpy.array([0.0, universe.repetitions[1]],
float)
if universe.cell.active[2]:
result.interval_c = numpy.array([0.0, universe.repetitions[2]],
float)
return result
def default_parameters(cls):
result = Parameters()
result.filter_atom1 = Expression()
result.filter_bond12 = Expression()
result.filter_atom2 = Expression()
result.filter_bond23 = Expression()
result.filter_atom3 = Expression()
result.filter_bond34 = Expression()
result.filter_atom4 = Expression()
return result
def fn():
context.application.model.file_open("test/input/springs.zml")
context.application.main.select_nodes(
context.application.model.universe.children[7:9][::-1] +
context.application.model.universe.children[2:6][::-1])
parameters = Parameters()
parameters.allow_rotation = True
parameters.update_interval = 0.4
parameters.update_steps = 1
OptimizeSprings = context.application.plugins.get_action(
"OptimizeSprings")
assert OptimizeSprings.analyze_selection(parameters)
OptimizeSprings(parameters)
def fn():
context.application.model.file_open("test/input/springs.zml")
context.application.main.select_nodes(
context.application.model.universe.children[7:9][::-1] +
context.application.model.universe.children[2:6][::-1]
)
parameters = Parameters()
parameters.allow_rotation = True
parameters.update_interval = 0.4
parameters.update_steps = 1
OptimizeSprings = context.application.plugins.get_action("OptimizeSprings")
assert OptimizeSprings.analyze_selection(parameters)
OptimizeSprings(parameters)
def fn():
context.application.model.file_open("test/input/precursor.zml")
context.application.main.select_nodes(
[context.application.model.universe])
parameters = Parameters()
parameters.filter_atom1 = Expression()
parameters.filter_bond12 = Expression()
parameters.filter_atom2 = Expression()
DistributionBondLengths = context.application.plugins.get_action(
"DistributionBondLengths")
assert DistributionBondLengths.analyze_selection(parameters)
DistributionBondLengths(parameters)
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 fn():
context.application.model.file_open("test/input/tpa.zml")
universe = context.application.model.universe
context.application.main.select_nodes([universe] + universe.children)
parameters = Parameters()
parameters.number1 = 6
parameters.number2 = 6
parameters.distance = 3.0
parameters.bond_type = BOND_SINGLE
AutoConnectParameters = context.application.plugins.get_action("AutoConnectParameters")
assert AutoConnectParameters.analyze_selection(parameters)
AutoConnectParameters(parameters)
Bond = context.application.plugins.get_node("Bond")
num_bonds = sum(isinstance(node,Bond) for node in universe.children)
assert num_bonds == 2*4
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 default_parameters(cls):
result = Parameters()
result.n = 5
result.m = 1
result.flat = False
result.max_length = 50 * angstrom
result.max_error = 0.01 * angstrom
result.tube_length = Undefined(50 * angstrom)
return result
def fn():
context.application.model.file_open("test/input/sod.zml")
parameters = Parameters()
parameters.interval_b = numpy.array([-0.5, 2.5], float)
parameters.interval_c = numpy.array([-1.5, 1.5], float)
UnitCellToCluster = context.application.plugins.get_action("UnitCellToCluster")
assert UnitCellToCluster.analyze_selection(parameters)
UnitCellToCluster(parameters)
# check the bond lengths
Bond = context.application.plugins.get_node("Bond")
universe = context.application.model.universe
for bond in context.application.model.universe.children:
if isinstance(bond, Bond):
delta = bond.children[0].target.transformation.t - bond.children[1].target.transformation.t
delta = universe.shortest_vector(delta)
distance = numpy.linalg.norm(delta)
assert distance < 4.0
def default_parameters(cls):
result = Parameters()
result.filter_atom1 = Expression()
result.filter_bond12 = Expression()
result.filter_atom2 = Expression()
result.filter_bond23 = Expression()
result.filter_atom3 = Expression()
result.filter_bond34 = Expression()
result.filter_atom4 = Expression()
return result
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
def fn():
context.application.model.file_open("test/input/silica_layer.zml")
parameters = Parameters()
parameters.n = 10
parameters.m = 4
parameters.flat = False
parameters.max_length = 300 * angstrom
parameters.max_error = 0.01 * angstrom
parameters.tube_length = Undefined(0.01 * angstrom)
CreateTube = context.application.plugins.get_action("CreateTube")
assert CreateTube.analyze_selection(parameters)
CreateTube(parameters)
def fn():
context.application.model.file_open("test/input/tpa.xyz")
Atom = context.application.plugins.get_node("Atom")
for child in context.application.model.universe.children[::-1]:
if isinstance(child, Atom) and child.number == 1:
context.application.model.universe.children.remove(child)
context.application.main.select_nodes([context.application.model.universe])
AutoConnectPhysical = context.application.plugins.get_action("AutoConnectPhysical")
assert AutoConnectPhysical.analyze_selection()
AutoConnectPhysical()
parameters = Parameters()
parameters.num_hydrogens = 2
parameters.valence_angle = 1.9093
context.application.main.select_nodes([context.application.model.universe.children[1]])
SaturateHydrogensManual = context.application.plugins.get_action("SaturateHydrogensManual")
assert SaturateHydrogensManual.analyze_selection(parameters)
SaturateHydrogensManual(parameters)
def default_parameters(cls):
result = Parameters()
result.n = 5
result.m = 1
result.flat = False
result.max_length = 50*angstrom
result.max_error = 0.01*angstrom
result.tube_length = Undefined(50*angstrom)
return result
def fn():
FileNew = context.application.plugins.get_action("FileNew")
FileNew()
context.application.main.select_nodes([context.application.model.folder])
AddFolder = context.application.plugins.get_action("AddFolder")
assert AddFolder.analyze_selection()
AddFolder()
context.application.main.select_nodes([context.application.model.folder])
AddNotes = context.application.plugins.get_action("AddNotes")
assert AddNotes.analyze_selection()
AddNotes()
context.application.main.select_nodes([context.application.model.folder])
SelectChildrenByExpression = context.application.plugins.get_action("SelectChildrenByExpression")
parameters = Parameters()
parameters.recursive = SelectChildrenByExpression.SELECT_PLAIN
parameters.expression = Expression("isinstance(node, Folder)")
assert SelectChildrenByExpression.analyze_selection(parameters)
SelectChildrenByExpression(parameters)
assert context.application.model.folder.children[0].selected
assert not context.application.model.folder.children[1].selected
def default_parameters(cls):
result = Parameters()
result.number1 = 6
result.number2 = 6
result.distance = 0.5
result.bond_type = BOND_SINGLE
return result
def fn():
context.application.model.file_open("test/input/silica_layer.zml")
parameters = Parameters()
parameters.n = 10
parameters.m = 4
parameters.flat = False
parameters.max_length = 300*angstrom
parameters.max_error = 0.01*angstrom
parameters.tube_length = Undefined(0.01*angstrom)
CreateTube = context.application.plugins.get_action("CreateTube")
assert CreateTube.analyze_selection(parameters)
CreateTube(parameters)
def fn():
context.application.model.file_open("test/input/tpa.xyz")
Atom = context.application.plugins.get_node("Atom")
for child in context.application.model.universe.children[::-1]:
if isinstance(child, Atom) and child.number == 1:
context.application.model.universe.children.remove(child)
context.application.main.select_nodes(
[context.application.model.universe])
AutoConnectPhysical = context.application.plugins.get_action(
"AutoConnectPhysical")
assert AutoConnectPhysical.analyze_selection()
AutoConnectPhysical()
parameters = Parameters()
parameters.num_hydrogens = 2
parameters.valence_angle = 1.9093
context.application.main.select_nodes(
[context.application.model.universe.children[1]])
SaturateHydrogensManual = context.application.plugins.get_action(
"SaturateHydrogensManual")
assert SaturateHydrogensManual.analyze_selection(parameters)
SaturateHydrogensManual(parameters)
def fn():
context.application.model.file_open("test/input/lau.zml")
context.application.main.select_nodes(
[context.application.model.universe])
parameters = Parameters()
parameters.number1 = 14
parameters.number2 = 14
parameters.distance = 6.0
parameters.bond_type = BOND_SINGLE
AutoConnectParameters = context.application.plugins.get_action(
"AutoConnectParameters")
assert AutoConnectParameters.analyze_selection(parameters)
AutoConnectParameters(parameters)
def fn():
context.application.model.file_open("test/input/tpa.zml")
universe = context.application.model.universe
context.application.main.select_nodes([universe] + universe.children)
parameters = Parameters()
parameters.number1 = 6
parameters.number2 = 6
parameters.distance = 3.0
parameters.bond_type = BOND_SINGLE
AutoConnectParameters = context.application.plugins.get_action(
"AutoConnectParameters")
assert AutoConnectParameters.analyze_selection(parameters)
AutoConnectParameters(parameters)
Bond = context.application.plugins.get_node("Bond")
num_bonds = sum(isinstance(node, Bond) for node in universe.children)
assert num_bonds == 2 * 4
def default_parameters(cls):
result = Parameters()
result.matrix = context.application.model.universe.cell.matrix.copy()
return result
def default_parameters(cls):
result = Parameters()
result.expression = Expression()
result.recursive = cls.SELECT_PLAIN
return result
def default_parameters(cls):
rotation2 = Rotation.from_properties(0.0, [1, 0, 0], False)
result = Parameters()
result.connect_description1 = (Expression("True"),
Expression("node.get_radius()"))
result.repulse_description1 = (Expression("True"),
Expression("node.get_radius()"))
result.connect_description2 = (Expression("True"),
Expression("node.get_radius()"))
result.repulse_description2 = (Expression("True"),
Expression("node.get_radius()"))
result.action_radius = 7 * angstrom
result.distance_tolerance = 0.1 * angstrom
result.hit_tolerance = 0.1 * angstrom
result.allow_inversions = True
result.minimum_triangle_size = 0.1 * angstrom
result.rotation_tolerance = 0.05
result.rotation2 = Undefined(rotation2)
return result
def default_parameters(cls):
result = Parameters()
result.num_hydrogens = 2
result.valence_angle = 109.4 * deg
return result
def default_parameters(cls):
result = Parameters()
result.matrix = context.application.model.universe.cell.matrix.copy()
return result
def default_parameters(cls):
result = Parameters()
result.center = numpy.zeros(3, float)
result.normal = numpy.zeros(3, float)
return result
def default_parameters(cls):
result = Parameters()
result.allow_rotation = True
result.update_interval = 0.4
result.update_steps = 1
return result
def default_parameters(cls):
result = Parameters()
result.center = Translation.identity()
result.rotation = Rotation.identity()
return result
def default_parameters(cls):
result = Parameters()
result.translation = Translation.identity()
return result
def default_parameters(cls):
result = Parameters()
result.center = numpy.zeros(3, float)
result.normal = numpy.zeros(3, float)
return result
def default_parameters(cls):
result = Parameters()
result.expression = Expression()
result.recursive = cls.SELECT_PLAIN
return result