""" Module contains helper functions to build microtubules, centrosomes
and interMT connectors"""
from abaqus import *
from abaqusConstants import *
import section
import regionToolset
import part
import material
import sketch
[docs]def create_MT_part( l, type, i, **kwargs ):
"""
Create an Abaqus object representing a single microtubule part
:param l: Length of the microtuble
:type l: float
:param type: Type of the MT: aMT or ipMT
:type type: str
:param i: sequential number of the MT
:type i: str
:param kwargs: model parameters
:type kwargs: dict
:return: part object, MTname
:rtype: object, str
"""
modelname = kwargs['modelname']
s = mdb.models[modelname].ConstrainedSketch(
name='__profile__',
sheetSize=1.0)
g, v, d, c = s.geometry, s.vertices, s.dimensions, s.constraints
s.sketchOptions.setValues(decimalPlaces=3)
s.setPrimaryObject(option=STANDALONE)
# create line
s.Line(point1=(0.0, 0.0), point2=(l, 0.0))
# create a name for MT
MTname = create_mt_name(l, type, i)
# Create part
p = mdb.models[modelname].Part(
name=MTname,
dimensionality=THREE_D,
type=DEFORMABLE_BODY)
p = mdb.models[modelname].parts[MTname]
p.BaseWire(sketch=s)
s.unsetPrimaryObject()
del mdb.models[modelname].sketches['__profile__']
return p, MTname
[docs]def create_connector_part( connectorname, length, **kwargs ):
"""
Create an Abaqus object that represents a single connector part
:param connectorname: Name of the connector
:type connectorname: str
:param length: Length of the connector
:type length: float
:param kwargs: model parameters
:type kwargs: dict
:return: Part object
:rtype: object
"""
modelname = kwargs['modelname']
s = mdb.models[modelname].ConstrainedSketch(
name='__profile__',
sheetSize=1)
g, v, d, c = s.geometry, s.vertices, s.dimensions, s.constraints
s.sketchOptions.setValues(decimalPlaces=4)
s.setPrimaryObject(option=STANDALONE)
# create line
s.Line(point1=(0.0, 0.0), point2=(0.0, length))
p = mdb.models[modelname].Part(
name=connectorname,
dimensionality=THREE_D,
type=DEFORMABLE_BODY)
p = mdb.models[modelname].parts[connectorname]
p.BaseWire(sketch=s)
s.unsetPrimaryObject()
del mdb.models[modelname].sketches['__profile__']
return p
[docs]def create_centrosome_sketch( l, r, **kwargs ):
"""
Create a 2D sketch of the centrosome middle cross-section
:param l: Length of the centrosome, e.g., dimension along z axis
:type l: float
:param r: Radius of the centrosome, e.g., radius of the centrosome cross-section
in x-y plane
:type r: float
:param kwargs: model parameters
:type kwargs: dict
:return: Sketch object
:rtype: object
"""
modelname = kwargs['modelname']
s = mdb.models[modelname].ConstrainedSketch(
name='__profile__', sheetSize=2.0)
g, v, d, c = s.geometry, s.vertices, s.dimensions, s.constraints
# Create cross-sectoion
s.setPrimaryObject(option=STANDALONE)
# Define an axis of revolution
s.ConstructionLine(point1=(0.0, -1.0), point2=(0.0, 1.0))
# Create a revolution sketch
s.FixedConstraint(entity=g[2])
s.Arc3Points(point1=(0.0, r), point2=(0.0, -r), point3=(l / 2, 0.0))
s.Line(point1=(0.0, -r), point2=(0.0, r))
s.VerticalConstraint(entity=g[4], addUndoState=False)
return s
[docs]def create_mt_name( l, type, i ):
"""
Specify a unique name to each created microtubule
:param l: Length of the MT
:type l: float
:param type: Type of the MT: aMT or ipMT
:type type: str
:param i: sequential number of the MT
:type i: int
:return: MTname
:rtype: str
"""
if type == 'ipMT':
MTname = 'ipMT_' + str(l * 100)[:3] + '_' + str(i)
print(MTname)
elif type == 'aMT':
MTname = 'aMT_' + str(i)
else:
raise ValueError('Only interpolar MTs (ipMT) and astral MTs (aMT) are currently supported')
return MTname
[docs]def create_section( sectionName, sectionProfile, sectionMaterial, **kwargs ):
"""
Create a beam section for the microtubule
:param sectionName: Name of the section. 'MT-section'
:type sectionName: str
:param sectionProfile: Type of the section profile. 'MT-profile'
:type sectionProfile: str
:param sectionMaterial: Name of the material assigned to the section. 'MT_material'
:type sectionMaterial: str
:param kwargs: model parameters
:type kwargs: dict
:return: Null
:rtype: Null
"""
modelname = kwargs['modelname']
mdb.models[modelname].BeamSection(
name=sectionName,
integration=DURING_ANALYSIS,
poissonRatio=0.0,
profile=sectionProfile,
material=sectionMaterial,
temperatureVar=LINEAR,
consistentMassMatrix=False)
[docs]def define_material( name, E, nu, **kwargs ):
"""
Define material parameters of microtubules, connectors and centrosomes specifying
its module of elasticity and Poisson's ratio
:param name: Name of the material
:type name: str
:param E: Module of elasticity
:type E: float
:param nu: Poisson's ratio
:type nu: float
:param kwargs: model parameters
:type kwargs: dict
:return: Null
:rtype: Null
"""
modelname = kwargs['modelname']
mdb.models[modelname].Material(name=name)
mdb.models[modelname].materials[name].Elastic(table=((E, nu),))
[docs]def assign_MT_section( part, MTname, **kwargs ):
"""
Assign a section to microtubules
:param part: Microtubule part to which section to be assigned
:type part: object
:param MTname: Name of the microtubule
:type MTname: str
:param kwargs: model parameters
:type kwargs: dict
:return: Null
:rtype: Null
"""
modelname = kwargs['modelname']
e = part.edges
edges = e.getByBoundingSphere((0.0, 0.0, 0.0), (kwargs['spindleLength']), )
region = part.Set(edges=edges, name='MT-set')
p = mdb.models[modelname].parts[MTname]
p.SectionAssignment(
region=region, sectionName='MT-section', offset=0.0,
offsetType=MIDDLE_SURFACE, offsetField='',
thicknessAssignment=FROM_SECTION)
[docs]def assign_MT_section_orientation( MTname, **kwargs ):
"""
Assign MT section orientation with respect to the local coordinates of the MT
:param MTname: Name of the microtubule
:type MTname: str
:param kwargs: model parameters
:type kwargs: dict
:return: Null
:rtype: Null
"""
modelname = kwargs['modelname']
p = mdb.models[modelname].parts[MTname]
e = p.edges
edges = e.getSequenceFromMask(mask=('[#1 ]',), )
region = p.Set(edges=edges, name='MT-set')
p = mdb.models[modelname].parts[MTname]
p.assignBeamSectionOrientation(
region=region,
method=N1_COSINES,
n1=(0.0, 0.0, -1.0))
[docs]def assign_connector_section( part, name, **kwargs ):
"""
Assign a section to each connector
:param part: Connector part to which section to be assigned
:type part: object
:param name: Name of the connector
:type name: str
:param kwargs: model parameters
:type kwargs: dict
:return: Region containing connector
:rtype: object
"""
e = part.edges
edges = e.getByBoundingSphere((0.0, 0.0, 0.0), (kwargs['spindleLength']), )
region = part.Set(edges=edges, name='connector-set')
part.SectionAssignment(
region=region, sectionName=name, offset=0.0,
offsetType=MIDDLE_SURFACE, offsetField='',
thicknessAssignment=FROM_SECTION)
return region
[docs]def create_centrosome_part( Centrosomesketch, name, **kwargs ):
"""
Create an Abaqus object containing centrosome geometry part
:param Centrosomesketch: Name of the centrosome sketch object
:type Centrosomesketch: str
:param name: Name of the centrosome part
:type name: object
:param kwargs: model parameters
:type kwargs: str
:return: Centrosome part
:rtype: object
"""
modelname = kwargs['modelname']
p = mdb.models[modelname].Part(
name=name,
dimensionality=THREE_D,
type=DEFORMABLE_BODY)
p = mdb.models[modelname].parts[name]
p.BaseSolidRevolve(sketch=Centrosomesketch, angle=360.0, flipRevolveDirection=OFF)
Centrosomesketch.unsetPrimaryObject()
p = mdb.models[modelname].parts[name]
del mdb.models[modelname].sketches['__profile__']
return p
[docs]def assign_centrosome_section( part, name, sectionName, **kwargs ):
"""
Assign section to the Centrosome part
:param part: Centrosome part to which the section is to be assigned
:type part: object
:param name: Name of the centrosome
:type name: str
:param sectionName: Name of the section to be assigned
:type sectionName: str
:param kwargs: model parameters
:type kwargs: dict
:return: Null
:rtype: Null
"""
modelname = kwargs['modelname']
c = part.cells
cells = c.getByBoundingSphere((0.0, 0.0, 0.0), (kwargs['spindleLength']), )
region = part.Set(cells=cells, name='centrosome-set')
p = mdb.models[modelname].parts[name]
p.SectionAssignment(
region=region,
sectionName=sectionName, offset=0.0,
offsetType=MIDDLE_SURFACE, offsetField='',
thicknessAssignment=FROM_SECTION)
[docs]def model( **kwargs ):
"""
Create Abaqus model for the mitotic spindle
:param kwargs: model parameters
:type kwargs: dict
:return: Null
:rtype: Null
"""
modelname = kwargs['modelname']
# Create and save model database
mdb.Model(name=modelname, modelType=STANDARD_EXPLICIT)
