mpacts.contact.models.collision. contractilerepulsive

In order to be able to use this module import it like this:

import mpacts.contact.models.collision.contractilerepulsive
#or assign it to a shorter name
import mpacts.contact.models.collision.contractilerepulsive as con

ContractileHertzRandomWalk2Matrix

Description: Contact model between 3D spherical cells (pc2) and other bodies that are contractile with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in pc2 in the direction of a given vector array. Geometry combinations available:

PC2 | PC1 - Sphere Rigid_Triangle Rigid_Sphere Rigid_RoundedTriangle Rigid_Quad Rigid_CylinderTop Rigid_CylinderBottom Rigid_Cylinder Rigid_Cone Rigid_Capsule Deformable_Triangle Deformable_RoundedTriangle Deformable_Line Deformable_Capsule
Sphere YES YES YES YES YES YES YES YES YES YES YES YES YES YES

ContractileHertzRandomWalk2Matrix (Deformable_Capsule Sphere)

Contact model between 3D spherical cells (pc2) and other bodies that are contractile with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in pc2 in the direction of a given vector array.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • Fc — Magnitude of the constant contractile force (Could be modified). Note that positive values indicate contractile (adhesive) forces here!
    • fraction_hardsphere — Fraction of radius below which hard sphere repulsion starts. Must be between ]0,1]
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu2 — Poisson ratio for hard-core repulsion material 2.
    • orientation1 — Vector which keeps the direction in which the particle tries to go for pc1.
    • orientation2 — Vector which keeps the direction in which the particle tries to go for pc2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • contact_data_storage_factory (default value = None) — The contact data storage factory to make contact data. Do not change! Especially vector in parallel is not a safe choice here.
    • contact_data (default value = None) — The contact data belonging to the DoF (parents) made by this model.
    • eta_front (default value = 0.14999999999999999) — protrusion threshold value
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • traction (default value = -1) — Traction applied to achieve relative motion. If not given, parameter ‘walk_force’ must be specified.
    • transpose (default value = 0) — switches around pc1 and pc2 for the ContactMatrix.
    • tune_angle (default value = 0.92729521800161219) — nu
    • walk_force (default value = -1) — Total walk force applied to achieve relative motion. If not given, parameter ‘traction’ must be specified.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataDeformable_Cylinder_1_DataCapsule_SphereN_ContractileForce2_HertzT_DirectedWalkN_T_AreaWeightedResistanceAssembleForces_2AssembleForces_DeformableCylinder_1Assemble_ContactArea_2Assemble_VirialStress_2ComputeContactMatrixElementOverdampedDeformableCapsuleDof_1SphereDof_2AssembleContactMatrix_ComposedParticleFeedback

ContractileHertzRandomWalk2Matrix (Deformable_Line Sphere)

Contact model between 3D spherical cells (pc2) and other bodies that are contractile with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in pc2 in the direction of a given vector array.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • Fc — Magnitude of the constant contractile force (Could be modified). Note that positive values indicate contractile (adhesive) forces here!
    • fraction_hardsphere — Fraction of radius below which hard sphere repulsion starts. Must be between ]0,1]
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu2 — Poisson ratio for hard-core repulsion material 2.
    • orientation1 — Vector which keeps the direction in which the particle tries to go for pc1.
    • orientation2 — Vector which keeps the direction in which the particle tries to go for pc2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • eta_front (default value = 0.14999999999999999) — protrusion threshold value
    • orthogonal_to (default value = 0 0 1) — Direction ‘out of plane’ for the 2D system. Default = (0,0,1).
    • reject_larger_radius (default value = 1) — If true, overlaps larger than the sphere’s radius will be rejected’
    • traction (default value = -1) — Traction applied to achieve relative motion. If not given, parameter ‘walk_force’ must be specified.
    • tune_angle (default value = 0.92729521800161219) — nu
    • walk_force (default value = -1) — Total walk force applied to achieve relative motion. If not given, parameter ‘traction’ must be specified.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataDeformable_Line_1_DataLine_SphereN_ContractileForce2_HertzT_DirectedWalkN_T_AreaWeightedResistanceAssembleForces_2AssembleForces_DeformableCylinder_1Assemble_ContactArea_2Assemble_VirialStress_2Feedback

ContractileHertzRandomWalk2Matrix (Deformable_RoundedTriangle Sphere)

Contact model between 3D spherical cells (pc2) and other bodies that are contractile with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in pc2 in the direction of a given vector array.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • Fc — Magnitude of the constant contractile force (Could be modified). Note that positive values indicate contractile (adhesive) forces here!
    • fraction_hardsphere — Fraction of radius below which hard sphere repulsion starts. Must be between ]0,1]
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu2 — Poisson ratio for hard-core repulsion material 2.
    • orientation1 — Vector which keeps the direction in which the particle tries to go for pc1.
    • orientation2 — Vector which keeps the direction in which the particle tries to go for pc2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • contact_data_storage_factory (default value = None) — The contact data storage factory to make contact data. Do not change! Especially vector in parallel is not a safe choice here.
    • contact_data (default value = None) — The contact data belonging to the DoF (parents) made by this model.
    • disable_warning_fake_rounded_triangle (default value = 0) — Disables the printing of the specified warning message.
    • eta_front (default value = 0.14999999999999999) — protrusion threshold value
    • flip_normals (default value = 0) — Optionally flip normals if sphere is more than its radius submerged. In most cases, we recommend that you leave this option to its default ‘false’.
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • reject_large_overlap (default value = 1) — Optionally reject overlaps reject_overlap_r times larger than the radius. Unless you have a fully concave ‘container’ geometry, we recommend that you leave this value to its default ‘true’.
    • reject_overlap_r (default value = 1) — If reject_large_overlap is True, this specifies the number of sphere radii of overlap that should be rejected (Default=1).
    • traction (default value = -1) — Traction applied to achieve relative motion. If not given, parameter ‘walk_force’ must be specified.
    • transpose (default value = 0) — switches around pc1 and pc2 for the ContactMatrix.
    • tune_angle (default value = 0.92729521800161219) — nu
    • walk_force (default value = -1) — Total walk force applied to achieve relative motion. If not given, parameter ‘traction’ must be specified.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataDeformable_NGon_1_Data  <3 >
  ↓
NGon_SphereWarningMessage  <WARN::FakeRoundedTriangle >
  ↓
N_ContractileForce2_HertzT_DirectedWalkN_T_AreaWeightedResistanceAssembleForces_DeformableTriangleBarycentric_1AssembleForces_2Assemble_ContactArea_2Assemble_VirialStress_2ComputeContactMatrixElementOverdampedDeformableTriangleBarycentricDof_1SphereDof_2AssembleContactMatrix_ComposedParticleFeedback

ContractileHertzRandomWalk2Matrix (Deformable_Triangle Sphere)

Contact model between 3D spherical cells (pc2) and other bodies that are contractile with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in pc2 in the direction of a given vector array.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • Fc — Magnitude of the constant contractile force (Could be modified). Note that positive values indicate contractile (adhesive) forces here!
    • fraction_hardsphere — Fraction of radius below which hard sphere repulsion starts. Must be between ]0,1]
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu2 — Poisson ratio for hard-core repulsion material 2.
    • orientation1 — Vector which keeps the direction in which the particle tries to go for pc1.
    • orientation2 — Vector which keeps the direction in which the particle tries to go for pc2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • contact_data_storage_factory (default value = None) — The contact data storage factory to make contact data. Do not change! Especially vector in parallel is not a safe choice here.
    • contact_data (default value = None) — The contact data belonging to the DoF (parents) made by this model.
    • eta_front (default value = 0.14999999999999999) — protrusion threshold value
    • flip_normals (default value = 0) — Optionally flip normals if sphere is more than its radius submerged. In most cases, we recommend that you leave this option to its default ‘false’.
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • reject_large_overlap (default value = 1) — Optionally reject overlaps reject_overlap_r times larger than the radius. Unless you have a fully concave ‘container’ geometry, we recommend that you leave this value to its default ‘true’.
    • reject_overlap_r (default value = 1) — If reject_large_overlap is True, this specifies the number of sphere radii of overlap that should be rejected (Default=1).
    • traction (default value = -1) — Traction applied to achieve relative motion. If not given, parameter ‘walk_force’ must be specified.
    • transpose (default value = 0) — switches around pc1 and pc2 for the ContactMatrix.
    • tune_angle (default value = 0.92729521800161219) — nu
    • walk_force (default value = -1) — Total walk force applied to achieve relative motion. If not given, parameter ‘traction’ must be specified.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataDeformable_NGon_1_Data  <3 >
  ↓
NGon_SphereN_ContractileForce2_HertzT_DirectedWalkN_T_AreaWeightedResistanceAssembleForces_DeformableTriangleBarycentric_1AssembleForces_2Assemble_ContactArea_2Assemble_VirialStress_2ComputeContactMatrixElementOverdampedDeformableTriangleBarycentricDof_1SphereDof_2AssembleContactMatrix_ComposedParticleFeedback

ContractileHertzRandomWalk2Matrix (Rigid_Capsule Sphere)

Contact model between 3D spherical cells (pc2) and other bodies that are contractile with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in pc2 in the direction of a given vector array.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • Fc — Magnitude of the constant contractile force (Could be modified). Note that positive values indicate contractile (adhesive) forces here!
    • fraction_hardsphere — Fraction of radius below which hard sphere repulsion starts. Must be between ]0,1]
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu2 — Poisson ratio for hard-core repulsion material 2.
    • orientation1 — Vector which keeps the direction in which the particle tries to go for pc1.
    • orientation2 — Vector which keeps the direction in which the particle tries to go for pc2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • eta_front (default value = 0.14999999999999999) — protrusion threshold value
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • traction (default value = -1) — Traction applied to achieve relative motion. If not given, parameter ‘walk_force’ must be specified.
    • tune_angle (default value = 0.92729521800161219) — nu
    • walk_force (default value = -1) — Total walk force applied to achieve relative motion. If not given, parameter ‘traction’ must be specified.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataRigid_Cylinder_1_DataCylinder_SphereN_ContractileForce2_HertzT_DirectedWalkN_T_AreaWeightedResistanceAssembleForcesAssemble_ContactArea_2Assemble_VirialStress_2ComputeContactMatrixElementOverdampedRigidBodyDof_1SphereDof_2AssembleContactMatrixToDiagonal_2FrictionMatrixForce_2Feedback

ContractileHertzRandomWalk2Matrix (Rigid_Cone Sphere)

Contact model between 3D spherical cells (pc2) and other bodies that are contractile with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in pc2 in the direction of a given vector array.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • Fc — Magnitude of the constant contractile force (Could be modified). Note that positive values indicate contractile (adhesive) forces here!
    • fraction_hardsphere — Fraction of radius below which hard sphere repulsion starts. Must be between ]0,1]
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu2 — Poisson ratio for hard-core repulsion material 2.
    • orientation1 — Vector which keeps the direction in which the particle tries to go for pc1.
    • orientation2 — Vector which keeps the direction in which the particle tries to go for pc2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • eta_front (default value = 0.14999999999999999) — protrusion threshold value
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • traction (default value = -1) — Traction applied to achieve relative motion. If not given, parameter ‘walk_force’ must be specified.
    • tune_angle (default value = 0.92729521800161219) — nu
    • walk_force (default value = -1) — Total walk force applied to achieve relative motion. If not given, parameter ‘traction’ must be specified.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataRigid_Cone_1_DataCone_SphereN_ContractileForce2_HertzT_DirectedWalkN_T_AreaWeightedResistanceAssembleForcesAssemble_ContactArea_2Assemble_VirialStress_2ComputeContactMatrixElementOverdampedRigidBodyDof_1SphereDof_2AssembleContactMatrixToDiagonal_2FrictionMatrixForce_2Feedback

ContractileHertzRandomWalk2Matrix (Rigid_Cylinder Sphere)

Contact model between 3D spherical cells (pc2) and other bodies that are contractile with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in pc2 in the direction of a given vector array.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • Fc — Magnitude of the constant contractile force (Could be modified). Note that positive values indicate contractile (adhesive) forces here!
    • fraction_hardsphere — Fraction of radius below which hard sphere repulsion starts. Must be between ]0,1]
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu2 — Poisson ratio for hard-core repulsion material 2.
    • orientation1 — Vector which keeps the direction in which the particle tries to go for pc1.
    • orientation2 — Vector which keeps the direction in which the particle tries to go for pc2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • eta_front (default value = 0.14999999999999999) — protrusion threshold value
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • traction (default value = -1) — Traction applied to achieve relative motion. If not given, parameter ‘walk_force’ must be specified.
    • tune_angle (default value = 0.92729521800161219) — nu
    • walk_force (default value = -1) — Total walk force applied to achieve relative motion. If not given, parameter ‘traction’ must be specified.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataRigid_Cylinder_1_DataCylinder_SphereN_ContractileForce2_HertzT_DirectedWalkN_T_AreaWeightedResistanceAssembleForcesAssemble_ContactArea_2Assemble_VirialStress_2ComputeContactMatrixElementOverdampedRigidBodyDof_1SphereDof_2AssembleContactMatrixToDiagonal_2FrictionMatrixForce_2Feedback

ContractileHertzRandomWalk2Matrix (Rigid_CylinderBottom Sphere)

Contact model between 3D spherical cells (pc2) and other bodies that are contractile with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in pc2 in the direction of a given vector array.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • Fc — Magnitude of the constant contractile force (Could be modified). Note that positive values indicate contractile (adhesive) forces here!
    • fraction_hardsphere — Fraction of radius below which hard sphere repulsion starts. Must be between ]0,1]
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu2 — Poisson ratio for hard-core repulsion material 2.
    • orientation1 — Vector which keeps the direction in which the particle tries to go for pc1.
    • orientation2 — Vector which keeps the direction in which the particle tries to go for pc2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • eta_front (default value = 0.14999999999999999) — protrusion threshold value
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • traction (default value = -1) — Traction applied to achieve relative motion. If not given, parameter ‘walk_force’ must be specified.
    • tune_angle (default value = 0.92729521800161219) — nu
    • walk_force (default value = -1) — Total walk force applied to achieve relative motion. If not given, parameter ‘traction’ must be specified.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataRigid_Cylinder_1_DataDisk_Sphere  <Bottom_Selector >
  ↓
N_ContractileForce2_HertzT_DirectedWalkN_T_AreaWeightedResistanceAssembleForcesAssemble_ContactArea_2Assemble_VirialStress_2ComputeContactMatrixElementOverdampedRigidBodyDof_1SphereDof_2AssembleContactMatrixToDiagonal_2FrictionMatrixForce_2Feedback

ContractileHertzRandomWalk2Matrix (Rigid_CylinderTop Sphere)

Contact model between 3D spherical cells (pc2) and other bodies that are contractile with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in pc2 in the direction of a given vector array.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • Fc — Magnitude of the constant contractile force (Could be modified). Note that positive values indicate contractile (adhesive) forces here!
    • fraction_hardsphere — Fraction of radius below which hard sphere repulsion starts. Must be between ]0,1]
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu2 — Poisson ratio for hard-core repulsion material 2.
    • orientation1 — Vector which keeps the direction in which the particle tries to go for pc1.
    • orientation2 — Vector which keeps the direction in which the particle tries to go for pc2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • eta_front (default value = 0.14999999999999999) — protrusion threshold value
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • traction (default value = -1) — Traction applied to achieve relative motion. If not given, parameter ‘walk_force’ must be specified.
    • tune_angle (default value = 0.92729521800161219) — nu
    • walk_force (default value = -1) — Total walk force applied to achieve relative motion. If not given, parameter ‘traction’ must be specified.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataRigid_Cylinder_1_DataDisk_Sphere  <Top_Selector >
  ↓
N_ContractileForce2_HertzT_DirectedWalkN_T_AreaWeightedResistanceAssembleForcesAssemble_ContactArea_2Assemble_VirialStress_2ComputeContactMatrixElementOverdampedRigidBodyDof_1SphereDof_2AssembleContactMatrixToDiagonal_2FrictionMatrixForce_2Feedback

ContractileHertzRandomWalk2Matrix (Rigid_Quad Sphere)

Contact model between 3D spherical cells (pc2) and other bodies that are contractile with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in pc2 in the direction of a given vector array.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • Fc — Magnitude of the constant contractile force (Could be modified). Note that positive values indicate contractile (adhesive) forces here!
    • fraction_hardsphere — Fraction of radius below which hard sphere repulsion starts. Must be between ]0,1]
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu2 — Poisson ratio for hard-core repulsion material 2.
    • orientation1 — Vector which keeps the direction in which the particle tries to go for pc1.
    • orientation2 — Vector which keeps the direction in which the particle tries to go for pc2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • eta_front (default value = 0.14999999999999999) — protrusion threshold value
    • flip_normals (default value = 0) — Optionally flip normals if sphere is more than its radius submerged. In most cases, we recommend that you leave this option to its default ‘false’.
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • reject_large_overlap (default value = 1) — Optionally reject overlaps reject_overlap_r times larger than the radius. Unless you have a fully concave ‘container’ geometry, we recommend that you leave this value to its default ‘true’.
    • reject_overlap_r (default value = 1) — If reject_large_overlap is True, this specifies the number of sphere radii of overlap that should be rejected (Default=1).
    • traction (default value = -1) — Traction applied to achieve relative motion. If not given, parameter ‘walk_force’ must be specified.
    • tune_angle (default value = 0.92729521800161219) — nu
    • walk_force (default value = -1) — Total walk force applied to achieve relative motion. If not given, parameter ‘traction’ must be specified.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataRigid_NGon_1_Data  <4 >
  ↓
NGon_SphereN_ContractileForce2_HertzT_DirectedWalkN_T_AreaWeightedResistanceAssembleForcesAssemble_ContactArea_2Assemble_VirialStress_2ComputeContactMatrixElementOverdampedRigidBodyDof_1SphereDof_2AssembleContactMatrixToDiagonal_2FrictionMatrixForce_2Feedback

ContractileHertzRandomWalk2Matrix (Rigid_RoundedTriangle Sphere)

Contact model between 3D spherical cells (pc2) and other bodies that are contractile with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in pc2 in the direction of a given vector array.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • Fc — Magnitude of the constant contractile force (Could be modified). Note that positive values indicate contractile (adhesive) forces here!
    • fraction_hardsphere — Fraction of radius below which hard sphere repulsion starts. Must be between ]0,1]
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu2 — Poisson ratio for hard-core repulsion material 2.
    • orientation1 — Vector which keeps the direction in which the particle tries to go for pc1.
    • orientation2 — Vector which keeps the direction in which the particle tries to go for pc2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • disable_warning_fake_rounded_triangle (default value = 0) — Disables the printing of the specified warning message.
    • eta_front (default value = 0.14999999999999999) — protrusion threshold value
    • flip_normals (default value = 0) — Optionally flip normals if sphere is more than its radius submerged. In most cases, we recommend that you leave this option to its default ‘false’.
    • reject_large_overlap (default value = 1) — Optionally reject overlaps reject_overlap_r times larger than the radius. Unless you have a fully concave ‘container’ geometry, we recommend that you leave this value to its default ‘true’.
    • reject_overlap_r (default value = 1) — If reject_large_overlap is True, this specifies the number of sphere radii of overlap that should be rejected (Default=1).
    • traction (default value = -1) — Traction applied to achieve relative motion. If not given, parameter ‘walk_force’ must be specified.
    • tune_angle (default value = 0.92729521800161219) — nu
    • walk_force (default value = -1) — Total walk force applied to achieve relative motion. If not given, parameter ‘traction’ must be specified.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataRigid_NGon_1_Data  <3 >
  ↓
NGon_SphereWarningMessage  <WARN::FakeRoundedTriangle >
  ↓
N_ContractileForce2_HertzT_DirectedWalkN_T_AreaWeightedResistanceAssembleForcesAssemble_ContactArea_2Assemble_VirialStress_2Feedback

ContractileHertzRandomWalk2Matrix (Rigid_Sphere Sphere)

Contact model between 3D spherical cells (pc2) and other bodies that are contractile with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in pc2 in the direction of a given vector array.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • Fc — Magnitude of the constant contractile force (Could be modified). Note that positive values indicate contractile (adhesive) forces here!
    • fraction_hardsphere — Fraction of radius below which hard sphere repulsion starts. Must be between ]0,1]
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu2 — Poisson ratio for hard-core repulsion material 2.
    • orientation1 — Vector which keeps the direction in which the particle tries to go for pc1.
    • orientation2 — Vector which keeps the direction in which the particle tries to go for pc2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • eta_front (default value = 0.14999999999999999) — protrusion threshold value
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • traction (default value = -1) — Traction applied to achieve relative motion. If not given, parameter ‘walk_force’ must be specified.
    • tune_angle (default value = 0.92729521800161219) — nu
    • walk_force (default value = -1) — Total walk force applied to achieve relative motion. If not given, parameter ‘traction’ must be specified.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataRigidSphere_1_DataSphere_SphereN_ContractileForce2_HertzT_DirectedWalkN_T_AreaWeightedResistanceAssembleForcesAssemble_ContactArea_2Assemble_VirialStress_2ComputeContactMatrixElementOverdampedRigidBodyDof_1SphereDof_2AssembleContactMatrixToDiagonal_2FrictionMatrixForce_2Feedback

ContractileHertzRandomWalk2Matrix (Rigid_Triangle Sphere)

Contact model between 3D spherical cells (pc2) and other bodies that are contractile with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in pc2 in the direction of a given vector array.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • Fc — Magnitude of the constant contractile force (Could be modified). Note that positive values indicate contractile (adhesive) forces here!
    • fraction_hardsphere — Fraction of radius below which hard sphere repulsion starts. Must be between ]0,1]
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu2 — Poisson ratio for hard-core repulsion material 2.
    • orientation1 — Vector which keeps the direction in which the particle tries to go for pc1.
    • orientation2 — Vector which keeps the direction in which the particle tries to go for pc2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • eta_front (default value = 0.14999999999999999) — protrusion threshold value
    • flip_normals (default value = 0) — Optionally flip normals if sphere is more than its radius submerged. In most cases, we recommend that you leave this option to its default ‘false’.
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • reject_large_overlap (default value = 1) — Optionally reject overlaps reject_overlap_r times larger than the radius. Unless you have a fully concave ‘container’ geometry, we recommend that you leave this value to its default ‘true’.
    • reject_overlap_r (default value = 1) — If reject_large_overlap is True, this specifies the number of sphere radii of overlap that should be rejected (Default=1).
    • traction (default value = -1) — Traction applied to achieve relative motion. If not given, parameter ‘walk_force’ must be specified.
    • tune_angle (default value = 0.92729521800161219) — nu
    • walk_force (default value = -1) — Total walk force applied to achieve relative motion. If not given, parameter ‘traction’ must be specified.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataRigid_NGon_1_Data  <3 >
  ↓
NGon_SphereN_ContractileForce2_HertzT_DirectedWalkN_T_AreaWeightedResistanceAssembleForcesAssemble_ContactArea_2Assemble_VirialStress_2ComputeContactMatrixElementOverdampedRigidBodyDof_1SphereDof_2AssembleContactMatrixToDiagonal_2FrictionMatrixForce_2Feedback

ContractileHertzRandomWalk2Matrix (Sphere Sphere)

Contact model between 3D spherical cells (pc2) and other bodies that are contractile with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in pc2 in the direction of a given vector array.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • Fc — Magnitude of the constant contractile force (Could be modified). Note that positive values indicate contractile (adhesive) forces here!
    • fraction_hardsphere — Fraction of radius below which hard sphere repulsion starts. Must be between ]0,1]
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu2 — Poisson ratio for hard-core repulsion material 2.
    • orientation1 — Vector which keeps the direction in which the particle tries to go for pc1.
    • orientation2 — Vector which keeps the direction in which the particle tries to go for pc2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • eta_front (default value = 0.14999999999999999) — protrusion threshold value
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • traction (default value = -1) — Traction applied to achieve relative motion. If not given, parameter ‘walk_force’ must be specified.
    • tune_angle (default value = 0.92729521800161219) — nu
    • walk_force (default value = -1) — Total walk force applied to achieve relative motion. If not given, parameter ‘traction’ must be specified.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereN_ContractileForce2_HertzT_DirectedWalkN_T_AreaWeightedResistanceAssembleForcesAssemble_ContactArea_2Assemble_VirialStress_2ComputeContactMatrixElementOverdampedAssembleContactMatrixFeedback

ContractileRepulsive

Description: Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope. No Friction Geometry combinations available:

PC2 | PC1 - Sphere Rigid_Triangle Rigid_Sphere Rigid_RoundedTriangle Rigid_Quad Rigid_CylinderTop Rigid_CylinderBottom Rigid_Cylinder Rigid_Cone Rigid_Capsule Deformable_Triangle Deformable_RoundedTriangle Deformable_Line Deformable_Capsule
Sphere YES YES YES YES YES YES YES YES YES YES YES YES YES YES

ContractileRepulsive (Deformable_Capsule Sphere)

Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope. No Friction

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • k — stiffness
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • F_adh (default value = 0) — adhesive force
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateSphere0_2_DataDeformable_Cylinder_1_DataCapsule_SphereN_Contractile_lineAssembleForces_2AssembleForces_DeformableCylinder_1Feedback

ContractileRepulsive (Deformable_Line Sphere)

Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope. No Friction

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • k — stiffness
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • F_adh (default value = 0) — adhesive force
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)
    • orthogonal_to (default value = 0 0 1) — Direction ‘out of plane’ for the 2D system. Default = (0,0,1).
    • reject_larger_radius (default value = 1) — If true, overlaps larger than the sphere’s radius will be rejected’

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateSphere0_2_DataDeformable_Line_1_DataLine_SphereN_Contractile_lineAssembleForces_2AssembleForces_DeformableCylinder_1Feedback

ContractileRepulsive (Deformable_RoundedTriangle Sphere)

Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope. No Friction

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • k — stiffness
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • F_adh (default value = 0) — adhesive force
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)
    • disable_warning_fake_rounded_triangle (default value = 0) — Disables the printing of the specified warning message.
    • flip_normals (default value = 0) — Optionally flip normals if sphere is more than its radius submerged. In most cases, we recommend that you leave this option to its default ‘false’.
    • reject_large_overlap (default value = 1) — Optionally reject overlaps reject_overlap_r times larger than the radius. Unless you have a fully concave ‘container’ geometry, we recommend that you leave this value to its default ‘true’.
    • reject_overlap_r (default value = 1) — If reject_large_overlap is True, this specifies the number of sphere radii of overlap that should be rejected (Default=1).

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateSphere0_2_DataDeformable_NGon_1_Data  <3 >
  ↓
NGon_SphereWarningMessage  <WARN::FakeRoundedTriangle >
  ↓
N_Contractile_lineAssembleForces_DeformableTriangleBarycentric_1AssembleForces_2Feedback

ContractileRepulsive (Deformable_Triangle Sphere)

Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope. No Friction

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • k — stiffness
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • F_adh (default value = 0) — adhesive force
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)
    • flip_normals (default value = 0) — Optionally flip normals if sphere is more than its radius submerged. In most cases, we recommend that you leave this option to its default ‘false’.
    • reject_large_overlap (default value = 1) — Optionally reject overlaps reject_overlap_r times larger than the radius. Unless you have a fully concave ‘container’ geometry, we recommend that you leave this value to its default ‘true’.
    • reject_overlap_r (default value = 1) — If reject_large_overlap is True, this specifies the number of sphere radii of overlap that should be rejected (Default=1).

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateSphere0_2_DataDeformable_NGon_1_Data  <3 >
  ↓
NGon_SphereN_Contractile_lineAssembleForces_DeformableTriangleBarycentric_1AssembleForces_2Feedback

ContractileRepulsive (Rigid_Capsule Sphere)

Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope. No Friction

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • k — stiffness
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • F_adh (default value = 0) — adhesive force
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateSphere0_2_DataRigid_Cylinder_1_DataCylinder_SphereN_Contractile_lineAssembleForcesFeedback

ContractileRepulsive (Rigid_Cone Sphere)

Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope. No Friction

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • k — stiffness
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • F_adh (default value = 0) — adhesive force
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateSphere0_2_DataRigid_Cone_1_DataCone_SphereN_Contractile_lineAssembleForcesFeedback

ContractileRepulsive (Rigid_Cylinder Sphere)

Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope. No Friction

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • k — stiffness
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • F_adh (default value = 0) — adhesive force
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateSphere0_2_DataRigid_Cylinder_1_DataCylinder_SphereN_Contractile_lineAssembleForcesFeedback

ContractileRepulsive (Rigid_CylinderBottom Sphere)

Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope. No Friction

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • k — stiffness
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • F_adh (default value = 0) — adhesive force
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateSphere0_2_DataRigid_Cylinder_1_DataDisk_Sphere  <Bottom_Selector >
  ↓
N_Contractile_lineAssembleForcesFeedback

ContractileRepulsive (Rigid_CylinderTop Sphere)

Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope. No Friction

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • k — stiffness
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • F_adh (default value = 0) — adhesive force
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateSphere0_2_DataRigid_Cylinder_1_DataDisk_Sphere  <Top_Selector >
  ↓
N_Contractile_lineAssembleForcesFeedback

ContractileRepulsive (Rigid_Quad Sphere)

Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope. No Friction

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • k — stiffness
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • F_adh (default value = 0) — adhesive force
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)
    • flip_normals (default value = 0) — Optionally flip normals if sphere is more than its radius submerged. In most cases, we recommend that you leave this option to its default ‘false’.
    • reject_large_overlap (default value = 1) — Optionally reject overlaps reject_overlap_r times larger than the radius. Unless you have a fully concave ‘container’ geometry, we recommend that you leave this value to its default ‘true’.
    • reject_overlap_r (default value = 1) — If reject_large_overlap is True, this specifies the number of sphere radii of overlap that should be rejected (Default=1).

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateSphere0_2_DataRigid_NGon_1_Data  <4 >
  ↓
NGon_SphereN_Contractile_lineAssembleForcesFeedback

ContractileRepulsive (Rigid_RoundedTriangle Sphere)

Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope. No Friction

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • k — stiffness
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • F_adh (default value = 0) — adhesive force
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)
    • disable_warning_fake_rounded_triangle (default value = 0) — Disables the printing of the specified warning message.
    • flip_normals (default value = 0) — Optionally flip normals if sphere is more than its radius submerged. In most cases, we recommend that you leave this option to its default ‘false’.
    • reject_large_overlap (default value = 1) — Optionally reject overlaps reject_overlap_r times larger than the radius. Unless you have a fully concave ‘container’ geometry, we recommend that you leave this value to its default ‘true’.
    • reject_overlap_r (default value = 1) — If reject_large_overlap is True, this specifies the number of sphere radii of overlap that should be rejected (Default=1).

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateSphere0_2_DataRigid_NGon_1_Data  <3 >
  ↓
NGon_SphereWarningMessage  <WARN::FakeRoundedTriangle >
  ↓
N_Contractile_lineAssembleForcesFeedback

ContractileRepulsive (Rigid_Sphere Sphere)

Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope. No Friction

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • k — stiffness
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • F_adh (default value = 0) — adhesive force
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateSphere0_2_DataRigidSphere_1_DataSphere_SphereN_Contractile_lineAssembleForcesFeedback

ContractileRepulsive (Rigid_Triangle Sphere)

Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope. No Friction

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • k — stiffness
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • F_adh (default value = 0) — adhesive force
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)
    • flip_normals (default value = 0) — Optionally flip normals if sphere is more than its radius submerged. In most cases, we recommend that you leave this option to its default ‘false’.
    • reject_large_overlap (default value = 1) — Optionally reject overlaps reject_overlap_r times larger than the radius. Unless you have a fully concave ‘container’ geometry, we recommend that you leave this value to its default ‘true’.
    • reject_overlap_r (default value = 1) — If reject_large_overlap is True, this specifies the number of sphere radii of overlap that should be rejected (Default=1).

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateSphere0_2_DataRigid_NGon_1_Data  <3 >
  ↓
NGon_SphereN_Contractile_lineAssembleForcesFeedback

ContractileRepulsive (Sphere Sphere)

Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope. No Friction

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • k — stiffness
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • F_adh (default value = 0) — adhesive force
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateSphere0_2_DataSphere0_1_DataSphere_SphereN_Contractile_lineAssembleForcesFeedback

ContractileRepulsiveCILActiveTensionMatrix

Description: Same as ‘Contractile_Repulsive_Matrix’ but with freedir assembler for CIL and virial stress assembly. Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

ContractileRepulsiveCILActiveTensionMatrix (Sphere Sphere)

Same as ‘Contractile_Repulsive_Matrix’ but with freedir assembler for CIL and virial stress assembly.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • Wa (m^2 . kg . s^-2) — Cell-substrate adhesion energy
    • Wc (m^2 . kg . s^-2) — Contractile energy
    • gamma_normal (kg . s^-1) — Normal friction coefficient (kg/s)
    • gamma_tangential (kg . s^-1) — Tangential friction coefficient (kg/s)
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)
    • dimension1 (default value = 0 0 1) — dimension in which the 1d force should be computed (default=z).
    • dimension2 (default value = 1 0 0) — orthogonal dimension used for computing the width (default=x).
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereN_ContractileN_T_ConstantResistanceAssembleForcesAssemble_ActiveTensionAssemble_FreeDirectionComputeContactMatrixElementOverdampedAssembleContactMatrixFeedback

ContractileRepulsiveCILDewetMatrix

Description: Same as ‘Contractile_Repulsive_Matrix’ but with freedir assembler for CIL and virial stress assembly. Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

ContractileRepulsiveCILDewetMatrix (Sphere Sphere)

Same as ‘Contractile_Repulsive_Matrix’ but with freedir assembler for CIL and virial stress assembly.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • Wa (m^2 . kg . s^-2) — Cell-substrate adhesion energy
    • Wc (m^2 . kg . s^-2) — Contractile energy
    • gamma_normal (kg . s^-1) — Normal friction coefficient (kg/s)
    • gamma_tangential (kg . s^-1) — Tangential friction coefficient (kg/s)
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • attrFactorMax (default value = 1) — maximum factor for contact state adhesion modifier
    • attrFactorMin (default value = 1) — minimum factor for contact state adhesion modifier
    • attrFactorTime (default value = 0) — time it takes to linearly increase from attrFactorMin to attrFactorMax
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • init_adhesion_modifier (default value = 0) — If ‘True’, will re-init the adhesion modfier of all current contacts the next execution of this contact model. After that, this property will be automatically re-set to ‘false’ for subsequent iterations.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereContactAdhesionModifierN_Contractile_dewetN_T_ConstantResistanceAssembleForcesAssemble_VirialTensionAssemble_VirialEnergyAssemble_FreeDirectionComputeContactMatrixElementOverdampedAssembleContactMatrixFeedback

ContractileRepulsiveCILDgradMatrix

Description: Same as ‘Contractile_Repulsive_Matrix’ but with freedir assembler for CIL and virial stress assembly. Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

ContractileRepulsiveCILDgradMatrix (Sphere Sphere)

Same as ‘Contractile_Repulsive_Matrix’ but with freedir assembler for CIL and virial stress assembly.

Parallel Compatible: No

Properties:

  • Required keywords:
    • Wa (m^2 . kg . s^-2) — Cell-substrate adhesion energy
    • Wc (m^2 . kg . s^-2) — Contractile energy
    • gamma_normal (kg . s^-1) — Normal friction coefficient (kg/s)
    • gamma_tangential (kg . s^-1) — Tangential friction coefficient (kg/s)
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereN_ContractileN_T_ConstantResistanceAssembleForcesAssemble_VirialTensionAssemble_VirialEnergyCountEffectiveContactsAssemble_DensityGradientAssemble_FreeDirectionComputeContactMatrixElementOverdampedAssembleContactMatrixFeedback

ContractileRepulsiveCILMatrix

Description: Same as ‘Contractile_Repulsive_Matrix’ but with freedir assembler for CIL and virial stress assembly. Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

ContractileRepulsiveCILMatrix (Sphere Sphere)

Same as ‘Contractile_Repulsive_Matrix’ but with freedir assembler for CIL and virial stress assembly.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • Wa (m^2 . kg . s^-2) — Cell-substrate adhesion energy
    • Wc (m^2 . kg . s^-2) — Contractile energy
    • gamma_normal (kg . s^-1) — Normal friction coefficient (kg/s)
    • gamma_tangential (kg . s^-1) — Tangential friction coefficient (kg/s)
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereN_ContractileN_T_ConstantResistanceAssembleForcesAssemble_VirialTensionAssemble_VirialEnergyAssemble_FreeDirectionComputeContactMatrixElementOverdampedAssembleContactMatrixFeedback

ContractileRepulsiveCILStrainMatrix

Description: Same as ‘Contractile_Repulsive_Matrix’ but with freedir assembler for CIL and virial stress assembly. Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

ContractileRepulsiveCILStrainMatrix (Sphere Sphere)

Same as ‘Contractile_Repulsive_Matrix’ but with freedir assembler for CIL and virial stress assembly.

Parallel Compatible: No

Properties:

  • Required keywords:
    • Wa (m^2 . kg . s^-2) — Cell-substrate adhesion energy
    • Wc (m^2 . kg . s^-2) — Contractile energy
    • gamma_normal (kg . s^-1) — Normal friction coefficient (kg/s)
    • gamma_tangential (kg . s^-1) — Tangential friction coefficient (kg/s)
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • v_array1 (default value = None) — array with velocities of pc1. If not given, the standard ‘v’ array is taken
    • v_array2 (default value = None) — array with velocities of pc2. If not given, the standard ‘v’ array is taken

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereN_ContractileN_T_ConstantResistanceAssembleForcesAssemble_ContractileEnergyAssemble_StrainRateCountEffectiveContactsAssemble_FreeDirectionComputeContactMatrixElementOverdampedAssembleContactMatrixFeedback

ContractileRepulsiveDividingMatrix

Description: Contractile-repulsive model with binary fission. Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

ContractileRepulsiveDividingMatrix (Sphere Sphere)

Contractile-repulsive model with binary fission.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • Wa (m^2 . kg . s^-2) — Cell-substrate adhesion energy
    • Wc (m^2 . kg . s^-2) — Contractile energy
    • division_force (kg . m . s^-2) — Maximum force applied between two dividing cells in order to keep the desired division trajectory
    • division_time (s) — time it takes for the cytokinesis to complete
    • divstiffatt (kg . s^-2) — attractive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • divstiffrep (kg . s^-2) — repulsive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • gamma_dividing — Normal friction coefficient for dividing cells (kg/s).
    • gamma_normal (kg . s^-1) — Normal friction coefficient (kg/s)
    • gamma_tangential (kg . s^-1) — Tangential friction coefficient (kg/s)
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
    • state_dividing — State value of cell which indicates that the cell is currently dividing.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereN_DividingN_ContractileN_T_ConstantResistanceN_DividingResistanceModifyForceAndFriction_AliveFractionAssembleForcesAssemble_VirialTensionComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackFeedbackDividing

ContractileRepulsiveHertzMatrix

Description: Linear contractility up to a user-specified overlap, after which repulsion follows a power-law slope added with an even increased repulsion (Hertz-like) at the point of zero contractility. Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

ContractileRepulsiveHertzMatrix (Sphere Sphere)

Linear contractility up to a user-specified overlap, after which repulsion follows a power-law slope added with an even increased repulsion (Hertz-like) at the point of zero contractility.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E1 — Youngs modulus for hard-core repulsion material 1.
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • Wa — Cell-matrix adhesion energy
    • Wc — Contractile energy
    • gamma_normal (kg . s^-1) — Normal friction coefficient (kg/s)
    • gamma_tangential (kg . s^-1) — Tangential friction coefficient (kg/s)
    • nu1 — Poisson ratio for hard-core repulsion material 1.
    • nu2 — Poisson ratio for hard-core repulsion material 2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereN_Contractile_HertzN_T_ConstantResistanceAssembleForcesComputeContactMatrixElementOverdampedAssembleContactMatrixFeedback

ContractileRepulsiveMatrix

Description: Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope. Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

ContractileRepulsiveMatrix (Sphere Sphere)

Linear contractility up to a user-specified, overlap, after which (hard) repulsion follows a power-law slope.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • Wa (m^2 . kg . s^-2) — Cell-substrate adhesion energy
    • Wc (m^2 . kg . s^-2) — Contractile energy
    • gamma_normal (kg . s^-1) — Normal friction coefficient (kg/s)
    • gamma_tangential (kg . s^-1) — Tangential friction coefficient (kg/s)
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • allow_dewet (default value = 1) — If false, the contact force never drops to zero when de-wetting (Warning, actual Wa would be higher in this case)
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereN_ContractileN_T_ConstantResistanceAssembleForcesComputeContactMatrixElementOverdampedAssembleContactMatrixFeedback

DelileRandomWalkMatrix

Description: To be documented Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

DelileRandomWalkMatrix (Sphere Sphere)

To be documented

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • orientation1 — Vector which keeps the direction in which the particle tries to go for pc1.
    • orientation2 — Vector which keeps the direction in which the particle tries to go for pc2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
    • w_rep — Repulsive ‘layer stiffness’
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • a (default value = 1.3696999999999999) — Contact area calibration factor.
    • attrConst (default value = -1) — Adhesion energy (in N/m).
    • attrFactorMax (default value = 1) — maximum factor for contact state adhesion modifier
    • attrFactorMin (default value = 1) — minimum factor for contact state adhesion modifier
    • attrFactorTime (default value = 0) — time it takes to linearly increase from attrFactorMin to attrFactorMax
    • c_eq (default value = 0.95230000000000004) — Relative equilibrium distance between two cells
    • c_max (default value = 1.2414000000000001) — Relative maximal distance between two cells
    • eta_front (default value = 0.14999999999999999) — protrusion threshold value
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • init_adhesion_modifier (default value = 0) — If ‘True’, will re-init the adhesion modfier of all current contacts the next execution of this contact model. After that, this property will be automatically re-set to ‘false’ for subsequent iterations.
    • traction (default value = -1) — Traction applied to achieve relative motion. If not given, parameter ‘walk_force’ must be specified.
    • tune_angle (default value = 0.92729521800161219) — nu
    • w_adh (default value = -1) — Adhesive ‘layer stiffness’ (Pa/m)
    • walk_force (default value = -1) — Total walk force applied to achieve relative motion. If not given, parameter ‘traction’ must be specified.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereN_DelileT_DirectedWalkN_T_AreaWeightedResistanceAssembleForcesContactAdhesionModifierAssemble_ContactArea_2Assemble_ContactArea_1Assemble_VirialStressComputeContactMatrixElementOverdampedAssembleContactMatrixFeedback

TensileModulusHertzRandomWalkMatrix

Description: Contact model for 3D spherical cells that pull linearly with strain with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in the direction of a given vector array. Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

TensileModulusHertzRandomWalkMatrix (Sphere Sphere)

Contact model for 3D spherical cells that pull linearly with strain with only viscous resistance up up to a ‘hard’-core inner radius, below which the contact is Hertz-like Moreover, a tangential random walk is performed by the cells in the direction of a given vector array.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E1 — Youngs modulus for hard-core repulsion material 1.
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • fraction_hardsphere — Fraction of radius below which hard sphere repulsion starts. Must be between ]0,1]
    • gamma_normal (kg . s^-1) — Normal friction coefficient (kg/s)
    • gamma_tangential (kg . s^-1) — Tangential friction coefficient (kg/s)
    • nu1 — Poisson ratio for hard-core repulsion material 1.
    • nu2 — Poisson ratio for hard-core repulsion material 2.
    • orientation1 — Vector which keeps the direction in which the particle tries to go for pc1.
    • orientation2 — Vector which keeps the direction in which the particle tries to go for pc2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
    • tensile_modulus — Tensile modulus: linear increase of contractile force with strain starting from fraction_hardsphere x radius (where contractile force=0)
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • attrFactorMax (default value = 1) — maximum factor for contact state adhesion modifier
    • attrFactorMin (default value = 1) — minimum factor for contact state adhesion modifier
    • attrFactorTime (default value = 0) — time it takes to linearly increase from attrFactorMin to attrFactorMax
    • eta_front (default value = 0.14999999999999999) — protrusion threshold value
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • init_adhesion_modifier (default value = 0) — If ‘True’, will re-init the adhesion modfier of all current contacts the next execution of this contact model. After that, this property will be automatically re-set to ‘false’ for subsequent iterations.
    • traction (default value = -1) — Traction applied to achieve relative motion. If not given, parameter ‘walk_force’ must be specified.
    • tune_angle (default value = 0.92729521800161219) — nu
    • walk_force (default value = -1) — Total walk force applied to achieve relative motion. If not given, parameter ‘traction’ must be specified.

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereN_ContractileModulus_HertzT_DirectedWalkN_T_ConstantResistanceAssembleForcesContactAdhesionModifierAssemble_ContactArea_2Assemble_ContactArea_1Assemble_VirialStressComputeContactMatrixElementOverdampedAssembleContactMatrixFeedback