mpacts.contact.models.continuum. compartmentmodel

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

import mpacts.contact.models.continuum.compartmentmodel
#or assign it to a shorter name
import mpacts.contact.models.continuum.compartmentmodel as com

CompartmentModel

Description: Compartment Model trial, should work for Geometry combinations available:

PC2 | PC1 - Sphere Rigid_Triangle Deformable_Triangle Deformable_RoundedTriangle
Sphere YES YES    
Rigid_Triangle   YES    
Deformable_Triangle     YES  
Deformable_RoundedTriangle       YES
ComposedParticle   YES    

CompartmentModel (Deformable_RoundedTriangle Deformable_RoundedTriangle)

Compartment Model trial, should work for

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • khat — Transfer rates - has to match the number of concentrations! Normally this is a rate (1/s), but for triangle-triangle commonedge contacts it’s a diffusivity (m^2/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.
    • species_names — List of array names of concentration arrays. For the flux-arrays, ‘dc_dt_‘ will be prepended, unless explicitely given.
  • Optional keywords:
    • feedback_concentration (default value = 0) — If ‘True’ we set -|flux| as the feedback for the contact detector. This way, you can skip the computation of ‘too small’ fluxes if you use a contact detector with VerletLists. To do so, set ‘keep_distance’ to MINUS minimal_concentration_to_repeat. Use with care as this over-rides the default meaning of ‘feedback’ to return a spatial distance. As such it is a bad idea to set this for contact detectors based on geometry (e.g. MultiGrid), and only make sense with contact detectors that are geometry-agnostic (e.g. FixedList and SmartBruteForce).
    • flux_species_names (default value = flux_species_names) — List of array names of flux-arrays.

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

DefaultBoilerPlateDeformable_NGon_1_Data  <3 >
  ↓
Deformable_NGon_2_Data  <3 >
  ↓
Triangle_Triangle_CommonEdge_DistanceCompartmentModel_DataAssemble_CompartmentModelFeedback

CompartmentModel (Deformable_Triangle Deformable_Triangle)

Compartment Model trial, should work for

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • khat — Transfer rates - has to match the number of concentrations! Normally this is a rate (1/s), but for triangle-triangle commonedge contacts it’s a diffusivity (m^2/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.
    • species_names — List of array names of concentration arrays. For the flux-arrays, ‘dc_dt_‘ will be prepended, unless explicitely given.
  • Optional keywords:
    • feedback_concentration (default value = 0) — If ‘True’ we set -|flux| as the feedback for the contact detector. This way, you can skip the computation of ‘too small’ fluxes if you use a contact detector with VerletLists. To do so, set ‘keep_distance’ to MINUS minimal_concentration_to_repeat. Use with care as this over-rides the default meaning of ‘feedback’ to return a spatial distance. As such it is a bad idea to set this for contact detectors based on geometry (e.g. MultiGrid), and only make sense with contact detectors that are geometry-agnostic (e.g. FixedList and SmartBruteForce).
    • flux_species_names (default value = flux_species_names) — List of array names of flux-arrays.

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

DefaultBoilerPlateDeformable_NGon_1_Data  <3 >
  ↓
Deformable_NGon_2_Data  <3 >
  ↓
Triangle_Triangle_CommonEdge_DistanceCompartmentModel_DataAssemble_CompartmentModelFeedback

CompartmentModel (Rigid_Triangle ComposedParticle)

Compartment Model trial, should work for

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • khat — Transfer rates - has to match the number of concentrations! Normally this is a rate (1/s), but for triangle-triangle commonedge contacts it’s a diffusivity (m^2/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.
    • species_names — List of array names of concentration arrays. For the flux-arrays, ‘dc_dt_‘ will be prepended, unless explicitely given.
  • Optional keywords:
    • feedback_concentration (default value = 0) — If ‘True’ we set -|flux| as the feedback for the contact detector. This way, you can skip the computation of ‘too small’ fluxes if you use a contact detector with VerletLists. To do so, set ‘keep_distance’ to MINUS minimal_concentration_to_repeat. Use with care as this over-rides the default meaning of ‘feedback’ to return a spatial distance. As such it is a bad idea to set this for contact detectors based on geometry (e.g. MultiGrid), and only make sense with contact detectors that are geometry-agnostic (e.g. FixedList and SmartBruteForce).
    • flip_normals (default value = 0) — If ‘True’, the normals of the N-Gon will be flipped.In most cases, we recommend that you leave this option to its default ‘false’. Contrary to the option ‘flip_normals’ in e.g. Ngon-Sphere contact, this option will always flip the normals, if enables, since points do not have any radius.
    • flux_species_names (default value = flux_species_names) — List of array names of flux-arrays.

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

DefaultBoilerPlatePosition_2_DataRigid_NGon_1_Data  <3 >
  ↓
NGon_PointCompartmentModel_DataAssemble_CompartmentModelFeedback

CompartmentModel (Rigid_Triangle Rigid_Triangle)

Compartment Model trial, should work for

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • khat — Transfer rates - has to match the number of concentrations! Normally this is a rate (1/s), but for triangle-triangle commonedge contacts it’s a diffusivity (m^2/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.
    • species_names — List of array names of concentration arrays. For the flux-arrays, ‘dc_dt_‘ will be prepended, unless explicitely given.
  • Optional keywords:
    • feedback_concentration (default value = 0) — If ‘True’ we set -|flux| as the feedback for the contact detector. This way, you can skip the computation of ‘too small’ fluxes if you use a contact detector with VerletLists. To do so, set ‘keep_distance’ to MINUS minimal_concentration_to_repeat. Use with care as this over-rides the default meaning of ‘feedback’ to return a spatial distance. As such it is a bad idea to set this for contact detectors based on geometry (e.g. MultiGrid), and only make sense with contact detectors that are geometry-agnostic (e.g. FixedList and SmartBruteForce).
    • flux_species_names (default value = flux_species_names) — List of array names of flux-arrays.

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

DefaultBoilerPlateRigid_NGon_1_Data  <3 >
  ↓
Rigid_NGon_2_Data  <3 >
  ↓
Triangle_Triangle_CommonEdge_DistanceCompartmentModel_DataAssemble_CompartmentModelFeedback

CompartmentModel (Rigid_Triangle Sphere)

Compartment Model trial, should work for

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • khat — Transfer rates - has to match the number of concentrations! Normally this is a rate (1/s), but for triangle-triangle commonedge contacts it’s a diffusivity (m^2/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.
    • species_names — List of array names of concentration arrays. For the flux-arrays, ‘dc_dt_‘ will be prepended, unless explicitely given.
  • Optional keywords:
    • feedback_concentration (default value = 0) — If ‘True’ we set -|flux| as the feedback for the contact detector. This way, you can skip the computation of ‘too small’ fluxes if you use a contact detector with VerletLists. To do so, set ‘keep_distance’ to MINUS minimal_concentration_to_repeat. Use with care as this over-rides the default meaning of ‘feedback’ to return a spatial distance. As such it is a bad idea to set this for contact detectors based on geometry (e.g. MultiGrid), and only make sense with contact detectors that are geometry-agnostic (e.g. FixedList and SmartBruteForce).
    • 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’.
    • flux_species_names (default value = flux_species_names) — List of array names of flux-arrays.
    • 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_SphereCompartmentModel_DataAssemble_CompartmentModelFeedback

CompartmentModel (Sphere Sphere)

Compartment Model trial, should work for

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • khat — Transfer rates - has to match the number of concentrations! Normally this is a rate (1/s), but for triangle-triangle commonedge contacts it’s a diffusivity (m^2/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.
    • species_names — List of array names of concentration arrays. For the flux-arrays, ‘dc_dt_‘ will be prepended, unless explicitely given.
  • Optional keywords:
    • feedback_concentration (default value = 0) — If ‘True’ we set -|flux| as the feedback for the contact detector. This way, you can skip the computation of ‘too small’ fluxes if you use a contact detector with VerletLists. To do so, set ‘keep_distance’ to MINUS minimal_concentration_to_repeat. Use with care as this over-rides the default meaning of ‘feedback’ to return a spatial distance. As such it is a bad idea to set this for contact detectors based on geometry (e.g. MultiGrid), and only make sense with contact detectors that are geometry-agnostic (e.g. FixedList and SmartBruteForce).
    • flux_species_names (default value = flux_species_names) — List of array names of flux-arrays.

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

DefaultBoilerPlateSphere0_1_DataSphere0_2_DataSphere_SphereCompartmentModel_DataAssemble_CompartmentModelFeedback

CompartmentModelGradient

Description: Compartment Model for diffusion that also assembles the gradients, only usable for spheres, for now... Geometry combinations available:

PC2 | PC1 - Rigid_Triangle Deformable_Triangle Deformable_RoundedTriangle
Rigid_Triangle YES    
Deformable_Triangle   YES  
Deformable_RoundedTriangle     YES
ComposedParticle YES    

CompartmentModelGradient (Deformable_RoundedTriangle Deformable_RoundedTriangle)

Compartment Model for diffusion that also assembles the gradients, only usable for spheres, for now...

Parallel Compatible: No

Properties:

  • Required keywords:
    • gradient_names — List of array names of gradient arrays. For the flux-arrays.
    • khat — Transfer rates - has to match the number of concentrations! Normally this is a rate (1/s), but for triangle-triangle commonedge contacts it’s a diffusivity (m^2/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.
    • species_names — List of array names of concentration arrays. For the flux-arrays, ‘dc_dt_‘ will be prepended, unless explicitely given.
  • Optional keywords:
    • feedback_concentration (default value = 0) — If ‘True’ we set -|flux| as the feedback for the contact detector. This way, you can skip the computation of ‘too small’ fluxes if you use a contact detector with VerletLists. To do so, set ‘keep_distance’ to MINUS minimal_concentration_to_repeat. Use with care as this over-rides the default meaning of ‘feedback’ to return a spatial distance. As such it is a bad idea to set this for contact detectors based on geometry (e.g. MultiGrid), and only make sense with contact detectors that are geometry-agnostic (e.g. FixedList and SmartBruteForce).
    • flux_species_names (default value = flux_species_names) — List of array names of flux-arrays.

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

DefaultBoilerPlateDeformable_NGon_1_Data  <3 >
  ↓
Deformable_NGon_2_Data  <3 >
  ↓
Triangle_Triangle_CommonEdge_DistanceCompartmentModel_DataAssemble_CompartmentModelAssemble_CompartmentGradientFeedback

CompartmentModelGradient (Deformable_Triangle Deformable_Triangle)

Compartment Model for diffusion that also assembles the gradients, only usable for spheres, for now...

Parallel Compatible: No

Properties:

  • Required keywords:
    • gradient_names — List of array names of gradient arrays. For the flux-arrays.
    • khat — Transfer rates - has to match the number of concentrations! Normally this is a rate (1/s), but for triangle-triangle commonedge contacts it’s a diffusivity (m^2/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.
    • species_names — List of array names of concentration arrays. For the flux-arrays, ‘dc_dt_‘ will be prepended, unless explicitely given.
  • Optional keywords:
    • feedback_concentration (default value = 0) — If ‘True’ we set -|flux| as the feedback for the contact detector. This way, you can skip the computation of ‘too small’ fluxes if you use a contact detector with VerletLists. To do so, set ‘keep_distance’ to MINUS minimal_concentration_to_repeat. Use with care as this over-rides the default meaning of ‘feedback’ to return a spatial distance. As such it is a bad idea to set this for contact detectors based on geometry (e.g. MultiGrid), and only make sense with contact detectors that are geometry-agnostic (e.g. FixedList and SmartBruteForce).
    • flux_species_names (default value = flux_species_names) — List of array names of flux-arrays.

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

DefaultBoilerPlateDeformable_NGon_1_Data  <3 >
  ↓
Deformable_NGon_2_Data  <3 >
  ↓
Triangle_Triangle_CommonEdge_DistanceCompartmentModel_DataAssemble_CompartmentModelAssemble_CompartmentGradientFeedback

CompartmentModelGradient (Rigid_Triangle ComposedParticle)

Compartment Model for diffusion that also assembles the gradients, only usable for spheres, for now...

Parallel Compatible: No

Properties:

  • Required keywords:
    • gradient_names — List of array names of gradient arrays. For the flux-arrays.
    • khat — Transfer rates - has to match the number of concentrations! Normally this is a rate (1/s), but for triangle-triangle commonedge contacts it’s a diffusivity (m^2/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.
    • species_names — List of array names of concentration arrays. For the flux-arrays, ‘dc_dt_‘ will be prepended, unless explicitely given.
  • Optional keywords:
    • feedback_concentration (default value = 0) — If ‘True’ we set -|flux| as the feedback for the contact detector. This way, you can skip the computation of ‘too small’ fluxes if you use a contact detector with VerletLists. To do so, set ‘keep_distance’ to MINUS minimal_concentration_to_repeat. Use with care as this over-rides the default meaning of ‘feedback’ to return a spatial distance. As such it is a bad idea to set this for contact detectors based on geometry (e.g. MultiGrid), and only make sense with contact detectors that are geometry-agnostic (e.g. FixedList and SmartBruteForce).
    • flip_normals (default value = 0) — If ‘True’, the normals of the N-Gon will be flipped.In most cases, we recommend that you leave this option to its default ‘false’. Contrary to the option ‘flip_normals’ in e.g. Ngon-Sphere contact, this option will always flip the normals, if enables, since points do not have any radius.
    • flux_species_names (default value = flux_species_names) — List of array names of flux-arrays.

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

DefaultBoilerPlatePosition_2_DataRigid_NGon_1_Data  <3 >
  ↓
NGon_PointCompartmentModel_DataAssemble_CompartmentModelAssemble_CompartmentGradientFeedback

CompartmentModelGradient (Rigid_Triangle Rigid_Triangle)

Compartment Model for diffusion that also assembles the gradients, only usable for spheres, for now...

Parallel Compatible: No

Properties:

  • Required keywords:
    • gradient_names — List of array names of gradient arrays. For the flux-arrays.
    • khat — Transfer rates - has to match the number of concentrations! Normally this is a rate (1/s), but for triangle-triangle commonedge contacts it’s a diffusivity (m^2/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.
    • species_names — List of array names of concentration arrays. For the flux-arrays, ‘dc_dt_‘ will be prepended, unless explicitely given.
  • Optional keywords:
    • feedback_concentration (default value = 0) — If ‘True’ we set -|flux| as the feedback for the contact detector. This way, you can skip the computation of ‘too small’ fluxes if you use a contact detector with VerletLists. To do so, set ‘keep_distance’ to MINUS minimal_concentration_to_repeat. Use with care as this over-rides the default meaning of ‘feedback’ to return a spatial distance. As such it is a bad idea to set this for contact detectors based on geometry (e.g. MultiGrid), and only make sense with contact detectors that are geometry-agnostic (e.g. FixedList and SmartBruteForce).
    • flux_species_names (default value = flux_species_names) — List of array names of flux-arrays.

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

DefaultBoilerPlateRigid_NGon_1_Data  <3 >
  ↓
Rigid_NGon_2_Data  <3 >
  ↓
Triangle_Triangle_CommonEdge_DistanceCompartmentModel_DataAssemble_CompartmentModelAssemble_CompartmentGradientFeedback

CompartmentModelTranslateGradient

Description: Compartment Model for diffusion that translates the gradient from pc1 to pc2 Geometry combinations available:

PC2 | PC1 - Rigid_Triangle
Sphere YES

CompartmentModelTranslateGradient (Rigid_Triangle Sphere)

Compartment Model for diffusion that translates the gradient from pc1 to pc2

Parallel Compatible: No

Properties:

  • Required keywords:
    • gradient_names — List of array names of gradient arrays.
    • khat — Transfer rates - has to match the number of concentrations! Normally this is a rate (1/s), but for triangle-triangle commonedge contacts it’s a diffusivity (m^2/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.
    • species_names — List of array names of concentration arrays. For the flux-arrays, ‘dc_dt_‘ will be prepended, unless explicitely given.
  • Optional keywords:
    • feedback_concentration (default value = 0) — If ‘True’ we set -|flux| as the feedback for the contact detector. This way, you can skip the computation of ‘too small’ fluxes if you use a contact detector with VerletLists. To do so, set ‘keep_distance’ to MINUS minimal_concentration_to_repeat. Use with care as this over-rides the default meaning of ‘feedback’ to return a spatial distance. As such it is a bad idea to set this for contact detectors based on geometry (e.g. MultiGrid), and only make sense with contact detectors that are geometry-agnostic (e.g. FixedList and SmartBruteForce).
    • 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’.
    • flux_species_names (default value = flux_species_names) — List of array names of flux-arrays.
    • 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_SphereCompartmentModel_DataAssemble_CompartmentModelAssemble_TranslateCompartmentGradient_2Feedback