migflow.scontact

Model for Immersed Granular Flow: Fluid user interface

Contact: jonathan.lambrechts@uclouvain.be Webpage: www.migflow.be

MigFlow computes immersed granular flows using an unresolved FEM-DEM model. The continuous phase (mixture) is computed by solving averaged Navier-Stokes equations on unstructured meshes with the continuous finite element method.

class migflow.scontact.ParticleProblem(dim)

Bases: object

Creates the numerical structure containing all the physical particles that appear in the problem

Builds the particle problem structure.

Parameters

dim (int) – Dimension of the problem

Raises

ValueError – If the dimension differs from 2 or 3
NameError – If C builder cannot be found

__del__(): Deletes the particle solver structure.

add_body(x, invertM, invertI)

Adds a body in the particle problem. — Only in 2D

Parameters

x (ndarray) – array of the position of the body
InvertM – inverse mass of the body
InvertI – inverse inertia of the body

Returns

body id

Return type

int

add_boundary_periodic_entity(dim, transform)

Adds a periodic entity .

Parameters

dim (int) – dimension of the entity
transform (ndarray) – array of the transformation to applied to the periodic entity

add_boundary_periodic_point(x, tag)

Adds a boundary periodic point.

Parameters

x (ndarray) – array of the coordinates of the point
tag (int) – entity tag

add_boundary_periodic_segment(x0, x1, tag)

Adds a boundary periodic segment.

Parameters

x0 (ndarray) – array of the coordinates of the first endpoint
x1 (ndarray) – array of the coordinates of the second endpoint
tag (int) – entity tag

add_boundary_periodic_triangle(x0, x1, x2, tag)

Adds a boundary periodic triangle.

Parameters

x0 (ndarray) – array of the coordinates of the first summit
x1 (ndarray) – array of the coordinates of the second summit
x2 (ndarray) – array of the coordinates of the third summit
tag (int) – tag of the periodic entity

add_boundary_segment(x0, x1, tag, material='default', r=0)

Adds a boundary segment.

Parameters

x0 (ndarray) – array of the coordinates of the first endpoint
x1 (ndarray) – array of the coordinates of the second endpoint
tag (str) – segment tag
r – if != 0, the segment is a cylinder
material (str) – segment material

add_boundary_triangle(x0, x1, x2, tag, material='default')

Adds a boundary triangle.

Parameters

x0 (ndarray) – array of the coordinates of the first summit
x1 (ndarray) – array of the coordinates of the second summit
x2 (ndarray) – array of the coordinates of the third summit
tag (str) – triangle tag
material (str) – triangle material

add_boundary_triangle_framed(x0, x1, x2, tag, material='default')

Adds a boundary triangle with segments framing it.

Parameters

x0 (ndarray) – array of the coordinates of the first summit
x1 (ndarray) – array of the coordinates of the second summit
x2 (ndarray) – array of the coordinates of the third summit
tag (str) – triangle tag
material (str) – triangle material

add_entities(xbody, invertM=0.0, invertI=0.0, particles_coordinates=None, particles_radius=None, particles_materials='default', segments_coordinates=None, segments_tags=None, segments_materials='default', triangles_coordinates=None, triangles_tags=None, triangles_materials='default', is_relative_position=True)

Adds entities (either particles, segments or triangles) to a body described by its position, inverse of mass and inverse of inertia.

Parameters

xbody (np.ndarray) – position of the body
invertM (float, optional) – inverse mass of the body. Defaults to 0.
invertI (float, optional) – inverse inertia of the body. Defaults to 0.
particles_coordinates (np.ndarray, optional) – position of the particles. Defaults to None.
particles_radius (Union[np.ndarray, float], optional) – array of the particles radii. Defaults to None.
particles_materials (Union[str, List[str]], optional) – array of the particles material. Defaults to “default”.
segments_coordinates (np.ndarray, optional) – array of the segments coordinates as n_segments x 2 x dimension. Defaults to None.
segments_tags (Union[str, List[str]], optional) – array of the segments tags. Defaults to None.
segments_materials (Union[str, List[str]], optional) – array of the segments materials. Defaults to “default”.
triangles_coordinates (np.ndarray, optional) – array of the segments coordinates as n_segments x 3 x dimension. Defaults to None.
triangles_tags (str, optional) – array of the triangles tags. Defaults to None.
triangles_materials (Union[str, List[str]], optional) – array of the triangles materials. Defaults to “default”.
is_relative_position (bool, optional) – flag if the given position is the relative position towards the body or the absolute position. Defaults to True.

Returns

body id

Return type

int

add_particle(x, r, m, material='default', forced=False, inverse_inertia=None)

Adds a particle in the particle container.

Parameters

x (ndarray) – array of the particle position
r (float) – particle radius
m (float) – particle mass
material (str) – particle material

Returns

body id

Return type

int

add_particle_body(positions, radii, masses, material='default', forced=False)

Adds a body in the particle problem with a list of constituting particles — Only in 2D

Parameters

positions (ndarray) – positions of the particles constituting the body
radii (ndarray) – radii of the particles
masses (ndarray) – masses of the particles
material (str) – material of the particles
forced (bool) – Flag indicating whether the body is forced or not

Returns

body id

Return type

int

add_particle_to_body(x, r, body, material='default')

Adds a particle to a body.

Parameters

x (ndarray) – array of the particle positon with respect to the body’s centre of mass
r (float) – Particle radius
body (int) – number of the body to which the particle will be added
material (str) – Particle material

add_particles(x, r, m, material='default', forced=False, inverse_inertia=None)

Adds particles in the particle container.

Parameters

x (ndarray) – array of tuple to set the centre particle position
r (ndarray) – array of particle radius
m (ndarray) – array of particle mass
material (str) – particle material

Returns

id of the added bodies

Return type

np.ndarray

add_segment_to_body(x0, x1, body, tag, material='default', radius=0)

Adds a segment to a body.

Parameters

x0 (np.ndarray) – array of the coordinates of the first endpoint
x1 (np.ndarray) – array of the coordinates of the second endpoint
body (int) – body id
tag (str) – boundary id associated to the segment
radius (float) – if not 0, the segment is a cylinder
material (str) – Segment material

add_triangle_to_body(x0, x1, x2, body, tag, material='default')

Adds a segment to a body.

Parameters

x0 (np.ndarray) – array of the coordinates of the first endpoint
x1 (np.ndarray) – array of the coordinates of the second endpoint
body (int) – body id
tag (str) – boundary id associated to the segment
material (str) – Segment material

body_constraint(): Returns the invert mases of the bodies. :returns: Array of the body invert masses :rtype: np.ndarray

body_invert_inertia(): Returns the invert inertias of the bodies. :returns: Array of the body invert inertias :rtype: np.ndarray

body_invert_mass(): Returns the invert mases of the bodies. :returns: Array of the body invert masses :rtype: np.ndarray

body_omega(): Returns the angular velocities of the bodies. :returns: Array of the body angular velocities :rtype: np.ndarray

body_position(): Returns the positions of the bodies. :returns: Array of the body positions :rtype: np.ndarray

body_theta(): Returns the array of the body angles. :returns: Array of the body angles :rtype: np.ndarray

body_velocity(): Returns the velocities of the bodies. :returns: Array of the body velocities :rtype: np.ndarray

bounding_box(padding_ratio=0.0): Returns the bounding box of the particle problem. :returns: position of the lower left corner, position of the upper right corner :rtype: Tuple[np.ndarray, np.ndarray]

compute_relative_position(mass_center, particles_position, theta)

compute_stress_tensor(nodes, radius)

Computes the stress tensor of the granular material :type nodes: ndarray :param nodes: Array of nodes at which to compute the stress tensor :param r: Radius within which the contact forces will be averaged

Returns: Array of stresses on the nodes of the grid
Return type: np.ndarray

contact_forces(): Returns the contact forces on each particle. :returns: Array of the particle contact forces :rtype: np.ndarray

contact_heat(ks, young_modulus, poisson_ratio, temperature, isolated_bodies=None)

Compute the thermal heat producted by the contact

Parameters

ks (np.ndarray) – conductibility
young_modulus (np.ndarray) – Bodies Young modulus
poisson_ratio (np.ndarray) – Bodies Poisson ratio
temperature (np.ndarray) – Bodies temperature
isolated_bodies (np.ndarray, optional) – Bodies which does not produce any heat. Defaults to None.

Raises

ValueError – Wrong shape

Returns

heat producted by the contact for each body.

Return type

np.ndarray

contacts(): Gives the contacts between the bodies. :returns: Array of contact forces between the particles :rtype: np.ndarray

delassus(): Returns the delassus operators of the particles. :returns: Array of the particle delassus operators :rtype: np.ndarray

dim(): Returns the dimension of the particle problem. :returns: Dimension of the problem :rtype: int

filter_new_particles(x, r)

Return type: ndarray

get_boundary_forces(tag='default')

Returns the forces acting on a boundary because of the contacts in the global basis. :type tag: str :param tag: Name of the boundary

Returns: Array of forces on boundary named tag
Return type: np.ndarray

get_current_quality(tol)

Returns worst current contact quality(min c.space)
Performs new init of contacts list (copy)

Return type: float

get_iters_contacts_solve(): Returns the number of iterations in the contacts solver during the iteration :returns: numbers of iterations in the contacts solver during the iteration :rtype: int

get_material_id(material)

Returns the number associated to a string material. :type material: str :param material: string material.

Returns: number associated to the string material
Return type: int

get_overall_quality()

returns and tracks the worst interpenetration (min c.space) contacts of the entire simulation

Return type: float

get_separation_threshold()

Get the separation threshold for oriented faces.

Returns: Separation threshold value.
Return type: float

get_tag_id(tag='default')

Returns the number associated to a string tag. :type tag: str :param tag: string tag.

Returns: number associated to the string tag
Return type: int

get_time_contacts_solve(): Returns time spent in the contacts solver during the iteration :returns: time spent in the contacts solver during the iteration :rtype: float

get_time_detection(): Returns time spent in the detection during the iteration :returns: time spent in the detection during the iteration :rtype: float

id(): Returns the ids of the particles. :returns: Array of the particle ids :rtype: np.ndarray

init_body(reference_position, relative_position, particle_masses, particle_radii, material='default')

Return type: int

iterate(dt, forces, body_forces=None, tol=1e-08, force_motion=0)

Computes iteratively the set of velocities that respect the non-interpenetration constrain.: Returns 1 if the computation converged, 0 otherwise.

Parameters

dt (float) – Numerical time step
forces (ndarray) – List of vectors containing the forces applied on the particles
body_forces (Optional[ndarray]) – List of forces applied to the bodies
tol (float) – Optional argument defining the interpenetration tolerance to stop the NLGS iterations of the NSCD
force_motion (int) – Optional argument allowing to move the grains if convergence has not been reached when set to 1

load_mesh_to_body(bodyid, filename, tags=None, shift=None, material='default', moving=False): Not here : periodic entities

load_msh_boundaries(filename, tags=None, shift=None, material='default')

Loads the numerical domain and set the physical boundaries the particles cannot go through.

Parameters

filename (str) – name of the msh file. If None the current gmsh model is loaded without the need to a msh file.
tags (Optional[str]) – tags of physical boundary defined in the msh file
shift (Optional[ndarray]) – optional argument to shift the numerical domain
material (str) – material of the boundary

material(): Returns the materials of the particles. :returns: Array of the particle materials :rtype: np.ndarray

mu(): Returns the array of the friction coefficients between materials. :returns: Array of the friction coefficients between materials. :rtype: np.ndarray

n_bodies(): Returns the number of bodies. :returns: number of bodies :rtype: int

n_particles(): Returns the number of particles. :returns: number of particles :rtype: int

omega(): Returns the omega of the particles. :returns: Array of the particle omega :rtype: np.ndarray

parse_type(tname)

particle_body()

Returns the bodies associated to each particle

Returns: body id
Return type: np.ndarray

particle_relative_position()

Returns the relative positions of the particles

Returns: Array of the relative positions
Return type: np.ndarray

particles(): Returns the array of particles. :returns: Array of particles :rtype: np.ndarray

periodic_entity(): Returns the array of periodic entities. :returns: Array of periodic entities :rtype: np.ndarray

periodic_points(): Returns the array of periodic points. :returns: Array of periodic points :rtype: np.ndarray

periodic_segments()

Returns the array of periodic segments.

Return type: ndarray

periodic_triangles(): Returns the array of periodic triangles. :returns: Array of periodic segments :rtype: np.ndarray

position(): Returns the positions of the particles. :returns: Array of the particle positions :rtype: np.ndarray

r(): Returns the raddi of the particles. :returns: Array of the particle radii :rtype: np.ndarray

read_mig(odir, t=None, iteration=None): Reads output files. :type odir: str :param odir: Directory in which to read the file :type t: Optional[float] :param t: Time at which to read the file :param iteration; iteration to read: :param -1 for last iteration:

remove_bodies_flag(flag): Removes particles based on given flag. :type flag: ndarray :param flag: flag with the same size as the number of bodies, with 0 for bodies to be removed and 1 for bodies to be kept

restore_state(): Restores the saved state of the particle problem.

save_state(): Saves the current state of the particle problem.

segments(): Returns the array of boundary segments. :returns: Array of boundary segments :rtype: np.ndarray

segments_position()

Returns the position of all segments.

Returns: edges coordinates of all segments
Return type: np.ndarray

set_boundary_velocity(tag, v): Sets the velocity of a boundary to a given value. :type tag: str :param tag: Name of the boundary :type v: ndarray :param v: Velocity vector to be given to the boundary

set_cohesion_coefficient(c, mat0='default', mat1='default')

Sets the cohesion coefficient between two materials.

Parameters

c (ndarray) – Value of the cohesion coefficients
mat0 (str) – First material
mat1 (str) – Second material

set_compute_contact_forces(compute_contact_forces=1): Enables the computation of the contact forces on each particle if 1 and disables it if 0.

set_detection_per_iteration(n)

Sets the number of iterations between two contact detection.

Parameters: n (int) – Number of iterations between two contact detection.

set_fixed_contact_geometry(flag)

Sets the management of the contact geometry, either fixed (default) or changing each time the contact is solved.

Parameters: flag (bool) – True for fixed False for changing.

set_friction_coefficient(mu, mat0='default', mat1='default')

Sets the friction coefficient between two materials.

Parameters

mu (float) – Value of the friction coefficient
mat0 (str) – First material
mat1 (str) – Second material

set_initial(initial=1): Sets the initial state of the particle problem.

set_jacobi_max_iters(maxit=10000)

set_jacobi_mode(jacobi_mode=0)

set_jacobi_relaxation(relax=0.5)

set_oriented_faces(flag)

Set whether the faces (triangles in 3d, or edges in 2d) are oriented. By default, set to false.

Parameters: flag (bool) – _description_

set_predict_basis(flag)

Set the management of the contact geometry, if true, a contact basis estimation is used in the contact resolution

Parameters: flag (bool) – True for the estimation

set_redblack_mode(redblack_mode=0)

set_separation_threshold(threshold)

Set the separation threshold for oriented faces.

Parameters: threshold (float) – Separation threshold value.

set_use_queue(use_queue=1): Enables the use of the queue if 1 and disables it if 0.

triangles(): Returns the array of boundary triangles. :returns: Array of boundary triangles :rtype: np.ndarray

velocity(): Returns the velocities of the particles. :returns: Array of the particle velocities :rtype: np.ndarray

volume(): Returns the volumes of the particles. :returns: Array of the particle volumes :rtype: np.ndarray

write_mig(output_dir, t, extra_fields={}, write_contacts=True): Writes output files for post-visualization. :type output_dir: str :param output_dir: Directory in which to write the file (expected to end in “.mig”) :type t: float :param t: Time at which the simulation is :type extra_fields: Dict[str, ndarray] :param extra_fields: extra field as a dictionnary {name : values}

write_residues_to_CSV(filename)

Writes the residues of the particle problem to a CSV file.

Parameters: filename (str) – Name of the output CSV file.

migflow.scontact.absolute_coord(position_bodies, theta_bodies, bodies, relative_position)

migflow.scontact.fastdeposit_2d(boundary, r, svgfilename=None)

Fast 2d deposit of particles in a simple domain. :type boundary: ndarray :param boundary: points describing the boundary (single loop counter-clockwise oriented, no holes). :type boundary: np.ndarray [n,2] :type r: ndarray :param r: radius of the particles. :type r: np.ndarray [m] :type svgfilename: Optional[str] :param svgfilename: if not None, a svg file is generated illustrating the algorithm

Returns: positions of the particles. np.ndarray [m,2]: radius of the particles.
Return type: np.ndarray [m,2]

migflow.scontact.get_particle_range(outputdir, field)

Returns the range associated to a particle field. :type field: str :param field: name of the field :type field: str

Returns: minimum and maximum values of the field
Return type: Tuple[np.ndarray, np.ndarray]

migflow.scontact.read_particle_field(outputdir, field, t)

Returns a particle field at a given time. :type outputdir: str :param outputdir: output directory of the simulation :type outputdir: str :type field: str :param field: name of the field :type field: str :type t: float :param t: time :type t: float

Returns: values of the field at time t
Return type: np.ndarray