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Dem insertion: clear and add (chaos-polymtl#1135)
Description of the problem LPBF spreading simulations requires a lots of particles. Most of them are useless during most of the simulation time, as they are deep the powder dispenser. It would be more efficient to only simulate the particles required for the layer N and not for the following layers. Description of the solution A new insertion method called "clear and add" has been implemented. This method is very similar to file insertion in that it reads particle position, diameter and velocity from input files. First, we define a clearing box, where particles will be deleted. Then, we insert new particles from an insertion file. Each insertion, a different insertion file can be use. How Has This Been Tested? Custom parameter file. (See slack) Comments I still need to do a test, and example and the documentation for this method. I have change the order for the parsing of the parameters. It is now in alphabetical order. It is cleaner IMO. Former-commit-id: f69c03c
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‎CHANGELOG.md

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All notable changes to the Lethe project will be documented in this file.
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The format is based on [Keep a Changelog](http://keepachangelog.com/).
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## [Master] - 2024-05-27
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### Changed
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- MINOR The "insertion file name" parameter has been renamed to "list of input files". It now supports a list of input files that will be used in order when inserting particles. [#1135](https://github.com/chaos-polymtl/lethe/pull/1135)
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## [Master] - 2024-05-26
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### Fixed

‎applications_tests/lethe-particles/CMakeLists.txt

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@@ -24,6 +24,8 @@ file(COPY periodic_gmsh_files/pipe.msh DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/
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file(COPY load_balancing_solid_object_files/square.msh DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/load_balancing_solid_object.${_build_type}")
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file(COPY insert_file_3d_files/particles.input DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/insert_file_3d.${_build_type}")
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file(COPY moving_float_files/square.msh DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/moving_float.${_build_type}")
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file(COPY insert_and_remove_with_files_files/particles_00.input DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/insert_and_remove_with_files.${_build_type}")
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file(COPY insert_and_remove_with_files_files/particles_01.input DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/insert_and_remove_with_files.${_build_type}")
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file(COPY moving_receptacle_files/restart.insertion_object DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/restart_moving_receptacle.${_build_type}/mpirun=1/")
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file(COPY moving_receptacle_files/restart.particles DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/restart_moving_receptacle.${_build_type}/mpirun=1/")

‎applications_tests/lethe-particles/insert_and_remove_with_files.prm

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# Listing of Parameters
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#----------------------
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set dimension = 3
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#---------------------------------------------------
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# Simulation Control
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#---------------------------------------------------
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subsection simulation control
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set time step = 1e-5
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set time end = 0.11
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set log frequency = 10000
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set output frequency = 0
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end
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#---------------------------------------------------
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# Timer
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#---------------------------------------------------
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subsection timer
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set type = none
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end
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#---------------------------------------------------
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# Test
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#---------------------------------------------------
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subsection test
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set enable = true
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end
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#---------------------------------------------------
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# Model parameters
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#---------------------------------------------------
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subsection model parameters
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subsection contact detection
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set contact detection method = dynamic
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set dynamic contact search size coefficient = 0.9
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set neighborhood threshold = 1.3
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end
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set particle particle contact force method = hertz_mindlin_limit_overlap
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set particle wall contact force method = nonlinear
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set rolling resistance torque method = constant_resistance
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set integration method = velocity_verlet
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end
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#---------------------------------------------------
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# Lagrangian Physical Properties
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#---------------------------------------------------
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subsection lagrangian physical properties
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set gx = 0.0
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set gy = 0.0
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set gz = 0.0
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set number of particle types = 1
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subsection particle type 0
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set size distribution type = uniform
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set diameter = 0.1
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set number of particles = 6
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set density particles = 1000
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set young modulus particles = 1000000
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set poisson ratio particles = 0.3
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set restitution coefficient particles = 0.3
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set friction coefficient particles = 0.1
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set rolling friction particles = 0.05
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end
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set young modulus wall = 1000000
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set poisson ratio wall = 0.3
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set restitution coefficient wall = 0.3
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set friction coefficient wall = 0.1
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set rolling friction wall = 0.05
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end
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#---------------------------------------------------
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# Insertion Info
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#---------------------------------------------------
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subsection insertion info
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set insertion method = file
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set insertion frequency = 100
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set list of input files = ../particles_00.input, ../particles_01.input
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set removal box points coordinates = 0., -1., -1.: 1., 1., 1.
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set remove particles = true
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end
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#---------------------------------------------------
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# Mesh
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#---------------------------------------------------
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subsection mesh
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set type = dealii
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set grid type = hyper_cube
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set grid arguments = -0.8 : 0.8 : false
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set initial refinement = 2
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set expand particle-wall contact search = false
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end
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‎applications_tests/lethe-particles/insert_and_remove_with_files.with_dealii.geq.9.6.mpirun=1.output

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*********************
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Running on 1 rank(s)
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*********************
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DEM time-step is 0.115554% of Rayleigh time step
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Warning: It is recommended to increase the time-step
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Reading triangulation
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Finished reading triangulation
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Warning: expansion of particle-wall contact list is disabled.
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This feature is useful in geometries with concave boundaries.
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*********************************************************************
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4 particles of type 0 were inserted, 2 particles of type 0 remaining
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*********************************************************************
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*********************************************************************
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2 particles of type 0 were inserted, 0 particles of type 0 remaining
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*********************************************************************
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*****************************************************************
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Transient iteration: 10000 Time: 0.1 Time step: 1e-05
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*****************************************************************
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| Variable | Min | Max | Average | Total |
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| Contact list generation | 0.0000e+00 | 1.0000e+02 | 1.0000e+02 | 1.0000e+02 |
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| Velocity magnitude | 0.0000e+00 | 2.2251e-308 | 0.0000e+00 | 0.0000e+00 |
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| Angular velocity magnitude | 0.0000e+00 | 2.2251e-308 | 0.0000e+00 | 0.0000e+00 |
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| Translational kinetic energy | 0.0000e+00 | 2.2251e-308 | 0.0000e+00 | 0.0000e+00 |
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| Rotational kinetic energy | 0.0000e+00 | 2.2251e-308 | 0.0000e+00 | 0.0000e+00 |
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id, type, dp, x, y, z
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0 0 0.10000 -0.2000 0.0000 0.0000
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1 0 0.10000 -0.2000 0.3000 0.0000
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2 0 0.10000 0.2000 0.0000 0.1000
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3 0 0.10000 0.2000 0.5000 0.1000

‎applications_tests/lethe-particles/insert_and_remove_with_files_files/particles_00.input

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p_x; p_y; p_z; v_x; v_y; v_z; w_x; w_y; w_z; diameters; fem_force_x; fem_force_y; fem_force_z; fem_torque_x; fem_torque_y; fem_torque_z
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-0.2; 0.0; 0.0; 0.0; 0.0; 0.0; 0.0; 0.0; 0.0; 0.1 ; 0.0 ; 0.0 ; 0.0 ; 0.0 ; 0.0 ; 0.0
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-0.2; 0.3; 0.0; 0.0; 0.0; 0.0; 0.0; 0.0; 0.0; 0.1 ; 0.0 ; 0.0 ; 0.0 ; 0.0 ; 0.0 ; 0.0
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0.2; 0.0; 0.0; 0.0; 0.0; 0.0; 0.0; 0.0; 0.0; 0.1 ; 0.0 ; 0.0 ; 0.0 ; 0.0 ; 0.0 ; 0.0
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0.2; 0.3; 0.0; 0.0; 0.0; 0.0; 0.0; 0.0; 0.0; 0.1 ; 0.0 ; 0.0 ; 0.0 ; 0.0 ; 0.0 ; 0.0

‎applications_tests/lethe-particles/insert_and_remove_with_files_files/particles_01.input

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p_x; p_y; p_z; v_x; v_y; v_z; w_x; w_y; w_z; diameters; fem_force_x; fem_force_y; fem_force_z; fem_torque_x; fem_torque_y; fem_torque_z
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0.2; 0.0; 0.1; 0.0; 0.0; 0.0; 0.0; 0.0; 0.0; 0.1 ; 0.0 ; 0.0 ; 0.0 ; 0.0 ; 0.0 ; 0.0
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0.2; 0.5; 0.1; 0.0; 0.0; 0.0; 0.0; 0.0; 0.0; 0.1 ; 0.0 ; 0.0 ; 0.0 ; 0.0 ; 0.0 ; 0.0

‎applications_tests/lethe-particles/insert_file_3d.prm

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subsection insertion info
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set insertion method = file
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set insertion file name = ../particles.input
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set list of input files = ../particles.input
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set insertion frequency = 5000
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end
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‎applications_tests/lethe-particles/insert_plane_3d.output

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28 0 0.01000 0.2079 -0.0069 0.3979
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29 0 0.01000 -0.0357 -0.0020 -0.3063
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30 0 0.01000 0.2206 0.0303 0.1907
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31 0 0.01000 -0.0391 0.0187 0.2174
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31 0 0.01000 -0.0391 0.0187 0.2174

‎doc/source/parameters/dem/insertion_info.rst

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@@ -15,6 +15,8 @@ In this subsection, insertion methods which are ``volume``, ``plane``, ``list``
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# Every method
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set insertion frequency = 20000
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set remove particles = false
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set removal box points coordinates = 0., 0., 0.: 1., 1., 1.
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# If method = volume
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set inserted number of particles at each time step = 100
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set list diameters = 0.
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# If method = file
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set insertion file name = particles.input
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set list of input files = particles.input
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end
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The ``insertion method`` parameter chooses the type of insertion. Acceptable choices are ``volume``, ``plane``, ``list`` and ``file``. Different insertion method can share the same parameter.
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* The ``insertion maximum offset`` and ``insertion prn seed`` parameters defines the random offset values to the initial positions of particles during a ``volume`` and ``plane`` insertion. The ``insertion maximum offset`` parameter defines the maximum value for an offset. The ``insertion prn seed`` parameter defines the pseudo-random number (PRN) with which offset values are getting generated.
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* The ``removal box points coordinates`` parameter defines a removal box where particles will be removed from the triangulation just before the insertion of new particles. This assures that there is no excessive overlap between new and previously inserted particles. If the ``remove particles`` parameter is set to ``false`` particle removal will not be performed.
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-------
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Volume
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-------
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---------------------
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File
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---------------------
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The ``file`` insertion method insert particles in a similar way to the ``list`` insertion method. The main difference between these two methods is the option to use an external file provided by the ``insertion file name`` parameter. This parameter is set at ``particles.input`` by default. This file has to follow this structure:
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The ``file`` insertion method inserts particles in a similar way to the ``list`` insertion method. The main difference between these two methods is the option to use external files provided by the ``list of input files`` parameter. This parameter is set at ``particles.input`` by default, but a file list can be specified. At each insertion time step, a different file will be used. If the end of the list is reached and there are still particles to be inserted, the list returns to the first file. An insertion file must follow this structure:
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.. code-block:: text
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The ``file`` insertion combine with the ``extract-particles-properties-from-vtu.py`` python code can be a useful tool. The loading of particles and the rest of the simulation can be performed in two different triangulations, witch is not the case of the the restart feature. This means that the loading triangulation can have smaller cells and a bigger domain to allow for the use of larger insertion boxes. Then, particles properties can be extracted and the remainder of the simulation can be performed in the appropriate triangulation.
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.. warning::
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The critical Rayleigh time step is computed from the parameters in the ``particle type`` subsections, not the ``insertion info`` subsection. It is the user's responsibility to fill the ``particle type`` subsections correctly according to the diameter values stored in the insertion input file, otherwise Rayleigh time percentage displayed at the start of every DEM simulation may not be accurate.
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The critical Rayleigh time step is computed from the parameters in the ``particle type`` subsections, not the ``insertion info`` subsection. It is the user's responsibility to fill the ``particle type`` subsections correctly according to the diameter values stored in the insertion input file, otherwise Rayleigh time percentage displayed at the start of every DEM simulation may not be accurate.

‎include/core/parameters.h

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std::vector<T> vector = Utilities::string_to_double(vector_of_string);
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return vector;
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}
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if constexpr (std::is_same<T, std::string>::value)
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{
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return vector_of_string;
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}
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}
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} // namespace Parameters

‎include/core/parameters_lagrangian.h

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178178
// Insertion frequency
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int insertion_frequency;
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// Direction (axis) of insertion of particles (1st, 2nd, 3rd)
182-
std::vector<unsigned int> direction_sequence;
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/* Removal box: */
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bool removing_particles_in_region;
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// Insertion box info (xmin,xmax,ymin,ymax,zmin,zmax)
185-
Point<3> insertion_box_point_1, insertion_box_point_2;
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// Clear box info (xmin,xmax,ymin,ymax,zmin,zmax)
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Point<3> clear_box_point_1, clear_box_point_2;
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/* File: */
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std::vector<std::string> list_of_input_files;
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/* Plane: */
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// Plane normal vector
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Tensor<1, 3> insertion_plane_normal_vector;
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// Plane point
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Point<3> insertion_plane_point;
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/* List */
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// Containers used for the list insertion method
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std::vector<double> list_x, list_y, list_z, list_vx, list_vy, list_vz,
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list_wx, list_wy, list_wz, list_d;
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/* Volume */
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// Direction sequence for the insertion of particles (1st, 2nd, 3rd)
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std::vector<unsigned int> direction_sequence;
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// Insertion box info (p_1 , p_2)
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Point<3> insertion_box_point_1, insertion_box_point_2;
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// Insertion initial velocity conditions
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Tensor<1, 3> initial_vel, initial_omega;
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// Insertion distance threshold
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double distance_threshold;
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// Insertion random number range
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double insertion_maximum_offset;
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// Insertion random number seed
197213
int seed_for_insertion;
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std::vector<double> list_x, list_y, list_z, list_vx, list_vy, list_vz,
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list_wx, list_wy, list_wz, list_d;
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std::string insertion_particles_file_name;
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// Insertion plane definition
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Tensor<1, 3> insertion_plane_normal_vector;
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Point<3> insertion_plane_point;
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static void
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declare_parameters(ParameterHandler &prm);
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void

‎include/dem/dem.h

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std::vector<std::shared_ptr<SerialSolid<dim - 1, dim>>> solids;
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// Distribution objects
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std::vector<std::shared_ptr<Distribution>> distribution_object_container;
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std::vector<std::shared_ptr<Distribution>> size_distribution_object_container;
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// Adaptive sparce contacts (ASC) in cells object
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AdaptiveSparseContacts<dim> sparse_contacts_object;

‎include/dem/input_parameter_inspection.h

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*
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* @param dem_parameters Input DEM parameters in the parameter handler file
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* @param pcout Printing in parallel
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* @param distribution_object_container Contain all the types of distribution
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* @param size_distribution_object_container Contain all the types of distribution
3434
* being used for each type of particle.
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*
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*/
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template <int dim>
3939
void
40-
input_parameter_inspection(
41-
const DEMSolverParameters<dim> &dem_parameters,
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const ConditionalOStream &pcout,
43-
const std::vector<shared_ptr<Distribution>> &distribution_object_container);
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input_parameter_inspection(const DEMSolverParameters<dim> &dem_parameters,
41+
const ConditionalOStream &pcout,
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const std::vector<shared_ptr<Distribution>>
43+
&size_distribution_object_container);
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#endif /* input_parameter_inspection_h */

‎include/dem/insertion.h

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* volume_insertion, plane_insertion, list_insertion and file_insertion
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* classes.
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*
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* @param distribution_object_container Contains all distribution for each
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* type of particle
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* @param size_distribution_object_container Contains all distribution for each
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* particle type
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* @param triangulation Triangulation to access the cells in which the
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* particles are inserted
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* @param dem_parameters DEM parameters declared in the .prm file
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*/
7073
Insertion(const std::vector<std::shared_ptr<Distribution>>
71-
&distribution_object_container);
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&size_distribution_object_container,
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const parallel::distributed::Triangulation<dim> &triangulation,
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const DEMSolverParameters<dim> &dem_parameters);
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/**
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* @brief This function is overridden by the volume_insertion, plane_insertion,
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const DEMSolverParameters<dim> &dem_parameters,
160165
const ConditionalOStream &pcout);
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/**
168+
* @brief Find every cell that are completely and partially inside de the
169+
* clearing box. For the cell completely inside the box, all the particles
170+
* will be deleted. For those partially inside, a fine verification is
171+
* required.
172+
*
173+
* @param triangulation Triangulation to access the cells in which the
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* particles deleted.
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*/
176+
void
177+
find_cells_in_removing_box(
178+
const parallel::distributed::Triangulation<dim> &triangulation);
179+
180+
/**
181+
* @brief Remove every particle located inside a predefined zone. Currently,
182+
* the zone is defined by a box.
183+
*
184+
* @param particle_handler The particle handler of particles which are being
185+
* removed.
186+
*/
187+
void
188+
remove_particles_in_box(Particles::ParticleHandler<dim> &particle_handler);
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162190
// Number of particles inserted at each insertion time step. This value can
163191
// change in the last insertion step to reach the desired number of particles
164192
unsigned int inserted_this_step;
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181209
// particle during an insertion time step
182210
std::vector<std::shared_ptr<Distribution>> distributions_objects;
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212+
// Clearing bool
213+
const bool removing_particles_in_region;
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215+
// Clearing box coordinates
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Point<dim> p_min, p_max;
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// Cell iterator containers for clearing
219+
std::set<typename Triangulation<dim>::active_cell_iterator> in_removal_box;
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std::set<typename Triangulation<dim>::active_cell_iterator>
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edge_of_removal_box;
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// For when the triangulation has changed (i.e. when load balancing)
224+
bool mark_for_update;
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boost::signals2::connection change_to_triangulation;
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private:
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// Stores particles diameters
186229
std::vector<double> particle_sizes;

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