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sanathkeshavsanathkeshav
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Merge branch 'develop' into feature/GBDiffusion
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‎.github/workflows/test_pyfans.yaml‎

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name: Test PyFans
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on: [push, pull_request]
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on:
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push:
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branches:
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- main
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- develop
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pull_request:
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branches:
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- "*"
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jobs:
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pyfans-run-test:
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test-pyfans:
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runs-on: ubuntu-latest
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container: unistuttgartdae/fans-ci:noble
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defaults:
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- name: Install dependencies
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run: |
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apt update
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apt install -y cmake make g++ python3 python3-numpy python3.12-dev
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apt install -y wget python3-venv
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- name: Install preCICE
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run: |
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wget https://github.com/precice/precice/releases/download/v3.2.0/libprecice3_3.2.0_noble.deb
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apt install -y ./libprecice3_3.2.0_noble.deb
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- name: Install the Micro Manager
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run: |
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python3 -m venv .venv
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. .venv/bin/activate
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pip install micro-manager-precice
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- name: Configure
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working-directory: ${{ env.FANS_BUILD_DIR }}
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run: |
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cmake .. -DFANS_LIBRARY_FOR_MICRO_MANAGER=ON
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make
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- name: Run FANS as a library via a Python script
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- name: Run a dummy macro-micro coupling test
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run: |
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. .venv/bin/activate
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cd test/test_pyfans
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python3 run_fans_as_library.py
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python3 macro-cube.py & micro-manager-precice micro-manager-config.json

‎CHANGELOG.md‎

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## latest
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- Add grain boundary diffusion material model for polycrystals https://github.com/DataAnalyticsEngineering/FANS/pull/52
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- Remove MPI initialization from pyFANS and add an integration test for it https://github.com/DataAnalyticsEngineering/FANS/pull/46
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- Native support for MacOS https://github.com/DataAnalyticsEngineering/FANS/pull/25
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- Remove Ubuntu 20.04 from testing and Docker support https://github.com/DataAnalyticsEngineering/FANS/pull/51
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- Add support for `--version` command line argument for checking the version of FANS

‎pyfans/micro.cpp‎

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// In this file we solve a micro problem with FANS which is controlled by the Micro Manager
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// This file is compiled with pybind11 to be available as a python module
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//
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// To check if python is able to import it, run:
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// python3 -c "import micro; micro.MicroSimulation(1)"
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// from the same directory
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#include "micro.hpp"
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#include "setup.h"
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MicroSimulation::MicroSimulation(int sim_id, char *input_file)
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{
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MPI_Init(NULL, NULL);
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// initialize fftw mpi
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fftw_mpi_init();
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‎test/test_pyfans/README.md‎

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Configure the FANS CMake build with the variable `FANS_LIB` set to `ON`.
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## Dependencies
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Install the following dependencies
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## Run the test
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Run
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The test runs a dummy macro problem (unit cube) which is coupled via preCICE to the Micro Manager. The Micro Manager controls micro simulations created using pyFANS. Run the test by running
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```bash
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python3 run_fans_as_library.py
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python macro-cube.py & micro-manager-precice micro-manager-config.json
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```
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The script creates a pyFANS object and calls the `solve()` method. The script only checks if the pyFANS object is created and the solve function is callable. The result is not checked for correctness.

‎test/test_pyfans/macro-cube.py‎

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"""
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Run FANS as a Python callable library.
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"""
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import numpy as np
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import precice
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def main():
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np_axis = 2
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# preCICE setup
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participant = precice.Participant("macro-cube", "precice-config.xml", 0, 1)
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mesh_name = "cube"
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# Coupling mesh - unit cube
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x_coords, y_coords, z_coords = np.meshgrid(
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np.linspace(0, 1, np_axis),
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np.linspace(0, 1, np_axis),
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np.linspace(0, 1, np_axis),
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)
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nv = np_axis ** participant.get_mesh_dimensions(mesh_name)
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coords = np.zeros((nv, participant.get_mesh_dimensions(mesh_name)))
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# Define unit cube coordinates
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for z in range(np_axis):
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for y in range(np_axis):
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for x in range(np_axis):
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n = x + y * np_axis + z * np_axis * np_axis
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coords[n, 0] = x_coords[x, y, z]
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coords[n, 1] = y_coords[x, y, z]
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coords[n, 2] = z_coords[x, y, z]
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vertex_ids = participant.set_mesh_vertices(mesh_name, coords)
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participant.initialize()
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dt = participant.get_max_time_step_size()
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strains1to3 = np.full((nv, 3), 0.005)
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strains4to6 = np.full((nv, 3), 0.0005)
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# time loop
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while participant.is_coupling_ongoing():
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stress1to3 = participant.read_data(mesh_name, "stresses1to3", vertex_ids, dt)
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stress4to6 = participant.read_data(mesh_name, "stresses4to6", vertex_ids, dt)
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cmat1 = participant.read_data(mesh_name, "cmat1", vertex_ids, dt)
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cmat2 = participant.read_data(mesh_name, "cmat2", vertex_ids, dt)
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cmat3 = participant.read_data(mesh_name, "cmat3", vertex_ids, dt)
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cmat4 = participant.read_data(mesh_name, "cmat4", vertex_ids, dt)
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cmat5 = participant.read_data(mesh_name, "cmat5", vertex_ids, dt)
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cmat6 = participant.read_data(mesh_name, "cmat6", vertex_ids, dt)
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cmat7 = participant.read_data(mesh_name, "cmat7", vertex_ids, dt)
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participant.write_data(mesh_name, "strains1to3", vertex_ids, strains1to3)
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participant.write_data(mesh_name, "strains4to6", vertex_ids, strains4to6)
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participant.advance(dt)
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dt = participant.get_max_time_step_size()
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participant.finalize()
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if __name__ == "__main__":
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main()

‎test/test_pyfans/micro-manager-config.json‎

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{
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"micro_file_name": "PyFANS",
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"coupling_params": {
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"precice_config_file_name": "precice-config.xml",
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"macro_mesh_name": "cube",
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"read_data_names": {"strains1to3": "vector",
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"strains4to6": "vector"
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},
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"write_data_names": {"stresses1to3": "vector",
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"stresses4to6": "vector",
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"cmat1":"vector",
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"cmat2":"vector",
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"cmat3":"vector",
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"cmat4":"vector",
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"cmat5":"vector",
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"cmat6":"vector",
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"cmat7":"vector"
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}
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},
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"simulation_params": {
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"micro_dt": 1e-1,
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"macro_domain_bounds": [0, 1, 0, 1, 0, 1]
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}
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}

‎test/test_pyfans/precice-config.xml‎

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<?xml version="1.0"?>
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<precice-configuration experimental="true">
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<log>
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<sink type="stream" output="stdout" filter= "%Severity% > debug" enabled="true" />
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</log>
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<data:vector name="stresses1to3"/>
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<data:vector name="stresses4to6"/>
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<data:vector name="strains1to3"/>
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<data:vector name="strains4to6"/>
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<data:vector name="cmat1"/>
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<data:vector name="cmat2"/>
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<data:vector name="cmat3"/>
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<data:vector name="cmat4"/>
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<data:vector name="cmat5"/>
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<data:vector name="cmat6"/>
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<data:vector name="cmat7"/>
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<mesh name="cube" dimensions="3">
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<use-data name="stresses1to3"/>
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<use-data name="stresses4to6"/>
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<use-data name="strains1to3"/>
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<use-data name="strains4to6"/>
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<use-data name="cmat1"/>
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<use-data name="cmat2"/>
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<use-data name="cmat3"/>
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<use-data name="cmat4"/>
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<use-data name="cmat5"/>
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<use-data name="cmat6"/>
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<use-data name="cmat7"/>
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</mesh>
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<participant name="macro-cube">
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<provide-mesh name="cube"/>
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<read-data name="stresses1to3" mesh="cube"/>
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<read-data name="stresses4to6" mesh="cube"/>
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<read-data name="cmat1" mesh="cube"/>
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<read-data name="cmat2" mesh="cube"/>
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<read-data name="cmat3" mesh="cube"/>
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<read-data name="cmat4" mesh="cube"/>
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<read-data name="cmat5" mesh="cube"/>
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<read-data name="cmat6" mesh="cube"/>
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<read-data name="cmat7" mesh="cube"/>
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<write-data name="strains1to3" mesh="cube"/>
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<write-data name="strains4to6" mesh="cube"/>
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</participant>
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<participant name="Micro-Manager">
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<receive-mesh name="cube" from="macro-cube" api-access="true" safety-factor="0.0"/>
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<read-data name="strains1to3" mesh="cube"/>
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<read-data name="strains4to6" mesh="cube"/>
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<write-data name="stresses1to3" mesh="cube"/>
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<write-data name="stresses4to6" mesh="cube"/>
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<write-data name="cmat1" mesh="cube"/>
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<write-data name="cmat2" mesh="cube"/>
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<write-data name="cmat3" mesh="cube"/>
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<write-data name="cmat4" mesh="cube"/>
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<write-data name="cmat5" mesh="cube"/>
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<write-data name="cmat6" mesh="cube"/>
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<write-data name="cmat7" mesh="cube"/>
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</participant>
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<m2n:sockets acceptor="macro-cube" connector="Micro-Manager"/>
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<coupling-scheme:serial-explicit>
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<participants first="Micro-Manager" second="macro-cube"/>
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<max-time value="0.2"/>
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<time-window-size value="0.1"/>
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<exchange data="stresses1to3" mesh="cube" from="Micro-Manager" to="macro-cube"/>
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<exchange data="stresses4to6" mesh="cube" from="Micro-Manager" to="macro-cube"/>
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<exchange data="cmat1" mesh="cube" from="Micro-Manager" to="macro-cube"/>
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<exchange data="cmat2" mesh="cube" from="Micro-Manager" to="macro-cube"/>
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<exchange data="cmat3" mesh="cube" from="Micro-Manager" to="macro-cube"/>
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<exchange data="cmat4" mesh="cube" from="Micro-Manager" to="macro-cube"/>
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<exchange data="cmat5" mesh="cube" from="Micro-Manager" to="macro-cube"/>
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<exchange data="cmat6" mesh="cube" from="Micro-Manager" to="macro-cube"/>
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<exchange data="cmat7" mesh="cube" from="Micro-Manager" to="macro-cube"/>
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<exchange data="strains1to3" mesh="cube" from="macro-cube" to="Micro-Manager"/>
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<exchange data="strains4to6" mesh="cube" from="macro-cube" to="Micro-Manager"/>
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</coupling-scheme:serial-explicit>
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</precice-configuration>

‎test/test_pyfans/run_fans_as_library.py‎

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