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OpenMP solvers#110

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joseestraguesbsc wants to merge 34 commits into
feature/mech-origfrom
dev/mech-orig
Open

OpenMP solvers#110
joseestraguesbsc wants to merge 34 commits into
feature/mech-origfrom
dev/mech-orig

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@joseestraguesbsc

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Includes #73. Significant change to discuss is that I had to move mesh to common to include mechanics.

@asmelko asmelko left a comment

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I see you updated vcpkg submodule. was there any concrete reason for that?

Comment thread .devcontainer/physicore-dev/dockerfile Outdated
Comment thread .devcontainer/physicore-dev/devcontainer.json Outdated
Comment thread Testing/Temporary/CTestCostData.txt Outdated
Comment thread Testing/Temporary/LastTest.log Outdated
Comment thread .github/workflows/cmake-multi-platform.yml Outdated
Comment thread reactions-diffusion/biofvm/include/biofvm/mesh.h Outdated
Comment thread reactions-diffusion/biofvm/include/biofvm/solver_registry.h Outdated
Comment thread common/include/common/registry.h Outdated
Comment thread reactions-diffusion/biofvm/include/biofvm/solver_registry.h Outdated
Comment thread CMakePresets.json Outdated
Comment thread mechanics/physicell/include/physicell/solver_registry.h
Comment thread mechanics/physicell/tests/test_environment.cpp
Comment thread mechanics/physicell/tests/test_vtk_agents_serializer.cpp Outdated
Comment thread mechanics/physicell/tests/test_vtk_agents_serializer.cpp Outdated
Comment thread mechanics/physicell/tests/test_solver_registry.cpp Outdated
Comment thread mechanics/physicell/src/solver_registry.cpp
Comment thread mechanics/physicell/include/physicell/agent_data.h
Comment thread mechanics/physicell/src/environment.cpp Outdated
Comment thread mechanics/physicell/src/environment.cpp Outdated
Comment thread mechanics/physicell/include/physicell/environment.h Outdated

@asmelko asmelko left a comment

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please, copy reactions-diffusion/biofvm/kernels/.clang-tidy file into kernels directory so that clang tidy does not complain about congnitive complexity

Comment thread mechanics/physicell/kernels/openmp_solver/src/openmp_solver.cpp
Comment thread mechanics/physicell/kernels/openmp_solver/src/cell_forces.cpp Outdated
Comment thread mechanics/physicell/kernels/openmp_solver/src/cell_neighbors.cpp Outdated
Comment thread mechanics/physicell/kernels/openmp_solver/src/position_solver.cpp Outdated
Comment thread mechanics/physicell/kernels/openmp_solver/tests/test_openmp_solver.cpp Outdated
Comment thread mechanics/physicell/kernels/openmp_solver/tests/test_solve_pair.cpp Outdated
Comment thread mechanics/physicell/kernels/openmp_solver/tests/test_solve_pair.cpp Outdated
Comment thread mechanics/physicell/kernels/openmp_solver/tests/test_solve_pair.cpp Outdated
Comment thread mechanics/physicell/kernels/openmp_solver/tests/test_solve_pair.cpp Outdated
Comment thread mechanics/physicell/kernels/openmp_solver/tests/test_solve_pair.cpp Outdated
Comment thread common/include/common/random.h Outdated
class random
{
public:
static random& instance();

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There is no need for the instance method when all the other methods are static


namespace physicore {

class random

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move random.h and .cpp to mechanics/physicell -> its used only there so far
if we put it into common module, randomness implementation should correctly support all possible kernels (now it supports only openmp and single core) so that it could be called from within them

@asmelko

asmelko commented Apr 7, 2026

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Please look into the Sonarqube code coverage and cover missing lines with some meaningful tests.
EDIT: seems like you just missed adding the new kernel test binary to the sonar config file

@sonarqubecloud

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@sonarqubecloud

sonarqubecloud Bot commented May 9, 2026

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Quality Gate Failed Quality Gate failed

Failed conditions
2 Security Hotspots
42.9% Coverage on New Code (required ≥ 80%)

See analysis details on SonarQube Cloud

@sonarqubecloud

sonarqubecloud Bot commented May 9, 2026

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Quality Gate Failed Quality Gate failed

Failed conditions
2 Security Hotspots
43.2% Coverage on New Code (required ≥ 80%)

See analysis details on SonarQube Cloud

@asmelko

asmelko commented May 9, 2026

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We should add motility and basement membrane tests

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3 participants