NMPDE project delivery - #80
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…the membrane tension and the auxilialies variables
… the auxiliar variables. they have to be impplementend yet. Just an examble for the fast inward current was done
- Create polymorphic `SolverAdapter` and `PreconditionAdapter` hierarchies to support runtime selection of solver (CG, GMRES, Direct) and preconditioner types (Jacobi, ILU, SSOR). - Refactor option parsing in `Args` using std::function lambdas to support extensible CLI arguments, including `--solver` and solver-specific parameters. - Implement stream operators (`operator<<`) for solvers, preconditioners, and args configuration, including printing the number of MPI processes. - Restrict arguments printout to MPI rank 0 in `exercise-01.cpp`. - Clean up workspace by removing `TODO.txt`.
…alization suite - Add comprehensive PBS job submission scripts for simulation sweeps: - convergence_sweep.sh: spatial mesh size (h) and time step (dt) sweeps - model_sweep.sh: cellular action potential model parameter sweeps - cpu_sweep.sh: MPI strong scalability benchmarks (1 to 28 cores) - solver_sweep.sh: linear solver and preconditioner performance comparison - euler_comparison.sh: time discretization scheme comparison - Add Python/ParaView automated 3D and 2D visualization tools: - plot_convergence_3d.py: 3D activation time surface and scatter plots with inverted X-axis, Z-gradient color mapping, and node labels - plot_model_activation.py: ParaView clip plane rendering with corner camera orientation and unified global color scale across models - plot_scaling.py, plot_performance.py: scaling and solver benchmark plotting - Fix C++ activation time VTU/PVTU output path handling in Current.cpp using std::filesystem - Fix system return check and suppress unused parameter compiler warnings in args.cpp - Update model definitions in models/models.csv
…sage - Rename auxiliary variables from v, w, s to w1, w2, w3. - Rename voltage variables from u to v (v_o, v_u) and adjust threshold/time constants (theta_w1, theta_w2, tau_w1_1_m, tau_w1_2_m). - Set the physical/membrane variable as static constants (beta_mm, Cm, and intracellular/extracellular conductivities). - Update system solvers, boundary conditions, initial values, and output mapping in Current class to use new naming conventions. - Rename activation_time() to check_activation_time() and adjust corresponding variables. - Align help message in args.cpp and add solver/preconditioner parameters (-p, --max_iter, --tol, --reduce, --ilu_fill, --ssor_omega).
- Rename temporary variables v_owned_old, w_owned_old, s_owned_old to w1_old, w2_old, w3_old inside Current::integrate_auxiliar_variables(). - Localize time constant variables (tau_w2_m, tau_w3) for updating w2 and w3. - Use the correct renamed w1_old/w2_old/w3_old states in the ODE integration formulas.
- Add scripts/run.sh to request a dedicated PBS interactive node, build the dealii_paraview.sif container, compile the project, and trigger sweep scripts (with a --init flag to skip sweeps). - Update convergence, CPU, model, and solver sweep scripts to execute simulations and plot scripts inside the new dealii_paraview.sif container. - Collect PBS job IDs in sweep scripts to schedule plotting tasks automatically using dependent jobs (qsub -W depend=afterany).
- Add dealii_paraview.def to build an Apptainer image containing dealii, ParaView, pvpython, and Python plotting dependencies. - Update defaults.cmake to set the default solver to cg, the default preconditioner to ilu, and default ILU fill-in to 0.
…pelines - Correct configuration repetition loop syntax in cpu_sweep.sh and solver_sweep.sh. - Add mean and standard deviation computation to performance and scaling plotting scripts to support repeated configuration runs. - Migrate all sweep scripts to target the updated dealii_paraview.sif container. - Update run.sh to compile projects inside the container and skip container builds if dealii_paraview.sif is already present. - Modify plot_convergence_3d.py to use pure vtkmodules XML readers, bypassing host-side ParaView/OpenXR import failures. - Implement plot_euler_comparison.py to plot 1D activation profiles along the (0,0,0) -> (20,7,3) line for discretization methods, including a zoomed view with lines only. - Refactor plot_model_activation.py to natively render square screenshots, extract a standalone colorbar legend and generate 1D line profiles for all models. - Integrate automated post-run plotting job dependencies using PBS job chaining in euler_comparison.sh.
…ation visualization scripts - Update plot_euler_comparison.py to generate a combined plot with a zoomed inset at the bottom-right corner for the last segment (x >= 20.5 mm). - Update plot_model_activation.py to generate a standalone zoomed plot (x < 1.0 mm) and a combined plot with an inset at the bottom-right corner zooming on the initial propagation segment (x < 1.0 mm).
- Update plot_scaling.py to display only the numeric core counts (e.g. 1, 2, 4, 8, 16, 32, 58) on the x-axis ticks and change the x-axis label to "Number of cores in use". - Create README.md detailing the local CMake compilation commands, Apptainer execution pattern, dealii_paraview.sif container toolset, MOX department cluster environment, and LLM-assisted sweep scripts. - Document in the README that the main.tex LaTeX report contains the mathematical discussion as well as the experimental results and plots generated by the scripts. - Document that run.sh with --init builds both the container image and compiles the exercise-01 binary while skipping the sweeps.
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This is the git repository of our project that we present tomorrow