Add one line installer and pulsatile case#6
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Feb 19, 2026
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- Add a one line installer for the svFSGe
- Add a pulsatile case using mean wss
- Add converted pulsatile Q waveform (pulsatile_flow.dat) from VMR source .flow files, converted from cm/s to mm/s to match kg/mm/s unit system - Update steady_full.xml inlet BC to use Unsteady time dependence with the pulsatile temporal values file - Add static BC file copy step in svfsi.py setup_files so pulsatile_flow.dat is staged into the run directory automatically - Include source .flow files from Vascular Model Repository Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
- Increase Number_of_time_steps from 10 to 960 (10 cardiac cycles at dt=0.01s) - Add run_fluid_only.py script for standalone fluid simulation without FSG coupling, handles mesh/BC file staging and runs svFSI directly Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
- Container named 'fsg-dev' now persists after exit - Rerunning the script reconnects to existing container - Uses 'sleep infinity' + 'docker exec' pattern for persistence - Updated pip install to use requirements.txt (includes meshio) - Shows container management commands on completion Users can now: - Exit and reconnect without losing setup - Stop/start the container as needed - See the container in 'docker ps -a' Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Instead of requiring requirements.txt, the script now has the package list hardcoded. This makes it work even if requirements.txt is missing or the repo state is inconsistent. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Creates a bootstrap script that can be downloaded and run via curl. Handles repo cloning and Docker setup in one command. Usage: curl -fsSL https://raw.githubusercontent.com/Eleven7825/svFSGe/master/scripts/install.sh | bash Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
- Prominently featured at the top of Quickstart section - Explains prerequisites and what the command does - Updated Quick Setup Script section to mention persistent container Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
- Add setup_singularity.sh for automated Singularity environment setup - Add install_singularity.sh for one-command installation on HPC - Add run_simulation.sh helper script for easy simulation execution - Update README.md with HPC installation instructions - Support for read-only containers with user-space Python package installation - Include verification step to ensure all dependencies are properly installed
…ive VTU copying - Copies folder structure and all files except VTU/BIN from pulsatile/steady/gr_restart - Copies only last 400 pulsatile VTU files to minimize transfer size - Copies only last 10 steady VTU files - Excludes all gr_restart VTU files completely - Uses SSH ControlMaster for single authentication - Strips carriage returns from remote SSH output for proper path handling
…from the json file
…be read from the json file" This reverts commit 7c671a3.
…_full_coarse.json
Informational prints in extract_pulsatile_time_average and extract_pulsatile_amplitude are now gated behind verbose=False by default. Enable with "debug": true in the JSON config. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- fsg.py/svfsi.py: add iqn_ils_debug option (off by default) to save V, W, Q, R, column counts before/after QR filtering, and cc coefficients each IQN-ILS call; saved to debug_qr.npy on archive - post.py: add plot_cc() to plot cc norm and heatmap with load-step transition lines; called automatically from main_arg when debug_qr.npy exists - in_sim/partitioned_full_steep.json: new steep profile case (nmax=5, profile_beta with beta_min=2/beta_max=10, iqn_ils_debug enabled) - in_svfsi_plus/gr_full_restart_steep.xml: solid XML with n_t_end=4 for steeper GR ramp (full load reached at t=3 out of 5 steps) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…verbose output - fsg.py/svfsi.py: save load step t and sub-iter n alongside each IQN-ILS debug entry, removing need for fragile formula to reconstruct transitions - post.py: derive transition lines directly from saved t array; fix path resolution for plot_cc in main_arg (two levels up from partitioned/converged) - svfsi.py: suppress "extracted from N geometries" print unless debug=true - in_sim/partitioned_full_debug.json: normal progressive profile case with iqn_ils_debug enabled for comparison against steep profile Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Draw a step line at ncols_after - 0.5 on the heatmap to clearly show the boundary between active coefficients and NaN, making filtering events (drops in the line) immediately visible. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
When iqn_ils_reset=true, mat_V and mat_W are cleared at n=0 of each new load step so IQN-ILS starts from scratch without reusing vectors from previous time steps. Default is false (existing behavior). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- fsg.py: add iqn_ils_debug saving (cc, t, n per call), iqn_ils_reset flag to clear history vectors at each new load step, fallback to relaxation when mat_V is empty after reset - post.py: add plot_cc() with 3-panel GridSpec figure (|c| heatmap log scale, ||c|| norm, coupling residual before/after IQN update); called from main_arg; use pcolormesh + dedicated colorbar column to fix x-axis alignment - in_sim/partitioned_full_steep.json: set q=5, reset=true, profile_beta=true
…ot_cc - Dummy invisible subplots in colorbar column for all rows so column widths match - MaxNLocator(integer=True) for integer x-axis ticks - Fix sharex() call (replace deprecated get_shared_x_axes().join()) - Remove legend from heatmap and norm subplots; residual shows only before/after/tol - Sparser y-ticks on heatmap (every 2)
Saves and restores all state needed to resume from a converged load step: - IQN-ILS history (mat_W, mat_V, dk, res, dtk) - Coupling error and relaxation history (err, omega) - Current and all previous converged solutions - svFSI binary restart files (stFile_last.bin) snapshotted at checkpoint time to avoid corruption from subsequent failed load steps Usage: set "save_restart": true in JSON to enable checkpointing. Restart via "restart": "path/to/restart.npz" in JSON or -restart CLI flag. Tested on steady case (nmax=2 + restart to nmax=3): sub-iteration counts, IQN-ILS residuals, and displacement fields match to floating-point precision.
The load profile (how the G&R insult is ramped over the load steps) was
hard-coded inside svMultiPhysics' gr_equilibrated.cpp and could not be
changed from here. Expose it through the GR_equilibrated material params
and inject it from the simulation JSON:
- svfsi.py set_gr_load(): reads an optional "gr_load" section and patches
the solid solver XML (<load_profile>/<load_steep>/<load_file>) per run,
using the same regex-on-XML approach as the pulsatile step-count patch.
profile: linear | tanh (default) | power | file
steep: tanh steepness / power exponent
curve: for "file", the load factor per step ([step, factor] pairs or
a plain list); step 0 = pre-stress, 1..nloads = G&R loads.
Omitting "gr_load" leaves the XML untouched -> svFSI defaults (tanh, 2.0),
reproducing the historical behavior.
- Rename the top-level G&R load-step count nmax -> nloads (it clashed with
coup["nmax"], the coupling-iteration cap). The old "nmax" is still
accepted for backward compatibility. coup["nmax"] is unchanged.
Verified: fsg.py in_sim/partitioned_test.json matches test_reference/nmax_2
with both the tanh default and an equivalent file curve.
Requires the matching gr_equilibrated.cpp parser changes in svMultiPhysics
(FSGe branch); without them an older binary rejects the injected XML tags.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Companion to the load-profile work: the aneurysm insult (the spatial
elastin/stimulus knock-down that localizes the lesion) was a super-Gaussian
hard-coded in svMultiPhysics' gr_equilibrated.cpp. Expose it and inject it
from the simulation JSON.
- svfsi.py set_gr_insult(): reads an optional "gr_insult" section and patches
the solid XML with the GR_equilibrated insult params, writing
gr_insult_curve.dat for profile=file. Refactor the XML-patch and curve-write
logic out of set_gr_load() into shared _patch_solid_xml()/_write_curve()
helpers used by both.
profile: gaussian (default) | file (axial shape; azimuth stays gaussian)
mag: peak elastin loss fraction
z_loc/z_wid/z_exp: axial center/width (frac of length)/exponent
asym, theta_wid/theta_exp: azimuthal localization
curve: for "file", axial factor f_axi vs normalized position z/lo
([z/lo, factor] pairs or a plain list)
Knock-down at a point = mag * f_axi(z) * f_cir(azimuth). Omitting "gr_insult"
leaves the XML untouched -> svFSI defaults reproduce the historical insult.
- partitioned_test.json: add an explicit gaussian gr_insult so the CI test
also exercises the injection path (behavior unchanged).
Verified: fsg.py in_sim/partitioned_test.json matches test_reference/nmax_2
with the injected gaussian insult.
Requires the matching gr_equilibrated.cpp parser changes in svMultiPhysics
(FSGe branch); an older binary would reject the injected insult_* XML tags.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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