hyphal-flow

Basilisk C simulations for drop transport in a single fungal hypha branch with three-phase, non-coalescing viscoelastic modeling.

Repository Layout

├── src-local/                               # Project-specific Basilisk headers
│   ├── log-conform-elastic.h
│   ├── log-conform-viscoelastic.h
│   ├── reduced-three-phase-nonCoalescing.h
│   ├── three-phase-nonCoalescing-elastic.h
│   └── three-phase-nonCoalescing-viscoelastic.h
├── simulationCases/                         # Simulation entry points + case dirs
│   ├── hypha.c
│   ├── hypha-capillary.c
│   ├── Hypha-capillary-length.c
│   ├── Makefile
│   └── runCodesInParallel.sh
├── postProcess/                             # Analysis and plotting utilities
│   ├── getData-elastic-nonCoalescence.c
│   ├── getFacet-threePhase.c
│   ├── plot_vcm_vs_time.py
│   ├── plot_hypha_width_vs_time.py
│   └── plot_vcm_vs_Ec_H.py
├── default.params                           # Base parameters for sweeps
├── sweep.params                             # Default MPI sweep config
├── sweep-128.params                         # Default serial-128 sweep config
├── runSweepHamilton.sbatch                  # MPI sweep runner
├── runSweepHamilton-serial-128.sbatch       # Serial compile + parallel launch
├── AGENTS.md                                # Authoritative project guidance
├── README.md
└── LICENSE

Requirements

• Basilisk qcc
• C compiler (GCC/Clang)
• mpicc and MPI runtime for MPI builds
• Python 3 (for plotting scripts and sweep value generation)

Quick Start

1. Compile a simulation case

OpenMP build:

qcc -Wall -O2 -fopenmp -I$(PWD)/src-local simulationCases/hypha.c -o hypha -lm

MPI build:

CC99='mpicc -std=c99' qcc -Wall -O2 -D_MPI=1 -disable-dimensions \
  -I$(PWD)/src-local simulationCases/hypha.c -o hyphaMPI -lm

2. Run locally

./hypha

or with MPI:

mpirun -np 8 ./hyphaMPI

3. Run a cluster sweep

The Hamilton job script performs an Ec_h sweep defined in the selected sweep config file and writes results to simulationCases/<CaseNo>/.

sbatch runSweepHamilton.sbatch

By default it reads sweep.params. You can pass a different sweep file:

sbatch runSweepHamilton.sbatch my-sweep.params

For the serial executable workflow (compile without MPI, launch all cases in parallel), use:

sbatch runSweepHamilton-serial-128.sbatch
sbatch runSweepHamilton-serial-128.sbatch my-sweep-128.params

Parameter Files

• default.params: base parameter values used by the sweep script.
• sweep.params: default sweep input for runSweepHamilton.sbatch (contains CASE_START, optional CASE_END, and SWEEP_Ec_h=... list).
• sweep-128.params: default sweep input for runSweepHamilton-serial-128.sbatch (128 Ec_h values, CASE_START=1506).

Post-Processing

postProcess/ contains extraction and plotting utilities. Typical usage is to run plotting scripts from inside a case directory containing log and/or hypha-def-log, for example:

python3 ../postProcess/plot_vcm_vs_time.py
python3 ../postProcess/plot_hypha_width_vs_time.py

For multi-case analysis (after collecting logs into one directory):

python3 postProcess/plot_vcm_vs_Ec_H.py --log_dir path/to/logs --pattern "log*"

Notes

• simulationCases/hypha.c reads Ec_h from a parameter interface (param_double(...)), so runtime parameter handling must be available in the configured Basilisk toolchain.
• Generated binaries, logs, restart files, local Basilisk checkouts, and .comphy-basilisk/ are intentionally not committed.

License

GPL-3.0. See LICENSE.