diff --git a/exec/reactDiff/test_Schlogl_2d/clean.sh b/exec/reactDiff/test_Schlogl_2d/clean.sh new file mode 100755 index 00000000..d5c9d18e --- /dev/null +++ b/exec/reactDiff/test_Schlogl_2d/clean.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +rm -rf slurm-*.out plt* averagedDensity.txt diff --git a/exec/reactDiff/test_Schlogl_2d/inputs_Schlogl_2d b/exec/reactDiff/test_Schlogl_2d/inputs_Schlogl_2d new file mode 100644 index 00000000..c54794ec --- /dev/null +++ b/exec/reactDiff/test_Schlogl_2d/inputs_Schlogl_2d @@ -0,0 +1,101 @@ +# Problem specification +prob_lo = 0.0 0.0 # physical lo coordinate +prob_hi = 32.0 32.0 # physical hi coordinate + +# number of cells in domain and maximum number of cells in a box +n_cells = 64 64 +max_grid_size = 16 16 + +# to compute cell volume in 2D problems +cell_depth = 1. + +# Time-step control +fixed_dt = 0.001 + +# Controls for number of steps between actions +max_step = 1000000 +plot_int = 100000 +struct_fact_int = 1 +n_steps_skip = 100000 + +seed = 0 + +nspecies = 1 +nreaction = 4 + +prob_type = 0 + +n_init_in_1 = 1000. + +integer_populations = 1 + +# 0=D+R (first-order splitting) +# 1=(1/2)R + D + (1/2)R (Strang option 1) +# 2=(1/2)D + R + (1/2)D (Strang option 2) +# -1=unsplit forward Euler +# -2=unsplit explicit midpoint +# -3=unsplit multinomial diffusion +# -4=unsplit implicit midpoint +temporal_integrator = 1 + +# only used for split schemes (temporal_integrator>=0) +# 0=explicit trapezoidal predictor/corrector +# 1=Crank-Nicolson semi-implicit +# 2=explicit midpoint +# 3=multinomial diffusion +# 4=forward Euler +reactDiff_diffusion_type = 0 + +# Fickian diffusion coeffs +D_Fick = 1. + +variance_coef_mass = 1. +initial_variance_mass = 1. + +# how to compute n on faces for stochastic weighting +# 1=arithmetic (with C0-Heaviside), 2=geometric, 3=harmonic +# 10=arithmetic average with discontinuous Heaviside function +# 11=arithmetic average with C1-smoothed Heaviside function +# 12=arithmetic average with C2-smoothed Heaviside function +avg_type = 1 + +# only used for split schemes (temporal_integrator>=0) +# 0=first-order (deterministic, tau leaping, CLE, or SSA) +# 1=second-order (determinisitc, tau leaping, or CLE only) +reactDiff_reaction_type = 0 + +# 0=deterministic; 1=CLE; 2=SSA; 3=tau leap +reaction_type = 2 + +# Schlog model is: +# (1) 2X --> 3X +# (2) 3X --> 2X +# (3) 0 --> X +# (4) X --> 0 +stoich_1R = 2 +stoich_1P = 3 +stoich_2R = 3 +stoich_2P = 2 +stoich_3R = 0 +stoich_3P = 1 +stoich_4R = 1 +stoich_4P = 0 + +# reaction rate constant for each reaction (assuming Law of Mass Action holds) +# using rate_multiplier, reaction rates can be changed by the same factor +# if include_discrete_LMA_correction, n^2 and n^3 in rate expressions become +# n*(n-1/dv) and n*(n-1/dv)*(n-2/dv). +#rate_const = 1e-4 1e-7 200. 0.2 # thermodynamic equilibrium +rate_const = 1e-4 2e-7 200. 0.1 # case where detailed balance is not satisfied + +rate_multiplier = 1. +include_discrete_LMA_correction = 1 + +# Boundary conditions +# ---------------------- +# BC specifications: +# -1 = periodic +# 1 = wall (Neumann) +# 2 = reservoir (Dirichlet) +bc_mass_lo = -1 -1 +bc_mass_hi = -1 -1 diff --git a/exec/reactDiff/test_Schlogl_2d/job_script.sh b/exec/reactDiff/test_Schlogl_2d/job_script.sh new file mode 100644 index 00000000..86337152 --- /dev/null +++ b/exec/reactDiff/test_Schlogl_2d/job_script.sh @@ -0,0 +1,9 @@ +#! /bin/bash -l +#SBATCH --nodes=1 +#SBATCH --ntasks-per-node=16 +#SBATCH --partition test +#SBATCH --time=0-00:30:00 + +# COMMANDS HERE + +srun -n 16 ../main2d.gnu.MPI.ex inputs_Schlogl_2d diff --git a/exec/reactDiff/test_Schlogl_2d/submit_job.sh b/exec/reactDiff/test_Schlogl_2d/submit_job.sh new file mode 100755 index 00000000..66c0ac81 --- /dev/null +++ b/exec/reactDiff/test_Schlogl_2d/submit_job.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +# LOAD NECESSARY MODULES + +sbatch job_script.sh