From 8bdab7224ab7b5aa5affe76618859fbab70b110a Mon Sep 17 00:00:00 2001
From: Matteo Polimeno <mpolimeno@rclogin01.cluster>
Date: Tue, 7 Nov 2023 11:23:27 -0800
Subject: [PATCH] updated input files for non equilibrium case for NO2
 dimerization

---
 .../inputs_NO2_dimerization_neq               | 133 ++++++++++++++++++
 1 file changed, 133 insertions(+)
 create mode 100644 exec/compressible_stag/test_NO2_dimerization_neq_kinetic_params/inputs_NO2_dimerization_neq

diff --git a/exec/compressible_stag/test_NO2_dimerization_neq_kinetic_params/inputs_NO2_dimerization_neq b/exec/compressible_stag/test_NO2_dimerization_neq_kinetic_params/inputs_NO2_dimerization_neq
new file mode 100644
index 00000000..3e5194d6
--- /dev/null
+++ b/exec/compressible_stag/test_NO2_dimerization_neq_kinetic_params/inputs_NO2_dimerization_neq
@@ -0,0 +1,133 @@
+# random number seed
+# 0 = unpredictable seed based on clock
+# positive = fixed seed
+seed = 0
+
+# Problem specification
+prob_lo = 0.0 0.0 0.0 # physical lo coordinate
+prob_hi = 1.28e-04 1.28e-04 1.28e-04 # physical hi coordinate
+
+# Number of ghost cells, conserved, and primitive variables
+# ---------------------
+ngc = 2 2 2
+nvars = 7
+nprimvars = 10
+
+# number of cells in domain
+n_cells = 16 16 16 
+# max number of cells in a box
+max_grid_size = 4 4 8 
+
+# Time-step control
+fixed_dt = 1.e-12
+
+# Controls for number of steps between actions
+# First run (equilibration) set max_step = 10000, set nreaction = 0 (no reaction)
+# Second run set max_step = 100000, set nreaction = 2 (see below)
+#max_step = 10000 # Comment (uncomment) this if restart = 100000 (-1)
+max_step = 100000  # Comment (uncomment) this if restart = -1 (100000)
+plot_int = 1000
+chk_int  = 10000
+#restart  = -1    # Comment (uncomment) this if max_step = 100000 (10000)
+restart = 10000   # Comment (uncomment) this if max_step = 10000 (100000)
+
+# Multispecies toggle
+# if algorithm_type = 1, single component
+# if algorithm_type = 2, multispecies
+algorithm_type = 2
+
+# Viscous tensor form
+# if visc_type = 1, L = not-symmetric (bulk viscosity = 0)
+# if visc_type = 2, L = symmetric (bulk viscosity = 0)
+# if visc_type = 3, L = symmetric + bulk viscosity
+visc_type = 2
+
+# Advection method
+# if advection_type = 1, interpolate primitive quantities
+# if advection_type = 2, interpolate conserved quantities
+advection_type = 2
+
+# Problem specification
+# if prob_type = 1, constant species concentration
+# if prob_type = 2, Rayleigh-Taylor instability
+# if prob_type = 3, diffusion barrier
+prob_type = 1
+
+# Initial parameters
+k_B = 1.38064852e-16	# [units: cm2*g*s-2*K-1]
+Runiv = 8.314462175e7
+T_init = 380.153 
+rho0 = 1.855335e-03 
+
+struct_fact_int = 0 
+n_steps_skip = 100000
+
+# Boundary conditions:
+# NOTE: setting bc_vel to periodic sets all the other bc's to periodic)
+# bc_vel:   -1 = periodic
+#            1 = slip
+#            2 = no-slip
+# bc_mass:  -1 = periodic
+#            1 = wall
+#            2 = concentration (set bc_Yk or bc_Xk in compressible namelist)
+#            3 = reservoir (set bc_Yk or bc_Xk in compressible namelist)
+# bc_therm: -1 = periodic
+#            1 = adiabatic
+#            2 = isothermal (set with t_lo/hi in common namelist)
+bc_vel_lo   = -1 -1 -1
+bc_vel_hi   = -1 -1 -1
+bc_mass_lo  = -1 -1 -1
+bc_mass_hi  = -1 -1 -1
+bc_therm_lo = -1 -1 -1
+bc_therm_hi = -1 -1 -1
+
+# Temperature if thermal BC specified
+t_hi = 350 350 350 
+t_lo = 350 350 350 
+
+#Kinetic species info
+#--------------
+nspecies = 2
+
+molmass = 46.0055 92.0110 
+diameter = 3.765e-08 4.621e-08 
+rhobar = 0.690422 0.309578 
+
+# Enter negative dof to use hcv & hcp values
+dof = 7.279582 18.049065
+hcv = -1 -1
+hcp = -1 -1
+e0 = 4.684542e+09 -1.730892e+09
+
+plot_means = 1
+plot_vars = 1
+
+# dimerization reaction
+# react1 : 2A -> A_2
+# react2 : A_2 -> 2A
+# spec1 = A
+# spec2 = A_2
+
+#nreaction = 0 # Comment (uncomment) this if max_step = 100000 (10000)
+nreaction = 2  # Comment (uncomment) this if max_step = 10000 (100000)
+
+T0_chem = 350
+
+rate_const = 2.929463e+26 1.307730e+27
+
+# These are the kinetic parameters for the expression of the rate constants
+#alpha_param = 0 0 # k(T) = k(T0)
+#beta_param  = 0 0 # k(T) = k(T0)
+alpha_param = -8.863943e-14 8.917095e-13 # Temperature Correction
+beta_param  = -1.355050 -2.100000        # Temperature Correction
+
+stoich_1R = 2 0
+stoich_1P = 0 1
+stoich_2R = 0 1
+stoich_2P = 2 0
+
+# 0 = Deterministic Chemistry
+# 1 = CLE (Chemical Langevin Equation)
+# 2 = SSA (Stochastic Simulation Algorithm)
+
+reaction_type = 1