Docs Update: Tutorials Folder and Running on ReadTheDocs

.gitignore

@@ -62,7 +62,6 @@ temp_print_trace.*
 *.plugin
 *.outp
 *.patch
-*.txt
 *.bib.bak
 *.out
 *.vtk

README.md

@@ -26,14 +26,16 @@ After installing MOOSE, make sure you have the following folder on your local ma
 
 `git submodule update --init moose`
 
+`mamba activate moose` 
+
 `make -jn` 
 
 where `n` is the number of logical processors on your computer. 
 
 **Step 3.**
 Run tests to make sure CRANE is installed properly. 
 
-`./run_tests`
+`./run_tests -jn`
 
 If all the tests pass, CRANE has been successfully installed. 
 

docs/source/running.rst

@@ -1,3 +1,38 @@
 Running
 =======
 
+Running a CRANE input file follows the syntax
+
+.. code-block:: bash
+
+    <path-from-intput-to-crane-opt> -i <input-file>
+
+while in the MOOSE environment. 
+The file ``crane-opt`` is generated upon successful compilation of CRANE, 
+and is located alongside the MAKEFILE. 
+For example, to want to run ``argon_test.i`` located in ``crane/problems/argon_microdischarge``,
+you would enter the following command while in ``argon_microdischarge`` directory:
+
+.. code-block:: bash
+
+    ../../crane-opt -i argon_test.i
+
+Each set of ``../`` denotes a step up through the directories. 
+Since ``argon_microdischarge`` is within ``problems``, which is within ``crane``,
+we need two sets of ``../`` to be in the directory in which ``crane-opt`` is located.
+
+To run an input file on multiple processors, 
+one would add the following command before the path to `crane-opt``:
+
+.. code-block:: bash
+
+    mpiexec -np n <path-from-intput-to-crane-opt> -i <input-file>
+
+where ``n`` is the number of processors you wish to use. For the ``argon_microdischarge`` example,
+you might run
+
+.. code-block:: bash
+
+    mpiexec -np 4 ../../crane-opt -i argon_test.i
+
+to run the input file using four cores.

tutorials/ArgonMicrodischarge/argon_density_plot.py

@@ -0,0 +1,28 @@
+#* This file is part of Crane, an open-source
+#* application for plasma chemistry and thermochemistry
+#* https://github.com/lcpp-org/crane
+#*
+#* Crane is powered by the MOOSE Framework
+#* https://www.mooseframework.org
+#*
+#* Licensed under LGPL 2.1, please see LICENSE for details
+#* https://www.gnu.org/licenses/lgpl-2.1.html
+
+import numpy as np
+import matplotlib.pyplot as plt
+import pandas as pd
+
+filename = 'argon_test_out.csv'
+data = pd.read_csv(filename)
+
+fig, ax = plt.subplots()
+ax.loglog(data['time'], data['e'], 'k', label='e')
+ax.loglog(data['time'], data['Ar+'], 'g', label='Ar$^+$')
+ax.loglog(data['time'], data['Ar2+'], 'r', label='Ar$_2^+$')
+ax.loglog(data['time'], data['Ar*'], 'c', label='Ar$^*$')
+ax.set_xlabel('Time (s)', fontsize=20)
+ax.set_ylabel('Density (cm$^{-3}$)', fontsize=20)
+ax.tick_params(axis='both', labelsize=15)
+ax.legend(fontsize=15)
+fig.savefig('argon_species.png', bbox_inches='tight')
+plt.show()

tutorials/ArgonMicrodischarge/argon_test.i

@@ -0,0 +1,211 @@
+[Mesh]
+  type = GeneratedMesh
+  dim = 1
+  xmin = 0
+  xmax = 1
+  nx = 1
+[]
+
+[Variables]
+  # ODE variables
+  [./e]
+    family = SCALAR
+    order = FIRST
+    initial_condition = 1e6
+    # scaling = 1e-2
+  [../]
+
+  [./Ar+]
+    family = SCALAR
+    order = FIRST
+    initial_condition = 1e6
+    # scaling = 1e-2
+  [../]
+
+  [./Ar]
+    family = SCALAR
+    order = FIRST
+    initial_condition = 3.21883e18
+    #scaling = 1e-15
+  [../]
+
+  [./Ar*]
+    family = SCALAR
+    order = FIRST
+    initial_condition = 1e6
+    # scaling = 1e-2
+  [../]
+
+  [./Ar2+]
+    family = SCALAR
+    order = FIRST
+    initial_condition = 1
+    # scaling = 1e-2
+  [../]
+[]
+
+[ScalarKernels]
+  [./de_dt]
+    type = ODETimeDerivative
+    variable = e
+  [../]
+
+  [./dAr+_dt]
+    type = ODETimeDerivative
+    variable = Ar+
+  [../]
+
+  [./dAr_dt]
+    type = ODETimeDerivative
+    variable = Ar
+  [../]
+
+  [./dAr*_dt]
+    type = ODETimeDerivative
+    variable = Ar*
+  [../]
+
+  [./dAr2_dt]
+    type = ODETimeDerivative
+    variable = Ar2+
+  [../]
+[]
+
+[GlobalReactions]
+  [argon]
+    species = 'e Ar* Ar+ Ar Ar2+'
+    file_location = 'data'
+
+    # These are parameters required equation-based rate coefficients
+    equation_constants = 'Tgas J pi'
+    equation_values = '300 2.405 3.141'
+    equation_variables = 'Te'
+    sampling_variable = 'reduced_field'
+
+
+    reactions = 'e + Ar -> e + e + Ar+          : EEDF (Ar_ionization)
+                 e + Ar -> Ar* + e              : EEDF (Ar_excitation)
+                 e + Ar* -> Ar + e              : EEDF (Ar*_deexcitation)
+                 e + Ar* -> Ar+ + e + e         : EEDF (Ar*_ionization)
+                 Ar2+ + e -> Ar* + Ar           : {8.5e-7*((Te/1.5)*11600/300.0)^(-0.67)}
+                 Ar2+ + Ar -> Ar+ + Ar + Ar     : {(6.06e-6/Tgas)*exp(-15130.0/Tgas)}
+                 Ar* + Ar* -> Ar2+ + e          : 6.0e-10
+                 Ar+ + e + e -> Ar + e          : {8.75e-27*((Te/1.5)^(-4.5))}
+                 Ar* + Ar + Ar -> Ar + Ar + Ar  : 1.399e-32
+                 Ar+ + Ar + Ar -> Ar2+ + Ar     : {2.25e-31*(Tgas/300.0)^(-0.4)}
+                 e -> W                         : {1.52*(760/100)*(Tgas/273.16)*(Te/1.5)*((J/0.4)^2 + (pi/0.4)^2)}
+                 Ar+ -> W                       : {1.52*(760/100)*(Tgas/273.16)*(Te/1.5)*((J/0.4)^2 + (pi/0.4)^2)}
+                 Ar2+ -> W                      : {1.52*(760/100)*(Tgas/273.16)*(Te/1.5)*((J/0.4)^2 + (pi/0.4)^2)}'
+  []
+[]
+
+[AuxVariables]
+  [./reduced_field]
+    order = FIRST
+    family = SCALAR
+    initial_condition = 7.7667949e-20
+  [../]
+
+  [./mobility]
+    order = FIRST
+    family = SCALAR
+  [../]
+
+  [./Te]
+    order = FIRST
+    family = SCALAR
+  [../]
+
+  [./current]
+    order = FIRST
+    family = SCALAR
+  [../]
+[]
+
+[AuxScalarKernels]
+  [reduced_field_calculate]
+    type = ParsedAuxScalar
+    variable = reduced_field
+    constant_names = 'V d qe R'
+    constant_expressions = '1000 0.004 1.602e-19 1e5'
+    args = 'reduced_field Ar current'
+    function = 'V/(d+R*current/(reduced_field*Ar*1e6))/(Ar*1e6)'
+    execute_on = 'TIMESTEP_END'
+  []
+
+  [e_drift]
+    type = ParsedAuxScalar
+    variable = current
+    constant_names = 'r pi'
+    constant_expressions = '0.004 3.1415926'
+    args = 'reduced_field mobility Ar e'
+    function = '(reduced_field * mobility * Ar*1e6) * 1.6e-19 * pi*(r^2.0) * (e*1e6)'
+    execute_on = 'TIMESTEP_BEGIN'
+  []
+
+  [mobility_calculation]
+    type = ScalarLinearInterpolation
+    variable = mobility
+    sampler = reduced_field
+    property_file = 'data/electron_mobility.txt'
+    execute_on = 'INITIAL TIMESTEP_BEGIN'
+  []
+
+  [temperature_calculation]
+    type = ScalarLinearInterpolation
+    variable = Te
+    sampler = reduced_field
+    property_file = 'data/electron_temperature.txt'
+    execute_on = 'INITIAL TIMESTEP_BEGIN'
+  []
+[]
+
+[Debug]
+  show_var_residual_norms = true
+[]
+
+#[UserObjects]
+#  active = 'value_provider'
+#
+  #[./value_provider]
+  #  type = ValueProvider
+  #  property_file = 'data/electron_temperature.txt'
+  #[../]
+#[]
+
+[Executioner]
+  type = Transient
+  end_time = 1e-3
+  solve_type = linear
+  dtmin = 1e-16
+  dtmax = 1e-6
+  line_search = none
+  steady_state_detection = true
+  [./TimeStepper]
+    type = IterationAdaptiveDT
+    cutback_factor = 0.9
+    dt = 1e-10
+    growth_factor = 1.01
+  [../]
+  #[TimeIntegrator]
+  #  type = LStableDirk2
+  #[]
+[]
+
+[Preconditioning]
+  [./smp]
+    type = SMP
+    full = true
+    #ksp_norm = none
+  [../]
+[]
+
+[Outputs]
+  [out]
+    type = CSV
+  []
+  [console]
+    type = Console
+    execute_scalars_on = 'none'
+  []
+[]