diff --git a/.gitignore b/.gitignore index 73fa666..09f355a 100644 --- a/.gitignore +++ b/.gitignore @@ -62,7 +62,6 @@ temp_print_trace.* *.plugin *.outp *.patch -*.txt *.bib.bak *.out *.vtk diff --git a/README.md b/README.md index feec712..08d265f 100644 --- a/README.md +++ b/README.md @@ -26,6 +26,8 @@ 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. @@ -33,7 +35,7 @@ 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. diff --git a/docs/source/running.rst b/docs/source/running.rst index 0403c3e..21d718e 100644 --- a/docs/source/running.rst +++ b/docs/source/running.rst @@ -1,3 +1,38 @@ Running ======= +Running a CRANE input file follows the syntax + +.. code-block:: bash + + -i + +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 -i + +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. \ No newline at end of file diff --git a/tutorials/ArgonMicrodischarge/argon_density_plot.py b/tutorials/ArgonMicrodischarge/argon_density_plot.py new file mode 100644 index 0000000..fe8bbe9 --- /dev/null +++ b/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() diff --git a/tutorials/ArgonMicrodischarge/argon_test.i b/tutorials/ArgonMicrodischarge/argon_test.i new file mode 100644 index 0000000..d7a8f84 --- /dev/null +++ b/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' + [] +[] diff --git a/tutorials/ArgonMicrodischarge/data/Ar*_deexcitation.txt b/tutorials/ArgonMicrodischarge/data/Ar*_deexcitation.txt new file mode 100644 index 0000000..61cd4fb --- /dev/null +++ b/tutorials/ArgonMicrodischarge/data/Ar*_deexcitation.txt @@ -0,0 +1,300 @@ 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b/tutorials/ArgonMicrodischarge/data/Ar*_ionization.txt new file mode 100644 index 0000000..83249a7 --- /dev/null +++ b/tutorials/ArgonMicrodischarge/data/Ar*_ionization.txt @@ -0,0 +1,300 @@ +1.0000e-22 0.0000e+00 +4.3410e-22 1.6910e-15 +7.6820e-22 3.1410e-12 +1.1020e-21 3.8990e-11 +1.4360e-21 1.3910e-10 +1.7710e-21 3.0820e-10 +2.1050e-21 5.2760e-10 +2.4390e-21 7.8600e-10 +2.7730e-21 1.0720e-09 +3.1070e-21 1.3740e-09 +3.4410e-21 1.6780e-09 +3.7750e-21 1.9660e-09 +4.1090e-21 2.2260e-09 +4.4430e-21 2.4510e-09 +4.7780e-21 2.6410e-09 +5.1120e-21 2.7990e-09 +5.4460e-21 2.9310e-09 +5.7800e-21 3.0420e-09 +6.1140e-21 3.1350e-09 +6.4480e-21 3.2150e-09 +6.7820e-21 3.2840e-09 +7.1160e-21 3.3450e-09 +7.4510e-21 3.4000e-09 +7.7850e-21 3.4490e-09 +8.1190e-21 3.4940e-09 +8.4530e-21 3.5350e-09 +8.7870e-21 3.5740e-09 +9.1210e-21 3.6100e-09 +9.4550e-21 3.6450e-09 +9.7890e-21 3.6770e-09 +1.0120e-20 3.7090e-09 +1.0460e-20 3.7390e-09 +1.0790e-20 3.7680e-09 +1.1130e-20 3.7960e-09 +1.1460e-20 3.8240e-09 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-0,0 +1,31 @@ +#* 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['rate_constant0'], 'k', label='Ionization') +ax.loglog(data['time'], data['rate_constant1'], 'g', label='Excitation') +ax.loglog(data['time'], data['rate_constant2'], 'r', label='De-excitation') +ax.loglog(data['time'], data['rate_constant3'], 'c', label='Stepwise Ionization') +print(min(data['rate_constant2'])) + +ax.set_xlabel('Time (s)', fontsize=20) +ax.set_ylabel('Rate Coefficients (cm$^3$ s$^{-1}$)', fontsize=20) +ax.tick_params(axis='both', labelsize=15) +ax.legend(fontsize=15) +fig.savefig('eedf_rate_coefficients.png', bbox_inches='tight') +plt.show() diff --git a/tutorials/ArgonMicrodischarge/reduced_field_plot.py b/tutorials/ArgonMicrodischarge/reduced_field_plot.py new file mode 100644 index 0000000..e7b8df6 --- /dev/null +++ b/tutorials/ArgonMicrodischarge/reduced_field_plot.py @@ -0,0 +1,27 @@ +#* 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.semilogx(data['time'], data['reduced_field'], 'k', label='E/N', linewidth=4) + +ax.set_xlabel('Time (s)', fontsize=20) +ax.set_ylabel('Reduced Field, E/N (V m$^{-2}$)', fontsize=20) +ax.tick_params(axis='both', labelsize=15) +ax.legend(fontsize=15) +fig.savefig('reduced_field.png', bbox_inches='tight') +plt.show() diff --git a/tutorials/TwoReactionArgon/Example1/reaction_e + Ar -> e + e + Ar+.txt b/tutorials/TwoReactionArgon/Example1/reaction_e + Ar -> e + e + Ar+.txt new file mode 100644 index 0000000..db41970 --- /dev/null +++ b/tutorials/TwoReactionArgon/Example1/reaction_e + Ar -> e + e + Ar+.txt @@ -0,0 +1,300 @@ +1.0000e-22 0.0000e+00 +4.3410e-22 0.0000e+00 +7.6820e-22 0.0000e+00 +1.1020e-21 0.0000e+00 +1.4360e-21 0.0000e+00 +1.7710e-21 0.0000e+00 +2.1050e-21 0.0000e+00 +2.4390e-21 0.0000e+00 +2.7730e-21 0.0000e+00 +3.1070e-21 0.0000e+00 +3.4410e-21 0.0000e+00 +3.7750e-21 0.0000e+00 +4.1090e-21 0.0000e+00 +4.4430e-21 0.0000e+00 +4.7780e-21 0.0000e+00 +5.1120e-21 2.4770e-23 +5.4460e-21 1.4310e-22 +5.7800e-21 6.6440e-22 +6.1140e-21 2.5810e-21 +6.4480e-21 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= 2.5e-19 + [../] +[] + +[ScalarKernels] + [./de_dt] + type = ODETimeDerivative + variable = e + [../] + + [./dAr+_dt] + type = ODETimeDerivative + variable = Ar+ + [../] + + [./dAr_dt] + type = ODETimeDerivative + variable = Ar + [../] +[] + +[ChemicalReactions] + [./ScalarNetwork] + species = 'e Ar+ Ar' + file_location = 'Example1' + interpolation_type = 'spline' + reactions = 'e + Ar -> e + e + Ar+ : EEDF + e + Ar+ + Ar -> Ar + Ar : 1e-25' + + [../] +[] + +[AuxVariables] + [./reduced_field] + order = FIRST + family = SCALAR + initial_condition = 51e-21 + [../] +[] + +[Executioner] + type = Transient + end_time = 0.25e-6 + dt = 1e-10 + solve_type = 'newton' + dtmin = 1e-20 + dtmax = 1e-8 + petsc_options_iname = '-snes_linesearch_type' + petsc_options_value = 'basic' +[] + +[Preconditioning] + active = 'smp' + + [./smp] + type = SMP + full = true + [../] + + [./fd] + type = FDP + full = true + [../] +[] + +[Outputs] + [./out] + type = Exodus + execute_on = 'TIMESTEP_END' + [../] +[]