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A bit of cleaning house #34

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merged 7 commits into from
Jun 3, 2019
Merged

A bit of cleaning house #34

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a18865a
Move 2D syntax checks from problems directory to tests
cticenhour May 31, 2019
f7a5574
Add geo files to 2D and TM tests
cticenhour May 31, 2019
47b6292
Removing old Notre Dame cluster build script and git diff
cticenhour May 31, 2019
a203098
Remove old build script
cticenhour May 31, 2019
52372d1
Move chemical reactions notes to doc folder and update README to refl…
cticenhour May 31, 2019
84ec316
Add missing material properties file
cticenhour May 31, 2019
40eacd3
Update submodule commands in README to include crane
cticenhour May 31, 2019
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12 changes: 6 additions & 6 deletions README.md
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Expand Up @@ -6,10 +6,10 @@ Zapdos
Free (in all senses of the word) and open source software for modelling atmospheric plasmas using finite elements.
This application is built on top of the MOOSE framework, which can be found at [http://mooseframework.org](http://mooseframework.org)

The best documentation so far for this project is in
[this thesis chapter.](http://169.229.198.106/ZapdosChapter.pdf) Some notes on
The best documentation so far for this project is in Chapter 3 of the thesis located at
`doc/Lindsay_thesis_coupling_of_plasmas_and_liquids.pdf`. Some notes on
understanding existing chemistry kernels and/or implementing new ones in
Zapdos/MOOSE are given in Chemical_Reactions.ipynb.
Zapdos/MOOSE are given in `doc/Chemical_Reactions.ipynb`.

**Instructions for installing Zapdos:**

Expand All @@ -22,8 +22,8 @@ Zapdos/MOOSE are given in Chemical_Reactions.ipynb.
<ul>
<li><code>git clone https://github.com/shannon-lab/zapdos</code></li>
<li><code>cd zapdos</code></li>
<li><code>git submodule init squirrel</code></li>
<li><code>git submodule update squirrel</code></li>
<li><code>git submodule init squirrel crane</code></li>
<li><code>git submodule update squirrel crane</code></li>
<li><code>make -jn</code> where "n" is the number of logical processors on
your computer</li>
</ul>
Expand All @@ -44,7 +44,7 @@ Zapdos/MOOSE are given in Chemical_Reactions.ipynb.
<li><code>make -jn</code></li>
</ul>
then continue to Step 4.</li>
<li>To make sure the installation is working correctly, execute <code>run_tests -jn</code>, substituting 'n' with your number of processors. All tests should pass with 'OK'
<li>To make sure the installation is working correctly, execute <code>./run_tests -jn</code>, substituting 'n' with your number of processors. All tests should pass with 'OK'
<li>If everything checks out, you should now be able to run input files using the <code>zapdos-opt</code> executable in the <code>~/projects/zapdos</code> directory. Input files demonstrating the capabilities of zapdos can be found in the sub-directories of <code>~/projects/zapdos/tests</code>. If you want to start modifying an input file, a good one to choose is <code>mean_en.i</code> in <code>~/projects/zapdos/problems</code>. I typically run an input file like <code>mean_en.i</code> using the following command:</li>
<ul>
<li><code>cd ~/projects/zapdos/problems; ../zapdos-opt -i mean_en.i --color off 2>&1 | tee log.txt</code></li>
Expand Down
8 changes: 0 additions & 8 deletions build_libmesh_and_zapdos.sh
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27 changes: 0 additions & 27 deletions compile.bash
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0 Chemical_Reactions.ipynb → doc/Chemical_Reactions.ipynb
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193 changes: 0 additions & 193 deletions gitdiff.txt
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71 changes: 71 additions & 0 deletions tests/2d_syntax/2d.geo
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@@ -0,0 +1,71 @@
dom0Mult = 1e3;

lc = .1 * 1e-3 * dom0Mult;
dc = 1; // Stands for don't care

// Needle tip
Point(5) = {0, 1e-3 * dom0Mult, 0, .005 * lc};

// Center of radius of curvature
Point(6) = {0, dom0Mult * (1e-3 + 30e-6), 0, dc};

// Point of needle at small radius
Point(7) = {30e-6 * dom0Mult, dom0Mult * (1e-3 + 30e-6), 0, .05 * lc};

// Point of needle at large radius (pesudo-bottom left of domain)
Point(8) = {dom0Mult * 180e-6, dom0Mult * 1.5e-3, 0, .5 * lc};

// Needle tip edge
Circle(1) = {5, 6, 7};

// Long needle edge
Line(2) = {7, 8};

// Top right of domain
Point(9) = {1e-3 * dom0Mult, 1.5e-3 * dom0Mult, 0, lc};

// Center of ground plane (bottom left of domain)
Point(10) = {0, 0, 0, lc};

// Outer bound of ground plane (top right of domain)
Point(11) = {1e-3 * dom0Mult, 0, 0, lc};

// Axis of symmetry
Line(3) = {5, 10};

// Anode
Line(4) = {10, 11};

// Wall 1
Line(5) = {11, 9};

// Wall 2
Line(6) = {9, 8};
Line Loop(7) = {5, 6, -2, -1, 3, 4};
Plane Surface(8) = {7};

// Plasma domain
Physical Surface("plasma") = {8};

// Physical Cathode
Physical Line("needle") = {2, 1};

// Physical Anode
Physical Line("dish") = {4};

// Physical Walls
Physical Line("walls") = {5, 6};

// Physical axis of symmetry
Physical Line("axis") = {3};

// Field[1] = BoundaryLayer;
// Field[1].EdgesList = {3};
// Field[1].hfar = .1;
// Field[1].hwall_n = .01;
// Field[1].hwall_t = .05;
// Field[1].thickness = .2;

// Field[2] = Min;
// Field[2].FieldsList = {1};
// Background Field = 2;
0 problems/2d.i → tests/2d_syntax/2d.i
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0 problems/2d.msh → tests/2d_syntax/2d.msh
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0 problems/2d_jac_test.i → tests/2d_syntax/2d_jac_test.i
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0 problems/2d_temp.i → tests/2d_syntax/2d_temp.i
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50 changes: 50 additions & 0 deletions tests/2d_syntax/td_argon_mean_en.txt
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0.000E+00 0.00000E+00 0.00000E+00 8.55793E+07 6.51633E-01 1.03878E+00
7.810E-01 0.00000E+00 0.00000E+00 8.55793E+07 6.51633E-01 1.03878E+00
8.732E-01 0.00000E+00 0.00000E+00 9.70712E+07 5.49353E-01 9.56873E-01
9.776E-01 0.00000E+00 0.00000E+00 1.09990E+08 4.62655E-01 8.81762E-01
1.095E+00 0.00000E+00 0.00000E+00 1.24513E+08 3.88982E-01 8.13442E-01
1.228E+00 0.00000E+00 0.00000E+00 1.40808E+08 3.26775E-01 7.51115E-01
1.376E+00 0.00000E+00 0.00000E+00 1.59158E+08 2.74357E-01 6.94382E-01
1.543E+00 0.00000E+00 0.00000E+00 1.79804E+08 2.30249E-01 6.43243E-01
1.730E+00 0.00000E+00 0.00000E+00 2.03143E+08 1.93053E-01 5.96098E-01
1.939E+00 0.00000E+00 0.00000E+00 2.29502E+08 1.61690E-01 5.53748E-01
2.169E+00 0.00000E+00 0.00000E+00 2.59539E+08 1.35121E-01 5.14994E-01
2.420E+00 0.00000E+00 0.00000E+00 2.94174E+08 1.12627E-01 4.79435E-01
2.696E+00 0.00000E+00 1.08196E-09 3.33627E+08 9.38095E-02 4.47473E-01
3.000E+00 0.00000E+00 3.58346E-08 3.78935E+08 7.81080E-02 4.16709E-01
3.337E+00 0.00000E+00 6.50619E-04 4.30074E+08 6.51233E-02 3.88782E-01
3.714E+00 0.00000E+00 5.01721E-01 4.88219E+08 5.43760E-02 3.62373E-01
4.137E+00 0.00000E+00 3.84772E+01 5.51169E+08 4.55863E-02 3.37922E-01
4.577E+00 0.00000E+00 5.76101E+02 5.94456E+08 3.94535E-02 3.17186E-01
4.928E+00 3.58790E-07 2.78116E+03 5.66928E+08 3.68726E-02 3.04362E-01
5.146E+00 1.74816E-04 6.82485E+03 4.82292E+08 3.67407E-02 2.99048E-01
5.280E+00 9.31602E-03 1.19806E+04 3.92465E+08 3.71762E-02 2.96930E-01
5.384E+00 2.05834E-01 1.79840E+04 3.18110E+08 3.73400E-02 2.95332E-01
5.484E+00 2.40146E+00 2.49744E+04 2.59722E+08 3.70923E-02 2.93414E-01
5.589E+00 1.73206E+01 3.32924E+04 2.13860E+08 3.65290E-02 2.91097E-01
5.705E+00 8.64399E+01 4.32086E+04 1.77132E+08 3.57579E-02 2.88181E-01
5.833E+00 3.24530E+02 5.50335E+04 1.47477E+08 3.48829E-02 2.85144E-01
5.972E+00 9.75954E+02 6.89572E+04 1.22926E+08 3.39760E-02 2.81868E-01
6.124E+00 2.46100E+03 8.50822E+04 1.02581E+08 3.30890E-02 2.78352E-01
6.290E+00 5.39539E+03 1.03287E+05 8.55780E+07 3.22460E-02 2.74716E-01
6.473E+00 1.05738E+04 1.23353E+05 7.13025E+07 3.14550E-02 2.70681E-01
6.679E+00 1.89518E+04 1.45188E+05 5.94010E+07 3.06998E-02 2.65967E-01
6.913E+00 3.16014E+04 1.68669E+05 4.94896E+07 2.99687E-02 2.60493E-01
7.185E+00 4.98398E+04 1.93947E+05 4.12864E+07 2.92416E-02 2.54580E-01
7.510E+00 7.50618E+04 2.20932E+05 3.44462E+07 2.85264E-02 2.48467E-01
7.906E+00 1.08938E+05 2.49840E+05 2.87712E+07 2.78073E-02 2.42794E-01
8.402E+00 1.53369E+05 2.80642E+05 2.40454E+07 2.71001E-02 2.38160E-01
9.038E+00 2.10485E+05 3.13144E+05 2.00631E+07 2.64289E-02 2.35283E-01
9.871E+00 2.82204E+05 3.47129E+05 1.66821E+07 2.57976E-02 2.35083E-01
1.098E+01 3.69700E+05 3.81745E+05 1.37939E+07 2.52263E-02 2.39118E-01
1.251E+01 4.72979E+05 4.15699E+05 1.13038E+07 2.47149E-02 2.49546E-01
1.459E+01 5.91150E+05 4.47847E+05 9.18649E+06 2.41516E-02 2.68084E-01
1.743E+01 7.19568E+05 4.75942E+05 7.40784E+06 2.34564E-02 2.96970E-01
2.131E+01 8.51968E+05 4.97265E+05 5.92900E+06 2.26254E-02 3.37922E-01
2.656E+01 9.81013E+05 5.09954E+05 4.71673E+06 2.16026E-02 3.92218E-01
3.366E+01 1.09799E+06 5.11194E+05 3.72604E+06 2.04639E-02 4.62256E-01
4.328E+01 1.19561E+06 5.00730E+05 2.92066E+06 1.91894E-02 5.52549E-01
5.662E+01 1.26138E+06 4.75742E+05 2.29185E+06 1.79269E-02 6.74006E-01
7.600E+01 1.28343E+06 4.36859E+05 1.77402E+06 1.68841E-02 8.50998E-01
1.051E+02 1.25238E+06 3.85078E+05 1.34091E+06 1.60930E-02 1.12547E+00
1.501E+02 1.16893E+06 3.25300E+05 9.88910E+05 1.55377E-02 1.56656E+00
0 problems/tests → tests/2d_syntax/tests
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