Merge pull request #34 from cticenhour/test-reorg

A bit of cleaning house
shannon-lab · Jun 3, 2019 · 091bef1 · 091bef1
2 parents 46193a1 + 40eacd3
commit 091bef1
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diff --git a/README.md b/README.md
@@ -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:**
 
@@ -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>
@@ -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>

diff --git a/build_libmesh_and_zapdos.sh b/build_libmesh_and_zapdos.sh
diff --git a/compile.bash b/compile.bash
diff --git a/Chemical_Reactions.ipynb → doc/Chemical_Reactions.ipynb b/Chemical_Reactions.ipynb → doc/Chemical_Reactions.ipynb
diff --git a/gitdiff.txt b/gitdiff.txt
diff --git a/tests/2d_syntax/2d.geo b/tests/2d_syntax/2d.geo
@@ -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;
diff --git a/problems/2d.i → tests/2d_syntax/2d.i b/problems/2d.i → tests/2d_syntax/2d.i
diff --git a/problems/2d.msh → tests/2d_syntax/2d.msh b/problems/2d.msh → tests/2d_syntax/2d.msh
diff --git a/problems/2d_jac_test.i → tests/2d_syntax/2d_jac_test.i b/problems/2d_jac_test.i → tests/2d_syntax/2d_jac_test.i
diff --git a/problems/2d_temp.i → tests/2d_syntax/2d_temp.i b/problems/2d_temp.i → tests/2d_syntax/2d_temp.i
diff --git a/tests/2d_syntax/td_argon_mean_en.txt b/tests/2d_syntax/td_argon_mean_en.txt
@@ -0,0 +1,50 @@
+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
diff --git a/problems/tests → tests/2d_syntax/tests b/problems/tests → tests/2d_syntax/tests