Merge pull request #198 from VirtualPlanetaryLaboratory/dev

Dev

Author: RoryBarnes

.gitignore

@@ -48,7 +48,8 @@ merge-from-private.sh
 vplot_config.py
 *.bst
 *.aux
-*.bbl
+*.bpa
+*.bpf
 *.blg
 */build
 */dist

docs/parametersweep.rst

@@ -146,12 +146,11 @@ Here’s the input file for :code:`BigPlanet`:
 
 .. code-block:: bash
 
-    sSrcFolder ~/vplanet/examples/EarthInterior
     sDestFolder ParameterSweep
     sArchiveFile ParameterSweep.bpa
+    sOutputFile ParameterSweep.bpf
 
-    saBodyFiles   sun.in earth.in
-
+    saBodyFiles   earth.in sun.in
     sPrimaryFile   vpl.in
 
     saKeyInclude earth:TCore:initial earth:40KPowerCore:final earth:RIC:final
@@ -160,9 +159,10 @@ Here’s the input file for :code:`BigPlanet`:
 This will create an `HDF5
 <https://en.wikipedia.org/wiki/Hierarchical_Data_Format>`_ file
 that shares the same name as the destfolder from the :code:`VSPACE` file, but with ".bpf" or ".bpa"
-appended, e.g. ParameterSweep.bpa. This file will now replace the directory structure
-created by :code:`VSPACE`. The -a option is for creation of an achvie file, which has **everything from
-the destfolder created with :code:`VSPACE` and the data generated from :code:`MultiPlanet`. Here is a 
+appended, depending on what type of BigPlanet file. In this case, we are creating ParameterSweep.bpf. 
+This file will now replace the directory structure created by :code:`VSPACE`. 
+The -a option is for creation of an archive file (the .bpa file), which has **everything** from
+the destfolder created with :code:`VSPACE` and the data generated from :code:`MultiPlanet`.
 
 .. note::
 

docs/run_examples.py

@@ -7,13 +7,13 @@
 path = pathlib.Path(__file__).parents[0].absolute()
 
 # gets the list of examples
-example_list = glob.glob(str(path.parents[0] / "examples" / "*" / "makeplot.py"))
+example_list = sorted(glob.glob(str(path.parents[0] / "examples" / "*" / "makeplot.py")))
 
 # list of examples that should not be ran in the test
-no_fly_list = ["AbioticO2", "ChaoticResonances", "DampedCBP", "TidalEarth", "SS_NBody"]
-
+no_fly_list = ["AbioticO2", "ChaoticResonances", "DampedCBP", "TidalEarth", "SS_NBody", "MagneticBreaking"]
 
 for example in example_list:
+    print(example)
 
     # Example name
     name = pathlib.Path(example).parents[0].name

environment.yml

@@ -6,15 +6,19 @@ dependencies:
   - pip>=20.3.3
   - scipy>=1.5.2
   - setuptools>=51.3.3
+  #- cm-super
+  #- texlive-fonts-recommended
+  #- texlive-fonts-extra
+  #- dvipng
   - pip:
-    - matplotlib>=3.3.3
-    - nose>=1.3.7
-    - parameterized>=0.8.1
-    - pytest>=6.2.4
-    - pytest-dependency>=0.5.1
-    - pytest-env>=0.6.2
-    - pytest-cov>=2.11.1
-    - sphinx>=4.0.1
-    - breathe>=4.30.0
-    - sphinxcontrib-bibtex>=2.2.0
-    - coverage>=5.5
+      - matplotlib>=3.3.3
+      - nose>=1.3.7
+      - parameterized>=0.8.1
+      - pytest>=6.2.4
+      - pytest-dependency>=0.5.1
+      - pytest-env>=0.6.2
+      - pytest-cov>=2.11.1
+      - sphinx>=4.0.1
+      - breathe>=4.30.0
+      - sphinxcontrib-bibtex>=2.2.0
+      - coverage>=5.5

examples/HLossTides/makeplot.py

@@ -16,7 +16,7 @@
 mpl.rcParams["font.size"] = 10.0
 
 # Run vplanet
-cplauto = vplanet.run(path / "Lopez12CPL" / "auto" / "vpl.in", units=False)
+cplauto = vplanet.run(path / "Lopez12CPL" / "Auto" / "vpl.in", units=False)
 cplbondi = vplanet.run(path / "Lopez12CPL" / "Bondi" / "vpl.in", units=False)
 cplelim = vplanet.run(path / "Lopez12CPL" / "ELim" / "vpl.in", units=False)
 cplrr = vplanet.run(path / "Lopez12CPL" / "RR" / "vpl.in", units=False)

examples/ParameterSweep/bpl.in

@@ -0,0 +1,8 @@
+sDestFolder ParameterSweep
+sArchiveFile ParameterSweep.bpa
+sOutputFile ParameterSweep.bpf
+
+saBodyFiles   earth.in sun.in
+sPrimaryFile   vpl.in
+
+saKeyInclude earth:TCore:initial earth:40KPowerCore:final earth:RIC:final

examples/ParameterSweep/makeplot.py

@@ -20,27 +20,33 @@
 
 # Run multi-planet
 if not (path / ".ParameterSweep").exists():
-    subprocess.check_output(["multi-planet", "vspace.in"], cwd=path)
+    subprocess.check_output(["multiplanet", "vspace.in"], cwd=path)
 
 # Run bigplanet
 if not (path / ".ParameterSweep_BPL").exists():
-    subprocess.check_output(["bigplanet", "vspace.in"], cwd=path)
+    subprocess.check_output(["bigplanet", "bpl.in"], cwd=path)
 
-data = bp.BPLFile(path / "ParameterSweep.bpl")
+data = bp.BPLFile(path / "ParameterSweep.bpf")
 
 mpl.rcParams["figure.figsize"] = (10, 8)
 fig = plt.figure()
 
-RIC = bp.ExtractColumn(data, "earth_RIC_final")
-RIC_units = bp.ExtractUnits(data, "earth_RIC_final")
+RIC = bp.ExtractColumn(data, "earth:RIC:final")
+RIC_units = bp.ExtractUnits(data, "earth:RIC:final")
 
-TCore_uniq = bp.ExtractUniqueValues(data, "earth_TCore_initial")
-TCore_units = bp.ExtractUnits(data, "earth_TCore_initial")
+TCore_uniq = bp.ExtractUniqueValues(data, "earth:TCore:initial")
+TCore_units = bp.ExtractUnits(data, "earth:TCore:initial")
 
-K40_uniq = bp.ExtractUniqueValues(data, "earth_40KPowerCore_final")
-K40_units = bp.ExtractUnits(data, "earth_40KPowerCore_final")
+K40_uniq = bp.ExtractUniqueValues(data, "earth:40KPowerCore:final")
+K40_units = bp.ExtractUnits(data, "earth:40KPowerCore:final")
 
-RIC_Matrix = bp.CreateMatrix(TCore_uniq, K40_uniq, RIC)
+
+
+print(TCore_uniq)
+
+RIC_Matrix = np.reshape(RIC,(len(TCore_uniq),len(K40_uniq)))
+
+#RIC_Matrix = bp.CreateMatrix(TCore_uniq, K40_uniq, RIC)
 
 contours = [0, 500, 1000, 1500, 2000, 2500]
 xlabel = "Initial Core Temperature (" + TCore_units + ")"