Merge pull request #261 from VirtualPlanetaryLaboratory/FlareCleanup

Flare cleanup
VirtualPlanetaryLaboratory · Feb 2, 2024 · a0b4594 · a0b4594
2 parents cefa35e + 644257b
commit a0b4594
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Showing 17 changed files with 479 additions and 543 deletions.
diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml
@@ -19,7 +19,7 @@ jobs:
           - python-version: '3.10'
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -35,7 +35,7 @@ jobs:
 
       - name: Set up Python
         id: setup_python
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: vplanet
           environment-file: environment.yml

diff --git a/.github/workflows/memcheck.yml b/.github/workflows/memcheck.yml
@@ -12,13 +12,13 @@ jobs:
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Set up Python
         id: setup_python
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: vplanet
           environment-file: environment.yml

diff --git a/.github/workflows/pip-install.yml b/.github/workflows/pip-install.yml
@@ -16,12 +16,12 @@ jobs:
           - os: ubuntu-22.04
             python-version: '3.6'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
           fetch-depth: 0
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: ${{ matrix.python }}
@@ -49,7 +49,7 @@ jobs:
           CIBW_SKIP: '*-manylinux_i686'
           CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           path: ./wheelhouse/*.whl
 
@@ -62,23 +62,23 @@ jobs:
           submodules: true
           fetch-depth: 0
 
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: ${{ matrix.python }}
 
       - name: Build sdist
         run: python setup.py sdist
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           path: dist/*.tar.gz
 
   upload_pypi:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: artifact
           path: dist

diff --git a/.github/workflows/tests-linux.yml b/.github/workflows/tests-linux.yml
@@ -21,13 +21,13 @@ jobs:
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Set up Python
         id: setup_python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -48,7 +48,7 @@ jobs:
 
       - name: Check test ouptut created
         id: check_test_file
-        uses: andstor/file-existence-action@v2
+        uses: andstor/file-existence-action@v3
         with:
           files: "/home/runner/work/vplanet/vplanet/junit/test-results.xml"
           fail: true
@@ -64,6 +64,6 @@ jobs:
           files: junit/test-*.xml
 
       - name: CodeCov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           files: ./.coverage
diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
@@ -13,16 +13,17 @@ jobs:
     strategy:
       matrix:
         os: [macos-11, macos-12, macos-13]
-        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11']
+
       fail-fast: false
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Set up Python
         id: setup_python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -37,19 +38,7 @@ jobs:
         if: steps.setup_python.outcome == 'success'
         run: make test
 
-      - name: Check test ouptut created
-        id: check_test_file
-        uses: andstor/file-existence-action@v2
-        with:
-          files: "/home/runner/work/vplanet/vplanet/junit/test-results.xml"
-          fail: true
-
       - name: Get unique id
         uses: Tiryoh/gha-jobid-action@v1
         id: jobs
 
-      - name: Publish unit test results
-        uses: EnricoMi/publish-unit-test-result-action/composite@v2
-        if: always()
-        with:
-          files: junit/test-*.xml
diff --git a/src/evolve.c b/src/evolve.c
@@ -632,8 +632,7 @@ void Evolve(BODY *body, CONTROL *control, FILES *files, MODULE *module,
   }
 
   /* Write out initial conditions */
-  WriteOutput(body, control, files, output, system, update, fnWrite,
-              control->Evolve.dTime, dDt);
+  WriteOutput(body, control, files, output, system, update, fnWrite);
 
   /* If Runge-Kutta need to copy actual update to that in
      control->Evolve. This transfer all the meta-data about the
@@ -670,9 +669,7 @@ void Evolve(BODY *body, CONTROL *control, FILES *files, MODULE *module,
     /* Halt? */
     if (fbCheckHalt(body, control, update, fnUpdate)) {
       fdGetUpdateInfo(body, control, system, update, fnUpdate);
-      WriteOutput(body, control, files, output, system, update, fnWrite,
-                  control->Evolve.dTime,
-                  control->Io.dOutputTime / control->Evolve.nSteps);
+      WriteOutput(body, control, files, output, system, update, fnWrite);
       return;
     }
 
@@ -686,12 +683,11 @@ void Evolve(BODY *body, CONTROL *control, FILES *files, MODULE *module,
     /* Time for Output? */
     if (control->Evolve.dTime >= control->Io.dNextOutput) {
       control->Evolve.nSteps += nSteps;
-      WriteOutput(body, control, files, output, system, update, fnWrite,
-                  control->Evolve.dTime,
-                  control->Io.dOutputTime / control->Evolve.nSteps);
+      WriteOutput(body, control, files, output, system, update, fnWrite);
       // Timesteps are synchronized with the output time, so this statement is
       // sufficient
       control->Io.dNextOutput += control->Io.dOutputTime;
+      //printf("%d\n",nSteps);
       nSteps = 0;
     }
 

diff --git a/src/flare.c b/src/flare.c
@@ -23,7 +23,7 @@ void BodyCopyFlare(BODY *dest, BODY *src, int foo, int iNumBodies, int iBody) {
   dest[iBody].iFlareFFD      = src[iBody].iFlareFFD;
   dest[iBody].iFlareBandPass = src[iBody].iFlareBandPass;
   // dest[iBody].iFlareSlopeUnits = src[iBody].iFlareSlopeUnits;
-  dest[iBody].dEnergyBin = src[iBody].dEnergyBin;
+  dest[iBody].iEnergyBin = src[iBody].iEnergyBin;
   // dest[iBody].dFlareSlope      = src[iBody].dFlareSlope;
   //  dest[iBody].dFlareYInt       = src[iBody].dFlareYInt;
 }
@@ -38,11 +38,11 @@ void ReadFlareEnergyBin(BODY *body,
                         int iFile) {
   // This parameter cannot exist in primary file
   int lTmp = -1;
-  double dTmp;
+  int iTmp;
 
-  AddOptionDouble(files->Infile[iFile].cIn,
+  AddOptionInt(files->Infile[iFile].cIn,
                   options->cName,
-                  &dTmp,
+                  &iTmp,
                   &lTmp,
                   control->Io.iVerbose);
   if (lTmp >= 0) {
@@ -51,10 +51,10 @@ void ReadFlareEnergyBin(BODY *body,
                     files->Infile[iFile].cIn,
                     lTmp,
                     control->Io.iVerbose);
-    body[iFile - 1].dEnergyBin = dTmp;
+    body[iFile - 1].iEnergyBin = iTmp;
     UpdateFoundOption(&files->Infile[iFile], options, lTmp, iFile);
   } else if (iFile > 0)
-    body[iFile - 1].dEnergyBin = options->dDefault;
+    body[iFile - 1].iEnergyBin = (int)options->dDefault;
 }
 
 void ReadFlareFFD(BODY *body,
@@ -525,14 +525,15 @@ void InitializeOptionsFlare(OPTIONS *options, fnReadOption fnRead[]) {
   sprintf(options[OPT_LXUVFLARECONST].cDimension, "energy/time");
   fnRead[OPT_LXUVFLARECONST] = &ReadLXUVFlareConst;
 
+  // XXX Change to iEnergyBin for next major release
   sprintf(options[OPT_FLAREENERGYBIN].cName, "dEnergyBin");
   sprintf(options[OPT_FLAREENERGYBIN].cDescr,
           "Number of energies consider between the minimum and maximum "
           "energies to calculate the luminosity by flares");
   sprintf(options[OPT_FLAREENERGYBIN].cDefault,
           "100 energies between dFlareMinEnergy and dFlareMaxEnergy");
-  options[OPT_FLAREENERGYBIN].dDefault   = 100.0;
-  options[OPT_FLAREENERGYBIN].iType      = 2;
+  options[OPT_FLAREENERGYBIN].dDefault   = 100;
+  options[OPT_FLAREENERGYBIN].iType      = 1;
   options[OPT_FLAREENERGYBIN].bMultiFile = 1;
   options[OPT_FLAREENERGYBIN].dNeg       = 1;
   sprintf(options[OPT_FLAREENERGYBIN].cNeg, "None");
@@ -921,15 +922,15 @@ void InitializeBodyFlare(BODY *body, CONTROL *control, UPDATE *update,
                          int iBody, int iModule) {
   // double *daEnergyERGXUV, *daLXUVFlare, *daFFD, *daEnergyJOUXUV, *daLogEner;
   // double *daLogEnerXUV, *daEnergyERG, *daEnergyJOU, *daEnerJOU;
-  body[iBody].daEnergyERGXUV = malloc(body[iBody].dEnergyBin * sizeof(double));
-  body[iBody].daLXUVFlare    = malloc(body[iBody].dEnergyBin * sizeof(double));
-  body[iBody].daFFD          = malloc(body[iBody].dEnergyBin * sizeof(double));
-  body[iBody].daEnergyJOUXUV = malloc(body[iBody].dEnergyBin * sizeof(double));
-  body[iBody].daLogEner      = malloc(body[iBody].dEnergyBin * sizeof(double));
-  body[iBody].daLogEnerXUV   = malloc(body[iBody].dEnergyBin * sizeof(double));
-  body[iBody].daEnergyERG    = malloc(body[iBody].dEnergyBin * sizeof(double));
-  body[iBody].daEnergyJOU    = malloc(body[iBody].dEnergyBin * sizeof(double));
-  body[iBody].daEnerJOU      = malloc(body[iBody].dEnergyBin * sizeof(double));
+  body[iBody].daEnergyERGXUV = malloc((body[iBody].iEnergyBin+1) * sizeof(double));
+  body[iBody].daLXUVFlare    = malloc((body[iBody].iEnergyBin+1) * sizeof(double));
+  body[iBody].daEnergyJOUXUV = malloc((body[iBody].iEnergyBin+1) * sizeof(double));
+  body[iBody].daFFD          = malloc((body[iBody].iEnergyBin+1) * sizeof(double));
+  body[iBody].daLogEner      = malloc((body[iBody].iEnergyBin+1) * sizeof(double));
+  body[iBody].daLogEnerXUV   = malloc((body[iBody].iEnergyBin+1) * sizeof(double));
+  body[iBody].daEnergyERG    = malloc((body[iBody].iEnergyBin+1) * sizeof(double));
+  body[iBody].daEnergyJOU    = malloc((body[iBody].iEnergyBin+1) * sizeof(double));
+  body[iBody].daEnerJOU      = malloc((body[iBody].iEnergyBin+1) * sizeof(double));
 
   body[iBody].dLXUVFlare = fdLXUVFlare(body, control->Evolve.dTimeStep, iBody);
 }
@@ -1678,12 +1679,11 @@ double fdLXUVFlare(BODY *body, double dDeltaTime, int iBody) {
   double dLXUVFlare = 0.0;
   double dLogEnergyMinERG, dLogEnergyMaxERG, dEnergyMin, dEnergyMax,
         dLogEnergyMin, dLogEnergyMax;
-  int iEnergyBin = 0;
   int i, iLogEnergyMinERG, iLogEnergyMaxERG, iLogEnergyMin, iLogEnergyMax;
   double dEnergyMinXUV, dEnergyMaxXUV, dLogEnergyMinXUV;
   int iLogEnergyMinERGXUV, iLogEnergyMaxERGXUV, iLogEnergyMinXUV,
         iLogEnergyMaxXUV;
-  double dEnergyStep, dEnergyStepXUV, dEnergyBin;
+  double dEnergyStep, dEnergyStepXUV;
 
 
   // ######################### 1. Choosing how to calculate FFD: slopes(age) or
@@ -1715,10 +1715,6 @@ double fdLXUVFlare(BODY *body, double dDeltaTime, int iBody) {
 
     dLogEnergyMinXUV = fdBandPassXUV(body, iBody, body[iBody].dFlareMinEnergy);
 
-    // Defining the array size (dEnergybin) of energies
-    dEnergyBin = body[iBody].dEnergyBin;
-    iEnergyBin = (int)dEnergyBin;
-
     // Declaring the XUV Energy arrays of size dEnergyBin
     // double daEnergyJOUXUV[iEnergyBin + 1], daLogEnerXUV[iEnergyBin + 1],
     //      daEnergyERGXUV[iEnergyBin + 1];
@@ -1738,7 +1734,7 @@ double fdLXUVFlare(BODY *body, double dDeltaTime, int iBody) {
 
     // Defining the energy step used in line 1097, 1099, and 1101 to fill the
     // energy arrays
-    dEnergyStep = (dLogEnergyMaxERG - dLogEnergyMinERG) / iEnergyBin;
+    dEnergyStep = (dLogEnergyMaxERG - dLogEnergyMinERG) / body[iBody].iEnergyBin;
 
     // Declaring the Kepler Energy arrays of size iEnergyBin
     // double daEnergyERG[iEnergyBin + 1], daEnergyJOU[iEnergyBin + 1],
@@ -1747,7 +1743,7 @@ double fdLXUVFlare(BODY *body, double dDeltaTime, int iBody) {
     // ############################ 4. Filling the energy arrays
     // ########################################################################
 
-    for (i = 0; i < iEnergyBin + 1; i++) {
+    for (i = 0; i < body[iBody].iEnergyBin + 1; i++) {
       // XUV energy (energy_joules)
       body[iBody].daEnergyJOUXUV[i] =
             fdEnergyJoulesXUV(dLogEnergyMinXUV + i * dEnergyStep);
@@ -1762,8 +1758,8 @@ double fdLXUVFlare(BODY *body, double dDeltaTime, int iBody) {
     body[iBody].dFlareEnergy3   = body[iBody].daEnerJOU[2];
     body[iBody].dFlareEnergy4   = body[iBody].daEnerJOU[3];
     body[iBody].dFlareEnergyMin = body[iBody].daEnerJOU[0];
-    body[iBody].dFlareEnergyMid = body[iBody].daEnerJOU[iEnergyBin / 2];
-    body[iBody].dFlareEnergyMax = body[iBody].daEnerJOU[iEnergyBin];
+    body[iBody].dFlareEnergyMid = body[iBody].daEnerJOU[(int)(body[iBody].iEnergyBin / 2.)];
+    body[iBody].dFlareEnergyMax = body[iBody].daEnerJOU[body[iBody].iEnergyBin];
     // ############################ 5. Filling the FFD arrays
     // ########################################################################
 
@@ -1772,7 +1768,7 @@ double fdLXUVFlare(BODY *body, double dDeltaTime, int iBody) {
     // double daFFD[iEnergyBin + 1];
 
     // When DAVENPORT or LACY are selected, we have to calculate the FFD first.
-    for (i = 0; i < iEnergyBin + 1; i++) {
+    for (i = 0; i < body[iBody].iEnergyBin + 1; i++) {
       body[iBody].daFFD[i] = fdFFD(body, iBody, body[iBody].daLogEner[i],
                                    dFlareSlope, dFlareYInt);
     }
@@ -1782,15 +1778,15 @@ double fdLXUVFlare(BODY *body, double dDeltaTime, int iBody) {
     body[iBody].dFlareFreq3   = body[iBody].daFFD[2];
     body[iBody].dFlareFreq4   = body[iBody].daFFD[3];
     body[iBody].dFlareFreqMin = body[iBody].daFFD[0];
-    body[iBody].dFlareFreqMid = body[iBody].daFFD[iEnergyBin / 2];
-    body[iBody].dFlareFreqMax = body[iBody].daFFD[iEnergyBin];
+    body[iBody].dFlareFreqMid = body[iBody].daFFD[(int)(body[iBody].iEnergyBin / 2)];
+    body[iBody].dFlareFreqMax = body[iBody].daFFD[body[iBody].iEnergyBin];
     // ############################ 6. Calculating the XUV luminosity by flares
     // ########################################################################
     //  double daLXUVFlare[iEnergyBin];
 
     // Calculating the luminosity by flares for DAVENPORT or LACY mode
     // if the user select to calculate the luminosity using a FFD model
-    for (i = 0; i < iEnergyBin; i++) {
+    for (i = 0; i < body[iBody].iEnergyBin; i++) {
       body[iBody].daLXUVFlare[i] =
             (body[iBody].daEnergyJOUXUV[i + 1] -
              body[iBody].daEnergyJOUXUV[i]) *

diff --git a/src/output.c b/src/output.c
@@ -2213,8 +2213,7 @@ void WriteLog(BODY *body, CONTROL *control, FILES *files, MODULE *module,
 }
 
 void WriteOutput(BODY *body, CONTROL *control, FILES *files, OUTPUT *output,
-                 SYSTEM *system, UPDATE *update, fnWriteOutput *fnWrite,
-                 double dTime, double dDt) {
+                 SYSTEM *system, UPDATE *update, fnWriteOutput *fnWrite) {
   int iBody, iCol, iOut, iSubOut, iExtra = 0, iGrid, iLat, jBody, j;
   double dCol[NUMOPT], *dTmp, dGrid[NUMOPT];
   FILE *fp;

diff --git a/src/output.h b/src/output.h
@@ -118,7 +118,7 @@ void WriteLogEntry(BODY *, CONTROL *, OUTPUT *, SYSTEM *, UPDATE *,
 
 void InitializeOutputFunctions(MODULE *, OUTPUT *, int);
 void WriteOutput(BODY *, CONTROL *, FILES *, OUTPUT *, SYSTEM *, UPDATE *,
-                 fnWriteOutput *, double, double);
+                 fnWriteOutput *);
 void WriteLog(BODY *, CONTROL *, FILES *, MODULE *, OPTIONS *, OUTPUT *,
               SYSTEM *, UPDATE *, fnUpdateVariable ***, fnWriteOutput *, int);
 void InitializeOutput(FILES*,OUTPUT *, fnWriteOutput *);

diff --git a/src/vplanet.h b/src/vplanet.h
@@ -878,7 +878,7 @@ struct BODY {
   int iFlareBandPass; /**< Option to choose in which band pass the input energy
                          are*/
   int iFlareSlopeUnits; /**< Mode to choose in which units the FFD slopes are*/
-  double dEnergyBin;    /**< Number of energies consider between the minimum and
+  int iEnergyBin;    /**< Number of energies consider between the minimum and
                            maximum energies to calculate the luminosity by flares*/
   double *daEnergyERG;
   double *daEnergyJOU;