Merge pull request #61 from ORNL-Fusion/master_dev

Master dev
ORNL-Fusion · Nov 21, 2024 · 64ae384 · 64ae384
2 parents 02d19e8 + 3b06790
commit 64ae384
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diff --git a/.github/workflows/ci_doxygen.yaml b/.github/workflows/ci_doxygen.yaml
@@ -0,0 +1,49 @@
+name: Build Documentation
+on:
+    workflow_dispatch:
+    push:
+        branches:
+          - 'master'
+jobs:
+    ci_doxygen:
+        if: ${{github.ref_name}} == 'master'
+        runs-on: ubuntu-latest
+        steps:
+            - name: Clone Repo
+              shell: bash
+              working-directory: ${{runner.workspace}}
+              run: |
+                git clone https://github.com/ORNL-Fusion/Stellarator-Tools.git ${{runner.workspace}}/Stellarator-Tools
+                git clone https://token:${{secrets.AUTH_TOKEN}}@github.com/ORNL-Fusion/Stellarator-Tools-Docs.git
+            - name: Create build directory.
+              shell: bash
+              working-directory: ${{runner.workspace}}/Stellarator-Tools
+              run: cmake -E make_directory build
+            - name: Install Libraries Linux
+              shell: bash
+              run: |
+                sudo apt update
+                sudo apt-get install libnetcdf-dev
+                sudo apt-get install libnetcdff-dev
+                sudo apt-get install libopenmpi-dev
+                sudo apt-get install libscalapack-openmpi-dev
+                sudo apt-get install doxygen
+            - name: Configure CMake
+              shell: bash
+              working-directory: ${{runner.workspace}}/Stellarator-Tools/build
+              run: cmake -DBUILD_BOOZ_XFORM=ON -DBUILD_V3FIT=ON -DBUILD_V3RFUN=ON -DBUILD_SIESTA=ON -DBUILD_LGRID=ON -DBUILD_SURFACE=ON -DBUILD_BMW=ON -DBUILD_PARVMEC=ON -DBUILD_DESCUR=ON -DDOXYGEN_OUTPUT_DIRECTORY=${{runner.workspace}}/Stellarator-Tools-Docs -DDOXYGEN_HTML_OUTPUT=docs ../
+            - name: Build
+              shell: bash
+              working-directory: ${{runner.workspace}}/Stellarator-Tools/build
+              run: make doc
+            - name: Push changes.
+              shell: bash
+              working-directory: ${{runner.workspace}}/Stellarator-Tools-Docs/docs
+              env:
+                GITHUB_TOKEN: ${{secrets.AUTH_TOKEN}}
+              run: |
+                git config user.name ${{secrets.AUTH_USER}}
+                git config user.email ${{secrets.AUTH_EMAIL}}
+                git add *
+                git commit . -m "Update Doxygen docs."
+                git push origin main
diff --git a/Sources/General/bcovar.f b/Sources/General/bcovar.f
@@ -1,3 +1,35 @@
+!-------------------------------------------------------------------------------
+!>  @brief Compute the covariant magnetic field.
+!>
+!>  The contravariant magnetic field are defined as.
+!>
+!>    B^u = 1/sqrt(g)(χ' - φ'dλ/dv)                                          (1)
+!>
+!>    B^v = 1/sqrt(g)(φ' + φ'dλ/du)                                          (2)
+!>
+!>  This can be converted to covariant components using the metric tensors.
+!>
+!>    g_uu = dr/du*dr/du + dz/du*dz/du                                       (3)
+!>
+!>    g_uv = dr/du*dr/dv + dz/du*dz/dv                                       (4)
+!>
+!>    g_uu = dr/dv*dr/dv + R^2 + dz/dv*dz/dv                                 (5)
+!>
+!>  The covariant magnetic field are
+!>
+!>    B_u = guu*B^u + guv*B^v                                                (6)
+!>
+!>    B_v = guv*B^u + gvv*B^v                                                (7)
+!>
+!>  On exit the parameter lu contains the quantity.
+!>
+!>   P = R(p + |B^2|/(2μ0))
+!>
+!>  @param[inout] lu       Poloidal derivative of lambda.
+!>  @param[inout] lv       Toroidal derivative of lambda.
+!>  @param[in]    tpxc
+!>  @param[inout] ier_flag Error status.
+!-------------------------------------------------------------------------------
       SUBROUTINE bcovar_par(lu, lv, tpxc, ier_flag)
       USE vmec_main, fpsi => bvco, p5 => cp5
       USE vmec_params, ONLY: ns4, signgs, pdamp, lamscale, ntmax,

diff --git a/Sources/General/forces.f b/Sources/General/forces.f
@@ -1,3 +1,10 @@
+!-------------------------------------------------------------------------------
+!>  @brief Compute variation in the forces.
+!>
+!>  The variation in the forces is defined as:
+!>
+!>    d/ds(dZ/du)
+!-------------------------------------------------------------------------------
       SUBROUTINE forces_par
       USE vmec_main, p5 => cp5
       USE realspace
@@ -40,7 +47,7 @@ SUBROUTINE forces_par
       DO l = nsmin, nsmax      
          guus(:,l) = pguu(:,l)*pshalf(:,l)
          guvs(:,l) = pguv(:,l)*pshalf(:,l)
-         gvvs(:,l) = pgvv(:,l)* pshalf(:,l)
+         gvvs(:,l) = pgvv(:,l)*pshalf(:,l)
 
          parmn_e(:,l) = ohs*zu12(:,l)*lu_e(:,l)
          pazmn_e(:,l) =-ohs*ru12(:,l)*lu_e(:,l)

diff --git a/Sources/General/jacobian.f b/Sources/General/jacobian.f
@@ -1,3 +1,13 @@
+!-------------------------------------------------------------------------------
+!>  @brief Compute quantities need to compute the jacobian.
+!>
+!>  The jacobian is defined by:
+!>
+!>    sqrt(g) = R(dZ/ds*dR/du - dR/ds*dZ/du)
+!>
+!>  Radial derivatives naturally fall on the half mesh so these quantities
+!>  become half mesh values.
+!-------------------------------------------------------------------------------
       SUBROUTINE jacobian_par
       USE vmec_input, ONLY: nzeta
       USE vmec_main, ONLY: ohs, nrzt, irst, nznt, iter2
@@ -31,9 +41,11 @@ SUBROUTINE jacobian_par
       irst = 1
 
       DO i = nsmin, nsmax
+!  drdu on the half mesh.
          pru12(:,i) = p5*(pru(:,i,meven) + pru(:,i-1,meven) +
      &                    pshalf(:,i)*(pru(:,i,modd) +
      &                                 pru(:,i-1,modd)))
+!  dzds on the half mesh.
          pzs(:,i)   = ohs*(pz1(:,i,meven) - pz1(:,i-1,meven) +
      &                     pshalf(:,i)*(pz1(:,i,modd) -
      &                                  pz1(:,i-1,modd)))
@@ -43,15 +55,15 @@ SUBROUTINE jacobian_par
      &                       (pru(:,i,meven)*pz1(:,i,modd) +
      &                        pru(:,i-1,meven)*pz1(:,i-1,modd)) /
      &                       pshalf(:,i))
-      END DO
-
-      DO i = nsmin, nsmax
+!  dzdu on the half mesh.
          pzu12(:,i) = p5*(pzu(:,i,meven) + pzu(:,i-1,meven) +
      &                    pshalf(:,i)*(pzu(:,i,modd) +
      &                                 pzu(:,i-1,modd)))
+!  drds on the half mesh.
          prs(:,i)   = ohs*(pr1(:,i,meven) - pr1(:,i-1,meven) +
      &                     pshalf(:,i)*(pr1(:,i,modd) -
      &                                  pr1(:,i-1,modd)))
+!  R on the half mesh.
          pr12(:,i)  = p5*(pr1(:,i,meven) + pr1(:,i-1,meven) +
      &                    pshalf(:,i)*(pr1(:,i,modd) +
      &                                 pr1(:,i-1,modd)))

diff --git a/Sources/General/totzsp_mod.f b/Sources/General/totzsp_mod.f
@@ -37,8 +37,8 @@ MODULE totzsp_mod
 !>  @param[out]   zv1       Real space dZ/dv.
 !>  @param[out]   lu1       Real space dlambda/du.
 !>  @param[out]   lv1       Real space dlambda/dv.
-!>  @param[out]   rcn1      Unknown R quantity.
-!>  @param[out]   zcn1      Unknown Z quantity.
+!>  @param[out]   rcn1      Constraint on R.
+!>  @param[out]   zcn1      Constraint on Z.
 !>  @param[out]   ier_flag  Status of the transform. Takes the value of
 !>                          @ref r01_bad_value_flag if rmnc(0,1) is zero.
 !>
@@ -277,8 +277,8 @@ END SUBROUTINE totzsps_par
 !>  @param[out]   zv1       Real space dZ/dv.
 !>  @param[out]   lu1       Real space dlambda/du.
 !>  @param[out]   lv1       Real space dlambda/dv.
-!>  @param[out]   rcn1      Unknown R quantity.
-!>  @param[out]   zcn1      Unknown Z quantity.
+!>  @param[out]   rcn1      Constraint on R.
+!>  @param[out]   zcn1      Constraint on Z.
 !>  @param[out]   ier_flag  Status of the transform. Takes the value of
 !>                          @ref r01_bad_value_flag if rmnc(0,1) is zero.
 !>