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Nek5000 · Jun 7, 2021 · 723cd46 · 723cd46
1 parent bcd890b
commit 723cd46
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Showing 51 changed files with 4,594 additions and 2,708 deletions.
diff --git a/3rd_party/gslib/ogs/ogs.hpp b/3rd_party/gslib/ogs/ogs.hpp
@@ -135,7 +135,7 @@ SOFTWARE.
 #define ogsMax "max"
 #define ogsMin "min"
 
-#define OGS_ENABLE_TIMER
+//#define OGS_ENABLE_TIMER
 
 // OCCA+gslib gather scatter
 typedef struct {

diff --git a/3rd_party/nek5000/.github/workflows/ci.yml b/3rd_party/nek5000/.github/workflows/ci.yml
@@ -0,0 +1,79 @@
+name: CI
+
+on:
+  # allows us to run workflows manually
+  workflow_dispatch:
+
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  MPICH_FC: gfortran
+
+jobs:
+  main:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        test_case: [ 
+            "Tools",
+            "Axi::test_PnPn_Parallel",
+            "CmtInviscidVortex::test_PnPn_Parallel",
+            "ConjHt::test_PnPn_Parallel",
+            "Eddy_EddyUv::test_PnPn_Parallel",
+            "Eddy_EddyUv::test_PnPn_Serial",
+            "Eddy_LegacySize::test_PnPn2_Parallel",
+            "Eddy_Neknek::test_PnPn2_Parallel",
+            "Eddy_Neknek::test_PnPn_Parallel",
+            "Eddy_Neknek_mv::test_PnPn2_Parallel",
+            "Eddy_Neknek_mv::test_PnPn_Parallel",
+            "Eddy_Rich::test_PnPn2_Parallel",
+            "Ethier::test_PnPn2_Parallel",
+            "Ethier::test_PnPn_Parallel",
+            "FsHydro::test_PnPn2_Parallel",
+            "InclDef::test_PnPn_Parallel",
+            "IO_Test::test_PnPn2_Parallel",
+            "KovStokes::test_PnPn2_Parallel",
+            "KovStokes::test_PnPn_Parallel",
+            "LowMachTest::test_PnPn_Parallel",
+            "MvCylCvode::test_PnPn_Parallel",
+            "chan2d::test_PnPn_Parallel",
+            "eddy_mv::test_PnPn_Parallel",
+            "lpm_one::test_PnPn_Parallel",
+            "lpm_two::test_PnPn_Parallel" 
+        ]
+        include:
+          - test_case: "Tools"
+            mpi: no
+          - test_case: "Eddy_EddyUv::test_PnPn_Serial"
+            mpi: no 
+          - test_case: "InclDef::test_PnPn_Parallel"
+            mpi: no
+      fail-fast: false
+
+    name: "${{ matrix.test_case }}"
+
+    env:
+      TEST_CASE: ${{ matrix.test_case }}
+      MPI: "${{ matrix.mpi == 'no' && '0' || '1' }}"
+      FC: "${{ matrix.mpi == 'no' && 'gfortran' || 'mpif77' }}"
+      CC: "${{ matrix.mpi == 'no' && 'gcc' || 'mpicc' }}"
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: apt dependencies
+        shell: bash
+        run: |
+          sudo apt -y update
+          sudo apt install -y gfortran mpich libmpich-dev python3-pytest
+
+      - name: test
+        shell: bash
+        run: |
+          pytest-3 -s -v short_tests/NekTests.py::$TEST_CASE
diff --git a/3rd_party/nek5000/.gitignore b/3rd_party/nek5000/.gitignore
@@ -19,3 +19,5 @@ bin/pretex
 bin/prex
 bin/re2torea
 bin/reatore2
+
+__pycache__
diff --git a/3rd_party/nek5000/.travis.yml b/3rd_party/nek5000/.travis.yml
diff --git a/3rd_party/nek5000/3rd_party/cvode/install b/3rd_party/nek5000/3rd_party/cvode/install
@@ -2,7 +2,6 @@
 set -e
 
 VER=2.7.0
-CHKSUM=3559c375ce9f875542e4a39978908f91792e6d57
 
 if [ "$1" == "clean" ]; then
   rm -rf sundials lib include 2>/dev/null 
@@ -14,13 +13,7 @@ if [ -f ./lib/libsundials_fcvode.a ]; then
 fi
 
 if [ ! -f v$VER.tar.gz ]; then
-  wget --no-check-certificate -O v$VER.tar.gz https://computation.llnl.gov/projects/sundials/download/sundials-$VER.tar.gz
-  SUM=`openssl dgst -sha1 v$VER.tar.gz | sed 's/^.* //'`
-  if [ $SUM != $CHKSUM ] ; then
-    echo 'Invalid checksum!'
-    rm -rf v$VER.tar.gz
-    exit 1
-  fi
+  wget --no-check-certificate -O v$VER.tar.gz https://github.com/LLNL/sundials/archive/refs/tags/v$VER.tar.gz
 fi
 
 rm -rf sundials 2>/dev/null

diff --git a/3rd_party/nek5000/core/NEKUSE b/3rd_party/nek5000/core/NEKUSE
@@ -2,15 +2,15 @@ c
 c     Nekuse
 c
       real x,y,z,r,theta,ux,uy,uz,un,u1,u2,trx,try,trz,trn,tr1,tr2,pa
-     $    ,p0,ffx,ffy,ffz,temp,flux,hc,hrad,tinf,qvol,udiff,utrans
+     $    ,p0,ffx,ffy,ffz,temp,flux,hc,hrad,tinf,qvol,avol,udiff,utrans
      $    ,si2,si3,sigma,turbk,turbe,ps(ldimt)
       common /nekuse/ x  ,y  ,z  ,r  ,theta
      $              , ux ,uy ,uz
      $              , un ,u1 ,u2
      $              , trx,try,trz
      $              , trn,tr1,tr2,pa,p0
      $              , ffx,ffy,ffz
-     $              , temp,flux,hc,hrad,tinf,qvol
+     $              , temp,flux,hc,hrad,tinf,qvol,avol
      $              , udiff,utrans
      $              , si2,si3,sigma
      $              , turbk,turbe

diff --git a/3rd_party/nek5000/core/SOLN b/3rd_party/nek5000/core/SOLN
@@ -11,8 +11,8 @@ c
 c
 c     Solution and data
 c
-      real bq(lx1,ly1,lz1,lelt,ldimt)
-      common /bqcb/ bq
+      real bq(lx1,ly1,lz1,lelt,ldimt),adq(lx1,ly1,lz1,lelt,ldimt)
+      common /bqcb/ bq,adq
 
 c     Can be used for post-processing runs (SIZE .gt. 10+3*LDIMT flds)
       real vxlag  (lx1,ly1,lz1,lelv,2)

diff --git a/3rd_party/nek5000/core/conduct.f b/3rd_party/nek5000/core/conduct.f
@@ -64,6 +64,7 @@ subroutine cdscal (igeom)
          call sethlm  (h1,h2,intype)
          call bcneusc (ta,-1)
          call add2    (h2,ta,n)
+         call add2    (h2,adq(1,1,1,1,ifield-1),n)
          call bcdirsc (t(1,1,1,1,ifield-1))
          call axhelm  (ta,t(1,1,1,1,ifield-1),h1,h2,imesh,ISD)
          call sub3    (tb,bq(1,1,1,1,ifield-1),ta,n)
@@ -119,15 +120,15 @@ subroutine makeuq
 
       if (nio.eq.0.and.loglevel.gt.2) 
      $   write(6,*) 'makeuq', ifield, time
-      call setqvol(bq(1,1,1,1,ifield-1))
+      call setqvol(bq(1,1,1,1,ifield-1),adq(1,1,1,1,ifield-1))
       call col2   (bq(1,1,1,1,ifield-1) ,bm1,n)
 
       if (.not.ifcvfld(ifield)) time = time+dt ! Restore time
 
       return
       end
 c-----------------------------------------------------------------------
-      subroutine setqvol(bql)
+      subroutine setqvol(bql,aql)
 
 c     Set user specified volumetric forcing function (e.g. heat source).
 
@@ -137,7 +138,7 @@ subroutine setqvol(bql)
       include 'TSTEP'
       include 'CTIMER'
 
-      real bql(lx1*ly1*lz1,lelt)
+      real bql(lx1*ly1*lz1,lelt),aql(lx1*ly1*lz1,lelt)
 
 #ifdef TIMER
       etime1=dnekclock()
@@ -149,7 +150,7 @@ subroutine setqvol(bql)
 
       do iel=1,nel
 
-         call nekuq (bql,iel) ! ONLY SUPPORT USERQ - pff, 3/08/16
+         call nekuq (bql,aql,iel) ! ONLY SUPPORT USERQ - pff, 3/08/16
 
 c        igrp = igroup(iel)
 c        if (matype(igrp,ifield).eq.1) then ! constant source within a group
@@ -172,7 +173,7 @@ subroutine setqvol(bql)
       return
       end
 C
-      subroutine nekuq (bql,iel)
+      subroutine nekuq (bql,aql,iel)
 C------------------------------------------------------------------
 C
 C     Generate user-specified volumetric source term (temp./p.s.)
@@ -186,16 +187,18 @@ subroutine nekuq (bql,iel)
       include 'NEKUSE'
       include 'INPUT'
 c
-      real bql(lx1,ly1,lz1,lelt)
+      real bql(lx1,ly1,lz1,lelt),aql(lx1,ly1,lz1,lelt)
 c
       ielg = lglel(iel)
       do 10 k=1,lz1
       do 10 j=1,ly1
       do 10 i=1,lx1
          if (optlevel.le.2) call nekasgn (i,j,k,iel)
          qvol = 0.0
+         avol = 0.0
          call userq   (i,j,k,ielg)
          bql(i,j,k,iel) = qvol
+         aql(i,j,k,iel) = avol
  10   continue
 
       return

diff --git a/3rd_party/nek5000/core/experimental/RANS_KOMG b/3rd_party/nek5000/core/experimental/RANS_KOMG
@@ -1,12 +1,17 @@
-      parameter (ncoeffs = 21)
+      integer ncoeffs,ifld_k,ifld_omega
+      parameter (ncoeffs = 30)
       common /rans_komg_i/ ifld_k, ifld_omega
       common /rans_komg_r/ kSrc  (lx1,ly1,lz1,lelv)
      $                   , omgSrc(lx1,ly1,lz1,lelv)
+     $                   , kDiag  (lx1,ly1,lz1,lelv)
+     $                   , omgDiag(lx1,ly1,lz1,lelv)
      $                   , mut   (lx1,ly1,lz1,lelv)
      $                   , mutsk (lx1,ly1,lz1,lelv)
      $                   , mutso (lx1,ly1,lz1,lelv)
      $                   , coeffs(ncoeffs)
 
+      real kSrc, omgSrc, kDiag, omgDiag, mut, mutsk, mutso, coeffs
+
       common /rans_komg_omegab/ f_omegb     (lx1,ly1,lz1,lelv)
      $                        , dfdx_omegb  (lx1,ly1,lz1,lelv)
      $                        , dfdy_omegb  (lx1,ly1,lz1,lelv)
@@ -16,12 +21,22 @@
      $                        , ywd         (lx1,ly1,lz1,lelv)
      $                        , ywdm1       (lx1,ly1,lz1,lelv)
 
-      real kSrc, omgSrc, mut, mutsk, mutso
+      real f_omegb, dfdx_omegb, dfdy_omegb, dfdz_omegb
+      real delfsq_omegb, delsqf_omegb, ywd, ywdm1
+      real k,mu_t,nu_t,mu,mu_k,mu_tp,nu, kv_min,omeg_max, mu_min
 
       common/ifrans/ifrans_komg_stndrd, ifrans_komg_lowRe
-     $             ,ifrans_komgSST_stndrd, ifrans_komgSST_lowRe
-     $             ,ifrans_komg_stndrd_noreg
+     $             ,ifrans_komgSST_stndrd
+     $             ,ifrans_komg_stndrd_noreg, ifrans_ktau_stndrd
+     $             ,ifrans_ktau_lowRe, ifrans_ktauSST_stndrd
+     $             ,ifrans_diag
       logical       ifrans_komg_stndrd, ifrans_komg_lowRe
-     $             ,ifrans_komgSST_stndrd, ifrans_komgSST_lowRe
-     $             ,ifrans_komg_stndrd_noreg
+     $             ,ifrans_komgSST_stndrd
+     $             ,ifrans_komg_stndrd_noreg, ifrans_ktau_stndrd
+     $             ,ifrans_ktau_lowRe, ifrans_ktauSST_stndrd
+     $             ,ifrans_diag
+
+      common /viscmol/mul   (lx1,ly1,lz1,lelv), mul_dx(lx1,ly1,lz1,lelv)
+     $               ,mul_dy(lx1,ly1,lz1,lelv), mul_dz(lx1,ly1,lz1,lelv)
+      real mul, mul_dx, mul_dy, mul_dz