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Merge branch 'development' into mrf
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@baperry2
baperry2 authored Oct 8, 2024
2 parents b2bee8b + c6e5e30 commit bd12db9
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Showing 5 changed files with 40 additions and 32 deletions.
13 changes: 9 additions & 4 deletions .github/workflows/docs.yml
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Expand Up @@ -37,11 +37,16 @@ jobs:
working-directory: ${{runner.workspace}}/build-docs
run: |
echo "::add-matcher::.github/problem-matchers/sphinx.json"
cmake --build ${{runner.workspace}}/build-docs
echo "::remove-matcher owner=sphinx-problem-matcher-loose-no-severity::"
echo "::remove-matcher owner=sphinx-problem-matcher-loose::"
echo "::remove-matcher owner=sphinx-problem-matcher::"
cmake --build ${{runner.workspace}}/build-docs 2>&1 | tee -a build-output.txt
touch ${{runner.workspace}}/build-docs/sphinx/html/.nojekyll
- name: Report
working-directory: ${{runner.workspace}}/build-docs
run: |
echo "::add-matcher::.github/problem-matchers/sphinx.json"
egrep "WARNING:|Warning:|ERROR:|Error:" build-output.txt | sort | uniq | \
awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > build-output-warnings.txt
cat build-output-warnings.txt
exit $(tail -n 1 build-output-warnings.txt | awk '{print $2}')
- name: Deploy
if: github.event_name == 'push' && github.ref == 'refs/heads/development'
uses: JamesIves/github-pages-deploy-action@releases/v3
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5 changes: 4 additions & 1 deletion Source/Diffterm.H
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Expand Up @@ -271,8 +271,8 @@ pc_diffusion_flux_eb(
coef[dComp_xi] * divu;
, tauz = coef[dComp_mu] * (dwdy + dvdz);)
} else if (dir == 2) {
#if AMREX_SPACEDIM == 3
const amrex::Real dudz = dxinv[dir] * (q(iv, QU) - q(ivm, QU));

const amrex::Real dvdz = dxinv[dir] * (q(iv, QV) - q(ivm, QV));
const amrex::Real dwdz = dxinv[dir] * (q(iv, QW) - q(ivm, QW));

Expand Down Expand Up @@ -313,6 +313,7 @@ pc_diffusion_flux_eb(
tauy = coef[dComp_mu] * (dvdz + dwdy);
tauz = coef[dComp_mu] * (2.0 * dwdz - 2.0 / 3.0 * divu) +
coef[dComp_xi] * divu;
#endif
}
}
const amrex::Real dTdd =
Expand Down Expand Up @@ -413,6 +414,7 @@ pc_diffusion_flux(
coef[dComp_mu] * (2.0 * dvdy - 2.0 / 3.0 * divu) + coef[dComp_xi] * divu;
AMREX_D_TERM(, , tauz = coef[dComp_mu] * (dwdy + dvdz););
} else if (dir == 2) {
#if AMREX_SPACEDIM == 3
const amrex::Real dudz = dxinv[dir] * (q(iv, QU) - q(ivm, QU));
const amrex::Real dvdz = dxinv[dir] * (q(iv, QV) - q(ivm, QV));
const amrex::Real dwdz = dxinv[dir] * (q(iv, QW) - q(ivm, QW));
Expand All @@ -434,6 +436,7 @@ pc_diffusion_flux(
tauy = coef[dComp_mu] * (dvdz + dwdy);
tauz =
coef[dComp_mu] * (2.0 * dwdz - 2.0 / 3.0 * divu) + coef[dComp_xi] * divu;
#endif
}
const amrex::Real dTdd = dxinv[dir] * (q(iv, QTEMP) - q(ivm, QTEMP));

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46 changes: 23 additions & 23 deletions Source/Geometry.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -159,23 +159,26 @@ ExtrudedTriangles::build(
problo = geom.ProbLo();
probhi = geom.ProbHi();

maxlen = amrex::max<amrex::Real>(
amrex::max<amrex::Real>(geom.ProbLength(0), geom.ProbLength(1)),
geom.ProbLength(2));
AMREX_D_TERM(maxlen = geom.ProbLength(0);
, maxlen = amrex::max<amrex::Real>(maxlen, geom.ProbLength(1));
, maxlen = amrex::max<amrex::Real>(maxlen, geom.ProbLength(2)););

// setting all triangles to be waaay outside the domain initially
for (int itri = 0; itri < max_tri; itri++) {
alltri[npts_in_tri * itri + 0][0] = problo[0] + 100.0 * maxlen;
alltri[npts_in_tri * itri + 0][1] = problo[1] - 100.0 * maxlen;
alltri[npts_in_tri * itri + 0][2] = 0.0;

alltri[npts_in_tri * itri + 1][0] = probhi[0] + 100.0 * maxlen;
alltri[npts_in_tri * itri + 1][1] = problo[1] - 100.0 * maxlen;
alltri[npts_in_tri * itri + 1][2] = 0.0;

alltri[npts_in_tri * itri + 2][0] = probhi[0] + 100.0 * maxlen;
alltri[npts_in_tri * itri + 2][1] = problo[1] + 100.0 * maxlen;
alltri[npts_in_tri * itri + 2][2] = 0.0;
AMREX_D_TERM(alltri[npts_in_tri * itri + 0][0] = problo[0] + 100.0 * maxlen;
,
alltri[npts_in_tri * itri + 0][1] = problo[1] - 100.0 * maxlen;
, alltri[npts_in_tri * itri + 0][2] = 0.0;);

AMREX_D_TERM(alltri[npts_in_tri * itri + 1][0] = probhi[0] + 100.0 * maxlen;
,
alltri[npts_in_tri * itri + 1][1] = problo[1] - 100.0 * maxlen;
, alltri[npts_in_tri * itri + 1][2] = 0.0;);

AMREX_D_TERM(alltri[npts_in_tri * itri + 2][0] = probhi[0] + 100.0 * maxlen;
,
alltri[npts_in_tri * itri + 2][1] = problo[1] + 100.0 * maxlen;
, alltri[npts_in_tri * itri + 2][2] = 0.0;);
}

// get user defined number of triangles
Expand Down Expand Up @@ -217,17 +220,14 @@ ExtrudedTriangles::build(
point1 = alltri[npts_in_tri * itri + 1];
point2 = alltri[npts_in_tri * itri + 2];

norm0[0] = -(point1[1] - point0[1]);
norm0[1] = (point1[0] - point0[0]);
norm0[2] = 0.0;
AMREX_D_TERM(norm0[0] = -(point1[1] - point0[1]);
, norm0[1] = (point1[0] - point0[0]);, norm0[2] = 0.0;);

norm1[0] = -(point2[1] - point1[1]);
norm1[1] = (point2[0] - point1[0]);
norm1[2] = 0.0;
AMREX_D_TERM(norm1[0] = -(point2[1] - point1[1]);
, norm1[1] = (point2[0] - point1[0]);, norm1[2] = 0.0;);

norm2[0] = -(point0[1] - point2[1]);
norm2[1] = (point0[0] - point2[0]);
norm2[2] = 0.0;
AMREX_D_TERM(norm2[0] = -(point0[1] - point2[1]);
, norm2[1] = (point0[0] - point2[0]);, norm2[2] = 0.0;);

// normalize so that magnitude is 1
amrex::Real norm = sqrt(norm0[0] * norm0[0] + norm0[1] * norm0[1]);
Expand Down
2 changes: 1 addition & 1 deletion Submodules/PelePhysics
Submodule PelePhysics updated 29 files
+7 −1 .github/workflows/ci.yml
+9 −4 .github/workflows/docs.yml
+2 −0 Docs/sphinx/Utility.rst
+2 −2 Mechanisms/Null/mechanism.cpp
+20 −5 README.md
+4 −4 Source/Eos/GammaLaw.H
+1 −1 Source/Eos/Manifold.H
+20 −35 Source/Reactions/ReactorArkode.cpp
+17 −0 Source/Reactions/ReactorBase.H
+7 −0 Source/Reactions/ReactorNull.H
+2 −1 Source/Reactions/ReactorNull.cpp
+7 −0 Source/Reactions/ReactorRK64.H
+12 −17 Source/Reactions/ReactorRK64.cpp
+13 −16 Source/Reactions/ReactorUtils.H
+7 −3 Source/Utility/Diagnostics/DiagFramePlane.cpp
+8 −5 Source/Utility/TurbInflow/turbinflow.H
+23 −36 Source/Utility/TurbInflow/turbinflow.cpp
+1 −1 Submodules/amrex
+1 −1 Submodules/sundials
+ − Support/CMLM/autoignition.ctb
+2 −0 Testing/Exec/EosEval/main.cpp
+13 −7 Testing/Exec/IgnitionDelay/GPU_misc.H
+1 −1 Testing/Exec/IgnitionDelay/README.md
+9 −1 Testing/Exec/IgnitionDelay/check_ignDelay.py
+17 −17 Testing/Exec/IgnitionDelay/computeIgnitionDelay.py
+3 −5 Testing/Exec/IgnitionDelay/exec_ignDelay.sh
+29 −0 Testing/Exec/IgnitionDelay/inputs/inputs.0d_manifold
+11 −1 Testing/Exec/IgnitionDelay/main.cpp
+12 −19 Testing/Exec/IgnitionDelay/utils/initFunctions.H
6 changes: 3 additions & 3 deletions Tests/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -255,7 +255,7 @@ add_test_r(eb-c10 EB-C10)
add_test_rv(eb-c11 EB-C11)
add_test_rv(eb-c12 EB-C12)
if(PELE_DIM EQUAL 2)
add_test_r(eb-flowpastcylinder-re500 EB-FlowPastCylinder)
add_test_r(eb-flowpastcylinder-re500 EB-FlowPastCylinder)
endif()
if(PELE_DIM EQUAL 2)
add_test_r(auxquantities_eb AuxQuantities)
Expand Down Expand Up @@ -304,13 +304,13 @@ add_test_re(zerod-1 zeroD)
add_test_re(spray-eb Spray-EB)
add_test_re(spray-a-wbreakup Spray-A-Wbreakup)
add_test_re(soot-flame Soot-Flame)
add_test_re(eb-c7 EB-C7)
add_test_re(eb-bluffbody-1 EB-BluffBody)
if(PELE_DIM GREATER 2)
add_test_re(eb-c8 EB-C8)
add_test_re(eb-c8-rere-mol EB-C8)
add_test_re(tg-3 TG)
add_test_re(tg-4 TG)
add_test_re(eb-c7 EB-C7)
add_test_re(eb-bluffbody-1 EB-BluffBody)
endif()

#=============================================================================
Expand Down

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