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Merge branch 'master' of github.com:liruipeng/UEDGE into omp_col
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liruipeng committed Mar 28, 2024
2 parents 171ee08 + a6245d2 commit 8d660b4
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163 changes: 163 additions & 0 deletions .github/workflows/run_testsuite.yml
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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: Build UEDGE and run test suite

on: [push, pull_request]

jobs:
fulltests:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.9]
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install pip dependencies
run: |
python -m pip install --upgrade pip
python -m pip install forthon mppl numpy h5py
python -m pip install flake8
python -m pip install pytest-isolate pytest-xdist
- name: Build UEDGE
run: |
python setup.py build
python setup.py install
- name: Return to pytests branch
uses: actions/checkout@v4
with:
ref: pytests
repository: LLNL/UEDGE
- name: Test with pytest
run: |
# Create a clean UEDGE instance for every test
pytest --isolate --tb=native pytests/fulltests
unittests_D-and-C:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.9]
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install pip dependencies
run: |
python -m pip install --upgrade pip
python -m pip install forthon mppl numpy h5py
python -m pip install flake8
python -m pip install pytest-isolate pytest-xdist
- name: Build UEDGE
run: |
python setup.py build
python setup.py install
- name: Return to pytests branch
uses: actions/checkout@v4
with:
ref: pytests
repository: LLNL/UEDGE
- name: Test with pytest
run: |
# Create a clean UEDGE instance for every test
pytest --isolate --tb=native pytests/unittests/D+C
unittests_D-mols:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.9]
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install pip dependencies
run: |
python -m pip install --upgrade pip
python -m pip install forthon mppl numpy h5py
python -m pip install flake8
python -m pip install pytest-isolate pytest-xdist
- name: Build UEDGE
run: |
python setup.py build
python setup.py install
- name: Return to pytests branch
uses: actions/checkout@v4
with:
ref: pytests
repository: LLNL/UEDGE
- name: Test with pytest
run: |
# Create a clean UEDGE instance for every test
pytest --isolate --tb=native pytests/unittests/D_mols
unittests_D-only:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.9]
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install pip dependencies
run: |
python -m pip install --upgrade pip
python -m pip install forthon mppl numpy h5py
python -m pip install flake8
python -m pip install pytest-isolate pytest-xdist
- name: Build UEDGE
run: |
python setup.py build
python setup.py install
- name: Return to pytests branch
uses: actions/checkout@v4
with:
ref: pytests
repository: LLNL/UEDGE
- name: Test with pytest
run: |
# Create a clean UEDGE instance for every test
pytest --isolate --tb=native pytests/unittests/D_only
unittests_slab-D-only:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.9]
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install pip dependencies
run: |
python -m pip install --upgrade pip
python -m pip install forthon mppl numpy h5py
python -m pip install flake8
python -m pip install pytest-isolate pytest-xdist
- name: Build UEDGE
run: |
python setup.py build
python setup.py install
- name: Return to pytests branch
uses: actions/checkout@v4
with:
ref: pytests
repository: LLNL/UEDGE
- name: Test with pytest
run: |
# Create a clean UEDGE instance for every test
pytest --isolate --tb=native pytests/unittests/slab_D_only
35 changes: 0 additions & 35 deletions .github/workflows/tests.yml

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10 changes: 8 additions & 2 deletions .gitignore
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*.pyc
*.F
a.out
*/build/
build/
.idea/
.DS_Store
*~
pyscripts/__src__.py
*.swp
a.out
PyUEDGE_tutorial/*
*.swo
pyscripts/__src__.py
pyscripts/__version__.py
dist/uedge-8.0.0-py3.7-macosx-10.9-x86_64.egg
uedge.egg-info
pyscripts/__src__.py
*.egg
*.c
*.f
pyscripts/__version__.py
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8 changes: 1 addition & 7 deletions Makefile.Forthon
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DEBUG = -v --fargs "-Ofast -DFORTHON -cpp" # -g #--fargs "-C=array" #--fargs "-CB -traceback"

SO = so
PUBLICHOME =
BUILDDIR = build
Expand All @@ -7,12 +8,6 @@ MYPYTHON = python3
FORTHON = Forthon3
BUILDBASE = -v --build-base $(BUILDDIR)
INSTALLARGS = --pkgbase uedge $(BUILDBASE) $(OMPFLAGS)
##MYPYTHON = /home1/rognlien/Python2/Python-2.4.2/python

# Following 2 variables set in Makefile.PETSc, if used (if unset, ignored)
# SETUPOPTS =
# PETSC-UEDGE =
# PETSC-COM =

all: mppl2f90 $(BUILDDIR)/compydep $(BUILDDIR)/grdpydep $(BUILDDIR)/flxpydep $(BUILDDIR)/bbbpydep $(BUILDDIR)/svrpydep $(BUILDDIR)/wdfpydep $(BUILDDIR)/aphpydep $(BUILDDIR)/apipydep $(BUILDDIR)/nclpydep
rm -f uedgeC.so
Expand Down Expand Up @@ -76,7 +71,6 @@ clean:
#--- Build command for opendx wrapper.
DX: pyDXObject.c
$(MYPYTHON) DXsetup.py build --build-platlib .
#cp pyDXObject.so /home/dave/scriptsnew

#----------------------------------------------------------------------------

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38 changes: 19 additions & 19 deletions aph/aph.v
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aph # Atomic physics (hydrogenic)

***** Physical_constants:
ev real /1.6022e-19/ # 1 electron volt in Joules
ev_aph real /1.6022e-19/ # 1 electron volt in Joules
m_prot real /1.67e-27/ # proton mass

***** Data_input:
Expand All @@ -15,7 +15,7 @@ aphdir character*120 # name of directory containing data files
data_directory character*120 # another dirname containing data files. This is to be be passed in

***** Ionization_energy:
erad real [eV] /25./ # tot elec engy loss/ioniz (rad+binding) if istabon=0
erad real [eV] /25./ +input # tot elec engy loss/ioniz (rad+binding) if istabon=0

***** Rtdata:
# hydrogenic rate table data from ADPAK via Braams' rate code
Expand Down Expand Up @@ -145,23 +145,23 @@ readehr2(fname:string) subroutine

***** Aphwrk:
# working arrays for 2-d spline interpolation
nxdata integer
nydata integer
xdata(1:nxdata) _real
ydata(1:nydata) _real
fdata(1:nxdata,1:nydata) _real
ldf integer
iflag integer
kxords integer /4/ # order of spline fit versus log(te)
# kxords=4 (default) is cubic interpolation
kyords integer /4/ # order of spline fit versus log10(ne)
# kyords=4 (default) is cubic interpolation
xknots(1:nxdata+kxords) _real
yknots(1:nydata+kyords) _real
workh(1:nxdata*nydata+2*kxords*(nxdata+1)) _real # work array
rsacoef(1:nxdata,1:nydata) _real # spline coeff's for ionization
rracoef(1:nxdata,1:nydata) _real # spline coeff's for recombination
rqacoef(1:nxdata,1:nydata) _real # spline coeff's for line emission
nxdata_aph integer
nydata_aph integer
xdata_aph(1:nxdata_aph) _real
ydata_aph(1:nydata_aph) _real
fdata_aph(1:nxdata_aph,1:nydata_aph) _real
ldf_aph integer
iflag_aph integer
kxords_aph integer /4/ # order of spline fit versus log(te)
# kxords_aph=4 (default) is cubic interpolation
kyords_aph integer /4/ # order of spline fit versus log10(ne)
# kyords_aph=4 (default) is cubic interpolation
xknots_aph(1:nxdata_aph+kxords_aph) _real
yknots_aph(1:nydata_aph+kyords_aph) _real
workh(1:nxdata_aph*nydata_aph+2*kxords_aph*(nxdata_aph+1)) _real # work array
rsacoef(1:nxdata_aph,1:nydata_aph) _real # spline coeff's for ionization
rracoef(1:nxdata_aph,1:nydata_aph) _real # spline coeff's for recombination
rqacoef(1:nxdata_aph,1:nydata_aph) _real # spline coeff's for line emission

***** Subs:
# Subroutines that can be called from the parser
Expand Down
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