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Prepare Release of CPCM-X (#25)
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Release CPCM-X
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MtoLStoN authored Jul 31, 2023
1 parent dfa7464 commit b41feaf
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121 changes: 121 additions & 0 deletions .github/workflows/fortran_build.yml
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name: CI
on: [push, pull_request]

env:
BUILD_DIR: _build

jobs:
gcc-meson-build:
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: [macos-latest, ubuntu-latest]
fc: [gfortran-11]
cc: [gcc-11]
include:
- os: ubuntu-latest
fc: gfortran-9
cc: gcc-9
- os: ubuntu-latest
fc: gfortran-10
cc: gcc-10

steps:
- name: Checkout code
uses: actions/checkout@v2

- name: Setup Python
uses: actions/setup-python@v1
with:
python-version: 3.x

- name: Install OpenBLAS (OSX)
if: ${{ contains(matrix.os, 'macos') }}
run: |
brew install openblas
echo "PKG_CONFIG_PATH=/usr/local/opt/openblas/lib/pkgconfig" >> $GITHUB_ENV
- name: Install meson
run: pip3 install meson==0.62.0 ninja cmake

- name: Configure build
run: >-
meson setup ${{ env.BUILD_DIR }}
--buildtype=release
${{ env.MESON_ARGS }}
env:
FC: ${{ matrix.fc }}
CC: ${{ matrix.cc }}
MESON_ARGS: ${{ contains(matrix.os, 'macos') && '-Dlapack=openblas' || '-Dlapack=netlib' }}

- name: Build project
run: meson compile -C ${{ env.BUILD_DIR }}

- name: Run unit tests
run: meson test -C ${{ env.BUILD_DIR }} --print-errorlogs --no-rebuild -t 120 --suite cpx

intel-meson-build:
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest]
fc: [ifort]
cc: [icc]
env:
FC: ${{ matrix.fc }}
CC: ${{ matrix.cc }}
APT_PACKAGES: >-
intel-oneapi-compiler-fortran
intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
intel-oneapi-mkl
intel-oneapi-mkl-devel
asciidoctor
steps:
- name: Checkout code
uses: actions/checkout@v2

- name: Setup Python
uses: actions/setup-python@v1
with:
python-version: 3.x

- run: pip3 install meson ninja --user

- name: Add Intel repository
if: contains(matrix.os, 'ubuntu')
run: |
wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
sudo apt-get update
- name: Install Intel oneAPI compiler
if: contains(matrix.os, 'ubuntu')
run: |
sudo apt-get install ${APT_PACKAGES}
source /opt/intel/oneapi/setvars.sh
printenv >> $GITHUB_ENV
- name: Configure meson build
run: >-
meson setup ${{ env.BUILD_DIR }}
--prefix=/ --libdir=lib
-Dfortran_link_args="-lifcoremt -static"
-Ddefault_library=static
-Dlapack=mkl
- name: Build project
run: ninja -C ${{ env.BUILD_DIR }}

- name: Run unit tests
run: >-
meson test -C ${{ env.BUILD_DIR }}
--print-errorlogs
--num-processes 1
--no-rebuild
--suite cpx
-t 12
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0.30880726
7540.06830745
-1.26119686
15813.08917624
0.00845974
16.58382447
-0.23040291
-0.13909842
-10.60951107
0.00000000
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0.26735274
6968.29354476
-0.85997768
16987.81891223
0.00881484
20.09563223
-0.19526441
-0.16800049
-10.80693208
0.00000000
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0.30880726
7540.06830745
-1.26119686
15813.08917624
0.00845974
16.58382447
-0.23040291
-0.13909842
-10.60951107
0.00000000
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0.53725564
1977.88495090
1.61721497
2664.61735599
0.00806820
57.11402448
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-0.08426734
-8.41974122
0.00000000
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#!/bin/python3

# Read .cosmo file and write a fortran file with the same data

import sys

# Break each line after every 120 characters
def break_lines(string):
if (len(string) < 132):
return string
new_string = ""
for i in range(0, len(string), 120):
new_string += string[i:i+120] + "&\n&"
return new_string[:-3]
# Read the file
with open(sys.argv[1], 'r') as f:
lines = f.readlines()

solvent = sys.argv[1].split('.')[0]

# Read area
area=0
for line in lines:
if "area" in line:
area = float(line.split('=')[1])
break
# Read volume (if it exists)
volume=0
for line in lines:
if "volume" in line:
volume = float(line.split('=')[1])
break
# Read COSMO energy
energy=0
for line in lines:
if "Total energy [a.u.]" in line:
energy = float(line.split('=')[1])
break

print(area, volume, energy)

# Read atom information
aid = []
axyz = []
aelement = []
i=0
while True:
if "#atom" in lines[i]:
break
i+=1
i+=1
tmp_element=""
while 'coord_car' not in lines[i]:
aid.append(int(lines[i].split()[0]))
axyz.append([float(lines[i].split()[1]), float(lines[i].split()[2]), float(lines[i].split()[3])])
tmp_element=lines[i].split()[4].lower()
if len(tmp_element) == 1:
tmp_element=tmp_element+" "
aelement.append(tmp_element)
i+=1

# Read segment information
su = []
sid = []
sarea = []
sxyz = []
spot = []
while True:
if "segment_information" in lines[i]:
break
i+=1
i+=11
while i < len(lines):
sid.append(int(lines[i].split()[1]))
sxyz.append([float(lines[i].split()[2]), float(lines[i].split()[3]), float(lines[i].split()[4])])
sarea.append(float(lines[i].split()[6]))
su.append(float(lines[i].split()[7]))
spot.append(float(lines[i].split()[8]))
i+=1

# Write the file
with open(solvent+".fh", 'w') as f:
f.write("!>COSMO file for "+solvent+" from xtb\n")
f.write(break_lines("real(wp), parameter :: area_"+solvent+"_xtb = "+str(area)+", volume_"+solvent+"_xtb = "+str(volume)+", energy_"+solvent+"_xtb = "+str(energy)+"\n"))
f.write(break_lines("integer, parameter, dimension("+str(len(aid))+") :: aid_"+solvent+"_xtb = (/ "+str(aid)[1:-1]+" /)\n"))
f.write(break_lines("real(wp), parameter, dimension("+str(len(aid))+",3) :: axyz_"+solvent+"_xtb = reshape(btoa*(/ "+str(axyz)[1:-1]+" /), shape(axyz_"+solvent+"_xtb),order=(/2,1/))\n"))
f.write(break_lines("character(len=2), parameter, dimension("+str(len(aid))+") :: aelement_"+solvent+"_xtb = (/ "+str(aelement)[1:-1]+" /)\n"))
f.write(break_lines("integer, parameter, dimension("+str(len(sid))+") :: sid_"+solvent+"_xtb = (/ "+str(sid)[1:-1]+" /)\n"))
f.write(break_lines("real(wp), parameter, dimension("+str(len(sid))+",3) :: sxyz_"+solvent+"_xtb = reshape(btoa*(/ "+str(sxyz)[1:-1]+" /), shape(sxyz_"+solvent+"_xtb),order=(/2,1/))\n"))
f.write(break_lines("real(wp), parameter, dimension("+str(len(sid))+") :: sarea_"+solvent+"_xtb = (/ "+str(sarea)[1:-1]+" /)\n"))
f.write(break_lines("real(wp), parameter, dimension("+str(len(sid))+") :: su_"+solvent+"_xtb = (/ "+str(su)[1:-1]+" /)\n"))
f.write(break_lines("real(wp), parameter, dimension("+str(len(sid))+") :: spot_"+solvent+"_xtb = (/ "+str(spot)[1:-1]+" /)\n"))


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