Commit ac93728e19e1e53bff0da424c6eb8d4ac8705301 - votca-xtp

+40

-0

.github/workflows/changelog.yml less more

	0	name: Changelog
	1	on:
	2	issue_comment:
	3	types: [created]
	4	jobs:
	5	edit:
	6	name: add entry
	7	if: ${{ startsWith(github.event.comment.body, '@votca-bot changelog:') }}
	8	runs-on: ubuntu-latest
	9	steps:
	10	- name: Check if message comes from PR
	11	uses: octokit/request-action@v2.x
	12	id: issue_info
	13	with:
	14	route: GET /repos/:repository/issues/:pull_number
	15	repository: ${{ github.repository }}
	16	pull_number: ${{ github.event.issue.number }}
	17	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	18	- name: Get PR info
	19	if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
	20	uses: octokit/request-action@v2.x
	21	id: pr_info
	22	with:
	23	route: GET /repos/:repository/pulls/:pull_number
	24	repository: ${{ github.repository }}
	25	pull_number: ${{ github.event.issue.number }}
	26	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	27	- name: Checkout head branch from PR
	28	if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
	29	uses: actions/checkout@v2.2.0
	30	with:
	31	repository: ${{ fromJSON(steps.pr_info.outputs.data).head.repo.full_name }}
	32	ref: ${{ fromJSON(steps.pr_info.outputs.data).head.ref }}
	33	token: ${{ secrets.VOTCA_BOT_TOKEN }}
	34	- name: Create and commit changelog entry
	35	if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
	36	uses: votca/actions/changelog@master
	37	with:
	38	message: ${{ github.event.comment.body }}
	39	pr_number: ${{ github.event.issue.number }}

+75

-0

.github/workflows/continuous-integration-workflow.yml less more

	0	name: CI
	1	on:
	2	pull_request:
	3	branches:
	4	- master
	5	- stable
	6
	7	jobs:
	8	CI:
	9	continue-on-error: ${{ matrix.distro == 'ubuntu_devel' \|\| matrix.distro == 'fedora_rawhide' \|\| matrix.continue-on-error == true }}
	10	strategy:
	11	matrix:
	12	distro: [latest, fedora_rawhide, opensuse, ubuntu, ubuntu_devel, ubuntu_rolling, ubuntu_18.04, intel]
	13	toolchain: [gnu, clang]
	14	cmake_build_type: [Release, Debug]
	15	minimal: [false]
	16	own_gmx: [false]
	17	module_build: [false]
	18	coverage: [false]
	19	no_regression_testing: [true]
	20	include:
	21	- distro: latest
	22	toolchain: gnu
	23	cmake_build_type: Release
	24	module_build: true
	25	no_regression_testing: true
	26	runs-on: ubuntu-latest
	27	container: votca/buildenv:${{ matrix.distro }}
	28	steps:
	29	- uses: actions/checkout@v2.2.0
	30	with:
	31	fetch-depth: 0
	32	- name: Run Votca Setup
	33	id: setup
	34	uses: votca/actions/setup@master
	35	with:
	36	distro: ${{ matrix.distro }}
	37	toolchain: ${{ matrix.toolchain }}
	38	minimal: ${{ matrix.minimal == true }}
	39	module: ${{ matrix.module_build == true }}
	40	own_gmx: ${{ matrix.own_gmx == true }}
	41	regression_testing: ${{ matrix.no_regression_testing != true }}
	42	coverage: ${{ matrix.coverage }}
	43	cmake_build_type: ${{ matrix.cmake_build_type }}
	44	ctest_args: ${{ matrix.ctest_args }}
	45	cmake_args: ${{ matrix.cmake_args }}
	46	- uses: actions/cache@v2
	47	with:
	48	path: ~/.ccache
	49	key: ${{ steps.setup.outputs.cache_key }}
	50	restore-keys: ${{ steps.setup.outputs.cache_restore_key }}
	51	- name: CMake
	52	run: mkdir builddir && cd builddir && cmake ${{ steps.setup.outputs.cmake_args }} ../votca
	53	- name: Build
	54	run: \|
	55	ccache -z
	56	cmake --build builddir -- -j ${{ steps.setup.outputs.jobs }}
	57	ccache -s
	58	- name: Tests
	59	run: ctest --output-on-failure ${{ steps.setup.outputs.ctest_args }}
	60	working-directory: builddir
	61	- name: Doxygen
	62	if: ${{ ! matrix.module_build }}
	63	run: cmake --build builddir --target doxygen
	64	- name: Build Sphinx
	65	if: ${{ steps.setup.outputs.build_sphinx == 'true' }}
	66	run: cmake --build builddir --target doc
	67	- name: Test DESTDIR Install
	68	if: ${{ ! matrix.module_build }}
	69	run: DESTDIR=${PWD}/install cmake --build builddir --target install && rm -rf ${PWD}/install/usr && rmdir ${PWD}/install
	70	- name: Install
	71	run: sudo cmake --build builddir --target install
	72	- name: Check Formatting
	73	if: ${{ steps.setup.outputs.check_format == 'true' }}
	74	run: cmake --build builddir --target format && git -C votca/${{ steps.setup.outputs.module }} diff --exit-code

+37

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.github/workflows/create-pr.yml less more

	0	name: Create PR
	1	on:
	2	push:
	3	branches:
	4	- stable
	5
	6	jobs:
	7	PR:
	8	name: Create
	9	if: github.repository_owner == 'votca'
	10	runs-on: ubuntu-latest
	11	steps:
	12	- name: Checkout code
	13	uses: actions/checkout@master
	14	with:
	15	ref: ${{ github.event.ref }}
	16	fetch-depth: 0
	17	token: ${{ secrets.VOTCA_BOT_TOKEN }}
	18	- name: Try to merge master branch
	19	run: \|
	20	git config --global user.name "Votca Bot"
	21	git config --global user.email "github@votca.org"
	22	git checkout -b stable_fixes
	23	git merge origin/master \|\| true
	24	git push origin stable_fixes
	25	- name: Create Pull Request
	26	uses: actions/github-script@0.3.0
	27	with:
	28	github-token: ${{ secrets.VOTCA_BOT_TOKEN }}
	29	script: \|
	30	github.pulls.create({
	31	owner: 'votca',
	32	repo: 'xtp',
	33	title: 'Fixes from stable',
	34	head: 'stable_fixes',
	35	base: 'master'
	36	})

+28

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.github/workflows/create-release.yml less more

	0	name: Make Release
	1	on:
	2	push:
	3	tags:
	4	- 'v[1-9]*'
	5
	6	jobs:
	7	release:
	8	name: Make Release
	9	if: github.repository_owner == 'votca'
	10	runs-on: ubuntu-latest
	11	steps:
	12	- name: Checkout code
	13	uses: actions/checkout@v2
	14	- name: Create Changlog
	15	uses: votca/actions/release_changelog@master
	16	with:
	17	version: ${{ github.ref }}
	18	changelog: 'release_changelog.md'
	19	- name: Create Release
	20	uses: actions/create-release@v1
	21	env:
	22	GITHUB_TOKEN: ${{ secrets.VOTCA_BOT_TOKEN }}
	23	with:
	24	tag_name: ${{ github.ref }}
	25	release_name: ${{ github.ref }}
	26	prerelease: ${{ contains(github.ref, 'rc') }}
	27	body_path: 'release_changelog.md'

+46

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.github/workflows/format.yml less more

	0	name: Format
	1	on:
	2	issue_comment:
	3	types: [created]
	4	jobs:
	5	edit:
	6	name: clang-format
	7	if: ${{ github.event.comment.body == '@votca-bot format' }}
	8	runs-on: ubuntu-latest
	9	container: votca/buildenv:format
	10	steps:
	11	- name: Check if message comes from PR
	12	uses: octokit/request-action@v2.x
	13	id: issue_info
	14	with:
	15	route: GET /repos/:repository/issues/:pull_number
	16	repository: ${{ github.repository }}
	17	pull_number: ${{ github.event.issue.number }}
	18	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	19	- name: Get PR info
	20	if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
	21	uses: octokit/request-action@v2.x
	22	id: pr_info
	23	with:
	24	route: GET /repos/:repository/pulls/:pull_number
	25	repository: ${{ github.repository }}
	26	pull_number: ${{ github.event.issue.number }}
	27	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	28	- name: Checkout head branch from PR
	29	if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
	30	uses: actions/checkout@master
	31	with:
	32	repository: ${{ fromJSON(steps.pr_info.outputs.data).head.repo.full_name }}
	33	ref: ${{ fromJSON(steps.pr_info.outputs.data).head.ref }}
	34	token: ${{ secrets.VOTCA_BOT_TOKEN }}
	35	- name: Run clang-format
	36	if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
	37	run: find . -type f -regex ".*\.$c\\|h\\|cc\\|cpp\\|hpp$" -print0 \| xargs -0 clang-format -i -style=file
	38	- name: Commit and push
	39	if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
	40	run: \|
	41	git config --global user.name "Votca Bot"
	42	git config --global user.email "github@votca.org"
	43	git add -u
	44	git commit -m "Format code using $(clang-format --version)" \|\| true
	45	git push

+18

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.github/workflows/forward-to-votca.yml less more

	0	name: Forward
	1	on:
	2	push:
	3	branches:
	4	- master
	5	- stable
	6
	7	jobs:
	8	VOTCA:
	9	if: github.repository_owner == 'votca'
	10	runs-on: ubuntu-latest
	11	steps:
	12	- name: Update submodule
	13	uses: votca/actions/forward@master
	14	with:
	15	module: ${{ github.repository }}
	16	token: ${{ secrets.VOTCA_BOT_TOKEN }}
	17

+5

-127

.gitlab-ci.yml less more

0	0	stages:
1		- canary
2	1	- build
3	2
4	3	.build_script:

34	33	- pushd build
35	34	- cmake .. -DCMAKE_VERBOSE_MAKEFILE=ON -DENABLE_TESTING=ON -DBUILD_XTP=ON -DENABLE_WERROR=ON
36	35	-DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
	36	${CMAKE_GENERATOR:+-G${CMAKE_GENERATOR}}
37	37	-DMODULE_BUILD=${MODULE_BUILD} ${MODULE_BUILD:+-DCMAKE_INSTALL_PREFIX=/home/votca/votca.install}
38		-DWITH_MKL=${WITH_MKL} -DCMAKE_DISABLE_FIND_PACKAGE_MKL=${DISABLE_MKL}
	38	-DCMAKE_DISABLE_FIND_PACKAGE_MKL=${DISABLE_MKL}
39	39	-DUSE_CUDA=${USE_CUDA}
40		- cmake --build . -- -j2
	40	- cmake --build . --parallel 2
41	41	- ctest --output-on-failure
42		- test -z "${MODULE_BUILD}" && DESTDIR=${PWD}/install cmake --build . --target install && rm -rf ${PWD}/install/usr && rmdir ${PWD}/install
43		- sudo cmake --build . --target install
	42	- test -z "${MODULE_BUILD}" && DESTDIR=${PWD}/install cmake --install . && rm -rf ${PWD}/install/usr && rmdir ${PWD}/install
	43	- sudo cmake --install .
44	44	- if [[ ${CLANG_FORMAT} ]]; then cmake --build . --target format && git -C ${CI_PROJECT_DIR}/votca/${CI_PROJECT_NAME} diff --exit-code; fi
45	45	- ccache -s
46	46

50	50	image: votca/buildenv:${DISTRO}
51	51	extends: .build_script
52	52
53		Debug GCC:
54		stage: canary
55		variables:
56		CC: "gcc"
57		CXX: "g++"
58		CMAKE_BUILD_TYPE: "Debug"
59		CLANG_FORMAT: "yes"
60		extends: .build
61
62		None GCC:
63		variables:
64		CC: "gcc"
65		CXX: "g++"
66		CMAKE_BUILD_TYPE: ""
67		extends: .build
68
69		None Clang:
70		variables:
71		CC: "clang"
72		CXX: "clang++"
73		CMAKE_BUILD_TYPE: ""
74		extends: .build
75
76		Debug Clang:
77		variables:
78		CC: "clang"
79		CXX: "clang++"
80		CMAKE_BUILD_TYPE: "Debug"
81		extends: .build
82
83		Release GCC:
84		variables:
85		CC: "gcc"
86		CXX: "g++"
87		CMAKE_BUILD_TYPE: "Release"
88		extends: .build
89
90		Release Clang:
91		variables:
92		CC: "clang"
93		CXX: "clang++"
94		CMAKE_BUILD_TYPE: "Release"
95		extends: .build
96
97		Debug GCC Ubuntu:
98		variables:
99		CC: "gcc"
100		CXX: "g++"
101		CMAKE_BUILD_TYPE: "Debug"
102		DISTRO: "ubuntu"
103		extends: .build
104
105		Debug Clang Ubuntu:
106		variables:
107		CC: "clang"
108		CXX: "clang++"
109		CMAKE_BUILD_TYPE: "Debug"
110		DISTRO: "ubuntu"
111		extends: .build
112
113		Release GCC Ubuntu:
114		variables:
115		CC: "gcc"
116		CXX: "g++"
117		CMAKE_BUILD_TYPE: "Release"
118		DISTRO: "ubuntu"
119		extends: .build
120
121		Release Clang Ubuntu:
122		variables:
123		CC: "clang"
124		CXX: "clang++"
125		CMAKE_BUILD_TYPE: "Release"
126		DISTRO: "ubuntu"
127		extends: .build
128
129		Debug GCC Rawhide:
130		variables:
131		CC: "gcc"
132		CXX: "g++"
133		CMAKE_BUILD_TYPE: "Debug"
134		DISTRO: "fedora_rawhide"
135		extends: .build
136		allow_failure: true
137
138		Debug Clang Rawhide:
139		variables:
140		CC: "clang"
141		CXX: "clang++"
142		CMAKE_BUILD_TYPE: "Debug"
143		DISTRO: "fedora_rawhide"
144		extends: .build
145		allow_failure: true
146
147		Release GCC Rawhide:
148		variables:
149		CC: "gcc"
150		CXX: "g++"
151		CMAKE_BUILD_TYPE: "Release"
152		DISTRO: "fedora_rawhide"
153		extends: .build
154		allow_failure: true
155
156		Release Clang Rawhide:
157		variables:
158		CC: "clang"
159		CXX: "clang++"
160		CMAKE_BUILD_TYPE: "Release"
161		DISTRO: "fedora_rawhide"
162		extends: .build
163		allow_failure: true
164
165		Release GCC Module:
166		variables:
167		CC: "gcc"
168		CXX: "g++"
169		CMAKE_BUILD_TYPE: "Release"
170		MODULE_BUILD: "yes"
171		extends: .build
172
173	53	Debug GPU Ubuntu:
174	54	variables:
175	55	CC: "gcc"
176	56	CXX: "g++"
177	57	CMAKE_BUILD_TYPE: "Debug"
178	58	USE_CUDA: "yes"
179		WITH_MKL: "no"
180	59	DISABLE_MKL: "yes"
181		NO_INSTALL: "yes"
182	60	before_script:
183	61	- source /opt/gromacs-2019/bin/GMXRC.bash
184	62	extends: .build_script

+0

-136

~~.travis.yml~~ less more

0		# the original source of this file can be found in votca/votca repository
1		# add changes there!
2		# To update:
3		# wget -O .travis.yml https://raw.githubusercontent.com/votca/votca/master/.travis.yml
4		language: cpp
5
6		sudo: required
7
8		services:
9		- docker
10
11		git:
12		quiet: true
13
14		stages:
15		- canary
16		- test
17		- deploy
18
19		jobs:
20		include:
21		- stage: canary
22		env: ENV=3
23		- stage: deploy
24		if: repo = votca/votca AND type != pull_request
25		env: ENV=1
26
27		env:
28		matrix:
29		- ENV=1
30		- ENV=2
31		- ENV=3
32		- ENV=4
33		- ENV=5
34		- ENV=6
35		- ENV=7
36		- ENV=8
37		- ENV=9
38		- ENV=10
39		- ENV=11
40		- ENV=12
41		- ENV=13
42		- ENV=14
43		- ENV=15
44		- ENV=16
45		- ENV=17
46		- ENV=18
47		- ENV=19
48		- ENV=20
49
50		before_script:
51		- git checkout -b current_commit
52		- cd ../../
53		- if [[ ${TRAVIS_REPO_SLUG} = */votca ]]; then
54		if [[ ${TRAVIS_BRANCH} = next ]]; then
55		git -C ${TRAVIS_REPO_SLUG} submodule foreach git checkout master;
56		git -C ${TRAVIS_REPO_SLUG} submodule foreach git pull;
57		fi;
58		cp -vr ${TRAVIS_REPO_SLUG}/docker ${HOME};
59		mv -v ${TRAVIS_REPO_SLUG} $HOME/docker;
60		else
61		git clone -q --recursive https://github.com/votca/votca.git $HOME/docker/votca;
62		if [[ ${TRAVIS_BRANCH} != master ]]; then
63		git -C ${HOME}/docker/votca checkout -b ${TRAVIS_BRANCH} ${TRAVIS_TAG:-origin/${TRAVIS_BRANCH}} && git -C ${HOME}/docker/votca submodule update --recursive --init;
64		fi;
65		git -C ${HOME}/docker/votca/${TRAVIS_REPO_SLUG#*/} fetch ${PWD}/${TRAVIS_REPO_SLUG} current_commit;
66		git -C ${HOME}/docker/votca/${TRAVIS_REPO_SLUG#*/} checkout -f FETCH_HEAD;
67		cp -vr ${HOME}/docker/votca/docker/* ${HOME}/docker;
68		if [[ -d ${TRAVIS_REPO_SLUG}/docker ]]; then cp -vr ${TRAVIS_REPO_SLUG}/docker/* ${HOME}/docker; fi;
69		fi
70		- source ${HOME}/docker/set_env.sh
71		- test -n "${SKIP}" \|\| cp -r $HOME/.ccache ${HOME}/docker/ccache
72		- sed -i "1s/latest/${DISTRO:-latest}/" ${HOME}/docker/Dockerfile
73		- if [[ ! ${SKIP} ]]; then
74		travis_retry timeout 540 docker pull $(sed -n '1s/FROM //p' ${HOME}/docker/Dockerfile) \| cat;
75		fi
76
77		script:
78		- if [[ ! ${SKIP} ]]; then
79		travis_retry docker build "${docker_opts[@]}"
80		${TRAVIS_TAG:+-t votca/votca:${TRAVIS_TAG}}
81		-t votca/votca:latest -t votca/votca:${TRAVIS_BRANCH} ${HOME}/docker/ &&
82		rm -rf $HOME/.ccache &&
83		CON=$(docker run -d votca/votca:${TRAVIS_BRANCH} /bin/bash) &&
84		docker cp ${CON}:/home/votca/.ccache ${HOME}/;
85		fi
86
87		after_success:
88		- if [[ ${TRAVIS_REPO_SLUG} != votca/votca \|\| ${TRAVIS_BUILD_STAGE_NAME} != "Deploy" \|\| ${SKIP} ]]; then travis_terminate 0; fi
89		- shopt -s extglob && [[ ${TRAVIS_BRANCH} = @(master\|stable\|v1.*) ]] && DEPLOY=yes
90		- if [[ ${TRAVIS_BRANCH} = master ]]; then DOCKER_TAG=latest; else DOCKER_TAG="${TRAVIS_BRANCH}"; fi
91		- if [[ ${DOCKER_USERNAME} && ${DOCKER_PASSWORD} && ${TRAVIS_PULL_REQUEST} == false && ${DEPLOY} ]]; then
92		docker login -u="$DOCKER_USERNAME" -p="$DOCKER_PASSWORD";
93		docker push "${TRAVIS_REPO_SLUG}:${DOCKER_TAG}";
94		fi
95		- if true; then
96		git clone --depth=1 https://github.com/votca/doxygen.git "$HOME/devdoc";
97		cd $HOME/devdoc;
98		rm -f *;
99		git checkout -- CNAME;
100		docker cp ${CON}:/home/votca/votca/build/share/doc/html . ;
101		mv html/* .; rmdir html;
102		docker cp ${CON}:/home/votca/votca/build/csg-manual/manual.pdf . ;
103		docker cp ${CON}:/home/votca/votca/build/xtp/manual/xtp-manual.pdf . ;
104		git add --all .;
105		if [[ ${TRAVIS_BRANCH} = master && ${encrypted_7abbb71c3ba6_key} && ${encrypted_7abbb71c3ba6_iv} && ${TRAVIS_PULL_REQUEST} == false ]]; then
106		git config --global user.name "Automatic Deployment (Travis CI)";
107		git config --global user.email "votca-commits@googlegroups.com";
108		git commit -m "Documentation Update";
109		openssl aes-256-cbc -K $encrypted_7abbb71c3ba6_key -iv $encrypted_7abbb71c3ba6_iv -in keys/deploy3.enc -out ~/.ssh/id_rsa -d;
110		chmod 600 ~/.ssh/id_rsa;
111		git push git@github.com:votca/doxygen.git gh-pages;
112		else
113		git status;
114		git diff --cached --no-color \| head -c 1k;
115		fi;
116		fi
117
118		branches:
119		only:
120		- master
121		- development
122		- stable
123		- next
124		- /^v\d+\.\d+(\.\d+\|_rc\d+)?$/
125
126		cache:
127		- ccache
128
129		compiler:
130		- gcc
131		- clang
132
133		notifications:
134		email:
135		- votca-commits@googlegroups.com

+5

-0

CHANGELOG.md less more

0	0	For more detailed information about the changes see the history of the
1	1	[repository](https://github.com/votca/xtp/commits/master).
	2
	3	## Version 1.6.2 (released 22.08.20)
	4	* move CI to GitHub Actions (#512, #514, #516, #519)
	5	* add more checks to the dft_parse_part (#521)
	6	* make unit tests work in parallel (#530)
2	7
3	8	## Version 1.6.1 (released 21.06.20)
4	9	* fix warnings on Ubuntu 20.04 (#438, #460)

+1

-1

CMakeLists.txt less more

1	1	project(votca-xtp)
2	2
3	3
4		set(PROJECT_VERSION "1.6.1")
	4	set(PROJECT_VERSION "1.6.2")
5	5	set(PROJECT_CONTACT "bugs@votca.org")
6	6	string(REGEX REPLACE "^[1-9]+\\.([1-9]+).*$" "\\1" SOVERSION "${PROJECT_VERSION}")
7	7	if (NOT ${SOVERSION} MATCHES "[1-9]+")

+1

-1

src/libxtp/jobcalculators/eqm.cc less more

227	227	WriteLoggerToFile(work_dir + "/dft.log", dft_logger);
228	228	}
229	229
230		if (!_do_dft_parse) {
	230	if (!_do_dft_parse && (_do_gwbse \|\| _do_esp)) {
231	231	// load the DFT data from serialized orbitals object
232	232	std::string ORB_FILE =
233	233	eqm_work_dir + "/molecules/" + frame_dir + "/" + orb_file;

+2

-1

src/tests/CMakeLists.txt less more

87	87	add_executable(unit_${PROG} ${PROG}.cc)
88	88	target_link_libraries(unit_${PROG} votca_xtp Boost::unit_test_framework)
89	89	target_compile_definitions(unit_${PROG} PRIVATE BOOST_TEST_DYN_LINK)
90		add_test(unit_${PROG} unit_${PROG})
	90	file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/Run_unit_${PROG})
	91	add_test(NAME unit_${PROG} COMMAND $<TARGET_FILE:unit_${PROG}> WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/Run_unit_${PROG})
91	92	# run tests for xtp (for coverage) as well
92	93	set_tests_properties(unit_${PROG} PROPERTIES LABELS "xtp;votca;unit")
93	94	endforeach(PROG)

+72

-0

tutorials/.github/workflows/continuous-integration-workflow.yml less more

	0	name: CI
	1	on:
	2	pull_request:
	3	branches:
	4	- master
	5	- stable
	6
	7	jobs:
	8	CI:
	9	continue-on-error: ${{ matrix.distro == 'ubuntu_devel' \|\| matrix.distro == 'fedora_rawhide' \|\| matrix.continue-on-error == true }}
	10	strategy:
	11	matrix:
	12	distro: [latest, fedora_rawhide, opensuse, ubuntu, ubuntu_devel, ubuntu_rolling, ubuntu_18.04]
	13	toolchain: [gnu]
	14	cmake_build_type: [Release]
	15	minimal: [false]
	16	own_gmx: [false]
	17	module_build: [false]
	18	coverage: [false]
	19	no_regression_testing: [true]
	20	include:
	21	- distro: latest
	22	toolchain: gnu
	23	cmake_build_type: Release
	24	module_build: true
	25	no_regression_testing: true
	26	runs-on: ubuntu-latest
	27	container: votca/buildenv:${{ matrix.distro }}
	28	steps:
	29	- uses: actions/checkout@v2.2.0
	30	with:
	31	fetch-depth: 0
	32	- name: Run Votca Setup
	33	id: setup
	34	uses: votca/actions/setup@master
	35	with:
	36	distro: ${{ matrix.distro }}
	37	toolchain: ${{ matrix.toolchain }}
	38	minimal: ${{ matrix.minimal == true }}
	39	module: ${{ matrix.module_build == true }}
	40	own_gmx: ${{ matrix.own_gmx == true }}
	41	regression_testing: ${{ matrix.no_regression_testing != true }}
	42	coverage: ${{ matrix.coverage }}
	43	cmake_build_type: ${{ matrix.cmake_build_type }}
	44	ctest_args: ${{ matrix.ctest_args }}
	45	cmake_args: ${{ matrix.cmake_args }}
	46	- uses: actions/cache@v2
	47	with:
	48	path: ~/.ccache
	49	key: ${{ steps.setup.outputs.cache_key }}
	50	restore-keys: ${{ steps.setup.outputs.cache_restore_key }}
	51	- name: CMake
	52	run: mkdir builddir && cd builddir && cmake ${{ steps.setup.outputs.cmake_args }} ../votca
	53	- name: Build
	54	run: \|
	55	ccache -z
	56	cmake --build builddir -- -j ${{ steps.setup.outputs.jobs }}
	57	ccache -s
	58	- name: Tests
	59	run: ctest --output-on-failure ${{ steps.setup.outputs.ctest_args }}
	60	working-directory: builddir
	61	- name: Build Sphinx
	62	if: ${{ steps.setup.outputs.build_sphinx == 'true' }}
	63	run: cmake --build builddir --target doc
	64	- name: Test DESTDIR Install
	65	if: ${{ ! matrix.module_build }}
	66	run: DESTDIR=${PWD}/install cmake --build builddir --target install && rm -rf ${PWD}/install/usr && rmdir ${PWD}/install
	67	- name: Install
	68	run: sudo cmake --build builddir --target install
	69	- name: Check for untracked files
	70	run: git status --porcelain && git status --porcelain \| sed Q1
	71	working-directory: votca/${{ steps.setup.outputs.module }}

+37

-0

tutorials/.github/workflows/create-pr.yml less more

	0	name: Create PR
	1	on:
	2	push:
	3	branches:
	4	- stable
	5
	6	jobs:
	7	PR:
	8	name: Create
	9	if: github.repository_owner == 'votca'
	10	runs-on: ubuntu-latest
	11	steps:
	12	- name: Checkout code
	13	uses: actions/checkout@master
	14	with:
	15	ref: ${{ github.event.ref }}
	16	fetch-depth: 0
	17	token: ${{ secrets.VOTCA_BOT_TOKEN }}
	18	- name: Try to merge master branch
	19	run: \|
	20	git config --global user.name "Votca Bot"
	21	git config --global user.email "github@votca.org"
	22	git checkout -b stable_fixes
	23	git merge origin/master \|\| true
	24	git push origin stable_fixes
	25	- name: Create Pull Request
	26	uses: actions/github-script@0.3.0
	27	with:
	28	github-token: ${{ secrets.VOTCA_BOT_TOKEN }}
	29	script: \|
	30	github.pulls.create({
	31	owner: 'votca',
	32	repo: 'xtp-tutorials',
	33	title: 'Fixes from stable',
	34	head: 'stable_fixes',
	35	base: 'master'
	36	})

+20

-0

tutorials/.github/workflows/create-release.yml less more

	0	name: Make Release
	1	on:
	2	push:
	3	tags:
	4	- 'v[1-9]*'
	5
	6	jobs:
	7	release:
	8	name: Make Release
	9	if: github.repository_owner == 'votca'
	10	runs-on: ubuntu-latest
	11	steps:
	12	- name: Create Release
	13	uses: actions/create-release@v1
	14	env:
	15	GITHUB_TOKEN: ${{ secrets.VOTCA_BOT_TOKEN }}
	16	with:
	17	tag_name: ${{ github.ref }}
	18	release_name: ${{ github.ref }}
	19	prerelease: ${{ contains(github.ref, 'rc') }}

+18

-0

tutorials/.github/workflows/forward-to-votca.yml less more

	0	name: Forward
	1	on:
	2	push:
	3	branches:
	4	- master
	5	- stable
	6
	7	jobs:
	8	VOTCA:
	9	if: github.repository_owner == 'votca'
	10	runs-on: ubuntu-latest
	11	steps:
	12	- name: Update submodule
	13	uses: votca/actions/forward@master
	14	with:
	15	module: ${{ github.repository }}
	16	token: ${{ secrets.VOTCA_BOT_TOKEN }}
	17

+5

-127

tutorials/.gitlab-ci.yml less more

0	0	stages:
1		- canary
2	1	- build
3	2
4	3	.build_script:

34	33	- pushd build
35	34	- cmake .. -DCMAKE_VERBOSE_MAKEFILE=ON -DENABLE_TESTING=ON -DBUILD_XTP=ON -DENABLE_WERROR=ON
36	35	-DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
	36	${CMAKE_GENERATOR:+-G${CMAKE_GENERATOR}}
37	37	-DMODULE_BUILD=${MODULE_BUILD} ${MODULE_BUILD:+-DCMAKE_INSTALL_PREFIX=/home/votca/votca.install}
38		-DWITH_MKL=${WITH_MKL} -DCMAKE_DISABLE_FIND_PACKAGE_MKL=${DISABLE_MKL}
	38	-DCMAKE_DISABLE_FIND_PACKAGE_MKL=${DISABLE_MKL}
39	39	-DUSE_CUDA=${USE_CUDA}
40		- cmake --build . -- -j2
	40	- cmake --build . --parallel 2
41	41	- ctest --output-on-failure
42		- test -z "${MODULE_BUILD}" && DESTDIR=${PWD}/install cmake --build . --target install && rm -rf ${PWD}/install/usr && rmdir ${PWD}/install
43		- sudo cmake --build . --target install
	42	- test -z "${MODULE_BUILD}" && DESTDIR=${PWD}/install cmake --install . && rm -rf ${PWD}/install/usr && rmdir ${PWD}/install
	43	- sudo cmake --install .
44	44	- if [[ ${CLANG_FORMAT} ]]; then cmake --build . --target format && git -C ${CI_PROJECT_DIR}/votca/${CI_PROJECT_NAME} diff --exit-code; fi
45	45	- ccache -s
46	46

50	50	image: votca/buildenv:${DISTRO}
51	51	extends: .build_script
52	52
53		Debug GCC:
54		stage: canary
55		variables:
56		CC: "gcc"
57		CXX: "g++"
58		CMAKE_BUILD_TYPE: "Debug"
59		CLANG_FORMAT: "yes"
60		extends: .build
61
62		None GCC:
63		variables:
64		CC: "gcc"
65		CXX: "g++"
66		CMAKE_BUILD_TYPE: ""
67		extends: .build
68
69		None Clang:
70		variables:
71		CC: "clang"
72		CXX: "clang++"
73		CMAKE_BUILD_TYPE: ""
74		extends: .build
75
76		Debug Clang:
77		variables:
78		CC: "clang"
79		CXX: "clang++"
80		CMAKE_BUILD_TYPE: "Debug"
81		extends: .build
82
83		Release GCC:
84		variables:
85		CC: "gcc"
86		CXX: "g++"
87		CMAKE_BUILD_TYPE: "Release"
88		extends: .build
89
90		Release Clang:
91		variables:
92		CC: "clang"
93		CXX: "clang++"
94		CMAKE_BUILD_TYPE: "Release"
95		extends: .build
96
97		Debug GCC Ubuntu:
98		variables:
99		CC: "gcc"
100		CXX: "g++"
101		CMAKE_BUILD_TYPE: "Debug"
102		DISTRO: "ubuntu"
103		extends: .build
104
105		Debug Clang Ubuntu:
106		variables:
107		CC: "clang"
108		CXX: "clang++"
109		CMAKE_BUILD_TYPE: "Debug"
110		DISTRO: "ubuntu"
111		extends: .build
112
113		Release GCC Ubuntu:
114		variables:
115		CC: "gcc"
116		CXX: "g++"
117		CMAKE_BUILD_TYPE: "Release"
118		DISTRO: "ubuntu"
119		extends: .build
120
121		Release Clang Ubuntu:
122		variables:
123		CC: "clang"
124		CXX: "clang++"
125		CMAKE_BUILD_TYPE: "Release"
126		DISTRO: "ubuntu"
127		extends: .build
128
129		Debug GCC Rawhide:
130		variables:
131		CC: "gcc"
132		CXX: "g++"
133		CMAKE_BUILD_TYPE: "Debug"
134		DISTRO: "fedora_rawhide"
135		extends: .build
136		allow_failure: true
137
138		Debug Clang Rawhide:
139		variables:
140		CC: "clang"
141		CXX: "clang++"
142		CMAKE_BUILD_TYPE: "Debug"
143		DISTRO: "fedora_rawhide"
144		extends: .build
145		allow_failure: true
146
147		Release GCC Rawhide:
148		variables:
149		CC: "gcc"
150		CXX: "g++"
151		CMAKE_BUILD_TYPE: "Release"
152		DISTRO: "fedora_rawhide"
153		extends: .build
154		allow_failure: true
155
156		Release Clang Rawhide:
157		variables:
158		CC: "clang"
159		CXX: "clang++"
160		CMAKE_BUILD_TYPE: "Release"
161		DISTRO: "fedora_rawhide"
162		extends: .build
163		allow_failure: true
164
165		Release GCC Module:
166		variables:
167		CC: "gcc"
168		CXX: "g++"
169		CMAKE_BUILD_TYPE: "Release"
170		MODULE_BUILD: "yes"
171		extends: .build
172
173	53	Debug GPU Ubuntu:
174	54	variables:
175	55	CC: "gcc"
176	56	CXX: "g++"
177	57	CMAKE_BUILD_TYPE: "Debug"
178	58	USE_CUDA: "yes"
179		WITH_MKL: "no"
180	59	DISABLE_MKL: "yes"
181		NO_INSTALL: "yes"
182	60	before_script:
183	61	- source /opt/gromacs-2019/bin/GMXRC.bash
184	62	extends: .build_script

+0

-136

~~tutorials/.travis.yml~~ less more

0		# the original source of this file can be found in votca/votca repository
1		# add changes there!
2		# To update:
3		# wget -O .travis.yml https://raw.githubusercontent.com/votca/votca/master/.travis.yml
4		language: cpp
5
6		sudo: required
7
8		services:
9		- docker
10
11		git:
12		quiet: true
13
14		stages:
15		- canary
16		- test
17		- deploy
18
19		jobs:
20		include:
21		- stage: canary
22		env: ENV=3
23		- stage: deploy
24		if: repo = votca/votca AND type != pull_request
25		env: ENV=1
26
27		env:
28		matrix:
29		- ENV=1
30		- ENV=2
31		- ENV=3
32		- ENV=4
33		- ENV=5
34		- ENV=6
35		- ENV=7
36		- ENV=8
37		- ENV=9
38		- ENV=10
39		- ENV=11
40		- ENV=12
41		- ENV=13
42		- ENV=14
43		- ENV=15
44		- ENV=16
45		- ENV=17
46		- ENV=18
47		- ENV=19
48		- ENV=20
49
50		before_script:
51		- git checkout -b current_commit
52		- cd ../../
53		- if [[ ${TRAVIS_REPO_SLUG} = */votca ]]; then
54		if [[ ${TRAVIS_BRANCH} = next ]]; then
55		git -C ${TRAVIS_REPO_SLUG} submodule foreach git checkout master;
56		git -C ${TRAVIS_REPO_SLUG} submodule foreach git pull;
57		fi;
58		cp -vr ${TRAVIS_REPO_SLUG}/docker ${HOME};
59		mv -v ${TRAVIS_REPO_SLUG} $HOME/docker;
60		else
61		git clone -q --recursive https://github.com/votca/votca.git $HOME/docker/votca;
62		if [[ ${TRAVIS_BRANCH} != master ]]; then
63		git -C ${HOME}/docker/votca checkout -b ${TRAVIS_BRANCH} ${TRAVIS_TAG:-origin/${TRAVIS_BRANCH}} && git -C ${HOME}/docker/votca submodule update --recursive --init;
64		fi;
65		git -C ${HOME}/docker/votca/${TRAVIS_REPO_SLUG#*/} fetch ${PWD}/${TRAVIS_REPO_SLUG} current_commit;
66		git -C ${HOME}/docker/votca/${TRAVIS_REPO_SLUG#*/} checkout -f FETCH_HEAD;
67		cp -vr ${HOME}/docker/votca/docker/* ${HOME}/docker;
68		if [[ -d ${TRAVIS_REPO_SLUG}/docker ]]; then cp -vr ${TRAVIS_REPO_SLUG}/docker/* ${HOME}/docker; fi;
69		fi
70		- source ${HOME}/docker/set_env.sh
71		- test -n "${SKIP}" \|\| cp -r $HOME/.ccache ${HOME}/docker/ccache
72		- sed -i "1s/latest/${DISTRO:-latest}/" ${HOME}/docker/Dockerfile
73		- if [[ ! ${SKIP} ]]; then
74		travis_retry timeout 540 docker pull $(sed -n '1s/FROM //p' ${HOME}/docker/Dockerfile) \| cat;
75		fi
76
77		script:
78		- if [[ ! ${SKIP} ]]; then
79		travis_retry docker build "${docker_opts[@]}"
80		${TRAVIS_TAG:+-t votca/votca:${TRAVIS_TAG}}
81		-t votca/votca:latest -t votca/votca:${TRAVIS_BRANCH} ${HOME}/docker/ &&
82		rm -rf $HOME/.ccache &&
83		CON=$(docker run -d votca/votca:${TRAVIS_BRANCH} /bin/bash) &&
84		docker cp ${CON}:/home/votca/.ccache ${HOME}/;
85		fi
86
87		after_success:
88		- if [[ ${TRAVIS_REPO_SLUG} != votca/votca \|\| ${TRAVIS_BUILD_STAGE_NAME} != "Deploy" \|\| ${SKIP} ]]; then travis_terminate 0; fi
89		- shopt -s extglob && [[ ${TRAVIS_BRANCH} = @(master\|stable\|v1.*) ]] && DEPLOY=yes
90		- if [[ ${TRAVIS_BRANCH} = master ]]; then DOCKER_TAG=latest; else DOCKER_TAG="${TRAVIS_BRANCH}"; fi
91		- if [[ ${DOCKER_USERNAME} && ${DOCKER_PASSWORD} && ${TRAVIS_PULL_REQUEST} == false && ${DEPLOY} ]]; then
92		docker login -u="$DOCKER_USERNAME" -p="$DOCKER_PASSWORD";
93		docker push "${TRAVIS_REPO_SLUG}:${DOCKER_TAG}";
94		fi
95		- if true; then
96		git clone --depth=1 https://github.com/votca/doxygen.git "$HOME/devdoc";
97		cd $HOME/devdoc;
98		rm -f *;
99		git checkout -- CNAME;
100		docker cp ${CON}:/home/votca/votca/build/share/doc/html . ;
101		mv html/* .; rmdir html;
102		docker cp ${CON}:/home/votca/votca/build/csg-manual/manual.pdf . ;
103		docker cp ${CON}:/home/votca/votca/build/xtp/manual/xtp-manual.pdf . ;
104		git add --all .;
105		if [[ ${TRAVIS_BRANCH} = master && ${encrypted_7abbb71c3ba6_key} && ${encrypted_7abbb71c3ba6_iv} && ${TRAVIS_PULL_REQUEST} == false ]]; then
106		git config --global user.name "Automatic Deployment (Travis CI)";
107		git config --global user.email "votca-commits@googlegroups.com";
108		git commit -m "Documentation Update";
109		openssl aes-256-cbc -K $encrypted_7abbb71c3ba6_key -iv $encrypted_7abbb71c3ba6_iv -in keys/deploy3.enc -out ~/.ssh/id_rsa -d;
110		chmod 600 ~/.ssh/id_rsa;
111		git push git@github.com:votca/doxygen.git gh-pages;
112		else
113		git status;
114		git diff --cached --no-color \| head -c 1k;
115		fi;
116		fi
117
118		branches:
119		only:
120		- master
121		- development
122		- stable
123		- next
124		- /^v\d+\.\d+(\.\d+\|_rc\d+)?$/
125
126		cache:
127		- ccache
128
129		compiler:
130		- gcc
131		- clang
132
133		notifications:
134		email:
135		- votca-commits@googlegroups.com

+1

-1

tutorials/CMakeLists.txt less more

1	1
2	2	project(xtp-tutorials)
3	3
4		set(PROJECT_VERSION "1.6.1")
	4	set(PROJECT_VERSION "1.6.2")
5	5
6	6	set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules)
7	7	include(GNUInstallDirs)

+20

-0

tutorials/GROMACS/Methane/QC_FILES/g09/anion_geo/polar/molpol.xml~ less more

	0	<options>
	1	<molpol help="Molecular polarizability calculator (and optimizer)" label="tool:molpol">
	2	<mpsfiles>
	3	<input help="mps input file">CH4_i.mps</input>
	4	<output help="mps output file">CH4_i.mps</output>
	5	<polar help="xml file with infos on polarizability tensor">output.xml</polar>
	6	</mpsfiles>
	7	<induction>
	8	<expdamp help="Thole sharpness parameter">0.39000</expdamp>
	9	<wSOR help="mixing factor for convergence">0.35000</wSOR>
	10	<maxiter help="maximum number of iterations">1024</maxiter>
	11	<tolerance help="rel. tolerance for induced moments">0.00001</tolerance>
	12	</induction>
	13	<target>
	14	<optimize help="if 'true', refine atomic polarizabilities to match molecular polarizable volume specified in target.molpol">true</optimize>
	15	<molpol help="target polarizability tensor in format xx xy xz yy yz zz (this should be in the eigen-frame, hence xy = xz = yz = 0), if optimize=true the associated polarizable volume will be matched iteratively and the resulting set of polar sites written to mpsfiles.output">2.3191 0.0 0.0 2.3199 0.0 2.3204</molpol>
	16	<tolerance help="relative tolerance when optimizing the polarizable volume">0.00001</tolerance>
	17	</target>
	18	</molpol>
	19	</options>

+20

-0

tutorials/GROMACS/Methane/QC_FILES/g09/cation_geo/polar/molpol.xml~ less more

	0	<options>
	1	<molpol help="Molecular polarizability calculator (and optimizer)" label="tool:molpol">
	2	<mpsfiles>
	3	<input help="mps input file">CH4_h.mps</input>
	4	<output help="mps output file">CH4_h.mps</output>
	5	<polar help="xml file with infos on polarizability tensor">output.xml</polar>
	6	</mpsfiles>
	7	<induction>
	8	<expdamp help="Thole sharpness parameter">0.39000</expdamp>
	9	<wSOR help="mixing factor for convergence">0.35000</wSOR>
	10	<maxiter help="maximum number of iterations">1024</maxiter>
	11	<tolerance help="rel. tolerance for induced moments">0.00001</tolerance>
	12	</induction>
	13	<target>
	14	<optimize help="if 'true', refine atomic polarizabilities to match molecular polarizable volume specified in target.molpol">true</optimize>
	15	<molpol help="target polarizability tensor in format xx xy xz yy yz zz (this should be in the eigen-frame, hence xy = xz = yz = 0), if optimize=true the associated polarizable volume will be matched iteratively and the resulting set of polar sites written to mpsfiles.output">1.4451 0.0 0.0 2.0267 0.0 2.0267</molpol>
	16	<tolerance help="relative tolerance when optimizing the polarizable volume">0.00001</tolerance>
	17	</target>
	18	</molpol>
	19	</options>

+20

-0

tutorials/GROMACS/Methane/QC_FILES/g09/neutral_geo/polar/molpol.xml~ less more

	0	<options>
	1	<molpol help="Molecular polarizability calculator (and optimizer)" label="tool:molpol">
	2	<mpsfiles>
	3	<input help="mps input file">CH4_n.mps</input>
	4	<output help="mps output file">CH4_n.mps</output>
	5	<polar help="xml file with infos on polarizability tensor">output.xml</polar>
	6	</mpsfiles>
	7	<induction>
	8	<expdamp help="Thole sharpness parameter">0.39000</expdamp>
	9	<wSOR help="mixing factor for convergence">0.35000</wSOR>
	10	<maxiter help="maximum number of iterations">1024</maxiter>
	11	<tolerance help="rel. tolerance for induced moments">0.00001</tolerance>
	12	</induction>
	13	<target>
	14	<optimize help="if 'true', refine atomic polarizabilities to match molecular polarizable volume specified in target.molpol">true</optimize>
	15	<molpol help="target polarizability tensor in format xx xy xz yy yz zz (this should be in the eigen-frame, hence xy = xz = yz = 0), if optimize=true the associated polarizable volume will be matched iteratively and the resulting set of polar sites written to mpsfiles.output">2.3191 0.0 0.0 2.3199 0.0 2.3204</molpol>
	16	<tolerance help="relative tolerance when optimizing the polarizable volume">0.00001</tolerance>
	17	</target>
	18	</molpol>
	19	</options>