Commit d0bbc744969133b025f37ae52a29cd8fb3a82a54 - votca-xtp

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~~.clang-format~~ less more

0		---
1		# BasedOnStyle: Google
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18		ExperimentalAutoDetectBinPacking: false
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43		SpaceBeforeAssignmentOperators: true
44		ContinuationIndentWidth: 4
45		...
46

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~~.codecov.yml~~ less more

0		coverage:
1		precision: 1
2		round: down
3		range: "70...100"
4		ignore:
5		- /usr/include/
6		- src/tests/

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~~.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 }}

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~~.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: ${{ matrix.distro == 'ubuntu:devel' \|\| matrix.distro == 'opensuse:latest' \|\| matrix.distro == 'fedora:rawhide' \|\| matrix.continue-on-error == true }}
10		strategy:
11		matrix:
12		distro: ['fedora:latest', 'fedora:rawhide', 'opensuse:latest', 'ubuntu:latest', 'ubuntu:devel', 'ubuntu:rolling', 'ubuntu:18.04', 'fedora:intel']
13		toolchain: [gnu, clang]
14		cmake_build_type: [Release, Debug]
15		minimal: [false]
16		own_gmx: [false]
17		module_build: [false]
18		coverage: [false]
19		no_regression_testing: [true]
20		include:
21		- distro: 'fedora:latest'
22		toolchain: gnu
23		cmake_build_type: Release
24		module_build: true
25		no_regression_testing: true
26		runs-on: ubuntu-latest
27		container: ghcr.io/votca/buildenv/${{ 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

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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		})

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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'

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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: ghcr.io/votca/buildenv/format:latest
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: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
37		run: \|
38		curl -OL https://github.com/votca/votca/raw/master/.clang-format
39		find . -type f -regex ".*\.$c\\|h\\|cc\\|cpp\\|hpp$" -print0 \| xargs -0 clang-format -i -style=file
40		- name: Commit and push
41		if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
42		run: \|
43		git config --global user.name "Votca Bot"
44		git config --global user.email "github@votca.org"
45		git add -u
46		git commit -m "Format code using $(clang-format --version)" \|\| true
47		git push

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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

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~~.gitignore~~ less more

0		*~
1		Makefile
2
3		libvotca*.a
4		libvotca*.so
5		libvotca.so.
6
7		share/doc/html
8		share/doc/Doxyfile
9
10		include/votca/xtp/votca_config.h
11		src/libxtp/gitversion.h
12		include/votca/xtp/votca_config.h
13
14		src/tools/xtp_dump
15		src/tools/xtp_parallel
16		src/tools/xtp_map
17		src/tools/xtp_run
18		src/tools/xtp_tools
19		src/tools/xtp_overlap
20		src/tools/xtp_kmc_run
21		src/dipro/*.mod
22		src/dipro/*.x
23		src/tools/*.man
24
25		scripts/xtp_dipro.out
26		scripts/xtp_dipro
27		scripts/xtp_update
28		scripts/xtp_update.out
29		scripts/xtp_testsuite
30		scripts/xtp_testsuite.out
31		scripts/xtp_update_exciton
32		scripts/xtp_update_exciton.out
33		scripts/xtp_basisset
34		scripts/xtp_basisset.out
35		scripts/xtp_makeauxbasis
36		scripts/xtp_makeauxbasis.out
37
38		netbeans
39		.dep.inc
40		*/nbproject/private
41
42		CMakeFiles
43		cmake_install.cmake
44		CMakeCache.txt
45		install_manifest.txt
46
47		/build

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~~CHANGELOG.md~~ less more

0		For more detailed information about the changes see the history of the
1		[repository](https://github.com/votca/xtp/commits/master).
2
3		## Version 1.6.4 (released 12.01.21)
4		* fix build on openSUSE (#622)
5		* Refactored logger (#625)
6
7		## Version 1.6.3 (released 09.12.20)
8		* switch to ghcr.io for CI (#555)
9		* fixing Gaussian guess read keyword (#562, #563)
10		* improved kmc output (#575)
11		* use master .clang-format in format action (#582, #584)
12		* strip windows line endings in readers (#596)
13
14		## Version 1.6.2 _SuperGitta_ (released 22.08.20)
15		* move CI to GitHub Actions (#512, #514, #516, #519)
16		* add more checks to the dft_parse_part (#521)
17		* make unit tests work in parallel (#530)
18
19		## Version 1.6.1 (released 21.06.20)
20		* fix warnings on Ubuntu 20.04 (#438, #460)
21		* remove obsolete boost define (#440)
22
23		## Version 1.6 _SuperPelagia_ (released 17.04.20)
24		* fix 32-bit build (#381, #380)
25		* remove duplicated basissets (#384, #386, #387)
26		* fix clang-10 warnings (#394)
27		* fix unit_test_eeinteractor on OpenSUSE (#341, #428)
28
29		## Version 1.6_rc2 (released 10.02.20)
30		* fix remove giant logo from tarball (#337)
31		* fix assertions related to GLIBCXX_ASSERTIONS (#345)
32		* remove unused boost serialisation (#346)
33		* fix build on 32-bit archs (#347)
34		* add ENABLE_HIGH_MEMORY_TESTS cmake option (#356)
35		* fix copyright (#363)
36		* remove old doxygen target (#365)
37		* fix some gcc10 warnings (#376)
38		* Add external fields to dft calculations (#351, #353)
39		* added def2 and cc basis sets (#355)
40		* added apdft (#350)
41		* added test to cubefile reader (#344)
42		* fix state tracker (#333)
43		* grid class refator (#335)
44		* changed ppm screening (#371)
45
46		## Version 1.6_rc1 (released 04.12.19)
47		* completely new statefile in hdf5 format for larger systems
48		* new electrostatics with PCG solver
49		* new QM/MM engine with freely configurable regions
50		* exact GW-BSE for small systems
51		* new iterative matrix solvers for large systems
52		* CUDA support for parts of GW-BSE
53		* full LAMMPS support
54		* improved testing
55		* new tutorial with more functionality
56		* deleted netbeans support
57		* removed old manual
58		* Major CMake refactor
59
60		## Version 1.5.1 (released 20.11.19)
61		* remove exit() calls in the library
62		* fix build on CentOs7
63
64		## Version 1.5 _SuperVictor_ (released 31.01.19)
65		* enable gitlab CI
66
67		## Version 1.5_rc3 (released 19.01.19)
68		* travis: fixed bug in building tags
69
70		## Version 1.5_rc2 (released 16.01.19)
71		* fix parallel build of manual
72		* fix usage on inkscape on arm arch
73		* clean up namespace in header
74
75		## Version 1.5_rc1 (released 28.12.18)
76		* optimized GW-BSE code and integral engine
77		* added closed shell DFT code which supports hybrid functionals
78		* removed ctp dependency
79		* atm no support for site energy calculation
80		* CHELPG fit for ground and excited states
81		* merged igwbse and idft into one calculator
82		* added unit and integration test
83		* improved geometry optimiser
84		* replaced ublas with Eigen3
85		* replaced boost serialisation with hdf5 files
86
87		## Version 1.4.1 (released 02.09.17)
88
89		* fix pkg-config file
90
91		## Version 1.4 (released 29.10.16)
92
93		* fixed a bug in gwbse
94		* added missing copyright
95		* cmake: fixed underlinking
96
97		## Version 1.4_rc1 (released 26.09.16)
98
99		* include manual
100		* an extension of the whole workflow from: electrons and holes, to singlet and triplet excitons
101		* a fully functional GW-BSE code optimized for: molecular properties, including excited state geometry optimizsation
102		* Inclusion of LIBXC to calculate Exchange correlation matrices
103		* allowing interfacing GW-BSE with many quantum mechanical packages
104		* support for ORCA DFT package
105		* framework to use stochastic models to generate larger system
106		* better performance of larger systems
107		* new calculators: egwbse,igwbse,ewald,.....
108		* support for intel mkl library and compilers for better performance
109		* A periodic polarisation embedding: to calculate classical configuration energies without cutoffs
110		* xtp_update_exciton to update state file to newest format
111		* integration of moo and kmc into xtp for easier installation
112		* kmc_lifetime calculator to simulate exciton movement with lifetimes
113		* partialcharges to extract atomic charges from qm calculation
114		* renaming from ctp to xtp
115		* many bugfixes
116
117		## Version 1.3 (released XX.09.15)
118
119		* new executables: ctp_tools, ctp_dump, ctp_parallel, xtp_testsuite, xtp_update
120		* ctp_tools wraps light-weight tools that assist e.g. in generating the system mapping file
121		* ctp_dump extracts information from the state file to human-readable format
122		* ctp_parallel wraps heavy-duty job-based calculators: allows synchronization across processes
123		* ctp_testsuite provides an easy-to-use environment to run: selected tests, individual calculators
124		* ctp_update updates an existent state file to the current version
125		* new calculators: edft, idft, pdb2map, xqmultipole, ...
126		* edft / idft: provide interfaces to the GAUSSIAN, TURBOMOLE & NWCHEM package, using packages computes: couplings, internal energies, partial charges
127		* pdb2map (generates a system mapping file from an input coordinate file)
128		* xqmultipole computes classical configuration energies of: charged clusters embedded in a molecular environment
129		* enhanced usability via the command-line help, tutorial & test-suite
130		* a GUI tutorial assists with the first practical steps in using VOTCA-CTP
131		* an extended and homogenized help system provides: short infos on individual calculator options from the command line
132
133		## Version 1.0 (released 23.10.11)
134
135		* parallel evaluation of site energies using: Thole model + GDMA - Tinker no longer required
136		* much clearer input files (and many more checks for input errors)
137		* most of calculators are parallel and can be used on a cluster
138		* bug in zindo/ctp interface fixed
139		* state file now contains: the atomistic trajectory, rigid fragments, conjugated segments
140		* support for several MD frames

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CHANGELOG.rst less more

	0	For more detailed information about the changes see the history of the
	1	`repository <https://github.com/votca/xtp/commits/master>`__.
	2
	3	Version 2021 (released 13.03.21)
	4	================================
	5
	6	- fix CI on rawhide (#663)
	7	- add xtp_qmmm2qm to cmake install (#665)
	8	- add auto-cancel workflow to GitHub Actions (#674)
	9
	10	Version 2021-rc.1 (released 13.03.21)
	11	=====================================
	12
	13	- G0W0 rpa energies are fixed in BSE (#383)
	14	- Hqp part of BSE can be separate from QP range (#388)
	15	- Fixed Cuda implementation (#391)
	16	- Plain, linear, and Anderson mixing in evGW
	17	- Use a general syntax to represent all QMPackages input (#318)
	18	- Remove support for both Gaussian and NWChem (#318)
	19	- Fixed executable path check (#400)
	20	- Usage of offdiagonal elements of Hqp in BSE optional, default: with
	21	offdiagonals (#402)
	22	- refactored MO reordering of external QMPackages (#406)
	23	- Add defaults to XML (#319, #413)
	24	- fix build with gcc-10 (#422, #424)
	25	- Add name command line argument (#426)
	26	- fix usage of PROJECT\_SOURCE\_DIR in cmake (#431)
	27	- check that temperature is positive for KMC (#432)
	28	- document cmake options and packages (#434)
	29	- remove long gone MKL option for gitlab-ci (#435)
	30	- add documentation using Sphinx (#433, #615)
	31	- add kokkos-based Ewald solver (#444, #446, #485)
	32	- allow multiple choices for the calculator options (#442, #445)
	33	- move bsecoupling defaults to xml (#451)
	34	- address missing includes (#452)
	35	- fix readjobfiles path (#453)
	36	- standardising include order and style in header files (#448)
	37	- changed to OpenMP reductions instead of hand crafted solutions (#466,
	38	#471, #493)
	39	- switch to GitHub Actions as CI (#467, #474, #477, #482, #500, #502,
	40	#518, #549, #637)
	41	- move tutorial to its own repo (#450)
	42	- removed share/packages folder (#475)
	43	- copy orca \*.gbw files in eqm (#472)
	44	- improve mkl support (#479)
	45	- add def2-tzvp, def2-tzvpp, def2-qzvp, def2-qzvpp for Rb,I,Ag,Xe
	46	(#480)
	47	- create a map between orca and libxc functional names (#461)
	48	- fix path to share/data (#486, #487)
	49	- remove special XML symbols (#488)
	50	- standardize includes in src files (#462)
	51	- add cmake exported target (#489)
	52	- update codacy badge (#490)
	53	- add mkl builds to CI (#496)
	54	- convert markdown to rst (#497)
	55	- enable CXX only in CMake (#499)
	56	- implement RPA correlation energy (#498)
	57	- added verbose option for rootfinder (#503)
	58	- fix orca pointcharges (#504)
	59	- remove constant cutoff from neighborlist (#508, #509)
	60	- fix default and flags properties issue (#511)
	61	- add more checks to the dft_parse_part (#510)
	62	- add NOSCF option for iqm in internal and external DFT (#483)
	63	- added versions to output files (#523)
	64	- write an empty state file if it does not exist yet (#526)
	65	- fix double unit conversion (#531)
	66	- Unittests can read input and reference values from files (#529)
	67	- fix double SCF in ORCA keyword line (#533)
	68	- xtp internally uses only single shells. (#539)
	69	- Refactor orbital reordering (#537)
	70	- fix build with clang-11 (#546)
	71	- Add a molden parser to xtp (#547)
	72	- Correct self-energy frequency derivative (#550)
	73	- fix multiline orca keyword (#552)
	74	- Contour Deformation Approach (CDA) for self-energy implemented (#4, #548)
	75	- BSE with perturbative dynamical screening (#3, #560)
	76	- Correction of full BSE energy contribution in analysis output (#560)
	77	- Bump required CMake version to 3.12 (#568)
	78	- Refactored calculator interface (#570)
	79	- Fixed boost test deprecation warnings (#569)
	80	- Refactored CUDA-OpenMP integration (#571)
	81	- replaced own integrals with the libint library (#559)
	82	- improved kmc output (#574)
	83	- fix build on Ubuntu 16.04 (#577)
	84	- use unique_ptr in factory (#581)
	85	- fix QMMM with QP (#590, #591)
	86	- fix bug in setCenter of AODipole (#593)
	87	- extra check in orca unit test (#594)
	88	- fixed atomid numbering while adding containers (#599)
	89	- added tool for automatic mapping file generation (#595)
	90	- Added GPU support for RPA (#601)
	91	- fixed int64 interface to RDKIT (#602)
	92	- remove kokkos dependent ewald (#612)
	93	- fixed Sphinx warnings (#609)
	94	- better error for exceeded angular momentum in libint (#613)
	95	- fixed wrong QP-QMMM energy with non-zero QPmin (#620)
	96	- fixed density analysis options (#627)
	97	- Use libint transformation matrices (#630)
	98	- Added script to extract orbitals from qmmm statefile (#629)
	99	- clean up XTP app message (#631)
	100	- fixed EXX 3c mode (#640)
	101
	102	Version 1.6.4 (released 12.01.21)
	103	=================================
	104
	105	- fix build on openSUSE (#622)
	106	- refactored logger (#625)
	107
	108	Version 1.6.3 (released 09.12.20)
	109	=================================
	110
	111	- switch to ghcr.io for CI (#555)
	112	- fixing Gaussian guess read keyword (#562, #563)
	113	- improved kmc output (#575)
	114	- use master .clang-format in format action (#582, #584)
	115	- strip windows line endings in readers (#596)
	116
	117	Version 1.6.2 SuperGitta (released 22.08.20)
	118	=================================
	119
	120	- move CI to GitHub Actions (#512, #514, #516,
	121	#519)
	122	- add more checks to the dft_parse_part (#521)
	123	- make unit tests work in parallel (#530)
	124
	125	Version 1.6.1 (released 21.06.20)
	126	=================================
	127
	128	- fix warnings on Ubuntu 20.04 (#438, #460)
	129	- remove obsolete boost define (#440)
	130
	131	Version 1.6 SuperPelagia (released 17.04.20)
	132	==============================================
	133
	134	- fix 32-bit build (#381, #380)
	135	- remove duplicated basissets (#384, #386, #387)
	136	- fix clang-10 warnings (#394)
	137	- fix unit\_test\_eeinteractor on OpenSUSE (#341, #428)
	138
	139	Version 1.6\_rc2 (released 10.02.20)
	140	====================================
	141
	142	- fix remove giant logo from tarball (#337)
	143	- fix assertions related to GLIBCXX\_ASSERTIONS (#345)
	144	- remove unused boost serialisation (#346)
	145	- fix build on 32-bit archs (#347)
	146	- add ENABLE\_HIGH\_MEMORY\_TESTS cmake option (#356)
	147	- fix copyright (#363)
	148	- remove old doxygen target (#365)
	149	- fix some gcc10 warnings (#376)
	150	- Add external fields to dft calculations (#351, #353)
	151	- added def2 and cc basis sets (#355)
	152	- added apdft (#350)
	153	- added test to cubefile reader (#344)
	154	- fix state tracker (#333)
	155	- grid class refator (#335)
	156	- changed ppm screening (#371)
	157
	158	Version 1.6\_rc1 (released 04.12.19)
	159	====================================
	160
	161	- completely new statefile in hdf5 format for larger systems
	162	- new electrostatics with PCG solver
	163	- new QM/MM engine with freely configurable regions
	164	- exact GW-BSE for small systems
	165	- new iterative matrix solvers for large systems
	166	- CUDA support for parts of GW-BSE
	167	- full LAMMPS support
	168	- improved testing
	169	- new tutorial with more functionality
	170	- deleted netbeans support
	171	- removed old manual
	172	- Major CMake refactor
	173
	174	Version 1.5.1 (released 20.11.19)
	175	=================================
	176
	177	- remove exit() calls in the library
	178	- fix build on CentOs7
	179
	180	Version 1.5 SuperVictor (released 31.01.19)
	181	=============================================
	182
	183	- enable gitlab CI
	184
	185	Version 1.5\_rc3 (released 19.01.19)
	186	====================================
	187
	188	- travis: fixed bug in building tags
	189
	190	Version 1.5\_rc2 (released 16.01.19)
	191	====================================
	192
	193	- fix parallel build of manual
	194	- fix usage on inkscape on arm arch
	195	- clean up namespace in header
	196
	197	Version 1.5\_rc1 (released 28.12.18)
	198	====================================
	199
	200	- optimized GW-BSE code and integral engine
	201	- added closed shell DFT code which supports hybrid functionals
	202	- removed ctp dependency
	203	- atm no support for site energy calculation
	204	- CHELPG fit for ground and excited states
	205	- merged igwbse and idft into one calculator
	206	- added unit and integration test
	207	- improved geometry optimiser
	208	- replaced ublas with Eigen3
	209	- replaced boost serialisation with hdf5 files
	210
	211	Version 1.4.1 (released 02.09.17)
	212	=================================
	213
	214	- fix pkg-config file
	215
	216	Version 1.4 (released 29.10.16)
	217	===============================
	218
	219	- fixed a bug in gwbse
	220	- added missing copyright
	221	- cmake: fixed underlinking
	222
	223	Version 1.4\_rc1 (released 26.09.16)
	224	====================================
	225
	226	- include manual
	227	- an extension of the whole workflow from: electrons and holes, to
	228	singlet and triplet excitons
	229	- a fully functional GW-BSE code optimized for: molecular properties,
	230	including excited state geometry optimizsation
	231	- Inclusion of LIBXC to calculate Exchange correlation matrices
	232	- allowing interfacing GW-BSE with many quantum mechanical packages
	233	- support for ORCA DFT package
	234	- framework to use stochastic models to generate larger system
	235	- better performance of larger systems
	236	- new calculators: egwbse,igwbse,ewald,.....
	237	- support for intel mkl library and compilers for better performance
	238	- A periodic polarisation embedding: to calculate classical
	239	configuration energies without cutoffs
	240	- xtp\_update\_exciton to update state file to newest format
	241	- integration of moo and kmc into xtp for easier installation
	242	- kmc\_lifetime calculator to simulate exciton movement with lifetimes
	243	- partialcharges to extract atomic charges from qm calculation
	244	- renaming from ctp to xtp
	245	- many bugfixes
	246
	247	Version 1.3 (released XX.09.15)
	248	===============================
	249
	250	- new executables: ctp\_tools, ctp\_dump, ctp\_parallel,
	251	xtp\_testsuite, xtp\_update
	252	- ctp\_tools wraps light-weight tools that assist e.g. in generating
	253	the system mapping file
	254	- ctp\_dump extracts information from the state file to human-readable
	255	format
	256	- ctp\_parallel wraps heavy-duty job-based calculators: allows
	257	synchronization across processes
	258	- ctp\_testsuite provides an easy-to-use environment to run: selected
	259	tests, individual calculators
	260	- ctp\_update updates an existent state file to the current version
	261	- new calculators: edft, idft, pdb2map, xqmultipole, ...
	262	- edft / idft: provide interfaces to the GAUSSIAN, TURBOMOLE & NWCHEM
	263	package, using packages computes: couplings, internal energies,
	264	partial charges
	265	- pdb2map (generates a system mapping file from an input coordinate
	266	file)
	267	- xqmultipole computes classical configuration energies of: charged
	268	clusters embedded in a molecular environment
	269	- enhanced usability via the command-line help, tutorial & test-suite
	270	- a GUI tutorial assists with the first practical steps in using
	271	VOTCA-CTP
	272	- an extended and homogenized help system provides: short infos on
	273	individual calculator options from the command line
	274
	275	Version 1.0 (released 23.10.11)
	276	===============================
	277
	278	- parallel evaluation of site energies using: Thole model + GDMA -
	279	Tinker no longer required
	280	- much clearer input files (and many more checks for input errors)
	281	- most of calculators are parallel and can be used on a cluster
	282	- bug in zindo/ctp interface fixed
	283	- state file now contains: the atomistic trajectory, rigid fragments,
	284	conjugated segments
	285	- support for several MD frames

+39

-31

CMakeLists.txt less more

0		cmake_minimum_required(VERSION 3.10)
1		project(votca-xtp)
	0	cmake_minimum_required(VERSION 3.12)
	1	project(votca-xtp LANGUAGES CXX)
2	2
3
4		set(PROJECT_VERSION "1.6.4")
5		set(PROJECT_CONTACT "bugs@votca.org")
6		string(REGEX REPLACE "^[1-9]+\\.([1-9]+).*$" "\\1" SOVERSION "${PROJECT_VERSION}")
7		if (NOT ${SOVERSION} MATCHES "[1-9]+")
8		message(FATAL_ERROR "Could not determind SOVERSION from ${PROJECT_VERSION}")
9		endif (NOT ${SOVERSION} MATCHES "[1-9]+")
	3	set(PROJECT_VERSION "2021")
	4	string(REGEX REPLACE "[-.].*$" "" SOVERSION "${PROJECT_VERSION}")
	5	if (NOT ${SOVERSION} MATCHES "^[0-9]+$")
	6	message(FATAL_ERROR "Could not determine SOVERSION (${SOVERSION}) from ${PROJECT_VERSION}")
	7	endif (NOT ${SOVERSION} MATCHES "^[0-9]+$")
	8	set(PROJECT_CONTACT "https://github.com/votca/xtp/issues")
10	9
11	10	# Cmake modules/macros are in a subdirectory to keep this file cleaner
12	11	set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules)

19	18	add_definitions(-DDEBUG)
20	19	endif()
21	20
22		enable_language(CXX)
23
24	21	######################################################################
25	22	# compiler tests
26	23	# these need ot be done early (before further tests).
27	24	#####################################################################
28	25
	26	include(FeatureSummary)
29	27	include(CheckCXXCompilerFlag)
30	28	set(CMAKE_CXX_STANDARD 14)
31	29	set(CMAKE_CXX_STANDARD_REQUIRED ON)
32	30	set(CMAKE_CXX_EXTENSIONS OFF) #...without compiler extensions like gnu++11
33	31
34		find_package(OpenMP)
35		if (OPENMP_FOUND)
36		set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
37		set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
	32	#openmp with clang smaller version 10 and user defined reductions is buggy https://bugs.llvm.org/show_bug.cgi?id=44134
	33	if (NOT CMAKE_CXX_COMPILER_ID STREQUAL "Clang" OR CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)
	34	find_package(OpenMP 4.5)
	35	set_package_properties(OpenMP PROPERTIES TYPE RECOMMENDED PURPOSE "Used for thread parallelization in xtp")
	36	else()
	37	# in case OpenMP was detected somewhere else
	38	unset(OpenMP_FOUND)
38	39	endif()
39	40
40	41	########################################################################
41	42	# User input options #
42	43	########################################################################
43	44
44		find_package(LIBXC REQUIRED)
	45
	46	find_package(PkgConfig REQUIRED)
	47	set_package_properties(PkgConfig PROPERTIES TYPE RECOMMENDED PURPOSE "Used to detect libxc and libint package")
	48	pkg_check_modules(LIBXC REQUIRED IMPORTED_TARGET libxc)
	49	if(NOT TARGET PkgConfig::LIBINT)
	50	pkg_check_modules(LIBINT REQUIRED IMPORTED_TARGET libint2>=2.6)
	51	endif()
	52
45	53	find_package(HDF5 1.8 REQUIRED COMPONENTS CXX)
	54	set_package_properties(HDF5 PROPERTIES TYPE REQUIRED PURPOSE "Used to read/write HDF5 data files")
46	55
47	56	if(HDF5_VERSION VERSION_GREATER 1.8)
48	57	message(WARNING "HDF5 will be used such that it is compatible with version 1.8.")

61	70	include(GNUInstallDirs)
62	71
63	72	option(USE_CUDA "Use a Nvidia GPU to speed up computations" OFF)
	73	add_feature_info(USE_CUDA USE_CUDA "Use CUDA for GPU acceleration")
64	74
65	75	option(ENABLE_TESTING "Build and enable testing stuff" OFF)
	76	add_feature_info(ENABLE_TESTING ENABLE_TESTING "Enable unit tests")
66	77	if(ENABLE_TESTING)
67	78	enable_testing()
68	79	endif(ENABLE_TESTING)

72	83	########################################################################
73	84	if(IS_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/.git)
74	85	find_package(Git)
	86	set_package_properties(Git PROPERTIES TYPE OPTIONAL PURPOSE "Generated version for development version")
75	87	endif(IS_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/.git)
76	88
77	89	find_package(Boost 1.57.0 REQUIRED COMPONENTS program_options filesystem system timer)
78	90	find_package(Eigen3 3.3.0 REQUIRED NO_MODULE)
	91	if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
	92	set_package_properties(Boost PROPERTIES TYPE REQUIRED PURPOSE "Extended C++ libraries")
	93	set_package_properties(Eigen3 PROPERTIES TYPE REQUIRED PURPOSE "C++ vector data structures")
	94	endif()
79	95	message(STATUS "Found Eigen3: ${Eigen3_DIR}")
80	96
81	97	option(BUILD_MANPAGES "Build manpages (might lead to problem on system without rpath" OFF)
	98	add_feature_info(BUILD_MANPAGES BUILD_MANPAGES "Build manpages (disable for cross-compile)")
82	99	#define this target here, so that individual man pages can append to it.
83	100	if(NOT TARGET manpages)
84	101	add_custom_target(manpages ALL)
85	102	endif()
86	103
87	104	find_package(VOTCA_TOOLS REQUIRED NO_MODULE)
	105	set_package_properties(VOTCA_TOOLS PROPERTIES TYPE REQUIRED PURPOSE "Votca base library")
88	106	if(DEFINED VOTCA_TOOLS_VERSION AND NOT VOTCA_TOOLS_VERSION STREQUAL PROJECT_VERSION)
89	107	message(FATAL_ERROR "Incompatible VOTCA Tools version found (needed ${PROJECT_VERSION}, found ${VOTCA_TOOLS_VERSION})")
90	108	endif()
91	109	message(STATUS "Found VOTCA_TOOLS: ${VOTCA_TOOLS_DIR}")
92	110	find_package(VOTCA_CSG REQUIRED NO_MODULE)
	111	set_package_properties(VOTCA_TOOLS PROPERTIES TYPE REQUIRED PURPOSE "Votca csg library")
93	112	if(DEFINED VOTCA_CSG_VERSION AND NOT VOTCA_CSG_VERSION STREQUAL PROJECT_VERSION)
94	113	message(FATAL_ERROR "Incompatible VOTCA CSG version found (needed ${PROJECT_VERSION}, found ${VOTCA_CSG_VERSION})")
95	114	endif()

97	116
98	117	if(USE_CUDA)
99	118	find_package(CUDA REQUIRED)
	119	set_package_properties(CUDA PROPERTIES TYPE REQUIRED PURPOSE "Used for GPU acceleration")
100	120	endif(USE_CUDA)
101	121
102	122	########################################################################

108	128	########################################################################
109	129	# Basic system tests (standard libraries, headers, functions, types) #
110	130	########################################################################
111		include(CheckIncludeFile)
112		foreach(HEADER assert.h)
113		check_include_file(${HEADER} FOUND_${HEADER})
114		if(NOT FOUND_${HEADER})
115		message(FATAL_ERROR "Could not find needed header - ${HEADER}")
116		endif(NOT FOUND_${HEADER})
117		endforeach(HEADER)
118
119	131	include(CheckIncludeFileCXX)
120	132	foreach(HEADER algorithm)
121	133	check_include_file_cxx(${HEADER} FOUND_${HEADER})

126	138
127	139	set(MATH_LIBRARIES "m" CACHE STRING "math library")
128	140	mark_as_advanced( MATH_LIBRARIES )
129		include(CheckLibraryExists)
130		foreach(FUNC sqrt)
131		check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES})
132		if(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
133		message(FATAL_ERROR "Could not find needed math function - ${FUNC}")
134		endif(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
135		endforeach(FUNC)
136	141
137	142	######################################
138	143	# Include the following subdirectory #

142	147	add_subdirectory(src)
143	148	add_subdirectory(share)
144	149
	150	if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
	151	feature_summary(INCLUDE_QUIET_PACKAGES WHAT ALL)
	152	endif (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)

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-47

~~CMakeModules/FindLIBXC.cmake~~ less more

0		# - Find libxc
1		# Find the native libxc headers and libraries.
2		#
3		# LIBXC_INCLUDE_DIRS - where to find xc.h, etc.
4		# LIBXC_LIBRARIES - List of libraries when using expat.
5		# LIBXC_FOUND - True if expat found.
6		#
7		# Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org)
8		#
9		# Licensed under the Apache License, Version 2.0 (the "License");
10		# you may not use this file except in compliance with the License.
11		# You may obtain a copy of the License at
12		#
13		# http://www.apache.org/licenses/LICENSE-2.0
14		#
15		# Unless required by applicable law or agreed to in writing, software
16		# distributed under the License is distributed on an "AS IS" BASIS,
17		# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
18		# See the License for the specific language governing permissions and
19		# limitations under the License.
20		#
21
22		# check if info is available via PkgConfig
23		find_package(PkgConfig)
24		pkg_check_modules(PC_libxc libxc)
25
26		find_path(LIBXC_INCLUDE_DIR NAMES xc.h HINTS HINTS ${PC_libxc_INCLUDE_DIRS})
27		find_library(LIBXC_LIBRARY NAMES xc HINTS ${PC_libxc_LIBRARY_DIRS} )
28
29		#include(FindPackageHandleStandardArgs)
30		# handle the QUIETLY and REQUIRED arguments and set LIBXC_FOUND to TRUE
31		# if all listed variables are TRUE
32		find_package_handle_standard_args(LIBXC DEFAULT_MSG LIBXC_LIBRARY LIBXC_INCLUDE_DIR )
33
34		if(LIBXC_FOUND)
35		set(LIBXC_LIBRARIES ${LIBXC_LIBRARY} )
36		set(LIBXC_INCLUDE_DIRS ${LIBXC_INCLUDE_DIR} )
37
38		if(NOT TARGET LIBXC::LIBXC)
39		add_library(LIBXC::LIBXC UNKNOWN IMPORTED)
40		set_target_properties(LIBXC::LIBXC PROPERTIES
41		IMPORTED_LOCATION "${LIBXC_LIBRARY}"
42		INTERFACE_INCLUDE_DIRECTORIES "${LIBXC_INCLUDE_DIRS}")
43		endif()
44		endif()
45
46		mark_as_advanced(LIBXC_INCLUDE_DIR LIBXC_LIBRARY )

+0

-75

~~CODE_OF_CONDUCT.md~~ less more

0		# Contributor Covenant Code of Conduct
1
2		## Our Pledge
3
4		In the interest of fostering an open and welcoming environment, we as
5		contributors and maintainers pledge to making participation in our project and
6		our community a harassment-free experience for everyone, regardless of age, body
7		size, disability, ethnicity, gender identity and expression, level of
8		experience, nationality, personal appearance, race, religion, or sexual identity
9		and orientation.
10
11		## Our Standards
12
13		Examples of behavior that contributes to creating a positive environment
14		include:
15
16		* Using welcoming and inclusive language
17		* Being respectful of differing viewpoints and experiences
18		* Gracefully accepting constructive criticism
19		* Focusing on what is best for the community
20		* Showing empathy towards other community members
21
22		Examples of unacceptable behavior by participants include:
23
24		* The use of sexualized language or imagery and unwelcome sexual attention or
25		advances
26		* Trolling, insulting/derogatory comments, and personal or political attacks
27		* Public or private harassment
28		* Publishing others' private information, such as a physical or electronic
29		address, without explicit permission
30		* Other conduct which could reasonably be considered inappropriate in a
31		professional setting
32
33		## Our Responsibilities
34
35		Project maintainers are responsible for clarifying the standards of acceptable
36		behavior and are expected to take appropriate and fair corrective action in
37		response to any instances of unacceptable behavior.
38
39		Project maintainers have the right and responsibility to remove, edit, or reject
40		comments, commits, code, wiki edits, issues, and other contributions that are
41		not aligned to this Code of Conduct, or to ban temporarily or permanently any
42		contributor for other behaviors that they deem inappropriate, threatening,
43		offensive, or harmful.
44
45		## Scope
46
47		This Code of Conduct applies both within project spaces and in public spaces
48		when an individual is representing the project or its community. Examples of
49		representing a project or community include using an official project e-mail
50		address, posting via an official social media account, or acting as an appointed
51		representative at an online or offline event. Representation of a project may be
52		further defined and clarified by project maintainers.
53
54		## Enforcement
55
56		Instances of abusive, harassing, or otherwise unacceptable behavior may be
57		reported by contacting the project team at votca@googlegroups.com. The project
58		team will review and investigate all complaints, and will respond in a way that
59		it deems appropriate to the circumstances. The project team is obligated to
60		maintain confidentiality with regard to the reporter of an incident. Further
61		details of specific enforcement policies may be posted separately.
62
63		Project maintainers who do not follow or enforce the Code of Conduct in good
64		faith may face temporary or permanent repercussions as determined by other
65		members of the project's leadership.
66
67		## Attribution
68
69		This Code of Conduct is adapted from the [Contributor Covenant][homepage],
70		version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
71
72		[homepage]: http://contributor-covenant.org
73
74		[version]: http://contributor-covenant.org/version/1/4/

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CODE_OF_CONDUCT.rst less more

	0	Contributor Covenant Code of Conduct
	1	====================================
	2
	3	Our Pledge
	4	----------
	5
	6	In the interest of fostering an open and welcoming environment, we as
	7	contributors and maintainers pledge to making participation in our
	8	project and our community a harassment-free experience for everyone,
	9	regardless of age, body size, disability, ethnicity, gender identity and
	10	expression, level of experience, nationality, personal appearance, race,
	11	religion, or sexual identity and orientation.
	12
	13	Our Standards
	14	-------------
	15
	16	Examples of behavior that contributes to creating a positive environment
	17	include:
	18
	19	- Using welcoming and inclusive language
	20	- Being respectful of differing viewpoints and experiences
	21	- Gracefully accepting constructive criticism
	22	- Focusing on what is best for the community
	23	- Showing empathy towards other community members
	24
	25	Examples of unacceptable behavior by participants include:
	26
	27	- The use of sexualized language or imagery and unwelcome sexual
	28	attention or advances
	29	- Trolling, insulting/derogatory comments, and personal or political
	30	attacks
	31	- Public or private harassment
	32	- Publishing others' private information, such as a physical or
	33	electronic address, without explicit permission
	34	- Other conduct which could reasonably be considered inappropriate in a
	35	professional setting
	36
	37	Our Responsibilities
	38	--------------------
	39
	40	Project maintainers are responsible for clarifying the standards of
	41	acceptable behavior and are expected to take appropriate and fair
	42	corrective action in response to any instances of unacceptable behavior.
	43
	44	Project maintainers have the right and responsibility to remove, edit,
	45	or reject comments, commits, code, wiki edits, issues, and other
	46	contributions that are not aligned to this Code of Conduct, or to ban
	47	temporarily or permanently any contributor for other behaviors that they
	48	deem inappropriate, threatening, offensive, or harmful.
	49
	50	Scope
	51	-----
	52
	53	This Code of Conduct applies both within project spaces and in public
	54	spaces when an individual is representing the project or its community.
	55	Examples of representing a project or community include using an
	56	official project e-mail address, posting via an official social media
	57	account, or acting as an appointed representative at an online or
	58	offline event. Representation of a project may be further defined and
	59	clarified by project maintainers.
	60
	61	Enforcement
	62	-----------
	63
	64	Instances of abusive, harassing, or otherwise unacceptable behavior may
	65	be reported by contacting the project team at votca@googlegroups.com.
	66	The project team will review and investigate all complaints, and will
	67	respond in a way that it deems appropriate to the circumstances. The
	68	project team is obligated to maintain confidentiality with regard to the
	69	reporter of an incident. Further details of specific enforcement
	70	policies may be posted separately.
	71
	72	Project maintainers who do not follow or enforce the Code of Conduct in
	73	good faith may face temporary or permanent repercussions as determined
	74	by other members of the project's leadership.
	75
	76	Attribution
	77	-----------
	78
	79	This Code of Conduct is adapted from the `Contributor
	80	Covenant <http://contributor-covenant.org>`__, version 1.4, available at
	81	`http://contributor-covenant.org/version/1/4 <http://contributor-covenant.org/version/1/4/>`__

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0		Apache License
1		Version 2.0, January 2004
2		http://www.apache.org/licenses/
3
4		TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
5
6		1. Definitions.
7
8		"License" shall mean the terms and conditions for use, reproduction,
9		and distribution as defined by Sections 1 through 9 of this document.
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200		limitations under the License.

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LICENSE.rst less more

	0	::
	1
	2	Apache License
	3	Version 2.0, January 2004
	4	http://www.apache.org/licenses/
	5
	6	TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
	7
	8	1. Definitions.
	9
	10	"License" shall mean the terms and conditions for use, reproduction, and
	11	distribution as defined by Sections 1 through 9 of this document.
	12
	13	"Licensor" shall mean the copyright owner or entity authorized by the
	14	copyright owner that is granting the License.
	15
	16	"Legal Entity" shall mean the union of the acting entity and all other
	17	entities that control, are controlled by, or are under common control
	18	with that entity. For the purposes of this definition, "control" means
	19	(i) the power, direct or indirect, to cause the direction or management
	20	of such entity, whether by contract or otherwise, or (ii) ownership of
	21	fifty percent (50%) or more of the outstanding shares, or (iii)
	22	beneficial ownership of such entity.
	23
	24	"You" (or "Your") shall mean an individual or Legal Entity exercising
	25	permissions granted by this License.
	26
	27	"Source" form shall mean the preferred form for making modifications,
	28	including but not limited to software source code, documentation source,
	29	and configuration files.
	30
	31	"Object" form shall mean any form resulting from mechanical
	32	transformation or translation of a Source form, including but not
	33	limited to compiled object code, generated documentation, and
	34	conversions to other media types.
	35
	36	"Work" shall mean the work of authorship, whether in Source or Object
	37	form, made available under the License, as indicated by a copyright
	38	notice that is included in or attached to the work (an example is
	39	provided in the Appendix below).
	40
	41	"Derivative Works" shall mean any work, whether in Source or Object
	42	form, that is based on (or derived from) the Work and for which the
	43	editorial revisions, annotations, elaborations, or other modifications
	44	represent, as a whole, an original work of authorship. For the purposes
	45	of this License, Derivative Works shall not include works that remain
	46	separable from, or merely link (or bind by name) to the interfaces of,
	47	the Work and Derivative Works thereof.
	48
	49	"Contribution" shall mean any work of authorship, including the original
	50	version of the Work and any modifications or additions to that Work or
	51	Derivative Works thereof, that is intentionally submitted to Licensor
	52	for inclusion in the Work by the copyright owner or by an individual or
	53	Legal Entity authorized to submit on behalf of the copyright owner. For
	54	the purposes of this definition, "submitted" means any form of
	55	electronic, verbal, or written communication sent to the Licensor or its
	56	representatives, including but not limited to communication on
	57	electronic mailing lists, source code control systems, and issue
	58	tracking systems that are managed by, or on behalf of, the Licensor for
	59	the purpose of discussing and improving the Work, but excluding
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	61	writing by the copyright owner as "Not a Contribution."
	62
	63	"Contributor" shall mean Licensor and any individual or Legal Entity on
	64	behalf of whom a Contribution has been received by Licensor and
	65	subsequently incorporated within the Work.
	66
	67	2. Grant of Copyright License. Subject to the terms and conditions of
	68	this License, each Contributor hereby grants to You a perpetual,
	69	worldwide, non-exclusive, no-charge, royalty-free, irrevocable
	70	copyright license to reproduce, prepare Derivative Works of, publicly
	71	display, publicly perform, sublicense, and distribute the Work and
	72	such Derivative Works in Source or Object form.
	73
	74	3. Grant of Patent License. Subject to the terms and conditions of this
	75	License, each Contributor hereby grants to You a perpetual,
	76	worldwide, non-exclusive, no-charge, royalty-free, irrevocable
	77	(except as stated in this section) patent license to make, have made,
	78	use, offer to sell, sell, import, and otherwise transfer the Work,
	79	where such license applies only to those patent claims licensable by
	80	such Contributor that are necessarily infringed by their
	81	Contribution(s) alone or by combination of their Contribution(s) with
	82	the Work to which such Contribution(s) was submitted. If You
	83	institute patent litigation against any entity (including a
	84	cross-claim or counterclaim in a lawsuit) alleging that the Work or a
	85	Contribution incorporated within the Work constitutes direct or
	86	contributory patent infringement, then any patent licenses granted to
	87	You under this License for that Work shall terminate as of the date
	88	such litigation is filed.
	89
	90	4. Redistribution. You may reproduce and distribute copies of the Work
	91	or Derivative Works thereof in any medium, with or without
	92	modifications, and in Source or Object form, provided that You meet
	93	the following conditions:
	94
	95	(a) You must give any other recipients of the Work or Derivative Works a
	96	copy of this License; and
	97
	98	(b) You must cause any modified files to carry prominent notices stating
	99	that You changed the files; and
	100
	101	(c) You must retain, in the Source form of any Derivative Works that You
	102	distribute, all copyright, patent, trademark, and attribution
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	106	(d) If the Work includes a "NOTICE" text file as part of its
	107	distribution, then any Derivative Works that You distribute must
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	111	places: within a NOTICE text file distributed as part of the
	112	Derivative Works; within the Source form or documentation, if
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	116	informational purposes only and do not modify the License. You may
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	119	Work, provided that such additional attribution notices cannot be
	120	construed as modifying the License.
	121
	122	You may add Your own copyright statement to Your modifications and may
	123	provide additional or different license terms and conditions for use,
	124	reproduction, or distribution of Your modifications, or for any such
	125	Derivative Works as a whole, provided Your use, reproduction, and
	126	distribution of the Work otherwise complies with the conditions stated
	127	in this License.
	128
	129	5. Submission of Contributions. Unless You explicitly state otherwise,
	130	any Contribution intentionally submitted for inclusion in the Work by
	131	You to the Licensor shall be under the terms and conditions of this
	132	License, without any additional terms or conditions. Notwithstanding
	133	the above, nothing herein shall supersede or modify the terms of any
	134	separate license agreement you may have executed with Licensor
	135	regarding such Contributions.
	136
	137	6. Trademarks. This License does not grant permission to use the trade
	138	names, trademarks, service marks, or product names of the Licensor,
	139	except as required for reasonable and customary use in describing the
	140	origin of the Work and reproducing the content of the NOTICE file.
	141
	142	7. Disclaimer of Warranty. Unless required by applicable law or agreed
	143	to in writing, Licensor provides the Work (and each Contributor
	144	provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES
	145	OR CONDITIONS OF ANY KIND, either express or implied, including,
	146	without limitation, any warranties or conditions of TITLE,
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	148	PURPOSE. You are solely responsible for determining the
	149	appropriateness of using or redistributing the Work and assume any
	150	risks associated with Your exercise of permissions under this
	151	License.
	152
	153	8. Limitation of Liability. In no event and under no legal theory,
	154	whether in tort (including negligence), contract, or otherwise,
	155	unless required by applicable law (such as deliberate and grossly
	156	negligent acts) or agreed to in writing, shall any Contributor be
	157	liable to You for damages, including any direct, indirect, special,
	158	incidental, or consequential damages of any character arising as a
	159	result of this License or out of the use or inability to use the Work
	160	(including but not limited to damages for loss of goodwill, work
	161	stoppage, computer failure or malfunction, or any and all other
	162	commercial damages or losses), even if such Contributor has been
	163	advised of the possibility of such damages.
	164
	165	9. Accepting Warranty or Additional Liability. While redistributing the
	166	Work or Derivative Works thereof, You may choose to offer, and charge
	167	a fee for, acceptance of support, warranty, indemnity, or other
	168	liability obligations and/or rights consistent with this License.
	169	However, in accepting such obligations, You may act only on Your own
	170	behalf and on Your sole responsibility, not on behalf of any other
	171	Contributor, and only if You agree to indemnify, defend, and hold
	172	each Contributor harmless for any liability incurred by, or claims
	173	asserted against, such Contributor by reason of your accepting any
	174	such warranty or additional liability.
	175
	176	END OF TERMS AND CONDITIONS
	177
	178	APPENDIX: How to apply the Apache License to your work.
	179
	180	::
	181
	182	To apply the Apache License to your work, attach the following
	183	boilerplate notice, with the fields enclosed by brackets "{}"
	184	replaced with your own identifying information. (Don't include
	185	the brackets!) The text should be enclosed in the appropriate
	186	comment syntax for the file format. We also recommend that a
	187	file or class name and description of purpose be included on the
	188	same "printed page" as the copyright notice for easier
	189	identification within third-party archives.
	190
	191	Copyright {yyyy} {name of copyright owner}
	192
	193	Licensed under the Apache License, Version 2.0 (the "License"); you may
	194	not use this file except in compliance with the License. You may obtain
	195	a copy of the License at
	196
	197	::
	198
	199	http://www.apache.org/licenses/LICENSE-2.0
	200
	201	Unless required by applicable law or agreed to in writing, software
	202	distributed under the License is distributed on an "AS IS" BASIS,
	203	WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
	204	See the License for the specific language governing permissions and
	205	limitations under the License.

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0		Versatile Object-oriented Toolkit for Coarse-graining Applications
1		Copyright 2009-2011 The VOTCA Development Team
2
3		This product includes software developed at
4		The VOTCA Development Team (http://www.votca.org).
5
6		This software contains code, which was
7		derived from VOTCA KMC, MOO and CTP project.

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	0	Versatile Object-oriented Toolkit for Coarse-graining Applications
	1	Copyright 2009-2020 The VOTCA Development Team
	2
	3	This product includes software developed at The VOTCA Development Team
	4	(http://www.votca.org).
	5
	6	This software contains code, which was derived from VOTCA KMC, MOO and
	7	CTP project.

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~~README.md~~ less more

0		[![Codacy Badge](https://api.codacy.com/project/badge/Grade/6e930e3c0f5a4a9b83aa3362cfdd21e1)](https://www.codacy.com/manual/votca-package/xtp?utm_source=github.com&utm_medium=referral&utm_content=votca/xtp&utm_campaign=Badge_Grade)
1		[![codecov](https://codecov.io/gh/votca/xtp/branch/master/graph/badge.svg)](https://codecov.io/gh/votca/xtp)
2		[![Build Status](https://travis-ci.org/votca/xtp.svg?branch=master)](https://travis-ci.org/votca/xtp)
3		[![pipeline status](https://gitlab.com/votca/xtp/badges/master/pipeline.svg)](https://gitlab.com/votca/xtp/commits/master)
4		[![DOI](https://zenodo.org/badge/50048374.svg)](https://zenodo.org/badge/latestdoi/50048374)
5
6		VOTCA-XTP is a library which allows you to calculate the electronic properties of organic materials, e.g.
7		- excited state properties via GW-BSE
8		- spectra using QM/MM in conjunction with excited state treatment via GW-BSE
9		- energetic disorder for electrons/holes and excitions via QM/MM or fast MM/MM multipole methods
10		- electron and hole mobilities using electronic couplings and kinetic Monte-Carlo
11		- electron, hole, singlet and triplet diffusion constants using electronic couplings and kinetic Monte-Carlo
12
13		Installation instructions and developer information can be found
14		[here](https://github.com/votca/votca/blob/master/share/doc/INSTALL.md)
15
16		For other questions, we provide an email list:
17
18		[google group](https://groups.google.com/forum/#!forum/votca)
19
20		and a slack channel:
21
22		[Slack](https://votca.slack.com/messages/C7XVBE9EG/?)
23
24		We have no manual for the moment but we have a complete tutorial here:
25
26		[Tutorial](https://github.com/votca/xtp-tutorials)
27
28		The development of VOTCA is mainly funded by academic research grants. If you
29		use this package, please cite the VOTCA papers:
30
31		* Electronic Excitations in Complex Molecular Environments: Many-Body Green’s
32		Functions Theory in VOTCA-XTP Jens Wehner, Lothar Brombacher, Joshua Brown,
33		Christoph Junghans, Onur Caylak, Yuriy Khalak, Pranav Madhikar, Gianluca
34		Tirimbo, Björn Baumeier J. Chem. Theory Comput. 14, 6353 (2018).
35
36		* Microscopic simulations of charge transport in disordered organic
37		semiconductors V. Ruehle, A. Lukyanov, F. May, M. Schrader, T. Vehoff, J.
38		Kirkpatrick, B. Baumeier and D. Andrienko J. Chem. Theo. Comp. 7, 3335-3345
39		(2011)
40
41		* Versatile Object-oriented Toolkit for Coarse-graining Applications, V.Ruehle,
42		C. Junghans, A. Lukyanov, K. Kremer, D. Andrienko, J. Chem. Theo. Comp. 5
43		(12), 3211 (2009)
44
45		In case of questions, please post them in the google discussion group for votca
46		at <http://groups.google.com/group/votca-xtp>
47
48		You can contact the VOTCA Development Team at devs@votca.org.

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	0	\|Codacy Badge\| \|codecov\| \|CI\| \|DOI\|
	1
	2	VOTCA-XTP is a library which allows you to calculate the electronic
	3	properties of organic materials, e.g. - excited state properties via
	4	GW-BSE - spectra using QM/MM in conjunction with excited state treatment
	5	via GW-BSE - energetic disorder for electrons/holes and excitons via
	6	QM/MM or fast MM/MM multipole methods - electron and hole mobilities
	7	using electronic couplings and kinetic Monte-Carlo - electron, hole,
	8	singlet and triplet diffusion constants using electronic couplings and
	9	kinetic Monte-Carlo
	10
	11	Installation instructions and developer information can be found
	12	`here <https://github.com/votca/votca/blob/master/share/doc/INSTALL.rst>`__
	13
	14	For other questions, we provide an email list:
	15
	16	`google group <https://groups.google.com/forum/#!forum/votca>`__
	17
	18	and a slack channel:
	19
	20	`Slack <https://votca.slack.com/messages/C7XVBE9EG/?>`__
	21
	22	We have no manual for the moment but we have a complete tutorial here:
	23
	24	`Tutorial <https://github.com/votca/xtp-tutorials>`__
	25
	26	The development of VOTCA is mainly funded by academic research grants.
	27	If you use this package, please cite the VOTCA papers:
	28
	29	- Excited-State Electronic Structure of Molecules Using Many-Body
	30	Green’s Functions: Quasiparticles and Electron-Hole Excitations with
	31	VOTCA-XTP. Gianluca Tirimbò, Vivek Sundaram, Onur Çaylak, Wouter
	32	Scharpach, Javier Sijen, Christoph Junghans, Joshua Brown, Felipe
	33	Zapata Ruiz, Nicolas Renaud, Jens Wehner, Björn Baumeier, J. Chem.
	34	Phys. 152, 114103 (2020).
	35
	36	- Electronic Excitations in Complex Molecular Environments: Many-Body
	37	Green’s Functions Theory in VOTCA-XTP. Jens Wehner, Lothar
	38	Brombacher, Joshua Brown, Christoph Junghans, Onur Caylak, Yuriy
	39	Khalak, Pranav Madhikar, Gianluca Tirimbo, Björn Baumeier, J. Chem.
	40	Theory Comput. 14, 6353 (2018).
	41
	42	- Microscopic simulations of charge transport in disordered organic
	43	semiconductors. V. Ruehle, A. Lukyanov, F. May, M. Schrader, T.
	44	Vehoff, J. Kirkpatrick, B. Baumeier and D. Andrienko, J. Chem. Theo.
	45	Comp. 7, 3335-3345 (2011).
	46
	47	- Versatile Object-oriented Toolkit for Coarse-graining Applications.
	48	V.Ruehle, C. Junghans, A. Lukyanov, K. Kremer, D. Andrienko, J. Chem.
	49	Theo. Comp. 5 (12), 3211 (2009).
	50
	51	In case of questions, please post them in the google discussion group
	52	for votca at http://groups.google.com/group/votca-xtp
	53
	54	You can contact the VOTCA Development Team at devs@votca.org.
	55
	56	.. \|Codacy Badge\| image:: https://app.codacy.com/project/badge/Grade/b9c7170d5c3440b7a2327a667cb1ec59
	57	:target: https://www.codacy.com/gh/votca/xtp?utm_source=github.com&utm_medium=referral&utm_content=votca/xtp&utm_campaign=Badge_Grade
	58	.. \|codecov\| image:: https://codecov.io/gh/votca/xtp/branch/master/graph/badge.svg
	59	:target: https://codecov.io/gh/votca/xtp
	60	.. \|CI\| image:: https://github.com/votca/votca/workflows/CI/badge.svg?branch=master
	61	:target: https://github.com/votca/votca/actions?query=workflow%3ACI+branch%3Amaster
	62	.. \|DOI\| image:: https://zenodo.org/badge/50048374.svg
	63	:target: https://zenodo.org/badge/latestdoi/50048374

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include/votca/xtp/CMakeLists.txt less more

0		configure_file(votca_config.h.in ${CMAKE_CURRENT_BINARY_DIR}/votca_config.h)
	0	configure_file(votca_xtp_config.h.in ${CMAKE_CURRENT_BINARY_DIR}/votca_xtp_config.h)
1	1
2		file(GLOB_RECURSE VOTCA_HEADERS *.h ${CMAKE_CURRENT_BINARY_DIR}/votca_config.h)
	2	file(GLOB_RECURSE VOTCA_HEADERS *.h ${CMAKE_CURRENT_BINARY_DIR}/votca_xtp_config.h)
3	3	install(FILES ${VOTCA_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/votca/xtp)

+54

-34

include/votca/xtp/ERIs.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team
	1	* Copyright 2009-2020 The VOTCA Development Team
2	2	* (http://www.votca.org)
3	3	*
4	4	* Licensed under the Apache License, Version 2.0 (the "License")

20	20	#ifndef VOTCA_XTP_ERIS_H
21	21	#define VOTCA_XTP_ERIS_H
22	22
23		#include <votca/xtp/fourcenter.h>
24		#include <votca/xtp/threecenter.h>
	23	// Local VOTCA includes
	24	#include "threecenter.h"
25	25
26	26	namespace votca {
27	27	namespace xtp {

30	30	* \brief Takes a density matrix and and an auxiliary basis set and calculates
31	31	* the electron repulsion integrals.
32	32	*
33		*
34		*
35	33	*/
36	34	class ERIs {
37	35
38	36	public:
39	37	void Initialize(const AOBasis& dftbasis, const AOBasis& auxbasis);
40		void Initialize_4c_small_molecule(const AOBasis& dftbasis);
41		void Initialize_4c_screening(const AOBasis& dftbasis,
42		double eps); // Pre-screening
	38	void Initialize_4c(const AOBasis& dftbasis);
43	39
44		Mat_p_Energy CalculateERIs(const Eigen::MatrixXd& DMAT) const;
45		Mat_p_Energy CalculateEXX(const Eigen::MatrixXd& DMAT) const;
46		Mat_p_Energy CalculateEXX(const Eigen::MatrixXd& occMos,
47		const Eigen::MatrixXd& DMAT) const;
48		Mat_p_Energy CalculateERIs_4c_small_molecule(
49		const Eigen::MatrixXd& DMAT) const;
50		Mat_p_Energy CalculateEXX_4c_small_molecule(
51		const Eigen::MatrixXd& DMAT) const;
	40	Eigen::MatrixXd CalculateERIs_3c(const Eigen::MatrixXd& DMAT) const;
52	41
53		Mat_p_Energy CalculateERIs_4c_direct(const AOBasis& dftbasis,
54		const Eigen::MatrixXd& DMAT) const;
	42	std::array<Eigen::MatrixXd, 2> CalculateERIs_EXX_3c(
	43	const Eigen::MatrixXd& occMos, const Eigen::MatrixXd& DMAT) const {
	44	std::array<Eigen::MatrixXd, 2> result;
	45	result[0] = CalculateERIs_3c(DMAT);
	46	if (occMos.rows() > 0 && occMos.cols() > 0) {
	47	assert(occMos.rows() == DMAT.rows() && "occMos.rows()==DMAT.rows()");
	48	result[1] = CalculateEXX_mos(occMos);
	49	} else {
	50	result[1] = CalculateEXX_dmat(DMAT);
	51	}
	52	return result;
	53	}
	54
	55	Eigen::MatrixXd CalculateERIs_4c(const Eigen::MatrixXd& DMAT,
	56	double error) const {
	57	return Compute4c<false>(DMAT, error)[0];
	58	}
	59
	60	std::array<Eigen::MatrixXd, 2> CalculateERIs_EXX_4c(
	61	const Eigen::MatrixXd& DMAT, double error) const {
	62	return Compute4c<true>(DMAT, error);
	63	}
55	64
56	65	Index Removedfunctions() const { return _threecenter.Removedfunctions(); }
57	66
	67	static double CalculateEnergy(const Eigen::MatrixXd& DMAT,
	68	const Eigen::MatrixXd& matrix_operator) {
	69	return matrix_operator.cwiseProduct(DMAT).sum();
	70	}
	71
58	72	private:
59		bool _with_screening = false;
60		double _screening_eps;
61		Eigen::MatrixXd _diagonals; // Square matrix containing <ab\|ab> for all basis
62		// functions a, b
	73	std::vector<libint2::Shell> basis_;
	74	std::vector<Index> starts_;
63	75
64		void CalculateERIsDiagonals(const AOBasis& dftbasis);
	76	std::vector<std::vector<Index>> shellpairs_;
	77	std::vector<std::vector<libint2::ShellPair>> shellpairdata_;
	78	Index maxnprim_;
	79	Index maxL_;
65	80
66		bool CheckScreen(double eps, const AOShell& shell_1, const AOShell& shell_2,
67		const AOShell& shell_3, const AOShell& shell_4) const;
	81	Eigen::MatrixXd CalculateEXX_dmat(const Eigen::MatrixXd& DMAT) const;
	82	Eigen::MatrixXd CalculateEXX_mos(const Eigen::MatrixXd& occMos) const;
	83
	84	std::vector<std::vector<libint2::ShellPair>> ComputeShellPairData(
	85	const std::vector<libint2::Shell>& basis,
	86	const std::vector<std::vector<Index>>& shellpairs) const;
	87
	88	Eigen::MatrixXd ComputeSchwarzShells(const AOBasis& dftbasis) const;
	89	Eigen::MatrixXd ComputeShellBlockNorm(const Eigen::MatrixXd& dmat) const;
	90
	91	template <bool with_exchange>
	92	std::array<Eigen::MatrixXd, 2> Compute4c(const Eigen::MatrixXd& dmat,
	93	double error) const;
68	94
69	95	TCMatrix_dft _threecenter;
70		FCMatrix _fourcenter;
71	96
72		double CalculateEnergy(const Eigen::MatrixXd& DMAT,
73		const Eigen::MatrixXd& matrix_operator) const;
74		template <bool transposed_block>
75		void FillERIsBlock(Eigen::MatrixXd& ERIsCur, const Eigen::MatrixXd& DMAT,
76		const Eigen::Tensor<double, 4>& block,
77		const AOShell& shell_1, const AOShell& shell_2,
78		const AOShell& shell_3, const AOShell& shell_4) const;
79		};
	97	Eigen::MatrixXd schwarzscreen_; // Square matrix containing <ab\|ab> for all
	98	// shells
	99	}; // namespace xtp
80	100
81	101	} // namespace xtp
82	102	} // namespace votca

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include/votca/xtp/GaussianQuadratureBase.h less more

	0	/*
	1	* Copyright 2009-2020 The VOTCA Development Team
	2	* (http://www.votca.org)
	3	*
	4	* Licensed under the Apache License, Version 2.0 (the "License")
	5	*
	6	* You may not use this file except in compliance with the License.
	7	* You may obtain a copy of the License at
	8	*
	9	* http://www.apache.org/licenses/LICENSE-2.0
	10	*
	11	* Unless required by applicable law or agreed to in writing, software
	12	* distributed under the License is distributed on an "AS IS" BASIS,
	13	* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
	14	* See the License for the specific language governing permissions and
	15	* limitations under the License.
	16	*
	17	*/
	18
	19	#pragma once
	20
	21	#ifndef VOTCA_XTP_GAUSSIANQUADRATUREBASE_H
	22	#define VOTCA_XTP_GAUSSIANQUADRATUREBASE_H
	23
	24	// Local VOTCA includes
	25	#include "eigen.h"
	26	#include <votca/tools/constants.h>
	27
	28	namespace votca {
	29	namespace xtp {
	30
	31	class GaussianQuadratureBase {
	32	public:
	33	GaussianQuadratureBase() = default;
	34
	35	void configure(Index order) {
	36	FillPoints();
	37	FillAdaptedWeights();
	38	CheckOrder(order, _map_points);
	39	CheckOrder(order, _map_AdaptedWeights);
	40	points_ = _map_points[order];
	41	weights_ = _map_AdaptedWeights[order];
	42	}
	43
	44	virtual ~GaussianQuadratureBase() = default;
	45
	46	Index Order() const { return points_.size(); }
	47
	48	template <typename F>
	49	double Integrate(const F& f) const {
	50	double result = 0.0;
	51	for (Index j = 0; j < Order(); ++j) {
	52	result += ScaledWeight(j) * f(j, ScaledPoint(j), UseSymmetry());
	53	}
	54	return result;
	55	}
	56	virtual double ScaledPoint(Index i) const = 0;
	57
	58	virtual double ScaledWeight(Index i) const = 0;
	59
	60	private:
	61	void CheckOrder(Index order,
	62	const std::map<Index, Eigen::VectorXd>& map) const;
	63
	64	protected:
	65	Eigen::VectorXd points_;
	66	Eigen::VectorXd weights_;
	67
	68	std::map<Index, Eigen::VectorXd> _map_points;
	69	std::map<Index, Eigen::VectorXd> _map_AdaptedWeights;
	70
	71	virtual bool UseSymmetry() const = 0;
	72
	73	virtual void FillPoints() = 0;
	74	virtual void FillAdaptedWeights() = 0;
	75	};
	76
	77	} // namespace xtp
	78	} // namespace votca
	79
	80	#endif // VOTCA_XTP_GAUSSIANQUADRATUREBASE_H

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include/votca/xtp/ImaginaryAxisIntegration.h less more

	0	/*
	1	* Copyright 2009-2020 The VOTCA Development Team
	2	* (http://www.votca.org)
	3	*
	4	* Licensed under the Apache License, Version 2.0 (the "License")
	5	*
	6	* You may not use this file except in compliance with the License.
	7	* You may obtain a copy of the License at
	8	*
	9	* http://www.apache.org/licenses/LICENSE-2.0
	10	*
	11	* Unless required by applicable law or agreed to in writing, software
	12	* distributed under the License is distributed on an "AS IS" BASIS,
	13	* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
	14	* See the License for the specific language governing permissions and
	15	* limitations under the License.
	16	*
	17	*/
	18
	19	#ifndef VOTCA_XTP_IMAGINARYAXISINTEGRATION_H
	20	#define VOTCA_XTP_IMAGINARYAXISINTEGRATION_H
	21
	22	#include "eigen.h"
	23	#include "quadrature_factory.h"
	24	#include "rpa.h"
	25	#include <memory>
	26
	27	// Computes the contribution from the Gauss-Laguerre quadrature to the
	28	// self-energy expectation matrix for given RPA and frequencies
	29	namespace votca {
	30	namespace xtp {
	31
	32	class ImaginaryAxisIntegration {
	33
	34	public:
	35	struct options {
	36	Index order;
	37	Index qptotal;
	38	Index qpmin;
	39	Index homo;
	40	Index rpamin;
	41	Index rpamax;
	42	std::string quadrature_scheme;
	43	double alpha;
	44	};
	45
	46	ImaginaryAxisIntegration(const Eigen::VectorXd& energies,
	47	const TCMatrix_gwbse& Mmn);
	48
	49	void configure(options opt, const RPA& rpa,
	50	const Eigen::MatrixXd& kDielMxInv_zero);
	51
	52	double SigmaGQDiag(double frequency, Index gw_level, double eta) const;
	53
	54	private:
	55	options _opt;
	56
	57	std::unique_ptr<GaussianQuadratureBase> _gq = nullptr;
	58
	59	// This function calculates and stores inverses of the microscopic dielectric
	60	// matrix in a matrix vector
	61	void CalcDielInvVector(const RPA& rpa,
	62	const Eigen::MatrixXd& kDielMxInv_zero);
	63	const Eigen::VectorXd& _energies;
	64	std::vector<Eigen::MatrixXd> _dielinv_matrices_r;
	65	const TCMatrix_gwbse& _Mmn;
	66	};
	67	} // namespace xtp
	68	} // namespace votca
	69	#endif // VOTCA_XTP_IMAGINARYAXISINTEGRATION_H

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-2

include/votca/xtp/IndexParser.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team
	1	* Copyright 2009-2020 The VOTCA Development Team
2	2	* (http://www.votca.org)
3	3	*
4	4	* Licensed under the Apache License, Version 2.0 (the "License")

20	20	#ifndef VOTCA_XTP_INDEXPARSER_H
21	21	#define VOTCA_XTP_INDEXPARSER_H
22	22
	23	// Standard includes
23	24	#include <string>
24	25	#include <vector>
	26
	27	// VOTCA includes
25	28	#include <votca/tools/types.h>
26	29
27	30	/**

43	46	} // namespace xtp
44	47	} // namespace votca
45	48
46		#endif // VOTCA_XTP_ATOMCONTAINER_H
	49	#endif // VOTCA_XTP_INDEXPARSER_H

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-5

include/votca/xtp/adiis.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team
	1	* Copyright 2009-2020 The VOTCA Development Team
2	2	* (http://www.votca.org)
3	3	*
4	4	* Licensed under the Apache License, Version 2.0 (the "License")

17	17	*/
18	18
19	19	#pragma once
20		#ifndef _VOTCA_XTP_ADIIS__H
21		#define _VOTCA_XTP_ADIIS__H
	20	#ifndef VOTCA_XTP_ADIIS_H
	21	#define VOTCA_XTP_ADIIS_H
22	22
	23	// Standard includes
23	24	#include <memory>
24	25	#include <vector>
25		#include <votca/xtp/eigen.h>
	26
	27	// Local VOTCA includes
	28	#include "eigen.h"
	29
26	30	namespace votca {
27	31	namespace xtp {
28	32

40	44	} // namespace xtp
41	45	} // namespace votca
42	46
43		#endif
	47	#endif // VOTCA_XTP_ADIIS_H

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include/votca/xtp/adiis_costfunction.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team
	1	* Copyright 2009-2020 The VOTCA Development Team
2	2	* (http://www.votca.org)
3	3	*
4	4	* Licensed under the Apache License, Version 2.0 (the "License")

20	20	#ifndef VOTCA_XTP_ADIIS_COSTFUNCTION_H
21	21	#define VOTCA_XTP_ADIIS_COSTFUNCTION_H
22	22
23		#include <votca/xtp/optimiser_costfunction.h>
	23	// Local VOTCA includes
	24	#include "optimiser_costfunction.h"
24	25
25	26	namespace votca {
26	27	namespace xtp {

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include/votca/xtp/amplitude_integration.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team
	1	* Copyright 2009-2020 The VOTCA Development Team
2	2	* (http://www.votca.org)
3	3	*
4	4	* Licensed under the Apache License, Version 2.0 (the "License")

17	17	*/
18	18
19	19	#pragma once
20		#ifndef XTP_AMPLITUDE_INTEGRATION_H
21		#define XTP_AMPLITUDE_INTEGRATION_H
	20	#ifndef VOTCA_XTP_AMPLITUDE_INTEGRATION_H
	21	#define VOTCA_XTP_AMPLITUDE_INTEGRATION_H
22	22
23		#include <votca/xtp/aobasis.h>
24		#include <votca/xtp/eigen.h>
25		#include <votca/xtp/regular_grid.h>
	23	// Local VOTCA includes
	24	#include "aobasis.h"
	25	#include "eigen.h"
	26	#include "regular_grid.h"
	27
26	28	namespace votca {
27	29	namespace xtp {
28	30

41	43
42	44	} // namespace xtp
43	45	} // namespace votca
44		#endif // XTP_NUMERICAL_INTEGRATION_H
	46	#endif // VOTCA_XTP_AMPLITUDE_INTEGRATION_H

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include/votca/xtp/anderson_mixing.h less more

	0	/*
	1	* Copyright 2009-2020 The VOTCA Development Team
	2	* (http://www.votca.org)
	3	*
	4	* Licensed under the Apache License, Version 2.0 (the "License")
	5	*
	6	* You may not use this file except in compliance with the License.
	7	* You may obtain a copy of the License at
	8	*
	9	* http://www.apache.org/licenses/LICENSE-2.0
	10	*
	11	* Unless required by applicable law or agreed to in writing, software
	12	* distributed under the License is distributed on an "AS IS" BASIS,
	13	* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
	14	* See the License for the specific language governing permissions and
	15	* limitations under the License.
	16	*
	17	*/
	18
	19	#pragma once
	20	#ifndef VOTCA_XTP_ANDERSON_MIXING_H
	21	#define VOTCA_XTP_ANDERSON_MIXING_H
	22
	23	// Standard includes
	24	#include <vector>
	25
	26	// Local VOTCA includes
	27	#include "eigen.h"
	28
	29	namespace votca {
	30	namespace xtp {
	31	/**
	32	* \brief Anderson mixing as convergence acceleration in SCF/fixed point
	33	* problems
	34	*
	35	* Keeps a history of input and output solution vectors during a self-consistent
	36	* fixed-point procedure and determines a new solution from an optimized mixing.
	37	* Requires specification of the order of the method (maximum history to take)
	38	* and a mixing parameter.
	39	*
	40	* B. Baumeier, Diploma Thesis, Appendix C (2005)
	41	*
	42	* I. Ramiere and T. Helfer, Iterative Residual-Based Vector Methods to
	43	* Accelerate Fixed Point Iterations, Comput. Math. Appl. 70, 2210 (2015)
	44	*/
	45	class Anderson {
	46	public:
	47	const Eigen::VectorXd MixHistory();
	48
	49	void UpdateOutput(const Eigen::VectorXd &newOutput);
	50	void UpdateInput(const Eigen::VectorXd &newInput);
	51	void Configure(const Index order, const double alpha);
	52
	53	private:
	54	std::vector<Eigen::VectorXd> _input;
	55	std::vector<Eigen::VectorXd> _output;
	56
	57	double _alpha = 0.7;
	58	Index _order = 25;
	59	};
	60
	61	} // namespace xtp
	62	} // namespace votca
	63
	64	#endif // VOTCA_XTP_ANDERSON_MIXING_H

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include/votca/xtp/aobasis.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team
	1	* Copyright 2009-2020 The VOTCA Development Team
2	2	* (http://www.votca.org)
3	3	*
4	4	* Licensed under the Apache License, Version 2.0 (the "License")

20	20	#ifndef VOTCA_XTP_AOBASIS_H
21	21	#define VOTCA_XTP_AOBASIS_H
22	22
23		#include <votca/xtp/aoshell.h>
24		#include <votca/xtp/eigen.h>
	23	// Local VOTCA includes
	24	#include "aoshell.h"
	25	#include "checkpoint.h"
	26	#include "eigen.h"
	27	#include <libint2/shell.h>
25	28
26	29	namespace votca {
27	30	namespace xtp {

35	38	*/
36	39	class AOBasis {
37	40	public:
38		void ReorderMOs(Eigen::MatrixXd& v, const std::string& start,
39		const std::string& target) const;
40
41	41	void Fill(const BasisSet& bs, const QMMolecule& atoms);
42	42
43	43	Index AOBasisSize() const { return _AOBasisSize; }

52	52
53	53	Index getNumofShells() const { return Index(_aoshells.size()); }
54	54
	55	Index getMaxNprim() const;
	56
	57	Index getMaxL() const;
	58
	59	std::vector<Index> getMapToBasisFunctions() const;
	60
55	61	const std::vector<Index>& getFuncPerAtom() const { return _FuncperAtom; }
56	62
57		private:
	63	std::vector<libint2::Shell> GenerateLibintBasis() const;
	64
	65	std::vector<std::vector<Index>> ComputeShellPairs(
	66	double threshold = 1e-20) const;
	67
58	68	AOShell& addShell(const Shell& shell, const QMAtom& atom, Index startIndex);
59	69
60		void MultiplyMOs(Eigen::MatrixXd& v,
61		const std::vector<Index>& multiplier) const;
	70	const std::string& Name() const { return _name; }
62	71
63		std::vector<Index> invertOrder(const std::vector<Index>& order) const;
	72	void UpdateShellPositions(const QMMolecule& mol);
64	73
65		std::vector<Index> getReorderVector(const std::string& start,
66		const std::string& target) const;
	74	void WriteToCpt(CheckpointWriter& w) const;
67	75
68		void addReorderShell(const std::string& start, const std::string& target,
69		const std::string& shell,
70		std::vector<Index>& neworder) const;
	76	void ReadFromCpt(CheckpointReader& r);
71	77
72		std::vector<Index> getMultiplierVector(const std::string& start,
73		const std::string& target) const;
	78	void add(const AOBasis& other);
74	79
75		void addMultiplierShell(const std::string& start, const std::string& target,
76		const std::string& shell,
77		std::vector<Index>& multiplier) const;
	80	friend std::ostream& operator<<(std::ostream& out, const AOBasis& aobasis);
	81
	82	private:
	83	void FillFuncperAtom();
	84
	85	void clear();
	86	std::string _name = "";
78	87
79	88	std::vector<AOShell> _aoshells;
80	89

+46

-30

include/votca/xtp/aomatrix.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team
	1	* Copyright 2009-2020 The VOTCA Development Team
2	2	* (http://www.votca.org)
3	3	*
4	4	* Licensed under the Apache License, Version 2.0 (the "License")

20	20	#ifndef VOTCA_XTP_AOMATRIX_H
21	21	#define VOTCA_XTP_AOMATRIX_H
22	22
23		#include <votca/xtp/aobasis.h>
	23	// Local VOTCA includes
	24	#include "aobasis.h"
24	25
25	26	namespace votca {
26	27	namespace xtp {
27	28
28	29	class AOMatrix {
29	30	public:
30		Index Dimension() { return _aomatrix.rows(); }
31		const Eigen::MatrixXd& Matrix() const { return _aomatrix; }
32		void Fill(const AOBasis& aobasis);
33
34		protected:
35		virtual void FillBlock(Eigen::Block<Eigen::MatrixXd>& matrix,
36		const AOShell& shell_row,
37		const AOShell& shell_col) const = 0;
38		Eigen::MatrixXd _aomatrix;
	31	virtual void Fill(const AOBasis& aobasis) = 0;
	32	virtual Index Dimension() = 0;
	33	using MatrixLibInt =
	34	Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>;
39	35	};
40	36
41	37	// derived class for kinetic energy
42	38	class AOKinetic : public AOMatrix {
43		protected:
44		void FillBlock(Eigen::Block<Eigen::MatrixXd>& matrix,
45		const AOShell& shell_row,
46		const AOShell& shell_col) const override;
	39	public:
	40	void Fill(const AOBasis& aobasis) final;
	41	Index Dimension() final { return _aomatrix.rows(); }
	42	const Eigen::MatrixXd& Matrix() const { return _aomatrix; }
	43
	44	private:
	45	Eigen::MatrixXd _aomatrix;
47	46	};
48	47
49	48	// derived class for atomic orbital overlap
50	49	class AOOverlap : public AOMatrix {
51	50	public:
52		Eigen::MatrixXd FillShell(const AOShell& shell) const;
	51	void Fill(const AOBasis& aobasis) final;
	52	Index Dimension() final { return _aomatrix.rows(); }
	53	const Eigen::MatrixXd& Matrix() const { return _aomatrix; }
	54
	55	Eigen::MatrixXd singleShellOverlap(const AOShell& shell) const;
53	56	Index Removedfunctions() const { return removedfunctions; }
54	57	double SmallestEigenValue() const { return smallestEigenvalue; }
55	58
56	59	Eigen::MatrixXd Pseudo_InvSqrt(double etol);
57	60	Eigen::MatrixXd Sqrt();
58	61
59		Eigen::MatrixXd Primitive_Overlap(const AOGaussianPrimitive& g_row,
60		const AOGaussianPrimitive& g_col,
61		Index l_offset = 0) const;
62
63		protected:
64		void FillBlock(Eigen::Block<Eigen::MatrixXd>& matrix,
65		const AOShell& shell_row,
66		const AOShell& shell_col) const override;
67
68	62	private:
69	63	Index removedfunctions;
70	64	double smallestEigenvalue;
	65	Eigen::MatrixXd _aomatrix;
71	66	};
72	67
73	68	// derived class for atomic orbital Coulomb interaction
74	69	class AOCoulomb : public AOMatrix {
75	70	public:
	71	void Fill(const AOBasis& aobasis) final;
	72	Index Dimension() final { return _aomatrix.rows(); }
	73	const Eigen::MatrixXd& Matrix() const { return _aomatrix; }
	74
76	75	Eigen::MatrixXd Pseudo_InvSqrt_GWBSE(const AOOverlap& auxoverlap,
77	76	double etol);
78	77	Eigen::MatrixXd Pseudo_InvSqrt(double etol);
79	78	Index Removedfunctions() const { return removedfunctions; }
80	79
81		protected:
82		void FillBlock(Eigen::Block<Eigen::MatrixXd>& matrix,
83		const AOShell& shell_row,
84		const AOShell& shell_col) const override;
	80	private:
	81	void computeCoulombIntegrals(const AOBasis& aobasis);
	82	Index removedfunctions;
	83	Eigen::MatrixXd _aomatrix;
	84	};
	85
	86	/* derived class for atomic orbital electrical dipole matrices, required for
	87	* electrical transition dipoles
	88	*/
	89	class AODipole : public AOMatrix {
	90	public:
	91	void Fill(const AOBasis& aobasis) final;
	92	Index Dimension() final { return _aomatrix[0].rows(); }
	93	const std::array<Eigen::MatrixXd, 3>& Matrix() const { return _aomatrix; }
	94
	95	void setCenter(const Eigen::Vector3d& r) {
	96	for (Index i = 0; i < 3; i++) {
	97	_r[i] = r[i];
	98	}
	99	} // definition of a center around which the moment should be calculated
85	100
86	101	private:
87		Index removedfunctions;
	102	std::array<Eigen::MatrixXd, 3> _aomatrix;
	103	std::array<libint2::Shell::real_t, 3> _r = {0, 0, 0};
88	104	};
89	105
90	106	} // namespace xtp

+0

-72

~~include/votca/xtp/aomatrix3d.h~~ less more

0		/*
1		* Copyright 2009-2019 The VOTCA Development Team
2		* (http://www.votca.org)
3		*
4		* Licensed under the Apache License, Version 2.0 (the "License")
5		*
6		* You may not use this file except in compliance with the License.
7		* You may obtain a copy of the License at
8		*
9		* http://www.apache.org/licenses/LICENSE-2.0
10		*
11		* Unless required by applicable law or agreed to in writing, software
12		* distributed under the License is distributed on an "AS IS" BASIS,
13		* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
14		* See the License for the specific language governing permissions and
15		* limitations under the License.
16		*
17		*/
18
19		#pragma once
20		#ifndef VOTCA_XTP_AOMATRIX3D_H
21		#define VOTCA_XTP_AOMATRIX3D_H
22
23		#include <votca/xtp/aobasis.h>
24
25		namespace votca {
26		namespace xtp {
27
28		class AOMatrix3D {
29		public:
30		const std::array<Eigen::MatrixXd, 3>& Matrix() const { return _aomatrix; }
31		void Fill(const AOBasis& aobasis);
32		Index Dimension() { return _aomatrix[0].rows(); }
33
34		protected:
35		std::array<Eigen::MatrixXd, 3> _aomatrix;
36		virtual void FillBlock(std::vector<Eigen::Block<Eigen::MatrixXd>>& matrix,
37		const AOShell& shell_row,
38		const AOShell& shell_col) const = 0;
39		};
40
41		/* derived class for atomic orbital gradient matrices, required for
42		* momentum transition dipoles
43		*/
44		class AOMomentum : public AOMatrix3D {
45		protected:
46		void FillBlock(std::vector<Eigen::Block<Eigen::MatrixXd>>& matrix,
47		const AOShell& shell_row,
48		const AOShell& shell_col) const override;
49		};
50
51		/* derived class for atomic orbital electrical dipole matrices, required for
52		* electrical transition dipoles
53		*/
54		class AODipole : public AOMatrix3D {
55		public:
56		void setCenter(const Eigen::Vector3d& r) {
57		_r = r;
58		} // definition of a center around which the moment should be calculated
59		protected:
60		void FillBlock(std::vector<Eigen::Block<Eigen::MatrixXd>>& matrix,
61		const AOShell& shell_row,
62		const AOShell& shell_col) const override;
63
64		private:
65		Eigen::Vector3d _r = Eigen::Vector3d::Zero();
66		};
67
68		} // namespace xtp
69		} // namespace votca
70
71		#endif // VOTCA_XTP_AOMATRIX3D_H

+6

-5

include/votca/xtp/aopotential.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team
	1	* Copyright 2009-2020 The VOTCA Development Team
2	2	* (http://www.votca.org)
3	3	*
4	4	* Licensed under the Apache License, Version 2.0 (the "License")

20	20	#ifndef VOTCA_XTP_AOPOTENTIAL_H
21	21	#define VOTCA_XTP_AOPOTENTIAL_H
22	22
23		#include <votca/xtp/aobasis.h>
24		#include <votca/xtp/ecpaobasis.h>
25		#include <votca/xtp/staticsite.h>
	23	// Local VOTCA includes
	24	#include "aobasis.h"
	25	#include "ecpaobasis.h"
	26	#include "staticsite.h"
26	27
27	28	namespace votca {
28	29	namespace xtp {

113	114	} // namespace xtp
114	115	} // namespace votca
115	116
116		#endif // VOTCA_XTP_AOMATRIX_H
	117	#endif // VOTCA_XTP_AOPOTENTIAL_H

+66

-78

include/votca/xtp/aoshell.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team
	1	* Copyright 2009-2020 The VOTCA Development Team
2	2	* (http://www.votca.org)
3	3	*
4	4	* Licensed under the Apache License, Version 2.0 (the "License")

20	20	#ifndef VOTCA_XTP_AOSHELL_H
21	21	#define VOTCA_XTP_AOSHELL_H
22	22
	23	// Third party includes
23	24	#include <boost/math/constants/constants.hpp>
	25
	26	// VOTCA includes
24	27	#include <votca/tools/constants.h>
25		#include <votca/xtp/eigen.h>
26	28
	29	// Local VOTCA includes
	30	#include "basisset.h"
	31	#include "eigen.h"
27	32	#include "qmatom.h"
28		#include <votca/xtp/basisset.h>
	33	// include libint last otherwise it overrides eigen
	34	#include <libint2/shell.h>
29	35
30	36	namespace votca {
31	37	namespace xtp {
32	38
	39	class AOShell;
33	40	class AOBasis;
34		class AOShell;
35	41
36	42	class AOGaussianPrimitive {
37		friend class AOShell;
	43	friend AOShell;
38	44
39	45	public:
	46	AOGaussianPrimitive(const GaussianPrimitive& gaussian,
	47	const AOShell& aoshell);
	48
	49	AOGaussianPrimitive(const AOGaussianPrimitive& gaussian,
	50	const AOShell& aoshell);
	51
	52	struct data {
	53	Index atomid;
	54	Index l;
	55	Index startindex;
	56	double decay;
	57	double contraction;
	58	double x;
	59	double y;
	60	double z;
	61	double scale;
	62	};
	63
	64	AOGaussianPrimitive(const AOGaussianPrimitive::data& d,
	65	const AOShell& aoshell)
	66	: _aoshell(aoshell) {
	67	_decay = d.decay;
	68	_contraction = d.contraction;
	69	_powfactor = CalcPowFactor(_decay);
	70	}
	71
	72	void SetupCptTable(CptTable& table) const;
	73
	74	void WriteData(data& d) const;
	75
40	76	double getPowfactor() const { return _powfactor; }
41	77	double getDecay() const { return _decay; }
42		const Eigen::VectorXd& getContraction() const { return _contraction; }
	78	double getContraction() const { return _contraction; }
43	79	const AOShell& getShell() const { return _aoshell; }
44	80
45	81	private:
	82	static double CalcPowFactor(double decay) {
	83	return std::pow(2.0 * decay / boost::math::constants::pi<double>(), 0.75);
	84	}
46	85	double _decay;
47		Eigen::VectorXd _contraction;
	86	double _contraction;
48	87	const AOShell& _aoshell;
49	88	double _powfactor; // used in evalspace to speed up DFT
50		// private constructor, only a shell can create a primitive
51		AOGaussianPrimitive(const GaussianPrimitive& gaussian, const AOShell& aoshell)
52		: _decay(gaussian.decay()), _aoshell(aoshell) {
53		_contraction = Eigen::VectorXd::Map(gaussian.Contractions().data(),
54		gaussian.Contractions().size());
55		_powfactor =
56		std::pow(2.0 * _decay / boost::math::constants::pi<double>(), 0.75);
57		}
58
59		AOGaussianPrimitive(const AOGaussianPrimitive& gaussian,
60		const AOShell& aoshell)
61		: _decay(gaussian._decay),
62		_contraction(gaussian._contraction),
63		_aoshell(aoshell),
64		_powfactor(gaussian._powfactor) {
65		;
66		}
67	89	};
68	90
69	91	/*
70	92	* shells in a Gaussian-basis expansion
71	93	*/
72	94	class AOShell {
73		friend class AOBasis;
	95	friend AOBasis;
74	96
75	97	public:
76		AOShell(const AOShell& shell) {
	98	AOShell(const Shell& shell, const QMAtom& atom, Index startIndex);
77	99
78		_type = shell._type;
79		_Lmax = shell._Lmax;
80		_Lmin = shell._Lmin;
81		_scale = shell._scale;
82		_numFunc = shell._numFunc;
83		_numcartFunc = shell._numcartFunc;
84		_mindecay = shell._mindecay;
85		_startIndex = shell._startIndex;
86		_offset = shell._offset;
87		_cartOffset = shell._cartOffset;
88		_pos = shell._pos;
89		_atomindex = shell._atomindex;
90		_gaussians.reserve(shell._gaussians.size());
91		for (const auto& gaus : shell._gaussians) {
92		_gaussians.push_back(AOGaussianPrimitive(gaus, *this));
93		}
	100	AOShell(const AOGaussianPrimitive::data& d) {
	101	_l = static_cast<L>(d.l);
	102	_scale = d.scale;
	103	_startIndex = d.startindex;
	104	_atomindex = d.atomid;
	105	_pos = Eigen::Vector3d(d.x, d.y, d.z);
	106	_gaussians.push_back(AOGaussianPrimitive(d, *this));
94	107	}
95	108
96		const std::string& getType() const { return _type; }
97		Index getNumFunc() const { return _numFunc; }
98		Index getCartesianNumFunc() const { return _numcartFunc; }
	109	AOShell(const AOShell& shell);
	110
	111	L getL() const { return _l; }
	112	Index getNumFunc() const { return NumFuncShell(_l); };
	113	Index getCartesianNumFunc() const { return NumFuncShell_cartesian(_l); };
99	114	Index getStartIndex() const { return _startIndex; }
100		Index getOffset() const { return _offset; }
101		Index getCartesianOffset() const { return _cartOffset; }
	115	Index getOffset() const { return OffsetFuncShell(_l); }
	116	Index getCartesianOffset() const { return OffsetFuncShell_cartesian(_l); }
102	117	Index getAtomIndex() const { return _atomindex; }
	118	Index getSize() const { return _gaussians.size(); }
103	119
104		Index getLmax() const { return _Lmax; }
105		Index getLmin() const { return _Lmin; }
106
107		bool isCombined() const { return _Lmax != _Lmin; }
	120	libint2::Shell LibintShell() const;
108	121
109	122	const Eigen::Vector3d& getPos() const { return _pos; }
110	123	double getScale() const { return _scale; }

112	125	void CalcMinDecay() {
113	126	_mindecay = std::numeric_limits<double>::max();
114	127	for (auto& gaussian : _gaussians) {
115		if (gaussian.getDecay() < _mindecay) {
116		_mindecay = gaussian.getDecay();
117		}
	128	_mindecay = std::min(_mindecay, gaussian.getDecay());
118	129	}
119		return;
120	130	}
121	131
122	132	double getMinDecay() const { return _mindecay; }

143	153	friend std::ostream& operator<<(std::ostream& out, const AOShell& shell);
144	154
145	155	private:
146		// only class aobasis can construct shells
147		AOShell(const Shell& shell, const QMAtom& atom, Index startIndex)
148		: _type(shell.getType()),
149		_Lmax(shell.getLmax()),
150		_Lmin(shell.getLmin()),
151		_scale(shell.getScale()),
152		_numFunc(shell.getnumofFunc()),
153		_numcartFunc(xtp::NumFuncShell_cartesian(shell.getType())),
154		_startIndex(startIndex),
155		_offset(shell.getOffset()),
156		_cartOffset(xtp::OffsetFuncShell_cartesian(shell.getType())),
157		_pos(atom.getPos()),
158		_atomindex(atom.getId()) {
159		;
160		}
161
162		std::string _type;
163		Index _Lmax;
164		Index _Lmin;
	156	L _l;
165	157	// scaling factor
166	158	double _scale;
167	159	// number of functions in shell
168		Index _numFunc;
169		Index _numcartFunc;
170	160	double _mindecay;
171	161	Index _startIndex;
172		Index _offset;
173		Index _cartOffset;
174	162	Eigen::Vector3d _pos;
175	163	Index _atomindex;
176	164

+8

-30

include/votca/xtp/aotransform.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team
	1	* Copyright 2009-2020 The VOTCA Development Team
2	2	* (http://www.votca.org)
3	3	*
4	4	* Licensed under the Apache License, Version 2.0 (the "License")

20	20	#ifndef VOTCA_XTP_AOTRANSFORM_H
21	21	#define VOTCA_XTP_AOTRANSFORM_H
22	22
23		#include <votca/xtp/aoshell.h>
24		#include <votca/xtp/eigen.h>
	23	// Local VOTCA includes
	24	#include "aoshell.h"
	25	#include "eigen.h"
25	26
26	27	namespace votca {
27	28	namespace xtp {

82	83	static std::array<int, 120> i_more_y();
83	84	static std::array<int, 120> i_more_z();
84	85
85		static Index getCartesianSize(Index l);
86		static Index getSphericalSize(Index l);
87	86	static Index getBlockSize(Index lmax);
88		static Eigen::MatrixXd getTrafo(const AOGaussianPrimitive& gaussian);
89	87	static Eigen::VectorXd XIntegrate(Index size, double U);
90	88
91		private:
92		// clang-format off
93		enum S { s };
94		enum P { x, y, z };
95		enum D { xx, xy, xz, yy, yz, zz };
96		enum F { xxx, xxy, xxz, xyy, xyz, xzz, yyy, yyz, yzz, zzz };
97		enum G {
98		xxxx, xxxy, xxxz, xxyy, xxyz, xxzz, xyyy, xyyz, xyzz, xzzz, yyyy,
99		yyyz, yyzz, yzzz, zzzz
100		};
101		enum H {
102		xxxxx, xxxxy, xxxxz, xxxyy, xxxyz, xxxzz, xxyyy, xxyyz, xxyzz, xxzzz,
103		xyyyy, xyyyz, xyyzz, xyzzz, xzzzz, yyyyy, yyyyz, yyyzz, yyzzz, yzzzz,
104		zzzzz
105		};
106		enum I {
107		xxxxxx, xxxxxy, xxxxxz, xxxxyy, xxxxyz, xxxxzz, xxxyyy, xxxyyz, xxxyzz,
108		xxxzzz, xxyyyy, xxyyyz, xxyyzz, xxyzzz, xxzzzz, xyyyyy, xyyyyz, xyyyzz,
109		xyyzzz, xyzzzz, xzzzzz, yyyyyy, yyyyyz, yyyyzz, yyyzzz, yyzzzz, yzzzzz,
110		zzzzzz
111		};
112		// clang-format on
	89	static double getNorm(L l, const AOGaussianPrimitive& gaussian);
113	90
114		static Eigen::MatrixXd getPrimitiveShellTrafo(Index l, double decay,
115		double contraction);
	91	/// transforms a cartesian shell to a spherical cartesian shell
	92	template <typename Matrix>
	93	static Matrix tform(L l_row, L l_col, const Matrix& cartesian);
116	94	};
117	95
118	96	} // namespace xtp

+6

-3

include/votca/xtp/atom.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team
	1	* Copyright 2009-2020 The VOTCA Development Team
2	2	* (http://www.votca.org)
3	3	*
4	4	* Licensed under the Apache License, Version 2.0 (the "License")

22	22	#ifndef VOTCA_XTP_ATOM_H
23	23	#define VOTCA_XTP_ATOM_H
24	24
	25	// Standard includes
25	26	#include <exception>
26	27	#include <map>
27	28	#include <string>
28		#include <votca/xtp/checkpointreader.h>
29		#include <votca/xtp/checkpointwriter.h>
	29
	30	// Local VOTCA includes
	31	#include "checkpointreader.h"
	32	#include "checkpointwriter.h"
30	33
31	34	namespace votca {
32	35	namespace xtp {

+9

-10

include/votca/xtp/atomcontainer.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team
	1	* Copyright 2009-2020 The VOTCA Development Team
2	2	* (http://www.votca.org)
3	3	*
4	4	* Licensed under the Apache License, Version 2.0 (the "License")

19	19	#pragma once
20	20	#ifndef VOTCA_XTP_ATOMCONTAINER_H
21	21	#define VOTCA_XTP_ATOMCONTAINER_H
	22
	23	// Standard includes
22	24	#include <limits>
23	25	#include <typeinfo>
	26
	27	// VOTCA includes
24	28	#include <votca/tools/elements.h>
25		#include <votca/xtp/checkpoint.h>
26		#include <votca/xtp/eigen.h>
	29
	30	// Local VOTCA includes
	31	#include "checkpoint.h"
	32	#include "eigen.h"
27	33
28	34	/**
29	35	* \brief Basic Container for QMAtoms,PolarSites and Atoms

59	65	}
60	66	void push_back(T&& atom) {
61	67	_atomlist.push_back(atom);
62		calcPos();
63		}
64
65		void AddContainer(const AtomContainer<T>& container) {
66		_type += "_" + container._type;
67		_atomlist.insert(_atomlist.end(), container._atomlist.begin(),
68		container._atomlist.end());
69	68	calcPos();
70	69	}
71	70

+30

-26

include/votca/xtp/basisset.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team
	1	* Copyright 2009-2020 The VOTCA Development Team
2	2	* (http://www.votca.org)
3	3	*
4	4	* Licensed under the Apache License, Version 2.0 (the "License")

20	20	#ifndef VOTCA_XTP_BASISSET_H
21	21	#define VOTCA_XTP_BASISSET_H
22	22
	23	// Standard includes
23	24	#include <iostream>
24	25	#include <map>
25	26	#include <memory>
26	27	#include <string>
27	28	#include <vector>
	29
	30	// VOTCA includes
28	31	#include <votca/tools/types.h>
29	32
30	33	namespace votca {
31	34	namespace xtp {
	35
	36	enum class L { S = 0, P = 1, D = 2, F = 3, G = 4, H = 5, I = 6 };
	37
	38	std::string EnumToString(L l);
	39
	40	L StringToEnum(const std::string& type);
	41	L StringToEnum(char type);
	42
32	43	// shell type (S, P, D))
33	44
34		Index FindLmax(const std::string& type);
	45	bool CheckShellType(const std::string& shelltype);
35	46
36		Index FindLmin(const std::string& type);
	47	Index OffsetFuncShell(L l);
37	48
38		Index OffsetFuncShell(const std::string& shell_type);
	49	Index NumFuncShell(L l);
	50	Index NumFuncShell_cartesian(L l);
39	51
40		Index NumFuncShell(const std::string& shell_type);
41		Index NumFuncShell_cartesian(const std::string& shell_type);
42
43		Index OffsetFuncShell_cartesian(const std::string& shell_type);
44
45		std::vector<Index> NumFuncSubShell(const std::string& shell_type);
	52	Index OffsetFuncShell_cartesian(L l);
46	53
47	54	// Gaussian function: contractionexp(-decayr^2)
48	55	class GaussianPrimitive {
49	56	public:
50		GaussianPrimitive(double decay, std::vector<double> contraction)
	57	GaussianPrimitive(double decay, double contraction)
51	58	: _decay(decay), _contraction(contraction) {}
52		const std::vector<double>& Contractions() const { return _contraction; }
	59	double contraction() const { return _contraction; }
53	60
54	61	double decay() const { return _decay; }
55	62
56	63	private:
57	64	double _decay;
58		std::vector<double> _contraction;
	65	double _contraction;
59	66	};
60	67
61	68	class Shell {
62	69
63	70	public:
64		Shell(std::string type, double scale) : _type(type), _scale(scale) { ; }
65		const std::string& getType() const { return _type; }
	71	Shell(L l, double scale) : _l(l), _scale(scale) { ; }
66	72
67		bool isCombined() const { return (_type.length() > 1); }
	73	L getL() const { return _l; }
68	74
69		Index getLmax() const { return FindLmax(_type); }
	75	Index getnumofFunc() const { return NumFuncShell(_l); };
70	76
71		Index getLmin() const { return FindLmin(_type); }
72
73		Index getnumofFunc() const { return NumFuncShell(_type); };
74
75		Index getOffset() const { return OffsetFuncShell(_type); }
	77	Index getOffset() const { return OffsetFuncShell(_l); }
76	78
77	79	double getScale() const { return _scale; }
78	80

86	88	}
87	89
88	90	// adds a Gaussian
89		GaussianPrimitive& addGaussian(double decay, std::vector<double> contraction);
	91	GaussianPrimitive& addGaussian(double decay, double contraction);
90	92	friend std::ostream& operator<<(std::ostream& out, const Shell& shell);
91	93
92	94	private:
93		std::string _type;
	95	L _l;
94	96	// scaling factor
95	97	double _scale;
96	98

111	113
112	114	const std::string& getType() const { return _type; }
113	115
114		Shell& addShell(const std::string& shellType, double shellScale) {
115		_shells.push_back(Shell(shellType, shellScale));
	116	Shell& addShell(L l, double shellScale) {
	117	_shells.push_back(Shell(l, shellScale));
116	118	return _shells.back();
117	119	}
118	120

146	148
147	149	friend std::ostream& operator<<(std::ostream& out, const BasisSet& basis);
148	150
	151	const std::string& Name() const { return _name; }
	152
149	153	private:
150	154	Element& addElement(std::string elementType);
151	155	std::string _name;

+0

-94

~~include/votca/xtp/bfgs-trm.h~~ less more

0		/*
1		* Copyright 2009-2019 The VOTCA Development Team
2		* (http://www.votca.org)
3		*
4		* Licensed under the Apache License, Version 2.0 (the "License")
5		*
6		* You may not use this file except in compliance with the License.
7		* You may obtain a copy of the License at
8		*
9		* http://www.apache.org/licenses/LICENSE-2.0
10		*
11		* Unless required by applicable law or agreed to in writing, software
12		* distributed under the License is distributed on an "AS IS" BASIS,
13		* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
14		* See the License for the specific language governing permissions and
15		* limitations under the License.
16		*
17		*/
18
19		#pragma once
20		#ifndef VOTCA_XTP_BFGSTRM_H
21		#define VOTCA_XTP_BFGSTRM_H
22
23		#include <functional>
24		#include <vector>
25		#include <votca/xtp/logger.h>
26		#include <votca/xtp/optimiser_costfunction.h>
27
28		namespace votca {
29		namespace xtp {
30
31		class BFGSTRM {
32		public:
33		BFGSTRM(Optimiser_costfunction& costfunction) : _costfunction(costfunction) {
34		_hessian = Eigen::MatrixXd::Identity(costfunction.NumParameters(),
35		costfunction.NumParameters());
36		}
37
38		void setLog(Logger* pLog) { _pLog = pLog; }
39
40		void setTrustRadius(double trust_radius) { _trust_radius = trust_radius; }
41
42		double getTrustRadius() const { return _trust_radius; }
43
44		void setCallbacks(const std::vector<std::function<void()> >& callbacks) {
45		_callbacks = callbacks;
46		}
47
48		void setNumofIterations(Index iterations) { _max_iteration = iterations; }
49
50		void Optimize(const Eigen::VectorXd& initialparameters);
51
52		bool Success() const { return _success; }
53		std::string getErrorMessage() const { return _errormessage; }
54
55		double getCost() const { return _cost; }
56
57		Index getIteration() const { return _iteration; }
58
59		const Eigen::VectorXd getParameters() const { return _parameters; }
60
61		void setInitialHessian(const Eigen::MatrixXd& hessian) { _hessian = hessian; }
62
63		private:
64		Optimiser_costfunction& _costfunction;
65
66		void UpdateHessian(const Eigen::VectorXd& delta_pos,
67		const Eigen::VectorXd& delta_gradient);
68		double QuadraticEnergy(const Eigen::VectorXd& gradient,
69		const Eigen::VectorXd& delta_pos) const;
70		bool AcceptRejectStep(const Eigen::VectorXd& delta_pos,
71		const Eigen::VectorXd& gradient, double energy_delta);
72
73		std::string _errormessage;
74		bool _success = true;
75		Index _iteration = 0;
76
77		std::vector<std::function<void()> > _callbacks;
78
79		Eigen::MatrixXd _hessian;
80		Eigen::VectorXd _parameters;
81
82		double _cost = std::numeric_limits<double>::max();
83
84		double _trust_radius = 0.1;
85
86		Index _max_iteration = 200;
87
88		Logger* _pLog;
89		};
90
91		} // namespace xtp
92		} // namespace votca
93		#endif // VOTCA_XTP_BFGSTRM_H

+97

-0

include/votca/xtp/bfgs_trm.h less more

	0	/*
	1	* Copyright 2009-2020 The VOTCA Development Team
	2	* (http://www.votca.org)
	3	*
	4	* Licensed under the Apache License, Version 2.0 (the "License")
	5	*
	6	* You may not use this file except in compliance with the License.
	7	* You may obtain a copy of the License at
	8	*
	9	* http://www.apache.org/licenses/LICENSE-2.0
	10	*
	11	* Unless required by applicable law or agreed to in writing, software
	12	* distributed under the License is distributed on an "AS IS" BASIS,
	13	* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
	14	* See the License for the specific language governing permissions and
	15	* limitations under the License.
	16	*
	17	*/
	18
	19	#pragma once
	20	#ifndef VOTCA_XTP_BFGS_TRM_H
	21	#define VOTCA_XTP_BFGS_TRM_H
	22
	23	// Standard includes
	24	#include <functional>
	25	#include <vector>
	26
	27	// Local VOTCA includes
	28	#include "logger.h"
	29	#include "optimiser_costfunction.h"
	30
	31	namespace votca {
	32	namespace xtp {
	33
	34	class BFGSTRM {
	35	public:
	36	BFGSTRM(Optimiser_costfunction& costfunction) : _costfunction(costfunction) {
	37	_hessian = Eigen::MatrixXd::Identity(costfunction.NumParameters(),
	38	costfunction.NumParameters());
	39	}
	40
	41	void setLog(Logger* pLog) { _pLog = pLog; }
	42
	43	void setTrustRadius(double trust_radius) { _trust_radius = trust_radius; }
	44
	45	double getTrustRadius() const { return _trust_radius; }
	46
	47	void setCallbacks(const std::vector<std::function<void()> >& callbacks) {
	48	_callbacks = callbacks;
	49	}
	50
	51	void setNumofIterations(Index iterations) { _max_iteration = iterations; }
	52
	53	void Optimize(const Eigen::VectorXd& initialparameters);
	54
	55	bool Success() const { return _success; }
	56	std::string getErrorMessage() const { return _errormessage; }
	57
	58	double getCost() const { return _cost; }
	59
	60	Index getIteration() const { return _iteration; }
	61
	62	const Eigen::VectorXd getParameters() const { return _parameters; }
	63
	64	void setInitialHessian(const Eigen::MatrixXd& hessian) { _hessian = hessian; }
	65
	66	private:
	67	Optimiser_costfunction& _costfunction;
	68
	69	void UpdateHessian(const Eigen::VectorXd& delta_pos,
	70	const Eigen::VectorXd& delta_gradient);
	71	double QuadraticEnergy(const Eigen::VectorXd& gradient,
	72	const Eigen::VectorXd& delta_pos) const;
	73	bool AcceptRejectStep(const Eigen::VectorXd& delta_pos,
	74	const Eigen::VectorXd& gradient, double energy_delta);
	75
	76	std::string _errormessage;
	77	bool _success = true;
	78	Index _iteration = 0;
	79
	80	std::vector<std::function<void()> > _callbacks;
	81
	82	Eigen::MatrixXd _hessian;
	83	Eigen::VectorXd _parameters;
	84
	85	double _cost = std::numeric_limits<double>::max();
	86
	87	double _trust_radius = 0.1;
	88
	89	Index _max_iteration = 200;
	90
	91	Logger* _pLog;
	92	};
	93
	94	} // namespace xtp
	95	} // namespace votca
	96	#endif // VOTCA_XTP_BFGS_TRM_H

+55

-27

include/votca/xtp/bse.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team
	1	* Copyright 2009-2020 The VOTCA Development Team
2	2	* (http://www.votca.org)
3	3	*
4	4	* Licensed under the Apache License, Version 2.0 (the "License")

17	17	*/
18	18
19	19	#pragma once
20		#ifndef _VOTCA_XTP_BSE_H
21		#define _VOTCA_XTP_BSE_H
	20	#ifndef VOTCA_XTP_BSE_H
	21	#define VOTCA_XTP_BSE_H
22	22
23		#include <votca/xtp/logger.h>
24		#include <votca/xtp/orbitals.h>
25		#include <votca/xtp/qmstate.h>
26		#include <votca/xtp/threecenter.h>
	23	// Local VOTCA includes
	24	#include "logger.h"
	25	#include "orbitals.h"
	26	#include "qmstate.h"
	27	#include "threecenter.h"
27	28
28	29	namespace votca {
29	30	namespace xtp {

38	39	class BSE {
39	40
40	41	public:
41		BSE(Logger& log, TCMatrix_gwbse& Mmn, const Eigen::MatrixXd& Hqp)
42		: _log(log), _Mmn(Mmn), _Hqp(Hqp){};
	42	// BSE(Logger& log, TCMatrix_gwbse& Mmn, const Eigen::MatrixXd& Hqp_in)
	43	// : _log(log), _Mmn(Mmn), _Hqp_in(Hqp_in){};
	44	BSE(Logger& log, TCMatrix_gwbse& Mmn) : _log(log), _Mmn(Mmn){};
43	45
44	46	struct options {
45	47	bool useTDA = true;

47	49	Index rpamin;
48	50	Index rpamax;
49	51	Index qpmin;
	52	Index qpmax;
50	53	Index vmin;
51	54	Index cmax;
52		Index nmax = 5; // number of eigenvectors to calculate
53		bool davidson = true; // use davidson to diagonalize the matrix
54		bool matrixfree = false; // use matrix free method
55		std::string davidson_correction = "DPR";
56		std::string davidson_ortho = "GS";
57		std::string davidson_tolerance = "normal";
58		std::string davidson_update = "safe";
59		Index davidson_maxiter = 50;
60		double min_print_weight =
61		0.5; // minimium contribution for state to print it
	55	Index nmax; // number of eigenvectors to calculate
	56	bool davidson; // use davidson to diagonalize the matrix
	57	bool matrixfree; // use matrix free method
	58	std::string davidson_correction;
	59	std::string davidson_ortho;
	60	std::string davidson_tolerance;
	61	std::string davidson_update;
	62	Index davidson_maxiter;
	63	double min_print_weight; // minimium contribution for state to print it
	64	bool use_Hqp_offdiag;
	65	Index max_dyn_iter;
	66	double dyn_tolerance;
62	67	};
63	68
64		void configure(const options& opt, const Eigen::VectorXd& DFTenergies);
	69	void configure(const options& opt, const Eigen::VectorXd& RPAEnergies,
	70	const Eigen::MatrixXd& Hqp_in);
65	71
66	72	void Solve_singlets(Orbitals& orb) const;
67	73	void Solve_triplets(Orbitals& orb) const;
	74
	75	Eigen::MatrixXd getHqp() const { return _Hqp; };
68	76
69	77	SingletOperator_TDA getSingletOperator_TDA() const;
70	78	TripletOperator_TDA getTripletOperator_TDA() const;

73	81	const Orbitals& orb) const;
74	82	void Analyze_triplets(std::vector<QMFragment<BSE_Population> > fragments,
75	83	const Orbitals& orb) const;
	84
	85	void Perturbative_DynamicalScreening(const QMStateType& type, Orbitals& orb);
76	86
77	87	private:
78	88	options _opt;

83	93	Eigen::VectorXd qp_contrib;
84	94	};
85	95
	96	struct ExpectationValues {
	97	Eigen::VectorXd direct_term;
	98	Eigen::VectorXd cross_term;
	99	};
	100
86	101	Logger& _log;
87	102	Index _bse_vmax;
88	103	Index _bse_cmin;

90	105	Index _bse_vtotal;
91	106	Index _bse_ctotal;
92	107
	108	Index _max_dyn_iter;
	109	double _dyn_tolerance;
	110
93	111	Eigen::VectorXd _epsilon_0_inv;
94	112
95	113	TCMatrix_gwbse& _Mmn;
96		const Eigen::MatrixXd& _Hqp;
	114	Eigen::MatrixXd _Hqp;
97	115
98	116	tools::EigenSystem Solve_singlets_TDA() const;
99	117	tools::EigenSystem Solve_singlets_BTDA() const;

107	125	void configureBSEOperator(BSE_OPERATOR& H) const;
108	126
109	127	template <typename BSE_OPERATOR>
110		tools::EigenSystem solve_hermitian(BSE_OPERATOR& H) const;
	128	tools::EigenSystem solve_hermitian(BSE_OPERATOR& h) const;
111	129
112	130	template <typename BSE_OPERATOR_ApB, typename BSE_OPERATOR_AmB>
113	131	tools::EigenSystem Solve_nonhermitian(BSE_OPERATOR_ApB& apb,

120	138	void printFragInfo(const std::vector<QMFragment<BSE_Population> >& frags,
121	139	Index state) const;
122	140	void printWeights(Index i_bse, double weight) const;
123		void SetupDirectInteractionOperator(const Eigen::VectorXd& DFTenergies);
	141	void SetupDirectInteractionOperator(const Eigen::VectorXd& DFTenergies,
	142	double energy);
	143
	144	Eigen::MatrixXd AdjustHqpSize(const Eigen::MatrixXd& Hqp_in,
	145	const Eigen::VectorXd& RPAInputEnergies);
124	146
125	147	Interaction Analyze_eh_interaction(const QMStateType& type,
126	148	const Orbitals& orb) const;
127	149	template <typename BSE_OPERATOR>
128		Eigen::VectorXd Analyze_IndividualContribution(const QMStateType& type,
129		const Orbitals& orb,
130		const BSE_OPERATOR& H) const;
	150	ExpectationValues ExpectationValue_Operator(const QMStateType& type,
	151	const Orbitals& orb,
	152	const BSE_OPERATOR& H) const;
	153
	154	template <typename BSE_OPERATOR>
	155	ExpectationValues ExpectationValue_Operator_State(const QMStateType& type,
	156	const Orbitals& orb,
	157	const BSE_OPERATOR& H,
	158	const Index state) const;
131	159	};
132	160	} // namespace xtp
133	161	} // namespace votca
134	162
135		#endif /* _VOTCA_XTP_BSE_H */
	163	#endif // VOTCA_XTP_BSE_H

+8

-7

include/votca/xtp/bse_operator.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team
	1	* Copyright 2009-2020 The VOTCA Development Team
2	2	* (http://www.votca.org)
3	3	*
4	4	* Licensed under the Apache License, Version 2.0 (the "License")

17	17	*/
18	18
19	19	#pragma once
20		#ifndef _VOTCA_XTP_BSE_OPERATOR_H
21		#define _VOTCA_XTP_BSE_OPERATOR_H
	20	#ifndef VOTCA_XTP_BSE_OPERATOR_H
	21	#define VOTCA_XTP_BSE_OPERATOR_H
22	22
23		#include <votca/xtp/eigen.h>
24		#include <votca/xtp/matrixfreeoperator.h>
25		#include <votca/xtp/threecenter.h>
	23	// Local VOTCA includes
	24	#include "eigen.h"
	25	#include "matrixfreeoperator.h"
	26	#include "threecenter.h"
26	27
27	28	namespace votca {
28	29	namespace xtp {

88	89	} // namespace xtp
89	90	} // namespace votca
90	91
91		#endif /* _VOTCA_XTP_BSE_OP_H */
	92	#endif // VOTCA_XTP_BSE_OPERATOR_H

+7

-6

include/votca/xtp/bse_population.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team
	1	* Copyright 2009-2020 The VOTCA Development Team
2	2	* (http://www.votca.org)
3	3	*
4	4	* Licensed under the Apache License, Version 2.0 (the "License")

17	17	*/
18	18
19	19	#pragma once
20		#ifndef VOTCA_XTP_BSE_POPULATIONS_H
21		#define VOTCA_XTP_BSE_POPULATIONS_H
	20	#ifndef VOTCA_XTP_BSE_POPULATION_H
	21	#define VOTCA_XTP_BSE_POPULATION_H
22	22
23		#include <votca/xtp/checkpoint.h>
24		#include <votca/xtp/eigen.h>
	23	// Local VOTCA includes
	24	#include "checkpoint.h"
	25	#include "eigen.h"
25	26
26	27	/**
27	28	* \brief Small container to keep occupation of BSE states for each atom

73	74	} // namespace xtp
74	75	} // namespace votca
75	76
76		#endif // VOTCA_XTP_BSE_POPULATIONS_H
	77	#endif // VOTCA_XTP_BSE_POPULATION_H

+11

-10

include/votca/xtp/bsecoupling.h less more

0	0	/*
1		* Copyright 2009-2019 The VOTCA Development Team