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https://github.com/TREX-CoE/trexio.git
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Merge pull request #104 from TREX-CoE/gammcor
Added Cholesky decomposition of ERI and RDM
This commit is contained in:
GitHub
commit
0c18b60f1d
10
.github/workflows/actions.yml
vendored
10
.github/workflows/actions.yml
vendored
@ -15,7 +15,7 @@ jobs:
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|||||||
|
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get_commit_message:
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get_commit_message:
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name: Get commit message
|
name: Get commit message
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runs-on: ubuntu-latest
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runs-on: ubuntu-20.04
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outputs:
|
outputs:
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||||||
message: ${{ steps.commit_message.outputs.message }}
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message: ${{ steps.commit_message.outputs.message }}
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steps:
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steps:
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@ -34,8 +34,8 @@ jobs:
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|
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trexio_ubuntu:
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trexio_ubuntu:
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|
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runs-on: ubuntu-latest
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runs-on: ubuntu-20.04
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name: x86 Ubuntu latest
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name: x86 Ubuntu 20.04
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needs: get_commit_message
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needs: get_commit_message
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|
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steps:
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steps:
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@ -101,8 +101,8 @@ jobs:
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trexio_macos:
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trexio_macos:
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|
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runs-on: macos-latest
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runs-on: macos-11
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name: x86 MacOS latest
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name: x86 MacOS 11
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|
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steps:
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v2
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6
.github/workflows/build-wheels.yml
vendored
6
.github/workflows/build-wheels.yml
vendored
@ -16,7 +16,7 @@ jobs:
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|||||||
get_commit_message:
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get_commit_message:
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if: ${{ github.event.workflow_run.conclusion == 'success' }}
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if: ${{ github.event.workflow_run.conclusion == 'success' }}
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name: Get commit message
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name: Get commit message
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runs-on: ubuntu-latest
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runs-on: ubuntu-20.04
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outputs:
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outputs:
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message: ${{ steps.commit_message.outputs.message }}
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message: ${{ steps.commit_message.outputs.message }}
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steps:
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steps:
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@ -39,7 +39,7 @@ jobs:
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if: >-
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if: >-
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contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
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contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
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(github.repository == 'TREX-CoE/trexio' && startsWith(github.ref, 'refs/tags/v'))
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(github.repository == 'TREX-CoE/trexio' && startsWith(github.ref, 'refs/tags/v'))
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runs-on: ubuntu-latest
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runs-on: ubuntu-20.04
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strategy:
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strategy:
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matrix:
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matrix:
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manylinux_tag: [2010_x86_64, 2014_x86_64, 2_24_x86_64]
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manylinux_tag: [2010_x86_64, 2014_x86_64, 2_24_x86_64]
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@ -182,7 +182,7 @@ jobs:
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publish_wheels:
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publish_wheels:
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name: Publish all wheels on PyPI
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name: Publish all wheels on PyPI
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needs: [build_linux_wheels, build_macos_wheels]
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needs: [build_linux_wheels, build_macos_wheels]
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runs-on: ubuntu-latest
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runs-on: ubuntu-20.04
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steps:
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steps:
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- name: Checkout the branch
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- name: Checkout the branch
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2
.github/workflows/gh-pages.yml
vendored
2
.github/workflows/gh-pages.yml
vendored
@ -20,7 +20,7 @@ jobs:
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run: sudo apt-get update
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run: sudo apt-get update
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- name: install dependencies
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- name: install dependencies
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run: sudo apt-get install emacs26
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run: sudo apt-get install emacs
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# this step is needed to pull the git submodule org-html-themes
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# this step is needed to pull the git submodule org-html-themes
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#- name: initialize submodules
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#- name: initialize submodules
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4
.gitmodules
vendored
4
.gitmodules
vendored
@ -1,6 +1,6 @@
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[submodule "python/examples"]
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[submodule "python/examples"]
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path = python/examples
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path = python/examples
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url = git@github.com:TREX-CoE/trexio-tutorials.git
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url = https://github.com/TREX-CoE/trexio-tutorials.git
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[submodule "docs/org-html-themes"]
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[submodule "docs/org-html-themes"]
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path = docs/org-html-themes
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path = docs/org-html-themes
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url = git@github.com:fniessen/org-html-themes.git
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url = https://github.com/fniessen/org-html-themes.git
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@ -17,6 +17,8 @@ CHANGES
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- Added OCaml binding
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- Added OCaml binding
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- Added spin and energy in MOs
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- Added spin and energy in MOs
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- Added CSF group
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- Added CSF group
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- Added Cholesky-decomposed two-electron integrals
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- Added Cholesky-decomposed RDMs for Gammcor
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- Added `trexio_flush` functionality
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- Added `trexio_flush` functionality
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- Optional compilation `--without-fortran`
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- Optional compilation `--without-fortran`
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@ -6,7 +6,7 @@
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# TREXIO_INCLUDE_DIRS - The TREXIO include directories;
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# TREXIO_INCLUDE_DIRS - The TREXIO include directories;
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# TREXIO_LIBRARIES - The libraries needed to use TREXIO;
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# TREXIO_LIBRARIES - The libraries needed to use TREXIO;
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|
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# If TREXIO has been installed in a non-standard location, one can set an
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# If TREXIO has been installed in a non-standard location, one can set an
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# environment variable $TREXIO_DIR in the current shell:
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# environment variable $TREXIO_DIR in the current shell:
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# $ export TREXIO_DIR=<custom_path>
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# $ export TREXIO_DIR=<custom_path>
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# to indicate the prefix used during the TREXIO installation
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# to indicate the prefix used during the TREXIO installation
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@ -45,13 +45,13 @@ set(TREXIO_SEARCH_PATHS
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/opt
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/opt
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)
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)
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find_path(TREXIO_INCLUDE_DIR
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find_path(TREXIO_INCLUDE_DIR
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NAMES trexio.h
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NAMES trexio.h
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HINTS $ENV{TREXIO_DIR}
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HINTS $ENV{TREXIO_DIR}
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PATH_SUFFIXES include/trexio include
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PATH_SUFFIXES include/trexio include
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PATHS ${TREXIO_SEARCH_PATHS}
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PATHS ${TREXIO_SEARCH_PATHS}
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)
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)
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# No need to specify platform-specific prefix (e.g. libtrexio on Unix) or
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# No need to specify platform-specific prefix (e.g. libtrexio on Unix) or
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# suffix (e.g. .so on Unix or .dylib on MacOS) in NAMES. CMake takes care of that.
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# suffix (e.g. .so on Unix or .dylib on MacOS) in NAMES. CMake takes care of that.
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@ -70,8 +70,8 @@ INCLUDE(FindPackageHandleStandardArgs)
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FIND_PACKAGE_HANDLE_STANDARD_ARGS(TREXIO DEFAULT_MSG TREXIO_LIBRARY TREXIO_INCLUDE_DIR )
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FIND_PACKAGE_HANDLE_STANDARD_ARGS(TREXIO DEFAULT_MSG TREXIO_LIBRARY TREXIO_INCLUDE_DIR )
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MARK_AS_ADVANCED(TREXIO_INCLUDE_DIR TREXIO_LIBRARY)
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MARK_AS_ADVANCED(TREXIO_INCLUDE_DIR TREXIO_LIBRARY)
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# Mot setting _INCLUDE_DIR and _LIBRARIES is considered a bug,
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# Mot setting _INCLUDE_DIR and _LIBRARIES is considered a bug,
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# see https://gitlab.kitware.com/cmake/community/-/wikis/doc/tutorials/How-To-Find-Libraries
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# see https://gitlab.kitware.com/cmake/community/-/wikis/doc/tutorials/How-To-Find-Libraries
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set(TREXIO_LIBRARIES ${TREXIO_LIBRARY})
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set(TREXIO_LIBRARIES ${TREXIO_LIBRARY})
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set(TREXIO_INCLUDE_DIRS ${TREXIO_INCLUDE_DIR})
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set(TREXIO_INCLUDE_DIRS ${TREXIO_INCLUDE_DIR})
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100
trex.org
100
trex.org
@ -651,15 +651,25 @@ prim_factor =
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** Two-electron integrals (~mo_2e_int~ group)
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** Two-electron integrals (~mo_2e_int~ group)
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The operators as the same as those defined in the
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The operators are the same as those defined in the
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[[#ao_two_e][AO two-electron integrals section]]. Here, the integrals are given in
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[[#ao_two_e][AO two-electron integrals section]]. Here, the integrals are given in
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the basis of molecular orbitals.
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the basis of molecular orbitals.
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The Cholesky decomposition of the integrals can also be stored:
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\[
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\A_{ijkl} = \sum_{\alpha} G_{il\alpha} G_{jl\alpha}
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\]
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#+NAME: mo_2e_int
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#+NAME: mo_2e_int
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| Variable | Type | Dimensions | Description |
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| Variable | Type | Dimensions | Description |
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|----------+----------------+------------------------------------+-----------------------------------------|
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|-----------------------+----------------+-----------------------------------------+-----------------------------------------------|
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| ~eri~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Electron repulsion integrals |
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| ~eri~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Electron repulsion integrals |
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| ~eri_lr~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Long-range Electron repulsion integrals |
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| ~eri_lr~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Long-range Electron repulsion integrals |
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| ~eri_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for ERI |
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| ~eri_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_cholesky_num)~ | Cholesky decomposition of the ERI |
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| ~eri_lr_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for long range ERI |
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| ~eri_lr_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_cholesky_num)~ | Cholesky decomposition of the long range ERI |
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#+CALL: json(data=mo_2e_int, title="mo_2e_int")
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#+CALL: json(data=mo_2e_int, title="mo_2e_int")
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@ -667,8 +677,12 @@ prim_factor =
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:results:
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:results:
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#+begin_src python :tangle trex.json
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#+begin_src python :tangle trex.json
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"mo_2e_int": {
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"mo_2e_int": {
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"eri" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
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"eri" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
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, "eri_lr" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
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, "eri_lr" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
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, "eri_cholesky_num" : [ "dim" , [] ]
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, "eri_cholesky" : [ "float sparse", [ "rdm.2e_cholesky_num", "mo.num", "mo.num" ] ]
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, "eri_lr_cholesky_num" : [ "dim" , [] ]
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, "eri_lr_cholesky" : [ "float sparse", [ "rdm.2e_cholesky_num", "mo.num", "mo.num" ] ]
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} ,
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} ,
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#+end_src
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#+end_src
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:end:
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:end:
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@ -833,17 +847,43 @@ prim_factor =
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\frac{1}{2} \sum_{ijlk} \Gamma_{ijkl} \langle k l | i j \rangle
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\frac{1}{2} \sum_{ijlk} \Gamma_{ijkl} \langle k l | i j \rangle
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\]
|
\]
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|
To compress the storage, the Cholesky decomposition of the RDMs can
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|
be stored:
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|
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|
\[
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|
\Gamma_{ijkl} = \sum_{\alpha} G_{ij\alpha} G_{kl\alpha}
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\]
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|
Warning: as opposed to electron repulsion integrals, the
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|
decomposition is made such that the Cholesky vectors are expanded
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|
in a two-electron basis
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|
$f_{ij}(\mathbf{r}_1,\mathbf{r}_2) = \phi_i(\mathbf{r}_1) \phi_j(\mathbf{r}_2)$,
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|
whereas in electron repulsion integrals each Cholesky vector is
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|
expressed in a basis of a one-electron function
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|
$g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)$.
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|
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#+NAME: rdm
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#+NAME: rdm
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| Variable | Type | Dimensions | Description |
|
| Variable | Type | Dimensions | Description |
|
||||||
|-----------+----------------+------------------------------------+-----------------------------------------------------------------------|
|
|------------------------+----------------+----------------------------------------------+-----------------------------------------------------------------------|
|
||||||
| ~1e~ | ~float~ | ~(mo.num, mo.num)~ | One body density matrix |
|
| ~1e~ | ~float~ | ~(mo.num, mo.num)~ | One body density matrix |
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| ~1e_up~ | ~float~ | ~(mo.num, mo.num)~ | \uparrow-spin component of the one body density matrix |
|
| ~1e_up~ | ~float~ | ~(mo.num, mo.num)~ | \uparrow-spin component of the one body density matrix |
|
||||||
| ~1e_dn~ | ~float~ | ~(mo.num, mo.num)~ | \downarrow-spin component of the one body density matrix |
|
| ~1e_dn~ | ~float~ | ~(mo.num, mo.num)~ | \downarrow-spin component of the one body density matrix |
|
||||||
| ~2e~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Two-body reduced density matrix (spin trace) |
|
| ~2e~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Two-body reduced density matrix (spin trace) |
|
||||||
| ~2e_upup~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\uparrow component of the two-body reduced density matrix |
|
| ~2e_upup~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\uparrow component of the two-body reduced density matrix |
|
||||||
| ~2e_dndn~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \downarrow\downarrow component of the two-body reduced density matrix |
|
| ~2e_dndn~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \downarrow\downarrow component of the two-body reduced density matrix |
|
||||||
| ~2e_updn~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\downarrow component of the two-body reduced density matrix |
|
| ~2e_updn~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\downarrow component of the two-body reduced density matrix |
|
||||||
| ~2e_dnup~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \downarrow\uparrow component of the two-body reduced density matrix |
|
| ~2e_dnup~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \downarrow\uparrow component of the two-body reduced density matrix |
|
||||||
|
| ~2e_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
|
||||||
|
| ~2e_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_cholesky_num)~ | Cholesky decomposition of the Two-body RDM (spin trace) |
|
||||||
|
| ~2e_upup_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
|
||||||
|
| ~2e_upup_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_upup_cholesky_num)~ | Cholesky decomposition of the Two-body RDM (\uparrow\uparrow) |
|
||||||
|
| ~2e_dndn_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
|
||||||
|
| ~2e_dndn_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_dndn_cholesky_num)~ | Cholesky decomposition of the Two-body RDM (\downarrow\downarrow) |
|
||||||
|
| ~2e_updn_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
|
||||||
|
| ~2e_updn_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_updn_cholesky_num)~ | Cholesky decomposition of the Two-body RDM (\uparrow\downarrow) |
|
||||||
|
| ~2e_dnup_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
|
||||||
|
| ~2e_dnup_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_dnup_cholesky_num)~ | Cholesky decomposition of the Two-body RDM (\downarrow\uparrow) |
|
||||||
|
|
||||||
#+CALL: json(data=rdm, title="rdm")
|
#+CALL: json(data=rdm, title="rdm")
|
||||||
|
|
||||||
@ -851,14 +891,24 @@ prim_factor =
|
|||||||
:results:
|
:results:
|
||||||
#+begin_src python :tangle trex.json
|
#+begin_src python :tangle trex.json
|
||||||
"rdm": {
|
"rdm": {
|
||||||
"1e" : [ "float" , [ "mo.num", "mo.num" ] ]
|
"1e" : [ "float" , [ "mo.num", "mo.num" ] ]
|
||||||
, "1e_up" : [ "float" , [ "mo.num", "mo.num" ] ]
|
, "1e_up" : [ "float" , [ "mo.num", "mo.num" ] ]
|
||||||
, "1e_dn" : [ "float" , [ "mo.num", "mo.num" ] ]
|
, "1e_dn" : [ "float" , [ "mo.num", "mo.num" ] ]
|
||||||
, "2e" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
, "2e" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
||||||
, "2e_upup" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
, "2e_upup" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
||||||
, "2e_dndn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
, "2e_dndn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
||||||
, "2e_updn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
, "2e_updn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
||||||
, "2e_dnup" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
, "2e_dnup" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
||||||
|
, "2e_cholesky_num" : [ "dim" , [] ]
|
||||||
|
, "2e_cholesky" : [ "float sparse", [ "rdm.2e_cholesky_num", "mo.num", "mo.num" ] ]
|
||||||
|
, "2e_upup_cholesky_num" : [ "dim" , [] ]
|
||||||
|
, "2e_upup_cholesky" : [ "float sparse", [ "rdm.2e_upup_cholesky_num", "mo.num", "mo.num" ] ]
|
||||||
|
, "2e_dndn_cholesky_num" : [ "dim" , [] ]
|
||||||
|
, "2e_dndn_cholesky" : [ "float sparse", [ "rdm.2e_dndn_cholesky_num", "mo.num", "mo.num" ] ]
|
||||||
|
, "2e_updn_cholesky_num" : [ "dim" , [] ]
|
||||||
|
, "2e_updn_cholesky" : [ "float sparse", [ "rdm.2e_updn_cholesky_num", "mo.num", "mo.num" ] ]
|
||||||
|
, "2e_dnup_cholesky_num" : [ "dim" , [] ]
|
||||||
|
, "2e_dnup_cholesky" : [ "float sparse", [ "rdm.2e_dnup_cholesky_num", "mo.num", "mo.num" ] ]
|
||||||
} ,
|
} ,
|
||||||
#+end_src
|
#+end_src
|
||||||
:end:
|
:end:
|
||||||
|
|||||||
Loading…
Reference in New Issue
Block a user