Merge pull request #104 from TREX-CoE/gammcor

Added Cholesky decomposition of ERI and RDM
2024-11-03 20:54:07 +01:00 · 2022-12-01 19:15:58 +01:00 · 2022-12-01 19:15:58 +01:00 · 0c18b60f1d
commit 0c18b60f1d
parent 813577e4a6 062ce5f113
7 changed files with 94 additions and 42 deletions
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@ -15,7 +15,7 @@ jobs:

  get_commit_message:
    name: Get commit message
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
    outputs:
      message: ${{ steps.commit_message.outputs.message }}
    steps:
@ -34,8 +34,8 @@ jobs:

  trexio_ubuntu:

-    runs-on: ubuntu-latest
-    name: x86 Ubuntu latest
+    runs-on: ubuntu-20.04
+    name: x86 Ubuntu 20.04
    needs: get_commit_message

    steps:
@ -101,8 +101,8 @@ jobs:

  trexio_macos:

-    runs-on: macos-latest
-    name: x86 MacOS latest
+    runs-on: macos-11
+    name: x86 MacOS 11

    steps:
      - uses: actions/checkout@v2
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@ -16,7 +16,7 @@ jobs:
  get_commit_message:
    if: ${{ github.event.workflow_run.conclusion == 'success' }}
    name: Get commit message
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
    outputs:
      message: ${{ steps.commit_message.outputs.message }}
    steps:
@ -39,7 +39,7 @@ jobs:
    if: >-
      contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
      (github.repository == 'TREX-CoE/trexio' && startsWith(github.ref, 'refs/tags/v'))
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
    strategy:
      matrix:
        manylinux_tag: [2010_x86_64, 2014_x86_64, 2_24_x86_64]
@ -182,7 +182,7 @@ jobs:
  publish_wheels:
    name: Publish all wheels on PyPI
    needs: [build_linux_wheels, build_macos_wheels]
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04

    steps:
      - name: Checkout the branch
--- a/.github/workflows/gh-pages.yml
+++ b/.github/workflows/gh-pages.yml
@ -20,7 +20,7 @@ jobs:
        run: sudo apt-get update

      - name: install dependencies
-        run: sudo apt-get install emacs26
+        run: sudo apt-get install emacs

      # this step is needed to pull the git submodule org-html-themes
      #- name: initialize submodules
--- a/.gitmodules
+++ b/.gitmodules
@ -1,6 +1,6 @@
 [submodule "python/examples"]
 	path = python/examples
-	url = git@github.com:TREX-CoE/trexio-tutorials.git
+	url = https://github.com/TREX-CoE/trexio-tutorials.git
 [submodule "docs/org-html-themes"]
 	path = docs/org-html-themes
-	url = git@github.com:fniessen/org-html-themes.git
+	url = https://github.com/fniessen/org-html-themes.git
--- a/2
+++ b/2
@ -17,6 +17,8 @@ CHANGES
 - Added OCaml binding
 - Added spin and energy in MOs
 - Added CSF group
+- Added Cholesky-decomposed two-electron integrals
+- Added Cholesky-decomposed RDMs for Gammcor
 - Added `trexio_flush` functionality
 - Optional compilation `--without-fortran`

--- a/cmake/FindTREXIO.cmake
+++ b/cmake/FindTREXIO.cmake
@ -6,7 +6,7 @@
 #  TREXIO_INCLUDE_DIRS - The TREXIO include directories;
 #  TREXIO_LIBRARIES - The libraries needed to use TREXIO;

-# If TREXIO has been installed in a non-standard location, one can set an 
+# If TREXIO has been installed in a non-standard location, one can set an
 # environment variable $TREXIO_DIR in the current shell:
 # $ export TREXIO_DIR=<custom_path>
 # to indicate the prefix used during the TREXIO installation
@ -45,13 +45,13 @@ set(TREXIO_SEARCH_PATHS
 	/opt
 )

-find_path(TREXIO_INCLUDE_DIR 
-	  NAMES trexio.h 
+find_path(TREXIO_INCLUDE_DIR
+	  NAMES trexio.h
 	  HINTS $ENV{TREXIO_DIR}
 	  PATH_SUFFIXES include/trexio include
 	  PATHS ${TREXIO_SEARCH_PATHS}
 	  )
-	        
+

 # No need to specify platform-specific prefix (e.g. libtrexio on Unix) or
 # suffix (e.g. .so on Unix or .dylib on MacOS) in NAMES. CMake takes care of that.
@ -70,8 +70,8 @@ INCLUDE(FindPackageHandleStandardArgs)
 FIND_PACKAGE_HANDLE_STANDARD_ARGS(TREXIO DEFAULT_MSG TREXIO_LIBRARY TREXIO_INCLUDE_DIR )
 MARK_AS_ADVANCED(TREXIO_INCLUDE_DIR TREXIO_LIBRARY)

-# Mot setting _INCLUDE_DIR and _LIBRARIES is considered a bug, 
+# Mot setting _INCLUDE_DIR and _LIBRARIES is considered a bug,
 # see https://gitlab.kitware.com/cmake/community/-/wikis/doc/tutorials/How-To-Find-Libraries
 set(TREXIO_LIBRARIES ${TREXIO_LIBRARY})
-set(TREXIO_INCLUDE_DIRS ${TREXIO_INCLUDE_DIR}) 
+set(TREXIO_INCLUDE_DIRS ${TREXIO_INCLUDE_DIR})

--- a/trex.org
+++ b/trex.org
@ -651,15 +651,25 @@ prim_factor =

 ** Two-electron integrals (~mo_2e_int~ group)

-   The operators as the same as those defined in the
+   The operators are the same as those defined in the
   [[#ao_two_e][AO two-electron integrals section]]. Here, the integrals are given in
   the basis of molecular orbitals.

+   The Cholesky decomposition of the integrals can also be stored:
+
+   \[
+   \A_{ijkl} = \sum_{\alpha} G_{il\alpha} G_{jl\alpha}
+   \]
+
   #+NAME: mo_2e_int
-  | Variable | Type           | Dimensions                         | Description                             |
-  |----------+----------------+------------------------------------+-----------------------------------------|
-  | ~eri~    | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Electron repulsion integrals            |
-  | ~eri_lr~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Long-range Electron repulsion integrals |
+  | Variable              | Type           | Dimensions                              | Description                                   |
+  |-----------------------+----------------+-----------------------------------------+-----------------------------------------------|
+  | ~eri~                 | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~      | Electron repulsion integrals                  |
+  | ~eri_lr~              | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~      | Long-range Electron repulsion integrals       |
+  | ~eri_cholesky_num~    | ~dim~          |                                         | Number of Cholesky vectors for ERI            |
+  | ~eri_cholesky~        | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_cholesky_num)~ | Cholesky decomposition of the ERI             |
+  | ~eri_lr_cholesky_num~ | ~dim~          |                                         | Number of Cholesky vectors for long range ERI |
+  | ~eri_lr_cholesky~     | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_cholesky_num)~ | Cholesky decomposition of the long range ERI  |

   #+CALL: json(data=mo_2e_int, title="mo_2e_int")

@ -667,8 +677,12 @@ prim_factor =
   :results:
   #+begin_src python :tangle trex.json
       "mo_2e_int": {
-              "eri" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
-         , "eri_lr" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
+                           "eri" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ]    ]
+         ,              "eri_lr" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ]    ]
+         ,    "eri_cholesky_num" : [ "dim"         , []                                            ]
+         ,        "eri_cholesky" : [ "float sparse", [ "rdm.2e_cholesky_num", "mo.num", "mo.num" ] ]
+         , "eri_lr_cholesky_num" : [ "dim"         , []                                            ]
+         ,     "eri_lr_cholesky" : [ "float sparse", [ "rdm.2e_cholesky_num", "mo.num", "mo.num" ] ]
       } ,
   #+end_src
   :end:
@ -833,17 +847,43 @@ prim_factor =
      \frac{1}{2} \sum_{ijlk} \Gamma_{ijkl} \langle k l | i j \rangle
  \]

+
+  To compress the storage, the Cholesky decomposition of the RDMs can
+  be stored:
+
+  \[
+    \Gamma_{ijkl} = \sum_{\alpha} G_{ij\alpha} G_{kl\alpha}
+  \]
+
+  Warning: as opposed to electron repulsion integrals, the
+  decomposition is made such that the Cholesky vectors are expanded
+  in a two-electron basis
+  $f_{ij}(\mathbf{r}_1,\mathbf{r}_2) = \phi_i(\mathbf{r}_1) \phi_j(\mathbf{r}_2)$,
+  whereas in electron repulsion integrals each Cholesky vector is
+  expressed in a basis of a one-electron function
+  $g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)$.
+  
  #+NAME: rdm
-  | Variable  | Type           | Dimensions                         | Description                                                           |
-  |-----------+----------------+------------------------------------+-----------------------------------------------------------------------|
-  | ~1e~      | ~float~        | ~(mo.num, mo.num)~                 | 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              |
-  | ~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_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_dnup~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \downarrow\uparrow component of the two-body reduced density matrix   |
+  | Variable               | Type           | Dimensions                                   | Description                                                           |
+  |------------------------+----------------+----------------------------------------------+-----------------------------------------------------------------------|
+  | ~1e~                   | ~float~        | ~(mo.num, mo.num)~                           | 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              |
+  | ~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_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_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")

@ -851,14 +891,24 @@ prim_factor =
  :results:
  #+begin_src python :tangle trex.json
      "rdm": {
-               "1e" : [ "float"       , [ "mo.num", "mo.num" ]                     ]
-        ,   "1e_up" : [ "float"       , [ "mo.num", "mo.num" ]                     ]
-        ,   "1e_dn" : [ "float"       , [ "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_dndn" : [ "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" ] ]
+                            "1e" : [ "float"       , [ "mo.num", "mo.num" ]                             ]
+        ,                "1e_up" : [ "float"       , [ "mo.num", "mo.num" ]                             ]
+        ,                "1e_dn" : [ "float"       , [ "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_dndn" : [ "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_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: