mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-08-25 06:31:43 +02:00
Merge branch 'TREX-CoE:master' into master
This commit is contained in:
joguenzl
GitHub
commit
7ed53ab71c
18
.github/workflows/actions.yml
vendored
18
.github/workflows/actions.yml
vendored
@ -112,8 +112,8 @@ jobs:
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run: make maintainer-clean
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trexio_macos:
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name: x86 MacOS 11
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runs-on: macos-11
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name: x86 MacOS 12
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runs-on: macos-12
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steps:
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- uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
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@ -121,13 +121,14 @@ jobs:
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- name: install dependencies
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run: |
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brew install emacs
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brew install hdf5
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brew install hdf5@1.12
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brew install automake
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brew --prefix hdf5
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- name: configure with autotools
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run: |
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./autogen.sh
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./configure FC=gfortran-10 --enable-silent-rules
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./configure FC=gfortran-12 --enable-silent-rules
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- name: compile TREXIO
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run: make -j3
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@ -135,6 +136,15 @@ jobs:
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- name: check TREXIO
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run: make -j3 check
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- name: compile Python API
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run: |
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export H5_CFLAGS="-I$(brew --prefix hdf5)/include"
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export H5_LDFLAGS="-L$(brew --prefix hdf5)/lib"
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make python-install
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- name: test Python API
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run: make python-test
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- name: Archive test log file
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if: failure()
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uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
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37
.github/workflows/build-wheels.yml
vendored
37
.github/workflows/build-wheels.yml
vendored
@ -21,7 +21,7 @@ jobs:
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message: ${{ steps.commit_message.outputs.message }}
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steps:
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- name: Checkout the repo
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uses: actions/checkout@v2
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uses: actions/checkout@v3
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# Gets the correct commit message for pull request
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with:
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ref: ${{ github.event.pull_request.head.sha }}
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@ -42,14 +42,14 @@ jobs:
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runs-on: ubuntu-20.04
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strategy:
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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: [2014_x86_64, 2_24_x86_64]
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steps:
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- name: Checkout the branch
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uses: actions/checkout@v2
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uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v1
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uses: actions/setup-python@v4
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with:
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python-version: '3.9'
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@ -103,22 +103,14 @@ jobs:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [macos-10.15]
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python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
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# TODO: normally, one could include macos-11 and the OS list above but the produced wheels receive an error upon installation:
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# ERROR: trexio-1.1.0-cp39-cp39-macosx_11_0_x86_64.whl is not a supported wheel on this platform.
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# This happens even with the MACOSX_DEPLOYMENT_TARGET trick. Perhaps it can be solved by configuring the build system
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# to produce the wheels for MacOS-11 from the very beginning
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#exclude:
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# - os: macos-11
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env:
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H5_LDFLAGS: '-L/usr/local/Cellar/hdf5/1.12.1/lib'
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H5_CFLAGS: '-I/usr/local/Cellar/hdf5/1.12.1/include'
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os: [macos-12]
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python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v2
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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@ -128,11 +120,6 @@ jobs:
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- name: Install HDF5
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run: brew install hdf5@1.12
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# This step is needed to produce wheels with the correct platform tag for MacOS-11 (Big Sur)
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#- name: Set MACOSX_DEPLOYMENT_TARGET environment variable
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# if: ${{ matrix.os == 'macos-11' }}
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# run: echo "MACOSX_DEPLOYMENT_TARGET=11.0" >> $GITHUB_ENV
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- name: Compute the PYTREXIO_VERSION environment variable
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run: echo "PYTREXIO_VERSION=$(grep __version__ python/pytrexio/_version.py | cut -d\ -f3 | tr -d '"')" >> $GITHUB_ENV
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@ -158,6 +145,8 @@ jobs:
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run: |
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mkdir wheelhouse/
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cd trexio-${{ env.PYTREXIO_VERSION }}/
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export H5_CFLAGS="-I$(brew --prefix hdf5)/include"
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export H5_LDFLAGS="-L$(brew --prefix hdf5)/lib"
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python -m build --wheel --outdir=./
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delocate-wheel trexio-*.whl
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mv trexio-*.whl ../wheelhouse/
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@ -186,10 +175,10 @@ jobs:
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steps:
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- name: Checkout the branch
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uses: actions/checkout@v2
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uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v1
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uses: actions/setup-python@v4
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with:
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python-version: '3.9'
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@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.16)
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# Initialize the CMake project.
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project(Trexio
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VERSION 2.4.0
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VERSION 2.3.1
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DESCRIPTION "TREX I/O library"
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LANGUAGES C Fortran
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)
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@ -2,7 +2,7 @@
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# Process this file with autoconf to produce a configure script.
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AC_PREREQ([2.69])
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AC_INIT([trexio],[2.4.0],[https://github.com/TREX-CoE/trexio/issues])
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AC_INIT([trexio],[2.3.1],[https://github.com/TREX-CoE/trexio/issues])
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AC_CONFIG_SRCDIR([Makefile.in])
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AC_CONFIG_HEADERS([include/config.h])
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@ -200,7 +200,7 @@ program print_energy
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#+begin_src f90
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call getarg(1, filename)
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f = trexio_open (filename, 'r', TREXIO_HDF5, rc)
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f = trexio_open (filename, 'r', TREXIO_AUTO, rc)
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if (rc /= TREXIO_SUCCESS) then
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call trexio_string_of_error(rc, err_msg)
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print *, 'Error opening TREXIO file: '//trim(err_msg)
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@ -410,6 +410,139 @@ program print_energy
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end program
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#+end_src
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** Python
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:PROPERTIES:
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:header-args: :tangle print_energy.py
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:END:
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#+begin_src python
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import sys
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import trexio
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import numpy as np
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BUFSIZE = 100000
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#+end_src
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This program computes the energy as:
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\[
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E = E_{\text{NN}} + \sum_{ij} \gamma_{ij}\, \langle j | h | i \rangle\,
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+\, \frac{1}{2} \sum_{ijkl} \Gamma_{ijkl}\, \langle k l | i j
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\rangle\; \textrm{ with } \; 0 < i,j,k,l \le n
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\]
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One needs to read from the TREXIO file:
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- $n$ :: The number of molecular orbitals
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- $E_{\text{NN}}$ :: The nuclear repulsion energy
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- $\gamma_{ij}$ :: The one-body reduced density matrix
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- $\langle j |h| i \rangle$ :: The one-electron Hamiltonian integrals
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- $\Gamma_{ijkl}$ :: The two-body reduced density matrix
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- $\langle k l | i j \rangle$ :: The electron repulsion integrals
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*** Obtain the name of the TREXIO file from the command line, and open it for reading
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#+begin_src python
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filename = sys.argv[1]
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f = trexio.File(filename, 'r', trexio.TREXIO_AUTO)
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#+end_src
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*** Read the nuclear repulsion energy
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#+begin_src python
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E_nn = trexio.read_nucleus_repulsion(f)
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#+end_src
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*** Read the number of molecular orbitals
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#+begin_src python
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n = trexio.read_mo_num(f)
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#+end_src
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*** Read one-electron quantities
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#+begin_src python
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if not trexio.has_mo_1e_int_core_hamiltonian(f):
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print("No core hamiltonian in file")
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sys.exit(-1)
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h0 = trexio.read_mo_1e_int_core_hamiltonian(f)
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if not trexio.has_rdm_1e(f):
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print("No 1e RDM in file")
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sys.exit(-1)
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D = trexio.read_rdm_1e(f)
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#+end_src
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*** Read two-electron quantities
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**** Electron repulsion integrals
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#+begin_src python
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if not trexio.has_mo_2e_int_eri(f):
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print("No electron repulsion integrals in file")
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sys.exit(-1)
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size_max = trexio.read_mo_2e_int_eri_size(f)
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offset = 0
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icount = BUFSIZE
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feof = False
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W = np.zeros( (n,n,n,n) )
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while not feof:
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buffer_index, buffer_values, icount, feof = trexio.read_mo_2e_int_eri(f, offset, icount)
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for m in range(icount):
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i, j, k, l = buffer_index[m]
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W[i,j,k,l] = buffer_values[m]
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W[k,j,i,l] = buffer_values[m]
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W[i,l,k,j] = buffer_values[m]
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W[k,l,i,j] = buffer_values[m]
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W[j,i,l,k] = buffer_values[m]
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W[j,k,l,i] = buffer_values[m]
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W[l,i,j,k] = buffer_values[m]
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W[l,k,j,i] = buffer_values[m]
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#+end_src
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**** Reduced density matrix
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#+begin_src python
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if not trexio.has_rdm_2e(f):
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print("No two-body density matrix in file")
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offset = 0
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icount = BUFSIZE
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feof = False
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G = np.zeros( (n,n,n,n) )
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while not feof:
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buffer_index, buffer_values, icount, feof = trexio.read_rdm_2e(f, offset, icount)
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for m in range(icount):
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i, j, k, l = buffer_index[m]
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G[i,j,k,l] = buffer_values[m]
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#+end_src
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*** Compute the energy
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When the orbitals are real, we can use
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\begin{eqnarray*}
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E &=& E_{\text{NN}} + \sum_{ij} \gamma_{ij}\, \langle j | h | i \rangle\,
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+\, \frac{1}{2} \sum_{ijkl} \Gamma_{ijkl}\, \langle k l | i j
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\rangle \\
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&=& E_{\text{NN}} + \sum_{ij} \gamma_{ij}\, \langle i | h | j \rangle\,
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+\, \frac{1}{2} \sum_{ijkl} \Gamma_{ijkl}\, \langle i j | k l
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\rangle \\
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\end{eqnarray*}
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#+begin_src python
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G = np.reshape(G, (n*n, n*n) )
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W = np.reshape(W, (n*n, n*n) )
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E = E_nn
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E += 0.5*sum( [ np.dot(G[:,l], W[:,l]) for l in range(n*n) ] )
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E += sum( [ np.dot(D[:,l], h0[:,l]) for l in range(n) ] )
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print (f"Energy: {E}")
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#+end_src
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* Reading determinants
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** Fortran
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@ -1 +1 @@
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__version__ = "1.4.0"
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__version__ = "1.3.2"
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@ -1,4 +1,4 @@
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setuptools>=42
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pkgconfig
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numpy<1.23.0
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numpy<1.24.0
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numpy>=1.17.3
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@ -34,14 +34,14 @@
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num variable is modified by address
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*/
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/* Return num variables as part of the output tuple */
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%apply int *OUTPUT { int32_t* const num};
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%apply int *OUTPUT { int64_t* const num};
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%apply int *OUTPUT { int32_t* const num_up};
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%apply int *OUTPUT { int32_t* const num_dn};
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%apply int *OUTPUT { int64_t* const num_up};
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%apply int *OUTPUT { int64_t* const num_dn};
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%apply int32_t *OUTPUT { int32_t* const num};
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%apply int64_t *OUTPUT { int64_t* const num};
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%apply int32_t *OUTPUT { int32_t* const num_up};
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%apply int32_t *OUTPUT { int32_t* const num_dn};
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%apply int64_t *OUTPUT { int64_t* const num_up};
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%apply int64_t *OUTPUT { int64_t* const num_dn};
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%apply float *OUTPUT { float* const num};
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%apply float *OUTPUT { double* const num};
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%apply double *OUTPUT { double* const num};
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/* Return TREXIO exit code from trexio_open as part of the output tuple */
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%apply int *OUTPUT { trexio_exit_code* const rc_open};
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/* Return number of sparse data points stored in the file as part of the output tuple */
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