Merge branch 'TREX-CoE:master' into master

.github/workflows/actions.yml

@@ -112,8 +112,8 @@ jobs:
         run: make maintainer-clean
 
   trexio_macos:
-    name: x86 MacOS 11
+    name: x86 MacOS 12
-    runs-on: macos-11
+    runs-on: macos-12
 
     steps:
       - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
@@ -121,13 +121,14 @@ jobs:
       - name: install dependencies
         run: |
           brew install emacs
-          brew install hdf5
+          brew install hdf5@1.12
           brew install automake
+          brew --prefix hdf5
 
       - name: configure with autotools
         run: |
           ./autogen.sh
-          ./configure FC=gfortran-10 --enable-silent-rules
+          ./configure FC=gfortran-12 --enable-silent-rules
 
       - name: compile TREXIO
         run: make -j3
@@ -135,6 +136,15 @@ jobs:
       - name: check TREXIO
         run: make -j3 check
       
+      - name: compile Python API
+        run: |
+          export H5_CFLAGS="-I$(brew --prefix hdf5)/include"
+          export H5_LDFLAGS="-L$(brew --prefix hdf5)/lib"
+          make python-install
+      
+      - name: test Python API
+        run: make python-test
+
       - name: Archive test log file
         if: failure()
         uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2

.github/workflows/build-wheels.yml

@@ -21,7 +21,7 @@ jobs:
       message: ${{ steps.commit_message.outputs.message }}
     steps:
       - name: Checkout the repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         # Gets the correct commit message for pull request
         with:
           ref: ${{ github.event.pull_request.head.sha }}
@@ -42,14 +42,14 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        manylinux_tag: [2010_x86_64, 2014_x86_64, 2_24_x86_64]
+        manylinux_tag: [2014_x86_64, 2_24_x86_64]
 
     steps:
       - name: Checkout the branch
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: '3.9'
 
@@ -103,22 +103,14 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-10.15]
+        os: [macos-12]
-        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
-# TODO: normally, one could include macos-11 and the OS list above but the produced wheels receive an error upon installation:
+
-# ERROR: trexio-1.1.0-cp39-cp39-macosx_11_0_x86_64.whl is not a supported wheel on this platform.
-# This happens even with the MACOSX_DEPLOYMENT_TARGET trick. Perhaps it can be solved by configuring the build system
-# to produce the wheels for MacOS-11 from the very beginning
-        #exclude:
-        #  - os: macos-11
-    env:
-        H5_LDFLAGS: '-L/usr/local/Cellar/hdf5/1.12.1/lib'
-        H5_CFLAGS: '-I/usr/local/Cellar/hdf5/1.12.1/include'
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -128,11 +120,6 @@ jobs:
       - name: Install HDF5
         run: brew install hdf5@1.12
 
-      # This step is needed to produce wheels with the correct platform tag for MacOS-11 (Big Sur)
-      #- name: Set MACOSX_DEPLOYMENT_TARGET environment variable
-      #  if: ${{ matrix.os == 'macos-11' }}
-      #  run: echo "MACOSX_DEPLOYMENT_TARGET=11.0" >> $GITHUB_ENV
-
       - name: Compute the PYTREXIO_VERSION environment variable
         run: echo "PYTREXIO_VERSION=$(grep __version__ python/pytrexio/_version.py | cut -d\  -f3 | tr -d '"')" >> $GITHUB_ENV
 
@@ -158,6 +145,8 @@ jobs:
         run: |
           mkdir wheelhouse/
           cd trexio-${{ env.PYTREXIO_VERSION }}/
+          export H5_CFLAGS="-I$(brew --prefix hdf5)/include"
+          export H5_LDFLAGS="-L$(brew --prefix hdf5)/lib"
           python -m build --wheel --outdir=./
           delocate-wheel trexio-*.whl
           mv trexio-*.whl ../wheelhouse/
@@ -186,10 +175,10 @@ jobs:
 
     steps:
       - name: Checkout the branch
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: '3.9'
 

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.16)
 
 # Initialize the CMake project.
 project(Trexio
-	VERSION 2.4.0
+	VERSION 2.3.1
 	DESCRIPTION "TREX I/O library"
 	LANGUAGES C Fortran
 	)

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.69])
-AC_INIT([trexio],[2.4.0],[https://github.com/TREX-CoE/trexio/issues])
+AC_INIT([trexio],[2.3.1],[https://github.com/TREX-CoE/trexio/issues])
 
 AC_CONFIG_SRCDIR([Makefile.in])
 AC_CONFIG_HEADERS([include/config.h])

docs/examples.org

@@ -200,7 +200,7 @@ program print_energy
    #+begin_src f90
   call getarg(1, filename)
 
-  f = trexio_open (filename, 'r', TREXIO_HDF5, rc)
+  f = trexio_open (filename, 'r', TREXIO_AUTO, rc)
   if (rc /= TREXIO_SUCCESS) then
      call trexio_string_of_error(rc, err_msg)
      print *, 'Error opening TREXIO file: '//trim(err_msg)
@@ -410,6 +410,139 @@ program print_energy
 end program
     #+end_src
 
+** Python
+  :PROPERTIES:
+  :header-args:    :tangle  print_energy.py
+  :END:
+   
+  #+begin_src python
+import sys
+import trexio
+import numpy as np
+
+BUFSIZE = 100000
+  #+end_src
+
+   This program computes the energy as:
+
+   \[
+   E = E_{\text{NN}} + \sum_{ij} \gamma_{ij}\, \langle j | h | i \rangle\,
+   +\, \frac{1}{2} \sum_{ijkl} \Gamma_{ijkl}\, \langle k l | i j
+   \rangle\; \textrm{ with } \; 0 < i,j,k,l \le n
+   \]
+   One needs to read from the TREXIO file:
+
+   - $n$ :: The number of molecular orbitals
+   - $E_{\text{NN}}$ :: The nuclear repulsion energy 
+   - $\gamma_{ij}$ :: The one-body reduced density matrix 
+   - $\langle j |h| i \rangle$ :: The one-electron Hamiltonian integrals 
+   - $\Gamma_{ijkl}$ :: The two-body reduced density matrix 
+   - $\langle k l  | i j \rangle$ :: The electron repulsion integrals
+
+*** Obtain the name of the TREXIO file from the command line, and open it for reading
+
+    #+begin_src python
+filename = sys.argv[1]
+f = trexio.File(filename, 'r', trexio.TREXIO_AUTO)
+    #+end_src
+
+*** Read the nuclear repulsion energy
+
+    #+begin_src python
+E_nn = trexio.read_nucleus_repulsion(f)
+    #+end_src
+
+*** Read the number of molecular orbitals
+
+    #+begin_src python
+n = trexio.read_mo_num(f)
+    #+end_src
+
+*** Read one-electron quantities
+    
+    #+begin_src python
+if not trexio.has_mo_1e_int_core_hamiltonian(f):
+  print("No core hamiltonian in file")
+  sys.exit(-1)
+  
+h0 = trexio.read_mo_1e_int_core_hamiltonian(f)
+
+if not trexio.has_rdm_1e(f):
+  print("No 1e RDM in file")
+  sys.exit(-1)
+  
+D = trexio.read_rdm_1e(f)
+    #+end_src
+  
+*** Read two-electron quantities
+    
+**** Electron repulsion integrals
+
+     #+begin_src python
+if not trexio.has_mo_2e_int_eri(f):
+  print("No electron repulsion integrals in file")
+  sys.exit(-1)
+
+size_max = trexio.read_mo_2e_int_eri_size(f)
+
+offset = 0
+icount = BUFSIZE
+feof = False
+W = np.zeros( (n,n,n,n) )
+while not feof:
+  buffer_index, buffer_values, icount, feof = trexio.read_mo_2e_int_eri(f, offset, icount)
+  for m in range(icount):
+    i, j, k, l = buffer_index[m]
+    W[i,j,k,l] = buffer_values[m]
+    W[k,j,i,l] = buffer_values[m]
+    W[i,l,k,j] = buffer_values[m]
+    W[k,l,i,j] = buffer_values[m]
+    W[j,i,l,k] = buffer_values[m]
+    W[j,k,l,i] = buffer_values[m]
+    W[l,i,j,k] = buffer_values[m]
+    W[l,k,j,i] = buffer_values[m]
+     #+end_src
+
+**** Reduced density matrix
+     
+     #+begin_src python
+if not trexio.has_rdm_2e(f):
+  print("No two-body density matrix in file")
+
+offset = 0
+icount = BUFSIZE
+feof = False
+G = np.zeros( (n,n,n,n) )
+while not feof:
+  buffer_index, buffer_values, icount, feof = trexio.read_rdm_2e(f, offset, icount)
+  for m in range(icount):
+    i, j, k, l = buffer_index[m]
+    G[i,j,k,l] = buffer_values[m]
+
+     #+end_src
+    
+*** Compute the energy
+    
+    When the orbitals are real, we can use
+   \begin{eqnarray*}
+   E &=& E_{\text{NN}} + \sum_{ij} \gamma_{ij}\, \langle j | h | i \rangle\,
+   +\, \frac{1}{2} \sum_{ijkl} \Gamma_{ijkl}\, \langle k l | i j
+   \rangle \\
+     &=& E_{\text{NN}} + \sum_{ij} \gamma_{ij}\, \langle i | h | j \rangle\,
+   +\, \frac{1}{2} \sum_{ijkl} \Gamma_{ijkl}\, \langle i j | k l
+   \rangle \\
+   \end{eqnarray*}
+
+    #+begin_src python
+G = np.reshape(G, (n*n, n*n) )
+W = np.reshape(W, (n*n, n*n) )
+E = E_nn
+E += 0.5*sum( [ np.dot(G[:,l], W[:,l]) for l in range(n*n) ] )
+E += sum( [ np.dot(D[:,l], h0[:,l]) for l in range(n) ] )
+
+print (f"Energy: {E}")
+    #+end_src
+
 * Reading determinants
   
 ** Fortran

python/pytrexio/_version.py

@@ -1 +1 @@
-__version__ = "1.4.0"
+__version__ = "1.3.2"

python/requirements.txt

@@ -1,4 +1,4 @@
 setuptools>=42
 pkgconfig
-numpy<1.23.0
+numpy<1.24.0
 numpy>=1.17.3

src/pytrexio.i

@@ -34,14 +34,14 @@
    num variable is modified by address
 */
 /* Return num variables as part of the output tuple */
-%apply int *OUTPUT { int32_t* const num};
+%apply int32_t *OUTPUT { int32_t* const num};
-%apply int *OUTPUT { int64_t* const num};
+%apply int64_t *OUTPUT { int64_t* const num};
-%apply int *OUTPUT { int32_t* const num_up};
+%apply int32_t *OUTPUT { int32_t* const num_up};
-%apply int *OUTPUT { int32_t* const num_dn};
+%apply int32_t *OUTPUT { int32_t* const num_dn};
-%apply int *OUTPUT { int64_t* const num_up};
+%apply int64_t *OUTPUT { int64_t* const num_up};
-%apply int *OUTPUT { int64_t* const num_dn};
+%apply int64_t *OUTPUT { int64_t* const num_dn};
 %apply float *OUTPUT { float* const num};
-%apply float *OUTPUT { double* const num};
+%apply double *OUTPUT { double* const num};
 /* Return TREXIO exit code from trexio_open as part of the output tuple */
 %apply int *OUTPUT { trexio_exit_code* const rc_open};
 /* Return number of sparse data points stored in the file as part of the output tuple */