Merge branch 'master' of https://github.com/joguenzl/trexio

.github/workflows/actions.yml

@@ -20,7 +20,7 @@ jobs:
       message: ${{ steps.commit_message.outputs.message }}
     steps:
       - name: Checkout the repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
         # Gets the correct commit message for pull request
         with:
           ref: ${{ github.event.pull_request.head.sha }}
@@ -31,15 +31,13 @@ jobs:
           COMMIT_MSG=$(git log --no-merges -1 --oneline)
           echo "::set-output name=message::$COMMIT_MSG"
 
-
   trexio_ubuntu:
-
-    runs-on: ubuntu-20.04
     name: x86 Ubuntu 20.04
+    runs-on: ubuntu-20.04
     needs: get_commit_message
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
 
       - name: install dependencies
         run: |
@@ -84,7 +82,7 @@ jobs:
         if: >-
           contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
           github.event_name == 'release'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
         with:
           name: pytrexio-source
           path: ./trexio-*.tar.gz
@@ -114,29 +112,38 @@ jobs:
         run: make maintainer-clean
 
   trexio_macos:
-
+    name: x86 MacOS 12
-    runs-on: macos-11
+    runs-on: macos-12
-    name: x86 MacOS 11
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
 
       - 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 -j 2
+        run: make -j3
 
       - name: check TREXIO
-        run: make check
+        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()

.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 2.3.0
+	VERSION 2.3.1
 	DESCRIPTION "TREX I/O library"
 	LANGUAGES C Fortran
 	)

README.md

@@ -22,8 +22,8 @@ TREX library for efficient I/O.
 2. `gzip -cd trexio-<version>.tar.gz | tar xvf -`
 3. `cd trexio-<version>`
 4. `./configure`
-5. `make`
+5. ```make -j`getconf _NPROCESSORS_ONLN` ```
-6. `make check`
+6. ```make -j`getconf _NPROCESSORS_ONLN` check```
 7. `sudo make install`
 
 
@@ -45,8 +45,8 @@ TREX library for efficient I/O.
 2. `cd trexio`
 3. `./autogen.sh`
 4. `./configure`
-5. `make`
+5. ```make -j`getconf _NPROCESSORS_ONLN` ```
-6. `make check`
+6. ```make -j`getconf _NPROCESSORS_ONLN` check```
 7. `sudo make install`
 
 ## Installation procedure for CMake users (from the tarball or GitHub repo clone):
@@ -56,8 +56,8 @@ The aforementioned instructions rely on [Autotools](https://www.gnu.org/software
 
 1. `cmake -S. -Bbuild`
 2. `cd build`
-3. `make`
+3. ```make -j`getconf _NPROCESSORS_ONLN` ```
-4. `ctest` (or `make test`)
+4. ```ctest -j`getconf _NPROCESSORS_ONLN` ```
 5. `sudo make install`
 
 **Note: on systems with no `sudo` access, one can add `-DCMAKE_INSTALL_PREFIX=build` as an argument to the `cmake` command so that `make install/uninstall` can be run without `sudo` privileges.**
@@ -73,7 +73,7 @@ The official releases of TREXIO `>2.0.0` are also available via the `conda-forge
 The pre-compiled stable binaries of `trexio` can be installed as follows:
 
 ```
-conda install trexio -c conda-forge
+conda install -c conda-forge trexio
 ```
 
 More details can be found in the corresponding [trexio-feedstock](https://github.com/conda-forge/trexio-feedstock).
@@ -88,7 +88,7 @@ Schema file contains the manifest specification for the `trexio` package.
 It can be installed as follows:
 
 ```
-guix package --cores=<n_cores> --install-from-file=trexio.scm
+guix package --cores=`getconf _NPROCESSORS_ONLN` --install-from-file=trexio.scm
 ```
 
 ## Installation procedure for Spack users
@@ -100,7 +100,7 @@ file contains the Spack specifications required to build different variants of `
 It can be installed as follows
 
 ```
-spack install --jobs <n_cores> trexio
+spack install --jobs `getconf _NPROCESSORS_ONLN` trexio
 ```
 
 ## Installation procedure for Debian/Ubuntu users
@@ -127,14 +127,14 @@ To build TREXIO without HDF5 back end, append `--without-hdf5` option to `config
 ## Linking to your program
 
 The `make install` command takes care of installing the TREXIO shared library on the user machine.
-Once installed, add `-ltrexio` to the list of compiler options.
+After installation, append `-ltrexio` to the list of compiler  (`$LIBS`) options.
 
-In some cases (e.g. when using custom `prefix` during configuration), the TREXIO library might end up installed in a directory, which is absent in the default `$LIBRARY_PATH`.
+In some cases (e.g. when using custom installation prefix during configuration), the TREXIO library might end up installed in a directory, which is absent in the default `$LD_LIBRARY_PATH`.
-In order to link the program against TREXIO, the search paths can be modified as follows:
+In order to link the program against TREXIO, the search path can be modified as follows:
 
-`export LIBRARY_PATH=$LIBRARY_PATH:<path_to_trexio>/lib`
+`export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<path_to_trexio>/lib`
 
-(same holds for `$LD_LIBRARY_PATH`). The `<path_to_trexio>` has to be replaced by the prefix used during the installation.
+where the `<path_to_trexio>` has to be replaced by the prefix used during the installation.
 
 If your project relies on CMake build system, feel free to use the
 [FindTREXIO.cmake](https://github.com/TREX-CoE/trexio/blob/master/cmake/FindTREXIO.cmake)

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.69])
-AC_INIT([trexio],[2.3.0],[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__ = "1.3.0"
+__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/CMakeLists.txt

@@ -66,7 +66,7 @@ option(ENABLE_HDF5 "Enable HDF5 support" ON)
 
 if(ENABLE_HDF5)
   # Try to detect HDF5 installation using built-in FindHDF5.cmake macro.
-  find_package(HDF5 REQUIRED COMPONENTS C HL)
+  find_package(HDF5 REQUIRED COMPONENTS C)
 
   if(HDF5_FOUND)
     message(STATUS "HDF5 version     :: ${HDF5_VERSION}")
@@ -87,9 +87,7 @@ if(ENABLE_HDF5)
   # - include directories with HDF5 header files
   target_include_directories(trexio PRIVATE ${HDF5_C_INCLUDE_DIRS})
   # - link to HDF5 C libraries
-  target_link_libraries(trexio PRIVATE
+  target_link_libraries(trexio PRIVATE ${HDF5_C_LIBRARIES})
-         ${HDF5_C_HL_LIBRARIES}
-         ${HDF5_C_LIBRARIES})
 endif()
 
 # Private headers have to be listed as sources, otherwise they are installed

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 */

src/templates_text/templator_text.org

@@ -145,10 +145,10 @@ trexio_text_inquire (const char* file_name)
   if (file_exists) {
 
     bool is_a_directory = false;
-#ifdef S_IFDIR
+#if defined(S_IFDIR)
     is_a_directory = st.st_mode & S_IFDIR;
-#elif S_ISDIR
+#elif defined(S_ISDIR)
-    is_a_directory = S_ISDIR(s.st_mode);
+    is_a_directory = S_ISDIR(st.st_mode);
 #else
     printf("Some important macros are missing for directory handling.\n");
     return TREXIO_FAILURE;
@@ -162,6 +162,29 @@ trexio_text_inquire (const char* file_name)
 }
     #+end_src
 
+On non-POSIX file systems, the function ~mkdtemp~ might is not defined.
+In that case, we define an alternate one, which is not as safe as the original one.
+
+    #+begin_src c :tangle basic_text.c
+#if defined _POSIX_C_SOURCE && (_POSIX_C_SOURCE - 0) >= 200809L
+#else
+
+char* mkdtemp(char* template) {
+    char* dir = NULL;
+    dir = tmpnam(dir);
+    if (dir == NULL) return NULL;
+
+    if (mkdir(dir, S_IRWXU | S_IRWXG | S_IRWXO) != 0) {
+        return NULL;
+    }
+
+    strcpy(template, dir);
+    return template;
+}
+
+#endif
+    #+end_src
+
     #+begin_src c :tangle basic_text.c
 trexio_exit_code
 trexio_text_init (trexio_t* const file)

tools/trexio.scm

@@ -60,8 +60,22 @@
 		"1n9n1gbk5hgvg73am991xrv7ap002rz719a3nvh8m8ff9x10qd76"
                 ))))))
 
+(define-public trexio-2.3
+  (package/inherit trexio-2.0
+    (version "2.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/TREX-CoE/trexio/releases/download/v" version
+				  "/trexio-" version
+                                  ".tar.gz"))
+              (sha256
+               (base32
+		;; the hash below is produced by guix download <url>
+		"183wljg1avsia2pf2wb59s2i2qw6y19qfw164ffy1g024b6362ii"
+                ))))))
+
 (define-public trexio
   ;; Default version of TREXIO.
-  trexio-2.2)
+  trexio-2.3)
 
 trexio