Merge branch 'master' into fix-rtd-build

.github/workflows/binder.yml

@@ -2,27 +2,39 @@ name: Build Notebook Container
 
 on:
   push:
+    branches:
+      - master
+      - release/*
   workflow_dispatch:
-  pull_request:
 
 concurrency:
-  group: latest-repo2docker-group
+  group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:
   build:
     runs-on: ubuntu-latest
     name: Run repo2docker
+
+    permissions:
+      contents: read
+      packages: write
+
     steps:
 
-    - name: checkout files in repo
-      uses: actions/checkout@v3
+      - name: checkout files in repo
+        uses: actions/checkout@v3
+
+      - name: downcase repository name
+        run: |
+          echo "REPO=${GITHUB_REPOSITORY,,}" >>${GITHUB_ENV}
 
-    - name: update jupyter dependencies with repo2docker
-      uses: jupyterhub/repo2docker-action@master
-      with:
-        DOCKER_USERNAME: ${{ github.repository_owner }}
-        DOCKER_PASSWORD: ${{ secrets.GITHUB_TOKEN }}
-        DOCKER_REGISTRY: ghcr.io
-        MYBINDERORG_TAG: ${{ github.event.ref }}
-        PUBLIC_REGISTRY_CHECK: true
+      - name: update jupyter dependencies with repo2docker
+        uses: jupyterhub/repo2docker-action@master
+        with:
+          DOCKER_USERNAME: ${{ github.repository_owner }}
+          DOCKER_PASSWORD: ${{ secrets.GITHUB_TOKEN }}
+          DOCKER_REGISTRY: ghcr.io
+          MYBINDERORG_TAG: ${{ github.event.ref }}
+          IMAGE_NAME: ${{ env.REPO }}
+          PUBLIC_REGISTRY_CHECK: true

.github/workflows/build-test.yml

@@ -13,6 +13,10 @@ on:
     types:
       - created
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 env:
   BUILD_TYPE: Release
 
@@ -22,7 +26,11 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        python-version:
+          - "3.8"
+          - "3.9"
+          - "3.10"
+          - "3.11"
 
     steps:
     - uses: actions/checkout@v3
@@ -44,7 +52,6 @@ jobs:
           environment-file: environment.yml
           channel-priority: true
           python-version: ${{ matrix.python-version }}
-          use-only-tar-bz2: true  # IMPORTANT: This needs to be set for caching to work properly!
 
     - name: Configure
       shell: bash -l {0}

.github/workflows/code-coverage.yml

@@ -8,6 +8,10 @@ on:
     branches:
       - master
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 env:
   BUILD_TYPE: Debug
 

.github/workflows/pip-install.yml

@@ -13,12 +13,20 @@ on:
     types:
       - created
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        python-version:
+          - "3.8"
+          - "3.9"
+          - "3.10"
+          - "3.11"
 
     steps:
     - uses: actions/checkout@v3

README.md

@@ -4,6 +4,7 @@
 [![License](https://img.shields.io/badge/license-%20LGPLv3-blue.svg)](../master/LICENSE)
 ![Build and test VAMPyR](https://github.com/MRChemSoft/vampyr/workflows/Build%20and%20test%20VAMPyR/badge.svg)
 [![codecov](https://codecov.io/gh/MRChemSoft/vampyr/branch/master/graph/badge.svg)](https://codecov.io/gh/MRChemSoft/vampyr)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/MRChemSoft/vampyr/master?urlpath=lab%2Ftree%2Fdocs%2Fnotebooks)
 
 The Very Accurate Multiresolution Python Routines (VAMPyR) package is a high
 level Python interface to the [MRCPP](https://github.com/MRChemSoft/mrcpp) code.
@@ -65,3 +66,34 @@ Note that the conda-forge package is _always_ built with OpenMP support enabled
 in the MRCPP backend.
 
 The VAMPyR module is now available whenever you have activated the `myenv` environment.
+
+### Creating a Conda environment from a .yml file
+
+You can also create a Conda environment from a .yml file that already specifies VAMPyR and
+other useful packages such as numpy, and matplotlib. Here's how:
+
+1. Write an `environment.yml` file, for example:
+
+    ```yaml
+    name: myenv
+    channels:
+      - conda-forge
+    dependencies:
+      - vampyr
+      - numpy
+      - matplotlib
+      - jupyterlab
+    ```
+
+2. Create the environment from the `environment.yml` file:
+
+    ```sh
+    $ conda env create -f environment.yml
+    ```
+3. Activate the environment:
+
+    ```sh
+    $ conda activate myenv
+    ```
+The VAMPyR module, along with numpy and matplotlib, is now available whenever
+you have activated the myenv environment.

binder/environment.yml

@@ -3,6 +3,7 @@ channels:
 dependencies:
   - cmake
   - cxx-compiler
+  - eigen
   #- mrcpp
   - matplotlib
   - ninja
@@ -11,3 +12,4 @@ dependencies:
   - pybind11
   - pytest
   - pytest-cov
+  - python >=3.8

binder/postBuild

@@ -2,6 +2,8 @@
 
 set -euxo
 
+type -P python
+
 # install current version of VAMPyR
 python -m pip install -vvv .
 

cmake/compiler_flags/Intel.CXX.cmake

@@ -2,7 +2,7 @@ if(NOT DEFINED ENV{CXXFLAGS})
     if(CMAKE_CXX_COMPILER_ID MATCHES Intel)
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ftz -fp-speculation=fast -fp-model fast -Wno-unknown-pragmas")
         set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG")
-        set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-O2 -debug -DNDEBUG")
+        set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-O2 -debug -DNDEBUG -g3 -parallel-source-info=2")
         set(CMAKE_CXX_FLAGS_DEBUG "-O0 -debug -DDEBUG")
     endif()
 endif()

cmake/custom/fetch_mrcpp.cmake

@@ -2,7 +2,7 @@
 set(_build_type ${CMAKE_BUILD_TYPE})
 set(CMAKE_BUILD_TYPE Release)
 
-find_package(MRCPP 1.4 CONFIG QUIET)
+find_package(MRCPP 1.5 CONFIG QUIET)
 
 # whether MRCPP was fetched and built locally
 set(MRCPP_FETCHED FALSE)
@@ -18,7 +18,7 @@ else()
     GIT_REPOSITORY
       https://github.com/MRChemSoft/mrcpp.git
     GIT_TAG
-      1a6d450ac356feffba5c5cb2d02b92a875dbb9aa
+      v1.5.0
     )
 
   set(CMAKE_CXX_COMPILER ${CMAKE_CXX_COMPILER})

cmake/custom/fetch_pybind11.cmake

@@ -1,4 +1,4 @@
-find_package(pybind11 2.6 CONFIG QUIET)
+find_package(pybind11 2.9 CONFIG QUIET)
 
 set(PYBIND11_CPP_STANDARD "-std=c++${CMAKE_CXX_STANDARD}")
 
@@ -10,9 +10,8 @@ else()
   FetchContent_Declare(pybind11
     QUIET
     URL
-      https://github.com/pybind/pybind11/archive/v2.7.1.tar.gz
+      https://github.com/pybind/pybind11/archive/v2.10.0.tar.gz
     )
   set(PYBIND11_TEST OFF CACHE BOOL "")
   FetchContent_MakeAvailable(pybind11)
 endif()
-

environment.yml

@@ -3,10 +3,12 @@ channels:
 dependencies:
   - cmake
   - cxx-compiler
-  - mrcpp
+  - eigen
+  #- mrcpp
   - ninja
   - numpy
   - pip
   - pybind11
   - pytest
   - pytest-cov
+  - python >=3.8

setup.cfg

@@ -13,15 +13,15 @@ classifiers =
     License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
     Programming Language :: Python
     Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     Programming Language :: C++
     Topic :: Scientific/Engineering :: Chemistry
 
 [options]
-python_requires = >= 3.7
+python_requires = >= 3.8
 
 setup_requires =
     pybind11-global >= 2.6

src/vampyr/CMakeLists.txt

@@ -20,6 +20,8 @@ target_link_libraries(_vampyr
     # extra linking needed to use std::filesystem: https://en.cppreference.com/w/cpp/filesystem
     # need to link against stdc++fs for GNU<9.1
     "$<$<AND:$<CXX_COMPILER_ID:GNU>,$<VERSION_LESS:$<CXX_COMPILER_VERSION>,9.1>>:-lstdc++fs>"
+    # same for Intel compiler because it uses whatever GNU standard C++ is around
+    "$<$<OR:$<CXX_COMPILER_ID:Intel>,$<CXX_COMPILER_ID:IntelLLVM>>:-lstdc++fs>"
     # need to link against c++fs for LLVM<9.0
     "$<$<AND:$<CXX_COMPILER_ID:Clang>,$<VERSION_LESS:$<CXX_COMPILER_VERSION>,9.0>>:-lc++fs>"
   )

src/vampyr/operators/convolutions.h

@@ -5,10 +5,12 @@
 #include <MRCPP/operators/HelmholtzOperator.h>
 #include <MRCPP/operators/IdentityConvolution.h>
 #include <MRCPP/operators/PoissonOperator.h>
+#include <MRCPP/operators/CartesianConvolution.h>
 #include <MRCPP/treebuilders/apply.h>
 
 namespace vampyr {
 
+void cartesian_convolution(pybind11::module &);
 void helmholtz_operator(pybind11::module &);
 void poisson_operator(pybind11::module &);
 
@@ -17,7 +19,19 @@ template <int D> void convolutions(pybind11::module &m) {
     using namespace mrcpp;
     using namespace pybind11::literals;
 
-    py::class_<ConvolutionOperator<D>>(m, "ConvolutionOperator");
+    py::class_<ConvolutionOperator<D>>(m, "ConvolutionOperator")
+        .def(py::init<const MultiResolutionAnalysis<D> &, GaussExp<1> &, double>(),
+             "mra"_a,
+             "kernel"_a,
+             "prec"_a)
+        .def(
+            "__call__",
+            [](ConvolutionOperator<D> &O, FunctionTree<D> *inp) {
+                auto out = std::make_unique<FunctionTree<D>>(inp->getMRA());
+                apply<D>(O.getBuildPrec(), *out, O, *inp);
+                return out;
+            },
+            "inp"_a);
 
     py::class_<IdentityConvolution<D>, ConvolutionOperator<D>>(m, "IdentityConvolution")
         .def(py::init<const MultiResolutionAnalysis<D> &, double>(), "mra"_a, "prec"_a)
@@ -35,10 +49,32 @@ template <int D> void convolutions(pybind11::module &m) {
             },
             "inp"_a);
 
+    if constexpr (D == 3) cartesian_convolution(m);
     if constexpr (D == 3) helmholtz_operator(m);
     if constexpr (D == 3) poisson_operator(m);
 }
 
+void cartesian_convolution(pybind11::module &m) {
+    namespace py = pybind11;
+    using namespace mrcpp;
+    using namespace pybind11::literals;
+
+    py::class_<CartesianConvolution, ConvolutionOperator<3>>(m, "CartesianConvolution")
+        .def(py::init<const MultiResolutionAnalysis<3> &, GaussExp<1> &, double>(),
+             "mra"_a,
+             "kernel"_a,
+             "prec"_a)
+        .def(
+            "__call__",
+            [](CartesianConvolution &O, FunctionTree<3> *inp) {
+                auto out = std::make_unique<FunctionTree<3>>(inp->getMRA());
+                apply<3>(O.getBuildPrec(), *out, O, *inp);
+                return out;
+            },
+            "inp"_a)
+        .def("setCartesianComponents", &CartesianConvolution::setCartesianComponents);
+}
+
 void poisson_operator(pybind11::module &m) {
     namespace py = pybind11;
     using namespace mrcpp;

src/vampyr/operators/derivatives.h

@@ -20,7 +20,6 @@ template <int D> void derivatives(pybind11::module &m) {
         An abstract base class for derivative operators
     )mydelimiter")
         // clang-format on
-        .def(py::init<const MultiResolutionAnalysis<D> &>(), "mra"_a)
         .def("getOrder", &DerivativeOperator<D>::getOrder)
         .def(
             "__call__",

src/vampyr/tests/test_convolutions_1d.py

@@ -17,6 +17,26 @@
 ffunc = vp.GaussFunc(alpha=alpha, beta=beta, position=r0)
 
 
+def test_GaussKernel():
+    beta = 1.0e5
+    alpha = (beta / np.pi) ** (1.0 / 2.0)
+    ifunc = vp.GaussFunc(alpha=alpha, beta=beta)
+    iexp = vp.GaussExp()
+    iexp.append(ifunc)
+    I = vp.ConvolutionOperator(mra, iexp, prec=epsilon)
+
+    ftree = vp.FunctionTree(mra)
+    vp.advanced.build_grid(out=ftree, inp=ffunc)
+    vp.advanced.project(prec=epsilon, out=ftree, inp=ffunc)
+
+    gtree = vp.FunctionTree(mra)
+    vp.advanced.apply(prec=epsilon, out=gtree, oper=I, inp=ftree)
+    assert gtree.integrate() == pytest.approx(ftree.integrate(), rel=epsilon)
+
+    gtree2 = I(ftree)
+    assert gtree2.integrate() == pytest.approx(ftree.integrate(), rel=epsilon)
+
+
 def test_Identity():
     I = vp.IdentityConvolution(mra, prec=epsilon)