Preparing v1.0rc1 (#114)

* Update readme

* Try to fix binder.yml workflow

* Do not run binder.yml on PRs

* Add quadrature to MWNode and FunctionTree

* Update src/vampyr/trees/trees.h

* Throw exceiption in 1D and 2D f_tree quadrature requests.

As suggested by Roberto. Thanks

* __add__ and __iadd__

* Update pybind so it works with newer python versions (#103)

* Fix RTD builds (#108)

* Moved dunders to impl__ implementation in trees (#104)




Co-authored-by: Roberto Di Remigio Eikås <roberto@totaltrash.xyz>

* Work on documentation

* Add hydrogen atom example

* Add helium atom

* Avoid killed kernel with badly defined analytic functions

* update convolution operator and add comment to error catch

* Add Beryllium atom notebook

* Update notebooks

* Update link to current mrcpp master

* Run clang-format

* Update MRCPP version to fetch

* Add matplotlib, safeguard in plotter.py

* Run black+isort on Python files

* better solvent notebook (#107)


Co-authored-by: Roberto Di Remigio Eikås <roberto@totaltrash.xyz>

* Add authorship and instruction cells above executable cells (#110)

* Remove repetition from `index.rst` (#112)

* linked vampyr to the timeevol branch of evgeniy's fork

* added _skbuild/ to .gitignore

* added complex apply

* added time evolution operator in 1d

* minor changes to convolutions.h

* Time evolution operator can now be imported

* added filter class to get filter matrices U, H0, and so on

* linked vampyr back to the master mrcpp branch

* added a time evolution test

* small changes proposed by a reviewer

* def test_time_evolution():

* documentation

* docs

* docs

* removed some stuff from notebook messing with other cells

* Preparing v1.0rc1

---------

Co-authored-by: Magnar Bjorgve <magnbjor@gmail.com>
Co-authored-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com>
Co-authored-by: Roberto Di Remigio Eikås <roberto@totaltrash.xyz>
Co-authored-by: Gabriel <gabriel.a.gerez.s@uit.no>
Co-authored-by: edinvay <evgeni36@yandex.ru>

.github/workflows/binder.yml

@@ -6,7 +6,6 @@ on:
       - master
       - release/*
   workflow_dispatch:
-  pull_request:
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -16,21 +15,26 @@ 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: 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 }}
-        IMAGE_NAME: ${{ env.REPO }}
-        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

@@ -28,13 +28,11 @@ jobs:
         os: [ubuntu-latest, macos-latest]
         python-version:
           - "3.8"
-          - "3.9"
-          - "3.10"
           - "3.11"
 
     steps:
     - uses: actions/checkout@v3
-    
+
     - name: Cache conda
       uses: actions/cache@v3
       env:
@@ -52,7 +50,7 @@ jobs:
           environment-file: environment.yml
           channel-priority: true
           python-version: ${{ matrix.python-version }}
-  
+
     - name: Configure
       shell: bash -l {0}
       env:

.github/workflows/pip-install.yml

@@ -24,8 +24,6 @@ jobs:
       matrix:
         python-version:
           - "3.8"
-          - "3.9"
-          - "3.10"
           - "3.11"
 
     steps:

.gitignore

@@ -3,12 +3,14 @@ install*
 debug*
 .idea
 .ipynb_checkpoints
-*.ipynb
 *.swp
 cmake-build-debug
 .direnv
 .pytest_cache
 
+# Editor junk
+.vscode
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -131,3 +133,6 @@ GTAGS
 # Validated input files produced during testing
 validated*.json
 .ccls-cache
+
+
+_skbuild/

.readthedocs.yml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "miniconda3-4.7"
+    python: "mambaforge-22.9"
 
 conda:
   environment: environment.yml

CHANGELOG.md

@@ -16,6 +16,10 @@ The format is based on [Keep a Changelog], and this project adheres to [Semantic
 
 ## [Unreleased]
 
+## [1.0rc1]
+
+Release candidate, added time evolution operator and docs.
+
 ## [1.0rc0]
 
 Third release candidate, closing in on major version.

README.md

@@ -66,3 +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.

VERSION

@@ -1 +1 @@
-1.0rc0
+1.0rc1

cmake/custom/fetch_mrcpp.cmake

@@ -18,7 +18,7 @@ else()
     GIT_REPOSITORY
       https://github.com/MRChemSoft/mrcpp.git
     GIT_TAG
-      v1.5.0
+      8107aabe28d6e75f04d66c95a94c157731484eae
     )
 
   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()
-

docs/bibliography.bib

@@ -35,3 +35,17 @@ @ARTICLE{Anderson2019-bx
   issn    = "2590-0552",
   doi     = "10.1016/j.jcpx.2019.100033"
 }
+
+@article{Tomasi2005,
+author = {Tomasi, Jacopo and Mennucci, Benedetta and Cammi, Roberto},
+title = {Quantum Mechanical Continuum Solvation Models},
+journal = {Chemical Reviews},
+volume = {105},
+number = {8},
+pages = {2999-3094},
+year = {2005},
+doi = {10.1021/cr9904009},
+note ={PMID: 16092826},
+URL = {  https://doi.org/10.1021/cr9904009},
+eprint = { https://doi.org/10.1021/cr9904009 }
+}

docs/conf.py

@@ -108,9 +108,4 @@ def version_from_file(f):
         "notebook_interface": "jupyterlab",
     },
 }
-html_sidebars = {
-    "**": [
-        "sidebar-logo.html",
-        "sbt-sidebar-nav.html",
-    ]
-}
+

docs/index.rst

@@ -19,8 +19,16 @@ Check out the :doc:`usage` section for further information, including how to :re
    :caption: Contents
 
    usage
-   notebooks/vampyr_intro
+   notebooks/introduction
+   notebooks/function_representations
+   notebooks/multiwavelets
+   notebooks/poisson_equation
+   notebooks/helmholtz_equation
+   notebooks/hydrogen_atom
+   notebooks/helium_atom
+   notebooks/beryllium_atom
    notebooks/PCMSolvent
+   notebooks/harmonic_oscillator_evolution
 
 .. toctree::
    :maxdepth: 2