Merge branch 'master' into node_xc

Author: gitpeterwind

.circleci/config.yml

@@ -1,9 +1,9 @@
 version: 2
 
 variables:
-  ubuntu-2004: &ubuntu-2004
+  ubuntu-2204: &ubuntu-2204
     docker:
-      - image: ghcr.io/mrchemsoft/metamr/circleci_ubuntu-20.04:sha-343e011
+      - image: ghcr.io/mrchemsoft/metamr/circleci_ubuntu-22.04:sha-9f6ecd4
         name: tsubame
         user: merzbow
     working_directory: ~/mrchem
@@ -52,14 +52,14 @@ variables:
 
 jobs:
   serial-py3:
-    <<: *ubuntu-2004
+    <<: *ubuntu-2204
     steps:
       - checkout
       - *configure-serial
       - *build
       - *tests
   omp-py3:
-    <<: *ubuntu-2004
+    <<: *ubuntu-2204
     environment:
       - OMP_NUM_THREADS: '2'
     steps:
@@ -68,7 +68,7 @@ jobs:
       - *build
       - *tests
   mpi-py3:
-    <<: *ubuntu-2004
+    <<: *ubuntu-2204
     steps:
       - checkout
       - *configure-mpi

.github/workflows/build-test.yml

@@ -42,19 +42,19 @@ jobs:
           activate-environment: mrchem-gha
           environment-file: .github/mrchem-gha.yml
           channel-priority: true
-          python-version: 3.6
+          python-version: 3.9
           use-only-tar-bz2: true  # IMPORTANT: This needs to be set for caching to work properly!
 
     - name: Configure
       shell: bash -l {0}
       run: |
         python ./setup --type=$BUILD_TYPE --omp --arch-flags=false --generator=Ninja --prefix=$GITHUB_WORKSPACE/Software/MRChem build
-        
+
     - name: Build
       shell: bash -l {0}
       run: |
         cmake --build build --config $BUILD_TYPE --target install -- -v -d stats
-        
+
     - name: Test
       shell: bash -l {0}
       run: |

.github/workflows/code-coverage.yml

@@ -26,18 +26,18 @@ jobs:
           activate-environment: mrchem-codecov
           environment-file: .github/mrchem-codecov.yml
           channel-priority: true
-          python-version: 3.6
+          python-version: 3.9
 
     - name: Configure
       shell: bash -l {0}
       run: |
         python ./setup --type=$BUILD_TYPE --arch-flags=false --coverage --generator=Ninja --prefix=$GITHUB_WORKSPACE/Software/MRChem build
-  
+
     - name: Build
       shell: bash -l {0}
       run: |
         cmake --build build --config $BUILD_TYPE --target install -- -v -d stats
-    
+
     - name: Test MRChem and generate coverage report
       shell: bash -l {0}
       run: |

doc/index.rst

@@ -42,6 +42,8 @@ Features in MRChem-1.1:
         - Electric field
     + Solvent effects
         - Cavity-free PCM
+        - Poisson-Boltzmann PCM
+        - Linearized Poisson-Boltzmann PCM
 * Properties:
     + Ground state energy
     + Dipole moment

doc/installation.rst

@@ -6,7 +6,7 @@ Installation
 Build prerequisites
 -------------------
 
-- Python-3.7 (or later)
+- Python-3.9 (or later)
 - CMake-3.14 (or later)
 - GNU-5.4 or Intel-17 (or later) compilers (C++14 standard)
 

doc/programmers/code_reference/environment.rst

@@ -21,11 +21,38 @@ Permittivity
    :protected-members:
    :private-members: 
 
-SCRF
+DHScreening
 ------------
 
-.. doxygenclass:: mrchem::SCRF
+.. doxygenclass:: mrchem::DHScreening
    :project: MRChem
    :members:  
    :protected-members:
    :private-members: 
+
+GPESolver
+------------
+
+.. doxygenclass:: mrchem::GPESolver
+   :project: MRChem
+   :members:  
+   :protected-members:
+   :private-members: 
+
+PBESolver
+------------
+
+.. doxygenclass:: mrchem::PBESolver
+   :project: MRChem
+   :members:  
+   :protected-members:
+   :private-members: 
+
+LPBESolver
+------------
+
+.. doxygenclass:: mrchem::LPBESolver
+   :project: MRChem
+   :members:  
+   :protected-members:
+   :private-members: 

doc/programming.bib

@@ -333,7 +333,6 @@ @article{Fosso-Tande2013
 abstract = {We describe and present results of the implementation of the surface and volume polarization for electrostatics (SVPE) solvation model. Unlike most other implementations of the solvation model where the solute and the solvent are described with multiple numerical representations, our implementation uses a multiresolution, adaptive multiwavelet basis to describe both the solute and the solvent. This requires reformulation to use integral equations throughout as well as a conscious management of numerical properties of the basis. {\textcopyright} 2013 Elsevier B.V. All rights reserved.},
 author = {Fosso-Tande, Jacob and Harrison, Robert J.},
 doi = {10.1016/j.cplett.2013.01.065},
-file = {:home/ggerez/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Fosso-Tande, Harrison - 2013 - Implicit solvation models in a multiresolution multiwavelet basis.pdf:pdf},
 issn = {00092614},
 journal = {Chem. Phys. Lett.},
 pages = {179--184},
@@ -343,3 +342,20 @@ @article{Fosso-Tande2013
 year = {2013}
 }
 
+@article{gerez2023,
+author = {Gerez S, Gabriel A. and Di Remigio Eikås, Roberto and Jensen, Stig Rune and Bjørgve, Magnar and Frediani, Luca},
+title = {Cavity-Free Continuum Solvation: Implementation and Parametrization in a Multiwavelet Framework},
+journal = {Journal of Chemical Theory and Computation},
+volume = {19},
+number = {7},
+pages = {1986-1997},
+year = {2023},
+doi = {10.1021/acs.jctc.2c01098},
+    note ={PMID: 36933225},
+URL = { 
+        https://doi.org/10.1021/acs.jctc.2c01098
+},
+eprint = { 
+        https://doi.org/10.1021/acs.jctc.2c01098
+}
+}

doc/users/user_inp.rst

@@ -200,7 +200,7 @@ as the ``world_origin`` is the true origin).
 WaveFunction
 ------------
 
-Here we give the wavefunction method and whether we run spin restricted (alpha
+Here we give the wavefunction method, environment used (for solvent models) and whether we run spin restricted (alpha
 and beta spins are forced to occupy the same spatial orbitals) or not (method
 must be specified, otherwise defaults are shown):
 
@@ -209,6 +209,7 @@ must be specified, otherwise defaults are shown):
     WaveFunction {
       method = <wavefunction_method>        # Core, Hartree, HF or DFT
       restricted = true                     # Spin restricted/unrestricted
+      environment = pcm                     # Environment (pcm, pcm-pb, pcm-lpb) defaults to none
     }
 
 There are currently four methods available: Core Hamiltonian, Hartree,
@@ -218,6 +219,11 @@ B3LYP``), *or* you can set ``method = DFT`` and specify a "non-standard"
 functional in the separate DFT section (see below). See
 :ref:`User input reference` for a list of available default functionals.
 
+The solvent model implemented is a cavity free PCM, described in :cite:`gerez2023`. 
+In this model we have implemented the Generalized Poisson equation solver, keyword ``pcm``, a 
+Poisson-Boltzmann solver, keyword ``pcm-pb`` and a Linearized Poisson-Boltzmann solver, keyword ``pcm-lpb``. 
+Further details for the calculation have to be included in the ``PCM`` section, see :ref: `User input reference` for details.
+
 .. note::
 
     Restricted open-shell wavefunctions are not supported.