Add poisson-boltzmann to the SCRF (#450)

* add poisson-boltzmann to the SCRF Add additional input for pb equation, all other tests passing, error with ion_radius variable add a harcoded to pass test for pb fix json error mid debug commit, the run_pb block produces different convergence despite being identical to the standard * PB working as intended (within a reasonable domain) Faster pb and lpb solver and proper test * add test for linearized pb * Rename SCRF to GPESolver in preparation for refactor. Use inheritance to implement PBESolver and LPBESolver Rename GPESolver::solveEquation to iterateEquation * Add new test references to pb and lpb solvent Update tests and Fix correct solvers running Add proper capitalisation to Debye-Huckel Co-authored-by: Roberto Di Remigio Eikås <[email protected]> Remove unused setters in Cavity Co-authored-by: Roberto Di Remigio Eikås <[email protected]> Pass parameters by const reference Co-authored-by: Roberto Di Remigio Eikås <[email protected]> * fix tests for pb solver * Add documentation to the solvent classes * Add DHScreening to the StepFunction hierarchy * Reorder includes * Update python/template.yml Co-authored-by: Roberto Di Remigio Eikås <[email protected]> * Update python/mrchem/api.py Co-authored-by: Roberto Di Remigio Eikås <[email protected]> * Post-rebase fixes * Formatting * debugging * more debugging * even more debugging * BUGFIX in PB_solver.cpp: rho_el was not zero and the ordering of the energy outputs of GPESolver was wrong * real BUGFIX: same as above but relax the thrs, we are running it with 1.0e-3 prec after all * attempt to fix test error * update python version for tests * update python version for singularity images * update python version for circleci config * Use newer base image with CircleCI * update minimum python requirements in installation.rst * create cavity even if we are running pb or lpb * use proper dividor * Be more consistent * Update input for PCM * rebase fix * rebase fix * all tests passing and PB_solver is correct --------- Co-authored-by: Roberto Di Remigio Eikås <[email protected]> Co-authored-by: Roberto Di Remigio Eikås <[email protected]>
MRChemSoft · Feb 14, 2024 · 698e74f · 698e74f
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diff --git a/.circleci/config.yml b/.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

diff --git a/.github/workflows/build-test.yml b/.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: |

diff --git a/.github/workflows/code-coverage.yml b/.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: |

diff --git a/doc/index.rst b/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

diff --git a/doc/installation.rst b/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)
 

diff --git a/doc/programmers/code_reference/environment.rst b/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: 
diff --git a/doc/programming.bib b/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
+}
+}
diff --git a/doc/users/user_inp.rst b/doc/users/user_inp.rst
@@ -194,7 +194,7 @@ 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):
 
@@ -203,6 +203,7 @@ 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,
@@ -212,6 +213,11 @@ 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.