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Refactor Green's functions, boundary integral operators and solvers
Disentangle design of Green's functions from that of the boundary integral operators and adapt solvers accordingly. The boundary integral operator is no longer implemented as a Visitor. This has two advantages: 1. It is no longer a template parameter to the Green's functions 2. It doesn't need to know about internal details of the Green's functions. The boundary integral operator appears now as an explicit argument to the solvers' `buildSystemMatrix` function.
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‎CHANGELOG.md‎

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non compliant. The hook generates a patch and shows the command needed to
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apply it.
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_NOT recommended_ The hook can be skipped by passing the `--no-verify` option to `git commit`
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- A pre-commit hook in `.githooks/pre-commit-license-maintainer` checking the license headers.
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**BREAKING CHANGE** Perl5 is needed to work on the code.
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The hook is based on this [project](https://github.com/NitorCreations/license-maintainer)
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and is configured based on the `.gitattributes` file.
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The list of authors is automatically extracted from the `license.author`
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field in `.git/config`. This can either be modified by hand or by invoking
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`git config license.author="list-of-authors"`.
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The hook will check the license headers, amend them where possible and abort
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where not possible, showing the commands needed to update the license.
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_NOT recommended_ The hook can be skipped by passing the `--no-verify` option to `git commit`
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- An `UNUSED` preprocessor macro to mark arguments as unused.
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- An `UNUSED_FUNCTION` preprocessor macro to mark functions as unused.
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### Changed
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- The Green's function, solver and boundary integral operator classes have been
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radically redesigned. This avoids coupling between integrators and Green's
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function that existed in the previous design.
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See the [Green's function code
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reference](http://pcmsolver.readthedocs.io/en/latest/code-reference/greens-functions.html)
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for a more detailed explanation.
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### Deprecated
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### Removed

‎doc/code-reference/greens-functions.rst‎

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IGreensFunction
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---------------
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.. doxygenclass:: IGreensFunction
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:project: PCMSolver
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:members:

‎doc/programmers/documentation.rst‎

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@@ -25,6 +25,15 @@ as extensive as for reStructuredText, see `these comments
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<https://blog.readthedocs.com/adding-markdown-support/>`_ Follow the guidelines
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in :cite:`Wilson2014` regarding what to document.
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Documeting methods in derived classes
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-------------------------------------
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Virtual methods should only be documented in the base classes.
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This avoids unnecessary verbosity and conforms to the principle: "Document
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_what_, not _how_" :cite:`Wilson2014`
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If you feel the _how_ needs to be explicitly documented, add some notes in the
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appropriate ``.rst`` file.
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How does this work?
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-------------------
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‎src/bi_operators/BIOperatorData.hpp‎

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/**
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* PCMSolver, an API for the Polarizable Continuum Model
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* Copyright (C) 2016 Roberto Di Remigio, Luca Frediani and collaborators.
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*
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* This file is part of PCMSolver.
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*
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* PCMSolver is free software: you can redistribute it and/or modify
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* it under the terms of the GNU Lesser General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* PCMSolver is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public License
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* along with PCMSolver. If not, see <http://www.gnu.org/licenses/>.
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*
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* For information on the complete list of contributors to the
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* PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
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*/
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#ifndef BIOPERATORDATA_HPP
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#define BIOPERATORDATA_HPP
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#include "Config.hpp"
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/*! @struct biOperatorData
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* @brief Contains all data defined from user input to set up the integrators
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*/
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struct biOperatorData {
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/*! Scaling for the diagonal of the approximate collocation matrices */
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double scaling;
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/*! Whether the structure was initialized with user input or not */
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bool empty;
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biOperatorData() { empty = true; }
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biOperatorData(double s) : scaling(s) { empty = false; }
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};
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#endif // BIOPERATORDATA_HPP

‎src/bi_operators/BoundaryIntegralOperator.cpp‎

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/**
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* PCMSolver, an API for the Polarizable Continuum Model
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* Copyright (C) 2016 Roberto Di Remigio, Luca Frediani and collaborators.
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*
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* This file is part of PCMSolver.
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*
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* PCMSolver is free software: you can redistribute it and/or modify
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* it under the terms of the GNU Lesser General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* PCMSolver is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public License
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* along with PCMSolver. If not, see <http://www.gnu.org/licenses/>.
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*
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* For information on the complete list of contributors to the
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* PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
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*/
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#include "BoundaryIntegralOperator.hpp"
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#include "Config.hpp"
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#include <Eigen/Core>
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#include "cavity/Cavity.hpp"
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#include "green/IGreensFunction.hpp"
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#include "utils/MathUtils.hpp"
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Eigen::MatrixXd BoundaryIntegralOperator::computeS(
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const Cavity & cav, const IGreensFunction & gf) const {
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Eigen::MatrixXd biop = computeS_impl(cav.elements(), gf);
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// Perform symmetry blocking
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// The total size of the cavity
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PCMSolverIndex cavitySize = cav.size();
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// The number of irreps in the group
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int nrBlocks = cav.pointGroup().nrIrrep();
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// The size of the irreducible portion of the cavity
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int dimBlock = cav.irreducible_size();
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if (cav.pointGroup().nrGenerators() != 0) {
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TIMER_ON("Symmetry blocking");
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symmetryBlocking(biop, cavitySize, dimBlock, nrBlocks);
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TIMER_OFF("Symmetry blocking");
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}
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return biop;
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}
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Eigen::MatrixXd BoundaryIntegralOperator::computeD(
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const Cavity & cav, const IGreensFunction & gf) const {
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Eigen::MatrixXd biop = computeD_impl(cav.elements(), gf);
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// Perform symmetry blocking
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// The total size of the cavity
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PCMSolverIndex cavitySize = cav.size();
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// The number of irreps in the group
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int nrBlocks = cav.pointGroup().nrIrrep();
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// The size of the irreducible portion of the cavity
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int dimBlock = cav.irreducible_size();
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if (cav.pointGroup().nrGenerators() != 0) {
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TIMER_ON("Symmetry blocking");
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symmetryBlocking(biop, cavitySize, dimBlock, nrBlocks);
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TIMER_OFF("Symmetry blocking");
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}
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return biop;
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}

‎src/bi_operators/BoundaryIntegralOperator.hpp‎

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/**
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* PCMSolver, an API for the Polarizable Continuum Model
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* Copyright (C) 2016 Roberto Di Remigio, Luca Frediani and collaborators.
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*
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* This file is part of PCMSolver.
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*
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* PCMSolver is free software: you can redistribute it and/or modify
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* it under the terms of the GNU Lesser General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* PCMSolver is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public License
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* along with PCMSolver. If not, see <http://www.gnu.org/licenses/>.
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*
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* For information on the complete list of contributors to the
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* PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
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*/
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#ifndef BOUNDARYINTEGRALOPERATORS_HPP
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#define BOUNDARYINTEGRALOPERATORS_HPP
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#include <vector>
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#include "Config.hpp"
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#include <Eigen/Core>
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class Cavity;
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class Element;
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class IGreensFunction;
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class BoundaryIntegralOperator {
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public:
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virtual ~BoundaryIntegralOperator() {}
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Eigen::MatrixXd computeS(const Cavity & cav, const IGreensFunction & gf) const;
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Eigen::MatrixXd computeD(const Cavity & cav, const IGreensFunction & gf) const;
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private:
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virtual Eigen::MatrixXd computeS_impl(const std::vector<Element> & elems,
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const IGreensFunction & gf) const = 0;
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virtual Eigen::MatrixXd computeD_impl(const std::vector<Element> & elems,
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const IGreensFunction & gf) const = 0;
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};
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#endif // BOUNDARYINTEGRALOPERATORS_HPP

‎src/bi_operators/CMakeLists.txt‎

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# List of headers
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list(APPEND headers_list CollocationIntegrator.hpp IntegratorForward.hpp IntegratorHelperFunctions.hpp IntegratorTypes.hpp NumericalIntegrator.hpp PurisimaIntegrator.hpp)
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list(APPEND headers_list BIOperatorData.hpp BoundaryIntegralOperator.hpp Collocation.hpp Purisima.hpp Numerical.hpp)
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# List of sources
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list(APPEND sources_list )
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list(APPEND sources_list BoundaryIntegralOperator.cpp Collocation.cpp Purisima.cpp Numerical.cpp)
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add_library(bi_operators OBJECT ${headers_list} ${sources_list})
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set_target_properties(bi_operators PROPERTIES POSITION_INDEPENDENT_CODE 1 )

‎src/bi_operators/Collocation.cpp‎

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/**
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* PCMSolver, an API for the Polarizable Continuum Model
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* Copyright (C) 2016 Roberto Di Remigio, Luca Frediani and collaborators.
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*
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* This file is part of PCMSolver.
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*
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* PCMSolver is free software: you can redistribute it and/or modify
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* it under the terms of the GNU Lesser General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* PCMSolver is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public License
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* along with PCMSolver. If not, see <http://www.gnu.org/licenses/>.
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*
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* For information on the complete list of contributors to the
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* PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
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*/
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#include "Collocation.hpp"
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#include "Config.hpp"
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#include <Eigen/Core>
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#include "cavity/Element.hpp"
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#include "green/IGreensFunction.hpp"
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#include "BIOperatorData.hpp"
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#include "utils/Factory.hpp"
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namespace integrator {
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Collocation::Collocation() : factor_(1.07) {}
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Collocation::Collocation(double fac) : factor_(fac) {}
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Eigen::MatrixXd Collocation::computeS_impl(const std::vector<Element> & elems,
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const IGreensFunction & gf) const {
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PCMSolverIndex cavitySize = elems.size();
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Eigen::MatrixXd S = Eigen::MatrixXd::Zero(cavitySize, cavitySize);
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for (PCMSolverIndex i = 0; i < cavitySize; ++i) {
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Element source = elems[i];
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S(i, i) = gf.singleLayer(source, factor_);
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for (PCMSolverIndex j = 0; j < cavitySize; ++j) {
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Element probe = elems[j];
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if (i != j)
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S(i, j) = gf.kernelS(source.center(), probe.center());
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}
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}
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return S;
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}
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Eigen::MatrixXd Collocation::computeD_impl(const std::vector<Element> & elems,
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const IGreensFunction & gf) const {
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PCMSolverIndex cavitySize = elems.size();
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Eigen::MatrixXd D = Eigen::MatrixXd::Zero(cavitySize, cavitySize);
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for (PCMSolverIndex i = 0; i < cavitySize; ++i) {
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Element source = elems[i];
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D(i, i) = gf.doubleLayer(source, factor_);
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for (PCMSolverIndex j = 0; j < cavitySize; ++j) {
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Element probe = elems[j];
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if (i != j)
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D(i, j) =
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gf.kernelD(probe.normal().normalized(), source.center(), probe.center());
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}
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}
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return D;
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}
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} // namespace integrator
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namespace {
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BoundaryIntegralOperator * createCollocation(const biOperatorData & data) {
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return new integrator::Collocation(data.scaling);
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}
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const std::string COLLOCATION("COLLOCATION");
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const bool registeredCollocation =
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Factory<BoundaryIntegralOperator, biOperatorData>::TheFactory().registerObject(
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COLLOCATION, createCollocation);
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}

‎src/bi_operators/Collocation.hpp‎

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/**
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* PCMSolver, an API for the Polarizable Continuum Model
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* Copyright (C) 2016 Roberto Di Remigio, Luca Frediani and collaborators.
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*
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* This file is part of PCMSolver.
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*
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* PCMSolver is free software: you can redistribute it and/or modify
8+
* it under the terms of the GNU Lesser General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
10+
* (at your option) any later version.
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*
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* PCMSolver is distributed in the hope that it will be useful,
13+
* but WITHOUT ANY WARRANTY; without even the implied warranty of
14+
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public License
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* along with PCMSolver. If not, see <http://www.gnu.org/licenses/>.
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*
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* For information on the complete list of contributors to the
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* PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
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*/
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#ifndef COLLOCATION_HPP
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#define COLLOCATION_HPP
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#include <vector>
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#include "Config.hpp"
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#include <Eigen/Core>
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class Element;
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class IGreensFunction;
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#include "BoundaryIntegralOperator.hpp"
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namespace integrator {
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/*! \file Collocation.hpp
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* \class Collocation
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* \brief Implementation of the single and double layer operators matrix
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*representation using one-point collocation
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* \author Roberto Di Remigio
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* \date 2015, 2016
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*
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* Calculates the diagonal elements of S as:
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* \f[
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* S_{ii} = factor * \sqrt{\frac{4\pi}{a_i}}
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* \f]
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* while the diagonal elements of D are:
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* \f[
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* D_{ii} = -factor * \sqrt{\frac{\pi}{a_i}} \frac{1}{R_I}
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* \f]
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*/
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class Collocation __final : public BoundaryIntegralOperator {
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public:
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Collocation();
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Collocation(double fac);
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virtual ~Collocation() {}
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private:
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/*! Scaling factor for the diagonal elements of the matrix representation of
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* the S and D operators
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*/
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double factor_;
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virtual Eigen::MatrixXd computeS_impl(const std::vector<Element> & elems,
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const IGreensFunction & gf) const __override;
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virtual Eigen::MatrixXd computeD_impl(const std::vector<Element> & elems,
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const IGreensFunction & gf) const __override;
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};
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} // namespace integrator
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#endif // COLLOCATION_HPP

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