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BotellaABotellaA
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Merge pull request #7 from Geode-solutions/gibbs_energy
feat(Energy Terms): set up energy term to build gibbs energy.
2 parents 53e1183 + aeadd66 commit bcad127

21 files changed

Lines changed: 1108 additions & 64 deletions

‎commitlint.config.js‎

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export default {
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extends: ["@commitlint/config-angular"],
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rules: {
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"scope-empty": [2, "never"],
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"subject-empty": [2, "never"],
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"subject-max-length": [0],
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"body-leading-blank": [0],
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"footer-leading-blank": [0],
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"header-max-length": [0],
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"scope-case": [0],
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"subject-case": [0],
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"subject-full-stop": [0],
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"type-case": [0],
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"type-empty": [0],
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},
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}

‎include/geode/stochastic/configuration/configuration.hpp‎

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void remove_object( index_t idx );
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index_t size() const;
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/**
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* @brief Bounds-checked access to the marked object at index @p idx.
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* Wrapper for std::vector::at().
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* @throws std::out_of_range if idx is out of range.
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*/
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const MarkedObject< Geometry >& object( index_t idx ) const;
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/**
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* @brief Unchecked access to the marked object at index @p idx.
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* Wrapper for std::vector::operator[]().
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*/
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const MarkedObject< Geometry >& operator[]( index_t idx ) const;
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std::vector< index_t > object_ids_with_mark( const Mark& mark );
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‎include/geode/stochastic/configuration/marked_object.hpp‎

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#include <geode/stochastic/common.hpp>
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#include <geode/geometry/basic_objects/segment.hpp>
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#include <geode/geometry/bounding_box.hpp>
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#include <geode/geometry/point.hpp>
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namespace geode
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{
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FORWARD_DECLARATION_DIMENSION_CLASS( Point );
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const std::optional< Mark >& mark() const;
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bool has_mark() const;
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decltype( auto ) bounding_box() const;
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decltype( auto ) barycenter() const;
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auto bounding_box() const
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{
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if constexpr( std::is_same_v< Geometry, Point2D > )
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{
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geode::BoundingBox< 2 > box;
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box.add_point( geometry_ );
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return box;
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}
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else if constexpr( std::is_same_v< Geometry, Point3D > )
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{
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geode::BoundingBox< 3 > box;
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box.add_point( geometry_ );
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return box;
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}
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else
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{
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return geometry_.bounding_box();
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}
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}
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auto barycenter() const
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{
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if constexpr( std::is_same_v< Geometry, Point2D >
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|| std::is_same_v< Geometry, Point3D > )
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{
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return geometry_;
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}
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else
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{
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return geometry_.barycenter();
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}
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}
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private:
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Geometry geometry_;

‎include/geode/stochastic/configuration/pairwise_interactions.hpp‎

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/*
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* Copyright (c) 2019 - 2025 Geode-solutions
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in
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* all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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* SOFTWARE.
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*
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*/
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#pragma once
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#include <geode/geometry/distance.hpp>
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#include <geode/geometry/point.hpp>
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#include <geode/stochastic/configuration/marked_object.hpp>
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namespace geode
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{
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struct DistanceCutoffInteraction
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{
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DistanceCutoffInteraction( double distance )
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: cutoff_distance( distance )
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{
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}
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template < typename Geometry >
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double operator()( const MarkedObject< Geometry >& object1,
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const MarkedObject< Geometry >& object2 ) const
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{
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auto dist = geode::point_point_distance(
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object1.barycenter(), object2.barycenter() );
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return dist <= cutoff_distance ? 1.0 : 0.0;
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}
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double cutoff_distance{ GLOBAL_EPSILON };
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};
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} // namespace geode

‎include/geode/stochastic/sampling/mcmc/models/components/energy_term.hpp‎

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/*
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* Copyright (c) 2019 - 2025 Geode-solutions
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in
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* all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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* SOFTWARE.
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*
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*/
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#pragma once
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#include <geode/stochastic/common.hpp>
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#include <geode/stochastic/configuration/configuration.hpp>
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namespace
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{
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struct NegLogParam
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{
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explicit NegLogParam( double param )
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{
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OPENGEODE_EXCEPTION( param >= 0.,
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"[Gibbs energy term] - The model parameter "
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"cannot be smaller than 0." );
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if( param >= geode::GLOBAL_EPSILON )
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{
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value = -std::log( param );
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}
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}
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double scale( double multiplier ) const
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{
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if( value )
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{
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return value.value() * multiplier;
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}
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return ( multiplier > 0 )
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? std::numeric_limits< double >::infinity()
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: 0.0;
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}
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double param() const
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{
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if( value )
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{
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return std::exp( -value.value() );
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}
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return 0.;
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}
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std::optional< double > value;
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};
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} // namespace
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namespace geode
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{
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template < typename Geometry >
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class EnergyTerm
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{
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public:
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explicit EnergyTerm( double parameter )
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: neg_log_parameter_( parameter )
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{
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}
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virtual ~EnergyTerm() = default;
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double parameter() const
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{
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return neg_log_parameter_.param();
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}
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virtual double log_total(
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const Configuration< Geometry >& state ) const = 0;
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virtual double log_delta_add( const Configuration< Geometry >& state,
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const MarkedObject< Geometry >& sample ) const = 0;
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virtual double log_delta_remove( const Configuration< Geometry >& state,
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index_t sample_id ) const = 0;
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virtual double log_delta_change( const Configuration< Geometry >& state,
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index_t old_sample_id,
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const MarkedObject< Geometry >& new_sample ) const = 0;
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virtual double statistic(
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const Configuration< Geometry >& state ) const = 0;
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protected:
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NegLogParam neg_log_parameter_;
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};
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} // namespace geode

‎include/geode/stochastic/sampling/mcmc/models/components/intensity_term.hpp‎

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/*
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* Copyright (c) 2019 - 2025 Geode-solutions
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
5+
* of this software and associated documentation files (the "Software"), to deal
6+
* in the Software without restriction, including without limitation the rights
7+
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
8+
* copies of the Software, and to permit persons to whom the Software is
9+
* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in
12+
* all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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* SOFTWARE.
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*
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*/
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#pragma once
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#include <geode/stochastic/configuration/configuration.hpp>
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#include <geode/stochastic/sampling/mcmc/models/components/energy_term.hpp>
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namespace geode
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{
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template < typename Geometry >
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class IntensityTerm : public EnergyTerm< Geometry >
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{
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public:
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explicit IntensityTerm( double lambda )
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: EnergyTerm< Geometry >( lambda )
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{
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}
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double log_total( const Configuration< Geometry >& state ) const final
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{
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const auto n = static_cast< double >( number_of_objects( state ) );
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return this->neg_log_parameter_.scale( n );
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}
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double log_delta_add( const Configuration< Geometry >& state,
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const MarkedObject< Geometry >& sample ) const final
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{
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return this->neg_log_parameter_.scale( 1. );
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}
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double log_delta_remove( const Configuration< Geometry >& state,
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index_t sample_id ) const final
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{
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return this->neg_log_parameter_.scale( -1. );
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}
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double log_delta_change( const Configuration< Geometry >& state,
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index_t old_sample_id,
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const MarkedObject< Geometry >& new_sample ) const final
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{
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return 0.0;
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}
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double statistic( const Configuration< Geometry >& state ) const final
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{
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return static_cast< double >( number_of_objects( state ) );
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}
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private:
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index_t number_of_objects(
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const Configuration< Geometry >& state ) const
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{
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return state.size();
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}
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};
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} // namespace geode

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