/* -------------------------------------------------------------------------- * * OpenMM * * -------------------------------------------------------------------------- * * This is part of the OpenMM molecular simulation toolkit originating from * * Simbios, the NIH National Center for Physics-Based Simulation of * * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * * Portions copyright (c) 2025 Stanford University and the Authors. * * Authors: Peter Eastman * * Contributors: * * * * Permission is hereby granted, free of charge, to any person obtaining a * * copy of this software and associated documentation files (the "Software"), * * to deal in the Software without restriction, including without limitation * * the rights to use, copy, modify, merge, publish, distribute, sublicense, * * and/or sell copies of the Software, and to permit persons to whom the * * Software is furnished to do so, subject to the following conditions: * * * * The above copyright notice and this permission notice shall be included in * * all copies or substantial portions of the Software. * * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL * * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, * * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR * * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE * * USE OR OTHER DEALINGS IN THE SOFTWARE. * * -------------------------------------------------------------------------- */ #include "openmm/serialization/DPDIntegratorProxy.h" #include using namespace std; using namespace OpenMM; DPDIntegratorProxy::DPDIntegratorProxy() : SerializationProxy("DPDIntegrator") { } void DPDIntegratorProxy::serialize(const void* object, SerializationNode& node) const { node.setIntProperty("version", 1); const DPDIntegrator& integrator = *reinterpret_cast(object); node.setDoubleProperty("stepSize", integrator.getStepSize()); node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance()); node.setDoubleProperty("temperature", integrator.getTemperature()); node.setDoubleProperty("defaultFriction", integrator.getDefaultFriction()); node.setDoubleProperty("defaultCutoff", integrator.getDefaultCutoff()); node.setIntProperty("randomSeed", integrator.getRandomNumberSeed()); node.setIntProperty("integrationForceGroups", integrator.getIntegrationForceGroups()); SerializationNode& types = node.createChildNode("ParticleTypes"); for (auto type: integrator.getParticleTypes()) types.createChildNode("Type").setIntProperty("particle", type.first).setIntProperty("type", type.second); SerializationNode& pairs = node.createChildNode("TypePairs"); for (int i = 0; i < integrator.getNumTypePairs(); i++) { int type1, type2; double friction, cutoff; integrator.getTypePairParameters(i, type1, type2, friction, cutoff); pairs.createChildNode("Pair").setIntProperty("type1", type1).setIntProperty("type2", type2).setDoubleProperty("friction", friction).setDoubleProperty("cutoff", cutoff); } } void* DPDIntegratorProxy::deserialize(const SerializationNode& node) const { if (node.getIntProperty("version") != 1) throw OpenMMException("Unsupported version number"); DPDIntegrator *integrator = new DPDIntegrator(node.getDoubleProperty("temperature"), node.getDoubleProperty("defaultFriction"), node.getDoubleProperty("defaultCutoff"), node.getDoubleProperty("stepSize")); integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance")); integrator->setRandomNumberSeed(node.getIntProperty("randomSeed")); integrator->setIntegrationForceGroups(node.getIntProperty("integrationForceGroups", 0xFFFFFFFF)); const SerializationNode& types = node.getChildNode("ParticleTypes"); for (auto& type: types.getChildren()) integrator->setParticleType(type.getIntProperty("particle"), type.getIntProperty("type")); const SerializationNode& pairs = node.getChildNode("TypePairs"); for (auto& pair: pairs.getChildren()) integrator->addTypePair(pair.getIntProperty("type1"), pair.getIntProperty("type2"), pair.getDoubleProperty("friction"), pair.getDoubleProperty("cutoff")); return integrator; }