mirror of
https://github.com/openmm/openmm
synced 2026-06-03 06:39:48 +09:00
baf7942c74
* Created CustomVolumeForce * Serialization for CustomVolumeForce * Documentation for CustomVolumeForce * Code simplification * Removed unused code
77 lines
4.1 KiB
C++
77 lines
4.1 KiB
C++
/* -------------------------------------------------------------------------- *
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* OpenMM *
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* -------------------------------------------------------------------------- *
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* This is part of the OpenMM molecular simulation toolkit originating from *
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* Simbios, the NIH National Center for Physics-Based Simulation of *
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* Biological Structures at Stanford, funded under the NIH Roadmap for *
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* Medical Research, grant U54 GM072970. See https://simtk.org. *
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* *
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* Portions copyright (c) 2025 Stanford University and the Authors. *
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* Authors: Peter Eastman *
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* Contributors: *
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* *
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* Permission is hereby granted, free of charge, to any person obtaining a *
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* copy of this software and associated documentation files (the "Software"), *
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* to deal in the Software without restriction, including without limitation *
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* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
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* and/or sell copies of the Software, and to permit persons to whom the *
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* Software is 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 *
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* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
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* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
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* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
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* USE OR OTHER DEALINGS IN THE SOFTWARE. *
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* -------------------------------------------------------------------------- */
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#include "openmm/internal/CustomVolumeForceImpl.h"
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#include "openmm/internal/ContextImpl.h"
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#include "lepton/ParsedExpression.h"
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#include "lepton/Parser.h"
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using namespace OpenMM;
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using namespace std;
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CustomVolumeForceImpl::CustomVolumeForceImpl(const CustomVolumeForce& owner) : CustomCPPForceImpl(owner), owner(owner) {
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Lepton::ParsedExpression expression = Lepton::Parser::parse(owner.getEnergyFunction());
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energyExpression = expression.createCompiledExpression();
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map<string, double*> variableLocations;
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globalParameterNames.resize(owner.getNumGlobalParameters());
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globalValues.resize(owner.getNumGlobalParameters());
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for (int i = 0; i < owner.getNumGlobalParameters(); i++) {
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string name = owner.getGlobalParameterName(i);
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defaultParameters[name] = owner.getGlobalParameterDefaultValue(i);
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globalParameterNames[i] = name;
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variableLocations[name] = &globalValues[i];
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}
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variableLocations["v"] = &volume;
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variableLocations["ax"] = &a[0];
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variableLocations["bx"] = &b[0];
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variableLocations["by"] = &b[1];
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variableLocations["cx"] = &c[0];
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variableLocations["cy"] = &c[1];
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variableLocations["cz"] = &c[2];
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energyExpression.setVariableLocations(variableLocations);
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}
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void CustomVolumeForceImpl::initialize(ContextImpl& context) {
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CustomCPPForceImpl::initialize(context);
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}
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double CustomVolumeForceImpl::computeForce(ContextImpl& context, const vector<Vec3>& positions, vector<Vec3>& forces) {
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for (int i = 0; i < globalParameterNames.size(); i++)
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globalValues[i] = context.getParameter(globalParameterNames[i]);
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context.getPeriodicBoxVectors(a, b, c);
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volume = a[0]*b[1]*c[2];
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return energyExpression.evaluate();
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}
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map<string, double> CustomVolumeForceImpl::getDefaultParameters() {
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return defaultParameters;
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}
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