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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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#include <fstream> |
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#include "integrators/LDForceManager.hpp" |
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#include "math/CholeskyDecomposition.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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namespace oopse { |
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|
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LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){ |
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Globals* simParams = info->getSimParams(); |
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std::map<std::string, HydroProp> hydroPropMap; |
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if (simParams->haveHydroPropFile()) { |
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hydroPropMap = parseFrictionFile(simParams->getHydroPropFile()); |
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} else { |
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//error |
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} |
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|
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
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if (iter != hydroPropMap.end()) { |
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hydroProps_.push_back(iter->second); |
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} else { |
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//error |
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} |
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|
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} |
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} |
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variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt(); |
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} |
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std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) { |
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std::map<std::string, HydroProp> props; |
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std::ifstream ifs(filename.c_str()); |
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if (ifs.is_open()) { |
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|
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} |
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|
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const unsigned int BufferSize = 65535; |
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char buffer[BufferSize]; |
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while (ifs.getline(buffer, BufferSize)) { |
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StringTokenizer tokenizer(buffer); |
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HydroProp currProp; |
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if (tokenizer.countTokens() >= 67) { |
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std::string atomName = tokenizer.nextToken(); |
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currProp.cod[0] = tokenizer.nextTokenAsDouble(); |
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currProp.cod[1] = tokenizer.nextTokenAsDouble(); |
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currProp.cod[2] = tokenizer.nextTokenAsDouble(); |
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|
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currProp.Ddtt(0,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtt(0,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtt(0,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtt(1,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtt(1,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtt(1,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtt(2,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtt(2,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtt(2,2) = tokenizer.nextTokenAsDouble(); |
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|
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currProp.Ddtr(0,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtr(0,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtr(0,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtr(1,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtr(1,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtr(1,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtr(2,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtr(2,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddtr(2,2) = tokenizer.nextTokenAsDouble(); |
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|
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currProp.Ddrr(0,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddrr(0,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddrr(0,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddrr(1,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddrr(1,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddrr(1,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddrr(2,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddrr(2,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Ddrr(2,2) = tokenizer.nextTokenAsDouble(); |
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|
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currProp.Xidtt(0,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidtt(0,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidtt(0,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidtt(1,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidtt(1,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidtt(1,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidtt(2,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidtt(2,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidtt(2,2) = tokenizer.nextTokenAsDouble(); |
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|
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currProp.Xidrt(0,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidrt(0,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidrt(0,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidrt(1,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidrt(1,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidrt(1,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidrt(2,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidrt(2,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidrt(2,2) = tokenizer.nextTokenAsDouble(); |
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|
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currProp.Xidtr(0,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidtr(0,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidtr(0,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidtr(1,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidtr(1,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidtr(1,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidtr(2,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidtr(2,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidtr(2,2) = tokenizer.nextTokenAsDouble(); |
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|
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currProp.Xidrr(0,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidrr(0,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidrr(0,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidrr(1,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidrr(1,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidrr(1,2) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidrr(2,0) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidrr(2,1) = tokenizer.nextTokenAsDouble(); |
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currProp.Xidrr(2,2) = tokenizer.nextTokenAsDouble(); |
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props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp)); |
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} |
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} |
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|
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return props; |
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} |
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|
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void LDForceManager::postCalculation() { |
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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Vector3d vel; |
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Vector3d pos; |
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Vector3d frc; |
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Mat3x3d A; |
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Mat3x3d Atrans; |
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Vector3d Tb; |
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Vector3d ji; |
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double mass; |
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unsigned int index = 0; |
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for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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|
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vel =integrableObject->getVel(); |
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if (integrableObject->isDirectional()){ |
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//calculate angular velocity in lab frame |
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Mat3x3d I = integrableObject->getI(); |
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Vector3d angMom = integrableObject->getJ(); |
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Vector3d omega; |
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|
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if (integrableObject->isLinear()) { |
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int linearAxis = integrableObject->linearAxis(); |
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int l = (linearAxis +1 )%3; |
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int m = (linearAxis +2 )%3; |
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omega[l] = angMom[l] /I(l, l); |
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omega[m] = angMom[m] /I(m, m); |
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|
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} else { |
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omega[0] = angMom[0] /I(0, 0); |
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omega[1] = angMom[1] /I(1, 1); |
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omega[2] = angMom[2] /I(2, 2); |
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} |
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|
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//apply friction force and torque at center of diffusion |
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A = integrableObject->getA(); |
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Atrans = A.transpose(); |
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Vector3d rcd = Atrans * hydroProps_[index].cod; |
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Vector3d vcd = vel + cross(omega, rcd); |
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vcd = A* vcd; |
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Vector3d frictionForce = -(hydroProps_[index].Xidtt * vcd + hydroProps_[index].Xidrt * omega); |
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frictionForce = Atrans*frictionForce; |
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integrableObject->addFrc(frictionForce); |
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Vector3d frictionTorque = - (hydroProps_[index].Xidtr * vcd + hydroProps_[index].Xidrr * omega); |
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frictionTorque = Atrans*frictionTorque; |
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integrableObject->addTrq(frictionTorque+ cross(rcd, frictionForce)); |
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|
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//apply random force and torque at center of diffustion |
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Vector3d randomForce; |
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Vector3d randomTorque; |
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genRandomForceAndTorque(randomForce, randomTorque, index, variance_); |
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randomForce = Atrans*randomForce; |
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randomTorque = Atrans* randomTorque; |
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integrableObject->addFrc(randomForce); |
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integrableObject->addTrq(randomTorque + cross(rcd, randomForce )); |
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|
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} else { |
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//spheric atom |
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Vector3d frictionForce = -(hydroProps_[index].Xidtt *vel); |
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Vector3d randomForce; |
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Vector3d randomTorque; |
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genRandomForceAndTorque(randomForce, randomTorque, index, variance_); |
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|
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//randomForce /= OOPSEConstant::energyConvert; |
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//randomTorque /= OOPSEConstant::energyConvert; |
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integrableObject->addFrc(frictionForce+randomForce); |
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} |
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|
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++index; |
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|
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} |
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} |
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|
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ForceManager::postCalculation(); |
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|
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|
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|
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} |
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|
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void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) { |
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/* |
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SquareMatrix<double, 6> Dd; |
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SquareMatrix<double, 6> S; |
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Vector<double, 6> Z; |
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Vector<double, 6> generalForce; |
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Dd.setSubMatrix(0, 0, hydroProps_[index].Ddtt); |
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Dd.setSubMatrix(0, 3, hydroProps_[index].Ddtr.transpose()); |
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Dd.setSubMatrix(3, 0, hydroProps_[index].Ddtr); |
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Dd.setSubMatrix(3, 3, hydroProps_[index].Ddrr); |
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CholeskyDecomposition(Dd, S); |
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*/ |
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|
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SquareMatrix<double, 6> Xid; |
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SquareMatrix<double, 6> S; |
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Vector<double, 6> Z; |
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Vector<double, 6> generalForce; |
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Xid.setSubMatrix(0, 0, hydroProps_[index].Xidtt); |
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Xid.setSubMatrix(0, 3, hydroProps_[index].Xidrt); |
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Xid.setSubMatrix(3, 0, hydroProps_[index].Xidtr); |
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Xid.setSubMatrix(3, 3, hydroProps_[index].Xidrr); |
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CholeskyDecomposition(Xid, S); |
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|
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/* |
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Xid *= variance; |
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Z[0] = randNumGen_.randNorm(0, 1.0); |
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Z[1] = randNumGen_.randNorm(0, 1.0); |
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Z[2] = randNumGen_.randNorm(0, 1.0); |
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Z[3] = randNumGen_.randNorm(0, 1.0); |
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Z[4] = randNumGen_.randNorm(0, 1.0); |
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Z[5] = randNumGen_.randNorm(0, 1.0); |
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*/ |
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|
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Z[0] = randNumGen_.randNorm(0, variance); |
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Z[1] = randNumGen_.randNorm(0, variance); |
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Z[2] = randNumGen_.randNorm(0, variance); |
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Z[3] = randNumGen_.randNorm(0, variance); |
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Z[4] = randNumGen_.randNorm(0, variance); |
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Z[5] = randNumGen_.randNorm(0, variance); |
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|
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|
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generalForce = S*Z; |
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|
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force[0] = generalForce[0]; |
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force[1] = generalForce[1]; |
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force[2] = generalForce[2]; |
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torque[0] = generalForce[3]; |
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torque[1] = generalForce[4]; |
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torque[2] = generalForce[5]; |
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|
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} |
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|
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} |
