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/* |
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* Copyright (c) 2009 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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|
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#include <cmath> |
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#include "restraints/RestraintForceManager.hpp" |
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#include "restraints/MolecularRestraint.hpp" |
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#include "restraints/ObjectRestraint.hpp" |
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#include "io/RestReader.hpp" |
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#include "utils/simError.h" |
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#include "utils/OOPSEConstant.hpp" |
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#include "utils/StringUtils.hpp" |
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#include "selection/SelectionEvaluator.hpp" |
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#include "selection/SelectionManager.hpp" |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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|
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|
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namespace oopse { |
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|
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RestraintForceManager::RestraintForceManager(SimInfo* info): ForceManager(info) { |
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|
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// order of affairs: |
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// |
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// 1) create restraints from the restraintStamps found in the MD |
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// file. |
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// |
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// 2) Create RestraintReader to parse the input files for the ideal |
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// structures. This reader will set reference structures, and will |
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// calculate molecular centers of mass, etc. |
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// |
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// 3) sit around and wait for calcForces to be called. When it comes, |
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// call the normal force manager calcForces, then loop through the |
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// restrained objects and do their restraint forces. |
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|
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currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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Globals* simParam = info_->getSimParams(); |
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|
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if (simParam->haveStatusTime()){ |
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restTime_ = simParam->getStatusTime(); |
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} else { |
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sprintf(painCave.errMsg, |
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"Restraint warning: If you use restraints without setting\n", |
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"\tstatusTime, no restraint data will be written to the rest\n", |
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"\tfile.\n"); |
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painCave.isFatal = 0; |
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simError(); |
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restTime_ = simParam->getRunTime(); |
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} |
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|
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int nRestraintStamps = simParam->getNRestraintStamps(); |
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std::vector<RestraintStamp*> stamp = simParam->getRestraintStamps(); |
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|
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for (int i = 0; i < nRestraintStamps; i++){ |
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|
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std::string myType = toUpperCopy(stamp[i]->getType()); |
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|
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if (myType.compare("MOLECULAR")==0){ |
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|
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int molIndex; |
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std::vector<Vector3d> ref; |
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Vector3d refCom; |
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|
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if (!stamp[i]->haveMolIndex()) { |
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sprintf(painCave.errMsg, |
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"Restraint Error: A molecular restraint was specified\n" |
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"\twithout providing a value for molIndex.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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molIndex = stamp[i]->getMolIndex(); |
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} |
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|
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Molecule* mol = info_->getMoleculeByGlobalIndex(molIndex); |
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|
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if (mol == NULL) { |
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sprintf(painCave.errMsg, |
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"Restraint Error: A molecular restraint was specified, but\n" |
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"\tno molecule was found with global index %d.\n", |
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molIndex); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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MolecularRestraint* rest = new MolecularRestraint(); |
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|
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std::string restPre("mol_"); |
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std::stringstream restName; |
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restName << restPre << molIndex; |
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rest->setRestraintName(restName.str()); |
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|
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if (stamp[i]->haveDisplacementSpringConstant()) { |
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rest->setDisplacementForceConstant(stamp[i]->getDisplacementSpringConstant()); |
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} |
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if (stamp[i]->haveTwistSpringConstant()) { |
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rest->setTwistForceConstant(stamp[i]->getTwistSpringConstant()); |
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} |
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if (stamp[i]->haveSwingXSpringConstant()) { |
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rest->setSwingXForceConstant(stamp[i]->getSwingXSpringConstant()); |
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} |
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if (stamp[i]->haveSwingYSpringConstant()) { |
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rest->setSwingYForceConstant(stamp[i]->getSwingYSpringConstant()); |
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} |
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if (stamp[i]->haveRestrainedTwistAngle()) { |
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rest->setRestrainedTwistAngle(stamp[i]->getRestrainedTwistAngle() * M_PI/180.0); |
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} |
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if (stamp[i]->haveRestrainedSwingYAngle()) { |
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rest->setRestrainedSwingYAngle(stamp[i]->getRestrainedSwingYAngle() * M_PI/180.0); |
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} |
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if (stamp[i]->haveRestrainedSwingXAngle()) { |
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rest->setRestrainedSwingXAngle(stamp[i]->getRestrainedSwingXAngle() * M_PI/180.0); |
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} |
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|
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restraints_.push_back(rest); |
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mol->addProperty(new RestraintData("Restraint", rest)); |
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restrainedMols_.push_back(mol); |
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|
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} else if (myType.compare("OBJECT") == 0) { |
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|
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std::string objectSelection; |
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|
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if (!stamp[i]->haveObjectSelection()) { |
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sprintf(painCave.errMsg, |
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"Restraint Error: An object restraint was specified\n" |
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"\twithout providing a selection script in the\n" |
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"\tobjectSelection variable.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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objectSelection = stamp[i]->getObjectSelection(); |
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} |
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|
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SelectionEvaluator evaluator(info); |
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SelectionManager seleMan(info); |
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|
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evaluator.loadScriptString(objectSelection); |
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seleMan.setSelectionSet(evaluator.evaluate()); |
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int selectionCount = seleMan.getSelectionCount(); |
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|
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sprintf(painCave.errMsg, |
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"Restraint Info: The specified restraint objectSelection,\n" |
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"\t\t%s\n" |
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"\twill result in %d integrable objects being\n" |
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"\trestrained.\n", objectSelection.c_str(), selectionCount); |
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painCave.isFatal = 0; |
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simError(); |
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|
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int selei; |
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StuntDouble* sd; |
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|
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for (sd = seleMan.beginSelected(selei); sd != NULL; |
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sd = seleMan.nextSelected(selei)) { |
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|
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ObjectRestraint* rest = new ObjectRestraint(); |
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|
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if (stamp[i]->haveDisplacementSpringConstant()) { |
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rest->setDisplacementForceConstant(stamp[i]->getDisplacementSpringConstant()); |
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} |
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if (stamp[i]->haveTwistSpringConstant()) { |
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rest->setTwistForceConstant(stamp[i]->getTwistSpringConstant()); |
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} |
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if (stamp[i]->haveSwingXSpringConstant()) { |
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rest->setSwingXForceConstant(stamp[i]->getSwingXSpringConstant()); |
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} |
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if (stamp[i]->haveSwingYSpringConstant()) { |
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rest->setSwingYForceConstant(stamp[i]->getSwingYSpringConstant()); |
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} |
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if (stamp[i]->haveRestrainedTwistAngle()) { |
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rest->setRestrainedTwistAngle(stamp[i]->getRestrainedTwistAngle()); |
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} |
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if (stamp[i]->haveRestrainedSwingXAngle()) { |
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rest->setRestrainedSwingXAngle(stamp[i]->getRestrainedSwingXAngle()); |
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} |
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if (stamp[i]->haveRestrainedSwingYAngle()) { |
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rest->setRestrainedSwingYAngle(stamp[i]->getRestrainedSwingYAngle()); |
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} |
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restraints_.push_back(rest); |
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sd->addProperty(new RestraintData("Restraint", rest)); |
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restrainedObjs_.push_back(sd); |
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} |
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|
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} |
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} |
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|
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// ThermodynamicIntegration subclasses RestraintForceManager, and there |
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// are times when it won't use restraints at all, so only open the |
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// restraint file if we are actually using restraints: |
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|
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if (simParam->getUseRestraints()) { |
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std::string refFile = simParam->getRestraint_file(); |
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RestReader* rr = new RestReader(info, refFile); |
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|
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rr->readReferenceStructure(); |
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} |
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|
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restOutput_ = getPrefix(info_->getFinalConfigFileName()) + ".rest"; |
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restOut = new RestWriter(info_, restOutput_.c_str(), restraints_); |
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|
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if(!restOut){ |
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sprintf(painCave.errMsg, "Restraint error: Failed to create RestWriter\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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// todo: figure out the scale factor. Right now, just scale them all to 1 |
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std::vector<Restraint*>::const_iterator resti; |
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for(resti=restraints_.begin(); resti != restraints_.end(); ++resti){ |
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(*resti)->setScaleFactor(1.0); |
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} |
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} |
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|
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RestraintForceManager::~RestraintForceManager(){ |
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if (restOut) |
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delete restOut; |
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} |
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|
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void RestraintForceManager::init() { |
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currRestTime_ = currSnapshot_->getTime(); |
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} |
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|
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void RestraintForceManager::calcForces(bool needPotential, bool needStress){ |
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|
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ForceManager::calcForces(needPotential, needStress); |
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RealType restPot_local, restPot; |
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|
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restPot_local = doRestraints(1.0); |
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|
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#ifdef IS_MPI |
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MPI::COMM_WORLD.Allreduce(&restPot_local, &restPot, 1, |
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MPI::REALTYPE, MPI::SUM); |
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#else |
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restPot = restPot_local; |
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#endif |
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currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += restPot; |
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currSnapshot_->statData[Stats::VHARM] = restPot; |
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|
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//write out forces and current positions of restrained molecules |
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if (currSnapshot_->getTime() >= currRestTime_){ |
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restOut->writeRest(restInfo_); |
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currRestTime_ += restTime_; |
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} |
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} |
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|
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RealType RestraintForceManager::doRestraints(RealType scalingFactor){ |
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std::vector<Molecule*>::const_iterator rm; |
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GenericData* data; |
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Molecule::IntegrableObjectIterator ioi; |
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MolecularRestraint* mRest; |
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StuntDouble* sd; |
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RealType pTot; |
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|
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std::vector<StuntDouble*>::const_iterator ro; |
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ObjectRestraint* oRest; |
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|
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std::map<int, Restraint::RealPair> restInfo; |
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|
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unscaledPotential_ = 0.0; |
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|
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restInfo_.clear(); |
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|
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for(rm=restrainedMols_.begin(); rm != restrainedMols_.end(); ++rm){ |
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|
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// make sure this molecule (*rm) has a generic data for restraints: |
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data = (*rm)->getPropertyByName("Restraint"); |
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if (data != NULL) { |
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// make sure we can reinterpret the generic data as restraint data: |
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RestraintData* restData= dynamic_cast<RestraintData*>(data); |
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if (restData != NULL) { |
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// make sure we can reinterpet the restraint data as a pointer to |
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// an MolecularRestraint: |
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mRest = dynamic_cast<MolecularRestraint*>(restData->getData()); |
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if (mRest == NULL) { |
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sprintf( painCave.errMsg, |
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"Can not cast RestraintData to MolecularRestraint\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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sprintf( painCave.errMsg, |
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"Can not cast GenericData to RestraintData\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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sprintf( painCave.errMsg, "Can not find Restraint for RestrainedObject\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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// phew. At this point, we should have the pointer to the |
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// correct MolecularRestraint in the variable mRest. |
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|
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Vector3d molCom = (*rm)->getCom(); |
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|
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std::vector<Vector3d> struc; |
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std::vector<Vector3d> forces; |
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|
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for(sd = (*rm)->beginIntegrableObject(ioi); sd != NULL; |
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sd = (*rm)->nextIntegrableObject(ioi)) { |
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struc.push_back(sd->getPos()); |
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} |
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|
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mRest->setScaleFactor(scalingFactor); |
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mRest->calcForce(struc, molCom); |
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forces = mRest->getRestraintForces(); |
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int index = 0; |
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|
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for(sd = (*rm)->beginIntegrableObject(ioi); sd != NULL; |
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sd = (*rm)->nextIntegrableObject(ioi)) { |
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sd->addFrc(forces[index]); |
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struc.push_back(sd->getPos()); |
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index++; |
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} |
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|
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unscaledPotential_ += mRest->getUnscaledPotential(); |
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|
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restInfo = mRest->getRestraintInfo(); |
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restInfo_.push_back(restInfo); |
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} |
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|
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for(ro=restrainedObjs_.begin(); ro != restrainedObjs_.end(); ++ro){ |
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// make sure this object (*ro) has a generic data for restraints: |
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data = (*ro)->getPropertyByName("Restraint"); |
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if (data != NULL) { |
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// make sure we can reinterpret the generic data as restraint data: |
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RestraintData* restData= dynamic_cast<RestraintData*>(data); |
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if (restData != NULL) { |
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// make sure we can reinterpet the restraint data as a pointer to |
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// an ObjectRestraint: |
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oRest = dynamic_cast<ObjectRestraint*>(restData->getData()); |
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if (oRest == NULL) { |
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sprintf( painCave.errMsg, |
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"Can not cast RestraintData to ObjectRestraint\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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sprintf( painCave.errMsg, |
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"Can not cast GenericData to RestraintData\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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sprintf( painCave.errMsg, "Can not find Restraint for RestrainedObject\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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// phew. At this point, we should have the pointer to the |
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// correct Object restraint in the variable oRest. |
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|
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oRest->setScaleFactor(scalingFactor); |
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|
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Vector3d pos = (*ro)->getPos(); |
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|
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if ( (*ro)->isDirectional() ) { |
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|
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// directional objects may have orientational restraints as well |
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// as positional, so get the rotation matrix first: |
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|
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RotMat3x3d A = (*ro)->getA(); |
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oRest->calcForce(pos, A); |
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(*ro)->addFrc(oRest->getRestraintForce()); |
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(*ro)->addTrq(oRest->getRestraintTorque()); |
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} else { |
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|
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// plain vanilla positional restraints: |
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|
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oRest->calcForce(pos); |
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(*ro)->addFrc(oRest->getRestraintForce()); |
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} |
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|
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unscaledPotential_ += oRest->getUnscaledPotential(); |
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|
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restInfo = oRest->getRestraintInfo(); |
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restInfo_.push_back(restInfo); |
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} |
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|
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return unscaledPotential_ * scalingFactor; |
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} |
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} |
