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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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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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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#include "config.h" |
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#include <cmath> |
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|
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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/PhysicalConstants.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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|
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namespace OpenMD { |
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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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std::vector<int> stuntDoubleIndex; |
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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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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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if (molIndex < 0) { |
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sprintf(painCave.errMsg, |
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"Restraint Error: A molecular restraint was specified\n" |
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"\twith a molIndex that was less than 0\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if (molIndex >= info_->getNGlobalMolecules()) { |
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sprintf(painCave.errMsg, |
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"Restraint Error: A molecular restraint was specified with\n" |
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"\ta molIndex that was greater than the total number of molecules\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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Molecule* mol = info_->getMoleculeByGlobalIndex(molIndex); |
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|
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if (mol == NULL) { |
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#ifdef IS_MPI |
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// getMoleculeByGlobalIndex returns a NULL in parallel if |
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// this proc doesn't have the molecule. Do a quick check to |
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// make sure another processor is supposed to have it. |
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|
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int myrank; |
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MPI_Comm_rank( MPI_COMM_WORLD, &myrank); |
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|
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if (info_->getMolToProc(molIndex) == myrank) { |
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|
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// If we were supposed to have it but got a null, then freak out. |
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#endif |
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|
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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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#ifdef IS_MPI |
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} |
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#endif |
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} |
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|
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|
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#ifdef IS_MPI |
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// only handle this molecular restraint if this processor owns the |
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// molecule |
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int myrank; |
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MPI_Comm_rank( MPI_COMM_WORLD, &myrank); |
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if (info_->getMolToProc(molIndex) == myrank) { |
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|
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#endif |
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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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if (stamp[i]->havePrint()) { |
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rest->setPrintRestraint(stamp[i]->getPrint()); |
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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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#ifdef IS_MPI |
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} |
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#endif |
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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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stuntDoubleIndex.push_back(sd->getGlobalIntegrableObjectIndex()); |
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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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if (stamp[i]->havePrint()) { |
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rest->setPrintRestraint(stamp[i]->getPrint()); |
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} |
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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, stuntDoubleIndex); |
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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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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(){ |
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|
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ForceManager::calcForces(); |
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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_Allreduce(&restPot_local, &restPot, 1, |
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MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
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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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RealType pot = currSnapshot_->getLongRangePotential(); |
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pot += restPot; |
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currSnapshot_->setLongRangePotential(pot); |
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currSnapshot_->setRestraintPotential(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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|
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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 = OPENMD_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 = OPENMD_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 = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
| 385 |
} |
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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; |
| 394 |
|
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for(sd = (*rm)->beginIntegrableObject(ioi); sd != NULL; |
| 396 |
sd = (*rm)->nextIntegrableObject(ioi)) { |
| 397 |
struc.push_back(sd->getPos()); |
| 398 |
} |
| 399 |
|
| 400 |
mRest->setScaleFactor(scalingFactor); |
| 401 |
mRest->calcForce(struc, molCom); |
| 402 |
forces = mRest->getRestraintForces(); |
| 403 |
int index = 0; |
| 404 |
|
| 405 |
for(sd = (*rm)->beginIntegrableObject(ioi); sd != NULL; |
| 406 |
sd = (*rm)->nextIntegrableObject(ioi)) { |
| 407 |
sd->addFrc(forces[index]); |
| 408 |
struc.push_back(sd->getPos()); |
| 409 |
index++; |
| 410 |
} |
| 411 |
|
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unscaledPotential_ += mRest->getUnscaledPotential(); |
| 413 |
|
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restInfo = mRest->getRestraintInfo(); |
| 415 |
|
| 416 |
// only collect data on restraints that we're going to print: |
| 417 |
if (mRest->getPrintRestraint()) |
| 418 |
restInfo_.push_back(restInfo); |
| 419 |
} |
| 420 |
|
| 421 |
for(ro=restrainedObjs_.begin(); ro != restrainedObjs_.end(); ++ro){ |
| 422 |
// make sure this object (*ro) has a generic data for restraints: |
| 423 |
data = (*ro)->getPropertyByName("Restraint"); |
| 424 |
if (data != NULL) { |
| 425 |
// make sure we can reinterpret the generic data as restraint data: |
| 426 |
RestraintData* restData= dynamic_cast<RestraintData*>(data); |
| 427 |
if (restData != NULL) { |
| 428 |
// make sure we can reinterpet the restraint data as a pointer to |
| 429 |
// an ObjectRestraint: |
| 430 |
oRest = dynamic_cast<ObjectRestraint*>(restData->getData()); |
| 431 |
if (oRest == NULL) { |
| 432 |
sprintf( painCave.errMsg, |
| 433 |
"Can not cast RestraintData to ObjectRestraint\n"); |
| 434 |
painCave.severity = OPENMD_ERROR; |
| 435 |
painCave.isFatal = 1; |
| 436 |
simError(); |
| 437 |
} |
| 438 |
} else { |
| 439 |
sprintf( painCave.errMsg, |
| 440 |
"Can not cast GenericData to RestraintData\n"); |
| 441 |
painCave.severity = OPENMD_ERROR; |
| 442 |
painCave.isFatal = 1; |
| 443 |
simError(); |
| 444 |
} |
| 445 |
} else { |
| 446 |
sprintf( painCave.errMsg, "Can not find Restraint for RestrainedObject\n"); |
| 447 |
painCave.severity = OPENMD_ERROR; |
| 448 |
painCave.isFatal = 1; |
| 449 |
simError(); |
| 450 |
} |
| 451 |
|
| 452 |
// phew. At this point, we should have the pointer to the |
| 453 |
// correct Object restraint in the variable oRest. |
| 454 |
|
| 455 |
oRest->setScaleFactor(scalingFactor); |
| 456 |
|
| 457 |
Vector3d pos = (*ro)->getPos(); |
| 458 |
|
| 459 |
if ( (*ro)->isDirectional() ) { |
| 460 |
|
| 461 |
// directional objects may have orientational restraints as well |
| 462 |
// as positional, so get the rotation matrix first: |
| 463 |
|
| 464 |
RotMat3x3d A = (*ro)->getA(); |
| 465 |
oRest->calcForce(pos, A); |
| 466 |
(*ro)->addFrc(oRest->getRestraintForce()); |
| 467 |
(*ro)->addTrq(oRest->getRestraintTorque()); |
| 468 |
} else { |
| 469 |
|
| 470 |
// plain vanilla positional restraints: |
| 471 |
|
| 472 |
oRest->calcForce(pos); |
| 473 |
(*ro)->addFrc(oRest->getRestraintForce()); |
| 474 |
} |
| 475 |
|
| 476 |
unscaledPotential_ += oRest->getUnscaledPotential(); |
| 477 |
|
| 478 |
restInfo = oRest->getRestraintInfo(); |
| 479 |
|
| 480 |
// only collect data on restraints that we're going to print: |
| 481 |
if (oRest->getPrintRestraint()) |
| 482 |
restInfo_.push_back(restInfo); |
| 483 |
} |
| 484 |
|
| 485 |
return unscaledPotential_ * scalingFactor; |
| 486 |
} |
| 487 |
} |
