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#include <iostream> |
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#include <stdlib.h> |
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#include <math.h> |
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#ifdef IS_MPI |
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#include "brains/mpiSimulation.hpp" |
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#include <unistd.h> |
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#endif //is_mpi |
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|
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#ifdef PROFILE |
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#include "profiling/mdProfile.hpp" |
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#endif // profile |
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|
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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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|
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#include "brains/Snapshot.hpp" |
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#include "integrators/Integrator.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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Integrator::Integrator(SimInfo* info) |
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: info_(info), forceMan_(NULL) , needPotential(false), needStress(false), velocitizer_(NULL), |
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needVelocityScaling(false), dumpWriter(NULL), statWriter(NULL), thermo(info), |
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currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) { |
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|
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Globals* simParams = info->getSimParams(); |
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|
|
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template<typename T> Integrator<T>::Integrator(SimInfo* theInfo, |
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ForceFields* the_ff){ |
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info = theInfo; |
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myFF = the_ff; |
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isFirst = 1; |
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|
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molecules = info->molecules; |
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nMols = info->n_mol; |
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|
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// give a little love back to the SimInfo object |
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|
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if (info->the_integrator != NULL){ |
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delete info->the_integrator; |
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} |
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|
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nAtoms = info->n_atoms; |
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integrableObjects = info->integrableObjects; |
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|
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|
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// check for constraints |
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|
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constrainedA = NULL; |
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constrainedB = NULL; |
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constrainedDsqr = NULL; |
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moving = NULL; |
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moved = NULL; |
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oldPos = NULL; |
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|
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nConstrained = 0; |
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|
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checkConstraints(); |
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|
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} |
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|
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template<typename T> Integrator<T>::~Integrator(){ |
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|
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if (nConstrained){ |
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delete[] constrainedA; |
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delete[] constrainedB; |
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delete[] constrainedDsqr; |
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delete[] moving; |
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delete[] moved; |
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delete[] oldPos; |
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} |
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|
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} |
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|
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|
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template<typename T> void Integrator<T>::checkConstraints(void){ |
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isConstrained = 0; |
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|
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Constraint* temp_con; |
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Constraint* dummy_plug; |
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temp_con = new Constraint[info->n_SRI]; |
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nConstrained = 0; |
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int constrained = 0; |
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|
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SRI** theArray; |
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for (int i = 0; i < nMols; i++){ |
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|
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theArray = (SRI * *) molecules[i].getMyBonds(); |
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for (int j = 0; j < molecules[i].getNBonds(); j++){ |
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constrained = theArray[j]->is_constrained(); |
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|
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if (constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a(dummy_plug->get_a()); |
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temp_con[nConstrained].set_b(dummy_plug->get_b()); |
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temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
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|
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nConstrained++; |
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constrained = 0; |
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} |
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if (simParams->haveDt()) { |
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dt = simParams->getDt(); |
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} else { |
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sprintf(painCave.errMsg, |
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"Integrator Error: dt is not set\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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theArray = (SRI * *) molecules[i].getMyBends(); |
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for (int j = 0; j < molecules[i].getNBends(); j++){ |
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constrained = theArray[j]->is_constrained(); |
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|
66 |
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if (constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a(dummy_plug->get_a()); |
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temp_con[nConstrained].set_b(dummy_plug->get_b()); |
100 |
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temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
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|
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nConstrained++; |
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constrained = 0; |
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} |
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|
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if (simParams->haveRunTime()) { |
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runTime = simParams->getRunTime(); |
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} else { |
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sprintf(painCave.errMsg, |
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"Integrator Error: runTime is not set\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
70 |
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|
71 |
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theArray = (SRI * *) molecules[i].getMyTorsions(); |
72 |
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for (int j = 0; j < molecules[i].getNTorsions(); j++){ |
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constrained = theArray[j]->is_constrained(); |
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|
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if (constrained){ |
76 |
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dummy_plug = theArray[j]->get_constraint(); |
113 |
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temp_con[nConstrained].set_a(dummy_plug->get_a()); |
114 |
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temp_con[nConstrained].set_b(dummy_plug->get_b()); |
115 |
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temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
116 |
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|
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nConstrained++; |
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constrained = 0; |
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} |
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// set the status, sample, and thermal kick times |
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if (simParams->haveSampleTime()){ |
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sampleTime = simParams->getSampleTime(); |
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statusTime = sampleTime; |
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} else{ |
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sampleTime = simParams->getRunTime(); |
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statusTime = sampleTime; |
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} |
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} |
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|
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|
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if (nConstrained > 0){ |
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isConstrained = 1; |
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|
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if (constrainedA != NULL) |
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delete[] constrainedA; |
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if (constrainedB != NULL) |
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delete[] constrainedB; |
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if (constrainedDsqr != NULL) |
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delete[] constrainedDsqr; |
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|
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constrainedA = new int[nConstrained]; |
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constrainedB = new int[nConstrained]; |
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constrainedDsqr = new double[nConstrained]; |
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|
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for (int i = 0; i < nConstrained; i++){ |
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constrainedA[i] = temp_con[i].get_a(); |
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constrainedB[i] = temp_con[i].get_b(); |
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constrainedDsqr[i] = temp_con[i].get_dsqr(); |
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if (simParams->haveStatusTime()){ |
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statusTime = simParams->getStatusTime(); |
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} |
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|
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|
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// save oldAtoms to check for lode balancing later on. |
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|
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oldAtoms = nAtoms; |
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|
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moving = new int[nAtoms]; |
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moved = new int[nAtoms]; |
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|
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oldPos = new double[nAtoms * 3]; |
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} |
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|
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delete[] temp_con; |
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} |
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|
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|
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template<typename T> void Integrator<T>::integrate(void){ |
160 |
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|
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double runTime = info->run_time; |
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double sampleTime = info->sampleTime; |
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double statusTime = info->statusTime; |
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double thermalTime = info->thermalTime; |
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double resetTime = info->resetTime; |
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|
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double difference; |
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double currSample; |
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double currThermal; |
170 |
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double currStatus; |
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< |
double currReset; |
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|
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int calcPot, calcStress; |
174 |
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|
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tStats = new Thermo(info); |
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statOut = new StatWriter(info); |
177 |
< |
dumpOut = new DumpWriter(info); |
178 |
< |
|
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atoms = info->atoms; |
180 |
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|
181 |
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dt = info->dt; |
182 |
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dt2 = 0.5 * dt; |
183 |
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|
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readyCheck(); |
185 |
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|
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// remove center of mass drift velocity (in case we passed in a configuration |
187 |
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// that was drifting |
188 |
< |
tStats->removeCOMdrift(); |
189 |
< |
|
190 |
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// initialize the retraints if necessary |
191 |
< |
if (info->useSolidThermInt && !info->useLiquidThermInt) { |
192 |
< |
myFF->initRestraints(); |
193 |
< |
} |
194 |
< |
|
195 |
< |
// initialize the forces before the first step |
196 |
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|
197 |
< |
calcForce(1, 1); |
198 |
< |
|
199 |
< |
//execute constraint algorithm to make sure at the very beginning the system is constrained |
200 |
< |
if(nConstrained){ |
201 |
< |
preMove(); |
202 |
< |
constrainA(); |
203 |
< |
calcForce(1, 1); |
204 |
< |
constrainB(); |
205 |
< |
} |
206 |
< |
|
207 |
< |
if (info->setTemp){ |
208 |
< |
thermalize(); |
209 |
< |
} |
210 |
< |
|
211 |
< |
calcPot = 0; |
212 |
< |
calcStress = 0; |
213 |
< |
currSample = sampleTime + info->getTime(); |
214 |
< |
currThermal = thermalTime+ info->getTime(); |
215 |
< |
currStatus = statusTime + info->getTime(); |
216 |
< |
currReset = resetTime + info->getTime(); |
217 |
< |
|
218 |
< |
dumpOut->writeDump(info->getTime()); |
219 |
< |
statOut->writeStat(info->getTime()); |
220 |
< |
|
221 |
< |
|
222 |
< |
#ifdef IS_MPI |
223 |
< |
strcpy(checkPointMsg, "The integrator is ready to go."); |
224 |
< |
MPIcheckPoint(); |
225 |
< |
#endif // is_mpi |
226 |
< |
|
227 |
< |
while (info->getTime() < runTime && !stopIntegrator()){ |
228 |
< |
difference = info->getTime() + dt - currStatus; |
229 |
< |
if (difference > 0 || fabs(difference) < 1e-4 ){ |
230 |
< |
calcPot = 1; |
231 |
< |
calcStress = 1; |
83 |
> |
if (simParams->haveThermalTime()){ |
84 |
> |
thermalTime = simParams->getThermalTime(); |
85 |
> |
} else { |
86 |
> |
thermalTime = simParams->getRunTime(); |
87 |
|
} |
88 |
|
|
89 |
< |
#ifdef PROFILE |
90 |
< |
startProfile( pro1 ); |
236 |
< |
#endif |
237 |
< |
|
238 |
< |
integrateStep(calcPot, calcStress); |
239 |
< |
|
240 |
< |
#ifdef PROFILE |
241 |
< |
endProfile( pro1 ); |
242 |
< |
|
243 |
< |
startProfile( pro2 ); |
244 |
< |
#endif // profile |
245 |
< |
|
246 |
< |
info->incrTime(dt); |
247 |
< |
|
248 |
< |
if (info->setTemp){ |
249 |
< |
if (info->getTime() >= currThermal){ |
250 |
< |
thermalize(); |
251 |
< |
currThermal += thermalTime; |
252 |
< |
} |
89 |
> |
if (!simParams->getUseInitTime()) { |
90 |
> |
currentSnapshot_->setTime(0.0); |
91 |
|
} |
254 |
– |
|
255 |
– |
if (info->getTime() >= currSample){ |
256 |
– |
dumpOut->writeDump(info->getTime()); |
257 |
– |
currSample += sampleTime; |
258 |
– |
} |
259 |
– |
|
260 |
– |
if (info->getTime() >= currStatus){ |
261 |
– |
statOut->writeStat(info->getTime()); |
262 |
– |
calcPot = 0; |
263 |
– |
calcStress = 0; |
264 |
– |
currStatus += statusTime; |
265 |
– |
} |
266 |
– |
|
267 |
– |
if (info->resetIntegrator){ |
268 |
– |
if (info->getTime() >= currReset){ |
269 |
– |
this->resetIntegrator(); |
270 |
– |
currReset += resetTime; |
271 |
– |
} |
272 |
– |
} |
92 |
|
|
93 |
< |
#ifdef PROFILE |
94 |
< |
endProfile( pro2 ); |
95 |
< |
#endif //profile |
277 |
< |
|
278 |
< |
#ifdef IS_MPI |
279 |
< |
strcpy(checkPointMsg, "successfully took a time step."); |
280 |
< |
MPIcheckPoint(); |
281 |
< |
#endif // is_mpi |
282 |
< |
} |
283 |
< |
|
284 |
< |
dumpOut->writeFinal(info->getTime()); |
285 |
< |
|
286 |
< |
// dump out a file containing the omega values for the final configuration |
287 |
< |
if (info->useSolidThermInt && !info->useLiquidThermInt) |
288 |
< |
myFF->dumpzAngle(); |
289 |
< |
|
290 |
< |
|
291 |
< |
delete dumpOut; |
292 |
< |
delete statOut; |
293 |
< |
} |
294 |
< |
|
295 |
< |
template<typename T> void Integrator<T>::integrateStep(int calcPot, |
296 |
< |
int calcStress){ |
297 |
< |
// Position full step, and velocity half step |
298 |
< |
|
299 |
< |
#ifdef PROFILE |
300 |
< |
startProfile(pro3); |
301 |
< |
#endif //profile |
302 |
< |
|
303 |
< |
//save old state (position, velocity etc) |
304 |
< |
preMove(); |
305 |
< |
#ifdef PROFILE |
306 |
< |
endProfile(pro3); |
307 |
< |
|
308 |
< |
startProfile(pro4); |
309 |
< |
#endif // profile |
310 |
< |
|
311 |
< |
moveA(); |
312 |
< |
|
313 |
< |
#ifdef PROFILE |
314 |
< |
endProfile(pro4); |
315 |
< |
|
316 |
< |
startProfile(pro5); |
317 |
< |
#endif//profile |
318 |
< |
|
319 |
< |
|
320 |
< |
#ifdef IS_MPI |
321 |
< |
strcpy(checkPointMsg, "Succesful moveA\n"); |
322 |
< |
MPIcheckPoint(); |
323 |
< |
#endif // is_mpi |
324 |
< |
|
325 |
< |
// calc forces |
326 |
< |
calcForce(calcPot, calcStress); |
327 |
< |
|
328 |
< |
#ifdef IS_MPI |
329 |
< |
strcpy(checkPointMsg, "Succesful doForces\n"); |
330 |
< |
MPIcheckPoint(); |
331 |
< |
#endif // is_mpi |
332 |
< |
|
333 |
< |
#ifdef PROFILE |
334 |
< |
endProfile( pro5 ); |
335 |
< |
|
336 |
< |
startProfile( pro6 ); |
337 |
< |
#endif //profile |
338 |
< |
|
339 |
< |
// finish the velocity half step |
340 |
< |
|
341 |
< |
moveB(); |
342 |
< |
|
343 |
< |
#ifdef PROFILE |
344 |
< |
endProfile(pro6); |
345 |
< |
#endif // profile |
346 |
< |
|
347 |
< |
#ifdef IS_MPI |
348 |
< |
strcpy(checkPointMsg, "Succesful moveB\n"); |
349 |
< |
MPIcheckPoint(); |
350 |
< |
#endif // is_mpi |
351 |
< |
} |
352 |
< |
|
353 |
< |
|
354 |
< |
template<typename T> void Integrator<T>::moveA(void){ |
355 |
< |
size_t i, j; |
356 |
< |
DirectionalAtom* dAtom; |
357 |
< |
double Tb[3], ji[3]; |
358 |
< |
double vel[3], pos[3], frc[3]; |
359 |
< |
double mass; |
360 |
< |
double omega; |
361 |
< |
|
362 |
< |
for (i = 0; i < integrableObjects.size() ; i++){ |
363 |
< |
integrableObjects[i]->getVel(vel); |
364 |
< |
integrableObjects[i]->getPos(pos); |
365 |
< |
integrableObjects[i]->getFrc(frc); |
366 |
< |
// std::cerr << "f = " << frc[0] << "\t" << frc[1] << "\t" << frc[2] << "\n"; |
93 |
> |
//create a default a ForceManager |
94 |
> |
//if the subclass want to using different ForceManager, use setForceManager |
95 |
> |
forceMan_ = new ForceManager(info); |
96 |
|
|
97 |
< |
mass = integrableObjects[i]->getMass(); |
97 |
> |
// check for the temperature set flag (velocity scaling) |
98 |
> |
if (simParams->haveTempSet()) { |
99 |
> |
needVelocityScaling = simParams->getTempSet(); |
100 |
|
|
101 |
< |
for (j = 0; j < 3; j++){ |
102 |
< |
// velocity half step |
103 |
< |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
104 |
< |
// position whole step |
105 |
< |
pos[j] += dt * vel[j]; |
106 |
< |
} |
376 |
< |
|
377 |
< |
integrableObjects[i]->setVel(vel); |
378 |
< |
integrableObjects[i]->setPos(pos); |
379 |
< |
|
380 |
< |
|
381 |
< |
if (integrableObjects[i]->isDirectional()){ |
382 |
< |
|
383 |
< |
// get and convert the torque to body frame |
384 |
< |
|
385 |
< |
integrableObjects[i]->getTrq(Tb); |
386 |
< |
|
387 |
< |
// std::cerr << "t = " << Tb[0] << "\t" << Tb[1] << "\t" << Tb[2] << "\n"; |
388 |
< |
integrableObjects[i]->lab2Body(Tb); |
389 |
< |
|
390 |
< |
// get the angular momentum, and propagate a half step |
391 |
< |
|
392 |
< |
integrableObjects[i]->getJ(ji); |
393 |
< |
|
394 |
< |
for (j = 0; j < 3; j++) |
395 |
< |
ji[j] += (dt2 * Tb[j]) * eConvert; |
396 |
< |
|
397 |
< |
this->rotationPropagation( integrableObjects[i], ji ); |
398 |
< |
|
399 |
< |
integrableObjects[i]->setJ(ji); |
400 |
< |
} |
401 |
< |
} |
402 |
< |
|
403 |
< |
if(nConstrained) |
404 |
< |
constrainA(); |
405 |
< |
} |
406 |
< |
|
407 |
< |
|
408 |
< |
template<typename T> void Integrator<T>::moveB(void){ |
409 |
< |
int i, j; |
410 |
< |
double Tb[3], ji[3]; |
411 |
< |
double vel[3], frc[3]; |
412 |
< |
double mass; |
413 |
< |
|
414 |
< |
for (i = 0; i < integrableObjects.size(); i++){ |
415 |
< |
integrableObjects[i]->getVel(vel); |
416 |
< |
integrableObjects[i]->getFrc(frc); |
417 |
< |
|
418 |
< |
mass = integrableObjects[i]->getMass(); |
419 |
< |
|
420 |
< |
// velocity half step |
421 |
< |
for (j = 0; j < 3; j++) |
422 |
< |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
423 |
< |
|
424 |
< |
integrableObjects[i]->setVel(vel); |
425 |
< |
|
426 |
< |
if (integrableObjects[i]->isDirectional()){ |
427 |
< |
|
428 |
< |
// get and convert the torque to body frame |
429 |
< |
|
430 |
< |
integrableObjects[i]->getTrq(Tb); |
431 |
< |
integrableObjects[i]->lab2Body(Tb); |
432 |
< |
|
433 |
< |
// get the angular momentum, and propagate a half step |
434 |
< |
|
435 |
< |
integrableObjects[i]->getJ(ji); |
436 |
< |
|
437 |
< |
for (j = 0; j < 3; j++) |
438 |
< |
ji[j] += (dt2 * Tb[j]) * eConvert; |
439 |
< |
|
440 |
< |
|
441 |
< |
integrableObjects[i]->setJ(ji); |
442 |
< |
} |
443 |
< |
} |
444 |
< |
|
445 |
< |
if(nConstrained) |
446 |
< |
constrainB(); |
447 |
< |
} |
448 |
< |
|
449 |
< |
|
450 |
< |
template<typename T> void Integrator<T>::preMove(void){ |
451 |
< |
int i, j; |
452 |
< |
double pos[3]; |
453 |
< |
|
454 |
< |
if (nConstrained){ |
455 |
< |
for (i = 0; i < nAtoms; i++){ |
456 |
< |
atoms[i]->getPos(pos); |
457 |
< |
|
458 |
< |
for (j = 0; j < 3; j++){ |
459 |
< |
oldPos[3 * i + j] = pos[j]; |
460 |
< |
} |
461 |
< |
} |
462 |
< |
} |
463 |
< |
} |
464 |
< |
|
465 |
< |
template<typename T> void Integrator<T>::constrainA(){ |
466 |
< |
int i, j; |
467 |
< |
int done; |
468 |
< |
double posA[3], posB[3]; |
469 |
< |
double velA[3], velB[3]; |
470 |
< |
double pab[3]; |
471 |
< |
double rab[3]; |
472 |
< |
int a, b, ax, ay, az, bx, by, bz; |
473 |
< |
double rma, rmb; |
474 |
< |
double dx, dy, dz; |
475 |
< |
double rpab; |
476 |
< |
double rabsq, pabsq, rpabsq; |
477 |
< |
double diffsq; |
478 |
< |
double gab; |
479 |
< |
int iteration; |
480 |
< |
|
481 |
< |
for (i = 0; i < nAtoms; i++){ |
482 |
< |
moving[i] = 0; |
483 |
< |
moved[i] = 1; |
484 |
< |
} |
485 |
< |
|
486 |
< |
iteration = 0; |
487 |
< |
done = 0; |
488 |
< |
while (!done && (iteration < maxIteration)){ |
489 |
< |
done = 1; |
490 |
< |
for (i = 0; i < nConstrained; i++){ |
491 |
< |
a = constrainedA[i]; |
492 |
< |
b = constrainedB[i]; |
493 |
< |
|
494 |
< |
ax = (a * 3) + 0; |
495 |
< |
ay = (a * 3) + 1; |
496 |
< |
az = (a * 3) + 2; |
497 |
< |
|
498 |
< |
bx = (b * 3) + 0; |
499 |
< |
by = (b * 3) + 1; |
500 |
< |
bz = (b * 3) + 2; |
501 |
< |
|
502 |
< |
if (moved[a] || moved[b]){ |
503 |
< |
atoms[a]->getPos(posA); |
504 |
< |
atoms[b]->getPos(posB); |
505 |
< |
|
506 |
< |
for (j = 0; j < 3; j++) |
507 |
< |
pab[j] = posA[j] - posB[j]; |
508 |
< |
|
509 |
< |
//periodic boundary condition |
510 |
< |
|
511 |
< |
info->wrapVector(pab); |
512 |
< |
|
513 |
< |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
514 |
< |
|
515 |
< |
rabsq = constrainedDsqr[i]; |
516 |
< |
diffsq = rabsq - pabsq; |
517 |
< |
|
518 |
< |
// the original rattle code from alan tidesley |
519 |
< |
if (fabs(diffsq) > (tol * rabsq * 2)){ |
520 |
< |
rab[0] = oldPos[ax] - oldPos[bx]; |
521 |
< |
rab[1] = oldPos[ay] - oldPos[by]; |
522 |
< |
rab[2] = oldPos[az] - oldPos[bz]; |
523 |
< |
|
524 |
< |
info->wrapVector(rab); |
525 |
< |
|
526 |
< |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
527 |
< |
|
528 |
< |
rpabsq = rpab * rpab; |
529 |
< |
|
530 |
< |
|
531 |
< |
if (rpabsq < (rabsq * -diffsq)){ |
532 |
< |
#ifdef IS_MPI |
533 |
< |
a = atoms[a]->getGlobalIndex(); |
534 |
< |
b = atoms[b]->getGlobalIndex(); |
535 |
< |
#endif //is_mpi |
536 |
< |
sprintf(painCave.errMsg, |
537 |
< |
"Constraint failure in constrainA at atom %d and %d.\n", a, |
538 |
< |
b); |
101 |
> |
if (simParams->haveTargetTemp()) { |
102 |
> |
targetScalingTemp = simParams->getTargetTemp(); |
103 |
> |
} |
104 |
> |
else { |
105 |
> |
sprintf(painCave.errMsg, |
106 |
> |
"Integrator Error: Target Temperature is not set\n"); |
107 |
|
painCave.isFatal = 1; |
108 |
|
simError(); |
541 |
– |
} |
109 |
|
|
543 |
– |
rma = 1.0 / atoms[a]->getMass(); |
544 |
– |
rmb = 1.0 / atoms[b]->getMass(); |
545 |
– |
|
546 |
– |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
547 |
– |
|
548 |
– |
dx = rab[0] * gab; |
549 |
– |
dy = rab[1] * gab; |
550 |
– |
dz = rab[2] * gab; |
551 |
– |
|
552 |
– |
posA[0] += rma * dx; |
553 |
– |
posA[1] += rma * dy; |
554 |
– |
posA[2] += rma * dz; |
555 |
– |
|
556 |
– |
atoms[a]->setPos(posA); |
557 |
– |
|
558 |
– |
posB[0] -= rmb * dx; |
559 |
– |
posB[1] -= rmb * dy; |
560 |
– |
posB[2] -= rmb * dz; |
561 |
– |
|
562 |
– |
atoms[b]->setPos(posB); |
563 |
– |
|
564 |
– |
dx = dx / dt; |
565 |
– |
dy = dy / dt; |
566 |
– |
dz = dz / dt; |
567 |
– |
|
568 |
– |
atoms[a]->getVel(velA); |
569 |
– |
|
570 |
– |
velA[0] += rma * dx; |
571 |
– |
velA[1] += rma * dy; |
572 |
– |
velA[2] += rma * dz; |
573 |
– |
|
574 |
– |
atoms[a]->setVel(velA); |
575 |
– |
|
576 |
– |
atoms[b]->getVel(velB); |
577 |
– |
|
578 |
– |
velB[0] -= rmb * dx; |
579 |
– |
velB[1] -= rmb * dy; |
580 |
– |
velB[2] -= rmb * dz; |
581 |
– |
|
582 |
– |
atoms[b]->setVel(velB); |
583 |
– |
|
584 |
– |
moving[a] = 1; |
585 |
– |
moving[b] = 1; |
586 |
– |
done = 0; |
110 |
|
} |
588 |
– |
} |
111 |
|
} |
590 |
– |
|
591 |
– |
for (i = 0; i < nAtoms; i++){ |
592 |
– |
moved[i] = moving[i]; |
593 |
– |
moving[i] = 0; |
594 |
– |
} |
595 |
– |
|
596 |
– |
iteration++; |
597 |
– |
} |
598 |
– |
|
599 |
– |
if (!done){ |
600 |
– |
sprintf(painCave.errMsg, |
601 |
– |
"Constraint failure in constrainA, too many iterations: %d\n", |
602 |
– |
iteration); |
603 |
– |
painCave.isFatal = 1; |
604 |
– |
simError(); |
605 |
– |
} |
606 |
– |
|
607 |
– |
} |
608 |
– |
|
609 |
– |
template<typename T> void Integrator<T>::constrainB(void){ |
610 |
– |
int i, j; |
611 |
– |
int done; |
612 |
– |
double posA[3], posB[3]; |
613 |
– |
double velA[3], velB[3]; |
614 |
– |
double vxab, vyab, vzab; |
615 |
– |
double rab[3]; |
616 |
– |
int a, b, ax, ay, az, bx, by, bz; |
617 |
– |
double rma, rmb; |
618 |
– |
double dx, dy, dz; |
619 |
– |
double rvab; |
620 |
– |
double gab; |
621 |
– |
int iteration; |
622 |
– |
|
623 |
– |
for (i = 0; i < nAtoms; i++){ |
624 |
– |
moving[i] = 0; |
625 |
– |
moved[i] = 1; |
626 |
– |
} |
627 |
– |
|
628 |
– |
done = 0; |
629 |
– |
iteration = 0; |
630 |
– |
while (!done && (iteration < maxIteration)){ |
631 |
– |
done = 1; |
632 |
– |
|
633 |
– |
for (i = 0; i < nConstrained; i++){ |
634 |
– |
a = constrainedA[i]; |
635 |
– |
b = constrainedB[i]; |
636 |
– |
|
637 |
– |
ax = (a * 3) + 0; |
638 |
– |
ay = (a * 3) + 1; |
639 |
– |
az = (a * 3) + 2; |
640 |
– |
|
641 |
– |
bx = (b * 3) + 0; |
642 |
– |
by = (b * 3) + 1; |
643 |
– |
bz = (b * 3) + 2; |
644 |
– |
|
645 |
– |
if (moved[a] || moved[b]){ |
646 |
– |
atoms[a]->getVel(velA); |
647 |
– |
atoms[b]->getVel(velB); |
648 |
– |
|
649 |
– |
vxab = velA[0] - velB[0]; |
650 |
– |
vyab = velA[1] - velB[1]; |
651 |
– |
vzab = velA[2] - velB[2]; |
652 |
– |
|
653 |
– |
atoms[a]->getPos(posA); |
654 |
– |
atoms[b]->getPos(posB); |
655 |
– |
|
656 |
– |
for (j = 0; j < 3; j++) |
657 |
– |
rab[j] = posA[j] - posB[j]; |
658 |
– |
|
659 |
– |
info->wrapVector(rab); |
660 |
– |
|
661 |
– |
rma = 1.0 / atoms[a]->getMass(); |
662 |
– |
rmb = 1.0 / atoms[b]->getMass(); |
663 |
– |
|
664 |
– |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
665 |
– |
|
666 |
– |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
667 |
– |
|
668 |
– |
if (fabs(gab) > tol){ |
669 |
– |
dx = rab[0] * gab; |
670 |
– |
dy = rab[1] * gab; |
671 |
– |
dz = rab[2] * gab; |
672 |
– |
|
673 |
– |
velA[0] += rma * dx; |
674 |
– |
velA[1] += rma * dy; |
675 |
– |
velA[2] += rma * dz; |
676 |
– |
|
677 |
– |
atoms[a]->setVel(velA); |
678 |
– |
|
679 |
– |
velB[0] -= rmb * dx; |
680 |
– |
velB[1] -= rmb * dy; |
681 |
– |
velB[2] -= rmb * dz; |
682 |
– |
|
683 |
– |
atoms[b]->setVel(velB); |
684 |
– |
|
685 |
– |
moving[a] = 1; |
686 |
– |
moving[b] = 1; |
687 |
– |
done = 0; |
688 |
– |
} |
689 |
– |
} |
690 |
– |
} |
691 |
– |
|
692 |
– |
for (i = 0; i < nAtoms; i++){ |
693 |
– |
moved[i] = moving[i]; |
694 |
– |
moving[i] = 0; |
695 |
– |
} |
696 |
– |
|
697 |
– |
iteration++; |
698 |
– |
} |
699 |
– |
|
700 |
– |
if (!done){ |
701 |
– |
sprintf(painCave.errMsg, |
702 |
– |
"Constraint failure in constrainB, too many iterations: %d\n", |
703 |
– |
iteration); |
704 |
– |
painCave.isFatal = 1; |
705 |
– |
simError(); |
706 |
– |
} |
707 |
– |
} |
708 |
– |
|
709 |
– |
template<typename T> void Integrator<T>::rotationPropagation |
710 |
– |
( StuntDouble* sd, double ji[3] ){ |
711 |
– |
|
712 |
– |
double angle; |
713 |
– |
double A[3][3], I[3][3]; |
714 |
– |
int i, j, k; |
715 |
– |
|
716 |
– |
// use the angular velocities to propagate the rotation matrix a |
717 |
– |
// full time step |
718 |
– |
|
719 |
– |
sd->getA(A); |
720 |
– |
sd->getI(I); |
721 |
– |
|
722 |
– |
if (sd->isLinear()) { |
723 |
– |
|
724 |
– |
i = sd->linearAxis(); |
725 |
– |
j = (i+1)%3; |
726 |
– |
k = (i+2)%3; |
727 |
– |
|
728 |
– |
angle = dt2 * ji[j] / I[j][j]; |
729 |
– |
this->rotate( k, i, angle, ji, A ); |
730 |
– |
|
731 |
– |
angle = dt * ji[k] / I[k][k]; |
732 |
– |
this->rotate( i, j, angle, ji, A); |
733 |
– |
|
734 |
– |
angle = dt2 * ji[j] / I[j][j]; |
735 |
– |
this->rotate( k, i, angle, ji, A ); |
736 |
– |
|
737 |
– |
} else { |
738 |
– |
// rotate about the x-axis |
739 |
– |
angle = dt2 * ji[0] / I[0][0]; |
740 |
– |
this->rotate( 1, 2, angle, ji, A ); |
112 |
|
|
113 |
< |
// rotate about the y-axis |
114 |
< |
angle = dt2 * ji[1] / I[1][1]; |
115 |
< |
this->rotate( 2, 0, angle, ji, A ); |
113 |
> |
//create a default a velocitizer |
114 |
> |
//if the subclass want to using different velocitizer, use setVelocitizer |
115 |
> |
velocitizer_ = new Velocitizer(info); |
116 |
|
|
746 |
– |
// rotate about the z-axis |
747 |
– |
angle = dt * ji[2] / I[2][2]; |
748 |
– |
sd->addZangle(angle); |
749 |
– |
this->rotate( 0, 1, angle, ji, A); |
750 |
– |
|
751 |
– |
// rotate about the y-axis |
752 |
– |
angle = dt2 * ji[1] / I[1][1]; |
753 |
– |
this->rotate( 2, 0, angle, ji, A ); |
754 |
– |
|
755 |
– |
// rotate about the x-axis |
756 |
– |
angle = dt2 * ji[0] / I[0][0]; |
757 |
– |
this->rotate( 1, 2, angle, ji, A ); |
758 |
– |
|
759 |
– |
} |
760 |
– |
sd->setA( A ); |
117 |
|
} |
118 |
|
|
119 |
< |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
120 |
< |
double angle, double ji[3], |
121 |
< |
double A[3][3]){ |
122 |
< |
int i, j, k; |
123 |
< |
double sinAngle; |
124 |
< |
double cosAngle; |
769 |
< |
double angleSqr; |
770 |
< |
double angleSqrOver4; |
771 |
< |
double top, bottom; |
772 |
< |
double rot[3][3]; |
773 |
< |
double tempA[3][3]; |
774 |
< |
double tempJ[3]; |
775 |
< |
|
776 |
< |
// initialize the tempA |
777 |
< |
|
778 |
< |
for (i = 0; i < 3; i++){ |
779 |
< |
for (j = 0; j < 3; j++){ |
780 |
< |
tempA[j][i] = A[i][j]; |
781 |
< |
} |
782 |
< |
} |
783 |
< |
|
784 |
< |
// initialize the tempJ |
785 |
< |
|
786 |
< |
for (i = 0; i < 3; i++) |
787 |
< |
tempJ[i] = ji[i]; |
788 |
< |
|
789 |
< |
// initalize rot as a unit matrix |
790 |
< |
|
791 |
< |
rot[0][0] = 1.0; |
792 |
< |
rot[0][1] = 0.0; |
793 |
< |
rot[0][2] = 0.0; |
794 |
< |
|
795 |
< |
rot[1][0] = 0.0; |
796 |
< |
rot[1][1] = 1.0; |
797 |
< |
rot[1][2] = 0.0; |
798 |
< |
|
799 |
< |
rot[2][0] = 0.0; |
800 |
< |
rot[2][1] = 0.0; |
801 |
< |
rot[2][2] = 1.0; |
802 |
< |
|
803 |
< |
// use a small angle aproximation for sin and cosine |
804 |
< |
|
805 |
< |
angleSqr = angle * angle; |
806 |
< |
angleSqrOver4 = angleSqr / 4.0; |
807 |
< |
top = 1.0 - angleSqrOver4; |
808 |
< |
bottom = 1.0 + angleSqrOver4; |
809 |
< |
|
810 |
< |
cosAngle = top / bottom; |
811 |
< |
sinAngle = angle / bottom; |
812 |
< |
|
813 |
< |
rot[axes1][axes1] = cosAngle; |
814 |
< |
rot[axes2][axes2] = cosAngle; |
815 |
< |
|
816 |
< |
rot[axes1][axes2] = sinAngle; |
817 |
< |
rot[axes2][axes1] = -sinAngle; |
818 |
< |
|
819 |
< |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
820 |
< |
|
821 |
< |
for (i = 0; i < 3; i++){ |
822 |
< |
ji[i] = 0.0; |
823 |
< |
for (k = 0; k < 3; k++){ |
824 |
< |
ji[i] += rot[i][k] * tempJ[k]; |
825 |
< |
} |
826 |
< |
} |
827 |
< |
|
828 |
< |
// rotate the Rotation matrix acording to: |
829 |
< |
// A[][] = A[][] * transpose(rot[][]) |
830 |
< |
|
831 |
< |
|
832 |
< |
// NOte for as yet unknown reason, we are performing the |
833 |
< |
// calculation as: |
834 |
< |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
835 |
< |
|
836 |
< |
for (i = 0; i < 3; i++){ |
837 |
< |
for (j = 0; j < 3; j++){ |
838 |
< |
A[j][i] = 0.0; |
839 |
< |
for (k = 0; k < 3; k++){ |
840 |
< |
A[j][i] += tempA[i][k] * rot[j][k]; |
841 |
< |
} |
842 |
< |
} |
843 |
< |
} |
119 |
> |
Integrator::~Integrator(){ |
120 |
> |
delete forceMan_; |
121 |
> |
delete velocitizer_; |
122 |
> |
|
123 |
> |
delete dumpWriter; |
124 |
> |
delete statWriter; |
125 |
|
} |
126 |
|
|
846 |
– |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
847 |
– |
myFF->doForces(calcPot, calcStress); |
848 |
– |
} |
127 |
|
|
850 |
– |
template<typename T> void Integrator<T>::thermalize(){ |
851 |
– |
tStats->velocitize(); |
128 |
|
} |
129 |
|
|
854 |
– |
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
855 |
– |
return tStats->getTotalE(); |
856 |
– |
} |
857 |
– |
template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
858 |
– |
//By default, return a null string |
859 |
– |
//The reason we use string instead of char* is that if we use char*, we will |
860 |
– |
//return a pointer point to local variable which might cause problem |
861 |
– |
return string(); |
862 |
– |
} |