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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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/* Uses the Helfand-moment method for calculating thermal |
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* conductivity using the relation kappa = (N,V)lim(t)->inf 1/(2*k_B*T^2*V*t) <[G_K(t)-G_K(0)]^2> |
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* where G_K is the Helfand moment for thermal conductivity definded as |
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* G_K(t) = sum_{a=1}{^N} x_a(E_a-<E_a>) and E_a is defined to be |
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* E_a = p_2^2/(2*m)+1/2 sum_{b.ne.a} u(r_ab) where p is momentum and u is pot energy for the |
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* particle pair a-b. This routine calculates E_a, <E_a> and does the correlation |
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* <[G_K(t)-G_K(0)]^2>. |
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* See Viscardy et al. JCP 126, 184513 (2007) |
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*/ |
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#include "applications/dynamicProps/EnergyCorrFunc.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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#include "brains/ForceManager.hpp" |
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#include "brains/Thermo.hpp" |
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namespace oopse { |
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// We need all of the positions, velocities, etc. so that we can |
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// recalculate pressures and actions on the fly: |
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EnergyCorrFunc::EnergyCorrFunc(SimInfo* info, const std::string& filename, |
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const std::string& sele1, |
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const std::string& sele2) |
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: FrameTimeCorrFunc(info, filename, sele1, sele2, |
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DataStorage::dslPosition | |
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DataStorage::dslVelocity | |
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DataStorage::dslForce | |
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DataStorage::dslTorque | |
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DataStorage::dslParticlePot ){ |
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setCorrFuncType("EnergyCorrFunc"); |
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setOutputName(getPrefix(dumpFilename_) + ".moment"); |
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histogram_.resize(nTimeBins_); |
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count_.resize(nTimeBins_); |
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} |
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void EnergyCorrFunc::correlateFrames(int frame1, int frame2) { |
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Snapshot* snapshot1 = bsMan_->getSnapshot(frame1); |
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Snapshot* snapshot2 = bsMan_->getSnapshot(frame2); |
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assert(snapshot1 && snapshot2); |
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RealType time1 = snapshot1->getTime(); |
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RealType time2 = snapshot2->getTime(); |
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int timeBin = int ((time2 - time1) /deltaTime_ + 0.5); |
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// //std::cerr << "Correlating Frame" << std::endl; |
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// Vector3d G_t_frame1 = G_t_[frame1]; |
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// Vector3d G_t_frame2 = G_t_[frame2]; |
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// |
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// |
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// RealType diff_x = G_t_frame1.x()-G_t_frame2.x(); |
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// RealType diff_x_sq = diff_x * diff_x; |
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// |
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// RealType diff_y = G_t_frame1.y()-G_t_frame2.y(); |
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// RealType diff_y_sq = diff_y * diff_y; |
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// |
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// RealType diff_z = G_t_frame1.z()-G_t_frame2.z(); |
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// RealType diff_z_sq = diff_z*diff_z; |
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// |
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// |
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// |
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// |
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// histogram_[timeBin][0] += diff_x_sq; |
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// histogram_[timeBin][1] += diff_y_sq; |
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// histogram_[timeBin][2] += diff_z_sq; |
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// |
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// count_[timeBin]++; |
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} |
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void EnergyCorrFunc::postCorrelate() { |
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for (int i =0 ; i < nTimeBins_; ++i) { |
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if (count_[i] > 0) { |
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histogram_[i] /= count_[i]; |
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} |
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} |
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} |
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void EnergyCorrFunc::preCorrelate() { |
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// Fill the histogram with empty 3x3 matrices: |
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std::fill(histogram_.begin(), histogram_.end(), 0.0); |
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// count array set to zero |
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std::fill(count_.begin(), count_.end(), 0); |
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SimInfo::MoleculeIterator mi; |
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Molecule::IntegrableObjectIterator mj; |
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Molecule* mol; |
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Molecule::AtomIterator ai; |
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Atom* atom; |
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std::vector<RealType > particleEnergies; |
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// We'll need the force manager to compute forces for the average pressure |
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ForceManager* forceMan = new ForceManager(info_); |
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forceMan->init(); |
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// We'll need thermo to compute the pressures from the virial |
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Thermo* thermo = new Thermo(info_); |
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// prepare the averages |
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RealType pSum = 0.0; |
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RealType vSum = 0.0; |
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int nsamp = 0; |
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// dump files can be enormous, so read them in block-by-block: |
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int nblocks = bsMan_->getNBlocks(); |
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bool firsttime = true; |
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int junkframe = 0; |
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for (int i = 0; i < nblocks; ++i) { |
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//std::cerr << "block = " << i << "\n"; |
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bsMan_->loadBlock(i); |
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assert(bsMan_->isBlockActive(i)); |
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SnapshotBlock block1 = bsMan_->getSnapshotBlock(i); |
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for (int j = block1.first; j < block1.second; ++j) { |
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// go snapshot-by-snapshot through this block: |
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Snapshot* snap = bsMan_->getSnapshot(j); |
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// update the positions and velocities of the atoms belonging |
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// to rigid bodies: |
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updateFrame(j); |
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// do the forces: |
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forceMan->calcForces(true, true); |
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int index = 0; |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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RealType mass = atom->getMass(); |
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Vector3d vel = atom->getVel(); |
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RealType kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]); |
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RealType eatom = (kinetic + atom->getParticlePot())/2.0; |
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particleEnergies.push_back(eatom); |
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if(firsttime) |
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{ |
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AvgE_a_.push_back(eatom); |
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}else{ |
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/* We assume the the number of atoms does not change.*/ |
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AvgE_a_[index] += eatom; |
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} |
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index++; |
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} |
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} |
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firsttime = false; |
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E_a_.push_back(particleEnergies); |
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} |
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bsMan_->unloadBlock(i); |
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} |
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int nframes = bsMan_->getNFrames(); |
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for (int i = 0; i < AvgE_a_.size(); i++){ |
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AvgE_a_[i] /= nframes; |
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} |
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int frame = 0; |
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// Do it again to compute G^(kappa)(t) for x,y,z |
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for (int i = 0; i < nblocks; ++i) { |
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//std::cerr << "block = " << i << "\n"; |
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bsMan_->loadBlock(i); |
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assert(bsMan_->isBlockActive(i)); |
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SnapshotBlock block1 = bsMan_->getSnapshotBlock(i); |
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for (int j = block1.first; j < block1.second; ++j) { |
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// go snapshot-by-snapshot through this block: |
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Snapshot* snap = bsMan_->getSnapshot(j); |
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updateFrame(j); |
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particleEnergies = E_a_[frame]; |
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int thisAtom = 0; |
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Vector3d G_t; |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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Vector3d pos = atom->getPos(); |
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G_t[0] += (particleEnergies[thisAtom]-AvgE_a_[thisAtom]); |
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G_t[1] += (particleEnergies[thisAtom]-AvgE_a_[thisAtom]); |
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G_t[2] += (particleEnergies[thisAtom]-AvgE_a_[thisAtom]); |
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thisAtom++; |
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} |
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} |
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G_t_.push_back(G_t); |
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frame++; |
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std::cerr <<"Frame: " << frame <<"\t" << G_t << std::endl; |
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} |
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bsMan_->unloadBlock(i); |
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} |
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} |
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void EnergyCorrFunc::writeCorrelate() { |
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std::ofstream ofs(getOutputFileName().c_str()); |
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if (ofs.is_open()) { |
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ofs << "#" << getCorrFuncType() << "\n"; |
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ofs << "#time\tK_x\tK_y\tK_z\n"; |
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for (int i = 0; i < nTimeBins_; ++i) { |
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ofs << time_[i] << "\t" << |
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histogram_[i].x() << "\t" << |
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histogram_[i].y() << "\t" << |
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histogram_[i].z() << "\t" << "\n"; |
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} |
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} else { |
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sprintf(painCave.errMsg, |
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"EnergyCorrFunc::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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ofs.close(); |
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} |
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} |
