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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. 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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/** |
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* @file Snapshot.cpp |
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* @author tlin |
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* @date 11/11/2004 |
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* @version 1.0 |
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*/ |
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|
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#include "brains/Snapshot.hpp" |
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#include "utils/NumericConstant.hpp" |
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#include "utils/simError.h" |
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#include "utils/Utility.hpp" |
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#include <cstdio> |
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|
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namespace OpenMD { |
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|
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Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups) : |
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atomData(nAtoms), rigidbodyData(nRigidbodies), |
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cgData(nCutoffGroups, DataStorage::dslPosition), |
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orthoTolerance_(1e-6) { |
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|
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frameData.id = -1; |
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frameData.currentTime = 0; |
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frameData.hmat = Mat3x3d(0.0); |
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frameData.invHmat = Mat3x3d(0.0); |
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frameData.orthoRhombic = false; |
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frameData.bondPotential = 0.0; |
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frameData.bendPotential = 0.0; |
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frameData.torsionPotential = 0.0; |
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frameData.inversionPotential = 0.0; |
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frameData.lrPotentials = potVec(0.0); |
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frameData.excludedPotentials = potVec(0.0); |
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frameData.restraintPotential = 0.0; |
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frameData.rawPotential = 0.0; |
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frameData.xyArea = 0.0; |
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frameData.volume = 0.0; |
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frameData.thermostat = make_pair(0.0, 0.0); |
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frameData.electronicThermostat = make_pair(0.0, 0.0); |
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frameData.barostat = Mat3x3d(0.0); |
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frameData.stressTensor = Mat3x3d(0.0); |
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frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0); |
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|
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clearDerivedProperties(); |
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} |
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|
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Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, |
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int storageLayout) : |
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atomData(nAtoms, storageLayout), |
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rigidbodyData(nRigidbodies, storageLayout), |
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cgData(nCutoffGroups, DataStorage::dslPosition), |
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orthoTolerance_(1e-6) { |
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|
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frameData.id = -1; |
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frameData.currentTime = 0; |
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frameData.hmat = Mat3x3d(0.0); |
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frameData.invHmat = Mat3x3d(0.0); |
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frameData.bBox = Mat3x3d(0.0); |
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frameData.invBbox = Mat3x3d(0.0); |
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frameData.orthoRhombic = false; |
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frameData.bondPotential = 0.0; |
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frameData.bendPotential = 0.0; |
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frameData.torsionPotential = 0.0; |
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frameData.inversionPotential = 0.0; |
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frameData.lrPotentials = potVec(0.0); |
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frameData.excludedPotentials = potVec(0.0); |
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frameData.restraintPotential = 0.0; |
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frameData.rawPotential = 0.0; |
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frameData.xyArea = 0.0; |
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frameData.volume = 0.0; |
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frameData.thermostat = make_pair(0.0, 0.0); |
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frameData.electronicThermostat = make_pair(0.0, 0.0); |
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frameData.barostat = Mat3x3d(0.0); |
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frameData.stressTensor = Mat3x3d(0.0); |
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frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0); |
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|
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clearDerivedProperties(); |
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} |
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|
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void Snapshot::clearDerivedProperties() { |
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frameData.totalEnergy = 0.0; |
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frameData.translationalKinetic = 0.0; |
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frameData.rotationalKinetic = 0.0; |
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frameData.kineticEnergy = 0.0; |
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frameData.potentialEnergy = 0.0; |
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frameData.shortRangePotential = 0.0; |
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frameData.longRangePotential = 0.0; |
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frameData.pressure = 0.0; |
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frameData.temperature = 0.0; |
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frameData.pressureTensor = Mat3x3d(0.0); |
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frameData.systemDipole = Vector3d(0.0); |
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frameData.convectiveHeatFlux = Vector3d(0.0, 0.0, 0.0); |
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frameData.electronicTemperature = 0.0; |
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frameData.COM = V3Zero; |
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frameData.COMvel = V3Zero; |
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frameData.COMw = V3Zero; |
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|
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hasTotalEnergy = false; |
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hasTranslationalKineticEnergy = false; |
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hasRotationalKineticEnergy = false; |
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hasKineticEnergy = false; |
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hasShortRangePotential = false; |
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hasLongRangePotential = false; |
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hasPotentialEnergy = false; |
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hasXYarea = false; |
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hasVolume = false; |
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hasPressure = false; |
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hasTemperature = false; |
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hasElectronicTemperature = false; |
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hasCOM = false; |
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hasCOMvel = false; |
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hasCOMw = false; |
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hasPressureTensor = false; |
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hasSystemDipole = false; |
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hasConvectiveHeatFlux = false; |
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hasInertiaTensor = false; |
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hasGyrationalVolume = false; |
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hasHullVolume = false; |
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hasConservedQuantity = false; |
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hasBoundingBox = false; |
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} |
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|
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/** Returns the id of this Snapshot */ |
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int Snapshot::getID() { |
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return frameData.id; |
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} |
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|
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/** Sets the id of this Snapshot */ |
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void Snapshot::setID(int id) { |
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frameData.id = id; |
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} |
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|
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int Snapshot::getSize() { |
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return atomData.getSize() + rigidbodyData.getSize(); |
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} |
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|
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/** Returns the number of atoms */ |
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int Snapshot::getNumberOfAtoms() { |
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return atomData.getSize(); |
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} |
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|
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/** Returns the number of rigid bodies */ |
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int Snapshot::getNumberOfRigidBodies() { |
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return rigidbodyData.getSize(); |
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} |
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|
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/** Returns the number of rigid bodies */ |
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int Snapshot::getNumberOfCutoffGroups() { |
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return cgData.getSize(); |
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} |
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|
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/** Returns the H-Matrix */ |
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Mat3x3d Snapshot::getHmat() { |
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return frameData.hmat; |
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} |
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|
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/** Sets the H-Matrix */ |
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void Snapshot::setHmat(const Mat3x3d& m) { |
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hasVolume = false; |
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frameData.hmat = m; |
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frameData.invHmat = frameData.hmat.inverse(); |
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|
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//determine whether the box is orthoTolerance or not |
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bool oldOrthoRhombic = frameData.orthoRhombic; |
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|
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RealType smallDiag = fabs(frameData.hmat(0, 0)); |
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if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1)); |
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if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2)); |
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RealType tol = smallDiag * orthoTolerance_; |
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|
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frameData.orthoRhombic = true; |
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|
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for (int i = 0; i < 3; i++ ) { |
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for (int j = 0 ; j < 3; j++) { |
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if (i != j) { |
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if (frameData.orthoRhombic) { |
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if ( fabs(frameData.hmat(i, j)) >= tol) |
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frameData.orthoRhombic = false; |
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} |
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} |
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} |
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} |
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|
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if( oldOrthoRhombic != frameData.orthoRhombic){ |
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|
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// It is finally time to suppress these warnings once and for |
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// all. They were annoying and not very informative. |
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|
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// if( frameData.orthoRhombic ) { |
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// sprintf( painCave.errMsg, |
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// "OpenMD is switching from the default Non-Orthorhombic\n" |
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// "\tto the faster Orthorhombic periodic boundary computations.\n" |
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// "\tThis is usually a good thing, but if you want the\n" |
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// "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
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// "\tvariable ( currently set to %G ) smaller.\n", |
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// orthoTolerance_); |
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// painCave.severity = OPENMD_INFO; |
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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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// "OpenMD is switching from the faster Orthorhombic to the more\n" |
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// "\tflexible Non-Orthorhombic periodic boundary computations.\n" |
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// "\tThis is usually because the box has deformed under\n" |
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// "\tNPTf integration. If you want to live on the edge with\n" |
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// "\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
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// "\tvariable ( currently set to %G ) larger.\n", |
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// orthoTolerance_); |
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// painCave.severity = OPENMD_WARNING; |
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// simError(); |
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// } |
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} |
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} |
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|
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/** Returns the inverse H-Matrix */ |
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Mat3x3d Snapshot::getInvHmat() { |
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return frameData.invHmat; |
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} |
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|
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/** Returns the Bounding Box */ |
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Mat3x3d Snapshot::getBoundingBox() { |
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return frameData.bBox; |
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} |
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|
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/** Sets the Bounding Box */ |
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void Snapshot::setBoundingBox(const Mat3x3d& m) { |
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frameData.bBox = m; |
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frameData.invBbox = frameData.bBox.inverse(); |
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hasBoundingBox = true; |
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} |
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|
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/** Returns the inverse Bounding Box */ |
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Mat3x3d Snapshot::getInvBoundingBox() { |
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return frameData.invBbox; |
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} |
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|
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RealType Snapshot::getXYarea() { |
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if (!hasXYarea) { |
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Vector3d x = frameData.hmat.getColumn(0); |
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Vector3d y = frameData.hmat.getColumn(1); |
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frameData.xyArea = cross(x,y).length(); |
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hasXYarea = true; |
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} |
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return frameData.xyArea; |
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} |
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|
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RealType Snapshot::getVolume() { |
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if (!hasVolume) { |
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frameData.volume = frameData.hmat.determinant(); |
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hasVolume = true; |
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} |
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return frameData.volume; |
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} |
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|
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void Snapshot::setVolume(RealType vol) { |
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hasVolume = true; |
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frameData.volume = vol; |
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} |
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|
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|
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/** Wrap a vector according to periodic boundary conditions */ |
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void Snapshot::wrapVector(Vector3d& pos) { |
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|
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if( !frameData.orthoRhombic ) { |
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Vector3d scaled = frameData.invHmat * pos; |
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for (int i = 0; i < 3; i++) { |
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scaled[i] -= roundMe( scaled[i] ); |
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} |
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
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pos = frameData.hmat * scaled; |
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} else { |
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RealType scaled; |
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for (int i=0; i<3; i++) { |
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scaled = pos[i] * frameData.invHmat(i,i); |
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scaled -= roundMe( scaled ); |
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pos[i] = scaled * frameData.hmat(i,i); |
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} |
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} |
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} |
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|
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/** Scaling a vector to multiples of the periodic box */ |
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inline Vector3d Snapshot::scaleVector(Vector3d& pos) { |
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|
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Vector3d scaled; |
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|
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if( !frameData.orthoRhombic ) |
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scaled = frameData.invHmat * pos; |
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else { |
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// calc the scaled coordinates. |
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for (int i=0; i<3; i++) |
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scaled[i] = pos[i] * frameData.invHmat(i, i); |
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} |
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|
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return scaled; |
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} |
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|
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void Snapshot::setCOM(const Vector3d& com) { |
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frameData.COM = com; |
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hasCOM = true; |
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} |
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|
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void Snapshot::setCOMvel(const Vector3d& comVel) { |
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frameData.COMvel = comVel; |
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hasCOMvel = true; |
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} |
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|
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void Snapshot::setCOMw(const Vector3d& comw) { |
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frameData.COMw = comw; |
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hasCOMw = true; |
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} |
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|
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Vector3d Snapshot::getCOM() { |
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return frameData.COM; |
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} |
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|
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Vector3d Snapshot::getCOMvel() { |
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return frameData.COMvel; |
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} |
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|
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Vector3d Snapshot::getCOMw() { |
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return frameData.COMw; |
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} |
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|
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RealType Snapshot::getTime() { |
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return frameData.currentTime; |
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} |
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|
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void Snapshot::increaseTime(RealType dt) { |
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setTime(getTime() + dt); |
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} |
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|
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void Snapshot::setTime(RealType time) { |
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frameData.currentTime = time; |
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} |
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|
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void Snapshot::setBondPotential(RealType bp) { |
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frameData.bondPotential = bp; |
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} |
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|
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void Snapshot::setBendPotential(RealType bp) { |
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frameData.bendPotential = bp; |
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} |
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|
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void Snapshot::setTorsionPotential(RealType tp) { |
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frameData.torsionPotential = tp; |
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} |
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|
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void Snapshot::setInversionPotential(RealType ip) { |
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frameData.inversionPotential = ip; |
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} |
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|
| 392 |
|
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RealType Snapshot::getBondPotential() { |
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return frameData.bondPotential; |
| 395 |
} |
| 396 |
RealType Snapshot::getBendPotential() { |
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return frameData.bendPotential; |
| 398 |
} |
| 399 |
RealType Snapshot::getTorsionPotential() { |
| 400 |
return frameData.torsionPotential; |
| 401 |
} |
| 402 |
RealType Snapshot::getInversionPotential() { |
| 403 |
return frameData.inversionPotential; |
| 404 |
} |
| 405 |
|
| 406 |
RealType Snapshot::getShortRangePotential() { |
| 407 |
if (!hasShortRangePotential) { |
| 408 |
frameData.shortRangePotential = frameData.bondPotential; |
| 409 |
frameData.shortRangePotential += frameData.bendPotential; |
| 410 |
frameData.shortRangePotential += frameData.torsionPotential; |
| 411 |
frameData.shortRangePotential += frameData.inversionPotential; |
| 412 |
hasShortRangePotential = true; |
| 413 |
} |
| 414 |
return frameData.shortRangePotential; |
| 415 |
} |
| 416 |
|
| 417 |
void Snapshot::setLongRangePotential(potVec lrPot) { |
| 418 |
frameData.lrPotentials = lrPot; |
| 419 |
} |
| 420 |
|
| 421 |
RealType Snapshot::getLongRangePotential() { |
| 422 |
if (!hasLongRangePotential) { |
| 423 |
for (int i = 0; i < N_INTERACTION_FAMILIES; i++) { |
| 424 |
frameData.longRangePotential += frameData.lrPotentials[i]; |
| 425 |
} |
| 426 |
hasLongRangePotential = true; |
| 427 |
} |
| 428 |
return frameData.longRangePotential; |
| 429 |
} |
| 430 |
|
| 431 |
potVec Snapshot::getLongRangePotentials() { |
| 432 |
return frameData.lrPotentials; |
| 433 |
} |
| 434 |
|
| 435 |
RealType Snapshot::getPotentialEnergy() { |
| 436 |
if (!hasPotentialEnergy) { |
| 437 |
frameData.potentialEnergy = this->getLongRangePotential(); |
| 438 |
frameData.potentialEnergy += this->getShortRangePotential(); |
| 439 |
hasPotentialEnergy = true; |
| 440 |
} |
| 441 |
return frameData.potentialEnergy; |
| 442 |
} |
| 443 |
|
| 444 |
void Snapshot::setExcludedPotentials(potVec exPot) { |
| 445 |
frameData.excludedPotentials = exPot; |
| 446 |
} |
| 447 |
|
| 448 |
potVec Snapshot::getExcludedPotentials() { |
| 449 |
return frameData.excludedPotentials; |
| 450 |
} |
| 451 |
|
| 452 |
void Snapshot::setRestraintPotential(RealType rp) { |
| 453 |
frameData.restraintPotential = rp; |
| 454 |
} |
| 455 |
|
| 456 |
RealType Snapshot::getRestraintPotential() { |
| 457 |
return frameData.restraintPotential; |
| 458 |
} |
| 459 |
|
| 460 |
void Snapshot::setRawPotential(RealType rp) { |
| 461 |
frameData.rawPotential = rp; |
| 462 |
} |
| 463 |
|
| 464 |
RealType Snapshot::getRawPotential() { |
| 465 |
return frameData.rawPotential; |
| 466 |
} |
| 467 |
|
| 468 |
RealType Snapshot::getTranslationalKineticEnergy() { |
| 469 |
return frameData.translationalKinetic; |
| 470 |
} |
| 471 |
|
| 472 |
RealType Snapshot::getRotationalKineticEnergy() { |
| 473 |
return frameData.rotationalKinetic; |
| 474 |
} |
| 475 |
|
| 476 |
RealType Snapshot::getKineticEnergy() { |
| 477 |
return frameData.kineticEnergy; |
| 478 |
} |
| 479 |
|
| 480 |
void Snapshot::setTranslationalKineticEnergy(RealType tke) { |
| 481 |
hasTranslationalKineticEnergy = true; |
| 482 |
frameData.translationalKinetic = tke; |
| 483 |
} |
| 484 |
|
| 485 |
void Snapshot::setRotationalKineticEnergy(RealType rke) { |
| 486 |
hasRotationalKineticEnergy = true; |
| 487 |
frameData.rotationalKinetic = rke; |
| 488 |
} |
| 489 |
|
| 490 |
void Snapshot::setKineticEnergy(RealType ke) { |
| 491 |
hasKineticEnergy = true; |
| 492 |
frameData.kineticEnergy = ke; |
| 493 |
} |
| 494 |
|
| 495 |
RealType Snapshot::getTotalEnergy() { |
| 496 |
return frameData.totalEnergy; |
| 497 |
} |
| 498 |
|
| 499 |
void Snapshot::setTotalEnergy(RealType te) { |
| 500 |
hasTotalEnergy = true; |
| 501 |
frameData.totalEnergy = te; |
| 502 |
} |
| 503 |
|
| 504 |
RealType Snapshot::getConservedQuantity() { |
| 505 |
return frameData.conservedQuantity; |
| 506 |
} |
| 507 |
|
| 508 |
void Snapshot::setConservedQuantity(RealType cq) { |
| 509 |
hasConservedQuantity = true; |
| 510 |
frameData.conservedQuantity = cq; |
| 511 |
} |
| 512 |
|
| 513 |
RealType Snapshot::getTemperature() { |
| 514 |
return frameData.temperature; |
| 515 |
} |
| 516 |
|
| 517 |
void Snapshot::setTemperature(RealType temp) { |
| 518 |
hasTemperature = true; |
| 519 |
frameData.temperature = temp; |
| 520 |
} |
| 521 |
|
| 522 |
RealType Snapshot::getElectronicTemperature() { |
| 523 |
return frameData.electronicTemperature; |
| 524 |
} |
| 525 |
|
| 526 |
void Snapshot::setElectronicTemperature(RealType eTemp) { |
| 527 |
hasElectronicTemperature = true; |
| 528 |
frameData.electronicTemperature = eTemp; |
| 529 |
} |
| 530 |
|
| 531 |
RealType Snapshot::getPressure() { |
| 532 |
return frameData.pressure; |
| 533 |
} |
| 534 |
|
| 535 |
void Snapshot::setPressure(RealType pressure) { |
| 536 |
hasPressure = true; |
| 537 |
frameData.pressure = pressure; |
| 538 |
} |
| 539 |
|
| 540 |
Mat3x3d Snapshot::getPressureTensor() { |
| 541 |
return frameData.pressureTensor; |
| 542 |
} |
| 543 |
|
| 544 |
|
| 545 |
void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) { |
| 546 |
hasPressureTensor = true; |
| 547 |
frameData.pressureTensor = pressureTensor; |
| 548 |
} |
| 549 |
|
| 550 |
void Snapshot::setStressTensor(const Mat3x3d& stressTensor) { |
| 551 |
frameData.stressTensor = stressTensor; |
| 552 |
} |
| 553 |
|
| 554 |
Mat3x3d Snapshot::getStressTensor() { |
| 555 |
return frameData.stressTensor; |
| 556 |
} |
| 557 |
|
| 558 |
void Snapshot::setConductiveHeatFlux(const Vector3d& chf) { |
| 559 |
frameData.conductiveHeatFlux = chf; |
| 560 |
} |
| 561 |
|
| 562 |
Vector3d Snapshot::getConductiveHeatFlux() { |
| 563 |
return frameData.conductiveHeatFlux; |
| 564 |
} |
| 565 |
|
| 566 |
Vector3d Snapshot::getConvectiveHeatFlux() { |
| 567 |
return frameData.convectiveHeatFlux; |
| 568 |
} |
| 569 |
|
| 570 |
void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) { |
| 571 |
hasConvectiveHeatFlux = true; |
| 572 |
frameData.convectiveHeatFlux = chf; |
| 573 |
} |
| 574 |
|
| 575 |
Vector3d Snapshot::getHeatFlux() { |
| 576 |
// BE CAREFUL WITH UNITS |
| 577 |
return getConductiveHeatFlux() + getConvectiveHeatFlux(); |
| 578 |
} |
| 579 |
|
| 580 |
Vector3d Snapshot::getSystemDipole() { |
| 581 |
return frameData.systemDipole; |
| 582 |
} |
| 583 |
|
| 584 |
void Snapshot::setSystemDipole(const Vector3d& bd) { |
| 585 |
hasSystemDipole = true; |
| 586 |
frameData.systemDipole = bd; |
| 587 |
} |
| 588 |
|
| 589 |
void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) { |
| 590 |
frameData.thermostat = thermostat; |
| 591 |
} |
| 592 |
|
| 593 |
pair<RealType, RealType> Snapshot::getThermostat() { |
| 594 |
return frameData.thermostat; |
| 595 |
} |
| 596 |
|
| 597 |
void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) { |
| 598 |
frameData.electronicThermostat = eTherm; |
| 599 |
} |
| 600 |
|
| 601 |
pair<RealType, RealType> Snapshot::getElectronicThermostat() { |
| 602 |
return frameData.electronicThermostat; |
| 603 |
} |
| 604 |
|
| 605 |
void Snapshot::setBarostat(const Mat3x3d& barostat) { |
| 606 |
frameData.barostat = barostat; |
| 607 |
} |
| 608 |
|
| 609 |
Mat3x3d Snapshot::getBarostat() { |
| 610 |
return frameData.barostat; |
| 611 |
} |
| 612 |
|
| 613 |
void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) { |
| 614 |
frameData.inertiaTensor = inertiaTensor; |
| 615 |
hasInertiaTensor = true; |
| 616 |
} |
| 617 |
|
| 618 |
Mat3x3d Snapshot::getInertiaTensor() { |
| 619 |
return frameData.inertiaTensor; |
| 620 |
} |
| 621 |
|
| 622 |
void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) { |
| 623 |
frameData.gyrationalVolume = gyrationalVolume; |
| 624 |
hasGyrationalVolume = true; |
| 625 |
} |
| 626 |
|
| 627 |
RealType Snapshot::getGyrationalVolume() { |
| 628 |
return frameData.gyrationalVolume; |
| 629 |
} |
| 630 |
|
| 631 |
void Snapshot::setHullVolume(const RealType hullVolume) { |
| 632 |
frameData.hullVolume = hullVolume; |
| 633 |
hasHullVolume = true; |
| 634 |
} |
| 635 |
|
| 636 |
RealType Snapshot::getHullVolume() { |
| 637 |
return frameData.hullVolume; |
| 638 |
} |
| 639 |
|
| 640 |
void Snapshot::setOrthoTolerance(RealType ot) { |
| 641 |
orthoTolerance_ = ot; |
| 642 |
} |
| 643 |
} |
