src/brains/Snapshot.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
  
/**
 * @file Snapshot.cpp
 * @author tlin
 * @date 11/11/2004
 * @version 1.0
 */

#include "brains/Snapshot.hpp"
#include "utils/NumericConstant.hpp"
#include "utils/simError.h"
#include "utils/Utility.hpp"
#include <cstdio>

namespace OpenMD {

  Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups) : 
    atomData(nAtoms), rigidbodyData(nRigidbodies),
    cgData(nCutoffGroups, DataStorage::dslPosition), 
    orthoTolerance_(1e-6) {
    
    frameData.id = -1;                   
    frameData.currentTime = 0;     
    frameData.hmat = Mat3x3d(0.0);             
    frameData.invHmat = Mat3x3d(0.0);          
    frameData.orthoRhombic = false;        
    frameData.bondPotential = 0.0;      
    frameData.bendPotential = 0.0;      
    frameData.torsionPotential = 0.0;   
    frameData.inversionPotential = 0.0; 
    frameData.lrPotentials = potVec(0.0);
    frameData.reciprocalPotential = 0.0;
    frameData.excludedPotentials = potVec(0.0); 
    frameData.restraintPotential = 0.0; 
    frameData.rawPotential = 0.0;   
    frameData.xyArea = 0.0;
    frameData.volume = 0.0;          
    frameData.thermostat = make_pair(0.0, 0.0);
    frameData.electronicThermostat = make_pair(0.0, 0.0);
    frameData.barostat = Mat3x3d(0.0);              
    frameData.stressTensor = Mat3x3d(0.0);              
    frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);

    clearDerivedProperties();
  }
  
  Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, 
                     int storageLayout) : 
    atomData(nAtoms, storageLayout), 
    rigidbodyData(nRigidbodies, storageLayout),
    cgData(nCutoffGroups, DataStorage::dslPosition),
    orthoTolerance_(1e-6) {
    
    frameData.id = -1;                   
    frameData.currentTime = 0;     
    frameData.hmat = Mat3x3d(0.0);             
    frameData.invHmat = Mat3x3d(0.0);      
    frameData.bBox = Mat3x3d(0.0);             
    frameData.invBbox = Mat3x3d(0.0);
    frameData.orthoRhombic = false;        
    frameData.bondPotential = 0.0;      
    frameData.bendPotential = 0.0;      
    frameData.torsionPotential = 0.0;   
    frameData.inversionPotential = 0.0; 
    frameData.lrPotentials = potVec(0.0);
    frameData.reciprocalPotential = 0.0;
    frameData.excludedPotentials = potVec(0.0); 
    frameData.restraintPotential = 0.0; 
    frameData.rawPotential = 0.0;       
    frameData.xyArea = 0.0;
    frameData.volume = 0.0;          
    frameData.thermostat = make_pair(0.0, 0.0);
    frameData.electronicThermostat = make_pair(0.0, 0.0);
    frameData.barostat = Mat3x3d(0.0);              
    frameData.stressTensor = Mat3x3d(0.0);              
    frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);

    clearDerivedProperties();
  }

  void Snapshot::clearDerivedProperties() {
    frameData.totalEnergy = 0.0;     
    frameData.translationalKinetic = 0.0;   
    frameData.rotationalKinetic = 0.0;   
    frameData.kineticEnergy = 0.0;   
    frameData.potentialEnergy = 0.0; 
    frameData.shortRangePotential = 0.0;
    frameData.longRangePotential = 0.0; 
    frameData.pressure = 0.0;        
    frameData.temperature = 0.0;
    frameData.pressureTensor = Mat3x3d(0.0);   
    frameData.systemDipole = Vector3d(0.0);            
    frameData.convectiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
    frameData.electronicTemperature = 0.0;
    frameData.COM = V3Zero;             
    frameData.COMvel = V3Zero;          
    frameData.COMw = V3Zero;  

    hasTotalEnergy = false;         
    hasTranslationalKineticEnergy = false;       
    hasRotationalKineticEnergy = false;       
    hasKineticEnergy = false;       
    hasShortRangePotential = false;
    hasLongRangePotential = false;
    hasPotentialEnergy = false;   
    hasXYarea = false;
    hasVolume = false;         
    hasPressure = false;       
    hasTemperature = false;    
    hasElectronicTemperature = false;
    hasCOM = false;
    hasCOMvel = false;
    hasCOMw = false;
    hasPressureTensor = false;    
    hasSystemDipole = false;      
    hasConvectiveHeatFlux = false;  
    hasInertiaTensor = false;
    hasGyrationalVolume = false;   
    hasHullVolume = false;
    hasConservedQuantity = false; 
    hasBoundingBox = false;
  }

  /** Returns the id of this Snapshot */
  int Snapshot::getID() {
    return frameData.id;
  }
  
  /** Sets the id of this Snapshot */
  void Snapshot::setID(int id) {
    frameData.id = id;
  }
  
  int Snapshot::getSize() {
    return atomData.getSize() + rigidbodyData.getSize();
  }
  
  /** Returns the number of atoms */
  int Snapshot::getNumberOfAtoms() {
    return atomData.getSize();
  }
  
  /** Returns the number of rigid bodies */
  int Snapshot::getNumberOfRigidBodies() {
    return rigidbodyData.getSize();
  }
  
  /** Returns the number of rigid bodies */
  int Snapshot::getNumberOfCutoffGroups() {
    return cgData.getSize();
  }

    /** Returns the number of bytes in a FrameData structure */
  int Snapshot::getFrameDataSize() {
    return sizeof(FrameData);
  }
  
  /** Returns the H-Matrix */
  Mat3x3d Snapshot::getHmat() {
    return frameData.hmat;
  }

  /** Sets the H-Matrix */  
  void Snapshot::setHmat(const Mat3x3d& m) {
    hasVolume = false;
    frameData.hmat = m;
    frameData.invHmat = frameData.hmat.inverse();
    
    //determine whether the box is orthoTolerance or not
    bool oldOrthoRhombic = frameData.orthoRhombic;
    
    RealType smallDiag = fabs(frameData.hmat(0, 0));
    if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
    if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));    
    RealType tol = smallDiag * orthoTolerance_;

    frameData.orthoRhombic = true;

    for (int i = 0; i < 3; i++ ) {
      for (int j = 0 ; j < 3; j++) {
        if (i != j) {
          if (frameData.orthoRhombic) {
            if ( fabs(frameData.hmat(i, j)) >= tol)
              frameData.orthoRhombic = false;
          }        
        }
      }
    }
    
    if( oldOrthoRhombic != frameData.orthoRhombic){
      
      // It is finally time to suppress these warnings once and for
      // all.  They were annoying and not very informative.

      // if( frameData.orthoRhombic ) {
      //   sprintf( painCave.errMsg,
      //         "OpenMD is switching from the default Non-Orthorhombic\n"
      //         "\tto the faster Orthorhombic periodic boundary computations.\n"
      //         "\tThis is usually a good thing, but if you want the\n"
      //         "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
      //         "\tvariable ( currently set to %G ) smaller.\n",
      //         orthoTolerance_);
      //   painCave.severity = OPENMD_INFO;
      //   simError();
      // }
      // else {
      //   sprintf( painCave.errMsg,
      //         "OpenMD is switching from the faster Orthorhombic to the more\n"
      //         "\tflexible Non-Orthorhombic periodic boundary computations.\n"
      //         "\tThis is usually because the box has deformed under\n"
      //         "\tNPTf integration. If you want to live on the edge with\n"
      //         "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
      //         "\tvariable ( currently set to %G ) larger.\n",
      //         orthoTolerance_);
      //   painCave.severity = OPENMD_WARNING;
      //   simError();
      // }
    }    
  }
  
  /** Returns the inverse H-Matrix */
  Mat3x3d Snapshot::getInvHmat() {
    return frameData.invHmat;
  }

  /** Returns the Bounding Box */
  Mat3x3d Snapshot::getBoundingBox() {
    return frameData.bBox;
  }

  /** Sets the Bounding Box */  
  void Snapshot::setBoundingBox(const Mat3x3d& m) {
    frameData.bBox = m;
    frameData.invBbox = frameData.bBox.inverse();
    hasBoundingBox = true;
  }

  /** Returns the inverse Bounding Box */
  Mat3x3d Snapshot::getInvBoundingBox() {
    return frameData.invBbox;
  }

  RealType Snapshot::getXYarea() {
    if (!hasXYarea) {
      Vector3d x = frameData.hmat.getColumn(0);
      Vector3d y = frameData.hmat.getColumn(1);
      frameData.xyArea = cross(x,y).length();
      hasXYarea = true;
    }
    return frameData.xyArea;
  }

  RealType Snapshot::getVolume() {
    if (!hasVolume) {
      frameData.volume = frameData.hmat.determinant();
      hasVolume = true;
    }
    return frameData.volume;
  }

  void Snapshot::setVolume(RealType vol) {
    hasVolume = true;
    frameData.volume = vol;
  }


  /** Wrap a vector according to periodic boundary conditions */
  void Snapshot::wrapVector(Vector3d& pos) {
    
    if( !frameData.orthoRhombic ) {
      Vector3d scaled = frameData.invHmat * pos;
      for (int i = 0; i < 3; i++) {
        scaled[i] -= roundMe( scaled[i] );        
      }
      // calc the wrapped real coordinates from the wrapped scaled coordinates
      pos = frameData.hmat * scaled;
    } else {
      RealType scaled;
      for (int i=0; i<3; i++) {      
        scaled = pos[i] * frameData.invHmat(i,i);
        scaled -= roundMe( scaled );
        pos[i] = scaled * frameData.hmat(i,i);
      }
    }
  }

  /** Scaling a vector to multiples of the periodic box */
  inline Vector3d Snapshot::scaleVector(Vector3d& pos) {   
    
    Vector3d scaled;

    if( !frameData.orthoRhombic )
      scaled = frameData.invHmat * pos;
    else {
      // calc the scaled coordinates.
      for (int i=0; i<3; i++) 
        scaled[i] = pos[i] * frameData.invHmat(i, i);
    }

    return scaled;
  }

  void Snapshot::setCOM(const Vector3d& com) {
    frameData.COM = com;
    hasCOM = true;
  }
  
  void Snapshot::setCOMvel(const Vector3d& comVel) {
    frameData.COMvel = comVel;
    hasCOMvel = true;
  }
  
  void Snapshot::setCOMw(const Vector3d& comw) {
    frameData.COMw = comw;
    hasCOMw = true;
  }
  
  Vector3d Snapshot::getCOM() {
    return frameData.COM;
  }
  
  Vector3d Snapshot::getCOMvel() {
    return frameData.COMvel;
  }
  
  Vector3d Snapshot::getCOMw() {
    return frameData.COMw;
  }
  
  RealType Snapshot::getTime() {
    return frameData.currentTime;
  }
  
  void Snapshot::increaseTime(RealType dt) {
    setTime(getTime() + dt);
  }
  
  void Snapshot::setTime(RealType time) {
    frameData.currentTime = time;
  }
 
  void Snapshot::setBondPotential(RealType bp) {
    frameData.bondPotential = bp;
  }
  
  void Snapshot::setBendPotential(RealType bp) {
    frameData.bendPotential = bp;
  }
  
  void Snapshot::setTorsionPotential(RealType tp) {
    frameData.torsionPotential = tp;
  }
  
  void Snapshot::setInversionPotential(RealType ip) {
    frameData.inversionPotential = ip;
  }


  RealType Snapshot::getBondPotential() {
    return frameData.bondPotential;
  }
  RealType Snapshot::getBendPotential() {
    return frameData.bendPotential;
  }
  RealType Snapshot::getTorsionPotential() {
    return frameData.torsionPotential;
  }
  RealType Snapshot::getInversionPotential() {
    return frameData.inversionPotential;
  }

  RealType Snapshot::getShortRangePotential() {
    if (!hasShortRangePotential) {
      frameData.shortRangePotential = frameData.bondPotential;
      frameData.shortRangePotential += frameData.bendPotential;
      frameData.shortRangePotential += frameData.torsionPotential;
      frameData.shortRangePotential += frameData.inversionPotential;
      hasShortRangePotential = true;
    }
    return frameData.shortRangePotential;
  }

  void Snapshot::setReciprocalPotential(RealType rp){
    frameData.reciprocalPotential = rp;
  }

  RealType Snapshot::getReciprocalPotential() {
    return frameData.reciprocalPotential;
  }

  void Snapshot::setLongRangePotential(potVec lrPot) {
    frameData.lrPotentials = lrPot;
  }
    
  RealType Snapshot::getLongRangePotential() {
    if (!hasLongRangePotential) {
      for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
        frameData.longRangePotential += frameData.lrPotentials[i];
      }
      frameData.longRangePotential += frameData.reciprocalPotential;
      hasLongRangePotential = true;
    }   
    return frameData.longRangePotential;
  }

  potVec Snapshot::getLongRangePotentials() {
    return frameData.lrPotentials;
  }

  RealType Snapshot::getPotentialEnergy() {
    if (!hasPotentialEnergy) {
      frameData.potentialEnergy = this->getLongRangePotential();
      frameData.potentialEnergy += this->getShortRangePotential();
      hasPotentialEnergy = true;
    }
    return frameData.potentialEnergy;
  }
    
  void Snapshot::setExcludedPotentials(potVec exPot) {
    frameData.excludedPotentials = exPot;
  }

  potVec Snapshot::getExcludedPotentials() {
    return frameData.excludedPotentials;
  }
      
  void Snapshot::setRestraintPotential(RealType rp) {
    frameData.restraintPotential = rp;
  }
  
  RealType Snapshot::getRestraintPotential() {
    return frameData.restraintPotential;
  }
  
  void Snapshot::setRawPotential(RealType rp) {
    frameData.rawPotential = rp;
  }
  
  RealType Snapshot::getRawPotential() {
    return frameData.rawPotential;
  }

  RealType Snapshot::getTranslationalKineticEnergy() {
    return frameData.translationalKinetic;
  }

  RealType Snapshot::getRotationalKineticEnergy() {
    return frameData.rotationalKinetic;
  }

  RealType Snapshot::getKineticEnergy() {
    return frameData.kineticEnergy;
  }

  void Snapshot::setTranslationalKineticEnergy(RealType tke) {
    hasTranslationalKineticEnergy = true;
    frameData.translationalKinetic = tke;
  }

  void Snapshot::setRotationalKineticEnergy(RealType rke) {
    hasRotationalKineticEnergy = true;
    frameData.rotationalKinetic = rke;
  }

  void Snapshot::setKineticEnergy(RealType ke) {
    hasKineticEnergy = true;
    frameData.kineticEnergy = ke;
  }

  RealType Snapshot::getTotalEnergy() {
    return frameData.totalEnergy;
  }

  void Snapshot::setTotalEnergy(RealType te) {
    hasTotalEnergy = true;
    frameData.totalEnergy = te;
  }

  RealType Snapshot::getConservedQuantity() {
    return frameData.conservedQuantity;
  }

  void Snapshot::setConservedQuantity(RealType cq) {
    hasConservedQuantity = true;
    frameData.conservedQuantity = cq;
  }

  RealType Snapshot::getTemperature() {
    return frameData.temperature;
  }

  void Snapshot::setTemperature(RealType temp) {
    hasTemperature = true;
    frameData.temperature = temp;
  }

  RealType Snapshot::getElectronicTemperature() {
    return frameData.electronicTemperature;
  }

  void Snapshot::setElectronicTemperature(RealType eTemp) {
    hasElectronicTemperature = true;
    frameData.electronicTemperature = eTemp;
  }

  RealType Snapshot::getPressure() {
    return frameData.pressure;
  }

  void Snapshot::setPressure(RealType pressure) {
    hasPressure = true;
    frameData.pressure = pressure;
  }

  Mat3x3d Snapshot::getPressureTensor() {
    return frameData.pressureTensor;
  }


  void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) {
    hasPressureTensor = true;
    frameData.pressureTensor = pressureTensor;
  }

  void Snapshot::setStressTensor(const Mat3x3d& stressTensor) {
    frameData.stressTensor = stressTensor;
  }

  Mat3x3d  Snapshot::getStressTensor() {
    return frameData.stressTensor;
  }

  void Snapshot::setConductiveHeatFlux(const Vector3d& chf) {
    frameData.conductiveHeatFlux = chf;
  }

  Vector3d Snapshot::getConductiveHeatFlux() {
    return frameData.conductiveHeatFlux;
  }
  
  Vector3d Snapshot::getConvectiveHeatFlux() {
    return frameData.convectiveHeatFlux;
  }

  void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) {    
    hasConvectiveHeatFlux = true;
    frameData.convectiveHeatFlux = chf;
  }

  Vector3d Snapshot::getHeatFlux() {
    // BE CAREFUL WITH UNITS
    return getConductiveHeatFlux() + getConvectiveHeatFlux();
  }

  Vector3d Snapshot::getSystemDipole() {
    return frameData.systemDipole;
  }

  void Snapshot::setSystemDipole(const Vector3d& bd) {    
    hasSystemDipole = true;
    frameData.systemDipole = bd;
  }

  void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) {
    frameData.thermostat = thermostat;
  }

  pair<RealType, RealType> Snapshot::getThermostat() {
    return frameData.thermostat;
  }

  void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) {
    frameData.electronicThermostat = eTherm;
  }

  pair<RealType, RealType> Snapshot::getElectronicThermostat() {
    return frameData.electronicThermostat;
  }
 
  void Snapshot::setBarostat(const Mat3x3d& barostat) {
    frameData.barostat = barostat;
  }

  Mat3x3d Snapshot::getBarostat() {
    return frameData.barostat;
  }

  void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) {
    frameData.inertiaTensor = inertiaTensor;
    hasInertiaTensor = true;
  }

  Mat3x3d Snapshot::getInertiaTensor() {
    return frameData.inertiaTensor;
  }

  void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) {
    frameData.gyrationalVolume = gyrationalVolume;
    hasGyrationalVolume = true;
  }

  RealType Snapshot::getGyrationalVolume() {
    return frameData.gyrationalVolume;
  }

  void Snapshot::setHullVolume(const RealType hullVolume) {
    frameData.hullVolume = hullVolume;
    hasHullVolume = true;
  }

  RealType Snapshot::getHullVolume() {
    return frameData.hullVolume;
  }

  void Snapshot::setOrthoTolerance(RealType ot) {
    orthoTolerance_ = ot;
  }
}
Revision:	1966
Committed:	Fri Jan 24 14:17:42 2014 UTC (11 years, 3 months ago) by gezelter
File size:	19460 byte(s)
Log Message:	More changes for memory management.
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	507	/**
44			* @file Snapshot.cpp
45			* @author tlin
46			* @date 11/11/2004
47			* @version 1.0
48			*/
49	gezelter	246
50			#include "brains/Snapshot.hpp"
51			#include "utils/NumericConstant.hpp"
52			#include "utils/simError.h"
53			#include "utils/Utility.hpp"
54	jmarr	1401	#include <cstdio>
55
56	gezelter	1390	namespace OpenMD {
57	gezelter	246
58	gezelter	1782	Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups) :
59			atomData(nAtoms), rigidbodyData(nRigidbodies),
60			cgData(nCutoffGroups, DataStorage::dslPosition),
61			orthoTolerance_(1e-6) {
62	gezelter	246
63	gezelter	1782	frameData.id = -1;
64			frameData.currentTime = 0;
65			frameData.hmat = Mat3x3d(0.0);
66			frameData.invHmat = Mat3x3d(0.0);
67			frameData.orthoRhombic = false;
68			frameData.bondPotential = 0.0;
69			frameData.bendPotential = 0.0;
70			frameData.torsionPotential = 0.0;
71			frameData.inversionPotential = 0.0;
72			frameData.lrPotentials = potVec(0.0);
73	gezelter	1925	frameData.reciprocalPotential = 0.0;
74	gezelter	1782	frameData.excludedPotentials = potVec(0.0);
75			frameData.restraintPotential = 0.0;
76			frameData.rawPotential = 0.0;
77			frameData.xyArea = 0.0;
78			frameData.volume = 0.0;
79			frameData.thermostat = make_pair(0.0, 0.0);
80			frameData.electronicThermostat = make_pair(0.0, 0.0);
81			frameData.barostat = Mat3x3d(0.0);
82			frameData.stressTensor = Mat3x3d(0.0);
83			frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
84	chuckv	1112
85	gezelter	1782	clearDerivedProperties();
86			}
87
88			Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
89			int storageLayout) :
90			atomData(nAtoms, storageLayout),
91			rigidbodyData(nRigidbodies, storageLayout),
92			cgData(nCutoffGroups, DataStorage::dslPosition),
93			orthoTolerance_(1e-6) {
94
95			frameData.id = -1;
96			frameData.currentTime = 0;
97			frameData.hmat = Mat3x3d(0.0);
98	gezelter	1879	frameData.invHmat = Mat3x3d(0.0);
99			frameData.bBox = Mat3x3d(0.0);
100			frameData.invBbox = Mat3x3d(0.0);
101	gezelter	1782	frameData.orthoRhombic = false;
102			frameData.bondPotential = 0.0;
103			frameData.bendPotential = 0.0;
104			frameData.torsionPotential = 0.0;
105			frameData.inversionPotential = 0.0;
106			frameData.lrPotentials = potVec(0.0);
107	gezelter	1925	frameData.reciprocalPotential = 0.0;
108	gezelter	1782	frameData.excludedPotentials = potVec(0.0);
109			frameData.restraintPotential = 0.0;
110			frameData.rawPotential = 0.0;
111			frameData.xyArea = 0.0;
112			frameData.volume = 0.0;
113			frameData.thermostat = make_pair(0.0, 0.0);
114			frameData.electronicThermostat = make_pair(0.0, 0.0);
115			frameData.barostat = Mat3x3d(0.0);
116			frameData.stressTensor = Mat3x3d(0.0);
117			frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
118	gezelter	246
119	gezelter	1782	clearDerivedProperties();
120			}
121
122			void Snapshot::clearDerivedProperties() {
123			frameData.totalEnergy = 0.0;
124			frameData.translationalKinetic = 0.0;
125			frameData.rotationalKinetic = 0.0;
126			frameData.kineticEnergy = 0.0;
127			frameData.potentialEnergy = 0.0;
128			frameData.shortRangePotential = 0.0;
129			frameData.longRangePotential = 0.0;
130			frameData.pressure = 0.0;
131			frameData.temperature = 0.0;
132			frameData.pressureTensor = Mat3x3d(0.0);
133			frameData.systemDipole = Vector3d(0.0);
134			frameData.convectiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
135			frameData.electronicTemperature = 0.0;
136			frameData.COM = V3Zero;
137			frameData.COMvel = V3Zero;
138	gezelter	1879	frameData.COMw = V3Zero;
139	gezelter	1782
140			hasTotalEnergy = false;
141			hasTranslationalKineticEnergy = false;
142			hasRotationalKineticEnergy = false;
143			hasKineticEnergy = false;
144			hasShortRangePotential = false;
145			hasLongRangePotential = false;
146			hasPotentialEnergy = false;
147			hasXYarea = false;
148			hasVolume = false;
149			hasPressure = false;
150			hasTemperature = false;
151			hasElectronicTemperature = false;
152			hasCOM = false;
153			hasCOMvel = false;
154			hasCOMw = false;
155			hasPressureTensor = false;
156			hasSystemDipole = false;
157			hasConvectiveHeatFlux = false;
158			hasInertiaTensor = false;
159			hasGyrationalVolume = false;
160			hasHullVolume = false;
161			hasConservedQuantity = false;
162	gezelter	1879	hasBoundingBox = false;
163	gezelter	1782	}
164
165			/** Returns the id of this Snapshot */
166			int Snapshot::getID() {
167			return frameData.id;
168			}
169
170			/** Sets the id of this Snapshot */
171			void Snapshot::setID(int id) {
172			frameData.id = id;
173			}
174
175			int Snapshot::getSize() {
176			return atomData.getSize() + rigidbodyData.getSize();
177			}
178
179			/** Returns the number of atoms */
180			int Snapshot::getNumberOfAtoms() {
181			return atomData.getSize();
182			}
183
184			/** Returns the number of rigid bodies */
185			int Snapshot::getNumberOfRigidBodies() {
186			return rigidbodyData.getSize();
187			}
188
189			/** Returns the number of rigid bodies */
190			int Snapshot::getNumberOfCutoffGroups() {
191			return cgData.getSize();
192			}
193	gezelter	1966
194			/** Returns the number of bytes in a FrameData structure */
195			int Snapshot::getFrameDataSize() {
196			return sizeof(FrameData);
197			}
198	gezelter	1782
199			/** Returns the H-Matrix */
200			Mat3x3d Snapshot::getHmat() {
201			return frameData.hmat;
202			}
203
204			/** Sets the H-Matrix */
205			void Snapshot::setHmat(const Mat3x3d& m) {
206			hasVolume = false;
207			frameData.hmat = m;
208			frameData.invHmat = frameData.hmat.inverse();
209
210	gezelter	246	//determine whether the box is orthoTolerance or not
211	gezelter	1782	bool oldOrthoRhombic = frameData.orthoRhombic;
212	gezelter	246
213	gezelter	1782	RealType smallDiag = fabs(frameData.hmat(0, 0));
214			if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
215			if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));
216	gezelter	1021	RealType tol = smallDiag * orthoTolerance_;
217	gezelter	246
218	gezelter	1782	frameData.orthoRhombic = true;
219	gezelter	246
220			for (int i = 0; i < 3; i++ ) {
221	gezelter	507	for (int j = 0 ; j < 3; j++) {
222			if (i != j) {
223	gezelter	1782	if (frameData.orthoRhombic) {
224			if ( fabs(frameData.hmat(i, j)) >= tol)
225			frameData.orthoRhombic = false;
226	gezelter	507	}
227			}
228			}
229	gezelter	246	}
230	gezelter	1782
231			if( oldOrthoRhombic != frameData.orthoRhombic){
232
233	gezelter	1879	// It is finally time to suppress these warnings once and for
234			// all. They were annoying and not very informative.
235
236			// if( frameData.orthoRhombic ) {
237			// sprintf( painCave.errMsg,
238			// "OpenMD is switching from the default Non-Orthorhombic\n"
239			// "\tto the faster Orthorhombic periodic boundary computations.\n"
240			// "\tThis is usually a good thing, but if you want the\n"
241			// "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
242			// "\tvariable ( currently set to %G ) smaller.\n",
243			// orthoTolerance_);
244			// painCave.severity = OPENMD_INFO;
245			// simError();
246			// }
247			// else {
248			// sprintf( painCave.errMsg,
249			// "OpenMD is switching from the faster Orthorhombic to the more\n"
250			// "\tflexible Non-Orthorhombic periodic boundary computations.\n"
251			// "\tThis is usually because the box has deformed under\n"
252			// "\tNPTf integration. If you want to live on the edge with\n"
253			// "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
254			// "\tvariable ( currently set to %G ) larger.\n",
255			// orthoTolerance_);
256			// painCave.severity = OPENMD_WARNING;
257			// simError();
258			// }
259	gezelter	246	}
260	gezelter	1782	}
261
262			/** Returns the inverse H-Matrix */
263			Mat3x3d Snapshot::getInvHmat() {
264			return frameData.invHmat;
265			}
266	gezelter	246
267	gezelter	1879	/** Returns the Bounding Box */
268			Mat3x3d Snapshot::getBoundingBox() {
269			return frameData.bBox;
270			}
271
272			/** Sets the Bounding Box */
273			void Snapshot::setBoundingBox(const Mat3x3d& m) {
274			frameData.bBox = m;
275			frameData.invBbox = frameData.bBox.inverse();
276			hasBoundingBox = true;
277			}
278
279			/** Returns the inverse Bounding Box */
280			Mat3x3d Snapshot::getInvBoundingBox() {
281			return frameData.invBbox;
282			}
283
284	gezelter	1782	RealType Snapshot::getXYarea() {
285			if (!hasXYarea) {
286			Vector3d x = frameData.hmat.getColumn(0);
287			Vector3d y = frameData.hmat.getColumn(1);
288			frameData.xyArea = cross(x,y).length();
289			hasXYarea = true;
290			}
291			return frameData.xyArea;
292	gezelter	507	}
293	gezelter	246
294	gezelter	1782	RealType Snapshot::getVolume() {
295			if (!hasVolume) {
296			frameData.volume = frameData.hmat.determinant();
297			hasVolume = true;
298			}
299			return frameData.volume;
300			}
301	gezelter	246
302	gezelter	1782	void Snapshot::setVolume(RealType vol) {
303			hasVolume = true;
304			frameData.volume = vol;
305			}
306
307	gezelter	1896
308	gezelter	1782	/** Wrap a vector according to periodic boundary conditions */
309	gezelter	507	void Snapshot::wrapVector(Vector3d& pos) {
310	gezelter	1782
311	gezelter	1895	if( !frameData.orthoRhombic ) {
312			Vector3d scaled = frameData.invHmat * pos;
313	gezelter	1896	for (int i = 0; i < 3; i++) {
314			scaled[i] -= roundMe( scaled[i] );
315			}
316	gezelter	1782	// calc the wrapped real coordinates from the wrapped scaled coordinates
317	gezelter	1895	pos = frameData.hmat * scaled;
318			} else {
319			RealType scaled;
320	gezelter	1896	for (int i=0; i<3; i++) {
321			scaled = pos[i] * frameData.invHmat(i,i);
322			scaled -= roundMe( scaled );
323			pos[i] = scaled * frameData.hmat(i,i);
324	gezelter	1895	}
325	gezelter	1782	}
326			}
327	gezelter	246
328	gezelter	1782	/** Scaling a vector to multiples of the periodic box */
329			inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
330
331	gezelter	246	Vector3d scaled;
332
333	gezelter	1782	if( !frameData.orthoRhombic )
334			scaled = frameData.invHmat * pos;
335			else {
336	gezelter	507	// calc the scaled coordinates.
337	gezelter	1782	for (int i=0; i<3; i++)
338			scaled[i] = pos[i] * frameData.invHmat(i, i);
339			}
340	gezelter	246
341	gezelter	1782	return scaled;
342			}
343	gezelter	246
344	gezelter	1782	void Snapshot::setCOM(const Vector3d& com) {
345			frameData.COM = com;
346			hasCOM = true;
347			}
348
349			void Snapshot::setCOMvel(const Vector3d& comVel) {
350			frameData.COMvel = comVel;
351			hasCOMvel = true;
352			}
353
354			void Snapshot::setCOMw(const Vector3d& comw) {
355			frameData.COMw = comw;
356			hasCOMw = true;
357			}
358
359			Vector3d Snapshot::getCOM() {
360			return frameData.COM;
361			}
362
363			Vector3d Snapshot::getCOMvel() {
364			return frameData.COMvel;
365			}
366
367			Vector3d Snapshot::getCOMw() {
368			return frameData.COMw;
369			}
370
371			RealType Snapshot::getTime() {
372			return frameData.currentTime;
373			}
374
375			void Snapshot::increaseTime(RealType dt) {
376			setTime(getTime() + dt);
377			}
378
379			void Snapshot::setTime(RealType time) {
380			frameData.currentTime = time;
381			}
382
383			void Snapshot::setBondPotential(RealType bp) {
384			frameData.bondPotential = bp;
385			}
386
387			void Snapshot::setBendPotential(RealType bp) {
388			frameData.bendPotential = bp;
389			}
390
391			void Snapshot::setTorsionPotential(RealType tp) {
392			frameData.torsionPotential = tp;
393			}
394
395			void Snapshot::setInversionPotential(RealType ip) {
396			frameData.inversionPotential = ip;
397			}
398	gezelter	246
399
400	gezelter	1782	RealType Snapshot::getBondPotential() {
401			return frameData.bondPotential;
402			}
403			RealType Snapshot::getBendPotential() {
404			return frameData.bendPotential;
405			}
406			RealType Snapshot::getTorsionPotential() {
407			return frameData.torsionPotential;
408			}
409			RealType Snapshot::getInversionPotential() {
410			return frameData.inversionPotential;
411			}
412
413			RealType Snapshot::getShortRangePotential() {
414			if (!hasShortRangePotential) {
415			frameData.shortRangePotential = frameData.bondPotential;
416			frameData.shortRangePotential += frameData.bendPotential;
417			frameData.shortRangePotential += frameData.torsionPotential;
418			frameData.shortRangePotential += frameData.inversionPotential;
419			hasShortRangePotential = true;
420	gezelter	246	}
421	gezelter	1782	return frameData.shortRangePotential;
422			}
423	gezelter	246
424	gezelter	1925	void Snapshot::setReciprocalPotential(RealType rp){
425			frameData.reciprocalPotential = rp;
426			}
427
428			RealType Snapshot::getReciprocalPotential() {
429			return frameData.reciprocalPotential;
430			}
431
432	gezelter	1782	void Snapshot::setLongRangePotential(potVec lrPot) {
433			frameData.lrPotentials = lrPot;
434	gezelter	507	}
435	gezelter	1782
436			RealType Snapshot::getLongRangePotential() {
437			if (!hasLongRangePotential) {
438			for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
439			frameData.longRangePotential += frameData.lrPotentials[i];
440			}
441	gezelter	1925	frameData.longRangePotential += frameData.reciprocalPotential;
442	gezelter	1782	hasLongRangePotential = true;
443			}
444			return frameData.longRangePotential;
445			}
446	gezelter	246
447	gezelter	1782	potVec Snapshot::getLongRangePotentials() {
448			return frameData.lrPotentials;
449			}
450
451			RealType Snapshot::getPotentialEnergy() {
452			if (!hasPotentialEnergy) {
453			frameData.potentialEnergy = this->getLongRangePotential();
454			frameData.potentialEnergy += this->getShortRangePotential();
455			hasPotentialEnergy = true;
456	gezelter	1104	}
457	gezelter	1782	return frameData.potentialEnergy;
458	gezelter	1104	}
459	gezelter	1782
460			void Snapshot::setExcludedPotentials(potVec exPot) {
461			frameData.excludedPotentials = exPot;
462			}
463
464			potVec Snapshot::getExcludedPotentials() {
465			return frameData.excludedPotentials;
466			}
467
468			void Snapshot::setRestraintPotential(RealType rp) {
469			frameData.restraintPotential = rp;
470			}
471	gezelter	1104
472	gezelter	1782	RealType Snapshot::getRestraintPotential() {
473			return frameData.restraintPotential;
474	gezelter	1104	}
475
476	gezelter	1782	void Snapshot::setRawPotential(RealType rp) {
477			frameData.rawPotential = rp;
478	gezelter	1104	}
479	gezelter	1782
480			RealType Snapshot::getRawPotential() {
481			return frameData.rawPotential;
482			}
483
484			RealType Snapshot::getTranslationalKineticEnergy() {
485			return frameData.translationalKinetic;
486			}
487
488			RealType Snapshot::getRotationalKineticEnergy() {
489			return frameData.rotationalKinetic;
490			}
491
492			RealType Snapshot::getKineticEnergy() {
493			return frameData.kineticEnergy;
494			}
495
496			void Snapshot::setTranslationalKineticEnergy(RealType tke) {
497			hasTranslationalKineticEnergy = true;
498			frameData.translationalKinetic = tke;
499			}
500
501			void Snapshot::setRotationalKineticEnergy(RealType rke) {
502			hasRotationalKineticEnergy = true;
503			frameData.rotationalKinetic = rke;
504			}
505
506			void Snapshot::setKineticEnergy(RealType ke) {
507			hasKineticEnergy = true;
508			frameData.kineticEnergy = ke;
509			}
510
511			RealType Snapshot::getTotalEnergy() {
512			return frameData.totalEnergy;
513			}
514
515			void Snapshot::setTotalEnergy(RealType te) {
516			hasTotalEnergy = true;
517			frameData.totalEnergy = te;
518			}
519
520			RealType Snapshot::getConservedQuantity() {
521			return frameData.conservedQuantity;
522			}
523
524			void Snapshot::setConservedQuantity(RealType cq) {
525			hasConservedQuantity = true;
526			frameData.conservedQuantity = cq;
527			}
528
529			RealType Snapshot::getTemperature() {
530			return frameData.temperature;
531			}
532
533			void Snapshot::setTemperature(RealType temp) {
534			hasTemperature = true;
535			frameData.temperature = temp;
536			}
537
538			RealType Snapshot::getElectronicTemperature() {
539			return frameData.electronicTemperature;
540			}
541
542			void Snapshot::setElectronicTemperature(RealType eTemp) {
543			hasElectronicTemperature = true;
544			frameData.electronicTemperature = eTemp;
545			}
546
547			RealType Snapshot::getPressure() {
548			return frameData.pressure;
549			}
550
551			void Snapshot::setPressure(RealType pressure) {
552			hasPressure = true;
553			frameData.pressure = pressure;
554			}
555
556			Mat3x3d Snapshot::getPressureTensor() {
557			return frameData.pressureTensor;
558			}
559
560
561			void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) {
562			hasPressureTensor = true;
563			frameData.pressureTensor = pressureTensor;
564			}
565
566			void Snapshot::setStressTensor(const Mat3x3d& stressTensor) {
567			frameData.stressTensor = stressTensor;
568			}
569
570			Mat3x3d Snapshot::getStressTensor() {
571			return frameData.stressTensor;
572			}
573
574			void Snapshot::setConductiveHeatFlux(const Vector3d& chf) {
575			frameData.conductiveHeatFlux = chf;
576			}
577
578			Vector3d Snapshot::getConductiveHeatFlux() {
579			return frameData.conductiveHeatFlux;
580			}
581
582			Vector3d Snapshot::getConvectiveHeatFlux() {
583			return frameData.convectiveHeatFlux;
584			}
585
586			void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) {
587			hasConvectiveHeatFlux = true;
588			frameData.convectiveHeatFlux = chf;
589			}
590
591			Vector3d Snapshot::getHeatFlux() {
592			// BE CAREFUL WITH UNITS
593			return getConductiveHeatFlux() + getConvectiveHeatFlux();
594			}
595
596			Vector3d Snapshot::getSystemDipole() {
597			return frameData.systemDipole;
598			}
599
600			void Snapshot::setSystemDipole(const Vector3d& bd) {
601			hasSystemDipole = true;
602			frameData.systemDipole = bd;
603			}
604
605			void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) {
606			frameData.thermostat = thermostat;
607			}
608
609			pair<RealType, RealType> Snapshot::getThermostat() {
610			return frameData.thermostat;
611			}
612
613			void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) {
614			frameData.electronicThermostat = eTherm;
615			}
616
617			pair<RealType, RealType> Snapshot::getElectronicThermostat() {
618			return frameData.electronicThermostat;
619			}
620	gezelter	1104
621	gezelter	1782	void Snapshot::setBarostat(const Mat3x3d& barostat) {
622			frameData.barostat = barostat;
623			}
624
625			Mat3x3d Snapshot::getBarostat() {
626			return frameData.barostat;
627			}
628
629			void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) {
630			frameData.inertiaTensor = inertiaTensor;
631			hasInertiaTensor = true;
632			}
633
634			Mat3x3d Snapshot::getInertiaTensor() {
635			return frameData.inertiaTensor;
636			}
637
638			void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) {
639			frameData.gyrationalVolume = gyrationalVolume;
640			hasGyrationalVolume = true;
641			}
642
643			RealType Snapshot::getGyrationalVolume() {
644			return frameData.gyrationalVolume;
645			}
646
647			void Snapshot::setHullVolume(const RealType hullVolume) {
648			frameData.hullVolume = hullVolume;
649			hasHullVolume = true;
650			}
651
652			RealType Snapshot::getHullVolume() {
653			return frameData.hullVolume;
654			}
655
656			void Snapshot::setOrthoTolerance(RealType ot) {
657			orthoTolerance_ = ot;
658			}
659	gezelter	246	}