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.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.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 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::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];
      }
      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:	1896
Committed:	Tue Jul 2 20:02:31 2013 UTC (11 years, 10 months ago) by gezelter
File size:	18979 byte(s)
Log Message:	Speedup tests
#	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			frameData.excludedPotentials = potVec(0.0);
74			frameData.restraintPotential = 0.0;
75			frameData.rawPotential = 0.0;
76			frameData.xyArea = 0.0;
77			frameData.volume = 0.0;
78			frameData.thermostat = make_pair(0.0, 0.0);
79			frameData.electronicThermostat = make_pair(0.0, 0.0);
80			frameData.barostat = Mat3x3d(0.0);
81			frameData.stressTensor = Mat3x3d(0.0);
82			frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
83	chuckv	1112
84	gezelter	1782	clearDerivedProperties();
85			}
86
87			Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
88			int storageLayout) :
89			atomData(nAtoms, storageLayout),
90			rigidbodyData(nRigidbodies, storageLayout),
91			cgData(nCutoffGroups, DataStorage::dslPosition),
92			orthoTolerance_(1e-6) {
93
94			frameData.id = -1;
95			frameData.currentTime = 0;
96			frameData.hmat = Mat3x3d(0.0);
97	gezelter	1879	frameData.invHmat = Mat3x3d(0.0);
98			frameData.bBox = Mat3x3d(0.0);
99			frameData.invBbox = Mat3x3d(0.0);
100	gezelter	1782	frameData.orthoRhombic = false;
101			frameData.bondPotential = 0.0;
102			frameData.bendPotential = 0.0;
103			frameData.torsionPotential = 0.0;
104			frameData.inversionPotential = 0.0;
105			frameData.lrPotentials = potVec(0.0);
106			frameData.excludedPotentials = potVec(0.0);
107			frameData.restraintPotential = 0.0;
108			frameData.rawPotential = 0.0;
109			frameData.xyArea = 0.0;
110			frameData.volume = 0.0;
111			frameData.thermostat = make_pair(0.0, 0.0);
112			frameData.electronicThermostat = make_pair(0.0, 0.0);
113			frameData.barostat = Mat3x3d(0.0);
114			frameData.stressTensor = Mat3x3d(0.0);
115			frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
116	gezelter	246
117	gezelter	1782	clearDerivedProperties();
118			}
119
120			void Snapshot::clearDerivedProperties() {
121			frameData.totalEnergy = 0.0;
122			frameData.translationalKinetic = 0.0;
123			frameData.rotationalKinetic = 0.0;
124			frameData.kineticEnergy = 0.0;
125			frameData.potentialEnergy = 0.0;
126			frameData.shortRangePotential = 0.0;
127			frameData.longRangePotential = 0.0;
128			frameData.pressure = 0.0;
129			frameData.temperature = 0.0;
130			frameData.pressureTensor = Mat3x3d(0.0);
131			frameData.systemDipole = Vector3d(0.0);
132			frameData.convectiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
133			frameData.electronicTemperature = 0.0;
134			frameData.COM = V3Zero;
135			frameData.COMvel = V3Zero;
136	gezelter	1879	frameData.COMw = V3Zero;
137	gezelter	1782
138			hasTotalEnergy = false;
139			hasTranslationalKineticEnergy = false;
140			hasRotationalKineticEnergy = false;
141			hasKineticEnergy = false;
142			hasShortRangePotential = false;
143			hasLongRangePotential = false;
144			hasPotentialEnergy = false;
145			hasXYarea = false;
146			hasVolume = false;
147			hasPressure = false;
148			hasTemperature = false;
149			hasElectronicTemperature = false;
150			hasCOM = false;
151			hasCOMvel = false;
152			hasCOMw = false;
153			hasPressureTensor = false;
154			hasSystemDipole = false;
155			hasConvectiveHeatFlux = false;
156			hasInertiaTensor = false;
157			hasGyrationalVolume = false;
158			hasHullVolume = false;
159			hasConservedQuantity = false;
160	gezelter	1879	hasBoundingBox = false;
161	gezelter	1782	}
162
163			/** Returns the id of this Snapshot */
164			int Snapshot::getID() {
165			return frameData.id;
166			}
167
168			/** Sets the id of this Snapshot */
169			void Snapshot::setID(int id) {
170			frameData.id = id;
171			}
172
173			int Snapshot::getSize() {
174			return atomData.getSize() + rigidbodyData.getSize();
175			}
176
177			/** Returns the number of atoms */
178			int Snapshot::getNumberOfAtoms() {
179			return atomData.getSize();
180			}
181
182			/** Returns the number of rigid bodies */
183			int Snapshot::getNumberOfRigidBodies() {
184			return rigidbodyData.getSize();
185			}
186
187			/** Returns the number of rigid bodies */
188			int Snapshot::getNumberOfCutoffGroups() {
189			return cgData.getSize();
190			}
191
192			/** Returns the H-Matrix */
193			Mat3x3d Snapshot::getHmat() {
194			return frameData.hmat;
195			}
196
197			/** Sets the H-Matrix */
198			void Snapshot::setHmat(const Mat3x3d& m) {
199			hasVolume = false;
200			frameData.hmat = m;
201			frameData.invHmat = frameData.hmat.inverse();
202
203	gezelter	246	//determine whether the box is orthoTolerance or not
204	gezelter	1782	bool oldOrthoRhombic = frameData.orthoRhombic;
205	gezelter	246
206	gezelter	1782	RealType smallDiag = fabs(frameData.hmat(0, 0));
207			if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
208			if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));
209	gezelter	1021	RealType tol = smallDiag * orthoTolerance_;
210	gezelter	246
211	gezelter	1782	frameData.orthoRhombic = true;
212	gezelter	246
213			for (int i = 0; i < 3; i++ ) {
214	gezelter	507	for (int j = 0 ; j < 3; j++) {
215			if (i != j) {
216	gezelter	1782	if (frameData.orthoRhombic) {
217			if ( fabs(frameData.hmat(i, j)) >= tol)
218			frameData.orthoRhombic = false;
219	gezelter	507	}
220			}
221			}
222	gezelter	246	}
223	gezelter	1782
224			if( oldOrthoRhombic != frameData.orthoRhombic){
225
226	gezelter	1879	// It is finally time to suppress these warnings once and for
227			// all. They were annoying and not very informative.
228
229			// if( frameData.orthoRhombic ) {
230			// sprintf( painCave.errMsg,
231			// "OpenMD is switching from the default Non-Orthorhombic\n"
232			// "\tto the faster Orthorhombic periodic boundary computations.\n"
233			// "\tThis is usually a good thing, but if you want the\n"
234			// "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
235			// "\tvariable ( currently set to %G ) smaller.\n",
236			// orthoTolerance_);
237			// painCave.severity = OPENMD_INFO;
238			// simError();
239			// }
240			// else {
241			// sprintf( painCave.errMsg,
242			// "OpenMD is switching from the faster Orthorhombic to the more\n"
243			// "\tflexible Non-Orthorhombic periodic boundary computations.\n"
244			// "\tThis is usually because the box has deformed under\n"
245			// "\tNPTf integration. If you want to live on the edge with\n"
246			// "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
247			// "\tvariable ( currently set to %G ) larger.\n",
248			// orthoTolerance_);
249			// painCave.severity = OPENMD_WARNING;
250			// simError();
251			// }
252	gezelter	246	}
253	gezelter	1782	}
254
255			/** Returns the inverse H-Matrix */
256			Mat3x3d Snapshot::getInvHmat() {
257			return frameData.invHmat;
258			}
259	gezelter	246
260	gezelter	1879	/** Returns the Bounding Box */
261			Mat3x3d Snapshot::getBoundingBox() {
262			return frameData.bBox;
263			}
264
265			/** Sets the Bounding Box */
266			void Snapshot::setBoundingBox(const Mat3x3d& m) {
267			frameData.bBox = m;
268			frameData.invBbox = frameData.bBox.inverse();
269			hasBoundingBox = true;
270			}
271
272			/** Returns the inverse Bounding Box */
273			Mat3x3d Snapshot::getInvBoundingBox() {
274			return frameData.invBbox;
275			}
276
277	gezelter	1782	RealType Snapshot::getXYarea() {
278			if (!hasXYarea) {
279			Vector3d x = frameData.hmat.getColumn(0);
280			Vector3d y = frameData.hmat.getColumn(1);
281			frameData.xyArea = cross(x,y).length();
282			hasXYarea = true;
283			}
284			return frameData.xyArea;
285	gezelter	507	}
286	gezelter	246
287	gezelter	1782	RealType Snapshot::getVolume() {
288			if (!hasVolume) {
289			frameData.volume = frameData.hmat.determinant();
290			hasVolume = true;
291			}
292			return frameData.volume;
293			}
294	gezelter	246
295	gezelter	1782	void Snapshot::setVolume(RealType vol) {
296			hasVolume = true;
297			frameData.volume = vol;
298			}
299
300	gezelter	1896
301	gezelter	1782	/** Wrap a vector according to periodic boundary conditions */
302	gezelter	507	void Snapshot::wrapVector(Vector3d& pos) {
303	gezelter	1782
304	gezelter	1895	if( !frameData.orthoRhombic ) {
305			Vector3d scaled = frameData.invHmat * pos;
306	gezelter	1896	for (int i = 0; i < 3; i++) {
307			scaled[i] -= roundMe( scaled[i] );
308			}
309	gezelter	1782	// calc the wrapped real coordinates from the wrapped scaled coordinates
310	gezelter	1895	pos = frameData.hmat * scaled;
311			} else {
312			RealType scaled;
313	gezelter	1896	for (int i=0; i<3; i++) {
314			scaled = pos[i] * frameData.invHmat(i,i);
315			scaled -= roundMe( scaled );
316			pos[i] = scaled * frameData.hmat(i,i);
317	gezelter	1895	}
318	gezelter	1782	}
319			}
320	gezelter	246
321	gezelter	1782	/** Scaling a vector to multiples of the periodic box */
322			inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
323
324	gezelter	246	Vector3d scaled;
325
326	gezelter	1782	if( !frameData.orthoRhombic )
327			scaled = frameData.invHmat * pos;
328			else {
329	gezelter	507	// calc the scaled coordinates.
330	gezelter	1782	for (int i=0; i<3; i++)
331			scaled[i] = pos[i] * frameData.invHmat(i, i);
332			}
333	gezelter	246
334	gezelter	1782	return scaled;
335			}
336	gezelter	246
337	gezelter	1782	void Snapshot::setCOM(const Vector3d& com) {
338			frameData.COM = com;
339			hasCOM = true;
340			}
341
342			void Snapshot::setCOMvel(const Vector3d& comVel) {
343			frameData.COMvel = comVel;
344			hasCOMvel = true;
345			}
346
347			void Snapshot::setCOMw(const Vector3d& comw) {
348			frameData.COMw = comw;
349			hasCOMw = true;
350			}
351
352			Vector3d Snapshot::getCOM() {
353			return frameData.COM;
354			}
355
356			Vector3d Snapshot::getCOMvel() {
357			return frameData.COMvel;
358			}
359
360			Vector3d Snapshot::getCOMw() {
361			return frameData.COMw;
362			}
363
364			RealType Snapshot::getTime() {
365			return frameData.currentTime;
366			}
367
368			void Snapshot::increaseTime(RealType dt) {
369			setTime(getTime() + dt);
370			}
371
372			void Snapshot::setTime(RealType time) {
373			frameData.currentTime = time;
374			}
375
376			void Snapshot::setBondPotential(RealType bp) {
377			frameData.bondPotential = bp;
378			}
379
380			void Snapshot::setBendPotential(RealType bp) {
381			frameData.bendPotential = bp;
382			}
383
384			void Snapshot::setTorsionPotential(RealType tp) {
385			frameData.torsionPotential = tp;
386			}
387
388			void Snapshot::setInversionPotential(RealType ip) {
389			frameData.inversionPotential = ip;
390			}
391	gezelter	246
392
393	gezelter	1782	RealType Snapshot::getBondPotential() {
394			return frameData.bondPotential;
395			}
396			RealType Snapshot::getBendPotential() {
397			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	gezelter	246	}
414	gezelter	1782	return frameData.shortRangePotential;
415			}
416	gezelter	246
417	gezelter	1782	void Snapshot::setLongRangePotential(potVec lrPot) {
418			frameData.lrPotentials = lrPot;
419	gezelter	507	}
420	gezelter	1782
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	gezelter	246
431	gezelter	1782	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	gezelter	1104	}
441	gezelter	1782	return frameData.potentialEnergy;
442	gezelter	1104	}
443	gezelter	1782
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	gezelter	1104
456	gezelter	1782	RealType Snapshot::getRestraintPotential() {
457			return frameData.restraintPotential;
458	gezelter	1104	}
459
460	gezelter	1782	void Snapshot::setRawPotential(RealType rp) {
461			frameData.rawPotential = rp;
462	gezelter	1104	}
463	gezelter	1782
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	gezelter	1104
605	gezelter	1782	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	gezelter	246	}