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 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:	1925
Committed:	Wed Aug 7 15:24:16 2013 UTC (11 years, 8 months ago) by gezelter
File size:	19324 byte(s)
Log Message:	More ewald fixes, reporting reciprocal potential in stats.
#	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
194			/** Returns the H-Matrix */
195			Mat3x3d Snapshot::getHmat() {
196			return frameData.hmat;
197			}
198
199			/** Sets the H-Matrix */
200			void Snapshot::setHmat(const Mat3x3d& m) {
201			hasVolume = false;
202			frameData.hmat = m;
203			frameData.invHmat = frameData.hmat.inverse();
204
205	gezelter	246	//determine whether the box is orthoTolerance or not
206	gezelter	1782	bool oldOrthoRhombic = frameData.orthoRhombic;
207	gezelter	246
208	gezelter	1782	RealType smallDiag = fabs(frameData.hmat(0, 0));
209			if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
210			if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));
211	gezelter	1021	RealType tol = smallDiag * orthoTolerance_;
212	gezelter	246
213	gezelter	1782	frameData.orthoRhombic = true;
214	gezelter	246
215			for (int i = 0; i < 3; i++ ) {
216	gezelter	507	for (int j = 0 ; j < 3; j++) {
217			if (i != j) {
218	gezelter	1782	if (frameData.orthoRhombic) {
219			if ( fabs(frameData.hmat(i, j)) >= tol)
220			frameData.orthoRhombic = false;
221	gezelter	507	}
222			}
223			}
224	gezelter	246	}
225	gezelter	1782
226			if( oldOrthoRhombic != frameData.orthoRhombic){
227
228	gezelter	1879	// It is finally time to suppress these warnings once and for
229			// all. They were annoying and not very informative.
230
231			// if( frameData.orthoRhombic ) {
232			// sprintf( painCave.errMsg,
233			// "OpenMD is switching from the default Non-Orthorhombic\n"
234			// "\tto the faster Orthorhombic periodic boundary computations.\n"
235			// "\tThis is usually a good thing, but if you want the\n"
236			// "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
237			// "\tvariable ( currently set to %G ) smaller.\n",
238			// orthoTolerance_);
239			// painCave.severity = OPENMD_INFO;
240			// simError();
241			// }
242			// else {
243			// sprintf( painCave.errMsg,
244			// "OpenMD is switching from the faster Orthorhombic to the more\n"
245			// "\tflexible Non-Orthorhombic periodic boundary computations.\n"
246			// "\tThis is usually because the box has deformed under\n"
247			// "\tNPTf integration. If you want to live on the edge with\n"
248			// "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
249			// "\tvariable ( currently set to %G ) larger.\n",
250			// orthoTolerance_);
251			// painCave.severity = OPENMD_WARNING;
252			// simError();
253			// }
254	gezelter	246	}
255	gezelter	1782	}
256
257			/** Returns the inverse H-Matrix */
258			Mat3x3d Snapshot::getInvHmat() {
259			return frameData.invHmat;
260			}
261	gezelter	246
262	gezelter	1879	/** Returns the Bounding Box */
263			Mat3x3d Snapshot::getBoundingBox() {
264			return frameData.bBox;
265			}
266
267			/** Sets the Bounding Box */
268			void Snapshot::setBoundingBox(const Mat3x3d& m) {
269			frameData.bBox = m;
270			frameData.invBbox = frameData.bBox.inverse();
271			hasBoundingBox = true;
272			}
273
274			/** Returns the inverse Bounding Box */
275			Mat3x3d Snapshot::getInvBoundingBox() {
276			return frameData.invBbox;
277			}
278
279	gezelter	1782	RealType Snapshot::getXYarea() {
280			if (!hasXYarea) {
281			Vector3d x = frameData.hmat.getColumn(0);
282			Vector3d y = frameData.hmat.getColumn(1);
283			frameData.xyArea = cross(x,y).length();
284			hasXYarea = true;
285			}
286			return frameData.xyArea;
287	gezelter	507	}
288	gezelter	246
289	gezelter	1782	RealType Snapshot::getVolume() {
290			if (!hasVolume) {
291			frameData.volume = frameData.hmat.determinant();
292			hasVolume = true;
293			}
294			return frameData.volume;
295			}
296	gezelter	246
297	gezelter	1782	void Snapshot::setVolume(RealType vol) {
298			hasVolume = true;
299			frameData.volume = vol;
300			}
301
302	gezelter	1896
303	gezelter	1782	/** Wrap a vector according to periodic boundary conditions */
304	gezelter	507	void Snapshot::wrapVector(Vector3d& pos) {
305	gezelter	1782
306	gezelter	1895	if( !frameData.orthoRhombic ) {
307			Vector3d scaled = frameData.invHmat * pos;
308	gezelter	1896	for (int i = 0; i < 3; i++) {
309			scaled[i] -= roundMe( scaled[i] );
310			}
311	gezelter	1782	// calc the wrapped real coordinates from the wrapped scaled coordinates
312	gezelter	1895	pos = frameData.hmat * scaled;
313			} else {
314			RealType scaled;
315	gezelter	1896	for (int i=0; i<3; i++) {
316			scaled = pos[i] * frameData.invHmat(i,i);
317			scaled -= roundMe( scaled );
318			pos[i] = scaled * frameData.hmat(i,i);
319	gezelter	1895	}
320	gezelter	1782	}
321			}
322	gezelter	246
323	gezelter	1782	/** Scaling a vector to multiples of the periodic box */
324			inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
325
326	gezelter	246	Vector3d scaled;
327
328	gezelter	1782	if( !frameData.orthoRhombic )
329			scaled = frameData.invHmat * pos;
330			else {
331	gezelter	507	// calc the scaled coordinates.
332	gezelter	1782	for (int i=0; i<3; i++)
333			scaled[i] = pos[i] * frameData.invHmat(i, i);
334			}
335	gezelter	246
336	gezelter	1782	return scaled;
337			}
338	gezelter	246
339	gezelter	1782	void Snapshot::setCOM(const Vector3d& com) {
340			frameData.COM = com;
341			hasCOM = true;
342			}
343
344			void Snapshot::setCOMvel(const Vector3d& comVel) {
345			frameData.COMvel = comVel;
346			hasCOMvel = true;
347			}
348
349			void Snapshot::setCOMw(const Vector3d& comw) {
350			frameData.COMw = comw;
351			hasCOMw = true;
352			}
353
354			Vector3d Snapshot::getCOM() {
355			return frameData.COM;
356			}
357
358			Vector3d Snapshot::getCOMvel() {
359			return frameData.COMvel;
360			}
361
362			Vector3d Snapshot::getCOMw() {
363			return frameData.COMw;
364			}
365
366			RealType Snapshot::getTime() {
367			return frameData.currentTime;
368			}
369
370			void Snapshot::increaseTime(RealType dt) {
371			setTime(getTime() + dt);
372			}
373
374			void Snapshot::setTime(RealType time) {
375			frameData.currentTime = time;
376			}
377
378			void Snapshot::setBondPotential(RealType bp) {
379			frameData.bondPotential = bp;
380			}
381
382			void Snapshot::setBendPotential(RealType bp) {
383			frameData.bendPotential = bp;
384			}
385
386			void Snapshot::setTorsionPotential(RealType tp) {
387			frameData.torsionPotential = tp;
388			}
389
390			void Snapshot::setInversionPotential(RealType ip) {
391			frameData.inversionPotential = ip;
392			}
393	gezelter	246
394
395	gezelter	1782	RealType Snapshot::getBondPotential() {
396			return frameData.bondPotential;
397			}
398			RealType Snapshot::getBendPotential() {
399			return frameData.bendPotential;
400			}
401			RealType Snapshot::getTorsionPotential() {
402			return frameData.torsionPotential;
403			}
404			RealType Snapshot::getInversionPotential() {
405			return frameData.inversionPotential;
406			}
407
408			RealType Snapshot::getShortRangePotential() {
409			if (!hasShortRangePotential) {
410			frameData.shortRangePotential = frameData.bondPotential;
411			frameData.shortRangePotential += frameData.bendPotential;
412			frameData.shortRangePotential += frameData.torsionPotential;
413			frameData.shortRangePotential += frameData.inversionPotential;
414			hasShortRangePotential = true;
415	gezelter	246	}
416	gezelter	1782	return frameData.shortRangePotential;
417			}
418	gezelter	246
419	gezelter	1925	void Snapshot::setReciprocalPotential(RealType rp){
420			frameData.reciprocalPotential = rp;
421			}
422
423			RealType Snapshot::getReciprocalPotential() {
424			return frameData.reciprocalPotential;
425			}
426
427	gezelter	1782	void Snapshot::setLongRangePotential(potVec lrPot) {
428			frameData.lrPotentials = lrPot;
429	gezelter	507	}
430	gezelter	1782
431			RealType Snapshot::getLongRangePotential() {
432			if (!hasLongRangePotential) {
433			for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
434			frameData.longRangePotential += frameData.lrPotentials[i];
435			}
436	gezelter	1925	frameData.longRangePotential += frameData.reciprocalPotential;
437	gezelter	1782	hasLongRangePotential = true;
438			}
439			return frameData.longRangePotential;
440			}
441	gezelter	246
442	gezelter	1782	potVec Snapshot::getLongRangePotentials() {
443			return frameData.lrPotentials;
444			}
445
446			RealType Snapshot::getPotentialEnergy() {
447			if (!hasPotentialEnergy) {
448			frameData.potentialEnergy = this->getLongRangePotential();
449			frameData.potentialEnergy += this->getShortRangePotential();
450			hasPotentialEnergy = true;
451	gezelter	1104	}
452	gezelter	1782	return frameData.potentialEnergy;
453	gezelter	1104	}
454	gezelter	1782
455			void Snapshot::setExcludedPotentials(potVec exPot) {
456			frameData.excludedPotentials = exPot;
457			}
458
459			potVec Snapshot::getExcludedPotentials() {
460			return frameData.excludedPotentials;
461			}
462
463			void Snapshot::setRestraintPotential(RealType rp) {
464			frameData.restraintPotential = rp;
465			}
466	gezelter	1104
467	gezelter	1782	RealType Snapshot::getRestraintPotential() {
468			return frameData.restraintPotential;
469	gezelter	1104	}
470
471	gezelter	1782	void Snapshot::setRawPotential(RealType rp) {
472			frameData.rawPotential = rp;
473	gezelter	1104	}
474	gezelter	1782
475			RealType Snapshot::getRawPotential() {
476			return frameData.rawPotential;
477			}
478
479			RealType Snapshot::getTranslationalKineticEnergy() {
480			return frameData.translationalKinetic;
481			}
482
483			RealType Snapshot::getRotationalKineticEnergy() {
484			return frameData.rotationalKinetic;
485			}
486
487			RealType Snapshot::getKineticEnergy() {
488			return frameData.kineticEnergy;
489			}
490
491			void Snapshot::setTranslationalKineticEnergy(RealType tke) {
492			hasTranslationalKineticEnergy = true;
493			frameData.translationalKinetic = tke;
494			}
495
496			void Snapshot::setRotationalKineticEnergy(RealType rke) {
497			hasRotationalKineticEnergy = true;
498			frameData.rotationalKinetic = rke;
499			}
500
501			void Snapshot::setKineticEnergy(RealType ke) {
502			hasKineticEnergy = true;
503			frameData.kineticEnergy = ke;
504			}
505
506			RealType Snapshot::getTotalEnergy() {
507			return frameData.totalEnergy;
508			}
509
510			void Snapshot::setTotalEnergy(RealType te) {
511			hasTotalEnergy = true;
512			frameData.totalEnergy = te;
513			}
514
515			RealType Snapshot::getConservedQuantity() {
516			return frameData.conservedQuantity;
517			}
518
519			void Snapshot::setConservedQuantity(RealType cq) {
520			hasConservedQuantity = true;
521			frameData.conservedQuantity = cq;
522			}
523
524			RealType Snapshot::getTemperature() {
525			return frameData.temperature;
526			}
527
528			void Snapshot::setTemperature(RealType temp) {
529			hasTemperature = true;
530			frameData.temperature = temp;
531			}
532
533			RealType Snapshot::getElectronicTemperature() {
534			return frameData.electronicTemperature;
535			}
536
537			void Snapshot::setElectronicTemperature(RealType eTemp) {
538			hasElectronicTemperature = true;
539			frameData.electronicTemperature = eTemp;
540			}
541
542			RealType Snapshot::getPressure() {
543			return frameData.pressure;
544			}
545
546			void Snapshot::setPressure(RealType pressure) {
547			hasPressure = true;
548			frameData.pressure = pressure;
549			}
550
551			Mat3x3d Snapshot::getPressureTensor() {
552			return frameData.pressureTensor;
553			}
554
555
556			void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) {
557			hasPressureTensor = true;
558			frameData.pressureTensor = pressureTensor;
559			}
560
561			void Snapshot::setStressTensor(const Mat3x3d& stressTensor) {
562			frameData.stressTensor = stressTensor;
563			}
564
565			Mat3x3d Snapshot::getStressTensor() {
566			return frameData.stressTensor;
567			}
568
569			void Snapshot::setConductiveHeatFlux(const Vector3d& chf) {
570			frameData.conductiveHeatFlux = chf;
571			}
572
573			Vector3d Snapshot::getConductiveHeatFlux() {
574			return frameData.conductiveHeatFlux;
575			}
576
577			Vector3d Snapshot::getConvectiveHeatFlux() {
578			return frameData.convectiveHeatFlux;
579			}
580
581			void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) {
582			hasConvectiveHeatFlux = true;
583			frameData.convectiveHeatFlux = chf;
584			}
585
586			Vector3d Snapshot::getHeatFlux() {
587			// BE CAREFUL WITH UNITS
588			return getConductiveHeatFlux() + getConvectiveHeatFlux();
589			}
590
591			Vector3d Snapshot::getSystemDipole() {
592			return frameData.systemDipole;
593			}
594
595			void Snapshot::setSystemDipole(const Vector3d& bd) {
596			hasSystemDipole = true;
597			frameData.systemDipole = bd;
598			}
599
600			void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) {
601			frameData.thermostat = thermostat;
602			}
603
604			pair<RealType, RealType> Snapshot::getThermostat() {
605			return frameData.thermostat;
606			}
607
608			void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) {
609			frameData.electronicThermostat = eTherm;
610			}
611
612			pair<RealType, RealType> Snapshot::getElectronicThermostat() {
613			return frameData.electronicThermostat;
614			}
615	gezelter	1104
616	gezelter	1782	void Snapshot::setBarostat(const Mat3x3d& barostat) {
617			frameData.barostat = barostat;
618			}
619
620			Mat3x3d Snapshot::getBarostat() {
621			return frameData.barostat;
622			}
623
624			void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) {
625			frameData.inertiaTensor = inertiaTensor;
626			hasInertiaTensor = true;
627			}
628
629			Mat3x3d Snapshot::getInertiaTensor() {
630			return frameData.inertiaTensor;
631			}
632
633			void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) {
634			frameData.gyrationalVolume = gyrationalVolume;
635			hasGyrationalVolume = true;
636			}
637
638			RealType Snapshot::getGyrationalVolume() {
639			return frameData.gyrationalVolume;
640			}
641
642			void Snapshot::setHullVolume(const RealType hullVolume) {
643			frameData.hullVolume = hullVolume;
644			hasHullVolume = true;
645			}
646
647			RealType Snapshot::getHullVolume() {
648			return frameData.hullVolume;
649			}
650
651			void Snapshot::setOrthoTolerance(RealType ot) {
652			orthoTolerance_ = ot;
653			}
654	gezelter	246	}