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; 
  }

  /** 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();
  }

  /** 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) {
    
    Vector3d scaled = scaleVector(pos);
    
    for (int i = 0; i < 3; i++) 
      scaled[i] -= roundMe(scaled[i]);
    
    if( !frameData.orthoRhombic )
      pos = frameData.hmat * scaled;    
    else {
      
      // calc the wrapped real coordinates from the wrapped scaled coordinates
      for (int i=0; i<3; i++) {
        pos[i] = scaled[i] * 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:	1858
Committed:	Wed Apr 3 21:32:13 2013 UTC (12 years, 1 month ago) by gezelter
File size:	18792 byte(s)
Log Message:	Some bugfixes for cell-linked-list-style neighbor lists when the simulation doesn't use periodic boundary conditions. Cleaning up some of the Hull stuff while we're in there.
#	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	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [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	1764	Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups) :
59			atomData(nAtoms), rigidbodyData(nRigidbodies),
60			cgData(nCutoffGroups, DataStorage::dslPosition),
61			orthoTolerance_(1e-6) {
62
63			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	gezelter	1774	frameData.rawPotential = 0.0;
76			frameData.xyArea = 0.0;
77	gezelter	1764	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
84			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	1858	frameData.invHmat = Mat3x3d(0.0);
98			frameData.bBox = Mat3x3d(0.0);
99			frameData.invBbox = Mat3x3d(0.0);
100	gezelter	1764	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	gezelter	1774	frameData.xyArea = 0.0;
110	gezelter	1764	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
117			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	1858	frameData.COMw = V3Zero;
137	gezelter	1764
138			hasTotalEnergy = false;
139			hasTranslationalKineticEnergy = false;
140			hasRotationalKineticEnergy = false;
141			hasKineticEnergy = false;
142			hasShortRangePotential = false;
143			hasLongRangePotential = false;
144	gezelter	1774	hasPotentialEnergy = false;
145			hasXYarea = false;
146	gezelter	1764	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			}
161
162			/** Returns the id of this Snapshot */
163			int Snapshot::getID() {
164			return frameData.id;
165			}
166
167			/** Sets the id of this Snapshot */
168			void Snapshot::setID(int id) {
169			frameData.id = id;
170			}
171
172			int Snapshot::getSize() {
173			return atomData.getSize() + rigidbodyData.getSize();
174			}
175
176			/** Returns the number of atoms */
177			int Snapshot::getNumberOfAtoms() {
178			return atomData.getSize();
179			}
180
181			/** Returns the number of rigid bodies */
182			int Snapshot::getNumberOfRigidBodies() {
183			return rigidbodyData.getSize();
184			}
185
186			/** Returns the number of rigid bodies */
187			int Snapshot::getNumberOfCutoffGroups() {
188			return cgData.getSize();
189			}
190
191			/** Returns the H-Matrix */
192			Mat3x3d Snapshot::getHmat() {
193			return frameData.hmat;
194			}
195
196			/** Sets the H-Matrix */
197			void Snapshot::setHmat(const Mat3x3d& m) {
198			hasVolume = false;
199	gezelter	1715	frameData.hmat = m;
200			frameData.invHmat = frameData.hmat.inverse();
201	gezelter	246
202			//determine whether the box is orthoTolerance or not
203	gezelter	1715	bool oldOrthoRhombic = frameData.orthoRhombic;
204	gezelter	246
205	gezelter	1715	RealType smallDiag = fabs(frameData.hmat(0, 0));
206			if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
207			if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));
208	gezelter	1021	RealType tol = smallDiag * orthoTolerance_;
209	gezelter	246
210	gezelter	1715	frameData.orthoRhombic = true;
211	gezelter	246
212			for (int i = 0; i < 3; i++ ) {
213	gezelter	507	for (int j = 0 ; j < 3; j++) {
214			if (i != j) {
215	gezelter	1715	if (frameData.orthoRhombic) {
216			if ( fabs(frameData.hmat(i, j)) >= tol)
217			frameData.orthoRhombic = false;
218	gezelter	507	}
219			}
220			}
221	gezelter	246	}
222	gezelter	1764
223	gezelter	1715	if( oldOrthoRhombic != frameData.orthoRhombic){
224	gezelter	1764
225	gezelter	1838	// It is finally time to suppress these warnings once and for
226			// all. They were annoying and not very informative.
227
228			// if( frameData.orthoRhombic ) {
229			// sprintf( painCave.errMsg,
230			// "OpenMD is switching from the default Non-Orthorhombic\n"
231			// "\tto the faster Orthorhombic periodic boundary computations.\n"
232			// "\tThis is usually a good thing, but if you want the\n"
233			// "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
234			// "\tvariable ( currently set to %G ) smaller.\n",
235			// orthoTolerance_);
236			// painCave.severity = OPENMD_INFO;
237			// simError();
238			// }
239			// else {
240			// sprintf( painCave.errMsg,
241			// "OpenMD is switching from the faster Orthorhombic to the more\n"
242			// "\tflexible Non-Orthorhombic periodic boundary computations.\n"
243			// "\tThis is usually because the box has deformed under\n"
244			// "\tNPTf integration. If you want to live on the edge with\n"
245			// "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
246			// "\tvariable ( currently set to %G ) larger.\n",
247			// orthoTolerance_);
248			// painCave.severity = OPENMD_WARNING;
249			// simError();
250			// }
251	gezelter	246	}
252	gezelter	507	}
253	gezelter	1764
254			/** Returns the inverse H-Matrix */
255			Mat3x3d Snapshot::getInvHmat() {
256			return frameData.invHmat;
257			}
258	gezelter	246
259	gezelter	1858	/** Returns the Bounding Box */
260			Mat3x3d Snapshot::getBoundingBox() {
261			return frameData.bBox;
262			}
263
264			/** Sets the Bounding Box */
265			void Snapshot::setBoundingBox(const Mat3x3d& m) {
266			frameData.bBox = m;
267			frameData.invBbox = frameData.bBox.inverse();
268			}
269
270			/** Returns the inverse Bounding Box */
271			Mat3x3d Snapshot::getInvBoundingBox() {
272			return frameData.invBbox;
273			}
274
275	gezelter	1774	RealType Snapshot::getXYarea() {
276			if (!hasXYarea) {
277			Vector3d x = frameData.hmat.getColumn(0);
278			Vector3d y = frameData.hmat.getColumn(1);
279			frameData.xyArea = cross(x,y).length();
280			hasXYarea = true;
281			}
282			return frameData.xyArea;
283			}
284
285	gezelter	1764	RealType Snapshot::getVolume() {
286			if (!hasVolume) {
287			frameData.volume = frameData.hmat.determinant();
288			hasVolume = true;
289			}
290			return frameData.volume;
291			}
292	gezelter	246
293	gezelter	1764	void Snapshot::setVolume(RealType vol) {
294			hasVolume = true;
295			frameData.volume = vol;
296			}
297
298			/** Wrap a vector according to periodic boundary conditions */
299	gezelter	1568	void Snapshot::wrapVector(Vector3d& pos) {
300	gezelter	1562
301			Vector3d scaled = scaleVector(pos);
302	gezelter	1568
303	gezelter	1562	for (int i = 0; i < 3; i++)
304			scaled[i] -= roundMe(scaled[i]);
305	gezelter	1764
306	gezelter	1715	if( !frameData.orthoRhombic )
307			pos = frameData.hmat * scaled;
308	gezelter	1562	else {
309	gezelter	1764
310	gezelter	507	// calc the wrapped real coordinates from the wrapped scaled coordinates
311	gezelter	1562	for (int i=0; i<3; i++) {
312	gezelter	1715	pos[i] = scaled[i] * frameData.hmat(i, i);
313	gezelter	1540	}
314	gezelter	246	}
315	gezelter	507	}
316	gezelter	246
317	gezelter	1764	/** Scaling a vector to multiples of the periodic box */
318	gezelter	1562	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
319
320			Vector3d scaled;
321
322	gezelter	1715	if( !frameData.orthoRhombic )
323			scaled = frameData.invHmat * pos;
324	gezelter	1562	else {
325			// calc the scaled coordinates.
326			for (int i=0; i<3; i++)
327	gezelter	1715	scaled[i] = pos[i] * frameData.invHmat(i, i);
328	gezelter	1562	}
329
330			return scaled;
331			}
332	gezelter	1764
333			void Snapshot::setCOM(const Vector3d& com) {
334			frameData.COM = com;
335			hasCOM = true;
336			}
337	gezelter	1562
338	gezelter	1764	void Snapshot::setCOMvel(const Vector3d& comVel) {
339			frameData.COMvel = comVel;
340			hasCOMvel = true;
341			}
342
343			void Snapshot::setCOMw(const Vector3d& comw) {
344			frameData.COMw = comw;
345			hasCOMw = true;
346			}
347
348	gezelter	1104	Vector3d Snapshot::getCOM() {
349	gezelter	1715	return frameData.COM;
350	gezelter	1104	}
351
352			Vector3d Snapshot::getCOMvel() {
353	gezelter	1715	return frameData.COMvel;
354	gezelter	1104	}
355
356			Vector3d Snapshot::getCOMw() {
357	gezelter	1715	return frameData.COMw;
358	gezelter	1104	}
359	gezelter	1764
360			RealType Snapshot::getTime() {
361			return frameData.currentTime;
362			}
363
364			void Snapshot::increaseTime(RealType dt) {
365			setTime(getTime() + dt);
366			}
367
368			void Snapshot::setTime(RealType time) {
369			frameData.currentTime = time;
370			}
371
372			void Snapshot::setBondPotential(RealType bp) {
373			frameData.bondPotential = bp;
374			}
375
376			void Snapshot::setBendPotential(RealType bp) {
377			frameData.bendPotential = bp;
378			}
379
380			void Snapshot::setTorsionPotential(RealType tp) {
381			frameData.torsionPotential = tp;
382			}
383
384			void Snapshot::setInversionPotential(RealType ip) {
385			frameData.inversionPotential = ip;
386			}
387
388
389			RealType Snapshot::getBondPotential() {
390			return frameData.bondPotential;
391			}
392			RealType Snapshot::getBendPotential() {
393			return frameData.bendPotential;
394			}
395			RealType Snapshot::getTorsionPotential() {
396			return frameData.torsionPotential;
397			}
398			RealType Snapshot::getInversionPotential() {
399			return frameData.inversionPotential;
400			}
401
402			RealType Snapshot::getShortRangePotential() {
403			if (!hasShortRangePotential) {
404			frameData.shortRangePotential = frameData.bondPotential;
405			frameData.shortRangePotential += frameData.bendPotential;
406			frameData.shortRangePotential += frameData.torsionPotential;
407			frameData.shortRangePotential += frameData.inversionPotential;
408			hasShortRangePotential = true;
409			}
410			return frameData.shortRangePotential;
411			}
412
413			void Snapshot::setLongRangePotential(potVec lrPot) {
414			frameData.lrPotentials = lrPot;
415			}
416
417			RealType Snapshot::getLongRangePotential() {
418			if (!hasLongRangePotential) {
419			for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
420			frameData.longRangePotential += frameData.lrPotentials[i];
421			}
422			hasLongRangePotential = true;
423			}
424			return frameData.longRangePotential;
425			}
426
427			potVec Snapshot::getLongRangePotentials() {
428			return frameData.lrPotentials;
429			}
430
431			RealType Snapshot::getPotentialEnergy() {
432			if (!hasPotentialEnergy) {
433			frameData.potentialEnergy = this->getLongRangePotential();
434			frameData.potentialEnergy += this->getShortRangePotential();
435			hasPotentialEnergy = true;
436			}
437			return frameData.potentialEnergy;
438			}
439
440			void Snapshot::setExcludedPotentials(potVec exPot) {
441			frameData.excludedPotentials = exPot;
442			}
443
444			potVec Snapshot::getExcludedPotentials() {
445			return frameData.excludedPotentials;
446			}
447
448			void Snapshot::setRestraintPotential(RealType rp) {
449			frameData.restraintPotential = rp;
450			}
451
452			RealType Snapshot::getRestraintPotential() {
453			return frameData.restraintPotential;
454			}
455
456			void Snapshot::setRawPotential(RealType rp) {
457			frameData.rawPotential = rp;
458			}
459
460			RealType Snapshot::getRawPotential() {
461			return frameData.rawPotential;
462			}
463
464			RealType Snapshot::getTranslationalKineticEnergy() {
465			return frameData.translationalKinetic;
466			}
467
468			RealType Snapshot::getRotationalKineticEnergy() {
469			return frameData.rotationalKinetic;
470			}
471
472			RealType Snapshot::getKineticEnergy() {
473			return frameData.kineticEnergy;
474			}
475
476			void Snapshot::setTranslationalKineticEnergy(RealType tke) {
477			hasTranslationalKineticEnergy = true;
478			frameData.translationalKinetic = tke;
479			}
480
481			void Snapshot::setRotationalKineticEnergy(RealType rke) {
482			hasRotationalKineticEnergy = true;
483			frameData.rotationalKinetic = rke;
484			}
485
486			void Snapshot::setKineticEnergy(RealType ke) {
487			hasKineticEnergy = true;
488			frameData.kineticEnergy = ke;
489			}
490
491			RealType Snapshot::getTotalEnergy() {
492			return frameData.totalEnergy;
493			}
494
495			void Snapshot::setTotalEnergy(RealType te) {
496			hasTotalEnergy = true;
497			frameData.totalEnergy = te;
498			}
499
500			RealType Snapshot::getConservedQuantity() {
501			return frameData.conservedQuantity;
502			}
503
504			void Snapshot::setConservedQuantity(RealType cq) {
505			hasConservedQuantity = true;
506			frameData.conservedQuantity = cq;
507			}
508
509			RealType Snapshot::getTemperature() {
510			return frameData.temperature;
511			}
512
513			void Snapshot::setTemperature(RealType temp) {
514			hasTemperature = true;
515			frameData.temperature = temp;
516			}
517
518			RealType Snapshot::getElectronicTemperature() {
519			return frameData.electronicTemperature;
520			}
521
522			void Snapshot::setElectronicTemperature(RealType eTemp) {
523			hasElectronicTemperature = true;
524			frameData.electronicTemperature = eTemp;
525			}
526
527			RealType Snapshot::getPressure() {
528			return frameData.pressure;
529			}
530
531			void Snapshot::setPressure(RealType pressure) {
532			hasPressure = true;
533			frameData.pressure = pressure;
534			}
535
536			Mat3x3d Snapshot::getPressureTensor() {
537			return frameData.pressureTensor;
538			}
539
540
541			void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) {
542			hasPressureTensor = true;
543			frameData.pressureTensor = pressureTensor;
544			}
545
546			void Snapshot::setStressTensor(const Mat3x3d& stressTensor) {
547			frameData.stressTensor = stressTensor;
548			}
549
550			Mat3x3d Snapshot::getStressTensor() {
551			return frameData.stressTensor;
552			}
553
554			void Snapshot::setConductiveHeatFlux(const Vector3d& chf) {
555			frameData.conductiveHeatFlux = chf;
556			}
557
558			Vector3d Snapshot::getConductiveHeatFlux() {
559			return frameData.conductiveHeatFlux;
560			}
561
562			Vector3d Snapshot::getConvectiveHeatFlux() {
563			return frameData.convectiveHeatFlux;
564			}
565
566			void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) {
567			hasConvectiveHeatFlux = true;
568			frameData.convectiveHeatFlux = chf;
569			}
570
571			Vector3d Snapshot::getHeatFlux() {
572			// BE CAREFUL WITH UNITS
573			return getConductiveHeatFlux() + getConvectiveHeatFlux();
574			}
575
576			Vector3d Snapshot::getSystemDipole() {
577			return frameData.systemDipole;
578			}
579
580			void Snapshot::setSystemDipole(const Vector3d& bd) {
581			hasSystemDipole = true;
582			frameData.systemDipole = bd;
583			}
584
585			void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) {
586			frameData.thermostat = thermostat;
587			}
588
589			pair<RealType, RealType> Snapshot::getThermostat() {
590			return frameData.thermostat;
591			}
592
593			void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) {
594			frameData.electronicThermostat = eTherm;
595			}
596
597			pair<RealType, RealType> Snapshot::getElectronicThermostat() {
598			return frameData.electronicThermostat;
599			}
600
601			void Snapshot::setBarostat(const Mat3x3d& barostat) {
602			frameData.barostat = barostat;
603			}
604
605			Mat3x3d Snapshot::getBarostat() {
606			return frameData.barostat;
607			}
608
609			void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) {
610			frameData.inertiaTensor = inertiaTensor;
611			hasInertiaTensor = true;
612			}
613
614			Mat3x3d Snapshot::getInertiaTensor() {
615			return frameData.inertiaTensor;
616			}
617
618			void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) {
619			frameData.gyrationalVolume = gyrationalVolume;
620			hasGyrationalVolume = true;
621			}
622
623			RealType Snapshot::getGyrationalVolume() {
624			return frameData.gyrationalVolume;
625			}
626
627			void Snapshot::setHullVolume(const RealType hullVolume) {
628			frameData.hullVolume = hullVolume;
629			hasHullVolume = true;
630			}
631
632			RealType Snapshot::getHullVolume() {
633			return frameData.hullVolume;
634			}
635
636			void Snapshot::setOrthoTolerance(RealType ot) {
637			orthoTolerance_ = ot;
638			}
639	gezelter	246	}