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) {
    
    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:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (11 years, 10 months ago) by gezelter
File size:	18847 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	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			/** Wrap a vector according to periodic boundary conditions */
301	gezelter	507	void Snapshot::wrapVector(Vector3d& pos) {
302	gezelter	1782
303			Vector3d scaled = scaleVector(pos);
304
305			for (int i = 0; i < 3; i++)
306			scaled[i] -= roundMe(scaled[i]);
307
308			if( !frameData.orthoRhombic )
309			pos = frameData.hmat * scaled;
310			else {
311
312			// calc the wrapped real coordinates from the wrapped scaled coordinates
313			for (int i=0; i<3; i++) {
314			pos[i] = scaled[i] * frameData.hmat(i, i);
315			}
316			}
317			}
318	gezelter	246
319	gezelter	1782	/** Scaling a vector to multiples of the periodic box */
320			inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
321
322	gezelter	246	Vector3d scaled;
323
324	gezelter	1782	if( !frameData.orthoRhombic )
325			scaled = frameData.invHmat * pos;
326			else {
327	gezelter	507	// calc the scaled coordinates.
328	gezelter	1782	for (int i=0; i<3; i++)
329			scaled[i] = pos[i] * frameData.invHmat(i, i);
330			}
331	gezelter	246
332	gezelter	1782	return scaled;
333			}
334	gezelter	246
335	gezelter	1782	void Snapshot::setCOM(const Vector3d& com) {
336			frameData.COM = com;
337			hasCOM = true;
338			}
339
340			void Snapshot::setCOMvel(const Vector3d& comVel) {
341			frameData.COMvel = comVel;
342			hasCOMvel = true;
343			}
344
345			void Snapshot::setCOMw(const Vector3d& comw) {
346			frameData.COMw = comw;
347			hasCOMw = true;
348			}
349
350			Vector3d Snapshot::getCOM() {
351			return frameData.COM;
352			}
353
354			Vector3d Snapshot::getCOMvel() {
355			return frameData.COMvel;
356			}
357
358			Vector3d Snapshot::getCOMw() {
359			return frameData.COMw;
360			}
361
362			RealType Snapshot::getTime() {
363			return frameData.currentTime;
364			}
365
366			void Snapshot::increaseTime(RealType dt) {
367			setTime(getTime() + dt);
368			}
369
370			void Snapshot::setTime(RealType time) {
371			frameData.currentTime = time;
372			}
373
374			void Snapshot::setBondPotential(RealType bp) {
375			frameData.bondPotential = bp;
376			}
377
378			void Snapshot::setBendPotential(RealType bp) {
379			frameData.bendPotential = bp;
380			}
381
382			void Snapshot::setTorsionPotential(RealType tp) {
383			frameData.torsionPotential = tp;
384			}
385
386			void Snapshot::setInversionPotential(RealType ip) {
387			frameData.inversionPotential = ip;
388			}
389	gezelter	246
390
391	gezelter	1782	RealType Snapshot::getBondPotential() {
392			return frameData.bondPotential;
393			}
394			RealType Snapshot::getBendPotential() {
395			return frameData.bendPotential;
396			}
397			RealType Snapshot::getTorsionPotential() {
398			return frameData.torsionPotential;
399			}
400			RealType Snapshot::getInversionPotential() {
401			return frameData.inversionPotential;
402			}
403
404			RealType Snapshot::getShortRangePotential() {
405			if (!hasShortRangePotential) {
406			frameData.shortRangePotential = frameData.bondPotential;
407			frameData.shortRangePotential += frameData.bendPotential;
408			frameData.shortRangePotential += frameData.torsionPotential;
409			frameData.shortRangePotential += frameData.inversionPotential;
410			hasShortRangePotential = true;
411	gezelter	246	}
412	gezelter	1782	return frameData.shortRangePotential;
413			}
414	gezelter	246
415	gezelter	1782	void Snapshot::setLongRangePotential(potVec lrPot) {
416			frameData.lrPotentials = lrPot;
417	gezelter	507	}
418	gezelter	1782
419			RealType Snapshot::getLongRangePotential() {
420			if (!hasLongRangePotential) {
421			for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
422			frameData.longRangePotential += frameData.lrPotentials[i];
423			}
424			hasLongRangePotential = true;
425			}
426			return frameData.longRangePotential;
427			}
428	gezelter	246
429	gezelter	1782	potVec Snapshot::getLongRangePotentials() {
430			return frameData.lrPotentials;
431			}
432
433			RealType Snapshot::getPotentialEnergy() {
434			if (!hasPotentialEnergy) {
435			frameData.potentialEnergy = this->getLongRangePotential();
436			frameData.potentialEnergy += this->getShortRangePotential();
437			hasPotentialEnergy = true;
438	gezelter	1104	}
439	gezelter	1782	return frameData.potentialEnergy;
440	gezelter	1104	}
441	gezelter	1782
442			void Snapshot::setExcludedPotentials(potVec exPot) {
443			frameData.excludedPotentials = exPot;
444			}
445
446			potVec Snapshot::getExcludedPotentials() {
447			return frameData.excludedPotentials;
448			}
449
450			void Snapshot::setRestraintPotential(RealType rp) {
451			frameData.restraintPotential = rp;
452			}
453	gezelter	1104
454	gezelter	1782	RealType Snapshot::getRestraintPotential() {
455			return frameData.restraintPotential;
456	gezelter	1104	}
457
458	gezelter	1782	void Snapshot::setRawPotential(RealType rp) {
459			frameData.rawPotential = rp;
460	gezelter	1104	}
461	gezelter	1782
462			RealType Snapshot::getRawPotential() {
463			return frameData.rawPotential;
464			}
465
466			RealType Snapshot::getTranslationalKineticEnergy() {
467			return frameData.translationalKinetic;
468			}
469
470			RealType Snapshot::getRotationalKineticEnergy() {
471			return frameData.rotationalKinetic;
472			}
473
474			RealType Snapshot::getKineticEnergy() {
475			return frameData.kineticEnergy;
476			}
477
478			void Snapshot::setTranslationalKineticEnergy(RealType tke) {
479			hasTranslationalKineticEnergy = true;
480			frameData.translationalKinetic = tke;
481			}
482
483			void Snapshot::setRotationalKineticEnergy(RealType rke) {
484			hasRotationalKineticEnergy = true;
485			frameData.rotationalKinetic = rke;
486			}
487
488			void Snapshot::setKineticEnergy(RealType ke) {
489			hasKineticEnergy = true;
490			frameData.kineticEnergy = ke;
491			}
492
493			RealType Snapshot::getTotalEnergy() {
494			return frameData.totalEnergy;
495			}
496
497			void Snapshot::setTotalEnergy(RealType te) {
498			hasTotalEnergy = true;
499			frameData.totalEnergy = te;
500			}
501
502			RealType Snapshot::getConservedQuantity() {
503			return frameData.conservedQuantity;
504			}
505
506			void Snapshot::setConservedQuantity(RealType cq) {
507			hasConservedQuantity = true;
508			frameData.conservedQuantity = cq;
509			}
510
511			RealType Snapshot::getTemperature() {
512			return frameData.temperature;
513			}
514
515			void Snapshot::setTemperature(RealType temp) {
516			hasTemperature = true;
517			frameData.temperature = temp;
518			}
519
520			RealType Snapshot::getElectronicTemperature() {
521			return frameData.electronicTemperature;
522			}
523
524			void Snapshot::setElectronicTemperature(RealType eTemp) {
525			hasElectronicTemperature = true;
526			frameData.electronicTemperature = eTemp;
527			}
528
529			RealType Snapshot::getPressure() {
530			return frameData.pressure;
531			}
532
533			void Snapshot::setPressure(RealType pressure) {
534			hasPressure = true;
535			frameData.pressure = pressure;
536			}
537
538			Mat3x3d Snapshot::getPressureTensor() {
539			return frameData.pressureTensor;
540			}
541
542
543			void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) {
544			hasPressureTensor = true;
545			frameData.pressureTensor = pressureTensor;
546			}
547
548			void Snapshot::setStressTensor(const Mat3x3d& stressTensor) {
549			frameData.stressTensor = stressTensor;
550			}
551
552			Mat3x3d Snapshot::getStressTensor() {
553			return frameData.stressTensor;
554			}
555
556			void Snapshot::setConductiveHeatFlux(const Vector3d& chf) {
557			frameData.conductiveHeatFlux = chf;
558			}
559
560			Vector3d Snapshot::getConductiveHeatFlux() {
561			return frameData.conductiveHeatFlux;
562			}
563
564			Vector3d Snapshot::getConvectiveHeatFlux() {
565			return frameData.convectiveHeatFlux;
566			}
567
568			void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) {
569			hasConvectiveHeatFlux = true;
570			frameData.convectiveHeatFlux = chf;
571			}
572
573			Vector3d Snapshot::getHeatFlux() {
574			// BE CAREFUL WITH UNITS
575			return getConductiveHeatFlux() + getConvectiveHeatFlux();
576			}
577
578			Vector3d Snapshot::getSystemDipole() {
579			return frameData.systemDipole;
580			}
581
582			void Snapshot::setSystemDipole(const Vector3d& bd) {
583			hasSystemDipole = true;
584			frameData.systemDipole = bd;
585			}
586
587			void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) {
588			frameData.thermostat = thermostat;
589			}
590
591			pair<RealType, RealType> Snapshot::getThermostat() {
592			return frameData.thermostat;
593			}
594
595			void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) {
596			frameData.electronicThermostat = eTherm;
597			}
598
599			pair<RealType, RealType> Snapshot::getElectronicThermostat() {
600			return frameData.electronicThermostat;
601			}
602	gezelter	1104
603	gezelter	1782	void Snapshot::setBarostat(const Mat3x3d& barostat) {
604			frameData.barostat = barostat;
605			}
606
607			Mat3x3d Snapshot::getBarostat() {
608			return frameData.barostat;
609			}
610
611			void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) {
612			frameData.inertiaTensor = inertiaTensor;
613			hasInertiaTensor = true;
614			}
615
616			Mat3x3d Snapshot::getInertiaTensor() {
617			return frameData.inertiaTensor;
618			}
619
620			void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) {
621			frameData.gyrationalVolume = gyrationalVolume;
622			hasGyrationalVolume = true;
623			}
624
625			RealType Snapshot::getGyrationalVolume() {
626			return frameData.gyrationalVolume;
627			}
628
629			void Snapshot::setHullVolume(const RealType hullVolume) {
630			frameData.hullVolume = hullVolume;
631			hasHullVolume = true;
632			}
633
634			RealType Snapshot::getHullVolume() {
635			return frameData.hullVolume;
636			}
637
638			void Snapshot::setOrthoTolerance(RealType ot) {
639			orthoTolerance_ = ot;
640			}
641	gezelter	246	}