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.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;
  }

  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:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 2 months ago) by gezelter
File size:	18332 byte(s)
Log Message:	Fixed a widespread typo in the license
#	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			frameData.invHmat = Mat3x3d(0.0);
98			frameData.orthoRhombic = false;
99			frameData.bondPotential = 0.0;
100			frameData.bendPotential = 0.0;
101			frameData.torsionPotential = 0.0;
102			frameData.inversionPotential = 0.0;
103			frameData.lrPotentials = potVec(0.0);
104			frameData.excludedPotentials = potVec(0.0);
105			frameData.restraintPotential = 0.0;
106			frameData.rawPotential = 0.0;
107	gezelter	1774	frameData.xyArea = 0.0;
108	gezelter	1764	frameData.volume = 0.0;
109			frameData.thermostat = make_pair(0.0, 0.0);
110			frameData.electronicThermostat = make_pair(0.0, 0.0);
111			frameData.barostat = Mat3x3d(0.0);
112			frameData.stressTensor = Mat3x3d(0.0);
113			frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
114
115			clearDerivedProperties();
116			}
117
118			void Snapshot::clearDerivedProperties() {
119			frameData.totalEnergy = 0.0;
120			frameData.translationalKinetic = 0.0;
121			frameData.rotationalKinetic = 0.0;
122			frameData.kineticEnergy = 0.0;
123			frameData.potentialEnergy = 0.0;
124			frameData.shortRangePotential = 0.0;
125			frameData.longRangePotential = 0.0;
126			frameData.pressure = 0.0;
127			frameData.temperature = 0.0;
128			frameData.pressureTensor = Mat3x3d(0.0);
129			frameData.systemDipole = Vector3d(0.0);
130			frameData.convectiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
131			frameData.electronicTemperature = 0.0;
132			frameData.COM = V3Zero;
133			frameData.COMvel = V3Zero;
134			frameData.COMw = V3Zero;
135
136			hasTotalEnergy = false;
137			hasTranslationalKineticEnergy = false;
138			hasRotationalKineticEnergy = false;
139			hasKineticEnergy = false;
140			hasShortRangePotential = false;
141			hasLongRangePotential = false;
142	gezelter	1774	hasPotentialEnergy = false;
143			hasXYarea = false;
144	gezelter	1764	hasVolume = false;
145			hasPressure = false;
146			hasTemperature = false;
147			hasElectronicTemperature = false;
148			hasCOM = false;
149			hasCOMvel = false;
150			hasCOMw = false;
151			hasPressureTensor = false;
152			hasSystemDipole = false;
153			hasConvectiveHeatFlux = false;
154			hasInertiaTensor = false;
155			hasGyrationalVolume = false;
156			hasHullVolume = false;
157			hasConservedQuantity = false;
158			}
159
160			/** Returns the id of this Snapshot */
161			int Snapshot::getID() {
162			return frameData.id;
163			}
164
165			/** Sets the id of this Snapshot */
166			void Snapshot::setID(int id) {
167			frameData.id = id;
168			}
169
170			int Snapshot::getSize() {
171			return atomData.getSize() + rigidbodyData.getSize();
172			}
173
174			/** Returns the number of atoms */
175			int Snapshot::getNumberOfAtoms() {
176			return atomData.getSize();
177			}
178
179			/** Returns the number of rigid bodies */
180			int Snapshot::getNumberOfRigidBodies() {
181			return rigidbodyData.getSize();
182			}
183
184			/** Returns the number of rigid bodies */
185			int Snapshot::getNumberOfCutoffGroups() {
186			return cgData.getSize();
187			}
188
189			/** Returns the H-Matrix */
190			Mat3x3d Snapshot::getHmat() {
191			return frameData.hmat;
192			}
193
194			/** Sets the H-Matrix */
195			void Snapshot::setHmat(const Mat3x3d& m) {
196			hasVolume = false;
197	gezelter	1715	frameData.hmat = m;
198			frameData.invHmat = frameData.hmat.inverse();
199	gezelter	246
200			//determine whether the box is orthoTolerance or not
201	gezelter	1715	bool oldOrthoRhombic = frameData.orthoRhombic;
202	gezelter	246
203	gezelter	1715	RealType smallDiag = fabs(frameData.hmat(0, 0));
204			if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
205			if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));
206	gezelter	1021	RealType tol = smallDiag * orthoTolerance_;
207	gezelter	246
208	gezelter	1715	frameData.orthoRhombic = true;
209	gezelter	246
210			for (int i = 0; i < 3; i++ ) {
211	gezelter	507	for (int j = 0 ; j < 3; j++) {
212			if (i != j) {
213	gezelter	1715	if (frameData.orthoRhombic) {
214			if ( fabs(frameData.hmat(i, j)) >= tol)
215			frameData.orthoRhombic = false;
216	gezelter	507	}
217			}
218			}
219	gezelter	246	}
220	gezelter	1764
221	gezelter	1715	if( oldOrthoRhombic != frameData.orthoRhombic){
222	gezelter	1764
223	gezelter	1838	// It is finally time to suppress these warnings once and for
224			// all. They were annoying and not very informative.
225
226			// if( frameData.orthoRhombic ) {
227			// sprintf( painCave.errMsg,
228			// "OpenMD is switching from the default Non-Orthorhombic\n"
229			// "\tto the faster Orthorhombic periodic boundary computations.\n"
230			// "\tThis is usually a good thing, but if you want the\n"
231			// "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
232			// "\tvariable ( currently set to %G ) smaller.\n",
233			// orthoTolerance_);
234			// painCave.severity = OPENMD_INFO;
235			// simError();
236			// }
237			// else {
238			// sprintf( painCave.errMsg,
239			// "OpenMD is switching from the faster Orthorhombic to the more\n"
240			// "\tflexible Non-Orthorhombic periodic boundary computations.\n"
241			// "\tThis is usually because the box has deformed under\n"
242			// "\tNPTf integration. If you want to live on the edge with\n"
243			// "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
244			// "\tvariable ( currently set to %G ) larger.\n",
245			// orthoTolerance_);
246			// painCave.severity = OPENMD_WARNING;
247			// simError();
248			// }
249	gezelter	246	}
250	gezelter	507	}
251	gezelter	1764
252			/** Returns the inverse H-Matrix */
253			Mat3x3d Snapshot::getInvHmat() {
254			return frameData.invHmat;
255			}
256	gezelter	246
257	gezelter	1774	RealType Snapshot::getXYarea() {
258			if (!hasXYarea) {
259			Vector3d x = frameData.hmat.getColumn(0);
260			Vector3d y = frameData.hmat.getColumn(1);
261			frameData.xyArea = cross(x,y).length();
262			hasXYarea = true;
263			}
264			return frameData.xyArea;
265			}
266
267	gezelter	1764	RealType Snapshot::getVolume() {
268			if (!hasVolume) {
269			frameData.volume = frameData.hmat.determinant();
270			hasVolume = true;
271			}
272			return frameData.volume;
273			}
274	gezelter	246
275	gezelter	1764	void Snapshot::setVolume(RealType vol) {
276			hasVolume = true;
277			frameData.volume = vol;
278			}
279
280			/** Wrap a vector according to periodic boundary conditions */
281	gezelter	1568	void Snapshot::wrapVector(Vector3d& pos) {
282	gezelter	1562
283			Vector3d scaled = scaleVector(pos);
284	gezelter	1568
285	gezelter	1562	for (int i = 0; i < 3; i++)
286			scaled[i] -= roundMe(scaled[i]);
287	gezelter	1764
288	gezelter	1715	if( !frameData.orthoRhombic )
289			pos = frameData.hmat * scaled;
290	gezelter	1562	else {
291	gezelter	1764
292	gezelter	507	// calc the wrapped real coordinates from the wrapped scaled coordinates
293	gezelter	1562	for (int i=0; i<3; i++) {
294	gezelter	1715	pos[i] = scaled[i] * frameData.hmat(i, i);
295	gezelter	1540	}
296	gezelter	246	}
297	gezelter	507	}
298	gezelter	246
299	gezelter	1764	/** Scaling a vector to multiples of the periodic box */
300	gezelter	1562	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
301
302			Vector3d scaled;
303
304	gezelter	1715	if( !frameData.orthoRhombic )
305			scaled = frameData.invHmat * pos;
306	gezelter	1562	else {
307			// calc the scaled coordinates.
308			for (int i=0; i<3; i++)
309	gezelter	1715	scaled[i] = pos[i] * frameData.invHmat(i, i);
310	gezelter	1562	}
311
312			return scaled;
313			}
314	gezelter	1764
315			void Snapshot::setCOM(const Vector3d& com) {
316			frameData.COM = com;
317			hasCOM = true;
318			}
319	gezelter	1562
320	gezelter	1764	void Snapshot::setCOMvel(const Vector3d& comVel) {
321			frameData.COMvel = comVel;
322			hasCOMvel = true;
323			}
324
325			void Snapshot::setCOMw(const Vector3d& comw) {
326			frameData.COMw = comw;
327			hasCOMw = true;
328			}
329
330	gezelter	1104	Vector3d Snapshot::getCOM() {
331	gezelter	1715	return frameData.COM;
332	gezelter	1104	}
333
334			Vector3d Snapshot::getCOMvel() {
335	gezelter	1715	return frameData.COMvel;
336	gezelter	1104	}
337
338			Vector3d Snapshot::getCOMw() {
339	gezelter	1715	return frameData.COMw;
340	gezelter	1104	}
341	gezelter	1764
342			RealType Snapshot::getTime() {
343			return frameData.currentTime;
344			}
345
346			void Snapshot::increaseTime(RealType dt) {
347			setTime(getTime() + dt);
348			}
349
350			void Snapshot::setTime(RealType time) {
351			frameData.currentTime = time;
352			}
353
354			void Snapshot::setBondPotential(RealType bp) {
355			frameData.bondPotential = bp;
356			}
357
358			void Snapshot::setBendPotential(RealType bp) {
359			frameData.bendPotential = bp;
360			}
361
362			void Snapshot::setTorsionPotential(RealType tp) {
363			frameData.torsionPotential = tp;
364			}
365
366			void Snapshot::setInversionPotential(RealType ip) {
367			frameData.inversionPotential = ip;
368			}
369
370
371			RealType Snapshot::getBondPotential() {
372			return frameData.bondPotential;
373			}
374			RealType Snapshot::getBendPotential() {
375			return frameData.bendPotential;
376			}
377			RealType Snapshot::getTorsionPotential() {
378			return frameData.torsionPotential;
379			}
380			RealType Snapshot::getInversionPotential() {
381			return frameData.inversionPotential;
382			}
383
384			RealType Snapshot::getShortRangePotential() {
385			if (!hasShortRangePotential) {
386			frameData.shortRangePotential = frameData.bondPotential;
387			frameData.shortRangePotential += frameData.bendPotential;
388			frameData.shortRangePotential += frameData.torsionPotential;
389			frameData.shortRangePotential += frameData.inversionPotential;
390			hasShortRangePotential = true;
391			}
392			return frameData.shortRangePotential;
393			}
394
395			void Snapshot::setLongRangePotential(potVec lrPot) {
396			frameData.lrPotentials = lrPot;
397			}
398
399			RealType Snapshot::getLongRangePotential() {
400			if (!hasLongRangePotential) {
401			for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
402			frameData.longRangePotential += frameData.lrPotentials[i];
403			}
404			hasLongRangePotential = true;
405			}
406			return frameData.longRangePotential;
407			}
408
409			potVec Snapshot::getLongRangePotentials() {
410			return frameData.lrPotentials;
411			}
412
413			RealType Snapshot::getPotentialEnergy() {
414			if (!hasPotentialEnergy) {
415			frameData.potentialEnergy = this->getLongRangePotential();
416			frameData.potentialEnergy += this->getShortRangePotential();
417			hasPotentialEnergy = true;
418			}
419			return frameData.potentialEnergy;
420			}
421
422			void Snapshot::setExcludedPotentials(potVec exPot) {
423			frameData.excludedPotentials = exPot;
424			}
425
426			potVec Snapshot::getExcludedPotentials() {
427			return frameData.excludedPotentials;
428			}
429
430			void Snapshot::setRestraintPotential(RealType rp) {
431			frameData.restraintPotential = rp;
432			}
433
434			RealType Snapshot::getRestraintPotential() {
435			return frameData.restraintPotential;
436			}
437
438			void Snapshot::setRawPotential(RealType rp) {
439			frameData.rawPotential = rp;
440			}
441
442			RealType Snapshot::getRawPotential() {
443			return frameData.rawPotential;
444			}
445
446			RealType Snapshot::getTranslationalKineticEnergy() {
447			return frameData.translationalKinetic;
448			}
449
450			RealType Snapshot::getRotationalKineticEnergy() {
451			return frameData.rotationalKinetic;
452			}
453
454			RealType Snapshot::getKineticEnergy() {
455			return frameData.kineticEnergy;
456			}
457
458			void Snapshot::setTranslationalKineticEnergy(RealType tke) {
459			hasTranslationalKineticEnergy = true;
460			frameData.translationalKinetic = tke;
461			}
462
463			void Snapshot::setRotationalKineticEnergy(RealType rke) {
464			hasRotationalKineticEnergy = true;
465			frameData.rotationalKinetic = rke;
466			}
467
468			void Snapshot::setKineticEnergy(RealType ke) {
469			hasKineticEnergy = true;
470			frameData.kineticEnergy = ke;
471			}
472
473			RealType Snapshot::getTotalEnergy() {
474			return frameData.totalEnergy;
475			}
476
477			void Snapshot::setTotalEnergy(RealType te) {
478			hasTotalEnergy = true;
479			frameData.totalEnergy = te;
480			}
481
482			RealType Snapshot::getConservedQuantity() {
483			return frameData.conservedQuantity;
484			}
485
486			void Snapshot::setConservedQuantity(RealType cq) {
487			hasConservedQuantity = true;
488			frameData.conservedQuantity = cq;
489			}
490
491			RealType Snapshot::getTemperature() {
492			return frameData.temperature;
493			}
494
495			void Snapshot::setTemperature(RealType temp) {
496			hasTemperature = true;
497			frameData.temperature = temp;
498			}
499
500			RealType Snapshot::getElectronicTemperature() {
501			return frameData.electronicTemperature;
502			}
503
504			void Snapshot::setElectronicTemperature(RealType eTemp) {
505			hasElectronicTemperature = true;
506			frameData.electronicTemperature = eTemp;
507			}
508
509			RealType Snapshot::getPressure() {
510			return frameData.pressure;
511			}
512
513			void Snapshot::setPressure(RealType pressure) {
514			hasPressure = true;
515			frameData.pressure = pressure;
516			}
517
518			Mat3x3d Snapshot::getPressureTensor() {
519			return frameData.pressureTensor;
520			}
521
522
523			void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) {
524			hasPressureTensor = true;
525			frameData.pressureTensor = pressureTensor;
526			}
527
528			void Snapshot::setStressTensor(const Mat3x3d& stressTensor) {
529			frameData.stressTensor = stressTensor;
530			}
531
532			Mat3x3d Snapshot::getStressTensor() {
533			return frameData.stressTensor;
534			}
535
536			void Snapshot::setConductiveHeatFlux(const Vector3d& chf) {
537			frameData.conductiveHeatFlux = chf;
538			}
539
540			Vector3d Snapshot::getConductiveHeatFlux() {
541			return frameData.conductiveHeatFlux;
542			}
543
544			Vector3d Snapshot::getConvectiveHeatFlux() {
545			return frameData.convectiveHeatFlux;
546			}
547
548			void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) {
549			hasConvectiveHeatFlux = true;
550			frameData.convectiveHeatFlux = chf;
551			}
552
553			Vector3d Snapshot::getHeatFlux() {
554			// BE CAREFUL WITH UNITS
555			return getConductiveHeatFlux() + getConvectiveHeatFlux();
556			}
557
558			Vector3d Snapshot::getSystemDipole() {
559			return frameData.systemDipole;
560			}
561
562			void Snapshot::setSystemDipole(const Vector3d& bd) {
563			hasSystemDipole = true;
564			frameData.systemDipole = bd;
565			}
566
567			void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) {
568			frameData.thermostat = thermostat;
569			}
570
571			pair<RealType, RealType> Snapshot::getThermostat() {
572			return frameData.thermostat;
573			}
574
575			void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) {
576			frameData.electronicThermostat = eTherm;
577			}
578
579			pair<RealType, RealType> Snapshot::getElectronicThermostat() {
580			return frameData.electronicThermostat;
581			}
582
583			void Snapshot::setBarostat(const Mat3x3d& barostat) {
584			frameData.barostat = barostat;
585			}
586
587			Mat3x3d Snapshot::getBarostat() {
588			return frameData.barostat;
589			}
590
591			void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) {
592			frameData.inertiaTensor = inertiaTensor;
593			hasInertiaTensor = true;
594			}
595
596			Mat3x3d Snapshot::getInertiaTensor() {
597			return frameData.inertiaTensor;
598			}
599
600			void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) {
601			frameData.gyrationalVolume = gyrationalVolume;
602			hasGyrationalVolume = true;
603			}
604
605			RealType Snapshot::getGyrationalVolume() {
606			return frameData.gyrationalVolume;
607			}
608
609			void Snapshot::setHullVolume(const RealType hullVolume) {
610			frameData.hullVolume = hullVolume;
611			hasHullVolume = true;
612			}
613
614			RealType Snapshot::getHullVolume() {
615			return frameData.hullVolume;
616			}
617
618			void Snapshot::setOrthoTolerance(RealType ot) {
619			orthoTolerance_ = ot;
620			}
621	gezelter	246	}