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, 24107 (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:	1838
Committed:	Tue Jan 22 16:20:11 2013 UTC (12 years, 3 months ago) by gezelter
File size:	18331 byte(s)
Log Message:	Unified the computation of storageLayout into SimCreator, but that value is stored in SimInfo. We used to compute storageLayout values in two places - now only one.
#	Content
1	/*
2	* 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	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	/**
44	* @file Snapshot.cpp
45	* @author tlin
46	* @date 11/11/2004
47	* @version 1.0
48	*/
49
50	#include "brains/Snapshot.hpp"
51	#include "utils/NumericConstant.hpp"
52	#include "utils/simError.h"
53	#include "utils/Utility.hpp"
54	#include <cstdio>
55
56	namespace OpenMD {
57
58	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	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
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	frameData.xyArea = 0.0;
108	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	hasPotentialEnergy = false;
143	hasXYarea = false;
144	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	frameData.hmat = m;
198	frameData.invHmat = frameData.hmat.inverse();
199
200	//determine whether the box is orthoTolerance or not
201	bool oldOrthoRhombic = frameData.orthoRhombic;
202
203	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	RealType tol = smallDiag * orthoTolerance_;
207
208	frameData.orthoRhombic = true;
209
210	for (int i = 0; i < 3; i++ ) {
211	for (int j = 0 ; j < 3; j++) {
212	if (i != j) {
213	if (frameData.orthoRhombic) {
214	if ( fabs(frameData.hmat(i, j)) >= tol)
215	frameData.orthoRhombic = false;
216	}
217	}
218	}
219	}
220
221	if( oldOrthoRhombic != frameData.orthoRhombic){
222
223	// 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	}
250	}
251
252	/** Returns the inverse H-Matrix */
253	Mat3x3d Snapshot::getInvHmat() {
254	return frameData.invHmat;
255	}
256
257	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	RealType Snapshot::getVolume() {
268	if (!hasVolume) {
269	frameData.volume = frameData.hmat.determinant();
270	hasVolume = true;
271	}
272	return frameData.volume;
273	}
274
275	void Snapshot::setVolume(RealType vol) {
276	hasVolume = true;
277	frameData.volume = vol;
278	}
279
280	/** Wrap a vector according to periodic boundary conditions */
281	void Snapshot::wrapVector(Vector3d& pos) {
282
283	Vector3d scaled = scaleVector(pos);
284
285	for (int i = 0; i < 3; i++)
286	scaled[i] -= roundMe(scaled[i]);
287
288	if( !frameData.orthoRhombic )
289	pos = frameData.hmat * scaled;
290	else {
291
292	// calc the wrapped real coordinates from the wrapped scaled coordinates
293	for (int i=0; i<3; i++) {
294	pos[i] = scaled[i] * frameData.hmat(i, i);
295	}
296	}
297	}
298
299	/** Scaling a vector to multiples of the periodic box */
300	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
301
302	Vector3d scaled;
303
304	if( !frameData.orthoRhombic )
305	scaled = frameData.invHmat * pos;
306	else {
307	// calc the scaled coordinates.
308	for (int i=0; i<3; i++)
309	scaled[i] = pos[i] * frameData.invHmat(i, i);
310	}
311
312	return scaled;
313	}
314
315	void Snapshot::setCOM(const Vector3d& com) {
316	frameData.COM = com;
317	hasCOM = true;
318	}
319
320	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	Vector3d Snapshot::getCOM() {
331	return frameData.COM;
332	}
333
334	Vector3d Snapshot::getCOMvel() {
335	return frameData.COMvel;
336	}
337
338	Vector3d Snapshot::getCOMw() {
339	return frameData.COMw;
340	}
341
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	}