src/brains/Snapshot.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
  
/**
 * @file Snapshot.cpp
 * @author tlin
 * @date 11/11/2004
 * @version 1.0
 */

#include "brains/Snapshot.hpp"
#include "utils/NumericConstant.hpp"
#include "utils/simError.h"
#include "utils/Utility.hpp"
#include <cstdio>

namespace OpenMD {

  Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups) : 
    atomData(nAtoms), rigidbodyData(nRigidbodies),
    cgData(nCutoffGroups, DataStorage::dslPosition), 
    orthoTolerance_(1e-6) {
    
    frameData.id = -1;                   
    frameData.currentTime = 0;     
    frameData.hmat = Mat3x3d(0.0);             
    frameData.invHmat = Mat3x3d(0.0);          
    frameData.orthoRhombic = false;        
    frameData.bondPotential = 0.0;      
    frameData.bendPotential = 0.0;      
    frameData.torsionPotential = 0.0;   
    frameData.inversionPotential = 0.0; 
    frameData.lrPotentials = potVec(0.0);
    frameData.excludedPotentials = potVec(0.0); 
    frameData.restraintPotential = 0.0; 
    frameData.rawPotential = 0.0;   
    frameData.xyArea = 0.0;
    frameData.volume = 0.0;          
    frameData.thermostat = make_pair(0.0, 0.0);
    frameData.electronicThermostat = make_pair(0.0, 0.0);
    frameData.barostat = Mat3x3d(0.0);              
    frameData.stressTensor = Mat3x3d(0.0);              
    frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);

    clearDerivedProperties();
  }
  
  Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, 
                     int storageLayout) : 
    atomData(nAtoms, storageLayout), 
    rigidbodyData(nRigidbodies, storageLayout),
    cgData(nCutoffGroups, DataStorage::dslPosition),
    orthoTolerance_(1e-6) {
    
    frameData.id = -1;                   
    frameData.currentTime = 0;     
    frameData.hmat = Mat3x3d(0.0);             
    frameData.invHmat = Mat3x3d(0.0);      
    frameData.bBox = Mat3x3d(0.0);             
    frameData.invBbox = Mat3x3d(0.0);
    frameData.orthoRhombic = false;        
    frameData.bondPotential = 0.0;      
    frameData.bendPotential = 0.0;      
    frameData.torsionPotential = 0.0;   
    frameData.inversionPotential = 0.0; 
    frameData.lrPotentials = potVec(0.0);
    frameData.excludedPotentials = potVec(0.0); 
    frameData.restraintPotential = 0.0; 
    frameData.rawPotential = 0.0;       
    frameData.xyArea = 0.0;
    frameData.volume = 0.0;          
    frameData.thermostat = make_pair(0.0, 0.0);
    frameData.electronicThermostat = make_pair(0.0, 0.0);
    frameData.barostat = Mat3x3d(0.0);              
    frameData.stressTensor = Mat3x3d(0.0);              
    frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);

    clearDerivedProperties();
  }

  void Snapshot::clearDerivedProperties() {
    frameData.totalEnergy = 0.0;     
    frameData.translationalKinetic = 0.0;   
    frameData.rotationalKinetic = 0.0;   
    frameData.kineticEnergy = 0.0;   
    frameData.potentialEnergy = 0.0; 
    frameData.shortRangePotential = 0.0;
    frameData.longRangePotential = 0.0; 
    frameData.pressure = 0.0;        
    frameData.temperature = 0.0;
    frameData.pressureTensor = Mat3x3d(0.0);   
    frameData.systemDipole = Vector3d(0.0);            
    frameData.convectiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
    frameData.electronicTemperature = 0.0;
    frameData.COM = V3Zero;             
    frameData.COMvel = V3Zero;          
    frameData.COMw = V3Zero;  

    hasTotalEnergy = false;         
    hasTranslationalKineticEnergy = false;       
    hasRotationalKineticEnergy = false;       
    hasKineticEnergy = false;       
    hasShortRangePotential = false;
    hasLongRangePotential = false;
    hasPotentialEnergy = false;   
    hasXYarea = false;
    hasVolume = false;         
    hasPressure = false;       
    hasTemperature = false;    
    hasElectronicTemperature = false;
    hasCOM = false;
    hasCOMvel = false;
    hasCOMw = false;
    hasPressureTensor = false;    
    hasSystemDipole = false;      
    hasConvectiveHeatFlux = false;  
    hasInertiaTensor = false;
    hasGyrationalVolume = false;   
    hasHullVolume = false;
    hasConservedQuantity = false; 
  }

  /** Returns the id of this Snapshot */
  int Snapshot::getID() {
    return frameData.id;
  }
  
  /** Sets the id of this Snapshot */
  void Snapshot::setID(int id) {
    frameData.id = id;
  }
  
  int Snapshot::getSize() {
    return atomData.getSize() + rigidbodyData.getSize();
  }
  
  /** Returns the number of atoms */
  int Snapshot::getNumberOfAtoms() {
    return atomData.getSize();
  }
  
  /** Returns the number of rigid bodies */
  int Snapshot::getNumberOfRigidBodies() {
    return rigidbodyData.getSize();
  }
  
  /** Returns the number of rigid bodies */
  int Snapshot::getNumberOfCutoffGroups() {
    return cgData.getSize();
  }
  
  /** Returns the H-Matrix */
  Mat3x3d Snapshot::getHmat() {
    return frameData.hmat;
  }

  /** Sets the H-Matrix */  
  void Snapshot::setHmat(const Mat3x3d& m) {
    hasVolume = false;
    frameData.hmat = m;
    frameData.invHmat = frameData.hmat.inverse();
    
    //determine whether the box is orthoTolerance or not
    bool oldOrthoRhombic = frameData.orthoRhombic;
    
    RealType smallDiag = fabs(frameData.hmat(0, 0));
    if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
    if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));    
    RealType tol = smallDiag * orthoTolerance_;

    frameData.orthoRhombic = true;

    for (int i = 0; i < 3; i++ ) {
      for (int j = 0 ; j < 3; j++) {
        if (i != j) {
          if (frameData.orthoRhombic) {
            if ( fabs(frameData.hmat(i, j)) >= tol)
              frameData.orthoRhombic = false;
          }        
        }
      }
    }
    
    if( oldOrthoRhombic != frameData.orthoRhombic){
      
      // It is finally time to suppress these warnings once and for
      // all.  They were annoying and not very informative.

      // if( frameData.orthoRhombic ) {
      //   sprintf( painCave.errMsg,
      //         "OpenMD is switching from the default Non-Orthorhombic\n"
      //         "\tto the faster Orthorhombic periodic boundary computations.\n"
      //         "\tThis is usually a good thing, but if you want the\n"
      //         "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
      //         "\tvariable ( currently set to %G ) smaller.\n",
      //         orthoTolerance_);
      //   painCave.severity = OPENMD_INFO;
      //   simError();
      // }
      // else {
      //   sprintf( painCave.errMsg,
      //         "OpenMD is switching from the faster Orthorhombic to the more\n"
      //         "\tflexible Non-Orthorhombic periodic boundary computations.\n"
      //         "\tThis is usually because the box has deformed under\n"
      //         "\tNPTf integration. If you want to live on the edge with\n"
      //         "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
      //         "\tvariable ( currently set to %G ) larger.\n",
      //         orthoTolerance_);
      //   painCave.severity = OPENMD_WARNING;
      //   simError();
      // }
    }    
  }
  
  /** Returns the inverse H-Matrix */
  Mat3x3d Snapshot::getInvHmat() {
    return frameData.invHmat;
  }

  /** Returns the Bounding Box */
  Mat3x3d Snapshot::getBoundingBox() {
    return frameData.bBox;
  }

  /** Sets the Bounding Box */  
  void Snapshot::setBoundingBox(const Mat3x3d& m) {
    frameData.bBox = m;
    frameData.invBbox = frameData.bBox.inverse();
  }

  /** Returns the inverse Bounding Box */
  Mat3x3d Snapshot::getInvBoundingBox() {
    return frameData.invBbox;
  }

  RealType Snapshot::getXYarea() {
    if (!hasXYarea) {
      Vector3d x = frameData.hmat.getColumn(0);
      Vector3d y = frameData.hmat.getColumn(1);
      frameData.xyArea = cross(x,y).length();
      hasXYarea = true;
    }
    return frameData.xyArea;
  }

  RealType Snapshot::getVolume() {
    if (!hasVolume) {
      frameData.volume = frameData.hmat.determinant();
      hasVolume = true;
    }
    return frameData.volume;
  }

  void Snapshot::setVolume(RealType vol) {
    hasVolume = true;
    frameData.volume = vol;
  }

  /** Wrap a vector according to periodic boundary conditions */
  void Snapshot::wrapVector(Vector3d& pos) {
    
    Vector3d scaled = scaleVector(pos);
    
    for (int i = 0; i < 3; i++) 
      scaled[i] -= roundMe(scaled[i]);
    
    if( !frameData.orthoRhombic )
      pos = frameData.hmat * scaled;    
    else {
      
      // calc the wrapped real coordinates from the wrapped scaled coordinates
      for (int i=0; i<3; i++) {
        pos[i] = scaled[i] * frameData.hmat(i, i);
      }   
    }
  }

  /** Scaling a vector to multiples of the periodic box */
  inline Vector3d Snapshot::scaleVector(Vector3d& pos) {   
    
    Vector3d scaled;

    if( !frameData.orthoRhombic )
      scaled = frameData.invHmat * pos;
    else {
      // calc the scaled coordinates.
      for (int i=0; i<3; i++) 
        scaled[i] = pos[i] * frameData.invHmat(i, i);
    }

    return scaled;
  }

  void Snapshot::setCOM(const Vector3d& com) {
    frameData.COM = com;
    hasCOM = true;
  }
  
  void Snapshot::setCOMvel(const Vector3d& comVel) {
    frameData.COMvel = comVel;
    hasCOMvel = true;
  }
  
  void Snapshot::setCOMw(const Vector3d& comw) {
    frameData.COMw = comw;
    hasCOMw = true;
  }
  
  Vector3d Snapshot::getCOM() {
    return frameData.COM;
  }
  
  Vector3d Snapshot::getCOMvel() {
    return frameData.COMvel;
  }
  
  Vector3d Snapshot::getCOMw() {
    return frameData.COMw;
  }
  
  RealType Snapshot::getTime() {
    return frameData.currentTime;
  }
  
  void Snapshot::increaseTime(RealType dt) {
    setTime(getTime() + dt);
  }
  
  void Snapshot::setTime(RealType time) {
    frameData.currentTime = time;
  }
 
  void Snapshot::setBondPotential(RealType bp) {
    frameData.bondPotential = bp;
  }
  
  void Snapshot::setBendPotential(RealType bp) {
    frameData.bendPotential = bp;
  }
  
  void Snapshot::setTorsionPotential(RealType tp) {
    frameData.torsionPotential = tp;
  }
  
  void Snapshot::setInversionPotential(RealType ip) {
    frameData.inversionPotential = ip;
  }


  RealType Snapshot::getBondPotential() {
    return frameData.bondPotential;
  }
  RealType Snapshot::getBendPotential() {
    return frameData.bendPotential;
  }
  RealType Snapshot::getTorsionPotential() {
    return frameData.torsionPotential;
  }
  RealType Snapshot::getInversionPotential() {
    return frameData.inversionPotential;
  }

  RealType Snapshot::getShortRangePotential() {
    if (!hasShortRangePotential) {
      frameData.shortRangePotential = frameData.bondPotential;
      frameData.shortRangePotential += frameData.bendPotential;
      frameData.shortRangePotential += frameData.torsionPotential;
      frameData.shortRangePotential += frameData.inversionPotential;
      hasShortRangePotential = true;
    }
    return frameData.shortRangePotential;
  }

  void Snapshot::setLongRangePotential(potVec lrPot) {
    frameData.lrPotentials = lrPot;
  }
    
  RealType Snapshot::getLongRangePotential() {
    if (!hasLongRangePotential) {
      for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
        frameData.longRangePotential += frameData.lrPotentials[i];
      }
      hasLongRangePotential = true;
    }   
    return frameData.longRangePotential;
  }

  potVec Snapshot::getLongRangePotentials() {
    return frameData.lrPotentials;
  }

  RealType Snapshot::getPotentialEnergy() {
    if (!hasPotentialEnergy) {
      frameData.potentialEnergy = this->getLongRangePotential();
      frameData.potentialEnergy += this->getShortRangePotential();
      hasPotentialEnergy = true;
    }
    return frameData.potentialEnergy;
  }
    
  void Snapshot::setExcludedPotentials(potVec exPot) {
    frameData.excludedPotentials = exPot;
  }

  potVec Snapshot::getExcludedPotentials() {
    return frameData.excludedPotentials;
  }
      
  void Snapshot::setRestraintPotential(RealType rp) {
    frameData.restraintPotential = rp;
  }
  
  RealType Snapshot::getRestraintPotential() {
    return frameData.restraintPotential;
  }
  
  void Snapshot::setRawPotential(RealType rp) {
    frameData.rawPotential = rp;
  }
  
  RealType Snapshot::getRawPotential() {
    return frameData.rawPotential;
  }

  RealType Snapshot::getTranslationalKineticEnergy() {
    return frameData.translationalKinetic;
  }

  RealType Snapshot::getRotationalKineticEnergy() {
    return frameData.rotationalKinetic;
  }

  RealType Snapshot::getKineticEnergy() {
    return frameData.kineticEnergy;
  }

  void Snapshot::setTranslationalKineticEnergy(RealType tke) {
    hasTranslationalKineticEnergy = true;
    frameData.translationalKinetic = tke;
  }

  void Snapshot::setRotationalKineticEnergy(RealType rke) {
    hasRotationalKineticEnergy = true;
    frameData.rotationalKinetic = rke;
  }

  void Snapshot::setKineticEnergy(RealType ke) {
    hasKineticEnergy = true;
    frameData.kineticEnergy = ke;
  }

  RealType Snapshot::getTotalEnergy() {
    return frameData.totalEnergy;
  }

  void Snapshot::setTotalEnergy(RealType te) {
    hasTotalEnergy = true;
    frameData.totalEnergy = te;
  }

  RealType Snapshot::getConservedQuantity() {
    return frameData.conservedQuantity;
  }

  void Snapshot::setConservedQuantity(RealType cq) {
    hasConservedQuantity = true;
    frameData.conservedQuantity = cq;
  }

  RealType Snapshot::getTemperature() {
    return frameData.temperature;
  }

  void Snapshot::setTemperature(RealType temp) {
    hasTemperature = true;
    frameData.temperature = temp;
  }

  RealType Snapshot::getElectronicTemperature() {
    return frameData.electronicTemperature;
  }

  void Snapshot::setElectronicTemperature(RealType eTemp) {
    hasElectronicTemperature = true;
    frameData.electronicTemperature = eTemp;
  }

  RealType Snapshot::getPressure() {
    return frameData.pressure;
  }

  void Snapshot::setPressure(RealType pressure) {
    hasPressure = true;
    frameData.pressure = pressure;
  }

  Mat3x3d Snapshot::getPressureTensor() {
    return frameData.pressureTensor;
  }


  void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) {
    hasPressureTensor = true;
    frameData.pressureTensor = pressureTensor;
  }

  void Snapshot::setStressTensor(const Mat3x3d& stressTensor) {
    frameData.stressTensor = stressTensor;
  }

  Mat3x3d  Snapshot::getStressTensor() {
    return frameData.stressTensor;
  }

  void Snapshot::setConductiveHeatFlux(const Vector3d& chf) {
    frameData.conductiveHeatFlux = chf;
  }

  Vector3d Snapshot::getConductiveHeatFlux() {
    return frameData.conductiveHeatFlux;
  }
  
  Vector3d Snapshot::getConvectiveHeatFlux() {
    return frameData.convectiveHeatFlux;
  }

  void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) {    
    hasConvectiveHeatFlux = true;
    frameData.convectiveHeatFlux = chf;
  }

  Vector3d Snapshot::getHeatFlux() {
    // BE CAREFUL WITH UNITS
    return getConductiveHeatFlux() + getConvectiveHeatFlux();
  }

  Vector3d Snapshot::getSystemDipole() {
    return frameData.systemDipole;
  }

  void Snapshot::setSystemDipole(const Vector3d& bd) {    
    hasSystemDipole = true;
    frameData.systemDipole = bd;
  }

  void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) {
    frameData.thermostat = thermostat;
  }

  pair<RealType, RealType> Snapshot::getThermostat() {
    return frameData.thermostat;
  }

  void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) {
    frameData.electronicThermostat = eTherm;
  }

  pair<RealType, RealType> Snapshot::getElectronicThermostat() {
    return frameData.electronicThermostat;
  }
 
  void Snapshot::setBarostat(const Mat3x3d& barostat) {
    frameData.barostat = barostat;
  }

  Mat3x3d Snapshot::getBarostat() {
    return frameData.barostat;
  }

  void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) {
    frameData.inertiaTensor = inertiaTensor;
    hasInertiaTensor = true;
  }

  Mat3x3d Snapshot::getInertiaTensor() {
    return frameData.inertiaTensor;
  }

  void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) {
    frameData.gyrationalVolume = gyrationalVolume;
    hasGyrationalVolume = true;
  }

  RealType Snapshot::getGyrationalVolume() {
    return frameData.gyrationalVolume;
  }

  void Snapshot::setHullVolume(const RealType hullVolume) {
    frameData.hullVolume = hullVolume;
    hasHullVolume = true;
  }

  RealType Snapshot::getHullVolume() {
    return frameData.hullVolume;
  }

  void Snapshot::setOrthoTolerance(RealType ot) {
    orthoTolerance_ = ot;
  }
}
Revision:	1858
Committed:	Wed Apr 3 21:32:13 2013 UTC (12 years ago) by gezelter
File size:	18792 byte(s)
Log Message:	Some bugfixes for cell-linked-list-style neighbor lists when the simulation doesn't use periodic boundary conditions. Cleaning up some of the Hull stuff while we're in there.
#	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, 234107 (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.bBox = Mat3x3d(0.0);
99	frameData.invBbox = Mat3x3d(0.0);
100	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
117	clearDerivedProperties();
118	}
119
120	void Snapshot::clearDerivedProperties() {
121	frameData.totalEnergy = 0.0;
122	frameData.translationalKinetic = 0.0;
123	frameData.rotationalKinetic = 0.0;
124	frameData.kineticEnergy = 0.0;
125	frameData.potentialEnergy = 0.0;
126	frameData.shortRangePotential = 0.0;
127	frameData.longRangePotential = 0.0;
128	frameData.pressure = 0.0;
129	frameData.temperature = 0.0;
130	frameData.pressureTensor = Mat3x3d(0.0);
131	frameData.systemDipole = Vector3d(0.0);
132	frameData.convectiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
133	frameData.electronicTemperature = 0.0;
134	frameData.COM = V3Zero;
135	frameData.COMvel = V3Zero;
136	frameData.COMw = V3Zero;
137
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	}
161
162	/** Returns the id of this Snapshot */
163	int Snapshot::getID() {
164	return frameData.id;
165	}
166
167	/** Sets the id of this Snapshot */
168	void Snapshot::setID(int id) {
169	frameData.id = id;
170	}
171
172	int Snapshot::getSize() {
173	return atomData.getSize() + rigidbodyData.getSize();
174	}
175
176	/** Returns the number of atoms */
177	int Snapshot::getNumberOfAtoms() {
178	return atomData.getSize();
179	}
180
181	/** Returns the number of rigid bodies */
182	int Snapshot::getNumberOfRigidBodies() {
183	return rigidbodyData.getSize();
184	}
185
186	/** Returns the number of rigid bodies */
187	int Snapshot::getNumberOfCutoffGroups() {
188	return cgData.getSize();
189	}
190
191	/** Returns the H-Matrix */
192	Mat3x3d Snapshot::getHmat() {
193	return frameData.hmat;
194	}
195
196	/** Sets the H-Matrix */
197	void Snapshot::setHmat(const Mat3x3d& m) {
198	hasVolume = false;
199	frameData.hmat = m;
200	frameData.invHmat = frameData.hmat.inverse();
201
202	//determine whether the box is orthoTolerance or not
203	bool oldOrthoRhombic = frameData.orthoRhombic;
204
205	RealType smallDiag = fabs(frameData.hmat(0, 0));
206	if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
207	if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));
208	RealType tol = smallDiag * orthoTolerance_;
209
210	frameData.orthoRhombic = true;
211
212	for (int i = 0; i < 3; i++ ) {
213	for (int j = 0 ; j < 3; j++) {
214	if (i != j) {
215	if (frameData.orthoRhombic) {
216	if ( fabs(frameData.hmat(i, j)) >= tol)
217	frameData.orthoRhombic = false;
218	}
219	}
220	}
221	}
222
223	if( oldOrthoRhombic != frameData.orthoRhombic){
224
225	// It is finally time to suppress these warnings once and for
226	// all. They were annoying and not very informative.
227
228	// if( frameData.orthoRhombic ) {
229	// sprintf( painCave.errMsg,
230	// "OpenMD is switching from the default Non-Orthorhombic\n"
231	// "\tto the faster Orthorhombic periodic boundary computations.\n"
232	// "\tThis is usually a good thing, but if you want the\n"
233	// "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
234	// "\tvariable ( currently set to %G ) smaller.\n",
235	// orthoTolerance_);
236	// painCave.severity = OPENMD_INFO;
237	// simError();
238	// }
239	// else {
240	// sprintf( painCave.errMsg,
241	// "OpenMD is switching from the faster Orthorhombic to the more\n"
242	// "\tflexible Non-Orthorhombic periodic boundary computations.\n"
243	// "\tThis is usually because the box has deformed under\n"
244	// "\tNPTf integration. If you want to live on the edge with\n"
245	// "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
246	// "\tvariable ( currently set to %G ) larger.\n",
247	// orthoTolerance_);
248	// painCave.severity = OPENMD_WARNING;
249	// simError();
250	// }
251	}
252	}
253
254	/** Returns the inverse H-Matrix */
255	Mat3x3d Snapshot::getInvHmat() {
256	return frameData.invHmat;
257	}
258
259	/** Returns the Bounding Box */
260	Mat3x3d Snapshot::getBoundingBox() {
261	return frameData.bBox;
262	}
263
264	/** Sets the Bounding Box */
265	void Snapshot::setBoundingBox(const Mat3x3d& m) {
266	frameData.bBox = m;
267	frameData.invBbox = frameData.bBox.inverse();
268	}
269
270	/** Returns the inverse Bounding Box */
271	Mat3x3d Snapshot::getInvBoundingBox() {
272	return frameData.invBbox;
273	}
274
275	RealType Snapshot::getXYarea() {
276	if (!hasXYarea) {
277	Vector3d x = frameData.hmat.getColumn(0);
278	Vector3d y = frameData.hmat.getColumn(1);
279	frameData.xyArea = cross(x,y).length();
280	hasXYarea = true;
281	}
282	return frameData.xyArea;
283	}
284
285	RealType Snapshot::getVolume() {
286	if (!hasVolume) {
287	frameData.volume = frameData.hmat.determinant();
288	hasVolume = true;
289	}
290	return frameData.volume;
291	}
292
293	void Snapshot::setVolume(RealType vol) {
294	hasVolume = true;
295	frameData.volume = vol;
296	}
297
298	/** Wrap a vector according to periodic boundary conditions */
299	void Snapshot::wrapVector(Vector3d& pos) {
300
301	Vector3d scaled = scaleVector(pos);
302
303	for (int i = 0; i < 3; i++)
304	scaled[i] -= roundMe(scaled[i]);
305
306	if( !frameData.orthoRhombic )
307	pos = frameData.hmat * scaled;
308	else {
309
310	// calc the wrapped real coordinates from the wrapped scaled coordinates
311	for (int i=0; i<3; i++) {
312	pos[i] = scaled[i] * frameData.hmat(i, i);
313	}
314	}
315	}
316
317	/** Scaling a vector to multiples of the periodic box */
318	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
319
320	Vector3d scaled;
321
322	if( !frameData.orthoRhombic )
323	scaled = frameData.invHmat * pos;
324	else {
325	// calc the scaled coordinates.
326	for (int i=0; i<3; i++)
327	scaled[i] = pos[i] * frameData.invHmat(i, i);
328	}
329
330	return scaled;
331	}
332
333	void Snapshot::setCOM(const Vector3d& com) {
334	frameData.COM = com;
335	hasCOM = true;
336	}
337
338	void Snapshot::setCOMvel(const Vector3d& comVel) {
339	frameData.COMvel = comVel;
340	hasCOMvel = true;
341	}
342
343	void Snapshot::setCOMw(const Vector3d& comw) {
344	frameData.COMw = comw;
345	hasCOMw = true;
346	}
347
348	Vector3d Snapshot::getCOM() {
349	return frameData.COM;
350	}
351
352	Vector3d Snapshot::getCOMvel() {
353	return frameData.COMvel;
354	}
355
356	Vector3d Snapshot::getCOMw() {
357	return frameData.COMw;
358	}
359
360	RealType Snapshot::getTime() {
361	return frameData.currentTime;
362	}
363
364	void Snapshot::increaseTime(RealType dt) {
365	setTime(getTime() + dt);
366	}
367
368	void Snapshot::setTime(RealType time) {
369	frameData.currentTime = time;
370	}
371
372	void Snapshot::setBondPotential(RealType bp) {
373	frameData.bondPotential = bp;
374	}
375
376	void Snapshot::setBendPotential(RealType bp) {
377	frameData.bendPotential = bp;
378	}
379
380	void Snapshot::setTorsionPotential(RealType tp) {
381	frameData.torsionPotential = tp;
382	}
383
384	void Snapshot::setInversionPotential(RealType ip) {
385	frameData.inversionPotential = ip;
386	}
387
388
389	RealType Snapshot::getBondPotential() {
390	return frameData.bondPotential;
391	}
392	RealType Snapshot::getBendPotential() {
393	return frameData.bendPotential;
394	}
395	RealType Snapshot::getTorsionPotential() {
396	return frameData.torsionPotential;
397	}
398	RealType Snapshot::getInversionPotential() {
399	return frameData.inversionPotential;
400	}
401
402	RealType Snapshot::getShortRangePotential() {
403	if (!hasShortRangePotential) {
404	frameData.shortRangePotential = frameData.bondPotential;
405	frameData.shortRangePotential += frameData.bendPotential;
406	frameData.shortRangePotential += frameData.torsionPotential;
407	frameData.shortRangePotential += frameData.inversionPotential;
408	hasShortRangePotential = true;
409	}
410	return frameData.shortRangePotential;
411	}
412
413	void Snapshot::setLongRangePotential(potVec lrPot) {
414	frameData.lrPotentials = lrPot;
415	}
416
417	RealType Snapshot::getLongRangePotential() {
418	if (!hasLongRangePotential) {
419	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
420	frameData.longRangePotential += frameData.lrPotentials[i];
421	}
422	hasLongRangePotential = true;
423	}
424	return frameData.longRangePotential;
425	}
426
427	potVec Snapshot::getLongRangePotentials() {
428	return frameData.lrPotentials;
429	}
430
431	RealType Snapshot::getPotentialEnergy() {
432	if (!hasPotentialEnergy) {
433	frameData.potentialEnergy = this->getLongRangePotential();
434	frameData.potentialEnergy += this->getShortRangePotential();
435	hasPotentialEnergy = true;
436	}
437	return frameData.potentialEnergy;
438	}
439
440	void Snapshot::setExcludedPotentials(potVec exPot) {
441	frameData.excludedPotentials = exPot;
442	}
443
444	potVec Snapshot::getExcludedPotentials() {
445	return frameData.excludedPotentials;
446	}
447
448	void Snapshot::setRestraintPotential(RealType rp) {
449	frameData.restraintPotential = rp;
450	}
451
452	RealType Snapshot::getRestraintPotential() {
453	return frameData.restraintPotential;
454	}
455
456	void Snapshot::setRawPotential(RealType rp) {
457	frameData.rawPotential = rp;
458	}
459
460	RealType Snapshot::getRawPotential() {
461	return frameData.rawPotential;
462	}
463
464	RealType Snapshot::getTranslationalKineticEnergy() {
465	return frameData.translationalKinetic;
466	}
467
468	RealType Snapshot::getRotationalKineticEnergy() {
469	return frameData.rotationalKinetic;
470	}
471
472	RealType Snapshot::getKineticEnergy() {
473	return frameData.kineticEnergy;
474	}
475
476	void Snapshot::setTranslationalKineticEnergy(RealType tke) {
477	hasTranslationalKineticEnergy = true;
478	frameData.translationalKinetic = tke;
479	}
480
481	void Snapshot::setRotationalKineticEnergy(RealType rke) {
482	hasRotationalKineticEnergy = true;
483	frameData.rotationalKinetic = rke;
484	}
485
486	void Snapshot::setKineticEnergy(RealType ke) {
487	hasKineticEnergy = true;
488	frameData.kineticEnergy = ke;
489	}
490
491	RealType Snapshot::getTotalEnergy() {
492	return frameData.totalEnergy;
493	}
494
495	void Snapshot::setTotalEnergy(RealType te) {
496	hasTotalEnergy = true;
497	frameData.totalEnergy = te;
498	}
499
500	RealType Snapshot::getConservedQuantity() {
501	return frameData.conservedQuantity;
502	}
503
504	void Snapshot::setConservedQuantity(RealType cq) {
505	hasConservedQuantity = true;
506	frameData.conservedQuantity = cq;
507	}
508
509	RealType Snapshot::getTemperature() {
510	return frameData.temperature;
511	}
512
513	void Snapshot::setTemperature(RealType temp) {
514	hasTemperature = true;
515	frameData.temperature = temp;
516	}
517
518	RealType Snapshot::getElectronicTemperature() {
519	return frameData.electronicTemperature;
520	}
521
522	void Snapshot::setElectronicTemperature(RealType eTemp) {
523	hasElectronicTemperature = true;
524	frameData.electronicTemperature = eTemp;
525	}
526
527	RealType Snapshot::getPressure() {
528	return frameData.pressure;
529	}
530
531	void Snapshot::setPressure(RealType pressure) {
532	hasPressure = true;
533	frameData.pressure = pressure;
534	}
535
536	Mat3x3d Snapshot::getPressureTensor() {
537	return frameData.pressureTensor;
538	}
539
540
541	void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) {
542	hasPressureTensor = true;
543	frameData.pressureTensor = pressureTensor;
544	}
545
546	void Snapshot::setStressTensor(const Mat3x3d& stressTensor) {
547	frameData.stressTensor = stressTensor;
548	}
549
550	Mat3x3d Snapshot::getStressTensor() {
551	return frameData.stressTensor;
552	}
553
554	void Snapshot::setConductiveHeatFlux(const Vector3d& chf) {
555	frameData.conductiveHeatFlux = chf;
556	}
557
558	Vector3d Snapshot::getConductiveHeatFlux() {
559	return frameData.conductiveHeatFlux;
560	}
561
562	Vector3d Snapshot::getConvectiveHeatFlux() {
563	return frameData.convectiveHeatFlux;
564	}
565
566	void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) {
567	hasConvectiveHeatFlux = true;
568	frameData.convectiveHeatFlux = chf;
569	}
570
571	Vector3d Snapshot::getHeatFlux() {
572	// BE CAREFUL WITH UNITS
573	return getConductiveHeatFlux() + getConvectiveHeatFlux();
574	}
575
576	Vector3d Snapshot::getSystemDipole() {
577	return frameData.systemDipole;
578	}
579
580	void Snapshot::setSystemDipole(const Vector3d& bd) {
581	hasSystemDipole = true;
582	frameData.systemDipole = bd;
583	}
584
585	void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) {
586	frameData.thermostat = thermostat;
587	}
588
589	pair<RealType, RealType> Snapshot::getThermostat() {
590	return frameData.thermostat;
591	}
592
593	void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) {
594	frameData.electronicThermostat = eTherm;
595	}
596
597	pair<RealType, RealType> Snapshot::getElectronicThermostat() {
598	return frameData.electronicThermostat;
599	}
600
601	void Snapshot::setBarostat(const Mat3x3d& barostat) {
602	frameData.barostat = barostat;
603	}
604
605	Mat3x3d Snapshot::getBarostat() {
606	return frameData.barostat;
607	}
608
609	void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) {
610	frameData.inertiaTensor = inertiaTensor;
611	hasInertiaTensor = true;
612	}
613
614	Mat3x3d Snapshot::getInertiaTensor() {
615	return frameData.inertiaTensor;
616	}
617
618	void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) {
619	frameData.gyrationalVolume = gyrationalVolume;
620	hasGyrationalVolume = true;
621	}
622
623	RealType Snapshot::getGyrationalVolume() {
624	return frameData.gyrationalVolume;
625	}
626
627	void Snapshot::setHullVolume(const RealType hullVolume) {
628	frameData.hullVolume = hullVolume;
629	hasHullVolume = true;
630	}
631
632	RealType Snapshot::getHullVolume() {
633	return frameData.hullVolume;
634	}
635
636	void Snapshot::setOrthoTolerance(RealType ot) {
637	orthoTolerance_ = ot;
638	}
639	}