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
 * @time 10:56am
 * @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.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.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;     
    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){
      
      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::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:	1764
Committed:	Tue Jul 3 18:32:27 2012 UTC (12 years, 9 months ago) by gezelter
File size:	17681 byte(s)
Log Message:	Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged 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, 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	* @time 10:56am
48	* @version 1.0
49	*/
50
51	#include "brains/Snapshot.hpp"
52	#include "utils/NumericConstant.hpp"
53	#include "utils/simError.h"
54	#include "utils/Utility.hpp"
55	#include <cstdio>
56
57	namespace OpenMD {
58
59	Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups) :
60	atomData(nAtoms), rigidbodyData(nRigidbodies),
61	cgData(nCutoffGroups, DataStorage::dslPosition),
62	orthoTolerance_(1e-6) {
63
64	frameData.id = -1;
65	frameData.currentTime = 0;
66	frameData.hmat = Mat3x3d(0.0);
67	frameData.invHmat = Mat3x3d(0.0);
68	frameData.orthoRhombic = false;
69	frameData.bondPotential = 0.0;
70	frameData.bendPotential = 0.0;
71	frameData.torsionPotential = 0.0;
72	frameData.inversionPotential = 0.0;
73	frameData.lrPotentials = potVec(0.0);
74	frameData.excludedPotentials = potVec(0.0);
75	frameData.restraintPotential = 0.0;
76	frameData.rawPotential = 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.volume = 0.0;
108	frameData.thermostat = make_pair(0.0, 0.0);
109	frameData.electronicThermostat = make_pair(0.0, 0.0);
110	frameData.barostat = Mat3x3d(0.0);
111	frameData.stressTensor = Mat3x3d(0.0);
112	frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
113
114	clearDerivedProperties();
115	}
116
117	void Snapshot::clearDerivedProperties() {
118	frameData.totalEnergy = 0.0;
119	frameData.translationalKinetic = 0.0;
120	frameData.rotationalKinetic = 0.0;
121	frameData.kineticEnergy = 0.0;
122	frameData.potentialEnergy = 0.0;
123	frameData.shortRangePotential = 0.0;
124	frameData.longRangePotential = 0.0;
125	frameData.pressure = 0.0;
126	frameData.temperature = 0.0;
127	frameData.pressureTensor = Mat3x3d(0.0);
128	frameData.systemDipole = Vector3d(0.0);
129	frameData.convectiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
130	frameData.electronicTemperature = 0.0;
131	frameData.COM = V3Zero;
132	frameData.COMvel = V3Zero;
133	frameData.COMw = V3Zero;
134
135	hasTotalEnergy = false;
136	hasTranslationalKineticEnergy = false;
137	hasRotationalKineticEnergy = false;
138	hasKineticEnergy = false;
139	hasShortRangePotential = false;
140	hasLongRangePotential = false;
141	hasPotentialEnergy = false;
142	hasVolume = false;
143	hasPressure = false;
144	hasTemperature = false;
145	hasElectronicTemperature = false;
146	hasCOM = false;
147	hasCOMvel = false;
148	hasCOMw = false;
149	hasPressureTensor = false;
150	hasSystemDipole = false;
151	hasConvectiveHeatFlux = false;
152	hasInertiaTensor = false;
153	hasGyrationalVolume = false;
154	hasHullVolume = false;
155	hasConservedQuantity = false;
156	}
157
158	/** Returns the id of this Snapshot */
159	int Snapshot::getID() {
160	return frameData.id;
161	}
162
163	/** Sets the id of this Snapshot */
164	void Snapshot::setID(int id) {
165	frameData.id = id;
166	}
167
168	int Snapshot::getSize() {
169	return atomData.getSize() + rigidbodyData.getSize();
170	}
171
172	/** Returns the number of atoms */
173	int Snapshot::getNumberOfAtoms() {
174	return atomData.getSize();
175	}
176
177	/** Returns the number of rigid bodies */
178	int Snapshot::getNumberOfRigidBodies() {
179	return rigidbodyData.getSize();
180	}
181
182	/** Returns the number of rigid bodies */
183	int Snapshot::getNumberOfCutoffGroups() {
184	return cgData.getSize();
185	}
186
187	/** Returns the H-Matrix */
188	Mat3x3d Snapshot::getHmat() {
189	return frameData.hmat;
190	}
191
192	/** Sets the H-Matrix */
193	void Snapshot::setHmat(const Mat3x3d& m) {
194	hasVolume = false;
195	frameData.hmat = m;
196	frameData.invHmat = frameData.hmat.inverse();
197
198	//determine whether the box is orthoTolerance or not
199	bool oldOrthoRhombic = frameData.orthoRhombic;
200
201	RealType smallDiag = fabs(frameData.hmat(0, 0));
202	if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
203	if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));
204	RealType tol = smallDiag * orthoTolerance_;
205
206	frameData.orthoRhombic = true;
207
208	for (int i = 0; i < 3; i++ ) {
209	for (int j = 0 ; j < 3; j++) {
210	if (i != j) {
211	if (frameData.orthoRhombic) {
212	if ( fabs(frameData.hmat(i, j)) >= tol)
213	frameData.orthoRhombic = false;
214	}
215	}
216	}
217	}
218
219	if( oldOrthoRhombic != frameData.orthoRhombic){
220
221	if( frameData.orthoRhombic ) {
222	sprintf( painCave.errMsg,
223	"OpenMD is switching from the default Non-Orthorhombic\n"
224	"\tto the faster Orthorhombic periodic boundary computations.\n"
225	"\tThis is usually a good thing, but if you want the\n"
226	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
227	"\tvariable ( currently set to %G ) smaller.\n",
228	orthoTolerance_);
229	painCave.severity = OPENMD_INFO;
230	simError();
231	}
232	else {
233	sprintf( painCave.errMsg,
234	"OpenMD is switching from the faster Orthorhombic to the more\n"
235	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
236	"\tThis is usually because the box has deformed under\n"
237	"\tNPTf integration. If you want to live on the edge with\n"
238	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
239	"\tvariable ( currently set to %G ) larger.\n",
240	orthoTolerance_);
241	painCave.severity = OPENMD_WARNING;
242	simError();
243	}
244	}
245	}
246
247	/** Returns the inverse H-Matrix */
248	Mat3x3d Snapshot::getInvHmat() {
249	return frameData.invHmat;
250	}
251
252	RealType Snapshot::getVolume() {
253	if (!hasVolume) {
254	frameData.volume = frameData.hmat.determinant();
255	hasVolume = true;
256	}
257	return frameData.volume;
258	}
259
260	void Snapshot::setVolume(RealType vol) {
261	hasVolume = true;
262	frameData.volume = vol;
263	}
264
265	/** Wrap a vector according to periodic boundary conditions */
266	void Snapshot::wrapVector(Vector3d& pos) {
267
268	Vector3d scaled = scaleVector(pos);
269
270	for (int i = 0; i < 3; i++)
271	scaled[i] -= roundMe(scaled[i]);
272
273	if( !frameData.orthoRhombic )
274	pos = frameData.hmat * scaled;
275	else {
276
277	// calc the wrapped real coordinates from the wrapped scaled coordinates
278	for (int i=0; i<3; i++) {
279	pos[i] = scaled[i] * frameData.hmat(i, i);
280	}
281	}
282	}
283
284	/** Scaling a vector to multiples of the periodic box */
285	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
286
287	Vector3d scaled;
288
289	if( !frameData.orthoRhombic )
290	scaled = frameData.invHmat * pos;
291	else {
292	// calc the scaled coordinates.
293	for (int i=0; i<3; i++)
294	scaled[i] = pos[i] * frameData.invHmat(i, i);
295	}
296
297	return scaled;
298	}
299
300	void Snapshot::setCOM(const Vector3d& com) {
301	frameData.COM = com;
302	hasCOM = true;
303	}
304
305	void Snapshot::setCOMvel(const Vector3d& comVel) {
306	frameData.COMvel = comVel;
307	hasCOMvel = true;
308	}
309
310	void Snapshot::setCOMw(const Vector3d& comw) {
311	frameData.COMw = comw;
312	hasCOMw = true;
313	}
314
315	Vector3d Snapshot::getCOM() {
316	return frameData.COM;
317	}
318
319	Vector3d Snapshot::getCOMvel() {
320	return frameData.COMvel;
321	}
322
323	Vector3d Snapshot::getCOMw() {
324	return frameData.COMw;
325	}
326
327	RealType Snapshot::getTime() {
328	return frameData.currentTime;
329	}
330
331	void Snapshot::increaseTime(RealType dt) {
332	setTime(getTime() + dt);
333	}
334
335	void Snapshot::setTime(RealType time) {
336	frameData.currentTime = time;
337	}
338
339	void Snapshot::setBondPotential(RealType bp) {
340	frameData.bondPotential = bp;
341	}
342
343	void Snapshot::setBendPotential(RealType bp) {
344	frameData.bendPotential = bp;
345	}
346
347	void Snapshot::setTorsionPotential(RealType tp) {
348	frameData.torsionPotential = tp;
349	}
350
351	void Snapshot::setInversionPotential(RealType ip) {
352	frameData.inversionPotential = ip;
353	}
354
355
356	RealType Snapshot::getBondPotential() {
357	return frameData.bondPotential;
358	}
359	RealType Snapshot::getBendPotential() {
360	return frameData.bendPotential;
361	}
362	RealType Snapshot::getTorsionPotential() {
363	return frameData.torsionPotential;
364	}
365	RealType Snapshot::getInversionPotential() {
366	return frameData.inversionPotential;
367	}
368
369	RealType Snapshot::getShortRangePotential() {
370	if (!hasShortRangePotential) {
371	frameData.shortRangePotential = frameData.bondPotential;
372	frameData.shortRangePotential += frameData.bendPotential;
373	frameData.shortRangePotential += frameData.torsionPotential;
374	frameData.shortRangePotential += frameData.inversionPotential;
375	hasShortRangePotential = true;
376	}
377	return frameData.shortRangePotential;
378	}
379
380	void Snapshot::setLongRangePotential(potVec lrPot) {
381	frameData.lrPotentials = lrPot;
382	}
383
384	RealType Snapshot::getLongRangePotential() {
385	if (!hasLongRangePotential) {
386	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
387	frameData.longRangePotential += frameData.lrPotentials[i];
388	}
389	hasLongRangePotential = true;
390	}
391	return frameData.longRangePotential;
392	}
393
394	potVec Snapshot::getLongRangePotentials() {
395	return frameData.lrPotentials;
396	}
397
398	RealType Snapshot::getPotentialEnergy() {
399	if (!hasPotentialEnergy) {
400	frameData.potentialEnergy = this->getLongRangePotential();
401	frameData.potentialEnergy += this->getShortRangePotential();
402	hasPotentialEnergy = true;
403	}
404	return frameData.potentialEnergy;
405	}
406
407	void Snapshot::setExcludedPotentials(potVec exPot) {
408	frameData.excludedPotentials = exPot;
409	}
410
411	potVec Snapshot::getExcludedPotentials() {
412	return frameData.excludedPotentials;
413	}
414
415	void Snapshot::setRestraintPotential(RealType rp) {
416	frameData.restraintPotential = rp;
417	}
418
419	RealType Snapshot::getRestraintPotential() {
420	return frameData.restraintPotential;
421	}
422
423	void Snapshot::setRawPotential(RealType rp) {
424	frameData.rawPotential = rp;
425	}
426
427	RealType Snapshot::getRawPotential() {
428	return frameData.rawPotential;
429	}
430
431	RealType Snapshot::getTranslationalKineticEnergy() {
432	return frameData.translationalKinetic;
433	}
434
435	RealType Snapshot::getRotationalKineticEnergy() {
436	return frameData.rotationalKinetic;
437	}
438
439	RealType Snapshot::getKineticEnergy() {
440	return frameData.kineticEnergy;
441	}
442
443	void Snapshot::setTranslationalKineticEnergy(RealType tke) {
444	hasTranslationalKineticEnergy = true;
445	frameData.translationalKinetic = tke;
446	}
447
448	void Snapshot::setRotationalKineticEnergy(RealType rke) {
449	hasRotationalKineticEnergy = true;
450	frameData.rotationalKinetic = rke;
451	}
452
453	void Snapshot::setKineticEnergy(RealType ke) {
454	hasKineticEnergy = true;
455	frameData.kineticEnergy = ke;
456	}
457
458	RealType Snapshot::getTotalEnergy() {
459	return frameData.totalEnergy;
460	}
461
462	void Snapshot::setTotalEnergy(RealType te) {
463	hasTotalEnergy = true;
464	frameData.totalEnergy = te;
465	}
466
467	RealType Snapshot::getConservedQuantity() {
468	return frameData.conservedQuantity;
469	}
470
471	void Snapshot::setConservedQuantity(RealType cq) {
472	hasConservedQuantity = true;
473	frameData.conservedQuantity = cq;
474	}
475
476	RealType Snapshot::getTemperature() {
477	return frameData.temperature;
478	}
479
480	void Snapshot::setTemperature(RealType temp) {
481	hasTemperature = true;
482	frameData.temperature = temp;
483	}
484
485	RealType Snapshot::getElectronicTemperature() {
486	return frameData.electronicTemperature;
487	}
488
489	void Snapshot::setElectronicTemperature(RealType eTemp) {
490	hasElectronicTemperature = true;
491	frameData.electronicTemperature = eTemp;
492	}
493
494	RealType Snapshot::getPressure() {
495	return frameData.pressure;
496	}
497
498	void Snapshot::setPressure(RealType pressure) {
499	hasPressure = true;
500	frameData.pressure = pressure;
501	}
502
503	Mat3x3d Snapshot::getPressureTensor() {
504	return frameData.pressureTensor;
505	}
506
507
508	void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) {
509	hasPressureTensor = true;
510	frameData.pressureTensor = pressureTensor;
511	}
512
513	void Snapshot::setStressTensor(const Mat3x3d& stressTensor) {
514	frameData.stressTensor = stressTensor;
515	}
516
517	Mat3x3d Snapshot::getStressTensor() {
518	return frameData.stressTensor;
519	}
520
521	void Snapshot::setConductiveHeatFlux(const Vector3d& chf) {
522	frameData.conductiveHeatFlux = chf;
523	}
524
525	Vector3d Snapshot::getConductiveHeatFlux() {
526	return frameData.conductiveHeatFlux;
527	}
528
529	Vector3d Snapshot::getConvectiveHeatFlux() {
530	return frameData.convectiveHeatFlux;
531	}
532
533	void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) {
534	hasConvectiveHeatFlux = true;
535	frameData.convectiveHeatFlux = chf;
536	}
537
538	Vector3d Snapshot::getHeatFlux() {
539	// BE CAREFUL WITH UNITS
540	return getConductiveHeatFlux() + getConvectiveHeatFlux();
541	}
542
543	Vector3d Snapshot::getSystemDipole() {
544	return frameData.systemDipole;
545	}
546
547	void Snapshot::setSystemDipole(const Vector3d& bd) {
548	hasSystemDipole = true;
549	frameData.systemDipole = bd;
550	}
551
552	void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) {
553	frameData.thermostat = thermostat;
554	}
555
556	pair<RealType, RealType> Snapshot::getThermostat() {
557	return frameData.thermostat;
558	}
559
560	void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) {
561	frameData.electronicThermostat = eTherm;
562	}
563
564	pair<RealType, RealType> Snapshot::getElectronicThermostat() {
565	return frameData.electronicThermostat;
566	}
567
568	void Snapshot::setBarostat(const Mat3x3d& barostat) {
569	frameData.barostat = barostat;
570	}
571
572	Mat3x3d Snapshot::getBarostat() {
573	return frameData.barostat;
574	}
575
576	void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) {
577	frameData.inertiaTensor = inertiaTensor;
578	hasInertiaTensor = true;
579	}
580
581	Mat3x3d Snapshot::getInertiaTensor() {
582	return frameData.inertiaTensor;
583	}
584
585	void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) {
586	frameData.gyrationalVolume = gyrationalVolume;
587	hasGyrationalVolume = true;
588	}
589
590	RealType Snapshot::getGyrationalVolume() {
591	return frameData.gyrationalVolume;
592	}
593
594	void Snapshot::setHullVolume(const RealType hullVolume) {
595	frameData.hullVolume = hullVolume;
596	hasHullVolume = true;
597	}
598
599	RealType Snapshot::getHullVolume() {
600	return frameData.hullVolume;
601	}
602
603	void Snapshot::setOrthoTolerance(RealType ot) {
604	orthoTolerance_ = ot;
605	}
606	}