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.reciprocalPotential = 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.reciprocalPotential = 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.systemQuadrupole = Mat3x3d(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;      
    hasSystemQuadrupole = false;
    hasConvectiveHeatFlux = false;  
    hasInertiaTensor = false;
    hasGyrationalVolume = false;   
    hasHullVolume = false;
    hasConservedQuantity = false; 
    hasBoundingBox = false;
  }

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

    /** Returns the number of bytes in a FrameData structure */
  int Snapshot::getFrameDataSize() {
    return sizeof(FrameData);
  }
  
  /** Returns the H-Matrix */
  Mat3x3d Snapshot::getHmat() {
    return frameData.hmat;
  }

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

    frameData.orthoRhombic = true;

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

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

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

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

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

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

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

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


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

  RealType Snapshot::getReciprocalPotential() {
    return frameData.reciprocalPotential;
  }

  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];
      }
      frameData.longRangePotential += frameData.reciprocalPotential;
      hasLongRangePotential = true;
    }   
    return frameData.longRangePotential;
  }

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

  RealType Snapshot::getPotentialEnergy() {
    if (!hasPotentialEnergy) {
      frameData.potentialEnergy = this->getLongRangePotential();
      frameData.potentialEnergy += this->getShortRangePotential();
      frameData.potentialEnergy += this->getRestraintPotential();
      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;
  }

  Mat3x3d Snapshot::getSystemQuadrupole() {
    return frameData.systemQuadrupole;
  }

  void Snapshot::setSystemQuadrupole(const Mat3x3d& bq) {    
    hasSystemQuadrupole = true;
    frameData.systemQuadrupole = bq;
  }

  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:	2024
Committed:	Thu Oct 16 19:13:51 2014 UTC (10 years, 6 months ago) by gezelter
File size:	19818 byte(s)
Log Message:	Added Radial and Z-projected velocity autocorrelation functions Started to add SequentialProps program Mucking about with angular restraint potentials
#	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.reciprocalPotential = 0.0;
74	frameData.excludedPotentials = potVec(0.0);
75	frameData.restraintPotential = 0.0;
76	frameData.rawPotential = 0.0;
77	frameData.xyArea = 0.0;
78	frameData.volume = 0.0;
79	frameData.thermostat = make_pair(0.0, 0.0);
80	frameData.electronicThermostat = make_pair(0.0, 0.0);
81	frameData.barostat = Mat3x3d(0.0);
82	frameData.stressTensor = Mat3x3d(0.0);
83	frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
84
85	clearDerivedProperties();
86	}
87
88	Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
89	int storageLayout) :
90	atomData(nAtoms, storageLayout),
91	rigidbodyData(nRigidbodies, storageLayout),
92	cgData(nCutoffGroups, DataStorage::dslPosition),
93	orthoTolerance_(1e-6) {
94
95	frameData.id = -1;
96	frameData.currentTime = 0;
97	frameData.hmat = Mat3x3d(0.0);
98	frameData.invHmat = Mat3x3d(0.0);
99	frameData.bBox = Mat3x3d(0.0);
100	frameData.invBbox = Mat3x3d(0.0);
101	frameData.orthoRhombic = false;
102	frameData.bondPotential = 0.0;
103	frameData.bendPotential = 0.0;
104	frameData.torsionPotential = 0.0;
105	frameData.inversionPotential = 0.0;
106	frameData.lrPotentials = potVec(0.0);
107	frameData.reciprocalPotential = 0.0;
108	frameData.excludedPotentials = potVec(0.0);
109	frameData.restraintPotential = 0.0;
110	frameData.rawPotential = 0.0;
111	frameData.xyArea = 0.0;
112	frameData.volume = 0.0;
113	frameData.thermostat = make_pair(0.0, 0.0);
114	frameData.electronicThermostat = make_pair(0.0, 0.0);
115	frameData.barostat = Mat3x3d(0.0);
116	frameData.stressTensor = Mat3x3d(0.0);
117	frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
118
119	clearDerivedProperties();
120	}
121
122	void Snapshot::clearDerivedProperties() {
123	frameData.totalEnergy = 0.0;
124	frameData.translationalKinetic = 0.0;
125	frameData.rotationalKinetic = 0.0;
126	frameData.kineticEnergy = 0.0;
127	frameData.potentialEnergy = 0.0;
128	frameData.shortRangePotential = 0.0;
129	frameData.longRangePotential = 0.0;
130	frameData.pressure = 0.0;
131	frameData.temperature = 0.0;
132	frameData.pressureTensor = Mat3x3d(0.0);
133	frameData.systemDipole = Vector3d(0.0);
134	frameData.systemQuadrupole = Mat3x3d(0.0);
135	frameData.convectiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
136	frameData.electronicTemperature = 0.0;
137	frameData.COM = V3Zero;
138	frameData.COMvel = V3Zero;
139	frameData.COMw = V3Zero;
140
141	hasTotalEnergy = false;
142	hasTranslationalKineticEnergy = false;
143	hasRotationalKineticEnergy = false;
144	hasKineticEnergy = false;
145	hasShortRangePotential = false;
146	hasLongRangePotential = false;
147	hasPotentialEnergy = false;
148	hasXYarea = false;
149	hasVolume = false;
150	hasPressure = false;
151	hasTemperature = false;
152	hasElectronicTemperature = false;
153	hasCOM = false;
154	hasCOMvel = false;
155	hasCOMw = false;
156	hasPressureTensor = false;
157	hasSystemDipole = false;
158	hasSystemQuadrupole = false;
159	hasConvectiveHeatFlux = false;
160	hasInertiaTensor = false;
161	hasGyrationalVolume = false;
162	hasHullVolume = false;
163	hasConservedQuantity = false;
164	hasBoundingBox = false;
165	}
166
167	/** Returns the id of this Snapshot */
168	int Snapshot::getID() {
169	return frameData.id;
170	}
171
172	/** Sets the id of this Snapshot */
173	void Snapshot::setID(int id) {
174	frameData.id = id;
175	}
176
177	int Snapshot::getSize() {
178	return atomData.getSize() + rigidbodyData.getSize();
179	}
180
181	/** Returns the number of atoms */
182	int Snapshot::getNumberOfAtoms() {
183	return atomData.getSize();
184	}
185
186	/** Returns the number of rigid bodies */
187	int Snapshot::getNumberOfRigidBodies() {
188	return rigidbodyData.getSize();
189	}
190
191	/** Returns the number of rigid bodies */
192	int Snapshot::getNumberOfCutoffGroups() {
193	return cgData.getSize();
194	}
195
196	/** Returns the number of bytes in a FrameData structure */
197	int Snapshot::getFrameDataSize() {
198	return sizeof(FrameData);
199	}
200
201	/** Returns the H-Matrix */
202	Mat3x3d Snapshot::getHmat() {
203	return frameData.hmat;
204	}
205
206	/** Sets the H-Matrix */
207	void Snapshot::setHmat(const Mat3x3d& m) {
208	hasVolume = false;
209	frameData.hmat = m;
210	frameData.invHmat = frameData.hmat.inverse();
211
212	//determine whether the box is orthoTolerance or not
213	bool oldOrthoRhombic = frameData.orthoRhombic;
214
215	RealType smallDiag = fabs(frameData.hmat(0, 0));
216	if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
217	if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));
218	RealType tol = smallDiag * orthoTolerance_;
219
220	frameData.orthoRhombic = true;
221
222	for (int i = 0; i < 3; i++ ) {
223	for (int j = 0 ; j < 3; j++) {
224	if (i != j) {
225	if (frameData.orthoRhombic) {
226	if ( fabs(frameData.hmat(i, j)) >= tol)
227	frameData.orthoRhombic = false;
228	}
229	}
230	}
231	}
232
233	if( oldOrthoRhombic != frameData.orthoRhombic){
234
235	// It is finally time to suppress these warnings once and for
236	// all. They were annoying and not very informative.
237
238	// if( frameData.orthoRhombic ) {
239	// sprintf( painCave.errMsg,
240	// "OpenMD is switching from the default Non-Orthorhombic\n"
241	// "\tto the faster Orthorhombic periodic boundary computations.\n"
242	// "\tThis is usually a good thing, but if you want the\n"
243	// "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
244	// "\tvariable ( currently set to %G ) smaller.\n",
245	// orthoTolerance_);
246	// painCave.severity = OPENMD_INFO;
247	// simError();
248	// }
249	// else {
250	// sprintf( painCave.errMsg,
251	// "OpenMD is switching from the faster Orthorhombic to the more\n"
252	// "\tflexible Non-Orthorhombic periodic boundary computations.\n"
253	// "\tThis is usually because the box has deformed under\n"
254	// "\tNPTf integration. If you want to live on the edge with\n"
255	// "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
256	// "\tvariable ( currently set to %G ) larger.\n",
257	// orthoTolerance_);
258	// painCave.severity = OPENMD_WARNING;
259	// simError();
260	// }
261	}
262	}
263
264	/** Returns the inverse H-Matrix */
265	Mat3x3d Snapshot::getInvHmat() {
266	return frameData.invHmat;
267	}
268
269	/** Returns the Bounding Box */
270	Mat3x3d Snapshot::getBoundingBox() {
271	return frameData.bBox;
272	}
273
274	/** Sets the Bounding Box */
275	void Snapshot::setBoundingBox(const Mat3x3d& m) {
276	frameData.bBox = m;
277	frameData.invBbox = frameData.bBox.inverse();
278	hasBoundingBox = true;
279	}
280
281	/** Returns the inverse Bounding Box */
282	Mat3x3d Snapshot::getInvBoundingBox() {
283	return frameData.invBbox;
284	}
285
286	RealType Snapshot::getXYarea() {
287	if (!hasXYarea) {
288	Vector3d x = frameData.hmat.getColumn(0);
289	Vector3d y = frameData.hmat.getColumn(1);
290	frameData.xyArea = cross(x,y).length();
291	hasXYarea = true;
292	}
293	return frameData.xyArea;
294	}
295
296	RealType Snapshot::getVolume() {
297	if (!hasVolume) {
298	frameData.volume = frameData.hmat.determinant();
299	hasVolume = true;
300	}
301	return frameData.volume;
302	}
303
304	void Snapshot::setVolume(RealType vol) {
305	hasVolume = true;
306	frameData.volume = vol;
307	}
308
309
310	/** Wrap a vector according to periodic boundary conditions */
311	void Snapshot::wrapVector(Vector3d& pos) {
312
313	if( !frameData.orthoRhombic ) {
314	Vector3d scaled = frameData.invHmat * pos;
315	for (int i = 0; i < 3; i++) {
316	scaled[i] -= roundMe( scaled[i] );
317	}
318	// calc the wrapped real coordinates from the wrapped scaled coordinates
319	pos = frameData.hmat * scaled;
320	} else {
321	RealType scaled;
322	for (int i=0; i<3; i++) {
323	scaled = pos[i] * frameData.invHmat(i,i);
324	scaled -= roundMe( scaled );
325	pos[i] = scaled * frameData.hmat(i,i);
326	}
327	}
328	}
329
330	/** Scaling a vector to multiples of the periodic box */
331	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
332
333	Vector3d scaled;
334
335	if( !frameData.orthoRhombic )
336	scaled = frameData.invHmat * pos;
337	else {
338	// calc the scaled coordinates.
339	for (int i=0; i<3; i++)
340	scaled[i] = pos[i] * frameData.invHmat(i, i);
341	}
342
343	return scaled;
344	}
345
346	void Snapshot::setCOM(const Vector3d& com) {
347	frameData.COM = com;
348	hasCOM = true;
349	}
350
351	void Snapshot::setCOMvel(const Vector3d& comVel) {
352	frameData.COMvel = comVel;
353	hasCOMvel = true;
354	}
355
356	void Snapshot::setCOMw(const Vector3d& comw) {
357	frameData.COMw = comw;
358	hasCOMw = true;
359	}
360
361	Vector3d Snapshot::getCOM() {
362	return frameData.COM;
363	}
364
365	Vector3d Snapshot::getCOMvel() {
366	return frameData.COMvel;
367	}
368
369	Vector3d Snapshot::getCOMw() {
370	return frameData.COMw;
371	}
372
373	RealType Snapshot::getTime() {
374	return frameData.currentTime;
375	}
376
377	void Snapshot::increaseTime(RealType dt) {
378	setTime(getTime() + dt);
379	}
380
381	void Snapshot::setTime(RealType time) {
382	frameData.currentTime = time;
383	}
384
385	void Snapshot::setBondPotential(RealType bp) {
386	frameData.bondPotential = bp;
387	}
388
389	void Snapshot::setBendPotential(RealType bp) {
390	frameData.bendPotential = bp;
391	}
392
393	void Snapshot::setTorsionPotential(RealType tp) {
394	frameData.torsionPotential = tp;
395	}
396
397	void Snapshot::setInversionPotential(RealType ip) {
398	frameData.inversionPotential = ip;
399	}
400
401
402	RealType Snapshot::getBondPotential() {
403	return frameData.bondPotential;
404	}
405	RealType Snapshot::getBendPotential() {
406	return frameData.bendPotential;
407	}
408	RealType Snapshot::getTorsionPotential() {
409	return frameData.torsionPotential;
410	}
411	RealType Snapshot::getInversionPotential() {
412	return frameData.inversionPotential;
413	}
414
415	RealType Snapshot::getShortRangePotential() {
416	if (!hasShortRangePotential) {
417	frameData.shortRangePotential = frameData.bondPotential;
418	frameData.shortRangePotential += frameData.bendPotential;
419	frameData.shortRangePotential += frameData.torsionPotential;
420	frameData.shortRangePotential += frameData.inversionPotential;
421	hasShortRangePotential = true;
422	}
423	return frameData.shortRangePotential;
424	}
425
426	void Snapshot::setReciprocalPotential(RealType rp){
427	frameData.reciprocalPotential = rp;
428	}
429
430	RealType Snapshot::getReciprocalPotential() {
431	return frameData.reciprocalPotential;
432	}
433
434	void Snapshot::setLongRangePotential(potVec lrPot) {
435	frameData.lrPotentials = lrPot;
436	}
437
438	RealType Snapshot::getLongRangePotential() {
439	if (!hasLongRangePotential) {
440	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
441	frameData.longRangePotential += frameData.lrPotentials[i];
442	}
443	frameData.longRangePotential += frameData.reciprocalPotential;
444	hasLongRangePotential = true;
445	}
446	return frameData.longRangePotential;
447	}
448
449	potVec Snapshot::getLongRangePotentials() {
450	return frameData.lrPotentials;
451	}
452
453	RealType Snapshot::getPotentialEnergy() {
454	if (!hasPotentialEnergy) {
455	frameData.potentialEnergy = this->getLongRangePotential();
456	frameData.potentialEnergy += this->getShortRangePotential();
457	frameData.potentialEnergy += this->getRestraintPotential();
458	hasPotentialEnergy = true;
459	}
460	return frameData.potentialEnergy;
461	}
462
463	void Snapshot::setExcludedPotentials(potVec exPot) {
464	frameData.excludedPotentials = exPot;
465	}
466
467	potVec Snapshot::getExcludedPotentials() {
468	return frameData.excludedPotentials;
469	}
470
471	void Snapshot::setRestraintPotential(RealType rp) {
472	frameData.restraintPotential = rp;
473	}
474
475	RealType Snapshot::getRestraintPotential() {
476	return frameData.restraintPotential;
477	}
478
479	void Snapshot::setRawPotential(RealType rp) {
480	frameData.rawPotential = rp;
481	}
482
483	RealType Snapshot::getRawPotential() {
484	return frameData.rawPotential;
485	}
486
487	RealType Snapshot::getTranslationalKineticEnergy() {
488	return frameData.translationalKinetic;
489	}
490
491	RealType Snapshot::getRotationalKineticEnergy() {
492	return frameData.rotationalKinetic;
493	}
494
495	RealType Snapshot::getKineticEnergy() {
496	return frameData.kineticEnergy;
497	}
498
499	void Snapshot::setTranslationalKineticEnergy(RealType tke) {
500	hasTranslationalKineticEnergy = true;
501	frameData.translationalKinetic = tke;
502	}
503
504	void Snapshot::setRotationalKineticEnergy(RealType rke) {
505	hasRotationalKineticEnergy = true;
506	frameData.rotationalKinetic = rke;
507	}
508
509	void Snapshot::setKineticEnergy(RealType ke) {
510	hasKineticEnergy = true;
511	frameData.kineticEnergy = ke;
512	}
513
514	RealType Snapshot::getTotalEnergy() {
515	return frameData.totalEnergy;
516	}
517
518	void Snapshot::setTotalEnergy(RealType te) {
519	hasTotalEnergy = true;
520	frameData.totalEnergy = te;
521	}
522
523	RealType Snapshot::getConservedQuantity() {
524	return frameData.conservedQuantity;
525	}
526
527	void Snapshot::setConservedQuantity(RealType cq) {
528	hasConservedQuantity = true;
529	frameData.conservedQuantity = cq;
530	}
531
532	RealType Snapshot::getTemperature() {
533	return frameData.temperature;
534	}
535
536	void Snapshot::setTemperature(RealType temp) {
537	hasTemperature = true;
538	frameData.temperature = temp;
539	}
540
541	RealType Snapshot::getElectronicTemperature() {
542	return frameData.electronicTemperature;
543	}
544
545	void Snapshot::setElectronicTemperature(RealType eTemp) {
546	hasElectronicTemperature = true;
547	frameData.electronicTemperature = eTemp;
548	}
549
550	RealType Snapshot::getPressure() {
551	return frameData.pressure;
552	}
553
554	void Snapshot::setPressure(RealType pressure) {
555	hasPressure = true;
556	frameData.pressure = pressure;
557	}
558
559	Mat3x3d Snapshot::getPressureTensor() {
560	return frameData.pressureTensor;
561	}
562
563
564	void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) {
565	hasPressureTensor = true;
566	frameData.pressureTensor = pressureTensor;
567	}
568
569	void Snapshot::setStressTensor(const Mat3x3d& stressTensor) {
570	frameData.stressTensor = stressTensor;
571	}
572
573	Mat3x3d Snapshot::getStressTensor() {
574	return frameData.stressTensor;
575	}
576
577	void Snapshot::setConductiveHeatFlux(const Vector3d& chf) {
578	frameData.conductiveHeatFlux = chf;
579	}
580
581	Vector3d Snapshot::getConductiveHeatFlux() {
582	return frameData.conductiveHeatFlux;
583	}
584
585	Vector3d Snapshot::getConvectiveHeatFlux() {
586	return frameData.convectiveHeatFlux;
587	}
588
589	void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) {
590	hasConvectiveHeatFlux = true;
591	frameData.convectiveHeatFlux = chf;
592	}
593
594	Vector3d Snapshot::getHeatFlux() {
595	// BE CAREFUL WITH UNITS
596	return getConductiveHeatFlux() + getConvectiveHeatFlux();
597	}
598
599	Vector3d Snapshot::getSystemDipole() {
600	return frameData.systemDipole;
601	}
602
603	void Snapshot::setSystemDipole(const Vector3d& bd) {
604	hasSystemDipole = true;
605	frameData.systemDipole = bd;
606	}
607
608	Mat3x3d Snapshot::getSystemQuadrupole() {
609	return frameData.systemQuadrupole;
610	}
611
612	void Snapshot::setSystemQuadrupole(const Mat3x3d& bq) {
613	hasSystemQuadrupole = true;
614	frameData.systemQuadrupole = bq;
615	}
616
617	void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) {
618	frameData.thermostat = thermostat;
619	}
620
621	pair<RealType, RealType> Snapshot::getThermostat() {
622	return frameData.thermostat;
623	}
624
625	void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) {
626	frameData.electronicThermostat = eTherm;
627	}
628
629	pair<RealType, RealType> Snapshot::getElectronicThermostat() {
630	return frameData.electronicThermostat;
631	}
632
633	void Snapshot::setBarostat(const Mat3x3d& barostat) {
634	frameData.barostat = barostat;
635	}
636
637	Mat3x3d Snapshot::getBarostat() {
638	return frameData.barostat;
639	}
640
641	void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) {
642	frameData.inertiaTensor = inertiaTensor;
643	hasInertiaTensor = true;
644	}
645
646	Mat3x3d Snapshot::getInertiaTensor() {
647	return frameData.inertiaTensor;
648	}
649
650	void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) {
651	frameData.gyrationalVolume = gyrationalVolume;
652	hasGyrationalVolume = true;
653	}
654
655	RealType Snapshot::getGyrationalVolume() {
656	return frameData.gyrationalVolume;
657	}
658
659	void Snapshot::setHullVolume(const RealType hullVolume) {
660	frameData.hullVolume = hullVolume;
661	hasHullVolume = true;
662	}
663
664	RealType Snapshot::getHullVolume() {
665	return frameData.hullVolume;
666	}
667
668	void Snapshot::setOrthoTolerance(RealType ot) {
669	orthoTolerance_ = ot;
670	}
671	}