[ViewVC] Diff of: OpenMD/branches/development/src/brains/Snapshot.hpp

Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1760 by gezelter, Thu Jun 21 19:26:46 2012 UTC

+ * redistribute this software in source and binary code form, provided
+ * that the following conditions are met:
-<
+ * 1. Acknowledgement of the program authors must be made in any
-<
+ *    publication of scientific results based in part on use of the
-<
+ *    program.  An acceptable form of acknowledgement is citation of
-<
+ *    the article in which the program was described (Matthew
-<
+ *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
-<
+ *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
-<
+ *    Parallel Simulation Engine for Molecular Dynamics,"
-<
+ *    J. Comput. Chem. 26, pp. 252-271 (2005))
-<
+ *
-<
+ * 2. Redistributions of source code must retain the above copyright
->
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
-<
+ * 3. Redistributions in binary form must reproduce the above copyright
->
+ * 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.
+ * 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.hpp
-–
+ * @author tlin
-–
+ * @date 10/20/2004
-–
+ * @time 23:56am
-–
+ * @version 1.0
-–
+ */
-–
+#ifndef BRAINS_SNAPSHOT_HPP
+#define BRAINS_SNAPSHOT_HPP
+#include <vector>
+#include "brains/DataStorage.hpp"
-+
+#include "nonbonded/NonBondedInteraction.hpp"
+#include "brains/Stats.hpp"
-–
+#include "UseTheForce/DarkSide/simulation_interface.h"
-<
+namespace oopse{
->
+namespace OpenMD{
+  /**
-<
+   * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
-<
+   * @brief Snapshot class is a repository class for storing dynamic data during
-<
+   *  Simulation
-<
+   * Every snapshot class will contain one DataStorage  for atoms and one DataStorage
-<
+   *  for rigid bodies.
->
+   * FrameData is a structure for holding system-wide dynamic data
->
+   * about the simulation.
+   */
-+
-+
+  struct FrameData {
-+
+    int id;                       /**< identification number of the snapshot */
-+
+    RealType currentTime;         /**< current time */
-+
+    Mat3x3d  hmat;                /**< axes of the periodic box in matrix form */
-+
+    Mat3x3d  invHmat;             /**< the inverse of the Hmat matrix */
-+
+    bool     orthoRhombic;        /**< is this an orthorhombic periodic box? */
-+
+    RealType volume;              /**< total volume of this frame */
-+
+    RealType pressure;            /**< pressure of this frame */
-+
+    RealType totalEnergy;         /**< total energy of this frame */
-+
+    RealType kineticEnergy;       /**< kinetic energy of this frame */
-+
+    RealType potentialEnergy;     /**< potential energy of this frame */
-+
+    RealType shortRangePotential; /**< short-range contributions to the potential*/
-+
+    RealType longRangePotential;  /**< long-range contributions to the potential */
-+
+    RealType bondPotential;       /**< bonded contribution to the potential */
-+
+    RealType bendPotential;       /**< angle-bending contribution to the potential */
-+
+    RealType torsionPotential;    /**< dihedral (torsion angle) contribution to the potential */
-+
+    RealType inversionPotential;  /**< inversion (planarity) contribution to the potential */
-+
+    potVec   lrPotentials;        /**< breakdown of long-range potentials by family */
-+
+    potVec   excludedPotentials;  /**< breakdown of excluded potentials by family */
-+
+    RealType restraintPotential;  /**< potential energy of restraints */
-+
+    RealType rawPotential;        /**< unrestrained potential energy (when restraints are applied) */
-+
+    RealType temperature;         /**< temperature of this frame */
-+
+    RealType chi;                 /**< thermostat velocity */
-+
+    RealType integralOfChiDt;     /**< thermostat position */
-+
+    RealType electronicTemperature; /**< temperature of the electronic degrees of freedom */
-+
+    RealType chiQ;                /**< fluctuating charge thermostat velocity */
-+
+    RealType integralOfChiQDt;    /**< fluctuating charge thermostat position */
-+
+    Mat3x3d  eta;                 /**< barostat matrix */
-+
+    Vector3d COM;                 /**< location of system center of mass */
-+
+    Vector3d COMvel;              /**< system center of mass velocity */
-+
+    Vector3d COMw;                /**< system center of mass angular velocity */
-+
+    Mat3x3d  stressTensor;        /**< stress tensor */
-+
+    Mat3x3d  pressureTensor;      /**< pressure tensor */
-+
+    Vector3d systemDipole;        /**< total system dipole moment */
-+
+    Vector3d conductiveHeatFlux;  /**< heat flux vector (conductive only) */
-+
+  };
-+
-+
-+
+  /**
-+
+   * @class Snapshot
-+
+   * @brief The Snapshot class is a repository storing dynamic data during a
-+
+   * Simulation.  Every Snapshot contains FrameData (for global information)
-+
+   * as well as DataStorage (one for Atoms, one for RigidBodies, and one for
-+
+   * CutoffGroups).
-+
+   */
+  class Snapshot {
-–
+  public:
-–
-–
+    Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies),
-–
+                                             currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {
-+
+  public:
-+
+    Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups) :
-+
+      atomData(nAtoms), rigidbodyData(nRigidbodies),
-+
+      cgData(nCutoffGroups, DataStorage::dslPosition),
-+
+      orthoTolerance_(1e-6), hasCOM_(false), hasVolume_(false),
-+
+      hasShortRangePotential_(false),
-+
+      hasBondPotential_(false), hasBendPotential_(false),
-+
+      hasTorsionPotential_(false), hasInversionPotential_(false),
-+
+      hasLongRangePotential_(false), hasLongRangePotentialFamilies_(false),
-+
+      hasRestraintPotential_(false), hasRawPotential_(false),
-+
+      hasExcludedPotentials_(false)
-+
+    {
-+
-+
+      frameData.id = -1;
-+
+      frameData.currentTime = 0;
-+
+      frameData.hmat = Mat3x3d(0.0);
-+
+      frameData.invHmat = Mat3x3d(0.0);
-+
+      frameData.orthoRhombic = false;
-+
+      frameData.volume = 0.0;
-+
+      frameData.pressure = 0.0;
-+
+      frameData.totalEnergy = 0.0;
-+
+      frameData.kineticEnergy = 0.0;
-+
+      frameData.potentialEnergy = 0.0;
-+
+      frameData.temperature = 0.0;
-+
+      frameData.chi = 0.0;
-+
+      frameData.integralOfChiDt = 0.0;
-+
+      frameData.electronicTemperature = 0.0;
-+
+      frameData.chiQ = 0.0;
-+
+      frameData.integralOfChiQDt = 0.0;
-+
+      frameData.eta = Mat3x3d(0.0);
-+
+      frameData.COM = V3Zero;
-+
+      frameData.COMvel = V3Zero;
-+
+      frameData.COMw = V3Zero;
-+
+      frameData.stressTensor = Mat3x3d(0.0);
-+
+      frameData.pressureTensor = Mat3x3d(0.0);
-+
+      frameData.systemDipole = Vector3d(0.0);
-+
+      frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
-<
+    Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
-<
+      : atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout),
-<
+        currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {
->
+    Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, int storageLayout) :
->
+      atomData(nAtoms, storageLayout),
->
+      rigidbodyData(nRigidbodies, storageLayout),
->
+      cgData(nCutoffGroups, DataStorage::dslPosition),
->
+      orthoTolerance_(1e-6), hasCOM_(false), hasVolume_(false),
->
+      hasShortRangePotential_(false),
->
+      hasBondPotential_(false), hasBendPotential_(false),
->
+      hasTorsionPotential_(false), hasInversionPotential_(false),
->
+      hasLongRangePotential_(false), hasLongRangePotentialFamilies_(false),
->
+      hasRestraintPotential_(false), hasRawPotential_(false),
->
+      hasExcludedPotentials_(false)
->
+    {
-<
+      }
-<
->
+      frameData.id = -1;
->
+      frameData.currentTime = 0;
->
+      frameData.hmat = Mat3x3d(0.0);
->
+      frameData.invHmat = Mat3x3d(0.0);
->
+      frameData.orthoRhombic = false;
->
+      frameData.volume = 0.0;
->
+      frameData.pressure = 0.0;
->
+      frameData.totalEnergy = 0.0;
->
+      frameData.kineticEnergy = 0.0;
->
+      frameData.potentialEnergy = 0.0;
->
+      frameData.temperature = 0.0;
->
+      frameData.chi = 0.0;
->
+      frameData.integralOfChiDt = 0.0;
->
+      frameData.electronicTemperature = 0.0;
->
+      frameData.chiQ = 0.0;
->
+      frameData.integralOfChiQDt = 0.0;
->
+      frameData.eta = Mat3x3d(0.0);
->
+      frameData.COM = V3Zero;
->
+      frameData.COMvel = V3Zero;
->
+      frameData.COMw = V3Zero;
->
+      frameData.stressTensor = Mat3x3d(0.0);
->
+      frameData.pressureTensor = Mat3x3d(0.0);
->
+      frameData.systemDipole = V3Zero;
->
+      frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
->
+    }
->
+    /** Returns the id of this Snapshot */
+    int getID() {
-<
+      return id_;
->
+      return frameData.id;
+    /** Sets the id of this Snapshot */
+    void setID(int id) {
-<
+      id_ = id;
->
+      frameData.id = id;
+    int getSize() {
+      return rigidbodyData.getSize();
-+
+    /** Returns the number of rigid bodies */
-+
+    int getNumberOfCutoffGroups() {
-+
+      return cgData.getSize();
-+
+    }
-+
+    /** Returns the H-Matrix */
+    Mat3x3d getHmat() {
-<
+      return hmat_;
->
+      return frameData.hmat;
+    /** Sets the H-Matrix */
+    void setHmat(const Mat3x3d& m);
+    RealType getVolume() {
-<
+      return hmat_.determinant();
->
+      if (!hasVolume_) {
->
+        frameData.volume = frameData.hmat.determinant();
->
+        hasVolume_ = true;
->
+      }
->
+      return frameData.volume;
-+
+    void setVolume(RealType volume){
-+
+      hasVolume_=true;
-+
+      frameData.volume = volume;
-+
+    }
-+
+    /** Returns the inverse H-Matrix */
+    Mat3x3d getInvHmat() {
-<
+      return invHmat_;
->
+      return frameData.invHmat;
+    /** Wrapping the vector according to periodic boundary condition*/
+    void wrapVector(Vector3d& v);
-+
+    /** Scaling a vector to multiples of the periodic box */
-+
+    Vector3d scaleVector(Vector3d &v);
-+
-+
+    Vector3d getCOM();
-+
+    Vector3d getCOMvel();
-+
+    Vector3d getCOMw();
+    RealType getTime() {
-<
+      return currentTime_;
->
+      return frameData.currentTime;
+    void increaseTime(RealType dt) {
+    void setTime(RealType time) {
-<
+      currentTime_ =time;
->
+      frameData.currentTime =time;
+      //time at statData is redundant
-<
+      statData[Stats::TIME] = currentTime_;
->
+      statData[Stats::TIME] = frameData.currentTime;
-+
+    void setShortRangePotential(RealType srp) {
-+
+      frameData.shortRangePotential = srp;
-+
+      hasShortRangePotential_ = true;
-+
+      statData[Stats::SHORT_RANGE_POTENTIAL] = frameData.shortRangePotential;
-+
+    }
-+
-+
+    RealType getShortRangePotential() {
-+
+      return frameData.shortRangePotential;
-+
+    }
-+
-+
+    void setBondPotential(RealType bp) {
-+
+      frameData.bondPotential = bp;
-+
+      hasBondPotential_ = true;
-+
+      statData[Stats::BOND_POTENTIAL] = frameData.bondPotential;
-+
+    }
-+
-+
+    void setBendPotential(RealType bp) {
-+
+      frameData.bendPotential = bp;
-+
+      hasBendPotential_ = true;
-+
+      statData[Stats::BEND_POTENTIAL] = frameData.bendPotential;
-+
+    }
-+
-+
+    void setTorsionPotential(RealType tp) {
-+
+      frameData.torsionPotential = tp;
-+
+      hasTorsionPotential_ = true;
-+
+      statData[Stats::DIHEDRAL_POTENTIAL] = frameData.torsionPotential;
-+
+    }
-+
-+
+    void setInversionPotential(RealType ip) {
-+
+      frameData.inversionPotential = ip;
-+
+      hasInversionPotential_ = true;
-+
+      statData[Stats::INVERSION_POTENTIAL] = frameData.inversionPotential;
-+
+    }
-+
-+
+    void setLongRangePotential(RealType lrp) {
-+
+      frameData.longRangePotential = lrp;
-+
+      hasLongRangePotential_ = true;
-+
+      statData[Stats::LONG_RANGE_POTENTIAL] = frameData.longRangePotential;
-+
+    }
-+
-+
+    RealType getLongRangePotential() {
-+
+      return frameData.longRangePotential;
-+
+    }
-+
-+
+    void setLongRangePotentialFamilies(potVec lrPot) {
-+
+      frameData.lrPotentials = lrPot;
-+
+      hasLongRangePotentialFamilies_ = true;
-+
+      statData[Stats::VANDERWAALS_POTENTIAL] = frameData.lrPotentials[VANDERWAALS_FAMILY];
-+
+      statData[Stats::ELECTROSTATIC_POTENTIAL] = frameData.lrPotentials[ELECTROSTATIC_FAMILY];
-+
+      statData[Stats::METALLIC_POTENTIAL] = frameData.lrPotentials[METALLIC_FAMILY];
-+
+      statData[Stats::HYDROGENBONDING_POTENTIAL] = frameData.lrPotentials[HYDROGENBONDING_FAMILY];
-+
+    }
-+
-+
+    potVec getLongRangePotentials() {
-+
+      return frameData.lrPotentials;
-+
+    }
-+
-+
+    void setExcludedPotentials(potVec exPot) {
-+
+      frameData.excludedPotentials = exPot;
-+
+      hasExcludedPotentials_ = true;
-+
+    }
-+
-+
+    potVec getExcludedPotentials() {
-+
+      return frameData.excludedPotentials;
-+
+    }
-+
-+
-+
+    void setRestraintPotential(RealType rp) {
-+
+      frameData.restraintPotential = rp;
-+
+      hasRestraintPotential_ = true;
-+
+      statData[Stats::RESTRAINT_POTENTIAL] = frameData.restraintPotential;
-+
+    }
-+
-+
+    RealType getRestraintPotential() {
-+
+      return frameData.restraintPotential;
-+
+    }
-+
-+
+    void setRawPotential(RealType rp) {
-+
+      frameData.rawPotential = rp;
-+
+      hasRawPotential_ = true;
-+
+      statData[Stats::RAW_POTENTIAL] = frameData.rawPotential;
-+
+    }
-+
-+
+    RealType getRawPotential() {
-+
+      return frameData.rawPotential;
-+
+    }
-+
+    RealType getChi() {
-<
+      return chi_;
->
+      return frameData.chi;
+    void setChi(RealType chi) {
-<
+      chi_ = chi;
->
+      frameData.chi = chi;
+    RealType getIntegralOfChiDt() {
-<
+      return integralOfChiDt_;
->
+      return frameData.integralOfChiDt;
+    void setIntegralOfChiDt(RealType integralOfChiDt) {
-<
+      integralOfChiDt_ = integralOfChiDt;
->
+      frameData.integralOfChiDt = integralOfChiDt;
-+
+    RealType getChiElectronic() {
-+
+      return frameData.chiQ;
-+
+    }
-+
-+
+    void setChiElectronic(RealType chiQ) {
-+
+      frameData.chiQ = chiQ;
-+
+    }
-+
-+
+    RealType getIntegralOfChiElectronicDt() {
-+
+      return frameData.integralOfChiQDt;
-+
+    }
-+
-+
+    void setIntegralOfChiElectronicDt(RealType integralOfChiQDt) {
-+
+      frameData.integralOfChiQDt = integralOfChiQDt;
-+
+    }
-+
-+
+    void setOrthoTolerance(RealType orthoTolerance) {
-+
+      orthoTolerance_ = orthoTolerance;
-+
+    }
-+
+    Mat3x3d getEta() {
-<
+      return eta_;
->
+      return frameData.eta;
+    void setEta(const Mat3x3d& eta) {
-<
+      eta_ = eta;
->
+      frameData.eta = eta;
-<
->
->
+    Mat3x3d getStressTensor() {
->
+      return frameData.stressTensor;
->
+    }
->
->
+    void setStressTensor(const Mat3x3d& stressTensor) {
->
+      frameData.stressTensor = stressTensor;
->
+    }
->
->
+    Vector3d getConductiveHeatFlux() {
->
+      return frameData.conductiveHeatFlux;
->
+    }
->
->
+    void setConductiveHeatFlux(const Vector3d& heatFlux) {
->
+      frameData.conductiveHeatFlux = heatFlux;
->
+    }
->
->
+    bool hasCOM() {
->
+      return hasCOM_;
->
+    }
->
->
+    void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
->
+      frameData.COM = COM;
->
+      frameData.COMvel = COMvel;
->
+      frameData.COMw = COMw;
->
+      hasCOM_ = true;
->
+    }
->
+    DataStorage atomData;
+    DataStorage rigidbodyData;
-+
+    DataStorage cgData;
-+
+    FrameData frameData;
+    Stats statData;
-–
-–
+  private:
-–
+    RealType currentTime_;
-<
+    Mat3x3d hmat_;
-<
+    Mat3x3d invHmat_;
-<
+    int orthoRhombic_;
-<
-<
+    RealType chi_;
-<
+    RealType integralOfChiDt_;
-<
+    Mat3x3d eta_;
-<
-<
+    int id_; /**< identification number of the snapshot */
->
+  private:
->
+    RealType orthoTolerance_;
->
+    bool hasCOM_;
->
+    bool hasVolume_;
->
+    bool hasShortRangePotential_;
->
+    bool hasBondPotential_;
->
+    bool hasBendPotential_;
->
+    bool hasTorsionPotential_;
->
+    bool hasInversionPotential_;
->
+    bool hasLongRangePotential_;
->
+    bool hasLongRangePotentialFamilies_;
->
+    bool hasRestraintPotential_;
->
+    bool hasRawPotential_;
->
+    bool hasExcludedPotentials_;
+  };
+  typedef DataStorage (Snapshot::*DataStoragePointer);

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1760 by gezelter, Thu Jun 21 19:26:46 2012 UTC

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Comparing: trunk/src/brains/Snapshot.hpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs. branches/development/src/brains/Snapshot.hpp (file contents), Revision 1760 by gezelter, Thu Jun 21 19:26:46 2012 UTC

Comparing: trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs. branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1760 by gezelter, Thu Jun 21 19:26:46 2012 UTC

Diff Legend

Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1760 by gezelter, Thu Jun 21 19:26:46 2012 UTC

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1760 by gezelter, Thu Jun 21 19:26:46 2012 UTC