Thermo.hpp

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 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#ifndef BRAINS_THERMO_HPP
#define BRAINS_THERMO_HPP
 
#include "brains/SimInfo.hpp"
#include "primitives/Atom.hpp"
#include "perturbations/VelocityField.hpp"
 
namespace OpenMD {
 
  class Thermo {
  public:
    Thermo(SimInfo* info);
 
    // note: all the following energies are in kcal/mol
 
    RealType getTranslationalKinetic();  // the translational kinetic energy
    RealType getRotationalKinetic();     // the rotational kinetic energy
    RealType getElectronicKinetic();     // the electronic kinetic energy
    RealType getKinetic();               // the total kinetic energy
    RealType getPotential();             // the total potential energy
    potVec getSelectionPotentials();     // the potential energy of a selection
 
    RealType getTotalEnergy();  // gets the total energy
 
    RealType getTemperature();            // Gives the instant temp. in K
    RealType getElectronicTemperature();  // gives the instant electronic
                                          // temperature in K
    RealType getNetCharge();       // gives the total net charge on the system
    RealType getChargeMomentum();  // gives the instantaneous charge momentum in
                                   // kcal fs / e / mol
    std::vector<Vector3d> getCurrentDensity();
 
    RealType getPressure();                // gives the instant pressure in atm;
    RealType getPressure(Snapshot* snap);  // gives the instant pressure in atm
                                           // for a given snapshot;
 
    /** \brief gives the pressure tensor in amu*fs^-2*Ang^-1 */
    Mat3x3d getPressureTensor();
    /** \brief gives the pressure tensor in amu*fs^-2*Ang^-1 for a given
     * snapshot */
    Mat3x3d getPressureTensor(Snapshot* snap);
 
    RealType getVolume();  // gives the volume in Ang^3
 
    /** \brief accumulate and return the simulation box dipole moment in C*m */
    Vector3d getSystemDipole();
 
    /** \brief accumulate and return the simulation box dipole moment in debye
     * Angstroms */
    Mat3x3d getSystemQuadrupole();
 
    Vector3d getHeatFlux();
 
    /** \brief Returns the center of the mass of the whole system.*/
    Vector3d getCom();
 
    /** \brief Returns the velocity of center of mass of the whole system.*/
    Vector3d getComVel();
 
    /** \brief Returns the center of the mass and Center of Mass velocity of
        the whole system.*/
    void getComAll(Vector3d& com, Vector3d& comVel);
 
    /** \brief Returns the inertia tensor and the total angular
        momentum for for the entire system
     * \param[out] inertiaTensor the inertia tensor
     * \param[out] angularMomentum the angular momentum vector
     * \ingroup surface
     */
    void getInertiaTensor(Mat3x3d& inertiaTensor, Vector3d& angularMomentum);
 
    /** \brief Returns the Axis-aligned bounding box for the current system.
     */
    Mat3x3d getBoundingBox();
 
    /** \brief Returns system angular momentum */
    Vector3d getAngularMomentum();
 
    /** \brief Returns volume of system as estimated by an ellipsoid defined
        by the radii of gyration */
    RealType getGyrationalVolume();
 
    /** \brief Overloaded version of gyrational volume that also returns
        det(I) so dV/dr can be calculated */
    void getGyrationalVolume(RealType& vol, RealType& detI);
 
    RealType getHullVolume();
 
    RealType getTaggedAtomPairDistance();
 
  private:
    SimInfo* info_ {nullptr};
    std::unique_ptr<VelocityField> velField_;
    bool usePeculiarVelocities_ {false};
 
  };
}  // namespace OpenMD
 
#endif