OpenMD 3.0
Molecular Dynamics in the Open
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Thermo.hpp
1/*
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31 * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
32 * research, please cite the appropriate papers when you publish your
33 * work. Good starting points are:
34 *
35 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
39 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
40 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
41 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
42 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
43 */
44
45#ifndef BRAINS_THERMO_HPP
46#define BRAINS_THERMO_HPP
47
48#include "brains/SimInfo.hpp"
49#include "primitives/Atom.hpp"
50
51namespace OpenMD {
52
53 class Thermo {
54 public:
55 Thermo(SimInfo* info) : info_(info) {}
56
57 // note: all the following energies are in kcal/mol
58
59 RealType getTranslationalKinetic(); // the translational kinetic energy
60 RealType getRotationalKinetic(); // the rotational kinetic energy
61 RealType getElectronicKinetic(); // the electronic kinetic energy
62 RealType getKinetic(); // the total kinetic energy
63 RealType getPotential(); // the total potential energy
64 potVec getSelectionPotentials(); // the potential energy of a selection
65
66 RealType getTotalEnergy(); // gets the total energy
67
68 RealType getTemperature(); // Gives the instant temp. in K
69 RealType getElectronicTemperature(); // gives the instant electronic
70 // temperature in K
71 RealType getNetCharge(); // gives the total net charge on the system
72 RealType getChargeMomentum(); // gives the instantaneous charge momentum in
73 // kcal fs / e / mol
74 std::vector<Vector3d> getCurrentDensity();
75
76 RealType getPressure(); // gives the instant pressure in atm;
77 RealType getPressure(Snapshot* snap); // gives the instant pressure in atm
78 // for a given snapshot;
79
80 /** \brief gives the pressure tensor in amu*fs^-2*Ang^-1 */
82 /** \brief gives the pressure tensor in amu*fs^-2*Ang^-1 for a given
83 * snapshot */
85
86 RealType getVolume(); // gives the volume in Ang^3
87
88 /** \brief accumulate and return the simulation box dipole moment in C*m */
90
91 /** \brief accumulate and return the simulation box dipole moment in debye
92 * Angstroms */
94
95 Vector3d getHeatFlux();
96
97 /** \brief Returns the center of the mass of the whole system.*/
99
100 /** \brief Returns the velocity of center of mass of the whole system.*/
102
103 /** \brief Returns the center of the mass and Center of Mass velocity of
104 the whole system.*/
105 void getComAll(Vector3d& com, Vector3d& comVel);
106
107 /** \brief Returns the inertia tensor and the total angular
108 momentum for for the entire system
109 * \param[out] inertiaTensor the inertia tensor
110 * \param[out] angularMomentum the angular momentum vector
111 * \ingroup surface
112 */
113 void getInertiaTensor(Mat3x3d& inertiaTensor, Vector3d& angularMomentum);
114
115 /** \brief Returns the Axis-aligned bounding box for the current system.
116 */
118
119 /** \brief Returns system angular momentum */
121
122 /** \brief Returns volume of system as estimated by an ellipsoid defined
123 by the radii of gyration */
124 RealType getGyrationalVolume();
125
126 /** \brief Overloaded version of gyrational volume that also returns
127 det(I) so dV/dr can be calculated */
128 void getGyrationalVolume(RealType& vol, RealType& detI);
129
130 RealType getHullVolume();
131
132 RealType getTaggedAtomPairDistance();
133
134 private:
135 SimInfo* info_ {nullptr};
136 };
137} // namespace OpenMD
138
139#endif
One of the heavy-weight classes of OpenMD, SimInfo maintains objects and variables relating to the cu...
Definition SimInfo.hpp:93
The Snapshot class is a repository storing dynamic data during a Simulation.
Definition Snapshot.hpp:147
Mat3x3d getPressureTensor()
gives the pressure tensor in amu*fs^-2*Ang^-1
Definition Thermo.cpp:443
Vector3d getSystemDipole()
accumulate and return the simulation box dipole moment in C*m
Definition Thermo.cpp:525
void getComAll(Vector3d &com, Vector3d &comVel)
Returns the center of the mass and Center of Mass velocity of the whole system.
Definition Thermo.cpp:839
void getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum)
Returns the inertia tensor and the total angular momentum for for the entire system.
Definition Thermo.cpp:888
RealType getGyrationalVolume()
Returns volume of system as estimated by an ellipsoid defined by the radii of gyration.
Definition Thermo.cpp:1066
Vector3d getCom()
Returns the center of the mass of the whole system.
Definition Thermo.cpp:805
Mat3x3d getSystemQuadrupole()
accumulate and return the simulation box dipole moment in debye Angstroms
Definition Thermo.cpp:622
Vector3d getAngularMomentum()
Returns system angular momentum.
Definition Thermo.cpp:1020
Vector3d getComVel()
Returns the velocity of center of mass of the whole system.
Definition Thermo.cpp:775
Mat3x3d getBoundingBox()
Returns the Axis-aligned bounding box for the current system.
Definition Thermo.cpp:964
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.