| 35 |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
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*/ |
| 52 |
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|
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public: |
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|
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< |
Thermo( SimInfo* info) : info_(info) {} |
| 55 |
> |
Thermo( SimInfo* info ) : info_(info) {} |
| 56 |
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|
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// note: all the following energies are in kcal/mol |
| 58 |
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|
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+ |
RealType getTranslationalKinetic(); // the translational kinetic energy |
| 60 |
+ |
RealType getRotationalKinetic(); // the rotational kinetic energy |
| 61 |
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RealType getKinetic(); // the total kinetic energy |
| 62 |
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RealType getPotential(); // the total potential energy |
| 63 |
< |
RealType getTotalE(); // gets the total energy |
| 63 |
> |
RealType getTotalEnergy(); // gets the total energy |
| 64 |
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|
| 65 |
< |
RealType getTemperature(); // gives the instant temp. in K |
| 65 |
> |
RealType getTemperature(); // Gives the instant temp. in K |
| 66 |
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RealType getElectronicTemperature(); // gives the instant electronic temperature in K |
| 67 |
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|
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RealType getPressure(); // gives the instant pressure in atm; |
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– |
RealType getPressureX() { return getPressure(0); } |
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– |
RealType getPressureY() { return getPressure(1); } |
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– |
RealType getPressureZ() { return getPressure(2); } |
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|
| 70 |
< |
// gives the pressure tensor in amu*fs^-2*Ang^-1 |
| 71 |
< |
Mat3x3d getPressureTensor(); |
| 70 |
> |
/** \brief gives the pressure tensor in amu*fs^-2*Ang^-1 */ |
| 71 |
> |
Mat3x3d getPressureTensor(); |
| 72 |
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RealType getVolume(); // gives the volume in Ang^3 |
| 73 |
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|
| 74 |
< |
// accumulate and return the simulation box dipole moment in C*m |
| 75 |
< |
Vector3d getBoxDipole(); |
| 74 |
> |
/** \brief accumulate and return the simulation box dipole moment in C*m */ |
| 75 |
> |
Vector3d getSystemDipole(); |
| 76 |
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Vector3d getHeatFlux(); |
| 77 |
< |
void saveStat(); |
| 77 |
> |
|
| 78 |
> |
/** \brief Returns the center of the mass of the whole system.*/ |
| 79 |
> |
Vector3d getCom(); |
| 80 |
> |
|
| 81 |
> |
/** \brief Returns the velocity of center of mass of the whole system.*/ |
| 82 |
> |
Vector3d getComVel(); |
| 83 |
> |
|
| 84 |
> |
/** \brief Returns the center of the mass and Center of Mass velocity of |
| 85 |
> |
the whole system.*/ |
| 86 |
> |
void getComAll(Vector3d& com,Vector3d& comVel); |
| 87 |
> |
|
| 88 |
> |
/** \brief Returns the inertia tensor and the total angular |
| 89 |
> |
momentum for for the entire system |
| 90 |
> |
* \param[out] inertiaTensor the inertia tensor |
| 91 |
> |
* \param[out] angularMomentum the angular momentum vector |
| 92 |
> |
* \ingroup surface |
| 93 |
> |
*/ |
| 94 |
> |
void getInertiaTensor(Mat3x3d &inertiaTensor,Vector3d &angularMomentum); |
| 95 |
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|
| 96 |
< |
private: |
| 97 |
< |
RealType getPressure(int direction); |
| 96 |
> |
/** \brief Returns the Axis-aligned bounding box for the current system. |
| 97 |
> |
*/ |
| 98 |
> |
Mat3x3d getBoundingBox(); |
| 99 |
> |
|
| 100 |
> |
/** \brief Returns system angular momentum */ |
| 101 |
> |
Vector3d getAngularMomentum(); |
| 102 |
> |
|
| 103 |
> |
/** \brief Returns volume of system as estimated by an ellipsoid defined |
| 104 |
> |
by the radii of gyration */ |
| 105 |
> |
RealType getGyrationalVolume(); |
| 106 |
> |
|
| 107 |
> |
/** \brief Overloaded version of gyrational volume that also returns |
| 108 |
> |
det(I) so dV/dr can be calculated */ |
| 109 |
> |
void getGyrationalVolume(RealType &vol, RealType &detI); |
| 110 |
> |
|
| 111 |
> |
RealType getHullVolume(); |
| 112 |
> |
|
| 113 |
> |
RealType getTaggedAtomPairDistance(); |
| 114 |
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|
| 115 |
+ |
private: |
| 116 |
|
SimInfo* info_; |
| 117 |
|
}; |
| 118 |
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|
