| 1 |
< |
#ifndef __THERMO_H__ |
| 2 |
< |
#define __THERMO_H__ |
| 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, 24107 (2008). |
| 39 |
> |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
> |
*/ |
| 41 |
> |
|
| 42 |
> |
#ifndef BRAINS_THERMO_HPP |
| 43 |
> |
#define BRAINS_THERMO_HPP |
| 44 |
|
|
| 45 |
|
#include "primitives/Atom.hpp" |
| 5 |
– |
#include "primitives/SRI.hpp" |
| 46 |
|
#include "brains/SimInfo.hpp" |
| 7 |
– |
#include "math/randomSPRNG.hpp" |
| 47 |
|
|
| 48 |
< |
class Thermo{ |
| 48 |
> |
namespace OpenMD { |
| 49 |
|
|
| 50 |
< |
public: |
| 12 |
< |
|
| 13 |
< |
Thermo( SimInfo* the_info ); |
| 14 |
< |
~Thermo(); |
| 50 |
> |
class Thermo{ |
| 51 |
|
|
| 52 |
< |
// note: all the following energies are in kcal/mol |
| 52 |
> |
public: |
| 53 |
|
|
| 54 |
< |
double getKinetic(); // the total kinetic energy |
| 19 |
< |
double getPotential(); // the total potential energy |
| 20 |
< |
double getTotalE(); // gets the total energy |
| 54 |
> |
Thermo( SimInfo* info) : info_(info) {} |
| 55 |
|
|
| 56 |
< |
double getTemperature(); // gives the instant temp. in K |
| 56 |
> |
// note: all the following energies are in kcal/mol |
| 57 |
|
|
| 58 |
< |
double getPressure(); // gives the instant pressure in atm; |
| 59 |
< |
double getPressureX(); // gives the instant pressure in atm; |
| 60 |
< |
double getPressureY(); // gives the instant pressure in atm; |
| 27 |
< |
double getPressureZ(); // gives the instant pressure in atm; |
| 58 |
> |
RealType getKinetic(); // the total kinetic energy |
| 59 |
> |
RealType getPotential(); // the total potential energy |
| 60 |
> |
RealType getTotalE(); // gets the total energy |
| 61 |
|
|
| 62 |
< |
void getPressureTensor(double press[3][3]); // gives the pressure |
| 30 |
< |
// tensor in |
| 31 |
< |
// amu*fs^-2*Ang^-1 |
| 32 |
< |
double getVolume(); // gives the volume in Ang^3 |
| 62 |
> |
RealType getTemperature(); // gives the instant temp. in K |
| 63 |
|
|
| 64 |
< |
int getNDF(); // get the number of degrees of freedom in the system |
| 65 |
< |
int getNDFraw(); // get the number of raw degrees of freedom in the system |
| 66 |
< |
// i.e. don't subtract constraints or system COM. |
| 67 |
< |
|
| 38 |
< |
void velocitize(); // set the temperature to the target temp in SimInfo |
| 39 |
< |
// NOTE: srand48 should be seeded before calling. |
| 40 |
< |
void getCOMVel(double vdrift[3]); |
| 41 |
< |
void getCOM(double COM[3]); |
| 42 |
< |
void removeCOMdrift(); |
| 64 |
> |
RealType getPressure(); // gives the instant pressure in atm; |
| 65 |
> |
RealType getPressureX() { return getPressure(0); } |
| 66 |
> |
RealType getPressureY() { return getPressure(1); } |
| 67 |
> |
RealType getPressureZ() { return getPressure(2); } |
| 68 |
|
|
| 69 |
< |
private: |
| 70 |
< |
SimInfo* info; |
| 71 |
< |
gaussianSPRNG *gaussStream; |
| 72 |
< |
}; |
| 69 |
> |
// gives the pressure tensor in amu*fs^-2*Ang^-1 |
| 70 |
> |
Mat3x3d getPressureTensor(); |
| 71 |
> |
RealType getVolume(); // gives the volume in Ang^3 |
| 72 |
> |
|
| 73 |
> |
// accumulate and return the simulation box dipole moment in C*m |
| 74 |
> |
Vector3d getBoxDipole(); |
| 75 |
> |
|
| 76 |
> |
void saveStat(); |
| 77 |
> |
|
| 78 |
> |
private: |
| 79 |
> |
RealType getPressure(int direction); |
| 80 |
> |
|
| 81 |
> |
SimInfo* info_; |
| 82 |
> |
}; |
| 83 |
> |
|
| 84 |
> |
} //end namespace OpenMD |
| 85 |
|
#endif |
