src/integrators/NPTi.cpp

#include "NPTi.hpp"
#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "integrators/NPT.hpp"
#include "primitives/Molecule.hpp"
#include "utils/OOPSEConstant.hpp"
#include "utils/simError.h"

namespace oopse {

// Basic isotropic thermostating and barostating via the Melchionna
// modification of the Hoover algorithm:
//
//    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
//       Molec. Phys., 78, 533.
//
//           and
//
//    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.

NPTi::NPTi ( SimInfo *info) : NPT(info){

    Globals* globals = info_->getGlobals();

}

void NPTi::evolveEtaA() {
    eta += dt2 * ( instaVol * (instaPress - targetPressure) /
         (OOPSEConstant::pressureConvert*NkBT*tb2));
    oldEta = eta;
}

void NPTi::evolveEtaB() {

    prevEta = eta;
    eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
         (OOPSEConstant::pressureConvert*NkBT*tb2));
}

void NPTi::calcVelScale() {
    vScale = chi + eta;
}

void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) {
    sc = vel * vScale;
}

void NPTi::getVelScaleB(Vector3d& sc, int index ){
    sc = oldVel[index] * vScale;    
}


void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM,
                           int index, Vector3d& sc){
    /**@todo*/
    sc  = oldPos[index] + pos/2.0 -COM;
    sc *= eta;
}

void NPTi::scaleSimBox(){

    double scaleFactor;

    scaleFactor = exp(dt*eta);

    if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
        sprintf( painCave.errMsg,
             "NPTi error: Attempting a Box scaling of more than 10 percent"
             " check your tauBarostat, as it is probably too small!\n"
             " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
             );
        painCave.isFatal = 1;
        simError();
    } else {
        Mat3x3d hmat = currentSnapshot_->getHmat();
        hmat *= scaleFactor;
        currentSnapshot_->setHmat(hmat);
    }

}

bool NPTi::etaConverged() {

    return ( fabs(prevEta - eta) <= etaTolerance );
}

double NPTi::calcConservedQuantity(){

    double conservedQuantity;
    double Energy;
    double thermostat_kinetic;
    double thermostat_potential;
    double barostat_kinetic;
    double barostat_potential;

    Energy =thermo.getTotalE();

    thermostat_kinetic = fkBT* tt2 * chi * chi / (2.0 * OOPSEConstant::energyConvert);

    thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;


    barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * OOPSEConstant::energyConvert);

    barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /
        OOPSEConstant::energyConvert;

    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
        barostat_kinetic + barostat_potential;

    return conservedQuantity;
}

void NPTi::loadEta() {
    Mat3x3d etaMat = currentSnapshot_->getEta();
    eta = etaMat(0,0);
    if (fabs(etaMat(1,1) - eta) >= oopse::epsilon || fabs(etaMat(1,1) - eta) >= oopse::epsilon || etaMat.isDiagonal()) {
        sprintf( painCave.errMsg,
                 "NPTi error: the diagonal elements of are eta matrix is not same or etaMat is not a diagonal matrix");
        painCave.isFatal = 1;
        simError();
    }
}

void NPTi::saveEta() {
    Mat3x3d etaMat(0.0);
    etaMat(0, 0) = eta;
    etaMat(1, 1) = eta;
    etaMat(2, 2) = eta;
    currentSnapshot_->setEta(etaMat);
}

}
Revision:	1822
Committed:	Thu Dec 2 02:08:29 2004 UTC (19 years, 9 months ago) by tim
File size:	3432 byte(s)
Log Message:	oopse get compiled, still has some linking problem
#	User	Rev	Content
1	tim	1822	#include "NPTi.hpp"
2	tim	1492	#include "brains/SimInfo.hpp"
3			#include "brains/Thermo.hpp"
4	tim	1822	#include "integrators/NPT.hpp"
5			#include "primitives/Molecule.hpp"
6			#include "utils/OOPSEConstant.hpp"
7	tim	1492	#include "utils/simError.h"
8	gezelter	1490
9	tim	1822	namespace oopse {
10	gezelter	1490
11			// Basic isotropic thermostating and barostating via the Melchionna
12			// modification of the Hoover algorithm:
13			//
14			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
15			// Molec. Phys., 78, 533.
16			//
17			// and
18			//
19			// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
20
21	tim	1822	NPTi::NPTi ( SimInfo *info) : NPT(info){
22	gezelter	1490
23	tim	1822	Globals* globals = info_->getGlobals();
24	gezelter	1490
25			}
26
27	tim	1774	void NPTi::evolveEtaA() {
28	tim	1822	eta += dt2 * ( instaVol * (instaPress - targetPressure) /
29			(OOPSEConstant::pressureConvertNkBTtb2));
30			oldEta = eta;
31	gezelter	1490	}
32
33	tim	1774	void NPTi::evolveEtaB() {
34	gezelter	1490
35	tim	1822	prevEta = eta;
36			eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
37			(OOPSEConstant::pressureConvertNkBTtb2));
38	gezelter	1490	}
39
40	tim	1774	void NPTi::calcVelScale() {
41	tim	1822	vScale = chi + eta;
42	gezelter	1490	}
43
44	tim	1774	void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) {
45			sc = vel * vScale;
46	gezelter	1490	}
47
48	tim	1774	void NPTi::getVelScaleB(Vector3d& sc, int index ){
49			sc = oldVel[index] * vScale;
50	gezelter	1490	}
51
52
53	tim	1774	void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM,
54	tim	1822	int index, Vector3d& sc){
55	tim	1774	/*@todo/
56			sc = oldPos[index] + pos/2.0 -COM;
57			sc *= eta;
58	gezelter	1490	}
59
60	tim	1774	void NPTi::scaleSimBox(){
61	gezelter	1490
62	tim	1822	double scaleFactor;
63	gezelter	1490
64	tim	1822	scaleFactor = exp(dt*eta);
65	gezelter	1490
66	tim	1822	if ((scaleFactor > 1.1) \|\| (scaleFactor < 0.9)) {
67			sprintf( painCave.errMsg,
68	gezelter	1490	"NPTi error: Attempting a Box scaling of more than 10 percent"
69			" check your tauBarostat, as it is probably too small!\n"
70			" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
71			);
72	tim	1822	painCave.isFatal = 1;
73			simError();
74			} else {
75			Mat3x3d hmat = currentSnapshot_->getHmat();
76			hmat *= scaleFactor;
77			currentSnapshot_->setHmat(hmat);
78			}
79	gezelter	1490
80			}
81
82	tim	1774	bool NPTi::etaConverged() {
83	gezelter	1490
84	tim	1822	return ( fabs(prevEta - eta) <= etaTolerance );
85	gezelter	1490	}
86
87	tim	1774	double NPTi::calcConservedQuantity(){
88	gezelter	1490
89	tim	1822	double conservedQuantity;
90			double Energy;
91			double thermostat_kinetic;
92			double thermostat_potential;
93			double barostat_kinetic;
94			double barostat_potential;
95	gezelter	1490
96	tim	1822	Energy =thermo.getTotalE();
97	gezelter	1490
98	tim	1822	thermostat_kinetic = fkBT* tt2 * chi * chi / (2.0 * OOPSEConstant::energyConvert);
99	gezelter	1490
100	tim	1822	thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;
101	gezelter	1490
102
103	tim	1822	barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * OOPSEConstant::energyConvert);
104	gezelter	1490
105	tim	1822	barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /
106			OOPSEConstant::energyConvert;
107	gezelter	1490
108	tim	1822	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
109			barostat_kinetic + barostat_potential;
110	gezelter	1490
111	tim	1822	return conservedQuantity;
112	gezelter	1490	}
113
114	tim	1822	void NPTi::loadEta() {
115			Mat3x3d etaMat = currentSnapshot_->getEta();
116			eta = etaMat(0,0);
117			if (fabs(etaMat(1,1) - eta) >= oopse::epsilon \|\| fabs(etaMat(1,1) - eta) >= oopse::epsilon \|\| etaMat.isDiagonal()) {
118			sprintf( painCave.errMsg,
119			"NPTi error: the diagonal elements of are eta matrix is not same or etaMat is not a diagonal matrix");
120			painCave.isFatal = 1;
121			simError();
122			}
123			}
124
125			void NPTi::saveEta() {
126			Mat3x3d etaMat(0.0);
127			etaMat(0, 0) = eta;
128			etaMat(1, 1) = eta;
129			etaMat(2, 2) = eta;
130			currentSnapshot_->setEta(etaMat);
131			}
132
133			}