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){

}

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(){

    chi= currentSnapshot_->getChi();
    integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
    loadEta();
    // We need NkBT a lot, so just set it here: This is the RAW number
    // of integrableObjects, so no subtraction or addition of constraints or
    // orientational degrees of freedom:
    NkBT = info_->getNGlobalIntegrableObjects()*OOPSEConstant::kB *targetTemp;

    // fkBT is used because the thermostat operates on more degrees of freedom
    // than the barostat (when there are particles with orientational degrees
    // of freedom).  
    fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp;    
    
    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  eta matrix are not the 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:	1913
Committed:	Mon Jan 10 22:04:20 2005 UTC (21 years, 5 months ago) by tim
File size:	4037 byte(s)
Log Message:	create a register module to register force fields, integrators and minimizers
#	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			}
24
25	tim	1774	void NPTi::evolveEtaA() {
26	tim	1822	eta += dt2 * ( instaVol * (instaPress - targetPressure) /
27			(OOPSEConstant::pressureConvertNkBTtb2));
28			oldEta = eta;
29	gezelter	1490	}
30
31	tim	1774	void NPTi::evolveEtaB() {
32	gezelter	1490
33	tim	1822	prevEta = eta;
34			eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
35			(OOPSEConstant::pressureConvertNkBTtb2));
36	gezelter	1490	}
37
38	tim	1774	void NPTi::calcVelScale() {
39	tim	1822	vScale = chi + eta;
40	gezelter	1490	}
41
42	tim	1774	void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) {
43			sc = vel * vScale;
44	gezelter	1490	}
45
46	tim	1774	void NPTi::getVelScaleB(Vector3d& sc, int index ){
47			sc = oldVel[index] * vScale;
48	gezelter	1490	}
49
50
51	tim	1774	void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM,
52	tim	1822	int index, Vector3d& sc){
53	tim	1774	/*@todo/
54	tim	1897	sc = (oldPos[index] + pos)/2.0 -COM;
55	tim	1774	sc *= eta;
56	gezelter	1490	}
57
58	tim	1774	void NPTi::scaleSimBox(){
59	gezelter	1490
60	tim	1822	double scaleFactor;
61	gezelter	1490
62	tim	1822	scaleFactor = exp(dt*eta);
63	gezelter	1490
64	tim	1822	if ((scaleFactor > 1.1) \|\| (scaleFactor < 0.9)) {
65			sprintf( painCave.errMsg,
66	gezelter	1490	"NPTi error: Attempting a Box scaling of more than 10 percent"
67			" check your tauBarostat, as it is probably too small!\n"
68			" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
69			);
70	tim	1822	painCave.isFatal = 1;
71			simError();
72			} else {
73			Mat3x3d hmat = currentSnapshot_->getHmat();
74			hmat *= scaleFactor;
75			currentSnapshot_->setHmat(hmat);
76			}
77	gezelter	1490
78			}
79
80	tim	1774	bool NPTi::etaConverged() {
81	gezelter	1490
82	tim	1822	return ( fabs(prevEta - eta) <= etaTolerance );
83	gezelter	1490	}
84
85	tim	1774	double NPTi::calcConservedQuantity(){
86	gezelter	1490
87	tim	1867	chi= currentSnapshot_->getChi();
88			integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
89			loadEta();
90			// We need NkBT a lot, so just set it here: This is the RAW number
91			// of integrableObjects, so no subtraction or addition of constraints or
92			// orientational degrees of freedom:
93			NkBT = info_->getNGlobalIntegrableObjects()OOPSEConstant::kB targetTemp;
94
95			// fkBT is used because the thermostat operates on more degrees of freedom
96			// than the barostat (when there are particles with orientational degrees
97			// of freedom).
98			fkBT = info_->getNdf()OOPSEConstant::kB targetTemp;
99
100	tim	1822	double conservedQuantity;
101			double Energy;
102			double thermostat_kinetic;
103			double thermostat_potential;
104			double barostat_kinetic;
105			double barostat_potential;
106	gezelter	1490
107	tim	1822	Energy =thermo.getTotalE();
108	gezelter	1490
109	tim	1822	thermostat_kinetic = fkBT* tt2 * chi * chi / (2.0 * OOPSEConstant::energyConvert);
110	gezelter	1490
111	tim	1822	thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;
112	gezelter	1490
113
114	tim	1822	barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * OOPSEConstant::energyConvert);
115	gezelter	1490
116	tim	1822	barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /
117			OOPSEConstant::energyConvert;
118	gezelter	1490
119	tim	1822	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
120			barostat_kinetic + barostat_potential;
121	tim	1907
122	tim	1822	return conservedQuantity;
123	gezelter	1490	}
124
125	tim	1822	void NPTi::loadEta() {
126			Mat3x3d etaMat = currentSnapshot_->getEta();
127			eta = etaMat(0,0);
128	tim	1883	//if (fabs(etaMat(1,1) - eta) >= oopse::epsilon \|\| fabs(etaMat(1,1) - eta) >= oopse::epsilon \|\| !etaMat.isDiagonal()) {
129			// sprintf( painCave.errMsg,
130			// "NPTi error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
131			// painCave.isFatal = 1;
132			// simError();
133			//}
134	tim	1822	}
135
136			void NPTi::saveEta() {
137			Mat3x3d etaMat(0.0);
138			etaMat(0, 0) = eta;
139			etaMat(1, 1) = eta;
140			etaMat(2, 2) = eta;
141			currentSnapshot_->setEta(etaMat);
142			}
143
144			}