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root/OpenMD/trunk/src/integrators/NPrT.cpp

Comparing trunk/src/integrators/NPrT.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 36 | Line 36
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).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include "brains/SimInfo.hpp"
#	Line 62 | Line 63 | namespace OpenMD {
63
64		}
65		void NPrT::evolveEtaA() {
66	<	Mat3x3d hmat = currentSnapshot_->getHmat();
66	>	Mat3x3d hmat = snap->getHmat();
67		RealType hz = hmat(2, 2);
68		RealType Axy = hmat(0,0) * hmat(1, 1);
69		RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert);
#	Line 74 | Line 75 | namespace OpenMD {
75		}
76
77		void NPrT::evolveEtaB() {
78	<	Mat3x3d hmat = currentSnapshot_->getHmat();
78	>	Mat3x3d hmat = snap->getHmat();
79		RealType hz = hmat(2, 2);
80		RealType Axy = hmat(0,0) * hmat(1, 1);
81		prevEta = eta;
#	Line 93 | Line 94 | namespace OpenMD {
94		vScale(i, j) = eta(i, j);
95
96		if (i == j) {
97	<	vScale(i, j) += chi;
97	>	vScale(i, j) += thermostat.first;
98		}
99		}
100		}
#	Line 120 | Line 121 | namespace OpenMD {
121		scaleMat(0, 0) = exp(dt*eta(0, 0));
122		scaleMat(1, 1) = exp(dt*eta(1, 1));
123		scaleMat(2, 2) = exp(dt*eta(2, 2));
124	<	Mat3x3d hmat = currentSnapshot_->getHmat();
124	>	Mat3x3d hmat = snap->getHmat();
125		hmat = hmat *scaleMat;
126	<	currentSnapshot_->setHmat(hmat);
126	>	snap->setHmat(hmat);
127
128		}
129
#	Line 141 | Line 142 | namespace OpenMD {
142		}
143
144		RealType NPrT::calcConservedQuantity(){
145	<
145	<	chi= currentSnapshot_->getChi();
146	<	integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
145	>	thermostat = snap->getThermostat();
146		loadEta();
147
148		// We need NkBT a lot, so just set it here: This is the RAW number
#	Line 157 | Line 156 | namespace OpenMD {
156		fkBT = info_->getNdf()*PhysicalConstants::kB *targetTemp;
157
158
159	<	RealType totalEnergy = thermo.getTotalE();
159	>	RealType totalEnergy = thermo.getTotalEnergy();
160
161	<	RealType thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * PhysicalConstants::energyConvert);
161	>	RealType thermostat_kinetic = fkBT * tt2 * thermostat.first * thermostat.first /(2.0 * PhysicalConstants::energyConvert);
162
163	<	RealType thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert;
163	>	RealType thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert;
164
165		SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
166		RealType trEta = tmp.trace();
#	Line 170 | Line 169 | namespace OpenMD {
169
170		RealType barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert;
171
172	<	Mat3x3d hmat = currentSnapshot_->getHmat();
172	>	Mat3x3d hmat = snap->getHmat();
173		RealType hz = hmat(2, 2);
174		RealType area = hmat(0,0) * hmat(1, 1);
175
#	Line 182 | Line 181 | namespace OpenMD {
181		}
182
183		void NPrT::loadEta() {
184	<	eta= currentSnapshot_->getEta();
184	>	eta= snap->getBarostat();
185
186		//if (!eta.isDiagonal()) {
187		//    sprintf( painCave.errMsg,
#	Line 193 | Line 192 | namespace OpenMD {
192		}
193
194		void NPrT::saveEta() {
195	<	currentSnapshot_->setEta(eta);
195	>	snap->setBarostat(eta);
196		}
197
198		}

Comparing trunk/src/integrators/NPrT.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 0 | Line 1
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