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

Comparing trunk/src/integrators/NPTi.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 35 | Line 35
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).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
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 "NPTi.hpp"
#	Line 77 | Line 78 | namespace OpenMD {
78		}
79
80		void NPTi::calcVelScale() {
81	<	vScale = chi + eta;
81	>	vScale = thermostat.first + eta;
82		}
83
84		void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) {
#	Line 111 | Line 112 | namespace OpenMD {
112		painCave.isFatal = 1;
113		simError();
114		} else {
115	<	Mat3x3d hmat = currentSnapshot_->getHmat();
115	>	Mat3x3d hmat = snap->getHmat();
116		hmat *= scaleFactor;
117	<	currentSnapshot_->setHmat(hmat);
117	>	snap->setHmat(hmat);
118		}
119
120		}
#	Line 125 | Line 126 | namespace OpenMD {
126
127		RealType NPTi::calcConservedQuantity(){
128
129	<	chi= currentSnapshot_->getChi();
129	<	integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
129	>	thermostat = snap->getThermostat();
130		loadEta();
131		// We need NkBT a lot, so just set it here: This is the RAW number
132		// of integrableObjects, so no subtraction or addition of constraints or
#	Line 145 | Line 145 | namespace OpenMD {
145		RealType barostat_kinetic;
146		RealType barostat_potential;
147
148	<	Energy =thermo.getTotalE();
148	>	Energy =thermo.getTotalEnergy();
149
150	<	thermostat_kinetic = fkBT* tt2 * chi * chi / (2.0 * PhysicalConstants::energyConvert);
150	>	thermostat_kinetic = fkBT* tt2 * thermostat.first *
151	>	thermostat.first / (2.0 * PhysicalConstants::energyConvert);
152
153	<	thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert;
153	>	thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert;
154
155
156		barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * PhysicalConstants::energyConvert);
#	Line 164 | Line 165 | namespace OpenMD {
165		}
166
167		void NPTi::loadEta() {
168	<	Mat3x3d etaMat = currentSnapshot_->getEta();
168	>	Mat3x3d etaMat = snap->getBarostat();
169		eta = etaMat(0,0);
170		//if (fabs(etaMat(1,1) - eta) >= OpenMD::epsilon || fabs(etaMat(1,1) - eta) >= OpenMD::epsilon || !etaMat.isDiagonal()) {
171		//    sprintf( painCave.errMsg,
#	Line 179 | Line 180 | namespace OpenMD {
180		etaMat(0, 0) = eta;
181		etaMat(1, 1) = eta;
182		etaMat(2, 2) = eta;
183	<	currentSnapshot_->setEta(etaMat);
183	>	snap->setBarostat(etaMat);
184		}
185		}

Comparing trunk/src/integrators/NPTi.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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