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root/OpenMD/branches/development/src/integrators/NPT.cpp

Comparing:
trunk/src/integrators/NPT.cpp (file contents), Revision 546 by tim, Sun May 29 00:06:14 2005 UTC vs.
branches/development/src/integrators/NPT.cpp (file contents), Revision 1759 by gezelter, Thu Jun 21 18:55:33 2012 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include <math.h>
#	Line 46 | Line 47
47		#include "integrators/NPT.hpp"
48		#include "math/SquareMatrix3.hpp"
49		#include "primitives/Molecule.hpp"
50	<	#include "utils/OOPSEConstant.hpp"
50	>	#include "utils/PhysicalConstants.hpp"
51		#include "utils/simError.h"
52
53		// Basic isotropic thermostating and barostating via the Melchionna
#	Line 59 | Line 60
60		//
61		//    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
62
63	<	namespace oopse {
63	>	namespace OpenMD {
64
65		NPT::NPT(SimInfo* info) :
66		VelocityVerletIntegrator(info), chiTolerance(1e-6), etaTolerance(1e-6), maxIterNum_(4) {
67
68		Globals* simParams = info_->getSimParams();
69
70	<	if (!simParams->getUseInitXSstate()) {
70	>	if (!simParams->getUseIntialExtendedSystemState()) {
71		Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
72		currSnapshot->setChi(0.0);
73		currSnapshot->setIntegralOfChiDt(0.0);
#	Line 76 | Line 77 | namespace oopse {
77		if (!simParams->haveTargetTemp()) {
78		sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp!\n");
79		painCave.isFatal = 1;
80	<	painCave.severity = OOPSE_ERROR;
80	>	painCave.severity = OPENMD_ERROR;
81		simError();
82		} else {
83		targetTemp = simParams->getTargetTemp();
#	Line 85 | Line 86 | namespace oopse {
86		// We must set tauThermostat
87		if (!simParams->haveTauThermostat()) {
88		sprintf(painCave.errMsg, "If you use the constant temperature\n"
89	<	"\tintegrator, you must set tauThermostat_.\n");
89	>	"\tintegrator, you must set tauThermostat.\n");
90
91	<	painCave.severity = OOPSE_ERROR;
91	>	painCave.severity = OPENMD_ERROR;
92		painCave.isFatal = 1;
93		simError();
94		} else {
#	Line 107 | Line 108 | namespace oopse {
108		if (!simParams->haveTauBarostat()) {
109		sprintf(painCave.errMsg,
110		"If you use the NPT integrator, you must set tauBarostat.\n");
111	<	painCave.severity = OOPSE_ERROR;
111	>	painCave.severity = OPENMD_ERROR;
112		painCave.isFatal = 1;
113		simError();
114		} else {
#	Line 117 | Line 118 | namespace oopse {
118		tt2 = tauThermostat * tauThermostat;
119		tb2 = tauBarostat * tauBarostat;
120
121	<	update();
121	>	updateSizes();
122		}
123
124		NPT::~NPT() {
125		}
126
127	<	void NPT::doUpdate() {
127	>	void NPT::doUpdateSizes() {
128
129		oldPos.resize(info_->getNIntegrableObjects());
130		oldVel.resize(info_->getNIntegrableObjects());
#	Line 137 | Line 138 | namespace oopse {
138		Molecule* mol;
139		StuntDouble* integrableObject;
140		Vector3d Tb, ji;
141	<	double mass;
141	>	RealType mass;
142		Vector3d vel;
143		Vector3d pos;
144		Vector3d frc;
#	Line 150 | Line 151 | namespace oopse {
151
152		instaTemp =thermo.getTemperature();
153		press = thermo.getPressureTensor();
154	<	instaPress = OOPSEConstant::pressureConvert* (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0;
154	>	instaPress = PhysicalConstants::pressureConvert* (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0;
155		instaVol =thermo.getVolume();
156
157		Vector3d  COM = info_->getCom();
#	Line 171 | Line 172 | namespace oopse {
172		getVelScaleA(sc, vel);
173
174		// velocity half step  (use chi from previous step here):
175	<	//vel[j] += dt2 * ((frc[j] / mass) * OOPSEConstant::energyConvert - sc[j]);
176	<	vel += dt2*OOPSEConstant::energyConvert/mass* frc - dt2*sc;
175	>	//vel[j] += dt2 * ((frc[j] / mass) * PhysicalConstants::energyConvert - sc[j]);
176	>	vel += dt2*PhysicalConstants::energyConvert/mass* frc - dt2*sc;
177		integrableObject->setVel(vel);
178
179		if (integrableObject->isDirectional()) {
#	Line 185 | Line 186 | namespace oopse {
186
187		ji = integrableObject->getJ();
188
189	<	//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
190	<	ji += dt2*OOPSEConstant::energyConvert * Tb - dt2*chi* ji;
189	>	//ji[j] += dt2 * (Tb[j] * PhysicalConstants::energyConvert - ji[j]*chi);
190	>	ji += dt2*PhysicalConstants::energyConvert * Tb - dt2*chi* ji;
191
192	<	rotAlgo->rotate(integrableObject, ji, dt);
192	>	rotAlgo_->rotate(integrableObject, ji, dt);
193
194		integrableObject->setJ(ji);
195		}
#	Line 204 | Line 205 | namespace oopse {
205		//calculate the integral of chidt
206		integralOfChidt += dt2 * chi;
207
208	+	flucQ_->moveA();
209	+
210	+
211		index = 0;
212		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
213		for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
#	Line 232 | Line 236 | namespace oopse {
236		}
237		}
238
239	<	rattle->constraintA();
239	>	rattle_->constraintA();
240		}
241
242		// Scale the box after all the positions have been moved:
#	Line 256 | Line 260 | namespace oopse {
260		Vector3d sc;
261		Vector3d vel;
262		Vector3d frc;
263	<	double mass;
263	>	RealType mass;
264
265
266		chi= currentSnapshot_->getChi();
267		integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
268	<	double oldChi  = chi;
269	<	double prevChi;
268	>	RealType oldChi  = chi;
269	>	RealType prevChi;
270
271		loadEta();
272
#	Line 273 | Line 277 | namespace oopse {
277		integrableObject = mol->nextIntegrableObject(j)) {
278
279		oldVel[index] = integrableObject->getVel();
280	<	oldJi[index] = integrableObject->getJ();
280	>
281	>	if (integrableObject->isDirectional())
282	>	oldJi[index] = integrableObject->getJ();
283	>
284		++index;
285		}
286		}
#	Line 306 | Line 313 | namespace oopse {
313		getVelScaleB(sc, index);
314
315		// velocity half step
316	<	//vel[j] = oldVel[3 * i + j] + dt2 *((frc[j] / mass) * OOPSEConstant::energyConvert - sc[j]);
317	<	vel = oldVel[index] + dt2*OOPSEConstant::energyConvert/mass* frc - dt2*sc;
316	>	//vel[j] = oldVel[3 * i + j] + dt2 *((frc[j] / mass) * PhysicalConstants::energyConvert - sc[j]);
317	>	vel = oldVel[index] + dt2*PhysicalConstants::energyConvert/mass* frc - dt2*sc;
318		integrableObject->setVel(vel);
319
320		if (integrableObject->isDirectional()) {
321		// get and convert the torque to body frame
322		Tb = integrableObject->lab2Body(integrableObject->getTrq());
323
324	<	//ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi[3*i+j]*chi);
325	<	ji = oldJi[index] + dt2*OOPSEConstant::energyConvert*Tb - dt2*chi*oldJi[index];
324	>	//ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * PhysicalConstants::energyConvert - oldJi[3*i+j]*chi);
325	>	ji = oldJi[index] + dt2*PhysicalConstants::energyConvert*Tb - dt2*chi*oldJi[index];
326		integrableObject->setJ(ji);
327		}
328
#	Line 323 | Line 330 | namespace oopse {
330		}
331		}
332
333	<	rattle->constraintB();
333	>	rattle_->constraintB();
334
335		if ((fabs(prevChi - chi) <= chiTolerance) && this->etaConverged())
336		break;
#	Line 335 | Line 342 | namespace oopse {
342		currentSnapshot_->setChi(chi);
343		currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
344
345	+	flucQ_->moveB();
346		saveEta();
347		}
348

Comparing:
trunk/src/integrators/NPT.cpp (property svn:keywords), Revision 546 by tim, Sun May 29 00:06:14 2005 UTC vs.
branches/development/src/integrators/NPT.cpp (property svn:keywords), Revision 1759 by gezelter, Thu Jun 21 18:55:33 2012 UTC

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