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

Comparing:
trunk/src/integrators/NPT.cpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/integrators/NPT.cpp (file contents), Revision 1759 by gezelter, Thu Jun 21 18:55:33 2012 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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) :
65	>	NPT::NPT(SimInfo* info) :
66		VelocityVerletIntegrator(info), chiTolerance(1e-6), etaTolerance(1e-6), maxIterNum_(4) {
67
68	<	Globals* simParams = info_->getSimParams();
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);
74		currSnapshot->setEta(Mat3x3d(0.0));
75	<	}
75	>	}
76
77	<	if (!simParams->haveTargetTemp()) {
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 {
82	>	} else {
83		targetTemp = simParams->getTargetTemp();
84	<	}
84	>	}
85
86	<	// We must set tauThermostat
87	<	if (!simParams->haveTauThermostat()) {
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 {
94	>	} else {
95		tauThermostat = simParams->getTauThermostat();
96	<	}
96	>	}
97
98	<	if (!simParams->haveTargetPressure()) {
98	>	if (!simParams->haveTargetPressure()) {
99		sprintf(painCave.errMsg, "NPT error: You can't use the NPT integrator\n"
100	<	"   without a targetPressure!\n");
100	>	"   without a targetPressure!\n");
101
102		painCave.isFatal = 1;
103		simError();
104	<	} else {
104	>	} else {
105		targetPressure = simParams->getTargetPressure();
106	<	}
106	>	}
107
108	<	if (!simParams->haveTauBarostat()) {
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 {
114	>	} else {
115		tauBarostat = simParams->getTauBarostat();
116	<	}
116	>	}
117
118	<	tt2 = tauThermostat * tauThermostat;
119	<	tb2 = tauBarostat * tauBarostat;
118	>	tt2 = tauThermostat * tauThermostat;
119	>	tb2 = tauBarostat * tauBarostat;
120
121	<	update();
122	<	}
121	>	updateSizes();
122	>	}
123
124	<	NPT::~NPT() {
125	<	}
124	>	NPT::~NPT() {
125	>	}
126
127	<	void NPT::doUpdate() {
127	>	void NPT::doUpdateSizes() {
128
129		oldPos.resize(info_->getNIntegrableObjects());
130		oldVel.resize(info_->getNIntegrableObjects());
131		oldJi.resize(info_->getNIntegrableObjects());
132
133	<	}
133	>	}
134
135	<	void NPT::moveA() {
135	>	void NPT::moveA() {
136		SimInfo::MoleculeIterator i;
137		Molecule::IntegrableObjectIterator  j;
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 | void NPT::moveA() {
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 160 | Line 161 | void NPT::moveA() {
161		calcVelScale();
162
163		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
164	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
165	<	integrableObject = mol->nextIntegrableObject(j)) {
164	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
165	>	integrableObject = mol->nextIntegrableObject(j)) {
166
167	<	vel = integrableObject->getVel();
168	<	frc = integrableObject->getFrc();
167	>	vel = integrableObject->getVel();
168	>	frc = integrableObject->getFrc();
169
170	<	mass = integrableObject->getMass();
170	>	mass = integrableObject->getMass();
171
172	<	getVelScaleA(sc, vel);
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;
177	<	integrableObject->setVel(vel);
174	>	// velocity half step  (use chi from previous step here):
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()) {
179	>	if (integrableObject->isDirectional()) {
180
181	<	// get and convert the torque to body frame
181	>	// get and convert the torque to body frame
182
183	<	Tb = integrableObject->lab2Body(integrableObject->getTrq());
183	>	Tb = integrableObject->lab2Body(integrableObject->getTrq());
184
185	<	// get the angular momentum, and propagate a half step
185	>	// get the angular momentum, and propagate a half step
186
187	<	ji = integrableObject->getJ();
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	<	}
194	>	integrableObject->setJ(ji);
195	>	}
196
197	<	}
197	>	}
198		}
199		// evolve chi and eta  half step
200
#	Line 204 | Line 205 | void NPT::moveA() {
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;
214	<	integrableObject = mol->nextIntegrableObject(j)) {
215	<	oldPos[index++] = integrableObject->getPos();
216	<	}
213	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
214	>	integrableObject = mol->nextIntegrableObject(j)) {
215	>	oldPos[index++] = integrableObject->getPos();
216	>	}
217		}
218
219		//the first estimation of r(t+dt) is equal to  r(t)
220
221		for(int k = 0; k < maxIterNum_; k++) {
222	<	index = 0;
223	<	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
224	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
225	<	integrableObject = mol->nextIntegrableObject(j)) {
222	>	index = 0;
223	>	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
224	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
225	>	integrableObject = mol->nextIntegrableObject(j)) {
226
227	<	vel = integrableObject->getVel();
228	<	pos = integrableObject->getPos();
227	>	vel = integrableObject->getVel();
228	>	pos = integrableObject->getPos();
229
230	<	this->getPosScale(pos, COM, index, sc);
230	>	this->getPosScale(pos, COM, index, sc);
231
232	<	pos = oldPos[index] + dt * (vel + sc);
233	<	integrableObject->setPos(pos);
232	>	pos = oldPos[index] + dt * (vel + sc);
233	>	integrableObject->setPos(pos);
234
235	<	++index;
236	<	}
237	<	}
235	>	++index;
236	>	}
237	>	}
238
239	<	rattle->constraintA();
239	>	rattle_->constraintA();
240		}
241
242		// Scale the box after all the positions have been moved:
#	Line 243 | Line 247 | void NPT::moveA() {
247		currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
248
249		saveEta();
250	<	}
250	>	}
251
252	<	void NPT::moveB(void) {
252	>	void NPT::moveB(void) {
253		SimInfo::MoleculeIterator i;
254		Molecule::IntegrableObjectIterator  j;
255		Molecule* mol;
#	Line 256 | Line 260 | void NPT::moveB(void) {
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
273		//save velocity and angular momentum
274		index = 0;
275		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
276	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
277	<	integrableObject = mol->nextIntegrableObject(j)) {
276	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
277	>	integrableObject = mol->nextIntegrableObject(j)) {
278
279	<	oldVel[index] = integrableObject->getVel();
280	<	oldJi[index] = integrableObject->getJ();
281	<	++index;
282	<	}
279	>	oldVel[index] = integrableObject->getVel();
280	>
281	>	if (integrableObject->isDirectional())
282	>	oldJi[index] = integrableObject->getJ();
283	>
284	>	++index;
285	>	}
286		}
287
288		// do the iteration:
289		instaVol =thermo.getVolume();
290
291		for(int k = 0; k < maxIterNum_; k++) {
292	<	instaTemp =thermo.getTemperature();
293	<	instaPress =thermo.getPressure();
292	>	instaTemp =thermo.getTemperature();
293	>	instaPress =thermo.getPressure();
294
295	<	// evolve chi another half step using the temperature at t + dt/2
296	<	prevChi = chi;
297	<	chi = oldChi + dt2 * (instaTemp / targetTemp - 1.0) / tt2;
295	>	// evolve chi another half step using the temperature at t + dt/2
296	>	prevChi = chi;
297	>	chi = oldChi + dt2 * (instaTemp / targetTemp - 1.0) / tt2;
298
299	<	//evolve eta
300	<	this->evolveEtaB();
301	<	this->calcVelScale();
299	>	//evolve eta
300	>	this->evolveEtaB();
301	>	this->calcVelScale();
302
303	<	index = 0;
304	<	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
305	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
306	<	integrableObject = mol->nextIntegrableObject(j)) {
303	>	index = 0;
304	>	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
305	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
306	>	integrableObject = mol->nextIntegrableObject(j)) {
307
308	<	frc = integrableObject->getFrc();
309	<	vel = integrableObject->getVel();
308	>	frc = integrableObject->getFrc();
309	>	vel = integrableObject->getVel();
310
311	<	mass = integrableObject->getMass();
311	>	mass = integrableObject->getMass();
312
313	<	getVelScaleB(sc, index);
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;
318	<	integrableObject->setVel(vel);
315	>	// velocity half step
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());
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];
326	<	integrableObject->setJ(ji);
327	<	}
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
329	<	++index;
330	<	}
331	<	}
329	>	++index;
330	>	}
331	>	}
332
333	<	rattle->constraintB();
333	>	rattle_->constraintB();
334
335	<	if ((fabs(prevChi - chi) <= chiTolerance) && this->etaConverged())
336	<	break;
335	>	if ((fabs(prevChi - chi) <= chiTolerance) && this->etaConverged())
336	>	break;
337		}
338
339		//calculate integral of chidt
#	Line 335 | Line 342 | void NPT::moveB(void) {
342		currentSnapshot_->setChi(chi);
343		currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
344
345	+	flucQ_->moveB();
346		saveEta();
347	<	}
347	>	}
348
349	+	void NPT::resetIntegrator(){
350	+	currentSnapshot_->setChi(0.0);
351	+	currentSnapshot_->setIntegralOfChiDt(0.0);
352	+	resetEta();
353	+	}
354	+
355	+
356	+	void NPT::resetEta() {
357	+	Mat3x3d etaMat(0.0);
358	+	currentSnapshot_->setEta(etaMat);
359	+	}
360	+
361		}

Comparing:
trunk/src/integrators/NPT.cpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 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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