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Comparing trunk/src/integrators/NVT.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

#	Line 1 | Line 1
1	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
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.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
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, 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 "integrators/NVT.hpp"
44	>	#include "primitives/Molecule.hpp"
45	>	#include "utils/simError.h"
46	>	#include "utils/PhysicalConstants.hpp"
47
48	<	#include "Atom.hpp"
4	<	#include "SRI.hpp"
5	<	#include "AbstractClasses.hpp"
6	<	#include "SimInfo.hpp"
7	<	#include "ForceFields.hpp"
8	<	#include "Thermo.hpp"
9	<	#include "ReadWrite.hpp"
10	<	#include "Integrator.hpp"
11	<	#include "simError.h"
48	>	namespace OpenMD {
49
50	+	NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), maxIterNum_(4),
51	+	chiTolerance_(1e-6) {
52
53	<	// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
53	>	Globals* simParams = info_->getSimParams();
54
55	<	template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff):
56	<	T( theInfo, the_ff )
57	<	{
19	<	GenericData* data;
20	<	DoubleData * chiValue;
21	<	DoubleData * integralOfChidtValue;
22	<
23	<	chiValue = NULL;
24	<	integralOfChidtValue = NULL;
25	<
26	<	chi = 0.0;
27	<	have_tau_thermostat = 0;
28	<	have_target_temp = 0;
29	<	have_chi_tolerance = 0;
30	<	integralOfChidt = 0.0;
31	<
32	<
33	<	if( theInfo->useInitXSstate ){
34	<
35	<	// retrieve chi and integralOfChidt from simInfo
36	<	data = info->getProperty(CHIVALUE_ID);
37	<	if(data){
38	<	chiValue = dynamic_cast<DoubleData*>(data);
55	>	if (!simParams->getUseIntialExtendedSystemState()) {
56	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
57	>	snap->setThermostat(make_pair(0.0, 0.0));
58		}
59
60	<	data = info->getProperty(INTEGRALOFCHIDT_ID);
61	<	if(data){
62	<	integralOfChidtValue = dynamic_cast<DoubleData*>(data);
60	>	if (!simParams->haveTargetTemp()) {
61	>	sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n");
62	>	painCave.isFatal = 1;
63	>	painCave.severity = OPENMD_ERROR;
64	>	simError();
65	>	} else {
66	>	targetTemp_ = simParams->getTargetTemp();
67		}
45	–
46	–	// chi and integralOfChidt should appear by pair
47	–	if(chiValue && integralOfChidtValue){
48	–	chi = chiValue->getData();
49	–	integralOfChidt = integralOfChidtValue->getData();
50	–	}
51	–	}
68
69	<	oldVel = new double[3*integrableObjects.size()];
54	<	oldJi = new double[3*integrableObjects.size()];
55	<	}
69	>	// We must set tauThermostat.
70
71	<	template<typename T> NVT<T>::~NVT() {
72	<	delete[] oldVel;
73	<	delete[] oldJi;
60	<	}
71	>	if (!simParams->haveTauThermostat()) {
72	>	sprintf(painCave.errMsg, "If you use the constant temperature\n"
73	>	"\tintegrator, you must set tauThermostat.\n");
74
75	<	template<typename T> void NVT<T>::moveA() {
75	>	painCave.severity = OPENMD_ERROR;
76	>	painCave.isFatal = 1;
77	>	simError();
78	>	} else {
79	>	tauThermostat_ = simParams->getTauThermostat();
80	>	}
81
82	<	int i, j;
83	<	DirectionalAtom* dAtom;
66	<	double Tb[3], ji[3];
67	<	double mass;
68	<	double vel[3], pos[3], frc[3];
82	>	updateSizes();
83	>	}
84
85	<	double instTemp;
85	>	void NVT::doUpdateSizes() {
86	>	oldVel_.resize(info_->getNIntegrableObjects());
87	>	oldJi_.resize(info_->getNIntegrableObjects());
88	>	}
89
90	<	// We need the temperature at time = t for the chi update below:
90	>	void NVT::moveA() {
91	>	SimInfo::MoleculeIterator i;
92	>	Molecule::IntegrableObjectIterator  j;
93	>	Molecule* mol;
94	>	StuntDouble* sd;
95	>	Vector3d Tb;
96	>	Vector3d ji;
97	>	RealType mass;
98	>	Vector3d vel;
99	>	Vector3d pos;
100	>	Vector3d frc;
101
102	<	instTemp = tStats->getTemperature();
102	>	pair<RealType, RealType> thermostat = snap->getThermostat();
103
104	<	for( i=0; i < integrableObjects.size(); i++ ){
104	>	// We need the temperature at time = t for the chi update below:
105
106	<	integrableObjects[i]->getVel( vel );
79	<	integrableObjects[i]->getPos( pos );
80	<	integrableObjects[i]->getFrc( frc );
106	>	RealType instTemp = thermo.getTemperature();
107
108	<	mass = integrableObjects[i]->getMass();
108	>	for (mol = info_->beginMolecule(i); mol != NULL;
109	>	mol = info_->nextMolecule(i)) {
110
111	<	for (j=0; j < 3; j++) {
112	<	// velocity half step  (use chi from previous step here):
86	<	vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
87	<	// position whole step
88	<	pos[j] += dt * vel[j];
89	<	}
111	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
112	>	sd = mol->nextIntegrableObject(j)) {
113
114	<	integrableObjects[i]->setVel( vel );
115	<	integrableObjects[i]->setPos( pos );
114	>	vel = sd->getVel();
115	>	pos = sd->getPos();
116	>	frc = sd->getFrc();
117
118	<	if( integrableObjects[i]->isDirectional() ){
118	>	mass = sd->getMass();
119
120	<	// get and convert the torque to body frame
120	>	// velocity half step (use chi from previous step here):
121	>	vel += dt2 *PhysicalConstants::energyConvert/mass*frc
122	>	- dt2*thermostat.first*vel;
123	>
124	>	// position whole step
125	>	pos += dt * vel;
126
127	<	integrableObjects[i]->getTrq( Tb );
128	<	integrableObjects[i]->lab2Body( Tb );
127	>	sd->setVel(vel);
128	>	sd->setPos(pos);
129
130	<	// get the angular momentum, and propagate a half step
130	>	if (sd->isDirectional()) {
131
132	<	integrableObjects[i]->getJ( ji );
132	>	//convert the torque to body frame
133	>	Tb = sd->lab2Body(sd->getTrq());
134
135	<	for (j=0; j < 3; j++)
106	<	ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
135	>	// get the angular momentum, and propagate a half step
136
137	<	this->rotationPropagation( integrableObjects[i], ji );
137	>	ji = sd->getJ();
138
139	<	integrableObjects[i]->setJ( ji );
140	<	}
112	<	}
113	<
114	<	if(nConstrained)
115	<	constrainA();
139	>	ji += dt2*PhysicalConstants::energyConvert*Tb
140	>	- dt2*thermostat.first *ji;
141
142	<	// Finally, evolve chi a half step (just like a velocity) using
118	<	// temperature at time t, not time t+dt/2
142	>	rotAlgo_->rotate(sd, ji, dt);
143
144	<	//std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n";
145	<
146	<	chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
123	<	integralOfChidt += chi*dt2;
144	>	sd->setJ(ji);
145	>	}
146	>	}
147
148	<	}
148	>	}
149	>
150	>	flucQ_->moveA();
151	>	rattle_->constraintA();
152
153	<	template<typename T> void NVT<T>::moveB( void ){
154	<	int i, j, k;
129	<	double Tb[3], ji[3];
130	<	double vel[3], frc[3];
131	<	double mass;
132	<	double instTemp;
133	<	double oldChi, prevChi;
153	>	// Finally, evolve chi a half step (just like a velocity) using
154	>	// temperature at time t, not time t+dt/2
155
156	<	// Set things up for the iteration:
156	>	thermostat.first += dt2 * (instTemp / targetTemp_ - 1.0)
157	>	/ (tauThermostat_ * tauThermostat_);
158	>	thermostat.second += thermostat.first * dt2;
159
160	<	oldChi = chi;
160	>	snap->setThermostat(thermostat);
161	>	}
162
163	<	for( i=0; i < integrableObjects.size(); i++ ){
164	<
165	<	integrableObjects[i]->getVel( vel );
166	<
167	<	for (j=0; j < 3; j++)
168	<	oldVel[3*i + j]  = vel[j];
169	<
170	<	if( integrableObjects[i]->isDirectional() ){
171	<
172	<	integrableObjects[i]->getJ( ji );
173	<
174	<	for (j=0; j < 3; j++)
175	<	oldJi[3*i + j] = ji[j];
163	>	void NVT::moveB() {
164	>	SimInfo::MoleculeIterator i;
165	>	Molecule::IntegrableObjectIterator  j;
166	>	Molecule* mol;
167	>	StuntDouble* sd;
168	>
169	>	Vector3d Tb;
170	>	Vector3d ji;
171	>	Vector3d vel;
172	>	Vector3d frc;
173	>	RealType mass;
174	>	RealType instTemp;
175	>	int index;
176	>	// Set things up for the iteration:
177
178	+	pair<RealType, RealType> thermostat = snap->getThermostat();
179	+	RealType oldChi = thermostat.first;
180	+	RealType  prevChi;
181	+
182	+	index = 0;
183	+	for (mol = info_->beginMolecule(i); mol != NULL;
184	+	mol = info_->nextMolecule(i)) {
185	+
186	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
187	+	sd = mol->nextIntegrableObject(j)) {
188	+
189	+	oldVel_[index] = sd->getVel();
190	+
191	+	if (sd->isDirectional())
192	+	oldJi_[index] = sd->getJ();
193	+
194	+	++index;
195	+	}
196		}
154	–	}
197
198	<	// do the iteration:
198	>	// do the iteration:
199
200	<	for (k=0; k < 4; k++) {
200	>	for(int k = 0; k < maxIterNum_; k++) {
201	>	index = 0;
202	>	instTemp = thermo.getTemperature();
203
204	<	instTemp = tStats->getTemperature();
204	>	// evolve chi another half step using the temperature at t + dt/2
205
206	<	// evolve chi another half step using the temperature at t + dt/2
206	>	prevChi = thermostat.first;
207	>	thermostat.first = oldChi + dt2 * (instTemp / targetTemp_ - 1.0)
208	>	/ (tauThermostat_ * tauThermostat_);
209
210	<	prevChi = chi;
211	<	chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
212	<	(tauThermostat*tauThermostat);
210	>	for (mol = info_->beginMolecule(i); mol != NULL;
211	>	mol = info_->nextMolecule(i)) {
212	>
213	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
214	>	sd = mol->nextIntegrableObject(j)) {
215
216	<	for( i=0; i < integrableObjects.size(); i++ ){
216	>	frc = sd->getFrc();
217	>	mass = sd->getMass();
218
219	<	integrableObjects[i]->getFrc( frc );
171	<	integrableObjects[i]->getVel(vel);
219	>	// velocity half step
220
221	<	mass = integrableObjects[i]->getMass();
221	>	vel = oldVel_[index]
222	>	+ dt2/mass*PhysicalConstants::energyConvert * frc
223	>	- dt2*thermostat.first*oldVel_[index];
224	>
225	>	sd->setVel(vel);
226
227	<	// velocity half step
176	<	for (j=0; j < 3; j++)
177	<	vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
227	>	if (sd->isDirectional()) {
228
229	<	integrableObjects[i]->setVel( vel );
229	>	// get and convert the torque to body frame
230
231	<	if( integrableObjects[i]->isDirectional() ){
231	>	Tb =  sd->lab2Body(sd->getTrq());
232
233	<	// get and convert the torque to body frame
233	>	ji = oldJi_[index] + dt2*PhysicalConstants::energyConvert*Tb
234	>	- dt2*thermostat.first *oldJi_[index];
235
236	<	integrableObjects[i]->getTrq( Tb );
237	<	integrableObjects[i]->lab2Body( Tb );
236	>	sd->setJ(ji);
237	>	}
238
188	–	for (j=0; j < 3; j++)
189	–	ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
239
240	<	integrableObjects[i]->setJ( ji );
240	>	++index;
241	>	}
242		}
193	–	}
243
244	<	if(nConstrained)
196	<	constrainB();
244	>	rattle_->constraintB();
245
246	<	if (fabs(prevChi - chi) <= chiTolerance) break;
247	<	}
246	>	if (fabs(prevChi - thermostat.first) <= chiTolerance_)
247	>	break;
248
249	<	integralOfChidt += dt2*chi;
202	<	}
249	>	}
250
251	<	template<typename T> void NVT<T>::resetIntegrator( void ){
251	>	flucQ_->moveB();
252
253	<	chi = 0.0;
254	<	integralOfChidt = 0.0;
208	<	}
209	<
210	<	template<typename T> int NVT<T>::readyCheck() {
211	<
212	<	//check parent's readyCheck() first
213	<	if (T::readyCheck() == -1)
214	<	return -1;
215	<
216	<	// First check to see if we have a target temperature.
217	<	// Not having one is fatal.
218	<
219	<	if (!have_target_temp) {
220	<	sprintf( painCave.errMsg,
221	<	"You can't use the NVT integrator without a targetTemp!\n"
222	<	);
223	<	painCave.isFatal = 1;
224	<	painCave.severity = OOPSE_ERROR;
225	<	simError();
226	<	return -1;
253	>	thermostat.second += dt2 * thermostat.first;
254	>	snap->setThermostat(thermostat);
255		}
256
257	<	// We must set tauThermostat.
258	<
231	<	if (!have_tau_thermostat) {
232	<	sprintf( painCave.errMsg,
233	<	"If you use the constant temperature\n"
234	<	"\tintegrator, you must set tauThermostat.\n");
235	<	painCave.severity = OOPSE_ERROR;
236	<	painCave.isFatal = 1;
237	<	simError();
238	<	return -1;
257	>	void NVT::resetIntegrator() {
258	>	snap->setThermostat(make_pair(0.0, 0.0));
259		}
260	+
261	+	RealType NVT::calcConservedQuantity() {
262
263	<	if (!have_chi_tolerance) {
264	<	sprintf( painCave.errMsg,
265	<	"In NVT integrator: setting chi tolerance to 1e-6\n");
266	<	chiTolerance = 1e-6;
267	<	have_chi_tolerance = 1;
268	<	painCave.severity = OOPSE_INFO;
269	<	painCave.isFatal = 0;
270	<	simError();
249	<	}
263	>	pair<RealType, RealType> thermostat = snap->getThermostat();
264	>	RealType conservedQuantity;
265	>	RealType fkBT;
266	>	RealType Energy;
267	>	RealType thermostat_kinetic;
268	>	RealType thermostat_potential;
269	>
270	>	fkBT = info_->getNdf() *PhysicalConstants::kB *targetTemp_;
271
272	<	return 1;
272	>	Energy = thermo.getTotalEnergy();
273
274	<	}
274	>	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * thermostat.first * thermostat.first / (2.0 * PhysicalConstants::energyConvert);
275
276	<	template<typename T> double NVT<T>::getConservedQuantity(void){
276	>	thermostat_potential = fkBT * thermostat.second / PhysicalConstants::energyConvert;
277
278	<	double conservedQuantity;
258	<	double fkBT;
259	<	double Energy;
260	<	double thermostat_kinetic;
261	<	double thermostat_potential;
278	>	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
279
280	<	fkBT = (double)(info->ndf) * kB * targetTemp;
280	>	return conservedQuantity;
281	>	}
282
265	–	Energy = tStats->getTotalE();
283
284	<	thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
268	<	(2.0 * eConvert);
269	<
270	<	thermostat_potential = fkBT * integralOfChidt / eConvert;
271	<
272	<	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
273	<
274	<	return conservedQuantity;
275	<	}
276	<
277	<	template<typename T> string NVT<T>::getAdditionalParameters(void){
278	<	string parameters;
279	<	const int BUFFERSIZE = 2000; // size of the read buffer
280	<	char buffer[BUFFERSIZE];
281	<
282	<	sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
283	<	parameters += buffer;
284	<
285	<	return parameters;
286	<	}
284	>	}//end namespace OpenMD

Comparing trunk/src/integrators/NVT.cpp (property svn:keywords):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

#	Line 0 | Line 1
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