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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 1879 by gezelter, Sun Jun 16 15:15:42 2013 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), chiTolerance_ (1e-6), maxIterNum_(4) {
51
52	<	// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
52	>	Globals* simParams = info_->getSimParams();
53
54	<	template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff):
55	<	T( theInfo, the_ff )
56	<	{
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);
54	>	if (!simParams->getUseIntialExtendedSystemState()) {
55	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
56	>	snap->setThermostat(make_pair(0.0, 0.0));
57		}
58
59	<	data = info->getProperty(INTEGRALOFCHIDT_ID);
60	<	if(data){
61	<	integralOfChidtValue = dynamic_cast<DoubleData*>(data);
59	>	if (!simParams->haveTargetTemp()) {
60	>	sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n");
61	>	painCave.isFatal = 1;
62	>	painCave.severity = OPENMD_ERROR;
63	>	simError();
64	>	} else {
65	>	targetTemp_ = simParams->getTargetTemp();
66		}
45	–
46	–	// chi and integralOfChidt should appear by pair
47	–	if(chiValue && integralOfChidtValue){
48	–	chi = chiValue->getData();
49	–	integralOfChidt = integralOfChidtValue->getData();
50	–	}
51	–	}
67
68	<	oldVel = new double[3*integrableObjects.size()];
54	<	oldJi = new double[3*integrableObjects.size()];
55	<	}
68	>	// We must set tauThermostat.
69
70	<	template<typename T> NVT<T>::~NVT() {
71	<	delete[] oldVel;
72	<	delete[] oldJi;
60	<	}
70	>	if (!simParams->haveTauThermostat()) {
71	>	sprintf(painCave.errMsg, "If you use the constant temperature\n"
72	>	"\tintegrator, you must set tauThermostat.\n");
73
74	<	template<typename T> void NVT<T>::moveA() {
74	>	painCave.severity = OPENMD_ERROR;
75	>	painCave.isFatal = 1;
76	>	simError();
77	>	} else {
78	>	tauThermostat_ = simParams->getTauThermostat();
79	>	}
80
81	<	int i, j;
82	<	DirectionalAtom* dAtom;
66	<	double Tb[3], ji[3];
67	<	double mass;
68	<	double vel[3], pos[3], frc[3];
81	>	updateSizes();
82	>	}
83
84	<	double instTemp;
84	>	void NVT::doUpdateSizes() {
85	>	oldVel_.resize(info_->getNIntegrableObjects());
86	>	oldJi_.resize(info_->getNIntegrableObjects());
87	>	}
88
89	<	// We need the temperature at time = t for the chi update below:
89	>	void NVT::moveA() {
90	>	SimInfo::MoleculeIterator i;
91	>	Molecule::IntegrableObjectIterator  j;
92	>	Molecule* mol;
93	>	StuntDouble* sd;
94	>	Vector3d Tb;
95	>	Vector3d ji;
96	>	RealType mass;
97	>	Vector3d vel;
98	>	Vector3d pos;
99	>	Vector3d frc;
100
101	<	instTemp = tStats->getTemperature();
101	>	pair<RealType, RealType> thermostat = snap->getThermostat();
102
103	<	for( i=0; i < integrableObjects.size(); i++ ){
103	>	// We need the temperature at time = t for the chi update below:
104
105	<	integrableObjects[i]->getVel( vel );
79	<	integrableObjects[i]->getPos( pos );
80	<	integrableObjects[i]->getFrc( frc );
105	>	RealType instTemp = thermo.getTemperature();
106
107	<	mass = integrableObjects[i]->getMass();
107	>	for (mol = info_->beginMolecule(i); mol != NULL;
108	>	mol = info_->nextMolecule(i)) {
109
110	<	for (j=0; j < 3; j++) {
111	<	// 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	<	}
110	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
111	>	sd = mol->nextIntegrableObject(j)) {
112
113	<	integrableObjects[i]->setVel( vel );
114	<	integrableObjects[i]->setPos( pos );
113	>	vel = sd->getVel();
114	>	pos = sd->getPos();
115	>	frc = sd->getFrc();
116
117	<	if( integrableObjects[i]->isDirectional() ){
117	>	mass = sd->getMass();
118
119	<	// get and convert the torque to body frame
119	>	// velocity half step (use chi from previous step here):
120	>	vel += dt2 *PhysicalConstants::energyConvert/mass*frc
121	>	- dt2*thermostat.first*vel;
122	>
123	>	// position whole step
124	>	pos += dt * vel;
125
126	<	integrableObjects[i]->getTrq( Tb );
127	<	integrableObjects[i]->lab2Body( Tb );
126	>	sd->setVel(vel);
127	>	sd->setPos(pos);
128
129	<	// get the angular momentum, and propagate a half step
129	>	if (sd->isDirectional()) {
130
131	<	integrableObjects[i]->getJ( ji );
131	>	//convert the torque to body frame
132	>	Tb = sd->lab2Body(sd->getTrq());
133
134	<	for (j=0; j < 3; j++)
106	<	ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
134	>	// get the angular momentum, and propagate a half step
135
136	<	this->rotationPropagation( integrableObjects[i], ji );
136	>	ji = sd->getJ();
137
138	<	integrableObjects[i]->setJ( ji );
139	<	}
112	<	}
113	<
114	<	if(nConstrained)
115	<	constrainA();
138	>	ji += dt2*PhysicalConstants::energyConvert*Tb
139	>	- dt2*thermostat.first *ji;
140
141	<	// Finally, evolve chi a half step (just like a velocity) using
118	<	// temperature at time t, not time t+dt/2
141	>	rotAlgo_->rotate(sd, ji, dt);
142
143	<	//std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n";
144	<
145	<	chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
123	<	integralOfChidt += chi*dt2;
143	>	sd->setJ(ji);
144	>	}
145	>	}
146
147	<	}
147	>	}
148	>
149	>	flucQ_->moveA();
150	>	rattle_->constraintA();
151
152	<	template<typename T> void NVT<T>::moveB( void ){
153	<	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;
152	>	// Finally, evolve chi a half step (just like a velocity) using
153	>	// temperature at time t, not time t+dt/2
154
155	<	// Set things up for the iteration:
155	>	thermostat.first += dt2 * (instTemp / targetTemp_ - 1.0)
156	>	/ (tauThermostat_ * tauThermostat_);
157	>	thermostat.second += thermostat.first * dt2;
158
159	<	oldChi = chi;
159	>	snap->setThermostat(thermostat);
160	>	}
161
162	<	for( i=0; i < integrableObjects.size(); i++ ){
163	<
164	<	integrableObjects[i]->getVel( vel );
165	<
166	<	for (j=0; j < 3; j++)
167	<	oldVel[3*i + j]  = vel[j];
168	<
169	<	if( integrableObjects[i]->isDirectional() ){
170	<
171	<	integrableObjects[i]->getJ( ji );
172	<
173	<	for (j=0; j < 3; j++)
174	<	oldJi[3*i + j] = ji[j];
162	>	void NVT::moveB() {
163	>	SimInfo::MoleculeIterator i;
164	>	Molecule::IntegrableObjectIterator  j;
165	>	Molecule* mol;
166	>	StuntDouble* sd;
167	>
168	>	Vector3d Tb;
169	>	Vector3d ji;
170	>	Vector3d vel;
171	>	Vector3d frc;
172	>	RealType mass;
173	>	RealType instTemp;
174	>	int index;
175	>	// Set things up for the iteration:
176
177	+	pair<RealType, RealType> thermostat = snap->getThermostat();
178	+	RealType oldChi = thermostat.first;
179	+	RealType  prevChi;
180	+
181	+	index = 0;
182	+	for (mol = info_->beginMolecule(i); mol != NULL;
183	+	mol = info_->nextMolecule(i)) {
184	+
185	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
186	+	sd = mol->nextIntegrableObject(j)) {
187	+
188	+	oldVel_[index] = sd->getVel();
189	+
190	+	if (sd->isDirectional())
191	+	oldJi_[index] = sd->getJ();
192	+
193	+	++index;
194	+	}
195		}
154	–	}
196
197	<	// do the iteration:
197	>	// do the iteration:
198
199	<	for (k=0; k < 4; k++) {
199	>	for(int k = 0; k < maxIterNum_; k++) {
200	>	index = 0;
201	>	instTemp = thermo.getTemperature();
202
203	<	instTemp = tStats->getTemperature();
203	>	// evolve chi another half step using the temperature at t + dt/2
204
205	<	// evolve chi another half step using the temperature at t + dt/2
205	>	prevChi = thermostat.first;
206	>	thermostat.first = oldChi + dt2 * (instTemp / targetTemp_ - 1.0)
207	>	/ (tauThermostat_ * tauThermostat_);
208
209	<	prevChi = chi;
210	<	chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
211	<	(tauThermostat*tauThermostat);
209	>	for (mol = info_->beginMolecule(i); mol != NULL;
210	>	mol = info_->nextMolecule(i)) {
211	>
212	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
213	>	sd = mol->nextIntegrableObject(j)) {
214
215	<	for( i=0; i < integrableObjects.size(); i++ ){
215	>	frc = sd->getFrc();
216	>	mass = sd->getMass();
217
218	<	integrableObjects[i]->getFrc( frc );
171	<	integrableObjects[i]->getVel(vel);
218	>	// velocity half step
219
220	<	mass = integrableObjects[i]->getMass();
220	>	vel = oldVel_[index]
221	>	+ dt2/mass*PhysicalConstants::energyConvert * frc
222	>	- dt2*thermostat.first*oldVel_[index];
223	>
224	>	sd->setVel(vel);
225
226	<	// 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);
226	>	if (sd->isDirectional()) {
227
228	<	integrableObjects[i]->setVel( vel );
228	>	// get and convert the torque to body frame
229
230	<	if( integrableObjects[i]->isDirectional() ){
230	>	Tb =  sd->lab2Body(sd->getTrq());
231
232	<	// get and convert the torque to body frame
232	>	ji = oldJi_[index] + dt2*PhysicalConstants::energyConvert*Tb
233	>	- dt2*thermostat.first *oldJi_[index];
234
235	<	integrableObjects[i]->getTrq( Tb );
236	<	integrableObjects[i]->lab2Body( Tb );
235	>	sd->setJ(ji);
236	>	}
237
188	–	for (j=0; j < 3; j++)
189	–	ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
238
239	<	integrableObjects[i]->setJ( ji );
239	>	++index;
240	>	}
241		}
193	–	}
242
243	<	if(nConstrained)
196	<	constrainB();
243	>	rattle_->constraintB();
244
245	<	if (fabs(prevChi - chi) <= chiTolerance) break;
246	<	}
245	>	if (fabs(prevChi - thermostat.first) <= chiTolerance_)
246	>	break;
247
248	<	integralOfChidt += dt2*chi;
202	<	}
248	>	}
249
250	<	template<typename T> void NVT<T>::resetIntegrator( void ){
250	>	flucQ_->moveB();
251
252	<	chi = 0.0;
253	<	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;
252	>	thermostat.second += dt2 * thermostat.first;
253	>	snap->setThermostat(thermostat);
254		}
255
256	<	// We must set tauThermostat.
257	<
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;
256	>	void NVT::resetIntegrator() {
257	>	snap->setThermostat(make_pair(0.0, 0.0));
258		}
259	+
260	+	RealType NVT::calcConservedQuantity() {
261
262	<	if (!have_chi_tolerance) {
263	<	sprintf( painCave.errMsg,
264	<	"In NVT integrator: setting chi tolerance to 1e-6\n");
265	<	chiTolerance = 1e-6;
266	<	have_chi_tolerance = 1;
267	<	painCave.severity = OOPSE_INFO;
268	<	painCave.isFatal = 0;
269	<	simError();
249	<	}
262	>	pair<RealType, RealType> thermostat = snap->getThermostat();
263	>	RealType conservedQuantity;
264	>	RealType fkBT;
265	>	RealType Energy;
266	>	RealType thermostat_kinetic;
267	>	RealType thermostat_potential;
268	>
269	>	fkBT = info_->getNdf() *PhysicalConstants::kB *targetTemp_;
270
271	<	return 1;
271	>	Energy = thermo.getTotalEnergy();
272
273	<	}
273	>	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * thermostat.first * thermostat.first / (2.0 * PhysicalConstants::energyConvert);
274
275	<	template<typename T> double NVT<T>::getConservedQuantity(void){
275	>	thermostat_potential = fkBT * thermostat.second / PhysicalConstants::energyConvert;
276
277	<	double conservedQuantity;
258	<	double fkBT;
259	<	double Energy;
260	<	double thermostat_kinetic;
261	<	double thermostat_potential;
277	>	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
278
279	<	fkBT = (double)(info->ndf) * kB * targetTemp;
279	>	return conservedQuantity;
280	>	}
281
265	–	Energy = tStats->getTotalE();
282
283	<	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	<	}
283	>	}//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 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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