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

Comparing:
trunk/src/integrators/NVT.cpp (file contents), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/integrators/NVT.cpp (file contents), Revision 1710 by gezelter, Fri May 18 21:44:02 2012 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, 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 "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	<	{
57	<	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* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
56	>	currSnapshot->setChi(0.0);
57	>	currSnapshot->setIntegralOfChiDt(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	>	update();
83	>	}
84
85	<	double instTemp;
85	>	void NVT::doUpdate() {
86	>	oldVel_.resize(info_->getNIntegrableObjects());
87	>	oldJi_.resize(info_->getNIntegrableObjects());
88	>	}
89	>	void NVT::moveA() {
90	>	SimInfo::MoleculeIterator i;
91	>	Molecule::IntegrableObjectIterator  j;
92	>	Molecule* mol;
93	>	StuntDouble* integrableObject;
94	>	Vector3d Tb;
95	>	Vector3d ji;
96	>	RealType mass;
97	>	Vector3d vel;
98	>	Vector3d pos;
99	>	Vector3d frc;
100
101	<	// We need the temperature at time = t for the chi update below:
101	>	RealType chi = currentSnapshot_->getChi();
102	>	RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
103	>
104	>	// We need the temperature at time = t for the chi update below:
105
106	<	instTemp = tStats->getTemperature();
106	>	RealType instTemp = thermo.getTemperature();
107
108	<	for( i=0; i < integrableObjects.size(); i++ ){
108	>	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
109	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
110	>	integrableObject = mol->nextIntegrableObject(j)) {
111
112	<	integrableObjects[i]->getVel( vel );
113	<	integrableObjects[i]->getPos( pos );
114	<	integrableObjects[i]->getFrc( frc );
112	>	vel = integrableObject->getVel();
113	>	pos = integrableObject->getPos();
114	>	frc = integrableObject->getFrc();
115
116	<	mass = integrableObjects[i]->getMass();
116	>	mass = integrableObject->getMass();
117
118	<	for (j=0; j < 3; j++) {
119	<	// velocity half step  (use chi from previous step here):
120	<	vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
121	<	// position whole step
122	<	pos[j] += dt * vel[j];
123	<	}
118	>	// velocity half step  (use chi from previous step here):
119	>	//vel[j] += dt2 * ((frc[j] / mass ) * PhysicalConstants::energyConvert - vel[j]*chi);
120	>	vel += dt2 *PhysicalConstants::energyConvert/mass*frc - dt2*chi*vel;
121	>
122	>	// position whole step
123	>	//pos[j] += dt * vel[j];
124	>	pos += dt * vel;
125
126	<	integrableObjects[i]->setVel( vel );
127	<	integrableObjects[i]->setPos( pos );
126	>	integrableObject->setVel(vel);
127	>	integrableObject->setPos(pos);
128
129	<	if( integrableObjects[i]->isDirectional() ){
129	>	if (integrableObject->isDirectional()) {
130
131	<	// get and convert the torque to body frame
131	>	//convert the torque to body frame
132	>	Tb = integrableObject->lab2Body(integrableObject->getTrq());
133
134	<	integrableObjects[i]->getTrq( Tb );
99	<	integrableObjects[i]->lab2Body( Tb );
134	>	// get the angular momentum, and propagate a half step
135
136	<	// get the angular momentum, and propagate a half step
136	>	ji = integrableObject->getJ();
137
138	<	integrableObjects[i]->getJ( ji );
138	>	//ji[j] += dt2 * (Tb[j] * PhysicalConstants::energyConvert - ji[j]*chi);
139	>	ji += dt2*PhysicalConstants::energyConvert*Tb - dt2*chi *ji;
140	>	rotAlgo->rotate(integrableObject, ji, dt);
141
142	<	for (j=0; j < 3; j++)
143	<	ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
142	>	integrableObject->setJ(ji);
143	>	}
144	>	}
145
108	–	this->rotationPropagation( integrableObjects[i], ji );
109	–
110	–	integrableObjects[i]->setJ( ji );
146		}
147	<	}
148	<
114	<	if(nConstrained)
115	<	constrainA();
147	>
148	>	rattle->constraintA();
149
150	<	// Finally, evolve chi a half step (just like a velocity) using
151	<	// temperature at time t, not time t+dt/2
150	>	// Finally, evolve chi a half step (just like a velocity) using
151	>	// temperature at time t, not time t+dt/2
152
153	<	//std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n";
154	<
155	<	chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
123	<	integralOfChidt += chi*dt2;
153	>
154	>	chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
155	>	integralOfChidt += chi * dt2;
156
157	<	}
157	>	currentSnapshot_->setChi(chi);
158	>	currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
159	>	}
160
161	<	template<typename T> void NVT<T>::moveB( void ){
162	<	int i, j, k;
163	<	double Tb[3], ji[3];
164	<	double vel[3], frc[3];
165	<	double mass;
166	<	double instTemp;
167	<	double oldChi, prevChi;
168	<
169	<	// Set things up for the iteration:
170	<
171	<	oldChi = chi;
172	<
173	<	for( i=0; i < integrableObjects.size(); i++ ){
174	<
141	<	integrableObjects[i]->getVel( vel );
142	<
143	<	for (j=0; j < 3; j++)
144	<	oldVel[3*i + j]  = vel[j];
145	<
146	<	if( integrableObjects[i]->isDirectional() ){
147	<
148	<	integrableObjects[i]->getJ( ji );
149	<
150	<	for (j=0; j < 3; j++)
151	<	oldJi[3*i + j] = ji[j];
161	>	void NVT::moveB() {
162	>	SimInfo::MoleculeIterator i;
163	>	Molecule::IntegrableObjectIterator  j;
164	>	Molecule* mol;
165	>	StuntDouble* integrableObject;
166	>
167	>	Vector3d Tb;
168	>	Vector3d ji;
169	>	Vector3d vel;
170	>	Vector3d frc;
171	>	RealType mass;
172	>	RealType instTemp;
173	>	int index;
174	>	// Set things up for the iteration:
175
176	+	RealType chi = currentSnapshot_->getChi();
177	+	RealType oldChi = chi;
178	+	RealType  prevChi;
179	+	RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
180	+
181	+	index = 0;
182	+	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
183	+	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
184	+	integrableObject = mol->nextIntegrableObject(j)) {
185	+
186	+	oldVel_[index] = integrableObject->getVel();
187	+
188	+	if (integrableObject->isDirectional())
189	+	oldJi_[index] = integrableObject->getJ();
190	+
191	+	++index;
192	+	}
193		}
154	–	}
194
195	<	// do the iteration:
195	>	// do the iteration:
196
197	<	for (k=0; k < 4; k++) {
197	>	for(int k = 0; k < maxIterNum_; k++) {
198	>	index = 0;
199	>	instTemp = thermo.getTemperature();
200
201	<	instTemp = tStats->getTemperature();
201	>	// evolve chi another half step using the temperature at t + dt/2
202
203	<	// evolve chi another half step using the temperature at t + dt/2
203	>	prevChi = chi;
204	>	chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
205
206	<	prevChi = chi;
207	<	chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
208	<	(tauThermostat*tauThermostat);
206	>	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
207	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
208	>	integrableObject = mol->nextIntegrableObject(j)) {
209
210	<	for( i=0; i < integrableObjects.size(); i++ ){
210	>	frc = integrableObject->getFrc();
211	>	vel = integrableObject->getVel();
212
213	<	integrableObjects[i]->getFrc( frc );
171	<	integrableObjects[i]->getVel(vel);
213	>	mass = integrableObject->getMass();
214
215	<	mass = integrableObjects[i]->getMass();
215	>	// velocity half step
216	>	//for(j = 0; j < 3; j++)
217	>	//    vel[j] = oldVel_[3*i+j] + dt2 * ((frc[j] / mass ) * PhysicalConstants::energyConvert - oldVel_[3*i + j]*chi);
218	>	vel = oldVel_[index] + dt2/mass*PhysicalConstants::energyConvert * frc - dt2*chi*oldVel_[index];
219	>
220	>	integrableObject->setVel(vel);
221
222	<	// 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);
222	>	if (integrableObject->isDirectional()) {
223
224	<	integrableObjects[i]->setVel( vel );
224	>	// get and convert the torque to body frame
225
226	<	if( integrableObjects[i]->isDirectional() ){
226	>	Tb =  integrableObject->lab2Body(integrableObject->getTrq());
227
228	<	// get and convert the torque to body frame
228	>	//for(j = 0; j < 3; j++)
229	>	//    ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * PhysicalConstants::energyConvert - oldJi_[3*i+j]*chi);
230	>	ji = oldJi_[index] + dt2*PhysicalConstants::energyConvert*Tb - dt2*chi *oldJi_[index];
231
232	<	integrableObjects[i]->getTrq( Tb );
233	<	integrableObjects[i]->lab2Body( Tb );
232	>	integrableObject->setJ(ji);
233	>	}
234
188	–	for (j=0; j < 3; j++)
189	–	ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
235
236	<	integrableObjects[i]->setJ( ji );
236	>	++index;
237	>	}
238		}
193	–	}
239
195	–	if(nConstrained)
196	–	constrainB();
240
241	<	if (fabs(prevChi - chi) <= chiTolerance) break;
199	<	}
241	>	rattle->constraintB();
242
243	<	integralOfChidt += dt2*chi;
244	<	}
243	>	if (fabs(prevChi - chi) <= chiTolerance_)
244	>	break;
245
246	<	template<typename T> void NVT<T>::resetIntegrator( void ){
246	>	}
247
248	<	chi = 0.0;
207	<	integralOfChidt = 0.0;
208	<	}
248	>	integralOfChidt += dt2 * chi;
249
250	<	template<typename T> int NVT<T>::readyCheck() {
251	<
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;
250	>	currentSnapshot_->setChi(chi);
251	>	currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
252		}
253
254	<	// We must set tauThermostat.
255	<
256	<	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;
254	>	void NVT::resetIntegrator() {
255	>	currentSnapshot_->setChi(0.0);
256	>	currentSnapshot_->setIntegralOfChiDt(0.0);
257		}
258	+
259	+	RealType NVT::calcConservedQuantity() {
260
261	<	if (!have_chi_tolerance) {
262	<	sprintf( painCave.errMsg,
263	<	"In NVT integrator: setting chi tolerance to 1e-6\n");
264	<	chiTolerance = 1e-6;
265	<	have_chi_tolerance = 1;
266	<	painCave.severity = OOPSE_INFO;
267	<	painCave.isFatal = 0;
268	<	simError();
269	<	}
261	>	RealType chi = currentSnapshot_->getChi();
262	>	RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
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.getTotalE();
272
273	<	}
273	>	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * PhysicalConstants::energyConvert);
274
275	<	template<typename T> double NVT<T>::getConservedQuantity(void){
275	>	thermostat_potential = fkBT * integralOfChidt / 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.
branches/development/src/integrators/NVT.cpp (property svn:keywords), Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

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