ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.cpp (file contents), Revision 546 by tim, Sun May 29 00:06:14 2005 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 50 | Line 50
50		#include "integrators/VelocityVerletIntegrator.hpp"
51		#include "integrators/DLM.hpp"
52		#include "utils/StringUtils.hpp"
53	+	#include "utils/ProgressBar.hpp"
54
55	<	namespace oopse {
55	>	namespace OpenMD {
56		VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
57		dt2 = 0.5 * dt;
58		rotAlgo = new DLM();
#	Line 67 | Line 68 | namespace oopse {
68
69		forceMan_->init();
70
71	<	// remove center of mass drift velocity (in case we passed in a configuration
72	<	// that was drifting
71	>	// remove center of mass drift velocity (in case we passed in a
72	>	// configuration that was drifting)
73		velocitizer_->removeComDrift();
74
75		// initialize the forces before the first step
76	<	calcForce(true, true);
76	>	calcForce();
77
78	<	//execute constraint algorithm to make sure at the very beginning the system is constrained
78	>	// execute the constraint algorithm to make sure that the system is
79	>	// constrained at the very beginning
80		if (info_->getNGlobalConstraints() > 0) {
81		rattle->constraintA();
82	<	calcForce(true, true);
83	<	rattle->constraintB();
84	<	info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot
82	>	calcForce();
83	>	rattle->constraintB();
84	>	//copy the current snapshot to previous snapshot
85	>	info_->getSnapshotManager()->advance();
86		}
87
88		if (needVelocityScaling) {
#	Line 89 | Line 92 | namespace oopse {
92		dumpWriter = createDumpWriter();
93
94		statWriter = createStatWriter();
95	<
93	<	if (simParams->getUseSolidThermInt()) {
94	<	restWriter = createRestWriter();
95	<	restWriter->writeZangle();
96	<	}
97	<
95	>
96		dumpWriter->writeDumpAndEor();
97	<
98	<
97	>
98	>	progressBar = new ProgressBar();
99	>
100		//save statistics, before writeStat,  we must save statistics
101		thermo.saveStat();
102		saveConservedQuantity();
103	+	if (simParams->getUseRNEMD())
104	+	rnemd_->getStarted();
105	+
106		statWriter->writeStat(currentSnapshot_->statData);
107
108		currSample = sampleTime + currentSnapshot_->getTime();
109	<	currStatus =  statusTime + currentSnapshot_->getTime();;
109	>	currStatus =  statusTime + currentSnapshot_->getTime();
110		currThermal = thermalTime + currentSnapshot_->getTime();
111		if (needReset) {
112		currReset = resetTime + currentSnapshot_->getTime();
113		}
114	+	if (simParams->getUseRNEMD()){
115	+	currRNEMD = RNEMD_exchangeTime + currentSnapshot_->getTime();
116	+	}
117		needPotential = false;
118		needStress = false;
119
120		}
121	<
121	>
122		void VelocityVerletIntegrator::doIntegrate() {
123
124
#	Line 126 | Line 131 | namespace oopse {
131		integrateStep();
132
133		postStep();
134	<
134	>
135		}
136
137		finalize();
#	Line 135 | Line 140 | namespace oopse {
140
141
142		void VelocityVerletIntegrator::preStep() {
143	<	double difference = currentSnapshot_->getTime() + dt - currStatus;
143	>	RealType difference = currentSnapshot_->getTime() + dt - currStatus;
144
145	<	if (difference > 0 || fabs(difference) < oopse::epsilon) {
145	>	if (difference > 0 || fabs(difference) < OpenMD::epsilon) {
146		needPotential = true;
147		needStress = true;
148		}
144	–
149		}
150
151		void VelocityVerletIntegrator::postStep() {
152	<
152	>
153		//save snapshot
154		info_->getSnapshotManager()->advance();
155
156		//increase time
157		currentSnapshot_->increaseTime(dt);
158	<
158	>
159		if (needVelocityScaling) {
160		if (currentSnapshot_->getTime() >= currThermal) {
161		velocitizer_->velocitize(targetScalingTemp);
162		currThermal += thermalTime;
163		}
164		}
165	<
165	>	if (useRNEMD) {
166	>	if (currentSnapshot_->getTime() >= currRNEMD) {
167	>	rnemd_->doRNEMD();
168	>	currRNEMD += RNEMD_exchangeTime;
169	>	}
170	>	rnemd_->collectData();
171	>	}
172	>
173		if (currentSnapshot_->getTime() >= currSample) {
174		dumpWriter->writeDumpAndEor();
175	<
165	<	if (simParams->getUseSolidThermInt())
166	<	restWriter->writeZangle();
167	<
175	>
176		currSample += sampleTime;
177		}
178	<
178	>
179		if (currentSnapshot_->getTime() >= currStatus) {
180		//save statistics, before writeStat,  we must save statistics
181		thermo.saveStat();
182		saveConservedQuantity();
183	+
184	+	if (simParams->getUseRNEMD()) {
185	+	rnemd_->getStatus();
186	+	}
187	+
188		statWriter->writeStat(currentSnapshot_->statData);
189	<
189	>
190	>	progressBar->setStatus(currentSnapshot_->getTime(), runTime);
191	>	progressBar->update();
192	>
193		needPotential = false;
194		needStress = false;
195		currStatus += statusTime;
196		}
197	<
198	<	if (needReset && currentSnapshot_->getTime() >= currReset) {
199	<	resetIntegrator();
200	<	currReset += resetTime;
201	<	}
186	<
197	>
198	>	if (needReset && currentSnapshot_->getTime() >= currReset) {
199	>	resetIntegrator();
200	>	currReset += resetTime;
201	>	}
202		}
203
204
205		void VelocityVerletIntegrator::finalize() {
206		dumpWriter->writeEor();
207
193	–	if (simParams->getUseSolidThermInt()) {
194	–	restWriter->writeZangle();
195	–	delete restWriter;
196	–	restWriter = NULL;
197	–	}
198	–
208		delete dumpWriter;
209		delete statWriter;
210
#	Line 207 | Line 216 | namespace oopse {
216		void VelocityVerletIntegrator::integrateStep() {
217
218		moveA();
219	<	calcForce(needPotential, needStress);
219	>	calcForce();
220		moveB();
221		}
222
223
224	<	void VelocityVerletIntegrator::calcForce(bool needPotential,
225	<	bool needStress) {
217	<	forceMan_->calcForces(needPotential, needStress);
224	>	void VelocityVerletIntegrator::calcForce() {
225	>	forceMan_->calcForces();
226		}
227
228		DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
#	Line 222 | Line 230 | namespace oopse {
230		}
231
232		StatWriter* VelocityVerletIntegrator::createStatWriter() {
233	<	// if solidThermInt is true, add extra information to the statfile
234	<	if (simParams->getUseSolidThermInt()){
235	<	StatsBitSet mask;
236	<	mask.set(Stats::TIME);
237	<	mask.set(Stats::TOTAL_ENERGY);
238	<	mask.set(Stats::POTENTIAL_ENERGY);
239	<	mask.set(Stats::KINETIC_ENERGY);
240	<	mask.set(Stats::TEMPERATURE);
241	<	mask.set(Stats::PRESSURE);
234	<	mask.set(Stats::VOLUME);
235	<	mask.set(Stats::CONSERVED_QUANTITY);
233	>
234	>	std::string statFileFormatString = simParams->getStatFileFormat();
235	>	StatsBitSet mask = parseStatFileFormat(statFileFormatString);
236	>
237	>	// if we're doing a thermodynamic integration, we'll want the raw
238	>	// potential as well as the full potential:
239	>
240	>
241	>	if (simParams->getUseThermodynamicIntegration())
242		mask.set(Stats::VRAW);
243	+
244	+	// if we've got restraints turned on, we'll also want a report of the
245	+	// total harmonic restraints
246	+	if (simParams->getUseRestraints()){
247		mask.set(Stats::VHARM);
238	–	return new StatWriter(info_->getStatFileName(), mask);
248		}
249
250	<	if (simParams->havePrintPressureTensor() && simParams->getPrintPressureTensor()){
251	<	StatsBitSet mask;
252	<	mask.set(Stats::TIME);
253	<	mask.set(Stats::TOTAL_ENERGY);
254	<	mask.set(Stats::POTENTIAL_ENERGY);
255	<	mask.set(Stats::KINETIC_ENERGY);
256	<	mask.set(Stats::TEMPERATURE);
257	<	mask.set(Stats::PRESSURE);
258	<	mask.set(Stats::VOLUME);
259	<	mask.set(Stats::CONSERVED_QUANTITY);
260	<	mask.set(Stats::PRESSURE_TENSOR_X);
252	<	mask.set(Stats::PRESSURE_TENSOR_Y);
253	<	mask.set(Stats::PRESSURE_TENSOR_Z);
254	<	return new StatWriter(info_->getStatFileName(), mask);
250	>	if (simParams->havePrintPressureTensor() &&
251	>	simParams->getPrintPressureTensor()){
252	>	mask.set(Stats::PRESSURE_TENSOR_XX);
253	>	mask.set(Stats::PRESSURE_TENSOR_XY);
254	>	mask.set(Stats::PRESSURE_TENSOR_XZ);
255	>	mask.set(Stats::PRESSURE_TENSOR_YX);
256	>	mask.set(Stats::PRESSURE_TENSOR_YY);
257	>	mask.set(Stats::PRESSURE_TENSOR_YZ);
258	>	mask.set(Stats::PRESSURE_TENSOR_ZX);
259	>	mask.set(Stats::PRESSURE_TENSOR_ZY);
260	>	mask.set(Stats::PRESSURE_TENSOR_ZZ);
261		}
262
263	<	return new StatWriter(info_->getStatFileName());
264	<	}
263	>	if (simParams->getAccumulateBoxDipole()) {
264	>	mask.set(Stats::BOX_DIPOLE_X);
265	>	mask.set(Stats::BOX_DIPOLE_Y);
266	>	mask.set(Stats::BOX_DIPOLE_Z);
267	>	}
268	>
269	>	if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
270	>	if (simParams->getPrintTaggedPairDistance()) {
271	>	mask.set(Stats::TAGGED_PAIR_DISTANCE);
272	>	}
273	>	}
274
275	<	RestWriter* VelocityVerletIntegrator::createRestWriter(){
276	<	return new RestWriter(info_);
275	>	if (simParams->getUseRNEMD()) {
276	>	mask.set(Stats::RNEMD_EXCHANGE_TOTAL);
277	>	}
278	>
279	>
280	>	return new StatWriter(info_->getStatFileName(), mask);
281		}
282
283
284	<	} //end namespace oopse
284	>	} //end namespace OpenMD

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.cpp (property svn:keywords), Revision 546 by tim, Sun May 29 00:06:14 2005 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines