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root/OpenMD/branches/development/src/visitors/ZconsVisitor.cpp

Comparing:
trunk/src/visitors/ZconsVisitor.cpp (file contents), Revision 407 by gezelter, Tue Mar 8 21:07:49 2005 UTC vs.
branches/development/src/visitors/ZconsVisitor.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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 <cmath>
44		#include "visitors/ZconsVisitor.hpp"
45		#include "primitives/Molecule.hpp"
46		#include "utils/StringUtils.hpp"
47	<	namespace oopse {
47	>	#include "types/ZconsStamp.hpp"
48	>	namespace OpenMD {
49
50	<	ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisitor(), info_(info), zconsReader_(NULL){
50	>	ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisitor(), info_(info), zconsReader_(NULL){
51
52		visitorName = "ZConsVisitor";
53		currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
54		Globals* simParam = info_->getSimParams();
55
56	<	if (simParam->haveZconstraintTime()){
57	<	zconsTime_ = simParam->getZconsTime();
56	>	if (simParam->haveZconsTime()){
57	>	zconsTime_ = simParam->getZconsTime();
58		}
59		else{
60	<	sprintf(painCave.errMsg,
61	<	"ZConstraint error: If you use a ZConstraint,\n"
62	<	"\tyou must set zconsTime.\n");
63	<	painCave.isFatal = 1;
64	<	simError();
60	>	sprintf(painCave.errMsg,
61	>	"ZConstraint error: If you use a ZConstraint,\n"
62	>	"\tyou must set zconsTime.\n");
63	>	painCave.isFatal = 1;
64	>	simError();
65		}
66
67		if (simParam->haveZconsTol()){
68	<	zconsTol_ = simParam->getZconsTol();
68	>	zconsTol_ = simParam->getZconsTol();
69		}
70		else{
71	<	zconsTol_ = 0.01;
72	<	sprintf(painCave.errMsg,
73	<	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
74	<	"\tOOPSE will use a default value of %f.\n"
75	<	"\tTo set the tolerance, use the zconsTol variable.\n",
76	<	zconsTol_);
77	<	painCave.isFatal = 0;
78	<	simError();
71	>	zconsTol_ = 0.01;
72	>	sprintf(painCave.errMsg,
73	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
74	>	"\tOpenMD will use a default value of %f.\n"
75	>	"\tTo set the tolerance, use the zconsTol variable.\n",
76	>	zconsTol_);
77	>	painCave.isFatal = 0;
78	>	simError();
79		}
80
81	<	int nZconstraints = simParam->getNzConstraints();
82	<	ZconStamp** stamp = simParam->getZconStamp();
81	>	int nZconstraints = simParam->getNZconsStamps();
82	>	std::vector<ZConsStamp*> stamp = simParam->getZconsStamps();
83		for (int i = 0; i < nZconstraints; i++){
84	<	int zmolIndex = stamp[i]->getMolIndex();
85	<	zmolStates_.insert(std::make_pair(zmolIndex, zsMoving));
84	>	int zmolIndex = stamp[i]->getMolIndex();
85	>	zmolStates_.insert(std::make_pair(zmolIndex, zsMoving));
86		}
87
88
#	Line 88 | Line 90 | ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisito
90		/** @todo only works for single version now*/
91		std::map<int, ZConsState>::iterator j;
92		for (j = zmolStates_.begin(); j != zmolStates_.end(); ++j) {
93	<	Molecule* mol = info_->getMoleculeByGlobalIndex(j->first);
94	<	assert(mol != NULL);
95	<	Molecule::AtomIterator ai;
96	<	Atom* at;
97	<	for (at = mol->beginAtom(ai); at != NULL; at = mol->nextAtom(ai)) {
98	<	zatomToZmol_.insert(std::make_pair(at->getGlobalIndex(), mol->getGlobalIndex()));
99	<	}
93	>	Molecule* mol = info_->getMoleculeByGlobalIndex(j->first);
94	>	assert(mol != NULL);
95	>	Molecule::AtomIterator ai;
96	>	Atom* at;
97	>	for (at = mol->beginAtom(ai); at != NULL; at = mol->nextAtom(ai)) {
98	>	zatomToZmol_.insert(std::make_pair(at->getGlobalIndex(), mol->getGlobalIndex()));
99	>	}
100		}
101
102		zconsFilename_ = getPrefix(info_->getFinalConfigFileName()) + ".fz";
#	Line 102 | Line 104 | ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisito
104		zconsReader_ = new ZConsReader(info);
105
106		if (zconsReader_->hasNextFrame())
107	<	zconsReader_->readNextFrame();
107	>	zconsReader_->readNextFrame();
108
109	<	}
109	>	}
110
111	<	ZConsVisitor::~ZConsVisitor(){
112	<	if(!zconsReader_)
113	<	delete zconsReader_;
111	>	ZConsVisitor::~ZConsVisitor(){
112	>	if(!zconsReader_)
113	>	delete zconsReader_;
114
115	<	}
115	>	}
116
117	<	void ZConsVisitor::visit(Atom* atom){
117	>	void ZConsVisitor::visit(Atom* atom){
118		std::string prefix;
119		if(isZconstraint(atom->getGlobalIndex(), prefix))
120	<	internalVisit(atom, prefix);
121	<	}
120	>	internalVisit(atom, prefix);
121	>	}
122
123	<	void ZConsVisitor::visit(DirectionalAtom* datom){
123	>	void ZConsVisitor::visit(DirectionalAtom* datom){
124		std::string prefix;
125
126		if(isZconstraint(datom->getGlobalIndex(), prefix))
127	<	internalVisit(datom, prefix);
128	<	}
127	>	internalVisit(datom, prefix);
128	>	}
129
130	<	void ZConsVisitor::visit(RigidBody* rb){
130	>	void ZConsVisitor::visit(RigidBody* rb){
131		std::string prefix;
132		std::vector<Atom*> atoms;
133
134		atoms = rb->getAtoms();
135
136		if(isZconstraint(atoms[0]->getGlobalIndex(), prefix))
137	<	internalVisit(rb, prefix);
138	<	}
137	>	internalVisit(rb, prefix);
138	>	}
139
140	<	void ZConsVisitor::update(){
140	>	void ZConsVisitor::update(){
141		Molecule* mol;
142		Vector3d com;
143		ZConsState state;
144		std::map<int, ZConsState>::iterator i;
145		for ( i = zmolStates_.begin(); i != zmolStates_.end(); ++i) {
146	<	i->second = zsMoving;
146	>	i->second = zsMoving;
147		}
148
149		readZconsFile(currSnapshot_->getTime());
#	Line 149 | Line 151 | void ZConsVisitor::update(){
151		const std::vector<ZconsData>& fixedZmolData = zconsReader_->getFixedZMolData();
152		std::vector<ZconsData>::const_iterator j;
153		for (j = fixedZmolData.begin(); j != fixedZmolData.end(); ++j) {
154	<	std::map<int, ZConsState>::iterator k = zmolStates_.find(j->zmolIndex);
155	<	assert(k != zmolStates_.end());
156	<	k->second = zsFixed;
154	>	std::map<int, ZConsState>::iterator k = zmolStates_.find(j->zmolIndex);
155	>	assert(k != zmolStates_.end());
156	>	k->second = zsFixed;
157		}
158
159	<	}
159	>	}
160
161	<	void ZConsVisitor::readZconsFile(double time) {
162	<	double tempTime;
161	>	void ZConsVisitor::readZconsFile(RealType time) {
162	>	RealType tempTime;
163		while(zconsReader_->hasNextFrame()){
164	<	tempTime = zconsReader_->getCurTime();
165	<	if(tempTime >= time) {
166	<	return;
167	<	}
164	>	tempTime = zconsReader_->getCurTime();
165	>	if(tempTime >= time) {
166	>	return;
167	>	}
168
169	<	zconsReader_->readNextFrame();
169	>	zconsReader_->readNextFrame();
170		}
171	<	}
171	>	}
172
173	<	void ZConsVisitor::internalVisit(StuntDouble* sd, const std::string& prefix){
173	>	void ZConsVisitor::internalVisit(StuntDouble* sd, const std::string& prefix){
174		GenericData* data;
175		AtomData* atomData;
176		AtomInfo* atomInfo;
#	Line 177 | Line 179 | void ZConsVisitor::internalVisit(StuntDouble* sd, cons
179		//if there is not atom data, just skip it
180		data = sd->getPropertyByName("ATOMDATA");
181		if(data != NULL){
182	<	atomData = dynamic_cast<AtomData*>(data);
183	<	if(atomData == NULL)
184	<	return;
185	<	}
182	>	atomData = dynamic_cast<AtomData*>(data);
183	>	if(atomData == NULL)
184	>	return;
185	>	}
186		else
187	<	return;
187	>	return;
188
189		for(atomInfo  = atomData->beginAtomInfo(iter); atomInfo; atomInfo = atomData->nextAtomInfo(iter))
190	<	(atomInfo->atomTypeName).insert(0, prefix);
191	<	}
190	>	(atomInfo->atomTypeName).insert(0, prefix);
191	>	}
192
193
194	<	bool ZConsVisitor::isZconstraint(int atomIndex, std::string& prefix){
194	>	bool ZConsVisitor::isZconstraint(int atomIndex, std::string& prefix){
195		std::string prefixString[] = {"ZF", "ZM"};
196		std::map<int, int>::iterator i = zatomToZmol_.find(atomIndex);
197		if (i ==  zatomToZmol_.end() ){
198	<	prefix = "";
199	<	return false;
198	>	prefix = "";
199	>	return false;
200		} else {
201
202	<	std::map<int, ZConsState>::iterator j = zmolStates_.find(i->second);
203	<	assert(j !=zmolStates_.end());
204	<	prefix = prefixString[j->second];
205	<	return true;
202	>	std::map<int, ZConsState>::iterator j = zmolStates_.find(i->second);
203	>	assert(j !=zmolStates_.end());
204	>	prefix = prefixString[j->second];
205	>	return true;
206		}
207	<	}
207	>	}
208
209	<	const std::string ZConsVisitor::toString(){
209	>	const std::string ZConsVisitor::toString(){
210		char buffer[65535];
211		std::string result;
212
#	Line 214 | Line 216 | const std::string ZConsVisitor::toString(){
216		sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
217		result += buffer;
218
219	<	sprintf(buffer , "number of zconstraint molecule: %d\n", zmolStates_.size());
219	>	sprintf(buffer , "number of zconstraint molecule: %d\n", (int) zmolStates_.size());
220		result += buffer;
221
222		sprintf(buffer , "zconstraint tolerance = %lf\n", zconsTol_);
#	Line 229 | Line 231 | const std::string ZConsVisitor::toString(){
231		std::map<int, ZConsState>::iterator i;
232		int j = 0;
233		for ( i = zmolStates_.begin(); i != zmolStates_.end(); ++i) {
234	<	sprintf(buffer ,"zconstraint molecule[%d] = %d\n", j++, i->first);
235	<	result += buffer;
234	>	sprintf(buffer ,"zconstraint molecule[%d] = %d\n", j++, i->first);
235	>	result += buffer;
236		}
237
238		sprintf(buffer ,"------------------------------------------------------------------\n");
239		result += buffer;
240
241		return result;
242	<	}
242	>	}
243
244
245	<	}//namespace oopse
245	>	}//namespace OpenMD

Comparing:
trunk/src/visitors/ZconsVisitor.cpp (property svn:keywords), Revision 407 by gezelter, Tue Mar 8 21:07:49 2005 UTC vs.
branches/development/src/visitors/ZconsVisitor.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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