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

Comparing:
trunk/src/visitors/ZconsVisitor.cpp (file contents), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 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	<	#include "ZconsVisitor.hpp"
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 <cmath>
44	+	#include "visitors/ZconsVisitor.hpp"
45	+	#include "primitives/Molecule.hpp"
46	+	#include "utils/StringUtils.hpp"
47	+	#include "types/ZconsStamp.hpp"
48	+	namespace OpenMD {
49
50	<	ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisitor(), zconsReader(NULL){
5	<	GenericData* data;
6	<	DoubleData* tolerance;
7	<	ZConsParaData* zConsParaData;
8	<	StringData* filename;
9	<	DoubleData* sampleTime;
10	<	vector<ZConsParaItem>* parameters;
50	>	ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisitor(), info_(info), zconsReader_(NULL){
51
52	<	this->info = info;
53	<	visitorName = "ZConsVisitor";
54	<
15	<	//retrieve tolerance for z-constraint molecuels
16	<	data = info->getProperty(ZCONSTOL_ID);
52	>	visitorName = "ZConsVisitor";
53	>	currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
54	>	Globals* simParam = info_->getSimParams();
55
56	<	if (!data){
57	<	cerr << "Can not get zconstraint tolerance from SimInfo" << endl;
20	<	haveZcons = false;
21	<	return;
22	<	}
23	<	else{
24	<	tolerance = dynamic_cast<DoubleData*>(data);
25	<
26	<	if (!tolerance){
27	<	cerr << "Can not get zconstraint tolerance  from SimInfo" << endl;
28	<	haveZcons = false;
29	<	return;
56	>	if (simParam->haveZconsTime()){
57	>	zconsTime_ = simParam->getZconsTime();
58		}
59		else{
60	<	zconsTol = tolerance->getData();
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		}
34	–	}
66
67	<	//retrieve sample time of z-contraint
68	<	data = info->getProperty(ZCONSTIME_ID);
38	<
39	<	if (!data){
40	<	cerr << "Can not get zcons time  from SimInfo" << endl;
41	<	haveZcons = false;
42	<	return;
43	<	}
44	<	else{
45	<	sampleTime = dynamic_cast<DoubleData*>(data);
46	<
47	<	if (!sampleTime){
48	<	cerr << "Can not get zcons time  from SimInfo" << endl;
49	<	haveZcons = false;
50	<	return;
67	>	if (simParam->haveZconsTol()){
68	>	zconsTol_ = simParam->getZconsTol();
69		}
70		else{
71	<	zconsTime = sampleTime->getData();
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->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));
86		}
55	–	}
87
57	–	//retrieve index of z-constraint molecules
58	–	data = info->getProperty(ZCONSPARADATA_ID);
59	–	if (!data){
60	–	cerr << "Can not get index of z-constraint molecules from SimInfo" << endl;
61	–	haveZcons = false;
62	–	return;
63	–	}
64	–	else{
65	–	zConsParaData = dynamic_cast<ZConsParaData*>(data);
88
89	<	if (!zConsParaData){
90	<	cerr << "Can not get index of z-constraint molecules from SimInfo" << endl;
91	<	haveZcons = false;
92	<	return;
89	>	//fill zatomToZmol_ array
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	>	}
100		}
72	–	else{
73	–	vector<ZConsParaItem>::iterator i;
74	–	Molecule* mol;
101
102	<	parameters = zConsParaData->getData();
103	<	for(i = parameters->begin(); i != parameters->end(); ++i){
102	>	zconsFilename_ = getPrefix(info_->getFinalConfigFileName()) + ".fz";
103	>
104	>	zconsReader_ = new ZConsReader(info);
105
106	<	mol = findZconsMol(i->zconsIndex);
107	<	if(mol != NULL)
108	<	zconsMol.push_back(mol);
106	>	if (zconsReader_->hasNextFrame())
107	>	zconsReader_->readNextFrame();
108	>
109	>	}
110
111	<	}
112	<
113	<	if(zconsMol.size() < 1){
86	<	cerr << "number of zconstraint molecules is less than one" << endl;
87	<	haveZcons = false;
88	<	return;
89	<	}
90	<
91	<	}//end if (!zConsParaData)
92	<
93	<	}//end  if (!data
111	>	ZConsVisitor::~ZConsVisitor(){
112	>	if(!zconsReader_)
113	>	delete zconsReader_;
114
95	–	//retrieve output filename of z force
96	–	data = info->getProperty(ZCONSFILENAME_ID);
97	–	if (!data){
98	–	cerr << "Can not get filename of z-constraint output from SimInfo" << endl;
99	–	haveZcons = false;
100	–	return;
115		}
102	–	else{
103	–	filename = dynamic_cast<StringData*>(data);
116
117	<	if (!filename){
118	<	cerr << "Can not get filename of z-constraint output from SimInfo" << endl;
119	<	haveZcons = false;
120	<	return;
109	<	}
110	<	else{
111	<	zconsFilename = filename->getData();
112	<	}
117	>	void ZConsVisitor::visit(Atom* atom){
118	>	std::string prefix;
119	>	if(isZconstraint(atom->getGlobalIndex(), prefix))
120	>	internalVisit(atom, prefix);
121		}
122
123	<	zconsReader = new ZConsReader(info);
123	>	void ZConsVisitor::visit(DirectionalAtom* datom){
124	>	std::string prefix;
125
126	<	if (zconsReader->hasNextFrame())
127	<	zconsReader->readNextFrame();
128	<
120	<	haveZcons = true;
121	<	}
126	>	if(isZconstraint(datom->getGlobalIndex(), prefix))
127	>	internalVisit(datom, prefix);
128	>	}
129
130	<	ZConsVisitor::~ZConsVisitor(){
131	<	if(!zconsReader)
132	<	delete zconsReader;
126	<
127	<	}
130	>	void ZConsVisitor::visit(RigidBody* rb){
131	>	std::string prefix;
132	>	std::vector<Atom*> atoms;
133
134	<	void ZConsVisitor::visit(Atom* atom){
130	<	string prefix;
131	<	if(isZconstraint(atom->getIndex(), prefix))
132	<	internalVisit(atom, prefix);
133	<	}
134	>	atoms = rb->getAtoms();
135
136	<	void ZConsVisitor::visit(DirectionalAtom* datom){
137	<	string prefix;
138	<
138	<	if(isZconstraint(datom->getIndex(), prefix))
139	<	internalVisit(datom, prefix);
140	<	}
136	>	if(isZconstraint(atoms[0]->getGlobalIndex(), prefix))
137	>	internalVisit(rb, prefix);
138	>	}
139
140	<	void ZConsVisitor::visit(RigidBody* rb){
141	<	string prefix;
142	<	vector<Atom*> atoms;
143	<
144	<	atoms = rb->getAtoms();
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;
147	>	}
148	>
149	>	readZconsFile(currSnapshot_->getTime());
150	>
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;
157	>	}
158
159	<	if(isZconstraint(atoms[0]->getIndex(), prefix))
149	<	internalVisit(rb, prefix);
150	<	}
159	>	}
160
161	<	Molecule* ZConsVisitor::findZconsMol(int index){
162	<	Molecule* mols;
163	<	mols = info->molecules;
164	<	for(int i =0; i < info->n_mol; i++)
165	<	if(index == mols[i].getMyIndex())
166	<	return &mols[i];
161	>	void ZConsVisitor::readZconsFile(RealType time) {
162	>	RealType tempTime;
163	>	while(zconsReader_->hasNextFrame()){
164	>	tempTime = zconsReader_->getCurTime();
165	>	if(tempTime >= time) {
166	>	return;
167	>	}
168	>
169	>	zconsReader_->readNextFrame();
170	>	}
171	>	}
172
173	<	return NULL;
174	<	}
173	>	void ZConsVisitor::internalVisit(StuntDouble* sd, const std::string& prefix){
174	>	GenericData* data;
175	>	AtomData* atomData;
176	>	AtomInfo* atomInfo;
177	>	std::vector<AtomInfo*>::iterator iter;
178
179	<	void ZConsVisitor::update(){
180	<	Molecule* mol;
181	<	double com[3];
182	<	ZConsState state;
183	<	Atom** atoms;
184	<	int natoms;
185	<
169	<	getZconsPos(info->currentTime);
170	<
171	<	for(size_t i = 0; i < zconsMol.size(); i++){
172	<	zconsMol[i]->getCOM(com);
173	<
174	<	if(fabs(com[2] - zconsPos[i]) < zconsTol)
175	<	state = zsFixed;
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	>	}
186		else
187	<	state = zsMoving;
187	>	return;
188
189	<	//update the state of zconstraint atom
190	<	natoms = zconsMol[i]->getNAtoms();
181	<	atoms = zconsMol[i]->getMyAtoms();
182	<	for(int j =0; j < natoms; j++)
183	<	zconsState[atoms[j]->getIndex()] = state;
189	>	for(atomInfo  = atomData->beginAtomInfo(iter); atomInfo; atomInfo = atomData->nextAtomInfo(iter))
190	>	(atomInfo->atomTypeName).insert(0, prefix);
191		}
185	–
186	–	}
192
188	–	void ZConsVisitor::getZconsPos(double time){
193
194	<	vector<double> tempPos;
195	<	vector<double> prevPos;
196	<	double tempTime;
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;
200	>	} else {
201
202	<	while(true){
203	<	tempTime = zconsReader->getCurTime();
204	<
205	<	zconsPos = zconsReader->getZConsPos();
206	<
199	<	if(tempTime >= time)
200	<	return;
201	<
202	<	zconsReader->readNextFrame();
203	<
204	<	}
205	<
206	<	}
207	<
208	<	void ZConsVisitor::internalVisit(StuntDouble* sd, const string& prefix){
209	<	GenericData* data;
210	<	AtomData* atomData;
211	<	AtomInfo* atomInfo;
212	<	vector<AtomInfo*>::iterator iter;
213	<
214	<
215	<	//if there is not atom data, just skip it
216	<	data = sd->getProperty("ATOMDATA");
217	<	if(data != NULL){
218	<	atomData = dynamic_cast<AtomData*>(data);
219	<	if(atomData == NULL)
220	<	return;
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		}
222	–	else
223	–	return;
208
209	<	for(atomInfo  = atomData->beginAtomInfo(iter); atomInfo; atomInfo = atomData->nextAtomInfo(iter))
210	<	(atomInfo->AtomType).insert(0, prefix);
211	<	}
209	>	const std::string ZConsVisitor::toString(){
210	>	char buffer[65535];
211	>	std::string result;
212
213	+	sprintf(buffer ,"------------------------------------------------------------------\n");
214	+	result += buffer;
215
216	<	bool ZConsVisitor::isZconstraint(int index, string& prefix){
217	<	map<int, ZConsState>::iterator i;
232	<	string prefixString[] = {"ZF", "ZM"};
233	<
234	<	i = zconsState.find(index);
235	<	if(i !=zconsState.end()){
236	<	prefix = prefixString[(*i).second];
237	<	return true;
238	<	}
239	<	else{
240	<	prefix = "";
241	<	return false;
242	<	}
243	<	}
216	>	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
217	>	result += buffer;
218
219	<	const string ZConsVisitor::toString(){
220	<	char buffer[65535];
247	<	string result;
248	<
249	<	sprintf(buffer ,"------------------------------------------------------------------\n");
250	<	result += buffer;
219	>	sprintf(buffer , "number of zconstraint molecule: %d\n", (int) zmolStates_.size());
220	>	result += buffer;
221
222	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
223	<	result += buffer;
254	<
255	<	sprintf(buffer , "number of zconstraint molecule: %d\n", zconsMol.size());
256	<	result += buffer;
222	>	sprintf(buffer , "zconstraint tolerance = %lf\n", zconsTol_);
223	>	result += buffer;
224
225	<	sprintf(buffer , "zconstraint tolerance = %lf\n", zconsTol);
226	<	result += buffer;
225	>	sprintf(buffer , "zconstraint sample time = %lf\n", zconsTime_);
226	>	result += buffer;
227
228	<	sprintf(buffer , "zconstraint sample time = %lf\n", zconsTime);
229	<	result += buffer;
228	>	sprintf(buffer , "zconstraint output filename = %s\n", zconsFilename_.c_str());
229	>	result += buffer;
230
231	<	sprintf(buffer , "zconstraint output filename = %s\n", zconsFilename.c_str());
232	<	result += buffer;
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;
236	>	}
237
238	<	for(size_t i = 0; i < zconsMol.size(); ++i){
268	<	sprintf(buffer ,"zconstraint molecule[%d] = %d\n", i, zconsMol[i]->getMyIndex());
238	>	sprintf(buffer ,"------------------------------------------------------------------\n");
239		result += buffer;
240
241	+	return result;
242		}
243
273	–
274	–	sprintf(buffer ,"------------------------------------------------------------------\n");
275	–	result += buffer;
244
245	<	return result;
278	<	}
245	>	}//namespace OpenMD

Comparing:
trunk/src/visitors/ZconsVisitor.cpp (property svn:keywords), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 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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