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root/OpenMD/trunk/src/visitors/ZconsVisitor.cpp

Comparing trunk/src/visitors/ZconsVisitor.cpp (file contents):
Revision 132 by tim, Thu Oct 21 16:22:01 2004 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

#	Line 1 | Line 1
1	<	#include "visitors/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, 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 <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	<	namespace oopse {
50	>	ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisitor(),
51	>	zconsReader_(NULL), info_(info){
52	>
53	>	visitorName = "ZConsVisitor";
54	>	currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
55	>	Globals* simParam = info_->getSimParams();
56
57	<	ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisitor(), zconsReader(NULL){
58	<	GenericData* data;
8	<	DoubleGenericData* tolerance;
9	<	ZConsParaData* zConsParaData;
10	<	StringGenericData* filename;
11	<	DoubleGenericData* sampleTime;
12	<	vector<ZConsParaItem>* parameters;
13	<
14	<	this->info = info;
15	<	visitorName = "ZConsVisitor";
16	<
17	<	//retrieve tolerance for z-constraint molecuels
18	<	data = info->getProperty(ZCONSTOL_ID);
19	<
20	<	if (!data){
21	<	cerr << "Can not get zconstraint tolerance from SimInfo" << endl;
22	<	haveZcons = false;
23	<	return;
24	<	}
25	<	else{
26	<	tolerance = dynamic_cast<DoubleGenericData*>(data);
27	<
28	<	if (!tolerance){
29	<	cerr << "Can not get zconstraint tolerance  from SimInfo" << endl;
30	<	haveZcons = false;
31	<	return;
57	>	if (simParam->haveZconsTime()){
58	>	zconsTime_ = simParam->getZconsTime();
59		}
60		else{
61	<	zconsTol = tolerance->getData();
61	>	sprintf(painCave.errMsg,
62	>	"ZConstraint error: If you use a ZConstraint,\n"
63	>	"\tyou must set zconsTime.\n");
64	>	painCave.isFatal = 1;
65	>	simError();
66		}
36	–	}
67
68	<	//retrieve sample time of z-contraint
69	<	data = info->getProperty(ZCONSTIME_ID);
40	<
41	<	if (!data){
42	<	cerr << "Can not get zcons time  from SimInfo" << endl;
43	<	haveZcons = false;
44	<	return;
45	<	}
46	<	else{
47	<	sampleTime = dynamic_cast<DoubleGenericData*>(data);
48	<
49	<	if (!sampleTime){
50	<	cerr << "Can not get zcons time  from SimInfo" << endl;
51	<	haveZcons = false;
52	<	return;
68	>	if (simParam->haveZconsTol()){
69	>	zconsTol_ = simParam->getZconsTol();
70		}
71		else{
72	<	zconsTime = sampleTime->getData();
72	>	zconsTol_ = 0.01;
73	>	sprintf(painCave.errMsg,
74	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
75	>	"\tOpenMD will use a default value of %f.\n"
76	>	"\tTo set the tolerance, use the zconsTol variable.\n",
77	>	zconsTol_);
78	>	painCave.isFatal = 0;
79	>	simError();
80	>	}
81	>
82	>	int nZconstraints = simParam->getNZconsStamps();
83	>	std::vector<ZConsStamp*> stamp = simParam->getZconsStamps();
84	>	for (int i = 0; i < nZconstraints; i++){
85	>	int zmolIndex = stamp[i]->getMolIndex();
86	>	zmolStates_.insert(std::make_pair(zmolIndex, zsMoving));
87		}
57	–	}
88
59	–	//retrieve index of z-constraint molecules
60	–	data = info->getProperty(ZCONSPARADATA_ID);
61	–	if (!data){
62	–	cerr << "Can not get index of z-constraint molecules from SimInfo" << endl;
63	–	haveZcons = false;
64	–	return;
65	–	}
66	–	else{
67	–	zConsParaData = dynamic_cast<ZConsParaData*>(data);
89
90	<	if (!zConsParaData){
91	<	cerr << "Can not get index of z-constraint molecules from SimInfo" << endl;
92	<	haveZcons = false;
93	<	return;
90	>	//fill zatomToZmol_ array
91	>	/** @todo only works for single version now*/
92	>	std::map<int, ZConsState>::iterator j;
93	>	for (j = zmolStates_.begin(); j != zmolStates_.end(); ++j) {
94	>	Molecule* mol = info_->getMoleculeByGlobalIndex(j->first);
95	>	assert(mol != NULL);
96	>	Molecule::AtomIterator ai;
97	>	Atom* at;
98	>	for (at = mol->beginAtom(ai); at != NULL; at = mol->nextAtom(ai)) {
99	>	zatomToZmol_.insert(std::make_pair(at->getGlobalIndex(), mol->getGlobalIndex()));
100	>	}
101		}
74	–	else{
75	–	vector<ZConsParaItem>::iterator i;
76	–	Molecule* mol;
102
103	<	parameters = zConsParaData->getData();
104	<	for(i = parameters->begin(); i != parameters->end(); ++i){
103	>	zconsFilename_ = getPrefix(info_->getFinalConfigFileName()) + ".fz";
104	>
105	>	zconsReader_ = new ZConsReader(info);
106
107	<	mol = findZconsMol(i->zconsIndex);
108	<	if(mol != NULL)
109	<	zconsMol.push_back(mol);
107	>	if (zconsReader_->hasNextFrame())
108	>	zconsReader_->readNextFrame();
109	>
110	>	}
111
112	<	}
113	<
114	<	if(zconsMol.size() < 1){
88	<	cerr << "number of zconstraint molecules is less than one" << endl;
89	<	haveZcons = false;
90	<	return;
91	<	}
92	<
93	<	}//end if (!zConsParaData)
94	<
95	<	}//end  if (!data
112	>	ZConsVisitor::~ZConsVisitor(){
113	>	if(!zconsReader_)
114	>	delete zconsReader_;
115
97	–	//retrieve output filename of z force
98	–	data = info->getProperty(ZCONSFILENAME_ID);
99	–	if (!data){
100	–	cerr << "Can not get filename of z-constraint output from SimInfo" << endl;
101	–	haveZcons = false;
102	–	return;
116		}
104	–	else{
105	–	filename = dynamic_cast<StringGenericData*>(data);
117
118	<	if (!filename){
119	<	cerr << "Can not get filename of z-constraint output from SimInfo" << endl;
120	<	haveZcons = false;
121	<	return;
111	<	}
112	<	else{
113	<	zconsFilename = filename->getData();
114	<	}
118	>	void ZConsVisitor::visit(Atom* atom){
119	>	std::string prefix;
120	>	if(isZconstraint(atom->getGlobalIndex(), prefix))
121	>	internalVisit(atom, prefix);
122		}
123
124	<	zconsReader = new ZConsReader(info);
124	>	void ZConsVisitor::visit(DirectionalAtom* datom){
125	>	std::string prefix;
126
127	<	if (zconsReader->hasNextFrame())
128	<	zconsReader->readNextFrame();
129	<
122	<	haveZcons = true;
123	<	}
127	>	if(isZconstraint(datom->getGlobalIndex(), prefix))
128	>	internalVisit(datom, prefix);
129	>	}
130
131	<	ZConsVisitor::~ZConsVisitor(){
132	<	if(!zconsReader)
133	<	delete zconsReader;
128	<
129	<	}
131	>	void ZConsVisitor::visit(RigidBody* rb){
132	>	std::string prefix;
133	>	std::vector<Atom*> atoms;
134
135	<	void ZConsVisitor::visit(Atom* atom){
132	<	string prefix;
133	<	if(isZconstraint(atom->getIndex(), prefix))
134	<	internalVisit(atom, prefix);
135	<	}
135	>	atoms = rb->getAtoms();
136
137	<	void ZConsVisitor::visit(DirectionalAtom* datom){
138	<	string prefix;
139	<
140	<	if(isZconstraint(datom->getIndex(), prefix))
141	<	internalVisit(datom, prefix);
142	<	}
137	>	if(isZconstraint(atoms[0]->getGlobalIndex(), prefix))
138	>	internalVisit(rb, prefix);
139	>	}
140
141	<	void ZConsVisitor::visit(RigidBody* rb){
142	<	string prefix;
143	<	vector<Atom*> atoms;
144	<
145	<	atoms = rb->getAtoms();
141	>	void ZConsVisitor::update(){
142	>	Vector3d com;
143	>	std::map<int, ZConsState>::iterator i;
144	>	for ( i = zmolStates_.begin(); i != zmolStates_.end(); ++i) {
145	>	i->second = zsMoving;
146	>	}
147	>
148	>	readZconsFile(currSnapshot_->getTime());
149	>
150	>	const std::vector<ZconsData>& fixedZmolData = zconsReader_->getFixedZMolData();
151	>	std::vector<ZconsData>::const_iterator j;
152	>	for (j = fixedZmolData.begin(); j != fixedZmolData.end(); ++j) {
153	>	std::map<int, ZConsState>::iterator k = zmolStates_.find(j->zmolIndex);
154	>	assert(k != zmolStates_.end());
155	>	k->second = zsFixed;
156	>	}
157
158	<	if(isZconstraint(atoms[0]->getIndex(), prefix))
151	<	internalVisit(rb, prefix);
152	<	}
158	>	}
159
160	<	Molecule* ZConsVisitor::findZconsMol(int index){
161	<	Molecule* mols;
162	<	mols = info->molecules;
163	<	for(int i =0; i < info->n_mol; i++)
164	<	if(index == mols[i].getMyIndex())
165	<	return &mols[i];
160	>	void ZConsVisitor::readZconsFile(RealType time) {
161	>	RealType tempTime;
162	>	while(zconsReader_->hasNextFrame()){
163	>	tempTime = zconsReader_->getCurTime();
164	>	if(tempTime >= time) {
165	>	return;
166	>	}
167	>
168	>	zconsReader_->readNextFrame();
169	>	}
170	>	}
171
172	<	return NULL;
173	<	}
172	>	void ZConsVisitor::internalVisit(StuntDouble* sd, const std::string& prefix){
173	>	GenericData* data;
174	>	AtomData* atomData;
175	>	AtomInfo* atomInfo;
176	>	std::vector<AtomInfo*>::iterator iter;
177
178	<	void ZConsVisitor::update(){
179	<	Molecule* mol;
180	<	double com[3];
181	<	ZConsState state;
182	<	Atom** atoms;
183	<	int natoms;
184	<
171	<	getZconsPos(info->currentTime);
172	<
173	<	for(size_t i = 0; i < zconsMol.size(); i++){
174	<	zconsMol[i]->getCOM(com);
175	<
176	<	if(fabs(com[2] - zconsPos[i]) < zconsTol)
177	<	state = zsFixed;
178	>	//if there is not atom data, just skip it
179	>	data = sd->getPropertyByName("ATOMDATA");
180	>	if(data != NULL){
181	>	atomData = dynamic_cast<AtomData*>(data);
182	>	if(atomData == NULL)
183	>	return;
184	>	}
185		else
186	<	state = zsMoving;
186	>	return;
187
188	<	//update the state of zconstraint atom
189	<	natoms = zconsMol[i]->getNAtoms();
183	<	atoms = zconsMol[i]->getMyAtoms();
184	<	for(int j =0; j < natoms; j++)
185	<	zconsState[atoms[j]->getIndex()] = state;
188	>	for(atomInfo  = atomData->beginAtomInfo(iter); atomInfo; atomInfo = atomData->nextAtomInfo(iter))
189	>	(atomInfo->atomTypeName).insert(0, prefix);
190		}
187	–
188	–	}
191
190	–	void ZConsVisitor::getZconsPos(double time){
192
193	<	vector<double> tempPos;
194	<	vector<double> prevPos;
195	<	double tempTime;
193	>	bool ZConsVisitor::isZconstraint(int atomIndex, std::string& prefix){
194	>	std::string prefixString[] = {"ZF", "ZM"};
195	>	std::map<int, int>::iterator i = zatomToZmol_.find(atomIndex);
196	>	if (i ==  zatomToZmol_.end() ){
197	>	prefix = "";
198	>	return false;
199	>	} else {
200
201	<	while(true){
202	<	tempTime = zconsReader->getCurTime();
203	<
204	<	zconsPos = zconsReader->getZConsPos();
205	<
201	<	if(tempTime >= time)
202	<	return;
203	<
204	<	zconsReader->readNextFrame();
205	<
206	<	}
207	<
208	<	}
209	<
210	<	void ZConsVisitor::internalVisit(StuntDouble* sd, const string& prefix){
211	<	GenericData* data;
212	<	AtomData* atomData;
213	<	AtomInfo* atomInfo;
214	<	vector<AtomInfo*>::iterator iter;
215	<
216	<
217	<	//if there is not atom data, just skip it
218	<	data = sd->getProperty("ATOMDATA");
219	<	if(data != NULL){
220	<	atomData = dynamic_cast<AtomData*>(data);
221	<	if(atomData == NULL)
222	<	return;
201	>	std::map<int, ZConsState>::iterator j = zmolStates_.find(i->second);
202	>	assert(j !=zmolStates_.end());
203	>	prefix = prefixString[j->second];
204	>	return true;
205	>	}
206		}
224	–	else
225	–	return;
207
208	<	for(atomInfo  = atomData->beginAtomInfo(iter); atomInfo; atomInfo = atomData->nextAtomInfo(iter))
209	<	(atomInfo->AtomType).insert(0, prefix);
210	<	}
208	>	const std::string ZConsVisitor::toString(){
209	>	char buffer[65535];
210	>	std::string result;
211
212	+	sprintf(buffer ,"------------------------------------------------------------------\n");
213	+	result += buffer;
214
215	<	bool ZConsVisitor::isZconstraint(int index, string& prefix){
216	<	map<int, ZConsState>::iterator i;
234	<	string prefixString[] = {"ZF", "ZM"};
235	<
236	<	i = zconsState.find(index);
237	<	if(i !=zconsState.end()){
238	<	prefix = prefixString[(*i).second];
239	<	return true;
240	<	}
241	<	else{
242	<	prefix = "";
243	<	return false;
244	<	}
245	<	}
215	>	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
216	>	result += buffer;
217
218	<	const string ZConsVisitor::toString(){
219	<	char buffer[65535];
249	<	string result;
250	<
251	<	sprintf(buffer ,"------------------------------------------------------------------\n");
252	<	result += buffer;
218	>	sprintf(buffer , "number of zconstraint molecule: %d\n", (int) zmolStates_.size());
219	>	result += buffer;
220
221	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
222	<	result += buffer;
256	<
257	<	sprintf(buffer , "number of zconstraint molecule: %d\n", zconsMol.size());
258	<	result += buffer;
221	>	sprintf(buffer , "zconstraint tolerance = %lf\n", zconsTol_);
222	>	result += buffer;
223
224	<	sprintf(buffer , "zconstraint tolerance = %lf\n", zconsTol);
225	<	result += buffer;
224	>	sprintf(buffer , "zconstraint sample time = %lf\n", zconsTime_);
225	>	result += buffer;
226
227	<	sprintf(buffer , "zconstraint sample time = %lf\n", zconsTime);
228	<	result += buffer;
227	>	sprintf(buffer , "zconstraint output filename = %s\n", zconsFilename_.c_str());
228	>	result += buffer;
229
230	<	sprintf(buffer , "zconstraint output filename = %s\n", zconsFilename.c_str());
231	<	result += buffer;
230	>	std::map<int, ZConsState>::iterator i;
231	>	int j = 0;
232	>	for ( i = zmolStates_.begin(); i != zmolStates_.end(); ++i) {
233	>	sprintf(buffer ,"zconstraint molecule[%d] = %d\n", j++, i->first);
234	>	result += buffer;
235	>	}
236
237	<	for(size_t i = 0; i < zconsMol.size(); ++i){
270	<	sprintf(buffer ,"zconstraint molecule[%d] = %d\n", i, zconsMol[i]->getMyIndex());
237	>	sprintf(buffer ,"------------------------------------------------------------------\n");
238		result += buffer;
239
240	+	return result;
241		}
242
275	–
276	–	sprintf(buffer ,"------------------------------------------------------------------\n");
277	–	result += buffer;
243
244	<	return result;
280	<	}
281	<
282	<
283	<	}//namespace oopse
244	>	}//namespace OpenMD

Comparing trunk/src/visitors/ZconsVisitor.cpp (property svn:keywords):
Revision 132 by tim, Thu Oct 21 16:22:01 2004 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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

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