src/visitors/ZconsVisitor.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#include <cmath>
#include "visitors/ZconsVisitor.hpp"
#include "primitives/Molecule.hpp"
#include "utils/StringUtils.hpp"
#include "types/ZconsStamp.hpp"
namespace oopse {

  ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisitor(), info_(info), zconsReader_(NULL){

    visitorName = "ZConsVisitor";
    currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
    Globals* simParam = info_->getSimParams();

    if (simParam->haveZconsTime()){
      zconsTime_ = simParam->getZconsTime();
    }
    else{
      sprintf(painCave.errMsg,
              "ZConstraint error: If you use a ZConstraint,\n"
              "\tyou must set zconsTime.\n");
      painCave.isFatal = 1;
      simError();
    }

    if (simParam->haveZconsTol()){
      zconsTol_ = simParam->getZconsTol();
    }
    else{
      zconsTol_ = 0.01;
      sprintf(painCave.errMsg,
              "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
              "\tOOPSE will use a default value of %f.\n"
              "\tTo set the tolerance, use the zconsTol variable.\n",
              zconsTol_);
      painCave.isFatal = 0;
      simError();      
    }    
         
    int nZconstraints = simParam->getNZconsStamps();
    std::vector<ZConsStamp*> stamp = simParam->getZconsStamps();
    for (int i = 0; i < nZconstraints; i++){
      int zmolIndex = stamp[i]->getMolIndex();
      zmolStates_.insert(std::make_pair(zmolIndex, zsMoving));
    }


    //fill zatomToZmol_ array
    /** @todo only works for single version now*/
    std::map<int, ZConsState>::iterator j;
    for (j = zmolStates_.begin(); j != zmolStates_.end(); ++j) {
      Molecule* mol = info_->getMoleculeByGlobalIndex(j->first);
      assert(mol != NULL);
      Molecule::AtomIterator ai;
      Atom* at;
      for (at = mol->beginAtom(ai); at != NULL; at = mol->nextAtom(ai)) {
        zatomToZmol_.insert(std::make_pair(at->getGlobalIndex(), mol->getGlobalIndex()));
      }
    }

    zconsFilename_ = getPrefix(info_->getFinalConfigFileName()) + ".fz"; 
    
    zconsReader_ = new ZConsReader(info);

    if (zconsReader_->hasNextFrame())
      zconsReader_->readNextFrame();
  
  }

  ZConsVisitor::~ZConsVisitor(){
    if(!zconsReader_) 
      delete zconsReader_;
  
  }

  void ZConsVisitor::visit(Atom* atom){
    std::string prefix;
    if(isZconstraint(atom->getGlobalIndex(), prefix))
      internalVisit(atom, prefix);
  }

  void ZConsVisitor::visit(DirectionalAtom* datom){
    std::string prefix;

    if(isZconstraint(datom->getGlobalIndex(), prefix))
      internalVisit(datom, prefix);
  }

  void ZConsVisitor::visit(RigidBody* rb){
    std::string prefix;
    std::vector<Atom*> atoms;

    atoms = rb->getAtoms();

    if(isZconstraint(atoms[0]->getGlobalIndex(), prefix))
      internalVisit(rb, prefix);
  }

  void ZConsVisitor::update(){
    Molecule* mol;
    Vector3d com;
    ZConsState state;
    std::map<int, ZConsState>::iterator i;
    for ( i = zmolStates_.begin(); i != zmolStates_.end(); ++i) {
      i->second = zsMoving;
    }
     
    readZconsFile(currSnapshot_->getTime());

    const std::vector<ZconsData>& fixedZmolData = zconsReader_->getFixedZMolData();
    std::vector<ZconsData>::const_iterator j;
    for (j = fixedZmolData.begin(); j != fixedZmolData.end(); ++j) {
      std::map<int, ZConsState>::iterator k = zmolStates_.find(j->zmolIndex);
      assert(k != zmolStates_.end());
      k->second = zsFixed;
    }
    
  }

  void ZConsVisitor::readZconsFile(double time) {
    double tempTime;
    while(zconsReader_->hasNextFrame()){
      tempTime = zconsReader_->getCurTime();
      if(tempTime >= time) {
        return;
      }
        
      zconsReader_->readNextFrame();
    } 
  }

  void ZConsVisitor::internalVisit(StuntDouble* sd, const std::string& prefix){
    GenericData* data;
    AtomData* atomData;
    AtomInfo* atomInfo;
    std::vector<AtomInfo*>::iterator iter;

    //if there is not atom data, just skip it
    data = sd->getPropertyByName("ATOMDATA");
    if(data != NULL){
      atomData = dynamic_cast<AtomData*>(data);  
      if(atomData == NULL)
        return;
    }
    else
      return;

    for(atomInfo  = atomData->beginAtomInfo(iter); atomInfo; atomInfo = atomData->nextAtomInfo(iter))
      (atomInfo->atomTypeName).insert(0, prefix);
  }


  bool ZConsVisitor::isZconstraint(int atomIndex, std::string& prefix){
    std::string prefixString[] = {"ZF", "ZM"};
    std::map<int, int>::iterator i = zatomToZmol_.find(atomIndex);
    if (i ==  zatomToZmol_.end() ){
      prefix = "";
      return false;
    } else {

      std::map<int, ZConsState>::iterator j = zmolStates_.find(i->second);
      assert(j !=zmolStates_.end());
      prefix = prefixString[j->second];
      return true;
    }
  }

  const std::string ZConsVisitor::toString(){
    char buffer[65535];
    std::string result;

    sprintf(buffer ,"------------------------------------------------------------------\n");
    result += buffer;

    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
    result += buffer;

    sprintf(buffer , "number of zconstraint molecule: %d\n", zmolStates_.size());
    result += buffer;

    sprintf(buffer , "zconstraint tolerance = %lf\n", zconsTol_);
    result += buffer;

    sprintf(buffer , "zconstraint sample time = %lf\n", zconsTime_);
    result += buffer;

    sprintf(buffer , "zconstraint output filename = %s\n", zconsFilename_.c_str());
    result += buffer;

    std::map<int, ZConsState>::iterator i;
    int j = 0;
    for ( i = zmolStates_.begin(); i != zmolStates_.end(); ++i) {
      sprintf(buffer ,"zconstraint molecule[%d] = %d\n", j++, i->first);
      result += buffer;
    }
  
    sprintf(buffer ,"------------------------------------------------------------------\n");
    result += buffer;

    return result;
  }


}//namespace oopse
Revision:	2469
Committed:	Fri Dec 2 15:38:03 2005 UTC (18 years, 7 months ago) by tim
File size:	7868 byte(s)
Log Message:	End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
#	Content
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. 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
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	#include <cmath>
43	#include "visitors/ZconsVisitor.hpp"
44	#include "primitives/Molecule.hpp"
45	#include "utils/StringUtils.hpp"
46	#include "types/ZconsStamp.hpp"
47	namespace oopse {
48
49	ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisitor(), info_(info), zconsReader_(NULL){
50
51	visitorName = "ZConsVisitor";
52	currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
53	Globals* simParam = info_->getSimParams();
54
55	if (simParam->haveZconsTime()){
56	zconsTime_ = simParam->getZconsTime();
57	}
58	else{
59	sprintf(painCave.errMsg,
60	"ZConstraint error: If you use a ZConstraint,\n"
61	"\tyou must set zconsTime.\n");
62	painCave.isFatal = 1;
63	simError();
64	}
65
66	if (simParam->haveZconsTol()){
67	zconsTol_ = simParam->getZconsTol();
68	}
69	else{
70	zconsTol_ = 0.01;
71	sprintf(painCave.errMsg,
72	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
73	"\tOOPSE will use a default value of %f.\n"
74	"\tTo set the tolerance, use the zconsTol variable.\n",
75	zconsTol_);
76	painCave.isFatal = 0;
77	simError();
78	}
79
80	int nZconstraints = simParam->getNZconsStamps();
81	std::vector<ZConsStamp*> stamp = simParam->getZconsStamps();
82	for (int i = 0; i < nZconstraints; i++){
83	int zmolIndex = stamp[i]->getMolIndex();
84	zmolStates_.insert(std::make_pair(zmolIndex, zsMoving));
85	}
86
87
88	//fill zatomToZmol_ array
89	/** @todo only works for single version now*/
90	std::map<int, ZConsState>::iterator j;
91	for (j = zmolStates_.begin(); j != zmolStates_.end(); ++j) {
92	Molecule* mol = info_->getMoleculeByGlobalIndex(j->first);
93	assert(mol != NULL);
94	Molecule::AtomIterator ai;
95	Atom* at;
96	for (at = mol->beginAtom(ai); at != NULL; at = mol->nextAtom(ai)) {
97	zatomToZmol_.insert(std::make_pair(at->getGlobalIndex(), mol->getGlobalIndex()));
98	}
99	}
100
101	zconsFilename_ = getPrefix(info_->getFinalConfigFileName()) + ".fz";
102
103	zconsReader_ = new ZConsReader(info);
104
105	if (zconsReader_->hasNextFrame())
106	zconsReader_->readNextFrame();
107
108	}
109
110	ZConsVisitor::~ZConsVisitor(){
111	if(!zconsReader_)
112	delete zconsReader_;
113
114	}
115
116	void ZConsVisitor::visit(Atom* atom){
117	std::string prefix;
118	if(isZconstraint(atom->getGlobalIndex(), prefix))
119	internalVisit(atom, prefix);
120	}
121
122	void ZConsVisitor::visit(DirectionalAtom* datom){
123	std::string prefix;
124
125	if(isZconstraint(datom->getGlobalIndex(), prefix))
126	internalVisit(datom, prefix);
127	}
128
129	void ZConsVisitor::visit(RigidBody* rb){
130	std::string prefix;
131	std::vector<Atom*> atoms;
132
133	atoms = rb->getAtoms();
134
135	if(isZconstraint(atoms[0]->getGlobalIndex(), prefix))
136	internalVisit(rb, prefix);
137	}
138
139	void ZConsVisitor::update(){
140	Molecule* mol;
141	Vector3d com;
142	ZConsState state;
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	}
159
160	void ZConsVisitor::readZconsFile(double time) {
161	double tempTime;
162	while(zconsReader_->hasNextFrame()){
163	tempTime = zconsReader_->getCurTime();
164	if(tempTime >= time) {
165	return;
166	}
167
168	zconsReader_->readNextFrame();
169	}
170	}
171
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	//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	return;
187
188	for(atomInfo = atomData->beginAtomInfo(iter); atomInfo; atomInfo = atomData->nextAtomInfo(iter))
189	(atomInfo->atomTypeName).insert(0, prefix);
190	}
191
192
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	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	}
207
208	const std::string ZConsVisitor::toString(){
209	char buffer[65535];
210	std::string result;
211
212	sprintf(buffer ,"------------------------------------------------------------------\n");
213	result += buffer;
214
215	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
216	result += buffer;
217
218	sprintf(buffer , "number of zconstraint molecule: %d\n", zmolStates_.size());
219	result += buffer;
220
221	sprintf(buffer , "zconstraint tolerance = %lf\n", zconsTol_);
222	result += buffer;
223
224	sprintf(buffer , "zconstraint sample time = %lf\n", zconsTime_);
225	result += buffer;
226
227	sprintf(buffer , "zconstraint output filename = %s\n", zconsFilename_.c_str());
228	result += buffer;
229
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	sprintf(buffer ,"------------------------------------------------------------------\n");
238	result += buffer;
239
240	return result;
241	}
242
243
244	}//namespace oopse