ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/visitors/ZconsVisitor.cpp
(Generate patch)

Comparing trunk/src/visitors/ZconsVisitor.cpp (file contents):
Revision 407 by gezelter, Tue Mar 8 21:07:49 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #include <cmath>
43   #include "visitors/ZconsVisitor.hpp"
44   #include "primitives/Molecule.hpp"
45   #include "utils/StringUtils.hpp"
46 < namespace oopse {
46 > #include "types/ZconsStamp.hpp"
47 > namespace OpenMD {
48  
49 < ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisitor(), info_(info), zconsReader_(NULL){
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->haveZconstraintTime()){
56 <        zconsTime_ = simParam->getZconsTime();
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();
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();
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();      
70 >      zconsTol_ = 0.01;
71 >      sprintf(painCave.errMsg,
72 >              "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
73 >              "\tOpenMD 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->getNzConstraints();
81 <    ZconStamp** stamp = simParam->getZconStamp();
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));
83 >      int zmolIndex = stamp[i]->getMolIndex();
84 >      zmolStates_.insert(std::make_pair(zmolIndex, zsMoving));
85      }
86  
87  
# Line 88 | Line 89 | ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisito
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 <        }
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";
# Line 102 | Line 103 | ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisito
103      zconsReader_ = new ZConsReader(info);
104  
105      if (zconsReader_->hasNextFrame())
106 <        zconsReader_->readNextFrame();
106 >      zconsReader_->readNextFrame();
107    
108 < }
108 >  }
109  
110 < ZConsVisitor::~ZConsVisitor(){
111 <  if(!zconsReader_)
112 <    delete zconsReader_;
110 >  ZConsVisitor::~ZConsVisitor(){
111 >    if(!zconsReader_)
112 >      delete zconsReader_;
113    
114 < }
114 >  }
115  
116 < void ZConsVisitor::visit(Atom* atom){
116 >  void ZConsVisitor::visit(Atom* atom){
117      std::string prefix;
118      if(isZconstraint(atom->getGlobalIndex(), prefix))
119 <        internalVisit(atom, prefix);
120 < }
119 >      internalVisit(atom, prefix);
120 >  }
121  
122 < void ZConsVisitor::visit(DirectionalAtom* datom){
122 >  void ZConsVisitor::visit(DirectionalAtom* datom){
123      std::string prefix;
124  
125      if(isZconstraint(datom->getGlobalIndex(), prefix))
126 <        internalVisit(datom, prefix);
127 < }
126 >      internalVisit(datom, prefix);
127 >  }
128  
129 < void ZConsVisitor::visit(RigidBody* rb){
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 < }
136 >      internalVisit(rb, prefix);
137 >  }
138  
139 < void ZConsVisitor::update(){
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;
145 >      i->second = zsMoving;
146      }
147      
148      readZconsFile(currSnapshot_->getTime());
# Line 149 | Line 150 | void ZConsVisitor::update(){
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;
153 >      std::map<int, ZConsState>::iterator k = zmolStates_.find(j->zmolIndex);
154 >      assert(k != zmolStates_.end());
155 >      k->second = zsFixed;
156      }
157      
158 < }
158 >  }
159  
160 < void ZConsVisitor::readZconsFile(double time) {
161 <    double tempTime;
160 >  void ZConsVisitor::readZconsFile(RealType time) {
161 >    RealType tempTime;
162      while(zconsReader_->hasNextFrame()){
163 <        tempTime = zconsReader_->getCurTime();
164 <        if(tempTime >= time) {
165 <            return;
166 <        }
163 >      tempTime = zconsReader_->getCurTime();
164 >      if(tempTime >= time) {
165 >        return;
166 >      }
167          
168 <        zconsReader_->readNextFrame();
168 >      zconsReader_->readNextFrame();
169      }
170 < }
170 >  }
171  
172 < void ZConsVisitor::internalVisit(StuntDouble* sd, const std::string& prefix){
172 >  void ZConsVisitor::internalVisit(StuntDouble* sd, const std::string& prefix){
173      GenericData* data;
174      AtomData* atomData;
175      AtomInfo* atomInfo;
# Line 177 | Line 178 | void ZConsVisitor::internalVisit(StuntDouble* sd, cons
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 <        }
181 >      atomData = dynamic_cast<AtomData*>(data);  
182 >      if(atomData == NULL)
183 >        return;
184 >    }
185      else
186 <        return;
186 >      return;
187  
188      for(atomInfo  = atomData->beginAtomInfo(iter); atomInfo; atomInfo = atomData->nextAtomInfo(iter))
189 <        (atomInfo->atomTypeName).insert(0, prefix);
190 < }
189 >      (atomInfo->atomTypeName).insert(0, prefix);
190 >  }
191  
192  
193 < bool ZConsVisitor::isZconstraint(int atomIndex, std::string& prefix){
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;
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;
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 < }
206 >  }
207  
208 < const std::string ZConsVisitor::toString(){
208 >  const std::string ZConsVisitor::toString(){
209      char buffer[65535];
210      std::string result;
211  
# Line 214 | Line 215 | const std::string ZConsVisitor::toString(){
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());
218 >    sprintf(buffer , "number of zconstraint molecule: %d\n", (int) zmolStates_.size());
219      result += buffer;
220  
221      sprintf(buffer , "zconstraint tolerance = %lf\n", zconsTol_);
# Line 229 | Line 230 | const std::string ZConsVisitor::toString(){
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;
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 < }
241 >  }
242  
243  
244 < }//namespace oopse
244 > }//namespace OpenMD

Diff Legend

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