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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#include <cmath>
#include "visitors/ZconsVisitor.hpp"
#include "primitives/Molecule.hpp"
#include "utils/StringUtils.hpp"
#include "types/ZconsStamp.hpp"
namespace OpenMD {

  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"
              "\tOpenMD 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(RealType time) {
    RealType 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", (int) 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 OpenMD
Revision:	1442
Committed:	Mon May 10 17:28:26 2010 UTC (15 years, 5 months ago) by gezelter
Original Path:	*trunk/src/visitors/ZconsVisitor.cpp*
File size:	7922 byte(s)
Log Message:	Adding property set to svn entries
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	gezelter	246	*/
41
42			#include <cmath>
43	tim	3	#include "visitors/ZconsVisitor.hpp"
44	gezelter	246	#include "primitives/Molecule.hpp"
45			#include "utils/StringUtils.hpp"
46	tim	770	#include "types/ZconsStamp.hpp"
47	gezelter	1390	namespace OpenMD {
48	tim	132
49	gezelter	507	ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisitor(), info_(info), zconsReader_(NULL){
50	gezelter	2
51	gezelter	246	visitorName = "ZConsVisitor";
52			currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
53			Globals* simParam = info_->getSimParams();
54	gezelter	2
55	tim	665	if (simParam->haveZconsTime()){
56	gezelter	507	zconsTime_ = simParam->getZconsTime();
57	gezelter	2	}
58			else{
59	gezelter	507	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	gezelter	2	}
65
66	gezelter	246	if (simParam->haveZconsTol()){
67	gezelter	507	zconsTol_ = simParam->getZconsTol();
68	gezelter	2	}
69			else{
70	gezelter	507	zconsTol_ = 0.01;
71			sprintf(painCave.errMsg,
72			"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
73	gezelter	1390	"\tOpenMD will use a default value of %f.\n"
74	gezelter	507	"\tTo set the tolerance, use the zconsTol variable.\n",
75			zconsTol_);
76			painCave.isFatal = 0;
77			simError();
78	gezelter	246	}
79
80	tim	770	int nZconstraints = simParam->getNZconsStamps();
81			std::vector<ZConsStamp*> stamp = simParam->getZconsStamps();
82	gezelter	246	for (int i = 0; i < nZconstraints; i++){
83	gezelter	507	int zmolIndex = stamp[i]->getMolIndex();
84			zmolStates_.insert(std::make_pair(zmolIndex, zsMoving));
85	gezelter	2	}
86
87
88	gezelter	246	//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	gezelter	507	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	gezelter	2	}
100
101	gezelter	246	zconsFilename_ = getPrefix(info_->getFinalConfigFileName()) + ".fz";
102
103			zconsReader_ = new ZConsReader(info);
104	gezelter	2
105	gezelter	246	if (zconsReader_->hasNextFrame())
106	gezelter	507	zconsReader_->readNextFrame();
107	gezelter	2
108	gezelter	507	}
109	gezelter	2
110	gezelter	507	ZConsVisitor::~ZConsVisitor(){
111			if(!zconsReader_)
112			delete zconsReader_;
113	gezelter	2
114	gezelter	507	}
115	gezelter	2
116	gezelter	507	void ZConsVisitor::visit(Atom* atom){
117	gezelter	246	std::string prefix;
118			if(isZconstraint(atom->getGlobalIndex(), prefix))
119	gezelter	507	internalVisit(atom, prefix);
120			}
121	gezelter	2
122	gezelter	507	void ZConsVisitor::visit(DirectionalAtom* datom){
123	gezelter	246	std::string prefix;
124
125			if(isZconstraint(datom->getGlobalIndex(), prefix))
126	gezelter	507	internalVisit(datom, prefix);
127			}
128	gezelter	2
129	gezelter	507	void ZConsVisitor::visit(RigidBody* rb){
130	gezelter	246	std::string prefix;
131			std::vector<Atom*> atoms;
132	gezelter	2
133	gezelter	246	atoms = rb->getAtoms();
134	gezelter	2
135	gezelter	246	if(isZconstraint(atoms[0]->getGlobalIndex(), prefix))
136	gezelter	507	internalVisit(rb, prefix);
137			}
138	gezelter	2
139	gezelter	507	void ZConsVisitor::update(){
140	gezelter	246	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	gezelter	507	i->second = zsMoving;
146	gezelter	246	}
147
148			readZconsFile(currSnapshot_->getTime());
149	gezelter	2
150	gezelter	246	const std::vector<ZconsData>& fixedZmolData = zconsReader_->getFixedZMolData();
151			std::vector<ZconsData>::const_iterator j;
152			for (j = fixedZmolData.begin(); j != fixedZmolData.end(); ++j) {
153	gezelter	507	std::map<int, ZConsState>::iterator k = zmolStates_.find(j->zmolIndex);
154			assert(k != zmolStates_.end());
155			k->second = zsFixed;
156	gezelter	246	}
157
158	gezelter	507	}
159	gezelter	2
160	tim	963	void ZConsVisitor::readZconsFile(RealType time) {
161			RealType tempTime;
162	gezelter	246	while(zconsReader_->hasNextFrame()){
163	gezelter	507	tempTime = zconsReader_->getCurTime();
164			if(tempTime >= time) {
165			return;
166			}
167	gezelter	246
168	gezelter	507	zconsReader_->readNextFrame();
169	gezelter	246	}
170	gezelter	507	}
171	gezelter	2
172	gezelter	507	void ZConsVisitor::internalVisit(StuntDouble* sd, const std::string& prefix){
173	gezelter	246	GenericData* data;
174			AtomData* atomData;
175			AtomInfo* atomInfo;
176			std::vector<AtomInfo*>::iterator iter;
177	gezelter	2
178	gezelter	246	//if there is not atom data, just skip it
179			data = sd->getPropertyByName("ATOMDATA");
180			if(data != NULL){
181	gezelter	507	atomData = dynamic_cast<AtomData*>(data);
182			if(atomData == NULL)
183			return;
184			}
185	gezelter	246	else
186	gezelter	507	return;
187	gezelter	2
188	gezelter	246	for(atomInfo = atomData->beginAtomInfo(iter); atomInfo; atomInfo = atomData->nextAtomInfo(iter))
189	gezelter	507	(atomInfo->atomTypeName).insert(0, prefix);
190			}
191	gezelter	2
192
193	gezelter	507	bool ZConsVisitor::isZconstraint(int atomIndex, std::string& prefix){
194	gezelter	246	std::string prefixString[] = {"ZF", "ZM"};
195			std::map<int, int>::iterator i = zatomToZmol_.find(atomIndex);
196			if (i == zatomToZmol_.end() ){
197	gezelter	507	prefix = "";
198			return false;
199	gezelter	246	} else {
200	gezelter	2
201	gezelter	507	std::map<int, ZConsState>::iterator j = zmolStates_.find(i->second);
202			assert(j !=zmolStates_.end());
203			prefix = prefixString[j->second];
204			return true;
205	gezelter	246	}
206	gezelter	507	}
207	gezelter	2
208	gezelter	507	const std::string ZConsVisitor::toString(){
209	gezelter	246	char buffer[65535];
210			std::string result;
211	gezelter	2
212	gezelter	246	sprintf(buffer ,"------------------------------------------------------------------\n");
213			result += buffer;
214	gezelter	2
215	gezelter	246	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
216			result += buffer;
217	gezelter	2
218	gezelter	1390	sprintf(buffer , "number of zconstraint molecule: %d\n", (int) zmolStates_.size());
219	gezelter	246	result += buffer;
220	gezelter	2
221	gezelter	246	sprintf(buffer , "zconstraint tolerance = %lf\n", zconsTol_);
222			result += buffer;
223	gezelter	2
224	gezelter	246	sprintf(buffer , "zconstraint sample time = %lf\n", zconsTime_);
225			result += buffer;
226	gezelter	2
227	gezelter	246	sprintf(buffer , "zconstraint output filename = %s\n", zconsFilename_.c_str());
228	gezelter	2	result += buffer;
229
230	gezelter	246	std::map<int, ZConsState>::iterator i;
231			int j = 0;
232			for ( i = zmolStates_.begin(); i != zmolStates_.end(); ++i) {
233	gezelter	507	sprintf(buffer ,"zconstraint molecule[%d] = %d\n", j++, i->first);
234			result += buffer;
235	gezelter	246	}
236	gezelter	2
237	gezelter	246	sprintf(buffer ,"------------------------------------------------------------------\n");
238			result += buffer;
239	gezelter	2
240	gezelter	246	return result;
241	gezelter	507	}
242	tim	132
243
244	gezelter	1390	}//namespace OpenMD