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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	7988 byte(s)
Log Message:	updated copyright notices
#	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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			#include <cmath>
44	tim	3	#include "visitors/ZconsVisitor.hpp"
45	gezelter	246	#include "primitives/Molecule.hpp"
46			#include "utils/StringUtils.hpp"
47	tim	770	#include "types/ZconsStamp.hpp"
48	gezelter	1390	namespace OpenMD {
49	tim	132
50	gezelter	507	ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisitor(), info_(info), zconsReader_(NULL){
51	gezelter	2
52	gezelter	246	visitorName = "ZConsVisitor";
53			currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
54			Globals* simParam = info_->getSimParams();
55	gezelter	2
56	tim	665	if (simParam->haveZconsTime()){
57	gezelter	507	zconsTime_ = simParam->getZconsTime();
58	gezelter	2	}
59			else{
60	gezelter	507	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	gezelter	2	}
66
67	gezelter	246	if (simParam->haveZconsTol()){
68	gezelter	507	zconsTol_ = simParam->getZconsTol();
69	gezelter	2	}
70			else{
71	gezelter	507	zconsTol_ = 0.01;
72			sprintf(painCave.errMsg,
73			"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
74	gezelter	1390	"\tOpenMD will use a default value of %f.\n"
75	gezelter	507	"\tTo set the tolerance, use the zconsTol variable.\n",
76			zconsTol_);
77			painCave.isFatal = 0;
78			simError();
79	gezelter	246	}
80
81	tim	770	int nZconstraints = simParam->getNZconsStamps();
82			std::vector<ZConsStamp*> stamp = simParam->getZconsStamps();
83	gezelter	246	for (int i = 0; i < nZconstraints; i++){
84	gezelter	507	int zmolIndex = stamp[i]->getMolIndex();
85			zmolStates_.insert(std::make_pair(zmolIndex, zsMoving));
86	gezelter	2	}
87
88
89	gezelter	246	//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	gezelter	507	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	gezelter	2	}
101
102	gezelter	246	zconsFilename_ = getPrefix(info_->getFinalConfigFileName()) + ".fz";
103
104			zconsReader_ = new ZConsReader(info);
105	gezelter	2
106	gezelter	246	if (zconsReader_->hasNextFrame())
107	gezelter	507	zconsReader_->readNextFrame();
108	gezelter	2
109	gezelter	507	}
110	gezelter	2
111	gezelter	507	ZConsVisitor::~ZConsVisitor(){
112			if(!zconsReader_)
113			delete zconsReader_;
114	gezelter	2
115	gezelter	507	}
116	gezelter	2
117	gezelter	507	void ZConsVisitor::visit(Atom* atom){
118	gezelter	246	std::string prefix;
119			if(isZconstraint(atom->getGlobalIndex(), prefix))
120	gezelter	507	internalVisit(atom, prefix);
121			}
122	gezelter	2
123	gezelter	507	void ZConsVisitor::visit(DirectionalAtom* datom){
124	gezelter	246	std::string prefix;
125
126			if(isZconstraint(datom->getGlobalIndex(), prefix))
127	gezelter	507	internalVisit(datom, prefix);
128			}
129	gezelter	2
130	gezelter	507	void ZConsVisitor::visit(RigidBody* rb){
131	gezelter	246	std::string prefix;
132			std::vector<Atom*> atoms;
133	gezelter	2
134	gezelter	246	atoms = rb->getAtoms();
135	gezelter	2
136	gezelter	246	if(isZconstraint(atoms[0]->getGlobalIndex(), prefix))
137	gezelter	507	internalVisit(rb, prefix);
138			}
139	gezelter	2
140	gezelter	507	void ZConsVisitor::update(){
141	gezelter	246	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	gezelter	507	i->second = zsMoving;
147	gezelter	246	}
148
149			readZconsFile(currSnapshot_->getTime());
150	gezelter	2
151	gezelter	246	const std::vector<ZconsData>& fixedZmolData = zconsReader_->getFixedZMolData();
152			std::vector<ZconsData>::const_iterator j;
153			for (j = fixedZmolData.begin(); j != fixedZmolData.end(); ++j) {
154	gezelter	507	std::map<int, ZConsState>::iterator k = zmolStates_.find(j->zmolIndex);
155			assert(k != zmolStates_.end());
156			k->second = zsFixed;
157	gezelter	246	}
158
159	gezelter	507	}
160	gezelter	2
161	tim	963	void ZConsVisitor::readZconsFile(RealType time) {
162			RealType tempTime;
163	gezelter	246	while(zconsReader_->hasNextFrame()){
164	gezelter	507	tempTime = zconsReader_->getCurTime();
165			if(tempTime >= time) {
166			return;
167			}
168	gezelter	246
169	gezelter	507	zconsReader_->readNextFrame();
170	gezelter	246	}
171	gezelter	507	}
172	gezelter	2
173	gezelter	507	void ZConsVisitor::internalVisit(StuntDouble* sd, const std::string& prefix){
174	gezelter	246	GenericData* data;
175			AtomData* atomData;
176			AtomInfo* atomInfo;
177			std::vector<AtomInfo*>::iterator iter;
178	gezelter	2
179	gezelter	246	//if there is not atom data, just skip it
180			data = sd->getPropertyByName("ATOMDATA");
181			if(data != NULL){
182	gezelter	507	atomData = dynamic_cast<AtomData*>(data);
183			if(atomData == NULL)
184			return;
185			}
186	gezelter	246	else
187	gezelter	507	return;
188	gezelter	2
189	gezelter	246	for(atomInfo = atomData->beginAtomInfo(iter); atomInfo; atomInfo = atomData->nextAtomInfo(iter))
190	gezelter	507	(atomInfo->atomTypeName).insert(0, prefix);
191			}
192	gezelter	2
193
194	gezelter	507	bool ZConsVisitor::isZconstraint(int atomIndex, std::string& prefix){
195	gezelter	246	std::string prefixString[] = {"ZF", "ZM"};
196			std::map<int, int>::iterator i = zatomToZmol_.find(atomIndex);
197			if (i == zatomToZmol_.end() ){
198	gezelter	507	prefix = "";
199			return false;
200	gezelter	246	} else {
201	gezelter	2
202	gezelter	507	std::map<int, ZConsState>::iterator j = zmolStates_.find(i->second);
203			assert(j !=zmolStates_.end());
204			prefix = prefixString[j->second];
205			return true;
206	gezelter	246	}
207	gezelter	507	}
208	gezelter	2
209	gezelter	507	const std::string ZConsVisitor::toString(){
210	gezelter	246	char buffer[65535];
211			std::string result;
212	gezelter	2
213	gezelter	246	sprintf(buffer ,"------------------------------------------------------------------\n");
214			result += buffer;
215	gezelter	2
216	gezelter	246	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
217			result += buffer;
218	gezelter	2
219	gezelter	1390	sprintf(buffer , "number of zconstraint molecule: %d\n", (int) zmolStates_.size());
220	gezelter	246	result += buffer;
221	gezelter	2
222	gezelter	246	sprintf(buffer , "zconstraint tolerance = %lf\n", zconsTol_);
223			result += buffer;
224	gezelter	2
225	gezelter	246	sprintf(buffer , "zconstraint sample time = %lf\n", zconsTime_);
226			result += buffer;
227	gezelter	2
228	gezelter	246	sprintf(buffer , "zconstraint output filename = %s\n", zconsFilename_.c_str());
229	gezelter	2	result += buffer;
230
231	gezelter	246	std::map<int, ZConsState>::iterator i;
232			int j = 0;
233			for ( i = zmolStates_.begin(); i != zmolStates_.end(); ++i) {
234	gezelter	507	sprintf(buffer ,"zconstraint molecule[%d] = %d\n", j++, i->first);
235			result += buffer;
236	gezelter	246	}
237	gezelter	2
238	gezelter	246	sprintf(buffer ,"------------------------------------------------------------------\n");
239			result += buffer;
240	gezelter	2
241	gezelter	246	return result;
242	gezelter	507	}
243	tim	132
244
245	gezelter	1390	}//namespace OpenMD