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, 234107 (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(), 
                                              zconsReader_(NULL), info_(info){
    
    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(){
    Vector3d com;
    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:	2071
Committed:	Sat Mar 7 21:41:51 2015 UTC (10 years, 7 months ago) by gezelter
File size:	7964 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	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. 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	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	if (simParam->haveZconsTime()){
58	zconsTime_ = simParam->getZconsTime();
59	}
60	else{
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	}
67
68	if (simParam->haveZconsTol()){
69	zconsTol_ = simParam->getZconsTol();
70	}
71	else{
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	}
88
89
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	}
102
103	zconsFilename_ = getPrefix(info_->getFinalConfigFileName()) + ".fz";
104
105	zconsReader_ = new ZConsReader(info);
106
107	if (zconsReader_->hasNextFrame())
108	zconsReader_->readNextFrame();
109
110	}
111
112	ZConsVisitor::~ZConsVisitor(){
113	if(!zconsReader_)
114	delete zconsReader_;
115
116	}
117
118	void ZConsVisitor::visit(Atom* atom){
119	std::string prefix;
120	if(isZconstraint(atom->getGlobalIndex(), prefix))
121	internalVisit(atom, prefix);
122	}
123
124	void ZConsVisitor::visit(DirectionalAtom* datom){
125	std::string prefix;
126
127	if(isZconstraint(datom->getGlobalIndex(), prefix))
128	internalVisit(datom, prefix);
129	}
130
131	void ZConsVisitor::visit(RigidBody* rb){
132	std::string prefix;
133	std::vector<Atom*> atoms;
134
135	atoms = rb->getAtoms();
136
137	if(isZconstraint(atoms[0]->getGlobalIndex(), prefix))
138	internalVisit(rb, prefix);
139	}
140
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	}
159
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	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", (int) 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 OpenMD