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"
namespace oopse {

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

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

    if (simParam->haveZconstraintTime()){
        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->getNzConstraints();
    ZconStamp** stamp = simParam->getZconStamp();
    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->AtomType).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:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	7922 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	User	Rev	Content
1	gezelter	1930	/*
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	tim	1492	#include "visitors/ZconsVisitor.hpp"
44	gezelter	1930	#include "primitives/Molecule.hpp"
45			#include "utils/StringUtils.hpp"
46	tim	1625	namespace oopse {
47
48	gezelter	1930	ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisitor(), info_(info), zconsReader_(NULL){
49	gezelter	1490
50	gezelter	1930	visitorName = "ZConsVisitor";
51			currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
52			Globals* simParam = info_->getSimParams();
53	gezelter	1490
54	gezelter	1930	if (simParam->haveZconstraintTime()){
55			zconsTime_ = simParam->getZconsTime();
56	gezelter	1490	}
57			else{
58	gezelter	1930	sprintf(painCave.errMsg,
59			"ZConstraint error: If you use a ZConstraint,\n"
60			"\tyou must set zconsTime.\n");
61			painCave.isFatal = 1;
62			simError();
63	gezelter	1490	}
64
65	gezelter	1930	if (simParam->haveZconsTol()){
66			zconsTol_ = simParam->getZconsTol();
67	gezelter	1490	}
68			else{
69	gezelter	1930	zconsTol_ = 0.01;
70			sprintf(painCave.errMsg,
71			"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
72			"\tOOPSE will use a default value of %f.\n"
73			"\tTo set the tolerance, use the zconsTol variable.\n",
74			zconsTol_);
75			painCave.isFatal = 0;
76			simError();
77			}
78
79			int nZconstraints = simParam->getNzConstraints();
80			ZconStamp** stamp = simParam->getZconStamp();
81			for (int i = 0; i < nZconstraints; i++){
82			int zmolIndex = stamp[i]->getMolIndex();
83			zmolStates_.insert(std::make_pair(zmolIndex, zsMoving));
84	gezelter	1490	}
85
86
87	gezelter	1930	//fill zatomToZmol_ array
88			/** @todo only works for single version now*/
89			std::map<int, ZConsState>::iterator j;
90			for (j = zmolStates_.begin(); j != zmolStates_.end(); ++j) {
91			Molecule* mol = info_->getMoleculeByGlobalIndex(j->first);
92			assert(mol != NULL);
93			Molecule::AtomIterator ai;
94			Atom* at;
95			for (at = mol->beginAtom(ai); at != NULL; at = mol->nextAtom(ai)) {
96			zatomToZmol_.insert(std::make_pair(at->getGlobalIndex(), mol->getGlobalIndex()));
97			}
98	gezelter	1490	}
99
100	gezelter	1930	zconsFilename_ = getPrefix(info_->getFinalConfigFileName()) + ".fz";
101
102			zconsReader_ = new ZConsReader(info);
103	gezelter	1490
104	gezelter	1930	if (zconsReader_->hasNextFrame())
105			zconsReader_->readNextFrame();
106	gezelter	1490
107			}
108
109			ZConsVisitor::~ZConsVisitor(){
110	gezelter	1930	if(!zconsReader_)
111			delete zconsReader_;
112	gezelter	1490
113			}
114
115			void ZConsVisitor::visit(Atom* atom){
116	gezelter	1930	std::string prefix;
117			if(isZconstraint(atom->getGlobalIndex(), prefix))
118			internalVisit(atom, prefix);
119	gezelter	1490	}
120
121			void ZConsVisitor::visit(DirectionalAtom* datom){
122	gezelter	1930	std::string prefix;
123
124			if(isZconstraint(datom->getGlobalIndex(), prefix))
125			internalVisit(datom, prefix);
126	gezelter	1490	}
127
128			void ZConsVisitor::visit(RigidBody* rb){
129	gezelter	1930	std::string prefix;
130			std::vector<Atom*> atoms;
131	gezelter	1490
132	gezelter	1930	atoms = rb->getAtoms();
133	gezelter	1490
134	gezelter	1930	if(isZconstraint(atoms[0]->getGlobalIndex(), prefix))
135			internalVisit(rb, prefix);
136	gezelter	1490	}
137
138			void ZConsVisitor::update(){
139	gezelter	1930	Molecule* mol;
140			Vector3d com;
141			ZConsState state;
142			std::map<int, ZConsState>::iterator i;
143			for ( i = zmolStates_.begin(); i != zmolStates_.end(); ++i) {
144			i->second = zsMoving;
145			}
146
147			readZconsFile(currSnapshot_->getTime());
148	gezelter	1490
149	gezelter	1930	const std::vector<ZconsData>& fixedZmolData = zconsReader_->getFixedZMolData();
150			std::vector<ZconsData>::const_iterator j;
151			for (j = fixedZmolData.begin(); j != fixedZmolData.end(); ++j) {
152			std::map<int, ZConsState>::iterator k = zmolStates_.find(j->zmolIndex);
153			assert(k != zmolStates_.end());
154			k->second = zsFixed;
155			}
156
157			}
158	gezelter	1490
159	gezelter	1930	void ZConsVisitor::readZconsFile(double time) {
160			double tempTime;
161			while(zconsReader_->hasNextFrame()){
162			tempTime = zconsReader_->getCurTime();
163			if(tempTime >= time) {
164			return;
165			}
166
167			zconsReader_->readNextFrame();
168			}
169	gezelter	1490	}
170
171	gezelter	1930	void ZConsVisitor::internalVisit(StuntDouble* sd, const std::string& prefix){
172			GenericData* data;
173			AtomData* atomData;
174			AtomInfo* atomInfo;
175			std::vector<AtomInfo*>::iterator iter;
176	gezelter	1490
177	gezelter	1930	//if there is not atom data, just skip it
178			data = sd->getPropertyByName("ATOMDATA");
179			if(data != NULL){
180			atomData = dynamic_cast<AtomData*>(data);
181			if(atomData == NULL)
182			return;
183			}
184			else
185			return;
186	gezelter	1490
187	gezelter	1930	for(atomInfo = atomData->beginAtomInfo(iter); atomInfo; atomInfo = atomData->nextAtomInfo(iter))
188			(atomInfo->AtomType).insert(0, prefix);
189	gezelter	1490	}
190
191
192	gezelter	1930	bool ZConsVisitor::isZconstraint(int atomIndex, std::string& prefix){
193			std::string prefixString[] = {"ZF", "ZM"};
194			std::map<int, int>::iterator i = zatomToZmol_.find(atomIndex);
195			if (i == zatomToZmol_.end() ){
196			prefix = "";
197			return false;
198			} else {
199	gezelter	1490
200	gezelter	1930	std::map<int, ZConsState>::iterator j = zmolStates_.find(i->second);
201			assert(j !=zmolStates_.end());
202			prefix = prefixString[j->second];
203			return true;
204			}
205	gezelter	1490	}
206
207	gezelter	1930	const std::string ZConsVisitor::toString(){
208			char buffer[65535];
209			std::string result;
210	gezelter	1490
211	gezelter	1930	sprintf(buffer ,"------------------------------------------------------------------\n");
212			result += buffer;
213	gezelter	1490
214	gezelter	1930	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
215			result += buffer;
216	gezelter	1490
217	gezelter	1930	sprintf(buffer , "number of zconstraint molecule: %d\n", zmolStates_.size());
218			result += buffer;
219	gezelter	1490
220	gezelter	1930	sprintf(buffer , "zconstraint tolerance = %lf\n", zconsTol_);
221			result += buffer;
222	gezelter	1490
223	gezelter	1930	sprintf(buffer , "zconstraint sample time = %lf\n", zconsTime_);
224			result += buffer;
225	gezelter	1490
226	gezelter	1930	sprintf(buffer , "zconstraint output filename = %s\n", zconsFilename_.c_str());
227	gezelter	1490	result += buffer;
228
229	gezelter	1930	std::map<int, ZConsState>::iterator i;
230			int j = 0;
231			for ( i = zmolStates_.begin(); i != zmolStates_.end(); ++i) {
232			sprintf(buffer ,"zconstraint molecule[%d] = %d\n", j++, i->first);
233			result += buffer;
234			}
235	gezelter	1490
236	gezelter	1930	sprintf(buffer ,"------------------------------------------------------------------\n");
237			result += buffer;
238	gezelter	1490
239	gezelter	1930	return result;
240	gezelter	1490	}
241	tim	1625
242
243			}//namespace oopse