src/visitors/AtomNameVisitor.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 <sstream> 
#include <fstream>
#include "visitors/AtomNameVisitor.hpp"
#include "utils/Trim.hpp"
#include "utils/StringTokenizer.hpp"


namespace OpenMD {
AtomNameVisitor::AtomNameVisitor(SimInfo* info) : BaseVisitor(), info_(info) {
    visitorName = "AtomNameVisitor";
    std::stringstream ss(defaultAtomTypeTable);
    readAtomTypes(ss);
}

AtomNameVisitor::AtomNameVisitor(SimInfo* info, const std::string& atomTypeFile) : BaseVisitor(), info_(info) {
    visitorName = "AtomNameVisitor";
    std::ifstream ifs(atomTypeFile.c_str());
    readAtomTypes(ifs);
}


void AtomNameVisitor::visitAtom(Atom* atom) {
    AtomData* atomData;
    GenericData* data;    
    bool haveAtomData;
    
    data = atom->getPropertyByName("ATOMDATA");
    if(data != NULL){
      atomData = dynamic_cast<AtomData*>(data);  
      if(atomData == NULL){
        std::cerr << "can not get Atom Data from " << atom->getType() << std::endl;
        atomData = new AtomData; 
        haveAtomData = false;      
      } else {
        haveAtomData = true;
      }
    } else {
      atomData = new AtomData;
      haveAtomData = false;
    }

    std::vector<AtomInfo*>::iterator i;
    for (AtomInfo* atomInfo = atomData->beginAtomInfo(i); atomInfo != NULL; atomInfo = atomData->nextAtomInfo(i)) {
        atomInfo->atomTypeName = getBaseAtomTypeName(atomInfo->atomTypeName);        
    }
    
}

void AtomNameVisitor::visit(RigidBody* rb) {
    std::vector<Atom*>::iterator i;

  for (Atom* atom = rb->beginAtom(i); atom != NULL; atom = rb->nextAtom(i)) {
    visit(atom);
  }
}


void AtomNameVisitor::readAtomTypes(std::istream& is) {
    const int bufferSize = 65535;
    char buffer[bufferSize];
    std::string line;
    while(is.getline(buffer, bufferSize)) {
      line = trimLeftCopy(buffer);
      //a line begins with "//" is comment
      // let's also call lines starting with # and ! as comments
     if ( line.empty() || 
                  (line.size() >= 2 && line[0] == '/' && line[1] == '/') ||
                  (line.size() >= 1 && line[0] == '#') || 
                  (line.size() >= 1 && line[0] == '!') ) {
        continue;
      } else {
        StringTokenizer tokenizer(line);
        if (tokenizer.countTokens() >= 2) {
            std::string atomName = tokenizer.nextToken();
            std::string baseAtomName = tokenizer.nextToken();
            atomNames_.insert(MapType::value_type(atomName, baseAtomName));
        }
      }
    }

}

std::string AtomNameVisitor::getBaseAtomTypeName(const std::string& atomTypeName) {
    MapType::iterator i;
    i = atomNames_.find(atomTypeName);
    return i != atomNames_.end() ? i->second : atomTypeName;
}


const std::string AtomNameVisitor::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,
            "Visitor Description: print base atom types\n");
    result += buffer;

    sprintf(buffer,
            "------------------------------------------------------------------\n");
    result += buffer;

    return result;
}

}
Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
File size:	5336 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	User	Rev	Content
1	tim	548	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	548	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	548	* 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	tim	548	*/
41			#include <sstream>
42			#include <fstream>
43			#include "visitors/AtomNameVisitor.hpp"
44			#include "utils/Trim.hpp"
45			#include "utils/StringTokenizer.hpp"
46
47
48	gezelter	1390	namespace OpenMD {
49	tim	548	AtomNameVisitor::AtomNameVisitor(SimInfo* info) : BaseVisitor(), info_(info) {
50			visitorName = "AtomNameVisitor";
51			std::stringstream ss(defaultAtomTypeTable);
52			readAtomTypes(ss);
53			}
54
55			AtomNameVisitor::AtomNameVisitor(SimInfo* info, const std::string& atomTypeFile) : BaseVisitor(), info_(info) {
56			visitorName = "AtomNameVisitor";
57			std::ifstream ifs(atomTypeFile.c_str());
58			readAtomTypes(ifs);
59			}
60
61
62			void AtomNameVisitor::visitAtom(Atom* atom) {
63			AtomData* atomData;
64			GenericData* data;
65			bool haveAtomData;
66
67			data = atom->getPropertyByName("ATOMDATA");
68			if(data != NULL){
69			atomData = dynamic_cast<AtomData*>(data);
70			if(atomData == NULL){
71			std::cerr << "can not get Atom Data from " << atom->getType() << std::endl;
72			atomData = new AtomData;
73			haveAtomData = false;
74			} else {
75			haveAtomData = true;
76			}
77			} else {
78			atomData = new AtomData;
79			haveAtomData = false;
80			}
81
82			std::vector<AtomInfo*>::iterator i;
83			for (AtomInfo* atomInfo = atomData->beginAtomInfo(i); atomInfo != NULL; atomInfo = atomData->nextAtomInfo(i)) {
84			atomInfo->atomTypeName = getBaseAtomTypeName(atomInfo->atomTypeName);
85			}
86
87			}
88
89			void AtomNameVisitor::visit(RigidBody* rb) {
90			std::vector<Atom*>::iterator i;
91
92			for (Atom* atom = rb->beginAtom(i); atom != NULL; atom = rb->nextAtom(i)) {
93			visit(atom);
94			}
95			}
96
97
98			void AtomNameVisitor::readAtomTypes(std::istream& is) {
99			const int bufferSize = 65535;
100			char buffer[bufferSize];
101			std::string line;
102			while(is.getline(buffer, bufferSize)) {
103			line = trimLeftCopy(buffer);
104			//a line begins with "//" is comment
105			// let's also call lines starting with # and ! as comments
106			if ( line.empty() \|\|
107			(line.size() >= 2 && line[0] == '/' && line[1] == '/') \|\|
108			(line.size() >= 1 && line[0] == '#') \|\|
109			(line.size() >= 1 && line[0] == '!') ) {
110			continue;
111			} else {
112			StringTokenizer tokenizer(line);
113			if (tokenizer.countTokens() >= 2) {
114			std::string atomName = tokenizer.nextToken();
115			std::string baseAtomName = tokenizer.nextToken();
116			atomNames_.insert(MapType::value_type(atomName, baseAtomName));
117			}
118			}
119			}
120
121			}
122
123			std::string AtomNameVisitor::getBaseAtomTypeName(const std::string& atomTypeName) {
124			MapType::iterator i;
125			i = atomNames_.find(atomTypeName);
126			return i != atomNames_.end() ? i->second : atomTypeName;
127			}
128
129
130			const std::string AtomNameVisitor::toString() {
131			char buffer[65535];
132			std::string result;
133
134			sprintf(buffer,
135			"------------------------------------------------------------------\n");
136			result += buffer;
137
138			sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
139			result += buffer;
140
141			sprintf(buffer,
142			"Visitor Description: print base atom types\n");
143			result += buffer;
144
145			sprintf(buffer,
146			"------------------------------------------------------------------\n");
147			result += buffer;
148
149			return result;
150			}
151
152			}