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


namespace oopse {
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:	2245
Committed:	Sun May 29 00:16:14 2005 UTC (19 years, 1 month ago) by tim
File size:	5294 byte(s)
Log Message:	adding AtomNameVisitor
#	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. 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	#include <sstream>
42	#include <fstream>
43	#include "visitors/AtomNameVisitor.hpp"
44	#include "utils/Trim.hpp"
45	#include "utils/StringTokenizer.hpp"
46
47
48	namespace oopse {
49	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	}