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Comparing:
trunk/src/visitors/AtomNameVisitor.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/visitors/AtomNameVisitor.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 1 | Line 1
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, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
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 OpenMD {
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	<	}
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, 24107 (2008).
39	>	* [4]  Vardeman & Gezelter, in progress (2009).
40	>	*/
41	>	#include <sstream>
42	>	#include <fstream>
43	>	#include "visitors/AtomNameVisitor.hpp"
44	>	#include "utils/Trim.hpp"
45	>	#include "utils/StringTokenizer.hpp"
46	>	#include "brains/SimInfo.hpp"
47	>
48	>
49	>	namespace OpenMD {
50	>	AtomNameVisitor::AtomNameVisitor(SimInfo* info) : BaseVisitor(),
51	>	info_(info) {
52	>	visitorName = "AtomNameVisitor";
53	>	ff_ = info_->getForceField();
54	>	}
55	>
56	>
57	>	void AtomNameVisitor::visitAtom(Atom* atom) {
58	>	AtomData* atomData;
59	>	GenericData* data;
60	>	bool haveAtomData;
61	>
62	>	data = atom->getPropertyByName("ATOMDATA");
63	>	if(data != NULL){
64	>	atomData = dynamic_cast<AtomData*>(data);
65	>	if(atomData == NULL){
66	>	std::cerr << "can not get Atom Data from " << atom->getType() << std::endl;
67	>	atomData = new AtomData;
68	>	haveAtomData = false;
69	>	} else {
70	>	haveAtomData = true;
71	>	}
72	>	} else {
73	>	atomData = new AtomData;
74	>	haveAtomData = false;
75	>	}
76	>
77	>	std::vector<AtomInfo*>::iterator i;
78	>	for (AtomInfo* atomInfo = atomData->beginAtomInfo(i);
79	>	atomInfo != NULL;
80	>	atomInfo = atomData->nextAtomInfo(i)) {
81	>
82	>	// query the force field for the AtomType associated with this
83	>	// atomTypeName:
84	>	AtomType* at = ff_->getAtomType(atomInfo->atomTypeName);
85	>	// get the chain of base types for this atom type:
86	>	std::vector<AtomType*> ayb = at->allYourBase();
87	>	// use the last type in the chain of base types for the name:
88	>	std::string bn = ayb[ayb.size()-1]->getName();
89	>
90	>	atomInfo->atomTypeName = bn;
91	>	}
92	>	}
93	>
94	>	void AtomNameVisitor::visit(RigidBody* rb) {
95	>	std::vector<Atom*>::iterator i;
96	>
97	>	for (Atom* atom = rb->beginAtom(i); atom != NULL; atom = rb->nextAtom(i)) {
98	>	visit(atom);
99	>	}
100	>	}
101	>
102	>
103	>	const std::string AtomNameVisitor::toString() {
104	>	char   buffer[65535];
105	>	std::string result;
106	>
107	>	sprintf(buffer,
108	>	"------------------------------------------------------------------\n");
109	>	result += buffer;
110	>
111	>	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
112	>	result += buffer;
113	>
114	>	sprintf(buffer,
115	>	"Visitor Description: print base atom types\n");
116	>	result += buffer;
117	>
118	>	sprintf(buffer,
119	>	"------------------------------------------------------------------\n");
120	>	result += buffer;
121	>
122	>	return result;
123	>	}
124	>
125	>	}

Comparing:
trunk/src/visitors/AtomNameVisitor.cpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/visitors/AtomNameVisitor.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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