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root/OpenMD/trunk/src/primitives/Element.hpp
Revision: 1210
Committed: Wed Jan 23 03:45:33 2008 UTC (17 years, 3 months ago) by gezelter
File size: 4575 byte(s)
Log Message: 
Removed older version of openbabel from our code.  We now have a
configure check to see if openbabel is installed and then we link to
the stuff we need.  Conversion to OOPSE's md format is handled by only
one application (atom2md), so most of the work went on there.
ElementsTable still needs some work to function in parallel.

File Contents

# Content
1 /**********************************************************************
2
3 This basic Element data-holding class was originally taken from the data.h
4 file in OpenBabel. The code has been modified to match the OOPSE coding style.
5
6 We have retained the OpenBabel copyright and GPL license on this class:
7
8 Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
9 Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
10
11 This file is part of the Open Babel project.
12 For more information, see <http://openbabel.sourceforge.net/>
13
14 This program is free software; you can redistribute it and/or modify
15 it under the terms of the GNU General Public License as published by
16 the Free Software Foundation version 2 of the License.
17
18 This program is distributed in the hope that it will be useful,
19 but WITHOUT ANY WARRANTY; without even the implied warranty of
20 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 GNU General Public License for more details.
22 ***********************************************************************/
23
24 /**
25 * @file Element.hpp
26 * @author gezelter
27 * @date 12/21/2007
28 * @version 1.0
29 */
30
31 #ifndef PRIMITIVES_ELEMENT_HPP
32 #define PRIMITIVES_ELEMENT_HPP
33 #include <string>
34 #include "config.h"
35
36 namespace oopse{
37 class Element {
38 public:
39 Element() {}
40 Element(int num, const char *sym, RealType rcov, RealType rvdw,
41 int maxbo, RealType mass, RealType elNeg, RealType ionize,
42 RealType elAffin, RealType red, RealType green, RealType blue,
43 std::string name) :
44 num_(num), name_(name), Rcov_(rcov), Rvdw_(rvdw), mass_(mass),
45 elNeg_(elNeg), ionize_(ionize), elAffinity_(elAffin),
46 red_(red), green_(green), blue_(blue),
47 maxbonds_(maxbo)
48 {
49 strncpy(symbol_, sym, 3);
50 }
51
52
53 /**
54 * Returns the atomic number of this element
55 * @return the atomic number of this element
56 */
57 int GetAtomicNum() {
58 return(num_);
59 }
60
61 /**
62 * Returns the atomic symbol for this element
63 * @return the atomic symbol for this element
64 */
65 char *GetSymbol() {
66 return(symbol_);
67 }
68
69 /**
70 * Returns the covalent radius of this element
71 * @return the covalent radius of this element
72 */
73 RealType GetCovalentRad() {
74 return(Rcov_);
75 }
76
77 /**
78 * Returns the van der Waals radius of this element
79 * @return the van der Waals radius of this element
80 */
81 RealType GetVdwRad() {
82 return(Rvdw_);
83 }
84
85 /**
86 * Returns the standard atomic mass for this element (in amu)
87 * @return the standard atomic mass for this element (in amu)
88 */
89 RealType GetMass() {
90 return(mass_);
91 }
92
93 /**
94 * Returns the maximum expected number of bonds to this element
95 * @return the maximum expected number of bonds to this element
96 */
97 int GetMaxBonds() {
98 return(maxbonds_);
99 }
100
101 /**
102 * Returns the Pauling electronegativity for this element
103 * @return the Pauling electronegativity for this element
104 */
105 RealType GetElectroNeg() {
106 return(elNeg_);
107 }
108
109 /**
110 * Returns the ionization potential (in eV) of this element
111 * @return the ionization potential (in eV) of this element
112 */
113 RealType GetIonization() {
114 return(ionize_);
115 }
116
117 /**
118 * Returns the electron affinity (in eV) of this element
119 * @return the electron affinity (in eV) of this element
120 */
121 RealType GetElectronAffinity() {
122 return(elAffinity_);
123 }
124
125 /**
126 * Returns the name of this element (in English)
127 * @return the name of this element (in English)
128 */
129 std::string GetName() {
130 return(name_);
131 }
132
133 /**
134 * Returns the red component of this element's default visualization color
135 * @return the red component of this element's default visualization color
136 */
137 RealType GetRed() {
138 return(red_);
139 }
140
141 /**
142 * Returns the green component of this element's default color
143 * @return the green component of this element's default color
144 */
145 RealType GetGreen() {
146 return(green_);
147 }
148
149 /**
150 * Returns the blue component of this element's default color
151 * @return the blue component of this element's default color
152 */
153 RealType GetBlue() {
154 return(blue_);
155 }
156
157 protected:
158 int num_;
159 char symbol_[3];
160 std::string name_;
161 RealType Rcov_, Rvdw_, mass_, elNeg_, ionize_, elAffinity_;
162 RealType red_, green_, blue_;
163 int maxbonds_;
164
165 };
166 }
167 #endif