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Comparing trunk/OOPSE-3.0/src/types/AtomType.hpp (file contents):
Revision 1632 by gezelter, Fri Oct 22 20:21:36 2004 UTC vs.
Revision 2427 by chuckv, Mon Nov 14 21:29:36 2005 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. 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   #ifndef TYPES_ATOMTYPE_HPP
43 +
44   #define TYPES_ATOMTYPE_HPP
45  
46 + #include <string>
47 +
48   #include "utils/PropertyMap.hpp"
49 +
50   #define __C
51   #include "types/AtomTypeProperties.h"
52   #include "UseTheForce/DarkSide/atype_interface.h"
# Line 11 | Line 56 | namespace oopse {
56     * @class AtomType
57     * AtomType is what OOPSE looks to for unchanging data about an atom.
58     * Things that belong to AtomType are universal properties (i.e. does
59 <   * this atom have a Charge?  What is it's mass?)  Dynamic properties of
59 >   * this atom have a Charge?  What is it's mass_?)  Dynamic properties of
60     * an atom are not intended to be properties of an atom type
61     */
62 <  class AtomType{
18 <    
62 >  class AtomType {
63    public:
64 <    
64 >
65      AtomType();
66 <    ~AtomType();
66 >
67 >    virtual ~AtomType() { } ;
68 >
69 >    virtual void complete();
70 >
71      /**
72       * Finishes off the AtomType by communicating the logical portions of the
73       * structure to the Fortran atype module
74       */
75 <    void    complete();
75 >    void makeFortranAtomType();
76 >            
77 >    void setMass(double m) {
78 >      mass_ = m;
79 >    }
80 >
81 >    double getMass(void) {
82 >      return mass_;
83 >    }
84 >
85 >    void setIdent(int id) {
86 >      atp.ident = id;
87 >    }
88 >
89 >    int getIdent() {
90 >      return atp.ident;
91 >    }
92 >
93 >    void setName(const std::string&name) {
94 >      name_ = name;
95 >    }
96 >
97 >    std::string getName() {
98 >      return name_;
99 >    }
100 >
101 >    void setLennardJones() {
102 >      atp.is_LennardJones = 1;
103 >    }
104 >
105 >    bool isLennardJones() {
106 >      return atp.is_LennardJones;
107 >    }
108 >
109 >
110 >    bool isElectrostatic() {
111 >      return isCharge() || isMultipole();
112 >    }
113 >
114 >    void setEAM() {
115 >      atp.is_EAM = 1;
116 >    }
117 >
118 >    bool isEAM() {
119 >      return atp.is_EAM;
120 >    }
121 >
122 >    void setCharge() {
123 >      atp.is_Charge = 1;
124 >    }
125 >
126 >    bool isCharge() {
127 >      return atp.is_Charge;
128 >    }
129 >
130 >    bool isDirectional() {
131 >      return atp.is_Directional;
132 >    }
133 >
134 >    bool isDipole() {
135 >      return atp.is_Dipole;
136 >    }
137 >
138 >    bool isSplitDipole() {
139 >      return atp.is_SplitDipole;
140 >    }
141 >
142 >    bool isQuadrupole() {
143 >      return atp.is_Quadrupole;
144 >    }
145 >            
146 >    bool isMultipole() {
147 >      return isDipole() || isQuadrupole();
148 >    }
149 >
150 >    bool isGayBerne() {
151 >      return atp.is_GayBerne;
152 >    }
153 >
154 >    bool isSticky() {
155 >      return atp.is_Sticky;
156 >    }
157      
158 <    void    setMass(double m) { mass = m; }
159 <    double  getMass(void) { return mass; }
158 >    bool isStickyPower() {
159 >      return atp.is_StickyPower;
160 >    }
161  
162 <    void    setIdent(int id) {atp.ident = id;}
163 <    int     getIdent() {return atp.ident;}
162 >    bool isShape() {
163 >      return atp.is_Shape;
164 >    }
165  
166 <    void    setName(char* n) {strcpy(name, n);}
167 <    char*   getName() {return name;}
166 >    bool isSC() {
167 >      return atp.is_SC;
168 >    }
169      
170 <    void    setLennardJones() { atp.is_LennardJones = 1; }
171 <    bool    isLennardJones()  { return atp.is_LennardJones; }
170 >    void setSC() {
171 >      atp.is_SC = 1;
172 >    }
173      
41 –    void    setElectrostatic() { atp.is_Electrostatic = 1; }
42 –    bool    isElectrostatic()  { return atp.is_Electrostatic; }
43 –            
44 –    void    setEAM() { atp.is_EAM = 1; }
45 –    bool    isEAM()  { return atp.is_EAM; }
46 –        
47 –    void    setCharge() { atp.is_Charge = 1; atp.is_Electrostatic = 1;}
48 –    bool    isCharge()  { return atp.is_Charge; }
49 –
50 –    PropertyMap properties;
51 –                
52 –  private:
174      
175 <    AtomTypeProperties atp;
176 <    double mass;
177 <    char* name;
175 >    bool isMEAM() {
176 >      return atp.is_MEAM;
177 >    }
178      
179 +    void setMEAM() {
180 +      atp.is_MEAM = 1;
181 +    }
182 +    
183 +    
184 +    //below functions are just forward functions
185 +    /**
186 +     * Adds property into property map
187 +     * @param genData GenericData to be added into PropertyMap
188 +     */
189 +    void addProperty(GenericData* genData);
190 +
191 +    /**
192 +     * Removes property from PropertyMap by name
193 +     * @param propName the name of property to be removed
194 +     */
195 +    void removeProperty(const std::string& propName);
196 +
197 +    /**
198 +     * clear all of the properties
199 +     */
200 +    void clearProperties();
201 +
202 +    /**
203 +     * Returns all names of properties
204 +     * @return all names of properties
205 +     */
206 +    std::vector<std::string> getPropertyNames();
207 +
208 +    /**
209 +     * Returns all of the properties in PropertyMap
210 +     * @return all of the properties in PropertyMap
211 +     */      
212 +    std::vector<GenericData*> getProperties();
213 +
214 +    /**
215 +     * Returns property
216 +     * @param propName name of property
217 +     * @return a pointer point to property with propName. If no property named propName
218 +     * exists, return NULL
219 +     */      
220 +    GenericData* getPropertyByName(const std::string& propName);
221 +
222 +  protected:
223 +
224 +    AtomTypeProperties atp;
225 +    double mass_;
226 +    std::string name_;
227 +
228 +  private:
229 +    //prevent copy construction and copy assignment, since property map contains
230 +    //pointers which can not be copied and managered safely, except make the generic data
231 +    //at PropertyMap as copy on write shared pointer
232 +    AtomType(const AtomType&);
233 +    AtomType& operator=(const AtomType& atomType);
234 +
235 +            
236 +    PropertyMap properties_;
237 +            
238    };
239 +
240 +  struct LJParam {
241 +    double epsilon;
242 +    double sigma;
243 +    int soft_pot;
244 +  };
245 +  typedef SimpleTypeData<LJParam> LJParamGenericData;
246 +
247 +  struct EAMParam {
248 +    double latticeConstant;        
249 +    int nrho;
250 +    double drho;
251 +    int nr;
252 +    double dr;
253 +    double rcut;
254 +    std::vector<double> rvals;
255 +    std::vector<double> rhovals;
256 +    std::vector<double> Frhovals;    
257 +  };
258 +
259 +  typedef SimpleTypeData<EAMParam> EAMParamGenericData;
260 +  
261 +  struct SCParam {
262 +    double c;
263 +    double m;
264 +    double n;
265 +    double alpha;
266 +    double epsilon;
267 +  };
268 +  typedef SimpleTypeData<SCParam> SCParamGenericData;
269 +  
270 +  
271 +  
272 +  
273   }
274 +
275   #endif

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