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Revision 1652 by gezelter, Tue Oct 26 22:25:19 2004 UTC vs.
Revision 1930 by gezelter, Wed Jan 12 22:41:40 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"
53  
11 – using namespace std;
12 –
54   namespace oopse {
14 –  /**
15 –   * @class AtomType
16 –   * AtomType is what OOPSE looks to for unchanging data about an atom.
17 –   * Things that belong to AtomType are universal properties (i.e. does
18 –   * this atom have a Charge?  What is it's mass?)  Dynamic properties of
19 –   * an atom are not intended to be properties of an atom type
20 –   */
21 –  class AtomType{
22 –    
23 –  public:
24 –    
25 –    AtomType();
26 –    virtual ~AtomType(){ };
55      /**
56 <     * Finishes off the AtomType by communicating the logical portions of the
57 <     * structure to the Fortran atype module
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
60 >     * an atom are not intended to be properties of an atom type
61       */
62 <    void    complete();
63 <    
33 <    void    setMass(double m) { mass = m; }
34 <    double  getMass(void) { return mass; }
62 >    class AtomType {
63 >        public:
64  
65 <    void    setIdent(int id) {atp.ident = id;}
37 <    int     getIdent() {return atp.ident;}
65 >            AtomType();
66  
67 <    void    setName(string n) {name = n;}
68 <    string  getName() {return name;}
69 <    
70 <    void    setLennardJones() { atp.is_LennardJones = 1; }
71 <    bool    isLennardJones()  { return atp.is_LennardJones; }
72 <    
73 <    void    setElectrostatic() { atp.is_Electrostatic = 1; }
74 <    bool    isElectrostatic()  { return atp.is_Electrostatic; }
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 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 isQuadrupole() {
139 >                return atp.is_Quadrupole;
140 >            }
141 >            
142 >            bool isMultipole() {
143 >                return isDipole() || isQuadrupole();
144 >            }
145 >
146 >            bool isGayBerne() {
147 >                return atp.is_GayBerne;
148 >            }
149 >
150 >            bool isSticky() {
151 >                return atp.is_Sticky;
152 >            }
153 >
154 >            bool isShape() {
155 >                return atp.is_Shape;
156 >            }
157 >
158 >            //below functions are just forward functions
159 >            /**
160 >             * Adds property into property map
161 >             * @param genData GenericData to be added into PropertyMap
162 >             */
163 >            void addProperty(GenericData* genData);
164 >
165 >            /**
166 >             * Removes property from PropertyMap by name
167 >             * @param propName the name of property to be removed
168 >             */
169 >            void removeProperty(const std::string& propName);
170 >
171 >            /**
172 >             * clear all of the properties
173 >             */
174 >            void clearProperties();
175 >
176 >            /**
177 >             * Returns all names of properties
178 >             * @return all names of properties
179 >             */
180 >            std::vector<std::string> getPropertyNames();
181 >
182 >            /**
183 >             * Returns all of the properties in PropertyMap
184 >             * @return all of the properties in PropertyMap
185 >             */      
186 >            std::vector<GenericData*> getProperties();
187 >
188 >            /**
189 >             * Returns property
190 >             * @param propName name of property
191 >             * @return a pointer point to property with propName. If no property named propName
192 >             * exists, return NULL
193 >             */      
194 >        GenericData* getPropertyByName(const std::string& propName);
195 >
196 >        protected:
197 >
198 >            AtomTypeProperties atp;
199 >            double mass_;
200 >            std::string name_;
201 >
202 >        private:
203 >            //prevent copy construction and copy assignment, since property map contains
204 >            //pointers which can not be copied and managered safely, except make the generic data
205 >            //at PropertyMap as copy on write shared pointer
206 >            AtomType(const AtomType&);
207 >            AtomType& operator=(const AtomType& atomType);
208 >
209 >            
210 >            PropertyMap properties_;
211              
212 <    void    setEAM() { atp.is_EAM = 1; }
49 <    bool    isEAM()  { return atp.is_EAM; }
50 <        
51 <    void    setCharge() { atp.is_Charge = 1; atp.is_Electrostatic = 1;}
52 <    bool    isCharge()  { return atp.is_Charge; }
212 >    };
213  
214 <    bool    isDirectional() { return atp.is_Directional; }
215 <    bool    isDipole()  { return atp.is_Dipole; }
216 <    bool    isGayBerne()  { return atp.is_GayBerne; }
217 <    bool    isSticky()  { return atp.is_Sticky; }
218 <    bool    isShape()  { return atp.is_Shape; }
214 >    struct LJParam {
215 >        double epsilon;
216 >        double sigma;
217 >    };
218 >    typedef SimpleTypeData<LJParam> LJParamGenericData;
219  
220 <    PropertyMap properties;
221 <                
222 <  protected:
223 <    
224 <    AtomTypeProperties atp;
225 <    double mass;
226 <    string name;
227 <    
228 <  };
220 >    struct EAMParam {
221 >        double latticeConstant;        
222 >        int nrho;
223 >        double drho;
224 >        int nr;
225 >        double dr;
226 >        double rcut;
227 >        std::vector<double> rvals;
228 >        std::vector<double> rhovals;
229 >        std::vector<double> Frhovals;    
230 >    };
231 >
232 >    typedef SimpleTypeData<EAMParam> EAMParamGenericData;
233   }
234 +
235   #endif

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