src/types/AtomType.hpp

 /*
 * 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.
 */
 
#ifndef TYPES_ATOMTYPE_HPP

#define TYPES_ATOMTYPE_HPP

#include <string>

#include "utils/PropertyMap.hpp"

#define __C
#include "types/AtomTypeProperties.h"
#include "UseTheForce/DarkSide/atype_interface.h"

namespace oopse {
    /**
     * @class AtomType
     * AtomType is what OOPSE looks to for unchanging data about an atom.
     * Things that belong to AtomType are universal properties (i.e. does
     * this atom have a Charge?  What is it's mass_?)  Dynamic properties of
     * an atom are not intended to be properties of an atom type
     */
    class AtomType {
        public:

            AtomType();

            virtual ~AtomType() { } ;

            virtual void complete();

            /**
             * Finishes off the AtomType by communicating the logical portions of the
             * structure to the Fortran atype module
             */
            void makeFortranAtomType();
            
            void setMass(double m) {
                mass_ = m;
            }

            double getMass(void) {
                return mass_;
            }

            void setIdent(int id) {
                atp.ident = id;
            }

            int getIdent() {
                return atp.ident;
            }

            void setName(const std::string&name) {
                name_ = name;
            }

            std::string getName() {
                return name_;
            }

            void setLennardJones() {
                atp.is_LennardJones = 1;
            }

            bool isLennardJones() {
                return atp.is_LennardJones;
            }


            bool isElectrostatic() {
                return isCharge() || isMultipole();
            }

            void setEAM() {
                atp.is_EAM = 1;
            }

            bool isEAM() {
                return atp.is_EAM;
            }

            void setCharge() {
                atp.is_Charge = 1;
            }

            bool isCharge() {
                return atp.is_Charge;
            }

            bool isDirectional() {
                return atp.is_Directional;
            }

            bool isDipole() {
                return atp.is_Dipole;
            }

            bool isQuadrupole() {
                return atp.is_Quadrupole;
            }
            
            bool isMultipole() {
                return isDipole() || isQuadrupole();
            }

            bool isGayBerne() {
                return atp.is_GayBerne;
            }

            bool isSticky() {
                return atp.is_Sticky;
            }

            bool isShape() {
                return atp.is_Shape;
            }

            //below functions are just forward functions
            /**
             * Adds property into property map
             * @param genData GenericData to be added into PropertyMap
             */
            void addProperty(GenericData* genData);

            /**
             * Removes property from PropertyMap by name
             * @param propName the name of property to be removed
             */
            void removeProperty(const std::string& propName);

            /**
             * clear all of the properties
             */
            void clearProperties();

            /**
             * Returns all names of properties
             * @return all names of properties
             */
            std::vector<std::string> getPropertyNames();

            /**
             * Returns all of the properties in PropertyMap
             * @return all of the properties in PropertyMap
             */      
            std::vector<GenericData*> getProperties();

            /**
             * Returns property 
             * @param propName name of property
             * @return a pointer point to property with propName. If no property named propName
             * exists, return NULL
             */      
        GenericData* getPropertyByName(const std::string& propName);

        protected:

            AtomTypeProperties atp;
            double mass_;
            std::string name_;

        private:
            //prevent copy construction and copy assignment, since property map contains
            //pointers which can not be copied and managered safely, except make the generic data
            //at PropertyMap as copy on write shared pointer
            AtomType(const AtomType&);
            AtomType& operator=(const AtomType& atomType);

            
            PropertyMap properties_;
             
    };

    struct LJParam {
        double epsilon;
        double sigma;
        int soft_pot;
    };
    typedef SimpleTypeData<LJParam> LJParamGenericData;

    struct EAMParam {
        double latticeConstant;         
        int nrho;
        double drho;
        int nr;
        double dr;
        double rcut;
        std::vector<double> rvals; 
        std::vector<double> rhovals;
        std::vector<double> Frhovals;    
    };

    typedef SimpleTypeData<EAMParam> EAMParamGenericData;
}

#endif
Revision:	2062
Committed:	Fri Feb 25 21:22:00 2005 UTC (19 years, 4 months ago) by tim
File size:	7095 byte(s)
Log Message:	adding soft potential to LJ Module
#	User	Rev	Content
1	gezelter	1930	/*
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	gezelter	1631	#ifndef TYPES_ATOMTYPE_HPP
43	gezelter	1930
44	gezelter	1631	#define TYPES_ATOMTYPE_HPP
45
46	gezelter	1652	#include <string>
47
48	gezelter	1631	#include "utils/PropertyMap.hpp"
49	gezelter	1930
50	gezelter	1631	#define __C
51			#include "types/AtomTypeProperties.h"
52			#include "UseTheForce/DarkSide/atype_interface.h"
53
54			namespace oopse {
55			/**
56	gezelter	1930	* @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	gezelter	1631	*/
62	gezelter	1930	class AtomType {
63			public:
64	gezelter	1631
65	gezelter	1930	AtomType();
66	gezelter	1632
67	gezelter	1930	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	gezelter	1632
212	gezelter	1930	};
213	gezelter	1632
214	gezelter	1930	struct LJParam {
215			double epsilon;
216			double sigma;
217	tim	2062	int soft_pot;
218	gezelter	1930	};
219			typedef SimpleTypeData<LJParam> LJParamGenericData;
220	gezelter	1652
221	gezelter	1930	struct EAMParam {
222			double latticeConstant;
223			int nrho;
224			double drho;
225			int nr;
226			double dr;
227			double rcut;
228			std::vector<double> rvals;
229			std::vector<double> rhovals;
230			std::vector<double> Frhovals;
231			};
232
233			typedef SimpleTypeData<EAMParam> EAMParamGenericData;
234	gezelter	1631	}
235	gezelter	1930
236	gezelter	1631	#endif