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 isSplitDipole() {
      return atp.is_SplitDipole;
    }

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

    bool isGayBerne() {
      return atp.is_GayBerne;
    }

    bool isSticky() {
      return atp.is_Sticky;
    }
    
    bool isStickyPower() {
      return atp.is_StickyPower;
    }

    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:	2220
Committed:	Thu May 5 14:47:35 2005 UTC (19 years, 2 months ago) by chrisfen
File size:	6228 byte(s)
Log Message:	OOPSE setup for TAP water. It's not parametrized, but OOPSE will now let me run it...
#	User	Rev	Content
1	gezelter	2094	/*
2	gezelter	1930	* 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	gezelter	2204	/**
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			class AtomType {
63			public:
64	gezelter	1631
65	gezelter	2204	AtomType();
66	gezelter	1632
67	gezelter	2204	virtual ~AtomType() { } ;
68	gezelter	1930
69	gezelter	2204	virtual void complete();
70	gezelter	1930
71	gezelter	2204	/**
72			* Finishes off the AtomType by communicating the logical portions of the
73			* structure to the Fortran atype module
74			*/
75			void makeFortranAtomType();
76	gezelter	1930
77	gezelter	2204	void setMass(double m) {
78			mass_ = m;
79			}
80	gezelter	1930
81	gezelter	2204	double getMass(void) {
82			return mass_;
83			}
84	gezelter	1930
85	gezelter	2204	void setIdent(int id) {
86			atp.ident = id;
87			}
88	gezelter	1930
89	gezelter	2204	int getIdent() {
90			return atp.ident;
91			}
92	gezelter	1930
93	gezelter	2204	void setName(const std::string&name) {
94			name_ = name;
95			}
96	gezelter	1930
97	gezelter	2204	std::string getName() {
98			return name_;
99			}
100	gezelter	1930
101	gezelter	2204	void setLennardJones() {
102			atp.is_LennardJones = 1;
103			}
104	gezelter	1930
105	gezelter	2204	bool isLennardJones() {
106			return atp.is_LennardJones;
107			}
108	gezelter	1930
109
110	gezelter	2204	bool isElectrostatic() {
111			return isCharge() \|\| isMultipole();
112			}
113	gezelter	1930
114	gezelter	2204	void setEAM() {
115			atp.is_EAM = 1;
116			}
117	gezelter	1930
118	gezelter	2204	bool isEAM() {
119			return atp.is_EAM;
120			}
121	gezelter	1930
122	gezelter	2204	void setCharge() {
123			atp.is_Charge = 1;
124			}
125	gezelter	1930
126	gezelter	2204	bool isCharge() {
127			return atp.is_Charge;
128			}
129	gezelter	1930
130	gezelter	2204	bool isDirectional() {
131			return atp.is_Directional;
132			}
133	gezelter	1930
134	gezelter	2204	bool isDipole() {
135			return atp.is_Dipole;
136			}
137	gezelter	1930
138	gezelter	2204	bool isSplitDipole() {
139			return atp.is_SplitDipole;
140			}
141	gezelter	2094
142	gezelter	2204	bool isQuadrupole() {
143			return atp.is_Quadrupole;
144			}
145	gezelter	1930
146	gezelter	2204	bool isMultipole() {
147			return isDipole() \|\| isQuadrupole();
148			}
149	gezelter	1930
150	gezelter	2204	bool isGayBerne() {
151			return atp.is_GayBerne;
152			}
153	gezelter	1930
154	gezelter	2204	bool isSticky() {
155			return atp.is_Sticky;
156			}
157	chrisfen	2220
158			bool isStickyPower() {
159			return atp.is_StickyPower;
160			}
161	gezelter	1930
162	gezelter	2204	bool isShape() {
163			return atp.is_Shape;
164			}
165	gezelter	1930
166	gezelter	2204	//below functions are just forward functions
167			/**
168			* Adds property into property map
169			* @param genData GenericData to be added into PropertyMap
170			*/
171			void addProperty(GenericData* genData);
172	gezelter	1930
173	gezelter	2204	/**
174			* Removes property from PropertyMap by name
175			* @param propName the name of property to be removed
176			*/
177			void removeProperty(const std::string& propName);
178	gezelter	1930
179	gezelter	2204	/**
180			* clear all of the properties
181			*/
182			void clearProperties();
183	gezelter	1930
184	gezelter	2204	/**
185			* Returns all names of properties
186			* @return all names of properties
187			*/
188			std::vector<std::string> getPropertyNames();
189	gezelter	1930
190	gezelter	2204	/**
191			* Returns all of the properties in PropertyMap
192			* @return all of the properties in PropertyMap
193			*/
194			std::vector<GenericData*> getProperties();
195	gezelter	1930
196	gezelter	2204	/**
197			* Returns property
198			* @param propName name of property
199			* @return a pointer point to property with propName. If no property named propName
200			* exists, return NULL
201			*/
202			GenericData* getPropertyByName(const std::string& propName);
203	gezelter	1930
204	gezelter	2204	protected:
205	gezelter	1930
206	gezelter	2204	AtomTypeProperties atp;
207			double mass_;
208			std::string name_;
209	gezelter	1930
210	gezelter	2204	private:
211			//prevent copy construction and copy assignment, since property map contains
212			//pointers which can not be copied and managered safely, except make the generic data
213			//at PropertyMap as copy on write shared pointer
214			AtomType(const AtomType&);
215			AtomType& operator=(const AtomType& atomType);
216	gezelter	1930
217
218	gezelter	2204	PropertyMap properties_;
219	gezelter	1632
220	gezelter	2204	};
221	gezelter	1632
222	gezelter	2204	struct LJParam {
223			double epsilon;
224			double sigma;
225			int soft_pot;
226			};
227			typedef SimpleTypeData<LJParam> LJParamGenericData;
228	gezelter	1652
229	gezelter	2204	struct EAMParam {
230			double latticeConstant;
231			int nrho;
232			double drho;
233			int nr;
234			double dr;
235			double rcut;
236			std::vector<double> rvals;
237			std::vector<double> rhovals;
238			std::vector<double> Frhovals;
239			};
240	gezelter	1930
241	gezelter	2204	typedef SimpleTypeData<EAMParam> EAMParamGenericData;
242	gezelter	1631	}
243	gezelter	1930
244	gezelter	1631	#endif