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...
#	Content
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
54	namespace oopse {
55	/**
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
65	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 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	bool isStickyPower() {
159	return atp.is_StickyPower;
160	}
161
162	bool isShape() {
163	return atp.is_Shape;
164	}
165
166	//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
173	/**
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
179	/**
180	* clear all of the properties
181	*/
182	void clearProperties();
183
184	/**
185	* Returns all names of properties
186	* @return all names of properties
187	*/
188	std::vector<std::string> getPropertyNames();
189
190	/**
191	* Returns all of the properties in PropertyMap
192	* @return all of the properties in PropertyMap
193	*/
194	std::vector<GenericData*> getProperties();
195
196	/**
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
204	protected:
205
206	AtomTypeProperties atp;
207	double mass_;
208	std::string name_;
209
210	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
217
218	PropertyMap properties_;
219
220	};
221
222	struct LJParam {
223	double epsilon;
224	double sigma;
225	int soft_pot;
226	};
227	typedef SimpleTypeData<LJParam> LJParamGenericData;
228
229	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
241	typedef SimpleTypeData<EAMParam> EAMParamGenericData;
242	}
243
244	#endif