src/UseTheForce/ForceFields.hpp

#ifndef __FORCEFIELDS_H__
#define __FORCEFIELDS_H__

#define MK_STR(s) # s
#define STR_DEFINE(t, s) t = MK_STR(s)

#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string>
#include <map>

#include "primitives/Atom.hpp"
#include "brains/SimInfo.hpp"
#include "primitives/StuntDouble.hpp"
#include "types/ShapeAtomType.hpp"
#include "io/basic_ifstrstream.hpp"

#ifdef IS_MPI
#include "UseTheForce/mpiForceField.h"
#endif

using namespace std;
using namespace oopse;

class bond_pair{
public:
  bond_pair(){}
  ~bond_pair(){}

  int a;
  int b;
};

class bend_set{
public:
  bend_set(){ isGhost = 0; }
  ~bend_set(){}

  int ghost;
  int isGhost;

  int a;
  int b;
  int c;
};

class torsion_set{
public:
  torsion_set(){}
  ~torsion_set(){}

  int a;
  int b;
  int c;
  int d;
};


class ForceFields{

public:
  ForceFields(){ 

    char* force_param_path;
    frcFile = NULL; 
    entry_plug = NULL; 
    has_variant=0;

    force_param_path = getenv("FORCE_PARAM_PATH");
    if (force_param_path != NULL) {
      ffPath = force_param_path;
    } else {
      ffPath = "";
    }

    if( ffPath.empty() ) {
      STR_DEFINE(ffPath, FRC_PATH );
    }   
  }
  ForceFields(const string &theVariant){ 
    char* force_param_path;
    frcFile = NULL; 
    entry_plug = NULL; 
    has_variant=1; 
    variant = theVariant;

    force_param_path = getenv("FORCE_PARAM_PATH");
    if (force_param_path != NULL) {
      ffPath = force_param_path;
    } else {
      ffPath = "";
    }

    if( ffPath.empty() ) {
      STR_DEFINE(ffPath, FRC_PATH );
    }   
  }
  virtual ~ForceFields(){}
  
  void setSimInfo( SimInfo* the_entry_plug ) { entry_plug = the_entry_plug; }
  
  virtual void readParams( void ) = 0;
  
  virtual void cleanMe( void ) = 0;


  virtual void initializeAtoms( int nAtoms, Atom** atomArray ) = 0;
  virtual void initializeBonds( int nBonds, Bond** bondArray,
                                bond_pair* the_bonds ) = 0;
  virtual void initializeBends( int nBends, Bend** bendArray,
                                bend_set* the_bends ) = 0;
  virtual void initializeTorsions( int nTorsions, Torsion** torsionArray,
                                   torsion_set* the_torsions ) = 0;
  virtual void initForceField() = 0;

  virtual void calcRcut( void );
  virtual void setRcut( double LJrcut );
  virtual void doForces( int calcPot, int calcStress );

protected:
  
  void initFortran( int useReactionField );
  
  FILE *frcFile;
  SimInfo* entry_plug;
  
  int lineNum;
  char readLine[500];
  char* eof_test;
  short int has_variant;
  double bigSigma;

  string ffPath;
  ifstrstream forceFile;
  bool hasVariant;
  string variant;
  map<string, AtomType*> atomTypeMap;
  // map<pair<string,string>, BondType*> bondTypeMap;
  // map<tuple3<string,string,string>, BendType*> bendTypeMap;
  // map<tuple4<string,string,string,string>, TorsionType*> torsionTypeMap;

};


class DUFF : public ForceFields{

public:
  DUFF();
  virtual ~DUFF();

  void readParams();
  void cleanMe( void );

  void initializeAtoms( int nAtoms, Atom** atomArray );
  void initializeBonds( int nBonds, Bond** bondArray,
                        bond_pair* the_bonds );
  void initializeBends( int nBends, Bend** bendArray,
                        bend_set* the_bends );
  void initializeTorsions( int nTorsions, Torsion** torsionArray,
                           torsion_set* the_torsions );

  void initForceField();

private:
  
  void fastForward( char* stopText, char* searchOwner );
};

class LJFF : public ForceFields{

public:
  LJFF();
  virtual ~LJFF();
  

  void readParams();
  void cleanMe( void );

  void initializeAtoms( int nAtoms, Atom** atomArray );
  void initializeBonds( int nBonds, Bond** bondArray,
                        bond_pair* the_bonds );
  void initializeBends( int nBends, Bend** bendArray,
                        bend_set* the_bends );
  void initializeTorsions( int nTorsions, Torsion** torsionArray,
                           torsion_set* the_torsions );

  void initForceField( );


private:

  void fastForward( char* stopText, char* searchOwner );

};

class EAM_FF : public ForceFields{

public:

  EAM_FF();
  EAM_FF(const string &theVariant);

  virtual ~EAM_FF();
  
  void readParams();
  void cleanMe( void );

  void initializeAtoms( int nAtoms, Atom** atomArray );
  void initializeBonds( int nBonds, Bond** bondArray,
                        bond_pair* the_bonds );
  void initializeBends( int nBends, Bend** bendArray,
                        bend_set* the_bends );
  void initializeTorsions( int nTorsions, Torsion** torsionArray,
                           torsion_set* the_torsions );

  void initForceField();

  void calcRcut( void );

private:

  void fastForward( char* stopText, char* searchOwner );
  
  double eamRcut;
};

class WATER : public ForceFields{

public:
  WATER();
  virtual ~WATER();

  void readParams();
  void cleanMe( void );
  void initializeAtoms( int nAtoms, Atom** atomArray );
  void initializeBonds( int nBonds, Bond** bondArray,
                        bond_pair* the_bonds );
  void initializeBends( int nBends, Bend** bendArray,
                        bend_set* the_bends );
  void initializeTorsions( int nTorsions, Torsion** torsionArray,
                           torsion_set* the_torsions );
  void initForceField();


private:
  
  void fastForward( char* stopText, char* searchOwner );
  void sectionSearch( char* secHead, char* stopText, char* searchOwner );

};

class Shapes_FF : public ForceFields{

public:
  Shapes_FF() : ForceFields() {};
  Shapes_FF(const string &the_variant) : ForceFields(the_variant) {};
  virtual ~Shapes_FF();
  
  void readParams();
  void cleanMe( void );

  void initializeAtoms( int nAtoms, Atom** atomArray );
  void initializeBonds( int nBonds, Bond** bondArray,
                        bond_pair* the_bonds );
  void initializeBends( int nBends, Bend** bendArray,
                        bend_set* the_bends );
  void initializeTorsions( int nTorsions, Torsion** torsionArray,
                           torsion_set* the_torsions );

  void initForceField();

  void calcRcut( void );

  void parseShapeFile(string shapeFileName, ShapeAtomType* st);

private:

  double findLargestContactDistance(ShapeAtomType* st);
  double findCutoffDistance(ShapeAtomType* st);
  double shapesRcut;
  double bigContact;

};


#endif

Revision:	1772
Committed:	Tue Nov 23 22:48:31 2004 UTC (19 years, 7 months ago) by chrisfen
File size:	5970 byte(s)
Log Message:	Improvements to restraints
#	Content
1	#ifndef __FORCEFIELDS_H__
2	#define __FORCEFIELDS_H__
3
4	#define MK_STR(s) # s
5	#define STR_DEFINE(t, s) t = MK_STR(s)
6
7	#include <stdio.h>
8	#include <stdlib.h>
9	#include <math.h>
10	#include <string>
11	#include <map>
12
13	#include "primitives/Atom.hpp"
14	#include "brains/SimInfo.hpp"
15	#include "primitives/StuntDouble.hpp"
16	#include "types/ShapeAtomType.hpp"
17	#include "io/basic_ifstrstream.hpp"
18
19	#ifdef IS_MPI
20	#include "UseTheForce/mpiForceField.h"
21	#endif
22
23	using namespace std;
24	using namespace oopse;
25
26	class bond_pair{
27	public:
28	bond_pair(){}
29	~bond_pair(){}
30
31	int a;
32	int b;
33	};
34
35	class bend_set{
36	public:
37	bend_set(){ isGhost = 0; }
38	~bend_set(){}
39
40	int ghost;
41	int isGhost;
42
43	int a;
44	int b;
45	int c;
46	};
47
48	class torsion_set{
49	public:
50	torsion_set(){}
51	~torsion_set(){}
52
53	int a;
54	int b;
55	int c;
56	int d;
57	};
58
59
60
61	class ForceFields{
62
63	public:
64	ForceFields(){
65
66	char* force_param_path;
67	frcFile = NULL;
68	entry_plug = NULL;
69	has_variant=0;
70
71	force_param_path = getenv("FORCE_PARAM_PATH");
72	if (force_param_path != NULL) {
73	ffPath = force_param_path;
74	} else {
75	ffPath = "";
76	}
77
78	if( ffPath.empty() ) {
79	STR_DEFINE(ffPath, FRC_PATH );
80	}
81	}
82	ForceFields(const string &theVariant){
83	char* force_param_path;
84	frcFile = NULL;
85	entry_plug = NULL;
86	has_variant=1;
87	variant = theVariant;
88
89	force_param_path = getenv("FORCE_PARAM_PATH");
90	if (force_param_path != NULL) {
91	ffPath = force_param_path;
92	} else {
93	ffPath = "";
94	}
95
96	if( ffPath.empty() ) {
97	STR_DEFINE(ffPath, FRC_PATH );
98	}
99	}
100	virtual ~ForceFields(){}
101
102	void setSimInfo( SimInfo* the_entry_plug ) { entry_plug = the_entry_plug; }
103
104	virtual void readParams( void ) = 0;
105
106	virtual void cleanMe( void ) = 0;
107
108
109	virtual void initializeAtoms( int nAtoms, Atom** atomArray ) = 0;
110	virtual void initializeBonds( int nBonds, Bond** bondArray,
111	bond_pair* the_bonds ) = 0;
112	virtual void initializeBends( int nBends, Bend** bendArray,
113	bend_set* the_bends ) = 0;
114	virtual void initializeTorsions( int nTorsions, Torsion** torsionArray,
115	torsion_set* the_torsions ) = 0;
116	virtual void initForceField() = 0;
117
118	virtual void calcRcut( void );
119	virtual void setRcut( double LJrcut );
120	virtual void doForces( int calcPot, int calcStress );
121
122	protected:
123
124	void initFortran( int useReactionField );
125
126	FILE *frcFile;
127	SimInfo* entry_plug;
128
129	int lineNum;
130	char readLine[500];
131	char* eof_test;
132	short int has_variant;
133	double bigSigma;
134
135	string ffPath;
136	ifstrstream forceFile;
137	bool hasVariant;
138	string variant;
139	map<string, AtomType*> atomTypeMap;
140	// map<pair<string,string>, BondType*> bondTypeMap;
141	// map<tuple3<string,string,string>, BendType*> bendTypeMap;
142	// map<tuple4<string,string,string,string>, TorsionType*> torsionTypeMap;
143
144	};
145
146
147	class DUFF : public ForceFields{
148
149	public:
150	DUFF();
151	virtual ~DUFF();
152
153	void readParams();
154	void cleanMe( void );
155
156	void initializeAtoms( int nAtoms, Atom** atomArray );
157	void initializeBonds( int nBonds, Bond** bondArray,
158	bond_pair* the_bonds );
159	void initializeBends( int nBends, Bend** bendArray,
160	bend_set* the_bends );
161	void initializeTorsions( int nTorsions, Torsion** torsionArray,
162	torsion_set* the_torsions );
163
164	void initForceField();
165
166	private:
167
168	void fastForward( char* stopText, char* searchOwner );
169	};
170
171	class LJFF : public ForceFields{
172
173	public:
174	LJFF();
175	virtual ~LJFF();
176
177
178	void readParams();
179	void cleanMe( void );
180
181	void initializeAtoms( int nAtoms, Atom** atomArray );
182	void initializeBonds( int nBonds, Bond** bondArray,
183	bond_pair* the_bonds );
184	void initializeBends( int nBends, Bend** bendArray,
185	bend_set* the_bends );
186	void initializeTorsions( int nTorsions, Torsion** torsionArray,
187	torsion_set* the_torsions );
188
189	void initForceField( );
190
191
192	private:
193
194	void fastForward( char* stopText, char* searchOwner );
195
196	};
197
198	class EAM_FF : public ForceFields{
199
200	public:
201
202	EAM_FF();
203	EAM_FF(const string &theVariant);
204
205	virtual ~EAM_FF();
206
207	void readParams();
208	void cleanMe( void );
209
210	void initializeAtoms( int nAtoms, Atom** atomArray );
211	void initializeBonds( int nBonds, Bond** bondArray,
212	bond_pair* the_bonds );
213	void initializeBends( int nBends, Bend** bendArray,
214	bend_set* the_bends );
215	void initializeTorsions( int nTorsions, Torsion** torsionArray,
216	torsion_set* the_torsions );
217
218	void initForceField();
219
220	void calcRcut( void );
221
222	private:
223
224	void fastForward( char* stopText, char* searchOwner );
225
226	double eamRcut;
227	};
228
229	class WATER : public ForceFields{
230
231	public:
232	WATER();
233	virtual ~WATER();
234
235	void readParams();
236	void cleanMe( void );
237	void initializeAtoms( int nAtoms, Atom** atomArray );
238	void initializeBonds( int nBonds, Bond** bondArray,
239	bond_pair* the_bonds );
240	void initializeBends( int nBends, Bend** bendArray,
241	bend_set* the_bends );
242	void initializeTorsions( int nTorsions, Torsion** torsionArray,
243	torsion_set* the_torsions );
244	void initForceField();
245
246
247	private:
248
249	void fastForward( char* stopText, char* searchOwner );
250	void sectionSearch( char* secHead, char* stopText, char* searchOwner );
251
252	};
253
254	class Shapes_FF : public ForceFields{
255
256	public:
257	Shapes_FF() : ForceFields() {};
258	Shapes_FF(const string &the_variant) : ForceFields(the_variant) {};
259	virtual ~Shapes_FF();
260
261	void readParams();
262	void cleanMe( void );
263
264	void initializeAtoms( int nAtoms, Atom** atomArray );
265	void initializeBonds( int nBonds, Bond** bondArray,
266	bond_pair* the_bonds );
267	void initializeBends( int nBends, Bend** bendArray,
268	bend_set* the_bends );
269	void initializeTorsions( int nTorsions, Torsion** torsionArray,
270	torsion_set* the_torsions );
271
272	void initForceField();
273
274	void calcRcut( void );
275
276	void parseShapeFile(string shapeFileName, ShapeAtomType* st);
277
278	private:
279
280	double findLargestContactDistance(ShapeAtomType* st);
281	double findCutoffDistance(ShapeAtomType* st);
282	double shapesRcut;
283	double bigContact;
284
285	};
286
287
288	#endif
289