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
#	User	Rev	Content
1	gezelter	1490	#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	gezelter	1650	#include <string>
11			#include <map>
12	gezelter	1490
13	tim	1492	#include "primitives/Atom.hpp"
14			#include "brains/SimInfo.hpp"
15			#include "primitives/StuntDouble.hpp"
16	gezelter	1650	#include "types/ShapeAtomType.hpp"
17			#include "io/basic_ifstrstream.hpp"
18	gezelter	1490
19			#ifdef IS_MPI
20	tim	1492	#include "UseTheForce/mpiForceField.h"
21	gezelter	1490	#endif
22
23	gezelter	1650	using namespace std;
24			using namespace oopse;
25
26	gezelter	1490	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	gezelter	1650	ForceFields(){
65	gezelter	1670
66			char* force_param_path;
67	gezelter	1650	frcFile = NULL;
68			entry_plug = NULL;
69			has_variant=0;
70	gezelter	1670
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	gezelter	1653	if( ffPath.empty() ) {
79	gezelter	1650	STR_DEFINE(ffPath, FRC_PATH );
80			}
81			}
82	gezelter	1670	ForceFields(const string &theVariant){
83			char* force_param_path;
84	gezelter	1650	frcFile = NULL;
85			entry_plug = NULL;
86			has_variant=1;
87	gezelter	1653	variant = theVariant;
88	gezelter	1670
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	gezelter	1653	if( ffPath.empty() ) {
97	gezelter	1650	STR_DEFINE(ffPath, FRC_PATH );
98			}
99			}
100	gezelter	1490	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	gezelter	1628	virtual void initForceField() = 0;
117	gezelter	1490
118			virtual void calcRcut( void );
119			virtual void setRcut( double LJrcut );
120			virtual void doForces( int calcPot, int calcStress );
121
122			protected:
123
124	gezelter	1628	void initFortran( int useReactionField );
125	chuckv	1617
126	gezelter	1490	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	gezelter	1653	string ffPath;
136	gezelter	1650	ifstrstream forceFile;
137	gezelter	1653	bool hasVariant;
138			string variant;
139	gezelter	1650	map<string, AtomType*> atomTypeMap;
140	gezelter	1653	// map<pair<string,string>, BondType*> bondTypeMap;
141			// map<tuple3<string,string,string>, BendType*> bendTypeMap;
142			// map<tuple4<string,string,string,string>, TorsionType*> torsionTypeMap;
143	gezelter	1650
144	gezelter	1490	};
145
146
147			class DUFF : public ForceFields{
148
149			public:
150	gezelter	1656	DUFF();
151	gezelter	1490	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	gezelter	1628	void initForceField();
165	gezelter	1490
166			private:
167
168			void fastForward( char* stopText, char* searchOwner );
169			};
170
171			class LJFF : public ForceFields{
172
173			public:
174	gezelter	1656	LJFF();
175	gezelter	1490	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	gezelter	1628	void initForceField( );
190	gezelter	1490
191	gezelter	1650
192	gezelter	1490	private:
193
194			void fastForward( char* stopText, char* searchOwner );
195
196			};
197
198			class EAM_FF : public ForceFields{
199
200			public:
201	gezelter	1656
202			EAM_FF();
203	gezelter	1670	EAM_FF(const string &theVariant);
204	gezelter	1656
205	gezelter	1490	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	gezelter	1628	void initForceField();
219	gezelter	1490
220			void calcRcut( void );
221	gezelter	1650
222	gezelter	1490	private:
223
224			void fastForward( char* stopText, char* searchOwner );
225
226			double eamRcut;
227			};
228
229			class WATER : public ForceFields{
230
231			public:
232	gezelter	1656	WATER();
233	gezelter	1490	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	gezelter	1628	void initForceField();
245	gezelter	1490
246	gezelter	1650
247	gezelter	1490	private:
248
249			void fastForward( char* stopText, char* searchOwner );
250			void sectionSearch( char* secHead, char* stopText, char* searchOwner );
251
252			};
253
254	gezelter	1520	class Shapes_FF : public ForceFields{
255
256			public:
257	gezelter	1650	Shapes_FF() : ForceFields() {};
258	gezelter	1670	Shapes_FF(const string &the_variant) : ForceFields(the_variant) {};
259	gezelter	1520	virtual ~Shapes_FF();
260
261	gezelter	1650	void readParams();
262	gezelter	1520	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	gezelter	1628	void initForceField();
273	gezelter	1520
274	chrisfen	1688	void calcRcut( void );
275
276	gezelter	1650	void parseShapeFile(string shapeFileName, ShapeAtomType* st);
277
278	gezelter	1520	private:
279	gezelter	1650
280			double findLargestContactDistance(ShapeAtomType* st);
281	chrisfen	1688	double findCutoffDistance(ShapeAtomType* st);
282	chrisfen	1646	double shapesRcut;
283	chrisfen	1688	double bigContact;
284	gezelter	1520
285			};
286
287
288	gezelter	1490	#endif
289