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 initRestraints();
  virtual void dumpzAngle();

  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 parseShapeFile(string shapeFileName, ShapeAtomType* st);

  void calcRcut( void );

private:

  double findLargestContactDistance(ShapeAtomType* st);
  double shapesRcut;

};


#endif

Revision:	1670
Committed:	Thu Oct 28 16:56:20 2004 UTC (19 years, 8 months ago) by gezelter
Original Path:	*trunk/OOPSE-2.0/src/UseTheForce/ForceFields.hpp*
File size:	5963 byte(s)
Log Message:	fixed duplicate declaration foo
#	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	virtual void initRestraints();
118			virtual void dumpzAngle();
119
120			virtual void calcRcut( void );
121			virtual void setRcut( double LJrcut );
122			virtual void doForces( int calcPot, int calcStress );
123
124			protected:
125
126	gezelter	1628	void initFortran( int useReactionField );
127	chuckv	1617
128	gezelter	1490	FILE *frcFile;
129			SimInfo* entry_plug;
130
131			int lineNum;
132			char readLine[500];
133			char* eof_test;
134			short int has_variant;
135			double bigSigma;
136
137	gezelter	1653	string ffPath;
138	gezelter	1650	ifstrstream forceFile;
139	gezelter	1653	bool hasVariant;
140			string variant;
141	gezelter	1650	map<string, AtomType*> atomTypeMap;
142	gezelter	1653	// map<pair<string,string>, BondType*> bondTypeMap;
143			// map<tuple3<string,string,string>, BendType*> bendTypeMap;
144			// map<tuple4<string,string,string,string>, TorsionType*> torsionTypeMap;
145	gezelter	1650
146	gezelter	1490	};
147
148
149			class DUFF : public ForceFields{
150
151			public:
152	gezelter	1656	DUFF();
153	gezelter	1490	virtual ~DUFF();
154
155			void readParams();
156			void cleanMe( void );
157
158			void initializeAtoms( int nAtoms, Atom** atomArray );
159			void initializeBonds( int nBonds, Bond** bondArray,
160			bond_pair* the_bonds );
161			void initializeBends( int nBends, Bend** bendArray,
162			bend_set* the_bends );
163			void initializeTorsions( int nTorsions, Torsion** torsionArray,
164			torsion_set* the_torsions );
165
166	gezelter	1628	void initForceField();
167	gezelter	1490
168			private:
169
170			void fastForward( char* stopText, char* searchOwner );
171			};
172
173			class LJFF : public ForceFields{
174
175			public:
176	gezelter	1656	LJFF();
177	gezelter	1490	virtual ~LJFF();
178
179
180			void readParams();
181			void cleanMe( void );
182
183			void initializeAtoms( int nAtoms, Atom** atomArray );
184			void initializeBonds( int nBonds, Bond** bondArray,
185			bond_pair* the_bonds );
186			void initializeBends( int nBends, Bend** bendArray,
187			bend_set* the_bends );
188			void initializeTorsions( int nTorsions, Torsion** torsionArray,
189			torsion_set* the_torsions );
190
191	gezelter	1628	void initForceField( );
192	gezelter	1490
193	gezelter	1650
194	gezelter	1490	private:
195
196			void fastForward( char* stopText, char* searchOwner );
197
198			};
199
200			class EAM_FF : public ForceFields{
201
202			public:
203	gezelter	1656
204			EAM_FF();
205	gezelter	1670	EAM_FF(const string &theVariant);
206	gezelter	1656
207	gezelter	1490	virtual ~EAM_FF();
208
209			void readParams();
210			void cleanMe( void );
211
212			void initializeAtoms( int nAtoms, Atom** atomArray );
213			void initializeBonds( int nBonds, Bond** bondArray,
214			bond_pair* the_bonds );
215			void initializeBends( int nBends, Bend** bendArray,
216			bend_set* the_bends );
217			void initializeTorsions( int nTorsions, Torsion** torsionArray,
218			torsion_set* the_torsions );
219
220	gezelter	1628	void initForceField();
221	gezelter	1490
222			void calcRcut( void );
223	gezelter	1650
224	gezelter	1490	private:
225
226			void fastForward( char* stopText, char* searchOwner );
227
228			double eamRcut;
229			};
230
231			class WATER : public ForceFields{
232
233			public:
234	gezelter	1656	WATER();
235	gezelter	1490	virtual ~WATER();
236
237			void readParams();
238			void cleanMe( void );
239			void initializeAtoms( int nAtoms, Atom** atomArray );
240			void initializeBonds( int nBonds, Bond** bondArray,
241			bond_pair* the_bonds );
242			void initializeBends( int nBends, Bend** bendArray,
243			bend_set* the_bends );
244			void initializeTorsions( int nTorsions, Torsion** torsionArray,
245			torsion_set* the_torsions );
246	gezelter	1628	void initForceField();
247	gezelter	1490
248	gezelter	1650
249	gezelter	1490	private:
250
251			void fastForward( char* stopText, char* searchOwner );
252			void sectionSearch( char* secHead, char* stopText, char* searchOwner );
253
254			};
255
256	gezelter	1520	class Shapes_FF : public ForceFields{
257
258			public:
259	gezelter	1650	Shapes_FF() : ForceFields() {};
260	gezelter	1670	Shapes_FF(const string &the_variant) : ForceFields(the_variant) {};
261	gezelter	1520	virtual ~Shapes_FF();
262
263	gezelter	1650	void readParams();
264	gezelter	1520	void cleanMe( void );
265
266			void initializeAtoms( int nAtoms, Atom** atomArray );
267			void initializeBonds( int nBonds, Bond** bondArray,
268			bond_pair* the_bonds );
269			void initializeBends( int nBends, Bend** bendArray,
270			bend_set* the_bends );
271			void initializeTorsions( int nTorsions, Torsion** torsionArray,
272			torsion_set* the_torsions );
273
274	gezelter	1628	void initForceField();
275	gezelter	1520
276	gezelter	1650	void parseShapeFile(string shapeFileName, ShapeAtomType* st);
277
278	gezelter	1520	void calcRcut( void );
279	chrisfen	1646
280	gezelter	1520	private:
281	gezelter	1650
282			double findLargestContactDistance(ShapeAtomType* st);
283	chrisfen	1646	double shapesRcut;
284	gezelter	1520
285			};
286
287
288	gezelter	1490	#endif
289