src/brains/SimSetup.hpp

#ifndef __SIMSETUP_H__
#define __SIMSETUP_H__
#include <string>
#include "utils/StringUtils.hpp"
#include "types/MakeStamps.hpp"
#include "io/Globals.hpp"
#include "UseTheForce/ForceFields.hpp"
#include "brains/SimInfo.hpp"
#include "io/ReadWrite.hpp"
#include "integrators/AllIntegrator.hpp"

using namespace std;
using namespace oopse;
// this routine is defined in BASS_interface.cpp
extern void set_interface_stamps( MakeStamps* ms, Globals* g );

string getPrefix(const string& str );

class SimSetup{

public:
  SimSetup();
  ~SimSetup();

  void setSimInfo( SimInfo* the_info ) { info = the_info; }
  void setSimInfo( SimInfo* the_info, int theNinfo );
  void suspendInit( void ) { initSuspend = true; }  
  void parseFile( char* fileName );
  void createSim( void );

  ForceFields* getForceField() {return the_ff;}
private:

#ifdef IS_MPI
  void receiveParse(void);
#endif

  void gatherInfo( void );
  void sysObjectsCreation( void );
  void finalInfoCheck( void );
  void initSystemCoords( void );
  void makeOutNames(void);
  void makeIntegrator(void);
  void initFortran(void);
  void makeMinimizer(void);

  void createFF( void );
  void compList( void );
  void calcSysValues( void );
  void makeSysArrays( void );

#ifdef IS_MPI
  void mpiMolDivide( void );

  int* mol2proc;
  int* molCompType;

#endif //is_mpi

  void initFromMetaDataFile( void );
  void makeMolecules( void );
  void makeElement( double x, double y, double z );

  int ensembleCase;
  int ffCase;

  MakeStamps* stamps;
  Globals* globals;
  char* inFileName;

  SimInfo* info;
  int isInfoArray;
  int nInfo;
  
  bool initSuspend;

  int n_components;
  int globalAtomCounter;
  int globalMolCounter;

  char force_field[100];
  char forcefield_variant[100];
  char ensemble[100];
  Component** the_components;

  int* components_nmol;
  MoleculeStamp** comp_stamps; //the stamps matching the components
  int tot_nmol;
  int tot_atoms;
  int tot_groups;
  int tot_rigid;
  int tot_bonds;
  int tot_bends;
  int tot_torsions;
  int tot_SRI;

  ForceFields* the_ff;

  // needed by makeElement

  int current_mol;
  int current_comp_mol;
  int current_comp;
  int current_atom_ndx;
  short int has_forcefield_variant;

  vector<int> globalAtomIndex;
  vector<int> globalGroupIndex;
  void setupZConstraint(SimInfo& theInfo);  //setup parameters for zconstraint method

};
#endif
Revision:	99
Committed:	Mon Oct 18 17:07:27 2004 UTC (20 years, 6 months ago) by tim
File size:	2367 byte(s)
Log Message:	fix some bugs in Quaternion class
#	User	Rev	Content
1	gezelter	2	#ifndef __SIMSETUP_H__
2			#define __SIMSETUP_H__
3			#include <string>
4	tim	3	#include "utils/StringUtils.hpp"
5			#include "types/MakeStamps.hpp"
6			#include "io/Globals.hpp"
7			#include "UseTheForce/ForceFields.hpp"
8			#include "brains/SimInfo.hpp"
9			#include "io/ReadWrite.hpp"
10			#include "integrators/AllIntegrator.hpp"
11	gezelter	2
12			using namespace std;
13	tim	99	using namespace oopse;
14	gezelter	2	// this routine is defined in BASS_interface.cpp
15			extern void set_interface_stamps( MakeStamps* ms, Globals* g );
16
17			string getPrefix(const string& str );
18
19			class SimSetup{
20
21			public:
22			SimSetup();
23			~SimSetup();
24
25			void setSimInfo( SimInfo* the_info ) { info = the_info; }
26			void setSimInfo( SimInfo* the_info, int theNinfo );
27			void suspendInit( void ) { initSuspend = true; }
28			void parseFile( char* fileName );
29			void createSim( void );
30
31			ForceFields* getForceField() {return the_ff;}
32			private:
33
34			#ifdef IS_MPI
35			void receiveParse(void);
36			#endif
37
38			void gatherInfo( void );
39			void sysObjectsCreation( void );
40			void finalInfoCheck( void );
41			void initSystemCoords( void );
42			void makeOutNames(void);
43			void makeIntegrator(void);
44			void initFortran(void);
45			void makeMinimizer(void);
46
47			void createFF( void );
48			void compList( void );
49			void calcSysValues( void );
50			void makeSysArrays( void );
51
52			#ifdef IS_MPI
53			void mpiMolDivide( void );
54
55			int* mol2proc;
56			int* molCompType;
57
58			#endif //is_mpi
59
60			void initFromMetaDataFile( void );
61			void makeMolecules( void );
62			void makeElement( double x, double y, double z );
63
64			int ensembleCase;
65			int ffCase;
66
67			MakeStamps* stamps;
68			Globals* globals;
69			char* inFileName;
70
71			SimInfo* info;
72			int isInfoArray;
73			int nInfo;
74
75			bool initSuspend;
76
77			int n_components;
78			int globalAtomCounter;
79			int globalMolCounter;
80
81			char force_field[100];
82			char forcefield_variant[100];
83			char ensemble[100];
84			Component** the_components;
85
86			int* components_nmol;
87			MoleculeStamp** comp_stamps; //the stamps matching the components
88			int tot_nmol;
89			int tot_atoms;
90			int tot_groups;
91			int tot_rigid;
92			int tot_bonds;
93			int tot_bends;
94			int tot_torsions;
95			int tot_SRI;
96
97			ForceFields* the_ff;
98
99			// needed by makeElement
100
101			int current_mol;
102			int current_comp_mol;
103			int current_comp;
104			int current_atom_ndx;
105			short int has_forcefield_variant;
106
107			vector<int> globalAtomIndex;
108			vector<int> globalGroupIndex;
109			void setupZConstraint(SimInfo& theInfo); //setup parameters for zconstraint method
110
111			};
112			#endif