cdsubs.h

一个很好的分子动力学程序

#ifndef __CDSUBS_H
#define __CDSUBS_H

/*
************************************************************************
Includes
************************************************************************
*/

#include <stdio.h>
#include "particle.h"


/*
************************************************************************
Defines
************************************************************************
*/

#define FALSE 0
#define TRUE  1


#define NFILE 10
#define NPL 	20 	/*  INITIAL MAXIMUM NUMBER OF PARTICLES			*/
#define NGL   100 	/*  INITIAL MAXIMUM LENGTH OF NEIGHBOR LIST		*/
#define NTYPE 10	  /*	MAXIMUM NUMBER OF PARTICLE TYPES 	*/
#define NSTR  256

/*  BOLTZMANN'S CONSTANT (IN ergs/K)  */
#define BK		 1.38e-16
/*  1/BK  */
#define K		 7.246377e15
/*  Atoms per mole  */
#define AVAG	 6.022e23
/*  Cm per Angstom  */
#define ANGS	 1.0e-8
/*  Angstroms per Cm  */
#define CM		 1.0e+8
/*  Ergs to Joules  */
#define JOULE	 1.0e-7
/*  Ergs to Electron Volts  */
#define EV		 6.24196e11
/*  Ergs to Hartrees  */
#define HARTREE (1.0/4.3596e-11)

/*  erg/cm^3 to MBAR */
#define MBAR 1e-12


/*  Constraint types  */
#define CONSTR_LINE  0
#define CONSTR_PLANE 1

/*
************************************************************************
Type Definitions
************************************************************************
*/

/*  Structure for printing output every n steps  */
typedef struct
	{
	char	  FileName[80];
	FILE	 *File;
	BOOLEAN Save;
	BOOLEAN IsFileNew;
	int	  StepIncrement;
	int	  CurrentStep;
	}
	StepOutput_t;

/*  SIMULATION CONTROL	*/
typedef struct
{
	double tempc, cutoff, cutmin, uratio, size;
	double dtime, cstep;
	int	 nrej, nacc, nstep;
	int	 quench, echo;
	char	 eulabel[20];
	double eunit;
	unsigned seed;

	/*  esave flag and file */
#if 0
	char	 ename[80];
	int	 eflag, estep, eistep, efilenew;
#endif

	/*  Periodic Step Output  */
	StepOutput_t EnergyStepOutput;
	StepOutput_t BoxStepOutput;
	StepOutput_t StressStepOutput;
	StepOutput_t TrajectoryStepOutput;

	/*  force, integrate and energy subroutine pointers  */
	void	 *forcepnt;
	void   *energylistpnt;
	void   *FreePotPtr;

	/*  Debug flag  */
	int	 debug;

	/*  Stop signal  */
	int	 signal;

	/*  Potential Name  */
	char	 pottype[10];

	/*  Compare Info	*/
	BOOLEAN UseCompare;
	BOOLEAN UseInverseCompare;
	BOOLEAN NewCompareFile;
	char	  CompareFileName[NSTR];
	double  CompareRadius;
	double  CompareEnergy;

	/*  Calculate stress of selected atoms only  */
	BOOLEAN UseSelectStress;

	/*  Have WRITE ?? commands omitt comments in output stream  */
   BOOLEAN UseVerboseOutputFile;

	/*  Shut off non-critical messages like *** NUMBER SELECT  */
	BOOLEAN PrintInfo;

	}
	Simulation_t;

/*  Function type for passing algorithm routines (through simulation)  */
typedef void PotFree_f   (void);
typedef void PotForce_f  (Particle_t *, Simulation_t * );
typedef void PotEnergy_f (Particle_t *, Simulation_t *, int);



/*
************************************************************************
Function Prototypes
************************************************************************
*/

void	  initrand (unsigned);
double  randfloat(void	);
void	  init(void);

/* 27 Mar 1992 - replaced with call to sortfx in sortsub.c	*/
/*
void	  sort (double *, int *, int, int);
*/

#if 0
double  sqr (double);
void	  copy_coord (int, double *, double *);
#endif

void    PrintWrapWarning(int);
void	  energy_all	  (Particle_t *, Simulation_t *, int);
void	  runmc			  (Particle_t *, Simulation_t *, int, double);
void	  runcmd 		  (Particle_t *, Simulation_t *, int		  );

/*  Kinetic Energy (from cdmd.c)  */
void CalcKineticEnergy     (Particle_t *, Simulation_t *);
double GetTemperature      (Particle_t *, Simulation_t *, BOOLEAN );
double GetKE               (Particle_t *, Simulation_t *, BOOLEAN );

/*  Simulation Statistics  */
long	  GetNumberOfMDSteps(void);
double  GetElapsedMDTime (void);
long	  GetNumNeighborSearchCalls (void);
double  GetElapsedNeighborSearchTime (void);

/*  STATE FUNCTIONS	*/
void	  writestate	  (Particle_t *, Simulation_t *, char *);
int	  readstate 	  (Particle_t **, Simulation_t *, char *);
void dumpstate  (char *);

/*  Quartic Potential Routines  */
void	  qu_energy_list (Particle_t *, Simulation_t *, int);
void	  qu_calcforc	  (Particle_t *, Simulation_t * );
void	  qu_read_potential (char *, char *);
/*  Tersoff Potential Routines  */
void	  csi_energy_list (Particle_t *, Simulation_t *, int);
void	  csi_calcforc	  (Particle_t *, Simulation_t * );
void	  csi_read_potential (char *, char *);
/*  Stillinger-Weber Potential Routines  */
void	  stil_energy_list (Particle_t *, Simulation_t *, int);
void	  stil_calcforc	  (Particle_t *, Simulation_t * );
void	  stil_read_potential (char *, char *);
void    STILL_Parse         (char *);
void    STILL_Init          (char *);
/*  EAM	Potential Routines  */
void	  em_energy_list (Particle_t *, Simulation_t *, int);
void	  em_calcforc	  (Particle_t *, Simulation_t * );
void	  em_read_potential (char *, char *);
/*  PAIR Potential Routines  */
void	  pr_energy_list (Particle_t *, Simulation_t *, int);
void	  pr_calcforc	  (Particle_t *, Simulation_t * );
void	  pr_read_potential (char *, char *);
/*  ION	Potential Routines  */
void	  io_energy_list (Particle_t *, Simulation_t *, int);
void	  io_calcforc	  (Particle_t *, Simulation_t * );
void	  io_read_potential (char *, char *);

void	read_command	(char *, int *);
int	GetNumberOfCommandErrors (void);
int	GetNumberOfWarnings		 (void);
void	IncrementNumberOfWarnings(void);


/*  Vector functions  */
#if 0
double GetMagnitude(double [NDIR]);
double GetDot      (double [NDIR], double [NDIR]);
void   Normalize   (double [NDIR]);
void   CalcCross   (double [NDIR], double [NDIR], double [NDIR]);
void   Orthogonalize (double [NDIR], double [NDIR]);
#endif

void	read_allocate	(char *);
void	read_bond		(char *);
void	read_box 		(char *);
void	read_bsave		(char *);
void	read_calc		(char *);
void	read_clamp		(char *);
void	read_cmd 		(char *);
void	read_compare	(char *);
void	read_constrain (char *);
void	read_cor 		(char *);
void	read_damp 	 	(char *);
void	read_debug		(char *);
void	read_disp		(char *);
void	read_dtime		(char *);
void	read_dup 		(char *);
void	read_echo		(char *);
void	read_erase		(char *);
void	read_esave		(char *);
void	read_eunit		(char *);
void	read_extforce	(char *);
void	read_extspring (char *);
void	read_fill 		(char *);
void	read_fix 		(char *);
void	read_itemp		(char *);
void	read_label		(char *);
void  read_macro     (char *);
void  read_macrof    (char *);
void	read_mass		(char *);
void	read_mc			(char *);
void	read_move		(char *);
void	read_nrange 	(char *);
void	read_particle	(char *);
void	read_posvel   	(char *);
void	read_potential (char *);
void	read_pressure 	(char *);
void	read_pstrain	(char *);
void	read_quench 	(char *);
void	read_rcv 		(char *);
void	read_read		(char *);
void	read_refstep	(char *);
void	read_remove 	(char *);
void	read_repeat 	(char *);
void	read_rotate 	(char *);
void	read_run 		(char *);
void	read_scale		(char *);
void	read_screw		(char *);
void	read_seed		(char *);
void	read_select 	(char *);
void	read_set 		(char *);
void	read_size		(char *);
void	read_ssave		(char *);
void	read_state		(char *);
void	read_step		(char *);
void	read_surface	(char *);
void	read_velocity	(char *);
void	read_tag 		(char *);
void	read_tsave		(char *);
void	read_type		(char *);
void	read_typelist	(char *);
void	read_typename	(char *);
void  read_verbose   (char *);
void	read_wave 		(char *);
void	read_write		(char *);

void	error_msg		(int, char *);

void x					(char *, ...);

void CheckForNoneSelected(void);

/*  Function for including atom coordinates symbollically  */
void EvaluateFormula
(
char   *InputFormula,
double *InputValues,
double  InputConversion,
double *OutputValues,
double  OutputConversion,
int     NumOutput
);

void UpdateNeighborList(Particle_t *);

void AddMacro (char *, char *);
void ReplaceMacro (char *OutputStr, int MaxLen);

int  GetTotalDOF (Particle_t *);

#endif