X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=484c45605529657c396d12fad349dff7f05c24a7;hb=58fd691b276fbe87593036714f26dbfe7486cbeb;hp=f2ccdb56343c9522efc5db74f3b976f0d91a0083;hpb=91e4a00285261865ffce4b9553d153b562c80ee6;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index f2ccdb5..484c456 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -84,14 +84,16 @@ typedef struct s_moldyn {
 
 	/* potential force function and parameter pointers */
 	int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
-	void *pot1b_params;
 	int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
-	int (*func2b_post)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
-	void *pot2b_params;
-	int (*func3b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,
-	              u8 bck);
-	void *pot3b_params;
-	//int (*potential_force_function)(struct s_moldyn *moldyn);
+	int (*func3b_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+	int (*func3b_j2)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+	int (*func3b_j3)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+	int (*func3b_k1)(struct s_moldyn *moldyn,
+	                 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+	int (*func3b_k2)(struct s_moldyn *moldyn,
+	                 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+	void *pot_params;
+	unsigned char run3bp;
 
 	double cutoff;		/* cutoff radius */
 	double cutoff_square;	/* square of the cutoff radius */
@@ -101,9 +103,21 @@ typedef struct s_moldyn {
 
 	double t_ref;		/* reference temperature */
 	double t;		/* actual temperature */
+	double t_sum;		/* sum over all t */
+	double mean_t;		/* mean value of t */
+
+	t_virial virial;	/* global virial (absolute coordinates) */
+	double gp;		/* pressure computed from global virial */
+	double gp_sum;		/* sum over all gp */
+	double mean_gp;		/* mean value of gp */
+
+	double mean_v;		/* mean of virial */
+	double virial_sum;	/* sum over all calculated virials */
 
 	double p_ref;		/* reference pressure */
 	double p;		/* actual pressure (computed by virial) */
+	double p_sum;		/* sum over all p */
+	double mean_p;		/* mean value of p */
 	t_3dvec tp;		/* thermodynamic pressure dU/dV */
 	double dv;		/* dV for thermodynamic pressure calc */
 
@@ -123,11 +137,24 @@ typedef struct s_moldyn {
 	double tau;		/* delta t */
 	double time;		/* absolute time */
 	double tau_square;	/* delta t squared */
-	double elapsed;		/* total elapsed time */
+	int total_steps;	/* total steps */
 
+	/* energy */
 	double energy;		/* potential energy */
 	double ekin;		/* kinetic energy */
 
+	/* energy averages & fluctuations */
+	double k_m;
+	double p_m;
+	double t_m;
+	double dk2_m;		/* mean square kinetic energy fluctuations */
+	double dp2_m;		/* mean square potential energy fluctuations */
+	double dt2_m;		/* mean square fluctuations in total energy */
+	
+	/* response functions */
+	double c_v_nve;		/* constant volume heat capacity (nve) */
+	double c_v_nvt;		/* constant volume heat capacity (nvt) */
+
 	char vlsdir[128];	/* visualization/log/save directory */
 	t_visual vis;		/* visualization interface structure */
 	u8 vlsprop;		/* log/vis/save properties */
@@ -135,12 +162,18 @@ typedef struct s_moldyn {
 	int efd;		/* fd for energy log */
 	unsigned int mwrite;	/* how often to log momentum */
 	int mfd;		/* fd for momentum log */
+	unsigned int pwrite;	/* how often to log pressure */
+	int pfd;		/* fd for pressure log */
+	unsigned int twrite;	/* how often to log temperature */
+	int tfd;		/* fd for temperature log */
 	unsigned int vwrite;	/* how often to visualize atom information */
 	unsigned int swrite;	/* how often to create a save file */
 	int rfd;		/* report file descriptor */
 	char rtitle[64];	/* report title */
 	char rauthor[64];	/* report author */
-	int pfd;		/* gnuplot script file descriptor */
+	int epfd;		/* energy gnuplot script file descriptor */
+	int ppfd;		/* pressure gnuplot script file descriptor */
+	int tpfd;		/* temperature gnuplot script file descriptor */
 
 	u8 status;		/* general moldyn properties */
 
@@ -149,6 +182,12 @@ typedef struct s_moldyn {
 	double debug;		/* debugging stuff, ignore */
 } t_moldyn;
 
+/*
+ *
+ *  defines
+ *
+ */
+
 #define MOLDYN_STAT_PBX			0x01	/* periodic boudaries in x */
 #define MOLDYN_STAT_PBY			0x02	/* y */
 #define MOLDYN_STAT_PBZ			0x04	/* and z direction */
@@ -165,116 +204,7 @@ typedef struct s_moldyn {
 #define P_SCALE_DIRECT			0x08	/* direct p control */
 
 /*
- *
- * potential parameter structures
- *
- */
-
-/*
- * harmonic oscillator potential parameter structure
- */
-
-typedef struct s_ho_params {
-	double spring_constant;
-	double equilibrium_distance;
-} t_ho_params;
-
-/*
- * lennard jones potential parameter structure
- */
-
-typedef struct s_lj_params {
-	double sigma6;
-	double sigma12;
-	double epsilon4;
-	double uc;
-} t_lj_params;
-
-/*
- * tersoff 
- */
-
-/* tersoff exchange structure to exchange 2bp and 3bp calculated values */
-typedef struct s_tersoff_exchange {
-	double f_c,df_c;
-	double f_a,df_a;
-
-	t_3dvec dist_ij;
-	double d_ij2;
-	double d_ij;
-
-	double chi;
-
-	double *beta_i;
-	double *beta_j;
-	double *n_i;
-	double *n_j;
-	double *c_i;
-	double *c_j;
-	double *d_i;
-	double *d_j;
-	double *h_i;
-	double *h_j;
-
-	double ci2;
-	double cj2;
-	double di2;
-	double dj2;
-	double ci2di2;
-	double cj2dj2;
-	double betaini;
-	double betajnj;
-
-	u8 run3bp;
-	u8 run2bp_post;
-	u8 d_ij_between_rs;
-
-	double zeta_ij;
-	double zeta_ji;
-	t_3dvec dzeta_ij;
-	t_3dvec dzeta_ji;
-} t_tersoff_exchange;
-
-/* tersoff mult (2!) potential parameters */
-typedef struct s_tersoff_mult_params {
-	double S[2];		/* tersoff cutoff radii */
-	double S2[2];		/* tersoff cutoff radii squared */
-	double R[2];		/* tersoff cutoff radii */
-	double Smixed;		/* mixed S radius */
-	double S2mixed;		/* mixed S radius squared */
-	double Rmixed;		/* mixed R radius */
-	double A[2];		/* factor of tersoff attractive part */
-	double B[2];		/* factor of tersoff repulsive part */
-	double Amixed;		/* mixed A factor */
-	double Bmixed;		/* mixed B factor */
-	double lambda[2];	/* tersoff lambda */
-	double lambda_m;	/* mixed lambda */
-	double mu[2];		/* tersoff mu */
-	double mu_m;		/* mixed mu */
-
-	double chi;
-
-	double beta[2];
-	double n[2];
-	double c[2];
-	double d[2];
-	double h[2];
-
-	t_tersoff_exchange exchange;	/* exchange between 2bp and 3bp calc */
-} t_tersoff_mult_params;
-
-
-
-/*
- *
- *  defines
- *
- */
-
-#define ONE_THIRD	(1.0/3.0)
-
-/*
- * default values
+ * default values & units
  *
  * - length unit: 1 A (1 A = 1e-10 m)
  * - time unit: 1 fs (1 fs = 1e-15 s)
@@ -290,7 +220,11 @@ typedef struct s_tersoff_mult_params {
 #define KILOGRAM			(1.0/AMU)		/* amu */
 #define NEWTON	(METER*KILOGRAM/(SECOND*SECOND))	/* A amu / fs^2 */
 #define PASCAL	(NEWTON/(METER*METER))			/* N / A^2 */
-#define ATM	((1.0133e5*PASCAL))			/* N / A^2 */
+#define BAR	((1.0e5*PASCAL))			/* N / A^2 */
+#define K_BOLTZMANN	(1.380650524e-23*METER*NEWTON)	/* NA/K */
+#define K_B2		(K_BOLTZMANN*K_BOLTZMANN)	/* (NA)^2/K^2 */
+#define EV		(1.6021765314e-19*METER*NEWTON)	/* NA */
+#define JOULE		(NEWTON*METER)			/* NA */
 
 #define MOLDYN_TEMP			273.0
 #define MOLDYN_TAU			1.0
@@ -306,9 +240,11 @@ typedef struct s_tersoff_mult_params {
 
 #define LOG_TOTAL_ENERGY		0x01
 #define LOG_TOTAL_MOMENTUM		0x02
-#define SAVE_STEP			0x04
-#define VISUAL_STEP			0x08
-#define CREATE_REPORT			0x10
+#define LOG_PRESSURE			0x04
+#define LOG_TEMPERATURE			0x08
+#define SAVE_STEP			0x10
+#define VISUAL_STEP			0x20
+#define CREATE_REPORT			0x40
 
 #define TRUE				1
 #define FALSE				0
@@ -316,45 +252,50 @@ typedef struct s_tersoff_mult_params {
 #define VERBOSE				1
 #define QUIET				0
 
+#define SCALE_UP			'u'
+#define SCALE_DOWN			'd'
+#define SCALE_DIRECT			'D'
+
 /*
- *
- * phsical values / constants
- *
+ * potential related phsical values / constants
  *
  */
 
-#define K_BOLTZMANN		(1.380650524e-23*METER*NEWTON)	/* NA/K */
-#define EV			(1.6021765314e-19*METER*NEWTON)	/* NA */
+#define ONE_THIRD		(1.0/3.0)
 
 #define C			0x06
+#define LC_C			3.567				/* A */
 #define M_C			12.011				/* amu */
 
 #define SI			0x0e
-#define LC_SI			(0.543105e-9*METER)		/* A */
+#define LC_SI			5.43105				/* A */
 #define M_SI			28.08553			/* amu */
 
-//#define LJ_SIGMA_SI		((0.25*sqrt(3.0)*LC_SI)/1.122462)	/* A */
-#define LJ_SIGMA_SI		(LC_SI/1.122462)			/* A */
+#define LC_3C_SIC		4.3596				/* A */
+
+#define LJ_SIGMA_SI		((0.25*sqrt(3.0)*LC_SI)/1.122462)	/* A */
+//#define LJ_SIGMA_SI		(LC_SI/1.122462)			/* A */
+//#define LJ_SIGMA_SI		(0.5*sqrt(2.0)*LC_SI/1.122462)		/* A */
 #define LJ_EPSILON_SI		(2.1678*EV)				/* NA */
 
-#define TM_R_SI			(2.7e-10*METER)			/* A */
-#define TM_S_SI			(3.0e-10*METER)			/* A */
+#define TM_R_SI			2.7				/* A */
+#define TM_S_SI			3.0				/* A */
 #define TM_A_SI			(1830.8*EV)			/* NA */
 #define TM_B_SI			(471.18*EV)			/* NA */
-#define TM_LAMBDA_SI		(2.4799e10/METER)		/* 1/A */
-#define TM_MU_SI		(1.7322e10/METER)		/* 1/A */
+#define TM_LAMBDA_SI		2.4799				/* 1/A */
+#define TM_MU_SI		1.7322				/* 1/A */
 #define TM_BETA_SI		1.1000e-6
 #define TM_N_SI			0.78734
 #define TM_C_SI			1.0039e5
 #define TM_D_SI			16.217
 #define TM_H_SI			-0.59825
 
-#define TM_R_C			(1.8e-10*METER)			/* A */
-#define TM_S_C			(2.1e-10*METER)			/* A */
+#define TM_R_C			1.8				/* A */
+#define TM_S_C			2.1				/* A */
 #define TM_A_C			(1393.6*EV)			/* NA */
 #define TM_B_C			(346.7*EV)			/* NA */
-#define TM_LAMBDA_C		(3.4879e10/METER)		/* 1/A */
-#define TM_MU_C			(2.2119e10/METER)		/* 1/A */
+#define TM_LAMBDA_C		3.4879				/* 1/A */
+#define TM_MU_C			2.2119				/* 1/A */
 #define TM_BETA_C		1.5724e-7
 #define TM_N_C			0.72751
 #define TM_C_C			3.8049e4
@@ -363,8 +304,53 @@ typedef struct s_tersoff_mult_params {
 
 #define TM_CHI_SIC		0.9776
 
+#define TM_LC_3C_SIC		(0.432e-9*METER)		/* A */
+
+#define ALBE_R_SI		(2.82-0.14)
+#define ALBE_S_SI		(2.82+0.14)
+#define ALBE_A_SI		(3.24*EV/0.842)
+#define ALBE_B_SI		(1.842*3.24*EV/0.842)
+#define ALBE_R0_SI		2.232
+#define ALBE_LAMBDA_SI		(1.4761*sqrt(2.0*1.842))
+#define ALBE_MU_SI		(1.4761*sqrt(2.0/1.842))
+#define ALBE_GAMMA_SI		0.114354
+#define ALBE_C_SI		2.00494
+#define ALBE_D_SI		0.81472
+#define ALBE_H_SI		0.259
+
+#define LC_SI_ALBE		5.429
+
+#define ALBE_R_C		(2.00-0.15)
+#define ALBE_S_C		(2.00+0.15)
+#define ALBE_A_C		(6.00*EV/1.167)
+#define ALBE_B_C		(2.167*6.00*EV/1.167)
+#define ALBE_R0_C		1.4276
+#define ALBE_LAMBDA_C		(2.0099*sqrt(2.0*2.167))
+#define ALBE_MU_C		(2.0099*sqrt(2.0/2.167))
+#define ALBE_GAMMA_C		0.11233
+#define ALBE_C_C		181.910
+#define ALBE_D_C		6.28433
+#define ALBE_H_C		0.5556
+
+#define LC_C_ALBE		3.566
+
+#define ALBE_R_SIC		(2.40-0.20)
+#define ALBE_S_SIC		(2.40+0.10)
+#define ALBE_A_SIC		(4.36*EV/0.847)
+#define ALBE_B_SIC		(1.847*4.36*EV/0.847)
+#define ALBE_R0_SIC		1.79
+#define ALBE_LAMBDA_SIC		(1.6991*sqrt(2.0*1.847))
+#define ALBE_MU_SIC		(1.6991*sqrt(2.0/1.847))
+#define ALBE_GAMMA_SIC		0.011877
+#define ALBE_C_SIC		273987
+#define ALBE_D_SIC		180.314
+#define ALBE_H_SIC		0.68
+
+#define LC_SIC_ALBE		4.359
+
+
 /*
- * lattice constants
+ * lattice types
  */
 
 #define CUBIC			0x01
@@ -378,10 +364,9 @@ typedef struct s_tersoff_mult_params {
  *
  */
 
-typedef int (*pf_func1b)(t_moldyn *,t_atom *ai);
-typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8 bc);
-typedef int (*pf_func2b_post)(t_moldyn *,t_atom *,t_atom *,u8 bc);
-typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8 bc);
+typedef int (*pf_func1b)(t_moldyn *,t_atom *);
+typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8);
+typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8);
 
 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
 int moldyn_shutdown(t_moldyn *moldyn);
@@ -394,10 +379,14 @@ int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
 int set_nn_dist(t_moldyn *moldyn,double dist);
 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
-int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params);
-int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params);
-int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params);
-int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params);
+int set_potential1b(t_moldyn *moldyn,pf_func1b func);
+int set_potential2b(t_moldyn *moldyn,pf_func2b func);
+int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func);
+int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func);
+int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func);
+int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func);
+int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func);
+int set_potential_params(t_moldyn *moldyn,void *params);
 
 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
@@ -405,7 +394,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
 int moldyn_log_shutdown(t_moldyn *moldyn);
 
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
-                   u8 attr,u8 brand,int a,int b,int c);
+                   u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin);
 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
@@ -421,11 +410,10 @@ double pressure_calc(t_moldyn *moldyn);
 double thermodynamic_pressure_calc(t_moldyn *moldyn);
 double get_pressure(t_moldyn *moldyn);
 int scale_volume(t_moldyn *moldyn);
-int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z);
-int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z);
+int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
+int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
 
-double get_e_kin(t_moldyn *moldyn);
-double update_e_kin(t_moldyn *moldyn);
+double e_kin_calc(t_moldyn *moldyn);
 double get_total_energy(t_moldyn *moldyn);
 t_3dvec get_total_p(t_moldyn *moldyn);
 
@@ -445,18 +433,17 @@ int moldyn_integrate(t_moldyn *moldyn);
 int velocity_verlet(t_moldyn *moldyn);
 
 int potential_force_calc(t_moldyn *moldyn);
-inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
-	__attribute__((always_inline));
-inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
-	__attribute__((always_inline));
-int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
-int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
-int tersoff_mult_complete_params(t_tersoff_mult_params *p);
-int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai);
-int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
-int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
-int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
+int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d);
+//inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
+//	__attribute__((always_inline));
+int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
+//inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
+//	__attribute__((always_inline));
 
 int moldyn_bc_check(t_moldyn *moldyn);
 
+int get_line(int fd,char *line,int max);
+int calc_fluctuations(double start,double end,t_moldyn *moldyn);
+int get_heat_capacity(t_moldyn *moldyn);
+
 #endif