X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=69cee96951e8ccf5ebe016ab0a9bd9086cb492a9;hb=4871747c5c848e5881bea7949a41ceb589263841;hp=c01bc9f6e5e81da8cca4ca56c8206ea21e4aed81;hpb=785f05e0c0ddb57428dc71b0a3f7798673799871;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index c01bc9f..69cee96 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -12,7 +12,6 @@
 #include "random/random.h"
 #include "list/list.h"
 
-
 /*
  * 
  * datatypes
@@ -22,15 +21,27 @@
 /* general */
 typedef unsigned char u8;
 
+/* virial */
+typedef struct s_virial {
+	double xx;	/*			| xx	 xy	xz |	*/
+	double yy;	/*	V	=	| yx	 yy	yz |	*/
+	double zz;	/*			| zx	 zy	zz |	*/
+	double xy;	/*						*/
+	double xz;	/*	with:	xy=yx, xz=zx, yz=zy		*/
+	double yz;	/*						*/
+} t_virial;
+
 /* the atom of the md simulation */
 typedef struct s_atom {
 	t_3dvec r;		/* position */
 	t_3dvec v;		/* velocity */
 	t_3dvec f;		/* force */
-	t_3dvec virial;		/* virial */
+	t_virial virial;	/* virial */
+	double e;		/* site energy */
 	int element;		/* number of element in pse */
 	double mass;		/* atom mass */
-	u8 bnum;		/* brand number */
+	u8 brand;		/* brand id */
+	int tag;		/* atom unique id (number of atom) */
 	u8 attr;		/* attributes */
 } t_atom;
 
@@ -55,10 +66,11 @@ typedef struct s_linkcell {
 
 /* moldyn schedule structure */
 typedef struct s_moldyn_schedule {
-	int content_count;
+	int count;
+	int total_sched;
 	int *runs;
 	double *tau;
-	int (*hook)(void *moldyn,void *hook);
+	int (*hook)(void *moldyn,void *hook_params);
 	void *hook_params;
 } t_moldyn_schedule;
 
@@ -91,7 +103,9 @@ typedef struct s_moldyn {
 	double t;		/* actual temperature */
 
 	double p_ref;		/* reference pressure */
-	double p;		/* actual pressure */
+	double p;		/* actual pressure (computed by virial) */
+	t_3dvec tp;		/* thermodynamic pressure dU/dV */
+	double dv;		/* dV for thermodynamic pressure calc */
 
 	/* pressure and temperature control (velocity/volume scaling) */
 	/* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
@@ -123,6 +137,10 @@ typedef struct s_moldyn {
 	int mfd;		/* fd for momentum 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 */
 
 	u8 status;		/* general moldyn properties */
 
@@ -146,7 +164,6 @@ typedef struct s_moldyn {
 #define P_SCALE_BERENDSEN		0x04	/* berendsen p control */
 #define P_SCALE_DIRECT			0x08	/* direct p control */
 
-
 /*
  *
  * potential parameter structures
@@ -170,6 +187,7 @@ typedef struct s_lj_params {
 	double sigma6;
 	double sigma12;
 	double epsilon4;
+	double uc;
 } t_lj_params;
 
 /*
@@ -182,6 +200,7 @@ typedef struct s_tersoff_exchange {
 	double f_a,df_a;
 
 	t_3dvec dist_ij;
+	double d_ij2;
 	double d_ij;
 
 	double chi;
@@ -219,8 +238,10 @@ typedef struct s_tersoff_exchange {
 /* tersoff multi (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 */
@@ -287,6 +308,7 @@ typedef struct s_tersoff_mult_params {
 #define LOG_TOTAL_MOMENTUM		0x02
 #define SAVE_STEP			0x04
 #define VISUAL_STEP			0x08
+#define CREATE_REPORT			0x10
 
 #define TRUE				1
 #define FALSE				0
@@ -307,6 +329,7 @@ typedef struct s_tersoff_mult_params {
 #define SI			0x0e
 #define LC_SI			(0.543105e-9*METER)		/* A */
 #define M_SI			28.08553			/* amu */
+
 #define LJ_SIGMA_SI		((0.25*sqrt(3.0)*LC_SI)/1.122462)	/* A */
 #define LJ_EPSILON_SI		(2.1678*EV)				/* NA */
 
@@ -340,8 +363,9 @@ typedef struct s_tersoff_mult_params {
  * lattice constants
  */
 
-#define FCC			0x01
-#define DIAMOND			0x02
+#define CUBIC			0x01
+#define FCC			0x02
+#define DIAMOND			0x04
 
 
 /*
@@ -372,23 +396,32 @@ 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 moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
+int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
 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 bnum,int a,int b,int c);
+                   u8 attr,u8 brand,int a,int b,int c);
+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);
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
              t_3dvec *r,t_3dvec *v);
 int destroy_atoms(t_moldyn *moldyn);
 
 int thermal_init(t_moldyn *moldyn,u8 equi_init);
+double temperature_calc(t_moldyn *moldyn);
+double get_temperature(t_moldyn *moldyn);
 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
+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);
 
 double get_e_kin(t_moldyn *moldyn);
-double get_e_pot(t_moldyn *moldyn);
+double update_e_kin(t_moldyn *moldyn);
 double get_total_energy(t_moldyn *moldyn);
 t_3dvec get_total_p(t_moldyn *moldyn);
 
@@ -399,16 +432,19 @@ int link_cell_update(t_moldyn *moldyn);
 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
 int link_cell_shutdown(t_moldyn *moldyn);
 
+typedef int (*set_hook)(void *,void *);
+
 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
-int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params);
+int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params);
 
 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 check_per_bound(t_moldyn *moldyn,t_3dvec *a);
 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);