X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=c5cc064cedc85c1cd417b8b65a7f20fb74c44311;hb=15b4727e1137600f8f46af027aefd2b5c7a56420;hp=9493f5fa9a6bea4986149dd1cc10ffae334015b1;hpb=9c2172b5fce9688fa6be8d8a30745f9ef0b31419;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index 9493f5f..c5cc064 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -22,12 +22,22 @@
 /* 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 (v_xx, v_yy, v_zz) */
+	t_virial virial;	/* virial */
 	double e;		/* site energy */
 	int element;		/* number of element in pse */
 	double mass;		/* atom mass */
@@ -57,7 +67,8 @@ 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);
@@ -71,6 +82,7 @@ typedef struct s_moldyn {
 
 	t_3dvec dim;		/* dimensions of the simulation volume */
 	double volume;		/* volume of sim cell (dim.x*dim.y*dim.z) */
+	double vt1,vt2;
 
 	/* potential force function and parameter pointers */
 	int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
@@ -172,6 +184,7 @@ typedef struct s_lj_params {
 	double sigma6;
 	double sigma12;
 	double epsilon4;
+	double uc;
 } t_lj_params;
 
 /*
@@ -184,6 +197,7 @@ typedef struct s_tersoff_exchange {
 	double f_a,df_a;
 
 	t_3dvec dist_ij;
+	double d_ij2;
 	double d_ij;
 
 	double chi;
@@ -221,8 +235,10 @@ 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 */
@@ -309,6 +325,7 @@ 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 */
 
@@ -386,11 +403,15 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 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 get_pressure(t_moldyn *moldyn);
 int scale_volume(t_moldyn *moldyn);
 
 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);
 
@@ -408,9 +429,10 @@ 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);