X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=7329099471555c62dfc7aec3fe37d2be387be34d;hb=f3e4193447ac49a8953515910d4b4e6ce2c7608b;hp=72ff30bdfb00ab876cce6261360b827298c77043;hpb=1d83ceb2ce2ff5150fd079f1066b7f583e38c8f4;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index 72ff30b..7329099 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -12,6 +12,7 @@
 #include "random/random.h"
 #include "list/list.h"
 
+#include "report/report.h"
 
 /*
  * 
@@ -22,14 +23,27 @@
 /* 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_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;
 
@@ -54,10 +68,11 @@ 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;
 
@@ -67,6 +82,7 @@ typedef struct s_moldyn {
 	t_atom *atom;		/* pointer to the atoms */
 
 	t_3dvec dim;		/* dimensions of the simulation volume */
+	double volume;		/* volume of sim cell (dim.x*dim.y*dim.z) */
 
 	/* potential force function and parameter pointers */
 	int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
@@ -89,10 +105,12 @@ 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) */
-	/* (in units of tau!) */
+	/* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
 	unsigned char pt_scale;	/* type of p and t scaling */
 	double t_tc;		/* t berendsen control time constant */
 	double p_tc;		/* p berendsen control time constant */
@@ -121,6 +139,10 @@ 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 */
 
@@ -129,20 +151,21 @@ typedef struct s_moldyn {
 	int debug;		/* debugging stuff, ignore */
 } t_moldyn;
 
-#define MOLDYN_STAT_PBX			0x08	/* periodic boudaries in x */
-#define MOLDYN_STAT_PBY			0x10	/* y */
-#define MOLDYN_STAT_PBZ			0x20	/* and z direction */
+#define MOLDYN_STAT_PBX			0x01	/* periodic boudaries in x */
+#define MOLDYN_STAT_PBY			0x02	/* y */
+#define MOLDYN_STAT_PBZ			0x04	/* and z direction */
+
+#define MOLDYN_PSCALE			0x08	/* size controlled by piston */
 
-#define MOLDYN_1BP			0x00	/* care about single */
-#define MOLDYN_2BP			0x01	/* 2 body */
-#define MOLDYN_3BP			0x02	/* and 3 body particle pots */
+#define MOLDYN_1BP			0x10	/* care about single */
+#define MOLDYN_2BP			0x20	/* 2 body */
+#define MOLDYN_3BP			0x40	/* and 3 body particle pots */
 
 #define T_SCALE_BERENDSEN		0x01	/* berendsen t control */
 #define T_SCALE_DIRECT			0x02	/* direct t control */
 #define P_SCALE_BERENDSEN		0x04	/* berendsen p control */
 #define P_SCALE_DIRECT			0x08	/* direct p control */
 
-
 /*
  *
  * potential parameter structures
@@ -166,6 +189,7 @@ typedef struct s_lj_params {
 	double sigma6;
 	double sigma12;
 	double epsilon4;
+	double uc;
 } t_lj_params;
 
 /*
@@ -178,6 +202,7 @@ typedef struct s_tersoff_exchange {
 	double f_a,df_a;
 
 	t_3dvec dist_ij;
+	double d_ij2;
 	double d_ij;
 
 	double chi;
@@ -215,8 +240,10 @@ 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 */
@@ -246,12 +273,17 @@ typedef struct s_tersoff_mult_params {
  *
  */
 
+#define ONE_THIRD	(1.0/3.0)
+
 /*
  * default values
  *
  * - length unit: 1 A (1 A = 1e-10 m)
  * - time unit: 1 fs (1 fs = 1e-15 s)
  * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg )
+ *
+ * fyi: in the following 1 N = (amu*A)/(fs*fs)
+ *
  */
 
 #define METER				1e10			/* A */
@@ -259,6 +291,8 @@ typedef struct s_tersoff_mult_params {
 #define AMU				1.6605388628e-27	/* kg */
 #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 MOLDYN_TEMP			273.0
 #define MOLDYN_TAU			1.0
@@ -276,6 +310,7 @@ 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
@@ -284,6 +319,7 @@ typedef struct s_tersoff_mult_params {
  *
  * phsical values / constants
  *
+ *
  */
 
 #define K_BOLTZMANN		(1.380650524e-23*METER*NEWTON)	/* NA/K */
@@ -295,6 +331,7 @@ 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 */
 
@@ -328,8 +365,9 @@ typedef struct s_tersoff_mult_params {
  * lattice constants
  */
 
-#define FCC			0x01
-#define DIAMOND			0x02
+#define CUBIC			0x01
+#define FCC			0x02
+#define DIAMOND			0x04
 
 
 /*
@@ -349,6 +387,7 @@ int moldyn_shutdown(t_moldyn *moldyn);
 int set_int_alg(t_moldyn *moldyn,u8 algo);
 int set_cutoff(t_moldyn *moldyn,double cutoff);
 int set_temperature(t_moldyn *moldyn,double t_ref);
+int set_pressure(t_moldyn *moldyn,double p_ref);
 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);
@@ -359,20 +398,32 @@ 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);
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
+                   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 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);
 
@@ -383,14 +434,19 @@ 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);
-int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
+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);