X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=13009982133b83e9df47ca46c8b690e84f2dc005;hb=296a35b943e922173ce648ec76a4472e287af108;hp=a2223c0345472043779822c5aa80883c2665b464;hpb=d9e7f195bbb219ad4c2de0e5f54d023ef9e669fb;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index a2223c0..1300998 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -12,7 +12,6 @@
 #include "random/random.h"
 #include "list/list.h"
 
-
 /*
  * 
  * datatypes
@@ -22,14 +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_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 +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;
 
@@ -67,16 +80,15 @@ 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);
-	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;
+	void *pot_params;
 	//int (*potential_force_function)(struct s_moldyn *moldyn);
 
 	double cutoff;		/* cutoff radius */
@@ -89,9 +101,12 @@ 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) */
+	/* (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 */
@@ -111,141 +126,47 @@ typedef struct s_moldyn {
 	double energy;		/* potential energy */
 	double ekin;		/* kinetic energy */
 
-	t_visual vis;		/* visualization/log/save interface structure */
-	u8 lvstat;		/* log & vis properties */
+	char vlsdir[128];	/* visualization/log/save directory */
+	t_visual vis;		/* visualization interface structure */
+	u8 vlsprop;		/* log/vis/save properties */
 	unsigned int ewrite;	/* how often to log energy */
 	int efd;		/* fd for energy log */
 	unsigned int mwrite;	/* how often to log momentum */
 	int mfd;		/* fd for momentum log */
 	unsigned int vwrite;	/* how often to visualize atom information */
-	char vfb[64];		/* visualization file name base */
-	//void *visual;		/* pointer (hack!) */
 	unsigned int swrite;	/* how often to create a save file */
-	char sfb[64];		/* visualization file name base */
+	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 */
 
 	t_random random;	/* random interface */
 
-	int debug;		/* debugging stuff, ignore */
+	double 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_1BP			0x00	/* care about single */
-#define MOLDYN_2BP			0x01	/* 2 body */
-#define MOLDYN_3BP			0x02	/* 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
+ *  defines
  *
  */
 
-/*
- * 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;
-} 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_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 multi (2!) potential parameters */
-typedef struct s_tersoff_mult_params {
-	double S[2];		/* tersoff cutoff radii */
-	double R[2];		/* tersoff cutoff radii */
-	double Smixed;		/* mixed S radius */
-	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;
+#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			0x10	/* care about single */
+#define MOLDYN_2BP			0x20	/* 2 body */
+#define MOLDYN_3BP			0x40	/* and 3 body particle pots */
 
-/*
- *
- *  defines
- *
- */
+#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 */
 
 /*
  * default values
@@ -253,6 +174,9 @@ typedef struct s_tersoff_mult_params {
  * - 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 */
@@ -260,6 +184,8 @@ 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
@@ -277,16 +203,23 @@ 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
 
+#define VERBOSE				1
+#define QUIET				0
+
 /*
  *
  * phsical values / constants
  *
+ *
  */
 
+#define ONE_THIRD		(1.0/3.0)
+
 #define K_BOLTZMANN		(1.380650524e-23*METER*NEWTON)	/* NA/K */
 #define EV			(1.6021765314e-19*METER*NEWTON)	/* NA */
 
@@ -296,7 +229,10 @@ 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_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 */
@@ -329,8 +265,9 @@ typedef struct s_tersoff_mult_params {
  * lattice constants
  */
 
-#define FCC			0x01
-#define DIAMOND			0x02
+#define CUBIC			0x01
+#define FCC			0x02
+#define DIAMOND			0x04
 
 
 /*
@@ -350,6 +287,7 @@ 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);
@@ -359,45 +297,58 @@ 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 moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer);
+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);
 
 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
 
-int link_cell_init(t_moldyn *moldyn);
+int link_cell_init(t_moldyn *moldyn,u8 vol);
 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 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);
-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);
+//inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
+//	__attribute__((always_inline));
 
 int moldyn_bc_check(t_moldyn *moldyn);