X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=83b3a86d8f41c6560cfe4d829523976dfac3fb6f;hb=a32468230b319b32819f1b20fd28aa9659574d45;hp=5160668f5379b72a1cee78db4aa31f7ca381299c;hpb=92ef07d77a4c879527180224acea73a3f6564497;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index 5160668..83b3a86 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -33,11 +33,13 @@ typedef struct s_virial {
 
 /* the atom of the md simulation */
 typedef struct s_atom {
+	t_3dvec r_0;		/* initial position */
 	t_3dvec r;		/* position */
 	t_3dvec v;		/* velocity */
 	t_3dvec f;		/* force */
 	t_virial virial;	/* virial */
 	double e;		/* site energy */
+	double ekin;		/* kinetic energy */
 	int element;		/* number of element in pse */
 	double mass;		/* atom mass */
 	u8 brand;		/* brand id */
@@ -47,6 +49,8 @@ typedef struct s_atom {
 
 #define ATOM_ATTR_FP	0x01	/* fixed position (bulk material) */
 #define ATOM_ATTR_HB	0x02	/* coupled to heat bath (velocity scaling) */
+#define ATOM_ATTR_VA	0x04	/* visualize this atom */
+#define ATOM_ATTR_VB	0x08	/* visualize the bond of this atom */
 
 #define ATOM_ATTR_1BP		0x10	/* single paricle potential */
 #define ATOM_ATTR_2BP		0x20	/* pair potential */
@@ -58,11 +62,15 @@ typedef struct s_linkcell {
 	int cells;		/* total amount of cells */
 	double len;		/* prefered cell edge length */
 	double x,y,z;		/* the actual cell lengthes */
+#ifdef STATIC_LISTS
+	int **subcell;		/* pointer to the cell lists */
+#else
 	t_list *subcell;	/* pointer to the cell lists */
+#endif
 	int dnlc;		/* direct neighbour lists counter */
 } t_linkcell;
 
-#include "visual/visual.h"
+#define MAX_ATOMS_PER_LIST	20
 
 /* moldyn schedule structure */
 typedef struct s_moldyn_schedule {
@@ -74,9 +82,20 @@ typedef struct s_moldyn_schedule {
 	void *hook_params;
 } t_moldyn_schedule;
 
+/* visualization structure */
+typedef struct s_visual {
+	int fd;			/* rasmol script file descriptor */
+	char fb[128];		/* basename of the save files */
+	t_3dvec dim;		/* dimensions of the simulation cell */
+} t_visual;
+
 /* moldyn main structure */
 typedef struct s_moldyn {
+	int argc;		/* number of arguments */
+	char **args;		/* pointer to arguments */
+
 	int count;		/* total amount of atoms */
+	double mass;		/* total system mass */
 	t_atom *atom;		/* pointer to the atoms */
 
 	t_3dvec dim;		/* dimensions of the simulation volume */
@@ -98,28 +117,40 @@ typedef struct s_moldyn {
 	double cutoff;		/* cutoff radius */
 	double cutoff_square;	/* square of the cutoff radius */
 	double nnd;		/* nearest neighbour distance (optional) */
+	double bondlen[3];	/* bond lengthes (only 2 atomic systems) */
 
 	t_linkcell lc;		/* linked cell list interface */
 
+	int avg_skip;		/* amount of steps without average calc */
+
 	double t_ref;		/* reference temperature */
 	double t;		/* actual temperature */
 	double t_sum;		/* sum over all t */
-	double mean_t;		/* mean value of t */
+	double t_avg;		/* average value of t */
+
+	t_virial gvir;		/* global virial (absolute coordinates) */
+	double gv;
+	double gv_sum;
+	double gv_avg;
 
-	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 gp_avg;		/* average value of gp */
 
-	double mean_v;		/* mean of virial */
+	t_virial vir;		/* actual virial */
+	double virial;
 	double virial_sum;	/* sum over all calculated virials */
+	double virial_avg;	/* average of virial */
 
 	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 */
+	double p_avg;		/* average value of p */
+
+	double tp;		/* thermodynamic pressure dU/dV */
+	double tp_sum;		/* sum over dU/dV pressure */
+	double tp_avg;		/* average value of dU/dV pressure */
+	int tp_cnt;		/* how often to do thermodynamic p calc */
 
 	/* pressure and temperature control (velocity/volume scaling) */
 	/* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
@@ -139,9 +170,26 @@ typedef struct s_moldyn {
 	double tau_square;	/* delta t squared */
 	int total_steps;	/* total steps */
 
+	/* energy */
 	double energy;		/* potential energy */
 	double ekin;		/* kinetic energy */
 
+	/* energy averages & fluctuations */
+	double k_sum;		/* sum of kinetic energy */
+	double v_sum;		/* sum of potential energy */
+	double k_avg;		/* average of kinetic energy */
+	double v_avg;		/* average of potential energy */
+	double k2_sum;		/* sum of kinetic energy squared */
+	double v2_sum;		/* sum of potential energy squared */
+	double k2_avg;		/* average of kinetic energy squared */
+	double v2_avg;		/* average of potential energy squared */
+	double dk2_avg;		/* mean square kinetic energy fluctuations */
+	double dv2_avg;		/* mean square potential energy fluctuations */
+	
+	/* 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 */
@@ -153,7 +201,9 @@ typedef struct s_moldyn {
 	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 vwrite;	/* how often to log volume */
+	int vfd;		/* fd for volume log */
+	unsigned int awrite;	/* 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 */
@@ -207,9 +257,12 @@ typedef struct s_moldyn {
 #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 GPA	(1e9*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
@@ -227,9 +280,10 @@ typedef struct s_moldyn {
 #define LOG_TOTAL_MOMENTUM		0x02
 #define LOG_PRESSURE			0x04
 #define LOG_TEMPERATURE			0x08
-#define SAVE_STEP			0x10
-#define VISUAL_STEP			0x20
-#define CREATE_REPORT			0x40
+#define LOG_VOLUME			0x10
+#define SAVE_STEP			0x20
+#define VISUAL_STEP			0x40
+#define CREATE_REPORT			0x80
 
 #define TRUE				1
 #define FALSE				0
@@ -289,12 +343,12 @@ typedef struct s_moldyn {
 
 #define TM_CHI_SIC		0.9776
 
-#define TM_LC_3C_SIC		(0.432e-9*METER)		/* A */
+#define TM_LC_SIC		4.32				/* 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_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))
@@ -303,12 +357,12 @@ typedef struct s_moldyn {
 #define ALBE_D_SI		0.81472
 #define ALBE_H_SI		0.259
 
-#define LC_SI_ALBE		5.429
+#define ALBE_LC_SI		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_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))
@@ -317,12 +371,12 @@ typedef struct s_moldyn {
 #define ALBE_D_C		6.28433
 #define ALBE_H_C		0.5556
 
-#define LC_C_ALBE		3.566
+#define ALBE_LC_C		3.566
 
 #define ALBE_R_SIC		(2.40-0.20)
-#define ALBE_S_SIC		(2.40+0.10)
+#define ALBE_S_SIC		(2.40+0.20)
 #define ALBE_A_SIC		(4.36*EV/0.847)
-#define ALBE_B_SIC		(1.847*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))
@@ -331,7 +385,7 @@ typedef struct s_moldyn {
 #define ALBE_D_SIC		180.314
 #define ALBE_H_SIC		0.68
 
-#define LC_SIC_ALBE		4.359
+#define ALBE_LC_SIC		4.359
 
 
 /*
@@ -342,7 +396,6 @@ typedef struct s_moldyn {
 #define FCC			0x02
 #define DIAMOND			0x04
 
-
 /*
  *
  * function prototypes
@@ -358,6 +411,7 @@ 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_bondlen(t_moldyn *moldyn,double b0,double b1,double bm);
 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);
@@ -373,6 +427,8 @@ 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 set_avg_skip(t_moldyn *moldyn,int skip);
+
 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);
@@ -380,18 +436,24 @@ 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,t_3dvec *origin);
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
+             t_3dvec *r,t_3dvec *v);
+int del_atom(t_moldyn *moldyn,int tag);
 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 total_mass_calc(t_moldyn *moldyn);
 double temperature_calc(t_moldyn *moldyn);
 double get_temperature(t_moldyn *moldyn);
 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
+double virial_sum(t_moldyn *moldyn);
 double pressure_calc(t_moldyn *moldyn);
+int average_reset(t_moldyn *moldyn);
+int average_and_fluctuation_calc(t_moldyn *moldyn);
+int get_heat_capacity(t_moldyn *moldyn);
 double thermodynamic_pressure_calc(t_moldyn *moldyn);
 double get_pressure(t_moldyn *moldyn);
 int scale_volume(t_moldyn *moldyn);
@@ -406,7 +468,11 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist);
 
 int link_cell_init(t_moldyn *moldyn,u8 vol);
 int link_cell_update(t_moldyn *moldyn);
+#ifdef STATIC_LISTS
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell);
+#else
 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
+#endif
 int link_cell_shutdown(t_moldyn *moldyn);
 
 typedef int (*set_hook)(void *,void *);
@@ -427,4 +493,16 @@ int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
 
 int moldyn_bc_check(t_moldyn *moldyn);
 
+int moldyn_read_save_file(t_moldyn *moldyn,char *file);
+int moldyn_load(t_moldyn *moldyn);
+int get_line(int fd,char *line,int max);
+
+int pair_correlation_init(t_moldyn *moldyn,double dr);
+int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc);
+int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr);
+
+int visual_init(t_moldyn *moldyn,char *filebase);
+int visual_atoms(t_moldyn *moldyn);
+
 #endif
+