#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 */
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 {
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 */
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 */
double gp_sum; /* sum over all gp */
double gp_avg; /* average value of gp */
- double virial; /* actual virial */
+ t_virial vir; /* actual virial */
+ double virial;
double virial_sum; /* sum over all calculated virials */
double virial_avg; /* average of virial */
double p_sum; /* sum over all p */
double p_avg; /* average value of p */
- t_3dvec tp; /* thermodynamic pressure dU/dV */
- double dv; /* dV for thermodynamic pressure calc */
+ 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.) */
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 */
#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 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
#define FCC 0x02
#define DIAMOND 0x04
-
/*
*
* function prototypes
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);
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 scale_velocity(t_moldyn *moldyn,u8 equi_init);
double virial_sum(t_moldyn *moldyn);
double pressure_calc(t_moldyn *moldyn);
-int energy_fluctuation_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 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 *);
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
+
projects / physik / posic.git / blobdiff