#include "random/random.h"
#include "list/list.h"
+#include "report/report.h"
/*
*
/* 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;
/* 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;
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);
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 */
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 */
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
double sigma6;
double sigma12;
double epsilon4;
+ double uc;
} t_lj_params;
/*
double f_a,df_a;
t_3dvec dist_ij;
+ double d_ij2;
double d_ij;
double chi;
/* 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 */
*
*/
+#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 */
#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
#define LOG_TOTAL_MOMENTUM 0x02
#define SAVE_STEP 0x04
#define VISUAL_STEP 0x08
+#define CREATE_REPORT 0x10
#define TRUE 1
#define FALSE 0
*
* phsical values / constants
*
+ *
*/
#define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
#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 */
* lattice constants
*/
-#define FCC 0x01
-#define DIAMOND 0x02
+#define CUBIC 0x01
+#define FCC 0x02
+#define DIAMOND 0x04
/*
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);
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);
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);
projects / physik / posic.git / blobdiff