/* 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 */
int tag; /* atom unique id (number of atom) */
u8 attr; /* attributes */
+ int pbc[3]; /* pb crossing in x, y and z direction */
} t_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 */ // TODO
+#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 */
+#define ATOM_ATTR_3BP 0x40 /* 3 body potential */
-#define ATOM_ATTR_1BP 0x10 /* single paricle potential */
-#define ATOM_ATTR_2BP 0x20 /* pair potential */
-#define ATOM_ATTR_3BP 0x40 /* 3 body potential */
+#define DEFAULT_ATOM_ATTR 0x74 // 1,2,3 body interaction + visualize
+
+/* special list structure for low mem approach */
+typedef struct s_lowmem_list {
+ int *head;
+ int *list;
+} t_lowmem_list;
/* cell lists */
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 */
+#elif LOWMEM_LISTS
+ t_lowmem_list *subcell; /* low mem approach list */
+#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 */
+ char **args; /* pointer to arguments */
+
int count; /* total amount of atoms */
double mass; /* total system mass */
t_atom *atom; /* pointer to the atoms */
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);
- int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
- int (*func3b_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
- int (*func3b_j2)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
- int (*func3b_j3)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
- int (*func3b_k1)(struct s_moldyn *moldyn,
- t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
- int (*func3b_k2)(struct s_moldyn *moldyn,
- t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+ int (*func_i0)(struct s_moldyn *moldyn,t_atom *ai);
+ int (*func_j0)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func_j0_k0)(struct s_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+ int (*func_j0e)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func_j1_k0)(struct s_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+ int (*func_j1c)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func_j1_k1)(struct s_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+ int (*func_j1e)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
void *pot_params;
unsigned char run3bp;
t_linkcell lc; /* linked cell list interface */
- int mean_skip; /* amount of steps without average calc */
+ 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 */
-
- 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 mean_v; /* mean of virial */
+ double t_avg; /* average value of t */
+
+ /* for sale! */
+ t_virial gvir; /* global virial (absolute coordinates) */
+ //double gv;
+ //double gv_sum;
+ //double gv_avg;
+ double sale1;
+ double sale2;
+ double sale3;
+
+ // gp stuff exchanged by kinetic energies
+ //double gp; /* pressure computed from global virial */
+ //double gp_sum; /* sum over all gp */
+ //double gp_avg; /* average value of gp */
+ double ekinx;
+ double ekiny;
+ double ekinz;
+
+ 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 px,py,pz; /* components of pressure */
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.) */
/* energy averages & fluctuations */
double k_sum; /* sum of kinetic energy */
double v_sum; /* sum of potential energy */
- double k_mean; /* average of kinetic energy */
- double v_mean; /* average 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_mean; /* average of kinetic energy squared */
- double v2_mean; /* average of potential energy squared */
- double dk2_mean; /* mean square kinetic energy fluctuations */
- double dv2_mean; /* mean square potential energy fluctuations */
+ 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) */
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 */
t_random random; /* random interface */
double debug; /* debugging stuff, ignore */
+
+ /* potential 2 body check function */
+ int (*check_2b_bond)(struct s_moldyn *moldyn,
+ t_atom *itom,t_atom *jtom,u8 bc);
} t_moldyn;
+typedef struct s_pcc {
+ int o1;
+ int o2;
+ double dr;
+ double *stat;
+} t_pcc;
+
+typedef struct s_ba {
+ int *acnt;
+ int *bcnt;
+ int tcnt;
+} t_ba;
+
+typedef struct s_vb {
+ int fd;
+} t_vb;
+
+typedef struct s_part_params {
+ u8 type;
+ double r;
+ t_3dvec p;
+ t_3dvec d;
+} t_part_params;
+
+#define PART_INSIDE_R 1
+#define PART_OUTSIDE_R 2
+#define PART_INSIDE_D 3
+#define PART_OUTSIDE_D 4
+
+typedef struct s_defect_params {
+ u8 type;
+ u8 stype;
+ double od;
+ double dd;
+ int element;
+ u8 brand;
+ u8 attr;
+} t_defect_params;
+
+#define DEFECT_TYPE_0D 1
+#define DEFECT_TYPE_1D 2
+#define DEFECT_TYPE_2D 3
+#define DEFECT_TYPE_3D 4
+
+#define DEFECT_STYPE_DB_X 1
+#define DEFECT_STYPE_DB_Y 2
+#define DEFECT_STYPE_DB_Z 3
+#define DEFECT_STYPE_DB_R 4
+
+typedef struct s_offset_params {
+ t_3dvec o;
+ u8 use;
+} t_offset_params;
+
/*
*
* defines
#define MOLDYN_2BP 0x20 /* 2 body */
#define MOLDYN_3BP 0x40 /* and 3 body particle pots */
+#define T_SCALE_NONE 0x00
#define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
#define T_SCALE_DIRECT 0x02 /* direct t control */
+#define T_SCALE_MASK 0x03
+
+#define P_SCALE_NONE 0x00
#define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
#define P_SCALE_DIRECT 0x08 /* direct p control */
+#define P_SCALE_MASK 0x0c
/*
* default values & units
#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 MOLDYN_POTENTIAL_HO 0x00
#define MOLDYN_POTENTIAL_LJ 0x01
#define MOLDYN_POTENTIAL_TM 0x02
+#define MOLDYN_POTENTIAL_AM 0x03
+#define MOLDYN_POTENTIAL_AO 0x04
#define LOG_TOTAL_ENERGY 0x01
#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 SCALE_DIRECT 'D'
/*
- * potential related phsical values / constants
- *
+ * usefull constants
*/
#define ONE_THIRD (1.0/3.0)
+/*
+ * element specific defines
+ */
+
#define C 0x06
#define LC_C 3.567 /* A */
#define M_C 12.011 /* amu */
#define LC_3C_SIC 4.3596 /* 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 2.7 /* A */
-#define TM_S_SI 3.0 /* A */
-#define TM_A_SI (1830.8*EV) /* NA */
-#define TM_B_SI (471.18*EV) /* NA */
-#define TM_LAMBDA_SI 2.4799 /* 1/A */
-#define TM_MU_SI 1.7322 /* 1/A */
-#define TM_BETA_SI 1.1000e-6
-#define TM_N_SI 0.78734
-#define TM_C_SI 1.0039e5
-#define TM_D_SI 16.217
-#define TM_H_SI -0.59825
-
-#define TM_R_C 1.8 /* A */
-#define TM_S_C 2.1 /* A */
-#define TM_A_C (1393.6*EV) /* NA */
-#define TM_B_C (346.7*EV) /* NA */
-#define TM_LAMBDA_C 3.4879 /* 1/A */
-#define TM_MU_C 2.2119 /* 1/A */
-#define TM_BETA_C 1.5724e-7
-#define TM_N_C 0.72751
-#define TM_C_C 3.8049e4
-#define TM_D_C 4.384
-#define TM_H_C -0.57058
-
-#define TM_CHI_SIC 0.9776
-
-#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_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))
-#define ALBE_GAMMA_SI 0.114354
-#define ALBE_C_SI 2.00494
-#define ALBE_D_SI 0.81472
-#define ALBE_H_SI 0.259
-
-#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_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))
-#define ALBE_GAMMA_C 0.11233
-#define ALBE_C_C 181.910
-#define ALBE_D_C 6.28433
-#define ALBE_H_C 0.5556
-
-#define ALBE_LC_C 3.566
-
-#define ALBE_R_SIC (2.40-0.20)
-#define ALBE_S_SIC (2.40+0.10)
-#define ALBE_A_SIC (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))
-#define ALBE_GAMMA_SIC 0.011877
-#define ALBE_C_SIC 273987
-#define ALBE_D_SIC 180.314
-#define ALBE_H_SIC 0.68
-
-#define ALBE_LC_SIC 4.359
-
-
/*
* lattice types
*/
#define CUBIC 0x01
#define FCC 0x02
#define DIAMOND 0x04
+#define ZINCBLENDE 0x08
+#define NONE 0x80
+
+/*
+ * more includes
+ */
+//#include "pse.h"
/*
*
*
*/
-typedef int (*pf_func1b)(t_moldyn *,t_atom *);
-typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8);
-typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8);
-
int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
int moldyn_shutdown(t_moldyn *moldyn);
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_p_scale(t_moldyn *moldyn,u8 ptype,double ptc);
+int set_t_scale(t_moldyn *moldyn,u8 ttype,double ttc);
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_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
-int set_potential1b(t_moldyn *moldyn,pf_func1b func);
-int set_potential2b(t_moldyn *moldyn,pf_func2b func);
-int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func);
-int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func);
-int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func);
-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_potential(t_moldyn *moldyn,u8 type);
-int set_mean_skip(t_moldyn *moldyn,int skip);
+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);
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 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,
+int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
+ u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin,
+ t_part_params *p_params,t_defect_params *d_params,
+ t_offset_params *o_params);
+int add_atom(t_moldyn *moldyn,int element,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,
+ t_part_params *p_params,t_defect_params *d_params);
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+ t_part_params *p_params,t_defect_params *d_params);
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+ t_part_params *p_params,t_defect_params *d_params);
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 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);
+#elif LOWMEM_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 *);
//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 check_per_bound_and_care_for_pbc(t_moldyn *moldyn,t_atom *a);
//inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
// __attribute__((always_inline));
int moldyn_bc_check(t_moldyn *moldyn);
+int moldyn_read_save_file(t_moldyn *moldyn,char *file);
+int moldyn_free_save_file(t_moldyn *moldyn);
+int moldyn_load(t_moldyn *moldyn);
+int process_2b_bonds(t_moldyn *moldyn,void *data,
+ int (*process)(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+ void *data,u8 bc));
+int process_neighbours(t_moldyn *moldyn,void *data,t_atom *atom,
+ int (*process)(t_moldyn *moldyn,t_atom *atom,t_atom *natom,
+ void *data,u8 bc));
+
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_msd(t_moldyn *moldyn,double *msd);
+int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
+ t_atom *jtom,void *data,u8 bc);
+int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr);
+int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+ void *data,u8 bc);
+int bond_analyze(t_moldyn *moldyn,double *quality);
+
+int visual_init(t_moldyn *moldyn,char *filebase);
+int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+ void *data,u8 bc);
+#ifdef VISUAL_THREAD
+void *visual_atoms(void *ptr);
+#else
+int visual_atoms(t_moldyn *moldyn);
#endif
+
+int fpu_set_rtd(void);
+
+#endif
+
projects / physik / posic.git / blobdiff