X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=moldyn.h;h=0670f3d19239ada190d6c7d65fd99317392af295;hp=38e4999b696405ea21139fd1b5a7588e290bd03b;hb=HEAD;hpb=c0a8b254109929fba10795e644187c51742108a8 diff --git a/moldyn.h b/moldyn.h index 38e4999..0670f3d 100644 --- a/moldyn.h +++ b/moldyn.h @@ -12,7 +12,6 @@ #include "random/random.h" #include "list/list.h" - /* * * datatypes @@ -22,26 +21,49 @@ /* 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_0; /* initial position */ t_3dvec r; /* position */ t_3dvec v; /* velocity */ t_3dvec f; /* force */ - t_3dvec virial; /* virial (v_xx, v_yy, v_zz) */ + 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 DEFAULT_ATOM_ATTR 0x74 // 1,2,3 body interaction + visualize -#define ATOM_ATTR_1BP 0x10 /* single paricle potential */ -#define ATOM_ATTR_2BP 0x20 /* pair potential */ -#define ATOM_ATTR_3BP 0x40 /* 3 body potential */ +/* 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 { @@ -49,11 +71,17 @@ 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 { @@ -61,28 +89,44 @@ typedef struct s_moldyn_schedule { 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; +/* 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 */ 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; - //int (*potential_force_function)(struct s_moldyn *moldyn); + 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; double cutoff; /* cutoff radius */ double cutoff_square; /* square of the cutoff radius */ @@ -90,11 +134,45 @@ typedef struct s_moldyn { 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 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 */ + double p; /* actual pressure (computed by virial) */ + double px,py,pz; /* components of pressure */ + double p_sum; /* sum over all p */ + 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.) */ @@ -112,11 +190,28 @@ typedef struct s_moldyn { double tau; /* delta t */ double time; /* absolute time */ double tau_square; /* delta t squared */ - double elapsed; /* total elapsed time */ + 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 */ @@ -124,16 +219,92 @@ typedef struct s_moldyn { 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 */ + unsigned int pwrite; /* how often to log pressure */ + 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 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 */ + char rauthor[64]; /* report author */ + int epfd; /* energy gnuplot script file descriptor */ + int ppfd; /* pressure gnuplot script file descriptor */ + int tpfd; /* temperature gnuplot script file descriptor */ u8 status; /* general moldyn properties */ t_random random; /* random interface */ - int debug; /* debugging stuff, ignore */ + 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_STAT_PBX 0x01 /* periodic boudaries in x */ #define MOLDYN_STAT_PBY 0x02 /* y */ #define MOLDYN_STAT_PBZ 0x04 /* and z direction */ @@ -144,119 +315,18 @@ typedef struct s_moldyn { #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 /* - * - * potential parameter structures - * - */ - -/* - * 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; - - - -/* - * - * defines - * - */ - -#define ONE_THIRD (1.0/3.0) - -/* - * default values + * default values & units * * - length unit: 1 A (1 A = 1e-10 m) * - time unit: 1 fs (1 fs = 1e-15 s) @@ -272,7 +342,12 @@ typedef struct s_tersoff_mult_params { #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 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 @@ -285,67 +360,63 @@ typedef struct s_tersoff_mult_params { #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 SAVE_STEP 0x04 -#define VISUAL_STEP 0x08 +#define LOG_PRESSURE 0x04 +#define LOG_TEMPERATURE 0x08 +#define LOG_VOLUME 0x10 +#define SAVE_STEP 0x20 +#define VISUAL_STEP 0x40 +#define CREATE_REPORT 0x80 #define TRUE 1 #define FALSE 0 +#define VERBOSE 1 +#define QUIET 0 + +#define SCALE_UP 'u' +#define SCALE_DOWN 'd' +#define SCALE_DIRECT 'D' + /* - * - * phsical values / constants - * - * + * usefull constants */ -#define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */ -#define EV (1.6021765314e-19*METER*NEWTON) /* NA */ +#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 SI 0x0e -#define LC_SI (0.543105e-9*METER) /* A */ +#define LC_SI 5.43105 /* 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 */ - -#define TM_R_SI (2.7e-10*METER) /* A */ -#define TM_S_SI (3.0e-10*METER) /* A */ -#define TM_A_SI (1830.8*EV) /* NA */ -#define TM_B_SI (471.18*EV) /* NA */ -#define TM_LAMBDA_SI (2.4799e10/METER) /* 1/A */ -#define TM_MU_SI (1.7322e10/METER) /* 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 (1.8e-10*METER) /* A */ -#define TM_S_C (2.1e-10*METER) /* A */ -#define TM_A_C (1393.6*EV) /* NA */ -#define TM_B_C (346.7*EV) /* NA */ -#define TM_LAMBDA_C (3.4879e10/METER) /* 1/A */ -#define TM_MU_C (2.2119e10/METER) /* 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 LC_3C_SIC 4.3596 /* A */ /* - * lattice constants + * lattice types */ -#define FCC 0x01 -#define DIAMOND 0x02 +#define CUBIC 0x01 +#define FCC 0x02 +#define DIAMOND 0x04 +#define ZINCBLENDE 0x08 +#define NONE 0x80 + +/* + * more includes + */ +//#include "pse.h" /* * @@ -353,11 +424,6 @@ typedef struct s_tersoff_mult_params { * */ -typedef int (*pf_func1b)(t_moldyn *,t_atom *ai); -typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8 bc); -typedef int (*pf_func2b_post)(t_moldyn *,t_atom *,t_atom *,u8 bc); -typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8 bc); - int moldyn_init(t_moldyn *moldyn,int argc,char **argv); int moldyn_shutdown(t_moldyn *moldyn); @@ -365,61 +431,120 @@ 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_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,void *params); -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 set_potential(t_moldyn *moldyn,u8 type); + +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); -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 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); +int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z); +int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z); -double get_e_kin(t_moldyn *moldyn); -double get_e_pot(t_moldyn *moldyn); +double e_kin_calc(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); +#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 *); + 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); -inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) - __attribute__((always_inline)); +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); +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 +