#include "random/random.h"
#include "list/list.h"
-
/*
*
* datatypes
/* 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_virial virial; /* virial */
+ double e; /* site energy */
+ double ekin; /* kinetic 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 */
+ 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 {
- 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;
+/* 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 */
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) */
- /* (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 */
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 */
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 */
-} 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_1BP 0x00 /* care about single */
-#define MOLDYN_2BP 0x01 /* 2 body */
-#define MOLDYN_3BP 0x02 /* and 3 body particle pots */
+ double debug; /* debugging stuff, ignore */
-#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 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;
/*
*
- * potential parameter structures
+ * defines
*
*/
-/*
- * harmonic oscillator potential parameter structure
- */
+#define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */
+#define MOLDYN_STAT_PBY 0x02 /* y */
+#define MOLDYN_STAT_PBZ 0x04 /* and z direction */
-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;
+#define MOLDYN_PSCALE 0x08 /* size controlled by piston */
+#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_NONE 0x00
+#define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
+#define T_SCALE_DIRECT 0x02 /* direct t control */
+#define T_SCALE_MASK 0x03
-/*
- *
- * defines
- *
- */
+#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
+ * default values & units
*
* - 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 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
#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"
/*
*
*
*/
-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);
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 bnum,int a,int b,int c);
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,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 get_e_kin(t_moldyn *moldyn);
-double get_e_pot(t_moldyn *moldyn);
+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 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);
+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
+
projects / physik / posic.git / blobdiff