#include "math/math.h"
#include "random/random.h"
-//#include "visual/visual.h"
+#include "list/list.h"
-/* datatypes */
+/*
+ *
+ * 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; /* positions */
- t_3dvec v; /* velocities */
- t_3dvec f; /* forces */
- int element; /* number of element in pse */
- double mass; /* atom mass */
- //t_list vicinity /* verlet neighbour list */
+ 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 brand; /* brand id */
+ int tag; /* atom unique id (number of atom) */
+ u8 attr; /* attributes */
} t_atom;
-typedef struct s_moldyn {
+#define ATOM_ATTR_FP 0x01 /* fixed position (bulk material) */
+#define ATOM_ATTR_HB 0x02 /* coupled to heat bath (velocity scaling) */
+
+#define ATOM_ATTR_1BP 0x10 /* single paricle potential */
+#define ATOM_ATTR_2BP 0x20 /* pair potential */
+#define ATOM_ATTR_3BP 0x40 /* 3 body potential */
+
+/* cell lists */
+typedef struct s_linkcell {
+ int nx,ny,nz; /* amount of cells in x, y and z direction */
+ int cells; /* total amount of cells */
+ double len; /* prefered cell edge length */
+ double x,y,z; /* the actual cell lengthes */
+ t_list *subcell; /* pointer to the cell lists */
+ int dnlc; /* direct neighbour lists counter */
+} t_linkcell;
+
+#include "visual/visual.h"
+
+/* moldyn schedule structure */
+typedef struct s_moldyn_schedule {
int count;
- t_atom *atom;
- double (*potential)(struct s_moldyn *moldyn);
+ int total_sched;
+ int *runs;
+ double *tau;
+ int (*hook)(void *moldyn,void *hook_params);
+ void *hook_params;
+} t_moldyn_schedule;
+
+/* moldyn main structure */
+typedef struct s_moldyn {
+ 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);
+ 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);
void *pot_params;
- int (*force)(struct s_moldyn *moldyn);
- double cutoff;
- double cutoff_square;
- t_3dvec dim;
+ unsigned char run3bp;
+
+ double cutoff; /* cutoff radius */
+ double cutoff_square; /* square of the cutoff radius */
+ double nnd; /* nearest neighbour distance (optional) */
+
+ 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 */
+
+ t_virial gvir; /* global virial (absolute coordinates) */
+ double gv;
+ double gv_sum;
+ double gv_avg;
+
+ double gp; /* pressure computed from global virial */
+ double gp_sum; /* sum over all gp */
+ double gp_avg; /* average value of gp */
+
+ double virial; /* actual 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 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 */
+
+ /* pressure and temperature control (velocity/volume scaling) */
+ /* (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 */
+
+ /* simulation schedule */
+ t_moldyn_schedule schedule;
+ int current; /* current position in schedule */
+
+ /* integration function pointer */
int (*integrate)(struct s_moldyn *moldyn);
- int time_steps;
- double tau;
- void *visual;
- int write;
- unsigned char status;
-} t_moldyn;
+ int time_steps; /* amount of iterations */
+ double tau; /* delta t */
+ double time; /* absolute time */
+ double tau_square; /* delta t squared */
+ int total_steps; /* total steps */
+
+ /* energy */
+ double energy; /* potential energy */
+ double ekin; /* kinetic energy */
-typedef struct s_ho_params {
- double spring_constant;
- double equilibrium_distance;
-} t_ho_params;
+ /* 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) */
-typedef struct s_lj_params {
- double sigma6;
- double sigma12;
- double epsilon;
-} t_lj_params;
+ char vlsdir[128]; /* visualization/log/save directory */
+ t_visual vis; /* visualization interface structure */
+ u8 vlsprop; /* log/vis/save properties */
+ unsigned int ewrite; /* how often to log energy */
+ int efd; /* fd for energy log */
+ unsigned int mwrite; /* how often to log momentum */
+ int mfd; /* fd for momentum log */
+ 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 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 */
+
+ double debug; /* debugging stuff, ignore */
+} t_moldyn;
/*
+ *
* defines
+ *
+ */
+
+#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 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 */
+
+/*
+ * 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)
+ *
*/
-/* general defines */
+#define METER 1e10 /* A */
+#define SECOND 1e15 /* fs */
+#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 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_STAT_POTENTIAL 0x01
-#define MOLDYN_STAT_FORCE 0x02
+#define MOLDYN_TEMP 273.0
+#define MOLDYN_TAU 1.0
+#define MOLDYN_CUTOFF 10.0
+#define MOLDYN_RUNS 1000000
-/* phsical values */
+#define MOLDYN_INTEGRATE_VERLET 0x00
+#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
-#define K_BOLTZMANN 1.3807e-27 /* Nm/K */
-#define AMU 1.660540e-27 /* kg */
+#define MOLDYN_POTENTIAL_HO 0x00
+#define MOLDYN_POTENTIAL_LJ 0x01
+#define MOLDYN_POTENTIAL_TM 0x02
-#define FCC 0x01
-#define DIAMOND 0x02
+#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 TRUE 1
+#define FALSE 0
+
+#define VERBOSE 1
+#define QUIET 0
+
+#define SCALE_UP 'u'
+#define SCALE_DOWN 'd'
+#define SCALE_DIRECT 'D'
+
+/*
+ * potential related phsical values / constants
+ *
+ */
+
+#define ONE_THIRD (1.0/3.0)
#define C 0x06
-#define M_C (12.011*AMU)
+#define LC_C 3.567 /* A */
+#define M_C 12.011 /* amu */
#define SI 0x0e
-#define LC_SI 0.543105e-9 /* m */
-#define M_SI (28.085*AMU) /* kg */
-#define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* m */
-#define LJ_EPSILON_SI (2.1678*1.60e-19) /* Nm */
-
-/* function prototypes */
-
-int create_lattice(unsigned char type,int element,double mass,double lc,
- int a,int b,int c,t_atom **atom);
-int destroy_lattice(t_atom *atom);
-int thermal_init(t_atom *atom,t_random *random,int count,double t);
-int scale_velocity(t_atom *atom,int count,double t);
-double get_e_kin(t_atom *atom,int count);
-double get_e_pot(t_moldyn *moldyn);
+#define LC_SI 5.43105 /* A */
+#define M_SI 28.08553 /* 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
+
+
+/*
+ *
+ * function prototypes
+ *
+ */
+
+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_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_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_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,
+ t_3dvec *r,t_3dvec *v);
+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 energy_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_atom *atom,int count);
+t_3dvec get_total_p(t_moldyn *moldyn);
-double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
+double estimate_time_step(t_moldyn *moldyn,double nn_dist);
+
+int link_cell_init(t_moldyn *moldyn,u8 vol);
+int link_cell_update(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,set_hook hook,void *hook_params);
int moldyn_integrate(t_moldyn *moldyn);
int velocity_verlet(t_moldyn *moldyn);
-double potential_harmonic_oscillator(t_moldyn *moldyn);
-int force_harmonic_oscillator(t_moldyn *moldyn);
-double potential_lennard_jones(t_moldyn *moldyn);
-int force_lennard_jones(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);
+//inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
+// __attribute__((always_inline));
+
+int moldyn_bc_check(t_moldyn *moldyn);
+
+int get_line(int fd,char *line,int max);
#endif
projects / physik / posic.git / blobdiff