fixed several stupid mistakes

[physik/posic.git] / moldyn.h

diff --git a/moldyn.h b/moldyn.h
index 53a22fd..3016bc4 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -18,14 +18,14 @@ typedef struct s_atom {
        t_3dvec r;      /* positions */
        t_3dvec v;      /* velocities */
        t_3dvec f;      /* forces */
-       t_3dvec dr;     /* delta r for verlet list updates */
        int element;    /* number of element in pse */
        double mass;    /* atom mass */
-       t_list verlet;  /* verlet neighbour list */
 } t_atom;
 
 typedef struct s_linkcell {
+       int listfd;
        int nx,ny,nz;
+       int cells;
        double x,y,z;
        t_list *subcell;
 } t_linkcell;
@@ -38,15 +38,11 @@ typedef struct s_moldyn {
        t_atom *atom;
        t_3dvec dim;
        /* potential, force & parameters */
-       double (*potential)(struct s_moldyn *moldyn);
-       int (*force)(struct s_moldyn *moldyn);
+       int (*potential_force_function)(struct s_moldyn *moldyn);
        void *pot_params;
-       /* cut off radius, verlet list & co */
+       /* cut off radius */
        double cutoff;
        double cutoff_square;
-       double r_verlet;
-       double dr_max1;
-       double dr_max2;
        /* linked list / cell method */
        t_linkcell lc;
        /* temperature */
@@ -55,7 +51,11 @@ typedef struct s_moldyn {
        int (*integrate)(struct s_moldyn *moldyn);
        int time_steps;
        double tau;
+       double tau_square;
+       /* energy */
+       double energy;
        /* logging & visualization */
+       t_visual vis;
        unsigned char lvstat;
        unsigned int ewrite;
        char efb[64];
@@ -74,6 +74,8 @@ typedef struct s_moldyn {
        void *visual;
        /* moldyn general status */
        unsigned char status;
+       /* random */
+       t_random random;
 } t_moldyn;
 
 typedef struct s_ho_params {
@@ -105,8 +107,16 @@ typedef struct s_lj_params {
 
 #define MOLDYN_TEMP                    273.0
 #define MOLDYN_TAU                     1.0e-15
+#define MOLDYN_CUTOFF                  10.0e-9
 #define MOLDYN_RUNS                    1000000
 
+#define MOLDYN_INTEGRATE_VERLET                0x00
+#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
+
+#define MOLDYN_POTENTIAL_HO            0x00
+#define MOLDYN_POTENTIAL_LJ            0x01
+#define MOLDYN_POTENTIAL_DEFAULT MOLDYN_POTENTIAL_LJ
+
 /* phsical values */
 
 #define K_BOLTZMANN            1.3807e-27                      /* Nm/K */
@@ -121,21 +131,22 @@ typedef struct s_lj_params {
 #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_SIGMA_SI            ((0.20*sqrt(3.0)*LC_SI)/1.122462)       /* m */
 #define LJ_EPSILON_SI          (2.1678*1.60e-19)                       /* Nm */
 
 /* function prototypes */
 
 int moldyn_usage(char **argv);
 int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv);
-int moldyn_log_init(t_moldyn *moldyn,void *v);
+int moldyn_log_init(t_moldyn *moldyn);
+int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
 int moldyn_shutdown(t_moldyn *moldyn);
 
 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_moldyn *moldyn,t_random *random,int count);
-int scale_velocity(t_moldyn *moldyn,int count);
+int thermal_init(t_moldyn *moldyn);
+int scale_velocity(t_moldyn *moldyn);
 double get_e_kin(t_atom *atom,int count);
 double get_e_pot(t_moldyn *moldyn);
 double get_total_energy(t_moldyn *moldyn);
@@ -143,19 +154,15 @@ t_3dvec get_total_p(t_atom *atom,int count);
 
 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
 
-int verlet_list_init(t_moldyn *moldyn);
 int link_cell_init(t_moldyn *moldyn);
-int verlet_list_update(t_moldyn *moldyn);
 int link_cell_update(t_moldyn *moldyn);
-int verlet_list_shutdown(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);
 
 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 harmonic_oscillator(t_moldyn *moldyn);
+int lennard_jones(t_moldyn *moldyn);
 
 #endif