more changes ...

diff --git a/moldyn.c b/moldyn.c
index 14ae320..8b80242 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -56,10 +56,6 @@ int moldyn_usage(char **argv) {
 int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
 
        int i;
-       t_ho_params hop;
-       t_lj_params ljp;
-       t_tersoff_params tp;
-       double s,e;
 
        memset(moldyn,0,sizeof(t_moldyn));
 
@@ -68,7 +64,6 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
        moldyn->tau=MOLDYN_TAU;
        moldyn->time_steps=MOLDYN_RUNS;
        moldyn->integrate=velocity_verlet;
-       moldyn->potential_force_function=lennard_jones;
 
        /* parse argv */
        for(i=1;i<argc;i++) {
@@ -562,7 +557,7 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 
 int moldyn_integrate(t_moldyn *moldyn) {
 
-       int i;
+       int i,sched;
        unsigned int e,m,s,d,v;
        t_3dvec p;
 
@@ -591,6 +586,12 @@ int moldyn_integrate(t_moldyn *moldyn) {
        /* calculate initial forces */
        moldyn->potential_force_function(moldyn);
 
+       for(sched=0;sched<moldyn->schedule.content_count;sched++) {
+               moldyn->tau=;
+               moldyn->tau_square=;
+
+       // hier weiter ...
+
        for(i=0;i<moldyn->time_steps;i++) {
 
                /* integration step */

diff --git a/moldyn.h b/moldyn.h
index 0a6b4f2..1df6dfa 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -13,12 +13,16 @@
 #include "list/list.h"
 
 
-/* datatypes */
+/*
+ * 
+ * datatypes
+ *
+ */
 
+/* general */
 typedef unsigned char u8;
 
 /* the atom of the md simulation */
-
 typedef struct s_atom {
        t_3dvec r;              /* position */
        t_3dvec v;              /* velocity */
@@ -37,7 +41,6 @@ typedef struct s_atom {
 #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 */
@@ -50,10 +53,17 @@ typedef struct s_linkcell {
 
 #include "visual/visual.h"
 
-# moldyn structure */
+# moldyn schedule structure */
+typedef struct s_moldyn_schedule {
+       int content_count;
+       int *runs;
+       int *tau;
+       int (*hook)(t_moldyn *,void *);
+       void *hook_params;
+} t_moldyn_schedule;
 
+/* moldyn main structure */
 typedef struct s_moldyn {
-
        int count;              /* total amount of atoms */
        t_atom *atom;           /* pointer to the atoms */
 
@@ -75,16 +85,21 @@ typedef struct s_moldyn {
 
        double t;               /* temperature */
 
+       /* simulation schedule */
+       t_moldyn_schedule schedule;
+       int current;            /* current position in schedule */
+
        /* integration function pointer */
        int (*integrate)(struct s_moldyn *moldyn);
        int time_steps;         /* amount of iterations */
        double tau;             /* delta t */
        double tau_square;      /* delta t squared */
+       double elapsed;         /* total elapsed time */
 
        double energy;          /* energy */
 
        t_visual vis;           /* visualization/log/save interface structure */
-       u8 lvstat;      /* log & vis properties */
+       u8 lvstat;              /* log & vis properties */
        unsigned int ewrite;    /* how often to log energy */
        char efb[64];           /* energy log filename */
        int efd;                /* fd for energy log */
@@ -96,7 +111,7 @@ typedef struct s_moldyn {
        void *visual;           /* pointer (hack!) */
        unsigned int swrite;    /* how often to create a save file */
 
-       u8 status;      /* general moldyn properties */
+       u8 status;              /* general moldyn properties */
 
        t_random random;        /* random interface */
 } t_moldyn;
@@ -111,19 +126,37 @@ typedef struct s_moldyn {
 #define MOLDYN_STAT_PBY                        0x10    /* y */
 #define MOLDYN_STAT_PBZ                        0x20    /* and z direction */
 
+
+/*
+ *
+ * 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 exchange structure to exchange 2bp and 3bp calculated values */
+/*
+ * tersoff 
+ */
 
+/* tersoff exchange structure to exchange 2bp and 3bp calculated values */
 typedef struct s_tersoff_exchange {
        double f_c,df_c;
 
@@ -151,7 +184,6 @@ typedef struct s_tersoff_exchange {
 } 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 */
@@ -177,15 +209,19 @@ typedef struct s_tersoff_mult_params {
        t_tersoff_exchange exchange;    /* exchange between 2bp and 3bp calc */
 } t_tersoff_params;
 
+
+
 /*
+ *
  *  defines
+ *
  */
 
-/* general defines */
+/* default values */
 
 #define MOLDYN_TEMP                    273.0
 #define MOLDYN_TAU                     1.0e-15
-#define MOLDYN_CUTOFF                  10.0e-9
+#define MOLDYN_CUTOFF                  1.0e-9
 #define MOLDYN_RUNS                    1000000
 
 #define MOLDYN_INTEGRATE_VERLET                0x00
@@ -193,9 +229,18 @@ typedef struct s_tersoff_mult_params {
 
 #define MOLDYN_POTENTIAL_HO            0x00
 #define MOLDYN_POTENTIAL_LJ            0x01
-#define MOLDYN_POTENTIAL_DEFAULT       MOLDYN_POTENTIAL_LJ
+#define MOLDYN_POTENTIAL_TM            0x02
 
-/* phsical values */
+#define MOLDYN_SET_POTENTIAL           0x00
+#define MOLDYN_SET_
+#define MOLDYN_SET_
+#define MOLDYN_SET_
+
+/*
+ *
+ * phsical values / constants
+ *
+ */
 
 #define K_BOLTZMANN            1.3807e-27                      /* Nm/K */
 #define AMU                    1.660540e-27                    /* kg */
@@ -212,7 +257,12 @@ typedef struct s_tersoff_mult_params {
 #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 */
+
+/*
+ *
+ * function prototypes
+ *
+ */
 
 int moldyn_usage(char **argv);
 int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv);

diff --git a/posic.c b/posic.c
index d53af6f..cd1a2e2 100644 (file)
--- a/posic.c
+++ b/posic.c
@@ -18,15 +18,15 @@ int main(int argc,char **argv) {
 
        t_moldyn md;
 
+       t_lj_params lj;
+       t_ho_params ho;
+       t_tersoff_mult_params tp;
+
        int a,b,c;
        double e;
        double help;
        t_3dvec p;
 
-       t_lj_params lj;
-       t_ho_params ho;
-       t_tersoff_params tp;
-
        /*
         *  moldyn init
         *