runtime schedule adding and injection of c atoms

diff --git a/sic.c b/sic.c
index ba7de3d..751cb06 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -21,8 +21,15 @@
 #include "potentials/tersoff.h"
 #endif
 
-#define INJECT         1
-#define NR_ATOMS       4
+#define INJECT         160
+#define NR_ATOMS       10
+
+typedef struct s_hp {
+       int a_count;    /* atom count */
+       u8 quit;        /* quit mark */
+} t_hp;
+
+#define TC             50
 
 int hook(void *moldyn,void *hook_params) {
 
@@ -32,22 +39,45 @@ int hook(void *moldyn,void *hook_params) {
        unsigned char run;
        int i,j;
        t_atom *atom;
+       t_hp *hp;
 
        md=moldyn;
+       hp=hook_params;
+
+       /* quit */
+       if(hp->quit)
+               return 0;
+
+       /* switch on t scaling */
+       if(md->schedule.count==0)
+               set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
+
+       /* last schedule add if there is enough carbon inside */
+       if(hp->a_count==(INJECT*NR_ATOMS)) {
+               hp->quit=1;
+               moldyn_add_schedule(md,10000,1.0);
+               return 0;
+       }
+
+       /* more relaxing time for too high temperatures */
+       if(md->t-md->t_ref>TC) {
+               moldyn_add_schedule(md,100,1.0);
+               return 0;
+       }
 
-       if(!(md->schedule.count%2)) {
-               /* add carbon at random place, and enable t scaling */
-               for(j=0;j<NR_ATOMS;j++) {
+       /* inject carbon atoms */
+       printf("injecting another 10 carbon atoms ...\n");
+       for(j=0;j<NR_ATOMS;j++) {
                run=1;
                while(run) {
-                       r.x=rand_get_double(&(md->random))*md->dim.x;
-                       r.y=rand_get_double(&(md->random))*md->dim.y;
-                       r.z=rand_get_double(&(md->random))*md->dim.z;
+                       r.x=rand_get_double(&(md->random))*md->dim.x*0.37;
+                       r.y=rand_get_double(&(md->random))*md->dim.y*0.37;
+                       r.z=rand_get_double(&(md->random))*md->dim.z*0.37;
                        for(i=0;i<md->count;i++) {
                                atom=&(md->atom[i]);
                                v3_sub(&dist,&(atom->r),&r);
                                d=v3_absolute_square(&dist);
-                               if(d>TM_R_C)
+                               if(d>1.0)
                                        run=0;
                        }
                }
@@ -55,15 +85,11 @@ int hook(void *moldyn,void *hook_params) {
                add_atom(md,C,M_C,1,
                         ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
                         &r,&v);
-               }
-               printf("adding atoms & enable t scaling\n");
-               set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
-       }
-       else {
-               /* disable t scaling */
-               printf("disabling t scaling\n");
-               set_pt_scale(md,0,0,0,0);
        }
+       hp->a_count+=NR_ATOMS;
+
+       /* add schedule for simulating injected atoms ;) */
+       moldyn_add_schedule(md,100,1.0);
 
        return 0;
 }
@@ -79,6 +105,9 @@ int main(int argc,char **argv) {
        /* main moldyn structure */
        t_moldyn md;
 
+       /* hook parameter structure */
+       t_hp hookparam;
+
        /* potential parameters */
        t_tersoff_mult_params tp;
        t_albe_mult_params ap;
@@ -202,9 +231,9 @@ int main(int argc,char **argv) {
 
        /* set (initial) dimensions of simulation volume */
 #ifdef ALBE
-       //set_dim(&md,8*ALBE_LC_SI,8*ALBE_LC_SI,8*ALBE_LC_SI,TRUE);
+       set_dim(&md,20*ALBE_LC_SI,20*ALBE_LC_SI,20*ALBE_LC_SI,TRUE);
        //set_dim(&md,8*ALBE_LC_C,8*ALBE_LC_C,8*ALBE_LC_C,TRUE);
-       set_dim(&md,8*ALBE_LC_SIC,8*ALBE_LC_SIC,8*ALBE_LC_SIC,TRUE);
+       //set_dim(&md,8*ALBE_LC_SIC,8*ALBE_LC_SIC,8*ALBE_LC_SIC,TRUE);
 #else
        //set_dim(&md,8*LC_SI,8*LC_SI,8*LC_SI,TRUE);
        //set_dim(&md,8*LC_C,8*LC_C,8*LC_C,TRUE);
@@ -216,18 +245,18 @@ int main(int argc,char **argv) {
 
        /* create the lattice / place atoms */
 #ifdef ALBE
-       //create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
+       create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
        //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
 #else
        //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 #endif
-       //               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+                      ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
        //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
-       //               0,8,8,8,NULL);
+                      0,20,20,20,NULL);
        //               1,8,8,8,NULL);
 
        /* create zinkblende structure */
-       /**/
+       /*
 #ifdef ALBE
        r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
        create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
@@ -247,7 +276,7 @@ int main(int argc,char **argv) {
                       ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
                       1,8,8,8,&r);
 #endif
-       /**/
+       */
 
        /* check for right atom placing */
        moldyn_bc_check(&md);
@@ -289,21 +318,20 @@ int main(int argc,char **argv) {
        set_pressure(&md,BAR);
 
        /* set amount of steps to skip before average calc */
-       set_avg_skip(&md,1000);
+       set_avg_skip(&md,500);
 
        /* set p/t scaling */
        //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
        //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
        //                 T_SCALE_BERENDSEN,100.0);
-       //set_pt_scale(&md,0,0,T_SCALE_dIRECT,1.0);
+       //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
        //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
        
        /* initial thermal fluctuations of particles (in equilibrium) */
        thermal_init(&md,TRUE);
 
        /* create the simulation schedule */
-       /* initial configuration */
-       moldyn_add_schedule(&md,10000,1.0);
+       moldyn_add_schedule(&md,1000,1.0);
        //moldyn_add_schedule(&md,1000,1.0);
        //moldyn_add_schedule(&md,1000,1.0);
        //moldyn_add_schedule(&md,1000,1.0);
@@ -311,15 +339,13 @@ int main(int argc,char **argv) {
        //moldyn_add_schedule(&md,1000,1.0);
        /* adding atoms */
        //for(inject=0;inject<INJECT;inject++) {
-       //      /* injecting atom and run with enabled t scaling */
-       //      moldyn_add_schedule(&md,900,1.0);
-       //      /* continue running with disabled t scaling */
-       //      moldyn_add_schedule(&md,1100,1.0);
+       //      /* injecting atoms */
+       //      moldyn_add_schedule(&md,10,1.0);
        //}
 
-
        /* schedule hook function */
-       moldyn_set_schedule_hook(&md,&hook,NULL);
+       memset(&hookparam,0,sizeof(t_hp));
+       moldyn_set_schedule_hook(&md,&hook,&hookparam);
 
        /* activate logging */
        moldyn_set_log_dir(&md,argv[1]);