add another way of calculating tersoff + small moldyn mods

[physik/posic.git] / sic.c

diff --git a/sic.c b/sic.c
index 167735f..a78f3a0 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -14,21 +14,53 @@
 #include "potentials/harmonic_oscillator.h"
 #include "potentials/lennard_jones.h"
 #include "potentials/tersoff.h"
+//#include "potentials/tersoff_orig.h"
+
+#define INJECT         1
+#define NR_ATOMS       4
 
 int hook(void *moldyn,void *hook_params) {
 
        t_moldyn *md;
+       t_3dvec r,v,dist;
+       double d;
+       unsigned char run;
+       int i,j;
+       t_atom *atom;
 
        md=moldyn;
 
-       /* switch to direct scaling in first hook */    
-       if(md->schedule.count==0)
+       printf("\nschedule hook: ");
+
+       if(!(md->schedule.count%2)) {
+               /* add carbon at random place, and enable t scaling */
+               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;
+                       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)
+                                       run=0;
+                       }
+               }
+               v.x=0; v.y=0; v.z=0;
+               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);
-       /* switch off temp scaling in second hook */
-       if(md->schedule.count==1)
+       }
+       else {
+               /* disable t scaling */
+               printf("disabling t scaling\n");
                set_pt_scale(md,0,0,0,0);
-               
-       //set_temperature(md,md->t_ref-100.0);
+       }
 
        return 0;
 }
@@ -49,6 +81,9 @@ int main(int argc,char **argv) {
        t_ho_params ho;
        t_tersoff_mult_params tp;
 
+       /* atom injection counter */
+       int inject;
+
        /* testing location & velocity vector */
        t_3dvec r,v;
        memset(&r,0,sizeof(t_3dvec));
@@ -63,8 +98,13 @@ int main(int argc,char **argv) {
        /* choose potential */
        set_potential1b(&md,tersoff_mult_1bp);
        set_potential2b(&md,tersoff_mult_2bp);
-       set_potential2b_post(&md,tersoff_mult_post_2bp);
-       set_potential3b(&md,tersoff_mult_3bp);
+       //set_potential3b_j1(&md,tersoff_mult_2bp);
+       //set_potential3b_k1(&md,tersoff_mult_3bp);
+       //set_potential3b_j3(&md,tersoff_mult_post_2bp);
+       set_potential3b_j1(&md,tersoff_mult_3bp_j1);
+       set_potential3b_k1(&md,tersoff_mult_3bp_k1);
+       set_potential3b_j2(&md,tersoff_mult_3bp_j2);
+       set_potential3b_k2(&md,tersoff_mult_3bp_k2);
        //set_potential2b(&md,lennard_jones);
        //set_potential2b(&md,harmonic_oscillator);
        set_potential_params(&md,&tp);
@@ -164,7 +204,7 @@ int main(int argc,char **argv) {
 
        /* set temperature & pressure */
        set_temperature(&md,atof(argv[2])+273.0);
-       set_pressure(&md,ATM);
+       set_pressure(&md,BAR);
 
        /* set p/t scaling */
        //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
@@ -176,18 +216,27 @@ int main(int argc,char **argv) {
        thermal_init(&md,TRUE);
 
        /* create the simulation schedule */
-       moldyn_add_schedule(&md,10001,1.0);
-       //moldyn_add_schedule(&md,501,1.0);
-       //moldyn_add_schedule(&md,501,1.0);
+       /* initial configuration */
+       moldyn_add_schedule(&md,10000,1.0);
+       /* 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);
+       //}
 
        /* schedule hook function */
-       //moldyn_set_schedule_hook(&md,&hook,NULL);
+       moldyn_set_schedule_hook(&md,&hook,NULL);
 
        /* activate logging */
        moldyn_set_log_dir(&md,argv[1]);
        moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
        moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
+       moldyn_set_log(&md,LOG_TEMPERATURE,1);
+       moldyn_set_log(&md,LOG_PRESSURE,1);
        moldyn_set_log(&md,VISUAL_STEP,100);
+       moldyn_set_log(&md,SAVE_STEP,100);
        moldyn_set_log(&md,CREATE_REPORT,0);
 
        /*