modified runmd scripts + added pressure debug line (commented) to moldyn

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index 4330396..b79dea6 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -113,7 +113,7 @@ int set_p_scale(t_moldyn *moldyn,u8 ptype,double ptc) {
        moldyn->pt_scale|=ptype;
        moldyn->p_tc=ptc;
 
-       printf("[moldyn] p/t scaling:\n");
+       printf("[moldyn] p scaling:\n");
 
        printf("  p: %s",ptype?"yes":"no ");
        if(ptype)
@@ -129,7 +129,7 @@ int set_t_scale(t_moldyn *moldyn,u8 ttype,double ttc) {
        moldyn->pt_scale|=ttype;
        moldyn->t_tc=ttc;
 
-       printf("[moldyn] p/t scaling:\n");
+       printf("[moldyn] t scaling:\n");
 
        printf("  t: %s",ttype?"yes":"no ");
        if(ttype)
@@ -220,7 +220,7 @@ int set_potential(t_moldyn *moldyn,u8 type) {
                        moldyn->func3b_k1=tersoff_mult_3bp_k1;
                        moldyn->func3b_j2=tersoff_mult_3bp_j2;
                        moldyn->func3b_k2=tersoff_mult_3bp_k2;
-                       // missing: check 2b bond func
+                       moldyn->check_2b_bond=tersoff_mult_check_2b_bond;
                        break;
                case MOLDYN_POTENTIAL_AM:
                        moldyn->func3b_j1=albe_mult_3bp_j1;
@@ -1579,8 +1579,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
                printf("[moldyn] WARNING: forces too high / tau too small!\n");
 
        /* zero absolute time */
-       moldyn->time=0.0;
-       moldyn->total_steps=0;
+       // should have right values!
+       //moldyn->time=0.0;
+       //moldyn->total_steps=0;
 
        /* debugging, ignore */
        moldyn->debug=0;
@@ -1697,6 +1698,7 @@ printf("\rsched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)",
        sched->count,i,moldyn->total_steps,
        moldyn->t,moldyn->t_avg,
        moldyn->p/BAR,moldyn->p_avg/BAR,
+       //moldyn->p/BAR,(moldyn->p-2.0*moldyn->ekin/(3.0*moldyn->volume))/BAR,
        moldyn->volume,
        (int)(t2.tv_sec-t1.tv_sec));
 
@@ -2586,8 +2588,6 @@ int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
        if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
                return 0;
 
-       d=sqrt(d);
-
        /* now count this bonding ... */
        ba=data;