more logging

[physik/posic.git] / mdrun.c

diff --git a/mdrun.c b/mdrun.c
index bd70d00..1bf983d 100644 (file)
--- a/mdrun.c
+++ b/mdrun.c
@@ -308,10 +308,12 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                                        fp.lz=atoi(word[++i]);
                                        fp.lc=atof(word[++i]);
                                        mdrun->lc=fp.lc;
+                                       continue;
                                }
                                if(!strncmp(word[i],"eb",2)) {
                                        fp.fill_element=atoi(word[++i]);
                                        fp.fill_brand=atoi(word[++i]);
+                                       continue;
                                }
                                if(word[i][0]=='p') {
                                        i+=1;
@@ -347,6 +349,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                                                fp.p_params.d.y=atof(word[++i]);
                                                fp.p_params.d.z=atof(word[++i]);
                                        }
+                                       continue;
                                }
                                if(word[i][0]=='d') {
                                        switch(word[++i][0]) {
@@ -387,6 +390,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                                                default:
                                                        break;
                                        }
+                                       continue;
 
                                }
                                i+=1;
@@ -463,7 +467,9 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                        csp.type=0;
                        for(i=1;i<wcnt;i++) {
                                if(!strncmp(word[i],"pctrl",5)) {
-                                       csp.ptau=0.01/(atof(word[++i])*GPA);
+                                       csp.ptau=atof(word[++i]);
+                                       if(csp.ptau>0)
+                                               csp.ptau=0.01/(csp.ptau*GPA);
                                        csp.type|=CHSATTR_PCTRL;
                                }
                                if(!strncmp(word[i],"tctrl",5)) {
@@ -1056,13 +1062,13 @@ int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
                if(csp->ptau>0)
                        set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
                else
-                       set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
+                       set_p_scale(moldyn,P_SCALE_NONE,1.0);
        }
        if(csp->type&CHSATTR_TCTRL) {
                if(csp->ttau>0)
                        set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
                else
-                       set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
+                       set_t_scale(moldyn,T_SCALE_NONE,1.0);
        }
        if(csp->type&CHSATTR_PRELAX) {
                if(csp->dp<0)
@@ -1255,8 +1261,9 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 
                                        create_lattice(moldyn,
                                                       fp->lattice,fp->lc,
-                                                      mdrun->element1,
-                                                      DEFAULT_ATOM_ATTR,0,
+                                                      fp->fill_element,
+                                                      DEFAULT_ATOM_ATTR,
+                                                      fp->fill_brand,
                                                       fp->lx,fp->ly,fp->lz,
                                                       NULL,
                                                       &(fp->p_params),