unstable but might run ...

[physik/posic.git] / mdrun.c

diff --git a/mdrun.c b/mdrun.c
index 63899a6..8c5cf71 100644 (file)
--- a/mdrun.c
+++ b/mdrun.c
@@ -140,7 +140,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
        char *wptr;
        char word[16][32];
        int wcnt;
-       int i;
+       int i,o;
 
        t_insert_atoms_params iap;
        t_continue_params cp;
@@ -255,6 +255,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                        mdrun->lx=atoi(word[2]);
                        mdrun->ly=atoi(word[3]);
                        mdrun->lz=atoi(word[4]);
+                       mdrun->lc=atof(word[5]);
                }
                else if(!strncmp(word[0],"aattr",5)) {
                        // for aatrib line we need a special stage
@@ -274,7 +275,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                                                break;
                                }
                        }
-                       i=1;
+                       i=2;
                        if(cap.type&CHAATTR_REGION) {
                                cap.x0=atof(word[1]);   
                                cap.y0=atof(word[2]);   
@@ -288,9 +289,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                                cap.element=atoi(word[i]);
                                i+=1;
                        }
-                       wptr=word[i];
-                       for(i=0;i<strlen(wptr);i++) {
-                               switch(word[2][i]) {
+                       for(o=0;o<strlen(word[i]);o++) {
+                               switch(word[i][o]) {
                                        case 'b':
                                                cap.attr|=ATOM_ATTR_VB;
                                                break;
@@ -674,7 +674,6 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 
        /* default steps and tau values */
        steps=mdrun->relax_steps;
-printf("-------> %d\n",mdrun->relax_steps);
        tau=mdrun->timestep;
 
        /* check whether relaxation steps are necessary */
@@ -767,8 +766,9 @@ int main(int argc,char **argv) {
        t_moldyn moldyn;
        t_3dvec o;
 
-       /* clear mdrun struct */
+       /* clear structs */
        memset(&mdrun,0,sizeof(t_mdrun));
+       memset(&moldyn,0,sizeof(t_moldyn));
 
        /* parse arguments */
        if(mdrun_parse_argv(&mdrun,argc,argv)<0)
@@ -790,7 +790,6 @@ int main(int argc,char **argv) {
        if(set_int_alg(&moldyn,mdrun.intalgo)<0)
                return -1;
        set_cutoff(&moldyn,mdrun.cutoff);
-       set_nn_dist(&moldyn,mdrun.nnd);
        if(set_potential(&moldyn,mdrun.potential)<0)
                return -1;
        switch(mdrun.potential) {
@@ -820,22 +819,22 @@ int main(int argc,char **argv) {
        switch(mdrun.lattice) {
                case FCC:
                        create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
-                                      mdrun.m1,0,0,mdrun.lx,
+                                      mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
                                       mdrun.ly,mdrun.lz,NULL);
                        break;
                case DIAMOND:
                        create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
-                                      mdrun.m1,0,0,mdrun.lx,
+                                      mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
                                       mdrun.ly,mdrun.lz,NULL);
                        break;
                case ZINCBLENDE:
                        o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
                        create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
-                                      mdrun.m1,0,0,mdrun.lx,
+                                      mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
                                       mdrun.ly,mdrun.lz,&o);
                        o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
                        create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
-                                      mdrun.m2,0,1,mdrun.lx,
+                                      mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
                                       mdrun.ly,mdrun.lz,&o);
                        break;
                default: