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added position insertion method + fixed positioning
[physik/posic.git] / mdrun.c
diff --git a/mdrun.c b/mdrun.c
index 63899a6..b2e67f3 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;
@@ -332,7 +332,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                                        csp.type|=CHSATTR_TCTRL;
                                }
                                if(!strncmp(word[i],"prelax",6)) {
-                                       csp.dp=atof(word[++i]);
+                                       csp.dp=atof(word[++i])*BAR;
                                        csp.type|=CHSATTR_PRELAX;
                                }
                                if(!strncmp(word[i],"trelax",6)) {
@@ -372,7 +372,6 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                                iap.ins_steps=atoi(word[2]);
                                iap.ins_atoms=atoi(word[3]);
                                iap.element=atoi(word[4]);
-                               iap.element=atoi(word[4]);
                                iap.brand=atoi(word[5]);
                                for(i=0;i<strlen(word[6]);i++) {
                                        switch(word[6][i]) {
@@ -401,17 +400,31 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                                                        break;
                                        }
                                }
-                               // only rand mode by now
-                               if(word[8][0]=='t')
-                                       iap.type=INS_TOTAL;
-                               else {
-                                       iap.type=INS_REGION;
-                                       iap.x0=atof(word[8]);
-                                       iap.y0=atof(word[9]);
-                                       iap.z0=atof(word[10]);
-                                       iap.x1=atof(word[11]);
-                                       iap.y1=atof(word[12]);
-                                       iap.z1=atof(word[13]);
+                               switch(word[7][0]) {
+                                       // insertion types
+                                       case 'p':
+                                               iap.type=INS_POS;
+                                               iap.x0=atof(word[8]);
+                                               iap.y0=atof(word[9]);
+                                               iap.z0=atof(word[10]);
+                                               break;
+                                       case 'r':
+                                               if(word[8][0]=='t') {
+                                                       iap.type=INS_TOTAL;
+                                                       iap.cr=atof(word[9]);
+                                               }
+                                               else {
+                                                       iap.type=INS_REGION;
+                                                       iap.x0=atof(word[8]);
+                                                       iap.y0=atof(word[9]);
+                                                       iap.z0=atof(word[10]);
+                                                       iap.x1=atof(word[11]);
+                                                       iap.y1=atof(word[12]);
+                                                       iap.z1=atof(word[13]);
+                                                       iap.cr=atof(word[14]);
+                                               }
+                                       default:
+                                               break;
                                }
                                add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
                        }
@@ -448,8 +461,9 @@ int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
 
        double delta;
 
-       if(!(mdrun->sattr&SATTR_PRELAX))
+       if(!(mdrun->sattr&SATTR_PRELAX)) {
                return TRUE;
+       }
 
        delta=moldyn->p_avg-moldyn->p_ref;
 
@@ -486,7 +500,7 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
        t_stage *stage;
        t_atom *atom;
        t_3dvec r,v,dist;
-       double d,dmin;
+       double d,dmin,o;
        int cnt,i;
        double x,y,z;
        double x0,y0,z0;
@@ -498,15 +512,32 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
        cr_check=FALSE;
 
        v.x=0.0; v.y=0.0; v.z=0.0;
+       x=0; y=0; z=0;
+       o=0; dmin=0;
+
+       switch(mdrun->lattice) {
+               case CUBIC:
+                       o=0.5*mdrun->lc;
+                       break;
+               case FCC:
+                       o=0.25*mdrun->lc;
+                       break;
+               case DIAMOND:
+               case ZINCBLENDE:
+                       o=0.125*mdrun->lc;
+                       break;
+               default:
+                       break;
+       }
 
        switch(iap->type) {
                case INS_TOTAL:
                        x=moldyn->dim.x;
-                       x0=0.0;
+                       x0=-x/2.0;
                        y=moldyn->dim.y;
-                       y0=0.0;
+                       y0=-y/2.0;
                        z=moldyn->dim.z;
-                       z0=0.0;
+                       z0=-z/2.0;
                        cr_check=TRUE;
                        break;
                case INS_REGION:
@@ -518,6 +549,12 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
                        z0=iap->z0;
                        cr_check=TRUE;
                        break;
+               case INS_POS:
+                       x0=iap->x0;
+                       y0=iap->y0;
+                       z0=iap->z0;
+                       cr_check=FALSE;
+                       break;
                default:
                        printf("%s unknown insertion mode: %02x\n",
                               ME,iap->type);
@@ -528,9 +565,25 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
        while(cnt<iap->ins_atoms) {
                run=1;
                while(run) {
-                       r.x=(rand_get_double(&(moldyn->random))-0.5)*x+x0;
-                       r.y=(rand_get_double(&(moldyn->random))-0.5)*y+y0;
-                       r.z=(rand_get_double(&(moldyn->random))-0.5)*z+z0;
+                       if(iap->type!=INS_POS) {
+                               r.x=rand_get_double(&(moldyn->random))*x;
+                               r.y=rand_get_double(&(moldyn->random))*y;
+                               r.z=rand_get_double(&(moldyn->random))*z;
+                       }
+                       else {
+                               r.x=0.0;
+                               r.y=0.0;
+                               r.z=0.0;
+                       }
+                       r.x+=x0;
+                       r.y+=y0;
+                       r.z+=z0;
+                       // offset
+                       if(iap->type!=INS_TOTAL) {
+                               r.x+=o;
+                               r.y+=o;
+                               r.z+=o;
+                       }
                        run=0;
                        if(cr_check==TRUE) {
                                dmin=1000;      // for sure too high!
@@ -550,8 +603,10 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
                }
                add_atom(moldyn,iap->element,pse_mass[iap->element],
                         iap->brand,iap->attr,&r,&v);
-               printf("%s atom inserted: %f %f %f | d squared = %f\n",
-                      ME,r.x,r.y,r.z,dmin);
+               printf("%s atom inserted (%d/%d): %f %f %f\n",
+                      ME,(iap->cnt_steps+1)*iap->ins_atoms,
+                      iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
+               printf("  -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
                cnt+=1;
        }
 
@@ -630,9 +685,9 @@ int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
        }
        if(csp->type&CHSATTR_AVGRST) {
                if(csp->avgrst)
-                       mdrun->sattr|=CHSATTR_AVGRST;
+                       mdrun->sattr|=SATTR_AVGRST;
                else
-                       mdrun->sattr&=(~(CHSATTR_AVGRST));
+                       mdrun->sattr&=(~(SATTR_AVGRST));
        }
        if(csp->type&CHSATTR_RSTEPS) {
                mdrun->relax_steps=csp->rsteps;
@@ -674,12 +729,11 @@ 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 */
-       if(!((check_pressure(moldyn,mdrun)==FALSE)|\
-            (check_temperature(moldyn,mdrun)==FALSE))) {
+       if((check_pressure(moldyn,mdrun)==TRUE)&\
+          (check_temperature(moldyn,mdrun)==TRUE)) {
        
                /* be verbose */
                stage_print("\n###########################\n");
@@ -714,7 +768,9 @@ printf("-------> %d\n",mdrun->relax_steps);
                                        change_stage=TRUE;
                                        break;
                                }
-                               set_temperature(moldyn,moldyn->t_ref+ap->dt);
+                               if(moldyn->t_ref+ap->dt>=0.0)
+                                       set_temperature(moldyn,
+                                                       moldyn->t_ref+ap->dt);
                                ap->count+=1;
                                break;
                        case STAGE_CHAATTR:
@@ -767,8 +823,9 @@ 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 +847,6 @@ 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 +876,22 @@ 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:
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