added position insertion method + fixed positioning

diff --git a/mdrun.c b/mdrun.c
index e5feda3aa4ceed4c52e53f6327d79738ebd97518..b2e67f371810946b5c4b67b82e6a03caab311dfe 100644 (file)
--- a/mdrun.c
+++ b/mdrun.c
@@ -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]) {
@@ -401,20 +400,31 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                                                        break;
                                        }
                                }
-                               // only rand mode by now
-                               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]);
+                               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);
                        }
@@ -490,7 +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;
@@ -502,15 +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:
@@ -522,6 +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);
@@ -532,9 +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!
@@ -719,7 +768,9 @@ int mdrun_hook(void *ptr1,void *ptr2) {
                                        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:

diff --git a/mdrun.h b/mdrun.h
index 83a8196d879f09f9a3f164ee923435466427dc47..fa169067643a6ca2b61926694545678f78838384 100644 (file)
--- a/mdrun.h
+++ b/mdrun.h
@@ -116,6 +116,7 @@ typedef struct s_insert_atoms_params {
 
 #define INS_TOTAL                              0x01
 #define INS_REGION                             0x02
+#define INS_POS                                        0x03
 
 typedef struct s_continue_params {
        int runs;