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tool to search for bonds
[physik/posic.git]
/
mdrun.c
diff --git
a/mdrun.c
b/mdrun.c
index
8c5cf71
..
b2e67f3
100644
(file)
--- a/
mdrun.c
+++ b/
mdrun.c
@@
-332,7
+332,7
@@
int mdrun_parse_config(t_mdrun *mdrun) {
csp.type|=CHSATTR_TCTRL;
}
if(!strncmp(word[i],"prelax",6)) {
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)) {
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.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]) {
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;
}
}
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);
}
}
add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
}
@@
-448,8
+461,9
@@
int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
double delta;
double delta;
- if(!(mdrun->sattr&SATTR_PRELAX))
+ if(!(mdrun->sattr&SATTR_PRELAX))
{
return TRUE;
return TRUE;
+ }
delta=moldyn->p_avg-moldyn->p_ref;
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;
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;
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;
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;
switch(iap->type) {
case INS_TOTAL:
x=moldyn->dim.x;
- x0=
0
.0;
+ x0=
-x/2
.0;
y=moldyn->dim.y;
y=moldyn->dim.y;
- y0=
0
.0;
+ y0=
-y/2
.0;
z=moldyn->dim.z;
z=moldyn->dim.z;
- z0=
0
.0;
+ z0=
-z/2
.0;
cr_check=TRUE;
break;
case INS_REGION:
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;
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);
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) {
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!
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);
}
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;
}
cnt+=1;
}
@@
-630,9
+685,9
@@
int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
}
if(csp->type&CHSATTR_AVGRST) {
if(csp->avgrst)
}
if(csp->type&CHSATTR_AVGRST) {
if(csp->avgrst)
- mdrun->sattr|=
CH
SATTR_AVGRST;
+ mdrun->sattr|=SATTR_AVGRST;
else
else
- mdrun->sattr&=(~(
CH
SATTR_AVGRST));
+ mdrun->sattr&=(~(SATTR_AVGRST));
}
if(csp->type&CHSATTR_RSTEPS) {
mdrun->relax_steps=csp->rsteps;
}
if(csp->type&CHSATTR_RSTEPS) {
mdrun->relax_steps=csp->rsteps;
@@
-677,8
+732,8
@@
int mdrun_hook(void *ptr1,void *ptr2) {
tau=mdrun->timestep;
/* check whether relaxation steps are necessary */
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");
/* be verbose */
stage_print("\n###########################\n");
@@
-713,7
+768,9
@@
int mdrun_hook(void *ptr1,void *ptr2) {
change_stage=TRUE;
break;
}
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:
ap->count+=1;
break;
case STAGE_CHAATTR: