#include "potentials/tersoff.h"
#endif
-
-/*
- * global variables, pse and atom colors (only needed here)
- */
-
-static char *pse_name[]={
- "*",
- "H",
- "He",
- "Li",
- "Be",
- "B",
- "C",
- "N",
- "O",
- "F",
- "Ne",
- "Na",
- "Mg",
- "Al",
- "Si",
- "P",
- "S",
- "Cl",
- "Ar",
-};
-
-static char *pse_col[]={
- "*",
- "White",
- "He",
- "Li",
- "Be",
- "B",
- "Gray",
- "N",
- "Blue",
- "F",
- "Ne",
- "Na",
- "Mg",
- "Al",
- "Yellow",
- "P",
- "S",
- "Cl",
- "Ar",
-};
-
/*
* the moldyn functions
*/
int set_cutoff(t_moldyn *moldyn,double cutoff) {
moldyn->cutoff=cutoff;
+ moldyn->cutoff_square=cutoff*cutoff;
printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
return 0;
}
-int set_bondlen(t_moldyn *moldyn,double b0,double b1,double bm) {
-
- moldyn->bondlen[0]=b0*b0;
- moldyn->bondlen[1]=b1*b1;
- if(bm<0)
- moldyn->bondlen[2]=b0*b1;
- else
- moldyn->bondlen[2]=bm*bm;
-
- return 0;
-}
-
int set_temperature(t_moldyn *moldyn,double t_ref) {
moldyn->t_ref=t_ref;
return 0;
}
+int set_p_scale(t_moldyn *moldyn,u8 ptype,double ptc) {
+
+ moldyn->pt_scale&=(~(P_SCALE_MASK));
+ moldyn->pt_scale|=ptype;
+ moldyn->p_tc=ptc;
+
+ printf("[moldyn] p scaling:\n");
+
+ printf(" p: %s",ptype?"yes":"no ");
+ if(ptype)
+ printf(" | type: %02x | factor: %f",ptype,ptc);
+ printf("\n");
+
+ return 0;
+}
+
+int set_t_scale(t_moldyn *moldyn,u8 ttype,double ttc) {
+
+ moldyn->pt_scale&=(~(T_SCALE_MASK));
+ moldyn->pt_scale|=ttype;
+ moldyn->t_tc=ttc;
+
+ printf("[moldyn] t scaling:\n");
+
+ printf(" t: %s",ttype?"yes":"no ");
+ if(ttype)
+ printf(" | type: %02x | factor: %f",ttype,ttc);
+ printf("\n");
+
+ return 0;
+}
+
int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
moldyn->pt_scale=(ptype|ttype);
switch(type) {
case MOLDYN_POTENTIAL_TM:
- moldyn->func1b=tersoff_mult_1bp;
- moldyn->func3b_j1=tersoff_mult_3bp_j1;
- moldyn->func3b_k1=tersoff_mult_3bp_k1;
- moldyn->func3b_j2=tersoff_mult_3bp_j2;
- moldyn->func3b_k2=tersoff_mult_3bp_k2;
- // missing: check 2b bond func
+ moldyn->func_i0=tersoff_mult_1bp;
+ moldyn->func_j1=tersoff_mult_3bp_j1;
+ moldyn->func_j1_k0=tersoff_mult_3bp_k1;
+ moldyn->func_j1c=tersoff_mult_3bp_j2;
+ moldyn->func_j1_k1=tersoff_mult_3bp_k2;
+ moldyn->check_2b_bond=tersoff_mult_check_2b_bond;
break;
+ /*
case MOLDYN_POTENTIAL_AM:
moldyn->func3b_j1=albe_mult_3bp_j1;
moldyn->func3b_k1=albe_mult_3bp_k1;
moldyn->func3b_k2=albe_mult_3bp_k2;
moldyn->check_2b_bond=albe_mult_check_2b_bond;
break;
+ */
+ case MOLDYN_POTENTIAL_AM:
+ moldyn->func_i0=albe_mult_i0;
+ moldyn->func_j0=albe_mult_i0_j0;
+ moldyn->func_j0_k0=albe_mult_i0_j0_k0;
+ moldyn->func_j0e=albe_mult_i0_j1;
+ moldyn->func_j1=albe_mult_i0_j2;
+ moldyn->func_j1_k0=albe_mult_i0_j2_k0;
+ moldyn->func_j1c=albe_mult_i0_j3;
+ moldyn->check_2b_bond=albe_mult_check_2b_bond;
+ break;
+ case MOLDYN_POTENTIAL_HO:
+ moldyn->func_j0=harmonic_oscillator;
+ moldyn->check_2b_bond=harmonic_oscillator_check_2b_bond;
+ break;
+ case MOLDYN_POTENTIAL_LJ:
+ moldyn->func_j0=lennard_jones;
+ moldyn->check_2b_bond=lennard_jones_check_2b_bond;
+ break;
default:
printf("[moldyn] set potential: unknown type %02x\n",
type);
t_3dvec orig;
void *ptr;
t_atom *atom;
+ char name[16];
new=a*b*c;
count=moldyn->count;
case CUBIC:
set_nn_dist(moldyn,lc);
ret=cubic_init(a,b,c,lc,atom,&orig);
+ strcpy(name,"cubic");
break;
case FCC:
if(!origin)
v3_scale(&orig,&orig,0.5);
set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
ret=fcc_init(a,b,c,lc,atom,&orig);
+ strcpy(name,"fcc");
break;
case DIAMOND:
if(!origin)
v3_scale(&orig,&orig,0.25);
set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
ret=diamond_init(a,b,c,lc,atom,&orig);
+ strcpy(name,"diamond");
break;
default:
printf("unknown lattice type (%02x)\n",type);
}
moldyn->count+=new;
- printf("[moldyn] created lattice with %d atoms\n",new);
+ printf("[moldyn] created %s lattice with %d atoms\n",name,new);
for(ret=0;ret<new;ret++) {
atom[ret].element=element;
/* sqaure of some variables */
moldyn->tau_square=moldyn->tau*moldyn->tau;
- moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
/* get current time */
gettimeofday(&t1,NULL);
printf("[moldyn] WARNING: forces too high / tau too small!\n");
/* zero absolute time */
- moldyn->time=0.0;
- moldyn->total_steps=0;
+ // should have right values!
+ //moldyn->time=0.0;
+ //moldyn->total_steps=0;
/* debugging, ignore */
moldyn->debug=0;
temperature_calc(moldyn);
virial_sum(moldyn);
pressure_calc(moldyn);
- //thermodynamic_pressure_calc(moldyn);
+ /*
+ thermodynamic_pressure_calc(moldyn);
+ printf("\n\nDEBUG: numeric pressure calc: %f\n\n",
+ moldyn->tp/BAR);
+ */
/* calculate fluctuations + averages */
average_and_fluctuation_calc(moldyn);
/* single particle potential/force */
if(itom[i].attr&ATOM_ATTR_1BP)
- if(moldyn->func1b)
- moldyn->func1b(moldyn,&(itom[i]));
+ if(moldyn->func_i0)
+ moldyn->func_i0(moldyn,&(itom[i]));
if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
continue;
dnlc=lc->dnlc;
+#ifndef STATIC_LISTS
+ /* check for later 3 body interaction */
+ if(itom[i].attr&ATOM_ATTR_3BP)
+ memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
+#endif
+
/* first loop over atoms j */
- if(moldyn->func2b) {
+ if(moldyn->func_j0) {
for(j=0;j<27;j++) {
bc_ij=(j<dnlc)?0:1;
jtom=&(atom[neighbour_i[j][p]]);
p++;
-
- if(jtom==&(itom[i]))
- continue;
-
- if((jtom->attr&ATOM_ATTR_2BP)&
- (itom[i].attr&ATOM_ATTR_2BP)) {
- moldyn->func2b(moldyn,
- &(itom[i]),
- jtom,
- bc_ij);
- }
- }
#else
this=&(neighbour_i[j]);
list_reset_f(this);
do {
jtom=this->current->data;
+#endif
if(jtom==&(itom[i]))
continue;
+ /* reset 3bp run */
+ moldyn->run3bp=1;
+
if((jtom->attr&ATOM_ATTR_2BP)&
(itom[i].attr&ATOM_ATTR_2BP)) {
- moldyn->func2b(moldyn,
- &(itom[i]),
- jtom,
- bc_ij);
+ moldyn->func_j0(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+ }
+
+ /* 3 body potential/force */
+
+ /* in j loop, 3bp run can be skipped */
+ if(!(moldyn->run3bp))
+ continue;
+
+ if(!(itom[i].attr&ATOM_ATTR_3BP))
+ continue;
+
+ if(!(jtom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ if(moldyn->func_j0_k0==NULL)
+ continue;
+
+ /* first loop over atoms k in first j loop */
+ for(k=0;k<27;k++) {
+
+ bc_ik=(k<dnlc)?0:1;
+#ifdef STATIC_LISTS
+ q=0;
+
+ while(neighbour_i[j][q]!=0) {
+
+ ktom=&(atom[neighbour_i[k][q]]);
+ q++;
+#else
+ that=&(neighbour_i2[k]);
+ list_reset_f(that);
+
+ if(that->start==NULL)
+ continue;
+
+ do {
+ ktom=that->current->data;
+#endif
+
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ //if(ktom==jtom)
+ // continue;
+
+ if(ktom==&(itom[i]))
+ continue;
+
+ moldyn->func_j0_k0(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
+#ifdef STATIC_LISTS
}
+#else
+ } while(list_next_f(that)!=\
+ L_NO_NEXT_ELEMENT);
+#endif
+
+ }
+
+ /* finish of first j loop after first k loop */
+ if(moldyn->func_j0e)
+ moldyn->func_j0e(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+
+#ifdef STATIC_LISTS
+ }
+#else
} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
#endif
}
}
- /* 3 body potential/force */
+ /* continued 3 body potential/force */
if(!(itom[i].attr&ATOM_ATTR_3BP))
continue;
- /* copy the neighbour lists */
-#ifdef STATIC_LISTS
- /* no copy needed for static lists */
-#else
- memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
-#endif
-
/* second loop over atoms j */
for(j=0;j<27;j++) {
/* reset 3bp run */
moldyn->run3bp=1;
- if(moldyn->func3b_j1)
- moldyn->func3b_j1(moldyn,
- &(itom[i]),
- jtom,
- bc_ij);
+ if(moldyn->func_j1)
+ moldyn->func_j1(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
- /* in first j loop, 3bp run can be skipped */
+ /* in j loop, 3bp run can be skipped */
if(!(moldyn->run3bp))
continue;
- /* first loop over atoms k */
- if(moldyn->func3b_k1) {
+ /* first loop over atoms k in second j loop */
+ if(moldyn->func_j1_k0) {
for(k=0;k<27;k++) {
if(!(ktom->attr&ATOM_ATTR_3BP))
continue;
- if(ktom==jtom)
- continue;
+ //if(ktom==jtom)
+ // continue;
if(ktom==&(itom[i]))
continue;
- moldyn->func3b_k1(moldyn,
- &(itom[i]),
- jtom,
- ktom,
- bc_ik|bc_ij);
+ moldyn->func_j1_k0(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
#ifdef STATIC_LISTS
}
#else
}
- if(moldyn->func3b_j2)
- moldyn->func3b_j2(moldyn,
- &(itom[i]),
- jtom,
- bc_ij);
+ /* continued j loop after first k loop */
+ if(moldyn->func_j1c)
+ moldyn->func_j1c(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
/* second loop over atoms k */
- if(moldyn->func3b_k2) {
+ if(moldyn->func_j1_k1) {
for(k=0;k<27;k++) {
if(!(ktom->attr&ATOM_ATTR_3BP))
continue;
- if(ktom==jtom)
- continue;
+ //if(ktom==jtom)
+ // continue;
if(ktom==&(itom[i]))
continue;
- moldyn->func3b_k2(moldyn,
- &(itom[i]),
- jtom,
- ktom,
- bc_ik|bc_ij);
+ moldyn->func_j1_k1(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
#ifdef STATIC_LISTS
}
}
- /* 2bp post function */
- if(moldyn->func3b_j3) {
- moldyn->func3b_j3(moldyn,
- &(itom[i]),
- jtom,bc_ij);
+ /* finish of j loop after second k loop */
+ if(moldyn->func_j1e) {
+ moldyn->func_j1e(moldyn,
+ &(itom[i]),
+ jtom,bc_ij);
}
#ifdef STATIC_LISTS
}
#endif
}
-
+
#ifdef DEBUG
//printf("\n\n");
#endif
t_list *this;
lc=&(moldyn->lc);
-
- link_cell_init(moldyn,VERBOSE);
-
itom=moldyn->atom;
for(i=0;i<moldyn->count;i++) {
ret=read(fd,line+count,1);
if(ret<=0) return ret;
if(line[count]=='\n') {
- line[count]='\0';
+ memset(line+count,0,max-count-1);
+ //line[count]='\0';
return count+1;
}
count+=1;
if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
return 0;
- d=sqrt(d);
-
/* now count this bonding ... */
ba=data;
return 0;
}
+int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+ void *data,u8 bc) {
+
+ t_vb *vb;
+
+ vb=data;
+
+ if(itom->tag>=jtom->tag)
+ return 0;
+
+ if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
+ return 0;
+
+ if((itom->attr&ATOM_ATTR_VB)|(jtom->attr&ATOM_ATTR_VB))
+ dprintf(vb->fd,"# [B] %f %f %f %f %f %f\n",
+ itom->r.x,itom->r.y,itom->r.z,
+ jtom->r.x,jtom->r.y,jtom->r.z);
+
+ return 0;
+}
+
int visual_atoms(t_moldyn *moldyn) {
- int i,j,fd;
+ int i;
char file[128+64];
t_3dvec dim;
double help;
t_visual *v;
t_atom *atom;
- t_atom *btom;
- t_linkcell *lc;
-#ifdef STATIC_LISTS
- int *neighbour[27];
- int p;
-#else
- t_list neighbour[27];
-#endif
- u8 bc;
- t_3dvec dist;
- double d2;
- u8 brand;
+ t_vb vb;
v=&(moldyn->vis);
dim.x=v->dim.x;
dim.y=v->dim.y;
dim.z=v->dim.z;
atom=moldyn->atom;
- lc=&(moldyn->lc);
help=(dim.x+dim.y);
sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,moldyn->time);
- fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
- if(fd<0) {
+ vb.fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
+ if(vb.fd<0) {
perror("open visual save file fd");
return -1;
}
/* write the actual data file */
// povray header
- dprintf(fd,"# [P] %d %07.f <%f,%f,%f>\n",
+ dprintf(vb.fd,"# [P] %d %07.f <%f,%f,%f>\n",
moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help);
// atomic configuration
- for(i=0;i<moldyn->count;i++) {
+ for(i=0;i<moldyn->count;i++)
// atom type, positions, color and kinetic energy
- dprintf(fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
- atom[i].r.x,
- atom[i].r.y,
- atom[i].r.z,
- pse_col[atom[i].element],
- atom[i].ekin);
-
- /*
- * bond detection should usually be done by potential
- * functions. brrrrr! EVIL!
- *
- * todo: potentials need to export a 'find_bonds' function!
- */
-
- // bonds between atoms
- if(!(atom[i].attr&ATOM_ATTR_VB))
- continue;
- link_cell_neighbour_index(moldyn,
- (atom[i].r.x+moldyn->dim.x/2)/lc->x,
- (atom[i].r.y+moldyn->dim.y/2)/lc->y,
- (atom[i].r.z+moldyn->dim.z/2)/lc->z,
- neighbour);
- for(j=0;j<27;j++) {
- bc=j<lc->dnlc?0:1;
-#ifdef STATIC_LISTS
- p=0;
- while(neighbour[j][p]!=0) {
- btom=&(atom[neighbour[j][p]]);
- p++;
-#else
- list_reset_f(&neighbour[j]);
- if(neighbour[j].start==NULL)
- continue;
- do {
- btom=neighbour[j].current->data;
-#endif
- if(btom==&atom[i]) // skip identical atoms
- continue;
- //if(btom<&atom[i]) // skip half of them
- // continue;
- v3_sub(&dist,&(atom[i].r),&(btom->r));
- if(bc) check_per_bound(moldyn,&dist);
- d2=v3_absolute_square(&dist);
- brand=atom[i].brand;
- if(brand==btom->brand) {
- if(d2>moldyn->bondlen[brand])
- continue;
- }
- else {
- if(d2>moldyn->bondlen[2])
- continue;
- }
- dprintf(fd,"# [B] %f %f %f %f %f %f\n",
- atom[i].r.x,atom[i].r.y,atom[i].r.z,
- btom->r.x,btom->r.y,btom->r.z);
-#ifdef STATIC_LISTS
- }
-#else
- } while(list_next_f(&neighbour[j])!=L_NO_NEXT_ELEMENT);
-#endif
- }
- }
-
+ dprintf(vb.fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
+ atom[i].r.x,
+ atom[i].r.y,
+ atom[i].r.z,
+ pse_col[atom[i].element],
+ atom[i].ekin);
+
+ // bonds between atoms
+ process_2b_bonds(moldyn,&vb,visual_bonds_process);
+
// boundaries
if(dim.x) {
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
-dim.x/2,-dim.y/2,-dim.z/2,
dim.x/2,-dim.y/2,-dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
-dim.x/2,-dim.y/2,-dim.z/2,
-dim.x/2,dim.y/2,-dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
dim.x/2,dim.y/2,-dim.z/2,
dim.x/2,-dim.y/2,-dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
-dim.x/2,dim.y/2,-dim.z/2,
dim.x/2,dim.y/2,-dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
-dim.x/2,-dim.y/2,dim.z/2,
dim.x/2,-dim.y/2,dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
-dim.x/2,-dim.y/2,dim.z/2,
-dim.x/2,dim.y/2,dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
dim.x/2,dim.y/2,dim.z/2,
dim.x/2,-dim.y/2,dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
-dim.x/2,dim.y/2,dim.z/2,
dim.x/2,dim.y/2,dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
-dim.x/2,-dim.y/2,dim.z/2,
-dim.x/2,-dim.y/2,-dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
-dim.x/2,dim.y/2,dim.z/2,
-dim.x/2,dim.y/2,-dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
dim.x/2,-dim.y/2,dim.z/2,
dim.x/2,-dim.y/2,-dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
dim.x/2,dim.y/2,dim.z/2,
dim.x/2,dim.y/2,-dim.z/2);
}
- close(fd);
+ close(vb.fd);
return 0;
}
projects / physik / posic.git / blobdiff