#include "moldyn.h"
-#include "math/math.h"
-#include "init/init.h"
-#include "random/random.h"
-#include "visual/visual.h"
-#include "list/list.h"
-
-
int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
- //int ret;
-
- //ret=moldyn_parse_argv(moldyn,argc,argv);
- //if(ret<0) return ret;
-
memset(moldyn,0,sizeof(t_moldyn));
rand_init(&(moldyn->random),NULL,1);
int moldyn_shutdown(t_moldyn *moldyn) {
+ printf("[moldyn] shutdown\n");
moldyn_log_shutdown(moldyn);
link_cell_shutdown(moldyn);
- moldyn_log_shutdown(moldyn);
rand_close(&(moldyn->random));
free(moldyn->atom);
return 0;
}
-int set_temperature(t_moldyn *moldyn,double t) {
-
- moldyn->t=t;
+int set_temperature(t_moldyn *moldyn,double t_ref) {
+
+ moldyn->t_ref=t_ref;
+
+ return 0;
+}
+
+int set_pressure(t_moldyn *moldyn,double p_ref) {
+
+ moldyn->p_ref=p_ref;
+
+ return 0;
+}
+
+int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
+
+ moldyn->pt_scale=(ptype|ttype);
+ moldyn->t_tc=ttc;
+ moldyn->p_tc=ptc;
return 0;
}
moldyn->dim.y=y;
moldyn->dim.z=z;
+ moldyn->volume=x*y*z;
+
if(visualize) {
moldyn->vis.dim.x=x;
moldyn->vis.dim.y=y;
moldyn->vis.dim.z=z;
}
+ printf("[moldyn] dimensions in A and A^3 respectively:\n");
+ printf(" x: %f\n",moldyn->dim.x);
+ printf(" y: %f\n",moldyn->dim.y);
+ printf(" z: %f\n",moldyn->dim.z);
+ printf(" volume: %f\n",moldyn->volume);
+ printf(" visualize simulation box: %s\n",visualize?"on":"off");
+
+ return 0;
+}
+
+int set_nn_dist(t_moldyn *moldyn,double dist) {
+
+ moldyn->nnd=dist;
+
return 0;
}
return 0;
}
+int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
+
+ moldyn->func2b_post=func;
+ moldyn->pot2b_params=params;
+
+ return 0;
+}
+
int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
moldyn->func3b=func;
return 0;
}
-int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
+int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
+
+ strncpy(moldyn->vlsdir,dir,127);
+
+ return 0;
+}
+
+int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
+
+ char filename[128];
+ int ret;
switch(type) {
case LOG_TOTAL_ENERGY:
moldyn->ewrite=timer;
- moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+ snprintf(filename,127,"%s/energy",moldyn->vlsdir);
+ moldyn->efd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
if(moldyn->efd<0) {
- perror("[moldyn] efd open");
+ perror("[moldyn] energy log fd open");
return moldyn->efd;
}
dprintf(moldyn->efd,"# total energy log file\n");
break;
case LOG_TOTAL_MOMENTUM:
moldyn->mwrite=timer;
- moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+ snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
+ moldyn->mfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
if(moldyn->mfd<0) {
- perror("[moldyn] mfd open");
+ perror("[moldyn] momentum log fd open");
return moldyn->mfd;
}
dprintf(moldyn->efd,"# total momentum log file\n");
break;
case SAVE_STEP:
moldyn->swrite=timer;
- strncpy(moldyn->sfb,fb,63);
break;
case VISUAL_STEP:
moldyn->vwrite=timer;
- strncpy(moldyn->vfb,fb,63);
- visual_init(&(moldyn->vis),fb);
+ ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
+ if(ret<0) {
+ printf("[moldyn] visual init failure\n");
+ return ret;
+ }
break;
default:
- printf("unknown log mechanism: %02x\n",type);
+ printf("[moldyn] unknown log mechanism: %02x\n",type);
return -1;
}
int moldyn_log_shutdown(t_moldyn *moldyn) {
+ printf("[moldyn] log shutdown\n");
if(moldyn->efd) close(moldyn->efd);
if(moldyn->mfd) close(moldyn->mfd);
- if(moldyn->visual) visual_tini(moldyn->visual);
+ if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
return 0;
}
+/*
+ * creating lattice functions
+ */
+
int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
u8 attr,u8 bnum,int a,int b,int c) {
int count;
int ret;
t_3dvec origin;
- t_atom *atom;
count=a*b*c;
- atom=moldyn->atom;
+ /* how many atoms do we expect */
if(type==FCC) count*=4;
-
if(type==DIAMOND) count*=8;
- atom=malloc(count*sizeof(t_atom));
- if(atom==NULL) {
+ /* allocate space for atoms */
+ moldyn->atom=malloc(count*sizeof(t_atom));
+ if(moldyn->atom==NULL) {
perror("malloc (atoms)");
return -1;
}
switch(type) {
case FCC:
- ret=fcc_init(a,b,c,lc,atom,&origin);
+ ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
break;
case DIAMOND:
- ret=diamond_init(a,b,c,lc,atom,&origin);
+ ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
break;
default:
printf("unknown lattice type (%02x)\n",type);
/* debug */
if(ret!=count) {
- printf("ok, there is something wrong ...\n");
- printf("calculated -> %d atoms\n",count);
- printf("created -> %d atoms\n",ret);
+ printf("[moldyn] creating lattice failed\n");
+ printf(" amount of atoms\n");
+ printf(" - expected: %d\n",count);
+ printf(" - created: %d\n",ret);
return -1;
}
moldyn->count=count;
+ printf("[moldyn] created lattice with %d atoms\n",count);
while(count) {
- atom[count-1].element=element;
- atom[count-1].mass=mass;
- atom[count-1].attr=attr;
- atom[count-1].bnum=bnum;
count-=1;
+ moldyn->atom[count].element=element;
+ moldyn->atom[count].mass=mass;
+ moldyn->atom[count].attr=attr;
+ moldyn->atom[count].bnum=bnum;
+ check_per_bound(moldyn,&(moldyn->atom[count].r));
}
return ret;
}
+/* fcc lattice init */
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+ int count;
+ int i,j;
+ t_3dvec o,r,n;
+ t_3dvec basis[3];
+ double help[3];
+ double x,y,z;
+
+ x=a*lc;
+ y=b*lc;
+ z=c*lc;
+
+ if(origin) v3_copy(&o,origin);
+ else v3_zero(&o);
+
+ /* construct the basis */
+ for(i=0;i<3;i++) {
+ for(j=0;j<3;j++) {
+ if(i!=j) help[j]=0.5*lc;
+ else help[j]=.0;
+ }
+ v3_set(&basis[i],help);
+ }
+
+ v3_zero(&r);
+ count=0;
+
+ /* fill up the room */
+ r.x=o.x;
+ while(r.x<x) {
+ r.y=o.y;
+ while(r.y<y) {
+ r.z=o.z;
+ while(r.z<z) {
+ v3_copy(&(atom[count].r),&r);
+ atom[count].element=1;
+ count+=1;
+ for(i=0;i<3;i++) {
+ v3_add(&n,&r,&basis[i]);
+ if((n.x<x+o.x)&&
+ (n.y<y+o.y)&&
+ (n.z<z+o.z)) {
+ v3_copy(&(atom[count].r),&n);
+ count+=1;
+ }
+ }
+ r.z+=lc;
+ }
+ r.y+=lc;
+ }
+ r.x+=lc;
+ }
+
+ /* coordinate transformation */
+ help[0]=x/2.0;
+ help[1]=y/2.0;
+ help[2]=z/2.0;
+ v3_set(&n,help);
+ for(i=0;i<count;i++)
+ v3_sub(&(atom[i].r),&(atom[i].r),&n);
+
+ return count;
+}
+
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+ int count;
+ t_3dvec o;
+
+ count=fcc_init(a,b,c,lc,atom,origin);
+
+ o.x=0.25*lc;
+ o.y=0.25*lc;
+ o.z=0.25*lc;
+
+ if(origin) v3_add(&o,&o,origin);
+
+ count+=fcc_init(a,b,c,lc,&atom[count],&o);
+
+ return count;
+}
+
int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
t_3dvec *r,t_3dvec *v) {
moldyn->atom=ptr;
atom=moldyn->atom;
- atom->r=*r;
- atom->v=*v;
- atom->element=element;
- atom->bnum=bnum;
- atom->attr=attr;
+ atom[count-1].r=*r;
+ atom[count-1].v=*v;
+ atom[count-1].element=element;
+ atom[count-1].mass=mass;
+ atom[count-1].bnum=bnum;
+ atom[count-1].attr=attr;
return 0;
}
return 0;
}
-int thermal_init(t_moldyn *moldyn) {
+int thermal_init(t_moldyn *moldyn,u8 equi_init) {
/*
* - gaussian distribution of velocities
/* gaussian distribution of velocities */
v3_zero(&p_total);
for(i=0;i<moldyn->count;i++) {
- sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
+ sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
/* x direction */
v=sigma*rand_get_gauss(random);
atom[i].v.x=v;
}
/* velocity scaling */
- scale_velocity(moldyn);
+ scale_velocity(moldyn,equi_init);
return 0;
}
-int scale_velocity(t_moldyn *moldyn) {
+int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
int i;
- double e,c;
+ double e,scale;
t_atom *atom;
+ int count;
atom=moldyn->atom;
/*
* - velocity scaling (E = 3/2 N k T), E: kinetic energy
*/
+
+ /* get kinetic energy / temperature & count involved atoms */
e=0.0;
+ count=0;
+ for(i=0;i<moldyn->count;i++) {
+ if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
+ e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ count+=1;
+ }
+ }
+ if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
+ else return 0; /* no atoms involved in scaling! */
+
+ /* (temporary) hack for e,t = 0 */
+ if(e==0.0) {
+ moldyn->t=0.0;
+ if(moldyn->t_ref!=0.0) {
+ thermal_init(moldyn,equi_init);
+ return 0;
+ }
+ else
+ return 0; /* no scaling needed */
+ }
+
+
+ /* get scaling factor */
+ scale=moldyn->t_ref/moldyn->t;
+ if(equi_init&TRUE)
+ scale*=2.0;
+ else
+ if(moldyn->pt_scale&T_SCALE_BERENDSEN)
+ scale=1.0+(scale-1.0)/moldyn->t_tc;
+ scale=sqrt(scale);
+
+ /* velocity scaling */
+ for(i=0;i<moldyn->count;i++) {
+ if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
+ v3_scale(&(atom[i].v),&(atom[i].v),scale);
+ }
+
+ return 0;
+}
+
+int scale_volume(t_moldyn *moldyn) {
+
+ t_atom *atom;
+ t_3dvec *dim,*vdim;
+ double virial,scale;
+ t_linkcell *lc;
+ int i;
+
+ atom=moldyn->atom;
+ dim=&(moldyn->dim);
+ vdim=&(moldyn->vis.dim);
+ lc=&(moldyn->lc);
+
for(i=0;i<moldyn->count;i++)
- e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
- c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
- for(i=0;i<moldyn->count;i++)
- v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
+ virial+=v3_norm(&(atom[i].virial));
+
+printf("%f\n",virial);
+ /* get pressure from virial */
+ moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*virial;
+ moldyn->p/=moldyn->volume;
+printf("%f\n",moldyn->p/(ATM));
+
+ /* scale factor */
+ if(moldyn->pt_scale&P_SCALE_BERENDSEN)
+ scale=3*sqrt(1-(moldyn->p_ref-moldyn->p)/moldyn->p_tc);
+ else
+ /* should actually never be used */
+ scale=pow(moldyn->p/moldyn->p_ref,1.0/3.0);
+
+printf("scale = %f\n",scale);
+ /* actual scaling */
+ dim->x*=scale;
+ dim->y*=scale;
+ dim->z*=scale;
+ if(vdim->x) vdim->x=dim->x;
+ if(vdim->y) vdim->y=dim->y;
+ if(vdim->z) vdim->z=dim->z;
+ moldyn->volume*=(scale*scale*scale);
+
+ /* check whether we need a new linkcell init */
+ if((dim->x/moldyn->cutoff!=lc->nx)||
+ (dim->y/moldyn->cutoff!=lc->ny)||
+ (dim->z/moldyn->cutoff!=lc->nx)) {
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn);
+ }
return 0;
+
}
double get_e_kin(t_moldyn *moldyn) {
/* nn_dist is the nearest neighbour distance */
- if(moldyn->t==5.0) {
- printf("[moldyn] i do not estimate timesteps below %f K!\n",
- MOLDYN_CRITICAL_EST_TEMP);
- return 23.42;
- }
-
tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
return tau;
t_linkcell *lc;
int i;
- int fd;
-
- fd=open("/dev/null",O_WRONLY);
lc=&(moldyn->lc);
printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
for(i=0;i<lc->cells;i++)
- //list_init(&(lc->subcell[i]),1);
- list_init(&(lc->subcell[i]),fd);
+ list_init_f(&(lc->subcell[i]));
link_cell_update(moldyn);
int link_cell_update(t_moldyn *moldyn) {
int count,i,j,k;
- int nx,ny,nz;
+ int nx,ny;
t_atom *atom;
t_linkcell *lc;
+ double x,y,z;
atom=moldyn->atom;
lc=&(moldyn->lc);
nx=lc->nx;
ny=lc->ny;
- nz=lc->nz;
+
+ x=moldyn->dim.x/2;
+ y=moldyn->dim.y/2;
+ z=moldyn->dim.z/2;
for(i=0;i<lc->cells;i++)
- list_destroy(&(moldyn->lc.subcell[i]));
+ list_destroy_f(&(lc->subcell[i]));
for(count=0;count<moldyn->count;count++) {
- i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
- j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
- k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
- list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
- &(atom[count]));
+ i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
+ j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
+ k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
+ list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+ &(atom[count]));
}
return 0;
count2=27;
a=nx*ny;
-
cell[0]=lc->subcell[i+j*nx+k*a];
for(ci=-1;ci<=1;ci++) {
bx=0;
}
}
- lc->dnlc=count2;
- lc->countn=27;
+ lc->dnlc=count1;
- return count2;
+ return count1;
}
int link_cell_shutdown(t_moldyn *moldyn) {
lc=&(moldyn->lc);
for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
- list_shutdown(&(moldyn->lc.subcell[i]));
+ list_destroy_f(&(moldyn->lc.subcell[i]));
+
+ free(lc->subcell);
return 0;
}
unsigned int e,m,s,v;
t_3dvec p;
t_moldyn_schedule *schedule;
-
+ t_atom *atom;
int fd;
- char fb[128];
+ char dir[128];
+ double ds;
schedule=&(moldyn->schedule);
+ atom=moldyn->atom;
/* initialize linked cell method */
link_cell_init(moldyn);
/* calculate initial forces */
potential_force_calc(moldyn);
+ /* some stupid checks before we actually start calculating bullshit */
+ if(moldyn->cutoff>0.5*moldyn->dim.x)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
+ if(moldyn->cutoff>0.5*moldyn->dim.y)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+ if(moldyn->cutoff>0.5*moldyn->dim.z)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
+ ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
+ if(ds>0.05*moldyn->nnd)
+ printf("[moldyn] warning: forces too high / tau too small!\n");
+
/* zero absolute time */
moldyn->time=0.0;
+ /* debugging, ignore */
+ moldyn->debug=0;
+
+ /* executing the schedule */
for(sched=0;sched<moldyn->schedule.content_count;sched++) {
/* setting amount of runs and finite time step size */
/* integration step */
moldyn->integrate(moldyn);
- /* increase absolute time */
- moldyn->time+=moldyn->tau;
+ /* p/t scaling */
+ if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
+ scale_velocity(moldyn,FALSE);
+ if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
+ scale_volume(moldyn);
/* check for log & visualization */
if(e) {
if(!(i%e))
dprintf(moldyn->efd,
- "%.15f %.45f %.45f %.45f\n",
+ "%f %f %f %f\n",
moldyn->time,update_e_kin(moldyn),
moldyn->energy,
get_total_energy(moldyn));
if(!(i%m)) {
p=get_total_p(moldyn);
dprintf(moldyn->mfd,
- "%.15f %.45f\n",moldyn->time,
- v3_norm(&p));
+ "%f %f\n",moldyn->time,v3_norm(&p));
}
}
if(s) {
if(!(i%s)) {
- snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
- moldyn->t,i*moldyn->tau);
- fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
+ snprintf(dir,128,"%s/s-%07.f.save",
+ moldyn->vlsdir,moldyn->time);
+ fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
if(fd<0) perror("[moldyn] save fd open");
else {
write(fd,moldyn,sizeof(t_moldyn));
if(!(i%v)) {
visual_atoms(&(moldyn->vis),moldyn->time,
moldyn->atom,moldyn->count);
- printf("\rsched: %d, steps: %d",sched,i);
+ printf("\rsched: %d, steps: %d, debug: %d",
+ sched,i,moldyn->debug);
fflush(stdout);
}
}
+ /* increase absolute time */
+ moldyn->time+=moldyn->tau;
+
}
/* check for hooks */
if(schedule->hook)
schedule->hook(moldyn,schedule->hook_params);
+ /* get a new info line */
+ printf("\n");
+
}
return 0;
v3_add(&(atom[i].r),&(atom[i].r),&delta);
v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
v3_add(&(atom[i].r),&(atom[i].r),&delta);
- v3_per_bound(&(atom[i].r),&(moldyn->dim));
+ check_per_bound(moldyn,&(atom[i].r));
/* velocities */
v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
/* forces depending on chosen potential */
potential_force_calc(moldyn);
- //moldyn->potential_force_function(moldyn);
for(i=0;i<count;i++) {
/* again velocities */
int potential_force_calc(t_moldyn *moldyn) {
int i,j,k,count;
- t_atom *atom,*btom,*ktom;
+ t_atom *itom,*jtom,*ktom;
t_linkcell *lc;
- t_list neighbour[27];
- t_list *this,*thisk,*neighbourk;
- u8 bc,bck;
- int countn,dnlc;
+ t_list neighbour_i[27];
+ t_list neighbour_i2[27];
+ t_list *this,*that;
+ u8 bc_ij,bc_ik;
+ int dnlc;
count=moldyn->count;
- atom=moldyn->atom;
+ itom=moldyn->atom;
lc=&(moldyn->lc);
/* reset energy */
moldyn->energy=0.0;
-
-printf("DEBUG: count = %d\n",count);
- for(i=0;i<count;i++) {
+ /* get energy and force of every atom */
+ for(i=0;i<count;i++) {
+
/* reset force */
- v3_zero(&(atom[i].f));
+ v3_zero(&(itom[i].f));
+
+ /* reset viral of atom i */
+ v3_zero(&(itom[i].virial));
/* single particle potential/force */
- if(atom[i].attr&ATOM_ATTR_1BP)
- moldyn->func1b(moldyn,&(atom[i]));
+ if(itom[i].attr&ATOM_ATTR_1BP)
+ moldyn->func1b(moldyn,&(itom[i]));
+
+ if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
+ continue;
/* 2 body pair potential/force */
- if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
-printf("DEBUG: processing atom %d\n",i);
- 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);
+ link_cell_neighbour_index(moldyn,
+ (itom[i].r.x+moldyn->dim.x/2)/lc->x,
+ (itom[i].r.y+moldyn->dim.y/2)/lc->y,
+ (itom[i].r.z+moldyn->dim.z/2)/lc->z,
+ neighbour_i);
- countn=lc->countn;
- dnlc=lc->dnlc;
+ dnlc=lc->dnlc;
-printf("DEBUG: countn = %d - dnslc = %d\n",countn,dnlc);
- for(j=0;j<countn;j++) {
+ for(j=0;j<27;j++) {
- this=&(neighbour[j]);
- list_reset(this);
+ this=&(neighbour_i[j]);
+ list_reset_f(this);
- if(this->start==NULL)
- continue;
+ if(this->start==NULL)
+ continue;
- bc=(j<dnlc)?0:1;
+ bc_ij=(j<dnlc)?0:1;
- do {
- btom=this->current->data;
+ do {
+ jtom=this->current->data;
- if(btom==&(atom[i]))
- continue;
+ if(jtom==&(itom[i]))
+ continue;
- if((btom->attr&ATOM_ATTR_2BP)&
- (atom[i].attr&ATOM_ATTR_2BP))
-printf("DEBUG: calling func2b\n");
- moldyn->func2b(moldyn,
- &(atom[i]),
- btom,
- bc);
+ if((jtom->attr&ATOM_ATTR_2BP)&
+ (itom[i].attr&ATOM_ATTR_2BP)) {
+ moldyn->func2b(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+ }
- /* 3 body potential/force */
+ /* 3 body potential/force */
- if(!(atom[i].attr&ATOM_ATTR_3BP)||
- !(btom->attr&ATOM_ATTR_3BP))
- continue;
+ if(!(itom[i].attr&ATOM_ATTR_3BP)||
+ !(jtom->attr&ATOM_ATTR_3BP))
+ continue;
- link_cell_neighbour_index(moldyn,
- (btom->r.x+moldyn->dim.x/2)/lc->x,
- (btom->r.y+moldyn->dim.y/2)/lc->y,
- (btom->r.z+moldyn->dim.z/2)/lc->z,
- neighbourk);
+ /* copy the neighbour lists */
+ memcpy(neighbour_i2,neighbour_i,
+ 27*sizeof(t_list));
- for(k=0;k<lc->countn;k++) {
+ /* get neighbours of i */
+ for(k=0;k<27;k++) {
- thisk=&(neighbourk[k]);
- list_reset(thisk);
+ that=&(neighbour_i2[k]);
+ list_reset_f(that);
- if(thisk->start==NULL)
- continue;
+ if(that->start==NULL)
+ continue;
- bck=(k<lc->dnlc)?0:1;
+ bc_ik=(k<dnlc)?0:1;
- do {
+ do {
- ktom=thisk->current->data;
+ ktom=that->current->data;
- if(!(ktom->attr&ATOM_ATTR_3BP))
- continue;
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
- if(ktom==btom)
- continue;
+ if(ktom==jtom)
+ continue;
- if(ktom==&(atom[i]))
- continue;
+ if(ktom==&(itom[i]))
+ continue;
- moldyn->func3b(moldyn,&(atom[i]),btom,ktom,bck);
+ moldyn->func3b(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
- } while(list_next(thisk)!=\
- L_NO_NEXT_ELEMENT);
+ } while(list_next_f(that)!=\
+ L_NO_NEXT_ELEMENT);
- }
+ }
+
+ /* 2bp post function */
+ if(moldyn->func2b_post) {
+ moldyn->func2b_post(moldyn,
+ &(itom[i]),
+ jtom,bc_ij);
+ }
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
- }
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+
}
+
}
return 0;
* periodic boundayr checking
*/
-int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
double x,y,z;
t_3dvec *dim;
dim=&(moldyn->dim);
- x=0.5*dim->x;
- y=0.5*dim->y;
- z=0.5*dim->z;
+ x=dim->x/2;
+ y=dim->y/2;
+ z=dim->z/2;
if(moldyn->status&MOLDYN_STAT_PBX) {
if(a->x>=x) a->x-=dim->x;
sc=params->spring_constant;
equi_dist=params->equilibrium_distance;
- v3_sub(&distance,&(ai->r),&(aj->r));
+ v3_sub(&distance,&(aj->r),&(ai->r));
- v3_per_bound(&distance,&(moldyn->dim));
if(bc) check_per_bound(moldyn,&distance);
d=v3_norm(&distance);
if(d<=moldyn->cutoff) {
/* energy is 1/2 (d-d0)^2, but we will add this twice ... */
moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
- v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
+ /* f = -grad E; grad r_ij = -1 1/r_ij distance */
+ v3_scale(&force,&distance,sc*(1.0-(equi_dist/d)));
v3_add(&(ai->f),&(ai->f),&force);
}
sig6=params->sigma6;
sig12=params->sigma12;
- v3_sub(&distance,&(ai->r),&(aj->r));
+ v3_sub(&distance,&(aj->r),&(ai->r));
if(bc) check_per_bound(moldyn,&distance);
d=v3_absolute_square(&distance); /* 1/r^2 */
if(d<=moldyn->cutoff_square) {
h1*=12*sig12;
d=+h1-h2;
d*=eps;
- v3_scale(&force,&distance,d);
- v3_add(&(ai->f),&(aj->f),&force);
+ v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
+ v3_add(&(ai->f),&(ai->f),&force);
}
return 0;
* tersoff potential & force for 2 sorts of atoms
*/
+/* create mixed terms from parameters and set them */
+int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
+
+ printf("[moldyn] tersoff parameter completion\n");
+ p->Smixed=sqrt(p->S[0]*p->S[1]);
+ p->Rmixed=sqrt(p->R[0]*p->R[1]);
+ p->Amixed=sqrt(p->A[0]*p->A[1]);
+ p->Bmixed=sqrt(p->B[0]*p->B[1]);
+ p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
+ p->mu_m=0.5*(p->mu[0]+p->mu[1]);
+
+ printf("[moldyn] tersoff mult parameter info:\n");
+ printf(" S (A) | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
+ printf(" R (A) | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
+ printf(" A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
+ printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
+ printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
+ p->lambda_m);
+ printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
+ printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
+ printf(" n | %f | %f\n",p->n[0],p->n[1]);
+ printf(" c | %f | %f\n",p->c[0],p->c[1]);
+ printf(" d | %f | %f\n",p->d[0],p->d[1]);
+ printf(" h | %f | %f\n",p->h[0],p->h[1]);
+ printf(" chi | %f \n",p->chi);
+
+ return 0;
+}
+
/* tersoff 1 body part */
int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
* their right values
*/
- exchange->beta=&(params->beta[num]);
- exchange->n=&(params->n[num]);
- exchange->c=&(params->c[num]);
- exchange->d=&(params->d[num]);
- exchange->h=&(params->h[num]);
+ exchange->beta_i=&(params->beta[num]);
+ exchange->n_i=&(params->n[num]);
+ exchange->c_i=&(params->c[num]);
+ exchange->d_i=&(params->d[num]);
+ exchange->h_i=&(params->h[num]);
- exchange->betan=pow(*(exchange->beta),*(exchange->n));
- exchange->c2=params->c[num]*params->c[num];
- exchange->d2=params->d[num]*params->d[num];
- exchange->c2d2=exchange->c2/exchange->d2;
+ exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
+ exchange->ci2=params->c[num]*params->c[num];
+ exchange->di2=params->d[num]*params->d[num];
+ exchange->ci2di2=exchange->ci2/exchange->di2;
return 0;
}
int num;
double s_r;
double arg;
- double scale;
params=moldyn->pot2b_params;
- num=ai->bnum;
+ num=aj->bnum;
exchange=&(params->exchange);
+ /* clear 3bp and 2bp post run */
exchange->run3bp=0;
+ exchange->run2bp_post=0;
+
+ /* reset S > r > R mark */
+ exchange->d_ij_between_rs=0;
/*
- * we need: f_c, df_c, f_r, df_r
+ * calc of 2bp contribution of V_ij and dV_ij/ji
+ *
+ * for Vij and dV_ij we need:
+ * - f_c_ij, df_c_ij
+ * - f_r_ij, df_r_ij
+ *
+ * for dV_ji we need:
+ * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
+ * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
*
- * therefore we need: R, S, A, lambda
*/
- v3_sub(&dist_ij,&(ai->r),&(aj->r));
-
+ /* dist_ij, d_ij */
+ v3_sub(&dist_ij,&(aj->r),&(ai->r));
if(bc) check_per_bound(moldyn,&dist_ij);
+ d_ij=v3_norm(&dist_ij);
- /* save for use in 3bp */ /* REALLY ?!?!?! */
+ /* save for use in 3bp */
+ exchange->d_ij=d_ij;
exchange->dist_ij=dist_ij;
/* constants */
- if(num==aj->bnum) {
+ if(num==ai->bnum) {
S=params->S[num];
R=params->R[num];
A=params->A[num];
+ B=params->B[num];
lambda=params->lambda[num];
- /* more constants depending of atoms i and j, needed in 3bp */
- params->exchange.B=&(params->B[num]);
- params->exchange.mu=&(params->mu[num]);
mu=params->mu[num];
- params->exchange.chi=1.0;
+ exchange->chi=1.0;
}
else {
S=params->Smixed;
R=params->Rmixed;
A=params->Amixed;
+ B=params->Bmixed;
lambda=params->lambda_m;
- /* more constants depending of atoms i and j, needed in 3bp */
- params->exchange.B=&(params->Bmixed);
- params->exchange.mu=&(params->mu_m);
mu=params->mu_m;
params->exchange.chi=params->chi;
}
- d_ij=v3_norm(&dist_ij);
-
- /* save for use in 3bp */
- exchange->d_ij=d_ij;
-
+ /* if d_ij > S => no force & potential energy contribution */
if(d_ij>S)
return 0;
+ /* more constants */
+ exchange->beta_j=&(params->beta[num]);
+ exchange->n_j=&(params->n[num]);
+ exchange->c_j=&(params->c[num]);
+ exchange->d_j=&(params->d[num]);
+ exchange->h_j=&(params->h[num]);
+ if(num==ai->bnum) {
+ exchange->betajnj=exchange->betaini;
+ exchange->cj2=exchange->ci2;
+ exchange->dj2=exchange->di2;
+ exchange->cj2dj2=exchange->ci2di2;
+ }
+ else {
+ exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
+ exchange->cj2=params->c[num]*params->c[num];
+ exchange->dj2=params->d[num]*params->d[num];
+ exchange->cj2dj2=exchange->cj2/exchange->dj2;
+ }
+
+ /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
f_r=A*exp(-lambda*d_ij);
- df_r=-lambda*f_r/d_ij;
+ df_r=lambda*f_r/d_ij;
- /* f_a, df_a calc + save for 3bp use */
+ /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
exchange->f_a=-B*exp(-mu*d_ij);
- exchange->df_a=-mu*exchange->f_a/d_ij;
+ exchange->df_a=mu*exchange->f_a/d_ij;
+ /* f_c, df_c calc (again, same for ij and ji) */
if(d_ij<R) {
/* f_c = 1, df_c = 0 */
f_c=1.0;
df_c=0.0;
- v3_scale(&force,&dist_ij,df_r);
+ /* two body contribution (ij, ji) */
+ v3_scale(&force,&dist_ij,-df_r);
}
else {
s_r=S-R;
arg=M_PI*(d_ij-R)/s_r;
f_c=0.5+0.5*cos(arg);
- df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
- scale=df_c*f_r+df_r*f_c;
- v3_scale(&force,&dist_ij,scale);
+ //df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij)); /* MARK! */
+ df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
+ /* two body contribution (ij, ji) */
+ v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
+ /* tell 3bp that S > r > R */
+ exchange->d_ij_between_rs=1;
}
- /* add forces */
+ /* add forces of 2bp (ij, ji) contribution
+ * dVij = dVji and we sum up both: no 1/2) */
v3_add(&(ai->f),&(ai->f),&force);
- /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
- moldyn->energy+=(0.25*f_r*f_c);
+
+ /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
+ moldyn->energy+=(0.5*f_r*f_c);
/* save for use in 3bp */
exchange->f_c=f_c;
exchange->df_c=df_c;
- /* enable the run of 3bp function */
+ /* enable the run of 3bp function and 2bp post processing */
exchange->run3bp=1;
+ exchange->run2bp_post=1;
+
+ /* reset 3bp sums */
+ exchange->zeta_ij=0.0;
+ exchange->zeta_ji=0.0;
+ v3_zero(&(exchange->dzeta_ij));
+ v3_zero(&(exchange->dzeta_ji));
+
+ return 0;
+}
+
+/* tersoff 2 body post part */
+
+int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+ /*
+ * here we have to allow for the 3bp sums
+ *
+ * that is:
+ * - zeta_ij, dzeta_ij
+ * - zeta_ji, dzeta_ji
+ *
+ * to compute the 3bp contribution to:
+ * - Vij, dVij
+ * - dVji
+ *
+ */
+
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+
+ t_3dvec force,temp;
+ t_3dvec *dist_ij;
+ double b,db,tmp;
+ double f_c,df_c,f_a,df_a;
+ double chi,ni,betaini,nj,betajnj;
+ double zeta;
+
+ params=moldyn->pot2b_params;
+ exchange=&(params->exchange);
+
+ /* we do not run if f_c_ij was detected to be 0! */
+ if(!(exchange->run2bp_post))
+ return 0;
+
+ f_c=exchange->f_c;
+ df_c=exchange->df_c;
+ f_a=exchange->f_a;
+ df_a=exchange->df_a;
+ betaini=exchange->betaini;
+ betajnj=exchange->betajnj;
+ ni=*(exchange->n_i);
+ nj=*(exchange->n_j);
+ chi=exchange->chi;
+ dist_ij=&(exchange->dist_ij);
+
+ /* Vij and dVij */
+ zeta=exchange->zeta_ij;
+ if(zeta==0.0) {
+ moldyn->debug++; /* just for debugging ... */
+ db=0.0;
+ b=chi;
+ v3_scale(&force,dist_ij,df_a*b*f_c);
+ }
+ else {
+ tmp=betaini*pow(zeta,ni-1.0); /* beta^n * zeta^n-1 */
+ b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
+ db=chi*pow(b,-1.0/(2*ni)-1); /* x(...)^(-1/2n - 1) */
+ b=db*b; /* b_ij */
+ db*=-0.5*tmp; /* db_ij */
+ v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
+ v3_scale(&temp,dist_ij,df_a*b);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,f_c);
+ }
+ v3_scale(&temp,dist_ij,df_c*b*f_a);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,-0.5);
+
+ /* add force */
+ v3_add(&(ai->f),&(ai->f),&force);
+
+ /* add energy of 3bp sum */
+ moldyn->energy+=(0.5*f_c*b*f_a);
+
+ /* dVji */
+ zeta=exchange->zeta_ji;
+ if(zeta==0.0) {
+ moldyn->debug++;
+ b=chi;
+ v3_scale(&force,dist_ij,df_a*b*f_c);
+ }
+ else {
+ tmp=betajnj*pow(zeta,nj-1.0); /* beta^n * zeta^n-1 */
+ b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
+ db=chi*pow(b,-1.0/(2*nj)-1); /* x(...)^(-1/2n - 1) */
+ b=db*b; /* b_ij */
+ db*=-0.5*tmp; /* db_ij */
+ v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
+ v3_scale(&temp,dist_ij,df_a*b);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,f_c);
+ }
+ v3_scale(&temp,dist_ij,df_c*b*f_a);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,-0.5);
+
+ /* add force */
+ v3_add(&(ai->f),&(ai->f),&force);
return 0;
}
t_tersoff_mult_params *params;
t_tersoff_exchange *exchange;
t_3dvec dist_ij,dist_ik,dist_jk;
- t_3dvec temp,force;
+ t_3dvec temp1,temp2;
+ t_3dvec *dzeta;
double R,S,s_r;
- double d_ij,d_ij2,d_ik,d_jk;
- double f_c,df_c,b_ij,f_a,df_a;
+ double B,mu;
+ double d_ij,d_ik,d_jk;
+ double rr,dd;
+ double f_c,df_c;
double f_c_ik,df_c_ik,arg;
- double scale;
- double chi;
- double n,c,d,h,beta,betan;
+ double f_c_jk;
+ double n,c,d,h;
double c2,d2,c2d2;
- double numer,denom;
- double theta,cos_theta,sin_theta;
- double d_theta,d_theta1,d_theta2;
- double h_cos,h_cos2,d2_h_cos2;
- double frac1,bracket1,bracket2,bracket2_n_1,bracket2_n;
- double bracket3,bracket3_pow_1,bracket3_pow;
+ double cos_theta,d_costheta1,d_costheta2;
+ double h_cos,d2_h_cos2;
+ double frac,g,zeta,chi;
+ double tmp;
int num;
params=moldyn->pot3b_params;
- num=ai->bnum;
exchange=&(params->exchange);
if(!(exchange->run3bp))
return 0;
/*
- * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
+ * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
+ * 2bp contribution of dV_jk
+ *
+ * for Vij and dV_ij we still need:
+ * - b_ij, db_ij (zeta_ij)
+ * - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
*
- * we got f_c, df_c, f_a, df_a from 2bp calculation
+ * for dV_ji we still need:
+ * - b_ji, db_ji (zeta_ji)
+ * - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
+ *
+ * for dV_jk we need:
+ * - f_c_jk
+ * - f_a_jk
+ * - db_jk (zeta_jk)
+ * - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
+ *
+ */
+
+ /*
+ * get exchange data
*/
+ /* dist_ij, d_ij - this is < S_ij ! */
+ dist_ij=exchange->dist_ij;
d_ij=exchange->d_ij;
- d_ij2=exchange->d_ij2;
- f_a=params->exchange.f_a;
- df_a=params->exchange.df_a;
-
- /* d_ij is <= S, as we didn't return so far! */
+ /* f_c_ij, df_c_ij (same for ji) */
+ f_c=exchange->f_c;
+ df_c=exchange->df_c;
/*
- * calc of b_ij (scalar) and db_ij (vector)
- *
- * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
- *
- * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
- * w_ik,
- *
+ * calculate unknown values now ...
*/
-
- v3_sub(&dist_ik,&(ai->r),&(ak->r));
+ /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
+
+ /* dist_ik, d_ik */
+ v3_sub(&dist_ik,&(ak->r),&(ai->r));
if(bc) check_per_bound(moldyn,&dist_ik);
d_ik=v3_norm(&dist_ik);
- /* constants for f_c_ik calc */
+ /* ik constants */
+ num=ai->bnum;
if(num==ak->bnum) {
R=params->R[num];
S=params->S[num];
S=params->Smixed;
}
- /* calc of f_c_ik */
- if(d_ik>S)
- return 0;
+ /* zeta_ij/dzeta_ij contribution only for d_ik < S */
+ if(d_ik<S) {
+
+ /* get constants_i from exchange data */
+ n=*(exchange->n_i);
+ c=*(exchange->c_i);
+ d=*(exchange->d_i);
+ h=*(exchange->h_i);
+ c2=exchange->ci2;
+ d2=exchange->di2;
+ c2d2=exchange->ci2di2;
+
+ /* cosine of theta_ijk by scalaproduct */
+ rr=v3_scalar_product(&dist_ij,&dist_ik);
+ dd=d_ij*d_ik;
+ cos_theta=rr/dd;
+
+ /* d_costheta */
+ tmp=1.0/dd;
+ d_costheta1=cos_theta/(d_ij*d_ij)-tmp;
+ d_costheta2=cos_theta/(d_ik*d_ik)-tmp;
+
+ /* some usefull values */
+ h_cos=(h-cos_theta);
+ d2_h_cos2=d2+(h_cos*h_cos);
+ frac=c2/(d2_h_cos2);
+
+ /* g(cos_theta) */
+ g=1.0+c2d2-frac;
+
+ /* d_costheta_ij and dg(cos_theta) - needed in any case! */
+ v3_scale(&temp1,&dist_ij,d_costheta1);
+ v3_scale(&temp2,&dist_ik,d_costheta2);
+ v3_add(&temp1,&temp1,&temp2);
+ v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
+
+ /* f_c_ik & df_c_ik + {d,}zeta contribution */
+ dzeta=&(exchange->dzeta_ij);
+ if(d_ik<R) {
+ /* {d,}f_c_ik */
+ // => f_c_ik=1.0;
+ // => df_c_ik=0.0; of course we do not set this!
+
+ /* zeta_ij */
+ exchange->zeta_ij+=g;
+
+ /* dzeta_ij */
+ v3_add(dzeta,dzeta,&temp1);
+ }
+ else {
+ /* {d,}f_c_ik */
+ s_r=S-R;
+ arg=M_PI*(d_ik-R)/s_r;
+ f_c_ik=0.5+0.5*cos(arg);
+ //df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik)); /* MARK */
+ df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
+
+ /* zeta_ij */
+ exchange->zeta_ij+=f_c_ik*g;
+
+ /* dzeta_ij */
+ v3_scale(&temp1,&temp1,f_c_ik);
+ v3_scale(&temp2,&dist_ik,g*df_c_ik);
+ v3_add(&temp1,&temp1,&temp2);
+ v3_add(dzeta,dzeta,&temp1);
+ }
+ }
+
+ /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
- if(d_ik<R) {
- /* f_c_ik = 1, df_c_ik = 0 */
- f_c_ik=1.0;
- df_c_ik=0.0;
+ /* dist_jk, d_jk */
+ v3_sub(&dist_jk,&(ak->r),&(aj->r));
+ if(bc) check_per_bound(moldyn,&dist_jk);
+ d_jk=v3_norm(&dist_jk);
+
+ /* jk constants */
+ num=aj->bnum;
+ if(num==ak->bnum) {
+ R=params->R[num];
+ S=params->S[num];
+ B=params->B[num];
+ mu=params->mu[num];
+ chi=1.0;
}
else {
- s_r=S-R;
- arg=M_PI*(d_ik-R)/s_r;
- f_c_ik=0.5+0.5*cos(arg);
- df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
+ R=params->Rmixed;
+ S=params->Smixed;
+ B=params->Bmixed;
+ mu=params->mu_m;
+ chi=params->chi;
}
-
- v3_sub(&dist_jk,&(aj->r),&(ak->r));
- if(bc) check_per_bound(moldyn,&dist_jk);
- d_jk=v3_norm(&dist_jk);
- beta=*(exchange->beta);
- betan=exchange->betan;
- n=*(exchange->n);
- c=*(exchange->c);
- d=*(exchange->d);
- h=*(exchange->h);
- c2=exchange->c2;
- d2=exchange->d2;
- c2d2=exchange->c2d2;
-
- numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
- denom=2*d_ij*d_ik;
- cos_theta=numer/denom;
- sin_theta=sqrt(1.0-(cos_theta*cos_theta));
- theta=acos(cos_theta);
- d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
- d_theta1=2*denom-numer*2*d_ik/d_ij;
- d_theta2=2*denom-numer*2*d_ij/d_ik;
- d_theta1*=d_theta;
- d_theta2*=d_theta;
-
- h_cos=(h-cos_theta);
- h_cos2=h_cos*h_cos;
- d2_h_cos2=d2-h_cos2;
-
- /* some usefull expressions */
- frac1=c2/(d2-h_cos2);
- bracket1=1+c2d2-frac1;
- bracket2=f_c_ik*bracket1;
- bracket2_n_1=pow(bracket2,n-1.0);
- bracket2_n=bracket2_n_1*bracket2;
- bracket3=1+betan*bracket2_n;
- bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
- bracket3_pow=bracket3_pow_1*bracket3;
-
- /* now go on with calc of b_ij and derivation of b_ij */
- b_ij=chi*bracket3_pow;
-
- /* derivation of theta */
- v3_scale(&force,&dist_ij,d_theta1);
- v3_scale(&temp,&dist_ik,d_theta2);
- v3_add(&force,&force,&temp);
+ /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
+ if(d_jk<S) {
+
+ /* constants_j from exchange data */
+ n=*(exchange->n_j);
+ c=*(exchange->c_j);
+ d=*(exchange->d_j);
+ h=*(exchange->h_j);
+ c2=exchange->cj2;
+ d2=exchange->dj2;
+ c2d2=exchange->cj2dj2;
+
+ /* cosine of theta_jik by scalaproduct */
+ rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
+ dd=d_ij*d_jk;
+ cos_theta=rr/dd;
+
+ /* d_costheta */
+ d_costheta1=1.0/dd;
+ d_costheta2=cos_theta/(d_ij*d_ij);
+
+ /* some usefull values */
+ h_cos=(h-cos_theta);
+ d2_h_cos2=d2+(h_cos*h_cos);
+ frac=c2/(d2_h_cos2);
+
+ /* g(cos_theta) */
+ g=1.0+c2d2-frac;
+
+ /* d_costheta_ij and dg(cos_theta) - needed in any case! */
+ v3_scale(&temp1,&dist_jk,d_costheta1);
+ v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
+ v3_add(&temp1,&temp1,&temp2);
+ v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
+
+ /* store dg in temp2 and use it for dVjk later */
+ v3_copy(&temp2,&temp1);
+
+ /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
+ dzeta=&(exchange->dzeta_ji);
+ if(d_jk<R) {
+ /* f_c_jk */
+ f_c_jk=1.0;
+
+ /* zeta_ji */
+ exchange->zeta_ji+=g;
+
+ /* dzeta_ji */
+ v3_add(dzeta,dzeta,&temp1);
+ }
+ else {
+ /* f_c_jk */
+ s_r=S-R;
+ arg=M_PI*(d_jk-R)/s_r;
+ f_c_jk=0.5+0.5*cos(arg);
+
+ /* zeta_ji */
+ exchange->zeta_ji+=f_c_jk*g;
+
+ /* dzeta_ji */
+ v3_scale(&temp1,&temp1,f_c_jk);
+ v3_add(dzeta,dzeta,&temp1);
+ }
- /* part 1 of derivation of b_ij */
- v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1);
+ /* dV_jk stuff | add force contribution on atom i immediately */
+ if(exchange->d_ij_between_rs) {
+ zeta=f_c*g;
+ v3_scale(&temp1,&temp2,f_c);
+ v3_scale(&temp2,&dist_ij,df_c*g);
+ v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
+ }
+ else {
+ zeta=g;
+ // dzeta_jk is simply dg, which is stored in temp2
+ }
+ /* betajnj * zeta_jk ^ nj-1 */
+ tmp=exchange->betajnj*pow(zeta,(n-1.0));
+ tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
+ v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
+ v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
+ /* scaled with 0.5 ^ */
- /* part 2 of derivation of b_ij */
- v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
+ }
- /* sum up and scale ... */
- v3_add(&temp,&temp,&force);
- scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
- v3_scale(&temp,&temp,scale);
+ return 0;
+}
- /* now construct an energy and a force out of that */
- v3_scale(&temp,&temp,f_a);
- v3_scale(&force,&dist_ij,df_a*b_ij);
- v3_add(&temp,&temp,&force);
- v3_scale(&temp,&temp,f_c);
- v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
- v3_add(&force,&force,&temp);
- /* add forces */
- v3_add(&(ai->f),&(ai->f),&force);
- /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
- moldyn->energy+=(0.25*f_a*b_ij*f_c);
-
+/*
+ * debugging / critical check functions
+ */
+
+int moldyn_bc_check(t_moldyn *moldyn) {
+
+ t_atom *atom;
+ t_3dvec *dim;
+ int i;
+double x;
+u8 byte;
+int j,k;
+
+ atom=moldyn->atom;
+ dim=&(moldyn->dim);
+x=dim->x/2;
+
+ for(i=0;i<moldyn->count;i++) {
+ if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
+ printf("FATAL: atom %d: x: %.20f (%.20f)\n",
+ i,atom[i].r.x,dim->x/2);
+ printf("diagnostic:\n");
+ printf("-----------\natom.r.x:\n");
+ for(j=0;j<8;j++) {
+ memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
+ for(k=0;k<8;k++)
+ printf("%d%c",
+ ((byte)&(1<<k))?1:0,
+ (k==7)?'\n':'|');
+ }
+ printf("---------------\nx=dim.x/2:\n");
+ for(j=0;j<8;j++) {
+ memcpy(&byte,(u8 *)(&x)+j,1);
+ for(k=0;k<8;k++)
+ printf("%d%c",
+ ((byte)&(1<<k))?1:0,
+ (k==7)?'\n':'|');
+ }
+ if(atom[i].r.x==x) printf("the same!\n");
+ else printf("different!\n");
+ }
+ if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
+ printf("FATAL: atom %d: y: %.20f (%.20f)\n",
+ i,atom[i].r.y,dim->y/2);
+ if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
+ printf("FATAL: atom %d: z: %.20f (%.20f)\n",
+ i,atom[i].r.z,dim->z/2);
+ }
+
return 0;
}
-
projects / physik / posic.git / blobdiff