#include "init/init.h"
#include "random/random.h"
#include "visual/visual.h"
+#include "list/list.h"
-int moldyn_usage(char **argv) {
- printf("\n%s usage:\n\n",argv[0]);
- printf("--- general options ---\n");
- printf("-E <steps> <file> (log total energy)\n");
- printf("-M <steps> <file> (log total momentum)\n");
- printf("-D <steps> <file> (dump total information)\n");
- printf("-S <steps> <filebase> (single save file)\n");
- printf("--- physics options ---\n");
- printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
- printf("-t <timestep tau> [s] (%f)\n",MOLDYN_TAU);
- printf("-R <runs> (%d)\n",MOLDYN_RUNS);
- printf("\n");
+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);
+ moldyn->random.status|=RAND_STAT_VERBOSE;
return 0;
}
-int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
+int moldyn_shutdown(t_moldyn *moldyn) {
- int i;
+ printf("[moldyn] shutdown\n");
+ moldyn_log_shutdown(moldyn);
+ link_cell_shutdown(moldyn);
+ rand_close(&(moldyn->random));
+ free(moldyn->atom);
- memset(moldyn,0,sizeof(t_moldyn));
+ return 0;
+}
- /* default values */
- moldyn->t=MOLDYN_TEMP;
- moldyn->tau=MOLDYN_TAU;
- moldyn->time_steps=MOLDYN_RUNS;
-
- /* parse argv */
- for(i=1;i<argc;i++) {
- if(argv[i][0]=='-') {
- switch(argv[i][1]){
- case 'E':
- moldyn->ewrite=atoi(argv[++i]);
- strncpy(moldyn->efb,argv[++i],64);
- break;
- case 'M':
- moldyn->mwrite=atoi(argv[++i]);
- strncpy(moldyn->mfb,argv[++i],64);
- break;
- case 'D':
- moldyn->dwrite=atoi(argv[++i]);
- strncpy(moldyn->dfb,argv[++i],64);
- break;
- case 'S':
- moldyn->swrite=atoi(argv[++i]);
- strncpy(moldyn->sfb,argv[++i],64);
- break;
- case 'T':
- break;
- moldyn->t=atof(argv[++i]);
- case 't':
- moldyn->tau=atof(argv[++i]);
- break;
- case 'R':
- moldyn->time_steps=atoi(argv[++i]);
- break;
- default:
- printf("unknown option %s\n",argv[i]);
- moldyn_usage(argv);
- return -1;
- }
- } else {
- moldyn_usage(argv);
+int set_int_alg(t_moldyn *moldyn,u8 algo) {
+
+ switch(algo) {
+ case MOLDYN_INTEGRATE_VERLET:
+ moldyn->integrate=velocity_verlet;
+ break;
+ default:
+ printf("unknown integration algorithm: %02x\n",algo);
return -1;
- }
}
return 0;
}
-int moldyn_log_init(t_moldyn *moldyn) {
+int set_cutoff(t_moldyn *moldyn,double cutoff) {
- moldyn->lvstat=0;
+ moldyn->cutoff=cutoff;
- if(moldyn->ewrite) {
- moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
- if(moldyn->efd<0) {
- perror("[moldyn] efd open");
- return moldyn->efd;
- }
- dprintf(moldyn->efd,"# moldyn total energy logfile\n");
- moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_E;
- }
+ return 0;
+}
- if(moldyn->mwrite) {
- moldyn->mfd=open(moldyn->mfb,O_WRONLY|O_CREAT|O_TRUNC);
- if(moldyn->mfd<0) {
- perror("[moldyn] mfd open");
- return moldyn->mfd;
- }
- dprintf(moldyn->mfd,"# moldyn total momentum logfile\n");
- moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_M;
+int set_temperature(t_moldyn *moldyn,double t_ref) {
+
+ moldyn->t_ref=t_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;
+}
+
+int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
+
+ moldyn->dim.x=x;
+ moldyn->dim.y=y;
+ moldyn->dim.z=z;
+
+ if(visualize) {
+ moldyn->vis.dim.x=x;
+ moldyn->vis.dim.y=y;
+ moldyn->vis.dim.z=z;
}
- if(moldyn->swrite)
- moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
+ return 0;
+}
- if(moldyn->dwrite) {
- moldyn->dfd=open(moldyn->dfb,O_WRONLY|O_CREAT|O_TRUNC);
- if(moldyn->dfd<0) {
- perror("[moldyn] dfd open");
- return moldyn->dfd;
- }
- write(moldyn->dfd,moldyn,sizeof(t_moldyn));
- moldyn->lvstat|=MOLDYN_LVSTAT_DUMP;
+int set_nn_dist(t_moldyn *moldyn,double dist) {
+
+ moldyn->nnd=dist;
+
+ return 0;
+}
+
+int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
+
+ if(x)
+ moldyn->status|=MOLDYN_STAT_PBX;
+
+ if(y)
+ moldyn->status|=MOLDYN_STAT_PBY;
+
+ if(z)
+ moldyn->status|=MOLDYN_STAT_PBZ;
+
+ return 0;
+}
+
+int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
+
+ moldyn->func1b=func;
+ moldyn->pot1b_params=params;
+
+ return 0;
+}
+
+int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
+
+ moldyn->func2b=func;
+ moldyn->pot2b_params=params;
+
+ return 0;
+}
+
+int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
+
+ moldyn->func3b=func;
+ moldyn->pot3b_params=params;
+
+ return 0;
+}
+
+int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
+
+ switch(type) {
+ case LOG_TOTAL_ENERGY:
+ moldyn->ewrite=timer;
+ moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+ if(moldyn->efd<0) {
+ perror("[moldyn] efd 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);
+ if(moldyn->mfd<0) {
+ perror("[moldyn] mfd 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);
+ break;
+ default:
+ printf("unknown log mechanism: %02x\n",type);
+ return -1;
}
- if(moldyn->dwrite)
- moldyn->lvstat|=MOLDYN_LVSTAT_VISUAL;
+ return 0;
+}
+
+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->vis)) visual_tini(&(moldyn->vis));
return 0;
}
-int create_lattice(unsigned char type,int element,double mass,double lc,
- int a,int b,int c,t_atom **atom) {
+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;
count=a*b*c;
if(type==FCC) count*=4;
+
if(type==DIAMOND) count*=8;
- *atom=malloc(count*sizeof(t_atom));
- if(*atom==NULL) {
+ 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);
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;
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;
}
-int destroy_lattice(t_atom *atom) {
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
+ t_3dvec *r,t_3dvec *v) {
- if(atom) free(atom);
+ t_atom *atom;
+ void *ptr;
+ int count;
+
+ atom=moldyn->atom;
+ count=++(moldyn->count);
+
+ ptr=realloc(atom,count*sizeof(t_atom));
+ if(!ptr) {
+ perror("[moldyn] realloc (add atom)");
+ return -1;
+ }
+ moldyn->atom=ptr;
+
+ atom=moldyn->atom;
+ 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;
+}
+
+int destroy_atoms(t_moldyn *moldyn) {
+
+ if(moldyn->atom) free(moldyn->atom);
return 0;
}
-int thermal_init(t_moldyn *moldyn,t_random *random,int count) {
+int thermal_init(t_moldyn *moldyn,u8 equi_init) {
/*
* - gaussian distribution of velocities
double v,sigma;
t_3dvec p_total,delta;
t_atom *atom;
+ t_random *random;
atom=moldyn->atom;
+ random=&(moldyn->random);
/* gaussian distribution of velocities */
v3_zero(&p_total);
- for(i=0;i<count;i++) {
- sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
+ for(i=0;i<moldyn->count;i++) {
+ 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;
}
/* zero total momentum */
- v3_scale(&p_total,&p_total,1.0/count);
- for(i=0;i<count;i++) {
+ v3_scale(&p_total,&p_total,1.0/moldyn->count);
+ for(i=0;i<moldyn->count;i++) {
v3_scale(&delta,&p_total,1.0/atom[i].mass);
v3_sub(&(atom[i].v),&(atom[i].v),&delta);
}
/* velocity scaling */
- scale_velocity(moldyn,count);
+ scale_velocity(moldyn,equi_init);
return 0;
}
-int scale_velocity(t_moldyn *moldyn,int count) {
+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;
- for(i=0;i<count;i++)
- e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
- c=sqrt((2.0*e)/(3.0*count*K_BOLTZMANN*moldyn->t));
- for(i=0;i<count;i++)
- v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
+ 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=(2.0*e)/(3.0*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);
+ 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+moldyn->tau*(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;
}
-double get_e_kin(t_atom *atom,int count) {
+double get_e_kin(t_moldyn *moldyn) {
int i;
- double e;
+ t_atom *atom;
- e=0.0;
+ atom=moldyn->atom;
+ moldyn->ekin=0.0;
- for(i=0;i<count;i++) {
- e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
- }
+ for(i=0;i<moldyn->count;i++)
+ moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
- return e;
+ return moldyn->ekin;
}
double get_e_pot(t_moldyn *moldyn) {
- return(moldyn->potential(moldyn));
+ return moldyn->energy;
}
-double get_total_energy(t_moldyn *moldyn) {
+double update_e_kin(t_moldyn *moldyn) {
- double e;
+ return(get_e_kin(moldyn));
+}
- e=get_e_kin(moldyn->atom,moldyn->count);
- e+=get_e_pot(moldyn);
+double get_total_energy(t_moldyn *moldyn) {
- return e;
+ return(moldyn->ekin+moldyn->energy);
}
-t_3dvec get_total_p(t_atom *atom, int count) {
+t_3dvec get_total_p(t_moldyn *moldyn) {
t_3dvec p,p_total;
int i;
+ t_atom *atom;
+
+ atom=moldyn->atom;
v3_zero(&p_total);
- for(i=0;i<count;i++) {
+ for(i=0;i<moldyn->count;i++) {
v3_scale(&p,&(atom[i].v),atom[i].mass);
v3_add(&p_total,&p_total,&p);
}
return p_total;
}
-double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
+double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
double tau;
- tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
- tau*=1.0E-9;
- if(tau<moldyn->tau)
- printf("[moldyn] warning: time step (%f > %.15f)\n",
- moldyn->tau,tau);
+ /* 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;
}
+/*
+ * numerical tricks
+ */
+
+/* linked list / cell method */
+
+int link_cell_init(t_moldyn *moldyn) {
+
+ t_linkcell *lc;
+ int i;
+ int fd;
+
+ fd=open("/dev/null",O_WRONLY);
+
+ lc=&(moldyn->lc);
+
+ /* partitioning the md cell */
+ lc->nx=moldyn->dim.x/moldyn->cutoff;
+ lc->x=moldyn->dim.x/lc->nx;
+ lc->ny=moldyn->dim.y/moldyn->cutoff;
+ lc->y=moldyn->dim.y/lc->ny;
+ lc->nz=moldyn->dim.z/moldyn->cutoff;
+ lc->z=moldyn->dim.z/lc->nz;
+
+ lc->cells=lc->nx*lc->ny*lc->nz;
+ lc->subcell=malloc(lc->cells*sizeof(t_list));
+
+ 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);
+
+ link_cell_update(moldyn);
+
+ return 0;
+}
+
+int link_cell_update(t_moldyn *moldyn) {
+
+ int count,i,j,k;
+ int nx,ny,nz;
+ t_atom *atom;
+ t_linkcell *lc;
+
+ atom=moldyn->atom;
+ lc=&(moldyn->lc);
+
+ nx=lc->nx;
+ ny=lc->ny;
+ nz=lc->nz;
+
+ for(i=0;i<lc->cells;i++)
+ list_destroy(&(moldyn->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]));
+ }
+
+ return 0;
+}
+
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
+
+ t_linkcell *lc;
+ int a;
+ int count1,count2;
+ int ci,cj,ck;
+ int nx,ny,nz;
+ int x,y,z;
+ u8 bx,by,bz;
+
+ lc=&(moldyn->lc);
+ nx=lc->nx;
+ ny=lc->ny;
+ nz=lc->nz;
+ count1=1;
+ count2=27;
+ a=nx*ny;
+
+ cell[0]=lc->subcell[i+j*nx+k*a];
+ for(ci=-1;ci<=1;ci++) {
+ bx=0;
+ x=i+ci;
+ if((x<0)||(x>=nx)) {
+ x=(x+nx)%nx;
+ bx=1;
+ }
+ for(cj=-1;cj<=1;cj++) {
+ by=0;
+ y=j+cj;
+ if((y<0)||(y>=ny)) {
+ y=(y+ny)%ny;
+ by=1;
+ }
+ for(ck=-1;ck<=1;ck++) {
+ bz=0;
+ z=k+ck;
+ if((z<0)||(z>=nz)) {
+ z=(z+nz)%nz;
+ bz=1;
+ }
+ if(!(ci|cj|ck)) continue;
+ if(bx|by|bz) {
+ cell[--count2]=lc->subcell[x+y*nx+z*a];
+ }
+ else {
+ cell[count1++]=lc->subcell[x+y*nx+z*a];
+ }
+ }
+ }
+ }
+
+ lc->dnlc=count1;
+ lc->countn=27;
+
+ return count2;
+}
+
+int link_cell_shutdown(t_moldyn *moldyn) {
+
+ int i;
+ t_linkcell *lc;
+
+ lc=&(moldyn->lc);
+
+ for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
+ list_shutdown(&(moldyn->lc.subcell[i]));
+
+ return 0;
+}
+
+int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
+
+ int count;
+ void *ptr;
+ t_moldyn_schedule *schedule;
+
+ schedule=&(moldyn->schedule);
+ count=++(schedule->content_count);
+
+ ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
+ if(!ptr) {
+ perror("[moldyn] realloc (runs)");
+ return -1;
+ }
+ moldyn->schedule.runs=ptr;
+ moldyn->schedule.runs[count-1]=runs;
+
+ ptr=realloc(schedule->tau,count*sizeof(double));
+ if(!ptr) {
+ perror("[moldyn] realloc (tau)");
+ return -1;
+ }
+ moldyn->schedule.tau=ptr;
+ moldyn->schedule.tau[count-1]=tau;
+
+ return 0;
+}
+
+int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
+
+ moldyn->schedule.hook=hook;
+ moldyn->schedule.hook_params=hook_params;
+
+ return 0;
+}
/*
*
int moldyn_integrate(t_moldyn *moldyn) {
- int i;
- unsigned int e,m,s,d,v;
- unsigned char lvstat;
+ int i,sched;
+ unsigned int e,m,s,v;
t_3dvec p;
-
+ t_moldyn_schedule *schedule;
+ t_atom *atom;
int fd;
char fb[128];
+ double ds;
+
+ schedule=&(moldyn->schedule);
+ atom=moldyn->atom;
+ /* initialize linked cell method */
+ link_cell_init(moldyn);
+
+ /* logging & visualization */
e=moldyn->ewrite;
m=moldyn->mwrite;
s=moldyn->swrite;
- d=moldyn->dwrite;
v=moldyn->vwrite;
- if(!(lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
- printf("[moldyn] warning, lv system not initialized\n");
- return -1;
- }
-
+ /* sqaure of some variables */
+ moldyn->tau_square=moldyn->tau*moldyn->tau;
+ moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
/* calculate initial forces */
- moldyn->force(moldyn);
+ potential_force_calc(moldyn);
+
+ /* do some 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;
+ for(sched=0;sched<moldyn->schedule.content_count;sched++) {
+
+ /* setting amount of runs and finite time step size */
+ moldyn->tau=schedule->tau[sched];
+ moldyn->tau_square=moldyn->tau*moldyn->tau;
+ moldyn->time_steps=schedule->runs[sched];
+
+ /* integration according to schedule */
for(i=0;i<moldyn->time_steps;i++) {
+
/* integration step */
moldyn->integrate(moldyn);
- /* check for log & visualiziation */
+ /* p/t scaling */
+ if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
+ scale_velocity(moldyn,FALSE);
+
+ /* increase absolute time */
+ moldyn->time+=moldyn->tau;
+
+ /* check for log & visualization */
if(e) {
if(!(i%e))
dprintf(moldyn->efd,
- "%.15f %.45f\n",i*moldyn->tau,
+ "%.15f %.45f %.45f %.45f\n",
+ moldyn->time,update_e_kin(moldyn),
+ moldyn->energy,
get_total_energy(moldyn));
}
if(m) {
if(!(i%m)) {
- p=get_total_p(moldyn->atom,moldyn->count);
+ p=get_total_p(moldyn);
dprintf(moldyn->mfd,
- "%.15f %.45f\n",i*moldyn->tau,
+ "%.15f %.45f\n",moldyn->time,
v3_norm(&p));
}
}
write(fd,moldyn->atom,
moldyn->count*sizeof(t_atom));
}
+ close(fd);
}
}
- if(d) {
- if(!(i%d))
- write(moldyn->dfd,moldyn->atom,
- moldyn->count*sizeof(t_atom));
-
- }
if(v) {
- if(!(i%v))
- visual_atoms(moldyn->visual,i*moldyn->tau,
+ if(!(i%v)) {
+ visual_atoms(&(moldyn->vis),moldyn->time,
moldyn->atom,moldyn->count);
+ printf("\rsched: %d, steps: %d",sched,i);
+ fflush(stdout);
+ }
}
+
+ }
+
+ /* check for hooks */
+ if(schedule->hook)
+ schedule->hook(moldyn,schedule->hook_params);
+
}
return 0;
atom=moldyn->atom;
count=moldyn->count;
tau=moldyn->tau;
-
- tau_square=tau*tau;
+ tau_square=moldyn->tau_square;
for(i=0;i<count;i++) {
/* new positions */
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);
v3_add(&(atom[i].v),&(atom[i].v),&delta);
}
+ /* neighbour list update */
+ link_cell_update(moldyn);
+
/* forces depending on chosen potential */
- moldyn->force(moldyn);
+ potential_force_calc(moldyn);
+ //moldyn->potential_force_function(moldyn);
for(i=0;i<count;i++) {
/* again velocities */
*
*/
-/* harmonic oscillator potential and force */
+/* generic potential and force calculation */
-double potential_harmonic_oscillator(t_moldyn *moldyn) {
+int potential_force_calc(t_moldyn *moldyn) {
- t_ho_params *params;
- t_atom *atom;
- int i,j;
- int count;
- t_3dvec distance;
- double d,u;
- double sc,equi_dist;
+ int i,j,k,count;
+ t_atom *itom,*jtom,*ktom;
+ t_linkcell *lc;
+ t_list neighbour_i[27];
+ t_list neighbour_i2[27];
+ //t_list neighbour_j[27];
+ t_list *this,*that;
+ u8 bc_ij,bc_ijk;
+ int countn,dnlc;
- params=moldyn->pot_params;
- atom=moldyn->atom;
- sc=params->spring_constant;
- equi_dist=params->equilibrium_distance;
count=moldyn->count;
+ itom=moldyn->atom;
+ lc=&(moldyn->lc);
+
+ /* reset energy */
+ moldyn->energy=0.0;
- u=0.0;
for(i=0;i<count;i++) {
- for(j=0;j<i;j++) {
- v3_sub(&distance,&(atom[i].r),&(atom[j].r));
- d=v3_norm(&distance);
- u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
+
+ /* reset force */
+ v3_zero(&(itom[i].f));
+
+ /* single particle potential/force */
+ if(itom[i].attr&ATOM_ATTR_1BP)
+ moldyn->func1b(moldyn,&(itom[i]));
+
+ /* 2 body pair potential/force */
+ if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
+
+ 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;
+
+ for(j=0;j<countn;j++) {
+
+ this=&(neighbour_i[j]);
+ list_reset(this);
+
+ if(this->start==NULL)
+ continue;
+
+ bc_ij=(j<dnlc)?0:1;
+
+ do {
+ jtom=this->current->data;
+
+ 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);
+
+ /* 3 body potential/force */
+
+ if(!(itom[i].attr&ATOM_ATTR_3BP)||
+ !(jtom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ /*
+ * according to mr. nordlund, we dont need to take the
+ * sum over all atoms now, as 'this is centered' around
+ * atom i ...
+ * i am not quite sure though! there is a not vanishing
+ * part even if f_c_ik is zero ...
+ * this analytical potentials suck!
+ * switching from mc to md to dft soon!
+ */
+
+ // link_cell_neighbour_index(moldyn,
+ // (jtom->r.x+moldyn->dim.x/2)/lc->x,
+ // (jtom->r.y+moldyn->dim.y/2)/lc->y,
+ // (jtom->r.z+moldyn->dim.z/2)/lc->z,
+ // neighbour_j);
+
+// /* neighbours of j */
+// for(k=0;k<lc->countn;k++) {
+//
+// that=&(neighbour_j[k]);
+// list_reset(that);
+//
+// if(that->start==NULL)
+// continue;
+//
+// bc_ijk=(k<lc->dnlc)?0:1;
+//
+// do {
+//
+// ktom=that->current->data;
+//
+// if(!(ktom->attr&ATOM_ATTR_3BP))
+// continue;
+//
+// if(ktom==jtom)
+// continue;
+//
+// if(ktom==&(itom[i]))
+// continue;
+//
+// moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
+//
+/* } while(list_next(that)!=\ */
+// L_NO_NEXT_ELEMENT);
+//
+// }
+
+ /* copy the neighbour lists */
+ memcpy(neighbour_i2,neighbour_i,
+ 27*sizeof(t_list));
+
+ /* get neighbours of i */
+ for(k=0;k<countn;k++) {
+
+ that=&(neighbour_i2[k]);
+ list_reset(that);
+
+ if(that->start==NULL)
+ continue;
+
+ bc_ijk=(k<dnlc)?0:1;
+
+ do {
+
+ ktom=that->current->data;
+
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ if(ktom==jtom)
+ continue;
+
+ if(ktom==&(itom[i]))
+ continue;
+
+printf("Debug: atom %d before 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
+ moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
+printf("Debug: atom %d after 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
+
+ } while(list_next(that)!=\
+ L_NO_NEXT_ELEMENT);
+
+ }
+
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+ }
}
}
- return u;
+ return 0;
+}
+
+/*
+ * periodic boundayr checking
+ */
+
+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;
+
+ if(moldyn->status&MOLDYN_STAT_PBX) {
+ if(a->x>=x) a->x-=dim->x;
+ else if(-a->x>x) a->x+=dim->x;
+ }
+ if(moldyn->status&MOLDYN_STAT_PBY) {
+ if(a->y>=y) a->y-=dim->y;
+ else if(-a->y>y) a->y+=dim->y;
+ }
+ if(moldyn->status&MOLDYN_STAT_PBZ) {
+ if(a->z>=z) a->z-=dim->z;
+ else if(-a->z>z) a->z+=dim->z;
+ }
+
+ return 0;
}
+
+
+/*
+ * example potentials
+ */
+
+/* harmonic oscillator potential and force */
-int force_harmonic_oscillator(t_moldyn *moldyn) {
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
t_ho_params *params;
- int i,j,count;
- t_atom *atom;
- t_3dvec distance;
- t_3dvec force;
+ t_3dvec force,distance;
double d;
double sc,equi_dist;
- atom=moldyn->atom;
- count=moldyn->count;
- params=moldyn->pot_params;
+ params=moldyn->pot2b_params;
sc=params->spring_constant;
equi_dist=params->equilibrium_distance;
- for(i=0;i<count;i++) v3_zero(&(atom[i].f));
-
- for(i=0;i<count;i++) {
- for(j=0;j<i;j++) {
- v3_sub(&distance,&(atom[i].r),&(atom[j].r));
- v3_per_bound(&distance,&(moldyn->dim));
- d=v3_norm(&distance);
- if(d<=moldyn->cutoff) {
- v3_scale(&force,&distance,
- (-sc*(1.0-(equi_dist/d))));
- v3_add(&(atom[i].f),&(atom[i].f),&force);
- v3_sub(&(atom[j].f),&(atom[j].f),&force);
- }
- }
+ v3_sub(&distance,&(ai->r),&(aj->r));
+
+ 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)));
+ v3_add(&(ai->f),&(ai->f),&force);
}
return 0;
}
-
/* lennard jones potential & force for one sort of atoms */
-double potential_lennard_jones(t_moldyn *moldyn) {
+int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
t_lj_params *params;
- t_atom *atom;
- int i,j;
- int count;
- t_3dvec distance;
- double d,help;
- double u;
+ t_3dvec force,distance;
+ double d,h1,h2;
double eps,sig6,sig12;
- params=moldyn->pot_params;
- atom=moldyn->atom;
- count=moldyn->count;
- eps=params->epsilon;
+ params=moldyn->pot2b_params;
+ eps=params->epsilon4;
sig6=params->sigma6;
sig12=params->sigma12;
- u=0.0;
- for(i=0;i<count;i++) {
- for(j=0;j<i;j++) {
- v3_sub(&distance,&(atom[j].r),&(atom[i].r));
- d=1.0/v3_absolute_square(&distance); /* 1/r^2 */
- help=d*d; /* 1/r^4 */
- help*=d; /* 1/r^6 */
- d=help*help; /* 1/r^12 */
- u+=eps*(sig12*d-sig6*help);
- }
+ v3_sub(&distance,&(ai->r),&(aj->r));
+ if(bc) check_per_bound(moldyn,&distance);
+ d=v3_absolute_square(&distance); /* 1/r^2 */
+ if(d<=moldyn->cutoff_square) {
+ d=1.0/d; /* 1/r^2 */
+ h2=d*d; /* 1/r^4 */
+ h2*=d; /* 1/r^6 */
+ h1=h2*h2; /* 1/r^12 */
+ /* energy is eps*..., but we will add this twice ... */
+ moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
+ h2*=d; /* 1/r^8 */
+ h1*=d; /* 1/r^14 */
+ h2*=6*sig6;
+ h1*=12*sig12;
+ d=+h1-h2;
+ d*=eps;
+ v3_scale(&force,&distance,d);
+ 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]);
+
+ return 0;
+}
+
+/* tersoff 1 body part */
+int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
+
+ int num;
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
- return u;
+ num=ai->bnum;
+ params=moldyn->pot1b_params;
+ exchange=&(params->exchange);
+
+ /*
+ * simple: point constant parameters only depending on atom i to
+ * 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->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;
+
+ return 0;
}
+
+/* tersoff 2 body part */
+int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+ t_3dvec dist_ij,force;
+ double d_ij;
+ double A,B,R,S,lambda,mu;
+ double f_r,df_r;
+ double f_c,df_c;
+ int num;
+ double s_r;
+ double arg;
+ double scale;
+
+ params=moldyn->pot2b_params;
+ num=ai->bnum;
+ exchange=&(params->exchange);
+
+ exchange->run3bp=0;
+
+ /*
+ * we need: f_c, df_c, f_r, df_r
+ *
+ * therefore we need: R, S, A, lambda
+ */
-int force_lennard_jones(t_moldyn *moldyn) {
+ v3_sub(&dist_ij,&(ai->r),&(aj->r));
- t_lj_params *params;
- int i,j,count;
- t_atom *atom;
- t_3dvec distance;
- t_3dvec force;
- double d,h1,h2;
- double eps,sig6,sig12;
+ if(bc) check_per_bound(moldyn,&dist_ij);
- atom=moldyn->atom;
- count=moldyn->count;
- params=moldyn->pot_params;
- eps=params->epsilon;
- sig6=params->sigma6;
- sig12=params->sigma12;
+ d_ij=v3_norm(&dist_ij);
- for(i=0;i<count;i++) v3_zero(&(atom[i].f));
+ /* save for use in 3bp */
+ exchange->dist_ij=dist_ij; /* <- needed ? */
+ exchange->d_ij=d_ij;
- for(i=0;i<count;i++) {
- for(j=0;j<i;j++) {
- v3_sub(&distance,&(atom[j].r),&(atom[i].r));
- v3_per_bound(&distance,&(moldyn->dim));
- d=v3_absolute_square(&distance);
- if(d<=moldyn->cutoff_square) {
- h1=1.0/d; /* 1/r^2 */
- d=h1*h1; /* 1/r^4 */
- h2=d*d; /* 1/r^8 */
- h1*=d; /* 1/r^6 */
- h1*=h2; /* 1/r^14 */
- h1*=sig12;
- h2*=sig6;
- d=12.0*h1-6.0*h2;
- d*=eps;
- v3_scale(&force,&distance,d);
- v3_add(&(atom[j].f),&(atom[j].f),&force);
- v3_sub(&(atom[i].f),&(atom[i].f),&force);
- }
- }
+ /* constants */
+ if(num==aj->bnum) {
+ S=params->S[num];
+ R=params->R[num];
+ A=params->A[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;
+ }
+ else {
+ S=params->Smixed;
+ R=params->Rmixed;
+ A=params->Amixed;
+ 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;
+ }
+
+ if(d_ij>S)
+ return 0;
+
+ f_r=A*exp(-lambda*d_ij);
+ df_r=-lambda*f_r/d_ij;
+
+ /* f_a, df_a calc + save for 3bp use */
+ exchange->f_a=-B*exp(-mu*d_ij);
+ exchange->df_a=-mu*exchange->f_a/d_ij;
+
+ 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);
+ }
+ 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);
+ }
+
+ /* add forces */
+ v3_add(&(ai->f),&(ai->f),&force);
+ /* energy 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 */
+ exchange->run3bp=1;
+
+ return 0;
+}
+
+/* tersoff 3 body part */
+
+int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
+
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+ t_3dvec dist_ij,dist_ik,dist_jk;
+ t_3dvec temp,force;
+ 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 f_c_ik,df_c_ik,arg;
+ double scale;
+ double chi;
+ double n,c,d,h,beta,betan;
+ 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;
+ 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
+ *
+ * we got f_c, df_c, f_a, df_a from 2bp calculation
+ */
+
+ 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! */
+
+ /*
+ * 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,
+ *
+ */
+
+
+ v3_sub(&dist_ik,&(ai->r),&(ak->r));
+ if(bc) check_per_bound(moldyn,&dist_ik);
+ d_ik=v3_norm(&dist_ik);
+
+ /* constants for f_c_ik calc */
+ if(num==ak->bnum) {
+ R=params->R[num];
+ S=params->S[num];
}
+ else {
+ R=params->Rmixed;
+ S=params->Smixed;
+ }
+
+ /* calc of f_c_ik */
+ if(d_ik>S)
+ return 0;
+ if(d_ik<R) {
+ /* f_c_ik = 1, df_c_ik = 0 */
+ f_c_ik=1.0;
+ df_c_ik=0.0;
+ }
+ 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));
+ }
+
+ 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);
+
+ /* part 1 of derivation of b_ij */
+ v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1);
+
+ /* 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);
+
+ /* 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);
+
return 0;
}
projects / physik / posic.git / blobdiff