2 * moldyn.c - molecular dynamics library main file
4 * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
12 #include <sys/types.h>
20 #include "math/math.h"
21 #include "init/init.h"
22 #include "random/random.h"
23 #include "visual/visual.h"
24 #include "list/list.h"
27 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
31 //ret=moldyn_parse_argv(moldyn,argc,argv);
32 //if(ret<0) return ret;
34 memset(moldyn,0,sizeof(t_moldyn));
36 rand_init(&(moldyn->random),NULL,1);
37 moldyn->random.status|=RAND_STAT_VERBOSE;
42 int moldyn_shutdown(t_moldyn *moldyn) {
44 printf("[moldyn] shutdown\n");
45 moldyn_log_shutdown(moldyn);
46 link_cell_shutdown(moldyn);
47 rand_close(&(moldyn->random));
53 int set_int_alg(t_moldyn *moldyn,u8 algo) {
56 case MOLDYN_INTEGRATE_VERLET:
57 moldyn->integrate=velocity_verlet;
60 printf("unknown integration algorithm: %02x\n",algo);
67 int set_cutoff(t_moldyn *moldyn,double cutoff) {
69 moldyn->cutoff=cutoff;
74 int set_temperature(t_moldyn *moldyn,double t_ref) {
81 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
83 moldyn->pt_scale=(ptype|ttype);
90 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
105 int set_nn_dist(t_moldyn *moldyn,double dist) {
112 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
115 moldyn->status|=MOLDYN_STAT_PBX;
118 moldyn->status|=MOLDYN_STAT_PBY;
121 moldyn->status|=MOLDYN_STAT_PBZ;
126 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
129 moldyn->pot1b_params=params;
134 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
137 moldyn->pot2b_params=params;
142 int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
144 moldyn->func2b_post=func;
145 moldyn->pot2b_params=params;
150 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
153 moldyn->pot3b_params=params;
158 int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
161 case LOG_TOTAL_ENERGY:
162 moldyn->ewrite=timer;
163 moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
165 perror("[moldyn] efd open");
168 dprintf(moldyn->efd,"# total energy log file\n");
170 case LOG_TOTAL_MOMENTUM:
171 moldyn->mwrite=timer;
172 moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
174 perror("[moldyn] mfd open");
177 dprintf(moldyn->efd,"# total momentum log file\n");
180 moldyn->swrite=timer;
181 strncpy(moldyn->sfb,fb,63);
184 moldyn->vwrite=timer;
185 strncpy(moldyn->vfb,fb,63);
186 visual_init(&(moldyn->vis),fb);
189 printf("unknown log mechanism: %02x\n",type);
196 int moldyn_log_shutdown(t_moldyn *moldyn) {
198 printf("[moldyn] log shutdown\n");
199 if(moldyn->efd) close(moldyn->efd);
200 if(moldyn->mfd) close(moldyn->mfd);
201 if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
206 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
207 u8 attr,u8 bnum,int a,int b,int c) {
215 if(type==FCC) count*=4;
217 if(type==DIAMOND) count*=8;
219 moldyn->atom=malloc(count*sizeof(t_atom));
220 if(moldyn->atom==NULL) {
221 perror("malloc (atoms)");
229 ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
232 ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
235 printf("unknown lattice type (%02x)\n",type);
241 printf("ok, there is something wrong ...\n");
242 printf("calculated -> %d atoms\n",count);
243 printf("created -> %d atoms\n",ret);
248 printf("[moldyn] created lattice with %d atoms\n",count);
252 moldyn->atom[count].element=element;
253 moldyn->atom[count].mass=mass;
254 moldyn->atom[count].attr=attr;
255 moldyn->atom[count].bnum=bnum;
256 check_per_bound(moldyn,&(moldyn->atom[count].r));
263 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
264 t_3dvec *r,t_3dvec *v) {
271 count=++(moldyn->count);
273 ptr=realloc(atom,count*sizeof(t_atom));
275 perror("[moldyn] realloc (add atom)");
283 atom[count-1].element=element;
284 atom[count-1].mass=mass;
285 atom[count-1].bnum=bnum;
286 atom[count-1].attr=attr;
291 int destroy_atoms(t_moldyn *moldyn) {
293 if(moldyn->atom) free(moldyn->atom);
298 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
301 * - gaussian distribution of velocities
302 * - zero total momentum
303 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
308 t_3dvec p_total,delta;
313 random=&(moldyn->random);
315 /* gaussian distribution of velocities */
317 for(i=0;i<moldyn->count;i++) {
318 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
320 v=sigma*rand_get_gauss(random);
322 p_total.x+=atom[i].mass*v;
324 v=sigma*rand_get_gauss(random);
326 p_total.y+=atom[i].mass*v;
328 v=sigma*rand_get_gauss(random);
330 p_total.z+=atom[i].mass*v;
333 /* zero total momentum */
334 v3_scale(&p_total,&p_total,1.0/moldyn->count);
335 for(i=0;i<moldyn->count;i++) {
336 v3_scale(&delta,&p_total,1.0/atom[i].mass);
337 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
340 /* velocity scaling */
341 scale_velocity(moldyn,equi_init);
346 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
356 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
359 /* get kinetic energy / temperature & count involved atoms */
362 for(i=0;i<moldyn->count;i++) {
363 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
364 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
368 if(count!=0) moldyn->t=(2.0*e)/(3.0*count*K_BOLTZMANN);
369 else return 0; /* no atoms involved in scaling! */
371 /* (temporary) hack for e,t = 0 */
374 if(moldyn->t_ref!=0.0)
375 thermal_init(moldyn,equi_init);
377 return 0; /* no scaling needed */
381 /* get scaling factor */
382 scale=moldyn->t_ref/moldyn->t;
386 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
387 scale=1.0+moldyn->tau*(scale-1.0)/moldyn->t_tc;
390 /* velocity scaling */
391 for(i=0;i<moldyn->count;i++)
392 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
393 v3_scale(&(atom[i].v),&(atom[i].v),scale);
398 double get_e_kin(t_moldyn *moldyn) {
406 for(i=0;i<moldyn->count;i++)
407 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
412 double get_e_pot(t_moldyn *moldyn) {
414 return moldyn->energy;
417 double update_e_kin(t_moldyn *moldyn) {
419 return(get_e_kin(moldyn));
422 double get_total_energy(t_moldyn *moldyn) {
424 return(moldyn->ekin+moldyn->energy);
427 t_3dvec get_total_p(t_moldyn *moldyn) {
436 for(i=0;i<moldyn->count;i++) {
437 v3_scale(&p,&(atom[i].v),atom[i].mass);
438 v3_add(&p_total,&p_total,&p);
444 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
448 /* nn_dist is the nearest neighbour distance */
451 printf("[moldyn] i do not estimate timesteps below %f K!\n",
452 MOLDYN_CRITICAL_EST_TEMP);
456 tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
465 /* linked list / cell method */
467 int link_cell_init(t_moldyn *moldyn) {
473 fd=open("/dev/null",O_WRONLY);
477 /* partitioning the md cell */
478 lc->nx=moldyn->dim.x/moldyn->cutoff;
479 lc->x=moldyn->dim.x/lc->nx;
480 lc->ny=moldyn->dim.y/moldyn->cutoff;
481 lc->y=moldyn->dim.y/lc->ny;
482 lc->nz=moldyn->dim.z/moldyn->cutoff;
483 lc->z=moldyn->dim.z/lc->nz;
485 lc->cells=lc->nx*lc->ny*lc->nz;
486 lc->subcell=malloc(lc->cells*sizeof(t_list));
488 printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
490 for(i=0;i<lc->cells;i++)
491 //list_init(&(lc->subcell[i]),1);
492 list_init(&(lc->subcell[i]),fd);
494 link_cell_update(moldyn);
499 int link_cell_update(t_moldyn *moldyn) {
513 for(i=0;i<lc->cells;i++)
514 list_destroy(&(moldyn->lc.subcell[i]));
516 for(count=0;count<moldyn->count;count++) {
517 i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
518 j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
519 k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
520 list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
527 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
545 cell[0]=lc->subcell[i+j*nx+k*a];
546 for(ci=-1;ci<=1;ci++) {
553 for(cj=-1;cj<=1;cj++) {
560 for(ck=-1;ck<=1;ck++) {
567 if(!(ci|cj|ck)) continue;
569 cell[--count2]=lc->subcell[x+y*nx+z*a];
572 cell[count1++]=lc->subcell[x+y*nx+z*a];
583 int link_cell_shutdown(t_moldyn *moldyn) {
590 for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
591 list_shutdown(&(moldyn->lc.subcell[i]));
596 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
600 t_moldyn_schedule *schedule;
602 schedule=&(moldyn->schedule);
603 count=++(schedule->content_count);
605 ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
607 perror("[moldyn] realloc (runs)");
610 moldyn->schedule.runs=ptr;
611 moldyn->schedule.runs[count-1]=runs;
613 ptr=realloc(schedule->tau,count*sizeof(double));
615 perror("[moldyn] realloc (tau)");
618 moldyn->schedule.tau=ptr;
619 moldyn->schedule.tau[count-1]=tau;
624 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
626 moldyn->schedule.hook=hook;
627 moldyn->schedule.hook_params=hook_params;
634 * 'integration of newtons equation' - algorithms
638 /* start the integration */
640 int moldyn_integrate(t_moldyn *moldyn) {
643 unsigned int e,m,s,v;
645 t_moldyn_schedule *schedule;
651 schedule=&(moldyn->schedule);
654 /* initialize linked cell method */
655 link_cell_init(moldyn);
657 /* logging & visualization */
663 /* sqaure of some variables */
664 moldyn->tau_square=moldyn->tau*moldyn->tau;
665 moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
667 /* calculate initial forces */
668 potential_force_calc(moldyn);
670 /* some stupid checks before we actually start calculating bullshit */
671 if(moldyn->cutoff>0.5*moldyn->dim.x)
672 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
673 if(moldyn->cutoff>0.5*moldyn->dim.y)
674 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
675 if(moldyn->cutoff>0.5*moldyn->dim.z)
676 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
677 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
678 if(ds>0.05*moldyn->nnd)
679 printf("[moldyn] warning: forces too high / tau too small!\n");
681 /* zero absolute time */
684 /* debugging, ignre */
687 /* executing the schedule */
688 for(sched=0;sched<moldyn->schedule.content_count;sched++) {
690 /* setting amount of runs and finite time step size */
691 moldyn->tau=schedule->tau[sched];
692 moldyn->tau_square=moldyn->tau*moldyn->tau;
693 moldyn->time_steps=schedule->runs[sched];
695 /* integration according to schedule */
697 for(i=0;i<moldyn->time_steps;i++) {
699 /* integration step */
700 moldyn->integrate(moldyn);
703 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
704 scale_velocity(moldyn,FALSE);
706 /* increase absolute time */
707 moldyn->time+=moldyn->tau;
709 /* check for log & visualization */
713 "%.15f %.45f %.45f %.45f\n",
714 moldyn->time,update_e_kin(moldyn),
716 get_total_energy(moldyn));
720 p=get_total_p(moldyn);
722 "%.15f %.45f\n",moldyn->time,
728 snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
729 moldyn->t,i*moldyn->tau);
730 fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
731 if(fd<0) perror("[moldyn] save fd open");
733 write(fd,moldyn,sizeof(t_moldyn));
734 write(fd,moldyn->atom,
735 moldyn->count*sizeof(t_atom));
742 visual_atoms(&(moldyn->vis),moldyn->time,
743 moldyn->atom,moldyn->count);
744 printf("\rsched: %d, steps: %d, theta: %d",
745 sched,i,moldyn->debug);
752 /* check for hooks */
754 schedule->hook(moldyn,schedule->hook_params);
756 /* get a new info line */
764 /* velocity verlet */
766 int velocity_verlet(t_moldyn *moldyn) {
769 double tau,tau_square;
776 tau_square=moldyn->tau_square;
778 for(i=0;i<count;i++) {
780 v3_scale(&delta,&(atom[i].v),tau);
781 v3_add(&(atom[i].r),&(atom[i].r),&delta);
782 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
783 v3_add(&(atom[i].r),&(atom[i].r),&delta);
784 check_per_bound(moldyn,&(atom[i].r));
787 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
788 v3_add(&(atom[i].v),&(atom[i].v),&delta);
791 /* neighbour list update */
792 link_cell_update(moldyn);
794 /* forces depending on chosen potential */
795 potential_force_calc(moldyn);
797 for(i=0;i<count;i++) {
798 /* again velocities */
799 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
800 v3_add(&(atom[i].v),&(atom[i].v),&delta);
809 * potentials & corresponding forces
813 /* generic potential and force calculation */
815 int potential_force_calc(t_moldyn *moldyn) {
818 t_atom *itom,*jtom,*ktom;
820 t_list neighbour_i[27];
821 t_list neighbour_i2[27];
822 //t_list neighbour_j[27];
834 /* get energy and force of every atom */
835 for(i=0;i<count;i++) {
838 v3_zero(&(itom[i].f));
840 /* single particle potential/force */
841 if(itom[i].attr&ATOM_ATTR_1BP)
842 moldyn->func1b(moldyn,&(itom[i]));
844 /* 2 body pair potential/force */
845 if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
847 link_cell_neighbour_index(moldyn,
848 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
849 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
850 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
857 this=&(neighbour_i[j]);
860 if(this->start==NULL)
866 jtom=this->current->data;
871 if((jtom->attr&ATOM_ATTR_2BP)&
872 (itom[i].attr&ATOM_ATTR_2BP))
873 moldyn->func2b(moldyn,
878 /* 3 body potential/force */
880 if(!(itom[i].attr&ATOM_ATTR_3BP)||
881 !(jtom->attr&ATOM_ATTR_3BP))
884 /* copy the neighbour lists */
885 memcpy(neighbour_i2,neighbour_i,
888 /* get neighbours of i */
891 that=&(neighbour_i2[k]);
894 if(that->start==NULL)
901 ktom=that->current->data;
903 if(!(ktom->attr&ATOM_ATTR_3BP))
912 moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ik|bc_ij);
914 } while(list_next(that)!=\
919 } while(list_next(this)!=L_NO_NEXT_ELEMENT);
921 /* 2bp post function */
922 if(moldyn->func2b_post) {
923 printf("pre(%d): %.15f %.15f %.15f\n",i,itom[i].f.x,itom[i].r.x,itom[i].v.x);
924 moldyn->func2b_post(moldyn,
927 printf("post(%d): %.15f %.15f %.15f\n",i,itom[i].f.x,itom[i].r.x,itom[i].v.x);
938 * periodic boundayr checking
941 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
952 if(moldyn->status&MOLDYN_STAT_PBX) {
953 if(a->x>=x) a->x-=dim->x;
954 else if(-a->x>x) a->x+=dim->x;
956 if(moldyn->status&MOLDYN_STAT_PBY) {
957 if(a->y>=y) a->y-=dim->y;
958 else if(-a->y>y) a->y+=dim->y;
960 if(moldyn->status&MOLDYN_STAT_PBZ) {
961 if(a->z>=z) a->z-=dim->z;
962 else if(-a->z>z) a->z+=dim->z;
973 /* harmonic oscillator potential and force */
975 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
978 t_3dvec force,distance;
982 params=moldyn->pot2b_params;
983 sc=params->spring_constant;
984 equi_dist=params->equilibrium_distance;
986 v3_sub(&distance,&(ai->r),&(aj->r));
988 if(bc) check_per_bound(moldyn,&distance);
989 d=v3_norm(&distance);
990 if(d<=moldyn->cutoff) {
991 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
992 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
993 v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
994 v3_add(&(ai->f),&(ai->f),&force);
1000 /* lennard jones potential & force for one sort of atoms */
1002 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1004 t_lj_params *params;
1005 t_3dvec force,distance;
1007 double eps,sig6,sig12;
1009 params=moldyn->pot2b_params;
1010 eps=params->epsilon4;
1011 sig6=params->sigma6;
1012 sig12=params->sigma12;
1014 v3_sub(&distance,&(ai->r),&(aj->r));
1015 if(bc) check_per_bound(moldyn,&distance);
1016 d=v3_absolute_square(&distance); /* 1/r^2 */
1017 if(d<=moldyn->cutoff_square) {
1018 d=1.0/d; /* 1/r^2 */
1021 h1=h2*h2; /* 1/r^12 */
1022 /* energy is eps*..., but we will add this twice ... */
1023 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
1030 v3_scale(&force,&distance,d);
1031 v3_add(&(ai->f),&(ai->f),&force);
1038 * tersoff potential & force for 2 sorts of atoms
1041 /* create mixed terms from parameters and set them */
1042 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
1044 printf("[moldyn] tersoff parameter completion\n");
1045 p->Smixed=sqrt(p->S[0]*p->S[1]);
1046 p->Rmixed=sqrt(p->R[0]*p->R[1]);
1047 p->Amixed=sqrt(p->A[0]*p->A[1]);
1048 p->Bmixed=sqrt(p->B[0]*p->B[1]);
1049 p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
1050 p->mu_m=0.5*(p->mu[0]+p->mu[1]);
1052 printf("[moldyn] tersoff mult parameter info:\n");
1053 printf(" S (m) | %.12f | %.12f | %.12f\n",p->S[0],p->S[1],p->Smixed);
1054 printf(" R (m) | %.12f | %.12f | %.12f\n",p->R[0],p->R[1],p->Rmixed);
1055 printf(" A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
1056 printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
1057 printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
1059 printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
1060 printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
1061 printf(" n | %f | %f\n",p->n[0],p->n[1]);
1062 printf(" c | %f | %f\n",p->c[0],p->c[1]);
1063 printf(" d | %f | %f\n",p->d[0],p->d[1]);
1064 printf(" h | %f | %f\n",p->h[0],p->h[1]);
1065 printf(" chi | %f \n",p->chi);
1070 /* tersoff 1 body part */
1071 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
1074 t_tersoff_mult_params *params;
1075 t_tersoff_exchange *exchange;
1078 params=moldyn->pot1b_params;
1079 exchange=&(params->exchange);
1082 * simple: point constant parameters only depending on atom i to
1083 * their right values
1086 exchange->beta=&(params->beta[num]);
1087 exchange->n=&(params->n[num]);
1088 exchange->c=&(params->c[num]);
1089 exchange->d=&(params->d[num]);
1090 exchange->h=&(params->h[num]);
1092 exchange->betan=pow(*(exchange->beta),*(exchange->n));
1093 exchange->n_betan=*(exchange->n)*exchange->betan;
1094 exchange->c2=params->c[num]*params->c[num];
1095 exchange->d2=params->d[num]*params->d[num];
1096 exchange->c2d2=exchange->c2/exchange->d2;
1101 /* tersoff 2 body part */
1102 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1104 t_tersoff_mult_params *params;
1105 t_tersoff_exchange *exchange;
1106 t_3dvec dist_ij,force;
1108 double A,B,R,S,lambda,mu;
1116 params=moldyn->pot2b_params;
1118 exchange=&(params->exchange);
1121 exchange->run2bp_post=0;
1124 * we need: f_c, df_c, f_r, df_r
1126 * therefore we need: R, S, A, lambda
1129 v3_sub(&dist_ij,&(ai->r),&(aj->r));
1131 if(bc) check_per_bound(moldyn,&dist_ij);
1133 d_ij=v3_norm(&dist_ij);
1135 /* save for use in 3bp */
1136 exchange->d_ij=d_ij;
1137 exchange->dist_ij=dist_ij;
1138 exchange->d_ij2=d_ij*d_ij;
1146 lambda=params->lambda[num];
1148 params->exchange.chi=1.0;
1155 lambda=params->lambda_m;
1157 params->exchange.chi=params->chi;
1162 f_r=A*exp(-lambda*d_ij);
1163 df_r=-lambda*f_r/d_ij;
1165 /* f_a, df_a calc + save for later use */
1166 exchange->f_a=-B*exp(-mu*d_ij);
1167 exchange->df_a=-mu*exchange->f_a/d_ij;
1170 /* f_c = 1, df_c = 0 */
1173 v3_scale(&force,&dist_ij,df_r);
1177 arg=M_PI*(d_ij-R)/s_r;
1178 f_c=0.5+0.5*cos(arg);
1179 df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
1180 scale=df_c*f_r+df_r*f_c;
1181 v3_scale(&force,&dist_ij,scale);
1185 v3_add(&(ai->f),&(ai->f),&force);
1186 /* energy is 0.5 f_r f_c ... */
1187 moldyn->energy+=(0.5*f_r*f_c);
1189 /* save for use in 3bp */
1191 exchange->df_c=df_c;
1193 /* enable the run of 3bp function and 2bp post processing */
1195 exchange->run2bp_post=1;
1197 /* reset 3bp sums */
1198 exchange->sum1_3bp=0.0;
1199 exchange->sum2_3bp=0.0;
1200 v3_zero(&(exchange->db_ij));
1205 /* tersoff 2 body post part */
1207 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1209 /* here we have to allow for the 3bp sums */
1211 t_tersoff_mult_params *params;
1212 t_tersoff_exchange *exchange;
1214 t_3dvec force,temp,*db_ij,*dist_ij;
1215 double db_ij_scale1,db_ij_scale2;
1217 double f_c,df_c,f_a,df_a;
1222 params=moldyn->pot2b_params;
1223 exchange=&(params->exchange);
1225 /* we do not run if f_c_ij was detected to be 0! */
1226 if(!(exchange->run2bp_post))
1229 db_ij=&(exchange->db_ij);
1231 df_c=exchange->df_c;
1233 df_a=exchange->df_a;
1234 betan=exchange->betan;
1237 dist_ij=&(exchange->dist_ij);
1239 db_ij_scale1=(1+betan*exchange->sum1_3bp);
1240 db_ij_scale2=(exchange->n_betan*exchange->sum2_3bp);
1241 help=pow(db_ij_scale1,-1.0/(2*n)-1);
1242 b_ij=chi*db_ij_scale1*help;
1243 db_ij_scale1=-chi/(2*n)*help;
1244 printf("debug: %.20f %.20f %.20f\n",db_ij->x,exchange->sum1_3bp,exchange->sum2_3bp);
1247 v3_scale(db_ij,db_ij,(db_ij_scale1*db_ij_scale2));
1248 v3_scale(db_ij,db_ij,f_a);
1251 v3_scale(&temp,dist_ij,b_ij*df_a);
1253 /* db_ij + df_a part */
1254 v3_add(&force,&temp,db_ij);
1255 v3_scale(&force,&force,f_c);
1258 v3_scale(&temp,dist_ij,f_a*b_ij*df_c);
1260 /* add energy of 3bp sum */
1261 moldyn->energy+=(0.5*f_c*b_ij*f_a);
1263 /* add force of 3bp calculation (all three parts) */
1264 v3_add(&(ai->f),&temp,&force);
1269 /* tersoff 3 body part */
1271 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1273 t_tersoff_mult_params *params;
1274 t_tersoff_exchange *exchange;
1275 t_3dvec dist_ij,dist_ik,dist_jk;
1278 double d_ij,d_ij2,d_ik,d_jk;
1279 double f_c,df_c,f_a,df_a;
1280 double f_c_ik,df_c_ik,arg;
1284 double theta,cos_theta,sin_theta;
1285 double d_theta,d_theta1,d_theta2;
1286 double h_cos,d2_h_cos2;
1287 double frac,bracket,bracket_n_1,bracket_n;
1291 params=moldyn->pot3b_params;
1293 exchange=&(params->exchange);
1295 if(!(exchange->run3bp))
1299 * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
1301 * we got f_c, df_c, f_a, df_a from 2bp calculation
1304 d_ij=exchange->d_ij;
1305 d_ij2=exchange->d_ij2;
1306 dist_ij=exchange->dist_ij;
1308 f_a=params->exchange.f_a;
1309 df_a=params->exchange.df_a;
1312 df_c=exchange->df_c;
1314 /* d_ij is <= S, as we didn't return so far! */
1317 * calc of b_ij (scalar) and db_ij (vector)
1319 * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
1321 * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
1326 v3_sub(&dist_ik,&(ai->r),&(ak->r));
1327 if(bc) check_per_bound(moldyn,&dist_ik);
1328 d_ik=v3_norm(&dist_ik);
1330 /* constants for f_c_ik calc */
1340 /* calc of f_c_ik */
1351 arg=M_PI*(d_ik-R)/s_r;
1352 f_c_ik=0.5+0.5*cos(arg);
1353 df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
1356 v3_sub(&dist_jk,&(aj->r),&(ak->r));
1357 if(bc) check_per_bound(moldyn,&dist_jk);
1358 d_jk=v3_norm(&dist_jk);
1360 /* get exchange data */
1367 c2d2=exchange->c2d2;
1369 /* cosine of theta by scalaproduct, *
1370 * derivation of theta by law of cosines! */
1371 numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
1373 cos_theta=numer/denom;
1374 cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
1375 printf("cos theta: %.25f\n",cos_theta);
1377 /* hack - cos theta machine accuracy problems! */
1378 if(cos_theta>1.0||cos_theta<-1.0) {
1380 if(fabs(cos_theta)>1.0+ACCEPTABLE_ERROR)
1381 printf("[moldyn] WARNING: cos theta failure!\n");
1386 printf("THETA CORRECTION\n");
1389 sin_theta=sqrt(1.0-(cos_theta*cos_theta));
1390 theta=acos(cos_theta);
1391 d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
1392 d_theta1=2*denom-numer*2*d_ik/d_ij;
1393 d_theta2=2*denom-numer*2*d_ij/d_ik;
1396 printf("FOO %.15f %.15f\n",sin_theta,cos_theta);
1398 h_cos=(h-cos_theta);
1399 d2_h_cos2=d2+(h_cos*h_cos);
1401 frac=c2/(d2_h_cos2);
1411 bracket_n_1=pow(bracket,n-1.0);
1412 bracket_n=bracket_n_1*bracket;
1415 /* calc of db_ij and the 2 sums */
1416 exchange->sum1_3bp+=bracket_n;
1417 exchange->sum2_3bp+=bracket_n_1;
1419 /* derivation of theta */
1420 v3_scale(&force,&dist_ij,d_theta1);
1421 v3_scale(&temp,&dist_ik,d_theta2);
1422 v3_add(&force,&force,&temp);
1424 printf("DA:%.20f %.20f %.20f\n",d_theta1,force.x,temp.x);
1425 /* part 1 of db_ij */
1426 v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac/d2_h_cos2);
1428 /* part 2 of db_ij */
1429 v3_scale(&temp,&dist_ik,df_c_ik*g);
1431 /* sum up and add to db_ij */
1432 v3_add(&temp,&temp,&force);
1433 v3_add(&(exchange->db_ij),&(exchange->db_ij),&temp);