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, ignore */
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, debug: %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 //if(i==0) printf("und dann %.20f\n",atom[i].r.x*1e10);
785 check_per_bound(moldyn,&(atom[i].r));
786 //if(i==0) printf("und danach %.20f\n",atom[i].r.x);
789 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
790 v3_add(&(atom[i].v),&(atom[i].v),&delta);
792 moldyn_bc_check(moldyn);
794 /* neighbour list update */
795 link_cell_update(moldyn);
797 /* forces depending on chosen potential */
798 potential_force_calc(moldyn);
800 for(i=0;i<count;i++) {
801 /* again velocities */
802 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
803 v3_add(&(atom[i].v),&(atom[i].v),&delta);
812 * potentials & corresponding forces
816 /* generic potential and force calculation */
818 int potential_force_calc(t_moldyn *moldyn) {
821 t_atom *itom,*jtom,*ktom;
823 t_list neighbour_i[27];
824 t_list neighbour_i2[27];
825 //t_list neighbour_j[27];
837 /* get energy and force of every atom */
838 for(i=0;i<count;i++) {
841 v3_zero(&(itom[i].f));
843 /* single particle potential/force */
844 if(itom[i].attr&ATOM_ATTR_1BP)
845 moldyn->func1b(moldyn,&(itom[i]));
847 /* 2 body pair potential/force */
848 if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
850 link_cell_neighbour_index(moldyn,
851 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
852 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
853 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
860 this=&(neighbour_i[j]);
863 if(this->start==NULL)
869 jtom=this->current->data;
874 if((jtom->attr&ATOM_ATTR_2BP)&
875 (itom[i].attr&ATOM_ATTR_2BP))
876 moldyn->func2b(moldyn,
881 /* 3 body potential/force */
883 if(!(itom[i].attr&ATOM_ATTR_3BP)||
884 !(jtom->attr&ATOM_ATTR_3BP))
887 /* copy the neighbour lists */
888 memcpy(neighbour_i2,neighbour_i,
891 /* get neighbours of i */
894 that=&(neighbour_i2[k]);
897 if(that->start==NULL)
904 ktom=that->current->data;
906 if(!(ktom->attr&ATOM_ATTR_3BP))
915 moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ik|bc_ij);
917 } while(list_next(that)!=\
922 } while(list_next(this)!=L_NO_NEXT_ELEMENT);
924 /* 2bp post function */
925 if(moldyn->func2b_post) {
926 moldyn->func2b_post(moldyn,
933 //printf("DEBUG: %.15f \n",itom[i].f.x);
940 * periodic boundayr checking
943 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
954 if(moldyn->status&MOLDYN_STAT_PBX) {
955 if(a->x>=x) a->x-=dim->x;
956 else if(-a->x>x) a->x+=dim->x;
958 if(moldyn->status&MOLDYN_STAT_PBY) {
959 if(a->y>=y) a->y-=dim->y;
960 else if(-a->y>y) a->y+=dim->y;
962 if(moldyn->status&MOLDYN_STAT_PBZ) {
963 if(a->z>=z) a->z-=dim->z;
964 else if(-a->z>z) a->z+=dim->z;
975 /* harmonic oscillator potential and force */
977 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
980 t_3dvec force,distance;
984 params=moldyn->pot2b_params;
985 sc=params->spring_constant;
986 equi_dist=params->equilibrium_distance;
988 v3_sub(&distance,&(aj->r),&(ai->r));
990 if(bc) check_per_bound(moldyn,&distance);
991 d=v3_norm(&distance);
992 if(d<=moldyn->cutoff) {
993 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
994 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
995 /* f = -grad E; grad r_ij = -1 1/r_ij distance */
996 v3_scale(&force,&distance,sc*(1.0-(equi_dist/d)));
997 v3_add(&(ai->f),&(ai->f),&force);
1003 /* lennard jones potential & force for one sort of atoms */
1005 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1007 t_lj_params *params;
1008 t_3dvec force,distance;
1010 double eps,sig6,sig12;
1012 params=moldyn->pot2b_params;
1013 eps=params->epsilon4;
1014 sig6=params->sigma6;
1015 sig12=params->sigma12;
1017 v3_sub(&distance,&(aj->r),&(ai->r));
1018 if(bc) check_per_bound(moldyn,&distance);
1019 d=v3_absolute_square(&distance); /* 1/r^2 */
1020 if(d<=moldyn->cutoff_square) {
1021 d=1.0/d; /* 1/r^2 */
1024 h1=h2*h2; /* 1/r^12 */
1025 /* energy is eps*..., but we will add this twice ... */
1026 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
1033 v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
1034 v3_add(&(ai->f),&(ai->f),&force);
1041 * tersoff potential & force for 2 sorts of atoms
1044 /* create mixed terms from parameters and set them */
1045 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
1047 printf("[moldyn] tersoff parameter completion\n");
1048 p->Smixed=sqrt(p->S[0]*p->S[1]);
1049 p->Rmixed=sqrt(p->R[0]*p->R[1]);
1050 p->Amixed=sqrt(p->A[0]*p->A[1]);
1051 p->Bmixed=sqrt(p->B[0]*p->B[1]);
1052 p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
1053 p->mu_m=0.5*(p->mu[0]+p->mu[1]);
1055 printf("[moldyn] tersoff mult parameter info:\n");
1056 printf(" S (m) | %.12f | %.12f | %.12f\n",p->S[0],p->S[1],p->Smixed);
1057 printf(" R (m) | %.12f | %.12f | %.12f\n",p->R[0],p->R[1],p->Rmixed);
1058 printf(" A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
1059 printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
1060 printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
1062 printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
1063 printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
1064 printf(" n | %f | %f\n",p->n[0],p->n[1]);
1065 printf(" c | %f | %f\n",p->c[0],p->c[1]);
1066 printf(" d | %f | %f\n",p->d[0],p->d[1]);
1067 printf(" h | %f | %f\n",p->h[0],p->h[1]);
1068 printf(" chi | %f \n",p->chi);
1073 /* tersoff 1 body part */
1074 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
1077 t_tersoff_mult_params *params;
1078 t_tersoff_exchange *exchange;
1081 params=moldyn->pot1b_params;
1082 exchange=&(params->exchange);
1085 * simple: point constant parameters only depending on atom i to
1086 * their right values
1089 exchange->beta_i=&(params->beta[num]);
1090 exchange->n_i=&(params->n[num]);
1091 exchange->c_i=&(params->c[num]);
1092 exchange->d_i=&(params->d[num]);
1093 exchange->h_i=&(params->h[num]);
1095 exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
1096 exchange->ci2=params->c[num]*params->c[num];
1097 exchange->di2=params->d[num]*params->d[num];
1098 exchange->ci2di2=exchange->ci2/exchange->di2;
1103 /* tersoff 2 body part */
1104 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1106 t_tersoff_mult_params *params;
1107 t_tersoff_exchange *exchange;
1108 t_3dvec dist_ij,force;
1110 double A,B,R,S,lambda,mu;
1117 params=moldyn->pot2b_params;
1119 exchange=&(params->exchange);
1121 /* clear 3bp and 2bp post run */
1123 exchange->run2bp_post=0;
1125 /* reset S > r > R mark */
1126 exchange->d_ij_between_rs=0;
1129 * calc of 2bp contribution of V_ij and dV_ij/ji
1131 * for Vij and dV_ij we need:
1135 * for dV_ji we need:
1136 * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
1137 * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
1142 v3_sub(&dist_ij,&(aj->r),&(ai->r));
1143 if(bc) check_per_bound(moldyn,&dist_ij);
1144 d_ij=v3_norm(&dist_ij);
1146 /* save for use in 3bp */
1147 exchange->d_ij=d_ij;
1148 exchange->dist_ij=dist_ij;
1156 lambda=params->lambda[num];
1165 lambda=params->lambda_m;
1167 params->exchange.chi=params->chi;
1170 /* if d_ij > S => no force & potential energy contribution */
1174 /* more constants */
1175 exchange->beta_j=&(params->beta[num]);
1176 exchange->n_j=&(params->n[num]);
1177 exchange->c_j=&(params->c[num]);
1178 exchange->d_j=&(params->d[num]);
1179 exchange->h_j=&(params->h[num]);
1181 exchange->betajnj=exchange->betaini;
1182 exchange->cj2=exchange->ci2;
1183 exchange->dj2=exchange->di2;
1184 exchange->cj2dj2=exchange->ci2di2;
1187 exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
1188 exchange->cj2=params->c[num]*params->c[num];
1189 exchange->dj2=params->d[num]*params->d[num];
1190 exchange->cj2dj2=exchange->cj2/exchange->dj2;
1193 /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
1194 f_r=A*exp(-lambda*d_ij);
1195 df_r=lambda*f_r/d_ij;
1197 /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
1198 exchange->f_a=-B*exp(-mu*d_ij);
1199 exchange->df_a=-mu*exchange->f_a/d_ij;
1201 /* f_c, df_c calc (again, same for ij and ji) */
1203 /* f_c = 1, df_c = 0 */
1206 /* two body contribution (ij, ji) */
1207 v3_scale(&force,&dist_ij,-df_r);
1211 arg=M_PI*(d_ij-R)/s_r;
1212 f_c=0.5+0.5*cos(arg);
1213 df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
1214 /* two body contribution (ij, ji) */
1215 v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
1216 /* tell 3bp that S > r > R */
1217 exchange->d_ij_between_rs=1;
1220 /* add forces of 2bp (ij, ji) contribution
1221 * dVij = dVji and we sum up both: no 1/2) */
1222 v3_add(&(ai->f),&(ai->f),&force);
1224 /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
1225 moldyn->energy+=(0.5*f_r*f_c);
1227 /* save for use in 3bp */
1229 exchange->df_c=df_c;
1231 /* enable the run of 3bp function and 2bp post processing */
1233 exchange->run2bp_post=1;
1235 /* reset 3bp sums */
1236 exchange->zeta_ij=0.0;
1237 exchange->zeta_ji=0.0;
1238 v3_zero(&(exchange->dzeta_ij));
1239 v3_zero(&(exchange->dzeta_ji));
1244 /* tersoff 2 body post part */
1246 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1249 * here we have to allow for the 3bp sums
1252 * - zeta_ij, dzeta_ij
1253 * - zeta_ji, dzeta_ji
1255 * to compute the 3bp contribution to:
1261 t_tersoff_mult_params *params;
1262 t_tersoff_exchange *exchange;
1267 double f_c,df_c,f_a,df_a;
1268 double chi,ni,betaini,nj,betajnj;
1271 params=moldyn->pot2b_params;
1272 exchange=&(params->exchange);
1274 /* we do not run if f_c_ij was detected to be 0! */
1275 if(!(exchange->run2bp_post))
1279 df_c=exchange->df_c;
1281 df_a=exchange->df_a;
1282 betaini=exchange->betaini;
1283 betajnj=exchange->betajnj;
1284 ni=*(exchange->n_i);
1285 nj=*(exchange->n_j);
1287 dist_ij=&(exchange->dist_ij);
1290 zeta=exchange->zeta_ij;
1292 moldyn->debug++; /* just for debugging ... */
1295 v3_scale(&force,dist_ij,df_a*b*f_c);
1298 tmp=betaini*pow(zeta,ni-1.0); /* beta^n * zeta^n-1 */
1299 b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
1300 db=chi*pow(b,-1.0/(2*ni)-1); /* x(...)^(-1/2n - 1) */
1302 db*=-0.5*tmp; /* db_ij */
1303 v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
1304 v3_scale(&temp,dist_ij,df_a*b);
1305 v3_add(&force,&force,&temp);
1306 v3_scale(&force,&force,f_c);
1308 v3_scale(&temp,dist_ij,df_c*b*f_a);
1309 v3_add(&force,&force,&temp);
1310 v3_scale(&force,&force,-0.5);
1313 v3_add(&(ai->f),&(ai->f),&force);
1315 /* add energy of 3bp sum */
1316 moldyn->energy+=(0.5*f_c*b*f_a);
1319 zeta=exchange->zeta_ji;
1323 v3_scale(&force,dist_ij,df_a*b*f_c);
1326 tmp=betajnj*pow(zeta,nj-1.0); /* beta^n * zeta^n-1 */
1327 b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
1328 db=chi*pow(b,-1.0/(2*nj)-1); /* x(...)^(-1/2n - 1) */
1330 db*=-0.5*tmp; /* db_ij */
1331 v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
1332 v3_scale(&temp,dist_ij,df_a*b);
1333 v3_add(&force,&force,&temp);
1334 v3_scale(&force,&force,f_c);
1336 v3_scale(&temp,dist_ij,df_c*b*f_a);
1337 v3_add(&force,&force,&temp);
1338 v3_scale(&force,&force,-0.5);
1341 v3_sub(&(ai->f),&(ai->f),&force);
1346 /* tersoff 3 body part */
1348 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1350 t_tersoff_mult_params *params;
1351 t_tersoff_exchange *exchange;
1352 t_3dvec dist_ij,dist_ik,dist_jk;
1353 t_3dvec temp1,temp2;
1357 double d_ij,d_ik,d_jk;
1360 double f_c_ik,df_c_ik,arg;
1364 double cos_theta,d_costheta1,d_costheta2;
1365 double h_cos,d2_h_cos2;
1366 double frac,g,zeta,chi;
1370 params=moldyn->pot3b_params;
1371 exchange=&(params->exchange);
1373 if(!(exchange->run3bp))
1377 * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
1378 * 2bp contribution of dV_jk
1380 * for Vij and dV_ij we still need:
1381 * - b_ij, db_ij (zeta_ij)
1382 * - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
1384 * for dV_ji we still need:
1385 * - b_ji, db_ji (zeta_ji)
1386 * - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
1388 * for dV_jk we need:
1392 * - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
1400 /* dist_ij, d_ij - this is < S_ij ! */
1401 dist_ij=exchange->dist_ij;
1402 d_ij=exchange->d_ij;
1404 /* f_c_ij, df_c_ij (same for ji) */
1406 df_c=exchange->df_c;
1409 * calculate unknown values now ...
1412 /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
1415 v3_sub(&dist_ik,&(ak->r),&(ai->r));
1416 if(bc) check_per_bound(moldyn,&dist_ik);
1417 d_ik=v3_norm(&dist_ik);
1430 /* zeta_ij/dzeta_ij contribution only for d_ik < S */
1433 /* get constants_i from exchange data */
1440 c2d2=exchange->ci2di2;
1442 /* cosine of theta_ijk by scalaproduct */
1443 rr=v3_scalar_product(&dist_ij,&dist_ik);
1449 d_costheta1=cos_theta/(d_ij*d_ij)-tmp;
1450 d_costheta2=cos_theta/(d_ik*d_ik)-tmp;
1452 /* some usefull values */
1453 h_cos=(h-cos_theta);
1454 d2_h_cos2=d2+(h_cos*h_cos);
1455 frac=c2/(d2_h_cos2);
1460 /* d_costheta_ij and dg(cos_theta) - needed in any case! */
1461 v3_scale(&temp1,&dist_ij,d_costheta1);
1462 v3_scale(&temp2,&dist_ik,d_costheta2);
1463 v3_add(&temp1,&temp1,&temp2);
1464 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
1466 /* f_c_ik & df_c_ik + {d,}zeta contribution */
1467 dzeta=&(exchange->dzeta_ij);
1471 // => df_c_ik=0.0; of course we do not set this!
1474 exchange->zeta_ij+=g;
1477 v3_add(dzeta,dzeta,&temp1);
1482 arg=M_PI*(d_ik-R)/s_r;
1483 f_c_ik=0.5+0.5*cos(arg);
1484 df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
1487 exchange->zeta_ij+=f_c_ik*g;
1490 v3_scale(&temp1,&temp1,f_c_ik);
1491 v3_scale(&temp2,&dist_ik,g*df_c_ik);
1492 v3_add(&temp1,&temp1,&temp2);
1493 v3_add(dzeta,dzeta,&temp1);
1497 /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
1500 v3_sub(&dist_jk,&(ak->r),&(aj->r));
1501 if(bc) check_per_bound(moldyn,&dist_jk);
1502 d_jk=v3_norm(&dist_jk);
1521 /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
1524 /* constants_j from exchange data */
1531 c2d2=exchange->cj2dj2;
1533 /* cosine of theta_jik by scalaproduct */
1534 rr=v3_scalar_product(&dist_ij,&dist_jk); /* times -1 */
1539 d_costheta1=1.0/(d_jk*d_ij);
1540 d_costheta2=cos_theta/(d_ij*d_ij); /* in fact -cos(), but ^ */
1542 /* some usefull values */
1543 h_cos=(h-cos_theta);
1544 d2_h_cos2=d2+(h_cos*h_cos);
1545 frac=c2/(d2_h_cos2);
1550 /* d_costheta_ij and dg(cos_theta) - needed in any case! */
1551 v3_scale(&temp1,&dist_jk,d_costheta1);
1552 v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
1553 v3_add(&temp1,&temp1,&temp2);
1554 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
1556 /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
1557 dzeta=&(exchange->dzeta_ji);
1563 exchange->zeta_ji+=g;
1566 v3_add(dzeta,dzeta,&temp1);
1571 arg=M_PI*(d_jk-R)/s_r;
1572 f_c_jk=0.5+0.5*cos(arg);
1575 exchange->zeta_ji+=f_c_jk*g;
1578 v3_scale(&temp1,&temp1,f_c_jk);
1579 v3_add(dzeta,dzeta,&temp1);
1582 /* dV_jk stuff | add force contribution on atom i immediately */
1583 if(exchange->d_ij_between_rs) {
1585 v3_scale(&temp1,&temp1,f_c);
1586 v3_scale(&temp2,&dist_ij,df_c);
1587 v3_add(&temp1,&temp1,&temp2);
1591 // dzeta_jk is simply dg, which is temp1
1593 /* betajnj * zeta_jk ^ nj-1 */
1594 tmp=exchange->betajnj*pow(zeta,(n-1.0));
1595 tmp=-chi/2.0*pow(1+tmp*zeta,-1.0/(2.0*n)-1)*tmp;
1596 v3_scale(&temp1,&temp1,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
1597 v3_add(&(ai->f),&(ai->f),&temp1); /* -1 skipped in f_a calc ^ */
1598 /* scaled with 0.5 ^ */
1606 * debugging / critical check functions
1609 int moldyn_bc_check(t_moldyn *moldyn) {
1618 for(i=0;i<moldyn->count;i++) {
1619 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2)
1620 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1621 i,atom[i].r.x*1e10,dim->x/2*1e10);
1622 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
1623 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
1624 i,atom[i].r.y*1e10,dim->y/2*1e10);
1625 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
1626 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
1627 i,atom[i].r.z*1e10,dim->z/2*1e10);