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 link_cell_shutdown(moldyn);
45 moldyn_log_shutdown(moldyn);
46 rand_close(&(moldyn->random));
52 int set_int_alg(t_moldyn *moldyn,u8 algo) {
55 case 'MOLDYN_INTEGRATE_VERLET':
56 moldyn->integrate=velocity_verlet;
59 printf("unknown integration algorithm: %02x\",alg);
66 int set_cutoff(t_moldyn *moldyn,double cutoff) {
68 moldyn->cutoff=cutoff;
73 int set_temperature(t_moldyn *moldyn,double t) {
80 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
95 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
98 moldyn->status|=MOLDYN_STAT_PBX;
101 moldyn->status|=MOLDYN_STAT_PBY;
104 moldyn->status|=MOLDYN_STAT_PBZ;
109 int set_potential(t_moldyn *moldyn,u8 type,(int *)(func),void *params) {
113 moldyn->pf_func1b=func;
114 moldyn->pot1b_params=params;
117 moldyn->pf_func2b=func;
118 moldyn->pot2b_params=params;
121 moldyn->pf_func3b=func;
122 moldyn->pot3b_params=params;
125 printf("unknown potential type: %02x\n",type);
132 int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
135 case LOG_TOTAL_ENERGY:
136 moldyn->ewrite=timer;
137 moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
139 perror("[moldyn] efd open");
142 dprintf("# moldyn total energy log file\n");
144 case LOG_TOTAL_MOMENTUM:
145 moldyn->mwrite=timer;
146 moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
148 perror("[moldyn] mfd open");
151 dprintf("# moldyn total momentum log file\n");
154 moldyn->swrite=timer;
155 strncpy(moldyn->sfb,fb,63);
158 moldyn->mwrite=timer;
159 strncpy(moldyn->vfb,fb,63);
160 visual_init(&(moldyn->vis),fb);
163 printf("unknown log mechanism: %02x\n",type);
170 int moldyn_log_shutdown(t_moldyn *moldyn) {
172 if(moldyn->efd) close(moldyn->efd);
173 if(moldyn->mfd) close(moldyn->mfd);
174 if(moldyn->visual) visual_tini(moldyn->visual);
179 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
180 u8 attr,u8 bnum,int a,int b,int c) {
190 if(type==FCC) count*=4;
192 if(type==DIAMOND) count*=8;
194 atom=malloc(count*sizeof(t_atom));
196 perror("malloc (atoms)");
204 ret=fcc_init(a,b,c,lc,atom,&origin);
207 ret=diamond_init(a,b,c,lc,atom,&origin);
210 printf("unknown lattice type (%02x)\n",type);
216 printf("ok, there is something wrong ...\n");
217 printf("calculated -> %d atoms\n",count);
218 printf("created -> %d atoms\n",ret);
225 atom[count-1].element=element;
226 atom[count-1].mass=mass;
227 atom[count-1].attr=attr;
228 atom[count-1].bnum=bnum;
235 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
236 t_3dvec r,t_3dvec v) {
243 count=++(moldyn->count);
245 ptr=realloc(atom,count*sizeof(t_atom));
247 perror("[moldyn] realloc (add atom)");
254 atom->element=element;
261 int destroy_atoms(t_moldyn *moldyn) {
263 if(moldyn->atom) free(moldyn->atom);
268 int thermal_init(t_moldyn *moldyn) {
271 * - gaussian distribution of velocities
272 * - zero total momentum
273 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
278 t_3dvec p_total,delta;
283 random=&(moldyn->random);
285 /* gaussian distribution of velocities */
287 for(i=0;i<moldyn->count;i++) {
288 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
290 v=sigma*rand_get_gauss(random);
292 p_total.x+=atom[i].mass*v;
294 v=sigma*rand_get_gauss(random);
296 p_total.y+=atom[i].mass*v;
298 v=sigma*rand_get_gauss(random);
300 p_total.z+=atom[i].mass*v;
303 /* zero total momentum */
304 v3_scale(&p_total,&p_total,1.0/moldyn->count);
305 for(i=0;i<moldyn->count;i++) {
306 v3_scale(&delta,&p_total,1.0/atom[i].mass);
307 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
310 /* velocity scaling */
311 scale_velocity(moldyn);
316 int scale_velocity(t_moldyn *moldyn) {
325 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
328 for(i=0;i<moldyn->count;i++)
329 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
330 c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
331 for(i=0;i<moldyn->count;i++)
332 v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
337 double get_e_kin(t_moldyn *moldyn) {
345 for(i=0;i<moldyn->count;i++)
346 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
351 double get_e_pot(t_moldyn *moldyn) {
353 return moldyn->energy;
356 double get_total_energy(t_moldyn *moldyn) {
358 return(get_e_kin(moldyn)+get_e_pot(moldyn));
361 t_3dvec get_total_p(t_moldyn *moldyn) {
370 for(i=0;i<count;i++) {
371 v3_scale(&p,&(atom[i].v),atom[i].mass);
372 v3_add(&p_total,&p_total,&p);
378 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
382 tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
385 printf("[moldyn] warning: time step (%f > %.15f)\n",
395 /* linked list / cell method */
397 int link_cell_init(t_moldyn *moldyn) {
405 lc->listfd=open("/dev/null",O_WRONLY);
407 /* partitioning the md cell */
408 lc->nx=moldyn->dim.x/moldyn->cutoff;
409 lc->x=moldyn->dim.x/lc->nx;
410 lc->ny=moldyn->dim.y/moldyn->cutoff;
411 lc->y=moldyn->dim.y/lc->ny;
412 lc->nz=moldyn->dim.z/moldyn->cutoff;
413 lc->z=moldyn->dim.z/lc->nz;
415 lc->cells=lc->nx*lc->ny*lc->nz;
416 lc->subcell=malloc(lc->cells*sizeof(t_list));
418 printf("initializing linked cells (%d)\n",lc->cells);
420 for(i=0;i<lc->cells;i++)
421 //list_init(&(lc->subcell[i]),1);
422 list_init(&(lc->subcell[i]));
424 link_cell_update(moldyn);
429 int link_cell_update(t_moldyn *moldyn) {
443 for(i=0;i<lc->cells;i++)
444 list_destroy(&(moldyn->lc.subcell[i]));
446 for(count=0;count<moedyn->count;count++) {
447 i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
448 j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
449 k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
450 list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
457 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
476 cell[0]=lc->subcell[i+j*nx+k*a];
477 for(ci=-1;ci<=1;ci++) {
484 for(cj=-1;cj<=1;cj++) {
491 for(ck=-1;ck<=1;ck++) {
498 if(!(ci|cj|ck)) continue;
500 cell[--count2]=lc->subcell[x+y*nx+z*a];
503 cell[count1++]=lc->subcell[x+y*nx+z*a];
515 int link_cell_shutdown(t_moldyn *moldyn) {
522 for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
523 list_shutdown(&(moldyn->lc.subcell[i]));
525 if(lc->listfd) close(lc->listfd);
530 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
534 t_moldyn_schedule *schedule;
536 schedule=moldyn->schedule;
537 count=++(schedule->content_count);
539 ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
541 perror("[moldyn] realloc (runs)");
544 moldyn->schedule.runs[count-1]=runs;
546 ptr=realloc(schedule->tau,count*sizeof(double));
548 perror("[moldyn] realloc (tau)");
551 moldyn->schedule.tau[count-1]=tau;
556 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
558 moldyn->schedule.hook=hook;
559 moldyn->schedule.hook_params=hook_params;
566 * 'integration of newtons equation' - algorithms
570 /* start the integration */
572 int moldyn_integrate(t_moldyn *moldyn) {
575 unsigned int e,m,s,d,v;
581 /* initialize linked cell method */
582 link_cell_init(moldyn);
584 /* logging & visualization */
591 if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
592 printf("[moldyn] warning, lv system not initialized\n");
596 /* sqaure of some variables */
597 moldyn->tau_square=moldyn->tau*moldyn->tau;
598 moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
600 /* calculate initial forces */
601 moldyn->potential_force_function(moldyn);
603 for(sched=0;sched<moldyn->schedule.content_count;sched++) {
605 /* setting amont of runs and finite time step size */
606 moldyn->tau=schedule->tau[sched];
607 moldyn->tau_square=moldyn->tau*moldyn->tau;
608 moldyn->timesteps=schedule->runs[sched];
610 /* integration according to schedule */
612 for(i=0;i<moldyn->time_steps;i++) {
614 /* integration step */
615 moldyn->integrate(moldyn);
617 /* check for log & visualization */
621 "%.15f %.45f\n",i*moldyn->tau,
622 get_total_energy(moldyn));
626 p=get_total_p(moldyn->atom,moldyn->count);
628 "%.15f %.45f\n",i*moldyn->tau,
634 snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
635 moldyn->t,i*moldyn->tau);
636 fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
637 if(fd<0) perror("[moldyn] save fd open");
639 write(fd,moldyn,sizeof(t_moldyn));
640 write(fd,moldyn->atom,
641 moldyn->count*sizeof(t_atom));
648 visual_atoms(moldyn->visual,i*moldyn->tau,
649 moldyn->atom,moldyn->count);
650 printf("\rsteps: %d",i);
656 /* check for hooks */
658 schedule->hook(moldyn,schedule->hook_params);
663 /* velocity verlet */
665 int velocity_verlet(t_moldyn *moldyn) {
668 double tau,tau_square;
675 tau_square=moldyn->tau_square;
677 for(i=0;i<count;i++) {
679 v3_scale(&delta,&(atom[i].v),tau);
680 v3_add(&(atom[i].r),&(atom[i].r),&delta);
681 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
682 v3_add(&(atom[i].r),&(atom[i].r),&delta);
683 v3_per_bound(&(atom[i].r),&(moldyn->dim));
686 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
687 v3_add(&(atom[i].v),&(atom[i].v),&delta);
690 /* neighbour list update */
691 printf("list update ...\n");
692 link_cell_update(moldyn);
695 /* forces depending on chosen potential */
696 printf("calc potential/force ...\n");
697 potential_force_calc(moldyn);
698 //moldyn->potential_force_function(moldyn);
701 for(i=0;i<count;i++) {
702 /* again velocities */
703 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
704 v3_add(&(atom[i].v),&(atom[i].v),&delta);
713 * potentials & corresponding forces
717 /* generic potential and force calculation */
719 int potential_force_calc(t_moldyn *moldyn) {
724 t_list neighbour[27];
737 for(i=0;i<count;i++) {
740 v3_zero(&(atom[i].f));
742 /* single particle potential/force */
743 if(atom[i].attr&ATOM_ATTR_1BP)
744 moldyn->pf_func1b(moldyn,&(atom[i]));
746 /* 2 body pair potential/force */
747 if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
749 link_cell_neighbour_index(moldyn,
750 (atom[i].r.x+moldyn->dim.x/2)/lc->x,
751 (atom[i].r.y+moldyn->dim.y/2)/lc->y,
752 (atom[i].r.z+moldyn->dim.z/2)/lc->z,
758 for(j=0;j<countn;j++) {
760 this=&(neighbour[j]);
763 if(this->start==NULL)
769 btom=this->current->data;
774 if((btom->attr&ATOM_ATTR_2BP)&
775 (atom[i].attr&ATOM_ATTR_2BP))
776 moldyn->pf_func2b(moldyn,
781 /* 3 body potential/force */
783 if(!(atom[i].attr&ATOM_ATTR_3BP)||
784 !(btom->attr&ATOM_ATTR_3BP))
787 link_cell_neighbour_index(moldyn,
788 (btom->r.x+moldyn->dim.x/2)/lc->x,
789 (btom->r.y+moldyn->dim.y/2)/lc->y,
790 (btom->r.z+moldyn->dim.z/2)/lc->z,
793 for(k=0;k<lc->countn;k++) {
795 thisk=&(neighbourk[k]);
798 if(thisk->start==NULL)
801 bck=(k<lc->dnlc)?0:1;
805 ktom=thisk->current->data;
807 if(!(ktom->attr&ATOM_ATTR_3BP))
816 moldyn->pf_func3b(moldyn,&(atom[i]),btom,ktom,bck);
818 } while(list_next(thisk)!=\
821 } while(list_next(this)!=L_NO_NEXT_ELEMENT);
830 * periodic boundayr checking
833 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
841 if(moldyn->MOLDYN_ATTR_PBX)
842 if(a->x>=x) a->x-=dim->x;
843 else if(-a->x>x) a->x+=dim->x;
844 if(moldyn->MOLDYN_ATTR_PBY)
845 if(a->y>=y) a->y-=dim->y;
846 else if(-a->y>y) a->y+=dim->y;
847 if(moldyn->MOLDYN_ATTR_PBZ)
848 if(a->z>=z) a->z-=dim->z;
849 else if(-a->z>z) a->z+=dim->z;
859 /* harmonic oscillator potential and force */
861 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc)) {
864 t_3dvec force,distance;
868 params=moldyn->pot2b_params;
869 sc=params->spring_constant;
870 equi_dist=params->equilibrium_distance;
872 v3_sub(&distance,&(ai->r),&(aj->r);
874 v3_per_bound(&distance,&(moldyn->dim));
875 if(bc) check_per_bound(moldyn,&distance);
876 d=v3_norm(&distance);
877 if(d<=moldyn->cutoff) {
878 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
879 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
880 v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
881 v3_add(&(ai->f),&(ai->f),&force);
887 /* lennard jones potential & force for one sort of atoms */
889 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
892 t_3dvec force,distance;
894 double eps,sig6,sig12;
896 params=moldyn->pot_params;
897 eps=params->epsilon4;
899 sig12=params->sigma12;
901 v3_sub(&distance,&(ai->r),&(aj->r));
902 if(bc) check_per_bound(moldyn,&distance);
903 d=v3_absolute_square(&distance); /* 1/r^2 */
904 if(d<=moldyn->cutoff_square) {
908 h1=h2*h2; /* 1/r^12 */
909 /* energy is eps*..., but we will add this twice ... */
910 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
917 v3_scale(&force,&distance,d);
918 v3_add(&(ai->f),&(aj->f),&force);
925 * tersoff potential & force for 2 sorts of atoms
928 /* tersoff 1 body part */
929 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
932 t_tersoff_mult_params *params;
933 t_tersoff_exchange *exchange;
936 params=moldyn->pot1b_params;
937 exchange=&(params->exchange);
940 * simple: point constant parameters only depending on atom i to
944 exchange->beta=&(params->beta[num]);
945 exchange->n=&(params->n[num]);
946 exchange->c=&(params->c[num]);
947 exchange->d=&(params->d[num]);
948 exchange->h=&(params->h[num]);
950 exchange->betan=pow(*(exchange->beta),*(exchange->n));
951 exchange->c2=params->c[num]*params->c[num];
952 exchange->d2=params->d[num]*params->d[num];
953 exchange->c2d2=exchange->c2/exchange->d2;
958 /* tersoff 2 body part */
959 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
961 t_tersoff_mult_params *params;
962 t_tersoff_exchange *exchange;
965 double A,B,R,S,lambda;
968 params=moldyn->pot_params;
970 exchange=&(params->exchange);
975 * we need: f_c, df_c, f_r, df_r
977 * therefore we need: R, S, A, lambda
980 v3_sub(&dist_ij,&(ai->r),&(aj->r));
982 if(bc) check_per_bound(moldyn,&dist_ij);
984 /* save for use in 3bp */ /* REALLY ?!?!?! */
985 exchange->dist_ij=dist_ij;
992 lambda=params->lambda[num];
993 /* more constants depending of atoms i and j, needed in 3bp */
994 params->exchange.B=&(params->B[num]);
995 params->exchange.mu=params->mu[num];
996 params->exchange.chi=1.0;
1002 lambda=params->lambda_m;
1003 /* more constants depending of atoms i and j, needed in 3bp */
1004 params->exchange.B=&(params->Bmixed);
1005 params->exchange.mu=&(params->mu_m);
1006 params->exchange.chi=params->chi;
1009 d_ij=v3_norm(&dist_ij);
1011 /* save for use in 3bp */
1012 exchange->d_ij=d_ij;
1017 f_r=A*exp(-lamda*d_ij);
1018 df_r=-lambda*f_r/d_ij;
1020 /* f_a, df_a calc + save for 3bp use */
1021 exchange->f_a=-B*exp(-mu*d_ij);
1022 exchange->df_a=-mu*exchange->f_a/d_ij;
1025 /* f_c = 1, df_c = 0 */
1028 v3_scale(&force,&dist_ij,df_r);
1032 arg=PI*(d_ij-R)/s_r;
1033 f_c=0.5+0.5*cos(arg);
1034 df_c=-0.5*sin(arg)*(PI/(s_r*d_ij));
1035 scale=df_c*f_r+df_r*f_c;
1036 v3_scale(&force,&dist_ij,scale);
1040 v3_add(&(ai->f),&(ai->f),&force);
1041 /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1042 moldyn->energy+=(0.25*f_r*f_c);
1044 /* save for use in 3bp */
1046 exchange->df_c=df_c;
1048 /* enable the run of 3bp function */
1054 /* tersoff 3 body part */
1056 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1058 t_tersoff_mult_params *params;
1059 t_tersoff_exchange *exchange;
1060 t_3dvec dist_ij,dist_ik,dist_jk;
1063 double d_ij,d_ik,d_jk;
1064 double f_c,df_c,b_ij,f_a,df_a;
1065 double n,c,d,h,neta,betan,betan_1;
1066 double theta,cos_theta,sin_theta;
1069 params=moldyn->pot_params;
1071 exchange=params->exchange;
1073 if(!(exchange->run3bp))
1077 * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
1079 * we got f_c, df_c, f_a, df_a from 2bp calculation
1082 d_ij=exchange->d_ij;
1083 d_ij2=exchange->d_ij2;
1085 f_a=params->exchange.f_a;
1086 df_a=params->exchange.df_a;
1088 /* d_ij is <= S, as we didn't return so far! */
1091 * calc of b_ij (scalar) and db_ij (vector)
1093 * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
1095 * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
1101 v3_sub(&dist_ik,&(aj->i),&(ak->r));
1102 if(bc) check_per_bound(moldyn,&dist_ik);
1103 d_ik=v3_norm(&dist_ik);
1105 /* constants for f_c_ik calc */
1115 /* calc of f_c_ik */
1120 /* f_c_ik = 1, df_c_ik = 0 */
1126 arg=PI*(d_ik-R)/s_r;
1127 f_c_ik=0.5+0.5*cos(arg);
1128 df_c_ik=-0.5*sin(arg)*(PI/(s_r*d_ik));
1131 v3_sub(&dist_jk,&(aj->r),&(ak->r));
1132 if(bc) check_per_bound(moldyn,&dist_jk);
1133 d_jk=v3_norm(&dist_jk);
1135 beta=*(exchange->beta);
1136 betan=exchange->betan;
1143 c2d2=exchange->c2d2;
1145 numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
1147 cos_theta=numer/denom;
1148 sin_theta=sqrt(1.0-(cos_theta*cos_theta));
1149 theta=arccos(cos_theta);
1150 d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
1151 d_theta1=2*denom-numer*2*d_ik/d_ij;
1152 d_theta2=2*denom-numer*2*d_ij/d_ik;
1156 h_cos=(h-cos_theta);
1158 d2_h_cos2=d2-h_cos2;
1160 /* some usefull expressions */
1161 frac1=c2/(d2-h_cos2);
1162 bracket1=1+c2d2-frac1;
1163 bracket2=f_c_ik*bracket1;
1164 bracket2_n_1=pow(bracket2,n-1.0);
1165 bracket2_n=bracket2_n_1*bracket2;
1166 bracket3=1+betan*bracket2_n;
1167 bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
1168 bracket3_pow=bracket3_pow_1*bracket3;
1170 /* now go on with calc of b_ij and derivation of b_ij */
1171 b_ij=chi*bracket3_pow;
1173 /* derivation of theta */
1174 v3_scale(&force,&dist_ij,d1_theta);
1175 v3_scale(&temp,&dist_ik,d_theta2);
1176 v3_add(&force,&force,&temp);
1178 /* part 1 of derivation of b_ij */
1179 v3_scale(&force,sin_theta*2*h_cos*f_c_ik*frac1);
1181 /* part 2 of derivation of b_ij */
1182 v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
1184 /* sum up and scale ... */
1185 v3_add(&temp,&temp,&force);
1186 scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
1187 v3_scale(&temp,&temp,scale);
1189 /* now construct an energy and a force out of that */
1190 v3_scale(&temp,&temp,f_a);
1191 v3_scale(&force,&dist_ij,df_a*b_ij);
1192 v3_add(&temp,&temp,&force);
1193 v3_scale(&temp,&temp,f_c);
1194 v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
1195 v3_add(&force,&force,&temp);
1198 v3_add(&(ai->f),&(ai->f),&force);
1199 /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1200 moldyn->energy+=(0.25*f_a*b_ij*f_c);