moldyn.c

   1 /*
   2  * moldyn.c - molecular dynamics library main file
   3  *
   4  * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
   5  *
   6  */
   7
   8 #define _GNU_SOURCE
   9 #include <stdio.h>
  10 #include <stdlib.h>
  11 #include <string.h>
  12 #include <sys/types.h>
  13 #include <sys/stat.h>
  14 #include <fcntl.h>
  15 #include <unistd.h>
  16 #include <math.h>
  17
  18 #include "moldyn.h"
  19
  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"
  25
  26
  27 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
  28
  29         //int ret;
  30
  31         //ret=moldyn_parse_argv(moldyn,argc,argv);
  32         //if(ret<0) return ret;
  33
  34         memset(moldyn,0,sizeof(t_moldyn));
  35
  36         rand_init(&(moldyn->random),NULL,1);
  37         moldyn->random.status|=RAND_STAT_VERBOSE;
  38
  39         return 0;
  40 }
  41
  42 int moldyn_shutdown(t_moldyn *moldyn) {
  43
  44         printf("[moldyn] shutdown\n");
  45         moldyn_log_shutdown(moldyn);
  46         link_cell_shutdown(moldyn);
  47         rand_close(&(moldyn->random));
  48         free(moldyn->atom);
  49
  50         return 0;
  51 }
  52
  53 int set_int_alg(t_moldyn *moldyn,u8 algo) {
  54
  55         switch(algo) {
  56                 case MOLDYN_INTEGRATE_VERLET:
  57                         moldyn->integrate=velocity_verlet;
  58                         break;
  59                 default:
  60                         printf("unknown integration algorithm: %02x\n",algo);
  61                         return -1;
  62         }
  63
  64         return 0;
  65 }
  66
  67 int set_cutoff(t_moldyn *moldyn,double cutoff) {
  68
  69         moldyn->cutoff=cutoff;
  70
  71         return 0;
  72 }
  73
  74 int set_temperature(t_moldyn *moldyn,double t_ref) {
  75
  76         moldyn->t_ref=t_ref;
  77
  78         return 0;
  79 }
  80
  81 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
  82
  83         moldyn->pt_scale=(ptype|ttype);
  84         moldyn->t_tc=ttc;
  85         moldyn->p_tc=ptc;
  86
  87         return 0;
  88 }
  89
  90 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
  91
  92         moldyn->dim.x=x;
  93         moldyn->dim.y=y;
  94         moldyn->dim.z=z;
  95
  96         if(visualize) {
  97                 moldyn->vis.dim.x=x;
  98                 moldyn->vis.dim.y=y;
  99                 moldyn->vis.dim.z=z;
 100         }
 101
 102         return 0;
 103 }
 104
 105 int set_nn_dist(t_moldyn *moldyn,double dist) {
 106
 107         moldyn->nnd=dist;
 108
 109         return 0;
 110 }
 111
 112 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 113
 114         if(x)
 115                 moldyn->status|=MOLDYN_STAT_PBX;
 116
 117         if(y)
 118                 moldyn->status|=MOLDYN_STAT_PBY;
 119
 120         if(z)
 121                 moldyn->status|=MOLDYN_STAT_PBZ;
 122
 123         return 0;
 124 }
 125
 126 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
 127
 128         moldyn->func1b=func;
 129         moldyn->pot1b_params=params;
 130
 131         return 0;
 132 }
 133
 134 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
 135
 136         moldyn->func2b=func;
 137         moldyn->pot2b_params=params;
 138
 139         return 0;
 140 }
 141
 142 int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
 143
 144         moldyn->func2b=func;
 145         moldyn->pot2b_params=params;
 146
 147         return 0;
 148 }
 149
 150 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
 151
 152         moldyn->func3b=func;
 153         moldyn->pot3b_params=params;
 154
 155         return 0;
 156 }
 157
 158 int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
 159
 160         switch(type) {
 161                 case LOG_TOTAL_ENERGY:
 162                         moldyn->ewrite=timer;
 163                         moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
 164                         if(moldyn->efd<0) {
 165                                 perror("[moldyn] efd open");
 166                                 return moldyn->efd;
 167                         }
 168                         dprintf(moldyn->efd,"# total energy log file\n");
 169                         break;
 170                 case LOG_TOTAL_MOMENTUM:
 171                         moldyn->mwrite=timer;
 172                         moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
 173                         if(moldyn->mfd<0) {
 174                                 perror("[moldyn] mfd open");
 175                                 return moldyn->mfd;
 176                         }
 177                         dprintf(moldyn->efd,"# total momentum log file\n");
 178                         break;
 179                 case SAVE_STEP:
 180                         moldyn->swrite=timer;
 181                         strncpy(moldyn->sfb,fb,63);
 182                         break;
 183                 case VISUAL_STEP:
 184                         moldyn->vwrite=timer;
 185                         strncpy(moldyn->vfb,fb,63);
 186                         visual_init(&(moldyn->vis),fb);
 187                         break;
 188                 default:
 189                         printf("unknown log mechanism: %02x\n",type);
 190                         return -1;
 191         }
 192
 193         return 0;
 194 }
 195
 196 int moldyn_log_shutdown(t_moldyn *moldyn) {
 197
 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));
 202
 203         return 0;
 204 }
 205
 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) {
 208
 209         int count;
 210         int ret;
 211         t_3dvec origin;
 212
 213         count=a*b*c;
 214
 215         if(type==FCC) count*=4;
 216
 217         if(type==DIAMOND) count*=8;
 218
 219         moldyn->atom=malloc(count*sizeof(t_atom));
 220         if(moldyn->atom==NULL) {
 221                 perror("malloc (atoms)");
 222                 return -1;
 223         }
 224
 225         v3_zero(&origin);
 226
 227         switch(type) {
 228                 case FCC:
 229                         ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
 230                         break;
 231                 case DIAMOND:
 232                         ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
 233                         break;
 234                 default:
 235                         printf("unknown lattice type (%02x)\n",type);
 236                         return -1;
 237         }
 238
 239         /* debug */
 240         if(ret!=count) {
 241                 printf("ok, there is something wrong ...\n");
 242                 printf("calculated -> %d atoms\n",count);
 243                 printf("created -> %d atoms\n",ret);
 244                 return -1;
 245         }
 246
 247         moldyn->count=count;
 248         printf("[moldyn] created lattice with %d atoms\n",count);
 249
 250         while(count) {
 251                 count-=1;
 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));
 257         }
 258
 259
 260         return ret;
 261 }
 262
 263 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 264              t_3dvec *r,t_3dvec *v) {
 265
 266         t_atom *atom;
 267         void *ptr;
 268         int count;
 269
 270         atom=moldyn->atom;
 271         count=++(moldyn->count);
 272
 273         ptr=realloc(atom,count*sizeof(t_atom));
 274         if(!ptr) {
 275                 perror("[moldyn] realloc (add atom)");
 276                 return -1;
 277         }
 278         moldyn->atom=ptr;
 279
 280         atom=moldyn->atom;
 281         atom[count-1].r=*r;
 282         atom[count-1].v=*v;
 283         atom[count-1].element=element;
 284         atom[count-1].mass=mass;
 285         atom[count-1].bnum=bnum;
 286         atom[count-1].attr=attr;
 287
 288         return 0;
 289 }
 290
 291 int destroy_atoms(t_moldyn *moldyn) {
 292
 293         if(moldyn->atom) free(moldyn->atom);
 294
 295         return 0;
 296 }
 297
 298 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 299
 300         /*
 301          * - gaussian distribution of velocities
 302          * - zero total momentum
 303          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 304          */
 305
 306         int i;
 307         double v,sigma;
 308         t_3dvec p_total,delta;
 309         t_atom *atom;
 310         t_random *random;
 311
 312         atom=moldyn->atom;
 313         random=&(moldyn->random);
 314
 315         /* gaussian distribution of velocities */
 316         v3_zero(&p_total);
 317         for(i=0;i<moldyn->count;i++) {
 318                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
 319                 /* x direction */
 320                 v=sigma*rand_get_gauss(random);
 321                 atom[i].v.x=v;
 322                 p_total.x+=atom[i].mass*v;
 323                 /* y direction */
 324                 v=sigma*rand_get_gauss(random);
 325                 atom[i].v.y=v;
 326                 p_total.y+=atom[i].mass*v;
 327                 /* z direction */
 328                 v=sigma*rand_get_gauss(random);
 329                 atom[i].v.z=v;
 330                 p_total.z+=atom[i].mass*v;
 331         }
 332
 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);
 338         }
 339
 340         /* velocity scaling */
 341         scale_velocity(moldyn,equi_init);
 342
 343         return 0;
 344 }
 345
 346 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 347
 348         int i;
 349         double e,scale;
 350         t_atom *atom;
 351         int count;
 352
 353         atom=moldyn->atom;
 354
 355         /*
 356          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 357          */
 358
 359         /* get kinetic energy / temperature & count involved atoms */
 360         e=0.0;
 361         count=0;
 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));
 365                         count+=1;
 366                 }
 367         }
 368         if(count!=0) moldyn->t=(2.0*e)/(3.0*count*K_BOLTZMANN);
 369         else return 0;  /* no atoms involved in scaling! */
 370
 371         /* (temporary) hack for e,t = 0 */
 372         if(e==0.0) {
 373         moldyn->t=0.0;
 374                 if(moldyn->t_ref!=0.0)
 375                         thermal_init(moldyn,equi_init);
 376                 else
 377                         return 0; /* no scaling needed */
 378         }
 379
 380
 381         /* get scaling factor */
 382         scale=moldyn->t_ref/moldyn->t;
 383         if(equi_init&TRUE)
 384                 scale*=2.0;
 385         else
 386                 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
 387                         scale=1.0+moldyn->tau*(scale-1.0)/moldyn->t_tc;
 388         scale=sqrt(scale);
 389
 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);
 394
 395         return 0;
 396 }
 397
 398 double get_e_kin(t_moldyn *moldyn) {
 399
 400         int i;
 401         t_atom *atom;
 402
 403         atom=moldyn->atom;
 404         moldyn->ekin=0.0;
 405
 406         for(i=0;i<moldyn->count;i++)
 407                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 408
 409         return moldyn->ekin;
 410 }
 411
 412 double get_e_pot(t_moldyn *moldyn) {
 413
 414         return moldyn->energy;
 415 }
 416
 417 double update_e_kin(t_moldyn *moldyn) {
 418
 419         return(get_e_kin(moldyn));
 420 }
 421
 422 double get_total_energy(t_moldyn *moldyn) {
 423
 424         return(moldyn->ekin+moldyn->energy);
 425 }
 426
 427 t_3dvec get_total_p(t_moldyn *moldyn) {
 428
 429         t_3dvec p,p_total;
 430         int i;
 431         t_atom *atom;
 432
 433         atom=moldyn->atom;
 434
 435         v3_zero(&p_total);
 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);
 439         }
 440
 441         return p_total;
 442 }
 443
 444 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 445
 446         double tau;
 447
 448         /* nn_dist is the nearest neighbour distance */
 449
 450         if(moldyn->t==5.0) {
 451                 printf("[moldyn] i do not estimate timesteps below %f K!\n",
 452                        MOLDYN_CRITICAL_EST_TEMP);
 453                 return 23.42;
 454         }
 455
 456         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
 457
 458         return tau;
 459 }
 460
 461 /*
 462  * numerical tricks
 463  */
 464
 465 /* linked list / cell method */
 466
 467 int link_cell_init(t_moldyn *moldyn) {
 468
 469         t_linkcell *lc;
 470         int i;
 471         int fd;
 472
 473         fd=open("/dev/null",O_WRONLY);
 474
 475         lc=&(moldyn->lc);
 476
 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;
 484
 485         lc->cells=lc->nx*lc->ny*lc->nz;
 486         lc->subcell=malloc(lc->cells*sizeof(t_list));
 487
 488         printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 489
 490         for(i=0;i<lc->cells;i++)
 491                 //list_init(&(lc->subcell[i]),1);
 492                 list_init(&(lc->subcell[i]),fd);
 493
 494         link_cell_update(moldyn);
 495
 496         return 0;
 497 }
 498
 499 int link_cell_update(t_moldyn *moldyn) {
 500
 501         int count,i,j,k;
 502         int nx,ny,nz;
 503         t_atom *atom;
 504         t_linkcell *lc;
 505
 506         atom=moldyn->atom;
 507         lc=&(moldyn->lc);
 508
 509         nx=lc->nx;
 510         ny=lc->ny;
 511         nz=lc->nz;
 512
 513         for(i=0;i<lc->cells;i++)
 514                 list_destroy(&(moldyn->lc.subcell[i]));
 515
 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]),
 521                                        &(atom[count]));
 522         }
 523
 524         return 0;
 525 }
 526
 527 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 528
 529         t_linkcell *lc;
 530         int a;
 531         int count1,count2;
 532         int ci,cj,ck;
 533         int nx,ny,nz;
 534         int x,y,z;
 535         u8 bx,by,bz;
 536
 537         lc=&(moldyn->lc);
 538         nx=lc->nx;
 539         ny=lc->ny;
 540         nz=lc->nz;
 541         count1=1;
 542         count2=27;
 543         a=nx*ny;
 544
 545         cell[0]=lc->subcell[i+j*nx+k*a];
 546         for(ci=-1;ci<=1;ci++) {
 547                 bx=0;
 548                 x=i+ci;
 549                 if((x<0)||(x>=nx)) {
 550                         x=(x+nx)%nx;
 551                         bx=1;
 552                 }
 553                 for(cj=-1;cj<=1;cj++) {
 554                         by=0;
 555                         y=j+cj;
 556                         if((y<0)||(y>=ny)) {
 557                                 y=(y+ny)%ny;
 558                                 by=1;
 559                         }
 560                         for(ck=-1;ck<=1;ck++) {
 561                                 bz=0;
 562                                 z=k+ck;
 563                                 if((z<0)||(z>=nz)) {
 564                                         z=(z+nz)%nz;
 565                                         bz=1;
 566                                 }
 567                                 if(!(ci|cj|ck)) continue;
 568                                 if(bx|by|bz) {
 569                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
 570                                 }
 571                                 else {
 572                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
 573                                 }
 574                         }
 575                 }
 576         }
 577
 578         lc->dnlc=count1;
 579         lc->countn=27;
 580
 581         return count2;
 582 }
 583
 584 int link_cell_shutdown(t_moldyn *moldyn) {
 585
 586         int i;
 587         t_linkcell *lc;
 588
 589         lc=&(moldyn->lc);
 590
 591         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 592                 list_shutdown(&(moldyn->lc.subcell[i]));
 593
 594         return 0;
 595 }
 596
 597 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 598
 599         int count;
 600         void *ptr;
 601         t_moldyn_schedule *schedule;
 602
 603         schedule=&(moldyn->schedule);
 604         count=++(schedule->content_count);
 605
 606         ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
 607         if(!ptr) {
 608                 perror("[moldyn] realloc (runs)");
 609                 return -1;
 610         }
 611         moldyn->schedule.runs=ptr;
 612         moldyn->schedule.runs[count-1]=runs;
 613
 614         ptr=realloc(schedule->tau,count*sizeof(double));
 615         if(!ptr) {
 616                 perror("[moldyn] realloc (tau)");
 617                 return -1;
 618         }
 619         moldyn->schedule.tau=ptr;
 620         moldyn->schedule.tau[count-1]=tau;
 621
 622         return 0;
 623 }
 624
 625 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 626
 627         moldyn->schedule.hook=hook;
 628         moldyn->schedule.hook_params=hook_params;
 629
 630         return 0;
 631 }
 632
 633 /*
 634  *
 635  * 'integration of newtons equation' - algorithms
 636  *
 637  */
 638
 639 /* start the integration */
 640
 641 int moldyn_integrate(t_moldyn *moldyn) {
 642
 643         int i,sched;
 644         unsigned int e,m,s,v;
 645         t_3dvec p;
 646         t_moldyn_schedule *schedule;
 647         t_atom *atom;
 648         int fd;
 649         char fb[128];
 650         double ds;
 651
 652         schedule=&(moldyn->schedule);
 653         atom=moldyn->atom;
 654
 655         /* initialize linked cell method */
 656         link_cell_init(moldyn);
 657
 658         /* logging & visualization */
 659         e=moldyn->ewrite;
 660         m=moldyn->mwrite;
 661         s=moldyn->swrite;
 662         v=moldyn->vwrite;
 663
 664         /* sqaure of some variables */
 665         moldyn->tau_square=moldyn->tau*moldyn->tau;
 666         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 667         /* calculate initial forces */
 668         potential_force_calc(moldyn);
 669
 670         /* do some 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");
 680
 681         /* zero absolute time */
 682         moldyn->time=0.0;
 683         for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 684
 685                 /* setting amount of runs and finite time step size */
 686                 moldyn->tau=schedule->tau[sched];
 687                 moldyn->tau_square=moldyn->tau*moldyn->tau;
 688                 moldyn->time_steps=schedule->runs[sched];
 689
 690         /* integration according to schedule */
 691
 692         for(i=0;i<moldyn->time_steps;i++) {
 693
 694                 /* integration step */
 695                 moldyn->integrate(moldyn);
 696
 697                 /* p/t scaling */
 698                 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
 699                         scale_velocity(moldyn,FALSE);
 700
 701                 /* increase absolute time */
 702                 moldyn->time+=moldyn->tau;
 703
 704                 /* check for log & visualization */
 705                 if(e) {
 706                         if(!(i%e))
 707                                 dprintf(moldyn->efd,
 708                                         "%.15f %.45f %.45f %.45f\n",
 709                                         moldyn->time,update_e_kin(moldyn),
 710                                         moldyn->energy,
 711                                         get_total_energy(moldyn));
 712                 }
 713                 if(m) {
 714                         if(!(i%m)) {
 715                                 p=get_total_p(moldyn);
 716                                 dprintf(moldyn->mfd,
 717                                         "%.15f %.45f\n",moldyn->time,
 718                                         v3_norm(&p));
 719                         }
 720                 }
 721                 if(s) {
 722                         if(!(i%s)) {
 723                                 snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
 724                                          moldyn->t,i*moldyn->tau);
 725                                 fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
 726                                 if(fd<0) perror("[moldyn] save fd open");
 727                                 else {
 728                                         write(fd,moldyn,sizeof(t_moldyn));
 729                                         write(fd,moldyn->atom,
 730                                               moldyn->count*sizeof(t_atom));
 731                                 }
 732                                 close(fd);
 733                         }
 734                 }
 735                 if(v) {
 736                         if(!(i%v)) {
 737                                 visual_atoms(&(moldyn->vis),moldyn->time,
 738                                              moldyn->atom,moldyn->count);
 739                                 printf("\rsched: %d, steps: %d",sched,i);
 740                                 fflush(stdout);
 741                         }
 742                 }
 743
 744         }
 745
 746                 /* check for hooks */
 747                 if(schedule->hook)
 748                         schedule->hook(moldyn,schedule->hook_params);
 749
 750         }
 751
 752         return 0;
 753 }
 754
 755 /* velocity verlet */
 756
 757 int velocity_verlet(t_moldyn *moldyn) {
 758
 759         int i,count;
 760         double tau,tau_square;
 761         t_3dvec delta;
 762         t_atom *atom;
 763
 764         atom=moldyn->atom;
 765         count=moldyn->count;
 766         tau=moldyn->tau;
 767         tau_square=moldyn->tau_square;
 768
 769         for(i=0;i<count;i++) {
 770                 /* new positions */
 771                 v3_scale(&delta,&(atom[i].v),tau);
 772                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 773                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 774                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 775                 check_per_bound(moldyn,&(atom[i].r));
 776
 777                 /* velocities */
 778                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 779                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 780         }
 781
 782         /* neighbour list update */
 783         link_cell_update(moldyn);
 784
 785         /* forces depending on chosen potential */
 786         potential_force_calc(moldyn);
 787         //moldyn->potential_force_function(moldyn);
 788
 789         for(i=0;i<count;i++) {
 790                 /* again velocities */
 791                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 792                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 793         }
 794
 795         return 0;
 796 }
 797
 798
 799 /*
 800  *
 801  * potentials & corresponding forces
 802  *
 803  */
 804
 805 /* generic potential and force calculation */
 806
 807 int potential_force_calc(t_moldyn *moldyn) {
 808
 809         int i,j,k,count;
 810         t_atom *itom,*jtom,*ktom;
 811         t_linkcell *lc;
 812         t_list neighbour_i[27];
 813         t_list neighbour_i2[27];
 814         //t_list neighbour_j[27];
 815         t_list *this,*that;
 816         u8 bc_ij,bc_ijk;
 817         int countn,dnlc;
 818
 819         count=moldyn->count;
 820         itom=moldyn->atom;
 821         lc=&(moldyn->lc);
 822
 823         /* reset energy */
 824         moldyn->energy=0.0;
 825
 826         for(i=0;i<count;i++) {
 827
 828                 /* reset force */
 829                 v3_zero(&(itom[i].f));
 830
 831                 /* single particle potential/force */
 832                 if(itom[i].attr&ATOM_ATTR_1BP)
 833                         moldyn->func1b(moldyn,&(itom[i]));
 834
 835                 /* 2 body pair potential/force */
 836                 if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 837
 838                         link_cell_neighbour_index(moldyn,
 839                                 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
 840                                 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
 841                                 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
 842                                 neighbour_i);
 843
 844                         countn=lc->countn;
 845                         dnlc=lc->dnlc;
 846
 847                         for(j=0;j<countn;j++) {
 848
 849                                 this=&(neighbour_i[j]);
 850                                 list_reset(this);
 851
 852                                 if(this->start==NULL)
 853                                         continue;
 854
 855                                 bc_ij=(j<dnlc)?0:1;
 856
 857                                 do {
 858                                         jtom=this->current->data;
 859
 860                                         if(jtom==&(itom[i]))
 861                                                 continue;
 862
 863                                         if((jtom->attr&ATOM_ATTR_2BP)&
 864                                            (itom[i].attr&ATOM_ATTR_2BP))
 865                                                 moldyn->func2b(moldyn,
 866                                                                &(itom[i]),
 867                                                                jtom,
 868                                                                bc_ij);
 869
 870                                         /* 3 body potential/force */
 871
 872                                         if(!(itom[i].attr&ATOM_ATTR_3BP)||
 873                                            !(jtom->attr&ATOM_ATTR_3BP))
 874                                                 continue;
 875
 876                         /*
 877                          * according to mr. nordlund, we dont need to take the
 878                          * sum over all atoms now, as 'this is centered' around
 879                          * atom i ...
 880                          * i am not quite sure though! there is a not vanishing
 881                          * part even if f_c_ik is zero ...
 882                          * this analytical potentials suck!
 883                          * switching from mc to md to dft soon!
 884                          */
 885
 886                         //              link_cell_neighbour_index(moldyn,
 887                         //                 (jtom->r.x+moldyn->dim.x/2)/lc->x,
 888                         //                 (jtom->r.y+moldyn->dim.y/2)/lc->y,
 889                         //                 (jtom->r.z+moldyn->dim.z/2)/lc->z,
 890                         //                 neighbour_j);
 891
 892 //                                      /* neighbours of j */
 893 //                                      for(k=0;k<lc->countn;k++) {
 894 //
 895 //                                              that=&(neighbour_j[k]);
 896 //                                              list_reset(that);
 897 //
 898 //                                              if(that->start==NULL)
 899 //                                                      continue;
 900 //
 901 //                                              bc_ijk=(k<lc->dnlc)?0:1;
 902 //
 903 //                                              do {
 904 //
 905 //                      ktom=that->current->data;
 906 //
 907 //                      if(!(ktom->attr&ATOM_ATTR_3BP))
 908 //                              continue;
 909 //
 910 //                      if(ktom==jtom)
 911 //                              continue;
 912 //
 913 //                      if(ktom==&(itom[i]))
 914 //                              continue;
 915 //
 916 //                      moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
 917 //
 918 /*                                              } while(list_next(that)!=\ */
 919 //                                                      L_NO_NEXT_ELEMENT);
 920 //
 921 //                                      }
 922
 923                                         /* copy the neighbour lists */
 924                                         memcpy(neighbour_i2,neighbour_i,
 925                                                27*sizeof(t_list));
 926
 927                                         /* get neighbours of i */
 928                                         for(k=0;k<countn;k++) {
 929
 930                                                 that=&(neighbour_i2[k]);
 931                                                 list_reset(that);
 932
 933                                                 if(that->start==NULL)
 934                                                         continue;
 935
 936                                                 bc_ijk=(k<dnlc)?0:1;
 937
 938                                                 do {
 939
 940                         ktom=that->current->data;
 941
 942                         if(!(ktom->attr&ATOM_ATTR_3BP))
 943                                 continue;
 944
 945                         if(ktom==jtom)
 946                                 continue;
 947
 948                         if(ktom==&(itom[i]))
 949                                 continue;
 950
 951 //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);
 952                         moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
 953 //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);
 954
 955                                                 } while(list_next(that)!=\
 956                                                         L_NO_NEXT_ELEMENT);
 957
 958                                         }
 959
 960                                 } while(list_next(this)!=L_NO_NEXT_ELEMENT);
 961
 962                                 /* 2bp post function */
 963                                 if(moldyn->func2b_post)
 964                                         moldyn->func2b_post(moldyn,
 965                                                             &(itom[i]),
 966                                                             jtom,bc_ij);
 967
 968                         }
 969                 }
 970         }
 971
 972         return 0;
 973 }
 974
 975 /*
 976  * periodic boundayr checking
 977  */
 978
 979 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 980
 981         double x,y,z;
 982         t_3dvec *dim;
 983
 984         dim=&(moldyn->dim);
 985
 986         x=0.5*dim->x;
 987         y=0.5*dim->y;
 988         z=0.5*dim->z;
 989
 990         if(moldyn->status&MOLDYN_STAT_PBX) {
 991                 if(a->x>=x) a->x-=dim->x;
 992                 else if(-a->x>x) a->x+=dim->x;
 993         }
 994         if(moldyn->status&MOLDYN_STAT_PBY) {
 995                 if(a->y>=y) a->y-=dim->y;
 996                 else if(-a->y>y) a->y+=dim->y;
 997         }
 998         if(moldyn->status&MOLDYN_STAT_PBZ) {
 999                 if(a->z>=z) a->z-=dim->z;
1000                 else if(-a->z>z) a->z+=dim->z;
1001         }
1002
1003         return 0;
1004 }
1005
1006
1007 /*
1008  * example potentials
1009  */
1010
1011 /* harmonic oscillator potential and force */
1012
1013 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1014
1015         t_ho_params *params;
1016         t_3dvec force,distance;
1017         double d;
1018         double sc,equi_dist;
1019
1020         params=moldyn->pot2b_params;
1021         sc=params->spring_constant;
1022         equi_dist=params->equilibrium_distance;
1023
1024         v3_sub(&distance,&(ai->r),&(aj->r));
1025
1026         if(bc) check_per_bound(moldyn,&distance);
1027         d=v3_norm(&distance);
1028         if(d<=moldyn->cutoff) {
1029                 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
1030                 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
1031                 v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
1032                 v3_add(&(ai->f),&(ai->f),&force);
1033         }
1034
1035         return 0;
1036 }
1037
1038 /* lennard jones potential & force for one sort of atoms */
1039
1040 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1041
1042         t_lj_params *params;
1043         t_3dvec force,distance;
1044         double d,h1,h2;
1045         double eps,sig6,sig12;
1046
1047         params=moldyn->pot2b_params;
1048         eps=params->epsilon4;
1049         sig6=params->sigma6;
1050         sig12=params->sigma12;
1051
1052         v3_sub(&distance,&(ai->r),&(aj->r));
1053         if(bc) check_per_bound(moldyn,&distance);
1054         d=v3_absolute_square(&distance);        /* 1/r^2 */
1055         if(d<=moldyn->cutoff_square) {
1056                 d=1.0/d;                        /* 1/r^2 */
1057                 h2=d*d;                         /* 1/r^4 */
1058                 h2*=d;                          /* 1/r^6 */
1059                 h1=h2*h2;                       /* 1/r^12 */
1060                 /* energy is eps*..., but we will add this twice ... */
1061                 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
1062                 h2*=d;                          /* 1/r^8 */
1063                 h1*=d;                          /* 1/r^14 */
1064                 h2*=6*sig6;
1065                 h1*=12*sig12;
1066                 d=+h1-h2;
1067                 d*=eps;
1068                 v3_scale(&force,&distance,d);
1069                 v3_add(&(ai->f),&(ai->f),&force);
1070         }
1071
1072         return 0;
1073 }
1074
1075 /*
1076  * tersoff potential & force for 2 sorts of atoms
1077  */
1078
1079 /* create mixed terms from parameters and set them */
1080 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
1081
1082         printf("[moldyn] tersoff parameter completion\n");
1083         p->Smixed=sqrt(p->S[0]*p->S[1]);
1084         p->Rmixed=sqrt(p->R[0]*p->R[1]);
1085         p->Amixed=sqrt(p->A[0]*p->A[1]);
1086         p->Bmixed=sqrt(p->B[0]*p->B[1]);
1087         p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
1088         p->mu_m=0.5*(p->mu[0]+p->mu[1]);
1089
1090         printf("[moldyn] tersoff mult parameter info:\n");
1091         printf("  S (m)  | %.12f | %.12f | %.12f\n",p->S[0],p->S[1],p->Smixed);
1092         printf("  R (m)  | %.12f | %.12f | %.12f\n",p->R[0],p->R[1],p->Rmixed);
1093         printf("  A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
1094         printf("  B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
1095         printf("  lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
1096                                           p->lambda_m);
1097         printf("  mu     | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
1098         printf("  beta   | %.10f | %.10f\n",p->beta[0],p->beta[1]);
1099         printf("  n      | %f | %f\n",p->n[0],p->n[1]);
1100         printf("  c      | %f | %f\n",p->c[0],p->c[1]);
1101         printf("  d      | %f | %f\n",p->d[0],p->d[1]);
1102         printf("  h      | %f | %f\n",p->h[0],p->h[1]);
1103         printf("  chi    | %f \n",p->chi);
1104
1105         return 0;
1106 }
1107
1108 /* tersoff 1 body part */
1109 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
1110
1111         int num;
1112         t_tersoff_mult_params *params;
1113         t_tersoff_exchange *exchange;
1114
1115         num=ai->bnum;
1116         params=moldyn->pot1b_params;
1117         exchange=&(params->exchange);
1118
1119         /*
1120          * simple: point constant parameters only depending on atom i to
1121          *         their right values
1122          */
1123
1124         exchange->beta=&(params->beta[num]);
1125         exchange->n=&(params->n[num]);
1126         exchange->c=&(params->c[num]);
1127         exchange->d=&(params->d[num]);
1128         exchange->h=&(params->h[num]);
1129
1130         exchange->betan=pow(*(exchange->beta),*(exchange->n));
1131         exchange->n_betan=*(exchange->n)*exchange->betan;
1132         exchange->c2=params->c[num]*params->c[num];
1133         exchange->d2=params->d[num]*params->d[num];
1134         exchange->c2d2=exchange->c2/exchange->d2;
1135
1136         return 0;
1137 }
1138
1139 /* tersoff 2 body part */
1140 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1141
1142         t_tersoff_mult_params *params;
1143         t_tersoff_exchange *exchange;
1144         t_3dvec dist_ij,force;
1145         double d_ij;
1146         double A,B,R,S,lambda,mu;
1147         double f_r,df_r;
1148         double f_c,df_c;
1149         int num;
1150         double s_r;
1151         double arg;
1152         double scale;
1153
1154         params=moldyn->pot2b_params;
1155         num=ai->bnum;
1156         exchange=&(params->exchange);
1157
1158         exchange->run3bp=0;
1159
1160         /*
1161          * we need: f_c, df_c, f_r, df_r
1162          *
1163          * therefore we need: R, S, A, lambda
1164          */
1165
1166         v3_sub(&dist_ij,&(ai->r),&(aj->r));
1167
1168         if(bc) check_per_bound(moldyn,&dist_ij);
1169
1170         d_ij=v3_norm(&dist_ij);
1171
1172         /* save for use in 3bp */
1173         exchange->d_ij=d_ij;
1174         exchange->dist_ij=dist_ij;
1175         exchange->d_ij2=d_ij*d_ij;
1176
1177         /* constants */
1178         if(num==aj->bnum) {
1179                 S=params->S[num];
1180                 R=params->R[num];
1181                 A=params->A[num];
1182                 B=params->B[num];
1183                 lambda=params->lambda[num];
1184                 mu=params->mu[num];
1185                 params->exchange.chi=1.0;
1186         }
1187         else {
1188                 S=params->Smixed;
1189                 R=params->Rmixed;
1190                 A=params->Amixed;
1191                 B=params->Bmixed;
1192                 lambda=params->lambda_m;
1193                 mu=params->mu_m;
1194                 params->exchange.chi=params->chi;
1195         }
1196
1197         if(d_ij>S)
1198                 return 0;
1199
1200         f_r=A*exp(-lambda*d_ij);
1201         df_r=-lambda*f_r/d_ij;
1202
1203         /* f_a, df_a calc + save for 3bp use */
1204         exchange->f_a=-B*exp(-mu*d_ij);
1205         exchange->df_a=-mu*exchange->f_a/d_ij;
1206
1207         if(d_ij<R) {
1208                 /* f_c = 1, df_c = 0 */
1209                 f_c=1.0;
1210                 df_c=0.0;
1211                 v3_scale(&force,&dist_ij,df_r);
1212         }
1213         else {
1214                 s_r=S-R;
1215                 arg=M_PI*(d_ij-R)/s_r;
1216                 f_c=0.5+0.5*cos(arg);
1217                 df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
1218                 scale=df_c*f_r+df_r*f_c;
1219                 v3_scale(&force,&dist_ij,scale);
1220         }
1221
1222         /* add forces */
1223         v3_add(&(ai->f),&(ai->f),&force);
1224         /* energy is 0.5 f_r f_c ... */
1225         moldyn->energy+=(0.5*f_r*f_c);
1226
1227         /* save for use in 3bp */
1228         exchange->f_c=f_c;
1229         exchange->df_c=df_c;
1230
1231         /* enable the run of 3bp function */
1232         exchange->run3bp=1;
1233
1234         /* reset 3bp sums */
1235         exchange->sum1_3bp=0.0;
1236         exchange->sum2_3bp=0.0;
1237         v3_zero(&(exchange->db_ij));
1238
1239         return 0;
1240 }
1241
1242 /* tersoff 2 body post part */
1243
1244 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1245
1246         /* here we have to allow for the 3bp sums */
1247
1248         t_tersoff_mult_params *params;
1249         t_tersoff_exchange *exchange;
1250
1251         t_3dvec force,temp,*db_ij,*dist_ij;
1252         double db_ij_scale1,db_ij_scale2;
1253         double b_ij;
1254         double f_c,df_c,f_a,df_a;
1255         double chi,betan;
1256         double help;
1257         double n;
1258
1259         params=moldyn->pot2b_params;
1260         exchange=&(params->exchange);
1261
1262         db_ij=&(exchange->db_ij);
1263         f_c=exchange->f_c;
1264         df_c=exchange->df_c;
1265         f_a=exchange->f_a;
1266         df_a=exchange->df_a;
1267         betan=exchange->betan;
1268         n=*(exchange->n);
1269         dist_ij=&(exchange->dist_ij);
1270
1271         db_ij_scale1=(1+betan*exchange->sum1_3bp);
1272         db_ij_scale2=(exchange->n_betan*exchange->sum2_3bp);
1273         help=pow(db_ij_scale1,-1.0/(2*n)-1);
1274         b_ij=chi*db_ij_scale1*help;
1275         db_ij_scale1=-chi/(2*n)*help;
1276
1277         v3_scale(db_ij,db_ij,(db_ij_scale1*db_ij_scale2));
1278         v3_scale(db_ij,db_ij,f_a);
1279
1280         v3_scale(&temp,dist_ij,b_ij*df_a);
1281
1282         v3_add(&force,&temp,db_ij);
1283         v3_scale(&force,&force,f_c);
1284
1285         v3_scale(&temp,dist_ij,f_a*b_ij*df_c);
1286
1287         /* add energy of 3bp sum */
1288         moldyn->energy+=(0.5*f_c*b_ij*f_a);
1289         /* add force of 3bp calculation */
1290         v3_add(&(ai->f),&temp,&force);
1291
1292         return 0;
1293 }
1294
1295 /* tersoff 3 body part */
1296
1297 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1298
1299         t_tersoff_mult_params *params;
1300         t_tersoff_exchange *exchange;
1301         t_3dvec dist_ij,dist_ik,dist_jk;
1302         t_3dvec temp,force;
1303         double R,S,s_r;
1304         double d_ij,d_ij2,d_ik,d_jk;
1305         double f_c,df_c,f_a,df_a;
1306         double f_c_ik,df_c_ik,arg;
1307         double n,c,d,h;
1308         double c2,d2,c2d2;
1309         double numer,denom;
1310         double theta,cos_theta,sin_theta;
1311         double d_theta,d_theta1,d_theta2;
1312         double h_cos,d2_h_cos2;
1313         double frac,bracket,bracket_n_1,bracket_n;
1314         double g;
1315         int num;
1316
1317         params=moldyn->pot3b_params;
1318         num=ai->bnum;
1319         exchange=&(params->exchange);
1320
1321         if(!(exchange->run3bp))
1322                 return 0;
1323
1324         /*
1325          * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
1326          *
1327          * we got f_c, df_c, f_a, df_a from 2bp calculation
1328          */
1329
1330         d_ij=exchange->d_ij;
1331         d_ij2=exchange->d_ij2;
1332         dist_ij=exchange->dist_ij;
1333
1334         f_a=params->exchange.f_a;
1335         df_a=params->exchange.df_a;
1336
1337         f_c=exchange->f_c;
1338         df_c=exchange->df_c;
1339
1340         /* d_ij is <= S, as we didn't return so far! */
1341
1342         /*
1343          * calc of b_ij (scalar) and db_ij (vector)
1344          *
1345          * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
1346          *
1347          * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
1348          *              w_ik,
1349          *
1350          */
1351
1352         v3_sub(&dist_ik,&(ai->r),&(ak->r));
1353         if(bc) check_per_bound(moldyn,&dist_ik);
1354         d_ik=v3_norm(&dist_ik);
1355
1356         /* constants for f_c_ik calc */
1357         if(num==ak->bnum) {
1358                 R=params->R[num];
1359                 S=params->S[num];
1360         }
1361         else {
1362                 R=params->Rmixed;
1363                 S=params->Smixed;
1364         }
1365
1366         /* calc of f_c_ik */
1367         if(d_ik>S) {
1368                 f_c_ik=0.0;
1369                 df_c_ik=0.0;
1370         }
1371         else if(d_ik<R) {
1372                 f_c_ik=1.0;
1373                 df_c_ik=0.0;
1374         }
1375         else {
1376                 s_r=S-R;
1377                 arg=M_PI*(d_ik-R)/s_r;
1378                 f_c_ik=0.5+0.5*cos(arg);
1379                 df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
1380         }
1381
1382         v3_sub(&dist_jk,&(aj->r),&(ak->r));
1383         if(bc) check_per_bound(moldyn,&dist_jk);
1384         d_jk=v3_norm(&dist_jk);
1385
1386         /* get exchange data */
1387         n=*(exchange->n);
1388         c=*(exchange->c);
1389         d=*(exchange->d);
1390         h=*(exchange->h);
1391         c2=exchange->c2;
1392         d2=exchange->d2;
1393         c2d2=exchange->c2d2;
1394
1395         numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
1396         denom=2*d_ij*d_ik;
1397         cos_theta=numer/denom;
1398         /* prefere law of cosines, dot product -> nan (often) */
1399         //cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
1400         sin_theta=sqrt(1.0-(cos_theta*cos_theta));
1401         theta=acos(cos_theta);
1402         d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
1403         d_theta1=2*denom-numer*2*d_ik/d_ij;
1404         d_theta2=2*denom-numer*2*d_ij/d_ik;
1405         d_theta1*=d_theta;
1406         d_theta2*=d_theta;
1407
1408         h_cos=(h-cos_theta);
1409         d2_h_cos2=d2+(h_cos*h_cos);
1410
1411         frac=c2/(d2_h_cos2);
1412         g=1.0+c2d2-frac;
1413
1414         if(f_c_ik==0.0) {
1415                 bracket=0.0;
1416                 bracket_n_1=0.0;
1417                 bracket_n=0.0;
1418                 printf("Foo -> 0: ");
1419         }
1420         else {
1421                 bracket=f_c_ik*g;
1422                 bracket_n_1=pow(bracket,n-1.0);
1423                 bracket_n=bracket_n_1*bracket;
1424                 printf("Foo -> 1: ");
1425         }
1426 //printf("%.15f %.15f %.15f\n",bracket_n_1,bracket_n,bracket);
1427
1428         /* calc of db_ij and the 2 sums */
1429         exchange->sum1_3bp+=bracket_n;
1430         exchange->sum2_3bp+=bracket_n_1;
1431
1432         /* derivation of theta */
1433         v3_scale(&force,&dist_ij,d_theta1);
1434         v3_scale(&temp,&dist_ik,d_theta2);
1435         v3_add(&force,&force,&temp);
1436
1437         /* part 1 of db_ij */
1438         v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac/d2_h_cos2);
1439
1440         /* part 2 of db_ij */
1441         v3_scale(&temp,&dist_ik,df_c_ik*g);
1442
1443         /* sum up and add to db_ij */
1444         v3_add(&temp,&temp,&force);
1445         v3_add(&(exchange->db_ij),&(exchange->db_ij),&temp);
1446
1447         return 0;
1448 }
1449