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 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
  21
  22         memset(moldyn,0,sizeof(t_moldyn));
  23
  24         rand_init(&(moldyn->random),NULL,1);
  25         moldyn->random.status|=RAND_STAT_VERBOSE;
  26
  27         return 0;
  28 }
  29
  30 int moldyn_shutdown(t_moldyn *moldyn) {
  31
  32         printf("[moldyn] shutdown\n");
  33         moldyn_log_shutdown(moldyn);
  34         link_cell_shutdown(moldyn);
  35         rand_close(&(moldyn->random));
  36         free(moldyn->atom);
  37
  38         return 0;
  39 }
  40
  41 int set_int_alg(t_moldyn *moldyn,u8 algo) {
  42
  43         switch(algo) {
  44                 case MOLDYN_INTEGRATE_VERLET:
  45                         moldyn->integrate=velocity_verlet;
  46                         break;
  47                 default:
  48                         printf("unknown integration algorithm: %02x\n",algo);
  49                         return -1;
  50         }
  51
  52         return 0;
  53 }
  54
  55 int set_cutoff(t_moldyn *moldyn,double cutoff) {
  56
  57         moldyn->cutoff=cutoff;
  58
  59         return 0;
  60 }
  61
  62 int set_temperature(t_moldyn *moldyn,double t_ref) {
  63
  64         moldyn->t_ref=t_ref;
  65
  66         return 0;
  67 }
  68
  69 int set_pressure(t_moldyn *moldyn,double p_ref) {
  70
  71         moldyn->p_ref=p_ref;
  72
  73         return 0;
  74 }
  75
  76 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
  77
  78         moldyn->pt_scale=(ptype|ttype);
  79         moldyn->t_tc=ttc;
  80         moldyn->p_tc=ptc;
  81
  82         return 0;
  83 }
  84
  85 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
  86
  87         moldyn->dim.x=x;
  88         moldyn->dim.y=y;
  89         moldyn->dim.z=z;
  90
  91         moldyn->volume=x*y*z;
  92
  93         if(visualize) {
  94                 moldyn->vis.dim.x=x;
  95                 moldyn->vis.dim.y=y;
  96                 moldyn->vis.dim.z=z;
  97         }
  98
  99         printf("[moldyn] dimensions in A and A^3 respectively:\n");
 100         printf("  x: %f\n",moldyn->dim.x);
 101         printf("  y: %f\n",moldyn->dim.y);
 102         printf("  z: %f\n",moldyn->dim.z);
 103         printf("  volume: %f\n",moldyn->volume);
 104         printf("  visualize simulation box: %s\n",visualize?"on":"off");
 105
 106         return 0;
 107 }
 108
 109 int set_nn_dist(t_moldyn *moldyn,double dist) {
 110
 111         moldyn->nnd=dist;
 112
 113         return 0;
 114 }
 115
 116 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 117
 118         if(x)
 119                 moldyn->status|=MOLDYN_STAT_PBX;
 120
 121         if(y)
 122                 moldyn->status|=MOLDYN_STAT_PBY;
 123
 124         if(z)
 125                 moldyn->status|=MOLDYN_STAT_PBZ;
 126
 127         return 0;
 128 }
 129
 130 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
 131
 132         moldyn->func1b=func;
 133         moldyn->pot1b_params=params;
 134
 135         return 0;
 136 }
 137
 138 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
 139
 140         moldyn->func2b=func;
 141         moldyn->pot2b_params=params;
 142
 143         return 0;
 144 }
 145
 146 int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
 147
 148         moldyn->func2b_post=func;
 149         moldyn->pot2b_params=params;
 150
 151         return 0;
 152 }
 153
 154 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
 155
 156         moldyn->func3b=func;
 157         moldyn->pot3b_params=params;
 158
 159         return 0;
 160 }
 161
 162 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
 163
 164         strncpy(moldyn->vlsdir,dir,127);
 165
 166         return 0;
 167 }
 168
 169 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 170
 171         char filename[128];
 172         int ret;
 173
 174         switch(type) {
 175                 case LOG_TOTAL_ENERGY:
 176                         moldyn->ewrite=timer;
 177                         snprintf(filename,127,"%s/energy",moldyn->vlsdir);
 178                         moldyn->efd=open(filename,
 179                                          O_WRONLY|O_CREAT|O_EXCL,
 180                                          S_IRUSR|S_IWUSR);
 181                         if(moldyn->efd<0) {
 182                                 perror("[moldyn] energy log fd open");
 183                                 return moldyn->efd;
 184                         }
 185                         dprintf(moldyn->efd,"# total energy log file\n");
 186                         break;
 187                 case LOG_TOTAL_MOMENTUM:
 188                         moldyn->mwrite=timer;
 189                         snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
 190                         moldyn->mfd=open(filename,
 191                                          O_WRONLY|O_CREAT|O_EXCL,
 192                                          S_IRUSR|S_IWUSR);
 193                         if(moldyn->mfd<0) {
 194                                 perror("[moldyn] momentum log fd open");
 195                                 return moldyn->mfd;
 196                         }
 197                         dprintf(moldyn->efd,"# total momentum log file\n");
 198                         break;
 199                 case SAVE_STEP:
 200                         moldyn->swrite=timer;
 201                         break;
 202                 case VISUAL_STEP:
 203                         moldyn->vwrite=timer;
 204                         ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
 205                         if(ret<0) {
 206                                 printf("[moldyn] visual init failure\n");
 207                                 return ret;
 208                         }
 209                         break;
 210                 default:
 211                         printf("[moldyn] unknown log mechanism: %02x\n",type);
 212                         return -1;
 213         }
 214
 215         return 0;
 216 }
 217
 218 int moldyn_log_shutdown(t_moldyn *moldyn) {
 219
 220         printf("[moldyn] log shutdown\n");
 221         if(moldyn->efd) close(moldyn->efd);
 222         if(moldyn->mfd) close(moldyn->mfd);
 223         if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 224
 225         return 0;
 226 }
 227
 228 /*
 229  * creating lattice functions
 230  */
 231
 232 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 233                    u8 attr,u8 brand,int a,int b,int c) {
 234
 235         int new,count;
 236         int ret;
 237         t_3dvec origin;
 238         void *ptr;
 239         t_atom *atom;
 240
 241         new=a*b*c;
 242         count=moldyn->count;
 243
 244         /* how many atoms do we expect */
 245         if(type==FCC) new*=4;
 246         if(type==DIAMOND) new*=8;
 247
 248         /* allocate space for atoms */
 249         ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
 250         if(!ptr) {
 251                 perror("[moldyn] realloc (create lattice)");
 252                 return -1;
 253         }
 254         moldyn->atom=ptr;
 255         atom=&(moldyn->atom[count]);
 256
 257         v3_zero(&origin);
 258
 259         switch(type) {
 260                 case FCC:
 261                         ret=fcc_init(a,b,c,lc,atom,&origin);
 262                         break;
 263                 case DIAMOND:
 264                         ret=diamond_init(a,b,c,lc,atom,&origin);
 265                         break;
 266                 default:
 267                         printf("unknown lattice type (%02x)\n",type);
 268                         return -1;
 269         }
 270
 271         /* debug */
 272         if(ret!=new) {
 273                 printf("[moldyn] creating lattice failed\n");
 274                 printf("  amount of atoms\n");
 275                 printf("  - expected: %d\n",new);
 276                 printf("  - created: %d\n",ret);
 277                 return -1;
 278         }
 279
 280         moldyn->count+=new;
 281         printf("[moldyn] created lattice with %d atoms\n",new);
 282
 283         for(ret=0;ret<new;ret++) {
 284                 atom[ret].element=element;
 285                 atom[ret].mass=mass;
 286                 atom[ret].attr=attr;
 287                 atom[ret].brand=brand;
 288                 atom[ret].tag=count+ret;
 289                 check_per_bound(moldyn,&(atom[ret].r));
 290         }
 291
 292         return ret;
 293 }
 294
 295 /* fcc lattice init */
 296 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 297
 298         int count;
 299         int i,j;
 300         t_3dvec o,r,n;
 301         t_3dvec basis[3];
 302         double help[3];
 303         double x,y,z;
 304
 305         x=a*lc;
 306         y=b*lc;
 307         z=c*lc;
 308
 309         if(origin) v3_copy(&o,origin);
 310         else v3_zero(&o);
 311
 312         /* construct the basis */
 313         for(i=0;i<3;i++) {
 314                 for(j=0;j<3;j++) {
 315                         if(i!=j) help[j]=0.5*lc;
 316                         else help[j]=.0;
 317                 }
 318                 v3_set(&basis[i],help);
 319         }
 320
 321         v3_zero(&r);
 322         count=0;
 323
 324         /* fill up the room */
 325         r.x=o.x;
 326         while(r.x<x) {
 327                 r.y=o.y;
 328                 while(r.y<y) {
 329                         r.z=o.z;
 330                         while(r.z<z) {
 331                                 v3_copy(&(atom[count].r),&r);
 332                                 atom[count].element=1;
 333                                 count+=1;
 334                                 for(i=0;i<3;i++) {
 335                                         v3_add(&n,&r,&basis[i]);
 336                                         if((n.x<x+o.x)&&
 337                                            (n.y<y+o.y)&&
 338                                            (n.z<z+o.z)) {
 339                                                 v3_copy(&(atom[count].r),&n);
 340                                                 count+=1;
 341                                         }
 342                                 }
 343                                 r.z+=lc;
 344                         }
 345                         r.y+=lc;
 346                 }
 347                 r.x+=lc;
 348         }
 349
 350         /* coordinate transformation */
 351         help[0]=x/2.0;
 352         help[1]=y/2.0;
 353         help[2]=z/2.0;
 354         v3_set(&n,help);
 355         for(i=0;i<count;i++)
 356                 v3_sub(&(atom[i].r),&(atom[i].r),&n);
 357
 358         return count;
 359 }
 360
 361 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 362
 363         int count;
 364         t_3dvec o;
 365
 366         count=fcc_init(a,b,c,lc,atom,origin);
 367
 368         o.x=0.25*lc;
 369         o.y=0.25*lc;
 370         o.z=0.25*lc;
 371
 372         if(origin) v3_add(&o,&o,origin);
 373
 374         count+=fcc_init(a,b,c,lc,&atom[count],&o);
 375
 376         return count;
 377 }
 378
 379 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 380              t_3dvec *r,t_3dvec *v) {
 381
 382         t_atom *atom;
 383         void *ptr;
 384         int count;
 385
 386         atom=moldyn->atom;
 387         count=(moldyn->count)++;
 388
 389         ptr=realloc(atom,(count+1)*sizeof(t_atom));
 390         if(!ptr) {
 391                 perror("[moldyn] realloc (add atom)");
 392                 return -1;
 393         }
 394         moldyn->atom=ptr;
 395
 396         atom=moldyn->atom;
 397         atom[count].r=*r;
 398         atom[count].v=*v;
 399         atom[count].element=element;
 400         atom[count].mass=mass;
 401         atom[count].brand=brand;
 402         atom[count].tag=count;
 403         atom[count].attr=attr;
 404
 405         return 0;
 406 }
 407
 408 int destroy_atoms(t_moldyn *moldyn) {
 409
 410         if(moldyn->atom) free(moldyn->atom);
 411
 412         return 0;
 413 }
 414
 415 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 416
 417         /*
 418          * - gaussian distribution of velocities
 419          * - zero total momentum
 420          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 421          */
 422
 423         int i;
 424         double v,sigma;
 425         t_3dvec p_total,delta;
 426         t_atom *atom;
 427         t_random *random;
 428
 429         atom=moldyn->atom;
 430         random=&(moldyn->random);
 431
 432         /* gaussian distribution of velocities */
 433         v3_zero(&p_total);
 434         for(i=0;i<moldyn->count;i++) {
 435                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
 436                 /* x direction */
 437                 v=sigma*rand_get_gauss(random);
 438                 atom[i].v.x=v;
 439                 p_total.x+=atom[i].mass*v;
 440                 /* y direction */
 441                 v=sigma*rand_get_gauss(random);
 442                 atom[i].v.y=v;
 443                 p_total.y+=atom[i].mass*v;
 444                 /* z direction */
 445                 v=sigma*rand_get_gauss(random);
 446                 atom[i].v.z=v;
 447                 p_total.z+=atom[i].mass*v;
 448         }
 449
 450         /* zero total momentum */
 451         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 452         for(i=0;i<moldyn->count;i++) {
 453                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 454                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 455         }
 456
 457         /* velocity scaling */
 458         scale_velocity(moldyn,equi_init);
 459
 460         return 0;
 461 }
 462
 463 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 464
 465         int i;
 466         double e,scale;
 467         t_atom *atom;
 468         int count;
 469
 470         atom=moldyn->atom;
 471
 472         /*
 473          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 474          */
 475
 476         /* get kinetic energy / temperature & count involved atoms */
 477         e=0.0;
 478         count=0;
 479         for(i=0;i<moldyn->count;i++) {
 480                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
 481                         e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 482                         count+=1;
 483                 }
 484         }
 485         if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
 486         else return 0;  /* no atoms involved in scaling! */
 487
 488         /* (temporary) hack for e,t = 0 */
 489         if(e==0.0) {
 490         moldyn->t=0.0;
 491                 if(moldyn->t_ref!=0.0) {
 492                         thermal_init(moldyn,equi_init);
 493                         return 0;
 494                 }
 495                 else
 496                         return 0; /* no scaling needed */
 497         }
 498
 499
 500         /* get scaling factor */
 501         scale=moldyn->t_ref/moldyn->t;
 502         if(equi_init&TRUE)
 503                 scale*=2.0;
 504         else
 505                 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
 506                         scale=1.0+(scale-1.0)/moldyn->t_tc;
 507         scale=sqrt(scale);
 508
 509         /* velocity scaling */
 510         for(i=0;i<moldyn->count;i++) {
 511                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
 512                         v3_scale(&(atom[i].v),&(atom[i].v),scale);
 513         }
 514
 515         return 0;
 516 }
 517
 518 int scale_volume(t_moldyn *moldyn) {
 519
 520         t_atom *atom;
 521         t_3dvec *dim,*vdim;
 522         double scale,v;
 523         t_virial virial;
 524         t_linkcell *lc;
 525         int i;
 526
 527         atom=moldyn->atom;
 528         dim=&(moldyn->dim);
 529         vdim=&(moldyn->vis.dim);
 530         lc=&(moldyn->lc);
 531
 532         memset(&virial,0,sizeof(t_virial));
 533
 534         for(i=0;i<moldyn->count;i++) {
 535                 virial.xx+=atom[i].virial.xx;
 536                 virial.yy+=atom[i].virial.yy;
 537                 virial.zz+=atom[i].virial.zz;
 538                 virial.xy+=atom[i].virial.xy;
 539                 virial.xz+=atom[i].virial.xz;
 540                 virial.yz+=atom[i].virial.yz;
 541         }
 542
 543         /* just a guess so far ... */
 544         v=sqrt(virial.xx*virial.xx+virial.yy*virial.yy+virial.zz+virial.zz);
 545
 546 printf("%f\n",v);
 547         /* get pressure from virial */
 548         moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*v;
 549         moldyn->p/=moldyn->volume;
 550 printf("%f\n",moldyn->p/(ATM));
 551
 552         /* scale factor */
 553         if(moldyn->pt_scale&P_SCALE_BERENDSEN)
 554                 scale=3*sqrt(1-(moldyn->p_ref-moldyn->p)/moldyn->p_tc);
 555         else
 556                 /* should actually never be used */
 557                 scale=pow(moldyn->p/moldyn->p_ref,1.0/3.0);
 558
 559 printf("scale = %f\n",scale);
 560         /* actual scaling */
 561         dim->x*=scale;
 562         dim->y*=scale;
 563         dim->z*=scale;
 564         if(vdim->x) vdim->x=dim->x;
 565         if(vdim->y) vdim->y=dim->y;
 566         if(vdim->z) vdim->z=dim->z;
 567         moldyn->volume*=(scale*scale*scale);
 568
 569         /* check whether we need a new linkcell init */
 570         if((dim->x/moldyn->cutoff!=lc->nx)||
 571            (dim->y/moldyn->cutoff!=lc->ny)||
 572            (dim->z/moldyn->cutoff!=lc->nx)) {
 573                 link_cell_shutdown(moldyn);
 574                 link_cell_init(moldyn);
 575         }
 576
 577         return 0;
 578
 579 }
 580
 581 double get_e_kin(t_moldyn *moldyn) {
 582
 583         int i;
 584         t_atom *atom;
 585
 586         atom=moldyn->atom;
 587         moldyn->ekin=0.0;
 588
 589         for(i=0;i<moldyn->count;i++)
 590                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 591
 592         return moldyn->ekin;
 593 }
 594
 595 double get_e_pot(t_moldyn *moldyn) {
 596
 597         return moldyn->energy;
 598 }
 599
 600 double update_e_kin(t_moldyn *moldyn) {
 601
 602         return(get_e_kin(moldyn));
 603 }
 604
 605 double get_total_energy(t_moldyn *moldyn) {
 606
 607         return(moldyn->ekin+moldyn->energy);
 608 }
 609
 610 t_3dvec get_total_p(t_moldyn *moldyn) {
 611
 612         t_3dvec p,p_total;
 613         int i;
 614         t_atom *atom;
 615
 616         atom=moldyn->atom;
 617
 618         v3_zero(&p_total);
 619         for(i=0;i<moldyn->count;i++) {
 620                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 621                 v3_add(&p_total,&p_total,&p);
 622         }
 623
 624         return p_total;
 625 }
 626
 627 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 628
 629         double tau;
 630
 631         /* nn_dist is the nearest neighbour distance */
 632
 633         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
 634
 635         return tau;
 636 }
 637
 638 /*
 639  * numerical tricks
 640  */
 641
 642 /* linked list / cell method */
 643
 644 int link_cell_init(t_moldyn *moldyn) {
 645
 646         t_linkcell *lc;
 647         int i;
 648
 649         lc=&(moldyn->lc);
 650
 651         /* partitioning the md cell */
 652         lc->nx=moldyn->dim.x/moldyn->cutoff;
 653         lc->x=moldyn->dim.x/lc->nx;
 654         lc->ny=moldyn->dim.y/moldyn->cutoff;
 655         lc->y=moldyn->dim.y/lc->ny;
 656         lc->nz=moldyn->dim.z/moldyn->cutoff;
 657         lc->z=moldyn->dim.z/lc->nz;
 658
 659         lc->cells=lc->nx*lc->ny*lc->nz;
 660         lc->subcell=malloc(lc->cells*sizeof(t_list));
 661
 662         printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 663
 664         for(i=0;i<lc->cells;i++)
 665                 list_init_f(&(lc->subcell[i]));
 666
 667         link_cell_update(moldyn);
 668
 669         return 0;
 670 }
 671
 672 int link_cell_update(t_moldyn *moldyn) {
 673
 674         int count,i,j,k;
 675         int nx,ny;
 676         t_atom *atom;
 677         t_linkcell *lc;
 678         double x,y,z;
 679
 680         atom=moldyn->atom;
 681         lc=&(moldyn->lc);
 682
 683         nx=lc->nx;
 684         ny=lc->ny;
 685
 686         x=moldyn->dim.x/2;
 687         y=moldyn->dim.y/2;
 688         z=moldyn->dim.z/2;
 689
 690         for(i=0;i<lc->cells;i++)
 691                 list_destroy_f(&(lc->subcell[i]));
 692
 693         for(count=0;count<moldyn->count;count++) {
 694                 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
 695                 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
 696                 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
 697                 list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 698                                      &(atom[count]));
 699         }
 700
 701         return 0;
 702 }
 703
 704 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 705
 706         t_linkcell *lc;
 707         int a;
 708         int count1,count2;
 709         int ci,cj,ck;
 710         int nx,ny,nz;
 711         int x,y,z;
 712         u8 bx,by,bz;
 713
 714         lc=&(moldyn->lc);
 715         nx=lc->nx;
 716         ny=lc->ny;
 717         nz=lc->nz;
 718         count1=1;
 719         count2=27;
 720         a=nx*ny;
 721
 722         cell[0]=lc->subcell[i+j*nx+k*a];
 723         for(ci=-1;ci<=1;ci++) {
 724                 bx=0;
 725                 x=i+ci;
 726                 if((x<0)||(x>=nx)) {
 727                         x=(x+nx)%nx;
 728                         bx=1;
 729                 }
 730                 for(cj=-1;cj<=1;cj++) {
 731                         by=0;
 732                         y=j+cj;
 733                         if((y<0)||(y>=ny)) {
 734                                 y=(y+ny)%ny;
 735                                 by=1;
 736                         }
 737                         for(ck=-1;ck<=1;ck++) {
 738                                 bz=0;
 739                                 z=k+ck;
 740                                 if((z<0)||(z>=nz)) {
 741                                         z=(z+nz)%nz;
 742                                         bz=1;
 743                                 }
 744                                 if(!(ci|cj|ck)) continue;
 745                                 if(bx|by|bz) {
 746                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
 747                                 }
 748                                 else {
 749                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
 750                                 }
 751                         }
 752                 }
 753         }
 754
 755         lc->dnlc=count1;
 756
 757         return count1;
 758 }
 759
 760 int link_cell_shutdown(t_moldyn *moldyn) {
 761
 762         int i;
 763         t_linkcell *lc;
 764
 765         lc=&(moldyn->lc);
 766
 767         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 768                 list_destroy_f(&(moldyn->lc.subcell[i]));
 769
 770         free(lc->subcell);
 771
 772         return 0;
 773 }
 774
 775 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 776
 777         int count;
 778         void *ptr;
 779         t_moldyn_schedule *schedule;
 780
 781         schedule=&(moldyn->schedule);
 782         count=++(schedule->total_sched);
 783
 784         ptr=realloc(schedule->runs,count*sizeof(int));
 785         if(!ptr) {
 786                 perror("[moldyn] realloc (runs)");
 787                 return -1;
 788         }
 789         schedule->runs=ptr;
 790         schedule->runs[count-1]=runs;
 791
 792         ptr=realloc(schedule->tau,count*sizeof(double));
 793         if(!ptr) {
 794                 perror("[moldyn] realloc (tau)");
 795                 return -1;
 796         }
 797         schedule->tau=ptr;
 798         schedule->tau[count-1]=tau;
 799
 800         return 0;
 801 }
 802
 803 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 804
 805         moldyn->schedule.hook=hook;
 806         moldyn->schedule.hook_params=hook_params;
 807
 808         return 0;
 809 }
 810
 811 /*
 812  *
 813  * 'integration of newtons equation' - algorithms
 814  *
 815  */
 816
 817 /* start the integration */
 818
 819 int moldyn_integrate(t_moldyn *moldyn) {
 820
 821         int i;
 822         unsigned int e,m,s,v;
 823         t_3dvec p;
 824         t_moldyn_schedule *sched;
 825         t_atom *atom;
 826         int fd;
 827         char dir[128];
 828         double ds;
 829
 830         sched=&(moldyn->schedule);
 831         atom=moldyn->atom;
 832
 833         /* initialize linked cell method */
 834         link_cell_init(moldyn);
 835
 836         /* logging & visualization */
 837         e=moldyn->ewrite;
 838         m=moldyn->mwrite;
 839         s=moldyn->swrite;
 840         v=moldyn->vwrite;
 841
 842         /* sqaure of some variables */
 843         moldyn->tau_square=moldyn->tau*moldyn->tau;
 844         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 845
 846         /* calculate initial forces */
 847         potential_force_calc(moldyn);
 848
 849         /* some stupid checks before we actually start calculating bullshit */
 850         if(moldyn->cutoff>0.5*moldyn->dim.x)
 851                 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
 852         if(moldyn->cutoff>0.5*moldyn->dim.y)
 853                 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
 854         if(moldyn->cutoff>0.5*moldyn->dim.z)
 855                 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
 856         ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
 857         if(ds>0.05*moldyn->nnd)
 858                 printf("[moldyn] warning: forces too high / tau too small!\n");
 859
 860         /* zero absolute time */
 861         moldyn->time=0.0;
 862
 863         /* debugging, ignore */
 864         moldyn->debug=0;
 865
 866         /* executing the schedule */
 867         for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
 868
 869                 /* setting amount of runs and finite time step size */
 870                 moldyn->tau=sched->tau[sched->count];
 871                 moldyn->tau_square=moldyn->tau*moldyn->tau;
 872                 moldyn->time_steps=sched->runs[sched->count];
 873
 874         /* integration according to schedule */
 875
 876         for(i=0;i<moldyn->time_steps;i++) {
 877
 878                 /* integration step */
 879                 moldyn->integrate(moldyn);
 880
 881                 /* p/t scaling */
 882                 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
 883                         scale_velocity(moldyn,FALSE);
 884                 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
 885                         scale_volume(moldyn);
 886
 887                 /* check for log & visualization */
 888                 if(e) {
 889                         if(!(i%e))
 890                                 dprintf(moldyn->efd,
 891                                         "%f %f %f %f\n",
 892                                         moldyn->time,update_e_kin(moldyn),
 893                                         moldyn->energy,
 894                                         get_total_energy(moldyn));
 895                 }
 896                 if(m) {
 897                         if(!(i%m)) {
 898                                 p=get_total_p(moldyn);
 899                                 dprintf(moldyn->mfd,
 900                                         "%f %f\n",moldyn->time,v3_norm(&p));
 901                         }
 902                 }
 903                 if(s) {
 904                         if(!(i%s)) {
 905                                 snprintf(dir,128,"%s/s-%07.f.save",
 906                                          moldyn->vlsdir,moldyn->time);
 907                                 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
 908                                 if(fd<0) perror("[moldyn] save fd open");
 909                                 else {
 910                                         write(fd,moldyn,sizeof(t_moldyn));
 911                                         write(fd,moldyn->atom,
 912                                               moldyn->count*sizeof(t_atom));
 913                                 }
 914                                 close(fd);
 915                         }
 916                 }
 917                 if(v) {
 918                         if(!(i%v)) {
 919                                 visual_atoms(&(moldyn->vis),moldyn->time,
 920                                              moldyn->atom,moldyn->count);
 921                                 printf("\rsched: %d, steps: %d, debug: %d",
 922                                        sched->count,i,moldyn->debug);
 923                                 fflush(stdout);
 924                         }
 925                 }
 926
 927                 /* increase absolute time */
 928                 moldyn->time+=moldyn->tau;
 929
 930         }
 931
 932                 /* check for hooks */
 933                 if(sched->hook)
 934                         sched->hook(moldyn,sched->hook_params);
 935
 936                 /* get a new info line */
 937                 printf("\n");
 938
 939         }
 940
 941         return 0;
 942 }
 943
 944 /* velocity verlet */
 945
 946 int velocity_verlet(t_moldyn *moldyn) {
 947
 948         int i,count;
 949         double tau,tau_square;
 950         t_3dvec delta;
 951         t_atom *atom;
 952
 953         atom=moldyn->atom;
 954         count=moldyn->count;
 955         tau=moldyn->tau;
 956         tau_square=moldyn->tau_square;
 957
 958         for(i=0;i<count;i++) {
 959                 /* new positions */
 960                 v3_scale(&delta,&(atom[i].v),tau);
 961                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 962                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 963                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 964                 check_per_bound(moldyn,&(atom[i].r));
 965
 966                 /* velocities */
 967                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 968                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 969         }
 970
 971         /* neighbour list update */
 972         link_cell_update(moldyn);
 973
 974         /* forces depending on chosen potential */
 975         potential_force_calc(moldyn);
 976
 977         for(i=0;i<count;i++) {
 978                 /* again velocities */
 979                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 980                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 981         }
 982
 983         return 0;
 984 }
 985
 986
 987 /*
 988  *
 989  * potentials & corresponding forces
 990  *
 991  */
 992
 993 /* generic potential and force calculation */
 994
 995 int potential_force_calc(t_moldyn *moldyn) {
 996
 997         int i,j,k,count;
 998         t_atom *itom,*jtom,*ktom;
 999         t_virial *virial;
1000         t_linkcell *lc;
1001         t_list neighbour_i[27];
1002         t_list neighbour_i2[27];
1003         t_list *this,*that;
1004         u8 bc_ij,bc_ik;
1005         int dnlc;
1006
1007         count=moldyn->count;
1008         itom=moldyn->atom;
1009         lc=&(moldyn->lc);
1010
1011         /* reset energy */
1012         moldyn->energy=0.0;
1013
1014         /* get energy and force of every atom */
1015         for(i=0;i<count;i++) {
1016
1017                 /* reset force */
1018                 v3_zero(&(itom[i].f));
1019
1020                 /* reset viral of atom i */
1021                 virial=&(itom[i].virial);
1022                 virial->xx=0.0;
1023                 virial->yy=0.0;
1024                 virial->zz=0.0;
1025                 virial->xy=0.0;
1026                 virial->xz=0.0;
1027                 virial->yz=0.0;
1028
1029                 /* reset site energy */
1030                 itom[i].e=0.0;
1031
1032                 /* single particle potential/force */
1033                 if(itom[i].attr&ATOM_ATTR_1BP)
1034                         moldyn->func1b(moldyn,&(itom[i]));
1035
1036                 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1037                         continue;
1038
1039                 /* 2 body pair potential/force */
1040
1041                 link_cell_neighbour_index(moldyn,
1042                                           (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1043                                           (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1044                                           (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1045                                           neighbour_i);
1046
1047                 dnlc=lc->dnlc;
1048
1049                 for(j=0;j<27;j++) {
1050
1051                         this=&(neighbour_i[j]);
1052                         list_reset_f(this);
1053
1054                         if(this->start==NULL)
1055                                 continue;
1056
1057                         bc_ij=(j<dnlc)?0:1;
1058
1059                         do {
1060                                 jtom=this->current->data;
1061
1062                                 if(jtom==&(itom[i]))
1063                                         continue;
1064
1065                                 if((jtom->attr&ATOM_ATTR_2BP)&
1066                                    (itom[i].attr&ATOM_ATTR_2BP)) {
1067                                         moldyn->func2b(moldyn,
1068                                                        &(itom[i]),
1069                                                        jtom,
1070                                                        bc_ij);
1071                                 }
1072
1073                                 /* 3 body potential/force */
1074
1075                                 if(!(itom[i].attr&ATOM_ATTR_3BP)||
1076                                    !(jtom->attr&ATOM_ATTR_3BP))
1077                                         continue;
1078
1079                                 /* copy the neighbour lists */
1080                                 memcpy(neighbour_i2,neighbour_i,
1081                                        27*sizeof(t_list));
1082
1083                                 /* get neighbours of i */
1084                                 for(k=0;k<27;k++) {
1085
1086                                         that=&(neighbour_i2[k]);
1087                                         list_reset_f(that);
1088
1089                                         if(that->start==NULL)
1090                                                 continue;
1091
1092                                         bc_ik=(k<dnlc)?0:1;
1093
1094                                         do {
1095
1096                                                 ktom=that->current->data;
1097
1098                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
1099                                                         continue;
1100
1101                                                 if(ktom==jtom)
1102                                                         continue;
1103
1104                                                 if(ktom==&(itom[i]))
1105                                                         continue;
1106
1107                                                 moldyn->func3b(moldyn,
1108                                                                &(itom[i]),
1109                                                                jtom,
1110                                                                ktom,
1111                                                                bc_ik|bc_ij);
1112
1113                                         } while(list_next_f(that)!=\
1114                                                 L_NO_NEXT_ELEMENT);
1115
1116                                 }
1117
1118                                 /* 2bp post function */
1119                                 if(moldyn->func2b_post) {
1120                                         moldyn->func2b_post(moldyn,
1121                                                             &(itom[i]),
1122                                                             jtom,bc_ij);
1123                                 }
1124
1125                         } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1126
1127                 }
1128
1129         }
1130 #ifdef DEBUG
1131 printf("\n\n");
1132 #endif
1133
1134         return 0;
1135 }
1136
1137 /*
1138  * periodic boundayr checking
1139  */
1140
1141 inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1142
1143         double x,y,z;
1144         t_3dvec *dim;
1145
1146         dim=&(moldyn->dim);
1147
1148         x=dim->x/2;
1149         y=dim->y/2;
1150         z=dim->z/2;
1151
1152         if(moldyn->status&MOLDYN_STAT_PBX) {
1153                 if(a->x>=x) a->x-=dim->x;
1154                 else if(-a->x>x) a->x+=dim->x;
1155         }
1156         if(moldyn->status&MOLDYN_STAT_PBY) {
1157                 if(a->y>=y) a->y-=dim->y;
1158                 else if(-a->y>y) a->y+=dim->y;
1159         }
1160         if(moldyn->status&MOLDYN_STAT_PBZ) {
1161                 if(a->z>=z) a->z-=dim->z;
1162                 else if(-a->z>z) a->z+=dim->z;
1163         }
1164
1165         return 0;
1166 }
1167
1168
1169 /*
1170  * example potentials
1171  */
1172
1173 /* harmonic oscillator potential and force */
1174
1175 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1176
1177         t_ho_params *params;
1178         t_3dvec force,distance;
1179         double d;
1180         double sc,equi_dist;
1181
1182         params=moldyn->pot2b_params;
1183         sc=params->spring_constant;
1184         equi_dist=params->equilibrium_distance;
1185
1186         v3_sub(&distance,&(aj->r),&(ai->r));
1187
1188         if(bc) check_per_bound(moldyn,&distance);
1189         d=v3_norm(&distance);
1190         if(d<=moldyn->cutoff) {
1191                 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
1192                 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
1193                 /* f = -grad E; grad r_ij = -1 1/r_ij distance */
1194                 v3_scale(&force,&distance,sc*(1.0-(equi_dist/d)));
1195                 v3_add(&(ai->f),&(ai->f),&force);
1196         }
1197
1198         return 0;
1199 }
1200
1201 /* lennard jones potential & force for one sort of atoms */
1202
1203 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1204
1205         t_lj_params *params;
1206         t_3dvec force,distance;
1207         double d,h1,h2;
1208         double eps,sig6,sig12;
1209
1210         params=moldyn->pot2b_params;
1211         eps=params->epsilon4;
1212         sig6=params->sigma6;
1213         sig12=params->sigma12;
1214
1215         v3_sub(&distance,&(aj->r),&(ai->r));
1216         if(bc) check_per_bound(moldyn,&distance);
1217         d=v3_absolute_square(&distance);        /* 1/r^2 */
1218         if(d<=moldyn->cutoff_square) {
1219                 d=1.0/d;                        /* 1/r^2 */
1220                 h2=d*d;                         /* 1/r^4 */
1221                 h2*=d;                          /* 1/r^6 */
1222                 h1=h2*h2;                       /* 1/r^12 */
1223                 /* energy is eps*..., but we will add this twice ... */
1224                 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
1225                 h2*=d;                          /* 1/r^8 */
1226                 h1*=d;                          /* 1/r^14 */
1227                 h2*=6*sig6;
1228                 h1*=12*sig12;
1229                 d=+h1-h2;
1230                 d*=eps;
1231                 v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
1232                 v3_add(&(ai->f),&(ai->f),&force);
1233         }
1234
1235         return 0;
1236 }
1237
1238 /*
1239  * tersoff potential & force for 2 sorts of atoms
1240  */
1241
1242 /* create mixed terms from parameters and set them */
1243 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
1244
1245         printf("[moldyn] tersoff parameter completion\n");
1246         p->S2[0]=p->S[0]*p->S[0];
1247         p->S2[1]=p->S[1]*p->S[1];
1248         p->Smixed=sqrt(p->S[0]*p->S[1]);
1249         p->S2mixed=p->Smixed*p->Smixed;
1250         p->Rmixed=sqrt(p->R[0]*p->R[1]);
1251         p->Amixed=sqrt(p->A[0]*p->A[1]);
1252         p->Bmixed=sqrt(p->B[0]*p->B[1]);
1253         p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
1254         p->mu_m=0.5*(p->mu[0]+p->mu[1]);
1255
1256         printf("[moldyn] tersoff mult parameter info:\n");
1257         printf("  S (A)  | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
1258         printf("  R (A)  | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
1259         printf("  A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
1260         printf("  B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
1261         printf("  lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
1262                                           p->lambda_m);
1263         printf("  mu     | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
1264         printf("  beta   | %.10f | %.10f\n",p->beta[0],p->beta[1]);
1265         printf("  n      | %f | %f\n",p->n[0],p->n[1]);
1266         printf("  c      | %f | %f\n",p->c[0],p->c[1]);
1267         printf("  d      | %f | %f\n",p->d[0],p->d[1]);
1268         printf("  h      | %f | %f\n",p->h[0],p->h[1]);
1269         printf("  chi    | %f \n",p->chi);
1270
1271         return 0;
1272 }
1273
1274 /* tersoff 1 body part */
1275 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
1276
1277         int brand;
1278         t_tersoff_mult_params *params;
1279         t_tersoff_exchange *exchange;
1280
1281         brand=ai->brand;
1282         params=moldyn->pot1b_params;
1283         exchange=&(params->exchange);
1284
1285         /*
1286          * simple: point constant parameters only depending on atom i to
1287          *         their right values
1288          */
1289
1290         exchange->beta_i=&(params->beta[brand]);
1291         exchange->n_i=&(params->n[brand]);
1292         exchange->c_i=&(params->c[brand]);
1293         exchange->d_i=&(params->d[brand]);
1294         exchange->h_i=&(params->h[brand]);
1295
1296         exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
1297         exchange->ci2=params->c[brand]*params->c[brand];
1298         exchange->di2=params->d[brand]*params->d[brand];
1299         exchange->ci2di2=exchange->ci2/exchange->di2;
1300
1301         return 0;
1302 }
1303
1304 /* tersoff 2 body part */
1305 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1306
1307         t_tersoff_mult_params *params;
1308         t_tersoff_exchange *exchange;
1309         t_3dvec dist_ij,force;
1310         double d_ij,d_ij2;
1311         double A,B,R,S,S2,lambda,mu;
1312         double f_r,df_r;
1313         double f_c,df_c;
1314         int brand;
1315         double s_r;
1316         double arg;
1317
1318         params=moldyn->pot2b_params;
1319         brand=aj->brand;
1320         exchange=&(params->exchange);
1321
1322         /* clear 3bp and 2bp post run */
1323         exchange->run3bp=0;
1324         exchange->run2bp_post=0;
1325
1326         /* reset S > r > R mark */
1327         exchange->d_ij_between_rs=0;
1328
1329         /*
1330          * calc of 2bp contribution of V_ij and dV_ij/ji
1331          *
1332          * for Vij and dV_ij we need:
1333          * - f_c_ij, df_c_ij
1334          * - f_r_ij, df_r_ij
1335          *
1336          * for dV_ji we need:
1337          * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
1338          * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
1339          *
1340          */
1341
1342         /* constants */
1343         if(brand==ai->brand) {
1344                 S=params->S[brand];
1345                 S2=params->S2[brand];
1346                 R=params->R[brand];
1347                 A=params->A[brand];
1348                 B=params->B[brand];
1349                 lambda=params->lambda[brand];
1350                 mu=params->mu[brand];
1351                 exchange->chi=1.0;
1352         }
1353         else {
1354                 S=params->Smixed;
1355                 S2=params->S2mixed;
1356                 R=params->Rmixed;
1357                 A=params->Amixed;
1358                 B=params->Bmixed;
1359                 lambda=params->lambda_m;
1360                 mu=params->mu_m;
1361                 params->exchange.chi=params->chi;
1362         }
1363
1364         /* dist_ij, d_ij */
1365         v3_sub(&dist_ij,&(aj->r),&(ai->r));
1366         if(bc) check_per_bound(moldyn,&dist_ij);
1367         d_ij2=v3_absolute_square(&dist_ij);
1368
1369         /* if d_ij2 > S2 => no force & potential energy contribution */
1370         if(d_ij2>S2)
1371                 return 0;
1372
1373         /* now we will need the distance */
1374         //d_ij=v3_norm(&dist_ij);
1375         d_ij=sqrt(d_ij2);
1376
1377         /* save for use in 3bp */
1378         exchange->d_ij=d_ij;
1379         exchange->dist_ij=dist_ij;
1380
1381         /* more constants */
1382         exchange->beta_j=&(params->beta[brand]);
1383         exchange->n_j=&(params->n[brand]);
1384         exchange->c_j=&(params->c[brand]);
1385         exchange->d_j=&(params->d[brand]);
1386         exchange->h_j=&(params->h[brand]);
1387         if(brand==ai->brand) {
1388                 exchange->betajnj=exchange->betaini;
1389                 exchange->cj2=exchange->ci2;
1390                 exchange->dj2=exchange->di2;
1391                 exchange->cj2dj2=exchange->ci2di2;
1392         }
1393         else {
1394                 exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
1395                 exchange->cj2=params->c[brand]*params->c[brand];
1396                 exchange->dj2=params->d[brand]*params->d[brand];
1397                 exchange->cj2dj2=exchange->cj2/exchange->dj2;
1398         }
1399
1400         /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
1401         f_r=A*exp(-lambda*d_ij);
1402         df_r=lambda*f_r/d_ij;
1403
1404         /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
1405         exchange->f_a=-B*exp(-mu*d_ij);
1406         exchange->df_a=mu*exchange->f_a/d_ij;
1407
1408         /* f_c, df_c calc (again, same for ij and ji) */
1409         if(d_ij<R) {
1410                 /* f_c = 1, df_c = 0 */
1411                 f_c=1.0;
1412                 df_c=0.0;
1413                 /* two body contribution (ij, ji) */
1414                 v3_scale(&force,&dist_ij,-df_r);
1415         }
1416         else {
1417                 s_r=S-R;
1418                 arg=M_PI*(d_ij-R)/s_r;
1419                 f_c=0.5+0.5*cos(arg);
1420                 df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
1421                 /* two body contribution (ij, ji) */
1422                 v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
1423                 /* tell 3bp that S > r > R */
1424                 exchange->d_ij_between_rs=1;
1425         }
1426
1427         /* add forces of 2bp (ij, ji) contribution
1428          * dVij = dVji and we sum up both: no 1/2) */
1429         v3_add(&(ai->f),&(ai->f),&force);
1430 #ifdef DEBUG
1431 if(ai==&(moldyn->atom[0])) {
1432         printf("dVij, dVji (2bp) contrib:\n");
1433         printf("%f | %f\n",force.x,ai->f.x);
1434         printf("%f | %f\n",force.y,ai->f.y);
1435         printf("%f | %f\n",force.z,ai->f.z);
1436 }
1437 #endif
1438
1439         /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
1440         moldyn->energy+=(0.5*f_r*f_c);
1441
1442         /* save for use in 3bp */
1443         exchange->f_c=f_c;
1444         exchange->df_c=df_c;
1445
1446         /* enable the run of 3bp function and 2bp post processing */
1447         exchange->run3bp=1;
1448         exchange->run2bp_post=1;
1449
1450         /* reset 3bp sums */
1451         exchange->zeta_ij=0.0;
1452         exchange->zeta_ji=0.0;
1453         v3_zero(&(exchange->dzeta_ij));
1454         v3_zero(&(exchange->dzeta_ji));
1455
1456         return 0;
1457 }
1458
1459 /* tersoff 2 body post part */
1460
1461 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1462
1463         /*
1464          * here we have to allow for the 3bp sums
1465          *
1466          * that is:
1467          * - zeta_ij, dzeta_ij
1468          * - zeta_ji, dzeta_ji
1469          *
1470          * to compute the 3bp contribution to:
1471          * - Vij, dVij
1472          * - dVji
1473          *
1474          */
1475
1476         t_tersoff_mult_params *params;
1477         t_tersoff_exchange *exchange;
1478
1479         t_3dvec force,temp;
1480         t_3dvec *dist_ij;
1481         double b,db,tmp;
1482         double f_c,df_c,f_a,df_a;
1483         double chi,ni,betaini,nj,betajnj;
1484         double zeta;
1485
1486         params=moldyn->pot2b_params;
1487         exchange=&(params->exchange);
1488
1489         /* we do not run if f_c_ij was detected to be 0! */
1490         if(!(exchange->run2bp_post))
1491                 return 0;
1492
1493         f_c=exchange->f_c;
1494         df_c=exchange->df_c;
1495         f_a=exchange->f_a;
1496         df_a=exchange->df_a;
1497         betaini=exchange->betaini;
1498         betajnj=exchange->betajnj;
1499         ni=*(exchange->n_i);
1500         nj=*(exchange->n_j);
1501         chi=exchange->chi;
1502         dist_ij=&(exchange->dist_ij);
1503
1504         /* Vij and dVij */
1505         zeta=exchange->zeta_ij;
1506         if(zeta==0.0) {
1507                 moldyn->debug++;                /* just for debugging ... */
1508                 db=0.0;
1509                 b=chi;
1510                 v3_scale(&force,dist_ij,df_a*b*f_c);
1511         }
1512         else {
1513                 tmp=betaini*pow(zeta,ni-1.0);           /* beta^n * zeta^n-1 */
1514                 b=(1+zeta*tmp);                         /* 1 + beta^n zeta^n */
1515                 db=chi*pow(b,-1.0/(2*ni)-1);            /* x(...)^(-1/2n - 1) */
1516                 b=db*b;                                 /* b_ij */
1517                 db*=-0.5*tmp;                           /* db_ij */
1518                 v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
1519                 v3_scale(&temp,dist_ij,df_a*b);
1520                 v3_add(&force,&force,&temp);
1521                 v3_scale(&force,&force,f_c);
1522         }
1523         v3_scale(&temp,dist_ij,df_c*b*f_a);
1524         v3_add(&force,&force,&temp);
1525         v3_scale(&force,&force,-0.5);
1526
1527         /* add force */
1528         v3_add(&(ai->f),&(ai->f),&force);
1529 #ifdef DEBUG
1530 if(ai==&(moldyn->atom[0])) {
1531         printf("dVij (3bp) contrib:\n");
1532         printf("%f | %f\n",force.x,ai->f.x);
1533         printf("%f | %f\n",force.y,ai->f.y);
1534         printf("%f | %f\n",force.z,ai->f.z);
1535 }
1536 #endif
1537
1538         /* add energy of 3bp sum */
1539         moldyn->energy+=(0.5*f_c*b*f_a);
1540
1541         /* dVji */
1542         zeta=exchange->zeta_ji;
1543         if(zeta==0.0) {
1544                 moldyn->debug++;
1545                 b=chi;
1546                 v3_scale(&force,dist_ij,df_a*b*f_c);
1547         }
1548         else {
1549                 tmp=betajnj*pow(zeta,nj-1.0);           /* beta^n * zeta^n-1 */
1550                 b=(1+zeta*tmp);                         /* 1 + beta^n zeta^n */
1551                 db=chi*pow(b,-1.0/(2*nj)-1);            /* x(...)^(-1/2n - 1) */
1552                 b=db*b;                                 /* b_ij */
1553                 db*=-0.5*tmp;                           /* db_ij */
1554                 v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
1555                 v3_scale(&temp,dist_ij,df_a*b);
1556                 v3_add(&force,&force,&temp);
1557                 v3_scale(&force,&force,f_c);
1558         }
1559         v3_scale(&temp,dist_ij,df_c*b*f_a);
1560         v3_add(&force,&force,&temp);
1561         v3_scale(&force,&force,-0.5);
1562
1563         /* add force */
1564         v3_add(&(ai->f),&(ai->f),&force);
1565 #ifdef DEBUG
1566 if(ai==&(moldyn->atom[0])) {
1567         printf("dVji (3bp) contrib:\n");
1568         printf("%f | %f\n",force.x,ai->f.x);
1569         printf("%f | %f\n",force.y,ai->f.y);
1570         printf("%f | %f\n",force.z,ai->f.z);
1571 }
1572 #endif
1573
1574         return 0;
1575 }
1576
1577 /* tersoff 3 body part */
1578
1579 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1580
1581         t_tersoff_mult_params *params;
1582         t_tersoff_exchange *exchange;
1583         t_3dvec dist_ij,dist_ik,dist_jk;
1584         t_3dvec temp1,temp2;
1585         t_3dvec *dzeta;
1586         double R,S,s_r;
1587         double B,mu;
1588         double d_ij,d_ik,d_jk;
1589         double rr,dd;
1590         double f_c,df_c;
1591         double f_c_ik,df_c_ik,arg;
1592         double f_c_jk;
1593         double n,c,d,h;
1594         double c2,d2,c2d2;
1595         double cos_theta,d_costheta1,d_costheta2;
1596         double h_cos,d2_h_cos2;
1597         double frac,g,zeta,chi;
1598         double tmp;
1599         int brand;
1600
1601         params=moldyn->pot3b_params;
1602         exchange=&(params->exchange);
1603
1604         if(!(exchange->run3bp))
1605                 return 0;
1606
1607         /*
1608          * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
1609          * 2bp contribution of dV_jk
1610          *
1611          * for Vij and dV_ij we still need:
1612          * - b_ij, db_ij (zeta_ij)
1613          *   - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
1614          *
1615          * for dV_ji we still need:
1616          * - b_ji, db_ji (zeta_ji)
1617          *   - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
1618          *
1619          * for dV_jk we need:
1620          * - f_c_jk
1621          * - f_a_jk
1622          * - db_jk (zeta_jk)
1623          *   - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
1624          *
1625          */
1626
1627         /*
1628          * get exchange data
1629          */
1630
1631         /* dist_ij, d_ij - this is < S_ij ! */
1632         dist_ij=exchange->dist_ij;
1633         d_ij=exchange->d_ij;
1634
1635         /* f_c_ij, df_c_ij (same for ji) */
1636         f_c=exchange->f_c;
1637         df_c=exchange->df_c;
1638
1639         /*
1640          * calculate unknown values now ...
1641          */
1642
1643         /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
1644
1645         /* dist_ik, d_ik */
1646         v3_sub(&dist_ik,&(ak->r),&(ai->r));
1647         if(bc) check_per_bound(moldyn,&dist_ik);
1648         d_ik=v3_norm(&dist_ik);
1649
1650         /* ik constants */
1651         brand=ai->brand;
1652         if(brand==ak->brand) {
1653                 R=params->R[brand];
1654                 S=params->S[brand];
1655         }
1656         else {
1657                 R=params->Rmixed;
1658                 S=params->Smixed;
1659         }
1660
1661         /* zeta_ij/dzeta_ij contribution only for d_ik < S */
1662         if(d_ik<S) {
1663
1664                 /* get constants_i from exchange data */
1665                 n=*(exchange->n_i);
1666                 c=*(exchange->c_i);
1667                 d=*(exchange->d_i);
1668                 h=*(exchange->h_i);
1669                 c2=exchange->ci2;
1670                 d2=exchange->di2;
1671                 c2d2=exchange->ci2di2;
1672
1673                 /* cosine of theta_ijk by scalaproduct */
1674                 rr=v3_scalar_product(&dist_ij,&dist_ik);
1675                 dd=d_ij*d_ik;
1676                 cos_theta=rr/dd;
1677
1678                 /* d_costheta */
1679                 tmp=1.0/dd;
1680                 d_costheta1=cos_theta/(d_ij*d_ij)-tmp;
1681                 d_costheta2=cos_theta/(d_ik*d_ik)-tmp;
1682
1683                 /* some usefull values */
1684                 h_cos=(h-cos_theta);
1685                 d2_h_cos2=d2+(h_cos*h_cos);
1686                 frac=c2/(d2_h_cos2);
1687
1688                 /* g(cos_theta) */
1689                 g=1.0+c2d2-frac;
1690
1691                 /* d_costheta_ij and dg(cos_theta) - needed in any case! */
1692                 v3_scale(&temp1,&dist_ij,d_costheta1);
1693                 v3_scale(&temp2,&dist_ik,d_costheta2);
1694                 v3_add(&temp1,&temp1,&temp2);
1695                 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
1696
1697                 /* f_c_ik & df_c_ik + {d,}zeta contribution */
1698                 dzeta=&(exchange->dzeta_ij);
1699                 if(d_ik<R) {
1700                         /* {d,}f_c_ik */
1701                         // => f_c_ik=1.0;
1702                         // => df_c_ik=0.0; of course we do not set this!
1703
1704                         /* zeta_ij */
1705                         exchange->zeta_ij+=g;
1706
1707                         /* dzeta_ij */
1708                         v3_add(dzeta,dzeta,&temp1);
1709                 }
1710                 else {
1711                         /* {d,}f_c_ik */
1712                         s_r=S-R;
1713                         arg=M_PI*(d_ik-R)/s_r;
1714                         f_c_ik=0.5+0.5*cos(arg);
1715                         df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
1716
1717                         /* zeta_ij */
1718                         exchange->zeta_ij+=f_c_ik*g;
1719
1720                         /* dzeta_ij */
1721                         v3_scale(&temp1,&temp1,f_c_ik);
1722                         v3_scale(&temp2,&dist_ik,g*df_c_ik);
1723                         v3_add(&temp1,&temp1,&temp2);
1724                         v3_add(dzeta,dzeta,&temp1);
1725                 }
1726         }
1727
1728         /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
1729
1730         /* dist_jk, d_jk */
1731         v3_sub(&dist_jk,&(ak->r),&(aj->r));
1732         if(bc) check_per_bound(moldyn,&dist_jk);
1733         d_jk=v3_norm(&dist_jk);
1734
1735         /* jk constants */
1736         brand=aj->brand;
1737         if(brand==ak->brand) {
1738                 R=params->R[brand];
1739                 S=params->S[brand];
1740                 B=params->B[brand];
1741                 mu=params->mu[brand];
1742                 chi=1.0;
1743         }
1744         else {
1745                 R=params->Rmixed;
1746                 S=params->Smixed;
1747                 B=params->Bmixed;
1748                 mu=params->mu_m;
1749                 chi=params->chi;
1750         }
1751
1752         /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
1753         if(d_jk<S) {
1754
1755                 /* constants_j from exchange data */
1756                 n=*(exchange->n_j);
1757                 c=*(exchange->c_j);
1758                 d=*(exchange->d_j);
1759                 h=*(exchange->h_j);
1760                 c2=exchange->cj2;
1761                 d2=exchange->dj2;
1762                 c2d2=exchange->cj2dj2;
1763
1764                 /* cosine of theta_jik by scalaproduct */
1765                 rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
1766                 dd=d_ij*d_jk;
1767                 cos_theta=rr/dd;
1768
1769                 /* d_costheta */
1770                 d_costheta1=1.0/dd;
1771                 d_costheta2=cos_theta/(d_ij*d_ij);
1772
1773                 /* some usefull values */
1774                 h_cos=(h-cos_theta);
1775                 d2_h_cos2=d2+(h_cos*h_cos);
1776                 frac=c2/(d2_h_cos2);
1777
1778                 /* g(cos_theta) */
1779                 g=1.0+c2d2-frac;
1780
1781                 /* d_costheta_ij and dg(cos_theta) - needed in any case! */
1782                 v3_scale(&temp1,&dist_jk,d_costheta1);
1783                 v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
1784                 v3_add(&temp1,&temp1,&temp2);
1785                 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
1786
1787                 /* store dg in temp2 and use it for dVjk later */
1788                 v3_copy(&temp2,&temp1);
1789
1790                 /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
1791                 dzeta=&(exchange->dzeta_ji);
1792                 if(d_jk<R) {
1793                         /* f_c_jk */
1794                         f_c_jk=1.0;
1795
1796                         /* zeta_ji */
1797                         exchange->zeta_ji+=g;
1798
1799                         /* dzeta_ji */
1800                         v3_add(dzeta,dzeta,&temp1);
1801                 }
1802                 else {
1803                         /* f_c_jk */
1804                         s_r=S-R;
1805                         arg=M_PI*(d_jk-R)/s_r;
1806                         f_c_jk=0.5+0.5*cos(arg);
1807
1808                         /* zeta_ji */
1809                         exchange->zeta_ji+=f_c_jk*g;
1810
1811                         /* dzeta_ji */
1812                         v3_scale(&temp1,&temp1,f_c_jk);
1813                         v3_add(dzeta,dzeta,&temp1);
1814                 }
1815
1816                 /* dV_jk stuff | add force contribution on atom i immediately */
1817                 if(exchange->d_ij_between_rs) {
1818                         zeta=f_c*g;
1819                         v3_scale(&temp1,&temp2,f_c);
1820                         v3_scale(&temp2,&dist_ij,df_c*g);
1821                         v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
1822                 }
1823                 else {
1824                         zeta=g;
1825                         // dzeta_jk is simply dg, which is stored in temp2
1826                 }
1827                 /* betajnj * zeta_jk ^ nj-1 */
1828                 tmp=exchange->betajnj*pow(zeta,(n-1.0));
1829                 tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
1830                 v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
1831                 v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
1832                                                   /* scaled with 0.5 ^ */
1833 #ifdef DEBUG
1834 if(ai==&(moldyn->atom[0])) {
1835         printf("dVjk (3bp) contrib:\n");
1836         printf("%f | %f\n",temp2.x,ai->f.x);
1837         printf("%f | %f\n",temp2.y,ai->f.y);
1838         printf("%f | %f\n",temp2.z,ai->f.z);
1839 }
1840 #endif
1841
1842         }
1843
1844         return 0;
1845 }
1846
1847
1848 /*
1849  * debugging / critical check functions
1850  */
1851
1852 int moldyn_bc_check(t_moldyn *moldyn) {
1853
1854         t_atom *atom;
1855         t_3dvec *dim;
1856         int i;
1857         double x;
1858         u8 byte;
1859         int j,k;
1860
1861         atom=moldyn->atom;
1862         dim=&(moldyn->dim);
1863         x=dim->x/2;
1864
1865         for(i=0;i<moldyn->count;i++) {
1866                 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1867                         printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1868                                i,atom[i].r.x,dim->x/2);
1869                         printf("diagnostic:\n");
1870                         printf("-----------\natom.r.x:\n");
1871                         for(j=0;j<8;j++) {
1872                                 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
1873                                 for(k=0;k<8;k++)
1874                                         printf("%d%c",
1875                                         ((byte)&(1<<k))?1:0,
1876                                         (k==7)?'\n':'|');
1877                         }
1878                         printf("---------------\nx=dim.x/2:\n");
1879                         for(j=0;j<8;j++) {
1880                                 memcpy(&byte,(u8 *)(&x)+j,1);
1881                                 for(k=0;k<8;k++)
1882                                         printf("%d%c",
1883                                         ((byte)&(1<<k))?1:0,
1884                                         (k==7)?'\n':'|');
1885                         }
1886                         if(atom[i].r.x==x) printf("the same!\n");
1887                         else printf("different!\n");
1888                 }
1889                 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
1890                         printf("FATAL: atom %d: y: %.20f (%.20f)\n",
1891                                i,atom[i].r.y,dim->y/2);
1892                 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
1893                         printf("FATAL: atom %d: z: %.20f (%.20f)\n",
1894                                i,atom[i].r.z,dim->z/2);
1895         }
1896
1897         return 0;
1898 }