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_pressure(t_moldyn *moldyn,double p_ref) {
  82
  83         moldyn->p_ref=p_ref;
  84
  85         return 0;
  86 }
  87
  88 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
  89
  90         moldyn->pt_scale=(ptype|ttype);
  91         moldyn->t_tc=ttc;
  92         moldyn->p_tc=ptc;
  93
  94         return 0;
  95 }
  96
  97 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
  98
  99         moldyn->dim.x=x;
 100         moldyn->dim.y=y;
 101         moldyn->dim.z=z;
 102
 103         moldyn->volume=x*y*z;
 104
 105         if(visualize) {
 106                 moldyn->vis.dim.x=x;
 107                 moldyn->vis.dim.y=y;
 108                 moldyn->vis.dim.z=z;
 109         }
 110
 111         printf("[moldyn] dimensions in A and A^2 respectively:\n");
 112         printf("  x: %f\n",moldyn->dim.x);
 113         printf("  y: %f\n",moldyn->dim.y);
 114         printf("  z: %f\n",moldyn->dim.z);
 115         printf("  volume: %f\n",moldyn->volume);
 116         printf("  visualize simulation box: %s\n",visualize?"on":"off");
 117
 118         return 0;
 119 }
 120
 121 int set_nn_dist(t_moldyn *moldyn,double dist) {
 122
 123         moldyn->nnd=dist;
 124
 125         return 0;
 126 }
 127
 128 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 129
 130         if(x)
 131                 moldyn->status|=MOLDYN_STAT_PBX;
 132
 133         if(y)
 134                 moldyn->status|=MOLDYN_STAT_PBY;
 135
 136         if(z)
 137                 moldyn->status|=MOLDYN_STAT_PBZ;
 138
 139         return 0;
 140 }
 141
 142 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
 143
 144         moldyn->func1b=func;
 145         moldyn->pot1b_params=params;
 146
 147         return 0;
 148 }
 149
 150 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
 151
 152         moldyn->func2b=func;
 153         moldyn->pot2b_params=params;
 154
 155         return 0;
 156 }
 157
 158 int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
 159
 160         moldyn->func2b_post=func;
 161         moldyn->pot2b_params=params;
 162
 163         return 0;
 164 }
 165
 166 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
 167
 168         moldyn->func3b=func;
 169         moldyn->pot3b_params=params;
 170
 171         return 0;
 172 }
 173
 174 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
 175
 176         strncpy(moldyn->vlsdir,dir,127);
 177
 178         return 0;
 179 }
 180
 181 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 182
 183         char filename[128];
 184         int ret;
 185
 186         switch(type) {
 187                 case LOG_TOTAL_ENERGY:
 188                         moldyn->ewrite=timer;
 189                         snprintf(filename,127,"%s/energy",moldyn->vlsdir);
 190                         moldyn->efd=open(filename,
 191                                          O_WRONLY|O_CREAT|O_EXCL,
 192                                          S_IRUSR|S_IWUSR);
 193                         if(moldyn->efd<0) {
 194                                 perror("[moldyn] energy log fd open");
 195                                 return moldyn->efd;
 196                         }
 197                         dprintf(moldyn->efd,"# total energy log file\n");
 198                         break;
 199                 case LOG_TOTAL_MOMENTUM:
 200                         moldyn->mwrite=timer;
 201                         snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
 202                         moldyn->mfd=open(filename,
 203                                          O_WRONLY|O_CREAT|O_EXCL,
 204                                          S_IRUSR|S_IWUSR);
 205                         if(moldyn->mfd<0) {
 206                                 perror("[moldyn] momentum log fd open");
 207                                 return moldyn->mfd;
 208                         }
 209                         dprintf(moldyn->efd,"# total momentum log file\n");
 210                         break;
 211                 case SAVE_STEP:
 212                         moldyn->swrite=timer;
 213                         break;
 214                 case VISUAL_STEP:
 215                         moldyn->vwrite=timer;
 216                         ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
 217                         if(ret<0) {
 218                                 printf("[moldyn] visual init failure\n");
 219                                 return ret;
 220                         }
 221                         break;
 222                 default:
 223                         printf("[moldyn] unknown log mechanism: %02x\n",type);
 224                         return -1;
 225         }
 226
 227         return 0;
 228 }
 229
 230 int moldyn_log_shutdown(t_moldyn *moldyn) {
 231
 232         printf("[moldyn] log shutdown\n");
 233         if(moldyn->efd) close(moldyn->efd);
 234         if(moldyn->mfd) close(moldyn->mfd);
 235         if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 236
 237         return 0;
 238 }
 239
 240 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 241                    u8 attr,u8 bnum,int a,int b,int c) {
 242
 243         int count;
 244         int ret;
 245         t_3dvec origin;
 246
 247         count=a*b*c;
 248
 249         /* how many atoms do we expect */
 250         if(type==FCC) count*=4;
 251         if(type==DIAMOND) count*=8;
 252
 253         /* allocate space for atoms */
 254         moldyn->atom=malloc(count*sizeof(t_atom));
 255         if(moldyn->atom==NULL) {
 256                 perror("malloc (atoms)");
 257                 return -1;
 258         }
 259
 260         v3_zero(&origin);
 261
 262         switch(type) {
 263                 case FCC:
 264                         ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
 265                         break;
 266                 case DIAMOND:
 267                         ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
 268                         break;
 269                 default:
 270                         printf("unknown lattice type (%02x)\n",type);
 271                         return -1;
 272         }
 273
 274         /* debug */
 275         if(ret!=count) {
 276                 printf("[moldyn] creating lattice failed\n");
 277                 printf("  amount of atoms\n");
 278                 printf("  - expected: %d\n",count);
 279                 printf("  - created: %d\n",ret);
 280                 return -1;
 281         }
 282
 283         moldyn->count=count;
 284         printf("[moldyn] created lattice with %d atoms\n",count);
 285
 286         while(count) {
 287                 count-=1;
 288                 moldyn->atom[count].element=element;
 289                 moldyn->atom[count].mass=mass;
 290                 moldyn->atom[count].attr=attr;
 291                 moldyn->atom[count].bnum=bnum;
 292                 check_per_bound(moldyn,&(moldyn->atom[count].r));
 293         }
 294
 295         return ret;
 296 }
 297
 298 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 299              t_3dvec *r,t_3dvec *v) {
 300
 301         t_atom *atom;
 302         void *ptr;
 303         int count;
 304
 305         atom=moldyn->atom;
 306         count=++(moldyn->count);
 307
 308         ptr=realloc(atom,count*sizeof(t_atom));
 309         if(!ptr) {
 310                 perror("[moldyn] realloc (add atom)");
 311                 return -1;
 312         }
 313         moldyn->atom=ptr;
 314
 315         atom=moldyn->atom;
 316         atom[count-1].r=*r;
 317         atom[count-1].v=*v;
 318         atom[count-1].element=element;
 319         atom[count-1].mass=mass;
 320         atom[count-1].bnum=bnum;
 321         atom[count-1].attr=attr;
 322
 323         return 0;
 324 }
 325
 326 int destroy_atoms(t_moldyn *moldyn) {
 327
 328         if(moldyn->atom) free(moldyn->atom);
 329
 330         return 0;
 331 }
 332
 333 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 334
 335         /*
 336          * - gaussian distribution of velocities
 337          * - zero total momentum
 338          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 339          */
 340
 341         int i;
 342         double v,sigma;
 343         t_3dvec p_total,delta;
 344         t_atom *atom;
 345         t_random *random;
 346
 347         atom=moldyn->atom;
 348         random=&(moldyn->random);
 349
 350         /* gaussian distribution of velocities */
 351         v3_zero(&p_total);
 352         for(i=0;i<moldyn->count;i++) {
 353                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
 354                 /* x direction */
 355                 v=sigma*rand_get_gauss(random);
 356                 atom[i].v.x=v;
 357                 p_total.x+=atom[i].mass*v;
 358                 /* y direction */
 359                 v=sigma*rand_get_gauss(random);
 360                 atom[i].v.y=v;
 361                 p_total.y+=atom[i].mass*v;
 362                 /* z direction */
 363                 v=sigma*rand_get_gauss(random);
 364                 atom[i].v.z=v;
 365                 p_total.z+=atom[i].mass*v;
 366         }
 367
 368         /* zero total momentum */
 369         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 370         for(i=0;i<moldyn->count;i++) {
 371                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 372                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 373         }
 374
 375         /* velocity scaling */
 376         scale_velocity(moldyn,equi_init);
 377
 378         return 0;
 379 }
 380
 381 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 382
 383         int i;
 384         double e,scale;
 385         t_atom *atom;
 386         int count;
 387
 388         atom=moldyn->atom;
 389
 390         /*
 391          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 392          */
 393
 394         /* get kinetic energy / temperature & count involved atoms */
 395         e=0.0;
 396         count=0;
 397         for(i=0;i<moldyn->count;i++) {
 398                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
 399                         e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 400                         count+=1;
 401                 }
 402         }
 403         if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
 404         else return 0;  /* no atoms involved in scaling! */
 405
 406         /* (temporary) hack for e,t = 0 */
 407         if(e==0.0) {
 408         moldyn->t=0.0;
 409                 if(moldyn->t_ref!=0.0) {
 410                         thermal_init(moldyn,equi_init);
 411                         return 0;
 412                 }
 413                 else
 414                         return 0; /* no scaling needed */
 415         }
 416
 417
 418         /* get scaling factor */
 419         scale=moldyn->t_ref/moldyn->t;
 420         if(equi_init&TRUE)
 421                 scale*=2.0;
 422         else
 423                 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
 424                         scale=1.0+(scale-1.0)/moldyn->t_tc;
 425         scale=sqrt(scale);
 426
 427         /* velocity scaling */
 428         for(i=0;i<moldyn->count;i++) {
 429                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
 430                         v3_scale(&(atom[i].v),&(atom[i].v),scale);
 431         }
 432
 433         return 0;
 434 }
 435
 436 int scale_volume(t_moldyn *moldyn) {
 437
 438         t_atom *atom;
 439         t_3dvec *dim,*vdim;
 440         double virial,scale;
 441         t_linkcell *lc;
 442         int i;
 443
 444         atom=moldyn->atom;
 445         dim=&(moldyn->dim);
 446         vdim=&(moldyn->vis.dim);
 447         lc=&(moldyn->lc);
 448
 449         for(i=0;i<moldyn->count;i++)
 450                 virial+=v3_norm(&(atom[i].virial));
 451
 452 printf("%f\n",virial);
 453         /* get pressure from virial */
 454         moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*virial;
 455         moldyn->p/=moldyn->volume;
 456 printf("%f\n",moldyn->p/(ATM));
 457
 458         /* scale factor */
 459         if(moldyn->pt_scale&P_SCALE_BERENDSEN)
 460                 scale=3*sqrt(1-(moldyn->p_ref-moldyn->p)/moldyn->p_tc);
 461         else
 462                 /* should actually never be used */
 463                 scale=pow(moldyn->p/moldyn->p_ref,1.0/3.0);
 464
 465 printf("scale = %f\n",scale);
 466         /* actual scaling */
 467         dim->x*=scale;
 468         dim->y*=scale;
 469         dim->z*=scale;
 470         if(vdim->x) vdim->x=dim->x;
 471         if(vdim->y) vdim->y=dim->y;
 472         if(vdim->z) vdim->z=dim->z;
 473         moldyn->volume*=(scale*scale*scale);
 474
 475         /* check whether we need a new linkcell init */
 476         if((dim->x/moldyn->cutoff!=lc->nx)||
 477            (dim->y/moldyn->cutoff!=lc->ny)||
 478            (dim->z/moldyn->cutoff!=lc->nx)) {
 479                 link_cell_shutdown(moldyn);
 480                 link_cell_init(moldyn);
 481         }
 482
 483         return 0;
 484
 485 }
 486
 487 double get_e_kin(t_moldyn *moldyn) {
 488
 489         int i;
 490         t_atom *atom;
 491
 492         atom=moldyn->atom;
 493         moldyn->ekin=0.0;
 494
 495         for(i=0;i<moldyn->count;i++)
 496                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 497
 498         return moldyn->ekin;
 499 }
 500
 501 double get_e_pot(t_moldyn *moldyn) {
 502
 503         return moldyn->energy;
 504 }
 505
 506 double update_e_kin(t_moldyn *moldyn) {
 507
 508         return(get_e_kin(moldyn));
 509 }
 510
 511 double get_total_energy(t_moldyn *moldyn) {
 512
 513         return(moldyn->ekin+moldyn->energy);
 514 }
 515
 516 t_3dvec get_total_p(t_moldyn *moldyn) {
 517
 518         t_3dvec p,p_total;
 519         int i;
 520         t_atom *atom;
 521
 522         atom=moldyn->atom;
 523
 524         v3_zero(&p_total);
 525         for(i=0;i<moldyn->count;i++) {
 526                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 527                 v3_add(&p_total,&p_total,&p);
 528         }
 529
 530         return p_total;
 531 }
 532
 533 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 534
 535         double tau;
 536
 537         /* nn_dist is the nearest neighbour distance */
 538
 539         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
 540
 541         return tau;
 542 }
 543
 544 /*
 545  * numerical tricks
 546  */
 547
 548 /* linked list / cell method */
 549
 550 int link_cell_init(t_moldyn *moldyn) {
 551
 552         t_linkcell *lc;
 553         int i;
 554         int fd;
 555
 556         fd=open("/dev/null",O_WRONLY);
 557
 558         lc=&(moldyn->lc);
 559
 560         /* partitioning the md cell */
 561         lc->nx=moldyn->dim.x/moldyn->cutoff;
 562         lc->x=moldyn->dim.x/lc->nx;
 563         lc->ny=moldyn->dim.y/moldyn->cutoff;
 564         lc->y=moldyn->dim.y/lc->ny;
 565         lc->nz=moldyn->dim.z/moldyn->cutoff;
 566         lc->z=moldyn->dim.z/lc->nz;
 567
 568         lc->cells=lc->nx*lc->ny*lc->nz;
 569         lc->subcell=malloc(lc->cells*sizeof(t_list));
 570
 571         printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 572
 573         for(i=0;i<lc->cells;i++)
 574                 //list_init(&(lc->subcell[i]),1);
 575                 list_init(&(lc->subcell[i]),fd);
 576
 577         link_cell_update(moldyn);
 578
 579         return 0;
 580 }
 581
 582 int link_cell_update(t_moldyn *moldyn) {
 583
 584         int count,i,j,k;
 585         int nx,ny,nz;
 586         t_atom *atom;
 587         t_linkcell *lc;
 588
 589         atom=moldyn->atom;
 590         lc=&(moldyn->lc);
 591
 592         nx=lc->nx;
 593         ny=lc->ny;
 594         nz=lc->nz;
 595
 596         for(i=0;i<lc->cells;i++)
 597                 list_destroy(&(moldyn->lc.subcell[i]));
 598
 599         for(count=0;count<moldyn->count;count++) {
 600                 i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
 601                 j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
 602                 k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
 603                 list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 604                                        &(atom[count]));
 605         }
 606
 607         return 0;
 608 }
 609
 610 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 611
 612         t_linkcell *lc;
 613         int a;
 614         int count1,count2;
 615         int ci,cj,ck;
 616         int nx,ny,nz;
 617         int x,y,z;
 618         u8 bx,by,bz;
 619
 620         lc=&(moldyn->lc);
 621         nx=lc->nx;
 622         ny=lc->ny;
 623         nz=lc->nz;
 624         count1=1;
 625         count2=27;
 626         a=nx*ny;
 627
 628         cell[0]=lc->subcell[i+j*nx+k*a];
 629         for(ci=-1;ci<=1;ci++) {
 630                 bx=0;
 631                 x=i+ci;
 632                 if((x<0)||(x>=nx)) {
 633                         x=(x+nx)%nx;
 634                         bx=1;
 635                 }
 636                 for(cj=-1;cj<=1;cj++) {
 637                         by=0;
 638                         y=j+cj;
 639                         if((y<0)||(y>=ny)) {
 640                                 y=(y+ny)%ny;
 641                                 by=1;
 642                         }
 643                         for(ck=-1;ck<=1;ck++) {
 644                                 bz=0;
 645                                 z=k+ck;
 646                                 if((z<0)||(z>=nz)) {
 647                                         z=(z+nz)%nz;
 648                                         bz=1;
 649                                 }
 650                                 if(!(ci|cj|ck)) continue;
 651                                 if(bx|by|bz) {
 652                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
 653                                 }
 654                                 else {
 655                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
 656                                 }
 657                         }
 658                 }
 659         }
 660
 661         lc->dnlc=count1;
 662
 663         return count1;
 664 }
 665
 666 int link_cell_shutdown(t_moldyn *moldyn) {
 667
 668         int i;
 669         t_linkcell *lc;
 670
 671         lc=&(moldyn->lc);
 672
 673         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 674                 list_shutdown(&(moldyn->lc.subcell[i]));
 675
 676         return 0;
 677 }
 678
 679 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 680
 681         int count;
 682         void *ptr;
 683         t_moldyn_schedule *schedule;
 684
 685         schedule=&(moldyn->schedule);
 686         count=++(schedule->content_count);
 687
 688         ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
 689         if(!ptr) {
 690                 perror("[moldyn] realloc (runs)");
 691                 return -1;
 692         }
 693         moldyn->schedule.runs=ptr;
 694         moldyn->schedule.runs[count-1]=runs;
 695
 696         ptr=realloc(schedule->tau,count*sizeof(double));
 697         if(!ptr) {
 698                 perror("[moldyn] realloc (tau)");
 699                 return -1;
 700         }
 701         moldyn->schedule.tau=ptr;
 702         moldyn->schedule.tau[count-1]=tau;
 703
 704         return 0;
 705 }
 706
 707 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 708
 709         moldyn->schedule.hook=hook;
 710         moldyn->schedule.hook_params=hook_params;
 711
 712         return 0;
 713 }
 714
 715 /*
 716  *
 717  * 'integration of newtons equation' - algorithms
 718  *
 719  */
 720
 721 /* start the integration */
 722
 723 int moldyn_integrate(t_moldyn *moldyn) {
 724
 725         int i,sched;
 726         unsigned int e,m,s,v;
 727         t_3dvec p;
 728         t_moldyn_schedule *schedule;
 729         t_atom *atom;
 730         int fd;
 731         char dir[128];
 732         double ds;
 733
 734         schedule=&(moldyn->schedule);
 735         atom=moldyn->atom;
 736
 737         /* initialize linked cell method */
 738         link_cell_init(moldyn);
 739
 740         /* logging & visualization */
 741         e=moldyn->ewrite;
 742         m=moldyn->mwrite;
 743         s=moldyn->swrite;
 744         v=moldyn->vwrite;
 745
 746         /* sqaure of some variables */
 747         moldyn->tau_square=moldyn->tau*moldyn->tau;
 748         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 749
 750         /* calculate initial forces */
 751         potential_force_calc(moldyn);
 752
 753         /* some stupid checks before we actually start calculating bullshit */
 754         if(moldyn->cutoff>0.5*moldyn->dim.x)
 755                 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
 756         if(moldyn->cutoff>0.5*moldyn->dim.y)
 757                 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
 758         if(moldyn->cutoff>0.5*moldyn->dim.z)
 759                 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
 760         ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
 761         if(ds>0.05*moldyn->nnd)
 762                 printf("[moldyn] warning: forces too high / tau too small!\n");
 763
 764         /* zero absolute time */
 765         moldyn->time=0.0;
 766
 767         /* debugging, ignore */
 768         moldyn->debug=0;
 769
 770         /* executing the schedule */
 771         for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 772
 773                 /* setting amount of runs and finite time step size */
 774                 moldyn->tau=schedule->tau[sched];
 775                 moldyn->tau_square=moldyn->tau*moldyn->tau;
 776                 moldyn->time_steps=schedule->runs[sched];
 777
 778         /* integration according to schedule */
 779
 780         for(i=0;i<moldyn->time_steps;i++) {
 781
 782                 /* integration step */
 783                 moldyn->integrate(moldyn);
 784
 785                 /* p/t scaling */
 786                 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
 787                         scale_velocity(moldyn,FALSE);
 788                 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
 789 {
 790 printf("going to do p scale ...\n");
 791                         scale_volume(moldyn);
 792 printf("done\n");
 793 }
 794
 795                 /* check for log & visualization */
 796                 if(e) {
 797                         if(!(i%e))
 798                                 dprintf(moldyn->efd,
 799                                         "%f %f %f %f\n",
 800                                         moldyn->time,update_e_kin(moldyn),
 801                                         moldyn->energy,
 802                                         get_total_energy(moldyn));
 803                 }
 804                 if(m) {
 805                         if(!(i%m)) {
 806                                 p=get_total_p(moldyn);
 807                                 dprintf(moldyn->mfd,
 808                                         "%f %f\n",moldyn->time,v3_norm(&p));
 809                         }
 810                 }
 811                 if(s) {
 812                         if(!(i%s)) {
 813                                 snprintf(dir,128,"%s/s-%07.f.save",
 814                                          moldyn->vlsdir,moldyn->time);
 815                                 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
 816                                 if(fd<0) perror("[moldyn] save fd open");
 817                                 else {
 818                                         write(fd,moldyn,sizeof(t_moldyn));
 819                                         write(fd,moldyn->atom,
 820                                               moldyn->count*sizeof(t_atom));
 821                                 }
 822                                 close(fd);
 823                         }
 824                 }
 825                 if(v) {
 826                         if(!(i%v)) {
 827                                 visual_atoms(&(moldyn->vis),moldyn->time,
 828                                              moldyn->atom,moldyn->count);
 829                                 printf("\rsched: %d, steps: %d, debug: %d",
 830                                        sched,i,moldyn->debug);
 831                                 fflush(stdout);
 832                         }
 833                 }
 834
 835                 /* increase absolute time */
 836                 moldyn->time+=moldyn->tau;
 837
 838         }
 839
 840                 /* check for hooks */
 841                 if(schedule->hook)
 842                         schedule->hook(moldyn,schedule->hook_params);
 843
 844                 /* get a new info line */
 845                 printf("\n");
 846
 847         }
 848
 849         return 0;
 850 }
 851
 852 /* velocity verlet */
 853
 854 int velocity_verlet(t_moldyn *moldyn) {
 855
 856         int i,count;
 857         double tau,tau_square;
 858         t_3dvec delta;
 859         t_atom *atom;
 860
 861         atom=moldyn->atom;
 862         count=moldyn->count;
 863         tau=moldyn->tau;
 864         tau_square=moldyn->tau_square;
 865
 866         for(i=0;i<count;i++) {
 867                 /* new positions */
 868                 v3_scale(&delta,&(atom[i].v),tau);
 869                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 870                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 871                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 872 //if(i==5) printf("v: %f %f %f\n",atom[i].r.x,(atom[i].r.x+moldyn->dim.x/2)/moldyn->lc.x,2*atom[i].r.x/moldyn->dim.x);
 873                 check_per_bound(moldyn,&(atom[i].r));
 874 //if(i==5) printf("n: %f %f %f\n",atom[i].r.x,(atom[i].r.x+moldyn->dim.x/2)/moldyn->lc.x,2*atom[i].r.x/moldyn->dim.x);
 875
 876                 /* velocities */
 877                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 878                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 879         }
 880
 881 //moldyn_bc_check(moldyn);
 882         /* neighbour list update */
 883         link_cell_update(moldyn);
 884
 885         /* forces depending on chosen potential */
 886         potential_force_calc(moldyn);
 887
 888         for(i=0;i<count;i++) {
 889                 /* again velocities */
 890                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 891                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 892         }
 893
 894         return 0;
 895 }
 896
 897
 898 /*
 899  *
 900  * potentials & corresponding forces
 901  *
 902  */
 903
 904 /* generic potential and force calculation */
 905
 906 int potential_force_calc(t_moldyn *moldyn) {
 907
 908         int i,j,k,count;
 909         t_atom *itom,*jtom,*ktom;
 910         t_linkcell *lc;
 911         t_list neighbour_i[27];
 912         t_list neighbour_i2[27];
 913         t_list *this,*that;
 914         u8 bc_ij,bc_ik;
 915         int dnlc;
 916
 917         count=moldyn->count;
 918         itom=moldyn->atom;
 919         lc=&(moldyn->lc);
 920
 921         /* reset energy */
 922         moldyn->energy=0.0;
 923
 924         /* get energy and force of every atom */
 925         for(i=0;i<count;i++) {
 926
 927                 /* reset force */
 928                 v3_zero(&(itom[i].f));
 929
 930                 /* reset viral of atom i */
 931                 v3_zero(&(itom[i].virial));
 932
 933                 /* single particle potential/force */
 934                 if(itom[i].attr&ATOM_ATTR_1BP)
 935                         moldyn->func1b(moldyn,&(itom[i]));
 936
 937                 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
 938                         continue;
 939
 940                 /* 2 body pair potential/force */
 941
 942                 link_cell_neighbour_index(moldyn,
 943                                           (itom[i].r.x+moldyn->dim.x/2)/lc->x,
 944                                           (itom[i].r.y+moldyn->dim.y/2)/lc->y,
 945                                           (itom[i].r.z+moldyn->dim.z/2)/lc->z,
 946                                           neighbour_i);
 947
 948                 dnlc=lc->dnlc;
 949
 950                 for(j=0;j<27;j++) {
 951
 952                         this=&(neighbour_i[j]);
 953                         list_reset(this);
 954
 955                         if(this->start==NULL)
 956                                 continue;
 957
 958                         bc_ij=(j<dnlc)?0:1;
 959
 960                         do {
 961                                 jtom=this->current->data;
 962
 963                                 if(jtom==&(itom[i]))
 964                                         continue;
 965
 966                                 if((jtom->attr&ATOM_ATTR_2BP)&
 967                                    (itom[i].attr&ATOM_ATTR_2BP)) {
 968                                         moldyn->func2b(moldyn,
 969                                                        &(itom[i]),
 970                                                        jtom,
 971                                                        bc_ij);
 972                                 }
 973
 974                                 /* 3 body potential/force */
 975
 976                                 if(!(itom[i].attr&ATOM_ATTR_3BP)||
 977                                    !(jtom->attr&ATOM_ATTR_3BP))
 978                                         continue;
 979
 980                                 /* copy the neighbour lists */
 981                                 memcpy(neighbour_i2,neighbour_i,
 982                                        27*sizeof(t_list));
 983
 984                                 /* get neighbours of i */
 985                                 for(k=0;k<27;k++) {
 986
 987                                         that=&(neighbour_i2[k]);
 988                                         list_reset(that);
 989
 990                                         if(that->start==NULL)
 991                                                 continue;
 992
 993                                         bc_ik=(k<dnlc)?0:1;
 994
 995                                         do {
 996
 997                                                 ktom=that->current->data;
 998
 999                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
1000                                                         continue;
1001
1002                                                 if(ktom==jtom)
1003                                                         continue;
1004
1005                                                 if(ktom==&(itom[i]))
1006                                                         continue;
1007
1008                                                 moldyn->func3b(moldyn,
1009                                                                &(itom[i]),
1010                                                                jtom,
1011                                                                ktom,
1012                                                                bc_ik|bc_ij);
1013
1014                                         } while(list_next(that)!=\
1015                                                 L_NO_NEXT_ELEMENT);
1016
1017                                 }
1018
1019                                 /* 2bp post function */
1020                                 if(moldyn->func2b_post) {
1021                                         moldyn->func2b_post(moldyn,
1022                                                             &(itom[i]),
1023                                                             jtom,bc_ij);
1024                                 }
1025
1026                         } while(list_next(this)!=L_NO_NEXT_ELEMENT);
1027
1028                 }
1029
1030         }
1031
1032         return 0;
1033 }
1034
1035 /*
1036  * periodic boundayr checking
1037  */
1038
1039 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1040
1041         double x,y,z;
1042         t_3dvec *dim;
1043
1044         dim=&(moldyn->dim);
1045
1046         x=dim->x/2;
1047         y=dim->y/2;
1048         z=dim->z/2;
1049
1050         if(moldyn->status&MOLDYN_STAT_PBX) {
1051                 if(a->x>=x) a->x-=dim->x;
1052                 else if(-a->x>x) a->x+=dim->x;
1053         }
1054         if(moldyn->status&MOLDYN_STAT_PBY) {
1055                 if(a->y>=y) a->y-=dim->y;
1056                 else if(-a->y>y) a->y+=dim->y;
1057         }
1058         if(moldyn->status&MOLDYN_STAT_PBZ) {
1059                 if(a->z>=z) a->z-=dim->z;
1060                 else if(-a->z>z) a->z+=dim->z;
1061         }
1062
1063         return 0;
1064 }
1065
1066
1067 /*
1068  * example potentials
1069  */
1070
1071 /* harmonic oscillator potential and force */
1072
1073 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1074
1075         t_ho_params *params;
1076         t_3dvec force,distance;
1077         double d;
1078         double sc,equi_dist;
1079
1080         params=moldyn->pot2b_params;
1081         sc=params->spring_constant;
1082         equi_dist=params->equilibrium_distance;
1083
1084         v3_sub(&distance,&(aj->r),&(ai->r));
1085
1086         if(bc) check_per_bound(moldyn,&distance);
1087         d=v3_norm(&distance);
1088         if(d<=moldyn->cutoff) {
1089                 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
1090                 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
1091                 /* f = -grad E; grad r_ij = -1 1/r_ij distance */
1092                 v3_scale(&force,&distance,sc*(1.0-(equi_dist/d)));
1093                 v3_add(&(ai->f),&(ai->f),&force);
1094         }
1095
1096         return 0;
1097 }
1098
1099 /* lennard jones potential & force for one sort of atoms */
1100
1101 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1102
1103         t_lj_params *params;
1104         t_3dvec force,distance;
1105         double d,h1,h2;
1106         double eps,sig6,sig12;
1107
1108         params=moldyn->pot2b_params;
1109         eps=params->epsilon4;
1110         sig6=params->sigma6;
1111         sig12=params->sigma12;
1112
1113         v3_sub(&distance,&(aj->r),&(ai->r));
1114         if(bc) check_per_bound(moldyn,&distance);
1115         d=v3_absolute_square(&distance);        /* 1/r^2 */
1116         if(d<=moldyn->cutoff_square) {
1117                 d=1.0/d;                        /* 1/r^2 */
1118                 h2=d*d;                         /* 1/r^4 */
1119                 h2*=d;                          /* 1/r^6 */
1120                 h1=h2*h2;                       /* 1/r^12 */
1121                 /* energy is eps*..., but we will add this twice ... */
1122                 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
1123                 h2*=d;                          /* 1/r^8 */
1124                 h1*=d;                          /* 1/r^14 */
1125                 h2*=6*sig6;
1126                 h1*=12*sig12;
1127                 d=+h1-h2;
1128                 d*=eps;
1129                 v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
1130                 v3_add(&(ai->f),&(ai->f),&force);
1131         }
1132
1133         return 0;
1134 }
1135
1136 /*
1137  * tersoff potential & force for 2 sorts of atoms
1138  */
1139
1140 /* create mixed terms from parameters and set them */
1141 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
1142
1143         printf("[moldyn] tersoff parameter completion\n");
1144         p->Smixed=sqrt(p->S[0]*p->S[1]);
1145         p->Rmixed=sqrt(p->R[0]*p->R[1]);
1146         p->Amixed=sqrt(p->A[0]*p->A[1]);
1147         p->Bmixed=sqrt(p->B[0]*p->B[1]);
1148         p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
1149         p->mu_m=0.5*(p->mu[0]+p->mu[1]);
1150
1151         printf("[moldyn] tersoff mult parameter info:\n");
1152         printf("  S (A)  | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
1153         printf("  R (A)  | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
1154         printf("  A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
1155         printf("  B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
1156         printf("  lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
1157                                           p->lambda_m);
1158         printf("  mu     | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
1159         printf("  beta   | %.10f | %.10f\n",p->beta[0],p->beta[1]);
1160         printf("  n      | %f | %f\n",p->n[0],p->n[1]);
1161         printf("  c      | %f | %f\n",p->c[0],p->c[1]);
1162         printf("  d      | %f | %f\n",p->d[0],p->d[1]);
1163         printf("  h      | %f | %f\n",p->h[0],p->h[1]);
1164         printf("  chi    | %f \n",p->chi);
1165
1166         return 0;
1167 }
1168
1169 /* tersoff 1 body part */
1170 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
1171
1172         int num;
1173         t_tersoff_mult_params *params;
1174         t_tersoff_exchange *exchange;
1175
1176         num=ai->bnum;
1177         params=moldyn->pot1b_params;
1178         exchange=&(params->exchange);
1179
1180         /*
1181          * simple: point constant parameters only depending on atom i to
1182          *         their right values
1183          */
1184
1185         exchange->beta_i=&(params->beta[num]);
1186         exchange->n_i=&(params->n[num]);
1187         exchange->c_i=&(params->c[num]);
1188         exchange->d_i=&(params->d[num]);
1189         exchange->h_i=&(params->h[num]);
1190
1191         exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
1192         exchange->ci2=params->c[num]*params->c[num];
1193         exchange->di2=params->d[num]*params->d[num];
1194         exchange->ci2di2=exchange->ci2/exchange->di2;
1195
1196         return 0;
1197 }
1198
1199 /* tersoff 2 body part */
1200 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1201
1202         t_tersoff_mult_params *params;
1203         t_tersoff_exchange *exchange;
1204         t_3dvec dist_ij,force;
1205         double d_ij;
1206         double A,B,R,S,lambda,mu;
1207         double f_r,df_r;
1208         double f_c,df_c;
1209         int num;
1210         double s_r;
1211         double arg;
1212
1213         params=moldyn->pot2b_params;
1214         num=aj->bnum;
1215         exchange=&(params->exchange);
1216
1217         /* clear 3bp and 2bp post run */
1218         exchange->run3bp=0;
1219         exchange->run2bp_post=0;
1220
1221         /* reset S > r > R mark */
1222         exchange->d_ij_between_rs=0;
1223
1224         /*
1225          * calc of 2bp contribution of V_ij and dV_ij/ji
1226          *
1227          * for Vij and dV_ij we need:
1228          * - f_c_ij, df_c_ij
1229          * - f_r_ij, df_r_ij
1230          *
1231          * for dV_ji we need:
1232          * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
1233          * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
1234          *
1235          */
1236
1237         /* dist_ij, d_ij */
1238         v3_sub(&dist_ij,&(aj->r),&(ai->r));
1239         if(bc) check_per_bound(moldyn,&dist_ij);
1240         d_ij=v3_norm(&dist_ij);
1241
1242         /* save for use in 3bp */
1243         exchange->d_ij=d_ij;
1244         exchange->dist_ij=dist_ij;
1245
1246         /* constants */
1247         if(num==ai->bnum) {
1248                 S=params->S[num];
1249                 R=params->R[num];
1250                 A=params->A[num];
1251                 B=params->B[num];
1252                 lambda=params->lambda[num];
1253                 mu=params->mu[num];
1254                 exchange->chi=1.0;
1255         }
1256         else {
1257                 S=params->Smixed;
1258                 R=params->Rmixed;
1259                 A=params->Amixed;
1260                 B=params->Bmixed;
1261                 lambda=params->lambda_m;
1262                 mu=params->mu_m;
1263                 params->exchange.chi=params->chi;
1264         }
1265
1266         /* if d_ij > S => no force & potential energy contribution */
1267         if(d_ij>S)
1268                 return 0;
1269
1270         /* more constants */
1271         exchange->beta_j=&(params->beta[num]);
1272         exchange->n_j=&(params->n[num]);
1273         exchange->c_j=&(params->c[num]);
1274         exchange->d_j=&(params->d[num]);
1275         exchange->h_j=&(params->h[num]);
1276         if(num==ai->bnum) {
1277                 exchange->betajnj=exchange->betaini;
1278                 exchange->cj2=exchange->ci2;
1279                 exchange->dj2=exchange->di2;
1280                 exchange->cj2dj2=exchange->ci2di2;
1281         }
1282         else {
1283                 exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
1284                 exchange->cj2=params->c[num]*params->c[num];
1285                 exchange->dj2=params->d[num]*params->d[num];
1286                 exchange->cj2dj2=exchange->cj2/exchange->dj2;
1287         }
1288
1289         /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
1290         f_r=A*exp(-lambda*d_ij);
1291         df_r=lambda*f_r/d_ij;
1292
1293         /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
1294         exchange->f_a=-B*exp(-mu*d_ij);
1295         exchange->df_a=mu*exchange->f_a/d_ij;
1296
1297         /* f_c, df_c calc (again, same for ij and ji) */
1298         if(d_ij<R) {
1299                 /* f_c = 1, df_c = 0 */
1300                 f_c=1.0;
1301                 df_c=0.0;
1302                 /* two body contribution (ij, ji) */
1303                 v3_scale(&force,&dist_ij,-df_r);
1304         }
1305         else {
1306                 s_r=S-R;
1307                 arg=M_PI*(d_ij-R)/s_r;
1308                 f_c=0.5+0.5*cos(arg);
1309                 //df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij)); /* MARK! */
1310                 df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
1311                 /* two body contribution (ij, ji) */
1312                 v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
1313                 /* tell 3bp that S > r > R */
1314                 exchange->d_ij_between_rs=1;
1315         }
1316
1317         /* add forces of 2bp (ij, ji) contribution
1318          * dVij = dVji and we sum up both: no 1/2) */
1319         v3_add(&(ai->f),&(ai->f),&force);
1320
1321         /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
1322         moldyn->energy+=(0.5*f_r*f_c);
1323
1324         /* save for use in 3bp */
1325         exchange->f_c=f_c;
1326         exchange->df_c=df_c;
1327
1328         /* enable the run of 3bp function and 2bp post processing */
1329         exchange->run3bp=1;
1330         exchange->run2bp_post=1;
1331
1332         /* reset 3bp sums */
1333         exchange->zeta_ij=0.0;
1334         exchange->zeta_ji=0.0;
1335         v3_zero(&(exchange->dzeta_ij));
1336         v3_zero(&(exchange->dzeta_ji));
1337
1338         return 0;
1339 }
1340
1341 /* tersoff 2 body post part */
1342
1343 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1344
1345         /*
1346          * here we have to allow for the 3bp sums
1347          *
1348          * that is:
1349          * - zeta_ij, dzeta_ij
1350          * - zeta_ji, dzeta_ji
1351          *
1352          * to compute the 3bp contribution to:
1353          * - Vij, dVij
1354          * - dVji
1355          *
1356          */
1357
1358         t_tersoff_mult_params *params;
1359         t_tersoff_exchange *exchange;
1360
1361         t_3dvec force,temp;
1362         t_3dvec *dist_ij;
1363         double b,db,tmp;
1364         double f_c,df_c,f_a,df_a;
1365         double chi,ni,betaini,nj,betajnj;
1366         double zeta;
1367
1368         params=moldyn->pot2b_params;
1369         exchange=&(params->exchange);
1370
1371         /* we do not run if f_c_ij was detected to be 0! */
1372         if(!(exchange->run2bp_post))
1373                 return 0;
1374
1375         f_c=exchange->f_c;
1376         df_c=exchange->df_c;
1377         f_a=exchange->f_a;
1378         df_a=exchange->df_a;
1379         betaini=exchange->betaini;
1380         betajnj=exchange->betajnj;
1381         ni=*(exchange->n_i);
1382         nj=*(exchange->n_j);
1383         chi=exchange->chi;
1384         dist_ij=&(exchange->dist_ij);
1385
1386         /* Vij and dVij */
1387         zeta=exchange->zeta_ij;
1388         if(zeta==0.0) {
1389                 moldyn->debug++;                /* just for debugging ... */
1390                 db=0.0;
1391                 b=chi;
1392                 v3_scale(&force,dist_ij,df_a*b*f_c);
1393         }
1394         else {
1395                 tmp=betaini*pow(zeta,ni-1.0);           /* beta^n * zeta^n-1 */
1396                 b=(1+zeta*tmp);                         /* 1 + beta^n zeta^n */
1397                 db=chi*pow(b,-1.0/(2*ni)-1);            /* x(...)^(-1/2n - 1) */
1398                 b=db*b;                                 /* b_ij */
1399                 db*=-0.5*tmp;                           /* db_ij */
1400                 v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
1401                 v3_scale(&temp,dist_ij,df_a*b);
1402                 v3_add(&force,&force,&temp);
1403                 v3_scale(&force,&force,f_c);
1404         }
1405         v3_scale(&temp,dist_ij,df_c*b*f_a);
1406         v3_add(&force,&force,&temp);
1407         v3_scale(&force,&force,-0.5);
1408
1409         /* add force */
1410         v3_add(&(ai->f),&(ai->f),&force);
1411
1412         /* add energy of 3bp sum */
1413         moldyn->energy+=(0.5*f_c*b*f_a);
1414
1415         /* dVji */
1416         zeta=exchange->zeta_ji;
1417         if(zeta==0.0) {
1418                 moldyn->debug++;
1419                 b=chi;
1420                 v3_scale(&force,dist_ij,df_a*b*f_c);
1421         }
1422         else {
1423                 tmp=betajnj*pow(zeta,nj-1.0);           /* beta^n * zeta^n-1 */
1424                 b=(1+zeta*tmp);                         /* 1 + beta^n zeta^n */
1425                 db=chi*pow(b,-1.0/(2*nj)-1);            /* x(...)^(-1/2n - 1) */
1426                 b=db*b;                                 /* b_ij */
1427                 db*=-0.5*tmp;                           /* db_ij */
1428                 v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
1429                 v3_scale(&temp,dist_ij,df_a*b);
1430                 v3_add(&force,&force,&temp);
1431                 v3_scale(&force,&force,f_c);
1432         }
1433         v3_scale(&temp,dist_ij,df_c*b*f_a);
1434         v3_add(&force,&force,&temp);
1435         v3_scale(&force,&force,-0.5);
1436
1437         /* add force */
1438         v3_add(&(ai->f),&(ai->f),&force);
1439
1440         return 0;
1441 }
1442
1443 /* tersoff 3 body part */
1444
1445 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1446
1447         t_tersoff_mult_params *params;
1448         t_tersoff_exchange *exchange;
1449         t_3dvec dist_ij,dist_ik,dist_jk;
1450         t_3dvec temp1,temp2;
1451         t_3dvec *dzeta;
1452         double R,S,s_r;
1453         double B,mu;
1454         double d_ij,d_ik,d_jk;
1455         double rr,dd;
1456         double f_c,df_c;
1457         double f_c_ik,df_c_ik,arg;
1458         double f_c_jk;
1459         double n,c,d,h;
1460         double c2,d2,c2d2;
1461         double cos_theta,d_costheta1,d_costheta2;
1462         double h_cos,d2_h_cos2;
1463         double frac,g,zeta,chi;
1464         double tmp;
1465         int num;
1466
1467         params=moldyn->pot3b_params;
1468         exchange=&(params->exchange);
1469
1470         if(!(exchange->run3bp))
1471                 return 0;
1472
1473         /*
1474          * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
1475          * 2bp contribution of dV_jk
1476          *
1477          * for Vij and dV_ij we still need:
1478          * - b_ij, db_ij (zeta_ij)
1479          *   - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
1480          *
1481          * for dV_ji we still need:
1482          * - b_ji, db_ji (zeta_ji)
1483          *   - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
1484          *
1485          * for dV_jk we need:
1486          * - f_c_jk
1487          * - f_a_jk
1488          * - db_jk (zeta_jk)
1489          *   - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
1490          *
1491          */
1492
1493         /*
1494          * get exchange data
1495          */
1496
1497         /* dist_ij, d_ij - this is < S_ij ! */
1498         dist_ij=exchange->dist_ij;
1499         d_ij=exchange->d_ij;
1500
1501         /* f_c_ij, df_c_ij (same for ji) */
1502         f_c=exchange->f_c;
1503         df_c=exchange->df_c;
1504
1505         /*
1506          * calculate unknown values now ...
1507          */
1508
1509         /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
1510
1511         /* dist_ik, d_ik */
1512         v3_sub(&dist_ik,&(ak->r),&(ai->r));
1513         if(bc) check_per_bound(moldyn,&dist_ik);
1514         d_ik=v3_norm(&dist_ik);
1515
1516         /* ik constants */
1517         num=ai->bnum;
1518         if(num==ak->bnum) {
1519                 R=params->R[num];
1520                 S=params->S[num];
1521         }
1522         else {
1523                 R=params->Rmixed;
1524                 S=params->Smixed;
1525         }
1526
1527         /* zeta_ij/dzeta_ij contribution only for d_ik < S */
1528         if(d_ik<S) {
1529
1530                 /* get constants_i from exchange data */
1531                 n=*(exchange->n_i);
1532                 c=*(exchange->c_i);
1533                 d=*(exchange->d_i);
1534                 h=*(exchange->h_i);
1535                 c2=exchange->ci2;
1536                 d2=exchange->di2;
1537                 c2d2=exchange->ci2di2;
1538
1539                 /* cosine of theta_ijk by scalaproduct */
1540                 rr=v3_scalar_product(&dist_ij,&dist_ik);
1541                 dd=d_ij*d_ik;
1542                 cos_theta=rr/dd;
1543
1544                 /* d_costheta */
1545                 tmp=1.0/dd;
1546                 d_costheta1=cos_theta/(d_ij*d_ij)-tmp;
1547                 d_costheta2=cos_theta/(d_ik*d_ik)-tmp;
1548
1549                 /* some usefull values */
1550                 h_cos=(h-cos_theta);
1551                 d2_h_cos2=d2+(h_cos*h_cos);
1552                 frac=c2/(d2_h_cos2);
1553
1554                 /* g(cos_theta) */
1555                 g=1.0+c2d2-frac;
1556
1557                 /* d_costheta_ij and dg(cos_theta) - needed in any case! */
1558                 v3_scale(&temp1,&dist_ij,d_costheta1);
1559                 v3_scale(&temp2,&dist_ik,d_costheta2);
1560                 v3_add(&temp1,&temp1,&temp2);
1561                 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
1562
1563                 /* f_c_ik & df_c_ik + {d,}zeta contribution */
1564                 dzeta=&(exchange->dzeta_ij);
1565                 if(d_ik<R) {
1566                         /* {d,}f_c_ik */
1567                         // => f_c_ik=1.0;
1568                         // => df_c_ik=0.0; of course we do not set this!
1569
1570                         /* zeta_ij */
1571                         exchange->zeta_ij+=g;
1572
1573                         /* dzeta_ij */
1574                         v3_add(dzeta,dzeta,&temp1);
1575                 }
1576                 else {
1577                         /* {d,}f_c_ik */
1578                         s_r=S-R;
1579                         arg=M_PI*(d_ik-R)/s_r;
1580                         f_c_ik=0.5+0.5*cos(arg);
1581                         //df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik)); /* MARK */
1582                         df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
1583
1584                         /* zeta_ij */
1585                         exchange->zeta_ij+=f_c_ik*g;
1586
1587                         /* dzeta_ij */
1588                         v3_scale(&temp1,&temp1,f_c_ik);
1589                         v3_scale(&temp2,&dist_ik,g*df_c_ik);
1590                         v3_add(&temp1,&temp1,&temp2);
1591                         v3_add(dzeta,dzeta,&temp1);
1592                 }
1593         }
1594
1595         /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
1596
1597         /* dist_jk, d_jk */
1598         v3_sub(&dist_jk,&(ak->r),&(aj->r));
1599         if(bc) check_per_bound(moldyn,&dist_jk);
1600         d_jk=v3_norm(&dist_jk);
1601
1602         /* jk constants */
1603         num=aj->bnum;
1604         if(num==ak->bnum) {
1605                 R=params->R[num];
1606                 S=params->S[num];
1607                 B=params->B[num];
1608                 mu=params->mu[num];
1609                 chi=1.0;
1610         }
1611         else {
1612                 R=params->Rmixed;
1613                 S=params->Smixed;
1614                 B=params->Bmixed;
1615                 mu=params->mu_m;
1616                 chi=params->chi;
1617         }
1618
1619         /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
1620         if(d_jk<S) {
1621
1622                 /* constants_j from exchange data */
1623                 n=*(exchange->n_j);
1624                 c=*(exchange->c_j);
1625                 d=*(exchange->d_j);
1626                 h=*(exchange->h_j);
1627                 c2=exchange->cj2;
1628                 d2=exchange->dj2;
1629                 c2d2=exchange->cj2dj2;
1630
1631                 /* cosine of theta_jik by scalaproduct */
1632                 rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
1633                 dd=d_ij*d_jk;
1634                 cos_theta=rr/dd;
1635
1636                 /* d_costheta */
1637                 d_costheta1=1.0/dd;
1638                 d_costheta2=cos_theta/(d_ij*d_ij);
1639
1640                 /* some usefull values */
1641                 h_cos=(h-cos_theta);
1642                 d2_h_cos2=d2+(h_cos*h_cos);
1643                 frac=c2/(d2_h_cos2);
1644
1645                 /* g(cos_theta) */
1646                 g=1.0+c2d2-frac;
1647
1648                 /* d_costheta_ij and dg(cos_theta) - needed in any case! */
1649                 v3_scale(&temp1,&dist_jk,d_costheta1);
1650                 v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
1651                 v3_add(&temp1,&temp1,&temp2);
1652                 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
1653
1654                 /* store dg in temp2 and use it for dVjk later */
1655                 v3_copy(&temp2,&temp1);
1656
1657                 /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
1658                 dzeta=&(exchange->dzeta_ji);
1659                 if(d_jk<R) {
1660                         /* f_c_jk */
1661                         f_c_jk=1.0;
1662
1663                         /* zeta_ji */
1664                         exchange->zeta_ji+=g;
1665
1666                         /* dzeta_ji */
1667                         v3_add(dzeta,dzeta,&temp1);
1668                 }
1669                 else {
1670                         /* f_c_jk */
1671                         s_r=S-R;
1672                         arg=M_PI*(d_jk-R)/s_r;
1673                         f_c_jk=0.5+0.5*cos(arg);
1674
1675                         /* zeta_ji */
1676                         exchange->zeta_ji+=f_c_jk*g;
1677
1678                         /* dzeta_ji */
1679                         v3_scale(&temp1,&temp1,f_c_jk);
1680                         v3_add(dzeta,dzeta,&temp1);
1681                 }
1682
1683                 /* dV_jk stuff | add force contribution on atom i immediately */
1684                 if(exchange->d_ij_between_rs) {
1685                         zeta=f_c*g;
1686                         v3_scale(&temp1,&temp2,f_c);
1687                         v3_scale(&temp2,&dist_ij,df_c*g);
1688                         v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
1689                 }
1690                 else {
1691                         zeta=g;
1692                         // dzeta_jk is simply dg, which is stored in temp2
1693                 }
1694                 /* betajnj * zeta_jk ^ nj-1 */
1695                 tmp=exchange->betajnj*pow(zeta,(n-1.0));
1696                 tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
1697                 v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
1698                 v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
1699                                                   /* scaled with 0.5 ^ */
1700
1701         }
1702
1703         return 0;
1704 }
1705
1706
1707 /*
1708  * debugging / critical check functions
1709  */
1710
1711 int moldyn_bc_check(t_moldyn *moldyn) {
1712
1713         t_atom *atom;
1714         t_3dvec *dim;
1715         int i;
1716 double x;
1717 u8 byte;
1718 int j,k;
1719
1720         atom=moldyn->atom;
1721         dim=&(moldyn->dim);
1722 x=dim->x/2;
1723
1724         for(i=0;i<moldyn->count;i++) {
1725                 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1726                         printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1727                                i,atom[i].r.x,dim->x/2);
1728                         printf("diagnostic:\n");
1729                         printf("-----------\natom.r.x:\n");
1730                         for(j=0;j<8;j++) {
1731                                 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
1732                                 for(k=0;k<8;k++)
1733                                         printf("%d%c",
1734                                         ((byte)&(1<<k))?1:0,
1735                                         (k==7)?'\n':'|');
1736                         }
1737                         printf("---------------\nx=dim.x/2:\n");
1738                         for(j=0;j<8;j++) {
1739                                 memcpy(&byte,(u8 *)(&x)+j,1);
1740                                 for(k=0;k<8;k++)
1741                                         printf("%d%c",
1742                                         ((byte)&(1<<k))?1:0,
1743                                         (k==7)?'\n':'|');
1744                         }
1745                         if(atom[i].r.x==x) printf("the same!\n");
1746                         else printf("different!\n");
1747                 }
1748                 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
1749                         printf("FATAL: atom %d: y: %.20f (%.20f)\n",
1750                                i,atom[i].r.y,dim->y/2);
1751                 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
1752                         printf("FATAL: atom %d: z: %.20f (%.20f)\n",
1753                                i,atom[i].r.z,dim->z/2);
1754         }
1755
1756         return 0;
1757 }
1758