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) {
  75
  76         moldyn->t=t;
  77
  78         return 0;
  79 }
  80
  81 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
  82
  83         moldyn->dim.x=x;
  84         moldyn->dim.y=y;
  85         moldyn->dim.z=z;
  86
  87         if(visualize) {
  88                 moldyn->vis.dim.x=x;
  89                 moldyn->vis.dim.y=y;
  90                 moldyn->vis.dim.z=z;
  91         }
  92
  93         return 0;
  94 }
  95
  96 int set_nn_dist(t_moldyn *moldyn,double dist) {
  97
  98         moldyn->nnd=dist;
  99
 100         return 0;
 101 }
 102
 103 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 104
 105         if(x)
 106                 moldyn->status|=MOLDYN_STAT_PBX;
 107
 108         if(y)
 109                 moldyn->status|=MOLDYN_STAT_PBY;
 110
 111         if(z)
 112                 moldyn->status|=MOLDYN_STAT_PBZ;
 113
 114         return 0;
 115 }
 116
 117 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
 118
 119         moldyn->func1b=func;
 120         moldyn->pot1b_params=params;
 121
 122         return 0;
 123 }
 124
 125 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
 126
 127         moldyn->func2b=func;
 128         moldyn->pot2b_params=params;
 129
 130         return 0;
 131 }
 132
 133 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
 134
 135         moldyn->func3b=func;
 136         moldyn->pot3b_params=params;
 137
 138         return 0;
 139 }
 140
 141 int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
 142
 143         switch(type) {
 144                 case LOG_TOTAL_ENERGY:
 145                         moldyn->ewrite=timer;
 146                         moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
 147                         if(moldyn->efd<0) {
 148                                 perror("[moldyn] efd open");
 149                                 return moldyn->efd;
 150                         }
 151                         dprintf(moldyn->efd,"# total energy log file\n");
 152                         break;
 153                 case LOG_TOTAL_MOMENTUM:
 154                         moldyn->mwrite=timer;
 155                         moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
 156                         if(moldyn->mfd<0) {
 157                                 perror("[moldyn] mfd open");
 158                                 return moldyn->mfd;
 159                         }
 160                         dprintf(moldyn->efd,"# total momentum log file\n");
 161                         break;
 162                 case SAVE_STEP:
 163                         moldyn->swrite=timer;
 164                         strncpy(moldyn->sfb,fb,63);
 165                         break;
 166                 case VISUAL_STEP:
 167                         moldyn->vwrite=timer;
 168                         strncpy(moldyn->vfb,fb,63);
 169                         visual_init(&(moldyn->vis),fb);
 170                         break;
 171                 default:
 172                         printf("unknown log mechanism: %02x\n",type);
 173                         return -1;
 174         }
 175
 176         return 0;
 177 }
 178
 179 int moldyn_log_shutdown(t_moldyn *moldyn) {
 180
 181         printf("[moldyn] log shutdown\n");
 182         if(moldyn->efd) close(moldyn->efd);
 183         if(moldyn->mfd) close(moldyn->mfd);
 184         if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 185
 186         return 0;
 187 }
 188
 189 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 190                    u8 attr,u8 bnum,int a,int b,int c) {
 191
 192         int count;
 193         int ret;
 194         t_3dvec origin;
 195
 196         count=a*b*c;
 197
 198         if(type==FCC) count*=4;
 199
 200         if(type==DIAMOND) count*=8;
 201
 202         moldyn->atom=malloc(count*sizeof(t_atom));
 203         if(moldyn->atom==NULL) {
 204                 perror("malloc (atoms)");
 205                 return -1;
 206         }
 207
 208         v3_zero(&origin);
 209
 210         switch(type) {
 211                 case FCC:
 212                         ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
 213                         break;
 214                 case DIAMOND:
 215                         ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
 216                         break;
 217                 default:
 218                         printf("unknown lattice type (%02x)\n",type);
 219                         return -1;
 220         }
 221
 222         /* debug */
 223         if(ret!=count) {
 224                 printf("ok, there is something wrong ...\n");
 225                 printf("calculated -> %d atoms\n",count);
 226                 printf("created -> %d atoms\n",ret);
 227                 return -1;
 228         }
 229
 230         moldyn->count=count;
 231         printf("[moldyn] created lattice with %d atoms\n",count);
 232
 233         while(count) {
 234                 count-=1;
 235                 moldyn->atom[count].element=element;
 236                 moldyn->atom[count].mass=mass;
 237                 moldyn->atom[count].attr=attr;
 238                 moldyn->atom[count].bnum=bnum;
 239                 check_per_bound(moldyn,&(moldyn->atom[count].r));
 240         }
 241
 242
 243         return ret;
 244 }
 245
 246 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 247              t_3dvec *r,t_3dvec *v) {
 248
 249         t_atom *atom;
 250         void *ptr;
 251         int count;
 252
 253         atom=moldyn->atom;
 254         count=++(moldyn->count);
 255
 256         ptr=realloc(atom,count*sizeof(t_atom));
 257         if(!ptr) {
 258                 perror("[moldyn] realloc (add atom)");
 259                 return -1;
 260         }
 261         moldyn->atom=ptr;
 262
 263         atom=moldyn->atom;
 264         atom[count-1].r=*r;
 265         atom[count-1].v=*v;
 266         atom[count-1].element=element;
 267         atom[count-1].mass=mass;
 268         atom[count-1].bnum=bnum;
 269         atom[count-1].attr=attr;
 270
 271         return 0;
 272 }
 273
 274 int destroy_atoms(t_moldyn *moldyn) {
 275
 276         if(moldyn->atom) free(moldyn->atom);
 277
 278         return 0;
 279 }
 280
 281 int thermal_init(t_moldyn *moldyn) {
 282
 283         /*
 284          * - gaussian distribution of velocities
 285          * - zero total momentum
 286          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 287          */
 288
 289         int i;
 290         double v,sigma;
 291         t_3dvec p_total,delta;
 292         t_atom *atom;
 293         t_random *random;
 294
 295         atom=moldyn->atom;
 296         random=&(moldyn->random);
 297
 298         /* gaussian distribution of velocities */
 299         v3_zero(&p_total);
 300         for(i=0;i<moldyn->count;i++) {
 301                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
 302                 /* x direction */
 303                 v=sigma*rand_get_gauss(random);
 304                 atom[i].v.x=v;
 305                 p_total.x+=atom[i].mass*v;
 306                 /* y direction */
 307                 v=sigma*rand_get_gauss(random);
 308                 atom[i].v.y=v;
 309                 p_total.y+=atom[i].mass*v;
 310                 /* z direction */
 311                 v=sigma*rand_get_gauss(random);
 312                 atom[i].v.z=v;
 313                 p_total.z+=atom[i].mass*v;
 314         }
 315
 316         /* zero total momentum */
 317         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 318         for(i=0;i<moldyn->count;i++) {
 319                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 320                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 321         }
 322
 323         /* velocity scaling */
 324         scale_velocity(moldyn,VSCALE_INIT_EQUI);
 325
 326         return 0;
 327 }
 328
 329 int scale_velocity(t_moldyn *moldyn,u8 type) {
 330
 331         int i;
 332         double e,scale;
 333         t_atom *atom;
 334         int count;
 335
 336         atom=moldyn->atom;
 337
 338         /*
 339          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 340          */
 341
 342         e=0.0;
 343         count=0;
 344         for(i=0;i<moldyn->count;i++) {
 345                 if(atom[i].attr&ATOM_ATTR_HB) {
 346                         e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 347                         count+=1;
 348                 }
 349         }
 350
 351         /* temporary hack for e,t = 0 */
 352         if(e==0.0) {
 353                 if(moldyn->t!=0.0)
 354                         thermal_init(moldyn);
 355                 else
 356                         return 0;
 357         }
 358
 359         /* direct scaling */
 360         scale=(1.5*count*K_BOLTZMANN*moldyn->t)/e;
 361         if(type&VSCALE_INIT_EQUI) scale*=2.0; /* equipartition theorem */
 362         scale=sqrt(scale);
 363         for(i=0;i<moldyn->count;i++)
 364                 if(atom[i].attr&ATOM_ATTR_HB)
 365                         v3_scale(&(atom[i].v),&(atom[i].v),scale);
 366
 367         return 0;
 368 }
 369
 370 double get_e_kin(t_moldyn *moldyn) {
 371
 372         int i;
 373         t_atom *atom;
 374
 375         atom=moldyn->atom;
 376         moldyn->ekin=0.0;
 377
 378         for(i=0;i<moldyn->count;i++)
 379                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 380
 381         return moldyn->ekin;
 382 }
 383
 384 double get_e_pot(t_moldyn *moldyn) {
 385
 386         return moldyn->energy;
 387 }
 388
 389 double update_e_kin(t_moldyn *moldyn) {
 390
 391         return(get_e_kin(moldyn));
 392 }
 393
 394 double get_total_energy(t_moldyn *moldyn) {
 395
 396         return(moldyn->ekin+moldyn->energy);
 397 }
 398
 399 t_3dvec get_total_p(t_moldyn *moldyn) {
 400
 401         t_3dvec p,p_total;
 402         int i;
 403         t_atom *atom;
 404
 405         atom=moldyn->atom;
 406
 407         v3_zero(&p_total);
 408         for(i=0;i<moldyn->count;i++) {
 409                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 410                 v3_add(&p_total,&p_total,&p);
 411         }
 412
 413         return p_total;
 414 }
 415
 416 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 417
 418         double tau;
 419
 420         /* nn_dist is the nearest neighbour distance */
 421
 422         if(moldyn->t==5.0) {
 423                 printf("[moldyn] i do not estimate timesteps below %f K!\n",
 424                        MOLDYN_CRITICAL_EST_TEMP);
 425                 return 23.42;
 426         }
 427
 428         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
 429
 430         return tau;
 431 }
 432
 433 /*
 434  * numerical tricks
 435  */
 436
 437 /* linked list / cell method */
 438
 439 int link_cell_init(t_moldyn *moldyn) {
 440
 441         t_linkcell *lc;
 442         int i;
 443         int fd;
 444
 445         fd=open("/dev/null",O_WRONLY);
 446
 447         lc=&(moldyn->lc);
 448
 449         /* partitioning the md cell */
 450         lc->nx=moldyn->dim.x/moldyn->cutoff;
 451         lc->x=moldyn->dim.x/lc->nx;
 452         lc->ny=moldyn->dim.y/moldyn->cutoff;
 453         lc->y=moldyn->dim.y/lc->ny;
 454         lc->nz=moldyn->dim.z/moldyn->cutoff;
 455         lc->z=moldyn->dim.z/lc->nz;
 456
 457         lc->cells=lc->nx*lc->ny*lc->nz;
 458         lc->subcell=malloc(lc->cells*sizeof(t_list));
 459
 460         printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 461
 462         for(i=0;i<lc->cells;i++)
 463                 //list_init(&(lc->subcell[i]),1);
 464                 list_init(&(lc->subcell[i]),fd);
 465
 466         link_cell_update(moldyn);
 467
 468         return 0;
 469 }
 470
 471 int link_cell_update(t_moldyn *moldyn) {
 472
 473         int count,i,j,k;
 474         int nx,ny,nz;
 475         t_atom *atom;
 476         t_linkcell *lc;
 477
 478         atom=moldyn->atom;
 479         lc=&(moldyn->lc);
 480
 481         nx=lc->nx;
 482         ny=lc->ny;
 483         nz=lc->nz;
 484
 485         for(i=0;i<lc->cells;i++)
 486                 list_destroy(&(moldyn->lc.subcell[i]));
 487
 488         for(count=0;count<moldyn->count;count++) {
 489                 i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
 490                 j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
 491                 k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
 492                 list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 493                                        &(atom[count]));
 494         }
 495
 496         return 0;
 497 }
 498
 499 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 500
 501         t_linkcell *lc;
 502         int a;
 503         int count1,count2;
 504         int ci,cj,ck;
 505         int nx,ny,nz;
 506         int x,y,z;
 507         u8 bx,by,bz;
 508
 509         lc=&(moldyn->lc);
 510         nx=lc->nx;
 511         ny=lc->ny;
 512         nz=lc->nz;
 513         count1=1;
 514         count2=27;
 515         a=nx*ny;
 516
 517         cell[0]=lc->subcell[i+j*nx+k*a];
 518         for(ci=-1;ci<=1;ci++) {
 519                 bx=0;
 520                 x=i+ci;
 521                 if((x<0)||(x>=nx)) {
 522                         x=(x+nx)%nx;
 523                         bx=1;
 524                 }
 525                 for(cj=-1;cj<=1;cj++) {
 526                         by=0;
 527                         y=j+cj;
 528                         if((y<0)||(y>=ny)) {
 529                                 y=(y+ny)%ny;
 530                                 by=1;
 531                         }
 532                         for(ck=-1;ck<=1;ck++) {
 533                                 bz=0;
 534                                 z=k+ck;
 535                                 if((z<0)||(z>=nz)) {
 536                                         z=(z+nz)%nz;
 537                                         bz=1;
 538                                 }
 539                                 if(!(ci|cj|ck)) continue;
 540                                 if(bx|by|bz) {
 541                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
 542                                 }
 543                                 else {
 544                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
 545                                 }
 546                         }
 547                 }
 548         }
 549
 550         lc->dnlc=count1;
 551         lc->countn=27;
 552
 553         return count2;
 554 }
 555
 556 int link_cell_shutdown(t_moldyn *moldyn) {
 557
 558         int i;
 559         t_linkcell *lc;
 560
 561         lc=&(moldyn->lc);
 562
 563         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 564                 list_shutdown(&(moldyn->lc.subcell[i]));
 565
 566         return 0;
 567 }
 568
 569 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 570
 571         int count;
 572         void *ptr;
 573         t_moldyn_schedule *schedule;
 574
 575         schedule=&(moldyn->schedule);
 576         count=++(schedule->content_count);
 577
 578         ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
 579         if(!ptr) {
 580                 perror("[moldyn] realloc (runs)");
 581                 return -1;
 582         }
 583         moldyn->schedule.runs=ptr;
 584         moldyn->schedule.runs[count-1]=runs;
 585
 586         ptr=realloc(schedule->tau,count*sizeof(double));
 587         if(!ptr) {
 588                 perror("[moldyn] realloc (tau)");
 589                 return -1;
 590         }
 591         moldyn->schedule.tau=ptr;
 592         moldyn->schedule.tau[count-1]=tau;
 593
 594         return 0;
 595 }
 596
 597 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 598
 599         moldyn->schedule.hook=hook;
 600         moldyn->schedule.hook_params=hook_params;
 601
 602         return 0;
 603 }
 604
 605 /*
 606  *
 607  * 'integration of newtons equation' - algorithms
 608  *
 609  */
 610
 611 /* start the integration */
 612
 613 int moldyn_integrate(t_moldyn *moldyn) {
 614
 615         int i,sched;
 616         unsigned int e,m,s,v;
 617         t_3dvec p;
 618         t_moldyn_schedule *schedule;
 619         t_atom *atom;
 620         int fd;
 621         char fb[128];
 622         double ds;
 623
 624         schedule=&(moldyn->schedule);
 625         atom=moldyn->atom;
 626
 627         /* initialize linked cell method */
 628         link_cell_init(moldyn);
 629
 630         /* logging & visualization */
 631         e=moldyn->ewrite;
 632         m=moldyn->mwrite;
 633         s=moldyn->swrite;
 634         v=moldyn->vwrite;
 635
 636         /* sqaure of some variables */
 637         moldyn->tau_square=moldyn->tau*moldyn->tau;
 638         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 639         /* calculate initial forces */
 640         potential_force_calc(moldyn);
 641
 642         /* do some checks before we actually start calculating bullshit */
 643         if(moldyn->cutoff>0.5*moldyn->dim.x)
 644                 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
 645         if(moldyn->cutoff>0.5*moldyn->dim.y)
 646                 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
 647         if(moldyn->cutoff>0.5*moldyn->dim.z)
 648                 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
 649         ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
 650         if(ds>0.05*moldyn->nnd)
 651                 printf("[moldyn] warning: forces too high / tau too small!\n");
 652
 653         /* zero absolute time */
 654         moldyn->time=0.0;
 655         for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 656
 657                 /* setting amount of runs and finite time step size */
 658                 moldyn->tau=schedule->tau[sched];
 659                 moldyn->tau_square=moldyn->tau*moldyn->tau;
 660                 moldyn->time_steps=schedule->runs[sched];
 661
 662         /* integration according to schedule */
 663
 664         for(i=0;i<moldyn->time_steps;i++) {
 665
 666                 /* integration step */
 667                 moldyn->integrate(moldyn);
 668
 669                 /* increase absolute time */
 670                 moldyn->time+=moldyn->tau;
 671
 672                 /* check for log & visualization */
 673                 if(e) {
 674                         if(!(i%e))
 675                                 dprintf(moldyn->efd,
 676                                         "%.15f %.45f %.45f %.45f\n",
 677                                         moldyn->time,update_e_kin(moldyn),
 678                                         moldyn->energy,
 679                                         get_total_energy(moldyn));
 680                 }
 681                 if(m) {
 682                         if(!(i%m)) {
 683                                 p=get_total_p(moldyn);
 684                                 dprintf(moldyn->mfd,
 685                                         "%.15f %.45f\n",moldyn->time,
 686                                         v3_norm(&p));
 687                         }
 688                 }
 689                 if(s) {
 690                         if(!(i%s)) {
 691                                 snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
 692                                          moldyn->t,i*moldyn->tau);
 693                                 fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
 694                                 if(fd<0) perror("[moldyn] save fd open");
 695                                 else {
 696                                         write(fd,moldyn,sizeof(t_moldyn));
 697                                         write(fd,moldyn->atom,
 698                                               moldyn->count*sizeof(t_atom));
 699                                 }
 700                                 close(fd);
 701                         }
 702                 }
 703                 if(v) {
 704                         if(!(i%v)) {
 705                                 visual_atoms(&(moldyn->vis),moldyn->time,
 706                                              moldyn->atom,moldyn->count);
 707                                 printf("\rsched: %d, steps: %d",sched,i);
 708                                 fflush(stdout);
 709                         }
 710                 }
 711
 712         }
 713
 714                 /* check for hooks */
 715                 if(schedule->hook)
 716                         schedule->hook(moldyn,schedule->hook_params);
 717
 718         }
 719
 720         return 0;
 721 }
 722
 723 /* velocity verlet */
 724
 725 int velocity_verlet(t_moldyn *moldyn) {
 726
 727         int i,count;
 728         double tau,tau_square;
 729         t_3dvec delta;
 730         t_atom *atom;
 731
 732         atom=moldyn->atom;
 733         count=moldyn->count;
 734         tau=moldyn->tau;
 735         tau_square=moldyn->tau_square;
 736
 737         for(i=0;i<count;i++) {
 738                 /* new positions */
 739                 v3_scale(&delta,&(atom[i].v),tau);
 740                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 741                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 742                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 743                 check_per_bound(moldyn,&(atom[i].r));
 744
 745                 /* velocities */
 746                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 747                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 748         }
 749
 750         /* neighbour list update */
 751         link_cell_update(moldyn);
 752
 753         /* forces depending on chosen potential */
 754         potential_force_calc(moldyn);
 755         //moldyn->potential_force_function(moldyn);
 756
 757         for(i=0;i<count;i++) {
 758                 /* again velocities */
 759                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 760                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 761         }
 762
 763         return 0;
 764 }
 765
 766
 767 /*
 768  *
 769  * potentials & corresponding forces
 770  *
 771  */
 772
 773 /* generic potential and force calculation */
 774
 775 int potential_force_calc(t_moldyn *moldyn) {
 776
 777         int i,j,k,count;
 778         t_atom *itom,*jtom,*ktom;
 779         t_linkcell *lc;
 780         t_list neighbour_i[27],neighbour_j[27];
 781         t_list *this,*that;
 782         u8 bc_ij,bc_ijk;
 783         int countn,dnlc;
 784
 785         count=moldyn->count;
 786         itom=moldyn->atom;
 787         lc=&(moldyn->lc);
 788
 789         /* reset energy */
 790         moldyn->energy=0.0;
 791
 792         for(i=0;i<count;i++) {
 793
 794                 /* reset force */
 795                 v3_zero(&(itom[i].f));
 796
 797                 /* single particle potential/force */
 798                 if(itom[i].attr&ATOM_ATTR_1BP)
 799                         moldyn->func1b(moldyn,&(itom[i]));
 800
 801                 /* 2 body pair potential/force */
 802                 if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 803
 804                         link_cell_neighbour_index(moldyn,
 805                                 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
 806                                 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
 807                                 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
 808                                 neighbour_i);
 809
 810                         countn=lc->countn;
 811                         dnlc=lc->dnlc;
 812
 813                         for(j=0;j<countn;j++) {
 814
 815                                 this=&(neighbour_i[j]);
 816                                 list_reset(this);
 817
 818                                 if(this->start==NULL)
 819                                         continue;
 820
 821                                 bc_ij=(j<dnlc)?0:1;
 822
 823                                 do {
 824                                         jtom=this->current->data;
 825
 826                                         if(jtom==&(itom[i]))
 827                                                 continue;
 828
 829                                         if((jtom->attr&ATOM_ATTR_2BP)&
 830                                            (itom[i].attr&ATOM_ATTR_2BP))
 831                                                 moldyn->func2b(moldyn,
 832                                                                &(itom[i]),
 833                                                                jtom,
 834                                                                bc_ij);
 835
 836                                         /* 3 body potential/force */
 837
 838                                         if(!(itom[i].attr&ATOM_ATTR_3BP)||
 839                                            !(jtom->attr&ATOM_ATTR_3BP))
 840                                                 continue;
 841
 842                                         link_cell_neighbour_index(moldyn,
 843                                            (jtom->r.x+moldyn->dim.x/2)/lc->x,
 844                                            (jtom->r.y+moldyn->dim.y/2)/lc->y,
 845                                            (jtom->r.z+moldyn->dim.z/2)/lc->z,
 846                                            neighbour_j);
 847
 848                                         /* neighbours of j */
 849                                         for(k=0;k<lc->countn;k++) {
 850
 851                                                 that=&(neighbour_j[k]);
 852                                                 list_reset(that);
 853
 854                                                 if(that->start==NULL)
 855                                                         continue;
 856
 857                                                 bc_ijk=(k<lc->dnlc)?0:1;
 858
 859                                                 do {
 860
 861                         ktom=that->current->data;
 862
 863                         if(!(ktom->attr&ATOM_ATTR_3BP))
 864                                 continue;
 865
 866                         if(ktom==jtom)
 867                                 continue;
 868
 869                         if(ktom==&(itom[i]))
 870                                 continue;
 871
 872                         moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
 873
 874                                                 } while(list_next(that)!=\
 875                                                         L_NO_NEXT_ELEMENT);
 876
 877                                         }
 878
 879                                         /* neighbours of i */
 880                                         for(k=0;k<countn;k++) {
 881
 882                                                 that=&(neighbour_i[k]);
 883                                                 list_reset(that);
 884
 885                                                 if(that->start==NULL)
 886                                                         continue;
 887
 888                                                 bc_ijk=(k<dnlc)?0:1;
 889
 890                                                 do {
 891
 892                         ktom=that->current->data;
 893
 894                         if(!(ktom->attr&ATOM_ATTR_3BP))
 895                                 continue;
 896
 897                         if(ktom==jtom)
 898                                 continue;
 899
 900                         if(ktom==&(itom[i]))
 901                                 continue;
 902
 903                         moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
 904
 905                                                 } while(list_next(that)!=\
 906                                                         L_NO_NEXT_ELEMENT);
 907
 908                                         }
 909
 910                                 } while(list_next(this)!=L_NO_NEXT_ELEMENT);
 911                         }
 912                 }
 913         }
 914
 915         return 0;
 916 }
 917
 918 /*
 919  * periodic boundayr checking
 920  */
 921
 922 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 923
 924         double x,y,z;
 925         t_3dvec *dim;
 926
 927         dim=&(moldyn->dim);
 928
 929         x=0.5*dim->x;
 930         y=0.5*dim->y;
 931         z=0.5*dim->z;
 932
 933         if(moldyn->status&MOLDYN_STAT_PBX) {
 934                 if(a->x>=x) a->x-=dim->x;
 935                 else if(-a->x>x) a->x+=dim->x;
 936         }
 937         if(moldyn->status&MOLDYN_STAT_PBY) {
 938                 if(a->y>=y) a->y-=dim->y;
 939                 else if(-a->y>y) a->y+=dim->y;
 940         }
 941         if(moldyn->status&MOLDYN_STAT_PBZ) {
 942                 if(a->z>=z) a->z-=dim->z;
 943                 else if(-a->z>z) a->z+=dim->z;
 944         }
 945
 946         return 0;
 947 }
 948
 949
 950 /*
 951  * example potentials
 952  */
 953
 954 /* harmonic oscillator potential and force */
 955
 956 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 957
 958         t_ho_params *params;
 959         t_3dvec force,distance;
 960         double d;
 961         double sc,equi_dist;
 962
 963         params=moldyn->pot2b_params;
 964         sc=params->spring_constant;
 965         equi_dist=params->equilibrium_distance;
 966
 967         v3_sub(&distance,&(ai->r),&(aj->r));
 968
 969         if(bc) check_per_bound(moldyn,&distance);
 970         d=v3_norm(&distance);
 971         if(d<=moldyn->cutoff) {
 972                 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
 973                 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
 974                 v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
 975                 v3_add(&(ai->f),&(ai->f),&force);
 976         }
 977
 978         return 0;
 979 }
 980
 981 /* lennard jones potential & force for one sort of atoms */
 982
 983 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 984
 985         t_lj_params *params;
 986         t_3dvec force,distance;
 987         double d,h1,h2;
 988         double eps,sig6,sig12;
 989
 990         params=moldyn->pot2b_params;
 991         eps=params->epsilon4;
 992         sig6=params->sigma6;
 993         sig12=params->sigma12;
 994
 995         v3_sub(&distance,&(ai->r),&(aj->r));
 996         if(bc) check_per_bound(moldyn,&distance);
 997         d=v3_absolute_square(&distance);        /* 1/r^2 */
 998         if(d<=moldyn->cutoff_square) {
 999                 d=1.0/d;                        /* 1/r^2 */
1000                 h2=d*d;                         /* 1/r^4 */
1001                 h2*=d;                          /* 1/r^6 */
1002                 h1=h2*h2;                       /* 1/r^12 */
1003                 /* energy is eps*..., but we will add this twice ... */
1004                 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
1005                 h2*=d;                          /* 1/r^8 */
1006                 h1*=d;                          /* 1/r^14 */
1007                 h2*=6*sig6;
1008                 h1*=12*sig12;
1009                 d=+h1-h2;
1010                 d*=eps;
1011                 v3_scale(&force,&distance,d);
1012                 v3_add(&(ai->f),&(ai->f),&force);
1013         }
1014
1015         return 0;
1016 }
1017
1018 /*
1019  * tersoff potential & force for 2 sorts of atoms
1020  */
1021
1022 /* create mixed terms from parameters and set them */
1023 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
1024
1025         printf("[moldyn] tersoff parameter completion\n");
1026         p->Smixed=sqrt(p->S[0]*p->S[1]);
1027         p->Rmixed=sqrt(p->R[0]*p->R[1]);
1028         p->Amixed=sqrt(p->A[0]*p->A[1]);
1029         p->Bmixed=sqrt(p->B[0]*p->B[1]);
1030         p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
1031         p->mu_m=0.5*(p->mu[0]+p->mu[1]);
1032
1033         return 0;
1034 }
1035
1036 /* tersoff 1 body part */
1037 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
1038
1039         int num;
1040         t_tersoff_mult_params *params;
1041         t_tersoff_exchange *exchange;
1042
1043         num=ai->bnum;
1044         params=moldyn->pot1b_params;
1045         exchange=&(params->exchange);
1046
1047         /*
1048          * simple: point constant parameters only depending on atom i to
1049          *         their right values
1050          */
1051
1052         exchange->beta=&(params->beta[num]);
1053         exchange->n=&(params->n[num]);
1054         exchange->c=&(params->c[num]);
1055         exchange->d=&(params->d[num]);
1056         exchange->h=&(params->h[num]);
1057
1058         exchange->betan=pow(*(exchange->beta),*(exchange->n));
1059         exchange->c2=params->c[num]*params->c[num];
1060         exchange->d2=params->d[num]*params->d[num];
1061         exchange->c2d2=exchange->c2/exchange->d2;
1062
1063         return 0;
1064 }
1065
1066 /* tersoff 2 body part */
1067 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1068
1069         t_tersoff_mult_params *params;
1070         t_tersoff_exchange *exchange;
1071         t_3dvec dist_ij,force;
1072         double d_ij;
1073         double A,B,R,S,lambda,mu;
1074         double f_r,df_r;
1075         double f_c,df_c;
1076         int num;
1077         double s_r;
1078         double arg;
1079         double scale;
1080
1081         params=moldyn->pot2b_params;
1082         num=ai->bnum;
1083         exchange=&(params->exchange);
1084
1085         exchange->run3bp=0;
1086
1087         /*
1088          * we need: f_c, df_c, f_r, df_r
1089          *
1090          * therefore we need: R, S, A, lambda
1091          */
1092
1093         v3_sub(&dist_ij,&(ai->r),&(aj->r));
1094
1095         if(bc) check_per_bound(moldyn,&dist_ij);
1096
1097         /* save for use in 3bp */ /* REALLY ?!?!?! */
1098         exchange->dist_ij=dist_ij;
1099
1100         /* constants */
1101         if(num==aj->bnum) {
1102                 S=params->S[num];
1103                 R=params->R[num];
1104                 A=params->A[num];
1105                 lambda=params->lambda[num];
1106                 /* more constants depending of atoms i and j, needed in 3bp */
1107                 params->exchange.B=&(params->B[num]);
1108                 params->exchange.mu=&(params->mu[num]);
1109                 mu=params->mu[num];
1110                 params->exchange.chi=1.0;
1111         }
1112         else {
1113                 S=params->Smixed;
1114                 R=params->Rmixed;
1115                 A=params->Amixed;
1116                 lambda=params->lambda_m;
1117                 /* more constants depending of atoms i and j, needed in 3bp */
1118                 params->exchange.B=&(params->Bmixed);
1119                 params->exchange.mu=&(params->mu_m);
1120                 mu=params->mu_m;
1121                 params->exchange.chi=params->chi;
1122         }
1123
1124         d_ij=v3_norm(&dist_ij);
1125
1126         /* save for use in 3bp */
1127         exchange->d_ij=d_ij;
1128
1129         if(d_ij>S)
1130                 return 0;
1131
1132         f_r=A*exp(-lambda*d_ij);
1133         df_r=-lambda*f_r/d_ij;
1134
1135         /* f_a, df_a calc + save for 3bp use */
1136         exchange->f_a=-B*exp(-mu*d_ij);
1137         exchange->df_a=-mu*exchange->f_a/d_ij;
1138
1139         if(d_ij<R) {
1140                 /* f_c = 1, df_c = 0 */
1141                 f_c=1.0;
1142                 df_c=0.0;
1143                 v3_scale(&force,&dist_ij,df_r);
1144         }
1145         else {
1146                 s_r=S-R;
1147                 arg=M_PI*(d_ij-R)/s_r;
1148                 f_c=0.5+0.5*cos(arg);
1149                 df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
1150                 scale=df_c*f_r+df_r*f_c;
1151                 v3_scale(&force,&dist_ij,scale);
1152         }
1153
1154         /* add forces */
1155         v3_add(&(ai->f),&(ai->f),&force);
1156         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1157         moldyn->energy+=(0.25*f_r*f_c);
1158
1159         /* save for use in 3bp */
1160         exchange->f_c=f_c;
1161         exchange->df_c=df_c;
1162
1163         /* enable the run of 3bp function */
1164         exchange->run3bp=1;
1165
1166         return 0;
1167 }
1168
1169 /* tersoff 3 body part */
1170
1171 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1172
1173         t_tersoff_mult_params *params;
1174         t_tersoff_exchange *exchange;
1175         t_3dvec dist_ij,dist_ik,dist_jk;
1176         t_3dvec temp,force;
1177         double R,S,s_r;
1178         double d_ij,d_ij2,d_ik,d_jk;
1179         double f_c,df_c,b_ij,f_a,df_a;
1180         double f_c_ik,df_c_ik,arg;
1181         double scale;
1182         double chi;
1183         double n,c,d,h,beta,betan;
1184         double c2,d2,c2d2;
1185         double numer,denom;
1186         double theta,cos_theta,sin_theta;
1187         double d_theta,d_theta1,d_theta2;
1188         double h_cos,h_cos2,d2_h_cos2;
1189         double frac1,bracket1,bracket2,bracket2_n_1,bracket2_n;
1190         double bracket3,bracket3_pow_1,bracket3_pow;
1191         int num;
1192
1193         params=moldyn->pot3b_params;
1194         num=ai->bnum;
1195         exchange=&(params->exchange);
1196
1197         if(!(exchange->run3bp))
1198                 return 0;
1199
1200         /*
1201          * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
1202          *
1203          * we got f_c, df_c, f_a, df_a from 2bp calculation
1204          */
1205
1206         d_ij=exchange->d_ij;
1207         d_ij2=exchange->d_ij2;
1208
1209         f_a=params->exchange.f_a;
1210         df_a=params->exchange.df_a;
1211
1212         /* d_ij is <= S, as we didn't return so far! */
1213
1214         /*
1215          * calc of b_ij (scalar) and db_ij (vector)
1216          *
1217          * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
1218          *
1219          * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
1220          *              w_ik,
1221          *
1222          */
1223
1224
1225         v3_sub(&dist_ik,&(ai->r),&(ak->r));
1226         if(bc) check_per_bound(moldyn,&dist_ik);
1227         d_ik=v3_norm(&dist_ik);
1228
1229         /* constants for f_c_ik calc */
1230         if(num==ak->bnum) {
1231                 R=params->R[num];
1232                 S=params->S[num];
1233         }
1234         else {
1235                 R=params->Rmixed;
1236                 S=params->Smixed;
1237         }
1238
1239         /* calc of f_c_ik */
1240         if(d_ik>S)
1241                 return 0;
1242
1243         if(d_ik<R) {
1244                 /* f_c_ik = 1, df_c_ik = 0 */
1245                 f_c_ik=1.0;
1246                 df_c_ik=0.0;
1247         }
1248         else {
1249                 s_r=S-R;
1250                 arg=M_PI*(d_ik-R)/s_r;
1251                 f_c_ik=0.5+0.5*cos(arg);
1252                 df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
1253         }
1254
1255         v3_sub(&dist_jk,&(aj->r),&(ak->r));
1256         if(bc) check_per_bound(moldyn,&dist_jk);
1257         d_jk=v3_norm(&dist_jk);
1258
1259         beta=*(exchange->beta);
1260         betan=exchange->betan;
1261         n=*(exchange->n);
1262         c=*(exchange->c);
1263         d=*(exchange->d);
1264         h=*(exchange->h);
1265         c2=exchange->c2;
1266         d2=exchange->d2;
1267         c2d2=exchange->c2d2;
1268
1269         numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
1270         denom=2*d_ij*d_ik;
1271         cos_theta=numer/denom;
1272         sin_theta=sqrt(1.0-(cos_theta*cos_theta));
1273         theta=acos(cos_theta);
1274         d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
1275         d_theta1=2*denom-numer*2*d_ik/d_ij;
1276         d_theta2=2*denom-numer*2*d_ij/d_ik;
1277         d_theta1*=d_theta;
1278         d_theta2*=d_theta;
1279
1280         h_cos=(h-cos_theta);
1281         h_cos2=h_cos*h_cos;
1282         d2_h_cos2=d2-h_cos2;
1283
1284         /* some usefull expressions */
1285         frac1=c2/(d2-h_cos2);
1286         bracket1=1+c2d2-frac1;
1287         bracket2=f_c_ik*bracket1;
1288         bracket2_n_1=pow(bracket2,n-1.0);
1289         bracket2_n=bracket2_n_1*bracket2;
1290         bracket3=1+betan*bracket2_n;
1291         bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
1292         bracket3_pow=bracket3_pow_1*bracket3;
1293
1294         /* now go on with calc of b_ij and derivation of b_ij */
1295         b_ij=chi*bracket3_pow;
1296
1297         /* derivation of theta */
1298         v3_scale(&force,&dist_ij,d_theta1);
1299         v3_scale(&temp,&dist_ik,d_theta2);
1300         v3_add(&force,&force,&temp);
1301
1302         /* part 1 of derivation of b_ij */
1303         v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1);
1304
1305         /* part 2 of derivation of b_ij */
1306         v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
1307
1308         /* sum up and scale ... */
1309         v3_add(&temp,&temp,&force);
1310         scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
1311         v3_scale(&temp,&temp,scale);
1312
1313         /* now construct an energy and a force out of that */
1314         v3_scale(&temp,&temp,f_a);
1315         v3_scale(&force,&dist_ij,df_a*b_ij);
1316         v3_add(&temp,&temp,&force);
1317         v3_scale(&temp,&temp,f_c);
1318         v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
1319         v3_add(&force,&force,&temp);
1320
1321         /* add forces */
1322         v3_add(&(ai->f),&(ai->f),&force);
1323         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1324         moldyn->energy+=(0.25*f_a*b_ij*f_c);
1325
1326         return 0;
1327 }
1328