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
 335         atom=moldyn->atom;
 336
 337         /*
 338          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 339          */
 340
 341         e=0.0;
 342         for(i=0;i<moldyn->count;i++)
 343                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 344         scale=(1.5*moldyn->count*K_BOLTZMANN*moldyn->t)/e;
 345         if(type&VSCALE_INIT_EQUI) scale*=2.0; /* equipartition theorem */
 346         scale=sqrt(scale);
 347         for(i=0;i<moldyn->count;i++)
 348                 v3_scale(&(atom[i].v),&(atom[i].v),scale);
 349
 350         return 0;
 351 }
 352
 353 double get_e_kin(t_moldyn *moldyn) {
 354
 355         int i;
 356         t_atom *atom;
 357
 358         atom=moldyn->atom;
 359         moldyn->ekin=0.0;
 360
 361         for(i=0;i<moldyn->count;i++)
 362                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 363
 364         return moldyn->ekin;
 365 }
 366
 367 double get_e_pot(t_moldyn *moldyn) {
 368
 369         return moldyn->energy;
 370 }
 371
 372 double update_e_kin(t_moldyn *moldyn) {
 373
 374         return(get_e_kin(moldyn));
 375 }
 376
 377 double get_total_energy(t_moldyn *moldyn) {
 378
 379         return(moldyn->ekin+moldyn->energy);
 380 }
 381
 382 t_3dvec get_total_p(t_moldyn *moldyn) {
 383
 384         t_3dvec p,p_total;
 385         int i;
 386         t_atom *atom;
 387
 388         atom=moldyn->atom;
 389
 390         v3_zero(&p_total);
 391         for(i=0;i<moldyn->count;i++) {
 392                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 393                 v3_add(&p_total,&p_total,&p);
 394         }
 395
 396         return p_total;
 397 }
 398
 399 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 400
 401         double tau;
 402
 403         /* nn_dist is the nearest neighbour distance */
 404
 405         if(moldyn->t==5.0) {
 406                 printf("[moldyn] i do not estimate timesteps below %f K!\n",
 407                        MOLDYN_CRITICAL_EST_TEMP);
 408                 return 23.42;
 409         }
 410
 411         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
 412
 413         return tau;
 414 }
 415
 416 /*
 417  * numerical tricks
 418  */
 419
 420 /* linked list / cell method */
 421
 422 int link_cell_init(t_moldyn *moldyn) {
 423
 424         t_linkcell *lc;
 425         int i;
 426         int fd;
 427
 428         fd=open("/dev/null",O_WRONLY);
 429
 430         lc=&(moldyn->lc);
 431
 432         /* partitioning the md cell */
 433         lc->nx=moldyn->dim.x/moldyn->cutoff;
 434         lc->x=moldyn->dim.x/lc->nx;
 435         lc->ny=moldyn->dim.y/moldyn->cutoff;
 436         lc->y=moldyn->dim.y/lc->ny;
 437         lc->nz=moldyn->dim.z/moldyn->cutoff;
 438         lc->z=moldyn->dim.z/lc->nz;
 439
 440         lc->cells=lc->nx*lc->ny*lc->nz;
 441         lc->subcell=malloc(lc->cells*sizeof(t_list));
 442
 443         printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 444
 445         for(i=0;i<lc->cells;i++)
 446                 //list_init(&(lc->subcell[i]),1);
 447                 list_init(&(lc->subcell[i]),fd);
 448
 449         link_cell_update(moldyn);
 450
 451         return 0;
 452 }
 453
 454 int link_cell_update(t_moldyn *moldyn) {
 455
 456         int count,i,j,k;
 457         int nx,ny,nz;
 458         t_atom *atom;
 459         t_linkcell *lc;
 460
 461         atom=moldyn->atom;
 462         lc=&(moldyn->lc);
 463
 464         nx=lc->nx;
 465         ny=lc->ny;
 466         nz=lc->nz;
 467
 468         for(i=0;i<lc->cells;i++)
 469                 list_destroy(&(moldyn->lc.subcell[i]));
 470
 471         for(count=0;count<moldyn->count;count++) {
 472                 i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
 473                 j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
 474                 k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
 475                 list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 476                                        &(atom[count]));
 477         }
 478
 479         return 0;
 480 }
 481
 482 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 483
 484         t_linkcell *lc;
 485         int a;
 486         int count1,count2;
 487         int ci,cj,ck;
 488         int nx,ny,nz;
 489         int x,y,z;
 490         u8 bx,by,bz;
 491
 492         lc=&(moldyn->lc);
 493         nx=lc->nx;
 494         ny=lc->ny;
 495         nz=lc->nz;
 496         count1=1;
 497         count2=27;
 498         a=nx*ny;
 499
 500
 501         cell[0]=lc->subcell[i+j*nx+k*a];
 502         for(ci=-1;ci<=1;ci++) {
 503                 bx=0;
 504                 x=i+ci;
 505                 if((x<0)||(x>=nx)) {
 506                         x=(x+nx)%nx;
 507                         bx=1;
 508                 }
 509                 for(cj=-1;cj<=1;cj++) {
 510                         by=0;
 511                         y=j+cj;
 512                         if((y<0)||(y>=ny)) {
 513                                 y=(y+ny)%ny;
 514                                 by=1;
 515                         }
 516                         for(ck=-1;ck<=1;ck++) {
 517                                 bz=0;
 518                                 z=k+ck;
 519                                 if((z<0)||(z>=nz)) {
 520                                         z=(z+nz)%nz;
 521                                         bz=1;
 522                                 }
 523                                 if(!(ci|cj|ck)) continue;
 524                                 if(bx|by|bz) {
 525                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
 526                                 }
 527                                 else {
 528                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
 529                                 }
 530                         }
 531                 }
 532         }
 533
 534         lc->dnlc=count1;
 535         lc->countn=27;
 536
 537         return count2;
 538 }
 539
 540 int link_cell_shutdown(t_moldyn *moldyn) {
 541
 542         int i;
 543         t_linkcell *lc;
 544
 545         lc=&(moldyn->lc);
 546
 547         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 548                 list_shutdown(&(moldyn->lc.subcell[i]));
 549
 550         return 0;
 551 }
 552
 553 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 554
 555         int count;
 556         void *ptr;
 557         t_moldyn_schedule *schedule;
 558
 559         schedule=&(moldyn->schedule);
 560         count=++(schedule->content_count);
 561
 562         ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
 563         if(!ptr) {
 564                 perror("[moldyn] realloc (runs)");
 565                 return -1;
 566         }
 567         moldyn->schedule.runs=ptr;
 568         moldyn->schedule.runs[count-1]=runs;
 569
 570         ptr=realloc(schedule->tau,count*sizeof(double));
 571         if(!ptr) {
 572                 perror("[moldyn] realloc (tau)");
 573                 return -1;
 574         }
 575         moldyn->schedule.tau=ptr;
 576         moldyn->schedule.tau[count-1]=tau;
 577
 578         return 0;
 579 }
 580
 581 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 582
 583         moldyn->schedule.hook=hook;
 584         moldyn->schedule.hook_params=hook_params;
 585
 586         return 0;
 587 }
 588
 589 /*
 590  *
 591  * 'integration of newtons equation' - algorithms
 592  *
 593  */
 594
 595 /* start the integration */
 596
 597 int moldyn_integrate(t_moldyn *moldyn) {
 598
 599         int i,sched;
 600         unsigned int e,m,s,v;
 601         t_3dvec p;
 602         t_moldyn_schedule *schedule;
 603         t_atom *atom;
 604         int fd;
 605         char fb[128];
 606         double ds;
 607
 608         schedule=&(moldyn->schedule);
 609         atom=moldyn->atom;
 610
 611         /* initialize linked cell method */
 612         link_cell_init(moldyn);
 613
 614         /* logging & visualization */
 615         e=moldyn->ewrite;
 616         m=moldyn->mwrite;
 617         s=moldyn->swrite;
 618         v=moldyn->vwrite;
 619
 620         /* sqaure of some variables */
 621         moldyn->tau_square=moldyn->tau*moldyn->tau;
 622         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 623         /* calculate initial forces */
 624         potential_force_calc(moldyn);
 625
 626         /* do some checks before we actually start calculating bullshit */
 627         if(moldyn->cutoff>0.5*moldyn->dim.x)
 628                 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
 629         if(moldyn->cutoff>0.5*moldyn->dim.y)
 630                 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
 631         if(moldyn->cutoff>0.5*moldyn->dim.z)
 632                 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
 633         ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
 634         if(ds>0.05*moldyn->nnd)
 635                 printf("[moldyn] warning: forces too high / tau too small!\n");
 636
 637         /* zero absolute time */
 638         moldyn->time=0.0;
 639
 640         for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 641
 642                 /* setting amount of runs and finite time step size */
 643                 moldyn->tau=schedule->tau[sched];
 644                 moldyn->tau_square=moldyn->tau*moldyn->tau;
 645                 moldyn->time_steps=schedule->runs[sched];
 646
 647         /* integration according to schedule */
 648
 649         for(i=0;i<moldyn->time_steps;i++) {
 650
 651                 /* integration step */
 652                 moldyn->integrate(moldyn);
 653
 654                 /* increase absolute time */
 655                 moldyn->time+=moldyn->tau;
 656
 657                 /* check for log & visualization */
 658                 if(e) {
 659                         if(!(i%e))
 660                                 dprintf(moldyn->efd,
 661                                         "%.15f %.45f %.45f %.45f\n",
 662                                         moldyn->time,update_e_kin(moldyn),
 663                                         moldyn->energy,
 664                                         get_total_energy(moldyn));
 665                 }
 666                 if(m) {
 667                         if(!(i%m)) {
 668                                 p=get_total_p(moldyn);
 669                                 dprintf(moldyn->mfd,
 670                                         "%.15f %.45f\n",moldyn->time,
 671                                         v3_norm(&p));
 672                         }
 673                 }
 674                 if(s) {
 675                         if(!(i%s)) {
 676                                 snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
 677                                          moldyn->t,i*moldyn->tau);
 678                                 fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
 679                                 if(fd<0) perror("[moldyn] save fd open");
 680                                 else {
 681                                         write(fd,moldyn,sizeof(t_moldyn));
 682                                         write(fd,moldyn->atom,
 683                                               moldyn->count*sizeof(t_atom));
 684                                 }
 685                                 close(fd);
 686                         }
 687                 }
 688                 if(v) {
 689                         if(!(i%v)) {
 690                                 visual_atoms(&(moldyn->vis),moldyn->time,
 691                                              moldyn->atom,moldyn->count);
 692                                 printf("\rsched: %d, steps: %d",sched,i);
 693                                 fflush(stdout);
 694                         }
 695                 }
 696
 697         }
 698
 699                 /* check for hooks */
 700                 if(schedule->hook)
 701                         schedule->hook(moldyn,schedule->hook_params);
 702
 703         }
 704
 705         return 0;
 706 }
 707
 708 /* velocity verlet */
 709
 710 int velocity_verlet(t_moldyn *moldyn) {
 711
 712         int i,count;
 713         double tau,tau_square;
 714         t_3dvec delta;
 715         t_atom *atom;
 716
 717         atom=moldyn->atom;
 718         count=moldyn->count;
 719         tau=moldyn->tau;
 720         tau_square=moldyn->tau_square;
 721
 722         for(i=0;i<count;i++) {
 723                 /* new positions */
 724                 v3_scale(&delta,&(atom[i].v),tau);
 725                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 726                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 727                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 728                 check_per_bound(moldyn,&(atom[i].r));
 729
 730                 /* velocities */
 731                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 732                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 733         }
 734
 735         /* neighbour list update */
 736         link_cell_update(moldyn);
 737
 738         /* forces depending on chosen potential */
 739         potential_force_calc(moldyn);
 740         //moldyn->potential_force_function(moldyn);
 741
 742         for(i=0;i<count;i++) {
 743                 /* again velocities */
 744                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 745                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 746         }
 747
 748         return 0;
 749 }
 750
 751
 752 /*
 753  *
 754  * potentials & corresponding forces
 755  *
 756  */
 757
 758 /* generic potential and force calculation */
 759
 760 int potential_force_calc(t_moldyn *moldyn) {
 761
 762         int i,j,k,count;
 763         t_atom *atom,*btom,*ktom;
 764         t_linkcell *lc;
 765         t_list neighbour[27];
 766         t_list *this,*thisk,*neighbourk;
 767         u8 bc,bck;
 768         int countn,dnlc;
 769
 770         count=moldyn->count;
 771         atom=moldyn->atom;
 772         lc=&(moldyn->lc);
 773
 774         /* reset energy */
 775         moldyn->energy=0.0;
 776
 777         for(i=0;i<count;i++) {
 778
 779                 /* reset force */
 780                 v3_zero(&(atom[i].f));
 781
 782                 /* single particle potential/force */
 783                 if(atom[i].attr&ATOM_ATTR_1BP)
 784                         moldyn->func1b(moldyn,&(atom[i]));
 785
 786                 /* 2 body pair potential/force */
 787                 if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 788
 789                         link_cell_neighbour_index(moldyn,
 790                                 (atom[i].r.x+moldyn->dim.x/2)/lc->x,
 791                                 (atom[i].r.y+moldyn->dim.y/2)/lc->y,
 792                                 (atom[i].r.z+moldyn->dim.z/2)/lc->z,
 793                                 neighbour);
 794
 795                         countn=lc->countn;
 796                         dnlc=lc->dnlc;
 797
 798                         for(j=0;j<countn;j++) {
 799
 800                                 this=&(neighbour[j]);
 801                                 list_reset(this);
 802
 803                                 if(this->start==NULL)
 804                                         continue;
 805
 806                                 bc=(j<dnlc)?0:1;
 807
 808                                 do {
 809                                         btom=this->current->data;
 810
 811                                         if(btom==&(atom[i]))
 812                                                 continue;
 813
 814                                         if((btom->attr&ATOM_ATTR_2BP)&
 815                                            (atom[i].attr&ATOM_ATTR_2BP))
 816                                                 moldyn->func2b(moldyn,
 817                                                                &(atom[i]),
 818                                                                btom,
 819                                                                bc);
 820
 821                                         /* 3 body potential/force */
 822
 823                                         if(!(atom[i].attr&ATOM_ATTR_3BP)||
 824                                            !(btom->attr&ATOM_ATTR_3BP))
 825                                                 continue;
 826
 827 printf("DEBUG: problem exists here ...\n");
 828                                         link_cell_neighbour_index(moldyn,
 829                                            (btom->r.x+moldyn->dim.x/2)/lc->x,
 830                                            (btom->r.y+moldyn->dim.y/2)/lc->y,
 831                                            (btom->r.z+moldyn->dim.z/2)/lc->z,
 832                                            neighbourk);
 833 printf("DEBUG: as you won't see that!\n");
 834
 835                                         for(k=0;k<lc->countn;k++) {
 836
 837                                                 thisk=&(neighbourk[k]);
 838                                                 list_reset(thisk);
 839
 840                                                 if(thisk->start==NULL)
 841                                                         continue;
 842
 843                                                 bck=(k<lc->dnlc)?0:1;
 844
 845                                                 do {
 846
 847                         ktom=thisk->current->data;
 848
 849                         if(!(ktom->attr&ATOM_ATTR_3BP))
 850                                 continue;
 851
 852                         if(ktom==btom)
 853                                 continue;
 854
 855                         if(ktom==&(atom[i]))
 856                                 continue;
 857
 858                         moldyn->func3b(moldyn,&(atom[i]),btom,ktom,bck);
 859
 860                                                 } while(list_next(thisk)!=\
 861                                                         L_NO_NEXT_ELEMENT);
 862
 863                                         }
 864
 865                                 } while(list_next(this)!=L_NO_NEXT_ELEMENT);
 866                         }
 867                 }
 868         }
 869
 870         return 0;
 871 }
 872
 873 /*
 874  * periodic boundayr checking
 875  */
 876
 877 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 878
 879         double x,y,z;
 880         t_3dvec *dim;
 881
 882         dim=&(moldyn->dim);
 883
 884         x=0.5*dim->x;
 885         y=0.5*dim->y;
 886         z=0.5*dim->z;
 887
 888         if(moldyn->status&MOLDYN_STAT_PBX) {
 889                 if(a->x>=x) a->x-=dim->x;
 890                 else if(-a->x>x) a->x+=dim->x;
 891         }
 892         if(moldyn->status&MOLDYN_STAT_PBY) {
 893                 if(a->y>=y) a->y-=dim->y;
 894                 else if(-a->y>y) a->y+=dim->y;
 895         }
 896         if(moldyn->status&MOLDYN_STAT_PBZ) {
 897                 if(a->z>=z) a->z-=dim->z;
 898                 else if(-a->z>z) a->z+=dim->z;
 899         }
 900
 901         return 0;
 902 }
 903
 904
 905 /*
 906  * example potentials
 907  */
 908
 909 /* harmonic oscillator potential and force */
 910
 911 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 912
 913         t_ho_params *params;
 914         t_3dvec force,distance;
 915         double d;
 916         double sc,equi_dist;
 917
 918         params=moldyn->pot2b_params;
 919         sc=params->spring_constant;
 920         equi_dist=params->equilibrium_distance;
 921
 922         v3_sub(&distance,&(ai->r),&(aj->r));
 923
 924         if(bc) check_per_bound(moldyn,&distance);
 925         d=v3_norm(&distance);
 926         if(d<=moldyn->cutoff) {
 927                 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
 928                 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
 929                 v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
 930                 v3_add(&(ai->f),&(ai->f),&force);
 931         }
 932
 933         return 0;
 934 }
 935
 936 /* lennard jones potential & force for one sort of atoms */
 937
 938 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 939
 940         t_lj_params *params;
 941         t_3dvec force,distance;
 942         double d,h1,h2;
 943         double eps,sig6,sig12;
 944
 945         params=moldyn->pot2b_params;
 946         eps=params->epsilon4;
 947         sig6=params->sigma6;
 948         sig12=params->sigma12;
 949
 950         v3_sub(&distance,&(ai->r),&(aj->r));
 951         if(bc) check_per_bound(moldyn,&distance);
 952         d=v3_absolute_square(&distance);        /* 1/r^2 */
 953         if(d<=moldyn->cutoff_square) {
 954                 d=1.0/d;                        /* 1/r^2 */
 955                 h2=d*d;                         /* 1/r^4 */
 956                 h2*=d;                          /* 1/r^6 */
 957                 h1=h2*h2;                       /* 1/r^12 */
 958                 /* energy is eps*..., but we will add this twice ... */
 959                 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
 960                 h2*=d;                          /* 1/r^8 */
 961                 h1*=d;                          /* 1/r^14 */
 962                 h2*=6*sig6;
 963                 h1*=12*sig12;
 964                 d=+h1-h2;
 965                 d*=eps;
 966                 v3_scale(&force,&distance,d);
 967                 v3_add(&(ai->f),&(ai->f),&force);
 968         }
 969
 970         return 0;
 971 }
 972
 973 /*
 974  * tersoff potential & force for 2 sorts of atoms
 975  */
 976
 977 /* create mixed terms from parameters and set them */
 978 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
 979
 980         printf("[moldyn] tersoff parameter completion\n");
 981         p->Smixed=sqrt(p->S[0]*p->S[1]);
 982         p->Rmixed=sqrt(p->R[0]*p->R[1]);
 983         p->Amixed=sqrt(p->A[0]*p->A[1]);
 984         p->Bmixed=sqrt(p->B[0]*p->B[1]);
 985         p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
 986         p->mu_m=0.5*(p->mu[0]+p->mu[1]);
 987
 988         return 0;
 989 }
 990
 991 /* tersoff 1 body part */
 992 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
 993
 994         int num;
 995         t_tersoff_mult_params *params;
 996         t_tersoff_exchange *exchange;
 997
 998         num=ai->bnum;
 999         params=moldyn->pot1b_params;
1000         exchange=&(params->exchange);
1001
1002         /*
1003          * simple: point constant parameters only depending on atom i to
1004          *         their right values
1005          */
1006
1007         exchange->beta=&(params->beta[num]);
1008         exchange->n=&(params->n[num]);
1009         exchange->c=&(params->c[num]);
1010         exchange->d=&(params->d[num]);
1011         exchange->h=&(params->h[num]);
1012
1013         exchange->betan=pow(*(exchange->beta),*(exchange->n));
1014         exchange->c2=params->c[num]*params->c[num];
1015         exchange->d2=params->d[num]*params->d[num];
1016         exchange->c2d2=exchange->c2/exchange->d2;
1017
1018         return 0;
1019 }
1020
1021 /* tersoff 2 body part */
1022 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1023
1024         t_tersoff_mult_params *params;
1025         t_tersoff_exchange *exchange;
1026         t_3dvec dist_ij,force;
1027         double d_ij;
1028         double A,B,R,S,lambda,mu;
1029         double f_r,df_r;
1030         double f_c,df_c;
1031         int num;
1032         double s_r;
1033         double arg;
1034         double scale;
1035
1036         params=moldyn->pot2b_params;
1037         num=ai->bnum;
1038         exchange=&(params->exchange);
1039
1040         exchange->run3bp=0;
1041
1042         /*
1043          * we need: f_c, df_c, f_r, df_r
1044          *
1045          * therefore we need: R, S, A, lambda
1046          */
1047
1048         v3_sub(&dist_ij,&(ai->r),&(aj->r));
1049
1050         if(bc) check_per_bound(moldyn,&dist_ij);
1051
1052         /* save for use in 3bp */ /* REALLY ?!?!?! */
1053         exchange->dist_ij=dist_ij;
1054
1055         /* constants */
1056         if(num==aj->bnum) {
1057                 S=params->S[num];
1058                 R=params->R[num];
1059                 A=params->A[num];
1060                 lambda=params->lambda[num];
1061                 /* more constants depending of atoms i and j, needed in 3bp */
1062                 params->exchange.B=&(params->B[num]);
1063                 params->exchange.mu=&(params->mu[num]);
1064                 mu=params->mu[num];
1065                 params->exchange.chi=1.0;
1066         }
1067         else {
1068                 S=params->Smixed;
1069                 R=params->Rmixed;
1070                 A=params->Amixed;
1071                 lambda=params->lambda_m;
1072                 /* more constants depending of atoms i and j, needed in 3bp */
1073                 params->exchange.B=&(params->Bmixed);
1074                 params->exchange.mu=&(params->mu_m);
1075                 mu=params->mu_m;
1076                 params->exchange.chi=params->chi;
1077         }
1078
1079         d_ij=v3_norm(&dist_ij);
1080
1081         /* save for use in 3bp */
1082         exchange->d_ij=d_ij;
1083
1084         if(d_ij>S)
1085                 return 0;
1086
1087         f_r=A*exp(-lambda*d_ij);
1088         df_r=-lambda*f_r/d_ij;
1089
1090         /* f_a, df_a calc + save for 3bp use */
1091         exchange->f_a=-B*exp(-mu*d_ij);
1092         exchange->df_a=-mu*exchange->f_a/d_ij;
1093
1094         if(d_ij<R) {
1095                 /* f_c = 1, df_c = 0 */
1096                 f_c=1.0;
1097                 df_c=0.0;
1098                 v3_scale(&force,&dist_ij,df_r);
1099         }
1100         else {
1101                 s_r=S-R;
1102                 arg=M_PI*(d_ij-R)/s_r;
1103                 f_c=0.5+0.5*cos(arg);
1104                 df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
1105                 scale=df_c*f_r+df_r*f_c;
1106                 v3_scale(&force,&dist_ij,scale);
1107         }
1108
1109         /* add forces */
1110         v3_add(&(ai->f),&(ai->f),&force);
1111         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1112         moldyn->energy+=(0.25*f_r*f_c);
1113
1114         /* save for use in 3bp */
1115         exchange->f_c=f_c;
1116         exchange->df_c=df_c;
1117
1118         /* enable the run of 3bp function */
1119         exchange->run3bp=1;
1120
1121         return 0;
1122 }
1123
1124 /* tersoff 3 body part */
1125
1126 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1127
1128         t_tersoff_mult_params *params;
1129         t_tersoff_exchange *exchange;
1130         t_3dvec dist_ij,dist_ik,dist_jk;
1131         t_3dvec temp,force;
1132         double R,S,s_r;
1133         double d_ij,d_ij2,d_ik,d_jk;
1134         double f_c,df_c,b_ij,f_a,df_a;
1135         double f_c_ik,df_c_ik,arg;
1136         double scale;
1137         double chi;
1138         double n,c,d,h,beta,betan;
1139         double c2,d2,c2d2;
1140         double numer,denom;
1141         double theta,cos_theta,sin_theta;
1142         double d_theta,d_theta1,d_theta2;
1143         double h_cos,h_cos2,d2_h_cos2;
1144         double frac1,bracket1,bracket2,bracket2_n_1,bracket2_n;
1145         double bracket3,bracket3_pow_1,bracket3_pow;
1146         int num;
1147
1148         params=moldyn->pot3b_params;
1149         num=ai->bnum;
1150         exchange=&(params->exchange);
1151
1152         if(!(exchange->run3bp))
1153                 return 0;
1154
1155         /*
1156          * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
1157          *
1158          * we got f_c, df_c, f_a, df_a from 2bp calculation
1159          */
1160
1161         d_ij=exchange->d_ij;
1162         d_ij2=exchange->d_ij2;
1163
1164         f_a=params->exchange.f_a;
1165         df_a=params->exchange.df_a;
1166
1167         /* d_ij is <= S, as we didn't return so far! */
1168
1169         /*
1170          * calc of b_ij (scalar) and db_ij (vector)
1171          *
1172          * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
1173          *
1174          * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
1175          *              w_ik,
1176          *
1177          */
1178
1179
1180         v3_sub(&dist_ik,&(ai->r),&(ak->r));
1181         if(bc) check_per_bound(moldyn,&dist_ik);
1182         d_ik=v3_norm(&dist_ik);
1183
1184         /* constants for f_c_ik calc */
1185         if(num==ak->bnum) {
1186                 R=params->R[num];
1187                 S=params->S[num];
1188         }
1189         else {
1190                 R=params->Rmixed;
1191                 S=params->Smixed;
1192         }
1193
1194         /* calc of f_c_ik */
1195         if(d_ik>S)
1196                 return 0;
1197
1198         if(d_ik<R) {
1199                 /* f_c_ik = 1, df_c_ik = 0 */
1200                 f_c_ik=1.0;
1201                 df_c_ik=0.0;
1202         }
1203         else {
1204                 s_r=S-R;
1205                 arg=M_PI*(d_ik-R)/s_r;
1206                 f_c_ik=0.5+0.5*cos(arg);
1207                 df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
1208         }
1209
1210         v3_sub(&dist_jk,&(aj->r),&(ak->r));
1211         if(bc) check_per_bound(moldyn,&dist_jk);
1212         d_jk=v3_norm(&dist_jk);
1213
1214         beta=*(exchange->beta);
1215         betan=exchange->betan;
1216         n=*(exchange->n);
1217         c=*(exchange->c);
1218         d=*(exchange->d);
1219         h=*(exchange->h);
1220         c2=exchange->c2;
1221         d2=exchange->d2;
1222         c2d2=exchange->c2d2;
1223
1224         numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
1225         denom=2*d_ij*d_ik;
1226         cos_theta=numer/denom;
1227         sin_theta=sqrt(1.0-(cos_theta*cos_theta));
1228         theta=acos(cos_theta);
1229         d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
1230         d_theta1=2*denom-numer*2*d_ik/d_ij;
1231         d_theta2=2*denom-numer*2*d_ij/d_ik;
1232         d_theta1*=d_theta;
1233         d_theta2*=d_theta;
1234
1235         h_cos=(h-cos_theta);
1236         h_cos2=h_cos*h_cos;
1237         d2_h_cos2=d2-h_cos2;
1238
1239         /* some usefull expressions */
1240         frac1=c2/(d2-h_cos2);
1241         bracket1=1+c2d2-frac1;
1242         bracket2=f_c_ik*bracket1;
1243         bracket2_n_1=pow(bracket2,n-1.0);
1244         bracket2_n=bracket2_n_1*bracket2;
1245         bracket3=1+betan*bracket2_n;
1246         bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
1247         bracket3_pow=bracket3_pow_1*bracket3;
1248
1249         /* now go on with calc of b_ij and derivation of b_ij */
1250         b_ij=chi*bracket3_pow;
1251
1252         /* derivation of theta */
1253         v3_scale(&force,&dist_ij,d_theta1);
1254         v3_scale(&temp,&dist_ik,d_theta2);
1255         v3_add(&force,&force,&temp);
1256
1257         /* part 1 of derivation of b_ij */
1258         v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1);
1259
1260         /* part 2 of derivation of b_ij */
1261         v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
1262
1263         /* sum up and scale ... */
1264         v3_add(&temp,&temp,&force);
1265         scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
1266         v3_scale(&temp,&temp,scale);
1267
1268         /* now construct an energy and a force out of that */
1269         v3_scale(&temp,&temp,f_a);
1270         v3_scale(&force,&dist_ij,df_a*b_ij);
1271         v3_add(&temp,&temp,&force);
1272         v3_scale(&temp,&temp,f_c);
1273         v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
1274         v3_add(&force,&force,&temp);
1275
1276         /* add forces */
1277         v3_add(&(ai->f),&(ai->f),&force);
1278         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1279         moldyn->energy+=(0.25*f_a*b_ij*f_c);
1280
1281         return 0;
1282 }
1283