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