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 int moldyn_usage(char **argv) {
  27
  28         printf("\n%s usage:\n\n",argv[0]);
  29         printf("--- general options ---\n");
  30         printf("-E <steps> <file> (log total energy)\n");
  31         printf("-M <steps> <file> (log total momentum)\n");
  32         printf("-D <steps> <file> (dump total information)\n");
  33         printf("-S <steps> <filebase> (single save file)\n");
  34         printf("-V <steps> <filebase> (rasmol file)\n");
  35         printf("--- physics options ---\n");
  36         printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
  37         printf("-t <timestep tau> [s] (%.15f)\n",MOLDYN_TAU);
  38         printf("-C <cutoff radius> [m] (%.15f)\n",MOLDYN_CUTOFF);
  39         printf("-R <runs> (%d)\n",MOLDYN_RUNS);
  40         printf(" -- integration algo --\n");
  41         printf("  -I <number> (%d)\n",MOLDYN_INTEGRATE_DEFAULT);
  42         printf("     0: velocity verlet\n");
  43         printf(" -- potential --\n");
  44         printf("  -P <number> <param1 param2 ...>\n");
  45         printf("     0: harmonic oscillator\n");
  46         printf("        param1: spring constant\n");
  47         printf("        param2: equilibrium distance\n");
  48         printf("     1: lennard jones\n");
  49         printf("        param1: epsilon\n");
  50         printf("        param2: sigma\n");
  51         printf("\n");
  52
  53         return 0;
  54 }
  55
  56 int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
  57
  58         int i;
  59
  60         memset(moldyn,0,sizeof(t_moldyn));
  61
  62         /* default values */
  63         moldyn->t=MOLDYN_TEMP;
  64         moldyn->tau=MOLDYN_TAU;
  65         moldyn->time_steps=MOLDYN_RUNS;
  66         moldyn->integrate=velocity_verlet;
  67
  68         /* parse argv */
  69         for(i=1;i<argc;i++) {
  70                 if(argv[i][0]=='-') {
  71                         switch(argv[i][1]){
  72                                 case 'E':
  73                                         moldyn->ewrite=atoi(argv[++i]);
  74                                         strncpy(moldyn->efb,argv[++i],64);
  75                                         break;
  76                                 case 'M':
  77                                         moldyn->mwrite=atoi(argv[++i]);
  78                                         strncpy(moldyn->mfb,argv[++i],64);
  79                                         break;
  80                                 case 'S':
  81                                         moldyn->swrite=atoi(argv[++i]);
  82                                         strncpy(moldyn->sfb,argv[++i],64);
  83                                         break;
  84                                 case 'V':
  85                                         moldyn->vwrite=atoi(argv[++i]);
  86                                         strncpy(moldyn->vfb,argv[++i],64);
  87                                         break;
  88                                 case 'T':
  89                                         moldyn->t=atof(argv[++i]);
  90                                         break;
  91                                 case 't':
  92                                         moldyn->tau=atof(argv[++i]);
  93                                         break;
  94                                 case 'C':
  95                                         moldyn->cutoff=atof(argv[++i]);
  96                                         break;
  97                                 case 'R':
  98                                         moldyn->time_steps=atoi(argv[++i]);
  99                                         break;
 100                                 case 'I':
 101         /* integration algorithm */
 102         switch(atoi(argv[++i])) {
 103                 case MOLDYN_INTEGRATE_VERLET:
 104                         moldyn->integrate=velocity_verlet;
 105                         break;
 106                 default:
 107                         printf("unknown integration algo %s\n",argv[i]);
 108                         moldyn_usage(argv);
 109                         return -1;
 110         }
 111
 112                                 case 'P':
 113         /* potential + params */
 114         switch(atoi(argv[++i])) {
 115                 case MOLDYN_POTENTIAL_HO:
 116                         hop.spring_constant=atof(argv[++i]);
 117                         hop.equilibrium_distance=atof(argv[++i]);
 118                         moldyn->pot_params=malloc(sizeof(t_ho_params));
 119                         memcpy(moldyn->pot_params,&hop,sizeof(t_ho_params));
 120                         moldyn->potential_force_function=harmonic_oscillator;
 121                         break;
 122                 case MOLDYN_POTENTIAL_LJ:
 123                         e=atof(argv[++i]);
 124                         s=atof(argv[++i]);
 125                         ljp.epsilon4=4*e;
 126                         ljp.sigma6=s*s*s*s*s*s;
 127                         ljp.sigma12=ljp.sigma6*ljp.sigma6;
 128                         moldyn->pot_params=malloc(sizeof(t_lj_params));
 129                         memcpy(moldyn->pot_params,&ljp,sizeof(t_lj_params));
 130                         moldyn->potential_force_function=lennard_jones;
 131                         break;
 132                 default:
 133                         printf("unknown potential %s\n",argv[i]);
 134                         moldyn_usage(argv);
 135                         return -1;
 136         }
 137
 138                                 default:
 139                                         printf("unknown option %s\n",argv[i]);
 140                                         moldyn_usage(argv);
 141                                         return -1;
 142                         }
 143                 } else {
 144                         moldyn_usage(argv);
 145                         return -1;
 146                 }
 147         }
 148
 149         return 0;
 150 }
 151
 152 int moldyn_log_init(t_moldyn *moldyn) {
 153
 154         moldyn->lvstat=0;
 155         t_visual *vis;
 156
 157         vis=&(moldyn->vis);
 158
 159         if(moldyn->ewrite) {
 160                 moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
 161                 if(moldyn->efd<0) {
 162                         perror("[moldyn] efd open");
 163                         return moldyn->efd;
 164                 }
 165                 dprintf(moldyn->efd,"# moldyn total energy logfile\n");
 166                 moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_E;
 167         }
 168
 169         if(moldyn->mwrite) {
 170                 moldyn->mfd=open(moldyn->mfb,O_WRONLY|O_CREAT|O_TRUNC);
 171                 if(moldyn->mfd<0) {
 172                         perror("[moldyn] mfd open");
 173                         return moldyn->mfd;
 174                 }
 175                 dprintf(moldyn->mfd,"# moldyn total momentum logfile\n");
 176                 moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_M;
 177         }
 178
 179         if(moldyn->swrite)
 180                 moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
 181
 182         if((moldyn->vwrite)&&(vis)) {
 183                 moldyn->visual=vis;
 184                 visual_init(vis,moldyn->vfb);
 185                 moldyn->lvstat|=MOLDYN_LVSTAT_VISUAL;
 186         }
 187
 188         moldyn->lvstat|=MOLDYN_LVSTAT_INITIALIZED;
 189
 190         return 0;
 191 }
 192
 193 int moldyn_log_shutdown(t_moldyn *moldyn) {
 194
 195         if(moldyn->efd) close(moldyn->efd);
 196         if(moldyn->mfd) close(moldyn->efd);
 197         if(moldyn->dfd) close(moldyn->efd);
 198         if(moldyn->visual) visual_tini(moldyn->visual);
 199
 200         return 0;
 201 }
 202
 203 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 204
 205         int ret;
 206
 207         ret=moldyn_parse_argv(moldyn,argc,argv);
 208         if(ret<0) return ret;
 209
 210         ret=moldyn_log_init(moldyn);
 211         if(ret<0) return ret;
 212
 213         rand_init(&(moldyn->random),NULL,1);
 214         moldyn->random.status|=RAND_STAT_VERBOSE;
 215
 216         moldyn->status=0;
 217
 218         return 0;
 219 }
 220
 221 int moldyn_shutdown(t_moldyn *moldyn) {
 222
 223         moldyn_log_shutdown(moldyn);
 224         rand_close(&(moldyn->random));
 225         free(moldyn->atom);
 226
 227         return 0;
 228 }
 229
 230 int create_lattice(u8 type,int element,double mass,double lc,
 231                    int a,int b,int c,t_atom **atom) {
 232
 233         int count;
 234         int ret;
 235         t_3dvec origin;
 236
 237         count=a*b*c;
 238
 239         if(type==FCC) count*=4;
 240         if(type==DIAMOND) count*=8;
 241
 242         *atom=malloc(count*sizeof(t_atom));
 243         if(*atom==NULL) {
 244                 perror("malloc (atoms)");
 245                 return -1;
 246         }
 247
 248         v3_zero(&origin);
 249
 250         switch(type) {
 251                 case FCC:
 252                         ret=fcc_init(a,b,c,lc,*atom,&origin);
 253                         break;
 254                 case DIAMOND:
 255                         ret=diamond_init(a,b,c,lc,*atom,&origin);
 256                         break;
 257                 default:
 258                         printf("unknown lattice type (%02x)\n",type);
 259                         return -1;
 260         }
 261
 262         /* debug */
 263         if(ret!=count) {
 264                 printf("ok, there is something wrong ...\n");
 265                 printf("calculated -> %d atoms\n",count);
 266                 printf("created -> %d atoms\n",ret);
 267                 return -1;
 268         }
 269
 270         while(count) {
 271                 (*atom)[count-1].element=element;
 272                 (*atom)[count-1].mass=mass;
 273                 count-=1;
 274         }
 275
 276         return ret;
 277 }
 278
 279 int destroy_lattice(t_atom *atom) {
 280
 281         if(atom) free(atom);
 282
 283         return 0;
 284 }
 285
 286 int thermal_init(t_moldyn *moldyn) {
 287
 288         /*
 289          * - gaussian distribution of velocities
 290          * - zero total momentum
 291          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 292          */
 293
 294         int i;
 295         double v,sigma;
 296         t_3dvec p_total,delta;
 297         t_atom *atom;
 298         t_random *random;
 299
 300         atom=moldyn->atom;
 301         random=&(moldyn->random);
 302
 303         /* gaussian distribution of velocities */
 304         v3_zero(&p_total);
 305         for(i=0;i<moldyn->count;i++) {
 306                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
 307                 /* x direction */
 308                 v=sigma*rand_get_gauss(random);
 309                 atom[i].v.x=v;
 310                 p_total.x+=atom[i].mass*v;
 311                 /* y direction */
 312                 v=sigma*rand_get_gauss(random);
 313                 atom[i].v.y=v;
 314                 p_total.y+=atom[i].mass*v;
 315                 /* z direction */
 316                 v=sigma*rand_get_gauss(random);
 317                 atom[i].v.z=v;
 318                 p_total.z+=atom[i].mass*v;
 319         }
 320
 321         /* zero total momentum */
 322         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 323         for(i=0;i<moldyn->count;i++) {
 324                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 325                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 326         }
 327
 328         /* velocity scaling */
 329         scale_velocity(moldyn);
 330
 331         return 0;
 332 }
 333
 334 int scale_velocity(t_moldyn *moldyn) {
 335
 336         int i;
 337         double e,c;
 338         t_atom *atom;
 339
 340         atom=moldyn->atom;
 341
 342         /*
 343          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 344          */
 345         e=0.0;
 346         for(i=0;i<moldyn->count;i++)
 347                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 348         c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
 349         for(i=0;i<moldyn->count;i++)
 350                 v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
 351
 352         return 0;
 353 }
 354
 355 double get_e_kin(t_atom *atom,int count) {
 356
 357         int i;
 358         double e;
 359
 360         e=0.0;
 361
 362         for(i=0;i<count;i++) {
 363                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 364         }
 365
 366         return e;
 367 }
 368
 369 double get_e_pot(t_moldyn *moldyn) {
 370
 371         return moldyn->energy;
 372 }
 373
 374 double get_total_energy(t_moldyn *moldyn) {
 375
 376         double e;
 377
 378         e=get_e_kin(moldyn->atom,moldyn->count);
 379         e+=get_e_pot(moldyn);
 380
 381         return e;
 382 }
 383
 384 t_3dvec get_total_p(t_atom *atom, int count) {
 385
 386         t_3dvec p,p_total;
 387         int i;
 388
 389         v3_zero(&p_total);
 390         for(i=0;i<count;i++) {
 391                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 392                 v3_add(&p_total,&p_total,&p);
 393         }
 394
 395         return p_total;
 396 }
 397
 398 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
 399
 400         double tau;
 401
 402         tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
 403         tau*=1.0E-9;
 404         if(tau<moldyn->tau)
 405                 printf("[moldyn] warning: time step  (%f > %.15f)\n",
 406                        moldyn->tau,tau);
 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
 422         lc=&(moldyn->lc);
 423
 424         /* list log fd */
 425         lc->listfd=open("/dev/null",O_WRONLY);
 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("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]));
 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<moedyn->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         if(lc->listfd) close(lc->listfd);
 546
 547         return 0;
 548 }
 549
 550 int moldyn_add_schedule(t_moldyn *moldyn,) {
 551
 552
 553         return 0;
 554 }
 555
 556 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 557
 558
 559         return 0;
 560 }
 561
 562 /*
 563  *
 564  * 'integration of newtons equation' - algorithms
 565  *
 566  */
 567
 568 /* start the integration */
 569
 570 int moldyn_integrate(t_moldyn *moldyn) {
 571
 572         int i,sched;
 573         unsigned int e,m,s,d,v;
 574         t_3dvec p;
 575
 576         int fd;
 577         char fb[128];
 578
 579         /* initialize linked cell method */
 580         link_cell_init(moldyn);
 581
 582         /* logging & visualization */
 583         e=moldyn->ewrite;
 584         m=moldyn->mwrite;
 585         s=moldyn->swrite;
 586         d=moldyn->dwrite;
 587         v=moldyn->vwrite;
 588
 589         if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
 590                 printf("[moldyn] warning, lv system not initialized\n");
 591                 return -1;
 592         }
 593
 594         /* sqaure of some variables */
 595         moldyn->tau_square=moldyn->tau*moldyn->tau;
 596         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 597
 598         /* calculate initial forces */
 599         moldyn->potential_force_function(moldyn);
 600
 601         for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 602
 603                 /* setting amont of runs and finite time step size */
 604                 moldyn->tau=schedule->tau[sched];
 605                 moldyn->tau_square=moldyn->tau*moldyn->tau;
 606                 moldyn->timesteps=schedule->runs[sched];
 607
 608         /* integration according to schedule */
 609
 610         for(i=0;i<moldyn->time_steps;i++) {
 611
 612                 /* integration step */
 613                 moldyn->integrate(moldyn);
 614
 615                 /* check for log & visualization */
 616                 if(e) {
 617                         if(!(i%e))
 618                                 dprintf(moldyn->efd,
 619                                         "%.15f %.45f\n",i*moldyn->tau,
 620                                         get_total_energy(moldyn));
 621                 }
 622                 if(m) {
 623                         if(!(i%m)) {
 624                                 p=get_total_p(moldyn->atom,moldyn->count);
 625                                 dprintf(moldyn->mfd,
 626                                         "%.15f %.45f\n",i*moldyn->tau,
 627                                         v3_norm(&p));
 628                         }
 629                 }
 630                 if(s) {
 631                         if(!(i%s)) {
 632                                 snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
 633                                          moldyn->t,i*moldyn->tau);
 634                                 fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
 635                                 if(fd<0) perror("[moldyn] save fd open");
 636                                 else {
 637                                         write(fd,moldyn,sizeof(t_moldyn));
 638                                         write(fd,moldyn->atom,
 639                                               moldyn->count*sizeof(t_atom));
 640                                 }
 641                                 close(fd);
 642                         }
 643                 }
 644                 if(v) {
 645                         if(!(i%v)) {
 646                                 visual_atoms(moldyn->visual,i*moldyn->tau,
 647                                              moldyn->atom,moldyn->count);
 648                                 printf("\rsteps: %d",i);
 649                                 fflush(stdout);
 650                         }
 651                 }
 652         }
 653
 654                 /* check for hooks */
 655                 if(schedule->hook)
 656                         schedule->hook(moldyn,schedule->hook_params);
 657
 658         return 0;
 659 }
 660
 661 /* velocity verlet */
 662
 663 int velocity_verlet(t_moldyn *moldyn) {
 664
 665         int i,count;
 666         double tau,tau_square;
 667         t_3dvec delta;
 668         t_atom *atom;
 669
 670         atom=moldyn->atom;
 671         count=moldyn->count;
 672         tau=moldyn->tau;
 673         tau_square=moldyn->tau_square;
 674
 675         for(i=0;i<count;i++) {
 676                 /* new positions */
 677                 v3_scale(&delta,&(atom[i].v),tau);
 678                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 679                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 680                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 681                 v3_per_bound(&(atom[i].r),&(moldyn->dim));
 682
 683                 /* velocities */
 684                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 685                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 686         }
 687
 688         /* neighbour list update */
 689 printf("list update ...\n");
 690         link_cell_update(moldyn);
 691 printf("done\n");
 692
 693         /* forces depending on chosen potential */
 694 printf("calc potential/force ...\n");
 695         potential_force_calc(moldyn);
 696         //moldyn->potential_force_function(moldyn);
 697 printf("done\n");
 698
 699         for(i=0;i<count;i++) {
 700                 /* again velocities */
 701                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 702                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 703         }
 704
 705         return 0;
 706 }
 707
 708
 709 /*
 710  *
 711  * potentials & corresponding forces
 712  *
 713  */
 714
 715 /* generic potential and force calculation */
 716
 717 int potential_force_calc(t_moldyn *moldyn) {
 718
 719         int i,count;
 720         t_atom *atom;
 721         t_linkcell *lc;
 722         t_list neighbour[27];
 723         t_list *this;
 724         double u;
 725         u8 bc,bc3;
 726         int countn,dnlc;
 727
 728         count=moldyn->count;
 729         atom=moldyn->atom;
 730         lc=&(moldyn->lc);
 731
 732         /* reset energy */
 733         moldyn->energy=0.0;
 734
 735         for(i=0;i<count;i++) {
 736
 737                 /* reset force */
 738                 v3_zero(&(atom[i].f));
 739
 740                 /* single particle potential/force */
 741                 if(atom[i].attr&ATOM_ATTR_1BP)
 742                         moldyn->pf_func1b(moldyn,&(atom[i]));
 743
 744                 /* 2 body pair potential/force */
 745                 if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 746
 747                         link_cell_neighbour_index(moldyn,
 748                                 (atom[i].r.x+moldyn->dim.x/2)/lc->x,
 749                                 (atom[i].r.y+moldyn->dim.y/2)/lc->y,
 750                                 (atom[i].r.z+moldyn->dim.z/2)/lc->z,
 751                                 neighbour);
 752
 753                         countn=lc->countn;
 754                         dnlc=lc->dnlc;
 755
 756                         for(j=0;j<countn;j++) {
 757
 758                                 this=&(neighbour[j]);
 759                                 list_reset(this);
 760
 761                                 if(this->start==NULL)
 762                                         continue;
 763
 764                                 bc=(j<dnlc)?0:1;
 765
 766                                 do {
 767                                         btom=this->current->data;
 768
 769                                         if(btom==&(atom[i]))
 770                                                 continue;
 771
 772                                         if((btom->attr&ATOM_ATTR_2BP)&
 773                                            (atom[i].attr&ATOM_ATTR_2BP))
 774                                                 moldyn->pf_func2b(moldyn,
 775                                                                   &(atom[i]),
 776                                                                   btom,
 777                                                                   bc);
 778
 779                                         /* 3 body potential/force */
 780
 781                                         if(!(atom[i].attr&ATOM_ATTR_3BP)||
 782                                            !(btom->attr&ATOM_ATTR_3BP))
 783                                                 continue;
 784
 785                                         link_cell_neighbour_index(moldyn,
 786                                            (btom->r.x+moldyn->dim.x/2)/lc->x,
 787                                            (btom->r.y+moldyn->dim.y/2)/lc->y,
 788                                            (btom->r.z+moldyn->dim.z/2)/lc->z,
 789                                            neighbourk);
 790
 791                                         for(k=0;k<lc->countn;k++) {
 792
 793                                                 thisk=&(neighbourk[k]);
 794                                                 list_reset(thisk);
 795
 796                                                 if(thisk->start==NULL)
 797                                                         continue;
 798
 799                                                 bck=(k<lc->dnlc)?0:1;
 800
 801                                                 do {
 802
 803                         ktom=thisk->current->data;
 804
 805                         if(!(ktom->attr&ATOM_ATTR_3BP))
 806                                 continue;
 807
 808                         if(ktom==btom)
 809                                 continue;
 810
 811                         if(ktom==&(atom[i]))
 812                                 continue;
 813
 814                         moldyn->pf_func3b(moldyn,&(atom[i]),btom,ktom,bck);
 815
 816                                                 } while(list_next(thisk)!=\
 817                                                         L_NO_NEXT_ELEMENT);
 818
 819                                 } while(list_next(this)!=L_NO_NEXT_ELEMENT);
 820                         }
 821                 }
 822         }
 823
 824         return 0;
 825 }
 826
 827 /*
 828  * periodic boundayr checking
 829  */
 830
 831 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 832
 833         double x,y,z;
 834
 835         x=0.5*dim->x;
 836         y=0.5*dim->y;
 837         z=0.5*dim->z;
 838
 839         if(moldyn->MOLDYN_ATTR_PBX)
 840                 if(a->x>=x) a->x-=dim->x;
 841                 else if(-a->x>x) a->x+=dim->x;
 842         if(moldyn->MOLDYN_ATTR_PBY)
 843                 if(a->y>=y) a->y-=dim->y;
 844                 else if(-a->y>y) a->y+=dim->y;
 845         if(moldyn->MOLDYN_ATTR_PBZ)
 846                 if(a->z>=z) a->z-=dim->z;
 847                 else if(-a->z>z) a->z+=dim->z;
 848
 849         return 0;
 850 }
 851
 852
 853 /*
 854  * example potentials
 855  */
 856
 857 /* harmonic oscillator potential and force */
 858
 859 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc)) {
 860
 861         t_ho_params *params;
 862         t_3dvec force,distance;
 863         double d;
 864         double sc,equi_dist;
 865
 866         params=moldyn->pot2b_params;
 867         sc=params->spring_constant;
 868         equi_dist=params->equilibrium_distance;
 869
 870         v3_sub(&distance,&(ai->r),&(aj->r);
 871
 872         v3_per_bound(&distance,&(moldyn->dim));
 873         if(bc) check_per_bound(moldyn,&distance);
 874         d=v3_norm(&distance);
 875         if(d<=moldyn->cutoff) {
 876                 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
 877                 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
 878                 v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
 879                 v3_add(&(ai->f),&(ai->f),&force);
 880         }
 881
 882         return 0;
 883 }
 884
 885 /* lennard jones potential & force for one sort of atoms */
 886
 887 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 888
 889         t_lj_params *params;
 890         t_3dvec force,distance;
 891         double d,h1,h2,u;
 892         double eps,sig6,sig12;
 893
 894         params=moldyn->pot_params;
 895         eps=params->epsilon4;
 896         sig6=params->sigma6;
 897         sig12=params->sigma12;
 898
 899         v3_sub(&distance,&(ai->r),&(aj->r));
 900         if(bc) check_per_bound(moldyn,&distance);
 901         d=v3_absolute_square(&distance);        /* 1/r^2 */
 902         if(d<=moldyn->cutoff_square) {
 903                 d=1.0/d;                        /* 1/r^2 */
 904                 h2=d*d;                         /* 1/r^4 */
 905                 h2*=d;                          /* 1/r^6 */
 906                 h1=h2*h2;                       /* 1/r^12 */
 907                 /* energy is eps*..., but we will add this twice ... */
 908                 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
 909                 h2*=d;                          /* 1/r^8 */
 910                 h1*=d;                          /* 1/r^14 */
 911                 h2*=6*sig6;
 912                 h1*=12*sig12;
 913                 d=+h1-h2;
 914                 d*=eps;
 915                 v3_scale(&force,&distance,d);
 916                 v3_add(&(ai->f),&(aj->f),&force);
 917         }
 918
 919         return 0;
 920 }
 921
 922 /*
 923  * tersoff potential & force for 2 sorts of atoms
 924  */
 925
 926 /* tersoff 1 body part */
 927 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
 928
 929         int num;
 930         t_tersoff_mult_params *params;
 931         t_tersoff_exchange *exchange;
 932
 933         num=ai->bnum;
 934         params=moldyn->pot1b_params;
 935         exchange=&(params->exchange);
 936
 937         /*
 938          * simple: point constant parameters only depending on atom i to
 939          *         their right values
 940          */
 941
 942         exchange->beta=&(params->beta[num]);
 943         exchange->n=&(params->n[num]);
 944         exchange->c=&(params->c[num]);
 945         exchange->d=&(params->d[num]);
 946         exchange->h=&(params->h[num]);
 947
 948         exchange->betan=pow(*(exchange->beta),*(exchange->n));
 949         exchange->c2=params->c[num]*params->c[num];
 950         exchange->d2=params->d[num]*params->d[num];
 951         exchange->c2d2=exchange->c2/exchange->d2;
 952
 953         return 0;
 954 }
 955
 956 /* tersoff 2 body part */
 957 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 958
 959         t_tersoff_mult_params *params;
 960         t_tersoff_exchange *exchange;
 961         t_3dvec dist_ij;
 962         double d_ij;
 963         double A,B,R,S,lambda;
 964         int num;
 965
 966         params=moldyn->pot_params;
 967         num=ai->bnum;
 968         exchange=&(params->exchange);
 969
 970         exchange->run3bp=0;
 971
 972         /*
 973          * we need: f_c, df_c, f_r, df_r
 974          *
 975          * therefore we need: R, S, A, lambda
 976          */
 977
 978         v3_sub(&dist_ij,&(ai->r),&(aj->r));
 979
 980         if(bc) check_per_bound(moldyn,&dist_ij);
 981
 982         /* save for use in 3bp */ /* REALLY ?!?!?! */
 983         exchange->dist_ij=dist_ij;
 984
 985         /* constants */
 986         if(num==aj->bnum) {
 987                 S=params->S[num];
 988                 R=params->R[num];
 989                 A=params->A[num];
 990                 lambda=params->lambda[num];
 991                 /* more constants depending of atoms i and j, needed in 3bp */
 992                 params->exchange.B=&(params->B[num]);
 993                 params->exchange.mu=params->mu[num];
 994                 params->exchange.chi=1.0;
 995         }
 996         else {
 997                 S=params->Smixed;
 998                 R=params->Rmixed;
 999                 A=params->Amixed;
1000                 lambda=params->lambda_m;
1001                 /* more constants depending of atoms i and j, needed in 3bp */
1002                 params->exchange.B=&(params->Bmixed);
1003                 params->exchange.mu=&(params->mu_m);
1004                 params->exchange.chi=params->chi;
1005         }
1006
1007         d_ij=v3_norm(&dist_ij);
1008
1009         /* save for use in 3bp */
1010         exchange->d_ij=d_ij;
1011
1012         if(d_ij>S)
1013                 return 0;
1014
1015         f_r=A*exp(-lamda*d_ij);
1016         df_r=-lambda*f_r/d_ij;
1017
1018         /* f_a, df_a calc + save for 3bp use */
1019         exchange->f_a=-B*exp(-mu*d_ij);
1020         exchange->df_a=-mu*exchange->f_a/d_ij;
1021
1022         if(d_ij<R) {
1023                 /* f_c = 1, df_c = 0 */
1024                 f_c=1.0;
1025                 df_c=0.0;
1026                 v3_scale(&force,&dist_ij,df_r);
1027         }
1028         else {
1029                 s_r=S-R;
1030                 arg=PI*(d_ij-R)/s_r;
1031                 f_c=0.5+0.5*cos(arg);
1032                 df_c=-0.5*sin(arg)*(PI/(s_r*d_ij));
1033                 scale=df_c*f_r+df_r*f_c;
1034                 v3_scale(&force,&dist_ij,scale);
1035         }
1036
1037         /* add forces */
1038         v3_add(&(ai->f),&(ai->f),&force);
1039         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1040         moldyn->energy+=(0.25*f_r*f_c);
1041
1042         /* save for use in 3bp */
1043         exchange->f_c=f_c;
1044         exchange->df_c=df_c;
1045
1046         /* enable the run of 3bp function */
1047         exchange->run3bp=1;
1048
1049         return 0;
1050 }
1051
1052 /* tersoff 3 body part */
1053
1054 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1055
1056         t_tersoff_mult_params *params;
1057         t_tersoff_exchange *exchange;
1058         t_3dvec dist_ij,dist_ik,dist_jk;
1059         t_3dvec temp,force;
1060         double R,S,s_r;
1061         double d_ij,d_ik,d_jk;
1062         double f_c,df_c,b_ij,f_a,df_a;
1063         double n,c,d,h,neta,betan,betan_1;
1064         double theta,cos_theta,sin_theta;
1065         int num;
1066
1067         params=moldyn->pot_params;
1068         num=ai->bnum;
1069         exchange=params->exchange;
1070
1071         if(!(exchange->run3bp))
1072                 return 0;
1073
1074         /*
1075          * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
1076          *
1077          * we got f_c, df_c, f_a, df_a from 2bp calculation
1078          */
1079
1080         d_ij=exchange->d_ij;
1081         d_ij2=exchange->d_ij2;
1082
1083         f_a=params->exchange.f_a;
1084         df_a=params->exchange.df_a;
1085
1086         /* d_ij is <= S, as we didn't return so far! */
1087
1088         /*
1089          * calc of b_ij (scalar) and db_ij (vector)
1090          *
1091          * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
1092          *
1093          * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
1094          *              w_ik,
1095          *
1096          */
1097
1098
1099         v3_sub(&dist_ik,&(aj->i),&(ak->r));
1100         if(bc) check_per_bound(moldyn,&dist_ik);
1101         d_ik=v3_norm(&dist_ik);
1102
1103         /* constants for f_c_ik calc */
1104         if(num==ak->bnum) {
1105                 R=params->R[num];
1106                 S=params->S[num];
1107         }
1108         else {
1109                 R=params->Rmixed;
1110                 S=params->Smixed;
1111         }
1112
1113         /* calc of f_c_ik */
1114         if(d_ik>S)
1115                 return 0;
1116
1117         if(d_ik<R) {
1118                 /* f_c_ik = 1, df_c_ik = 0 */
1119                 f_c_ik=1.0;
1120                 df_c_ik=0.0;
1121         }
1122         else {
1123                 s_r=S-R;
1124                 arg=PI*(d_ik-R)/s_r;
1125                 f_c_ik=0.5+0.5*cos(arg);
1126                 df_c_ik=-0.5*sin(arg)*(PI/(s_r*d_ik));
1127         }
1128
1129         v3_sub(&dist_jk,&(aj->r),&(ak->r));
1130         if(bc) check_per_bound(moldyn,&dist_jk);
1131         d_jk=v3_norm(&dist_jk);
1132
1133         beta=*(exchange->beta);
1134         betan=exchange->betan;
1135         n=*(exchange->n);
1136         c=*(exchange->c);
1137         d=*(exchange->d);
1138         h=*(exchange->h);
1139         c2=exchange->c2;
1140         d2=exchange->d2;
1141         c2d2=exchange->c2d2;
1142
1143         numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
1144         denom=2*d_ij*d_ik;
1145         cos_theta=numer/denom;
1146         sin_theta=sqrt(1.0-(cos_theta*cos_theta));
1147         theta=arccos(cos_theta);
1148         d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
1149         d_theta1=2*denom-numer*2*d_ik/d_ij;
1150         d_theta2=2*denom-numer*2*d_ij/d_ik;
1151         d_theta1*=d_theta;
1152         d_theta2*=d_theta;
1153
1154         h_cos=(h-cos_theta);
1155         h_cos2=h_cos*h_cos;
1156         d2_h_cos2=d2-h_cos2;
1157
1158         /* some usefull expressions */
1159         frac1=c2/(d2-h_cos2);
1160         bracket1=1+c2d2-frac1;
1161         bracket2=f_c_ik*bracket1;
1162         bracket2_n_1=pow(bracket2,n-1.0);
1163         bracket2_n=bracket2_n_1*bracket2;
1164         bracket3=1+betan*bracket2_n;
1165         bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
1166         bracket3_pow=bracket3_pow_1*bracket3;
1167
1168         /* now go on with calc of b_ij and derivation of b_ij */
1169         b_ij=chi*bracket3_pow;
1170
1171         /* derivation of theta */
1172         v3_scale(&force,&dist_ij,d1_theta);
1173         v3_scale(&temp,&dist_ik,d_theta2);
1174         v3_add(&force,&force,&temp);
1175
1176         /* part 1 of derivation of b_ij */
1177         v3_scale(&force,sin_theta*2*h_cos*f_c_ik*frac1);
1178
1179         /* part 2 of derivation of b_ij */
1180         v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
1181
1182         /* sum up and scale ... */
1183         v3_add(&temp,&temp,&force);
1184         scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
1185         v3_scale(&temp,&temp,scale);
1186
1187         /* now construct an energy and a force out of that */
1188         v3_scale(&temp,&temp,f_a);
1189         v3_scale(&force,&dist_ij,df_a*b_ij);
1190         v3_add(&temp,&temp,&force);
1191         v3_scale(&temp,&temp,f_c);
1192         v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
1193         v3_add(&force,&force,&temp);
1194
1195         /* add forces */
1196         v3_add(&(ai->f),&(ai->f),&force);
1197         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1198         moldyn->energy+=(0.25*f_a*b_ij*f_c);
1199
1200         return 0;
1201 }
1202