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(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 231                    u8 attr,u8 bnum,int a,int b,int c) {
 232
 233         int count;
 234         int ret;
 235         t_3dvec origin;
 236         t_atom *atom;
 237
 238         count=a*b*c;
 239         atom=moldyn->atom;
 240
 241         if(type==FCC) count*=4;
 242         if(type==DIAMOND) count*=8;
 243
 244         atom=malloc(count*sizeof(t_atom));
 245         if(atom==NULL) {
 246                 perror("malloc (atoms)");
 247                 return -1;
 248         }
 249
 250         v3_zero(&origin);
 251
 252         switch(type) {
 253                 case FCC:
 254                         ret=fcc_init(a,b,c,lc,atom,&origin);
 255                         break;
 256                 case DIAMOND:
 257                         ret=diamond_init(a,b,c,lc,atom,&origin);
 258                         break;
 259                 default:
 260                         printf("unknown lattice type (%02x)\n",type);
 261                         return -1;
 262         }
 263
 264         /* debug */
 265         if(ret!=count) {
 266                 printf("ok, there is something wrong ...\n");
 267                 printf("calculated -> %d atoms\n",count);
 268                 printf("created -> %d atoms\n",ret);
 269                 return -1;
 270         }
 271
 272         while(count) {
 273                 atom[count-1].element=element;
 274                 atom[count-1].mass=mass;
 275                 atom[count-1].attr=attr;
 276                 atom[count-1].bnum=bnum;
 277                 count-=1;
 278         }
 279
 280         return ret;
 281 }
 282
 283 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 284              t_3dvec r,t_3dvec v) {
 285
 286         t_atom *atom;
 287         void *ptr;
 288         int count;
 289
 290         atom=moldyn->atom;
 291         count=++(moldyn->count);
 292
 293         ptr=realloc(atom,count*sizeof(t_atom));
 294         if(!ptr) {
 295                 perror("[moldyn] realloc (add atom)");
 296                 return -1;
 297         }
 298
 299         atom=ptr;
 300         atom->r=r;
 301         atom->v=v;
 302         atom->element=element;
 303         atom->bnum=bnum;
 304         atom->attr=attr;
 305
 306         return 0;
 307 }
 308
 309 int destroy_atoms(t_moldyn *moldyn) {
 310
 311         if(moldyn->atom) free(moldyn->atom);
 312
 313         return 0;
 314 }
 315
 316 int thermal_init(t_moldyn *moldyn) {
 317
 318         /*
 319          * - gaussian distribution of velocities
 320          * - zero total momentum
 321          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 322          */
 323
 324         int i;
 325         double v,sigma;
 326         t_3dvec p_total,delta;
 327         t_atom *atom;
 328         t_random *random;
 329
 330         atom=moldyn->atom;
 331         random=&(moldyn->random);
 332
 333         /* gaussian distribution of velocities */
 334         v3_zero(&p_total);
 335         for(i=0;i<moldyn->count;i++) {
 336                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
 337                 /* x direction */
 338                 v=sigma*rand_get_gauss(random);
 339                 atom[i].v.x=v;
 340                 p_total.x+=atom[i].mass*v;
 341                 /* y direction */
 342                 v=sigma*rand_get_gauss(random);
 343                 atom[i].v.y=v;
 344                 p_total.y+=atom[i].mass*v;
 345                 /* z direction */
 346                 v=sigma*rand_get_gauss(random);
 347                 atom[i].v.z=v;
 348                 p_total.z+=atom[i].mass*v;
 349         }
 350
 351         /* zero total momentum */
 352         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 353         for(i=0;i<moldyn->count;i++) {
 354                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 355                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 356         }
 357
 358         /* velocity scaling */
 359         scale_velocity(moldyn);
 360
 361         return 0;
 362 }
 363
 364 int scale_velocity(t_moldyn *moldyn) {
 365
 366         int i;
 367         double e,c;
 368         t_atom *atom;
 369
 370         atom=moldyn->atom;
 371
 372         /*
 373          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 374          */
 375         e=0.0;
 376         for(i=0;i<moldyn->count;i++)
 377                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 378         c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
 379         for(i=0;i<moldyn->count;i++)
 380                 v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
 381
 382         return 0;
 383 }
 384
 385 double get_e_kin(t_atom *atom,int count) {
 386
 387         int i;
 388         double e;
 389
 390         e=0.0;
 391
 392         for(i=0;i<count;i++) {
 393                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 394         }
 395
 396         return e;
 397 }
 398
 399 double get_e_pot(t_moldyn *moldyn) {
 400
 401         return moldyn->energy;
 402 }
 403
 404 double get_total_energy(t_moldyn *moldyn) {
 405
 406         double e;
 407
 408         e=get_e_kin(moldyn->atom,moldyn->count);
 409         e+=get_e_pot(moldyn);
 410
 411         return e;
 412 }
 413
 414 t_3dvec get_total_p(t_atom *atom, int count) {
 415
 416         t_3dvec p,p_total;
 417         int i;
 418
 419         v3_zero(&p_total);
 420         for(i=0;i<count;i++) {
 421                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 422                 v3_add(&p_total,&p_total,&p);
 423         }
 424
 425         return p_total;
 426 }
 427
 428 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
 429
 430         double tau;
 431
 432         tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
 433         tau*=1.0E-9;
 434         if(tau<moldyn->tau)
 435                 printf("[moldyn] warning: time step  (%f > %.15f)\n",
 436                        moldyn->tau,tau);
 437
 438         return tau;
 439 }
 440
 441 /*
 442  * numerical tricks
 443  */
 444
 445 /* linked list / cell method */
 446
 447 int link_cell_init(t_moldyn *moldyn) {
 448
 449         t_linkcell *lc;
 450         int i;
 451
 452         lc=&(moldyn->lc);
 453
 454         /* list log fd */
 455         lc->listfd=open("/dev/null",O_WRONLY);
 456
 457         /* partitioning the md cell */
 458         lc->nx=moldyn->dim.x/moldyn->cutoff;
 459         lc->x=moldyn->dim.x/lc->nx;
 460         lc->ny=moldyn->dim.y/moldyn->cutoff;
 461         lc->y=moldyn->dim.y/lc->ny;
 462         lc->nz=moldyn->dim.z/moldyn->cutoff;
 463         lc->z=moldyn->dim.z/lc->nz;
 464
 465         lc->cells=lc->nx*lc->ny*lc->nz;
 466         lc->subcell=malloc(lc->cells*sizeof(t_list));
 467
 468         printf("initializing linked cells (%d)\n",lc->cells);
 469
 470         for(i=0;i<lc->cells;i++)
 471                 //list_init(&(lc->subcell[i]),1);
 472                 list_init(&(lc->subcell[i]));
 473
 474         link_cell_update(moldyn);
 475
 476         return 0;
 477 }
 478
 479 int link_cell_update(t_moldyn *moldyn) {
 480
 481         int count,i,j,k;
 482         int nx,ny,nz;
 483         t_atom *atom;
 484         t_linkcell *lc;
 485
 486         atom=moldyn->atom;
 487         lc=&(moldyn->lc);
 488
 489         nx=lc->nx;
 490         ny=lc->ny;
 491         nz=lc->nz;
 492
 493         for(i=0;i<lc->cells;i++)
 494                 list_destroy(&(moldyn->lc.subcell[i]));
 495
 496         for(count=0;count<moedyn->count;count++) {
 497                 i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
 498                 j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
 499                 k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
 500                 list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 501                                        &(atom[count]));
 502         }
 503
 504         return 0;
 505 }
 506
 507 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 508
 509         t_linkcell *lc;
 510         int a;
 511         int count1,count2;
 512         int ci,cj,ck;
 513         int nx,ny,nz;
 514         int x,y,z;
 515         u8 bx,by,bz;
 516
 517         lc=&(moldyn->lc);
 518         nx=lc->nx;
 519         ny=lc->ny;
 520         nz=lc->nz;
 521         count1=1;
 522         count2=27;
 523         a=nx*ny;
 524
 525
 526         cell[0]=lc->subcell[i+j*nx+k*a];
 527         for(ci=-1;ci<=1;ci++) {
 528                 bx=0;
 529                 x=i+ci;
 530                 if((x<0)||(x>=nx)) {
 531                         x=(x+nx)%nx;
 532                         bx=1;
 533                 }
 534                 for(cj=-1;cj<=1;cj++) {
 535                         by=0;
 536                         y=j+cj;
 537                         if((y<0)||(y>=ny)) {
 538                                 y=(y+ny)%ny;
 539                                 by=1;
 540                         }
 541                         for(ck=-1;ck<=1;ck++) {
 542                                 bz=0;
 543                                 z=k+ck;
 544                                 if((z<0)||(z>=nz)) {
 545                                         z=(z+nz)%nz;
 546                                         bz=1;
 547                                 }
 548                                 if(!(ci|cj|ck)) continue;
 549                                 if(bx|by|bz) {
 550                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
 551                                 }
 552                                 else {
 553                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
 554                                 }
 555                         }
 556                 }
 557         }
 558
 559         lc->dnlc=count2;
 560         lc->countn=27;
 561
 562         return count2;
 563 }
 564
 565 int link_cell_shutdown(t_moldyn *moldyn) {
 566
 567         int i;
 568         t_linkcell *lc;
 569
 570         lc=&(moldyn->lc);
 571
 572         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 573                 list_shutdown(&(moldyn->lc.subcell[i]));
 574
 575         if(lc->listfd) close(lc->listfd);
 576
 577         return 0;
 578 }
 579
 580 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau ) {
 581
 582         int count;
 583         void *ptr;
 584         t_moldyn_schedule *schedule;
 585
 586         schedule=moldyn->schedule;
 587         count=++(schedule->content_count);
 588
 589         ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
 590         if(!ptr) {
 591                 perror("[moldyn] realloc (runs)");
 592                 return -1;
 593         }
 594         moldyn->schedule.runs[count-1]=runs;
 595
 596         ptr=realloc(schedule->tau,count*sizeof(double));
 597         if(!ptr) {
 598                 perror("[moldyn] realloc (tau)");
 599                 return -1;
 600         }
 601         moldyn->schedule.tau[count-1]=tau;
 602
 603         return 0;
 604 }
 605
 606 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 607
 608         moldyn->schedule.hook=hook;
 609         moldyn->schedule.hook_params=hook_params;
 610
 611         return 0;
 612 }
 613
 614 /*
 615  *
 616  * 'integration of newtons equation' - algorithms
 617  *
 618  */
 619
 620 /* start the integration */
 621
 622 int moldyn_integrate(t_moldyn *moldyn) {
 623
 624         int i,sched;
 625         unsigned int e,m,s,d,v;
 626         t_3dvec p;
 627
 628         int fd;
 629         char fb[128];
 630
 631         /* initialize linked cell method */
 632         link_cell_init(moldyn);
 633
 634         /* logging & visualization */
 635         e=moldyn->ewrite;
 636         m=moldyn->mwrite;
 637         s=moldyn->swrite;
 638         d=moldyn->dwrite;
 639         v=moldyn->vwrite;
 640
 641         if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
 642                 printf("[moldyn] warning, lv system not initialized\n");
 643                 return -1;
 644         }
 645
 646         /* sqaure of some variables */
 647         moldyn->tau_square=moldyn->tau*moldyn->tau;
 648         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 649
 650         /* calculate initial forces */
 651         moldyn->potential_force_function(moldyn);
 652
 653         for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 654
 655                 /* setting amont of runs and finite time step size */
 656                 moldyn->tau=schedule->tau[sched];
 657                 moldyn->tau_square=moldyn->tau*moldyn->tau;
 658                 moldyn->timesteps=schedule->runs[sched];
 659
 660         /* integration according to schedule */
 661
 662         for(i=0;i<moldyn->time_steps;i++) {
 663
 664                 /* integration step */
 665                 moldyn->integrate(moldyn);
 666
 667                 /* check for log & visualization */
 668                 if(e) {
 669                         if(!(i%e))
 670                                 dprintf(moldyn->efd,
 671                                         "%.15f %.45f\n",i*moldyn->tau,
 672                                         get_total_energy(moldyn));
 673                 }
 674                 if(m) {
 675                         if(!(i%m)) {
 676                                 p=get_total_p(moldyn->atom,moldyn->count);
 677                                 dprintf(moldyn->mfd,
 678                                         "%.15f %.45f\n",i*moldyn->tau,
 679                                         v3_norm(&p));
 680                         }
 681                 }
 682                 if(s) {
 683                         if(!(i%s)) {
 684                                 snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
 685                                          moldyn->t,i*moldyn->tau);
 686                                 fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
 687                                 if(fd<0) perror("[moldyn] save fd open");
 688                                 else {
 689                                         write(fd,moldyn,sizeof(t_moldyn));
 690                                         write(fd,moldyn->atom,
 691                                               moldyn->count*sizeof(t_atom));
 692                                 }
 693                                 close(fd);
 694                         }
 695                 }
 696                 if(v) {
 697                         if(!(i%v)) {
 698                                 visual_atoms(moldyn->visual,i*moldyn->tau,
 699                                              moldyn->atom,moldyn->count);
 700                                 printf("\rsteps: %d",i);
 701                                 fflush(stdout);
 702                         }
 703                 }
 704         }
 705
 706                 /* check for hooks */
 707                 if(schedule->hook)
 708                         schedule->hook(moldyn,schedule->hook_params);
 709
 710         return 0;
 711 }
 712
 713 /* velocity verlet */
 714
 715 int velocity_verlet(t_moldyn *moldyn) {
 716
 717         int i,count;
 718         double tau,tau_square;
 719         t_3dvec delta;
 720         t_atom *atom;
 721
 722         atom=moldyn->atom;
 723         count=moldyn->count;
 724         tau=moldyn->tau;
 725         tau_square=moldyn->tau_square;
 726
 727         for(i=0;i<count;i++) {
 728                 /* new positions */
 729                 v3_scale(&delta,&(atom[i].v),tau);
 730                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 731                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 732                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 733                 v3_per_bound(&(atom[i].r),&(moldyn->dim));
 734
 735                 /* velocities */
 736                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 737                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 738         }
 739
 740         /* neighbour list update */
 741 printf("list update ...\n");
 742         link_cell_update(moldyn);
 743 printf("done\n");
 744
 745         /* forces depending on chosen potential */
 746 printf("calc potential/force ...\n");
 747         potential_force_calc(moldyn);
 748         //moldyn->potential_force_function(moldyn);
 749 printf("done\n");
 750
 751         for(i=0;i<count;i++) {
 752                 /* again velocities */
 753                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 754                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 755         }
 756
 757         return 0;
 758 }
 759
 760
 761 /*
 762  *
 763  * potentials & corresponding forces
 764  *
 765  */
 766
 767 /* generic potential and force calculation */
 768
 769 int potential_force_calc(t_moldyn *moldyn) {
 770
 771         int i,count;
 772         t_atom *atom;
 773         t_linkcell *lc;
 774         t_list neighbour[27];
 775         t_list *this;
 776         double u;
 777         u8 bc,bc3;
 778         int countn,dnlc;
 779
 780         count=moldyn->count;
 781         atom=moldyn->atom;
 782         lc=&(moldyn->lc);
 783
 784         /* reset energy */
 785         moldyn->energy=0.0;
 786
 787         for(i=0;i<count;i++) {
 788
 789                 /* reset force */
 790                 v3_zero(&(atom[i].f));
 791
 792                 /* single particle potential/force */
 793                 if(atom[i].attr&ATOM_ATTR_1BP)
 794                         moldyn->pf_func1b(moldyn,&(atom[i]));
 795
 796                 /* 2 body pair potential/force */
 797                 if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 798
 799                         link_cell_neighbour_index(moldyn,
 800                                 (atom[i].r.x+moldyn->dim.x/2)/lc->x,
 801                                 (atom[i].r.y+moldyn->dim.y/2)/lc->y,
 802                                 (atom[i].r.z+moldyn->dim.z/2)/lc->z,
 803                                 neighbour);
 804
 805                         countn=lc->countn;
 806                         dnlc=lc->dnlc;
 807
 808                         for(j=0;j<countn;j++) {
 809
 810                                 this=&(neighbour[j]);
 811                                 list_reset(this);
 812
 813                                 if(this->start==NULL)
 814                                         continue;
 815
 816                                 bc=(j<dnlc)?0:1;
 817
 818                                 do {
 819                                         btom=this->current->data;
 820
 821                                         if(btom==&(atom[i]))
 822                                                 continue;
 823
 824                                         if((btom->attr&ATOM_ATTR_2BP)&
 825                                            (atom[i].attr&ATOM_ATTR_2BP))
 826                                                 moldyn->pf_func2b(moldyn,
 827                                                                   &(atom[i]),
 828                                                                   btom,
 829                                                                   bc);
 830
 831                                         /* 3 body potential/force */
 832
 833                                         if(!(atom[i].attr&ATOM_ATTR_3BP)||
 834                                            !(btom->attr&ATOM_ATTR_3BP))
 835                                                 continue;
 836
 837                                         link_cell_neighbour_index(moldyn,
 838                                            (btom->r.x+moldyn->dim.x/2)/lc->x,
 839                                            (btom->r.y+moldyn->dim.y/2)/lc->y,
 840                                            (btom->r.z+moldyn->dim.z/2)/lc->z,
 841                                            neighbourk);
 842
 843                                         for(k=0;k<lc->countn;k++) {
 844
 845                                                 thisk=&(neighbourk[k]);
 846                                                 list_reset(thisk);
 847
 848                                                 if(thisk->start==NULL)
 849                                                         continue;
 850
 851                                                 bck=(k<lc->dnlc)?0:1;
 852
 853                                                 do {
 854
 855                         ktom=thisk->current->data;
 856
 857                         if(!(ktom->attr&ATOM_ATTR_3BP))
 858                                 continue;
 859
 860                         if(ktom==btom)
 861                                 continue;
 862
 863                         if(ktom==&(atom[i]))
 864                                 continue;
 865
 866                         moldyn->pf_func3b(moldyn,&(atom[i]),btom,ktom,bck);
 867
 868                                                 } while(list_next(thisk)!=\
 869                                                         L_NO_NEXT_ELEMENT);
 870
 871                                 } while(list_next(this)!=L_NO_NEXT_ELEMENT);
 872                         }
 873                 }
 874         }
 875
 876         return 0;
 877 }
 878
 879 /*
 880  * periodic boundayr checking
 881  */
 882
 883 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 884
 885         double x,y,z;
 886
 887         x=0.5*dim->x;
 888         y=0.5*dim->y;
 889         z=0.5*dim->z;
 890
 891         if(moldyn->MOLDYN_ATTR_PBX)
 892                 if(a->x>=x) a->x-=dim->x;
 893                 else if(-a->x>x) a->x+=dim->x;
 894         if(moldyn->MOLDYN_ATTR_PBY)
 895                 if(a->y>=y) a->y-=dim->y;
 896                 else if(-a->y>y) a->y+=dim->y;
 897         if(moldyn->MOLDYN_ATTR_PBZ)
 898                 if(a->z>=z) a->z-=dim->z;
 899                 else if(-a->z>z) a->z+=dim->z;
 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         v3_per_bound(&distance,&(moldyn->dim));
 925         if(bc) check_per_bound(moldyn,&distance);
 926         d=v3_norm(&distance);
 927         if(d<=moldyn->cutoff) {
 928                 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
 929                 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
 930                 v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
 931                 v3_add(&(ai->f),&(ai->f),&force);
 932         }
 933
 934         return 0;
 935 }
 936
 937 /* lennard jones potential & force for one sort of atoms */
 938
 939 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 940
 941         t_lj_params *params;
 942         t_3dvec force,distance;
 943         double d,h1,h2,u;
 944         double eps,sig6,sig12;
 945
 946         params=moldyn->pot_params;
 947         eps=params->epsilon4;
 948         sig6=params->sigma6;
 949         sig12=params->sigma12;
 950
 951         v3_sub(&distance,&(ai->r),&(aj->r));
 952         if(bc) check_per_bound(moldyn,&distance);
 953         d=v3_absolute_square(&distance);        /* 1/r^2 */
 954         if(d<=moldyn->cutoff_square) {
 955                 d=1.0/d;                        /* 1/r^2 */
 956                 h2=d*d;                         /* 1/r^4 */
 957                 h2*=d;                          /* 1/r^6 */
 958                 h1=h2*h2;                       /* 1/r^12 */
 959                 /* energy is eps*..., but we will add this twice ... */
 960                 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
 961                 h2*=d;                          /* 1/r^8 */
 962                 h1*=d;                          /* 1/r^14 */
 963                 h2*=6*sig6;
 964                 h1*=12*sig12;
 965                 d=+h1-h2;
 966                 d*=eps;
 967                 v3_scale(&force,&distance,d);
 968                 v3_add(&(ai->f),&(aj->f),&force);
 969         }
 970
 971         return 0;
 972 }
 973
 974 /*
 975  * tersoff potential & force for 2 sorts of atoms
 976  */
 977
 978 /* tersoff 1 body part */
 979 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
 980
 981         int num;
 982         t_tersoff_mult_params *params;
 983         t_tersoff_exchange *exchange;
 984
 985         num=ai->bnum;
 986         params=moldyn->pot1b_params;
 987         exchange=&(params->exchange);
 988
 989         /*
 990          * simple: point constant parameters only depending on atom i to
 991          *         their right values
 992          */
 993
 994         exchange->beta=&(params->beta[num]);
 995         exchange->n=&(params->n[num]);
 996         exchange->c=&(params->c[num]);
 997         exchange->d=&(params->d[num]);
 998         exchange->h=&(params->h[num]);
 999
1000         exchange->betan=pow(*(exchange->beta),*(exchange->n));
1001         exchange->c2=params->c[num]*params->c[num];
1002         exchange->d2=params->d[num]*params->d[num];
1003         exchange->c2d2=exchange->c2/exchange->d2;
1004
1005         return 0;
1006 }
1007
1008 /* tersoff 2 body part */
1009 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1010
1011         t_tersoff_mult_params *params;
1012         t_tersoff_exchange *exchange;
1013         t_3dvec dist_ij;
1014         double d_ij;
1015         double A,B,R,S,lambda;
1016         int num;
1017
1018         params=moldyn->pot_params;
1019         num=ai->bnum;
1020         exchange=&(params->exchange);
1021
1022         exchange->run3bp=0;
1023
1024         /*
1025          * we need: f_c, df_c, f_r, df_r
1026          *
1027          * therefore we need: R, S, A, lambda
1028          */
1029
1030         v3_sub(&dist_ij,&(ai->r),&(aj->r));
1031
1032         if(bc) check_per_bound(moldyn,&dist_ij);
1033
1034         /* save for use in 3bp */ /* REALLY ?!?!?! */
1035         exchange->dist_ij=dist_ij;
1036
1037         /* constants */
1038         if(num==aj->bnum) {
1039                 S=params->S[num];
1040                 R=params->R[num];
1041                 A=params->A[num];
1042                 lambda=params->lambda[num];
1043                 /* more constants depending of atoms i and j, needed in 3bp */
1044                 params->exchange.B=&(params->B[num]);
1045                 params->exchange.mu=params->mu[num];
1046                 params->exchange.chi=1.0;
1047         }
1048         else {
1049                 S=params->Smixed;
1050                 R=params->Rmixed;
1051                 A=params->Amixed;
1052                 lambda=params->lambda_m;
1053                 /* more constants depending of atoms i and j, needed in 3bp */
1054                 params->exchange.B=&(params->Bmixed);
1055                 params->exchange.mu=&(params->mu_m);
1056                 params->exchange.chi=params->chi;
1057         }
1058
1059         d_ij=v3_norm(&dist_ij);
1060
1061         /* save for use in 3bp */
1062         exchange->d_ij=d_ij;
1063
1064         if(d_ij>S)
1065                 return 0;
1066
1067         f_r=A*exp(-lamda*d_ij);
1068         df_r=-lambda*f_r/d_ij;
1069
1070         /* f_a, df_a calc + save for 3bp use */
1071         exchange->f_a=-B*exp(-mu*d_ij);
1072         exchange->df_a=-mu*exchange->f_a/d_ij;
1073
1074         if(d_ij<R) {
1075                 /* f_c = 1, df_c = 0 */
1076                 f_c=1.0;
1077                 df_c=0.0;
1078                 v3_scale(&force,&dist_ij,df_r);
1079         }
1080         else {
1081                 s_r=S-R;
1082                 arg=PI*(d_ij-R)/s_r;
1083                 f_c=0.5+0.5*cos(arg);
1084                 df_c=-0.5*sin(arg)*(PI/(s_r*d_ij));
1085                 scale=df_c*f_r+df_r*f_c;
1086                 v3_scale(&force,&dist_ij,scale);
1087         }
1088
1089         /* add forces */
1090         v3_add(&(ai->f),&(ai->f),&force);
1091         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1092         moldyn->energy+=(0.25*f_r*f_c);
1093
1094         /* save for use in 3bp */
1095         exchange->f_c=f_c;
1096         exchange->df_c=df_c;
1097
1098         /* enable the run of 3bp function */
1099         exchange->run3bp=1;
1100
1101         return 0;
1102 }
1103
1104 /* tersoff 3 body part */
1105
1106 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1107
1108         t_tersoff_mult_params *params;
1109         t_tersoff_exchange *exchange;
1110         t_3dvec dist_ij,dist_ik,dist_jk;
1111         t_3dvec temp,force;
1112         double R,S,s_r;
1113         double d_ij,d_ik,d_jk;
1114         double f_c,df_c,b_ij,f_a,df_a;
1115         double n,c,d,h,neta,betan,betan_1;
1116         double theta,cos_theta,sin_theta;
1117         int num;
1118
1119         params=moldyn->pot_params;
1120         num=ai->bnum;
1121         exchange=params->exchange;
1122
1123         if(!(exchange->run3bp))
1124                 return 0;
1125
1126         /*
1127          * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
1128          *
1129          * we got f_c, df_c, f_a, df_a from 2bp calculation
1130          */
1131
1132         d_ij=exchange->d_ij;
1133         d_ij2=exchange->d_ij2;
1134
1135         f_a=params->exchange.f_a;
1136         df_a=params->exchange.df_a;
1137
1138         /* d_ij is <= S, as we didn't return so far! */
1139
1140         /*
1141          * calc of b_ij (scalar) and db_ij (vector)
1142          *
1143          * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
1144          *
1145          * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
1146          *              w_ik,
1147          *
1148          */
1149
1150
1151         v3_sub(&dist_ik,&(aj->i),&(ak->r));
1152         if(bc) check_per_bound(moldyn,&dist_ik);
1153         d_ik=v3_norm(&dist_ik);
1154
1155         /* constants for f_c_ik calc */
1156         if(num==ak->bnum) {
1157                 R=params->R[num];
1158                 S=params->S[num];
1159         }
1160         else {
1161                 R=params->Rmixed;
1162                 S=params->Smixed;
1163         }
1164
1165         /* calc of f_c_ik */
1166         if(d_ik>S)
1167                 return 0;
1168
1169         if(d_ik<R) {
1170                 /* f_c_ik = 1, df_c_ik = 0 */
1171                 f_c_ik=1.0;
1172                 df_c_ik=0.0;
1173         }
1174         else {
1175                 s_r=S-R;
1176                 arg=PI*(d_ik-R)/s_r;
1177                 f_c_ik=0.5+0.5*cos(arg);
1178                 df_c_ik=-0.5*sin(arg)*(PI/(s_r*d_ik));
1179         }
1180
1181         v3_sub(&dist_jk,&(aj->r),&(ak->r));
1182         if(bc) check_per_bound(moldyn,&dist_jk);
1183         d_jk=v3_norm(&dist_jk);
1184
1185         beta=*(exchange->beta);
1186         betan=exchange->betan;
1187         n=*(exchange->n);
1188         c=*(exchange->c);
1189         d=*(exchange->d);
1190         h=*(exchange->h);
1191         c2=exchange->c2;
1192         d2=exchange->d2;
1193         c2d2=exchange->c2d2;
1194
1195         numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
1196         denom=2*d_ij*d_ik;
1197         cos_theta=numer/denom;
1198         sin_theta=sqrt(1.0-(cos_theta*cos_theta));
1199         theta=arccos(cos_theta);
1200         d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
1201         d_theta1=2*denom-numer*2*d_ik/d_ij;
1202         d_theta2=2*denom-numer*2*d_ij/d_ik;
1203         d_theta1*=d_theta;
1204         d_theta2*=d_theta;
1205
1206         h_cos=(h-cos_theta);
1207         h_cos2=h_cos*h_cos;
1208         d2_h_cos2=d2-h_cos2;
1209
1210         /* some usefull expressions */
1211         frac1=c2/(d2-h_cos2);
1212         bracket1=1+c2d2-frac1;
1213         bracket2=f_c_ik*bracket1;
1214         bracket2_n_1=pow(bracket2,n-1.0);
1215         bracket2_n=bracket2_n_1*bracket2;
1216         bracket3=1+betan*bracket2_n;
1217         bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
1218         bracket3_pow=bracket3_pow_1*bracket3;
1219
1220         /* now go on with calc of b_ij and derivation of b_ij */
1221         b_ij=chi*bracket3_pow;
1222
1223         /* derivation of theta */
1224         v3_scale(&force,&dist_ij,d1_theta);
1225         v3_scale(&temp,&dist_ik,d_theta2);
1226         v3_add(&force,&force,&temp);
1227
1228         /* part 1 of derivation of b_ij */
1229         v3_scale(&force,sin_theta*2*h_cos*f_c_ik*frac1);
1230
1231         /* part 2 of derivation of b_ij */
1232         v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
1233
1234         /* sum up and scale ... */
1235         v3_add(&temp,&temp,&force);
1236         scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
1237         v3_scale(&temp,&temp,scale);
1238
1239         /* now construct an energy and a force out of that */
1240         v3_scale(&temp,&temp,f_a);
1241         v3_scale(&force,&dist_ij,df_a*b_ij);
1242         v3_add(&temp,&temp,&force);
1243         v3_scale(&temp,&temp,f_c);
1244         v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
1245         v3_add(&force,&force,&temp);
1246
1247         /* add forces */
1248         v3_add(&(ai->f),&(ai->f),&force);
1249         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1250         moldyn->energy+=(0.25*f_a*b_ij*f_c);
1251
1252         return 0;
1253 }
1254