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("-R <runs> (%d)\n",MOLDYN_RUNS);
  39         printf("\n");
  40
  41         return 0;
  42 }
  43
  44 int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
  45
  46         int i;
  47
  48         memset(moldyn,0,sizeof(t_moldyn));
  49
  50         /* default values */
  51         moldyn->t=MOLDYN_TEMP;
  52         moldyn->tau=MOLDYN_TAU;
  53         moldyn->time_steps=MOLDYN_RUNS;
  54
  55         /* parse argv */
  56         for(i=1;i<argc;i++) {
  57                 if(argv[i][0]=='-') {
  58                         switch(argv[i][1]){
  59                                 case 'E':
  60                                         moldyn->ewrite=atoi(argv[++i]);
  61                                         strncpy(moldyn->efb,argv[++i],64);
  62                                         break;
  63                                 case 'M':
  64                                         moldyn->mwrite=atoi(argv[++i]);
  65                                         strncpy(moldyn->mfb,argv[++i],64);
  66                                         break;
  67                                 case 'D':
  68                                         moldyn->dwrite=atoi(argv[++i]);
  69                                         strncpy(moldyn->dfb,argv[++i],64);
  70                                         break;
  71                                 case 'S':
  72                                         moldyn->swrite=atoi(argv[++i]);
  73                                         strncpy(moldyn->sfb,argv[++i],64);
  74                                         break;
  75                                 case 'V':
  76                                         moldyn->vwrite=atoi(argv[++i]);
  77                                         strncpy(moldyn->vfb,argv[++i],64);
  78                                         break;
  79                                 case 'T':
  80                                         moldyn->t=atof(argv[++i]);
  81                                         break;
  82                                 case 't':
  83                                         moldyn->tau=atof(argv[++i]);
  84                                         break;
  85                                 case 'R':
  86                                         moldyn->time_steps=atoi(argv[++i]);
  87                                         break;
  88                                 default:
  89                                         printf("unknown option %s\n",argv[i]);
  90                                         moldyn_usage(argv);
  91                                         return -1;
  92                         }
  93                 } else {
  94                         moldyn_usage(argv);
  95                         return -1;
  96                 }
  97         }
  98
  99         return 0;
 100 }
 101
 102 int moldyn_log_init(t_moldyn *moldyn,void *v) {
 103
 104         moldyn->lvstat=0;
 105         t_visual *vis;
 106
 107         vis=v;
 108
 109         if(moldyn->ewrite) {
 110                 moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
 111                 if(moldyn->efd<0) {
 112                         perror("[moldyn] efd open");
 113                         return moldyn->efd;
 114                 }
 115                 dprintf(moldyn->efd,"# moldyn total energy logfile\n");
 116                 moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_E;
 117         }
 118
 119         if(moldyn->mwrite) {
 120                 moldyn->mfd=open(moldyn->mfb,O_WRONLY|O_CREAT|O_TRUNC);
 121                 if(moldyn->mfd<0) {
 122                         perror("[moldyn] mfd open");
 123                         return moldyn->mfd;
 124                 }
 125                 dprintf(moldyn->mfd,"# moldyn total momentum logfile\n");
 126                 moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_M;
 127         }
 128
 129         if(moldyn->swrite)
 130                 moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
 131
 132         if(moldyn->dwrite) {
 133                 moldyn->dfd=open(moldyn->dfb,O_WRONLY|O_CREAT|O_TRUNC);
 134                 if(moldyn->dfd<0) {
 135                         perror("[moldyn] dfd open");
 136                         return moldyn->dfd;
 137                 }
 138                 write(moldyn->dfd,moldyn,sizeof(t_moldyn));
 139                 moldyn->lvstat|=MOLDYN_LVSTAT_DUMP;
 140         }
 141
 142         if((moldyn->vwrite)&&(vis)) {
 143                 moldyn->visual=vis;
 144                 visual_init(vis,moldyn->vfb);
 145                 moldyn->lvstat|=MOLDYN_LVSTAT_VISUAL;
 146         }
 147
 148         moldyn->lvstat|=MOLDYN_LVSTAT_INITIALIZED;
 149
 150         return 0;
 151 }
 152
 153 int moldyn_shutdown(t_moldyn *moldyn) {
 154
 155         if(moldyn->efd) close(moldyn->efd);
 156         if(moldyn->mfd) close(moldyn->efd);
 157         if(moldyn->dfd) close(moldyn->efd);
 158         if(moldyn->visual) visual_tini(moldyn->visual);
 159
 160         return 0;
 161 }
 162
 163 int create_lattice(unsigned char type,int element,double mass,double lc,
 164                    int a,int b,int c,t_atom **atom) {
 165
 166         int count;
 167         int ret;
 168         t_3dvec origin;
 169
 170         count=a*b*c;
 171
 172         if(type==FCC) count*=4;
 173         if(type==DIAMOND) count*=8;
 174
 175         *atom=malloc(count*sizeof(t_atom));
 176         if(*atom==NULL) {
 177                 perror("malloc (atoms)");
 178                 return -1;
 179         }
 180
 181         v3_zero(&origin);
 182
 183         switch(type) {
 184                 case FCC:
 185                         ret=fcc_init(a,b,c,lc,*atom,&origin);
 186                         break;
 187                 case DIAMOND:
 188                         ret=diamond_init(a,b,c,lc,*atom,&origin);
 189                         break;
 190                 default:
 191                         printf("unknown lattice type (%02x)\n",type);
 192                         return -1;
 193         }
 194
 195         /* debug */
 196         if(ret!=count) {
 197                 printf("ok, there is something wrong ...\n");
 198                 printf("calculated -> %d atoms\n",count);
 199                 printf("created -> %d atoms\n",ret);
 200                 return -1;
 201         }
 202
 203         while(count) {
 204                 (*atom)[count-1].element=element;
 205                 (*atom)[count-1].mass=mass;
 206                 count-=1;
 207         }
 208
 209         return ret;
 210 }
 211
 212 int destroy_lattice(t_atom *atom) {
 213
 214         if(atom) free(atom);
 215
 216         return 0;
 217 }
 218
 219 int thermal_init(t_moldyn *moldyn,t_random *random,int count) {
 220
 221         /*
 222          * - gaussian distribution of velocities
 223          * - zero total momentum
 224          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 225          */
 226
 227         int i;
 228         double v,sigma;
 229         t_3dvec p_total,delta;
 230         t_atom *atom;
 231
 232         atom=moldyn->atom;
 233
 234         /* gaussian distribution of velocities */
 235         v3_zero(&p_total);
 236         for(i=0;i<count;i++) {
 237                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
 238                 /* x direction */
 239                 v=sigma*rand_get_gauss(random);
 240                 atom[i].v.x=v;
 241                 p_total.x+=atom[i].mass*v;
 242                 /* y direction */
 243                 v=sigma*rand_get_gauss(random);
 244                 atom[i].v.y=v;
 245                 p_total.y+=atom[i].mass*v;
 246                 /* z direction */
 247                 v=sigma*rand_get_gauss(random);
 248                 atom[i].v.z=v;
 249                 p_total.z+=atom[i].mass*v;
 250         }
 251
 252         /* zero total momentum */
 253         v3_scale(&p_total,&p_total,1.0/count);
 254         for(i=0;i<count;i++) {
 255                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 256                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 257         }
 258
 259         /* velocity scaling */
 260         scale_velocity(moldyn,count);
 261
 262         return 0;
 263 }
 264
 265 int scale_velocity(t_moldyn *moldyn,int count) {
 266
 267         int i;
 268         double e,c;
 269         t_atom *atom;
 270
 271         atom=moldyn->atom;
 272
 273         /*
 274          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 275          */
 276         e=0.0;
 277         for(i=0;i<count;i++)
 278                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 279         c=sqrt((2.0*e)/(3.0*count*K_BOLTZMANN*moldyn->t));
 280         for(i=0;i<count;i++)
 281                 v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
 282
 283         return 0;
 284 }
 285
 286 double get_e_kin(t_atom *atom,int count) {
 287
 288         int i;
 289         double e;
 290
 291         e=0.0;
 292
 293         for(i=0;i<count;i++) {
 294                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 295         }
 296
 297         return e;
 298 }
 299
 300 double get_e_pot(t_moldyn *moldyn) {
 301
 302         return(moldyn->potential(moldyn));
 303 }
 304
 305 double get_total_energy(t_moldyn *moldyn) {
 306
 307         double e;
 308
 309         e=get_e_kin(moldyn->atom,moldyn->count);
 310         e+=get_e_pot(moldyn);
 311
 312         return e;
 313 }
 314
 315 t_3dvec get_total_p(t_atom *atom, int count) {
 316
 317         t_3dvec p,p_total;
 318         int i;
 319
 320         v3_zero(&p_total);
 321         for(i=0;i<count;i++) {
 322                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 323                 v3_add(&p_total,&p_total,&p);
 324         }
 325
 326         return p_total;
 327 }
 328
 329 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
 330
 331         double tau;
 332
 333         tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
 334         tau*=1.0E-9;
 335         if(tau<moldyn->tau)
 336                 printf("[moldyn] warning: time step  (%f > %.15f)\n",
 337                        moldyn->tau,tau);
 338
 339         return tau;
 340 }
 341
 342 /*
 343  * numerical tricks
 344  */
 345
 346 /* verlet list */
 347
 348 int verlet_list_init(t_moldyn *moldyn) {
 349
 350         int i,fd;
 351
 352         fd=open("/dev/null",O_WRONLY);
 353
 354         for(i=0;i<moldyn->count;i++)
 355                 list_init(&(moldyn->atom[i].verlet),fd);
 356
 357         moldyn->r_verlet=1.1*moldyn->cutoff;
 358         /* +moldyn->tau*\
 359                 sqrt(3.0*K_BOLTZMANN*moldyn->t/moldyn->atom[0].mass); */
 360
 361         printf("debug: r verlet = %.15f\n",moldyn->r_verlet);
 362         printf("       r cutoff = %.15f\n",moldyn->cutoff);
 363         printf("       dim      = %.15f\n",moldyn->dim.x);
 364
 365         /* make sure to update the list in the beginning */
 366         moldyn->dr_max1=moldyn->r_verlet;
 367         moldyn->dr_max2=moldyn->r_verlet;
 368
 369         return 0;
 370 }
 371
 372 int link_cell_init(t_moldyn *moldyn) {
 373
 374         t_linkcell *lc;
 375
 376         lc=&(moldyn->lc);
 377
 378         /* partitioning the md cell */
 379         lc->nx=moldyn->dim.x/moldyn->cutoff;
 380         lc->x=moldyn->dim.x/lc->nx;
 381         lc->ny=moldyn->dim.y/moldyn->cutoff;
 382         lc->y=moldyn->dim.y/lc->ny;
 383         lc->nz=moldyn->dim.z/moldyn->cutoff;
 384         lc->z=moldyn->dim.z/lc->nz;
 385
 386         lc->subcell=malloc(lc->nx*lc->ny*lc->nz*sizeof(t_list));
 387
 388         link_cell_update(moldyn);
 389
 390         return 0;
 391 }
 392
 393 int verlet_list_update(t_moldyn *moldyn) {
 394
 395         int i,j;
 396         t_3dvec d;
 397         t_atom *atom;
 398
 399         atom=moldyn->atom;
 400
 401         puts("debug: list update start");
 402
 403         for(i=0;i<moldyn->count;i++) {
 404                 list_destroy(&(atom[i].verlet));
 405                 for(j=0;j<moldyn->count;j++) {
 406                         if(i!=j) {
 407                                 v3_sub(&d,&(atom[i].r),&(atom[j].r));
 408                                 v3_per_bound(&d,&(moldyn->dim));
 409                                 if(v3_norm(&d)<=moldyn->r_verlet)
 410                                         list_add_immediate_ptr(&(atom[i].verlet),&(atom[j]));
 411                         }
 412                 }
 413         }
 414
 415         moldyn->dr_max1=0.0;
 416         moldyn->dr_max2=0.0;
 417
 418         puts("debug: list update end");
 419
 420         return 0;
 421 }
 422
 423 int link_cell_update(t_moldyn *moldyn) {
 424
 425         int count,i,j,k;
 426         int nx,ny,nz;
 427         t_atom *atom;
 428
 429         atom=moldyn->atom;
 430         nx=moldyn->lc.nx; ny=moldyn->lc.ny; nz=moldyn->lc.nz;
 431
 432         for(i=0;i<nx*ny*nz;i++)
 433                 list_destroy(&(moldyn->lc.subcell[i]));
 434
 435         for(count=0;count<moldyn->count;count++) {
 436                 for(i=0;i<nx;i++) {
 437                         if((atom[count].r.x>=i*moldyn->dim.x) && \
 438                            (atom[count].r.x<(i+1)*moldyn->dim.x))
 439                                 break;
 440                 }
 441                 for(j=0;j<ny;j++) {
 442                         if((atom[count].r.y>=j*moldyn->dim.y) && \
 443                            (atom[count].r.y<(j+1)*moldyn->dim.y))
 444                                 break;
 445                 }
 446                 for(k=0;k<nz;k++) {
 447                         if((atom[count].r.z>=k*moldyn->dim.z) && \
 448                            (atom[count].r.z<(k+1)*moldyn->dim.z))
 449                                 break;
 450                 }
 451                 list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 452                                        &(atom[count]));
 453         }
 454
 455         return 0;
 456 }
 457
 458 int verlet_list_shutdown(t_moldyn *moldyn) {
 459
 460         int i;
 461
 462         for(i=0;i<moldyn->count;i++)
 463                 list_shutdown(&(moldyn->atom[i].verlet));
 464
 465         return 0;
 466 }
 467
 468 int link_cell_shutdown(t_moldyn *moldyn) {
 469
 470         int i;
 471         t_linkcell *lc;
 472
 473         lc=&(moldyn->lc);
 474
 475         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 476                 list_shutdown(&(moldyn->lc.subcell[i]));
 477
 478         return 0;
 479 }
 480
 481 /*
 482  *
 483  * 'integration of newtons equation' - algorithms
 484  *
 485  */
 486
 487 /* start the integration */
 488
 489 int moldyn_integrate(t_moldyn *moldyn) {
 490
 491         int i;
 492         unsigned int e,m,s,d,v;
 493         t_3dvec p;
 494         double rlc;
 495
 496         int fd;
 497         char fb[128];
 498
 499         /* logging & visualization */
 500         e=moldyn->ewrite;
 501         m=moldyn->mwrite;
 502         s=moldyn->swrite;
 503         d=moldyn->dwrite;
 504         v=moldyn->vwrite;
 505
 506         /* verlet list */
 507         rlc=moldyn->r_verlet-moldyn->cutoff;
 508
 509         if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
 510                 printf("[moldyn] warning, lv system not initialized\n");
 511                 return -1;
 512         }
 513
 514         /* create the verlet list */
 515         verlet_list_update(moldyn);
 516
 517         /* calculate initial forces */
 518         moldyn->force(moldyn);
 519
 520         for(i=0;i<moldyn->time_steps;i++) {
 521                 /* check for velet list update */
 522                 printf(".");
 523                 if(moldyn->dr_max1+moldyn->dr_max2>rlc) {
 524                         printf("\n");
 525                         verlet_list_update(moldyn);
 526                 }
 527
 528                 /* integration step */
 529                 moldyn->integrate(moldyn);
 530
 531                 /* check for log & visualiziation */
 532                 if(e) {
 533                         if(!(i%e))
 534                                 dprintf(moldyn->efd,
 535                                         "%.15f %.45f\n",i*moldyn->tau,
 536                                         get_total_energy(moldyn));
 537                 }
 538                 if(m) {
 539                         if(!(i%m)) {
 540                                 p=get_total_p(moldyn->atom,moldyn->count);
 541                                 dprintf(moldyn->mfd,
 542                                         "%.15f %.45f\n",i*moldyn->tau,
 543                                         v3_norm(&p));
 544                         }
 545                 }
 546                 if(s) {
 547                         if(!(i%s)) {
 548                                 snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
 549                                          moldyn->t,i*moldyn->tau);
 550                                 fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
 551                                 if(fd<0) perror("[moldyn] save fd open");
 552                                 else {
 553                                         write(fd,moldyn,sizeof(t_moldyn));
 554                                         write(fd,moldyn->atom,
 555                                               moldyn->count*sizeof(t_atom));
 556                                 }
 557                         }
 558                 }
 559                 if(d) {
 560                         if(!(i%d))
 561                                 write(moldyn->dfd,moldyn->atom,
 562                                       moldyn->count*sizeof(t_atom));
 563
 564                 }
 565                 if(v) {
 566                         if(!(i%v))
 567                                 visual_atoms(moldyn->visual,i*moldyn->tau,
 568                                              moldyn->atom,moldyn->count);
 569                 }
 570         }
 571
 572         return 0;
 573 }
 574
 575 /* velocity verlet */
 576
 577 int velocity_verlet(t_moldyn *moldyn) {
 578
 579         int i,count;
 580         double tau,tau_square,dr;
 581         t_3dvec delta;
 582         t_atom *atom;
 583
 584         atom=moldyn->atom;
 585         count=moldyn->count;
 586         tau=moldyn->tau;
 587
 588         tau_square=tau*tau;
 589
 590         for(i=0;i<count;i++) {
 591                 /* new positions */
 592                 v3_scale(&delta,&(atom[i].v),tau);
 593                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 594                 v3_add(&(atom[i].dr),&(atom[i].dr),&delta);
 595                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 596                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 597                 v3_add(&(atom[i].dr),&(atom[i].dr),&delta);
 598                 v3_per_bound(&(atom[i].r),&(moldyn->dim));
 599
 600                 /* set maximum dr (possible list update) */
 601                 dr=v3_norm(&(atom[i].dr));
 602                 if(dr>moldyn->dr_max1) {
 603                         moldyn->dr_max2=moldyn->dr_max1;
 604                         moldyn->dr_max1=dr;
 605                 }
 606                 else if(dr>moldyn->dr_max2) moldyn->dr_max2=dr;
 607
 608                 /* velocities */
 609                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 610                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 611         }
 612
 613         /* forces depending on chosen potential */
 614         moldyn->force(moldyn);
 615
 616         for(i=0;i<count;i++) {
 617                 /* again velocities */
 618                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 619                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 620         }
 621
 622         return 0;
 623 }
 624
 625
 626 /*
 627  *
 628  * potentials & corresponding forces
 629  *
 630  */
 631
 632 /* harmonic oscillator potential and force */
 633
 634 double potential_harmonic_oscillator(t_moldyn *moldyn) {
 635
 636         t_ho_params *params;
 637         t_atom *atom;
 638         int i,j;
 639         int count;
 640         t_3dvec distance;
 641         double d,u;
 642         double sc,equi_dist;
 643
 644         params=moldyn->pot_params;
 645         atom=moldyn->atom;
 646         sc=params->spring_constant;
 647         equi_dist=params->equilibrium_distance;
 648         count=moldyn->count;
 649
 650         u=0.0;
 651         for(i=0;i<count;i++) {
 652                 for(j=0;j<i;j++) {
 653                         v3_sub(&distance,&(atom[i].r),&(atom[j].r));
 654                         d=v3_norm(&distance);
 655                         u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
 656                 }
 657         }
 658
 659         return u;
 660 }
 661
 662 int force_harmonic_oscillator(t_moldyn *moldyn) {
 663
 664         t_ho_params *params;
 665         int i,j,count;
 666         t_atom *atom;
 667         t_3dvec distance;
 668         t_3dvec force;
 669         double d;
 670         double sc,equi_dist;
 671
 672         atom=moldyn->atom;
 673         count=moldyn->count;
 674         params=moldyn->pot_params;
 675         sc=params->spring_constant;
 676         equi_dist=params->equilibrium_distance;
 677
 678         for(i=0;i<count;i++) v3_zero(&(atom[i].f));
 679
 680         for(i=0;i<count;i++) {
 681                 for(j=0;j<i;j++) {
 682                         v3_sub(&distance,&(atom[i].r),&(atom[j].r));
 683                         v3_per_bound(&distance,&(moldyn->dim));
 684                         d=v3_norm(&distance);
 685                         if(d<=moldyn->cutoff) {
 686                                 v3_scale(&force,&distance,
 687                                          -sc*(1.0-(equi_dist/d)));
 688                                 v3_add(&(atom[i].f),&(atom[i].f),&force);
 689                                 v3_sub(&(atom[j].f),&(atom[j].f),&force);
 690                         }
 691                 }
 692         }
 693
 694         return 0;
 695 }
 696
 697
 698 /* lennard jones potential & force for one sort of atoms */
 699
 700 double potential_lennard_jones(t_moldyn *moldyn) {
 701
 702         t_lj_params *params;
 703         t_atom *atom,*btom;
 704         int i;
 705         int count;
 706         t_3dvec distance;
 707         double d,help;
 708         double u;
 709         double eps,sig6,sig12;
 710
 711         params=moldyn->pot_params;
 712         atom=moldyn->atom;
 713         count=moldyn->count;
 714         eps=params->epsilon4;
 715         sig6=params->sigma6;
 716         sig12=params->sigma12;
 717
 718         u=0.0;
 719         for(i=0;i<count;i++) {
 720                 list_reset(&(atom[i].verlet));
 721                 if(atom[i].verlet.current==NULL) continue;
 722                 while(1) {
 723                         btom=atom[i].verlet.current->data;
 724                         v3_sub(&distance,&(atom[i].r),&(btom->r));
 725                         v3_per_bound(&distance,&(moldyn->dim));
 726                         d=1.0/v3_absolute_square(&distance);    /* 1/r^2 */
 727                         help=d*d;                               /* 1/r^4 */
 728                         help*=d;                                /* 1/r^6 */
 729                         d=help*help;                            /* 1/r^12 */
 730                         u+=eps*(sig12*d-sig6*help);
 731                         if(list_next(&(atom[i].verlet))==L_NO_NEXT_ELEMENT)
 732                                 break;
 733                 }
 734         }
 735
 736         return u;
 737 }
 738
 739 int force_lennard_jones(t_moldyn *moldyn) {
 740
 741         t_lj_params *params;
 742         int i,count;
 743         t_atom *atom,*btom;
 744         t_3dvec distance;
 745         t_3dvec force;
 746         double d,h1,h2;
 747         double eps,sig6,sig12;
 748
 749         atom=moldyn->atom;
 750         count=moldyn->count;
 751         params=moldyn->pot_params;
 752         eps=params->epsilon4;
 753         sig6=6*params->sigma6;
 754         sig12=12*params->sigma12;
 755
 756         for(i=0;i<count;i++) v3_zero(&(atom[i].f));
 757
 758         for(i=0;i<count;i++) {
 759                 list_reset(&(atom[i].verlet));
 760                 if(atom[i].verlet.current==NULL) continue;
 761                 while(1) {
 762                         btom=atom[i].verlet.current->data;
 763                         v3_sub(&distance,&(atom[i].r),&(btom->r));
 764                         v3_per_bound(&distance,&(moldyn->dim));
 765                         d=v3_absolute_square(&distance);
 766                         if(d<=moldyn->cutoff_square) {
 767                                 h1=1.0/d;                       /* 1/r^2 */
 768                                 d=h1*h1;                        /* 1/r^4 */
 769                                 h2=d*d;                         /* 1/r^8 */
 770                                 h1*=d;                          /* 1/r^6 */
 771                                 h1*=h2;                         /* 1/r^14 */
 772                                 h1*=sig12;
 773                                 h2*=sig6;
 774                                 /* actually there would be a '-',       *
 775                                  * but f=-d/dr potential                */
 776                                 d=h1+h2;
 777                                 d*=eps;
 778                                 v3_scale(&force,&distance,d);
 779                                 v3_add(&(atom[i].f),&(atom[i].f),&force);
 780                                 //v3_sub(&(atom[j].f),&(atom[j].f),&force);
 781                         }
 782                         if(list_next(&(atom[i].verlet))==L_NO_NEXT_ELEMENT)
 783                                 break;
 784                 }
 785         }
 786
 787         return 0;
 788 }
 789