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 #include "report/report.h"
  20
  21 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
  22
  23         printf("[moldyn] init\n");
  24
  25         memset(moldyn,0,sizeof(t_moldyn));
  26
  27         rand_init(&(moldyn->random),NULL,1);
  28         moldyn->random.status|=RAND_STAT_VERBOSE;
  29
  30         return 0;
  31 }
  32
  33 int moldyn_shutdown(t_moldyn *moldyn) {
  34
  35         printf("[moldyn] shutdown\n");
  36
  37         moldyn_log_shutdown(moldyn);
  38         link_cell_shutdown(moldyn);
  39         rand_close(&(moldyn->random));
  40         free(moldyn->atom);
  41
  42         return 0;
  43 }
  44
  45 int set_int_alg(t_moldyn *moldyn,u8 algo) {
  46
  47         printf("[moldyn] integration algorithm: ");
  48
  49         switch(algo) {
  50                 case MOLDYN_INTEGRATE_VERLET:
  51                         moldyn->integrate=velocity_verlet;
  52                         printf("velocity verlet\n");
  53                         break;
  54                 default:
  55                         printf("unknown integration algorithm: %02x\n",algo);
  56                         printf("unknown\n");
  57                         return -1;
  58         }
  59
  60         return 0;
  61 }
  62
  63 int set_cutoff(t_moldyn *moldyn,double cutoff) {
  64
  65         moldyn->cutoff=cutoff;
  66
  67         printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
  68
  69         return 0;
  70 }
  71
  72 int set_temperature(t_moldyn *moldyn,double t_ref) {
  73
  74         moldyn->t_ref=t_ref;
  75
  76         printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
  77
  78         return 0;
  79 }
  80
  81 int set_pressure(t_moldyn *moldyn,double p_ref) {
  82
  83         moldyn->p_ref=p_ref;
  84
  85         printf("[moldyn] pressure [atm]: %f\n",moldyn->p_ref/ATM);
  86
  87         return 0;
  88 }
  89
  90 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
  91
  92         moldyn->pt_scale=(ptype|ttype);
  93         moldyn->t_tc=ttc;
  94         moldyn->p_tc=ptc;
  95
  96         printf("[moldyn] p/t scaling:\n");
  97
  98         printf("  p: %s",ptype?"yes":"no ");
  99         if(ptype)
 100                 printf(" | type: %02x | factor: %f",ptype,ptc);
 101         printf("\n");
 102
 103         printf("  t: %s",ttype?"yes":"no ");
 104         if(ttype)
 105                 printf(" | type: %02x | factor: %f",ttype,ttc);
 106         printf("\n");
 107
 108         return 0;
 109 }
 110
 111 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 112
 113         moldyn->dim.x=x;
 114         moldyn->dim.y=y;
 115         moldyn->dim.z=z;
 116
 117         moldyn->volume=x*y*z;
 118
 119         if(visualize) {
 120                 moldyn->vis.dim.x=x;
 121                 moldyn->vis.dim.y=y;
 122                 moldyn->vis.dim.z=z;
 123         }
 124
 125         moldyn->dv=0.000001*moldyn->volume;
 126
 127         printf("[moldyn] dimensions in A and A^3 respectively:\n");
 128         printf("  x: %f\n",moldyn->dim.x);
 129         printf("  y: %f\n",moldyn->dim.y);
 130         printf("  z: %f\n",moldyn->dim.z);
 131         printf("  volume: %f\n",moldyn->volume);
 132         printf("  visualize simulation box: %s\n",visualize?"yes":"no");
 133         printf("  delta volume (pressure calc): %f\n",moldyn->dv);
 134
 135         return 0;
 136 }
 137
 138 int set_nn_dist(t_moldyn *moldyn,double dist) {
 139
 140         moldyn->nnd=dist;
 141
 142         return 0;
 143 }
 144
 145 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 146
 147         printf("[moldyn] periodic boundary conditions:\n");
 148
 149         if(x)
 150                 moldyn->status|=MOLDYN_STAT_PBX;
 151
 152         if(y)
 153                 moldyn->status|=MOLDYN_STAT_PBY;
 154
 155         if(z)
 156                 moldyn->status|=MOLDYN_STAT_PBZ;
 157
 158         printf("  x: %s\n",x?"yes":"no");
 159         printf("  y: %s\n",y?"yes":"no");
 160         printf("  z: %s\n",z?"yes":"no");
 161
 162         return 0;
 163 }
 164
 165 int set_potential1b(t_moldyn *moldyn,pf_func1b func) {
 166
 167         moldyn->func1b=func;
 168
 169         return 0;
 170 }
 171
 172 int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
 173
 174         moldyn->func2b=func;
 175
 176         return 0;
 177 }
 178
 179 int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func) {
 180
 181         moldyn->func2b_post=func;
 182
 183         return 0;
 184 }
 185
 186 int set_potential3b(t_moldyn *moldyn,pf_func3b func) {
 187
 188         moldyn->func3b=func;
 189
 190         return 0;
 191 }
 192
 193 int set_potential_params(t_moldyn *moldyn,void *params) {
 194
 195         moldyn->pot_params=params;
 196
 197         return 0;
 198 }
 199
 200 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
 201
 202         strncpy(moldyn->vlsdir,dir,127);
 203
 204         return 0;
 205 }
 206
 207 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
 208
 209         strncpy(moldyn->rauthor,author,63);
 210         strncpy(moldyn->rtitle,title,63);
 211
 212         return 0;
 213 }
 214
 215 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 216
 217         char filename[128];
 218         int ret;
 219
 220         printf("[moldyn] set log: ");
 221
 222         switch(type) {
 223                 case LOG_TOTAL_ENERGY:
 224                         moldyn->ewrite=timer;
 225                         snprintf(filename,127,"%s/energy",moldyn->vlsdir);
 226                         moldyn->efd=open(filename,
 227                                          O_WRONLY|O_CREAT|O_EXCL,
 228                                          S_IRUSR|S_IWUSR);
 229                         if(moldyn->efd<0) {
 230                                 perror("[moldyn] energy log fd open");
 231                                 return moldyn->efd;
 232                         }
 233                         dprintf(moldyn->efd,"# total energy log file\n");
 234                         printf("total energy (%d)\n",timer);
 235                         break;
 236                 case LOG_TOTAL_MOMENTUM:
 237                         moldyn->mwrite=timer;
 238                         snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
 239                         moldyn->mfd=open(filename,
 240                                          O_WRONLY|O_CREAT|O_EXCL,
 241                                          S_IRUSR|S_IWUSR);
 242                         if(moldyn->mfd<0) {
 243                                 perror("[moldyn] momentum log fd open");
 244                                 return moldyn->mfd;
 245                         }
 246                         dprintf(moldyn->efd,"# total momentum log file\n");
 247                         printf("total momentum (%d)\n",timer);
 248                         break;
 249                 case LOG_PRESSURE:
 250                         moldyn->pwrite=timer;
 251                         snprintf(filename,127,"%s/pressure",moldyn->vlsdir);
 252                         moldyn->pfd=open(filename,
 253                                          O_WRONLY|O_CREAT|O_EXCL,
 254                                          S_IRUSR|S_IWUSR);
 255                         if(moldyn->pfd<0) {
 256                                 perror("[moldyn] pressure log file\n");
 257                                 return moldyn->pfd;
 258                         }
 259                         dprintf(moldyn->pfd,"# pressure log file\n");
 260                         printf("pressure (%d)\n",timer);
 261                         break;
 262                 case LOG_TEMPERATURE:
 263                         moldyn->twrite=timer;
 264                         snprintf(filename,127,"%s/temperature",moldyn->vlsdir);
 265                         moldyn->tfd=open(filename,
 266                                          O_WRONLY|O_CREAT|O_EXCL,
 267                                          S_IRUSR|S_IWUSR);
 268                         if(moldyn->tfd<0) {
 269                                 perror("[moldyn] temperature log file\n");
 270                                 return moldyn->tfd;
 271                         }
 272                         dprintf(moldyn->tfd,"# temperature log file\n");
 273                         printf("temperature (%d)\n",timer);
 274                         break;
 275                 case SAVE_STEP:
 276                         moldyn->swrite=timer;
 277                         printf("save file (%d)\n",timer);
 278                         break;
 279                 case VISUAL_STEP:
 280                         moldyn->vwrite=timer;
 281                         ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
 282                         if(ret<0) {
 283                                 printf("[moldyn] visual init failure\n");
 284                                 return ret;
 285                         }
 286                         printf("visual file (%d)\n",timer);
 287                         break;
 288                 case CREATE_REPORT:
 289                         snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
 290                         moldyn->rfd=open(filename,
 291                                          O_WRONLY|O_CREAT|O_EXCL,
 292                                          S_IRUSR|S_IWUSR);
 293                         if(moldyn->rfd<0) {
 294                                 perror("[moldyn] report fd open");
 295                                 return moldyn->rfd;
 296                         }
 297                         if(moldyn->efd) {
 298                                 snprintf(filename,127,"%s/e_plot.scr",
 299                                          moldyn->vlsdir);
 300                                 moldyn->epfd=open(filename,
 301                                                  O_WRONLY|O_CREAT|O_EXCL,
 302                                                  S_IRUSR|S_IWUSR);
 303                                 if(moldyn->epfd<0) {
 304                                         perror("[moldyn] energy plot fd open");
 305                                         return moldyn->epfd;
 306                                 }
 307                                 dprintf(moldyn->epfd,e_plot_script);
 308                                 close(moldyn->epfd);
 309                         }
 310                         if(moldyn->pfd) {
 311                                 snprintf(filename,127,"%s/pressure_plot.scr",
 312                                          moldyn->vlsdir);
 313                                 moldyn->ppfd=open(filename,
 314                                                   O_WRONLY|O_CREAT|O_EXCL,
 315                                                   S_IRUSR|S_IWUSR);
 316                                 if(moldyn->ppfd<0) {
 317                                         perror("[moldyn] p plot fd open");
 318                                         return moldyn->ppfd;
 319                                 }
 320                                 dprintf(moldyn->ppfd,pressure_plot_script);
 321                                 close(moldyn->ppfd);
 322                         }
 323                         if(moldyn->tfd) {
 324                                 snprintf(filename,127,"%s/temperature_plot.scr",
 325                                          moldyn->vlsdir);
 326                                 moldyn->tpfd=open(filename,
 327                                                   O_WRONLY|O_CREAT|O_EXCL,
 328                                                   S_IRUSR|S_IWUSR);
 329                                 if(moldyn->tpfd<0) {
 330                                         perror("[moldyn] t plot fd open");
 331                                         return moldyn->tpfd;
 332                                 }
 333                                 dprintf(moldyn->tpfd,temperature_plot_script);
 334                                 close(moldyn->tpfd);
 335                         }
 336                         dprintf(moldyn->rfd,report_start,
 337                                 moldyn->rauthor,moldyn->rtitle);
 338                         break;
 339                 default:
 340                         printf("unknown log type: %02x\n",type);
 341                         return -1;
 342         }
 343
 344         return 0;
 345 }
 346
 347 int moldyn_log_shutdown(t_moldyn *moldyn) {
 348
 349         char sc[256];
 350
 351         printf("[moldyn] log shutdown\n");
 352         if(moldyn->efd) {
 353                 close(moldyn->efd);
 354                 if(moldyn->rfd) {
 355                         dprintf(moldyn->rfd,report_energy);
 356                         snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
 357                                  moldyn->vlsdir);
 358                         system(sc);
 359                 }
 360         }
 361         if(moldyn->mfd) close(moldyn->mfd);
 362         if(moldyn->pfd) {
 363                 close(moldyn->pfd);
 364                 if(moldyn->rfd)
 365                         dprintf(moldyn->rfd,report_pressure);
 366                         snprintf(sc,255,"cd %s && gnuplot pressure_plot.scr",
 367                                  moldyn->vlsdir);
 368                         system(sc);
 369         }
 370         if(moldyn->tfd) {
 371                 close(moldyn->tfd);
 372                 if(moldyn->rfd)
 373                         dprintf(moldyn->rfd,report_temperature);
 374                         snprintf(sc,255,"cd %s && gnuplot temperature_plot.scr",
 375                                  moldyn->vlsdir);
 376                         system(sc);
 377         }
 378         if(moldyn->rfd) {
 379                 dprintf(moldyn->rfd,report_end);
 380                 close(moldyn->rfd);
 381                 snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
 382                 system(sc);
 383                 snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
 384                 system(sc);
 385                 snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
 386                 system(sc);
 387         }
 388         if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 389
 390         return 0;
 391 }
 392
 393 /*
 394  * creating lattice functions
 395  */
 396
 397 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 398                    u8 attr,u8 brand,int a,int b,int c) {
 399
 400         int new,count;
 401         int ret;
 402         t_3dvec origin;
 403         void *ptr;
 404         t_atom *atom;
 405
 406         new=a*b*c;
 407         count=moldyn->count;
 408
 409         /* how many atoms do we expect */
 410         if(type==CUBIC) new*=1;
 411         if(type==FCC) new*=4;
 412         if(type==DIAMOND) new*=8;
 413
 414         /* allocate space for atoms */
 415         ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
 416         if(!ptr) {
 417                 perror("[moldyn] realloc (create lattice)");
 418                 return -1;
 419         }
 420         moldyn->atom=ptr;
 421         atom=&(moldyn->atom[count]);
 422
 423         /* no atoms on the boundaries (only reason: it looks better!) */
 424         origin.x=0.5*lc;
 425         origin.y=0.5*lc;
 426         origin.z=0.5*lc;
 427
 428         switch(type) {
 429                 case CUBIC:
 430                         set_nn_dist(moldyn,lc);
 431                         ret=cubic_init(a,b,c,lc,atom,&origin);
 432                         break;
 433                 case FCC:
 434                         v3_scale(&origin,&origin,0.5);
 435                         set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
 436                         ret=fcc_init(a,b,c,lc,atom,&origin);
 437                         break;
 438                 case DIAMOND:
 439                         v3_scale(&origin,&origin,0.25);
 440                         set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
 441                         ret=diamond_init(a,b,c,lc,atom,&origin);
 442                         break;
 443                 default:
 444                         printf("unknown lattice type (%02x)\n",type);
 445                         return -1;
 446         }
 447
 448         /* debug */
 449         if(ret!=new) {
 450                 printf("[moldyn] creating lattice failed\n");
 451                 printf("  amount of atoms\n");
 452                 printf("  - expected: %d\n",new);
 453                 printf("  - created: %d\n",ret);
 454                 return -1;
 455         }
 456
 457         moldyn->count+=new;
 458         printf("[moldyn] created lattice with %d atoms\n",new);
 459
 460         for(ret=0;ret<new;ret++) {
 461                 atom[ret].element=element;
 462                 atom[ret].mass=mass;
 463                 atom[ret].attr=attr;
 464                 atom[ret].brand=brand;
 465                 atom[ret].tag=count+ret;
 466                 check_per_bound(moldyn,&(atom[ret].r));
 467         }
 468
 469         return ret;
 470 }
 471
 472 /* cubic init */
 473 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 474
 475         int count;
 476         t_3dvec r;
 477         int i,j,k;
 478         t_3dvec o;
 479
 480         count=0;
 481         if(origin)
 482                 v3_copy(&o,origin);
 483         else
 484                 v3_zero(&o);
 485
 486         r.x=o.x;
 487         for(i=0;i<a;i++) {
 488                 r.y=o.y;
 489                 for(j=0;j<b;j++) {
 490                         r.z=o.z;
 491                         for(k=0;k<c;k++) {
 492                                 v3_copy(&(atom[count].r),&r);
 493                                 count+=1;
 494                                 r.z+=lc;
 495                         }
 496                         r.y+=lc;
 497                 }
 498                 r.x+=lc;
 499         }
 500
 501         for(i=0;i<count;i++) {
 502                 atom[i].r.x-=(a*lc)/2.0;
 503                 atom[i].r.y-=(b*lc)/2.0;
 504                 atom[i].r.z-=(c*lc)/2.0;
 505         }
 506
 507         return count;
 508 }
 509
 510 /* fcc lattice init */
 511 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 512
 513         int count;
 514         int i,j,k,l;
 515         t_3dvec o,r,n;
 516         t_3dvec basis[3];
 517
 518         count=0;
 519         if(origin)
 520                 v3_copy(&o,origin);
 521         else
 522                 v3_zero(&o);
 523
 524         /* construct the basis */
 525         memset(basis,0,3*sizeof(t_3dvec));
 526         basis[0].x=0.5*lc;
 527         basis[0].y=0.5*lc;
 528         basis[1].x=0.5*lc;
 529         basis[1].z=0.5*lc;
 530         basis[2].y=0.5*lc;
 531         basis[2].z=0.5*lc;
 532
 533         /* fill up the room */
 534         r.x=o.x;
 535         for(i=0;i<a;i++) {
 536                 r.y=o.y;
 537                 for(j=0;j<b;j++) {
 538                         r.z=o.z;
 539                         for(k=0;k<c;k++) {
 540                                 /* first atom */
 541                                 v3_copy(&(atom[count].r),&r);
 542                                 count+=1;
 543                                 r.z+=lc;
 544                                 /* the three face centered atoms */
 545                                 for(l=0;l<3;l++) {
 546                                         v3_add(&n,&r,&basis[l]);
 547                                         v3_copy(&(atom[count].r),&n);
 548                                         count+=1;
 549                                 }
 550                         }
 551                         r.y+=lc;
 552                 }
 553                 r.x+=lc;
 554         }
 555
 556         /* coordinate transformation */
 557         for(i=0;i<count;i++) {
 558                 atom[i].r.x-=(a*lc)/2.0;
 559                 atom[i].r.y-=(b*lc)/2.0;
 560                 atom[i].r.z-=(c*lc)/2.0;
 561         }
 562
 563         return count;
 564 }
 565
 566 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 567
 568         int count;
 569         t_3dvec o;
 570
 571         count=fcc_init(a,b,c,lc,atom,origin);
 572
 573         o.x=0.25*lc;
 574         o.y=0.25*lc;
 575         o.z=0.25*lc;
 576
 577         if(origin) v3_add(&o,&o,origin);
 578
 579         count+=fcc_init(a,b,c,lc,&atom[count],&o);
 580
 581         return count;
 582 }
 583
 584 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 585              t_3dvec *r,t_3dvec *v) {
 586
 587         t_atom *atom;
 588         void *ptr;
 589         int count;
 590
 591         atom=moldyn->atom;
 592         count=(moldyn->count)++;
 593
 594         ptr=realloc(atom,(count+1)*sizeof(t_atom));
 595         if(!ptr) {
 596                 perror("[moldyn] realloc (add atom)");
 597                 return -1;
 598         }
 599         moldyn->atom=ptr;
 600
 601         atom=moldyn->atom;
 602         atom[count].r=*r;
 603         atom[count].v=*v;
 604         atom[count].element=element;
 605         atom[count].mass=mass;
 606         atom[count].brand=brand;
 607         atom[count].tag=count;
 608         atom[count].attr=attr;
 609
 610         return 0;
 611 }
 612
 613 int destroy_atoms(t_moldyn *moldyn) {
 614
 615         if(moldyn->atom) free(moldyn->atom);
 616
 617         return 0;
 618 }
 619
 620 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 621
 622         /*
 623          * - gaussian distribution of velocities
 624          * - zero total momentum
 625          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 626          */
 627
 628         int i;
 629         double v,sigma;
 630         t_3dvec p_total,delta;
 631         t_atom *atom;
 632         t_random *random;
 633
 634         atom=moldyn->atom;
 635         random=&(moldyn->random);
 636
 637         printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
 638
 639         /* gaussian distribution of velocities */
 640         v3_zero(&p_total);
 641         for(i=0;i<moldyn->count;i++) {
 642                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
 643                 /* x direction */
 644                 v=sigma*rand_get_gauss(random);
 645                 atom[i].v.x=v;
 646                 p_total.x+=atom[i].mass*v;
 647                 /* y direction */
 648                 v=sigma*rand_get_gauss(random);
 649                 atom[i].v.y=v;
 650                 p_total.y+=atom[i].mass*v;
 651                 /* z direction */
 652                 v=sigma*rand_get_gauss(random);
 653                 atom[i].v.z=v;
 654                 p_total.z+=atom[i].mass*v;
 655         }
 656
 657         /* zero total momentum */
 658         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 659         for(i=0;i<moldyn->count;i++) {
 660                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 661                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 662         }
 663
 664         /* velocity scaling */
 665         scale_velocity(moldyn,equi_init);
 666
 667         return 0;
 668 }
 669
 670 double temperature_calc(t_moldyn *moldyn) {
 671
 672         /* assume up to date kinetic energy, which is 3/2 N k_B T */
 673
 674         moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
 675
 676         return moldyn->t;
 677 }
 678
 679 double get_temperature(t_moldyn *moldyn) {
 680
 681         return moldyn->t;
 682 }
 683
 684 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 685
 686         int i;
 687         double e,scale;
 688         t_atom *atom;
 689         int count;
 690
 691         atom=moldyn->atom;
 692
 693         /*
 694          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 695          */
 696
 697         /* get kinetic energy / temperature & count involved atoms */
 698         e=0.0;
 699         count=0;
 700         for(i=0;i<moldyn->count;i++) {
 701                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
 702                         e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
 703                         count+=1;
 704                 }
 705         }
 706         e*=0.5;
 707         if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
 708         else return 0;  /* no atoms involved in scaling! */
 709
 710         /* (temporary) hack for e,t = 0 */
 711         if(e==0.0) {
 712         moldyn->t=0.0;
 713                 if(moldyn->t_ref!=0.0) {
 714                         thermal_init(moldyn,equi_init);
 715                         return 0;
 716                 }
 717                 else
 718                         return 0; /* no scaling needed */
 719         }
 720
 721
 722         /* get scaling factor */
 723         scale=moldyn->t_ref/moldyn->t;
 724         if(equi_init&TRUE)
 725                 scale*=2.0;
 726         else
 727                 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
 728                         scale=1.0+(scale-1.0)/moldyn->t_tc;
 729         scale=sqrt(scale);
 730
 731         /* velocity scaling */
 732         for(i=0;i<moldyn->count;i++) {
 733                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
 734                         v3_scale(&(atom[i].v),&(atom[i].v),scale);
 735         }
 736
 737         return 0;
 738 }
 739
 740 double ideal_gas_law_pressure(t_moldyn *moldyn) {
 741
 742         double p;
 743
 744         p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
 745
 746         return p;
 747 }
 748
 749 double pressure_calc(t_moldyn *moldyn) {
 750
 751         int i;
 752         double v;
 753         t_virial *virial;
 754
 755         /*
 756          * PV = NkT + <W>
 757          * W = 1/3 sum_i f_i r_i
 758          * virial = sum_i f_i r_i
 759          *
 760          * => P = (2 Ekin + virial) / (3V)
 761          */
 762
 763         v=0.0;
 764         for(i=0;i<moldyn->count;i++) {
 765                 virial=&(moldyn->atom[i].virial);
 766                 v+=(virial->xx+virial->yy+virial->zz);
 767         }
 768
 769         /* assume up to date kinetic energy */
 770         moldyn->p=2.0*moldyn->ekin+v;
 771         moldyn->p/=(3.0*moldyn->volume);
 772
 773         return moldyn->p;
 774 }
 775
 776 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 777
 778         t_3dvec dim,*tp;
 779         double u,p;
 780         double scale,dv;
 781         t_atom *store;
 782
 783         /*
 784          * dU = - p dV
 785          *
 786          * => p = - dU/dV
 787          *
 788          * dV: dx,y,z = 0.001 x,y,z
 789          */
 790
 791         scale=1.00001;
 792 printf("\n\nP-DEBUG:\n");
 793
 794         tp=&(moldyn->tp);
 795         store=malloc(moldyn->count*sizeof(t_atom));
 796         if(store==NULL) {
 797                 printf("[moldyn] allocating store mem failed\n");
 798                 return -1;
 799         }
 800
 801         /* save unscaled potential energy + atom/dim configuration */
 802         u=moldyn->energy;
 803         memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
 804         dim=moldyn->dim;
 805
 806         /* derivative with respect to x direction */
 807         scale_dim(moldyn,scale,TRUE,0,0);
 808         scale_atoms(moldyn,scale,TRUE,0,0);
 809         dv=0.00001*moldyn->dim.x*moldyn->dim.y*moldyn->dim.z;
 810         link_cell_shutdown(moldyn);
 811         link_cell_init(moldyn,QUIET);
 812         potential_force_calc(moldyn);
 813         tp->x=(moldyn->energy-u)/dv;
 814         p=tp->x*tp->x;
 815 printf("e: %f eV de: %f eV dV: %f A^3\n",moldyn->energy/moldyn->count/EV,(moldyn->energy-u)/moldyn->count/EV,dv);
 816
 817         /* restore atomic configuration + dim */
 818         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 819         moldyn->dim=dim;
 820
 821         /* derivative with respect to y direction */
 822         scale_dim(moldyn,scale,0,TRUE,0);
 823         scale_atoms(moldyn,scale,0,TRUE,0);
 824         dv=0.00001*moldyn->dim.y*moldyn->dim.x*moldyn->dim.z;
 825         link_cell_shutdown(moldyn);
 826         link_cell_init(moldyn,QUIET);
 827         potential_force_calc(moldyn);
 828         tp->y=(moldyn->energy-u)/dv;
 829         p+=tp->y*tp->y;
 830
 831         /* restore atomic configuration + dim */
 832         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 833         moldyn->dim=dim;
 834
 835         /* derivative with respect to z direction */
 836         scale_dim(moldyn,scale,0,0,TRUE);
 837         scale_atoms(moldyn,scale,0,0,TRUE);
 838         dv=0.00001*moldyn->dim.z*moldyn->dim.x*moldyn->dim.y;
 839         link_cell_shutdown(moldyn);
 840         link_cell_init(moldyn,QUIET);
 841         potential_force_calc(moldyn);
 842         tp->z=(moldyn->energy-u)/dv;
 843         p+=tp->z*tp->z;
 844
 845         /* restore atomic configuration + dim */
 846         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 847         moldyn->dim=dim;
 848
 849         /* restore energy */
 850         moldyn->energy=u;
 851
 852         link_cell_shutdown(moldyn);
 853         link_cell_init(moldyn,QUIET);
 854
 855         return sqrt(p);
 856 }
 857
 858 double get_pressure(t_moldyn *moldyn) {
 859
 860         return moldyn->p;
 861
 862 }
 863
 864 int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
 865
 866         t_3dvec *dim;
 867
 868         dim=&(moldyn->dim);
 869
 870         if(x) dim->x*=scale;
 871         if(y) dim->y*=scale;
 872         if(z) dim->z*=scale;
 873
 874         return 0;
 875 }
 876
 877 int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
 878
 879         int i;
 880         t_3dvec *r;
 881
 882         for(i=0;i<moldyn->count;i++) {
 883                 r=&(moldyn->atom[i].r);
 884                 if(x) r->x*=scale;
 885                 if(y) r->y*=scale;
 886                 if(z) r->z*=scale;
 887         }
 888
 889         return 0;
 890 }
 891
 892 int scale_volume(t_moldyn *moldyn) {
 893
 894         t_3dvec *dim,*vdim;
 895         double scale;
 896         t_linkcell *lc;
 897
 898         vdim=&(moldyn->vis.dim);
 899         dim=&(moldyn->dim);
 900         lc=&(moldyn->lc);
 901
 902         /* scaling factor */
 903         if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
 904                 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
 905                 scale=pow(scale,ONE_THIRD);
 906         }
 907         else {
 908                 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
 909         }
 910 moldyn->debug=scale;
 911
 912         /* scale the atoms and dimensions */
 913         scale_atoms(moldyn,scale,TRUE,TRUE,TRUE);
 914         scale_dim(moldyn,scale,TRUE,TRUE,TRUE);
 915
 916         /* visualize dimensions */
 917         if(vdim->x!=0) {
 918                 vdim->x=dim->x;
 919                 vdim->y=dim->y;
 920                 vdim->z=dim->z;
 921         }
 922
 923         /* recalculate scaled volume */
 924         moldyn->volume=dim->x*dim->y*dim->z;
 925
 926         /* adjust/reinit linkcell */
 927         if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
 928            ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
 929            ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
 930                 link_cell_shutdown(moldyn);
 931                 link_cell_init(moldyn,QUIET);
 932         } else {
 933                 lc->x*=scale;
 934                 lc->y*=scale;
 935                 lc->z*=scale;
 936         }
 937
 938         return 0;
 939
 940 }
 941
 942 double get_e_kin(t_moldyn *moldyn) {
 943
 944         int i;
 945         t_atom *atom;
 946
 947         atom=moldyn->atom;
 948         moldyn->ekin=0.0;
 949
 950         for(i=0;i<moldyn->count;i++)
 951                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 952
 953         return moldyn->ekin;
 954 }
 955
 956 double update_e_kin(t_moldyn *moldyn) {
 957
 958         return(get_e_kin(moldyn));
 959 }
 960
 961 double get_total_energy(t_moldyn *moldyn) {
 962
 963         return(moldyn->ekin+moldyn->energy);
 964 }
 965
 966 t_3dvec get_total_p(t_moldyn *moldyn) {
 967
 968         t_3dvec p,p_total;
 969         int i;
 970         t_atom *atom;
 971
 972         atom=moldyn->atom;
 973
 974         v3_zero(&p_total);
 975         for(i=0;i<moldyn->count;i++) {
 976                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 977                 v3_add(&p_total,&p_total,&p);
 978         }
 979
 980         return p_total;
 981 }
 982
 983 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 984
 985         double tau;
 986
 987         /* nn_dist is the nearest neighbour distance */
 988
 989         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
 990
 991         return tau;
 992 }
 993
 994 /*
 995  * numerical tricks
 996  */
 997
 998 /* linked list / cell method */
 999
1000 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1001
1002         t_linkcell *lc;
1003         int i;
1004
1005         lc=&(moldyn->lc);
1006
1007         /* partitioning the md cell */
1008         lc->nx=moldyn->dim.x/moldyn->cutoff;
1009         lc->x=moldyn->dim.x/lc->nx;
1010         lc->ny=moldyn->dim.y/moldyn->cutoff;
1011         lc->y=moldyn->dim.y/lc->ny;
1012         lc->nz=moldyn->dim.z/moldyn->cutoff;
1013         lc->z=moldyn->dim.z/lc->nz;
1014
1015         lc->cells=lc->nx*lc->ny*lc->nz;
1016         lc->subcell=malloc(lc->cells*sizeof(t_list));
1017
1018         if(lc->cells<27)
1019                 printf("[moldyn] FATAL: less then 27 subcells!\n");
1020
1021         if(vol) printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
1022
1023         for(i=0;i<lc->cells;i++)
1024                 list_init_f(&(lc->subcell[i]));
1025
1026         link_cell_update(moldyn);
1027
1028         return 0;
1029 }
1030
1031 int link_cell_update(t_moldyn *moldyn) {
1032
1033         int count,i,j,k;
1034         int nx,ny;
1035         t_atom *atom;
1036         t_linkcell *lc;
1037         double x,y,z;
1038
1039         atom=moldyn->atom;
1040         lc=&(moldyn->lc);
1041
1042         nx=lc->nx;
1043         ny=lc->ny;
1044
1045         x=moldyn->dim.x/2;
1046         y=moldyn->dim.y/2;
1047         z=moldyn->dim.z/2;
1048
1049         for(i=0;i<lc->cells;i++)
1050                 list_destroy_f(&(lc->subcell[i]));
1051
1052         for(count=0;count<moldyn->count;count++) {
1053                 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1054                 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1055                 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1056                 list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
1057                                      &(atom[count]));
1058         }
1059
1060         return 0;
1061 }
1062
1063 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1064
1065         t_linkcell *lc;
1066         int a;
1067         int count1,count2;
1068         int ci,cj,ck;
1069         int nx,ny,nz;
1070         int x,y,z;
1071         u8 bx,by,bz;
1072
1073         lc=&(moldyn->lc);
1074         nx=lc->nx;
1075         ny=lc->ny;
1076         nz=lc->nz;
1077         count1=1;
1078         count2=27;
1079         a=nx*ny;
1080
1081         cell[0]=lc->subcell[i+j*nx+k*a];
1082         for(ci=-1;ci<=1;ci++) {
1083                 bx=0;
1084                 x=i+ci;
1085                 if((x<0)||(x>=nx)) {
1086                         x=(x+nx)%nx;
1087                         bx=1;
1088                 }
1089                 for(cj=-1;cj<=1;cj++) {
1090                         by=0;
1091                         y=j+cj;
1092                         if((y<0)||(y>=ny)) {
1093                                 y=(y+ny)%ny;
1094                                 by=1;
1095                         }
1096                         for(ck=-1;ck<=1;ck++) {
1097                                 bz=0;
1098                                 z=k+ck;
1099                                 if((z<0)||(z>=nz)) {
1100                                         z=(z+nz)%nz;
1101                                         bz=1;
1102                                 }
1103                                 if(!(ci|cj|ck)) continue;
1104                                 if(bx|by|bz) {
1105                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
1106                                 }
1107                                 else {
1108                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
1109                                 }
1110                         }
1111                 }
1112         }
1113
1114         lc->dnlc=count1;
1115
1116         return count1;
1117 }
1118
1119 int link_cell_shutdown(t_moldyn *moldyn) {
1120
1121         int i;
1122         t_linkcell *lc;
1123
1124         lc=&(moldyn->lc);
1125
1126         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1127                 list_destroy_f(&(moldyn->lc.subcell[i]));
1128
1129         free(lc->subcell);
1130
1131         return 0;
1132 }
1133
1134 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1135
1136         int count;
1137         void *ptr;
1138         t_moldyn_schedule *schedule;
1139
1140         schedule=&(moldyn->schedule);
1141         count=++(schedule->total_sched);
1142
1143         ptr=realloc(schedule->runs,count*sizeof(int));
1144         if(!ptr) {
1145                 perror("[moldyn] realloc (runs)");
1146                 return -1;
1147         }
1148         schedule->runs=ptr;
1149         schedule->runs[count-1]=runs;
1150
1151         ptr=realloc(schedule->tau,count*sizeof(double));
1152         if(!ptr) {
1153                 perror("[moldyn] realloc (tau)");
1154                 return -1;
1155         }
1156         schedule->tau=ptr;
1157         schedule->tau[count-1]=tau;
1158
1159         printf("[moldyn] schedule added:\n");
1160         printf("  number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1161
1162
1163         return 0;
1164 }
1165
1166 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1167
1168         moldyn->schedule.hook=hook;
1169         moldyn->schedule.hook_params=hook_params;
1170
1171         return 0;
1172 }
1173
1174 /*
1175  *
1176  * 'integration of newtons equation' - algorithms
1177  *
1178  */
1179
1180 /* start the integration */
1181
1182 int moldyn_integrate(t_moldyn *moldyn) {
1183
1184         int i;
1185         unsigned int e,m,s,v,p,t;
1186         t_3dvec momentum;
1187         t_moldyn_schedule *sched;
1188         t_atom *atom;
1189         int fd;
1190         char dir[128];
1191         double ds;
1192         double energy_scale;
1193         //double tp;
1194
1195         sched=&(moldyn->schedule);
1196         atom=moldyn->atom;
1197
1198         /* initialize linked cell method */
1199         link_cell_init(moldyn,VERBOSE);
1200
1201         /* logging & visualization */
1202         e=moldyn->ewrite;
1203         m=moldyn->mwrite;
1204         s=moldyn->swrite;
1205         v=moldyn->vwrite;
1206         p=moldyn->pwrite;
1207         t=moldyn->twrite;
1208
1209         /* sqaure of some variables */
1210         moldyn->tau_square=moldyn->tau*moldyn->tau;
1211         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1212
1213         /* energy scaling factor */
1214         energy_scale=moldyn->count*EV;
1215
1216         /* calculate initial forces */
1217         potential_force_calc(moldyn);
1218
1219         /* some stupid checks before we actually start calculating bullshit */
1220         if(moldyn->cutoff>0.5*moldyn->dim.x)
1221                 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1222         if(moldyn->cutoff>0.5*moldyn->dim.y)
1223                 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1224         if(moldyn->cutoff>0.5*moldyn->dim.z)
1225                 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1226         ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1227         if(ds>0.05*moldyn->nnd)
1228                 printf("[moldyn] warning: forces too high / tau too small!\n");
1229
1230         /* zero absolute time */
1231         moldyn->time=0.0;
1232
1233         /* debugging, ignore */
1234         moldyn->debug=0;
1235
1236         /* tell the world */
1237         printf("[moldyn] integration start, go get a coffee ...\n");
1238
1239         /* executing the schedule */
1240         for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
1241
1242                 /* setting amount of runs and finite time step size */
1243                 moldyn->tau=sched->tau[sched->count];
1244                 moldyn->tau_square=moldyn->tau*moldyn->tau;
1245                 moldyn->time_steps=sched->runs[sched->count];
1246
1247         /* integration according to schedule */
1248
1249         for(i=0;i<moldyn->time_steps;i++) {
1250
1251                 /* integration step */
1252                 moldyn->integrate(moldyn);
1253
1254                 /* calculate kinetic energy, temperature and pressure */
1255                 update_e_kin(moldyn);
1256                 temperature_calc(moldyn);
1257                 pressure_calc(moldyn);
1258                 //tp=thermodynamic_pressure_calc(moldyn);
1259
1260                 /* p/t scaling */
1261                 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1262                         scale_velocity(moldyn,FALSE);
1263                 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1264                         scale_volume(moldyn);
1265
1266                 /* check for log & visualization */
1267                 if(e) {
1268                         if(!(i%e))
1269                                 dprintf(moldyn->efd,
1270                                         "%f %f %f %f\n",
1271                                         moldyn->time,moldyn->ekin/energy_scale,
1272                                         moldyn->energy/energy_scale,
1273                                         get_total_energy(moldyn)/energy_scale);
1274                 }
1275                 if(m) {
1276                         if(!(i%m)) {
1277                                 momentum=get_total_p(moldyn);
1278                                 dprintf(moldyn->mfd,
1279                                         "%f %f %f %f %f\n",moldyn->time,
1280                                         momentum.x,momentum.y,momentum.z,
1281                                         v3_norm(&momentum));
1282                         }
1283                 }
1284                 if(p) {
1285                         if(!(i%p)) {
1286                                 dprintf(moldyn->pfd,
1287                                         "%f %f\n",moldyn->time,moldyn->p/ATM);
1288                         }
1289                 }
1290                 if(t) {
1291                         if(!(i%t)) {
1292                                 dprintf(moldyn->tfd,
1293                                         "%f %f\n",moldyn->time,moldyn->t);
1294                         }
1295                 }
1296                 if(s) {
1297                         if(!(i%s)) {
1298                                 snprintf(dir,128,"%s/s-%07.f.save",
1299                                          moldyn->vlsdir,moldyn->time);
1300                                 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
1301                                 if(fd<0) perror("[moldyn] save fd open");
1302                                 else {
1303                                         write(fd,moldyn,sizeof(t_moldyn));
1304                                         write(fd,moldyn->atom,
1305                                               moldyn->count*sizeof(t_atom));
1306                                 }
1307                                 close(fd);
1308                         }
1309                 }
1310                 if(v) {
1311                         if(!(i%v)) {
1312                                 visual_atoms(&(moldyn->vis),moldyn->time,
1313                                              moldyn->atom,moldyn->count);
1314                         }
1315                 }
1316
1317                 /* display progress */
1318                 if(!(i%10)) {
1319                         printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f",
1320                                sched->count,i,
1321                                moldyn->t,moldyn->p/ATM,moldyn->volume);
1322                         fflush(stdout);
1323                 }
1324
1325                 /* increase absolute time */
1326                 moldyn->time+=moldyn->tau;
1327
1328         }
1329
1330                 /* check for hooks */
1331                 if(sched->hook)
1332                         sched->hook(moldyn,sched->hook_params);
1333
1334                 /* get a new info line */
1335                 printf("\n");
1336
1337         }
1338
1339         return 0;
1340 }
1341
1342 /* velocity verlet */
1343
1344 int velocity_verlet(t_moldyn *moldyn) {
1345
1346         int i,count;
1347         double tau,tau_square,h;
1348         t_3dvec delta;
1349         t_atom *atom;
1350
1351         atom=moldyn->atom;
1352         count=moldyn->count;
1353         tau=moldyn->tau;
1354         tau_square=moldyn->tau_square;
1355
1356         for(i=0;i<count;i++) {
1357                 /* new positions */
1358                 h=0.5/atom[i].mass;
1359                 v3_scale(&delta,&(atom[i].v),tau);
1360                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1361                 v3_scale(&delta,&(atom[i].f),h*tau_square);
1362                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1363                 check_per_bound(moldyn,&(atom[i].r));
1364
1365                 /* velocities [actually v(t+tau/2)] */
1366                 v3_scale(&delta,&(atom[i].f),h*tau);
1367                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1368         }
1369
1370         /* neighbour list update */
1371         link_cell_update(moldyn);
1372
1373         /* forces depending on chosen potential */
1374         potential_force_calc(moldyn);
1375
1376         for(i=0;i<count;i++) {
1377                 /* again velocities [actually v(t+tau)] */
1378                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1379                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1380         }
1381
1382         return 0;
1383 }
1384
1385
1386 /*
1387  *
1388  * potentials & corresponding forces & virial routine
1389  *
1390  */
1391
1392 /* generic potential and force calculation */
1393
1394 int potential_force_calc(t_moldyn *moldyn) {
1395
1396         int i,j,k,count;
1397         t_atom *itom,*jtom,*ktom;
1398         t_virial *virial;
1399         t_linkcell *lc;
1400         t_list neighbour_i[27];
1401         t_list neighbour_i2[27];
1402         t_list *this,*that;
1403         u8 bc_ij,bc_ik;
1404         int dnlc;
1405
1406         count=moldyn->count;
1407         itom=moldyn->atom;
1408         lc=&(moldyn->lc);
1409
1410         /* reset energy */
1411         moldyn->energy=0.0;
1412
1413         /* reset force, site energy and virial of every atom */
1414         for(i=0;i<count;i++) {
1415
1416                 /* reset force */
1417                 v3_zero(&(itom[i].f));
1418
1419                 /* reset virial */
1420                 virial=(&(itom[i].virial));
1421                 virial->xx=0.0;
1422                 virial->yy=0.0;
1423                 virial->zz=0.0;
1424                 virial->xy=0.0;
1425                 virial->xz=0.0;
1426                 virial->yz=0.0;
1427
1428                 /* reset site energy */
1429                 itom[i].e=0.0;
1430
1431         }
1432
1433         /* get energy,force and virial of every atom */
1434         for(i=0;i<count;i++) {
1435
1436                 /* single particle potential/force */
1437                 if(itom[i].attr&ATOM_ATTR_1BP)
1438                         moldyn->func1b(moldyn,&(itom[i]));
1439
1440                 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1441                         continue;
1442
1443                 /* 2 body pair potential/force */
1444
1445                 link_cell_neighbour_index(moldyn,
1446                                           (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1447                                           (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1448                                           (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1449                                           neighbour_i);
1450
1451                 dnlc=lc->dnlc;
1452
1453                 for(j=0;j<27;j++) {
1454
1455                         this=&(neighbour_i[j]);
1456                         list_reset_f(this);
1457
1458                         if(this->start==NULL)
1459                                 continue;
1460
1461                         bc_ij=(j<dnlc)?0:1;
1462
1463                         do {
1464                                 jtom=this->current->data;
1465
1466                                 if(jtom==&(itom[i]))
1467                                         continue;
1468
1469                                 if((jtom->attr&ATOM_ATTR_2BP)&
1470                                    (itom[i].attr&ATOM_ATTR_2BP)) {
1471                                         moldyn->func2b(moldyn,
1472                                                        &(itom[i]),
1473                                                        jtom,
1474                                                        bc_ij);
1475                                 }
1476
1477                                 /* 3 body potential/force */
1478
1479                                 if(!(itom[i].attr&ATOM_ATTR_3BP)||
1480                                    !(jtom->attr&ATOM_ATTR_3BP))
1481                                         continue;
1482
1483                                 /* copy the neighbour lists */
1484                                 memcpy(neighbour_i2,neighbour_i,
1485                                        27*sizeof(t_list));
1486
1487                                 /* get neighbours of i */
1488                                 for(k=0;k<27;k++) {
1489
1490                                         that=&(neighbour_i2[k]);
1491                                         list_reset_f(that);
1492
1493                                         if(that->start==NULL)
1494                                                 continue;
1495
1496                                         bc_ik=(k<dnlc)?0:1;
1497
1498                                         do {
1499
1500                                                 ktom=that->current->data;
1501
1502                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
1503                                                         continue;
1504
1505                                                 if(ktom==jtom)
1506                                                         continue;
1507
1508                                                 if(ktom==&(itom[i]))
1509                                                         continue;
1510
1511                                                 moldyn->func3b(moldyn,
1512                                                                &(itom[i]),
1513                                                                jtom,
1514                                                                ktom,
1515                                                                bc_ik|bc_ij);
1516
1517                                         } while(list_next_f(that)!=\
1518                                                 L_NO_NEXT_ELEMENT);
1519
1520                                 }
1521
1522                                 /* 2bp post function */
1523                                 if(moldyn->func2b_post) {
1524                                         moldyn->func2b_post(moldyn,
1525                                                             &(itom[i]),
1526                                                             jtom,bc_ij);
1527                                 }
1528
1529                         } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1530
1531                 }
1532
1533         }
1534
1535 #ifdef DEBUG
1536 printf("\n\n");
1537 #endif
1538 #ifdef VDEBUG
1539 printf("\n\n");
1540 #endif
1541
1542         return 0;
1543 }
1544
1545 /*
1546  * virial calculation
1547  */
1548
1549 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1550 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1551
1552         a->virial.xx+=f->x*d->x;
1553         a->virial.yy+=f->y*d->y;
1554         a->virial.zz+=f->z*d->z;
1555         a->virial.xy+=f->x*d->y;
1556         a->virial.xz+=f->x*d->z;
1557         a->virial.yz+=f->y*d->z;
1558
1559         return 0;
1560 }
1561
1562 /*
1563  * periodic boundayr checking
1564  */
1565
1566 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1567 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1568
1569         double x,y,z;
1570         t_3dvec *dim;
1571
1572         dim=&(moldyn->dim);
1573
1574         x=dim->x/2;
1575         y=dim->y/2;
1576         z=dim->z/2;
1577
1578         if(moldyn->status&MOLDYN_STAT_PBX) {
1579                 if(a->x>=x) a->x-=dim->x;
1580                 else if(-a->x>x) a->x+=dim->x;
1581         }
1582         if(moldyn->status&MOLDYN_STAT_PBY) {
1583                 if(a->y>=y) a->y-=dim->y;
1584                 else if(-a->y>y) a->y+=dim->y;
1585         }
1586         if(moldyn->status&MOLDYN_STAT_PBZ) {
1587                 if(a->z>=z) a->z-=dim->z;
1588                 else if(-a->z>z) a->z+=dim->z;
1589         }
1590
1591         return 0;
1592 }
1593
1594 /*
1595  * debugging / critical check functions
1596  */
1597
1598 int moldyn_bc_check(t_moldyn *moldyn) {
1599
1600         t_atom *atom;
1601         t_3dvec *dim;
1602         int i;
1603         double x;
1604         u8 byte;
1605         int j,k;
1606
1607         atom=moldyn->atom;
1608         dim=&(moldyn->dim);
1609         x=dim->x/2;
1610
1611         for(i=0;i<moldyn->count;i++) {
1612                 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1613                         printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1614                                i,atom[i].r.x,dim->x/2);
1615                         printf("diagnostic:\n");
1616                         printf("-----------\natom.r.x:\n");
1617                         for(j=0;j<8;j++) {
1618                                 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
1619                                 for(k=0;k<8;k++)
1620                                         printf("%d%c",
1621                                         ((byte)&(1<<k))?1:0,
1622                                         (k==7)?'\n':'|');
1623                         }
1624                         printf("---------------\nx=dim.x/2:\n");
1625                         for(j=0;j<8;j++) {
1626                                 memcpy(&byte,(u8 *)(&x)+j,1);
1627                                 for(k=0;k<8;k++)
1628                                         printf("%d%c",
1629                                         ((byte)&(1<<k))?1:0,
1630                                         (k==7)?'\n':'|');
1631                         }
1632                         if(atom[i].r.x==x) printf("the same!\n");
1633                         else printf("different!\n");
1634                 }
1635                 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
1636                         printf("FATAL: atom %d: y: %.20f (%.20f)\n",
1637                                i,atom[i].r.y,dim->y/2);
1638                 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
1639                         printf("FATAL: atom %d: z: %.20f (%.20f)\n",
1640                                i,atom[i].r.z,dim->z/2);
1641         }
1642
1643         return 0;
1644 }