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 <sys/time.h>
  17 #include <time.h>
  18 #include <math.h>
  19
  20 #include "moldyn.h"
  21 #include "report/report.h"
  22
  23 /*
  24  * global variables, pse and atom colors (only needed here)
  25  */
  26
  27 static char *pse_name[]={
  28         "*",
  29         "H",
  30         "He",
  31         "Li",
  32         "Be",
  33         "B",
  34         "C",
  35         "N",
  36         "O",
  37         "F",
  38         "Ne",
  39         "Na",
  40         "Mg",
  41         "Al",
  42         "Si",
  43         "P",
  44         "S",
  45         "Cl",
  46         "Ar",
  47 };
  48
  49 static char *pse_col[]={
  50         "*",
  51         "White",
  52         "He",
  53         "Li",
  54         "Be",
  55         "B",
  56         "Gray",
  57         "N",
  58         "Blue",
  59         "F",
  60         "Ne",
  61         "Na",
  62         "Mg",
  63         "Al",
  64         "Yellow",
  65         "P",
  66         "S",
  67         "Cl",
  68         "Ar",
  69 };
  70
  71 /*
  72  * the moldyn functions
  73  */
  74
  75 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
  76
  77         printf("[moldyn] init\n");
  78
  79         memset(moldyn,0,sizeof(t_moldyn));
  80
  81         moldyn->argc=argc;
  82         moldyn->args=argv;
  83
  84         rand_init(&(moldyn->random),NULL,1);
  85         moldyn->random.status|=RAND_STAT_VERBOSE;
  86
  87         return 0;
  88 }
  89
  90 int moldyn_shutdown(t_moldyn *moldyn) {
  91
  92         printf("[moldyn] shutdown\n");
  93
  94         moldyn_log_shutdown(moldyn);
  95         link_cell_shutdown(moldyn);
  96         rand_close(&(moldyn->random));
  97         free(moldyn->atom);
  98
  99         return 0;
 100 }
 101
 102 int set_int_alg(t_moldyn *moldyn,u8 algo) {
 103
 104         printf("[moldyn] integration algorithm: ");
 105
 106         switch(algo) {
 107                 case MOLDYN_INTEGRATE_VERLET:
 108                         moldyn->integrate=velocity_verlet;
 109                         printf("velocity verlet\n");
 110                         break;
 111                 default:
 112                         printf("unknown integration algorithm: %02x\n",algo);
 113                         printf("unknown\n");
 114                         return -1;
 115         }
 116
 117         return 0;
 118 }
 119
 120 int set_cutoff(t_moldyn *moldyn,double cutoff) {
 121
 122         moldyn->cutoff=cutoff;
 123
 124         printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
 125
 126         return 0;
 127 }
 128
 129 int set_bondlen(t_moldyn *moldyn,double b0,double b1,double bm) {
 130
 131         moldyn->bondlen[0]=b0*b0;
 132         moldyn->bondlen[1]=b1*b1;
 133         if(bm<0)
 134                 moldyn->bondlen[2]=b0*b1;
 135         else
 136                 moldyn->bondlen[2]=bm*bm;
 137
 138         return 0;
 139 }
 140
 141 int set_temperature(t_moldyn *moldyn,double t_ref) {
 142
 143         moldyn->t_ref=t_ref;
 144
 145         printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
 146
 147         return 0;
 148 }
 149
 150 int set_pressure(t_moldyn *moldyn,double p_ref) {
 151
 152         moldyn->p_ref=p_ref;
 153
 154         printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
 155
 156         return 0;
 157 }
 158
 159 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
 160
 161         moldyn->pt_scale=(ptype|ttype);
 162         moldyn->t_tc=ttc;
 163         moldyn->p_tc=ptc;
 164
 165         printf("[moldyn] p/t scaling:\n");
 166
 167         printf("  p: %s",ptype?"yes":"no ");
 168         if(ptype)
 169                 printf(" | type: %02x | factor: %f",ptype,ptc);
 170         printf("\n");
 171
 172         printf("  t: %s",ttype?"yes":"no ");
 173         if(ttype)
 174                 printf(" | type: %02x | factor: %f",ttype,ttc);
 175         printf("\n");
 176
 177         return 0;
 178 }
 179
 180 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 181
 182         moldyn->dim.x=x;
 183         moldyn->dim.y=y;
 184         moldyn->dim.z=z;
 185
 186         moldyn->volume=x*y*z;
 187
 188         if(visualize) {
 189                 moldyn->vis.dim.x=x;
 190                 moldyn->vis.dim.y=y;
 191                 moldyn->vis.dim.z=z;
 192         }
 193
 194         moldyn->dv=0.000001*moldyn->volume;
 195
 196         printf("[moldyn] dimensions in A and A^3 respectively:\n");
 197         printf("  x: %f\n",moldyn->dim.x);
 198         printf("  y: %f\n",moldyn->dim.y);
 199         printf("  z: %f\n",moldyn->dim.z);
 200         printf("  volume: %f\n",moldyn->volume);
 201         printf("  visualize simulation box: %s\n",visualize?"yes":"no");
 202         printf("  delta volume (pressure calc): %f\n",moldyn->dv);
 203
 204         return 0;
 205 }
 206
 207 int set_nn_dist(t_moldyn *moldyn,double dist) {
 208
 209         moldyn->nnd=dist;
 210
 211         return 0;
 212 }
 213
 214 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 215
 216         printf("[moldyn] periodic boundary conditions:\n");
 217
 218         if(x)
 219                 moldyn->status|=MOLDYN_STAT_PBX;
 220
 221         if(y)
 222                 moldyn->status|=MOLDYN_STAT_PBY;
 223
 224         if(z)
 225                 moldyn->status|=MOLDYN_STAT_PBZ;
 226
 227         printf("  x: %s\n",x?"yes":"no");
 228         printf("  y: %s\n",y?"yes":"no");
 229         printf("  z: %s\n",z?"yes":"no");
 230
 231         return 0;
 232 }
 233
 234 int set_potential1b(t_moldyn *moldyn,pf_func1b func) {
 235
 236         moldyn->func1b=func;
 237
 238         return 0;
 239 }
 240
 241 int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
 242
 243         moldyn->func2b=func;
 244
 245         return 0;
 246 }
 247
 248 int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
 249
 250         moldyn->func3b_j1=func;
 251
 252         return 0;
 253 }
 254
 255 int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) {
 256
 257         moldyn->func3b_j2=func;
 258
 259         return 0;
 260 }
 261
 262 int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func) {
 263
 264         moldyn->func3b_j3=func;
 265
 266         return 0;
 267 }
 268
 269 int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func) {
 270
 271         moldyn->func3b_k1=func;
 272
 273         return 0;
 274 }
 275
 276 int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func) {
 277
 278         moldyn->func3b_k2=func;
 279
 280         return 0;
 281 }
 282
 283 int set_potential_params(t_moldyn *moldyn,void *params) {
 284
 285         moldyn->pot_params=params;
 286
 287         return 0;
 288 }
 289
 290 int set_avg_skip(t_moldyn *moldyn,int skip) {
 291
 292         printf("[moldyn] skip %d steps before starting average calc\n",skip);
 293         moldyn->avg_skip=skip;
 294
 295         return 0;
 296 }
 297
 298 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
 299
 300         strncpy(moldyn->vlsdir,dir,127);
 301
 302         return 0;
 303 }
 304
 305 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
 306
 307         strncpy(moldyn->rauthor,author,63);
 308         strncpy(moldyn->rtitle,title,63);
 309
 310         return 0;
 311 }
 312
 313 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 314
 315         char filename[128];
 316         int ret;
 317
 318         printf("[moldyn] set log: ");
 319
 320         switch(type) {
 321                 case LOG_TOTAL_ENERGY:
 322                         moldyn->ewrite=timer;
 323                         snprintf(filename,127,"%s/energy",moldyn->vlsdir);
 324                         moldyn->efd=open(filename,
 325                                          O_WRONLY|O_CREAT|O_EXCL,
 326                                          S_IRUSR|S_IWUSR);
 327                         if(moldyn->efd<0) {
 328                                 perror("[moldyn] energy log fd open");
 329                                 return moldyn->efd;
 330                         }
 331                         dprintf(moldyn->efd,"# total energy log file\n");
 332                         printf("total energy (%d)\n",timer);
 333                         break;
 334                 case LOG_TOTAL_MOMENTUM:
 335                         moldyn->mwrite=timer;
 336                         snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
 337                         moldyn->mfd=open(filename,
 338                                          O_WRONLY|O_CREAT|O_EXCL,
 339                                          S_IRUSR|S_IWUSR);
 340                         if(moldyn->mfd<0) {
 341                                 perror("[moldyn] momentum log fd open");
 342                                 return moldyn->mfd;
 343                         }
 344                         dprintf(moldyn->efd,"# total momentum log file\n");
 345                         printf("total momentum (%d)\n",timer);
 346                         break;
 347                 case LOG_PRESSURE:
 348                         moldyn->pwrite=timer;
 349                         snprintf(filename,127,"%s/pressure",moldyn->vlsdir);
 350                         moldyn->pfd=open(filename,
 351                                          O_WRONLY|O_CREAT|O_EXCL,
 352                                          S_IRUSR|S_IWUSR);
 353                         if(moldyn->pfd<0) {
 354                                 perror("[moldyn] pressure log file\n");
 355                                 return moldyn->pfd;
 356                         }
 357                         dprintf(moldyn->pfd,"# pressure log file\n");
 358                         printf("pressure (%d)\n",timer);
 359                         break;
 360                 case LOG_TEMPERATURE:
 361                         moldyn->twrite=timer;
 362                         snprintf(filename,127,"%s/temperature",moldyn->vlsdir);
 363                         moldyn->tfd=open(filename,
 364                                          O_WRONLY|O_CREAT|O_EXCL,
 365                                          S_IRUSR|S_IWUSR);
 366                         if(moldyn->tfd<0) {
 367                                 perror("[moldyn] temperature log file\n");
 368                                 return moldyn->tfd;
 369                         }
 370                         dprintf(moldyn->tfd,"# temperature log file\n");
 371                         printf("temperature (%d)\n",timer);
 372                         break;
 373                 case SAVE_STEP:
 374                         moldyn->swrite=timer;
 375                         printf("save file (%d)\n",timer);
 376                         break;
 377                 case VISUAL_STEP:
 378                         moldyn->vwrite=timer;
 379                         ret=visual_init(moldyn,moldyn->vlsdir);
 380                         if(ret<0) {
 381                                 printf("[moldyn] visual init failure\n");
 382                                 return ret;
 383                         }
 384                         printf("visual file (%d)\n",timer);
 385                         break;
 386                 case CREATE_REPORT:
 387                         snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
 388                         moldyn->rfd=open(filename,
 389                                          O_WRONLY|O_CREAT|O_EXCL,
 390                                          S_IRUSR|S_IWUSR);
 391                         if(moldyn->rfd<0) {
 392                                 perror("[moldyn] report fd open");
 393                                 return moldyn->rfd;
 394                         }
 395                         printf("report -> ");
 396                         if(moldyn->efd) {
 397                                 snprintf(filename,127,"%s/e_plot.scr",
 398                                          moldyn->vlsdir);
 399                                 moldyn->epfd=open(filename,
 400                                                  O_WRONLY|O_CREAT|O_EXCL,
 401                                                  S_IRUSR|S_IWUSR);
 402                                 if(moldyn->epfd<0) {
 403                                         perror("[moldyn] energy plot fd open");
 404                                         return moldyn->epfd;
 405                                 }
 406                                 dprintf(moldyn->epfd,e_plot_script);
 407                                 close(moldyn->epfd);
 408                                 printf("energy ");
 409                         }
 410                         if(moldyn->pfd) {
 411                                 snprintf(filename,127,"%s/pressure_plot.scr",
 412                                          moldyn->vlsdir);
 413                                 moldyn->ppfd=open(filename,
 414                                                   O_WRONLY|O_CREAT|O_EXCL,
 415                                                   S_IRUSR|S_IWUSR);
 416                                 if(moldyn->ppfd<0) {
 417                                         perror("[moldyn] p plot fd open");
 418                                         return moldyn->ppfd;
 419                                 }
 420                                 dprintf(moldyn->ppfd,pressure_plot_script);
 421                                 close(moldyn->ppfd);
 422                                 printf("pressure ");
 423                         }
 424                         if(moldyn->tfd) {
 425                                 snprintf(filename,127,"%s/temperature_plot.scr",
 426                                          moldyn->vlsdir);
 427                                 moldyn->tpfd=open(filename,
 428                                                   O_WRONLY|O_CREAT|O_EXCL,
 429                                                   S_IRUSR|S_IWUSR);
 430                                 if(moldyn->tpfd<0) {
 431                                         perror("[moldyn] t plot fd open");
 432                                         return moldyn->tpfd;
 433                                 }
 434                                 dprintf(moldyn->tpfd,temperature_plot_script);
 435                                 close(moldyn->tpfd);
 436                                 printf("temperature ");
 437                         }
 438                         dprintf(moldyn->rfd,report_start,
 439                                 moldyn->rauthor,moldyn->rtitle);
 440                         printf("\n");
 441                         break;
 442                 default:
 443                         printf("unknown log type: %02x\n",type);
 444                         return -1;
 445         }
 446
 447         return 0;
 448 }
 449
 450 int moldyn_log_shutdown(t_moldyn *moldyn) {
 451
 452         char sc[256];
 453
 454         printf("[moldyn] log shutdown\n");
 455         if(moldyn->efd) {
 456                 close(moldyn->efd);
 457                 if(moldyn->rfd) {
 458                         dprintf(moldyn->rfd,report_energy);
 459                         snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
 460                                  moldyn->vlsdir);
 461                         system(sc);
 462                 }
 463         }
 464         if(moldyn->mfd) close(moldyn->mfd);
 465         if(moldyn->pfd) {
 466                 close(moldyn->pfd);
 467                 if(moldyn->rfd)
 468                         dprintf(moldyn->rfd,report_pressure);
 469                         snprintf(sc,255,"cd %s && gnuplot pressure_plot.scr",
 470                                  moldyn->vlsdir);
 471                         system(sc);
 472         }
 473         if(moldyn->tfd) {
 474                 close(moldyn->tfd);
 475                 if(moldyn->rfd)
 476                         dprintf(moldyn->rfd,report_temperature);
 477                         snprintf(sc,255,"cd %s && gnuplot temperature_plot.scr",
 478                                  moldyn->vlsdir);
 479                         system(sc);
 480         }
 481         if(moldyn->rfd) {
 482                 dprintf(moldyn->rfd,report_end);
 483                 close(moldyn->rfd);
 484                 snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
 485                          moldyn->vlsdir);
 486                 system(sc);
 487                 snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
 488                          moldyn->vlsdir);
 489                 system(sc);
 490                 snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
 491                          moldyn->vlsdir);
 492                 system(sc);
 493         }
 494
 495         return 0;
 496 }
 497
 498 /*
 499  * creating lattice functions
 500  */
 501
 502 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 503                    u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
 504
 505         int new,count;
 506         int ret;
 507         t_3dvec orig;
 508         void *ptr;
 509         t_atom *atom;
 510
 511         new=a*b*c;
 512         count=moldyn->count;
 513
 514         /* how many atoms do we expect */
 515         if(type==CUBIC) new*=1;
 516         if(type==FCC) new*=4;
 517         if(type==DIAMOND) new*=8;
 518
 519         /* allocate space for atoms */
 520         ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
 521         if(!ptr) {
 522                 perror("[moldyn] realloc (create lattice)");
 523                 return -1;
 524         }
 525         moldyn->atom=ptr;
 526         atom=&(moldyn->atom[count]);
 527
 528         /* no atoms on the boundaries (only reason: it looks better!) */
 529         if(!origin) {
 530                 orig.x=0.5*lc;
 531                 orig.y=0.5*lc;
 532                 orig.z=0.5*lc;
 533         }
 534         else {
 535                 orig.x=origin->x;
 536                 orig.y=origin->y;
 537                 orig.z=origin->z;
 538         }
 539
 540         switch(type) {
 541                 case CUBIC:
 542                         set_nn_dist(moldyn,lc);
 543                         ret=cubic_init(a,b,c,lc,atom,&orig);
 544                         break;
 545                 case FCC:
 546                         if(!origin)
 547                                 v3_scale(&orig,&orig,0.5);
 548                         set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
 549                         ret=fcc_init(a,b,c,lc,atom,&orig);
 550                         break;
 551                 case DIAMOND:
 552                         if(!origin)
 553                                 v3_scale(&orig,&orig,0.25);
 554                         set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
 555                         ret=diamond_init(a,b,c,lc,atom,&orig);
 556                         break;
 557                 default:
 558                         printf("unknown lattice type (%02x)\n",type);
 559                         return -1;
 560         }
 561
 562         /* debug */
 563         if(ret!=new) {
 564                 printf("[moldyn] creating lattice failed\n");
 565                 printf("  amount of atoms\n");
 566                 printf("  - expected: %d\n",new);
 567                 printf("  - created: %d\n",ret);
 568                 return -1;
 569         }
 570
 571         moldyn->count+=new;
 572         printf("[moldyn] created lattice with %d atoms\n",new);
 573
 574         for(ret=0;ret<new;ret++) {
 575                 atom[ret].element=element;
 576                 atom[ret].mass=mass;
 577                 atom[ret].attr=attr;
 578                 atom[ret].brand=brand;
 579                 atom[ret].tag=count+ret;
 580                 check_per_bound(moldyn,&(atom[ret].r));
 581                 atom[ret].r_0=atom[ret].r;
 582         }
 583
 584         /* update total system mass */
 585         total_mass_calc(moldyn);
 586
 587         return ret;
 588 }
 589
 590 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 591              t_3dvec *r,t_3dvec *v) {
 592
 593         t_atom *atom;
 594         void *ptr;
 595         int count;
 596
 597         atom=moldyn->atom;
 598         count=(moldyn->count)++;
 599
 600         ptr=realloc(atom,(count+1)*sizeof(t_atom));
 601         if(!ptr) {
 602                 perror("[moldyn] realloc (add atom)");
 603                 return -1;
 604         }
 605         moldyn->atom=ptr;
 606
 607         atom=moldyn->atom;
 608         atom[count].r=*r;
 609         atom[count].v=*v;
 610         atom[count].element=element;
 611         atom[count].mass=mass;
 612         atom[count].brand=brand;
 613         atom[count].tag=count;
 614         atom[count].attr=attr;
 615         check_per_bound(moldyn,&(atom[count].r));
 616         atom[count].r_0=atom[count].r;
 617
 618         /* update total system mass */
 619         total_mass_calc(moldyn);
 620
 621         return 0;
 622 }
 623
 624 int del_atom(t_moldyn *moldyn,int tag) {
 625
 626         t_atom *new,*old;
 627         int cnt;
 628
 629         old=moldyn->atom;
 630
 631         new=(t_atom *)malloc((moldyn->count-1)*sizeof(t_atom));
 632         if(!new) {
 633                 perror("[moldyn]malloc (del atom)");
 634                 return -1;
 635         }
 636
 637         for(cnt=0;cnt<tag;cnt++)
 638                 new[cnt]=old[cnt];
 639
 640         for(cnt=tag+1;cnt<moldyn->count;cnt++) {
 641                 new[cnt-1]=old[cnt];
 642                 new[cnt-1].tag=cnt-1;
 643         }
 644
 645         moldyn->count-=1;
 646         moldyn->atom=new;
 647
 648         free(old);
 649
 650         return 0;
 651 }
 652
 653 /* cubic init */
 654 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 655
 656         int count;
 657         t_3dvec r;
 658         int i,j,k;
 659         t_3dvec o;
 660
 661         count=0;
 662         if(origin)
 663                 v3_copy(&o,origin);
 664         else
 665                 v3_zero(&o);
 666
 667         r.x=o.x;
 668         for(i=0;i<a;i++) {
 669                 r.y=o.y;
 670                 for(j=0;j<b;j++) {
 671                         r.z=o.z;
 672                         for(k=0;k<c;k++) {
 673                                 v3_copy(&(atom[count].r),&r);
 674                                 count+=1;
 675                                 r.z+=lc;
 676                         }
 677                         r.y+=lc;
 678                 }
 679                 r.x+=lc;
 680         }
 681
 682         for(i=0;i<count;i++) {
 683                 atom[i].r.x-=(a*lc)/2.0;
 684                 atom[i].r.y-=(b*lc)/2.0;
 685                 atom[i].r.z-=(c*lc)/2.0;
 686         }
 687
 688         return count;
 689 }
 690
 691 /* fcc lattice init */
 692 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 693
 694         int count;
 695         int i,j,k,l;
 696         t_3dvec o,r,n;
 697         t_3dvec basis[3];
 698
 699         count=0;
 700         if(origin)
 701                 v3_copy(&o,origin);
 702         else
 703                 v3_zero(&o);
 704
 705         /* construct the basis */
 706         memset(basis,0,3*sizeof(t_3dvec));
 707         basis[0].x=0.5*lc;
 708         basis[0].y=0.5*lc;
 709         basis[1].x=0.5*lc;
 710         basis[1].z=0.5*lc;
 711         basis[2].y=0.5*lc;
 712         basis[2].z=0.5*lc;
 713
 714         /* fill up the room */
 715         r.x=o.x;
 716         for(i=0;i<a;i++) {
 717                 r.y=o.y;
 718                 for(j=0;j<b;j++) {
 719                         r.z=o.z;
 720                         for(k=0;k<c;k++) {
 721                                 /* first atom */
 722                                 v3_copy(&(atom[count].r),&r);
 723                                 count+=1;
 724                                 r.z+=lc;
 725                                 /* the three face centered atoms */
 726                                 for(l=0;l<3;l++) {
 727                                         v3_add(&n,&r,&basis[l]);
 728                                         v3_copy(&(atom[count].r),&n);
 729                                         count+=1;
 730                                 }
 731                         }
 732                         r.y+=lc;
 733                 }
 734                 r.x+=lc;
 735         }
 736
 737         /* coordinate transformation */
 738         for(i=0;i<count;i++) {
 739                 atom[i].r.x-=(a*lc)/2.0;
 740                 atom[i].r.y-=(b*lc)/2.0;
 741                 atom[i].r.z-=(c*lc)/2.0;
 742         }
 743
 744         return count;
 745 }
 746
 747 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 748
 749         int count;
 750         t_3dvec o;
 751
 752         count=fcc_init(a,b,c,lc,atom,origin);
 753
 754         o.x=0.25*lc;
 755         o.y=0.25*lc;
 756         o.z=0.25*lc;
 757
 758         if(origin) v3_add(&o,&o,origin);
 759
 760         count+=fcc_init(a,b,c,lc,&atom[count],&o);
 761
 762         return count;
 763 }
 764
 765 int destroy_atoms(t_moldyn *moldyn) {
 766
 767         if(moldyn->atom) free(moldyn->atom);
 768
 769         return 0;
 770 }
 771
 772 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 773
 774         /*
 775          * - gaussian distribution of velocities
 776          * - zero total momentum
 777          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 778          */
 779
 780         int i;
 781         double v,sigma;
 782         t_3dvec p_total,delta;
 783         t_atom *atom;
 784         t_random *random;
 785
 786         atom=moldyn->atom;
 787         random=&(moldyn->random);
 788
 789         printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
 790
 791         /* gaussian distribution of velocities */
 792         v3_zero(&p_total);
 793         for(i=0;i<moldyn->count;i++) {
 794                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
 795                 /* x direction */
 796                 v=sigma*rand_get_gauss(random);
 797                 atom[i].v.x=v;
 798                 p_total.x+=atom[i].mass*v;
 799                 /* y direction */
 800                 v=sigma*rand_get_gauss(random);
 801                 atom[i].v.y=v;
 802                 p_total.y+=atom[i].mass*v;
 803                 /* z direction */
 804                 v=sigma*rand_get_gauss(random);
 805                 atom[i].v.z=v;
 806                 p_total.z+=atom[i].mass*v;
 807         }
 808
 809         /* zero total momentum */
 810         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 811         for(i=0;i<moldyn->count;i++) {
 812                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 813                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 814         }
 815
 816         /* velocity scaling */
 817         scale_velocity(moldyn,equi_init);
 818
 819         return 0;
 820 }
 821
 822 double total_mass_calc(t_moldyn *moldyn) {
 823
 824         int i;
 825
 826         moldyn->mass=0.0;
 827
 828         for(i=0;i<moldyn->count;i++)
 829                 moldyn->mass+=moldyn->atom[i].mass;
 830
 831         return moldyn->mass;
 832 }
 833
 834 double temperature_calc(t_moldyn *moldyn) {
 835
 836         /* assume up to date kinetic energy, which is 3/2 N k_B T */
 837
 838         moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
 839
 840         return moldyn->t;
 841 }
 842
 843 double get_temperature(t_moldyn *moldyn) {
 844
 845         return moldyn->t;
 846 }
 847
 848 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 849
 850         int i;
 851         double e,scale;
 852         t_atom *atom;
 853         int count;
 854
 855         atom=moldyn->atom;
 856
 857         /*
 858          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 859          */
 860
 861         /* get kinetic energy / temperature & count involved atoms */
 862         e=0.0;
 863         count=0;
 864         for(i=0;i<moldyn->count;i++) {
 865                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
 866                         e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
 867                         count+=1;
 868                 }
 869         }
 870         e*=0.5;
 871         if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
 872         else return 0;  /* no atoms involved in scaling! */
 873
 874         /* (temporary) hack for e,t = 0 */
 875         if(e==0.0) {
 876         moldyn->t=0.0;
 877                 if(moldyn->t_ref!=0.0) {
 878                         thermal_init(moldyn,equi_init);
 879                         return 0;
 880                 }
 881                 else
 882                         return 0; /* no scaling needed */
 883         }
 884
 885
 886         /* get scaling factor */
 887         scale=moldyn->t_ref/moldyn->t;
 888         if(equi_init&TRUE)
 889                 scale*=2.0;
 890         else
 891                 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
 892                         scale=1.0+(scale-1.0)/moldyn->t_tc;
 893         scale=sqrt(scale);
 894
 895         /* velocity scaling */
 896         for(i=0;i<moldyn->count;i++) {
 897                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
 898                         v3_scale(&(atom[i].v),&(atom[i].v),scale);
 899         }
 900
 901         return 0;
 902 }
 903
 904 double ideal_gas_law_pressure(t_moldyn *moldyn) {
 905
 906         double p;
 907
 908         p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
 909
 910         return p;
 911 }
 912
 913 double virial_sum(t_moldyn *moldyn) {
 914
 915         int i;
 916         double v;
 917         t_virial *virial;
 918
 919         /* virial (sum over atom virials) */
 920         v=0.0;
 921         for(i=0;i<moldyn->count;i++) {
 922                 virial=&(moldyn->atom[i].virial);
 923                 v+=(virial->xx+virial->yy+virial->zz);
 924         }
 925         moldyn->virial=v;
 926
 927         /* global virial (absolute coordinates) */
 928         virial=&(moldyn->gvir);
 929         moldyn->gv=virial->xx+virial->yy+virial->zz;
 930
 931         return moldyn->virial;
 932 }
 933
 934 double pressure_calc(t_moldyn *moldyn) {
 935
 936         /*
 937          * PV = NkT + <W>
 938          * with W = 1/3 sum_i f_i r_i (- skipped!)
 939          * virial = sum_i f_i r_i
 940          *
 941          * => P = (2 Ekin + virial) / (3V)
 942          */
 943
 944         /* assume up to date virial & up to date kinetic energy */
 945
 946         /* pressure (atom virials) */
 947         moldyn->p=2.0*moldyn->ekin+moldyn->virial;
 948         moldyn->p/=(3.0*moldyn->volume);
 949
 950         /* pressure (absolute coordinates) */
 951         moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
 952         moldyn->gp/=(3.0*moldyn->volume);
 953
 954         return moldyn->p;
 955 }
 956
 957 int average_and_fluctuation_calc(t_moldyn *moldyn) {
 958
 959         int denom;
 960
 961         if(moldyn->total_steps<moldyn->avg_skip)
 962                 return 0;
 963
 964         denom=moldyn->total_steps+1-moldyn->avg_skip;
 965
 966         /* assume up to date energies, temperature, pressure etc */
 967
 968         /* kinetic energy */
 969         moldyn->k_sum+=moldyn->ekin;
 970         moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
 971         moldyn->k_avg=moldyn->k_sum/denom;
 972         moldyn->k2_avg=moldyn->k2_sum/denom;
 973         moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg);
 974
 975         /* potential energy */
 976         moldyn->v_sum+=moldyn->energy;
 977         moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
 978         moldyn->v_avg=moldyn->v_sum/denom;
 979         moldyn->v2_avg=moldyn->v2_sum/denom;
 980         moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
 981
 982         /* temperature */
 983         moldyn->t_sum+=moldyn->t;
 984         moldyn->t_avg=moldyn->t_sum/denom;
 985
 986         /* virial */
 987         moldyn->virial_sum+=moldyn->virial;
 988         moldyn->virial_avg=moldyn->virial_sum/denom;
 989         moldyn->gv_sum+=moldyn->gv;
 990         moldyn->gv_avg=moldyn->gv_sum/denom;
 991
 992         /* pressure */
 993         moldyn->p_sum+=moldyn->p;
 994         moldyn->p_avg=moldyn->p_sum/denom;
 995         moldyn->gp_sum+=moldyn->gp;
 996         moldyn->gp_avg=moldyn->gp_sum/denom;
 997
 998         return 0;
 999 }
1000
1001 int get_heat_capacity(t_moldyn *moldyn) {
1002
1003         double temp2,ighc;
1004
1005         /* averages needed for heat capacity calc */
1006         if(moldyn->total_steps<moldyn->avg_skip)
1007                 return 0;
1008
1009         /* (temperature average)^2 */
1010         temp2=moldyn->t_avg*moldyn->t_avg;
1011         printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
1012                moldyn->t_avg);
1013
1014         /* ideal gas contribution */
1015         ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
1016         printf("  ideal gas contribution: %f\n",
1017                ighc/moldyn->mass*KILOGRAM/JOULE);
1018
1019         /* specific heat for nvt ensemble */
1020         moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc;
1021         moldyn->c_v_nvt/=moldyn->mass;
1022
1023         /* specific heat for nve ensemble */
1024         moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_avg/(ighc*K_BOLTZMANN*temp2)));
1025         moldyn->c_v_nve/=moldyn->mass;
1026
1027         printf("  NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
1028         printf("  NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
1029 printf("  --> <dV2> sim: %f experimental: %f\n",moldyn->dv2_avg,1.5*moldyn->count*K_B2*moldyn->t_avg*moldyn->t_avg*(1.0-1.5*moldyn->count*K_BOLTZMANN/(700*moldyn->mass*JOULE/KILOGRAM)));
1030
1031         return 0;
1032 }
1033
1034 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
1035
1036         t_3dvec dim;
1037         //t_3dvec *tp;
1038         double u_up,u_down,dv;
1039         double scale,p;
1040         t_atom *store;
1041
1042         /*
1043          * dU = - p dV
1044          *
1045          * => p = - dU/dV
1046          *
1047          */
1048
1049         scale=0.00001;
1050         dv=8*scale*scale*scale*moldyn->volume;
1051
1052         store=malloc(moldyn->count*sizeof(t_atom));
1053         if(store==NULL) {
1054                 printf("[moldyn] allocating store mem failed\n");
1055                 return -1;
1056         }
1057
1058         /* save unscaled potential energy + atom/dim configuration */
1059         memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
1060         dim=moldyn->dim;
1061
1062         /* scale up dimension and atom positions */
1063         scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
1064         scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
1065         link_cell_shutdown(moldyn);
1066         link_cell_init(moldyn,QUIET);
1067         potential_force_calc(moldyn);
1068         u_up=moldyn->energy;
1069
1070         /* restore atomic configuration + dim */
1071         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
1072         moldyn->dim=dim;
1073
1074         /* scale down dimension and atom positions */
1075         scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
1076         scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
1077         link_cell_shutdown(moldyn);
1078         link_cell_init(moldyn,QUIET);
1079         potential_force_calc(moldyn);
1080         u_down=moldyn->energy;
1081
1082         /* calculate pressure */
1083         p=-(u_up-u_down)/dv;
1084 printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR);
1085
1086         /* restore atomic configuration + dim */
1087         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
1088         moldyn->dim=dim;
1089
1090         /* restore energy */
1091         potential_force_calc(moldyn);
1092
1093         link_cell_shutdown(moldyn);
1094         link_cell_init(moldyn,QUIET);
1095
1096         return p;
1097 }
1098
1099 double get_pressure(t_moldyn *moldyn) {
1100
1101         return moldyn->p;
1102
1103 }
1104
1105 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1106
1107         t_3dvec *dim;
1108
1109         dim=&(moldyn->dim);
1110
1111         if(dir==SCALE_UP)
1112                 scale=1.0+scale;
1113
1114         if(dir==SCALE_DOWN)
1115                 scale=1.0-scale;
1116
1117         if(x) dim->x*=scale;
1118         if(y) dim->y*=scale;
1119         if(z) dim->z*=scale;
1120
1121         return 0;
1122 }
1123
1124 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1125
1126         int i;
1127         t_3dvec *r;
1128
1129         if(dir==SCALE_UP)
1130                 scale=1.0+scale;
1131
1132         if(dir==SCALE_DOWN)
1133                 scale=1.0-scale;
1134
1135         for(i=0;i<moldyn->count;i++) {
1136                 r=&(moldyn->atom[i].r);
1137                 if(x) r->x*=scale;
1138                 if(y) r->y*=scale;
1139                 if(z) r->z*=scale;
1140         }
1141
1142         return 0;
1143 }
1144
1145 int scale_volume(t_moldyn *moldyn) {
1146
1147         t_3dvec *dim,*vdim;
1148         double scale;
1149         t_linkcell *lc;
1150
1151         vdim=&(moldyn->vis.dim);
1152         dim=&(moldyn->dim);
1153         lc=&(moldyn->lc);
1154
1155         /* scaling factor */
1156         if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
1157                 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
1158                 scale=pow(scale,ONE_THIRD);
1159         }
1160         else {
1161                 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
1162         }
1163 moldyn->debug=scale;
1164
1165         /* scale the atoms and dimensions */
1166         scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1167         scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1168
1169         /* visualize dimensions */
1170         if(vdim->x!=0) {
1171                 vdim->x=dim->x;
1172                 vdim->y=dim->y;
1173                 vdim->z=dim->z;
1174         }
1175
1176         /* recalculate scaled volume */
1177         moldyn->volume=dim->x*dim->y*dim->z;
1178
1179         /* adjust/reinit linkcell */
1180         if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
1181            ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
1182            ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
1183                 link_cell_shutdown(moldyn);
1184                 link_cell_init(moldyn,QUIET);
1185         } else {
1186                 lc->x*=scale;
1187                 lc->y*=scale;
1188                 lc->z*=scale;
1189         }
1190
1191         return 0;
1192
1193 }
1194
1195 double e_kin_calc(t_moldyn *moldyn) {
1196
1197         int i;
1198         t_atom *atom;
1199
1200         atom=moldyn->atom;
1201         moldyn->ekin=0.0;
1202
1203         for(i=0;i<moldyn->count;i++) {
1204                 atom[i].ekin=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
1205                 moldyn->ekin+=atom[i].ekin;
1206         }
1207
1208         return moldyn->ekin;
1209 }
1210
1211 double get_total_energy(t_moldyn *moldyn) {
1212
1213         return(moldyn->ekin+moldyn->energy);
1214 }
1215
1216 t_3dvec get_total_p(t_moldyn *moldyn) {
1217
1218         t_3dvec p,p_total;
1219         int i;
1220         t_atom *atom;
1221
1222         atom=moldyn->atom;
1223
1224         v3_zero(&p_total);
1225         for(i=0;i<moldyn->count;i++) {
1226                 v3_scale(&p,&(atom[i].v),atom[i].mass);
1227                 v3_add(&p_total,&p_total,&p);
1228         }
1229
1230         return p_total;
1231 }
1232
1233 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
1234
1235         double tau;
1236
1237         /* nn_dist is the nearest neighbour distance */
1238
1239         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
1240
1241         return tau;
1242 }
1243
1244 /*
1245  * numerical tricks
1246  */
1247
1248 /* linked list / cell method */
1249
1250 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1251
1252         t_linkcell *lc;
1253         int i;
1254
1255         lc=&(moldyn->lc);
1256
1257         /* partitioning the md cell */
1258         lc->nx=moldyn->dim.x/moldyn->cutoff;
1259         lc->x=moldyn->dim.x/lc->nx;
1260         lc->ny=moldyn->dim.y/moldyn->cutoff;
1261         lc->y=moldyn->dim.y/lc->ny;
1262         lc->nz=moldyn->dim.z/moldyn->cutoff;
1263         lc->z=moldyn->dim.z/lc->nz;
1264         lc->cells=lc->nx*lc->ny*lc->nz;
1265
1266 #ifdef STATIC_LISTS
1267         lc->subcell=malloc(lc->cells*sizeof(int*));
1268 #else
1269         lc->subcell=malloc(lc->cells*sizeof(t_list));
1270 #endif
1271
1272         if(lc->subcell==NULL) {
1273                 perror("[moldyn] cell init (malloc)");
1274                 return -1;
1275         }
1276
1277         if(lc->cells<27)
1278                 printf("[moldyn] FATAL: less then 27 subcells!\n");
1279
1280         if(vol) {
1281 #ifdef STATIC_LISTS
1282                 printf("[moldyn] initializing 'static' linked cells (%d)\n",
1283                        lc->cells);
1284 #else
1285                 printf("[moldyn] initializing 'dynamic' linked cells (%d)\n",
1286                        lc->cells);
1287 #endif
1288                 printf("  x: %d x %f A\n",lc->nx,lc->x);
1289                 printf("  y: %d x %f A\n",lc->ny,lc->y);
1290                 printf("  z: %d x %f A\n",lc->nz,lc->z);
1291         }
1292
1293 #ifdef STATIC_LISTS
1294         /* list init */
1295         for(i=0;i<lc->cells;i++) {
1296                 lc->subcell[i]=malloc((MAX_ATOMS_PER_LIST+1)*sizeof(int));
1297                 if(lc->subcell[i]==NULL) {
1298                         perror("[moldyn] list init (malloc)");
1299                         return -1;
1300                 }
1301                 /*
1302                 if(i==0)
1303                         printf(" ---> %d malloc %p (%p)\n",
1304                                i,lc->subcell[0],lc->subcell);
1305                 */
1306         }
1307 #else
1308         for(i=0;i<lc->cells;i++)
1309                 list_init_f(&(lc->subcell[i]));
1310 #endif
1311
1312         /* update the list */
1313         link_cell_update(moldyn);
1314
1315         return 0;
1316 }
1317
1318 int link_cell_update(t_moldyn *moldyn) {
1319
1320         int count,i,j,k;
1321         int nx,ny;
1322         t_atom *atom;
1323         t_linkcell *lc;
1324 #ifdef STATIC_LISTS
1325         int p;
1326 #endif
1327
1328         atom=moldyn->atom;
1329         lc=&(moldyn->lc);
1330
1331         nx=lc->nx;
1332         ny=lc->ny;
1333
1334         for(i=0;i<lc->cells;i++)
1335 #ifdef STATIC_LISTS
1336                 memset(lc->subcell[i],0,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
1337 #else
1338                 list_destroy_f(&(lc->subcell[i]));
1339 #endif
1340
1341         for(count=0;count<moldyn->count;count++) {
1342                 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1343                 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1344                 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1345
1346 #ifdef STATIC_LISTS
1347                 p=0;
1348                 while(lc->subcell[i+j*nx+k*nx*ny][p]!=0)
1349                         p++;
1350
1351                 if(p>=MAX_ATOMS_PER_LIST) {
1352                         printf("[moldyn] FATAL: amount of atoms too high!\n");
1353                         return -1;
1354                 }
1355
1356                 lc->subcell[i+j*nx+k*nx*ny][p]=count;
1357 #else
1358                 list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
1359                                      &(atom[count]));
1360                 /*
1361                 if(j==0&&k==0)
1362                         printf(" ---> %d %d malloc %p (%p)\n",
1363                                i,count,lc->subcell[i].current,lc->subcell);
1364                 */
1365 #endif
1366         }
1367
1368         return 0;
1369 }
1370
1371 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
1372 #ifdef STATIC_LISTS
1373                               int **cell
1374 #else
1375                               t_list *cell
1376 #endif
1377                              ) {
1378
1379         t_linkcell *lc;
1380         int a;
1381         int count1,count2;
1382         int ci,cj,ck;
1383         int nx,ny,nz;
1384         int x,y,z;
1385         u8 bx,by,bz;
1386
1387         lc=&(moldyn->lc);
1388         nx=lc->nx;
1389         ny=lc->ny;
1390         nz=lc->nz;
1391         count1=1;
1392         count2=27;
1393         a=nx*ny;
1394
1395         cell[0]=lc->subcell[i+j*nx+k*a];
1396         for(ci=-1;ci<=1;ci++) {
1397                 bx=0;
1398                 x=i+ci;
1399                 if((x<0)||(x>=nx)) {
1400                         x=(x+nx)%nx;
1401                         bx=1;
1402                 }
1403                 for(cj=-1;cj<=1;cj++) {
1404                         by=0;
1405                         y=j+cj;
1406                         if((y<0)||(y>=ny)) {
1407                                 y=(y+ny)%ny;
1408                                 by=1;
1409                         }
1410                         for(ck=-1;ck<=1;ck++) {
1411                                 bz=0;
1412                                 z=k+ck;
1413                                 if((z<0)||(z>=nz)) {
1414                                         z=(z+nz)%nz;
1415                                         bz=1;
1416                                 }
1417                                 if(!(ci|cj|ck)) continue;
1418                                 if(bx|by|bz) {
1419                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
1420                                 }
1421                                 else {
1422                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
1423                                 }
1424                         }
1425                 }
1426         }
1427
1428         lc->dnlc=count1;
1429
1430         return count1;
1431 }
1432
1433 int link_cell_shutdown(t_moldyn *moldyn) {
1434
1435         int i;
1436         t_linkcell *lc;
1437
1438         lc=&(moldyn->lc);
1439
1440         for(i=0;i<lc->cells;i++) {
1441 #ifdef STATIC_LISTS
1442                 free(lc->subcell[i]);
1443 #else
1444                 //printf(" ---> %d free %p\n",i,lc->subcell[i].start);
1445                 list_destroy_f(&(lc->subcell[i]));
1446 #endif
1447         }
1448
1449         free(lc->subcell);
1450
1451         return 0;
1452 }
1453
1454 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1455
1456         int count;
1457         void *ptr;
1458         t_moldyn_schedule *schedule;
1459
1460         schedule=&(moldyn->schedule);
1461         count=++(schedule->total_sched);
1462
1463         ptr=realloc(schedule->runs,count*sizeof(int));
1464         if(!ptr) {
1465                 perror("[moldyn] realloc (runs)");
1466                 return -1;
1467         }
1468         schedule->runs=ptr;
1469         schedule->runs[count-1]=runs;
1470
1471         ptr=realloc(schedule->tau,count*sizeof(double));
1472         if(!ptr) {
1473                 perror("[moldyn] realloc (tau)");
1474                 return -1;
1475         }
1476         schedule->tau=ptr;
1477         schedule->tau[count-1]=tau;
1478
1479         printf("[moldyn] schedule added:\n");
1480         printf("  number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1481
1482
1483         return 0;
1484 }
1485
1486 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1487
1488         moldyn->schedule.hook=hook;
1489         moldyn->schedule.hook_params=hook_params;
1490
1491         return 0;
1492 }
1493
1494 /*
1495  *
1496  * 'integration of newtons equation' - algorithms
1497  *
1498  */
1499
1500 /* start the integration */
1501
1502 int moldyn_integrate(t_moldyn *moldyn) {
1503
1504         int i;
1505         unsigned int e,m,s,v,p,t;
1506         t_3dvec momentum;
1507         t_moldyn_schedule *sched;
1508         t_atom *atom;
1509         int fd;
1510         char dir[128];
1511         double ds;
1512         double energy_scale;
1513         struct timeval t1,t2;
1514         //double tp;
1515
1516         sched=&(moldyn->schedule);
1517         atom=moldyn->atom;
1518
1519         /* initialize linked cell method */
1520         link_cell_init(moldyn,VERBOSE);
1521
1522         /* logging & visualization */
1523         e=moldyn->ewrite;
1524         m=moldyn->mwrite;
1525         s=moldyn->swrite;
1526         v=moldyn->vwrite;
1527         p=moldyn->pwrite;
1528         t=moldyn->twrite;
1529
1530         /* sqaure of some variables */
1531         moldyn->tau_square=moldyn->tau*moldyn->tau;
1532         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1533
1534         /* get current time */
1535         gettimeofday(&t1,NULL);
1536
1537         /* calculate initial forces */
1538         potential_force_calc(moldyn);
1539 #ifdef DEBUG
1540 //return 0;
1541 #endif
1542
1543         /* some stupid checks before we actually start calculating bullshit */
1544         if(moldyn->cutoff>0.5*moldyn->dim.x)
1545                 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1546         if(moldyn->cutoff>0.5*moldyn->dim.y)
1547                 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1548         if(moldyn->cutoff>0.5*moldyn->dim.z)
1549                 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1550         ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1551         if(ds>0.05*moldyn->nnd)
1552                 printf("[moldyn] warning: forces too high / tau too small!\n");
1553
1554         /* zero absolute time */
1555         moldyn->time=0.0;
1556         moldyn->total_steps=0;
1557
1558         /* debugging, ignore */
1559         moldyn->debug=0;
1560
1561         /* tell the world */
1562         printf("[moldyn] integration start, go get a coffee ...\n");
1563
1564         /* executing the schedule */
1565         sched->count=0;
1566         while(sched->count<sched->total_sched) {
1567
1568                 /* setting amount of runs and finite time step size */
1569                 moldyn->tau=sched->tau[sched->count];
1570                 moldyn->tau_square=moldyn->tau*moldyn->tau;
1571                 moldyn->time_steps=sched->runs[sched->count];
1572
1573                 /* energy scaling factor (might change!) */
1574                 energy_scale=moldyn->count*EV;
1575
1576         /* integration according to schedule */
1577
1578         for(i=0;i<moldyn->time_steps;i++) {
1579
1580                 /* integration step */
1581                 moldyn->integrate(moldyn);
1582
1583                 /* calculate kinetic energy, temperature and pressure */
1584                 e_kin_calc(moldyn);
1585                 temperature_calc(moldyn);
1586                 virial_sum(moldyn);
1587                 pressure_calc(moldyn);
1588                 average_and_fluctuation_calc(moldyn);
1589
1590                 /* p/t scaling */
1591                 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1592                         scale_velocity(moldyn,FALSE);
1593                 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1594                         scale_volume(moldyn);
1595
1596                 /* check for log & visualization */
1597                 if(e) {
1598                         if(!(moldyn->total_steps%e))
1599                                 dprintf(moldyn->efd,
1600                                         "%f %f %f %f\n",
1601                                         moldyn->time,moldyn->ekin/energy_scale,
1602                                         moldyn->energy/energy_scale,
1603                                         get_total_energy(moldyn)/energy_scale);
1604                 }
1605                 if(m) {
1606                         if(!(moldyn->total_steps%m)) {
1607                                 momentum=get_total_p(moldyn);
1608                                 dprintf(moldyn->mfd,
1609                                         "%f %f %f %f %f\n",moldyn->time,
1610                                         momentum.x,momentum.y,momentum.z,
1611                                         v3_norm(&momentum));
1612                         }
1613                 }
1614                 if(p) {
1615                         if(!(moldyn->total_steps%p)) {
1616                                 dprintf(moldyn->pfd,
1617                                         "%f %f %f %f %f\n",moldyn->time,
1618                                          moldyn->p/BAR,moldyn->p_avg/BAR,
1619                                          moldyn->gp/BAR,moldyn->gp_avg/BAR);
1620                         }
1621                 }
1622                 if(t) {
1623                         if(!(moldyn->total_steps%t)) {
1624                                 dprintf(moldyn->tfd,
1625                                         "%f %f %f\n",
1626                                         moldyn->time,moldyn->t,moldyn->t_avg);
1627                         }
1628                 }
1629                 if(s) {
1630                         if(!(moldyn->total_steps%s)) {
1631                                 snprintf(dir,128,"%s/s-%07.f.save",
1632                                          moldyn->vlsdir,moldyn->time);
1633                                 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
1634                                         S_IRUSR|S_IWUSR);
1635                                 if(fd<0) perror("[moldyn] save fd open");
1636                                 else {
1637                                         write(fd,moldyn,sizeof(t_moldyn));
1638                                         write(fd,moldyn->atom,
1639                                               moldyn->count*sizeof(t_atom));
1640                                 }
1641                                 close(fd);
1642                         }
1643                 }
1644                 if(v) {
1645                         if(!(moldyn->total_steps%v)) {
1646                                 visual_atoms(moldyn);
1647                         }
1648                 }
1649
1650                 /* display progress */
1651                 //if(!(moldyn->total_steps%10)) {
1652                         /* get current time */
1653                         gettimeofday(&t2,NULL);
1654
1655 printf("\rsched:%d, steps:%d/%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
1656        sched->count,i,moldyn->total_steps,
1657        moldyn->t,moldyn->t_avg,
1658        moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
1659        moldyn->volume,
1660        (int)(t2.tv_sec-t1.tv_sec));
1661
1662                         fflush(stdout);
1663
1664                         /* copy over time */
1665                         t1=t2;
1666                 //}
1667
1668                 /* increase absolute time */
1669                 moldyn->time+=moldyn->tau;
1670                 moldyn->total_steps+=1;
1671
1672         }
1673
1674                 /* check for hooks */
1675                 if(sched->hook) {
1676                         printf("\n ## schedule hook %d start ##\n",
1677                                sched->count);
1678                         sched->hook(moldyn,sched->hook_params);
1679                         printf(" ## schedule hook end ##\n");
1680                 }
1681
1682                 /* increase the schedule counter */
1683                 sched->count+=1;
1684
1685         }
1686
1687         return 0;
1688 }
1689
1690 /* velocity verlet */
1691
1692 int velocity_verlet(t_moldyn *moldyn) {
1693
1694         int i,count;
1695         double tau,tau_square,h;
1696         t_3dvec delta;
1697         t_atom *atom;
1698
1699         atom=moldyn->atom;
1700         count=moldyn->count;
1701         tau=moldyn->tau;
1702         tau_square=moldyn->tau_square;
1703
1704         for(i=0;i<count;i++) {
1705                 /* new positions */
1706                 h=0.5/atom[i].mass;
1707                 v3_scale(&delta,&(atom[i].v),tau);
1708                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1709                 v3_scale(&delta,&(atom[i].f),h*tau_square);
1710                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1711                 check_per_bound(moldyn,&(atom[i].r));
1712
1713                 /* velocities [actually v(t+tau/2)] */
1714                 v3_scale(&delta,&(atom[i].f),h*tau);
1715                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1716         }
1717
1718         /* neighbour list update */
1719         link_cell_update(moldyn);
1720
1721         /* forces depending on chosen potential */
1722         potential_force_calc(moldyn);
1723
1724         for(i=0;i<count;i++) {
1725                 /* again velocities [actually v(t+tau)] */
1726                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1727                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1728         }
1729
1730         return 0;
1731 }
1732
1733
1734 /*
1735  *
1736  * potentials & corresponding forces & virial routine
1737  *
1738  */
1739
1740 /* generic potential and force calculation */
1741
1742 int potential_force_calc(t_moldyn *moldyn) {
1743
1744         int i,j,k,count;
1745         t_atom *itom,*jtom,*ktom;
1746         t_virial *virial;
1747         t_linkcell *lc;
1748 #ifdef STATIC_LISTS
1749         int *neighbour_i[27];
1750         int p,q;
1751         t_atom *atom;
1752 #else
1753         t_list neighbour_i[27];
1754         t_list neighbour_i2[27];
1755         t_list *this,*that;
1756 #endif
1757         u8 bc_ij,bc_ik;
1758         int dnlc;
1759
1760         count=moldyn->count;
1761         itom=moldyn->atom;
1762         lc=&(moldyn->lc);
1763 #ifdef STATIC_LISTS
1764         atom=moldyn->atom;
1765 #endif
1766
1767         /* reset energy */
1768         moldyn->energy=0.0;
1769
1770         /* reset global virial */
1771         memset(&(moldyn->gvir),0,sizeof(t_virial));
1772
1773         /* reset force, site energy and virial of every atom */
1774         for(i=0;i<count;i++) {
1775
1776                 /* reset force */
1777                 v3_zero(&(itom[i].f));
1778
1779                 /* reset virial */
1780                 virial=(&(itom[i].virial));
1781                 virial->xx=0.0;
1782                 virial->yy=0.0;
1783                 virial->zz=0.0;
1784                 virial->xy=0.0;
1785                 virial->xz=0.0;
1786                 virial->yz=0.0;
1787
1788                 /* reset site energy */
1789                 itom[i].e=0.0;
1790
1791         }
1792
1793         /* get energy, force and virial of every atom */
1794
1795         /* first (and only) loop over atoms i */
1796         for(i=0;i<count;i++) {
1797
1798                 /* single particle potential/force */
1799                 if(itom[i].attr&ATOM_ATTR_1BP)
1800                         if(moldyn->func1b)
1801                                 moldyn->func1b(moldyn,&(itom[i]));
1802
1803                 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1804                         continue;
1805
1806                 /* 2 body pair potential/force */
1807
1808                 link_cell_neighbour_index(moldyn,
1809                                           (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1810                                           (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1811                                           (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1812                                           neighbour_i);
1813
1814                 dnlc=lc->dnlc;
1815
1816                 /* first loop over atoms j */
1817                 if(moldyn->func2b) {
1818                         for(j=0;j<27;j++) {
1819
1820                                 bc_ij=(j<dnlc)?0:1;
1821 #ifdef STATIC_LISTS
1822                                 p=0;
1823
1824                                 while(neighbour_i[j][p]!=0) {
1825
1826                                         jtom=&(atom[neighbour_i[j][p]]);
1827                                         p++;
1828
1829                                         if(jtom==&(itom[i]))
1830                                                 continue;
1831
1832                                         if((jtom->attr&ATOM_ATTR_2BP)&
1833                                            (itom[i].attr&ATOM_ATTR_2BP)) {
1834                                                 moldyn->func2b(moldyn,
1835                                                                &(itom[i]),
1836                                                                jtom,
1837                                                                bc_ij);
1838                                         }
1839                                 }
1840 #else
1841                                 this=&(neighbour_i[j]);
1842                                 list_reset_f(this);
1843
1844                                 if(this->start==NULL)
1845                                         continue;
1846
1847                                 do {
1848                                         jtom=this->current->data;
1849
1850                                         if(jtom==&(itom[i]))
1851                                                 continue;
1852
1853                                         if((jtom->attr&ATOM_ATTR_2BP)&
1854                                            (itom[i].attr&ATOM_ATTR_2BP)) {
1855                                                 moldyn->func2b(moldyn,
1856                                                                &(itom[i]),
1857                                                                jtom,
1858                                                                bc_ij);
1859                                         }
1860                                 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1861 #endif
1862
1863                         }
1864                 }
1865
1866                 /* 3 body potential/force */
1867
1868                 if(!(itom[i].attr&ATOM_ATTR_3BP))
1869                         continue;
1870
1871                 /* copy the neighbour lists */
1872 #ifdef STATIC_LISTS
1873                 /* no copy needed for static lists */
1874 #else
1875                 memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
1876 #endif
1877
1878                 /* second loop over atoms j */
1879                 for(j=0;j<27;j++) {
1880
1881                         bc_ij=(j<dnlc)?0:1;
1882 #ifdef STATIC_LISTS
1883                         p=0;
1884
1885                         while(neighbour_i[j][p]!=0) {
1886
1887                                 jtom=&(atom[neighbour_i[j][p]]);
1888                                 p++;
1889 #else
1890                         this=&(neighbour_i[j]);
1891                         list_reset_f(this);
1892
1893                         if(this->start==NULL)
1894                                 continue;
1895
1896                         do {
1897
1898                                 jtom=this->current->data;
1899 #endif
1900
1901                                 if(jtom==&(itom[i]))
1902                                         continue;
1903
1904                                 if(!(jtom->attr&ATOM_ATTR_3BP))
1905                                         continue;
1906
1907                                 /* reset 3bp run */
1908                                 moldyn->run3bp=1;
1909
1910                                 if(moldyn->func3b_j1)
1911                                         moldyn->func3b_j1(moldyn,
1912                                                           &(itom[i]),
1913                                                           jtom,
1914                                                           bc_ij);
1915
1916                                 /* in first j loop, 3bp run can be skipped */
1917                                 if(!(moldyn->run3bp))
1918                                         continue;
1919
1920                                 /* first loop over atoms k */
1921                                 if(moldyn->func3b_k1) {
1922
1923                                 for(k=0;k<27;k++) {
1924
1925                                         bc_ik=(k<dnlc)?0:1;
1926 #ifdef STATIC_LISTS
1927                                         q=0;
1928
1929                                         while(neighbour_i[j][q]!=0) {
1930
1931                                                 ktom=&(atom[neighbour_i[k][q]]);
1932                                                 q++;
1933 #else
1934                                         that=&(neighbour_i2[k]);
1935                                         list_reset_f(that);
1936
1937                                         if(that->start==NULL)
1938                                                 continue;
1939
1940                                         do {
1941                                                 ktom=that->current->data;
1942 #endif
1943
1944                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
1945                                                         continue;
1946
1947                                                 if(ktom==jtom)
1948                                                         continue;
1949
1950                                                 if(ktom==&(itom[i]))
1951                                                         continue;
1952
1953                                                 moldyn->func3b_k1(moldyn,
1954                                                                   &(itom[i]),
1955                                                                   jtom,
1956                                                                   ktom,
1957                                                                   bc_ik|bc_ij);
1958 #ifdef STATIC_LISTS
1959                                         }
1960 #else
1961                                         } while(list_next_f(that)!=\
1962                                                 L_NO_NEXT_ELEMENT);
1963 #endif
1964
1965                                 }
1966
1967                                 }
1968
1969                                 if(moldyn->func3b_j2)
1970                                         moldyn->func3b_j2(moldyn,
1971                                                           &(itom[i]),
1972                                                           jtom,
1973                                                           bc_ij);
1974
1975                                 /* second loop over atoms k */
1976                                 if(moldyn->func3b_k2) {
1977
1978                                 for(k=0;k<27;k++) {
1979
1980                                         bc_ik=(k<dnlc)?0:1;
1981 #ifdef STATIC_LISTS
1982                                         q=0;
1983
1984                                         while(neighbour_i[j][q]!=0) {
1985
1986                                                 ktom=&(atom[neighbour_i[k][q]]);
1987                                                 q++;
1988 #else
1989                                         that=&(neighbour_i2[k]);
1990                                         list_reset_f(that);
1991
1992                                         if(that->start==NULL)
1993                                                 continue;
1994
1995                                         do {
1996                                                 ktom=that->current->data;
1997 #endif
1998
1999                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
2000                                                         continue;
2001
2002                                                 if(ktom==jtom)
2003                                                         continue;
2004
2005                                                 if(ktom==&(itom[i]))
2006                                                         continue;
2007
2008                                                 moldyn->func3b_k2(moldyn,
2009                                                                   &(itom[i]),
2010                                                                   jtom,
2011                                                                   ktom,
2012                                                                   bc_ik|bc_ij);
2013
2014 #ifdef STATIC_LISTS
2015                                         }
2016 #else
2017                                         } while(list_next_f(that)!=\
2018                                                 L_NO_NEXT_ELEMENT);
2019 #endif
2020
2021                                 }
2022
2023                                 }
2024
2025                                 /* 2bp post function */
2026                                 if(moldyn->func3b_j3) {
2027                                         moldyn->func3b_j3(moldyn,
2028                                                           &(itom[i]),
2029                                                           jtom,bc_ij);
2030                                 }
2031 #ifdef STATIC_LISTS
2032                         }
2033 #else
2034                         } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
2035 #endif
2036
2037                 }
2038
2039 #ifdef DEBUG
2040         //printf("\n\n");
2041 #endif
2042 #ifdef VDEBUG
2043         printf("\n\n");
2044 #endif
2045
2046         }
2047
2048 #ifdef DEBUG
2049         //printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
2050         if(moldyn->time>DSTART&&moldyn->time<DEND) {
2051                 printf("force:\n");
2052                 printf("  x: %0.40f\n",moldyn->atom[5832].f.x);
2053                 printf("  y: %0.40f\n",moldyn->atom[5832].f.y);
2054                 printf("  z: %0.40f\n",moldyn->atom[5832].f.z);
2055         }
2056 #endif
2057
2058         /* calculate global virial */
2059         for(i=0;i<count;i++) {
2060                 moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
2061                 moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
2062                 moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
2063                 moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
2064                 moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
2065                 moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
2066         }
2067
2068         return 0;
2069 }
2070
2071 /*
2072  * virial calculation
2073  */
2074
2075 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
2076 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
2077
2078         a->virial.xx+=f->x*d->x;
2079         a->virial.yy+=f->y*d->y;
2080         a->virial.zz+=f->z*d->z;
2081         a->virial.xy+=f->x*d->y;
2082         a->virial.xz+=f->x*d->z;
2083         a->virial.yz+=f->y*d->z;
2084
2085         return 0;
2086 }
2087
2088 /*
2089  * periodic boundary checking
2090  */
2091
2092 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
2093 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
2094
2095         double x,y,z;
2096         t_3dvec *dim;
2097
2098         dim=&(moldyn->dim);
2099
2100         x=dim->x/2;
2101         y=dim->y/2;
2102         z=dim->z/2;
2103
2104         if(moldyn->status&MOLDYN_STAT_PBX) {
2105                 if(a->x>=x) a->x-=dim->x;
2106                 else if(-a->x>x) a->x+=dim->x;
2107         }
2108         if(moldyn->status&MOLDYN_STAT_PBY) {
2109                 if(a->y>=y) a->y-=dim->y;
2110                 else if(-a->y>y) a->y+=dim->y;
2111         }
2112         if(moldyn->status&MOLDYN_STAT_PBZ) {
2113                 if(a->z>=z) a->z-=dim->z;
2114                 else if(-a->z>z) a->z+=dim->z;
2115         }
2116
2117         return 0;
2118 }
2119
2120 /*
2121  * debugging / critical check functions
2122  */
2123
2124 int moldyn_bc_check(t_moldyn *moldyn) {
2125
2126         t_atom *atom;
2127         t_3dvec *dim;
2128         int i;
2129         double x;
2130         u8 byte;
2131         int j,k;
2132
2133         atom=moldyn->atom;
2134         dim=&(moldyn->dim);
2135         x=dim->x/2;
2136
2137         for(i=0;i<moldyn->count;i++) {
2138                 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
2139                         printf("FATAL: atom %d: x: %.20f (%.20f)\n",
2140                                i,atom[i].r.x,dim->x/2);
2141                         printf("diagnostic:\n");
2142                         printf("-----------\natom.r.x:\n");
2143                         for(j=0;j<8;j++) {
2144                                 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
2145                                 for(k=0;k<8;k++)
2146                                         printf("%d%c",
2147                                         ((byte)&(1<<k))?1:0,
2148                                         (k==7)?'\n':'|');
2149                         }
2150                         printf("---------------\nx=dim.x/2:\n");
2151                         for(j=0;j<8;j++) {
2152                                 memcpy(&byte,(u8 *)(&x)+j,1);
2153                                 for(k=0;k<8;k++)
2154                                         printf("%d%c",
2155                                         ((byte)&(1<<k))?1:0,
2156                                         (k==7)?'\n':'|');
2157                         }
2158                         if(atom[i].r.x==x) printf("the same!\n");
2159                         else printf("different!\n");
2160                 }
2161                 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
2162                         printf("FATAL: atom %d: y: %.20f (%.20f)\n",
2163                                i,atom[i].r.y,dim->y/2);
2164                 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
2165                         printf("FATAL: atom %d: z: %.20f (%.20f)\n",
2166                                i,atom[i].r.z,dim->z/2);
2167         }
2168
2169         return 0;
2170 }
2171
2172 /*
2173  * restore function
2174  */
2175
2176 int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
2177
2178         int fd;
2179         int cnt,size;
2180
2181         fd=open(file,O_RDONLY);
2182         if(fd<0) {
2183                 perror("[moldyn] load save file open");
2184                 return fd;
2185         }
2186
2187         size=sizeof(t_moldyn);
2188
2189         while(size) {
2190                 cnt=read(fd,moldyn,size);
2191                 if(cnt<0) {
2192                         perror("[moldyn] load save file read (moldyn)");
2193                         return cnt;
2194                 }
2195                 size-=cnt;
2196         }
2197
2198         size=moldyn->count*sizeof(t_atom);
2199
2200         moldyn->atom=(t_atom *)malloc(size);
2201         if(moldyn->atom==NULL) {
2202                 perror("[moldyn] load save file malloc (atoms)");
2203                 return -1;
2204         }
2205
2206         while(size) {
2207                 cnt=read(fd,moldyn->atom,size);
2208                 if(cnt<0) {
2209                         perror("[moldyn] load save file read (atoms)");
2210                         return cnt;
2211                 }
2212                 size-=cnt;
2213         }
2214
2215         // hooks etc ...
2216
2217         return 0;
2218 }
2219
2220 int moldyn_load(t_moldyn *moldyn) {
2221
2222         // later ...
2223
2224         return 0;
2225 }
2226
2227 /*
2228  * post processing functions
2229  */
2230
2231 int get_line(int fd,char *line,int max) {
2232
2233         int count,ret;
2234
2235         count=0;
2236
2237         while(1) {
2238                 if(count==max) return count;
2239                 ret=read(fd,line+count,1);
2240                 if(ret<=0) return ret;
2241                 if(line[count]=='\n') {
2242                         line[count]='\0';
2243                         return count+1;
2244                 }
2245                 count+=1;
2246         }
2247 }
2248
2249 int pair_correlation_init(t_moldyn *moldyn,double dr) {
2250
2251
2252         return 0;
2253 }
2254
2255 int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
2256
2257         int slots;
2258         double *stat;
2259         int i,j;
2260         t_linkcell *lc;
2261 #ifdef STATIC_LISTS
2262         int *neighbour[27];
2263         int p;
2264 #else
2265         t_list neighbour[27];
2266 #endif
2267         t_atom *itom,*jtom;
2268         t_list *this;
2269         unsigned char bc;
2270         t_3dvec dist;
2271         double d;
2272         //double norm;
2273         int o,s;
2274         unsigned char ibrand;
2275
2276         lc=&(moldyn->lc);
2277
2278         slots=moldyn->cutoff/dr;
2279         o=2*slots;
2280
2281         printf("[moldyn] pair correlation calc info:\n");
2282         printf("  time: %f\n",moldyn->time);
2283         printf("  count: %d\n",moldyn->count);
2284         printf("  cutoff: %f\n",moldyn->cutoff);
2285         printf("  temperature: cur=%f avg=%f\n",moldyn->t,moldyn->t_avg);
2286
2287         if(ptr!=NULL) {
2288                 stat=(double *)ptr;
2289         }
2290         else {
2291                 stat=(double *)malloc(3*slots*sizeof(double));
2292                 if(stat==NULL) {
2293                         perror("[moldyn] pair correlation malloc");
2294                         return -1;
2295                 }
2296         }
2297
2298         memset(stat,0,3*slots*sizeof(double));
2299
2300         link_cell_init(moldyn,VERBOSE);
2301
2302         itom=moldyn->atom;
2303
2304         for(i=0;i<moldyn->count;i++) {
2305                 /* neighbour indexing */
2306                 link_cell_neighbour_index(moldyn,
2307                                           (itom[i].r.x+moldyn->dim.x/2)/lc->x,
2308                                           (itom[i].r.y+moldyn->dim.y/2)/lc->x,
2309                                           (itom[i].r.z+moldyn->dim.z/2)/lc->x,
2310                                           neighbour);
2311
2312                 /* brand of atom i */
2313                 ibrand=itom[i].brand;
2314
2315                 for(j=0;j<27;j++) {
2316
2317                         bc=(j<lc->dnlc)?0:1;
2318
2319 #ifdef STATIC_LISTS
2320                         p=0;
2321
2322                         while(neighbour[j][p]!=0) {
2323
2324                                 jtom=&(moldyn->atom[neighbour[j][p]]);
2325                                 p++;
2326 #else
2327                         this=&(neighbour[j]);
2328                         list_reset_f(this);
2329
2330                         if(this->start==NULL)
2331                                 continue;
2332
2333                         do {
2334
2335                                 jtom=this->current->data;
2336 #endif
2337                                 /* only count pairs once,
2338                                  * skip same atoms */
2339                                 if(itom[i].tag>=jtom->tag)
2340                                         continue;
2341
2342                                 /*
2343                                  * pair correlation calc
2344                                  */
2345
2346                                 /* distance */
2347                                 v3_sub(&dist,&(jtom->r),&(itom[i].r));
2348                                 if(bc) check_per_bound(moldyn,&dist);
2349                                 d=v3_absolute_square(&dist);
2350
2351                                 /* ignore if greater or equal cutoff */
2352                                 if(d>=moldyn->cutoff_square)
2353                                         continue;
2354
2355                                 /* fill the slots */
2356                                 d=sqrt(d);
2357                                 s=(int)(d/dr);
2358
2359                                 /* should never happen but it does 8) -
2360                                  * related to -ffloat-store problem! */
2361                                 if(s>=slots) s=slots-1;
2362
2363                                 if(ibrand!=jtom->brand) {
2364                                         /* mixed */
2365                                         stat[s]+=1;
2366                                 }
2367                                 else {
2368                                         /* type a - type a bonds */
2369                                         if(ibrand==0)
2370                                                 stat[s+slots]+=1;
2371                                         else
2372                                         /* type b - type b bonds */
2373                                                 stat[s+o]+=1;
2374                                 }
2375 #ifdef STATIC_LISTS
2376                         }
2377 #else
2378                         } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
2379 #endif
2380                 }
2381         }
2382
2383         /* normalization
2384         for(i=1;i<slots;i++) {
2385                  // normalization: 4 pi r r dr
2386                  // here: not double counting pairs -> 2 pi r r dr
2387                 norm=2*M_PI*moldyn->count*(i*dr*i*dr)*dr;
2388                 stat[i]/=norm;
2389                 stat[slots+i]/=norm;
2390                 stat[o+i]/=norm;
2391         }
2392         */
2393
2394         if(ptr==NULL) {
2395                 /* todo: store/print pair correlation function */
2396                 free(stat);
2397         }
2398
2399         free(moldyn->atom);
2400
2401         link_cell_shutdown(moldyn);
2402
2403         return 0;
2404 }
2405
2406 int analyze_bonds(t_moldyn *moldyn) {
2407
2408
2409
2410
2411         return 0;
2412 }
2413
2414 /*
2415  * visualization code
2416  */
2417
2418 int visual_init(t_moldyn *moldyn,char *filebase) {
2419
2420         strncpy(moldyn->vis.fb,filebase,128);
2421
2422         return 0;
2423 }
2424
2425 int visual_atoms(t_moldyn *moldyn) {
2426
2427         int i,j,fd;
2428         char file[128+64];
2429         t_3dvec dim;
2430         double help;
2431         t_visual *v;
2432         t_atom *atom;
2433         t_atom *btom;
2434         t_linkcell *lc;
2435 #ifdef STATIC_LISTS
2436         int *neighbour[27];
2437         int p;
2438 #else
2439         t_list neighbour[27];
2440 #endif
2441         u8 bc;
2442         t_3dvec dist;
2443         double d2;
2444         u8 brand;
2445
2446         v=&(moldyn->vis);
2447         dim.x=v->dim.x;
2448         dim.y=v->dim.y;
2449         dim.z=v->dim.z;
2450         atom=moldyn->atom;
2451         lc=&(moldyn->lc);
2452
2453         help=(dim.x+dim.y);
2454
2455         sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,moldyn->time);
2456         fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
2457         if(fd<0) {
2458                 perror("open visual save file fd");
2459                 return -1;
2460         }
2461
2462         /* write the actual data file */
2463
2464         // povray header
2465         dprintf(fd,"# [P] %d %07.f <%f,%f,%f>\n",
2466                 moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help);
2467
2468         // atomic configuration
2469         for(i=0;i<moldyn->count;i++) {
2470                 // atom type, positions, color and kinetic energy
2471                 dprintf(fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
2472                                                  atom[i].r.x,
2473                                                  atom[i].r.y,
2474                                                  atom[i].r.z,
2475                                                  pse_col[atom[i].element],
2476                                                  atom[i].ekin);
2477
2478                 /*
2479                  * bond detection should usually be done by potential
2480                  * functions. brrrrr! EVIL!
2481                  *
2482                  * todo: potentials need to export a 'find_bonds' function!
2483                  */
2484
2485                 // bonds between atoms
2486                 if(!(atom[i].attr&ATOM_ATTR_VB))
2487                         continue;
2488                 link_cell_neighbour_index(moldyn,
2489                                           (atom[i].r.x+moldyn->dim.x/2)/lc->x,
2490                                           (atom[i].r.y+moldyn->dim.y/2)/lc->y,
2491                                           (atom[i].r.z+moldyn->dim.z/2)/lc->z,
2492                                           neighbour);
2493                 for(j=0;j<27;j++) {
2494                         bc=j<lc->dnlc?0:1;
2495 #ifdef STATIC_LISTS
2496                         p=0;
2497                         while(neighbour[j][p]!=0) {
2498                                 btom=&(atom[neighbour[j][p]]);
2499                                 p++;
2500 #else
2501                         list_reset_f(&neighbour[j]);
2502                         if(neighbour[j].start==NULL)
2503                                 continue;
2504                         do {
2505                                 btom=neighbour[j].current->data;
2506 #endif
2507                                 if(btom==&atom[i])      // skip identical atoms
2508                                         continue;
2509                                 //if(btom<&atom[i])     // skip half of them
2510                                 //      continue;
2511                                 v3_sub(&dist,&(atom[i].r),&(btom->r));
2512                                 if(bc) check_per_bound(moldyn,&dist);
2513                                 d2=v3_absolute_square(&dist);
2514                                 brand=atom[i].brand;
2515                                 if(brand==btom->brand) {
2516                                         if(d2>moldyn->bondlen[brand])
2517                                                 continue;
2518                                 }
2519                                 else {
2520                                         if(d2>moldyn->bondlen[2])
2521                                                 continue;
2522                                 }
2523                                 dprintf(fd,"# [B] %f %f %f %f %f %f\n",
2524                                         atom[i].r.x,atom[i].r.y,atom[i].r.z,
2525                                         btom->r.x,btom->r.y,btom->r.z);
2526 #ifdef STATIC_LISTS
2527                         }
2528 #else
2529                         } while(list_next_f(&neighbour[j])!=L_NO_NEXT_ELEMENT);
2530 #endif
2531                 }
2532         }
2533
2534         // boundaries
2535         if(dim.x) {
2536                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2537                         -dim.x/2,-dim.y/2,-dim.z/2,
2538                         dim.x/2,-dim.y/2,-dim.z/2);
2539                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2540                         -dim.x/2,-dim.y/2,-dim.z/2,
2541                         -dim.x/2,dim.y/2,-dim.z/2);
2542                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2543                         dim.x/2,dim.y/2,-dim.z/2,
2544                         dim.x/2,-dim.y/2,-dim.z/2);
2545                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2546                         -dim.x/2,dim.y/2,-dim.z/2,
2547                         dim.x/2,dim.y/2,-dim.z/2);
2548
2549                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2550                         -dim.x/2,-dim.y/2,dim.z/2,
2551                         dim.x/2,-dim.y/2,dim.z/2);
2552                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2553                         -dim.x/2,-dim.y/2,dim.z/2,
2554                         -dim.x/2,dim.y/2,dim.z/2);
2555                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2556                         dim.x/2,dim.y/2,dim.z/2,
2557                         dim.x/2,-dim.y/2,dim.z/2);
2558                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2559                         -dim.x/2,dim.y/2,dim.z/2,
2560                         dim.x/2,dim.y/2,dim.z/2);
2561
2562                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2563                         -dim.x/2,-dim.y/2,dim.z/2,
2564                         -dim.x/2,-dim.y/2,-dim.z/2);
2565                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2566                         -dim.x/2,dim.y/2,dim.z/2,
2567                         -dim.x/2,dim.y/2,-dim.z/2);
2568                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2569                         dim.x/2,-dim.y/2,dim.z/2,
2570                         dim.x/2,-dim.y/2,-dim.z/2);
2571                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2572                         dim.x/2,dim.y/2,dim.z/2,
2573                         dim.x/2,dim.y/2,-dim.z/2);
2574         }
2575
2576         close(fd);
2577
2578         return 0;
2579 }
2580