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         if(moldyn->total_steps<moldyn->avg_skip)
 960                 return 0;
 961
 962         int denom=moldyn->total_steps+1-moldyn->avg_skip;
 963
 964         /* assume up to date energies, temperature, pressure etc */
 965
 966         /* kinetic energy */
 967         moldyn->k_sum+=moldyn->ekin;
 968         moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
 969         moldyn->k_avg=moldyn->k_sum/denom;
 970         moldyn->k2_avg=moldyn->k2_sum/denom;
 971         moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg);
 972
 973         /* potential energy */
 974         moldyn->v_sum+=moldyn->energy;
 975         moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
 976         moldyn->v_avg=moldyn->v_sum/denom;
 977         moldyn->v2_avg=moldyn->v2_sum/denom;
 978         moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
 979
 980         /* temperature */
 981         moldyn->t_sum+=moldyn->t;
 982         moldyn->t_avg=moldyn->t_sum/denom;
 983
 984         /* virial */
 985         moldyn->virial_sum+=moldyn->virial;
 986         moldyn->virial_avg=moldyn->virial_sum/denom;
 987         moldyn->gv_sum+=moldyn->gv;
 988         moldyn->gv_avg=moldyn->gv_sum/denom;
 989
 990         /* pressure */
 991         moldyn->p_sum+=moldyn->p;
 992         moldyn->p_avg=moldyn->p_sum/denom;
 993         moldyn->gp_sum+=moldyn->gp;
 994         moldyn->gp_avg=moldyn->gp_sum/denom;
 995
 996         return 0;
 997 }
 998
 999 int get_heat_capacity(t_moldyn *moldyn) {
1000
1001         double temp2,ighc;
1002
1003         /* averages needed for heat capacity calc */
1004         if(moldyn->total_steps<moldyn->avg_skip)
1005                 return 0;
1006
1007         /* (temperature average)^2 */
1008         temp2=moldyn->t_avg*moldyn->t_avg;
1009         printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
1010                moldyn->t_avg);
1011
1012         /* ideal gas contribution */
1013         ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
1014         printf("  ideal gas contribution: %f\n",
1015                ighc/moldyn->mass*KILOGRAM/JOULE);
1016
1017         /* specific heat for nvt ensemble */
1018         moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc;
1019         moldyn->c_v_nvt/=moldyn->mass;
1020
1021         /* specific heat for nve ensemble */
1022         moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_avg/(ighc*K_BOLTZMANN*temp2)));
1023         moldyn->c_v_nve/=moldyn->mass;
1024
1025         printf("  NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
1026         printf("  NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
1027 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)));
1028
1029         return 0;
1030 }
1031
1032 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
1033
1034         t_3dvec dim,*tp;
1035         double u_up,u_down,dv;
1036         double scale,p;
1037         t_atom *store;
1038
1039         /*
1040          * dU = - p dV
1041          *
1042          * => p = - dU/dV
1043          *
1044          */
1045
1046         scale=0.00001;
1047         dv=8*scale*scale*scale*moldyn->volume;
1048
1049         store=malloc(moldyn->count*sizeof(t_atom));
1050         if(store==NULL) {
1051                 printf("[moldyn] allocating store mem failed\n");
1052                 return -1;
1053         }
1054
1055         /* save unscaled potential energy + atom/dim configuration */
1056         memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
1057         dim=moldyn->dim;
1058
1059         /* scale up dimension and atom positions */
1060         scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
1061         scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
1062         link_cell_shutdown(moldyn);
1063         link_cell_init(moldyn,QUIET);
1064         potential_force_calc(moldyn);
1065         u_up=moldyn->energy;
1066
1067         /* restore atomic configuration + dim */
1068         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
1069         moldyn->dim=dim;
1070
1071         /* scale down dimension and atom positions */
1072         scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
1073         scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
1074         link_cell_shutdown(moldyn);
1075         link_cell_init(moldyn,QUIET);
1076         potential_force_calc(moldyn);
1077         u_down=moldyn->energy;
1078
1079         /* calculate pressure */
1080         p=-(u_up-u_down)/dv;
1081 printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR);
1082
1083         /* restore atomic configuration + dim */
1084         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
1085         moldyn->dim=dim;
1086
1087         /* restore energy */
1088         potential_force_calc(moldyn);
1089
1090         link_cell_shutdown(moldyn);
1091         link_cell_init(moldyn,QUIET);
1092
1093         return p;
1094 }
1095
1096 double get_pressure(t_moldyn *moldyn) {
1097
1098         return moldyn->p;
1099
1100 }
1101
1102 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1103
1104         t_3dvec *dim;
1105
1106         dim=&(moldyn->dim);
1107
1108         if(dir==SCALE_UP)
1109                 scale=1.0+scale;
1110
1111         if(dir==SCALE_DOWN)
1112                 scale=1.0-scale;
1113
1114         if(x) dim->x*=scale;
1115         if(y) dim->y*=scale;
1116         if(z) dim->z*=scale;
1117
1118         return 0;
1119 }
1120
1121 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1122
1123         int i;
1124         t_3dvec *r;
1125
1126         if(dir==SCALE_UP)
1127                 scale=1.0+scale;
1128
1129         if(dir==SCALE_DOWN)
1130                 scale=1.0-scale;
1131
1132         for(i=0;i<moldyn->count;i++) {
1133                 r=&(moldyn->atom[i].r);
1134                 if(x) r->x*=scale;
1135                 if(y) r->y*=scale;
1136                 if(z) r->z*=scale;
1137         }
1138
1139         return 0;
1140 }
1141
1142 int scale_volume(t_moldyn *moldyn) {
1143
1144         t_3dvec *dim,*vdim;
1145         double scale;
1146         t_linkcell *lc;
1147
1148         vdim=&(moldyn->vis.dim);
1149         dim=&(moldyn->dim);
1150         lc=&(moldyn->lc);
1151
1152         /* scaling factor */
1153         if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
1154                 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
1155                 scale=pow(scale,ONE_THIRD);
1156         }
1157         else {
1158                 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
1159         }
1160 moldyn->debug=scale;
1161
1162         /* scale the atoms and dimensions */
1163         scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1164         scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1165
1166         /* visualize dimensions */
1167         if(vdim->x!=0) {
1168                 vdim->x=dim->x;
1169                 vdim->y=dim->y;
1170                 vdim->z=dim->z;
1171         }
1172
1173         /* recalculate scaled volume */
1174         moldyn->volume=dim->x*dim->y*dim->z;
1175
1176         /* adjust/reinit linkcell */
1177         if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
1178            ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
1179            ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
1180                 link_cell_shutdown(moldyn);
1181                 link_cell_init(moldyn,QUIET);
1182         } else {
1183                 lc->x*=scale;
1184                 lc->y*=scale;
1185                 lc->z*=scale;
1186         }
1187
1188         return 0;
1189
1190 }
1191
1192 double e_kin_calc(t_moldyn *moldyn) {
1193
1194         int i;
1195         t_atom *atom;
1196
1197         atom=moldyn->atom;
1198         moldyn->ekin=0.0;
1199
1200         for(i=0;i<moldyn->count;i++) {
1201                 atom[i].ekin=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
1202                 moldyn->ekin+=atom[i].ekin;
1203         }
1204
1205         return moldyn->ekin;
1206 }
1207
1208 double get_total_energy(t_moldyn *moldyn) {
1209
1210         return(moldyn->ekin+moldyn->energy);
1211 }
1212
1213 t_3dvec get_total_p(t_moldyn *moldyn) {
1214
1215         t_3dvec p,p_total;
1216         int i;
1217         t_atom *atom;
1218
1219         atom=moldyn->atom;
1220
1221         v3_zero(&p_total);
1222         for(i=0;i<moldyn->count;i++) {
1223                 v3_scale(&p,&(atom[i].v),atom[i].mass);
1224                 v3_add(&p_total,&p_total,&p);
1225         }
1226
1227         return p_total;
1228 }
1229
1230 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
1231
1232         double tau;
1233
1234         /* nn_dist is the nearest neighbour distance */
1235
1236         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
1237
1238         return tau;
1239 }
1240
1241 /*
1242  * numerical tricks
1243  */
1244
1245 /* linked list / cell method */
1246
1247 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1248
1249         t_linkcell *lc;
1250         int i;
1251
1252         lc=&(moldyn->lc);
1253
1254         /* partitioning the md cell */
1255         lc->nx=moldyn->dim.x/moldyn->cutoff;
1256         lc->x=moldyn->dim.x/lc->nx;
1257         lc->ny=moldyn->dim.y/moldyn->cutoff;
1258         lc->y=moldyn->dim.y/lc->ny;
1259         lc->nz=moldyn->dim.z/moldyn->cutoff;
1260         lc->z=moldyn->dim.z/lc->nz;
1261         lc->cells=lc->nx*lc->ny*lc->nz;
1262
1263 #ifdef STATIC_LISTS
1264         lc->subcell=malloc(lc->cells*sizeof(int*));
1265 #else
1266         lc->subcell=malloc(lc->cells*sizeof(t_list));
1267 #endif
1268
1269         if(lc->subcell==NULL) {
1270                 perror("[moldyn] cell init (malloc)");
1271                 return -1;
1272         }
1273
1274         if(lc->cells<27)
1275                 printf("[moldyn] FATAL: less then 27 subcells!\n");
1276
1277         if(vol) {
1278 #ifdef STATIC_LISTS
1279                 printf("[moldyn] initializing 'static' linked cells (%d)\n",
1280                        lc->cells);
1281 #else
1282                 printf("[moldyn] initializing 'dynamic' linked cells (%d)\n",
1283                        lc->cells);
1284 #endif
1285                 printf("  x: %d x %f A\n",lc->nx,lc->x);
1286                 printf("  y: %d x %f A\n",lc->ny,lc->y);
1287                 printf("  z: %d x %f A\n",lc->nz,lc->z);
1288         }
1289
1290 #ifdef STATIC_LISTS
1291         /* list init */
1292         for(i=0;i<lc->cells;i++) {
1293                 lc->subcell[i]=malloc((MAX_ATOMS_PER_LIST+1)*sizeof(int));
1294                 if(lc->subcell[i]==NULL) {
1295                         perror("[moldyn] list init (malloc)");
1296                         return -1;
1297                 }
1298                 /*
1299                 if(i==0)
1300                         printf(" ---> %d malloc %p (%p)\n",
1301                                i,lc->subcell[0],lc->subcell);
1302                 */
1303         }
1304 #else
1305         for(i=0;i<lc->cells;i++)
1306                 list_init_f(&(lc->subcell[i]));
1307 #endif
1308
1309         /* update the list */
1310         link_cell_update(moldyn);
1311
1312         return 0;
1313 }
1314
1315 int link_cell_update(t_moldyn *moldyn) {
1316
1317         int count,i,j,k;
1318         int nx,ny;
1319         t_atom *atom;
1320         t_linkcell *lc;
1321 #ifdef STATIC_LISTS
1322         int p;
1323 #endif
1324
1325         atom=moldyn->atom;
1326         lc=&(moldyn->lc);
1327
1328         nx=lc->nx;
1329         ny=lc->ny;
1330
1331         for(i=0;i<lc->cells;i++)
1332 #ifdef STATIC_LISTS
1333                 memset(lc->subcell[i],0,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
1334 #else
1335                 list_destroy_f(&(lc->subcell[i]));
1336 #endif
1337
1338         for(count=0;count<moldyn->count;count++) {
1339                 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1340                 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1341                 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1342
1343 #ifdef STATIC_LISTS
1344                 p=0;
1345                 while(lc->subcell[i+j*nx+k*nx*ny][p]!=0)
1346                         p++;
1347
1348                 if(p>=MAX_ATOMS_PER_LIST) {
1349                         printf("[moldyn] FATAL: amount of atoms too high!\n");
1350                         return -1;
1351                 }
1352
1353                 lc->subcell[i+j*nx+k*nx*ny][p]=count;
1354 #else
1355                 list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
1356                                      &(atom[count]));
1357                 /*
1358                 if(j==0&&k==0)
1359                         printf(" ---> %d %d malloc %p (%p)\n",
1360                                i,count,lc->subcell[i].current,lc->subcell);
1361                 */
1362 #endif
1363         }
1364
1365         return 0;
1366 }
1367
1368 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
1369 #ifdef STATIC_LISTS
1370                               int **cell
1371 #else
1372                               t_list *cell
1373 #endif
1374                              ) {
1375
1376         t_linkcell *lc;
1377         int a;
1378         int count1,count2;
1379         int ci,cj,ck;
1380         int nx,ny,nz;
1381         int x,y,z;
1382         u8 bx,by,bz;
1383
1384         lc=&(moldyn->lc);
1385         nx=lc->nx;
1386         ny=lc->ny;
1387         nz=lc->nz;
1388         count1=1;
1389         count2=27;
1390         a=nx*ny;
1391
1392         cell[0]=lc->subcell[i+j*nx+k*a];
1393         for(ci=-1;ci<=1;ci++) {
1394                 bx=0;
1395                 x=i+ci;
1396                 if((x<0)||(x>=nx)) {
1397                         x=(x+nx)%nx;
1398                         bx=1;
1399                 }
1400                 for(cj=-1;cj<=1;cj++) {
1401                         by=0;
1402                         y=j+cj;
1403                         if((y<0)||(y>=ny)) {
1404                                 y=(y+ny)%ny;
1405                                 by=1;
1406                         }
1407                         for(ck=-1;ck<=1;ck++) {
1408                                 bz=0;
1409                                 z=k+ck;
1410                                 if((z<0)||(z>=nz)) {
1411                                         z=(z+nz)%nz;
1412                                         bz=1;
1413                                 }
1414                                 if(!(ci|cj|ck)) continue;
1415                                 if(bx|by|bz) {
1416                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
1417                                 }
1418                                 else {
1419                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
1420                                 }
1421                         }
1422                 }
1423         }
1424
1425         lc->dnlc=count1;
1426
1427         return count1;
1428 }
1429
1430 int link_cell_shutdown(t_moldyn *moldyn) {
1431
1432         int i;
1433         t_linkcell *lc;
1434
1435         lc=&(moldyn->lc);
1436
1437         for(i=0;i<lc->cells;i++) {
1438 #ifdef STATIC_LISTS
1439                 //printf(" ---> %d free %p\n",i,lc->subcell[i]);
1440                 free(lc->subcell[i]);
1441 #else
1442                 //printf(" ---> %d free %p\n",i,lc->subcell[i].start);
1443                 list_destroy_f(&(lc->subcell[i]));
1444 #endif
1445         }
1446
1447         free(lc->subcell);
1448
1449         return 0;
1450 }
1451
1452 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1453
1454         int count;
1455         void *ptr;
1456         t_moldyn_schedule *schedule;
1457
1458         schedule=&(moldyn->schedule);
1459         count=++(schedule->total_sched);
1460
1461         ptr=realloc(schedule->runs,count*sizeof(int));
1462         if(!ptr) {
1463                 perror("[moldyn] realloc (runs)");
1464                 return -1;
1465         }
1466         schedule->runs=ptr;
1467         schedule->runs[count-1]=runs;
1468
1469         ptr=realloc(schedule->tau,count*sizeof(double));
1470         if(!ptr) {
1471                 perror("[moldyn] realloc (tau)");
1472                 return -1;
1473         }
1474         schedule->tau=ptr;
1475         schedule->tau[count-1]=tau;
1476
1477         printf("[moldyn] schedule added:\n");
1478         printf("  number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1479
1480
1481         return 0;
1482 }
1483
1484 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1485
1486         moldyn->schedule.hook=hook;
1487         moldyn->schedule.hook_params=hook_params;
1488
1489         return 0;
1490 }
1491
1492 /*
1493  *
1494  * 'integration of newtons equation' - algorithms
1495  *
1496  */
1497
1498 /* start the integration */
1499
1500 int moldyn_integrate(t_moldyn *moldyn) {
1501
1502         int i;
1503         unsigned int e,m,s,v,p,t;
1504         t_3dvec momentum;
1505         t_moldyn_schedule *sched;
1506         t_atom *atom;
1507         int fd;
1508         char dir[128];
1509         double ds;
1510         double energy_scale;
1511         struct timeval t1,t2;
1512         //double tp;
1513
1514         sched=&(moldyn->schedule);
1515         atom=moldyn->atom;
1516
1517         /* initialize linked cell method */
1518         link_cell_init(moldyn,VERBOSE);
1519
1520         /* logging & visualization */
1521         e=moldyn->ewrite;
1522         m=moldyn->mwrite;
1523         s=moldyn->swrite;
1524         v=moldyn->vwrite;
1525         p=moldyn->pwrite;
1526         t=moldyn->twrite;
1527
1528         /* sqaure of some variables */
1529         moldyn->tau_square=moldyn->tau*moldyn->tau;
1530         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1531
1532         /* get current time */
1533         gettimeofday(&t1,NULL);
1534
1535         /* calculate initial forces */
1536         potential_force_calc(moldyn);
1537 #ifdef DEBUG
1538 //return 0;
1539 #endif
1540
1541         /* some stupid checks before we actually start calculating bullshit */
1542         if(moldyn->cutoff>0.5*moldyn->dim.x)
1543                 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1544         if(moldyn->cutoff>0.5*moldyn->dim.y)
1545                 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1546         if(moldyn->cutoff>0.5*moldyn->dim.z)
1547                 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1548         ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1549         if(ds>0.05*moldyn->nnd)
1550                 printf("[moldyn] warning: forces too high / tau too small!\n");
1551
1552         /* zero absolute time */
1553         moldyn->time=0.0;
1554         moldyn->total_steps=0;
1555
1556         /* debugging, ignore */
1557         moldyn->debug=0;
1558
1559         /* tell the world */
1560         printf("[moldyn] integration start, go get a coffee ...\n");
1561
1562         /* executing the schedule */
1563         sched->count=0;
1564         while(sched->count<sched->total_sched) {
1565
1566                 /* setting amount of runs and finite time step size */
1567                 moldyn->tau=sched->tau[sched->count];
1568                 moldyn->tau_square=moldyn->tau*moldyn->tau;
1569                 moldyn->time_steps=sched->runs[sched->count];
1570
1571                 /* energy scaling factor (might change!) */
1572                 energy_scale=moldyn->count*EV;
1573
1574         /* integration according to schedule */
1575
1576         for(i=0;i<moldyn->time_steps;i++) {
1577
1578                 /* integration step */
1579                 moldyn->integrate(moldyn);
1580
1581                 /* calculate kinetic energy, temperature and pressure */
1582                 e_kin_calc(moldyn);
1583                 temperature_calc(moldyn);
1584                 virial_sum(moldyn);
1585                 pressure_calc(moldyn);
1586                 average_and_fluctuation_calc(moldyn);
1587
1588                 /* p/t scaling */
1589                 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1590                         scale_velocity(moldyn,FALSE);
1591                 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1592                         scale_volume(moldyn);
1593
1594                 /* check for log & visualization */
1595                 if(e) {
1596                         if(!(moldyn->total_steps%e))
1597                                 dprintf(moldyn->efd,
1598                                         "%f %f %f %f\n",
1599                                         moldyn->time,moldyn->ekin/energy_scale,
1600                                         moldyn->energy/energy_scale,
1601                                         get_total_energy(moldyn)/energy_scale);
1602                 }
1603                 if(m) {
1604                         if(!(moldyn->total_steps%m)) {
1605                                 momentum=get_total_p(moldyn);
1606                                 dprintf(moldyn->mfd,
1607                                         "%f %f %f %f %f\n",moldyn->time,
1608                                         momentum.x,momentum.y,momentum.z,
1609                                         v3_norm(&momentum));
1610                         }
1611                 }
1612                 if(p) {
1613                         if(!(moldyn->total_steps%p)) {
1614                                 dprintf(moldyn->pfd,
1615                                         "%f %f %f %f %f\n",moldyn->time,
1616                                          moldyn->p/BAR,moldyn->p_avg/BAR,
1617                                          moldyn->gp/BAR,moldyn->gp_avg/BAR);
1618                         }
1619                 }
1620                 if(t) {
1621                         if(!(moldyn->total_steps%t)) {
1622                                 dprintf(moldyn->tfd,
1623                                         "%f %f %f\n",
1624                                         moldyn->time,moldyn->t,moldyn->t_avg);
1625                         }
1626                 }
1627                 if(s) {
1628                         if(!(moldyn->total_steps%s)) {
1629                                 snprintf(dir,128,"%s/s-%07.f.save",
1630                                          moldyn->vlsdir,moldyn->time);
1631                                 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
1632                                         S_IRUSR|S_IWUSR);
1633                                 if(fd<0) perror("[moldyn] save fd open");
1634                                 else {
1635                                         write(fd,moldyn,sizeof(t_moldyn));
1636                                         write(fd,moldyn->atom,
1637                                               moldyn->count*sizeof(t_atom));
1638                                 }
1639                                 close(fd);
1640                         }
1641                 }
1642                 if(v) {
1643                         if(!(moldyn->total_steps%v)) {
1644                                 visual_atoms(moldyn);
1645                         }
1646                 }
1647
1648                 /* display progress */
1649                 //if(!(moldyn->total_steps%10)) {
1650                         /* get current time */
1651                         gettimeofday(&t2,NULL);
1652
1653         printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
1654                sched->count,i,
1655                moldyn->t,moldyn->t_avg,
1656                moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
1657                moldyn->volume,
1658                (int)(t2.tv_sec-t1.tv_sec));
1659         fflush(stdout);
1660
1661                         /* copy over time */
1662                         t1=t2;
1663                 //}
1664
1665                 /* increase absolute time */
1666                 moldyn->time+=moldyn->tau;
1667                 moldyn->total_steps+=1;
1668
1669         }
1670
1671                 /* check for hooks */
1672                 if(sched->hook) {
1673                         printf("\n ## schedule hook %d/%d start ##\n",
1674                                sched->count+1,sched->total_sched-1);
1675                         sched->hook(moldyn,sched->hook_params);
1676                         printf(" ## schedule hook end ##\n");
1677                 }
1678
1679                 /* increase the schedule counter */
1680                 sched->count+=1;
1681
1682         }
1683
1684         return 0;
1685 }
1686
1687 /* velocity verlet */
1688
1689 int velocity_verlet(t_moldyn *moldyn) {
1690
1691         int i,count;
1692         double tau,tau_square,h;
1693         t_3dvec delta;
1694         t_atom *atom;
1695
1696         atom=moldyn->atom;
1697         count=moldyn->count;
1698         tau=moldyn->tau;
1699         tau_square=moldyn->tau_square;
1700
1701         for(i=0;i<count;i++) {
1702                 /* new positions */
1703                 h=0.5/atom[i].mass;
1704                 v3_scale(&delta,&(atom[i].v),tau);
1705                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1706                 v3_scale(&delta,&(atom[i].f),h*tau_square);
1707                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1708                 check_per_bound(moldyn,&(atom[i].r));
1709
1710                 /* velocities [actually v(t+tau/2)] */
1711                 v3_scale(&delta,&(atom[i].f),h*tau);
1712                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1713         }
1714
1715         /* neighbour list update */
1716         link_cell_update(moldyn);
1717
1718         /* forces depending on chosen potential */
1719         potential_force_calc(moldyn);
1720
1721         for(i=0;i<count;i++) {
1722                 /* again velocities [actually v(t+tau)] */
1723                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1724                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1725         }
1726
1727         return 0;
1728 }
1729
1730
1731 /*
1732  *
1733  * potentials & corresponding forces & virial routine
1734  *
1735  */
1736
1737 /* generic potential and force calculation */
1738
1739 int potential_force_calc(t_moldyn *moldyn) {
1740
1741         int i,j,k,count;
1742         t_atom *itom,*jtom,*ktom;
1743         t_virial *virial;
1744         t_linkcell *lc;
1745 #ifdef STATIC_LISTS
1746         int *neighbour_i[27];
1747         int p,q;
1748         t_atom *atom;
1749 #else
1750         t_list neighbour_i[27];
1751         t_list neighbour_i2[27];
1752         t_list *this,*that;
1753 #endif
1754         u8 bc_ij,bc_ik;
1755         int dnlc;
1756
1757         count=moldyn->count;
1758         itom=moldyn->atom;
1759         lc=&(moldyn->lc);
1760 #ifdef STATIC_LISTS
1761         atom=moldyn->atom;
1762 #endif
1763
1764         /* reset energy */
1765         moldyn->energy=0.0;
1766
1767         /* reset global virial */
1768         memset(&(moldyn->gvir),0,sizeof(t_virial));
1769
1770         /* reset force, site energy and virial of every atom */
1771         for(i=0;i<count;i++) {
1772
1773                 /* reset force */
1774                 v3_zero(&(itom[i].f));
1775
1776                 /* reset virial */
1777                 virial=(&(itom[i].virial));
1778                 virial->xx=0.0;
1779                 virial->yy=0.0;
1780                 virial->zz=0.0;
1781                 virial->xy=0.0;
1782                 virial->xz=0.0;
1783                 virial->yz=0.0;
1784
1785                 /* reset site energy */
1786                 itom[i].e=0.0;
1787
1788         }
1789
1790         /* get energy, force and virial of every atom */
1791
1792         /* first (and only) loop over atoms i */
1793         for(i=0;i<count;i++) {
1794
1795                 /* single particle potential/force */
1796                 if(itom[i].attr&ATOM_ATTR_1BP)
1797                         if(moldyn->func1b)
1798                                 moldyn->func1b(moldyn,&(itom[i]));
1799
1800                 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1801                         continue;
1802
1803                 /* 2 body pair potential/force */
1804
1805                 link_cell_neighbour_index(moldyn,
1806                                           (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1807                                           (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1808                                           (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1809                                           neighbour_i);
1810
1811                 dnlc=lc->dnlc;
1812
1813                 /* first loop over atoms j */
1814                 if(moldyn->func2b) {
1815                         for(j=0;j<27;j++) {
1816
1817                                 bc_ij=(j<dnlc)?0:1;
1818 #ifdef STATIC_LISTS
1819                                 p=0;
1820
1821                                 while(neighbour_i[j][p]!=0) {
1822
1823                                         jtom=&(atom[neighbour_i[j][p]]);
1824                                         p++;
1825
1826                                         if(jtom==&(itom[i]))
1827                                                 continue;
1828
1829                                         if((jtom->attr&ATOM_ATTR_2BP)&
1830                                            (itom[i].attr&ATOM_ATTR_2BP)) {
1831                                                 moldyn->func2b(moldyn,
1832                                                                &(itom[i]),
1833                                                                jtom,
1834                                                                bc_ij);
1835                                         }
1836                                 }
1837 #else
1838                                 this=&(neighbour_i[j]);
1839                                 list_reset_f(this);
1840
1841                                 if(this->start==NULL)
1842                                         continue;
1843
1844                                 do {
1845                                         jtom=this->current->data;
1846
1847                                         if(jtom==&(itom[i]))
1848                                                 continue;
1849
1850                                         if((jtom->attr&ATOM_ATTR_2BP)&
1851                                            (itom[i].attr&ATOM_ATTR_2BP)) {
1852                                                 moldyn->func2b(moldyn,
1853                                                                &(itom[i]),
1854                                                                jtom,
1855                                                                bc_ij);
1856                                         }
1857                                 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1858 #endif
1859
1860                         }
1861                 }
1862
1863                 /* 3 body potential/force */
1864
1865                 if(!(itom[i].attr&ATOM_ATTR_3BP))
1866                         continue;
1867
1868                 /* copy the neighbour lists */
1869 #ifdef STATIC_LISTS
1870                 /* no copy needed for static lists */
1871 #else
1872                 memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
1873 #endif
1874
1875                 /* second loop over atoms j */
1876                 for(j=0;j<27;j++) {
1877
1878                         bc_ij=(j<dnlc)?0:1;
1879 #ifdef STATIC_LISTS
1880                         p=0;
1881
1882                         while(neighbour_i[j][p]!=0) {
1883
1884                                 jtom=&(atom[neighbour_i[j][p]]);
1885                                 p++;
1886 #else
1887                         this=&(neighbour_i[j]);
1888                         list_reset_f(this);
1889
1890                         if(this->start==NULL)
1891                                 continue;
1892
1893                         do {
1894
1895                                 jtom=this->current->data;
1896 #endif
1897
1898                                 if(jtom==&(itom[i]))
1899                                         continue;
1900
1901                                 if(!(jtom->attr&ATOM_ATTR_3BP))
1902                                         continue;
1903
1904                                 /* reset 3bp run */
1905                                 moldyn->run3bp=1;
1906
1907                                 if(moldyn->func3b_j1)
1908                                         moldyn->func3b_j1(moldyn,
1909                                                           &(itom[i]),
1910                                                           jtom,
1911                                                           bc_ij);
1912
1913                                 /* in first j loop, 3bp run can be skipped */
1914                                 if(!(moldyn->run3bp))
1915                                         continue;
1916
1917                                 /* first loop over atoms k */
1918                                 if(moldyn->func3b_k1) {
1919
1920                                 for(k=0;k<27;k++) {
1921
1922                                         bc_ik=(k<dnlc)?0:1;
1923 #ifdef STATIC_LISTS
1924                                         q=0;
1925
1926                                         while(neighbour_i[j][q]!=0) {
1927
1928                                                 ktom=&(atom[neighbour_i[k][q]]);
1929                                                 q++;
1930 #else
1931                                         that=&(neighbour_i2[k]);
1932                                         list_reset_f(that);
1933
1934                                         if(that->start==NULL)
1935                                                 continue;
1936
1937                                         do {
1938                                                 ktom=that->current->data;
1939 #endif
1940
1941                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
1942                                                         continue;
1943
1944                                                 if(ktom==jtom)
1945                                                         continue;
1946
1947                                                 if(ktom==&(itom[i]))
1948                                                         continue;
1949
1950                                                 moldyn->func3b_k1(moldyn,
1951                                                                   &(itom[i]),
1952                                                                   jtom,
1953                                                                   ktom,
1954                                                                   bc_ik|bc_ij);
1955 #ifdef STATIC_LISTS
1956                                         }
1957 #else
1958                                         } while(list_next_f(that)!=\
1959                                                 L_NO_NEXT_ELEMENT);
1960 #endif
1961
1962                                 }
1963
1964                                 }
1965
1966                                 if(moldyn->func3b_j2)
1967                                         moldyn->func3b_j2(moldyn,
1968                                                           &(itom[i]),
1969                                                           jtom,
1970                                                           bc_ij);
1971
1972                                 /* second loop over atoms k */
1973                                 if(moldyn->func3b_k2) {
1974
1975                                 for(k=0;k<27;k++) {
1976
1977                                         bc_ik=(k<dnlc)?0:1;
1978 #ifdef STATIC_LISTS
1979                                         q=0;
1980
1981                                         while(neighbour_i[j][q]!=0) {
1982
1983                                                 ktom=&(atom[neighbour_i[k][q]]);
1984                                                 q++;
1985 #else
1986                                         that=&(neighbour_i2[k]);
1987                                         list_reset_f(that);
1988
1989                                         if(that->start==NULL)
1990                                                 continue;
1991
1992                                         do {
1993                                                 ktom=that->current->data;
1994 #endif
1995
1996                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
1997                                                         continue;
1998
1999                                                 if(ktom==jtom)
2000                                                         continue;
2001
2002                                                 if(ktom==&(itom[i]))
2003                                                         continue;
2004
2005                                                 moldyn->func3b_k2(moldyn,
2006                                                                   &(itom[i]),
2007                                                                   jtom,
2008                                                                   ktom,
2009                                                                   bc_ik|bc_ij);
2010
2011 #ifdef STATIC_LISTS
2012                                         }
2013 #else
2014                                         } while(list_next_f(that)!=\
2015                                                 L_NO_NEXT_ELEMENT);
2016 #endif
2017
2018                                 }
2019
2020                                 }
2021
2022                                 /* 2bp post function */
2023                                 if(moldyn->func3b_j3) {
2024                                         moldyn->func3b_j3(moldyn,
2025                                                           &(itom[i]),
2026                                                           jtom,bc_ij);
2027                                 }
2028 #ifdef STATIC_LISTS
2029                         }
2030 #else
2031                         } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
2032 #endif
2033
2034                 }
2035
2036 #ifdef DEBUG
2037         //printf("\n\n");
2038 #endif
2039 #ifdef VDEBUG
2040         printf("\n\n");
2041 #endif
2042
2043         }
2044
2045 #ifdef DEBUG
2046         //printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
2047         if(moldyn->time>DSTART&&moldyn->time<DEND) {
2048                 printf("force:\n");
2049                 printf("  x: %0.40f\n",moldyn->atom[5832].f.x);
2050                 printf("  y: %0.40f\n",moldyn->atom[5832].f.y);
2051                 printf("  z: %0.40f\n",moldyn->atom[5832].f.z);
2052         }
2053 #endif
2054
2055         /* calculate global virial */
2056         for(i=0;i<count;i++) {
2057                 moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
2058                 moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
2059                 moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
2060                 moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
2061                 moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
2062                 moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
2063         }
2064
2065         return 0;
2066 }
2067
2068 /*
2069  * virial calculation
2070  */
2071
2072 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
2073 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
2074
2075         a->virial.xx+=f->x*d->x;
2076         a->virial.yy+=f->y*d->y;
2077         a->virial.zz+=f->z*d->z;
2078         a->virial.xy+=f->x*d->y;
2079         a->virial.xz+=f->x*d->z;
2080         a->virial.yz+=f->y*d->z;
2081
2082         return 0;
2083 }
2084
2085 /*
2086  * periodic boundary checking
2087  */
2088
2089 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
2090 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
2091
2092         double x,y,z;
2093         t_3dvec *dim;
2094
2095         dim=&(moldyn->dim);
2096
2097         x=dim->x/2;
2098         y=dim->y/2;
2099         z=dim->z/2;
2100
2101         if(moldyn->status&MOLDYN_STAT_PBX) {
2102                 if(a->x>=x) a->x-=dim->x;
2103                 else if(-a->x>x) a->x+=dim->x;
2104         }
2105         if(moldyn->status&MOLDYN_STAT_PBY) {
2106                 if(a->y>=y) a->y-=dim->y;
2107                 else if(-a->y>y) a->y+=dim->y;
2108         }
2109         if(moldyn->status&MOLDYN_STAT_PBZ) {
2110                 if(a->z>=z) a->z-=dim->z;
2111                 else if(-a->z>z) a->z+=dim->z;
2112         }
2113
2114         return 0;
2115 }
2116
2117 /*
2118  * debugging / critical check functions
2119  */
2120
2121 int moldyn_bc_check(t_moldyn *moldyn) {
2122
2123         t_atom *atom;
2124         t_3dvec *dim;
2125         int i;
2126         double x;
2127         u8 byte;
2128         int j,k;
2129
2130         atom=moldyn->atom;
2131         dim=&(moldyn->dim);
2132         x=dim->x/2;
2133
2134         for(i=0;i<moldyn->count;i++) {
2135                 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
2136                         printf("FATAL: atom %d: x: %.20f (%.20f)\n",
2137                                i,atom[i].r.x,dim->x/2);
2138                         printf("diagnostic:\n");
2139                         printf("-----------\natom.r.x:\n");
2140                         for(j=0;j<8;j++) {
2141                                 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
2142                                 for(k=0;k<8;k++)
2143                                         printf("%d%c",
2144                                         ((byte)&(1<<k))?1:0,
2145                                         (k==7)?'\n':'|');
2146                         }
2147                         printf("---------------\nx=dim.x/2:\n");
2148                         for(j=0;j<8;j++) {
2149                                 memcpy(&byte,(u8 *)(&x)+j,1);
2150                                 for(k=0;k<8;k++)
2151                                         printf("%d%c",
2152                                         ((byte)&(1<<k))?1:0,
2153                                         (k==7)?'\n':'|');
2154                         }
2155                         if(atom[i].r.x==x) printf("the same!\n");
2156                         else printf("different!\n");
2157                 }
2158                 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
2159                         printf("FATAL: atom %d: y: %.20f (%.20f)\n",
2160                                i,atom[i].r.y,dim->y/2);
2161                 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
2162                         printf("FATAL: atom %d: z: %.20f (%.20f)\n",
2163                                i,atom[i].r.z,dim->z/2);
2164         }
2165
2166         return 0;
2167 }
2168
2169 /*
2170  * restore function
2171  */
2172
2173 int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
2174
2175         int fd;
2176         int cnt,size;
2177
2178         fd=open(file,O_RDONLY);
2179         if(fd<0) {
2180                 perror("[moldyn] load save file open");
2181                 return fd;
2182         }
2183
2184         size=sizeof(t_moldyn);
2185         cnt=read(fd,moldyn,size);
2186         if(cnt!=size) {
2187                 perror("[moldyn] load save file read (moldyn)");
2188                 return cnt;
2189         }
2190
2191         size=moldyn->count*sizeof(t_atom);
2192
2193         moldyn->atom=(t_atom *)malloc(size);
2194         if(moldyn->atom==NULL) {
2195                 perror("[moldyn] load save file malloc (atoms)");
2196                 return -1;
2197         }
2198
2199         cnt=read(fd,moldyn->atom,size);
2200         if(cnt!=size) {
2201                 perror("[moldyn] load save file read (atoms)");
2202                 return cnt;
2203         }
2204
2205         // hooks etc ...
2206
2207         return 0;
2208 }
2209
2210 int moldyn_load(t_moldyn *moldyn) {
2211
2212         // later ...
2213
2214         return 0;
2215 }
2216
2217 /*
2218  * post processing functions
2219  */
2220
2221 int get_line(int fd,char *line,int max) {
2222
2223         int count,ret;
2224
2225         count=0;
2226
2227         while(1) {
2228                 if(count==max) return count;
2229                 ret=read(fd,line+count,1);
2230                 if(ret<=0) return ret;
2231                 if(line[count]=='\n') {
2232                         line[count]='\0';
2233                         return count+1;
2234                 }
2235                 count+=1;
2236         }
2237 }
2238
2239 int pair_correlation_init(t_moldyn *moldyn,double dr) {
2240
2241
2242         return 0;
2243 }
2244
2245 int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
2246
2247         int slots;
2248         double *stat;
2249         int i,j;
2250         t_linkcell *lc;
2251 #ifdef STATIC_LISTS
2252         int *neighbour[27];
2253         int p;
2254 #else
2255         t_list neighbour[27];
2256 #endif
2257         t_atom *itom,*jtom;
2258         t_list *this;
2259         unsigned char bc;
2260         t_3dvec dist;
2261         double d,norm;
2262         int o,s;
2263         unsigned char ibrand;
2264
2265         lc=&(moldyn->lc);
2266
2267         slots=(int)(moldyn->cutoff/dr);
2268         o=2*slots;
2269
2270         printf("[moldyn] pair correlation calc info:\n");
2271         printf("  time: %f\n",moldyn->time);
2272         printf("  count: %d\n",moldyn->count);
2273         printf("  cutoff: %f\n",moldyn->cutoff);
2274         printf("  temperature: cur=%f avg=%f\n",moldyn->t,moldyn->t_avg);
2275
2276         if(ptr!=NULL) {
2277                 stat=(double *)ptr;
2278         }
2279         else {
2280                 stat=(double *)malloc(3*slots*sizeof(double));
2281                 if(stat==NULL) {
2282                         perror("[moldyn] pair correlation malloc");
2283                         return -1;
2284                 }
2285         }
2286
2287         memset(stat,0,3*slots*sizeof(double));
2288
2289         link_cell_init(moldyn,VERBOSE);
2290
2291         itom=moldyn->atom;
2292
2293         for(i=0;i<moldyn->count;i++) {
2294                 /* neighbour indexing */
2295                 link_cell_neighbour_index(moldyn,
2296                                           (itom[i].r.x+moldyn->dim.x/2)/lc->x,
2297                                           (itom[i].r.y+moldyn->dim.y/2)/lc->x,
2298                                           (itom[i].r.z+moldyn->dim.z/2)/lc->x,
2299                                           neighbour);
2300
2301                 /* brand of atom i */
2302                 ibrand=itom[i].brand;
2303
2304                 for(j=0;j<27;j++) {
2305
2306                         bc=(j<lc->dnlc)?0:1;
2307
2308 #ifdef STATIC_LISTS
2309                         p=0;
2310
2311                         while(neighbour[j][p]!=0) {
2312
2313                                 jtom=&(moldyn->atom[neighbour[j][p]]);
2314                                 p++;
2315 #else
2316                         this=&(neighbour[j]);
2317                         list_reset_f(this);
2318
2319                         if(this->start==NULL)
2320                                 continue;
2321
2322                         do {
2323
2324                                 jtom=this->current->data;
2325 #endif
2326
2327                                 if(jtom==&(itom[i]))
2328                                         continue;
2329
2330                                 /* only count pairs once */
2331                                 if(itom[i].tag>jtom->tag)
2332                                         continue;
2333
2334                                 /*
2335                                  * pair correlation calc
2336                                  */
2337
2338                                 /* distance */
2339                                 v3_sub(&dist,&(jtom->r),&(itom[i].r));
2340                                 if(bc) check_per_bound(moldyn,&dist);
2341                                 d=v3_absolute_square(&dist);
2342
2343                                 /* ignore if greater cutoff */
2344                                 if(d>moldyn->cutoff_square)
2345                                         continue;
2346
2347                                 /* fill the slots */
2348                                 d=sqrt(d);
2349                                 s=(int)(d/dr);
2350
2351                                 if(ibrand!=jtom->brand) {
2352                                         /* mixed */
2353                                         stat[s]+=1;
2354                                 }
2355                                 else {
2356                                         /* type a - type a bonds */
2357                                         if(ibrand==0)
2358                                                 stat[s+slots]+=1;
2359                                         else
2360                                         /* type b - type b bonds */
2361                                                 stat[s+o]+=1;
2362                                 }
2363
2364 #ifdef STATIC_LISTS
2365                         }
2366 #else
2367                         } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
2368 #endif
2369                 }
2370         }
2371
2372         /* normalization
2373         for(i=1;i<slots;i++) {
2374                  // normalization: 4 pi r r dr
2375                  // here: not double counting pairs -> 2 pi r r dr
2376                 norm=2*M_PI*moldyn->count*(i*dr*i*dr)*dr;
2377                 stat[i]/=norm;
2378                 stat[slots+i]/=norm;
2379                 stat[o+i]/=norm;
2380         }
2381         */
2382
2383         if(ptr==NULL) {
2384                 /* todo: store/print pair correlation function */
2385                 free(stat);
2386         }
2387
2388         free(moldyn->atom);
2389
2390         link_cell_shutdown(moldyn);
2391
2392         return 0;
2393 }
2394
2395 int analyze_bonds(t_moldyn *moldyn) {
2396
2397
2398
2399
2400         return 0;
2401 }
2402
2403 /*
2404  * visualization code
2405  */
2406
2407 int visual_init(t_moldyn *moldyn,char *filebase) {
2408
2409         strncpy(moldyn->vis.fb,filebase,128);
2410
2411         return 0;
2412 }
2413
2414 int visual_atoms(t_moldyn *moldyn) {
2415
2416         int i,j,fd;
2417         char file[128+64];
2418         t_3dvec dim;
2419         double help;
2420         t_visual *v;
2421         t_atom *atom;
2422         t_atom *btom;
2423         t_linkcell *lc;
2424 #ifdef STATIC_LISTS
2425         int *neighbour[27];
2426         int p;
2427 #else
2428         t_list neighbour[27];
2429 #endif
2430         u8 bc;
2431         t_3dvec dist;
2432         double d2;
2433         u8 brand;
2434
2435         v=&(moldyn->vis);
2436         dim.x=v->dim.x;
2437         dim.y=v->dim.y;
2438         dim.z=v->dim.z;
2439         atom=moldyn->atom;
2440         lc=&(moldyn->lc);
2441
2442         help=(dim.x+dim.y);
2443
2444         sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,moldyn->time);
2445         fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
2446         if(fd<0) {
2447                 perror("open visual save file fd");
2448                 return -1;
2449         }
2450
2451         /* write the actual data file */
2452
2453         // povray header
2454         dprintf(fd,"# [P] %d %07.f <%f,%f,%f>\n",
2455                 moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help);
2456
2457         // atomic configuration
2458         for(i=0;i<moldyn->count;i++) {
2459                 // atom type, positions, color and kinetic energy
2460                 dprintf(fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
2461                                                  atom[i].r.x,
2462                                                  atom[i].r.y,
2463                                                  atom[i].r.z,
2464                                                  pse_col[atom[i].element],
2465                                                  atom[i].ekin);
2466
2467                 /*
2468                  * bond detection should usually be done by potential
2469                  * functions. brrrrr! EVIL!
2470                  *
2471                  * todo: potentials need to export a 'find_bonds' function!
2472                  */
2473
2474                 // bonds between atoms
2475                 if(!(atom[i].attr&ATOM_ATTR_VB))
2476                         continue;
2477                 link_cell_neighbour_index(moldyn,
2478                                           (atom[i].r.x+moldyn->dim.x/2)/lc->x,
2479                                           (atom[i].r.y+moldyn->dim.y/2)/lc->y,
2480                                           (atom[i].r.z+moldyn->dim.z/2)/lc->z,
2481                                           neighbour);
2482                 for(j=0;j<27;j++) {
2483                         bc=j<lc->dnlc?0:1;
2484 #ifdef STATIC_LISTS
2485                         p=0;
2486                         while(neighbour[j][p]!=0) {
2487                                 btom=&(atom[neighbour[j][p]]);
2488                                 p++;
2489 #else
2490                         list_reset_f(&neighbour[j]);
2491                         if(neighbour[j].start==NULL)
2492                                 continue;
2493                         do {
2494                                 btom=neighbour[j].current->data;
2495 #endif
2496                                 if(btom==&atom[i])      // skip identical atoms
2497                                         continue;
2498                                 //if(btom<&atom[i])     // skip half of them
2499                                 //      continue;
2500                                 v3_sub(&dist,&(atom[i].r),&(btom->r));
2501                                 if(bc) check_per_bound(moldyn,&dist);
2502                                 d2=v3_absolute_square(&dist);
2503                                 brand=atom[i].brand;
2504                                 if(brand==btom->brand) {
2505                                         if(d2>moldyn->bondlen[brand])
2506                                                 continue;
2507                                 }
2508                                 else {
2509                                         if(d2>moldyn->bondlen[2])
2510                                                 continue;
2511                                 }
2512                                 dprintf(fd,"# [B] %f %f %f %f %f %f\n",
2513                                         atom[i].r.x,atom[i].r.y,atom[i].r.z,
2514                                         btom->r.x,btom->r.y,btom->r.z);
2515 #ifdef STATIC_LISTS
2516                         }
2517 #else
2518                         } while(list_next_f(&neighbour[j])!=L_NO_NEXT_ELEMENT);
2519 #endif
2520                 }
2521         }
2522
2523         // boundaries
2524         if(dim.x) {
2525                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2526                         -dim.x/2,-dim.y/2,-dim.z/2,
2527                         dim.x/2,-dim.y/2,-dim.z/2);
2528                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2529                         -dim.x/2,-dim.y/2,-dim.z/2,
2530                         -dim.x/2,dim.y/2,-dim.z/2);
2531                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2532                         dim.x/2,dim.y/2,-dim.z/2,
2533                         dim.x/2,-dim.y/2,-dim.z/2);
2534                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2535                         -dim.x/2,dim.y/2,-dim.z/2,
2536                         dim.x/2,dim.y/2,-dim.z/2);
2537
2538                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2539                         -dim.x/2,-dim.y/2,dim.z/2,
2540                         dim.x/2,-dim.y/2,dim.z/2);
2541                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2542                         -dim.x/2,-dim.y/2,dim.z/2,
2543                         -dim.x/2,dim.y/2,dim.z/2);
2544                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2545                         dim.x/2,dim.y/2,dim.z/2,
2546                         dim.x/2,-dim.y/2,dim.z/2);
2547                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2548                         -dim.x/2,dim.y/2,dim.z/2,
2549                         dim.x/2,dim.y/2,dim.z/2);
2550
2551                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2552                         -dim.x/2,-dim.y/2,dim.z/2,
2553                         -dim.x/2,-dim.y/2,-dim.z/2);
2554                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2555                         -dim.x/2,dim.y/2,dim.z/2,
2556                         -dim.x/2,dim.y/2,-dim.z/2);
2557                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2558                         dim.x/2,-dim.y/2,dim.z/2,
2559                         dim.x/2,-dim.y/2,-dim.z/2);
2560                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2561                         dim.x/2,dim.y/2,dim.z/2,
2562                         dim.x/2,dim.y/2,-dim.z/2);
2563         }
2564
2565         close(fd);
2566
2567         return 0;
2568 }
2569