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
1262         lc->cells=lc->nx*lc->ny*lc->nz;
1263         lc->subcell=malloc(lc->cells*sizeof(t_list));
1264
1265         if(lc->cells<27)
1266                 printf("[moldyn] FATAL: less then 27 subcells!\n");
1267
1268         if(vol) {
1269                 printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
1270                 printf("  x: %d x %f A\n",lc->nx,lc->x);
1271                 printf("  y: %d x %f A\n",lc->ny,lc->y);
1272                 printf("  z: %d x %f A\n",lc->nz,lc->z);
1273         }
1274
1275         for(i=0;i<lc->cells;i++)
1276                 list_init_f(&(lc->subcell[i]));
1277
1278         link_cell_update(moldyn);
1279
1280         return 0;
1281 }
1282
1283 int link_cell_update(t_moldyn *moldyn) {
1284
1285         int count,i,j,k;
1286         int nx,ny;
1287         t_atom *atom;
1288         t_linkcell *lc;
1289         double x,y,z;
1290
1291         atom=moldyn->atom;
1292         lc=&(moldyn->lc);
1293
1294         nx=lc->nx;
1295         ny=lc->ny;
1296
1297         x=moldyn->dim.x/2;
1298         y=moldyn->dim.y/2;
1299         z=moldyn->dim.z/2;
1300
1301         for(i=0;i<lc->cells;i++)
1302                 list_destroy_f(&(lc->subcell[i]));
1303
1304         for(count=0;count<moldyn->count;count++) {
1305                 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1306                 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1307                 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1308                 list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
1309                                      &(atom[count]));
1310         }
1311
1312         return 0;
1313 }
1314
1315 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1316
1317         t_linkcell *lc;
1318         int a;
1319         int count1,count2;
1320         int ci,cj,ck;
1321         int nx,ny,nz;
1322         int x,y,z;
1323         u8 bx,by,bz;
1324
1325         lc=&(moldyn->lc);
1326         nx=lc->nx;
1327         ny=lc->ny;
1328         nz=lc->nz;
1329         count1=1;
1330         count2=27;
1331         a=nx*ny;
1332
1333         cell[0]=lc->subcell[i+j*nx+k*a];
1334         for(ci=-1;ci<=1;ci++) {
1335                 bx=0;
1336                 x=i+ci;
1337                 if((x<0)||(x>=nx)) {
1338                         x=(x+nx)%nx;
1339                         bx=1;
1340                 }
1341                 for(cj=-1;cj<=1;cj++) {
1342                         by=0;
1343                         y=j+cj;
1344                         if((y<0)||(y>=ny)) {
1345                                 y=(y+ny)%ny;
1346                                 by=1;
1347                         }
1348                         for(ck=-1;ck<=1;ck++) {
1349                                 bz=0;
1350                                 z=k+ck;
1351                                 if((z<0)||(z>=nz)) {
1352                                         z=(z+nz)%nz;
1353                                         bz=1;
1354                                 }
1355                                 if(!(ci|cj|ck)) continue;
1356                                 if(bx|by|bz) {
1357                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
1358                                 }
1359                                 else {
1360                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
1361                                 }
1362                         }
1363                 }
1364         }
1365
1366         lc->dnlc=count1;
1367
1368         return count1;
1369 }
1370
1371 int link_cell_shutdown(t_moldyn *moldyn) {
1372
1373         int i;
1374         t_linkcell *lc;
1375
1376         lc=&(moldyn->lc);
1377
1378         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1379                 list_destroy_f(&(moldyn->lc.subcell[i]));
1380
1381         free(lc->subcell);
1382
1383         return 0;
1384 }
1385
1386 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1387
1388         int count;
1389         void *ptr;
1390         t_moldyn_schedule *schedule;
1391
1392         schedule=&(moldyn->schedule);
1393         count=++(schedule->total_sched);
1394
1395         ptr=realloc(schedule->runs,count*sizeof(int));
1396         if(!ptr) {
1397                 perror("[moldyn] realloc (runs)");
1398                 return -1;
1399         }
1400         schedule->runs=ptr;
1401         schedule->runs[count-1]=runs;
1402
1403         ptr=realloc(schedule->tau,count*sizeof(double));
1404         if(!ptr) {
1405                 perror("[moldyn] realloc (tau)");
1406                 return -1;
1407         }
1408         schedule->tau=ptr;
1409         schedule->tau[count-1]=tau;
1410
1411         printf("[moldyn] schedule added:\n");
1412         printf("  number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1413
1414
1415         return 0;
1416 }
1417
1418 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1419
1420         moldyn->schedule.hook=hook;
1421         moldyn->schedule.hook_params=hook_params;
1422
1423         return 0;
1424 }
1425
1426 /*
1427  *
1428  * 'integration of newtons equation' - algorithms
1429  *
1430  */
1431
1432 /* start the integration */
1433
1434 int moldyn_integrate(t_moldyn *moldyn) {
1435
1436         int i;
1437         unsigned int e,m,s,v,p,t;
1438         t_3dvec momentum;
1439         t_moldyn_schedule *sched;
1440         t_atom *atom;
1441         int fd;
1442         char dir[128];
1443         double ds;
1444         double energy_scale;
1445         struct timeval t1,t2;
1446         //double tp;
1447
1448         sched=&(moldyn->schedule);
1449         atom=moldyn->atom;
1450
1451         /* initialize linked cell method */
1452         link_cell_init(moldyn,VERBOSE);
1453
1454         /* logging & visualization */
1455         e=moldyn->ewrite;
1456         m=moldyn->mwrite;
1457         s=moldyn->swrite;
1458         v=moldyn->vwrite;
1459         p=moldyn->pwrite;
1460         t=moldyn->twrite;
1461
1462         /* sqaure of some variables */
1463         moldyn->tau_square=moldyn->tau*moldyn->tau;
1464         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1465
1466         /* get current time */
1467         gettimeofday(&t1,NULL);
1468
1469         /* calculate initial forces */
1470         potential_force_calc(moldyn);
1471 #ifdef DEBUG
1472 //return 0;
1473 #endif
1474
1475         /* some stupid checks before we actually start calculating bullshit */
1476         if(moldyn->cutoff>0.5*moldyn->dim.x)
1477                 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1478         if(moldyn->cutoff>0.5*moldyn->dim.y)
1479                 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1480         if(moldyn->cutoff>0.5*moldyn->dim.z)
1481                 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1482         ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1483         if(ds>0.05*moldyn->nnd)
1484                 printf("[moldyn] warning: forces too high / tau too small!\n");
1485
1486         /* zero absolute time */
1487         moldyn->time=0.0;
1488         moldyn->total_steps=0;
1489
1490         /* debugging, ignore */
1491         moldyn->debug=0;
1492
1493         /* tell the world */
1494         printf("[moldyn] integration start, go get a coffee ...\n");
1495
1496         /* executing the schedule */
1497         sched->count=0;
1498         while(sched->count<sched->total_sched) {
1499
1500                 /* setting amount of runs and finite time step size */
1501                 moldyn->tau=sched->tau[sched->count];
1502                 moldyn->tau_square=moldyn->tau*moldyn->tau;
1503                 moldyn->time_steps=sched->runs[sched->count];
1504
1505                 /* energy scaling factor (might change!) */
1506                 energy_scale=moldyn->count*EV;
1507
1508         /* integration according to schedule */
1509
1510         for(i=0;i<moldyn->time_steps;i++) {
1511
1512                 /* integration step */
1513                 moldyn->integrate(moldyn);
1514
1515                 /* calculate kinetic energy, temperature and pressure */
1516                 e_kin_calc(moldyn);
1517                 temperature_calc(moldyn);
1518                 virial_sum(moldyn);
1519                 pressure_calc(moldyn);
1520                 average_and_fluctuation_calc(moldyn);
1521
1522                 /* p/t scaling */
1523                 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1524                         scale_velocity(moldyn,FALSE);
1525                 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1526                         scale_volume(moldyn);
1527
1528                 /* check for log & visualization */
1529                 if(e) {
1530                         if(!(moldyn->total_steps%e))
1531                                 dprintf(moldyn->efd,
1532                                         "%f %f %f %f\n",
1533                                         moldyn->time,moldyn->ekin/energy_scale,
1534                                         moldyn->energy/energy_scale,
1535                                         get_total_energy(moldyn)/energy_scale);
1536                 }
1537                 if(m) {
1538                         if(!(moldyn->total_steps%m)) {
1539                                 momentum=get_total_p(moldyn);
1540                                 dprintf(moldyn->mfd,
1541                                         "%f %f %f %f %f\n",moldyn->time,
1542                                         momentum.x,momentum.y,momentum.z,
1543                                         v3_norm(&momentum));
1544                         }
1545                 }
1546                 if(p) {
1547                         if(!(moldyn->total_steps%p)) {
1548                                 dprintf(moldyn->pfd,
1549                                         "%f %f %f %f %f\n",moldyn->time,
1550                                          moldyn->p/BAR,moldyn->p_avg/BAR,
1551                                          moldyn->gp/BAR,moldyn->gp_avg/BAR);
1552                         }
1553                 }
1554                 if(t) {
1555                         if(!(moldyn->total_steps%t)) {
1556                                 dprintf(moldyn->tfd,
1557                                         "%f %f %f\n",
1558                                         moldyn->time,moldyn->t,moldyn->t_avg);
1559                         }
1560                 }
1561                 if(s) {
1562                         if(!(moldyn->total_steps%s)) {
1563                                 snprintf(dir,128,"%s/s-%07.f.save",
1564                                          moldyn->vlsdir,moldyn->time);
1565                                 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
1566                                         S_IRUSR|S_IWUSR);
1567                                 if(fd<0) perror("[moldyn] save fd open");
1568                                 else {
1569                                         write(fd,moldyn,sizeof(t_moldyn));
1570                                         write(fd,moldyn->atom,
1571                                               moldyn->count*sizeof(t_atom));
1572                                 }
1573                                 close(fd);
1574                         }
1575                 }
1576                 if(v) {
1577                         if(!(moldyn->total_steps%v)) {
1578                                 visual_atoms(moldyn);
1579                         }
1580                 }
1581
1582                 /* display progress */
1583                 //if(!(moldyn->total_steps%10)) {
1584                         /* get current time */
1585                         gettimeofday(&t2,NULL);
1586
1587         printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
1588                sched->count,i,
1589                moldyn->t,moldyn->t_avg,
1590                moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
1591                moldyn->volume,
1592                (int)(t2.tv_sec-t1.tv_sec));
1593         fflush(stdout);
1594
1595                         /* copy over time */
1596                         t1=t2;
1597                 //}
1598
1599                 /* increase absolute time */
1600                 moldyn->time+=moldyn->tau;
1601                 moldyn->total_steps+=1;
1602
1603         }
1604
1605                 /* check for hooks */
1606                 if(sched->hook) {
1607                         printf("\n ## schedule hook %d/%d start ##\n",
1608                                sched->count+1,sched->total_sched-1);
1609                         sched->hook(moldyn,sched->hook_params);
1610                         printf(" ## schedule hook end ##\n");
1611                 }
1612
1613                 /* increase the schedule counter */
1614                 sched->count+=1;
1615
1616         }
1617
1618         return 0;
1619 }
1620
1621 /* velocity verlet */
1622
1623 int velocity_verlet(t_moldyn *moldyn) {
1624
1625         int i,count;
1626         double tau,tau_square,h;
1627         t_3dvec delta;
1628         t_atom *atom;
1629
1630         atom=moldyn->atom;
1631         count=moldyn->count;
1632         tau=moldyn->tau;
1633         tau_square=moldyn->tau_square;
1634
1635         for(i=0;i<count;i++) {
1636                 /* new positions */
1637                 h=0.5/atom[i].mass;
1638                 v3_scale(&delta,&(atom[i].v),tau);
1639                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1640                 v3_scale(&delta,&(atom[i].f),h*tau_square);
1641                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1642                 check_per_bound(moldyn,&(atom[i].r));
1643
1644                 /* velocities [actually v(t+tau/2)] */
1645                 v3_scale(&delta,&(atom[i].f),h*tau);
1646                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1647         }
1648
1649         /* neighbour list update */
1650         link_cell_update(moldyn);
1651
1652         /* forces depending on chosen potential */
1653         potential_force_calc(moldyn);
1654
1655         for(i=0;i<count;i++) {
1656                 /* again velocities [actually v(t+tau)] */
1657                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1658                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1659         }
1660
1661         return 0;
1662 }
1663
1664
1665 /*
1666  *
1667  * potentials & corresponding forces & virial routine
1668  *
1669  */
1670
1671 /* generic potential and force calculation */
1672
1673 int potential_force_calc(t_moldyn *moldyn) {
1674
1675         int i,j,k,count;
1676         t_atom *itom,*jtom,*ktom;
1677         t_virial *virial;
1678         t_linkcell *lc;
1679         t_list neighbour_i[27];
1680         t_list neighbour_i2[27];
1681         t_list *this,*that;
1682         u8 bc_ij,bc_ik;
1683         int dnlc;
1684
1685         count=moldyn->count;
1686         itom=moldyn->atom;
1687         lc=&(moldyn->lc);
1688
1689         /* reset energy */
1690         moldyn->energy=0.0;
1691
1692         /* reset global virial */
1693         memset(&(moldyn->gvir),0,sizeof(t_virial));
1694
1695         /* reset force, site energy and virial of every atom */
1696         for(i=0;i<count;i++) {
1697
1698                 /* reset force */
1699                 v3_zero(&(itom[i].f));
1700
1701                 /* reset virial */
1702                 virial=(&(itom[i].virial));
1703                 virial->xx=0.0;
1704                 virial->yy=0.0;
1705                 virial->zz=0.0;
1706                 virial->xy=0.0;
1707                 virial->xz=0.0;
1708                 virial->yz=0.0;
1709
1710                 /* reset site energy */
1711                 itom[i].e=0.0;
1712
1713         }
1714
1715         /* get energy, force and virial of every atom */
1716
1717         /* first (and only) loop over atoms i */
1718         for(i=0;i<count;i++) {
1719
1720                 /* single particle potential/force */
1721                 if(itom[i].attr&ATOM_ATTR_1BP)
1722                         if(moldyn->func1b)
1723                                 moldyn->func1b(moldyn,&(itom[i]));
1724
1725                 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1726                         continue;
1727
1728                 /* 2 body pair potential/force */
1729
1730                 link_cell_neighbour_index(moldyn,
1731                                           (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1732                                           (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1733                                           (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1734                                           neighbour_i);
1735
1736                 dnlc=lc->dnlc;
1737
1738                 /* first loop over atoms j */
1739                 if(moldyn->func2b) {
1740                         for(j=0;j<27;j++) {
1741
1742                                 this=&(neighbour_i[j]);
1743                                 list_reset_f(this);
1744
1745                                 if(this->start==NULL)
1746                                         continue;
1747
1748                                 bc_ij=(j<dnlc)?0:1;
1749
1750                                 do {
1751                                         jtom=this->current->data;
1752
1753                                         if(jtom==&(itom[i]))
1754                                                 continue;
1755
1756                                         if((jtom->attr&ATOM_ATTR_2BP)&
1757                                            (itom[i].attr&ATOM_ATTR_2BP)) {
1758                                                 moldyn->func2b(moldyn,
1759                                                                &(itom[i]),
1760                                                                jtom,
1761                                                                bc_ij);
1762                                         }
1763                                 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1764
1765                         }
1766                 }
1767
1768                 /* 3 body potential/force */
1769
1770                 if(!(itom[i].attr&ATOM_ATTR_3BP))
1771                         continue;
1772
1773                 /* copy the neighbour lists */
1774                 memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
1775
1776                 /* second loop over atoms j */
1777                 for(j=0;j<27;j++) {
1778
1779                         this=&(neighbour_i[j]);
1780                         list_reset_f(this);
1781
1782                         if(this->start==NULL)
1783                                 continue;
1784
1785                         bc_ij=(j<dnlc)?0:1;
1786
1787                         do {
1788                                 jtom=this->current->data;
1789
1790                                 if(jtom==&(itom[i]))
1791                                         continue;
1792
1793                                 if(!(jtom->attr&ATOM_ATTR_3BP))
1794                                         continue;
1795
1796                                 /* reset 3bp run */
1797                                 moldyn->run3bp=1;
1798
1799                                 if(moldyn->func3b_j1)
1800                                         moldyn->func3b_j1(moldyn,
1801                                                           &(itom[i]),
1802                                                           jtom,
1803                                                           bc_ij);
1804
1805                                 /* in first j loop, 3bp run can be skipped */
1806                                 if(!(moldyn->run3bp))
1807                                         continue;
1808
1809                                 /* first loop over atoms k */
1810                                 if(moldyn->func3b_k1) {
1811
1812                                 for(k=0;k<27;k++) {
1813
1814                                         that=&(neighbour_i2[k]);
1815                                         list_reset_f(that);
1816
1817                                         if(that->start==NULL)
1818                                                 continue;
1819
1820                                         bc_ik=(k<dnlc)?0:1;
1821
1822                                         do {
1823
1824                                                 ktom=that->current->data;
1825
1826                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
1827                                                         continue;
1828
1829                                                 if(ktom==jtom)
1830                                                         continue;
1831
1832                                                 if(ktom==&(itom[i]))
1833                                                         continue;
1834
1835                                                 moldyn->func3b_k1(moldyn,
1836                                                                   &(itom[i]),
1837                                                                   jtom,
1838                                                                   ktom,
1839                                                                   bc_ik|bc_ij);
1840
1841                                         } while(list_next_f(that)!=\
1842                                                 L_NO_NEXT_ELEMENT);
1843
1844                                 }
1845
1846                                 }
1847
1848                                 if(moldyn->func3b_j2)
1849                                         moldyn->func3b_j2(moldyn,
1850                                                           &(itom[i]),
1851                                                           jtom,
1852                                                           bc_ij);
1853
1854                                 /* second loop over atoms k */
1855                                 if(moldyn->func3b_k2) {
1856
1857                                 for(k=0;k<27;k++) {
1858
1859                                         that=&(neighbour_i2[k]);
1860                                         list_reset_f(that);
1861
1862                                         if(that->start==NULL)
1863                                                 continue;
1864
1865                                         bc_ik=(k<dnlc)?0:1;
1866
1867                                         do {
1868
1869                                                 ktom=that->current->data;
1870
1871                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
1872                                                         continue;
1873
1874                                                 if(ktom==jtom)
1875                                                         continue;
1876
1877                                                 if(ktom==&(itom[i]))
1878                                                         continue;
1879
1880                                                 moldyn->func3b_k2(moldyn,
1881                                                                   &(itom[i]),
1882                                                                   jtom,
1883                                                                   ktom,
1884                                                                   bc_ik|bc_ij);
1885
1886                                         } while(list_next_f(that)!=\
1887                                                 L_NO_NEXT_ELEMENT);
1888
1889                                 }
1890
1891                                 }
1892
1893                                 /* 2bp post function */
1894                                 if(moldyn->func3b_j3) {
1895                                         moldyn->func3b_j3(moldyn,
1896                                                           &(itom[i]),
1897                                                           jtom,bc_ij);
1898                                 }
1899
1900                         } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1901
1902                 }
1903
1904 #ifdef DEBUG
1905         //printf("\n\n");
1906 #endif
1907 #ifdef VDEBUG
1908         printf("\n\n");
1909 #endif
1910
1911         }
1912
1913 #ifdef DEBUG
1914         //printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
1915         if(moldyn->time>DSTART&&moldyn->time<DEND) {
1916                 printf("force:\n");
1917                 printf("  x: %0.40f\n",moldyn->atom[5832].f.x);
1918                 printf("  y: %0.40f\n",moldyn->atom[5832].f.y);
1919                 printf("  z: %0.40f\n",moldyn->atom[5832].f.z);
1920         }
1921 #endif
1922
1923         /* calculate global virial */
1924         for(i=0;i<count;i++) {
1925                 moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
1926                 moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
1927                 moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
1928                 moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
1929                 moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
1930                 moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
1931         }
1932
1933         return 0;
1934 }
1935
1936 /*
1937  * virial calculation
1938  */
1939
1940 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1941 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1942
1943         a->virial.xx+=f->x*d->x;
1944         a->virial.yy+=f->y*d->y;
1945         a->virial.zz+=f->z*d->z;
1946         a->virial.xy+=f->x*d->y;
1947         a->virial.xz+=f->x*d->z;
1948         a->virial.yz+=f->y*d->z;
1949
1950         return 0;
1951 }
1952
1953 /*
1954  * periodic boundary checking
1955  */
1956
1957 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1958 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1959
1960         double x,y,z;
1961         t_3dvec *dim;
1962
1963         dim=&(moldyn->dim);
1964
1965         x=dim->x/2;
1966         y=dim->y/2;
1967         z=dim->z/2;
1968
1969         if(moldyn->status&MOLDYN_STAT_PBX) {
1970                 if(a->x>=x) a->x-=dim->x;
1971                 else if(-a->x>x) a->x+=dim->x;
1972         }
1973         if(moldyn->status&MOLDYN_STAT_PBY) {
1974                 if(a->y>=y) a->y-=dim->y;
1975                 else if(-a->y>y) a->y+=dim->y;
1976         }
1977         if(moldyn->status&MOLDYN_STAT_PBZ) {
1978                 if(a->z>=z) a->z-=dim->z;
1979                 else if(-a->z>z) a->z+=dim->z;
1980         }
1981
1982         return 0;
1983 }
1984
1985 /*
1986  * debugging / critical check functions
1987  */
1988
1989 int moldyn_bc_check(t_moldyn *moldyn) {
1990
1991         t_atom *atom;
1992         t_3dvec *dim;
1993         int i;
1994         double x;
1995         u8 byte;
1996         int j,k;
1997
1998         atom=moldyn->atom;
1999         dim=&(moldyn->dim);
2000         x=dim->x/2;
2001
2002         for(i=0;i<moldyn->count;i++) {
2003                 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
2004                         printf("FATAL: atom %d: x: %.20f (%.20f)\n",
2005                                i,atom[i].r.x,dim->x/2);
2006                         printf("diagnostic:\n");
2007                         printf("-----------\natom.r.x:\n");
2008                         for(j=0;j<8;j++) {
2009                                 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
2010                                 for(k=0;k<8;k++)
2011                                         printf("%d%c",
2012                                         ((byte)&(1<<k))?1:0,
2013                                         (k==7)?'\n':'|');
2014                         }
2015                         printf("---------------\nx=dim.x/2:\n");
2016                         for(j=0;j<8;j++) {
2017                                 memcpy(&byte,(u8 *)(&x)+j,1);
2018                                 for(k=0;k<8;k++)
2019                                         printf("%d%c",
2020                                         ((byte)&(1<<k))?1:0,
2021                                         (k==7)?'\n':'|');
2022                         }
2023                         if(atom[i].r.x==x) printf("the same!\n");
2024                         else printf("different!\n");
2025                 }
2026                 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
2027                         printf("FATAL: atom %d: y: %.20f (%.20f)\n",
2028                                i,atom[i].r.y,dim->y/2);
2029                 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
2030                         printf("FATAL: atom %d: z: %.20f (%.20f)\n",
2031                                i,atom[i].r.z,dim->z/2);
2032         }
2033
2034         return 0;
2035 }
2036
2037 /*
2038  * restore function
2039  */
2040
2041 int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
2042
2043         int fd;
2044         int cnt,size;
2045
2046         fd=open(file,O_RDONLY);
2047         if(fd<0) {
2048                 perror("[moldyn] load save file open");
2049                 return fd;
2050         }
2051
2052         size=sizeof(t_moldyn);
2053         cnt=read(fd,moldyn,size);
2054         if(cnt!=size) {
2055                 perror("[moldyn] load save file read (moldyn)");
2056                 return cnt;
2057         }
2058
2059         size=moldyn->count*sizeof(t_atom);
2060         cnt=read(fd,moldyn->atom,size);
2061         if(cnt!=size) {
2062                 perror("[moldyn] load save file read (atoms)");
2063                 return cnt;
2064         }
2065
2066         // hooks
2067
2068         return 0;
2069 }
2070
2071 int moldyn_load(t_moldyn *moldyn) {
2072
2073         // later ...
2074
2075         return 0;
2076 }
2077
2078 /*
2079  * post processing functions
2080  */
2081
2082 int get_line(int fd,char *line,int max) {
2083
2084         int count,ret;
2085
2086         count=0;
2087
2088         while(1) {
2089                 if(count==max) return count;
2090                 ret=read(fd,line+count,1);
2091                 if(ret<=0) return ret;
2092                 if(line[count]=='\n') {
2093                         line[count]='\0';
2094                         return count+1;
2095                 }
2096                 count+=1;
2097         }
2098 }
2099
2100 int pair_correlation_init(t_moldyn *moldyn,double dr) {
2101
2102
2103         return 0;
2104 }
2105
2106 int calculate_pair_correlation(t_moldyn *moldyn,double dr) {
2107
2108         int slots;
2109         int *stat;
2110         int i;
2111         t_linkcell *lc;
2112         t_list neighbour[27];
2113         t_atom *itom,*jtom;
2114         t_list *this;
2115
2116         lc=&(moldyn->lc);
2117
2118         slots=(int)(moldyn->cutoff/dr);
2119
2120         stat=(int *)malloc(3*slots*sizeof(int));
2121         if(stat==NULL) {
2122                 perror("[moldyn] pair correlation malloc");
2123                 return -1;
2124         }
2125
2126         link_cell_init(moldyn,VERBOSE);
2127
2128         for(i=0;i<lc->cells;i++) {
2129                 /* check for atoms */
2130                 itom=lc->subcell[i].current->data;
2131                 if(itom==NULL)
2132                         continue;
2133
2134                 /* pick first atom and do neighbour indexing */
2135                 link_cell_neighbour_index(moldyn,
2136                                           (itom->r.x+moldyn->dim.x/2)/lc->x,
2137                                           (itom->r.y+moldyn->dim.y/2)/lc->x,
2138                                           (itom->r.z+moldyn->dim.z/2)/lc->x,
2139                                           neighbour);
2140
2141                 /* calculation of g(r) */
2142                 do {
2143                         itom=lc->subcell[i].current->data;
2144 // GO ON HERE ...
2145                 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT););
2146
2147         }
2148
2149         link_cell_shutdown(moldyn);
2150
2151         return 0;
2152 }
2153
2154 int analyze_bonds(t_moldyn *moldyn) {
2155
2156
2157
2158
2159         return 0;
2160 }
2161
2162 /*
2163  * visualization code
2164  */
2165
2166 int visual_init(t_moldyn *moldyn,char *filebase) {
2167
2168         strncpy(moldyn->vis.fb,filebase,128);
2169
2170         return 0;
2171 }
2172
2173 int visual_atoms(t_moldyn *moldyn) {
2174
2175         int i,j,fd;
2176         char file[128+64];
2177         t_3dvec dim;
2178         double help;
2179         t_visual *v;
2180         t_atom *atom;
2181         t_atom *btom;
2182         t_linkcell *lc;
2183         t_list neighbour[27];
2184         u8 bc;
2185         t_3dvec dist;
2186         double d2;
2187         u8 brand;
2188
2189         v=&(moldyn->vis);
2190         dim.x=v->dim.x;
2191         dim.y=v->dim.y;
2192         dim.z=v->dim.z;
2193         atom=moldyn->atom;
2194         lc=&(moldyn->lc);
2195
2196         help=(dim.x+dim.y);
2197
2198         sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,moldyn->time);
2199         fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
2200         if(fd<0) {
2201                 perror("open visual save file fd");
2202                 return -1;
2203         }
2204
2205         /* write the actual data file */
2206
2207         // povray header
2208         dprintf(fd,"# [P] %d %07.f <%f,%f,%f>\n",
2209                 moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help);
2210
2211         // atomic configuration
2212         for(i=0;i<moldyn->count;i++) {
2213                 // atom type, positions, color and kinetic energy
2214                 dprintf(fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
2215                                                  atom[i].r.x,
2216                                                  atom[i].r.y,
2217                                                  atom[i].r.z,
2218                                                  pse_col[atom[i].element],
2219                                                  atom[i].ekin);
2220
2221                 /*
2222                  * bond detection should usually be done by potential
2223                  * functions. brrrrr! EVIL!
2224                  *
2225                  * todo: potentials need to export a 'find_bonds' function!
2226                  */
2227
2228                 // bonds between atoms
2229                 if(!(atom[i].attr&ATOM_ATTR_VB))
2230                         continue;
2231                 link_cell_neighbour_index(moldyn,
2232                                           (atom[i].r.x+moldyn->dim.x/2)/lc->x,
2233                                           (atom[i].r.y+moldyn->dim.y/2)/lc->y,
2234                                           (atom[i].r.z+moldyn->dim.z/2)/lc->z,
2235                                           neighbour);
2236                 for(j=0;j<27;j++) {
2237                         list_reset_f(&neighbour[j]);
2238                         if(neighbour[j].start==NULL)
2239                                 continue;
2240                         bc=j<lc->dnlc?0:1;
2241                         do {
2242                                 btom=neighbour[j].current->data;
2243                                 if(btom==&atom[i])      // skip identical atoms
2244                                         continue;
2245                                 //if(btom<&atom[i])     // skip half of them
2246                                 //      continue;
2247                                 v3_sub(&dist,&(atom[i].r),&(btom->r));
2248                                 if(bc) check_per_bound(moldyn,&dist);
2249                                 d2=v3_absolute_square(&dist);
2250                                 brand=atom[i].brand;
2251                                 if(brand==btom->brand) {
2252                                         if(d2>moldyn->bondlen[brand])
2253                                                 continue;
2254                                 }
2255                                 else {
2256                                         if(d2>moldyn->bondlen[2])
2257                                                 continue;
2258                                 }
2259                                 dprintf(fd,"# [B] %f %f %f %f %f %f\n",
2260                                         atom[i].r.x,atom[i].r.y,atom[i].r.z,
2261                                         btom->r.x,btom->r.y,btom->r.z);
2262                         } while(list_next_f(&neighbour[j])!=L_NO_NEXT_ELEMENT);
2263                 }
2264         }
2265
2266         // boundaries
2267         if(dim.x) {
2268                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2269                         -dim.x/2,-dim.y/2,-dim.z/2,
2270                         dim.x/2,-dim.y/2,-dim.z/2);
2271                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2272                         -dim.x/2,-dim.y/2,-dim.z/2,
2273                         -dim.x/2,dim.y/2,-dim.z/2);
2274                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2275                         dim.x/2,dim.y/2,-dim.z/2,
2276                         dim.x/2,-dim.y/2,-dim.z/2);
2277                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2278                         -dim.x/2,dim.y/2,-dim.z/2,
2279                         dim.x/2,dim.y/2,-dim.z/2);
2280
2281                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2282                         -dim.x/2,-dim.y/2,dim.z/2,
2283                         dim.x/2,-dim.y/2,dim.z/2);
2284                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2285                         -dim.x/2,-dim.y/2,dim.z/2,
2286                         -dim.x/2,dim.y/2,dim.z/2);
2287                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2288                         dim.x/2,dim.y/2,dim.z/2,
2289                         dim.x/2,-dim.y/2,dim.z/2);
2290                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2291                         -dim.x/2,dim.y/2,dim.z/2,
2292                         dim.x/2,dim.y/2,dim.z/2);
2293
2294                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2295                         -dim.x/2,-dim.y/2,dim.z/2,
2296                         -dim.x/2,-dim.y/2,-dim.z/2);
2297                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2298                         -dim.x/2,dim.y/2,dim.z/2,
2299                         -dim.x/2,dim.y/2,-dim.z/2);
2300                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2301                         dim.x/2,-dim.y/2,dim.z/2,
2302                         dim.x/2,-dim.y/2,-dim.z/2);
2303                 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2304                         dim.x/2,dim.y/2,dim.z/2,
2305                         dim.x/2,dim.y/2,-dim.z/2);
2306         }
2307
2308         close(fd);
2309
2310         return 0;
2311 }
2312