mdrun.c

   1 /*
   2  * mdrun.c - main code to run a md simulation
   3  *
   4  * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
   5  *
   6  */
   7
   8 #include "mdrun.h"
   9
  10 /* potential */
  11 #include "potentials/harmonic_oscillator.h"
  12 #include "potentials/lennard_jones.h"
  13 #include "potentials/albe.h"
  14 #ifdef TERSOFF_ORIG
  15 #include "potentials/tersoff_orig.h"
  16 #else
  17 #include "potentials/tersoff.h"
  18 #endif
  19
  20 #define ME      "[mdrun]"
  21
  22 /*
  23  * parse function
  24  */
  25
  26 int mdrun_usage(void) {
  27
  28         printf("%s usage:\n",ME);
  29
  30         return 0;
  31 }
  32
  33 int mdrun_parse_argv(t_mdrun *mdrun,int argc,char **argv) {
  34
  35         int i;
  36
  37         for(i=1;i<argc;i++) {
  38
  39                 if(argv[i][0]!='-') {
  40                         printf("%s unknown switch: %s\n",ME,argv[i]);
  41                         return -1;
  42                 }
  43
  44                 switch(argv[i][1]) {
  45                         case 'c':
  46                                 strncpy(mdrun->cfile,argv[++i],128);
  47                                 break;
  48                         case 's':
  49                                 strncpy(mdrun->sdir,argv[++i],128);
  50                                 break;
  51                         case 'h':
  52                                 mdrun_usage();
  53                                 break;
  54                         default:
  55                                 printf("%s unknown option: %s\n",ME,argv[i]);
  56                                 mdrun_usage();
  57                                 return -1;
  58                 }
  59
  60         }
  61
  62         return 0;
  63 }
  64
  65 int del_stages(t_mdrun *mdrun) {
  66
  67         t_list *sl;
  68         t_stage *stage;
  69
  70         sl=&(mdrun->stage);
  71
  72         list_reset_f(sl);
  73
  74         if(sl->start==NULL)
  75                 return 0;
  76
  77         do {
  78                 stage=sl->current->data;
  79                 free(stage->params);
  80                 free(stage);
  81         } while(list_next_f(sl)!=L_NO_NEXT_ELEMENT);
  82
  83         return 0;
  84 }
  85
  86 int add_stage(t_mdrun *mdrun,u8 type,void *params) {
  87
  88         int psize;
  89
  90         t_stage *stage;
  91
  92         switch(type) {
  93                 case STAGE_DISPLACE_ATOM:
  94                         psize=sizeof(t_displace_atom_params);
  95                         break;
  96                 case STAGE_INSERT_ATOMS:
  97                         psize=sizeof(t_insert_atoms_params);
  98                         break;
  99                 case STAGE_CONTINUE:
 100                         psize=sizeof(t_continue_params);
 101                         break;
 102                 case STAGE_ANNEAL:
 103                         psize=sizeof(t_anneal_params);
 104                         break;
 105                 case STAGE_CHAATTR:
 106                         psize=sizeof(t_chaattr_params);
 107                         break;
 108                 case STAGE_CHSATTR:
 109                         psize=sizeof(t_chsattr_params);
 110                         break;
 111                 default:
 112                         printf("%s unknown stage type: %02x\n",ME,type);
 113                         return -1;
 114         }
 115
 116         stage=malloc(sizeof(t_stage));
 117         if(stage==NULL) {
 118                 perror("[mdrun] malloc (add stage)");
 119                 return -1;
 120         }
 121
 122         stage->type=type;
 123         stage->executed=FALSE;
 124
 125         stage->params=malloc(psize);
 126         if(stage->params==NULL) {
 127                 perror("[mdrun] malloc (stage params)");
 128                 return -1;
 129         }
 130
 131         memcpy(stage->params,params,psize);
 132
 133         list_add_immediate_f(&(mdrun->stage),stage);
 134
 135         return 0;
 136 }
 137
 138 int mdrun_parse_config(t_mdrun *mdrun) {
 139
 140         int fd,ret;
 141         char error[128];
 142         char line[128];
 143         char *wptr;
 144         char word[16][32];
 145         int wcnt;
 146         int i,o;
 147
 148         t_displace_atom_params dap;
 149         t_insert_atoms_params iap;
 150         t_continue_params cp;
 151         t_anneal_params ap;
 152         t_chaattr_params cap;
 153         t_chsattr_params csp;
 154
 155         /* open config file */
 156         fd=open(mdrun->cfile,O_RDONLY);
 157         if(fd<0) {
 158                 snprintf(error,128,"%s open cfile %s",ME,mdrun->cfile);
 159                 perror(error);
 160                 return fd;
 161         }
 162
 163         /* read, parse, set */
 164         ret=1;
 165         while(ret>0) {
 166
 167                 /* read */
 168                 ret=get_line(fd,line,128);
 169
 170                 /* parse */
 171
 172                 // ignore # lines and \n
 173                 if((line[0]=='#')|(ret==1))
 174                         continue;
 175
 176                 // reset
 177                 memset(&iap,0,sizeof(t_insert_atoms_params));
 178                 memset(&cp,0,sizeof(t_continue_params));
 179                 memset(&ap,0,sizeof(t_anneal_params));
 180                 memset(&cap,0,sizeof(t_chaattr_params));
 181                 memset(&csp,0,sizeof(t_chsattr_params));
 182
 183                 // get command + args
 184                 wcnt=0;
 185                 while(1) {
 186                         if(wcnt)
 187                                 wptr=strtok(NULL," \t");
 188                         else
 189                                 wptr=strtok(line," \t");
 190                         if(wptr==NULL)
 191                                 break;
 192                         strncpy(word[wcnt],wptr,32);
 193                         wcnt+=1;
 194                 }
 195
 196                 if(!strncmp(word[0],"potential",9)) {
 197                         if(!strncmp(word[1],"albe",4))
 198                                 mdrun->potential=MOLDYN_POTENTIAL_AM;
 199                         if(!strncmp(word[1],"tersoff",7))
 200                                 mdrun->potential=MOLDYN_POTENTIAL_TM;
 201                         if(!strncmp(word[1],"ho",2))
 202                                 mdrun->potential=MOLDYN_POTENTIAL_HO;
 203                         if(!strncmp(word[1],"lj",2))
 204                                 mdrun->potential=MOLDYN_POTENTIAL_LJ;
 205                 }
 206                 else if(!strncmp(word[0],"cutoff",6))
 207                         mdrun->cutoff=atof(word[1]);
 208                 else if(!strncmp(word[0],"nnd",3))
 209                         mdrun->nnd=atof(word[1]);
 210                 else if(!strncmp(word[0],"intalgo",7)) {
 211                         if(!strncmp(word[1],"verlet",5))
 212                                 mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
 213                 }
 214                 else if(!strncmp(word[0],"timestep",8))
 215                         mdrun->timestep=atof(word[1]);
 216                 else if(!strncmp(word[0],"volume",6)) {
 217                         mdrun->dim.x=atof(word[1]);
 218                         mdrun->dim.y=atof(word[2]);
 219                         mdrun->dim.z=atof(word[3]);
 220                         if(strncmp(word[4],"0",1))
 221                                 mdrun->vis=TRUE;
 222                 }
 223                 else if(!strncmp(word[0],"pbc",3)) {
 224                         if(strncmp(word[1],"0",1))
 225                                 mdrun->pbcx=TRUE;
 226                         else
 227                                 mdrun->pbcx=FALSE;
 228                         if(strncmp(word[2],"0",1))
 229                                 mdrun->pbcy=TRUE;
 230                         else
 231                                 mdrun->pbcy=FALSE;
 232                         if(strncmp(word[3],"0",1))
 233                                 mdrun->pbcz=TRUE;
 234                         else
 235                                 mdrun->pbcz=FALSE;
 236                 }
 237                 else if(!strncmp(word[0],"temperature",11))
 238                         mdrun->temperature=atof(word[1]);
 239                 else if(!strncmp(word[0],"pressure",8))
 240                         mdrun->pressure=atof(word[1]);
 241                 else if(!strncmp(word[0],"lattice",7)) {
 242                         if(!strncmp(word[1],"zincblende",10))
 243                                 mdrun->lattice=ZINCBLENDE;
 244                         if(!strncmp(word[1],"fcc",3))
 245                                 mdrun->lattice=FCC;
 246                         if(!strncmp(word[1],"diamond",7))
 247                                 mdrun->lattice=DIAMOND;
 248                 }
 249                 else if(!strncmp(word[0],"element1",8)) {
 250                         mdrun->element1=atoi(word[1]);
 251                         mdrun->m1=pse_mass[mdrun->element1];
 252                 }
 253                 else if(!strncmp(word[0],"element2",8)) {
 254                         mdrun->element2=atoi(word[1]);
 255                         mdrun->m2=pse_mass[mdrun->element2];
 256                 }
 257                 else if(!strncmp(word[0],"fill",6)) {
 258                         // only lc mode by now
 259                         mdrun->lx=atoi(word[2]);
 260                         mdrun->ly=atoi(word[3]);
 261                         mdrun->lz=atoi(word[4]);
 262                         mdrun->lc=atof(word[5]);
 263                 }
 264                 else if(!strncmp(word[0],"aattr",5)) {
 265                         // for aatrib line we need a special stage
 266                         // containing one schedule of 0 loops ...
 267                         for(i=0;i<strlen(word[1]);i++) {
 268                                 switch(word[1][i]) {
 269                                         case 't':
 270                                                 cap.type|=CHAATTR_TOTALV;
 271                                                 break;
 272                                         case 'r':
 273                                                 cap.type|=CHAATTR_REGION;
 274                                                 break;
 275                                         case 'e':
 276                                                 cap.type|=CHAATTR_ELEMENT;
 277                                                 break;
 278                                         default:
 279                                                 break;
 280                                 }
 281                         }
 282                         i=2;
 283                         if(cap.type&CHAATTR_REGION) {
 284                                 cap.x0=atof(word[1]);
 285                                 cap.y0=atof(word[2]);
 286                                 cap.z0=atof(word[3]);
 287                                 cap.x1=atof(word[4]);
 288                                 cap.y1=atof(word[5]);
 289                                 cap.z1=atof(word[6]);
 290                                 i+=6;
 291                         }
 292                         if(cap.type&CHAATTR_ELEMENT) {
 293                                 cap.element=atoi(word[i]);
 294                                 i+=1;
 295                         }
 296                         for(o=0;o<strlen(word[i]);o++) {
 297                                 switch(word[i][o]) {
 298                                         case 'b':
 299                                                 cap.attr|=ATOM_ATTR_VB;
 300                                                 break;
 301                                         case 'h':
 302                                                 cap.attr|=ATOM_ATTR_HB;
 303                                                 break;
 304                                         case 'v':
 305                                                 cap.attr|=ATOM_ATTR_VA;
 306                                                 break;
 307                                         case 'f':
 308                                                 cap.attr|=ATOM_ATTR_FP;
 309                                                 break;
 310                                         case '1':
 311                                                 cap.attr|=ATOM_ATTR_1BP;
 312                                                 break;
 313                                         case '2':
 314                                                 cap.attr|=ATOM_ATTR_2BP;
 315                                                 break;
 316                                         case '3':
 317                                                 cap.attr|=ATOM_ATTR_3BP;
 318                                                 break;
 319                                         default:
 320                                                 break;
 321                                 }
 322                         }
 323                         add_stage(mdrun,STAGE_CHAATTR,&cap);
 324                 }
 325                 else if(!strncmp(word[0],"sattr",5)) {
 326                         // for satrib line we need a special stage
 327                         // containing one schedule of 0 loops ...
 328                         csp.type=0;
 329                         for(i=1;i<wcnt;i++) {
 330                                 if(!strncmp(word[i],"pctrl",5)) {
 331                                         csp.ptau=0.01/(atof(word[++i])*GPA);
 332                                         csp.type|=CHSATTR_PCTRL;
 333                                 }
 334                                 if(!strncmp(word[i],"tctrl",5)) {
 335                                         csp.ttau=atof(word[++i]);
 336                                         csp.type|=CHSATTR_TCTRL;
 337                                 }
 338                                 if(!strncmp(word[i],"prelax",6)) {
 339                                         csp.dp=atof(word[++i])*BAR;
 340                                         csp.type|=CHSATTR_PRELAX;
 341                                 }
 342                                 if(!strncmp(word[i],"trelax",6)) {
 343                                         csp.dt=atof(word[++i]);
 344                                         csp.type|=CHSATTR_TRELAX;
 345                                 }
 346                                 if(!strncmp(word[i],"rsteps",6)) {
 347                                         csp.rsteps=atoi(word[++i]);
 348                                         csp.type|=CHSATTR_RSTEPS;
 349                                 }
 350                                 if(!strncmp(word[i],"avgrst",6)) {
 351                                         csp.avgrst=atoi(word[++i]);
 352                                         csp.type|=CHSATTR_AVGRST;
 353                                 }
 354                         }
 355                         add_stage(mdrun,STAGE_CHSATTR,&csp);
 356                 }
 357                 else if(!strncmp(word[0],"prerun",6))
 358                         mdrun->prerun=atoi(word[1]);
 359                 else if(!strncmp(word[0],"avgskip",7))
 360                         mdrun->avgskip=atoi(word[1]);
 361                 else if(!strncmp(word[0],"elog",4))
 362                         mdrun->elog=atoi(word[1]);
 363                 else if(!strncmp(word[0],"tlog",4))
 364                         mdrun->tlog=atoi(word[1]);
 365                 else if(!strncmp(word[0],"plog",4))
 366                         mdrun->plog=atoi(word[1]);
 367                 else if(!strncmp(word[0],"vlog",4))
 368                         mdrun->vlog=atoi(word[1]);
 369                 else if(!strncmp(word[0],"save",4))
 370                         mdrun->save=atoi(word[1]);
 371                 else if(!strncmp(word[0],"visualize",9))
 372                         mdrun->visualize=atoi(word[1]);
 373                 else if(!strncmp(word[0],"stage",5)) {
 374                         // for every stage line, add a stage
 375                         if(!strncmp(word[1],"displace",8)) {
 376                                 dap.nr=atoi(word[2]);
 377                                 dap.dx=atof(word[3]);
 378                                 dap.dy=atof(word[4]);
 379                                 dap.dz=atof(word[5]);
 380                                 add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
 381                         }
 382                         else if(!strncmp(word[1],"ins_atoms",9)) {
 383                                 iap.ins_steps=atoi(word[2]);
 384                                 iap.ins_atoms=atoi(word[3]);
 385                                 iap.element=atoi(word[4]);
 386                                 iap.brand=atoi(word[5]);
 387                                 for(i=0;i<strlen(word[6]);i++) {
 388                                         switch(word[6][i]) {
 389                                                 case 'b':
 390                                                         iap.attr|=ATOM_ATTR_VB;
 391                                                         break;
 392                                                 case 'h':
 393                                                         iap.attr|=ATOM_ATTR_HB;
 394                                                         break;
 395                                                 case 'v':
 396                                                         iap.attr|=ATOM_ATTR_VA;
 397                                                         break;
 398                                                 case 'f':
 399                                                         iap.attr|=ATOM_ATTR_FP;
 400                                                         break;
 401                                                 case '1':
 402                                                         iap.attr|=ATOM_ATTR_1BP;
 403                                                         break;
 404                                                 case '2':
 405                                                         iap.attr|=ATOM_ATTR_2BP;
 406                                                         break;
 407                                                 case '3':
 408                                                         iap.attr|=ATOM_ATTR_3BP;
 409                                                         break;
 410                                                 default:
 411                                                         break;
 412                                         }
 413                                 }
 414                                 switch(word[7][0]) {
 415                                         // insertion types
 416                                         case 'p':
 417                                                 iap.type=INS_POS;
 418                                                 iap.x0=atof(word[8]);
 419                                                 iap.y0=atof(word[9]);
 420                                                 iap.z0=atof(word[10]);
 421                                                 break;
 422                                         case 'r':
 423                                                 if(word[8][0]=='t') {
 424                                                         iap.type=INS_TOTAL;
 425                                                         iap.cr=atof(word[9]);
 426                                                 }
 427                                                 else {
 428                                                         iap.type=INS_REGION;
 429                                                         iap.x0=atof(word[8]);
 430                                                         iap.y0=atof(word[9]);
 431                                                         iap.z0=atof(word[10]);
 432                                                         iap.x1=atof(word[11]);
 433                                                         iap.y1=atof(word[12]);
 434                                                         iap.z1=atof(word[13]);
 435                                                         iap.cr=atof(word[14]);
 436                                                 }
 437                                         default:
 438                                                 break;
 439                                 }
 440                                 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
 441                         }
 442                         else if(!strncmp(word[1],"continue",8)) {
 443                                 cp.runs=atoi(word[2]);
 444                                 add_stage(mdrun,STAGE_CONTINUE,&cp);
 445                         }
 446                         else if(!strncmp(word[1],"anneal",6)) {
 447                                 ap.count=0;
 448                                 ap.runs=atoi(word[2]);
 449                                 ap.dt=atof(word[3]);
 450                                 add_stage(mdrun,STAGE_ANNEAL,&ap);
 451                         }
 452                         else {
 453                                 printf("%s unknown stage type: %s\n",
 454                                        ME,word[1]);
 455                                 return -1;
 456                         }
 457                 }
 458                 else {
 459                         printf("%s unknown keyword '%s', skipped!\n",
 460                                ME,word[0]);
 461                         continue;
 462                 }
 463         }
 464
 465         /* close file */
 466         close(fd);
 467
 468         return 0;
 469 }
 470
 471 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
 472
 473         double delta;
 474
 475         if(!(mdrun->sattr&SATTR_PRELAX)) {
 476                 return TRUE;
 477         }
 478
 479         delta=moldyn->p_avg-moldyn->p_ref;
 480
 481         if(delta<0)
 482                 delta=-delta;
 483
 484         if(delta>mdrun->dp)
 485                 return FALSE;
 486
 487         return TRUE;
 488 }
 489
 490 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 491
 492         double delta;
 493
 494         if(!(mdrun->sattr&SATTR_TRELAX))
 495                 return TRUE;
 496
 497         delta=moldyn->t_avg-moldyn->t_ref;
 498
 499         if(delta<0)
 500                 delta=-delta;
 501
 502         if(delta>mdrun->dt)
 503                 return FALSE;
 504
 505         return TRUE;
 506 }
 507
 508 int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
 509
 510         t_displace_atom_params *dap;
 511         t_stage *stage;
 512         t_atom *atom;
 513
 514         stage=mdrun->stage.current->data;
 515         dap=stage->params;
 516
 517         atom=&(moldyn->atom[dap->nr]);
 518         atom->r.x+=dap->dx;
 519         atom->r.y+=dap->dy;
 520         atom->r.z+=dap->dz;
 521
 522         return 0;
 523 }
 524
 525 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 526
 527         t_insert_atoms_params *iap;
 528         t_stage *stage;
 529         t_atom *atom;
 530         t_3dvec r,v,dist;
 531         double d,dmin,o;
 532         int cnt,i;
 533         double x,y,z;
 534         double x0,y0,z0;
 535         u8 cr_check,run;
 536
 537         stage=mdrun->stage.current->data;
 538         iap=stage->params;
 539
 540         cr_check=FALSE;
 541
 542         v.x=0.0; v.y=0.0; v.z=0.0;
 543         x=0; y=0; z=0;
 544         o=0; dmin=0;
 545
 546         switch(mdrun->lattice) {
 547                 case CUBIC:
 548                         o=0.5*mdrun->lc;
 549                         break;
 550                 case FCC:
 551                         o=0.25*mdrun->lc;
 552                         break;
 553                 case DIAMOND:
 554                 case ZINCBLENDE:
 555                         o=0.125*mdrun->lc;
 556                         break;
 557                 default:
 558                         break;
 559         }
 560
 561         switch(iap->type) {
 562                 case INS_TOTAL:
 563                         x=moldyn->dim.x;
 564                         x0=-x/2.0;
 565                         y=moldyn->dim.y;
 566                         y0=-y/2.0;
 567                         z=moldyn->dim.z;
 568                         z0=-z/2.0;
 569                         cr_check=TRUE;
 570                         break;
 571                 case INS_REGION:
 572                         x=iap->x1-iap->x0;
 573                         x0=iap->x0;
 574                         y=iap->y1-iap->y0;
 575                         y0=iap->y0;
 576                         z=iap->z1-iap->z0;
 577                         z0=iap->z0;
 578                         cr_check=TRUE;
 579                         break;
 580                 case INS_POS:
 581                         x0=iap->x0;
 582                         y0=iap->y0;
 583                         z0=iap->z0;
 584                         cr_check=FALSE;
 585                         break;
 586                 default:
 587                         printf("%s unknown insertion mode: %02x\n",
 588                                ME,iap->type);
 589                         return -1;
 590         }
 591
 592         cnt=0;
 593         while(cnt<iap->ins_atoms) {
 594                 run=1;
 595                 while(run) {
 596                         if(iap->type!=INS_POS) {
 597                                 r.x=rand_get_double(&(moldyn->random))*x;
 598                                 r.y=rand_get_double(&(moldyn->random))*y;
 599                                 r.z=rand_get_double(&(moldyn->random))*z;
 600                         }
 601                         else {
 602                                 r.x=0.0;
 603                                 r.y=0.0;
 604                                 r.z=0.0;
 605                         }
 606                         r.x+=x0;
 607                         r.y+=y0;
 608                         r.z+=z0;
 609                         // offset
 610                         if(iap->type!=INS_TOTAL) {
 611                                 r.x+=o;
 612                                 r.y+=o;
 613                                 r.z+=o;
 614                         }
 615                         run=0;
 616                         if(cr_check==TRUE) {
 617                                 dmin=1000;      // for sure too high!
 618                                 for(i=0;i<moldyn->count;i++) {
 619                                         atom=&(moldyn->atom[i]);
 620                                         v3_sub(&dist,&(atom->r),&r);
 621                                         check_per_bound(moldyn,&dist);
 622                                         d=v3_absolute_square(&dist);
 623                                         if(d<(iap->cr*iap->cr)) {
 624                                                 run=1;
 625                                                 break;
 626                                         }
 627                                         if(d<dmin)
 628                                                 dmin=d;
 629                                 }
 630                         }
 631                 }
 632                 add_atom(moldyn,iap->element,pse_mass[iap->element],
 633                          iap->brand,iap->attr,&r,&v);
 634                 printf("%s atom inserted (%d/%d): %f %f %f\n",
 635                        ME,(iap->cnt_steps+1)*iap->ins_atoms,
 636                        iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
 637                 printf("  -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
 638                 cnt+=1;
 639         }
 640
 641         return 0;
 642 }
 643
 644 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 645
 646         t_stage *stage;
 647         t_chaattr_params *cap;
 648         t_atom *atom;
 649         int i;
 650
 651         stage=mdrun->stage.current->data;
 652         cap=stage->params;
 653
 654         for(i=0;i<moldyn->count;i++) {
 655                 atom=&(moldyn->atom[i]);
 656                 if(cap->type&CHAATTR_ELEMENT) {
 657                         if(cap->element!=atom->element)
 658                                 continue;
 659                 }
 660                 if(cap->type&CHAATTR_REGION) {
 661                         if(cap->x0<atom->r.x)
 662                                 continue;
 663                         if(cap->y0<atom->r.y)
 664                                 continue;
 665                         if(cap->z0<atom->r.z)
 666                                 continue;
 667                         if(cap->x1>atom->r.x)
 668                                 continue;
 669                         if(cap->y1>atom->r.y)
 670                                 continue;
 671                         if(cap->z1>atom->r.z)
 672                                 continue;
 673                 }
 674                 atom->attr=cap->attr;
 675         }
 676
 677         return 0;
 678 }
 679
 680 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 681
 682         t_stage *stage;
 683         t_chsattr_params *csp;
 684
 685         stage=mdrun->stage.current->data;
 686         csp=stage->params;
 687
 688         if(csp->type&CHSATTR_PCTRL) {
 689                 if(csp->ptau>0)
 690                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 691                 else
 692                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 693         }
 694         if(csp->type&CHSATTR_TCTRL) {
 695                 if(csp->ttau>0)
 696                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 697                 else
 698                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 699         }
 700         if(csp->type&CHSATTR_PRELAX) {
 701                 if(csp->dp<0)
 702                         mdrun->sattr&=(~(SATTR_PRELAX));
 703                 else
 704                         mdrun->sattr|=SATTR_PRELAX;
 705                 mdrun->dp=csp->dp;
 706         }
 707         if(csp->type&CHSATTR_TRELAX) {
 708                 if(csp->dt<0)
 709                         mdrun->sattr&=(~(SATTR_TRELAX));
 710                 else
 711                         mdrun->sattr|=SATTR_TRELAX;
 712                 mdrun->dt=csp->dt;
 713         }
 714         if(csp->type&CHSATTR_AVGRST) {
 715                 if(csp->avgrst)
 716                         mdrun->sattr|=SATTR_AVGRST;
 717                 else
 718                         mdrun->sattr&=(~(SATTR_AVGRST));
 719         }
 720         if(csp->type&CHSATTR_RSTEPS) {
 721                 mdrun->relax_steps=csp->rsteps;
 722         }
 723
 724         return 0;
 725 }
 726
 727 #define stage_print(m)  if(!(stage->executed)) \
 728                                 printf("%s",m)
 729
 730 int mdrun_hook(void *ptr1,void *ptr2) {
 731
 732         t_moldyn *moldyn;
 733         t_mdrun *mdrun;
 734         t_stage *stage;
 735         t_list *sl;
 736         int steps;
 737         double tau;
 738         u8 change_stage;
 739
 740         t_insert_atoms_params *iap;
 741         t_continue_params *cp;
 742         t_anneal_params *ap;
 743
 744         moldyn=ptr1;
 745         mdrun=ptr2;
 746
 747         sl=&(mdrun->stage);
 748
 749         change_stage=FALSE;
 750
 751         /* return immediately if there are no more stage */
 752         if(sl->current==NULL)
 753                 return 0;
 754
 755         /* get stage description */
 756         stage=sl->current->data;
 757
 758         /* default steps and tau values */
 759         steps=mdrun->relax_steps;
 760         tau=mdrun->timestep;
 761
 762         /* check whether relaxation steps are necessary */
 763         if((check_pressure(moldyn,mdrun)==TRUE)&\
 764            (check_temperature(moldyn,mdrun)==TRUE)) {
 765
 766                 /* be verbose */
 767                 stage_print("\n###########################\n");
 768                 stage_print("# [mdrun] executing stage #\n");
 769                 stage_print("###########################\n\n");
 770
 771                 /* stage specific stuff */
 772                 switch(stage->type) {
 773                         case STAGE_DISPLACE_ATOM:
 774                                 stage_print("  -> displace atom\n\n");
 775                                 displace_atom(moldyn,mdrun);
 776                                 change_stage=TRUE;
 777                                 break;
 778                         case STAGE_INSERT_ATOMS:
 779                                 stage_print("  -> insert atoms\n\n");
 780                                 iap=stage->params;
 781                                 if(iap->cnt_steps==iap->ins_steps) {
 782                                         change_stage=TRUE;
 783                                         break;
 784                                 }
 785                                 insert_atoms(moldyn,mdrun);
 786                                 iap->cnt_steps+=1;
 787                                 break;
 788                         case STAGE_CONTINUE:
 789                                 stage_print("  -> continue\n\n");
 790                                 if(stage->executed==TRUE) {
 791                                         change_stage=TRUE;
 792                                         break;
 793                                 }
 794                                 cp=stage->params;
 795                                 steps=cp->runs;
 796                                 break;
 797                         case STAGE_ANNEAL:
 798                                 stage_print("  -> anneal\n\n");
 799                                 ap=stage->params;
 800                                 if(ap->count==ap->runs) {
 801                                         change_stage=TRUE;
 802                                         break;
 803                                 }
 804                                 if(moldyn->t_ref+ap->dt>=0.0)
 805                                         set_temperature(moldyn,
 806                                                         moldyn->t_ref+ap->dt);
 807                                 ap->count+=1;
 808                                 break;
 809                         case STAGE_CHAATTR:
 810                                 stage_print("  -> chaattr\n\n");
 811                                 chaatr(moldyn,mdrun);
 812                                 change_stage=TRUE;
 813                                 break;
 814                         case STAGE_CHSATTR:
 815                                 stage_print("  -> chsattr\n\n");
 816                                 chsattr(moldyn,mdrun);
 817                                 change_stage=TRUE;
 818                                 break;
 819                         default:
 820                                 printf("%s unknwon stage type\n",ME);
 821                                 break;
 822                 }
 823
 824                 /* mark as executed */
 825                 stage->executed=TRUE;
 826
 827                 /* change state */
 828                 if(change_stage==TRUE) {
 829                         printf("%s finished stage\n",ME);
 830                         if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
 831                                 printf("%s no more stages\n",ME);
 832                                 return 0;
 833                         }
 834                         steps=0;
 835                         tau=mdrun->timestep;
 836                 }
 837
 838         }
 839         else {
 840
 841                 /* averages */
 842                 if(mdrun->sattr&SATTR_AVGRST)
 843                         average_reset(moldyn);
 844
 845         }
 846
 847         /* continue simulation */
 848         moldyn_add_schedule(moldyn,steps,tau);
 849
 850         return 0;
 851 }
 852
 853 int main(int argc,char **argv) {
 854
 855         t_mdrun mdrun;
 856         t_moldyn moldyn;
 857         t_3dvec o;
 858
 859         /* clear structs */
 860         memset(&mdrun,0,sizeof(t_mdrun));
 861         memset(&moldyn,0,sizeof(t_moldyn));
 862
 863         /* parse arguments */
 864         if(mdrun_parse_argv(&mdrun,argc,argv)<0)
 865                 return -1;
 866
 867         /* initialize list system */
 868         list_init_f(&(mdrun.stage));
 869
 870         /* parse config file */
 871         mdrun_parse_config(&mdrun);
 872
 873         /* reset the stage list */
 874         list_reset_f(&(mdrun.stage));
 875
 876         /* sanity check! */
 877
 878         /* prepare simulation */
 879         moldyn_init(&moldyn,argc,argv);
 880         if(set_int_alg(&moldyn,mdrun.intalgo)<0)
 881                 return -1;
 882         set_cutoff(&moldyn,mdrun.cutoff);
 883         if(set_potential(&moldyn,mdrun.potential)<0)
 884                 return -1;
 885         switch(mdrun.potential) {
 886                 case MOLDYN_POTENTIAL_AM:
 887                         albe_mult_set_params(&moldyn,
 888                                              mdrun.element1,
 889                                              mdrun.element2);
 890                         break;
 891                 case MOLDYN_POTENTIAL_TM:
 892                         tersoff_mult_set_params(&moldyn,
 893                                                 mdrun.element1,
 894                                                 mdrun.element2);
 895                         break;
 896                 case MOLDYN_POTENTIAL_HO:
 897                         harmonic_oscillator_set_params(&moldyn,mdrun.element1);
 898                         break;
 899                 case MOLDYN_POTENTIAL_LJ:
 900                         lennard_jones_set_params(&moldyn,mdrun.element1);
 901                         break;
 902                 default:
 903                         printf("%s unknown potential: %02x\n",
 904                                ME,mdrun.potential);
 905                         return -1;
 906         }
 907         set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
 908         set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
 909         switch(mdrun.lattice) {
 910                 case FCC:
 911                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
 912                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 913                                        mdrun.ly,mdrun.lz,NULL);
 914                         break;
 915                 case DIAMOND:
 916                         create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
 917                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 918                                        mdrun.ly,mdrun.lz,NULL);
 919                         break;
 920                 case ZINCBLENDE:
 921                         o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 922                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
 923                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 924                                        mdrun.ly,mdrun.lz,&o);
 925                         o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 926                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
 927                                        mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
 928                                        mdrun.ly,mdrun.lz,&o);
 929                         break;
 930                 default:
 931                         printf("%s unknown lattice type: %02x\n",
 932                                ME,mdrun.lattice);
 933                         return -1;
 934         }
 935         moldyn_bc_check(&moldyn);
 936         set_temperature(&moldyn,mdrun.temperature);
 937         set_pressure(&moldyn,mdrun.pressure);
 938         thermal_init(&moldyn,TRUE);
 939         moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
 940         moldyn_set_log_dir(&moldyn,mdrun.sdir);
 941         moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
 942         if(mdrun.elog)
 943                 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
 944         if(mdrun.tlog)
 945                 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
 946         if(mdrun.plog)
 947                 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
 948         if(mdrun.vlog)
 949                 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
 950         if(mdrun.visualize)
 951                 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
 952         if(mdrun.save)
 953                 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
 954         moldyn_set_log(&moldyn,CREATE_REPORT,0);
 955         set_avg_skip(&moldyn,mdrun.avgskip);
 956
 957         /* prepare the hook function */
 958         moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
 959
 960         /* run the simulation */
 961         moldyn_integrate(&moldyn);
 962
 963         /* shutdown */
 964         moldyn_shutdown(&moldyn);
 965         del_stages(&mdrun);
 966         list_destroy_f(&(mdrun.stage));
 967
 968         return 0;
 969 }