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][64];
 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,64);
 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],"continue",8))
 207                         strncpy(mdrun->continue_file,word[1],128);
 208                 else if(!strncmp(word[0],"cutoff",6))
 209                         mdrun->cutoff=atof(word[1]);
 210                 else if(!strncmp(word[0],"nnd",3))
 211                         mdrun->nnd=atof(word[1]);
 212                 else if(!strncmp(word[0],"intalgo",7)) {
 213                         if(!strncmp(word[1],"verlet",5))
 214                                 mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
 215                 }
 216                 else if(!strncmp(word[0],"timestep",8))
 217                         mdrun->timestep=atof(word[1]);
 218                 else if(!strncmp(word[0],"volume",6)) {
 219                         mdrun->dim.x=atof(word[1]);
 220                         mdrun->dim.y=atof(word[2]);
 221                         mdrun->dim.z=atof(word[3]);
 222                         if(strncmp(word[4],"0",1))
 223                                 mdrun->vis=TRUE;
 224                 }
 225                 else if(!strncmp(word[0],"pbc",3)) {
 226                         if(strncmp(word[1],"0",1))
 227                                 mdrun->pbcx=TRUE;
 228                         else
 229                                 mdrun->pbcx=FALSE;
 230                         if(strncmp(word[2],"0",1))
 231                                 mdrun->pbcy=TRUE;
 232                         else
 233                                 mdrun->pbcy=FALSE;
 234                         if(strncmp(word[3],"0",1))
 235                                 mdrun->pbcz=TRUE;
 236                         else
 237                                 mdrun->pbcz=FALSE;
 238                 }
 239                 else if(!strncmp(word[0],"temperature",11))
 240                         mdrun->temperature=atof(word[1]);
 241                 else if(!strncmp(word[0],"pressure",8))
 242                         mdrun->pressure=atof(word[1]);
 243                 else if(!strncmp(word[0],"lattice",7)) {
 244                         if(!strncmp(word[1],"zincblende",10))
 245                                 mdrun->lattice=ZINCBLENDE;
 246                         if(!strncmp(word[1],"fcc",3))
 247                                 mdrun->lattice=FCC;
 248                         if(!strncmp(word[1],"diamond",7))
 249                                 mdrun->lattice=DIAMOND;
 250                 }
 251                 else if(!strncmp(word[0],"element1",8)) {
 252                         mdrun->element1=atoi(word[1]);
 253                         mdrun->m1=pse_mass[mdrun->element1];
 254                 }
 255                 else if(!strncmp(word[0],"element2",8)) {
 256                         mdrun->element2=atoi(word[1]);
 257                         mdrun->m2=pse_mass[mdrun->element2];
 258                 }
 259                 else if(!strncmp(word[0],"fill",6)) {
 260                         // only lc mode by now
 261                         mdrun->lx=atoi(word[2]);
 262                         mdrun->ly=atoi(word[3]);
 263                         mdrun->lz=atoi(word[4]);
 264                         mdrun->lc=atof(word[5]);
 265                 }
 266                 else if(!strncmp(word[0],"aattr",5)) {
 267                         // for aatrib line we need a special stage
 268                         // containing one schedule of 0 loops ...
 269                         for(i=0;i<strlen(word[1]);i++) {
 270                                 switch(word[1][i]) {
 271                                         case 't':
 272                                                 cap.type|=CHAATTR_TOTALV;
 273                                                 break;
 274                                         case 'r':
 275                                                 cap.type|=CHAATTR_REGION;
 276                                                 break;
 277                                         case 'e':
 278                                                 cap.type|=CHAATTR_ELEMENT;
 279                                                 break;
 280                                         default:
 281                                                 break;
 282                                 }
 283                         }
 284                         i=2;
 285                         if(cap.type&CHAATTR_REGION) {
 286                                 cap.x0=atof(word[1]);
 287                                 cap.y0=atof(word[2]);
 288                                 cap.z0=atof(word[3]);
 289                                 cap.x1=atof(word[4]);
 290                                 cap.y1=atof(word[5]);
 291                                 cap.z1=atof(word[6]);
 292                                 i+=6;
 293                         }
 294                         if(cap.type&CHAATTR_ELEMENT) {
 295                                 cap.element=atoi(word[i]);
 296                                 i+=1;
 297                         }
 298                         for(o=0;o<strlen(word[i]);o++) {
 299                                 switch(word[i][o]) {
 300                                         case 'b':
 301                                                 cap.attr|=ATOM_ATTR_VB;
 302                                                 break;
 303                                         case 'h':
 304                                                 cap.attr|=ATOM_ATTR_HB;
 305                                                 break;
 306                                         case 'v':
 307                                                 cap.attr|=ATOM_ATTR_VA;
 308                                                 break;
 309                                         case 'f':
 310                                                 cap.attr|=ATOM_ATTR_FP;
 311                                                 break;
 312                                         case '1':
 313                                                 cap.attr|=ATOM_ATTR_1BP;
 314                                                 break;
 315                                         case '2':
 316                                                 cap.attr|=ATOM_ATTR_2BP;
 317                                                 break;
 318                                         case '3':
 319                                                 cap.attr|=ATOM_ATTR_3BP;
 320                                                 break;
 321                                         default:
 322                                                 break;
 323                                 }
 324                         }
 325                         add_stage(mdrun,STAGE_CHAATTR,&cap);
 326                 }
 327                 else if(!strncmp(word[0],"sattr",5)) {
 328                         // for satrib line we need a special stage
 329                         // containing one schedule of 0 loops ...
 330                         csp.type=0;
 331                         for(i=1;i<wcnt;i++) {
 332                                 if(!strncmp(word[i],"pctrl",5)) {
 333                                         csp.ptau=0.01/(atof(word[++i])*GPA);
 334                                         csp.type|=CHSATTR_PCTRL;
 335                                 }
 336                                 if(!strncmp(word[i],"tctrl",5)) {
 337                                         csp.ttau=atof(word[++i]);
 338                                         csp.type|=CHSATTR_TCTRL;
 339                                 }
 340                                 if(!strncmp(word[i],"prelax",6)) {
 341                                         csp.dp=atof(word[++i])*BAR;
 342                                         csp.type|=CHSATTR_PRELAX;
 343                                 }
 344                                 if(!strncmp(word[i],"trelax",6)) {
 345                                         csp.dt=atof(word[++i]);
 346                                         csp.type|=CHSATTR_TRELAX;
 347                                 }
 348                                 if(!strncmp(word[i],"rsteps",6)) {
 349                                         csp.rsteps=atoi(word[++i]);
 350                                         csp.type|=CHSATTR_RSTEPS;
 351                                 }
 352                                 if(!strncmp(word[i],"avgrst",6)) {
 353                                         csp.avgrst=atoi(word[++i]);
 354                                         csp.type|=CHSATTR_AVGRST;
 355                                 }
 356                         }
 357                         add_stage(mdrun,STAGE_CHSATTR,&csp);
 358                 }
 359                 else if(!strncmp(word[0],"prerun",6))
 360                         mdrun->prerun=atoi(word[1]);
 361                 else if(!strncmp(word[0],"avgskip",7))
 362                         mdrun->avgskip=atoi(word[1]);
 363                 else if(!strncmp(word[0],"elog",4))
 364                         mdrun->elog=atoi(word[1]);
 365                 else if(!strncmp(word[0],"tlog",4))
 366                         mdrun->tlog=atoi(word[1]);
 367                 else if(!strncmp(word[0],"plog",4))
 368                         mdrun->plog=atoi(word[1]);
 369                 else if(!strncmp(word[0],"vlog",4))
 370                         mdrun->vlog=atoi(word[1]);
 371                 else if(!strncmp(word[0],"save",4))
 372                         mdrun->save=atoi(word[1]);
 373                 else if(!strncmp(word[0],"visualize",9))
 374                         mdrun->visualize=atoi(word[1]);
 375                 else if(!strncmp(word[0],"stage",5)) {
 376                         // for every stage line, add a stage
 377                         if(!strncmp(word[1],"displace",8)) {
 378                                 dap.nr=atoi(word[2]);
 379                                 dap.dx=atof(word[3]);
 380                                 dap.dy=atof(word[4]);
 381                                 dap.dz=atof(word[5]);
 382                                 add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
 383                         }
 384                         else if(!strncmp(word[1],"ins_atoms",9)) {
 385                                 iap.ins_steps=atoi(word[2]);
 386                                 iap.ins_atoms=atoi(word[3]);
 387                                 iap.element=atoi(word[4]);
 388                                 iap.brand=atoi(word[5]);
 389                                 for(i=0;i<strlen(word[6]);i++) {
 390                                         switch(word[6][i]) {
 391                                                 case 'b':
 392                                                         iap.attr|=ATOM_ATTR_VB;
 393                                                         break;
 394                                                 case 'h':
 395                                                         iap.attr|=ATOM_ATTR_HB;
 396                                                         break;
 397                                                 case 'v':
 398                                                         iap.attr|=ATOM_ATTR_VA;
 399                                                         break;
 400                                                 case 'f':
 401                                                         iap.attr|=ATOM_ATTR_FP;
 402                                                         break;
 403                                                 case '1':
 404                                                         iap.attr|=ATOM_ATTR_1BP;
 405                                                         break;
 406                                                 case '2':
 407                                                         iap.attr|=ATOM_ATTR_2BP;
 408                                                         break;
 409                                                 case '3':
 410                                                         iap.attr|=ATOM_ATTR_3BP;
 411                                                         break;
 412                                                 default:
 413                                                         break;
 414                                         }
 415                                 }
 416                                 switch(word[7][0]) {
 417                                         // insertion types
 418                                         case 'p':
 419                                                 iap.type=INS_POS;
 420                                                 iap.x0=atof(word[8]);
 421                                                 iap.y0=atof(word[9]);
 422                                                 iap.z0=atof(word[10]);
 423                                                 break;
 424                                         case 'r':
 425                                                 if(word[8][0]=='t') {
 426                                                         iap.type=INS_TOTAL;
 427                                                         iap.cr=atof(word[9]);
 428                                                 }
 429                                                 else {
 430                                                         iap.type=INS_REGION;
 431                                                         iap.x0=atof(word[8]);
 432                                                         iap.y0=atof(word[9]);
 433                                                         iap.z0=atof(word[10]);
 434                                                         iap.x1=atof(word[11]);
 435                                                         iap.y1=atof(word[12]);
 436                                                         iap.z1=atof(word[13]);
 437                                                         iap.cr=atof(word[14]);
 438                                                 }
 439                                         default:
 440                                                 break;
 441                                 }
 442                                 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
 443                         }
 444                         else if(!strncmp(word[1],"continue",8)) {
 445                                 cp.runs=atoi(word[2]);
 446                                 add_stage(mdrun,STAGE_CONTINUE,&cp);
 447                         }
 448                         else if(!strncmp(word[1],"anneal",6)) {
 449                                 ap.count=0;
 450                                 ap.runs=atoi(word[2]);
 451                                 ap.dt=atof(word[3]);
 452                                 add_stage(mdrun,STAGE_ANNEAL,&ap);
 453                         }
 454                         else {
 455                                 printf("%s unknown stage type: %s\n",
 456                                        ME,word[1]);
 457                                 return -1;
 458                         }
 459                 }
 460                 else {
 461                         printf("%s unknown keyword '%s', skipped!\n",
 462                                ME,word[0]);
 463                         continue;
 464                 }
 465         }
 466
 467         /* close file */
 468         close(fd);
 469
 470         return 0;
 471 }
 472
 473 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
 474
 475         double delta;
 476
 477         if(!(mdrun->sattr&SATTR_PRELAX)) {
 478                 return TRUE;
 479         }
 480
 481         delta=moldyn->p_avg-moldyn->p_ref;
 482
 483         if(delta<0)
 484                 delta=-delta;
 485
 486         if(delta>mdrun->dp)
 487                 return FALSE;
 488
 489         return TRUE;
 490 }
 491
 492 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 493
 494         double delta;
 495
 496         if(!(mdrun->sattr&SATTR_TRELAX))
 497                 return TRUE;
 498
 499         delta=moldyn->t_avg-moldyn->t_ref;
 500
 501         if(delta<0)
 502                 delta=-delta;
 503
 504         if(delta>mdrun->dt)
 505                 return FALSE;
 506
 507         return TRUE;
 508 }
 509
 510 int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
 511
 512         t_displace_atom_params *dap;
 513         t_stage *stage;
 514         t_atom *atom;
 515
 516         stage=mdrun->stage.current->data;
 517         dap=stage->params;
 518
 519         atom=&(moldyn->atom[dap->nr]);
 520         atom->r.x+=dap->dx;
 521         atom->r.y+=dap->dy;
 522         atom->r.z+=dap->dz;
 523
 524         return 0;
 525 }
 526
 527 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 528
 529         t_insert_atoms_params *iap;
 530         t_stage *stage;
 531         t_atom *atom;
 532         t_3dvec r,v,dist;
 533         double d,dmin,o;
 534         int cnt,i;
 535         double x,y,z;
 536         double x0,y0,z0;
 537         u8 cr_check,run;
 538
 539         stage=mdrun->stage.current->data;
 540         iap=stage->params;
 541
 542         cr_check=FALSE;
 543
 544         v.x=0.0; v.y=0.0; v.z=0.0;
 545         x=0; y=0; z=0;
 546         o=0; dmin=0;
 547
 548         switch(mdrun->lattice) {
 549                 case CUBIC:
 550                         o=0.5*mdrun->lc;
 551                         break;
 552                 case FCC:
 553                         o=0.25*mdrun->lc;
 554                         break;
 555                 case DIAMOND:
 556                 case ZINCBLENDE:
 557                         o=0.125*mdrun->lc;
 558                         break;
 559                 default:
 560                         break;
 561         }
 562
 563         switch(iap->type) {
 564                 case INS_TOTAL:
 565                         x=moldyn->dim.x;
 566                         x0=-x/2.0;
 567                         y=moldyn->dim.y;
 568                         y0=-y/2.0;
 569                         z=moldyn->dim.z;
 570                         z0=-z/2.0;
 571                         cr_check=TRUE;
 572                         break;
 573                 case INS_REGION:
 574                         x=iap->x1-iap->x0;
 575                         x0=iap->x0;
 576                         y=iap->y1-iap->y0;
 577                         y0=iap->y0;
 578                         z=iap->z1-iap->z0;
 579                         z0=iap->z0;
 580                         cr_check=TRUE;
 581                         break;
 582                 case INS_POS:
 583                         x0=iap->x0;
 584                         y0=iap->y0;
 585                         z0=iap->z0;
 586                         cr_check=FALSE;
 587                         break;
 588                 default:
 589                         printf("%s unknown insertion mode: %02x\n",
 590                                ME,iap->type);
 591                         return -1;
 592         }
 593
 594         cnt=0;
 595         while(cnt<iap->ins_atoms) {
 596                 run=1;
 597                 while(run) {
 598                         if(iap->type!=INS_POS) {
 599                                 r.x=rand_get_double(&(moldyn->random))*x;
 600                                 r.y=rand_get_double(&(moldyn->random))*y;
 601                                 r.z=rand_get_double(&(moldyn->random))*z;
 602                         }
 603                         else {
 604                                 r.x=0.0;
 605                                 r.y=0.0;
 606                                 r.z=0.0;
 607                         }
 608                         r.x+=x0;
 609                         r.y+=y0;
 610                         r.z+=z0;
 611                         // offset
 612                         if(iap->type!=INS_TOTAL) {
 613                                 r.x+=o;
 614                                 r.y+=o;
 615                                 r.z+=o;
 616                         }
 617                         run=0;
 618                         if(cr_check==TRUE) {
 619                                 dmin=1000;      // for sure too high!
 620                                 for(i=0;i<moldyn->count;i++) {
 621                                         atom=&(moldyn->atom[i]);
 622                                         v3_sub(&dist,&(atom->r),&r);
 623                                         check_per_bound(moldyn,&dist);
 624                                         d=v3_absolute_square(&dist);
 625                                         if(d<(iap->cr*iap->cr)) {
 626                                                 run=1;
 627                                                 break;
 628                                         }
 629                                         if(d<dmin)
 630                                                 dmin=d;
 631                                 }
 632                         }
 633                 }
 634                 add_atom(moldyn,iap->element,pse_mass[iap->element],
 635                          iap->brand,iap->attr,&r,&v);
 636                 printf("%s atom inserted (%d/%d): %f %f %f\n",
 637                        ME,(iap->cnt_steps+1)*iap->ins_atoms,
 638                        iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
 639                 printf("  -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
 640                 cnt+=1;
 641         }
 642
 643         return 0;
 644 }
 645
 646 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 647
 648         t_stage *stage;
 649         t_chaattr_params *cap;
 650         t_atom *atom;
 651         int i;
 652
 653         stage=mdrun->stage.current->data;
 654         cap=stage->params;
 655
 656         for(i=0;i<moldyn->count;i++) {
 657                 atom=&(moldyn->atom[i]);
 658                 if(cap->type&CHAATTR_ELEMENT) {
 659                         if(cap->element!=atom->element)
 660                                 continue;
 661                 }
 662                 if(cap->type&CHAATTR_REGION) {
 663                         if(cap->x0<atom->r.x)
 664                                 continue;
 665                         if(cap->y0<atom->r.y)
 666                                 continue;
 667                         if(cap->z0<atom->r.z)
 668                                 continue;
 669                         if(cap->x1>atom->r.x)
 670                                 continue;
 671                         if(cap->y1>atom->r.y)
 672                                 continue;
 673                         if(cap->z1>atom->r.z)
 674                                 continue;
 675                 }
 676                 atom->attr=cap->attr;
 677         }
 678
 679         return 0;
 680 }
 681
 682 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 683
 684         t_stage *stage;
 685         t_chsattr_params *csp;
 686
 687         stage=mdrun->stage.current->data;
 688         csp=stage->params;
 689
 690         if(csp->type&CHSATTR_PCTRL) {
 691                 if(csp->ptau>0)
 692                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 693                 else
 694                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 695         }
 696         if(csp->type&CHSATTR_TCTRL) {
 697                 if(csp->ttau>0)
 698                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 699                 else
 700                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 701         }
 702         if(csp->type&CHSATTR_PRELAX) {
 703                 if(csp->dp<0)
 704                         mdrun->sattr&=(~(SATTR_PRELAX));
 705                 else
 706                         mdrun->sattr|=SATTR_PRELAX;
 707                 mdrun->dp=csp->dp;
 708         }
 709         if(csp->type&CHSATTR_TRELAX) {
 710                 if(csp->dt<0)
 711                         mdrun->sattr&=(~(SATTR_TRELAX));
 712                 else
 713                         mdrun->sattr|=SATTR_TRELAX;
 714                 mdrun->dt=csp->dt;
 715         }
 716         if(csp->type&CHSATTR_AVGRST) {
 717                 if(csp->avgrst)
 718                         mdrun->sattr|=SATTR_AVGRST;
 719                 else
 720                         mdrun->sattr&=(~(SATTR_AVGRST));
 721         }
 722         if(csp->type&CHSATTR_RSTEPS) {
 723                 mdrun->relax_steps=csp->rsteps;
 724         }
 725
 726         return 0;
 727 }
 728
 729 #define stage_print(m)  if(!(stage->executed)) \
 730                                 printf("%s",m)
 731
 732 int mdrun_hook(void *ptr1,void *ptr2) {
 733
 734         t_moldyn *moldyn;
 735         t_mdrun *mdrun;
 736         t_stage *stage;
 737         t_list *sl;
 738         int steps;
 739         double tau;
 740         u8 change_stage;
 741
 742         t_insert_atoms_params *iap;
 743         t_continue_params *cp;
 744         t_anneal_params *ap;
 745
 746         moldyn=ptr1;
 747         mdrun=ptr2;
 748
 749         sl=&(mdrun->stage);
 750
 751         change_stage=FALSE;
 752
 753         /* return immediately if there are no more stage */
 754         if(sl->current==NULL)
 755                 return 0;
 756
 757         /* get stage description */
 758         stage=sl->current->data;
 759
 760         /* default steps and tau values */
 761         steps=mdrun->relax_steps;
 762         tau=mdrun->timestep;
 763
 764         /* check whether relaxation steps are necessary */
 765         if((check_pressure(moldyn,mdrun)==TRUE)&\
 766            (check_temperature(moldyn,mdrun)==TRUE)) {
 767
 768                 /* be verbose */
 769                 stage_print("\n###########################\n");
 770                 stage_print("# [mdrun] executing stage #\n");
 771                 stage_print("###########################\n\n");
 772
 773                 /* stage specific stuff */
 774                 switch(stage->type) {
 775                         case STAGE_DISPLACE_ATOM:
 776                                 stage_print("  -> displace atom\n\n");
 777                                 displace_atom(moldyn,mdrun);
 778                                 change_stage=TRUE;
 779                                 break;
 780                         case STAGE_INSERT_ATOMS:
 781                                 stage_print("  -> insert atoms\n\n");
 782                                 iap=stage->params;
 783                                 if(iap->cnt_steps==iap->ins_steps) {
 784                                         change_stage=TRUE;
 785                                         break;
 786                                 }
 787                                 insert_atoms(moldyn,mdrun);
 788                                 iap->cnt_steps+=1;
 789                                 break;
 790                         case STAGE_CONTINUE:
 791                                 stage_print("  -> continue\n\n");
 792                                 if(stage->executed==TRUE) {
 793                                         change_stage=TRUE;
 794                                         break;
 795                                 }
 796                                 cp=stage->params;
 797                                 steps=cp->runs;
 798                                 break;
 799                         case STAGE_ANNEAL:
 800                                 stage_print("  -> anneal\n\n");
 801                                 ap=stage->params;
 802                                 if(ap->count==ap->runs) {
 803                                         change_stage=TRUE;
 804                                         break;
 805                                 }
 806                                 if(moldyn->t_ref+ap->dt>=0.0)
 807                                         set_temperature(moldyn,
 808                                                         moldyn->t_ref+ap->dt);
 809                                 ap->count+=1;
 810                                 break;
 811                         case STAGE_CHAATTR:
 812                                 stage_print("  -> chaattr\n\n");
 813                                 chaatr(moldyn,mdrun);
 814                                 change_stage=TRUE;
 815                                 break;
 816                         case STAGE_CHSATTR:
 817                                 stage_print("  -> chsattr\n\n");
 818                                 chsattr(moldyn,mdrun);
 819                                 change_stage=TRUE;
 820                                 break;
 821                         default:
 822                                 printf("%s unknwon stage type\n",ME);
 823                                 break;
 824                 }
 825
 826                 /* mark as executed */
 827                 stage->executed=TRUE;
 828
 829                 /* change state */
 830                 if(change_stage==TRUE) {
 831                         printf("%s finished stage\n",ME);
 832                         if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
 833                                 printf("%s no more stages\n",ME);
 834                                 return 0;
 835                         }
 836                         steps=0;
 837                         tau=mdrun->timestep;
 838                 }
 839
 840         }
 841         else {
 842
 843                 /* averages */
 844                 if(mdrun->sattr&SATTR_AVGRST)
 845                         average_reset(moldyn);
 846
 847         }
 848
 849         /* continue simulation */
 850         moldyn_add_schedule(moldyn,steps,tau);
 851
 852         return 0;
 853 }
 854
 855 int main(int argc,char **argv) {
 856
 857         t_mdrun mdrun;
 858         t_moldyn moldyn;
 859         t_3dvec o;
 860
 861         /* clear structs */
 862         memset(&mdrun,0,sizeof(t_mdrun));
 863         memset(&moldyn,0,sizeof(t_moldyn));
 864
 865         /* parse arguments */
 866         if(mdrun_parse_argv(&mdrun,argc,argv)<0)
 867                 return -1;
 868
 869         /* initialize list system */
 870         list_init_f(&(mdrun.stage));
 871
 872         /* parse config file */
 873         mdrun_parse_config(&mdrun);
 874
 875         /* reset the stage list */
 876         list_reset_f(&(mdrun.stage));
 877
 878         /* sanity check! */
 879
 880         /* prepare simulation */
 881
 882         moldyn_init(&moldyn,argc,argv);
 883
 884         if(mdrun.continue_file)
 885                 moldyn_read_save_file(&moldyn,mdrun.continue_file);
 886
 887         if(set_int_alg(&moldyn,mdrun.intalgo)<0)
 888                 return -1;
 889
 890         /* potential */
 891         set_cutoff(&moldyn,mdrun.cutoff);
 892         if(set_potential(&moldyn,mdrun.potential)<0)
 893                 return -1;
 894         switch(mdrun.potential) {
 895                 case MOLDYN_POTENTIAL_AM:
 896                         albe_mult_set_params(&moldyn,
 897                                              mdrun.element1,
 898                                              mdrun.element2);
 899                         break;
 900                 case MOLDYN_POTENTIAL_TM:
 901                         tersoff_mult_set_params(&moldyn,
 902                                                 mdrun.element1,
 903                                                 mdrun.element2);
 904                         break;
 905                 case MOLDYN_POTENTIAL_HO:
 906                         harmonic_oscillator_set_params(&moldyn,mdrun.element1);
 907                         break;
 908                 case MOLDYN_POTENTIAL_LJ:
 909                         lennard_jones_set_params(&moldyn,mdrun.element1);
 910                         break;
 911                 default:
 912                         printf("%s unknown potential: %02x\n",
 913                                ME,mdrun.potential);
 914                         return -1;
 915         }
 916
 917         /* if it is a continue run, reset schedule and skip lattice init */
 918         if(mdrun.continue_file) {
 919                 memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
 920                 goto addsched;
 921         }
 922
 923         /* initial lattice and dimensions */
 924         set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
 925         set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
 926         switch(mdrun.lattice) {
 927                 case FCC:
 928                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
 929                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 930                                        mdrun.ly,mdrun.lz,NULL);
 931                         break;
 932                 case DIAMOND:
 933                         create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
 934                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 935                                        mdrun.ly,mdrun.lz,NULL);
 936                         break;
 937                 case ZINCBLENDE:
 938                         o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 939                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
 940                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 941                                        mdrun.ly,mdrun.lz,&o);
 942                         o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 943                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
 944                                        mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
 945                                        mdrun.ly,mdrun.lz,&o);
 946                         break;
 947                 default:
 948                         printf("%s unknown lattice type: %02x\n",
 949                                ME,mdrun.lattice);
 950                         return -1;
 951         }
 952         moldyn_bc_check(&moldyn);
 953
 954         /* temperature and pressure */
 955         set_temperature(&moldyn,mdrun.temperature);
 956         set_pressure(&moldyn,mdrun.pressure);
 957         thermal_init(&moldyn,TRUE);
 958
 959 addsched:
 960         /* first schedule */
 961         moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
 962
 963         /* log */
 964         moldyn_set_log_dir(&moldyn,mdrun.sdir);
 965         moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
 966         if(mdrun.elog)
 967                 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
 968         if(mdrun.tlog)
 969                 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
 970         if(mdrun.plog)
 971                 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
 972         if(mdrun.vlog)
 973                 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
 974         if(mdrun.visualize)
 975                 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
 976         if(mdrun.save)
 977                 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
 978         moldyn_set_log(&moldyn,CREATE_REPORT,0);
 979         set_avg_skip(&moldyn,mdrun.avgskip);
 980
 981         /* prepare the hook function */
 982         moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
 983
 984         /* run the simulation */
 985         moldyn_integrate(&moldyn);
 986
 987         /* shutdown */
 988         moldyn_shutdown(&moldyn);
 989         del_stages(&mdrun);
 990         list_destroy_f(&(mdrun.stage));
 991
 992         return 0;
 993 }