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_INSERT_MIXED_ATOMS:
 100                         psize=sizeof(t_insert_mixed_atoms_params);
 101                         break;
 102                 case STAGE_CONTINUE:
 103                         psize=sizeof(t_continue_params);
 104                         break;
 105                 case STAGE_ANNEAL:
 106                         psize=sizeof(t_anneal_params);
 107                         break;
 108                 case STAGE_CHAATTR:
 109                         psize=sizeof(t_chaattr_params);
 110                         break;
 111                 case STAGE_CHSATTR:
 112                         psize=sizeof(t_chsattr_params);
 113                         break;
 114                 default:
 115                         printf("%s unknown stage type: %02x\n",ME,type);
 116                         return -1;
 117         }
 118
 119         stage=malloc(sizeof(t_stage));
 120         if(stage==NULL) {
 121                 perror("[mdrun] malloc (add stage)");
 122                 return -1;
 123         }
 124
 125         stage->type=type;
 126         stage->executed=FALSE;
 127
 128         stage->params=malloc(psize);
 129         if(stage->params==NULL) {
 130                 perror("[mdrun] malloc (stage params)");
 131                 return -1;
 132         }
 133
 134         memcpy(stage->params,params,psize);
 135
 136         list_add_immediate_f(&(mdrun->stage),stage);
 137
 138         return 0;
 139 }
 140
 141 int mdrun_parse_config(t_mdrun *mdrun) {
 142
 143         int fd,ret;
 144         char error[128];
 145         char line[128];
 146         char *wptr;
 147         char word[16][64];
 148         int wcnt;
 149         int i,o;
 150
 151         t_displace_atom_params dap;
 152         t_insert_atoms_params iap;
 153         t_insert_mixed_atoms_params imp;
 154         t_continue_params cp;
 155         t_anneal_params ap;
 156         t_chaattr_params cap;
 157         t_chsattr_params csp;
 158
 159         /* open config file */
 160         fd=open(mdrun->cfile,O_RDONLY);
 161         if(fd<0) {
 162                 snprintf(error,128,"%s open cfile %s",ME,mdrun->cfile);
 163                 perror(error);
 164                 return fd;
 165         }
 166
 167         /* read, parse, set */
 168         ret=1;
 169         while(ret>0) {
 170
 171                 /* read */
 172                 ret=get_line(fd,line,128);
 173
 174                 /* parse */
 175
 176                 // ignore # lines and \n
 177                 if((line[0]=='#')|(ret==1))
 178                         continue;
 179
 180                 // reset
 181                 memset(&iap,0,sizeof(t_insert_atoms_params));
 182                 memset(&imp,0,sizeof(t_insert_mixed_atoms_params));
 183                 memset(&cp,0,sizeof(t_continue_params));
 184                 memset(&ap,0,sizeof(t_anneal_params));
 185                 memset(&cap,0,sizeof(t_chaattr_params));
 186                 memset(&csp,0,sizeof(t_chsattr_params));
 187
 188                 // get command + args
 189                 wcnt=0;
 190                 while(1) {
 191                         if(wcnt)
 192                                 wptr=strtok(NULL," \t");
 193                         else
 194                                 wptr=strtok(line," \t");
 195                         if(wptr==NULL)
 196                                 break;
 197                         strncpy(word[wcnt],wptr,64);
 198                         wcnt+=1;
 199                 }
 200
 201                 if(!strncmp(word[0],"potential",9)) {
 202                         if(!strncmp(word[1],"albe",4))
 203                                 mdrun->potential=MOLDYN_POTENTIAL_AM;
 204                         if(!strncmp(word[1],"tersoff",7))
 205                                 mdrun->potential=MOLDYN_POTENTIAL_TM;
 206                         if(!strncmp(word[1],"ho",2))
 207                                 mdrun->potential=MOLDYN_POTENTIAL_HO;
 208                         if(!strncmp(word[1],"lj",2))
 209                                 mdrun->potential=MOLDYN_POTENTIAL_LJ;
 210                 }
 211                 else if(!strncmp(word[0],"continue",8))
 212                         strncpy(mdrun->continue_file,word[1],128);
 213                 else if(!strncmp(word[0],"cutoff",6))
 214                         mdrun->cutoff=atof(word[1]);
 215                 else if(!strncmp(word[0],"nnd",3))
 216                         mdrun->nnd=atof(word[1]);
 217                 else if(!strncmp(word[0],"intalgo",7)) {
 218                         if(!strncmp(word[1],"verlet",5))
 219                                 mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
 220                 }
 221                 else if(!strncmp(word[0],"timestep",8))
 222                         mdrun->timestep=atof(word[1]);
 223                 else if(!strncmp(word[0],"volume",6)) {
 224                         mdrun->dim.x=atof(word[1]);
 225                         mdrun->dim.y=atof(word[2]);
 226                         mdrun->dim.z=atof(word[3]);
 227                         if(strncmp(word[4],"0",1))
 228                                 mdrun->vis=TRUE;
 229                 }
 230                 else if(!strncmp(word[0],"pbc",3)) {
 231                         if(strncmp(word[1],"0",1))
 232                                 mdrun->pbcx=TRUE;
 233                         else
 234                                 mdrun->pbcx=FALSE;
 235                         if(strncmp(word[2],"0",1))
 236                                 mdrun->pbcy=TRUE;
 237                         else
 238                                 mdrun->pbcy=FALSE;
 239                         if(strncmp(word[3],"0",1))
 240                                 mdrun->pbcz=TRUE;
 241                         else
 242                                 mdrun->pbcz=FALSE;
 243                 }
 244                 else if(!strncmp(word[0],"temperature",11))
 245                         mdrun->temperature=atof(word[1]);
 246                 else if(!strncmp(word[0],"pressure",8))
 247                         mdrun->pressure=atof(word[1]);
 248                 else if(!strncmp(word[0],"lattice",7)) {
 249                         if(!strncmp(word[1],"zincblende",10))
 250                                 mdrun->lattice=ZINCBLENDE;
 251                         if(!strncmp(word[1],"fcc",3))
 252                                 mdrun->lattice=FCC;
 253                         if(!strncmp(word[1],"diamond",7))
 254                                 mdrun->lattice=DIAMOND;
 255                         if(!strncmp(word[1],"none",4))
 256                                 mdrun->lattice=NONE;
 257                 }
 258                 else if(!strncmp(word[0],"element1",8)) {
 259                         mdrun->element1=atoi(word[1]);
 260                         mdrun->m1=pse_mass[mdrun->element1];
 261                 }
 262                 else if(!strncmp(word[0],"element2",8)) {
 263                         mdrun->element2=atoi(word[1]);
 264                         mdrun->m2=pse_mass[mdrun->element2];
 265                 }
 266                 else if(!strncmp(word[0],"fill",6)) {
 267                         // only lc mode by now
 268                         mdrun->lx=atoi(word[2]);
 269                         mdrun->ly=atoi(word[3]);
 270                         mdrun->lz=atoi(word[4]);
 271                         mdrun->lc=atof(word[5]);
 272                 }
 273                 else if(!strncmp(word[0],"aattr",5)) {
 274                         // for aatrib line we need a special stage
 275                         // containing one schedule of 0 loops ...
 276                         for(i=0;i<strlen(word[1]);i++) {
 277                                 switch(word[1][i]) {
 278                                         case 't':
 279                                                 cap.type|=CHAATTR_TOTALV;
 280                                                 break;
 281                                         case 'r':
 282                                                 cap.type|=CHAATTR_REGION;
 283                                                 break;
 284                                         case 'e':
 285                                                 cap.type|=CHAATTR_ELEMENT;
 286                                                 break;
 287                                         default:
 288                                                 break;
 289                                 }
 290                         }
 291                         i=2;
 292                         if(cap.type&CHAATTR_REGION) {
 293                                 cap.x0=atof(word[1]);
 294                                 cap.y0=atof(word[2]);
 295                                 cap.z0=atof(word[3]);
 296                                 cap.x1=atof(word[4]);
 297                                 cap.y1=atof(word[5]);
 298                                 cap.z1=atof(word[6]);
 299                                 i+=6;
 300                         }
 301                         if(cap.type&CHAATTR_ELEMENT) {
 302                                 cap.element=atoi(word[i]);
 303                                 i+=1;
 304                         }
 305                         for(o=0;o<strlen(word[i]);o++) {
 306                                 switch(word[i][o]) {
 307                                         case 'b':
 308                                                 cap.attr|=ATOM_ATTR_VB;
 309                                                 break;
 310                                         case 'h':
 311                                                 cap.attr|=ATOM_ATTR_HB;
 312                                                 break;
 313                                         case 'v':
 314                                                 cap.attr|=ATOM_ATTR_VA;
 315                                                 break;
 316                                         case 'f':
 317                                                 cap.attr|=ATOM_ATTR_FP;
 318                                                 break;
 319                                         case '1':
 320                                                 cap.attr|=ATOM_ATTR_1BP;
 321                                                 break;
 322                                         case '2':
 323                                                 cap.attr|=ATOM_ATTR_2BP;
 324                                                 break;
 325                                         case '3':
 326                                                 cap.attr|=ATOM_ATTR_3BP;
 327                                                 break;
 328                                         default:
 329                                                 break;
 330                                 }
 331                         }
 332                         add_stage(mdrun,STAGE_CHAATTR,&cap);
 333                 }
 334                 else if(!strncmp(word[0],"sattr",5)) {
 335                         // for satrib line we need a special stage
 336                         // containing one schedule of 0 loops ...
 337                         csp.type=0;
 338                         for(i=1;i<wcnt;i++) {
 339                                 if(!strncmp(word[i],"pctrl",5)) {
 340                                         csp.ptau=0.01/(atof(word[++i])*GPA);
 341                                         csp.type|=CHSATTR_PCTRL;
 342                                 }
 343                                 if(!strncmp(word[i],"tctrl",5)) {
 344                                         csp.ttau=atof(word[++i]);
 345                                         csp.type|=CHSATTR_TCTRL;
 346                                 }
 347                                 if(!strncmp(word[i],"prelax",6)) {
 348                                         csp.dp=atof(word[++i])*BAR;
 349                                         csp.type|=CHSATTR_PRELAX;
 350                                 }
 351                                 if(!strncmp(word[i],"trelax",6)) {
 352                                         csp.dt=atof(word[++i]);
 353                                         csp.type|=CHSATTR_TRELAX;
 354                                 }
 355                                 if(!strncmp(word[i],"rsteps",6)) {
 356                                         csp.rsteps=atoi(word[++i]);
 357                                         csp.type|=CHSATTR_RSTEPS;
 358                                 }
 359                                 if(!strncmp(word[i],"avgrst",6)) {
 360                                         csp.avgrst=atoi(word[++i]);
 361                                         csp.type|=CHSATTR_AVGRST;
 362                                 }
 363                         }
 364                         add_stage(mdrun,STAGE_CHSATTR,&csp);
 365                 }
 366                 else if(!strncmp(word[0],"prerun",6))
 367                         mdrun->prerun=atoi(word[1]);
 368                 else if(!strncmp(word[0],"avgskip",7))
 369                         mdrun->avgskip=atoi(word[1]);
 370                 else if(!strncmp(word[0],"elog",4))
 371                         mdrun->elog=atoi(word[1]);
 372                 else if(!strncmp(word[0],"tlog",4))
 373                         mdrun->tlog=atoi(word[1]);
 374                 else if(!strncmp(word[0],"plog",4))
 375                         mdrun->plog=atoi(word[1]);
 376                 else if(!strncmp(word[0],"vlog",4))
 377                         mdrun->vlog=atoi(word[1]);
 378                 else if(!strncmp(word[0],"save",4))
 379                         mdrun->save=atoi(word[1]);
 380                 else if(!strncmp(word[0],"visualize",9))
 381                         mdrun->visualize=atoi(word[1]);
 382                 else if(!strncmp(word[0],"stage",5)) {
 383                         // for every stage line, add a stage
 384                         if(!strncmp(word[1],"displace",8)) {
 385                                 dap.nr=atoi(word[2]);
 386                                 dap.dx=atof(word[3]);
 387                                 dap.dy=atof(word[4]);
 388                                 dap.dz=atof(word[5]);
 389                                 add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
 390                         }
 391                         else if(!strncmp(word[1],"ins_atoms",9)) {
 392                                 iap.ins_steps=atoi(word[2]);
 393                                 iap.ins_atoms=atoi(word[3]);
 394                                 iap.element=atoi(word[4]);
 395                                 iap.brand=atoi(word[5]);
 396                                 for(i=0;i<strlen(word[6]);i++) {
 397                                         switch(word[6][i]) {
 398                                                 case 'b':
 399                                                         iap.attr|=ATOM_ATTR_VB;
 400                                                         break;
 401                                                 case 'h':
 402                                                         iap.attr|=ATOM_ATTR_HB;
 403                                                         break;
 404                                                 case 'v':
 405                                                         iap.attr|=ATOM_ATTR_VA;
 406                                                         break;
 407                                                 case 'f':
 408                                                         iap.attr|=ATOM_ATTR_FP;
 409                                                         break;
 410                                                 case '1':
 411                                                         iap.attr|=ATOM_ATTR_1BP;
 412                                                         break;
 413                                                 case '2':
 414                                                         iap.attr|=ATOM_ATTR_2BP;
 415                                                         break;
 416                                                 case '3':
 417                                                         iap.attr|=ATOM_ATTR_3BP;
 418                                                         break;
 419                                                 default:
 420                                                         break;
 421                                         }
 422                                 }
 423                                 switch(word[7][0]) {
 424                                         // insertion types
 425                                         case 'p':
 426                                                 iap.type=INS_POS;
 427                                                 iap.x0=atof(word[8]);
 428                                                 iap.y0=atof(word[9]);
 429                                                 iap.z0=atof(word[10]);
 430                                                 break;
 431                                         case 'r':
 432                                                 if(word[8][0]=='t') {
 433                                                         iap.type=INS_TOTAL;
 434                                                         iap.cr=atof(word[9]);
 435                                                 }
 436                                                 else {
 437                                                         iap.type=INS_REGION;
 438                                                         iap.x0=atof(word[8]);
 439                                                         iap.y0=atof(word[9]);
 440                                                         iap.z0=atof(word[10]);
 441                                                         iap.x1=atof(word[11]);
 442                                                         iap.y1=atof(word[12]);
 443                                                         iap.z1=atof(word[13]);
 444                                                         iap.cr=atof(word[14]);
 445                                                 }
 446                                         default:
 447                                                 break;
 448                                 }
 449                                 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
 450                         }
 451
 452
 453                         // HERE WE GO ...
 454
 455                         else if(!strncmp(word[1],"ins_m_atoms",11)) {
 456                                 imp.element1=atoi(word[2]);
 457                                 imp.element2=atoi(word[3]);
 458                                 imp.amount1=atoi(word[4]);
 459                                 imp.amount2=atoi(word[5]);
 460                                 imp.brand1=atoi(word[6]);
 461                                 imp.brand2=atoi(word[7]);
 462                                 imp.cr=atof(word[8]);
 463                                 /* do this later ...
 464                                 for(i=0;i<strlen(word[8]);i++) {
 465                                         switch(word[8][i]) {
 466                                                 case 'b':
 467                                                         imp.attr|=ATOM_ATTR_VB;
 468                                                         break;
 469                                                 case 'h':
 470                                                         imp.attr|=ATOM_ATTR_HB;
 471                                                         break;
 472                                                 case 'v':
 473                                                         imp.attr|=ATOM_ATTR_VA;
 474                                                         break;
 475                                                 case 'f':
 476                                                         imp.attr|=ATOM_ATTR_FP;
 477                                                         break;
 478                                                 case '1':
 479                                                         imp.attr|=ATOM_ATTR_1BP;
 480                                                         break;
 481                                                 case '2':
 482                                                         imp.attr|=ATOM_ATTR_2BP;
 483                                                         break;
 484                                                 case '3':
 485                                                         imp.attr|=ATOM_ATTR_3BP;
 486                                                         break;
 487                                                 default:
 488                                                         break;
 489                                         }
 490                                 }
 491                                 */
 492                                 imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
 493                                 imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
 494                                 add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
 495                         }
 496
 497
 498
 499
 500
 501                         else if(!strncmp(word[1],"continue",8)) {
 502                                 cp.runs=atoi(word[2]);
 503                                 add_stage(mdrun,STAGE_CONTINUE,&cp);
 504                         }
 505                         else if(!strncmp(word[1],"anneal",6)) {
 506                                 ap.count=0;
 507                                 ap.runs=atoi(word[2]);
 508                                 ap.dt=atof(word[3]);
 509                                 add_stage(mdrun,STAGE_ANNEAL,&ap);
 510                         }
 511                         else {
 512                                 printf("%s unknown stage type: %s\n",
 513                                        ME,word[1]);
 514                                 return -1;
 515                         }
 516                 }
 517                 else {
 518                         printf("%s unknown keyword '%s', skipped!\n",
 519                                ME,word[0]);
 520                         continue;
 521                 }
 522         }
 523
 524         /* close file */
 525         close(fd);
 526
 527         return 0;
 528 }
 529
 530 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
 531
 532         double delta;
 533
 534         if(!(mdrun->sattr&SATTR_PRELAX)) {
 535                 return TRUE;
 536         }
 537
 538         delta=moldyn->p_avg-moldyn->p_ref;
 539
 540         if(delta<0)
 541                 delta=-delta;
 542
 543         if(delta>mdrun->dp)
 544                 return FALSE;
 545
 546         return TRUE;
 547 }
 548
 549 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 550
 551         double delta;
 552
 553         if(!(mdrun->sattr&SATTR_TRELAX))
 554                 return TRUE;
 555
 556         delta=moldyn->t_avg-moldyn->t_ref;
 557
 558         if(delta<0)
 559                 delta=-delta;
 560
 561         if(delta>mdrun->dt)
 562                 return FALSE;
 563
 564         return TRUE;
 565 }
 566
 567 int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
 568
 569         t_displace_atom_params *dap;
 570         t_stage *stage;
 571         t_atom *atom;
 572
 573         stage=mdrun->stage.current->data;
 574         dap=stage->params;
 575
 576         atom=&(moldyn->atom[dap->nr]);
 577         atom->r.x+=dap->dx;
 578         atom->r.y+=dap->dy;
 579         atom->r.z+=dap->dz;
 580
 581         return 0;
 582 }
 583
 584 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 585
 586         t_insert_atoms_params *iap;
 587         t_stage *stage;
 588         t_atom *atom;
 589         t_3dvec r,v,dist;
 590         double d,dmin,o;
 591         int cnt,i;
 592         double x,y,z;
 593         double x0,y0,z0;
 594         u8 cr_check,run;
 595
 596         stage=mdrun->stage.current->data;
 597         iap=stage->params;
 598
 599         cr_check=FALSE;
 600
 601         v.x=0.0; v.y=0.0; v.z=0.0;
 602         x=0; y=0; z=0;
 603         o=0; dmin=0;
 604
 605         switch(mdrun->lattice) {
 606                 case CUBIC:
 607                         o=0.5*mdrun->lc;
 608                         break;
 609                 case FCC:
 610                         o=0.25*mdrun->lc;
 611                         break;
 612                 case DIAMOND:
 613                 case ZINCBLENDE:
 614                         o=0.125*mdrun->lc;
 615                         break;
 616                 default:
 617                         break;
 618         }
 619
 620         switch(iap->type) {
 621                 case INS_TOTAL:
 622                         x=moldyn->dim.x;
 623                         x0=-x/2.0;
 624                         y=moldyn->dim.y;
 625                         y0=-y/2.0;
 626                         z=moldyn->dim.z;
 627                         z0=-z/2.0;
 628                         cr_check=TRUE;
 629                         break;
 630                 case INS_REGION:
 631                         x=iap->x1-iap->x0;
 632                         x0=iap->x0;
 633                         y=iap->y1-iap->y0;
 634                         y0=iap->y0;
 635                         z=iap->z1-iap->z0;
 636                         z0=iap->z0;
 637                         cr_check=TRUE;
 638                         break;
 639                 case INS_POS:
 640                         x0=iap->x0;
 641                         y0=iap->y0;
 642                         z0=iap->z0;
 643                         cr_check=FALSE;
 644                         break;
 645                 default:
 646                         printf("%s unknown insertion mode: %02x\n",
 647                                ME,iap->type);
 648                         return -1;
 649         }
 650
 651         cnt=0;
 652         while(cnt<iap->ins_atoms) {
 653                 run=1;
 654                 while(run) {
 655                         if(iap->type!=INS_POS) {
 656                                 r.x=rand_get_double(&(moldyn->random))*x;
 657                                 r.y=rand_get_double(&(moldyn->random))*y;
 658                                 r.z=rand_get_double(&(moldyn->random))*z;
 659                         }
 660                         else {
 661                                 r.x=0.0;
 662                                 r.y=0.0;
 663                                 r.z=0.0;
 664                         }
 665                         r.x+=x0;
 666                         r.y+=y0;
 667                         r.z+=z0;
 668                         // offset
 669                         if(iap->type!=INS_TOTAL) {
 670                                 r.x+=o;
 671                                 r.y+=o;
 672                                 r.z+=o;
 673                         }
 674                         run=0;
 675                         if(cr_check==TRUE) {
 676                                 dmin=1000;      // for sure too high!
 677                                 for(i=0;i<moldyn->count;i++) {
 678                                         atom=&(moldyn->atom[i]);
 679                                         v3_sub(&dist,&(atom->r),&r);
 680                                         check_per_bound(moldyn,&dist);
 681                                         d=v3_absolute_square(&dist);
 682                                         if(d<(iap->cr*iap->cr)) {
 683                                                 run=1;
 684                                                 break;
 685                                         }
 686                                         if(d<dmin)
 687                                                 dmin=d;
 688                                 }
 689                         }
 690                 }
 691                 add_atom(moldyn,iap->element,pse_mass[iap->element],
 692                          iap->brand,iap->attr,&r,&v);
 693                 printf("%s atom inserted (%d/%d): %f %f %f\n",
 694                        ME,(iap->cnt_steps+1)*iap->ins_atoms,
 695                        iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
 696                 printf("  -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
 697                 cnt+=1;
 698         }
 699
 700         return 0;
 701 }
 702
 703 int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 704
 705         t_stage *stage;
 706         t_insert_mixed_atoms_params *imp;
 707         t_atom *atom;
 708         double x,x0,y,y0,z,z0;
 709         double dmin,d,c;
 710         u8 retry;
 711         t_3dvec r,v,dist;
 712         int i;
 713
 714
 715         stage=mdrun->stage.current->data;
 716         imp=stage->params;
 717
 718         x=moldyn->dim.x;
 719         x0=-x/2.0;
 720         y=moldyn->dim.y;
 721         y0=-y/2.0;
 722         z=moldyn->dim.z;
 723         z0=-z/2.0;
 724
 725         v.x=0.0;
 726         v.y=0.0;
 727         v.z=0.0;
 728
 729         c=imp->cr*imp->cr;
 730
 731         while(imp->amount1|imp->amount2) {
 732                 if(imp->amount1) {
 733                         retry=1;
 734                         while(retry) {
 735                                 retry=0;
 736                                 r.x=rand_get_double(&(moldyn->random))*x;
 737                                 r.y=rand_get_double(&(moldyn->random))*y;
 738                                 r.z=rand_get_double(&(moldyn->random))*z;
 739                                 r.x+=x0;
 740                                 r.y+=y0;
 741                                 r.z+=z0;
 742                                 dmin=1000.0;    // for sure too high!
 743                                 for(i=0;i<moldyn->count;i++) {
 744                                         atom=&(moldyn->atom[i]);
 745                                         v3_sub(&dist,&(atom->r),&r);
 746                                         check_per_bound(moldyn,&dist);
 747                                         d=v3_absolute_square(&dist);
 748                                         if(d<c) {
 749                                                 retry=1;
 750                                                 break;
 751                                         }
 752                                         if(d<dmin)
 753                                                 dmin=d;
 754
 755                                 }
 756                         }
 757                         add_atom(moldyn,imp->element1,pse_mass[imp->element1],
 758                                  imp->brand1,imp->attr1,&r,&v);
 759                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
 760                                ME,imp->amount1,r.x,r.y,r.z);
 761                         printf("  -> d2 = %f/%f\n",dmin,c);
 762                         imp->amount1-=1;
 763                 }
 764                 if(imp->amount2) {
 765                         retry=1;
 766                         while(retry) {
 767                                 retry=0;
 768                                 r.x=rand_get_double(&(moldyn->random))*x;
 769                                 r.y=rand_get_double(&(moldyn->random))*y;
 770                                 r.z=rand_get_double(&(moldyn->random))*z;
 771                                 r.x+=x0;
 772                                 r.y+=y0;
 773                                 r.z+=z0;
 774                                 dmin=1000.0;    // for sure too high!
 775                                 for(i=0;i<moldyn->count;i++) {
 776                                         atom=&(moldyn->atom[i]);
 777                                         v3_sub(&dist,&(atom->r),&r);
 778                                         check_per_bound(moldyn,&dist);
 779                                         d=v3_absolute_square(&dist);
 780                                         if(d<c) {
 781                                                 retry=1;
 782                                                 break;
 783                                         }
 784                                         if(d<dmin)
 785                                                 dmin=d;
 786
 787                                 }
 788                         }
 789                         add_atom(moldyn,imp->element2,pse_mass[imp->element2],
 790                                  imp->brand2,imp->attr2,&r,&v);
 791                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
 792                                ME,imp->amount2,r.x,r.y,r.z);
 793                         printf("  -> d2 = %f/%f\n",dmin,c);
 794                         imp->amount2-=1;
 795                 }
 796         }
 797
 798         return 0;
 799 }
 800
 801 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 802
 803         t_stage *stage;
 804         t_chaattr_params *cap;
 805         t_atom *atom;
 806         int i;
 807
 808         stage=mdrun->stage.current->data;
 809         cap=stage->params;
 810
 811         for(i=0;i<moldyn->count;i++) {
 812                 atom=&(moldyn->atom[i]);
 813                 if(cap->type&CHAATTR_ELEMENT) {
 814                         if(cap->element!=atom->element)
 815                                 continue;
 816                 }
 817                 if(cap->type&CHAATTR_REGION) {
 818                         if(cap->x0<atom->r.x)
 819                                 continue;
 820                         if(cap->y0<atom->r.y)
 821                                 continue;
 822                         if(cap->z0<atom->r.z)
 823                                 continue;
 824                         if(cap->x1>atom->r.x)
 825                                 continue;
 826                         if(cap->y1>atom->r.y)
 827                                 continue;
 828                         if(cap->z1>atom->r.z)
 829                                 continue;
 830                 }
 831                 atom->attr=cap->attr;
 832         }
 833
 834         return 0;
 835 }
 836
 837 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 838
 839         t_stage *stage;
 840         t_chsattr_params *csp;
 841
 842         stage=mdrun->stage.current->data;
 843         csp=stage->params;
 844
 845         if(csp->type&CHSATTR_PCTRL) {
 846                 if(csp->ptau>0)
 847                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 848                 else
 849                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 850         }
 851         if(csp->type&CHSATTR_TCTRL) {
 852                 if(csp->ttau>0)
 853                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 854                 else
 855                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 856         }
 857         if(csp->type&CHSATTR_PRELAX) {
 858                 if(csp->dp<0)
 859                         mdrun->sattr&=(~(SATTR_PRELAX));
 860                 else
 861                         mdrun->sattr|=SATTR_PRELAX;
 862                 mdrun->dp=csp->dp;
 863         }
 864         if(csp->type&CHSATTR_TRELAX) {
 865                 if(csp->dt<0)
 866                         mdrun->sattr&=(~(SATTR_TRELAX));
 867                 else
 868                         mdrun->sattr|=SATTR_TRELAX;
 869                 mdrun->dt=csp->dt;
 870         }
 871         if(csp->type&CHSATTR_AVGRST) {
 872                 if(csp->avgrst)
 873                         mdrun->sattr|=SATTR_AVGRST;
 874                 else
 875                         mdrun->sattr&=(~(SATTR_AVGRST));
 876         }
 877         if(csp->type&CHSATTR_RSTEPS) {
 878                 mdrun->relax_steps=csp->rsteps;
 879         }
 880
 881         return 0;
 882 }
 883
 884 #define stage_print(m)  if(!(stage->executed)) \
 885                                 printf("%s",m)
 886
 887 int mdrun_hook(void *ptr1,void *ptr2) {
 888
 889         t_moldyn *moldyn;
 890         t_mdrun *mdrun;
 891         t_stage *stage;
 892         t_list *sl;
 893         int steps;
 894         double tau;
 895         u8 change_stage;
 896
 897         t_insert_atoms_params *iap;
 898         t_insert_mixed_atoms_params *imp;
 899         t_continue_params *cp;
 900         t_anneal_params *ap;
 901
 902         moldyn=ptr1;
 903         mdrun=ptr2;
 904
 905         sl=&(mdrun->stage);
 906
 907         change_stage=FALSE;
 908
 909         /* return immediately if there are no more stage */
 910         if(sl->current==NULL)
 911                 return 0;
 912
 913         /* get stage description */
 914         stage=sl->current->data;
 915
 916         /* default steps and tau values */
 917         steps=mdrun->relax_steps;
 918         tau=mdrun->timestep;
 919
 920         /* check whether relaxation steps are necessary */
 921         if((check_pressure(moldyn,mdrun)==TRUE)&\
 922            (check_temperature(moldyn,mdrun)==TRUE)) {
 923
 924                 /* be verbose */
 925                 stage_print("\n###########################\n");
 926                 stage_print("# [mdrun] executing stage #\n");
 927                 stage_print("###########################\n\n");
 928
 929                 /* stage specific stuff */
 930                 switch(stage->type) {
 931                         case STAGE_DISPLACE_ATOM:
 932                                 stage_print("  -> displace atom\n\n");
 933                                 displace_atom(moldyn,mdrun);
 934                                 change_stage=TRUE;
 935                                 break;
 936                         case STAGE_INSERT_ATOMS:
 937                                 stage_print("  -> insert atoms\n\n");
 938                                 iap=stage->params;
 939                                 if(iap->cnt_steps==iap->ins_steps) {
 940                                         change_stage=TRUE;
 941                                         break;
 942                                 }
 943                                 insert_atoms(moldyn,mdrun);
 944                                 iap->cnt_steps+=1;
 945                                 break;
 946
 947
 948
 949                         case STAGE_INSERT_MIXED_ATOMS:
 950                                 stage_print("  -> insert mixed atoms\n\n");
 951                                 imp=stage->params;
 952                                 insert_mixed_atoms(moldyn,mdrun);
 953                                 break;
 954
 955
 956
 957                         case STAGE_CONTINUE:
 958                                 stage_print("  -> continue\n\n");
 959                                 if(stage->executed==TRUE) {
 960                                         change_stage=TRUE;
 961                                         break;
 962                                 }
 963                                 cp=stage->params;
 964                                 steps=cp->runs;
 965                                 break;
 966                         case STAGE_ANNEAL:
 967                                 stage_print("  -> anneal\n\n");
 968                                 ap=stage->params;
 969                                 if(ap->count==ap->runs) {
 970                                         change_stage=TRUE;
 971                                         break;
 972                                 }
 973                                 if(moldyn->t_ref+ap->dt>=0.0)
 974                                         set_temperature(moldyn,
 975                                                         moldyn->t_ref+ap->dt);
 976                                 ap->count+=1;
 977                                 break;
 978                         case STAGE_CHAATTR:
 979                                 stage_print("  -> chaattr\n\n");
 980                                 chaatr(moldyn,mdrun);
 981                                 change_stage=TRUE;
 982                                 break;
 983                         case STAGE_CHSATTR:
 984                                 stage_print("  -> chsattr\n\n");
 985                                 chsattr(moldyn,mdrun);
 986                                 change_stage=TRUE;
 987                                 break;
 988                         default:
 989                                 printf("%s unknwon stage type\n",ME);
 990                                 break;
 991                 }
 992
 993                 /* mark as executed */
 994                 stage->executed=TRUE;
 995
 996                 /* change state */
 997                 if(change_stage==TRUE) {
 998                         printf("%s finished stage\n",ME);
 999                         if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
1000                                 printf("%s no more stages\n",ME);
1001                                 return 0;
1002                         }
1003                         steps=0;
1004                         tau=mdrun->timestep;
1005                 }
1006
1007         }
1008         else {
1009
1010                 /* averages */
1011                 if(mdrun->sattr&SATTR_AVGRST)
1012                         average_reset(moldyn);
1013
1014         }
1015
1016         /* continue simulation */
1017         moldyn_add_schedule(moldyn,steps,tau);
1018
1019         return 0;
1020 }
1021
1022 int main(int argc,char **argv) {
1023
1024         t_mdrun mdrun;
1025         t_moldyn moldyn;
1026         t_3dvec o;
1027
1028         /* clear structs */
1029         memset(&mdrun,0,sizeof(t_mdrun));
1030         memset(&moldyn,0,sizeof(t_moldyn));
1031
1032         /* parse arguments */
1033         if(mdrun_parse_argv(&mdrun,argc,argv)<0)
1034                 return -1;
1035
1036         /* initialize list system */
1037         list_init_f(&(mdrun.stage));
1038
1039         /* parse config file */
1040         mdrun_parse_config(&mdrun);
1041
1042         /* reset the stage list */
1043         list_reset_f(&(mdrun.stage));
1044
1045         /* sanity check! */
1046
1047         /* prepare simulation */
1048
1049         if(mdrun.continue_file[0]) {
1050                 // read the save file
1051                 moldyn_read_save_file(&moldyn,mdrun.continue_file);
1052                 // manualaadjusting some stuff
1053                 moldyn.argc=argc;
1054                 moldyn.args=argv;
1055                 rand_init(&(moldyn.random),NULL,1);
1056                 moldyn.random.status|=RAND_STAT_VERBOSE;
1057         }
1058         else {
1059                 moldyn_init(&moldyn,argc,argv);
1060         }
1061
1062         if(set_int_alg(&moldyn,mdrun.intalgo)<0)
1063                 return -1;
1064
1065         /* potential */
1066         set_cutoff(&moldyn,mdrun.cutoff);
1067         if(set_potential(&moldyn,mdrun.potential)<0)
1068                 return -1;
1069         switch(mdrun.potential) {
1070                 case MOLDYN_POTENTIAL_AM:
1071                         albe_mult_set_params(&moldyn,
1072                                              mdrun.element1,
1073                                              mdrun.element2);
1074                         break;
1075                 case MOLDYN_POTENTIAL_TM:
1076                         tersoff_mult_set_params(&moldyn,
1077                                                 mdrun.element1,
1078                                                 mdrun.element2);
1079                         break;
1080                 case MOLDYN_POTENTIAL_HO:
1081                         harmonic_oscillator_set_params(&moldyn,mdrun.element1);
1082                         break;
1083                 case MOLDYN_POTENTIAL_LJ:
1084                         lennard_jones_set_params(&moldyn,mdrun.element1);
1085                         break;
1086                 default:
1087                         printf("%s unknown potential: %02x\n",
1088                                ME,mdrun.potential);
1089                         return -1;
1090         }
1091
1092         /* if it is a continue run, reset schedule and skip lattice init */
1093         if(mdrun.continue_file[0]) {
1094                 memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
1095                 goto addsched;
1096         }
1097
1098         /* initial lattice and dimensions */
1099         set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
1100         set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
1101         switch(mdrun.lattice) {
1102                 case FCC:
1103                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
1104                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1105                                        mdrun.ly,mdrun.lz,NULL);
1106                         break;
1107                 case DIAMOND:
1108                         create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
1109                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1110                                        mdrun.ly,mdrun.lz,NULL);
1111                         break;
1112                 case ZINCBLENDE:
1113                         o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1114                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
1115                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1116                                        mdrun.ly,mdrun.lz,&o);
1117                         o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1118                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
1119                                        mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
1120                                        mdrun.ly,mdrun.lz,&o);
1121                         break;
1122                 case NONE:
1123                         break;
1124                 default:
1125                         printf("%s unknown lattice type: %02x\n",
1126                                ME,mdrun.lattice);
1127                         return -1;
1128         }
1129         moldyn_bc_check(&moldyn);
1130
1131         /* temperature and pressure */
1132         set_temperature(&moldyn,mdrun.temperature);
1133         set_pressure(&moldyn,mdrun.pressure);
1134         thermal_init(&moldyn,TRUE);
1135
1136 addsched:
1137         /* first schedule */
1138         moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
1139
1140         /* log */
1141         moldyn_set_log_dir(&moldyn,mdrun.sdir);
1142         moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
1143         if(mdrun.elog)
1144                 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
1145         if(mdrun.tlog)
1146                 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
1147         if(mdrun.plog)
1148                 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
1149         if(mdrun.vlog)
1150                 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
1151         if(mdrun.visualize)
1152                 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
1153         if(mdrun.save)
1154                 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
1155         moldyn_set_log(&moldyn,CREATE_REPORT,0);
1156         set_avg_skip(&moldyn,mdrun.avgskip);
1157
1158         /* prepare the hook function */
1159         moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
1160
1161         /* run the simulation */
1162         moldyn_integrate(&moldyn);
1163
1164         /* shutdown */
1165         moldyn_shutdown(&moldyn);
1166         del_stages(&mdrun);
1167         list_destroy_f(&(mdrun.stage));
1168
1169         return 0;
1170 }