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_DEL_ATOMS:
  97                         psize=sizeof(t_del_atoms_params);
  98                         break;
  99                 case STAGE_MODIFY_ATOMS:
 100                         psize=sizeof(t_modify_atoms_params);
 101                         break;
 102                 case STAGE_INSERT_ATOMS:
 103                         psize=sizeof(t_insert_atoms_params);
 104                         break;
 105                 case STAGE_INSERT_MIXED_ATOMS:
 106                         psize=sizeof(t_insert_mixed_atoms_params);
 107                         break;
 108                 case STAGE_CONTINUE:
 109                         psize=sizeof(t_continue_params);
 110                         break;
 111                 case STAGE_ANNEAL:
 112                         psize=sizeof(t_anneal_params);
 113                         break;
 114                 case STAGE_CHAATTR:
 115                         psize=sizeof(t_chaattr_params);
 116                         break;
 117                 case STAGE_CHSATTR:
 118                         psize=sizeof(t_chsattr_params);
 119                         break;
 120                 case STAGE_SET_TEMP:
 121                         psize=sizeof(t_set_temp_params);
 122                         break;
 123                 case STAGE_SET_TIMESTEP:
 124                         psize=sizeof(t_set_timestep_params);
 125                         break;
 126                 case STAGE_FILL:
 127                         psize=sizeof(t_fill_params);
 128                         break;
 129                 case STAGE_THERMAL_INIT:
 130                         psize=0;
 131                         break;
 132                 default:
 133                         printf("%s unknown stage type: %02x\n",ME,type);
 134                         return -1;
 135         }
 136
 137         stage=malloc(sizeof(t_stage));
 138         if(stage==NULL) {
 139                 perror("[mdrun] malloc (add stage)");
 140                 return -1;
 141         }
 142
 143         stage->type=type;
 144         stage->executed=FALSE;
 145
 146         stage->params=malloc(psize);
 147         if(stage->params==NULL) {
 148                 perror("[mdrun] malloc (stage params)");
 149                 return -1;
 150         }
 151
 152         memcpy(stage->params,params,psize);
 153
 154         list_add_immediate_f(&(mdrun->stage),stage);
 155
 156         return 0;
 157 }
 158
 159 int mdrun_parse_config(t_mdrun *mdrun) {
 160
 161         int fd,ret;
 162         char error[128];
 163         char line[128];
 164         char *wptr;
 165         char word[32][64];
 166         int wcnt;
 167         int i,o;
 168
 169         t_displace_atom_params dap;
 170         t_modify_atoms_params map;
 171         t_insert_atoms_params iap;
 172         t_insert_mixed_atoms_params imp;
 173         t_continue_params cp;
 174         t_anneal_params ap;
 175         t_chaattr_params cap;
 176         t_chsattr_params csp;
 177         t_set_temp_params stp;
 178         t_set_timestep_params stsp;
 179         t_fill_params fp;
 180         t_del_atoms_params delp;
 181
 182         /* open config file */
 183         fd=open(mdrun->cfile,O_RDONLY);
 184         if(fd<0) {
 185                 snprintf(error,128,"%s open cfile %s",ME,mdrun->cfile);
 186                 perror(error);
 187                 return fd;
 188         }
 189
 190         /* read, parse, set */
 191         ret=1;
 192         while(ret>0) {
 193
 194                 /* read */
 195                 ret=get_line(fd,line,128);
 196
 197                 /* parse */
 198
 199                 // ignore # lines and \n
 200                 if((line[0]=='#')|(ret==1))
 201                         continue;
 202
 203                 // reset
 204                 memset(&iap,0,sizeof(t_insert_atoms_params));
 205                 memset(&map,0,sizeof(t_modify_atoms_params));
 206                 memset(&imp,0,sizeof(t_insert_mixed_atoms_params));
 207                 memset(&cp,0,sizeof(t_continue_params));
 208                 memset(&ap,0,sizeof(t_anneal_params));
 209                 memset(&cap,0,sizeof(t_chaattr_params));
 210                 memset(&csp,0,sizeof(t_chsattr_params));
 211                 memset(&stp,0,sizeof(t_set_temp_params));
 212                 memset(&stsp,0,sizeof(t_set_timestep_params));
 213                 memset(&fp,0,sizeof(t_fill_params));
 214                 memset(&delp,0,sizeof(t_del_atoms_params));
 215
 216                 // get command + args
 217                 wcnt=0;
 218                 while(1) {
 219                         if(wcnt)
 220                                 wptr=strtok(NULL," \t");
 221                         else
 222                                 wptr=strtok(line," \t");
 223                         if(wptr==NULL)
 224                                 break;
 225                         strncpy(word[wcnt],wptr,64);
 226                         wcnt+=1;
 227                 }
 228
 229                 if(!strncmp(word[0],"potential",9)) {
 230                         if(!strncmp(word[1],"albe",4))
 231                                 mdrun->potential=MOLDYN_POTENTIAL_AM;
 232                         if(!strncmp(word[1],"tersoff",7))
 233                                 mdrun->potential=MOLDYN_POTENTIAL_TM;
 234                         if(!strncmp(word[1],"ho",2))
 235                                 mdrun->potential=MOLDYN_POTENTIAL_HO;
 236                         if(!strncmp(word[1],"lj",2))
 237                                 mdrun->potential=MOLDYN_POTENTIAL_LJ;
 238                 }
 239                 else if(!strncmp(word[0],"continue",8))
 240                         strncpy(mdrun->continue_file,word[1],128);
 241                 else if(!strncmp(word[0],"cutoff",6))
 242                         mdrun->cutoff=atof(word[1]);
 243                 else if(!strncmp(word[0],"nnd",3))
 244                         mdrun->nnd=atof(word[1]);
 245                 else if(!strncmp(word[0],"intalgo",7)) {
 246                         if(!strncmp(word[1],"verlet",5))
 247                                 mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
 248                 }
 249                 else if(!strncmp(word[0],"timestep",8))
 250                         mdrun->timestep=atof(word[1]);
 251                 else if(!strncmp(word[0],"volume",6)) {
 252                         mdrun->dim.x=atof(word[1]);
 253                         mdrun->dim.y=atof(word[2]);
 254                         mdrun->dim.z=atof(word[3]);
 255                         if(strncmp(word[4],"0",1))
 256                                 mdrun->vis=TRUE;
 257                 }
 258                 else if(!strncmp(word[0],"pbc",3)) {
 259                         if(strncmp(word[1],"0",1))
 260                                 mdrun->pbcx=TRUE;
 261                         else
 262                                 mdrun->pbcx=FALSE;
 263                         if(strncmp(word[2],"0",1))
 264                                 mdrun->pbcy=TRUE;
 265                         else
 266                                 mdrun->pbcy=FALSE;
 267                         if(strncmp(word[3],"0",1))
 268                                 mdrun->pbcz=TRUE;
 269                         else
 270                                 mdrun->pbcz=FALSE;
 271                 }
 272                 else if(!strncmp(word[0],"temperature",11))
 273                         mdrun->temperature=atof(word[1]);
 274                 else if(!strncmp(word[0],"pressure",8))
 275                         mdrun->pressure=atof(word[1]);
 276                 else if(!strncmp(word[0],"lattice",7)) {
 277                         if(!strncmp(word[1],"zincblende",10))
 278                                 mdrun->lattice=ZINCBLENDE;
 279                         if(!strncmp(word[1],"fcc",3))
 280                                 mdrun->lattice=FCC;
 281                         if(!strncmp(word[1],"diamond",7))
 282                                 mdrun->lattice=DIAMOND;
 283                         if(!strncmp(word[1],"none",4))
 284                                 mdrun->lattice=NONE;
 285                         if(wcnt==3)
 286                                 mdrun->lc=atof(word[2]);
 287                 }
 288                 else if(!strncmp(word[0],"element1",8)) {
 289                         mdrun->element1=atoi(word[1]);
 290                 }
 291                 else if(!strncmp(word[0],"element2",8)) {
 292                         mdrun->element2=atoi(word[1]);
 293                 }
 294                 else if(!strncmp(word[0],"fill",6)) {
 295                         // default values
 296                         fp.fill_element=mdrun->element1;
 297                         fp.fill_brand=0;
 298                         fp.lattice=mdrun->lattice;
 299                         fp.p_params.type=0;
 300                         fp.d_params.type=0;
 301                         fp.d_params.stype=0;
 302                         // parse fill command
 303                         i=1;
 304                         while(i<wcnt) {
 305                                 if(!strncmp(word[i],"lc",2)) {
 306                                         fp.lx=atoi(word[++i]);
 307                                         fp.ly=atoi(word[++i]);
 308                                         fp.lz=atoi(word[++i]);
 309                                         fp.lc=atof(word[++i]);
 310                                         mdrun->lc=fp.lc;
 311                                         continue;
 312                                 }
 313                                 if(!strncmp(word[i],"eb",2)) {
 314                                         fp.fill_element=atoi(word[++i]);
 315                                         fp.fill_brand=atoi(word[++i]);
 316                                         continue;
 317                                 }
 318                                 if(word[i][0]=='p') {
 319                                         i+=1;
 320                                         switch(word[i][0]) {
 321                                         case 'i':
 322                                                 if(word[i][1]=='r')
 323                                                 fp.p_params.type=PART_INSIDE_R;
 324                                                 else
 325                                                 fp.p_params.type=PART_INSIDE_D;
 326                                                 break;
 327                                         case 'o':
 328                                                 if(word[i][1]=='r')
 329                                                 fp.p_params.type=PART_OUTSIDE_R;
 330                                                 else
 331                                                 fp.p_params.type=PART_OUTSIDE_D;
 332                                                 break;
 333                                         default:
 334                                                 break;
 335                                         }
 336                                         if((fp.p_params.type==PART_INSIDE_R)||
 337                                           (fp.p_params.type==PART_OUTSIDE_R)) {
 338                                                 fp.p_params.r=atof(word[++i]);
 339                                                 fp.p_params.p.x=atof(word[++i]);
 340                                                 fp.p_params.p.y=atof(word[++i]);
 341                                                 fp.p_params.p.z=atof(word[++i]);
 342                                         }
 343                                         if((fp.p_params.type==PART_INSIDE_D)||
 344                                            (fp.p_params.type==PART_OUTSIDE_D)) {
 345                                                 fp.p_params.p.x=atof(word[++i]);
 346                                                 fp.p_params.p.y=atof(word[++i]);
 347                                                 fp.p_params.p.z=atof(word[++i]);
 348                                                 fp.p_params.d.x=atof(word[++i]);
 349                                                 fp.p_params.d.y=atof(word[++i]);
 350                                                 fp.p_params.d.z=atof(word[++i]);
 351                                         }
 352                                         continue;
 353                                 }
 354                                 if(word[i][0]=='d') {
 355                                         switch(word[++i][0]) {
 356                                                 case '0':
 357
 358                                 fp.d_params.type=DEFECT_TYPE_0D;
 359                                 if(!strncmp(word[i+1],"dbx",3)) {
 360                                         fp.d_params.stype=DEFECT_STYPE_DB_X;
 361                                 }
 362                                 if(!strncmp(word[i+1],"dby",3)) {
 363                                         fp.d_params.stype=DEFECT_STYPE_DB_Y;
 364                                 }
 365                                 if(!strncmp(word[i+1],"dbz",3)) {
 366                                         fp.d_params.stype=DEFECT_STYPE_DB_Z;
 367                                 }
 368                                 if(!strncmp(word[i+1],"dbr",3)) {
 369                                         fp.d_params.stype=DEFECT_STYPE_DB_R;
 370                                 }
 371                                 i+=1;
 372                                 fp.d_params.od=atof(word[++i]);
 373                                 fp.d_params.dd=atof(word[++i]);
 374                                 fp.d_params.element=atoi(word[++i]);
 375                                 fp.d_params.brand=atoi(word[++i]);
 376                                 // parsed in future
 377                 fp.d_params.attr=ATOM_ATTR_HB|ATOM_ATTR_VA;
 378                 fp.d_params.attr|=ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
 379                                 break;
 380
 381                                                 case '1':
 382                                 fp.d_params.type=DEFECT_TYPE_1D;
 383                                 break;
 384                                                 case '2':
 385                                 fp.d_params.type=DEFECT_TYPE_2D;
 386                                 break;
 387                                                 case '3':
 388                                 fp.d_params.type=DEFECT_TYPE_3D;
 389                                 break;
 390                                                 default:
 391                                                         break;
 392                                         }
 393                                         continue;
 394
 395                                 }
 396                                 i+=1;
 397                         }
 398                         add_stage(mdrun,STAGE_FILL,&fp);
 399                 }
 400                 else if(!strncmp(word[0],"thermal_init",12)) {
 401                         add_stage(mdrun,STAGE_THERMAL_INIT,NULL);
 402                 }
 403                 else if(!strncmp(word[0],"aattr",5)) {
 404                         // for aatrib line we need a special stage
 405                         // containing one schedule of 0 loops ...
 406                         for(i=0;i<strlen(word[1]);i++) {
 407                                 switch(word[1][i]) {
 408                                         case 't':
 409                                                 cap.type|=CHAATTR_TOTALV;
 410                                                 break;
 411                                         case 'r':
 412                                                 cap.type|=CHAATTR_REGION;
 413                                                 break;
 414                                         case 'e':
 415                                                 cap.type|=CHAATTR_ELEMENT;
 416                                                 break;
 417                                         default:
 418                                                 break;
 419                                 }
 420                         }
 421                         i=2;
 422                         if(cap.type&CHAATTR_REGION) {
 423                                 cap.x0=atof(word[2]);
 424                                 cap.y0=atof(word[3]);
 425                                 cap.z0=atof(word[4]);
 426                                 cap.x1=atof(word[5]);
 427                                 cap.y1=atof(word[6]);
 428                                 cap.z1=atof(word[7]);
 429                                 i+=6;
 430                         }
 431                         if(cap.type&CHAATTR_ELEMENT) {
 432                                 cap.element=atoi(word[i]);
 433                                 i+=1;
 434                         }
 435                         for(o=0;o<strlen(word[i]);o++) {
 436                                 switch(word[i][o]) {
 437                                         case 'b':
 438                                                 cap.attr|=ATOM_ATTR_VB;
 439                                                 break;
 440                                         case 'h':
 441                                                 cap.attr|=ATOM_ATTR_HB;
 442                                                 break;
 443                                         case 'v':
 444                                                 cap.attr|=ATOM_ATTR_VA;
 445                                                 break;
 446                                         case 'f':
 447                                                 cap.attr|=ATOM_ATTR_FP;
 448                                                 break;
 449                                         case '1':
 450                                                 cap.attr|=ATOM_ATTR_1BP;
 451                                                 break;
 452                                         case '2':
 453                                                 cap.attr|=ATOM_ATTR_2BP;
 454                                                 break;
 455                                         case '3':
 456                                                 cap.attr|=ATOM_ATTR_3BP;
 457                                                 break;
 458                                         default:
 459                                                 break;
 460                                 }
 461                         }
 462                         add_stage(mdrun,STAGE_CHAATTR,&cap);
 463                 }
 464                 else if(!strncmp(word[0],"sattr",5)) {
 465                         // for satrib line we need a special stage
 466                         // containing one schedule of 0 loops ...
 467                         csp.type=0;
 468                         for(i=1;i<wcnt;i++) {
 469                                 if(!strncmp(word[i],"pctrl",5)) {
 470                                         csp.ptau=atof(word[++i]);
 471                                         if(csp.ptau>0)
 472                                                 csp.ptau=0.01/(csp.ptau*GPA);
 473                                         csp.type|=CHSATTR_PCTRL;
 474                                 }
 475                                 if(!strncmp(word[i],"tctrl",5)) {
 476                                         csp.ttau=atof(word[++i]);
 477                                         csp.type|=CHSATTR_TCTRL;
 478                                 }
 479                                 if(!strncmp(word[i],"prelax",6)) {
 480                                         csp.dp=atof(word[++i])*BAR;
 481                                         csp.type|=CHSATTR_PRELAX;
 482                                 }
 483                                 if(!strncmp(word[i],"trelax",6)) {
 484                                         csp.dt=atof(word[++i]);
 485                                         csp.type|=CHSATTR_TRELAX;
 486                                 }
 487                                 if(!strncmp(word[i],"rsteps",6)) {
 488                                         csp.rsteps=atoi(word[++i]);
 489                                         csp.type|=CHSATTR_RSTEPS;
 490                                 }
 491                                 if(!strncmp(word[i],"avgrst",6)) {
 492                                         csp.avgrst=atoi(word[++i]);
 493                                         csp.type|=CHSATTR_AVGRST;
 494                                 }
 495                         }
 496                         add_stage(mdrun,STAGE_CHSATTR,&csp);
 497                 }
 498                 else if(!strncmp(word[0],"prerun",6))
 499                         mdrun->prerun=atoi(word[1]);
 500                 else if(!strncmp(word[0],"avgskip",7))
 501                         mdrun->avgskip=atoi(word[1]);
 502                 else if(!strncmp(word[0],"elog",4))
 503                         mdrun->elog=atoi(word[1]);
 504                 else if(!strncmp(word[0],"tlog",4))
 505                         mdrun->tlog=atoi(word[1]);
 506                 else if(!strncmp(word[0],"plog",4))
 507                         mdrun->plog=atoi(word[1]);
 508                 else if(!strncmp(word[0],"vlog",4))
 509                         mdrun->vlog=atoi(word[1]);
 510                 else if(!strncmp(word[0],"save",4))
 511                         mdrun->save=atoi(word[1]);
 512                 else if(!strncmp(word[0],"visualize",9))
 513                         mdrun->visualize=atoi(word[1]);
 514                 else if(!strncmp(word[0],"stage",5)) {
 515                         // for every stage line, add a stage
 516                         if(!strncmp(word[1],"displace",8)) {
 517                                 dap.nr=atoi(word[2]);
 518                                 dap.dx=atof(word[3]);
 519                                 dap.dy=atof(word[4]);
 520                                 dap.dz=atof(word[5]);
 521                                 add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
 522                         }
 523                         else if(!strncmp(word[1],"del_atoms",9)) {
 524                                 delp.o.x=atof(word[2]);
 525                                 delp.o.y=atof(word[3]);
 526                                 delp.o.z=atof(word[4]);
 527                                 delp.r=atof(word[5]);
 528                                 add_stage(mdrun,STAGE_DEL_ATOMS,&delp);
 529                         }
 530                         else if(!strncmp(word[1],"mod_atoms",8)) {
 531                                 i=2;
 532                                 while(i<wcnt) {
 533                                         if(!strncmp(word[i],"t",1)) {
 534                                                 map.tag=atoi(word[++i]);
 535                                                 i+=1;
 536                                         }
 537                                         if(!strncmp(word[i],"ekin",5)) {
 538                                                 map.ekin.x=atof(word[++i])*EV;
 539                                                 map.ekin.y=atof(word[++i])*EV;
 540                                                 map.ekin.z=atof(word[++i])*EV;
 541                                                 i+=1;
 542                                         }
 543                                 }
 544                                 add_stage(mdrun,STAGE_MODIFY_ATOMS,&map);
 545                         }
 546                         else if(!strncmp(word[1],"ins_atoms",9)) {
 547                                 iap.ins_steps=atoi(word[2]);
 548                                 iap.ins_atoms=atoi(word[3]);
 549                                 iap.element=atoi(word[4]);
 550                                 iap.brand=atoi(word[5]);
 551                                 for(i=0;i<strlen(word[6]);i++) {
 552                                         switch(word[6][i]) {
 553                                                 case 'b':
 554                                                         iap.attr|=ATOM_ATTR_VB;
 555                                                         break;
 556                                                 case 'h':
 557                                                         iap.attr|=ATOM_ATTR_HB;
 558                                                         break;
 559                                                 case 'v':
 560                                                         iap.attr|=ATOM_ATTR_VA;
 561                                                         break;
 562                                                 case 'f':
 563                                                         iap.attr|=ATOM_ATTR_FP;
 564                                                         break;
 565                                                 case '1':
 566                                                         iap.attr|=ATOM_ATTR_1BP;
 567                                                         break;
 568                                                 case '2':
 569                                                         iap.attr|=ATOM_ATTR_2BP;
 570                                                         break;
 571                                                 case '3':
 572                                                         iap.attr|=ATOM_ATTR_3BP;
 573                                                         break;
 574                                                 default:
 575                                                         break;
 576                                         }
 577                                 }
 578                                 switch(word[7][0]) {
 579                                         // insertion types
 580                                         case 'p':
 581                                                 iap.type=INS_POS;
 582                                                 iap.x0=atof(word[8]);
 583                                                 iap.y0=atof(word[9]);
 584                                                 iap.z0=atof(word[10]);
 585                                                 break;
 586                                         case 'r':
 587                                                 switch(word[8][0]) {
 588
 589                                                 case 't':
 590                                                         iap.type=INS_TOTAL;
 591                                                         iap.cr=atof(word[9]);
 592                                                         break;
 593                                                 case 'r':
 594                                                         iap.type=INS_RECT;
 595                                                         iap.x0=atof(word[9]);
 596                                                         iap.y0=atof(word[10]);
 597                                                         iap.z0=atof(word[11]);
 598                                                         iap.x1=atof(word[12]);
 599                                                         iap.y1=atof(word[13]);
 600                                                         iap.z1=atof(word[14]);
 601                                                         iap.cr=atof(word[15]);
 602                                                         break;
 603                                                 case 's':
 604                                                         iap.type=INS_SPHERE;
 605                                                         iap.x0=atof(word[9]);
 606                                                         iap.y0=atof(word[10]);
 607                                                         iap.z0=atof(word[11]);
 608                                                         iap.x1=atof(word[12]);
 609                                                         iap.cr=atof(word[13]);
 610                                                         break;
 611                                                 default:
 612                                                         break;
 613                                                 }
 614                                         default:
 615                                                 break;
 616                                 }
 617                                 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
 618                         }
 619
 620
 621                         // HERE WE GO ...
 622
 623                         else if(!strncmp(word[1],"ins_m_atoms",11)) {
 624                                 imp.element1=atoi(word[2]);
 625                                 imp.element2=atoi(word[3]);
 626                                 imp.amount1=atoi(word[4]);
 627                                 imp.amount2=atoi(word[5]);
 628                                 imp.brand1=atoi(word[6]);
 629                                 imp.brand2=atoi(word[7]);
 630                                 imp.crmin=atof(word[8]);
 631                                 imp.crmax=atof(word[9]);
 632                                 /* do this later ...
 633                                 for(i=0;i<strlen(word[8]);i++) {
 634                                         switch(word[8][i]) {
 635                                                 case 'b':
 636                                                         imp.attr|=ATOM_ATTR_VB;
 637                                                         break;
 638                                                 case 'h':
 639                                                         imp.attr|=ATOM_ATTR_HB;
 640                                                         break;
 641                                                 case 'v':
 642                                                         imp.attr|=ATOM_ATTR_VA;
 643                                                         break;
 644                                                 case 'f':
 645                                                         imp.attr|=ATOM_ATTR_FP;
 646                                                         break;
 647                                                 case '1':
 648                                                         imp.attr|=ATOM_ATTR_1BP;
 649                                                         break;
 650                                                 case '2':
 651                                                         imp.attr|=ATOM_ATTR_2BP;
 652                                                         break;
 653                                                 case '3':
 654                                                         imp.attr|=ATOM_ATTR_3BP;
 655                                                         break;
 656                                                 default:
 657                                                         break;
 658                                         }
 659                                 }
 660                                 */
 661                                 imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 662                                 imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 663                                 add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
 664                         }
 665
 666
 667
 668
 669
 670                         else if(!strncmp(word[1],"continue",8)) {
 671                                 cp.runs=atoi(word[2]);
 672                                 add_stage(mdrun,STAGE_CONTINUE,&cp);
 673                         }
 674                         else if(!strncmp(word[1],"anneal",6)) {
 675                                 ap.count=0;
 676                                 ap.runs=atoi(word[2]);
 677                                 ap.dt=atof(word[3]);
 678                                 ap.interval=atoi(word[4]);
 679                                 add_stage(mdrun,STAGE_ANNEAL,&ap);
 680                         }
 681                         else if(!strncmp(word[1],"set_temp",8)) {
 682                                 if(word[2][0]=='c') {
 683                                         stp.type=SET_TEMP_CURRENT;
 684                                         stp.val=0.0;
 685                                 }
 686                                 else {
 687                                         stp.type=SET_TEMP_VALUE;
 688                                         stp.val=atof(word[2]);
 689                                 }
 690                                 add_stage(mdrun,STAGE_SET_TEMP,&stp);
 691                         }
 692                         else if(!strncmp(word[1],"set_timestep",12)) {
 693                                 stsp.tau=atof(word[2]);
 694                                 add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
 695                         }
 696                         else {
 697                                 printf("%s unknown stage type: %s\n",
 698                                        ME,word[1]);
 699                                 return -1;
 700                         }
 701                 }
 702                 else {
 703                         printf("%s unknown keyword '%s', skipped!\n",
 704                                ME,word[0]);
 705                         continue;
 706                 }
 707         }
 708
 709         /* close file */
 710         close(fd);
 711
 712         return 0;
 713 }
 714
 715 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
 716
 717         double delta;
 718
 719         if(!(mdrun->sattr&SATTR_PRELAX)) {
 720                 return TRUE;
 721         }
 722
 723         delta=moldyn->p_avg-moldyn->p_ref;
 724
 725         if(delta<0)
 726                 delta=-delta;
 727
 728         if(delta>mdrun->dp)
 729                 return FALSE;
 730
 731         return TRUE;
 732 }
 733
 734 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 735
 736         double delta;
 737
 738         if(!(mdrun->sattr&SATTR_TRELAX))
 739                 return TRUE;
 740
 741         delta=moldyn->t_avg-moldyn->t_ref;
 742
 743         if(delta<0)
 744                 delta=-delta;
 745
 746         if(delta>mdrun->dt)
 747                 return FALSE;
 748
 749         return TRUE;
 750 }
 751
 752 int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
 753
 754         t_displace_atom_params *dap;
 755         t_stage *stage;
 756         t_atom *atom;
 757
 758         stage=mdrun->stage.current->data;
 759         dap=stage->params;
 760
 761         atom=&(moldyn->atom[dap->nr]);
 762         atom->r.x+=dap->dx;
 763         atom->r.y+=dap->dy;
 764         atom->r.z+=dap->dz;
 765
 766         return 0;
 767 }
 768
 769 int del_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 770
 771         t_stage *stage;
 772         t_del_atoms_params *delp;
 773         int i;
 774         t_3dvec dist;
 775
 776         stage=mdrun->stage.current->data;
 777         delp=stage->params;
 778
 779         for(i=0;i<moldyn->count;i++) {
 780                 v3_sub(&dist,&(delp->o),&(moldyn->atom[i].r));
 781 //printf("%d ----> %f %f %f = %f | %f\n",i,dist.x,dist.y,dist.z,v3_absolute_square(&dist),delp->r*delp->r);
 782                 if(v3_absolute_square(&dist)<=(delp->r*delp->r)) {
 783                         del_atom(moldyn,moldyn->atom[i].tag);
 784                         printf("%s atom deleted: %d %d %d\n",ME,
 785                                moldyn->atom[i].tag,moldyn->atom[i].element,
 786                                moldyn->atom[i].brand);
 787                 }
 788         }
 789
 790         return 0;
 791 }
 792
 793 int modify_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 794
 795         t_modify_atoms_params *map;
 796         t_stage *stage;
 797         t_atom *atom;
 798         t_3dvec v;
 799         int i;
 800
 801         atom=moldyn->atom;
 802         stage=mdrun->stage.current->data;
 803         map=stage->params;
 804         v.x=0.0; v.y=0.0; v.z=0.0;
 805
 806         for(i=0;i<moldyn->count;i++) {
 807                 if(atom[i].tag==map->tag) {
 808                         v.x=sqrt(2.0*fabs(map->ekin.x)/atom[i].mass);
 809                         if(map->ekin.x<0.0)
 810                                 v.x=-v.x;
 811                         v.y=sqrt(2.0*fabs(map->ekin.y)/atom[i].mass);
 812                         if(map->ekin.y<0.0)
 813                                 v.y=-v.y;
 814                         v.z=sqrt(2.0*fabs(map->ekin.z)/atom[i].mass);
 815                         if(map->ekin.z<0.0)
 816                                 v.z=-v.z;
 817                         v3_copy(&(atom[i].v),&v);
 818                         printf("%s atom modified: v = (%f %f %f)\n",
 819                                ME,v.x,v.y,v.z);
 820                 }
 821         }
 822
 823         return 0;
 824 }
 825
 826 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 827
 828         t_insert_atoms_params *iap;
 829         t_stage *stage;
 830         t_atom *atom;
 831         t_3dvec r,v,dist;
 832         double d,dmin,o;
 833         int cnt,i;
 834         double x,y,z;
 835         double x0,y0,z0;
 836         u8 cr_check,run;
 837
 838         stage=mdrun->stage.current->data;
 839         iap=stage->params;
 840
 841         cr_check=FALSE;
 842
 843         v.x=0.0; v.y=0.0; v.z=0.0;
 844         x=0; y=0; z=0;
 845         o=0; dmin=0;
 846
 847         switch(mdrun->lattice) {
 848                 case CUBIC:
 849                         o=0.5*mdrun->lc;
 850                         break;
 851                 case FCC:
 852                         o=0.25*mdrun->lc;
 853                         break;
 854                 case DIAMOND:
 855                 case ZINCBLENDE:
 856                         o=0.125*mdrun->lc;
 857                         break;
 858                 default:
 859                         break;
 860         }
 861
 862         switch(iap->type) {
 863                 case INS_TOTAL:
 864                         x=moldyn->dim.x;
 865                         x0=-x/2.0;
 866                         y=moldyn->dim.y;
 867                         y0=-y/2.0;
 868                         z=moldyn->dim.z;
 869                         z0=-z/2.0;
 870                         cr_check=TRUE;
 871                         break;
 872                 case INS_RECT:
 873                         x=iap->x1-iap->x0;
 874                         x0=iap->x0;
 875                         y=iap->y1-iap->y0;
 876                         y0=iap->y0;
 877                         z=iap->z1-iap->z0;
 878                         z0=iap->z0;
 879                         cr_check=TRUE;
 880                         break;
 881                 case INS_SPHERE:
 882                         x=2.0*iap->x1;
 883                         x0=iap->x0-iap->x1;
 884                         y=x;
 885                         y0=iap->y0-iap->x1;
 886                         z=x;
 887                         z0=iap->z0-iap->x1;
 888                         cr_check=TRUE;
 889                         break;
 890                 case INS_POS:
 891                         x0=iap->x0;
 892                         y0=iap->y0;
 893                         z0=iap->z0;
 894                         cr_check=FALSE;
 895                         break;
 896                 default:
 897                         printf("%s unknown insertion mode: %02x\n",
 898                                ME,iap->type);
 899                         return -1;
 900         }
 901
 902         cnt=0;
 903         while(cnt<iap->ins_atoms) {
 904                 run=1;
 905                 while(run) {
 906                         if(iap->type!=INS_POS) {
 907                                 r.x=rand_get_double(&(moldyn->random))*x;
 908                                 r.y=rand_get_double(&(moldyn->random))*y;
 909                                 r.z=rand_get_double(&(moldyn->random))*z;
 910                         }
 911                         else {
 912                                 r.x=0.0;
 913                                 r.y=0.0;
 914                                 r.z=0.0;
 915                         }
 916                         r.x+=x0;
 917                         r.y+=y0;
 918                         r.z+=z0;
 919                         // offset
 920                         if(iap->type!=INS_TOTAL) {
 921                                 r.x+=o;
 922                                 r.y+=o;
 923                                 r.z+=o;
 924                         }
 925                         run=0;
 926                         if(cr_check==TRUE) {
 927                                 dmin=1000;      // for sure too high!
 928                                 for(i=0;i<moldyn->count;i++) {
 929                                         atom=&(moldyn->atom[i]);
 930                                         v3_sub(&dist,&(atom->r),&r);
 931                                         check_per_bound(moldyn,&dist);
 932                                         d=v3_absolute_square(&dist);
 933                                         if(d<(iap->cr*iap->cr)) {
 934                                                 run=1;
 935                                                 break;
 936                                         }
 937                                         if(d<dmin)
 938                                                 dmin=d;
 939                                 }
 940                         }
 941                         if(iap->type==INS_SPHERE) {
 942                                 if((r.x-iap->x0)*(r.x-iap->x0)+
 943                                    (r.y-iap->y0)*(r.y-iap->y0)+
 944                                    (r.z-iap->z0)*(r.z-iap->z0)>
 945                                    (iap->x1*iap->x1)) {
 946                                         run=1;
 947                                 }
 948                         }
 949                 }
 950                 add_atom(moldyn,iap->element,
 951                          iap->brand,iap->attr,&r,&v);
 952                 printf("%s atom inserted (%d/%d): %f %f %f\n",
 953                        ME,(iap->cnt_steps+1)*iap->ins_atoms,
 954                        iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
 955                 printf("  attributes: ");
 956                 if(iap->attr&ATOM_ATTR_VB)
 957                         printf("b ");
 958                 if(iap->attr&ATOM_ATTR_HB)
 959                         printf("h ");
 960                 if(iap->attr&ATOM_ATTR_VA)
 961                         printf("v ");
 962                 if(iap->attr&ATOM_ATTR_FP)
 963                         printf("f ");
 964                 if(iap->attr&ATOM_ATTR_1BP)
 965                         printf("1 ");
 966                 if(iap->attr&ATOM_ATTR_2BP)
 967                         printf("2 ");
 968                 if(iap->attr&ATOM_ATTR_3BP)
 969                         printf("3 ");
 970                 printf("\n");
 971                 printf("  d2 = %f/%f\n",dmin,iap->cr*iap->cr);
 972                 cnt+=1;
 973         }
 974
 975         return 0;
 976 }
 977
 978 int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 979
 980         t_stage *stage;
 981         t_insert_mixed_atoms_params *imp;
 982         t_atom *atom;
 983         double x,x0,y,y0,z,z0;
 984         double dmin,d,cmin,cmax;
 985         u8 retry;
 986         t_3dvec r,v,dist;
 987         int i;
 988
 989
 990         stage=mdrun->stage.current->data;
 991         imp=stage->params;
 992
 993         x=moldyn->dim.x;
 994         x0=-x/2.0;
 995         y=moldyn->dim.y;
 996         y0=-y/2.0;
 997         z=moldyn->dim.z;
 998         z0=-z/2.0;
 999
1000         v.x=0.0;
1001         v.y=0.0;
1002         v.z=0.0;
1003
1004         cmin=imp->crmin*imp->crmin;
1005         cmax=imp->crmax*imp->crmax;
1006
1007         while(imp->amount1|imp->amount2) {
1008                 if(imp->amount1) {
1009                         retry=1;
1010                         while(retry) {
1011                                 retry=0;
1012                                 r.x=rand_get_double(&(moldyn->random))*x;
1013                                 r.y=rand_get_double(&(moldyn->random))*y;
1014                                 r.z=rand_get_double(&(moldyn->random))*z;
1015                                 r.x+=x0;
1016                                 r.y+=y0;
1017                                 r.z+=z0;
1018                                 dmin=1000.0;    // for sure too high!
1019                                 for(i=0;i<moldyn->count;i++) {
1020                                         atom=&(moldyn->atom[i]);
1021                                         v3_sub(&dist,&(atom->r),&r);
1022                                         check_per_bound(moldyn,&dist);
1023                                         d=v3_absolute_square(&dist);
1024                                         if(d<cmin) {
1025                                                 retry=1;
1026                                                 break;
1027                                         }
1028                                         if(d<dmin)
1029                                                 dmin=d;
1030                                 }
1031                                 if(dmin!=1000.0)
1032                                         if(dmin>cmax)
1033                                                 retry=1;
1034                         }
1035                         add_atom(moldyn,imp->element1,
1036                                  imp->brand1,imp->attr1,&r,&v);
1037                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
1038                                ME,imp->amount1,r.x,r.y,r.z);
1039                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
1040                         imp->amount1-=1;
1041                 }
1042                 if(imp->amount2) {
1043                         retry=1;
1044                         while(retry) {
1045                                 retry=0;
1046                                 r.x=rand_get_double(&(moldyn->random))*x;
1047                                 r.y=rand_get_double(&(moldyn->random))*y;
1048                                 r.z=rand_get_double(&(moldyn->random))*z;
1049                                 r.x+=x0;
1050                                 r.y+=y0;
1051                                 r.z+=z0;
1052                                 dmin=1000.0;    // for sure too high!
1053                                 for(i=0;i<moldyn->count;i++) {
1054                                         atom=&(moldyn->atom[i]);
1055                                         v3_sub(&dist,&(atom->r),&r);
1056                                         check_per_bound(moldyn,&dist);
1057                                         d=v3_absolute_square(&dist);
1058                                         if(d<cmin) {
1059                                                 retry=1;
1060                                                 break;
1061                                         }
1062                                         if(d<dmin)
1063                                                 dmin=d;
1064                                 }
1065                                 if(dmin!=1000.0)
1066                                         if(dmin>cmax)
1067                                                 retry=1;
1068                         }
1069                         add_atom(moldyn,imp->element2,
1070                                  imp->brand2,imp->attr2,&r,&v);
1071                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
1072                                ME,imp->amount2,r.x,r.y,r.z);
1073                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
1074                         imp->amount2-=1;
1075                 }
1076         }
1077
1078         return 0;
1079 }
1080
1081 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
1082
1083         t_stage *stage;
1084         t_chaattr_params *cap;
1085         t_atom *atom;
1086         int i;
1087
1088         stage=mdrun->stage.current->data;
1089         cap=stage->params;
1090
1091         for(i=0;i<moldyn->count;i++) {
1092                 atom=&(moldyn->atom[i]);
1093                 if(cap->type&CHAATTR_ELEMENT) {
1094                         if(cap->element!=atom->element)
1095                                 continue;
1096                 }
1097                 if(cap->type&CHAATTR_REGION) {
1098                         if(cap->x0>atom->r.x)
1099                                 continue;
1100                         if(cap->y0>atom->r.y)
1101                                 continue;
1102                         if(cap->z0>atom->r.z)
1103                                 continue;
1104                         if(cap->x1<atom->r.x)
1105                                 continue;
1106                         if(cap->y1<atom->r.y)
1107                                 continue;
1108                         if(cap->z1<atom->r.z)
1109                                 continue;
1110                 }
1111                 printf("  changing attributes of atom %d (0x%x)\n",i,cap->attr);
1112                 atom->attr=cap->attr;
1113         }
1114
1115         printf("\n\n");
1116
1117         return 0;
1118 }
1119
1120 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
1121
1122         t_stage *stage;
1123         t_chsattr_params *csp;
1124
1125         stage=mdrun->stage.current->data;
1126         csp=stage->params;
1127
1128         if(csp->type&CHSATTR_PCTRL) {
1129                 if(csp->ptau>0)
1130                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
1131                 else
1132                         set_p_scale(moldyn,P_SCALE_NONE,1.0);
1133         }
1134         if(csp->type&CHSATTR_TCTRL) {
1135                 if(csp->ttau>0)
1136                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
1137                 else
1138                         set_t_scale(moldyn,T_SCALE_NONE,1.0);
1139         }
1140         if(csp->type&CHSATTR_PRELAX) {
1141                 if(csp->dp<0)
1142                         mdrun->sattr&=(~(SATTR_PRELAX));
1143                 else
1144                         mdrun->sattr|=SATTR_PRELAX;
1145                 mdrun->dp=csp->dp;
1146         }
1147         if(csp->type&CHSATTR_TRELAX) {
1148                 if(csp->dt<0)
1149                         mdrun->sattr&=(~(SATTR_TRELAX));
1150                 else
1151                         mdrun->sattr|=SATTR_TRELAX;
1152                 mdrun->dt=csp->dt;
1153         }
1154         if(csp->type&CHSATTR_AVGRST) {
1155                 if(csp->avgrst)
1156                         mdrun->sattr|=SATTR_AVGRST;
1157                 else
1158                         mdrun->sattr&=(~(SATTR_AVGRST));
1159         }
1160         if(csp->type&CHSATTR_RSTEPS) {
1161                 mdrun->relax_steps=csp->rsteps;
1162         }
1163
1164         return 0;
1165 }
1166
1167 #define stage_print(m)  if(!(stage->executed)) \
1168                                 printf("%s",m)
1169
1170 int mdrun_hook(void *ptr1,void *ptr2) {
1171
1172         t_moldyn *moldyn;
1173         t_mdrun *mdrun;
1174         t_stage *stage;
1175         t_list *sl;
1176         int steps;
1177         u8 change_stage;
1178         t_3dvec o;
1179
1180         t_insert_atoms_params *iap;
1181         t_insert_mixed_atoms_params *imp;
1182         t_continue_params *cp;
1183         t_anneal_params *ap;
1184         t_set_temp_params *stp;
1185         t_set_timestep_params *stsp;
1186         t_fill_params *fp;
1187
1188         moldyn=ptr1;
1189         mdrun=ptr2;
1190
1191         sl=&(mdrun->stage);
1192
1193         change_stage=FALSE;
1194
1195         /* return immediately if there are no more stage */
1196         if(sl->current==NULL)
1197                 return 0;
1198
1199         /* get stage description */
1200         stage=sl->current->data;
1201
1202         /* steps in next schedule */
1203         steps=mdrun->relax_steps;
1204
1205         /* check whether relaxation steps are necessary */
1206         if((check_pressure(moldyn,mdrun)==TRUE)&\
1207            (check_temperature(moldyn,mdrun)==TRUE)) {
1208
1209                 /* be verbose */
1210                 stage_print("\n###########################\n");
1211                 stage_print("# [mdrun] executing stage #\n");
1212                 stage_print("###########################\n\n");
1213
1214                 /* stage specific stuff */
1215                 switch(stage->type) {
1216                         case STAGE_DISPLACE_ATOM:
1217                                 stage_print("  -> displace atom\n\n");
1218                                 displace_atom(moldyn,mdrun);
1219                                 change_stage=TRUE;
1220                                 break;
1221                         case STAGE_DEL_ATOMS:
1222                                 stage_print(" -> del atoms\n\n");
1223                                 del_atoms(moldyn,mdrun);
1224                                 change_stage=TRUE;
1225                                 break;
1226                         case STAGE_MODIFY_ATOMS:
1227                                 stage_print(" -> modify atoms\n\n");
1228                                 modify_atoms(moldyn,mdrun);
1229                                 change_stage=TRUE;
1230                                 break;
1231                         case STAGE_INSERT_ATOMS:
1232                                 stage_print("  -> insert atoms\n\n");
1233                                 iap=stage->params;
1234                                 if(iap->cnt_steps==iap->ins_steps) {
1235                                         change_stage=TRUE;
1236                                         break;
1237                                 }
1238                                 insert_atoms(moldyn,mdrun);
1239                                 iap->cnt_steps+=1;
1240                                 break;
1241
1242
1243
1244                         case STAGE_INSERT_MIXED_ATOMS:
1245                                 stage_print("  -> insert mixed atoms\n\n");
1246                                 imp=stage->params;
1247                                 insert_mixed_atoms(moldyn,mdrun);
1248                                 change_stage=TRUE;
1249                                 break;
1250
1251
1252
1253                         case STAGE_CONTINUE:
1254                                 stage_print("  -> continue\n\n");
1255                                 if(stage->executed==TRUE) {
1256                                         change_stage=TRUE;
1257                                         break;
1258                                 }
1259                                 cp=stage->params;
1260                                 steps=cp->runs;
1261                                 break;
1262                         case STAGE_ANNEAL:
1263                                 stage_print("  -> anneal\n\n");
1264                                 ap=stage->params;
1265                                 if(ap->count==ap->runs) {
1266                                         change_stage=TRUE;
1267                                         break;
1268                                 }
1269                                 if(moldyn->t_ref+ap->dt>=0.0)
1270                                         set_temperature(moldyn,
1271                                                         moldyn->t_ref+ap->dt);
1272                                 ap->count+=1;
1273                                 steps=ap->interval;
1274                                 break;
1275                         case STAGE_CHAATTR:
1276                                 stage_print("  -> change atom attributes\n\n");
1277                                 chaatr(moldyn,mdrun);
1278                                 change_stage=TRUE;
1279                                 break;
1280                         case STAGE_CHSATTR:
1281                                 stage_print("  -> change sys attributes\n\n");
1282                                 chsattr(moldyn,mdrun);
1283                                 change_stage=TRUE;
1284                                 break;
1285                         case STAGE_SET_TEMP:
1286                                 stage_print("  -> set temperature\n\n");
1287                                 stp=stage->params;
1288                                 if(stp->type&SET_TEMP_CURRENT) {
1289                                         set_temperature(moldyn,moldyn->t_avg);
1290                                 }
1291                                 else {
1292                                         set_temperature(moldyn,stp->val);
1293                                 }
1294                                 change_stage=TRUE;
1295                                 break;
1296                         case STAGE_SET_TIMESTEP:
1297                                 stage_print("  -> set timestep\n\n");
1298                                 stsp=stage->params;
1299                                 mdrun->timestep=stsp->tau;
1300                                 change_stage=TRUE;
1301                                 break;
1302                         case STAGE_FILL:
1303                                 stage_print("  -> fill lattice\n\n");
1304                                 fp=stage->params;
1305                                 switch(fp->lattice) {
1306                                         case ZINCBLENDE:
1307
1308                                         o.x=0.5*0.25*fp->lc;
1309                                         o.y=o.x;
1310                                         o.z=o.x;
1311                                         create_lattice(moldyn,
1312                                                        FCC,fp->lc,
1313                                                        mdrun->element1,
1314                                                        DEFAULT_ATOM_ATTR,0,
1315                                                        fp->lx,fp->ly,fp->lz,
1316                                                        &o,
1317                                                        &(fp->p_params),
1318                                                        &(fp->d_params));
1319                                         o.x+=0.25*fp->lc;
1320                                         o.y=o.x;
1321                                         o.z=o.x;
1322                                         create_lattice(moldyn,
1323                                                        FCC,fp->lc,
1324                                                        mdrun->element2,
1325                                                        DEFAULT_ATOM_ATTR,1,
1326                                                        fp->lx,fp->ly,fp->lz,
1327                                                        &o,
1328                                                        &(fp->p_params),
1329                                                        &(fp->d_params));
1330                                         break;
1331
1332                                         default:
1333
1334                                         create_lattice(moldyn,
1335                                                        fp->lattice,fp->lc,
1336                                                        fp->fill_element,
1337                                                        DEFAULT_ATOM_ATTR,
1338                                                        fp->fill_brand,
1339                                                        fp->lx,fp->ly,fp->lz,
1340                                                        NULL,
1341                                                        &(fp->p_params),
1342                                                        &(fp->d_params));
1343                                         break;
1344                                 }
1345                                 moldyn_bc_check(moldyn);
1346                                 change_stage=TRUE;
1347                                 break;
1348                         case STAGE_THERMAL_INIT:
1349                                 stage_print("  -> thermal init\n\n");
1350                                 thermal_init(moldyn,TRUE);
1351                                 change_stage=TRUE;
1352                                 break;
1353                         default:
1354                                 printf("%s unknwon stage type\n",ME);
1355                                 break;
1356                 }
1357
1358                 /* mark as executed */
1359                 stage->executed=TRUE;
1360
1361                 /* change state */
1362                 if(change_stage==TRUE) {
1363                         printf("%s finished stage\n",ME);
1364                         if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
1365                                 printf("%s no more stages\n",ME);
1366                                 return 0;
1367                         }
1368                         steps=0;
1369                 }
1370
1371         }
1372         else {
1373
1374                 /* averages */
1375                 if(mdrun->sattr&SATTR_AVGRST)
1376                         average_reset(moldyn);
1377
1378         }
1379
1380         /* continue simulation */
1381         moldyn_add_schedule(moldyn,steps,mdrun->timestep);
1382
1383         return 0;
1384 }
1385
1386 int main(int argc,char **argv) {
1387
1388         t_mdrun mdrun;
1389         t_moldyn moldyn;
1390         //t_3dvec o;
1391
1392         /* clear structs */
1393         memset(&mdrun,0,sizeof(t_mdrun));
1394         memset(&moldyn,0,sizeof(t_moldyn));
1395
1396         /* parse arguments */
1397         if(mdrun_parse_argv(&mdrun,argc,argv)<0)
1398                 return -1;
1399
1400         /* initialize list system */
1401         list_init_f(&(mdrun.stage));
1402
1403         /* parse config file */
1404         mdrun_parse_config(&mdrun);
1405
1406         /* reset the stage list */
1407         list_reset_f(&(mdrun.stage));
1408
1409         /* sanity check! */
1410
1411         /* prepare simulation */
1412
1413         if(mdrun.continue_file[0]) {
1414                 // read the save file
1415                 moldyn_read_save_file(&moldyn,mdrun.continue_file);
1416                 // manualaadjusting some stuff
1417                 moldyn.argc=argc;
1418                 moldyn.args=argv;
1419                 rand_init(&(moldyn.random),NULL,1);
1420                 moldyn.random.status|=RAND_STAT_VERBOSE;
1421         }
1422         else {
1423                 moldyn_init(&moldyn,argc,argv);
1424         }
1425
1426         if(set_int_alg(&moldyn,mdrun.intalgo)<0)
1427                 return -1;
1428
1429         /* potential */
1430         set_cutoff(&moldyn,mdrun.cutoff);
1431         if(set_potential(&moldyn,mdrun.potential)<0)
1432                 return -1;
1433         switch(mdrun.potential) {
1434                 case MOLDYN_POTENTIAL_AM:
1435                         albe_mult_set_params(&moldyn,
1436                                              mdrun.element1,
1437                                              mdrun.element2);
1438                         break;
1439                 case MOLDYN_POTENTIAL_TM:
1440                         tersoff_mult_set_params(&moldyn,
1441                                                 mdrun.element1,
1442                                                 mdrun.element2);
1443                         break;
1444                 case MOLDYN_POTENTIAL_HO:
1445                         harmonic_oscillator_set_params(&moldyn,mdrun.element1);
1446                         break;
1447                 case MOLDYN_POTENTIAL_LJ:
1448                         lennard_jones_set_params(&moldyn,mdrun.element1);
1449                         break;
1450                 default:
1451                         printf("%s unknown potential: %02x\n",
1452                                ME,mdrun.potential);
1453                         return -1;
1454         }
1455
1456         /* if it is a continue run, reset schedule and skip lattice init */
1457         if(mdrun.continue_file[0]) {
1458                 memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
1459                 goto addsched;
1460         }
1461
1462         /* initial lattice and dimensions */
1463         set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
1464         set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
1465         /* replaced by fill stage !!
1466         switch(mdrun.lattice) {
1467                 case FCC:
1468                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
1469                                        mdrun.m1,DEFAULT_ATOM_ATTR,
1470                                        mdrun.fill_brand,mdrun.lx,
1471                                        mdrun.ly,mdrun.lz,NULL,0,NULL);
1472                         break;
1473                 case DIAMOND:
1474                         create_lattice(&moldyn,DIAMOND,mdrun.lc,
1475                                        mdrun.fill_element,
1476                                        mdrun.m1,DEFAULT_ATOM_ATTR,
1477                                        mdrun.fill_brand,mdrun.lx,
1478                                        mdrun.ly,mdrun.lz,NULL,0,NULL);
1479                         break;
1480                 case ZINCBLENDE:
1481                         o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1482                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
1483                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1484                                        mdrun.ly,mdrun.lz,&o,0,NULL);
1485                         o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1486                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
1487                                        mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
1488                                        mdrun.ly,mdrun.lz,&o,0,NULL);
1489                         break;
1490                 case NONE:
1491                         set_nn_dist(&moldyn,mdrun.nnd);
1492                         break;
1493                 default:
1494                         printf("%s unknown lattice type: %02x\n",
1495                                ME,mdrun.lattice);
1496                         return -1;
1497         }
1498         moldyn_bc_check(&moldyn);
1499         replaced by fill stage !! */
1500
1501         /* temperature and pressure */
1502         set_temperature(&moldyn,mdrun.temperature);
1503         set_pressure(&moldyn,mdrun.pressure);
1504         /* replaced thermal_init stage
1505         thermal_init(&moldyn,TRUE);
1506         */
1507
1508 addsched:
1509         /* first schedule */
1510         moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
1511
1512         /* log */
1513         moldyn_set_log_dir(&moldyn,mdrun.sdir);
1514         moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
1515         if(mdrun.elog)
1516                 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
1517         if(mdrun.tlog)
1518                 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
1519         if(mdrun.plog)
1520                 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
1521         if(mdrun.vlog)
1522                 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
1523         if(mdrun.visualize)
1524                 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
1525         if(mdrun.save)
1526                 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
1527         moldyn_set_log(&moldyn,CREATE_REPORT,0);
1528         set_avg_skip(&moldyn,mdrun.avgskip);
1529
1530         /* prepare the hook function */
1531         moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
1532
1533         /* run the simulation */
1534         moldyn_integrate(&moldyn);
1535
1536         /* shutdown */
1537         moldyn_shutdown(&moldyn);
1538         del_stages(&mdrun);
1539         list_destroy_f(&(mdrun.stage));
1540
1541         return 0;
1542 }