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 /* pse */
  21 #define PSE_MASS
  22 #include "pse.h"
  23 #undef PSE_MASS
  24
  25 #define ME      "[mdrun]"
  26
  27 /*
  28  * parse function
  29  */
  30
  31 int mdrun_usage(void) {
  32
  33         printf("%s usage:\n",ME);
  34
  35         return 0;
  36 }
  37
  38 int mdrun_parse_argv(t_mdrun *mdrun,int argc,char **argv) {
  39
  40         int i;
  41
  42         for(i=1;i<argc;i++) {
  43
  44                 if(argv[i][0]!='-') {
  45                         printf("%s unknown switch: %s\n",ME,argv[i]);
  46                         return -1;
  47                 }
  48
  49                 switch(argv[i][1]) {
  50                         case 'c':
  51                                 strncpy(mdrun->cfile,argv[++i],128);
  52                                 break;
  53                         case 's':
  54                                 strncpy(mdrun->sdir,argv[++i],128);
  55                                 break;
  56                         case 'h':
  57                                 mdrun_usage();
  58                                 break;
  59                         default:
  60                                 printf("%s unknown option: %s\n",ME,argv[i]);
  61                                 mdrun_usage();
  62                                 return -1;
  63                 }
  64
  65         }
  66
  67         return 0;
  68 }
  69
  70 int del_stages(t_mdrun *mdrun) {
  71
  72         t_list *sl;
  73         t_stage *stage;
  74
  75         sl=&(mdrun->stage);
  76
  77         list_reset_f(sl);
  78
  79         if(sl->start==NULL)
  80                 return 0;
  81
  82         do {
  83                 stage=sl->current->data;
  84                 free(stage->params);
  85                 free(stage);
  86         } while(list_next_f(sl)!=L_NO_NEXT_ELEMENT);
  87
  88         return 0;
  89 }
  90
  91 int add_stage(t_mdrun *mdrun,u8 type,void *params) {
  92
  93         int psize;
  94
  95         t_stage *stage;
  96
  97         switch(type) {
  98                 case STAGE_DISPLACE_ATOM:
  99                         psize=sizeof(t_displace_atom_params);
 100                         break;
 101                 case STAGE_DEL_ATOMS:
 102                         psize=sizeof(t_del_atoms_params);
 103                         break;
 104                 case STAGE_INSERT_ATOMS:
 105                         psize=sizeof(t_insert_atoms_params);
 106                         break;
 107                 case STAGE_INSERT_MIXED_ATOMS:
 108                         psize=sizeof(t_insert_mixed_atoms_params);
 109                         break;
 110                 case STAGE_CONTINUE:
 111                         psize=sizeof(t_continue_params);
 112                         break;
 113                 case STAGE_ANNEAL:
 114                         psize=sizeof(t_anneal_params);
 115                         break;
 116                 case STAGE_CHAATTR:
 117                         psize=sizeof(t_chaattr_params);
 118                         break;
 119                 case STAGE_CHSATTR:
 120                         psize=sizeof(t_chsattr_params);
 121                         break;
 122                 case STAGE_SET_TEMP:
 123                         psize=sizeof(t_set_temp_params);
 124                         break;
 125                 case STAGE_SET_TIMESTEP:
 126                         psize=sizeof(t_set_timestep_params);
 127                         break;
 128                 case STAGE_FILL:
 129                         psize=sizeof(t_fill_params);
 130                         break;
 131                 case STAGE_THERMAL_INIT:
 132                         psize=0;
 133                         break;
 134                 default:
 135                         printf("%s unknown stage type: %02x\n",ME,type);
 136                         return -1;
 137         }
 138
 139         stage=malloc(sizeof(t_stage));
 140         if(stage==NULL) {
 141                 perror("[mdrun] malloc (add stage)");
 142                 return -1;
 143         }
 144
 145         stage->type=type;
 146         stage->executed=FALSE;
 147
 148         stage->params=malloc(psize);
 149         if(stage->params==NULL) {
 150                 perror("[mdrun] malloc (stage params)");
 151                 return -1;
 152         }
 153
 154         memcpy(stage->params,params,psize);
 155
 156         list_add_immediate_f(&(mdrun->stage),stage);
 157
 158         return 0;
 159 }
 160
 161 int mdrun_parse_config(t_mdrun *mdrun) {
 162
 163         int fd,ret;
 164         char error[128];
 165         char line[128];
 166         char *wptr;
 167         char word[32][64];
 168         int wcnt;
 169         int i,o;
 170
 171         t_displace_atom_params dap;
 172         t_insert_atoms_params iap;
 173         t_insert_mixed_atoms_params imp;
 174         t_continue_params cp;
 175         t_anneal_params ap;
 176         t_chaattr_params cap;
 177         t_chsattr_params csp;
 178         t_set_temp_params stp;
 179         t_set_timestep_params stsp;
 180         t_fill_params fp;
 181         t_del_atoms_params delp;
 182
 183         /* open config file */
 184         fd=open(mdrun->cfile,O_RDONLY);
 185         if(fd<0) {
 186                 snprintf(error,128,"%s open cfile %s",ME,mdrun->cfile);
 187                 perror(error);
 188                 return fd;
 189         }
 190
 191         /* read, parse, set */
 192         ret=1;
 193         while(ret>0) {
 194
 195                 /* read */
 196                 ret=get_line(fd,line,128);
 197
 198                 /* parse */
 199
 200                 // ignore # lines and \n
 201                 if((line[0]=='#')|(ret==1))
 202                         continue;
 203
 204                 // reset
 205                 memset(&iap,0,sizeof(t_insert_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                                 }
 312                                 if(!strncmp(word[i],"eb",2)) {
 313                                         fp.fill_element=atoi(word[++i]);
 314                                         fp.fill_brand=atoi(word[++i]);
 315                                 }
 316                                 if(word[i][0]=='p') {
 317                                         i+=1;
 318                                         switch(word[i][0]) {
 319                                         case 'i':
 320                                                 if(word[i][1]=='r')
 321                                                 fp.p_params.type=PART_INSIDE_R;
 322                                                 else
 323                                                 fp.p_params.type=PART_INSIDE_D;
 324                                                 break;
 325                                         case 'o':
 326                                                 if(word[i][1]=='r')
 327                                                 fp.p_params.type=PART_OUTSIDE_R;
 328                                                 else
 329                                                 fp.p_params.type=PART_OUTSIDE_D;
 330                                                 break;
 331                                         default:
 332                                                 break;
 333                                         }
 334                                         if((fp.p_params.type==PART_INSIDE_R)||
 335                                           (fp.p_params.type==PART_OUTSIDE_R)) {
 336                                                 fp.p_params.r=atof(word[++i]);
 337                                                 fp.p_params.p.x=atof(word[++i]);
 338                                                 fp.p_params.p.y=atof(word[++i]);
 339                                                 fp.p_params.p.z=atof(word[++i]);
 340                                         }
 341                                         if((fp.p_params.type==PART_INSIDE_D)||
 342                                            (fp.p_params.type==PART_OUTSIDE_D)) {
 343                                                 fp.p_params.p.x=atof(word[++i]);
 344                                                 fp.p_params.p.y=atof(word[++i]);
 345                                                 fp.p_params.p.z=atof(word[++i]);
 346                                                 fp.p_params.d.x=atof(word[++i]);
 347                                                 fp.p_params.d.y=atof(word[++i]);
 348                                                 fp.p_params.d.z=atof(word[++i]);
 349                                         }
 350                                 }
 351                                 if(word[i][0]=='d') {
 352                                         switch(word[++i][0]) {
 353                                                 case '0':
 354
 355                                 fp.d_params.type=DEFECT_TYPE_0D;
 356                                 if(!strncmp(word[i+1],"dbx",3)) {
 357                                         fp.d_params.stype=DEFECT_STYPE_DB_X;
 358                                 }
 359                                 if(!strncmp(word[i+1],"dby",3)) {
 360                                         fp.d_params.stype=DEFECT_STYPE_DB_Y;
 361                                 }
 362                                 if(!strncmp(word[i+1],"dbz",3)) {
 363                                         fp.d_params.stype=DEFECT_STYPE_DB_Z;
 364                                 }
 365                                 if(!strncmp(word[i+1],"dbr",3)) {
 366                                         fp.d_params.stype=DEFECT_STYPE_DB_R;
 367                                 }
 368                                 i+=1;
 369                                 fp.d_params.od=atof(word[++i]);
 370                                 fp.d_params.dd=atof(word[++i]);
 371                                 fp.d_params.element=atoi(word[++i]);
 372                                 fp.d_params.brand=atoi(word[++i]);
 373                                 // parsed in future
 374                 fp.d_params.attr=ATOM_ATTR_HB|ATOM_ATTR_VA;
 375                 fp.d_params.attr|=ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
 376                                 break;
 377
 378                                                 case '1':
 379                                 fp.d_params.type=DEFECT_TYPE_1D;
 380                                 break;
 381                                                 case '2':
 382                                 fp.d_params.type=DEFECT_TYPE_2D;
 383                                 break;
 384                                                 case '3':
 385                                 fp.d_params.type=DEFECT_TYPE_3D;
 386                                 break;
 387                                                 default:
 388                                                         break;
 389                                         }
 390
 391                                 }
 392                                 i+=1;
 393                         }
 394                         add_stage(mdrun,STAGE_FILL,&fp);
 395                 }
 396                 else if(!strncmp(word[0],"thermal_init",12)) {
 397                         add_stage(mdrun,STAGE_THERMAL_INIT,NULL);
 398                 }
 399                 else if(!strncmp(word[0],"aattr",5)) {
 400                         // for aatrib line we need a special stage
 401                         // containing one schedule of 0 loops ...
 402                         for(i=0;i<strlen(word[1]);i++) {
 403                                 switch(word[1][i]) {
 404                                         case 't':
 405                                                 cap.type|=CHAATTR_TOTALV;
 406                                                 break;
 407                                         case 'r':
 408                                                 cap.type|=CHAATTR_REGION;
 409                                                 break;
 410                                         case 'e':
 411                                                 cap.type|=CHAATTR_ELEMENT;
 412                                                 break;
 413                                         default:
 414                                                 break;
 415                                 }
 416                         }
 417                         i=2;
 418                         if(cap.type&CHAATTR_REGION) {
 419                                 cap.x0=atof(word[1]);
 420                                 cap.y0=atof(word[2]);
 421                                 cap.z0=atof(word[3]);
 422                                 cap.x1=atof(word[4]);
 423                                 cap.y1=atof(word[5]);
 424                                 cap.z1=atof(word[6]);
 425                                 i+=6;
 426                         }
 427                         if(cap.type&CHAATTR_ELEMENT) {
 428                                 cap.element=atoi(word[i]);
 429                                 i+=1;
 430                         }
 431                         for(o=0;o<strlen(word[i]);o++) {
 432                                 switch(word[i][o]) {
 433                                         case 'b':
 434                                                 cap.attr|=ATOM_ATTR_VB;
 435                                                 break;
 436                                         case 'h':
 437                                                 cap.attr|=ATOM_ATTR_HB;
 438                                                 break;
 439                                         case 'v':
 440                                                 cap.attr|=ATOM_ATTR_VA;
 441                                                 break;
 442                                         case 'f':
 443                                                 cap.attr|=ATOM_ATTR_FP;
 444                                                 break;
 445                                         case '1':
 446                                                 cap.attr|=ATOM_ATTR_1BP;
 447                                                 break;
 448                                         case '2':
 449                                                 cap.attr|=ATOM_ATTR_2BP;
 450                                                 break;
 451                                         case '3':
 452                                                 cap.attr|=ATOM_ATTR_3BP;
 453                                                 break;
 454                                         default:
 455                                                 break;
 456                                 }
 457                         }
 458                         add_stage(mdrun,STAGE_CHAATTR,&cap);
 459                 }
 460                 else if(!strncmp(word[0],"sattr",5)) {
 461                         // for satrib line we need a special stage
 462                         // containing one schedule of 0 loops ...
 463                         csp.type=0;
 464                         for(i=1;i<wcnt;i++) {
 465                                 if(!strncmp(word[i],"pctrl",5)) {
 466                                         csp.ptau=0.01/(atof(word[++i])*GPA);
 467                                         csp.type|=CHSATTR_PCTRL;
 468                                 }
 469                                 if(!strncmp(word[i],"tctrl",5)) {
 470                                         csp.ttau=atof(word[++i]);
 471                                         csp.type|=CHSATTR_TCTRL;
 472                                 }
 473                                 if(!strncmp(word[i],"prelax",6)) {
 474                                         csp.dp=atof(word[++i])*BAR;
 475                                         csp.type|=CHSATTR_PRELAX;
 476                                 }
 477                                 if(!strncmp(word[i],"trelax",6)) {
 478                                         csp.dt=atof(word[++i]);
 479                                         csp.type|=CHSATTR_TRELAX;
 480                                 }
 481                                 if(!strncmp(word[i],"rsteps",6)) {
 482                                         csp.rsteps=atoi(word[++i]);
 483                                         csp.type|=CHSATTR_RSTEPS;
 484                                 }
 485                                 if(!strncmp(word[i],"avgrst",6)) {
 486                                         csp.avgrst=atoi(word[++i]);
 487                                         csp.type|=CHSATTR_AVGRST;
 488                                 }
 489                         }
 490                         add_stage(mdrun,STAGE_CHSATTR,&csp);
 491                 }
 492                 else if(!strncmp(word[0],"prerun",6))
 493                         mdrun->prerun=atoi(word[1]);
 494                 else if(!strncmp(word[0],"avgskip",7))
 495                         mdrun->avgskip=atoi(word[1]);
 496                 else if(!strncmp(word[0],"elog",4))
 497                         mdrun->elog=atoi(word[1]);
 498                 else if(!strncmp(word[0],"tlog",4))
 499                         mdrun->tlog=atoi(word[1]);
 500                 else if(!strncmp(word[0],"plog",4))
 501                         mdrun->plog=atoi(word[1]);
 502                 else if(!strncmp(word[0],"vlog",4))
 503                         mdrun->vlog=atoi(word[1]);
 504                 else if(!strncmp(word[0],"save",4))
 505                         mdrun->save=atoi(word[1]);
 506                 else if(!strncmp(word[0],"visualize",9))
 507                         mdrun->visualize=atoi(word[1]);
 508                 else if(!strncmp(word[0],"stage",5)) {
 509                         // for every stage line, add a stage
 510                         if(!strncmp(word[1],"displace",8)) {
 511                                 dap.nr=atoi(word[2]);
 512                                 dap.dx=atof(word[3]);
 513                                 dap.dy=atof(word[4]);
 514                                 dap.dz=atof(word[5]);
 515                                 add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
 516                         }
 517                         else if(!strncmp(word[1],"del_atoms",9)) {
 518                                 delp.o.x=atof(word[2]);
 519                                 delp.o.y=atof(word[3]);
 520                                 delp.o.z=atof(word[4]);
 521                                 delp.r=atof(word[5]);
 522                                 add_stage(mdrun,STAGE_DEL_ATOMS,&delp);
 523                         }
 524                         else if(!strncmp(word[1],"ins_atoms",9)) {
 525                                 iap.ins_steps=atoi(word[2]);
 526                                 iap.ins_atoms=atoi(word[3]);
 527                                 iap.element=atoi(word[4]);
 528                                 iap.brand=atoi(word[5]);
 529                                 for(i=0;i<strlen(word[6]);i++) {
 530                                         switch(word[6][i]) {
 531                                                 case 'b':
 532                                                         iap.attr|=ATOM_ATTR_VB;
 533                                                         break;
 534                                                 case 'h':
 535                                                         iap.attr|=ATOM_ATTR_HB;
 536                                                         break;
 537                                                 case 'v':
 538                                                         iap.attr|=ATOM_ATTR_VA;
 539                                                         break;
 540                                                 case 'f':
 541                                                         iap.attr|=ATOM_ATTR_FP;
 542                                                         break;
 543                                                 case '1':
 544                                                         iap.attr|=ATOM_ATTR_1BP;
 545                                                         break;
 546                                                 case '2':
 547                                                         iap.attr|=ATOM_ATTR_2BP;
 548                                                         break;
 549                                                 case '3':
 550                                                         iap.attr|=ATOM_ATTR_3BP;
 551                                                         break;
 552                                                 default:
 553                                                         break;
 554                                         }
 555                                 }
 556                                 switch(word[7][0]) {
 557                                         // insertion types
 558                                         case 'p':
 559                                                 iap.type=INS_POS;
 560                                                 iap.x0=atof(word[8]);
 561                                                 iap.y0=atof(word[9]);
 562                                                 iap.z0=atof(word[10]);
 563                                                 break;
 564                                         case 'r':
 565                                                 switch(word[8][0]) {
 566
 567                                                 case 't':
 568                                                         iap.type=INS_TOTAL;
 569                                                         iap.cr=atof(word[9]);
 570                                                         break;
 571                                                 case 'r':
 572                                                         iap.type=INS_RECT;
 573                                                         iap.x0=atof(word[9]);
 574                                                         iap.y0=atof(word[10]);
 575                                                         iap.z0=atof(word[11]);
 576                                                         iap.x1=atof(word[12]);
 577                                                         iap.y1=atof(word[13]);
 578                                                         iap.z1=atof(word[14]);
 579                                                         iap.cr=atof(word[15]);
 580                                                         break;
 581                                                 case 's':
 582                                                         iap.type=INS_SPHERE;
 583                                                         iap.x0=atof(word[9]);
 584                                                         iap.y0=atof(word[10]);
 585                                                         iap.z0=atof(word[11]);
 586                                                         iap.x1=atof(word[12]);
 587                                                         iap.cr=atof(word[13]);
 588                                                         break;
 589                                                 default:
 590                                                         break;
 591                                                 }
 592                                         default:
 593                                                 break;
 594                                 }
 595                                 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
 596                         }
 597
 598
 599                         // HERE WE GO ...
 600
 601                         else if(!strncmp(word[1],"ins_m_atoms",11)) {
 602                                 imp.element1=atoi(word[2]);
 603                                 imp.element2=atoi(word[3]);
 604                                 imp.amount1=atoi(word[4]);
 605                                 imp.amount2=atoi(word[5]);
 606                                 imp.brand1=atoi(word[6]);
 607                                 imp.brand2=atoi(word[7]);
 608                                 imp.crmin=atof(word[8]);
 609                                 imp.crmax=atof(word[9]);
 610                                 /* do this later ...
 611                                 for(i=0;i<strlen(word[8]);i++) {
 612                                         switch(word[8][i]) {
 613                                                 case 'b':
 614                                                         imp.attr|=ATOM_ATTR_VB;
 615                                                         break;
 616                                                 case 'h':
 617                                                         imp.attr|=ATOM_ATTR_HB;
 618                                                         break;
 619                                                 case 'v':
 620                                                         imp.attr|=ATOM_ATTR_VA;
 621                                                         break;
 622                                                 case 'f':
 623                                                         imp.attr|=ATOM_ATTR_FP;
 624                                                         break;
 625                                                 case '1':
 626                                                         imp.attr|=ATOM_ATTR_1BP;
 627                                                         break;
 628                                                 case '2':
 629                                                         imp.attr|=ATOM_ATTR_2BP;
 630                                                         break;
 631                                                 case '3':
 632                                                         imp.attr|=ATOM_ATTR_3BP;
 633                                                         break;
 634                                                 default:
 635                                                         break;
 636                                         }
 637                                 }
 638                                 */
 639                                 imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 640                                 imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 641                                 add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
 642                         }
 643
 644
 645
 646
 647
 648                         else if(!strncmp(word[1],"continue",8)) {
 649                                 cp.runs=atoi(word[2]);
 650                                 add_stage(mdrun,STAGE_CONTINUE,&cp);
 651                         }
 652                         else if(!strncmp(word[1],"anneal",6)) {
 653                                 ap.count=0;
 654                                 ap.runs=atoi(word[2]);
 655                                 ap.dt=atof(word[3]);
 656                                 ap.interval=atoi(word[4]);
 657                                 add_stage(mdrun,STAGE_ANNEAL,&ap);
 658                         }
 659                         else if(!strncmp(word[1],"set_temp",8)) {
 660                                 if(word[2][0]=='c') {
 661                                         stp.type=SET_TEMP_CURRENT;
 662                                         stp.val=0.0;
 663                                 }
 664                                 else {
 665                                         stp.type=SET_TEMP_VALUE;
 666                                         stp.val=atof(word[2]);
 667                                 }
 668                                 add_stage(mdrun,STAGE_SET_TEMP,&stp);
 669                         }
 670                         else if(!strncmp(word[1],"set_timestep",12)) {
 671                                 stsp.tau=atof(word[2]);
 672                                 add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
 673                         }
 674                         else {
 675                                 printf("%s unknown stage type: %s\n",
 676                                        ME,word[1]);
 677                                 return -1;
 678                         }
 679                 }
 680                 else {
 681                         printf("%s unknown keyword '%s', skipped!\n",
 682                                ME,word[0]);
 683                         continue;
 684                 }
 685         }
 686
 687         /* close file */
 688         close(fd);
 689
 690         return 0;
 691 }
 692
 693 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
 694
 695         double delta;
 696
 697         if(!(mdrun->sattr&SATTR_PRELAX)) {
 698                 return TRUE;
 699         }
 700
 701         delta=moldyn->p_avg-moldyn->p_ref;
 702
 703         if(delta<0)
 704                 delta=-delta;
 705
 706         if(delta>mdrun->dp)
 707                 return FALSE;
 708
 709         return TRUE;
 710 }
 711
 712 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 713
 714         double delta;
 715
 716         if(!(mdrun->sattr&SATTR_TRELAX))
 717                 return TRUE;
 718
 719         delta=moldyn->t_avg-moldyn->t_ref;
 720
 721         if(delta<0)
 722                 delta=-delta;
 723
 724         if(delta>mdrun->dt)
 725                 return FALSE;
 726
 727         return TRUE;
 728 }
 729
 730 int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
 731
 732         t_displace_atom_params *dap;
 733         t_stage *stage;
 734         t_atom *atom;
 735
 736         stage=mdrun->stage.current->data;
 737         dap=stage->params;
 738
 739         atom=&(moldyn->atom[dap->nr]);
 740         atom->r.x+=dap->dx;
 741         atom->r.y+=dap->dy;
 742         atom->r.z+=dap->dz;
 743
 744         return 0;
 745 }
 746
 747 int del_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 748
 749         t_stage *stage;
 750         t_del_atoms_params *delp;
 751         int i;
 752         t_3dvec dist;
 753
 754         stage=mdrun->stage.current->data;
 755         delp=stage->params;
 756
 757         for(i=0;i<moldyn->count;i++) {
 758                 v3_sub(&dist,&(delp->o),&(moldyn->atom[i].r));
 759 //printf("%d ----> %f %f %f = %f | %f\n",i,dist.x,dist.y,dist.z,v3_absolute_square(&dist),delp->r*delp->r);
 760                 if(v3_absolute_square(&dist)<=(delp->r*delp->r)) {
 761                         del_atom(moldyn,moldyn->atom[i].tag);
 762                         printf("%s atom deleted: %d %d %d\n",ME,
 763                                moldyn->atom[i].tag,moldyn->atom[i].element,
 764                                moldyn->atom[i].brand);
 765                 }
 766         }
 767
 768         return 0;
 769
 770 }
 771
 772 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 773
 774         t_insert_atoms_params *iap;
 775         t_stage *stage;
 776         t_atom *atom;
 777         t_3dvec r,v,dist;
 778         double d,dmin,o;
 779         int cnt,i;
 780         double x,y,z;
 781         double x0,y0,z0;
 782         u8 cr_check,run;
 783
 784         stage=mdrun->stage.current->data;
 785         iap=stage->params;
 786
 787         cr_check=FALSE;
 788
 789         v.x=0.0; v.y=0.0; v.z=0.0;
 790         x=0; y=0; z=0;
 791         o=0; dmin=0;
 792
 793         switch(mdrun->lattice) {
 794                 case CUBIC:
 795                         o=0.5*mdrun->lc;
 796                         break;
 797                 case FCC:
 798                         o=0.25*mdrun->lc;
 799                         break;
 800                 case DIAMOND:
 801                 case ZINCBLENDE:
 802                         o=0.125*mdrun->lc;
 803                         break;
 804                 default:
 805                         break;
 806         }
 807
 808         switch(iap->type) {
 809                 case INS_TOTAL:
 810                         x=moldyn->dim.x;
 811                         x0=-x/2.0;
 812                         y=moldyn->dim.y;
 813                         y0=-y/2.0;
 814                         z=moldyn->dim.z;
 815                         z0=-z/2.0;
 816                         cr_check=TRUE;
 817                         break;
 818                 case INS_RECT:
 819                         x=iap->x1-iap->x0;
 820                         x0=iap->x0;
 821                         y=iap->y1-iap->y0;
 822                         y0=iap->y0;
 823                         z=iap->z1-iap->z0;
 824                         z0=iap->z0;
 825                         cr_check=TRUE;
 826                         break;
 827                 case INS_SPHERE:
 828                         x=2.0*iap->x1;
 829                         x0=iap->x0-iap->x1;
 830                         y=x;
 831                         y0=iap->y0-iap->x1;
 832                         z=x;
 833                         z0=iap->z0-iap->x1;
 834                         cr_check=TRUE;
 835                         break;
 836                 case INS_POS:
 837                         x0=iap->x0;
 838                         y0=iap->y0;
 839                         z0=iap->z0;
 840                         cr_check=FALSE;
 841                         break;
 842                 default:
 843                         printf("%s unknown insertion mode: %02x\n",
 844                                ME,iap->type);
 845                         return -1;
 846         }
 847
 848         cnt=0;
 849         while(cnt<iap->ins_atoms) {
 850                 run=1;
 851                 while(run) {
 852                         if(iap->type!=INS_POS) {
 853                                 r.x=rand_get_double(&(moldyn->random))*x;
 854                                 r.y=rand_get_double(&(moldyn->random))*y;
 855                                 r.z=rand_get_double(&(moldyn->random))*z;
 856                         }
 857                         else {
 858                                 r.x=0.0;
 859                                 r.y=0.0;
 860                                 r.z=0.0;
 861                         }
 862                         r.x+=x0;
 863                         r.y+=y0;
 864                         r.z+=z0;
 865                         // offset
 866                         if(iap->type!=INS_TOTAL) {
 867                                 r.x+=o;
 868                                 r.y+=o;
 869                                 r.z+=o;
 870                         }
 871                         run=0;
 872                         if(cr_check==TRUE) {
 873                                 dmin=1000;      // for sure too high!
 874                                 for(i=0;i<moldyn->count;i++) {
 875                                         atom=&(moldyn->atom[i]);
 876                                         v3_sub(&dist,&(atom->r),&r);
 877                                         check_per_bound(moldyn,&dist);
 878                                         d=v3_absolute_square(&dist);
 879                                         if(d<(iap->cr*iap->cr)) {
 880                                                 run=1;
 881                                                 break;
 882                                         }
 883                                         if(d<dmin)
 884                                                 dmin=d;
 885                                 }
 886                         }
 887                         if(iap->type==INS_SPHERE) {
 888                                 if((r.x-iap->x0)*(r.x-iap->x0)+
 889                                    (r.y-iap->y0)*(r.y-iap->y0)+
 890                                    (r.z-iap->z0)*(r.z-iap->z0)>
 891                                    (iap->x1*iap->x1)) {
 892                                         run=1;
 893                                 }
 894                         }
 895                 }
 896                 add_atom(moldyn,iap->element,
 897                          iap->brand,iap->attr,&r,&v);
 898                 printf("%s atom inserted (%d/%d): %f %f %f\n",
 899                        ME,(iap->cnt_steps+1)*iap->ins_atoms,
 900                        iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
 901                 printf("  -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
 902                 cnt+=1;
 903         }
 904
 905         return 0;
 906 }
 907
 908 int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 909
 910         t_stage *stage;
 911         t_insert_mixed_atoms_params *imp;
 912         t_atom *atom;
 913         double x,x0,y,y0,z,z0;
 914         double dmin,d,cmin,cmax;
 915         u8 retry;
 916         t_3dvec r,v,dist;
 917         int i;
 918
 919
 920         stage=mdrun->stage.current->data;
 921         imp=stage->params;
 922
 923         x=moldyn->dim.x;
 924         x0=-x/2.0;
 925         y=moldyn->dim.y;
 926         y0=-y/2.0;
 927         z=moldyn->dim.z;
 928         z0=-z/2.0;
 929
 930         v.x=0.0;
 931         v.y=0.0;
 932         v.z=0.0;
 933
 934         cmin=imp->crmin*imp->crmin;
 935         cmax=imp->crmax*imp->crmax;
 936
 937         while(imp->amount1|imp->amount2) {
 938                 if(imp->amount1) {
 939                         retry=1;
 940                         while(retry) {
 941                                 retry=0;
 942                                 r.x=rand_get_double(&(moldyn->random))*x;
 943                                 r.y=rand_get_double(&(moldyn->random))*y;
 944                                 r.z=rand_get_double(&(moldyn->random))*z;
 945                                 r.x+=x0;
 946                                 r.y+=y0;
 947                                 r.z+=z0;
 948                                 dmin=1000.0;    // for sure too high!
 949                                 for(i=0;i<moldyn->count;i++) {
 950                                         atom=&(moldyn->atom[i]);
 951                                         v3_sub(&dist,&(atom->r),&r);
 952                                         check_per_bound(moldyn,&dist);
 953                                         d=v3_absolute_square(&dist);
 954                                         if(d<cmin) {
 955                                                 retry=1;
 956                                                 break;
 957                                         }
 958                                         if(d<dmin)
 959                                                 dmin=d;
 960                                 }
 961                                 if(dmin!=1000.0)
 962                                         if(dmin>cmax)
 963                                                 retry=1;
 964                         }
 965                         add_atom(moldyn,imp->element1,
 966                                  imp->brand1,imp->attr1,&r,&v);
 967                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
 968                                ME,imp->amount1,r.x,r.y,r.z);
 969                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
 970                         imp->amount1-=1;
 971                 }
 972                 if(imp->amount2) {
 973                         retry=1;
 974                         while(retry) {
 975                                 retry=0;
 976                                 r.x=rand_get_double(&(moldyn->random))*x;
 977                                 r.y=rand_get_double(&(moldyn->random))*y;
 978                                 r.z=rand_get_double(&(moldyn->random))*z;
 979                                 r.x+=x0;
 980                                 r.y+=y0;
 981                                 r.z+=z0;
 982                                 dmin=1000.0;    // for sure too high!
 983                                 for(i=0;i<moldyn->count;i++) {
 984                                         atom=&(moldyn->atom[i]);
 985                                         v3_sub(&dist,&(atom->r),&r);
 986                                         check_per_bound(moldyn,&dist);
 987                                         d=v3_absolute_square(&dist);
 988                                         if(d<cmin) {
 989                                                 retry=1;
 990                                                 break;
 991                                         }
 992                                         if(d<dmin)
 993                                                 dmin=d;
 994                                 }
 995                                 if(dmin!=1000.0)
 996                                         if(dmin>cmax)
 997                                                 retry=1;
 998                         }
 999                         add_atom(moldyn,imp->element2,
1000                                  imp->brand2,imp->attr2,&r,&v);
1001                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
1002                                ME,imp->amount2,r.x,r.y,r.z);
1003                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
1004                         imp->amount2-=1;
1005                 }
1006         }
1007
1008         return 0;
1009 }
1010
1011 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
1012
1013         t_stage *stage;
1014         t_chaattr_params *cap;
1015         t_atom *atom;
1016         int i;
1017
1018         stage=mdrun->stage.current->data;
1019         cap=stage->params;
1020
1021         for(i=0;i<moldyn->count;i++) {
1022                 atom=&(moldyn->atom[i]);
1023                 if(cap->type&CHAATTR_ELEMENT) {
1024                         if(cap->element!=atom->element)
1025                                 continue;
1026                 }
1027                 if(cap->type&CHAATTR_REGION) {
1028                         if(cap->x0<atom->r.x)
1029                                 continue;
1030                         if(cap->y0<atom->r.y)
1031                                 continue;
1032                         if(cap->z0<atom->r.z)
1033                                 continue;
1034                         if(cap->x1>atom->r.x)
1035                                 continue;
1036                         if(cap->y1>atom->r.y)
1037                                 continue;
1038                         if(cap->z1>atom->r.z)
1039                                 continue;
1040                 }
1041                 atom->attr=cap->attr;
1042         }
1043
1044         return 0;
1045 }
1046
1047 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
1048
1049         t_stage *stage;
1050         t_chsattr_params *csp;
1051
1052         stage=mdrun->stage.current->data;
1053         csp=stage->params;
1054
1055         if(csp->type&CHSATTR_PCTRL) {
1056                 if(csp->ptau>0)
1057                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
1058                 else
1059                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
1060         }
1061         if(csp->type&CHSATTR_TCTRL) {
1062                 if(csp->ttau>0)
1063                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
1064                 else
1065                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
1066         }
1067         if(csp->type&CHSATTR_PRELAX) {
1068                 if(csp->dp<0)
1069                         mdrun->sattr&=(~(SATTR_PRELAX));
1070                 else
1071                         mdrun->sattr|=SATTR_PRELAX;
1072                 mdrun->dp=csp->dp;
1073         }
1074         if(csp->type&CHSATTR_TRELAX) {
1075                 if(csp->dt<0)
1076                         mdrun->sattr&=(~(SATTR_TRELAX));
1077                 else
1078                         mdrun->sattr|=SATTR_TRELAX;
1079                 mdrun->dt=csp->dt;
1080         }
1081         if(csp->type&CHSATTR_AVGRST) {
1082                 if(csp->avgrst)
1083                         mdrun->sattr|=SATTR_AVGRST;
1084                 else
1085                         mdrun->sattr&=(~(SATTR_AVGRST));
1086         }
1087         if(csp->type&CHSATTR_RSTEPS) {
1088                 mdrun->relax_steps=csp->rsteps;
1089         }
1090
1091         return 0;
1092 }
1093
1094 #define stage_print(m)  if(!(stage->executed)) \
1095                                 printf("%s",m)
1096
1097 int mdrun_hook(void *ptr1,void *ptr2) {
1098
1099         t_moldyn *moldyn;
1100         t_mdrun *mdrun;
1101         t_stage *stage;
1102         t_list *sl;
1103         int steps;
1104         u8 change_stage;
1105         t_3dvec o;
1106
1107         t_insert_atoms_params *iap;
1108         t_insert_mixed_atoms_params *imp;
1109         t_continue_params *cp;
1110         t_anneal_params *ap;
1111         t_set_temp_params *stp;
1112         t_set_timestep_params *stsp;
1113         t_fill_params *fp;
1114
1115         moldyn=ptr1;
1116         mdrun=ptr2;
1117
1118         sl=&(mdrun->stage);
1119
1120         change_stage=FALSE;
1121
1122         /* return immediately if there are no more stage */
1123         if(sl->current==NULL)
1124                 return 0;
1125
1126         /* get stage description */
1127         stage=sl->current->data;
1128
1129         /* steps in next schedule */
1130         steps=mdrun->relax_steps;
1131
1132         /* check whether relaxation steps are necessary */
1133         if((check_pressure(moldyn,mdrun)==TRUE)&\
1134            (check_temperature(moldyn,mdrun)==TRUE)) {
1135
1136                 /* be verbose */
1137                 stage_print("\n###########################\n");
1138                 stage_print("# [mdrun] executing stage #\n");
1139                 stage_print("###########################\n\n");
1140
1141                 /* stage specific stuff */
1142                 switch(stage->type) {
1143                         case STAGE_DISPLACE_ATOM:
1144                                 stage_print("  -> displace atom\n\n");
1145                                 displace_atom(moldyn,mdrun);
1146                                 change_stage=TRUE;
1147                                 break;
1148                         case STAGE_DEL_ATOMS:
1149                                 stage_print(" -> del atoms\n\n");
1150                                 del_atoms(moldyn,mdrun);
1151                                 change_stage=TRUE;
1152                                 break;
1153                         case STAGE_INSERT_ATOMS:
1154                                 stage_print("  -> insert atoms\n\n");
1155                                 iap=stage->params;
1156                                 if(iap->cnt_steps==iap->ins_steps) {
1157                                         change_stage=TRUE;
1158                                         break;
1159                                 }
1160                                 insert_atoms(moldyn,mdrun);
1161                                 iap->cnt_steps+=1;
1162                                 break;
1163
1164
1165
1166                         case STAGE_INSERT_MIXED_ATOMS:
1167                                 stage_print("  -> insert mixed atoms\n\n");
1168                                 imp=stage->params;
1169                                 insert_mixed_atoms(moldyn,mdrun);
1170                                 change_stage=TRUE;
1171                                 break;
1172
1173
1174
1175                         case STAGE_CONTINUE:
1176                                 stage_print("  -> continue\n\n");
1177                                 if(stage->executed==TRUE) {
1178                                         change_stage=TRUE;
1179                                         break;
1180                                 }
1181                                 cp=stage->params;
1182                                 steps=cp->runs;
1183                                 break;
1184                         case STAGE_ANNEAL:
1185                                 stage_print("  -> anneal\n\n");
1186                                 ap=stage->params;
1187                                 if(ap->count==ap->runs) {
1188                                         change_stage=TRUE;
1189                                         break;
1190                                 }
1191                                 if(moldyn->t_ref+ap->dt>=0.0)
1192                                         set_temperature(moldyn,
1193                                                         moldyn->t_ref+ap->dt);
1194                                 ap->count+=1;
1195                                 steps=ap->interval;
1196                                 break;
1197                         case STAGE_CHAATTR:
1198                                 stage_print("  -> change atom attributes\n\n");
1199                                 chaatr(moldyn,mdrun);
1200                                 change_stage=TRUE;
1201                                 break;
1202                         case STAGE_CHSATTR:
1203                                 stage_print("  -> change sys attributes\n\n");
1204                                 chsattr(moldyn,mdrun);
1205                                 change_stage=TRUE;
1206                                 break;
1207                         case STAGE_SET_TEMP:
1208                                 stage_print("  -> set temperature\n\n");
1209                                 stp=stage->params;
1210                                 if(stp->type&SET_TEMP_CURRENT) {
1211                                         set_temperature(moldyn,moldyn->t_avg);
1212                                 }
1213                                 else {
1214                                         set_temperature(moldyn,stp->val);
1215                                 }
1216                                 change_stage=TRUE;
1217                                 break;
1218                         case STAGE_SET_TIMESTEP:
1219                                 stage_print("  -> set timestep\n\n");
1220                                 stsp=stage->params;
1221                                 mdrun->timestep=stsp->tau;
1222                                 change_stage=TRUE;
1223                                 break;
1224                         case STAGE_FILL:
1225                                 stage_print("  -> fill lattice\n\n");
1226                                 fp=stage->params;
1227                                 switch(fp->lattice) {
1228                                         case ZINCBLENDE:
1229
1230                                         o.x=0.5*0.25*fp->lc;
1231                                         o.y=o.x;
1232                                         o.z=o.x;
1233                                         create_lattice(moldyn,
1234                                                        FCC,fp->lc,
1235                                                        mdrun->element1,
1236                                                        DEFAULT_ATOM_ATTR,0,
1237                                                        fp->lx,fp->ly,fp->lz,
1238                                                        &o,
1239                                                        &(fp->p_params),
1240                                                        &(fp->d_params));
1241                                         o.x+=0.25*fp->lc;
1242                                         o.y=o.x;
1243                                         o.z=o.x;
1244                                         create_lattice(moldyn,
1245                                                        FCC,fp->lc,
1246                                                        mdrun->element2,
1247                                                        DEFAULT_ATOM_ATTR,1,
1248                                                        fp->lx,fp->ly,fp->lz,
1249                                                        &o,
1250                                                        &(fp->p_params),
1251                                                        &(fp->d_params));
1252                                         break;
1253
1254                                         default:
1255
1256                                         create_lattice(moldyn,
1257                                                        fp->lattice,fp->lc,
1258                                                        mdrun->element1,
1259                                                        DEFAULT_ATOM_ATTR,0,
1260                                                        fp->lx,fp->ly,fp->lz,
1261                                                        NULL,
1262                                                        &(fp->p_params),
1263                                                        &(fp->d_params));
1264                                         break;
1265                                 }
1266                                 moldyn_bc_check(moldyn);
1267                                 change_stage=TRUE;
1268                                 break;
1269                         case STAGE_THERMAL_INIT:
1270                                 stage_print("  -> thermal init\n\n");
1271                                 thermal_init(moldyn,TRUE);
1272                                 change_stage=TRUE;
1273                                 break;
1274                         default:
1275                                 printf("%s unknwon stage type\n",ME);
1276                                 break;
1277                 }
1278
1279                 /* mark as executed */
1280                 stage->executed=TRUE;
1281
1282                 /* change state */
1283                 if(change_stage==TRUE) {
1284                         printf("%s finished stage\n",ME);
1285                         if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
1286                                 printf("%s no more stages\n",ME);
1287                                 return 0;
1288                         }
1289                         steps=0;
1290                 }
1291
1292         }
1293         else {
1294
1295                 /* averages */
1296                 if(mdrun->sattr&SATTR_AVGRST)
1297                         average_reset(moldyn);
1298
1299         }
1300
1301         /* continue simulation */
1302         moldyn_add_schedule(moldyn,steps,mdrun->timestep);
1303
1304         return 0;
1305 }
1306
1307 int main(int argc,char **argv) {
1308
1309         t_mdrun mdrun;
1310         t_moldyn moldyn;
1311         //t_3dvec o;
1312
1313         /* clear structs */
1314         memset(&mdrun,0,sizeof(t_mdrun));
1315         memset(&moldyn,0,sizeof(t_moldyn));
1316
1317         /* parse arguments */
1318         if(mdrun_parse_argv(&mdrun,argc,argv)<0)
1319                 return -1;
1320
1321         /* initialize list system */
1322         list_init_f(&(mdrun.stage));
1323
1324         /* parse config file */
1325         mdrun_parse_config(&mdrun);
1326
1327         /* reset the stage list */
1328         list_reset_f(&(mdrun.stage));
1329
1330         /* sanity check! */
1331
1332         /* prepare simulation */
1333
1334         if(mdrun.continue_file[0]) {
1335                 // read the save file
1336                 moldyn_read_save_file(&moldyn,mdrun.continue_file);
1337                 // manualaadjusting some stuff
1338                 moldyn.argc=argc;
1339                 moldyn.args=argv;
1340                 rand_init(&(moldyn.random),NULL,1);
1341                 moldyn.random.status|=RAND_STAT_VERBOSE;
1342         }
1343         else {
1344                 moldyn_init(&moldyn,argc,argv);
1345         }
1346
1347         if(set_int_alg(&moldyn,mdrun.intalgo)<0)
1348                 return -1;
1349
1350         /* potential */
1351         set_cutoff(&moldyn,mdrun.cutoff);
1352         if(set_potential(&moldyn,mdrun.potential)<0)
1353                 return -1;
1354         switch(mdrun.potential) {
1355                 case MOLDYN_POTENTIAL_AM:
1356                         albe_mult_set_params(&moldyn,
1357                                              mdrun.element1,
1358                                              mdrun.element2);
1359                         break;
1360                 case MOLDYN_POTENTIAL_TM:
1361                         tersoff_mult_set_params(&moldyn,
1362                                                 mdrun.element1,
1363                                                 mdrun.element2);
1364                         break;
1365                 case MOLDYN_POTENTIAL_HO:
1366                         harmonic_oscillator_set_params(&moldyn,mdrun.element1);
1367                         break;
1368                 case MOLDYN_POTENTIAL_LJ:
1369                         lennard_jones_set_params(&moldyn,mdrun.element1);
1370                         break;
1371                 default:
1372                         printf("%s unknown potential: %02x\n",
1373                                ME,mdrun.potential);
1374                         return -1;
1375         }
1376
1377         /* if it is a continue run, reset schedule and skip lattice init */
1378         if(mdrun.continue_file[0]) {
1379                 memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
1380                 goto addsched;
1381         }
1382
1383         /* initial lattice and dimensions */
1384         set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
1385         set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
1386         /* replaced by fill stage !!
1387         switch(mdrun.lattice) {
1388                 case FCC:
1389                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
1390                                        mdrun.m1,DEFAULT_ATOM_ATTR,
1391                                        mdrun.fill_brand,mdrun.lx,
1392                                        mdrun.ly,mdrun.lz,NULL,0,NULL);
1393                         break;
1394                 case DIAMOND:
1395                         create_lattice(&moldyn,DIAMOND,mdrun.lc,
1396                                        mdrun.fill_element,
1397                                        mdrun.m1,DEFAULT_ATOM_ATTR,
1398                                        mdrun.fill_brand,mdrun.lx,
1399                                        mdrun.ly,mdrun.lz,NULL,0,NULL);
1400                         break;
1401                 case ZINCBLENDE:
1402                         o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1403                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
1404                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1405                                        mdrun.ly,mdrun.lz,&o,0,NULL);
1406                         o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1407                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
1408                                        mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
1409                                        mdrun.ly,mdrun.lz,&o,0,NULL);
1410                         break;
1411                 case NONE:
1412                         set_nn_dist(&moldyn,mdrun.nnd);
1413                         break;
1414                 default:
1415                         printf("%s unknown lattice type: %02x\n",
1416                                ME,mdrun.lattice);
1417                         return -1;
1418         }
1419         moldyn_bc_check(&moldyn);
1420         replaced by fill stage !! */
1421
1422         /* temperature and pressure */
1423         set_temperature(&moldyn,mdrun.temperature);
1424         set_pressure(&moldyn,mdrun.pressure);
1425         /* replaced thermal_init stage
1426         thermal_init(&moldyn,TRUE);
1427         */
1428
1429 addsched:
1430         /* first schedule */
1431         moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
1432
1433         /* log */
1434         moldyn_set_log_dir(&moldyn,mdrun.sdir);
1435         moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
1436         if(mdrun.elog)
1437                 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
1438         if(mdrun.tlog)
1439                 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
1440         if(mdrun.plog)
1441                 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
1442         if(mdrun.vlog)
1443                 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
1444         if(mdrun.visualize)
1445                 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
1446         if(mdrun.save)
1447                 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
1448         moldyn_set_log(&moldyn,CREATE_REPORT,0);
1449         set_avg_skip(&moldyn,mdrun.avgskip);
1450
1451         /* prepare the hook function */
1452         moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
1453
1454         /* run the simulation */
1455         moldyn_integrate(&moldyn);
1456
1457         /* shutdown */
1458         moldyn_shutdown(&moldyn);
1459         del_stages(&mdrun);
1460         list_destroy_f(&(mdrun.stage));
1461
1462         return 0;
1463 }