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