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_INSERT_ATOMS:
 102                         psize=sizeof(t_insert_atoms_params);
 103                         break;
 104                 case STAGE_INSERT_MIXED_ATOMS:
 105                         psize=sizeof(t_insert_mixed_atoms_params);
 106                         break;
 107                 case STAGE_CONTINUE:
 108                         psize=sizeof(t_continue_params);
 109                         break;
 110                 case STAGE_ANNEAL:
 111                         psize=sizeof(t_anneal_params);
 112                         break;
 113                 case STAGE_CHAATTR:
 114                         psize=sizeof(t_chaattr_params);
 115                         break;
 116                 case STAGE_CHSATTR:
 117                         psize=sizeof(t_chsattr_params);
 118                         break;
 119                 case STAGE_SET_TEMP:
 120                         psize=sizeof(t_set_temp_params);
 121                         break;
 122                 case STAGE_SET_TIMESTEP:
 123                         psize=sizeof(t_set_timestep_params);
 124                         break;
 125                 case STAGE_FILL:
 126                         psize=sizeof(t_fill_params);
 127                         break;
 128                 case STAGE_THERMAL_INIT:
 129                         psize=0;
 130                         break;
 131                 default:
 132                         printf("%s unknown stage type: %02x\n",ME,type);
 133                         return -1;
 134         }
 135
 136         stage=malloc(sizeof(t_stage));
 137         if(stage==NULL) {
 138                 perror("[mdrun] malloc (add stage)");
 139                 return -1;
 140         }
 141
 142         stage->type=type;
 143         stage->executed=FALSE;
 144
 145         stage->params=malloc(psize);
 146         if(stage->params==NULL) {
 147                 perror("[mdrun] malloc (stage params)");
 148                 return -1;
 149         }
 150
 151         memcpy(stage->params,params,psize);
 152
 153         list_add_immediate_f(&(mdrun->stage),stage);
 154
 155         return 0;
 156 }
 157
 158 int mdrun_parse_config(t_mdrun *mdrun) {
 159
 160         int fd,ret;
 161         char error[128];
 162         char line[128];
 163         char *wptr;
 164         char word[16][64];
 165         int wcnt;
 166         int i,o;
 167
 168         t_displace_atom_params dap;
 169         t_insert_atoms_params iap;
 170         t_insert_mixed_atoms_params imp;
 171         t_continue_params cp;
 172         t_anneal_params ap;
 173         t_chaattr_params cap;
 174         t_chsattr_params csp;
 175         t_set_temp_params stp;
 176         t_set_timestep_params stsp;
 177         t_fill_params fp;
 178
 179         /* open config file */
 180         fd=open(mdrun->cfile,O_RDONLY);
 181         if(fd<0) {
 182                 snprintf(error,128,"%s open cfile %s",ME,mdrun->cfile);
 183                 perror(error);
 184                 return fd;
 185         }
 186
 187         /* read, parse, set */
 188         ret=1;
 189         while(ret>0) {
 190
 191                 /* read */
 192                 ret=get_line(fd,line,128);
 193
 194                 /* parse */
 195
 196                 // ignore # lines and \n
 197                 if((line[0]=='#')|(ret==1))
 198                         continue;
 199
 200                 // reset
 201                 memset(&iap,0,sizeof(t_insert_atoms_params));
 202                 memset(&imp,0,sizeof(t_insert_mixed_atoms_params));
 203                 memset(&cp,0,sizeof(t_continue_params));
 204                 memset(&ap,0,sizeof(t_anneal_params));
 205                 memset(&cap,0,sizeof(t_chaattr_params));
 206                 memset(&csp,0,sizeof(t_chsattr_params));
 207                 memset(&stp,0,sizeof(t_set_temp_params));
 208                 memset(&stsp,0,sizeof(t_set_timestep_params));
 209                 memset(&fp,0,sizeof(t_fill_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                 }
 281                 else if(!strncmp(word[0],"element1",8)) {
 282                         mdrun->element1=atoi(word[1]);
 283                         mdrun->m1=pse_mass[mdrun->element1];
 284                 }
 285                 else if(!strncmp(word[0],"element2",8)) {
 286                         mdrun->element2=atoi(word[1]);
 287                         mdrun->m2=pse_mass[mdrun->element2];
 288                 }
 289                 else if(!strncmp(word[0],"fill",6)) {
 290                         fp.lx=atoi(word[2]);
 291                         fp.ly=atoi(word[3]);
 292                         fp.lz=atoi(word[4]);
 293                         fp.lc=atof(word[5]);
 294                         mdrun->lc=fp.lc;
 295                         if(!strncmp(word[1],"lc",2)) {
 296                                 if(wcnt==8) {
 297                                         fp.fill_element=atoi(word[6]);
 298                                         fp.fill_brand=atoi(word[7]);
 299                                 }
 300                                 else {
 301                                         fp.fill_element=mdrun->element1;
 302                                         fp.fill_brand=0;
 303                                 }
 304                         }
 305                         else {
 306                                 switch(word[6][0]) {
 307                                         case 'i':
 308                                                 if(word[6][1]=='r')
 309                                                         fp.p_type=PART_INSIDE_R;
 310                                                 else
 311                                                         fp.p_type=PART_INSIDE_D;
 312                                                 break;
 313                                         case 'o':
 314                                                 if(word[6][1]=='r')
 315                                                 fp.p_type=PART_OUTSIDE_R;
 316                                                 else
 317                                                 fp.p_type=PART_OUTSIDE_D;
 318                                                 break;
 319                                         default:
 320                                                 break;
 321                                 }
 322                         }
 323                         if((fp.p_type==PART_INSIDE_R)||
 324                            (fp.p_type==PART_OUTSIDE_R)) {
 325                                 fp.p_vals.r=atof(word[7]);
 326                                 fp.p_vals.p.x=atof(word[8]);
 327                                 fp.p_vals.p.y=atof(word[9]);
 328                                 fp.p_vals.p.z=atof(word[10]);
 329                         }
 330                         if((fp.p_type==PART_INSIDE_D)||
 331                            (fp.p_type==PART_OUTSIDE_D)) {
 332                                 fp.p_vals.p.x=atof(word[7]);
 333                                 fp.p_vals.p.y=atof(word[8]);
 334                                 fp.p_vals.p.z=atof(word[9]);
 335                                 fp.p_vals.d.x=atof(word[10]);
 336                                 fp.p_vals.d.y=atof(word[11]);
 337                                 fp.p_vals.d.z=atof(word[12]);
 338                         }
 339                         fp.lattice=mdrun->lattice;
 340                         add_stage(mdrun,STAGE_FILL,&fp);
 341                 }
 342                 else if(!strncmp(word[0],"thermal_init",12)) {
 343                         add_stage(mdrun,STAGE_THERMAL_INIT,NULL);
 344                 }
 345                 else if(!strncmp(word[0],"aattr",5)) {
 346                         // for aatrib line we need a special stage
 347                         // containing one schedule of 0 loops ...
 348                         for(i=0;i<strlen(word[1]);i++) {
 349                                 switch(word[1][i]) {
 350                                         case 't':
 351                                                 cap.type|=CHAATTR_TOTALV;
 352                                                 break;
 353                                         case 'r':
 354                                                 cap.type|=CHAATTR_REGION;
 355                                                 break;
 356                                         case 'e':
 357                                                 cap.type|=CHAATTR_ELEMENT;
 358                                                 break;
 359                                         default:
 360                                                 break;
 361                                 }
 362                         }
 363                         i=2;
 364                         if(cap.type&CHAATTR_REGION) {
 365                                 cap.x0=atof(word[1]);
 366                                 cap.y0=atof(word[2]);
 367                                 cap.z0=atof(word[3]);
 368                                 cap.x1=atof(word[4]);
 369                                 cap.y1=atof(word[5]);
 370                                 cap.z1=atof(word[6]);
 371                                 i+=6;
 372                         }
 373                         if(cap.type&CHAATTR_ELEMENT) {
 374                                 cap.element=atoi(word[i]);
 375                                 i+=1;
 376                         }
 377                         for(o=0;o<strlen(word[i]);o++) {
 378                                 switch(word[i][o]) {
 379                                         case 'b':
 380                                                 cap.attr|=ATOM_ATTR_VB;
 381                                                 break;
 382                                         case 'h':
 383                                                 cap.attr|=ATOM_ATTR_HB;
 384                                                 break;
 385                                         case 'v':
 386                                                 cap.attr|=ATOM_ATTR_VA;
 387                                                 break;
 388                                         case 'f':
 389                                                 cap.attr|=ATOM_ATTR_FP;
 390                                                 break;
 391                                         case '1':
 392                                                 cap.attr|=ATOM_ATTR_1BP;
 393                                                 break;
 394                                         case '2':
 395                                                 cap.attr|=ATOM_ATTR_2BP;
 396                                                 break;
 397                                         case '3':
 398                                                 cap.attr|=ATOM_ATTR_3BP;
 399                                                 break;
 400                                         default:
 401                                                 break;
 402                                 }
 403                         }
 404                         add_stage(mdrun,STAGE_CHAATTR,&cap);
 405                 }
 406                 else if(!strncmp(word[0],"sattr",5)) {
 407                         // for satrib line we need a special stage
 408                         // containing one schedule of 0 loops ...
 409                         csp.type=0;
 410                         for(i=1;i<wcnt;i++) {
 411                                 if(!strncmp(word[i],"pctrl",5)) {
 412                                         csp.ptau=0.01/(atof(word[++i])*GPA);
 413                                         csp.type|=CHSATTR_PCTRL;
 414                                 }
 415                                 if(!strncmp(word[i],"tctrl",5)) {
 416                                         csp.ttau=atof(word[++i]);
 417                                         csp.type|=CHSATTR_TCTRL;
 418                                 }
 419                                 if(!strncmp(word[i],"prelax",6)) {
 420                                         csp.dp=atof(word[++i])*BAR;
 421                                         csp.type|=CHSATTR_PRELAX;
 422                                 }
 423                                 if(!strncmp(word[i],"trelax",6)) {
 424                                         csp.dt=atof(word[++i]);
 425                                         csp.type|=CHSATTR_TRELAX;
 426                                 }
 427                                 if(!strncmp(word[i],"rsteps",6)) {
 428                                         csp.rsteps=atoi(word[++i]);
 429                                         csp.type|=CHSATTR_RSTEPS;
 430                                 }
 431                                 if(!strncmp(word[i],"avgrst",6)) {
 432                                         csp.avgrst=atoi(word[++i]);
 433                                         csp.type|=CHSATTR_AVGRST;
 434                                 }
 435                         }
 436                         add_stage(mdrun,STAGE_CHSATTR,&csp);
 437                 }
 438                 else if(!strncmp(word[0],"prerun",6))
 439                         mdrun->prerun=atoi(word[1]);
 440                 else if(!strncmp(word[0],"avgskip",7))
 441                         mdrun->avgskip=atoi(word[1]);
 442                 else if(!strncmp(word[0],"elog",4))
 443                         mdrun->elog=atoi(word[1]);
 444                 else if(!strncmp(word[0],"tlog",4))
 445                         mdrun->tlog=atoi(word[1]);
 446                 else if(!strncmp(word[0],"plog",4))
 447                         mdrun->plog=atoi(word[1]);
 448                 else if(!strncmp(word[0],"vlog",4))
 449                         mdrun->vlog=atoi(word[1]);
 450                 else if(!strncmp(word[0],"save",4))
 451                         mdrun->save=atoi(word[1]);
 452                 else if(!strncmp(word[0],"visualize",9))
 453                         mdrun->visualize=atoi(word[1]);
 454                 else if(!strncmp(word[0],"stage",5)) {
 455                         // for every stage line, add a stage
 456                         if(!strncmp(word[1],"displace",8)) {
 457                                 dap.nr=atoi(word[2]);
 458                                 dap.dx=atof(word[3]);
 459                                 dap.dy=atof(word[4]);
 460                                 dap.dz=atof(word[5]);
 461                                 add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
 462                         }
 463                         else if(!strncmp(word[1],"ins_atoms",9)) {
 464                                 iap.ins_steps=atoi(word[2]);
 465                                 iap.ins_atoms=atoi(word[3]);
 466                                 iap.element=atoi(word[4]);
 467                                 iap.brand=atoi(word[5]);
 468                                 for(i=0;i<strlen(word[6]);i++) {
 469                                         switch(word[6][i]) {
 470                                                 case 'b':
 471                                                         iap.attr|=ATOM_ATTR_VB;
 472                                                         break;
 473                                                 case 'h':
 474                                                         iap.attr|=ATOM_ATTR_HB;
 475                                                         break;
 476                                                 case 'v':
 477                                                         iap.attr|=ATOM_ATTR_VA;
 478                                                         break;
 479                                                 case 'f':
 480                                                         iap.attr|=ATOM_ATTR_FP;
 481                                                         break;
 482                                                 case '1':
 483                                                         iap.attr|=ATOM_ATTR_1BP;
 484                                                         break;
 485                                                 case '2':
 486                                                         iap.attr|=ATOM_ATTR_2BP;
 487                                                         break;
 488                                                 case '3':
 489                                                         iap.attr|=ATOM_ATTR_3BP;
 490                                                         break;
 491                                                 default:
 492                                                         break;
 493                                         }
 494                                 }
 495                                 switch(word[7][0]) {
 496                                         // insertion types
 497                                         case 'p':
 498                                                 iap.type=INS_POS;
 499                                                 iap.x0=atof(word[8]);
 500                                                 iap.y0=atof(word[9]);
 501                                                 iap.z0=atof(word[10]);
 502                                                 break;
 503                                         case 'r':
 504                                                 if(word[8][0]=='t') {
 505                                                         iap.type=INS_TOTAL;
 506                                                         iap.cr=atof(word[9]);
 507                                                 }
 508                                                 else {
 509                                                         iap.type=INS_REGION;
 510                                                         iap.x0=atof(word[8]);
 511                                                         iap.y0=atof(word[9]);
 512                                                         iap.z0=atof(word[10]);
 513                                                         iap.x1=atof(word[11]);
 514                                                         iap.y1=atof(word[12]);
 515                                                         iap.z1=atof(word[13]);
 516                                                         iap.cr=atof(word[14]);
 517                                                 }
 518                                         default:
 519                                                 break;
 520                                 }
 521                                 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
 522                         }
 523
 524
 525                         // HERE WE GO ...
 526
 527                         else if(!strncmp(word[1],"ins_m_atoms",11)) {
 528                                 imp.element1=atoi(word[2]);
 529                                 imp.element2=atoi(word[3]);
 530                                 imp.amount1=atoi(word[4]);
 531                                 imp.amount2=atoi(word[5]);
 532                                 imp.brand1=atoi(word[6]);
 533                                 imp.brand2=atoi(word[7]);
 534                                 imp.crmin=atof(word[8]);
 535                                 imp.crmax=atof(word[9]);
 536                                 /* do this later ...
 537                                 for(i=0;i<strlen(word[8]);i++) {
 538                                         switch(word[8][i]) {
 539                                                 case 'b':
 540                                                         imp.attr|=ATOM_ATTR_VB;
 541                                                         break;
 542                                                 case 'h':
 543                                                         imp.attr|=ATOM_ATTR_HB;
 544                                                         break;
 545                                                 case 'v':
 546                                                         imp.attr|=ATOM_ATTR_VA;
 547                                                         break;
 548                                                 case 'f':
 549                                                         imp.attr|=ATOM_ATTR_FP;
 550                                                         break;
 551                                                 case '1':
 552                                                         imp.attr|=ATOM_ATTR_1BP;
 553                                                         break;
 554                                                 case '2':
 555                                                         imp.attr|=ATOM_ATTR_2BP;
 556                                                         break;
 557                                                 case '3':
 558                                                         imp.attr|=ATOM_ATTR_3BP;
 559                                                         break;
 560                                                 default:
 561                                                         break;
 562                                         }
 563                                 }
 564                                 */
 565                                 imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 566                                 imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 567                                 add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
 568                         }
 569
 570
 571
 572
 573
 574                         else if(!strncmp(word[1],"continue",8)) {
 575                                 cp.runs=atoi(word[2]);
 576                                 add_stage(mdrun,STAGE_CONTINUE,&cp);
 577                         }
 578                         else if(!strncmp(word[1],"anneal",6)) {
 579                                 ap.count=0;
 580                                 ap.runs=atoi(word[2]);
 581                                 ap.dt=atof(word[3]);
 582                                 ap.interval=atoi(word[4]);
 583                                 add_stage(mdrun,STAGE_ANNEAL,&ap);
 584                         }
 585                         else if(!strncmp(word[1],"set_temp",8)) {
 586                                 if(word[2][0]=='c') {
 587                                         stp.type=SET_TEMP_CURRENT;
 588                                         stp.val=0.0;
 589                                 }
 590                                 else {
 591                                         stp.type=SET_TEMP_VALUE;
 592                                         stp.val=atof(word[2]);
 593                                 }
 594                                 add_stage(mdrun,STAGE_SET_TEMP,&stp);
 595                         }
 596                         else if(!strncmp(word[1],"set_timestep",12)) {
 597                                 stsp.tau=atof(word[2]);
 598                                 add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
 599                         }
 600                         else {
 601                                 printf("%s unknown stage type: %s\n",
 602                                        ME,word[1]);
 603                                 return -1;
 604                         }
 605                 }
 606                 else {
 607                         printf("%s unknown keyword '%s', skipped!\n",
 608                                ME,word[0]);
 609                         continue;
 610                 }
 611         }
 612
 613         /* close file */
 614         close(fd);
 615
 616         return 0;
 617 }
 618
 619 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
 620
 621         double delta;
 622
 623         if(!(mdrun->sattr&SATTR_PRELAX)) {
 624                 return TRUE;
 625         }
 626
 627         delta=moldyn->p_avg-moldyn->p_ref;
 628
 629         if(delta<0)
 630                 delta=-delta;
 631
 632         if(delta>mdrun->dp)
 633                 return FALSE;
 634
 635         return TRUE;
 636 }
 637
 638 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 639
 640         double delta;
 641
 642         if(!(mdrun->sattr&SATTR_TRELAX))
 643                 return TRUE;
 644
 645         delta=moldyn->t_avg-moldyn->t_ref;
 646
 647         if(delta<0)
 648                 delta=-delta;
 649
 650         if(delta>mdrun->dt)
 651                 return FALSE;
 652
 653         return TRUE;
 654 }
 655
 656 int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
 657
 658         t_displace_atom_params *dap;
 659         t_stage *stage;
 660         t_atom *atom;
 661
 662         stage=mdrun->stage.current->data;
 663         dap=stage->params;
 664
 665         atom=&(moldyn->atom[dap->nr]);
 666         atom->r.x+=dap->dx;
 667         atom->r.y+=dap->dy;
 668         atom->r.z+=dap->dz;
 669
 670         return 0;
 671 }
 672
 673 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 674
 675         t_insert_atoms_params *iap;
 676         t_stage *stage;
 677         t_atom *atom;
 678         t_3dvec r,v,dist;
 679         double d,dmin,o;
 680         int cnt,i;
 681         double x,y,z;
 682         double x0,y0,z0;
 683         u8 cr_check,run;
 684
 685         stage=mdrun->stage.current->data;
 686         iap=stage->params;
 687
 688         cr_check=FALSE;
 689
 690         v.x=0.0; v.y=0.0; v.z=0.0;
 691         x=0; y=0; z=0;
 692         o=0; dmin=0;
 693
 694         switch(mdrun->lattice) {
 695                 case CUBIC:
 696                         o=0.5*mdrun->lc;
 697                         break;
 698                 case FCC:
 699                         o=0.25*mdrun->lc;
 700                         break;
 701                 case DIAMOND:
 702                 case ZINCBLENDE:
 703                         o=0.125*mdrun->lc;
 704                         break;
 705                 default:
 706                         break;
 707         }
 708
 709         switch(iap->type) {
 710                 case INS_TOTAL:
 711                         x=moldyn->dim.x;
 712                         x0=-x/2.0;
 713                         y=moldyn->dim.y;
 714                         y0=-y/2.0;
 715                         z=moldyn->dim.z;
 716                         z0=-z/2.0;
 717                         cr_check=TRUE;
 718                         break;
 719                 case INS_REGION:
 720                         x=iap->x1-iap->x0;
 721                         x0=iap->x0;
 722                         y=iap->y1-iap->y0;
 723                         y0=iap->y0;
 724                         z=iap->z1-iap->z0;
 725                         z0=iap->z0;
 726                         cr_check=TRUE;
 727                         break;
 728                 case INS_POS:
 729                         x0=iap->x0;
 730                         y0=iap->y0;
 731                         z0=iap->z0;
 732                         cr_check=FALSE;
 733                         break;
 734                 default:
 735                         printf("%s unknown insertion mode: %02x\n",
 736                                ME,iap->type);
 737                         return -1;
 738         }
 739
 740         cnt=0;
 741         while(cnt<iap->ins_atoms) {
 742                 run=1;
 743                 while(run) {
 744                         if(iap->type!=INS_POS) {
 745                                 r.x=rand_get_double(&(moldyn->random))*x;
 746                                 r.y=rand_get_double(&(moldyn->random))*y;
 747                                 r.z=rand_get_double(&(moldyn->random))*z;
 748                         }
 749                         else {
 750                                 r.x=0.0;
 751                                 r.y=0.0;
 752                                 r.z=0.0;
 753                         }
 754                         r.x+=x0;
 755                         r.y+=y0;
 756                         r.z+=z0;
 757                         // offset
 758                         if(iap->type!=INS_TOTAL) {
 759                                 r.x+=o;
 760                                 r.y+=o;
 761                                 r.z+=o;
 762                         }
 763                         run=0;
 764                         if(cr_check==TRUE) {
 765                                 dmin=1000;      // for sure too high!
 766                                 for(i=0;i<moldyn->count;i++) {
 767                                         atom=&(moldyn->atom[i]);
 768                                         v3_sub(&dist,&(atom->r),&r);
 769                                         check_per_bound(moldyn,&dist);
 770                                         d=v3_absolute_square(&dist);
 771                                         if(d<(iap->cr*iap->cr)) {
 772                                                 run=1;
 773                                                 break;
 774                                         }
 775                                         if(d<dmin)
 776                                                 dmin=d;
 777                                 }
 778                         }
 779                 }
 780                 add_atom(moldyn,iap->element,pse_mass[iap->element],
 781                          iap->brand,iap->attr,&r,&v);
 782                 printf("%s atom inserted (%d/%d): %f %f %f\n",
 783                        ME,(iap->cnt_steps+1)*iap->ins_atoms,
 784                        iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
 785                 printf("  -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
 786                 cnt+=1;
 787         }
 788
 789         return 0;
 790 }
 791
 792 int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 793
 794         t_stage *stage;
 795         t_insert_mixed_atoms_params *imp;
 796         t_atom *atom;
 797         double x,x0,y,y0,z,z0;
 798         double dmin,d,cmin,cmax;
 799         u8 retry;
 800         t_3dvec r,v,dist;
 801         int i;
 802
 803
 804         stage=mdrun->stage.current->data;
 805         imp=stage->params;
 806
 807         x=moldyn->dim.x;
 808         x0=-x/2.0;
 809         y=moldyn->dim.y;
 810         y0=-y/2.0;
 811         z=moldyn->dim.z;
 812         z0=-z/2.0;
 813
 814         v.x=0.0;
 815         v.y=0.0;
 816         v.z=0.0;
 817
 818         cmin=imp->crmin*imp->crmin;
 819         cmax=imp->crmax*imp->crmax;
 820
 821         while(imp->amount1|imp->amount2) {
 822                 if(imp->amount1) {
 823                         retry=1;
 824                         while(retry) {
 825                                 retry=0;
 826                                 r.x=rand_get_double(&(moldyn->random))*x;
 827                                 r.y=rand_get_double(&(moldyn->random))*y;
 828                                 r.z=rand_get_double(&(moldyn->random))*z;
 829                                 r.x+=x0;
 830                                 r.y+=y0;
 831                                 r.z+=z0;
 832                                 dmin=1000.0;    // for sure too high!
 833                                 for(i=0;i<moldyn->count;i++) {
 834                                         atom=&(moldyn->atom[i]);
 835                                         v3_sub(&dist,&(atom->r),&r);
 836                                         check_per_bound(moldyn,&dist);
 837                                         d=v3_absolute_square(&dist);
 838                                         if(d<cmin) {
 839                                                 retry=1;
 840                                                 break;
 841                                         }
 842                                         if(d<dmin)
 843                                                 dmin=d;
 844                                 }
 845                                 if(dmin!=1000.0)
 846                                         if(dmin>cmax)
 847                                                 retry=1;
 848                         }
 849                         add_atom(moldyn,imp->element1,pse_mass[imp->element1],
 850                                  imp->brand1,imp->attr1,&r,&v);
 851                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
 852                                ME,imp->amount1,r.x,r.y,r.z);
 853                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
 854                         imp->amount1-=1;
 855                 }
 856                 if(imp->amount2) {
 857                         retry=1;
 858                         while(retry) {
 859                                 retry=0;
 860                                 r.x=rand_get_double(&(moldyn->random))*x;
 861                                 r.y=rand_get_double(&(moldyn->random))*y;
 862                                 r.z=rand_get_double(&(moldyn->random))*z;
 863                                 r.x+=x0;
 864                                 r.y+=y0;
 865                                 r.z+=z0;
 866                                 dmin=1000.0;    // for sure too high!
 867                                 for(i=0;i<moldyn->count;i++) {
 868                                         atom=&(moldyn->atom[i]);
 869                                         v3_sub(&dist,&(atom->r),&r);
 870                                         check_per_bound(moldyn,&dist);
 871                                         d=v3_absolute_square(&dist);
 872                                         if(d<cmin) {
 873                                                 retry=1;
 874                                                 break;
 875                                         }
 876                                         if(d<dmin)
 877                                                 dmin=d;
 878                                 }
 879                                 if(dmin!=1000.0)
 880                                         if(dmin>cmax)
 881                                                 retry=1;
 882                         }
 883                         add_atom(moldyn,imp->element2,pse_mass[imp->element2],
 884                                  imp->brand2,imp->attr2,&r,&v);
 885                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
 886                                ME,imp->amount2,r.x,r.y,r.z);
 887                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
 888                         imp->amount2-=1;
 889                 }
 890         }
 891
 892         return 0;
 893 }
 894
 895 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 896
 897         t_stage *stage;
 898         t_chaattr_params *cap;
 899         t_atom *atom;
 900         int i;
 901
 902         stage=mdrun->stage.current->data;
 903         cap=stage->params;
 904
 905         for(i=0;i<moldyn->count;i++) {
 906                 atom=&(moldyn->atom[i]);
 907                 if(cap->type&CHAATTR_ELEMENT) {
 908                         if(cap->element!=atom->element)
 909                                 continue;
 910                 }
 911                 if(cap->type&CHAATTR_REGION) {
 912                         if(cap->x0<atom->r.x)
 913                                 continue;
 914                         if(cap->y0<atom->r.y)
 915                                 continue;
 916                         if(cap->z0<atom->r.z)
 917                                 continue;
 918                         if(cap->x1>atom->r.x)
 919                                 continue;
 920                         if(cap->y1>atom->r.y)
 921                                 continue;
 922                         if(cap->z1>atom->r.z)
 923                                 continue;
 924                 }
 925                 atom->attr=cap->attr;
 926         }
 927
 928         return 0;
 929 }
 930
 931 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 932
 933         t_stage *stage;
 934         t_chsattr_params *csp;
 935
 936         stage=mdrun->stage.current->data;
 937         csp=stage->params;
 938
 939         if(csp->type&CHSATTR_PCTRL) {
 940                 if(csp->ptau>0)
 941                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 942                 else
 943                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 944         }
 945         if(csp->type&CHSATTR_TCTRL) {
 946                 if(csp->ttau>0)
 947                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 948                 else
 949                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 950         }
 951         if(csp->type&CHSATTR_PRELAX) {
 952                 if(csp->dp<0)
 953                         mdrun->sattr&=(~(SATTR_PRELAX));
 954                 else
 955                         mdrun->sattr|=SATTR_PRELAX;
 956                 mdrun->dp=csp->dp;
 957         }
 958         if(csp->type&CHSATTR_TRELAX) {
 959                 if(csp->dt<0)
 960                         mdrun->sattr&=(~(SATTR_TRELAX));
 961                 else
 962                         mdrun->sattr|=SATTR_TRELAX;
 963                 mdrun->dt=csp->dt;
 964         }
 965         if(csp->type&CHSATTR_AVGRST) {
 966                 if(csp->avgrst)
 967                         mdrun->sattr|=SATTR_AVGRST;
 968                 else
 969                         mdrun->sattr&=(~(SATTR_AVGRST));
 970         }
 971         if(csp->type&CHSATTR_RSTEPS) {
 972                 mdrun->relax_steps=csp->rsteps;
 973         }
 974
 975         return 0;
 976 }
 977
 978 #define stage_print(m)  if(!(stage->executed)) \
 979                                 printf("%s",m)
 980
 981 int mdrun_hook(void *ptr1,void *ptr2) {
 982
 983         t_moldyn *moldyn;
 984         t_mdrun *mdrun;
 985         t_stage *stage;
 986         t_list *sl;
 987         int steps;
 988         u8 change_stage;
 989         t_3dvec o;
 990
 991         t_insert_atoms_params *iap;
 992         t_insert_mixed_atoms_params *imp;
 993         t_continue_params *cp;
 994         t_anneal_params *ap;
 995         t_set_temp_params *stp;
 996         t_set_timestep_params *stsp;
 997         t_fill_params *fp;
 998
 999         moldyn=ptr1;
1000         mdrun=ptr2;
1001
1002         sl=&(mdrun->stage);
1003
1004         change_stage=FALSE;
1005
1006         /* return immediately if there are no more stage */
1007         if(sl->current==NULL)
1008                 return 0;
1009
1010         /* get stage description */
1011         stage=sl->current->data;
1012
1013         /* steps in next schedule */
1014         steps=mdrun->relax_steps;
1015
1016         /* check whether relaxation steps are necessary */
1017         if((check_pressure(moldyn,mdrun)==TRUE)&\
1018            (check_temperature(moldyn,mdrun)==TRUE)) {
1019
1020                 /* be verbose */
1021                 stage_print("\n###########################\n");
1022                 stage_print("# [mdrun] executing stage #\n");
1023                 stage_print("###########################\n\n");
1024
1025                 /* stage specific stuff */
1026                 switch(stage->type) {
1027                         case STAGE_DISPLACE_ATOM:
1028                                 stage_print("  -> displace atom\n\n");
1029                                 displace_atom(moldyn,mdrun);
1030                                 change_stage=TRUE;
1031                                 break;
1032                         case STAGE_INSERT_ATOMS:
1033                                 stage_print("  -> insert atoms\n\n");
1034                                 iap=stage->params;
1035                                 if(iap->cnt_steps==iap->ins_steps) {
1036                                         change_stage=TRUE;
1037                                         break;
1038                                 }
1039                                 insert_atoms(moldyn,mdrun);
1040                                 iap->cnt_steps+=1;
1041                                 break;
1042
1043
1044
1045                         case STAGE_INSERT_MIXED_ATOMS:
1046                                 stage_print("  -> insert mixed atoms\n\n");
1047                                 imp=stage->params;
1048                                 insert_mixed_atoms(moldyn,mdrun);
1049                                 change_stage=TRUE;
1050                                 break;
1051
1052
1053
1054                         case STAGE_CONTINUE:
1055                                 stage_print("  -> continue\n\n");
1056                                 if(stage->executed==TRUE) {
1057                                         change_stage=TRUE;
1058                                         break;
1059                                 }
1060                                 cp=stage->params;
1061                                 steps=cp->runs;
1062                                 break;
1063                         case STAGE_ANNEAL:
1064                                 stage_print("  -> anneal\n\n");
1065                                 ap=stage->params;
1066                                 if(ap->count==ap->runs) {
1067                                         change_stage=TRUE;
1068                                         break;
1069                                 }
1070                                 if(moldyn->t_ref+ap->dt>=0.0)
1071                                         set_temperature(moldyn,
1072                                                         moldyn->t_ref+ap->dt);
1073                                 ap->count+=1;
1074                                 steps=ap->interval;
1075                                 break;
1076                         case STAGE_CHAATTR:
1077                                 stage_print("  -> change atom attributes\n\n");
1078                                 chaatr(moldyn,mdrun);
1079                                 change_stage=TRUE;
1080                                 break;
1081                         case STAGE_CHSATTR:
1082                                 stage_print("  -> change sys attributes\n\n");
1083                                 chsattr(moldyn,mdrun);
1084                                 change_stage=TRUE;
1085                                 break;
1086                         case STAGE_SET_TEMP:
1087                                 stage_print("  -> set temperature\n\n");
1088                                 stp=stage->params;
1089                                 if(stp->type&SET_TEMP_CURRENT) {
1090                                         set_temperature(moldyn,moldyn->t_avg);
1091                                 }
1092                                 else {
1093                                         set_temperature(moldyn,stp->val);
1094                                 }
1095                                 change_stage=TRUE;
1096                                 break;
1097                         case STAGE_SET_TIMESTEP:
1098                                 stage_print("  -> set timestep\n\n");
1099                                 stsp=stage->params;
1100                                 mdrun->timestep=stsp->tau;
1101                                 change_stage=TRUE;
1102                                 break;
1103                         case STAGE_FILL:
1104                                 stage_print("  -> fill lattice\n\n");
1105                                 fp=stage->params;
1106                                 if(fp->lattice!=ZINCBLENDE) {
1107                                         create_lattice(moldyn,
1108                                                        fp->lattice,fp->lc,
1109                                                        mdrun->element1,
1110                                                        mdrun->m1,
1111                                                        DEFAULT_ATOM_ATTR,0,
1112                                                        fp->lx,fp->ly,fp->lz,
1113                                                        NULL,fp->p_type,
1114                                                        &(fp->p_vals));
1115                                 }
1116                                 else {
1117                                         o.x=0.5*0.25*fp->lc;
1118                                         o.y=o.x;
1119                                         o.z=o.x;
1120                                         create_lattice(moldyn,
1121                                                        FCC,fp->lc,
1122                                                        mdrun->element1,
1123                                                        mdrun->m1,
1124                                                        DEFAULT_ATOM_ATTR,0,
1125                                                        fp->lx,fp->ly,fp->lz,
1126                                                        &o,fp->p_type,
1127                                                        &(fp->p_vals));
1128                                         o.x+=0.25*fp->lc;
1129                                         o.y=o.x;
1130                                         o.z=o.x;
1131                                         create_lattice(moldyn,
1132                                                        FCC,fp->lc,
1133                                                        mdrun->element2,
1134                                                        mdrun->m2,
1135                                                        DEFAULT_ATOM_ATTR,1,
1136                                                        fp->lx,fp->ly,fp->lz,
1137                                                        &o,fp->p_type,
1138                                                        &(fp->p_vals));
1139                                 }
1140                                 moldyn_bc_check(moldyn);
1141                                 change_stage=TRUE;
1142                                 break;
1143                         case STAGE_THERMAL_INIT:
1144                                 stage_print("  -> thermal init\n\n");
1145                                 thermal_init(moldyn,TRUE);
1146                                 change_stage=TRUE;
1147                                 break;
1148                         default:
1149                                 printf("%s unknwon stage type\n",ME);
1150                                 break;
1151                 }
1152
1153                 /* mark as executed */
1154                 stage->executed=TRUE;
1155
1156                 /* change state */
1157                 if(change_stage==TRUE) {
1158                         printf("%s finished stage\n",ME);
1159                         if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
1160                                 printf("%s no more stages\n",ME);
1161                                 return 0;
1162                         }
1163                         steps=0;
1164                 }
1165
1166         }
1167         else {
1168
1169                 /* averages */
1170                 if(mdrun->sattr&SATTR_AVGRST)
1171                         average_reset(moldyn);
1172
1173         }
1174
1175         /* continue simulation */
1176         moldyn_add_schedule(moldyn,steps,mdrun->timestep);
1177
1178         return 0;
1179 }
1180
1181 int main(int argc,char **argv) {
1182
1183         t_mdrun mdrun;
1184         t_moldyn moldyn;
1185         //t_3dvec o;
1186
1187         /* clear structs */
1188         memset(&mdrun,0,sizeof(t_mdrun));
1189         memset(&moldyn,0,sizeof(t_moldyn));
1190
1191         /* parse arguments */
1192         if(mdrun_parse_argv(&mdrun,argc,argv)<0)
1193                 return -1;
1194
1195         /* initialize list system */
1196         list_init_f(&(mdrun.stage));
1197
1198         /* parse config file */
1199         mdrun_parse_config(&mdrun);
1200
1201         /* reset the stage list */
1202         list_reset_f(&(mdrun.stage));
1203
1204         /* sanity check! */
1205
1206         /* prepare simulation */
1207
1208         if(mdrun.continue_file[0]) {
1209                 // read the save file
1210                 moldyn_read_save_file(&moldyn,mdrun.continue_file);
1211                 // manualaadjusting some stuff
1212                 moldyn.argc=argc;
1213                 moldyn.args=argv;
1214                 rand_init(&(moldyn.random),NULL,1);
1215                 moldyn.random.status|=RAND_STAT_VERBOSE;
1216         }
1217         else {
1218                 moldyn_init(&moldyn,argc,argv);
1219         }
1220
1221         if(set_int_alg(&moldyn,mdrun.intalgo)<0)
1222                 return -1;
1223
1224         /* potential */
1225         set_cutoff(&moldyn,mdrun.cutoff);
1226         if(set_potential(&moldyn,mdrun.potential)<0)
1227                 return -1;
1228         switch(mdrun.potential) {
1229                 case MOLDYN_POTENTIAL_AM:
1230                         albe_mult_set_params(&moldyn,
1231                                              mdrun.element1,
1232                                              mdrun.element2);
1233                         break;
1234                 case MOLDYN_POTENTIAL_TM:
1235                         tersoff_mult_set_params(&moldyn,
1236                                                 mdrun.element1,
1237                                                 mdrun.element2);
1238                         break;
1239                 case MOLDYN_POTENTIAL_HO:
1240                         harmonic_oscillator_set_params(&moldyn,mdrun.element1);
1241                         break;
1242                 case MOLDYN_POTENTIAL_LJ:
1243                         lennard_jones_set_params(&moldyn,mdrun.element1);
1244                         break;
1245                 default:
1246                         printf("%s unknown potential: %02x\n",
1247                                ME,mdrun.potential);
1248                         return -1;
1249         }
1250
1251         /* if it is a continue run, reset schedule and skip lattice init */
1252         if(mdrun.continue_file[0]) {
1253                 memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
1254                 goto addsched;
1255         }
1256
1257         /* initial lattice and dimensions */
1258         set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
1259         set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
1260         /* replaced by fill stage !!
1261         switch(mdrun.lattice) {
1262                 case FCC:
1263                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
1264                                        mdrun.m1,DEFAULT_ATOM_ATTR,
1265                                        mdrun.fill_brand,mdrun.lx,
1266                                        mdrun.ly,mdrun.lz,NULL,0,NULL);
1267                         break;
1268                 case DIAMOND:
1269                         create_lattice(&moldyn,DIAMOND,mdrun.lc,
1270                                        mdrun.fill_element,
1271                                        mdrun.m1,DEFAULT_ATOM_ATTR,
1272                                        mdrun.fill_brand,mdrun.lx,
1273                                        mdrun.ly,mdrun.lz,NULL,0,NULL);
1274                         break;
1275                 case ZINCBLENDE:
1276                         o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1277                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
1278                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1279                                        mdrun.ly,mdrun.lz,&o,0,NULL);
1280                         o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1281                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
1282                                        mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
1283                                        mdrun.ly,mdrun.lz,&o,0,NULL);
1284                         break;
1285                 case NONE:
1286                         set_nn_dist(&moldyn,mdrun.nnd);
1287                         break;
1288                 default:
1289                         printf("%s unknown lattice type: %02x\n",
1290                                ME,mdrun.lattice);
1291                         return -1;
1292         }
1293         moldyn_bc_check(&moldyn);
1294         replaced by fill stage !! */
1295
1296         /* temperature and pressure */
1297         set_temperature(&moldyn,mdrun.temperature);
1298         set_pressure(&moldyn,mdrun.pressure);
1299         /* replaced thermal_init stage
1300         thermal_init(&moldyn,TRUE);
1301         */
1302
1303 addsched:
1304         /* first schedule */
1305         moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
1306
1307         /* log */
1308         moldyn_set_log_dir(&moldyn,mdrun.sdir);
1309         moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
1310         if(mdrun.elog)
1311                 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
1312         if(mdrun.tlog)
1313                 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
1314         if(mdrun.plog)
1315                 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
1316         if(mdrun.vlog)
1317                 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
1318         if(mdrun.visualize)
1319                 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
1320         if(mdrun.save)
1321                 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
1322         moldyn_set_log(&moldyn,CREATE_REPORT,0);
1323         set_avg_skip(&moldyn,mdrun.avgskip);
1324
1325         /* prepare the hook function */
1326         moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
1327
1328         /* run the simulation */
1329         moldyn_integrate(&moldyn);
1330
1331         /* shutdown */
1332         moldyn_shutdown(&moldyn);
1333         del_stages(&mdrun);
1334         list_destroy_f(&(mdrun.stage));
1335
1336         return 0;
1337 }