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                 default:
 126                         printf("%s unknown stage type: %02x\n",ME,type);
 127                         return -1;
 128         }
 129
 130         stage=malloc(sizeof(t_stage));
 131         if(stage==NULL) {
 132                 perror("[mdrun] malloc (add stage)");
 133                 return -1;
 134         }
 135
 136         stage->type=type;
 137         stage->executed=FALSE;
 138
 139         stage->params=malloc(psize);
 140         if(stage->params==NULL) {
 141                 perror("[mdrun] malloc (stage params)");
 142                 return -1;
 143         }
 144
 145         memcpy(stage->params,params,psize);
 146
 147         list_add_immediate_f(&(mdrun->stage),stage);
 148
 149         return 0;
 150 }
 151
 152 int mdrun_parse_config(t_mdrun *mdrun) {
 153
 154         int fd,ret;
 155         char error[128];
 156         char line[128];
 157         char *wptr;
 158         char word[16][64];
 159         int wcnt;
 160         int i,o;
 161
 162         t_displace_atom_params dap;
 163         t_insert_atoms_params iap;
 164         t_insert_mixed_atoms_params imp;
 165         t_continue_params cp;
 166         t_anneal_params ap;
 167         t_chaattr_params cap;
 168         t_chsattr_params csp;
 169         t_set_temp_params stp;
 170         t_set_timestep_params stsp;
 171
 172         /* open config file */
 173         fd=open(mdrun->cfile,O_RDONLY);
 174         if(fd<0) {
 175                 snprintf(error,128,"%s open cfile %s",ME,mdrun->cfile);
 176                 perror(error);
 177                 return fd;
 178         }
 179
 180         /* read, parse, set */
 181         ret=1;
 182         while(ret>0) {
 183
 184                 /* read */
 185                 ret=get_line(fd,line,128);
 186
 187                 /* parse */
 188
 189                 // ignore # lines and \n
 190                 if((line[0]=='#')|(ret==1))
 191                         continue;
 192
 193                 // reset
 194                 memset(&iap,0,sizeof(t_insert_atoms_params));
 195                 memset(&imp,0,sizeof(t_insert_mixed_atoms_params));
 196                 memset(&cp,0,sizeof(t_continue_params));
 197                 memset(&ap,0,sizeof(t_anneal_params));
 198                 memset(&cap,0,sizeof(t_chaattr_params));
 199                 memset(&csp,0,sizeof(t_chsattr_params));
 200                 memset(&stp,0,sizeof(t_set_temp_params));
 201                 memset(&stsp,0,sizeof(t_set_timestep_params));
 202
 203                 // get command + args
 204                 wcnt=0;
 205                 while(1) {
 206                         if(wcnt)
 207                                 wptr=strtok(NULL," \t");
 208                         else
 209                                 wptr=strtok(line," \t");
 210                         if(wptr==NULL)
 211                                 break;
 212                         strncpy(word[wcnt],wptr,64);
 213                         wcnt+=1;
 214                 }
 215
 216                 if(!strncmp(word[0],"potential",9)) {
 217                         if(!strncmp(word[1],"albe",4))
 218                                 mdrun->potential=MOLDYN_POTENTIAL_AM;
 219                         if(!strncmp(word[1],"tersoff",7))
 220                                 mdrun->potential=MOLDYN_POTENTIAL_TM;
 221                         if(!strncmp(word[1],"ho",2))
 222                                 mdrun->potential=MOLDYN_POTENTIAL_HO;
 223                         if(!strncmp(word[1],"lj",2))
 224                                 mdrun->potential=MOLDYN_POTENTIAL_LJ;
 225                 }
 226                 else if(!strncmp(word[0],"continue",8))
 227                         strncpy(mdrun->continue_file,word[1],128);
 228                 else if(!strncmp(word[0],"cutoff",6))
 229                         mdrun->cutoff=atof(word[1]);
 230                 else if(!strncmp(word[0],"nnd",3))
 231                         mdrun->nnd=atof(word[1]);
 232                 else if(!strncmp(word[0],"intalgo",7)) {
 233                         if(!strncmp(word[1],"verlet",5))
 234                                 mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
 235                 }
 236                 else if(!strncmp(word[0],"timestep",8))
 237                         mdrun->timestep=atof(word[1]);
 238                 else if(!strncmp(word[0],"volume",6)) {
 239                         mdrun->dim.x=atof(word[1]);
 240                         mdrun->dim.y=atof(word[2]);
 241                         mdrun->dim.z=atof(word[3]);
 242                         if(strncmp(word[4],"0",1))
 243                                 mdrun->vis=TRUE;
 244                 }
 245                 else if(!strncmp(word[0],"pbc",3)) {
 246                         if(strncmp(word[1],"0",1))
 247                                 mdrun->pbcx=TRUE;
 248                         else
 249                                 mdrun->pbcx=FALSE;
 250                         if(strncmp(word[2],"0",1))
 251                                 mdrun->pbcy=TRUE;
 252                         else
 253                                 mdrun->pbcy=FALSE;
 254                         if(strncmp(word[3],"0",1))
 255                                 mdrun->pbcz=TRUE;
 256                         else
 257                                 mdrun->pbcz=FALSE;
 258                 }
 259                 else if(!strncmp(word[0],"temperature",11))
 260                         mdrun->temperature=atof(word[1]);
 261                 else if(!strncmp(word[0],"pressure",8))
 262                         mdrun->pressure=atof(word[1]);
 263                 else if(!strncmp(word[0],"lattice",7)) {
 264                         if(!strncmp(word[1],"zincblende",10))
 265                                 mdrun->lattice=ZINCBLENDE;
 266                         if(!strncmp(word[1],"fcc",3))
 267                                 mdrun->lattice=FCC;
 268                         if(!strncmp(word[1],"diamond",7))
 269                                 mdrun->lattice=DIAMOND;
 270                         if(!strncmp(word[1],"none",4))
 271                                 mdrun->lattice=NONE;
 272                 }
 273                 else if(!strncmp(word[0],"element1",8)) {
 274                         mdrun->element1=atoi(word[1]);
 275                         mdrun->m1=pse_mass[mdrun->element1];
 276                 }
 277                 else if(!strncmp(word[0],"element2",8)) {
 278                         mdrun->element2=atoi(word[1]);
 279                         mdrun->m2=pse_mass[mdrun->element2];
 280                 }
 281                 else if(!strncmp(word[0],"fill",6)) {
 282                         // only lc mode by now
 283                         mdrun->lx=atoi(word[2]);
 284                         mdrun->ly=atoi(word[3]);
 285                         mdrun->lz=atoi(word[4]);
 286                         mdrun->lc=atof(word[5]);
 287                         if(wcnt==8) {
 288                                 mdrun->fill_element=atoi(word[6]);
 289                                 mdrun->fill_brand=atoi(word[7]);
 290                         }
 291                         else {
 292                                 mdrun->fill_element=mdrun->element1;
 293                                 mdrun->fill_brand=0;
 294                         }
 295                 }
 296                 else if(!strncmp(word[0],"aattr",5)) {
 297                         // for aatrib line we need a special stage
 298                         // containing one schedule of 0 loops ...
 299                         for(i=0;i<strlen(word[1]);i++) {
 300                                 switch(word[1][i]) {
 301                                         case 't':
 302                                                 cap.type|=CHAATTR_TOTALV;
 303                                                 break;
 304                                         case 'r':
 305                                                 cap.type|=CHAATTR_REGION;
 306                                                 break;
 307                                         case 'e':
 308                                                 cap.type|=CHAATTR_ELEMENT;
 309                                                 break;
 310                                         default:
 311                                                 break;
 312                                 }
 313                         }
 314                         i=2;
 315                         if(cap.type&CHAATTR_REGION) {
 316                                 cap.x0=atof(word[1]);
 317                                 cap.y0=atof(word[2]);
 318                                 cap.z0=atof(word[3]);
 319                                 cap.x1=atof(word[4]);
 320                                 cap.y1=atof(word[5]);
 321                                 cap.z1=atof(word[6]);
 322                                 i+=6;
 323                         }
 324                         if(cap.type&CHAATTR_ELEMENT) {
 325                                 cap.element=atoi(word[i]);
 326                                 i+=1;
 327                         }
 328                         for(o=0;o<strlen(word[i]);o++) {
 329                                 switch(word[i][o]) {
 330                                         case 'b':
 331                                                 cap.attr|=ATOM_ATTR_VB;
 332                                                 break;
 333                                         case 'h':
 334                                                 cap.attr|=ATOM_ATTR_HB;
 335                                                 break;
 336                                         case 'v':
 337                                                 cap.attr|=ATOM_ATTR_VA;
 338                                                 break;
 339                                         case 'f':
 340                                                 cap.attr|=ATOM_ATTR_FP;
 341                                                 break;
 342                                         case '1':
 343                                                 cap.attr|=ATOM_ATTR_1BP;
 344                                                 break;
 345                                         case '2':
 346                                                 cap.attr|=ATOM_ATTR_2BP;
 347                                                 break;
 348                                         case '3':
 349                                                 cap.attr|=ATOM_ATTR_3BP;
 350                                                 break;
 351                                         default:
 352                                                 break;
 353                                 }
 354                         }
 355                         add_stage(mdrun,STAGE_CHAATTR,&cap);
 356                 }
 357                 else if(!strncmp(word[0],"sattr",5)) {
 358                         // for satrib line we need a special stage
 359                         // containing one schedule of 0 loops ...
 360                         csp.type=0;
 361                         for(i=1;i<wcnt;i++) {
 362                                 if(!strncmp(word[i],"pctrl",5)) {
 363                                         csp.ptau=0.01/(atof(word[++i])*GPA);
 364                                         csp.type|=CHSATTR_PCTRL;
 365                                 }
 366                                 if(!strncmp(word[i],"tctrl",5)) {
 367                                         csp.ttau=atof(word[++i]);
 368                                         csp.type|=CHSATTR_TCTRL;
 369                                 }
 370                                 if(!strncmp(word[i],"prelax",6)) {
 371                                         csp.dp=atof(word[++i])*BAR;
 372                                         csp.type|=CHSATTR_PRELAX;
 373                                 }
 374                                 if(!strncmp(word[i],"trelax",6)) {
 375                                         csp.dt=atof(word[++i]);
 376                                         csp.type|=CHSATTR_TRELAX;
 377                                 }
 378                                 if(!strncmp(word[i],"rsteps",6)) {
 379                                         csp.rsteps=atoi(word[++i]);
 380                                         csp.type|=CHSATTR_RSTEPS;
 381                                 }
 382                                 if(!strncmp(word[i],"avgrst",6)) {
 383                                         csp.avgrst=atoi(word[++i]);
 384                                         csp.type|=CHSATTR_AVGRST;
 385                                 }
 386                         }
 387                         add_stage(mdrun,STAGE_CHSATTR,&csp);
 388                 }
 389                 else if(!strncmp(word[0],"prerun",6))
 390                         mdrun->prerun=atoi(word[1]);
 391                 else if(!strncmp(word[0],"avgskip",7))
 392                         mdrun->avgskip=atoi(word[1]);
 393                 else if(!strncmp(word[0],"elog",4))
 394                         mdrun->elog=atoi(word[1]);
 395                 else if(!strncmp(word[0],"tlog",4))
 396                         mdrun->tlog=atoi(word[1]);
 397                 else if(!strncmp(word[0],"plog",4))
 398                         mdrun->plog=atoi(word[1]);
 399                 else if(!strncmp(word[0],"vlog",4))
 400                         mdrun->vlog=atoi(word[1]);
 401                 else if(!strncmp(word[0],"save",4))
 402                         mdrun->save=atoi(word[1]);
 403                 else if(!strncmp(word[0],"visualize",9))
 404                         mdrun->visualize=atoi(word[1]);
 405                 else if(!strncmp(word[0],"stage",5)) {
 406                         // for every stage line, add a stage
 407                         if(!strncmp(word[1],"displace",8)) {
 408                                 dap.nr=atoi(word[2]);
 409                                 dap.dx=atof(word[3]);
 410                                 dap.dy=atof(word[4]);
 411                                 dap.dz=atof(word[5]);
 412                                 add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
 413                         }
 414                         else if(!strncmp(word[1],"ins_atoms",9)) {
 415                                 iap.ins_steps=atoi(word[2]);
 416                                 iap.ins_atoms=atoi(word[3]);
 417                                 iap.element=atoi(word[4]);
 418                                 iap.brand=atoi(word[5]);
 419                                 for(i=0;i<strlen(word[6]);i++) {
 420                                         switch(word[6][i]) {
 421                                                 case 'b':
 422                                                         iap.attr|=ATOM_ATTR_VB;
 423                                                         break;
 424                                                 case 'h':
 425                                                         iap.attr|=ATOM_ATTR_HB;
 426                                                         break;
 427                                                 case 'v':
 428                                                         iap.attr|=ATOM_ATTR_VA;
 429                                                         break;
 430                                                 case 'f':
 431                                                         iap.attr|=ATOM_ATTR_FP;
 432                                                         break;
 433                                                 case '1':
 434                                                         iap.attr|=ATOM_ATTR_1BP;
 435                                                         break;
 436                                                 case '2':
 437                                                         iap.attr|=ATOM_ATTR_2BP;
 438                                                         break;
 439                                                 case '3':
 440                                                         iap.attr|=ATOM_ATTR_3BP;
 441                                                         break;
 442                                                 default:
 443                                                         break;
 444                                         }
 445                                 }
 446                                 switch(word[7][0]) {
 447                                         // insertion types
 448                                         case 'p':
 449                                                 iap.type=INS_POS;
 450                                                 iap.x0=atof(word[8]);
 451                                                 iap.y0=atof(word[9]);
 452                                                 iap.z0=atof(word[10]);
 453                                                 break;
 454                                         case 'r':
 455                                                 if(word[8][0]=='t') {
 456                                                         iap.type=INS_TOTAL;
 457                                                         iap.cr=atof(word[9]);
 458                                                 }
 459                                                 else {
 460                                                         iap.type=INS_REGION;
 461                                                         iap.x0=atof(word[8]);
 462                                                         iap.y0=atof(word[9]);
 463                                                         iap.z0=atof(word[10]);
 464                                                         iap.x1=atof(word[11]);
 465                                                         iap.y1=atof(word[12]);
 466                                                         iap.z1=atof(word[13]);
 467                                                         iap.cr=atof(word[14]);
 468                                                 }
 469                                         default:
 470                                                 break;
 471                                 }
 472                                 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
 473                         }
 474
 475
 476                         // HERE WE GO ...
 477
 478                         else if(!strncmp(word[1],"ins_m_atoms",11)) {
 479                                 imp.element1=atoi(word[2]);
 480                                 imp.element2=atoi(word[3]);
 481                                 imp.amount1=atoi(word[4]);
 482                                 imp.amount2=atoi(word[5]);
 483                                 imp.brand1=atoi(word[6]);
 484                                 imp.brand2=atoi(word[7]);
 485                                 imp.crmin=atof(word[8]);
 486                                 imp.crmax=atof(word[9]);
 487                                 /* do this later ...
 488                                 for(i=0;i<strlen(word[8]);i++) {
 489                                         switch(word[8][i]) {
 490                                                 case 'b':
 491                                                         imp.attr|=ATOM_ATTR_VB;
 492                                                         break;
 493                                                 case 'h':
 494                                                         imp.attr|=ATOM_ATTR_HB;
 495                                                         break;
 496                                                 case 'v':
 497                                                         imp.attr|=ATOM_ATTR_VA;
 498                                                         break;
 499                                                 case 'f':
 500                                                         imp.attr|=ATOM_ATTR_FP;
 501                                                         break;
 502                                                 case '1':
 503                                                         imp.attr|=ATOM_ATTR_1BP;
 504                                                         break;
 505                                                 case '2':
 506                                                         imp.attr|=ATOM_ATTR_2BP;
 507                                                         break;
 508                                                 case '3':
 509                                                         imp.attr|=ATOM_ATTR_3BP;
 510                                                         break;
 511                                                 default:
 512                                                         break;
 513                                         }
 514                                 }
 515                                 */
 516                                 imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 517                                 imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 518                                 add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
 519                         }
 520
 521
 522
 523
 524
 525                         else if(!strncmp(word[1],"continue",8)) {
 526                                 cp.runs=atoi(word[2]);
 527                                 add_stage(mdrun,STAGE_CONTINUE,&cp);
 528                         }
 529                         else if(!strncmp(word[1],"anneal",6)) {
 530                                 ap.count=0;
 531                                 ap.runs=atoi(word[2]);
 532                                 ap.dt=atof(word[3]);
 533                                 ap.interval=atoi(word[4]);
 534                                 add_stage(mdrun,STAGE_ANNEAL,&ap);
 535                         }
 536                         else if(!strncmp(word[1],"set_temp",8)) {
 537                                 if(word[2][0]=='c') {
 538                                         stp.type=SET_TEMP_CURRENT;
 539                                         stp.val=0.0;
 540                                 }
 541                                 else {
 542                                         stp.type=SET_TEMP_VALUE;
 543                                         stp.val=atof(word[2]);
 544                                 }
 545                                 add_stage(mdrun,STAGE_SET_TEMP,&stp);
 546                         }
 547                         else if(!strncmp(word[1],"set_timestep",12)) {
 548                                 stsp.tau=atof(word[2]);
 549                                 add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
 550                         }
 551                         else {
 552                                 printf("%s unknown stage type: %s\n",
 553                                        ME,word[1]);
 554                                 return -1;
 555                         }
 556                 }
 557                 else {
 558                         printf("%s unknown keyword '%s', skipped!\n",
 559                                ME,word[0]);
 560                         continue;
 561                 }
 562         }
 563
 564         /* close file */
 565         close(fd);
 566
 567         return 0;
 568 }
 569
 570 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
 571
 572         double delta;
 573
 574         if(!(mdrun->sattr&SATTR_PRELAX)) {
 575                 return TRUE;
 576         }
 577
 578         delta=moldyn->p_avg-moldyn->p_ref;
 579
 580         if(delta<0)
 581                 delta=-delta;
 582
 583         if(delta>mdrun->dp)
 584                 return FALSE;
 585
 586         return TRUE;
 587 }
 588
 589 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 590
 591         double delta;
 592
 593         if(!(mdrun->sattr&SATTR_TRELAX))
 594                 return TRUE;
 595
 596         delta=moldyn->t_avg-moldyn->t_ref;
 597
 598         if(delta<0)
 599                 delta=-delta;
 600
 601         if(delta>mdrun->dt)
 602                 return FALSE;
 603
 604         return TRUE;
 605 }
 606
 607 int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
 608
 609         t_displace_atom_params *dap;
 610         t_stage *stage;
 611         t_atom *atom;
 612
 613         stage=mdrun->stage.current->data;
 614         dap=stage->params;
 615
 616         atom=&(moldyn->atom[dap->nr]);
 617         atom->r.x+=dap->dx;
 618         atom->r.y+=dap->dy;
 619         atom->r.z+=dap->dz;
 620
 621         return 0;
 622 }
 623
 624 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 625
 626         t_insert_atoms_params *iap;
 627         t_stage *stage;
 628         t_atom *atom;
 629         t_3dvec r,v,dist;
 630         double d,dmin,o;
 631         int cnt,i;
 632         double x,y,z;
 633         double x0,y0,z0;
 634         u8 cr_check,run;
 635
 636         stage=mdrun->stage.current->data;
 637         iap=stage->params;
 638
 639         cr_check=FALSE;
 640
 641         v.x=0.0; v.y=0.0; v.z=0.0;
 642         x=0; y=0; z=0;
 643         o=0; dmin=0;
 644
 645         switch(mdrun->lattice) {
 646                 case CUBIC:
 647                         o=0.5*mdrun->lc;
 648                         break;
 649                 case FCC:
 650                         o=0.25*mdrun->lc;
 651                         break;
 652                 case DIAMOND:
 653                 case ZINCBLENDE:
 654                         o=0.125*mdrun->lc;
 655                         break;
 656                 default:
 657                         break;
 658         }
 659
 660         switch(iap->type) {
 661                 case INS_TOTAL:
 662                         x=moldyn->dim.x;
 663                         x0=-x/2.0;
 664                         y=moldyn->dim.y;
 665                         y0=-y/2.0;
 666                         z=moldyn->dim.z;
 667                         z0=-z/2.0;
 668                         cr_check=TRUE;
 669                         break;
 670                 case INS_REGION:
 671                         x=iap->x1-iap->x0;
 672                         x0=iap->x0;
 673                         y=iap->y1-iap->y0;
 674                         y0=iap->y0;
 675                         z=iap->z1-iap->z0;
 676                         z0=iap->z0;
 677                         cr_check=TRUE;
 678                         break;
 679                 case INS_POS:
 680                         x0=iap->x0;
 681                         y0=iap->y0;
 682                         z0=iap->z0;
 683                         cr_check=FALSE;
 684                         break;
 685                 default:
 686                         printf("%s unknown insertion mode: %02x\n",
 687                                ME,iap->type);
 688                         return -1;
 689         }
 690
 691         cnt=0;
 692         while(cnt<iap->ins_atoms) {
 693                 run=1;
 694                 while(run) {
 695                         if(iap->type!=INS_POS) {
 696                                 r.x=rand_get_double(&(moldyn->random))*x;
 697                                 r.y=rand_get_double(&(moldyn->random))*y;
 698                                 r.z=rand_get_double(&(moldyn->random))*z;
 699                         }
 700                         else {
 701                                 r.x=0.0;
 702                                 r.y=0.0;
 703                                 r.z=0.0;
 704                         }
 705                         r.x+=x0;
 706                         r.y+=y0;
 707                         r.z+=z0;
 708                         // offset
 709                         if(iap->type!=INS_TOTAL) {
 710                                 r.x+=o;
 711                                 r.y+=o;
 712                                 r.z+=o;
 713                         }
 714                         run=0;
 715                         if(cr_check==TRUE) {
 716                                 dmin=1000;      // for sure too high!
 717                                 for(i=0;i<moldyn->count;i++) {
 718                                         atom=&(moldyn->atom[i]);
 719                                         v3_sub(&dist,&(atom->r),&r);
 720                                         check_per_bound(moldyn,&dist);
 721                                         d=v3_absolute_square(&dist);
 722                                         if(d<(iap->cr*iap->cr)) {
 723                                                 run=1;
 724                                                 break;
 725                                         }
 726                                         if(d<dmin)
 727                                                 dmin=d;
 728                                 }
 729                         }
 730                 }
 731                 add_atom(moldyn,iap->element,pse_mass[iap->element],
 732                          iap->brand,iap->attr,&r,&v);
 733                 printf("%s atom inserted (%d/%d): %f %f %f\n",
 734                        ME,(iap->cnt_steps+1)*iap->ins_atoms,
 735                        iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
 736                 printf("  -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
 737                 cnt+=1;
 738         }
 739
 740         return 0;
 741 }
 742
 743 int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 744
 745         t_stage *stage;
 746         t_insert_mixed_atoms_params *imp;
 747         t_atom *atom;
 748         double x,x0,y,y0,z,z0;
 749         double dmin,d,cmin,cmax;
 750         u8 retry;
 751         t_3dvec r,v,dist;
 752         int i;
 753
 754
 755         stage=mdrun->stage.current->data;
 756         imp=stage->params;
 757
 758         x=moldyn->dim.x;
 759         x0=-x/2.0;
 760         y=moldyn->dim.y;
 761         y0=-y/2.0;
 762         z=moldyn->dim.z;
 763         z0=-z/2.0;
 764
 765         v.x=0.0;
 766         v.y=0.0;
 767         v.z=0.0;
 768
 769         cmin=imp->crmin*imp->crmin;
 770         cmax=imp->crmax*imp->crmax;
 771
 772         while(imp->amount1|imp->amount2) {
 773                 if(imp->amount1) {
 774                         retry=1;
 775                         while(retry) {
 776                                 retry=0;
 777                                 r.x=rand_get_double(&(moldyn->random))*x;
 778                                 r.y=rand_get_double(&(moldyn->random))*y;
 779                                 r.z=rand_get_double(&(moldyn->random))*z;
 780                                 r.x+=x0;
 781                                 r.y+=y0;
 782                                 r.z+=z0;
 783                                 dmin=1000.0;    // for sure too high!
 784                                 for(i=0;i<moldyn->count;i++) {
 785                                         atom=&(moldyn->atom[i]);
 786                                         v3_sub(&dist,&(atom->r),&r);
 787                                         check_per_bound(moldyn,&dist);
 788                                         d=v3_absolute_square(&dist);
 789                                         if(d<cmin) {
 790                                                 retry=1;
 791                                                 break;
 792                                         }
 793                                         if(d<dmin)
 794                                                 dmin=d;
 795                                 }
 796                                 if(dmin!=1000.0)
 797                                         if(dmin>cmax)
 798                                                 retry=1;
 799                         }
 800                         add_atom(moldyn,imp->element1,pse_mass[imp->element1],
 801                                  imp->brand1,imp->attr1,&r,&v);
 802                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
 803                                ME,imp->amount1,r.x,r.y,r.z);
 804                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
 805                         imp->amount1-=1;
 806                 }
 807                 if(imp->amount2) {
 808                         retry=1;
 809                         while(retry) {
 810                                 retry=0;
 811                                 r.x=rand_get_double(&(moldyn->random))*x;
 812                                 r.y=rand_get_double(&(moldyn->random))*y;
 813                                 r.z=rand_get_double(&(moldyn->random))*z;
 814                                 r.x+=x0;
 815                                 r.y+=y0;
 816                                 r.z+=z0;
 817                                 dmin=1000.0;    // for sure too high!
 818                                 for(i=0;i<moldyn->count;i++) {
 819                                         atom=&(moldyn->atom[i]);
 820                                         v3_sub(&dist,&(atom->r),&r);
 821                                         check_per_bound(moldyn,&dist);
 822                                         d=v3_absolute_square(&dist);
 823                                         if(d<cmin) {
 824                                                 retry=1;
 825                                                 break;
 826                                         }
 827                                         if(d<dmin)
 828                                                 dmin=d;
 829                                 }
 830                                 if(dmin!=1000.0)
 831                                         if(dmin>cmax)
 832                                                 retry=1;
 833                         }
 834                         add_atom(moldyn,imp->element2,pse_mass[imp->element2],
 835                                  imp->brand2,imp->attr2,&r,&v);
 836                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
 837                                ME,imp->amount2,r.x,r.y,r.z);
 838                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
 839                         imp->amount2-=1;
 840                 }
 841         }
 842
 843         return 0;
 844 }
 845
 846 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 847
 848         t_stage *stage;
 849         t_chaattr_params *cap;
 850         t_atom *atom;
 851         int i;
 852
 853         stage=mdrun->stage.current->data;
 854         cap=stage->params;
 855
 856         for(i=0;i<moldyn->count;i++) {
 857                 atom=&(moldyn->atom[i]);
 858                 if(cap->type&CHAATTR_ELEMENT) {
 859                         if(cap->element!=atom->element)
 860                                 continue;
 861                 }
 862                 if(cap->type&CHAATTR_REGION) {
 863                         if(cap->x0<atom->r.x)
 864                                 continue;
 865                         if(cap->y0<atom->r.y)
 866                                 continue;
 867                         if(cap->z0<atom->r.z)
 868                                 continue;
 869                         if(cap->x1>atom->r.x)
 870                                 continue;
 871                         if(cap->y1>atom->r.y)
 872                                 continue;
 873                         if(cap->z1>atom->r.z)
 874                                 continue;
 875                 }
 876                 atom->attr=cap->attr;
 877         }
 878
 879         return 0;
 880 }
 881
 882 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 883
 884         t_stage *stage;
 885         t_chsattr_params *csp;
 886
 887         stage=mdrun->stage.current->data;
 888         csp=stage->params;
 889
 890         if(csp->type&CHSATTR_PCTRL) {
 891                 if(csp->ptau>0)
 892                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 893                 else
 894                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 895         }
 896         if(csp->type&CHSATTR_TCTRL) {
 897                 if(csp->ttau>0)
 898                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 899                 else
 900                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 901         }
 902         if(csp->type&CHSATTR_PRELAX) {
 903                 if(csp->dp<0)
 904                         mdrun->sattr&=(~(SATTR_PRELAX));
 905                 else
 906                         mdrun->sattr|=SATTR_PRELAX;
 907                 mdrun->dp=csp->dp;
 908         }
 909         if(csp->type&CHSATTR_TRELAX) {
 910                 if(csp->dt<0)
 911                         mdrun->sattr&=(~(SATTR_TRELAX));
 912                 else
 913                         mdrun->sattr|=SATTR_TRELAX;
 914                 mdrun->dt=csp->dt;
 915         }
 916         if(csp->type&CHSATTR_AVGRST) {
 917                 if(csp->avgrst)
 918                         mdrun->sattr|=SATTR_AVGRST;
 919                 else
 920                         mdrun->sattr&=(~(SATTR_AVGRST));
 921         }
 922         if(csp->type&CHSATTR_RSTEPS) {
 923                 mdrun->relax_steps=csp->rsteps;
 924         }
 925
 926         return 0;
 927 }
 928
 929 #define stage_print(m)  if(!(stage->executed)) \
 930                                 printf("%s",m)
 931
 932 int mdrun_hook(void *ptr1,void *ptr2) {
 933
 934         t_moldyn *moldyn;
 935         t_mdrun *mdrun;
 936         t_stage *stage;
 937         t_list *sl;
 938         int steps;
 939         u8 change_stage;
 940
 941         t_insert_atoms_params *iap;
 942         t_insert_mixed_atoms_params *imp;
 943         t_continue_params *cp;
 944         t_anneal_params *ap;
 945         t_set_temp_params *stp;
 946         t_set_timestep_params *stsp;
 947
 948         moldyn=ptr1;
 949         mdrun=ptr2;
 950
 951         sl=&(mdrun->stage);
 952
 953         change_stage=FALSE;
 954
 955         /* return immediately if there are no more stage */
 956         if(sl->current==NULL)
 957                 return 0;
 958
 959         /* get stage description */
 960         stage=sl->current->data;
 961
 962         /* steps in next schedule */
 963         steps=mdrun->relax_steps;
 964
 965         /* check whether relaxation steps are necessary */
 966         if((check_pressure(moldyn,mdrun)==TRUE)&\
 967            (check_temperature(moldyn,mdrun)==TRUE)) {
 968
 969                 /* be verbose */
 970                 stage_print("\n###########################\n");
 971                 stage_print("# [mdrun] executing stage #\n");
 972                 stage_print("###########################\n\n");
 973
 974                 /* stage specific stuff */
 975                 switch(stage->type) {
 976                         case STAGE_DISPLACE_ATOM:
 977                                 stage_print("  -> displace atom\n\n");
 978                                 displace_atom(moldyn,mdrun);
 979                                 change_stage=TRUE;
 980                                 break;
 981                         case STAGE_INSERT_ATOMS:
 982                                 stage_print("  -> insert atoms\n\n");
 983                                 iap=stage->params;
 984                                 if(iap->cnt_steps==iap->ins_steps) {
 985                                         change_stage=TRUE;
 986                                         break;
 987                                 }
 988                                 insert_atoms(moldyn,mdrun);
 989                                 iap->cnt_steps+=1;
 990                                 break;
 991
 992
 993
 994                         case STAGE_INSERT_MIXED_ATOMS:
 995                                 stage_print("  -> insert mixed atoms\n\n");
 996                                 imp=stage->params;
 997                                 insert_mixed_atoms(moldyn,mdrun);
 998                                 change_stage=TRUE;
 999                                 break;
1000
1001
1002
1003                         case STAGE_CONTINUE:
1004                                 stage_print("  -> continue\n\n");
1005                                 if(stage->executed==TRUE) {
1006                                         change_stage=TRUE;
1007                                         break;
1008                                 }
1009                                 cp=stage->params;
1010                                 steps=cp->runs;
1011                                 break;
1012                         case STAGE_ANNEAL:
1013                                 stage_print("  -> anneal\n\n");
1014                                 ap=stage->params;
1015                                 if(ap->count==ap->runs) {
1016                                         change_stage=TRUE;
1017                                         break;
1018                                 }
1019                                 if(moldyn->t_ref+ap->dt>=0.0)
1020                                         set_temperature(moldyn,
1021                                                         moldyn->t_ref+ap->dt);
1022                                 ap->count+=1;
1023                                 steps=ap->interval;
1024                                 break;
1025                         case STAGE_CHAATTR:
1026                                 stage_print("  -> change atom attributes\n\n");
1027                                 chaatr(moldyn,mdrun);
1028                                 change_stage=TRUE;
1029                                 break;
1030                         case STAGE_CHSATTR:
1031                                 stage_print("  -> change sys attributes\n\n");
1032                                 chsattr(moldyn,mdrun);
1033                                 change_stage=TRUE;
1034                                 break;
1035                         case STAGE_SET_TEMP:
1036                                 stage_print("  -> set temperature\n\n");
1037                                 stp=stage->params;
1038                                 if(stp->type&SET_TEMP_CURRENT) {
1039                                         set_temperature(moldyn,moldyn->t_avg);
1040                                 }
1041                                 else {
1042                                         set_temperature(moldyn,stp->val);
1043                                 }
1044                                 change_stage=TRUE;
1045                                 break;
1046                         case STAGE_SET_TIMESTEP:
1047                                 stage_print("  -> set timestep\n\n");
1048                                 stsp=stage->params;
1049                                 mdrun->timestep=stsp->tau;
1050                                 change_stage=TRUE;
1051                                 break;
1052                         default:
1053                                 printf("%s unknwon stage type\n",ME);
1054                                 break;
1055                 }
1056
1057                 /* mark as executed */
1058                 stage->executed=TRUE;
1059
1060                 /* change state */
1061                 if(change_stage==TRUE) {
1062                         printf("%s finished stage\n",ME);
1063                         if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
1064                                 printf("%s no more stages\n",ME);
1065                                 return 0;
1066                         }
1067                         steps=0;
1068                 }
1069
1070         }
1071         else {
1072
1073                 /* averages */
1074                 if(mdrun->sattr&SATTR_AVGRST)
1075                         average_reset(moldyn);
1076
1077         }
1078
1079         /* continue simulation */
1080         moldyn_add_schedule(moldyn,steps,mdrun->timestep);
1081
1082         return 0;
1083 }
1084
1085 int main(int argc,char **argv) {
1086
1087         t_mdrun mdrun;
1088         t_moldyn moldyn;
1089         t_3dvec o;
1090
1091         /* clear structs */
1092         memset(&mdrun,0,sizeof(t_mdrun));
1093         memset(&moldyn,0,sizeof(t_moldyn));
1094
1095         /* parse arguments */
1096         if(mdrun_parse_argv(&mdrun,argc,argv)<0)
1097                 return -1;
1098
1099         /* initialize list system */
1100         list_init_f(&(mdrun.stage));
1101
1102         /* parse config file */
1103         mdrun_parse_config(&mdrun);
1104
1105         /* reset the stage list */
1106         list_reset_f(&(mdrun.stage));
1107
1108         /* sanity check! */
1109
1110         /* prepare simulation */
1111
1112         if(mdrun.continue_file[0]) {
1113                 // read the save file
1114                 moldyn_read_save_file(&moldyn,mdrun.continue_file);
1115                 // manualaadjusting some stuff
1116                 moldyn.argc=argc;
1117                 moldyn.args=argv;
1118                 rand_init(&(moldyn.random),NULL,1);
1119                 moldyn.random.status|=RAND_STAT_VERBOSE;
1120         }
1121         else {
1122                 moldyn_init(&moldyn,argc,argv);
1123         }
1124
1125         if(set_int_alg(&moldyn,mdrun.intalgo)<0)
1126                 return -1;
1127
1128         /* potential */
1129         set_cutoff(&moldyn,mdrun.cutoff);
1130         if(set_potential(&moldyn,mdrun.potential)<0)
1131                 return -1;
1132         switch(mdrun.potential) {
1133                 case MOLDYN_POTENTIAL_AM:
1134                         albe_mult_set_params(&moldyn,
1135                                              mdrun.element1,
1136                                              mdrun.element2);
1137                         break;
1138                 case MOLDYN_POTENTIAL_TM:
1139                         tersoff_mult_set_params(&moldyn,
1140                                                 mdrun.element1,
1141                                                 mdrun.element2);
1142                         break;
1143                 case MOLDYN_POTENTIAL_HO:
1144                         harmonic_oscillator_set_params(&moldyn,mdrun.element1);
1145                         break;
1146                 case MOLDYN_POTENTIAL_LJ:
1147                         lennard_jones_set_params(&moldyn,mdrun.element1);
1148                         break;
1149                 default:
1150                         printf("%s unknown potential: %02x\n",
1151                                ME,mdrun.potential);
1152                         return -1;
1153         }
1154
1155         /* if it is a continue run, reset schedule and skip lattice init */
1156         if(mdrun.continue_file[0]) {
1157                 memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
1158                 goto addsched;
1159         }
1160
1161         /* initial lattice and dimensions */
1162         set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
1163         set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
1164         switch(mdrun.lattice) {
1165                 case FCC:
1166                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
1167                                        mdrun.m1,DEFAULT_ATOM_ATTR,
1168                                        mdrun.fill_brand,mdrun.lx,
1169                                        mdrun.ly,mdrun.lz,NULL,0,NULL);
1170                         break;
1171                 case DIAMOND:
1172                         create_lattice(&moldyn,DIAMOND,mdrun.lc,
1173                                        mdrun.fill_element,
1174                                        mdrun.m1,DEFAULT_ATOM_ATTR,
1175                                        mdrun.fill_brand,mdrun.lx,
1176                                        mdrun.ly,mdrun.lz,NULL,0,NULL);
1177                         break;
1178                 case ZINCBLENDE:
1179                         o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1180                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
1181                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1182                                        mdrun.ly,mdrun.lz,&o,0,NULL);
1183                         o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1184                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
1185                                        mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
1186                                        mdrun.ly,mdrun.lz,&o,0,NULL);
1187                         break;
1188                 case NONE:
1189                         set_nn_dist(&moldyn,mdrun.nnd);
1190                         break;
1191                 default:
1192                         printf("%s unknown lattice type: %02x\n",
1193                                ME,mdrun.lattice);
1194                         return -1;
1195         }
1196         moldyn_bc_check(&moldyn);
1197
1198         /* temperature and pressure */
1199         set_temperature(&moldyn,mdrun.temperature);
1200         set_pressure(&moldyn,mdrun.pressure);
1201         thermal_init(&moldyn,TRUE);
1202
1203 addsched:
1204         /* first schedule */
1205         moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
1206
1207         /* log */
1208         moldyn_set_log_dir(&moldyn,mdrun.sdir);
1209         moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
1210         if(mdrun.elog)
1211                 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
1212         if(mdrun.tlog)
1213                 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
1214         if(mdrun.plog)
1215                 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
1216         if(mdrun.vlog)
1217                 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
1218         if(mdrun.visualize)
1219                 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
1220         if(mdrun.save)
1221                 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
1222         moldyn_set_log(&moldyn,CREATE_REPORT,0);
1223         set_avg_skip(&moldyn,mdrun.avgskip);
1224
1225         /* prepare the hook function */
1226         moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
1227
1228         /* run the simulation */
1229         moldyn_integrate(&moldyn);
1230
1231         /* shutdown */
1232         moldyn_shutdown(&moldyn);
1233         del_stages(&mdrun);
1234         list_destroy_f(&(mdrun.stage));
1235
1236         return 0;
1237 }