src/gromacs/gmxpreprocess/topdirs.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "topdirs.h"
  40
  41 #include <stdarg.h>
  42 #include <stdio.h>
  43
  44 #include "gromacs/utility/cstringutil.h"
  45 #include "gromacs/utility/fatalerror.h"
  46 #include "gromacs/utility/smalloc.h"
  47
  48 /* Must correspond to the directive enum in grompp-impl.h */
  49 static const char *directive_names[d_maxdir+1] = {
  50     "defaults",
  51     "atomtypes",
  52     "bondtypes",
  53     "constrainttypes",
  54     "pairtypes",
  55     "angletypes",
  56     "dihedraltypes",
  57     "nonbond_params",
  58     "implicit_genborn_params",
  59     "implicit_surface_params",
  60     "cmaptypes",
  61     /* All the directives above can not appear after moleculetype */
  62     "moleculetype",
  63     "atoms",
  64     "virtual_sites2",
  65     "virtual_sites3",
  66     "virtual_sites4",
  67     "virtual_sitesn",
  68     "bonds",
  69     "exclusions",
  70     "pairs",
  71     "pairs_nb",
  72     "angles",
  73     "dihedrals",
  74     "constraints",
  75     "settles",
  76     "polarization",
  77     "water_polarization",
  78     "thole_polarization",
  79     "system",
  80     "molecules",
  81     "position_restraints",
  82     "angle_restraints",
  83     "angle_restraints_z",
  84     "distance_restraints",
  85     "orientation_restraints",
  86     "dihedral_restraints",
  87     "cmap",
  88     "intermolecular_interactions",
  89     "invalid"
  90 };
  91
  92 int ifunc_index(directive d, int type)
  93 {
  94     switch (d)
  95     {
  96         case d_bondtypes:
  97         case d_bonds:
  98             switch (type)
  99             {
 100                 case 1:
 101                     return F_BONDS;
 102                 case 2:
 103                     return F_G96BONDS;
 104                 case 3:
 105                     return F_MORSE;
 106                 case 4:
 107                     return F_CUBICBONDS;
 108                 case 5:
 109                     return F_CONNBONDS;
 110                 case 6:
 111                     return F_HARMONIC;
 112                 case 7:
 113                     return F_FENEBONDS;
 114                 case 8:
 115                     return F_TABBONDS;
 116                 case 9:
 117                     return F_TABBONDSNC;
 118                 case 10:
 119                     return F_RESTRBONDS;
 120                 default:
 121                     gmx_fatal(FARGS, "Invalid bond type %d", type);
 122                     break;
 123             }
 124             break;
 125         case d_angles:
 126         case d_angletypes:
 127             switch (type)
 128             {
 129                 case 1:
 130                     return F_ANGLES;
 131                 case 2:
 132                     return F_G96ANGLES;
 133                 case 3:
 134                     return F_CROSS_BOND_BONDS;
 135                 case 4:
 136                     return F_CROSS_BOND_ANGLES;
 137                 case 5:
 138                     return F_UREY_BRADLEY;
 139                 case 6:
 140                     return F_QUARTIC_ANGLES;
 141                 case 8:
 142                     return F_TABANGLES;
 143                 case 9:
 144                     return F_LINEAR_ANGLES;
 145                 case 10:
 146                     return F_RESTRANGLES;
 147                 default:
 148                     gmx_fatal(FARGS, "Invalid angle type %d", type);
 149                     break;
 150             }
 151             break;
 152         case d_pairs:
 153         case d_pairtypes:
 154             if (type == 1 || (d == d_pairtypes && type == 2))
 155             {
 156                 return F_LJ14;
 157             }
 158             else if (type == 2)
 159             {
 160                 return F_LJC14_Q;
 161             }
 162             else
 163             {
 164                 gmx_fatal(FARGS, "Invalid pairs type %d", type);
 165             }
 166             break;
 167         case d_pairs_nb:
 168             return F_LJC_PAIRS_NB;
 169         case d_dihedrals:
 170         case d_dihedraltypes:
 171             switch (type)
 172             {
 173                 case 1:
 174                     return F_PDIHS;
 175                 case 2:
 176                     return F_IDIHS;
 177                 case 3:
 178                     return F_RBDIHS;
 179                 case 4:
 180                     return F_PIDIHS;
 181                 case 5:
 182                     return F_FOURDIHS;
 183                 case 8:
 184                     return F_TABDIHS;
 185                 case 9:
 186                     return F_PDIHS; /* proper dihedrals where we allow multiple terms over single bond */
 187                 case 10:
 188                     return F_RESTRDIHS;
 189                 case 11:
 190                     return F_CBTDIHS;
 191                 default:
 192                     gmx_fatal(FARGS, "Invalid dihedral type %d", type);
 193             }
 194             break;
 195         case d_cmaptypes:
 196         case d_cmap:
 197             return F_CMAP;
 198
 199         case d_nonbond_params:
 200             if (type == 1)
 201             {
 202                 return F_LJ;
 203             }
 204             else
 205             {
 206                 return F_BHAM;
 207             }
 208         case d_vsites2:
 209             return F_VSITE2;
 210         case d_vsites3:
 211             switch (type)
 212             {
 213                 case 1:
 214                     return F_VSITE3;
 215                 case 2:
 216                     return F_VSITE3FD;
 217                 case 3:
 218                     return F_VSITE3FAD;
 219                 case 4:
 220                     return F_VSITE3OUT;
 221                 default:
 222                     gmx_fatal(FARGS, "Invalid vsites3 type %d", type);
 223             }
 224             break;
 225         case d_vsites4:
 226             switch (type)
 227             {
 228                 case 1:
 229                     return F_VSITE4FD;
 230                 case 2:
 231                     return F_VSITE4FDN;
 232                 default:
 233                     gmx_fatal(FARGS, "Invalid vsites4 type %d", type);
 234             }
 235             break;
 236         case d_vsitesn:
 237             return F_VSITEN;
 238         case d_constraints:
 239         case d_constrainttypes:
 240             switch (type)
 241             {
 242                 case 1:
 243                     return F_CONSTR;
 244                 case 2:
 245                     return F_CONSTRNC;
 246                 default:
 247                     gmx_fatal(FARGS, "Invalid constraints type %d", type);
 248             }
 249             break;
 250         case d_settles:
 251             return F_SETTLE;
 252         case d_position_restraints:
 253             switch (type)
 254             {
 255                 case 1:
 256                     return F_POSRES;
 257                 case 2:
 258                     return F_FBPOSRES;
 259                 default:
 260                     gmx_fatal(FARGS, "Invalid position restraint type %d", type);
 261             }
 262             break;
 263         case d_polarization:
 264             switch (type)
 265             {
 266                 case 1:
 267                     return F_POLARIZATION;
 268                 case 2:
 269                     return F_ANHARM_POL;
 270                 default:
 271                     gmx_fatal(FARGS, "Invalid polarization type %d", type);
 272             }
 273             break;
 274         case d_thole_polarization:
 275             return F_THOLE_POL;
 276         case d_water_polarization:
 277             return F_WATER_POL;
 278         case d_angle_restraints:
 279             return F_ANGRES;
 280         case d_angle_restraints_z:
 281             return F_ANGRESZ;
 282         case d_distance_restraints:
 283             return F_DISRES;
 284         case d_orientation_restraints:
 285             return F_ORIRES;
 286         case d_dihedral_restraints:
 287             return F_DIHRES;
 288         default:
 289             gmx_fatal(FARGS, "invalid directive %s in ifunc_index (%s:%s)",
 290                       dir2str(d), __FILE__, __LINE__);
 291     }
 292     return -1;
 293 }
 294
 295 const char *dir2str (directive d)
 296 {
 297     if (d < d_maxdir)
 298     {
 299         return directive_names[d];
 300     }
 301     else
 302     {
 303         return directive_names[d_maxdir];
 304     }
 305 }
 306
 307 directive str2dir (char *dstr)
 308 {
 309     int  d;
 310     char buf[STRLEN], *ptr;
 311
 312     /* Hack to be able to read old topologies */
 313     if (gmx_strncasecmp_min(dstr, "dummies", 7) == 0)
 314     {
 315         sprintf(buf, "virtual_sites%s", dstr+7);
 316         ptr = buf;
 317     }
 318     else
 319     {
 320         ptr = dstr;
 321     }
 322
 323     for (d = 0; (d < d_maxdir); d++)
 324     {
 325         if (gmx_strcasecmp_min(ptr, dir2str((directive)d)) == 0)
 326         {
 327             return (directive)d;
 328         }
 329     }
 330
 331     return d_invalid;
 332 }
 333
 334 static directive **necessary = nullptr;
 335
 336 static void set_nec(directive **n, ...)
 337 /* Must always have at least one extra argument */
 338 {
 339     va_list   ap;
 340     int       ind = 0;
 341     directive d;
 342
 343     va_start(ap, n);
 344     do
 345     {
 346         d = (directive)va_arg(ap, int);
 347         srenew(*n, ++ind);
 348         (*n)[ind-1] = d;
 349     }
 350     while (d != d_none);
 351     va_end(ap);
 352 }
 353
 354 void DS_Init(DirStack **DS)
 355 {
 356     if (necessary == nullptr)
 357     {
 358         int i;
 359
 360         snew(necessary, d_maxdir);
 361         set_nec(&(necessary[d_defaults]), d_none);
 362         set_nec(&(necessary[d_atomtypes]), d_defaults, d_none);
 363         set_nec(&(necessary[d_bondtypes]), d_atomtypes, d_none);
 364         set_nec(&(necessary[d_constrainttypes]), d_atomtypes, d_none);
 365         set_nec(&(necessary[d_pairtypes]), d_atomtypes, d_none);
 366         set_nec(&(necessary[d_angletypes]), d_atomtypes, d_none);
 367         set_nec(&(necessary[d_dihedraltypes]), d_atomtypes, d_none);
 368         set_nec(&(necessary[d_nonbond_params]), d_atomtypes, d_none);
 369         set_nec(&(necessary[d_implicit_genborn_params]), d_atomtypes, d_none);
 370         set_nec(&(necessary[d_implicit_surface_params]), d_atomtypes, d_none);
 371         set_nec(&(necessary[d_cmaptypes]), d_atomtypes, d_none);
 372         set_nec(&(necessary[d_moleculetype]), d_atomtypes, d_none);
 373         set_nec(&(necessary[d_atoms]), d_moleculetype, d_none);
 374         set_nec(&(necessary[d_vsites2]), d_atoms, d_none);
 375         set_nec(&(necessary[d_vsites3]), d_atoms, d_none);
 376         set_nec(&(necessary[d_vsites4]), d_atoms, d_none);
 377         set_nec(&(necessary[d_vsitesn]), d_atoms, d_none);
 378         set_nec(&(necessary[d_bonds]), d_atoms, d_none);
 379         set_nec(&(necessary[d_exclusions]), d_bonds, d_constraints, d_settles, d_none);
 380         set_nec(&(necessary[d_pairs]), d_atoms, d_none);
 381         set_nec(&(necessary[d_pairs_nb]), d_atoms, d_none);
 382         set_nec(&(necessary[d_angles]), d_atoms, d_none);
 383         set_nec(&(necessary[d_polarization]), d_atoms, d_none);
 384         set_nec(&(necessary[d_water_polarization]), d_atoms, d_none);
 385         set_nec(&(necessary[d_thole_polarization]), d_atoms, d_none);
 386         set_nec(&(necessary[d_dihedrals]), d_atoms, d_none);
 387         set_nec(&(necessary[d_constraints]), d_atoms, d_none);
 388         set_nec(&(necessary[d_settles]), d_atoms, d_none);
 389         set_nec(&(necessary[d_system]), d_moleculetype, d_none);
 390         set_nec(&(necessary[d_molecules]), d_system, d_none);
 391         set_nec(&(necessary[d_position_restraints]), d_atoms, d_none);
 392         set_nec(&(necessary[d_angle_restraints]), d_atoms, d_none);
 393         set_nec(&(necessary[d_angle_restraints_z]), d_atoms, d_none);
 394         set_nec(&(necessary[d_distance_restraints]), d_atoms, d_none);
 395         set_nec(&(necessary[d_orientation_restraints]), d_atoms, d_none);
 396         set_nec(&(necessary[d_dihedral_restraints]), d_atoms, d_none);
 397         set_nec(&(necessary[d_cmap]), d_atoms, d_none);
 398         set_nec(&(necessary[d_intermolecular_interactions]), d_molecules, d_none);
 399
 400         for (i = 0; (i < d_maxdir); i++)
 401         {
 402             if (debug)
 403             {
 404                 fprintf(debug, "%20s:  ", dir2str((directive)i));
 405             }
 406             if (necessary[i])
 407             {
 408                 directive d;
 409                 int       j = 0;
 410                 do
 411                 {
 412                     d = necessary[i][j++];
 413                     if (debug)
 414                     {
 415                         fprintf(debug, "%20s  ", dir2str(d));
 416                     }
 417                 }
 418                 while (d != d_none);
 419             }
 420             if (debug)
 421             {
 422                 fprintf(debug, "\n");
 423             }
 424         }
 425     }
 426     *DS = nullptr;
 427
 428 }
 429
 430 void DS_Done (DirStack **DS)
 431 {
 432     DirStack *D;
 433
 434     while (*DS != nullptr)
 435     {
 436         D   = *DS;
 437         *DS = (*DS)->prev;
 438         sfree (D);
 439     }
 440 }
 441
 442 void DS_Push (DirStack **DS, directive d)
 443 {
 444     DirStack *D;
 445
 446     snew(D, 1);
 447     D->d    = d;
 448     D->prev = *DS;
 449     *DS     = D;
 450 }
 451
 452 int DS_Search(DirStack *DS, directive d)
 453 {
 454     DirStack *D;
 455
 456     D = DS;
 457     while ((D != nullptr) && (D->d != d))
 458     {
 459         D = D->prev;
 460     }
 461
 462     return (D != nullptr);
 463 }
 464
 465 int DS_Check_Order(DirStack *DS, directive d)
 466 {
 467     directive d0;
 468     int       i = 0;
 469
 470     /* Check if parameter definitions appear after a moleculetype directive */
 471     if (d < d_moleculetype && DS_Search(DS, d_moleculetype))
 472     {
 473         return FALSE;
 474     }
 475
 476     /* Check if all the necessary directives have appeared before directive d */
 477     if (necessary[d][0] == d_none)
 478     {
 479         return TRUE;
 480     }
 481     else
 482     {
 483         do
 484         {
 485             d0 = necessary[d][i++];
 486             if (DS_Search(DS, d0))
 487             {
 488                 return TRUE;
 489             }
 490         }
 491         while (d0 != d_none);
 492     }
 493     return FALSE;
 494 }