src/gromacs/gmxpreprocess/topdirs.cpp

   1 /*
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   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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   6  * Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
   7  * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
   8  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   9  * and including many others, as listed in the AUTHORS file in the
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  38 #include "gmxpre.h"
  39
  40 #include "topdirs.h"
  41
  42 #include <cstdarg>
  43 #include <cstdio>
  44
  45 #include <algorithm>
  46
  47 #include "gromacs/topology/idef.h"
  48 #include "gromacs/utility/cstringutil.h"
  49 #include "gromacs/utility/enumerationhelpers.h"
  50 #include "gromacs/utility/fatalerror.h"
  51 #include "gromacs/utility/smalloc.h"
  52
  53 /* Must correspond to the Directive enum in grompp_impl.h */
  54 static gmx::EnumerationArray<Directive, const char*> directive_names = {
  55     { "defaults",
  56       "atomtypes",
  57       "bondtypes",
  58       "constrainttypes",
  59       "pairtypes",
  60       "angletypes",
  61       "dihedraltypes",
  62       "nonbond_params",
  63       "implicit_genborn_params",
  64       "implicit_surface_params",
  65       "cmaptypes",
  66       /* All the directives above can not appear after moleculetype */
  67       "moleculetype",
  68       "atoms",
  69       "virtual_sites1",
  70       "virtual_sites2",
  71       "virtual_sites3",
  72       "virtual_sites4",
  73       "virtual_sitesn",
  74       "bonds",
  75       "exclusions",
  76       "pairs",
  77       "pairs_nb",
  78       "angles",
  79       "dihedrals",
  80       "constraints",
  81       "settles",
  82       "polarization",
  83       "water_polarization",
  84       "thole_polarization",
  85       "system",
  86       "molecules",
  87       "position_restraints",
  88       "angle_restraints",
  89       "angle_restraints_z",
  90       "distance_restraints",
  91       "orientation_restraints",
  92       "dihedral_restraints",
  93       "cmap",
  94       "intermolecular_interactions",
  95       "maxdirs",
  96       "invalid",
  97       "none" }
  98 };
  99
 100 int ifunc_index(Directive d, int type)
 101 {
 102     switch (d)
 103     {
 104         case Directive::d_bondtypes:
 105         case Directive::d_bonds:
 106             switch (type)
 107             {
 108                 case 1: return F_BONDS;
 109                 case 2: return F_G96BONDS;
 110                 case 3: return F_MORSE;
 111                 case 4: return F_CUBICBONDS;
 112                 case 5: return F_CONNBONDS;
 113                 case 6: return F_HARMONIC;
 114                 case 7: return F_FENEBONDS;
 115                 case 8: return F_TABBONDS;
 116                 case 9: return F_TABBONDSNC;
 117                 case 10: return F_RESTRBONDS;
 118                 default: gmx_fatal(FARGS, "Invalid bond type %d", type);
 119             }
 120         case Directive::d_angles:
 121         case Directive::d_angletypes:
 122             switch (type)
 123             {
 124                 case 1: return F_ANGLES;
 125                 case 2: return F_G96ANGLES;
 126                 case 3: return F_CROSS_BOND_BONDS;
 127                 case 4: return F_CROSS_BOND_ANGLES;
 128                 case 5: return F_UREY_BRADLEY;
 129                 case 6: return F_QUARTIC_ANGLES;
 130                 case 8: return F_TABANGLES;
 131                 case 9: return F_LINEAR_ANGLES;
 132                 case 10: return F_RESTRANGLES;
 133                 default: gmx_fatal(FARGS, "Invalid angle type %d", type);
 134             }
 135         case Directive::d_pairs:
 136         case Directive::d_pairtypes:
 137             if (type == 1 || (d == Directive::d_pairtypes && type == 2))
 138             {
 139                 return F_LJ14;
 140             }
 141             else if (type == 2)
 142             {
 143                 return F_LJC14_Q;
 144             }
 145             else
 146             {
 147                 gmx_fatal(FARGS, "Invalid pairs type %d", type);
 148             }
 149         case Directive::d_pairs_nb: return F_LJC_PAIRS_NB;
 150         case Directive::d_dihedrals:
 151         case Directive::d_dihedraltypes:
 152             switch (type)
 153             {
 154                 case 1: return F_PDIHS;
 155                 case 2: return F_IDIHS;
 156                 case 3: return F_RBDIHS;
 157                 case 4: return F_PIDIHS;
 158                 case 5: return F_FOURDIHS;
 159                 case 8: return F_TABDIHS;
 160                 case 9:
 161                     return F_PDIHS; /* proper dihedrals where we allow multiple terms over single bond */
 162                 case 10: return F_RESTRDIHS;
 163                 case 11: return F_CBTDIHS;
 164                 default: gmx_fatal(FARGS, "Invalid dihedral type %d", type);
 165             }
 166         case Directive::d_cmaptypes:
 167         case Directive::d_cmap: return F_CMAP;
 168
 169         case Directive::d_nonbond_params:
 170             if (type == 1)
 171             {
 172                 return F_LJ;
 173             }
 174             else
 175             {
 176                 return F_BHAM;
 177             }
 178         case Directive::d_vsites1:
 179             if (type == 1)
 180             {
 181                 return F_VSITE1;
 182             }
 183             else
 184             {
 185                 gmx_fatal(FARGS, "Invalid vsites1 type %d", type);
 186             }
 187         case Directive::d_vsites2:
 188             switch (type)
 189             {
 190                 case 1: return F_VSITE2;
 191                 case 2: return F_VSITE2FD;
 192                 default: gmx_fatal(FARGS, "Invalid vsites2 type %d", type);
 193             }
 194         case Directive::d_vsites3:
 195             switch (type)
 196             {
 197                 case 1: return F_VSITE3;
 198                 case 2: return F_VSITE3FD;
 199                 case 3: return F_VSITE3FAD;
 200                 case 4: return F_VSITE3OUT;
 201                 default: gmx_fatal(FARGS, "Invalid vsites3 type %d", type);
 202             }
 203         case Directive::d_vsites4:
 204             switch (type)
 205             {
 206                 case 1: return F_VSITE4FD;
 207                 case 2: return F_VSITE4FDN;
 208                 default: gmx_fatal(FARGS, "Invalid vsites4 type %d", type);
 209             }
 210         case Directive::d_vsitesn: return F_VSITEN;
 211         case Directive::d_constraints:
 212         case Directive::d_constrainttypes:
 213             switch (type)
 214             {
 215                 case 1: return F_CONSTR;
 216                 case 2: return F_CONSTRNC;
 217                 default: gmx_fatal(FARGS, "Invalid constraints type %d", type);
 218             }
 219         case Directive::d_settles: return F_SETTLE;
 220         case Directive::d_position_restraints:
 221             switch (type)
 222             {
 223                 case 1: return F_POSRES;
 224                 case 2: return F_FBPOSRES;
 225                 default: gmx_fatal(FARGS, "Invalid position restraint type %d", type);
 226             }
 227         case Directive::d_polarization:
 228             switch (type)
 229             {
 230                 case 1: return F_POLARIZATION;
 231                 case 2: return F_ANHARM_POL;
 232                 default: gmx_fatal(FARGS, "Invalid polarization type %d", type);
 233             }
 234         case Directive::d_thole_polarization: return F_THOLE_POL;
 235         case Directive::d_water_polarization: return F_WATER_POL;
 236         case Directive::d_angle_restraints: return F_ANGRES;
 237         case Directive::d_angle_restraints_z: return F_ANGRESZ;
 238         case Directive::d_distance_restraints: return F_DISRES;
 239         case Directive::d_orientation_restraints: return F_ORIRES;
 240         case Directive::d_dihedral_restraints: return F_DIHRES;
 241         default:
 242             gmx_fatal(FARGS, "invalid directive %s in ifunc_index (%s:%d)", dir2str(d), __FILE__, __LINE__);
 243     }
 244 }
 245
 246 const char* dir2str(Directive d)
 247 {
 248     int index = static_cast<int>(d);
 249     return directive_names[index];
 250 }
 251
 252 Directive str2dir(char* dstr)
 253 {
 254     char buf[STRLEN], *ptr;
 255
 256     /* Hack to be able to read old topologies */
 257     if (gmx_strncasecmp_min(dstr, "dummies", 7) == 0)
 258     {
 259         sprintf(buf, "virtual_sites%s", dstr + 7);
 260         ptr = buf;
 261     }
 262     else
 263     {
 264         ptr = dstr;
 265     }
 266
 267     for (auto d : gmx::EnumerationWrapper<Directive>())
 268     {
 269         if (gmx_strcasecmp_min(ptr, dir2str(static_cast<Directive>(d))) == 0)
 270         {
 271             return static_cast<Directive>(d);
 272         }
 273     }
 274
 275     return Directive::d_invalid;
 276 }
 277
 278 static gmx::EnumerationArray<Directive, Directive*> necessary = { { nullptr } };
 279
 280 static void set_nec(Directive** n, ...)
 281 /* Must always have at least one extra argument */
 282 {
 283     va_list   ap;
 284     int       ind = 0;
 285     Directive d;
 286
 287     va_start(ap, n);
 288     do
 289     {
 290         d = static_cast<Directive>(va_arg(ap, int));
 291         srenew(*n, ++ind);
 292         (*n)[ind - 1] = d;
 293     } while (d != Directive::d_none);
 294     va_end(ap);
 295 }
 296
 297 void DS_Init(DirStack** DS)
 298 {
 299     if (necessary[0] == nullptr)
 300     {
 301         set_nec(&(necessary[Directive::d_defaults]), Directive::d_none);
 302         set_nec(&(necessary[Directive::d_atomtypes]), Directive::d_defaults, Directive::d_none);
 303         set_nec(&(necessary[Directive::d_bondtypes]), Directive::d_atomtypes, Directive::d_none);
 304         set_nec(&(necessary[Directive::d_constrainttypes]), Directive::d_atomtypes, Directive::d_none);
 305         set_nec(&(necessary[Directive::d_pairtypes]), Directive::d_atomtypes, Directive::d_none);
 306         set_nec(&(necessary[Directive::d_angletypes]), Directive::d_atomtypes, Directive::d_none);
 307         set_nec(&(necessary[Directive::d_dihedraltypes]), Directive::d_atomtypes, Directive::d_none);
 308         set_nec(&(necessary[Directive::d_nonbond_params]), Directive::d_atomtypes, Directive::d_none);
 309         // Note that the content of the next two directives are
 310         // ignored, but if grompp reads them in old force field files,
 311         // it still needs to understand that they are in a valid place
 312         // in the .top structure. It doesn't have to require them to
 313         // be in the same place that was valid in old versions (ie. child
 314         // directive of [atomtypes]) but any relevant case will
 315         // satisfy that.
 316         set_nec(&(necessary[Directive::d_implicit_genborn_params]), Directive::d_atomtypes, Directive::d_none);
 317         set_nec(&(necessary[Directive::d_implicit_surface_params]), Directive::d_atomtypes, Directive::d_none);
 318         set_nec(&(necessary[Directive::d_cmaptypes]), Directive::d_atomtypes, Directive::d_none);
 319         set_nec(&(necessary[Directive::d_moleculetype]), Directive::d_atomtypes, Directive::d_none);
 320         set_nec(&(necessary[Directive::d_atoms]), Directive::d_moleculetype, Directive::d_none);
 321         set_nec(&(necessary[Directive::d_vsites1]), Directive::d_atoms, Directive::d_none);
 322         set_nec(&(necessary[Directive::d_vsites2]), Directive::d_atoms, Directive::d_none);
 323         set_nec(&(necessary[Directive::d_vsites3]), Directive::d_atoms, Directive::d_none);
 324         set_nec(&(necessary[Directive::d_vsites4]), Directive::d_atoms, Directive::d_none);
 325         set_nec(&(necessary[Directive::d_vsitesn]), Directive::d_atoms, Directive::d_none);
 326         set_nec(&(necessary[Directive::d_bonds]), Directive::d_atoms, Directive::d_none);
 327         set_nec(&(necessary[Directive::d_exclusions]),
 328                 Directive::d_bonds,
 329                 Directive::d_constraints,
 330                 Directive::d_settles,
 331                 Directive::d_none);
 332         set_nec(&(necessary[Directive::d_pairs]), Directive::d_atoms, Directive::d_none);
 333         set_nec(&(necessary[Directive::d_pairs_nb]), Directive::d_atoms, Directive::d_none);
 334         set_nec(&(necessary[Directive::d_angles]), Directive::d_atoms, Directive::d_none);
 335         set_nec(&(necessary[Directive::d_polarization]), Directive::d_atoms, Directive::d_none);
 336         set_nec(&(necessary[Directive::d_water_polarization]), Directive::d_atoms, Directive::d_none);
 337         set_nec(&(necessary[Directive::d_thole_polarization]), Directive::d_atoms, Directive::d_none);
 338         set_nec(&(necessary[Directive::d_dihedrals]), Directive::d_atoms, Directive::d_none);
 339         set_nec(&(necessary[Directive::d_constraints]), Directive::d_atoms, Directive::d_none);
 340         set_nec(&(necessary[Directive::d_settles]), Directive::d_atoms, Directive::d_none);
 341         set_nec(&(necessary[Directive::d_system]), Directive::d_moleculetype, Directive::d_none);
 342         set_nec(&(necessary[Directive::d_molecules]), Directive::d_system, Directive::d_none);
 343         set_nec(&(necessary[Directive::d_position_restraints]), Directive::d_atoms, Directive::d_none);
 344         set_nec(&(necessary[Directive::d_angle_restraints]), Directive::d_atoms, Directive::d_none);
 345         set_nec(&(necessary[Directive::d_angle_restraints_z]), Directive::d_atoms, Directive::d_none);
 346         set_nec(&(necessary[Directive::d_distance_restraints]), Directive::d_atoms, Directive::d_none);
 347         set_nec(&(necessary[Directive::d_orientation_restraints]), Directive::d_atoms, Directive::d_none);
 348         set_nec(&(necessary[Directive::d_dihedral_restraints]), Directive::d_atoms, Directive::d_none);
 349         set_nec(&(necessary[Directive::d_cmap]), Directive::d_atoms, Directive::d_none);
 350         set_nec(&(necessary[Directive::d_intermolecular_interactions]),
 351                 Directive::d_molecules,
 352                 Directive::d_none);
 353     }
 354     *DS = nullptr;
 355 }
 356
 357 void DS_Done(DirStack** DS)
 358 {
 359     DirStack* D;
 360
 361     while (*DS != nullptr)
 362     {
 363         D   = *DS;
 364         *DS = (*DS)->prev;
 365         sfree(D);
 366     }
 367 }
 368
 369 void DS_Push(DirStack** DS, Directive d)
 370 {
 371     DirStack* D;
 372
 373     snew(D, 1);
 374     D->d    = d;
 375     D->prev = *DS;
 376     *DS     = D;
 377 }
 378
 379 int DS_Search(DirStack* DS, Directive d)
 380 {
 381     DirStack* D;
 382
 383     D = DS;
 384     while ((D != nullptr) && (D->d != d))
 385     {
 386         D = D->prev;
 387     }
 388
 389     return static_cast<int>(D != nullptr);
 390 }
 391
 392 int DS_Check_Order(DirStack* DS, Directive d)
 393 {
 394     Directive d0;
 395     int       i = 0;
 396
 397     /* Check if parameter definitions appear after a moleculetype directive */
 398     if (d < Directive::d_moleculetype && DS_Search(DS, Directive::d_moleculetype))
 399     {
 400         return FALSE;
 401     }
 402
 403     /* Check if all the necessary directives have appeared before directive d */
 404     if (necessary[d][0] == Directive::d_none)
 405     {
 406         return TRUE;
 407     }
 408     else
 409     {
 410         do
 411         {
 412             d0 = necessary[d][i++];
 413             if (DS_Search(DS, d0))
 414             {
 415                 return TRUE;
 416             }
 417         } while (d0 != Directive::d_none);
 418     }
 419     return FALSE;
 420 }