src/gromacs/gmxpreprocess/topdirs.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
   7  * Copyright (c) 2019,2020, 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", "atomtypes", "bondtypes", "constrainttypes", "pairtypes", "angletypes",
  56       "dihedraltypes", "nonbond_params", "implicit_genborn_params", "implicit_surface_params",
  57       "cmaptypes",
  58       /* All the directives above can not appear after moleculetype */
  59       "moleculetype", "atoms", "virtual_sites2", "virtual_sites3", "virtual_sites4",
  60       "virtual_sitesn", "bonds", "exclusions", "pairs", "pairs_nb", "angles", "dihedrals",
  61       "constraints", "settles", "polarization", "water_polarization", "thole_polarization",
  62       "system", "molecules", "position_restraints", "angle_restraints", "angle_restraints_z",
  63       "distance_restraints", "orientation_restraints", "dihedral_restraints", "cmap",
  64       "intermolecular_interactions", "maxdirs", "invalid", "none" }
  65 };
  66
  67 int ifunc_index(Directive d, int type)
  68 {
  69     switch (d)
  70     {
  71         case Directive::d_bondtypes:
  72         case Directive::d_bonds:
  73             switch (type)
  74             {
  75                 case 1: return F_BONDS;
  76                 case 2: return F_G96BONDS;
  77                 case 3: return F_MORSE;
  78                 case 4: return F_CUBICBONDS;
  79                 case 5: return F_CONNBONDS;
  80                 case 6: return F_HARMONIC;
  81                 case 7: return F_FENEBONDS;
  82                 case 8: return F_TABBONDS;
  83                 case 9: return F_TABBONDSNC;
  84                 case 10: return F_RESTRBONDS;
  85                 default: gmx_fatal(FARGS, "Invalid bond type %d", type);
  86             }
  87         case Directive::d_angles:
  88         case Directive::d_angletypes:
  89             switch (type)
  90             {
  91                 case 1: return F_ANGLES;
  92                 case 2: return F_G96ANGLES;
  93                 case 3: return F_CROSS_BOND_BONDS;
  94                 case 4: return F_CROSS_BOND_ANGLES;
  95                 case 5: return F_UREY_BRADLEY;
  96                 case 6: return F_QUARTIC_ANGLES;
  97                 case 8: return F_TABANGLES;
  98                 case 9: return F_LINEAR_ANGLES;
  99                 case 10: return F_RESTRANGLES;
 100                 default: gmx_fatal(FARGS, "Invalid angle type %d", type);
 101             }
 102         case Directive::d_pairs:
 103         case Directive::d_pairtypes:
 104             if (type == 1 || (d == Directive::d_pairtypes && type == 2))
 105             {
 106                 return F_LJ14;
 107             }
 108             else if (type == 2)
 109             {
 110                 return F_LJC14_Q;
 111             }
 112             else
 113             {
 114                 gmx_fatal(FARGS, "Invalid pairs type %d", type);
 115             }
 116         case Directive::d_pairs_nb: return F_LJC_PAIRS_NB;
 117         case Directive::d_dihedrals:
 118         case Directive::d_dihedraltypes:
 119             switch (type)
 120             {
 121                 case 1: return F_PDIHS;
 122                 case 2: return F_IDIHS;
 123                 case 3: return F_RBDIHS;
 124                 case 4: return F_PIDIHS;
 125                 case 5: return F_FOURDIHS;
 126                 case 8: return F_TABDIHS;
 127                 case 9:
 128                     return F_PDIHS; /* proper dihedrals where we allow multiple terms over single bond */
 129                 case 10: return F_RESTRDIHS;
 130                 case 11: return F_CBTDIHS;
 131                 default: gmx_fatal(FARGS, "Invalid dihedral type %d", type);
 132             }
 133         case Directive::d_cmaptypes:
 134         case Directive::d_cmap: return F_CMAP;
 135
 136         case Directive::d_nonbond_params:
 137             if (type == 1)
 138             {
 139                 return F_LJ;
 140             }
 141             else
 142             {
 143                 return F_BHAM;
 144             }
 145         case Directive::d_vsites2:
 146             switch (type)
 147             {
 148                 case 1: return F_VSITE2;
 149                 case 2: return F_VSITE2FD;
 150                 default: gmx_fatal(FARGS, "Invalid vsites2 type %d", type);
 151             }
 152         case Directive::d_vsites3:
 153             switch (type)
 154             {
 155                 case 1: return F_VSITE3;
 156                 case 2: return F_VSITE3FD;
 157                 case 3: return F_VSITE3FAD;
 158                 case 4: return F_VSITE3OUT;
 159                 default: gmx_fatal(FARGS, "Invalid vsites3 type %d", type);
 160             }
 161         case Directive::d_vsites4:
 162             switch (type)
 163             {
 164                 case 1: return F_VSITE4FD;
 165                 case 2: return F_VSITE4FDN;
 166                 default: gmx_fatal(FARGS, "Invalid vsites4 type %d", type);
 167             }
 168         case Directive::d_vsitesn: return F_VSITEN;
 169         case Directive::d_constraints:
 170         case Directive::d_constrainttypes:
 171             switch (type)
 172             {
 173                 case 1: return F_CONSTR;
 174                 case 2: return F_CONSTRNC;
 175                 default: gmx_fatal(FARGS, "Invalid constraints type %d", type);
 176             }
 177         case Directive::d_settles: return F_SETTLE;
 178         case Directive::d_position_restraints:
 179             switch (type)
 180             {
 181                 case 1: return F_POSRES;
 182                 case 2: return F_FBPOSRES;
 183                 default: gmx_fatal(FARGS, "Invalid position restraint type %d", type);
 184             }
 185         case Directive::d_polarization:
 186             switch (type)
 187             {
 188                 case 1: return F_POLARIZATION;
 189                 case 2: return F_ANHARM_POL;
 190                 default: gmx_fatal(FARGS, "Invalid polarization type %d", type);
 191             }
 192         case Directive::d_thole_polarization: return F_THOLE_POL;
 193         case Directive::d_water_polarization: return F_WATER_POL;
 194         case Directive::d_angle_restraints: return F_ANGRES;
 195         case Directive::d_angle_restraints_z: return F_ANGRESZ;
 196         case Directive::d_distance_restraints: return F_DISRES;
 197         case Directive::d_orientation_restraints: return F_ORIRES;
 198         case Directive::d_dihedral_restraints: return F_DIHRES;
 199         default:
 200             gmx_fatal(FARGS, "invalid directive %s in ifunc_index (%s:%d)", dir2str(d), __FILE__, __LINE__);
 201     }
 202 }
 203
 204 const char* dir2str(Directive d)
 205 {
 206     int index = static_cast<int>(d);
 207     return directive_names[index];
 208 }
 209
 210 Directive str2dir(char* dstr)
 211 {
 212     char buf[STRLEN], *ptr;
 213
 214     /* Hack to be able to read old topologies */
 215     if (gmx_strncasecmp_min(dstr, "dummies", 7) == 0)
 216     {
 217         sprintf(buf, "virtual_sites%s", dstr + 7);
 218         ptr = buf;
 219     }
 220     else
 221     {
 222         ptr = dstr;
 223     }
 224
 225     for (auto d : gmx::EnumerationWrapper<Directive>())
 226     {
 227         if (gmx_strcasecmp_min(ptr, dir2str(static_cast<Directive>(d))) == 0)
 228         {
 229             return static_cast<Directive>(d);
 230         }
 231     }
 232
 233     return Directive::d_invalid;
 234 }
 235
 236 static gmx::EnumerationArray<Directive, Directive*> necessary = { { nullptr } };
 237
 238 static void set_nec(Directive** n, ...)
 239 /* Must always have at least one extra argument */
 240 {
 241     va_list   ap;
 242     int       ind = 0;
 243     Directive d;
 244
 245     va_start(ap, n);
 246     do
 247     {
 248         d = static_cast<Directive>(va_arg(ap, int));
 249         srenew(*n, ++ind);
 250         (*n)[ind - 1] = d;
 251     } while (d != Directive::d_none);
 252     va_end(ap);
 253 }
 254
 255 void DS_Init(DirStack** DS)
 256 {
 257     if (necessary[0] == nullptr)
 258     {
 259         set_nec(&(necessary[Directive::d_defaults]), Directive::d_none);
 260         set_nec(&(necessary[Directive::d_atomtypes]), Directive::d_defaults, Directive::d_none);
 261         set_nec(&(necessary[Directive::d_bondtypes]), Directive::d_atomtypes, Directive::d_none);
 262         set_nec(&(necessary[Directive::d_constrainttypes]), Directive::d_atomtypes, Directive::d_none);
 263         set_nec(&(necessary[Directive::d_pairtypes]), Directive::d_atomtypes, Directive::d_none);
 264         set_nec(&(necessary[Directive::d_angletypes]), Directive::d_atomtypes, Directive::d_none);
 265         set_nec(&(necessary[Directive::d_dihedraltypes]), Directive::d_atomtypes, Directive::d_none);
 266         set_nec(&(necessary[Directive::d_nonbond_params]), Directive::d_atomtypes, Directive::d_none);
 267         // Note that the content of the next two directives are
 268         // ignored, but if grompp reads them in old force field files,
 269         // it still needs to understand that they are in a valid place
 270         // in the .top structure. It doesn't have to require them to
 271         // be in the same place that was valid in old versions (ie. child
 272         // directive of [atomtypes]) but any relevant case will
 273         // satisfy that.
 274         set_nec(&(necessary[Directive::d_implicit_genborn_params]), Directive::d_atomtypes,
 275                 Directive::d_none);
 276         set_nec(&(necessary[Directive::d_implicit_surface_params]), Directive::d_atomtypes,
 277                 Directive::d_none);
 278         set_nec(&(necessary[Directive::d_cmaptypes]), Directive::d_atomtypes, Directive::d_none);
 279         set_nec(&(necessary[Directive::d_moleculetype]), Directive::d_atomtypes, Directive::d_none);
 280         set_nec(&(necessary[Directive::d_atoms]), Directive::d_moleculetype, Directive::d_none);
 281         set_nec(&(necessary[Directive::d_vsites2]), Directive::d_atoms, Directive::d_none);
 282         set_nec(&(necessary[Directive::d_vsites3]), Directive::d_atoms, Directive::d_none);
 283         set_nec(&(necessary[Directive::d_vsites4]), Directive::d_atoms, Directive::d_none);
 284         set_nec(&(necessary[Directive::d_vsitesn]), Directive::d_atoms, Directive::d_none);
 285         set_nec(&(necessary[Directive::d_bonds]), Directive::d_atoms, Directive::d_none);
 286         set_nec(&(necessary[Directive::d_exclusions]), Directive::d_bonds, Directive::d_constraints,
 287                 Directive::d_settles, Directive::d_none);
 288         set_nec(&(necessary[Directive::d_pairs]), Directive::d_atoms, Directive::d_none);
 289         set_nec(&(necessary[Directive::d_pairs_nb]), Directive::d_atoms, Directive::d_none);
 290         set_nec(&(necessary[Directive::d_angles]), Directive::d_atoms, Directive::d_none);
 291         set_nec(&(necessary[Directive::d_polarization]), Directive::d_atoms, Directive::d_none);
 292         set_nec(&(necessary[Directive::d_water_polarization]), Directive::d_atoms, Directive::d_none);
 293         set_nec(&(necessary[Directive::d_thole_polarization]), Directive::d_atoms, Directive::d_none);
 294         set_nec(&(necessary[Directive::d_dihedrals]), Directive::d_atoms, Directive::d_none);
 295         set_nec(&(necessary[Directive::d_constraints]), Directive::d_atoms, Directive::d_none);
 296         set_nec(&(necessary[Directive::d_settles]), Directive::d_atoms, Directive::d_none);
 297         set_nec(&(necessary[Directive::d_system]), Directive::d_moleculetype, Directive::d_none);
 298         set_nec(&(necessary[Directive::d_molecules]), Directive::d_system, Directive::d_none);
 299         set_nec(&(necessary[Directive::d_position_restraints]), Directive::d_atoms, Directive::d_none);
 300         set_nec(&(necessary[Directive::d_angle_restraints]), Directive::d_atoms, Directive::d_none);
 301         set_nec(&(necessary[Directive::d_angle_restraints_z]), Directive::d_atoms, Directive::d_none);
 302         set_nec(&(necessary[Directive::d_distance_restraints]), Directive::d_atoms, Directive::d_none);
 303         set_nec(&(necessary[Directive::d_orientation_restraints]), Directive::d_atoms, Directive::d_none);
 304         set_nec(&(necessary[Directive::d_dihedral_restraints]), Directive::d_atoms, Directive::d_none);
 305         set_nec(&(necessary[Directive::d_cmap]), Directive::d_atoms, Directive::d_none);
 306         set_nec(&(necessary[Directive::d_intermolecular_interactions]), Directive::d_molecules,
 307                 Directive::d_none);
 308     }
 309     *DS = nullptr;
 310 }
 311
 312 void DS_Done(DirStack** DS)
 313 {
 314     DirStack* D;
 315
 316     while (*DS != nullptr)
 317     {
 318         D   = *DS;
 319         *DS = (*DS)->prev;
 320         sfree(D);
 321     }
 322 }
 323
 324 void DS_Push(DirStack** DS, Directive d)
 325 {
 326     DirStack* D;
 327
 328     snew(D, 1);
 329     D->d    = d;
 330     D->prev = *DS;
 331     *DS     = D;
 332 }
 333
 334 int DS_Search(DirStack* DS, Directive d)
 335 {
 336     DirStack* D;
 337
 338     D = DS;
 339     while ((D != nullptr) && (D->d != d))
 340     {
 341         D = D->prev;
 342     }
 343
 344     return static_cast<int>(D != nullptr);
 345 }
 346
 347 int DS_Check_Order(DirStack* DS, Directive d)
 348 {
 349     Directive d0;
 350     int       i = 0;
 351
 352     /* Check if parameter definitions appear after a moleculetype directive */
 353     if (d < Directive::d_moleculetype && DS_Search(DS, Directive::d_moleculetype))
 354     {
 355         return FALSE;
 356     }
 357
 358     /* Check if all the necessary directives have appeared before directive d */
 359     if (necessary[d][0] == Directive::d_none)
 360     {
 361         return TRUE;
 362     }
 363     else
 364     {
 365         do
 366         {
 367             d0 = necessary[d][i++];
 368             if (DS_Search(DS, d0))
 369             {
 370                 return TRUE;
 371             }
 372         } while (d0 != Directive::d_none);
 373     }
 374     return FALSE;
 375 }