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