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",
  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_sites2",
  70       "virtual_sites3",
  71       "virtual_sites4",
  72       "virtual_sitesn",
  73       "bonds",
  74       "exclusions",
  75       "pairs",
  76       "pairs_nb",
  77       "angles",
  78       "dihedrals",
  79       "constraints",
  80       "settles",
  81       "polarization",
  82       "water_polarization",
  83       "thole_polarization",
  84       "system",
  85       "molecules",
  86       "position_restraints",
  87       "angle_restraints",
  88       "angle_restraints_z",
  89       "distance_restraints",
  90       "orientation_restraints",
  91       "dihedral_restraints",
  92       "cmap",
  93       "intermolecular_interactions",
  94       "maxdirs",
  95       "invalid",
  96       "none" }
  97 };
  98
  99 int ifunc_index(Directive d, int type)
 100 {
 101     switch (d)
 102     {
 103         case Directive::d_bondtypes:
 104         case Directive::d_bonds:
 105             switch (type)
 106             {
 107                 case 1: return F_BONDS;
 108                 case 2: return F_G96BONDS;
 109                 case 3: return F_MORSE;
 110                 case 4: return F_CUBICBONDS;
 111                 case 5: return F_CONNBONDS;
 112                 case 6: return F_HARMONIC;
 113                 case 7: return F_FENEBONDS;
 114                 case 8: return F_TABBONDS;
 115                 case 9: return F_TABBONDSNC;
 116                 case 10: return F_RESTRBONDS;
 117                 default: gmx_fatal(FARGS, "Invalid bond type %d", type);
 118             }
 119         case Directive::d_angles:
 120         case Directive::d_angletypes:
 121             switch (type)
 122             {
 123                 case 1: return F_ANGLES;
 124                 case 2: return F_G96ANGLES;
 125                 case 3: return F_CROSS_BOND_BONDS;
 126                 case 4: return F_CROSS_BOND_ANGLES;
 127                 case 5: return F_UREY_BRADLEY;
 128                 case 6: return F_QUARTIC_ANGLES;
 129                 case 8: return F_TABANGLES;
 130                 case 9: return F_LINEAR_ANGLES;
 131                 case 10: return F_RESTRANGLES;
 132                 default: gmx_fatal(FARGS, "Invalid angle type %d", type);
 133             }
 134         case Directive::d_pairs:
 135         case Directive::d_pairtypes:
 136             if (type == 1 || (d == Directive::d_pairtypes && type == 2))
 137             {
 138                 return F_LJ14;
 139             }
 140             else if (type == 2)
 141             {
 142                 return F_LJC14_Q;
 143             }
 144             else
 145             {
 146                 gmx_fatal(FARGS, "Invalid pairs type %d", type);
 147             }
 148         case Directive::d_pairs_nb: return F_LJC_PAIRS_NB;
 149         case Directive::d_dihedrals:
 150         case Directive::d_dihedraltypes:
 151             switch (type)
 152             {
 153                 case 1: return F_PDIHS;
 154                 case 2: return F_IDIHS;
 155                 case 3: return F_RBDIHS;
 156                 case 4: return F_PIDIHS;
 157                 case 5: return F_FOURDIHS;
 158                 case 8: return F_TABDIHS;
 159                 case 9:
 160                     return F_PDIHS; /* proper dihedrals where we allow multiple terms over single bond */
 161                 case 10: return F_RESTRDIHS;
 162                 case 11: return F_CBTDIHS;
 163                 default: gmx_fatal(FARGS, "Invalid dihedral type %d", type);
 164             }
 165         case Directive::d_cmaptypes:
 166         case Directive::d_cmap: return F_CMAP;
 167
 168         case Directive::d_nonbond_params:
 169             if (type == 1)
 170             {
 171                 return F_LJ;
 172             }
 173             else
 174             {
 175                 return F_BHAM;
 176             }
 177         case Directive::d_vsites2:
 178             switch (type)
 179             {
 180                 case 1: return F_VSITE2;
 181                 case 2: return F_VSITE2FD;
 182                 default: gmx_fatal(FARGS, "Invalid vsites2 type %d", type);
 183             }
 184         case Directive::d_vsites3:
 185             switch (type)
 186             {
 187                 case 1: return F_VSITE3;
 188                 case 2: return F_VSITE3FD;
 189                 case 3: return F_VSITE3FAD;
 190                 case 4: return F_VSITE3OUT;
 191                 default: gmx_fatal(FARGS, "Invalid vsites3 type %d", type);
 192             }
 193         case Directive::d_vsites4:
 194             switch (type)
 195             {
 196                 case 1: return F_VSITE4FD;
 197                 case 2: return F_VSITE4FDN;
 198                 default: gmx_fatal(FARGS, "Invalid vsites4 type %d", type);
 199             }
 200         case Directive::d_vsitesn: return F_VSITEN;
 201         case Directive::d_constraints:
 202         case Directive::d_constrainttypes:
 203             switch (type)
 204             {
 205                 case 1: return F_CONSTR;
 206                 case 2: return F_CONSTRNC;
 207                 default: gmx_fatal(FARGS, "Invalid constraints type %d", type);
 208             }
 209         case Directive::d_settles: return F_SETTLE;
 210         case Directive::d_position_restraints:
 211             switch (type)
 212             {
 213                 case 1: return F_POSRES;
 214                 case 2: return F_FBPOSRES;
 215                 default: gmx_fatal(FARGS, "Invalid position restraint type %d", type);
 216             }
 217         case Directive::d_polarization:
 218             switch (type)
 219             {
 220                 case 1: return F_POLARIZATION;
 221                 case 2: return F_ANHARM_POL;
 222                 default: gmx_fatal(FARGS, "Invalid polarization type %d", type);
 223             }
 224         case Directive::d_thole_polarization: return F_THOLE_POL;
 225         case Directive::d_water_polarization: return F_WATER_POL;
 226         case Directive::d_angle_restraints: return F_ANGRES;
 227         case Directive::d_angle_restraints_z: return F_ANGRESZ;
 228         case Directive::d_distance_restraints: return F_DISRES;
 229         case Directive::d_orientation_restraints: return F_ORIRES;
 230         case Directive::d_dihedral_restraints: return F_DIHRES;
 231         default:
 232             gmx_fatal(FARGS, "invalid directive %s in ifunc_index (%s:%d)", dir2str(d), __FILE__, __LINE__);
 233     }
 234 }
 235
 236 const char* dir2str(Directive d)
 237 {
 238     int index = static_cast<int>(d);
 239     return directive_names[index];
 240 }
 241
 242 Directive str2dir(char* dstr)
 243 {
 244     char buf[STRLEN], *ptr;
 245
 246     /* Hack to be able to read old topologies */
 247     if (gmx_strncasecmp_min(dstr, "dummies", 7) == 0)
 248     {
 249         sprintf(buf, "virtual_sites%s", dstr + 7);
 250         ptr = buf;
 251     }
 252     else
 253     {
 254         ptr = dstr;
 255     }
 256
 257     for (auto d : gmx::EnumerationWrapper<Directive>())
 258     {
 259         if (gmx_strcasecmp_min(ptr, dir2str(static_cast<Directive>(d))) == 0)
 260         {
 261             return static_cast<Directive>(d);
 262         }
 263     }
 264
 265     return Directive::d_invalid;
 266 }
 267
 268 static gmx::EnumerationArray<Directive, Directive*> necessary = { { nullptr } };
 269
 270 static void set_nec(Directive** n, ...)
 271 /* Must always have at least one extra argument */
 272 {
 273     va_list   ap;
 274     int       ind = 0;
 275     Directive d;
 276
 277     va_start(ap, n);
 278     do
 279     {
 280         d = static_cast<Directive>(va_arg(ap, int));
 281         srenew(*n, ++ind);
 282         (*n)[ind - 1] = d;
 283     } while (d != Directive::d_none);
 284     va_end(ap);
 285 }
 286
 287 void DS_Init(DirStack** DS)
 288 {
 289     if (necessary[0] == nullptr)
 290     {
 291         set_nec(&(necessary[Directive::d_defaults]), Directive::d_none);
 292         set_nec(&(necessary[Directive::d_atomtypes]), Directive::d_defaults, Directive::d_none);
 293         set_nec(&(necessary[Directive::d_bondtypes]), Directive::d_atomtypes, Directive::d_none);
 294         set_nec(&(necessary[Directive::d_constrainttypes]), Directive::d_atomtypes, Directive::d_none);
 295         set_nec(&(necessary[Directive::d_pairtypes]), Directive::d_atomtypes, Directive::d_none);
 296         set_nec(&(necessary[Directive::d_angletypes]), Directive::d_atomtypes, Directive::d_none);
 297         set_nec(&(necessary[Directive::d_dihedraltypes]), Directive::d_atomtypes, Directive::d_none);
 298         set_nec(&(necessary[Directive::d_nonbond_params]), Directive::d_atomtypes, Directive::d_none);
 299         // Note that the content of the next two directives are
 300         // ignored, but if grompp reads them in old force field files,
 301         // it still needs to understand that they are in a valid place
 302         // in the .top structure. It doesn't have to require them to
 303         // be in the same place that was valid in old versions (ie. child
 304         // directive of [atomtypes]) but any relevant case will
 305         // satisfy that.
 306         set_nec(&(necessary[Directive::d_implicit_genborn_params]), Directive::d_atomtypes, Directive::d_none);
 307         set_nec(&(necessary[Directive::d_implicit_surface_params]), Directive::d_atomtypes, Directive::d_none);
 308         set_nec(&(necessary[Directive::d_cmaptypes]), Directive::d_atomtypes, Directive::d_none);
 309         set_nec(&(necessary[Directive::d_moleculetype]), Directive::d_atomtypes, Directive::d_none);
 310         set_nec(&(necessary[Directive::d_atoms]), Directive::d_moleculetype, Directive::d_none);
 311         set_nec(&(necessary[Directive::d_vsites2]), Directive::d_atoms, Directive::d_none);
 312         set_nec(&(necessary[Directive::d_vsites3]), Directive::d_atoms, Directive::d_none);
 313         set_nec(&(necessary[Directive::d_vsites4]), Directive::d_atoms, Directive::d_none);
 314         set_nec(&(necessary[Directive::d_vsitesn]), Directive::d_atoms, Directive::d_none);
 315         set_nec(&(necessary[Directive::d_bonds]), Directive::d_atoms, Directive::d_none);
 316         set_nec(&(necessary[Directive::d_exclusions]),
 317                 Directive::d_bonds,
 318                 Directive::d_constraints,
 319                 Directive::d_settles,
 320                 Directive::d_none);
 321         set_nec(&(necessary[Directive::d_pairs]), Directive::d_atoms, Directive::d_none);
 322         set_nec(&(necessary[Directive::d_pairs_nb]), Directive::d_atoms, Directive::d_none);
 323         set_nec(&(necessary[Directive::d_angles]), Directive::d_atoms, Directive::d_none);
 324         set_nec(&(necessary[Directive::d_polarization]), Directive::d_atoms, Directive::d_none);
 325         set_nec(&(necessary[Directive::d_water_polarization]), Directive::d_atoms, Directive::d_none);
 326         set_nec(&(necessary[Directive::d_thole_polarization]), Directive::d_atoms, Directive::d_none);
 327         set_nec(&(necessary[Directive::d_dihedrals]), Directive::d_atoms, Directive::d_none);
 328         set_nec(&(necessary[Directive::d_constraints]), Directive::d_atoms, Directive::d_none);
 329         set_nec(&(necessary[Directive::d_settles]), Directive::d_atoms, Directive::d_none);
 330         set_nec(&(necessary[Directive::d_system]), Directive::d_moleculetype, Directive::d_none);
 331         set_nec(&(necessary[Directive::d_molecules]), Directive::d_system, Directive::d_none);
 332         set_nec(&(necessary[Directive::d_position_restraints]), Directive::d_atoms, Directive::d_none);
 333         set_nec(&(necessary[Directive::d_angle_restraints]), Directive::d_atoms, Directive::d_none);
 334         set_nec(&(necessary[Directive::d_angle_restraints_z]), Directive::d_atoms, Directive::d_none);
 335         set_nec(&(necessary[Directive::d_distance_restraints]), Directive::d_atoms, Directive::d_none);
 336         set_nec(&(necessary[Directive::d_orientation_restraints]), Directive::d_atoms, Directive::d_none);
 337         set_nec(&(necessary[Directive::d_dihedral_restraints]), Directive::d_atoms, Directive::d_none);
 338         set_nec(&(necessary[Directive::d_cmap]), Directive::d_atoms, Directive::d_none);
 339         set_nec(&(necessary[Directive::d_intermolecular_interactions]),
 340                 Directive::d_molecules,
 341                 Directive::d_none);
 342     }
 343     *DS = nullptr;
 344 }
 345
 346 void DS_Done(DirStack** DS)
 347 {
 348     DirStack* D;
 349
 350     while (*DS != nullptr)
 351     {
 352         D   = *DS;
 353         *DS = (*DS)->prev;
 354         sfree(D);
 355     }
 356 }
 357
 358 void DS_Push(DirStack** DS, Directive d)
 359 {
 360     DirStack* D;
 361
 362     snew(D, 1);
 363     D->d    = d;
 364     D->prev = *DS;
 365     *DS     = D;
 366 }
 367
 368 int DS_Search(DirStack* DS, Directive d)
 369 {
 370     DirStack* D;
 371
 372     D = DS;
 373     while ((D != nullptr) && (D->d != d))
 374     {
 375         D = D->prev;
 376     }
 377
 378     return static_cast<int>(D != nullptr);
 379 }
 380
 381 int DS_Check_Order(DirStack* DS, Directive d)
 382 {
 383     Directive d0;
 384     int       i = 0;
 385
 386     /* Check if parameter definitions appear after a moleculetype directive */
 387     if (d < Directive::d_moleculetype && DS_Search(DS, Directive::d_moleculetype))
 388     {
 389         return FALSE;
 390     }
 391
 392     /* Check if all the necessary directives have appeared before directive d */
 393     if (necessary[d][0] == Directive::d_none)
 394     {
 395         return TRUE;
 396     }
 397     else
 398     {
 399         do
 400         {
 401             d0 = necessary[d][i++];
 402             if (DS_Search(DS, d0))
 403             {
 404                 return TRUE;
 405             }
 406         } while (d0 != Directive::d_none);
 407     }
 408     return FALSE;
 409 }