src/gromacs/topology/idef.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) 2013,2014,2015,2016,2018 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
  10  * top-level source directory and at http://www.gromacs.org.
  11  *
  12  * GROMACS is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU Lesser General Public License
  14  * as published by the Free Software Foundation; either version 2.1
  15  * of the License, or (at your option) any later version.
  16  *
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  20  * Lesser General Public License for more details.
  21  *
  22  * You should have received a copy of the GNU Lesser General Public
  23  * License along with GROMACS; if not, see
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  26  *
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  29  * control is crucial - bugs must be traceable. We will be happy to
  30  * consider code for inclusion in the official distribution, but
  31  * derived work must not be called official GROMACS. Details are found
  32  * in the README & COPYING files - if they are missing, get the
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  34  *
  35  * To help us fund GROMACS development, we humbly ask that you cite
  36  * the research papers on the package. Check out http://www.gromacs.org.
  37  */
  38 #include "gmxpre.h"
  39
  40 #include "idef.h"
  41
  42 #include <cstdio>
  43
  44 #include "gromacs/topology/forcefieldparameters.h"
  45 #include "gromacs/topology/ifunc.h"
  46 #include "gromacs/utility/fatalerror.h"
  47 #include "gromacs/utility/smalloc.h"
  48 #include "gromacs/utility/stringstream.h"
  49 #include "gromacs/utility/textwriter.h"
  50 #include "gromacs/utility/txtdump.h"
  51
  52 static void printHarmonicInteraction(gmx::TextWriter* writer,
  53                                      const t_iparams& iparams,
  54                                      const char*      r,
  55                                      const char*      kr)
  56 {
  57     writer->writeLineFormatted("%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e", r,
  58                                iparams.harmonic.rA, kr, iparams.harmonic.krA, r,
  59                                iparams.harmonic.rB, kr, iparams.harmonic.krB);
  60 }
  61
  62 void pr_iparams(FILE* fp, t_functype ftype, const t_iparams& iparams)
  63 {
  64     gmx::StringOutputStream stream;
  65     {
  66         gmx::TextWriter writer(&stream);
  67         printInteractionParameters(&writer, ftype, iparams);
  68     }
  69     fputs(stream.toString().c_str(), fp);
  70 }
  71
  72 void printInteractionParameters(gmx::TextWriter* writer, t_functype ftype, const t_iparams& iparams)
  73 {
  74     switch (ftype)
  75     {
  76         case F_ANGLES:
  77         case F_G96ANGLES: printHarmonicInteraction(writer, iparams, "th", "ct"); break;
  78         case F_CROSS_BOND_BONDS:
  79             writer->writeLineFormatted("r1e=%15.8e, r2e=%15.8e, krr=%15.8e", iparams.cross_bb.r1e,
  80                                        iparams.cross_bb.r2e, iparams.cross_bb.krr);
  81             break;
  82         case F_CROSS_BOND_ANGLES:
  83             writer->writeLineFormatted("r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e",
  84                                        iparams.cross_ba.r1e, iparams.cross_ba.r2e,
  85                                        iparams.cross_ba.r3e, iparams.cross_ba.krt);
  86             break;
  87         case F_LINEAR_ANGLES:
  88             writer->writeLineFormatted("klinA=%15.8e, aA=%15.8e, klinB=%15.8e, aB=%15.8e",
  89                                        iparams.linangle.klinA, iparams.linangle.aA,
  90                                        iparams.linangle.klinB, iparams.linangle.aB);
  91             break;
  92         case F_UREY_BRADLEY:
  93             writer->writeLineFormatted(
  94                     "thetaA=%15.8e, kthetaA=%15.8e, r13A=%15.8e, kUBA=%15.8e, thetaB=%15.8e, "
  95                     "kthetaB=%15.8e, r13B=%15.8e, kUBB=%15.8e",
  96                     iparams.u_b.thetaA, iparams.u_b.kthetaA, iparams.u_b.r13A, iparams.u_b.kUBA,
  97                     iparams.u_b.thetaB, iparams.u_b.kthetaB, iparams.u_b.r13B, iparams.u_b.kUBB);
  98             break;
  99         case F_QUARTIC_ANGLES:
 100             writer->writeStringFormatted("theta=%15.8e", iparams.qangle.theta);
 101             for (int i = 0; i < 5; i++)
 102             {
 103                 writer->writeStringFormatted(", c%c=%15.8e", '0' + i, iparams.qangle.c[i]);
 104             }
 105             writer->ensureLineBreak();
 106             break;
 107         case F_BHAM:
 108             writer->writeLineFormatted("a=%15.8e, b=%15.8e, c=%15.8e", iparams.bham.a,
 109                                        iparams.bham.b, iparams.bham.c);
 110             break;
 111         case F_BONDS:
 112         case F_G96BONDS:
 113         case F_HARMONIC: printHarmonicInteraction(writer, iparams, "b0", "cb"); break;
 114         case F_IDIHS: printHarmonicInteraction(writer, iparams, "xi", "cx"); break;
 115         case F_MORSE:
 116             writer->writeLineFormatted(
 117                     "b0A=%15.8e, cbA=%15.8e, betaA=%15.8e, b0B=%15.8e, cbB=%15.8e, betaB=%15.8e",
 118                     iparams.morse.b0A, iparams.morse.cbA, iparams.morse.betaA, iparams.morse.b0B,
 119                     iparams.morse.cbB, iparams.morse.betaB);
 120             break;
 121         case F_CUBICBONDS:
 122             writer->writeLineFormatted("b0=%15.8e, kb=%15.8e, kcub=%15.8e", iparams.cubic.b0,
 123                                        iparams.cubic.kb, iparams.cubic.kcub);
 124             break;
 125         case F_CONNBONDS: writer->ensureEmptyLine(); break;
 126         case F_FENEBONDS:
 127             writer->writeLineFormatted("bm=%15.8e, kb=%15.8e", iparams.fene.bm, iparams.fene.kb);
 128             break;
 129         case F_RESTRBONDS:
 130             writer->writeLineFormatted(
 131                     "lowA=%15.8e, up1A=%15.8e, up2A=%15.8e, kA=%15.8e, lowB=%15.8e, up1B=%15.8e, "
 132                     "up2B=%15.8e, kB=%15.8e,",
 133                     iparams.restraint.lowA, iparams.restraint.up1A, iparams.restraint.up2A,
 134                     iparams.restraint.kA, iparams.restraint.lowB, iparams.restraint.up1B,
 135                     iparams.restraint.up2B, iparams.restraint.kB);
 136             break;
 137         case F_TABBONDS:
 138         case F_TABBONDSNC:
 139         case F_TABANGLES:
 140         case F_TABDIHS:
 141             writer->writeLineFormatted("tab=%d, kA=%15.8e, kB=%15.8e", iparams.tab.table,
 142                                        iparams.tab.kA, iparams.tab.kB);
 143             break;
 144         case F_POLARIZATION:
 145             writer->writeLineFormatted("alpha=%15.8e", iparams.polarize.alpha);
 146             break;
 147         case F_ANHARM_POL:
 148             writer->writeLineFormatted("alpha=%15.8e drcut=%15.8e khyp=%15.8e",
 149                                        iparams.anharm_polarize.alpha, iparams.anharm_polarize.drcut,
 150                                        iparams.anharm_polarize.khyp);
 151             break;
 152         case F_THOLE_POL:
 153             writer->writeLineFormatted("a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e",
 154                                        iparams.thole.a, iparams.thole.alpha1, iparams.thole.alpha2,
 155                                        iparams.thole.rfac);
 156             break;
 157         case F_WATER_POL:
 158             writer->writeLineFormatted(
 159                     "al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f",
 160                     iparams.wpol.al_x, iparams.wpol.al_y, iparams.wpol.al_z, iparams.wpol.rOH,
 161                     iparams.wpol.rHH, iparams.wpol.rOD);
 162             break;
 163         case F_LJ:
 164             writer->writeLineFormatted("c6=%15.8e, c12=%15.8e", iparams.lj.c6, iparams.lj.c12);
 165             break;
 166         case F_LJ14:
 167             writer->writeLineFormatted("c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e",
 168                                        iparams.lj14.c6A, iparams.lj14.c12A, iparams.lj14.c6B,
 169                                        iparams.lj14.c12B);
 170             break;
 171         case F_LJC14_Q:
 172             writer->writeLineFormatted("fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e",
 173                                        iparams.ljc14.fqq, iparams.ljc14.qi, iparams.ljc14.qj,
 174                                        iparams.ljc14.c6, iparams.ljc14.c12);
 175             break;
 176         case F_LJC_PAIRS_NB:
 177             writer->writeLineFormatted("qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e", iparams.ljcnb.qi,
 178                                        iparams.ljcnb.qj, iparams.ljcnb.c6, iparams.ljcnb.c12);
 179             break;
 180         case F_PDIHS:
 181         case F_PIDIHS:
 182         case F_ANGRES:
 183         case F_ANGRESZ:
 184             writer->writeLineFormatted("phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d",
 185                                        iparams.pdihs.phiA, iparams.pdihs.cpA, iparams.pdihs.phiB,
 186                                        iparams.pdihs.cpB, iparams.pdihs.mult);
 187             break;
 188         case F_DISRES:
 189             writer->writeLineFormatted(
 190                     "label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)",
 191                     iparams.disres.label, iparams.disres.type, iparams.disres.low,
 192                     iparams.disres.up1, iparams.disres.up2, iparams.disres.kfac);
 193             break;
 194         case F_ORIRES:
 195             writer->writeLineFormatted(
 196                     "ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)",
 197                     iparams.orires.ex, iparams.orires.label, iparams.orires.power, iparams.orires.c,
 198                     iparams.orires.obs, iparams.orires.kfac);
 199             break;
 200         case F_DIHRES:
 201             writer->writeLineFormatted(
 202                     "phiA=%15.8e, dphiA=%15.8e, kfacA=%15.8e, phiB=%15.8e, dphiB=%15.8e, "
 203                     "kfacB=%15.8e",
 204                     iparams.dihres.phiA, iparams.dihres.dphiA, iparams.dihres.kfacA,
 205                     iparams.dihres.phiB, iparams.dihres.dphiB, iparams.dihres.kfacB);
 206             break;
 207         case F_POSRES:
 208             writer->writeLineFormatted(
 209                     "pos0A=(%15.8e,%15.8e,%15.8e), fcA=(%15.8e,%15.8e,%15.8e), "
 210                     "pos0B=(%15.8e,%15.8e,%15.8e), fcB=(%15.8e,%15.8e,%15.8e)",
 211                     iparams.posres.pos0A[XX], iparams.posres.pos0A[YY], iparams.posres.pos0A[ZZ],
 212                     iparams.posres.fcA[XX], iparams.posres.fcA[YY], iparams.posres.fcA[ZZ],
 213                     iparams.posres.pos0B[XX], iparams.posres.pos0B[YY], iparams.posres.pos0B[ZZ],
 214                     iparams.posres.fcB[XX], iparams.posres.fcB[YY], iparams.posres.fcB[ZZ]);
 215             break;
 216         case F_FBPOSRES:
 217             writer->writeLineFormatted(
 218                     "pos0=(%15.8e,%15.8e,%15.8e), geometry=%d, r=%15.8e, k=%15.8e",
 219                     iparams.fbposres.pos0[XX], iparams.fbposres.pos0[YY], iparams.fbposres.pos0[ZZ],
 220                     iparams.fbposres.geom, iparams.fbposres.r, iparams.fbposres.k);
 221             break;
 222         case F_RBDIHS:
 223             for (int i = 0; i < NR_RBDIHS; i++)
 224             {
 225                 writer->writeStringFormatted("%srbcA[%d]=%15.8e", i == 0 ? "" : ", ", i,
 226                                              iparams.rbdihs.rbcA[i]);
 227             }
 228             writer->ensureLineBreak();
 229             for (int i = 0; i < NR_RBDIHS; i++)
 230             {
 231                 writer->writeStringFormatted("%srbcB[%d]=%15.8e", i == 0 ? "" : ", ", i,
 232                                              iparams.rbdihs.rbcB[i]);
 233             }
 234             writer->ensureLineBreak();
 235             break;
 236         case F_FOURDIHS:
 237         {
 238             /* Use the OPLS -> Ryckaert-Bellemans formula backwards to get
 239              * the OPLS potential constants back.
 240              */
 241             const real* rbcA = iparams.rbdihs.rbcA;
 242             const real* rbcB = iparams.rbdihs.rbcB;
 243             real        VA[4], VB[4];
 244
 245             VA[3] = -0.25 * rbcA[4];
 246             VA[2] = -0.5 * rbcA[3];
 247             VA[1] = 4.0 * VA[3] - rbcA[2];
 248             VA[0] = 3.0 * VA[2] - 2.0 * rbcA[1];
 249
 250             VB[3] = -0.25 * rbcB[4];
 251             VB[2] = -0.5 * rbcB[3];
 252             VB[1] = 4.0 * VB[3] - rbcB[2];
 253             VB[0] = 3.0 * VB[2] - 2.0 * rbcB[1];
 254
 255             for (int i = 0; i < NR_FOURDIHS; i++)
 256             {
 257                 writer->writeStringFormatted("%sFourA[%d]=%15.8e", i == 0 ? "" : ", ", i, VA[i]);
 258             }
 259             writer->ensureLineBreak();
 260             for (int i = 0; i < NR_FOURDIHS; i++)
 261             {
 262                 writer->writeStringFormatted("%sFourB[%d]=%15.8e", i == 0 ? "" : ", ", i, VB[i]);
 263             }
 264             writer->ensureLineBreak();
 265             break;
 266         }
 267
 268         case F_CONSTR:
 269         case F_CONSTRNC:
 270             writer->writeLineFormatted("dA=%15.8e, dB=%15.8e", iparams.constr.dA, iparams.constr.dB);
 271             break;
 272         case F_SETTLE:
 273             writer->writeLineFormatted("doh=%15.8e, dhh=%15.8e", iparams.settle.doh, iparams.settle.dhh);
 274             break;
 275         case F_VSITE1: writer->ensureEmptyLine(); break;
 276         case F_VSITE2: writer->writeLineFormatted("a=%15.8e", iparams.vsite.a); break;
 277         case F_VSITE3:
 278         case F_VSITE3FD:
 279         case F_VSITE3FAD:
 280             writer->writeLineFormatted("a=%15.8e, b=%15.8e", iparams.vsite.a, iparams.vsite.b);
 281             break;
 282         case F_VSITE3OUT:
 283         case F_VSITE4FD:
 284         case F_VSITE4FDN:
 285             writer->writeLineFormatted("a=%15.8e, b=%15.8e, c=%15.8e", iparams.vsite.a,
 286                                        iparams.vsite.b, iparams.vsite.c);
 287             break;
 288         case F_VSITEN:
 289             writer->writeLineFormatted("n=%2d, a=%15.8e", iparams.vsiten.n, iparams.vsiten.a);
 290             break;
 291         case F_GB12_NOLONGERUSED:
 292         case F_GB13_NOLONGERUSED:
 293         case F_GB14_NOLONGERUSED:
 294             // These could only be generated by grompp, not written in
 295             // a .top file. Now that implicit solvent is not
 296             // supported, they can't be generated, and the values are
 297             // ignored if read from an old .tpr file. So there is
 298             // nothing to print.
 299             break;
 300         case F_CMAP:
 301             writer->writeLineFormatted("cmapA=%1d, cmapB=%1d", iparams.cmap.cmapA, iparams.cmap.cmapB);
 302             break;
 303         case F_RESTRANGLES: printHarmonicInteraction(writer, iparams, "ktheta", "costheta0"); break;
 304         case F_RESTRDIHS:
 305             writer->writeLineFormatted("phiA=%15.8e, cpA=%15.8e", iparams.pdihs.phiA, iparams.pdihs.cpA);
 306             break;
 307         case F_CBTDIHS:
 308             writer->writeLineFormatted("kphi=%15.8e", iparams.cbtdihs.cbtcA[0]);
 309             for (int i = 1; i < NR_CBTDIHS; i++)
 310             {
 311                 writer->writeStringFormatted(", cbtcA[%d]=%15.8e", i - 1, iparams.cbtdihs.cbtcA[i]);
 312             }
 313             writer->ensureLineBreak();
 314             break;
 315         default:
 316             gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d", ftype,
 317                       interaction_function[ftype].name, __FILE__, __LINE__);
 318     }
 319 }
 320
 321 template<typename T>
 322 static void printIlist(FILE*             fp,
 323                        int               indent,
 324                        const char*       title,
 325                        const t_functype* functype,
 326                        const T&          ilist,
 327                        gmx_bool          bShowNumbers,
 328                        gmx_bool          bShowParameters,
 329                        const t_iparams*  iparams)
 330 {
 331     int i, j, k, type, ftype;
 332
 333     indent = pr_title(fp, indent, title);
 334     pr_indent(fp, indent);
 335     fprintf(fp, "nr: %d\n", ilist.size());
 336     if (!ilist.empty())
 337     {
 338         pr_indent(fp, indent);
 339         fprintf(fp, "iatoms:\n");
 340         for (i = j = 0; i < ilist.size();)
 341         {
 342             pr_indent(fp, indent + INDENT);
 343             type  = ilist.iatoms[i];
 344             ftype = functype[type];
 345             if (bShowNumbers)
 346             {
 347                 fprintf(fp, "%d type=%d ", j, type);
 348             }
 349             j++;
 350             printf("(%s)", interaction_function[ftype].name);
 351             for (k = 0; k < interaction_function[ftype].nratoms; k++)
 352             {
 353                 fprintf(fp, " %3d", ilist.iatoms[i + 1 + k]);
 354             }
 355             if (bShowParameters)
 356             {
 357                 fprintf(fp, "  ");
 358                 pr_iparams(fp, ftype, iparams[type]);
 359             }
 360             fprintf(fp, "\n");
 361             i += 1 + interaction_function[ftype].nratoms;
 362         }
 363     }
 364 }
 365
 366 void pr_ilist(FILE*                  fp,
 367               int                    indent,
 368               const char*            title,
 369               const t_functype*      functype,
 370               const InteractionList& ilist,
 371               gmx_bool               bShowNumbers,
 372               gmx_bool               bShowParameters,
 373               const t_iparams*       iparams)
 374 {
 375     printIlist(fp, indent, title, functype, ilist, bShowNumbers, bShowParameters, iparams);
 376 }
 377
 378 void pr_idef(FILE* fp, int indent, const char* title, const t_idef* idef, gmx_bool bShowNumbers, gmx_bool bShowParameters)
 379 {
 380     int i, j;
 381
 382     if (available(fp, idef, indent, title))
 383     {
 384         indent = pr_title(fp, indent, title);
 385         pr_indent(fp, indent);
 386         fprintf(fp, "atnr=%d\n", idef->atnr);
 387         pr_indent(fp, indent);
 388         fprintf(fp, "ntypes=%d\n", idef->ntypes);
 389         for (i = 0; i < idef->ntypes; i++)
 390         {
 391             pr_indent(fp, indent + INDENT);
 392             fprintf(fp, "functype[%d]=%s, ", bShowNumbers ? i : -1,
 393                     interaction_function[idef->functype[i]].name);
 394             pr_iparams(fp, idef->functype[i], idef->iparams[i]);
 395         }
 396         pr_real(fp, indent, "fudgeQQ", idef->fudgeQQ);
 397
 398         for (j = 0; (j < F_NRE); j++)
 399         {
 400             printIlist(fp, indent, interaction_function[j].longname, idef->functype, idef->il[j],
 401                        bShowNumbers, bShowParameters, idef->iparams);
 402         }
 403     }
 404 }
 405
 406 void init_idef(t_idef* idef)
 407 {
 408     idef->ntypes           = 0;
 409     idef->atnr             = 0;
 410     idef->functype         = nullptr;
 411     idef->iparams          = nullptr;
 412     idef->fudgeQQ          = 0.0;
 413     idef->iparams_posres   = nullptr;
 414     idef->iparams_fbposres = nullptr;
 415     for (int f = 0; f < F_NRE; ++f)
 416     {
 417         idef->il[f].iatoms = nullptr;
 418         idef->il[f].nalloc = 0;
 419         idef->il[f].nr     = 0;
 420     }
 421 }
 422
 423 InteractionDefinitions::InteractionDefinitions(const gmx_ffparams_t& ffparams) :
 424     iparams(ffparams.iparams),
 425     functype(ffparams.functype),
 426     cmap_grid(ffparams.cmap_grid)
 427 {
 428 }
 429
 430 void InteractionDefinitions::clear()
 431 {
 432     /* Clear the counts */
 433     for (auto& ilist : il)
 434     {
 435         ilist.clear();
 436     }
 437     iparams_posres.clear();
 438     iparams_fbposres.clear();
 439 }
 440
 441 void done_idef(t_idef* idef)
 442 {
 443     sfree(idef->functype);
 444     sfree(idef->iparams);
 445     sfree(idef->iparams_posres);
 446     sfree(idef->iparams_fbposres);
 447     for (int f = 0; f < F_NRE; ++f)
 448     {
 449         sfree(idef->il[f].iatoms);
 450     }
 451
 452     init_idef(idef);
 453 }