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
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  11  *
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  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.
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  31  * derived work must not be called official GROMACS. Details are found
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  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",
  58                                r,
  59                                iparams.harmonic.rA,
  60                                kr,
  61                                iparams.harmonic.krA,
  62                                r,
  63                                iparams.harmonic.rB,
  64                                kr,
  65                                iparams.harmonic.krB);
  66 }
  67
  68 void pr_iparams(FILE* fp, t_functype ftype, const t_iparams& iparams)
  69 {
  70     gmx::StringOutputStream stream;
  71     {
  72         gmx::TextWriter writer(&stream);
  73         printInteractionParameters(&writer, ftype, iparams);
  74     }
  75     fputs(stream.toString().c_str(), fp);
  76 }
  77
  78 void printInteractionParameters(gmx::TextWriter* writer, t_functype ftype, const t_iparams& iparams)
  79 {
  80     switch (ftype)
  81     {
  82         case F_ANGLES:
  83         case F_G96ANGLES: printHarmonicInteraction(writer, iparams, "th", "ct"); break;
  84         case F_CROSS_BOND_BONDS:
  85             writer->writeLineFormatted("r1e=%15.8e, r2e=%15.8e, krr=%15.8e",
  86                                        iparams.cross_bb.r1e,
  87                                        iparams.cross_bb.r2e,
  88                                        iparams.cross_bb.krr);
  89             break;
  90         case F_CROSS_BOND_ANGLES:
  91             writer->writeLineFormatted("r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e",
  92                                        iparams.cross_ba.r1e,
  93                                        iparams.cross_ba.r2e,
  94                                        iparams.cross_ba.r3e,
  95                                        iparams.cross_ba.krt);
  96             break;
  97         case F_LINEAR_ANGLES:
  98             writer->writeLineFormatted("klinA=%15.8e, aA=%15.8e, klinB=%15.8e, aB=%15.8e",
  99                                        iparams.linangle.klinA,
 100                                        iparams.linangle.aA,
 101                                        iparams.linangle.klinB,
 102                                        iparams.linangle.aB);
 103             break;
 104         case F_UREY_BRADLEY:
 105             writer->writeLineFormatted(
 106                     "thetaA=%15.8e, kthetaA=%15.8e, r13A=%15.8e, kUBA=%15.8e, thetaB=%15.8e, "
 107                     "kthetaB=%15.8e, r13B=%15.8e, kUBB=%15.8e",
 108                     iparams.u_b.thetaA,
 109                     iparams.u_b.kthetaA,
 110                     iparams.u_b.r13A,
 111                     iparams.u_b.kUBA,
 112                     iparams.u_b.thetaB,
 113                     iparams.u_b.kthetaB,
 114                     iparams.u_b.r13B,
 115                     iparams.u_b.kUBB);
 116             break;
 117         case F_QUARTIC_ANGLES:
 118             writer->writeStringFormatted("theta=%15.8e", iparams.qangle.theta);
 119             for (int i = 0; i < 5; i++)
 120             {
 121                 writer->writeStringFormatted(", c%c=%15.8e", '0' + i, iparams.qangle.c[i]);
 122             }
 123             writer->ensureLineBreak();
 124             break;
 125         case F_BHAM:
 126             writer->writeLineFormatted(
 127                     "a=%15.8e, b=%15.8e, c=%15.8e", iparams.bham.a, iparams.bham.b, iparams.bham.c);
 128             break;
 129         case F_BONDS:
 130         case F_G96BONDS:
 131         case F_HARMONIC: printHarmonicInteraction(writer, iparams, "b0", "cb"); break;
 132         case F_IDIHS: printHarmonicInteraction(writer, iparams, "xi", "cx"); break;
 133         case F_MORSE:
 134             writer->writeLineFormatted(
 135                     "b0A=%15.8e, cbA=%15.8e, betaA=%15.8e, b0B=%15.8e, cbB=%15.8e, betaB=%15.8e",
 136                     iparams.morse.b0A,
 137                     iparams.morse.cbA,
 138                     iparams.morse.betaA,
 139                     iparams.morse.b0B,
 140                     iparams.morse.cbB,
 141                     iparams.morse.betaB);
 142             break;
 143         case F_CUBICBONDS:
 144             writer->writeLineFormatted("b0=%15.8e, kb=%15.8e, kcub=%15.8e",
 145                                        iparams.cubic.b0,
 146                                        iparams.cubic.kb,
 147                                        iparams.cubic.kcub);
 148             break;
 149         case F_CONNBONDS: writer->ensureEmptyLine(); break;
 150         case F_FENEBONDS:
 151             writer->writeLineFormatted("bm=%15.8e, kb=%15.8e", iparams.fene.bm, iparams.fene.kb);
 152             break;
 153         case F_RESTRBONDS:
 154             writer->writeLineFormatted(
 155                     "lowA=%15.8e, up1A=%15.8e, up2A=%15.8e, kA=%15.8e, lowB=%15.8e, up1B=%15.8e, "
 156                     "up2B=%15.8e, kB=%15.8e,",
 157                     iparams.restraint.lowA,
 158                     iparams.restraint.up1A,
 159                     iparams.restraint.up2A,
 160                     iparams.restraint.kA,
 161                     iparams.restraint.lowB,
 162                     iparams.restraint.up1B,
 163                     iparams.restraint.up2B,
 164                     iparams.restraint.kB);
 165             break;
 166         case F_TABBONDS:
 167         case F_TABBONDSNC:
 168         case F_TABANGLES:
 169         case F_TABDIHS:
 170             writer->writeLineFormatted(
 171                     "tab=%d, kA=%15.8e, kB=%15.8e", iparams.tab.table, iparams.tab.kA, iparams.tab.kB);
 172             break;
 173         case F_POLARIZATION:
 174             writer->writeLineFormatted("alpha=%15.8e", iparams.polarize.alpha);
 175             break;
 176         case F_ANHARM_POL:
 177             writer->writeLineFormatted("alpha=%15.8e drcut=%15.8e khyp=%15.8e",
 178                                        iparams.anharm_polarize.alpha,
 179                                        iparams.anharm_polarize.drcut,
 180                                        iparams.anharm_polarize.khyp);
 181             break;
 182         case F_THOLE_POL:
 183             writer->writeLineFormatted("a=%15.8e, alpha1=%15.8e, alpha2=%15.8e",
 184                                        iparams.thole.a,
 185                                        iparams.thole.alpha1,
 186                                        iparams.thole.alpha2);
 187             break;
 188         case F_WATER_POL:
 189             writer->writeLineFormatted(
 190                     "al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f",
 191                     iparams.wpol.al_x,
 192                     iparams.wpol.al_y,
 193                     iparams.wpol.al_z,
 194                     iparams.wpol.rOH,
 195                     iparams.wpol.rHH,
 196                     iparams.wpol.rOD);
 197             break;
 198         case F_LJ:
 199             writer->writeLineFormatted("c6=%15.8e, c12=%15.8e", iparams.lj.c6, iparams.lj.c12);
 200             break;
 201         case F_LJ14:
 202             writer->writeLineFormatted("c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e",
 203                                        iparams.lj14.c6A,
 204                                        iparams.lj14.c12A,
 205                                        iparams.lj14.c6B,
 206                                        iparams.lj14.c12B);
 207             break;
 208         case F_LJC14_Q:
 209             writer->writeLineFormatted("fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e",
 210                                        iparams.ljc14.fqq,
 211                                        iparams.ljc14.qi,
 212                                        iparams.ljc14.qj,
 213                                        iparams.ljc14.c6,
 214                                        iparams.ljc14.c12);
 215             break;
 216         case F_LJC_PAIRS_NB:
 217             writer->writeLineFormatted("qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e",
 218                                        iparams.ljcnb.qi,
 219                                        iparams.ljcnb.qj,
 220                                        iparams.ljcnb.c6,
 221                                        iparams.ljcnb.c12);
 222             break;
 223         case F_PDIHS:
 224         case F_PIDIHS:
 225         case F_ANGRES:
 226         case F_ANGRESZ:
 227             writer->writeLineFormatted("phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d",
 228                                        iparams.pdihs.phiA,
 229                                        iparams.pdihs.cpA,
 230                                        iparams.pdihs.phiB,
 231                                        iparams.pdihs.cpB,
 232                                        iparams.pdihs.mult);
 233             break;
 234         case F_DISRES:
 235             writer->writeLineFormatted(
 236                     "label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)",
 237                     iparams.disres.label,
 238                     iparams.disres.type,
 239                     iparams.disres.low,
 240                     iparams.disres.up1,
 241                     iparams.disres.up2,
 242                     iparams.disres.kfac);
 243             break;
 244         case F_ORIRES:
 245             writer->writeLineFormatted(
 246                     "ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)",
 247                     iparams.orires.ex,
 248                     iparams.orires.label,
 249                     iparams.orires.power,
 250                     iparams.orires.c,
 251                     iparams.orires.obs,
 252                     iparams.orires.kfac);
 253             break;
 254         case F_DIHRES:
 255             writer->writeLineFormatted(
 256                     "phiA=%15.8e, dphiA=%15.8e, kfacA=%15.8e, phiB=%15.8e, dphiB=%15.8e, "
 257                     "kfacB=%15.8e",
 258                     iparams.dihres.phiA,
 259                     iparams.dihres.dphiA,
 260                     iparams.dihres.kfacA,
 261                     iparams.dihres.phiB,
 262                     iparams.dihres.dphiB,
 263                     iparams.dihres.kfacB);
 264             break;
 265         case F_POSRES:
 266             writer->writeLineFormatted(
 267                     "pos0A=(%15.8e,%15.8e,%15.8e), fcA=(%15.8e,%15.8e,%15.8e), "
 268                     "pos0B=(%15.8e,%15.8e,%15.8e), fcB=(%15.8e,%15.8e,%15.8e)",
 269                     iparams.posres.pos0A[XX],
 270                     iparams.posres.pos0A[YY],
 271                     iparams.posres.pos0A[ZZ],
 272                     iparams.posres.fcA[XX],
 273                     iparams.posres.fcA[YY],
 274                     iparams.posres.fcA[ZZ],
 275                     iparams.posres.pos0B[XX],
 276                     iparams.posres.pos0B[YY],
 277                     iparams.posres.pos0B[ZZ],
 278                     iparams.posres.fcB[XX],
 279                     iparams.posres.fcB[YY],
 280                     iparams.posres.fcB[ZZ]);
 281             break;
 282         case F_FBPOSRES:
 283             writer->writeLineFormatted(
 284                     "pos0=(%15.8e,%15.8e,%15.8e), geometry=%d, r=%15.8e, k=%15.8e",
 285                     iparams.fbposres.pos0[XX],
 286                     iparams.fbposres.pos0[YY],
 287                     iparams.fbposres.pos0[ZZ],
 288                     iparams.fbposres.geom,
 289                     iparams.fbposres.r,
 290                     iparams.fbposres.k);
 291             break;
 292         case F_RBDIHS:
 293             for (int i = 0; i < NR_RBDIHS; i++)
 294             {
 295                 writer->writeStringFormatted(
 296                         "%srbcA[%d]=%15.8e", i == 0 ? "" : ", ", i, iparams.rbdihs.rbcA[i]);
 297             }
 298             writer->ensureLineBreak();
 299             for (int i = 0; i < NR_RBDIHS; i++)
 300             {
 301                 writer->writeStringFormatted(
 302                         "%srbcB[%d]=%15.8e", i == 0 ? "" : ", ", i, iparams.rbdihs.rbcB[i]);
 303             }
 304             writer->ensureLineBreak();
 305             break;
 306         case F_FOURDIHS:
 307         {
 308             /* Use the OPLS -> Ryckaert-Bellemans formula backwards to get
 309              * the OPLS potential constants back.
 310              */
 311             const real* rbcA = iparams.rbdihs.rbcA;
 312             const real* rbcB = iparams.rbdihs.rbcB;
 313             real        VA[4], VB[4];
 314
 315             VA[3] = -0.25 * rbcA[4];
 316             VA[2] = -0.5 * rbcA[3];
 317             VA[1] = 4.0 * VA[3] - rbcA[2];
 318             VA[0] = 3.0 * VA[2] - 2.0 * rbcA[1];
 319
 320             VB[3] = -0.25 * rbcB[4];
 321             VB[2] = -0.5 * rbcB[3];
 322             VB[1] = 4.0 * VB[3] - rbcB[2];
 323             VB[0] = 3.0 * VB[2] - 2.0 * rbcB[1];
 324
 325             for (int i = 0; i < NR_FOURDIHS; i++)
 326             {
 327                 writer->writeStringFormatted("%sFourA[%d]=%15.8e", i == 0 ? "" : ", ", i, VA[i]);
 328             }
 329             writer->ensureLineBreak();
 330             for (int i = 0; i < NR_FOURDIHS; i++)
 331             {
 332                 writer->writeStringFormatted("%sFourB[%d]=%15.8e", i == 0 ? "" : ", ", i, VB[i]);
 333             }
 334             writer->ensureLineBreak();
 335             break;
 336         }
 337
 338         case F_CONSTR:
 339         case F_CONSTRNC:
 340             writer->writeLineFormatted("dA=%15.8e, dB=%15.8e", iparams.constr.dA, iparams.constr.dB);
 341             break;
 342         case F_SETTLE:
 343             writer->writeLineFormatted("doh=%15.8e, dhh=%15.8e", iparams.settle.doh, iparams.settle.dhh);
 344             break;
 345         case F_VSITE1: writer->ensureEmptyLine(); break;
 346         case F_VSITE2: writer->writeLineFormatted("a=%15.8e", iparams.vsite.a); break;
 347         case F_VSITE3:
 348         case F_VSITE3FD:
 349         case F_VSITE3FAD:
 350             writer->writeLineFormatted("a=%15.8e, b=%15.8e", iparams.vsite.a, iparams.vsite.b);
 351             break;
 352         case F_VSITE3OUT:
 353         case F_VSITE4FD:
 354         case F_VSITE4FDN:
 355             writer->writeLineFormatted(
 356                     "a=%15.8e, b=%15.8e, c=%15.8e", iparams.vsite.a, iparams.vsite.b, iparams.vsite.c);
 357             break;
 358         case F_VSITEN:
 359             writer->writeLineFormatted("n=%2d, a=%15.8e", iparams.vsiten.n, iparams.vsiten.a);
 360             break;
 361         case F_GB12_NOLONGERUSED:
 362         case F_GB13_NOLONGERUSED:
 363         case F_GB14_NOLONGERUSED:
 364             // These could only be generated by grompp, not written in
 365             // a .top file. Now that implicit solvent is not
 366             // supported, they can't be generated, and the values are
 367             // ignored if read from an old .tpr file. So there is
 368             // nothing to print.
 369             break;
 370         case F_CMAP:
 371             writer->writeLineFormatted("cmapA=%1d, cmapB=%1d", iparams.cmap.cmapA, iparams.cmap.cmapB);
 372             break;
 373         case F_RESTRANGLES: printHarmonicInteraction(writer, iparams, "ktheta", "costheta0"); break;
 374         case F_RESTRDIHS:
 375             writer->writeLineFormatted("phiA=%15.8e, cpA=%15.8e", iparams.pdihs.phiA, iparams.pdihs.cpA);
 376             break;
 377         case F_CBTDIHS:
 378             writer->writeLineFormatted("kphi=%15.8e", iparams.cbtdihs.cbtcA[0]);
 379             for (int i = 1; i < NR_CBTDIHS; i++)
 380             {
 381                 writer->writeStringFormatted(", cbtcA[%d]=%15.8e", i - 1, iparams.cbtdihs.cbtcA[i]);
 382             }
 383             writer->ensureLineBreak();
 384             break;
 385         default:
 386             gmx_fatal(FARGS,
 387                       "unknown function type %d (%s) in %s line %d",
 388                       ftype,
 389                       interaction_function[ftype].name,
 390                       __FILE__,
 391                       __LINE__);
 392     }
 393 }
 394
 395 template<typename T>
 396 static void printIlist(FILE*             fp,
 397                        int               indent,
 398                        const char*       title,
 399                        const t_functype* functype,
 400                        const T&          ilist,
 401                        gmx_bool          bShowNumbers,
 402                        gmx_bool          bShowParameters,
 403                        const t_iparams*  iparams)
 404 {
 405     indent = pr_title(fp, indent, title);
 406     pr_indent(fp, indent);
 407     fprintf(fp, "nr: %d\n", ilist.size());
 408     if (!ilist.empty())
 409     {
 410         pr_indent(fp, indent);
 411         fprintf(fp, "iatoms:\n");
 412         int j = 0;
 413         for (int i = 0; i < ilist.size();)
 414         {
 415             pr_indent(fp, indent + INDENT);
 416             const int type  = ilist.iatoms[i];
 417             const int ftype = functype[type];
 418             if (bShowNumbers)
 419             {
 420                 fprintf(fp, "%d type=%d ", j, type);
 421             }
 422             j++;
 423             printf("(%s)", interaction_function[ftype].name);
 424             for (int k = 0; k < interaction_function[ftype].nratoms; k++)
 425             {
 426                 fprintf(fp, " %3d", ilist.iatoms[i + 1 + k]);
 427             }
 428             if (bShowParameters)
 429             {
 430                 fprintf(fp, "  ");
 431                 pr_iparams(fp, ftype, iparams[type]);
 432             }
 433             fprintf(fp, "\n");
 434             i += 1 + interaction_function[ftype].nratoms;
 435         }
 436     }
 437 }
 438
 439 void pr_ilist(FILE*                  fp,
 440               int                    indent,
 441               const char*            title,
 442               const t_functype*      functype,
 443               const InteractionList& ilist,
 444               gmx_bool               bShowNumbers,
 445               gmx_bool               bShowParameters,
 446               const t_iparams*       iparams)
 447 {
 448     printIlist(fp, indent, title, functype, ilist, bShowNumbers, bShowParameters, iparams);
 449 }
 450
 451 void pr_idef(FILE* fp, int indent, const char* title, const t_idef* idef, gmx_bool bShowNumbers, gmx_bool bShowParameters)
 452 {
 453     if (available(fp, idef, indent, title))
 454     {
 455         indent = pr_title(fp, indent, title);
 456         pr_indent(fp, indent);
 457         fprintf(fp, "atnr=%d\n", idef->atnr);
 458         pr_indent(fp, indent);
 459         fprintf(fp, "ntypes=%d\n", idef->ntypes);
 460         for (int i = 0; i < idef->ntypes; i++)
 461         {
 462             pr_indent(fp, indent + INDENT);
 463             fprintf(fp,
 464                     "functype[%d]=%s, ",
 465                     bShowNumbers ? i : -1,
 466                     interaction_function[idef->functype[i]].name);
 467             pr_iparams(fp, idef->functype[i], idef->iparams[i]);
 468         }
 469         pr_real(fp, indent, "fudgeQQ", idef->fudgeQQ);
 470
 471         for (int j = 0; (j < F_NRE); j++)
 472         {
 473             printIlist(fp,
 474                        indent,
 475                        interaction_function[j].longname,
 476                        idef->functype,
 477                        idef->il[j],
 478                        bShowNumbers,
 479                        bShowParameters,
 480                        idef->iparams);
 481         }
 482     }
 483 }
 484
 485 void init_idef(t_idef* idef)
 486 {
 487     idef->ntypes           = 0;
 488     idef->atnr             = 0;
 489     idef->functype         = nullptr;
 490     idef->iparams          = nullptr;
 491     idef->fudgeQQ          = 0.0;
 492     idef->iparams_posres   = nullptr;
 493     idef->iparams_fbposres = nullptr;
 494     for (int f = 0; f < F_NRE; ++f)
 495     {
 496         idef->il[f].iatoms = nullptr;
 497         idef->il[f].nalloc = 0;
 498         idef->il[f].nr     = 0;
 499     }
 500 }
 501
 502 InteractionDefinitions::InteractionDefinitions(const gmx_ffparams_t& ffparams) :
 503     iparams(ffparams.iparams), functype(ffparams.functype), cmap_grid(ffparams.cmap_grid)
 504 {
 505 }
 506
 507 void InteractionDefinitions::clear()
 508 {
 509     /* Clear the counts */
 510     for (auto& ilist : il)
 511     {
 512         ilist.clear();
 513     }
 514     iparams_posres.clear();
 515     iparams_fbposres.clear();
 516 }
 517
 518 void done_idef(t_idef* idef)
 519 {
 520     sfree(idef->functype);
 521     sfree(idef->iparams);
 522     sfree(idef->iparams_posres);
 523     sfree(idef->iparams_fbposres);
 524     for (int f = 0; f < F_NRE; ++f)
 525     {
 526         sfree(idef->il[f].iatoms);
 527     }
 528
 529     init_idef(idef);
 530 }