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, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 #include "gmxpre.h"
  38
  39 #include "idef.h"
  40
  41 #include <cstdio>
  42
  43 #include "gromacs/topology/ifunc.h"
  44 #include "gromacs/utility/fatalerror.h"
  45 #include "gromacs/utility/txtdump.h"
  46
  47 static void pr_harm(FILE *fp, const t_iparams *iparams, const char *r, const char *kr)
  48 {
  49     fprintf(fp, "%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e\n",
  50             r, iparams->harmonic.rA, kr, iparams->harmonic.krA,
  51             r, iparams->harmonic.rB, kr, iparams->harmonic.krB);
  52 }
  53
  54 void pr_iparams(FILE *fp, t_functype ftype, const t_iparams *iparams)
  55 {
  56     switch (ftype)
  57     {
  58         case F_ANGLES:
  59         case F_G96ANGLES:
  60             pr_harm(fp, iparams, "th", "ct");
  61             break;
  62         case F_CROSS_BOND_BONDS:
  63             fprintf(fp, "r1e=%15.8e, r2e=%15.8e, krr=%15.8e\n",
  64                     iparams->cross_bb.r1e, iparams->cross_bb.r2e,
  65                     iparams->cross_bb.krr);
  66             break;
  67         case F_CROSS_BOND_ANGLES:
  68             fprintf(fp, "r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e\n",
  69                     iparams->cross_ba.r1e, iparams->cross_ba.r2e,
  70                     iparams->cross_ba.r3e, iparams->cross_ba.krt);
  71             break;
  72         case F_LINEAR_ANGLES:
  73             fprintf(fp, "klinA=%15.8e, aA=%15.8e, klinB=%15.8e, aB=%15.8e\n",
  74                     iparams->linangle.klinA, iparams->linangle.aA,
  75                     iparams->linangle.klinB, iparams->linangle.aB);
  76             break;
  77         case F_UREY_BRADLEY:
  78             fprintf(fp, "thetaA=%15.8e, kthetaA=%15.8e, r13A=%15.8e, kUBA=%15.8e, thetaB=%15.8e, kthetaB=%15.8e, r13B=%15.8e, kUBB=%15.8e\n", iparams->u_b.thetaA, iparams->u_b.kthetaA, iparams->u_b.r13A, iparams->u_b.kUBA, iparams->u_b.thetaB, iparams->u_b.kthetaB, iparams->u_b.r13B, iparams->u_b.kUBB);
  79             break;
  80         case F_QUARTIC_ANGLES:
  81             fprintf(fp, "theta=%15.8e", iparams->qangle.theta);
  82             for (int i = 0; i < 5; i++)
  83             {
  84                 fprintf(fp, ", c%c=%15.8e", '0'+i, iparams->qangle.c[i]);
  85             }
  86             fprintf(fp, "\n");
  87             break;
  88         case F_BHAM:
  89             fprintf(fp, "a=%15.8e, b=%15.8e, c=%15.8e\n",
  90                     iparams->bham.a, iparams->bham.b, iparams->bham.c);
  91             break;
  92         case F_BONDS:
  93         case F_G96BONDS:
  94         case F_HARMONIC:
  95             pr_harm(fp, iparams, "b0", "cb");
  96             break;
  97         case F_IDIHS:
  98             pr_harm(fp, iparams, "xi", "cx");
  99             break;
 100         case F_MORSE:
 101             fprintf(fp, "b0A=%15.8e, cbA=%15.8e, betaA=%15.8e, b0B=%15.8e, cbB=%15.8e, betaB=%15.8e\n",
 102                     iparams->morse.b0A, iparams->morse.cbA, iparams->morse.betaA,
 103                     iparams->morse.b0B, iparams->morse.cbB, iparams->morse.betaB);
 104             break;
 105         case F_CUBICBONDS:
 106             fprintf(fp, "b0=%15.8e, kb=%15.8e, kcub=%15.8e\n",
 107                     iparams->cubic.b0, iparams->cubic.kb, iparams->cubic.kcub);
 108             break;
 109         case F_CONNBONDS:
 110             fprintf(fp, "\n");
 111             break;
 112         case F_FENEBONDS:
 113             fprintf(fp, "bm=%15.8e, kb=%15.8e\n", iparams->fene.bm, iparams->fene.kb);
 114             break;
 115         case F_RESTRBONDS:
 116             fprintf(fp, "lowA=%15.8e, up1A=%15.8e, up2A=%15.8e, kA=%15.8e, lowB=%15.8e, up1B=%15.8e, up2B=%15.8e, kB=%15.8e,\n",
 117                     iparams->restraint.lowA, iparams->restraint.up1A,
 118                     iparams->restraint.up2A, iparams->restraint.kA,
 119                     iparams->restraint.lowB, iparams->restraint.up1B,
 120                     iparams->restraint.up2B, iparams->restraint.kB);
 121             break;
 122         case F_TABBONDS:
 123         case F_TABBONDSNC:
 124         case F_TABANGLES:
 125         case F_TABDIHS:
 126             fprintf(fp, "tab=%d, kA=%15.8e, kB=%15.8e\n",
 127                     iparams->tab.table, iparams->tab.kA, iparams->tab.kB);
 128             break;
 129         case F_POLARIZATION:
 130             fprintf(fp, "alpha=%15.8e\n", iparams->polarize.alpha);
 131             break;
 132         case F_ANHARM_POL:
 133             fprintf(fp, "alpha=%15.8e drcut=%15.8e khyp=%15.8e\n",
 134                     iparams->anharm_polarize.alpha,
 135                     iparams->anharm_polarize.drcut,
 136                     iparams->anharm_polarize.khyp);
 137             break;
 138         case F_THOLE_POL:
 139             fprintf(fp, "a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e\n",
 140                     iparams->thole.a, iparams->thole.alpha1, iparams->thole.alpha2,
 141                     iparams->thole.rfac);
 142             break;
 143         case F_WATER_POL:
 144             fprintf(fp, "al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f\n",
 145                     iparams->wpol.al_x, iparams->wpol.al_y, iparams->wpol.al_z,
 146                     iparams->wpol.rOH, iparams->wpol.rHH, iparams->wpol.rOD);
 147             break;
 148         case F_LJ:
 149             fprintf(fp, "c6=%15.8e, c12=%15.8e\n", iparams->lj.c6, iparams->lj.c12);
 150             break;
 151         case F_LJ14:
 152             fprintf(fp, "c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e\n",
 153                     iparams->lj14.c6A, iparams->lj14.c12A,
 154                     iparams->lj14.c6B, iparams->lj14.c12B);
 155             break;
 156         case F_LJC14_Q:
 157             fprintf(fp, "fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
 158                     iparams->ljc14.fqq,
 159                     iparams->ljc14.qi, iparams->ljc14.qj,
 160                     iparams->ljc14.c6, iparams->ljc14.c12);
 161             break;
 162         case F_LJC_PAIRS_NB:
 163             fprintf(fp, "qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
 164                     iparams->ljcnb.qi, iparams->ljcnb.qj,
 165                     iparams->ljcnb.c6, iparams->ljcnb.c12);
 166             break;
 167         case F_PDIHS:
 168         case F_PIDIHS:
 169         case F_ANGRES:
 170         case F_ANGRESZ:
 171             fprintf(fp, "phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d\n",
 172                     iparams->pdihs.phiA, iparams->pdihs.cpA,
 173                     iparams->pdihs.phiB, iparams->pdihs.cpB,
 174                     iparams->pdihs.mult);
 175             break;
 176         case F_DISRES:
 177             fprintf(fp, "label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)\n",
 178                     iparams->disres.label, iparams->disres.type,
 179                     iparams->disres.low, iparams->disres.up1,
 180                     iparams->disres.up2, iparams->disres.kfac);
 181             break;
 182         case F_ORIRES:
 183             fprintf(fp, "ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)\n",
 184                     iparams->orires.ex, iparams->orires.label, iparams->orires.power,
 185                     iparams->orires.c, iparams->orires.obs, iparams->orires.kfac);
 186             break;
 187         case F_DIHRES:
 188             fprintf(fp, "phiA=%15.8e, dphiA=%15.8e, kfacA=%15.8e, phiB=%15.8e, dphiB=%15.8e, kfacB=%15.8e\n",
 189                     iparams->dihres.phiA, iparams->dihres.dphiA, iparams->dihres.kfacA,
 190                     iparams->dihres.phiB, iparams->dihres.dphiB, iparams->dihres.kfacB);
 191             break;
 192         case F_POSRES:
 193             fprintf(fp, "pos0A=(%15.8e,%15.8e,%15.8e), fcA=(%15.8e,%15.8e,%15.8e), pos0B=(%15.8e,%15.8e,%15.8e), fcB=(%15.8e,%15.8e,%15.8e)\n",
 194                     iparams->posres.pos0A[XX], iparams->posres.pos0A[YY],
 195                     iparams->posres.pos0A[ZZ], iparams->posres.fcA[XX],
 196                     iparams->posres.fcA[YY], iparams->posres.fcA[ZZ],
 197                     iparams->posres.pos0B[XX], iparams->posres.pos0B[YY],
 198                     iparams->posres.pos0B[ZZ], iparams->posres.fcB[XX],
 199                     iparams->posres.fcB[YY], iparams->posres.fcB[ZZ]);
 200             break;
 201         case F_FBPOSRES:
 202             fprintf(fp, "pos0=(%15.8e,%15.8e,%15.8e), geometry=%d, r=%15.8e, k=%15.8e\n",
 203                     iparams->fbposres.pos0[XX], iparams->fbposres.pos0[YY],
 204                     iparams->fbposres.pos0[ZZ], iparams->fbposres.geom,
 205                     iparams->fbposres.r,        iparams->fbposres.k);
 206             break;
 207         case F_RBDIHS:
 208             for (int i = 0; i < NR_RBDIHS; i++)
 209             {
 210                 fprintf(fp, "%srbcA[%d]=%15.8e", i == 0 ? "" : ", ", i, iparams->rbdihs.rbcA[i]);
 211             }
 212             fprintf(fp, "\n");
 213             for (int i = 0; i < NR_RBDIHS; i++)
 214             {
 215                 fprintf(fp, "%srbcB[%d]=%15.8e", i == 0 ? "" : ", ", i, iparams->rbdihs.rbcB[i]);
 216             }
 217             fprintf(fp, "\n");
 218             break;
 219         case F_FOURDIHS:
 220         {
 221             /* Use the OPLS -> Ryckaert-Bellemans formula backwards to get
 222              * the OPLS potential constants back.
 223              */
 224             const real *rbcA = iparams->rbdihs.rbcA;
 225             const real *rbcB = iparams->rbdihs.rbcB;
 226             real        VA[4], VB[4];
 227
 228             VA[3] = -0.25*rbcA[4];
 229             VA[2] = -0.5*rbcA[3];
 230             VA[1] = 4.0*VA[3]-rbcA[2];
 231             VA[0] = 3.0*VA[2]-2.0*rbcA[1];
 232
 233             VB[3] = -0.25*rbcB[4];
 234             VB[2] = -0.5*rbcB[3];
 235             VB[1] = 4.0*VB[3]-rbcB[2];
 236             VB[0] = 3.0*VB[2]-2.0*rbcB[1];
 237
 238             for (int i = 0; i < NR_FOURDIHS; i++)
 239             {
 240                 fprintf(fp, "%sFourA[%d]=%15.8e", i == 0 ? "" : ", ", i, VA[i]);
 241             }
 242             fprintf(fp, "\n");
 243             for (int i = 0; i < NR_FOURDIHS; i++)
 244             {
 245                 fprintf(fp, "%sFourB[%d]=%15.8e", i == 0 ? "" : ", ", i, VB[i]);
 246             }
 247             fprintf(fp, "\n");
 248             break;
 249         }
 250
 251         case F_CONSTR:
 252         case F_CONSTRNC:
 253             fprintf(fp, "dA=%15.8e, dB=%15.8e\n", iparams->constr.dA, iparams->constr.dB);
 254             break;
 255         case F_SETTLE:
 256             fprintf(fp, "doh=%15.8e, dhh=%15.8e\n", iparams->settle.doh,
 257                     iparams->settle.dhh);
 258             break;
 259         case F_VSITE2:
 260             fprintf(fp, "a=%15.8e\n", iparams->vsite.a);
 261             break;
 262         case F_VSITE3:
 263         case F_VSITE3FD:
 264         case F_VSITE3FAD:
 265             fprintf(fp, "a=%15.8e, b=%15.8e\n", iparams->vsite.a, iparams->vsite.b);
 266             break;
 267         case F_VSITE3OUT:
 268         case F_VSITE4FD:
 269         case F_VSITE4FDN:
 270             fprintf(fp, "a=%15.8e, b=%15.8e, c=%15.8e\n",
 271                     iparams->vsite.a, iparams->vsite.b, iparams->vsite.c);
 272             break;
 273         case F_VSITEN:
 274             fprintf(fp, "n=%2d, a=%15.8e\n", iparams->vsiten.n, iparams->vsiten.a);
 275             break;
 276         case F_GB12_NOLONGERUSED:
 277         case F_GB13_NOLONGERUSED:
 278         case F_GB14_NOLONGERUSED:
 279             // These could only be generated by grompp, not written in
 280             // a .top file. Now that implicit solvent is not
 281             // supported, they can't be generated, and the values are
 282             // ignored if read from an old .tpr file. So there is
 283             // nothing to print.
 284             break;
 285         case F_CMAP:
 286             fprintf(fp, "cmapA=%1d, cmapB=%1d\n", iparams->cmap.cmapA, iparams->cmap.cmapB);
 287             break;
 288         case  F_RESTRANGLES:
 289             pr_harm(fp, iparams, "ktheta", "costheta0");
 290             break;
 291         case  F_RESTRDIHS:
 292             fprintf(fp, "phiA=%15.8e, cpA=%15.8e",
 293                     iparams->pdihs.phiA, iparams->pdihs.cpA);
 294             break;
 295         case  F_CBTDIHS:
 296             fprintf(fp, "kphi=%15.8e", iparams->cbtdihs.cbtcA[0]);
 297             for (int i = 1; i < NR_CBTDIHS; i++)
 298             {
 299                 fprintf(fp, ", cbtcA[%d]=%15.8e", i-1, iparams->cbtdihs.cbtcA[i]);
 300             }
 301             fprintf(fp, "\n");
 302             break;
 303         default:
 304             gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d",
 305                       ftype, interaction_function[ftype].name, __FILE__, __LINE__);
 306     }
 307 }
 308
 309 template <typename T>
 310 static void
 311 printIlist(FILE *fp, int indent, const char *title,
 312            const t_functype *functype, const T &ilist,
 313            gmx_bool bShowNumbers,
 314            gmx_bool bShowParameters, const t_iparams *iparams)
 315 {
 316     int      i, j, k, type, ftype;
 317
 318     indent = pr_title(fp, indent, title);
 319     pr_indent(fp, indent);
 320     fprintf(fp, "nr: %d\n", ilist.size());
 321     if (ilist.size() > 0)
 322     {
 323         pr_indent(fp, indent);
 324         fprintf(fp, "iatoms:\n");
 325         for (i = j = 0; i < ilist.size(); )
 326         {
 327             pr_indent(fp, indent+INDENT);
 328             type  = ilist.iatoms[i];
 329             ftype = functype[type];
 330             if (bShowNumbers)
 331             {
 332                 fprintf(fp, "%d type=%d ", j, type);
 333             }
 334             j++;
 335             printf("(%s)", interaction_function[ftype].name);
 336             for (k = 0; k < interaction_function[ftype].nratoms; k++)
 337             {
 338                 fprintf(fp, " %3d", ilist.iatoms[i + 1 + k]);
 339             }
 340             if (bShowParameters)
 341             {
 342                 fprintf(fp, "  ");
 343                 pr_iparams(fp, ftype,  &iparams[type]);
 344             }
 345             fprintf(fp, "\n");
 346             i += 1+interaction_function[ftype].nratoms;
 347         }
 348     }
 349 }
 350
 351 void pr_ilist(FILE *fp, int indent, const char *title,
 352               const t_functype *functype, const InteractionList &ilist,
 353               gmx_bool bShowNumbers,
 354               gmx_bool bShowParameters, const t_iparams *iparams)
 355 {
 356     printIlist(fp, indent, title, functype, ilist,
 357                bShowNumbers, bShowParameters, iparams);
 358 }
 359
 360 static void pr_cmap(FILE *fp, int indent, const char *title,
 361                     const gmx_cmap_t *cmap_grid, gmx_bool bShowNumbers)
 362 {
 363     int  i, j, nelem;
 364     real dx, idx;
 365
 366     dx    = 360.0 / cmap_grid->grid_spacing;
 367     nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
 368
 369     if (available(fp, cmap_grid, indent, title))
 370     {
 371         fprintf(fp, "%s\n", title);
 372
 373         for (i = 0; i < cmap_grid->ngrid; i++)
 374         {
 375             idx = -180.0;
 376             fprintf(fp, "%8s %8s %8s %8s\n", "V", "dVdx", "dVdy", "d2dV");
 377
 378             fprintf(fp, "grid[%3d]={\n", bShowNumbers ? i : -1);
 379
 380             for (j = 0; j < nelem; j++)
 381             {
 382                 if ( (j%cmap_grid->grid_spacing) == 0)
 383                 {
 384                     fprintf(fp, "%8.1f\n", idx);
 385                     idx += dx;
 386                 }
 387
 388                 fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4]);
 389                 fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4+1]);
 390                 fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4+2]);
 391                 fprintf(fp, "%8.3f\n", cmap_grid->cmapdata[i].cmap[j*4+3]);
 392             }
 393             fprintf(fp, "\n");
 394         }
 395     }
 396
 397 }
 398
 399 void pr_ffparams(FILE *fp, int indent, const char *title,
 400                  const gmx_ffparams_t *ffparams,
 401                  gmx_bool bShowNumbers)
 402 {
 403     int i;
 404
 405     indent = pr_title(fp, indent, title);
 406     pr_indent(fp, indent);
 407     fprintf(fp, "atnr=%d\n", ffparams->atnr);
 408     pr_indent(fp, indent);
 409     fprintf(fp, "ntypes=%d\n", ffparams->ntypes);
 410     for (i = 0; i < ffparams->ntypes; i++)
 411     {
 412         pr_indent(fp, indent+INDENT);
 413         fprintf(fp, "functype[%d]=%s, ",
 414                 bShowNumbers ? i : -1,
 415                 interaction_function[ffparams->functype[i]].name);
 416         pr_iparams(fp, ffparams->functype[i], &ffparams->iparams[i]);
 417     }
 418     pr_double(fp, indent, "reppow", ffparams->reppow);
 419     pr_real(fp, indent, "fudgeQQ", ffparams->fudgeQQ);
 420     pr_cmap(fp, indent, "cmap", &ffparams->cmap_grid, bShowNumbers);
 421 }
 422
 423 void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef,
 424              gmx_bool bShowNumbers, gmx_bool bShowParameters)
 425 {
 426     int i, j;
 427
 428     if (available(fp, idef, indent, title))
 429     {
 430         indent = pr_title(fp, indent, title);
 431         pr_indent(fp, indent);
 432         fprintf(fp, "atnr=%d\n", idef->atnr);
 433         pr_indent(fp, indent);
 434         fprintf(fp, "ntypes=%d\n", idef->ntypes);
 435         for (i = 0; i < idef->ntypes; i++)
 436         {
 437             pr_indent(fp, indent+INDENT);
 438             fprintf(fp, "functype[%d]=%s, ",
 439                     bShowNumbers ? i : -1,
 440                     interaction_function[idef->functype[i]].name);
 441             pr_iparams(fp, idef->functype[i], &idef->iparams[i]);
 442         }
 443         pr_real(fp, indent, "fudgeQQ", idef->fudgeQQ);
 444
 445         for (j = 0; (j < F_NRE); j++)
 446         {
 447             printIlist(fp, indent, interaction_function[j].longname,
 448                        idef->functype, idef->il[j], bShowNumbers,
 449                        bShowParameters, idef->iparams);
 450         }
 451     }
 452 }