src/gromacs/gmxpreprocess/readrot.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) 2013,2014,2015,2016,2017,2018, 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 "gromacs/fileio/readinp.h"
  40 #include "gromacs/fileio/trrio.h"
  41 #include "gromacs/fileio/warninp.h"
  42 #include "gromacs/gmxpreprocess/readir.h"
  43 #include "gromacs/math/vec.h"
  44 #include "gromacs/math/vecdump.h"
  45 #include "gromacs/mdtypes/inputrec.h"
  46 #include "gromacs/mdtypes/md_enums.h"
  47 #include "gromacs/topology/block.h"
  48 #include "gromacs/utility/cstringutil.h"
  49 #include "gromacs/utility/fatalerror.h"
  50 #include "gromacs/utility/futil.h"
  51 #include "gromacs/utility/smalloc.h"
  52
  53 static const char *RotStr = "Enforced rotation:";
  54
  55
  56 static char s_vec[STRLEN];
  57
  58
  59 static void string2dvec(char buf[], dvec nums)
  60 {
  61     if (sscanf(buf, "%lf%lf%lf", &nums[0], &nums[1], &nums[2]) != 3)
  62     {
  63         gmx_fatal(FARGS, "Expected three numbers at input line %s", buf);
  64     }
  65 }
  66
  67
  68 extern char **read_rotparams(int *ninp_p, t_inpfile **inp_p, t_rot *rot,
  69                              warninp_t wi)
  70 {
  71     int         g, m;
  72     char      **grpbuf;
  73     char        buf[STRLEN];
  74     char        warn_buf[STRLEN];
  75     dvec        vec;
  76     t_rotgrp   *rotg;
  77
  78     /* read rotation parameters */
  79     printStringNoNewline(ninp_p, inp_p, "Output frequency for angle, torque and rotation potential energy for the whole group");
  80     rot->nstrout = get_eint(ninp_p, inp_p, "rot-nstrout", 100, wi);
  81     printStringNoNewline(ninp_p, inp_p, "Output frequency for per-slab data (angles, torques and slab centers)");
  82     rot->nstsout = get_eint(ninp_p, inp_p, "rot-nstsout", 1000, wi);
  83     printStringNoNewline(ninp_p, inp_p, "Number of rotation groups");
  84     rot->ngrp = get_eint(ninp_p, inp_p, "rot-ngroups", 1, wi);
  85
  86     if (rot->ngrp < 1)
  87     {
  88         gmx_fatal(FARGS, "rot-ngroups should be >= 1");
  89     }
  90
  91     snew(rot->grp, rot->ngrp);
  92
  93     /* Read the rotation groups */
  94     snew(grpbuf, rot->ngrp);
  95     for (g = 0; g < rot->ngrp; g++)
  96     {
  97         rotg = &rot->grp[g];
  98         snew(grpbuf[g], STRLEN);
  99         printStringNoNewline(ninp_p, inp_p, "Rotation group name");
 100         sprintf(buf, "rot-group%d", g);
 101         setStringEntry(ninp_p, inp_p, buf, grpbuf[g], "");
 102
 103         printStringNoNewline(ninp_p, inp_p, "Rotation potential. Can be iso, iso-pf, pm, pm-pf, rm, rm-pf, rm2, rm2-pf, flex, flex-t, flex2, flex2-t");
 104         sprintf(buf, "rot-type%d", g);
 105         rotg->eType = get_eenum(ninp_p, inp_p, buf, erotg_names);
 106
 107         printStringNoNewline(ninp_p, inp_p, "Use mass-weighting of the rotation group positions");
 108         sprintf(buf, "rot-massw%d", g);
 109         rotg->bMassW = get_eenum(ninp_p, inp_p, buf, yesno_names);
 110
 111         printStringNoNewline(ninp_p, inp_p, "Rotation vector, will get normalized");
 112         sprintf(buf, "rot-vec%d", g);
 113         setStringEntry(ninp_p, inp_p, buf, s_vec, "1.0 0.0 0.0");
 114         string2dvec(s_vec, vec);
 115         /* Normalize the rotation vector */
 116         if (dnorm(vec) != 0)
 117         {
 118             dsvmul(1.0/dnorm(vec), vec, vec);
 119         }
 120         else
 121         {
 122             sprintf(warn_buf, "rot-vec%d = 0", g);
 123             warning_error(wi, warn_buf);
 124         }
 125         fprintf(stderr, "%s Group %d (%s) normalized rot. vector: %f %f %f\n",
 126                 RotStr, g, erotg_names[rotg->eType], vec[0], vec[1], vec[2]);
 127         for (m = 0; m < DIM; m++)
 128         {
 129             rotg->vec[m] = vec[m];
 130         }
 131
 132         printStringNoNewline(ninp_p, inp_p, "Pivot point for the potentials iso, pm, rm, and rm2 (nm)");
 133         sprintf(buf, "rot-pivot%d", g);
 134         setStringEntry(ninp_p, inp_p, buf, s_vec, "0.0 0.0 0.0");
 135         clear_dvec(vec);
 136         if ( (rotg->eType == erotgISO) || (rotg->eType == erotgPM) || (rotg->eType == erotgRM) || (rotg->eType == erotgRM2) )
 137         {
 138             string2dvec(s_vec, vec);
 139         }
 140         for (m = 0; m < DIM; m++)
 141         {
 142             rotg->pivot[m] = vec[m];
 143         }
 144
 145         printStringNoNewline(ninp_p, inp_p, "Rotation rate (degree/ps) and force constant (kJ/(mol*nm^2))");
 146         sprintf(buf, "rot-rate%d", g);
 147         rotg->rate = get_ereal(ninp_p, inp_p, buf, 0.0, wi);
 148
 149         sprintf(buf, "rot-k%d", g);
 150         rotg->k = get_ereal(ninp_p, inp_p, buf, 0.0, wi);
 151         if (rotg->k <= 0.0)
 152         {
 153             sprintf(warn_buf, "rot-k%d <= 0", g);
 154             warning_note(wi, warn_buf);
 155         }
 156
 157         printStringNoNewline(ninp_p, inp_p, "Slab distance for flexible axis rotation (nm)");
 158         sprintf(buf, "rot-slab-dist%d", g);
 159         rotg->slab_dist = get_ereal(ninp_p, inp_p, buf, 1.5, wi);
 160         if (rotg->slab_dist <= 0.0)
 161         {
 162             sprintf(warn_buf, "rot-slab-dist%d <= 0", g);
 163             warning_error(wi, warn_buf);
 164         }
 165
 166         printStringNoNewline(ninp_p, inp_p, "Minimum value of Gaussian function for the force to be evaluated (for flex* potentials)");
 167         sprintf(buf, "rot-min-gauss%d", g);
 168         rotg->min_gaussian = get_ereal(ninp_p, inp_p, buf, 1e-3, wi);
 169         if (rotg->min_gaussian <= 0.0)
 170         {
 171             sprintf(warn_buf, "rot-min-gauss%d <= 0", g);
 172             warning_error(wi, warn_buf);
 173         }
 174
 175         printStringNoNewline(ninp_p, inp_p, "Value of additive constant epsilon' (nm^2) for rm2* and flex2* potentials");
 176         sprintf(buf, "rot-eps%d", g);
 177         rotg->eps = get_ereal(ninp_p, inp_p, buf, 1e-4, wi);
 178         if ( (rotg->eps <= 0.0) && (rotg->eType == erotgRM2 || rotg->eType == erotgFLEX2) )
 179         {
 180             sprintf(warn_buf, "rot-eps%d <= 0", g);
 181             warning_error(wi, warn_buf);
 182         }
 183
 184         printStringNoNewline(ninp_p, inp_p, "Fitting method to determine angle of rotation group (rmsd, norm, or potential)");
 185         sprintf(buf, "rot-fit-method%d", g);
 186         rotg->eFittype = get_eenum(ninp_p, inp_p, buf, erotg_fitnames);
 187         printStringNoNewline(ninp_p, inp_p, "For fit type 'potential', nr. of angles around the reference for which the pot. is evaluated");
 188         sprintf(buf, "rot-potfit-nsteps%d", g);
 189         rotg->PotAngle_nstep = get_eint(ninp_p, inp_p, buf, 21, wi);
 190         if ( (rotg->eFittype == erotgFitPOT) && (rotg->PotAngle_nstep < 1) )
 191         {
 192             sprintf(warn_buf, "rot-potfit-nsteps%d < 1", g);
 193             warning_error(wi, warn_buf);
 194         }
 195         printStringNoNewline(ninp_p, inp_p, "For fit type 'potential', distance in degrees between two consecutive angles");
 196         sprintf(buf, "rot-potfit-step%d", g);
 197         rotg->PotAngle_step = get_ereal(ninp_p, inp_p, buf, 0.25, wi);
 198     }
 199
 200     return grpbuf;
 201 }
 202
 203
 204 /* Check whether the box is unchanged */
 205 static void check_box_unchanged(matrix f_box, matrix box, char fn[], warninp_t wi)
 206 {
 207     int      i, ii;
 208     gmx_bool bSame = TRUE;
 209     char     warn_buf[STRLEN];
 210
 211
 212     for (i = 0; i < DIM; i++)
 213     {
 214         for (ii = 0; ii < DIM; ii++)
 215         {
 216             if (f_box[i][ii] != box[i][ii])
 217             {
 218                 bSame = FALSE;
 219             }
 220         }
 221     }
 222     if (!bSame)
 223     {
 224         sprintf(warn_buf, "%s Box size in reference file %s differs from actual box size!",
 225                 RotStr, fn);
 226         warning(wi, warn_buf);
 227         pr_rvecs(stderr, 0, "Your box is:", box, 3);
 228         pr_rvecs(stderr, 0, "Box in file:", f_box, 3);
 229     }
 230 }
 231
 232
 233 /* Extract the reference positions for the rotation group(s) */
 234 extern void set_reference_positions(
 235         t_rot *rot, rvec *x, matrix box,
 236         const char *fn, gmx_bool bSet, warninp_t wi)
 237 {
 238     int              g, i, ii;
 239     t_rotgrp        *rotg;
 240     gmx_trr_header_t header;    /* Header information of reference file */
 241     char             base[STRLEN], extension[STRLEN], reffile[STRLEN];
 242     char            *extpos;
 243     rvec             f_box[3]; /* Box from reference file */
 244
 245
 246     /* Base name and extension of the reference file: */
 247     strncpy(base, fn, STRLEN - 1);
 248     base[STRLEN-1] = '\0';
 249     extpos         = strrchr(base, '.');
 250     strcpy(extension, extpos+1);
 251     *extpos = '\0';
 252
 253
 254     for (g = 0; g < rot->ngrp; g++)
 255     {
 256         rotg = &rot->grp[g];
 257         fprintf(stderr, "%s group %d has %d reference positions.\n", RotStr, g, rotg->nat);
 258         snew(rotg->x_ref, rotg->nat);
 259
 260         /* Construct the name for the file containing the reference positions for this group: */
 261         sprintf(reffile, "%s.%d.%s", base, g, extension);
 262
 263         /* If the base filename for the reference position files was explicitly set by
 264          * the user, we issue a fatal error if the group file can not be found */
 265         if (bSet && !gmx_fexist(reffile))
 266         {
 267             gmx_fatal(FARGS, "%s The file containing the reference positions was not found.\n"
 268                       "Expected the file '%s' for group %d.\n",
 269                       RotStr, reffile, g);
 270         }
 271
 272         if (gmx_fexist(reffile))
 273         {
 274             fprintf(stderr, "  Reading them from %s.\n", reffile);
 275             gmx_trr_read_single_header(reffile, &header);
 276             if (rotg->nat != header.natoms)
 277             {
 278                 gmx_fatal(FARGS, "Number of atoms in file %s (%d) does not match the number of atoms in rotation group (%d)!\n",
 279                           reffile, header.natoms, rotg->nat);
 280             }
 281             gmx_trr_read_single_frame(reffile, &header.step, &header.t, &header.lambda, f_box, &header.natoms, rotg->x_ref, nullptr, nullptr);
 282
 283             /* Check whether the box is unchanged and output a warning if not: */
 284             check_box_unchanged(f_box, box, reffile, wi);
 285         }
 286         else
 287         {
 288             fprintf(stderr, " Saving them to %s.\n", reffile);
 289             for (i = 0; i < rotg->nat; i++)
 290             {
 291                 ii = rotg->ind[i];
 292                 copy_rvec(x[ii], rotg->x_ref[i]);
 293             }
 294             gmx_trr_write_single_frame(reffile, g, 0.0, 0.0, box, rotg->nat, rotg->x_ref, nullptr, nullptr);
 295         }
 296     }
 297 }
 298
 299
 300 extern void make_rotation_groups(t_rot *rot, char **rotgnames, t_blocka *grps, char **gnames)
 301 {
 302     int       g, ig = -1, i;
 303     t_rotgrp *rotg;
 304
 305
 306     for (g = 0; g < rot->ngrp; g++)
 307     {
 308         rotg      = &rot->grp[g];
 309         ig        = search_string(rotgnames[g], grps->nr, gnames);
 310         rotg->nat = grps->index[ig+1] - grps->index[ig];
 311
 312         if (rotg->nat > 0)
 313         {
 314             fprintf(stderr, "Rotation group %d '%s' has %d atoms\n", g, rotgnames[g], rotg->nat);
 315             snew(rotg->ind, rotg->nat);
 316             for (i = 0; i < rotg->nat; i++)
 317             {
 318                 rotg->ind[i] = grps->a[grps->index[ig]+i];
 319             }
 320         }
 321         else
 322         {
 323             gmx_fatal(FARGS, "Rotation group %d '%s' is empty", g, rotgnames[g]);
 324         }
 325     }
 326 }