src/gromacs/gmxpreprocess/readrot.cpp

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  38 #include "gmxpre.h"
  39
  40 #include <string>
  41
  42 #include "gromacs/fileio/readinp.h"
  43 #include "gromacs/fileio/trrio.h"
  44 #include "gromacs/fileio/warninp.h"
  45 #include "gromacs/gmxpreprocess/readir.h"
  46 #include "gromacs/math/vec.h"
  47 #include "gromacs/math/vecdump.h"
  48 #include "gromacs/mdtypes/inputrec.h"
  49 #include "gromacs/mdtypes/md_enums.h"
  50 #include "gromacs/topology/block.h"
  51 #include "gromacs/utility/arrayref.h"
  52 #include "gromacs/utility/cstringutil.h"
  53 #include "gromacs/utility/fatalerror.h"
  54 #include "gromacs/utility/futil.h"
  55 #include "gromacs/utility/path.h"
  56 #include "gromacs/utility/smalloc.h"
  57 #include "gromacs/utility/stringutil.h"
  58
  59 static const char* RotStr = "Enforced rotation:";
  60
  61
  62 static char s_vec[STRLEN];
  63
  64
  65 static void string2dvec(char buf[], dvec nums)
  66 {
  67     if (sscanf(buf, "%lf%lf%lf", &nums[0], &nums[1], &nums[2]) != 3)
  68     {
  69         gmx_fatal(FARGS, "Expected three numbers at input line %s", buf);
  70     }
  71 }
  72
  73
  74 extern std::vector<std::string> read_rotparams(std::vector<t_inpfile>* inp, t_rot* rot, warninp_t wi)
  75 {
  76     int       g, m;
  77     char      buf[STRLEN];
  78     char      warn_buf[STRLEN];
  79     dvec      vec;
  80     t_rotgrp* rotg;
  81
  82     /* read rotation parameters */
  83     printStringNoNewline(
  84             inp,
  85             "Output frequency for angle, torque and rotation potential energy for the whole group");
  86     rot->nstrout = get_eint(inp, "rot-nstrout", 100, wi);
  87     printStringNoNewline(inp,
  88                          "Output frequency for per-slab data (angles, torques and slab centers)");
  89     rot->nstsout = get_eint(inp, "rot-nstsout", 1000, wi);
  90     printStringNoNewline(inp, "Number of rotation groups");
  91     rot->ngrp = get_eint(inp, "rot-ngroups", 1, wi);
  92
  93     if (rot->ngrp < 1)
  94     {
  95         gmx_fatal(FARGS, "rot-ngroups should be >= 1");
  96     }
  97
  98     snew(rot->grp, rot->ngrp);
  99
 100     /* Read the rotation groups */
 101     std::vector<std::string> rotateGroups(rot->ngrp);
 102     char                     readBuffer[STRLEN];
 103     for (g = 0; g < rot->ngrp; g++)
 104     {
 105         rotg = &rot->grp[g];
 106         printStringNoNewline(inp, "Rotation group name");
 107         sprintf(buf, "rot-group%d", g);
 108         setStringEntry(inp, buf, readBuffer, "");
 109         rotateGroups[g] = readBuffer;
 110         printStringNoNewline(inp,
 111                              "Rotation potential. Can be iso, iso-pf, pm, pm-pf, rm, rm-pf, rm2, "
 112                              "rm2-pf, flex, flex-t, flex2, flex2-t");
 113         sprintf(buf, "rot-type%d", g);
 114         rotg->eType = get_eenum(inp, buf, erotg_names);
 115
 116         printStringNoNewline(inp, "Use mass-weighting of the rotation group positions");
 117         sprintf(buf, "rot-massw%d", g);
 118         rotg->bMassW = get_eenum(inp, buf, yesno_names);
 119
 120         printStringNoNewline(inp, "Rotation vector, will get normalized");
 121         sprintf(buf, "rot-vec%d", g);
 122         setStringEntry(inp, buf, s_vec, "1.0 0.0 0.0");
 123         string2dvec(s_vec, vec);
 124         /* Normalize the rotation vector */
 125         if (dnorm(vec) != 0)
 126         {
 127             dsvmul(1.0 / dnorm(vec), vec, vec);
 128         }
 129         else
 130         {
 131             sprintf(warn_buf, "rot-vec%d = 0", g);
 132             warning_error(wi, warn_buf);
 133         }
 134         fprintf(stderr, "%s Group %d (%s) normalized rot. vector: %f %f %f\n", RotStr, g,
 135                 erotg_names[rotg->eType], vec[0], vec[1], vec[2]);
 136         for (m = 0; m < DIM; m++)
 137         {
 138             rotg->inputVec[m] = vec[m];
 139         }
 140
 141         printStringNoNewline(inp, "Pivot point for the potentials iso, pm, rm, and rm2 (nm)");
 142         sprintf(buf, "rot-pivot%d", g);
 143         setStringEntry(inp, buf, s_vec, "0.0 0.0 0.0");
 144         clear_dvec(vec);
 145         if ((rotg->eType == erotgISO) || (rotg->eType == erotgPM) || (rotg->eType == erotgRM)
 146             || (rotg->eType == erotgRM2))
 147         {
 148             string2dvec(s_vec, vec);
 149         }
 150         for (m = 0; m < DIM; m++)
 151         {
 152             rotg->pivot[m] = vec[m];
 153         }
 154
 155         printStringNoNewline(inp, "Rotation rate (degree/ps) and force constant (kJ/(mol*nm^2))");
 156         sprintf(buf, "rot-rate%d", g);
 157         rotg->rate = get_ereal(inp, buf, 0.0, wi);
 158
 159         sprintf(buf, "rot-k%d", g);
 160         rotg->k = get_ereal(inp, buf, 0.0, wi);
 161         if (rotg->k <= 0.0)
 162         {
 163             sprintf(warn_buf, "rot-k%d <= 0", g);
 164             warning_note(wi, warn_buf);
 165         }
 166
 167         printStringNoNewline(inp, "Slab distance for flexible axis rotation (nm)");
 168         sprintf(buf, "rot-slab-dist%d", g);
 169         rotg->slab_dist = get_ereal(inp, buf, 1.5, wi);
 170         if (rotg->slab_dist <= 0.0)
 171         {
 172             sprintf(warn_buf, "rot-slab-dist%d <= 0", g);
 173             warning_error(wi, warn_buf);
 174         }
 175
 176         printStringNoNewline(inp,
 177                              "Minimum value of Gaussian function for the force to be evaluated "
 178                              "(for flex* potentials)");
 179         sprintf(buf, "rot-min-gauss%d", g);
 180         rotg->min_gaussian = get_ereal(inp, buf, 1e-3, wi);
 181         if (rotg->min_gaussian <= 0.0)
 182         {
 183             sprintf(warn_buf, "rot-min-gauss%d <= 0", g);
 184             warning_error(wi, warn_buf);
 185         }
 186
 187         printStringNoNewline(
 188                 inp, "Value of additive constant epsilon' (nm^2) for rm2* and flex2* potentials");
 189         sprintf(buf, "rot-eps%d", g);
 190         rotg->eps = get_ereal(inp, buf, 1e-4, wi);
 191         if ((rotg->eps <= 0.0) && (rotg->eType == erotgRM2 || rotg->eType == erotgFLEX2))
 192         {
 193             sprintf(warn_buf, "rot-eps%d <= 0", g);
 194             warning_error(wi, warn_buf);
 195         }
 196
 197         printStringNoNewline(
 198                 inp,
 199                 "Fitting method to determine angle of rotation group (rmsd, norm, or potential)");
 200         sprintf(buf, "rot-fit-method%d", g);
 201         rotg->eFittype = get_eenum(inp, buf, erotg_fitnames);
 202         printStringNoNewline(inp,
 203                              "For fit type 'potential', nr. of angles around the reference for "
 204                              "which the pot. is evaluated");
 205         sprintf(buf, "rot-potfit-nsteps%d", g);
 206         rotg->PotAngle_nstep = get_eint(inp, buf, 21, wi);
 207         if ((rotg->eFittype == erotgFitPOT) && (rotg->PotAngle_nstep < 1))
 208         {
 209             sprintf(warn_buf, "rot-potfit-nsteps%d < 1", g);
 210             warning_error(wi, warn_buf);
 211         }
 212         printStringNoNewline(
 213                 inp,
 214                 "For fit type 'potential', distance in degrees between two consecutive angles");
 215         sprintf(buf, "rot-potfit-step%d", g);
 216         rotg->PotAngle_step = get_ereal(inp, buf, 0.25, wi);
 217     }
 218
 219     return rotateGroups;
 220 }
 221
 222
 223 /* Check whether the box is unchanged */
 224 static void check_box_unchanged(matrix f_box, matrix box, const char fn[], warninp_t wi)
 225 {
 226     int  i, ii;
 227     bool bSame = TRUE;
 228     char warn_buf[STRLEN];
 229
 230
 231     for (i = 0; i < DIM; i++)
 232     {
 233         for (ii = 0; ii < DIM; ii++)
 234         {
 235             if (f_box[i][ii] != box[i][ii])
 236             {
 237                 bSame = FALSE;
 238             }
 239         }
 240     }
 241     if (!bSame)
 242     {
 243         sprintf(warn_buf, "%s Box size in reference file %s differs from actual box size!", RotStr, fn);
 244         warning(wi, warn_buf);
 245         pr_rvecs(stderr, 0, "Your box is:", box, 3);
 246         pr_rvecs(stderr, 0, "Box in file:", f_box, 3);
 247     }
 248 }
 249
 250
 251 /* Extract the reference positions for the rotation group(s) */
 252 extern void set_reference_positions(t_rot* rot, rvec* x, matrix box, const char* fn, bool bSet, warninp_t wi)
 253 {
 254     int              g, i, ii;
 255     t_rotgrp*        rotg;
 256     gmx_trr_header_t header;   /* Header information of reference file */
 257     rvec             f_box[3]; /* Box from reference file */
 258
 259     for (g = 0; g < rot->ngrp; g++)
 260     {
 261         rotg = &rot->grp[g];
 262         fprintf(stderr, "%s group %d has %d reference positions.\n", RotStr, g, rotg->nat);
 263         snew(rotg->x_ref, rotg->nat);
 264
 265         /* Construct the name for the file containing the reference positions for this group: */
 266         std::string reffileString =
 267                 gmx::Path::concatenateBeforeExtension(fn, gmx::formatString(".%d", g));
 268         const char* reffile = reffileString.c_str();
 269
 270         /* If the base filename for the reference position files was explicitly set by
 271          * the user, we issue a fatal error if the group file can not be found */
 272         if (bSet && !gmx_fexist(reffile))
 273         {
 274             gmx_fatal(FARGS,
 275                       "%s The file containing the reference positions was not found.\n"
 276                       "Expected the file '%s' for group %d.\n",
 277                       RotStr, reffile, g);
 278         }
 279
 280         if (gmx_fexist(reffile))
 281         {
 282             fprintf(stderr, "  Reading them from %s.\n", reffile);
 283             gmx_trr_read_single_header(reffile, &header);
 284             if (rotg->nat != header.natoms)
 285             {
 286                 gmx_fatal(FARGS,
 287                           "Number of atoms in file %s (%d) does not match the number of atoms in "
 288                           "rotation group (%d)!\n",
 289                           reffile, header.natoms, rotg->nat);
 290             }
 291             gmx_trr_read_single_frame(reffile, &header.step, &header.t, &header.lambda, f_box,
 292                                       &header.natoms, rotg->x_ref, nullptr, nullptr);
 293
 294             /* Check whether the box is unchanged and output a warning if not: */
 295             check_box_unchanged(f_box, box, reffile, wi);
 296         }
 297         else
 298         {
 299             fprintf(stderr, " Saving them to %s.\n", reffile);
 300             for (i = 0; i < rotg->nat; i++)
 301             {
 302                 ii = rotg->ind[i];
 303                 copy_rvec(x[ii], rotg->x_ref[i]);
 304             }
 305             gmx_trr_write_single_frame(reffile, g, 0.0, 0.0, box, rotg->nat, rotg->x_ref, nullptr, nullptr);
 306         }
 307     }
 308 }
 309
 310
 311 extern void make_rotation_groups(t_rot*                           rot,
 312                                  gmx::ArrayRef<const std::string> rotateGroupNames,
 313                                  t_blocka*                        grps,
 314                                  char**                           gnames)
 315 {
 316     int       g, ig = -1, i;
 317     t_rotgrp* rotg;
 318
 319
 320     for (g = 0; g < rot->ngrp; g++)
 321     {
 322         rotg      = &rot->grp[g];
 323         ig        = search_string(rotateGroupNames[g].c_str(), grps->nr, gnames);
 324         rotg->nat = grps->index[ig + 1] - grps->index[ig];
 325
 326         if (rotg->nat > 0)
 327         {
 328             fprintf(stderr, "Rotation group %d '%s' has %d atoms\n", g, rotateGroupNames[g].c_str(),
 329                     rotg->nat);
 330             snew(rotg->ind, rotg->nat);
 331             for (i = 0; i < rotg->nat; i++)
 332             {
 333                 rotg->ind[i] = grps->a[grps->index[ig] + i];
 334             }
 335         }
 336         else
 337         {
 338             gmx_fatal(FARGS, "Rotation group %d '%s' is empty", g, rotateGroupNames[g].c_str());
 339         }
 340     }
 341 }