src/gromacs/gmxana/gmx_saltbr.cpp

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  37 #include "gmxpre.h"
  38
  39 #include <cmath>
  40 #include <cstring>
  41
  42 #include "gromacs/commandline/filenm.h"
  43 #include "gromacs/commandline/pargs.h"
  44 #include "gromacs/fileio/trxio.h"
  45 #include "gromacs/fileio/xvgr.h"
  46 #include "gromacs/gmxana/gmx_ana.h"
  47 #include "gromacs/math/vec.h"
  48 #include "gromacs/pbcutil/pbc.h"
  49 #include "gromacs/topology/topology.h"
  50 #include "gromacs/utility/arraysize.h"
  51 #include "gromacs/utility/cstringutil.h"
  52 #include "gromacs/utility/fatalerror.h"
  53 #include "gromacs/utility/futil.h"
  54 #include "gromacs/utility/smalloc.h"
  55
  56 typedef struct {
  57     char *label;
  58     int   cg;
  59     real  q;
  60 } t_charge;
  61
  62 static t_charge *mk_charge(const t_atoms *atoms, const t_block *cgs, int *nncg)
  63 {
  64     t_charge *cg = nullptr;
  65     char      buf[32];
  66     int       i, j, ncg, resnr, anr;
  67     real      qq;
  68
  69     /* Find the charged groups */
  70     ncg = 0;
  71     for (i = 0; (i < cgs->nr); i++)
  72     {
  73         qq = 0.0;
  74         for (j = cgs->index[i]; (j < cgs->index[i+1]); j++)
  75         {
  76             qq += atoms->atom[j].q;
  77         }
  78         if (std::abs(qq) > 1.0e-5)
  79         {
  80             srenew(cg, ncg+1);
  81             cg[ncg].q  = qq;
  82             cg[ncg].cg = i;
  83             anr        = cgs->index[i];
  84             resnr      = atoms->atom[anr].resind;
  85             sprintf(buf, "%s%d-%d",
  86                     *(atoms->resinfo[resnr].name),
  87                     atoms->resinfo[resnr].nr,
  88                     anr+1);
  89             cg[ncg].label = gmx_strdup(buf);
  90             ncg++;
  91         }
  92     }
  93     *nncg = ncg;
  94
  95     for (i = 0; (i < ncg); i++)
  96     {
  97         printf("CG: %10s Q: %6g  Atoms:",
  98                cg[i].label, cg[i].q);
  99         for (j = cgs->index[cg[i].cg]; (j < cgs->index[cg[i].cg+1]); j++)
 100         {
 101             printf(" %4d", j);
 102         }
 103         printf("\n");
 104     }
 105
 106     return cg;
 107 }
 108
 109 static real calc_dist(t_pbc *pbc, rvec x[], const t_block *cgs, int icg, int jcg)
 110 {
 111     int  i, j;
 112     rvec dx;
 113     real d2, mindist2 = 1000;
 114
 115     for (i = cgs->index[icg]; (i < cgs->index[icg+1]); i++)
 116     {
 117         for (j = cgs->index[jcg]; (j < cgs->index[jcg+1]); j++)
 118         {
 119             pbc_dx(pbc, x[i], x[j], dx);
 120             d2 = norm2(dx);
 121             if (d2 < mindist2)
 122             {
 123                 mindist2 = d2;
 124             }
 125         }
 126     }
 127     return std::sqrt(mindist2);
 128 }
 129
 130 int gmx_saltbr(int argc, char *argv[])
 131 {
 132     const char     *desc[] = {
 133         "[THISMODULE] plots the distance between all combination of charged groups",
 134         "as a function of time. The groups are combined in different ways.",
 135         "A minimum distance can be given (i.e. a cut-off), such that groups",
 136         "that are never closer than that distance will not be plotted.[PAR]",
 137         "Output will be in a number of fixed filenames, [TT]min-min.xvg[tt], [TT]plus-min.xvg[tt]",
 138         "and [TT]plus-plus.xvg[tt], or files for every individual ion pair if the [TT]-sep[tt]",
 139         "option is selected. In this case, files are named as [TT]sb-(Resname)(Resnr)-(Atomnr)[tt].",
 140         "There may be [BB]many[bb] such files."
 141     };
 142     static gmx_bool bSep     = FALSE;
 143     static real     truncate = 1000.0;
 144     t_pargs         pa[]     = {
 145         { "-t",   FALSE, etREAL, {&truncate},
 146           "Groups that are never closer than this distance are not plotted" },
 147         { "-sep", FALSE, etBOOL, {&bSep},
 148           "Use separate files for each interaction (may be MANY)" }
 149     };
 150     t_filenm        fnm[] = {
 151         { efTRX, "-f",  nullptr, ffREAD },
 152         { efTPR, nullptr,  nullptr, ffREAD },
 153     };
 154 #define NFILE asize(fnm)
 155
 156     FILE              *out[3], *fp;
 157     static const char *title[3] = {
 158         "Distance between positively charged groups",
 159         "Distance between negatively charged groups",
 160         "Distance between oppositely charged groups"
 161     };
 162     static const char *fn[3] = {
 163         "plus-plus.xvg",
 164         "min-min.xvg",
 165         "plus-min.xvg"
 166     };
 167     int                nset[3] = {0, 0, 0};
 168
 169     t_topology        *top;
 170     int                ePBC;
 171     char              *buf;
 172     t_trxstatus       *status;
 173     int                i, j, k, m, nnn, teller, ncg;
 174     real               t, *time, qi, qj;
 175     t_charge          *cg;
 176     real            ***cgdist;
 177     int              **nWithin;
 178
 179     t_pbc              pbc;
 180     rvec              *x;
 181     matrix             box;
 182     gmx_output_env_t  *oenv;
 183
 184     if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
 185                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
 186     {
 187         return 0;
 188     }
 189
 190     top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
 191     cg  = mk_charge(&top->atoms, &(top->cgs), &ncg);
 192     snew(cgdist, ncg);
 193     snew(nWithin, ncg);
 194     for (i = 0; (i < ncg); i++)
 195     {
 196         snew(cgdist[i], ncg);
 197         snew(nWithin[i], ncg);
 198     }
 199
 200     read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
 201
 202     teller = 0;
 203     time   = nullptr;
 204     do
 205     {
 206         srenew(time, teller+1);
 207         time[teller] = t;
 208
 209         set_pbc(&pbc, ePBC, box);
 210
 211         for (i = 0; (i < ncg); i++)
 212         {
 213             for (j = i+1; (j < ncg); j++)
 214             {
 215                 srenew(cgdist[i][j], teller+1);
 216                 cgdist[i][j][teller] =
 217                     calc_dist(&pbc, x, &(top->cgs), cg[i].cg, cg[j].cg);
 218                 if (cgdist[i][j][teller] < truncate)
 219                 {
 220                     nWithin[i][j] = 1;
 221                 }
 222             }
 223         }
 224
 225         teller++;
 226     }
 227     while (read_next_x(oenv, status, &t, x, box));
 228     fprintf(stderr, "\n");
 229     close_trx(status);
 230
 231     if (bSep)
 232     {
 233         snew(buf, 256);
 234         for (i = 0; (i < ncg); i++)
 235         {
 236             for (j = i+1; (j < ncg); j++)
 237             {
 238                 if (nWithin[i][j])
 239                 {
 240                     sprintf(buf, "sb-%s:%s.xvg", cg[i].label, cg[j].label);
 241                     fp = xvgropen(buf, buf, "Time (ps)", "Distance (nm)", oenv);
 242                     for (k = 0; (k < teller); k++)
 243                     {
 244                         fprintf(fp, "%10g  %10g\n", time[k], cgdist[i][j][k]);
 245                     }
 246                     xvgrclose(fp);
 247                 }
 248             }
 249         }
 250         sfree(buf);
 251     }
 252     else
 253     {
 254
 255         for (m = 0; (m < 3); m++)
 256         {
 257             out[m] = xvgropen(fn[m], title[m], "Time (ps)", "Distance (nm)", oenv);
 258         }
 259
 260         snew(buf, 256);
 261         for (i = 0; (i < ncg); i++)
 262         {
 263             qi = cg[i].q;
 264             for (j = i+1; (j < ncg); j++)
 265             {
 266                 qj = cg[j].q;
 267                 if (nWithin[i][j])
 268                 {
 269                     sprintf(buf, "%s:%s", cg[i].label, cg[j].label);
 270                     if (qi*qj < 0)
 271                     {
 272                         nnn = 2;
 273                     }
 274                     else if (qi+qj > 0)
 275                     {
 276                         nnn = 0;
 277                     }
 278                     else
 279                     {
 280                         nnn = 1;
 281                     }
 282
 283                     if (nset[nnn] == 0)
 284                     {
 285                         xvgr_legend(out[nnn], 1, &buf, oenv);
 286                     }
 287                     else
 288                     {
 289                         if (output_env_get_xvg_format(oenv) == exvgXMGR)
 290                         {
 291                             fprintf(out[nnn], "@ legend string %d \"%s\"\n", nset[nnn], buf);
 292                         }
 293                         else if (output_env_get_xvg_format(oenv) == exvgXMGRACE)
 294                         {
 295                             fprintf(out[nnn], "@ s%d legend \"%s\"\n", nset[nnn], buf);
 296                         }
 297                     }
 298                     nset[nnn]++;
 299                     nWithin[i][j] = nnn+1;
 300                 }
 301             }
 302         }
 303         for (k = 0; (k < teller); k++)
 304         {
 305             for (m = 0; (m < 3); m++)
 306             {
 307                 fprintf(out[m], "%10g", time[k]);
 308             }
 309
 310             for (i = 0; (i < ncg); i++)
 311             {
 312                 for (j = i+1; (j < ncg); j++)
 313                 {
 314                     nnn = nWithin[i][j];
 315                     if (nnn > 0)
 316                     {
 317                         fprintf(out[nnn-1], "  %10g", cgdist[i][j][k]);
 318                     }
 319                 }
 320             }
 321             for (m = 0; (m < 3); m++)
 322             {
 323                 fprintf(out[m], "\n");
 324             }
 325         }
 326         for (m = 0; (m < 3); m++)
 327         {
 328             xvgrclose(out[m]);
 329             if (nset[m] == 0)
 330             {
 331                 remove(fn[m]);
 332             }
 333         }
 334     }
 335
 336     return 0;
 337 }