src/gromacs/gmxana/gmx_principal.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, 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 <cmath>
  40 #include <cstring>
  41
  42 #include "gromacs/commandline/pargs.h"
  43 #include "gromacs/fileio/confio.h"
  44 #include "gromacs/fileio/trxio.h"
  45 #include "gromacs/fileio/xvgr.h"
  46 #include "gromacs/gmxana/gmx_ana.h"
  47 #include "gromacs/gmxana/gstat.h"
  48 #include "gromacs/gmxana/princ.h"
  49 #include "gromacs/math/vec.h"
  50 #include "gromacs/pbcutil/rmpbc.h"
  51 #include "gromacs/topology/index.h"
  52 #include "gromacs/topology/topology.h"
  53 #include "gromacs/utility/arraysize.h"
  54 #include "gromacs/utility/cstringutil.h"
  55 #include "gromacs/utility/futil.h"
  56 #include "gromacs/utility/smalloc.h"
  57
  58
  59 void
  60 calc_principal_axes(const t_topology *top,
  61                     rvec             *x,
  62                     int              *index,
  63                     int               n,
  64                     matrix            axes,
  65                     rvec              inertia)
  66 {
  67     rvec   xcm;
  68
  69     sub_xcm(x, n, index, top->atoms.atom, xcm, FALSE);
  70     principal_comp(n, index, top->atoms.atom, x, axes, inertia);
  71 }
  72
  73 int gmx_principal(int argc, char *argv[])
  74 {
  75     const char       *desc[] = {
  76         "[THISMODULE] calculates the three principal axes of inertia for a group",
  77         "of atoms. NOTE: Old versions of GROMACS wrote the output data in a",
  78         "strange transposed way. As of GROMACS 5.0, the output file paxis1.dat",
  79         "contains the x/y/z components of the first (major) principal axis for",
  80         "each frame, and similarly for the middle and minor axes in paxis2.dat",
  81         "and paxis3.dat."
  82     };
  83     static gmx_bool   foo = FALSE;
  84
  85     t_pargs           pa[] = {
  86         { "-foo",      FALSE, etBOOL, {&foo}, "Dummy option to avoid empty array" }
  87     };
  88     t_trxstatus      *status;
  89     t_topology        top;
  90     int               ePBC;
  91     real              t;
  92     rvec        *     x;
  93
  94     int               natoms;
  95     char             *grpname;
  96     int               i, gnx;
  97     int              *index;
  98     rvec              moi;
  99     FILE        *     axis1;
 100     FILE        *     axis2;
 101     FILE        *     axis3;
 102     FILE        *     fmoi;
 103     matrix            axes, box;
 104     gmx_output_env_t *oenv;
 105     gmx_rmpbc_t       gpbc = nullptr;
 106     char   **         legend;
 107
 108     t_filenm          fnm[] = {
 109         { efTRX, "-f",   nullptr,       ffREAD },
 110         { efTPS, nullptr,   nullptr,       ffREAD },
 111         { efNDX, nullptr,   nullptr,       ffOPTRD },
 112         { efXVG, "-a1",  "paxis1",   ffWRITE },
 113         { efXVG, "-a2",  "paxis2",   ffWRITE },
 114         { efXVG, "-a3",  "paxis3",   ffWRITE },
 115         { efXVG, "-om",  "moi",      ffWRITE }
 116     };
 117 #define NFILE asize(fnm)
 118
 119     if (!parse_common_args(&argc, argv,
 120                            PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
 121                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
 122     {
 123         return 0;
 124     }
 125
 126     snew(legend, DIM);
 127     for (i = 0; i < DIM; i++)
 128     {
 129         snew(legend[i], STRLEN);
 130         sprintf(legend[i], "%c component", 'X'+i);
 131     }
 132
 133     axis1 = xvgropen(opt2fn("-a1", NFILE, fnm), "Principal axis 1 (major axis)",
 134                      output_env_get_xvgr_tlabel(oenv), "Component (nm)", oenv);
 135     xvgr_legend(axis1, DIM, (const char **)legend, oenv);
 136
 137     axis2 = xvgropen(opt2fn("-a2", NFILE, fnm), "Principal axis 2 (middle axis)",
 138                      output_env_get_xvgr_tlabel(oenv), "Component (nm)", oenv);
 139     xvgr_legend(axis2, DIM, (const char **)legend, oenv);
 140
 141     axis3 = xvgropen(opt2fn("-a3", NFILE, fnm), "Principal axis 3 (minor axis)",
 142                      output_env_get_xvgr_tlabel(oenv), "Component (nm)", oenv);
 143     xvgr_legend(axis3, DIM, (const char **)legend, oenv);
 144
 145     sprintf(legend[XX], "Axis 1 (major)");
 146     sprintf(legend[YY], "Axis 2 (middle)");
 147     sprintf(legend[ZZ], "Axis 3 (minor)");
 148
 149     fmoi  = xvgropen(opt2fn("-om", NFILE, fnm), "Moments of inertia around inertial axes",
 150                      output_env_get_xvgr_tlabel(oenv), "I (au nm\\S2\\N)", oenv);
 151     xvgr_legend(fmoi, DIM, (const char **)legend, oenv);
 152
 153     for (i = 0; i < DIM; i++)
 154     {
 155         sfree(legend[i]);
 156     }
 157     sfree(legend);
 158
 159     read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, nullptr, nullptr, box, TRUE);
 160
 161     get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
 162
 163     natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
 164
 165     gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
 166
 167     do
 168     {
 169         gmx_rmpbc(gpbc, natoms, box, x);
 170
 171         calc_principal_axes(&top, x, index, gnx, axes, moi);
 172
 173         fprintf(axis1, "%15.10f     %15.10f  %15.10f  %15.10f\n", t, axes[XX][XX], axes[XX][YY], axes[XX][ZZ]);
 174         fprintf(axis2, "%15.10f     %15.10f  %15.10f  %15.10f\n", t, axes[YY][XX], axes[YY][YY], axes[YY][ZZ]);
 175         fprintf(axis3, "%15.10f     %15.10f  %15.10f  %15.10f\n", t, axes[ZZ][XX], axes[ZZ][YY], axes[ZZ][ZZ]);
 176         fprintf(fmoi,  "%15.10f     %15.10f  %15.10f  %15.10f\n", t, moi[XX], moi[YY], moi[ZZ]);
 177     }
 178     while (read_next_x(oenv, status, &t, x, box));
 179
 180     gmx_rmpbc_done(gpbc);
 181
 182     close_trx(status);
 183
 184     xvgrclose(axis1);
 185     xvgrclose(axis2);
 186     xvgrclose(axis3);
 187     xvgrclose(fmoi);
 188
 189     return 0;
 190 }