src/gromacs/gmxana/gmx_principal.c

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  37 #include "gmxpre.h"
  38
  39 #include "config.h"
  40
  41 #include <math.h>
  42 #include <string.h>
  43
  44 #include "gromacs/commandline/pargs.h"
  45 #include "gromacs/legacyheaders/typedefs.h"
  46 #include "gromacs/utility/smalloc.h"
  47 #include "gromacs/legacyheaders/macros.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/utility/futil.h"
  50 #include "gromacs/topology/index.h"
  51 #include "princ.h"
  52 #include "gromacs/pbcutil/rmpbc.h"
  53 #include "gromacs/legacyheaders/txtdump.h"
  54 #include "gromacs/fileio/tpxio.h"
  55 #include "gromacs/fileio/trxio.h"
  56 #include "gromacs/fileio/xvgr.h"
  57 #include "gstat.h"
  58 #include "gmx_ana.h"
  59
  60
  61 void
  62 calc_principal_axes(t_topology *   top,
  63                     rvec *         x,
  64                     atom_id *      index,
  65                     int            n,
  66                     matrix         axes,
  67                     rvec           inertia)
  68 {
  69     rvec   xcm;
  70
  71     sub_xcm(x, n, index, top->atoms.atom, xcm, FALSE);
  72     principal_comp(n, index, top->atoms.atom, x, axes, inertia);
  73 }
  74
  75 int gmx_principal(int argc, char *argv[])
  76 {
  77     const char     *desc[] = {
  78         "[THISMODULE] calculates the three principal axes of inertia for a group",
  79         "of atoms. NOTE: Old versions of Gromacs wrote the output data in a",
  80         "strange transposed way. As of Gromacs-5.0, the output file paxis1.dat",
  81         "contains the x/y/z components of the first (major) principal axis for",
  82         "each frame, and similarly for the middle and minor axes in paxis2.dat",
  83         "and paxis3.dat."
  84     };
  85     static gmx_bool foo = FALSE;
  86
  87     t_pargs         pa[] = {
  88         { "-foo",      FALSE, etBOOL, {&foo}, "Dummy option to avoid empty array" }
  89     };
  90     t_trxstatus    *status;
  91     t_topology      top;
  92     int             ePBC;
  93     real            t;
  94     rvec      *     x;
  95
  96     int             natoms;
  97     char           *grpname, title[256];
  98     int             i, j, m, gnx, nam, mol;
  99     atom_id        *index;
 100     rvec            a1, a2, a3, moi;
 101     FILE      *     axis1;
 102     FILE      *     axis2;
 103     FILE      *     axis3;
 104     FILE      *     fmoi;
 105     matrix          axes, box;
 106     output_env_t    oenv;
 107     gmx_rmpbc_t     gpbc = NULL;
 108     char **         legend;
 109
 110     t_filenm        fnm[] = {
 111         { efTRX, "-f",   NULL,       ffREAD },
 112         { efTPS, NULL,   NULL,       ffREAD },
 113         { efNDX, NULL,   NULL,       ffOPTRD },
 114         { efXVG, "-a1",  "paxis1",   ffWRITE },
 115         { efXVG, "-a2",  "paxis2",   ffWRITE },
 116         { efXVG, "-a3",  "paxis3",   ffWRITE },
 117         { efXVG, "-om",  "moi",      ffWRITE }
 118     };
 119 #define NFILE asize(fnm)
 120
 121     if (!parse_common_args(&argc, argv,
 122                            PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
 123                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
 124     {
 125         return 0;
 126     }
 127
 128     snew(legend, DIM);
 129     for (i = 0; i < DIM; i++)
 130     {
 131         snew(legend[i], STRLEN);
 132         sprintf(legend[i], "%c component", 'X'+i);
 133     }
 134
 135     axis1 = xvgropen(opt2fn("-a1", NFILE, fnm), "Principal axis 1 (major axis)",
 136                      output_env_get_xvgr_tlabel(oenv), "Component (nm)", oenv);
 137     xvgr_legend(axis1, DIM, (const char **)legend, oenv);
 138
 139     axis2 = xvgropen(opt2fn("-a2", NFILE, fnm), "Principal axis 2 (middle axis)",
 140                      output_env_get_xvgr_tlabel(oenv), "Component (nm)", oenv);
 141     xvgr_legend(axis2, DIM, (const char **)legend, oenv);
 142
 143     axis3 = xvgropen(opt2fn("-a3", NFILE, fnm), "Principal axis 3 (minor axis)",
 144                      output_env_get_xvgr_tlabel(oenv), "Component (nm)", oenv);
 145     xvgr_legend(axis3, DIM, (const char **)legend, oenv);
 146
 147     sprintf(legend[XX], "Axis 1 (major)");
 148     sprintf(legend[YY], "Axis 2 (middle)");
 149     sprintf(legend[ZZ], "Axis 3 (minor)");
 150
 151     fmoi  = xvgropen(opt2fn("-om", NFILE, fnm), "Moments of inertia around inertial axes",
 152                      output_env_get_xvgr_tlabel(oenv), "I (au nm\\S2\\N)", oenv);
 153     xvgr_legend(fmoi, DIM, (const char **)legend, oenv);
 154
 155     for (i = 0; i < DIM; i++)
 156     {
 157         sfree(legend[i]);
 158     }
 159     sfree(legend);
 160
 161     read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box, TRUE);
 162
 163     get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
 164
 165     natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
 166
 167     gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
 168
 169     do
 170     {
 171         gmx_rmpbc(gpbc, natoms, box, x);
 172
 173         calc_principal_axes(&top, x, index, gnx, axes, moi);
 174
 175         fprintf(axis1, "%15.10f     %15.10f  %15.10f  %15.10f\n", t, axes[XX][XX], axes[XX][YY], axes[XX][ZZ]);
 176         fprintf(axis2, "%15.10f     %15.10f  %15.10f  %15.10f\n", t, axes[YY][XX], axes[YY][YY], axes[YY][ZZ]);
 177         fprintf(axis3, "%15.10f     %15.10f  %15.10f  %15.10f\n", t, axes[ZZ][XX], axes[ZZ][YY], axes[ZZ][ZZ]);
 178         fprintf(fmoi,  "%15.10f     %15.10f  %15.10f  %15.10f\n", t, moi[XX], moi[YY], moi[ZZ]);
 179     }
 180     while (read_next_x(oenv, status, &t, x, box));
 181
 182     gmx_rmpbc_done(gpbc);
 183
 184     close_trj(status);
 185
 186     xvgrclose(axis1);
 187     xvgrclose(axis2);
 188     xvgrclose(axis3);
 189     xvgrclose(fmoi);
 190
 191     return 0;
 192 }