src/gromacs/gmxana/gmx_principal.cpp

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