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42 #include "gromacs/commandline/pargs.h"
43 #include "gromacs/legacyheaders/typedefs.h"
44 #include "gromacs/utility/smalloc.h"
45 #include "gromacs/legacyheaders/macros.h"
46 #include "gromacs/math/vec.h"
47 #include "gromacs/utility/futil.h"
48 #include "gromacs/topology/index.h"
49 #include "gromacs/fileio/xvgr.h"
50 #include "gromacs/legacyheaders/viewit.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"
59 #include "gromacs/utility/fatalerror.h"
61 real calc_gyro(rvec x[], int gnx, atom_id index[], t_atom atom[], real tm,
62 rvec gvec, rvec d, gmx_bool bQ, gmx_bool bRot, gmx_bool bMOI, matrix trans)
65 real gyro, dx2, m0, Itot;
70 principal_comp(gnx, index, atom, x, trans, d);
76 for (m = 0; (m < DIM); m++)
81 pr_rvecs(stderr, 0, "trans", trans, DIM);
83 /* rotate_atoms(gnx,index,x,trans); */
86 for (i = 0; (i < gnx); i++)
91 m0 = fabs(atom[ii].q);
97 for (m = 0; (m < DIM); m++)
99 dx2 = x[ii][m]*x[ii][m];
103 gyro = comp[XX]+comp[YY]+comp[ZZ];
105 for (m = 0; (m < DIM); m++)
107 gvec[m] = sqrt((gyro-comp[m])/tm);
110 return sqrt(gyro/tm);
113 void calc_gyro_z(rvec x[], matrix box,
114 int gnx, atom_id index[], t_atom atom[],
115 int nz, real time, FILE *out)
117 static dvec *inertia = NULL;
118 static double *tm = NULL;
120 real zf, w, sdet, e1, e2;
128 for (i = 0; i < nz; i++)
130 clear_dvec(inertia[i]);
134 for (i = 0; (i < gnx); i++)
137 zf = nz*x[ii][ZZ]/box[ZZ][ZZ];
146 for (j = 0; j < 2; j++)
153 w = atom[ii].m*(1 + cos(M_PI*(zf - zi)));
154 inertia[zi][0] += w*sqr(x[ii][YY]);
155 inertia[zi][1] += w*sqr(x[ii][XX]);
156 inertia[zi][2] -= w*x[ii][XX]*x[ii][YY];
160 fprintf(out, "%10g", time);
161 for (j = 0; j < nz; j++)
163 for (i = 0; i < 3; i++)
165 inertia[j][i] /= tm[j];
167 sdet = sqrt(sqr(inertia[j][0] - inertia[j][1]) + 4*sqr(inertia[j][2]));
168 e1 = sqrt(0.5*(inertia[j][0] + inertia[j][1] + sdet));
169 e2 = sqrt(0.5*(inertia[j][0] + inertia[j][1] - sdet));
170 fprintf(out, " %5.3f %5.3f", e1, e2);
175 int gmx_gyrate(int argc, char *argv[])
177 const char *desc[] = {
178 "[THISMODULE] computes the radius of gyration of a molecule",
179 "and the radii of gyration about the [IT]x[it]-, [IT]y[it]- and [IT]z[it]-axes,",
180 "as a function of time. The atoms are explicitly mass weighted.[PAR]",
181 "With the [TT]-nmol[tt] option the radius of gyration will be calculated",
182 "for multiple molecules by splitting the analysis group in equally",
184 "With the option [TT]-nz[tt] 2D radii of gyration in the [IT]x-y[it] plane",
185 "of slices along the [IT]z[it]-axis are calculated."
187 static int nmol = 1, nz = 0;
188 static gmx_bool bQ = FALSE, bRot = FALSE, bMOI = FALSE;
190 { "-nmol", FALSE, etINT, {&nmol},
191 "The number of molecules to analyze" },
192 { "-q", FALSE, etBOOL, {&bQ},
193 "Use absolute value of the charge of an atom as weighting factor instead of mass" },
194 { "-p", FALSE, etBOOL, {&bRot},
195 "Calculate the radii of gyration about the principal axes." },
196 { "-moi", FALSE, etBOOL, {&bMOI},
197 "Calculate the moments of inertia (defined by the principal axes)." },
198 { "-nz", FALSE, etINT, {&nz},
199 "Calculate the 2D radii of gyration of this number of slices along the z-axis" },
206 rvec xcm, gvec, gvec1;
209 real **moi_trans = NULL;
210 int max_moi = 0, delta_moi = 100;
211 rvec d, d1; /* eigenvalues of inertia tensor */
212 real t, t0, tm, gyro;
214 char *grpname, title[256];
215 int i, j, m, gnx, nam, mol;
218 gmx_rmpbc_t gpbc = NULL;
219 const char *leg[] = { "Rg", "RgX", "RgY", "RgZ" };
220 const char *legI[] = { "Itot", "I1", "I2", "I3" };
221 #define NLEG asize(leg)
223 { efTRX, "-f", NULL, ffREAD },
224 { efTPS, NULL, NULL, ffREAD },
225 { efNDX, NULL, NULL, ffOPTRD },
226 { efXVG, NULL, "gyrate", ffWRITE },
227 { efXVG, "-acf", "moi-acf", ffOPTWR },
229 #define NFILE asize(fnm)
234 ppa = add_acf_pargs(&npargs, pa);
236 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
237 NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
241 bACF = opt2bSet("-acf", NFILE, fnm);
242 if (bACF && nmol != 1)
244 gmx_fatal(FARGS, "Can only do acf with nmol=1");
246 bRot = bRot || bMOI || bACF;
253 printf("Will rotate system along principal axes\n");
254 snew(moi_trans, DIM);
258 printf("Will print moments of inertia\n");
263 printf("Will print radius normalised by charge\n");
266 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x, NULL, box, TRUE);
267 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
269 if (nmol > gnx || gnx % nmol != 0)
271 gmx_fatal(FARGS, "The number of atoms in the group (%d) is not a multiple of nmol (%d)", gnx, nmol);
275 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
282 out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
283 "Radius of Charge", "Time (ps)", "Rg (nm)", oenv);
287 out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
288 "Moments of inertia", "Time (ps)", "I (a.m.u. nm\\S2\\N)", oenv);
292 out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
293 "Radius of gyration", "Time (ps)", "Rg (nm)", oenv);
297 xvgr_legend(out, NLEG, legI, oenv);
303 if (output_env_get_print_xvgr_codes(oenv))
305 fprintf(out, "@ subtitle \"Axes are principal component axes\"\n");
308 xvgr_legend(out, NLEG, leg, oenv);
312 gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
318 gmx_rmpbc_copy(gpbc, natoms, box, x, x_s);
323 for (mol = 0; mol < nmol; mol++)
325 tm = sub_xcm(nz == 0 ? x_s : x, nam, index+mol*nam, top.atoms.atom, xcm, bQ);
328 gyro += calc_gyro(x_s, nam, index+mol*nam, top.atoms.atom,
329 tm, gvec1, d1, bQ, bRot, bMOI, trans);
333 calc_gyro_z(x, box, nam, index+mol*nam, top.atoms.atom, nz, t, out);
335 rvec_inc(gvec, gvec1);
341 svmul(1.0/nmol, gvec, gvec);
342 svmul(1.0/nmol, d, d);
351 max_moi += delta_moi;
352 for (m = 0; (m < DIM); m++)
354 srenew(moi_trans[m], max_moi*DIM);
357 for (m = 0; (m < DIM); m++)
359 copy_rvec(trans[m], moi_trans[m]+DIM*j);
361 fprintf(out, "%10g %10g %10g %10g %10g\n",
362 t, gyro, d[XX], d[YY], d[ZZ]);
366 fprintf(out, "%10g %10g %10g %10g %10g\n",
367 t, gyro, gvec[XX], gvec[YY], gvec[ZZ]);
372 while (read_next_x(oenv, status, &t, x, box));
376 gmx_rmpbc_done(gpbc);
383 int mode = eacVector;
385 do_autocorr(opt2fn("-acf", NFILE, fnm), oenv,
386 "Moment of inertia vector ACF",
387 j, 3, moi_trans, (t-t0)/j, mode, FALSE);
388 do_view(oenv, opt2fn("-acf", NFILE, fnm), "-nxy");
391 do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");