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45 #include "gromacs/fileio/futil.h"
49 #include "gmx_fatal.h"
54 #include "gromacs/fileio/trxio.h"
57 int gmx_rotacf(int argc, char *argv[])
59 const char *desc[] = {
60 "[THISMODULE] calculates the rotational correlation function",
61 "for molecules. Atom triplets (i,j,k) must be given in the index",
62 "file, defining two vectors ij and jk. The rotational ACF",
63 "is calculated as the autocorrelation function of the vector",
64 "n = ij x jk, i.e. the cross product of the two vectors.",
65 "Since three atoms span a plane, the order of the three atoms",
66 "does not matter. Optionally, by invoking the [TT]-d[tt] switch, you can",
67 "calculate the rotational correlation function for linear molecules",
68 "by specifying atom pairs (i,j) in the index file.",
71 "[TT]gmx rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1",
72 "-fa expfit-x-P1 -beginfit 2.5 -endfit 20.0[tt][PAR]",
73 "This will calculate the rotational correlation function using a first",
74 "order Legendre polynomial of the angle of a vector defined by the index",
75 "file. The correlation function will be fitted from 2.5 ps until 20.0 ps",
76 "to a two-parameter exponential."
78 static gmx_bool bVec = FALSE, bAver = TRUE;
81 { "-d", FALSE, etBOOL, {&bVec},
82 "Use index doublets (vectors) for correlation function instead of triplets (planes)" },
83 { "-aver", FALSE, etBOOL, {&bAver},
84 "Average over molecules" }
95 int i, m, teller, n_alloc, natoms, nvec, ai, aj, ak;
98 gmx_rmpbc_t gpbc = NULL;
102 { efTRX, "-f", NULL, ffREAD },
103 { efTPX, NULL, NULL, ffREAD },
104 { efNDX, NULL, NULL, ffREAD },
105 { efXVG, "-o", "rotacf", ffWRITE }
107 #define NFILE asize(fnm)
114 ppa = add_acf_pargs(&npargs, pa);
116 if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
117 NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
122 rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
133 if (((isize % 3) != 0) && !bVec)
135 gmx_fatal(FARGS, "number of index elements not multiple of 3, "
136 "these can not be atom triplets\n");
138 if (((isize % 2) != 0) && bVec)
140 gmx_fatal(FARGS, "number of index elements not multiple of 2, "
141 "these can not be atom doublets\n");
144 top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
147 for (i = 0; (i < nvec); i++)
153 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
156 gpbc = gmx_rmpbc_init(&(top->idef), ePBC, natoms);
158 /* Start the loop over frames */
163 if (teller >= n_alloc)
166 for (i = 0; (i < nvec); i++)
168 srenew(c1[i], DIM*n_alloc);
173 /* Remove periodicity */
174 gmx_rmpbc_copy(gpbc, natoms, box, x, x_s);
176 /* Compute crossproducts for all vectors, if triplets.
177 * else, just get the vectors in case of doublets.
181 for (i = 0; (i < nvec); i++)
186 rvec_sub(x_s[ai], x_s[aj], xij);
187 rvec_sub(x_s[aj], x_s[ak], xjk);
189 for (m = 0; (m < DIM); m++)
191 c1[i][DIM*teller+m] = n[m];
197 for (i = 0; (i < nvec); i++)
201 rvec_sub(x_s[ai], x_s[aj], n);
202 for (m = 0; (m < DIM); m++)
204 c1[i][DIM*teller+m] = n[m];
208 /* Increment loop counter */
211 while (read_next_x(oenv, status, &t, x, box));
213 fprintf(stderr, "\nDone with trajectory\n");
215 gmx_rmpbc_done(gpbc);
218 /* Autocorrelation function */
221 fprintf(stderr, "Not enough frames for correlation function\n");
225 dt = (t1 - t0)/(teller-1);
229 do_autocorr(ftp2fn(efXVG, NFILE, fnm), oenv, "Rotational Correlation Function",
230 teller, nvec, c1, dt, mode, bAver);
233 do_view(oenv, ftp2fn(efXVG, NFILE, fnm), NULL);