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44 #include "gromacs/commandline/pargs.h"
49 #include "gmx_fatal.h"
51 #include "gromacs/fileio/futil.h"
53 #include "gromacs/fileio/pdbio.h"
54 #include "gromacs/fileio/tpxio.h"
55 #include "gromacs/fileio/trxio.h"
63 int gmx_nmens(int argc, char *argv[])
65 const char *desc[] = {
66 "[THISMODULE] generates an ensemble around an average structure",
67 "in a subspace that is defined by a set of normal modes (eigenvectors).",
68 "The eigenvectors are assumed to be mass-weighted.",
69 "The position along each eigenvector is randomly taken from a Gaussian",
70 "distribution with variance kT/eigenvalue.[PAR]",
71 "By default the starting eigenvector is set to 7, since the first six",
72 "normal modes are the translational and rotational degrees of freedom."
74 static int nstruct = 100, first = 7, last = -1, seed = -1;
75 static real temp = 300.0;
77 { "-temp", FALSE, etREAL, {&temp},
78 "Temperature in Kelvin" },
79 { "-seed", FALSE, etINT, {&seed},
80 "Random seed, -1 generates a seed from time and pid" },
81 { "-num", FALSE, etINT, {&nstruct},
82 "Number of structures to generate" },
83 { "-first", FALSE, etINT, {&first},
84 "First eigenvector to use (-1 is select)" },
85 { "-last", FALSE, etINT, {&last},
86 "Last eigenvector to use (-1 is till the last)" }
95 rvec *xtop, *xref, *xav, *xout1, *xout2;
96 gmx_bool bDMR, bDMA, bFit;
97 int nvec, *eignr = NULL;
100 real *eigval, totmass, *invsqrtm, t, disp;
102 char *grpname, title[STRLEN];
103 const char *indexfile;
105 int nout, *iout, noutvec, *outvec;
107 real rfac, invfr, rhalf, jr;
112 const unsigned long im = 0xffff;
113 const unsigned long ia = 1093;
114 const unsigned long ic = 18257;
118 { efTRN, "-v", "eigenvec", ffREAD },
119 { efXVG, "-e", "eigenval", ffREAD },
120 { efTPS, NULL, NULL, ffREAD },
121 { efNDX, NULL, NULL, ffOPTRD },
122 { efTRO, "-o", "ensemble", ffWRITE }
124 #define NFILE asize(fnm)
126 if (!parse_common_args(&argc, argv, PCA_BE_NICE,
127 NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
132 indexfile = ftp2fn_null(efNDX, NFILE, fnm);
134 read_eigenvectors(opt2fn("-v", NFILE, fnm), &natoms, &bFit,
135 &xref, &bDMR, &xav, &bDMA, &nvec, &eignr, &eigvec, &eigval);
137 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &xtop, NULL, box, bDMA);
140 printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n", natoms);
141 get_index(atoms, indexfile, 1, &i, &index, &grpname);
144 gmx_fatal(FARGS, "you selected a group with %d elements instead of %d",
149 snew(invsqrtm, natoms);
152 for (i = 0; (i < natoms); i++)
154 invsqrtm[i] = gmx_invsqrt(atoms->atom[index[i]].m);
159 for (i = 0; (i < natoms); i++)
171 /* make an index from first to last */
174 for (i = 0; i < nout; i++)
181 printf("Select eigenvectors for output, end your selection with 0\n");
187 srenew(iout, nout+1);
188 if (1 != scanf("%d", &iout[nout]))
190 gmx_fatal(FARGS, "Error reading user input");
194 while (iout[nout] >= 0);
198 /* make an index of the eigenvectors which are present */
201 for (i = 0; i < nout; i++)
204 while ((j < nvec) && (eignr[j] != iout[i]))
208 if ((j < nvec) && (eignr[j] == iout[i]))
211 iout[noutvec] = iout[i];
216 fprintf(stderr, "%d eigenvectors selected for output\n", noutvec);
222 fprintf(stderr, "Using seed %d and a temperature of %g K\n", seed, temp);
225 snew(xout2, atoms->nr);
226 out = open_trx(ftp2fn(efTRO, NFILE, fnm), "w");
227 jran = (unsigned long)((real)im*rando(&seed));
228 for (s = 0; s < nstruct; s++)
230 for (i = 0; i < natoms; i++)
232 copy_rvec(xav[i], xout1[i]);
234 for (j = 0; j < noutvec; j++)
237 /* (r-0.5) n times: var_n = n * var_1 = n/12
238 n=4: var_n = 1/3, so multiply with 3 */
240 rfac = sqrt(3.0 * BOLTZ*temp/eigval[iout[j]]);
242 rfac = rfac/(real)im;
244 jran = (jran*ia+ic) & im;
246 jran = (jran*ia+ic) & im;
248 jran = (jran*ia+ic) & im;
250 jran = (jran*ia+ic) & im;
252 disp = rfac * jr - rhalf;
254 for (i = 0; i < natoms; i++)
256 for (d = 0; d < DIM; d++)
258 xout1[i][d] += disp*eigvec[v][i][d]*invsqrtm[i];
262 for (i = 0; i < natoms; i++)
264 copy_rvec(xout1[i], xout2[index[i]]);
267 write_trx(out, natoms, index, atoms, 0, t, box, xout2, NULL, NULL);
268 fprintf(stderr, "\rGenerated %d structures", s+1);
270 fprintf(stderr, "\n");