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42 #include "gromacs/commandline/pargs.h"
43 #include "gromacs/fileio/confio.h"
44 #include "gromacs/fileio/pdbio.h"
45 #include "gromacs/fileio/trxio.h"
46 #include "gromacs/gmxana/eigio.h"
47 #include "gromacs/gmxana/gmx_ana.h"
48 #include "gromacs/math/functions.h"
49 #include "gromacs/math/units.h"
50 #include "gromacs/math/vec.h"
51 #include "gromacs/random/threefry.h"
52 #include "gromacs/random/uniformintdistribution.h"
53 #include "gromacs/topology/index.h"
54 #include "gromacs/topology/topology.h"
55 #include "gromacs/utility/arraysize.h"
56 #include "gromacs/utility/cstringutil.h"
57 #include "gromacs/utility/fatalerror.h"
58 #include "gromacs/utility/futil.h"
59 #include "gromacs/utility/smalloc.h"
62 int gmx_nmens(int argc, char* argv[])
64 const char* desc[] = {
65 "[THISMODULE] generates an ensemble around an average structure",
66 "in a subspace that is defined by a set of normal modes (eigenvectors).",
67 "The eigenvectors are assumed to be mass-weighted.",
68 "The position along each eigenvector is randomly taken from a Gaussian",
69 "distribution with variance kT/eigenvalue.[PAR]",
70 "By default the starting eigenvector is set to 7, since the first six",
71 "normal modes are the translational and rotational degrees of freedom."
73 static int nstruct = 100, first = 7, last = -1, seed = 0;
74 static real temp = 300.0;
76 { "-temp", FALSE, etREAL, { &temp }, "Temperature in Kelvin" },
77 { "-seed", FALSE, etINT, { &seed }, "Random seed (0 means generate)" },
78 { "-num", FALSE, etINT, { &nstruct }, "Number of structures to generate" },
79 { "-first", FALSE, etINT, { &first }, "First eigenvector to use (-1 is select)" },
80 { "-last", FALSE, etINT, { &last }, "Last eigenvector to use (-1 is till the last)" }
88 rvec * xtop, *xref, *xav, *xout1, *xout2;
89 gmx_bool bDMR, bDMA, bFit;
90 int nvec, *eignr = nullptr;
91 rvec** eigvec = nullptr;
93 real * eigval, *invsqrtm, t, disp;
96 const char* indexfile;
98 int nout, *iout, noutvec, *outvec;
100 real rfac, rhalf, jr;
101 gmx_output_env_t* oenv;
103 const unsigned long im = 0xffff;
104 const unsigned long ia = 1093;
105 const unsigned long ic = 18257;
108 t_filenm fnm[] = { { efTRN, "-v", "eigenvec", ffREAD },
109 { efXVG, "-e", "eigenval", ffREAD },
110 { efTPS, nullptr, nullptr, ffREAD },
111 { efNDX, nullptr, nullptr, ffOPTRD },
112 { efTRO, "-o", "ensemble", ffWRITE } };
113 #define NFILE asize(fnm)
115 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
120 indexfile = ftp2fn_null(efNDX, NFILE, fnm);
122 read_eigenvectors(opt2fn("-v", NFILE, fnm), &natoms, &bFit, &xref, &bDMR, &xav, &bDMA, &nvec,
123 &eignr, &eigvec, &eigval);
125 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, nullptr, box, bDMA);
128 printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n", natoms);
129 get_index(atoms, indexfile, 1, &i, &index, &grpname);
132 gmx_fatal(FARGS, "you selected a group with %d elements instead of %d", i, natoms);
136 snew(invsqrtm, natoms);
139 for (i = 0; (i < natoms); i++)
141 invsqrtm[i] = gmx::invsqrt(atoms->atom[index[i]].m);
146 for (i = 0; (i < natoms); i++)
158 /* make an index from first to last */
159 nout = last - first + 1;
161 for (i = 0; i < nout; i++)
163 iout[i] = first - 1 + i;
168 printf("Select eigenvectors for output, end your selection with 0\n");
174 srenew(iout, nout + 1);
175 if (1 != scanf("%d", &iout[nout]))
177 gmx_fatal(FARGS, "Error reading user input");
180 } while (iout[nout] >= 0);
184 /* make an index of the eigenvectors which are present */
187 for (i = 0; i < nout; i++)
190 while ((j < nvec) && (eignr[j] != iout[i]))
194 if ((j < nvec) && (eignr[j] == iout[i]))
197 iout[noutvec] = iout[i];
202 fprintf(stderr, "%d eigenvectors selected for output\n", noutvec);
207 // Make do with 32 bits for now to avoid changing user input to hex
208 seed = static_cast<int>(gmx::makeRandomSeed());
211 gmx::DefaultRandomEngine rng(seed);
213 fprintf(stderr, "Using random seed %d and a temperature of %g K.\n", seed, temp);
215 gmx::UniformIntDistribution<int> dist(0, im - 1);
219 snew(xout2, atoms->nr);
220 out = open_trx(ftp2fn(efTRO, NFILE, fnm), "w");
222 for (s = 0; s < nstruct; s++)
224 for (i = 0; i < natoms; i++)
226 copy_rvec(xav[i], xout1[i]);
228 for (j = 0; j < noutvec; j++)
231 /* (r-0.5) n times: var_n = n * var_1 = n/12
232 n=4: var_n = 1/3, so multiply with 3 */
234 rfac = std::sqrt(3.0 * BOLTZ * temp / eigval[iout[j]]);
238 jran = (jran * ia + ic) & im;
240 jran = (jran * ia + ic) & im;
242 jran = (jran * ia + ic) & im;
244 jran = (jran * ia + ic) & im;
246 disp = rfac * jr - rhalf;
248 for (i = 0; i < natoms; i++)
250 for (d = 0; d < DIM; d++)
252 xout1[i][d] += disp * eigvec[v][i][d] * invsqrtm[i];
256 for (i = 0; i < natoms; i++)
258 copy_rvec(xout1[i], xout2[index[i]]);
261 write_trx(out, natoms, index, atoms, 0, t, box, xout2, nullptr, nullptr);
262 fprintf(stderr, "\rGenerated %d structures", s + 1);
265 fprintf(stderr, "\n");