2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
39 #include "gromacs/math/utilities.h"
41 #include "gromacs/utility/smalloc.h"
42 #include "gromacs/fileio/confio.h"
43 #include "gromacs/commandline/pargs.h"
45 #include "gromacs/random/random.h"
46 #include "gromacs/math/3dview.h"
50 #include "sortwater.h"
51 #include "gromacs/fileio/trxio.h"
53 #include "gromacs/utility/fatalerror.h"
55 static void rand_rot(int natoms, rvec x[], rvec v[], vec4 xrot[], vec4 vrot[],
56 gmx_rng_t rng, rvec max_rot)
58 mat4 mt1, mt2, mr[DIM], mtemp1, mtemp2, mtemp3, mxtot, mvtot;
64 for (i = 0; (i < natoms); i++)
66 for (m = 0; (m < DIM); m++)
68 xcm[m] += x[i][m]/natoms; /* get center of mass of one molecule */
71 fprintf(stderr, "center of geometry: %f, %f, %f\n", xcm[0], xcm[1], xcm[2]);
73 translate(-xcm[XX], -xcm[YY], -xcm[ZZ], mt1); /* move c.o.ma to origin */
74 for (m = 0; (m < DIM); m++)
76 phi = M_PI*max_rot[m]*(2*gmx_rng_uniform_real(rng) - 1)/180;
77 rotate(m, phi, mr[m]);
79 translate(xcm[XX], xcm[YY], xcm[ZZ], mt2);
81 /* For mult_matrix we need to multiply in the opposite order
82 * compared to normal mathematical notation.
84 mult_matrix(mtemp1, mt1, mr[XX]);
85 mult_matrix(mtemp2, mr[YY], mr[ZZ]);
86 mult_matrix(mtemp3, mtemp1, mtemp2);
87 mult_matrix(mxtot, mtemp3, mt2);
88 mult_matrix(mvtot, mr[XX], mtemp2);
90 for (i = 0; (i < natoms); i++)
92 m4_op(mxtot, x[i], xrot[i]);
93 m4_op(mvtot, v[i], vrot[i]);
97 static void move_x(int natoms, rvec x[], matrix box)
103 for (i = 0; (i < natoms); i++)
105 for (m = 0; (m < DIM); m++)
110 for (m = 0; (m < DIM); m++)
112 xcm[m] = 0.5*box[m][m]-xcm[m]/natoms;
114 for (i = 0; (i < natoms); i++)
116 for (m = 0; (m < DIM); m++)
123 int gmx_genconf(int argc, char *argv[])
125 const char *desc[] = {
126 "[THISMODULE] multiplies a given coordinate file by simply stacking them",
127 "on top of each other, like a small child playing with wooden blocks.",
128 "The program makes a grid of [IT]user-defined[it]",
129 "proportions ([TT]-nbox[tt]), ",
130 "and interspaces the grid point with an extra space [TT]-dist[tt].[PAR]",
131 "When option [TT]-rot[tt] is used the program does not check for overlap",
132 "between molecules on grid points. It is recommended to make the box in",
133 "the input file at least as big as the coordinates + ",
134 "van der Waals radius.[PAR]",
135 "If the optional trajectory file is given, conformations are not",
136 "generated, but read from this file and translated appropriately to",
140 const char *bugs[] = {
141 "The program should allow for random displacement of lattice points."
145 t_atoms *atoms; /* list with all atoms */
147 rvec *x, *xx, *v; /* coordinates? */
151 matrix box, boxx; /* box length matrix */
153 int natoms; /* number of atoms in one molecule */
154 int nres; /* number of molecules? */
155 int i, j, k, l, m, ndx, nrdx, nx, ny, nz;
162 { efSTX, "-f", "conf", ffREAD },
163 { efSTO, "-o", "out", ffWRITE },
164 { efTRX, "-trj", NULL, ffOPTRD }
166 #define NFILE asize(fnm)
167 static rvec nrbox = {1, 1, 1};
168 static int seed = 0; /* seed for random number generator */
169 static int nmolat = 3;
170 static int nblock = 1;
171 static gmx_bool bShuffle = FALSE;
172 static gmx_bool bSort = FALSE;
173 static gmx_bool bRandom = FALSE; /* False: no random rotations */
174 static gmx_bool bRenum = TRUE; /* renumber residues */
175 static rvec dist = {0, 0, 0}; /* space added between molecules ? */
176 static rvec max_rot = {180, 180, 180}; /* maximum rotation */
178 { "-nbox", FALSE, etRVEC, {nrbox}, "Number of boxes" },
179 { "-dist", FALSE, etRVEC, {dist}, "Distance between boxes" },
180 { "-seed", FALSE, etINT, {&seed},
181 "Random generator seed, if 0 generated from the time" },
182 { "-rot", FALSE, etBOOL, {&bRandom}, "Randomly rotate conformations" },
183 { "-shuffle", FALSE, etBOOL, {&bShuffle}, "Random shuffling of molecules" },
184 { "-sort", FALSE, etBOOL, {&bSort}, "Sort molecules on X coord" },
185 { "-block", FALSE, etINT, {&nblock},
186 "Divide the box in blocks on this number of cpus" },
187 { "-nmolat", FALSE, etINT, {&nmolat},
188 "Number of atoms per molecule, assumed to start from 0. "
189 "If you set this wrong, it will screw up your system!" },
190 { "-maxrot", FALSE, etRVEC, {max_rot}, "Maximum random rotation" },
191 { "-renumber", FALSE, etBOOL, {&bRenum}, "Renumber residues" }
194 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
195 asize(desc), desc, asize(bugs), bugs, &oenv))
202 rng = gmx_rng_init(gmx_rng_make_seed());
206 rng = gmx_rng_init(seed);
209 bTRX = ftp2bSet(efTRX, NFILE, fnm);
210 nx = (int)(nrbox[XX]+0.5);
211 ny = (int)(nrbox[YY]+0.5);
212 nz = (int)(nrbox[ZZ]+0.5);
214 if ((nx <= 0) || (ny <= 0) || (nz <= 0))
216 gmx_fatal(FARGS, "Number of boxes (-nbox) should be larger than zero");
218 if ((nmolat <= 0) && bShuffle)
220 gmx_fatal(FARGS, "Can not shuffle if the molecules only have %d atoms",
224 vol = nx*ny*nz; /* calculate volume in grid points (= nr. molecules) */
226 get_stx_coordnum(opt2fn("-f", NFILE, fnm), &natoms);
228 /* make space for all the atoms */
229 init_t_atoms(atoms, natoms*vol, FALSE);
230 snew(x, natoms*vol); /* get space for coordinates of all atoms */
231 snew(xrot, natoms); /* get space for rotation matrix? */
232 snew(v, natoms*vol); /* velocities. not really needed? */
234 /* set atoms->nr to the number in one box *
235 * to avoid complaints in read_stx_conf *
238 read_stx_conf(opt2fn("-f", NFILE, fnm), title, atoms, x, v, &ePBC, box);
240 nres = atoms->nres; /* nr of residues in one element? */
244 if (!read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &xx, boxx))
246 gmx_fatal(FARGS, "No atoms in trajectory %s", ftp2fn(efTRX, NFILE, fnm));
252 for (i = 0; i < natoms; i++)
254 copy_rvec(x[i], xx[i]);
259 for (k = 0; (k < nz); k++) /* loop over all gridpositions */
261 shift[ZZ] = k*(dist[ZZ]+box[ZZ][ZZ]);
263 for (j = 0; (j < ny); j++)
265 shift[YY] = j*(dist[YY]+box[YY][YY])+k*box[ZZ][YY];
267 for (i = 0; (i < nx); i++)
269 shift[XX] = i*(dist[XX]+box[XX][XX])+j*box[YY][XX]+k*box[ZZ][XX];
271 ndx = (i*ny*nz+j*nz+k)*natoms;
272 nrdx = (i*ny*nz+j*nz+k)*nres;
274 /* Random rotation on input coords */
277 rand_rot(natoms, xx, v, xrot, vrot, rng, max_rot);
280 for (l = 0; (l < natoms); l++)
282 for (m = 0; (m < DIM); m++)
286 x[ndx+l][m] = xrot[l][m];
287 v[ndx+l][m] = vrot[l][m];
291 x[ndx+l][m] = xx[l][m];
292 v[ndx+l][m] = v[l][m];
295 if (ePBC == epbcSCREW && i % 2 == 1)
297 /* Rotate around x axis */
298 for (m = YY; m <= ZZ; m++)
300 x[ndx+l][m] = box[YY][m] + box[ZZ][m] - x[ndx+l][m];
301 v[ndx+l][m] = -v[ndx+l][m];
304 for (m = 0; (m < DIM); m++)
306 x[ndx+l][m] += shift[m];
308 atoms->atom[ndx+l].resind = nrdx + atoms->atom[l].resind;
309 atoms->atomname[ndx+l] = atoms->atomname[l];
312 for (l = 0; (l < nres); l++)
314 atoms->resinfo[nrdx+l] = atoms->resinfo[l];
317 atoms->resinfo[nrdx+l].nr += nrdx;
322 if (!read_next_x(oenv, status, &t, xx, boxx) &&
323 ((i+1)*(j+1)*(k+1) < vol))
325 gmx_fatal(FARGS, "Not enough frames in trajectory");
336 /* make box bigger */
337 for (m = 0; (m < DIM); m++)
339 box[m][m] += dist[m];
341 svmul(nx, box[XX], box[XX]);
342 svmul(ny, box[YY], box[YY]);
343 svmul(nz, box[ZZ], box[ZZ]);
344 if (ePBC == epbcSCREW && nx % 2 == 0)
346 /* With an even number of boxes in x we can forgot about the screw */
350 /* move_x(natoms*vol,x,box); */ /* put atoms in box? */
355 /*depending on how you look at it, this is either a nasty hack or the way it should work*/
358 for (i = 0; i < atoms->nres; i++)
360 atoms->resinfo[i].nr = i+1;
367 randwater(0, atoms->nr/nmolat, nmolat, x, v, rng);
371 sortwater(0, atoms->nr/nmolat, nmolat, x, v);
373 else if (opt2parg_bSet("-block", asize(pa), pa))
375 mkcompact(0, atoms->nr/nmolat, nmolat, x, v, nblock, box);
377 gmx_rng_destroy(rng);
379 write_sto_conf(opt2fn("-o", NFILE, fnm), title, atoms, x, v, ePBC, box);