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41 #include "gromacs/math/utilities.h"
42 #include "gromacs/legacyheaders/macros.h"
43 #include "gromacs/fileio/confio.h"
44 #include "gromacs/legacyheaders/txtdump.h"
45 #include "gromacs/legacyheaders/readinp.h"
46 #include "gromacs/legacyheaders/names.h"
47 #include "sortwater.h"
48 #include "gromacs/fileio/trxio.h"
50 #include "gromacs/commandline/pargs.h"
51 #include "gromacs/math/3dtransforms.h"
52 #include "gromacs/math/vec.h"
53 #include "gromacs/random/random.h"
54 #include "gromacs/utility/fatalerror.h"
55 #include "gromacs/utility/smalloc.h"
57 static void rand_rot(int natoms, rvec x[], rvec v[], vec4 xrot[], vec4 vrot[],
58 gmx_rng_t rng, rvec max_rot)
60 mat4 mt1, mt2, mr[DIM], mtemp1, mtemp2, mtemp3, mxtot, mvtot;
66 for (i = 0; (i < natoms); i++)
68 for (m = 0; (m < DIM); m++)
70 xcm[m] += x[i][m]/natoms; /* get center of mass of one molecule */
73 fprintf(stderr, "center of geometry: %f, %f, %f\n", xcm[0], xcm[1], xcm[2]);
75 /* move c.o.ma to origin */
76 gmx_mat4_init_translation(-xcm[XX], -xcm[YY], -xcm[ZZ], mt1);
77 for (m = 0; (m < DIM); m++)
79 phi = M_PI*max_rot[m]*(2*gmx_rng_uniform_real(rng) - 1)/180;
80 gmx_mat4_init_rotation(m, phi, mr[m]);
82 gmx_mat4_init_translation(xcm[XX], xcm[YY], xcm[ZZ], mt2);
84 /* For gmx_mat4_mmul() we need to multiply in the opposite order
85 * compared to normal mathematical notation.
87 gmx_mat4_mmul(mtemp1, mt1, mr[XX]);
88 gmx_mat4_mmul(mtemp2, mr[YY], mr[ZZ]);
89 gmx_mat4_mmul(mtemp3, mtemp1, mtemp2);
90 gmx_mat4_mmul(mxtot, mtemp3, mt2);
91 gmx_mat4_mmul(mvtot, mr[XX], mtemp2);
93 for (i = 0; (i < natoms); i++)
95 gmx_mat4_transform_point(mxtot, x[i], xrot[i]);
96 gmx_mat4_transform_point(mvtot, v[i], vrot[i]);
100 static void move_x(int natoms, rvec x[], matrix box)
106 for (i = 0; (i < natoms); i++)
108 for (m = 0; (m < DIM); m++)
113 for (m = 0; (m < DIM); m++)
115 xcm[m] = 0.5*box[m][m]-xcm[m]/natoms;
117 for (i = 0; (i < natoms); i++)
119 for (m = 0; (m < DIM); m++)
126 int gmx_genconf(int argc, char *argv[])
128 const char *desc[] = {
129 "[THISMODULE] multiplies a given coordinate file by simply stacking them",
130 "on top of each other, like a small child playing with wooden blocks.",
131 "The program makes a grid of [IT]user-defined[it]",
132 "proportions ([TT]-nbox[tt]), ",
133 "and interspaces the grid point with an extra space [TT]-dist[tt].[PAR]",
134 "When option [TT]-rot[tt] is used the program does not check for overlap",
135 "between molecules on grid points. It is recommended to make the box in",
136 "the input file at least as big as the coordinates + ",
137 "van der Waals radius.[PAR]",
138 "If the optional trajectory file is given, conformations are not",
139 "generated, but read from this file and translated appropriately to",
143 const char *bugs[] = {
144 "The program should allow for random displacement of lattice points."
148 t_atoms *atoms; /* list with all atoms */
150 rvec *x, *xx, *v; /* coordinates? */
154 matrix box, boxx; /* box length matrix */
156 int natoms; /* number of atoms in one molecule */
157 int nres; /* number of molecules? */
158 int i, j, k, l, m, ndx, nrdx, nx, ny, nz;
165 { efSTX, "-f", "conf", ffREAD },
166 { efSTO, "-o", "out", ffWRITE },
167 { efTRX, "-trj", NULL, ffOPTRD }
169 #define NFILE asize(fnm)
170 static rvec nrbox = {1, 1, 1};
171 static int seed = 0; /* seed for random number generator */
172 static int nmolat = 3;
173 static int nblock = 1;
174 static gmx_bool bShuffle = FALSE;
175 static gmx_bool bSort = FALSE;
176 static gmx_bool bRandom = FALSE; /* False: no random rotations */
177 static gmx_bool bRenum = TRUE; /* renumber residues */
178 static rvec dist = {0, 0, 0}; /* space added between molecules ? */
179 static rvec max_rot = {180, 180, 180}; /* maximum rotation */
181 { "-nbox", FALSE, etRVEC, {nrbox}, "Number of boxes" },
182 { "-dist", FALSE, etRVEC, {dist}, "Distance between boxes" },
183 { "-seed", FALSE, etINT, {&seed},
184 "Random generator seed, if 0 generated from the time" },
185 { "-rot", FALSE, etBOOL, {&bRandom}, "Randomly rotate conformations" },
186 { "-shuffle", FALSE, etBOOL, {&bShuffle}, "Random shuffling of molecules" },
187 { "-sort", FALSE, etBOOL, {&bSort}, "Sort molecules on X coord" },
188 { "-block", FALSE, etINT, {&nblock},
189 "Divide the box in blocks on this number of cpus" },
190 { "-nmolat", FALSE, etINT, {&nmolat},
191 "Number of atoms per molecule, assumed to start from 0. "
192 "If you set this wrong, it will screw up your system!" },
193 { "-maxrot", FALSE, etRVEC, {max_rot}, "Maximum random rotation" },
194 { "-renumber", FALSE, etBOOL, {&bRenum}, "Renumber residues" }
197 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
198 asize(desc), desc, asize(bugs), bugs, &oenv))
205 rng = gmx_rng_init(gmx_rng_make_seed());
209 rng = gmx_rng_init(seed);
212 bTRX = ftp2bSet(efTRX, NFILE, fnm);
213 nx = (int)(nrbox[XX]+0.5);
214 ny = (int)(nrbox[YY]+0.5);
215 nz = (int)(nrbox[ZZ]+0.5);
217 if ((nx <= 0) || (ny <= 0) || (nz <= 0))
219 gmx_fatal(FARGS, "Number of boxes (-nbox) should be larger than zero");
221 if ((nmolat <= 0) && bShuffle)
223 gmx_fatal(FARGS, "Can not shuffle if the molecules only have %d atoms",
227 vol = nx*ny*nz; /* calculate volume in grid points (= nr. molecules) */
229 get_stx_coordnum(opt2fn("-f", NFILE, fnm), &natoms);
231 /* make space for all the atoms */
232 init_t_atoms(atoms, natoms*vol, FALSE);
233 snew(x, natoms*vol); /* get space for coordinates of all atoms */
234 snew(xrot, natoms); /* get space for rotation matrix? */
235 snew(v, natoms*vol); /* velocities. not really needed? */
237 /* set atoms->nr to the number in one box *
238 * to avoid complaints in read_stx_conf *
241 read_stx_conf(opt2fn("-f", NFILE, fnm), title, atoms, x, v, &ePBC, box);
243 nres = atoms->nres; /* nr of residues in one element? */
247 if (!read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &xx, boxx))
249 gmx_fatal(FARGS, "No atoms in trajectory %s", ftp2fn(efTRX, NFILE, fnm));
255 for (i = 0; i < natoms; i++)
257 copy_rvec(x[i], xx[i]);
262 for (k = 0; (k < nz); k++) /* loop over all gridpositions */
264 shift[ZZ] = k*(dist[ZZ]+box[ZZ][ZZ]);
266 for (j = 0; (j < ny); j++)
268 shift[YY] = j*(dist[YY]+box[YY][YY])+k*box[ZZ][YY];
270 for (i = 0; (i < nx); i++)
272 shift[XX] = i*(dist[XX]+box[XX][XX])+j*box[YY][XX]+k*box[ZZ][XX];
274 ndx = (i*ny*nz+j*nz+k)*natoms;
275 nrdx = (i*ny*nz+j*nz+k)*nres;
277 /* Random rotation on input coords */
280 rand_rot(natoms, xx, v, xrot, vrot, rng, max_rot);
283 for (l = 0; (l < natoms); l++)
285 for (m = 0; (m < DIM); m++)
289 x[ndx+l][m] = xrot[l][m];
290 v[ndx+l][m] = vrot[l][m];
294 x[ndx+l][m] = xx[l][m];
295 v[ndx+l][m] = v[l][m];
298 if (ePBC == epbcSCREW && i % 2 == 1)
300 /* Rotate around x axis */
301 for (m = YY; m <= ZZ; m++)
303 x[ndx+l][m] = box[YY][m] + box[ZZ][m] - x[ndx+l][m];
304 v[ndx+l][m] = -v[ndx+l][m];
307 for (m = 0; (m < DIM); m++)
309 x[ndx+l][m] += shift[m];
311 atoms->atom[ndx+l].resind = nrdx + atoms->atom[l].resind;
312 atoms->atomname[ndx+l] = atoms->atomname[l];
315 for (l = 0; (l < nres); l++)
317 atoms->resinfo[nrdx+l] = atoms->resinfo[l];
320 atoms->resinfo[nrdx+l].nr += nrdx;
325 if (!read_next_x(oenv, status, &t, xx, boxx) &&
326 ((i+1)*(j+1)*(k+1) < vol))
328 gmx_fatal(FARGS, "Not enough frames in trajectory");
339 /* make box bigger */
340 for (m = 0; (m < DIM); m++)
342 box[m][m] += dist[m];
344 svmul(nx, box[XX], box[XX]);
345 svmul(ny, box[YY], box[YY]);
346 svmul(nz, box[ZZ], box[ZZ]);
347 if (ePBC == epbcSCREW && nx % 2 == 0)
349 /* With an even number of boxes in x we can forgot about the screw */
353 /* move_x(natoms*vol,x,box); */ /* put atoms in box? */
358 /*depending on how you look at it, this is either a nasty hack or the way it should work*/
361 for (i = 0; i < atoms->nres; i++)
363 atoms->resinfo[i].nr = i+1;
370 randwater(0, atoms->nr/nmolat, nmolat, x, v, rng);
374 sortwater(0, atoms->nr/nmolat, nmolat, x, v);
376 else if (opt2parg_bSet("-block", asize(pa), pa))
378 mkcompact(0, atoms->nr/nmolat, nmolat, x, v, nblock, box);
380 gmx_rng_destroy(rng);
382 write_sto_conf(opt2fn("-o", NFILE, fnm), title, atoms, x, v, ePBC, box);