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39 #include "gromacs/math/utilities.h"
40 #include "gromacs/legacyheaders/macros.h"
41 #include "gromacs/fileio/confio.h"
42 #include "gromacs/legacyheaders/txtdump.h"
43 #include "gromacs/legacyheaders/readinp.h"
44 #include "gromacs/legacyheaders/names.h"
45 #include "sortwater.h"
46 #include "gromacs/fileio/trxio.h"
48 #include "gromacs/commandline/pargs.h"
49 #include "gromacs/math/3dtransforms.h"
50 #include "gromacs/math/vec.h"
51 #include "gromacs/random/random.h"
52 #include "gromacs/utility/fatalerror.h"
53 #include "gromacs/utility/smalloc.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 /* move c.o.ma to origin */
74 gmx_mat4_init_translation(-xcm[XX], -xcm[YY], -xcm[ZZ], mt1);
75 for (m = 0; (m < DIM); m++)
77 phi = M_PI*max_rot[m]*(2*gmx_rng_uniform_real(rng) - 1)/180;
78 gmx_mat4_init_rotation(m, phi, mr[m]);
80 gmx_mat4_init_translation(xcm[XX], xcm[YY], xcm[ZZ], mt2);
82 /* For gmx_mat4_mmul() we need to multiply in the opposite order
83 * compared to normal mathematical notation.
85 gmx_mat4_mmul(mtemp1, mt1, mr[XX]);
86 gmx_mat4_mmul(mtemp2, mr[YY], mr[ZZ]);
87 gmx_mat4_mmul(mtemp3, mtemp1, mtemp2);
88 gmx_mat4_mmul(mxtot, mtemp3, mt2);
89 gmx_mat4_mmul(mvtot, mr[XX], mtemp2);
91 for (i = 0; (i < natoms); i++)
93 gmx_mat4_transform_point(mxtot, x[i], xrot[i]);
94 gmx_mat4_transform_point(mvtot, v[i], vrot[i]);
98 static void move_x(int natoms, rvec x[], matrix box)
104 for (i = 0; (i < natoms); i++)
106 for (m = 0; (m < DIM); m++)
111 for (m = 0; (m < DIM); m++)
113 xcm[m] = 0.5*box[m][m]-xcm[m]/natoms;
115 for (i = 0; (i < natoms); i++)
117 for (m = 0; (m < DIM); m++)
124 int gmx_genconf(int argc, char *argv[])
126 const char *desc[] = {
127 "[THISMODULE] multiplies a given coordinate file by simply stacking them",
128 "on top of each other, like a small child playing with wooden blocks.",
129 "The program makes a grid of [IT]user-defined[it]",
130 "proportions ([TT]-nbox[tt]), ",
131 "and interspaces the grid point with an extra space [TT]-dist[tt].[PAR]",
132 "When option [TT]-rot[tt] is used the program does not check for overlap",
133 "between molecules on grid points. It is recommended to make the box in",
134 "the input file at least as big as the coordinates + ",
135 "van der Waals radius.[PAR]",
136 "If the optional trajectory file is given, conformations are not",
137 "generated, but read from this file and translated appropriately to",
141 const char *bugs[] = {
142 "The program should allow for random displacement of lattice points."
146 t_atoms *atoms; /* list with all atoms */
148 rvec *x, *xx, *v; /* coordinates? */
152 matrix box, boxx; /* box length matrix */
154 int natoms; /* number of atoms in one molecule */
155 int nres; /* number of molecules? */
156 int i, j, k, l, m, ndx, nrdx, nx, ny, nz;
163 { efSTX, "-f", "conf", ffREAD },
164 { efSTO, "-o", "out", ffWRITE },
165 { efTRX, "-trj", NULL, ffOPTRD }
167 #define NFILE asize(fnm)
168 static rvec nrbox = {1, 1, 1};
169 static int seed = 0; /* seed for random number generator */
170 static int nmolat = 3;
171 static int nblock = 1;
172 static gmx_bool bShuffle = FALSE;
173 static gmx_bool bSort = FALSE;
174 static gmx_bool bRandom = FALSE; /* False: no random rotations */
175 static gmx_bool bRenum = TRUE; /* renumber residues */
176 static rvec dist = {0, 0, 0}; /* space added between molecules ? */
177 static rvec max_rot = {180, 180, 180}; /* maximum rotation */
179 { "-nbox", FALSE, etRVEC, {nrbox}, "Number of boxes" },
180 { "-dist", FALSE, etRVEC, {dist}, "Distance between boxes" },
181 { "-seed", FALSE, etINT, {&seed},
182 "Random generator seed, if 0 generated from the time" },
183 { "-rot", FALSE, etBOOL, {&bRandom}, "Randomly rotate conformations" },
184 { "-shuffle", FALSE, etBOOL, {&bShuffle}, "Random shuffling of molecules" },
185 { "-sort", FALSE, etBOOL, {&bSort}, "Sort molecules on X coord" },
186 { "-block", FALSE, etINT, {&nblock},
187 "Divide the box in blocks on this number of cpus" },
188 { "-nmolat", FALSE, etINT, {&nmolat},
189 "Number of atoms per molecule, assumed to start from 0. "
190 "If you set this wrong, it will screw up your system!" },
191 { "-maxrot", FALSE, etRVEC, {max_rot}, "Maximum random rotation" },
192 { "-renumber", FALSE, etBOOL, {&bRenum}, "Renumber residues" }
195 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
196 asize(desc), desc, asize(bugs), bugs, &oenv))
203 rng = gmx_rng_init(gmx_rng_make_seed());
207 rng = gmx_rng_init(seed);
210 bTRX = ftp2bSet(efTRX, NFILE, fnm);
211 nx = (int)(nrbox[XX]+0.5);
212 ny = (int)(nrbox[YY]+0.5);
213 nz = (int)(nrbox[ZZ]+0.5);
215 if ((nx <= 0) || (ny <= 0) || (nz <= 0))
217 gmx_fatal(FARGS, "Number of boxes (-nbox) should be larger than zero");
219 if ((nmolat <= 0) && bShuffle)
221 gmx_fatal(FARGS, "Can not shuffle if the molecules only have %d atoms",
225 vol = nx*ny*nz; /* calculate volume in grid points (= nr. molecules) */
227 get_stx_coordnum(opt2fn("-f", NFILE, fnm), &natoms);
229 /* make space for all the atoms */
230 init_t_atoms(atoms, natoms*vol, FALSE);
231 snew(x, natoms*vol); /* get space for coordinates of all atoms */
232 snew(xrot, natoms); /* get space for rotation matrix? */
233 snew(v, natoms*vol); /* velocities. not really needed? */
235 /* set atoms->nr to the number in one box *
236 * to avoid complaints in read_stx_conf *
239 read_stx_conf(opt2fn("-f", NFILE, fnm), title, atoms, x, v, &ePBC, box);
241 nres = atoms->nres; /* nr of residues in one element? */
245 if (!read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &xx, boxx))
247 gmx_fatal(FARGS, "No atoms in trajectory %s", ftp2fn(efTRX, NFILE, fnm));
253 for (i = 0; i < natoms; i++)
255 copy_rvec(x[i], xx[i]);
260 for (k = 0; (k < nz); k++) /* loop over all gridpositions */
262 shift[ZZ] = k*(dist[ZZ]+box[ZZ][ZZ]);
264 for (j = 0; (j < ny); j++)
266 shift[YY] = j*(dist[YY]+box[YY][YY])+k*box[ZZ][YY];
268 for (i = 0; (i < nx); i++)
270 shift[XX] = i*(dist[XX]+box[XX][XX])+j*box[YY][XX]+k*box[ZZ][XX];
272 ndx = (i*ny*nz+j*nz+k)*natoms;
273 nrdx = (i*ny*nz+j*nz+k)*nres;
275 /* Random rotation on input coords */
278 rand_rot(natoms, xx, v, xrot, vrot, rng, max_rot);
281 for (l = 0; (l < natoms); l++)
283 for (m = 0; (m < DIM); m++)
287 x[ndx+l][m] = xrot[l][m];
288 v[ndx+l][m] = vrot[l][m];
292 x[ndx+l][m] = xx[l][m];
293 v[ndx+l][m] = v[l][m];
296 if (ePBC == epbcSCREW && i % 2 == 1)
298 /* Rotate around x axis */
299 for (m = YY; m <= ZZ; m++)
301 x[ndx+l][m] = box[YY][m] + box[ZZ][m] - x[ndx+l][m];
302 v[ndx+l][m] = -v[ndx+l][m];
305 for (m = 0; (m < DIM); m++)
307 x[ndx+l][m] += shift[m];
309 atoms->atom[ndx+l].resind = nrdx + atoms->atom[l].resind;
310 atoms->atomname[ndx+l] = atoms->atomname[l];
313 for (l = 0; (l < nres); l++)
315 atoms->resinfo[nrdx+l] = atoms->resinfo[l];
318 atoms->resinfo[nrdx+l].nr += nrdx;
323 if (!read_next_x(oenv, status, &t, xx, boxx) &&
324 ((i+1)*(j+1)*(k+1) < vol))
326 gmx_fatal(FARGS, "Not enough frames in trajectory");
337 /* make box bigger */
338 for (m = 0; (m < DIM); m++)
340 box[m][m] += dist[m];
342 svmul(nx, box[XX], box[XX]);
343 svmul(ny, box[YY], box[YY]);
344 svmul(nz, box[ZZ], box[ZZ]);
345 if (ePBC == epbcSCREW && nx % 2 == 0)
347 /* With an even number of boxes in x we can forgot about the screw */
351 /* move_x(natoms*vol,x,box); */ /* put atoms in box? */
356 /*depending on how you look at it, this is either a nasty hack or the way it should work*/
359 for (i = 0; i < atoms->nres; i++)
361 atoms->resinfo[i].nr = i+1;
368 randwater(0, atoms->nr/nmolat, nmolat, x, v, rng);
372 sortwater(0, atoms->nr/nmolat, nmolat, x, v);
374 else if (opt2parg_bSet("-block", asize(pa), pa))
376 mkcompact(0, atoms->nr/nmolat, nmolat, x, v, nblock, box);
378 gmx_rng_destroy(rng);
380 write_sto_conf(opt2fn("-o", NFILE, fnm), title, atoms, x, v, ePBC, box);