| File: | gromacs/tools/dump.c |
| Location: | line 147, column 13 |
| Description: | Function call argument is an uninitialized value |
| 1 | /* | |||||
| 2 | * This file is part of the GROMACS molecular simulation package. | |||||
| 3 | * | |||||
| 4 | * Copyright (c) 1991-2000, University of Groningen, The Netherlands. | |||||
| 5 | * Copyright (c) 2001-2013, 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. | |||||
| 10 | * | |||||
| 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. | |||||
| 15 | * | |||||
| 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. | |||||
| 20 | * | |||||
| 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. | |||||
| 25 | * | |||||
| 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. | |||||
| 33 | * | |||||
| 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. | |||||
| 36 | */ | |||||
| 37 | #ifdef HAVE_CONFIG_H1 | |||||
| 38 | #include <config.h> | |||||
| 39 | #endif | |||||
| 40 | ||||||
| 41 | #include <stdio.h> | |||||
| 42 | #include <string.h> | |||||
| 43 | #include <math.h> | |||||
| 44 | #include <assert.h> | |||||
| 45 | #include "macros.h" | |||||
| 46 | #include "gromacs/commandline/pargs.h" | |||||
| 47 | #include "txtdump.h" | |||||
| 48 | #include "gromacs/utility/fatalerror.h" | |||||
| 49 | #include "gromacs/utility/smalloc.h" | |||||
| 50 | #include "names.h" | |||||
| 51 | #include "txtdump.h" | |||||
| 52 | #include "gromacs/gmxpreprocess/gmxcpp.h" | |||||
| 53 | #include "checkpoint.h" | |||||
| 54 | #include "mtop_util.h" | |||||
| 55 | #include "gromacs/fileio/xtcio.h" | |||||
| 56 | #include "gromacs/fileio/enxio.h" | |||||
| 57 | #include "gromacs/fileio/gmxfio.h" | |||||
| 58 | #include "gromacs/fileio/tpxio.h" | |||||
| 59 | #include "gromacs/fileio/trnio.h" | |||||
| 60 | #include "gromacs/utility/futil.h" | |||||
| 61 | #include "gromacs/fileio/tngio.h" | |||||
| 62 | #include "gromacs/fileio/tngio_for_tools.h" | |||||
| 63 | ||||||
| 64 | #ifdef HAVE_UNISTD_H | |||||
| 65 | #include <unistd.h> | |||||
| 66 | #endif | |||||
| 67 | ||||||
| 68 | #include "gromacs/linearalgebra/mtxio.h" | |||||
| 69 | #include "gromacs/linearalgebra/sparsematrix.h" | |||||
| 70 | ||||||
| 71 | ||||||
| 72 | static void list_tpx(const char *fn, gmx_bool bShowNumbers, const char *mdpfn, | |||||
| 73 | gmx_bool bSysTop) | |||||
| 74 | { | |||||
| 75 | FILE *gp; | |||||
| 76 | int fp, indent, i, j, **gcount, atot; | |||||
| 77 | t_state state; | |||||
| 78 | rvec *f = NULL((void*)0); | |||||
| 79 | t_inputrec ir; | |||||
| 80 | t_tpxheader tpx; | |||||
| 81 | gmx_mtop_t mtop; | |||||
| 82 | gmx_groups_t *groups; | |||||
| 83 | t_topology top; | |||||
| 84 | ||||||
| 85 | read_tpxheader(fn, &tpx, TRUE1, NULL((void*)0), NULL((void*)0)); | |||||
| 86 | ||||||
| 87 | read_tpx_state(fn, | |||||
| 88 | tpx.bIr ? &ir : NULL((void*)0), | |||||
| ||||||
| 89 | &state, tpx.bF ? f : NULL((void*)0), | |||||
| 90 | tpx.bTop ? &mtop : NULL((void*)0)); | |||||
| 91 | ||||||
| 92 | if (mdpfn && tpx.bIr) | |||||
| 93 | { | |||||
| 94 | gp = gmx_fio_fopen(mdpfn, "w"); | |||||
| 95 | pr_inputrec(gp, 0, NULL((void*)0), &(ir), TRUE1); | |||||
| 96 | gmx_fio_fclose(gp); | |||||
| 97 | } | |||||
| 98 | ||||||
| 99 | if (!mdpfn) | |||||
| 100 | { | |||||
| 101 | if (bSysTop) | |||||
| 102 | { | |||||
| 103 | top = gmx_mtop_t_to_t_topology(&mtop); | |||||
| 104 | } | |||||
| 105 | ||||||
| 106 | if (available(stdoutstdout, &tpx, 0, fn)) | |||||
| 107 | { | |||||
| 108 | indent = 0; | |||||
| 109 | indent = pr_title(stdoutstdout, indent, fn); | |||||
| 110 | pr_inputrec(stdoutstdout, 0, "inputrec", tpx.bIr ? &(ir) : NULL((void*)0), FALSE0); | |||||
| 111 | ||||||
| 112 | indent = 0; | |||||
| 113 | pr_header(stdoutstdout, indent, "header", &(tpx)); | |||||
| 114 | ||||||
| 115 | if (!bSysTop) | |||||
| 116 | { | |||||
| 117 | pr_mtop(stdoutstdout, indent, "topology", &(mtop), bShowNumbers); | |||||
| 118 | } | |||||
| 119 | else | |||||
| 120 | { | |||||
| 121 | pr_top(stdoutstdout, indent, "topology", &(top), bShowNumbers); | |||||
| 122 | } | |||||
| 123 | ||||||
| 124 | pr_rvecs(stdoutstdout, indent, "box", tpx.bBox ? state.box : NULL((void*)0), DIM3); | |||||
| 125 | pr_rvecs(stdoutstdout, indent, "box_rel", tpx.bBox ? state.box_rel : NULL((void*)0), DIM3); | |||||
| 126 | pr_rvecs(stdoutstdout, indent, "boxv", tpx.bBox ? state.boxv : NULL((void*)0), DIM3); | |||||
| 127 | pr_rvecs(stdoutstdout, indent, "pres_prev", tpx.bBox ? state.pres_prev : NULL((void*)0), DIM3); | |||||
| 128 | pr_rvecs(stdoutstdout, indent, "svir_prev", tpx.bBox ? state.svir_prev : NULL((void*)0), DIM3); | |||||
| 129 | pr_rvecs(stdoutstdout, indent, "fvir_prev", tpx.bBox ? state.fvir_prev : NULL((void*)0), DIM3); | |||||
| 130 | /* leave nosehoover_xi in for now to match the tpr version */ | |||||
| 131 | pr_doubles(stdoutstdout, indent, "nosehoover_xi", state.nosehoover_xi, state.ngtc); | |||||
| 132 | /*pr_doubles(stdout,indent,"nosehoover_vxi",state.nosehoover_vxi,state.ngtc);*/ | |||||
| 133 | /*pr_doubles(stdout,indent,"therm_integral",state.therm_integral,state.ngtc);*/ | |||||
| 134 | pr_rvecs(stdoutstdout, indent, "x", tpx.bX ? state.x : NULL((void*)0), state.natoms); | |||||
| 135 | pr_rvecs(stdoutstdout, indent, "v", tpx.bV ? state.v : NULL((void*)0), state.natoms); | |||||
| 136 | if (tpx.bF) | |||||
| 137 | { | |||||
| 138 | pr_rvecs(stdoutstdout, indent, "f", f, state.natoms); | |||||
| 139 | } | |||||
| 140 | } | |||||
| 141 | ||||||
| 142 | groups = &mtop.groups; | |||||
| 143 | ||||||
| 144 | snew(gcount, egcNR)(gcount) = save_calloc("gcount", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 144, (egcNR), sizeof(*(gcount))); | |||||
| 145 | for (i = 0; (i < egcNR); i++) | |||||
| 146 | { | |||||
| 147 | snew(gcount[i], groups->grps[i].nr)(gcount[i]) = save_calloc("gcount[i]", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 147, (groups->grps[i].nr), sizeof(*(gcount[i]))); | |||||
| ||||||
| 148 | } | |||||
| 149 | ||||||
| 150 | for (i = 0; (i < mtop.natoms); i++) | |||||
| 151 | { | |||||
| 152 | for (j = 0; (j < egcNR); j++) | |||||
| 153 | { | |||||
| 154 | gcount[j][ggrpnr(groups, j, i)((groups)->grpnr[j] ? (groups)->grpnr[j][i] : 0)]++; | |||||
| 155 | } | |||||
| 156 | } | |||||
| 157 | printf("Group statistics\n"); | |||||
| 158 | for (i = 0; (i < egcNR); i++) | |||||
| 159 | { | |||||
| 160 | atot = 0; | |||||
| 161 | printf("%-12s: ", gtypes[i]); | |||||
| 162 | for (j = 0; (j < groups->grps[i].nr); j++) | |||||
| 163 | { | |||||
| 164 | printf(" %5d", gcount[i][j]); | |||||
| 165 | atot += gcount[i][j]; | |||||
| 166 | } | |||||
| 167 | printf(" (total %d atoms)\n", atot); | |||||
| 168 | sfree(gcount[i])save_free("gcount[i]", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 168, (gcount[i])); | |||||
| 169 | } | |||||
| 170 | sfree(gcount)save_free("gcount", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 170, (gcount)); | |||||
| 171 | } | |||||
| 172 | done_state(&state); | |||||
| 173 | sfree(f)save_free("f", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 173, (f)); | |||||
| 174 | } | |||||
| 175 | ||||||
| 176 | static void list_top(const char *fn) | |||||
| 177 | { | |||||
| 178 | int status, done; | |||||
| 179 | #define BUFLEN256 256 | |||||
| 180 | char buf[BUFLEN256]; | |||||
| 181 | gmx_cpp_t handle; | |||||
| 182 | char *cppopts[] = { NULL((void*)0) }; | |||||
| 183 | ||||||
| 184 | status = cpp_open_file(fn, &handle, cppopts); | |||||
| 185 | if (status != 0) | |||||
| 186 | { | |||||
| 187 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c", 187, cpp_error(&handle, status)); | |||||
| 188 | } | |||||
| 189 | do | |||||
| 190 | { | |||||
| 191 | status = cpp_read_line(&handle, BUFLEN256, buf); | |||||
| 192 | done = (status == eCPP_EOF); | |||||
| 193 | if (!done) | |||||
| 194 | { | |||||
| 195 | if (status != eCPP_OK) | |||||
| 196 | { | |||||
| 197 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c", 197, cpp_error(&handle, status)); | |||||
| 198 | } | |||||
| 199 | else | |||||
| 200 | { | |||||
| 201 | printf("%s\n", buf); | |||||
| 202 | } | |||||
| 203 | } | |||||
| 204 | } | |||||
| 205 | while (!done); | |||||
| 206 | status = cpp_close_file(&handle); | |||||
| 207 | if (status != eCPP_OK) | |||||
| 208 | { | |||||
| 209 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c", 209, cpp_error(&handle, status)); | |||||
| 210 | } | |||||
| 211 | } | |||||
| 212 | ||||||
| 213 | static void list_trn(const char *fn) | |||||
| 214 | { | |||||
| 215 | t_fileio *fpread, *fpwrite; | |||||
| 216 | int nframe, indent; | |||||
| 217 | char buf[256]; | |||||
| 218 | rvec *x, *v, *f; | |||||
| 219 | matrix box; | |||||
| 220 | t_trnheader trn; | |||||
| 221 | gmx_bool bOK; | |||||
| 222 | ||||||
| 223 | fpread = open_trn(fn, "r"); | |||||
| 224 | fpwrite = open_tpx(NULL((void*)0), "w"); | |||||
| 225 | gmx_fio_setdebug(fpwrite, TRUE1); | |||||
| 226 | ||||||
| 227 | nframe = 0; | |||||
| 228 | while (fread_trnheader(fpread, &trn, &bOK)) | |||||
| 229 | { | |||||
| 230 | snew(x, trn.natoms)(x) = save_calloc("x", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 230, (trn.natoms), sizeof(*(x))); | |||||
| 231 | snew(v, trn.natoms)(v) = save_calloc("v", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 231, (trn.natoms), sizeof(*(v))); | |||||
| 232 | snew(f, trn.natoms)(f) = save_calloc("f", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 232, (trn.natoms), sizeof(*(f))); | |||||
| 233 | if (fread_htrn(fpread, &trn, | |||||
| 234 | trn.box_size ? box : NULL((void*)0), | |||||
| 235 | trn.x_size ? x : NULL((void*)0), | |||||
| 236 | trn.v_size ? v : NULL((void*)0), | |||||
| 237 | trn.f_size ? f : NULL((void*)0))) | |||||
| 238 | { | |||||
| 239 | sprintf(buf, "%s frame %d", fn, nframe); | |||||
| 240 | indent = 0; | |||||
| 241 | indent = pr_title(stdoutstdout, indent, buf); | |||||
| 242 | pr_indent(stdoutstdout, indent); | |||||
| 243 | fprintf(stdoutstdout, "natoms=%10d step=%10d time=%12.7e lambda=%10g\n", | |||||
| 244 | trn.natoms, trn.step, trn.t, trn.lambda); | |||||
| 245 | if (trn.box_size) | |||||
| 246 | { | |||||
| 247 | pr_rvecs(stdoutstdout, indent, "box", box, DIM3); | |||||
| 248 | } | |||||
| 249 | if (trn.x_size) | |||||
| 250 | { | |||||
| 251 | pr_rvecs(stdoutstdout, indent, "x", x, trn.natoms); | |||||
| 252 | } | |||||
| 253 | if (trn.v_size) | |||||
| 254 | { | |||||
| 255 | pr_rvecs(stdoutstdout, indent, "v", v, trn.natoms); | |||||
| 256 | } | |||||
| 257 | if (trn.f_size) | |||||
| 258 | { | |||||
| 259 | pr_rvecs(stdoutstdout, indent, "f", f, trn.natoms); | |||||
| 260 | } | |||||
| 261 | } | |||||
| 262 | else | |||||
| 263 | { | |||||
| 264 | fprintf(stderrstderr, "\nWARNING: Incomplete frame: nr %d, t=%g\n", | |||||
| 265 | nframe, trn.t); | |||||
| 266 | } | |||||
| 267 | ||||||
| 268 | sfree(x)save_free("x", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 268, (x)); | |||||
| 269 | sfree(v)save_free("v", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 269, (v)); | |||||
| 270 | sfree(f)save_free("f", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 270, (f)); | |||||
| 271 | nframe++; | |||||
| 272 | } | |||||
| 273 | if (!bOK) | |||||
| 274 | { | |||||
| 275 | fprintf(stderrstderr, "\nWARNING: Incomplete frame header: nr %d, t=%g\n", | |||||
| 276 | nframe, trn.t); | |||||
| 277 | } | |||||
| 278 | close_tpx(fpwrite); | |||||
| 279 | close_trn(fpread); | |||||
| 280 | } | |||||
| 281 | ||||||
| 282 | void list_xtc(const char *fn) | |||||
| 283 | { | |||||
| 284 | t_fileio *xd; | |||||
| 285 | int indent; | |||||
| 286 | char buf[256]; | |||||
| 287 | rvec *x; | |||||
| 288 | matrix box; | |||||
| 289 | int nframe, natoms, step; | |||||
| 290 | real prec, time; | |||||
| 291 | gmx_bool bOK; | |||||
| 292 | ||||||
| 293 | xd = open_xtc(fn, "r"); | |||||
| 294 | read_first_xtc(xd, &natoms, &step, &time, box, &x, &prec, &bOK); | |||||
| 295 | ||||||
| 296 | nframe = 0; | |||||
| 297 | do | |||||
| 298 | { | |||||
| 299 | sprintf(buf, "%s frame %d", fn, nframe); | |||||
| 300 | indent = 0; | |||||
| 301 | indent = pr_title(stdoutstdout, indent, buf); | |||||
| 302 | pr_indent(stdoutstdout, indent); | |||||
| 303 | fprintf(stdoutstdout, "natoms=%10d step=%10d time=%12.7e prec=%10g\n", | |||||
| 304 | natoms, step, time, prec); | |||||
| 305 | pr_rvecs(stdoutstdout, indent, "box", box, DIM3); | |||||
| 306 | pr_rvecs(stdoutstdout, indent, "x", x, natoms); | |||||
| 307 | nframe++; | |||||
| 308 | } | |||||
| 309 | while (read_next_xtc(xd, natoms, &step, &time, box, x, &prec, &bOK)); | |||||
| 310 | if (!bOK) | |||||
| 311 | { | |||||
| 312 | fprintf(stderrstderr, "\nWARNING: Incomplete frame at time %g\n", time); | |||||
| 313 | } | |||||
| 314 | sfree(x)save_free("x", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 314, (x)); | |||||
| 315 | close_xtc(xd); | |||||
| 316 | } | |||||
| 317 | ||||||
| 318 | /*! \brief Callback used by list_tng_for_gmx_dump. */ | |||||
| 319 | static void list_tng_inner(const char *fn, | |||||
| 320 | gmx_bool bFirstFrame, | |||||
| 321 | real *values, | |||||
| 322 | gmx_int64_t step, | |||||
| 323 | double frame_time, | |||||
| 324 | gmx_int64_t n_values_per_frame, | |||||
| 325 | gmx_int64_t n_atoms, | |||||
| 326 | real prec, | |||||
| 327 | gmx_int64_t nframe, | |||||
| 328 | char *block_name) | |||||
| 329 | { | |||||
| 330 | char buf[256]; | |||||
| 331 | int indent = 0; | |||||
| 332 | ||||||
| 333 | if (bFirstFrame) | |||||
| 334 | { | |||||
| 335 | sprintf(buf, "%s frame %" GMX_PRId64"l" "d", fn, nframe); | |||||
| 336 | indent = 0; | |||||
| 337 | indent = pr_title(stdoutstdout, indent, buf); | |||||
| 338 | pr_indent(stdoutstdout, indent); | |||||
| 339 | fprintf(stdoutstdout, "natoms=%10" GMX_PRId64"l" "d" " step=%10" GMX_PRId64"l" "d" " time=%12.7e", | |||||
| 340 | n_atoms, step, frame_time); | |||||
| 341 | if (prec > 0) | |||||
| 342 | { | |||||
| 343 | fprintf(stdoutstdout, " prec=%10g", prec); | |||||
| 344 | } | |||||
| 345 | fprintf(stdoutstdout, "\n"); | |||||
| 346 | } | |||||
| 347 | pr_reals_of_dim(stdoutstdout, indent, block_name, values, n_atoms, n_values_per_frame); | |||||
| 348 | } | |||||
| 349 | ||||||
| 350 | static void list_tng(const char gmx_unused__attribute__ ((unused)) *fn) | |||||
| 351 | { | |||||
| 352 | #ifdef GMX_USE_TNG | |||||
| 353 | tng_trajectory_t tng; | |||||
| 354 | gmx_int64_t nframe = 0; | |||||
| 355 | gmx_int64_t i, *block_ids = NULL((void*)0), step, ndatablocks; | |||||
| 356 | gmx_bool bOK; | |||||
| 357 | ||||||
| 358 | gmx_tng_open(fn, 'r', &tng); | |||||
| 359 | gmx_print_tng_molecule_system(tng, stdoutstdout); | |||||
| 360 | ||||||
| 361 | bOK = gmx_get_tng_data_block_types_of_next_frame(tng, -1, | |||||
| 362 | 0, | |||||
| 363 | NULL((void*)0), | |||||
| 364 | &step, &ndatablocks, | |||||
| 365 | &block_ids); | |||||
| 366 | do | |||||
| 367 | { | |||||
| 368 | for (i = 0; i < ndatablocks; i++) | |||||
| 369 | { | |||||
| 370 | double frame_time; | |||||
| 371 | real prec, *values = NULL((void*)0); | |||||
| 372 | gmx_int64_t n_values_per_frame, n_atoms; | |||||
| 373 | char block_name[STRLEN4096]; | |||||
| 374 | ||||||
| 375 | gmx_get_tng_data_next_frame_of_block_type(tng, block_ids[i], &values, | |||||
| 376 | &step, &frame_time, | |||||
| 377 | &n_values_per_frame, &n_atoms, | |||||
| 378 | &prec, | |||||
| 379 | block_name, STRLEN4096, &bOK); | |||||
| 380 | if (!bOK) | |||||
| 381 | { | |||||
| 382 | /* Can't write any output because we don't know what | |||||
| 383 | arrays are valid. */ | |||||
| 384 | fprintf(stderrstderr, "\nWARNING: Incomplete frame at time %g, will not write output\n", frame_time); | |||||
| 385 | list_tng_inner(fn, (0 == i), values, step, frame_time, | |||||
| 386 | n_values_per_frame, n_atoms, prec, nframe, block_name); | |||||
| 387 | } | |||||
| 388 | } | |||||
| 389 | nframe++; | |||||
| 390 | } | |||||
| 391 | while (gmx_get_tng_data_block_types_of_next_frame(tng, step, | |||||
| 392 | 0, | |||||
| 393 | NULL((void*)0), | |||||
| 394 | &step, | |||||
| 395 | &ndatablocks, | |||||
| 396 | &block_ids)); | |||||
| 397 | ||||||
| 398 | if (block_ids) | |||||
| 399 | { | |||||
| 400 | sfree(block_ids)save_free("block_ids", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 400, (block_ids)); | |||||
| 401 | } | |||||
| 402 | ||||||
| 403 | gmx_tng_close(&tng); | |||||
| 404 | #endif | |||||
| 405 | } | |||||
| 406 | ||||||
| 407 | void list_trx(const char *fn) | |||||
| 408 | { | |||||
| 409 | int ftp; | |||||
| 410 | ||||||
| 411 | ftp = fn2ftp(fn); | |||||
| 412 | if (ftp == efXTC) | |||||
| 413 | { | |||||
| 414 | list_xtc(fn); | |||||
| 415 | } | |||||
| 416 | else if ((ftp == efTRR) || (ftp == efTRJ)) | |||||
| 417 | { | |||||
| 418 | list_trn(fn); | |||||
| 419 | } | |||||
| 420 | else if (ftp == efTNG) | |||||
| 421 | { | |||||
| 422 | list_tng(fn); | |||||
| 423 | } | |||||
| 424 | else | |||||
| 425 | { | |||||
| 426 | fprintf(stderrstderr, "File %s is of an unsupported type. Try using the command\n 'less %s'\n", | |||||
| 427 | fn, fn); | |||||
| 428 | } | |||||
| 429 | } | |||||
| 430 | ||||||
| 431 | void list_ene(const char *fn) | |||||
| 432 | { | |||||
| 433 | int ndr; | |||||
| 434 | ener_file_t in; | |||||
| 435 | gmx_bool bCont; | |||||
| 436 | gmx_enxnm_t *enm = NULL((void*)0); | |||||
| 437 | t_enxframe *fr; | |||||
| 438 | int i, j, nre, b; | |||||
| 439 | real rav, minthird; | |||||
| 440 | char buf[22]; | |||||
| 441 | ||||||
| 442 | printf("gmx dump: %s\n", fn); | |||||
| 443 | in = open_enx(fn, "r"); | |||||
| 444 | do_enxnms(in, &nre, &enm); | |||||
| 445 | assert(enm)((void) (0)); | |||||
| 446 | ||||||
| 447 | printf("energy components:\n"); | |||||
| 448 | for (i = 0; (i < nre); i++) | |||||
| 449 | { | |||||
| 450 | printf("%5d %-24s (%s)\n", i, enm[i].name, enm[i].unit); | |||||
| 451 | } | |||||
| 452 | ||||||
| 453 | minthird = -1.0/3.0; | |||||
| 454 | snew(fr, 1)(fr) = save_calloc("fr", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 454, (1), sizeof(*(fr))); | |||||
| 455 | do | |||||
| 456 | { | |||||
| 457 | bCont = do_enx(in, fr); | |||||
| 458 | ||||||
| 459 | if (bCont) | |||||
| 460 | { | |||||
| 461 | printf("\n%24s %12.5e %12s %12s\n", "time:", | |||||
| 462 | fr->t, "step:", gmx_step_str(fr->step, buf)); | |||||
| 463 | printf("%24s %12s %12s %12s\n", | |||||
| 464 | "", "", "nsteps:", gmx_step_str(fr->nsteps, buf)); | |||||
| 465 | printf("%24s %12.5e %12s %12s\n", | |||||
| 466 | "delta_t:", fr->dt, "sum steps:", gmx_step_str(fr->nsum, buf)); | |||||
| 467 | if (fr->nre == nre) | |||||
| 468 | { | |||||
| 469 | printf("%24s %12s %12s %12s\n", | |||||
| 470 | "Component", "Energy", "Av. Energy", "Sum Energy"); | |||||
| 471 | if (fr->nsum > 0) | |||||
| 472 | { | |||||
| 473 | for (i = 0; (i < nre); i++) | |||||
| 474 | { | |||||
| 475 | printf("%24s %12.5e %12.5e %12.5e\n", | |||||
| 476 | enm[i].name, fr->ener[i].e, fr->ener[i].eav, | |||||
| 477 | fr->ener[i].esum); | |||||
| 478 | } | |||||
| 479 | } | |||||
| 480 | else | |||||
| 481 | { | |||||
| 482 | for (i = 0; (i < nre); i++) | |||||
| 483 | { | |||||
| 484 | printf("%24s %12.5e\n", | |||||
| 485 | enm[i].name, fr->ener[i].e); | |||||
| 486 | } | |||||
| 487 | } | |||||
| 488 | } | |||||
| 489 | for (b = 0; b < fr->nblock; b++) | |||||
| 490 | { | |||||
| 491 | const char *typestr = ""; | |||||
| 492 | ||||||
| 493 | t_enxblock *eb = &(fr->block[b]); | |||||
| 494 | printf("Block data %2d (%3d subblocks, id=%d)\n", | |||||
| 495 | b, eb->nsub, eb->id); | |||||
| 496 | ||||||
| 497 | if (eb->id < enxNR) | |||||
| 498 | { | |||||
| 499 | typestr = enx_block_id_name[eb->id]; | |||||
| 500 | } | |||||
| 501 | printf(" id='%s'\n", typestr); | |||||
| 502 | for (i = 0; i < eb->nsub; i++) | |||||
| 503 | { | |||||
| 504 | t_enxsubblock *sb = &(eb->sub[i]); | |||||
| 505 | printf(" Sub block %3d (%5d elems, type=%s) values:\n", | |||||
| 506 | i, sb->nr, xdr_datatype_names[sb->type]); | |||||
| 507 | ||||||
| 508 | switch (sb->type) | |||||
| 509 | { | |||||
| 510 | case xdr_datatype_float: | |||||
| 511 | for (j = 0; j < sb->nr; j++) | |||||
| 512 | { | |||||
| 513 | printf("%14d %8.4f\n", j, sb->fval[j]); | |||||
| 514 | } | |||||
| 515 | break; | |||||
| 516 | case xdr_datatype_double: | |||||
| 517 | for (j = 0; j < sb->nr; j++) | |||||
| 518 | { | |||||
| 519 | printf("%14d %10.6f\n", j, sb->dval[j]); | |||||
| 520 | } | |||||
| 521 | break; | |||||
| 522 | case xdr_datatype_int: | |||||
| 523 | for (j = 0; j < sb->nr; j++) | |||||
| 524 | { | |||||
| 525 | printf("%14d %10d\n", j, sb->ival[j]); | |||||
| 526 | } | |||||
| 527 | break; | |||||
| 528 | case xdr_datatype_int64: | |||||
| 529 | for (j = 0; j < sb->nr; j++) | |||||
| 530 | { | |||||
| 531 | printf("%14d %s\n", | |||||
| 532 | j, gmx_step_str(sb->lval[j], buf)); | |||||
| 533 | } | |||||
| 534 | break; | |||||
| 535 | case xdr_datatype_char: | |||||
| 536 | for (j = 0; j < sb->nr; j++) | |||||
| 537 | { | |||||
| 538 | printf("%14d %1c\n", j, sb->cval[j]); | |||||
| 539 | } | |||||
| 540 | break; | |||||
| 541 | case xdr_datatype_string: | |||||
| 542 | for (j = 0; j < sb->nr; j++) | |||||
| 543 | { | |||||
| 544 | printf("%14d %80s\n", j, sb->sval[j]); | |||||
| 545 | } | |||||
| 546 | break; | |||||
| 547 | default: | |||||
| 548 | gmx_incons("Unknown subblock type")_gmx_error("incons", "Unknown subblock type", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 548); | |||||
| 549 | } | |||||
| 550 | } | |||||
| 551 | } | |||||
| 552 | } | |||||
| 553 | } | |||||
| 554 | while (bCont); | |||||
| 555 | ||||||
| 556 | close_enx(in); | |||||
| 557 | ||||||
| 558 | free_enxframe(fr); | |||||
| 559 | sfree(fr)save_free("fr", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 559, (fr)); | |||||
| 560 | sfree(enm)save_free("enm", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 560, (enm)); | |||||
| 561 | } | |||||
| 562 | ||||||
| 563 | static void list_mtx(const char *fn) | |||||
| 564 | { | |||||
| 565 | int nrow, ncol, i, j, k; | |||||
| 566 | real *full = NULL((void*)0), value; | |||||
| 567 | gmx_sparsematrix_t * sparse = NULL((void*)0); | |||||
| 568 | ||||||
| 569 | gmx_mtxio_read(fn, &nrow, &ncol, &full, &sparse); | |||||
| 570 | ||||||
| 571 | if (full == NULL((void*)0)) | |||||
| 572 | { | |||||
| 573 | snew(full, nrow*ncol)(full) = save_calloc("full", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 573, (nrow*ncol), sizeof(*(full))); | |||||
| 574 | for (i = 0; i < nrow*ncol; i++) | |||||
| 575 | { | |||||
| 576 | full[i] = 0; | |||||
| 577 | } | |||||
| 578 | ||||||
| 579 | for (i = 0; i < sparse->nrow; i++) | |||||
| 580 | { | |||||
| 581 | for (j = 0; j < sparse->ndata[i]; j++) | |||||
| 582 | { | |||||
| 583 | k = sparse->data[i][j].col; | |||||
| 584 | value = sparse->data[i][j].value; | |||||
| 585 | full[i*ncol+k] = value; | |||||
| 586 | full[k*ncol+i] = value; | |||||
| 587 | } | |||||
| 588 | } | |||||
| 589 | gmx_sparsematrix_destroy(sparse); | |||||
| 590 | } | |||||
| 591 | ||||||
| 592 | printf("%d %d\n", nrow, ncol); | |||||
| 593 | for (i = 0; i < nrow; i++) | |||||
| 594 | { | |||||
| 595 | for (j = 0; j < ncol; j++) | |||||
| 596 | { | |||||
| 597 | printf(" %g", full[i*ncol+j]); | |||||
| 598 | } | |||||
| 599 | printf("\n"); | |||||
| 600 | } | |||||
| 601 | ||||||
| 602 | sfree(full)save_free("full", "/home/alexxy/Develop/gromacs/src/gromacs/tools/dump.c" , 602, (full)); | |||||
| 603 | } | |||||
| 604 | ||||||
| 605 | int gmx_dump(int argc, char *argv[]) | |||||
| 606 | { | |||||
| 607 | const char *desc[] = { | |||||
| 608 | "[THISMODULE] reads a run input file ([TT].tpa[tt]/[TT].tpr[tt]/[TT].tpb[tt]),", | |||||
| 609 | "a trajectory ([TT].trj[tt]/[TT].trr[tt]/[TT].xtc[tt]), an energy", | |||||
| 610 | "file ([TT].ene[tt]/[TT].edr[tt]), or a checkpoint file ([TT].cpt[tt])", | |||||
| 611 | "and prints that to standard output in a readable format.", | |||||
| 612 | "This program is essential for checking your run input file in case of", | |||||
| 613 | "problems.[PAR]", | |||||
| 614 | "The program can also preprocess a topology to help finding problems.", | |||||
| 615 | "Note that currently setting [TT]GMXLIB[tt] is the only way to customize", | |||||
| 616 | "directories used for searching include files.", | |||||
| 617 | }; | |||||
| 618 | const char *bugs[] = { | |||||
| 619 | "Position restraint output from -sys -s is broken" | |||||
| 620 | }; | |||||
| 621 | t_filenm fnm[] = { | |||||
| 622 | { efTPX, "-s", NULL((void*)0), ffOPTRD(1<<1 | 1<<3) }, | |||||
| 623 | { efTRX, "-f", NULL((void*)0), ffOPTRD(1<<1 | 1<<3) }, | |||||
| 624 | { efEDR, "-e", NULL((void*)0), ffOPTRD(1<<1 | 1<<3) }, | |||||
| 625 | { efCPT, NULL((void*)0), NULL((void*)0), ffOPTRD(1<<1 | 1<<3) }, | |||||
| 626 | { efTOP, "-p", NULL((void*)0), ffOPTRD(1<<1 | 1<<3) }, | |||||
| 627 | { efMTX, "-mtx", "hessian", ffOPTRD(1<<1 | 1<<3) }, | |||||
| 628 | { efMDP, "-om", NULL((void*)0), ffOPTWR(1<<2| 1<<3) } | |||||
| 629 | }; | |||||
| 630 | #define NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))) asize(fnm)((int)(sizeof(fnm)/sizeof((fnm)[0]))) | |||||
| 631 | ||||||
| 632 | output_env_t oenv; | |||||
| 633 | /* Command line options */ | |||||
| 634 | static gmx_bool bShowNumbers = TRUE1; | |||||
| 635 | static gmx_bool bSysTop = FALSE0; | |||||
| 636 | t_pargs pa[] = { | |||||
| 637 | { "-nr", FALSE0, etBOOL, {&bShowNumbers}, "Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)" }, | |||||
| 638 | { "-sys", FALSE0, etBOOL, {&bSysTop}, "List the atoms and bonded interactions for the whole system instead of for each molecule type" } | |||||
| 639 | }; | |||||
| 640 | ||||||
| 641 | if (!parse_common_args(&argc, argv, 0, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm, asize(pa)((int)(sizeof(pa)/sizeof((pa)[0]))), pa, | |||||
| 642 | asize(desc)((int)(sizeof(desc)/sizeof((desc)[0]))), desc, asize(bugs)((int)(sizeof(bugs)/sizeof((bugs)[0]))), bugs, &oenv)) | |||||
| 643 | { | |||||
| 644 | return 0; | |||||
| 645 | } | |||||
| 646 | ||||||
| 647 | ||||||
| 648 | if (ftp2bSet(efTPX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm)) | |||||
| 649 | { | |||||
| 650 | list_tpx(ftp2fn(efTPX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), bShowNumbers, | |||||
| 651 | ftp2fn_null(efMDP, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), bSysTop); | |||||
| 652 | } | |||||
| 653 | else if (ftp2bSet(efTRX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm)) | |||||
| 654 | { | |||||
| 655 | list_trx(ftp2fn(efTRX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm)); | |||||
| 656 | } | |||||
| 657 | else if (ftp2bSet(efEDR, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm)) | |||||
| 658 | { | |||||
| 659 | list_ene(ftp2fn(efEDR, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm)); | |||||
| 660 | } | |||||
| 661 | else if (ftp2bSet(efCPT, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm)) | |||||
| 662 | { | |||||
| 663 | list_checkpoint(ftp2fn(efCPT, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), stdoutstdout); | |||||
| 664 | } | |||||
| 665 | else if (ftp2bSet(efTOP, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm)) | |||||
| 666 | { | |||||
| 667 | list_top(ftp2fn(efTOP, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm)); | |||||
| 668 | } | |||||
| 669 | else if (ftp2bSet(efMTX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm)) | |||||
| 670 | { | |||||
| 671 | list_mtx(ftp2fn(efMTX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm)); | |||||
| 672 | } | |||||
| 673 | ||||||
| 674 | return 0; | |||||
| 675 | } |