Bug Summary

File:gromacs/fileio/tpxio.c
Location:line 2901, column 13
Description:Value stored to 'ip' is never read

Annotated Source Code

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) 2001-2004, 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.
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/* This file is completely threadsafe - keep it that way! */
42
43#include <stdlib.h>
44#include <string.h>
45
46#include "gromacs/utility/smalloc.h"
47#include "gromacs/utility/cstringutil.h"
48#include "gromacs/utility/fatalerror.h"
49#include "macros.h"
50#include "names.h"
51#include "symtab.h"
52#include "gromacs/utility/futil.h"
53#include "filenm.h"
54#include "gmxfio.h"
55#include "tpxio.h"
56#include "txtdump.h"
57#include "confio.h"
58#include "atomprop.h"
59#include "copyrite.h"
60#include "gromacs/math/vec.h"
61#include "mtop_util.h"
62
63#define TPX_TAG_RELEASE"release" "release"
64
65/*! \brief Tag string for the file format written to run input files
66 * written by this version of the code.
67 *
68 * Change this if you want to change the run input format in a feature
69 * branch. This ensures that there will not be different run input
70 * formats around which cannot be distinguished, while not causing
71 * problems rebasing the feature branch onto upstream changes. When
72 * merging with mainstream GROMACS, set this tag string back to
73 * TPX_TAG_RELEASE, and instead add an element to tpxv and set
74 * tpx_version to that.
75 */
76static const char *tpx_tag = TPX_TAG_RELEASE"release";
77
78/*! \brief Enum of values that describe the contents of a tpr file
79 * whose format matches a version number
80 *
81 * The enum helps the code be more self-documenting and ensure merges
82 * do not silently resolve when two patches make the same bump. When
83 * adding new functionality, add a new element to the end of this
84 * enumeration, change the definition of tpx_version, and write code
85 * below that does the right thing according to the value of
86 * file_version. */
87enum tpxv {
88 tpxv_ComputationalElectrophysiology = 96, /**< support for ion/water position swaps (computational electrophysiology) */
89 tpxv_Use64BitRandomSeed, /**< change ld_seed from int to gmx_int64_t */
90 tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, /**< potentials for supporting coarse-grained force fields */
91 tpxv_InteractiveMolecularDynamics /**< interactive molecular dynamics (IMD) */
92};
93
94/*! \brief Version number of the file format written to run input
95 * files by this version of the code.
96 *
97 * The tpx_version number should be increased whenever the file format
98 * in the main development branch changes, generally to the highest
99 * value present in tpxv. Backward compatibility for reading old run
100 * input files is maintained by checking this version number against
101 * that of the file and then using the correct code path.
102 *
103 * When developing a feature branch that needs to change the run input
104 * file format, change tpx_tag instead. */
105static const int tpx_version = tpxv_InteractiveMolecularDynamics;
106
107
108/* This number should only be increased when you edit the TOPOLOGY section
109 * or the HEADER of the tpx format.
110 * This way we can maintain forward compatibility too for all analysis tools
111 * and/or external programs that only need to know the atom/residue names,
112 * charges, and bond connectivity.
113 *
114 * It first appeared in tpx version 26, when I also moved the inputrecord
115 * to the end of the tpx file, so we can just skip it if we only
116 * want the topology.
117 *
118 * In particular, it must be increased when adding new elements to
119 * ftupd, so that old code can read new .tpr files.
120 */
121static const int tpx_generation = 26;
122
123/* This number should be the most recent backwards incompatible version
124 * I.e., if this number is 9, we cannot read tpx version 9 with this code.
125 */
126static const int tpx_incompatible_version = 9;
127
128
129
130/* Struct used to maintain tpx compatibility when function types are added */
131typedef struct {
132 int fvnr; /* file version number in which the function type first appeared */
133 int ftype; /* function type */
134} t_ftupd;
135
136/*
137 * The entries should be ordered in:
138 * 1. ascending file version number
139 * 2. ascending function type number
140 */
141/*static const t_ftupd ftupd[] = {
142 { 20, F_CUBICBONDS },
143 { 20, F_CONNBONDS },
144 { 20, F_HARMONIC },
145 { 20, F_EQM, },
146 { 22, F_DISRESVIOL },
147 { 22, F_ORIRES },
148 { 22, F_ORIRESDEV },
149 { 26, F_FOURDIHS },
150 { 26, F_PIDIHS },
151 { 26, F_DIHRES },
152 { 26, F_DIHRESVIOL },
153 { 30, F_CROSS_BOND_BONDS },
154 { 30, F_CROSS_BOND_ANGLES },
155 { 30, F_UREY_BRADLEY },
156 { 30, F_POLARIZATION },
157 { 54, F_DHDL_CON },
158 };*/
159/*
160 * The entries should be ordered in:
161 * 1. ascending function type number
162 * 2. ascending file version number
163 */
164/* question; what is the purpose of the commented code above? */
165static const t_ftupd ftupd[] = {
166 { 20, F_CUBICBONDS },
167 { 20, F_CONNBONDS },
168 { 20, F_HARMONIC },
169 { 34, F_FENEBONDS },
170 { 43, F_TABBONDS },
171 { 43, F_TABBONDSNC },
172 { 70, F_RESTRBONDS },
173 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRANGLES },
174 { 76, F_LINEAR_ANGLES },
175 { 30, F_CROSS_BOND_BONDS },
176 { 30, F_CROSS_BOND_ANGLES },
177 { 30, F_UREY_BRADLEY },
178 { 34, F_QUARTIC_ANGLES },
179 { 43, F_TABANGLES },
180 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRDIHS },
181 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_CBTDIHS },
182 { 26, F_FOURDIHS },
183 { 26, F_PIDIHS },
184 { 43, F_TABDIHS },
185 { 65, F_CMAP },
186 { 60, F_GB12 },
187 { 61, F_GB13 },
188 { 61, F_GB14 },
189 { 72, F_GBPOL },
190 { 72, F_NPSOLVATION },
191 { 41, F_LJC14_Q },
192 { 41, F_LJC_PAIRS_NB },
193 { 32, F_BHAM_LR },
194 { 32, F_RF_EXCL },
195 { 32, F_COUL_RECIP },
196 { 93, F_LJ_RECIP },
197 { 46, F_DPD },
198 { 30, F_POLARIZATION },
199 { 36, F_THOLE_POL },
200 { 90, F_FBPOSRES },
201 { 22, F_DISRESVIOL },
202 { 22, F_ORIRES },
203 { 22, F_ORIRESDEV },
204 { 26, F_DIHRES },
205 { 26, F_DIHRESVIOL },
206 { 49, F_VSITE4FDN },
207 { 50, F_VSITEN },
208 { 46, F_COM_PULL },
209 { 20, F_EQM },
210 { 46, F_ECONSERVED },
211 { 69, F_VTEMP_NOLONGERUSED},
212 { 66, F_PDISPCORR },
213 { 54, F_DVDL_CONSTR },
214 { 76, F_ANHARM_POL },
215 { 79, F_DVDL_COUL },
216 { 79, F_DVDL_VDW, },
217 { 79, F_DVDL_BONDED, },
218 { 79, F_DVDL_RESTRAINT },
219 { 79, F_DVDL_TEMPERATURE },
220};
221#define NFTUPD((int)(sizeof(ftupd)/sizeof((ftupd)[0]))) asize(ftupd)((int)(sizeof(ftupd)/sizeof((ftupd)[0])))
222
223/* Needed for backward compatibility */
224#define MAXNODES256 256
225
226static void _do_section(t_fileio *fio, int key, gmx_bool bRead, const char *src,
227 int line)
228{
229 char buf[STRLEN4096];
230 gmx_bool bDbg;
231
232 if (gmx_fio_getftp(fio) == efTPA)
233 {
234 if (!bRead)
235 {
236 gmx_fio_write_string(fio, itemstr[key])gmx_fio_writee_string(fio, itemstr[key], ("itemstr[key]"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 236);
237 bDbg = gmx_fio_getdebug(fio);
238 gmx_fio_setdebug(fio, FALSE0);
239 gmx_fio_write_string(fio, comment_str[key])gmx_fio_writee_string(fio, comment_str[key], ("comment_str[key]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
239);
240 gmx_fio_setdebug(fio, bDbg);
241 }
242 else
243 {
244 if (gmx_fio_getdebug(fio))
245 {
246 fprintf(stderrstderr, "Looking for section %s (%s, %d)",
247 itemstr[key], src, line);
248 }
249
250 do
251 {
252 gmx_fio_do_string(fio, buf)gmx_fio_doe_string(fio, buf, ("buf"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 252);
253 }
254 while ((gmx_strcasecmp(buf, itemstr[key]) != 0));
255
256 if (gmx_strcasecmp(buf, itemstr[key]) != 0)
257 {
258 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
258, "\nCould not find section heading %s", itemstr[key]);
259 }
260 else if (gmx_fio_getdebug(fio))
261 {
262 fprintf(stderrstderr, " and found it\n");
263 }
264 }
265 }
266}
267
268#define do_section(fio, key, bRead)_do_section(fio, key, bRead, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 268) _do_section(fio, key, bRead, __FILE__"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", __LINE__268)
269
270/**************************************************************
271 *
272 * Now the higer level routines that do io of the structures and arrays
273 *
274 **************************************************************/
275static void do_pullgrp_tpx_pre95(t_fileio *fio,
276 t_pull_group *pgrp,
277 t_pull_coord *pcrd,
278 gmx_bool bRead,
279 int file_version)
280{
281 int i;
282 rvec tmp;
283
284 gmx_fio_do_int(fio, pgrp->nat)gmx_fio_doe_int(fio, &pgrp->nat, ("pgrp->nat"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 284);
285 if (bRead)
286 {
287 snew(pgrp->ind, pgrp->nat)(pgrp->ind) = save_calloc("pgrp->ind", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 287, (pgrp->nat), sizeof(*(pgrp->ind)));
288 }
289 gmx_fio_ndo_int(fio, pgrp->ind, pgrp->nat)gmx_fio_ndoe_int(fio, pgrp->ind, pgrp->nat, ("pgrp->ind"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
289);
290 gmx_fio_do_int(fio, pgrp->nweight)gmx_fio_doe_int(fio, &pgrp->nweight, ("pgrp->nweight"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
290);
291 if (bRead)
292 {
293 snew(pgrp->weight, pgrp->nweight)(pgrp->weight) = save_calloc("pgrp->weight", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 293, (pgrp->nweight), sizeof(*(pgrp->weight)));
294 }
295 gmx_fio_ndo_real(fio, pgrp->weight, pgrp->nweight)gmx_fio_ndoe_real(fio, pgrp->weight, pgrp->nweight, ("pgrp->weight"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
295);
296 gmx_fio_do_int(fio, pgrp->pbcatom)gmx_fio_doe_int(fio, &pgrp->pbcatom, ("pgrp->pbcatom"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
296);
297 gmx_fio_do_rvec(fio, pcrd->vec)gmx_fio_doe_rvec(fio, &pcrd->vec, ("pcrd->vec"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 297);
298 clear_rvec(pcrd->origin);
299 gmx_fio_do_rvec(fio, tmp)gmx_fio_doe_rvec(fio, &tmp, ("tmp"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 299);
300 pcrd->init = tmp[0];
301 gmx_fio_do_real(fio, pcrd->rate)gmx_fio_doe_real(fio, &pcrd->rate, ("pcrd->rate"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 301);
302 gmx_fio_do_real(fio, pcrd->k)gmx_fio_doe_real(fio, &pcrd->k, ("pcrd->k"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 302);
303 if (file_version >= 56)
304 {
305 gmx_fio_do_real(fio, pcrd->kB)gmx_fio_doe_real(fio, &pcrd->kB, ("pcrd->kB"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 305);
306 }
307 else
308 {
309 pcrd->kB = pcrd->k;
310 }
311}
312
313static void do_pull_group(t_fileio *fio, t_pull_group *pgrp, gmx_bool bRead)
314{
315 int i;
316
317 gmx_fio_do_int(fio, pgrp->nat)gmx_fio_doe_int(fio, &pgrp->nat, ("pgrp->nat"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 317);
318 if (bRead)
319 {
320 snew(pgrp->ind, pgrp->nat)(pgrp->ind) = save_calloc("pgrp->ind", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 320, (pgrp->nat), sizeof(*(pgrp->ind)));
321 }
322 gmx_fio_ndo_int(fio, pgrp->ind, pgrp->nat)gmx_fio_ndoe_int(fio, pgrp->ind, pgrp->nat, ("pgrp->ind"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
322);
323 gmx_fio_do_int(fio, pgrp->nweight)gmx_fio_doe_int(fio, &pgrp->nweight, ("pgrp->nweight"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
323);
324 if (bRead)
325 {
326 snew(pgrp->weight, pgrp->nweight)(pgrp->weight) = save_calloc("pgrp->weight", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 326, (pgrp->nweight), sizeof(*(pgrp->weight)));
327 }
328 gmx_fio_ndo_real(fio, pgrp->weight, pgrp->nweight)gmx_fio_ndoe_real(fio, pgrp->weight, pgrp->nweight, ("pgrp->weight"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
328);
329 gmx_fio_do_int(fio, pgrp->pbcatom)gmx_fio_doe_int(fio, &pgrp->pbcatom, ("pgrp->pbcatom"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
329);
330}
331
332static void do_pull_coord(t_fileio *fio, t_pull_coord *pcrd)
333{
334 int i;
335
336 gmx_fio_do_int(fio, pcrd->group[0])gmx_fio_doe_int(fio, &pcrd->group[0], ("pcrd->group[0]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
336);
337 gmx_fio_do_int(fio, pcrd->group[1])gmx_fio_doe_int(fio, &pcrd->group[1], ("pcrd->group[1]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
337);
338 gmx_fio_do_rvec(fio, pcrd->origin)gmx_fio_doe_rvec(fio, &pcrd->origin, ("pcrd->origin"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
338);
339 gmx_fio_do_rvec(fio, pcrd->vec)gmx_fio_doe_rvec(fio, &pcrd->vec, ("pcrd->vec"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 339);
340 gmx_fio_do_real(fio, pcrd->init)gmx_fio_doe_real(fio, &pcrd->init, ("pcrd->init"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 340);
341 gmx_fio_do_real(fio, pcrd->rate)gmx_fio_doe_real(fio, &pcrd->rate, ("pcrd->rate"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 341);
342 gmx_fio_do_real(fio, pcrd->k)gmx_fio_doe_real(fio, &pcrd->k, ("pcrd->k"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 342);
343 gmx_fio_do_real(fio, pcrd->kB)gmx_fio_doe_real(fio, &pcrd->kB, ("pcrd->kB"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 343);
344}
345
346static void do_expandedvals(t_fileio *fio, t_expanded *expand, t_lambda *fepvals, gmx_bool bRead, int file_version)
347{
348 /* i is used in the ndo_double macro*/
349 int i;
350 real fv;
351 real rdum;
352 int n_lambda = fepvals->n_lambda;
353
354 /* reset the lambda calculation window */
355 fepvals->lambda_start_n = 0;
356 fepvals->lambda_stop_n = n_lambda;
357 if (file_version >= 79)
358 {
359 if (n_lambda > 0)
360 {
361 if (bRead)
362 {
363 snew(expand->init_lambda_weights, n_lambda)(expand->init_lambda_weights) = save_calloc("expand->init_lambda_weights"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 363
, (n_lambda), sizeof(*(expand->init_lambda_weights)));
364 }
365 gmx_fio_ndo_real(fio, expand->init_lambda_weights, n_lambda)gmx_fio_ndoe_real(fio, expand->init_lambda_weights, n_lambda
, ("expand->init_lambda_weights"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 365);
366 gmx_fio_do_gmx_bool(fio, expand->bInit_weights)gmx_fio_doe_gmx_bool(fio, &expand->bInit_weights, ("expand->bInit_weights"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
366);
367 }
368
369 gmx_fio_do_int(fio, expand->nstexpanded)gmx_fio_doe_int(fio, &expand->nstexpanded, ("expand->nstexpanded"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
369);
370 gmx_fio_do_int(fio, expand->elmcmove)gmx_fio_doe_int(fio, &expand->elmcmove, ("expand->elmcmove"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
370);
371 gmx_fio_do_int(fio, expand->elamstats)gmx_fio_doe_int(fio, &expand->elamstats, ("expand->elamstats"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
371);
372 gmx_fio_do_int(fio, expand->lmc_repeats)gmx_fio_doe_int(fio, &expand->lmc_repeats, ("expand->lmc_repeats"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
372);
373 gmx_fio_do_int(fio, expand->gibbsdeltalam)gmx_fio_doe_int(fio, &expand->gibbsdeltalam, ("expand->gibbsdeltalam"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
373);
374 gmx_fio_do_int(fio, expand->lmc_forced_nstart)gmx_fio_doe_int(fio, &expand->lmc_forced_nstart, ("expand->lmc_forced_nstart"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
374);
375 gmx_fio_do_int(fio, expand->lmc_seed)gmx_fio_doe_int(fio, &expand->lmc_seed, ("expand->lmc_seed"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
375);
376 gmx_fio_do_real(fio, expand->mc_temp)gmx_fio_doe_real(fio, &expand->mc_temp, ("expand->mc_temp"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
376);
377 gmx_fio_do_int(fio, expand->bSymmetrizedTMatrix)gmx_fio_doe_int(fio, &expand->bSymmetrizedTMatrix, ("expand->bSymmetrizedTMatrix"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
377);
378 gmx_fio_do_int(fio, expand->nstTij)gmx_fio_doe_int(fio, &expand->nstTij, ("expand->nstTij"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
378);
379 gmx_fio_do_int(fio, expand->minvarmin)gmx_fio_doe_int(fio, &expand->minvarmin, ("expand->minvarmin"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
379);
380 gmx_fio_do_int(fio, expand->c_range)gmx_fio_doe_int(fio, &expand->c_range, ("expand->c_range"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
380);
381 gmx_fio_do_real(fio, expand->wl_scale)gmx_fio_doe_real(fio, &expand->wl_scale, ("expand->wl_scale"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
381);
382 gmx_fio_do_real(fio, expand->wl_ratio)gmx_fio_doe_real(fio, &expand->wl_ratio, ("expand->wl_ratio"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
382);
383 gmx_fio_do_real(fio, expand->init_wl_delta)gmx_fio_doe_real(fio, &expand->init_wl_delta, ("expand->init_wl_delta"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
383);
384 gmx_fio_do_gmx_bool(fio, expand->bWLoneovert)gmx_fio_doe_gmx_bool(fio, &expand->bWLoneovert, ("expand->bWLoneovert"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
384);
385 gmx_fio_do_int(fio, expand->elmceq)gmx_fio_doe_int(fio, &expand->elmceq, ("expand->elmceq"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
385);
386 gmx_fio_do_int(fio, expand->equil_steps)gmx_fio_doe_int(fio, &expand->equil_steps, ("expand->equil_steps"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
386);
387 gmx_fio_do_int(fio, expand->equil_samples)gmx_fio_doe_int(fio, &expand->equil_samples, ("expand->equil_samples"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
387);
388 gmx_fio_do_int(fio, expand->equil_n_at_lam)gmx_fio_doe_int(fio, &expand->equil_n_at_lam, ("expand->equil_n_at_lam"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
388);
389 gmx_fio_do_real(fio, expand->equil_wl_delta)gmx_fio_doe_real(fio, &expand->equil_wl_delta, ("expand->equil_wl_delta"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
389);
390 gmx_fio_do_real(fio, expand->equil_ratio)gmx_fio_doe_real(fio, &expand->equil_ratio, ("expand->equil_ratio"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
390);
391 }
392}
393
394static void do_simtempvals(t_fileio *fio, t_simtemp *simtemp, int n_lambda, gmx_bool bRead,
395 int file_version)
396{
397 if (file_version >= 79)
398 {
399 gmx_fio_do_int(fio, simtemp->eSimTempScale)gmx_fio_doe_int(fio, &simtemp->eSimTempScale, ("simtemp->eSimTempScale"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
399);
400 gmx_fio_do_real(fio, simtemp->simtemp_high)gmx_fio_doe_real(fio, &simtemp->simtemp_high, ("simtemp->simtemp_high"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
400);
401 gmx_fio_do_real(fio, simtemp->simtemp_low)gmx_fio_doe_real(fio, &simtemp->simtemp_low, ("simtemp->simtemp_low"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
401);
402 if (n_lambda > 0)
403 {
404 if (bRead)
405 {
406 snew(simtemp->temperatures, n_lambda)(simtemp->temperatures) = save_calloc("simtemp->temperatures"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 406
, (n_lambda), sizeof(*(simtemp->temperatures)));
407 }
408 gmx_fio_ndo_real(fio, simtemp->temperatures, n_lambda)gmx_fio_ndoe_real(fio, simtemp->temperatures, n_lambda, ("simtemp->temperatures"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
408);
409 }
410 }
411}
412
413static void do_imd(t_fileio *fio, t_IMD *imd, gmx_bool bRead)
414{
415 gmx_fio_do_int(fio, imd->nat)gmx_fio_doe_int(fio, &imd->nat, ("imd->nat"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 415);
416 if (bRead)
417 {
418 snew(imd->ind, imd->nat)(imd->ind) = save_calloc("imd->ind", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 418, (imd->nat), sizeof(*(imd->ind)));
419 }
420 gmx_fio_ndo_int(fio, imd->ind, imd->nat)gmx_fio_ndoe_int(fio, imd->ind, imd->nat, ("imd->ind"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
420);
421}
422
423static void do_fepvals(t_fileio *fio, t_lambda *fepvals, gmx_bool bRead, int file_version)
424{
425 /* i is defined in the ndo_double macro; use g to iterate. */
426 int i, g;
427 real fv;
428 real rdum;
429
430 /* free energy values */
431
432 if (file_version >= 79)
433 {
434 gmx_fio_do_int(fio, fepvals->init_fep_state)gmx_fio_doe_int(fio, &fepvals->init_fep_state, ("fepvals->init_fep_state"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
434);
435 gmx_fio_do_double(fio, fepvals->init_lambda)gmx_fio_doe_double(fio, &fepvals->init_lambda, ("fepvals->init_lambda"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
435);
436 gmx_fio_do_double(fio, fepvals->delta_lambda)gmx_fio_doe_double(fio, &fepvals->delta_lambda, ("fepvals->delta_lambda"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
436);
437 }
438 else if (file_version >= 59)
439 {
440 gmx_fio_do_double(fio, fepvals->init_lambda)gmx_fio_doe_double(fio, &fepvals->init_lambda, ("fepvals->init_lambda"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
440);
441 gmx_fio_do_double(fio, fepvals->delta_lambda)gmx_fio_doe_double(fio, &fepvals->delta_lambda, ("fepvals->delta_lambda"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
441);
442 }
443 else
444 {
445 gmx_fio_do_real(fio, rdum)gmx_fio_doe_real(fio, &rdum, ("rdum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 445);
446 fepvals->init_lambda = rdum;
447 gmx_fio_do_real(fio, rdum)gmx_fio_doe_real(fio, &rdum, ("rdum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 447);
448 fepvals->delta_lambda = rdum;
449 }
450 if (file_version >= 79)
451 {
452 gmx_fio_do_int(fio, fepvals->n_lambda)gmx_fio_doe_int(fio, &fepvals->n_lambda, ("fepvals->n_lambda"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
452);
453 if (bRead)
454 {
455 snew(fepvals->all_lambda, efptNR)(fepvals->all_lambda) = save_calloc("fepvals->all_lambda"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 455
, (efptNR), sizeof(*(fepvals->all_lambda)));
456 }
457 for (g = 0; g < efptNR; g++)
458 {
459 if (fepvals->n_lambda > 0)
460 {
461 if (bRead)
462 {
463 snew(fepvals->all_lambda[g], fepvals->n_lambda)(fepvals->all_lambda[g]) = save_calloc("fepvals->all_lambda[g]"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 463
, (fepvals->n_lambda), sizeof(*(fepvals->all_lambda[g])
));
464 }
465 gmx_fio_ndo_double(fio, fepvals->all_lambda[g], fepvals->n_lambda)gmx_fio_ndoe_double(fio, fepvals->all_lambda[g], fepvals->
n_lambda, ("fepvals->all_lambda[g]"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 465);
466 gmx_fio_ndo_int(fio, fepvals->separate_dvdl, efptNR)gmx_fio_ndoe_int(fio, fepvals->separate_dvdl, efptNR, ("fepvals->separate_dvdl"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
466);
467 }
468 else if (fepvals->init_lambda >= 0)
469 {
470 fepvals->separate_dvdl[efptFEP] = TRUE1;
471 }
472 }
473 }
474 else if (file_version >= 64)
475 {
476 gmx_fio_do_int(fio, fepvals->n_lambda)gmx_fio_doe_int(fio, &fepvals->n_lambda, ("fepvals->n_lambda"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
476);
477 if (bRead)
478 {
479 int g;
480
481 snew(fepvals->all_lambda, efptNR)(fepvals->all_lambda) = save_calloc("fepvals->all_lambda"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 481
, (efptNR), sizeof(*(fepvals->all_lambda)));
482 /* still allocate the all_lambda array's contents. */
483 for (g = 0; g < efptNR; g++)
484 {
485 if (fepvals->n_lambda > 0)
486 {
487 snew(fepvals->all_lambda[g], fepvals->n_lambda)(fepvals->all_lambda[g]) = save_calloc("fepvals->all_lambda[g]"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 487
, (fepvals->n_lambda), sizeof(*(fepvals->all_lambda[g])
));
488 }
489 }
490 }
491 gmx_fio_ndo_double(fio, fepvals->all_lambda[efptFEP],gmx_fio_ndoe_double(fio, fepvals->all_lambda[efptFEP], fepvals
->n_lambda, ("fepvals->all_lambda[efptFEP]"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 492)
492 fepvals->n_lambda)gmx_fio_ndoe_double(fio, fepvals->all_lambda[efptFEP], fepvals
->n_lambda, ("fepvals->all_lambda[efptFEP]"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 492);
493 if (fepvals->init_lambda >= 0)
494 {
495 int g, h;
496
497 fepvals->separate_dvdl[efptFEP] = TRUE1;
498
499 if (bRead)
500 {
501 /* copy the contents of the efptFEP lambda component to all
502 the other components */
503 for (g = 0; g < efptNR; g++)
504 {
505 for (h = 0; h < fepvals->n_lambda; h++)
506 {
507 if (g != efptFEP)
508 {
509 fepvals->all_lambda[g][h] =
510 fepvals->all_lambda[efptFEP][h];
511 }
512 }
513 }
514 }
515 }
516 }
517 else
518 {
519 fepvals->n_lambda = 0;
520 fepvals->all_lambda = NULL((void*)0);
521 if (fepvals->init_lambda >= 0)
522 {
523 fepvals->separate_dvdl[efptFEP] = TRUE1;
524 }
525 }
526 if (file_version >= 13)
527 {
528 gmx_fio_do_real(fio, fepvals->sc_alpha)gmx_fio_doe_real(fio, &fepvals->sc_alpha, ("fepvals->sc_alpha"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
528);
529 }
530 else
531 {
532 fepvals->sc_alpha = 0;
533 }
534 if (file_version >= 38)
535 {
536 gmx_fio_do_int(fio, fepvals->sc_power)gmx_fio_doe_int(fio, &fepvals->sc_power, ("fepvals->sc_power"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
536);
537 }
538 else
539 {
540 fepvals->sc_power = 2;
541 }
542 if (file_version >= 79)
543 {
544 gmx_fio_do_real(fio, fepvals->sc_r_power)gmx_fio_doe_real(fio, &fepvals->sc_r_power, ("fepvals->sc_r_power"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
544);
545 }
546 else
547 {
548 fepvals->sc_r_power = 6.0;
549 }
550 if (file_version >= 15)
551 {
552 gmx_fio_do_real(fio, fepvals->sc_sigma)gmx_fio_doe_real(fio, &fepvals->sc_sigma, ("fepvals->sc_sigma"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
552);
553 }
554 else
555 {
556 fepvals->sc_sigma = 0.3;
557 }
558 if (bRead)
559 {
560 if (file_version >= 71)
561 {
562 fepvals->sc_sigma_min = fepvals->sc_sigma;
563 }
564 else
565 {
566 fepvals->sc_sigma_min = 0;
567 }
568 }
569 if (file_version >= 79)
570 {
571 gmx_fio_do_int(fio, fepvals->bScCoul)gmx_fio_doe_int(fio, &fepvals->bScCoul, ("fepvals->bScCoul"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
571);
572 }
573 else
574 {
575 fepvals->bScCoul = TRUE1;
576 }
577 if (file_version >= 64)
578 {
579 gmx_fio_do_int(fio, fepvals->nstdhdl)gmx_fio_doe_int(fio, &fepvals->nstdhdl, ("fepvals->nstdhdl"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
579);
580 }
581 else
582 {
583 fepvals->nstdhdl = 1;
584 }
585
586 if (file_version >= 73)
587 {
588 gmx_fio_do_int(fio, fepvals->separate_dhdl_file)gmx_fio_doe_int(fio, &fepvals->separate_dhdl_file, ("fepvals->separate_dhdl_file"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
588);
589 gmx_fio_do_int(fio, fepvals->dhdl_derivatives)gmx_fio_doe_int(fio, &fepvals->dhdl_derivatives, ("fepvals->dhdl_derivatives"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
589);
590 }
591 else
592 {
593 fepvals->separate_dhdl_file = esepdhdlfileYES;
594 fepvals->dhdl_derivatives = edhdlderivativesYES;
595 }
596 if (file_version >= 71)
597 {
598 gmx_fio_do_int(fio, fepvals->dh_hist_size)gmx_fio_doe_int(fio, &fepvals->dh_hist_size, ("fepvals->dh_hist_size"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
598);
599 gmx_fio_do_double(fio, fepvals->dh_hist_spacing)gmx_fio_doe_double(fio, &fepvals->dh_hist_spacing, ("fepvals->dh_hist_spacing"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
599);
600 }
601 else
602 {
603 fepvals->dh_hist_size = 0;
604 fepvals->dh_hist_spacing = 0.1;
605 }
606 if (file_version >= 79)
607 {
608 gmx_fio_do_int(fio, fepvals->bPrintEnergy)gmx_fio_doe_int(fio, &fepvals->bPrintEnergy, ("fepvals->bPrintEnergy"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
608);
609 }
610 else
611 {
612 fepvals->bPrintEnergy = FALSE0;
613 }
614
615 /* handle lambda_neighbors */
616 if ((file_version >= 83 && file_version < 90) || file_version >= 92)
617 {
618 gmx_fio_do_int(fio, fepvals->lambda_neighbors)gmx_fio_doe_int(fio, &fepvals->lambda_neighbors, ("fepvals->lambda_neighbors"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
618);
619 if ( (fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0) &&
620 (fepvals->init_lambda < 0) )
621 {
622 fepvals->lambda_start_n = (fepvals->init_fep_state -
623 fepvals->lambda_neighbors);
624 fepvals->lambda_stop_n = (fepvals->init_fep_state +
625 fepvals->lambda_neighbors + 1);
626 if (fepvals->lambda_start_n < 0)
627 {
628 fepvals->lambda_start_n = 0;;
629 }
630 if (fepvals->lambda_stop_n >= fepvals->n_lambda)
631 {
632 fepvals->lambda_stop_n = fepvals->n_lambda;
633 }
634 }
635 else
636 {
637 fepvals->lambda_start_n = 0;
638 fepvals->lambda_stop_n = fepvals->n_lambda;
639 }
640 }
641 else
642 {
643 fepvals->lambda_start_n = 0;
644 fepvals->lambda_stop_n = fepvals->n_lambda;
645 }
646}
647
648static void do_pull(t_fileio *fio, t_pull *pull, gmx_bool bRead, int file_version)
649{
650 int g;
651
652 if (file_version >= 95)
653 {
654 gmx_fio_do_int(fio, pull->ngroup)gmx_fio_doe_int(fio, &pull->ngroup, ("pull->ngroup"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
654);
655 }
656 gmx_fio_do_int(fio, pull->ncoord)gmx_fio_doe_int(fio, &pull->ncoord, ("pull->ncoord"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
656);
657 if (file_version < 95)
658 {
659 pull->ngroup = pull->ncoord + 1;
660 }
661 gmx_fio_do_int(fio, pull->eGeom)gmx_fio_doe_int(fio, &pull->eGeom, ("pull->eGeom"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 661
);
662 gmx_fio_do_ivec(fio, pull->dim)gmx_fio_doe_ivec(fio, &pull->dim, ("pull->dim"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 662);
663 gmx_fio_do_real(fio, pull->cyl_r1)gmx_fio_doe_real(fio, &pull->cyl_r1, ("pull->cyl_r1"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
663);
664 gmx_fio_do_real(fio, pull->cyl_r0)gmx_fio_doe_real(fio, &pull->cyl_r0, ("pull->cyl_r0"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
664);
665 gmx_fio_do_real(fio, pull->constr_tol)gmx_fio_doe_real(fio, &pull->constr_tol, ("pull->constr_tol"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
665);
666 if (file_version >= 95)
667 {
668 gmx_fio_do_int(fio, pull->bPrintRef)gmx_fio_doe_int(fio, &pull->bPrintRef, ("pull->bPrintRef"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
668);
669 }
670 gmx_fio_do_int(fio, pull->nstxout)gmx_fio_doe_int(fio, &pull->nstxout, ("pull->nstxout"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
670);
671 gmx_fio_do_int(fio, pull->nstfout)gmx_fio_doe_int(fio, &pull->nstfout, ("pull->nstfout"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
671);
672 if (bRead)
673 {
674 snew(pull->group, pull->ngroup)(pull->group) = save_calloc("pull->group", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 674, (pull->ngroup), sizeof(*(pull->group)));
675 snew(pull->coord, pull->ncoord)(pull->coord) = save_calloc("pull->coord", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 675, (pull->ncoord), sizeof(*(pull->coord)));
676 }
677 if (file_version < 95)
678 {
679 /* epullgPOS for position pulling, before epullgDIRPBC was removed */
680 if (pull->eGeom == epullgDIRPBC)
681 {
682 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
682, "pull-geometry=position is no longer supported");
683 }
684 if (pull->eGeom > epullgDIRPBC)
685 {
686 pull->eGeom -= 1;
687 }
688
689 for (g = 0; g < pull->ngroup; g++)
690 {
691 /* We read and ignore a pull coordinate for group 0 */
692 do_pullgrp_tpx_pre95(fio, &pull->group[g], &pull->coord[max(g-1, 0)(((g-1) > (0)) ? (g-1) : (0) )],
693 bRead, file_version);
694 if (g > 0)
695 {
696 pull->coord[g-1].group[0] = 0;
697 pull->coord[g-1].group[1] = g;
698 }
699 }
700
701 pull->bPrintRef = (pull->group[0].nat > 0);
702 }
703 else
704 {
705 for (g = 0; g < pull->ngroup; g++)
706 {
707 do_pull_group(fio, &pull->group[g], bRead);
708 }
709 for (g = 0; g < pull->ncoord; g++)
710 {
711 do_pull_coord(fio, &pull->coord[g]);
712 }
713 }
714}
715
716
717static void do_rotgrp(t_fileio *fio, t_rotgrp *rotg, gmx_bool bRead)
718{
719 int i;
720
721 gmx_fio_do_int(fio, rotg->eType)gmx_fio_doe_int(fio, &rotg->eType, ("rotg->eType"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 721
);
722 gmx_fio_do_int(fio, rotg->bMassW)gmx_fio_doe_int(fio, &rotg->bMassW, ("rotg->bMassW"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
722);
723 gmx_fio_do_int(fio, rotg->nat)gmx_fio_doe_int(fio, &rotg->nat, ("rotg->nat"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 723);
724 if (bRead)
725 {
726 snew(rotg->ind, rotg->nat)(rotg->ind) = save_calloc("rotg->ind", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 726, (rotg->nat), sizeof(*(rotg->ind)));
727 }
728 gmx_fio_ndo_int(fio, rotg->ind, rotg->nat)gmx_fio_ndoe_int(fio, rotg->ind, rotg->nat, ("rotg->ind"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
728);
729 if (bRead)
730 {
731 snew(rotg->x_ref, rotg->nat)(rotg->x_ref) = save_calloc("rotg->x_ref", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 731, (rotg->nat), sizeof(*(rotg->x_ref)));
732 }
733 gmx_fio_ndo_rvec(fio, rotg->x_ref, rotg->nat)gmx_fio_ndoe_rvec(fio, rotg->x_ref, rotg->nat, ("rotg->x_ref"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
733);
734 gmx_fio_do_rvec(fio, rotg->vec)gmx_fio_doe_rvec(fio, &rotg->vec, ("rotg->vec"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 734);
735 gmx_fio_do_rvec(fio, rotg->pivot)gmx_fio_doe_rvec(fio, &rotg->pivot, ("rotg->pivot")
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 735
);
736 gmx_fio_do_real(fio, rotg->rate)gmx_fio_doe_real(fio, &rotg->rate, ("rotg->rate"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 736);
737 gmx_fio_do_real(fio, rotg->k)gmx_fio_doe_real(fio, &rotg->k, ("rotg->k"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 737);
738 gmx_fio_do_real(fio, rotg->slab_dist)gmx_fio_doe_real(fio, &rotg->slab_dist, ("rotg->slab_dist"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
738);
739 gmx_fio_do_real(fio, rotg->min_gaussian)gmx_fio_doe_real(fio, &rotg->min_gaussian, ("rotg->min_gaussian"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
739);
740 gmx_fio_do_real(fio, rotg->eps)gmx_fio_doe_real(fio, &rotg->eps, ("rotg->eps"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 740);
741 gmx_fio_do_int(fio, rotg->eFittype)gmx_fio_doe_int(fio, &rotg->eFittype, ("rotg->eFittype"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
741);
742 gmx_fio_do_int(fio, rotg->PotAngle_nstep)gmx_fio_doe_int(fio, &rotg->PotAngle_nstep, ("rotg->PotAngle_nstep"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
742);
743 gmx_fio_do_real(fio, rotg->PotAngle_step)gmx_fio_doe_real(fio, &rotg->PotAngle_step, ("rotg->PotAngle_step"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
743);
744}
745
746static void do_rot(t_fileio *fio, t_rot *rot, gmx_bool bRead)
747{
748 int g;
749
750 gmx_fio_do_int(fio, rot->ngrp)gmx_fio_doe_int(fio, &rot->ngrp, ("rot->ngrp"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 750);
751 gmx_fio_do_int(fio, rot->nstrout)gmx_fio_doe_int(fio, &rot->nstrout, ("rot->nstrout"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
751);
752 gmx_fio_do_int(fio, rot->nstsout)gmx_fio_doe_int(fio, &rot->nstsout, ("rot->nstsout"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
752);
753 if (bRead)
754 {
755 snew(rot->grp, rot->ngrp)(rot->grp) = save_calloc("rot->grp", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 755, (rot->ngrp), sizeof(*(rot->grp)));
756 }
757 for (g = 0; g < rot->ngrp; g++)
758 {
759 do_rotgrp(fio, &rot->grp[g], bRead);
760 }
761}
762
763
764static void do_swapcoords(t_fileio *fio, t_swapcoords *swap, gmx_bool bRead)
765{
766 int i, j;
767
768
769 gmx_fio_do_int(fio, swap->nat)gmx_fio_doe_int(fio, &swap->nat, ("swap->nat"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 769);
770 gmx_fio_do_int(fio, swap->nat_sol)gmx_fio_doe_int(fio, &swap->nat_sol, ("swap->nat_sol"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
770);
771 for (j = 0; j < 2; j++)
772 {
773 gmx_fio_do_int(fio, swap->nat_split[j])gmx_fio_doe_int(fio, &swap->nat_split[j], ("swap->nat_split[j]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
773);
774 gmx_fio_do_int(fio, swap->massw_split[j])gmx_fio_doe_int(fio, &swap->massw_split[j], ("swap->massw_split[j]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
774);
775 }
776 gmx_fio_do_int(fio, swap->nstswap)gmx_fio_doe_int(fio, &swap->nstswap, ("swap->nstswap"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
776);
777 gmx_fio_do_int(fio, swap->nAverage)gmx_fio_doe_int(fio, &swap->nAverage, ("swap->nAverage"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
777);
778 gmx_fio_do_real(fio, swap->threshold)gmx_fio_doe_real(fio, &swap->threshold, ("swap->threshold"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
778);
779 gmx_fio_do_real(fio, swap->cyl0r)gmx_fio_doe_real(fio, &swap->cyl0r, ("swap->cyl0r")
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 779
);
780 gmx_fio_do_real(fio, swap->cyl0u)gmx_fio_doe_real(fio, &swap->cyl0u, ("swap->cyl0u")
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 780
);
781 gmx_fio_do_real(fio, swap->cyl0l)gmx_fio_doe_real(fio, &swap->cyl0l, ("swap->cyl0l")
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 781
);
782 gmx_fio_do_real(fio, swap->cyl1r)gmx_fio_doe_real(fio, &swap->cyl1r, ("swap->cyl1r")
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 782
);
783 gmx_fio_do_real(fio, swap->cyl1u)gmx_fio_doe_real(fio, &swap->cyl1u, ("swap->cyl1u")
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 783
);
784 gmx_fio_do_real(fio, swap->cyl1l)gmx_fio_doe_real(fio, &swap->cyl1l, ("swap->cyl1l")
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 784
);
785
786 if (bRead)
787 {
788 snew(swap->ind, swap->nat)(swap->ind) = save_calloc("swap->ind", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 788, (swap->nat), sizeof(*(swap->ind)));
789 snew(swap->ind_sol, swap->nat_sol)(swap->ind_sol) = save_calloc("swap->ind_sol", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 789, (swap->nat_sol), sizeof(*(swap->ind_sol)));
790 for (j = 0; j < 2; j++)
791 {
792 snew(swap->ind_split[j], swap->nat_split[j])(swap->ind_split[j]) = save_calloc("swap->ind_split[j]"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 792
, (swap->nat_split[j]), sizeof(*(swap->ind_split[j])));
793 }
794 }
795
796 gmx_fio_ndo_int(fio, swap->ind, swap->nat)gmx_fio_ndoe_int(fio, swap->ind, swap->nat, ("swap->ind"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
796);
797 gmx_fio_ndo_int(fio, swap->ind_sol, swap->nat_sol)gmx_fio_ndoe_int(fio, swap->ind_sol, swap->nat_sol, ("swap->ind_sol"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
797);
798 for (j = 0; j < 2; j++)
799 {
800 gmx_fio_ndo_int(fio, swap->ind_split[j], swap->nat_split[j])gmx_fio_ndoe_int(fio, swap->ind_split[j], swap->nat_split
[j], ("swap->ind_split[j]"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 800);
801 }
802
803 for (j = 0; j < eCompNR; j++)
804 {
805 gmx_fio_do_int(fio, swap->nanions[j])gmx_fio_doe_int(fio, &swap->nanions[j], ("swap->nanions[j]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
805);
806 gmx_fio_do_int(fio, swap->ncations[j])gmx_fio_doe_int(fio, &swap->ncations[j], ("swap->ncations[j]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
806);
807 }
808
809}
810
811
812static void do_inputrec(t_fileio *fio, t_inputrec *ir, gmx_bool bRead,
813 int file_version, real *fudgeQQ)
814{
815 int i, j, k, *tmp, idum = 0;
816 real rdum, bd_temp;
817 rvec vdum;
818 gmx_bool bSimAnn;
819 real zerotemptime, finish_t, init_temp, finish_temp;
820
821 if (file_version != tpx_version)
822 {
823 /* Give a warning about features that are not accessible */
824 fprintf(stderrstderr, "Note: file tpx version %d, software tpx version %d\n",
825 file_version, tpx_version);
826 }
827
828 if (bRead)
829 {
830 init_inputrec(ir);
831 }
832
833 if (file_version == 0)
834 {
835 return;
836 }
837
838 /* Basic inputrec stuff */
839 gmx_fio_do_int(fio, ir->eI)gmx_fio_doe_int(fio, &ir->eI, ("ir->eI"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 839);
840 if (file_version >= 62)
841 {
842 gmx_fio_do_int64(fio, ir->nsteps)gmx_fio_doe_int64(fio, &ir->nsteps, ("ir->nsteps"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 842
);
843 }
844 else
845 {
846 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 846);
847 ir->nsteps = idum;
848 }
849 if (file_version > 25)
850 {
851 if (file_version >= 62)
852 {
853 gmx_fio_do_int64(fio, ir->init_step)gmx_fio_doe_int64(fio, &ir->init_step, ("ir->init_step"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
853);
854 }
855 else
856 {
857 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 857);
858 ir->init_step = idum;
859 }
860 }
861 else
862 {
863 ir->init_step = 0;
864 }
865
866 if (file_version >= 58)
867 {
868 gmx_fio_do_int(fio, ir->simulation_part)gmx_fio_doe_int(fio, &ir->simulation_part, ("ir->simulation_part"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
868);
869 }
870 else
871 {
872 ir->simulation_part = 1;
873 }
874
875 if (file_version >= 67)
876 {
877 gmx_fio_do_int(fio, ir->nstcalcenergy)gmx_fio_doe_int(fio, &ir->nstcalcenergy, ("ir->nstcalcenergy"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
877);
878 }
879 else
880 {
881 ir->nstcalcenergy = 1;
882 }
883 if (file_version < 53)
884 {
885 /* The pbc info has been moved out of do_inputrec,
886 * since we always want it, also without reading the inputrec.
887 */
888 gmx_fio_do_int(fio, ir->ePBC)gmx_fio_doe_int(fio, &ir->ePBC, ("ir->ePBC"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 888);
889 if ((file_version <= 15) && (ir->ePBC == 2))
890 {
891 ir->ePBC = epbcNONE;
892 }
893 if (file_version >= 45)
894 {
895 gmx_fio_do_int(fio, ir->bPeriodicMols)gmx_fio_doe_int(fio, &ir->bPeriodicMols, ("ir->bPeriodicMols"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
895);
896 }
897 else
898 {
899 if (ir->ePBC == 2)
900 {
901 ir->ePBC = epbcXYZ;
902 ir->bPeriodicMols = TRUE1;
903 }
904 else
905 {
906 ir->bPeriodicMols = FALSE0;
907 }
908 }
909 }
910 if (file_version >= 81)
911 {
912 gmx_fio_do_int(fio, ir->cutoff_scheme)gmx_fio_doe_int(fio, &ir->cutoff_scheme, ("ir->cutoff_scheme"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
912);
913 if (file_version < 94)
914 {
915 ir->cutoff_scheme = 1 - ir->cutoff_scheme;
916 }
917 }
918 else
919 {
920 ir->cutoff_scheme = ecutsGROUP;
921 }
922 gmx_fio_do_int(fio, ir->ns_type)gmx_fio_doe_int(fio, &ir->ns_type, ("ir->ns_type"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 922
);
923 gmx_fio_do_int(fio, ir->nstlist)gmx_fio_doe_int(fio, &ir->nstlist, ("ir->nstlist"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 923
);
924 gmx_fio_do_int(fio, ir->ndelta)gmx_fio_doe_int(fio, &ir->ndelta, ("ir->ndelta"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 924);
925 if (file_version < 41)
926 {
927 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 927);
928 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 928);
929 }
930 if (file_version >= 45)
931 {
932 gmx_fio_do_real(fio, ir->rtpi)gmx_fio_doe_real(fio, &ir->rtpi, ("ir->rtpi"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 932);
933 }
934 else
935 {
936 ir->rtpi = 0.05;
937 }
938 gmx_fio_do_int(fio, ir->nstcomm)gmx_fio_doe_int(fio, &ir->nstcomm, ("ir->nstcomm"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 938
);
939 if (file_version > 34)
940 {
941 gmx_fio_do_int(fio, ir->comm_mode)gmx_fio_doe_int(fio, &ir->comm_mode, ("ir->comm_mode"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
941);
942 }
943 else if (ir->nstcomm < 0)
944 {
945 ir->comm_mode = ecmANGULAR;
946 }
947 else
948 {
949 ir->comm_mode = ecmLINEAR;
950 }
951 ir->nstcomm = abs(ir->nstcomm);
952
953 if (file_version > 25)
954 {
955 gmx_fio_do_int(fio, ir->nstcheckpoint)gmx_fio_doe_int(fio, &ir->nstcheckpoint, ("ir->nstcheckpoint"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
955);
956 }
957 else
958 {
959 ir->nstcheckpoint = 0;
960 }
961
962 gmx_fio_do_int(fio, ir->nstcgsteep)gmx_fio_doe_int(fio, &ir->nstcgsteep, ("ir->nstcgsteep"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
962);
963
964 if (file_version >= 30)
965 {
966 gmx_fio_do_int(fio, ir->nbfgscorr)gmx_fio_doe_int(fio, &ir->nbfgscorr, ("ir->nbfgscorr"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
966);
967 }
968 else if (bRead)
969 {
970 ir->nbfgscorr = 10;
971 }
972
973 gmx_fio_do_int(fio, ir->nstlog)gmx_fio_doe_int(fio, &ir->nstlog, ("ir->nstlog"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 973);
974 gmx_fio_do_int(fio, ir->nstxout)gmx_fio_doe_int(fio, &ir->nstxout, ("ir->nstxout"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 974
);
975 gmx_fio_do_int(fio, ir->nstvout)gmx_fio_doe_int(fio, &ir->nstvout, ("ir->nstvout"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 975
);
976 gmx_fio_do_int(fio, ir->nstfout)gmx_fio_doe_int(fio, &ir->nstfout, ("ir->nstfout"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 976
);
977 gmx_fio_do_int(fio, ir->nstenergy)gmx_fio_doe_int(fio, &ir->nstenergy, ("ir->nstenergy"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
977);
978 gmx_fio_do_int(fio, ir->nstxout_compressed)gmx_fio_doe_int(fio, &ir->nstxout_compressed, ("ir->nstxout_compressed"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
978);
979 if (file_version >= 59)
980 {
981 gmx_fio_do_double(fio, ir->init_t)gmx_fio_doe_double(fio, &ir->init_t, ("ir->init_t")
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 981
);
982 gmx_fio_do_double(fio, ir->delta_t)gmx_fio_doe_double(fio, &ir->delta_t, ("ir->delta_t"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
982);
983 }
984 else
985 {
986 gmx_fio_do_real(fio, rdum)gmx_fio_doe_real(fio, &rdum, ("rdum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 986);
987 ir->init_t = rdum;
988 gmx_fio_do_real(fio, rdum)gmx_fio_doe_real(fio, &rdum, ("rdum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 988);
989 ir->delta_t = rdum;
990 }
991 gmx_fio_do_real(fio, ir->x_compression_precision)gmx_fio_doe_real(fio, &ir->x_compression_precision, ("ir->x_compression_precision"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
991);
992 if (file_version < 19)
993 {
994 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 994);
995 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 995);
996 }
997 if (file_version < 18)
998 {
999 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 999);
1000 }
1001 if (file_version >= 81)
1002 {
1003 gmx_fio_do_real(fio, ir->verletbuf_tol)gmx_fio_doe_real(fio, &ir->verletbuf_tol, ("ir->verletbuf_tol"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1003);
1004 }
1005 else
1006 {
1007 ir->verletbuf_tol = 0;
1008 }
1009 gmx_fio_do_real(fio, ir->rlist)gmx_fio_doe_real(fio, &ir->rlist, ("ir->rlist"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1009);
1010 if (file_version >= 67)
1011 {
1012 gmx_fio_do_real(fio, ir->rlistlong)gmx_fio_doe_real(fio, &ir->rlistlong, ("ir->rlistlong"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1012);
1013 }
1014 if (file_version >= 82 && file_version != 90)
1015 {
1016 gmx_fio_do_int(fio, ir->nstcalclr)gmx_fio_doe_int(fio, &ir->nstcalclr, ("ir->nstcalclr"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1016);
1017 }
1018 else
1019 {
1020 /* Calculate at NS steps */
1021 ir->nstcalclr = ir->nstlist;
1022 }
1023 gmx_fio_do_int(fio, ir->coulombtype)gmx_fio_doe_int(fio, &ir->coulombtype, ("ir->coulombtype"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1023);
1024 if (file_version < 32 && ir->coulombtype == eelRF)
1025 {
1026 ir->coulombtype = eelRF_NEC;
1027 }
1028 if (file_version >= 81)
1029 {
1030 gmx_fio_do_int(fio, ir->coulomb_modifier)gmx_fio_doe_int(fio, &ir->coulomb_modifier, ("ir->coulomb_modifier"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1030);
1031 }
1032 else
1033 {
1034 ir->coulomb_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
1035 }
1036 gmx_fio_do_real(fio, ir->rcoulomb_switch)gmx_fio_doe_real(fio, &ir->rcoulomb_switch, ("ir->rcoulomb_switch"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1036);
1037 gmx_fio_do_real(fio, ir->rcoulomb)gmx_fio_doe_real(fio, &ir->rcoulomb, ("ir->rcoulomb"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1037);
1038 gmx_fio_do_int(fio, ir->vdwtype)gmx_fio_doe_int(fio, &ir->vdwtype, ("ir->vdwtype"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1038
);
1039 if (file_version >= 81)
1040 {
1041 gmx_fio_do_int(fio, ir->vdw_modifier)gmx_fio_doe_int(fio, &ir->vdw_modifier, ("ir->vdw_modifier"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1041);
1042 }
1043 else
1044 {
1045 ir->vdw_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
1046 }
1047 gmx_fio_do_real(fio, ir->rvdw_switch)gmx_fio_doe_real(fio, &ir->rvdw_switch, ("ir->rvdw_switch"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1047);
1048 gmx_fio_do_real(fio, ir->rvdw)gmx_fio_doe_real(fio, &ir->rvdw, ("ir->rvdw"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1048);
1049 if (file_version < 67)
1050 {
1051 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
1052 }
1053 gmx_fio_do_int(fio, ir->eDispCorr)gmx_fio_doe_int(fio, &ir->eDispCorr, ("ir->eDispCorr"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1053);
1054 gmx_fio_do_real(fio, ir->epsilon_r)gmx_fio_doe_real(fio, &ir->epsilon_r, ("ir->epsilon_r"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1054);
1055 if (file_version >= 37)
1056 {
1057 gmx_fio_do_real(fio, ir->epsilon_rf)gmx_fio_doe_real(fio, &ir->epsilon_rf, ("ir->epsilon_rf"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1057);
1058 }
1059 else
1060 {
1061 if (EEL_RF(ir->coulombtype)((ir->coulombtype) == eelRF || (ir->coulombtype) == eelGRF
|| (ir->coulombtype) == eelRF_NEC || (ir->coulombtype)
== eelRF_ZERO ))
1062 {
1063 ir->epsilon_rf = ir->epsilon_r;
1064 ir->epsilon_r = 1.0;
1065 }
1066 else
1067 {
1068 ir->epsilon_rf = 1.0;
1069 }
1070 }
1071 if (file_version >= 29)
1072 {
1073 gmx_fio_do_real(fio, ir->tabext)gmx_fio_doe_real(fio, &ir->tabext, ("ir->tabext"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1073);
1074 }
1075 else
1076 {
1077 ir->tabext = 1.0;
1078 }
1079
1080 if (file_version > 25)
1081 {
1082 gmx_fio_do_int(fio, ir->gb_algorithm)gmx_fio_doe_int(fio, &ir->gb_algorithm, ("ir->gb_algorithm"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1082);
1083 gmx_fio_do_int(fio, ir->nstgbradii)gmx_fio_doe_int(fio, &ir->nstgbradii, ("ir->nstgbradii"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1083);
1084 gmx_fio_do_real(fio, ir->rgbradii)gmx_fio_doe_real(fio, &ir->rgbradii, ("ir->rgbradii"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1084);
1085 gmx_fio_do_real(fio, ir->gb_saltconc)gmx_fio_doe_real(fio, &ir->gb_saltconc, ("ir->gb_saltconc"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1085);
1086 gmx_fio_do_int(fio, ir->implicit_solvent)gmx_fio_doe_int(fio, &ir->implicit_solvent, ("ir->implicit_solvent"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1086);
1087 }
1088 else
1089 {
1090 ir->gb_algorithm = egbSTILL;
1091 ir->nstgbradii = 1;
1092 ir->rgbradii = 1.0;
1093 ir->gb_saltconc = 0;
1094 ir->implicit_solvent = eisNO;
1095 }
1096 if (file_version >= 55)
1097 {
1098 gmx_fio_do_real(fio, ir->gb_epsilon_solvent)gmx_fio_doe_real(fio, &ir->gb_epsilon_solvent, ("ir->gb_epsilon_solvent"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1098);
1099 gmx_fio_do_real(fio, ir->gb_obc_alpha)gmx_fio_doe_real(fio, &ir->gb_obc_alpha, ("ir->gb_obc_alpha"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1099);
1100 gmx_fio_do_real(fio, ir->gb_obc_beta)gmx_fio_doe_real(fio, &ir->gb_obc_beta, ("ir->gb_obc_beta"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1100);
1101 gmx_fio_do_real(fio, ir->gb_obc_gamma)gmx_fio_doe_real(fio, &ir->gb_obc_gamma, ("ir->gb_obc_gamma"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1101);
1102 if (file_version >= 60)
1103 {
1104 gmx_fio_do_real(fio, ir->gb_dielectric_offset)gmx_fio_doe_real(fio, &ir->gb_dielectric_offset, ("ir->gb_dielectric_offset"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1104);
1105 gmx_fio_do_int(fio, ir->sa_algorithm)gmx_fio_doe_int(fio, &ir->sa_algorithm, ("ir->sa_algorithm"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1105);
1106 }
1107 else
1108 {
1109 ir->gb_dielectric_offset = 0.009;
1110 ir->sa_algorithm = esaAPPROX;
1111 }
1112 gmx_fio_do_real(fio, ir->sa_surface_tension)gmx_fio_doe_real(fio, &ir->sa_surface_tension, ("ir->sa_surface_tension"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1112);
1113
1114 /* Override sa_surface_tension if it is not changed in the mpd-file */
1115 if (ir->sa_surface_tension < 0)
1116 {
1117 if (ir->gb_algorithm == egbSTILL)
1118 {
1119 ir->sa_surface_tension = 0.0049 * 100 * CAL2JOULE(4.184);
1120 }
1121 else if (ir->gb_algorithm == egbHCT || ir->gb_algorithm == egbOBC)
1122 {
1123 ir->sa_surface_tension = 0.0054 * 100 * CAL2JOULE(4.184);
1124 }
1125 }
1126
1127 }
1128 else
1129 {
1130 /* Better use sensible values than insane (0.0) ones... */
1131 ir->gb_epsilon_solvent = 80;
1132 ir->gb_obc_alpha = 1.0;
1133 ir->gb_obc_beta = 0.8;
1134 ir->gb_obc_gamma = 4.85;
1135 ir->sa_surface_tension = 2.092;
1136 }
1137
1138
1139 if (file_version >= 81)
1140 {
1141 gmx_fio_do_real(fio, ir->fourier_spacing)gmx_fio_doe_real(fio, &ir->fourier_spacing, ("ir->fourier_spacing"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1141);
1142 }
1143 else
1144 {
1145 ir->fourier_spacing = 0.0;
1146 }
1147 gmx_fio_do_int(fio, ir->nkx)gmx_fio_doe_int(fio, &ir->nkx, ("ir->nkx"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1147);
1148 gmx_fio_do_int(fio, ir->nky)gmx_fio_doe_int(fio, &ir->nky, ("ir->nky"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1148);
1149 gmx_fio_do_int(fio, ir->nkz)gmx_fio_doe_int(fio, &ir->nkz, ("ir->nkz"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1149);
1150 gmx_fio_do_int(fio, ir->pme_order)gmx_fio_doe_int(fio, &ir->pme_order, ("ir->pme_order"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1150);
1151 gmx_fio_do_real(fio, ir->ewald_rtol)gmx_fio_doe_real(fio, &ir->ewald_rtol, ("ir->ewald_rtol"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1151);
1152
1153 if (file_version >= 93)
1154 {
1155 gmx_fio_do_real(fio, ir->ewald_rtol_lj)gmx_fio_doe_real(fio, &ir->ewald_rtol_lj, ("ir->ewald_rtol_lj"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1155);
1156 }
1157 else
1158 {
1159 ir->ewald_rtol_lj = ir->ewald_rtol;
1160 }
1161
1162 if (file_version >= 24)
1163 {
1164 gmx_fio_do_int(fio, ir->ewald_geometry)gmx_fio_doe_int(fio, &ir->ewald_geometry, ("ir->ewald_geometry"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1164);
1165 }
1166 else
1167 {
1168 ir->ewald_geometry = eewg3D;
1169 }
1170
1171 if (file_version <= 17)
1172 {
1173 ir->epsilon_surface = 0;
1174 if (file_version == 17)
1175 {
1176 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1176);
1177 }
1178 }
1179 else
1180 {
1181 gmx_fio_do_real(fio, ir->epsilon_surface)gmx_fio_doe_real(fio, &ir->epsilon_surface, ("ir->epsilon_surface"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1181);
1182 }
1183
1184 gmx_fio_do_gmx_bool(fio, ir->bOptFFT)gmx_fio_doe_gmx_bool(fio, &ir->bOptFFT, ("ir->bOptFFT"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1184);
1185
1186 if (file_version >= 93)
1187 {
1188 gmx_fio_do_int(fio, ir->ljpme_combination_rule)gmx_fio_doe_int(fio, &ir->ljpme_combination_rule, ("ir->ljpme_combination_rule"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1188);
1189 }
1190 gmx_fio_do_gmx_bool(fio, ir->bContinuation)gmx_fio_doe_gmx_bool(fio, &ir->bContinuation, ("ir->bContinuation"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1190);
1191 gmx_fio_do_int(fio, ir->etc)gmx_fio_doe_int(fio, &ir->etc, ("ir->etc"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1191);
1192 /* before version 18, ir->etc was a gmx_bool (ir->btc),
1193 * but the values 0 and 1 still mean no and
1194 * berendsen temperature coupling, respectively.
1195 */
1196 if (file_version >= 79)
1197 {
1198 gmx_fio_do_gmx_bool(fio, ir->bPrintNHChains)gmx_fio_doe_gmx_bool(fio, &ir->bPrintNHChains, ("ir->bPrintNHChains"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1198);
1199 }
1200 if (file_version >= 71)
1201 {
1202 gmx_fio_do_int(fio, ir->nsttcouple)gmx_fio_doe_int(fio, &ir->nsttcouple, ("ir->nsttcouple"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1202);
1203 }
1204 else
1205 {
1206 ir->nsttcouple = ir->nstcalcenergy;
1207 }
1208 if (file_version <= 15)
1209 {
1210 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1210);
1211 }
1212 if (file_version <= 17)
1213 {
1214 gmx_fio_do_int(fio, ir->epct)gmx_fio_doe_int(fio, &ir->epct, ("ir->epct"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1214);
1215 if (file_version <= 15)
1216 {
1217 if (ir->epct == 5)
1218 {
1219 ir->epct = epctSURFACETENSION;
1220 }
1221 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1221);
1222 }
1223 ir->epct -= 1;
1224 /* we have removed the NO alternative at the beginning */
1225 if (ir->epct == -1)
1226 {
1227 ir->epc = epcNO;
1228 ir->epct = epctISOTROPIC;
1229 }
1230 else
1231 {
1232 ir->epc = epcBERENDSEN;
1233 }
1234 }
1235 else
1236 {
1237 gmx_fio_do_int(fio, ir->epc)gmx_fio_doe_int(fio, &ir->epc, ("ir->epc"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1237);
1238 gmx_fio_do_int(fio, ir->epct)gmx_fio_doe_int(fio, &ir->epct, ("ir->epct"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1238);
1239 }
1240 if (file_version >= 71)
1241 {
1242 gmx_fio_do_int(fio, ir->nstpcouple)gmx_fio_doe_int(fio, &ir->nstpcouple, ("ir->nstpcouple"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1242);
1243 }
1244 else
1245 {
1246 ir->nstpcouple = ir->nstcalcenergy;
1247 }
1248 gmx_fio_do_real(fio, ir->tau_p)gmx_fio_doe_real(fio, &ir->tau_p, ("ir->tau_p"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1248);
1249 if (file_version <= 15)
1250 {
1251 gmx_fio_do_rvec(fio, vdum)gmx_fio_doe_rvec(fio, &vdum, ("vdum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1251);
1252 clear_mat(ir->ref_p);
1253 for (i = 0; i < DIM3; i++)
1254 {
1255 ir->ref_p[i][i] = vdum[i];
1256 }
1257 }
1258 else
1259 {
1260 gmx_fio_do_rvec(fio, ir->ref_p[XX])gmx_fio_doe_rvec(fio, &ir->ref_p[0], ("ir->ref_p[XX]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1260);
1261 gmx_fio_do_rvec(fio, ir->ref_p[YY])gmx_fio_doe_rvec(fio, &ir->ref_p[1], ("ir->ref_p[YY]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1261);
1262 gmx_fio_do_rvec(fio, ir->ref_p[ZZ])gmx_fio_doe_rvec(fio, &ir->ref_p[2], ("ir->ref_p[ZZ]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1262);
1263 }
1264 if (file_version <= 15)
1265 {
1266 gmx_fio_do_rvec(fio, vdum)gmx_fio_doe_rvec(fio, &vdum, ("vdum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1266);
1267 clear_mat(ir->compress);
1268 for (i = 0; i < DIM3; i++)
1269 {
1270 ir->compress[i][i] = vdum[i];
1271 }
1272 }
1273 else
1274 {
1275 gmx_fio_do_rvec(fio, ir->compress[XX])gmx_fio_doe_rvec(fio, &ir->compress[0], ("ir->compress[XX]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1275);
1276 gmx_fio_do_rvec(fio, ir->compress[YY])gmx_fio_doe_rvec(fio, &ir->compress[1], ("ir->compress[YY]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1276);
1277 gmx_fio_do_rvec(fio, ir->compress[ZZ])gmx_fio_doe_rvec(fio, &ir->compress[2], ("ir->compress[ZZ]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1277);
1278 }
1279 if (file_version >= 47)
1280 {
1281 gmx_fio_do_int(fio, ir->refcoord_scaling)gmx_fio_doe_int(fio, &ir->refcoord_scaling, ("ir->refcoord_scaling"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1281);
1282 gmx_fio_do_rvec(fio, ir->posres_com)gmx_fio_doe_rvec(fio, &ir->posres_com, ("ir->posres_com"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1282);
1283 gmx_fio_do_rvec(fio, ir->posres_comB)gmx_fio_doe_rvec(fio, &ir->posres_comB, ("ir->posres_comB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1283);
1284 }
1285 else
1286 {
1287 ir->refcoord_scaling = erscNO;
1288 clear_rvec(ir->posres_com);
1289 clear_rvec(ir->posres_comB);
1290 }
1291 if ((file_version > 25) && (file_version < 79))
1292 {
1293 gmx_fio_do_int(fio, ir->andersen_seed)gmx_fio_doe_int(fio, &ir->andersen_seed, ("ir->andersen_seed"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1293);
1294 }
1295 else
1296 {
1297 ir->andersen_seed = 0;
1298 }
1299 if (file_version < 26)
1300 {
1301 gmx_fio_do_gmx_bool(fio, bSimAnn)gmx_fio_doe_gmx_bool(fio, &bSimAnn, ("bSimAnn"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1301);
1302 gmx_fio_do_real(fio, zerotemptime)gmx_fio_doe_real(fio, &zerotemptime, ("zerotemptime"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1302);
1303 }
1304
1305 if (file_version < 37)
1306 {
1307 gmx_fio_do_real(fio, rdum)gmx_fio_doe_real(fio, &rdum, ("rdum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1307);
1308 }
1309
1310 gmx_fio_do_real(fio, ir->shake_tol)gmx_fio_doe_real(fio, &ir->shake_tol, ("ir->shake_tol"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1310);
1311 if (file_version < 54)
1312 {
1313 gmx_fio_do_real(fio, *fudgeQQ)gmx_fio_doe_real(fio, &*fudgeQQ, ("*fudgeQQ"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1313);
1314 }
1315
1316 gmx_fio_do_int(fio, ir->efep)gmx_fio_doe_int(fio, &ir->efep, ("ir->efep"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1316);
1317 if (file_version <= 14 && ir->efep != efepNO)
1318 {
1319 ir->efep = efepYES;
1320 }
1321 do_fepvals(fio, ir->fepvals, bRead, file_version);
1322
1323 if (file_version >= 79)
1324 {
1325 gmx_fio_do_gmx_bool(fio, ir->bSimTemp)gmx_fio_doe_gmx_bool(fio, &ir->bSimTemp, ("ir->bSimTemp"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1325);
1326 if (ir->bSimTemp)
1327 {
1328 ir->bSimTemp = TRUE1;
1329 }
1330 }
1331 else
1332 {
1333 ir->bSimTemp = FALSE0;
1334 }
1335 if (ir->bSimTemp)
1336 {
1337 do_simtempvals(fio, ir->simtempvals, ir->fepvals->n_lambda, bRead, file_version);
1338 }
1339
1340 if (file_version >= 79)
1341 {
1342 gmx_fio_do_gmx_bool(fio, ir->bExpanded)gmx_fio_doe_gmx_bool(fio, &ir->bExpanded, ("ir->bExpanded"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1342);
1343 if (ir->bExpanded)
1344 {
1345 ir->bExpanded = TRUE1;
1346 }
1347 else
1348 {
1349 ir->bExpanded = FALSE0;
1350 }
1351 }
1352 if (ir->bExpanded)
1353 {
1354 do_expandedvals(fio, ir->expandedvals, ir->fepvals, bRead, file_version);
1355 }
1356 if (file_version >= 57)
1357 {
1358 gmx_fio_do_int(fio, ir->eDisre)gmx_fio_doe_int(fio, &ir->eDisre, ("ir->eDisre"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1358);
1359 }
1360 gmx_fio_do_int(fio, ir->eDisreWeighting)gmx_fio_doe_int(fio, &ir->eDisreWeighting, ("ir->eDisreWeighting"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1360);
1361 if (file_version < 22)
1362 {
1363 if (ir->eDisreWeighting == 0)
1364 {
1365 ir->eDisreWeighting = edrwEqual;
1366 }
1367 else
1368 {
1369 ir->eDisreWeighting = edrwConservative;
1370 }
1371 }
1372 gmx_fio_do_gmx_bool(fio, ir->bDisreMixed)gmx_fio_doe_gmx_bool(fio, &ir->bDisreMixed, ("ir->bDisreMixed"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1372);
1373 gmx_fio_do_real(fio, ir->dr_fc)gmx_fio_doe_real(fio, &ir->dr_fc, ("ir->dr_fc"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1373);
1374 gmx_fio_do_real(fio, ir->dr_tau)gmx_fio_doe_real(fio, &ir->dr_tau, ("ir->dr_tau"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1374);
1375 gmx_fio_do_int(fio, ir->nstdisreout)gmx_fio_doe_int(fio, &ir->nstdisreout, ("ir->nstdisreout"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1375);
1376 if (file_version >= 22)
1377 {
1378 gmx_fio_do_real(fio, ir->orires_fc)gmx_fio_doe_real(fio, &ir->orires_fc, ("ir->orires_fc"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1378);
1379 gmx_fio_do_real(fio, ir->orires_tau)gmx_fio_doe_real(fio, &ir->orires_tau, ("ir->orires_tau"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1379);
1380 gmx_fio_do_int(fio, ir->nstorireout)gmx_fio_doe_int(fio, &ir->nstorireout, ("ir->nstorireout"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1380);
1381 }
1382 else
1383 {
1384 ir->orires_fc = 0;
1385 ir->orires_tau = 0;
1386 ir->nstorireout = 0;
1387 }
1388 if (file_version >= 26 && file_version < 79)
1389 {
1390 gmx_fio_do_real(fio, ir->dihre_fc)gmx_fio_doe_real(fio, &ir->dihre_fc, ("ir->dihre_fc"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1390);
1391 if (file_version < 56)
1392 {
1393 gmx_fio_do_real(fio, rdum)gmx_fio_doe_real(fio, &rdum, ("rdum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1393);
1394 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1394);
1395 }
1396 }
1397 else
1398 {
1399 ir->dihre_fc = 0;
1400 }
1401
1402 gmx_fio_do_real(fio, ir->em_stepsize)gmx_fio_doe_real(fio, &ir->em_stepsize, ("ir->em_stepsize"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1402);
1403 gmx_fio_do_real(fio, ir->em_tol)gmx_fio_doe_real(fio, &ir->em_tol, ("ir->em_tol"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1403);
1404 if (file_version >= 22)
1405 {
1406 gmx_fio_do_gmx_bool(fio, ir->bShakeSOR)gmx_fio_doe_gmx_bool(fio, &ir->bShakeSOR, ("ir->bShakeSOR"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1406);
1407 }
1408 else if (bRead)
1409 {
1410 ir->bShakeSOR = TRUE1;
1411 }
1412 if (file_version >= 11)
1413 {
1414 gmx_fio_do_int(fio, ir->niter)gmx_fio_doe_int(fio, &ir->niter, ("ir->niter"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1414);
1415 }
1416 else if (bRead)
1417 {
1418 ir->niter = 25;
1419 fprintf(stderrstderr, "Note: niter not in run input file, setting it to %d\n",
1420 ir->niter);
1421 }
1422 if (file_version >= 21)
1423 {
1424 gmx_fio_do_real(fio, ir->fc_stepsize)gmx_fio_doe_real(fio, &ir->fc_stepsize, ("ir->fc_stepsize"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1424);
1425 }
1426 else
1427 {
1428 ir->fc_stepsize = 0;
1429 }
1430 gmx_fio_do_int(fio, ir->eConstrAlg)gmx_fio_doe_int(fio, &ir->eConstrAlg, ("ir->eConstrAlg"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1430);
1431 gmx_fio_do_int(fio, ir->nProjOrder)gmx_fio_doe_int(fio, &ir->nProjOrder, ("ir->nProjOrder"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1431);
1432 gmx_fio_do_real(fio, ir->LincsWarnAngle)gmx_fio_doe_real(fio, &ir->LincsWarnAngle, ("ir->LincsWarnAngle"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1432);
1433 if (file_version <= 14)
1434 {
1435 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1435);
1436 }
1437 if (file_version >= 26)
1438 {
1439 gmx_fio_do_int(fio, ir->nLincsIter)gmx_fio_doe_int(fio, &ir->nLincsIter, ("ir->nLincsIter"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1439);
1440 }
1441 else if (bRead)
1442 {
1443 ir->nLincsIter = 1;
1444 fprintf(stderrstderr, "Note: nLincsIter not in run input file, setting it to %d\n",
1445 ir->nLincsIter);
1446 }
1447 if (file_version < 33)
1448 {
1449 gmx_fio_do_real(fio, bd_temp)gmx_fio_doe_real(fio, &bd_temp, ("bd_temp"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1449);
1450 }
1451 gmx_fio_do_real(fio, ir->bd_fric)gmx_fio_doe_real(fio, &ir->bd_fric, ("ir->bd_fric")
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1451
);
1452 if (file_version >= tpxv_Use64BitRandomSeed)
1453 {
1454 gmx_fio_do_int64(fio, ir->ld_seed)gmx_fio_doe_int64(fio, &ir->ld_seed, ("ir->ld_seed"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1454);
1455 }
1456 else
1457 {
1458 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1458);
1459 ir->ld_seed = idum;
1460 }
1461 if (file_version >= 33)
1462 {
1463 for (i = 0; i < DIM3; i++)
1464 {
1465 gmx_fio_do_rvec(fio, ir->deform[i])gmx_fio_doe_rvec(fio, &ir->deform[i], ("ir->deform[i]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1465);
1466 }
1467 }
1468 else
1469 {
1470 for (i = 0; i < DIM3; i++)
1471 {
1472 clear_rvec(ir->deform[i]);
1473 }
1474 }
1475 if (file_version >= 14)
1476 {
1477 gmx_fio_do_real(fio, ir->cos_accel)gmx_fio_doe_real(fio, &ir->cos_accel, ("ir->cos_accel"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1477);
1478 }
1479 else if (bRead)
1480 {
1481 ir->cos_accel = 0;
1482 }
1483 gmx_fio_do_int(fio, ir->userint1)gmx_fio_doe_int(fio, &ir->userint1, ("ir->userint1"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1483);
1484 gmx_fio_do_int(fio, ir->userint2)gmx_fio_doe_int(fio, &ir->userint2, ("ir->userint2"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1484);
1485 gmx_fio_do_int(fio, ir->userint3)gmx_fio_doe_int(fio, &ir->userint3, ("ir->userint3"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1485);
1486 gmx_fio_do_int(fio, ir->userint4)gmx_fio_doe_int(fio, &ir->userint4, ("ir->userint4"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1486);
1487 gmx_fio_do_real(fio, ir->userreal1)gmx_fio_doe_real(fio, &ir->userreal1, ("ir->userreal1"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1487);
1488 gmx_fio_do_real(fio, ir->userreal2)gmx_fio_doe_real(fio, &ir->userreal2, ("ir->userreal2"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1488);
1489 gmx_fio_do_real(fio, ir->userreal3)gmx_fio_doe_real(fio, &ir->userreal3, ("ir->userreal3"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1489);
1490 gmx_fio_do_real(fio, ir->userreal4)gmx_fio_doe_real(fio, &ir->userreal4, ("ir->userreal4"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1490);
1491
1492 /* AdResS stuff */
1493 if (file_version >= 77)
1494 {
1495 gmx_fio_do_gmx_bool(fio, ir->bAdress)gmx_fio_doe_gmx_bool(fio, &ir->bAdress, ("ir->bAdress"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1495);
1496 if (ir->bAdress)
1497 {
1498 if (bRead)
1499 {
1500 snew(ir->adress, 1)(ir->adress) = save_calloc("ir->adress", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1500, (1), sizeof(*(ir->adress)));
1501 }
1502 gmx_fio_do_int(fio, ir->adress->type)gmx_fio_doe_int(fio, &ir->adress->type, ("ir->adress->type"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1502);
1503 gmx_fio_do_real(fio, ir->adress->const_wf)gmx_fio_doe_real(fio, &ir->adress->const_wf, ("ir->adress->const_wf"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1503);
1504 gmx_fio_do_real(fio, ir->adress->ex_width)gmx_fio_doe_real(fio, &ir->adress->ex_width, ("ir->adress->ex_width"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1504);
1505 gmx_fio_do_real(fio, ir->adress->hy_width)gmx_fio_doe_real(fio, &ir->adress->hy_width, ("ir->adress->hy_width"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1505);
1506 gmx_fio_do_int(fio, ir->adress->icor)gmx_fio_doe_int(fio, &ir->adress->icor, ("ir->adress->icor"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1506);
1507 gmx_fio_do_int(fio, ir->adress->site)gmx_fio_doe_int(fio, &ir->adress->site, ("ir->adress->site"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1507);
1508 gmx_fio_do_rvec(fio, ir->adress->refs)gmx_fio_doe_rvec(fio, &ir->adress->refs, ("ir->adress->refs"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1508);
1509 gmx_fio_do_int(fio, ir->adress->n_tf_grps)gmx_fio_doe_int(fio, &ir->adress->n_tf_grps, ("ir->adress->n_tf_grps"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1509);
1510 gmx_fio_do_real(fio, ir->adress->ex_forcecap)gmx_fio_doe_real(fio, &ir->adress->ex_forcecap, ("ir->adress->ex_forcecap"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1510);
1511 gmx_fio_do_int(fio, ir->adress->n_energy_grps)gmx_fio_doe_int(fio, &ir->adress->n_energy_grps, ("ir->adress->n_energy_grps"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1511);
1512 gmx_fio_do_int(fio, ir->adress->do_hybridpairs)gmx_fio_doe_int(fio, &ir->adress->do_hybridpairs, (
"ir->adress->do_hybridpairs"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1512);
1513
1514 if (bRead)
1515 {
1516 snew(ir->adress->tf_table_index, ir->adress->n_tf_grps)(ir->adress->tf_table_index) = save_calloc("ir->adress->tf_table_index"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1516
, (ir->adress->n_tf_grps), sizeof(*(ir->adress->tf_table_index
)));
1517 }
1518 if (ir->adress->n_tf_grps > 0)
1519 {
1520 gmx_fio_ndo_int(fio, ir->adress->tf_table_index, ir->adress->n_tf_grps)gmx_fio_ndoe_int(fio, ir->adress->tf_table_index, ir->
adress->n_tf_grps, ("ir->adress->tf_table_index"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1520);
1521 }
1522 if (bRead)
1523 {
1524 snew(ir->adress->group_explicit, ir->adress->n_energy_grps)(ir->adress->group_explicit) = save_calloc("ir->adress->group_explicit"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1524
, (ir->adress->n_energy_grps), sizeof(*(ir->adress->
group_explicit)));
1525 }
1526 if (ir->adress->n_energy_grps > 0)
1527 {
1528 gmx_fio_ndo_int(fio, ir->adress->group_explicit, ir->adress->n_energy_grps)gmx_fio_ndoe_int(fio, ir->adress->group_explicit, ir->
adress->n_energy_grps, ("ir->adress->group_explicit"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1528);
1529 }
1530 }
1531 }
1532 else
1533 {
1534 ir->bAdress = FALSE0;
1535 }
1536
1537 /* pull stuff */
1538 if (file_version >= 48)
1539 {
1540 gmx_fio_do_int(fio, ir->ePull)gmx_fio_doe_int(fio, &ir->ePull, ("ir->ePull"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1540);
1541 if (ir->ePull != epullNO)
1542 {
1543 if (bRead)
1544 {
1545 snew(ir->pull, 1)(ir->pull) = save_calloc("ir->pull", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1545, (1), sizeof(*(ir->pull)));
1546 }
1547 do_pull(fio, ir->pull, bRead, file_version);
1548 }
1549 }
1550 else
1551 {
1552 ir->ePull = epullNO;
1553 }
1554
1555 /* Enforced rotation */
1556 if (file_version >= 74)
1557 {
1558 gmx_fio_do_int(fio, ir->bRot)gmx_fio_doe_int(fio, &ir->bRot, ("ir->bRot"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1558);
1559 if (ir->bRot == TRUE1)
1560 {
1561 if (bRead)
1562 {
1563 snew(ir->rot, 1)(ir->rot) = save_calloc("ir->rot", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1563, (1), sizeof(*(ir->rot)));
1564 }
1565 do_rot(fio, ir->rot, bRead);
1566 }
1567 }
1568 else
1569 {
1570 ir->bRot = FALSE0;
1571 }
1572
1573 /* Interactive molecular dynamics */
1574 if (file_version >= tpxv_InteractiveMolecularDynamics)
1575 {
1576 gmx_fio_do_int(fio, ir->bIMD)gmx_fio_doe_int(fio, &ir->bIMD, ("ir->bIMD"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1576);
1577 if (TRUE1 == ir->bIMD)
1578 {
1579 if (bRead)
1580 {
1581 snew(ir->imd, 1)(ir->imd) = save_calloc("ir->imd", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1581, (1), sizeof(*(ir->imd)));
1582 }
1583 do_imd(fio, ir->imd, bRead);
1584 }
1585 }
1586 else
1587 {
1588 /* We don't support IMD sessions for old .tpr files */
1589 ir->bIMD = FALSE0;
1590 }
1591
1592 /* grpopts stuff */
1593 gmx_fio_do_int(fio, ir->opts.ngtc)gmx_fio_doe_int(fio, &ir->opts.ngtc, ("ir->opts.ngtc"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1593);
1594 if (file_version >= 69)
1595 {
1596 gmx_fio_do_int(fio, ir->opts.nhchainlength)gmx_fio_doe_int(fio, &ir->opts.nhchainlength, ("ir->opts.nhchainlength"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1596);
1597 }
1598 else
1599 {
1600 ir->opts.nhchainlength = 1;
1601 }
1602 gmx_fio_do_int(fio, ir->opts.ngacc)gmx_fio_doe_int(fio, &ir->opts.ngacc, ("ir->opts.ngacc"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1602);
1603 gmx_fio_do_int(fio, ir->opts.ngfrz)gmx_fio_doe_int(fio, &ir->opts.ngfrz, ("ir->opts.ngfrz"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1603);
1604 gmx_fio_do_int(fio, ir->opts.ngener)gmx_fio_doe_int(fio, &ir->opts.ngener, ("ir->opts.ngener"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1604);
1605
1606 if (bRead)
1607 {
1608 snew(ir->opts.nrdf, ir->opts.ngtc)(ir->opts.nrdf) = save_calloc("ir->opts.nrdf", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1608, (ir->opts.ngtc), sizeof(*(ir->opts.nrdf)));
1609 snew(ir->opts.ref_t, ir->opts.ngtc)(ir->opts.ref_t) = save_calloc("ir->opts.ref_t", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1609, (ir->opts.ngtc), sizeof(*(ir->opts.ref_t)));
1610 snew(ir->opts.annealing, ir->opts.ngtc)(ir->opts.annealing) = save_calloc("ir->opts.annealing"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1610
, (ir->opts.ngtc), sizeof(*(ir->opts.annealing)));
1611 snew(ir->opts.anneal_npoints, ir->opts.ngtc)(ir->opts.anneal_npoints) = save_calloc("ir->opts.anneal_npoints"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1611
, (ir->opts.ngtc), sizeof(*(ir->opts.anneal_npoints)));
1612 snew(ir->opts.anneal_time, ir->opts.ngtc)(ir->opts.anneal_time) = save_calloc("ir->opts.anneal_time"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1612
, (ir->opts.ngtc), sizeof(*(ir->opts.anneal_time)));
1613 snew(ir->opts.anneal_temp, ir->opts.ngtc)(ir->opts.anneal_temp) = save_calloc("ir->opts.anneal_temp"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1613
, (ir->opts.ngtc), sizeof(*(ir->opts.anneal_temp)));
1614 snew(ir->opts.tau_t, ir->opts.ngtc)(ir->opts.tau_t) = save_calloc("ir->opts.tau_t", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1614, (ir->opts.ngtc), sizeof(*(ir->opts.tau_t)));
1615 snew(ir->opts.nFreeze, ir->opts.ngfrz)(ir->opts.nFreeze) = save_calloc("ir->opts.nFreeze", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1615, (ir->opts.ngfrz), sizeof(*(ir->opts.nFreeze)));
1616 snew(ir->opts.acc, ir->opts.ngacc)(ir->opts.acc) = save_calloc("ir->opts.acc", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1616, (ir->opts.ngacc), sizeof(*(ir->opts.acc)));
1617 snew(ir->opts.egp_flags, ir->opts.ngener*ir->opts.ngener)(ir->opts.egp_flags) = save_calloc("ir->opts.egp_flags"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1617
, (ir->opts.ngener*ir->opts.ngener), sizeof(*(ir->opts
.egp_flags)));
1618 }
1619 if (ir->opts.ngtc > 0)
1620 {
1621 if (bRead && file_version < 13)
1622 {
1623 snew(tmp, ir->opts.ngtc)(tmp) = save_calloc("tmp", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1623, (ir->opts.ngtc), sizeof(*(tmp)));
1624 gmx_fio_ndo_int(fio, tmp, ir->opts.ngtc)gmx_fio_ndoe_int(fio, tmp, ir->opts.ngtc, ("tmp"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1624);
1625 for (i = 0; i < ir->opts.ngtc; i++)
1626 {
1627 ir->opts.nrdf[i] = tmp[i];
1628 }
1629 sfree(tmp)save_free("tmp", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1629, (tmp));
1630 }
1631 else
1632 {
1633 gmx_fio_ndo_real(fio, ir->opts.nrdf, ir->opts.ngtc)gmx_fio_ndoe_real(fio, ir->opts.nrdf, ir->opts.ngtc, ("ir->opts.nrdf"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1633);
1634 }
1635 gmx_fio_ndo_real(fio, ir->opts.ref_t, ir->opts.ngtc)gmx_fio_ndoe_real(fio, ir->opts.ref_t, ir->opts.ngtc, (
"ir->opts.ref_t"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1635);
1636 gmx_fio_ndo_real(fio, ir->opts.tau_t, ir->opts.ngtc)gmx_fio_ndoe_real(fio, ir->opts.tau_t, ir->opts.ngtc, (
"ir->opts.tau_t"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1636);
1637 if (file_version < 33 && ir->eI == eiBD)
1638 {
1639 for (i = 0; i < ir->opts.ngtc; i++)
1640 {
1641 ir->opts.tau_t[i] = bd_temp;
1642 }
1643 }
1644 }
1645 if (ir->opts.ngfrz > 0)
1646 {
1647 gmx_fio_ndo_ivec(fio, ir->opts.nFreeze, ir->opts.ngfrz)gmx_fio_ndoe_ivec(fio, ir->opts.nFreeze, ir->opts.ngfrz
, ("ir->opts.nFreeze"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1647);
1648 }
1649 if (ir->opts.ngacc > 0)
1650 {
1651 gmx_fio_ndo_rvec(fio, ir->opts.acc, ir->opts.ngacc)gmx_fio_ndoe_rvec(fio, ir->opts.acc, ir->opts.ngacc, ("ir->opts.acc"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1651);
1652 }
1653 if (file_version >= 12)
1654 {
1655 gmx_fio_ndo_int(fio, ir->opts.egp_flags,gmx_fio_ndoe_int(fio, ir->opts.egp_flags, ir->opts.ngener
*ir->opts.ngener, ("ir->opts.egp_flags"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1656)
1656 ir->opts.ngener*ir->opts.ngener)gmx_fio_ndoe_int(fio, ir->opts.egp_flags, ir->opts.ngener
*ir->opts.ngener, ("ir->opts.egp_flags"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1656);
1657 }
1658
1659 if (bRead && file_version < 26)
1660 {
1661 for (i = 0; i < ir->opts.ngtc; i++)
1662 {
1663 if (bSimAnn)
1664 {
1665 ir->opts.annealing[i] = eannSINGLE;
1666 ir->opts.anneal_npoints[i] = 2;
1667 snew(ir->opts.anneal_time[i], 2)(ir->opts.anneal_time[i]) = save_calloc("ir->opts.anneal_time[i]"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1667
, (2), sizeof(*(ir->opts.anneal_time[i])));
1668 snew(ir->opts.anneal_temp[i], 2)(ir->opts.anneal_temp[i]) = save_calloc("ir->opts.anneal_temp[i]"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1668
, (2), sizeof(*(ir->opts.anneal_temp[i])));
1669 /* calculate the starting/ending temperatures from reft, zerotemptime, and nsteps */
1670 finish_t = ir->init_t + ir->nsteps * ir->delta_t;
1671 init_temp = ir->opts.ref_t[i]*(1-ir->init_t/zerotemptime);
1672 finish_temp = ir->opts.ref_t[i]*(1-finish_t/zerotemptime);
1673 ir->opts.anneal_time[i][0] = ir->init_t;
1674 ir->opts.anneal_time[i][1] = finish_t;
1675 ir->opts.anneal_temp[i][0] = init_temp;
1676 ir->opts.anneal_temp[i][1] = finish_temp;
1677 }
1678 else
1679 {
1680 ir->opts.annealing[i] = eannNO;
1681 ir->opts.anneal_npoints[i] = 0;
1682 }
1683 }
1684 }
1685 else
1686 {
1687 /* file version 26 or later */
1688 /* First read the lists with annealing and npoints for each group */
1689 gmx_fio_ndo_int(fio, ir->opts.annealing, ir->opts.ngtc)gmx_fio_ndoe_int(fio, ir->opts.annealing, ir->opts.ngtc
, ("ir->opts.annealing"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1689);
1690 gmx_fio_ndo_int(fio, ir->opts.anneal_npoints, ir->opts.ngtc)gmx_fio_ndoe_int(fio, ir->opts.anneal_npoints, ir->opts
.ngtc, ("ir->opts.anneal_npoints"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1690);
1691 for (j = 0; j < (ir->opts.ngtc); j++)
1692 {
1693 k = ir->opts.anneal_npoints[j];
1694 if (bRead)
1695 {
1696 snew(ir->opts.anneal_time[j], k)(ir->opts.anneal_time[j]) = save_calloc("ir->opts.anneal_time[j]"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1696
, (k), sizeof(*(ir->opts.anneal_time[j])));
1697 snew(ir->opts.anneal_temp[j], k)(ir->opts.anneal_temp[j]) = save_calloc("ir->opts.anneal_temp[j]"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1697
, (k), sizeof(*(ir->opts.anneal_temp[j])));
1698 }
1699 gmx_fio_ndo_real(fio, ir->opts.anneal_time[j], k)gmx_fio_ndoe_real(fio, ir->opts.anneal_time[j], k, ("ir->opts.anneal_time[j]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1699);
1700 gmx_fio_ndo_real(fio, ir->opts.anneal_temp[j], k)gmx_fio_ndoe_real(fio, ir->opts.anneal_temp[j], k, ("ir->opts.anneal_temp[j]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1700);
1701 }
1702 }
1703 /* Walls */
1704 if (file_version >= 45)
1705 {
1706 gmx_fio_do_int(fio, ir->nwall)gmx_fio_doe_int(fio, &ir->nwall, ("ir->nwall"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1706);
1707 gmx_fio_do_int(fio, ir->wall_type)gmx_fio_doe_int(fio, &ir->wall_type, ("ir->wall_type"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1707);
1708 if (file_version >= 50)
1709 {
1710 gmx_fio_do_real(fio, ir->wall_r_linpot)gmx_fio_doe_real(fio, &ir->wall_r_linpot, ("ir->wall_r_linpot"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1710);
1711 }
1712 else
1713 {
1714 ir->wall_r_linpot = -1;
1715 }
1716 gmx_fio_do_int(fio, ir->wall_atomtype[0])gmx_fio_doe_int(fio, &ir->wall_atomtype[0], ("ir->wall_atomtype[0]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1716);
1717 gmx_fio_do_int(fio, ir->wall_atomtype[1])gmx_fio_doe_int(fio, &ir->wall_atomtype[1], ("ir->wall_atomtype[1]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1717);
1718 gmx_fio_do_real(fio, ir->wall_density[0])gmx_fio_doe_real(fio, &ir->wall_density[0], ("ir->wall_density[0]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1718);
1719 gmx_fio_do_real(fio, ir->wall_density[1])gmx_fio_doe_real(fio, &ir->wall_density[1], ("ir->wall_density[1]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1719);
1720 gmx_fio_do_real(fio, ir->wall_ewald_zfac)gmx_fio_doe_real(fio, &ir->wall_ewald_zfac, ("ir->wall_ewald_zfac"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1720);
1721 }
1722 else
1723 {
1724 ir->nwall = 0;
1725 ir->wall_type = 0;
1726 ir->wall_atomtype[0] = -1;
1727 ir->wall_atomtype[1] = -1;
1728 ir->wall_density[0] = 0;
1729 ir->wall_density[1] = 0;
1730 ir->wall_ewald_zfac = 3;
1731 }
1732 /* Cosine stuff for electric fields */
1733 for (j = 0; (j < DIM3); j++)
1734 {
1735 gmx_fio_do_int(fio, ir->ex[j].n)gmx_fio_doe_int(fio, &ir->ex[j].n, ("ir->ex[j].n"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1735
);
1736 gmx_fio_do_int(fio, ir->et[j].n)gmx_fio_doe_int(fio, &ir->et[j].n, ("ir->et[j].n"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1736
);
1737 if (bRead)
1738 {
1739 snew(ir->ex[j].a, ir->ex[j].n)(ir->ex[j].a) = save_calloc("ir->ex[j].a", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1739, (ir->ex[j].n), sizeof(*(ir->ex[j].a)));
1740 snew(ir->ex[j].phi, ir->ex[j].n)(ir->ex[j].phi) = save_calloc("ir->ex[j].phi", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1740, (ir->ex[j].n), sizeof(*(ir->ex[j].phi)));
1741 snew(ir->et[j].a, ir->et[j].n)(ir->et[j].a) = save_calloc("ir->et[j].a", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1741, (ir->et[j].n), sizeof(*(ir->et[j].a)));
1742 snew(ir->et[j].phi, ir->et[j].n)(ir->et[j].phi) = save_calloc("ir->et[j].phi", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1742, (ir->et[j].n), sizeof(*(ir->et[j].phi)));
1743 }
1744 gmx_fio_ndo_real(fio, ir->ex[j].a, ir->ex[j].n)gmx_fio_ndoe_real(fio, ir->ex[j].a, ir->ex[j].n, ("ir->ex[j].a"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1744);
1745 gmx_fio_ndo_real(fio, ir->ex[j].phi, ir->ex[j].n)gmx_fio_ndoe_real(fio, ir->ex[j].phi, ir->ex[j].n, ("ir->ex[j].phi"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1745);
1746 gmx_fio_ndo_real(fio, ir->et[j].a, ir->et[j].n)gmx_fio_ndoe_real(fio, ir->et[j].a, ir->et[j].n, ("ir->et[j].a"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1746);
1747 gmx_fio_ndo_real(fio, ir->et[j].phi, ir->et[j].n)gmx_fio_ndoe_real(fio, ir->et[j].phi, ir->et[j].n, ("ir->et[j].phi"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1747);
1748 }
1749
1750 /* Swap ions */
1751 if (file_version >= tpxv_ComputationalElectrophysiology)
1752 {
1753 gmx_fio_do_int(fio, ir->eSwapCoords)gmx_fio_doe_int(fio, &ir->eSwapCoords, ("ir->eSwapCoords"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1753);
1754 if (ir->eSwapCoords != eswapNO)
1755 {
1756 if (bRead)
1757 {
1758 snew(ir->swap, 1)(ir->swap) = save_calloc("ir->swap", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1758, (1), sizeof(*(ir->swap)));
1759 }
1760 do_swapcoords(fio, ir->swap, bRead);
1761 }
1762 }
1763
1764 /* QMMM stuff */
1765 if (file_version >= 39)
1766 {
1767 gmx_fio_do_gmx_bool(fio, ir->bQMMM)gmx_fio_doe_gmx_bool(fio, &ir->bQMMM, ("ir->bQMMM")
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1767
);
1768 gmx_fio_do_int(fio, ir->QMMMscheme)gmx_fio_doe_int(fio, &ir->QMMMscheme, ("ir->QMMMscheme"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1768);
1769 gmx_fio_do_real(fio, ir->scalefactor)gmx_fio_doe_real(fio, &ir->scalefactor, ("ir->scalefactor"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1769);
1770 gmx_fio_do_int(fio, ir->opts.ngQM)gmx_fio_doe_int(fio, &ir->opts.ngQM, ("ir->opts.ngQM"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1770);
1771 if (bRead)
1772 {
1773 snew(ir->opts.QMmethod, ir->opts.ngQM)(ir->opts.QMmethod) = save_calloc("ir->opts.QMmethod", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1773, (ir->opts.ngQM), sizeof(*(ir->opts.QMmethod)));
1774 snew(ir->opts.QMbasis, ir->opts.ngQM)(ir->opts.QMbasis) = save_calloc("ir->opts.QMbasis", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1774, (ir->opts.ngQM), sizeof(*(ir->opts.QMbasis)));
1775 snew(ir->opts.QMcharge, ir->opts.ngQM)(ir->opts.QMcharge) = save_calloc("ir->opts.QMcharge", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1775, (ir->opts.ngQM), sizeof(*(ir->opts.QMcharge)));
1776 snew(ir->opts.QMmult, ir->opts.ngQM)(ir->opts.QMmult) = save_calloc("ir->opts.QMmult", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1776, (ir->opts.ngQM), sizeof(*(ir->opts.QMmult)));
1777 snew(ir->opts.bSH, ir->opts.ngQM)(ir->opts.bSH) = save_calloc("ir->opts.bSH", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1777, (ir->opts.ngQM), sizeof(*(ir->opts.bSH)));
1778 snew(ir->opts.CASorbitals, ir->opts.ngQM)(ir->opts.CASorbitals) = save_calloc("ir->opts.CASorbitals"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1778
, (ir->opts.ngQM), sizeof(*(ir->opts.CASorbitals)));
1779 snew(ir->opts.CASelectrons, ir->opts.ngQM)(ir->opts.CASelectrons) = save_calloc("ir->opts.CASelectrons"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 1779
, (ir->opts.ngQM), sizeof(*(ir->opts.CASelectrons)));
1780 snew(ir->opts.SAon, ir->opts.ngQM)(ir->opts.SAon) = save_calloc("ir->opts.SAon", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1780, (ir->opts.ngQM), sizeof(*(ir->opts.SAon)));
1781 snew(ir->opts.SAoff, ir->opts.ngQM)(ir->opts.SAoff) = save_calloc("ir->opts.SAoff", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1781, (ir->opts.ngQM), sizeof(*(ir->opts.SAoff)));
1782 snew(ir->opts.SAsteps, ir->opts.ngQM)(ir->opts.SAsteps) = save_calloc("ir->opts.SAsteps", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1782, (ir->opts.ngQM), sizeof(*(ir->opts.SAsteps)));
1783 snew(ir->opts.bOPT, ir->opts.ngQM)(ir->opts.bOPT) = save_calloc("ir->opts.bOPT", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1783, (ir->opts.ngQM), sizeof(*(ir->opts.bOPT)));
1784 snew(ir->opts.bTS, ir->opts.ngQM)(ir->opts.bTS) = save_calloc("ir->opts.bTS", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1784, (ir->opts.ngQM), sizeof(*(ir->opts.bTS)));
1785 }
1786 if (ir->opts.ngQM > 0)
1787 {
1788 gmx_fio_ndo_int(fio, ir->opts.QMmethod, ir->opts.ngQM)gmx_fio_ndoe_int(fio, ir->opts.QMmethod, ir->opts.ngQM,
("ir->opts.QMmethod"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1788);
1789 gmx_fio_ndo_int(fio, ir->opts.QMbasis, ir->opts.ngQM)gmx_fio_ndoe_int(fio, ir->opts.QMbasis, ir->opts.ngQM, (
"ir->opts.QMbasis"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1789);
1790 gmx_fio_ndo_int(fio, ir->opts.QMcharge, ir->opts.ngQM)gmx_fio_ndoe_int(fio, ir->opts.QMcharge, ir->opts.ngQM,
("ir->opts.QMcharge"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1790);
1791 gmx_fio_ndo_int(fio, ir->opts.QMmult, ir->opts.ngQM)gmx_fio_ndoe_int(fio, ir->opts.QMmult, ir->opts.ngQM, (
"ir->opts.QMmult"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1791);
1792 gmx_fio_ndo_gmx_bool(fio, ir->opts.bSH, ir->opts.ngQM)gmx_fio_ndoe_gmx_bool(fio, ir->opts.bSH, ir->opts.ngQM,
("ir->opts.bSH"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1792);
1793 gmx_fio_ndo_int(fio, ir->opts.CASorbitals, ir->opts.ngQM)gmx_fio_ndoe_int(fio, ir->opts.CASorbitals, ir->opts.ngQM
, ("ir->opts.CASorbitals"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1793);
1794 gmx_fio_ndo_int(fio, ir->opts.CASelectrons, ir->opts.ngQM)gmx_fio_ndoe_int(fio, ir->opts.CASelectrons, ir->opts.ngQM
, ("ir->opts.CASelectrons"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1794);
1795 gmx_fio_ndo_real(fio, ir->opts.SAon, ir->opts.ngQM)gmx_fio_ndoe_real(fio, ir->opts.SAon, ir->opts.ngQM, ("ir->opts.SAon"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1795);
1796 gmx_fio_ndo_real(fio, ir->opts.SAoff, ir->opts.ngQM)gmx_fio_ndoe_real(fio, ir->opts.SAoff, ir->opts.ngQM, (
"ir->opts.SAoff"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1796);
1797 gmx_fio_ndo_int(fio, ir->opts.SAsteps, ir->opts.ngQM)gmx_fio_ndoe_int(fio, ir->opts.SAsteps, ir->opts.ngQM, (
"ir->opts.SAsteps"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1797);
1798 gmx_fio_ndo_gmx_bool(fio, ir->opts.bOPT, ir->opts.ngQM)gmx_fio_ndoe_gmx_bool(fio, ir->opts.bOPT, ir->opts.ngQM
, ("ir->opts.bOPT"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1798);
1799 gmx_fio_ndo_gmx_bool(fio, ir->opts.bTS, ir->opts.ngQM)gmx_fio_ndoe_gmx_bool(fio, ir->opts.bTS, ir->opts.ngQM,
("ir->opts.bTS"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1799);
1800 }
1801 /* end of QMMM stuff */
1802 }
1803}
1804
1805
1806static void do_harm(t_fileio *fio, t_iparams *iparams)
1807{
1808 gmx_fio_do_real(fio, iparams->harmonic.rA)gmx_fio_doe_real(fio, &iparams->harmonic.rA, ("iparams->harmonic.rA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1808);
1809 gmx_fio_do_real(fio, iparams->harmonic.krA)gmx_fio_doe_real(fio, &iparams->harmonic.krA, ("iparams->harmonic.krA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1809);
1810 gmx_fio_do_real(fio, iparams->harmonic.rB)gmx_fio_doe_real(fio, &iparams->harmonic.rB, ("iparams->harmonic.rB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1810);
1811 gmx_fio_do_real(fio, iparams->harmonic.krB)gmx_fio_doe_real(fio, &iparams->harmonic.krB, ("iparams->harmonic.krB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1811);
1812}
1813
1814void do_iparams(t_fileio *fio, t_functype ftype, t_iparams *iparams,
1815 gmx_bool bRead, int file_version)
1816{
1817 int idum;
1818 real rdum;
1819
1820 if (!bRead)
1821 {
1822 gmx_fio_set_comment(fio, interaction_function[ftype].name);
1823 }
1824 switch (ftype)
1825 {
1826 case F_ANGLES:
1827 case F_G96ANGLES:
1828 case F_BONDS:
1829 case F_G96BONDS:
1830 case F_HARMONIC:
1831 case F_IDIHS:
1832 do_harm(fio, iparams);
1833 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && bRead)
1834 {
1835 /* Correct incorrect storage of parameters */
1836 iparams->pdihs.phiB = iparams->pdihs.phiA;
1837 iparams->pdihs.cpB = iparams->pdihs.cpA;
1838 }
1839 break;
1840 case F_RESTRANGLES:
1841 gmx_fio_do_real(fio, iparams->harmonic.rA)gmx_fio_doe_real(fio, &iparams->harmonic.rA, ("iparams->harmonic.rA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1841);
1842 gmx_fio_do_real(fio, iparams->harmonic.krA)gmx_fio_doe_real(fio, &iparams->harmonic.krA, ("iparams->harmonic.krA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1842);
1843 break;
1844 case F_LINEAR_ANGLES:
1845 gmx_fio_do_real(fio, iparams->linangle.klinA)gmx_fio_doe_real(fio, &iparams->linangle.klinA, ("iparams->linangle.klinA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1845);
1846 gmx_fio_do_real(fio, iparams->linangle.aA)gmx_fio_doe_real(fio, &iparams->linangle.aA, ("iparams->linangle.aA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1846);
1847 gmx_fio_do_real(fio, iparams->linangle.klinB)gmx_fio_doe_real(fio, &iparams->linangle.klinB, ("iparams->linangle.klinB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1847);
1848 gmx_fio_do_real(fio, iparams->linangle.aB)gmx_fio_doe_real(fio, &iparams->linangle.aB, ("iparams->linangle.aB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1848);
1849 break;
1850 case F_FENEBONDS:
1851 gmx_fio_do_real(fio, iparams->fene.bm)gmx_fio_doe_real(fio, &iparams->fene.bm, ("iparams->fene.bm"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1851);
1852 gmx_fio_do_real(fio, iparams->fene.kb)gmx_fio_doe_real(fio, &iparams->fene.kb, ("iparams->fene.kb"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1852);
1853 break;
1854
1855 case F_RESTRBONDS:
1856 gmx_fio_do_real(fio, iparams->restraint.lowA)gmx_fio_doe_real(fio, &iparams->restraint.lowA, ("iparams->restraint.lowA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1856);
1857 gmx_fio_do_real(fio, iparams->restraint.up1A)gmx_fio_doe_real(fio, &iparams->restraint.up1A, ("iparams->restraint.up1A"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1857);
1858 gmx_fio_do_real(fio, iparams->restraint.up2A)gmx_fio_doe_real(fio, &iparams->restraint.up2A, ("iparams->restraint.up2A"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1858);
1859 gmx_fio_do_real(fio, iparams->restraint.kA)gmx_fio_doe_real(fio, &iparams->restraint.kA, ("iparams->restraint.kA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1859);
1860 gmx_fio_do_real(fio, iparams->restraint.lowB)gmx_fio_doe_real(fio, &iparams->restraint.lowB, ("iparams->restraint.lowB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1860);
1861 gmx_fio_do_real(fio, iparams->restraint.up1B)gmx_fio_doe_real(fio, &iparams->restraint.up1B, ("iparams->restraint.up1B"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1861);
1862 gmx_fio_do_real(fio, iparams->restraint.up2B)gmx_fio_doe_real(fio, &iparams->restraint.up2B, ("iparams->restraint.up2B"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1862);
1863 gmx_fio_do_real(fio, iparams->restraint.kB)gmx_fio_doe_real(fio, &iparams->restraint.kB, ("iparams->restraint.kB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1863);
1864 break;
1865 case F_TABBONDS:
1866 case F_TABBONDSNC:
1867 case F_TABANGLES:
1868 case F_TABDIHS:
1869 gmx_fio_do_real(fio, iparams->tab.kA)gmx_fio_doe_real(fio, &iparams->tab.kA, ("iparams->tab.kA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1869);
1870 gmx_fio_do_int(fio, iparams->tab.table)gmx_fio_doe_int(fio, &iparams->tab.table, ("iparams->tab.table"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1870);
1871 gmx_fio_do_real(fio, iparams->tab.kB)gmx_fio_doe_real(fio, &iparams->tab.kB, ("iparams->tab.kB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1871);
1872 break;
1873 case F_CROSS_BOND_BONDS:
1874 gmx_fio_do_real(fio, iparams->cross_bb.r1e)gmx_fio_doe_real(fio, &iparams->cross_bb.r1e, ("iparams->cross_bb.r1e"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1874);
1875 gmx_fio_do_real(fio, iparams->cross_bb.r2e)gmx_fio_doe_real(fio, &iparams->cross_bb.r2e, ("iparams->cross_bb.r2e"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1875);
1876 gmx_fio_do_real(fio, iparams->cross_bb.krr)gmx_fio_doe_real(fio, &iparams->cross_bb.krr, ("iparams->cross_bb.krr"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1876);
1877 break;
1878 case F_CROSS_BOND_ANGLES:
1879 gmx_fio_do_real(fio, iparams->cross_ba.r1e)gmx_fio_doe_real(fio, &iparams->cross_ba.r1e, ("iparams->cross_ba.r1e"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1879);
1880 gmx_fio_do_real(fio, iparams->cross_ba.r2e)gmx_fio_doe_real(fio, &iparams->cross_ba.r2e, ("iparams->cross_ba.r2e"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1880);
1881 gmx_fio_do_real(fio, iparams->cross_ba.r3e)gmx_fio_doe_real(fio, &iparams->cross_ba.r3e, ("iparams->cross_ba.r3e"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1881);
1882 gmx_fio_do_real(fio, iparams->cross_ba.krt)gmx_fio_doe_real(fio, &iparams->cross_ba.krt, ("iparams->cross_ba.krt"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1882);
1883 break;
1884 case F_UREY_BRADLEY:
1885 gmx_fio_do_real(fio, iparams->u_b.thetaA)gmx_fio_doe_real(fio, &iparams->u_b.thetaA, ("iparams->u_b.thetaA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1885);
1886 gmx_fio_do_real(fio, iparams->u_b.kthetaA)gmx_fio_doe_real(fio, &iparams->u_b.kthetaA, ("iparams->u_b.kthetaA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1886);
1887 gmx_fio_do_real(fio, iparams->u_b.r13A)gmx_fio_doe_real(fio, &iparams->u_b.r13A, ("iparams->u_b.r13A"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1887);
1888 gmx_fio_do_real(fio, iparams->u_b.kUBA)gmx_fio_doe_real(fio, &iparams->u_b.kUBA, ("iparams->u_b.kUBA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1888);
1889 if (file_version >= 79)
1890 {
1891 gmx_fio_do_real(fio, iparams->u_b.thetaB)gmx_fio_doe_real(fio, &iparams->u_b.thetaB, ("iparams->u_b.thetaB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1891);
1892 gmx_fio_do_real(fio, iparams->u_b.kthetaB)gmx_fio_doe_real(fio, &iparams->u_b.kthetaB, ("iparams->u_b.kthetaB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1892);
1893 gmx_fio_do_real(fio, iparams->u_b.r13B)gmx_fio_doe_real(fio, &iparams->u_b.r13B, ("iparams->u_b.r13B"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1893);
1894 gmx_fio_do_real(fio, iparams->u_b.kUBB)gmx_fio_doe_real(fio, &iparams->u_b.kUBB, ("iparams->u_b.kUBB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1894);
1895 }
1896 else
1897 {
1898 iparams->u_b.thetaB = iparams->u_b.thetaA;
1899 iparams->u_b.kthetaB = iparams->u_b.kthetaA;
1900 iparams->u_b.r13B = iparams->u_b.r13A;
1901 iparams->u_b.kUBB = iparams->u_b.kUBA;
1902 }
1903 break;
1904 case F_QUARTIC_ANGLES:
1905 gmx_fio_do_real(fio, iparams->qangle.theta)gmx_fio_doe_real(fio, &iparams->qangle.theta, ("iparams->qangle.theta"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1905);
1906 gmx_fio_ndo_real(fio, iparams->qangle.c, 5)gmx_fio_ndoe_real(fio, iparams->qangle.c, 5, ("iparams->qangle.c"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1906);
1907 break;
1908 case F_BHAM:
1909 gmx_fio_do_real(fio, iparams->bham.a)gmx_fio_doe_real(fio, &iparams->bham.a, ("iparams->bham.a"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1909);
1910 gmx_fio_do_real(fio, iparams->bham.b)gmx_fio_doe_real(fio, &iparams->bham.b, ("iparams->bham.b"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1910);
1911 gmx_fio_do_real(fio, iparams->bham.c)gmx_fio_doe_real(fio, &iparams->bham.c, ("iparams->bham.c"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1911);
1912 break;
1913 case F_MORSE:
1914 gmx_fio_do_real(fio, iparams->morse.b0A)gmx_fio_doe_real(fio, &iparams->morse.b0A, ("iparams->morse.b0A"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1914);
1915 gmx_fio_do_real(fio, iparams->morse.cbA)gmx_fio_doe_real(fio, &iparams->morse.cbA, ("iparams->morse.cbA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1915);
1916 gmx_fio_do_real(fio, iparams->morse.betaA)gmx_fio_doe_real(fio, &iparams->morse.betaA, ("iparams->morse.betaA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1916);
1917 if (file_version >= 79)
1918 {
1919 gmx_fio_do_real(fio, iparams->morse.b0B)gmx_fio_doe_real(fio, &iparams->morse.b0B, ("iparams->morse.b0B"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1919);
1920 gmx_fio_do_real(fio, iparams->morse.cbB)gmx_fio_doe_real(fio, &iparams->morse.cbB, ("iparams->morse.cbB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1920);
1921 gmx_fio_do_real(fio, iparams->morse.betaB)gmx_fio_doe_real(fio, &iparams->morse.betaB, ("iparams->morse.betaB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1921);
1922 }
1923 else
1924 {
1925 iparams->morse.b0B = iparams->morse.b0A;
1926 iparams->morse.cbB = iparams->morse.cbA;
1927 iparams->morse.betaB = iparams->morse.betaA;
1928 }
1929 break;
1930 case F_CUBICBONDS:
1931 gmx_fio_do_real(fio, iparams->cubic.b0)gmx_fio_doe_real(fio, &iparams->cubic.b0, ("iparams->cubic.b0"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1931);
1932 gmx_fio_do_real(fio, iparams->cubic.kb)gmx_fio_doe_real(fio, &iparams->cubic.kb, ("iparams->cubic.kb"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1932);
1933 gmx_fio_do_real(fio, iparams->cubic.kcub)gmx_fio_doe_real(fio, &iparams->cubic.kcub, ("iparams->cubic.kcub"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1933);
1934 break;
1935 case F_CONNBONDS:
1936 break;
1937 case F_POLARIZATION:
1938 gmx_fio_do_real(fio, iparams->polarize.alpha)gmx_fio_doe_real(fio, &iparams->polarize.alpha, ("iparams->polarize.alpha"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1938);
1939 break;
1940 case F_ANHARM_POL:
1941 gmx_fio_do_real(fio, iparams->anharm_polarize.alpha)gmx_fio_doe_real(fio, &iparams->anharm_polarize.alpha,
("iparams->anharm_polarize.alpha"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1941);
1942 gmx_fio_do_real(fio, iparams->anharm_polarize.drcut)gmx_fio_doe_real(fio, &iparams->anharm_polarize.drcut,
("iparams->anharm_polarize.drcut"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1942);
1943 gmx_fio_do_real(fio, iparams->anharm_polarize.khyp)gmx_fio_doe_real(fio, &iparams->anharm_polarize.khyp, (
"iparams->anharm_polarize.khyp"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 1943);
1944 break;
1945 case F_WATER_POL:
1946 if (file_version < 31)
1947 {
1948 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1948, "Old tpr files with water_polarization not supported. Make a new.");
1949 }
1950 gmx_fio_do_real(fio, iparams->wpol.al_x)gmx_fio_doe_real(fio, &iparams->wpol.al_x, ("iparams->wpol.al_x"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1950);
1951 gmx_fio_do_real(fio, iparams->wpol.al_y)gmx_fio_doe_real(fio, &iparams->wpol.al_y, ("iparams->wpol.al_y"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1951);
1952 gmx_fio_do_real(fio, iparams->wpol.al_z)gmx_fio_doe_real(fio, &iparams->wpol.al_z, ("iparams->wpol.al_z"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1952);
1953 gmx_fio_do_real(fio, iparams->wpol.rOH)gmx_fio_doe_real(fio, &iparams->wpol.rOH, ("iparams->wpol.rOH"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1953);
1954 gmx_fio_do_real(fio, iparams->wpol.rHH)gmx_fio_doe_real(fio, &iparams->wpol.rHH, ("iparams->wpol.rHH"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1954);
1955 gmx_fio_do_real(fio, iparams->wpol.rOD)gmx_fio_doe_real(fio, &iparams->wpol.rOD, ("iparams->wpol.rOD"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1955);
1956 break;
1957 case F_THOLE_POL:
1958 gmx_fio_do_real(fio, iparams->thole.a)gmx_fio_doe_real(fio, &iparams->thole.a, ("iparams->thole.a"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1958);
1959 gmx_fio_do_real(fio, iparams->thole.alpha1)gmx_fio_doe_real(fio, &iparams->thole.alpha1, ("iparams->thole.alpha1"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1959);
1960 gmx_fio_do_real(fio, iparams->thole.alpha2)gmx_fio_doe_real(fio, &iparams->thole.alpha2, ("iparams->thole.alpha2"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1960);
1961 gmx_fio_do_real(fio, iparams->thole.rfac)gmx_fio_doe_real(fio, &iparams->thole.rfac, ("iparams->thole.rfac"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1961);
1962 break;
1963 case F_LJ:
1964 gmx_fio_do_real(fio, iparams->lj.c6)gmx_fio_doe_real(fio, &iparams->lj.c6, ("iparams->lj.c6"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1964);
1965 gmx_fio_do_real(fio, iparams->lj.c12)gmx_fio_doe_real(fio, &iparams->lj.c12, ("iparams->lj.c12"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1965);
1966 break;
1967 case F_LJ14:
1968 gmx_fio_do_real(fio, iparams->lj14.c6A)gmx_fio_doe_real(fio, &iparams->lj14.c6A, ("iparams->lj14.c6A"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1968);
1969 gmx_fio_do_real(fio, iparams->lj14.c12A)gmx_fio_doe_real(fio, &iparams->lj14.c12A, ("iparams->lj14.c12A"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1969);
1970 gmx_fio_do_real(fio, iparams->lj14.c6B)gmx_fio_doe_real(fio, &iparams->lj14.c6B, ("iparams->lj14.c6B"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1970);
1971 gmx_fio_do_real(fio, iparams->lj14.c12B)gmx_fio_doe_real(fio, &iparams->lj14.c12B, ("iparams->lj14.c12B"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1971);
1972 break;
1973 case F_LJC14_Q:
1974 gmx_fio_do_real(fio, iparams->ljc14.fqq)gmx_fio_doe_real(fio, &iparams->ljc14.fqq, ("iparams->ljc14.fqq"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1974);
1975 gmx_fio_do_real(fio, iparams->ljc14.qi)gmx_fio_doe_real(fio, &iparams->ljc14.qi, ("iparams->ljc14.qi"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1975);
1976 gmx_fio_do_real(fio, iparams->ljc14.qj)gmx_fio_doe_real(fio, &iparams->ljc14.qj, ("iparams->ljc14.qj"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1976);
1977 gmx_fio_do_real(fio, iparams->ljc14.c6)gmx_fio_doe_real(fio, &iparams->ljc14.c6, ("iparams->ljc14.c6"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1977);
1978 gmx_fio_do_real(fio, iparams->ljc14.c12)gmx_fio_doe_real(fio, &iparams->ljc14.c12, ("iparams->ljc14.c12"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1978);
1979 break;
1980 case F_LJC_PAIRS_NB:
1981 gmx_fio_do_real(fio, iparams->ljcnb.qi)gmx_fio_doe_real(fio, &iparams->ljcnb.qi, ("iparams->ljcnb.qi"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1981);
1982 gmx_fio_do_real(fio, iparams->ljcnb.qj)gmx_fio_doe_real(fio, &iparams->ljcnb.qj, ("iparams->ljcnb.qj"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1982);
1983 gmx_fio_do_real(fio, iparams->ljcnb.c6)gmx_fio_doe_real(fio, &iparams->ljcnb.c6, ("iparams->ljcnb.c6"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1983);
1984 gmx_fio_do_real(fio, iparams->ljcnb.c12)gmx_fio_doe_real(fio, &iparams->ljcnb.c12, ("iparams->ljcnb.c12"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1984);
1985 break;
1986 case F_PDIHS:
1987 case F_PIDIHS:
1988 case F_ANGRES:
1989 case F_ANGRESZ:
1990 gmx_fio_do_real(fio, iparams->pdihs.phiA)gmx_fio_doe_real(fio, &iparams->pdihs.phiA, ("iparams->pdihs.phiA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1990);
1991 gmx_fio_do_real(fio, iparams->pdihs.cpA)gmx_fio_doe_real(fio, &iparams->pdihs.cpA, ("iparams->pdihs.cpA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1991);
1992 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && file_version < 42)
1993 {
1994 /* Read the incorrectly stored multiplicity */
1995 gmx_fio_do_real(fio, iparams->harmonic.rB)gmx_fio_doe_real(fio, &iparams->harmonic.rB, ("iparams->harmonic.rB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1995);
1996 gmx_fio_do_real(fio, iparams->harmonic.krB)gmx_fio_doe_real(fio, &iparams->harmonic.krB, ("iparams->harmonic.krB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
1996);
1997 iparams->pdihs.phiB = iparams->pdihs.phiA;
1998 iparams->pdihs.cpB = iparams->pdihs.cpA;
1999 }
2000 else
2001 {
2002 gmx_fio_do_real(fio, iparams->pdihs.phiB)gmx_fio_doe_real(fio, &iparams->pdihs.phiB, ("iparams->pdihs.phiB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2002);
2003 gmx_fio_do_real(fio, iparams->pdihs.cpB)gmx_fio_doe_real(fio, &iparams->pdihs.cpB, ("iparams->pdihs.cpB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2003);
2004 gmx_fio_do_int(fio, iparams->pdihs.mult)gmx_fio_doe_int(fio, &iparams->pdihs.mult, ("iparams->pdihs.mult"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2004);
2005 }
2006 break;
2007 case F_RESTRDIHS:
2008 gmx_fio_do_real(fio, iparams->pdihs.phiA)gmx_fio_doe_real(fio, &iparams->pdihs.phiA, ("iparams->pdihs.phiA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2008);
2009 gmx_fio_do_real(fio, iparams->pdihs.cpA)gmx_fio_doe_real(fio, &iparams->pdihs.cpA, ("iparams->pdihs.cpA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2009);
2010 break;
2011 case F_DISRES:
2012 gmx_fio_do_int(fio, iparams->disres.label)gmx_fio_doe_int(fio, &iparams->disres.label, ("iparams->disres.label"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2012);
2013 gmx_fio_do_int(fio, iparams->disres.type)gmx_fio_doe_int(fio, &iparams->disres.type, ("iparams->disres.type"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2013);
2014 gmx_fio_do_real(fio, iparams->disres.low)gmx_fio_doe_real(fio, &iparams->disres.low, ("iparams->disres.low"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2014);
2015 gmx_fio_do_real(fio, iparams->disres.up1)gmx_fio_doe_real(fio, &iparams->disres.up1, ("iparams->disres.up1"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2015);
2016 gmx_fio_do_real(fio, iparams->disres.up2)gmx_fio_doe_real(fio, &iparams->disres.up2, ("iparams->disres.up2"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2016);
2017 gmx_fio_do_real(fio, iparams->disres.kfac)gmx_fio_doe_real(fio, &iparams->disres.kfac, ("iparams->disres.kfac"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2017);
2018 break;
2019 case F_ORIRES:
2020 gmx_fio_do_int(fio, iparams->orires.ex)gmx_fio_doe_int(fio, &iparams->orires.ex, ("iparams->orires.ex"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2020);
2021 gmx_fio_do_int(fio, iparams->orires.label)gmx_fio_doe_int(fio, &iparams->orires.label, ("iparams->orires.label"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2021);
2022 gmx_fio_do_int(fio, iparams->orires.power)gmx_fio_doe_int(fio, &iparams->orires.power, ("iparams->orires.power"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2022);
2023 gmx_fio_do_real(fio, iparams->orires.c)gmx_fio_doe_real(fio, &iparams->orires.c, ("iparams->orires.c"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2023);
2024 gmx_fio_do_real(fio, iparams->orires.obs)gmx_fio_doe_real(fio, &iparams->orires.obs, ("iparams->orires.obs"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2024);
2025 gmx_fio_do_real(fio, iparams->orires.kfac)gmx_fio_doe_real(fio, &iparams->orires.kfac, ("iparams->orires.kfac"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2025);
2026 break;
2027 case F_DIHRES:
2028 if (file_version < 82)
2029 {
2030 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2030);
2031 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2031);
2032 }
2033 gmx_fio_do_real(fio, iparams->dihres.phiA)gmx_fio_doe_real(fio, &iparams->dihres.phiA, ("iparams->dihres.phiA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2033);
2034 gmx_fio_do_real(fio, iparams->dihres.dphiA)gmx_fio_doe_real(fio, &iparams->dihres.dphiA, ("iparams->dihres.dphiA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2034);
2035 gmx_fio_do_real(fio, iparams->dihres.kfacA)gmx_fio_doe_real(fio, &iparams->dihres.kfacA, ("iparams->dihres.kfacA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2035);
2036 if (file_version >= 82)
2037 {
2038 gmx_fio_do_real(fio, iparams->dihres.phiB)gmx_fio_doe_real(fio, &iparams->dihres.phiB, ("iparams->dihres.phiB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2038);
2039 gmx_fio_do_real(fio, iparams->dihres.dphiB)gmx_fio_doe_real(fio, &iparams->dihres.dphiB, ("iparams->dihres.dphiB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2039);
2040 gmx_fio_do_real(fio, iparams->dihres.kfacB)gmx_fio_doe_real(fio, &iparams->dihres.kfacB, ("iparams->dihres.kfacB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2040);
2041 }
2042 else
2043 {
2044 iparams->dihres.phiB = iparams->dihres.phiA;
2045 iparams->dihres.dphiB = iparams->dihres.dphiA;
2046 iparams->dihres.kfacB = iparams->dihres.kfacA;
2047 }
2048 break;
2049 case F_POSRES:
2050 gmx_fio_do_rvec(fio, iparams->posres.pos0A)gmx_fio_doe_rvec(fio, &iparams->posres.pos0A, ("iparams->posres.pos0A"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2050);
2051 gmx_fio_do_rvec(fio, iparams->posres.fcA)gmx_fio_doe_rvec(fio, &iparams->posres.fcA, ("iparams->posres.fcA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2051);
2052 if (bRead && file_version < 27)
2053 {
2054 copy_rvec(iparams->posres.pos0A, iparams->posres.pos0B);
2055 copy_rvec(iparams->posres.fcA, iparams->posres.fcB);
2056 }
2057 else
2058 {
2059 gmx_fio_do_rvec(fio, iparams->posres.pos0B)gmx_fio_doe_rvec(fio, &iparams->posres.pos0B, ("iparams->posres.pos0B"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2059);
2060 gmx_fio_do_rvec(fio, iparams->posres.fcB)gmx_fio_doe_rvec(fio, &iparams->posres.fcB, ("iparams->posres.fcB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2060);
2061 }
2062 break;
2063 case F_FBPOSRES:
2064 gmx_fio_do_int(fio, iparams->fbposres.geom)gmx_fio_doe_int(fio, &iparams->fbposres.geom, ("iparams->fbposres.geom"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2064);
2065 gmx_fio_do_rvec(fio, iparams->fbposres.pos0)gmx_fio_doe_rvec(fio, &iparams->fbposres.pos0, ("iparams->fbposres.pos0"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2065);
2066 gmx_fio_do_real(fio, iparams->fbposres.r)gmx_fio_doe_real(fio, &iparams->fbposres.r, ("iparams->fbposres.r"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2066);
2067 gmx_fio_do_real(fio, iparams->fbposres.k)gmx_fio_doe_real(fio, &iparams->fbposres.k, ("iparams->fbposres.k"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2067);
2068 break;
2069 case F_CBTDIHS:
2070 gmx_fio_ndo_real(fio, iparams->cbtdihs.cbtcA, NR_CBTDIHS)gmx_fio_ndoe_real(fio, iparams->cbtdihs.cbtcA, 6, ("iparams->cbtdihs.cbtcA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2070);
2071 break;
2072 case F_RBDIHS:
2073 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcA, NR_RBDIHS)gmx_fio_ndoe_real(fio, iparams->rbdihs.rbcA, 6, ("iparams->rbdihs.rbcA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2073);
2074 if (file_version >= 25)
2075 {
2076 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcB, NR_RBDIHS)gmx_fio_ndoe_real(fio, iparams->rbdihs.rbcB, 6, ("iparams->rbdihs.rbcB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2076);
2077 }
2078 break;
2079 case F_FOURDIHS:
2080 /* Fourier dihedrals are internally represented
2081 * as Ryckaert-Bellemans since those are faster to compute.
2082 */
2083 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcA, NR_RBDIHS)gmx_fio_ndoe_real(fio, iparams->rbdihs.rbcA, 6, ("iparams->rbdihs.rbcA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2083);
2084 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcB, NR_RBDIHS)gmx_fio_ndoe_real(fio, iparams->rbdihs.rbcB, 6, ("iparams->rbdihs.rbcB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2084);
2085 break;
2086 case F_CONSTR:
2087 case F_CONSTRNC:
2088 gmx_fio_do_real(fio, iparams->constr.dA)gmx_fio_doe_real(fio, &iparams->constr.dA, ("iparams->constr.dA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2088);
2089 gmx_fio_do_real(fio, iparams->constr.dB)gmx_fio_doe_real(fio, &iparams->constr.dB, ("iparams->constr.dB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2089);
2090 break;
2091 case F_SETTLE:
2092 gmx_fio_do_real(fio, iparams->settle.doh)gmx_fio_doe_real(fio, &iparams->settle.doh, ("iparams->settle.doh"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2092);
2093 gmx_fio_do_real(fio, iparams->settle.dhh)gmx_fio_doe_real(fio, &iparams->settle.dhh, ("iparams->settle.dhh"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2093);
2094 break;
2095 case F_VSITE2:
2096 gmx_fio_do_real(fio, iparams->vsite.a)gmx_fio_doe_real(fio, &iparams->vsite.a, ("iparams->vsite.a"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2096);
2097 break;
2098 case F_VSITE3:
2099 case F_VSITE3FD:
2100 case F_VSITE3FAD:
2101 gmx_fio_do_real(fio, iparams->vsite.a)gmx_fio_doe_real(fio, &iparams->vsite.a, ("iparams->vsite.a"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2101);
2102 gmx_fio_do_real(fio, iparams->vsite.b)gmx_fio_doe_real(fio, &iparams->vsite.b, ("iparams->vsite.b"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2102);
2103 break;
2104 case F_VSITE3OUT:
2105 case F_VSITE4FD:
2106 case F_VSITE4FDN:
2107 gmx_fio_do_real(fio, iparams->vsite.a)gmx_fio_doe_real(fio, &iparams->vsite.a, ("iparams->vsite.a"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2107);
2108 gmx_fio_do_real(fio, iparams->vsite.b)gmx_fio_doe_real(fio, &iparams->vsite.b, ("iparams->vsite.b"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2108);
2109 gmx_fio_do_real(fio, iparams->vsite.c)gmx_fio_doe_real(fio, &iparams->vsite.c, ("iparams->vsite.c"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2109);
2110 break;
2111 case F_VSITEN:
2112 gmx_fio_do_int(fio, iparams->vsiten.n)gmx_fio_doe_int(fio, &iparams->vsiten.n, ("iparams->vsiten.n"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2112);
2113 gmx_fio_do_real(fio, iparams->vsiten.a)gmx_fio_doe_real(fio, &iparams->vsiten.a, ("iparams->vsiten.a"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2113);
2114 break;
2115 case F_GB12:
2116 case F_GB13:
2117 case F_GB14:
2118 /* We got rid of some parameters in version 68 */
2119 if (bRead && file_version < 68)
2120 {
2121 gmx_fio_do_real(fio, rdum)gmx_fio_doe_real(fio, &rdum, ("rdum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2121);
2122 gmx_fio_do_real(fio, rdum)gmx_fio_doe_real(fio, &rdum, ("rdum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2122);
2123 gmx_fio_do_real(fio, rdum)gmx_fio_doe_real(fio, &rdum, ("rdum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2123);
2124 gmx_fio_do_real(fio, rdum)gmx_fio_doe_real(fio, &rdum, ("rdum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2124);
2125 }
2126 gmx_fio_do_real(fio, iparams->gb.sar)gmx_fio_doe_real(fio, &iparams->gb.sar, ("iparams->gb.sar"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2126);
2127 gmx_fio_do_real(fio, iparams->gb.st)gmx_fio_doe_real(fio, &iparams->gb.st, ("iparams->gb.st"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2127);
2128 gmx_fio_do_real(fio, iparams->gb.pi)gmx_fio_doe_real(fio, &iparams->gb.pi, ("iparams->gb.pi"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2128);
2129 gmx_fio_do_real(fio, iparams->gb.gbr)gmx_fio_doe_real(fio, &iparams->gb.gbr, ("iparams->gb.gbr"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2129);
2130 gmx_fio_do_real(fio, iparams->gb.bmlt)gmx_fio_doe_real(fio, &iparams->gb.bmlt, ("iparams->gb.bmlt"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2130);
2131 break;
2132 case F_CMAP:
2133 gmx_fio_do_int(fio, iparams->cmap.cmapA)gmx_fio_doe_int(fio, &iparams->cmap.cmapA, ("iparams->cmap.cmapA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2133);
2134 gmx_fio_do_int(fio, iparams->cmap.cmapB)gmx_fio_doe_int(fio, &iparams->cmap.cmapB, ("iparams->cmap.cmapB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2134);
2135 break;
2136 default:
2137 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2137, "unknown function type %d (%s) in %s line %d",
2138 ftype, interaction_function[ftype].name, __FILE__"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", __LINE__2138);
2139 }
2140 if (!bRead)
2141 {
2142 gmx_fio_unset_comment(fio);
2143 }
2144}
2145
2146static void do_ilist(t_fileio *fio, t_ilist *ilist, gmx_bool bRead, int file_version,
2147 int ftype)
2148{
2149 int i, k, idum;
2150
2151 if (!bRead)
2152 {
2153 gmx_fio_set_comment(fio, interaction_function[ftype].name);
2154 }
2155 if (file_version < 44)
2156 {
2157 for (i = 0; i < MAXNODES256; i++)
2158 {
2159 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2159);
2160 }
2161 }
2162 gmx_fio_do_int(fio, ilist->nr)gmx_fio_doe_int(fio, &ilist->nr, ("ilist->nr"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2162);
2163 if (bRead)
2164 {
2165 snew(ilist->iatoms, ilist->nr)(ilist->iatoms) = save_calloc("ilist->iatoms", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2165, (ilist->nr), sizeof(*(ilist->iatoms)));
2166 }
2167 gmx_fio_ndo_int(fio, ilist->iatoms, ilist->nr)gmx_fio_ndoe_int(fio, ilist->iatoms, ilist->nr, ("ilist->iatoms"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2167);
2168 if (!bRead)
2169 {
2170 gmx_fio_unset_comment(fio);
2171 }
2172}
2173
2174static void do_ffparams(t_fileio *fio, gmx_ffparams_t *ffparams,
2175 gmx_bool bRead, int file_version)
2176{
2177 int idum, i, j;
2178 unsigned int k;
2179
2180 gmx_fio_do_int(fio, ffparams->atnr)gmx_fio_doe_int(fio, &ffparams->atnr, ("ffparams->atnr"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2180);
2181 if (file_version < 57)
2182 {
2183 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2183);
2184 }
2185 gmx_fio_do_int(fio, ffparams->ntypes)gmx_fio_doe_int(fio, &ffparams->ntypes, ("ffparams->ntypes"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2185);
2186 if (bRead && debug)
2187 {
2188 fprintf(debug, "ffparams->atnr = %d, ntypes = %d\n",
2189 ffparams->atnr, ffparams->ntypes);
2190 }
2191 if (bRead)
2192 {
2193 snew(ffparams->functype, ffparams->ntypes)(ffparams->functype) = save_calloc("ffparams->functype"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 2193
, (ffparams->ntypes), sizeof(*(ffparams->functype)));
2194 snew(ffparams->iparams, ffparams->ntypes)(ffparams->iparams) = save_calloc("ffparams->iparams", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2194, (ffparams->ntypes), sizeof(*(ffparams->iparams)
));
2195 }
2196 /* Read/write all the function types */
2197 gmx_fio_ndo_int(fio, ffparams->functype, ffparams->ntypes)gmx_fio_ndoe_int(fio, ffparams->functype, ffparams->ntypes
, ("ffparams->functype"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2197);
2198 if (bRead && debug)
2199 {
2200 pr_ivec(debug, 0, "functype", ffparams->functype, ffparams->ntypes, TRUE1);
2201 }
2202
2203 if (file_version >= 66)
2204 {
2205 gmx_fio_do_double(fio, ffparams->reppow)gmx_fio_doe_double(fio, &ffparams->reppow, ("ffparams->reppow"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2205);
2206 }
2207 else
2208 {
2209 ffparams->reppow = 12.0;
2210 }
2211
2212 if (file_version >= 57)
2213 {
2214 gmx_fio_do_real(fio, ffparams->fudgeQQ)gmx_fio_doe_real(fio, &ffparams->fudgeQQ, ("ffparams->fudgeQQ"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2214);
2215 }
2216
2217 /* Check whether all these function types are supported by the code.
2218 * In practice the code is backwards compatible, which means that the
2219 * numbering may have to be altered from old numbering to new numbering
2220 */
2221 for (i = 0; (i < ffparams->ntypes); i++)
2222 {
2223 if (bRead)
2224 {
2225 /* Loop over file versions */
2226 for (k = 0; (k < NFTUPD((int)(sizeof(ftupd)/sizeof((ftupd)[0])))); k++)
2227 {
2228 /* Compare the read file_version to the update table */
2229 if ((file_version < ftupd[k].fvnr) &&
2230 (ffparams->functype[i] >= ftupd[k].ftype))
2231 {
2232 ffparams->functype[i] += 1;
2233 if (debug)
2234 {
2235 fprintf(debug, "Incrementing function type %d to %d (due to %s)\n",
2236 i, ffparams->functype[i],
2237 interaction_function[ftupd[k].ftype].longname);
2238 fflush(debug);
2239 }
2240 }
2241 }
2242 }
2243
2244 do_iparams(fio, ffparams->functype[i], &ffparams->iparams[i], bRead,
2245 file_version);
2246 if (bRead && debug)
2247 {
2248 pr_iparams(debug, ffparams->functype[i], &ffparams->iparams[i]);
2249 }
2250 }
2251}
2252
2253static void add_settle_atoms(t_ilist *ilist)
2254{
2255 int i;
2256
2257 /* Settle used to only store the first atom: add the other two */
2258 srenew(ilist->iatoms, 2*ilist->nr)(ilist->iatoms) = save_realloc("ilist->iatoms", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2258, (ilist->iatoms), (2*ilist->nr), sizeof(*(ilist->
iatoms)));
2259 for (i = ilist->nr/2-1; i >= 0; i--)
2260 {
2261 ilist->iatoms[4*i+0] = ilist->iatoms[2*i+0];
2262 ilist->iatoms[4*i+1] = ilist->iatoms[2*i+1];
2263 ilist->iatoms[4*i+2] = ilist->iatoms[2*i+1] + 1;
2264 ilist->iatoms[4*i+3] = ilist->iatoms[2*i+1] + 2;
2265 }
2266 ilist->nr = 2*ilist->nr;
2267}
2268
2269static void do_ilists(t_fileio *fio, t_ilist *ilist, gmx_bool bRead,
2270 int file_version)
2271{
2272 int i, j, renum[F_NRE];
2273 gmx_bool bClear;
2274 unsigned int k;
2275
2276 for (j = 0; (j < F_NRE); j++)
2277 {
2278 bClear = FALSE0;
2279 if (bRead)
2280 {
2281 for (k = 0; k < NFTUPD((int)(sizeof(ftupd)/sizeof((ftupd)[0]))); k++)
2282 {
2283 if ((file_version < ftupd[k].fvnr) && (j == ftupd[k].ftype))
2284 {
2285 bClear = TRUE1;
2286 }
2287 }
2288 }
2289 if (bClear)
2290 {
2291 ilist[j].nr = 0;
2292 ilist[j].iatoms = NULL((void*)0);
2293 }
2294 else
2295 {
2296 do_ilist(fio, &ilist[j], bRead, file_version, j);
2297 if (file_version < 78 && j == F_SETTLE && ilist[j].nr > 0)
2298 {
2299 add_settle_atoms(&ilist[j]);
2300 }
2301 }
2302 /*
2303 if (bRead && gmx_debug_at)
2304 pr_ilist(debug,0,interaction_function[j].longname,
2305 functype,&ilist[j],TRUE);
2306 */
2307 }
2308}
2309
2310static void do_idef(t_fileio *fio, gmx_ffparams_t *ffparams, gmx_moltype_t *molt,
2311 gmx_bool bRead, int file_version)
2312{
2313 do_ffparams(fio, ffparams, bRead, file_version);
2314
2315 if (file_version >= 54)
2316 {
2317 gmx_fio_do_real(fio, ffparams->fudgeQQ)gmx_fio_doe_real(fio, &ffparams->fudgeQQ, ("ffparams->fudgeQQ"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2317);
2318 }
2319
2320 do_ilists(fio, molt->ilist, bRead, file_version);
2321}
2322
2323static void do_block(t_fileio *fio, t_block *block, gmx_bool bRead, int file_version)
2324{
2325 int i, idum, dum_nra, *dum_a;
2326
2327 if (file_version < 44)
2328 {
2329 for (i = 0; i < MAXNODES256; i++)
2330 {
2331 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2331);
2332 }
2333 }
2334 gmx_fio_do_int(fio, block->nr)gmx_fio_doe_int(fio, &block->nr, ("block->nr"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2334);
2335 if (file_version < 51)
2336 {
2337 gmx_fio_do_int(fio, dum_nra)gmx_fio_doe_int(fio, &dum_nra, ("dum_nra"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2337);
2338 }
2339 if (bRead)
2340 {
2341 if ((block->nalloc_index > 0) && (NULL((void*)0) != block->index))
2342 {
2343 sfree(block->index)save_free("block->index", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2343, (block->index));
2344 }
2345 block->nalloc_index = block->nr+1;
2346 snew(block->index, block->nalloc_index)(block->index) = save_calloc("block->index", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2346, (block->nalloc_index), sizeof(*(block->index)));
2347 }
2348 gmx_fio_ndo_int(fio, block->index, block->nr+1)gmx_fio_ndoe_int(fio, block->index, block->nr+1, ("block->index"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2348);
2349
2350 if (file_version < 51 && dum_nra > 0)
2351 {
2352 snew(dum_a, dum_nra)(dum_a) = save_calloc("dum_a", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2352, (dum_nra), sizeof(*(dum_a)));
2353 gmx_fio_ndo_int(fio, dum_a, dum_nra)gmx_fio_ndoe_int(fio, dum_a, dum_nra, ("dum_a"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2353);
2354 sfree(dum_a)save_free("dum_a", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2354, (dum_a));
2355 }
2356}
2357
2358static void do_blocka(t_fileio *fio, t_blocka *block, gmx_bool bRead,
2359 int file_version)
2360{
2361 int i, idum;
2362
2363 if (file_version < 44)
2364 {
2365 for (i = 0; i < MAXNODES256; i++)
2366 {
2367 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2367);
2368 }
2369 }
2370 gmx_fio_do_int(fio, block->nr)gmx_fio_doe_int(fio, &block->nr, ("block->nr"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2370);
2371 gmx_fio_do_int(fio, block->nra)gmx_fio_doe_int(fio, &block->nra, ("block->nra"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2371);
2372 if (bRead)
2373 {
2374 block->nalloc_index = block->nr+1;
2375 snew(block->index, block->nalloc_index)(block->index) = save_calloc("block->index", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2375, (block->nalloc_index), sizeof(*(block->index)));
2376 block->nalloc_a = block->nra;
2377 snew(block->a, block->nalloc_a)(block->a) = save_calloc("block->a", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2377, (block->nalloc_a), sizeof(*(block->a)));
2378 }
2379 gmx_fio_ndo_int(fio, block->index, block->nr+1)gmx_fio_ndoe_int(fio, block->index, block->nr+1, ("block->index"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2379);
2380 gmx_fio_ndo_int(fio, block->a, block->nra)gmx_fio_ndoe_int(fio, block->a, block->nra, ("block->a"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2380);
2381}
2382
2383static void do_atom(t_fileio *fio, t_atom *atom, int ngrp, gmx_bool bRead,
2384 int file_version, gmx_groups_t *groups, int atnr)
2385{
2386 int i, myngrp;
2387
2388 gmx_fio_do_real(fio, atom->m)gmx_fio_doe_real(fio, &atom->m, ("atom->m"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2388);
2389 gmx_fio_do_real(fio, atom->q)gmx_fio_doe_real(fio, &atom->q, ("atom->q"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2389);
2390 gmx_fio_do_real(fio, atom->mB)gmx_fio_doe_real(fio, &atom->mB, ("atom->mB"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2390);
2391 gmx_fio_do_real(fio, atom->qB)gmx_fio_doe_real(fio, &atom->qB, ("atom->qB"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2391);
2392 gmx_fio_do_ushort(fio, atom->type)gmx_fio_doe_ushort(fio, &atom->type, ("atom->type")
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 2392
);
2393 gmx_fio_do_ushort(fio, atom->typeB)gmx_fio_doe_ushort(fio, &atom->typeB, ("atom->typeB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2393);
2394 gmx_fio_do_int(fio, atom->ptype)gmx_fio_doe_int(fio, &atom->ptype, ("atom->ptype"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 2394
);
2395 gmx_fio_do_int(fio, atom->resind)gmx_fio_doe_int(fio, &atom->resind, ("atom->resind"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2395);
2396 if (file_version >= 52)
2397 {
2398 gmx_fio_do_int(fio, atom->atomnumber)gmx_fio_doe_int(fio, &atom->atomnumber, ("atom->atomnumber"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2398);
2399 }
2400 else if (bRead)
2401 {
2402 atom->atomnumber = NOTSET-12345;
2403 }
2404 if (file_version < 23)
2405 {
2406 myngrp = 8;
2407 }
2408 else if (file_version < 39)
2409 {
2410 myngrp = 9;
2411 }
2412 else
2413 {
2414 myngrp = ngrp;
2415 }
2416
2417 if (file_version < 57)
2418 {
2419 unsigned char uchar[egcNR];
2420 gmx_fio_ndo_uchar(fio, uchar, myngrp)gmx_fio_ndoe_uchar(fio, uchar, myngrp, ("uchar"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2420);
2421 for (i = myngrp; (i < ngrp); i++)
2422 {
2423 uchar[i] = 0;
2424 }
2425 /* Copy the old data format to the groups struct */
2426 for (i = 0; i < ngrp; i++)
2427 {
2428 groups->grpnr[i][atnr] = uchar[i];
2429 }
2430 }
2431}
2432
2433static void do_grps(t_fileio *fio, int ngrp, t_grps grps[], gmx_bool bRead,
2434 int file_version)
2435{
2436 int i, j, myngrp;
2437
2438 if (file_version < 23)
2439 {
2440 myngrp = 8;
2441 }
2442 else if (file_version < 39)
2443 {
2444 myngrp = 9;
2445 }
2446 else
2447 {
2448 myngrp = ngrp;
2449 }
2450
2451 for (j = 0; (j < ngrp); j++)
2452 {
2453 if (j < myngrp)
2454 {
2455 gmx_fio_do_int(fio, grps[j].nr)gmx_fio_doe_int(fio, &grps[j].nr, ("grps[j].nr"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2455);
2456 if (bRead)
2457 {
2458 snew(grps[j].nm_ind, grps[j].nr)(grps[j].nm_ind) = save_calloc("grps[j].nm_ind", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2458, (grps[j].nr), sizeof(*(grps[j].nm_ind)));
2459 }
2460 gmx_fio_ndo_int(fio, grps[j].nm_ind, grps[j].nr)gmx_fio_ndoe_int(fio, grps[j].nm_ind, grps[j].nr, ("grps[j].nm_ind"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2460);
2461 }
2462 else
2463 {
2464 grps[j].nr = 1;
2465 snew(grps[j].nm_ind, grps[j].nr)(grps[j].nm_ind) = save_calloc("grps[j].nm_ind", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2465, (grps[j].nr), sizeof(*(grps[j].nm_ind)));
2466 }
2467 }
2468}
2469
2470static void do_symstr(t_fileio *fio, char ***nm, gmx_bool bRead, t_symtab *symtab)
2471{
2472 int ls;
2473
2474 if (bRead)
2475 {
2476 gmx_fio_do_int(fio, ls)gmx_fio_doe_int(fio, &ls, ("ls"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2476);
2477 *nm = get_symtab_handle(symtab, ls);
2478 }
2479 else
2480 {
2481 ls = lookup_symtab(symtab, *nm);
2482 gmx_fio_do_int(fio, ls)gmx_fio_doe_int(fio, &ls, ("ls"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2482);
2483 }
2484}
2485
2486static void do_strstr(t_fileio *fio, int nstr, char ***nm, gmx_bool bRead,
2487 t_symtab *symtab)
2488{
2489 int j;
2490
2491 for (j = 0; (j < nstr); j++)
2492 {
2493 do_symstr(fio, &(nm[j]), bRead, symtab);
2494 }
2495}
2496
2497static void do_resinfo(t_fileio *fio, int n, t_resinfo *ri, gmx_bool bRead,
2498 t_symtab *symtab, int file_version)
2499{
2500 int j;
2501
2502 for (j = 0; (j < n); j++)
2503 {
2504 do_symstr(fio, &(ri[j].name), bRead, symtab);
2505 if (file_version >= 63)
2506 {
2507 gmx_fio_do_int(fio, ri[j].nr)gmx_fio_doe_int(fio, &ri[j].nr, ("ri[j].nr"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2507);
2508 gmx_fio_do_uchar(fio, ri[j].ic)gmx_fio_doe_uchar(fio, &ri[j].ic, ("ri[j].ic"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2508);
2509 }
2510 else
2511 {
2512 ri[j].nr = j + 1;
2513 ri[j].ic = ' ';
2514 }
2515 }
2516}
2517
2518static void do_atoms(t_fileio *fio, t_atoms *atoms, gmx_bool bRead, t_symtab *symtab,
2519 int file_version,
2520 gmx_groups_t *groups)
2521{
2522 int i;
2523
2524 gmx_fio_do_int(fio, atoms->nr)gmx_fio_doe_int(fio, &atoms->nr, ("atoms->nr"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2524);
2525 gmx_fio_do_int(fio, atoms->nres)gmx_fio_doe_int(fio, &atoms->nres, ("atoms->nres"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 2525
);
2526 if (file_version < 57)
2527 {
2528 gmx_fio_do_int(fio, groups->ngrpname)gmx_fio_doe_int(fio, &groups->ngrpname, ("groups->ngrpname"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2528);
2529 for (i = 0; i < egcNR; i++)
2530 {
2531 groups->ngrpnr[i] = atoms->nr;
2532 snew(groups->grpnr[i], groups->ngrpnr[i])(groups->grpnr[i]) = save_calloc("groups->grpnr[i]", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2532, (groups->ngrpnr[i]), sizeof(*(groups->grpnr[i])
));
2533 }
2534 }
2535 if (bRead)
2536 {
2537 snew(atoms->atom, atoms->nr)(atoms->atom) = save_calloc("atoms->atom", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2537, (atoms->nr), sizeof(*(atoms->atom)));
2538 snew(atoms->atomname, atoms->nr)(atoms->atomname) = save_calloc("atoms->atomname", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2538, (atoms->nr), sizeof(*(atoms->atomname)));
2539 snew(atoms->atomtype, atoms->nr)(atoms->atomtype) = save_calloc("atoms->atomtype", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2539, (atoms->nr), sizeof(*(atoms->atomtype)));
2540 snew(atoms->atomtypeB, atoms->nr)(atoms->atomtypeB) = save_calloc("atoms->atomtypeB", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2540, (atoms->nr), sizeof(*(atoms->atomtypeB)));
2541 snew(atoms->resinfo, atoms->nres)(atoms->resinfo) = save_calloc("atoms->resinfo", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2541, (atoms->nres), sizeof(*(atoms->resinfo)));
2542 if (file_version < 57)
2543 {
2544 snew(groups->grpname, groups->ngrpname)(groups->grpname) = save_calloc("groups->grpname", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2544, (groups->ngrpname), sizeof(*(groups->grpname)));
2545 }
2546 atoms->pdbinfo = NULL((void*)0);
2547 }
2548 for (i = 0; (i < atoms->nr); i++)
2549 {
2550 do_atom(fio, &atoms->atom[i], egcNR, bRead, file_version, groups, i);
2551 }
2552 do_strstr(fio, atoms->nr, atoms->atomname, bRead, symtab);
2553 if (bRead && (file_version <= 20))
2554 {
2555 for (i = 0; i < atoms->nr; i++)
2556 {
2557 atoms->atomtype[i] = put_symtab(symtab, "?");
2558 atoms->atomtypeB[i] = put_symtab(symtab, "?");
2559 }
2560 }
2561 else
2562 {
2563 do_strstr(fio, atoms->nr, atoms->atomtype, bRead, symtab);
2564 do_strstr(fio, atoms->nr, atoms->atomtypeB, bRead, symtab);
2565 }
2566 do_resinfo(fio, atoms->nres, atoms->resinfo, bRead, symtab, file_version);
2567
2568 if (file_version < 57)
2569 {
2570 do_strstr(fio, groups->ngrpname, groups->grpname, bRead, symtab);
2571
2572 do_grps(fio, egcNR, groups->grps, bRead, file_version);
2573 }
2574}
2575
2576static void do_groups(t_fileio *fio, gmx_groups_t *groups,
2577 gmx_bool bRead, t_symtab *symtab,
2578 int file_version)
2579{
2580 int g, n, i;
2581
2582 do_grps(fio, egcNR, groups->grps, bRead, file_version);
2583 gmx_fio_do_int(fio, groups->ngrpname)gmx_fio_doe_int(fio, &groups->ngrpname, ("groups->ngrpname"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2583);
2584 if (bRead)
2585 {
2586 snew(groups->grpname, groups->ngrpname)(groups->grpname) = save_calloc("groups->grpname", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2586, (groups->ngrpname), sizeof(*(groups->grpname)));
2587 }
2588 do_strstr(fio, groups->ngrpname, groups->grpname, bRead, symtab);
2589 for (g = 0; g < egcNR; g++)
2590 {
2591 gmx_fio_do_int(fio, groups->ngrpnr[g])gmx_fio_doe_int(fio, &groups->ngrpnr[g], ("groups->ngrpnr[g]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2591);
2592 if (groups->ngrpnr[g] == 0)
2593 {
2594 if (bRead)
2595 {
2596 groups->grpnr[g] = NULL((void*)0);
2597 }
2598 }
2599 else
2600 {
2601 if (bRead)
2602 {
2603 snew(groups->grpnr[g], groups->ngrpnr[g])(groups->grpnr[g]) = save_calloc("groups->grpnr[g]", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2603, (groups->ngrpnr[g]), sizeof(*(groups->grpnr[g])
));
2604 }
2605 gmx_fio_ndo_uchar(fio, groups->grpnr[g], groups->ngrpnr[g])gmx_fio_ndoe_uchar(fio, groups->grpnr[g], groups->ngrpnr
[g], ("groups->grpnr[g]"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2605);
2606 }
2607 }
2608}
2609
2610static void do_atomtypes(t_fileio *fio, t_atomtypes *atomtypes, gmx_bool bRead,
2611 int file_version)
2612{
2613 int i, j;
2614
2615 if (file_version > 25)
2616 {
2617 gmx_fio_do_int(fio, atomtypes->nr)gmx_fio_doe_int(fio, &atomtypes->nr, ("atomtypes->nr"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2617);
2618 j = atomtypes->nr;
2619 if (bRead)
2620 {
2621 snew(atomtypes->radius, j)(atomtypes->radius) = save_calloc("atomtypes->radius", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2621, (j), sizeof(*(atomtypes->radius)));
2622 snew(atomtypes->vol, j)(atomtypes->vol) = save_calloc("atomtypes->vol", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2622, (j), sizeof(*(atomtypes->vol)));
2623 snew(atomtypes->surftens, j)(atomtypes->surftens) = save_calloc("atomtypes->surftens"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 2623
, (j), sizeof(*(atomtypes->surftens)));
2624 snew(atomtypes->atomnumber, j)(atomtypes->atomnumber) = save_calloc("atomtypes->atomnumber"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 2624
, (j), sizeof(*(atomtypes->atomnumber)));
2625 snew(atomtypes->gb_radius, j)(atomtypes->gb_radius) = save_calloc("atomtypes->gb_radius"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 2625
, (j), sizeof(*(atomtypes->gb_radius)));
2626 snew(atomtypes->S_hct, j)(atomtypes->S_hct) = save_calloc("atomtypes->S_hct", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2626, (j), sizeof(*(atomtypes->S_hct)));
2627 }
2628 gmx_fio_ndo_real(fio, atomtypes->radius, j)gmx_fio_ndoe_real(fio, atomtypes->radius, j, ("atomtypes->radius"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2628);
2629 gmx_fio_ndo_real(fio, atomtypes->vol, j)gmx_fio_ndoe_real(fio, atomtypes->vol, j, ("atomtypes->vol"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2629);
2630 gmx_fio_ndo_real(fio, atomtypes->surftens, j)gmx_fio_ndoe_real(fio, atomtypes->surftens, j, ("atomtypes->surftens"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2630);
2631 if (file_version >= 40)
2632 {
2633 gmx_fio_ndo_int(fio, atomtypes->atomnumber, j)gmx_fio_ndoe_int(fio, atomtypes->atomnumber, j, ("atomtypes->atomnumber"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2633);
2634 }
2635 if (file_version >= 60)
2636 {
2637 gmx_fio_ndo_real(fio, atomtypes->gb_radius, j)gmx_fio_ndoe_real(fio, atomtypes->gb_radius, j, ("atomtypes->gb_radius"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2637);
2638 gmx_fio_ndo_real(fio, atomtypes->S_hct, j)gmx_fio_ndoe_real(fio, atomtypes->S_hct, j, ("atomtypes->S_hct"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2638);
2639 }
2640 }
2641 else
2642 {
2643 /* File versions prior to 26 cannot do GBSA,
2644 * so they dont use this structure
2645 */
2646 atomtypes->nr = 0;
2647 atomtypes->radius = NULL((void*)0);
2648 atomtypes->vol = NULL((void*)0);
2649 atomtypes->surftens = NULL((void*)0);
2650 atomtypes->atomnumber = NULL((void*)0);
2651 atomtypes->gb_radius = NULL((void*)0);
2652 atomtypes->S_hct = NULL((void*)0);
2653 }
2654}
2655
2656static void do_symtab(t_fileio *fio, t_symtab *symtab, gmx_bool bRead)
2657{
2658 int i, nr;
2659 t_symbuf *symbuf;
2660 char buf[STRLEN4096];
2661
2662 gmx_fio_do_int(fio, symtab->nr)gmx_fio_doe_int(fio, &symtab->nr, ("symtab->nr"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2662);
2663 nr = symtab->nr;
2664 if (bRead)
2665 {
2666 snew(symtab->symbuf, 1)(symtab->symbuf) = save_calloc("symtab->symbuf", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2666, (1), sizeof(*(symtab->symbuf)));
2667 symbuf = symtab->symbuf;
2668 symbuf->bufsize = nr;
2669 snew(symbuf->buf, nr)(symbuf->buf) = save_calloc("symbuf->buf", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2669, (nr), sizeof(*(symbuf->buf)));
2670 for (i = 0; (i < nr); i++)
2671 {
2672 gmx_fio_do_string(fio, buf)gmx_fio_doe_string(fio, buf, ("buf"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2672);
2673 symbuf->buf[i] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
2674 }
2675 }
2676 else
2677 {
2678 symbuf = symtab->symbuf;
2679 while (symbuf != NULL((void*)0))
2680 {
2681 for (i = 0; (i < symbuf->bufsize) && (i < nr); i++)
2682 {
2683 gmx_fio_do_string(fio, symbuf->buf[i])gmx_fio_doe_string(fio, symbuf->buf[i], ("symbuf->buf[i]"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2683);
2684 }
2685 nr -= i;
2686 symbuf = symbuf->next;
2687 }
2688 if (nr != 0)
2689 {
2690 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2690, "nr of symtab strings left: %d", nr);
2691 }
2692 }
2693}
2694
2695static void do_cmap(t_fileio *fio, gmx_cmap_t *cmap_grid, gmx_bool bRead)
2696{
2697 int i, j, ngrid, gs, nelem;
2698
2699 gmx_fio_do_int(fio, cmap_grid->ngrid)gmx_fio_doe_int(fio, &cmap_grid->ngrid, ("cmap_grid->ngrid"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2699);
2700 gmx_fio_do_int(fio, cmap_grid->grid_spacing)gmx_fio_doe_int(fio, &cmap_grid->grid_spacing, ("cmap_grid->grid_spacing"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2700);
2701
2702 ngrid = cmap_grid->ngrid;
2703 gs = cmap_grid->grid_spacing;
2704 nelem = gs * gs;
2705
2706 if (bRead)
2707 {
2708 snew(cmap_grid->cmapdata, ngrid)(cmap_grid->cmapdata) = save_calloc("cmap_grid->cmapdata"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 2708
, (ngrid), sizeof(*(cmap_grid->cmapdata)));
2709
2710 for (i = 0; i < cmap_grid->ngrid; i++)
2711 {
2712 snew(cmap_grid->cmapdata[i].cmap, 4*nelem)(cmap_grid->cmapdata[i].cmap) = save_calloc("cmap_grid->cmapdata[i].cmap"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 2712
, (4*nelem), sizeof(*(cmap_grid->cmapdata[i].cmap)));
2713 }
2714 }
2715
2716 for (i = 0; i < cmap_grid->ngrid; i++)
2717 {
2718 for (j = 0; j < nelem; j++)
2719 {
2720 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4])gmx_fio_doe_real(fio, &cmap_grid->cmapdata[i].cmap[j*4
], ("cmap_grid->cmapdata[i].cmap[j*4]"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2720);
2721 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+1])gmx_fio_doe_real(fio, &cmap_grid->cmapdata[i].cmap[j*4
+1], ("cmap_grid->cmapdata[i].cmap[j*4+1]"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2721);
2722 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+2])gmx_fio_doe_real(fio, &cmap_grid->cmapdata[i].cmap[j*4
+2], ("cmap_grid->cmapdata[i].cmap[j*4+2]"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2722);
2723 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+3])gmx_fio_doe_real(fio, &cmap_grid->cmapdata[i].cmap[j*4
+3], ("cmap_grid->cmapdata[i].cmap[j*4+3]"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2723);
2724 }
2725 }
2726}
2727
2728
2729void tpx_make_chain_identifiers(t_atoms *atoms, t_block *mols)
2730{
2731 int m, a, a0, a1, r;
2732 char c, chainid;
2733 int chainnum;
2734
2735 /* We always assign a new chain number, but save the chain id characters
2736 * for larger molecules.
2737 */
2738#define CHAIN_MIN_ATOMS15 15
2739
2740 chainnum = 0;
2741 chainid = 'A';
2742 for (m = 0; m < mols->nr; m++)
2743 {
2744 a0 = mols->index[m];
2745 a1 = mols->index[m+1];
2746 if ((a1-a0 >= CHAIN_MIN_ATOMS15) && (chainid <= 'Z'))
2747 {
2748 c = chainid;
2749 chainid++;
2750 }
2751 else
2752 {
2753 c = ' ';
2754 }
2755 for (a = a0; a < a1; a++)
2756 {
2757 atoms->resinfo[atoms->atom[a].resind].chainnum = chainnum;
2758 atoms->resinfo[atoms->atom[a].resind].chainid = c;
2759 }
2760 chainnum++;
2761 }
2762
2763 /* Blank out the chain id if there was only one chain */
2764 if (chainid == 'B')
2765 {
2766 for (r = 0; r < atoms->nres; r++)
2767 {
2768 atoms->resinfo[r].chainid = ' ';
2769 }
2770 }
2771}
2772
2773static void do_moltype(t_fileio *fio, gmx_moltype_t *molt, gmx_bool bRead,
2774 t_symtab *symtab, int file_version,
2775 gmx_groups_t *groups)
2776{
2777 int i;
2778
2779 if (file_version >= 57)
2780 {
2781 do_symstr(fio, &(molt->name), bRead, symtab);
2782 }
2783
2784 do_atoms(fio, &molt->atoms, bRead, symtab, file_version, groups);
2785
2786 if (bRead && gmx_debug_at)
2787 {
2788 pr_atoms(debug, 0, "atoms", &molt->atoms, TRUE1);
2789 }
2790
2791 if (file_version >= 57)
2792 {
2793 do_ilists(fio, molt->ilist, bRead, file_version);
2794
2795 do_block(fio, &molt->cgs, bRead, file_version);
2796 if (bRead && gmx_debug_at)
2797 {
2798 pr_block(debug, 0, "cgs", &molt->cgs, TRUE1);
2799 }
2800 }
2801
2802 /* This used to be in the atoms struct */
2803 do_blocka(fio, &molt->excls, bRead, file_version);
2804}
2805
2806static void do_molblock(t_fileio *fio, gmx_molblock_t *molb, gmx_bool bRead)
2807{
2808 int i;
2809
2810 gmx_fio_do_int(fio, molb->type)gmx_fio_doe_int(fio, &molb->type, ("molb->type"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2810);
2811 gmx_fio_do_int(fio, molb->nmol)gmx_fio_doe_int(fio, &molb->nmol, ("molb->nmol"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2811);
2812 gmx_fio_do_int(fio, molb->natoms_mol)gmx_fio_doe_int(fio, &molb->natoms_mol, ("molb->natoms_mol"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2812);
2813 /* Position restraint coordinates */
2814 gmx_fio_do_int(fio, molb->nposres_xA)gmx_fio_doe_int(fio, &molb->nposres_xA, ("molb->nposres_xA"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2814);
2815 if (molb->nposres_xA > 0)
2816 {
2817 if (bRead)
2818 {
2819 snew(molb->posres_xA, molb->nposres_xA)(molb->posres_xA) = save_calloc("molb->posres_xA", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2819, (molb->nposres_xA), sizeof(*(molb->posres_xA)));
2820 }
2821 gmx_fio_ndo_rvec(fio, molb->posres_xA, molb->nposres_xA)gmx_fio_ndoe_rvec(fio, molb->posres_xA, molb->nposres_xA
, ("molb->posres_xA"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2821);
2822 }
2823 gmx_fio_do_int(fio, molb->nposres_xB)gmx_fio_doe_int(fio, &molb->nposres_xB, ("molb->nposres_xB"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
2823);
2824 if (molb->nposres_xB > 0)
2825 {
2826 if (bRead)
2827 {
2828 snew(molb->posres_xB, molb->nposres_xB)(molb->posres_xB) = save_calloc("molb->posres_xB", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2828, (molb->nposres_xB), sizeof(*(molb->posres_xB)));
2829 }
2830 gmx_fio_ndo_rvec(fio, molb->posres_xB, molb->nposres_xB)gmx_fio_ndoe_rvec(fio, molb->posres_xB, molb->nposres_xB
, ("molb->posres_xB"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2830);
2831 }
2832
2833}
2834
2835static t_block mtop_mols(gmx_mtop_t *mtop)
2836{
2837 int mb, m, a, mol;
2838 t_block mols;
2839
2840 mols.nr = 0;
2841 for (mb = 0; mb < mtop->nmolblock; mb++)
2842 {
2843 mols.nr += mtop->molblock[mb].nmol;
2844 }
2845 mols.nalloc_index = mols.nr + 1;
2846 snew(mols.index, mols.nalloc_index)(mols.index) = save_calloc("mols.index", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2846, (mols.nalloc_index), sizeof(*(mols.index)));
2847
2848 a = 0;
2849 m = 0;
2850 mols.index[m] = a;
2851 for (mb = 0; mb < mtop->nmolblock; mb++)
2852 {
2853 for (mol = 0; mol < mtop->molblock[mb].nmol; mol++)
2854 {
2855 a += mtop->molblock[mb].natoms_mol;
2856 m++;
2857 mols.index[m] = a;
2858 }
2859 }
2860
2861 return mols;
2862}
2863
2864static void add_posres_molblock(gmx_mtop_t *mtop)
2865{
2866 t_ilist *il, *ilfb;
2867 int am, i, mol, a;
2868 gmx_bool bFE;
2869 gmx_molblock_t *molb;
2870 t_iparams *ip;
2871
2872 /* posres reference positions are stored in ip->posres (if present) and
2873 in ip->fbposres (if present). If normal and flat-bottomed posres are present,
2874 posres.pos0A are identical to fbposres.pos0. */
2875 il = &mtop->moltype[0].ilist[F_POSRES];
2876 ilfb = &mtop->moltype[0].ilist[F_FBPOSRES];
2877 if (il->nr == 0 && ilfb->nr == 0)
2878 {
2879 return;
2880 }
2881 am = 0;
2882 bFE = FALSE0;
2883 for (i = 0; i < il->nr; i += 2)
2884 {
2885 ip = &mtop->ffparams.iparams[il->iatoms[i]];
2886 am = max(am, il->iatoms[i+1])(((am) > (il->iatoms[i+1])) ? (am) : (il->iatoms[i+1
]) );
2887 if (ip->posres.pos0B[XX0] != ip->posres.pos0A[XX0] ||
2888 ip->posres.pos0B[YY1] != ip->posres.pos0A[YY1] ||
2889 ip->posres.pos0B[ZZ2] != ip->posres.pos0A[ZZ2])
2890 {
2891 bFE = TRUE1;
2892 }
2893 }
2894 /* This loop is required if we have only flat-bottomed posres:
2895 - set am
2896 - bFE == FALSE (no B-state for flat-bottomed posres) */
2897 if (il->nr == 0)
2898 {
2899 for (i = 0; i < ilfb->nr; i += 2)
2900 {
2901 ip = &mtop->ffparams.iparams[ilfb->iatoms[i]];
Value stored to 'ip' is never read
2902 am = max(am, ilfb->iatoms[i+1])(((am) > (ilfb->iatoms[i+1])) ? (am) : (ilfb->iatoms
[i+1]) );
2903 }
2904 }
2905 /* Make the posres coordinate block end at a molecule end */
2906 mol = 0;
2907 while (am >= mtop->mols.index[mol+1])
2908 {
2909 mol++;
2910 }
2911 molb = &mtop->molblock[0];
2912 molb->nposres_xA = mtop->mols.index[mol+1];
2913 snew(molb->posres_xA, molb->nposres_xA)(molb->posres_xA) = save_calloc("molb->posres_xA", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2913, (molb->nposres_xA), sizeof(*(molb->posres_xA)));
2914 if (bFE)
2915 {
2916 molb->nposres_xB = molb->nposres_xA;
2917 snew(molb->posres_xB, molb->nposres_xB)(molb->posres_xB) = save_calloc("molb->posres_xB", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 2917, (molb->nposres_xB), sizeof(*(molb->posres_xB)));
2918 }
2919 else
2920 {
2921 molb->nposres_xB = 0;
2922 }
2923 for (i = 0; i < il->nr; i += 2)
2924 {
2925 ip = &mtop->ffparams.iparams[il->iatoms[i]];
2926 a = il->iatoms[i+1];
2927 molb->posres_xA[a][XX0] = ip->posres.pos0A[XX0];
2928 molb->posres_xA[a][YY1] = ip->posres.pos0A[YY1];
2929 molb->posres_xA[a][ZZ2] = ip->posres.pos0A[ZZ2];
2930 if (bFE)
2931 {
2932 molb->posres_xB[a][XX0] = ip->posres.pos0B[XX0];
2933 molb->posres_xB[a][YY1] = ip->posres.pos0B[YY1];
2934 molb->posres_xB[a][ZZ2] = ip->posres.pos0B[ZZ2];
2935 }
2936 }
2937 if (il->nr == 0)
2938 {
2939 /* If only flat-bottomed posres are present, take reference pos from them.
2940 Here: bFE == FALSE */
2941 for (i = 0; i < ilfb->nr; i += 2)
2942 {
2943 ip = &mtop->ffparams.iparams[ilfb->iatoms[i]];
2944 a = ilfb->iatoms[i+1];
2945 molb->posres_xA[a][XX0] = ip->fbposres.pos0[XX0];
2946 molb->posres_xA[a][YY1] = ip->fbposres.pos0[YY1];
2947 molb->posres_xA[a][ZZ2] = ip->fbposres.pos0[ZZ2];
2948 }
2949 }
2950}
2951
2952static void set_disres_npair(gmx_mtop_t *mtop)
2953{
2954 int mt, i, npair;
2955 t_iparams *ip;
2956 t_ilist *il;
2957 t_iatom *a;
2958
2959 ip = mtop->ffparams.iparams;
2960
2961 for (mt = 0; mt < mtop->nmoltype; mt++)
2962 {
2963 il = &mtop->moltype[mt].ilist[F_DISRES];
2964 if (il->nr > 0)
2965 {
2966 a = il->iatoms;
2967 npair = 0;
2968 for (i = 0; i < il->nr; i += 3)
2969 {
2970 npair++;
2971 if (i+3 == il->nr || ip[a[i]].disres.label != ip[a[i+3]].disres.label)
2972 {
2973 ip[a[i]].disres.npair = npair;
2974 npair = 0;
2975 }
2976 }
2977 }
2978 }
2979}
2980
2981static void do_mtop(t_fileio *fio, gmx_mtop_t *mtop, gmx_bool bRead,
2982 int file_version)
2983{
2984 int mt, mb, i;
2985 t_blocka dumb;
2986
2987 if (bRead)
2988 {
2989 init_mtop(mtop);
2990 }
2991 do_symtab(fio, &(mtop->symtab), bRead);
2992 if (bRead && debug)
2993 {
2994 pr_symtab(debug, 0, "symtab", &mtop->symtab);
2995 }
2996
2997 do_symstr(fio, &(mtop->name), bRead, &(mtop->symtab));
2998
2999 if (file_version >= 57)
3000 {
3001 do_ffparams(fio, &mtop->ffparams, bRead, file_version);
3002
3003 gmx_fio_do_int(fio, mtop->nmoltype)gmx_fio_doe_int(fio, &mtop->nmoltype, ("mtop->nmoltype"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
3003);
3004 }
3005 else
3006 {
3007 mtop->nmoltype = 1;
3008 }
3009 if (bRead)
3010 {
3011 snew(mtop->moltype, mtop->nmoltype)(mtop->moltype) = save_calloc("mtop->moltype", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3011, (mtop->nmoltype), sizeof(*(mtop->moltype)));
3012 if (file_version < 57)
3013 {
3014 mtop->moltype[0].name = mtop->name;
3015 }
3016 }
3017 for (mt = 0; mt < mtop->nmoltype; mt++)
3018 {
3019 do_moltype(fio, &mtop->moltype[mt], bRead, &mtop->symtab, file_version,
3020 &mtop->groups);
3021 }
3022
3023 if (file_version >= 57)
3024 {
3025 gmx_fio_do_int(fio, mtop->nmolblock)gmx_fio_doe_int(fio, &mtop->nmolblock, ("mtop->nmolblock"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
3025);
3026 }
3027 else
3028 {
3029 mtop->nmolblock = 1;
3030 }
3031 if (bRead)
3032 {
3033 snew(mtop->molblock, mtop->nmolblock)(mtop->molblock) = save_calloc("mtop->molblock", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3033, (mtop->nmolblock), sizeof(*(mtop->molblock)));
3034 }
3035 if (file_version >= 57)
3036 {
3037 for (mb = 0; mb < mtop->nmolblock; mb++)
3038 {
3039 do_molblock(fio, &mtop->molblock[mb], bRead);
3040 }
3041 gmx_fio_do_int(fio, mtop->natoms)gmx_fio_doe_int(fio, &mtop->natoms, ("mtop->natoms"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
3041);
3042 }
3043 else
3044 {
3045 mtop->molblock[0].type = 0;
3046 mtop->molblock[0].nmol = 1;
3047 mtop->molblock[0].natoms_mol = mtop->moltype[0].atoms.nr;
3048 mtop->molblock[0].nposres_xA = 0;
3049 mtop->molblock[0].nposres_xB = 0;
3050 }
3051
3052 do_atomtypes (fio, &(mtop->atomtypes), bRead, file_version);
3053 if (bRead && debug)
3054 {
3055 pr_atomtypes(debug, 0, "atomtypes", &mtop->atomtypes, TRUE1);
3056 }
3057
3058 if (file_version < 57)
3059 {
3060 /* Debug statements are inside do_idef */
3061 do_idef (fio, &mtop->ffparams, &mtop->moltype[0], bRead, file_version);
3062 mtop->natoms = mtop->moltype[0].atoms.nr;
3063 }
3064
3065 if (file_version >= 65)
3066 {
3067 do_cmap(fio, &mtop->ffparams.cmap_grid, bRead);
3068 }
3069 else
3070 {
3071 mtop->ffparams.cmap_grid.ngrid = 0;
3072 mtop->ffparams.cmap_grid.grid_spacing = 0;
3073 mtop->ffparams.cmap_grid.cmapdata = NULL((void*)0);
3074 }
3075
3076 if (file_version >= 57)
3077 {
3078 do_groups(fio, &mtop->groups, bRead, &(mtop->symtab), file_version);
3079 }
3080
3081 if (file_version < 57)
3082 {
3083 do_block(fio, &mtop->moltype[0].cgs, bRead, file_version);
3084 if (bRead && gmx_debug_at)
3085 {
3086 pr_block(debug, 0, "cgs", &mtop->moltype[0].cgs, TRUE1);
3087 }
3088 do_block(fio, &mtop->mols, bRead, file_version);
3089 /* Add the posres coordinates to the molblock */
3090 add_posres_molblock(mtop);
3091 }
3092 if (bRead)
3093 {
3094 if (file_version >= 57)
3095 {
3096 done_block(&mtop->mols);
3097 mtop->mols = mtop_mols(mtop);
3098 }
3099 if (gmx_debug_at)
3100 {
3101 pr_block(debug, 0, "mols", &mtop->mols, TRUE1);
3102 }
3103 }
3104
3105 if (file_version < 51)
3106 {
3107 /* Here used to be the shake blocks */
3108 do_blocka(fio, &dumb, bRead, file_version);
3109 if (dumb.nr > 0)
3110 {
3111 sfree(dumb.index)save_free("dumb.index", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3111, (dumb.index));
3112 }
3113 if (dumb.nra > 0)
3114 {
3115 sfree(dumb.a)save_free("dumb.a", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3115, (dumb.a));
3116 }
3117 }
3118
3119 if (bRead)
3120 {
3121 close_symtab(&(mtop->symtab));
3122 }
3123}
3124
3125/* If TopOnlyOK is TRUE then we can read even future versions
3126 * of tpx files, provided the file_generation hasn't changed.
3127 * If it is FALSE, we need the inputrecord too, and bail out
3128 * if the file is newer than the program.
3129 *
3130 * The version and generation if the topology (see top of this file)
3131 * are returned in the two last arguments.
3132 *
3133 * If possible, we will read the inputrec even when TopOnlyOK is TRUE.
3134 */
3135static void do_tpxheader(t_fileio *fio, gmx_bool bRead, t_tpxheader *tpx,
3136 gmx_bool TopOnlyOK, int *file_version,
3137 int *file_generation)
3138{
3139 char buf[STRLEN4096];
3140 char file_tag[STRLEN4096];
3141 gmx_bool bDouble;
3142 int precision;
3143 int fver, fgen;
3144 int idum = 0;
3145 real rdum = 0;
3146
3147 gmx_fio_checktype(fio);
3148 gmx_fio_setdebug(fio, bDebugMode());
3149
3150 /* NEW! XDR tpb file */
3151 precision = sizeof(real);
3152 if (bRead)
3153 {
3154 gmx_fio_do_string(fio, buf)gmx_fio_doe_string(fio, buf, ("buf"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3154);
3155 if (strncmp(buf, "VERSION", 7)(__extension__ (__builtin_constant_p (7) && ((__builtin_constant_p
(buf) && strlen (buf) < ((size_t) (7))) || (__builtin_constant_p
("VERSION") && strlen ("VERSION") < ((size_t) (7)
))) ? __extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(buf) && __builtin_constant_p ("VERSION") &&
(__s1_len = strlen (buf), __s2_len = strlen ("VERSION"), (!(
(size_t)(const void *)((buf) + 1) - (size_t)(const void *)(buf
) == 1) || __s1_len >= 4) && (!((size_t)(const void
*)(("VERSION") + 1) - (size_t)(const void *)("VERSION") == 1
) || __s2_len >= 4)) ? __builtin_strcmp (buf, "VERSION") :
(__builtin_constant_p (buf) && ((size_t)(const void *
)((buf) + 1) - (size_t)(const void *)(buf) == 1) && (
__s1_len = strlen (buf), __s1_len < 4) ? (__builtin_constant_p
("VERSION") && ((size_t)(const void *)(("VERSION") +
1) - (size_t)(const void *)("VERSION") == 1) ? __builtin_strcmp
(buf, "VERSION") : (__extension__ ({ const unsigned char *__s2
= (const unsigned char *) (const char *) ("VERSION"); int __result
= (((const unsigned char *) (const char *) (buf))[0] - __s2[
0]); if (__s1_len > 0 && __result == 0) { __result
= (((const unsigned char *) (const char *) (buf))[1] - __s2[
1]); if (__s1_len > 1 && __result == 0) { __result
= (((const unsigned char *) (const char *) (buf))[2] - __s2[
2]); if (__s1_len > 2 && __result == 0) __result =
(((const unsigned char *) (const char *) (buf))[3] - __s2[3]
); } } __result; }))) : (__builtin_constant_p ("VERSION") &&
((size_t)(const void *)(("VERSION") + 1) - (size_t)(const void
*)("VERSION") == 1) && (__s2_len = strlen ("VERSION"
), __s2_len < 4) ? (__builtin_constant_p (buf) && (
(size_t)(const void *)((buf) + 1) - (size_t)(const void *)(buf
) == 1) ? __builtin_strcmp (buf, "VERSION") : (- (__extension__
({ const unsigned char *__s2 = (const unsigned char *) (const
char *) (buf); int __result = (((const unsigned char *) (const
char *) ("VERSION"))[0] - __s2[0]); if (__s2_len > 0 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) ("VERSION"))[1] - __s2[1]); if (__s2_len > 1 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) ("VERSION"))[2] - __s2[2]); if (__s2_len > 2 &&
__result == 0) __result = (((const unsigned char *) (const char
*) ("VERSION"))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp
(buf, "VERSION")))); }) : strncmp (buf, "VERSION", 7))))
3156 {
3157 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
3157, "Can not read file %s,\n"
3158 " this file is from a Gromacs version which is older than 2.0\n"
3159 " Make a new one with grompp or use a gro or pdb file, if possible",
3160 gmx_fio_getname(fio));
3161 }
3162 gmx_fio_do_int(fio, precision)gmx_fio_doe_int(fio, &precision, ("precision"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3162);
3163 bDouble = (precision == sizeof(double));
3164 if ((precision != sizeof(float)) && !bDouble)
3165 {
3166 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
3166, "Unknown precision in file %s: real is %d bytes "
3167 "instead of %d or %d",
3168 gmx_fio_getname(fio), precision, sizeof(float), sizeof(double));
3169 }
3170 gmx_fio_setprecision(fio, bDouble);
3171 fprintf(stderrstderr, "Reading file %s, %s (%s precision)\n",
3172 gmx_fio_getname(fio), buf, bDouble ? "double" : "single");
3173 }
3174 else
3175 {
3176 gmx_fio_write_string(fio, GromacsVersion())gmx_fio_writee_string(fio, GromacsVersion(), ("GromacsVersion()"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
3176);
3177 bDouble = (precision == sizeof(double));
3178 gmx_fio_setprecision(fio, bDouble);
3179 gmx_fio_do_int(fio, precision)gmx_fio_doe_int(fio, &precision, ("precision"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3179);
3180 fver = tpx_version;
3181 sprintf(file_tag, "%s", tpx_tag);
3182 fgen = tpx_generation;
3183 }
3184
3185 /* Check versions! */
3186 gmx_fio_do_int(fio, fver)gmx_fio_doe_int(fio, &fver, ("fver"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3186);
3187
3188 /* This is for backward compatibility with development versions 77-79
3189 * where the tag was, mistakenly, placed before the generation,
3190 * which would cause a segv instead of a proper error message
3191 * when reading the topology only from tpx with <77 code.
3192 */
3193 if (fver >= 77 && fver <= 79)
3194 {
3195 gmx_fio_do_string(fio, file_tag)gmx_fio_doe_string(fio, file_tag, ("file_tag"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3195);
3196 }
3197
3198 if (fver >= 26)
3199 {
3200 gmx_fio_do_int(fio, fgen)gmx_fio_doe_int(fio, &fgen, ("fgen"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3200);
3201 }
3202 else
3203 {
3204 fgen = 0;
3205 }
3206
3207 if (fver >= 81)
3208 {
3209 gmx_fio_do_string(fio, file_tag)gmx_fio_doe_string(fio, file_tag, ("file_tag"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3209);
3210 }
3211 if (bRead)
3212 {
3213 if (fver < 77)
3214 {
3215 /* Versions before 77 don't have the tag, set it to release */
3216 sprintf(file_tag, "%s", TPX_TAG_RELEASE"release");
3217 }
3218
3219 if (strcmp(file_tag, tpx_tag)__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(file_tag) && __builtin_constant_p (tpx_tag) &&
(__s1_len = strlen (file_tag), __s2_len = strlen (tpx_tag), (
!((size_t)(const void *)((file_tag) + 1) - (size_t)(const void
*)(file_tag) == 1) || __s1_len >= 4) && (!((size_t
)(const void *)((tpx_tag) + 1) - (size_t)(const void *)(tpx_tag
) == 1) || __s2_len >= 4)) ? __builtin_strcmp (file_tag, tpx_tag
) : (__builtin_constant_p (file_tag) && ((size_t)(const
void *)((file_tag) + 1) - (size_t)(const void *)(file_tag) ==
1) && (__s1_len = strlen (file_tag), __s1_len < 4
) ? (__builtin_constant_p (tpx_tag) && ((size_t)(const
void *)((tpx_tag) + 1) - (size_t)(const void *)(tpx_tag) == 1
) ? __builtin_strcmp (file_tag, tpx_tag) : (__extension__ ({ const
unsigned char *__s2 = (const unsigned char *) (const char *)
(tpx_tag); int __result = (((const unsigned char *) (const char
*) (file_tag))[0] - __s2[0]); if (__s1_len > 0 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) (file_tag))[1] - __s2[1]); if (__s1_len > 1 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) (file_tag))[2] - __s2[2]); if (__s1_len > 2 &&
__result == 0) __result = (((const unsigned char *) (const char
*) (file_tag))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p
(tpx_tag) && ((size_t)(const void *)((tpx_tag) + 1) -
(size_t)(const void *)(tpx_tag) == 1) && (__s2_len =
strlen (tpx_tag), __s2_len < 4) ? (__builtin_constant_p (
file_tag) && ((size_t)(const void *)((file_tag) + 1) -
(size_t)(const void *)(file_tag) == 1) ? __builtin_strcmp (file_tag
, tpx_tag) : (- (__extension__ ({ const unsigned char *__s2 =
(const unsigned char *) (const char *) (file_tag); int __result
= (((const unsigned char *) (const char *) (tpx_tag))[0] - __s2
[0]); if (__s2_len > 0 && __result == 0) { __result
= (((const unsigned char *) (const char *) (tpx_tag))[1] - __s2
[1]); if (__s2_len > 1 && __result == 0) { __result
= (((const unsigned char *) (const char *) (tpx_tag))[2] - __s2
[2]); if (__s2_len > 2 && __result == 0) __result =
(((const unsigned char *) (const char *) (tpx_tag))[3] - __s2
[3]); } } __result; })))) : __builtin_strcmp (file_tag, tpx_tag
)))); }) != 0)
3220 {
3221 fprintf(stderrstderr, "Note: file tpx tag '%s', software tpx tag '%s'\n",
3222 file_tag, tpx_tag);
3223
3224 /* We only support reading tpx files with the same tag as the code
3225 * or tpx files with the release tag and with lower version number.
3226 */
3227 if (!strcmp(file_tag, TPX_TAG_RELEASE)__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(file_tag) && __builtin_constant_p ("release") &&
(__s1_len = strlen (file_tag), __s2_len = strlen ("release")
, (!((size_t)(const void *)((file_tag) + 1) - (size_t)(const void
*)(file_tag) == 1) || __s1_len >= 4) && (!((size_t
)(const void *)(("release") + 1) - (size_t)(const void *)("release"
) == 1) || __s2_len >= 4)) ? __builtin_strcmp (file_tag, "release"
) : (__builtin_constant_p (file_tag) && ((size_t)(const
void *)((file_tag) + 1) - (size_t)(const void *)(file_tag) ==
1) && (__s1_len = strlen (file_tag), __s1_len < 4
) ? (__builtin_constant_p ("release") && ((size_t)(const
void *)(("release") + 1) - (size_t)(const void *)("release")
== 1) ? __builtin_strcmp (file_tag, "release") : (__extension__
({ const unsigned char *__s2 = (const unsigned char *) (const
char *) ("release"); int __result = (((const unsigned char *
) (const char *) (file_tag))[0] - __s2[0]); if (__s1_len >
0 && __result == 0) { __result = (((const unsigned char
*) (const char *) (file_tag))[1] - __s2[1]); if (__s1_len >
1 && __result == 0) { __result = (((const unsigned char
*) (const char *) (file_tag))[2] - __s2[2]); if (__s1_len >
2 && __result == 0) __result = (((const unsigned char
*) (const char *) (file_tag))[3] - __s2[3]); } } __result; }
))) : (__builtin_constant_p ("release") && ((size_t)(
const void *)(("release") + 1) - (size_t)(const void *)("release"
) == 1) && (__s2_len = strlen ("release"), __s2_len <
4) ? (__builtin_constant_p (file_tag) && ((size_t)(const
void *)((file_tag) + 1) - (size_t)(const void *)(file_tag) ==
1) ? __builtin_strcmp (file_tag, "release") : (- (__extension__
({ const unsigned char *__s2 = (const unsigned char *) (const
char *) (file_tag); int __result = (((const unsigned char *)
(const char *) ("release"))[0] - __s2[0]); if (__s2_len >
0 && __result == 0) { __result = (((const unsigned char
*) (const char *) ("release"))[1] - __s2[1]); if (__s2_len >
1 && __result == 0) { __result = (((const unsigned char
*) (const char *) ("release"))[2] - __s2[2]); if (__s2_len >
2 && __result == 0) __result = (((const unsigned char
*) (const char *) ("release"))[3] - __s2[3]); } } __result; }
)))) : __builtin_strcmp (file_tag, "release")))); }) == 0 && fver < tpx_version)
3228 {
3229 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
3229, "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' with program for tpx version %d, tag '%s'",
3230 gmx_fio_getname(fio), fver, file_tag,
3231 tpx_version, tpx_tag);
3232 }
3233 }
3234 }
3235
3236 if (file_version != NULL((void*)0))
3237 {
3238 *file_version = fver;
3239 }
3240 if (file_generation != NULL((void*)0))
3241 {
3242 *file_generation = fgen;
3243 }
3244
3245
3246 if ((fver <= tpx_incompatible_version) ||
3247 ((fver > tpx_version) && !TopOnlyOK) ||
3248 (fgen > tpx_generation) ||
3249 tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
3250 {
3251 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
3251, "reading tpx file (%s) version %d with version %d program",
3252 gmx_fio_getname(fio), fver, tpx_version);
3253 }
3254
3255 do_section(fio, eitemHEADER, bRead)_do_section(fio, eitemHEADER, bRead, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3255);
3256 gmx_fio_do_int(fio, tpx->natoms)gmx_fio_doe_int(fio, &tpx->natoms, ("tpx->natoms"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 3256
);
3257 if (fver >= 28)
3258 {
3259 gmx_fio_do_int(fio, tpx->ngtc)gmx_fio_doe_int(fio, &tpx->ngtc, ("tpx->ngtc"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3259);
3260 }
3261 else
3262 {
3263 tpx->ngtc = 0;
3264 }
3265 if (fver < 62)
3266 {
3267 gmx_fio_do_int(fio, idum)gmx_fio_doe_int(fio, &idum, ("idum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3267);
3268 gmx_fio_do_real(fio, rdum)gmx_fio_doe_real(fio, &rdum, ("rdum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3268);
3269 }
3270 /*a better decision will eventually (5.0 or later) need to be made
3271 on how to treat the alchemical state of the system, which can now
3272 vary through a simulation, and cannot be completely described
3273 though a single lambda variable, or even a single state
3274 index. Eventually, should probably be a vector. MRS*/
3275 if (fver >= 79)
3276 {
3277 gmx_fio_do_int(fio, tpx->fep_state)gmx_fio_doe_int(fio, &tpx->fep_state, ("tpx->fep_state"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
3277);
3278 }
3279 gmx_fio_do_real(fio, tpx->lambda)gmx_fio_doe_real(fio, &tpx->lambda, ("tpx->lambda")
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 3279
);
3280 gmx_fio_do_int(fio, tpx->bIr)gmx_fio_doe_int(fio, &tpx->bIr, ("tpx->bIr"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3280);
3281 gmx_fio_do_int(fio, tpx->bTop)gmx_fio_doe_int(fio, &tpx->bTop, ("tpx->bTop"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3281);
3282 gmx_fio_do_int(fio, tpx->bX)gmx_fio_doe_int(fio, &tpx->bX, ("tpx->bX"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3282);
3283 gmx_fio_do_int(fio, tpx->bV)gmx_fio_doe_int(fio, &tpx->bV, ("tpx->bV"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3283);
3284 gmx_fio_do_int(fio, tpx->bF)gmx_fio_doe_int(fio, &tpx->bF, ("tpx->bF"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3284);
3285 gmx_fio_do_int(fio, tpx->bBox)gmx_fio_doe_int(fio, &tpx->bBox, ("tpx->bBox"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3285);
3286
3287 if ((fgen > tpx_generation))
3288 {
3289 /* This can only happen if TopOnlyOK=TRUE */
3290 tpx->bIr = FALSE0;
3291 }
3292}
3293
3294static int do_tpx(t_fileio *fio, gmx_bool bRead,
3295 t_inputrec *ir, t_state *state, rvec *f, gmx_mtop_t *mtop,
3296 gmx_bool bXVallocated)
3297{
3298 t_tpxheader tpx;
3299 t_inputrec dum_ir;
3300 gmx_mtop_t dum_top;
3301 gmx_bool TopOnlyOK;
3302 int file_version, file_generation;
3303 int i;
3304 rvec *xptr, *vptr;
3305 int ePBC;
3306 gmx_bool bPeriodicMols;
3307
3308 if (!bRead)
3309 {
3310 tpx.natoms = state->natoms;
3311 tpx.ngtc = state->ngtc; /* need to add nnhpres here? */
3312 tpx.fep_state = state->fep_state;
3313 tpx.lambda = state->lambda[efptFEP];
3314 tpx.bIr = (ir != NULL((void*)0));
3315 tpx.bTop = (mtop != NULL((void*)0));
3316 tpx.bX = (state->x != NULL((void*)0));
3317 tpx.bV = (state->v != NULL((void*)0));
3318 tpx.bF = (f != NULL((void*)0));
3319 tpx.bBox = TRUE1;
3320 }
3321
3322 TopOnlyOK = (ir == NULL((void*)0));
3323
3324 do_tpxheader(fio, bRead, &tpx, TopOnlyOK, &file_version, &file_generation);
3325
3326 if (bRead)
3327 {
3328 state->flags = 0;
3329 /* state->lambda = tpx.lambda;*/ /*remove this eventually? */
3330 /* The init_state calls initialize the Nose-Hoover xi integrals to zero */
3331 if (bXVallocated)
3332 {
3333 xptr = state->x;
3334 vptr = state->v;
3335 init_state(state, 0, tpx.ngtc, 0, 0, 0); /* nose-hoover chains */ /* eventually, need to add nnhpres here? */
3336 state->natoms = tpx.natoms;
3337 state->nalloc = tpx.natoms;
3338 state->x = xptr;
3339 state->v = vptr;
3340 }
3341 else
3342 {
3343 init_state(state, tpx.natoms, tpx.ngtc, 0, 0, 0); /* nose-hoover chains */
3344 }
3345 }
3346
3347#define do_test(fio, b, p)if (bRead && (p != ((void*)0)) && !b) gmx_fatal
(0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3347, "No %s in %s","p", gmx_fio_getname(fio)) if (bRead && (p != NULL((void*)0)) && !b) gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
3347, "No %s in %s",#p, gmx_fio_getname(fio))
3348
3349 do_test(fio, tpx.bBox, state->box)if (bRead && (state->box != ((void*)0)) &&
!tpx.bBox) gmx_fatal(0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3349, "No %s in %s","state->box", gmx_fio_getname(fio));
3350 do_section(fio, eitemBOX, bRead)_do_section(fio, eitemBOX, bRead, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3350);
3351 if (tpx.bBox)
3352 {
3353 gmx_fio_ndo_rvec(fio, state->box, DIM)gmx_fio_ndoe_rvec(fio, state->box, 3, ("state->box"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3353);
3354 if (file_version >= 51)
3355 {
3356 gmx_fio_ndo_rvec(fio, state->box_rel, DIM)gmx_fio_ndoe_rvec(fio, state->box_rel, 3, ("state->box_rel"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
3356);
3357 }
3358 else
3359 {
3360 /* We initialize box_rel after reading the inputrec */
3361 clear_mat(state->box_rel);
3362 }
3363 if (file_version >= 28)
3364 {
3365 gmx_fio_ndo_rvec(fio, state->boxv, DIM)gmx_fio_ndoe_rvec(fio, state->boxv, 3, ("state->boxv"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c", 3365
);
3366 if (file_version < 56)
3367 {
3368 matrix mdum;
3369 gmx_fio_ndo_rvec(fio, mdum, DIM)gmx_fio_ndoe_rvec(fio, mdum, 3, ("mdum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3369);
3370 }
3371 }
3372 }
3373
3374 if (state->ngtc > 0 && file_version >= 28)
3375 {
3376 real *dumv;
3377 /*ndo_double(state->nosehoover_xi,state->ngtc,bDum);*/
3378 /*ndo_double(state->nosehoover_vxi,state->ngtc,bDum);*/
3379 /*ndo_double(state->therm_integral,state->ngtc,bDum);*/
3380 snew(dumv, state->ngtc)(dumv) = save_calloc("dumv", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3380, (state->ngtc), sizeof(*(dumv)));
3381 if (file_version < 69)
3382 {
3383 gmx_fio_ndo_real(fio, dumv, state->ngtc)gmx_fio_ndoe_real(fio, dumv, state->ngtc, ("dumv"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3383);
3384 }
3385 /* These used to be the Berendsen tcoupl_lambda's */
3386 gmx_fio_ndo_real(fio, dumv, state->ngtc)gmx_fio_ndoe_real(fio, dumv, state->ngtc, ("dumv"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3386);
3387 sfree(dumv)save_free("dumv", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3387, (dumv));
3388 }
3389
3390 /* Prior to tpx version 26, the inputrec was here.
3391 * I moved it to enable partial forward-compatibility
3392 * for analysis/viewer programs.
3393 */
3394 if (file_version < 26)
3395 {
3396 do_test(fio, tpx.bIr, ir)if (bRead && (ir != ((void*)0)) && !tpx.bIr) gmx_fatal
(0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3396, "No %s in %s","ir", gmx_fio_getname(fio));
3397 do_section(fio, eitemIR, bRead)_do_section(fio, eitemIR, bRead, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3397);
3398 if (tpx.bIr)
3399 {
3400 if (ir)
3401 {
3402 do_inputrec(fio, ir, bRead, file_version,
3403 mtop ? &mtop->ffparams.fudgeQQ : NULL((void*)0));
3404 if (bRead && debug)
3405 {
3406 pr_inputrec(debug, 0, "inputrec", ir, FALSE0);
3407 }
3408 }
3409 else
3410 {
3411 do_inputrec(fio, &dum_ir, bRead, file_version,
3412 mtop ? &mtop->ffparams.fudgeQQ : NULL((void*)0));
3413 if (bRead && debug)
3414 {
3415 pr_inputrec(debug, 0, "inputrec", &dum_ir, FALSE0);
3416 }
3417 done_inputrec(&dum_ir);
3418 }
3419
3420 }
3421 }
3422
3423 do_test(fio, tpx.bTop, mtop)if (bRead && (mtop != ((void*)0)) && !tpx.bTop
) gmx_fatal(0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3423, "No %s in %s","mtop", gmx_fio_getname(fio));
3424 do_section(fio, eitemTOP, bRead)_do_section(fio, eitemTOP, bRead, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3424);
3425 if (tpx.bTop)
3426 {
3427 if (mtop)
3428 {
3429 do_mtop(fio, mtop, bRead, file_version);
3430 }
3431 else
3432 {
3433 do_mtop(fio, &dum_top, bRead, file_version);
3434 done_mtop(&dum_top, TRUE1);
3435 }
3436 }
3437 do_test(fio, tpx.bX, state->x)if (bRead && (state->x != ((void*)0)) && !
tpx.bX) gmx_fatal(0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3437, "No %s in %s","state->x", gmx_fio_getname(fio));
3438 do_section(fio, eitemX, bRead)_do_section(fio, eitemX, bRead, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3438);
3439 if (tpx.bX)
3440 {
3441 if (bRead)
3442 {
3443 state->flags |= (1<<estX);
3444 }
3445 gmx_fio_ndo_rvec(fio, state->x, state->natoms)gmx_fio_ndoe_rvec(fio, state->x, state->natoms, ("state->x"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
3445);
3446 }
3447
3448 do_test(fio, tpx.bV, state->v)if (bRead && (state->v != ((void*)0)) && !
tpx.bV) gmx_fatal(0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3448, "No %s in %s","state->v", gmx_fio_getname(fio));
3449 do_section(fio, eitemV, bRead)_do_section(fio, eitemV, bRead, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3449);
3450 if (tpx.bV)
3451 {
3452 if (bRead)
3453 {
3454 state->flags |= (1<<estV);
3455 }
3456 gmx_fio_ndo_rvec(fio, state->v, state->natoms)gmx_fio_ndoe_rvec(fio, state->v, state->natoms, ("state->v"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
3456);
3457 }
3458
3459 do_test(fio, tpx.bF, f)if (bRead && (f != ((void*)0)) && !tpx.bF) gmx_fatal
(0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3459, "No %s in %s","f", gmx_fio_getname(fio));
3460 do_section(fio, eitemF, bRead)_do_section(fio, eitemF, bRead, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3460);
3461 if (tpx.bF)
3462 {
3463 gmx_fio_ndo_rvec(fio, f, state->natoms)gmx_fio_ndoe_rvec(fio, f, state->natoms, ("f"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3463);
3464 }
3465
3466 /* Starting with tpx version 26, we have the inputrec
3467 * at the end of the file, so we can ignore it
3468 * if the file is never than the software (but still the
3469 * same generation - see comments at the top of this file.
3470 *
3471 *
3472 */
3473 ePBC = -1;
3474 bPeriodicMols = FALSE0;
3475 if (file_version >= 26)
3476 {
3477 do_test(fio, tpx.bIr, ir)if (bRead && (ir != ((void*)0)) && !tpx.bIr) gmx_fatal
(0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3477, "No %s in %s","ir", gmx_fio_getname(fio));
3478 do_section(fio, eitemIR, bRead)_do_section(fio, eitemIR, bRead, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3478);
3479 if (tpx.bIr)
3480 {
3481 if (file_version >= 53)
3482 {
3483 /* Removed the pbc info from do_inputrec, since we always want it */
3484 if (!bRead)
3485 {
3486 ePBC = ir->ePBC;
3487 bPeriodicMols = ir->bPeriodicMols;
3488 }
3489 gmx_fio_do_int(fio, ePBC)gmx_fio_doe_int(fio, &ePBC, ("ePBC"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3489);
3490 gmx_fio_do_gmx_bool(fio, bPeriodicMols)gmx_fio_doe_gmx_bool(fio, &bPeriodicMols, ("bPeriodicMols"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c",
3490);
3491 }
3492 if (file_generation <= tpx_generation && ir)
3493 {
3494 do_inputrec(fio, ir, bRead, file_version, mtop ? &mtop->ffparams.fudgeQQ : NULL((void*)0));
3495 if (bRead && debug)
3496 {
3497 pr_inputrec(debug, 0, "inputrec", ir, FALSE0);
3498 }
3499 if (file_version < 51)
3500 {
3501 set_box_rel(ir, state);
3502 }
3503 if (file_version < 53)
3504 {
3505 ePBC = ir->ePBC;
3506 bPeriodicMols = ir->bPeriodicMols;
3507 }
3508 }
3509 if (bRead && ir && file_version >= 53)
3510 {
3511 /* We need to do this after do_inputrec, since that initializes ir */
3512 ir->ePBC = ePBC;
3513 ir->bPeriodicMols = bPeriodicMols;
3514 }
3515 }
3516 }
3517
3518 if (bRead)
3519 {
3520 if (tpx.bIr && ir)
3521 {
3522 if (state->ngtc == 0)
3523 {
3524 /* Reading old version without tcoupl state data: set it */
3525 init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength);
3526 }
3527 if (tpx.bTop && mtop)
3528 {
3529 if (file_version < 57)
3530 {
3531 if (mtop->moltype[0].ilist[F_DISRES].nr > 0)
3532 {
3533 ir->eDisre = edrSimple;
3534 }
3535 else
3536 {
3537 ir->eDisre = edrNone;
3538 }
3539 }
3540 set_disres_npair(mtop);
3541 }
3542 }
3543
3544 if (tpx.bTop && mtop)
3545 {
3546 gmx_mtop_finalize(mtop);
3547 }
3548
3549 if (file_version >= 57)
3550 {
3551 char *env;
3552 int ienv;
3553 env = getenv("GMX_NOCHARGEGROUPS");
3554 if (env != NULL((void*)0))
3555 {
3556 sscanf(env, "%d", &ienv);
3557 fprintf(stderrstderr, "\nFound env.var. GMX_NOCHARGEGROUPS = %d\n",
3558 ienv);
3559 if (ienv > 0)
3560 {
3561 fprintf(stderrstderr,
3562 "Will make single atomic charge groups in non-solvent%s\n",
3563 ienv > 1 ? " and solvent" : "");
3564 gmx_mtop_make_atomic_charge_groups(mtop, ienv == 1);
3565 }
3566 fprintf(stderrstderr, "\n");
3567 }
3568 }
3569 }
3570
3571 return ePBC;
3572}
3573
3574/************************************************************
3575 *
3576 * The following routines are the exported ones
3577 *
3578 ************************************************************/
3579
3580t_fileio *open_tpx(const char *fn, const char *mode)
3581{
3582 return gmx_fio_open(fn, mode);
3583}
3584
3585void close_tpx(t_fileio *fio)
3586{
3587 gmx_fio_close(fio);
3588}
3589
3590void read_tpxheader(const char *fn, t_tpxheader *tpx, gmx_bool TopOnlyOK,
3591 int *file_version, int *file_generation)
3592{
3593 t_fileio *fio;
3594
3595 fio = open_tpx(fn, "r");
3596 do_tpxheader(fio, TRUE1, tpx, TopOnlyOK, file_version, file_generation);
3597 close_tpx(fio);
3598}
3599
3600void write_tpx_state(const char *fn,
3601 t_inputrec *ir, t_state *state, gmx_mtop_t *mtop)
3602{
3603 t_fileio *fio;
3604
3605 fio = open_tpx(fn, "w");
3606 do_tpx(fio, FALSE0, ir, state, NULL((void*)0), mtop, FALSE0);
3607 close_tpx(fio);
3608}
3609
3610void read_tpx_state(const char *fn,
3611 t_inputrec *ir, t_state *state, rvec *f, gmx_mtop_t *mtop)
3612{
3613 t_fileio *fio;
3614
3615 fio = open_tpx(fn, "r");
3616 do_tpx(fio, TRUE1, ir, state, f, mtop, FALSE0);
3617 close_tpx(fio);
3618}
3619
3620int read_tpx(const char *fn,
3621 t_inputrec *ir, matrix box, int *natoms,
3622 rvec *x, rvec *v, rvec *f, gmx_mtop_t *mtop)
3623{
3624 t_fileio *fio;
3625 t_state state;
3626 int ePBC;
3627
3628 state.x = x;
3629 state.v = v;
3630 fio = open_tpx(fn, "r");
3631 ePBC = do_tpx(fio, TRUE1, ir, &state, f, mtop, TRUE1);
3632 close_tpx(fio);
3633 *natoms = state.natoms;
3634 if (box)
3635 {
3636 copy_mat(state.box, box);
3637 }
3638 state.x = NULL((void*)0);
3639 state.v = NULL((void*)0);
3640 done_state(&state);
3641
3642 return ePBC;
3643}
3644
3645int read_tpx_top(const char *fn,
3646 t_inputrec *ir, matrix box, int *natoms,
3647 rvec *x, rvec *v, rvec *f, t_topology *top)
3648{
3649 gmx_mtop_t mtop;
3650 t_topology *ltop;
3651 int ePBC;
3652
3653 ePBC = read_tpx(fn, ir, box, natoms, x, v, f, &mtop);
3654
3655 *top = gmx_mtop_t_to_t_topology(&mtop);
3656
3657 return ePBC;
3658}
3659
3660gmx_bool fn2bTPX(const char *file)
3661{
3662 switch (fn2ftp(file))
3663 {
3664 case efTPR:
3665 case efTPB:
3666 case efTPA:
3667 return TRUE1;
3668 default:
3669 return FALSE0;
3670 }
3671}
3672
3673static void done_gmx_groups_t(gmx_groups_t *g)
3674{
3675 int i;
3676
3677 for (i = 0; (i < egcNR); i++)
3678 {
3679 if (NULL((void*)0) != g->grps[i].nm_ind)
3680 {
3681 sfree(g->grps[i].nm_ind)save_free("g->grps[i].nm_ind", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3681, (g->grps[i].nm_ind));
3682 g->grps[i].nm_ind = NULL((void*)0);
3683 }
3684 if (NULL((void*)0) != g->grpnr[i])
3685 {
3686 sfree(g->grpnr[i])save_free("g->grpnr[i]", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3686, (g->grpnr[i]));
3687 g->grpnr[i] = NULL((void*)0);
3688 }
3689 }
3690 /* The contents of this array is in symtab, don't free it here */
3691 sfree(g->grpname)save_free("g->grpname", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3691, (g->grpname));
3692}
3693
3694gmx_bool read_tps_conf(const char *infile, char *title, t_topology *top, int *ePBC,
3695 rvec **x, rvec **v, matrix box, gmx_bool bMass)
3696{
3697 t_tpxheader header;
3698 int natoms, i, version, generation;
3699 gmx_bool bTop, bXNULL = FALSE0;
3700 gmx_mtop_t *mtop;
3701 t_topology *topconv;
3702 gmx_atomprop_t aps;
3703
3704 bTop = fn2bTPX(infile);
3705 *ePBC = -1;
3706 if (bTop)
3707 {
3708 read_tpxheader(infile, &header, TRUE1, &version, &generation);
3709 if (x)
3710 {
3711 snew(*x, header.natoms)(*x) = save_calloc("*x", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3711, (header.natoms), sizeof(*(*x)));
3712 }
3713 if (v)
3714 {
3715 snew(*v, header.natoms)(*v) = save_calloc("*v", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3715, (header.natoms), sizeof(*(*v)));
3716 }
3717 snew(mtop, 1)(mtop) = save_calloc("mtop", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3717, (1), sizeof(*(mtop)));
3718 *ePBC = read_tpx(infile, NULL((void*)0), box, &natoms,
3719 (x == NULL((void*)0)) ? NULL((void*)0) : *x, (v == NULL((void*)0)) ? NULL((void*)0) : *v, NULL((void*)0), mtop);
3720 *top = gmx_mtop_t_to_t_topology(mtop);
3721 /* In this case we need to throw away the group data too */
3722 done_gmx_groups_t(&mtop->groups);
3723 sfree(mtop)save_free("mtop", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3723, (mtop));
3724 strcpy(title, *top->name);
3725 tpx_make_chain_identifiers(&top->atoms, &top->mols);
3726 }
3727 else
3728 {
3729 get_stx_coordnum(infile, &natoms);
3730 init_t_atoms(&top->atoms, natoms, (fn2ftp(infile) == efPDB));
3731 if (x == NULL((void*)0))
3732 {
3733 snew(x, 1)(x) = save_calloc("x", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3733, (1), sizeof(*(x)));
3734 bXNULL = TRUE1;
3735 }
3736 snew(*x, natoms)(*x) = save_calloc("*x", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3736, (natoms), sizeof(*(*x)));
3737 if (v)
3738 {
3739 snew(*v, natoms)(*v) = save_calloc("*v", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3739, (natoms), sizeof(*(*v)));
3740 }
3741 read_stx_conf(infile, title, &top->atoms, *x, (v == NULL((void*)0)) ? NULL((void*)0) : *v, ePBC, box);
3742 if (bXNULL)
3743 {
3744 sfree(*x)save_free("*x", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3744, (*x));
3745 sfree(x)save_free("x", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/tpxio.c"
, 3745, (x));
3746 }
3747 if (bMass)
3748 {
3749 aps = gmx_atomprop_init();
3750 for (i = 0; (i < natoms); i++)
3751 {
3752 if (!gmx_atomprop_query(aps, epropMass,
3753 *top->atoms.resinfo[top->atoms.atom[i].resind].name,
3754 *top->atoms.atomname[i],
3755 &(top->atoms.atom[i].m)))
3756 {
3757 if (debug)
3758 {
3759 fprintf(debug, "Can not find mass for atom %s %d %s, setting to 1\n",
3760 *top->atoms.resinfo[top->atoms.atom[i].resind].name,
3761 top->atoms.resinfo[top->atoms.atom[i].resind].nr,
3762 *top->atoms.atomname[i]);
3763 }
3764 }
3765 }
3766 gmx_atomprop_destroy(aps);
3767 }
3768 top->idef.ntypes = -1;
3769 }
3770
3771 return bTop;
3772}