2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
37 /* This file is completely threadsafe - keep it that way! */
40 #include "cstringutil.h"
51 #include <sys/types.h>
52 #ifdef HAVE_SYS_TIME_H
62 #include "gromacs/utility/basedefinitions.h"
63 #include "gromacs/utility/basenetwork.h"
64 #include "gromacs/utility/fatalerror.h"
65 #include "gromacs/utility/futil.h"
66 #include "gromacs/utility/smalloc.h"
68 int continuing(char *s)
75 if ((sl > 0) && (s[sl-1] == CONTINUE))
88 char *fgets2(char *line, int n, FILE *stream)
91 if (fgets(line, n, stream) == NULL)
95 if ((c = strchr(line, '\n')) != NULL)
101 /* A line not ending in a newline can only occur at the end of a file,
102 * or because of n being too small.
103 * Since both cases occur very infrequently, we can check for EOF.
107 gmx_fatal(FARGS, "An input file contains a line longer than %d characters, while the buffer passed to fgets2 has size %d. The line starts with: '%20.20s'", n, n, line);
110 if ((c = strchr(line, '\r')) != NULL)
118 void strip_comment (char *line)
127 /* search for a comment mark and replace it by a zero */
128 if ((c = strchr(line, COMMENTSIGN)) != NULL)
134 void upstring (char *str)
138 for (i = 0; (i < (int)strlen(str)); i++)
140 str[i] = toupper(str[i]);
144 void ltrim (char *str)
155 while (('\0' != str[c]) && isspace(str[c]))
161 for (i = c; ('\0' != str[i]); i++)
169 void rtrim (char *str)
179 while ((nul > 0) && ((str[nul] == ' ') || (str[nul] == '\t')) )
186 void trim (char *str)
193 gmx_ctime_r(const time_t *clock, char *buf, int n)
197 ctime_s( buf, n, clock );
198 #elif defined(GMX_NATIVE_WINDOWS)
199 char *tmpbuf = ctime( clock );
200 strncpy(buf, tmpbuf, n-1);
202 #elif (defined(__sun))
204 ctime_r(clock, buf, n);
207 ctime_r(clock, tmpbuf);
208 strncpy(buf, tmpbuf, n-1);
214 void nice_header (FILE *out, const char *fn)
216 const char *unk = "onbekend";
226 char timebuf[STRLEN];
231 /* Print a nice header above the file */
233 fprintf (out, "%c\n", COMMENTSIGN);
234 fprintf (out, "%c\tFile '%s' was generated\n", COMMENTSIGN, fn ? fn : unk);
239 gh = gmx_gethostname(buf, 255);
240 /* pw returns null on error (e.g. compute nodes lack /etc/passwd) */
241 user = pw ? pw->pw_name : unk;
248 gmx_ctime_r(&clock, timebuf, STRLEN);
249 fprintf (out, "%c\tBy user: %s (%d)\n", COMMENTSIGN,
250 user ? user : unk, (int) uid);
251 fprintf(out, "%c\tOn host: %s\n", COMMENTSIGN, (gh == 0) ? buf : unk);
253 fprintf (out, "%c\tAt date: %s", COMMENTSIGN, timebuf);
254 fprintf (out, "%c\n", COMMENTSIGN);
258 int gmx_strcasecmp_min(const char *str1, const char *str2)
266 ch1 = toupper(*(str1++));
268 while ((ch1 == '-') || (ch1 == '_'));
271 ch2 = toupper(*(str2++));
273 while ((ch2 == '-') || (ch2 == '_'));
284 int gmx_strncasecmp_min(const char *str1, const char *str2, int n)
289 stri1 = (char *)str1;
290 stri2 = (char *)str2;
295 ch1 = toupper(*(str1++));
297 while ((ch1 == '-') || (ch1 == '_'));
300 ch2 = toupper(*(str2++));
302 while ((ch2 == '-') || (ch2 == '_'));
309 while (ch1 && (str1-stri1 < n) && (str2-stri2 < n));
313 int gmx_strcasecmp(const char *str1, const char *str2)
319 ch1 = toupper(*(str1++));
320 ch2 = toupper(*(str2++));
330 int gmx_strncasecmp(const char *str1, const char *str2, int n)
341 ch1 = toupper(*(str1++));
342 ch2 = toupper(*(str2++));
353 char *gmx_strdup(const char *src)
357 snew(dest, strlen(src)+1);
364 gmx_strndup(const char *src, int n)
375 strncpy(dest, src, len);
380 /* Magic hash init number for Dan J. Bernsteins algorithm.
381 * Do NOT use any other value unless you really know what you are doing.
384 gmx_string_hash_init = 5381;
388 gmx_string_fullhash_func(const char *s, unsigned int hash_init)
392 while ((c = (*s++)) != '\0')
394 hash_init = ((hash_init << 5) + hash_init) ^ c; /* (hash * 33) xor c */
400 gmx_string_hash_func(const char *s, unsigned int hash_init)
404 while ((c = toupper(*s++)) != '\0')
408 hash_init = ((hash_init << 5) + hash_init) ^ c; /* (hash * 33) xor c */
415 gmx_wcmatch(const char *pattern, const char *str)
421 /* Skip multiple wildcards in a sequence */
422 while (*pattern == '*' || *pattern == '?')
425 /* For ?, we need to check that there are characters left
431 return GMX_NO_WCMATCH;
439 /* If the pattern ends after the star, we have a match */
444 /* Match the rest against each possible suffix of str */
447 /* Only do the recursive call if the first character
448 * matches. We don't have to worry about wildcards here,
449 * since we have processed them above. */
450 if (*pattern == *str)
453 /* Match the suffix, and return if a match or an error */
454 rc = gmx_wcmatch(pattern, str);
455 if (rc != GMX_NO_WCMATCH)
462 /* If no suffix of str matches, we don't have a match */
463 return GMX_NO_WCMATCH;
465 else if ((*pattern == '?' && *str != 0) || *pattern == *str)
471 return GMX_NO_WCMATCH;
475 /* When the pattern runs out, we have a match if the string has ended. */
476 return (*str == 0) ? 0 : GMX_NO_WCMATCH;
479 char *wrap_lines(const char *buf, int line_width, int indent, gmx_bool bIndentFirst)
482 int i, i0, i2, j, b2len, lspace = 0, l2space = 0;
483 gmx_bool bFirst, bFitsOnLine;
485 /* characters are copied from buf to b2 with possible spaces changed
486 * into newlines and extra space added for indentation.
487 * i indexes buf (source buffer) and i2 indexes b2 (destination buffer)
488 * i0 points to the beginning of the current line (in buf, source)
489 * lspace and l2space point to the last space on the current line
490 * bFirst is set to prevent indentation of first line
491 * bFitsOnLine says if the first space occurred before line_width, if
492 * that is not the case, we have a word longer than line_width which
493 * will also not fit on the next line, so we might as well keep it on
494 * the current line (where it also won't fit, but looks better)
498 b2len = strlen(buf)+1+indent;
503 for (i2 = 0; (i2 < indent); i2++)
512 /* find the last space before end of line */
513 for (i = i0; ((i-i0 < line_width) || (l2space == -1)) && (buf[i]); i++)
516 /* remember the position of a space */
522 /* if we have a newline before the line is full, reset counters */
523 if (buf[i] == '\n' && buf[i+1])
528 /* add indentation after the newline */
529 for (j = 0; (j < indent); j++)
535 /* If we are at the last newline, copy it */
536 if (buf[i] == '\n' && !buf[i+1])
540 /* if we're not at the end of the string */
543 /* check if one word does not fit on the line */
544 bFitsOnLine = (i-i0 <= line_width);
545 /* reset line counters to just after the space */
548 /* if the words fit on the line, and we're beyond the indentation part */
549 if ( (bFitsOnLine) && (l2space >= indent) )
551 /* start a new line */
553 /* and add indentation */
558 line_width -= indent;
563 for (j = 0; (j < indent); j++)
567 /* no extra spaces after indent; */
568 while (buf[i0] == ' ')
583 str_to_int64_t(const char *str, char **endptr)
586 return strtoll(str, endptr, 10);
588 return _strtoi64(str, endptr, 10);
592 char *gmx_step_str(gmx_int64_t i, char *buf)
594 sprintf(buf, "%"GMX_PRId64, i);
598 void parse_digits_from_plain_string(const char *digitstring, int *ndigits, int **digitlist)
602 if (NULL == digitstring)
609 *ndigits = strlen(digitstring);
611 snew(*digitlist, *ndigits);
613 for (i = 0; i < *ndigits; i++)
615 if (digitstring[i] < '0' || digitstring[i] > '9')
617 gmx_fatal(FARGS, "Invalid character in digit-only string: '%c'\n",
620 (*digitlist)[i] = digitstring[i] - '0';
624 static void parse_digits_from_csv_string(const char gmx_unused *digitstring, int gmx_unused *ndigits, int gmx_unused *digitlist)
626 /* TODO Implement csv format to support (e.g.) more than 10
627 different GPUs in a node. */
628 gmx_incons("Not implemented yet");