src/gromacs/commandline/filenm.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "filenm.h"
  40
  41 #include <cctype>
  42 #include <cstdio>
  43 #include <cstring>
  44
  45 #include "gromacs/compat/string_view.h"
  46 #include "gromacs/fileio/filetypes.h"
  47 #include "gromacs/utility/basedefinitions.h"
  48 #include "gromacs/utility/cstringutil.h"
  49 #include "gromacs/utility/gmxassert.h"
  50 #include "gromacs/utility/path.h"
  51 #include "gromacs/utility/smalloc.h"
  52 #include "gromacs/utility/stringutil.h"
  53
  54 /* Use bitflag ... */
  55 static bool IS_SET(const t_filenm &fileOption)
  56 {
  57     return (fileOption.flag & ffSET) != 0;
  58 }
  59
  60 static bool IS_OPT(const t_filenm &fileOption)
  61 {
  62     return (fileOption.flag & ffOPT) != 0;
  63 }
  64
  65 static const t_filenm *getFileOption(const char *opt, int nfile, const t_filenm fnm[])
  66 {
  67     GMX_RELEASE_ASSERT(nfile == 0 || fnm, "need a valid list of filenames");
  68
  69     for (int i = 0; i < nfile; i++)
  70     {
  71         if ((fnm[i].opt != nullptr && strcmp(opt, fnm[i].opt) == 0) ||
  72             (fnm[i].opt == nullptr && strcmp(opt, ftp2defopt(fnm[i].ftp)) == 0))
  73         {
  74             return &fnm[i];
  75         }
  76     }
  77
  78     return nullptr;
  79 }
  80
  81 const char *opt2fn(const char *opt, int nfile, const t_filenm fnm[])
  82 {
  83     const t_filenm *fileOption = getFileOption(opt, nfile, fnm);
  84
  85     if (fileOption)
  86     {
  87         return fileOption->filenames[0].c_str();
  88     }
  89
  90     GMX_RELEASE_ASSERT(false, "opt2fn should be called with a valid option");
  91
  92     return nullptr;
  93 }
  94
  95 gmx::ArrayRef<const std::string>
  96 opt2fns(const char *opt, int nfile, const t_filenm fnm[])
  97 {
  98     const t_filenm *fileOption = getFileOption(opt, nfile, fnm);
  99
 100     if (fileOption)
 101     {
 102         return fileOption->filenames;
 103     }
 104
 105     GMX_RELEASE_ASSERT(false, "opt2fns should be called with a valid option");
 106
 107     return {};
 108 }
 109
 110 gmx::ArrayRef<const std::string>
 111 opt2fnsIfOptionSet(const char *opt, int nfile, const t_filenm fnm[])
 112 {
 113     if (opt2bSet(opt, nfile, fnm))
 114     {
 115         return opt2fns(opt, nfile, fnm);
 116     }
 117     else
 118     {
 119         return {};
 120     }
 121 }
 122
 123 const char *ftp2fn(int ftp, int nfile, const t_filenm fnm[])
 124 {
 125     int i;
 126
 127     for (i = 0; (i < nfile); i++)
 128     {
 129         if (ftp == fnm[i].ftp)
 130         {
 131             return fnm[i].filenames[0].c_str();
 132         }
 133     }
 134
 135     GMX_RELEASE_ASSERT(false, "ftp2fn should be called with a valid option");
 136
 137     return nullptr;
 138 }
 139
 140 gmx::ArrayRef<const std::string>
 141 ftp2fns(int ftp, int nfile, const t_filenm fnm[])
 142 {
 143     for (int i = 0; (i < nfile); i++)
 144     {
 145         if (ftp == fnm[i].ftp)
 146         {
 147             return fnm[i].filenames;
 148         }
 149     }
 150
 151     GMX_RELEASE_ASSERT(false, "ftp2fns should be called with a valid option");
 152
 153     return {};
 154 }
 155
 156 gmx_bool ftp2bSet(int ftp, int nfile, const t_filenm fnm[])
 157 {
 158     int i;
 159
 160     for (i = 0; (i < nfile); i++)
 161     {
 162         if (ftp == fnm[i].ftp)
 163         {
 164             return static_cast<gmx_bool>(IS_SET(fnm[i]));
 165         }
 166     }
 167
 168     GMX_RELEASE_ASSERT(false, "ftp2bSet should be called with a valid option");
 169
 170     return FALSE;
 171 }
 172
 173 gmx_bool opt2bSet(const char *opt, int nfile, const t_filenm fnm[])
 174 {
 175     const t_filenm *fileOption = getFileOption(opt, nfile, fnm);
 176
 177     if (fileOption)
 178     {
 179         return static_cast<gmx_bool>(IS_SET(*fileOption));
 180     }
 181
 182     GMX_RELEASE_ASSERT(false, "opt2bSet should be called with a valid option");
 183
 184     return FALSE;
 185 }
 186
 187 const char *opt2fn_null(const char *opt, int nfile, const t_filenm fnm[])
 188 {
 189     const t_filenm *fileOption = getFileOption(opt, nfile, fnm);
 190
 191     if (fileOption)
 192     {
 193         if (IS_OPT(*fileOption) && !IS_SET(*fileOption))
 194         {
 195             return nullptr;
 196         }
 197         else
 198         {
 199             return fileOption->filenames[0].c_str();
 200         }
 201     }
 202
 203     GMX_RELEASE_ASSERT(false, "opt2fn_null should be called with a valid option");
 204
 205     return nullptr;
 206 }
 207
 208 const char *ftp2fn_null(int ftp, int nfile, const t_filenm fnm[])
 209 {
 210     int i;
 211
 212     for (i = 0; (i < nfile); i++)
 213     {
 214         if (ftp == fnm[i].ftp)
 215         {
 216             if (IS_OPT(fnm[i]) && !IS_SET(fnm[i]))
 217             {
 218                 return nullptr;
 219             }
 220             else
 221             {
 222                 return fnm[i].filenames[0].c_str();
 223             }
 224         }
 225     }
 226
 227     GMX_RELEASE_ASSERT(false, "ftp2fn_null should be called with a valid option");
 228
 229     return nullptr;
 230 }
 231
 232 gmx_bool is_optional(const t_filenm *fnm)
 233 {
 234     return ((fnm->flag & ffOPT) == ffOPT);
 235 }
 236
 237 gmx_bool is_output(const t_filenm *fnm)
 238 {
 239     return ((fnm->flag & ffWRITE) == ffWRITE);
 240 }
 241
 242 gmx_bool is_set(const t_filenm *fnm)
 243 {
 244     return ((fnm->flag & ffSET) == ffSET);
 245 }
 246
 247 namespace
 248 {
 249
 250 /*! \brief Return the first position within \c filename of the ".partNNNN"
 251  * interior sequence produced by mdrun -noappend, or npos if not found. */
 252 size_t findSuffixFromNoAppendPosition(const gmx::compat::string_view filename)
 253 {
 254     size_t partPosition = filename.find(".part");
 255     if ((partPosition != decltype(filename) ::npos) &&
 256         (filename.length() - partPosition >= 10) &&
 257         (std::isdigit(filename[partPosition + 5])) &&
 258         (std::isdigit(filename[partPosition + 6])) &&
 259         (std::isdigit(filename[partPosition + 7])) &&
 260         (std::isdigit(filename[partPosition + 8])) &&
 261         filename[partPosition + 9] == '.')
 262     {
 263         return partPosition;
 264     }
 265     return decltype(filename) ::npos;
 266 }
 267
 268 } // namespace
 269
 270 bool hasSuffixFromNoAppend(const gmx::compat::string_view filename)
 271 {
 272     return (findSuffixFromNoAppendPosition(filename) != decltype(filename) ::npos);
 273 }
 274
 275 int add_suffix_to_output_names(t_filenm *fnm, int nfile, const char *suffix)
 276 {
 277     for (int i = 0; i < nfile; i++)
 278     {
 279         if (is_output(&fnm[i]) && fnm[i].ftp != efCPT)
 280         {
 281             /* We never use multiple _outputs_, but we might as well check
 282                for it, just in case... */
 283             for (std::string &filename : fnm[i].filenames)
 284             {
 285                 // mdrun should not generate files like
 286                 // md.part0002.part0003.log. mdrun should permit users
 287                 // to name files like md.equil.part0002.log. So,
 288                 // before we use Path::concatenateBeforeExtension to
 289                 // add the requested suffix, we need to check for
 290                 // files matching mdrun's pattern for adding part
 291                 // numbers. Then we can remove that if needed.
 292                 for (size_t partPosition; (partPosition = findSuffixFromNoAppendPosition(filename)) != std::string::npos; )
 293                 {
 294                     // Remove the ".partNNNN" that we have found,
 295                     // and then run the loop again to make sure
 296                     // there isn't another one to remove, somehow.
 297                     std::string temporary = filename.substr(0, partPosition);
 298                     temporary += filename.substr(partPosition + 9);
 299                     filename.swap(temporary);
 300                 }
 301                 filename = gmx::Path::concatenateBeforeExtension(filename, suffix);
 302             }
 303         }
 304     }
 305     return 0;
 306 }