src/gromacs/commandline/filenm.cpp

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  38 #include "gmxpre.h"
  39
  40 #include "filenm.h"
  41
  42 #include <cctype>
  43 #include <cstdio>
  44 #include <cstring>
  45
  46 #include <string_view>
  47
  48 #include "gromacs/fileio/filetypes.h"
  49 #include "gromacs/utility/arrayref.h"
  50 #include "gromacs/utility/basedefinitions.h"
  51 #include "gromacs/utility/cstringutil.h"
  52 #include "gromacs/utility/gmxassert.h"
  53 #include "gromacs/utility/path.h"
  54 #include "gromacs/utility/smalloc.h"
  55 #include "gromacs/utility/stringutil.h"
  56
  57 /* Use bitflag ... */
  58 static bool IS_SET(const t_filenm& fileOption)
  59 {
  60     return (fileOption.flag & ffSET) != 0;
  61 }
  62
  63 static bool IS_OPT(const t_filenm& fileOption)
  64 {
  65     return (fileOption.flag & ffOPT) != 0;
  66 }
  67
  68 static const t_filenm* getFileOption(const char* opt, int nfile, const t_filenm fnm[])
  69 {
  70     GMX_RELEASE_ASSERT(nfile == 0 || fnm, "need a valid list of filenames");
  71
  72     for (int i = 0; i < nfile; i++)
  73     {
  74         if ((fnm[i].opt != nullptr && strcmp(opt, fnm[i].opt) == 0)
  75             || (fnm[i].opt == nullptr && strcmp(opt, ftp2defopt(fnm[i].ftp)) == 0))
  76         {
  77             return &fnm[i];
  78         }
  79     }
  80
  81     return nullptr;
  82 }
  83
  84 const char* opt2fn(const char* opt, int nfile, const t_filenm fnm[])
  85 {
  86     const t_filenm* fileOption = getFileOption(opt, nfile, fnm);
  87
  88     if (fileOption)
  89     {
  90         return fileOption->filenames[0].c_str();
  91     }
  92
  93     GMX_RELEASE_ASSERT(false, "opt2fn should be called with a valid option");
  94
  95     return nullptr;
  96 }
  97
  98 gmx::ArrayRef<const std::string> opt2fns(const char* opt, int nfile, const t_filenm fnm[])
  99 {
 100     const t_filenm* fileOption = getFileOption(opt, nfile, fnm);
 101
 102     if (fileOption)
 103     {
 104         return fileOption->filenames;
 105     }
 106
 107     GMX_RELEASE_ASSERT(false, "opt2fns should be called with a valid option");
 108
 109     return {};
 110 }
 111
 112 gmx::ArrayRef<const std::string> opt2fnsIfOptionSet(const char* opt, int nfile, const t_filenm fnm[])
 113 {
 114     if (opt2bSet(opt, nfile, fnm))
 115     {
 116         return opt2fns(opt, nfile, fnm);
 117     }
 118     else
 119     {
 120         return {};
 121     }
 122 }
 123
 124 const char* ftp2fn(int ftp, int nfile, const t_filenm fnm[])
 125 {
 126     int i;
 127
 128     for (i = 0; (i < nfile); i++)
 129     {
 130         if (ftp == fnm[i].ftp)
 131         {
 132             return fnm[i].filenames[0].c_str();
 133         }
 134     }
 135
 136     GMX_RELEASE_ASSERT(false, "ftp2fn should be called with a valid option");
 137
 138     return nullptr;
 139 }
 140
 141 gmx::ArrayRef<const std::string> 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 std::string_view filename)
 253 {
 254     size_t partPosition = filename.find(".part");
 255     if ((partPosition != decltype(filename)::npos) && (filename.length() - partPosition >= 10)
 256         && (std::isdigit(filename[partPosition + 5])) && (std::isdigit(filename[partPosition + 6]))
 257         && (std::isdigit(filename[partPosition + 7])) && (std::isdigit(filename[partPosition + 8]))
 258         && filename[partPosition + 9] == '.')
 259     {
 260         return partPosition;
 261     }
 262     return decltype(filename)::npos;
 263 }
 264
 265 } // namespace
 266
 267 bool hasSuffixFromNoAppend(const std::string_view filename)
 268 {
 269     return (findSuffixFromNoAppendPosition(filename) != decltype(filename)::npos);
 270 }
 271
 272 int add_suffix_to_output_names(t_filenm* fnm, int nfile, const char* suffix)
 273 {
 274     for (int i = 0; i < nfile; i++)
 275     {
 276         if (is_output(&fnm[i]) && fnm[i].ftp != efCPT)
 277         {
 278             /* We never use multiple _outputs_, but we might as well check
 279                for it, just in case... */
 280             for (std::string& filename : fnm[i].filenames)
 281             {
 282                 // mdrun should not generate files like
 283                 // md.part0002.part0003.log. mdrun should permit users
 284                 // to name files like md.equil.part0002.log. So,
 285                 // before we use Path::concatenateBeforeExtension to
 286                 // add the requested suffix, we need to check for
 287                 // files matching mdrun's pattern for adding part
 288                 // numbers. Then we can remove that if needed.
 289                 for (size_t partPosition;
 290                      (partPosition = findSuffixFromNoAppendPosition(filename)) != std::string::npos;)
 291                 {
 292                     // Remove the ".partNNNN" that we have found,
 293                     // and then run the loop again to make sure
 294                     // there isn't another one to remove, somehow.
 295                     std::string temporary = filename.substr(0, partPosition);
 296                     temporary += filename.substr(partPosition + 9);
 297                     filename.swap(temporary);
 298                 }
 299                 filename = gmx::Path::concatenateBeforeExtension(filename, suffix);
 300             }
 301         }
 302     }
 303     return 0;
 304 }