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lammps/src/utils.h
Axel Kohlmeyer 5f2b947b99 fix typo
2021-07-29 11:48:24 -04:00

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_UTILS_H
#define LMP_UTILS_H
/*! \file utils.h */
#include "fmt/format.h"
#include "lmptype.h"
#include <mpi.h>
#include <cstdio>
#include <string>
#include <vector>
namespace LAMMPS_NS {
// forward declarations
class Error;
class LAMMPS;
namespace utils {
/*! Match text against a simplified regex pattern
*
* \param text the text to be matched against the pattern
* \param pattern the search pattern, which may contain regexp markers
* \return true if the pattern matches, false if not */
bool strmatch(const std::string &text, const std::string &pattern);
/*! Find sub-string that matches a simplified regex pattern
*
* \param text the text to be matched against the pattern
* \param pattern the search pattern, which may contain regexp markers
* \return the string that matches the pattern or an empty one */
std::string strfind(const std::string &text, const std::string &pattern);
/* Internal function handling the argument list for logmesg(). */
void fmtargs_logmesg(LAMMPS *lmp, fmt::string_view format, fmt::format_args args);
/*! Send formatted message to screen and logfile, if available
*
* This function simplifies the repetitive task of outputting some
* message to both the screen and/or the log file. The template
* wrapper with fmtlib format and argument processing allows
* this function to work similar to ``fmt::print()``.
*
* \param lmp pointer to LAMMPS class instance
* \param format format string of message to be printed
* \param args arguments to format string */
template <typename S, typename... Args> void logmesg(LAMMPS *lmp, const S &format, Args &&...args)
{
fmtargs_logmesg(lmp, format, fmt::make_args_checked<Args...>(format, args...));
}
/*! \overload
*
* \param lmp pointer to LAMMPS class instance
* \param mesg string with message to be printed */
void logmesg(LAMMPS *lmp, const std::string &mesg);
/*! Return a string representing the current system error status
*
* This is a wrapper around calling strerror(errno).
*
* \return error string */
std::string getsyserror();
/*! Wrapper around fgets() which reads whole lines but truncates the
* data to the buffer size and ensures a newline char at the end.
*
* This function is useful for reading line based text files with
* possible comments that should be parsed later. This applies to
* data files, potential files, atomfile variable files and so on.
* It is used instead of fgets() by utils::read_lines_from_file().
*
* \param s buffer for storing the result of fgets()
* \param size size of buffer s (max number of bytes returned)
* \param fp file pointer used by fgets() */
char *fgets_trunc(char *s, int size, FILE *fp);
/*! Safe wrapper around fgets() which aborts on errors
* or EOF and prints a suitable error message to help debugging.
*
* Use nullptr as the error parameter to avoid the abort on EOF or error.
*
* \param srcname name of the calling source file (from FLERR macro)
* \param srcline line in the calling source file (from FLERR macro)
* \param s buffer for storing the result of fgets()
* \param size size of buffer s (max number of bytes read by fgets())
* \param fp file pointer used by fgets()
* \param filename file name associated with fp (may be a null pointer; then LAMMPS will try to detect)
* \param error pointer to Error class instance (for abort) or nullptr */
void sfgets(const char *srcname, int srcline, char *s, int size, FILE *fp, const char *filename,
Error *error);
/*! Safe wrapper around fread() which aborts on errors
* or EOF and prints a suitable error message to help debugging.
*
* Use nullptr as the error parameter to avoid the abort on EOF or error.
*
* \param srcname name of the calling source file (from FLERR macro)
* \param srcline line in the calling source file (from FLERR macro)
* \param s buffer for storing the result of fread()
* \param size size of data elements read by fread()
* \param num number of data elements read by fread()
* \param fp file pointer used by fread()
* \param filename file name associated with fp (may be a null pointer; then LAMMPS will try to detect)
* \param error pointer to Error class instance (for abort) or nullptr */
void sfread(const char *srcname, int srcline, void *s, size_t size, size_t num, FILE *fp,
const char *filename, Error *error);
/*! Read N lines of text from file into buffer and broadcast them
*
* This function uses repeated calls to fread() to fill a buffer with
* newline terminated text. If a line does not end in a newline (e.g.
* at the end of a file), it is added. The caller has to allocate an
* nlines by nmax sized buffer for storing the text data.
* Reading is done by MPI rank 0 of the given communicator only, and
* thus only MPI rank 0 needs to provide a valid file pointer.
*
* \param fp file pointer used by fread
* \param nlines number of lines to be read
* \param nmax maximum length of a single line
* \param buffer buffer for storing the data.
* \param me MPI rank of calling process in MPI communicator
* \param comm MPI communicator for broadcast
* \return 1 if the read was short, 0 if read was successful */
int read_lines_from_file(FILE *fp, int nlines, int nmax, char *buffer, int me, MPI_Comm comm);
/*! Report if a requested style is in a package or may have a typo
*
* \param style type of style that is to be checked for
* \param name name of style that was not found
* \param lmp pointer to top-level LAMMPS class instance
* \return string usable for error messages */
std::string check_packages_for_style(const std::string &style, const std::string &name,
LAMMPS *lmp);
/*! Convert a string to a floating point number while checking
* if it is a valid floating point or integer number
*
* \param file name of source file for error message
* \param line line number in source file for error message
* \param str string to be converted to number
* \param do_abort determines whether to call Error::one() or Error::all()
* \param lmp pointer to top-level LAMMPS class instance
* \return double precision floating point number */
double numeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp);
/*! Convert a string to an integer number while checking
* if it is a valid integer number (regular int)
*
* \param file name of source file for error message
* \param line line number in source file for error message
* \param str string to be converted to number
* \param do_abort determines whether to call Error::one() or Error::all()
* \param lmp pointer to top-level LAMMPS class instance
* \return integer number (regular int) */
int inumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp);
/*! Convert a string to an integer number while checking
* if it is a valid integer number (bigint)
*
* \param file name of source file for error message
* \param line line number in source file for error message
* \param str string to be converted to number
* \param do_abort determines whether to call Error::one() or Error::all()
* \param lmp pointer to top-level LAMMPS class instance
* \return integer number (bigint) */
bigint bnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp);
/*! Convert a string to an integer number while checking
* if it is a valid integer number (tagint)
*
* \param file name of source file for error message
* \param line line number in source file for error message
* \param str string to be converted to number
* \param do_abort determines whether to call Error::one() or Error::all()
* \param lmp pointer to top-level LAMMPS class instance
* \return integer number (tagint) */
tagint tnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp);
/*! Compute index bounds derived from a string with a possible wildcard
*
* This functions processes the string in *str* and set the values of *nlo*
* and *nhi* according to the following five cases:
*
* - a single number, i: nlo = i; nhi = i;
* - a single asterisk, \*: nlo = nmin; nhi = nmax;
* - a single number followed by an asterisk, i\*: nlo = i; nhi = nmax;
* - a single asterisk followed by a number, \*i: nlo = nmin; nhi = i;
* - two numbers with an asterisk in between. i\*j: nlo = i; nhi = j;
*
* \param file name of source file for error message
* \param line line number in source file for error message
* \param str string to be processed
* \param nmin smallest possible lower bound
* \param nmax largest allowed upper bound
* \param nlo lower bound
* \param nhi upper bound
* \param error pointer to Error class for out-of-bounds messages */
template <typename TYPE>
void bounds(const char *file, int line, const std::string &str, bigint nmin, bigint nmax,
TYPE &nlo, TYPE &nhi, Error *error);
/*! Expand list of arguments when containing fix/compute wildcards
*
* This function searches the list of arguments in *arg* for strings
* of the kind c_ID[*] or f_ID[*] referring to computes or fixes.
* Any such strings are replaced by one or more strings with the
* '*' character replaced by the corresponding possible numbers as
* determined from the fix or compute instance. Other strings are
* just copied. If the *mode* parameter is set to 0, expand global
* vectors, but not global arrays; if it is set to 1, expand global
* arrays (by column) but not global vectors.
*
* If any expansion happens, the earg list and all its
* strings are new allocations and must be freed explicitly by the
* caller. Otherwise arg and earg will point to the same address
* and no explicit de-allocation is needed by the caller.
*
* \param file name of source file for error message
* \param line line number in source file for error message
* \param narg number of arguments in current list
* \param arg argument list, possibly containing wildcards
* \param mode select between global vectors(=0) and arrays (=1)
* \param earg new argument list with wildcards expanded
* \param lmp pointer to top-level LAMMPS class instance
* \return number of arguments in expanded list */
int expand_args(const char *file, int line, int narg, char **arg, int mode, char **&earg,
LAMMPS *lmp);
/*! Make C-style copy of string in new storage
*
* This allocates a storage buffer and copies the C-style or
* C++ style string into it. The buffer is allocated with "new"
* and thus needs to be deallocated with "delete[]".
*
* \param text string that should be copied
* \return new buffer with copy of string */
char *strdup(const std::string &text);
/*! Trim leading and trailing whitespace. Like TRIM() in Fortran.
*
* \param line string that should be trimmed
* \return new string without whitespace (string) */
std::string trim(const std::string &line);
/*! Return string with anything from '#' onward removed
*
* \param line string that should be trimmed
* \return new string without comment (string) */
std::string trim_comment(const std::string &line);
/*! Check if a string will likely have UTF-8 encoded characters
*
* UTF-8 uses the 7-bit standard ASCII table for the first 127 characters and
* all other characters are encoded as multiple bytes. For the multi-byte
* characters the first byte has either the highest two, three, or four bits
* set followed by a zero bit and followed by one, two, or three more bytes,
* respectively, where the highest bit is set and the second highest bit set
* to 0. The remaining bits combined are the character code, which is thus
* limited to 21-bits.
*
* For the sake of efficiency this test only checks if a character in the string
* has the highest bit set and thus is very likely an UTF-8 character. It will
* not be able to tell this this is a valid UTF-8 character or whether it is a
* 2-byte, 3-byte, or 4-byte character.
*
\verbatim embed:rst
*See also*
:cpp:func:`utils::utf8_subst`
\endverbatim
* \param line string that should be checked
* \return true if string contains UTF-8 encoded characters (bool) */
inline bool has_utf8(const std::string &line)
{
for (auto c : line)
if (c & 0x80U) return true;
return false;
}
/*! Replace known UTF-8 characters with ASCII equivalents
*
\verbatim embed:rst
*See also*
:cpp:func:`utils::has_utf8`
\endverbatim
* \param line string that should be converted
* \return new string with ascii replacements (string) */
std::string utf8_subst(const std::string &line);
/*! Count words in string with custom choice of separating characters
*
* \param text string that should be searched
* \param separators string containing characters that will be treated as whitespace
* \return number of words found */
size_t count_words(const std::string &text, const std::string &separators);
/*! Count words in string, ignore any whitespace matching " \t\r\n\f"
*
* \param text string that should be searched
* \return number of words found */
size_t count_words(const std::string &text);
/*! Count words in C-string, ignore any whitespace matching " \t\r\n\f"
*
* \param text string that should be searched
* \return number of words found */
size_t count_words(const char *text);
/*! Count words in a single line, trim anything from '#' onward
*
* \param text string that should be trimmed and searched
* \param separators string containing characters that will be treated as whitespace
* \return number of words found */
size_t trim_and_count_words(const std::string &text, const std::string &separators = " \t\r\n\f");
/*! Take text and split into non-whitespace words.
*
* This can handle strings with single and double quotes, escaped quotes,
* and escaped codes within quotes, but due to using an STL container and
* STL strings is rather slow because of making copies. Designed for
* parsing command lines and similar text and not for time critical
* processing. Use a tokenizer class if performance matters.
*
\verbatim embed:rst
*See also*
:cpp:class:`Tokenizer`, :cpp:class:`ValueTokenizer`
\endverbatim
* \param text string that should be split
* \return STL vector with the words */
std::vector<std::string> split_words(const std::string &text);
/*! Take multi-line text and split into lines
*
* \param text string that should be split
* \return STL vector with the lines */
std::vector<std::string> split_lines(const std::string &text);
/*! Check if string can be converted to valid integer
*
* \param str string that should be checked
* \return true, if string contains valid a integer, false otherwise */
bool is_integer(const std::string &str);
/*! Check if string can be converted to valid floating-point number
*
* \param str string that should be checked
* \return true, if string contains valid number, false otherwise */
bool is_double(const std::string &str);
/*! Check if string is a valid ID
* ID strings may contain only letters, numbers, and underscores.
*
* \param str string that should be checked
* \return true, if string contains valid id, false otherwise */
bool is_id(const std::string &str);
/*! Try to detect pathname from FILE pointer.
*
* Currently only supported on Linux, otherwise will report "(unknown)".
*
* \param buf storage buffer for pathname. output will be truncated if not large enough
* \param len size of storage buffer. output will be truncated to this length - 1
* \param fp FILE pointer struct from STDIO library for which we want to detect the name
* \return pointer to the storage buffer, i.e. buf */
const char *guesspath(char *buf, int len, FILE *fp);
/*! Strip off leading part of path, return just the filename
*
* \param path file path
* \return file name */
std::string path_basename(const std::string &path);
/*! Return the directory part of a path. Return "." if empty
*
* \param path file path
* \return directory name */
std::string path_dirname(const std::string &path);
/*! Join two pathname segments
*
* This uses the forward slash '/' character unless LAMMPS is compiled
* for Windows where it used the equivalent backward slash '\\'.
*
* \param a first path
* \param b second path
* \return combined path */
std::string path_join(const std::string &a, const std::string &b);
/*! Check if file exists and is readable
*
* \param path file path
* \return true if file exists and is readable */
bool file_is_readable(const std::string &path);
/*! Determine full path of potential file. If file is not found in current directory,
* search directories listed in LAMMPS_POTENTIALS environment variable
*
* \param path file path
* \return full path to potential file */
std::string get_potential_file_path(const std::string &path);
/*! Read potential file and return DATE field if it is present
*
* \param path file path
* \param potential_name name of potential that is being read
* \return DATE field if present */
std::string get_potential_date(const std::string &path, const std::string &potential_name);
/*! Read potential file and return UNITS field if it is present
*
* \param path file path
* \param potential_name name of potential that is being read
* \return UNITS field if present */
std::string get_potential_units(const std::string &path, const std::string &potential_name);
enum { NOCONVERT = 0, METAL2REAL = 1, REAL2METAL = 1 << 1 };
enum { UNKNOWN = 0, ENERGY };
/*! Return bitmask of available conversion factors for a given property
*
* \param property property to be converted
* \return bitmask indicating available conversions */
int get_supported_conversions(const int property);
/*! Return unit conversion factor for given property and selected from/to units
*
* \param property property to be converted
* \param conversion constant indicating the conversion
* \return conversion factor */
double get_conversion_factor(const int property, const int conversion);
/*! Open a potential file as specified by *name*
*
* If opening the file directly fails, the function will search for
* it in the list of folder pointed to by the environment variable
* ``LAMMPS_POTENTIALS`` (if it is set).
*
* If the potential file has a ``UNITS`` tag in the first line, the
* tag's value is compared to the current unit style setting.
* The behavior of the function then depends on the value of the
* *auto_convert* parameter. If it is a null pointer, then the unit
* values must match or else the open will fail with an error. Otherwise
* the bitmask that *auto_convert* points to is used check for
* compatibility with possible automatic conversions by the calling
* function. If compatible, the bitmask is set to the required
* conversion or ``utils::NOCONVERT``.
*
* \param name file- or pathname of the potential file
* \param lmp pointer to top-level LAMMPS class instance
* \param auto_convert pointer to unit conversion bitmask or ``nullptr``
* \return FILE pointer of the opened potential file or ``nullptr`` */
FILE *open_potential(const std::string &name, LAMMPS *lmp, int *auto_convert);
/*! Convert a time string to seconds
*
* The strings "off" and "unlimited" result in -1
*
* \param timespec a string in the following format: ([[HH:]MM:]SS)
* \return total in seconds */
double timespec2seconds(const std::string &timespec);
/*! Convert a LAMMPS version date to a number
*
* This will generate a number YYYYMMDD from a date string
* (with or without blanks) that is suitable for numerical
* comparisons, i.e. later dates will generate a larger number.
*
* The day may or may not have a leading zero, the month
* is identified by the first 3 letters (so there may be more)
* and the year may be 2 or 4 digits (the missing 2 digits will
* be assumed as 20. That is 04 corresponds to 2004).
*
* No check is made whether the date is valid.
*
* \param date string in the format (Day Month Year)
* \return date code */
int date2num(const std::string &date);
/*! Custom merge sort implementation
*
* This function provides a custom upward hybrid merge sort
* implementation with support to pass an opaque pointer to
* the comparison function, e.g. for access to class members.
* This avoids having to use global variables. For improved
* performance, it uses an in-place insertion sort on initial
* chunks of up to 64 elements and switches to merge sort from
* then on.
*
* \param index Array with indices to be sorted
* \param num Length of the index array
* \param ptr Pointer to opaque object passed to comparison function
* \param comp Pointer to comparison function */
void merge_sort(int *index, int num, void *ptr, int (*comp)(int, int, void *));
} // namespace utils
} // namespace LAMMPS_NS
#endif
/* ERROR/WARNING messages:
*/
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