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apply clang-format to all headers with some exceptions

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This commit is contained in:
Axel Kohlmeyer
2021-05-14 19:16:07 -04:00
parent 60e41a90c2
commit 7fcd449864
1651 changed files with 15108 additions and 15948 deletions
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235
src/utils.h
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@ -16,8 +16,8 @@
/*! \file utils.h */
#include "lmptype.h"
#include "fmt/format.h"
#include "lmptype.h"
#include <mpi.h>
@ -27,34 +27,33 @@
namespace LAMMPS_NS {
// forward declarations
class Error;
class LAMMPS;
// forward declarations
class Error;
class LAMMPS;
namespace utils {
namespace utils {
/** Match text against a simplified regex pattern
/** 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);
bool strmatch(const std::string &text, const std::string &pattern);
/** Find sub-string that matches a simplified regex 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 patters or an empty one */
std::string strfind(const std::string &text, const std::string &pattern);
std::string strfind(const std::string &text, const std::string &pattern);
/* Internal function handling the argument list for logmesg(). */
/* Internal function handling the argument list for logmesg(). */
void fmtargs_logmesg(LAMMPS *lmp, fmt::string_view format,
fmt::format_args args);
void fmtargs_logmesg(LAMMPS *lmp, fmt::string_view format, fmt::format_args args);
/** Send formatted message to screen and logfile, if available
/** 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
@ -65,28 +64,27 @@ namespace LAMMPS_NS {
* \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...));
}
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
/** \overload
*
* \param lmp pointer to LAMMPS class instance
* \param mesg string with message to be printed */
void logmesg(LAMMPS *lmp, const std::string &mesg);
void logmesg(LAMMPS *lmp, const std::string &mesg);
/** Return a string representing the current system error status
/** Return a string representing the current system error status
*
* This is a wrapper around calling strerror(errno).
*
* \return error string */
std::string getsyserror();
std::string getsyserror();
/** Wrapper around fgets() which reads whole lines but truncates the
/** 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
@ -98,9 +96,9 @@ namespace LAMMPS_NS {
* \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);
char *fgets_trunc(char *s, int size, FILE *fp);
/** Safe wrapper around fgets() which aborts on errors
/** 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.
@ -113,10 +111,10 @@ namespace LAMMPS_NS {
* \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);
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
/** 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.
@ -130,10 +128,10 @@ namespace LAMMPS_NS {
* \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);
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
/** 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.
@ -150,20 +148,19 @@ namespace LAMMPS_NS {
* \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);
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
/** 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);
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
/** 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
@ -173,10 +170,9 @@ namespace LAMMPS_NS {
* \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);
double numeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp);
/** Convert a string to an integer number while checking
/** 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
@ -186,10 +182,9 @@ namespace LAMMPS_NS {
* \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);
int inumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp);
/** Convert a string to an integer number while checking
/** 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
@ -199,10 +194,9 @@ namespace LAMMPS_NS {
* \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);
bigint bnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp);
/** Convert a string to an integer number while checking
/** 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
@ -212,10 +206,9 @@ namespace LAMMPS_NS {
* \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);
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
/** 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:
@ -235,11 +228,11 @@ namespace LAMMPS_NS {
* \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);
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
/** 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.
@ -264,10 +257,10 @@ namespace LAMMPS_NS {
* \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);
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
/** 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"
@ -276,23 +269,23 @@ namespace LAMMPS_NS {
* \param text string that should be copied
* \return new buffer with copy of string */
char *strdup(const std::string &text);
char *strdup(const std::string &text);
/** Trim leading and trailing whitespace. Like TRIM() in Fortran.
/** 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);
std::string trim(const std::string &line);
/** Return string with anything from '#' onward removed
/** 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);
std::string trim_comment(const std::string &line);
/** Check if a string will likely have UTF-8 encoded characters
/** 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
@ -316,13 +309,14 @@ namespace LAMMPS_NS {
* \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;
}
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
/** Replace known UTF-8 characters with ASCII equivalents
*
\verbatim embed:rst
@ -333,39 +327,39 @@ namespace LAMMPS_NS {
* \param line string that should be converted
* \return new string with ascii replacements (string) */
std::string utf8_subst(const std::string &line);
std::string utf8_subst(const std::string &line);
/** Count words in string with custom choice of separating characters
/** 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);
size_t count_words(const std::string &text, const std::string &separators);
/** Count words in string, ignore any whitespace matching " \t\r\n\f"
/** 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);
size_t count_words(const std::string &text);
/** Count words in C-string, ignore any whitespace matching " \t\r\n\f"
/** 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);
size_t count_words(const char *text);
/** Count words in a single line, trim anything from '#' onward
/** 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");
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.
/** 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
@ -382,37 +376,37 @@ namespace LAMMPS_NS {
* \param text string that should be split
* \return STL vector with the words */
std::vector<std::string> split_words(const std::string &text);
std::vector<std::string> split_words(const std::string &text);
/** Take multi-line text and split into lines
/** 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);
std::vector<std::string> split_lines(const std::string &text);
/** Check if string can be converted to valid integer
/** 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);
bool is_integer(const std::string &str);
/** Check if string can be converted to valid floating-point number
/** 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);
bool is_double(const std::string &str);
/** Check if string is a valid ID
/** 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);
bool is_id(const std::string &str);
/** Try to detect pathname from FILE pointer.
/** Try to detect pathname from FILE pointer.
*
* Currently only supported on Linux, otherwise will report "(unknown)".
*
@ -421,23 +415,23 @@ namespace LAMMPS_NS {
* \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);
const char *guesspath(char *buf, int len, FILE *fp);
/** Strip off leading part of path, return just the filename
/** 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);
std::string path_basename(const std::string &path);
/** Return the directory part of a path. Return "." if empty
/** 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);
std::string path_dirname(const std::string &path);
/** Join two pathname segments
/** Join two pathname segments
*
* This uses the forward slash '/' character unless LAMMPS is compiled
* for Windows where it used the equivalent backward slash '\\'.
@ -446,59 +440,57 @@ namespace LAMMPS_NS {
* \param b second path
* \return combined path */
std::string path_join(const std::string &a, const std::string &b);
std::string path_join(const std::string &a, const std::string &b);
/** Check if file exists and is readable
/** 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);
bool file_is_readable(const std::string &path);
/** Determine full path of potential file. If file is not found in current directory,
/** 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);
std::string get_potential_file_path(const std::string &path);
/** Read potential file and return DATE field if it is present
/** 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);
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
/** 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);
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 };
enum { NOCONVERT = 0, METAL2REAL = 1, REAL2METAL = 1 << 1 };
enum { UNKNOWN = 0, ENERGY };
/** Return bitmask of available conversion factors for a given property
/** 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);
int get_supported_conversions(const int property);
/** Return unit conversion factor for given property and selected from/to units
/** 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);
double get_conversion_factor(const int property, const int conversion);
/** Open a potential file as specified by *name*
/** 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
@ -519,18 +511,18 @@ namespace LAMMPS_NS {
* \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);
FILE *open_potential(const std::string &name, LAMMPS *lmp, int *auto_convert);
/** Convert a time string to seconds
/** 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);
double timespec2seconds(const std::string &timespec);
/** Convert a LAMMPS version date to a number
/** 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
@ -545,9 +537,9 @@ namespace LAMMPS_NS {
*
* \param date string in the format (Day Month Year)
* \return date code */
int date2num(const std::string &date);
int date2num(const std::string &date);
/** Custom merge sort implementation
/** Custom merge sort implementation
*
* This function provides a custom upward hybrid merge sort
* implementation with support to pass an opaque pointer to
@ -562,10 +554,9 @@ namespace LAMMPS_NS {
* \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 *));
}
}
void merge_sort(int *index, int num, void *ptr, int (*comp)(int, int, void *));
} // namespace utils
} // namespace LAMMPS_NS
#endif