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move merge sort to utils namespace

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This commit is contained in:
Axel Kohlmeyer
2020-09-06 17:38:53 -04:00
parent d995ed0d87
commit 485a169ef2
8 changed files with 218 additions and 199 deletions
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150
src/utils.h
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@ -33,23 +33,23 @@ namespace LAMMPS_NS {
*
* \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
*/
* \return true if the pattern matches, false if not */
bool strmatch(const std::string &text, const std::string &pattern);
/** Send message to screen and logfile, if available
*
* \param lmp pointer to LAMMPS class instance
* \param mesg message to be printed
*/
* \param mesg 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
*/
* \return error string */
std::string getsyserror();
/** safe wrapper around fgets() which aborts on errors
@ -61,8 +61,8 @@ namespace LAMMPS_NS {
* \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 NULL; then LAMMPS will try to detect)
* \param error pointer to Error class instance (for abort)
*/
* \param error pointer to Error class instance (for abort) */
void sfgets(const char *srcname, int srcline, char *s, int size,
FILE *fp, const char *filename, Error *error);
@ -76,8 +76,8 @@ namespace LAMMPS_NS {
* \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 NULL; then LAMMPS will try to detect)
* \param error pointer to Error class instance (for abort)
*/
* \param error pointer to Error class instance (for abort) */
void sfread(const char *srcname, int srcline, void *s, size_t size,
size_t num, FILE *fp, const char *filename, Error *error);
@ -86,8 +86,8 @@ namespace LAMMPS_NS {
* \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
*/
* \return string usable for error messages */
std::string check_packages_for_style(const std::string &style,
const std::string &name, LAMMPS *lmp);
@ -112,8 +112,8 @@ namespace LAMMPS_NS {
* \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)
*/
* \return integer number (regular int) */
int inumeric(const char *file, int line, const char *str,
bool do_abort, LAMMPS *lmp);
@ -125,8 +125,8 @@ namespace LAMMPS_NS {
* \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)
*/
* \return integer number (bigint) */
bigint bnumeric(const char *file, int line, const char *str,
bool do_abort, LAMMPS *lmp);
@ -162,6 +162,7 @@ namespace LAMMPS_NS {
* \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);
@ -197,45 +198,45 @@ namespace LAMMPS_NS {
/** Trim leading and trailing whitespace. Like TRIM() in Fortran.
*
* \param line string that should be trimmed
* \return new string without whitespace (string)
*/
* \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)
*/
* \return new string without comment (string) */
std::string trim_comment(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
*/
* \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
*/
* \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
*/
* \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
*/
* \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.
@ -247,22 +248,22 @@ namespace LAMMPS_NS {
* Use a tokenizer class for that.
*
* \param text string that should be split
* \return STL vector with the words
*/
* \return STL vector with the words */
std::vector<std::string> split_words(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 integer, false otherwise
*/
* \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 floating-point number, false otherwise
*/
* \return true, if string contains valid number, false otherwise */
bool is_double(const std::string &str);
/** Try to detect pathname from FILE pointer.
@ -272,55 +273,60 @@ namespace LAMMPS_NS {
* \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
*/
* \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
*/
* \return file name */
std::string path_basename(const std::string &path);
/**
* \brief Join two paths
* \param a first path
* \param b second path
* \return combined 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);
/**
* \brief 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
*/
* \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
*/
* \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);
* \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);
* \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 };
@ -328,16 +334,15 @@ namespace LAMMPS_NS {
/** Return bitmask of available conversion factors for a given property
*
* \param property property to be converted
* \return bitmask indicating available conversions
*/
* \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
*/
* \return conversion factor */
double get_conversion_factor(const int property, const int conversion);
/** Open a potential file as specified by *name*
@ -368,8 +373,8 @@ namespace LAMMPS_NS {
* The strings "off" and "unlimited" result in -1
*
* \param timespec a string in the following format: ([[HH:]MM:]SS)
* \return total in seconds
*/
* \return total in seconds */
double timespec2seconds(const std::string &timespec);
/** Convert a LAMMPS version date to a number
@ -386,9 +391,26 @@ namespace LAMMPS_NS {
* No check is made whether the date is valid.
*
* \param date string in the format (Day Month Year)
* \return date code
*/
* \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 *));
}
}