4.8. Utility functions

The utils sub-namespace inside the LAMMPS_NS namespace provides a collection of convenience functions and utilities that perform common tasks that are required repeatedly throughout the LAMMPS code like reading or writing to files with error checking or translation of strings into specific types of numbers with checking for validity. This reduces redundant implementations and encourages consistent behavior.

4.8.1. I/O with status check

These are wrappers around the corresponding C library calls like fgets() or fread(). They will check if there were errors on reading or an unexpected end-of-file state was reached. In that case, the functions will stop the calculation with an error message, indicating the name of the problematic file, if possible.

void LAMMPS_NS::utils::sfgets(const char *srcname, int srcline, char *s, int size, FILE *fp, const char *filename, Error *error)

safe wrapper around fgets() which aborts on errors or EOF and prints a suitable error message to help debugging

Parameters

srcname: name of the calling source file (from FLERR macro)
srcline: line in the calling source file (from FLERR macro)
s: buffer for storing the result of fgets()
size: size of buffer s (max number of bytes read by fgets())
fp: file pointer used by fgets()
filename: file name associated with fp (may be a null pointer; then LAMMPS will try to detect)
error: pointer to Error class instance (for abort)

void LAMMPS_NS::utils::sfread(const char *srcname, int srcline, void *s, size_t size, size_t num, 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

Parameters

srcname: name of the calling source file (from FLERR macro)
srcline: line in the calling source file (from FLERR macro)
s: buffer for storing the result of fread()
size: size of data elements read by fread()
num: number of data elements read by fread()
fp: file pointer used by fread()
filename: file name associated with fp (may be a null pointer; then LAMMPS will try to detect)
error: pointer to Error class instance (for abort)

4.8.2. String to number conversions with validity check

These functions should be used to convert strings to numbers. They are are strongly preferred over C library calls like atoi() or atof() since they check if the entire provided string is a valid (floating-point or integer) number, and will error out instead of silently returning the result of a partial conversion or zero in cases where the string is not a valid number. This behavior allows to more easily detect typos or issues when processing input files.

The do_abort flag should be set to true in case this function is called only on a single MPI rank, as that will then trigger the a call to Error::one() for errors instead of Error::all() and avoids a “hanging” calculation when run in parallel.

Please also see is_integer() and is_double() for testing strings for compliance without conversion.

double LAMMPS_NS::utils::numeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)

Convert a string to a floating point number while checking if it is a valid floating point or integer number

Return

double precision floating point number

Parameters

file: name of source file for error message
line: line number in source file for error message
str: string to be converted to number
do_abort: determines whether to call Error::one() or Error::all()
lmp: pointer to top-level LAMMPS class instance

int LAMMPS_NS::utils::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 (regular int)

Return

integer number (regular int)

Parameters

file: name of source file for error message
line: line number in source file for error message
str: string to be converted to number
do_abort: determines whether to call Error::one() or Error::all()
lmp: pointer to top-level LAMMPS class instance

bigint LAMMPS_NS::utils::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 (bigint)

Return

integer number (bigint)

Parameters

file: name of source file for error message
line: line number in source file for error message
str: string to be converted to number
do_abort: determines whether to call Error::one() or Error::all()
lmp: pointer to top-level LAMMPS class instance

tagint LAMMPS_NS::utils::tnumeric(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)

Return

integer number (tagint)

Parameters

file: name of source file for error message
line: line number in source file for error message
str: string to be converted to number
do_abort: determines whether to call Error::one() or Error::all()
lmp: pointer to top-level LAMMPS class instance

4.8.3. String processing

The following are functions to help with processing strings and parsing files or arguments.

std::string LAMMPS_NS::utils::trim(const std::string &line)

Trim leading and trailing whitespace. Like TRIM() in Fortran.

Return

new string without whitespace (string)

Parameters

line: string that should be trimmed

std::string LAMMPS_NS::utils::trim_comment(const std::string &line)

Return string with anything from ‘#’ onward removed

Return

new string without comment (string)

Parameters

line: string that should be trimmed

size_t LAMMPS_NS::utils::count_words(const char *text)

Count words in C-string, ignore any whitespace matching ” \t\r\n\f”

Return

number of words found

Parameters

text: string that should be searched

size_t LAMMPS_NS::utils::count_words(const std::string &text)

Count words in string, ignore any whitespace matching ” \t\r\n\f”

Return

number of words found

Parameters

text: string that should be searched

size_t LAMMPS_NS::utils::count_words(const std::string &text, const std::string &separators)

Count words in string with custom choice of separating characters

Return

number of words found

Parameters

text: string that should be searched
separators: string containing characters that will be treated as whitespace

size_t LAMMPS_NS::utils::trim_and_count_words(const std::string &text, const std::string &separators = " \t\r\n\f")

Count words in a single line, trim anything from ‘#’ onward

Return

number of words found

Parameters

text: string that should be trimmed and searched
separators: string containing characters that will be treated as whitespace

std::vector<std::string> LAMMPS_NS::utils::split_words(const std::string &text)

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 for that.

See also: Tokenizer, ValueTokenizer

   \param text string that should be split
   \return STL vector with the words

bool LAMMPS_NS::utils::strmatch(const std::string &text, const std::string &pattern)

Match text against a simplified regex pattern

More flexible and specific matching of a string against a pattern. This function is supposed to be a more safe, more specific and simple to use API to find pattern matches. The purpose is to replace uses of either strncmp() or strstr() in the code base to find sub-strings safely. With strncmp() finding prefixes, the number of characters to match must be counted, which can lead to errors, while using “^pattern” will do the same with less problems. Matching for suffixes using strstr() is not as specific as ‘pattern$’, and complex matches, e.g. “^rigid.*\/small.*”, to match all small body optimized rigid fixes require only one test.

Return

true if the pattern matches, false if not

Parameters

text: the text to be matched against the pattern
pattern: the search pattern, which may contain regexp markers

The use of std::string arguments allows for simple concatenation even with char * type variables. Example: utils::strmatch(text, std::string(“^”) + charptr)

bool LAMMPS_NS::utils::is_integer(const std::string &str)

Check if string can be converted to valid integer

Return

true, if string contains valid a integer, false otherwise

Parameters

str: string that should be checked

bool LAMMPS_NS::utils::is_double(const std::string &str)

Check if string can be converted to valid floating-point number

Return

true, if string contains valid number, false otherwise

Parameters

str: string that should be checked

4.8.4. File and path functions

const char *LAMMPS_NS::utils::guesspath(char *buf, int len, FILE *fp)

Try to detect pathname from FILE pointer.

Currently only supported on Linux, otherwise will report “(unknown)”.

On Linux the folder /proc/self/fd holds symbolic links to the actual pathnames associated with each open file descriptor of the current process.

Return

pointer to the storage buffer, i.e. buf

Parameters

buf: storage buffer for pathname. output will be truncated if not large enough
len: size of storage buffer. output will be truncated to this length - 1
fp: FILE pointer struct from STDIO library for which we want to detect the name

This function is used to provide a filename with error messages in functions where the filename is not passed as an argument, but the FILE * pointer.

std::string LAMMPS_NS::utils::path_basename(const std::string &path)

Strip off leading part of path, return just the filename

Return

file name

Parameters

path: file path

std::string LAMMPS_NS::utils::path_join(const std::string &a, const std::string &b)

Join two pathname segments

This uses the forward slash ‘/’ character unless LAMMPS is compiled for Windows where it used the equivalent backward slash ‘'.

Return

combined path

Parameters

a: first path
b: second path

bool LAMMPS_NS::utils::file_is_readable(const std::string &path)

Check if file exists and is readable

Return

true if file exists and is readable

Parameters

path: file path

4.8.5. Potential file functions

std::string LAMMPS_NS::utils::get_potential_file_path(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

Return

full path to potential file

Parameters

path: file path

std::string LAMMPS_NS::utils::get_potential_date(const std::string &path, const std::string &potential_name)

Read potential file and return DATE field if it is present

Return

DATE field if present

Parameters

path: file path
potential_name: name of potential that is being read

std::string LAMMPS_NS::utils::get_potential_units(const std::string &path, const std::string &potential_name)

Read potential file and return UNITS field if it is present

Return

UNITS field if present

Parameters

path: file path
potential_name: name of potential that is being read

int LAMMPS_NS::utils::get_supported_conversions(const int property)

Return bitmask of available conversion factors for a given property

Return

bitmask indicating available conversions

Parameters

property: property to be converted

double LAMMPS_NS::utils::get_conversion_factor(const int property, const int conversion)

Return unit conversion factor for given property and selected from/to units

Return

conversion factor

Parameters

property: property to be converted
conversion: constant indicating the conversion

FILE *LAMMPS_NS::utils::open_potential(const std::string &name, LAMMPS *lmp, int *auto_convert)

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.

Return

FILE pointer of the opened potential file or nullptr

Parameters

name: file- or pathname of the potential file
lmp: pointer to top-level LAMMPS class instance
auto_convert: pointer to unit conversion bitmask or nullptr

4.8.6. Argument processing

template<typename TYPE> void LAMMPS_NS::utils::bounds(const char *file, int line, const std::string &str, bigint nmin, bigint nmax, TYPE &nlo, TYPE &nhi, Error *error)

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;

Parameters

file: name of source file for error message
line: line number in source file for error message
str: string to be processed
nmin: smallest possible lower bound
nmax: largest allowed upper bound
nlo: lower bound
nhi: upper bound
error: pointer to Error class for out-of-bounds messages

int LAMMPS_NS::utils::expand_args(const char *file, int line, int narg, char **arg, int mode, char **&earg, LAMMPS *lmp)

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.

Return

number of arguments in expanded list

Parameters

file: name of source file for error message
line: line number in source file for error message
narg: number of arguments in current list
arg: argument list, possibly containing wildcards
mode: select between global vectors(=0) and arrays (=1)
earg: new argument list with wildcards expanded
lmp: pointer to top-level LAMMPS class instance

4.8.7. Convenience functions

void LAMMPS_NS::utils::logmesg(LAMMPS *lmp, const std::string &mesg)

Send 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. In combination with using fmt::format(), which returns the formatted text in a std::string() instance, this can be used to reduce operations previously requiring several lines of code to a single statement.

Parameters

lmp: pointer to LAMMPS class instance
mesg: message to be printed

std::string LAMMPS_NS::utils::getsyserror()

return a string representing the current system error status

This is a wrapper around calling strerror(errno).

Return: error string

std::string LAMMPS_NS::utils::check_packages_for_style(const std::string &style, const std::string &name, LAMMPS *lmp)

Report if a requested style is in a package or may have a typo

Return

string usable for error messages

Parameters

style: type of style that is to be checked for
name: name of style that was not found
lmp: pointer to top-level LAMMPS class instance

double LAMMPS_NS::utils::timespec2seconds(const std::string &timespec)

Convert a time string to seconds

The strings “off” and “unlimited” result in -1

Return

total in seconds

Parameters

timespec: a string in the following format: ([[HH:]MM:]SS)

int LAMMPS_NS::utils::date2num(const std::string &date)

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.

Return

date code

Parameters

date: string in the format (Day Month Year)

4.8.8. Customized standard functions

void LAMMPS_NS::utils::merge_sort(int *index, int num, void *ptr, int (*comp)(int, int, void*))

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.

Parameters

index: Array with indices to be sorted
num: Length of the index array
ptr: Pointer to opaque object passed to comparison function
comp: Pointer to comparison function

4.9. Tokenizer classes

The purpose of the tokenizer classes is to simplify the recurring task of breaking lines of text down into words and/or numbers. Traditionally, LAMMPS code would be using the strtok() function from the C library for that purpose, but that function has two significant disadvantages: 1) it cannot be used concurrently from different LAMMPS instances since it stores its status in a global variable and 2) it modifies the string that it is processing. These classes were implemented to avoid both of these issues and also to reduce the amount of code that needs to be written.

The basic procedure is to create an instance of the tokenizer class with the string to be processed as an argument and then do a loop until all available tokens are read. The constructor has a default set of separator characters, but that can be overridden. The default separators are all “whitespace” characters, i.e. the space character, the tabulator character, the carriage return character, the linefeed character, and the form feed character.

Tokenizer class example listing entries of the PATH environment variable

#include "tokenizer.h"
#include <cstdlib>
#include <string>
#include <iostream>

using namespace LAMMPS_NS;

int main(int, char **)
{
    const char *path = getenv("PATH");

    if (path != nullptr) {
        Tokenizer p(path,":");
        while (p.has_next())
            std::cout << "Entry: " << p.next() << "\n";
    }
    return 0;
}

Most tokenizer operations cannot fail except for LAMMPS_NS::Tokenizer::next() (when used without first checking with LAMMPS_NS::Tokenizer::has_next()) and LAMMPS_NS::Tokenizer::skip(). In case of failure, the class will throw an exception, so you may need to wrap the code using the tokenizer into a try / catch block to handle errors. The LAMMPS_NS::ValueTokenizer class may also throw an exception when a (type of) number is requested as next token that is not compatible with the string representing the next word.

ValueTokenizer class example with exception handling

#include "tokenizer.h"
#include <cstdlib>
#include <string>
#include <iostream>

using namespace LAMMPS_NS;

int main(int, char **)
{
    const char *text = "1 2 3 4 5 20.0 21 twentytwo 2.3";
    double num1(0),num2(0),num3(0),num4(0);

    ValueTokenizer t(text);
    // read 4 doubles after skipping over 5 numbers
    try {
        t.skip(5);
        num1 = t.next_double();
        num2 = t.next_double();
        num3 = t.next_double();
        num4 = t.next_double();
    } catch (TokenizerException &e) {
        std::cout << "Reading numbers failed: " << e.what() << "\n";
    }
    std::cout << "Values: " << num1 << " " << num2 << " " << num3 << " " << num4 << "\n";
    return 0;
}

This code example should produce the following output:

Reading numbers failed: Not a valid floating-point number: 'twentytwo'
Values: 20 21 0 0

class LAMMPS_NS::Tokenizer

Public Functions

Tokenizer(const std::string &str, const std::string &separators = TOKENIZER_DEFAULT_SEPARATORS)

Class for splitting text into words

This tokenizer will break down a string into sub-strings (i.e words) separated by the given separator characters.

See also: ValueTokenizer, utils::split_words()

Parameters

str: string to be processed
separators: string with separator characters (default: ” \t\r\n\f”)

void reset(): Re-position the tokenizer state to the first word, i.e. the first non-separator character

void skip(int n)

Skip over a given number of tokens

Parameters

n: number of tokens to skip over

bool has_next() const

Indicate whether more tokens are available

Return: true if there are more tokens, false if not

bool contains(const std::string &str) const

Search the text to be processed for a sub-string.

Return

true if string was found, false if not

Parameters

str: string to be searched for

std::string next()

Retrieve next token.

Return: string with the next token

size_t count()

Count number of tokens in text.

Return: number of counted tokens

std::vector<std::string> as_vector()

Retrieve the entire text converted to an STL vector of tokens.

Return: The STL vector

class LAMMPS_NS::TokenizerException : public exception

Subclassed by InvalidFloatException, InvalidIntegerException

Public Functions

TokenizerException(const std::string &msg, const std::string &token)

Thrown during retrieving or skipping tokens

Parameters

msg: String with error message
token: String of the token/word that caused the error

const char *what() const

Retrieve message describing the thrown exception

Return: string with error message

class LAMMPS_NS::ValueTokenizer

Public Functions

ValueTokenizer(const std::string &str, const std::string &separators = TOKENIZER_DEFAULT_SEPARATORS)

Class for reading text with numbers

See also: Tokenizer

See

Tokenizer InvalidIntegerException InvalidFloatException

Parameters

str: String to be processed
separators: String with separator characters (default: ” \t\r\n\f”)

std::string next_string()

Retrieve next token

Return: string with next token

tagint next_tagint()

Retrieve next token and convert to tagint

Return: value of next token

bigint next_bigint()

Retrieve next token and convert to bigint

Return: value of next token

int next_int()

Retrieve next token and convert to int

Return: value of next token

double next_double()

Retrieve next token and convert to double

Return: value of next token

bool has_next() const

Indicate whether more tokens are available

Return: true if there are more tokens, false if not

bool contains(const std::string &value) const

Search the text to be processed for a sub-string.

Return

true if string was found, false if not

Parameters

value: string with value to be searched for

void skip(int ntokens)

Skip over a given number of tokens

Parameters

n: number of tokens to skip over

size_t count()

Count number of tokens in text.

Return: number of counted tokens

class InvalidIntegerException : public TokenizerException

class InvalidFloatException : public TokenizerException

4.10. File reader classes

The purpose of the file reader classes is to simplify the recurring task of reading and parsing files. They can use the LAMMPS_NS::ValueTokenizer class to process the read in text. The LAMMPS_NS::TextFileReader is a more general version while LAMMPS_NS::PotentialFileReader is specialized to implement the behavior expected for looking up and reading/parsing files with potential parameters in LAMMPS. The potential file reader class requires a LAMMPS instance, requires to be run on MPI rank 0 only, will use the LAMMPS_NS::utils::get_potential_file_path() function to look up and open the file, and will call the LAMMPS_NS::Error class in case of failures to read or to convert numbers, so that LAMMPS will be aborted.

Use of PotentialFileReader class in pair style coul/streitz

 PotentialFileReader reader(lmp, file, "coul/streitz");
 char * line;

 while((line = reader.next_line(NPARAMS_PER_LINE))) {
   try {
     ValueTokenizer values(line);
     std::string iname = values.next_string();

     int ielement;
     for (ielement = 0; ielement < nelements; ielement++)
       if (iname == elements[ielement]) break;

     if (nparams == maxparam) {
       maxparam += DELTA;
       params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
                                           "pair:params");
     }

     params[nparams].ielement = ielement;
     params[nparams].chi = values.next_double();
     params[nparams].eta = values.next_double();
     params[nparams].gamma = values.next_double();
     params[nparams].zeta = values.next_double();
     params[nparams].zcore = values.next_double();

   } catch (TokenizerException & e) {
     error->one(FLERR, e.what());
   }
   nparams++;
 }

A file that would be parsed by the reader code fragment looks like this:

# DATE: 2015-02-19 UNITS: metal CONTRIBUTOR: Ray Shan CITATION: Streitz and Mintmire, Phys Rev B, 50, 11996-12003 (1994)
#
# X (eV)                J (eV)          gamma (1/AA)   zeta (1/AA)    Z (e)

Al      0.000000        10.328655       0.000000        0.968438        0.763905
O       5.484763        14.035715       0.000000        2.143957        0.000000

class LAMMPS_NS::TextFileReader

Public Functions

TextFileReader(const std::string &filename, const std::string &filetype)

Class for reading and parsing text files

The value of the class member variable ignore_comments controls whether any text following the pound sign (#) should be ignored (true) or not (false). Default: true, i.e. ignore.

See also: TextFileReader

Parameters

filename: Name of file to be read
filetype: Description of file type for error messages

~TextFileReader(): Closes the file

void skip_line(): Read the next line and ignore it

char *next_line(int nparams = 0)

Read the next line(s) until nparams words have been read.

This reads a line and counts the words in it, if the number is less than the requested number, it will read the next line, as well. Output will be a string with all read lines combined. The purpose is to somewhat replicate the reading behavior of formatted files in Fortran.

If the ignore_comments class member has the value true, then any text read in is truncated at the first ‘#’ character.

Return

String with the concatenated text

Parameters

nparams: Number of words that must be read. Default: 0

void next_dvector(double *list, int n)

Read lines until n doubles have been read and stored in array list

This reads lines from the file using the next_line() function, and splits them into floating-point numbers using the ValueTokenizer class and stores the number is the provided list.

Parameters

list: Pointer to array with suitable storage for n doubles
n: Number of doubles to be read

ValueTokenizer next_values(int nparams, const std::string &separators = TOKENIZER_DEFAULT_SEPARATORS)

Read text until nparams words are read and passed to a tokenizer object for custom parsing.

This reads lines from the file using the next_line() function, and splits them into floating-point numbers using the ValueTokenizer class and stores the number is the provided list.

Return

ValueTokenizer object for read in text

Parameters

nparams: Number of words to be read
separators: String with list of separators.

Public Members

bool ignore_comments: Controls whether comments are ignored.

class LAMMPS_NS::PotentialFileReader : protected Pointers

Public Functions

PotentialFileReader(class LAMMPS *lmp, const std::string &filename, const std::string &potential_name, const int auto_convert = 0)

Class for reading and parsing LAMMPS potential files

The value of the class member variable ignore_comments controls whether any text following the pound sign (#) should be ignored (true) or not (false). Default: true, i.e. ignore.

See also: TextFileReader

Parameters

lmp: Pointer to LAMMPS instance
filename: Name of file to be read
potential_name: Name of potential style for error messages
auto_convert: Bitmask of supported unit conversions

~PotentialFileReader(): Closes the file

void ignore_comments(bool value)

Set comment (= text after ‘#’) handling preference for the file to be read

Parameters

value: Comment text is ignored if true, or not if false

void skip_line(): Read a line but ignore its content

char *next_line(int nparams = 0)

Read the next line(s) until nparams words have been read.

This reads a line and counts the words in it, if the number is less than the requested number, it will read the next line, as well. Output will be a string with all read lines combined. The purpose is to somewhat replicate the reading behavior of formatted files in Fortran.

Return

String with the concatenated text

Parameters

nparams: Number of words that must be read. Default: 0

void next_dvector(double *list, int n)

Read lines until n doubles have been read and stored in array list

This reads lines from the file using the next_line() function, and splits them into floating-point numbers using the ValueTokenizer class and stores the number is the provided list.

Parameters

list: Pointer to array with suitable storage for n doubles
n: Number of doubles to be read

ValueTokenizer next_values(int nparams, const std::string &separators = TOKENIZER_DEFAULT_SEPARATORS)

Read text until nparams words are read and passed to a tokenizer object for custom parsing.

This reads lines from the file using the next_line() function, and splits them into floating-point numbers using the ValueTokenizer class and stores the number is the provided list.

Return

ValueTokenizer object for read in text

Parameters

nparams: Number of words to be read
separators: String with list of separators.

double next_double()

Read next line and convert first word to a double

Return: Value of first word in line as double

int next_int()

Read next line and convert first word to an int

Return: Value of first word in line as int

tagint next_tagint()

Read next line and convert first word to a tagint

Return: Value of first word in line as tagint

bigint next_bigint()

Read next line and convert first word to a bigint

Return: Value of first word in line as bigint

std::string next_string()

4.11. Memory pool classes

The memory pool classes are used for cases where otherwise many small memory allocations would be needed and where the data would be either all used or all freed. One example for that is the storage of neighbor lists. The memory management strategy is based on the assumption that allocations will be in chunks of similar sizes. The allocation is then not done per individual call for a reserved chunk of memory, but for a “page” that can hold multiple chunks of data. A parameter for the maximum chunk size must be provided, as that is used to determine whether a new page of memory must be used.

The MyPage class offers two ways to reserve a chunk: 1) with get() the chunk size needs to be known in advance, 2) with vget() a pointer to the next chunk is returned, but its size is registered later with vgot().

Example of using MyPage

   #include "my_page.h"
   using namespace LAMMPS_NS;

   MyPage<double> *dpage = new MyPage<double>;
   // max size of chunk: 256, size of page: 10240 doubles (=81920 bytes)
   dpage->init(256,10240);

   double **build_some_lists(int num)
   {
       dpage->reset();
       double **dlist = new double*[num];
       for (int i=0; i < num; ++i) {
           double *dptr = dpage.vget();
           int jnum = 0;
           for (int j=0; j < jmax; ++j) {
               // compute some dvalue for eligible loop index j
               dptr[j] = dvalue;
               ++jnum;
           }
           if (dpage.status() != 0) {
               // handle out of memory or jnum too large errors
           }
           dpage.vgot(jnum);
           dlist[i] = dptr;
       }
       return dlist;
   }

template<class T> class LAMMPS_NS::MyPage

Templated class for storing chunks of datums in pages.

The size of the chunk may vary from call to call, but must be less or equal than the maxchunk setting. The chunks are not returnable like with malloc() (i.e. you cannot call free() on them individually). One can only reset and start over. The purpose of this class is to replace many small memory allocations via malloc() with a few large ones. Since the pages are never freed until the class is re-initialized, they can be re-used without having to re-allocate them by calling the reset() method.

The settings maxchunk, pagesize, and pagedelta control the memory allocation strategy. The maxchunk value represents the expected largest number of items per chunk. If there is less space left on the current page, a new page is allocated for the next chunk. The pagesize value represents how many items can fit on a single page. It should have space for multiple chunks of size maxchunk. The combination of these two parameters determines how much memory is wasted by either switching to the next page too soon or allocating too large pages that never get properly used. It is an error, if a requested chunk is larger than maxchunk. The pagedelta parameter determines how many pages are allocated in one go. In combination with the pagesize setting, this determines how often blocks of memory get allocated (fewer allocations will result in faster execution).

Note: This is a template class with explicit instantiation. If the class is used with a new data type a new explicit instantiation may need to be added at the end of the file src/my_page.cpp to avoid symbol lookup errors.

Public Functions

MyPage()

Create a class instance

Need to call init() before use to define allocation settings

int init(int user_maxchunk = 1, int user_pagesize = 1024, int user_pagedelta = 1)

(Re-)initialize the set of pages and allocation parameters.

This also frees all previously allocated storage and allocates the first page(s).

Return

1 if there were invalid parameters, 2 if there was an allocation error or 0 if successful

Parameters

user_maxchunk: Expected maximum number of items for one chunk
user_pagesize: Number of items on a single memory page
user_pagedelta: Number of pages to allocate with one malloc

T *get(int n = 1)

Pointer to location that can store N items.

This will allocate more pages as needed. If the parameter N is larger than the maxchunk setting an error is flagged.

Return

memory location or null pointer, if error or allocation failed

Parameters

n: number of items for which storage is requested

T *vget()

Get pointer to location that can store maxchunk items.

This will return the same pointer as the previous call to this function unless vgot() is called afterwards to record how many items of the chunk were actually used.

Return: pointer to chunk of memory or null pointer if run out of memory

void vgot(int n)

Mark N items as used of the chunk reserved with a preceding call to vget().

This will advance the internal pointer inside the current memory page. It is not necessary to call this function for N = 0, that is the reserved storage was not used. A following call to vget() will then reserve the same location again. It is an error if N > maxchunk.

Parameters

n: Number of items used in previously reserved chunk

void reset(): Reset state of memory pool without freeing any memory

double size() const

Return total size of allocated pages

Return: total storage used in bytes

int status() const

Return error status

Return: 0 if no error, 1 requested chunk size > maxchunk, 2 if malloc failed

template<class T> class LAMMPS_NS::MyPoolChunk

Templated class for storing chunks of datums in pages.

The size of the chunk may vary from call to call between the minchunk and maxchunk setting. Chunks may be returned to the pool for re-use. Chunks can be reserved in nbin different sizes between minchunk and maxchunk. The chunksperpage setting specifies how many chunks are stored on any page and the pagedelta setting determines how many pages are allocated in one go. Pages are never freed, so they can be re-used without re-allocation.

Note: This is a template class with explicit instantiation. If the class is used with a new data type a new explicit instantiation may need to be added at the end of the file src/my_pool_chunk.cpp to avoid symbol lookup errors.

Public Functions

MyPoolChunk(int user_minchunk = 1, int user_maxchunk = 1, int user_nbin = 1, int user_chunkperpage = 1024, int user_pagedelta = 1)

Create a class instance and set memory pool parameters

Parameters

user_minchunk: Minimal chunk size
user_maxchunk: Maximal chunk size
user_nbin: Number of bins of different chunk sizes
user_chunkperpage: Number of chunks per page
user_pagedelta: Number of pages to allocate in one go

~MyPoolChunk(): Destroy class instance and free all allocated memory

T *get(int &index)

Return pointer/index of unused chunk of size maxchunk

Return

Pointer to requested chunk of storage

Parameters

index: Index of chunk in memory pool

T *get(int n, int &index)

Return pointer/index of unused chunk of size N

Return

Pointer to requested chunk of storage

Parameters

n: Size of chunk
index: Index of chunk in memory pool

void put(int index)

Put indexed chunk back into memory pool via free list

Parameters

index: Memory chunk index returned by call to get()

double size() const

Return total size of allocated pages

Return: total storage used in bytes

int status() const

Return error status

Return: 0 if no error, 1 if invalid input, 2 if malloc() failed, 3 if chunk > maxchunk

4.12. Eigensolver functions

The MathEigen sub-namespace of the LAMMPS_NS namespace contains functions and classes for eigensolvers. Currently only the jacobi3 function is used in various places in LAMMPS. That function is built on top of a group of more generic eigensolvers that are maintained in the math_eigen_impl.h header file. This header contains the implementation of three template classes:

“Jacobi” calculates all of the eigenvalues and eigenvectors of a dense, symmetric, real matrix.
The “PEigenDense” class only calculates the principal eigenvalue (ie. the largest or smallest eigenvalue), and its corresponding eigenvector. However it is much more efficient than “Jacobi” when applied to large matrices (larger than 13x13). PEigenDense also can understand complex-valued Hermitian matrices.
The “LambdaLanczos” class is a generalization of “PEigenDense” which can be applied to arbitrary sparse matrices.

The “math_eigen_impl.h” code is an amalgamation of jacobi_pd by Andrew Jewett at Scripps Research (under CC0-1.0 license) and Lambda Lanczos by Yuya Kurebayashi at Tohoku University (under MIT license)

int MathEigen::jacobi3(double const *const *mat, double *eval, double **evec)

A specialized function which finds the eigenvalues and eigenvectors of a 3x3 matrix (in double ** format).

Return

0 if eigenvalue calculation converged, 1 if it failed

Parameters

mat: the 3x3 matrix you wish to diagonalize
eval: store the eigenvalues here
evec: store the eigenvectors here…

int MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3]): This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

4.13. Communication buffer coding with ubuf

LAMMPS uses communication buffers where it collects data from various class instances and then exchanges the data with neighboring sub-domains. For simplicity those buffers are defined as double buffers and used for doubles and integer numbers. This presents a unique problem when 64-bit integers are used. While the storage needed for a double is also 64-bit, it cannot be used by a simple assignment. To get around that limitation, LAMMPS uses the ubuf union. It is used in the various “pack” and “unpack” functions in the LAMMPS classes to store and retrieve integers that may be 64-bit from the communication buffers.

union LAMMPS_NS::ubuf

#include <lmptype.h>

Data structure for packing 32-bit and 64-bit integers into double (communication) buffers

Using this union avoids aliasing issues by having member types (double, int) referencing the same buffer memory location.

The explicit constructor for 32-bit integers prevents compilers from (incorrectly) calling the double constructor when storing an int into a double buffer.

Usage:

To copy an integer into a double buffer:

double buf[2];
int    foo =   1;
tagint bar = 2<<40;
buf[1] = ubuf(foo).d;
buf[2] = ubuf(bar).d;

To copy from a double buffer back to an int:

foo = (int)    ubuf(buf[1]).i;
bar = (tagint) ubuf(buf[2]).i;

The typecasts prevent compiler warnings about possible truncation issues.

Public Functions

ubuf(const double &arg)

ubuf(const int64_t &arg)

ubuf(const int &arg)

Public Members

double d

int64_t i