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0b147704688faaf69d722914923fe14a0559f1df
lammps/src/utils.cpp
Steve Plimpton 0b14770468 merge with current master
2021-01-11 16:13:33 -07:00

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, 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.
------------------------------------------------------------------------- */
#include "utils.h"
#include "comm.h"
#include "compute.h"
#include "error.h"
#include "fix.h"
#include "memory.h"
#include "modify.h"
#include "text_file_reader.h"
#include "tokenizer.h"
#include "update.h"
#include <cctype>
#include <cerrno>
#include <cstring>
#if defined(__linux__)
#include <unistd.h> // for readlink
#endif
/*! \file utils.cpp */
/*
* Mini regex-module adapted from https://github.com/kokke/tiny-regex-c
* which is in the public domain.
*
* Supports:
* ---------
* '.' Dot, matches any character
* '^' Start anchor, matches beginning of string
* '$' End anchor, matches end of string
* '*' Asterisk, match zero or more (greedy)
* '+' Plus, match one or more (greedy)
* '?' Question, match zero or one (non-greedy)
* '[abc]' Character class, match if one of {'a', 'b', 'c'}
* '[a-zA-Z]' Character ranges, the character set of the ranges { a-z | A-Z }
* '\s' Whitespace, \t \f \r \n \v and spaces
* '\S' Non-whitespace
* '\w' Alphanumeric, [a-zA-Z0-9_]
* '\W' Non-alphanumeric
* '\d' Digits, [0-9]
* '\D' Non-digits
* '\i' Integer chars, [0-9], '+' and '-'
* '\I' Non-integers
* '\f' Floating point number chars, [0-9], '.', 'e', 'E', '+' and '-'
* '\F' Non-floats
*
* *NOT* supported:
* '[^abc]' Inverted class
* 'a|b' Branches
* '(abc)+' Groups
*/
extern "C"
{
/** Match text against a (simplified) regular expression
* (regexp will be compiled automatically). */
static int re_match(const char *text, const char *pattern);
}
////////////////////////////////////////////////////////////////////////
// Merge sort support functions
static void do_merge(int *idx, int *buf, int llo, int lhi, int rlo, int rhi,
void *ptr, int (*comp)(int, int, void *));
static void insertion_sort(int *index, int num, void *ptr,
int (*comp)(int, int, void*));
////////////////////////////////////////////////////////////////////////
using namespace LAMMPS_NS;
/** More flexible and specific matching of a string against a pattern.
* This function is supposed to be a more safe, more specific and
* simple to use API to find pattern matches. The purpose is to replace
* uses of either strncmp() or strstr() in the code base to find
* sub-strings safely. With strncmp() finding prefixes, the number of
* characters to match must be counted, which can lead to errors,
* while using "^pattern" will do the same with less problems.
* Matching for suffixes using strstr() is not as specific as 'pattern$',
* and complex matches, e.g. "^rigid.*\/small.*", to match all small
* body optimized rigid fixes require only one test.
*
* The use of std::string arguments allows for simple concatenation
* even with char * type variables.
* Example: utils::strmatch(text, std::string("^") + charptr)
*/
bool utils::strmatch(const std::string &text, const std::string &pattern)
{
const int pos = re_match(text.c_str(),pattern.c_str());
return (pos >= 0);
}
/** 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. */
void utils::logmesg(LAMMPS *lmp, const std::string &mesg)
{
if (lmp->screen) fputs(mesg.c_str(), lmp->screen);
if (lmp->logfile) fputs(mesg.c_str(), lmp->logfile);
}
/* define this here, so we won't have to include the headers
everywhere and utils.h will more likely be included anyway. */
std::string utils::getsyserror()
{
return std::string(strerror(errno));
}
/** On Linux the folder /proc/self/fd holds symbolic links to the actual
* pathnames associated with each open file descriptor of the current process.
*
* 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.
*/
const char *utils::guesspath(char *buf, int len, FILE *fp)
{
memset(buf,0,len);
#if defined(__linux__)
int fd = fileno(fp);
// get pathname from /proc or copy (unknown)
if (readlink(fmt::format("/proc/self/fd/{}",fd).c_str(),buf,len-1) <= 0)
strncpy(buf,"(unknown)",len-1);
#else
strncpy(buf,"(unknown)",len-1);
#endif
return buf;
}
#define MAXPATHLENBUF 1024
/* like fgets() but aborts with an error or EOF is encountered */
void utils::sfgets(const char *srcname, int srcline, char *s, int size,
FILE *fp, const char *filename, Error *error)
{
char *rv = fgets(s,size,fp);
if (rv == nullptr) { // something went wrong
char buf[MAXPATHLENBUF];
std::string errmsg;
// try to figure out the file name from the file pointer
if (!filename)
filename = guesspath(buf,MAXPATHLENBUF,fp);
if (feof(fp)) {
errmsg = "Unexpected end of file while reading file '";
} else if (ferror(fp)) {
errmsg = "Unexpected error while reading file '";
} else {
errmsg = "Unexpected short read while reading file '";
}
errmsg += filename;
errmsg += "'";
if (error) error->one(srcname,srcline,errmsg);
if (s) *s = '\0'; // truncate string to empty in case error is null pointer
}
return;
}
/* like fread() but aborts with an error or EOF is encountered */
void utils::sfread(const char *srcname, int srcline, void *s, size_t size,
size_t num, FILE *fp, const char *filename, Error *error)
{
size_t rv = fread(s,size,num,fp);
if (rv != num) { // something went wrong
char buf[MAXPATHLENBUF];
std::string errmsg;
// try to figure out the file name from the file pointer
if (!filename)
filename = guesspath(buf,MAXPATHLENBUF,fp);
if (feof(fp)) {
errmsg = "Unexpected end of file while reading file '";
} else if (ferror(fp)) {
errmsg = "Unexpected error while reading file '";
} else {
errmsg = "Unexpected short read while reading file '";
}
errmsg += filename;
errmsg += "'";
if (error) error->one(srcname,srcline,errmsg);
}
return;
}
/* ------------------------------------------------------------------ */
std::string utils::check_packages_for_style(const std::string &style,
const std::string &name,
LAMMPS *lmp)
{
std::string errmsg = "Unrecognized " + style + " style '" + name + "'";
const char *pkg = lmp->match_style(style.c_str(),name.c_str());
if (pkg) {
errmsg += fmt::format(" is part of the {} package",pkg);
if (lmp->is_installed_pkg(pkg))
errmsg += ", but seems to be missing because of a dependency";
else
errmsg += " which is not enabled in this LAMMPS binary.";
}
return errmsg;
}
/* ----------------------------------------------------------------------
read a floating point value from a string
generate an error if not a legitimate floating point value
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
double utils::numeric(const char *file, int line, const char *str,
bool do_abort, LAMMPS *lmp)
{
int n = 0;
if (str) n = strlen(str);
if (n == 0) {
if (do_abort)
lmp->error->one(file,line,"Expected floating point parameter instead of"
" NULL or empty string in input script or data file");
else
lmp->error->all(file,line,"Expected floating point parameter instead of"
" NULL or empty string in input script or data file");
}
for (int i = 0; i < n; i++) {
if (isdigit(str[i])) continue;
if (str[i] == '-' || str[i] == '+' || str[i] == '.') continue;
if (str[i] == 'e' || str[i] == 'E') continue;
std::string msg("Expected floating point parameter instead of '");
msg += str;
msg += "' in input script or data file";
if (do_abort)
lmp->error->one(file,line,msg);
else
lmp->error->all(file,line,msg);
}
return atof(str);
}
/* ----------------------------------------------------------------------
read an integer value from a string
generate an error if not a legitimate integer value
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
int utils::inumeric(const char *file, int line, const char *str,
bool do_abort, LAMMPS *lmp)
{
int n = 0;
if (str) n = strlen(str);
if (n == 0) {
if (do_abort)
lmp->error->one(file,line,"Expected integer parameter instead of "
"NULL or empty string in input script or data file");
else
lmp->error->all(file,line,"Expected integer parameter instead of "
"NULL or empty string in input script or data file");
}
for (int i = 0; i < n; i++) {
if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue;
std::string msg("Expected integer parameter instead of '");
msg += str;
msg += "' in input script or data file";
if (do_abort)
lmp->error->one(file,line,msg);
else
lmp->error->all(file,line,msg);
}
return atoi(str);
}
/* ----------------------------------------------------------------------
read a big integer value from a string
generate an error if not a legitimate integer value
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
bigint utils::bnumeric(const char *file, int line, const char *str,
bool do_abort, LAMMPS *lmp)
{
int n = 0;
if (str) n = strlen(str);
if (n == 0) {
if (do_abort)
lmp->error->one(file,line,"Expected integer parameter instead of "
"NULL or empty string in input script or data file");
else
lmp->error->all(file,line,"Expected integer parameter instead of "
"NULL or empty string in input script or data file");
}
for (int i = 0; i < n; i++) {
if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue;
std::string msg("Expected integer parameter instead of '");
msg += str;
msg += "' in input script or data file";
if (do_abort)
lmp->error->one(file,line,msg);
else
lmp->error->all(file,line,msg);
}
return ATOBIGINT(str);
}
/* ----------------------------------------------------------------------
read a tag integer value from a string
generate an error if not a legitimate integer value
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
tagint utils::tnumeric(const char *file, int line, const char *str,
bool do_abort, LAMMPS *lmp)
{
int n = 0;
if (str) n = strlen(str);
if (n == 0) {
if (do_abort)
lmp->error->one(file,line,"Expected integer parameter instead of "
"NULL or empty string in input script or data file");
else
lmp->error->all(file,line,"Expected integer parameter instead of "
"NULL or empty string in input script or data file");
}
for (int i = 0; i < n; i++) {
if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue;
std::string msg("Expected integer parameter instead of '");
msg += str;
msg += "' in input script or data file";
if (do_abort)
lmp->error->one(file,line,msg);
else
lmp->error->all(file,line,msg);
}
return ATOTAGINT(str);
}
/* ----------------------------------------------------------------------
compute bounds implied by numeric str with a possible wildcard asterisk
------------------------------------------------------------------------- */
template<typename TYPE>
void utils::bounds(const char *file, int line, const std::string &str,
bigint nmin, bigint nmax, TYPE &nlo, TYPE &nhi, Error *error)
{
size_t found = str.find_first_of("*");
nlo = nhi = -1;
if (found == std::string::npos) { // contains no '*'
nlo = nhi = strtol(str.c_str(),nullptr,10);
} else if (str.size() == 1) { // is only '*'
nlo = nmin;
nhi = nmax;
} else if (found == 0) { // is '*j'
nlo = nmin;
nhi = strtol(str.substr(1).c_str(),nullptr,10);
} else if (str.size() == found+1) { // is 'i*'
nlo = strtol(str.c_str(),nullptr,10);
nhi = nmax;
} else { // is 'i*j'
nlo = strtol(str.c_str(),nullptr,10);
nhi = strtol(str.substr(found+1).c_str(),nullptr,10);
}
if (error) {
if (nlo < nmin)
error->all(file,line,fmt::format("Numeric index {} is out of bounds"
"({}-{})",nlo,nmin,nmax));
else if (nhi > nmax)
error->all(file,line,fmt::format("Numeric index {} is out of bounds"
"({}-{})",nhi,nmin,nmax));
else if (nlo > nhi)
error->all(file,line,fmt::format("Numeric index {} is out of bounds"
"({}-{})",nlo,nmin,nhi));
}
}
template void utils::bounds<>(const char *, int, const std::string &,
bigint, bigint, int &, int &, Error *);
template void utils::bounds<>(const char *, int, const std::string &,
bigint, bigint, long &, long &, Error *);
template void utils::bounds<>(const char *, int, const std::string &,
bigint, bigint, long long &, long long &, Error *);
/* -------------------------------------------------------------------------
Expand list of arguments in arg to earg if arg contains wildcards
------------------------------------------------------------------------- */
int utils::expand_args(const char *file, int line, int narg, char **arg,
int mode, char **&earg, LAMMPS *lmp)
{
int n,iarg,index,nlo,nhi,nmax,expandflag,icompute,ifix;
char *ptr1,*ptr2,*str;
ptr1 = nullptr;
for (iarg = 0; iarg < narg; iarg++) {
ptr1 = strchr(arg[iarg],'*');
if (ptr1) break;
}
if (!ptr1) {
earg = arg;
return narg;
}
// maxarg should always end up equal to newarg, so caller can free earg
int maxarg = narg-iarg;
earg = (char **) lmp->memory->smalloc(maxarg*sizeof(char *),"input:earg");
int newarg = 0;
for (iarg = 0; iarg < narg; iarg++) {
expandflag = 0;
if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0) {
ptr1 = strchr(&arg[iarg][2],'[');
if (ptr1) {
ptr2 = strchr(ptr1,']');
if (ptr2) {
*ptr2 = '\0';
if (strchr(ptr1,'*')) {
if (arg[iarg][0] == 'c') {
*ptr1 = '\0';
icompute = lmp->modify->find_compute(&arg[iarg][2]);
*ptr1 = '[';
// check for global vector/array, peratom array, local array
if (icompute >= 0) {
if (mode == 0 && lmp->modify->compute[icompute]->vector_flag) {
nmax = lmp->modify->compute[icompute]->size_vector;
expandflag = 1;
} else if (mode == 1 && lmp->modify->compute[icompute]->array_flag) {
nmax = lmp->modify->compute[icompute]->size_array_cols;
expandflag = 1;
} else if (lmp->modify->compute[icompute]->peratom_flag &&
lmp->modify->compute[icompute]->size_peratom_cols) {
nmax = lmp->modify->compute[icompute]->size_peratom_cols;
expandflag = 1;
} else if (lmp->modify->compute[icompute]->local_flag &&
lmp->modify->compute[icompute]->size_local_cols) {
nmax = lmp->modify->compute[icompute]->size_local_cols;
expandflag = 1;
}
}
} else if (arg[iarg][0] == 'f') {
*ptr1 = '\0';
ifix = lmp->modify->find_fix(&arg[iarg][2]);
*ptr1 = '[';
// check for global vector/array, peratom array, local array
if (ifix >= 0) {
if (mode == 0 && lmp->modify->fix[ifix]->vector_flag) {
nmax = lmp->modify->fix[ifix]->size_vector;
expandflag = 1;
} else if (mode == 1 && lmp->modify->fix[ifix]->array_flag) {
nmax = lmp->modify->fix[ifix]->size_array_cols;
expandflag = 1;
} else if (lmp->modify->fix[ifix]->peratom_flag &&
lmp->modify->fix[ifix]->size_peratom_cols) {
nmax = lmp->modify->fix[ifix]->size_peratom_cols;
expandflag = 1;
} else if (lmp->modify->fix[ifix]->local_flag &&
lmp->modify->fix[ifix]->size_local_cols) {
nmax = lmp->modify->fix[ifix]->size_local_cols;
expandflag = 1;
}
}
} else if (arg[iarg][0] == 'i') {
*ptr1 = '\0';
int flag,cols;
int icustom = atom->find_custom(&arg[iarg][3],flag,cols);
*ptr1 = '[';
// check for custom per-atom integer array
if (icustom >= 0) {
if (mode == 1 && !flag && cols) {
nmax = cols;
expandflag = 1;
}
}
} else if (arg[iarg][0] == 'd') {
*ptr1 = '\0';
int flag,cols;
int icustom = atom->find_custom(&arg[iarg][3],flag,cols);
*ptr1 = '[';
// check for custom per-atom floating point array
if (icustom >= 0) {
if (mode == 1 && flag && cols) {
nmax = cols;
expandflag = 1;
}
}
}
}
*ptr2 = ']';
}
}
}
if (expandflag) {
*ptr2 = '\0';
bounds(file,line,ptr1+1,1,nmax,nlo,nhi,lmp->error);
*ptr2 = ']';
if (newarg+nhi-nlo+1 > maxarg) {
maxarg += nhi-nlo+1;
earg = (char **)
lmp->memory->srealloc(earg,maxarg*sizeof(char *),"input:earg");
}
for (index = nlo; index <= nhi; index++) {
n = strlen(arg[iarg]) + 16; // 16 = space for large inserted integer
str = earg[newarg] = new char[n];
strncpy(str,arg[iarg],ptr1+1-arg[iarg]);
sprintf(&str[ptr1+1-arg[iarg]],"%d",index);
strcat(str,ptr2);
newarg++;
}
} else {
if (newarg == maxarg) {
maxarg++;
earg = (char **)
lmp->memory->srealloc(earg,maxarg*sizeof(char *),"input:earg");
}
n = strlen(arg[iarg]) + 1;
earg[newarg] = new char[n];
strcpy(earg[newarg],arg[iarg]);
newarg++;
}
}
//printf("NEWARG %d\n",newarg);
//for (int i = 0; i < newarg; i++)
// printf(" arg %d: %s\n",i,earg[i]);
return newarg;
}
/* ----------------------------------------------------------------------
Return string without leading or trailing whitespace
------------------------------------------------------------------------- */
std::string utils::trim(const std::string &line) {
int beg = re_match(line.c_str(),"\\S+");
int end = re_match(line.c_str(),"\\s+$");
if (beg < 0) beg = 0;
if (end < 0) end = line.size();
return line.substr(beg,end-beg);
}
/* ----------------------------------------------------------------------
Return string without trailing # comment
------------------------------------------------------------------------- */
std::string utils::trim_comment(const std::string &line) {
auto end = line.find_first_of("#");
if (end != std::string::npos) {
return line.substr(0, end);
}
return std::string(line);
}
/* ----------------------------------------------------------------------
return number of words
------------------------------------------------------------------------- */
size_t utils::count_words(const char *text) {
size_t count = 0;
const char * buf = text;
char c = *buf;
while (c) {
if (c == ' ' || c == '\t' || c == '\r' || c == '\n' || c == '\f') {
c = *++buf;
continue;
};
++count;
c = *++buf;
while (c) {
if (c == ' ' || c == '\t' || c == '\r' || c == '\n' || c == '\f') {
break;
}
c = *++buf;
}
}
return count;
}
/* ----------------------------------------------------------------------
return number of words
------------------------------------------------------------------------- */
size_t utils::count_words(const std::string &text) {
return utils::count_words(text.c_str());
}
/* ----------------------------------------------------------------------
Return number of words
------------------------------------------------------------------------- */
size_t utils::count_words(const std::string &text, const std::string &separators) {
size_t count = 0;
size_t start = text.find_first_not_of(separators);
while (start != std::string::npos) {
size_t end = text.find_first_of(separators, start);
++count;
if (end == std::string::npos) {
return count;
} else {
start = text.find_first_not_of(separators, end + 1);
}
}
return count;
}
/* ----------------------------------------------------------------------
Trim comment from string and return number of words
------------------------------------------------------------------------- */
size_t utils::trim_and_count_words(const std::string &text, const std::string &separators) {
return utils::count_words(utils::trim_comment(text), separators);
}
/* ----------------------------------------------------------------------
Convert string into words on whitespace while handling single and
double quotes.
------------------------------------------------------------------------- */
std::vector<std::string> utils::split_words(const std::string &text)
{
std::vector<std::string> list;
const char *buf = text.c_str();
std::size_t beg = 0;
std::size_t len = 0;
std::size_t add = 0;
char c = *buf;
while (c) {
// leading whitespace
if (c == ' ' || c == '\t' || c == '\r' || c == '\n' || c == '\f') {
c = *++buf;
++beg;
continue;
};
len = 0;
// handle escaped/quoted text.
quoted:
// handle single quote
if (c == '\'') {
++beg;
add = 1;
c = *++buf;
while (((c != '\'') && (c != '\0'))
|| ((c == '\\') && (buf[1] == '\''))) {
if ((c == '\\') && (buf[1] == '\'')) {
++buf;
++len;
}
c = *++buf;
++len;
}
if (c != '\'') ++len;
c = *++buf;
// handle double quote
} else if (c == '"') {
++beg;
add = 1;
c = *++buf;
while (((c != '"') && (c != '\0'))
|| ((c == '\\') && (buf[1] == '"'))) {
if ((c == '\\') && (buf[1] == '"')) {
++buf;
++len;
}
c = *++buf;
++len;
}
if (c != '"') ++len;
c = *++buf;
}
// unquoted
while (1) {
if ((c == '\'') || (c == '"')) goto quoted;
// skip escaped quote
if ((c == '\\') && ((buf[1] == '\'') || (buf[1] == '"'))) {
++buf;
++len;
c = *++buf;
++len;
}
if ((c == ' ') || (c == '\t') || (c == '\r') || (c == '\n')
|| (c == '\f') || (c == '\0')) {
list.push_back(text.substr(beg,len));
beg += len + add;
break;
}
c = *++buf;
++len;
}
}
return list;
}
/* ----------------------------------------------------------------------
Return whether string is a valid integer number
------------------------------------------------------------------------- */
bool utils::is_integer(const std::string &str) {
if (str.size() == 0) {
return false;
}
for (auto c : str) {
if (isdigit(c) || c == '-' || c == '+') continue;
return false;
}
return true;
}
/* ----------------------------------------------------------------------
Return whether string is a valid floating-point number
------------------------------------------------------------------------- */
bool utils::is_double(const std::string &str) {
if (str.size() == 0) {
return false;
}
for (auto c : str) {
if (isdigit(c)) continue;
if (c == '-' || c == '+' || c == '.') continue;
if (c == 'e' || c == 'E') continue;
return false;
}
return true;
}
/* ----------------------------------------------------------------------
strip off leading part of path, return just the filename
------------------------------------------------------------------------- */
std::string utils::path_basename(const std::string &path) {
#if defined(_WIN32)
size_t start = path.find_last_of("/\\");
#else
size_t start = path.find_last_of("/");
#endif
if (start == std::string::npos) {
start = 0;
} else {
start += 1;
}
return path.substr(start);
}
/* ----------------------------------------------------------------------
Return only the leading part of a path, return just the directory
------------------------------------------------------------------------- */
std::string utils::path_dirname(const std::string &path) {
#if defined(_WIN32)
size_t start = path.find_last_of("/\\");
#else
size_t start = path.find_last_of("/");
#endif
if (start == std::string::npos) return ".";
return path.substr(0,start);
}
/* ----------------------------------------------------------------------
join two paths
------------------------------------------------------------------------- */
std::string utils::path_join(const std::string &a, const std::string &b) {
#if defined(_WIN32)
return fmt::format("{}\\{}", a, b);
#else
return fmt::format("{}/{}", a, b);
#endif
}
/* ----------------------------------------------------------------------
try to open file for reading
------------------------------------------------------------------------- */
bool utils::file_is_readable(const std::string &path) {
FILE * fp = fopen(path.c_str(), "r");
if (fp) {
fclose(fp);
return true;
}
return false;
}
/* ----------------------------------------------------------------------
try to find potential file as specified by name
search current directory and the LAMMPS_POTENTIALS directory if
specified
------------------------------------------------------------------------- */
#if defined(_WIN32)
#define OS_PATH_VAR_SEP ";"
#else
#define OS_PATH_VAR_SEP ":"
#endif
std::string utils::get_potential_file_path(const std::string &path) {
std::string filepath = path;
std::string filename = utils::path_basename(path);
if (utils::file_is_readable(filepath)) {
return filepath;
} else {
// try the environment variable directory
const char *var = getenv("LAMMPS_POTENTIALS");
if (var != nullptr) {
Tokenizer dirs(var,OS_PATH_VAR_SEP);
while (dirs.has_next()) {
auto pot = utils::path_basename(filepath);
auto path = dirs.next();
filepath = utils::path_join(path, pot);
if (utils::file_is_readable(filepath)) {
return filepath;
}
}
}
}
return "";
}
#undef OS_PATH_VAR_SEP
/* ----------------------------------------------------------------------
read first line of potential file
if it has a DATE field, return the following word
------------------------------------------------------------------------- */
std::string utils::get_potential_date(const std::string &path, const std::string &potential_name) {
TextFileReader reader(path, potential_name);
reader.ignore_comments = false;
char *line = reader.next_line();
if (line == nullptr) return "";
Tokenizer words(line);
while (words.has_next()) {
if (words.next() == "DATE:") {
if (words.has_next()) return words.next();
}
}
return "";
}
/* ----------------------------------------------------------------------
read first line of potential file
if it has UNITS field, return following word
------------------------------------------------------------------------- */
std::string utils::get_potential_units(const std::string &path, const std::string &potential_name) {
TextFileReader reader(path, potential_name);
reader.ignore_comments = false;
char *line = reader.next_line();
if (line == nullptr) return "";
Tokenizer words(line);
while (words.has_next()) {
if (words.next() == "UNITS:") {
if (words.has_next()) return words.next();
}
}
return "";
}
/* ----------------------------------------------------------------------
return bitmask of supported conversions for a given property
------------------------------------------------------------------------- */
int utils::get_supported_conversions(const int property)
{
if (property == ENERGY) {
return METAL2REAL | REAL2METAL;
}
return NOCONVERT;
}
/* ----------------------------------------------------------------------
return conversion factor for a given property and conversion setting
return 0.0 if unknown.
------------------------------------------------------------------------- */
double utils::get_conversion_factor(const int property, const int conversion)
{
if (property == ENERGY) {
if (conversion == NOCONVERT) {
return 1.0;
} else if (conversion == METAL2REAL) {
return 23.060549;
} else if (conversion == REAL2METAL) {
return 1.0/23.060549;
}
}
return 0.0;
}
/* ----------------------------------------------------------------------
open a potential file as specified by name
if fails, search in dir specified by env variable LAMMPS_POTENTIALS
------------------------------------------------------------------------- */
FILE *utils::open_potential(const std::string &name, LAMMPS *lmp,
int *auto_convert)
{
auto error = lmp->error;
auto me = lmp->comm->me;
std::string filepath = get_potential_file_path(name);
if (!filepath.empty()) {
std::string unit_style = lmp->update->unit_style;
std::string date = get_potential_date(filepath, "potential");
std::string units = get_potential_units(filepath, "potential");
if (!date.empty() && (me == 0)) {
logmesg(lmp, fmt::format("Reading potential file {} "
"with DATE: {}\n", name, date));
}
if (auto_convert == nullptr) {
if (!units.empty() && (units != unit_style) && (me == 0)) {
error->one(FLERR, fmt::format("Potential file {} requires {} units "
"but {} units are in use", name, units,
unit_style));
return nullptr;
}
} else {
if (units.empty() || units == unit_style) {
*auto_convert = NOCONVERT;
} else {
if ((units == "metal") && (unit_style == "real")
&& (*auto_convert & METAL2REAL)) {
*auto_convert = METAL2REAL;
} else if ((units == "real") && (unit_style == "metal")
&& (*auto_convert & REAL2METAL)) {
*auto_convert = REAL2METAL;
} else {
error->one(FLERR, fmt::format("Potential file {} requires {} units "
"but {} units are in use", name,
units, unit_style));
return nullptr;
}
}
if ((*auto_convert != NOCONVERT) && (me == 0))
error->warning(FLERR, fmt::format("Converting potential file in "
"{} units to {} units",
units, unit_style));
}
return fopen(filepath.c_str(), "r");
}
return nullptr;
}
/* ----------------------------------------------------------------------
convert a timespec ([[HH:]MM:]SS) to seconds
the strings "off" and "unlimited" result in -1.0;
------------------------------------------------------------------------- */
double utils::timespec2seconds(const std::string &timespec)
{
double vals[3];
int i = 0;
// first handle allowed textual inputs
if (timespec == "off") return -1.0;
if (timespec == "unlimited") return -1.0;
vals[0] = vals[1] = vals[2] = 0;
ValueTokenizer values(timespec, ":");
try {
for (i = 0; i < 3; i++) {
if (!values.has_next()) break;
vals[i] = values.next_int();
}
} catch (TokenizerException &e) {
return -1.0;
}
if (i == 3) return (vals[0]*60 + vals[1])*60 + vals[2];
else if (i == 2) return vals[0]*60 + vals[1];
return vals[0];
}
/* ----------------------------------------------------------------------
convert a LAMMPS version date (1Jan01) to a number
------------------------------------------------------------------------- */
int utils::date2num(const std::string &date)
{
std::size_t found = date.find_first_not_of("0123456789 ");
int num = strtol(date.substr(0,found).c_str(),nullptr,10);
auto month = date.substr(found);
found = month.find_first_of("0123456789 ");
num += strtol(month.substr(found).c_str(),nullptr,10)*10000;
if (num < 1000000) num += 20000000;
if (strmatch(month,"^Jan")) num += 100;
else if (strmatch(month,"^Feb")) num += 200;
else if (strmatch(month,"^Mar")) num += 300;
else if (strmatch(month,"^Apr")) num += 400;
else if (strmatch(month,"^May")) num += 500;
else if (strmatch(month,"^Jun")) num += 600;
else if (strmatch(month,"^Jul")) num += 700;
else if (strmatch(month,"^Aug")) num += 800;
else if (strmatch(month,"^Sep")) num += 900;
else if (strmatch(month,"^Oct")) num += 1000;
else if (strmatch(month,"^Nov")) num += 1100;
else if (strmatch(month,"^Dec")) num += 1200;
return num;
}
/* ----------------------------------------------------------------------
* Merge sort part 1: Loop over sublists doubling in size with each iteration.
* Pre-sort small sublists with insertion sort for better overall performance.
------------------------------------------------------------------------- */
void utils::merge_sort(int *index, int num, void *ptr,
int (*comp)(int, int, void *))
{
if (num < 2) return;
int chunk,i,j;
// do insertion sort on chunks of up to 64 elements
chunk = 64;
for (i=0; i < num; i += chunk) {
j = (i+chunk > num) ? num-i : chunk;
insertion_sort(index+i,j,ptr,comp);
}
// already done?
if (chunk >= num) return;
// continue with merge sort on the pre-sorted chunks.
// we need an extra buffer for temporary storage and two
// pointers to operate on, so we can swap the pointers
// rather than copying to the hold buffer in each pass
int *buf = new int[num];
int *dest = index;
int *hold = buf;
while (chunk < num) {
int m;
// swap hold and destination buffer
int *tmp = dest; dest = hold; hold = tmp;
// merge from hold array to destination array
for (i=0; i < num-1; i += 2*chunk) {
j = i + 2*chunk;
if (j > num) j=num;
m = i+chunk;
if (m > num) m=num;
do_merge(dest,hold,i,m,m,j,ptr,comp);
}
// copy all indices not handled by the chunked merge sort loop
for (; i < num ; i++) dest[i] = hold[i];
chunk *= 2;
}
// if the final sorted data is in buf, copy back to index
if (dest == buf) memcpy(index,buf,sizeof(int)*num);
delete[] buf;
}
/* ------------------------------------------------------------------ */
/* ----------------------------------------------------------------------
* Merge sort part 2: Insertion sort for pre-sorting of small chunks
------------------------------------------------------------------------- */
void insertion_sort(int *index, int num, void *ptr,
int (*comp)(int, int, void*))
{
if (num < 2) return;
for (int i=1; i < num; ++i) {
int tmp = index[i];
for (int j=i-1; j >= 0; --j) {
if ((*comp)(index[j],tmp,ptr) > 0) {
index[j+1] = index[j];
} else {
index[j+1] = tmp;
break;
}
if (j == 0) index[0] = tmp;
}
}
}
/* ----------------------------------------------------------------------
* Merge sort part 3: Merge two sublists
------------------------------------------------------------------------- */
static void do_merge(int *idx, int *buf, int llo, int lhi, int rlo, int rhi,
void *ptr, int (*comp)(int, int, void *))
{
int i = llo;
int l = llo;
int r = rlo;
while ((l < lhi) && (r < rhi)) {
if ((*comp)(buf[l],buf[r],ptr) < 0)
idx[i++] = buf[l++];
else idx[i++] = buf[r++];
}
while (l < lhi) idx[i++] = buf[l++];
while (r < rhi) idx[i++] = buf[r++];
}
/* ------------------------------------------------------------------ */
extern "C" {
/* Typedef'd pointer to get abstract datatype. */
typedef struct regex_t *re_t;
/* Compile regex string pattern to a regex_t-array. */
static re_t re_compile(const char *pattern);
/* Find matches of the compiled pattern inside text. */
static int re_matchp(const char *text, re_t pattern);
/* Definitions: */
#define MAX_REGEXP_OBJECTS 30 /* Max number of regex symbols in expression. */
#define MAX_CHAR_CLASS_LEN 40 /* Max length of character-class buffer in. */
enum { UNUSED, DOT, BEGIN, END, QUESTIONMARK, STAR, PLUS,
CHAR, CHAR_CLASS, INV_CHAR_CLASS, DIGIT, NOT_DIGIT,
INTEGER, NOT_INTEGER, FLOAT, NOT_FLOAT,
ALPHA, NOT_ALPHA, WHITESPACE, NOT_WHITESPACE /*, BRANCH */ };
typedef struct regex_t {
unsigned char type; /* CHAR, STAR, etc. */
union {
unsigned char ch; /* the character itself */
unsigned char *ccl; /* OR a pointer to characters in class */
};
} regex_t;
/* Private function declarations: */
static int matchpattern(regex_t *pattern, const char *text);
static int matchcharclass(char c, const char *str);
static int matchstar(regex_t p, regex_t *pattern, const char *text);
static int matchplus(regex_t p, regex_t *pattern, const char *text);
static int matchone(regex_t p, char c);
static int matchdigit(char c);
static int matchint(char c);
static int matchfloat(char c);
static int matchalpha(char c);
static int matchwhitespace(char c);
static int matchmetachar(char c, const char *str);
static int matchrange(char c, const char *str);
static int ismetachar(char c);
/* Semi-public functions: */
int re_match(const char *text, const char *pattern)
{
return re_matchp(text, re_compile(pattern));
}
int re_matchp(const char *text, re_t pattern)
{
if (pattern != 0) {
if (pattern[0].type == BEGIN) {
return ((matchpattern(&pattern[1], text)) ? 0 : -1);
} else {
int idx = -1;
do {
idx += 1;
if (matchpattern(pattern, text)) {
if (text[0] == '\0')
return -1;
return idx;
}
}
while (*text++ != '\0');
}
}
return -1;
}
re_t re_compile(const char *pattern)
{
/* The sizes of the two static arrays below substantiates the static RAM usage of this module.
MAX_REGEXP_OBJECTS is the max number of symbols in the expression.
MAX_CHAR_CLASS_LEN determines the size of buffer for chars in all char-classes in the expression. */
static regex_t re_compiled[MAX_REGEXP_OBJECTS];
static unsigned char ccl_buf[MAX_CHAR_CLASS_LEN];
int ccl_bufidx = 1;
char c; /* current char in pattern */
int i = 0; /* index into pattern */
int j = 0; /* index into re_compiled */
while (pattern[i] != '\0' && (j+1 < MAX_REGEXP_OBJECTS)) {
c = pattern[i];
switch (c) {
/* Meta-characters: */
case '^': { re_compiled[j].type = BEGIN; } break;
case '$': { re_compiled[j].type = END; } break;
case '.': { re_compiled[j].type = DOT; } break;
case '*': { re_compiled[j].type = STAR; } break;
case '+': { re_compiled[j].type = PLUS; } break;
case '?': { re_compiled[j].type = QUESTIONMARK; } break;
/* Escaped character-classes (\s \w ...): */
case '\\': {
if (pattern[i+1] != '\0') {
/* Skip the escape-char '\\' */
i += 1;
/* ... and check the next */
switch (pattern[i]) {
/* Meta-character: */
case 'd': { re_compiled[j].type = DIGIT; } break;
case 'D': { re_compiled[j].type = NOT_DIGIT; } break;
case 'i': { re_compiled[j].type = INTEGER; } break;
case 'I': { re_compiled[j].type = NOT_INTEGER; } break;
case 'f': { re_compiled[j].type = FLOAT; } break;
case 'F': { re_compiled[j].type = NOT_FLOAT; } break;
case 'w': { re_compiled[j].type = ALPHA; } break;
case 'W': { re_compiled[j].type = NOT_ALPHA; } break;
case 's': { re_compiled[j].type = WHITESPACE; } break;
case 'S': { re_compiled[j].type = NOT_WHITESPACE; } break;
/* Escaped character, e.g. '.' or '$' */
default: {
re_compiled[j].type = CHAR;
re_compiled[j].ch = pattern[i];
} break;
}
}
/* '\\' as last char in pattern -> invalid regular expression. */
} break;
/* Character class: */
case '[': {
/* Remember where the char-buffer starts. */
int buf_begin = ccl_bufidx;
/* Look-ahead to determine if negated */
if (pattern[i+1] == '^') {
re_compiled[j].type = INV_CHAR_CLASS;
i += 1; /* Increment i to avoid including '^' in the char-buffer */
} else {
re_compiled[j].type = CHAR_CLASS;
}
/* Copy characters inside [..] to buffer */
while ((pattern[++i] != ']') && (pattern[i] != '\0')) {
/* Missing ] */
if (pattern[i] == '\\') {
if (ccl_bufidx >= MAX_CHAR_CLASS_LEN - 1) {
return 0;
}
ccl_buf[ccl_bufidx++] = pattern[i++];
} else if (ccl_bufidx >= MAX_CHAR_CLASS_LEN) {
return 0;
}
ccl_buf[ccl_bufidx++] = pattern[i];
}
if (ccl_bufidx >= MAX_CHAR_CLASS_LEN) {
/* Catches cases such as [00000000000000000000000000000000000000][ */
return 0;
}
/* Null-terminate string end */
ccl_buf[ccl_bufidx++] = 0;
re_compiled[j].ccl = &ccl_buf[buf_begin];
} break;
/* Other characters: */
default: {
re_compiled[j].type = CHAR;
re_compiled[j].ch = c;
} break;
}
i += 1;
j += 1;
}
/* 'UNUSED' is a sentinel used to indicate end-of-pattern */
re_compiled[j].type = UNUSED;
return (re_t) re_compiled;
}
/* Private functions: */
static int matchdigit(char c)
{
return ((c >= '0') && (c <= '9'));
}
static int matchint(char c)
{
return (matchdigit(c) || (c == '-') || (c == '+'));
}
static int matchfloat(char c)
{
return (matchint(c) || (c == '.') || (c == 'e') || (c == 'E'));
}
static int matchalpha(char c)
{
return ((c >= 'a') && (c <= 'z')) || ((c >= 'A') && (c <= 'Z'));
}
static int matchwhitespace(char c)
{
return ((c == ' ') || (c == '\t') || (c == '\n') || (c == '\r') || (c == '\f') || (c == '\v'));
}
static int matchalphanum(char c)
{
return ((c == '_') || matchalpha(c) || matchdigit(c));
}
static int matchrange(char c, const char *str)
{
return ((c != '-') && (str[0] != '\0')
&& (str[0] != '-') && (str[1] == '-')
&& (str[1] != '\0') && (str[2] != '\0')
&& ((c >= str[0]) && (c <= str[2])));
}
static int ismetachar(char c)
{
return ((c == 's') || (c == 'S')
|| (c == 'w') || (c == 'W')
|| (c == 'd') || (c == 'D'));
}
static int matchmetachar(char c, const char *str)
{
switch (str[0]) {
case 'd': return matchdigit(c);
case 'D': return !matchdigit(c);
case 'i': return matchint(c);
case 'I': return !matchint(c);
case 'f': return matchfloat(c);
case 'F': return !matchfloat(c);
case 'w': return matchalphanum(c);
case 'W': return !matchalphanum(c);
case 's': return matchwhitespace(c);
case 'S': return !matchwhitespace(c);
default: return (c == str[0]);
}
}
static int matchcharclass(char c, const char *str)
{
do {
if (matchrange(c, str)) {
return 1;
} else if (str[0] == '\\') {
/* Escape-char: increment str-ptr and match on next char */
str += 1;
if (matchmetachar(c, str)) {
return 1;
} else if ((c == str[0]) && !ismetachar(c)) {
return 1;
}
} else if (c == str[0]) {
if (c == '-') {
return ((str[-1] == '\0') || (str[1] == '\0'));
} else {
return 1;
}
}
}
while (*str++ != '\0');
return 0;
}
static int matchone(regex_t p, char c)
{
switch (p.type) {
case DOT: return 1;
case CHAR_CLASS: return matchcharclass(c, (const char *)p.ccl);
case INV_CHAR_CLASS: return !matchcharclass(c, (const char *)p.ccl);
case DIGIT: return matchdigit(c);
case NOT_DIGIT: return !matchdigit(c);
case INTEGER: return matchint(c);
case NOT_INTEGER: return !matchint(c);
case FLOAT: return matchfloat(c);
case NOT_FLOAT: return !matchfloat(c);
case ALPHA: return matchalphanum(c);
case NOT_ALPHA: return !matchalphanum(c);
case WHITESPACE: return matchwhitespace(c);
case NOT_WHITESPACE: return !matchwhitespace(c);
default: return (p.ch == c);
}
}
static int matchstar(regex_t p, regex_t *pattern, const char *text)
{
do {
if (matchpattern(pattern, text))
return 1;
}
while ((text[0] != '\0') && matchone(p, *text++));
return 0;
}
static int matchplus(regex_t p, regex_t *pattern, const char *text)
{
while ((text[0] != '\0') && matchone(p, *text++)) {
if (matchpattern(pattern, text))
return 1;
}
return 0;
}
static int matchquestion(regex_t p, regex_t *pattern, const char *text)
{
if (p.type == UNUSED)
return 1;
if (matchpattern(pattern, text))
return 1;
if (*text && matchone(p, *text++))
return matchpattern(pattern, text);
return 0;
}
/* Iterative matching */
static int matchpattern(regex_t *pattern, const char *text)
{
do {
if ((pattern[0].type == UNUSED) || (pattern[1].type == QUESTIONMARK)) {
return matchquestion(pattern[0], &pattern[2], text);
} else if (pattern[1].type == STAR) {
return matchstar(pattern[0], &pattern[2], text);
} else if (pattern[1].type == PLUS) {
return matchplus(pattern[0], &pattern[2], text);
} else if ((pattern[0].type == END) && pattern[1].type == UNUSED) {
return (text[0] == '\0');
}
}
while ((text[0] != '\0') && matchone(*pattern++, *text++));
return 0;
}
}
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