Reads and analyzes settings file and stores parameters. More...

#include <Settings.h>

Inheritance diagram for nnp::settings::Settings:

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Public Types
typedef std::multimap< std::string, std::pair< std::string, std::size_t > >	KeyMap

typedef std::pair< KeyMap::const_iterator, KeyMap::const_iterator >	KeyRange

typedef std::map< std::string, std::shared_ptr< Key > > const	KeywordList

Public Member Functions
std::string	operator[] (std::string const &keyword) const
	Overload [] operator. More...

std::size_t	loadFile (std::string const &fileName="input.nn")
	Load a file with settings. More...

bool	keywordExists (Key const &key, bool const exact=false) const override

bool	keywordExists (std::string const &keyword, bool exact=false) const
	Check if keyword is present in settings file. More...

std::string	keywordCheck (std::string const &keyword) const
	Check for keyword and alternatives, throw exception if not present. More...

std::string	getValue (Key const &key) const override

std::string	getValue (std::string const &keyword) const
	Get value for given keyword. More...

KeyRange	getValues (std::string const &keyword) const
	Get all keyword-value pairs for given keyword. More...

std::vector< std::string >	info () const
	Get logged information about settings file. More...

std::vector< std::string >	getSettingsLines () const
	Get complete settings file. More...

void	writeSettingsFile (std::ofstream *const &file, std::map< std::size_t, std::string > const &replacements={}) const
	Write complete settings file. More...

virtual bool	keywordExists (Key const &key, bool const exact=false) const =0

virtual std::string	getValue (Key const &key) const =0

Private Member Functions
void	readFile ()
	Read file once and save all lines in lines vector. More...

std::size_t	parseLines ()
	Parse lines and create contents map. More...

std::pair< std::size_t, std::size_t >	sanityCheck ()
	Check if all keywords are in known-keywords database and for duplicates. More...

Private Attributes
std::vector< std::string >	lines
	Vector of all lines in settings file. More...

std::vector< std::string >	log
	Vector with log lines. More...

KeyMap	contents
	Map containing all keyword-value pairs. More...

std::string	fileName
	Settings file name. More...

Static Private Attributes
static KeywordList	knownKeywords = createKnownKeywordsMap()
	Map containing all known keywords and a description. More...

Detailed Description

Reads and analyzes settings file and stores parameters.

Definition at line 37 of file Settings.h.

Member Typedef Documentation

◆ KeyMap

typedef std::multimap<std::string, std::pair<std::string, std::size_t> > nnp::settings::Settings::KeyMap

Definition at line 42 of file Settings.h.

◆ KeyRange

typedef std::pair<KeyMap::const_iterator, KeyMap::const_iterator> nnp::settings::Settings::KeyRange

Definition at line 44 of file Settings.h.

◆ KeywordList

typedef std::map<std::string, std::shared_ptr<Key> > const nnp::settings::Settings::KeywordList

Definition at line 46 of file Settings.h.

Member Function Documentation

◆ operator[]()

string Settings::operator[] ( std::string const & keyword ) const

Overload [] operator.

Parameters

[in] keyword Keyword string.

Returns: Value string corresponding to keyword.

Internally calls getValue().

Definition at line 181 of file Settings.cpp.

{
    return getValue(keyword);
}

References getValue().

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◆ loadFile()

size_t Settings::loadFile ( std::string const & fileName = "input.nn" )

Load a file with settings.

Parameters

[in] fileName Name of file containing settings.

Returns: Number of critical problems detected.

Definition at line 187 of file Settings.cpp.

{
    this->fileName = fileName;
 
    readFile();
    return parseLines();
}

References fileName, parseLines(), and readFile().

Referenced by nnp::Mode::loadSettingsFile().

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◆ keywordExists() [1/2]

bool Settings::keywordExists	(	Key const &	key,
		bool const	exact = `false`
	)		const

overridevirtual

Implements nnp::settings::ISettings.

Definition at line 194 of file Settings.cpp.

{
    return keywordExists(key.getMainKeyword(), exact);
}

References nnp::settings::Key::getMainKeyword(), and keywordExists().

Referenced by nnp::Training::dataSetNormalization(), nnp::Training::initializeWeights(), keywordCheck(), keywordExists(), nnp::Mode::loadSettingsFile(), nnp::Training::randomizeNeuralNetworkWeights(), nnp::Training::setStage(), nnp::Mode::settingsKeywordExists(), nnp::Mode::setupElectrostatics(), nnp::Mode::setupElements(), nnp::Training::setupFileOutput(), nnp::Mode::setupNeuralNetwork(), nnp::Mode::setupNormalization(), nnp::Training::setupSelectionMode(), nnp::Mode::setupSymmetryFunctionScaling(), nnp::Training::setupTraining(), and nnp::Training::setupUpdatePlan().

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◆ keywordExists() [2/2]

bool Settings::keywordExists	(	std::string const &	keyword,
		bool	exact = `false`
	)		const

Check if keyword is present in settings file.

Parameters

[in]	keyword	Keyword string.
[in]	exact	If `True` check only for exact spelling, no alternative keywords allowed.

Returns: True if keyword exists, False otherwise.

Note: This throws an error if the keyword is not in the list of known keywords.

Definition at line 199 of file Settings.cpp.

{
    if (knownKeywords.find(keyword) == knownKeywords.end())
    {
        throw runtime_error("ERROR: Not in the list of allowed keyword: \"" +
                            keyword + "\".\n");
    }
    if (exact || knownKeywords.at(keyword)->hasUniqueKeyword())
    {
        return (contents.find(keyword) != contents.end());
    }
    else
    {
        for (auto alternative : *knownKeywords.at(keyword))
        {
            if (contents.find(alternative) != contents.end()) return true;
        }
    }
 
    return false;
}

References contents, and knownKeywords.

◆ keywordCheck()

string Settings::keywordCheck ( std::string const & keyword ) const

Check for keyword and alternatives, throw exception if not present.

Parameters

[in] keyword Original keyword for which alternatives should be searched.

Returns: Keyword or alternative found in file contents.

Definition at line 221 of file Settings.cpp.

{
    bool exists = keywordExists(keyword, false);
    bool unique = knownKeywords.at(keyword)->hasUniqueKeyword();
    if (!exists)
    {
        if (unique)
        {
            throw std::runtime_error("ERROR: Keyword \"" + keyword
                                     + "\" not found.\n");
        }
        else
        {
            throw std::runtime_error("ERROR: Neither keyword \"" + keyword
                                     + "\" nor alternative keywords found.\n");
        }
    }
 
    bool exact = keywordExists(keyword, true);
    if (!exact)
    {
        for (auto const& alt : *knownKeywords.at(keyword))
        {
            if (contents.find(alt) != contents.end()) return alt;
        }
    }
 
    return keyword;
}

References contents, keywordExists(), and knownKeywords.

Referenced by getValue(), and getValues().

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◆ getValue() [1/2]

string Settings::getValue ( Key const & key ) const

overridevirtual

Implements nnp::settings::ISettings.

Definition at line 251 of file Settings.cpp.

{
    return contents.find(key.getMainKeyword())->second.first;
}

References contents, and nnp::settings::Key::getMainKeyword().

Referenced by operator[](), and nnp::Mode::settingsGetValue().

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◆ getValue() [2/2]

string Settings::getValue ( std::string const & keyword ) const

Get value for given keyword.

Parameters

[in] keyword Keyword string.

Returns: Value string corresponding to keyword.

If keyword is present multiple times only the value of the first keyword-value pair is returned (use getValues() instead).

Definition at line 256 of file Settings.cpp.

{
    return contents.find(keywordCheck(keyword))->second.first;
}

References contents, and keywordCheck().

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◆ getValues()

Settings::KeyRange Settings::getValues ( std::string const & keyword ) const

Get all keyword-value pairs for given keyword.

Parameters

[in] keyword Keyword string.

Returns: Pair with begin and end values for iteration.

Useful if keyword appears multiple times. Returns a pair representing begin and end for an iterator over all corresponding keyword-value pairs. Use like this:

Settings* s = new Settings("input.nn");
Settings::KeyRange r = s->getValues("symfunction_short");
for (Settings::KeyMap::const_iterator i = r.first; i != r.second; i++)
{
    cout << "keyword: " << i->first
         << " value: " << i->second.first
         << " line : " << i->second.second << "\n";
}

Definition at line 261 of file Settings.cpp.

{
    return contents.equal_range(keywordCheck(keyword));
}

References contents, and keywordCheck().

Referenced by nnp::Mode::setupElectrostatics(), nnp::Mode::setupElements(), nnp::Mode::setupNeuralNetwork(), and nnp::Mode::setupSymmetryFunctions().

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◆ info()

vector< string > Settings::info ( ) const

Get logged information about settings file.

Returns: Vector with log lines.

Definition at line 266 of file Settings.cpp.

{
    return log;
}

References log.

Referenced by nnp::Mode::loadSettingsFile().

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◆ getSettingsLines()

vector< string > Settings::getSettingsLines ( ) const

Get complete settings file.

Returns: Vector with settings file lines.

Definition at line 271 of file Settings.cpp.

{
    return lines;
}

References lines.

Referenced by nnp::Training::dataSetNormalization(), and nnp::Mode::writePrunedSettingsFile().

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◆ writeSettingsFile()

void Settings::writeSettingsFile	(	std::ofstream *const &	file,
		std::map< std::size_t, std::string > const &	replacements = `{}`
	)		const

Write complete settings file.

Parameters

[in,out]	file	Settings file.
[in]	replacements	Map of line numbers with alternative content.

Definition at line 301 of file Settings.cpp.

{
    if (!file->is_open())
    {
        runtime_error("ERROR: Could not write to file.\n");
    }
 
    size_t i = 0;
    for (auto const& l : lines)
    {
        if (replacements.find(i) != replacements.end())
        {
            (*file) << replacements.at(i);
        }
        else (*file) << l << '\n';
        i++;
    }
 
    return;
}

References lines.

Referenced by nnp::Training::dataSetNormalization(), and nnp::Mode::writeSettingsFile().

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◆ readFile()

void Settings::readFile ( )

private

Read file once and save all lines in lines vector.

Definition at line 276 of file Settings.cpp.

{
    ifstream file;
    string   line;
 
    log.push_back(strpr("Settings file name: %s\n", fileName.c_str()));
    file.open(fileName.c_str());
    if (!file.is_open())
    {
        throw runtime_error("ERROR: Could not open file: \"" + fileName
                            + "\".\n");
    }
 
    while (getline(file, line))
    {
        lines.push_back(line);
    }
 
    file.close();
 
    log.push_back(strpr("Read %zu lines.\n", lines.size()));
 
    return;
}

References fileName, lines, log, and nnp::strpr().

Referenced by loadFile().

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◆ parseLines()

size_t Settings::parseLines ( )

private

Parse lines and create contents map.

Returns: Number of critical problems detected.

Definition at line 323 of file Settings.cpp.

{
    for (size_t i = 0; i < lines.size(); ++i)
    {
        string line = lines.at(i);
 
        // ignore empty and comment lines
        if (line.empty())
        {
            continue;
        }
        // check for empty lines in Windows format
        if (line == "\r")
        {
            continue;
        }
        if (line.find('#') != string::npos)
        {
            line.erase(line.find('#'));
        }
        if (line.find('!') != string::npos)
        {
            line.erase(line.find('!'));
        }
        if (line.find_first_not_of(' ') == string::npos)
        {
            continue;
        }
 
        // remove leading and trailing whitespaces and trim separating spaces
        line = reduce(line);
 
        // find separator position
        size_t const separatorPosition = line.find_first_of(" ");
        string key;
        pair<string, size_t> value;
 
        if (separatorPosition == string::npos)
        {
            // first check for single keyword without value
            key = line;
            value = pair<string, size_t>("", i);
        }
        else
        {
            // one or more arguments
            key = line.substr(0, separatorPosition);
            value = pair<string, size_t>(line.erase(0, separatorPosition + 1),
                                         i);
        }
 
        contents.insert(pair<string, pair<string, size_t> >(key, value));
    }
 
    size_t numProblems = 0;
    size_t numCritical = 0;
    tie(numProblems, numCritical) = sanityCheck();
    if (numProblems > 0)
    {
        log.push_back(strpr("WARNING: %zu problems detected (%zu critical).\n",
                            numProblems, numCritical));
    }
 
    log.push_back(strpr("Found %zu lines with keywords.\n", contents.size()));
 
    return numCritical;
}

References contents, lines, log, nnp::reduce(), sanityCheck(), and nnp::strpr().

Referenced by loadFile().

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◆ sanityCheck()

pair< size_t, size_t > Settings::sanityCheck ( )

private

Check if all keywords are in known-keywords database and for duplicates.

Returns: Number of detected/critical problems.

Definition at line 391 of file Settings.cpp.

{
    size_t countProblems = 0;
    size_t countCritical = 0;
 
    // check for unknown keywords
    for (multimap<string, pair<string, size_t> >::const_iterator
         it = contents.begin(); it != contents.end(); ++it)
    {
        if (knownKeywords.find((*it).first) == knownKeywords.end())
        {
            countProblems++;
            log.push_back(strpr(
                "WARNING: Unknown keyword \"%s\" at line %zu.\n",
                (*it).first.c_str(),
                (*it).second.second + 1));
        }
    }
 
    // check for multiple instances of known keywords (with exceptions)
    for (KeywordList::const_iterator it = knownKeywords.begin();
         it != knownKeywords.end(); ++it)
    {
        if (contents.count((*it).first) > 1
            && (*it).first != "symfunction"
            && (*it).first != "symfunction_short"
            && (*it).first != "atom_energy"
            && (*it).first != "element_nodes_short"
            && (*it).first != "fixed_gausswidth"
            && (*it).first != "initial_hardness")
        {
            countProblems++;
            countCritical++;
            log.push_back(strpr(
                "WARNING (CRITICAL): Multiple instances of \"%s\" detected.\n",
                (*it).first.c_str()));
        }
    }
 
    // Check for usage of multiple keyword versions.
    for (KeywordList::const_iterator it = knownKeywords.begin();
         it != knownKeywords.end(); ++it)
    {
        if (it->second->hasUniqueKeyword()) continue;
        vector<string> duplicates;
        for (auto keyword : *it->second)
        {
            if (contents.find(keyword) != contents.end())
            {
                duplicates.push_back(keyword);
            }
        }
        if (duplicates.size() > 1)
        {
            countProblems++;
            countCritical++;
            log.push_back(strpr(
                "WARNING (CRITICAL): Multiple alternative versions of keyword "
                "\"%s\" detected:.\n", (*it).first.c_str()));
            for (auto d : duplicates)
            {
                log.push_back(strpr(
                    "                    - \"%s\"\n", d.c_str()));
            }
        }
    }
 
    return make_pair(countProblems, countCritical);
}

References contents, d, knownKeywords, log, and nnp::strpr().

Referenced by parseLines().

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Member Data Documentation

◆ lines

std::vector<std::string> nnp::settings::Settings::lines

private

Vector of all lines in settings file.

Definition at line 143 of file Settings.h.

Referenced by getSettingsLines(), parseLines(), readFile(), and writeSettingsFile().

◆ log

std::vector<std::string> nnp::settings::Settings::log

private

Vector with log lines.

Definition at line 145 of file Settings.h.

Referenced by info(), parseLines(), readFile(), and sanityCheck().

◆ contents

KeyMap nnp::settings::Settings::contents

private

Map containing all keyword-value pairs.

Definition at line 147 of file Settings.h.

Referenced by getValue(), getValues(), keywordCheck(), keywordExists(), parseLines(), and sanityCheck().

◆ knownKeywords

Settings::KeywordList Settings::knownKeywords = createKnownKeywordsMap()

staticprivate

Map containing all known keywords and a description.

Definition at line 149 of file Settings.h.

Referenced by keywordCheck(), keywordExists(), and sanityCheck().

◆ fileName

std::string nnp::settings::Settings::fileName

private

Settings file name.

Definition at line 151 of file Settings.h.

Referenced by loadFile(), and readFile().

The documentation for this class was generated from the following files:

/home/runner/work/n2p2/n2p2/src/libnnp/Settings.h
/home/runner/work/n2p2/n2p2/src/libnnp/Settings.cpp

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Typedef Documentation

◆ KeyMap

◆ KeyRange

◆ KeywordList

Member Function Documentation

◆ operator[]()

◆ loadFile()

◆ keywordExists() [1/2]

◆ keywordExists() [2/2]

◆ keywordCheck()

◆ getValue() [1/2]

◆ getValue() [2/2]

◆ getValues()

◆ info()

◆ getSettingsLines()

◆ writeSettingsFile()

◆ readFile()

◆ parseLines()

◆ sanityCheck()

Member Data Documentation

◆ lines

◆ log

◆ contents

◆ knownKeywords

◆ fileName