ComChemKit API¶

Comprehensive API documentation for the ComChemKit.

Class Hierarchy¶

- Namespace calc
  - Struct ThermoResult
- Namespace symmetry
  - Struct SymmetryData
  - Struct Vector3D
  - Class SymmetryDetector
- Namespace ThermoInterface
  - Struct ThermoResult
  - Struct ThermoSettings
- Namespace util
  - Enum QuantumChemistryProgram
- Struct Atom
- Struct CheckSummary
- Struct CommandContext
- Struct ConfigValue
- Struct CreateSummary
- Struct ExecutionConfig
- Struct ExtractSummary
- Struct FileCreationResult
- Struct HighLevelEnergyData
- Struct JobCheckResult
- Struct JobResources
- Struct ProcessingContext
- Struct Result
- Struct SystemData
- Class CheckerCommand
- Class CommandParser
- Class CommandRegistry
- Class ConfigManager
- Class CoordExtractor
- Class CreateInput
- Class CreateInputCommand
- Class ExtractCommand
- Class ExtractCoordsCommand
- Class FileHandleManager
  - Class FileHandleManager::FileGuard
- Class HighLevelCommand
- Class HighLevelEnergyCalculator
- Class ICommand
- Class JobChecker
- Class JobSchedulerDetector
- Class LoadFile
- Class MemoryMonitor
- Class ParameterParser
- Class ThermoCommand
- Class ThreadPool
- Class ThreadSafeErrorCollector
- Enum BavPreset
- Enum CalculationType
- Enum CommandType
- Enum ConfigCategory
- Enum FileReadMode
- Enum JobStatus
- Enum LowVibTreatment
- Enum OMPStrategy
- Enum SchedulerType

File Hierarchy¶

- Directory commands
  - File checker_command.h
  - File command_registry.h
  - File command_system.h
  - File create_input_command.h
  - File extract_command.h
  - File extract_coords_command.h
  - File high_level_command.h
  - File icommand.h
  - File signal_handler.h
  - File thermo_command.h
- Directory extraction
  - File coord_extractor.h
  - File qc_extractor.h
- Directory high_level
  - File high_level_energy.h
- Directory input_gen
  - File create_input.h
  - File parameter_parser.h
- Directory job_management
  - File job_checker.h
  - File job_scheduler.h
- Directory thermo
  - File atommass.h
  - File calc.h
  - File chemsys.h
  - File help_utils.h
  - File loadfile.h
  - File omp_config.h
  - File symmetry.h
  - File thermo.h
  - File util.h
  - File version.h
- Directory ui
  - File help_utils.h
  - File interactive_mode.h
- Directory utilities
  - File config_manager.h
  - File loadfile.h
  - File metadata.h
  - File utils.h
  - File version.h

Full API¶

Classes and Structs¶

Struct Atom
- Struct Documentation
  - Atom
    - index
    - x
    - y
    - z
    - mass

Struct CheckSummary
- Struct Documentation
  - CheckSummary

Struct CommandContext
- Struct Documentation
  - CommandContext

Struct ConfigValue
- Struct Documentation
  - ConfigValue

Struct CreateSummary
- Struct Documentation
  - CreateSummary

Struct ExecutionConfig
- Struct Documentation
  - ExecutionConfig

Struct ExtractSummary
- Struct Documentation
  - ExtractSummary

Struct FileCreationResult
- Struct Documentation
  - FileCreationResult

Struct HighLevelEnergyData
- Struct Documentation
  - HighLevelEnergyData

Struct JobCheckResult
- Struct Documentation
  - JobCheckResult

Struct JobResources
- Struct Documentation
  - JobResources

Struct ProcessingContext
- Struct Documentation
  - ProcessingContext

Struct Result
- Struct Documentation
  - Result
    - file_name
    - etgkj
    - lf
    - GibbsFreeHartree
    - nucleare
    - scf
    - zpe
    - status
    - phaseCorr
    - copyright_count

Struct SymmetryData
- Struct Documentation
  - symmetry::SymmetryData
    - max_pgs
    - max_subgroups
    - pgsymb
    - nsgb
    - nsgr
    - sg
    - ng
    - cg

Struct Vector3D
- Struct Documentation
  - symmetry::Vector3D
    - Vector3D()
    - Vector3D()
    - Vector3D()
    - data()
    - data()
    - x
    - y
    - z

Struct ThermoResult
- Struct Documentation
  - ThermoInterface::ThermoResult

Class CheckerCommand
- Inheritance Relationships
  - Base Type
- Class Documentation
  - CheckerCommand

Class CommandParser
- Class Documentation
  - CommandParser

Class CommandRegistry
- Class Documentation
  - CommandRegistry

Class ConfigManager
- Class Documentation
  - ConfigManager
    - ConfigManager()

Class CoordExtractor
- Class Documentation
  - CoordExtractor

Class CreateInputCommand
- Inheritance Relationships
  - Base Type
- Class Documentation
  - CreateInputCommand

Class ExtractCommand
- Inheritance Relationships
  - Base Type
- Class Documentation
  - ExtractCommand

Class ExtractCoordsCommand
- Inheritance Relationships
  - Base Type
- Class Documentation
  - ExtractCoordsCommand

Class FileHandleManager
- Nested Relationships
  - Nested Types
- Class Documentation
  - FileHandleManager

Class FileHandleManager::FileGuard
- Nested Relationships
- Class Documentation
  - FileHandleManager::FileGuard

Class HighLevelCommand
- Inheritance Relationships
  - Base Type
- Class Documentation
  - HighLevelCommand

Class HighLevelEnergyCalculator
- Class Documentation
  - HighLevelEnergyCalculator
    - HighLevelEnergyCalculator()
    - HighLevelEnergyCalculator()

Class ICommand
- Inheritance Relationships
  - Derived Types
- Class Documentation
  - ICommand

Class JobChecker
- Class Documentation
  - JobChecker
    - JobChecker()

Class JobSchedulerDetector
- Class Documentation
  - JobSchedulerDetector

Class LoadFile
- Class Documentation
  - LoadFile

Class MemoryMonitor
- Class Documentation
  - MemoryMonitor

Class ParameterParser
- Class Documentation
  - ParameterParser

Class SymmetryDetector
- Class Documentation
  - symmetry::SymmetryDetector
    - detectPG()
    - PGname2rotsym()
    - ncenter
    - a
    - a_index
    - PGnameinit
    - PGname
    - rotsym

Class ThermoCommand
- Inheritance Relationships
  - Base Type
- Class Documentation
  - ThermoCommand

Class ThreadPool
- Class Documentation
  - ThreadPool

Class ThreadSafeErrorCollector
- Class Documentation
  - ThreadSafeErrorCollector

Enums¶

Enum BavPreset
- Enum Documentation
  - BavPreset
    - QChem
    - Grimme

Enum CalculationType
- Enum Documentation
  - CalculationType

Enum CommandType
- Enum Documentation
  - CommandType

Enum ConfigCategory
- Enum Documentation
  - ConfigCategory

Enum FileReadMode
- Enum Documentation
  - FileReadMode
    - FULL
    - TAIL
    - SMART

Enum JobStatus
- Enum Documentation
  - JobStatus

Enum LowVibTreatment
- Enum Documentation
  - LowVibTreatment

Enum OMPStrategy
- Enum Documentation
  - OMPStrategy
    - Outer
    - Inner

Enum SchedulerType
- Enum Documentation
  - SchedulerType
    - NONE
    - SLURM
    - PBS
    - SGE
    - LSF
    - UNKNOWN_CLUSTER

Enum QuantumChemistryProgram
- Enum Documentation
  - QuantumChemistryProgram
    - Unknown
    - Gaussian
    - Orca
    - Gamess
    - Nwchem
    - Cp2k
    - Xtb
    - Vasp
    - Otm
    - QChem

Functions¶

Function atommass::initmass
- Function Documentation
  - initmass()

Function bavPresetName
- Function Documentation
  - bavPresetName()

Function bavPresetValue
- Function Documentation
  - bavPresetValue()

Function calc::calcinertia
- Function Documentation
  - calcinertia()

Function calc::calcthermo(const SystemData&, double, double)
- Function Documentation
  - calcthermo()

Function calc::calcthermo(const SystemData&, double, double, double&, double&, double&, double&, double&, double&, double&, double&)
- Function Documentation
  - calcthermo()

Function calc::ensemble
- Function Documentation
  - ensemble()

Function calc::file_exists
- Function Documentation
  - file_exists()

Function calc::getGconc
- Function Documentation
  - getGconc()

Function calc::getvibcontri(const SystemData&, int, double, double&, double&, double&, double&)
- Function Documentation
  - getvibcontri()

Function calc::getvibcontri(const SystemData&, double, double&, double&, double&, double&)
- Function Documentation
  - getvibcontri()

Function calc::showthermo
- Function Documentation
  - showthermo()

Function calc::showvibdetail
- Function Documentation
  - showvibdetail()

Function calculateSafeMemoryLimit
- Function Documentation

Function calculateSafeThreadCount
- Function Documentation

Function ComChemKit::get_full_version
- Function Documentation

Function ComChemKit::get_header_info
- Function Documentation

Function ComChemKit::get_version
- Function Documentation

Function ComChemKit::get_version_info
- Function Documentation

Function ComChemKit::is_version_at_least
- Function Documentation

Function compareResults
- Function Documentation

Function configure_openmp
- Function Documentation
  - configure_openmp()

Function ConfigUtils::bool_to_string
- Function Documentation

Function ConfigUtils::file_exists
- Function Documentation

Function ConfigUtils::get_config_search_paths
- Function Documentation

Function ConfigUtils::get_config_version
- Function Documentation

Function ConfigUtils::get_executable_directory
- Function Documentation

Function ConfigUtils::is_readable
- Function Documentation

Function ConfigUtils::is_valid_concentration
- Function Documentation

Function ConfigUtils::is_valid_extension
- Function Documentation

Function ConfigUtils::is_valid_file_size
- Function Documentation

Function ConfigUtils::is_valid_pressure
- Function Documentation

Function ConfigUtils::is_valid_temperature
- Function Documentation

Function ConfigUtils::is_valid_thread_count
- Function Documentation

Function ConfigUtils::is_writable
- Function Documentation

Function ConfigUtils::join_strings
- Function Documentation

Function ConfigUtils::migrate_config_if_needed
- Function Documentation

Function ConfigUtils::split_string
- Function Documentation

Function ConfigUtils::string_to_bool
- Function Documentation

Function detect_physical_cores
- Function Documentation
  - detect_physical_cores()

Function detect_scheduler_cpus
- Function Documentation
  - detect_scheduler_cpus()

Function execute_directory_command
- Function Documentation
  - execute_directory_command()

Function execute_utility_command
- Function Documentation
  - execute_utility_command()

Function extract
- Function Documentation

Function findLogFiles()
- Function Documentation

Function findLogFiles()
- Function Documentation

Function findLogFiles()
- Function Documentation

Function findLogFiles()
- Function Documentation

Function formatMemorySize
- Function Documentation

Function get_default_threads
- Function Documentation
  - get_default_threads()

Function HelpUtils::create_default_config
- Function Documentation
  - create_default_config()

Function HelpUtils::print_command_help
- Function Documentation
  - print_command_help()

Function HelpUtils::print_config_help
- Function Documentation
  - print_config_help()

Function HelpUtils::print_help
- Function Documentation
  - print_help()

Function HighLevelEnergyUtils::extract_frequencies
- Function Documentation

Function HighLevelEnergyUtils::find_lowest_frequency
- Function Documentation

Function HighLevelEnergyUtils::get_current_directory_name
- Function Documentation

Function HighLevelEnergyUtils::hartree_to_ev
- Function Documentation

Function HighLevelEnergyUtils::hartree_to_kj_mol
- Function Documentation

Function HighLevelEnergyUtils::is_valid_high_level_directory()
- Function Documentation

Function HighLevelEnergyUtils::is_valid_high_level_directory()
- Function Documentation

Function HighLevelEnergyUtils::parse_energy_value
- Function Documentation

Function HighLevelEnergyUtils::validate_concentration
- Function Documentation

Function HighLevelEnergyUtils::validate_energy_data
- Function Documentation

Function HighLevelEnergyUtils::validate_temperature
- Function Documentation

Function is_directory_command
- Function Documentation
  - is_directory_command()

Function is_shell_command
- Function Documentation
  - is_shell_command()

Function is_utility_command
- Function Documentation
  - is_utility_command()

Function JobCheckerUtils::file_exists
- Function Documentation

Function JobCheckerUtils::get_file_extension
- Function Documentation

Function JobCheckerUtils::is_valid_log_file
- Function Documentation

Function Metadata::header
- Function Documentation
  - header()

Function omp_get_level
- Function Documentation
  - omp_get_level()

Function omp_get_max_threads
- Function Documentation
  - omp_get_max_threads()

Function omp_get_num_threads
- Function Documentation
  - omp_get_num_threads()

Function omp_get_thread_num
- Function Documentation
  - omp_get_thread_num()

Function omp_set_num_threads
- Function Documentation
  - omp_set_num_threads()

Function printJobResourceInfo
- Function Documentation

Function printResourceUsage
- Function Documentation

Function processAndOutputResults
- Function Documentation

Function run_interactive_loop
- Function Documentation
  - run_interactive_loop()

Function safe_stod
- Function Documentation

Function safe_stoi
- Function Documentation

Function safe_stoul
- Function Documentation

Function select_strategy
- Function Documentation
  - select_strategy()

Function setup_signal_handlers
- Function Documentation
  - setup_signal_handlers()

Function strategy_description
- Function Documentation
  - strategy_description()

Function symmetry::add_Cn
- Function Documentation
  - add_Cn()

Function symmetry::add_perm
- Function Documentation
  - add_perm()

Function symmetry::add_SG
- Function Documentation
  - add_SG()

Function symmetry::PG_determ
- Function Documentation
  - PG_determ()

Function symmetry::sym_elements
- Function Documentation
  - sym_elements()

Function symmetry::symclass
- Function Documentation
  - symclass()

Function symmetry::symm_check
- Function Documentation
  - symm_check()

Function symmetry::symm_cmass
- Function Documentation
  - symm_cmass()

Function symmetry::symm_crossp
- Function Documentation
  - symm_crossp()

Function symmetry::symm_cshift
- Function Documentation
  - symm_cshift()

Function symmetry::symm_dot
- Function Documentation
  - symm_dot()

Function symmetry::symm_igcd
- Function Documentation
  - symm_igcd()

Function symmetry::symm_inversion
- Function Documentation
  - symm_inversion()

Function symmetry::symm_point_group
- Function Documentation
  - symm_point_group()

Function symmetry::symm_reflect
- Function Documentation
  - symm_reflect()

Function symmetry::symm_rotate
- Function Documentation
  - symm_rotate()

Function symmetry::symm_srotate
- Function Documentation
  - symm_srotate()

Function ThermoHelpUtils::print_help
- Function Documentation
  - print_help()

Function ThermoHelpUtils::print_input_help
- Function Documentation
  - print_input_help()

Function ThermoHelpUtils::print_option_help
- Function Documentation
  - print_option_help()

Function ThermoHelpUtils::print_output_help
- Function Documentation
  - print_output_help()

Function ThermoHelpUtils::print_settings_help
- Function Documentation
  - print_settings_help()

Function ThermoHelpUtils::print_version
- Function Documentation
  - print_version()

Function ThermoInterface::calculate_thermal_corrections
- Function Documentation
  - calculate_thermal_corrections()

Function ThermoInterface::cleanup_thermo_module
- Function Documentation
  - cleanup_thermo_module()

Function ThermoInterface::create_system_data
- Function Documentation
  - create_system_data()

Function ThermoInterface::display_molecular_info
- Function Documentation
  - display_molecular_info()

Function ThermoInterface::extract_basic_properties
- Function Documentation
  - extract_basic_properties()

Function ThermoInterface::identify_program
- Function Documentation
  - identify_program()

Function ThermoInterface::initialize_thermo_module
- Function Documentation
  - initialize_thermo_module()

Function ThermoInterface::print_program_header
- Function Documentation
  - print_program_header()

Function ThermoInterface::process_batch
- Function Documentation
  - process_batch()

Function ThermoInterface::process_file
- Function Documentation
  - process_file()

Function util::create_default_settings_file
- Function Documentation
  - create_default_settings_file()

Function util::deterprog
- Function Documentation
  - deterprog()

Function util::diagmat
- Function Documentation
  - diagmat()

Function util::get_option_str
- Function Documentation
  - get_option_str()

Function util::loadarguments
- Function Documentation
  - loadarguments()

Function util::loadsettings
- Function Documentation
  - loadsettings()

Function util::loclabel
- Function Documentation
  - loclabel()

Function util::matmul
- Function Documentation
  - matmul()

Function util::modmass
- Function Documentation
  - modmass()

Function util::outotmfile
- Function Documentation
  - outotmfile()

Function util::parseLowVibTreatment
- Function Documentation
  - parseLowVibTreatment()

Function util::transpose
- Function Documentation
  - transpose()

Function Utils::generate_unique_filename
- Function Documentation
  - generate_unique_filename()

Function Utils::parseExtraKeywords
- Function Documentation
  - parseExtraKeywords()

Function Utils::read_file_unified
- Function Documentation
  - read_file_unified()

Function validate_thread_count
- Function Documentation
  - validate_thread_count()

Function validateFileSize
- Function Documentation

Variables¶

Variable ALT_CONFIG_FILENAME
- Variable Documentation
  - ALT_CONFIG_FILENAME

Variable amu2kg
- Variable Documentation
  - amu2kg

Variable atm2Pa
- Variable Documentation
  - atm2Pa

Variable au2cm_1
- Variable Documentation
  - au2cm_1

Variable au2eV
- Variable Documentation
  - au2eV

Variable au2J
- Variable Documentation
  - au2J

Variable au2kcal_mol
- Variable Documentation
  - au2kcal_mol

Variable au2kJ_mol
- Variable Documentation
  - au2kJ_mol

Variable b2a
- Variable Documentation
  - b2a

Variable cal2J
- Variable Documentation
  - cal2J

Variable DEFAULT_CONFIG_FILENAME
- Variable Documentation
  - DEFAULT_CONFIG_FILENAME

Variable DEFAULT_MAX_FILE_SIZE_MB
- Variable Documentation
  - DEFAULT_MAX_FILE_SIZE_MB

Variable DEFAULT_MEMORY_MB
- Variable Documentation
  - DEFAULT_MEMORY_MB

Variable elemass
- Variable Documentation
  - elemass

Variable g_config_manager
- Variable Documentation
  - g_config_manager

Variable g_shutdown_requested
- Variable Documentation
  - g_shutdown_requested

Variable h
- Variable Documentation
  - h

Variable HARTREE_TO_EV
- Variable Documentation
  - HARTREE_TO_EV

Variable HARTREE_TO_KJ_MOL
- Variable Documentation
  - HARTREE_TO_KJ_MOL

Variable ind2name
- Variable Documentation
  - ind2name

Variable isomass
- Variable Documentation
  - isomass

Variable isowei
- Variable Documentation
  - isowei

Variable kB
- Variable Documentation
  - kB

Variable kb
- Variable Documentation
  - kb

Variable KB_CONSTANT
- Variable Documentation
  - KB_CONSTANT

Variable MAX_FILE_HANDLES
- Variable Documentation
  - MAX_FILE_HANDLES

Variable MAX_MEMORY_MB
- Variable Documentation
  - MAX_MEMORY_MB

Variable maxiso
- Variable Documentation
  - maxiso

Variable MIN_MEMORY_MB
- Variable Documentation
  - MIN_MEMORY_MB

Variable NA
- Variable Documentation
  - NA

Variable nelesupp
- Variable Documentation
  - nelesupp

Variable OpenThermo::AUTHORS
- Variable Documentation
  - AUTHORS

Variable OpenThermo::PROJECT_URL
- Variable Documentation
  - PROJECT_URL

Variable OpenThermo::RELEASE_DATE
- Variable Documentation
  - RELEASE_DATE

Variable OpenThermo::VERSION
- Variable Documentation
  - VERSION

Variable PHASE_CORR_FACTOR
- Variable Documentation
  - PHASE_CORR_FACTOR

Variable pi
- Variable Documentation
  - pi

Variable Po
- Variable Documentation
  - Po

Variable PO_CONSTANT
- Variable Documentation
  - PO_CONSTANT

Variable R
- Variable Documentation
  - R

Variable R
- Variable Documentation
  - R

Variable R_CONSTANT
- Variable Documentation
  - R_CONSTANT

Variable wave2freq
- Variable Documentation
  - wave2freq

Defines¶

Define COMCHEMKIT_AUTHOR
- Define Documentation
  - COMCHEMKIT_AUTHOR

Define COMCHEMKIT_COPYRIGHT
- Define Documentation
  - COMCHEMKIT_COPYRIGHT

Define COMCHEMKIT_DESCRIPTION
- Define Documentation
  - COMCHEMKIT_DESCRIPTION

Define COMCHEMKIT_MAJOR
- Define Documentation
  - COMCHEMKIT_MAJOR

Define COMCHEMKIT_MINOR
- Define Documentation
  - COMCHEMKIT_MINOR

Define COMCHEMKIT_NAME
- Define Documentation
  - COMCHEMKIT_NAME

Define COMCHEMKIT_PATCH
- Define Documentation
  - COMCHEMKIT_PATCH

Define COMCHEMKIT_REPOSITORY
- Define Documentation
  - COMCHEMKIT_REPOSITORY

Define COMCHEMKIT_STRING
- Define Documentation
  - COMCHEMKIT_STRING

Define CONFIG_GET_BOOL
- Define Documentation
  - CONFIG_GET_BOOL

Define CONFIG_GET_DOUBLE
- Define Documentation
  - CONFIG_GET_DOUBLE

Define CONFIG_GET_INT
- Define Documentation
  - CONFIG_GET_INT

Define CONFIG_GET_STRING
- Define Documentation
  - CONFIG_GET_STRING

Define CONFIG_GET_UINT
- Define Documentation
  - CONFIG_GET_UINT

Define HAS_EXECUTION_POLICIES
- Define Documentation
  - HAS_EXECUTION_POLICIES