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ComChemKit 0.000.6 documentation
ComChemKit 0.000.6 documentation

User Guide:

  • Installation Guide
  • Installation Methods
  • Post-Installation Setup
  • Troubleshooting
  • Performance Optimization
  • Uninstallation
  • Getting Help
  • Usage Guide
  • Core Commands
  • Configuration and Customization
  • Performance and Resource Management
  • Safety Features
  • Advanced Workflows
  • Troubleshooting
  • Best Practices
  • Command Reference
  • Getting Help

Developer Guide:

  • Developer Guide
  • Project Overview
  • Development Setup
  • Coding Standards
  • Contributing
  • Testing Guidelines
  • Continuous Integration
  • Release Process
  • Support and Communication

API Reference:

  • ComChemKit API
    • Namespace atommass
    • Namespace calc
    • Namespace ComChemKit
    • Namespace ConfigUtils
    • Namespace FileUtils
    • Namespace HelpUtils
    • Namespace HighLevelEnergyUtils
    • Namespace JobCheckerUtils
    • Namespace Metadata
    • Namespace OpenThermo
    • Namespace symmetry
    • Namespace ThermoHelpUtils
    • Namespace ThermoInterface
    • Namespace util
    • Namespace Utils
    • Struct Atom
    • Struct ThermoResult
    • 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 SymmetryData
    • Struct Vector3D
    • Struct SystemData
    • Struct ThermoResult
    • Struct ThermoSettings
    • 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 SymmetryDetector
    • Class ThermoCommand
    • Class ThreadPool
    • Class ThreadSafeErrorCollector
    • Enum BavPreset
    • Enum CalculationType
    • Enum CommandType
    • Enum ConfigCategory
    • Enum FileReadMode
    • Enum JobStatus
    • Enum LowVibTreatment
    • Enum OMPStrategy
    • Enum SchedulerType
    • Enum QuantumChemistryProgram
    • Function atommass::initmass
    • Function bavPresetName
    • Function bavPresetValue
    • Function calc::calcinertia
    • Function calc::calcthermo(const SystemData&, double, double)
    • Function calc::calcthermo(const SystemData&, double, double, double&, double&, double&, double&, double&, double&, double&, double&)
    • Function calc::ensemble
    • Function calc::file_exists
    • Function calc::getGconc
    • Function calc::getvibcontri(const SystemData&, int, double, double&, double&, double&, double&)
    • Function calc::getvibcontri(const SystemData&, double, double&, double&, double&, double&)
    • Function calc::showthermo
    • Function calc::showvibdetail
    • Function calculateSafeMemoryLimit
    • Function calculateSafeThreadCount
    • Function ComChemKit::get_full_version
    • Function ComChemKit::get_header_info
    • Function ComChemKit::get_version
    • Function ComChemKit::get_version_info
    • Function ComChemKit::is_version_at_least
    • Function compareResults
    • Function configure_openmp
    • Function ConfigUtils::bool_to_string
    • Function ConfigUtils::file_exists
    • Function ConfigUtils::get_config_search_paths
    • Function ConfigUtils::get_config_version
    • Function ConfigUtils::get_executable_directory
    • Function ConfigUtils::is_readable
    • Function ConfigUtils::is_valid_concentration
    • Function ConfigUtils::is_valid_extension
    • Function ConfigUtils::is_valid_file_size
    • Function ConfigUtils::is_valid_pressure
    • Function ConfigUtils::is_valid_temperature
    • Function ConfigUtils::is_valid_thread_count
    • Function ConfigUtils::is_writable
    • Function ConfigUtils::join_strings
    • Function ConfigUtils::migrate_config_if_needed
    • Function ConfigUtils::split_string
    • Function ConfigUtils::string_to_bool
    • Function detect_physical_cores
    • Function detect_scheduler_cpus
    • Function execute_directory_command
    • Function execute_utility_command
    • Function extract
    • Function findLogFiles()
    • Function findLogFiles()
    • Function findLogFiles()
    • Function findLogFiles()
    • Function formatMemorySize
    • Function get_default_threads
    • Function HelpUtils::create_default_config
    • Function HelpUtils::print_command_help
    • Function HelpUtils::print_config_help
    • Function HelpUtils::print_help
    • Function HighLevelEnergyUtils::extract_frequencies
    • Function HighLevelEnergyUtils::find_lowest_frequency
    • Function HighLevelEnergyUtils::get_current_directory_name
    • Function HighLevelEnergyUtils::hartree_to_ev
    • Function HighLevelEnergyUtils::hartree_to_kj_mol
    • Function HighLevelEnergyUtils::is_valid_high_level_directory()
    • Function HighLevelEnergyUtils::is_valid_high_level_directory()
    • Function HighLevelEnergyUtils::parse_energy_value
    • Function HighLevelEnergyUtils::validate_concentration
    • Function HighLevelEnergyUtils::validate_energy_data
    • Function HighLevelEnergyUtils::validate_temperature
    • Function is_directory_command
    • Function is_shell_command
    • Function is_utility_command
    • Function JobCheckerUtils::file_exists
    • Function JobCheckerUtils::get_file_extension
    • Function JobCheckerUtils::is_valid_log_file
    • Function Metadata::header
    • Function omp_get_level
    • Function omp_get_max_threads
    • Function omp_get_num_threads
    • Function omp_get_thread_num
    • Function omp_set_num_threads
    • Function printJobResourceInfo
    • Function printResourceUsage
    • Function processAndOutputResults
    • Function run_interactive_loop
    • Function safe_stod
    • Function safe_stoi
    • Function safe_stoul
    • Function select_strategy
    • Function setup_signal_handlers
    • Function strategy_description
    • Function symmetry::add_Cn
    • Function symmetry::add_perm
    • Function symmetry::add_SG
    • Function symmetry::PG_determ
    • Function symmetry::sym_elements
    • Function symmetry::symclass
    • Function symmetry::symm_check
    • Function symmetry::symm_cmass
    • Function symmetry::symm_crossp
    • Function symmetry::symm_cshift
    • Function symmetry::symm_dot
    • Function symmetry::symm_igcd
    • Function symmetry::symm_inversion
    • Function symmetry::symm_point_group
    • Function symmetry::symm_reflect
    • Function symmetry::symm_rotate
    • Function symmetry::symm_srotate
    • Function ThermoHelpUtils::print_help
    • Function ThermoHelpUtils::print_input_help
    • Function ThermoHelpUtils::print_option_help
    • Function ThermoHelpUtils::print_output_help
    • Function ThermoHelpUtils::print_settings_help
    • Function ThermoHelpUtils::print_version
    • Function ThermoInterface::calculate_thermal_corrections
    • Function ThermoInterface::cleanup_thermo_module
    • Function ThermoInterface::create_system_data
    • Function ThermoInterface::display_molecular_info
    • Function ThermoInterface::extract_basic_properties
    • Function ThermoInterface::identify_program
    • Function ThermoInterface::initialize_thermo_module
    • Function ThermoInterface::print_program_header
    • Function ThermoInterface::process_batch
    • Function ThermoInterface::process_file
    • Function util::create_default_settings_file
    • Function util::deterprog
    • Function util::diagmat
    • Function util::get_option_str
    • Function util::loadarguments
    • Function util::loadsettings
    • Function util::loclabel
    • Function util::matmul
    • Function util::modmass
    • Function util::outotmfile
    • Function util::parseLowVibTreatment
    • Function util::transpose
    • Function Utils::generate_unique_filename
    • Function Utils::parseExtraKeywords
    • Function Utils::read_file_unified
    • Function validate_thread_count
    • Function validateFileSize
    • Variable ALT_CONFIG_FILENAME
    • Variable amu2kg
    • Variable atm2Pa
    • Variable au2cm_1
    • Variable au2eV
    • Variable au2J
    • Variable au2kcal_mol
    • Variable au2kJ_mol
    • Variable b2a
    • Variable cal2J
    • Variable DEFAULT_CONFIG_FILENAME
    • Variable DEFAULT_MAX_FILE_SIZE_MB
    • Variable DEFAULT_MEMORY_MB
    • Variable elemass
    • Variable g_config_manager
    • Variable g_shutdown_requested
    • Variable h
    • Variable HARTREE_TO_EV
    • Variable HARTREE_TO_KJ_MOL
    • Variable ind2name
    • Variable isomass
    • Variable isowei
    • Variable kB
    • Variable kb
    • Variable KB_CONSTANT
    • Variable MAX_FILE_HANDLES
    • Variable MAX_MEMORY_MB
    • Variable maxiso
    • Variable MIN_MEMORY_MB
    • Variable NA
    • Variable nelesupp
    • Variable OpenThermo::AUTHORS
    • Variable OpenThermo::PROJECT_URL
    • Variable OpenThermo::RELEASE_DATE
    • Variable OpenThermo::VERSION
    • Variable PHASE_CORR_FACTOR
    • Variable pi
    • Variable Po
    • Variable PO_CONSTANT
    • Variable R
    • Variable R
    • Variable R_CONSTANT
    • Variable wave2freq
    • Define COMCHEMKIT_AUTHOR
    • Define COMCHEMKIT_COPYRIGHT
    • Define COMCHEMKIT_DESCRIPTION
    • Define COMCHEMKIT_MAJOR
    • Define COMCHEMKIT_MINOR
    • Define COMCHEMKIT_NAME
    • Define COMCHEMKIT_PATCH
    • Define COMCHEMKIT_REPOSITORY
    • Define COMCHEMKIT_STRING
    • Define CONFIG_GET_BOOL
    • Define CONFIG_GET_DOUBLE
    • Define CONFIG_GET_INT
    • Define CONFIG_GET_STRING
    • Define CONFIG_GET_UINT
    • Define HAS_EXECUTION_POLICIES
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  • File coord_extractor.h

  • File qc_extractor.h

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