chemsmart package

Subpackages

• chemsmart.cli package
  • Subpackages
    • chemsmart.cli.gaussian package
      • Submodules
      • chemsmart.cli.gaussian.com module
      • chemsmart.cli.gaussian.crest module
      • chemsmart.cli.gaussian.custom module
      • chemsmart.cli.gaussian.dias module
      • chemsmart.cli.gaussian.gaussian module
      • chemsmart.cli.gaussian.irc module
      • chemsmart.cli.gaussian.link module
      • chemsmart.cli.gaussian.modred module
      • chemsmart.cli.gaussian.nci module
      • chemsmart.cli.gaussian.opt module
      • chemsmart.cli.gaussian.qmmm module
      • chemsmart.cli.gaussian.resp module
      • chemsmart.cli.gaussian.traj module
      • chemsmart.cli.gaussian.scan module
      • chemsmart.cli.gaussian.singlepoint module
      • chemsmart.cli.gaussian.tddft module
      • chemsmart.cli.gaussian.ts module
      • chemsmart.cli.gaussian.wbi module
      • Module contents
    • chemsmart.cli.mol package
      • Submodules
      • chemsmart.cli.mol.irc module
      • chemsmart.cli.mol.mol module
      • chemsmart.cli.mol.movie module
      • chemsmart.cli.mol.visualize module
      • Module contents
    • chemsmart.cli.orca package
      • Submodules
      • chemsmart.cli.orca.inp module
      • chemsmart.cli.orca.irc module
      • chemsmart.cli.orca.modred module
      • chemsmart.cli.orca.neb module
      • chemsmart.cli.orca.opt module
      • chemsmart.cli.orca.qmmm module
      • chemsmart.cli.orca.orca module
      • chemsmart.cli.orca.scan module
      • chemsmart.cli.orca.singlepoint module
      • chemsmart.cli.orca.ts module
      • Module contents
  • Submodules
  • chemsmart.cli.config module
    • Config
      • Config.chemsmart_dest
      • Config.chemsmart_gaussian
      • Config.chemsmart_orca
      • Config.chemsmart_package_path
      • Config.chemsmart_server
      • Config.chemsmart_template
      • Config.conda_folder
      • Config.conda_path
      • Config.configure_conda_in_server_yaml()
      • Config.configure_paths_interactively()
      • Config.env_vars
      • Config.powershell_profiles
      • Config.ps_env_vars
      • Config.setup_environment()
      • Config.shell_config
    • add_lines_in_yaml_files()
    • update_yaml_files()
  • chemsmart.cli.job module
    • click_file_label_and_index_options()
    • click_filename_options()
    • click_filenames_options()
    • click_folder_options()
    • click_job_options()
    • click_molecule_vibrational_displacement_options()
    • click_pubchem_options()
  • chemsmart.cli.jobrunner module
    • click_jobrunner_options()
  • chemsmart.cli.logger module
    • logger_options()
  • chemsmart.cli.main module
    • main()
  • chemsmart.cli.run module
    • process_pipeline()
  • chemsmart.cli.sub module
    • process_pipeline()
  • chemsmart.cli.subcommands module
  • chemsmart.cli.update module
    • Updater
      • Updater.docs_conf_file_path
      • Updater.package_path
      • Updater.pyproject_path
      • Updater.update_pyproject_toml()
      • Updater.update_version_number()
      • Updater.version_file_path
  • Module contents
• chemsmart.settings package
  • Submodules
  • chemsmart.settings.executable module
    • Executable
      • Executable.PROGRAM
      • Executable.available_servers
      • Executable.env
      • Executable.from_servername()
      • Executable.scratch_dir
    • GaussianExecutable
      • GaussianExecutable.PROGRAM
      • GaussianExecutable.get_executable()
    • NCIPLOTExecutable
      • NCIPLOTExecutable.PROGRAM
      • NCIPLOTExecutable.get_executable()
    • ORCAExecutable
      • ORCAExecutable.PROGRAM
      • ORCAExecutable.get_executable()
  • chemsmart.settings.gaussian module
    • GaussianProjectSettings
      • GaussianProjectSettings.PROJECT_NAME
      • GaussianProjectSettings.functional
      • GaussianProjectSettings.small_basis
      • GaussianProjectSettings.large_basis
      • GaussianProjectSettings.PROJECT_NAME
      • GaussianProjectSettings.from_project()
      • GaussianProjectSettings.functional
      • GaussianProjectSettings.irc_settings()
      • GaussianProjectSettings.large_basis
      • GaussianProjectSettings.main_settings()
      • GaussianProjectSettings.modred_settings()
      • GaussianProjectSettings.nci_settings()
      • GaussianProjectSettings.opt_settings()
      • GaussianProjectSettings.qmmm_settings()
      • GaussianProjectSettings.scan_settings()
      • GaussianProjectSettings.small_basis
      • GaussianProjectSettings.sp_settings()
      • GaussianProjectSettings.ts_settings()
      • GaussianProjectSettings.wbi_settings()
    • GaussianProjectSettingsManager
      • GaussianProjectSettingsManager.filename
      • GaussianProjectSettingsManager.create()
    • YamlGaussianProjectSettings
      • YamlGaussianProjectSettings.PROJECT_NAME
      • YamlGaussianProjectSettings.PROJECT_NAME
      • YamlGaussianProjectSettings.from_yaml()
      • YamlGaussianProjectSettings.irc_settings()
      • YamlGaussianProjectSettings.modred_settings()
      • YamlGaussianProjectSettings.nci_settings()
      • YamlGaussianProjectSettings.opt_settings()
      • YamlGaussianProjectSettings.qmmm_settings()
      • YamlGaussianProjectSettings.scan_settings()
      • YamlGaussianProjectSettings.sp_settings()
      • YamlGaussianProjectSettings.td_settings()
      • YamlGaussianProjectSettings.ts_settings()
      • YamlGaussianProjectSettings.wbi_settings()
    • YamlGaussianProjectSettingsBuilder
      • YamlGaussianProjectSettingsBuilder.filename
      • YamlGaussianProjectSettingsBuilder.build()
  • chemsmart.settings.orca module
    • ORCAProjectSettings
      • ORCAProjectSettings.PROJECT_NAME
      • ORCAProjectSettings.functional
      • ORCAProjectSettings.small_basis
      • ORCAProjectSettings.large_basis
      • ORCAProjectSettings.PROJECT_NAME
      • ORCAProjectSettings.from_project()
      • ORCAProjectSettings.functional
      • ORCAProjectSettings.irc_settings()
      • ORCAProjectSettings.large_basis
      • ORCAProjectSettings.main_settings()
      • ORCAProjectSettings.modred_settings()
      • ORCAProjectSettings.nci_settings()
      • ORCAProjectSettings.neb_settings()
      • ORCAProjectSettings.opt_settings()
      • ORCAProjectSettings.qmmm_settings()
      • ORCAProjectSettings.scan_settings()
      • ORCAProjectSettings.small_basis
      • ORCAProjectSettings.sp_settings()
      • ORCAProjectSettings.ts_settings()
      • ORCAProjectSettings.wbi_settings()
    • ORCAProjectSettingsManager
      • ORCAProjectSettingsManager.filename
      • ORCAProjectSettingsManager.create()
    • YamlORCAProjectSettings
      • YamlORCAProjectSettings.PROJECT_NAME
      • YamlORCAProjectSettings._opt_settings
      • YamlORCAProjectSettings._modred_settings
      • YamlORCAProjectSettings._ts_settings
      • YamlORCAProjectSettings._irc_settings
      • YamlORCAProjectSettings._scan_settings
      • YamlORCAProjectSettings._nci_settings
      • YamlORCAProjectSettings._sp_settings
      • YamlORCAProjectSettings._td_settings
      • YamlORCAProjectSettings._wbi_settings
      • YamlORCAProjectSettings.PROJECT_NAME
      • YamlORCAProjectSettings.from_yaml()
      • YamlORCAProjectSettings.irc_settings()
      • YamlORCAProjectSettings.modred_settings()
      • YamlORCAProjectSettings.nci_settings()
      • YamlORCAProjectSettings.neb_settings()
      • YamlORCAProjectSettings.opt_settings()
      • YamlORCAProjectSettings.qmmm_settings()
      • YamlORCAProjectSettings.scan_settings()
      • YamlORCAProjectSettings.sp_settings()
      • YamlORCAProjectSettings.td_settings()
      • YamlORCAProjectSettings.ts_settings()
      • YamlORCAProjectSettings.wbi_settings()
    • YamlORCAProjectSettingsBuilder
      • YamlORCAProjectSettingsBuilder.filename
      • YamlORCAProjectSettingsBuilder.build()
  • chemsmart.settings.server module
    • LSFServer
      • LSFServer.NAME
      • LSFServer.SCHEDULER_TYPE
      • LSFServer.name
      • LSFServer.kwargs
      • LSFServer._num_hours
      • LSFServer._queue_name
      • LSFServer.NAME
      • LSFServer.SCHEDULER_TYPE
    • PBSServer
      • PBSServer.NAME
      • PBSServer.SCHEDULER_TYPE
      • PBSServer.name
      • PBSServer.kwargs
      • PBSServer._num_hours
      • PBSServer._queue_name
      • PBSServer.NAME
      • PBSServer.SCHEDULER_TYPE
    • SGE_Server
      • SGE_Server.NAME
      • SGE_Server.SCHEDULER_TYPE
      • SGE_Server.name
      • SGE_Server.kwargs
      • SGE_Server._num_hours
      • SGE_Server._queue_name
      • SGE_Server.NAME
      • SGE_Server.SCHEDULER_TYPE
    • SLURMServer
      • SLURMServer.NAME
      • SLURMServer.SCHEDULER_TYPE
      • SLURMServer.name
      • SLURMServer.kwargs
      • SLURMServer._num_hours
      • SLURMServer._queue_name
      • SLURMServer.NAME
      • SLURMServer.SCHEDULER_TYPE
    • Server
      • Server.name
      • Server.kwargs
      • Server._num_hours
      • Server._queue_name
      • Server.current()
      • Server.detect_server_scheduler()
      • Server.extra_commands
      • Server.from_dict()
      • Server.from_scheduler_type()
      • Server.from_servername()
      • Server.from_yaml()
      • Server.get_submitter()
      • Server.mem_gb
      • Server.num_cores
      • Server.num_gpus
      • Server.num_hours
      • Server.num_threads
      • Server.queue_name
      • Server.register()
      • Server.scheduler
      • Server.scratch
      • Server.scratch_dir
      • Server.submit()
      • Server.submit_command
      • Server.use_hosts
    • ServerSettingsManager
      • ServerSettingsManager.filename
      • ServerSettingsManager.create()
    • YamlServerSettings
      • YamlServerSettings.NAME
      • YamlServerSettings.name
      • YamlServerSettings.kwargs
      • YamlServerSettings._num_hours
      • YamlServerSettings._queue_name
      • YamlServerSettings.NAME
      • YamlServerSettings.from_yaml()
      • YamlServerSettings.register()
  • chemsmart.settings.submitters module
    • FUGAKUSubmitter
      • FUGAKUSubmitter.NAME
      • FUGAKUSubmitter.name
      • FUGAKUSubmitter.job
      • FUGAKUSubmitter.server
      • FUGAKUSubmitter.kwargs
      • FUGAKUSubmitter.NAME
    • PBSSubmitter
      • PBSSubmitter.NAME
      • PBSSubmitter.name
      • PBSSubmitter.job
      • PBSSubmitter.server
      • PBSSubmitter.kwargs
      • PBSSubmitter.NAME
    • RunScript
      • RunScript.filename
      • RunScript.batch
      • RunScript.cli_args
      • RunScript.write()
    • SLFSubmitter
      • SLFSubmitter.NAME
      • SLFSubmitter.name
      • SLFSubmitter.job
      • SLFSubmitter.server
      • SLFSubmitter.kwargs
      • SLFSubmitter.NAME
    • SLURMSubmitter
      • SLURMSubmitter.NAME
      • SLURMSubmitter.name
      • SLURMSubmitter.job
      • SLURMSubmitter.server
      • SLURMSubmitter.kwargs
      • SLURMSubmitter.NAME
    • Submitter
      • Submitter.NAME
      • Submitter.name
      • Submitter.job
      • Submitter.server
      • Submitter.kwargs
      • Submitter.NAME
      • Submitter.executable
      • Submitter.from_dict()
      • Submitter.from_scheduler_type()
      • Submitter.run_script
      • Submitter.submit_folder
      • Submitter.submit_script
      • Submitter.write()
  • chemsmart.settings.user module
    • ChemsmartUserSettings
      • ChemsmartUserSettings.USER_YAML_FILE
      • ChemsmartUserSettings.USER_CONFIG_DIR
      • ChemsmartUserSettings.yaml
      • ChemsmartUserSettings.config_dir
      • ChemsmartUserSettings.data
      • ChemsmartUserSettings.USER_CONFIG_DIR
      • ChemsmartUserSettings.USER_YAML_FILE
      • ChemsmartUserSettings.all_available_gaussian_projects
      • ChemsmartUserSettings.all_available_orca_projects
      • ChemsmartUserSettings.all_available_servers
      • ChemsmartUserSettings.email
      • ChemsmartUserSettings.gaussian_project_yaml_files
      • ChemsmartUserSettings.orca_project_yaml_files
      • ChemsmartUserSettings.project
      • ChemsmartUserSettings.scratch
      • ChemsmartUserSettings.server_yaml_files
      • ChemsmartUserSettings.user_gaussian_envars
      • ChemsmartUserSettings.user_gaussian_modules
      • ChemsmartUserSettings.user_gaussian_script
      • ChemsmartUserSettings.user_gaussian_settings_dir
      • ChemsmartUserSettings.user_orca_envars
      • ChemsmartUserSettings.user_orca_modules
      • ChemsmartUserSettings.user_orca_script
      • ChemsmartUserSettings.user_orca_settings_dir
      • ChemsmartUserSettings.user_server_dir
  • Module contents

Module contents