Index

_

__enter__() (calypso.dispatchers.orchestrator.toolkit.ThreadLock method) __exit__() (calypso.dispatchers.orchestrator.toolkit.ThreadLock method)

__init__() (calypso.dispatchers.orchestrator.toolkit.ThreadLock method) __str__() (calypso.formula.Formula method) _exception (calypso.dispatchers.orchestrator.toolkit.ThreadWithException attribute)

A

acquire() (calypso.dispatchers.orchestrator.toolkit.ThreadLock method), [1] add_parser() (in module calypso.tools.cli_convert) (in module calypso.tools.cli_wyckcomb) (in module calypso.utils.cleancache) additional_head_setting (calypso.dispatchers.orchestrator.machine.MachineData attribute) ADSORPTION (calypso.config.config.IType attribute) ALPHABET (calypso.formula.FormulaFmt attribute) anonymous_formula (calypso.formula.Formula property)

are_jobs_finished() (calypso.dispatchers.orchestrator.Orchestrator method) (calypso.dispatchers.orchestrator.orchestrator.Orchestrator method) as_dict() (calypso.dispatchers.orchestrator.machine.Machine method) (calypso.dispatchers.orchestrator.machine.MachineData method) (calypso.dispatchers.orchestrator.Orchestrator method) (calypso.dispatchers.orchestrator.orchestrator.Orchestrator method) as_numbers() (calypso.symbols.Symbols method) as_strings() (calypso.symbols.Symbols method)

B

BaseExecutor (class in calypso.dispatchers.orchestrator.executor.base_executor) BaseScheduler (class in calypso.dispatchers.orchestrator.scheduler.base_scheduler)

BCM (calypso.config.config.ISim attribute) block (calypso.data.atomic.Element property) (calypso.data.Element property)

C

caly_velo (calypso.site.Site property) calypso module, [1] calypso.cli module calypso.config module calypso.config.config module calypso.config.read_dat module calypso.constants module calypso.data module calypso.data.atomic module calypso.data.manage_group module calypso.descriptors.nan module calypso.dispatchers module calypso.dispatchers.dispatcher module calypso.dispatchers.orchestrator module calypso.dispatchers.orchestrator.executor module calypso.dispatchers.orchestrator.executor.base_executor module calypso.dispatchers.orchestrator.executor.local module calypso.dispatchers.orchestrator.executor.ssh module calypso.dispatchers.orchestrator.jobs module calypso.dispatchers.orchestrator.log module calypso.dispatchers.orchestrator.machine module calypso.dispatchers.orchestrator.orchestrator module calypso.dispatchers.orchestrator.scheduler module calypso.dispatchers.orchestrator.scheduler.base_scheduler module calypso.dispatchers.orchestrator.scheduler.lsf module calypso.dispatchers.orchestrator.scheduler.pbs module calypso.dispatchers.orchestrator.scheduler.shell module calypso.dispatchers.orchestrator.scheduler.slurm module calypso.dispatchers.orchestrator.toolkit module calypso.fitnesses.enthalpy module calypso.fitnesses.nan module calypso.formula module calypso.logo module

calypso.site module calypso.symbols module calypso.tools module calypso.tools.cli_convert module calypso.tools.cli_wyckcomb module calypso.utils module calypso.utils.cleancache module calypso.utils.factory module calypso.utils.hash module calypso.utils.lazyloader module calypso.utils.log module calypso.utils.registry module calypso.utils.rotate_dir module calypso.utils.seed module calypso.utils.singleton module calypso.utils.str_parser module calypso.utils.to_toml module CalypsoFiles (class in calypso.constants) cartpos (calypso.site.Site property) CASTEP (calypso.config.config.ICode attribute) CCF (calypso.config.config.ISim attribute) check_dtype() (calypso.site.Site method) check_value() (calypso.dispatchers.orchestrator.toolkit.TimeParser static method) clean_handlers() (in module calypso.utils.log) cleancache() (in module calypso.utils.cleancache) cli_func() (in module calypso.tools.cli_convert) (in module calypso.tools.cli_wyckcomb) cli_main() (in module calypso.cli) CLUSTER (calypso.config.config.IType attribute) command (calypso.dispatchers.orchestrator.jobs.Job attribute) (calypso.dispatchers.orchestrator.machine.MachineData attribute) comment (calypso.dispatchers.orchestrator.jobs.Job attribute) Config (class in calypso.config) (class in calypso.config.config) connect() (calypso.dispatchers.orchestrator.executor.ssh.SSHClient method) convert() (in module calypso.config.config) copy() (calypso.site.Site method) count (calypso.formula.Formula property) count() (calypso.formula.Formula method) covalent_radius (calypso.data.atomic.DummyElement property) (calypso.data.atomic.Element property) (calypso.data.Element property) covalent_volume (calypso.data.atomic.DummyElement property) (calypso.data.atomic.Element property) (calypso.data.Element property) CP2K (calypso.config.config.ICode attribute) create() (calypso.constants.CalypsoFiles method) CRYSTAL (calypso.config.config.IType attribute) CUSTOM (calypso.config.config.ICode attribute)

D

DEBUG (calypso.config.config.IDisp attribute) default() (calypso.dispatchers.orchestrator.toolkit.JobStatusEncoder method) del_all_instances() (calypso.utils.singleton.ParameterizedSingletonMeta class method) del_instance() (calypso.utils.singleton.ParameterizedSingletonMeta class method) describe() (calypso.descriptors.nan.NANDescriptor method) DFTBPLUS (calypso.config.config.ICode attribute) dict_to_toml() (in module calypso.utils.to_toml) disconnect() (calypso.dispatchers.orchestrator.executor.ssh.SSHClient method) Dispatcher (class in calypso.dispatchers.dispatcher) download_file() (calypso.dispatchers.orchestrator.executor.ssh.SSHClient method)

download_files (calypso.dispatchers.orchestrator.jobs.Job attribute) download_job() (calypso.dispatchers.orchestrator.executor.base_executor.BaseExecutor method) (calypso.dispatchers.orchestrator.executor.local.Local method) (calypso.dispatchers.orchestrator.executor.ssh.SSHExecutor method) download_jobs() (calypso.dispatchers.orchestrator.machine.Machine method) download_remote_file() (calypso.dispatchers.orchestrator.executor.base_executor.BaseExecutor method) (calypso.dispatchers.orchestrator.executor.local.Local method) (calypso.dispatchers.orchestrator.executor.ssh.SSHExecutor method) DUMMY (calypso.config.config.ICode attribute) (calypso.config.config.IType attribute) DummyElement (class in calypso.data.atomic)

E

Element (class in calypso.data) (class in calypso.data.atomic) elements (calypso.formula.Formula property) ENTHALPY (calypso.config.config.IFit attribute) EnthalpyFitness (class in calypso.fitnesses.enthalpy) envs (calypso.dispatchers.orchestrator.machine.MachineData attribute) equal() (calypso.descriptors.nan.NANDescriptor method) error (calypso.dispatchers.orchestrator.jobs.JobStatus attribute)

example module execute() (calypso.dispatchers.orchestrator.executor.base_executor.BaseExecutor method) (calypso.dispatchers.orchestrator.executor.local.Local method) (calypso.dispatchers.orchestrator.executor.ssh.SSHExecutor method) execute_command() (calypso.dispatchers.orchestrator.executor.ssh.SSHClient method) executor (calypso.dispatchers.orchestrator.machine.MachineData attribute) external_command (calypso.dispatchers.orchestrator.machine.MachineData attribute)

F

Factory (class in calypso.utils.factory) failed (calypso.dispatchers.orchestrator.jobs.JobStatus attribute) file_exist() (calypso.dispatchers.orchestrator.executor.ssh.SSHClient method) files_exist() (calypso.dispatchers.orchestrator.executor.base_executor.BaseExecutor method) (calypso.dispatchers.orchestrator.executor.local.Local method) (calypso.dispatchers.orchestrator.executor.ssh.SSHClient method) (calypso.dispatchers.orchestrator.executor.ssh.SSHExecutor method) find_file_map() (calypso.formula.FormulaUnit method) finished (calypso.dispatchers.orchestrator.jobs.JobStatus attribute) fix (calypso.site.Site property) force (calypso.site.Site property) format() (calypso.data.manage_group.NumpyPrettyPrinter method) (calypso.formula.Formula method)

format_list() (in module calypso.utils.to_toml) format_value() (in module calypso.utils.to_toml) formula (calypso.symbols.Symbols property) Formula (class in calypso.formula) FormulaFmt (class in calypso.formula) FormulaUnit (class in calypso.formula) from_kwargs() (calypso.dispatchers.orchestrator.machine.MachineData class method) from_list() (calypso.dispatchers.orchestrator.toolkit.TimeParser class method) from_minutes() (calypso.dispatchers.orchestrator.toolkit.TimeParser class method) from_row_and_group() (calypso.data.atomic.Element class method) (calypso.data.Element class method) from_seconds() (calypso.dispatchers.orchestrator.toolkit.TimeParser class method) from_str() (calypso.dispatchers.orchestrator.toolkit.TimeParser class method)

G

GAUSSIAN (calypso.config.config.ICode attribute) generate_env() (calypso.dispatchers.orchestrator.scheduler.pbs.PBS method) generate_head() (calypso.dispatchers.orchestrator.scheduler.pbs.PBS method) generate_job_script() (calypso.dispatchers.orchestrator.scheduler.base_scheduler.BaseScheduler method) (calypso.dispatchers.orchestrator.scheduler.lsf.LSF method) (calypso.dispatchers.orchestrator.scheduler.shell.Shell method) (calypso.dispatchers.orchestrator.scheduler.slurm.Slurm method) generate_main() (calypso.dispatchers.orchestrator.scheduler.pbs.PBS method) generate_script() (calypso.dispatchers.orchestrator.scheduler.pbs.PBS method) generate_task_env() (calypso.dispatchers.orchestrator.scheduler.base_scheduler.BaseScheduler method) (calypso.dispatchers.orchestrator.scheduler.lsf.LSF method) (calypso.dispatchers.orchestrator.scheduler.shell.Shell method) (calypso.dispatchers.orchestrator.scheduler.slurm.Slurm method) generate_task_head() (calypso.dispatchers.orchestrator.scheduler.base_scheduler.BaseScheduler method) (calypso.dispatchers.orchestrator.scheduler.lsf.LSF method) (calypso.dispatchers.orchestrator.scheduler.shell.Shell method) (calypso.dispatchers.orchestrator.scheduler.slurm.Slurm method) generate_task_script() (calypso.dispatchers.orchestrator.scheduler.base_scheduler.BaseScheduler method) (calypso.dispatchers.orchestrator.scheduler.lsf.LSF method) (calypso.dispatchers.orchestrator.scheduler.shell.Shell method) (calypso.dispatchers.orchestrator.scheduler.slurm.Slurm method) generate_task_script_name() (calypso.dispatchers.orchestrator.scheduler.base_scheduler.BaseScheduler method) get_anonymous_formula() (calypso.formula.Formula method) get_cache_dir() (in module calypso.constants) get_calculator_config() (calypso.config.Config method) (calypso.config.config.Config method) get_config_dict() (in module calypso.utils.log) get_covalent_volume() (in module calypso.data) (in module calypso.data.atomic) get_dispatcher_config() (calypso.config.Config method) (calypso.config.config.Config method)

get_exception() (calypso.dispatchers.orchestrator.toolkit.ThreadWithException method) get_executor() (in module calypso.dispatchers.orchestrator.executor) get_file_obj() (calypso.dispatchers.orchestrator.executor.ssh.SSHClient method) get_generator_config() (calypso.config.Config method) (calypso.config.config.Config method) get_hours() (calypso.dispatchers.orchestrator.toolkit.TimeParser method) get_minutes() (calypso.dispatchers.orchestrator.toolkit.TimeParser method) get_pseudo_formula() (calypso.formula.FormulaUnit method) get_reduced_formula() (calypso.formula.Formula method) get_remote_file_obj() (calypso.dispatchers.orchestrator.executor.base_executor.BaseExecutor method) (calypso.dispatchers.orchestrator.executor.local.Local method) (calypso.dispatchers.orchestrator.executor.ssh.SSHExecutor method) get_results() (calypso.dispatchers.dispatcher.Dispatcher method) (calypso.dispatchers.orchestrator.Orchestrator method) (calypso.dispatchers.orchestrator.orchestrator.Orchestrator method) get_results_done() (calypso.dispatchers.dispatcher.Dispatcher method) (calypso.dispatchers.orchestrator.Orchestrator method) (calypso.dispatchers.orchestrator.orchestrator.Orchestrator method) get_scheduler() (in module calypso.dispatchers.orchestrator.scheduler) get_seconds() (calypso.dispatchers.orchestrator.toolkit.TimeParser method) get_structure_template() (calypso.formula.FormulaUnit method) GIBBS (calypso.config.config.IFit attribute) GPSO (calypso.config.config.IAlgo attribute) graceful_monitoring() (calypso.dispatchers.orchestrator.Orchestrator method) (calypso.dispatchers.orchestrator.orchestrator.Orchestrator method) group (calypso.data.atomic.Element property) (calypso.data.Element property) group_size (calypso.dispatchers.orchestrator.machine.MachineData attribute) GULP (calypso.config.config.ICode attribute)

H

handle_unexpected_state() (calypso.dispatchers.orchestrator.Orchestrator method) (calypso.dispatchers.orchestrator.orchestrator.Orchestrator method) HARDNESS (calypso.config.config.IFit attribute) hash_str() (in module calypso.utils.hash) hash_uints() (in module calypso.utils.hash)

hashstr() (in module calypso.dispatchers.orchestrator.toolkit) HILL (calypso.formula.FormulaFmt attribute) host (calypso.dispatchers.orchestrator.machine.MachineData attribute) how_jobs_going() (calypso.dispatchers.orchestrator.Orchestrator method) (calypso.dispatchers.orchestrator.orchestrator.Orchestrator method)

I

IAlgo (class in calypso.config.config) ICode (class in calypso.config.config) IDisp (class in calypso.config.config) IFit (class in calypso.config.config) inherit_default() (calypso.config.Config class method) (calypso.config.config.Config class method) inherit_default_and_from_file() (calypso.config.Config class method) (calypso.config.config.Config class method) init() (in module calypso.utils.log) init_job_status() (calypso.dispatchers.orchestrator.jobs.Job method) INTERFACE (calypso.config.config.IType attribute) IRunner (class in calypso.config.config) is_accessible() (calypso.dispatchers.orchestrator.machine.Machine method) is_actinoid (calypso.data.atomic.Element property) (calypso.data.Element property) is_alkali (calypso.data.atomic.Element property) (calypso.data.Element property) is_alkaline (calypso.data.atomic.Element property) (calypso.data.Element property) is_chalcogen (calypso.data.atomic.Element property) (calypso.data.Element property)

is_halogen (calypso.data.atomic.Element property) (calypso.data.Element property) is_lanthanoid (calypso.data.atomic.Element property) (calypso.data.Element property) is_metal (calypso.data.atomic.Element property) (calypso.data.Element property) is_metalloid (calypso.data.atomic.Element property) (calypso.data.Element property) is_new() (calypso.descriptors.nan.NANDescriptor method) is_noble_gas (calypso.data.atomic.Element property) (calypso.data.Element property) is_post_transition_metal (calypso.data.atomic.Element property) (calypso.data.Element property) is_radioactive (calypso.data.atomic.Element property) (calypso.data.Element property) is_rare_earth (calypso.data.atomic.Element property) (calypso.data.Element property) is_transition_metal (calypso.data.atomic.Element property) (calypso.data.Element property) ISim (class in calypso.config.config) IType (class in calypso.config.config)

J

Job (class in calypso.dispatchers.orchestrator.jobs) job_id (calypso.dispatchers.orchestrator.jobs.Job attribute)

JobStatus (class in calypso.dispatchers.orchestrator.jobs) JobStatusEncoder (class in calypso.dispatchers.orchestrator.toolkit)

K

key_filename (calypso.dispatchers.orchestrator.machine.MachineData attribute) kill() (calypso.dispatchers.orchestrator.scheduler.base_scheduler.BaseScheduler method) (calypso.dispatchers.orchestrator.scheduler.lsf.LSF method) (calypso.dispatchers.orchestrator.scheduler.pbs.PBS method) (calypso.dispatchers.orchestrator.scheduler.shell.Shell method) (calypso.dispatchers.orchestrator.scheduler.slurm.Slurm method)

kwargs (calypso.dispatchers.orchestrator.machine.MachineData attribute)

L

LAMMPS (calypso.config.config.ICode attribute) LAYER (calypso.config.config.IType attribute) lazy_import() (in module calypso.utils.lazyloader) LazyLoader (class in calypso.utils) (class in calypso.utils.lazyloader) Local (class in calypso.dispatchers.orchestrator.executor.local) local_root (calypso.dispatchers.orchestrator.jobs.Job attribute) local_work_dir (calypso.dispatchers.orchestrator.jobs.Job attribute) locally_files_exist() (calypso.dispatchers.orchestrator.executor.ssh.SSHExecutor method)

locally_rglob() (calypso.dispatchers.orchestrator.executor.base_executor.BaseExecutor method) (calypso.dispatchers.orchestrator.executor.ssh.SSHExecutor method) log_if_fail() (in module calypso.utils.log) log_init() (in module calypso.utils) LogAdapter (class in calypso.utils.log) LogicLine (class in calypso.config.read_dat) lower_case_key() (in module calypso.dispatchers.orchestrator.toolkit) LPSO (calypso.config.config.IAlgo attribute) LSF (class in calypso.dispatchers.orchestrator.scheduler.lsf)

M

Machine (class in calypso.dispatchers.orchestrator.machine) machine_capacity (calypso.dispatchers.orchestrator.machine.MachineData attribute) machine_id (calypso.dispatchers.orchestrator.jobs.Job attribute) machine_name (calypso.dispatchers.orchestrator.jobs.Job attribute) MachineData (class in calypso.dispatchers.orchestrator.machine) MAGMOM (calypso.config.config.IFit attribute) magmom (calypso.site.Site property) make_remote_dir() (calypso.dispatchers.orchestrator.executor.base_executor.BaseExecutor method) (calypso.dispatchers.orchestrator.executor.local.Local method) (calypso.dispatchers.orchestrator.executor.ssh.SSHExecutor method) map_v7tov8() (in module calypso.config.read_dat) mass (calypso.data.atomic.DummyElement property) (calypso.data.atomic.Element property) (calypso.data.Element property) (calypso.site.Site property) max_retry (calypso.dispatchers.orchestrator.jobs.Job attribute) (calypso.dispatchers.orchestrator.machine.MachineData attribute) max_run_time (calypso.dispatchers.orchestrator.machine.MachineData attribute) merge_dict() (in module calypso.config.config) METAL (calypso.formula.FormulaFmt attribute) metallic_radius (calypso.data.atomic.DummyElement property) (calypso.data.atomic.Element property) (calypso.data.Element property) mkdir() (calypso.dispatchers.orchestrator.executor.ssh.SSHClient method) MLP (calypso.config.config.ICode attribute) module calypso, [1] calypso.cli calypso.config calypso.config.config calypso.config.read_dat calypso.constants calypso.data calypso.data.atomic calypso.data.manage_group calypso.descriptors.nan calypso.dispatchers calypso.dispatchers.dispatcher calypso.dispatchers.orchestrator calypso.dispatchers.orchestrator.executor calypso.dispatchers.orchestrator.executor.base_executor calypso.dispatchers.orchestrator.executor.local calypso.dispatchers.orchestrator.executor.ssh calypso.dispatchers.orchestrator.jobs calypso.dispatchers.orchestrator.log calypso.dispatchers.orchestrator.machine calypso.dispatchers.orchestrator.orchestrator calypso.dispatchers.orchestrator.scheduler calypso.dispatchers.orchestrator.scheduler.base_scheduler calypso.dispatchers.orchestrator.scheduler.lsf calypso.dispatchers.orchestrator.scheduler.pbs calypso.dispatchers.orchestrator.scheduler.shell calypso.dispatchers.orchestrator.scheduler.slurm calypso.dispatchers.orchestrator.toolkit calypso.fitnesses.enthalpy calypso.fitnesses.nan calypso.formula calypso.logo calypso.site calypso.symbols calypso.tools calypso.tools.cli_convert calypso.tools.cli_wyckcomb calypso.utils calypso.utils.cleancache calypso.utils.factory calypso.utils.hash calypso.utils.lazyloader calypso.utils.log calypso.utils.registry calypso.utils.rotate_dir calypso.utils.seed calypso.utils.singleton calypso.utils.str_parser calypso.utils.to_toml example

MOLECULAR (calypso.config.config.IType attribute) monitoring() (calypso.dispatchers.orchestrator.Orchestrator method) (calypso.dispatchers.orchestrator.orchestrator.Orchestrator method) multiline() (in module calypso.config.read_dat) myClass (class in example) myMethod() (example.myClass method)

N

name (calypso.data.atomic.DummyElement property) (calypso.data.atomic.Element property) (calypso.data.Element property) (calypso.dispatchers.orchestrator.jobs.Job attribute) (calypso.dispatchers.orchestrator.machine.MachineData attribute) NAN (calypso.config.config.IFit attribute) (calypso.config.config.ISim attribute) NANDescriptor (class in calypso.descriptors.nan) NanFitness (class in calypso.fitnesses.nan) NestedMongoDict (class in calypso.config.config)

numb_cpu_per_node (calypso.dispatchers.orchestrator.machine.MachineData attribute) numb_node (calypso.dispatchers.orchestrator.machine.MachineData attribute) number (calypso.data.atomic.DummyElement property) (calypso.data.atomic.Element property) (calypso.data.Element property) (calypso.site.Site property) number2symbol() (in module calypso.data) (in module calypso.data.atomic) numbers2symbols() (in module calypso.data) (in module calypso.data.atomic) NumpyPrettyPrinter (class in calypso.data.manage_group)

O

ORCH (calypso.config.config.IDisp attribute) orchestrate() (calypso.dispatchers.orchestrator.Orchestrator method) (calypso.dispatchers.orchestrator.orchestrator.Orchestrator method)

Orchestrator (class in calypso.dispatchers.orchestrator) (class in calypso.dispatchers.orchestrator.orchestrator)

P

ParameterizedSingletonMeta (class in calypso.utils.singleton) parse_job_state() (calypso.dispatchers.orchestrator.scheduler.pbs.PBS method) parse_slice() (in module calypso.utils.str_parser) parser_spg() (in module calypso.config.config) password (calypso.dispatchers.orchestrator.machine.MachineData attribute) PBS (class in calypso.dispatchers.orchestrator.scheduler.pbs) PERIODIC (calypso.formula.FormulaFmt attribute)

pickup_from_old_submit() (calypso.dispatchers.orchestrator.Orchestrator method) (calypso.dispatchers.orchestrator.orchestrator.Orchestrator method) port (calypso.dispatchers.orchestrator.machine.MachineData attribute) pre_process_config() (in module calypso.config.config) process() (calypso.utils.log.LogAdapter method) ProcInfo (class in calypso.dispatchers.orchestrator.toolkit) PWSCF (calypso.config.config.ICode attribute)

Q

query() (calypso.dispatchers.orchestrator.scheduler.base_scheduler.BaseScheduler method) (calypso.dispatchers.orchestrator.scheduler.lsf.LSF method) (calypso.dispatchers.orchestrator.scheduler.pbs.PBS method) (calypso.dispatchers.orchestrator.scheduler.shell.Shell method) (calypso.dispatchers.orchestrator.scheduler.slurm.Slurm method)

queue (calypso.dispatchers.orchestrator.machine.MachineData attribute) queueing (calypso.dispatchers.orchestrator.jobs.JobStatus attribute)

R

read_file() (calypso.dispatchers.orchestrator.executor.ssh.SSHClient method) read_group_raw_csv() (in module calypso.data.manage_group) read_inputdat() (in module calypso.config.read_dat) read_remote_file() (calypso.dispatchers.orchestrator.executor.base_executor.BaseExecutor method) (calypso.dispatchers.orchestrator.executor.local.Local method) (calypso.dispatchers.orchestrator.executor.ssh.SSHExecutor method) read_subgroup_raw_csv() (in module calypso.data.manage_group) recursive_update() (in module calypso.config.config) reduce (calypso.formula.Formula property) register() (calypso.utils.factory.Factory method) register_module() (calypso.utils.Registry method) (calypso.utils.registry.Registry method) Registry (class in calypso.utils) (class in calypso.utils.registry) release() (calypso.dispatchers.orchestrator.toolkit.ThreadLock method), [1] remote_file_exist() (calypso.dispatchers.orchestrator.executor.ssh.SSHExecutor method) remote_log_file (calypso.dispatchers.orchestrator.jobs.Job attribute)

remote_rglob() (calypso.dispatchers.orchestrator.executor.ssh.SSHClient method) remote_root (calypso.dispatchers.orchestrator.jobs.Job attribute) (calypso.dispatchers.orchestrator.machine.MachineData attribute) remote_running_script (calypso.dispatchers.orchestrator.jobs.Job attribute) remote_work_dir (calypso.dispatchers.orchestrator.jobs.Job attribute) remove() (calypso.constants.CalypsoFiles method) resubmitted (calypso.dispatchers.orchestrator.jobs.JobStatus attribute) retry (calypso.dispatchers.orchestrator.jobs.Job attribute) returncode (calypso.dispatchers.orchestrator.toolkit.ProcInfo attribute) rglob() (calypso.dispatchers.orchestrator.executor.base_executor.BaseExecutor method) (calypso.dispatchers.orchestrator.executor.local.Local method) (calypso.dispatchers.orchestrator.executor.ssh.SSHExecutor method) rotate_name() (in module calypso.utils.rotate_dir) row (calypso.data.atomic.Element property) (calypso.data.Element property) run() (calypso.dispatchers.orchestrator.toolkit.ThreadWithException method) running (calypso.dispatchers.orchestrator.jobs.JobStatus attribute)

S

SABC (calypso.config.config.IAlgo attribute) sample_range() (calypso.formula.FormulaUnit static method) (in module calypso.formula) scheduler (calypso.dispatchers.orchestrator.machine.MachineData attribute) scheduler_env (calypso.dispatchers.orchestrator.machine.MachineData attribute) seed_everything() (in module calypso.utils) (in module calypso.utils.seed) serialize() (calypso.dispatchers.orchestrator.machine.Machine method) (calypso.dispatchers.orchestrator.Orchestrator method) (calypso.dispatchers.orchestrator.orchestrator.Orchestrator method) Shell (class in calypso.dispatchers.orchestrator.scheduler.shell) SIESTA (calypso.config.config.ICode attribute) singleline() (in module calypso.config.read_dat) singleton() (in module calypso.utils) (in module calypso.utils.singleton) SingletonMeta (class in calypso.utils.singleton) Site (class in calypso.site) Slurm (class in calypso.dispatchers.orchestrator.scheduler.slurm) SPLIT (calypso.config.config.IRunner attribute) split_list() (in module calypso.dispatchers.orchestrator.toolkit) SplitBlock() (in module calypso.config.read_dat) SplitLine (class in calypso.config.read_dat) SSHClient (class in calypso.dispatchers.orchestrator.executor.ssh) SSHExecutor (class in calypso.dispatchers.orchestrator.executor.ssh) start() (calypso.dispatchers.orchestrator.Orchestrator method) (calypso.dispatchers.orchestrator.orchestrator.Orchestrator method)

start_monitoring() (calypso.dispatchers.orchestrator.Orchestrator method) (calypso.dispatchers.orchestrator.orchestrator.Orchestrator method) status (calypso.dispatchers.orchestrator.jobs.Job attribute) stderr (calypso.dispatchers.orchestrator.toolkit.ProcInfo attribute) stdout (calypso.dispatchers.orchestrator.toolkit.ProcInfo attribute) stop() (calypso.dispatchers.orchestrator.Orchestrator method) (calypso.dispatchers.orchestrator.orchestrator.Orchestrator method) stopping (calypso.dispatchers.orchestrator.jobs.JobStatus attribute) store() (calypso.descriptors.nan.NANDescriptor method) StructureMessage (class in calypso.utils.log) submit() (calypso.dispatchers.orchestrator.scheduler.base_scheduler.BaseScheduler method) (calypso.dispatchers.orchestrator.scheduler.lsf.LSF method) (calypso.dispatchers.orchestrator.scheduler.pbs.PBS method) (calypso.dispatchers.orchestrator.scheduler.shell.Shell method) (calypso.dispatchers.orchestrator.scheduler.slurm.Slurm method) submit_batch (calypso.dispatchers.orchestrator.jobs.Job attribute) submit_task() (calypso.dispatchers.orchestrator.machine.Machine method) SURFACE (calypso.config.config.IType attribute) symbol (calypso.data.atomic.DummyElement property) (calypso.data.atomic.Element property) (calypso.data.Element property) (calypso.site.Site property) symbol2number() (in module calypso.data) (in module calypso.data.atomic) Symbols (class in calypso.symbols) symbols2numbers() (in module calypso.data) (in module calypso.data.atomic)

T

task_done() (calypso.dispatchers.dispatcher.Dispatcher method) terminate_monitoring() (calypso.dispatchers.orchestrator.Orchestrator method) (calypso.dispatchers.orchestrator.orchestrator.Orchestrator method) terminated (calypso.dispatchers.orchestrator.jobs.JobStatus attribute) THREAD (calypso.config.config.IRunner attribute) ThreadLock (class in calypso.dispatchers.orchestrator.toolkit)

ThreadWithException (class in calypso.dispatchers.orchestrator.toolkit) TimeParser (class in calypso.dispatchers.orchestrator.toolkit) to_dict() (calypso.config.config.NestedMongoDict method) to_lower_configdict() (in module calypso.config.config) to_string() (calypso.dispatchers.orchestrator.toolkit.TimeParser method) TRANSITION (calypso.config.config.IType attribute)

U

uint2base64() (in module calypso.utils.hash) unknown (calypso.dispatchers.orchestrator.jobs.JobStatus attribute) unknown_cli_func() (in module calypso.cli) unsubmitted (calypso.dispatchers.orchestrator.jobs.JobStatus attribute) update_job_state() (calypso.dispatchers.orchestrator.machine.Machine method) upload_file() (calypso.dispatchers.orchestrator.executor.ssh.SSHClient method) upload_file_to_remote() (calypso.dispatchers.orchestrator.executor.base_executor.BaseExecutor method) (calypso.dispatchers.orchestrator.executor.local.Local method) (calypso.dispatchers.orchestrator.executor.ssh.SSHExecutor method)

upload_files (calypso.dispatchers.orchestrator.jobs.Job attribute) upload_job() (calypso.dispatchers.orchestrator.executor.base_executor.BaseExecutor method) (calypso.dispatchers.orchestrator.executor.local.Local method) (calypso.dispatchers.orchestrator.executor.ssh.SSHExecutor method) upload_jobs() (calypso.dispatchers.orchestrator.machine.Machine method) upload_share_files (calypso.dispatchers.orchestrator.jobs.Job attribute) username (calypso.dispatchers.orchestrator.machine.MachineData attribute)

V

VASP (calypso.config.config.ICode attribute) vdw_radius (calypso.data.atomic.DummyElement property) (calypso.data.atomic.Element property) (calypso.data.Element property)

velocity (calypso.site.Site property) verify_config() (in module calypso.config.config)

W

WeakParameterizedSingletonMeta (class in calypso.utils.singleton) write_file() (calypso.dispatchers.orchestrator.executor.ssh.SSHClient method) write_group_raw_csv() (in module calypso.data.manage_group) write_into_remote_file() (calypso.dispatchers.orchestrator.executor.base_executor.BaseExecutor method) (calypso.dispatchers.orchestrator.executor.local.Local method) (calypso.dispatchers.orchestrator.executor.ssh.SSHExecutor method)

write_subgroup_raw_csv() (in module calypso.data.manage_group) write_toml() (in module calypso.utils.to_toml)

X

XRD (calypso.config.config.IFit attribute)