pyiron.atomistics.master.structure module¶
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class
pyiron.atomistics.master.structure.
StructureJobGenerator
(master)[source]¶ Bases:
pyiron_base.master.parallel.JobGenerator
JobGenerator for the StructureListMaster - this class implements the functions to generate the parameter list, modify the individual jobs according to the parameter list and generate the new job names according to the parameter list.
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static
job_name
(parameter)[source]¶ Generate job name for a give set of parameters
- Parameters
parameter – For the StructureListMaster the structures are simply numbered - struct_0, struct_1, …
- Returns
job name for the next job
- Return type
str
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modify_job
(job, parameter)[source]¶ Modify the next job by setting the structure for the specific parameter
- Parameters
job (GenericJob) – next job object to be executed
parameter – includes the atomistic structure
- Returns
- Return type
GenericJob
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property
parameter_list
¶ Returns: (list): [[index(int), pyiron.atomistics.structure.atoms.Atoms], …]
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static
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class
pyiron.atomistics.master.structure.
StructureListMaster
(project, job_name)[source]¶ Bases:
pyiron_base.master.parallel.ParallelMaster
The GenericMaster is the template class for all meta jobs - meaning all jobs which contain multiple other jobs. It defines the shared functionality of the different kind of job series.
- Parameters
project (ProjectHDFio) – ProjectHDFio instance which points to the HDF5 file the job is stored in
job_name (str) – name of the job, which has to be unique within the project
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.. attribute:: job_name
name of the job, which has to be unique within the project
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.. attribute:: status
- execution status of the job, can be one of the following [initialized, appended, created, submitted,
running, aborted, collect, suspended, refresh, busy, finished]
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.. attribute:: job_id
unique id to identify the job in the pyiron database
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.. attribute:: parent_id
job id of the predecessor job - the job which was executed before the current one in the current job series
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.. attribute:: master_id
job id of the master job - a meta job which groups a series of jobs, which are executed either in parallel or in serial.
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.. attribute:: child_ids
list of child job ids - only meta jobs have child jobs - jobs which list the meta job as their master
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.. attribute:: project
Project instance the jobs is located in
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.. attribute:: project_hdf5
ProjectHDFio instance which points to the HDF5 file the job is stored in
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.. attribute:: job_info_str
short string to describe the job by it is job_name and job ID - mainly used for logging
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.. attribute:: working_directory
working directory of the job is executed in - outside the HDF5 file
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.. attribute:: path
path to the job as a combination of absolute file system path and path within the HDF5 file.
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.. attribute:: version
Version of the hamiltonian, which is also the version of the executable unless a custom executable is used.
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.. attribute:: executable
Executable used to run the job - usually the path to an external executable.
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.. attribute:: library_activated
For job types which offer a Python library pyiron can use the python library instead of an external executable.
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.. attribute:: server
Server object to handle the execution environment for the job.
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.. attribute:: queue_id
the ID returned from the queuing system - it is most likely not the same as the job ID.
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.. attribute:: logger
logger object to monitor the external execution and internal pyiron warnings.
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.. attribute:: restart_file_list
list of files which are used to restart the calculation from these files.
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.. attribute:: job_type
- Job type object with all the available job types: [‘ExampleJob’, ‘SerialMaster’, ‘ParallelMaster’,
‘ScriptJob’, ‘ListMaster’]
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.. attribute:: child_names
Dictionary matching the child ID to the child job name.
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from_hdf
(hdf=None, group_name=None)[source]¶ Restore the StructureListMaster object in the HDF5 File
- Parameters
hdf (ProjectHDFio) – HDF5 group object - optional
group_name (str) – HDF5 subgroup name - optional
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property
structure_lst
¶