run module¶
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run.
addatexit__
(command, *args, **kwargs)[source]¶ Wrapper to add function to be run at exit
Parameters: - command (func) – function to be run
- *args – arguments for command
Keyword Arguments: **kwargs – Keyword arguments for command
Returns: None
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run.
bands
(calcs, engine='', execPrefix=None, execPostfix=' ', holdFlag=True, config=None)[source]¶ Wrapper to set up Electronic Band Structure calculation
Parameters: calcs (dict) – Dictionary of dictionaries of calculations
Keyword Arguments: - engine (str) – executable that you are calling to run the calculations
- execPrefix (str) – commands to go before the executable when run (ex. mpiexec nice -n 19 <executable>) (default = None)
- execPostfix (str) – commands to go after the executable when run (ex. <execPrefix> <executable> -ndiag 12 -nimage 2) (default = None)
- holdFlag (bool) – DEFUNCT. NEEDS REMOVAL
- config (str) – DEFUNCT. NEEDS REMOVAL
Returns: None
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run.
clean_cell_params
(output)[source]¶ Parses the atomic shifts in a supercell from fd.x outputted pw.x input files to correct for formatting issues when they are imported to AFLOWpi
Parameters: output (str) – pw.x input files generated by fd.x Keyword Arguments: None – Returns: pw.x input files generated by fd.x (cleaned by AFLOWpi) Return type: output (str)
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run.
cleanup
(calcs)[source]¶ Deletes all files a calculation set’s directory tree that are prepended with ‘_’
Parameters: calcs (dict) – Dictionary of dictionaries of calculations Keyword Arguments: None – Returns: None
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run.
dos
(calcs, engine='', execPrefix=None, execPostfix=None, holdFlag=True, config=None)[source]¶ Wrapper to set up DOS nscf calculation
Parameters: calcs (dict) – Dictionary of dictionaries of calculations
Keyword Arguments: - engine (str) – executable that you are calling to run the calculations
- execPrefix (str) – commands to go before the executable when run (ex. mpiexec nice -n 19 <executable>) (default = None)
- execPostfix (str) – commands to go after the executable when run (ex. <execPrefix> <executable> -ndiag 12 -nimage 2) (default = None)
- holdFlag (bool) – DEFUNCT. NEEDS REMOVAL
- config (str) – DEFUNCT. NEEDS REMOVAL
Returns: None
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run.
emr
(calcs, engine='', execPrefix=None, execPostfix=None, holdFlag=True, config=None)[source]¶ Wrapper to set up GIPAW EMR calculation
Parameters: calcs (dict) – Dictionary of dictionaries of calculations
Keyword Arguments: - engine (str) – executable that you are calling to run the calculations
- execPrefix (str) – commands to go before the executable when run (ex. mpiexec nice -n 19 <executable>) (default = None)
- execPostfix (str) – commands to go after the executable when run (ex. <execPrefix> <executable> -ndiag 12 -nimage 2) (default = None)
- holdFlag (bool) – DEFUNCT. NEEDS REMOVAL
- config (str) – DEFUNCT. NEEDS REMOVAL
Returns: None
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run.
generateSubRef
(qsubRefFileString, oneCalc, ID)[source]¶ Reads in the reference cluster submission file specified in “jobreffile” in the config used. Tries to insert a few parameters.
OBSOLETE PLANNED FOR REMOVAL
Parameters: - qsubRefFileString (str) – string of the “reference” cluster submission file
- oneCalc (dict) – dictionary of one of the calculations
- ID (str) – ID of calculation
Keyword Arguments: None –
Returns: string cluster submission file
Return type: clusterTypeDict (dict)
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run.
gvectors
(calcs, engine='', execPrefix=None, execPostfix=None, holdFlag=True, config=None)[source]¶ Wrapper to set up GIPAW gvectors calculation
Parameters: calcs (dict) – Dictionary of dictionaries of calculations
Keyword Arguments: - engine (str) – executable that you are calling to run the calculations
- execPrefix (str) – commands to go before the executable when run (ex. mpiexec nice -n 19 <executable>) (default = None)
- execPostfix (str) – commands to go after the executable when run (ex. <execPrefix> <executable> -ndiag 12 -nimage 2) (default = None)
- holdFlag (bool) – DEFUNCT. NEEDS REMOVAL
- config (str) – DEFUNCT. NEEDS REMOVAL
Returns: None
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run.
hyperfine
(calcs, engine='', execPrefix=None, execPostfix=None, holdFlag=True, config=None, isotope=())[source]¶ Wrapper to set up GIPAW hyperfine calculation
Parameters: calcs (dict) – Dictionary of dictionaries of calculations
Keyword Arguments: - engine (str) – executable that you are calling to run the calculations
- execPrefix (str) – commands to go before the executable when run (ex. mpiexec nice -n 19 <executable>) (default = None)
- execPostfix (str) – commands to go after the executable when run (ex. <execPrefix> <executable> -ndiag 12 -nimage 2) (default = None)
- holdFlag (bool) – DEFUNCT. NEEDS REMOVAL
- config (str) – DEFUNCT. NEEDS REMOVAL
Returns: None
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run.
nmr
(calcs, engine='', execPrefix=None, execPostfix=None, holdFlag=True, config=None)[source]¶ Wrapper to set up GIPAW NMR calculation
Parameters: calcs (dict) – Dictionary of dictionaries of calculations
Keyword Arguments: - engine (str) – executable that you are calling to run the calculations
- execPrefix (str) – commands to go before the executable when run (ex. mpiexec nice -n 19 <executable>) (default = None)
- execPostfix (str) – commands to go after the executable when run (ex. <execPrefix> <executable> -ndiag 12 -nimage 2) (default = None)
- holdFlag (bool) – DEFUNCT. NEEDS REMOVAL
- config (str) – DEFUNCT. NEEDS REMOVAL
Returns: None
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run.
pdos
(calcs, engine='', execPrefix=None, execPostfix='', holdFlag=True, config=None)[source]¶ Wrapper to set up DOS projection calculation
Parameters: calcs (dict) – Dictionary of dictionaries of calculations
Keyword Arguments: - engine (str) – executable that you are calling to run the calculations
- execPrefix (str) – commands to go before the executable when run (ex. mpiexec nice -n 19 <executable>) (default = None)
- execPostfix (str) – commands to go after the executable when run (ex. <execPrefix> <executable> -ndiag 12 -nimage 2) (default = None)
- holdFlag (bool) – DEFUNCT. NEEDS REMOVAL
- config (str) – DEFUNCT. NEEDS REMOVAL
Returns: None
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run.
prep_fd
(__submitNodeName__, oneCalc, ID, nrx1=2, nrx2=2, nrx3=2, innx=2, de=0.01, atom_sym=True, disp_sym=True, proj_phDOS=True)[source]¶ Generates input files for fd.x, fd_ifc.x, and matdyn.x for the finite difference phonon calculations.
Parameters: - __submitNodeName__ (str) – String of hostname that cluster jobs should be submitted from
- oneCalc (dict) – dictionary of one of the calculations
- ID (str) – ID of calculation
Keyword Arguments: - nrx1 (int) – supercell size for first primitive lattice vector
- nrx2 (int) – supercell size for second primitive lattice vector
- nrx3 (int) – supercell size for third primitive lattice vector
- innx (int) – how many differernt shifts in each direction for finite difference phonon calculation
- de (float) – amount to shift the atoms for finite differences
Returns: None
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run.
reset_logs
(calcs)[source]¶ Removes log files from AFLOWpi directory
Parameters: calcs (dict) – Dictionary of dictionaries of calculations Keyword Arguments: None – Returns: None
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run.
resubmit
(calcs)[source]¶ Stages loaded calculation set to be resubmitted on a cluster
Parameters: calcs (dict) – Dictionary of dictionaries of calculations Keyword Arguments: None – Returns: None
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run.
scf
(calcs, engine='', execPrefix=None, execPostfix=None, holdFlag=True, config=None, exit_on_error=True)[source]¶ Wrapper to set up self-consitent calculation
Parameters: calcs (dict) – Dictionary of dictionaries of calculations
Keyword Arguments: - engine (str) – executable that you are calling to run the calculations
- execPrefix (str) – commands to go before the executable when run (ex. mpiexec nice -n 19 <executable>) (default = None)
- execPostfix (str) – commands to go after the executable when run (ex. <execPrefix> <executable> -ndiag 12 -nimage 2) (default = None)
- holdFlag (bool) – DEFUNCT. NEEDS REMOVAL
- config (str) – DEFUNCT. NEEDS REMOVAL
Returns:
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run.
submit
()[source]¶ sets global __submit__flag__ so calculations will start when user script completes
Parameters: None – Keyword Arguments: None – Returns: None
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run.
submitFirstCalcs__
(calcs)[source]¶ Submits the first step of a calculation’s pipeline
Parameters: calcs (dict) – Dictionary of dictionaries of calculations Keyword Arguments: None – Returns: None
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run.
testOne
(calcs, calcType='scf', engine='', execPrefix=None, execPostfix=None, holdFlag=True, config=None)[source]¶ Run all the calculation in the dictionary with a specific engine
Parameters: calcs (dict) – Dictionary of dictionaries of calculations
Keyword Arguments: - engine (str) – executable that you are calling to run the calculations
- execPrefix (str) – commands to go before the executable when run (ex. mpiexec nice -n 19 <executable>) (default = None)
- execPostfix (str) – commands to go after the executable when run (ex. <execPrefix> <executable> -ndiag 12 -nimage 2) (default = None)
Returns: None
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run.
write_fdx_template
(oneCalc, ID, nrx1=2, nrx2=2, nrx3=2, innx=2, de=0.01, atom_sym=True, disp_sym=True, proj_phDOS=True)[source]¶ Generates input files for fd.x, fd_ifc.x, and matdyn.x for the finite difference phonon calculations.
Parameters: - oneCalc (dict) – dictionary of one of the calculations
- ID (str) – ID of calculation
Keyword Arguments: - nrx1 (int) – supercell size for first primitive lattice vector
- nrx2 (int) – supercell size for second primitive lattice vector
- nrx3 (int) – supercell size for third primitive lattice vector
- innx (int) – how many differernt shifts in each direction for finite difference phonon calculation
- de (float) – amount to shift the atoms for finite differences
Returns: None