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Configuration

Configuration#

Configuration is handled with ade.Config and can be modified for full customization of the calculations. By default, high-level optimisations are performed at PBE0-D3BJ/def2-SVP and single points at PBE0-D3BJ/def2-TZVP.

Calculations#

General#

The high-level electronic structure code defaults to the first available from {ORCA, Gaussian09, Gaussian16, NWChem, QChem} and the low-level from {XTB, MOPAC}. To select Gaussian09 as the high-level method:

>>> import autode as ade
>>> ade.Config.hcode = 'g09'

Similarly, with the low-level:

>>> ade.Config.lcode = 'MOPAC'

To set the number of cores available and the memory per core (in MB), to use a maximum of 32 GB for the whole calculation:

>>> ade.Config.n_cores = 8
>>> ade.Config.max_core = 4000

Keywords#

autodE uses wrappers around common keywords used in QM calculations to allow easy setting of e.g. a DFT functional.

>>> kwds = ade.Config.ORCA.keywords.sp
>>> kwds.functional
Functional(pbe0)

To modify the functional for single point energies, in ORCA:

>>> kwds.functional = 'B3LYP'

Alternatively, reassign to a whole new set of keywords:

>>> ade.Config.ORCA.keywords.sp = ['SP', 'B3LYP', 'def2-TZVP']

To add diffuse functions with the ma scheme to the def2-SVP default basis set for optimisations:

>>> ade.Config.ORCA.keywords.set_opt_basis_set('ma-def2-SVP')

Note

set_opt_basis_set sets the basis set in keywords.grad, keywords.opt_ts keywords.opt, keywords.low_opt and keywords.hess.

Temporary configuration#

It is also possible to change configuration temporarily, by using the context manager:

>>> ade.Config.ORCA.keywords.opt.functional
Functional(pbe0)
>>> ade.Config.n_cores = 4
>>> mol = ade.Molecule(smiles='CCO')
>>> with ade.temporary_config():
>>>     ade.Config.n_cores = 9
>>>     ade.Config.ORCA.keywords.opt.funcitonal = 'B3LYP'
>>>     # this calculation will run with 9 cores and B3LYP functional
>>>     mol.optimise(method=ade.methods.ORCA())
>>> # when context manager returns previous state of Config is restored
>>> ade.Config.n_cores
4
>>> ade.Config.ORCA.keywords.opt.functional
Functional(pbe0)

When the context manager exits, the previous state of the configuration is restored.

Warning

Note that the context manager works by saving the state of the Config when it is called and restoring the state when it exits. The way Python handles object references means that any references taken before or inside the context manager will become useless after it exits. Please see the example below for details.

>>> kwds = ade.Config.ORCA.keywords  # kwds refers to an object inside Config.ORCA
>>> with temporary_config():
...     kwds.opt.functional = 'B3LYP'
...     mol.optimise(method=ade.method.ORCA())
...     # this works successfully
>>> # when context manager exits, all variables in Config are restored, including Config.ORCA
>>> # But kwds still refers to an object from old Config.ORCA
>>> kwds.opt.functional
Functional(B3LYP)
>>> ade.Config.ORCA.opt.functional  # current config
Functional(pbe0)

As seen from the above example, the variable kwds is useless once the context manager exits, and changes to kwds no longer affects autodE. It is best to always modify Config directly.

XTB as a hmethod#

To use XTB as the hmethod for minima and TS optimisations within Gaussian use the xtb-gaussian wrapper and some default options. Note that the string to call xtb-gaussian will need to be modified with the appropriate keywords for spin and solvent, e.g., “xtb-gaussian –alpb water”.

>>> kwds = ade.Config.G16.keywords
>>> kwds.sp = ["External='xtb-gaussian'", "IOp(3/5=30)"]
>>> kwds.low_opt = ["External='xtb-gaussian'", "Opt(Loose, NoMicro)", "IOp(3/5=30)"]
>>> kwds.opt = ["External='xtb-gaussian'", "Opt(NoMicro)", "IOp(3/5=30)"]
>>> kwds.opt_ts = ["External='xtb-gaussian'", "Opt(TS, CalcFC, NoEigenTest, MaxCycles=100, MaxStep=10, NoTrustUpdate, NoMicro)", "IOp(3/5=30)"]
>>> kwds.hess = ["External='xtb-gaussian'", "Freq", "Geom(Redundant)", "IOp(3/5=30)"]
>>> kwds.grad = ["External='xtb-gaussian'", 'Force(NoStep)', "IOp(3/5=30)"]

To use XTB within ORCA copy the xtb binary to the folder where the orca binary is located and rename it otool_xtb, then set the keywords to use. For example

>>> kwds = ade.Config.ORCA.keywords
>>> kwds.sp = ['SP', 'PBE0', 'def2-SVP']
>>> kwds.opt = ['Opt', 'XTB2']
>>> kwds.low_opt = ['Opt', 'XTB2']
>>> kwds.hess = ['NumFreq', 'XTB2']
>>> kwds.grad = ['EnGrad', 'XTB2']
>>> kwds.opt_ts = ['OptTS', 'NumFreq', 'XTB2\n',
  '%geom\n'
  'NumHess true\n'
  'Calc_Hess true\n'
  'Recalc_Hess 30\n'
  'Trust -0.1\n'
  'MaxIter 150\n'
  'end']

Other#

See the config file to see all the options.

Note

NWChem currently only supports solvents for DFT, other methods must not have a solvent.

Logging#

To set the logging level to one of {DEBUG, INFO, WARNING, ERROR} set the AUTODE_LOG_LEVEL environment variable, in bash:

$ export AUTODE_LOG_LEVEL=INFO

To output the log to a file set e.g. autode.log:

$ export AUTODE_LOG_FILE=autode.log

To log with timestamps and colours:

$ conda install coloredlogs

To set the logging level permanently add the above export statements to your bash_profile.

In case of Windows command prompt, use the set command to set environment variables:

> set AUTODE_LOG_LEVEL=INFO

For powershell, use $env:

> $env:AUTODE_LOG_FILE = 'INFO'
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