Writers

QM-only input

class QMzyme.Writers.QMWriter(filename, memory, nprocs, full_region=None)

Writes a QM input file for ORCA or Gaussian using AQME qprep.

Parameters:

  • filename (str (required) Example: filename='1oh0_cutoff3') -- Name to be given to calculation input file. Does not need to contain file format suffix.

  • memory (str (optional, default memory='24GB')) -- Memory for the QM calculation (i) Gaussian: total memory; (ii) ORCA: memory per processor.

  • nprocs (int (optional, default nprocs=12)) -- Number of processors used in the QM calculation.

write()
reference()

QM/QM2 input

class QMzyme.Writers.QMQM2Writer(filename, memory, nprocs, full_region=None, total_charge=None, total_mult=None, high_region=None, low_region=None)

Writes a QM input file for ORCA or Gaussian using AQME qprep.

Parameters:

  • filename (str, required) -- Name to be given to calculation input file. Does not need to contain file format suffix. Example: filename='1oh0_cutoff3'.

  • memory (str, default='12GB') -- Memory for the QM calculation (i) Gaussian: total memory; (ii) ORCA: memory per processor.

  • nprocs (int, default nprocs=12) -- Number of processors used in the QM calculation.

  • high_region (QMzymeRegion, optional) -- QMzymeRegion with assigned QM method. If not provided, the code will search in CalculateModel.calculation for the 'QM' entry.

  • low_region (QMzymeRegion, optional) -- QMzymeRegion with assigned QM method. If not provided, the code will search in CalculateModel.calculation for the 'QM2' entry.

Notes:

Useful reminder for developers: Example text added to QM input file: .. code-block:: bash

!QM/QM2 WB97X-D3 DEF2-TZVP %QMMM QM2CUSTOMMETHOD "PBE D3BJ DEF2-SVP" QMATOMS {2:3} {6:13} END

The charge and multiplicity above the coordinates section is assigned to the high region (QM atoms).

write(full_region, high_region)
reference()

QM/xTB input

class QMzyme.Writers.QMXTBWriter(filename, memory, nprocs, full_region=None, high_region=None, low_region=None, total_charge=None, total_mult=None)

Writes a QM input file for ORCA or Gaussian using AQME qprep.

Parameters:

  • filename (str, required) -- Name to be given to calculation input file. Does not need to contain file format suffix. Example: filename='1oh0_cutoff3'

  • memory (str, default='12GB') -- Memory for the QM calculation (i) Gaussian: total memory; (ii) ORCA: memory per processor.

  • nprocs (int, default=12) -- Number of processors used in the QM calculation.

  • high_region (QMzymeRegion, optional) -- QMzymeRegion with assigned QM method. If not provided, the code will search in CalculateModel.calculation for the 'QM' entry.

  • low_region (QMzymeRegion, optional) -- QMzymeRegion with assigned xTB method. If not provided, the code will search in CalculateModel.calculation for the 'XTB' entry.

Notes:

Useful for developers. Example input: .. code-block:: bash

!QM/XTB WB97X-D3 DEF2-TZVP %QMMM QMATOMS {2:3} {6:13} END

The charge and mult above the coordinates section is assigned to the high region (QM atoms).

write(full_region, high_region)
reference()

QM/MM input

class QMzyme.Writers.QMMMWriter(filename, memory, nprocs, full_region)

Under development.

Developer Classes

If you are interesed in contributing to the QMzyme project by adding a new concrete Writer class, you will need to be familiar with these developer classes. Read more about it in the QMzyme Documentation.

We hope to support multi-scale methods beyond 2 layers in the bear future.

class QMzyme.Writers.Writer(filename, memory, nprocs, full_region)

Abstract Base Class for all calculation input file concrete writer classes. This class provides a rigid structure that imposes the required methods of all concrete writer classes to support community contributions.

If you are interested in contribute to QMzyme by creating a new writer class, see the QMzyme Documentation.

abstractmethod write()
abstractmethod reference()
set_constraints()
class QMzyme.Writers.WriterFactory

Factory Class to Register Concrete Writer Classes.

writers = {'QM': <class 'QMzyme.Writers.QMWriter'>, 'QMChargeField': <class 'QMzyme.Writers.QMMMWriter'>, 'QMQM2': <class 'QMzyme.Writers.QMQM2Writer'>, 'QMXTB': <class 'QMzyme.Writers.QMXTBWriter'>}
static register_writer(writer_type, writer)
static make_writer(writer_type, filename, memory, nprocs, **kwargs)

Instantiates and returns the specific concrete writer subclass.