PolTensor¶
This module defines the PolTensor workflow.
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class
mybigdft.workflows.poltensor.PolTensor(ground_state, ef_amplitudes=None, order=1)[source]¶ Bases:
mybigdft.workflows.workflow.AbstractWorkflowThis workflow allows to compute the (electronic) polarizability tensor of a given system.
The polarizability tensor represents the response of the charges of a system (its dipole) to the application of an external electric field.
To compute this polarizability tensor, some BigDFT calculations are performed, where the system is subject to an external electric field along each direction of space (\(x\), \(y\) and \(z\)). The elements of the polarizability tensor are then defined by the ratio of the delta of the dipole in one direction and the delta of the electric field amplitudes:
\[\alpha_{ij} = \frac{\Delta D_i}{\Delta E_j}\]where \(i, j \in \{x, y, z\}\), \(\Delta D_i\) is the variation of the dipole along the \(i\) direction and \(\Delta E_j\) is the variation of the electric field amplitude along the \(j\) direction.
A PolTensor workflow is initialized by the job of the ground- state of the system and three electric field amplitudes.
- Parameters
ground_state (Job) – Job used to compute the ground state of the system under consideration.
ef_amplitudes (list or numpy array of length 3) – Amplitude of the electric field to be applied in the three directions of space (\(x\), \(y\), \(z\)).
order (int) – Order of the numerical differentiation used to compute the polarizability tensor. If second order (resp. first), then six (resp. three) calculations per atom are to be performed.
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property
ground_state¶ - Returns
Job of the ground state of the system under consideration.
- Return type
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property
ef_amplitudes¶ - Returns
Amplitude of the electric field to be applied in the three directions of space (\(x\), \(y\), \(z\)).
- Return type
list or numpy array of length 3
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property
order¶ - Returns
order – Order of the numerical differentiation used to compute the polarizability tensor. If second order (resp. first), then six (resp. three) calculations per atom are to be performed.
- Return type
int
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property
pol_tensor¶ - Returns
Polarizability tensor of the system (units: atomic).
- Return type
numpy.array
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property
mean_polarizability¶ - Returns
Mean (electronic) polarizability of the system (units: atomic).
- Return type
float
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property
efields¶ - Returns
Electric fields the system must undergo before computing the polarizability tensor as post-processing. There are three or six of them (one or two per space coordinate, depending on the order of the numerical derivative procedure) if the forward or central difference scheme is used, respectively.
- Return type
OrderedDict of length 3 or 6
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post_proc()[source]¶ Compute the polarisability tensor and set its value (you can access its value via the attribute
pol_tensor).
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property
is_completed¶ - Returns
True if all the post-processing attributes are no longer set to their default value.
- Return type
bool
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property
logfiles¶ - Returns
A dictionary of all the logfiles of the workflow, with the name of the associated job as key.
- Return type
dict
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property
queue¶ - Returns
All the jobs of the workflow.
- Return type
list
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run(nmpi=1, nomp=1, force_run=False, dry_run=False, restart_if_incomplete=False, timeout=None)¶ Run all the calculations if the post-processing was not already performed.
Warning
If force_run or dry_run is set to True, then any previous value of the post-processing attributes is deleted and set back to their default value, so that the post-processing is not considered as being performed.
- Parameters
nmpi (int) – Number of MPI tasks.
nomp (int) – Number of OpenMP tasks.
force_run (bool) – If True, the calculations are run even though a logfile already exists.
dry_run (bool) – If True, the input files are written on disk, but the bigdft-tool command is run instead of the bigdft one.
restart_if_incomplete (bool) – If True, the job is restarted if the existing logfile is incomplete.
timeout (float or int or None) – Number of minutes after which each job must be stopped.
- Warns
UserWarning – If the post-processing was already completed.
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class
mybigdft.workflows.poltensor.ElectricField[source]¶ Bases:
mybigdft.workflows.poltensor.ElectricFieldThis class defines an electric field from the coordinate index and the amplitude of the electric field in that direction.
Create new instance of ElectricField(i_coord, amplitude)
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property
vector¶ - Returns
ElectricField vector.
- Return type
list
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property
amplitude¶ Alias for field number 1
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count()¶ Return number of occurrences of value.
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property
i_coord¶ Alias for field number 0
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index()¶ Return first index of value.
Raises ValueError if the value is not present.
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property