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Mode: electronic polarization

Syntax

atomsk --electronic-polarization <file> [options]

atomsk -PE <file> [options]

Description

This mode computes the electronic polarization of each ion in the framework of an ionic core-shell model, defined by the displacement of the electonic shell with respect to the ionic core, i.e. for ion i:

       Pi = 0.5*(|Qi|+|qi|) (Ri-ri)

where Q_i and R_i are the charge and position of the ionic core, and q_i and r_i are the charge and position of the electronic shell.

This mode will not compute anything if the charges for the ionic cores and shells are not set, or if there are no shells at all in the system. The charges can be defined thanks to the option -properties. For instance consider a fictitious system made of ions A and B, then the charges can be written in a file with the following format and read with the option -properties:

If some ions have no shell (so-called "rigid ions"), then their electronic polarization will be set to zero.

Output consists of the following files:

• *_PE.cfg: file in the CFG format containing the positions of ionic cores, and the polarization vector and amplitude as auxiliary properties;
• *_PE.xsf: file in the XSF format containing the positions of ionic cores and the polarization vector of the ion; xCrySDen can read this file and display vectors; beware that xCrySDen understands these vectors as FORCES (not as polarization vectors), so it may be tricky to set these vectors to the correct scale.

Note that when Atomsk reads a file containing shells, it tries to associate each shell to a core. If this association is wrong (most likely because cores and shell appear in random orders in the input file), it can be fixed with the option -bind-shells.

If this mode is used with one or several options they will be applied to the system before computing the electronic polarization.

Examples

• atomsk --electronic-polarization MgO.xsf

  This will not compute anything because the charges of cores and shells are not set.

• mgo.txt

  charge
Mg 1.58 0.42
O 0.513 -2.513


  atomsk -PE MgO.gin -prop mgo.txt

  This will read the positions of cores and shells from MgO.gin, and their charges from mgo.txt (Mg cores will have a charge of 1.58e, Mg shells 0.42e, and oxygen cores a charge of 0.513e and oxygen shells -2.513e). Then the polarization of each ion will be computed.

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