forked from lijiext/lammps
convert the remainder of raw html typesetting in pair style smtbq
This commit is contained in:
Axel Kohlmeyer
parent
228a0bfa2e
commit
8662733dcd
|
|
@ -47,13 +47,13 @@ smooth convergence to zero interaction.
|
|||
|
||||
The parameters appearing in the upper expressions are set in the
|
||||
ffield.SMTBQ.Syst file where Syst corresponds to the selected system
|
||||
(e.g. field.SMTBQ.Al2O3). Examples for TiO2,
|
||||
Al2O3 are provided. A single pair\_coeff command
|
||||
(e.g. field.SMTBQ.Al2O3). Examples for :math:`\mathrm{TiO_2}`,
|
||||
:math:`\mathrm{Al_2O_3}` are provided. A single pair\_coeff command
|
||||
is used with the SMTBQ styles which provides the path to the potential
|
||||
file with parameters for needed elements. These are mapped to LAMMPS
|
||||
atom types by specifying additional arguments after the potential
|
||||
filename in the pair\_coeff command. Note that atom type 1 must always
|
||||
correspond to oxygen atoms. As an example, to simulate a TiO2 system,
|
||||
correspond to oxygen atoms. As an example, to simulate a :math:`\mathrm{TiO_2}` system,
|
||||
atom type 1 has to be oxygen and atom type 2 Ti. The following
|
||||
pair\_coeff command should then be used:
|
||||
|
||||
|
|
@ -76,7 +76,7 @@ Interaction between oxygen, :math:`E_{OO}`, consists of two parts,
|
|||
an attractive and a repulsive part. The attractive part is effective
|
||||
only at short range (< :math:`r_2^{OO}`). The attractive
|
||||
contribution was optimized to study surfaces reconstruction
|
||||
(e.g. :ref:`SMTB-Q\_2 <SMTB-Q_2>` in TiO2) and is not necessary
|
||||
(e.g. :ref:`SMTB-Q\_2 <SMTB-Q_2>` in :math:`\mathrm{TiO_2}`) and is not necessary
|
||||
for oxide bulk modeling. The repulsive part is the Pauli interaction
|
||||
between the electron clouds of oxygen. The Pauli repulsion and the
|
||||
coulombic electrostatic interaction have same cut off value. In the
|
||||
|
|
@ -99,7 +99,7 @@ ffield.SMTBQ.Syst. The energy band term is given by:
|
|||
\delta Q_i & = | Q_i^{F} | - | Q_i |
|
||||
|
||||
|
||||
where :math:\eta_i` is the stoichiometry of atom *i*\ ,
|
||||
where :math:`\eta_i` is the stoichiometry of atom *i*\ ,
|
||||
:math:`\delta Q_i` is the charge delocalization of atom *i*\ ,
|
||||
compared to its formal charge
|
||||
:math:`Q^F_i`. :math:`n_0`, the number of hybridized
|
||||
|
|
@ -118,7 +118,7 @@ two visions is explained in appendix A of the article in the
|
|||
SrTiO3 :ref:`SMTB-Q\_3 <SMTB-Q_3>` (parameter :math:`\beta` shown in
|
||||
this article is in fact the :math:`\beta_O`). To summarize the
|
||||
relationship between the hopping integral :math:`\xi^O` and the
|
||||
others, we have in an oxide CnOm the following
|
||||
others, we have in an oxide :math:`\mathrm{C_n O_m}` the following
|
||||
relationship:
|
||||
|
||||
.. math::
|
||||
|
|
@ -127,7 +127,7 @@ relationship:
|
|||
\frac{\beta_O}{\sqrt{m}} & = \frac{\beta_C}{\sqrt{n}} = \xi^0 \frac{\sqrt{m}+\sqrt{n}}{2}
|
||||
|
||||
|
||||
Thus parameter :math:`\mu`, indicated above, is given by :math:`\mu = (\sqrt{n} + \sqrt{m}) / 2`
|
||||
Thus parameter :math:`\mu`, indicated above, is given by :math:`\mu = \frac{1}{2}(\sqrt{n}+\sqrt{m})`
|
||||
|
||||
The potential offers the possibility to consider the polarizability of
|
||||
the electron clouds of oxygen by changing the slater radius of the
|
||||
|
|
@ -158,7 +158,7 @@ quotation marks ('').
|
|||
1) Number of different element in the oxide:
|
||||
|
||||
* N_elem= 2 or 3
|
||||
* Dividing line
|
||||
* Divider line
|
||||
|
||||
2) Atomic parameters
|
||||
|
||||
|
|
@ -166,68 +166,111 @@ For the anion (oxygen)
|
|||
|
||||
* Name of element (char) and stoichiometry in oxide
|
||||
* Formal charge and mass of element
|
||||
* Principal quantum number of outer orbital n), electronegativity (:math:`\xi^0_i`) and hardness (:math:`J^0_i`)
|
||||
* Principal quantum number of outer orbital n), electronegativity (:math:`\chi^0_i`) and hardness (:math:`J^0_i`)
|
||||
* Ionic radius parameters : max coordination number (\ *coordBB* = 6 by default), bulk coordination number *(coordB)*\ , surface coordination number *(coordS)* and *rBB, rB and rS* the slater radius for each coordination number. (**note : If you don't want to change the slater radius, use three identical radius values**)
|
||||
* Number of orbital shared by the element in the oxide (:math:`d_i`)
|
||||
* Dividing line
|
||||
* Divider line
|
||||
|
||||
For each cations (metal):
|
||||
|
||||
* Name of element (char) and stoichiometry in oxide
|
||||
* Formal charge and mass of element
|
||||
* Number of electron in outer orbital *(ne)*\ , electronegativity (\ *χ<sup>0</sup><sub>i</simulationub>*\ ), hardness (\ *J<sup>0</sup><sub>i</sub>*\ ) and *r<sub>Salter</sub>* the slater radius for the cation.
|
||||
* Number of orbitals shared by the elements in the oxide (\ *d<sub>i</sub>*\ )
|
||||
* Dividing line
|
||||
* Number of electron in outer orbital *(ne)*\ , electronegativity (:math:`\chi^0_i`), hardness (:math:`J^0_i`) and :math:`r_{Slater}` the slater radius for the cation.
|
||||
* Number of orbitals shared by the elements in the oxide (:math:`d_i`)
|
||||
* Divider line
|
||||
|
||||
3) Potential parameters:
|
||||
|
||||
* Keyword for element1, element2 and interaction potential ('second\_moment' or 'buck' or 'buckPlusAttr') between element 1 and 2. If the potential is 'second\_moment', specify 'oxide' or 'metal' for metal-oxygen or metal-metal interactions respectively.
|
||||
* Potential parameter: <pre><br/> If type of potential is 'second\_moment' : *A (eV)*\ , *p*\ , *ξ<sup>0</sup>* (eV) and *q* <br/> *r<sub>c1</sub>* (Å), *r<sub>c2</sub>* (Å) and *r<sub>0</sub>* (Å) <br/> If type of potential is 'buck' : *C* (eV) and *ρ* (Å) <br/> If type of potential is 'buckPlusAttr' : *C* (eV) and *ρ* (Å) <br/> *D* (eV), *B* (Å<sup>-1</sup>), *r<sub>1</sub><sup>OO</sup>* (Å) and *r<sub>2</sub><sup>OO</sup>* (Å) </pre>
|
||||
* Dividing line
|
||||
* Keyword for element1, element2 and interaction potential
|
||||
('second\_moment' or 'buck' or 'buckPlusAttr') between element 1
|
||||
and 2. If the potential is 'second\_moment', specify 'oxide' or
|
||||
'metal' for metal-oxygen or metal-metal interactions respectively.
|
||||
* Potential parameter:
|
||||
|
||||
- If type of potential is 'second\_moment' : A (eV), *p*,
|
||||
:math:`\zeta^0` (eV) and *q*, :math:`r_{c1} (\mathrm{\mathring{A}})`, :math:`r_{c2}
|
||||
(\mathrm{\mathring{A}})` and :math:`r_0 (\mathrm{\mathring{A}})`
|
||||
- If type of potential is 'buck' : *C* (eV) and :math:`\rho (\mathrm{\mathring{A}})`
|
||||
- If type of potential is 'buckPlusAttr' : *C* (eV) and :math:`\rho
|
||||
(\mathrm{\mathring{A}})` *D* (eV), *B* :math:`(\mathrm{\mathring{A}}^{-1})`, :math:`r^{OO}_1 (\mathrm{\mathring{A}})` and
|
||||
:math:`r^{OO}_2 (\mathrm{\mathring{A}})`
|
||||
* Divider line
|
||||
|
||||
4) Tables parameters:
|
||||
|
||||
* Cutoff radius for the Coulomb interaction (\ *R<sub>coul</sub>*\ )
|
||||
* Starting radius (\ *r<sub>min</sub>* = 1,18845 Å) and increments (\ *dr* = 0,001 Å) for creating the potential table.
|
||||
* Dividing line
|
||||
* Cutoff radius for the Coulomb interaction (:math:`R_{coul}`)
|
||||
* Starting radius (:math:`r_{min} = 1,18845 \mathrm{\mathring{A}}`) and increments
|
||||
(:math:`dr = 0.001 \mathrm{\mathring{A}}`) for creating the potential table.
|
||||
* Divider line
|
||||
|
||||
5) Rick model parameter:
|
||||
|
||||
* *Nevery* : parameter to set the frequency (\ *1/Nevery*\ ) of the charge resolution. The charges are evaluated each *Nevery* time steps.
|
||||
* Max number of iterative loop (\ *loopmax*\ ) and precision criterion (\ *prec*\ ) in eV of the charge resolution
|
||||
* Dividing line
|
||||
* *Nevery* : parameter to set the frequency of the charge
|
||||
resolution. The charges are evaluated each *Nevery* time steps.
|
||||
* Max number of iterative loop (\ *loopmax*\ ) and convergence criterion
|
||||
(\ *prec*\ ) in eV of the charge resolution
|
||||
* Divider line
|
||||
|
||||
6) Coordination parameter:
|
||||
|
||||
* First (\ *r<sub>1n</sub>*\ ) and second (\ *r<sub>2n</sub>*\ ) neighbor distances in Å
|
||||
* Dividing line
|
||||
* First (:math:`r_{1n}`) and second (:math:`r_{2n}`) neighbor distances
|
||||
in angstrom
|
||||
* Divider line
|
||||
|
||||
7) Charge initialization mode:
|
||||
|
||||
* Keyword (\ *QInitMode*\ ) and initial oxygen charge (\ *Q<sub>init</sub>*\ ). If keyword = 'true', all oxygen charges are initially set equal to *Q<sub>init</sub>*\ . The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create\_atom"#create\_atom command or the charge specified in the file structure using :doc:`read_data <read_data>` command.
|
||||
* Dividing line
|
||||
* Keyword (\ *QInitMode*\ ) and initial oxygen charge
|
||||
(:math:`Q_{init}`). If keyword = 'true', all oxygen charges are
|
||||
initially set equal to :math:`Q_{init}`. The charges on the cations
|
||||
are initially set in order to respect the neutrality of the box. If
|
||||
keyword = 'false', all atom charges are initially set equal to 0 if
|
||||
you use the :doc:`create_atoms <create_atoms>` command or the charge
|
||||
specified in the file structure using :doc:`read_data <read_data>`
|
||||
command.
|
||||
* Divider line
|
||||
|
||||
8) Mode for the electronegativity equalization (Qeq)
|
||||
8) Mode for the electronegativity equalization (Qeq)
|
||||
|
||||
* Keyword (\ *mode*\ ) followed by:
|
||||
|
||||
- QEqAll (one QEq group) \| no parameters
|
||||
- QEqAllParallel (several QEq groups) \| no parameters
|
||||
- Surface \| zlim (QEq only for z>zlim)
|
||||
|
||||
* Keyword mode: <pre> <br/> QEqAll (one QEq group) \| no parameters <br/> QEqAllParallel (several QEq groups) \| no parameters <br/> Surface \| zlim (QEq only for z>zlim) </pre>
|
||||
* Parameter if necessary
|
||||
* Dividing line
|
||||
* Divider line
|
||||
|
||||
9) Verbose
|
||||
|
||||
* If you want the code to work in verbose mode or not : 'true' or 'false'
|
||||
* If you want to print or not in file 'Energy\_component.txt' the three main contributions to the energy of the system according to the description presented above : 'true' or 'false' and *N<sub>Energy</sub>*\ . This option writes in file every *N<sub>Energy</sub>* time step. If the value is 'false' then *N<sub>Energy</sub>* = 0. The file take into account the possibility to have several QEq group *g* then it writes: time step, number of atoms in group *g*\ , electrostatic part of energy, *E<sub>ES</sub>*\ , the interaction between oxygen, *E<sub>OO</sub>*\ , and short range metal-oxygen interaction, *E<sub>MO</sub>*\ .
|
||||
* If you want to print in file 'Electroneg\_component.txt' the electronegativity component (\ *∂E<sub>tot</sub> ⁄∂Q<sub>i</sub>*\ ) or not: 'true' or 'false' and *N<sub>Electroneg</sub>*\ .This option writes in file every *N<sub>Electroneg</sub>* time step. If the value is 'false' then *N<sub>Electroneg</sub>* = 0. The file consist in atom number *i*\ , atom type (1 for oxygen and # higher than 1 for metal), atom position: *x*\ , *y* and *z*\ , atomic charge of atom *i*\ , electrostatic part of atom *i* electronegativity, covalent part of atom *i* electronegativity, the hopping integral of atom *i* *(Zβ<sup>2</sup>)<sub>i<sub>* and box electronegativity.
|
||||
* If you want to print or not in the file 'Energy\_component.txt' the
|
||||
three main contributions to the energy of the system according to the
|
||||
description presented above : 'true' or 'false' and
|
||||
:math:`N_{Energy}`. This option writes to the file every
|
||||
:math:`N_{Energy}` time steps. If the value is 'false' then
|
||||
:math:`N_{Energy} = 0`. The file takes into account the possibility to
|
||||
have several QEq groups *g* then it writes: time step, number of atoms
|
||||
in group *g*\ , electrostatic part of energy, :math:`E_{ES}`, the
|
||||
interaction between oxygen, :math:`E_{OO}`, and short range
|
||||
metal-oxygen interaction, :math:`E_{MO}`.
|
||||
* If you want to print to the file 'Electroneg\_component.txt' the
|
||||
electronegativity component (:math:`\frac{\partial E_{tot}}{\partial
|
||||
Q_i}`) or not: 'true' or 'false' and :math:`N_{Electroneg}`. This
|
||||
option writes to the file every :math:`N_{Electroneg}` time steps. If
|
||||
the value is 'false' then :math:`N_{Electroneg} = 0`. The file
|
||||
consist of atom number *i*\ , atom type (1 for oxygen and # higher
|
||||
than 1 for metal), atom position: *x*\ , *y* and *z*\ , atomic charge
|
||||
of atom *i*\ , electrostatic part of atom *i* electronegativity,
|
||||
covalent part of atom *i* electronegativity, the hopping integral of
|
||||
atom *i* :math:`(Z\beta^2)_i` and box electronegativity.
|
||||
|
||||
.. note::
|
||||
|
||||
This last option slows down the calculation dramatically. Use
|
||||
only with a single processor simulation.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
**Mixing, shift, table, tail correction, restart, rRESPA info:**
|
||||
|
||||
This pair style does not support the :doc:`pair_modify <pair_modify>`
|
||||
|
|
@ -241,10 +284,8 @@ This pair style can only be used via the *pair* keyword of the
|
|||
:doc:`run_style respa <run_style>` command. It does not support the
|
||||
*inner*\ , *middle*\ , *outer* keywords.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
**Restriction:**
|
||||
|
||||
This pair style is part of the USER-SMTBQ package and is only enabled
|
||||
|
|
@ -259,50 +300,36 @@ for pair interactions.
|
|||
The SMTB-Q potential files provided with LAMMPS (see the potentials
|
||||
directory) are parameterized for metal :doc:`units <units>`.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
**Citing this work:**
|
||||
|
||||
Please cite related publication: N. Salles, O. Politano, E. Amzallag
|
||||
and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
.. _SMTB-Q\_1:
|
||||
|
||||
|
||||
|
||||
**(SMTB-Q\_1)** N. Salles, O. Politano, E. Amzallag, R. Tetot,
|
||||
Comput. Mater. Sci. 111 (2016) 181-189
|
||||
|
||||
.. _SMTB-Q\_2:
|
||||
|
||||
|
||||
|
||||
**(SMTB-Q\_2)** E. Maras, N. Salles, R. Tetot, T. Ala-Nissila,
|
||||
H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399
|
||||
|
||||
.. _SMTB-Q\_3:
|
||||
|
||||
|
||||
|
||||
**(SMTB-Q\_3)** R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface
|
||||
Science 616, 19-8722 28 (2013)
|
||||
|
||||
.. _Wolf2:
|
||||
|
||||
|
||||
|
||||
**(Wolf)** D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
|
||||
Phys, 110, 8254 (1999).
|
||||
|
||||
.. _Rick3:
|
||||
|
||||
|
||||
|
||||
**(Rick)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
|
||||
(1994).
|
||||
|
|
|
|||
Loading…
Reference in New Issue