ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

address spelling and achor issues, and integrate into style overview tables

Browse Source
This commit is contained in:
Axel Kohlmeyer
2022-02-16 08:04:12 -05:00
parent 78b123fa4d
commit 8b627f92f0
8 changed files with 25 additions and 18 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
doc/src/Commands_pair.rst
View File

@ -124,6 +124,7 @@ OPT.
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>` * :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
* :doc:`hdnnp <pair_hdnnp>` * :doc:`hdnnp <pair_hdnnp>`
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` * :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
* :doc:`ilp/tmd <pair_ilp_tmd>`
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>` * :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
* :doc:`lcbop <pair_lcbop>` * :doc:`lcbop <pair_lcbop>`
@ -241,6 +242,7 @@ OPT.
* :doc:`reaxff (ko) <pair_reaxff>` * :doc:`reaxff (ko) <pair_reaxff>`
* :doc:`rebo (io) <pair_airebo>` * :doc:`rebo (io) <pair_airebo>`
* :doc:`resquared (go) <pair_resquared>` * :doc:`resquared (go) <pair_resquared>`
* :doc:`saip/metal <pair_saip_metal>`
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
* :doc:`smd/hertz <pair_smd_hertz>` * :doc:`smd/hertz <pair_smd_hertz>`
* :doc:`smd/tlsph <pair_smd_tlsph>` * :doc:`smd/tlsph <pair_smd_tlsph>`

18
doc/src/pair_ilp_tmd.rst
View File

@ -30,8 +30,8 @@ Description
""""""""""" """""""""""
The *ilp/tmd* style computes the registry-dependent interlayer The *ilp/tmd* style computes the registry-dependent interlayer
potential (ILP) potential for itransition metal dichalcogenide (TMD) potential (ILP) potential for transition metal dichalcogenides (TMD)
as described in :ref:`(Ouyang3) <Ouyang3>`. as described in :ref:`(Ouyang7) <Ouyang7>`.
.. math:: .. math::
@ -58,11 +58,11 @@ calculating the normals.
.. note:: .. note::
Since each MX2 (M = Mo, W and X = S, Se Te) layer contains two Since each MX2 (M = Mo, W and X = S, Se Te) layer contains two
sublayers of X atoms and one sublayer of M atoms, the definition of the sub-layers of X atoms and one sub-layer of M atoms, the definition of the
normal vectors used for graphene and h-BN is no longer valid for TMDs. normal vectors used for graphene and h-BN is no longer valid for TMDs.
In :ref:`(Ouyang3) <Ouyang3>`, a new definition is proposed, where for In :ref:`(Ouyang7) <Ouyang7>`, a new definition is proposed, where for
each atom `i`, its six nearest neighboring atoms belonging to the same each atom `i`, its six nearest neighboring atoms belonging to the same
sublayer are chosen to define the normal vector `{\bf n}_i`. sub-layer are chosen to define the normal vector `{\bf n}_i`.
The parameter file (e.g. TMD.ILP), is intended for use with *metal* The parameter file (e.g. TMD.ILP), is intended for use with *metal*
:doc:`units <units>`, with energies in meV. Two additional parameters, :doc:`units <units>`, with energies in meV. Two additional parameters,
@ -72,14 +72,14 @@ list for calculating the normals for each atom pair.
.. note:: .. note::
The parameters presented in the parameter file (e.g. BNCH.ILP), The parameters presented in the parameter file (e.g. TMD.ILP),
are fitted with taper function by setting the cutoff equal to 16.0 are fitted with taper function by setting the cutoff equal to 16.0
Angstrom. Using different cutoff or taper function should be careful. Angstrom. Using different cutoff or taper function should be careful.
These parameters provide a good description in both short- and long-range These parameters provide a good description in both short- and long-range
interaction regimes. This feature is essential for simulations in high pressure interaction regimes. This feature is essential for simulations in high pressure
regime (i.e., the interlayer distance is smaller than the equilibrium regime (i.e., the interlayer distance is smaller than the equilibrium
distance). The benchmark tests and comparison of these parameters can distance). The benchmark tests and comparison of these parameters can
be found in :ref:`(Ouyang3) <Ouyang3>`. be found in :ref:`(Ouyang7) <Ouyang7>`.
This potential must be used in combination with hybrid/overlay. This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style *none*\ . Other interactions can be set to zero using pair_style *none*\ .
@ -152,6 +152,6 @@ tap_flag = 1
---------- ----------
.. _Ouyang3: .. _Ouyang7:
**(Ouyang3)** W. Ouyang, et al., J. Chem. Theory Comput. 17, 7237 (2021). **(Ouyang7)** W. Ouyang, et al., J. Chem. Theory Comput. 17, 7237 (2021).

12
doc/src/pair_saip_metal.rst
View File

@ -30,8 +30,8 @@ Description
""""""""""" """""""""""
The *saip/metal* style computes the registry-dependent interlayer The *saip/metal* style computes the registry-dependent interlayer
potential (ILP) potential for heterojunctions formed with hexagonal potential (ILP) potential for hetero-junctions formed with hexagonal
2D materials and metal surfaces, as described in :ref:`(Ouyang4) <Ouyang4>`. 2D materials and metal surfaces, as described in :ref:`(Ouyang6) <Ouyang6>`.
.. math:: .. math::
@ -63,9 +63,9 @@ calculating the normals.
assumption is suitable for many bulk material surfaces, for assumption is suitable for many bulk material surfaces, for
example, for systems possessing s-type valence orbitals or example, for systems possessing s-type valence orbitals or
metallic surfaces, whose valence electrons are mostly metallic surfaces, whose valence electrons are mostly
delocalized, such that their Pauli repulsions with the electrons delocalized, such that their Pauli repulsion with the electrons
of adjacent surfaces are isotropic. Caution should be used in of adjacent surfaces are isotropic. Caution should be used in
the case of very small gold contacts, for example, nanoclusters, the case of very small gold contacts, for example, nano-clusters,
where edge effects may become relevant. where edge effects may become relevant.
The parameter file (e.g. CHAu.ILP), is intended for use with *metal* The parameter file (e.g. CHAu.ILP), is intended for use with *metal*
@ -151,6 +151,6 @@ tap_flag = 1
---------- ----------
.. _Ouyang4: .. _Ouyang6:
**(Ouyang4)** W. Ouyang, O. Hod, and R. Guerra, J. Chem. Theory Comput. 17, 7215 (2021). **(Ouyang6)** W. Ouyang, O. Hod, and R. Guerra, J. Chem. Theory Comput. 17, 7215 (2021).

2
doc/src/pair_style.rst
View File

@ -188,6 +188,7 @@ accelerated styles exist.
* :doc:`hbond/dreiding/morse <pair_hbond_dreiding>` - DREIDING hydrogen bonding Morse potential * :doc:`hbond/dreiding/morse <pair_hbond_dreiding>` - DREIDING hydrogen bonding Morse potential
* :doc:`hdnnp <pair_hdnnp>` - High-dimensional neural network potential * :doc:`hdnnp <pair_hdnnp>` - High-dimensional neural network potential
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` - registry-dependent interlayer potential (ILP) * :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` - registry-dependent interlayer potential (ILP)
* :doc:`ilp/tmd <pair_ilp_tmd>` - interlayer potential (ILP) potential for transition metal dichalcogenides (TMD)
* :doc:`kim <pair_kim>` - interface to potentials provided by KIM project * :doc:`kim <pair_kim>` - interface to potentials provided by KIM project
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` - Kolmogorov-Crespi (KC) potential with no simplifications * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` - Kolmogorov-Crespi (KC) potential with no simplifications
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>` - Kolmogorov-Crespi (KC) potential with normals along z-axis * :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>` - Kolmogorov-Crespi (KC) potential with normals along z-axis
@ -305,6 +306,7 @@ accelerated styles exist.
* :doc:`reaxff <pair_reaxff>` - ReaxFF potential * :doc:`reaxff <pair_reaxff>` - ReaxFF potential
* :doc:`rebo <pair_airebo>` - second generation REBO potential of Brenner * :doc:`rebo <pair_airebo>` - second generation REBO potential of Brenner
* :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential * :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential
* :doc:`saip/metal <pair_saip_metal>` - interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions
* :doc:`smd/hertz <pair_smd_hertz>` - * :doc:`smd/hertz <pair_smd_hertz>` -
* :doc:`smd/tlsph <pair_smd_tlsph>` - * :doc:`smd/tlsph <pair_smd_tlsph>` -

4
doc/src/pair_sw.rst
View File

@ -69,7 +69,7 @@ and K of atom I within a cutoff distance :math:`a `\sigma`.
The *sw/mod* style is designed for simulations of materials when The *sw/mod* style is designed for simulations of materials when
distinguishing three-body angles are necessary, such as borophene distinguishing three-body angles are necessary, such as borophene
and transition metal dichalcogenide, which cannot be described and transition metal dichalcogenides, which cannot be described
by the original code for the Stillinger-Weber potential. by the original code for the Stillinger-Weber potential.
For instance, there are several types of angles around each Mo atom in `MoS_2`, For instance, there are several types of angles around each Mo atom in `MoS_2`,
and some unnecessary angle types should be excluded in the three-body interaction. and some unnecessary angle types should be excluded in the three-body interaction.
@ -99,7 +99,7 @@ This smoothly turns off the energy and force contributions for :math:`\left| \de
It is suggested that :math:`\delta 1` and :math:`\delta_2` to be the value around It is suggested that :math:`\delta 1` and :math:`\delta_2` to be the value around
:math:`0.5 \left| \cos \theta_1 - \cos \theta_2 \right|`, with :math:`0.5 \left| \cos \theta_1 - \cos \theta_2 \right|`, with
:math:`\theta_1` and :math:`\theta_2` as the different types of angles around an atom. :math:`\theta_1` and :math:`\theta_2` as the different types of angles around an atom.
For borophene and transition metal dichalcogenide, :math:`\delta_1 = 0.25` and :math:`\delta_2 = 0.35`. For borophene and transition metal dichalcogenides, :math:`\delta_1 = 0.25` and :math:`\delta_2 = 0.35`.
This value enables the cut-off function to exclude unnecessary angles in the three-body SW terms. This value enables the cut-off function to exclude unnecessary angles in the three-body SW terms.
.. note:: .. note::

3
doc/utils/sphinx-config/false_positives.txt
View File

@ -692,7 +692,7 @@ diagonalizers
diagonalizing diagonalizing
Diallo Diallo
diblock diblock
dichalcogenide dichalcogenides
Dickel Dickel
diel diel
Dietz Dietz
@ -2954,6 +2954,7 @@ safezone
Safran Safran
Sagui Sagui
Saidi Saidi
saip
Salanne Salanne
Salles Salles
sandia sandia

1
examples/PACKAGES/interlayer/ilp_graphene_hbn/BNCH.ILP Symbolic link
View File

@ -0,0 +1 @@
../../../../potentials/BNCH.ILP

1
examples/PACKAGES/interlayer/ilp_graphene_hbn/CH.rebo Symbolic link
View File

@ -0,0 +1 @@
../../../../potentials/CH.rebo