diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index a226d73b36..7d8c5c31e8 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -124,6 +124,7 @@ OPT. * :doc:`hbond/dreiding/morse (o) ` * :doc:`hdnnp ` * :doc:`ilp/graphene/hbn ` + * :doc:`ilp/tmd ` * :doc:`kolmogorov/crespi/full ` * :doc:`kolmogorov/crespi/z ` * :doc:`lcbop ` @@ -241,6 +242,7 @@ OPT. * :doc:`reaxff (ko) ` * :doc:`rebo (io) ` * :doc:`resquared (go) ` + * :doc:`saip/metal ` * :doc:`sdpd/taitwater/isothermal ` * :doc:`smd/hertz ` * :doc:`smd/tlsph ` diff --git a/doc/src/pair_ilp_tmd.rst b/doc/src/pair_ilp_tmd.rst index b2fd405a39..1ee619ec91 100644 --- a/doc/src/pair_ilp_tmd.rst +++ b/doc/src/pair_ilp_tmd.rst @@ -30,8 +30,8 @@ Description """"""""""" The *ilp/tmd* style computes the registry-dependent interlayer -potential (ILP) potential for itransition metal dichalcogenide (TMD) -as described in :ref:`(Ouyang3) `. +potential (ILP) potential for transition metal dichalcogenides (TMD) +as described in :ref:`(Ouyang7) `. .. math:: @@ -58,11 +58,11 @@ calculating the normals. .. note:: 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sub-layers of X atoms and one sub-layer of M atoms, the definition of the normal vectors used for graphene and h-BN is no longer valid for TMDs. - In :ref:`(Ouyang3) `, a new definition is proposed, where for + In :ref:`(Ouyang7) `, a new definition is proposed, where for 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* :doc:`units `, with energies in meV. Two additional parameters, @@ -72,14 +72,14 @@ list for calculating the normals for each atom pair. .. 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 Angstrom. Using different cutoff or taper function should be careful. These parameters provide a good description in both short- and long-range interaction regimes. This feature is essential for simulations in high pressure regime (i.e., the interlayer distance is smaller than the equilibrium distance). The benchmark tests and comparison of these parameters can - be found in :ref:`(Ouyang3) `. + be found in :ref:`(Ouyang7) `. This potential must be used in combination with hybrid/overlay. 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). diff --git a/doc/src/pair_saip_metal.rst b/doc/src/pair_saip_metal.rst index 4e6e480fbc..19e85d9416 100644 --- a/doc/src/pair_saip_metal.rst +++ b/doc/src/pair_saip_metal.rst @@ -30,8 +30,8 @@ Description """"""""""" The *saip/metal* style computes the registry-dependent interlayer -potential (ILP) potential for heterojunctions formed with hexagonal -2D materials and metal surfaces, as described in :ref:`(Ouyang4) `. +potential (ILP) potential for hetero-junctions formed with hexagonal +2D materials and metal surfaces, as described in :ref:`(Ouyang6) `. .. math:: @@ -63,9 +63,9 @@ calculating the normals. assumption is suitable for many bulk material surfaces, for example, for systems possessing s-type valence orbitals or 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 - 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. 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). diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 4f1f1e733f..f2afe959f3 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -188,6 +188,7 @@ accelerated styles exist. * :doc:`hbond/dreiding/morse ` - DREIDING hydrogen bonding Morse potential * :doc:`hdnnp ` - High-dimensional neural network potential * :doc:`ilp/graphene/hbn ` - registry-dependent interlayer potential (ILP) +* :doc:`ilp/tmd ` - interlayer potential (ILP) potential for transition metal dichalcogenides (TMD) * :doc:`kim ` - interface to potentials provided by KIM project * :doc:`kolmogorov/crespi/full ` - Kolmogorov-Crespi (KC) potential with no simplifications * :doc:`kolmogorov/crespi/z ` - Kolmogorov-Crespi (KC) potential with normals along z-axis @@ -305,6 +306,7 @@ accelerated styles exist. * :doc:`reaxff ` - ReaxFF potential * :doc:`rebo ` - second generation REBO potential of Brenner * :doc:`resquared ` - Everaers RE-Squared ellipsoidal potential +* :doc:`saip/metal ` - interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces * :doc:`sdpd/taitwater/isothermal ` - smoothed dissipative particle dynamics for water at isothermal conditions * :doc:`smd/hertz ` - * :doc:`smd/tlsph ` - diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index b6c645065c..0a6b284b96 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -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 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. 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. @@ -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 :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. -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. .. note:: diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 02dce2f3c2..18ae834078 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -692,7 +692,7 @@ diagonalizers diagonalizing Diallo diblock -dichalcogenide +dichalcogenides Dickel diel Dietz @@ -2954,6 +2954,7 @@ safezone Safran Sagui Saidi +saip Salanne Salles sandia diff --git a/examples/PACKAGES/interlayer/ilp_graphene_hbn/BNCH.ILP b/examples/PACKAGES/interlayer/ilp_graphene_hbn/BNCH.ILP new file mode 120000 index 0000000000..d999bd5e31 --- /dev/null +++ b/examples/PACKAGES/interlayer/ilp_graphene_hbn/BNCH.ILP @@ -0,0 +1 @@ +../../../../potentials/BNCH.ILP \ No newline at end of file diff --git a/examples/PACKAGES/interlayer/ilp_graphene_hbn/CH.rebo b/examples/PACKAGES/interlayer/ilp_graphene_hbn/CH.rebo new file mode 120000 index 0000000000..c5a6a40100 --- /dev/null +++ b/examples/PACKAGES/interlayer/ilp_graphene_hbn/CH.rebo @@ -0,0 +1 @@ +../../../../potentials/CH.rebo \ No newline at end of file