Merge branch 'master' of https://github.com/oywg11/lammps into ilp-update (918030bf) · Commits · 郑智淋 / lammps

doc/src/pair_coul_shield.txt

+7 −1

Original line number	Diff line number	Diff line
		@@ -38,7 +38,7 @@ charge and molecule ID information is included.

		Where Tap(r_ij) is the taper function which provides a continuous cutoff
		(up to third derivative) for inter-atomic separations larger than r_c
		"(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that
		"(Leven1)"_#Leven3, "(Leven2)"_#Leven4 and "(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that
		eliminates the short-range singularity of the classical mono-polar
		electrostatic interaction expression "(Maaravi)"_#Maaravi1.

		@@ -82,5 +82,11 @@ package"_Build_package.html doc page for more info.

		:line

		:link(Leven3)
		[(Leven1)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).

		:link(Leven4)
		[(Leven2)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).

		:link(Maaravi1)
		[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).

doc/src/pair_ilp_graphene_hbn.txt

+18 −15

Original line number	Diff line number	Diff line
		@@ -31,7 +31,7 @@ pair_coeff 2 2 coul/shield 0.69 :pre
		[Description:]

		The {ilp/graphene/hbn} style computes the registry-dependent interlayer
		potential (ILP) potential as described in "(Leven)"_#Leven and
		potential (ILP) potential as described in "(Leven1)"_#Leven1, "(Leven2)"_#Leven2 and
		"(Maaravi)"_#Maaravi2. The normals are calculated in the way as described
		in "(Kolmogorov)"_#Kolmogorov2.

		@@ -39,8 +39,9 @@ in "(Kolmogorov)"_#Kolmogorov2.

		Where Tap(r_ij) is the taper function which provides a continuous
		cutoff (up to third derivative) for interatomic separations larger than
		r_c "(Maaravi)"_#Maaravi2. The definitions of each parameter in the above
		equation can be found in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2.
		r_c "(Maaravi)"_#Maaravi2. The definitons of each parameter in the above
		equation can be found in "(Leven1)"_#Leven1 and "(Maaravi)"_#Maaravi2.


		It is important to include all the pairs to build the neighbor list for
		calculating the normals.
		@@ -61,13 +62,12 @@ NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP),
		are fitted with taper function by setting the cutoff equal to 16.0
		Angstrom. Using different cutoff or taper function should be careful.

		NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal Materials
		are presented in "(Ouyang)"_#Ouyang1. These parameters provide a good description
		in both short- and long-range interaction regime, while the old ILP parameters
		published in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2 are only suitable for
		long-range interaction regime. This feature is essential for simulations in
		high-pressure regime (i.e., the interlayer distance smaller than the equilibrium distance).
		The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
		NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal Materials are presented in "(Ouyang)"_#Ouyang.
		These parameters provide a good description in both short- and long-range interaction regimes.
		While the old ILP parameters published in "(Leven2)"_#Leven2 and "(Maaravi)"_#Maaravi2 are
		only suitable for long-range interaction regime. 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 "(Ouyang)"_#Ouyang.

		This potential must be used in combination with hybrid/overlay.
		Other interactions can be set to zero using pair_style {none}.
		@@ -112,14 +112,17 @@ units, if your simulation does not use {metal} units.

		:line

		:link(Leven)
		[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016)
		:link(Leven1)
		[(Leven1)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).

		:link(Leven2)
		[(Leven2)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).

		:link(Maaravi2)
		[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).

		:link(Kolmogorov2)
		[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
		[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005).

		:link(Ouyang1)
		[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh, O. Hod, arXiv:1806.09555 (2018).
		:link(Ouyang)
		[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).

doc/src/pair_kolmogorov_crespi_full.txt

+20 −17

Original line number	Diff line number	Diff line
		@@ -19,11 +19,11 @@ tap_flag = 0/1 to turn off/on the taper function

		pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0
		pair_coeff * * none
		pair_coeff * * kolmogorov/crespi/full CC.KC C C :pre
		pair_coeff * * kolmogorov/crespi/full CH.KC C C :pre

		pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
		pair_coeff * * rebo CH.airebo C C
		pair_coeff * * kolmogorov/crespi/full CC.KC C C :pre
		pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
		pair_coeff * * rebo CH.airebo C H
		pair_coeff * * kolmogorov/crespi/full CH_taper.KC C H :pre

		[Description:]

		@@ -38,27 +38,30 @@ forces and to include all the pairs to build the neighbor list for
		calculating the normals. Energies are shifted so that they go
		continuously to zero at the cutoff assuming that the exponential part of
		{Vij} (first term) decays sufficiently fast. This shift is achieved by
		the last term in the equation for {Vij} above.
		the last term in the equation for {Vij} above. This is essential only
		when the tapper function is turned off. The formula of taper function
		can be found in pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.

		NOTE: This potential is intended for interactions between two different
		graphene layers. Therefore, to avoid interaction within the same layers,
		each layer should have a separate molecule id and is recommended to use
		"full" atom style in the data file.

		The parameter file (e.g. CC.KC), is intended for use with {metal}
		The parameter file (e.g. CH.KC), is intended for use with {metal}
		"units"_units.html, with energies in meV. Two additional parameters, {S},
		and {rcut} are included in the parameter file. {S} is designed to
		facilitate scaling of energies. {rcut} is designed to build the neighbor
		list for calculating the normals for each atom pair.

		NOTE: A new set of parameters of KC potential for hydrocarbons (CH.KC)
		is presented in "(Ouyang)"_#Ouyang2. The parameters in CH.KC provides
		a good description in both short- and long-range interaction regime,
		while the original parameters (CC.KC) published in "(Kolmogorov)"_#Kolmogorov1
		are only suitable for long-range interaction regime.
		This feature is essential for simulations in high-pressure regime
		(i.e., the interlayer distance smaller than the equilibrium distance).
		The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang2.
		NOTE: Two new sets of parameters of KC potential for hydrocarbons, CH.KC (without the taper function)
		and CH_taper.KC (with the taper function) are presented in "(Ouyang)"_#Ouyang1.
		The energy for the KC potential with the taper function goes continuously to zero at the cutoff.
		The parameters in both CH.KC and CH_taper.KC provide a good description in
		both short- and long-range interaction regimes. While the original parameters (CC.KC)
		published in "(Kolmogorov)"_#Kolmogorov1 are only suitable for long-range interaction regime.
		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 "(Ouyang)"_#Ouyang1.

		This potential must be used in combination with hybrid/overlay.
		Other interactions can be set to zero using pair_style {none}.
		@@ -84,7 +87,7 @@ package"_Build_package.html doc page for more info.
		This pair potential requires the newton setting to be {on} for pair
		interactions.

		The CC.KC potential file provided with LAMMPS (see the potentials
		The CH.KC potential file provided with LAMMPS (see the potentials
		folder) are parameterized for metal units. You can use this potential
		with any LAMMPS units, but you would need to create your own custom
		CC.KC potential file with all coefficients converted to the appropriate
		@@ -105,5 +108,5 @@ units.
		:link(Kolmogorov1)
		[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)

		:link(Ouyang2)
		[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh, O. Hod, arXiv:1806.09555 (2018).
		:link(Ouyang1)
		[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
		No newline at end of file

potentials/BNCH.ILP

+1 −1

Original line number	Diff line number	Diff line
		# Interlayer Potential (ILP) for graphene/graphene, graphene/hBN and hBN/hBN junctions
		#
		# Cite as Wengen Ouyang,Davide Mandelli, Michael Urbakh, Oded Hod, arXiv:1806.09555 (2018).
		# Cite as W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Letters 18, 6009-6016 (2018).
		#
		# ----------------- Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************
		# beta(A) alpha delta(A) epsilon(meV) C(meV) d sR reff(A) C6(meV*A^6) S rcut

potentials/CH.KC

+2 −2

Original line number	Diff line number	Diff line
		# Refined parameters for Kolmogorov-Crespi Potential
		# Refined parameters for Kolmogorov-Crespi Potential without taper function
		#
		# Cite as Wengen Ouyang,Davide Mandelli, Michael Urbakh, Oded Hod, arXiv:1806.09555 (2018).
		# Cite as W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Letters 18, 6009-6016 (2018).
		#
		# z0 C0 C2 C4 C delta lambda A S rcut
		C C 3.328819 21.847167 12.060173 4.711099 6.678908e-4 0.7718101 3.143921 12.660270 1.0 2.0

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