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Merge pull request lammps#4780 from oywg11/saip-TMDC-Metal
Semi-anisotropic Interfacial Potential for Interfaces of TMDC with Metal
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‎doc/src/pair_ilp_tmd.rst‎

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.. versionadded:: 17Feb2022
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The *ilp/tmd* style computes the registry-dependent interlayer
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potential (ILP) potential for transition metal dichalcogenides (TMD)
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as described in :ref:`(Ouyang7) <Ouyang7>` and :ref:`(Jiang) <Jiang>`.
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potential (ILP) potential for heterointerfaces of transition metal dichalcogenides (TMD)/TMD,
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TMD/graphene, and TMD / hexagonal boron nitride (h-BN), as described in
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:ref:`(Ouyang7) <Ouyang7>`, :ref:`(Jiang1) <Jiang1>` and :ref:`(Jiang2) <Jiang2>`.
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.. math::
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**(Ouyang7)** W. Ouyang, et al., J. Chem. Theory Comput. 17, 7237 (2021).
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.. _Jiang:
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.. _Jiang1:
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**(Jiang)** W. Jiang, et al., J. Phys. Chem. A, 127, 46, 9820-9830 (2023).
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**(Jiang1)** W. Jiang, ... , W. Ouyang, et al., J. Phys. Chem. A, 127, 46, 9820-9830 (2023).
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.. _Jiang2:
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**(Jiang2)** W. Jiang, ..., W. Ouyang, J. Phys. Chem. C, 129, 2, 1417-1427 (2024).

‎doc/src/pair_saip_metal.rst‎

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.. index:: pair_style saip/metal
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.. index:: pair_style saip/metal/opt
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.. index:: pair_style saip/metal/tmd
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.. index:: pair_style saip/metal/tmd/opt
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pair_style saip/metal command
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===================================
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Accelerator Variant: *saip/metal/opt*
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pair_style saip/metal/tmd command
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===================================
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Accelerator Variant: *saip/metal/tmd/opt*
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Syntax
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""""""
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.. code-block:: LAMMPS
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pair_style [hybrid/overlay ...] saip/metal cutoff tap_flag
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pair_style [hybrid/overlay ...] style cutoff tap_flag
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* style = *saip/metal* or *saip/metal/tmd*
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* cutoff = global cutoff (distance units)
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* tap_flag = 0/1 to turn off/on the taper function
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pair_style hybrid/overlay eam rebo saip/metal 16.0
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pair_coeff 1 1 eam Au_u3.eam Au NULL NULL
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pair_coeff * * rebo CH.rebo NULL C H
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pair_coeff * * saip/metal CHAu.ILP Au C H
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pair_coeff * * saip/metal CHAu.ILP Au C H
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pair_style hybrid/overlay eam sw/mod saip/metal/tmd 16.0
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pair_coeff 1 1 eam Au_u3.eam Au NULL NULL
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pair_coeff * * sw/mod tmd.sw.mod NULL S Mo S
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pair_coeff * * saip/metal/tmd TMDAu.SAIP Au S Mo S
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Description
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"""""""""""
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.. versionadded:: 17Feb2022
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The *saip/metal* style computes the registry-dependent interlayer
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potential (ILP) potential for hetero-junctions formed with hexagonal
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2D materials and metal surfaces, as described in :ref:`(Ouyang6) <Ouyang6>`.
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The *saip/metal* style computes the semi-anisotropic interfacial
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potential (SAIP) potential for hetero-junctions formed with hexagonal
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2D materials and metal surfaces, as described in :ref:`(Ouyang6) <Ouyang6>` and :ref:`(Yao1) <Yao1>`.
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.. versionadded:: TBD
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The *saip/metal/tmd* style computes the semi-anisotropic interfacial
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potential (SAIP) potential for hetero-junctions formed with transition
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metal dichalcogenides (TMDCs) and metal surfaces, as described in :ref:`(Yao2) <Yao2>`.
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.. math::
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.. note::
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The parameters presented in the parameter file (e.g. BNCH.ILP),
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The parameters presented in the parameter file (e.g. TMDAu.SAIP),
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are fitted with taper function by setting the cutoff equal to 16.0
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Angstrom. Using different cutoff or taper function should be careful.
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This pair style requires the newton setting to be *on* for pair
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interactions.
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The CHAu.ILP potential file provided with LAMMPS (see the potentials
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The CHAu.ILP and TMDAu.SAIP potential file provided with LAMMPS (see the potentials
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directory) are parameterized for *metal* units. You can use this
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potential with any LAMMPS units, but you would need to create your own
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custom CHAu.ILP potential file with coefficients listed in the appropriate
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.. _Ouyang6:
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**(Ouyang6)** W. Ouyang, O. Hod, and R. Guerra, J. Chem. Theory Comput. 17, 7215 (2021).
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.. _Yao1:
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**(Yao1)** Y. Yao, ..., W. Ouyang, J. Phys. Chem. C, 128, 6836 (2024).
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.. _Yao2:
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**(Yao2)** Y. Yao, ..., W. Ouyang, Adv. Sci. 12, 2415884 (2025).

‎examples/PACKAGES/interlayer/saip_metal_tmd/3Lgold_1Lmos2.data‎

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‎examples/PACKAGES/interlayer/saip_metal_tmd/Au_u3.eam‎

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../../../../potentials/Au_u3.eam

‎examples/PACKAGES/interlayer/saip_metal_tmd/TMDAu.SAIP‎

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../../../../potentials/TMDAu.SAIP

‎examples/PACKAGES/interlayer/saip_metal_tmd/in.au_mos2‎

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# Initialization
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units metal
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boundary p p p
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atom_style full
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processors * * 1 # domain decomposition over x and y
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read_data ./3Lgold_1Lmos2.data
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mass 1 196.96657 # gold mass (g/mole)
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mass 2 32.065 # sulfur mass (g/mole)
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mass 3 95.95 # molybdenum mass (g/mole)
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mass 4 32.065 # sulfur mass (g/mole)
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# Separate atom groups
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group gold type 1
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group mos2 type 2 3 4
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######################## Potential defition ##############################
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# Interlayer potential
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pair_style hybrid/overlay eam sw/mod saip/metal/tmd 16.0 1
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####################################################################
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pair_coeff 1 1 eam ./Au_u3.eam
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pair_coeff * * sw/mod tmd.sw.mod NULL S Mo S
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pair_coeff * * saip/metal/tmd ./TMDAu.SAIP Au S Mo S
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####################################################################
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# Calculate pair energy
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compute 0 all pair eam
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compute 1 all pair sw/mod
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compute 2 all pair saip/metal/tmd
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variable EAM equal c_0
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variable SWMOD equal c_1
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variable SAIP equal c_2
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############# Output ##############
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thermo_style custom step etotal pe ke v_EAM v_SWMOD v_SAIP temp
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thermo 100
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thermo_modify lost error
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velocity all set 0.0 0.0 0.0
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velocity mos2 create 300.0 4928459 mom yes rot yes dist gaussian
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velocity gold create 300.0 4928459 mom yes rot yes dist gaussian
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fix intsub gold nve
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fix intrib mos2 nve
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timestep 1e-3
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run 1000

‎examples/PACKAGES/interlayer/saip_metal_tmd/log.10Sep25.au_mos2.g++.1‎

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LAMMPS (10 Sep 2025)
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# Initialization
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units metal
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boundary p p p
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atom_style full
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processors * * 1 # domain decomposition over x and y
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read_data ./3Lgold_1Lmos2.data
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Reading data file ...
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orthogonal box = (0.52363376 0.3023078 0) to (59.415066 34.303292 100)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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1590 atoms
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reading velocities ...
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1590 velocities
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.002 seconds
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read_data CPU = 0.043 seconds
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mass 1 196.96657 # gold mass (g/mole)
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mass 2 32.065 # sulfur mass (g/mole)
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mass 3 95.95 # molybdenum mass (g/mole)
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mass 4 32.065 # sulfur mass (g/mole)
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# Separate atom groups
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group gold type 1
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864 atoms in group gold
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group mos2 type 2 3 4
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726 atoms in group mos2
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######################## Potential defition ##############################
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# Interlayer potential
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pair_style hybrid/overlay eam sw/mod saip/metal/tmd 16.0 1
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####################################################################
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pair_coeff 1 1 eam ./Au_u3.eam
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Reading eam potential file ./Au_u3.eam with DATE: 2007-06-11
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pair_coeff * * sw/mod tmd.sw.mod NULL S Mo S
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Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
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pair_coeff * * saip/metal/tmd ./TMDAu.SAIP Au S Mo S
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Reading saip/metal/tmd potential file ./TMDAu.SAIP with DATE: 2025-04-04
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####################################################################
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# Calculate pair energy
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compute 0 all pair eam
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compute 1 all pair sw/mod
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compute 2 all pair saip/metal/tmd
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variable EAM equal c_0
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variable SWMOD equal c_1
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variable SAIP equal c_2
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############# Output ##############
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thermo_style custom step etotal pe ke v_EAM v_SWMOD v_SAIP temp
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thermo 100
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thermo_modify lost error
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velocity all set 0.0 0.0 0.0
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velocity mos2 create 300.0 4928459 mom yes rot yes dist gaussian
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velocity gold create 300.0 4928459 mom yes rot yes dist gaussian
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fix intsub gold nve
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fix intrib mos2 nve
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timestep 1e-3
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run 1000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
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@Article{Ouyang2018
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author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
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title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
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journal = {Nano Letters},
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volume = 18,
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pages = 6009,
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year = 2018,
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}
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- ilp/tmd potential doi:10.1021/acs.jctc.1c00782
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@Article{Ouyang2021
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author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
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A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},
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title = {Anisotropic Interlayer Force Field for Transition
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Metal Dichalcogenides: The Case of Molybdenum Disulfide},
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journal = {J.~Chem.\ Theory Comput.},
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volume = 17,
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pages = {7237--7245}
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year = 2021,
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}
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- saip/metal/tmd potential doi.org/10.1002/advs.202415884
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@Article{Ouyang2021
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author = {Y. Yao, Y. Song, B. Wu, S. Scherb, S. Huang, A. Hinaut, T. Glatzel, E. Meyer, Z. Liu, and W. Ouyang},
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title = {Unraveling the Interfacial Properties of Twisted Single-Crystal Au(111)/MoS2 Heterostructures: A Pathway to Robust Superlubricity},
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journal = {Adv. Sci.},
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volume = 12,
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pages = {2415884}
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year = 2025,
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 18
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ghost atom cutoff = 18
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binsize = 9, bins = 7 4 12
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5 neighbor lists, perpetual/occasional/extra = 5 0 0
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(1) pair eam, perpetual, skip from (5)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(2) pair sw/mod, perpetual, skip from (4)
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attributes: full, newton on
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pair build: skip
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stencil: none
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bin: none
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(3) pair saip/metal/tmd, perpetual
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attributes: full, newton on, ghost, cut 18
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pair build: full/bin/ghost
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stencil: full/ghost/bin/3d
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bin: standard
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(4) neighbor class addition, perpetual, copy from (3)
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attributes: full, newton on
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pair build: copy
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stencil: none
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bin: none
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(5) neighbor class addition, perpetual, half/full from (4)
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attributes: half, newton on
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pair build: halffull/newton
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 36.31 | 36.31 | 36.31 Mbytes
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Step TotEng PotEng KinEng v_EAM v_SWMOD v_SAIP Temp
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0 -4094.783 -4156.3625 61.579533 -3200.3073 -897.8971 -58.158136 299.8112
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100 -4094.7686 -4117.4877 22.71912 -3175.3866 -884.85097 -57.25016 110.61218
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200 -4094.7717 -4125.4148 30.643106 -3183.1956 -884.8818 -57.337423 149.19156
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300 -4094.7681 -4127.9027 33.134528 -3186.359 -883.41654 -58.127078 161.3215
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400 -4094.7722 -4126.5176 31.745428 -3182.8465 -885.26606 -58.405041 154.55841
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500 -4094.7701 -4127.6359 32.865884 -3184.0679 -884.73218 -58.835847 160.01356
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600 -4094.7721 -4128.7852 34.013058 -3183.4466 -885.94185 -59.396778 165.59879
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700 -4094.768 -4125.8024 31.034423 -3183.589 -882.00781 -60.2056 151.09675
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800 -4094.7702 -4127.4862 32.715987 -3182.9462 -883.47351 -61.066547 159.28376
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900 -4094.7696 -4126.9742 32.204602 -3182.4139 -883.06824 -61.492096 156.79399
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1000 -4094.7701 -4127.507 32.736928 -3182.2687 -883.48512 -61.75318 159.38571
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Loop time of 99.4509 on 1 procs for 1000 steps with 1590 atoms
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Performance: 0.869 ns/day, 27.625 hours/ns, 10.055 timesteps/s, 15.988 katom-step/s
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100.0% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 99.395 | 99.395 | 99.395 | 0.0 | 99.94
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Bond | 9.0611e-05 | 9.0611e-05 | 9.0611e-05 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.017015 | 0.017015 | 0.017015 | 0.0 | 0.02
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Output | 0.00043061 | 0.00043061 | 0.00043061 | 0.0 | 0.00
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Modify | 0.027927 | 0.027927 | 0.027927 | 0.0 | 0.03
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Other | | 0.01061 | | | 0.01
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Nlocal: 1590 ave 1590 max 1590 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3704 ave 3704 max 3704 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 1.17592e+06 ave 1.17592e+06 max 1.17592e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1175920
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Ave neighs/atom = 739.57233
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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:01:39

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