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

Merge branch 'ilp-tmd-update' of github.com:oywg11/lammps into collected-small-fixes

Browse Source
This commit is contained in:
Axel Kohlmeyer
2023-12-22 14:45:43 -05:00
parent 8cf958e241 e98df7018b
commit 4ea40ed2fd
7 changed files with 41 additions and 12 deletions
Download Patch File Download Diff File Expand all files Collapse all files

20
doc/src/pair_ilp_tmd.rst
View File

@ -22,12 +22,12 @@ Examples
.. code-block:: LAMMPS .. code-block:: LAMMPS
pair_style hybrid/overlay ilp/tmd 16.0 1 pair_style hybrid/overlay ilp/tmd 16.0 1
pair_coeff * * ilp/tmd MoS2.ILP Mo S S pair_coeff * * ilp/tmd TMD.ILP Mo S S
pair_style hybrid/overlay sw/mod sw/mod ilp/tmd 16.0 pair_style hybrid/overlay sw/mod sw/mod ilp/tmd 16.0
pair_coeff * * sw/mod 1 tmd.sw.mod Mo S S NULL NULL NULL pair_coeff * * sw/mod 1 tmd.sw.mod Mo S S NULL NULL NULL
pair_coeff * * sw/mod 2 tmd.sw.mod NULL NULL NULL Mo S S pair_coeff * * sw/mod 2 tmd.sw.mod NULL NULL NULL W Se Se
pair_coeff * * ilp/tmd MoS2.ILP Mo S S Mo S S pair_coeff * * ilp/tmd TMD.ILP Mo S S W Se Se
Description Description
""""""""""" """""""""""
@ -36,7 +36,7 @@ Description
The *ilp/tmd* style computes the registry-dependent interlayer The *ilp/tmd* style computes the registry-dependent interlayer
potential (ILP) potential for transition metal dichalcogenides (TMD) potential (ILP) potential for transition metal dichalcogenides (TMD)
as described in :ref:`(Ouyang7) <Ouyang7>`. as described in :ref:`(Ouyang7) <Ouyang7>` and :ref:`(Jiang) <Jiang>`.
.. math:: .. math::
@ -69,7 +69,7 @@ calculating the normals.
each atom `i`, its six nearest neighboring atoms belonging to the same each atom `i`, its six nearest neighboring atoms belonging to the same
sub-layer 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. MoS2.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,
*S*, and *rcut* are included in the parameter file. *S* is designed to *S*, and *rcut* are included in the parameter file. *S* is designed to
facilitate scaling of energies. *rcut* is designed to build the neighbor facilitate scaling of energies. *rcut* is designed to build the neighbor
@ -77,7 +77,7 @@ list for calculating the normals for each atom pair.
.. note:: .. note::
The parameters presented in the parameter file (e.g. MoS2.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
@ -133,10 +133,10 @@ if LAMMPS was built with that package. See the :doc:`Build package
This pair style requires the newton setting to be *on* for pair This pair style requires the newton setting to be *on* for pair
interactions. interactions.
The MoS2.ILP potential file provided with LAMMPS (see the potentials The TMD.ILP potential file provided with LAMMPS (see the potentials
directory) are parameterized for *metal* units. You can use this directory) are parameterized for *metal* units. You can use this
potential with any LAMMPS units, but you would need to create your own potential with any LAMMPS units, but you would need to create your own
custom MoS2.ILP potential file with coefficients listed in the appropriate custom TMD.ILP potential file with coefficients listed in the appropriate
units, if your simulation does not use *metal* units. units, if your simulation does not use *metal* units.
Related commands Related commands
@ -164,3 +164,7 @@ tap_flag = 1
.. _Ouyang7: .. _Ouyang7:
**(Ouyang7)** W. Ouyang, et al., J. Chem. Theory Comput. 17, 7237 (2021). **(Ouyang7)** W. Ouyang, et al., J. Chem. Theory Comput. 17, 7237 (2021).
.. _Jiang:
**(Jiang)** W. Jiang, et al., J. Phys. Chem. A, 127, 46, 9820–9830 (2023).

1
examples/PACKAGES/interlayer/ilp_tmds/MoS2.ILP
View File

@ -1 +0,0 @@
../../../../potentials/MoS2.ILP

1
examples/PACKAGES/interlayer/ilp_tmds/TMD.ILP Symbolic link
View File

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

2
examples/PACKAGES/interlayer/ilp_tmds/in.mos2
View File

@ -12,7 +12,7 @@ mass 4 95.94
pair_style hybrid/overlay sw/mod sw/mod ilp/tmd 16.0 pair_style hybrid/overlay sw/mod sw/mod ilp/tmd 16.0
pair_coeff * * sw/mod 1 tmd.sw.mod Mo S S NULL NULL NULL pair_coeff * * sw/mod 1 tmd.sw.mod Mo S S NULL NULL NULL
pair_coeff * * sw/mod 2 tmd.sw.mod NULL NULL NULL Mo S S pair_coeff * * sw/mod 2 tmd.sw.mod NULL NULL NULL Mo S S
pair_coeff * * ilp/tmd MoS2.ILP Mo S S Mo S S pair_coeff * * ilp/tmd TMD.ILP Mo S S Mo S S
# Calculate the pair potential # Calculate the pair potential
compute 0 all pair ilp/tmd compute 0 all pair ilp/tmd

25
potentials/TMD.ILP Normal file
View File

@ -0,0 +1,25 @@
# DATE: 2021-12-02 UNITS: metal CONTRIBUTOR: Wengen Ouyang w.g.ouyang@gmail.com
# CITATION: W. Ouyang, et al., J. Chem. Theory Comput. 17, 7237 (2021).
# CITATION: W. Jiang, et al., J. Phys. Chem. A, 127, 46, 9820–9830 (2023).
# Interlayer Potential (ILP) for bilayer and bulk Group-VI Transition Metal Dichalcogenides.
# The parameters below are fitted against the HSE + MBD-NL DFT reference data.
#
# -------------------- Repulsion Potential -------------------++++++++++++++++ Vdw Potential ++++++++++++++++*********
# beta(A) alpha delta(A) epsilon(meV) C(meV) d sR reff(A) C6(meV*A^6) S rcut
Mo Mo 5.579450 9.377662 2.027222 144.151775 97.978570 89.437597 2.059031 5.122055 491850.316195 1.0 4.0
W W 5.530854 6.624992 1.983208 0.271792 140.174059 107.392585 1.356333 4.437591 691850.243962 1.0 4.0
S S 3.161402 8.093263 1.953140 4.586764 118.065466 58.809416 0.215367 4.299600 148811.243409 1.0 4.0
Se Se 3.938627 10.515924 2.415783 3.012583 22.400612 116.864517 0.151121 5.884241 112506.195626 1.0 4.0
Mo W 5.412298 8.647128 2.108665 51.177950 184.342860 201.281256 2.547743 2.492287 99996.913401 1.0 4.0
Mo S 3.627152 19.971375 7.585031 76.101931 3.317496 45.720328 0.947470 4.410425 150597.857716 1.0 4.0
Mo Se 6.196447 4.844134 14.362005 7.407221 0.058823 27.156223 0.976771 3.979186 786029.840651 1.0 4.0
W S 3.680136 11.163004 32.254117 110.019679 79.381335 138.340438 0.900750 8.875776 250600.809034 1.0 4.0
W Se 3.559392 20.638856 1.202717 20.478669 197.422484 10.005271 1.052738 3.815817 288321.561114 1.0 4.0
S Se 2.820092 7.491151 1.933323 141.532559 293.127817 90.470904 0.390492 4.170885 117688.987069 1.0 4.0
# Symmetric Atom Pair
W Mo 5.412298 8.647128 2.108665 51.177950 184.342860 201.281256 2.547743 2.492287 99996.913401 1.0 4.0
S Mo 3.627152 19.971375 7.585031 76.101931 3.317496 45.720328 0.947470 4.410425 150597.857716 1.0 4.0
Se Mo 6.196447 4.844134 14.362005 7.407221 0.058823 27.156223 0.976771 3.979186 786029.840651 1.0 4.0
S W 3.680136 11.163004 32.254117 110.019679 79.381335 138.340438 0.900750 8.875776 250600.809034 1.0 4.0
Se W 3.559392 20.638856 1.202717 20.478669 197.422484 10.005271 1.052738 3.815817 288321.561114 1.0 4.0
Se S 2.820092 7.491151 1.933323 141.532559 293.127817 90.470904 0.390492 4.170885 117688.987069 1.0 4.0

2
src/INTERLAYER/pair_ilp_tmd.cpp
View File

@ -210,7 +210,7 @@ void PairILPTMD::calc_FRep(int eflag, int /* vflag */)
delki[1] = x[k][1] - x[i][1]; delki[1] = x[k][1] - x[i][1];
delki[2] = x[k][2] - x[i][2]; delki[2] = x[k][2] - x[i][2];
if (evflag) if (evflag)
ev_tally_xyz(k, j, nlocal, newton_pair, 0.0, 0.0, fk[0], fk[1], fk[2], delki[0], ev_tally_xyz(k, i, nlocal, newton_pair, 0.0, 0.0, fk[0], fk[1], fk[2], delki[0],
delki[1], delki[2]); delki[1], delki[2]);
} }

2
src/INTERLAYER/pair_kolmogorov_crespi_full.cpp
View File

@ -590,7 +590,7 @@ void PairKolmogorovCrespiFull::calc_FRep(int eflag, int /* vflag */)
delki[1] = x[k][1] - x[i][1]; delki[1] = x[k][1] - x[i][1];
delki[2] = x[k][2] - x[i][2]; delki[2] = x[k][2] - x[i][2];
if (evflag) if (evflag)
ev_tally_xyz(k, j, nlocal, newton_pair, 0.0, 0.0, fk[0], fk[1], fk[2], delki[0], ev_tally_xyz(k, i, nlocal, newton_pair, 0.0, 0.0, fk[0], fk[1], fk[2], delki[0],
delki[1], delki[2]); delki[1], delki[2]);
} }