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Merge pull request #3041 from oywg11/modified-sw-potential

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A modified Stillinger-Weber potential for transition metal dichalcogenide
This commit is contained in:
Axel Kohlmeyer
2021-12-09 09:43:49 -05:00
committed by GitHub
parent 5cee58a9c8 1238f1b273
commit 754610b9ee
20 changed files with 1835 additions and 15 deletions
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1
doc/src/Commands_pair.rst
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@ -262,6 +262,7 @@ OPT.
* :doc:`spin/neel <pair_spin_neel>`
* :doc:`srp <pair_srp>`
* :doc:`sw (giko) <pair_sw>`
* :doc:`sw/mod (o) <pair_sw>`
* :doc:`table (gko) <pair_table>`
* :doc:`table/rx (k) <pair_table_rx>`
* :doc:`tdpd <pair_mesodpd>`

5
doc/src/Howto_drude2.rst
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@ -491,11 +491,6 @@ NPT ensemble using Nose-Hoover thermostat:
**(Schroeder)** Schroeder and Steinhauser, J Chem Phys, 133,
154511 (2010).
.. _Jiang2:
**(Jiang)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux,
J Phys Chem Lett, 2, 87-92 (2011).
.. _Thole2:
**(Thole)** Chem Phys, 59, 341 (1981).

4
doc/src/fix_langevin_drude.rst
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@ -40,7 +40,7 @@ Example input scripts available: examples/PACKAGES/drude
Description
"""""""""""
Apply two Langevin thermostats as described in :ref:`(Jiang) <Jiang1>` for
Apply two Langevin thermostats as described in :ref:`(Jiang1) <Jiang1>` for
thermalizing the reduced degrees of freedom of Drude oscillators.
This link describes how to use the :doc:`thermalized Drude oscillator model <Howto_drude>` in LAMMPS and polarizable models in LAMMPS
are discussed on the :doc:`Howto polarizable <Howto_polarizable>` doc
@ -300,5 +300,5 @@ The option defaults are zero = no.
.. _Jiang1:
**(Jiang)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J
**(Jiang1)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J
Phys Chem Lett, 2, 87-92 (2011).

1
doc/src/pair_style.rst
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@ -327,6 +327,7 @@ accelerated styles exist.
* :doc:`spin/neel <pair_spin_neel>` -
* :doc:`srp <pair_srp>` -
* :doc:`sw <pair_sw>` - Stillinger-Weber 3-body potential
* :doc:`sw/mod <pair_sw>` - modified Stillinger-Weber 3-body potential
* :doc:`table <pair_table>` - tabulated pair potential
* :doc:`table/rx <pair_table_rx>` -
* :doc:`tdpd <pair_mesodpd>` - tDPD particle interactions

80
doc/src/pair_sw.rst
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@ -3,18 +3,34 @@
.. index:: pair_style sw/intel
.. index:: pair_style sw/kk
.. index:: pair_style sw/omp
.. index:: pair_style sw/mod
.. index:: pair_style sw/mod/omp
pair_style sw command
=====================
Accelerator Variants: *sw/gpu*, *sw/intel*, *sw/kk*, *sw/omp*
pair_style sw/mod command
=========================
Accelerator Variants: *sw/mod/omp*
Syntax
""""""
.. code-block:: LAMMPS
pair_style sw
pair_style style keyword values
* style = *sw* or *sw/mod*
* keyword = *maxdelcs*
.. parsed-literal::
*maxdelcs* value = delta1 delta2 (optional)
delta1 = The minimum thershold for cosine of three-body angle
delta2 = The maximum threshold for cosine of three-body angle
Examples
""""""""
@ -25,6 +41,9 @@ Examples
pair_coeff * * si.sw Si
pair_coeff * * GaN.sw Ga N Ga
pair_style sw/mod maxdelcs 0.25 0.35
pair_coeff * * tmd.sw.mod Mo S S
Description
"""""""""""
@ -48,8 +67,52 @@ where :math:`\phi_2` is a two-body term and :math:`\phi_3` is a
three-body term. The summations in the formula are over all neighbors J
and K of atom I within a cutoff distance :math:`a `\sigma`.
Only a single pair_coeff command is used with the *sw* style which
specifies a Stillinger-Weber potential file with parameters for all
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
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.
Such exclusion may be realized by selecting proper angle types directly.
The exclusion of unnecessary angles is achieved here by the cut-off function (`f_C(\delta)`),
which induces only minimum modifications for LAMMPS.
Validation, benchmark tests, and applications of the *sw/mod* style
can be found in :ref:`(Jiang2) <Jiang2>` and :ref:`(Jiang3) <Jiang3>`.
The *sw/mod* style computes the energy E of a system of atoms, whose potential
function is mostly the same as the Stillinger-Weber potential. The only modification
is in the three-body term, where the value of :math:`\delta = \cos \theta_{ijk} - \cos \theta_{0ijk}`
used in the original energy and force expression is scaled by a switching factor :math:`f_C(\delta)`:
.. math::
f_C(\delta) & = \left\{ \begin{array} {r@{\quad:\quad}l}
1 & \left| \delta \right| < \delta_1 \\
\frac{1}{2} + \frac{1}{2} \cos \left( \pi \frac{\left| \delta \right| - \delta_1}{\delta_2 - \delta_1} \right) &
\delta_1 < \left| \delta \right| < \delta_2 \\
0 & \left| \delta \right| > \delta_2
\end{array} \right. \\
This cut-off function decreases smoothly from 1 to 0 over the range :math:`[\delta_1, \delta_2]`.
This smoothly turns off the energy and force contributions for :math:`\left| \delta \right| > \delta_2`.
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`.
This value enables the cut-off function to exclude unnecessary angles in the three-body SW terms.
.. note::
The cut-off function is just to be used as a technique to exclude some unnecessary angles,
and it has no physical meaning. It should be noted that the force and potential are inconsistent
with each other in the decaying range of the cut-off function, as the angle dependence for the
cut-off function is not implemented in the force (first derivation of potential).
However, the angle variation is much smaller than the given threshold value for actual simulations,
so the inconsistency between potential and force can be neglected in actual simulations.
Only a single pair_coeff command is used with the *sw* and *sw/mod* styles
which specifies a Stillinger-Weber potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
@ -213,10 +276,19 @@ Related commands
Default
"""""""
none
The default values for the *maxdelcs* setting of the *sw/mod* pair
style are *delta1* = 0.25 and *delta2* = 0.35`.
----------
.. _Stillinger2:
**(Stillinger)** Stillinger and Weber, Phys Rev B, 31, 5262 (1985).
.. _Jiang2:
**(Jiang2)** J.-W. Jiang, Nanotechnology 26, 315706 (2015).
.. _Jiang3:
**(Jiang3)** J.-W. Jiang, Acta Mech. Solida. Sin 32, 17 (2019).

4
doc/utils/sphinx-config/false_positives.txt
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@ -308,6 +308,7 @@ boolean
boostostat
boostostatting
Boresch
borophene
Botero
Botu
Bouguet
@ -688,6 +689,7 @@ diagonalizers
diagonalizing
Diallo
diblock
dichalcogenide
Dickel
diel
differentiable
@ -2390,6 +2392,7 @@ ohenrich
ok
Okabe
Okamoto
O'Hearn
O'Keefe
OKeefe
oldlace
@ -3078,6 +3081,7 @@ snav
Snodin
Sodani
Soderlind
Solida
solvated
solvation
someuser

30
examples/threebody/in.mos2.sw.mod Normal file
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@ -0,0 +1,30 @@
# monolayer MoS2
units metal
boundary p p f
processors * * 1
atom_style atomic
read_data single_layer_MoS2.data
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
########################## Define potentials ################################
pair_style sw/mod maxdelcs 0.25 0.35
pair_coeff * * tmd.sw.mod Mo S S
#########################################################################
### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
############################
# Output
thermo 500
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 5000

92
examples/threebody/log.27Oct21.mos2_sw_mod.g++.1 Normal file
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@ -0,0 +1,92 @@
LAMMPS (27 Oct 2021)
# monolayer MoS2
units metal
boundary p p f
processors * * 1
atom_style atomic
read_data single_layer_MoS2.data
Reading data file ...
triclinic box = (0.0000000 0.0000000 -100.00000) to (51.152320 44.299209 100.00000) with tilt (25.576160 0.0000000 0.0000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
768 atoms
read_data CPU = 0.043 seconds
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
########################## Define potentials ################################
pair_style sw/mod maxdelcs 0.25 0.35
pair_coeff * * tmd.sw.mod Mo S S
Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
#########################################################################
### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
############################
# Output
thermo 500
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.158796
ghost atom cutoff = 5.158796
binsize = 2.579398, bins = 30 18 78
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw/mod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.466 | 3.466 | 3.466 Mbytes
Step TotEng PotEng KinEng Temp
0 -899.28605 -929.02881 29.742759 300
500 -899.28626 -922.45519 23.168929 233.69313
1000 -899.29247 -925.86547 26.573002 268.02828
1500 -899.27957 -916.95478 17.675214 178.28084
2000 -899.28171 -918.38728 19.105573 192.70814
2500 -899.28732 -922.50423 23.21691 234.17709
3000 -899.28195 -918.74112 19.459174 196.27473
3500 -899.27944 -918.03105 18.751604 189.13784
4000 -899.28397 -920.50737 21.223397 214.06955
4500 -899.28386 -919.79154 20.507685 206.85053
5000 -899.28077 -918.78947 19.508698 196.77425
Loop time of 5.84317 on 1 procs for 5000 steps with 768 atoms
Performance: 73.932 ns/day, 0.325 hours/ns, 855.700 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.6796 | 5.6796 | 5.6796 | 0.0 | 97.20
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.026354 | 0.026354 | 0.026354 | 0.0 | 0.45
Output | 0.0014959 | 0.0014959 | 0.0014959 | 0.0 | 0.03
Modify | 0.090437 | 0.090437 | 0.090437 | 0.0 | 1.55
Other | | 0.04524 | | | 0.77
Nlocal: 768.000 ave 768 max 768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 354.000 ave 354 max 354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 20480.0 ave 20480 max 20480 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 20480
Ave neighs/atom = 26.666667
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:06

781
examples/threebody/single_layer_MoS2.data Normal file
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@ -0,0 +1,781 @@
Single layer MoS2
768 atoms
3 atom types
0.0000000000000000 51.1523200000000177 xlo xhi
0.0000000000000000 44.2992085825108320 ylo yhi
-100.0000000000000000 100.0000000000000000 zlo zhi
25.5761600000000088 0.0000000000000000 0.0000000000000000 xy xz yz
Atoms
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examples/threebody/tmd.sw.mod Symbolic link
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../../potentials/tmd.sw.mod

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# DATE: 2018-03-26 UNITS: metal CONTRIBUTOR: Jin-Wu Jiang jwjiang5918@hotmail.com
# CITATION: J.-W. Jiang, Acta Mech. Solida. Sin 32, 17 (2019).
# The Stillinger-Weber parameters, for transition-metal dichalcogenide (TMD) lateral heterostructures.
# M = Mo, W; X = S, Se, Te
# these entries are in LAMMPS "metal" units:
# epsilon = eV; sigma = Angstroms
# other quantities are unitless
# format of a single entry (one or more lines):
# element 1, element 2, element 3,
# epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol
# M-X-X terms
Mo S S 1.000 1.252 2.523 67.883 1.000 0.143 6.918 7.223 4 0 0.0
Mo Se Se 1.000 0.913 3.672 32.526 1.000 0.143 5.737 27.084 4 0 0.0
Mo Te Te 1.000 0.880 4.097 23.705 1.000 0.143 5.086 40.810 4 0 0.0
W S S 1.000 0.889 3.558 37.687 1.000 0.143 5.664 24.525 4 0 0.0
W Se Se 1.000 0.706 4.689 25.607 1.000 0.143 5.476 65.662 4 0 0.0
W Te Te 1.000 0.778 4.632 21.313 1.000 0.143 4.326 62.148 4 0 0.0
# X-M-M terms
S Mo Mo 1.000 1.252 2.523 62.449 1.000 0.143 6.918 7.223 4 0 0.0
S W W 1.000 0.889 3.558 33.553 1.000 0.143 5.664 24.525 4 0 0.0
Se Mo Mo 1.000 0.913 3.672 27.079 1.000 0.143 5.737 27.084 4 0 0.0
Se W W 1.000 0.706 4.689 23.218 1.000 0.143 5.476 65.662 4 0 0.0
Te Mo Mo 1.000 0.880 4.097 20.029 1.000 0.143 5.086 40.810 4 0 0.0
Te W W 1.000 0.778 4.632 17.370 1.000 0.143 4.326 62.148 4 0 0.0
# M-X1-X2 terms
Mo S Se 1.000 0.000 0.000 46.989 1.000 0.143 0.000 0.000 4 0 0.0
Mo S Te 1.000 0.000 0.000 40.114 1.000 0.143 0.000 0.000 4 0 0.0
Mo Se S 1.000 0.000 0.000 46.989 1.000 0.143 0.000 0.000 4 0 0.0
Mo Se Te 1.000 0.000 0.000 27.767 1.000 0.143 0.000 0.000 4 0 0.0
Mo Te S 1.000 0.000 0.000 40.114 1.000 0.143 0.000 0.000 4 0 0.0
Mo Te Se 1.000 0.000 0.000 27.767 1.000 0.143 0.000 0.000 4 0 0.0
W S Se 1.000 0.000 0.000 31.065 1.000 0.143 0.000 0.000 4 0 0.0
W S Te 1.000 0.000 0.000 28.341 1.000 0.143 0.000 0.000 4 0 0.0
W Se S 1.000 0.000 0.000 31.065 1.000 0.143 0.000 0.000 4 0 0.0
W Se Te 1.000 0.000 0.000 23.362 1.000 0.143 0.000 0.000 4 0 0.0
W Te S 1.000 0.000 0.000 28.341 1.000 0.143 0.000 0.000 4 0 0.0
W Te Se 1.000 0.000 0.000 23.362 1.000 0.143 0.000 0.000 4 0 0.0
# X-M1-M2 terms
S Mo W 1.000 0.000 0.000 45.775 1.000 0.143 0.000 0.000 4 0 0.0
S W Mo 1.000 0.000 0.000 45.775 1.000 0.143 0.000 0.000 4 0 0.0
Se Mo W 1.000 0.000 0.000 25.074 1.000 0.143 0.000 0.000 4 0 0.0
Se W Mo 1.000 0.000 0.000 25.074 1.000 0.143 0.000 0.000 4 0 0.0
Te Mo W 1.000 0.000 0.000 18.652 1.000 0.143 0.000 0.000 4 0 0.0
Te W Mo 1.000 0.000 0.000 18.652 1.000 0.143 0.000 0.000 4 0 0.0
# zero terms
Mo Mo Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Mo W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Mo S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Mo Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Mo Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo W Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo W W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo W S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo W Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo W Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo S Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo S W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Se Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Se W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Te Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Te W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Mo Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Mo W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Mo S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Mo Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Mo Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W W Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W W W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W W S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W W Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W W Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W S Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W S W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Se Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Se W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Te Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Te W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Mo S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Mo Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Mo Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S W S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S W Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S W Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S S Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S S W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S S S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S S Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S S Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Se Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Se W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Se S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Se Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Se Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Te Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Te W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Te S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Te Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Te Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Mo S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Mo Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Mo Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se W S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se W Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se W Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se S Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se S W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se S S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se S Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se S Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Se Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Se W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Se S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Se Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Se Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Te Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Te W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Te S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Te Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Te Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Mo S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Mo Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Mo Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te W S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te W Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te W Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te S Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te S W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te S S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te S Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te S Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Se Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Se W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Se S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Se Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Se Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Te Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Te W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Te S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Te Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Te Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0

2
src/.gitignore vendored
View File

@ -1208,6 +1208,8 @@
/pair_sph_taitwater_morris.h
/pair_sw.cpp
/pair_sw.h
/pair_sw_mod.cpp
/pair_sw_mod.h
/pair_tersoff.cpp
/pair_tersoff.h
/pair_tersoff_mod.cpp

5
src/MANYBODY/pair_sw.cpp
View File

@ -293,7 +293,7 @@ void PairSW::read_file(char *file)
if (comm->me == 0) {
PotentialFileReader reader(lmp, file, "sw", unit_convert_flag);
char *line;
char * line;
// transparently convert units for supported conversions
@ -328,7 +328,8 @@ void PairSW::read_file(char *file)
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),"pair:params");
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
"pair:params");
// make certain all addional allocated storage is initialized
// to avoid false positives when checking with valgrind

4
src/MANYBODY/pair_sw.h
View File

@ -29,7 +29,6 @@ class PairSW : public Pair {
PairSW(class LAMMPS *);
virtual ~PairSW();
virtual void compute(int, int);
void settings(int, char **);
virtual void coeff(int, char **);
virtual double init_one(int, int);
virtual void init_style();
@ -54,11 +53,12 @@ class PairSW : public Pair {
int maxshort; // size of short neighbor list array
int *neighshort; // short neighbor list array
virtual void settings(int, char **);
virtual void allocate();
void read_file(char *);
virtual void setup_params();
void twobody(Param *, double, double &, int, double &);
void threebody(Param *, Param *, Param *, double, double, double *, double *, double *, double *,
virtual void threebody(Param *, Param *, Param *, double, double, double *, double *, double *, double *,
int, double &);
};

123
src/MANYBODY/pair_sw_mod.cpp Normal file
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@ -0,0 +1,123 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Jin-Wu Jiang (Shanghai U) and Wengen Ouyang (Wuhan U)
------------------------------------------------------------------------- */
#include "pair_sw_mod.h"
#include "error.h"
#include "math_const.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
PairSWMOD::PairSWMOD(LAMMPS *lmp) : PairSW(lmp)
{
delta1 = 0.25;
delta2 = 0.35;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairSWMOD::settings(int narg, char **arg)
{
// process optional keywords
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"maxdelcs") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style command");
delta1 = utils::numeric(FLERR,arg[iarg+1],false,lmp);
delta2 = utils::numeric(FLERR,arg[iarg+2],false,lmp);
iarg += 3;
if ((delta1 < 0.0) || (delta1 > 1.0) || (delta2 < 0.0) || (delta2 > 1.0) || (delta1 > delta2))
error->all(FLERR,"Illegal values for maxdelcs keyword");
} else error->all(FLERR,"Illegal pair_style command");
}
PairSW::settings(narg-iarg,arg+iarg);
}
/* ---------------------------------------------------------------------- */
void PairSWMOD::threebody(Param *paramij, Param *paramik, Param *paramijk,
double rsq1, double rsq2,
double *delr1, double *delr2,
double *fj, double *fk, int eflag, double &eng)
{
double r1,rinvsq1,rainv1,gsrainv1,gsrainvsq1,expgsrainv1;
double r2,rinvsq2,rainv2,gsrainv2,gsrainvsq2,expgsrainv2;
double rinv12,cs,delcs,delcssq,facexp,facrad,frad1,frad2;
double facang,facang12,csfacang,csfac1,csfac2,factor;
r1 = sqrt(rsq1);
rinvsq1 = 1.0/rsq1;
rainv1 = 1.0/(r1 - paramij->cut);
gsrainv1 = paramij->sigma_gamma * rainv1;
gsrainvsq1 = gsrainv1*rainv1/r1;
expgsrainv1 = exp(gsrainv1);
r2 = sqrt(rsq2);
rinvsq2 = 1.0/rsq2;
rainv2 = 1.0/(r2 - paramik->cut);
gsrainv2 = paramik->sigma_gamma * rainv2;
gsrainvsq2 = gsrainv2*rainv2/r2;
expgsrainv2 = exp(gsrainv2);
rinv12 = 1.0/(r1*r2);
cs = (delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2]) * rinv12;
delcs = cs - paramijk->costheta;
// Modification to delcs
if(fabs(delcs) >= delta2) delcs = 0.0;
else if(fabs(delcs) < delta2 && fabs(delcs) > delta1) {
factor = 0.5 + 0.5*cos(MY_PI*(fabs(delcs) - delta1)/(delta2 - delta1));
delcs *= factor;
}
delcssq = delcs*delcs;
facexp = expgsrainv1*expgsrainv2;
// facrad = sqrt(paramij->lambda_epsilon*paramik->lambda_epsilon) *
// facexp*delcssq;
facrad = paramijk->lambda_epsilon * facexp*delcssq;
frad1 = facrad*gsrainvsq1;
frad2 = facrad*gsrainvsq2;
facang = paramijk->lambda_epsilon2 * facexp*delcs;
facang12 = rinv12*facang;
csfacang = cs*facang;
csfac1 = rinvsq1*csfacang;
fj[0] = delr1[0]*(frad1+csfac1)-delr2[0]*facang12;
fj[1] = delr1[1]*(frad1+csfac1)-delr2[1]*facang12;
fj[2] = delr1[2]*(frad1+csfac1)-delr2[2]*facang12;
csfac2 = rinvsq2*csfacang;
fk[0] = delr2[0]*(frad2+csfac2)-delr1[0]*facang12;
fk[1] = delr2[1]*(frad2+csfac2)-delr1[1]*facang12;
fk[2] = delr2[2]*(frad2+csfac2)-delr1[2]*facang12;
if (eflag) eng = facrad;
}

94
src/MANYBODY/pair_sw_mod.h Normal file
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@ -0,0 +1,94 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(sw/mod,PairSWMOD);
// clang-format on
#else
#ifndef LMP_PAIR_SW_MOD_H
#define LMP_PAIR_SW_MOD_H
#include "pair_sw.h"
namespace LAMMPS_NS {
class PairSWMOD : public PairSW {
public:
PairSWMOD(class LAMMPS *);
virtual ~PairSWMOD() {}
protected:
double delta1;
double delta2;
void settings(int, char **);
void threebody(Param *, Param *, Param *, double, double, double *, double *, double *, double *,
int, double &);
};
} // namespace LAMMPS_NS
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: Pair style Stillinger-Weber requires atom IDs
This is a requirement to use the SW potential.
E: Pair style Stillinger-Weber requires newton pair on
See the newton command. This is a restriction to use the SW
potential.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: Cannot open Stillinger-Weber potential file %s
The specified SW potential file cannot be opened. Check that the path
and name are correct.
E: Incorrect format in Stillinger-Weber potential file
Incorrect number of words per line in the potential file.
E: Illegal Stillinger-Weber parameter
One or more of the coefficients defined in the potential file is
invalid.
E: Potential file has duplicate entry
The potential file has more than one entry for the same element.
E: Potential file is missing an entry
The potential file does not have a needed entry.
*/

119
src/OPENMP/pair_sw_mod_omp.cpp Normal file
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@ -0,0 +1,119 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
This software is distributed under the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
and Wengen Ouyang (Wuhan U)
------------------------------------------------------------------------- */
#include "pair_sw_mod_omp.h"
#include "error.h"
#include "math_const.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
PairSWMODOMP::PairSWMODOMP(LAMMPS *lmp) : PairSWOMP(lmp)
{
delta1 = 0.25;
delta2 = 0.35;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairSWMODOMP::settings(int narg, char **arg)
{
// process optional keywords
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"maxdelcs") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style command");
delta1 = utils::numeric(FLERR,arg[iarg+1],false,Pointers::lmp);
delta2 = utils::numeric(FLERR,arg[iarg+2],false,Pointers::lmp);
iarg += 3;
if ((delta1 < 0.0) || (delta1 > 1.0) || (delta2 < 0.0) || (delta2 > 1.0) || (delta1 > delta2))
error->all(FLERR,"Illegal values for maxdelcs keyword");
} else error->all(FLERR,"Illegal pair_style command");
}
PairSWOMP::settings(narg-iarg,arg+iarg);
}
/* ---------------------------------------------------------------------- */
void PairSWMODOMP::threebody(Param *paramij, Param *paramik, Param *paramijk,
double rsq1, double rsq2,
double *delr1, double *delr2,
double *fj, double *fk, int eflag, double &eng)
{
double r1,rinvsq1,rainv1,gsrainv1,gsrainvsq1,expgsrainv1;
double r2,rinvsq2,rainv2,gsrainv2,gsrainvsq2,expgsrainv2;
double rinv12,cs,delcs,delcssq,facexp,facrad,frad1,frad2;
double facang,facang12,csfacang,csfac1,csfac2,factor;
r1 = sqrt(rsq1);
rinvsq1 = 1.0/rsq1;
rainv1 = 1.0/(r1 - paramij->cut);
gsrainv1 = paramij->sigma_gamma * rainv1;
gsrainvsq1 = gsrainv1*rainv1/r1;
expgsrainv1 = exp(gsrainv1);
r2 = sqrt(rsq2);
rinvsq2 = 1.0/rsq2;
rainv2 = 1.0/(r2 - paramik->cut);
gsrainv2 = paramik->sigma_gamma * rainv2;
gsrainvsq2 = gsrainv2*rainv2/r2;
expgsrainv2 = exp(gsrainv2);
rinv12 = 1.0/(r1*r2);
cs = (delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2]) * rinv12;
delcs = cs - paramijk->costheta;
// Modification to delcs
if(fabs(delcs) >= delta2) delcs = 0.0;
else if(fabs(delcs) < delta2 && fabs(delcs) > delta1) {
factor = 0.5 + 0.5*cos(MY_PI*(fabs(delcs) - delta1)/(delta2 - delta1));
delcs *= factor;
}
delcssq = delcs*delcs;
facexp = expgsrainv1*expgsrainv2;
// facrad = sqrt(paramij->lambda_epsilon*paramik->lambda_epsilon) *
// facexp*delcssq;
facrad = paramijk->lambda_epsilon * facexp*delcssq;
frad1 = facrad*gsrainvsq1;
frad2 = facrad*gsrainvsq2;
facang = paramijk->lambda_epsilon2 * facexp*delcs;
facang12 = rinv12*facang;
csfacang = cs*facang;
csfac1 = rinvsq1*csfacang;
fj[0] = delr1[0]*(frad1+csfac1)-delr2[0]*facang12;
fj[1] = delr1[1]*(frad1+csfac1)-delr2[1]*facang12;
fj[2] = delr1[2]*(frad1+csfac1)-delr2[2]*facang12;
csfac2 = rinvsq2*csfacang;
fk[0] = delr2[0]*(frad2+csfac2)-delr1[0]*facang12;
fk[1] = delr2[1]*(frad2+csfac2)-delr1[1]*facang12;
fk[2] = delr2[2]*(frad2+csfac2)-delr1[2]*facang12;
if (eflag) eng = facrad;
}

49
src/OPENMP/pair_sw_mod_omp.h Normal file
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@ -0,0 +1,49 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(sw/mod/omp,PairSWMODOMP);
// clang-format on
#else
#ifndef LMP_PAIR_SW_MOD_OMP_H
#define LMP_PAIR_SW_MOD_OMP_H
#include "pair_sw_omp.h"
namespace LAMMPS_NS {
class PairSWMODOMP : public PairSWOMP {
public:
PairSWMODOMP(class LAMMPS *);
virtual ~PairSWMODOMP() {}
protected:
double delta1;
double delta2;
void settings(int, char **);
void threebody(Param *, Param *, Param *, double, double, double *, double *, double *, double *,
int, double &);
};
} // namespace LAMMPS_NS
#endif
#endif

156
unittest/force-styles/tests/manybody-pair-sw-mod-maxdelcs.yaml Normal file
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@ -0,0 +1,156 @@
---
lammps_version: 27 Oct 2021
date_generated: Fri Dec 3 17:14:23 2021
epsilon: 2e-08
skip_tests:
prerequisites: ! |
pair sw/mod
pre_commands: ! |
variable newton_pair delete
if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on"
post_commands: ! ""
input_file: in.manybody
pair_style: sw/mod maxdelcs 0.20 0.40
pair_coeff: ! |
* * CdTe.sw Cd Cd Cd Cd Te Te Te Te
extract: ! ""
natoms: 64
init_vdwl: -102.90155182016774
init_coul: 0
init_stress: ! |-
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init_forces: ! |2
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64 1.9765285883417301e+00 2.0768686745001230e+00 5.0210256117812220e+00
run_vdwl: -102.8863066387519
run_coul: 0
run_stress: ! |-
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run_forces: ! |2
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62 -2.7071779218109575e+00 2.0159966095690671e+00 -1.0872338761779961e+00
63 1.1764921309976299e+00 -3.5078075687694996e+00 9.5738583931291754e-02
64 2.0160799277578452e+00 2.1172152881764932e+00 5.0470647349337190e+00
...

156
unittest/force-styles/tests/manybody-pair-sw-mod-multi.yaml Normal file
View File

@ -0,0 +1,156 @@
---
lammps_version: 27 Oct 2021
date_generated: Fri Dec 3 17:00:11 2021
epsilon: 2e-08
skip_tests:
prerequisites: ! |
pair sw/mod
pre_commands: ! |
variable newton_pair delete
if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on"
post_commands: ! ""
input_file: in.manybody
pair_style: sw/mod
pair_coeff: ! |
* * CdTe.sw Cd Cd Cd Cd Te Te Te Te
extract: ! ""
natoms: 64
init_vdwl: -102.37263341910496
init_coul: 0
init_stress: ! |-
-1.9299390308487332e+01 -1.8776425549919630e+01 -1.9374721168707158e+01 -9.9622288974183402e+00 2.8070027242773669e+01 2.3879337940188838e+00
init_forces: ! |2
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2 -2.2306493745023439e+00 -8.0714318418132680e-01 -2.1923062020153332e+00
3 4.2806028767962845e-01 -4.3590991678773050e-01 -5.0075218062879157e-01
4 -1.5656435682231125e+00 2.5915183820303294e+00 1.5040666120009878e+00
5 -6.9060643334495364e-01 -1.0647727077215563e+00 1.0180213728505660e-01
6 1.5642465056067236e+00 3.1396473681405714e+00 2.3641961557945523e-01
7 -8.6200824722768510e-01 -3.1293943422778392e-01 5.8408431260171700e-01
8 -4.0266618929934772e-02 3.9766986295109796e-01 -2.5739252841289817e-01
9 -1.0121360928146172e-01 -2.1107078034640070e+00 -1.6464009666060164e+00
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18 8.0983992795309412e-01 1.9375641754963246e-01 3.0453558733140791e+00
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58 1.8947653213983979e+00 -1.2696890878445555e+00 1.1075578262554551e+00
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60 -1.3722628021690451e+00 -4.7890295934897642e+00 -2.6044795996416212e+00
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