diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index 1b2a4a4b1d..7d795e0430 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -14,7 +14,15 @@ Syntax .. code-block:: LAMMPS - pair_style sw + pair_style style keywords values + +* style = *sw* or *sw/gpu* or *sw/omp* +* keyword = *modify* + + .. parsed-literal:: + + *modify* value = flag + flag = 0/1 to turn off/on the modification Examples """""""" @@ -25,6 +33,9 @@ Examples pair_coeff * * si.sw Si pair_coeff * * GaN.sw Ga N Ga + pair_style sw modify 1 + pair_coeff * * tmd.sw Mo S S + Description """"""""""" @@ -157,16 +168,52 @@ used for anything and can be set to 0.0 if desired. This is also true for the parameters in :math:`\phi_3` that are taken from the ij and ik pairs (:math:`\sigma`, *a*, :math:`\gamma`) +The *modify* keyword computes the energy E of a system of atoms, whose +formula is the same as the Stillinger-Weber potential. The only modification +is in the three-body term, where :math:`\delta = \cos \theta_{ijk} - \cos \theta_{0ijk}` +is modified with the following function: + +.. math:: + + g_C(\delta) & = \left\{ \begin{array} {r@{\quad:\quad}l} + 1 & \delta < \delta_1 \\ + \frac{1}{2} + \frac{1}{2} \cos \left( \pi \frac{\delta-\delta_1}{\delta_2 - \delta_1} \right) & + \delta_1 < \delta < \delta_2 \\ + 0 & \delta > \delta_2 + \end{array} \right. \\ + + +The *modify* keyword 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. Validation, +benchmark tests, and applications of the *modify* keyword can be found in +:ref:`(Jiang_1) ` and :ref:`(Jiang_2) `. + ---------- -.. include:: accel_styles.rst +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the :doc:`Speed packages ` doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. -.. note:: +These accelerated styles are part of the GPU, INTEL, KOKKOS, +OPENMP and OPT packages, respectively. They are only enabled if +LAMMPS was built with those packages. See the :doc:`Build package ` page for more info. - When using the INTEL package with this style, there is an additional - 5 to 10 percent performance improvement when the Stillinger-Weber - parameters p and q are set to 4 and 0 respectively. These - parameters are common for modeling silicon and water. +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the +:doc:`suffix ` command in your input script. + +When using the INTEL package with this style, there is an +additional 5 to 10 percent performance improvement when the +Stillinger-Weber parameters p and q are set to 4 and 0 respectively. +These parameters are common for modeling silicon and water. + +See the :doc:`Speed packages ` page for more +instructions on how to use the accelerated styles effectively. ---------- @@ -220,3 +267,11 @@ none .. _Stillinger2: **(Stillinger)** Stillinger and Weber, Phys Rev B, 31, 5262 (1985). + +.. _Jiang1: + +**(Jiang_1)** J.-W. Jiang, Nanotechnology 26, 315706 (2015). + +.. _Jiang2: + +**(Jiang_2)** J.-W. Jiang, Acta Mech. Solida. Sin 32, 17 (2019). diff --git a/examples/sw/in.mos2 b/examples/sw/in.mos2 new file mode 100644 index 0000000000..6c8a54494f --- /dev/null +++ b/examples/sw/in.mos2 @@ -0,0 +1,33 @@ +# bilayer MoS2 +units metal +boundary p p f +processors * * 1 + +atom_style full +read_data ./single_layer_MoS2.data + +variable mS equal 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg +variable mMo equal 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg + +mass * ${mS} +mass 1 ${mMo} + +########################## Define potentials ################################ +pair_style sw modify 1 +pair_coeff * * tmd.sw 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 diff --git a/examples/sw/log.27Oct21.mos2.icc.1.lmp b/examples/sw/log.27Oct21.mos2.icc.1.lmp new file mode 100644 index 0000000000..746afd05d1 --- /dev/null +++ b/examples/sw/log.27Oct21.mos2.icc.1.lmp @@ -0,0 +1,109 @@ +LAMMPS (27 Oct 2021) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# bilayer MoS2 +units metal +boundary p p f +processors * * 1 + +atom_style full +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 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.006 seconds + +variable mS equal 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg +variable mMo equal 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg + +mass * ${mS} +mass * 32.065 +mass 1 ${mMo} +mass 1 95.94 + +########################## Define potentials ################################ +pair_style sw modify 1 +pair_coeff * * tmd.sw Mo S S +Reading sw potential file tmd.sw 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, perpetual + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.538 | 6.538 | 6.538 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 3.13855 on 1 procs for 5000 steps with 768 atoms + +Performance: 137.643 ns/day, 0.174 hours/ns, 1593.092 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.0292 | 3.0292 | 3.0292 | 0.0 | 96.52 +Bond | 0.0033211 | 0.0033211 | 0.0033211 | 0.0 | 0.11 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.020003 | 0.020003 | 0.020003 | 0.0 | 0.64 +Output | 0.0005136 | 0.0005136 | 0.0005136 | 0.0 | 0.02 +Modify | 0.051294 | 0.051294 | 0.051294 | 0.0 | 1.63 +Other | | 0.03422 | | | 1.09 + +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 +Ave special neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/sw/single_layer_MoS2.data b/examples/sw/single_layer_MoS2.data new file mode 100644 index 0000000000..07bca1e4c2 --- /dev/null +++ b/examples/sw/single_layer_MoS2.data @@ -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 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26.764105185266961 0.000000000000000 + 751 1 2 -0.26 63.940400000000022 27.687005364069270 -1.596930000000000 + 752 1 3 -0.26 63.940400000000022 27.687005364069270 1.596930000000000 + 753 1 1 0.52 63.940400000000022 29.532805721673888 0.000000000000000 + 754 1 2 -0.26 65.538910000000023 30.455705900476197 -1.596930000000000 + 755 1 3 -0.26 65.538910000000023 30.455705900476197 1.596930000000000 + 756 1 1 0.52 65.538910000000023 32.301506258080815 0.000000000000000 + 757 1 2 -0.26 67.137420000000023 33.224406436883124 -1.596930000000000 + 758 1 3 -0.26 67.137420000000023 33.224406436883124 1.596930000000000 + 759 1 1 0.52 67.137420000000023 35.070206794487742 0.000000000000000 + 760 1 2 -0.26 68.735930000000024 35.993106973290051 -1.596930000000000 + 761 1 3 -0.26 68.735930000000024 35.993106973290051 1.596930000000000 + 762 1 1 0.52 68.735930000000024 37.838907330894669 0.000000000000000 + 763 1 2 -0.26 70.334440000000024 38.761807509696978 -1.596930000000000 + 764 1 3 -0.26 70.334440000000024 38.761807509696978 1.596930000000000 + 765 1 1 0.52 70.334440000000024 40.607607867301596 0.000000000000000 + 766 1 2 -0.26 71.932950000000025 41.530508046103905 -1.596930000000000 + 767 1 3 -0.26 71.932950000000025 41.530508046103905 1.596930000000000 + 768 1 1 0.52 71.932950000000025 43.376308403708523 0.000000000000000 diff --git a/examples/sw/tmd.sw b/examples/sw/tmd.sw new file mode 100644 index 0000000000..b88390ee26 --- /dev/null +++ b/examples/sw/tmd.sw @@ -0,0 +1,143 @@ +# 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 diff --git a/potentials/tmd.sw b/potentials/tmd.sw new file mode 100644 index 0000000000..b88390ee26 --- /dev/null +++ b/potentials/tmd.sw @@ -0,0 +1,143 @@ +# 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 diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index fcdda9ef9e..268cd840bf 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -28,11 +28,13 @@ #include "neighbor.h" #include "potential_file_reader.h" #include "tokenizer.h" +#include "math_const.h" #include #include using namespace LAMMPS_NS; +using namespace MathConst; #define DELTA 4 @@ -231,9 +233,24 @@ void PairSW::allocate() global settings ------------------------------------------------------------------------- */ -void PairSW::settings(int narg, char **/*arg*/) +void PairSW::settings(int narg, char **arg) { - if (narg != 0) error->all(FLERR,"Illegal pair_style command"); + //if (narg != 0) error->all(FLERR,"Illegal pair_style command"); + // default values + + modify_flag = 0; + + // process optional keywords + + int iarg = 0; + + while (iarg < narg) { + if (strcmp(arg[iarg],"modify") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style command"); + modify_flag = utils::numeric(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + } else error->all(FLERR,"Illegal pair_style command"); + } } /* ---------------------------------------------------------------------- @@ -485,7 +502,7 @@ void PairSW::threebody(Param *paramij, Param *paramik, Param *paramijk, 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; + double facang,facang12,csfacang,csfac1,csfac2,factor; r1 = sqrt(rsq1); rinvsq1 = 1.0/rsq1; @@ -504,6 +521,14 @@ void PairSW::threebody(Param *paramij, Param *paramik, Param *paramijk, rinv12 = 1.0/(r1*r2); cs = (delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2]) * rinv12; delcs = cs - paramijk->costheta; + // Modification + if(modify_flag) { + if(fabs(delcs) >= 0.35) delcs = 0.0; + else if(fabs(delcs) < 0.35 && fabs(delcs) > 0.25) { + factor = 0.5 + 0.5*cos(MY_PI*(delcs-0.25)/(0.35-0.25)); + delcs *= factor; + } + } delcssq = delcs*delcs; facexp = expgsrainv1*expgsrainv2; diff --git a/src/MANYBODY/pair_sw.h b/src/MANYBODY/pair_sw.h index 5f6f51b57c..ce8c4da56a 100644 --- a/src/MANYBODY/pair_sw.h +++ b/src/MANYBODY/pair_sw.h @@ -54,6 +54,8 @@ class PairSW : public Pair { int maxshort; // size of short neighbor list array int *neighshort; // short neighbor list array + int modify_flag; // flag to turn on/off the modification + virtual void allocate(); void read_file(char *); virtual void setup_params();