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Commit 2d0d0809 authored by Zbigniew Koziol's avatar Zbigniew Koziol
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Another attempt to add Lebedeva potential

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doc/src/Eqs/pair_lebedeva.png

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
pair_style lebedeva command :h3
[Syntax:]
pair_style hybrid/overlay lebedeva cutoff :pre
[Examples:]
pair_style hybrid/overlay lebedeva 20.0
pair_coeff * * none
pair_coeff 1 2 lebedeva CC.Lebedeva C C :pre
pair_style hybrid/overlay rebo lebedeva 14.0
pair_coeff * * rebo CH.airebo C C
pair_coeff 1 2 lebedeva CC.Lebedeva C C :pre
[Description:]
The {lebedeva} style computes the Lebedeva interaction
potential as described in "(Lebedeva et al.)"_#Leb01. An important simplification is made,
which is to take all normals along the z-axis.
:c,image(Eqs/pair_lebedeva.png)
It is important to have a sufficiently large cutoff to ensure smooth forces.
Energies are shifted so that they go continuously to zero at the cutoff assuming
that the exponential part of {Vij} (first term) decays sufficiently fast.
This shift is achieved by the last term in the equation for {Vij} above.
The parameter file (e.g. CC.Lebedeva), is intended for use with metal
"units"_units.html, with energies in meV. An additional parameter, {S},
is available to facilitate scaling of energies.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style {none}.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html
"pair_none"_pair_none.html
"pair_style hybrid/overlay"_pair_hybrid.html
[Default:] none
:line
:link(Leb01)
[(Lebedeva et al.)] I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
examples/USER/misc/lebedeva/2particles.dat 0 → 100644
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Ideal graphene structure in YZ plane created with create_graphen.pl
2 atoms
2 atom types
0.0 20 xlo xhi
0.0 20 ylo yhi
0.0 5 zlo zhi
Atoms
1 1 10 10 0.0
2 2 0 0 3.35
examples/USER/misc/lebedeva/2particles.in 0 → 100644
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# After running LAMMPS with this input script a number of dump files is created.
# To extract the data from there I used grep script:
# grep '^2 ' *cfg > LammpsResult.dat
# After that after removing some text from LammpsResult.dat,
# the data can be viewed by lebedeva00.plot
#
# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland
# Email: softquake@gmail.com
# ---------- Start simulation ---------------------
clear
units metal
dimension 3
boundary f f f
atom_style atomic
# ========================== Create Atomistic Structure ===========================
region whole block 0 20 0 20 0 10
create_box 2 whole
read_data 2particles.dat add append
region graphite block INF INF INF INF 0 10 units box
group graphite type 1 2
group graphene1 type 1
group graphene2 type 2
pair_style hybrid/overlay lebedeva 20
pair_coeff * * none
pair_coeff 1 2 lebedeva CC.Lebedeva C C
mass 1 12.01 # Carbon
mass 2 12.01 # Carbon
neighbor 0.3 bin
neigh_modify delay 1 check yes
compute peratom all pe/atom
dump 1 all custom 1 dump_lebedeva_*.cfg id x y z c_peratom fx fy fz
dump_modify 1 pad 3
thermo 10
thermo_style custom step pe press temp
thermo_modify lost ignore
label STEP_LOOP
variable MYSTEP loop 0 400 pad # in degrees
variable DELTA_STEP equal 0.05
displace_atoms graphene2 move ${DELTA_STEP} ${DELTA_STEP} 0
run 1
next MYSTEP
jump SELF STEP_LOOP
print "all done"
examples/USER/misc/lebedeva/CC.Lebedeva 0 → 100644
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# Lebedeva Potential. Original values from Lebedeva. May be played with ;)
#
# Cite as: Irina V. Lebedeva, Andrey A. Knizhnik, Andrey M. Popov, Yurii E. Lozovik, Boris V. Potapkin,
# Modeling of graphene-based NEMS
# Physica E 44 (6), 949 (2012)
# https://doi.org/10.1016/j.physe.2011.07.018
#
# Parameters must be in this order as here, otherwise their values may be changed.
# The last one, S, is convenient for scaling the potential amplitude. S is a multiplication factor for A, B, C
# A B C z0 alpha D1 D2 lambda1 lambda2 S
# These are values according to Levedeva et al
#C C 10.510 11.6523.34 35.883 3.34 4.16 -0.86232 0.10049 0.48703 0.46445 1.0
# These are values by Z. Koziol et al.: https://arxiv.org/abs/1803.05162
C C 14.558 21.204 1.8 3.198 4.16 -0.862 0.10049 0.6 0.4 1.0
examples/USER/misc/lebedeva/LammpsResult.dat 0 → 100644
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dump_lebedeva_000.cfg:2 0.05 0.05 3.35 -7.28468e-07 4.85145e-07 4.85145e-07 -1.6334e-07
dump_lebedeva_001.cfg:2 0.05 0.05 3.35 -7.28468e-07 4.85145e-07 4.85145e-07 -1.6334e-07
dump_lebedeva_002.cfg:2 0.1 0.1 3.35 -7.5313e-07 5.01468e-07 5.01468e-07 -1.69689e-07
dump_lebedeva_003.cfg:2 0.15 0.15 3.35 -7.78625e-07 5.18417e-07 5.18417e-07 -1.76314e-07
dump_lebedeva_004.cfg:2 0.2 0.2 3.35 -8.04983e-07 5.36017e-07 5.36017e-07 -1.8323e-07
dump_lebedeva_005.cfg:2 0.25 0.25 3.35 -8.32238e-07 5.54298e-07 5.54298e-07 -1.90451e-07
dump_lebedeva_006.cfg:2 0.3 0.3 3.35 -8.60425e-07 5.73288e-07 5.73288e-07 -1.97991e-07
dump_lebedeva_007.cfg:2 0.35 0.35 3.35 -8.89579e-07 5.93019e-07 5.93019e-07 -2.05867e-07
dump_lebedeva_008.cfg:2 0.4 0.4 3.35 -9.19739e-07 6.13522e-07 6.13522e-07 -2.14094e-07
dump_lebedeva_009.cfg:2 0.45 0.45 3.35 -9.50945e-07 6.34832e-07 6.34832e-07 -2.2269e-07
dump_lebedeva_010.cfg:2 0.5 0.5 3.35 -9.83237e-07 6.56984e-07 6.56984e-07 -2.31673e-07
dump_lebedeva_011.cfg:2 0.55 0.55 3.35 -1.01666e-06 6.80016e-07 6.80016e-07 -2.41064e-07
dump_lebedeva_012.cfg:2 0.6 0.6 3.35 -1.05125e-06 7.03966e-07 7.03966e-07 -2.50881e-07
dump_lebedeva_013.cfg:2 0.65 0.65 3.35 -1.08707e-06 7.28875e-07 7.28875e-07 -2.61148e-07
dump_lebedeva_014.cfg:2 0.7 0.7 3.35 -1.12416e-06 7.54787e-07 7.54787e-07 -2.71886e-07
dump_lebedeva_015.cfg:2 0.75 0.75 3.35 -1.16257e-06 7.81747e-07 7.81747e-07 -2.83119e-07
dump_lebedeva_016.cfg:2 0.8 0.8 3.35 -1.20235e-06 8.09802e-07 8.09802e-07 -2.94873e-07
dump_lebedeva_017.cfg:2 0.85 0.85 3.35 -1.24357e-06 8.39001e-07 8.39001e-07 -3.07175e-07
dump_lebedeva_018.cfg:2 0.9 0.9 3.35 -1.28627e-06 8.69398e-07 8.69398e-07 -3.20053e-07
dump_lebedeva_019.cfg:2 0.95 0.95 3.35 -1.33053e-06 9.01046e-07 9.01046e-07 -3.33537e-07
dump_lebedeva_020.cfg:2 1 1 3.35 -1.3764e-06 9.34005e-07 9.34005e-07 -3.47657e-07
dump_lebedeva_021.cfg:2 1.05 1.05 3.35 -1.42395e-06 9.68333e-07 9.68333e-07 -3.62449e-07
dump_lebedeva_022.cfg:2 1.1 1.1 3.35 -1.47325e-06 1.0041e-06 1.0041e-06 -3.77946e-07
dump_lebedeva_023.cfg:2 1.15 1.15 3.35 -1.52438e-06 1.04136e-06 1.04136e-06 -3.94187e-07
dump_lebedeva_024.cfg:2 1.2 1.2 3.35 -1.57742e-06 1.08019e-06 1.08019e-06 -4.1121e-07
dump_lebedeva_025.cfg:2 1.25 1.25 3.35 -1.63243e-06 1.12067e-06 1.12067e-06 -4.29058e-07
dump_lebedeva_026.cfg:2 1.3 1.3 3.35 -1.68951e-06 1.16288e-06 1.16288e-06 -4.47775e-07
dump_lebedeva_027.cfg:2 1.35 1.35 3.35 -1.74875e-06 1.20689e-06 1.20689e-06 -4.67407e-07
dump_lebedeva_028.cfg:2 1.4 1.4 3.35 -1.81023e-06 1.25279e-06 1.25279e-06 -4.88004e-07
dump_lebedeva_029.cfg:2 1.45 1.45 3.35 -1.87406e-06 1.30067e-06 1.30067e-06 -5.0962e-07
dump_lebedeva_030.cfg:2 1.5 1.5 3.35 -1.94033e-06 1.35063e-06 1.35063e-06 -5.32308e-07
dump_lebedeva_031.cfg:2 1.55 1.55 3.35 -2.00916e-06 1.40277e-06 1.40277e-06 -5.56129e-07
dump_lebedeva_032.cfg:2 1.6 1.6 3.35 -2.08065e-06 1.4572e-06 1.4572e-06 -5.81145e-07
dump_lebedeva_033.cfg:2 1.65 1.65 3.35 -2.15492e-06 1.51402e-06 1.51402e-06 -6.07422e-07
dump_lebedeva_034.cfg:2 1.7 1.7 3.35 -2.23209e-06 1.57336e-06 1.57336e-06 -6.3503e-07
dump_lebedeva_035.cfg:2 1.75 1.75 3.35 -2.3123e-06 1.63533e-06 1.63533e-06 -6.64045e-07
dump_lebedeva_036.cfg:2 1.8 1.8 3.35 -2.39567e-06 1.70008e-06 1.70008e-06 -6.94545e-07
dump_lebedeva_037.cfg:2 1.85 1.85 3.35 -2.48236e-06 1.76774e-06 1.76774e-06 -7.26615e-07
dump_lebedeva_038.cfg:2 1.9 1.9 3.35 -2.5725e-06 1.83844e-06 1.83844e-06 -7.60344e-07
dump_lebedeva_039.cfg:2 1.95 1.95 3.35 -2.66625e-06 1.91236e-06 1.91236e-06 -7.95827e-07
dump_lebedeva_040.cfg:2 2 2 3.35 -2.76379e-06 1.98965e-06 1.98965e-06 -8.33165e-07
dump_lebedeva_041.cfg:2 2.05 2.05 3.35 -2.86528e-06 2.07047e-06 2.07047e-06 -8.72464e-07
dump_lebedeva_042.cfg:2 2.1 2.1 3.35 -2.9709e-06 2.15503e-06 2.15503e-06 -9.1384e-07
dump_lebedeva_043.cfg:2 2.15 2.15 3.35 -3.08085e-06 2.24349e-06 2.24349e-06 -9.57413e-07
dump_lebedeva_044.cfg:2 2.2 2.2 3.35 -3.19532e-06 2.33607e-06 2.33607e-06 -1.00331e-06
dump_lebedeva_045.cfg:2 2.25 2.25 3.35 -3.31452e-06 2.43298e-06 2.43298e-06 -1.05167e-06
dump_lebedeva_046.cfg:2 2.3 2.3 3.35 -3.43869e-06 2.53444e-06 2.53444e-06 -1.10265e-06
dump_lebedeva_047.cfg:2 2.35 2.35 3.35 -3.56805e-06 2.6407e-06 2.6407e-06 -1.15638e-06
dump_lebedeva_048.cfg:2 2.4 2.4 3.35 -3.70284e-06 2.752e-06 2.752e-06 -1.21305e-06
dump_lebedeva_049.cfg:2 2.45 2.45 3.35 -3.84334e-06 2.86861e-06 2.86861e-06 -1.27283e-06
dump_lebedeva_050.cfg:2 2.5 2.5 3.35 -3.9898e-06 2.99082e-06 2.99082e-06 -1.3359e-06
dump_lebedeva_051.cfg:2 2.55 2.55 3.35 -4.14252e-06 3.11892e-06 3.11892e-06 -1.40247e-06
dump_lebedeva_052.cfg:2 2.6 2.6 3.35 -4.30179e-06 3.25323e-06 3.25323e-06 -1.47275e-06
dump_lebedeva_053.cfg:2 2.65 2.65 3.35 -4.46795e-06 3.39408e-06 3.39408e-06 -1.54696e-06
dump_lebedeva_054.cfg:2 2.7 2.7 3.35 -4.64132e-06 3.54184e-06 3.54184e-06 -1.62536e-06
dump_lebedeva_055.cfg:2 2.75 2.75 3.35 -4.82225e-06 3.69686e-06 3.69686e-06 -1.70821e-06
dump_lebedeva_056.cfg:2 2.8 2.8 3.35 -5.01113e-06 3.85956e-06 3.85956e-06 -1.79577e-06
dump_lebedeva_057.cfg:2 2.85 2.85 3.35 -5.20835e-06 4.03036e-06 4.03036e-06 -1.88835e-06
dump_lebedeva_058.cfg:2 2.9 2.9 3.35 -5.41431e-06 4.2097e-06 4.2097e-06 -1.98627e-06
dump_lebedeva_059.cfg:2 2.95 2.95 3.35 -5.62947e-06 4.39805e-06 4.39805e-06 -2.08985e-06
dump_lebedeva_060.cfg:2 3 3 3.35 -5.85427e-06 4.59593e-06 4.59593e-06 -2.19948e-06
dump_lebedeva_061.cfg:2 3.05 3.05 3.35 -6.08923e-06 4.80386e-06 4.80386e-06 -2.31553e-06
dump_lebedeva_062.cfg:2 3.1 3.1 3.35 -6.33484e-06 5.02241e-06 5.02241e-06 -2.43842e-06
dump_lebedeva_063.cfg:2 3.15 3.15 3.35 -6.59165e-06 5.25219e-06 5.25219e-06 -2.56859e-06
dump_lebedeva_064.cfg:2 3.2 3.2 3.35 -6.86025e-06 5.49384e-06 5.49384e-06 -2.70652e-06
dump_lebedeva_065.cfg:2 3.25 3.25 3.35 -7.14125e-06 5.74802e-06 5.74802e-06 -2.85272e-06
dump_lebedeva_066.cfg:2 3.3 3.3 3.35 -7.43528e-06 6.01548e-06 6.01548e-06 -3.00774e-06
dump_lebedeva_067.cfg:2 3.35 3.35 3.35 -7.74303e-06 6.29696e-06 6.29696e-06 -3.17215e-06
dump_lebedeva_068.cfg:2 3.4 3.4 3.35 -8.06522e-06 6.5933e-06 6.5933e-06 -3.3466e-06
dump_lebedeva_069.cfg:2 3.45 3.45 3.35 -8.40262e-06 6.90535e-06 6.90535e-06 -3.53174e-06
dump_lebedeva_070.cfg:2 3.5 3.5 3.35 -8.75603e-06 7.23404e-06 7.23404e-06 -3.72831e-06
dump_lebedeva_071.cfg:2 3.55 3.55 3.35 -9.12632e-06 7.58035e-06 7.58035e-06 -3.93708e-06
dump_lebedeva_072.cfg:2 3.6 3.6 3.35 -9.51438e-06 7.94533e-06 7.94533e-06 -4.15889e-06
dump_lebedeva_073.cfg:2 3.65 3.65 3.35 -9.92118e-06 8.33009e-06 8.33009e-06 -4.39462e-06
dump_lebedeva_074.cfg:2 3.7 3.7 3.35 -1.03477e-05 8.73582e-06 8.73582e-06 -4.64524e-06
dump_lebedeva_075.cfg:2 3.75 3.75 3.35 -1.07951e-05 9.16377e-06 9.16377e-06 -4.91178e-06
dump_lebedeva_076.cfg:2 3.8 3.8 3.35 -1.12645e-05 9.61529e-06 9.61529e-06 -5.19536e-06
dump_lebedeva_077.cfg:2 3.85 3.85 3.35 -1.17571e-05 1.00918e-05 1.00918e-05 -5.49717e-06
dump_lebedeva_078.cfg:2 3.9 3.9 3.35 -1.22741e-05 1.05949e-05 1.05949e-05 -5.8185e-06
dump_lebedeva_079.cfg:2 3.95 3.95 3.35 -1.2817e-05 1.11261e-05 1.11261e-05 -6.16074e-06
dump_lebedeva_080.cfg:2 4 4 3.35 -1.33872e-05 1.16872e-05 1.16872e-05 -6.52537e-06
dump_lebedeva_081.cfg:2 4.05 4.05 3.35 -1.39863e-05 1.22801e-05 1.22801e-05 -6.91402e-06
dump_lebedeva_082.cfg:2 4.1 4.1 3.35 -1.46158e-05 1.29067e-05 1.29067e-05 -7.32841e-06
dump_lebedeva_083.cfg:2 4.15 4.15 3.35 -1.52776e-05 1.35692e-05 1.35692e-05 -7.77041e-06
dump_lebedeva_084.cfg:2 4.2 4.2 3.35 -1.59734e-05 1.42698e-05 1.42698e-05 -8.24204e-06
dump_lebedeva_085.cfg:2 4.25 4.25 3.35 -1.67052e-05 1.50109e-05 1.50109e-05 -8.74547e-06
dump_lebedeva_086.cfg:2 4.3 4.3 3.35 -1.74752e-05 1.57951e-05 1.57951e-05 -9.28307e-06
dump_lebedeva_087.cfg:2 4.35 4.35 3.35 -1.82855e-05 1.66251e-05 1.66251e-05 -9.85736e-06
dump_lebedeva_088.cfg:2 4.4 4.4 3.35 -1.91385e-05 1.75039e-05 1.75039e-05 -1.04711e-05
dump_lebedeva_089.cfg:2 4.45 4.45 3.35 -2.00367e-05 1.84346e-05 1.84346e-05 -1.11272e-05
dump_lebedeva_090.cfg:2 4.5 4.5 3.35 -2.09829e-05 1.94207e-05 1.94207e-05 -1.1829e-05
dump_lebedeva_091.cfg:2 4.55 4.55 3.35 -2.19798e-05 2.04656e-05 2.04656e-05 -1.25798e-05
dump_lebedeva_092.cfg:2 4.6 4.6 3.35 -2.30305e-05 2.15733e-05 2.15733e-05 -1.33834e-05
dump_lebedeva_093.cfg:2 4.65 4.65 3.35 -2.41382e-05 2.27478e-05 2.27478e-05 -1.42439e-05
dump_lebedeva_094.cfg:2 4.7 4.7 3.35 -2.53065e-05 2.39936e-05 2.39936e-05 -1.51657e-05
dump_lebedeva_095.cfg:2 4.75 4.75 3.35 -2.65389e-05 2.53153e-05 2.53153e-05 -1.61536e-05
dump_lebedeva_096.cfg:2 4.8 4.8 3.35 -2.78393e-05 2.67182e-05 2.67182e-05 -1.72127e-05
dump_lebedeva_097.cfg:2 4.85 4.85 3.35 -2.92121e-05 2.82074e-05 2.82074e-05 -1.83485e-05
dump_lebedeva_098.cfg:2 4.9 4.9 3.35 -3.06616e-05 2.9789e-05 2.9789e-05 -1.95673e-05
dump_lebedeva_099.cfg:2 4.95 4.95 3.35 -3.21926e-05 3.1469e-05 3.1469e-05 -2.08755e-05
dump_lebedeva_100.cfg:2 5 5 3.35 -3.38103e-05 3.32542e-05 3.32542e-05 -2.22803e-05
dump_lebedeva_101.cfg:2 5.05 5.05 3.35 -3.55199e-05 3.51516e-05 3.51516e-05 -2.37895e-05
dump_lebedeva_102.cfg:2 5.1 5.1 3.35 -3.73274e-05 3.7169e-05 3.7169e-05 -2.54115e-05
dump_lebedeva_103.cfg:2 5.15 5.15 3.35 -3.9239e-05 3.93146e-05 3.93146e-05 -2.71554e-05
dump_lebedeva_104.cfg:2 5.2 5.2 3.35 -4.12612e-05 4.15971e-05 4.15971e-05 -2.90313e-05
dump_lebedeva_105.cfg:2 5.25 5.25 3.35 -4.34011e-05 4.4026e-05 4.4026e-05 -3.10499e-05
dump_lebedeva_106.cfg:2 5.3 5.3 3.35 -4.56664e-05 4.66115e-05 4.66115e-05 -3.32231e-05
dump_lebedeva_107.cfg:2 5.35 5.35 3.35 -4.80651e-05 4.93643e-05 4.93643e-05 -3.55636e-05
dump_lebedeva_108.cfg:2 5.4 5.4 3.35 -5.06058e-05 5.22962e-05 5.22962e-05 -3.80853e-05
dump_lebedeva_109.cfg:2 5.45 5.45 3.35 -5.32979e-05 5.54196e-05 5.54196e-05 -4.08035e-05
dump_lebedeva_110.cfg:2 5.5 5.5 3.35 -5.61512e-05 5.8748e-05 5.8748e-05 -4.37346e-05
dump_lebedeva_111.cfg:2 5.55 5.55 3.35 -5.91763e-05 6.22957e-05 6.22957e-05 -4.68968e-05
dump_lebedeva_112.cfg:2 5.6 5.6 3.35 -6.23847e-05 6.60782e-05 6.60782e-05 -5.03095e-05
dump_lebedeva_113.cfg:2 5.65 5.65 3.35 -6.57883e-05 7.01119e-05 7.01119e-05 -5.39942e-05
dump_lebedeva_114.cfg:2 5.7 5.7 3.35 -6.94003e-05 7.44146e-05 7.44146e-05 -5.79742e-05
dump_lebedeva_115.cfg:2 5.75 5.75 3.35 -7.32346e-05 7.90054e-05 7.90054e-05 -6.22749e-05
dump_lebedeva_116.cfg:2 5.8 5.8 3.35 -7.7306e-05 8.39045e-05 8.39045e-05 -6.69239e-05
dump_lebedeva_117.cfg:2 5.85 5.85 3.35 -8.16306e-05 8.91338e-05 8.91338e-05 -7.19515e-05
dump_lebedeva_118.cfg:2 5.9 5.9 3.35 -8.62253e-05 9.47167e-05 9.47167e-05 -7.73906e-05
dump_lebedeva_119.cfg:2 5.95 5.95 3.35 -9.11085e-05 0.000100678 0.000100678 -8.32771e-05
dump_lebedeva_120.cfg:2 6 6 3.35 -9.62998e-05 0.000107044 0.000107044 -8.96501e-05
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dump_lebedeva_295.cfg:2 14.75 14.75 3.35 -4.34011e-05 -4.4026e-05 -4.4026e-05 -3.10499e-05
dump_lebedeva_296.cfg:2 14.8 14.8 3.35 -4.12612e-05 -4.15971e-05 -4.15971e-05 -2.90313e-05
dump_lebedeva_297.cfg:2 14.85 14.85 3.35 -3.9239e-05 -3.93146e-05 -3.93146e-05 -2.71554e-05
dump_lebedeva_298.cfg:2 14.9 14.9 3.35 -3.73274e-05 -3.7169e-05 -3.7169e-05 -2.54115e-05
dump_lebedeva_299.cfg:2 14.95 14.95 3.35 -3.55199e-05 -3.51516e-05 -3.51516e-05 -2.37895e-05
dump_lebedeva_300.cfg:2 15 15 3.35 -3.38103e-05 -3.32542e-05 -3.32542e-05 -2.22803e-05
dump_lebedeva_301.cfg:2 15.05 15.05 3.35 -3.21926e-05 -3.1469e-05 -3.1469e-05 -2.08755e-05
dump_lebedeva_302.cfg:2 15.1 15.1 3.35 -3.06616e-05 -2.9789e-05 -2.9789e-05 -1.95673e-05
dump_lebedeva_303.cfg:2 15.15 15.15 3.35 -2.92121e-05 -2.82074e-05 -2.82074e-05 -1.83485e-05
dump_lebedeva_304.cfg:2 15.2 15.2 3.35 -2.78393e-05 -2.67182e-05 -2.67182e-05 -1.72127e-05
dump_lebedeva_305.cfg:2 15.25 15.25 3.35 -2.65389e-05 -2.53153e-05 -2.53153e-05 -1.61536e-05
dump_lebedeva_306.cfg:2 15.3 15.3 3.35 -2.53065e-05 -2.39936e-05 -2.39936e-05 -1.51657e-05
dump_lebedeva_307.cfg:2 15.35 15.35 3.35 -2.41382e-05 -2.27478e-05 -2.27478e-05 -1.42439e-05
dump_lebedeva_308.cfg:2 15.4 15.4 3.35 -2.30305e-05 -2.15733e-05 -2.15733e-05 -1.33834e-05
dump_lebedeva_309.cfg:2 15.45 15.45 3.35 -2.19798e-05 -2.04656e-05 -2.04656e-05 -1.25798e-05
dump_lebedeva_310.cfg:2 15.5 15.5 3.35 -2.09829e-05 -1.94207e-05 -1.94207e-05 -1.1829e-05
dump_lebedeva_311.cfg:2 15.55 15.55 3.35 -2.00367e-05 -1.84346e-05 -1.84346e-05 -1.11272e-05
dump_lebedeva_312.cfg:2 15.6 15.6 3.35 -1.91385e-05 -1.75039e-05 -1.75039e-05 -1.04711e-05
dump_lebedeva_313.cfg:2 15.65 15.65 3.35 -1.82855e-05 -1.66251e-05 -1.66251e-05 -9.85736e-06
dump_lebedeva_314.cfg:2 15.7 15.7 3.35 -1.74752e-05 -1.57951e-05 -1.57951e-05 -9.28307e-06
dump_lebedeva_315.cfg:2 15.75 15.75 3.35 -1.67052e-05 -1.50109e-05 -1.50109e-05 -8.74547e-06
dump_lebedeva_316.cfg:2 15.8 15.8 3.35 -1.59734e-05 -1.42698e-05 -1.42698e-05 -8.24204e-06
dump_lebedeva_317.cfg:2 15.85 15.85 3.35 -1.52776e-05 -1.35692e-05 -1.35692e-05 -7.77041e-06
dump_lebedeva_318.cfg:2 15.9 15.9 3.35 -1.46158e-05 -1.29067e-05 -1.29067e-05 -7.32841e-06
dump_lebedeva_319.cfg:2 15.95 15.95 3.35 -1.39863e-05 -1.22801e-05 -1.22801e-05 -6.91402e-06
dump_lebedeva_320.cfg:2 16 16 3.35 -1.33872e-05 -1.16872e-05 -1.16872e-05 -6.52537e-06
dump_lebedeva_321.cfg:2 16.05 16.05 3.35 -1.2817e-05 -1.11261e-05 -1.11261e-05 -6.16074e-06
dump_lebedeva_322.cfg:2 16.1 16.1 3.35 -1.22741e-05 -1.05949e-05 -1.05949e-05 -5.8185e-06
dump_lebedeva_323.cfg:2 16.15 16.15 3.35 -1.17571e-05 -1.00918e-05 -1.00918e-05 -5.49717e-06
dump_lebedeva_324.cfg:2 16.2 16.2 3.35 -1.12645e-05 -9.61529e-06 -9.61529e-06 -5.19536e-06
dump_lebedeva_325.cfg:2 16.25 16.25 3.35 -1.07951e-05 -9.16377e-06 -9.16377e-06 -4.91178e-06
dump_lebedeva_326.cfg:2 16.3 16.3 3.35 -1.03477e-05 -8.73582e-06 -8.73582e-06 -4.64524e-06
dump_lebedeva_327.cfg:2 16.35 16.35 3.35 -9.92118e-06 -8.33009e-06 -8.33009e-06 -4.39462e-06
dump_lebedeva_328.cfg:2 16.4 16.4 3.35 -9.51438e-06 -7.94533e-06 -7.94533e-06 -4.15889e-06
dump_lebedeva_329.cfg:2 16.45 16.45 3.35 -9.12632e-06 -7.58035e-06 -7.58035e-06 -3.93708e-06
dump_lebedeva_330.cfg:2 16.5 16.5 3.35 -8.75603e-06 -7.23404e-06 -7.23404e-06 -3.72831e-06
dump_lebedeva_331.cfg:2 16.55 16.55 3.35 -8.40262e-06 -6.90535e-06 -6.90535e-06 -3.53174e-06
dump_lebedeva_332.cfg:2 16.6 16.6 3.35 -8.06522e-06 -6.5933e-06 -6.5933e-06 -3.3466e-06
dump_lebedeva_333.cfg:2 16.65 16.65 3.35 -7.74303e-06 -6.29696e-06 -6.29696e-06 -3.17215e-06
dump_lebedeva_334.cfg:2 16.7 16.7 3.35 -7.43528e-06 -6.01548e-06 -6.01548e-06 -3.00774e-06
dump_lebedeva_335.cfg:2 16.75 16.75 3.35 -7.14125e-06 -5.74802e-06 -5.74802e-06 -2.85272e-06
dump_lebedeva_336.cfg:2 16.8 16.8 3.35 -6.86025e-06 -5.49384e-06 -5.49384e-06 -2.70652e-06
dump_lebedeva_337.cfg:2 16.85 16.85 3.35 -6.59165e-06 -5.25219e-06 -5.25219e-06 -2.56859e-06
dump_lebedeva_338.cfg:2 16.9 16.9 3.35 -6.33484e-06 -5.02241e-06 -5.02241e-06 -2.43842e-06
dump_lebedeva_339.cfg:2 16.95 16.95 3.35 -6.08923e-06 -4.80386e-06 -4.80386e-06 -2.31553e-06
dump_lebedeva_340.cfg:2 17 17 3.35 -5.85427e-06 -4.59593e-06 -4.59593e-06 -2.19948e-06
dump_lebedeva_341.cfg:2 17.05 17.05 3.35 -5.62947e-06 -4.39805e-06 -4.39805e-06 -2.08985e-06
dump_lebedeva_342.cfg:2 17.1 17.1 3.35 -5.41431e-06 -4.2097e-06 -4.2097e-06 -1.98627e-06
dump_lebedeva_343.cfg:2 17.15 17.15 3.35 -5.20835e-06 -4.03036e-06 -4.03036e-06 -1.88835e-06
dump_lebedeva_344.cfg:2 17.2 17.2 3.35 -5.01113e-06 -3.85956e-06 -3.85956e-06 -1.79577e-06
dump_lebedeva_345.cfg:2 17.25 17.25 3.35 -4.82225e-06 -3.69686e-06 -3.69686e-06 -1.70821e-06
dump_lebedeva_346.cfg:2 17.3 17.3 3.35 -4.64132e-06 -3.54184e-06 -3.54184e-06 -1.62536e-06
dump_lebedeva_347.cfg:2 17.35 17.35 3.35 -4.46795e-06 -3.39408e-06 -3.39408e-06 -1.54696e-06
dump_lebedeva_348.cfg:2 17.4 17.4 3.35 -4.30179e-06 -3.25323e-06 -3.25323e-06 -1.47275e-06
dump_lebedeva_349.cfg:2 17.45 17.45 3.35 -4.14252e-06 -3.11892e-06 -3.11892e-06 -1.40247e-06
dump_lebedeva_350.cfg:2 17.5 17.5 3.35 -3.9898e-06 -2.99082e-06 -2.99082e-06 -1.3359e-06
dump_lebedeva_351.cfg:2 17.55 17.55 3.35 -3.84334e-06 -2.86861e-06 -2.86861e-06 -1.27283e-06
dump_lebedeva_352.cfg:2 17.6 17.6 3.35 -3.70284e-06 -2.752e-06 -2.752e-06 -1.21305e-06
dump_lebedeva_353.cfg:2 17.65 17.65 3.35 -3.56805e-06 -2.6407e-06 -2.6407e-06 -1.15638e-06
dump_lebedeva_354.cfg:2 17.7 17.7 3.35 -3.43869e-06 -2.53444e-06 -2.53444e-06 -1.10265e-06
dump_lebedeva_355.cfg:2 17.75 17.75 3.35 -3.31452e-06 -2.43298e-06 -2.43298e-06 -1.05167e-06
dump_lebedeva_356.cfg:2 17.8 17.8 3.35 -3.19532e-06 -2.33607e-06 -2.33607e-06 -1.00331e-06
dump_lebedeva_357.cfg:2 17.85 17.85 3.35 -3.08085e-06 -2.24349e-06 -2.24349e-06 -9.57413e-07
dump_lebedeva_358.cfg:2 17.9 17.9 3.35 -2.9709e-06 -2.15503e-06 -2.15503e-06 -9.1384e-07
dump_lebedeva_359.cfg:2 17.95 17.95 3.35 -2.86528e-06 -2.07047e-06 -2.07047e-06 -8.72464e-07
dump_lebedeva_360.cfg:2 18 18 3.35 -2.76379e-06 -1.98965e-06 -1.98965e-06 -8.33165e-07
dump_lebedeva_361.cfg:2 18.05 18.05 3.35 -2.66625e-06 -1.91236e-06 -1.91236e-06 -7.95827e-07
dump_lebedeva_362.cfg:2 18.1 18.1 3.35 -2.5725e-06 -1.83844e-06 -1.83844e-06 -7.60344e-07
dump_lebedeva_363.cfg:2 18.15 18.15 3.35 -2.48236e-06 -1.76774e-06 -1.76774e-06 -7.26615e-07
dump_lebedeva_364.cfg:2 18.2 18.2 3.35 -2.39567e-06 -1.70008e-06 -1.70008e-06 -6.94545e-07
dump_lebedeva_365.cfg:2 18.25 18.25 3.35 -2.3123e-06 -1.63533e-06 -1.63533e-06 -6.64045e-07
dump_lebedeva_366.cfg:2 18.3 18.3 3.35 -2.23209e-06 -1.57336e-06 -1.57336e-06 -6.3503e-07
dump_lebedeva_367.cfg:2 18.35 18.35 3.35 -2.15492e-06 -1.51402e-06 -1.51402e-06 -6.07422e-07
dump_lebedeva_368.cfg:2 18.4 18.4 3.35 -2.08065e-06 -1.4572e-06 -1.4572e-06 -5.81145e-07
dump_lebedeva_369.cfg:2 18.45 18.45 3.35 -2.00916e-06 -1.40277e-06 -1.40277e-06 -5.56129e-07
dump_lebedeva_370.cfg:2 18.5 18.5 3.35 -1.94033e-06 -1.35063e-06 -1.35063e-06 -5.32308e-07
dump_lebedeva_371.cfg:2 18.55 18.55 3.35 -1.87406e-06 -1.30067e-06 -1.30067e-06 -5.0962e-07
dump_lebedeva_372.cfg:2 18.6 18.6 3.35 -1.81023e-06 -1.25279e-06 -1.25279e-06 -4.88004e-07
dump_lebedeva_373.cfg:2 18.65 18.65 3.35 -1.74875e-06 -1.20689e-06 -1.20689e-06 -4.67407e-07
dump_lebedeva_374.cfg:2 18.7 18.7 3.35 -1.68951e-06 -1.16288e-06 -1.16288e-06 -4.47775e-07
dump_lebedeva_375.cfg:2 18.75 18.75 3.35 -1.63243e-06 -1.12067e-06 -1.12067e-06 -4.29058e-07
dump_lebedeva_376.cfg:2 18.8 18.8 3.35 -1.57742e-06 -1.08019e-06 -1.08019e-06 -4.1121e-07
dump_lebedeva_377.cfg:2 18.85 18.85 3.35 -1.52438e-06 -1.04136e-06 -1.04136e-06 -3.94187e-07
dump_lebedeva_378.cfg:2 18.9 18.9 3.35 -1.47325e-06 -1.0041e-06 -1.0041e-06 -3.77946e-07
dump_lebedeva_379.cfg:2 18.95 18.95 3.35 -1.42395e-06 -9.68333e-07 -9.68333e-07 -3.62449e-07
dump_lebedeva_380.cfg:2 19 19 3.35 -1.3764e-06 -9.34005e-07 -9.34005e-07 -3.47657e-07
dump_lebedeva_381.cfg:2 19.05 19.05 3.35 -1.33053e-06 -9.01046e-07 -9.01046e-07 -3.33537e-07
dump_lebedeva_382.cfg:2 19.1 19.1 3.35 -1.28627e-06 -8.69398e-07 -8.69398e-07 -3.20053e-07
dump_lebedeva_383.cfg:2 19.15 19.15 3.35 -1.24357e-06 -8.39001e-07 -8.39001e-07 -3.07175e-07
dump_lebedeva_384.cfg:2 19.2 19.2 3.35 -1.20235e-06 -8.09802e-07 -8.09802e-07 -2.94873e-07
dump_lebedeva_385.cfg:2 19.25 19.25 3.35 -1.16257e-06 -7.81747e-07 -7.81747e-07 -2.83119e-07
dump_lebedeva_386.cfg:2 19.3 19.3 3.35 -1.12416e-06 -7.54787e-07 -7.54787e-07 -2.71886e-07
dump_lebedeva_387.cfg:2 19.35 19.35 3.35 -1.08707e-06 -7.28875e-07 -7.28875e-07 -2.61148e-07
dump_lebedeva_388.cfg:2 19.4 19.4 3.35 -1.05125e-06 -7.03966e-07 -7.03966e-07 -2.50881e-07
dump_lebedeva_389.cfg:2 19.45 19.45 3.35 -1.01666e-06 -6.80016e-07 -6.80016e-07 -2.41064e-07
dump_lebedeva_390.cfg:2 19.5 19.5 3.35 -9.83237e-07 -6.56984e-07 -6.56984e-07 -2.31673e-07
dump_lebedeva_391.cfg:2 19.55 19.55 3.35 -9.50945e-07 -6.34832e-07 -6.34832e-07 -2.2269e-07
dump_lebedeva_392.cfg:2 19.6 19.6 3.35 -9.19739e-07 -6.13522e-07 -6.13522e-07 -2.14094e-07
dump_lebedeva_393.cfg:2 19.65 19.65 3.35 -8.89579e-07 -5.93019e-07 -5.93019e-07 -2.05867e-07
dump_lebedeva_394.cfg:2 19.7 19.7 3.35 -8.60425e-07 -5.73288e-07 -5.73288e-07 -1.97991e-07
dump_lebedeva_395.cfg:2 19.75 19.75 3.35 -8.32238e-07 -5.54298e-07 -5.54298e-07 -1.90451e-07
dump_lebedeva_396.cfg:2 19.8 19.8 3.35 -8.04983e-07 -5.36017e-07 -5.36017e-07 -1.8323e-07
dump_lebedeva_397.cfg:2 19.85 19.85 3.35 -7.78625e-07 -5.18417e-07 -5.18417e-07 -1.76314e-07
dump_lebedeva_398.cfg:2 19.9 19.9 3.35 -7.5313e-07 -5.01468e-07 -5.01468e-07 -1.69689e-07
dump_lebedeva_399.cfg:2 19.95 19.95 3.35 -7.28468e-07 -4.85145e-07 -4.85145e-07 -1.6334e-07
examples/USER/misc/lebedeva/LebDer.pl 0 → 100755
+ 90
− 0
View file @ 2d0d0809
#!/usr/bin/perl
# Computes potential energy of atom as a function of distance from another atom
# and computes numerical derivates of potential.
# The script was used to check if results from LAMMPS (using 2particles.in)
# are the same as these computed b this script.
# Prints results to STDOUT.
# Hence, use it like this:
# ./LebDer.pl > PerlResult.dat
# After that use lebedeva00.plot
#
# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland
# Email: softquake@gmail.com
# Parameters used by ZJK for Lebedeva
my $LEB_A = -14.558;
my $LEB_B = 21.204;
my $LEB_alpha = 4.16;
my $LEB_C = 1.8;
my $LEB_D1 = -0.862;
my $LEB_D2 = 0.10049; # has very strong influence on position of minimum
my $LEB_lambda1 = 0.6; # has influance on splitting of AB-AA.
my $LEB_lambda2 = 0.4; # has strong influence on position of minimum
my $LEB_z0 = 3.198;
my $LEBSCALE =1.0;
$Z0=3.35;
$CX0 = 10;
$CY0 = 10;
for (my $t=0; $t<400; $t++) {
my $X0 = 0.001 + 0.05*$t;
my $Y0 = 0.001 + 0.05*$t;
my $Z = $Z0;
print $X0, "\t", $Y0, "\t", $Z, "\t",&LEB($X0, $Y0, $Z), "\t", &DLEBX($X0, $Y0, $Z),"\t",&DLEBY($X0, $Y0, $Z), "\t", &DLEBZ($X0, $Y0, $Z),"\n";
}
###############################################################################################
sub LEB {
my $x = shift;
my $y = shift;
my $z = shift;
my $rho2 = ($x-$CX0)*($x-$CX0) + ($y-$CY0)*($y-$CY0);
my $r = sqrt($rho2 + ($Z0)*($Z0));
my $zr = ($LEB_z0/$r)*($LEB_z0/$r);
my $zr6 = $zr*$zr*$zr;
my $ONE = $LEB_C*(1+$LEB_D1*$rho2+$LEB_D2*$rho2*$rho2);
my $TWO = exp(-$LEB_lambda1*$rho2)*exp(-$LEB_lambda2*($z*$z-$LEB_z0*$LEB_z0));
my $U = $LEB_A*$zr6 +$LEB_B*exp(-$LEB_alpha*($r-$LEB_z0)) + $ONE*$TWO;
return $U;
}
sub DLEBX { # finding derivative at $x
my $x = shift;
my $y = shift;
my $z = shift;
my $h = 0.0001;
my $D = (&LEB($x+$h, $y, $z)-&LEB($x-$h, $y, $z))/(2*$h);
return $D;
}
sub DLEBY { # finding derivative at $y
my $x = shift;
my $y = shift;
my $z = shift;
my $h = 0.0001;
my $D = (&LEB($x, $y+$h, $z)-&LEB($x, $y-$h, $z))/(2*$h);
return $D;
}
sub DLEBZ { # finding derivative at $z
my $x = shift;
my $y = shift;
my $z = shift;
my $h = 0.0001;
my $D = (&LEB($x, $y, $z+$h)-&LEB($x, $y, $z-$h))/(2*$h);
return $D;
}
examples/USER/misc/lebedeva/lebedeva00.plot 0 → 100644
+ 34
− 0
View file @ 2d0d0809
# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland
# Email: softquake@gmail.com
set term x11;
unset log
unset title
set size 1.0,1.0
set encoding iso_8859_1
#set term postscript eps enhanced color "Helvetica" 18;
#set output "lebedeva00.eps"
set zero 1e-018;
set xlabel "x,y [{\305}]" font "Helvetica,18";
set ylabel "U [eV/atom]" font "Helvetica,18";
set key font ",18"
set key right
set key top
set pointsize 1.2
set xrange [0:20]
set yrange [-0.002:0.001]
#set yrange [-0.01:0.01]
#set yrange [*:*]
plot \
"LamppsResult.dat" u 2:5 t "Leb LAMMPS",\
"PerlResult.dat" u 1:($4*0.001/2.) w l t "Leb Perl"
exit
potentials/CC.Lebedeva 0 → 100644
+ 14
− 0
View file @ 2d0d0809
# Lebedeva Potential. Original values from Lebedeva. May be played with ;)
#
# Cite as: Irina V. Lebedeva, Andrey A. Knizhnik, Andrey M. Popov, Yurii E. Lozovik, Boris V. Potapkin,
# Modeling of graphene-based NEMS
# Physica E 44 (6), 949 (2012)
# https://doi.org/10.1016/j.physe.2011.07.018
#
# Parameters must be in this order as here, otherwise their values may be changed.
# The last one, S, is convenient for scaling the potential amplitude. S is a multiplication factor for A, B, C
# A B C z0 alpha D1 D2 lambda1 lambda2 S
# These are values according to Levedeva et al
#C C 10.510 11.6523.34 35.883 3.34 4.16 -0.86232 0.10049 0.48703 0.46445 1.0
# These are values by Z. Koziol et al.: https://arxiv.org/abs/1803.05162
C C 14.558 21.204 1.8 3.198 4.16 -0.862 0.10049 0.6 0.4 1.0
src/USER-MISC/pair_lebedeva.cpp 0 → 100644
+ 436
− 0
View file @ 2d0d0809
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, 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: Zbigniew Koziol
(National Center for Nuclear Research, Poland)
e-mail: softquake at gmail dot com
Writing this was based on C code of Kolmogorov-Crespi potential
of Jaap Kroes and others.
This is potential described in
[Lebedeva et al., Physica E, 44(6), 949-954, 2012.]
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_lebedeva.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
#define DELTA 4
/* ---------------------------------------------------------------------- */
PairLebedeva::PairLebedeva(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
// initialize element to parameter maps
nelements = 0;
elements = NULL;
nparams = maxparam = 0;
params = NULL;
elem2param = NULL;
map = NULL;
// always compute energy offset
offset_flag = 1;
}
/* ---------------------------------------------------------------------- */
PairLebedeva::~PairLebedeva()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(offset);
}
if (elements)
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
memory->destroy(params);
memory->destroy(elem2param);
if (allocated) delete [] map;
}
/* ---------------------------------------------------------------------- */
void PairLebedeva::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,der;
double rsq,r,rhosq,rho,exp1,exp2,exp3,r6,r8;
double frho,sumD,Ulm,fxy,fz,rdsq;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
// rho^2 = r^2 - z^2
rhosq = delx*delx + dely*dely;
rho = sqrt(rhosq);
rsq = rhosq + delz*delz;
if (rsq < cutsq[itype][jtype]) {
int iparam_ij = elem2param[map[itype]][map[jtype]];
Param& p = params[iparam_ij];
r = sqrt(rsq);
r6 = rsq*rsq*rsq;
r8 = r6*rsq;
// store exponents
exp1 = exp(-p.alpha*(r-p.z0));
exp2 = exp(-p.lambda1*rhosq);
exp3 = exp(-p.lambda2*(delz*delz-p.z02));
sumD = 1+p.D1*rhosq+p.D2*rhosq*rhosq;
Ulm = -p.A*p.z06/r6+ p.B*exp1+p.C*sumD*exp2*exp3;
// derivatives
fpair = -6.0*p.A*p.z06/r8+p.B*p.alpha*exp1/r; // used for x,y,z
der = p.D1+2*p.D2*rhosq-p.lambda1*sumD; // used for x,y
fxy = fpair - 2*p.C*exp2*exp3*der;
fz = fpair + 2*p.C*p.lambda2*sumD*exp2*exp3;
f[i][0] += delx*fxy;
f[i][1] += dely*fxy;
f[i][2] += delz*fz;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fxy;
f[j][1] -= dely*fxy;
f[j][2] -= delz*fz;
}
if (eflag) {
evdwl = Ulm - offset[itype][jtype];
}
if (evflag){
ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0,
-fxy,-fxy,-fz,delx,dely,delz);
}
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLebedeva::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(offset,n+1,n+1,"pair:offset");
map = new int[atom->ntypes+1];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairLebedeva::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
if (strcmp(force->pair_style,"hybrid/overlay")!=0)
error->all(FLERR,"ERROR: requires hybrid/overlay pair_style");
cut_global = force->numeric(FLERR,arg[0]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairLebedeva::coeff(int narg, char **arg)
{
int i,j,n;
if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
// nelements = # of unique elements
// elements = list of element names
if (elements) {
for (i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
}
elements = new char*[atom->ntypes];
for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
nelements = 0;
for (i = 3; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
map[i-2] = -1;
continue;
}
for (j = 0; j < nelements; j++)
if (strcmp(arg[i],elements[j]) == 0) break;
map[i-2] = j;
if (j == nelements) {
n = strlen(arg[i]) + 1;
elements[j] = new char[n];
strcpy(elements[j],arg[i]);
nelements++;
}
}
read_file(arg[2]);
double cut_one = cut_global;
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLebedeva::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
if (offset_flag && (cut[i][j] > 0.0)) {
int iparam_ij = elem2param[map[i]][map[j]];
Param& p = params[iparam_ij];
offset[i][j] = -p.A*pow(p.z0/cut[i][j],6);
} else offset[i][j] = 0.0;
offset[j][i] = offset[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
read Lebedeva potential file
------------------------------------------------------------------------- */
void PairLebedeva::read_file(char *filename)
{
int params_per_line = 12;
char **words = new char*[params_per_line+1];
memory->sfree(params);
params = NULL;
nparams = maxparam = 0;
// open file on proc 0
FILE *fp;
if (comm->me == 0) {
fp = force->open_potential(filename);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open Lebedeva potential file %s",filename);
error->one(FLERR,str);
}
}
// read each line out of file, skipping blank lines or leading '#'
// store line of params if all 3 element tags are in element list
int i,j,n,m,nwords,ielement,jelement;
char line[MAXLINE],*ptr;
int eof = 0;
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
// strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
if (nwords == 0) continue;
// concatenate additional lines until have params_per_line words
while (nwords < params_per_line) {
n = strlen(line);
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
}
if (nwords != params_per_line)
error->all(FLERR,"Insufficient format in Lebedeva potential file");
// words = ptrs to all words in line
nwords = 0;
words[nwords++] = strtok(line," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
// ielement,jelement = 1st args
// if these 2 args are in element list, then parse this line
// else skip to next line (continue)
for (ielement = 0; ielement < nelements; ielement++)
if (strcmp(words[0],elements[ielement]) == 0) break;
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (strcmp(words[1],elements[jelement]) == 0) break;
if (jelement == nelements) continue;
// load up parameter settings and error check their values
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
"pair:params");
}
params[nparams].ielement = ielement;
params[nparams].jelement = jelement;
params[nparams].A = atof(words[2]);
params[nparams].B = atof(words[3]);
params[nparams].C = atof(words[4]);
params[nparams].z0 = atof(words[5]);
params[nparams].alpha = atof(words[6]);
params[nparams].D1 = atof(words[7]);
params[nparams].D2 = atof(words[8]);
params[nparams].lambda1 = atof(words[9]);
params[nparams].lambda2 = atof(words[10]);
// S provides a convenient scaling of all energies
params[nparams].S = atof(words[11]);
// energies in meV further scaled by S
double meV = 1.0e-3*params[nparams].S;
params[nparams].A *= meV;
params[nparams].B *= meV;
params[nparams].C *= meV;
// precompute some quantities. That speeds up later process
params[nparams].z02 = pow(params[nparams].z0,2);
params[nparams].z06 = pow(params[nparams].z0,6);
nparams++;
if(nparams >= pow(atom->ntypes,3)) break;
}
memory->destroy(elem2param);
memory->create(elem2param,nelements,nelements,"pair:elem2param");
for (i = 0; i < nelements; i++) {
for (j = 0; j < nelements; j++) {
n = -1;
for (m = 0; m < nparams; m++) {
if (i == params[m].ielement && j == params[m].jelement) {
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = m;
}
}
if (n < 0) error->all(FLERR,"Potential file is missing an entry");
elem2param[i][j] = n;
}
}
delete [] words;
}
/* ---------------------------------------------------------------------- */
src/USER-MISC/pair_lebedeva.h 0 → 100644
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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, 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
PairStyle(lebedeva,PairLebedeva)
#else
#ifndef LMP_PAIR_Lebedeva_H
#define LMP_PAIR_Lebedeva_H
#include "pair.h"
namespace LAMMPS_NS {
class PairLebedeva : public Pair {
public:
PairLebedeva(class LAMMPS *);
virtual ~PairLebedeva();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
protected:
int me;
struct Param {
double z0,A,B,C,alpha,D1,D2,lambda1,lambda2,S;
double z02,z06;
int ielement,jelement;
};
Param *params; // parameter set for I-J interactions
char **elements; // names of unique elements
int **elem2param; // mapping from element pairs to parameters
int *map; // mapping from atom types to elements
int nelements; // # of unique elements
int nparams; // # of stored parameter sets
int maxparam; // max # of parameter sets
double cut_global;
double **cut;
double **offset;
void read_file( char * );
void allocate();
};
}
#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: 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.
*/
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