diff --git a/doc/src/Eqs/pair_lebedeva.png b/doc/src/Eqs/pair_lebedeva.png new file mode 100644 index 0000000000000000000000000000000000000000..af2ac876538ddca8a27b6dc0bf2944adf208b0b5 Binary files /dev/null and b/doc/src/Eqs/pair_lebedeva.png differ diff --git a/doc/src/pair_lebedeva.txt b/doc/src/pair_lebedeva.txt new file mode 100644 index 0000000000000000000000000000000000000000..6b9eabc611d48435e7c988cc49a170df4bad4de0 --- /dev/null +++ b/doc/src/pair_lebedeva.txt @@ -0,0 +1,63 @@ +"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) + diff --git a/examples/USER/misc/lebedeva/2particles.dat b/examples/USER/misc/lebedeva/2particles.dat new file mode 100644 index 0000000000000000000000000000000000000000..43eabd7d24608f5db46203ffb69213ac2f4de335 --- /dev/null +++ b/examples/USER/misc/lebedeva/2particles.dat @@ -0,0 +1,14 @@ +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 diff --git a/examples/USER/misc/lebedeva/2particles.in b/examples/USER/misc/lebedeva/2particles.in new file mode 100644 index 0000000000000000000000000000000000000000..2a9851f383b5d05dfe20d9f54945407ce31a7672 --- /dev/null +++ b/examples/USER/misc/lebedeva/2particles.in @@ -0,0 +1,63 @@ +# 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" + + diff --git a/examples/USER/misc/lebedeva/CC.Lebedeva b/examples/USER/misc/lebedeva/CC.Lebedeva new file mode 100644 index 0000000000000000000000000000000000000000..930f7b43288fc5cafcfc7654a1d737d140e1f6dd --- /dev/null +++ b/examples/USER/misc/lebedeva/CC.Lebedeva @@ -0,0 +1,14 @@ +# 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 diff --git a/examples/USER/misc/lebedeva/LammpsResult.dat b/examples/USER/misc/lebedeva/LammpsResult.dat new file mode 100644 index 0000000000000000000000000000000000000000..ff9dfe19495a087de72d0ecb08abd62c3c301efa --- /dev/null +++ b/examples/USER/misc/lebedeva/LammpsResult.dat @@ -0,0 +1,400 @@ +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 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+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 diff --git a/examples/USER/misc/lebedeva/LebDer.pl b/examples/USER/misc/lebedeva/LebDer.pl new file mode 100755 index 0000000000000000000000000000000000000000..5b449358d3f69f87460611c6623e89008908758c --- /dev/null +++ b/examples/USER/misc/lebedeva/LebDer.pl @@ -0,0 +1,90 @@ +#!/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; +} diff --git a/examples/USER/misc/lebedeva/lebedeva00.plot b/examples/USER/misc/lebedeva/lebedeva00.plot new file mode 100644 index 0000000000000000000000000000000000000000..a598c3e6b1e1c46c359e70007fea8ebe53dc46d0 --- /dev/null +++ b/examples/USER/misc/lebedeva/lebedeva00.plot @@ -0,0 +1,34 @@ +# 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 diff --git a/potentials/CC.Lebedeva b/potentials/CC.Lebedeva new file mode 100644 index 0000000000000000000000000000000000000000..930f7b43288fc5cafcfc7654a1d737d140e1f6dd --- /dev/null +++ b/potentials/CC.Lebedeva @@ -0,0 +1,14 @@ +# 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 diff --git a/src/USER-MISC/pair_lebedeva.cpp b/src/USER-MISC/pair_lebedeva.cpp new file mode 100644 index 0000000000000000000000000000000000000000..ed43550610c798a05dd2232241de64097d86ff7d --- /dev/null +++ b/src/USER-MISC/pair_lebedeva.cpp @@ -0,0 +1,436 @@ +/* ---------------------------------------------------------------------- + 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; +} + +/* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/pair_lebedeva.h b/src/USER-MISC/pair_lebedeva.h new file mode 100644 index 0000000000000000000000000000000000000000..6db8f66d6a1c88e16618d6a9a51c7b61f01b2f9f --- /dev/null +++ b/src/USER-MISC/pair_lebedeva.h @@ -0,0 +1,83 @@ +/* -*- 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. + +*/ +