diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 7cf4e7635b..1c05eb9384 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -262,6 +262,7 @@ OPT. * :doc:`spin/neel ` * :doc:`srp ` * :doc:`sw (giko) ` + * :doc:`sw/mod (o) ` * :doc:`table (gko) ` * :doc:`table/rx (k) ` * :doc:`tdpd ` diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst index 589e9d7b9a..00289a989a 100644 --- a/doc/src/Howto_drude2.rst +++ b/doc/src/Howto_drude2.rst @@ -491,11 +491,6 @@ NPT ensemble using Nose-Hoover thermostat: **(Schroeder)** Schroeder and Steinhauser, J Chem Phys, 133, 154511 (2010). -.. _Jiang2: - -**(Jiang)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, - J Phys Chem Lett, 2, 87-92 (2011). - .. _Thole2: **(Thole)** Chem Phys, 59, 341 (1981). diff --git a/doc/src/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst index 89ea28cf08..5e62e4f416 100644 --- a/doc/src/fix_langevin_drude.rst +++ b/doc/src/fix_langevin_drude.rst @@ -40,7 +40,7 @@ Example input scripts available: examples/PACKAGES/drude Description """"""""""" -Apply two Langevin thermostats as described in :ref:`(Jiang) ` for +Apply two Langevin thermostats as described in :ref:`(Jiang1) ` for thermalizing the reduced degrees of freedom of Drude oscillators. This link describes how to use the :doc:`thermalized Drude oscillator model ` in LAMMPS and polarizable models in LAMMPS are discussed on the :doc:`Howto polarizable ` doc @@ -300,5 +300,5 @@ The option defaults are zero = no. .. _Jiang1: -**(Jiang)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J +**(Jiang1)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J Phys Chem Lett, 2, 87-92 (2011). diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 1cf033ddba..7f88d97657 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -327,6 +327,7 @@ accelerated styles exist. * :doc:`spin/neel ` - * :doc:`srp ` - * :doc:`sw ` - Stillinger-Weber 3-body potential +* :doc:`sw/mod ` - modified Stillinger-Weber 3-body potential * :doc:`table ` - tabulated pair potential * :doc:`table/rx ` - * :doc:`tdpd ` - tDPD particle interactions diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index 1b2a4a4b1d..d71999b2d4 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -3,18 +3,34 @@ .. index:: pair_style sw/intel .. index:: pair_style sw/kk .. index:: pair_style sw/omp +.. index:: pair_style sw/mod +.. index:: pair_style sw/mod/omp pair_style sw command ===================== Accelerator Variants: *sw/gpu*, *sw/intel*, *sw/kk*, *sw/omp* +pair_style sw/mod command +========================= + +Accelerator Variants: *sw/mod/omp* + Syntax """""" .. code-block:: LAMMPS - pair_style sw + pair_style style keyword values + +* style = *sw* or *sw/mod* +* keyword = *maxdelcs* + + .. parsed-literal:: + + *maxdelcs* value = delta1 delta2 (optional) + delta1 = The minimum thershold for cosine of three-body angle + delta2 = The maximum threshold for cosine of three-body angle Examples """""""" @@ -25,6 +41,9 @@ Examples pair_coeff * * si.sw Si pair_coeff * * GaN.sw Ga N Ga + pair_style sw/mod maxdelcs 0.25 0.35 + pair_coeff * * tmd.sw.mod Mo S S + Description """"""""""" @@ -48,8 +67,52 @@ where :math:`\phi_2` is a two-body term and :math:`\phi_3` is a three-body term. The summations in the formula are over all neighbors J and K of atom I within a cutoff distance :math:`a `\sigma`. -Only a single pair_coeff command is used with the *sw* style which -specifies a Stillinger-Weber potential file with parameters for all +The *sw/mod* style is designed for simulations of materials when +distinguishing three-body angles are necessary, such as borophene +and transition metal dichalcogenide, which cannot be described +by the original code for the Stillinger-Weber potential. +For instance, there are several types of angles around each Mo atom in `MoS_2`, +and some unnecessary angle types should be excluded in the three-body interaction. +Such exclusion may be realized by selecting proper angle types directly. +The exclusion of unnecessary angles is achieved here by the cut-off function (`f_C(\delta)`), +which induces only minimum modifications for LAMMPS. + +Validation, benchmark tests, and applications of the *sw/mod* style +can be found in :ref:`(Jiang2) ` and :ref:`(Jiang3) `. + +The *sw/mod* style computes the energy E of a system of atoms, whose potential +function is mostly the same as the Stillinger-Weber potential. The only modification +is in the three-body term, where the value of :math:`\delta = \cos \theta_{ijk} - \cos \theta_{0ijk}` +used in the original energy and force expression is scaled by a switching factor :math:`f_C(\delta)`: + +.. math:: + + f_C(\delta) & = \left\{ \begin{array} {r@{\quad:\quad}l} + 1 & \left| \delta \right| < \delta_1 \\ + \frac{1}{2} + \frac{1}{2} \cos \left( \pi \frac{\left| \delta \right| - \delta_1}{\delta_2 - \delta_1} \right) & + \delta_1 < \left| \delta \right| < \delta_2 \\ + 0 & \left| \delta \right| > \delta_2 + \end{array} \right. \\ + +This cut-off function decreases smoothly from 1 to 0 over the range :math:`[\delta_1, \delta_2]`. +This smoothly turns off the energy and force contributions for :math:`\left| \delta \right| > \delta_2`. +It is suggested that :math:`\delta 1` and :math:`\delta_2` to be the value around +:math:`0.5 \left| \cos \theta_1 - \cos \theta_2 \right|`, with +:math:`\theta_1` and :math:`\theta_2` as the different types of angles around an atom. +For borophene and transition metal dichalcogenide, :math:`\delta_1 = 0.25` and :math:`\delta_2 = 0.35`. +This value enables the cut-off function to exclude unnecessary angles in the three-body SW terms. + +.. note:: + + The cut-off function is just to be used as a technique to exclude some unnecessary angles, + and it has no physical meaning. It should be noted that the force and potential are inconsistent + with each other in the decaying range of the cut-off function, as the angle dependence for the + cut-off function is not implemented in the force (first derivation of potential). + However, the angle variation is much smaller than the given threshold value for actual simulations, + so the inconsistency between potential and force can be neglected in actual simulations. + +Only a single pair_coeff command is used with the *sw* and *sw/mod* styles +which specifies a Stillinger-Weber potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying N additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: @@ -213,10 +276,19 @@ Related commands Default """"""" -none +The default values for the *maxdelcs* setting of the *sw/mod* pair +style are *delta1* = 0.25 and *delta2* = 0.35`. ---------- .. _Stillinger2: **(Stillinger)** Stillinger and Weber, Phys Rev B, 31, 5262 (1985). + +.. _Jiang2: + +**(Jiang2)** J.-W. Jiang, Nanotechnology 26, 315706 (2015). + +.. _Jiang3: + +**(Jiang3)** J.-W. Jiang, Acta Mech. Solida. Sin 32, 17 (2019). diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index c8e41faa4c..942895dbb3 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -308,6 +308,7 @@ boolean boostostat boostostatting Boresch +borophene Botero Botu Bouguet @@ -688,6 +689,7 @@ diagonalizers diagonalizing Diallo diblock +dichalcogenide Dickel diel differentiable @@ -2390,6 +2392,7 @@ ohenrich ok Okabe Okamoto +O'Hearn O'Keefe OKeefe oldlace @@ -3078,6 +3081,7 @@ snav Snodin Sodani Soderlind +Solida solvated solvation someuser diff --git a/examples/threebody/in.mos2.sw.mod b/examples/threebody/in.mos2.sw.mod new file mode 100644 index 0000000000..d5ddd356e0 --- /dev/null +++ b/examples/threebody/in.mos2.sw.mod @@ -0,0 +1,30 @@ +# monolayer MoS2 +units metal +boundary p p f +processors * * 1 + +atom_style atomic +read_data single_layer_MoS2.data + +mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg +mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg + +########################## Define potentials ################################ +pair_style sw/mod maxdelcs 0.25 0.35 +pair_coeff * * tmd.sw.mod Mo S S +######################################################################### + +### Simulation settings #### +timestep 0.001 +velocity all create 300.0 12345 + +############################ + +# Output +thermo 500 +thermo_style custom step etotal pe ke temp +thermo_modify lost warn + +###### Run molecular dynamics ###### +fix thermostat all nve +run 5000 diff --git a/examples/threebody/log.27Oct21.mos2_sw_mod.g++.1 b/examples/threebody/log.27Oct21.mos2_sw_mod.g++.1 new file mode 100644 index 0000000000..4dda8e9d1c --- /dev/null +++ b/examples/threebody/log.27Oct21.mos2_sw_mod.g++.1 @@ -0,0 +1,92 @@ +LAMMPS (27 Oct 2021) +# monolayer MoS2 +units metal +boundary p p f +processors * * 1 + +atom_style atomic +read_data single_layer_MoS2.data +Reading data file ... + triclinic box = (0.0000000 0.0000000 -100.00000) to (51.152320 44.299209 100.00000) with tilt (25.576160 0.0000000 0.0000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 768 atoms + read_data CPU = 0.043 seconds + +mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg +mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg + +########################## Define potentials ################################ +pair_style sw/mod maxdelcs 0.25 0.35 +pair_coeff * * tmd.sw.mod Mo S S +Reading sw potential file tmd.sw.mod with DATE: 2018-03-26 +######################################################################### + +### Simulation settings #### +timestep 0.001 +velocity all create 300.0 12345 + +############################ + +# Output +thermo 500 +thermo_style custom step etotal pe ke temp +thermo_modify lost warn + +###### Run molecular dynamics ###### +fix thermostat all nve +run 5000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.158796 + ghost atom cutoff = 5.158796 + binsize = 2.579398, bins = 30 18 78 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair sw/mod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.466 | 3.466 | 3.466 Mbytes +Step TotEng PotEng KinEng Temp + 0 -899.28605 -929.02881 29.742759 300 + 500 -899.28626 -922.45519 23.168929 233.69313 + 1000 -899.29247 -925.86547 26.573002 268.02828 + 1500 -899.27957 -916.95478 17.675214 178.28084 + 2000 -899.28171 -918.38728 19.105573 192.70814 + 2500 -899.28732 -922.50423 23.21691 234.17709 + 3000 -899.28195 -918.74112 19.459174 196.27473 + 3500 -899.27944 -918.03105 18.751604 189.13784 + 4000 -899.28397 -920.50737 21.223397 214.06955 + 4500 -899.28386 -919.79154 20.507685 206.85053 + 5000 -899.28077 -918.78947 19.508698 196.77425 +Loop time of 5.84317 on 1 procs for 5000 steps with 768 atoms + +Performance: 73.932 ns/day, 0.325 hours/ns, 855.700 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.6796 | 5.6796 | 5.6796 | 0.0 | 97.20 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.026354 | 0.026354 | 0.026354 | 0.0 | 0.45 +Output | 0.0014959 | 0.0014959 | 0.0014959 | 0.0 | 0.03 +Modify | 0.090437 | 0.090437 | 0.090437 | 0.0 | 1.55 +Other | | 0.04524 | | | 0.77 + +Nlocal: 768.000 ave 768 max 768 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 354.000 ave 354 max 354 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 20480.0 ave 20480 max 20480 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 20480 +Ave neighs/atom = 26.666667 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:06 diff --git a/examples/threebody/single_layer_MoS2.data b/examples/threebody/single_layer_MoS2.data new file mode 100644 index 0000000000..e68230987c --- /dev/null +++ b/examples/threebody/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 100.0000000000000000 zlo zhi + 25.5761600000000088 0.0000000000000000 0.0000000000000000 xy xz yz + + Atoms + + 1 2 0.000000000000000 0.000000000000000 -1.596930000000000 + 2 3 0.000000000000000 0.000000000000000 1.596930000000000 + 3 1 0.000000000000000 1.845800357604618 0.000000000000000 + 4 2 1.598510000000001 2.768700536406927 -1.596930000000000 + 5 3 1.598510000000001 2.768700536406927 1.596930000000000 + 6 1 1.598510000000001 4.614500894011545 0.000000000000000 + 7 2 3.197020000000001 5.537401072813854 -1.596930000000000 + 8 3 3.197020000000001 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71.932950000000025 43.376308403708523 0.000000000000000 diff --git a/examples/threebody/tmd.sw.mod b/examples/threebody/tmd.sw.mod new file mode 120000 index 0000000000..0affacdd40 --- /dev/null +++ b/examples/threebody/tmd.sw.mod @@ -0,0 +1 @@ +../../potentials/tmd.sw.mod \ No newline at end of file diff --git a/potentials/tmd.sw.mod b/potentials/tmd.sw.mod new file mode 100644 index 0000000000..b88390ee26 --- /dev/null +++ b/potentials/tmd.sw.mod @@ -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/.gitignore b/src/.gitignore index 5c6d732a69..e826633004 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -1208,6 +1208,8 @@ /pair_sph_taitwater_morris.h /pair_sw.cpp /pair_sw.h +/pair_sw_mod.cpp +/pair_sw_mod.h /pair_tersoff.cpp /pair_tersoff.h /pair_tersoff_mod.cpp diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index fcdda9ef9e..75ece1dc71 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -293,7 +293,7 @@ void PairSW::read_file(char *file) if (comm->me == 0) { PotentialFileReader reader(lmp, file, "sw", unit_convert_flag); - char *line; + char * line; // transparently convert units for supported conversions @@ -328,7 +328,8 @@ void PairSW::read_file(char *file) if (nparams == maxparam) { maxparam += DELTA; - params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),"pair:params"); + params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), + "pair:params"); // make certain all addional allocated storage is initialized // to avoid false positives when checking with valgrind diff --git a/src/MANYBODY/pair_sw.h b/src/MANYBODY/pair_sw.h index 5f6f51b57c..6509c460d6 100644 --- a/src/MANYBODY/pair_sw.h +++ b/src/MANYBODY/pair_sw.h @@ -29,7 +29,6 @@ class PairSW : public Pair { PairSW(class LAMMPS *); virtual ~PairSW(); virtual void compute(int, int); - void settings(int, char **); virtual void coeff(int, char **); virtual double init_one(int, int); virtual void init_style(); @@ -54,11 +53,12 @@ class PairSW : public Pair { int maxshort; // size of short neighbor list array int *neighshort; // short neighbor list array + virtual void settings(int, char **); virtual void allocate(); void read_file(char *); virtual void setup_params(); void twobody(Param *, double, double &, int, double &); - void threebody(Param *, Param *, Param *, double, double, double *, double *, double *, double *, + virtual void threebody(Param *, Param *, Param *, double, double, double *, double *, double *, double *, int, double &); }; diff --git a/src/MANYBODY/pair_sw_mod.cpp b/src/MANYBODY/pair_sw_mod.cpp new file mode 100644 index 0000000000..ce24952fc7 --- /dev/null +++ b/src/MANYBODY/pair_sw_mod.cpp @@ -0,0 +1,123 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Jin-Wu Jiang (Shanghai U) and Wengen Ouyang (Wuhan U) +------------------------------------------------------------------------- */ + +#include "pair_sw_mod.h" + +#include "error.h" +#include "math_const.h" + +#include +#include + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairSWMOD::PairSWMOD(LAMMPS *lmp) : PairSW(lmp) +{ + delta1 = 0.25; + delta2 = 0.35; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairSWMOD::settings(int narg, char **arg) +{ + // process optional keywords + + int iarg = 0; + + while (iarg < narg) { + if (strcmp(arg[iarg],"maxdelcs") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style command"); + delta1 = utils::numeric(FLERR,arg[iarg+1],false,lmp); + delta2 = utils::numeric(FLERR,arg[iarg+2],false,lmp); + iarg += 3; + if ((delta1 < 0.0) || (delta1 > 1.0) || (delta2 < 0.0) || (delta2 > 1.0) || (delta1 > delta2)) + error->all(FLERR,"Illegal values for maxdelcs keyword"); + } else error->all(FLERR,"Illegal pair_style command"); + } + PairSW::settings(narg-iarg,arg+iarg); +} + +/* ---------------------------------------------------------------------- */ + +void PairSWMOD::threebody(Param *paramij, Param *paramik, Param *paramijk, + double rsq1, double rsq2, + double *delr1, double *delr2, + double *fj, double *fk, int eflag, double &eng) +{ + double r1,rinvsq1,rainv1,gsrainv1,gsrainvsq1,expgsrainv1; + double r2,rinvsq2,rainv2,gsrainv2,gsrainvsq2,expgsrainv2; + double rinv12,cs,delcs,delcssq,facexp,facrad,frad1,frad2; + double facang,facang12,csfacang,csfac1,csfac2,factor; + + r1 = sqrt(rsq1); + rinvsq1 = 1.0/rsq1; + rainv1 = 1.0/(r1 - paramij->cut); + gsrainv1 = paramij->sigma_gamma * rainv1; + gsrainvsq1 = gsrainv1*rainv1/r1; + expgsrainv1 = exp(gsrainv1); + + r2 = sqrt(rsq2); + rinvsq2 = 1.0/rsq2; + rainv2 = 1.0/(r2 - paramik->cut); + gsrainv2 = paramik->sigma_gamma * rainv2; + gsrainvsq2 = gsrainv2*rainv2/r2; + expgsrainv2 = exp(gsrainv2); + + rinv12 = 1.0/(r1*r2); + cs = (delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2]) * rinv12; + delcs = cs - paramijk->costheta; + + // Modification to delcs + if(fabs(delcs) >= delta2) delcs = 0.0; + else if(fabs(delcs) < delta2 && fabs(delcs) > delta1) { + factor = 0.5 + 0.5*cos(MY_PI*(fabs(delcs) - delta1)/(delta2 - delta1)); + delcs *= factor; + } + delcssq = delcs*delcs; + + facexp = expgsrainv1*expgsrainv2; + + // facrad = sqrt(paramij->lambda_epsilon*paramik->lambda_epsilon) * + // facexp*delcssq; + + facrad = paramijk->lambda_epsilon * facexp*delcssq; + frad1 = facrad*gsrainvsq1; + frad2 = facrad*gsrainvsq2; + facang = paramijk->lambda_epsilon2 * facexp*delcs; + facang12 = rinv12*facang; + csfacang = cs*facang; + csfac1 = rinvsq1*csfacang; + + fj[0] = delr1[0]*(frad1+csfac1)-delr2[0]*facang12; + fj[1] = delr1[1]*(frad1+csfac1)-delr2[1]*facang12; + fj[2] = delr1[2]*(frad1+csfac1)-delr2[2]*facang12; + + csfac2 = rinvsq2*csfacang; + + fk[0] = delr2[0]*(frad2+csfac2)-delr1[0]*facang12; + fk[1] = delr2[1]*(frad2+csfac2)-delr1[1]*facang12; + fk[2] = delr2[2]*(frad2+csfac2)-delr1[2]*facang12; + + if (eflag) eng = facrad; +} diff --git a/src/MANYBODY/pair_sw_mod.h b/src/MANYBODY/pair_sw_mod.h new file mode 100644 index 0000000000..580f031e00 --- /dev/null +++ b/src/MANYBODY/pair_sw_mod.h @@ -0,0 +1,94 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(sw/mod,PairSWMOD); +// clang-format on +#else + +#ifndef LMP_PAIR_SW_MOD_H +#define LMP_PAIR_SW_MOD_H + +#include "pair_sw.h" + +namespace LAMMPS_NS { + +class PairSWMOD : public PairSW { + public: + PairSWMOD(class LAMMPS *); + virtual ~PairSWMOD() {} + + protected: + double delta1; + double delta2; + + void settings(int, char **); + void threebody(Param *, Param *, Param *, double, double, double *, double *, double *, double *, + int, double &); +}; + +} // namespace LAMMPS_NS + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair style Stillinger-Weber requires atom IDs + +This is a requirement to use the SW potential. + +E: Pair style Stillinger-Weber requires newton pair on + +See the newton command. This is a restriction to use the SW +potential. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +E: Cannot open Stillinger-Weber potential file %s + +The specified SW potential file cannot be opened. Check that the path +and name are correct. + +E: Incorrect format in Stillinger-Weber potential file + +Incorrect number of words per line in the potential file. + +E: Illegal Stillinger-Weber parameter + +One or more of the coefficients defined in the potential file is +invalid. + +E: Potential file has duplicate entry + +The potential file has more than one entry for the same element. + +E: Potential file is missing an entry + +The potential file does not have a needed entry. + +*/ diff --git a/src/OPENMP/pair_sw_mod_omp.cpp b/src/OPENMP/pair_sw_mod_omp.cpp new file mode 100644 index 0000000000..d87abc1d2c --- /dev/null +++ b/src/OPENMP/pair_sw_mod_omp.cpp @@ -0,0 +1,119 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + This software is distributed under the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) + and Wengen Ouyang (Wuhan U) +------------------------------------------------------------------------- */ + +#include "pair_sw_mod_omp.h" + +#include "error.h" +#include "math_const.h" + +#include +#include + +using namespace LAMMPS_NS; +using namespace MathConst; + +PairSWMODOMP::PairSWMODOMP(LAMMPS *lmp) : PairSWOMP(lmp) +{ + delta1 = 0.25; + delta2 = 0.35; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairSWMODOMP::settings(int narg, char **arg) +{ + // process optional keywords + + int iarg = 0; + + while (iarg < narg) { + if (strcmp(arg[iarg],"maxdelcs") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style command"); + delta1 = utils::numeric(FLERR,arg[iarg+1],false,Pointers::lmp); + delta2 = utils::numeric(FLERR,arg[iarg+2],false,Pointers::lmp); + iarg += 3; + if ((delta1 < 0.0) || (delta1 > 1.0) || (delta2 < 0.0) || (delta2 > 1.0) || (delta1 > delta2)) + error->all(FLERR,"Illegal values for maxdelcs keyword"); + } else error->all(FLERR,"Illegal pair_style command"); + } + PairSWOMP::settings(narg-iarg,arg+iarg); +} + +/* ---------------------------------------------------------------------- */ + +void PairSWMODOMP::threebody(Param *paramij, Param *paramik, Param *paramijk, + double rsq1, double rsq2, + double *delr1, double *delr2, + double *fj, double *fk, int eflag, double &eng) +{ + double r1,rinvsq1,rainv1,gsrainv1,gsrainvsq1,expgsrainv1; + double r2,rinvsq2,rainv2,gsrainv2,gsrainvsq2,expgsrainv2; + double rinv12,cs,delcs,delcssq,facexp,facrad,frad1,frad2; + double facang,facang12,csfacang,csfac1,csfac2,factor; + + r1 = sqrt(rsq1); + rinvsq1 = 1.0/rsq1; + rainv1 = 1.0/(r1 - paramij->cut); + gsrainv1 = paramij->sigma_gamma * rainv1; + gsrainvsq1 = gsrainv1*rainv1/r1; + expgsrainv1 = exp(gsrainv1); + + r2 = sqrt(rsq2); + rinvsq2 = 1.0/rsq2; + rainv2 = 1.0/(r2 - paramik->cut); + gsrainv2 = paramik->sigma_gamma * rainv2; + gsrainvsq2 = gsrainv2*rainv2/r2; + expgsrainv2 = exp(gsrainv2); + + rinv12 = 1.0/(r1*r2); + cs = (delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2]) * rinv12; + delcs = cs - paramijk->costheta; + + // Modification to delcs + if(fabs(delcs) >= delta2) delcs = 0.0; + else if(fabs(delcs) < delta2 && fabs(delcs) > delta1) { + factor = 0.5 + 0.5*cos(MY_PI*(fabs(delcs) - delta1)/(delta2 - delta1)); + delcs *= factor; + } + delcssq = delcs*delcs; + + facexp = expgsrainv1*expgsrainv2; + + // facrad = sqrt(paramij->lambda_epsilon*paramik->lambda_epsilon) * + // facexp*delcssq; + + facrad = paramijk->lambda_epsilon * facexp*delcssq; + frad1 = facrad*gsrainvsq1; + frad2 = facrad*gsrainvsq2; + facang = paramijk->lambda_epsilon2 * facexp*delcs; + facang12 = rinv12*facang; + csfacang = cs*facang; + csfac1 = rinvsq1*csfacang; + + fj[0] = delr1[0]*(frad1+csfac1)-delr2[0]*facang12; + fj[1] = delr1[1]*(frad1+csfac1)-delr2[1]*facang12; + fj[2] = delr1[2]*(frad1+csfac1)-delr2[2]*facang12; + + csfac2 = rinvsq2*csfacang; + + fk[0] = delr2[0]*(frad2+csfac2)-delr1[0]*facang12; + fk[1] = delr2[1]*(frad2+csfac2)-delr1[1]*facang12; + fk[2] = delr2[2]*(frad2+csfac2)-delr1[2]*facang12; + + if (eflag) eng = facrad; +} diff --git a/src/OPENMP/pair_sw_mod_omp.h b/src/OPENMP/pair_sw_mod_omp.h new file mode 100644 index 0000000000..7e69ca283b --- /dev/null +++ b/src/OPENMP/pair_sw_mod_omp.h @@ -0,0 +1,49 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(sw/mod/omp,PairSWMODOMP); +// clang-format on +#else + +#ifndef LMP_PAIR_SW_MOD_OMP_H +#define LMP_PAIR_SW_MOD_OMP_H + +#include "pair_sw_omp.h" + +namespace LAMMPS_NS { + +class PairSWMODOMP : public PairSWOMP { + + public: + PairSWMODOMP(class LAMMPS *); + virtual ~PairSWMODOMP() {} + + protected: + double delta1; + double delta2; + + void settings(int, char **); + void threebody(Param *, Param *, Param *, double, double, double *, double *, double *, double *, + int, double &); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/unittest/force-styles/tests/manybody-pair-sw-mod-maxdelcs.yaml b/unittest/force-styles/tests/manybody-pair-sw-mod-maxdelcs.yaml new file mode 100644 index 0000000000..02c4afee71 --- /dev/null +++ b/unittest/force-styles/tests/manybody-pair-sw-mod-maxdelcs.yaml @@ -0,0 +1,156 @@ +--- +lammps_version: 27 Oct 2021 +date_generated: Fri Dec 3 17:14:23 2021 +epsilon: 2e-08 +skip_tests: +prerequisites: ! | + pair sw/mod +pre_commands: ! | + variable newton_pair delete + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" +post_commands: ! "" +input_file: in.manybody +pair_style: sw/mod maxdelcs 0.20 0.40 +pair_coeff: ! | + * * CdTe.sw Cd Cd Cd Cd Te Te Te Te +extract: ! 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"" +input_file: in.manybody +pair_style: sw/mod +pair_coeff: ! | + * * CdTe.sw Cd Cd Cd Cd Te Te Te Te +extract: ! 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