forked from lijiext/lammps
import multi-element compatible pair style edip as edip/multi
This commit is contained in:
Axel Kohlmeyer
parent
06c151421c
commit
35e92733e9
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@ -1016,6 +1016,7 @@ package"_Section_start.html#start_3.
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"dpd/fdt/energy"_pair_dpd_fdt.html,
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"eam/cd (o)"_pair_eam.html,
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"edip (o)"_pair_edip.html,
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"edip/multi"_pair_edip.html,
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"eff/cut"_pair_eff.html,
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"exp6/rx"_pair_exp6_rx.html,
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"gauss/cut"_pair_gauss.html,
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@ -12,6 +12,7 @@ pair_style edip command :h3
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pair_style edip :pre
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pair_style edip/omp :pre
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pair_style edip/multi :pre
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[Examples:]
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@ -20,11 +21,14 @@ pair_coeff * * Si.edip Si
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[Description:]
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The {edip} style computes a 3-body "EDIP"_#EDIP potential which is
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popular for modeling silicon materials where it can have advantages
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over other models such as the "Stillinger-Weber"_pair_sw.html or
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"Tersoff"_pair_tersoff.html potentials. In EDIP, the energy E of a
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system of atoms is
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The {edip} and {edip/multi} styles compute a 3-body "EDIP"_#EDIP
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potential which is popular for modeling silicon materials where
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it can have advantages over other models such as the
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"Stillinger-Weber"_pair_sw.html or "Tersoff"_pair_tersoff.html
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potentials. The {edip} style has been programmed for single element
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potentials, while {edip/multi} supports multi-element EDIP runs.
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In EDIP, the energy E of a system of atoms is
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:c,image(Eqs/pair_edip.jpg)
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@ -142,7 +146,7 @@ This pair style can only be used via the {pair} keyword of the
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[Restrictions:]
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This angle style can only be used if LAMMPS was built with the
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This pair style can only be used if LAMMPS was built with the
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USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info on packages.
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@ -151,7 +155,7 @@ for pair interactions.
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The EDIP potential files provided with LAMMPS (see the potentials directory)
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are parameterized for metal "units"_units.html.
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You can use the SW potential with any LAMMPS units, but you would need
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You can use the EDIP potential with any LAMMPS units, but you would need
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to create your own EDIP potential file with coefficients listed in the
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appropriate units if your simulation doesn't use "metal" units.
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@ -0,0 +1,26 @@
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# DATE: 2011-09-15 CONTRIBUTOR: Unknown CITATION: Justo, Bazant, Kaxiras, Bulatov and Yip, Phys Rev B, 58, 2539 (1998)
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# EDIP parameters for various elements and mixtures
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# multiple entries can be added to this file, LAMMPS reads the ones it needs
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# these entries are in LAMMPS "metal" units
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# format of a single entry (one or more lines)
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#
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# element 1, element 2, element 3,
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# A B cutoffA cutoffC alpha beta eta
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# gamma lambda mu rho sigma Q0
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# u1 u2 u3 u4
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#
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# units for each parameters:
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# A , lambda are in eV
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# B, cutoffA, cutoffC, gamma, sigma are in Angstrom
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# alpha, beta, eta, mu, rho, Q0, u1-u4 are pure numbers
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# Here are the original parameters in metal units, for Silicon from:
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# J. F. Justo, M. Z. Bazant, E. Kaxiras, V. V. Bulatov, S. Yip
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# Phys. Rev. B 58, 2539 (1998)
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#
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Si Si Si 7.9821730 1.5075463 3.1213820 2.5609104 3.1083847 0.0070975 0.2523244
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1.1247945 1.4533108 0.6966326 1.2085196 0.5774108 312.1341346
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-0.165799 32.557 0.286198 0.66
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@ -0,0 +1,38 @@
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# DATE: 2017-05-16 CONTRIBUTOR: Laurent Pizzagalli CITATION: G. Lucas, M. Bertolus, and L. Pizzagalli, J. Phys. : Condens. Matter 22, 035802 (2010)
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# element 1, element 2, element 3,
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# A B cutoffA cutoffC alpha beta eta
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# gamma lambda mu rho sigma Q0
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# u1 u2 u3 u4
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#
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Si Si Si 5.488043 1.446435 2.941586 2.540193 3.066580 0.008593 0.589390
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1.135256 2.417497 0.629131 1.343679 0.298443 208.924548
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-0.165799 32.557 0.286198 0.66
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C C C 10.222599 0.959814 2.212263 1.741598 1.962090 0.025661 0.275605
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1.084183 3.633621 0.594236 2.827634 0.536561 289.305617
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-0.165799 32.557 0.286198 0.66
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C Si Si 7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.432497
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1.191567 3.025559 0.611684 2.061835 0.423863 249.115082
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-0.165799 32.557000 0.286198 0.660000
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Si C C 7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.432497
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1.191567 3.025559 0.611684 2.061835 0.423863 249.115082
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-0.165799 32.557000 0.286198 0.660000
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Si Si C 5.488043 1.446435 2.941586 2.540193 3.066580 0.008593 0.510944
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1.135256 2.721528 0.620407 1.343679 0.298443 229.019815
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-0.165799 32.557000 0.286198 0.660000
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Si C Si 7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.510944
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1.191567 2.721528 0.620407 2.061835 0.423863 229.019815
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-0.165799 32.557000 0.286198 0.660000
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C C Si 10.222599 0.959814 2.212263 1.741598 1.962090 0.025661 0.354051
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1.084183 3.329590 0.602960 2.827634 0.536561 269.210350
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-0.165799 32.557000 0.286198 0.660000
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C Si C 7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.354051
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1.191567 3.329590 0.602960 2.061835 0.423863 269.210350
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-0.165799 32.557000 0.286198 0.660000
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@ -0,0 +1,138 @@
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Position data for Silicon-Carbon system
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128 atoms
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2 atom types
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-6.00 5.97232152 xlo xhi
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-6.00 5.97232152 ylo yhi
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-6.00 5.97232152 zlo zhi
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Atoms
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1 2 -2.9378454 -4.4592615 -4.8109196
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2 2 5.6222143 -2.7335026 -1.7157569
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3 2 -2.6614623 -5.5431059 1.6353686
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4 2 -5.4326838 -4.6174577 5.9452279
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5 2 5.8679239 -0.1120535 -3.5839373
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6 2 -3.7174621 -0.6623311 -0.3714789
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7 2 -5.0724728 -2.5671623 4.4103461
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8 2 -3.3951436 0.9341126 4.9310702
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9 2 -5.4347593 1.9523767 -5.6180938
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10 2 -4.5884719 2.2904528 -1.0597739
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11 2 -5.9058662 0.6212406 2.0127574
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12 2 -4.7680660 0.1965740 4.3267764
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13 2 -5.4228882 5.2569673 -4.5162920
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14 2 -5.2683965 -5.9193658 -2.8648668
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15 2 -2.8610884 1.0484664 2.0299077
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16 2 -4.0711084 5.3133026 3.8009514
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17 2 -0.1947147 -4.1677696 -5.6950931
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18 2 -2.9892710 -3.1647368 -1.6173910
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19 2 -0.9129311 -4.3819066 -0.1601859
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20 2 -2.4513693 -5.2466501 4.8882912
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21 2 -2.8879952 -0.1633446 -3.3401150
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22 1 -4.6738762 -1.3807254 -2.2946777
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23 2 -0.6973948 -1.4885343 0.6005156
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24 1 -2.7392164 -2.4774843 0.2387186
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25 2 -2.6551254 -2.7229952 2.6350264
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26 1 -3.4644263 -4.6028144 3.3817786
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27 2 0.7227614 -2.0709446 2.9214737
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28 1 -2.1000577 -3.2131296 5.7273437
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29 2 -3.1057649 2.3204819 -2.2725622
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30 1 -2.2298751 0.7168389 -1.3107201
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31 2 -1.8698261 1.4006751 0.7265108
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32 1 -4.1103409 -0.7093340 1.9341753
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33 2 -0.3505581 3.2707182 -0.2880656
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34 1 -3.4045407 -1.4383961 4.3903527
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35 2 -3.0940529 1.4132478 -5.3635505
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36 1 -4.4560663 1.2072875 -3.7310176
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37 2 -2.6061002 4.6373499 -4.6903941
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38 1 -3.3477444 4.6768137 -2.6284678
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39 2 0.8121697 4.8602418 -4.6710946
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40 1 -2.5756922 3.3740738 -0.2136350
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41 2 -0.3867976 5.8745611 -2.1119905
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42 1 -1.6766249 1.3374292 3.8741477
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43 2 -0.8770613 3.3735941 4.3846975
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44 1 -1.8609254 3.3158245 -5.9786556
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45 1 -5.2732321 -4.6073253 -0.9581754
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46 1 -2.7888697 -5.6910152 -0.7922023
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47 1 -2.4717165 4.5801880 2.5083210
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48 1 -3.8819950 5.8456589 -5.7563384
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49 2 2.2314782 -2.7729214 -5.2356862
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50 2 0.2981976 -3.1385279 -3.1608167
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51 2 2.8810785 -3.4658695 -0.5823196
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52 2 0.2509625 -5.7595229 2.7389761
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53 2 -0.2934120 -0.8029431 -3.3698507
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54 1 -1.0075690 -2.0481922 -1.9419298
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55 2 2.0729069 1.4922441 -2.3898096
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56 1 1.1110944 -3.2004208 0.9491078
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57 2 1.6774298 -0.7901860 2.5158773
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58 1 -0.8342297 -4.3342518 2.0971458
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59 2 3.2747406 -1.3107897 4.7884706
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60 1 1.7126246 -3.3691471 4.5581012
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61 2 0.4770605 1.7769008 -5.3339915
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62 1 0.2944391 0.5892781 -2.2030106
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63 2 2.2039275 3.1557557 -2.0276796
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64 1 -0.0404494 0.4767818 1.0396418
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65 2 1.1395867 2.3763443 2.3481007
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66 1 -0.9738374 -1.6325161 3.7538567
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67 2 -0.3291998 0.2996990 5.2770809
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68 1 -1.6185604 -0.3964274 -5.1771220
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69 2 2.5999949 -5.1977715 5.8230717
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70 1 -1.6270675 2.3210900 -3.6299941
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71 2 3.6532700 4.9282597 -5.4319276
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72 1 0.0788934 4.0241037 -2.5011530
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73 2 2.8556507 2.6168653 2.1125546
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74 1 0.9738989 2.6255364 4.3412121
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75 2 3.7452938 3.4521356 4.5946426
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76 1 2.0805182 4.7039015 5.3280260
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77 1 -1.0324174 -5.8155041 -4.3265820
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78 1 0.7622442 -4.3631629 -1.3156572
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79 1 0.3263684 3.9937357 1.6172321
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80 1 -0.4350105 -5.7997058 4.5959134
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81 2 3.9161132 -4.6052788 -3.3191717
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82 2 1.9240657 5.7345079 -1.9754251
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83 2 -5.9794488 -4.2369359 1.8646522
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84 2 4.3339975 -4.4845227 5.3737440
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85 2 2.2755456 -0.6327737 -5.7931837
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86 1 1.8728190 -1.5504906 -3.4560010
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87 2 3.4558100 -1.1054068 -1.8333071
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88 1 4.3788172 -1.9466494 -0.3284637
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89 2 2.5999235 -3.7548996 2.5740569
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90 1 3.9983910 -4.4856603 1.1968663
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91 2 -5.7295580 -2.1475672 -5.9963645
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92 1 4.2664051 -2.6988975 -5.8005478
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93 2 4.5254685 2.2906832 -3.4765798
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94 1 2.3603088 1.3416442 -4.4173836
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95 2 4.7767057 1.4061217 -0.7524620
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96 1 1.8072666 -0.7835973 -0.4581995
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97 2 4.4745018 0.3736224 2.1068274
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98 1 3.6081170 -1.7315713 2.4019053
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99 2 4.6281423 -0.2865409 4.4756524
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100 1 1.7975239 0.2893530 4.2330830
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101 2 5.8341452 4.4986472 -5.9664541
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102 1 3.2401308 4.1655227 -3.5070029
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103 2 4.8720339 4.8709982 -2.3364366
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104 1 3.5526476 1.2262752 0.6926826
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105 2 -5.8173342 4.5420479 1.5578881
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106 1 3.9683224 1.5441137 3.8284375
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107 2 -5.5349308 1.9067049 3.7504113
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108 1 4.4728615 2.6415574 -5.5952809
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109 1 1.7000950 -4.8115440 -4.1953920
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110 1 1.7221527 4.1878404 -0.3712681
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111 1 3.9218156 4.5935583 1.3263407
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112 1 3.1310195 -5.8922481 3.6001155
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113 1 4.7558719 -2.2877771 -3.4742052
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114 1 -5.5050300 -2.7027381 0.8748867
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115 1 5.8418594 -4.6064370 3.8714113
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116 1 -4.7516868 -3.1691984 -4.4099768
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117 1 3.9404971 0.7188702 -2.2898786
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118 1 -5.6869740 0.2042380 -0.1916738
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119 1 5.8949589 -1.2422560 3.1201292
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120 1 5.9675804 -0.0712572 5.8964022
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121 1 -5.6208517 3.3600036 -2.9493510
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122 1 5.2065263 3.4517912 -0.3800894
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123 1 -4.6994522 2.5489583 1.8297431
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124 1 -4.0758407 3.0726196 5.0647973
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125 1 4.1587591 -5.0896820 -1.1443498
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126 1 -4.6963753 -5.7429833 1.1357818
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127 1 5.5994192 4.6887008 3.5948264
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128 1 5.0988369 -5.3774409 -4.9051267
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@ -0,0 +1,72 @@
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units metal
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atom_style atomic
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atom_modify map array
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boundary p p p
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atom_modify sort 0 0.0
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# temperature
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variable t equal 1800.0
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# coordination number cutoff
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variable r equal 2.835
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# minimization parameters
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variable etol equal 1.0e-5
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variable ftol equal 1.0e-5
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variable maxiter equal 100
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variable maxeval equal 100
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variable dmax equal 1.0e-1
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# diamond unit cell
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variable a equal 5.431
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lattice custom $a &
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a1 1.0 0.0 0.0 &
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a2 0.0 1.0 0.0 &
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a3 0.0 0.0 1.0 &
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basis 0.0 0.0 0.0 &
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basis 0.0 0.5 0.5 &
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basis 0.5 0.0 0.5 &
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basis 0.5 0.5 0.0 &
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basis 0.25 0.25 0.25 &
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basis 0.25 0.75 0.75 &
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basis 0.75 0.25 0.75 &
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basis 0.75 0.75 0.25
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region myreg block 0 4 &
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0 4 &
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0 4
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create_box 1 myreg
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create_atoms 1 region myreg
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mass 1 28.06
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group Si type 1
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velocity all create $t 5287287 mom yes rot yes dist gaussian
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# make a vacancy
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group del id 300
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delete_atoms group del
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pair_style edip
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pair_coeff * * Si.edip Si
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thermo 10
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fix 1 all nvt temp $t $t 0.1
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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# equilibrate
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run 500
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@ -0,0 +1,72 @@
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units metal
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atom_style atomic
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atom_modify map array
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boundary p p p
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atom_modify sort 0 0.0
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# temperature
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variable t equal 1800.0
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# coordination number cutoff
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variable r equal 2.835
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# minimization parameters
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variable etol equal 1.0e-5
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variable ftol equal 1.0e-5
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variable maxiter equal 100
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variable maxeval equal 100
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variable dmax equal 1.0e-1
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# diamond unit cell
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variable a equal 5.431
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lattice custom $a &
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a1 1.0 0.0 0.0 &
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a2 0.0 1.0 0.0 &
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a3 0.0 0.0 1.0 &
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basis 0.0 0.0 0.0 &
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basis 0.0 0.5 0.5 &
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basis 0.5 0.0 0.5 &
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basis 0.5 0.5 0.0 &
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basis 0.25 0.25 0.25 &
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basis 0.25 0.75 0.75 &
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basis 0.75 0.25 0.75 &
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basis 0.75 0.75 0.25
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region myreg block 0 4 &
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0 4 &
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0 4
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||||
create_box 1 myreg
|
||||
create_atoms 1 region myreg
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
||||
delete_atoms group del
|
||||
|
||||
pair_style edip/multi
|
||||
pair_coeff * * Si.edip Si
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
# equilibrate
|
||||
|
||||
run 500
|
||||
|
||||
|
|
@ -0,0 +1,33 @@
|
|||
# Test of MEAM potential for SiC system
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.SiC
|
||||
|
||||
pair_style edip/multi
|
||||
pair_coeff * * SiC.edip Si C
|
||||
|
||||
mass 1 28.085
|
||||
mass 2 12.001
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 1
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 50 dump.meam
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Si C
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Si C
|
||||
|
||||
run 100
|
||||
|
|
@ -0,0 +1,167 @@
|
|||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# minimization parameters
|
||||
|
||||
variable etol equal 1.0e-5
|
||||
variable ftol equal 1.0e-5
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 100
|
||||
variable dmax equal 1.0e-1
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
create_box 1 myreg
|
||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region myreg
|
||||
Created 512 atoms
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
512 atoms in group Si
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
velocity all create 1800 5287287 mom yes rot yes dist gaussian
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
||||
1 atoms in group del
|
||||
delete_atoms group del
|
||||
Deleted 1 atoms, new total = 511
|
||||
|
||||
pair_style edip/multi
|
||||
pair_coeff * * Si.edip Si
|
||||
Reading potential file Si.edip with DATE: 2011-09-15
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
# equilibrate
|
||||
|
||||
run 500
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.12138
|
||||
ghost atom cutoff = 4.12138
|
||||
binsize = 2.06069, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair edip/multi, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.979 | 2.979 | 2.979 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1802.5039 -2372.6618 0 -2253.8359 12261.807
|
||||
10 952.62744 -2316.428 0 -2253.6283 723.08194
|
||||
20 549.13801 -2289.442 0 -2253.2413 -2444.5204
|
||||
30 1047.0106 -2321.1523 0 -2252.1305 9013.201
|
||||
40 663.46141 -2294.2083 0 -2250.4711 2942.5348
|
||||
50 504.74535 -2282.849 0 -2249.5748 -461.44909
|
||||
60 1019.2173 -2315.5639 0 -2248.3744 7706.4286
|
||||
70 844.51195 -2302.5251 0 -2246.8526 3116.8302
|
||||
80 814.90407 -2299.3372 0 -2245.6166 794.77455
|
||||
90 1269.5636 -2327.4775 0 -2243.7845 7729.3968
|
||||
100 977.61563 -2306.1118 0 -2241.6647 2969.9939
|
||||
110 843.08539 -2295.6547 0 -2240.0763 1393.4039
|
||||
120 1161.6968 -2314.6587 0 -2238.0766 7398.3492
|
||||
130 918.19451 -2296.4321 0 -2235.9022 2537.3997
|
||||
140 881.42548 -2292.2768 0 -2234.1709 1550.3339
|
||||
150 1231.1005 -2313.1054 0 -2231.9479 8112.7566
|
||||
160 967.01862 -2293.332 0 -2229.5836 3422.9627
|
||||
170 833.51248 -2282.7489 0 -2227.8015 43.991459
|
||||
180 1240.8488 -2307.3633 0 -2225.5632 6557.8651
|
||||
190 1126.4621 -2297.1922 0 -2222.9328 4289.0067
|
||||
200 947.59571 -2283.29 0 -2220.822 586.2811
|
||||
210 1228.153 -2299.4702 0 -2218.5071 5315.0425
|
||||
220 1215.4104 -2295.9408 0 -2215.8176 4870.3417
|
||||
230 1112.436 -2286.7552 0 -2213.4204 2527.1879
|
||||
240 1300.081 -2296.6013 0 -2210.8965 5738.3708
|
||||
250 1192.5738 -2286.8463 0 -2208.2286 4076.49
|
||||
260 1004.7055 -2272.1753 0 -2205.9424 359.37589
|
||||
270 1241.2018 -2285.3632 0 -2203.5399 4160.5763
|
||||
280 1360.1974 -2290.325 0 -2200.6572 5802.3902
|
||||
290 1151.9365 -2273.9467 0 -2198.008 1418.8887
|
||||
300 1174.3518 -2273.0089 0 -2195.5925 1998.229
|
||||
310 1329.2727 -2280.5049 0 -2192.8757 4721.7297
|
||||
320 1284.4414 -2274.7519 0 -2190.0781 2985.4674
|
||||
330 1328.3761 -2274.9545 0 -2187.3844 4543.2109
|
||||
340 1446.3847 -2279.8693 0 -2184.5198 6254.4059
|
||||
350 1366.2165 -2271.7475 0 -2181.6828 3637.8335
|
||||
360 1358.9609 -2268.5982 0 -2179.0118 3049.5798
|
||||
370 1552.208 -2278.4802 0 -2176.1545 6334.0058
|
||||
380 1562.5295 -2276.1793 0 -2173.1732 5787.5547
|
||||
390 1415.5498 -2263.7824 0 -2170.4655 3438.5766
|
||||
400 1323.1568 -2255.1641 0 -2167.938 2427.2294
|
||||
410 1260.7186 -2248.5373 0 -2165.4273 1208.6299
|
||||
420 1282.1118 -2247.3718 0 -2162.8516 462.65374
|
||||
430 1451.944 -2255.7551 0 -2160.0391 2037.8025
|
||||
440 1568.9415 -2260.417 0 -2156.9882 3531.1602
|
||||
450 1565.8262 -2257.2396 0 -2154.0162 2586.7886
|
||||
460 1677.7143 -2261.7214 0 -2151.122 4112.9756
|
||||
470 1762.9071 -2264.4244 0 -2148.2089 5053.2139
|
||||
480 1704.5898 -2257.8678 0 -2145.4967 4077.4626
|
||||
490 1731.2619 -2257.1048 0 -2142.9753 4710.5263
|
||||
500 1723.9777 -2254.161 0 -2140.5118 4760.7295
|
||||
Loop time of 0.679564 on 1 procs for 500 steps with 511 atoms
|
||||
|
||||
Performance: 63.570 ns/day, 0.378 hours/ns, 735.765 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.65181 | 0.65181 | 0.65181 | 0.0 | 95.92
|
||||
Neigh | 0.013857 | 0.013857 | 0.013857 | 0.0 | 2.04
|
||||
Comm | 0.0033884 | 0.0033884 | 0.0033884 | 0.0 | 0.50
|
||||
Output | 0.00070739 | 0.00070739 | 0.00070739 | 0.0 | 0.10
|
||||
Modify | 0.0083694 | 0.0083694 | 0.0083694 | 0.0 | 1.23
|
||||
Other | | 0.001432 | | | 0.21
|
||||
|
||||
Nlocal: 511 ave 511 max 511 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 845 ave 845 max 845 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 7902 ave 7902 max 7902 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7902
|
||||
Ave neighs/atom = 15.4638
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,167 @@
|
|||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# minimization parameters
|
||||
|
||||
variable etol equal 1.0e-5
|
||||
variable ftol equal 1.0e-5
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 100
|
||||
variable dmax equal 1.0e-1
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
create_box 1 myreg
|
||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 region myreg
|
||||
Created 512 atoms
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
512 atoms in group Si
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
velocity all create 1800 5287287 mom yes rot yes dist gaussian
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
||||
1 atoms in group del
|
||||
delete_atoms group del
|
||||
Deleted 1 atoms, new total = 511
|
||||
|
||||
pair_style edip/multi
|
||||
pair_coeff * * Si.edip Si
|
||||
Reading potential file Si.edip with DATE: 2011-09-15
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
# equilibrate
|
||||
|
||||
run 500
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.12138
|
||||
ghost atom cutoff = 4.12138
|
||||
binsize = 2.06069, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair edip/multi, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.955 | 2.955 | 2.955 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1802.3816 -2372.6618 0 -2253.844 12260.967
|
||||
10 938.75954 -2315.5185 0 -2253.6329 558.21646
|
||||
20 534.27233 -2288.4721 0 -2253.2514 -2710.768
|
||||
30 1043.7796 -2320.9485 0 -2252.1398 8679.4381
|
||||
40 658.0916 -2293.8597 0 -2250.4765 2165.3742
|
||||
50 517.93009 -2283.7238 0 -2249.5805 -1124.9373
|
||||
60 1063.3594 -2318.4409 0 -2248.3414 7277.8526
|
||||
70 868.14006 -2304.0134 0 -2246.7832 2050.2848
|
||||
80 826.37805 -2300.0187 0 -2245.5416 91.099408
|
||||
90 1289.6772 -2328.7151 0 -2243.6961 8180.7423
|
||||
100 976.36208 -2305.9371 0 -2241.5727 3614.0499
|
||||
110 810.81713 -2293.4705 0 -2240.0193 1359.368
|
||||
120 1165.707 -2314.9026 0 -2238.056 7336.45
|
||||
130 929.81245 -2297.139 0 -2235.8432 2793.8451
|
||||
140 804.47874 -2287.2074 0 -2234.174 704.92455
|
||||
150 1182.4141 -2310.0266 0 -2232.0787 7822.2337
|
||||
160 979.92391 -2294.2969 0 -2229.6977 3206.7458
|
||||
170 830.14748 -2282.6079 0 -2227.8824 -296.87377
|
||||
180 1271.1133 -2309.4274 0 -2225.6322 7199.614
|
||||
190 1209.6006 -2302.6407 0 -2222.9006 5528.3784
|
||||
200 954.67693 -2283.6621 0 -2220.7273 47.02795
|
||||
210 1260.814 -2301.5582 0 -2218.442 4829.788
|
||||
220 1274.9954 -2299.7285 0 -2215.6774 5518.0597
|
||||
230 1048.0074 -2282.398 0 -2213.3106 1754.4144
|
||||
240 1261.7072 -2294.1108 0 -2210.9356 5233.2712
|
||||
250 1272.6178 -2292.0793 0 -2208.1849 4795.9325
|
||||
260 989.14205 -2271.0278 0 -2205.8209 -820.1828
|
||||
270 1212.0445 -2283.4212 0 -2203.52 3395.8634
|
||||
280 1391.9572 -2292.3809 0 -2200.6194 6666.2451
|
||||
290 1093.1204 -2270.0421 0 -2197.9807 206.94523
|
||||
300 1159.4831 -2272.102 0 -2195.6657 778.53806
|
||||
310 1407.3528 -2285.6228 0 -2192.8463 5223.048
|
||||
320 1236.7163 -2271.5389 0 -2190.0113 1865.3943
|
||||
330 1258.8275 -2270.4611 0 -2187.4758 2333.3209
|
||||
340 1507.9519 -2283.9906 0 -2184.5824 6775.5456
|
||||
350 1366.5116 -2271.7287 0 -2181.6446 3432.115
|
||||
360 1305.2829 -2265.1092 0 -2179.0614 1498.4073
|
||||
370 1581.4335 -2280.4645 0 -2176.2122 6518.5597
|
||||
380 1589.5319 -2277.9428 0 -2173.1567 6334.6506
|
||||
390 1402.6781 -2262.9323 0 -2170.464 3278.3038
|
||||
400 1374.9587 -2258.5717 0 -2167.9307 3608.7284
|
||||
410 1295.7416 -2250.7752 0 -2165.3565 1877.5222
|
||||
420 1278.6727 -2247.1099 0 -2162.8164 1599.4181
|
||||
430 1508.1328 -2259.4245 0 -2160.0044 4300.2224
|
||||
440 1624.2957 -2263.9806 0 -2156.9026 4432.625
|
||||
450 1597.3356 -2259.263 0 -2153.9624 3370.3816
|
||||
460 1772.0922 -2267.9106 0 -2151.0895 5788.3214
|
||||
470 1806.4047 -2267.304 0 -2148.221 5950.1166
|
||||
480 1593.0406 -2250.7469 0 -2145.7294 2518.0576
|
||||
490 1660.9767 -2252.894 0 -2143.398 4282.1643
|
||||
500 1714.283 -2253.9295 0 -2140.9194 5740.0247
|
||||
Loop time of 0.205398 on 4 procs for 500 steps with 511 atoms
|
||||
|
||||
Performance: 210.324 ns/day, 0.114 hours/ns, 2434.304 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.16285 | 0.1688 | 0.17446 | 1.1 | 82.18
|
||||
Neigh | 0.0035172 | 0.0036234 | 0.0038214 | 0.2 | 1.76
|
||||
Comm | 0.018727 | 0.024851 | 0.030996 | 2.9 | 12.10
|
||||
Output | 0.0013061 | 0.0014012 | 0.0015635 | 0.3 | 0.68
|
||||
Modify | 0.0046582 | 0.0048603 | 0.0050988 | 0.2 | 2.37
|
||||
Other | | 0.001861 | | | 0.91
|
||||
|
||||
Nlocal: 127.75 ave 131 max 124 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 433.75 ave 441 max 426 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1979.5 ave 2040 max 1895 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 7918
|
||||
Ave neighs/atom = 15.4951
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,167 @@
|
|||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# minimization parameters
|
||||
|
||||
variable etol equal 1.0e-5
|
||||
variable ftol equal 1.0e-5
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 100
|
||||
variable dmax equal 1.0e-1
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
create_box 1 myreg
|
||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region myreg
|
||||
Created 512 atoms
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
512 atoms in group Si
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
velocity all create 1800 5287287 mom yes rot yes dist gaussian
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
||||
1 atoms in group del
|
||||
delete_atoms group del
|
||||
Deleted 1 atoms, new total = 511
|
||||
|
||||
pair_style edip
|
||||
pair_coeff * * Si.edip Si
|
||||
Reading potential file Si.edip with DATE: 2011-09-15
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
# equilibrate
|
||||
|
||||
run 500
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.12138
|
||||
ghost atom cutoff = 4.12138
|
||||
binsize = 2.06069, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair edip, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.979 | 2.979 | 2.979 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1802.5039 -2372.6618 0 -2253.8359 12261.807
|
||||
10 952.62744 -2316.428 0 -2253.6283 723.08283
|
||||
20 549.138 -2289.442 0 -2253.2413 -2444.5194
|
||||
30 1047.0106 -2321.1522 0 -2252.1305 9013.2015
|
||||
40 663.46143 -2294.2083 0 -2250.4711 2942.5358
|
||||
50 504.74533 -2282.849 0 -2249.5748 -461.44817
|
||||
60 1019.2173 -2315.5639 0 -2248.3744 7706.429
|
||||
70 844.51197 -2302.5251 0 -2246.8526 3116.8313
|
||||
80 814.90406 -2299.3372 0 -2245.6165 794.77536
|
||||
90 1269.5635 -2327.4775 0 -2243.7845 7729.3971
|
||||
100 977.61566 -2306.1118 0 -2241.6647 2969.9952
|
||||
110 843.08538 -2295.6547 0 -2240.0763 1393.4046
|
||||
120 1161.6968 -2314.6587 0 -2238.0766 7398.3495
|
||||
130 918.19453 -2296.4321 0 -2235.9022 2537.4011
|
||||
140 881.42546 -2292.2768 0 -2234.1709 1550.3345
|
||||
150 1231.1005 -2313.1054 0 -2231.9479 8112.7568
|
||||
160 967.01865 -2293.332 0 -2229.5836 3422.964
|
||||
170 833.51246 -2282.7489 0 -2227.8015 43.99251
|
||||
180 1240.8487 -2307.3633 0 -2225.5632 6557.8652
|
||||
190 1126.4621 -2297.1922 0 -2222.9328 4289.0083
|
||||
200 947.5957 -2283.29 0 -2220.8219 586.28203
|
||||
210 1228.153 -2299.4702 0 -2218.5071 5315.0427
|
||||
220 1215.4104 -2295.9407 0 -2215.8176 4870.343
|
||||
230 1112.436 -2286.7552 0 -2213.4204 2527.1887
|
||||
240 1300.081 -2296.6013 0 -2210.8965 5738.3711
|
||||
250 1192.5739 -2286.8463 0 -2208.2286 4076.4913
|
||||
260 1004.7055 -2272.1753 0 -2205.9424 359.3769
|
||||
270 1241.2018 -2285.3632 0 -2203.5399 4160.5764
|
||||
280 1360.1974 -2290.325 0 -2200.6572 5802.3912
|
||||
290 1151.9366 -2273.9467 0 -2198.008 1418.8905
|
||||
300 1174.3518 -2273.0089 0 -2195.5925 1998.2297
|
||||
310 1329.2726 -2280.5049 0 -2192.8757 4721.7304
|
||||
320 1284.4414 -2274.7519 0 -2190.0781 2985.4687
|
||||
330 1328.3761 -2274.9545 0 -2187.3844 4543.2115
|
||||
340 1446.3847 -2279.8693 0 -2184.5198 6254.4071
|
||||
350 1366.2165 -2271.7475 0 -2181.6828 3637.8351
|
||||
360 1358.9609 -2268.5982 0 -2179.0118 3049.5811
|
||||
370 1552.2079 -2278.4802 0 -2176.1545 6334.0061
|
||||
380 1562.5295 -2276.1793 0 -2173.1731 5787.5565
|
||||
390 1415.5498 -2263.7823 0 -2170.4655 3438.5782
|
||||
400 1323.1568 -2255.1641 0 -2167.938 2427.2311
|
||||
410 1260.7186 -2248.5373 0 -2165.4273 1208.6316
|
||||
420 1282.1118 -2247.3718 0 -2162.8516 462.65508
|
||||
430 1451.9439 -2255.7551 0 -2160.0391 2037.8027
|
||||
440 1568.9415 -2260.417 0 -2156.9882 3531.1613
|
||||
450 1565.8261 -2257.2396 0 -2154.0161 2586.7896
|
||||
460 1677.7143 -2261.7214 0 -2151.122 4112.976
|
||||
470 1762.9071 -2264.4244 0 -2148.2089 5053.2148
|
||||
480 1704.5898 -2257.8678 0 -2145.4966 4077.4649
|
||||
490 1731.2619 -2257.1048 0 -2142.9753 4710.5276
|
||||
500 1723.9777 -2254.161 0 -2140.5118 4760.7316
|
||||
Loop time of 0.312472 on 1 procs for 500 steps with 511 atoms
|
||||
|
||||
Performance: 138.252 ns/day, 0.174 hours/ns, 1600.143 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.28525 | 0.28525 | 0.28525 | 0.0 | 91.29
|
||||
Neigh | 0.013753 | 0.013753 | 0.013753 | 0.0 | 4.40
|
||||
Comm | 0.0033333 | 0.0033333 | 0.0033333 | 0.0 | 1.07
|
||||
Output | 0.00071096 | 0.00071096 | 0.00071096 | 0.0 | 0.23
|
||||
Modify | 0.008044 | 0.008044 | 0.008044 | 0.0 | 2.57
|
||||
Other | | 0.001385 | | | 0.44
|
||||
|
||||
Nlocal: 511 ave 511 max 511 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 845 ave 845 max 845 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 7902 ave 7902 max 7902 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7902
|
||||
Ave neighs/atom = 15.4638
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,167 @@
|
|||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# minimization parameters
|
||||
|
||||
variable etol equal 1.0e-5
|
||||
variable ftol equal 1.0e-5
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 100
|
||||
variable dmax equal 1.0e-1
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
create_box 1 myreg
|
||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 region myreg
|
||||
Created 512 atoms
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
512 atoms in group Si
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
velocity all create 1800 5287287 mom yes rot yes dist gaussian
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
||||
1 atoms in group del
|
||||
delete_atoms group del
|
||||
Deleted 1 atoms, new total = 511
|
||||
|
||||
pair_style edip
|
||||
pair_coeff * * Si.edip Si
|
||||
Reading potential file Si.edip with DATE: 2011-09-15
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
# equilibrate
|
||||
|
||||
run 500
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.12138
|
||||
ghost atom cutoff = 4.12138
|
||||
binsize = 2.06069, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair edip, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.955 | 2.955 | 2.955 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1802.3816 -2372.6618 0 -2253.8439 12260.967
|
||||
10 938.75954 -2315.5185 0 -2253.6329 558.21736
|
||||
20 534.27232 -2288.4721 0 -2253.2514 -2710.767
|
||||
30 1043.7796 -2320.9485 0 -2252.1398 8679.4385
|
||||
40 658.09162 -2293.8597 0 -2250.4765 2165.3752
|
||||
50 517.93008 -2283.7238 0 -2249.5805 -1124.9362
|
||||
60 1063.3594 -2318.4409 0 -2248.3414 7277.853
|
||||
70 868.14007 -2304.0133 0 -2246.7832 2050.2859
|
||||
80 826.37803 -2300.0187 0 -2245.5416 91.100098
|
||||
90 1289.6772 -2328.7151 0 -2243.6961 8180.7427
|
||||
100 976.36211 -2305.9371 0 -2241.5727 3614.0511
|
||||
110 810.81711 -2293.4705 0 -2240.0193 1359.3687
|
||||
120 1165.707 -2314.9026 0 -2238.056 7336.4505
|
||||
130 929.81248 -2297.139 0 -2235.8432 2793.8463
|
||||
140 804.47872 -2287.2074 0 -2234.174 704.92524
|
||||
150 1182.414 -2310.0266 0 -2232.0787 7822.2339
|
||||
160 979.92395 -2294.2969 0 -2229.6977 3206.7474
|
||||
170 830.14746 -2282.6079 0 -2227.8824 -296.87288
|
||||
180 1271.1133 -2309.4274 0 -2225.6322 7199.614
|
||||
190 1209.6006 -2302.6407 0 -2222.9006 5528.3799
|
||||
200 954.67692 -2283.6621 0 -2220.7272 47.02925
|
||||
210 1260.814 -2301.5582 0 -2218.442 4829.7879
|
||||
220 1274.9954 -2299.7285 0 -2215.6774 5518.0611
|
||||
230 1048.0074 -2282.398 0 -2213.3106 1754.4157
|
||||
240 1261.7071 -2294.1107 0 -2210.9356 5233.2714
|
||||
250 1272.6179 -2292.0793 0 -2208.1849 4795.934
|
||||
260 989.14207 -2271.0278 0 -2205.8209 -820.18098
|
||||
270 1212.0444 -2283.4212 0 -2203.52 3395.8631
|
||||
280 1391.9572 -2292.3809 0 -2200.6194 6666.2464
|
||||
290 1093.1205 -2270.0421 0 -2197.9807 206.94752
|
||||
300 1159.483 -2272.102 0 -2195.6657 778.53823
|
||||
310 1407.3528 -2285.6227 0 -2192.8463 5223.0487
|
||||
320 1236.7164 -2271.5389 0 -2190.0112 1865.3963
|
||||
330 1258.8275 -2270.4611 0 -2187.4758 2333.321
|
||||
340 1507.9519 -2283.9906 0 -2184.5824 6775.546
|
||||
350 1366.5116 -2271.7287 0 -2181.6446 3432.1175
|
||||
360 1305.2828 -2265.1091 0 -2179.0614 1498.4079
|
||||
370 1581.4334 -2280.4645 0 -2176.2122 6518.5598
|
||||
380 1589.5319 -2277.9428 0 -2173.1566 6334.6527
|
||||
390 1402.6782 -2262.9323 0 -2170.464 3278.3048
|
||||
400 1374.9587 -2258.5717 0 -2167.9307 3608.7293
|
||||
410 1295.7416 -2250.7752 0 -2165.3565 1877.5245
|
||||
420 1278.6727 -2247.1099 0 -2162.8164 1599.4189
|
||||
430 1508.1328 -2259.4245 0 -2160.0044 4300.2235
|
||||
440 1624.2957 -2263.9806 0 -2156.9026 4432.6267
|
||||
450 1597.3356 -2259.263 0 -2153.9623 3370.3829
|
||||
460 1772.0921 -2267.9105 0 -2151.0895 5788.3219
|
||||
470 1806.4047 -2267.304 0 -2148.221 5950.1188
|
||||
480 1593.0406 -2250.7469 0 -2145.7294 2518.0601
|
||||
490 1660.9766 -2252.894 0 -2143.398 4282.1654
|
||||
500 1714.2831 -2253.9295 0 -2140.9194 5740.0268
|
||||
Loop time of 0.109584 on 4 procs for 500 steps with 511 atoms
|
||||
|
||||
Performance: 394.220 ns/day, 0.061 hours/ns, 4562.726 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.074678 | 0.077817 | 0.084705 | 1.4 | 71.01
|
||||
Neigh | 0.0036662 | 0.0037943 | 0.0039661 | 0.2 | 3.46
|
||||
Comm | 0.013665 | 0.020312 | 0.023178 | 2.7 | 18.54
|
||||
Output | 0.0010247 | 0.0010931 | 0.0012922 | 0.3 | 1.00
|
||||
Modify | 0.0043213 | 0.0047521 | 0.0051889 | 0.6 | 4.34
|
||||
Other | | 0.001814 | | | 1.66
|
||||
|
||||
Nlocal: 127.75 ave 131 max 124 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 433.75 ave 441 max 426 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1979.5 ave 2040 max 1895 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 7918
|
||||
Ave neighs/atom = 15.4951
|
||||
Neighbor list builds = 19
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,92 @@
|
|||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Test of MEAM potential for SiC system
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.SiC
|
||||
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
128 atoms
|
||||
|
||||
pair_style edip/multi
|
||||
pair_coeff * * SiC.edip Si C
|
||||
Reading potential file SiC.edip with DATE: 2017-05-16
|
||||
|
||||
mass 1 28.085
|
||||
mass 2 12.001
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 1
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 50 dump.meam
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Si C
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Si C
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 1 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.94159
|
||||
ghost atom cutoff = 3.94159
|
||||
binsize = 1.97079, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair edip/multi, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.692 | 2.692 | 2.692 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -563.61621 0 -563.61621 -726147.34
|
||||
10 4224.3601 -633.24829 0 -563.90103 -312355.55
|
||||
20 4528.5661 -638.15183 0 -563.81071 -20091.291
|
||||
30 4817.3654 -642.92111 0 -563.83905 106625.5
|
||||
40 4619.4324 -639.6884 0 -563.85562 107180.42
|
||||
50 4783.0025 -642.26961 0 -563.75166 75134.335
|
||||
60 4525.145 -638.06177 0 -563.77681 71591.713
|
||||
70 4685.2578 -640.72377 0 -563.8104 63956.042
|
||||
80 4621.8393 -639.75912 0 -563.88682 18177.383
|
||||
90 4834.7702 -643.34582 0 -563.97805 15282.823
|
||||
100 4424.0589 -636.60208 0 -563.97656 47963.501
|
||||
Loop time of 0.0552888 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 156.270 ns/day, 0.154 hours/ns, 1808.685 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.051872 | 0.051872 | 0.051872 | 0.0 | 93.82
|
||||
Neigh | 0.0023525 | 0.0023525 | 0.0023525 | 0.0 | 4.25
|
||||
Comm | 0.0004518 | 0.0004518 | 0.0004518 | 0.0 | 0.82
|
||||
Output | 0.00014806 | 0.00014806 | 0.00014806 | 0.0 | 0.27
|
||||
Modify | 0.00024796 | 0.00024796 | 0.00024796 | 0.0 | 0.45
|
||||
Other | | 0.0002165 | | | 0.39
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 473 ave 473 max 473 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2376 ave 2376 max 2376 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2376
|
||||
Ave neighs/atom = 18.5625
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,92 @@
|
|||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Test of MEAM potential for SiC system
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.SiC
|
||||
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
128 atoms
|
||||
|
||||
pair_style edip/multi
|
||||
pair_coeff * * SiC.edip Si C
|
||||
Reading potential file SiC.edip with DATE: 2017-05-16
|
||||
|
||||
mass 1 28.085
|
||||
mass 2 12.001
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 1
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 50 dump.meam
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Si C
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Si C
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 1 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.94159
|
||||
ghost atom cutoff = 3.94159
|
||||
binsize = 1.97079, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair edip/multi, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.686 | 2.686 | 2.686 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -563.61621 0 -563.61621 -726147.34
|
||||
10 4224.3601 -633.24829 0 -563.90103 -312355.55
|
||||
20 4528.5661 -638.15183 0 -563.81071 -20091.291
|
||||
30 4817.3654 -642.92111 0 -563.83905 106625.5
|
||||
40 4619.4324 -639.6884 0 -563.85562 107180.42
|
||||
50 4783.0025 -642.26961 0 -563.75166 75134.335
|
||||
60 4525.145 -638.06177 0 -563.77681 71591.713
|
||||
70 4685.2578 -640.72377 0 -563.8104 63956.042
|
||||
80 4621.8393 -639.75912 0 -563.88682 18177.383
|
||||
90 4834.7702 -643.34582 0 -563.97805 15282.823
|
||||
100 4424.0589 -636.60208 0 -563.97656 47963.501
|
||||
Loop time of 0.020755 on 4 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 416.285 ns/day, 0.058 hours/ns, 4818.118 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.011816 | 0.013825 | 0.016871 | 1.6 | 66.61
|
||||
Neigh | 0.00061321 | 0.00066817 | 0.00074816 | 0.0 | 3.22
|
||||
Comm | 0.0023363 | 0.0054012 | 0.0075014 | 2.7 | 26.02
|
||||
Output | 0.00020909 | 0.00022268 | 0.00025558 | 0.0 | 1.07
|
||||
Modify | 8.3208e-05 | 9.346e-05 | 0.00010395 | 0.0 | 0.45
|
||||
Other | | 0.0005446 | | | 2.62
|
||||
|
||||
Nlocal: 32 ave 36 max 25 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
Nghost: 262.75 ave 273 max 255 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 594 ave 687 max 453 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 2376
|
||||
Ave neighs/atom = 18.5625
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -637,6 +637,8 @@
|
|||
/pair_eam_fs_opt.h
|
||||
/pair_edip.cpp
|
||||
/pair_edip.h
|
||||
/pair_edip_multi.cpp
|
||||
/pair_edip_multi.h
|
||||
/pair_eff_cut.cpp
|
||||
/pair_eff_cut.h
|
||||
/pair_eff_inline.h
|
||||
|
|
|
|||
|
|
@ -798,6 +798,9 @@ void PairEDIP::coeff(int narg, char **arg)
|
|||
}
|
||||
}
|
||||
|
||||
if (nelements != 1)
|
||||
error->all(FLERR,"Pair style edip only supports single element potentials");
|
||||
|
||||
// read potential file and initialize potential parameters
|
||||
|
||||
read_file(arg[2]);
|
||||
|
|
@ -836,7 +839,7 @@ void PairEDIP::coeff(int narg, char **arg)
|
|||
void PairEDIP::init_style()
|
||||
{
|
||||
if (force->newton_pair == 0)
|
||||
error->all(FLERR,"Pair style EDIP requires newton pair on");
|
||||
error->all(FLERR,"Pair style edip requires newton pair on");
|
||||
|
||||
// need a full neighbor list
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,784 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Environment Dependent Interatomic Potential
|
||||
|
||||
Contributing author: Chao Jiang
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <float.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "pair_edip_multi.h"
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "force.h"
|
||||
#include "comm.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define MAXLINE 1024
|
||||
#define DELTA 4
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairEDIPMulti::PairEDIPMulti(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
single_enable = 0;
|
||||
restartinfo = 0;
|
||||
one_coeff = 1;
|
||||
manybody_flag = 1;
|
||||
|
||||
nelements = 0;
|
||||
elements = NULL;
|
||||
nparams = maxparam = 0;
|
||||
params = NULL;
|
||||
elem2param = NULL;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
check if allocated, since class can be destructed when incomplete
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
PairEDIPMulti::~PairEDIPMulti()
|
||||
{
|
||||
if (elements)
|
||||
for (int i = 0; i < nelements; i++) delete [] elements[i];
|
||||
delete [] elements;
|
||||
memory->destroy(params);
|
||||
memory->destroy(elem2param);
|
||||
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
delete [] map;
|
||||
|
||||
//XXX deallocateGrids();
|
||||
deallocatePreLoops();
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairEDIPMulti::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,k,ii,jj,kk,inum,jnum;
|
||||
int itype,jtype,ktype,ijparam,ikparam,ijkparam;
|
||||
double xtmp,ytmp,ztmp,evdwl;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
register int preForceCoord_counter;
|
||||
|
||||
double zeta_i;
|
||||
double dzetair;
|
||||
double fpair;
|
||||
double costheta;
|
||||
double dpairZ,dtripleZ;
|
||||
|
||||
// eflag != 0 means compute energy contributions in this step
|
||||
// vflag != 0 means compute virial contributions in this step
|
||||
|
||||
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;//total number of atoms in the cell
|
||||
ilist = list->ilist;//list of atoms
|
||||
numneigh = list->numneigh;//number of near neighbors
|
||||
firstneigh = list->firstneigh;//list of neighbors
|
||||
|
||||
// loop over full neighbor list of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
zeta_i = 0.0;
|
||||
int numForceCoordPairs = 0;
|
||||
|
||||
i = ilist[ii];
|
||||
itype = map[type[i]];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
|
||||
// all the neighbors of atom i
|
||||
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
// pre-loop to compute environment coordination f(Z)
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
double delx, dely, delz, r_ij;
|
||||
|
||||
delx = x[j][0] - xtmp;
|
||||
dely = x[j][1] - ytmp;
|
||||
delz = x[j][2] - ztmp;
|
||||
r_ij = delx * delx + dely * dely + delz * delz;
|
||||
|
||||
jtype = map[type[j]];
|
||||
ijparam = elem2param[itype][jtype][jtype];
|
||||
if (r_ij > params[ijparam].cutsq) continue;
|
||||
|
||||
r_ij = sqrt(r_ij);
|
||||
|
||||
// zeta and its derivative dZ/dr
|
||||
|
||||
if (r_ij < params[ijparam].cutoffC) zeta_i += 1.0;
|
||||
else {
|
||||
double f, fdr;
|
||||
edip_fc(r_ij, ¶ms[ijparam], f, fdr);
|
||||
zeta_i += f;
|
||||
dzetair = -fdr / r_ij;
|
||||
|
||||
preForceCoord_counter=numForceCoordPairs*5;
|
||||
preForceCoord[preForceCoord_counter+0]=dzetair;
|
||||
preForceCoord[preForceCoord_counter+1]=delx;
|
||||
preForceCoord[preForceCoord_counter+2]=dely;
|
||||
preForceCoord[preForceCoord_counter+3]=delz;
|
||||
preForceCoord[preForceCoord_counter+4]=j;
|
||||
numForceCoordPairs++;
|
||||
}
|
||||
}
|
||||
|
||||
// two-body interactions
|
||||
|
||||
dpairZ=0;
|
||||
dtripleZ=0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
double dr_ij[3], r_ij, f_ij[3];
|
||||
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
dr_ij[0] = x[j][0] - xtmp;
|
||||
dr_ij[1] = x[j][1] - ytmp;
|
||||
dr_ij[2] = x[j][2] - ztmp;
|
||||
r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2];
|
||||
|
||||
jtype = map[type[j]];
|
||||
ijparam = elem2param[itype][jtype][jtype];
|
||||
if (r_ij > params[ijparam].cutsq) continue;
|
||||
|
||||
r_ij = sqrt(r_ij);
|
||||
|
||||
// potential energy and force
|
||||
// since pair i-j is different from pair j-i, double counting is
|
||||
// already considered in constructing the potential
|
||||
|
||||
double fdr, fdZ;
|
||||
edip_pair(r_ij, zeta_i, ¶ms[ijparam], evdwl, fdr, fdZ);
|
||||
fpair = -fdr / r_ij;
|
||||
dpairZ += fdZ;
|
||||
|
||||
f[i][0] -= fpair * dr_ij[0];
|
||||
f[i][1] -= fpair * dr_ij[1];
|
||||
f[i][2] -= fpair * dr_ij[2];
|
||||
|
||||
f[j][0] += fpair * dr_ij[0];
|
||||
f[j][1] += fpair * dr_ij[1];
|
||||
f[j][2] += fpair * dr_ij[2];
|
||||
|
||||
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, -dr_ij[0], -dr_ij[1], -dr_ij[2]);
|
||||
|
||||
// three-body Forces
|
||||
|
||||
for (kk = jj + 1; kk < jnum; kk++) {
|
||||
double dr_ik[3], r_ik, f_ik[3];
|
||||
|
||||
k = jlist[kk];
|
||||
k &= NEIGHMASK;
|
||||
ktype = map[type[k]];
|
||||
ikparam = elem2param[itype][ktype][ktype];
|
||||
ijkparam = elem2param[itype][jtype][ktype];
|
||||
|
||||
dr_ik[0] = x[k][0] - xtmp;
|
||||
dr_ik[1] = x[k][1] - ytmp;
|
||||
dr_ik[2] = x[k][2] - ztmp;
|
||||
r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
|
||||
|
||||
if (r_ik > params[ikparam].cutsq) continue;
|
||||
|
||||
r_ik = sqrt(r_ik);
|
||||
|
||||
costheta=vec3_dot(dr_ij, dr_ik) / r_ij / r_ik;
|
||||
|
||||
double v1, v2, v3, v4, v5, v6, v7;
|
||||
|
||||
edip_fcut3(r_ij, ¶ms[ijparam], v1, v2);
|
||||
edip_fcut3(r_ik, ¶ms[ikparam], v3, v4);
|
||||
edip_h(costheta, zeta_i, ¶ms[ijkparam], v5, v6, v7);
|
||||
|
||||
// potential energy and forces
|
||||
evdwl = v1 * v3 * v5;
|
||||
dtripleZ += v1 * v3 * v7;
|
||||
|
||||
double dri[3], drj[3], drk[3];
|
||||
double dhl, dfr;
|
||||
|
||||
dhl = v1 * v3 * v6;
|
||||
|
||||
costheta_d(dr_ij, r_ij, dr_ik, r_ik, dri, drj, drk);
|
||||
|
||||
f_ij[0] = -dhl * drj[0];
|
||||
f_ij[1] = -dhl * drj[1];
|
||||
f_ij[2] = -dhl * drj[2];
|
||||
f_ik[0] = -dhl * drk[0];
|
||||
f_ik[1] = -dhl * drk[1];
|
||||
f_ik[2] = -dhl * drk[2];
|
||||
|
||||
dfr = v2 * v3 * v5;
|
||||
fpair = -dfr / r_ij;
|
||||
|
||||
f_ij[0] += fpair * dr_ij[0];
|
||||
f_ij[1] += fpair * dr_ij[1];
|
||||
f_ij[2] += fpair * dr_ij[2];
|
||||
|
||||
dfr = v1 * v4 * v5;
|
||||
fpair = -dfr / r_ik;
|
||||
|
||||
f_ik[0] += fpair * dr_ik[0];
|
||||
f_ik[1] += fpair * dr_ik[1];
|
||||
f_ik[2] += fpair * dr_ik[2];
|
||||
|
||||
f[j][0] += f_ij[0];
|
||||
f[j][1] += f_ij[1];
|
||||
f[j][2] += f_ij[2];
|
||||
|
||||
f[k][0] += f_ik[0];
|
||||
f[k][1] += f_ik[1];
|
||||
f[k][2] += f_ik[2];
|
||||
|
||||
f[i][0] -= f_ij[0] + f_ik[0];
|
||||
f[i][1] -= f_ij[1] + f_ik[1];
|
||||
f[i][2] -= f_ij[2] + f_ik[2];
|
||||
|
||||
if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik);
|
||||
}
|
||||
}
|
||||
|
||||
// forces due to environment coordination f(Z)
|
||||
for (int idx = 0; idx < numForceCoordPairs; idx++) {
|
||||
double delx, dely, delz;
|
||||
|
||||
preForceCoord_counter = idx * 5;
|
||||
dzetair = preForceCoord[preForceCoord_counter+0];
|
||||
delx = preForceCoord[preForceCoord_counter+1];
|
||||
dely = preForceCoord[preForceCoord_counter+2];
|
||||
delz = preForceCoord[preForceCoord_counter+3];
|
||||
j = static_cast<int> (preForceCoord[preForceCoord_counter+4]);
|
||||
|
||||
dzetair *= (dpairZ + dtripleZ);
|
||||
|
||||
f[j][0] += dzetair * delx;
|
||||
f[j][1] += dzetair * dely;
|
||||
f[j][2] += dzetair * delz;
|
||||
|
||||
f[i][0] -= dzetair * delx;
|
||||
f[i][1] -= dzetair * dely;
|
||||
f[i][2] -= dzetair * delz;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, dzetair, -delx, -dely, -delz);
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
double sqr(double x)
|
||||
{
|
||||
return x * x;
|
||||
}
|
||||
|
||||
//pair Vij, partial derivatives dVij(r,Z)/dr and dVij(r,Z)/dZ
|
||||
void PairEDIPMulti::edip_pair(double r, double z, Param *param, double &eng,
|
||||
double &fdr, double &fZ)
|
||||
{
|
||||
double A = param->A;
|
||||
double B = param->B;
|
||||
double rho = param->rho;
|
||||
double beta = param->beta;
|
||||
double v1,v2,v3,v4;
|
||||
|
||||
v1 = pow(B / r, rho);
|
||||
v2 = exp(-beta * z * z);
|
||||
edip_fcut2(r, param, v3, v4);
|
||||
|
||||
eng = A * (v1 - v2) * v3;
|
||||
fdr = A * (v1 - v2) * v4 + A * (-rho * v1 / r) * v3;
|
||||
fZ = A * (2 * beta * z * v2) * v3;
|
||||
}
|
||||
|
||||
//function fc(r) in calculating coordination Z and derivative fc'(r)
|
||||
void PairEDIPMulti::edip_fc(double r, Param *param, double &f, double &fdr)
|
||||
{
|
||||
double a = param->cutoffA;
|
||||
double c = param->cutoffC;
|
||||
double alpha = param->alpha;
|
||||
double x;
|
||||
double v1, v2, v3;
|
||||
|
||||
if(r < c + 1E-6)
|
||||
{
|
||||
f=1.0;
|
||||
fdr=0.0;
|
||||
return;
|
||||
}
|
||||
|
||||
if(r > a - 1E-6)
|
||||
{
|
||||
f=0.0;
|
||||
fdr=0.0;
|
||||
return;
|
||||
}
|
||||
|
||||
x = (a - c) / (r - c);
|
||||
v1 = x * x * x;
|
||||
v2 = 1.0 / (1.0 - v1);
|
||||
|
||||
f = exp(alpha * v2);
|
||||
fdr = (3.0 * x * v1 / (a - c)) * (-alpha * v2 * v2) * f;
|
||||
}
|
||||
|
||||
//cut-off function for Vij and its derivative fcut2'(r)
|
||||
void PairEDIPMulti::edip_fcut2(double r, Param *param, double &f, double &fdr)
|
||||
{
|
||||
double sigma = param->sigma;
|
||||
double a = param->cutoffA;
|
||||
double v1;
|
||||
|
||||
if(r > a - 1E-6)
|
||||
{
|
||||
f=0.0;
|
||||
fdr=0.0;
|
||||
return;
|
||||
}
|
||||
|
||||
v1 = 1.0 / (r - a);
|
||||
f = exp(sigma * v1);
|
||||
fdr = (-sigma * v1 * v1) * f;
|
||||
}
|
||||
|
||||
//function tau(Z) and its derivative tau'(Z)
|
||||
void PairEDIPMulti::edip_tau(double z, Param *param, double &f, double &fdZ)
|
||||
{
|
||||
double u1 = param->u1;
|
||||
double u2 = param->u2;
|
||||
double u3 = param->u3;
|
||||
double u4 = param->u4;
|
||||
double v1, v2;
|
||||
|
||||
v1 = exp(-u4 * z);
|
||||
v2 = exp(-2.0 * u4 * z);
|
||||
|
||||
f = u1 + u2 * u3 * v1 - u2 * v2;
|
||||
fdZ = -u2 * u3 * u4 * v1 + 2.0 * u2 * u4 * v2;
|
||||
}
|
||||
|
||||
//function h(l,Z) and its partial derivatives dh(l,Z)/dl and dh(l,Z)/dZ
|
||||
void PairEDIPMulti::edip_h(double l, double z, Param *param, double &f,
|
||||
double &fdl, double &fdZ)
|
||||
{
|
||||
double lambda = param->lambda;
|
||||
double eta = param->eta;
|
||||
double Q0 = param->Q0;
|
||||
double mu = param->mu;
|
||||
double Q, QdZ, Tau, TaudZ;
|
||||
double u2, du2l, du2Z;
|
||||
double v1, v2, v3;
|
||||
|
||||
//function Q(Z)
|
||||
Q = Q0 * exp(-mu * z);
|
||||
//derivative Q'(Z)
|
||||
QdZ= -mu * Q;
|
||||
|
||||
edip_tau(z, param, Tau, TaudZ);
|
||||
|
||||
v1 = sqr(l + Tau);
|
||||
u2 = Q * v1;
|
||||
v2 = exp(-u2);
|
||||
|
||||
f = lambda * (1 - v2 + eta * u2);
|
||||
|
||||
//df/du2
|
||||
v3 = lambda * (v2 + eta);
|
||||
|
||||
//du2/dl
|
||||
du2l = Q * 2 * (l + Tau);
|
||||
fdl = v3 * du2l;
|
||||
|
||||
//du2/dZ
|
||||
du2Z = QdZ * v1 + Q * 2 * (l + Tau) * TaudZ;
|
||||
fdZ = v3 * du2Z;
|
||||
}
|
||||
|
||||
//cut-off function for Vijk and its derivative fcut3'(r)
|
||||
void PairEDIPMulti::edip_fcut3(double r, Param *param, double &f, double &fdr)
|
||||
{
|
||||
double gamma = param->gamma;
|
||||
double a = param->cutoffA;
|
||||
double v1;
|
||||
|
||||
if(r > a - 1E-6)
|
||||
{
|
||||
f=0.0;
|
||||
fdr=0.0;
|
||||
return;
|
||||
}
|
||||
|
||||
v1 = 1.0 / (r - a);
|
||||
f = exp(gamma * v1);
|
||||
fdr = (-gamma * v1 * v1) * f;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
pre-calculated structures
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairEDIPMulti::allocatePreLoops(void)
|
||||
{
|
||||
int nthreads = comm->nthreads;
|
||||
|
||||
memory->create(preForceCoord,5*nthreads*leadDimInteractionList,"edip:preForceCoord");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
deallocate preLoops
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairEDIPMulti::deallocatePreLoops(void)
|
||||
{
|
||||
memory->destroy(preForceCoord);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairEDIPMulti::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
|
||||
map = new int[n+1];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairEDIPMulti::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairEDIPMulti::coeff(int narg, char **arg)
|
||||
{
|
||||
int i,j,n;
|
||||
|
||||
if (!allocated) allocate();
|
||||
|
||||
if (narg != 3 + atom->ntypes)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
|
||||
// insure I,J args are * *
|
||||
|
||||
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
|
||||
// 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 potential file and initialize potential parameters
|
||||
|
||||
read_file(arg[2]);
|
||||
setup();
|
||||
|
||||
// clear setflag since coeff() called once with I,J = * *
|
||||
|
||||
n = atom->ntypes;
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
// set setflag i,j for type pairs where both are mapped to elements
|
||||
|
||||
int count = 0;
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
if (map[i] >= 0 && map[j] >= 0) {
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
|
||||
// allocate tables and internal structures
|
||||
|
||||
allocatePreLoops();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairEDIPMulti::init_style()
|
||||
{
|
||||
if (atom->tag_enable == 0)
|
||||
error->all(FLERR,"Pair style edip/multi requires atom IDs");
|
||||
if (force->newton_pair == 0)
|
||||
error->all(FLERR,"Pair style edip/multi requires newton pair on");
|
||||
|
||||
// need a full neighbor list
|
||||
|
||||
int irequest = neighbor->request(this,instance_me);
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
neighbor->requests[irequest]->full = 1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairEDIPMulti::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
|
||||
|
||||
return cutmax;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairEDIPMulti::read_file(char *file)
|
||||
{
|
||||
int params_per_line = 20;
|
||||
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(file);
|
||||
if (fp == NULL) {
|
||||
char str[128];
|
||||
sprintf(str,"Cannot open EDIP potential file %s",file);
|
||||
error->one(FLERR,str);
|
||||
}
|
||||
}
|
||||
|
||||
// read each set of params from potential file
|
||||
// one set of params can span multiple lines
|
||||
// store params if all 3 element tags are in element list
|
||||
|
||||
int n,nwords,ielement,jelement,kelement;
|
||||
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,"Incorrect format in EDIP 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,kelement = 1st args
|
||||
// if all 3 args are in element list, then parse this line
|
||||
// else skip to next entry in file
|
||||
|
||||
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;
|
||||
for (kelement = 0; kelement < nelements; kelement++)
|
||||
if (strcmp(words[2],elements[kelement]) == 0) break;
|
||||
if (kelement == 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].kelement = kelement;
|
||||
params[nparams].A = atof(words[3]);
|
||||
params[nparams].B = atof(words[4]);
|
||||
params[nparams].cutoffA = atof(words[5]);
|
||||
params[nparams].cutoffC = atof(words[6]);
|
||||
params[nparams].alpha = atof(words[7]);
|
||||
params[nparams].beta = atof(words[8]);
|
||||
params[nparams].eta = atof(words[9]);
|
||||
params[nparams].gamma = atof(words[10]);
|
||||
params[nparams].lambda = atof(words[11]);
|
||||
params[nparams].mu = atof(words[12]);
|
||||
params[nparams].rho = atof(words[13]);
|
||||
params[nparams].sigma = atof(words[14]);
|
||||
params[nparams].Q0 = atof(words[15]);
|
||||
params[nparams].u1 = atof(words[16]);
|
||||
params[nparams].u2 = atof(words[17]);
|
||||
params[nparams].u3 = atof(words[18]);
|
||||
params[nparams].u4 = atof(words[19]);
|
||||
|
||||
if (params[nparams].A < 0.0 || params[nparams].B < 0.0 ||
|
||||
params[nparams].cutoffA < 0.0 || params[nparams].cutoffC < 0.0 ||
|
||||
params[nparams].alpha < 0.0 || params[nparams].beta < 0.0 ||
|
||||
params[nparams].eta < 0.0 || params[nparams].gamma < 0.0 ||
|
||||
params[nparams].lambda < 0.0 || params[nparams].mu < 0.0 ||
|
||||
params[nparams].rho < 0.0 || params[nparams].sigma < 0.0)
|
||||
error->all(FLERR,"Illegal EDIP parameter");
|
||||
|
||||
nparams++;
|
||||
}
|
||||
|
||||
delete [] words;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairEDIPMulti::setup()
|
||||
{
|
||||
int i,j,k,m,n;
|
||||
double rtmp;
|
||||
|
||||
// set elem2param for all triplet combinations
|
||||
// must be a single exact match to lines read from file
|
||||
// do not allow for ACB in place of ABC
|
||||
|
||||
memory->destroy(elem2param);
|
||||
memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");
|
||||
|
||||
for (i = 0; i < nelements; i++)
|
||||
for (j = 0; j < nelements; j++)
|
||||
for (k = 0; k < nelements; k++) {
|
||||
n = -1;
|
||||
for (m = 0; m < nparams; m++) {
|
||||
if (i == params[m].ielement && j == params[m].jelement &&
|
||||
k == params[m].kelement) {
|
||||
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][k] = n;
|
||||
}
|
||||
|
||||
// set cutoff square
|
||||
|
||||
for (m = 0; m < nparams; m++) {
|
||||
params[m].cutsq = params[m].cutoffA*params[m].cutoffA;
|
||||
}
|
||||
|
||||
// set cutmax to max of all params
|
||||
|
||||
cutmax = 0.0;
|
||||
for (m = 0; m < nparams; m++) {
|
||||
rtmp = sqrt(params[m].cutsq);
|
||||
if (rtmp > cutmax) cutmax = rtmp;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,113 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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(edip/multi,PairEDIPMulti)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_EDIP_MULTI_H
|
||||
#define LMP_PAIR_EDIP_MULTI_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairEDIPMulti : public Pair {
|
||||
public:
|
||||
PairEDIPMulti(class LAMMPS *);
|
||||
virtual ~PairEDIPMulti();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
double init_one(int, int);
|
||||
void init_style();
|
||||
|
||||
protected:
|
||||
struct Param {
|
||||
double A, B;//coefficients for pair interaction I-J
|
||||
double cutoffA;//cut-off distance for pair interaction I-J
|
||||
double cutoffC;//lower cut-off distance for calculating Z_I
|
||||
double alpha;//coefficient for calculating Z_I
|
||||
double beta;//attractive term for pair I-J
|
||||
double sigma;//cut-off coefficient for pair I-J
|
||||
double rho;//pair I-J
|
||||
double gamma;//coefficient for three-body interaction I-J-K
|
||||
double eta, lambda;//coefficients for function h(l,Z)
|
||||
double mu, Q0;//coefficients for function Q(Z)
|
||||
double u1, u2, u3, u4;//coefficients for function tau(Z)
|
||||
double cutsq;
|
||||
int ielement,jelement,kelement;
|
||||
};
|
||||
|
||||
double *preForceCoord;
|
||||
|
||||
double cutmax; // max cutoff for all elements
|
||||
int nelements; // # of unique elements
|
||||
char **elements; // names of unique elements
|
||||
int ***elem2param; // mapping from element triplets to parameters
|
||||
int *map; // mapping from atom types to elements
|
||||
int nparams; // # of stored parameter sets
|
||||
int maxparam; // max # of parameter sets
|
||||
Param *params; // parameter set for an I-J-K interaction
|
||||
|
||||
// max number of interaction per atom for f(Z) environment potential
|
||||
|
||||
static const int leadDimInteractionList = 64;
|
||||
|
||||
void allocate();
|
||||
void allocatePreLoops(void);
|
||||
void deallocatePreLoops(void);
|
||||
|
||||
void read_file(char *);
|
||||
void setup();
|
||||
|
||||
void edip_pair(double, double, Param *, double &, double &, double &);
|
||||
void edip_fc(double, Param *, double &, double &);
|
||||
void edip_fcut2(double, Param *, double &, double &);
|
||||
void edip_tau(double, Param *, double &, double &);
|
||||
void edip_h(double, double, Param *, double &, double &, double &);
|
||||
void edip_fcut3(double, Param *, double &, double &);
|
||||
|
||||
double vec3_dot(double x[3], double y[3])
|
||||
{
|
||||
return x[0]*y[0] + x[1]*y[1] + x[2]*y[2];
|
||||
}
|
||||
|
||||
void vec3_add(double k1, double x[3], double k2, double y[3], double *z)
|
||||
{
|
||||
z[0] = k1 * x[0] + k2 * y[0];
|
||||
z[1] = k1 * x[1] + k2 * y[1];
|
||||
z[2] = k1 * x[2] + k2 * y[2];
|
||||
}
|
||||
|
||||
//dr_ij=r_j - r_i
|
||||
//dr_ik=r_k - r_i
|
||||
void costheta_d(double *dr_ij, double r_ij, double *dr_ik, double r_ik,
|
||||
double *dri, double *drj, double *drk)
|
||||
{
|
||||
double costheta;
|
||||
|
||||
costheta = vec3_dot(dr_ij, dr_ik) / r_ij / r_ik;
|
||||
vec3_add(1 / r_ij / r_ik, dr_ik, -costheta / r_ij / r_ij, dr_ij, drj);
|
||||
vec3_add(1 / r_ij / r_ik, dr_ij, -costheta / r_ik / r_ik, dr_ik, drk);
|
||||
vec3_add(-1, drj, -1, drk, dri);
|
||||
}
|
||||
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue