186 lines
12 KiB
Groff
186 lines
12 KiB
Groff
LAMMPS (27 Jun 2024)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# Created 2011-01-07
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# General parameters
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variable sname index Si2H6
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units electron
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newton on
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boundary f f f
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atom_style electron
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read_data data.${sname}
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read_data data.Si2H6
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Reading data file ...
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orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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22 atoms
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read_data CPU = 0.001 seconds
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pair_style eff/cut 1000.0 ecp 1 Si
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pair_coeff * *
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compute energies all pair eff/cut
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variable eke equal c_energies[1]
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variable epauli equal c_energies[2]
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variable estatics equal c_energies[3]
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variable errestrain equal c_energies[4]
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comm_modify vel yes
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compute peratom all stress/atom NULL
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compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
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variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
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compute effTemp all temp/eff
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compute effPress all pressure effTemp
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thermo 2
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thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
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thermo_modify temp effTemp press effPress
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# Minimization
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min_style cg
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#dump 1 all xyz 2 ${sname}.min.xyz
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compute 1 all property/atom spin eradius erforce
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#dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
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min_modify line quadratic
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minimize 0 1.0e-5 1000 10000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- EFF package: doi:10.1002/jcc.21637
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@Article{Jaramillo-Botero11,
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author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
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title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
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journal = {J.~Comp.\ Chem.},
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year = 2011,
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volume = 32,
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number = 3,
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pages = {497--512}
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}
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- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
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@Article{Gissinger24,
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author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
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title = {Type Label Framework for Bonded Force Fields in LAMMPS},
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journal = {J. Phys. Chem. B},
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year = 2024,
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volume = 128,
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number = 13,
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pages = {3282–-3297}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1002
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ghost atom cutoff = 1002
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binsize = 501, bins = 4 4 4
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair eff/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 6.113 | 6.113 | 6.113 Mbytes
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Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
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0 -8.5010994 -8.5010994 0 5.4885963 1.6463577 -15.636053 0 0 3948.0425 3948.0425
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2 -8.67691 -8.67691 0 5.5258385 1.589403 -15.792152 0 0 3880.1721 3880.1721
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4 -8.848848 -8.848848 0 5.5663359 1.5311327 -15.946317 0 0 3788.6697 3788.6697
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6 -9.0177692 -9.0177692 0 5.6106795 1.4710658 -16.099514 0 0 3671.1737 3671.1737
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8 -9.185303 -9.185303 0 5.6598348 1.4083124 -16.25345 0 0 3523.4287 3523.4287
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10 -9.3547798 -9.3547798 0 5.7155927 1.3410774 -16.41145 0 0 3336.9891 3336.9891
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12 -9.5342746 -9.5342746 0 5.7820671 1.2650232 -16.581365 0 0 3091.6153 3091.6153
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14 -9.753773 -9.753773 0 5.8743943 1.1639 -16.792067 0 0 2711.1247 2711.1247
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16 -10.097143 -10.097143 0 6.0386279 0.98467639 -17.120448 0 0 1912.0559 1912.0559
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18 -10.206415 -10.206415 0 6.0972556 0.92111471 -17.224785 0 0 1604.9272 1604.9272
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20 -10.28471 -10.28471 0 6.1543746 0.86786676 -17.306951 0 0 1325.3681 1325.3681
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22 -10.343227 -10.343227 0 6.2122367 0.82042286 -17.375887 0 0 1062.6534 1062.6534
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24 -10.386164 -10.386164 0 6.2699963 0.77763016 -17.43379 0 0 820.84479 820.84479
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26 -10.416263 -10.416263 0 6.3255676 0.73934069 -17.481171 0 0 608.7375 608.7375
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28 -10.436521 -10.436521 0 6.3761026 0.70612619 -17.51875 0 0 434.68899 434.68899
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30 -10.450247 -10.450247 0 6.4147546 0.68147364 -17.546475 0 0 302.62232 302.62232
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32 -10.456683 -10.456683 0 6.416721 0.67361461 -17.547019 0 0 223.07929 223.07929
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34 -10.458069 -10.458069 0 6.3974543 0.66990042 -17.525424 0 0 164.78914 164.78914
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36 -10.458558 -10.458558 0 6.3763802 0.66472241 -17.49966 0 0 100.618 100.618
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38 -10.459231 -10.459231 0 6.3293189 0.66038284 -17.448933 0 0 -3.1075375 -3.1075375
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40 -10.459346 -10.459346 0 6.3132377 0.65807627 -17.43066 0 0 -29.981737 -29.981737
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42 -10.459366 -10.459366 0 6.3179452 0.65719131 -17.434503 0 0 -45.500522 -45.500522
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44 -10.459413 -10.459413 0 6.2985544 0.66239121 -17.420359 0 0 14.638842 14.638842
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46 -10.459499 -10.459499 0 6.3129457 0.65696218 -17.429407 0 0 -46.926115 -46.926115
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48 -10.459522 -10.459522 0 6.3120038 0.65909539 -17.430621 0 0 -27.058486 -27.058486
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50 -10.459532 -10.459532 0 6.3113769 0.65958039 -17.430489 0 0 -16.067028 -16.067028
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52 -10.459536 -10.459536 0 6.3181474 0.65939215 -17.437076 0 0 -15.311525 -15.311525
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54 -10.459539 -10.459539 0 6.3204818 0.66055005 -17.440571 0 0 -0.1004938 -0.1004938
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56 -10.459539 -10.459539 0 6.320264 0.6605463 -17.440349 0 0 -0.12138436 -0.12138436
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58 -10.459539 -10.459539 0 6.3204128 0.66045741 -17.440409 0 0 -1.2175176 -1.2175176
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60 -10.459539 -10.459539 0 6.3201688 0.66048114 -17.440189 0 0 -0.80979946 -0.80979946
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62 -10.459539 -10.459539 0 6.3201369 0.6605348 -17.440211 0 0 -0.85945162 -0.85945162
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64 -10.459539 -10.459539 0 6.3201036 0.66047761 -17.44012 0 0 -0.95534903 -0.95534903
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66 -10.459539 -10.459539 0 6.3201475 0.66049137 -17.440178 0 0 -0.89220297 -0.89220297
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68 -10.459539 -10.459539 0 6.3201605 0.6605388 -17.440238 0 0 -0.44631358 -0.44631358
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70 -10.459539 -10.459539 0 6.3202978 0.66049413 -17.440331 0 0 -0.72919322 -0.72919322
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72 -10.459539 -10.459539 0 6.3202928 0.66056005 -17.440392 0 0 -0.049401694 -0.049401694
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74 -10.459539 -10.459539 0 6.3204368 0.66055883 -17.440535 0 0 -0.025056381 -0.025056381
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76 -10.459539 -10.459539 0 6.3204403 0.66054902 -17.440528 0 0 -0.010774653 -0.010774653
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78 -10.459539 -10.459539 0 6.3203876 0.66056716 -17.440494 0 0 0.087250755 0.087250755
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80 -10.459539 -10.459539 0 6.3203944 0.66054525 -17.440479 0 0 -0.13822694 -0.13822694
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82 -10.459539 -10.459539 0 6.3203511 0.66055332 -17.440443 0 0 -0.043784806 -0.043784806
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84 -10.459539 -10.459539 0 6.32037 0.66054937 -17.440458 0 0 -0.10833935 -0.10833935
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86 -10.459539 -10.459539 0 6.3203586 0.66055472 -17.440452 0 0 -0.047719128 -0.047719128
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88 -10.459539 -10.459539 0 6.3203709 0.66055294 -17.440463 0 0 -0.055818341 -0.055818341
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Loop time of 0.00213866 on 4 procs for 88 steps with 22 atoms
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95.0% CPU use with 4 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = force tolerance
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Energy initial, next-to-last, final =
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-8.50109938620958 -10.4595390706543 -10.459539070672
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Force two-norm initial, final = 3.2945156 4.7997573e-06
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Force max component initial, final = 1.8019385 2.1386971e-06
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Final line search alpha, max atom move = 1 2.1386971e-06
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Iterations, force evaluations = 88 127
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.00027642 | 0.00052972 | 0.00096856 | 0.0 | 24.77
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00035997 | 0.00081245 | 0.0010746 | 0.0 | 37.99
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Output | 0.00037064 | 0.00039193 | 0.00045231 | 0.0 | 18.33
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.0004046 | | | 18.92
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Nlocal: 5.5 ave 7 max 3 min
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Histogram: 1 0 0 0 0 0 0 2 0 1
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Nghost: 16.5 ave 19 max 15 min
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Histogram: 1 0 2 0 0 0 0 0 0 1
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Neighs: 57.75 ave 109 max 29 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Total # of neighbors = 231
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Ave neighs/atom = 10.5
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Neighbor list builds = 0
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Dangerous builds = 0
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#undump 1
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#undump 2
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Total wall time: 0:00:00
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