fixed lost atoms error with smaller time step for energy conservation and added reference log files for PACKAGES/eff/Auger-Adamantane
This commit is contained in:
Trung Nguyen
@ -16,7 +16,7 @@ comm_modify vel yes
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compute effTemp all temp/eff
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thermo 1000
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thermo_style custom step pe temp press
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thermo_style custom step pe temp etotal press
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thermo_modify temp effTemp
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# Minimization
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@ -36,7 +36,7 @@ undump 2
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#velocity all create 300.0 4928459 dist uniform
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# NVE
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timestep 0.001
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timestep 0.0001
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fix 1 all nve/eff
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dump 1 all xyz 1000 ${sname}.nve.xyz
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@ -0,0 +1,367 @@
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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
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using 1 OpenMP thread(s) per MPI task
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variable sname index adamantane_ionized
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units electron
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newton on
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boundary f f f
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atom_style electron
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read_data data.${sname}
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read_data data.adamantane_ionized
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Reading data file ...
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orthogonal box = (-50 -50 -50) to (50 50 50)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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101 atoms
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read_data CPU = 0.038 seconds
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pair_style eff/cut 100.0
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pair_coeff * *
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comm_modify vel yes
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compute effTemp all temp/eff
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thermo 1000
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thermo_style custom step pe temp etotal press
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thermo_modify temp effTemp
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# Minimization
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min_style cg
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dump 1 all xyz 500 ${sname}.min.xyz
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dump 1 all xyz 500 adamantane_ionized.min.xyz
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compute 1 all property/atom spin eradius erforce
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dump 2 all custom 500 ${sname}.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
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dump 2 all custom 500 adamantane_ionized.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
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min_modify line quadratic
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minimize 0.0 1.0e-5 10000 100000
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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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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 = 102
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ghost atom cutoff = 102
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binsize = 51, bins = 2 2 2
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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) = 5.222 | 5.222 | 5.222 Mbytes
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Step PotEng Temp TotEng Press
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0 -320.50186 0 -320.50186 -45590269
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571 -324.30072 0 -324.30072 21193099
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Loop time of 2.61846 on 1 procs for 571 steps with 101 atoms
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = linesearch alpha is zero
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Energy initial, next-to-last, final =
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-320.501859657303 -324.30071870307 -324.30071870307
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Force two-norm initial, final = 2.8135352 2.2777398
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Force max component initial, final = 1.7194878 2.093044
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Final line search alpha, max atom move = 2.2781994e-09 4.7683716e-09
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Iterations, force evaluations = 571 5621
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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 | 2.602 | 2.602 | 2.602 | 0.0 | 99.37
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Neigh | 2.5097e-05 | 2.5097e-05 | 2.5097e-05 | 0.0 | 0.00
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Comm | 0.00046417 | 0.00046417 | 0.00046417 | 0.0 | 0.02
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Output | 0.00029579 | 0.00029579 | 0.00029579 | 0.0 | 0.01
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.0157 | | | 0.60
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Nlocal: 101 ave 101 max 101 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 5050 ave 5050 max 5050 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 5050
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Ave neighs/atom = 50
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Neighbor list builds = 1
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Dangerous builds = 0
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undump 1
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undump 2
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#restart timestep
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# set velocities for nve
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#velocity all create 300.0 4928459 dist uniform
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# NVE
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timestep 0.0001
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fix 1 all nve/eff
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dump 1 all xyz 1000 ${sname}.nve.xyz
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dump 1 all xyz 1000 adamantane_ionized.nve.xyz
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dump 2 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
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dump 2 all custom 1000 adamantane_ionized.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
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#restart 1000 ${sname}.nve.restart1 ${sname}.nve.restart2
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run 200000
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Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 4.097 | 4.097 | 4.097 Mbytes
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Step PotEng Temp TotEng Press
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571 -324.30072 0 -324.30072 21193099
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1000 -324.00833 75606.318 -315.02966 1.9184325e+08
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2000 -322.45879 62558.11 -315.02966 1.4564261e+08
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3000 -322.01495 58820.681 -315.02966 1.3051251e+08
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4000 -321.3178 52950.225 -315.02966 75989118
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5000 -320.89488 49388.959 -315.02966 55413771
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6000 -320.97564 50069.086 -315.02966 67105302
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7000 -320.9772 50082.172 -315.02966 90728737
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8000 -320.76927 48331.305 -315.02966 1.1054849e+08
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9000 -320.40821 45290.936 -315.02966 1.1325434e+08
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10000 -320.10216 42713.788 -315.02966 1.0766253e+08
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11000 -320.00263 41875.679 -315.02966 1.0831982e+08
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12000 -319.92006 41180.36 -315.02966 1.0888686e+08
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13000 -319.85913 40667.331 -315.02966 1.0763265e+08
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14000 -319.86056 40679.317 -315.02966 1.1159571e+08
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15000 -319.79071 40091.129 -315.02966 1.1261281e+08
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16000 -319.7393 39658.231 -315.02966 1.0983394e+08
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17000 -319.74963 39745.211 -315.02966 1.12573e+08
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18000 -319.70347 39356.518 -315.02966 1.1249278e+08
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19000 -319.68924 39236.684 -315.02966 1.084432e+08
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20000 -319.74747 39727.04 -315.02966 1.109151e+08
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21000 -319.76264 39854.793 -315.02966 1.0990745e+08
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22000 -319.7997 40166.86 -315.02966 1.0446598e+08
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23000 -319.91061 41100.771 -315.02966 1.0605289e+08
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24000 -319.98762 41749.299 -315.02966 1.0312843e+08
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25000 -320.06842 42429.669 -315.02966 96790253
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26000 -320.2321 43807.92 -315.02966 98941422
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27000 -320.43008 45475.083 -315.02966 99172853
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28000 -320.75368 48199.998 -315.02966 1.0304506e+08
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29000 -321.43727 53956.239 -315.02966 1.2359013e+08
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30000 -322.86003 65936.838 -315.02966 1.6426506e+08
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31000 -325.85698 91173.108 -315.02966 2.3460809e+08
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32000 -323.96663 75255.122 -315.02967 1.4386254e+08
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33000 -324.31173 78161.078 -315.02966 1.9611146e+08
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34000 -321.81048 57098.954 -315.02966 1.3183304e+08
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35000 -321.11553 51247.011 -315.02966 1.1860383e+08
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36000 -320.7006 47753.061 -315.02966 1.0988072e+08
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37000 -320.42875 45463.834 -315.02966 1.0486186e+08
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38000 -320.37522 45013.139 -315.02966 1.0667734e+08
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39000 -320.16625 43253.419 -315.02966 1.0141734e+08
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40000 -320.09034 42614.247 -315.02966 1.0082579e+08
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41000 -320.21558 43668.822 -315.02966 1.0548768e+08
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42000 -320.19431 43489.747 -315.02966 1.0242614e+08
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43000 -320.35932 44879.232 -315.02966 1.0646487e+08
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44000 -320.67457 47533.878 -315.02966 1.1366565e+08
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45000 -320.83512 48885.757 -315.02966 1.111537e+08
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46000 -321.16647 51675.946 -315.02966 1.1302624e+08
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||||
47000 -321.38122 53484.331 -315.02966 1.0507686e+08
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48000 -321.06774 50844.617 -315.02966 74672082
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49000 -322.49756 62884.615 -315.02966 1.044115e+08
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||||
50000 -325.97731 92186.422 -315.02966 2.2498335e+08
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51000 -320.66106 47420.072 -315.02966 34605338
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52000 -323.2278 69033.706 -315.02966 1.4817693e+08
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||||
53000 -322.82489 65640.939 -315.02966 1.6065307e+08
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||||
54000 -321.95574 58322.133 -315.02966 1.3860454e+08
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||||
55000 -321.41375 53758.198 -315.02966 1.1831887e+08
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56000 -320.82121 48768.626 -315.02966 97374067
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57000 -320.39876 45211.333 -315.02966 85881342
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||||
58000 -320.26394 44076.088 -315.02966 80873235
|
||||
59000 -320.06828 42428.515 -315.02966 75885502
|
||||
60000 -320.12912 42940.809 -315.02966 83005858
|
||||
61000 -320.34086 44723.765 -315.02966 90748569
|
||||
62000 -320.3942 45172.977 -315.02966 93992240
|
||||
63000 -320.63122 47168.811 -315.02966 1.0726441e+08
|
||||
64000 -320.86235 49115.084 -315.02966 1.1515294e+08
|
||||
65000 -320.95075 49859.439 -315.02966 1.1705259e+08
|
||||
66000 -321.28995 52715.744 -315.02966 1.3144493e+08
|
||||
67000 -321.69035 56087.363 -315.02966 1.4188253e+08
|
||||
68000 -322.28755 61116.149 -315.02966 1.5220904e+08
|
||||
69000 -323.31574 69774.213 -315.02966 1.5914511e+08
|
||||
70000 -322.98352 66976.685 -315.02966 1.0382488e+08
|
||||
71000 -323.42006 70652.696 -315.02966 1.1257889e+08
|
||||
72000 -322.38839 61965.354 -315.02966 1.213394e+08
|
||||
73000 -321.62733 55556.719 -315.02966 1.2062207e+08
|
||||
74000 -321.10333 51144.304 -315.02966 1.0628135e+08
|
||||
75000 -320.84916 49004.001 -315.02966 1.0188029e+08
|
||||
76000 -320.51651 46202.858 -315.02966 94118114
|
||||
77000 -320.47427 45847.17 -315.02966 91437540
|
||||
78000 -320.52773 46297.312 -315.02966 95165197
|
||||
79000 -320.43972 45556.265 -315.02966 95366722
|
||||
80000 -320.58645 46791.792 -315.02966 1.0182068e+08
|
||||
81000 -320.75509 48211.862 -315.02966 1.0907204e+08
|
||||
82000 -320.77091 48345.056 -315.02966 1.1257336e+08
|
||||
83000 -321.02219 50461.057 -315.02966 1.2376776e+08
|
||||
84000 -321.20064 51963.656 -315.02966 1.2909546e+08
|
||||
85000 -321.2856 52679.138 -315.02966 1.3104703e+08
|
||||
86000 -321.67229 55935.33 -315.02966 1.4072532e+08
|
||||
87000 -322.11917 59698.307 -315.02966 1.4404812e+08
|
||||
88000 -324.23523 77516.896 -315.02966 1.9731217e+08
|
||||
89000 -320.62579 47123.095 -315.02966 75893884
|
||||
90000 -324.35107 78492.385 -315.02966 2.1044355e+08
|
||||
91000 -322.47803 62720.127 -315.02966 1.5538903e+08
|
||||
92000 -321.71623 56305.3 -315.02966 1.3227964e+08
|
||||
93000 -321.22259 52148.564 -315.02966 1.1511464e+08
|
||||
94000 -320.89326 49375.312 -315.02966 1.0320494e+08
|
||||
95000 -320.60652 46960.796 -315.02966 93163389
|
||||
96000 -320.42504 45432.671 -315.02966 82638699
|
||||
97000 -320.35025 44802.889 -315.02966 77728012
|
||||
98000 -320.38016 45054.714 -315.02966 76753988
|
||||
99000 -320.64823 47312.019 -315.02966 79089183
|
||||
100000 -321.20665 52014.291 -315.02966 90654215
|
||||
101000 -322.45176 62498.949 -315.02966 1.1671692e+08
|
||||
102000 -325.27551 86276.757 -315.02966 1.7450838e+08
|
||||
103000 -324.86597 82828.164 -315.02967 1.5358223e+08
|
||||
104000 -323.50288 71350.092 -315.02966 1.3914499e+08
|
||||
105000 -321.83206 57280.642 -315.02966 1.1374062e+08
|
||||
106000 -321.23029 52213.369 -315.02966 1.0154377e+08
|
||||
107000 -320.79552 48552.352 -315.02966 93581739
|
||||
108000 -320.85374 49042.571 -315.02966 1.0230141e+08
|
||||
109000 -320.711 47840.638 -315.02966 98035102
|
||||
110000 -320.92927 49678.547 -315.02966 1.0291687e+08
|
||||
111000 -321.37088 53397.184 -315.02966 1.161465e+08
|
||||
112000 -321.64623 55715.825 -315.02966 1.2178973e+08
|
||||
113000 -323.29623 69609.916 -315.02966 1.5738912e+08
|
||||
114000 -326.43458 96036.881 -315.02966 2.2117147e+08
|
||||
115000 -326.29249 94840.366 -315.02967 2.1727072e+08
|
||||
116000 -323.49398 71275.138 -315.02966 1.6236371e+08
|
||||
117000 -321.69956 56164.918 -315.02966 1.2248665e+08
|
||||
118000 -321.03061 50531.902 -315.02966 1.114646e+08
|
||||
119000 -320.58664 46793.421 -315.02966 1.0201646e+08
|
||||
120000 -320.31068 44469.633 -315.02966 92788900
|
||||
121000 -320.33764 44696.673 -315.02966 96573809
|
||||
122000 -320.29533 44340.406 -315.02966 96276795
|
||||
123000 -320.48178 45910.447 -315.02966 96702563
|
||||
124000 -320.99926 50267.91 -315.02966 1.1042709e+08
|
||||
125000 -321.72882 56411.316 -315.02966 1.2653574e+08
|
||||
126000 -323.76935 73593.887 -315.02966 1.6411768e+08
|
||||
127000 -323.84136 74200.288 -315.02967 1.2684596e+08
|
||||
128000 -325.27771 86295.322 -315.02966 1.7908195e+08
|
||||
129000 -322.44151 62412.6 -315.02966 1.2334056e+08
|
||||
130000 -321.33424 53088.672 -315.02966 1.0110915e+08
|
||||
131000 -320.74694 48143.276 -315.02966 87343006
|
||||
132000 -320.58456 46775.879 -315.02966 84619630
|
||||
133000 -320.42884 45464.64 -315.02966 80256772
|
||||
134000 -320.41844 45377.068 -315.02966 79998095
|
||||
135000 -320.67167 47509.417 -315.02966 88059739
|
||||
136000 -320.94223 49787.695 -315.02966 94538899
|
||||
137000 -321.61703 55469.964 -315.02966 1.1016475e+08
|
||||
138000 -323.12933 68204.503 -315.02966 1.4202379e+08
|
||||
139000 -326.08028 93053.485 -315.02966 1.894649e+08
|
||||
140000 -326.22688 94287.865 -315.02967 1.9082785e+08
|
||||
141000 -323.43485 70777.215 -315.02966 1.4698731e+08
|
||||
142000 -321.79035 56929.435 -315.02966 1.1785802e+08
|
||||
143000 -321.17113 51715.2 -315.02966 1.0630317e+08
|
||||
144000 -320.72407 47950.681 -315.02966 94302254
|
||||
145000 -320.53771 46381.4 -315.02966 89962864
|
||||
146000 -320.57538 46698.572 -315.02966 90769921
|
||||
147000 -320.65873 47400.459 -315.02966 88297290
|
||||
148000 -321.05389 50727.942 -315.02966 95860956
|
||||
149000 -321.86647 57570.413 -315.02966 1.1210695e+08
|
||||
150000 -323.71338 73122.627 -315.02966 1.4277977e+08
|
||||
151000 -325.52965 88416.746 -315.02967 1.7216009e+08
|
||||
152000 -325.82817 90930.57 -315.02966 1.8312663e+08
|
||||
153000 -322.5891 63655.44 -315.02966 1.2089115e+08
|
||||
154000 -321.32957 53049.334 -315.02966 96494848
|
||||
155000 -320.66612 47462.65 -315.02966 81236441
|
||||
156000 -320.47196 45827.713 -315.02966 78679995
|
||||
157000 -320.33169 44646.581 -315.02966 75407967
|
||||
158000 -320.42358 45420.371 -315.02966 76161171
|
||||
159000 -320.79103 48514.483 -315.02966 84173108
|
||||
160000 -321.27968 52629.281 -315.02966 92130817
|
||||
161000 -322.50401 62938.95 -315.02966 1.138272e+08
|
||||
162000 -325.40267 87347.575 -315.02966 1.6576028e+08
|
||||
163000 -323.59983 72166.432 -315.02967 1.1072655e+08
|
||||
164000 -324.04378 75904.823 -315.02966 1.4709858e+08
|
||||
165000 -322.01605 58829.972 -315.02966 1.0400742e+08
|
||||
166000 -321.15747 51600.213 -315.02966 82397014
|
||||
167000 -320.8409 48934.422 -315.02966 73988066
|
||||
168000 -320.58861 46810.029 -315.02966 64925698
|
||||
169000 -320.54312 46426.959 -315.02966 61942158
|
||||
170000 -320.68604 47630.438 -315.02966 64309567
|
||||
171000 -320.77008 48338.134 -315.02966 63324927
|
||||
172000 -321.08474 50987.727 -315.02966 69721832
|
||||
173000 -321.6134 55439.431 -315.02966 80485473
|
||||
174000 -322.41904 62223.44 -315.02966 94329801
|
||||
175000 -324.95819 83604.705 -315.02966 1.5681125e+08
|
||||
176000 -321.71907 56329.278 -315.02966 45217519
|
||||
177000 -324.24577 77605.673 -315.02966 1.5164385e+08
|
||||
178000 -322.34082 61564.766 -315.02966 1.0677988e+08
|
||||
179000 -321.3229 52993.228 -315.02966 80528491
|
||||
180000 -320.91614 49567.992 -315.02966 70928167
|
||||
181000 -320.79771 48570.793 -315.02966 70105356
|
||||
182000 -320.43289 45498.72 -315.02966 62263793
|
||||
183000 -320.59821 46890.81 -315.02966 67986358
|
||||
184000 -320.64879 47316.739 -315.02966 70175355
|
||||
185000 -320.52287 46256.459 -315.02966 68704646
|
||||
186000 -320.94252 49790.187 -315.02966 81368769
|
||||
187000 -321.10174 51130.914 -315.02966 84251825
|
||||
188000 -321.38014 53475.167 -315.02966 91376642
|
||||
189000 -322.14722 59934.547 -315.02966 1.1198813e+08
|
||||
190000 -322.9004 66276.794 -315.02966 1.2823518e+08
|
||||
191000 -323.63455 72458.807 -315.02966 1.6144592e+08
|
||||
192000 -324.3348 78355.338 -315.02966 1.5544396e+08
|
||||
193000 -321.63344 55608.185 -315.02966 85813641
|
||||
194000 -323.54261 71684.651 -315.02966 1.4340251e+08
|
||||
195000 -323.1577 68443.449 -315.02966 1.5089288e+08
|
||||
196000 -322.90055 66278.083 -315.02966 1.4392954e+08
|
||||
197000 -322.45751 62547.374 -315.02966 1.2607137e+08
|
||||
198000 -322.18257 60232.201 -315.02966 1.137101e+08
|
||||
199000 -322.24297 60740.76 -315.02966 1.0950975e+08
|
||||
200000 -322.47749 62715.575 -315.02966 1.070732e+08
|
||||
200571 -323.24897 69211.97 -315.02966 1.1694375e+08
|
||||
Loop time of 86.0986 on 1 procs for 200000 steps with 101 atoms
|
||||
|
||||
Performance: 20070.020 fs/day, 0.001 hours/fs, 2322.919 timesteps/s, 234.615 katom-step/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 85.691 | 85.691 | 85.691 | 0.0 | 99.53
|
||||
Neigh | 0.0010104 | 0.0010104 | 0.0010104 | 0.0 | 0.00
|
||||
Comm | 0.016762 | 0.016762 | 0.016762 | 0.0 | 0.02
|
||||
Output | 0.061098 | 0.061098 | 0.061098 | 0.0 | 0.07
|
||||
Modify | 0.22948 | 0.22948 | 0.22948 | 0.0 | 0.27
|
||||
Other | | 0.09905 | | | 0.12
|
||||
|
||||
Nlocal: 101 ave 101 max 101 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 5050 ave 5050 max 5050 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 5050
|
||||
Ave neighs/atom = 50
|
||||
Neighbor list builds = 46
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
Total wall time: 0:01:28
|
||||
@ -0,0 +1,367 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index adamantane_ionized
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.adamantane_ionized
|
||||
Reading data file ...
|
||||
orthogonal box = (-50 -50 -50) to (50 50 50)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
101 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp etotal press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
# Minimization
|
||||
min_style cg
|
||||
dump 1 all xyz 500 ${sname}.min.xyz
|
||||
dump 1 all xyz 500 adamantane_ionized.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
dump 2 all custom 500 ${sname}.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
|
||||
dump 2 all custom 500 adamantane_ionized.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
|
||||
min_modify line quadratic
|
||||
minimize 0.0 1.0e-5 10000 100000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
|
||||
@Article{Jaramillo-Botero11,
|
||||
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||
journal = {J.~Comp.\ Chem.},
|
||||
year = 2011,
|
||||
volume = 32,
|
||||
number = 3,
|
||||
pages = {497--512}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 102
|
||||
ghost atom cutoff = 102
|
||||
binsize = 51, bins = 2 2 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.253 | 5.253 | 5.253 Mbytes
|
||||
Step PotEng Temp TotEng Press
|
||||
0 -320.50186 0 -320.50186 -45590269
|
||||
493 -324.31743 0 -324.31743 20971271
|
||||
Loop time of 0.883439 on 4 procs for 493 steps with 101 atoms
|
||||
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = linesearch alpha is zero
|
||||
Energy initial, next-to-last, final =
|
||||
-320.501859657306 -324.317430790588 -324.317430790588
|
||||
Force two-norm initial, final = 2.8135352 1.2148731
|
||||
Force max component initial, final = 1.7194878 1.1232786
|
||||
Final line search alpha, max atom move = 4.245048e-09 4.7683716e-09
|
||||
Iterations, force evaluations = 493 3804
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.24614 | 0.45831 | 0.84299 | 34.7 | 51.88
|
||||
Neigh | 1.1159e-05 | 1.2751e-05 | 1.5479e-05 | 0.0 | 0.00
|
||||
Comm | 0.019423 | 0.40607 | 0.62032 | 37.1 | 45.97
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.01905 | | | 2.16
|
||||
|
||||
Nlocal: 25.25 ave 30 max 17 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 75.75 ave 84 max 71 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 1262.5 ave 2394 max 663 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 5050
|
||||
Ave neighs/atom = 50
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
#restart timestep
|
||||
|
||||
# set velocities for nve
|
||||
#velocity all create 300.0 4928459 dist uniform
|
||||
|
||||
# NVE
|
||||
timestep 0.0001
|
||||
|
||||
fix 1 all nve/eff
|
||||
dump 1 all xyz 1000 ${sname}.nve.xyz
|
||||
dump 1 all xyz 1000 adamantane_ionized.nve.xyz
|
||||
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
|
||||
dump 2 all custom 1000 adamantane_ionized.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
|
||||
#restart 1000 ${sname}.nve.restart1 ${sname}.nve.restart2
|
||||
|
||||
run 200000
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.128 | 4.128 | 4.128 Mbytes
|
||||
Step PotEng Temp TotEng Press
|
||||
493 -324.31743 0 -324.31743 20971271
|
||||
1000 -324.2963 3994.2535 -323.82196 29875505
|
||||
2000 -324.14448 2715.8412 -323.82196 24005899
|
||||
3000 -323.9446 1032.7299 -323.82196 16224812
|
||||
4000 -323.83425 103.47941 -323.82196 11886177
|
||||
5000 -323.87559 451.59681 -323.82196 13395168
|
||||
6000 -324.05446 1957.8271 -323.82196 20034811
|
||||
7000 -324.24814 3588.7467 -323.82196 28092249
|
||||
8000 -324.3149 4150.7958 -323.82197 31632418
|
||||
9000 -324.25366 3635.1689 -323.82196 27760974
|
||||
10000 -324.05069 1926.0777 -323.82196 19436396
|
||||
11000 -323.88484 529.46541 -323.82196 13264080
|
||||
12000 -323.86286 344.37477 -323.82196 12741952
|
||||
13000 -324.00393 1532.3029 -323.82196 17720089
|
||||
14000 -324.20987 3266.4109 -323.82196 25528615
|
||||
15000 -324.34308 4388.1934 -323.82196 30700580
|
||||
16000 -324.30475 4065.4216 -323.82196 29168176
|
||||
17000 -324.12375 2541.2612 -323.82196 21928164
|
||||
18000 -323.93619 961.92262 -323.82196 14363951
|
||||
19000 -323.87105 413.39974 -323.82196 11446320
|
||||
20000 -323.9713 1257.5055 -323.82196 15118972
|
||||
21000 -324.16564 2894.0212 -323.82196 22749979
|
||||
22000 -324.32073 4199.9228 -323.82196 29044099
|
||||
23000 -324.34614 4413.8921 -323.82196 29514541
|
||||
24000 -324.20431 3219.6717 -323.82196 23595226
|
||||
25000 -324.01211 1601.1964 -323.82196 15812197
|
||||
26000 -323.90577 705.76969 -323.82196 11992491
|
||||
27000 -323.95668 1134.4631 -323.82196 14679820
|
||||
28000 -324.12645 2564.0146 -323.82196 21299092
|
||||
29000 -324.29158 3954.5234 -323.82196 28120074
|
||||
30000 -324.32731 4255.3405 -323.82196 31311574
|
||||
31000 -324.27771 3837.6901 -323.82196 28270491
|
||||
32000 -324.09259 2278.8862 -323.82196 21338356
|
||||
33000 -323.95465 1117.2898 -323.82196 15833338
|
||||
34000 -323.95469 1117.6477 -323.82196 16034624
|
||||
35000 -324.08796 2239.9037 -323.82196 22076527
|
||||
36000 -324.26866 3761.5323 -323.82196 29147703
|
||||
37000 -324.3502 4448.1533 -323.82196 33380564
|
||||
38000 -324.29459 3979.8076 -323.82196 31533851
|
||||
39000 -324.1694 2925.6774 -323.82196 25161011
|
||||
40000 -324.01365 1614.1815 -323.82196 19145060
|
||||
41000 -323.97015 1247.8234 -323.82196 16994462
|
||||
42000 -324.04755 1899.62 -323.82196 19654332
|
||||
43000 -324.22071 3357.7354 -323.82196 25666317
|
||||
44000 -324.35528 4490.9023 -323.82196 30318540
|
||||
45000 -324.35807 4514.3651 -323.82196 30645986
|
||||
46000 -324.24462 3559.0921 -323.82196 25690532
|
||||
47000 -324.09319 2283.909 -323.82196 18529309
|
||||
48000 -324.00266 1521.597 -323.82196 14177383
|
||||
49000 -324.04261 1858.0104 -323.82196 15780869
|
||||
50000 -324.19619 3151.2862 -323.82196 21070555
|
||||
51000 -324.32727 4255.0227 -323.82196 26451705
|
||||
52000 -324.3917 4797.6094 -323.82196 28066000
|
||||
53000 -324.30169 4039.6086 -323.82196 24214730
|
||||
54000 -324.14884 2752.5491 -323.82196 17848175
|
||||
55000 -324.02946 1747.258 -323.82196 13686029
|
||||
56000 -324.05031 1922.825 -323.82196 14113758
|
||||
57000 -324.16944 2925.9624 -323.82196 18723794
|
||||
58000 -324.30745 4088.1772 -323.82196 24387592
|
||||
59000 -324.36463 4569.6324 -323.82196 27059420
|
||||
60000 -324.32147 4206.1707 -323.82196 25012812
|
||||
61000 -324.18133 3026.1579 -323.82196 19500659
|
||||
62000 -324.07027 2090.9001 -323.82196 14626096
|
||||
63000 -324.04536 1881.129 -323.82196 13606034
|
||||
64000 -324.14417 2713.2333 -323.82196 17524492
|
||||
65000 -324.28817 3925.7771 -323.82196 23261363
|
||||
66000 -324.37816 4683.5409 -323.82196 26852878
|
||||
67000 -324.34311 4388.4452 -323.82196 25854003
|
||||
68000 -324.24346 3549.2763 -323.82196 20818195
|
||||
69000 -324.1067 2397.6992 -323.82196 15550338
|
||||
70000 -324.05471 1959.908 -323.82196 13178617
|
||||
71000 -324.12382 2541.8769 -323.82196 15655087
|
||||
72000 -324.25986 3687.3615 -323.82196 20831733
|
||||
73000 -324.37345 4643.9165 -323.82196 25082640
|
||||
74000 -324.38407 4733.3013 -323.82196 25377064
|
||||
75000 -324.28752 3920.3485 -323.82196 21185087
|
||||
76000 -324.14479 2718.409 -323.82196 15093238
|
||||
77000 -324.06273 2027.4447 -323.82196 11357895
|
||||
78000 -324.1027 2363.9918 -323.82196 12682184
|
||||
79000 -324.24431 3556.4784 -323.82196 17923460
|
||||
80000 -324.37329 4642.461 -323.82197 22977159
|
||||
81000 -324.40875 4941.1418 -323.82196 24175202
|
||||
82000 -324.33677 4334.993 -323.82196 20418362
|
||||
83000 -324.18471 3054.6117 -323.82196 14173787
|
||||
84000 -324.08262 2194.902 -323.82196 10107358
|
||||
85000 -324.07536 2133.7765 -323.82196 9748952.1
|
||||
86000 -324.18707 3074.432 -323.82196 13462472
|
||||
87000 -324.32091 4201.5211 -323.82196 19096674
|
||||
88000 -324.44557 5251.2038 -323.82196 22573960
|
||||
89000 -324.39988 4866.4678 -323.82196 21348490
|
||||
90000 -324.25685 3662.0864 -323.82196 15903121
|
||||
91000 -324.0755 2135.0001 -323.82196 10233161
|
||||
92000 -324.06354 2034.2765 -323.82196 7509452
|
||||
93000 -324.15185 2777.9236 -323.82196 9750370.3
|
||||
94000 -324.30478 4065.6146 -323.82196 15561885
|
||||
95000 -324.42696 5094.5186 -323.82196 20667693
|
||||
96000 -324.44094 5212.1846 -323.82196 21153174
|
||||
97000 -324.33283 4301.8232 -323.82196 16435314
|
||||
98000 -324.1883 3084.8099 -323.82196 10336860
|
||||
99000 -324.09656 2312.304 -323.82196 6808669.9
|
||||
100000 -324.13298 2619.0245 -323.82196 7675912.4
|
||||
101000 -324.25984 3687.2237 -323.82196 11868042
|
||||
102000 -324.40322 4894.6055 -323.82196 17007266
|
||||
103000 -324.44333 5232.3546 -323.82196 19025190
|
||||
104000 -324.39727 4844.4421 -323.82196 15980570
|
||||
105000 -324.25 3604.3886 -323.82196 9668044.1
|
||||
106000 -324.08507 2215.5839 -323.82196 4405958.8
|
||||
107000 -324.11835 2495.8211 -323.82196 3436936.2
|
||||
108000 -324.21008 3268.2404 -323.82196 6028268.3
|
||||
109000 -324.34118 4372.1743 -323.82196 10939013
|
||||
110000 -324.40282 4891.1987 -323.82196 14333667
|
||||
111000 -324.45353 5318.1927 -323.82196 13380345
|
||||
112000 -324.33795 4344.9374 -323.82196 7923709.9
|
||||
113000 -324.19654 3154.2192 -323.82196 1970263.7
|
||||
114000 -324.12867 2582.7343 -323.82196 -1481413.1
|
||||
115000 -324.17132 2941.8126 -323.82196 -290956.43
|
||||
116000 -324.33613 4329.6247 -323.82196 5245770.9
|
||||
117000 -324.41548 4997.8222 -323.82196 10354303
|
||||
118000 -324.48518 5584.7558 -323.82196 11795673
|
||||
119000 -324.41046 4955.5092 -323.82196 8031391.3
|
||||
120000 -324.24749 3583.2536 -323.82196 1845177.6
|
||||
121000 -324.14124 2688.5331 -323.82196 -2784584.1
|
||||
122000 -324.14467 2717.4458 -323.82196 -2261498.4
|
||||
123000 -324.28472 3896.7771 -323.82196 3080452.1
|
||||
124000 -324.43687 5177.9121 -323.82196 9819540.9
|
||||
125000 -324.51452 5831.8132 -323.82196 13180239
|
||||
126000 -324.47691 5515.0823 -323.82196 11018721
|
||||
127000 -324.31812 4178.0163 -323.82196 4976672.9
|
||||
128000 -324.16884 2920.9366 -323.82196 -186371.44
|
||||
129000 -324.13025 2596.0395 -323.82196 -1883126.3
|
||||
130000 -324.22275 3374.922 -323.82196 1526423.1
|
||||
131000 -324.41343 4980.5335 -323.82196 8415685
|
||||
132000 -324.45089 5296.046 -323.82196 13250300
|
||||
133000 -324.51148 5806.2229 -323.82196 12827560
|
||||
134000 -324.39463 4822.239 -323.82196 7049805.8
|
||||
135000 -324.20254 3204.6979 -323.82196 -187723.51
|
||||
136000 -324.1379 2660.4388 -323.82196 -3970679.9
|
||||
137000 -324.18473 3054.7443 -323.82196 -2351010.9
|
||||
138000 -324.35172 4460.9406 -323.82196 3024494.5
|
||||
139000 -324.48743 5603.6722 -323.82196 8652609.2
|
||||
140000 -324.53668 6018.4343 -323.82196 9612584.9
|
||||
141000 -324.43638 5173.8016 -323.82196 4805500.8
|
||||
142000 -324.28353 3886.746 -323.82196 -2740880.4
|
||||
143000 -324.14169 2692.2995 -323.82196 -8310197.6
|
||||
144000 -324.13063 2599.1788 -323.82196 -9603391.1
|
||||
145000 -324.27459 3811.4423 -323.82196 -5690559.8
|
||||
146000 -324.4342 5155.4519 -323.82196 431484.28
|
||||
147000 -324.55834 6200.7798 -323.82196 4166801.6
|
||||
148000 -324.51567 5841.5105 -323.82196 2299540.9
|
||||
149000 -324.34424 4397.967 -323.82196 -4487220.6
|
||||
150000 -324.20348 3212.6032 -323.82196 -10852097
|
||||
151000 -324.13211 2611.6979 -323.82196 -12942852
|
||||
152000 -324.20634 3236.7635 -323.82196 -10732036
|
||||
153000 -324.35827 4516.0788 -323.82196 -4665668.3
|
||||
154000 -324.5074 5771.8121 -323.82196 1703175.2
|
||||
155000 -324.51881 5867.9505 -323.82196 2959605.5
|
||||
156000 -324.44762 5268.4581 -323.82196 -1706620
|
||||
157000 -324.25179 3619.4025 -323.82196 -8511782.3
|
||||
158000 -324.13478 2634.1695 -323.82196 -11767435
|
||||
159000 -324.17085 2937.9043 -323.82196 -10356431
|
||||
160000 -324.28946 3936.6179 -323.82196 -5252437.9
|
||||
161000 -324.47596 5507.0864 -323.82196 1737812.2
|
||||
162000 -324.52686 5935.7476 -323.82196 5782720.9
|
||||
163000 -324.5121 5811.4236 -323.82196 4273238.8
|
||||
164000 -324.35265 4468.7315 -323.82196 -1590319.8
|
||||
165000 -324.19582 3148.1193 -323.82196 -6770200.2
|
||||
166000 -324.15306 2788.0507 -323.82196 -8385908.5
|
||||
167000 -324.24186 3535.8588 -323.82196 -4776412.5
|
||||
168000 -324.4 4867.4913 -323.82196 2207883.7
|
||||
169000 -324.52732 5939.6216 -323.82196 7770368.9
|
||||
170000 -324.53787 6028.4604 -323.82196 8163057.7
|
||||
171000 -324.42167 5049.9129 -323.82196 2893037
|
||||
172000 -324.25784 3670.3642 -323.82196 -4020286
|
||||
173000 -324.16815 2915.1362 -323.82196 -7461767.8
|
||||
174000 -324.21774 3332.737 -323.82196 -5214520.3
|
||||
175000 -324.37502 4657.1185 -323.82196 -81968.156
|
||||
176000 -324.5128 5817.2882 -323.82196 5130806.8
|
||||
177000 -324.4983 5695.2281 -323.82196 6394017.7
|
||||
178000 -324.47309 5482.9629 -323.82196 2466372.3
|
||||
179000 -324.31526 4153.8777 -323.82196 -4378953.5
|
||||
180000 -324.2046 3222.0434 -323.82196 -9221400.9
|
||||
181000 -324.21978 3349.8648 -323.82196 -9338327.2
|
||||
182000 -324.33867 4351.0162 -323.82196 -5586765.2
|
||||
183000 -324.44483 5244.9523 -323.82196 -706564.21
|
||||
184000 -324.54787 6112.6128 -323.82196 1971109.1
|
||||
185000 -324.49436 5662.0508 -323.82196 -1239.0449
|
||||
186000 -324.38425 4734.8404 -323.82196 -5595239.9
|
||||
187000 -324.25734 3666.1954 -323.82196 -10793981
|
||||
188000 -324.21303 3293.0496 -323.82196 -11574584
|
||||
189000 -324.28662 3912.7067 -323.82196 -8579023.4
|
||||
190000 -324.4316 5133.5815 -323.82196 -2888022.8
|
||||
191000 -324.51735 5855.6722 -323.82196 1558206.4
|
||||
192000 -324.55207 6147.9783 -323.82196 1897782.9
|
||||
193000 -324.43491 5161.4381 -323.82196 -1998628.2
|
||||
194000 -324.28751 3920.2514 -323.82196 -6841627.4
|
||||
195000 -324.24114 3529.7564 -323.82196 -8565471.5
|
||||
196000 -324.30158 4038.6851 -323.82196 -5634096.8
|
||||
197000 -324.44261 5226.2386 -323.82196 443851.89
|
||||
198000 -324.53354 5991.9831 -323.82196 5993350.1
|
||||
199000 -324.5697 6296.4193 -323.82196 7393255.8
|
||||
200000 -324.46863 5445.3485 -323.82196 4272906.2
|
||||
200493 -324.39372 4814.6196 -323.82196 1812660.2
|
||||
Loop time of 42.6156 on 4 procs for 200000 steps with 101 atoms
|
||||
|
||||
Performance: 40548.540 fs/day, 0.001 hours/fs, 4693.118 timesteps/s, 474.005 katom-step/s
|
||||
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 11.576 | 22.615 | 40.956 | 235.7 | 53.07
|
||||
Neigh | 1.9114e-05 | 2.3629e-05 | 2.5892e-05 | 0.0 | 0.00
|
||||
Comm | 0.99241 | 19.433 | 30.581 | 255.9 | 45.60
|
||||
Output | 0.03344 | 0.035732 | 0.037864 | 0.8 | 0.08
|
||||
Modify | 0.066393 | 0.082377 | 0.09318 | 3.4 | 0.19
|
||||
Other | | 0.4486 | | | 1.05
|
||||
|
||||
Nlocal: 25.25 ave 31 max 21 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Nghost: 75.75 ave 80 max 70 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Neighs: 1262.5 ave 2143 max 476 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 5050
|
||||
Ave neighs/atom = 50
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
Total wall time: 0:00:43
|
||||
Reference in New Issue
Block a user