forked from lijiext/lammps
206 lines
13 KiB
Groff
206 lines
13 KiB
Groff
LAMMPS (31 Mar 2017)
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# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
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units real
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neigh_modify delay 2 every 1
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#newton off
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boundary p p p
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atom_style full
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bond_style harmonic
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angle_style charmm
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dihedral_style charmmfsw
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improper_style harmonic
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pair_style lj/charmmfsw/coul/charmmfsh 8 12
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pair_modify mix arithmetic
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fix cmap all cmap charmm22.cmap
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Reading potential file charmm22.cmap with DATE: 2016-09-26
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fix_modify cmap energy yes
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read_data gagg.data fix cmap crossterm CMAP
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orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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34 atoms
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scanning bonds ...
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4 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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12 = max dihedrals/atom
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scanning impropers ...
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1 = max impropers/atom
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reading bonds ...
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33 bonds
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reading angles ...
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57 angles
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reading dihedrals ...
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75 dihedrals
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reading impropers ...
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7 impropers
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4 = max # of 1-2 neighbors
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7 = max # of 1-3 neighbors
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13 = max # of 1-4 neighbors
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16 = max # of special neighbors
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special_bonds charmm
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fix 1 all nve
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#fix 1 all nvt temp 300 300 100.0
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#fix 2 all shake 1e-9 500 0 m 1.0
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velocity all create 0.0 12345678 dist uniform
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thermo 1000
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thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
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timestep 2.0
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run 100000
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Neighbor list info ...
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update every 1 steps, delay 2 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 12 12 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/charmmfsw/coul/charmmfsh, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 14.94 | 15.57 | 16.2 Mbytes
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Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
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0 16.287573 -0.85933785 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023
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1000 18.816462 -0.84379243 0.78931817 2.7554247 4.4371421 -2.7762038 0.12697656
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2000 18.091571 -1.045888 0.72306589 3.0951524 4.6725102 -2.3580092 0.22712496
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3000 17.835596 -1.2171641 0.72666403 2.6696491 5.4373798 -2.0737041 0.075101693
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4000 16.211232 -0.42713611 0.99472642 3.8961462 5.2009895 -2.5626866 0.17356243
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5000 17.72183 -0.57081189 0.90733068 3.4376382 4.5457582 -2.3727543 0.12354518
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6000 18.753977 -1.5772499 0.81468321 2.9236782 4.6033216 -2.3380859 0.12835782
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7000 18.186024 -0.84205609 0.58996181 3.0329584 4.7221473 -2.5733244 0.10047631
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8000 18.214306 -1.1360934 0.72597583 3.7493032 4.7319959 -2.8957975 0.20060467
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9000 17.248415 -0.48642024 0.90266262 2.9721744 4.7651003 -2.1473349 0.13020438
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10000 17.760663 -1.2968458 0.92384687 3.7007432 4.7378917 -2.2147799 0.06940514
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11000 17.63395 -0.57366075 0.84871737 3.4276851 4.2853865 -2.2369491 0.17205075
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12000 18.305713 -1.0672299 0.75876262 2.8852171 4.6850229 -2.4090072 0.087568888
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13000 17.383367 -0.99678627 0.66712651 3.8060954 5.233865 -2.4180629 0.062014239
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14000 17.510901 -0.68723297 0.92448551 3.7550867 4.7321218 -2.6059088 0.11504409
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15000 18.080165 -1.13316 0.99982253 3.09947 4.8171402 -2.2713372 0.14580371
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16000 17.383245 -0.4535296 0.57826268 3.6453593 4.6541138 -2.2434512 0.13285609
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17000 17.111153 -0.3414839 0.73667584 3.7485311 4.6262965 -2.6166049 0.12635815
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18000 16.862046 -1.3592061 1.2371142 4.4878937 4.2937117 -2.2112584 0.066145125
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19000 18.313891 -1.654238 0.90644101 3.3934089 4.550735 -2.1862171 0.081267736
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20000 19.083561 -1.3081747 0.56257812 2.7633848 4.6211438 -2.5196707 0.13763071
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21000 18.23741 -1.051353 0.64408722 3.1735565 4.6912533 -2.2491947 0.099394904
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22000 17.914515 -0.89769621 0.61793801 3.1224992 4.8683543 -2.282475 0.14524537
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23000 16.756122 -0.98277883 1.2554905 3.7916115 4.7301443 -2.3094994 0.10226772
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24000 16.109857 -0.54593177 0.86934462 4.4293574 4.926985 -2.2652264 0.11414331
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25000 18.590559 -1.497327 1.1898361 2.9134403 4.7854107 -2.4437918 0.067416154
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26000 18.493391 -1.0533797 0.4889578 3.6563013 4.6171721 -2.3240835 0.11607829
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27000 18.646522 -1.1229601 0.67956815 2.7937638 4.8991207 -2.4068997 0.10109147
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28000 18.545103 -1.7237438 0.72488022 3.8041665 4.6459974 -2.4339333 0.21943258
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29000 17.840505 -1.0909667 0.88133248 3.3698456 5.0311644 -2.5116617 0.08102693
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30000 17.649527 -0.65409177 0.86781692 3.24112 4.9903073 -2.6234925 0.14799777
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31000 18.156812 -0.77476556 0.83192789 2.9620784 4.9160635 -2.8571635 0.22283201
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32000 18.251583 -1.3384075 0.8059007 3.2588176 4.4365328 -2.1875071 0.087883637
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33000 17.702785 -0.88311587 0.98573641 3.4645713 4.2650091 -2.0909158 0.14233004
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34000 17.123413 -1.4873429 1.0419563 4.2628178 4.6318762 -2.2292095 0.105354
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35000 18.162061 -1.0136007 0.82436129 3.6365024 4.5801677 -2.6856989 0.28648222
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36000 17.65618 -1.094718 0.8872444 3.5075241 4.6382423 -2.3895134 0.18116961
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37000 17.336475 -1.0657995 0.98869254 3.9252927 4.4383632 -2.2048244 0.22285949
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38000 17.369467 -0.97623132 0.6712095 4.1349304 4.597754 -2.4088341 0.14608514
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39000 18.170206 -1.2344285 0.77546195 3.6451049 4.7482287 -2.9895286 0.25768859
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40000 16.210866 -0.81407781 0.99246271 4.2676233 5.0253763 -2.2929865 0.13348624
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41000 17.641798 -1.0868157 0.80119513 3.4302526 5.280872 -2.4025406 0.22747391
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42000 18.349848 -1.613759 1.1497004 3.7800682 4.3237683 -2.8676401 0.2120425
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43000 19.130245 -1.196778 0.71845659 2.9325758 4.3684415 -2.433424 0.12240982
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44000 18.061321 -1.2410101 1.0329373 3.0751569 4.7138313 -2.2880904 0.075814461
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45000 18.162713 -1.4414622 1.009159 4.2298758 4.589593 -2.8502298 0.21606844
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46000 18.591574 -0.99730412 1.0955215 3.3965004 4.359466 -3.1049731 0.17322629
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47000 18.380259 -1.2717381 0.72291269 3.3958016 4.6099628 -2.4605065 0.19825185
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48000 18.130478 -1.5051279 1.2087492 3.2488529 4.6690881 -2.2518174 0.05633061
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49000 16.419912 -0.89320635 0.98926144 4.0388252 4.9919488 -2.1699511 0.15646479
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50000 16.453196 -1.0433497 0.778346 4.6078069 4.7320614 -2.3760788 0.17161976
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51000 18.245221 -0.89550444 0.9310446 3.0758194 4.3944595 -2.3082379 0.19983428
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52000 17.839632 -1.0221781 0.76425017 3.3331547 4.5368437 -2.0988773 0.21098435
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53000 18.693035 -1.4231915 0.76333082 3.1612761 4.583242 -2.4485762 0.089191206
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54000 16.334672 -0.36309884 1.0200365 4.6700448 4.1628702 -2.1713841 0.11431995
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55000 17.33842 -0.61522682 0.89847366 3.4970659 4.673495 -2.4743036 0.068004878
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56000 17.790294 -1.0150845 0.73697112 3.6000297 4.5988343 -2.4822509 0.11434632
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57000 18.913486 -1.0985507 1.0231848 2.7483267 4.4421755 -2.574424 0.1763388
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58000 17.586896 -0.98284126 0.96965633 3.3330357 4.5325543 -2.1936869 0.083230915
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59000 17.77788 -1.1649953 0.83092298 3.8004148 4.3940176 -2.3136642 0.017207608
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60000 17.013042 -0.21728023 1.1688832 3.5374476 4.5462244 -2.4425301 0.15028297
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61000 17.236242 -1.1342147 1.0301086 3.685948 4.6842331 -2.328108 0.070210812
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62000 17.529852 -1.2961547 1.0323133 3.4474598 5.1435839 -2.4553423 0.060842687
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63000 18.754704 -1.1816999 0.51806039 3.140172 4.5832701 -2.2713213 0.06327871
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64000 17.54594 -1.3592836 0.9694558 4.1363258 4.3547729 -2.3818433 0.12634448
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65000 16.962312 -0.54192775 0.90321315 4.0788618 4.2008255 -2.1376711 0.039504515
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66000 18.078619 -1.3552947 1.0716861 3.3285374 4.7229362 -2.3331115 0.21978698
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67000 17.132732 -1.4376876 0.91486534 4.4461852 4.6894176 -2.3655045 0.068150385
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68000 18.69286 -1.2856207 0.3895394 3.0620063 4.9922992 -2.3459189 0.079879643
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69000 18.329552 -1.1545957 0.88632275 3.1741058 4.4562418 -2.7094867 0.25329613
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70000 16.681168 -0.94434373 1.2450393 4.5737944 4.4902996 -2.4581775 0.15313095
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71000 17.375032 -1.0514442 1.0741595 3.4896146 4.8407713 -2.5302576 0.13640847
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72000 17.833013 -0.9047134 0.87067876 3.1658924 4.8825932 -2.4398117 0.2343991
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73000 17.421411 -1.2190741 0.73706811 4.2895 4.6464636 -2.3872727 0.19696525
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74000 17.383158 -0.34208984 0.71333984 3.2718891 4.2718495 -2.2484281 0.10827022
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75000 17.20885 -1.2710479 1.125102 3.8414467 5.3222741 -2.375505 0.12910797
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76000 16.811578 -0.545162 0.59076961 3.9118604 4.8031296 -2.2777895 0.063015508
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77000 16.679231 -0.080955983 0.7253398 3.4203454 5.0987608 -2.379614 0.12961874
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78000 18.164524 -1.3115525 0.92526408 3.5764487 4.3814882 -2.3712488 0.073436724
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79000 17.738686 -1.0697859 1.2186866 3.0593848 4.6551053 -2.2505871 0.075340661
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80000 16.767483 -0.84777477 1.03128 4.1982958 4.6992227 -2.4146425 0.079774219
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81000 16.257265 0.62803774 0.84032194 3.3873471 5.0961071 -2.7219776 0.20467848
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82000 18.232082 -1.2129302 0.50746051 3.9207128 4.5073437 -2.599371 0.094522372
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83000 16.618985 -0.60917055 0.8825847 3.805497 4.9560959 -2.2194726 0.14852687
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84000 17.90762 -0.82336075 0.90504161 3.0324198 4.7444271 -2.5036073 0.15860682
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85000 16.699883 -0.50297228 0.83405307 3.8598996 4.7971968 -2.2427788 0.10338668
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86000 16.353038 -0.0096880616 0.80705167 4.0865115 4.5364338 -2.4548873 0.098456203
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87000 17.887331 -0.75281219 1.0030148 4.0117123 4.3443074 -2.9774392 0.16190152
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88000 18.583708 -1.4867053 0.86324814 3.3971237 4.3526221 -2.221239 0.14459352
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89000 17.684828 -1.283764 1.0021118 3.5426808 4.9057005 -2.3921967 0.05844702
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90000 17.2597 -0.84306489 0.99797936 3.8896866 4.4315457 -2.5662899 0.18270206
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91000 16.705581 -0.44704047 0.75239556 3.470805 4.976868 -2.1894571 0.12312848
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92000 17.548071 -1.2222664 0.92898812 4.0813773 4.3432647 -2.1631158 0.14071343
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93000 17.163675 -0.94994776 0.96876981 3.9137692 4.4388666 -2.1260232 0.13187968
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94000 18.842071 -1.2822113 0.58767049 3.1393475 4.5820965 -2.7264682 0.10406266
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95000 18.112287 -1.1011381 0.63546648 3.4672667 4.486275 -2.2991936 0.041589685
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96000 17.102713 -0.6877313 0.8389032 3.6892719 4.5676004 -2.1905327 0.13507011
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97000 16.778253 -1.2902153 1.1588744 4.2820083 4.9537657 -2.4798159 0.35696636
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98000 18.34638 -1.2908146 1.185356 3.0739807 4.4575453 -2.3959144 0.22407922
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99000 17.995148 -1.3939639 0.7727299 3.8774144 4.4345458 -2.1142776 0.13550099
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100000 18.444746 -1.2456693 0.86061526 3.468696 4.5264336 -2.4239851 0.074369539
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Loop time of 2.52011 on 4 procs for 100000 steps with 34 atoms
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Performance: 6856.851 ns/day, 0.004 hours/ns, 39680.850 timesteps/s
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98.8% CPU use with 4 MPI tasks x no OpenMP threads
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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 | 0.072506 | 0.28131 | 0.69088 | 46.2 | 11.16
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Bond | 0.050544 | 0.45307 | 0.9416 | 57.6 | 17.98
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Neigh | 0.0060885 | 0.0061619 | 0.0062056 | 0.1 | 0.24
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Comm | 0.44686 | 1.3679 | 2.0111 | 53.5 | 54.28
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Output | 0.0028057 | 0.0029956 | 0.003264 | 0.3 | 0.12
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Modify | 0.028202 | 0.095174 | 0.15782 | 19.8 | 3.78
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Other | | 0.3135 | | | 12.44
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Nlocal: 8.5 ave 14 max 2 min
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Histogram: 1 0 1 0 0 0 0 0 0 2
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Nghost: 25.5 ave 32 max 20 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Neighs: 98.75 ave 242 max 31 min
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Histogram: 2 0 1 0 0 0 0 0 0 1
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Total # of neighbors = 395
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Ave neighs/atom = 11.6176
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Ave special neighs/atom = 9.52941
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Neighbor list builds = 246
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Dangerous builds = 0
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Total wall time: 0:00:02
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