forked from lijiext/lammps
208 lines
13 KiB
Groff
208 lines
13 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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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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Switching to CHARMM coulomb energy conversion constant (src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp:55)
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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 1 by 1 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) = 14.96 | 14.96 | 14.96 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 16.28796 -0.85933785 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023
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1000 18.817034 -0.84376064 0.78927748 2.7554954 4.4369572 -2.7762224 0.12700913
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2000 18.091506 -1.0458619 0.72328506 3.0956514 4.6724302 -2.3582544 0.22717594
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3000 17.841047 -1.2177066 0.72658478 2.6693344 5.4322049 -2.0735857 0.075472354
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4000 16.203768 -0.43010212 0.99813471 3.9020929 5.2015958 -2.562376 0.17393693
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5000 17.74278 -0.58387686 0.9095749 3.4440437 4.5474453 -2.3771369 0.12369887
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6000 18.84065 -1.5987004 0.81046711 2.9214019 4.5243733 -2.3180496 0.12365723
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7000 18.84546 -0.96510756 0.57164583 3.0069325 4.6579161 -2.8966842 0.186473
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8000 16.965729 -0.85937109 0.62698075 3.6416157 5.2427548 -2.4812956 0.14018019
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9000 16.847152 -0.23916172 0.76630295 3.8009862 4.4066861 -2.2021529 0.1798796
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10000 17.553635 -1.2829068 1.1657706 3.9123497 5.0547767 -2.9598952 0.34416632
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11000 17.985843 -1.5465483 0.84770758 3.3368358 5.662125 -2.6329553 0.24353243
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12000 17.803319 -1.0407393 0.74246545 3.6148795 4.7651004 -2.5084817 0.10619442
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13000 18.979266 -1.3899293 0.54141439 2.8249302 4.7550121 -2.5037554 0.11955235
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14000 17.009105 -0.79638876 0.94514282 3.8784001 4.5107273 -2.2861709 0.076774568
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15000 16.52792 -0.099911028 0.73468109 3.6878436 5.0897919 -2.6694045 0.1846061
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16000 18.602333 -1.2207715 0.73683889 3.5724426 4.2967652 -2.1185335 0.14454439
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17000 18.548631 -1.4459452 0.87132388 3.1082541 4.4173372 -2.1488103 0.05085499
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18000 18.274944 -0.9082365 0.78279222 3.2003259 4.2230915 -2.0279073 0.067678678
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19000 18.363395 -1.5446376 0.84278631 3.5192748 4.5827839 -2.3655766 0.16111203
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20000 17.92959 -0.78977685 0.83244452 3.3573732 4.5008538 -2.7568218 0.18551385
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21000 16.294685 -0.43068016 1.0820062 4.1094083 4.6392086 -2.4608104 0.1504371
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22000 17.945194 -1.12622 0.86476498 3.3577152 4.673294 -2.4760964 0.081229709
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23000 18.59629 -1.3692394 0.67592321 3.493029 4.5943035 -2.221834 0.13764568
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24000 17.636587 -0.46892268 0.59584902 3.2114851 4.7133747 -2.4081857 0.26633414
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25000 16.620668 -0.75136289 1.0243884 4.0835198 5.1451753 -2.6824535 0.24777903
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26000 18.59225 -1.0967117 0.56177724 3.2556596 4.3523235 -2.4816091 0.1788868
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27000 19.188088 -1.871277 0.96616357 3.0120122 4.3122826 -2.2148745 0.10347086
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28000 17.912724 -0.90553766 1.1257482 3.2754041 4.2225708 -2.4365707 0.1807316
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29000 17.81248 -1.1502128 0.95470623 3.4118416 4.6659831 -2.1613317 0.11462518
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30000 17.018989 -0.89064809 0.84950442 4.1712342 4.4636021 -2.3306882 0.15623897
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31000 18.547066 -1.5339831 0.89944952 3.3517223 4.7396826 -2.6121868 0.15212539
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32000 17.200059 -1.0016932 0.81295912 4.0695758 4.5595904 -2.3605079 0.1387539
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33000 17.531814 -0.70849955 0.75743835 3.226091 4.476408 -2.1190694 0.055884538
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34000 18.325131 -1.2897672 0.89479605 3.1671187 4.2968993 -1.9697837 0.17312732
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35000 18.289817 -1.0149458 0.75194781 3.4275427 4.5914578 -2.3206357 0.12126296
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36000 17.111721 -0.59386121 0.84127598 3.5534448 5.0274338 -2.36455 0.090112107
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37000 17.748767 -0.91029178 0.77689229 3.8018169 4.7249541 -2.4255194 0.054726961
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38000 17.2172 -0.43070288 0.88086005 3.5586613 4.3203841 -2.0587465 0.050764106
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39000 18.482481 -0.75351762 0.87677942 2.9007389 4.7178108 -2.6463003 0.25313342
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40000 18.465192 -1.4076534 0.92705504 3.3546181 4.4030743 -2.3873054 0.071878288
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41000 18.12592 -1.5839327 0.6979962 3.2851401 5.2815413 -2.3054411 0.11390788
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42000 18.376705 -1.0077349 0.70647799 2.9499245 4.6421626 -2.3504786 0.17673009
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43000 16.929642 -0.72975766 0.90203733 3.7176511 4.7292387 -2.2860424 0.084829761
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44000 17.271104 -0.99868378 1.0201679 4.1153184 4.2727269 -2.1172719 0.1029166
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45000 18.230889 -1.0093287 0.85777597 2.8550682 4.3913999 -2.0720155 0.073553812
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46000 18.241544 -1.7077516 0.95512232 3.8878131 4.3812806 -2.3031674 0.10194331
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47000 18.12818 -0.83919194 0.71483948 2.7541388 4.7432398 -2.2644558 0.053413336
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48000 17.965762 -0.92946694 0.70540637 3.4567259 4.5010549 -2.3038276 0.15002746
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49000 16.815211 0.19052416 1.0076747 3.1045662 4.9638411 -2.3712162 0.1057081
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50000 17.193025 -0.89817177 1.2261029 3.7515175 4.4880145 -2.2643247 0.29712734
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51000 18.665005 -0.84670757 0.56076732 3.0839868 4.458076 -2.2261738 0.046374416
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52000 17.619937 -0.89986585 0.64159147 3.7530936 4.8769799 -2.3791391 0.13429701
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53000 16.916466 -0.58872911 0.96495189 3.6755814 4.7419669 -2.3886804 0.20915197
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54000 17.199476 -0.88155666 0.64336469 3.927811 4.8019389 -2.2773601 0.18734294
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55000 18.158496 -0.81126798 0.68333055 2.9741959 4.4463001 -2.1864535 0.071857857
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56000 17.860471 -1.6993 1.2366001 3.7857634 4.7701817 -2.4192649 0.15619688
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57000 18.444698 -0.82854071 0.63506471 3.1823771 4.4432216 -2.2987011 0.1407306
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58000 18.047238 -1.4404915 1.0095109 3.7328328 4.6385391 -2.1656547 0.068584173
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59000 16.990212 -0.81630542 0.73745944 4.2847598 5.1556617 -2.4218952 0.044901478
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60000 18.164864 -0.68273809 0.60589655 3.1085907 4.5637459 -2.2379342 0.11464892
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61000 17.772457 -1.1890999 0.80411722 3.7218185 4.7750335 -2.4439724 0.11358571
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62000 17.192042 -0.095008686 0.71713238 3.2284848 4.9345758 -2.4377098 0.12788027
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63000 16.877969 -0.62181425 0.8931036 3.6147379 5.3541158 -2.302381 0.072736635
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64000 17.934695 -1.1664658 0.74610888 3.5102215 4.6537266 -2.3495291 0.18818648
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65000 17.034947 -0.59670985 0.7590603 3.4896411 5.0725358 -2.3057016 0.067650159
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66000 18.259418 -0.57940688 0.55125252 3.2917088 4.4949827 -2.3128319 0.17052154
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67000 16.656512 -1.1797815 0.88985636 4.3326457 4.7143632 -2.4187476 0.35820295
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68000 18.218359 -0.98502226 0.8053151 2.8694875 4.6774476 -2.2750794 0.027475615
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69000 18.591716 -1.2961393 0.85778116 3.4232791 4.3626988 -2.2150059 0.047420611
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70000 18.282862 -1.5115081 1.1486318 3.1099158 4.5945816 -2.1742452 0.15701805
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71000 17.722244 -1.3606013 0.98913854 3.9050958 4.4617942 -2.1980629 0.16665753
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72000 17.578225 -1.0672968 1.1898075 3.3110576 4.6292013 -2.1893929 0.15802869
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73000 17.700619 -1.1203382 0.68447774 3.7617044 4.5508307 -2.2031338 0.046795482
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74000 18.864586 -1.3377627 0.54243736 3.1047677 4.6094993 -2.2506839 0.0618695
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75000 17.252732 -0.75791613 0.79934329 3.6289993 4.8336985 -2.3716023 0.048355835
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76000 15.625117 -0.17710917 1.0083339 4.5957493 4.3952808 -2.0145142 0.2165007
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77000 18.663599 -1.214034 0.73808593 3.1282966 4.1967921 -2.04274 0.20129707
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78000 16.687112 -0.81273153 1.0670946 3.5384094 5.3755076 -2.1922472 0.025711096
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79000 18.169502 -1.443215 1.1859821 3.4043489 4.3415317 -2.3447052 0.11854425
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80000 18.787124 -1.6654307 1.0501597 3.0298408 4.2077733 -1.9985344 0.26128514
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81000 17.807683 -1.3429276 0.83231514 3.8051489 4.659607 -2.3866437 0.20196892
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82000 17.331324 -0.78827019 0.95190013 3.7412416 4.3529018 -2.307155 0.073785492
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83000 17.597954 -0.36573657 0.84239516 3.1227374 4.5709276 -2.2732398 0.12571923
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84000 17.961063 -1.2301714 0.65709128 3.5308724 4.5505295 -2.4116051 0.14784451
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85000 18.034924 -1.1445169 1.1114893 3.2704327 4.4570221 -2.3336871 0.084147643
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86000 18.35847 -1.0687438 0.71638387 3.2994265 4.7224093 -2.6523985 0.2338977
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87000 17.297387 -0.36290631 0.67031988 3.9566445 4.6234059 -2.8008118 0.22786876
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88000 17.179923 -0.40756603 1.0448818 3.4777257 4.454146 -2.420876 0.18845717
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89000 17.548178 -1.2104623 0.81223923 3.8553959 4.8092953 -2.3606086 0.16057241
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90000 18.203445 -1.2476535 0.93776844 3.3519306 4.5880767 -2.3299626 0.13273664
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91000 17.577661 -0.9536919 0.98278572 3.6805268 4.269043 -2.2758847 0.16458677
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92000 17.249982 -1.2620718 1.2379068 4.077245 4.6893055 -2.3623079 0.080584665
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93000 17.263474 -1.1194017 0.56075789 3.9937658 4.9398469 -2.458799 0.1178667
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94000 17.794002 -0.94808955 0.82296171 3.4988835 4.723922 -2.4525227 0.093849723
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95000 17.380526 -1.3184326 1.2273125 4.01341 4.3749028 -2.1577427 0.12183053
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96000 17.421883 -1.0247407 0.98739686 4.1656417 4.5509065 -2.5533884 0.15050166
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97000 18.097453 -0.82643049 0.58678318 3.5934164 4.2844244 -2.187686 0.1173314
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98000 17.110826 -0.9875292 1.1047966 3.5373119 4.9434687 -2.3951197 0.051018748
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99000 17.497671 -0.72505537 1.1343346 3.3335263 4.7133241 -2.3170405 0.18322857
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100000 17.502653 -1.2246734 0.85121721 4.132924 4.6912393 -2.605162 0.24425609
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Loop time of 2.20757 on 1 procs for 100000 steps with 34 atoms
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Performance: 7827.606 ns/day, 0.003 hours/ns, 45298.646 timesteps/s
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99.5% CPU use with 1 MPI tasks x 1 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 | 0.80344 | 0.80344 | 0.80344 | 0.0 | 36.39
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Bond | 1.0867 | 1.0867 | 1.0867 | 0.0 | 49.22
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Neigh | 0.0081377 | 0.0081377 | 0.0081377 | 0.0 | 0.37
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Comm | 0.017823 | 0.017823 | 0.017823 | 0.0 | 0.81
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Output | 0.0011017 | 0.0011017 | 0.0011017 | 0.0 | 0.05
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Modify | 0.21444 | 0.21444 | 0.21444 | 0.0 | 9.71
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Other | | 0.07595 | | | 3.44
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Nlocal: 34 ave 34 max 34 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: 395 ave 395 max 395 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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 = 230
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Dangerous builds = 0
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Total wall time: 0:00:02
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