165 lines
9.0 KiB
Groff
165 lines
9.0 KiB
Groff
LAMMPS (29 Sep 2021)
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# test script for fix mol/swap
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# initial system is 50/50 chains of type 1 and type 2
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# b/c epsilon12 is set to 1.1 (stronger than 1/1 or 2/2) the
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# system will go to equilibrium as mostly one type or the other
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# fix mol/swap helps this happen quickly
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# see the last 2 columns of thermo output for counts of 2 chain types
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units lj
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atom_style angle
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neighbor 0.36 bin
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neigh_modify delay 0
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pair_style lj/cut 1.1224620483
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bond_style fene
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angle_style cosine
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special_bonds lj 0.0 1.0 1.0
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read_data data.bead
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Reading data file ...
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orthogonal box = (-8.2115700 -8.2115700 -8.2115700) to (8.2115700 8.2115700 8.2115700)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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4000 atoms
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scanning bonds ...
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1 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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3900 bonds
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reading angles ...
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3800 angles
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 1 1
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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4 = max # of 1-4 neighbors
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6 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.034 seconds
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pair_coeff * * 1.0 1.0 1.1224620483
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pair_coeff 1 2 1.1 1.0 1.1224620483
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bond_coeff 1 30.0 1.5 1.0 1.0
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angle_coeff 1 1.500
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pair_modify shift yes
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variable vt1 atom type==1
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variable vt2 atom type==2
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group g1 dynamic all var vt1 every 100
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dynamic group g1 defined
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group g2 dynamic all var vt2 every 100
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dynamic group g2 defined
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variable count1 equal count(g1)
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variable count2 equal count(g2)
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timestep 0.010
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fix 1 all langevin 1.0 1.0 100.0 702547
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fix 2 all nve
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fix 3 all mol/swap 100 1 1 2 482794 1.0
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compute p all pressure thermo_temp
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thermo 1000
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thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
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run 50000
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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 = 1.482462
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ghost atom cutoff = 1.482462
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binsize = 0.74123102, bins = 23 23 23
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, 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
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bin: standard
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WARNING: Communication cutoff 1.4824620483 is shorter than a bond length based estimate of 1.815. This may lead to errors. (../comm.cpp:728)
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Per MPI rank memory allocation (min/avg/max) = 5.313 | 5.314 | 5.314 Mbytes
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Step Temp TotEng Press f_3[1] f_3[2] v_count1 v_count2
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0 0 21.4699 5.230121 0 0 2000 2000
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1000 0.50228459 21.61044 4.3659303 10 9 1960 2040
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2000 0.55721903 21.75955 4.5695439 20 17 1960 2040
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3000 0.61139287 21.892943 4.6514755 30 26 2240 1760
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4000 0.65767189 22.002303 5.1854503 40 33 2280 1720
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5000 0.69383416 22.110271 5.3803498 50 41 2280 1720
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6000 0.72692038 22.205887 5.1756569 60 49 2280 1720
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7000 0.77151336 22.306777 5.5743555 70 56 2240 1760
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8000 0.78606858 22.37036 5.7745208 80 64 2560 1440
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9000 0.79363653 22.420931 5.7369418 90 71 2680 1320
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10000 0.82352629 22.488759 6.0238896 100 76 2720 1280
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11000 0.83867685 22.534887 6.1263771 110 82 2800 1200
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12000 0.85335127 22.590281 6.1499954 120 86 2800 1200
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13000 0.86430985 22.632068 6.1654016 130 89 2760 1240
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14000 0.88057592 22.680253 6.2162735 140 94 2800 1200
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15000 0.89326694 22.719731 6.4789839 150 97 2760 1240
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16000 0.90667644 22.737367 6.214481 160 101 2760 1240
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17000 0.91190336 22.758572 6.2293336 170 105 2600 1400
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18000 0.93182455 22.782019 6.2865382 180 111 2680 1320
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19000 0.93002139 22.797048 6.5579988 190 117 2600 1400
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20000 0.92396243 22.796108 6.6207461 200 122 2800 1200
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21000 0.92949808 22.802813 6.3753268 210 125 2920 1080
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22000 0.93415719 22.807112 6.4696121 220 130 3040 960
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23000 0.9214833 22.82116 6.4146288 230 131 3080 920
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24000 0.95693685 22.839738 6.4035728 240 135 2920 1080
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25000 0.95421851 22.865199 6.4510751 250 138 2880 1120
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26000 0.95476555 22.878082 6.4652888 260 145 3000 1000
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27000 0.95773535 22.880671 6.757952 270 149 3000 1000
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28000 0.95405332 22.896053 6.7425175 280 155 3080 920
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29000 0.95955713 22.904144 6.6672832 290 161 3240 760
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30000 0.95521498 22.886699 6.6197941 300 164 3360 640
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31000 0.96431176 22.91094 6.6373887 310 168 3440 560
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32000 0.96592495 22.903679 6.4245884 320 172 3520 480
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33000 0.96457971 22.922681 6.6987987 330 175 3480 520
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34000 0.96541889 22.92116 6.5992755 340 178 3600 400
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35000 0.96892691 22.923361 6.7973298 350 178 3600 400
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36000 0.97267726 22.923431 6.6577403 360 179 3640 360
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37000 0.97514714 22.939979 6.4028068 370 183 3640 360
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38000 0.98638599 22.952022 6.6518868 380 183 3640 360
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39000 0.97864891 22.962534 6.3906837 390 184 3680 320
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40000 0.9933016 22.975785 6.6819613 400 185 3720 280
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41000 0.9861477 22.977271 6.6747347 410 187 3800 200
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42000 0.98157369 22.963129 6.830028 420 187 3800 200
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43000 0.98202452 22.966947 6.5257905 430 187 3800 200
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44000 0.99540503 22.971262 6.5546513 440 187 3800 200
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45000 0.98433653 22.978028 6.4316725 450 189 3800 200
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46000 0.97912775 22.981328 6.9139851 460 189 3800 200
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47000 0.9791927 22.981131 6.6417971 470 190 3840 160
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48000 0.99601024 22.998536 6.6756953 480 191 3880 120
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49000 0.99589958 22.998489 6.9262843 490 191 3880 120
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50000 0.99294715 23.00399 6.6976013 500 192 3920 80
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Loop time of 19.5161 on 4 procs for 50000 steps with 4000 atoms
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Performance: 2213556.537 tau/day, 2561.987 timesteps/s
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95.0% 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 | 2.6256 | 2.7183 | 2.8265 | 5.2 | 13.93
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Bond | 2.3363 | 2.4406 | 2.5197 | 4.8 | 12.51
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Neigh | 7.382 | 7.3884 | 7.3936 | 0.2 | 37.86
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Comm | 3.014 | 3.2136 | 3.3994 | 9.4 | 16.47
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Output | 0.0014574 | 0.0017086 | 0.0020613 | 0.5 | 0.01
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Modify | 3.0282 | 3.1295 | 3.2034 | 4.1 | 16.04
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Other | | 0.624 | | | 3.20
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Nlocal: 1000.00 ave 1011 max 993 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Nghost: 1187.25 ave 1202 max 1179 min
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Histogram: 2 0 0 1 0 0 0 0 0 1
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Neighs: 4939.25 ave 5067 max 4850 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Total # of neighbors = 19757
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Ave neighs/atom = 4.9392500
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Ave special neighs/atom = 5.7000000
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Neighbor list builds = 10714
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Dangerous builds = 0
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Total wall time: 0:00:19
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