forked from lijiext/lammps
279 lines
16 KiB
Groff
279 lines
16 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# Testsystem for core-shell model compared to Mitchell and Fincham
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# Hendrik Heenen, June 2014
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# ------------------------ INITIALIZATION ----------------------------
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units metal
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dimension 3
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boundary p p p
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atom_style full
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# ----------------------- ATOM DEFINITION ----------------------------
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fix csinfo all property/atom i_CSID
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read_data data.coreshell fix csinfo NULL CS-Info
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orthogonal box = (0 0 0) to (24.096 24.096 24.096)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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432 atoms
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scanning bonds ...
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1 = max bonds/atom
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reading bonds ...
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216 bonds
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1 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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group cores type 1 2
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216 atoms in group cores
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group shells type 3 4
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216 atoms in group shells
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neighbor 2.0 bin
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comm_modify vel yes
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# ------------------------ FORCE FIELDS ------------------------------
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kspace_style ewald 1.0e-6
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pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
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pair_coeff * * 0.0 1.000 0.00 0.00 0.00
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pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
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pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
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pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
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bond_style harmonic
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bond_coeff 1 63.014 0.0
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bond_coeff 2 25.724 0.0
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# ------------------------ Equilibration Run -------------------------------
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reset_timestep 0
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thermo 50
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thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
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compute CStemp all temp/cs cores shells
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compute thermo_press_lmp all pressure thermo_temp # press for correct kinetic scalar
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# output via chunk method
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#compute prop all property/atom i_CSID
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#compute cs_chunk all chunk/atom c_prop
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#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
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#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
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thermo_modify temp CStemp press thermo_press_lmp
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# 2 fmsec timestep
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timestep 0.002
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# velocity bias option
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velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CStemp
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Ewald initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.175257
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estimated absolute RMS force accuracy = 1.49563e-05
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estimated relative force accuracy = 1.03866e-06
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KSpace vectors: actual max1d max3d = 257 5 665
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kxmax kymax kzmax = 5 5 5
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 22
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ghost atom cutoff = 22
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binsize = 11, bins = 3 3 3
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair born/coul/long/cs, 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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velocity all scale 1427 temp CStemp
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# thermostating using the core/shell decoupling
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fix thermoberendsen all temp/berendsen 1427 1427 0.4
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fix nve all nve
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fix_modify thermoberendsen temp CStemp
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run 500
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Ewald initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.175257
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estimated absolute RMS force accuracy = 1.49563e-05
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estimated relative force accuracy = 1.03866e-06
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KSpace vectors: actual max1d max3d = 257 5 665
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kxmax kymax kzmax = 5 5 5
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Per MPI rank memory allocation (min/avg/max) = 17.29 | 17.29 | 17.29 Mbytes
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Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
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0 -635.44099 -675.09865 39.657659 1427 -20613.612 -675.09865 1.6320365 1018.8211 -1695.5518 0 2.7895988e-14 3.594347e-15 13990.5
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50 -634.17327 -666.17818 32.004909 1151.6314 -4029.8418 -667.9562 37.809071 989.23283 -1694.9981 1.7780231 9.7133792 2.191797 13990.5
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100 -631.93507 -661.91226 29.977186 1078.6679 -3171.7799 -664.06719 39.33341 991.36934 -1694.7699 2.1549313 11.091423 2.1704389 13990.5
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150 -630.16811 -663.12417 32.956056 1185.8565 143.26508 -665.48036 46.253769 982.97454 -1694.7087 2.3561935 11.467913 2.1652595 13990.5
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200 -628.62323 -663.64922 35.025998 1260.3391 -1622.4126 -665.96878 41.661879 986.81675 -1694.4474 2.3195587 10.597709 2.9538262 13990.5
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250 -627.31045 -662.01825 34.7078 1248.8894 -1509.6621 -664.50312 42.101718 987.90197 -1694.5068 2.4848739 10.392757 1.6933711 13990.5
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300 -626.57622 -660.97494 34.39872 1237.7678 -1637.8094 -663.48087 41.653234 989.53228 -1694.6664 2.5059303 11.204361 2.2809738 13990.5
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350 -625.91962 -665.35837 39.438749 1419.123 -1351.4779 -667.6167 41.582456 985.53382 -1694.733 2.2583289 10.83106 1.8963347 13990.5
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400 -625.24849 -660.77642 35.527934 1278.4003 -424.45104 -663.12602 43.890331 987.75201 -1694.7684 2.3495966 11.521966 2.175931 13990.5
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450 -624.67743 -662.88678 38.209353 1374.8857 1109.0155 -665.43212 46.964803 982.35208 -1694.749 2.5453383 11.002405 2.0014356 13990.5
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500 -624.30215 -661.97859 37.676437 1355.7098 -998.57286 -664.60382 42.373117 987.59021 -1694.5671 2.625227 11.153883 2.8270306 13990.5
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Loop time of 6.42035 on 1 procs for 500 steps with 432 atoms
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Performance: 13.457 ns/day, 1.783 hours/ns, 77.877 timesteps/s
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99.8% 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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Pair | 5.5082 | 5.5082 | 5.5082 | 0.0 | 85.79
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Bond | 0.0019779 | 0.0019779 | 0.0019779 | 0.0 | 0.03
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Kspace | 0.57472 | 0.57472 | 0.57472 | 0.0 | 8.95
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Neigh | 0.23256 | 0.23256 | 0.23256 | 0.0 | 3.62
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Comm | 0.086275 | 0.086275 | 0.086275 | 0.0 | 1.34
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Output | 0.00044322 | 0.00044322 | 0.00044322 | 0.0 | 0.01
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Modify | 0.012263 | 0.012263 | 0.012263 | 0.0 | 0.19
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Other | | 0.003893 | | | 0.06
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Nlocal: 432 ave 432 max 432 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 9338 ave 9338 max 9338 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 297354 ave 297354 max 297354 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 297354
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Ave neighs/atom = 688.319
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Ave special neighs/atom = 1
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Neighbor list builds = 22
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Dangerous builds = 0
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unfix thermoberendsen
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unfix nve
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fix npt_equ all npt temp 1427 1427 0.04 iso 0 0 0.4
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fix_modify npt_equ temp CStemp press thermo_press_lmp # pressure for correct kinetic scalar
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run 500
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Ewald initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.175257
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estimated absolute RMS force accuracy = 1.49563e-05
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estimated relative force accuracy = 1.03866e-06
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KSpace vectors: actual max1d max3d = 257 5 665
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kxmax kymax kzmax = 5 5 5
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Per MPI rank memory allocation (min/avg/max) = 17.29 | 17.29 | 17.29 Mbytes
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Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
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500 -624.30215 -661.97859 37.676437 1355.7098 -998.57286 -664.60382 42.373117 987.59021 -1694.5671 2.625227 11.153883 2.8270306 13990.5
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550 -615.79469 -659.53309 43.738406 1573.8374 1470.2728 -662.39233 46.796275 985.55051 -1694.7391 2.8592421 11.816222 2.0435827 13959.536
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600 -620.1583 -658.0606 37.902298 1363.8369 -1976.0423 -660.62151 39.901722 994.0484 -1694.5716 2.5609098 10.333069 1.7024274 14344.949
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650 -614.79177 -655.16909 40.377318 1452.8955 1369.3632 -658.06385 47.296696 989.25356 -1694.6141 2.8947623 12.7805 2.1488232 14305.838
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700 -619.96986 -659.64497 39.675118 1427.6282 455.78012 -662.19977 45.29754 986.93209 -1694.4294 2.554791 10.780261 2.0068563 14432.96
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750 -616.0691 -654.36205 38.29295 1377.8937 -241.86552 -657.41633 43.727007 993.62088 -1694.7642 3.0542755 11.706048 3.3689413 14829.924
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800 -614.16673 -652.57617 38.409441 1382.0854 -552.93403 -655.00904 42.769389 996.79939 -1694.5778 2.4328709 11.05387 1.3686986 15324.864
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850 -611.92307 -653.97912 42.056053 1513.3013 -685.21581 -656.44468 42.244804 996.03742 -1694.7269 2.4655655 11.681335 1.9879277 15467.594
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900 -615.2753 -658.9358 43.660499 1571.034 -243.69139 -661.50959 43.098716 989.8049 -1694.4132 2.573788 10.674681 1.6541594 14964.747
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950 -617.05845 -655.42907 38.370623 1380.6886 607.78657 -658.13583 45.497112 991.02201 -1694.6549 2.7067567 12.70332 2.4561886 14472.808
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1000 -618.16527 -657.57073 39.405466 1417.9254 416.69904 -660.62844 45.155689 988.77163 -1694.5558 3.0577092 11.730529 1.8247965 14362.255
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Loop time of 6.22988 on 1 procs for 500 steps with 432 atoms
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Performance: 13.869 ns/day, 1.731 hours/ns, 80.258 timesteps/s
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99.8% 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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Pair | 5.2759 | 5.2759 | 5.2759 | 0.0 | 84.69
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Bond | 0.0028615 | 0.0028615 | 0.0028615 | 0.0 | 0.05
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Kspace | 0.57661 | 0.57661 | 0.57661 | 0.0 | 9.26
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Neigh | 0.24735 | 0.24735 | 0.24735 | 0.0 | 3.97
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Comm | 0.083591 | 0.083591 | 0.083591 | 0.0 | 1.34
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Output | 0.0004077 | 0.0004077 | 0.0004077 | 0.0 | 0.01
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Modify | 0.03937 | 0.03937 | 0.03937 | 0.0 | 0.63
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Other | | 0.003794 | | | 0.06
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Nlocal: 432 ave 432 max 432 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 9025 ave 9025 max 9025 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 290026 ave 290026 max 290026 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 290026
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Ave neighs/atom = 671.356
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Ave special neighs/atom = 1
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Neighbor list builds = 24
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Dangerous builds = 0
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unfix npt_equ
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# ------------------------ Dynamic Run -------------------------------
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fix npt_dyn all npt temp 1427 1427 0.04 iso 0 0 0.4
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fix_modify npt_dyn temp CStemp press thermo_press_lmp # pressure for correct kinetic scalar
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run 1000
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Ewald initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.175163
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estimated absolute RMS force accuracy = 1.51081e-05
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estimated relative force accuracy = 1.0492e-06
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KSpace vectors: actual max1d max3d = 257 5 665
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kxmax kymax kzmax = 5 5 5
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Per MPI rank memory allocation (min/avg/max) = 17.29 | 17.29 | 17.29 Mbytes
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Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
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1000 -618.16527 -657.57073 39.405466 1417.9254 428.20902 -660.62844 45.155689 987.86858 -1693.6527 3.0577092 11.730529 1.8247964 14362.255
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1050 -624.47216 -659.74932 35.277161 1269.3767 1023.4005 -662.65642 47.132969 983.86865 -1693.658 2.9071018 11.128238 2.4855361 14240.043
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1100 -617.14258 -658.07887 40.936282 1473.0087 -664.49152 -660.92582 42.224469 990.57675 -1693.727 2.8469569 11.75658 2.4149634 14408.926
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1150 -619.61978 -657.61169 37.991909 1367.0614 -465.46433 -660.31084 43.105221 989.99318 -1693.4092 2.699159 10.782062 2.1690057 14554.158
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1200 -615.99237 -657.2408 41.248432 1484.2407 -813.35983 -660.07564 41.678196 991.8399 -1693.5937 2.8348373 10.545446 2.1121233 14555.425
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1250 -626.68392 -658.41883 31.734906 1141.9159 -539.79478 -660.84299 44.20365 988.80199 -1693.8486 2.4241661 11.395962 2.135851 14575.926
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1300 -617.50678 -657.21802 39.711239 1428.928 1685.6002 -659.90723 48.138182 985.72575 -1693.7712 2.6892077 12.721388 1.8776177 14369.009
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1350 -622.21239 -658.79581 36.583414 1316.3796 -799.75314 -661.51494 42.733724 989.2771 -1693.5258 2.7191347 11.211319 2.3809801 14613.392
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1400 -614.34638 -654.89562 40.549232 1459.0815 1192.2924 -657.82292 46.886633 988.93592 -1693.6455 2.927306 11.818277 2.0357932 15050.984
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1450 -614.74459 -651.08463 36.340044 1307.6224 -941.42354 -653.80733 42.373988 997.48406 -1693.6654 2.7226961 11.57117 1.9107106 15667.952
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1500 -608.59499 -648.39988 39.804894 1432.2979 -1036.978 -651.42193 41.284322 1000.5742 -1693.2804 3.0220531 10.965804 1.9225015 15657.799
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1550 -616.75971 -653.701 36.941282 1329.2567 956.80287 -656.37213 46.958724 990.63147 -1693.9623 2.6711387 11.270035 2.1646421 15283.769
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1600 -614.00249 -655.22129 41.218796 1483.1743 162.86851 -658.03388 44.578553 990.97117 -1693.5836 2.8125894 12.001595 2.1613558 15014.979
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1650 -620.21853 -658.7696 38.551071 1387.1817 -15.994219 -661.3575 44.417732 988.12137 -1693.8966 2.5879024 11.60402 2.2188998 14421.685
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1700 -621.65896 -660.14043 38.481472 1384.6773 374.01196 -662.88364 45.046442 985.61668 -1693.5468 2.7432107 11.020422 2.0354876 13843.115
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1750 -626.52363 -662.7125 36.188873 1302.1828 246.87832 -665.23873 45.613954 983.17191 -1694.0246 2.5262291 12.801515 2.4291407 13584.377
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1800 -620.84342 -658.64915 37.805737 1360.3624 1419.6927 -661.54346 47.476679 984.72199 -1693.7421 2.8943029 13.331926 2.1690676 13249.778
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1850 -618.96345 -661.03809 42.074638 1513.9701 1692.1613 -663.74409 47.099139 982.71413 -1693.5574 2.7060076 11.521214 1.6552929 13269.978
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1900 -622.60007 -658.68592 36.085857 1298.476 -1580.4079 -661.4614 41.163528 991.0778 -1693.7027 2.7754739 10.427911 1.946547 14057.045
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1950 -613.97975 -656.9327 42.952955 1545.5745 -1163.9497 -659.48701 40.688202 993.61603 -1693.7912 2.5543044 10.621596 2.2183688 14489.331
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2000 -613.52562 -654.78948 41.263864 1484.796 646.07695 -657.76756 45.489785 990.40525 -1693.6626 2.978081 12.135455 2.3293 14760.827
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Loop time of 12.672 on 1 procs for 1000 steps with 432 atoms
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Performance: 13.636 ns/day, 1.760 hours/ns, 78.914 timesteps/s
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99.8% 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 | 10.73 | 10.73 | 10.73 | 0.0 | 84.67
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Bond | 0.0057325 | 0.0057325 | 0.0057325 | 0.0 | 0.05
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Kspace | 1.1532 | 1.1532 | 1.1532 | 0.0 | 9.10
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Neigh | 0.52571 | 0.52571 | 0.52571 | 0.0 | 4.15
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Comm | 0.17069 | 0.17069 | 0.17069 | 0.0 | 1.35
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Output | 0.00081754 | 0.00081754 | 0.00081754 | 0.0 | 0.01
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Modify | 0.078469 | 0.078469 | 0.078469 | 0.0 | 0.62
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Other | | 0.007788 | | | 0.06
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Nlocal: 432 ave 432 max 432 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 8927 ave 8927 max 8927 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 281696 ave 281696 max 281696 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 281696
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Ave neighs/atom = 652.074
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Ave special neighs/atom = 1
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Neighbor list builds = 50
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Dangerous builds = 0
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Total wall time: 0:00:25
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