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 2 by 2 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) = 15.58 | 15.58 | 15.58 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 2.9851021e-14 4.2188475e-15 13990.5
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50 -634.17349 -666.17817 32.004686 1151.6234 -4029.8405 -667.9562 37.809075 989.23283 -1694.9981 1.778024 9.7133822 2.1917966 13990.5
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100 -631.93517 -661.91227 29.977104 1078.665 -3171.8044 -664.0672 39.333371 991.36937 -1694.7699 2.1549315 11.091441 2.1704346 13990.5
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150 -630.16822 -663.12423 32.956001 1185.8545 143.24615 -665.48041 46.253736 982.97453 -1694.7087 2.3561828 11.467862 2.1651517 13990.5
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200 -628.6223 -663.6493 35.026994 1260.375 -1622.4428 -665.96885 41.661825 986.81675 -1694.4474 2.3195537 10.597709 2.9538132 13990.5
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250 -627.31146 -662.01843 34.706968 1248.8595 -1509.7149 -664.50329 42.10159 987.90193 -1694.5068 2.4848612 10.392642 1.693337 13990.5
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300 -626.57661 -660.97479 34.398178 1237.7483 -1637.8266 -663.48071 41.653258 989.53241 -1694.6664 2.5059269 11.20455 2.2814851 13990.5
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350 -625.91971 -665.3583 39.438589 1419.1172 -1351.5076 -667.61665 41.582479 985.53388 -1694.733 2.2583457 10.831559 1.8963688 13990.5
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400 -625.24855 -660.7758 35.527253 1278.3758 -423.70384 -663.1256 43.89223 987.7506 -1694.7684 2.349799 11.523597 2.1775994 13990.5
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450 -624.6774 -662.88749 38.210092 1374.9123 1108.7784 -665.43272 46.964156 982.35233 -1694.7492 2.5452316 11.002239 2.001871 13990.5
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500 -624.30227 -661.97992 37.677648 1355.7533 -998.38049 -664.60501 42.373269 987.58935 -1694.5676 2.6250971 11.151918 2.8270144 13990.5
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Loop time of 1.9161 on 4 procs for 500 steps with 432 atoms
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Performance: 45.092 ns/day, 0.532 hours/ns, 260.946 timesteps/s
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98.1% CPU use with 4 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 | 1.3101 | 1.4046 | 1.5088 | 5.9 | 73.31
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Bond | 0.00073409 | 0.00074953 | 0.00076699 | 0.0 | 0.04
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Kspace | 0.20996 | 0.30779 | 0.39708 | 12.0 | 16.06
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Neigh | 0.065428 | 0.065516 | 0.065591 | 0.0 | 3.42
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Comm | 0.12002 | 0.12628 | 0.13124 | 1.2 | 6.59
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Output | 0.00047278 | 0.00062203 | 0.0010662 | 0.0 | 0.03
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Modify | 0.0061893 | 0.0064721 | 0.0066924 | 0.2 | 0.34
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Other | | 0.004042 | | | 0.21
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Nlocal: 108 ave 119 max 102 min
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Histogram: 1 1 1 0 0 0 0 0 0 1
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Nghost: 6516 ave 6545 max 6491 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Neighs: 74337.8 ave 81248 max 69989 min
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Histogram: 1 0 2 0 0 0 0 0 0 1
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Total # of neighbors = 297351
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Ave neighs/atom = 688.312
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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) = 15.59 | 15.65 | 15.84 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 -661.97992 37.677763 1355.7575 -998.38049 -664.60501 42.373269 987.58935 -1694.5676 2.6250971 11.151918 2.8270144 13990.5
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550 -615.79609 -659.53283 43.736746 1573.7776 1474.8922 -662.39181 46.806896 985.54114 -1694.7399 2.858983 11.812288 2.0388938 13959.445
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600 -620.14312 -658.02816 37.88504 1363.2159 -1969.137 -660.59055 39.918958 994.06227 -1694.5718 2.5623852 10.344301 1.7265857 14345.491
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650 -614.8194 -655.14772 40.328319 1451.1323 1362.2165 -658.04338 47.289196 989.28021 -1694.6128 2.8956629 12.77476 2.1533941 14308.181
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700 -620.02982 -659.67169 39.641877 1426.4321 437.18253 -662.22416 45.260412 986.94645 -1694.431 2.5524634 10.78512 2.0136405 14434.476
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750 -616.07569 -654.50017 38.424477 1382.6265 -256.57498 -657.55133 43.657506 993.54515 -1694.754 3.0511562 11.572553 3.3391993 14823.696
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800 -614.14966 -652.72914 38.579477 1388.2038 -584.44437 -655.14057 42.618194 996.80921 -1694.568 2.4114337 10.916418 1.4113651 15315.148
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850 -612.16455 -653.84169 41.677135 1499.6667 -441.98725 -656.42973 42.922374 995.29998 -1694.6521 2.5880353 11.829353 2.135168 15445.115
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900 -615.1092 -656.96201 41.85281 1505.988 374.2354 -659.60969 44.82627 989.96538 -1694.4013 2.6476821 11.074704 1.5105804 14959.613
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950 -620.11829 -657.30032 37.18203 1337.9196 237.21273 -659.92487 44.925824 990.04501 -1694.8957 2.6245445 11.636019 2.6504684 14536.194
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1000 -614.74144 -660.36077 45.619322 1641.5183 890.12037 -663.18359 45.139971 986.56616 -1694.8897 2.8228194 11.867666 2.4545613 14093.503
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Loop time of 1.93169 on 4 procs for 500 steps with 432 atoms
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Performance: 44.728 ns/day, 0.537 hours/ns, 258.841 timesteps/s
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98.0% CPU use with 4 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 | 1.239 | 1.3639 | 1.4951 | 8.2 | 70.61
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Bond | 0.0009706 | 0.0010555 | 0.0010962 | 0.2 | 0.05
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Kspace | 0.22414 | 0.34623 | 0.46491 | 15.4 | 17.92
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Neigh | 0.069416 | 0.069507 | 0.06959 | 0.0 | 3.60
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Comm | 0.11461 | 0.12363 | 0.13004 | 1.6 | 6.40
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Output | 0.00040793 | 0.0006547 | 0.001394 | 0.0 | 0.03
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Modify | 0.022097 | 0.022964 | 0.023674 | 0.4 | 1.19
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Other | | 0.003751 | | | 0.19
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Nlocal: 108 ave 130 max 94 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Nghost: 6344.5 ave 6406 max 6272 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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Neighs: 72679.5 ave 88315 max 61830 min
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Histogram: 1 0 1 0 1 0 0 0 0 1
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Total # of neighbors = 290718
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Ave neighs/atom = 672.958
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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) = 0.17523
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estimated absolute RMS force accuracy = 1.49925e-05
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estimated relative force accuracy = 1.04117e-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) = 15.59 | 15.71 | 15.84 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 -614.74144 -660.36077 45.619322 1641.5183 897.55556 -663.18359 45.139971 986.31352 -1694.6371 2.8228194 11.867665 2.4545613 14093.503
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1050 -618.94984 -658.03173 39.081888 1406.2821 5.4174147 -660.68647 43.84377 989.81944 -1694.3497 2.6547475 10.009866 1.6559553 14124.735
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1100 -616.115 -652.50083 36.385826 1309.2698 246.27221 -655.60386 44.678646 993.96562 -1694.2481 3.1030335 12.845497 2.1365385 14269.044
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1150 -612.77698 -655.40444 42.627458 1533.8622 -394.23637 -658.16511 42.232098 993.95417 -1694.3514 2.7606635 10.588799 2.0797438 14526.576
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1200 -614.12785 -652.61572 38.487865 1384.9074 -1232.5709 -655.35877 40.844849 997.88225 -1694.0859 2.7430549 11.246738 2.4837618 14939.435
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1250 -612.01665 -651.53067 39.514016 1421.8313 -532.88057 -654.28679 42.767165 997.1403 -1694.1943 2.7561288 12.258706 3.8726564 15369.672
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1300 -616.56459 -654.91454 38.349957 1379.945 -41.331568 -657.57515 44.211159 992.57496 -1694.3613 2.6606091 11.147615 2.3545887 15492.237
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1350 -609.61162 -652.77366 43.162036 1553.0979 672.33089 -655.82423 44.690532 993.39227 -1693.907 3.0505702 11.680426 1.9918324 15294.141
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1400 -616.08355 -652.13969 36.056138 1297.4066 -1202.7428 -654.77053 41.470863 998.3537 -1694.5951 2.6308398 10.12054 1.9139605 15206.436
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1450 -613.53416 -655.92542 42.391264 1525.3632 -225.70273 -658.53945 42.800387 993.30095 -1694.6408 2.61403 10.475263 1.5543043 14786.088
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1500 -618.90281 -658.01769 39.114877 1407.4691 1689.1895 -660.56762 47.983304 985.87237 -1694.4233 2.5499298 12.160031 2.121879 14225.24
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1550 -619.95625 -660.95261 40.996357 1475.1703 162.48311 -663.63715 44.435076 986.14893 -1694.2212 2.6845396 11.400162 2.1028833 14097.469
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1600 -621.01142 -658.90113 37.889708 1363.3839 -1426.7573 -661.45407 41.336331 991.32904 -1694.1194 2.5529431 10.96667 1.8785672 14124.398
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1650 -616.93204 -657.21145 40.27941 1449.3725 1600.8152 -659.95623 47.433021 987.26391 -1694.6532 2.7447834 12.068379 2.0232824 13868.26
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1700 -613.94971 -656.25711 42.307399 1522.3455 -17.243012 -658.67143 43.416284 992.19931 -1694.287 2.4143179 10.33501 1.9231274 14268.199
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1750 -614.52671 -652.83727 38.310551 1378.5271 -1505.7623 -655.2978 40.639683 998.21477 -1694.1523 2.4605373 10.777496 1.8915025 14892.754
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1800 -608.85779 -650.27052 41.412727 1490.1526 -426.82921 -653.21627 42.824093 998.13559 -1694.176 2.9457492 12.624136 2.1758155 15177.014
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1850 -614.3254 -653.44307 39.117675 1407.5698 -10.449183 -656.43604 44.1397 993.33969 -1693.9154 2.992966 11.306721 2.0406266 14987.262
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1900 -617.0898 -655.8162 38.726395 1393.4904 -810.27608 -658.56819 42.357417 993.51569 -1694.4413 2.751989 11.117505 1.8829772 14850.207
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1950 -615.58194 -657.41631 41.834372 1505.3246 1466.9904 -660.21529 47.446402 986.51421 -1694.1759 2.7989828 12.408148 2.0449602 14609.998
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2000 -617.98223 -655.26933 37.287095 1341.7001 -728.80528 -658.12982 42.660772 993.38817 -1694.1788 2.8604933 11.117049 2.0691895 14608.511
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Loop time of 4.08624 on 4 procs for 1000 steps with 432 atoms
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Performance: 42.288 ns/day, 0.568 hours/ns, 244.724 timesteps/s
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97.6% CPU use with 4 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 | 2.5272 | 2.7629 | 3.169 | 14.9 | 67.62
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Bond | 0.001961 | 0.0021452 | 0.0023017 | 0.3 | 0.05
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Kspace | 0.48303 | 0.85591 | 1.0735 | 24.7 | 20.95
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Neigh | 0.14933 | 0.14943 | 0.14956 | 0.0 | 3.66
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Comm | 0.22499 | 0.25699 | 0.27433 | 3.8 | 6.29
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Output | 0.00085068 | 0.001357 | 0.0028689 | 2.4 | 0.03
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Modify | 0.048769 | 0.049731 | 0.051893 | 0.6 | 1.22
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Other | | 0.00775 | | | 0.19
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Nlocal: 108 ave 118 max 100 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Nghost: 6291.25 ave 6323 max 6256 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Neighs: 71221.2 ave 77896 max 66643 min
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Histogram: 1 1 0 0 1 0 0 0 0 1
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Total # of neighbors = 284885
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Ave neighs/atom = 659.456
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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: 0:00:07
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