forked from lijiext/lammps
219 lines
12 KiB
Groff
219 lines
12 KiB
Groff
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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 Mitchel and Finchham
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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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# 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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# 2 fmsec timestep
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timestep 0.002
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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 1.9801 on 4 procs for 500 steps with 432 atoms
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Performance: 43.634 ns/day, 0.550 hours/ns, 252.513 timesteps/s
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98.3% 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 | 1.3316 | 1.4349 | 1.5717 | 7.8 | 72.46
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Bond | 0.00071955 | 0.00073642 | 0.00075316 | 0.0 | 0.04
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Kspace | 0.20621 | 0.33644 | 0.43824 | 15.7 | 16.99
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Neigh | 0.065812 | 0.065825 | 0.065829 | 0.0 | 3.32
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Comm | 0.11763 | 0.12492 | 0.12828 | 1.2 | 6.31
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Output | 0.0004766 | 0.0020956 | 0.0069461 | 6.1 | 0.11
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Modify | 0.0063045 | 0.0071256 | 0.0079646 | 1.0 | 0.36
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Other | | 0.008101 | | | 0.41
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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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# ------------------------ Dynamic Run -------------------------------
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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) = 0.175257
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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 -624.307 -662.13312 37.826117 1361.0957 331.61441 -664.76755 45.316291 984.7202 -1694.804 2.6344363 10.876847 1.9725627 13990.5
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600 -624.30999 -661.82604 37.516052 1349.9386 -977.02006 -664.34278 42.382897 987.88146 -1694.6071 2.5167365 10.214195 1.7874159 13990.5
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650 -624.30519 -659.19917 34.89398 1255.5887 549.29026 -661.95827 46.555452 986.06834 -1694.5821 2.7590968 13.15971 2.150802 13990.5
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700 -624.30925 -661.91134 37.60209 1353.0346 -173.75617 -664.45296 44.284848 985.83333 -1694.5711 2.5416162 10.971743 1.9844905 13990.5
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750 -624.30957 -660.4111 36.101528 1299.0399 1224.7615 -663.20844 47.513495 984.09149 -1694.8134 2.7973427 11.760288 2.1436426 13990.5
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800 -624.30443 -660.29859 35.994159 1295.1764 274.44426 -663.2484 45.216978 986.25498 -1694.7204 2.9498134 11.512509 4.0054687 13990.5
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850 -624.30771 -663.64907 39.341363 1415.6187 339.0107 -666.13161 45.126833 983.39086 -1694.6493 2.4825413 11.020953 2.1719529 13990.5
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900 -624.30318 -658.79061 34.487426 1240.9597 326.93573 -661.83606 45.870868 987.13858 -1694.8455 3.0454534 12.639272 1.9516031 13990.5
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950 -624.30275 -663.63565 39.332892 1415.3139 -668.82258 -665.98818 43.090661 985.63359 -1694.7124 2.3525337 11.014784 2.0742438 13990.5
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1000 -624.30302 -660.58037 36.27735 1305.3665 -725.43356 -663.2066 42.991534 988.36047 -1694.5586 2.6262239 10.521127 1.8763991 13990.5
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1050 -624.30291 -660.75751 36.454601 1311.7445 834.87442 -663.66586 46.551242 984.37581 -1694.5929 2.908347 11.20897 2.1312758 13990.5
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1100 -624.30709 -663.05705 38.749955 1394.3381 -709.57897 -665.5853 42.840927 986.33077 -1694.757 2.5282501 10.630015 2.6077838 13990.5
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1150 -624.31167 -663.16861 38.856933 1398.1875 -202.93169 -665.68694 43.83137 985.37199 -1694.8903 2.5183367 10.924515 2.9847813 13990.5
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1200 -624.30447 -660.45656 36.152088 1300.8592 -490.40029 -663.44614 43.512278 987.25887 -1694.2173 2.9895748 11.017505 2.1685389 13990.5
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1250 -624.3046 -661.95895 37.654347 1354.9149 -1405.9374 -664.49438 41.407094 988.59571 -1694.4972 2.5354305 11.05786 2.0138426 13990.5
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1300 -624.30002 -659.01152 34.711493 1249.0223 414.13124 -661.65532 45.873988 986.98863 -1694.5179 2.6438076 11.612439 2.2823703 13990.5
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1350 -624.31114 -659.05277 34.741631 1250.1068 795.03396 -661.48604 46.584896 986.7784 -1694.8493 2.43327 10.382832 1.616191 13990.5
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1400 -624.30512 -661.30058 36.995459 1331.2062 -1144.6328 -663.78961 41.970109 989.12976 -1694.8895 2.4890256 9.9264597 2.1371617 13990.5
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1450 -624.30479 -657.8718 33.567014 1207.8406 980.42716 -660.87614 47.207833 986.87048 -1694.9545 3.004339 11.783025 2.7986076 13990.5
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1500 -624.30058 -658.54923 34.248643 1232.3676 -728.22612 -661.1865 43.605107 989.73327 -1694.5249 2.6372721 11.688084 2.5466244 13990.5
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Loop time of 4.08004 on 4 procs for 1000 steps with 432 atoms
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Performance: 42.353 ns/day, 0.567 hours/ns, 245.096 timesteps/s
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97.7% 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 | 2.7379 | 2.8952 | 3.2162 | 11.5 | 70.96
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Bond | 0.0014176 | 0.0015033 | 0.0016136 | 0.2 | 0.04
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Kspace | 0.47825 | 0.7808 | 0.93251 | 20.9 | 19.14
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Neigh | 0.13731 | 0.13815 | 0.13904 | 0.2 | 3.39
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Comm | 0.23139 | 0.25066 | 0.2586 | 2.2 | 6.14
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Output | 0.0010233 | 0.0015535 | 0.0031006 | 2.3 | 0.04
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Modify | 0.0025311 | 0.0026742 | 0.0028279 | 0.2 | 0.07
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Other | | 0.00951 | | | 0.23
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Nlocal: 108 ave 116 max 98 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Nghost: 6461.75 ave 6504 max 6437 min
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Histogram: 2 0 0 0 1 0 0 0 0 1
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Neighs: 74412.8 ave 81159 max 68634 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Total # of neighbors = 297651
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Ave neighs/atom = 689.007
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Ave special neighs/atom = 1
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Neighbor list builds = 46
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Dangerous builds = 0
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Total wall time: 0:00:06
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