clean up doc src
This commit is contained in:
Steve Plimpton
209
examples/coreshell/log.5Oct16.coreshell.g++.1
Normal file
209
examples/coreshell/log.5Oct16.coreshell.g++.1
Normal file
@ -0,0 +1,209 @@
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LAMMPS (5 Oct 2016)
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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 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 CSequ all temp/cs cores shells
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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 CSequ
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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 CSequ
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Ewald initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
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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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1 neighbor list requests
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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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velocity all scale 1427 temp CSequ
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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 CSequ
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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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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
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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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Memory usage per processor = 15.7472 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 -4030.3308 -667.95621 37.809071 989.23282 -1694.9981 1.7780231 9.7133792 2.1917971 13990.5
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100 -631.93508 -661.91226 29.977186 1078.6679 -3172.6296 -664.0672 39.333409 991.36934 -1694.7699 2.1549314 11.091424 2.1704389 13990.5
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150 -630.1681 -663.12416 32.956057 1185.8565 142.25543 -665.48036 46.253767 982.97455 -1694.7087 2.3561935 11.467914 2.1652594 13990.5
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200 -628.62323 -663.64923 35.025998 1260.3391 -1623.5465 -665.96879 41.661877 986.81675 -1694.4474 2.3195587 10.597709 2.9538263 13990.5
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250 -627.31045 -662.01825 34.707801 1248.8894 -1510.5567 -664.50313 42.101716 987.90197 -1694.5068 2.4848735 10.392755 1.6933702 13990.5
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300 -626.57622 -660.97494 34.398716 1237.7677 -1638.6653 -663.48087 41.653234 989.53228 -1694.6664 2.5059308 11.204363 2.2809764 13990.5
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350 -625.91962 -665.35838 39.438756 1419.1232 -1352.4038 -667.6167 41.582459 985.53381 -1694.733 2.2583269 10.83105 1.8963306 13990.5
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400 -625.24851 -660.77642 35.527912 1278.3995 -425.3358 -663.12602 43.890329 987.75201 -1694.7684 2.3495978 11.521967 2.1759207 13990.5
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450 -624.67742 -662.88674 38.209317 1374.8844 1108.0844 -665.43207 46.964873 982.35206 -1694.749 2.5453361 11.002418 2.0014401 13990.5
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500 -624.30218 -661.97851 37.676336 1355.7061 -999.37887 -664.60374 42.373166 987.59022 -1694.5671 2.6252269 11.153982 2.8270477 13990.5
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Loop time of 8.64071 on 1 procs for 500 steps with 432 atoms
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Performance: 9.999 ns/day, 2.400 hours/ns, 57.866 timesteps/s
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99.9% CPU use with 1 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 | 7.824 | 7.824 | 7.824 | 0.0 | 90.55
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Bond | 0.0024104 | 0.0024104 | 0.0024104 | 0.0 | 0.03
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Kspace | 0.53534 | 0.53534 | 0.53534 | 0.0 | 6.20
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Neigh | 0.19522 | 0.19522 | 0.19522 | 0.0 | 2.26
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Comm | 0.066091 | 0.066091 | 0.066091 | 0.0 | 0.76
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Output | 0.0003643 | 0.0003643 | 0.0003643 | 0.0 | 0.00
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Modify | 0.011435 | 0.011435 | 0.011435 | 0.0 | 0.13
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Other | | 0.005869 | | | 0.07
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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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# ------------------------ Dynamic Run -------------------------------
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run 1000
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Ewald initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
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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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Memory usage per processor = 15.7472 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 -624.30218 -661.97851 37.676336 1355.7061 -999.37887 -664.60374 42.373166 987.59022 -1694.5671 2.6252269 11.153982 2.8270477 13990.5
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550 -624.30708 -662.13355 37.826467 1361.1083 326.46254 -664.76811 45.306636 984.72863 -1694.8034 2.6345547 10.879989 1.9751675 13990.5
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600 -624.30994 -661.8449 37.534969 1350.6193 -984.35215 -664.36139 42.366573 987.8789 -1694.6069 2.516489 10.211098 1.7890339 13990.5
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650 -624.30501 -659.20596 34.900952 1255.8396 554.8226 -661.96471 46.567453 986.05088 -1694.583 2.7587454 13.15403 2.1657286 13990.5
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700 -624.30907 -661.85064 37.541572 1350.8569 -135.38668 -664.3843 44.382641 985.80654 -1694.5735 2.5336521 10.991882 2.0402026 13990.5
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750 -624.30999 -660.52853 36.21854 1303.2503 1196.4145 -663.29701 47.437312 984.08773 -1694.822 2.7684838 11.681986 2.0756933 13990.5
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800 -624.30488 -659.87594 35.571053 1279.9518 361.87762 -662.81183 45.49882 986.40712 -1694.7178 2.935891 11.519352 3.7801343 13990.5
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850 -624.30607 -663.64735 39.341278 1415.6157 -42.214824 -666.11278 44.277011 984.33678 -1694.7266 2.4654311 11.03941 1.9211474 13990.5
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900 -624.30048 -659.04455 34.744072 1250.1946 386.10592 -662.10941 45.864611 986.90301 -1694.877 3.0648637 12.126864 2.467969 13990.5
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950 -624.30795 -663.3468 39.038856 1404.7337 289.90291 -665.76693 45.27444 983.7762 -1694.8176 2.420128 11.735744 2.053808 13990.5
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1000 -624.303 -659.5513 35.248296 1268.3381 -896.7132 -662.30776 42.985505 989.11655 -1694.4098 2.7564586 11.38686 1.8136876 13990.5
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1050 -624.30433 -659.21593 34.911606 1256.223 273.26272 -661.98578 45.834363 986.93885 -1694.759 2.7698415 12.201066 1.9804734 13990.5
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1100 -624.3035 -660.37975 36.076254 1298.1305 40.2604 -662.88712 45.266447 986.77782 -1694.9314 2.5073688 11.366839 2.2452799 13990.5
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1150 -624.30832 -658.16356 33.855242 1218.2119 905.45817 -660.85689 47.381273 986.61927 -1694.8574 2.6933378 13.157497 2.3062872 13990.5
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1200 -624.30971 -665.57285 41.263142 1484.77 -2010.9356 -667.71783 39.858615 987.32002 -1694.8965 2.1449751 9.3563352 1.7115187 13990.5
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1250 -624.3069 -662.41936 38.112468 1371.3994 223.85833 -665.01906 45.021425 984.67299 -1694.7135 2.5997021 10.137667 1.8129534 13990.5
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1300 -624.3116 -661.73044 37.418835 1346.4405 524.83698 -664.46475 45.716001 983.98856 -1694.1693 2.734311 11.475107 2.5468008 13990.5
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1350 -624.30917 -661.34529 37.036121 1332.6693 399.81653 -663.86813 45.373759 985.3362 -1694.5781 2.5228434 10.819603 2.2048214 13990.5
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1400 -624.31545 -660.75213 36.43668 1311.0996 193.18853 -663.43944 45.172084 985.90744 -1694.519 2.6873128 10.597955 1.9090871 13990.5
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1450 -624.30419 -660.88131 36.577122 1316.1532 530.40423 -663.62017 46.21726 984.89723 -1694.7347 2.7388564 12.015146 2.6454091 13990.5
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1500 -624.30236 -660.40336 36.100999 1299.0209 -759.2259 -663.48374 43.382233 987.65506 -1694.521 3.0803837 12.48163 2.2113083 13990.5
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Loop time of 17.2383 on 1 procs for 1000 steps with 432 atoms
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Performance: 10.024 ns/day, 2.394 hours/ns, 58.011 timesteps/s
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99.9% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 15.619 | 15.619 | 15.619 | 0.0 | 90.61
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Bond | 0.0048032 | 0.0048032 | 0.0048032 | 0.0 | 0.03
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Kspace | 1.068 | 1.068 | 1.068 | 0.0 | 6.20
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Neigh | 0.39623 | 0.39623 | 0.39623 | 0.0 | 2.30
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Comm | 0.13052 | 0.13052 | 0.13052 | 0.0 | 0.76
|
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Output | 0.00067472 | 0.00067472 | 0.00067472 | 0.0 | 0.00
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Modify | 0.0071197 | 0.0071197 | 0.0071197 | 0.0 | 0.04
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Other | | 0.01175 | | | 0.07
|
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|
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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: 9327 ave 9327 max 9327 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 297525 ave 297525 max 297525 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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|
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Total # of neighbors = 297525
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||||
Ave neighs/atom = 688.715
|
||||
Ave special neighs/atom = 1
|
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Neighbor list builds = 45
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Dangerous builds = 0
|
||||
Total wall time: 0:00:25
|
||||
209
examples/coreshell/log.5Oct16.coreshell.g++.4
Normal file
209
examples/coreshell/log.5Oct16.coreshell.g++.4
Normal file
@ -0,0 +1,209 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Testsystem for core-shell model compared to Mitchel and Finchham
|
||||
# Hendrik Heenen, June 2014
|
||||
|
||||
# ------------------------ INITIALIZATION ----------------------------
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style full
|
||||
|
||||
# ----------------------- ATOM DEFINITION ----------------------------
|
||||
|
||||
fix csinfo all property/atom i_CSID
|
||||
read_data data.coreshell fix csinfo NULL CS-Info
|
||||
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
432 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
216 bonds
|
||||
1 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
|
||||
group cores type 1 2
|
||||
216 atoms in group cores
|
||||
group shells type 3 4
|
||||
216 atoms in group shells
|
||||
|
||||
neighbor 2.0 bin
|
||||
comm_modify vel yes
|
||||
|
||||
# ------------------------ FORCE FIELDS ------------------------------
|
||||
|
||||
kspace_style ewald 1.0e-6
|
||||
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
|
||||
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
|
||||
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
|
||||
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
|
||||
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 63.014 0.0
|
||||
bond_coeff 2 25.724 0.0
|
||||
|
||||
# ------------------------ Equilibration Run -------------------------------
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
|
||||
|
||||
compute CSequ all temp/cs cores shells
|
||||
|
||||
# output via chunk method
|
||||
|
||||
#compute prop all property/atom i_CSID
|
||||
#compute cs_chunk all chunk/atom c_prop
|
||||
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
|
||||
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
|
||||
|
||||
thermo_modify temp CSequ
|
||||
|
||||
# velocity bias option
|
||||
|
||||
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
|
||||
Ewald initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 22
|
||||
ghost atom cutoff = 22
|
||||
binsize = 11 -> bins = 3 3 3
|
||||
velocity all scale 1427 temp CSequ
|
||||
|
||||
fix thermoberendsen all temp/berendsen 1427 1427 0.4
|
||||
fix nve all nve
|
||||
fix_modify thermoberendsen temp CSequ
|
||||
|
||||
# 2 fmsec timestep
|
||||
|
||||
timestep 0.002
|
||||
run 500
|
||||
Ewald initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Memory usage per processor = 15.2111 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
|
||||
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
|
||||
50 -634.17349 -666.17817 32.004686 1151.6234 -4030.346 -667.9562 37.809075 989.23283 -1694.9981 1.7780241 9.7133824 2.1917971 13990.5
|
||||
100 -631.93518 -661.91229 29.977104 1078.665 -3172.6554 -664.06722 39.333371 991.36935 -1694.7699 2.1549316 11.09144 2.1704351 13990.5
|
||||
150 -630.16821 -663.12421 32.956001 1185.8545 142.23746 -665.48039 46.253735 982.97455 -1694.7087 2.3561823 11.467862 2.1651502 13990.5
|
||||
200 -628.62229 -663.64928 35.026994 1260.375 -1623.495 -665.96883 41.661825 986.81676 -1694.4474 2.3195535 10.597709 2.9538127 13990.5
|
||||
250 -627.31146 -662.01843 34.706969 1248.8595 -1510.677 -664.50329 42.10159 987.90193 -1694.5068 2.4848607 10.392642 1.6933333 13990.5
|
||||
300 -626.57662 -660.97479 34.398174 1237.7482 -1638.7013 -663.48072 41.653268 989.53239 -1694.6664 2.5059279 11.204558 2.2814875 13990.5
|
||||
350 -625.91972 -665.3583 39.438581 1419.1169 -1352.428 -667.61665 41.5825 985.53386 -1694.733 2.2583465 10.831573 1.8963653 13990.5
|
||||
400 -625.24854 -660.77581 35.527271 1278.3764 -424.57407 -663.12561 43.89225 987.75056 -1694.7684 2.3497967 11.523588 2.1775908 13990.5
|
||||
450 -624.67739 -662.88749 38.210098 1374.9125 1107.8255 -665.43273 46.964166 982.35231 -1694.7492 2.5452345 11.00224 2.0018738 13990.5
|
||||
500 -624.30227 -661.98003 37.677766 1355.7576 -999.27326 -664.60512 42.373091 987.58943 -1694.5676 2.6250858 11.151835 2.8270448 13990.5
|
||||
Loop time of 2.40619 on 4 procs for 500 steps with 432 atoms
|
||||
|
||||
Performance: 35.907 ns/day, 0.668 hours/ns, 207.797 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.7876 | 1.9016 | 2.0542 | 7.0 | 79.03
|
||||
Bond | 0.00064754 | 0.0006901 | 0.00074625 | 0.1 | 0.03
|
||||
Kspace | 0.16854 | 0.31596 | 0.42594 | 16.5 | 13.13
|
||||
Neigh | 0.051607 | 0.051768 | 0.051931 | 0.1 | 2.15
|
||||
Comm | 0.11933 | 0.12412 | 0.12769 | 0.9 | 5.16
|
||||
Output | 0.00039911 | 0.00042087 | 0.00047565 | 0.2 | 0.02
|
||||
Modify | 0.0059447 | 0.0063215 | 0.0067348 | 0.4 | 0.26
|
||||
Other | | 0.005341 | | | 0.22
|
||||
|
||||
Nlocal: 108 ave 119 max 102 min
|
||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||
Nghost: 6516 ave 6545 max 6491 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Neighs: 74337.8 ave 81248 max 69989 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 297351
|
||||
Ave neighs/atom = 688.312
|
||||
Ave special neighs/atom = 1
|
||||
Neighbor list builds = 22
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix thermoberendsen
|
||||
|
||||
# ------------------------ Dynamic Run -------------------------------
|
||||
|
||||
run 1000
|
||||
Ewald initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Memory usage per processor = 15.213 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
|
||||
500 -624.30215 -661.98003 37.677882 1355.7618 -999.26443 -664.60512 42.373091 987.58943 -1694.5676 2.6250858 11.151835 2.8270448 13990.5
|
||||
550 -624.30702 -662.13315 37.826126 1361.096 330.71041 -664.76759 45.316349 984.7201 -1694.804 2.6344423 10.876902 1.9726348 13990.5
|
||||
600 -624.31001 -661.82602 37.516015 1349.9373 -978.11503 -664.34272 42.382797 987.88159 -1694.6071 2.5166949 10.21416 1.787289 13990.5
|
||||
650 -624.30516 -659.19843 34.893268 1255.5631 548.43865 -661.95754 46.556222 986.06829 -1694.582 2.7591048 13.16005 2.1511562 13990.5
|
||||
700 -624.30926 -661.91108 37.601819 1353.0248 -175.1339 -664.4528 44.284398 985.834 -1694.5712 2.5417263 10.972065 1.9847042 13990.5
|
||||
750 -624.30955 -660.4096 36.100048 1298.9866 1222.5932 -663.20741 47.511377 984.09471 -1694.8135 2.7978144 11.761903 2.1481489 13990.5
|
||||
800 -624.30447 -660.30683 36.002357 1295.4714 270.6639 -663.25589 45.210122 986.25515 -1694.7212 2.9490566 11.50988 4.0037749 13990.5
|
||||
850 -624.30774 -663.65149 39.343757 1415.7049 339.356 -666.13397 45.12874 983.38616 -1694.6489 2.4824719 11.01305 2.1691298 13990.5
|
||||
900 -624.30311 -658.78647 34.483353 1240.8132 309.88983 -661.8322 45.836842 987.17541 -1694.8445 3.045732 12.635589 1.9594437 13990.5
|
||||
950 -624.303 -663.59545 39.292454 1413.8588 -649.78872 -665.94289 43.141981 985.63193 -1694.7168 2.347436 11.012602 2.0685819 13990.5
|
||||
1000 -624.3032 -660.59776 36.294555 1305.9856 -753.87453 -663.22012 42.930848 988.41708 -1694.568 2.6223608 10.526403 1.8887197 13990.5
|
||||
1050 -624.3023 -660.7017 36.399405 1309.7584 790.88591 -663.6376 46.453299 984.4785 -1694.5694 2.9359001 11.210429 2.1822375 13990.5
|
||||
1100 -624.30545 -662.76291 38.457457 1383.8132 -853.19698 -665.29416 42.533854 986.84955 -1694.6776 2.5312537 10.517674 2.6445601 13990.5
|
||||
1150 -624.31539 -663.03811 38.722722 1393.3582 -380.13868 -665.58847 43.476852 985.81618 -1694.8815 2.5503626 10.818389 1.9559813 13990.5
|
||||
1200 -624.3093 -659.85835 35.549055 1279.1603 44.140107 -662.93041 44.773497 986.67501 -1694.3789 3.0720506 11.310516 2.2601607 13990.5
|
||||
1250 -624.30277 -663.46462 39.161852 1409.1594 -352.57297 -666.0144 43.477124 984.93408 -1694.4256 2.5497829 10.720231 1.8458373 13990.5
|
||||
1300 -624.30329 -660.15937 35.85608 1290.2079 -348.83001 -662.73568 43.884677 988.07413 -1694.6945 2.5763161 11.369766 2.2580977 13990.5
|
||||
1350 -624.30469 -662.72631 38.421619 1382.5236 1338.9038 -665.20399 47.35379 982.28307 -1694.8408 2.4776776 10.587886 1.7677665 13990.5
|
||||
1400 -624.30499 -662.12513 37.820139 1360.8806 132.00801 -664.73589 44.55252 985.34275 -1694.6312 2.6107622 11.193448 2.1613441 13990.5
|
||||
1450 -624.30207 -661.42856 37.126485 1335.9209 2069.8075 -664.07373 49.544418 981.20445 -1694.8226 2.6451763 13.011189 3.3987593 13990.5
|
||||
1500 -624.29727 -656.99924 32.701969 1176.7137 504.56835 -660.08591 46.605885 987.7602 -1694.452 3.0866635 13.271242 3.025272 13990.5
|
||||
Loop time of 4.96339 on 4 procs for 1000 steps with 432 atoms
|
||||
|
||||
Performance: 34.815 ns/day, 0.689 hours/ns, 201.475 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.6491 | 3.8484 | 4.2642 | 12.4 | 77.54
|
||||
Bond | 0.0013638 | 0.0014506 | 0.0016019 | 0.2 | 0.03
|
||||
Kspace | 0.3347 | 0.73521 | 0.92903 | 27.3 | 14.81
|
||||
Neigh | 0.10979 | 0.11008 | 0.11042 | 0.1 | 2.22
|
||||
Comm | 0.23785 | 0.25289 | 0.2601 | 1.8 | 5.10
|
||||
Output | 0.0008378 | 0.00088245 | 0.00098872 | 0.2 | 0.02
|
||||
Modify | 0.0022187 | 0.0024077 | 0.0026662 | 0.3 | 0.05
|
||||
Other | | 0.01206 | | | 0.24
|
||||
|
||||
Nlocal: 108 ave 112 max 102 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Nghost: 6500.75 ave 6612 max 6392 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 74275 ave 77543 max 69706 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
|
||||
Total # of neighbors = 297100
|
||||
Ave neighs/atom = 687.731
|
||||
Ave special neighs/atom = 1
|
||||
Neighbor list builds = 45
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:07
|
||||
@ -1,188 +0,0 @@
|
||||
LAMMPS (5 Mar 2015)
|
||||
# Testsystem for core-shell model compared to Mitchel and Finchham
|
||||
# Hendrik Heenen, June 2014
|
||||
|
||||
# ------------------------ INITIALIZATION ----------------------------
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style full
|
||||
|
||||
# ----------------------- ATOM DEFINITION ----------------------------
|
||||
|
||||
fix csinfo all property/atom i_CSID
|
||||
read_data data.coreshell fix csinfo NULL CS-Info
|
||||
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
432 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
216 bonds
|
||||
1 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
|
||||
group cores type 1 2
|
||||
216 atoms in group cores
|
||||
group shells type 3 4
|
||||
216 atoms in group shells
|
||||
|
||||
neighbor 2.0 bin
|
||||
comm_modify vel yes
|
||||
|
||||
# ------------------------ FORCE FIELDS ------------------------------
|
||||
|
||||
kspace_style ewald 1.0e-6
|
||||
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
|
||||
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
|
||||
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
|
||||
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
|
||||
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 63.014 0.0
|
||||
bond_coeff 2 25.724 0.0
|
||||
|
||||
# ------------------------ Equilibration Run -------------------------------
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
|
||||
|
||||
compute CSequ all temp/cs cores shells
|
||||
|
||||
# output via chunk method
|
||||
|
||||
#compute prop all property/atom i_CSID
|
||||
#compute cs_chunk all chunk/atom c_prop
|
||||
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
|
||||
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
|
||||
|
||||
thermo_modify temp CSequ
|
||||
|
||||
# velocity bias option
|
||||
|
||||
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
|
||||
Ewald initialization ...
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
master list distance cutoff = 22
|
||||
velocity all scale 1427 temp CSequ
|
||||
|
||||
fix thermoberendsen all temp/berendsen 1427 1427 0.4
|
||||
fix nve all nve
|
||||
fix_modify thermoberendsen temp CSequ
|
||||
|
||||
# 2 fmsec timestep
|
||||
|
||||
timestep 0.002
|
||||
run 500
|
||||
Ewald initialization ...
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Memory usage per processor = 6.86279 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
|
||||
0 -628.35255 -668.0717 39.719144 1427 -20608.918 -668.0717 1.6320365 1025.8481 -1695.5518 0 3.4602128e-14 4.1910919e-15 13990.5
|
||||
50 -632.83924 -664.88103 32.041787 1151.1736 -4098.5062 -668.28414 37.966205 988.74855 -1694.9989 3.4031081 25.060198 9.2894103 13990.5
|
||||
100 -630.51517 -660.52949 30.014321 1078.3323 -3202.2416 -664.01378 39.505874 991.23277 -1694.7524 3.4842892 26.36833 10.674509 13990.5
|
||||
150 -628.58401 -661.59121 33.007195 1185.8581 106.75378 -665.3449 46.400029 982.93422 -1694.6791 3.7536882 27.270427 10.826035 13990.5
|
||||
200 -627.39592 -662.45902 35.063102 1259.7212 -1672.1319 -665.61583 41.658839 987.14579 -1694.4205 3.1568106 23.525213 6.58382 13990.5
|
||||
250 -625.74143 -660.30023 34.558805 1241.6032 -1596.9927 -664.13159 42.148927 988.19127 -1694.4718 3.8313604 27.156726 8.5397995 13990.5
|
||||
300 -625.07332 -659.68738 34.614061 1243.5884 -1525.4995 -663.38119 42.077062 989.22231 -1694.6806 3.6938081 26.233327 9.2896507 13990.5
|
||||
350 -623.86869 -663.20518 39.336492 1413.2524 -1932.3573 -667.15923 40.519069 986.96395 -1694.6422 3.9540529 30.551213 14.69189 13990.5
|
||||
400 -623.55169 -660.39199 36.840301 1323.5711 -1747.3638 -664.07907 41.004982 989.66515 -1694.7492 3.6870716 27.463501 11.288658 13990.5
|
||||
450 -623.03498 -658.41209 35.377106 1271.0025 1243.4895 -662.14754 48.097573 984.42115 -1694.6663 3.735455 24.531264 6.5614635 13990.5
|
||||
500 -622.34231 -660.50992 38.167608 1371.2576 -1301.9479 -664.26607 41.813817 988.57955 -1694.6594 3.7561473 23.595051 5.844275 13990.5
|
||||
Loop time of 8.51483 on 1 procs for 500 steps with 432 atoms
|
||||
|
||||
Pair time (%) = 7.73226 (90.8093)
|
||||
Bond time (%) = 0.00232315 (0.0272836)
|
||||
Kspce time (%) = 0.518208 (6.08594)
|
||||
Neigh time (%) = 0.17925 (2.10514)
|
||||
Comm time (%) = 0.0653358 (0.767317)
|
||||
Outpt time (%) = 0.000309229 (0.00363165)
|
||||
Other time (%) = 0.0171449 (0.201354)
|
||||
|
||||
Nlocal: 432 ave 432 max 432 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 9307 ave 9307 max 9307 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 297357 ave 297357 max 297357 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 297357
|
||||
Ave neighs/atom = 688.326
|
||||
Ave special neighs/atom = 1
|
||||
Neighbor list builds = 21
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix thermoberendsen
|
||||
|
||||
# ------------------------ Dynamic Run -------------------------------
|
||||
|
||||
run 1000
|
||||
Ewald initialization ...
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Memory usage per processor = 6.86279 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
|
||||
500 -622.34231 -660.50992 38.167608 1371.2576 -1301.9479 -664.26607 41.813817 988.57955 -1694.6594 3.7561473 23.595051 5.844275 13990.5
|
||||
550 -622.53283 -661.59223 39.059403 1403.2973 -385.2836 -664.93615 43.738024 985.8195 -1694.4937 3.3439143 21.675844 3.5834691 13990.5
|
||||
600 -622.20391 -659.47921 37.275306 1339.1996 473.13042 -663.45898 46.093667 985.15793 -1694.7106 3.9797724 25.783443 9.4059533 13990.5
|
||||
650 -622.3473 -660.85461 38.507306 1383.462 -1021.6262 -664.41457 42.581674 987.48335 -1694.4796 3.5599548 24.069859 6.9189396 13990.5
|
||||
700 -621.9195 -660.92044 39.000937 1401.1968 71.427836 -664.81486 44.86887 985.26444 -1694.9482 3.894424 28.397753 9.3904596 13990.5
|
||||
750 -622.28852 -658.93918 36.650662 1316.7579 -1249.2306 -662.31101 41.915549 990.48822 -1694.7148 3.3718339 24.259772 4.9454879 13990.5
|
||||
800 -622.31982 -657.72021 35.400389 1271.839 254.0237 -661.60518 45.506498 987.48185 -1694.5935 3.8849638 24.386892 7.4962982 13990.5
|
||||
850 -622.31623 -661.4936 39.177375 1407.5357 37.74414 -665.02673 44.380924 985.14989 -1694.5575 3.5331239 23.316952 5.5622744 13990.5
|
||||
900 -621.83183 -660.10965 38.277816 1375.2171 1738.9676 -664.10328 48.428909 981.86752 -1694.3997 3.9936342 28.519154 11.384782 13990.5
|
||||
950 -622.03652 -659.97862 37.942096 1363.1555 -49.888312 -663.91816 44.582637 986.15057 -1694.6514 3.9395363 27.011672 8.4915326 13990.5
|
||||
1000 -621.71637 -660.69133 38.97496 1400.2635 -46.518055 -665.12412 44.669238 984.85534 -1694.6487 4.432789 29.799247 9.5235093 13990.5
|
||||
1050 -621.90579 -658.42698 36.521187 1312.1062 27.913475 -662.80273 44.953547 986.65365 -1694.4099 4.3757505 28.035827 8.4898226 13990.5
|
||||
1100 -621.92929 -661.57742 39.648126 1424.4485 820.11499 -665.35048 46.491843 982.84734 -1694.6897 3.7730563 27.803982 8.4955015 13990.5
|
||||
1150 -622.36518 -659.3383 36.973112 1328.3426 -799.63876 -662.87451 43.109263 988.96432 -1694.9481 3.5362185 23.473216 4.2340288 13990.5
|
||||
1200 -621.80278 -659.38996 37.587182 1350.4045 173.56518 -663.76385 45.4017 985.49478 -1694.6603 4.3738897 29.25765 11.540749 13990.5
|
||||
1250 -621.89233 -658.13657 36.244239 1302.1562 -194.31216 -662.25387 44.600608 987.50208 -1694.3566 4.1173041 27.781148 11.737589 13990.5
|
||||
1300 -622.01575 -659.4502 37.43445 1344.9172 419.91066 -663.67863 46.041458 984.96293 -1694.683 4.2284307 27.725967 9.666138 13990.5
|
||||
1350 -621.64918 -658.52586 36.876681 1324.8781 -1542.8395 -662.92795 41.627963 989.87571 -1694.4316 4.4020823 30.153096 11.999079 13990.5
|
||||
1400 -621.65713 -657.77765 36.120515 1297.7112 -2133.9795 -662.63382 40.620287 991.32101 -1694.5751 4.8561686 30.546416 11.476013 13990.5
|
||||
1450 -621.92858 -659.45137 37.522795 1348.0912 217.78723 -663.34796 45.334127 985.96702 -1694.6491 3.8965883 27.625033 7.3805255 13990.5
|
||||
1500 -621.9432 -657.57884 35.635634 1280.2907 632.02267 -661.89128 46.527064 986.00347 -1694.4218 4.3124408 28.010625 8.740067 13990.5
|
||||
Loop time of 17.041 on 1 procs for 1000 steps with 432 atoms
|
||||
|
||||
Pair time (%) = 15.4577 (90.7085)
|
||||
Bond time (%) = 0.00465488 (0.0273157)
|
||||
Kspce time (%) = 1.03763 (6.08902)
|
||||
Neigh time (%) = 0.390329 (2.29052)
|
||||
Comm time (%) = 0.131336 (0.770706)
|
||||
Outpt time (%) = 0.000611782 (0.00359005)
|
||||
Other time (%) = 0.0188062 (0.110358)
|
||||
|
||||
Nlocal: 432 ave 432 max 432 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 9406 ave 9406 max 9406 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 297120 ave 297120 max 297120 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 297120
|
||||
Ave neighs/atom = 687.778
|
||||
Ave special neighs/atom = 1
|
||||
Neighbor list builds = 46
|
||||
Dangerous builds = 0
|
||||
@ -1,188 +0,0 @@
|
||||
LAMMPS (5 Mar 2015)
|
||||
# Testsystem for core-shell model compared to Mitchel and Finchham
|
||||
# Hendrik Heenen, June 2014
|
||||
|
||||
# ------------------------ INITIALIZATION ----------------------------
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style full
|
||||
|
||||
# ----------------------- ATOM DEFINITION ----------------------------
|
||||
|
||||
fix csinfo all property/atom i_CSID
|
||||
read_data data.coreshell fix csinfo NULL CS-Info
|
||||
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
432 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
216 bonds
|
||||
1 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
|
||||
group cores type 1 2
|
||||
216 atoms in group cores
|
||||
group shells type 3 4
|
||||
216 atoms in group shells
|
||||
|
||||
neighbor 2.0 bin
|
||||
comm_modify vel yes
|
||||
|
||||
# ------------------------ FORCE FIELDS ------------------------------
|
||||
|
||||
kspace_style ewald 1.0e-6
|
||||
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
|
||||
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
|
||||
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
|
||||
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
|
||||
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 63.014 0.0
|
||||
bond_coeff 2 25.724 0.0
|
||||
|
||||
# ------------------------ Equilibration Run -------------------------------
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
|
||||
|
||||
compute CSequ all temp/cs cores shells
|
||||
|
||||
# output via chunk method
|
||||
|
||||
#compute prop all property/atom i_CSID
|
||||
#compute cs_chunk all chunk/atom c_prop
|
||||
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
|
||||
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
|
||||
|
||||
thermo_modify temp CSequ
|
||||
|
||||
# velocity bias option
|
||||
|
||||
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
|
||||
Ewald initialization ...
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
master list distance cutoff = 22
|
||||
velocity all scale 1427 temp CSequ
|
||||
|
||||
fix thermoberendsen all temp/berendsen 1427 1427 0.4
|
||||
fix nve all nve
|
||||
fix_modify thermoberendsen temp CSequ
|
||||
|
||||
# 2 fmsec timestep
|
||||
|
||||
timestep 0.002
|
||||
run 500
|
||||
Ewald initialization ...
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Memory usage per processor = 6.15182 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
|
||||
0 -628.35255 -668.0717 39.719144 1427 -20608.918 -668.0717 1.6320365 1025.8481 -1695.5518 0 3.6635741e-14 5.3290705e-15 13990.5
|
||||
50 -632.86102 -664.881 32.019982 1150.3902 -4100.2367 -668.28423 37.966091 988.74858 -1694.9989 3.403224 25.060809 9.2893842 13990.5
|
||||
100 -630.51552 -660.52959 30.014075 1078.3235 -3202.4205 -664.01411 39.505563 991.23276 -1694.7524 3.4845198 26.369799 10.674421 13990.5
|
||||
150 -628.58443 -661.59141 33.006978 1185.8503 106.65351 -665.34508 46.399848 982.93423 -1694.6792 3.7536698 27.270648 10.826129 13990.5
|
||||
200 -627.39641 -662.45927 35.062861 1259.7125 -1672.2627 -665.61606 41.658596 987.1458 -1694.4205 3.1567877 23.525464 6.5838195 13990.5
|
||||
250 -625.74093 -660.30053 34.559597 1241.6316 -1597.1305 -664.13208 42.148526 988.19121 -1694.4718 3.831555 27.157597 8.5399516 13990.5
|
||||
300 -625.07349 -659.68703 34.613535 1243.5695 -1525.6663 -663.38085 42.076798 989.22292 -1694.6806 3.6938245 26.233967 9.2898941 13990.5
|
||||
350 -623.86899 -663.20625 39.337263 1413.2801 -1933.067 -667.16008 40.51735 986.96485 -1694.6423 3.9538285 30.550701 14.691984 13990.5
|
||||
400 -623.55154 -660.39034 36.838804 1323.5173 -1746.896 -664.07771 41.006288 989.66515 -1694.7492 3.687369 27.463762 11.289238 13990.5
|
||||
450 -623.03522 -658.41494 35.37972 1271.0964 1245.1415 -662.15059 48.1009 984.41515 -1694.6666 3.7356529 24.533936 6.5615795 13990.5
|
||||
500 -622.34349 -660.51826 38.174772 1371.515 -1306.7035 -664.27406 41.802611 988.58329 -1694.66 3.7557939 23.595131 5.801075 13990.5
|
||||
Loop time of 2.53127 on 4 procs for 500 steps with 432 atoms
|
||||
|
||||
Pair time (%) = 1.94114 (76.6863)
|
||||
Bond time (%) = 0.000725508 (0.0286618)
|
||||
Kspce time (%) = 0.353945 (13.9829)
|
||||
Neigh time (%) = 0.0488738 (1.9308)
|
||||
Comm time (%) = 0.17332 (6.84714)
|
||||
Outpt time (%) = 0.000516713 (0.0204132)
|
||||
Other time (%) = 0.012753 (0.503818)
|
||||
|
||||
Nlocal: 108 ave 132 max 90 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Nghost: 6500 ave 6530 max 6448 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Neighs: 74339.8 ave 91261 max 61188 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 297359
|
||||
Ave neighs/atom = 688.331
|
||||
Ave special neighs/atom = 1
|
||||
Neighbor list builds = 21
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix thermoberendsen
|
||||
|
||||
# ------------------------ Dynamic Run -------------------------------
|
||||
|
||||
run 1000
|
||||
Ewald initialization ...
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Memory usage per processor = 6.15373 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
|
||||
500 -622.34349 -660.51826 38.174772 1371.515 -1306.7035 -664.27406 41.802611 988.58329 -1694.66 3.7557939 23.595131 5.801075 13990.5
|
||||
550 -622.53431 -661.60445 39.070141 1403.6831 -388.25413 -664.94784 43.727803 985.81836 -1694.494 3.3433892 21.667306 3.5808033 13990.5
|
||||
600 -622.20561 -659.56223 37.356624 1342.1211 428.9464 -663.53655 45.982645 985.19136 -1694.7106 3.974322 25.725869 9.3871295 13990.5
|
||||
650 -622.35823 -660.82051 38.462275 1381.8442 -1009.0888 -664.38771 42.618521 987.47881 -1694.485 3.5671985 24.149905 7.00428 13990.5
|
||||
700 -621.97407 -660.92034 38.946267 1399.2327 142.95891 -664.75916 45.033131 985.16618 -1694.9585 3.8388194 27.934663 8.7392159 13990.5
|
||||
750 -622.29209 -658.81919 36.527095 1312.3185 -952.526 -662.17886 42.618062 989.9262 -1694.7231 3.3596669 24.324239 4.9087128 13990.5
|
||||
800 -622.33521 -658.14785 35.812637 1286.6499 135.34005 -661.96381 45.178323 987.39314 -1694.5353 3.815955 24.107767 7.0978979 13990.5
|
||||
850 -622.37957 -660.474 38.094424 1368.6283 857.3439 -663.9925 46.509627 984.19258 -1694.6947 3.5185004 23.581763 5.0835354 13990.5
|
||||
900 -622.29844 -660.66771 38.369271 1378.5028 2861.462 -664.35013 50.97682 979.13332 -1694.4603 3.6824207 24.493416 6.3661215 13990.5
|
||||
950 -622.35097 -659.43438 37.083412 1332.3054 705.55718 -663.24413 46.294781 984.74433 -1694.2832 3.8097517 24.11493 4.1360943 13990.5
|
||||
1000 -622.08622 -658.28773 36.201516 1300.6213 421.181 -662.27058 45.865645 986.51483 -1694.6511 3.98285 26.774991 7.4172909 13990.5
|
||||
1050 -622.10558 -657.21399 35.108408 1261.3489 -464.31761 -661.46995 44.291275 988.69737 -1694.4586 4.2559609 25.983762 5.4926993 13990.5
|
||||
1100 -622.29369 -658.21246 35.918767 1290.4629 123.81951 -662.20344 45.651482 986.92119 -1694.7761 3.990985 25.85199 5.2327524 13990.5
|
||||
1150 -621.98418 -658.28218 36.297998 1304.0876 546.02432 -662.38868 46.194374 985.7826 -1694.3657 4.1065008 27.128736 6.901853 13990.5
|
||||
1200 -621.76032 -658.36996 36.60964 1315.2841 198.92215 -662.79546 45.536182 986.45023 -1694.7819 4.4255014 30.59935 9.4790152 13990.5
|
||||
1250 -621.77583 -657.79539 36.019569 1294.0844 521.16569 -662.12132 46.16971 986.26128 -1694.5523 4.3259289 29.294668 9.6073346 13990.5
|
||||
1300 -622.0461 -659.54559 37.499494 1347.2541 -854.68333 -663.33538 42.882224 988.27569 -1694.4933 3.7897892 26.707354 8.861147 13990.5
|
||||
1350 -621.7984 -657.10932 35.310914 1268.6244 -1010.1044 -661.35487 42.90716 990.41696 -1694.679 4.2455538 29.623565 10.702495 13990.5
|
||||
1400 -622.2597 -660.89426 38.634556 1388.0337 2292.235 -664.36487 49.907981 980.3269 -1694.5997 3.4706065 25.34727 6.8458703 13990.5
|
||||
1450 -622.36952 -660.43856 38.069033 1367.716 199.44207 -664.44407 45.483438 984.89046 -1694.818 4.0055092 24.149259 3.9431126 13990.5
|
||||
1500 -621.84913 -659.73606 37.886922 1361.1733 -1274.5089 -663.96475 42.049386 988.31676 -1694.3309 4.2286938 28.927291 10.527466 13990.5
|
||||
Loop time of 5.06693 on 4 procs for 1000 steps with 432 atoms
|
||||
|
||||
Pair time (%) = 3.90916 (77.1504)
|
||||
Bond time (%) = 0.00148368 (0.0292816)
|
||||
Kspce time (%) = 0.657798 (12.9822)
|
||||
Neigh time (%) = 0.108943 (2.15008)
|
||||
Comm time (%) = 0.373417 (7.36968)
|
||||
Outpt time (%) = 0.00109911 (0.0216918)
|
||||
Other time (%) = 0.0150309 (0.296647)
|
||||
|
||||
Nlocal: 108 ave 113 max 100 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Nghost: 6461 ave 6519 max 6372 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Neighs: 74316.8 ave 77778 max 69869 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
|
||||
Total # of neighbors = 297267
|
||||
Ave neighs/atom = 688.118
|
||||
Ave special neighs/atom = 1
|
||||
Neighbor list builds = 46
|
||||
Dangerous builds = 0
|
||||
Reference in New Issue
Block a user