210 lines
12 KiB
Groff
210 lines
12 KiB
Groff
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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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:
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Section | min time | avg time | max time |%varavg| %total
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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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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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Total # of neighbors = 297525
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Ave neighs/atom = 688.715
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Ave special neighs/atom = 1
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Neighbor list builds = 45
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Dangerous builds = 0
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Total wall time: 0:00:25
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