forked from lijiext/lammps
192 lines
11 KiB
Groff
192 lines
11 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 Mitchel and Finchham
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# Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation.
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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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pair_style born/coul/wolf/cs 0.1 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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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/wolf/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 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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Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 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 -637.41039 -677.06805 39.657659 1427 -21302.622 -677.06805 1.6320365 -678.70009 0 0 1.2935454e-14 3.3306691e-15 13990.5
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50 -635.62711 -667.67134 32.044236 1153.0465 -4533.0717 -669.45724 37.76997 -707.22721 0 1.7858938 9.684452 2.2001656 13990.5
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100 -632.76337 -662.83035 30.066977 1081.8989 -3492.8736 -664.98454 39.197093 -704.18164 0 2.1541967 11.063962 2.1543406 13990.5
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150 -630.82538 -663.70056 32.875182 1182.9464 -74.33032 -666.12202 46.263665 -712.38569 0 2.4214607 11.739683 2.7558416 13990.5
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200 -629.1541 -664.54637 35.39227 1273.5187 -1707.5508 -666.87772 41.796197 -708.67391 0 2.3313445 10.594804 3.0025376 13990.5
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250 -627.86587 -662.60879 34.742918 1250.1531 -1258.7537 -665.21416 43.017024 -708.23118 0 2.6053655 10.576999 1.8400987 13990.5
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300 -627.10755 -664.12897 37.021419 1332.1403 -1891.3466 -666.39618 40.769593 -707.16577 0 2.2672094 9.412943 1.2434258 13990.5
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350 -626.27558 -665.04303 38.767449 1394.9676 -1436.8514 -667.47081 41.854746 -709.32556 0 2.4277827 10.304721 1.977594 13990.5
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400 -625.55098 -661.86388 36.312896 1306.6455 -331.92076 -664.4632 44.426542 -708.88975 0 2.599325 11.081635 2.1734468 13990.5
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450 -624.88626 -661.07359 36.187328 1302.1272 -2325.834 -663.6031 39.662697 -703.26579 0 2.5295037 9.9810051 1.3068928 13990.5
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500 -623.87093 -660.24145 36.370525 1308.7192 410.85327 -662.86944 45.869201 -708.73864 0 2.6279857 10.592786 1.8162328 13990.5
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Loop time of 9.56959 on 1 procs for 500 steps with 432 atoms
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Performance: 9.029 ns/day, 2.658 hours/ns, 52.249 timesteps/s
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99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 9.2366 | 9.2366 | 9.2366 | 0.0 | 96.52
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Bond | 0.0020828 | 0.0020828 | 0.0020828 | 0.0 | 0.02
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Neigh | 0.22581 | 0.22581 | 0.22581 | 0.0 | 2.36
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Comm | 0.087387 | 0.087387 | 0.087387 | 0.0 | 0.91
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Output | 0.00043035 | 0.00043035 | 0.00043035 | 0.0 | 0.00
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Modify | 0.013176 | 0.013176 | 0.013176 | 0.0 | 0.14
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Other | | 0.004087 | | | 0.04
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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: 9328 ave 9328 max 9328 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 297280 ave 297280 max 297280 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 297280
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Ave neighs/atom = 688.148
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Ave special neighs/atom = 1
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Neighbor list builds = 21
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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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Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 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 -623.87093 -660.24145 36.370525 1308.7192 410.85327 -662.86944 45.869201 -708.73864 0 2.6279857 10.592786 1.8162328 13990.5
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550 -623.95762 -659.99899 36.041371 1296.8752 -442.62441 -662.68699 44.004419 -706.69141 0 2.6879934 10.936057 1.7358509 13990.5
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600 -624.04214 -661.21748 37.175332 1337.6785 47.61587 -663.76133 45.009742 -708.77107 0 2.5438549 11.431366 2.1185465 13990.5
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650 -623.98279 -661.85255 37.86976 1362.6661 -1708.3824 -664.31138 40.933446 -705.24482 0 2.4588297 9.7960192 1.4159906 13990.5
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700 -624.02941 -661.57484 37.545431 1350.9958 -124.09619 -663.95322 44.666399 -708.61962 0 2.3783802 10.518712 2.0854583 13990.5
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750 -624.03935 -661.11619 37.076842 1334.1346 -1163.274 -663.82553 42.121895 -705.94743 0 2.70934 10.634855 1.9381646 13990.5
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800 -623.98709 -659.43647 35.449379 1275.5736 -285.65541 -662.23781 44.650237 -706.88805 0 2.8013481 11.83459 3.4506393 13990.5
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850 -623.96081 -661.77923 37.81842 1360.8187 -814.33165 -664.3816 42.860208 -707.24181 0 2.6023716 10.766441 2.9211138 13990.5
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900 -623.96136 -662.9842 39.02284 1404.1573 308.1419 -665.65877 45.053211 -710.71198 0 2.674576 11.028802 1.8494293 13990.5
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950 -623.91049 -660.63827 36.727782 1321.5743 -445.29549 -663.79804 43.948376 -707.74641 0 3.1597692 11.852029 1.8238312 13990.5
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1000 -623.90541 -661.03472 37.129304 1336.0223 522.59285 -663.50211 45.8633 -709.36541 0 2.4673901 10.949322 1.8613502 13990.5
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1050 -624.01134 -660.99086 36.979522 1330.6327 -1710.3266 -663.6777 41.055997 -704.7337 0 2.6868396 10.865335 2.2154562 13990.5
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1100 -624.02639 -660.86653 36.840144 1325.6175 1151.2194 -663.50657 47.207655 -710.71423 0 2.6400422 11.298226 1.8901962 13990.5
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1150 -624.04418 -661.29792 37.253732 1340.4996 161.18555 -663.7371 45.222823 -708.95992 0 2.4391845 11.26132 2.2249572 13990.5
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1200 -624.08629 -662.39857 38.312276 1378.5891 -1404.3216 -664.93056 41.729944 -706.6605 0 2.5319943 10.45796 2.1150356 13990.5
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1250 -624.03031 -661.25639 37.226081 1339.5046 61.673399 -663.72681 45.083327 -708.81014 0 2.4704185 11.764377 2.2300033 13990.5
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1300 -623.97477 -661.56221 37.587436 1352.5072 -766.14948 -663.8091 42.864064 -706.67316 0 2.2468911 10.098925 1.7609776 13990.5
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1350 -623.93106 -660.2936 36.362535 1308.4317 -2387.7331 -663.03485 39.756427 -702.79127 0 2.7412491 10.88663 2.66284 13990.5
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1400 -623.86405 -658.43845 34.574407 1244.0896 2274.8627 -660.9465 50.133006 -711.0795 0 2.5080438 11.530504 1.7943496 13990.5
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1450 -623.85491 -661.52972 37.674807 1355.6511 -1417.2183 -664.20085 41.731022 -705.93187 0 2.6711331 11.299254 1.9911762 13990.5
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1500 -623.80036 -659.86071 36.060348 1297.5581 -193.90288 -662.71759 44.340486 -707.05807 0 2.8568759 11.042693 2.2234298 13990.5
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Loop time of 19.4477 on 1 procs for 1000 steps with 432 atoms
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Performance: 8.885 ns/day, 2.701 hours/ns, 51.420 timesteps/s
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98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 18.754 | 18.754 | 18.754 | 0.0 | 96.43
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Bond | 0.0046136 | 0.0046136 | 0.0046136 | 0.0 | 0.02
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Neigh | 0.49116 | 0.49116 | 0.49116 | 0.0 | 2.53
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Comm | 0.17734 | 0.17734 | 0.17734 | 0.0 | 0.91
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Output | 0.00094318 | 0.00094318 | 0.00094318 | 0.0 | 0.00
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Modify | 0.007426 | 0.007426 | 0.007426 | 0.0 | 0.04
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Other | | 0.0122 | | | 0.06
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Nlocal: 432 ave 432 max 432 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 9382 ave 9382 max 9382 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 297191 ave 297191 max 297191 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 297191
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Ave neighs/atom = 687.942
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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: 0:00:29
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