update example outputs
This commit is contained in:
Axel Kohlmeyer
@ -21,14 +21,11 @@ read_data data.spce
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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pair_style hybrid/overlay coul/long 12.0 python 12.0
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kspace_style pppm 1.0e-6
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pair_style hybrid/overlay coul/cut 12.0 python 12.0
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pair_coeff * * coul/long
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pair_coeff * * coul/cut
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pair_coeff * * python py_pot.LJCutSPCE OW NULL
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pair_modify table 0
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bond_style harmonic
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angle_style harmonic
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dihedral_style none
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@ -54,15 +51,6 @@ fix 2 all nvt temp 300.0 300.0 100.0
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# create combined lj/coul table for all atom types
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# generate tabulated potential from python variant
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pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
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PPPM initialization ...
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WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.279652
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grid = 40 40 40
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000394206
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estimated relative force accuracy = 1.18714e-06
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using double precision FFTs
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3d grid and FFT values/proc = 34263 16000
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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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@ -70,7 +58,7 @@ Neighbor list info ...
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ghost atom cutoff = 14
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binsize = 7, bins = 6 6 6
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair coul/long, perpetual
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(1) pair coul/cut, 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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@ -81,25 +69,7 @@ Neighbor list info ...
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stencil: none
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bin: none
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pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
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PPPM initialization ...
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WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.279652
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grid = 40 40 40
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000394206
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estimated relative force accuracy = 1.18714e-06
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using double precision FFTs
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3d grid and FFT values/proc = 34263 16000
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pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
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PPPM initialization ...
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WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.279652
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grid = 40 40 40
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000394206
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estimated relative force accuracy = 1.18714e-06
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using double precision FFTs
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3d grid and FFT values/proc = 34263 16000
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# switch to tabulated potential
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pair_style table linear 2000 pppm
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@ -109,15 +79,6 @@ pair_coeff 2 2 spce.table HW-HW
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thermo 10
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run 100
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PPPM initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.279652
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grid = 40 40 40
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000394674
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estimated relative force accuracy = 1.18855e-06
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using double precision FFTs
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3d grid and FFT values/proc = 34263 16000
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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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@ -130,49 +91,48 @@ Neighbor list info ...
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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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Per MPI rank memory allocation (min/avg/max) = 13.05 | 13.05 | 13.05 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 9.962 | 9.963 | 9.963 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -100272.97 0 -100272.97 -1282.0708
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10 120.61568 -101350.63 0 -100272.39 -4077.5051
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20 136.11379 -101465.43 0 -100248.65 -5136.5677
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30 137.01602 -101455.3 0 -100230.46 -5347.8311
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40 153.424 -101582.46 0 -100210.93 -5223.1676
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50 167.73654 -101686.24 0 -100186.77 -4468.6687
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60 163.11642 -101618.16 0 -100159.99 -3291.7815
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70 169.64512 -101647.89 0 -100131.35 -2611.638
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80 182.9979 -101737.01 0 -100101.11 -2390.6293
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90 191.33873 -101778.71 0 -100068.24 -2239.386
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100 194.7458 -101775.84 0 -100034.92 -1951.9128
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Loop time of 2.35848 on 4 procs for 100 steps with 4500 atoms
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0 0 -18284.922 0 -18284.922 -2080.7739
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10 146.83806 -19552.072 0 -18239.421 -4865.31
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20 183.15761 -18706.872 0 -17069.543 -4865.6695
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30 205.96203 -18901.541 0 -17060.354 -4454.8634
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40 241.62768 -18323.117 0 -16163.099 -3269.1475
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50 265.98384 -19883.562 0 -17505.813 -2788.5194
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60 274.01897 -21320.575 0 -18870.996 -2387.0708
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70 288.7601 -19849.269 0 -17267.913 -1235.818
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80 300.64724 -20958.602 0 -18270.981 -1714.7988
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90 304.19113 -21580.4 0 -18861.099 -2144.1614
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100 304.22027 -21239.014 0 -18519.452 -2092.6759
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Loop time of 1.7361 on 4 procs for 100 steps with 4500 atoms
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Performance: 3.663 ns/day, 6.551 hours/ns, 42.400 timesteps/s
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99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
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Performance: 4.977 ns/day, 4.823 hours/ns, 57.600 timesteps/s
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99.2% 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 | 1.5061 | 1.5612 | 1.6879 | 5.9 | 66.20
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Bond | 9.5129e-05 | 0.00012672 | 0.00014567 | 0.0 | 0.01
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Kspace | 0.52033 | 0.64456 | 0.69933 | 9.1 | 27.33
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Neigh | 0.066265 | 0.066342 | 0.06644 | 0.0 | 2.81
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Comm | 0.03394 | 0.036139 | 0.038043 | 0.8 | 1.53
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Output | 0.00040889 | 0.00044978 | 0.00056887 | 0.0 | 0.02
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Modify | 0.04557 | 0.045813 | 0.046082 | 0.1 | 1.94
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Other | | 0.003826 | | | 0.16
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Pair | 1.4424 | 1.5149 | 1.6066 | 5.3 | 87.26
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Bond | 8.9407e-05 | 0.00010258 | 0.00012374 | 0.0 | 0.01
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Neigh | 0.064205 | 0.064241 | 0.064295 | 0.0 | 3.70
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Comm | 0.023643 | 0.1155 | 0.18821 | 19.2 | 6.65
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Output | 0.00038004 | 0.00042355 | 0.00054145 | 0.0 | 0.02
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Modify | 0.037507 | 0.037787 | 0.038042 | 0.1 | 2.18
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Other | | 0.003148 | | | 0.18
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Nlocal: 1125 ave 1154 max 1092 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Nghost: 12256.2 ave 12296 max 12213 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Neighs: 650442 ave 678824 max 626375 min
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Histogram: 1 0 0 0 2 0 0 0 0 1
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Nlocal: 1125 ave 1162 max 1098 min
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Histogram: 1 1 0 0 0 1 0 0 0 1
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Nghost: 12267.8 ave 12302 max 12238 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Neighs: 649416 ave 681458 max 630541 min
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Histogram: 1 0 2 0 0 0 0 0 0 1
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Total # of neighbors = 2601766
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Ave neighs/atom = 578.17
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Total # of neighbors = 2597662
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Ave neighs/atom = 577.258
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Ave special neighs/atom = 2
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Neighbor list builds = 3
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Dangerous builds = 0
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shell rm spce.table
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Total wall time: 0:00:02
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Total wall time: 0:00:01
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