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lammps/examples/USER/hadress/Relaxation/log.long_setup
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LAMMPS (28 Jun 2016-ICMS)
# SPC/E water box benchmark
# HAdResS Relaxation Setup
# Maziar Heidari, Max Planck Institute for Polymer Research
# (heidari@mpip-mainz.mpg.de))
units real
atom_style full/hars
boundary p p p
#read_data HAdResS_SPC.data
#read_restart restart.waterT300.10000
variable root index waterT300
variable Nrun equal 5000
variable Nf equal 100
variable Ne equal 10
variable Nr equal ${Nf}/${Ne}
variable Nr equal 100/${Ne}
variable Nr equal 100/10
variable Ndump equal 1000
variable Nrestart equal 10000
variable Nr_rdf equal 0.5*${Nrun}/${Ne}
variable Nr_rdf equal 0.5*5000/${Ne}
variable Nr_rdf equal 0.5*5000/10
variable Text equal 300.0
variable Pext equal 1.0
variable x index 1
variable y index 1
variable z index 1
variable xx equal 40*$x
variable xx equal 40*1
variable yy equal 8*$y
variable yy equal 8*1
variable zz equal 8*$z
variable zz equal 8*1
variable half_xx equal 0.5*${xx}
variable half_xx equal 0.5*40
variable half_yy equal 0.5*${yy}
variable half_yy equal 0.5*8
variable half_zz equal 0.5*${zz}
variable half_zz equal 0.5*8
#######################################################################
molecule mol1 molecule
Read molecule mol1:
3 atoms with 2 types
2 bonds with 1 types
1 angles with 1 types
0 dihedrals with 0 types
0 impropers with 0 types
lattice fcc 5.0
Lattice spacing in x,y,z = 5 5 5
region box block -${half_xx} ${half_xx} -${half_yy} ${half_yy} -${half_zz} ${half_zz}
region box block -20 ${half_xx} -${half_yy} ${half_yy} -${half_zz} ${half_zz}
region box block -20 20 -${half_yy} ${half_yy} -${half_zz} ${half_zz}
region box block -20 20 -4 ${half_yy} -${half_zz} ${half_zz}
region box block -20 20 -4 4 -${half_zz} ${half_zz}
region box block -20 20 -4 4 -4 ${half_zz}
region box block -20 20 -4 4 -4 4
create_box 2 box bond/types 1 extra/bond/per/atom 2 angle/types 1 extra/angle/per/atom 1 dihedral/types 0 improper/types 0 extra/special/per/atom 2
Created orthogonal box = (-100 -20 -20) to (100 20 20)
8 by 1 by 1 MPI processor grid
create_atoms 0 box mol mol1 10
Created 30720 atoms
mass 1 15.9994
mass 2 1.00794
pair_style lj/cut/coul/dsf 0.2 10.0 12.0
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
########################################################################
bond_style harmonic
angle_style harmonic
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
neigh_modify every 1 delay 2 check yes
fix 1 all shake 0.0001 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
10240 = # of frozen angles
fix 2 all npt temp ${Text} ${Text} 100.0 iso ${Pext} ${Pext} 1000.0
fix 2 all npt temp 300 ${Text} 100.0 iso ${Pext} ${Pext} 1000.0
fix 2 all npt temp 300 300 100.0 iso ${Pext} ${Pext} 1000.0
fix 2 all npt temp 300 300 100.0 iso 1 ${Pext} 1000.0
fix 2 all npt temp 300 300 100.0 iso 1 1 1000.0
velocity all create 300 432567 dist uniform
timestep 1.0
########################################################################
compute FFX all property/atom fx
compute SumFFX all reduce sum c_FFX
compute FFY all property/atom fy
compute SumFFY all reduce sum c_FFY
compute FFZ all property/atom fz
compute SumFFZ all reduce sum c_FFZ
compute T all temp
fix TempAve all ave/time ${Ne} ${Nr} ${Nf} c_T
fix TempAve all ave/time 10 ${Nr} ${Nf} c_T
fix TempAve all ave/time 10 10 ${Nf} c_T
fix TempAve all ave/time 10 10 100 c_T
compute Pperatom all stress/atom NULL
variable Patom atom -1.0*c_Pperatom[1]/(3*0.5*(yhi-ylo)*(zhi-zlo))
variable P equal press
fix PressAve all ave/time ${Ne} ${Nr} ${Nf} v_P
fix PressAve all ave/time 10 ${Nr} ${Nf} v_P
fix PressAve all ave/time 10 10 ${Nf} v_P
fix PressAve all ave/time 10 10 100 v_P
compute xbin all chunk/atom bin/1d x lower 1.0
fix PressureP all ave/chunk 10 100 1000 xbin v_Patom ave one file Pres.profile
fix DensityD all ave/chunk 10 100 1000 xbin density/number ave one file Dens.profile
compute rdf all rdf 100 1 1 # oxygen-oxygen
fix rdf all ave/time 10 100 1000 c_rdf file O.rdf mode vector
########################################################################
thermo_style custom step temp f_TempAve press f_PressAve density vol ke ebond eangle evdwl ecoul etotal c_SumFFX c_SumFFY c_SumFFZ
thermo ${Nf}
thermo 100
#dump trj all atom ${Ndump} wat.lammpstrj
restart ${Nrestart} restart.${root}
restart 10000 restart.${root}
restart 10000 restart.waterT300
run ${Nrun}
run 5000
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7 -> bins = 29 6 6
Memory usage per processor = 24.5041 Mbytes
Step Temp TempAve Press PressAve Density Volume KinEng E_bond E_angle E_vdwl E_coul TotEng SumFFX SumFFY SumFFZ
0 300 0 3061.0504 0 0.95728236 320000 18313.203 0 0 -8410.406 -10520.398 -617.60182 -2.9558578e-12 -4.7748472e-12 2.0463631e-12
100 722.42113 726.26629 669.99751 -3728.8038 0.96964164 315921.2 44099.482 0 0 1229.0472 -60800.341 -15471.812 -2.0747848e-12 -2.4868996e-13 -2.1174174e-12
200 672.30193 700.99675 3870.2449 2874.3101 0.97049545 315643.27 41040.005 0 0 8601.5314 -78428.949 -28787.412 1.0729195e-12 3.8653525e-12 -3.9790393e-13
300 592.58544 628.382 3069.1097 3522.3169 0.9555818 320569.47 36173.791 0 0 10948.789 -88620.009 -41497.43 2.2737368e-13 -7.0343731e-13 -1.3784529e-12
400 520.30907 552.49065 1943.348 2496.8422 0.94359548 324641.61 31761.752 0 0 12369.025 -96387.62 -52256.843 3.1903369e-12 -8.2067686e-12 -3.225864e-12
500 459.59206 486.86334 549.40597 1133.6295 0.93537771 327493.75 28055.342 0 0 12949.619 -102053.93 -61048.965 1.3784529e-12 1.6342483e-12 3.8511416e-12
600 415.38949 433.75352 1.4569256 201.61025 0.9313777 328900.25 25357.04 0 0 14176.571 -107686.88 -68153.274 -3.9932502e-12 -2.4087399e-12 -7.1054274e-13
700 385.71613 397.44463 -631.11439 -320.97111 0.93039984 329245.92 23545.659 0 0 15055.033 -112669.59 -74068.897 1.2505552e-12 -3.6806114e-12 7.1764816e-13
800 356.11937 367.27862 -671.82952 -640.63686 0.93266027 328447.95 21738.954 0 0 16326.055 -117045.52 -78980.514 -1.6910917e-12 2.7711167e-13 -2.3163693e-12
900 338.91012 345.50897 -640.19805 -635.51626 0.93690765 326958.96 20688.432 0 0 17640.855 -121408.48 -83079.189 -1.0942358e-12 -4.2135184e-12 2.7711167e-13
1000 319.53052 327.60563 -545.21295 -553.87233 0.94151289 325359.7 19505.424 0 0 18713.383 -124685.23 -86466.421 4.813927e-13 3.225864e-12 -3.3395509e-12
1100 308.8326 314.58069 -761.29703 -763.03497 0.94632538 323705.1 18852.38 0 0 19166.571 -127189.49 -89170.539 1.4210855e-12 2.8066438e-12 -9.3791641e-13
1200 301.76115 304.81367 -440.39604 -540.52035 0.95118939 322049.8 18420.71 0 0 20259.633 -129952.26 -91271.912 -2.2737368e-13 5.1016968e-12 3.0482283e-12
1300 296.49263 297.24181 -675.72951 -644.35564 0.95543431 320618.96 18099.099 0 0 20283.49 -131069.78 -92687.193 2.3234747e-12 2.3163693e-12 3.9790393e-13
1400 294.9624 295.69622 -357.34776 -442.82857 0.95965753 319207.99 18005.687 0 0 20928.701 -132387.37 -93452.979 2.5011104e-12 -6.3735683e-12 -4.8601123e-12
1500 296.02595 296.39461 -333.87184 -347.78361 0.96297909 318106.96 18070.61 0 0 21064.998 -132849.58 -93713.971 -2.5792701e-12 4.8316906e-13 -2.3234747e-12
1600 300.18717 298.41552 -102.6141 -216.44008 0.96572244 317203.31 18324.628 0 0 21348.52 -133266.22 -93593.066 -2.0747848e-12 4.8743232e-12 -4.2987836e-12
1700 302.98621 300.74468 -155.46265 -133.22884 0.96766255 316567.33 18495.493 0 0 21259.158 -133174.23 -93419.581 7.1054274e-14 5.968559e-13 1.0729195e-12
1800 301.95843 302.37343 -1.7195682 -93.781454 0.96915745 316079.04 18432.753 0 0 21436.481 -133299.2 -93429.965 3.0979663e-12 -1.0373924e-12 4.7606363e-13
1900 301.86985 302.15919 -319.10585 -141.98502 0.97039749 315675.13 18427.346 0 0 21115.718 -133313.58 -93770.517 -2.4371616e-12 2.8421709e-13 3.5527137e-13
2000 298.84343 298.91301 -151.49568 -257.29626 0.97233695 315045.47 18242.601 0 0 21386.431 -133789.41 -94160.382 -5.4711791e-12 -1.0196288e-12 -5.6843419e-13
2100 299.03003 298.21981 -23.788734 -58.23207 0.97419484 314444.65 18253.992 0 0 21631.286 -134244.6 -94359.324 6.4659389e-13 -4.2987836e-13 4.7961635e-13
2200 299.25013 298.69936 -33.63205 12.201447 0.97529292 314090.62 18267.427 0 0 21592.352 -134217.82 -94358.042 1.4992452e-12 -3.7374548e-12 3.2684966e-13
2300 300.76612 299.84547 -42.337862 -77.507918 0.97612851 313821.75 18359.97 0 0 21579.897 -134218.91 -94279.039 -6.8460793e-12 -5.2935434e-12 8.5265128e-14
2400 299.85945 301.31106 15.332163 8.7186875 0.97680703 313603.76 18304.623 0 0 21568.169 -134138.74 -94265.943 -7.4606987e-13 -5.4356519e-13 -5.7234217e-12
2500 303.40614 300.90682 -18.509074 13.533787 0.97717378 313486.06 18521.127 0 0 21644.079 -134534.62 -94369.418 -2.0961011e-12 -2.5863756e-12 -4.4479975e-12
2600 297.22973 299.20115 -273.9953 -110.07731 0.97751498 313376.63 18144.094 0 0 21224.278 -133911.3 -94542.924 -1.4210855e-14 -8.9528385e-13 -1.3127277e-12
2700 299.89005 298.4368 63.181662 -145.68542 0.97886893 312943.18 18306.491 0 0 21826.535 -134671.5 -94538.47 2.2026825e-13 1.8474111e-12 -3.8227199e-12
2800 300.63193 301.37555 118.11423 104.73468 0.97965067 312693.46 18351.778 0 0 21839.657 -134671.38 -94479.941 -2.0250468e-12 -3.3963943e-12 1.7692514e-12
2900 299.07735 300.27547 90.740202 123.04219 0.97944357 312759.57 18256.88 0 0 21803.823 -134631.21 -94570.506 -1.563194e-13 4.9169557e-12 8.6686214e-13
3000 298.49324 299.98395 -35.534874 -53.419852 0.97916136 312849.72 18221.224 0 0 21658.245 -134572.24 -94692.772 -1.4210855e-14 4.1708859e-12 1.3855583e-13
3100 298.40189 299.31074 70.947639 -15.61549 0.97929095 312808.32 18215.648 0 0 21841.392 -134813.06 -94756.023 9.0238927e-13 -1.6768809e-12 4.0785153e-12
3200 299.34848 299.19741 204.29487 117.89327 0.97907611 312876.96 18273.431 0 0 22048.069 -135048.44 -94726.939 2.3305802e-12 3.3928416e-12 3.7800874e-12
3300 300.08533 300.65279 91.483556 68.128506 0.97819385 313159.15 18318.412 0 0 21879.018 -134865.38 -94667.952 -1.5027979e-12 -1.8012258e-12 -3.9293013e-12
3400 298.89082 299.72369 -286.87405 -71.674846 0.97736873 313423.53 18245.494 0 0 21356.306 -134277.55 -94675.754 1.3358203e-12 -9.0238927e-13 5.2295945e-12
3500 299.82257 298.74339 -192.7363 -294.10617 0.97821225 313153.26 18302.372 0 0 21433.428 -134288.66 -94552.857 -6.1106675e-13 9.094947e-13 -1.8900437e-12
3600 302.32438 302.77239 29.64575 -70.226344 0.98000754 312579.59 18455.092 0 0 21734.458 -134674.06 -94484.51 -1.563194e-13 -1.2398971e-12 -1.5702994e-12
3700 303.7171 302.14897 40.275294 155.93014 0.9810237 312255.81 18540.109 0 0 21894.857 -135188.68 -94753.714 -2.9629632e-12 -2.8776981e-13 -3.4106051e-12
3800 298.64705 299.66245 -56.946617 -68.650559 0.98145448 312118.76 18230.613 0 0 21849.373 -135256.72 -95176.737 -2.8421709e-13 1.7053026e-13 5.186962e-13
3900 295.55247 296.41268 -77.871707 -76.88407 0.98214624 311898.92 18041.707 0 0 21778.477 -135167.24 -95347.054 -1.1795009e-12 1.7408297e-13 1.8474111e-13
4000 298.61303 297.97338 115.58333 -5.4708305 0.98319193 311567.2 18228.537 0 0 22039.698 -135426.68 -95158.44 2.6645353e-12 -1.9966251e-12 1.2363444e-12
4100 302.80542 301.38195 -251.31558 -74.852328 0.98385963 311355.75 18484.457 0 0 21444.49 -134800.39 -94871.439 -6.2527761e-13 -1.2079227e-13 4.0891734e-12
4200 302.1423 301.42782 -60.437893 -100.59492 0.98517973 310938.55 18443.977 0 0 21611.427 -134854.94 -94799.536 -2.4407143e-12 -1.7053026e-13 -6.2954086e-12
4300 299.39357 301.20687 145.79629 51.790098 0.98629196 310587.91 18276.184 0 0 21897.867 -135063.15 -94889.1 3.5527137e-12 2.3305802e-12 -4.7535309e-12
4400 297.40216 298.64321 -152.77353 -88.689698 0.9869834 310370.32 18154.62 0 0 21452.59 -134621.86 -95014.649 -5.6132876e-13 2.643219e-12 9.9475983e-14
4500 302.20515 299.31375 16.093279 -68.268591 0.98829845 309957.34 18447.814 0 0 21732.46 -135122.05 -94941.778 2.692957e-12 -1.4850343e-12 1.7763568e-12
4600 300.35271 301.81947 203.49961 93.951145 0.98920774 309672.42 18334.734 0 0 21970.953 -135262.07 -94956.386 -3.1832315e-12 2.9842795e-12 2.5828228e-12
4700 298.87318 300.33458 188.5356 104.76773 0.98916566 309685.59 18244.417 0 0 21974.821 -135334.46 -95115.226 -1.4566126e-12 -5.4853899e-12 1.2931878e-12
4800 299.07179 299.53258 -77.183596 -2.1556589 0.98868938 309834.78 18256.541 0 0 21655.155 -135173.49 -95261.794 3.7800874e-12 3.6219916e-12 2.0250468e-12
4900 296.47561 298.45007 166.72211 63.731555 0.98844502 309911.37 18098.06 0 0 21993.847 -135411.96 -95320.052 -3.2684966e-13 -8.2422957e-13 4.156675e-12
5000 300.98135 298.55831 -49.673601 -8.122336 0.98781835 310107.98 18373.108 0 0 21722.687 -135248.71 -95152.911 -2.8279601e-12 -3.1832315e-12 1.4495072e-12
Loop time of 776.07 on 8 procs for 5000 steps with 30720 atoms
Performance: 0.557 ns/day, 43.115 hours/ns, 6.443 timesteps/s
99.8% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 676.25 | 685.7 | 696.97 | 22.7 | 88.36
Bond | 0.17369 | 0.21555 | 0.2631 | 8.8 | 0.03
Neigh | 27.284 | 27.45 | 27.597 | 2.5 | 3.54
Comm | 21.218 | 28.484 | 38.047 | 99.1 | 3.67
Output | 0.015086 | 0.01526 | 0.015404 | 0.1 | 0.00
Modify | 28.463 | 32.87 | 40.007 | 69.6 | 4.24
Other | | 1.338 | | | 0.17
Nlocal: 3840 ave 3867 max 3803 min
Histogram: 1 0 1 2 0 0 0 1 0 3
Nghost: 20033.2 ave 20139 max 19912 min
Histogram: 1 1 0 0 2 0 2 0 0 2
Neighs: 2.18456e+06 ave 2.21417e+06 max 2.1601e+06 min
Histogram: 3 0 1 0 1 0 0 0 0 3
Total # of neighbors = 17476467
Ave neighs/atom = 568.895
Ave special neighs/atom = 2
Neighbor list builds = 309
Dangerous builds = 0
write_restart restart.waterT300
Total wall time: 0:12:56
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