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add lj example for fix widom

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Axel Kohlmeyer
2020-07-17 15:02:11 -04:00
parent 29e2c82d71
commit c9342aec31
4 changed files with 2225 additions and 0 deletions
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examples/gcmc/data.widom.lj Normal file
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# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
units lj
atom_style atomic
pair_style lj/cut 2.5
pair_modify shift yes
read_data data.widom.lj
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 1 2 1.5 0.8 2.0
pair_coeff 2 2 0.5 0.88 2.2
neighbor 0.3 bin
neigh_modify delay 0 every 5 check yes
fix mywidom all widom 10 100000 2 29494 0.75
fix 1 all langevin 0.75 0.75 0.1 48279 zero yes
fix 2 all nve
timestep 0.002
thermo_style custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
thermo 10
run 100

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examples/gcmc/log.30Jun20.widom.lj.g++.1 Normal file
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LAMMPS (30 Jun 2020)
using 1 OpenMP thread(s) per MPI task
# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
units lj
atom_style atomic
pair_style lj/cut 2.5
pair_modify shift yes
read_data data.widom.lj
orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4000000 9.4000000 9.4000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
1000 atoms
reading velocities ...
1000 velocities
read_data CPU = 0.003 seconds
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 1 2 1.5 0.8 2.0
pair_coeff 2 2 0.5 0.88 2.2
neighbor 0.3 bin
neigh_modify delay 0 every 5 check yes
fix mywidom all widom 10 100000 2 29494 0.75
fix 1 all langevin 0.75 0.75 0.1 48279 zero yes
fix 2 all nve
timestep 0.002
thermo_style custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
thermo 10
run 100
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.181 | 3.181 | 3.181 Mbytes
Step Temp PotEng TotEng Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
0 0.75021245 -6.4204308 -5.2962374 7.2962696 830.584 1.2039721 0 0 830.584
10 0.7358936 -6.4405082 -5.3377717 7.1699962 830.584 1.2039721 -3.8577501 171.3429 830.584
20 0.75426414 -6.4267946 -5.2965298 7.2833985 830.584 1.2039721 -4.0708206 227.63895 830.584
30 0.72947489 -6.4064078 -5.3132896 7.3872583 830.584 1.2039721 -4.4304803 367.7146 830.584
40 0.73504751 -6.4248725 -5.3234038 7.2927069 830.584 1.2039721 -4.1904189 266.99373 830.584
50 0.76497439 -6.4352472 -5.2889331 7.3046861 830.584 1.2039721 -3.8628472 172.51133 830.584
60 0.75752861 -6.4147051 -5.2795485 7.4416 830.584 1.2039721 -3.5355467 111.5042 830.584
70 0.77775078 -6.4210798 -5.2556202 7.4473703 830.584 1.2039721 -3.4754802 102.92223 830.584
80 0.80937104 -6.4320008 -5.2191583 7.4121087 830.584 1.2039721 -3.9287513 188.35625 830.584
90 0.76321255 -6.4203633 -5.2766893 7.4307727 830.584 1.2039721 -4.2257529 279.87337 830.584
100 0.74561743 -6.4010576 -5.2837499 7.52907 830.584 1.2039721 -3.6817835 135.5099 830.584
Loop time of 25.8264 on 1 procs for 100 steps with 1000 atoms
Performance: 669.082 tau/day, 3.872 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.08186 | 0.08186 | 0.08186 | 0.0 | 0.32
Neigh | 0.023613 | 0.023613 | 0.023613 | 0.0 | 0.09
Comm | 0.0053532 | 0.0053532 | 0.0053532 | 0.0 | 0.02
Output | 0.00037837 | 0.00037837 | 0.00037837 | 0.0 | 0.00
Modify | 25.715 | 25.715 | 25.715 | 0.0 | 99.57
Other | | 0.0005643 | | | 0.00
Nlocal: 1000.00 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3049.00 ave 3049 max 3049 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 46176.0 ave 46176 max 46176 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46176
Ave neighs/atom = 46.176000
Neighbor list builds = 10
Dangerous builds = 0
Total wall time: 0:00:25

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LAMMPS (30 Jun 2020)
using 1 OpenMP thread(s) per MPI task
# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
units lj
atom_style atomic
pair_style lj/cut 2.5
pair_modify shift yes
read_data data.widom.lj
orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4000000 9.4000000 9.4000000)
1 by 2 by 2 MPI processor grid
reading atoms ...
1000 atoms
reading velocities ...
1000 velocities
read_data CPU = 0.002 seconds
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 1 2 1.5 0.8 2.0
pair_coeff 2 2 0.5 0.88 2.2
neighbor 0.3 bin
neigh_modify delay 0 every 5 check yes
fix mywidom all widom 10 100000 2 29494 0.75
fix 1 all langevin 0.75 0.75 0.1 48279 zero yes
fix 2 all nve
timestep 0.002
thermo_style custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
thermo 10
run 100
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.13 | 3.13 | 3.131 Mbytes
Step Temp PotEng TotEng Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
0 0.75021245 -6.4204308 -5.2962374 7.2962696 830.584 1.2039721 0 0 830.584
10 0.74279259 -6.4332442 -5.3201696 7.2071344 830.584 1.2039721 -3.4462258 98.984938 830.584
20 0.73016272 -6.4222911 -5.3281423 7.2714238 830.584 1.2039721 -4.4887329 397.41346 830.584
30 0.74416342 -6.429139 -5.3140101 7.2713375 830.584 1.2039721 -4.3313574 322.19056 830.584
40 0.73295457 -6.4370942 -5.3387618 7.227091 830.584 1.2039721 -4.7419281 557.00309 830.584
50 0.76914235 -6.4473959 -5.2948361 7.2179148 830.584 1.2039721 -3.1794069 69.352982 830.584
60 0.74099083 -6.4433012 -5.3329265 7.204973 830.584 1.2039721 -3.5231065 109.66994 830.584
70 0.74514671 -6.4288463 -5.312244 7.2771269 830.584 1.2039721 -1.0154832 3.8727995 830.584
80 0.72787097 -6.4457574 -5.3550427 7.1130709 830.584 1.2039721 -3.6691709 133.2501 830.584
90 0.78452846 -6.5034376 -5.3278217 6.8238659 830.584 1.2039721 -2.0798339 16.008373 830.584
100 0.77188499 -6.487313 -5.3306433 6.9133194 830.584 1.2039721 -2.066579 15.727938 830.584
Loop time of 3.37748 on 4 procs for 100 steps with 1000 atoms
Performance: 5116.239 tau/day, 29.608 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.02025 | 0.020952 | 0.021322 | 0.3 | 0.62
Neigh | 0.0059071 | 0.0060568 | 0.0061543 | 0.1 | 0.18
Comm | 0.016558 | 0.059554 | 0.094282 | 12.2 | 1.76
Output | 0.00022173 | 0.00042927 | 0.0010471 | 0.0 | 0.01
Modify | 3.2552 | 3.2902 | 3.3335 | 1.7 | 97.42
Other | | 0.0003003 | | | 0.01
Nlocal: 250.000 ave 256 max 242 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 1666.00 ave 1670 max 1659 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 11538.0 ave 11832 max 11091 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 46152
Ave neighs/atom = 46.152000
Neighbor list builds = 10
Dangerous builds = 0
Total wall time: 0:00:03