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update fix orient/eco example to be aligned with LAMMPS conventions

This commit is contained in:
Axel Kohlmeyer 2020-06-06 10:36:35 -04:00
parent 4832de4a76
commit 8bfabcab56
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7 changed files with 203 additions and 17 deletions
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examples/USER/misc/orient_eco/Ni_u3.eam Symbolic link
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../../../../potentials/Ni_u3.eam

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examples/USER/misc/orient_eco/sigma5.lammps → examples/USER/misc/orient_eco/data.sigma5 Executable file → Normal file
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examples/USER/misc/orient_eco/in.orient_eco Normal file
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units metal
atom_style atomic
read_data data.sigma5
pair_style eam
pair_coeff * * Ni_u3.eam
timestep 0.001
fix integrator all npt temp 750 750 0.1 iso 0 0 0.1
fix eco all orient/eco 0.08 0.25 3.6 sigma5.ori
thermo 100
thermo_style custom step temp etotal press vol f_eco
velocity all create 750 18527782
#dump save all custom 100 orient_eco.dump xs ys zs f_eco[1] f_eco[2]
#dump_modify save sort id
run 1000

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examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.1 Normal file
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LAMMPS (5 May 2020)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style atomic
read_data data.sigma5
orthogonal box = (-90.272 -4.42719e-07 0) to (90.272 88.5438 17.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
25600 atoms
read_data CPU = 0.0209658 secs
pair_style eam
pair_coeff * * Ni_u3.eam
Reading potential file Ni_u3.eam with DATE: 2007-06-11
timestep 0.001
fix integrator all npt temp 750 750 0.1 iso 0 0 0.1
fix eco all orient/eco 0.08 0.25 3.6 sigma5.ori
thermo 100
thermo_style custom step temp etotal press vol f_eco
velocity all create 750 18527782
#dump save all custom 100 orient_eco.dump xs ys zs f_eco[1] f_eco[2]
#dump_modify save sort id
run 1000
fix orient/eco: cutoff=3.600000 norm_fac=30.012844 neighbors=18
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 54 27 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair eam, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix orient/eco, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 107.4 | 107.4 | 107.4 Mbytes
Step Temp TotEng Press Volume f_eco
0 750 -111027.95 15148.458 279755.85 8.7507522e-10
100 422.27806 -110928.76 213.95562 285332.65 -0.9445869
200 388.82804 -110721.03 -482.03081 286441.76 -0.62401498
300 441.96877 -110478.76 -174.17824 286638.76 -0.84438548
400 486.68584 -110211.69 60.449185 287024.35 -1.1228851
500 530.74819 -109923.82 96.672717 287554.06 -2.2396258
600 569.97656 -109623.63 -77.584646 288223.23 -3.1029924
700 615.98095 -109318.75 -64.920979 288793.81 -5.0459701
800 664.91881 -109021.02 -62.347415 289323.84 -6.1930838
900 704.83039 -108741.73 365.8898 289827.26 -9.8340949
1000 734.71441 -108502.96 1119.6572 290190 -12.049805
Loop time of 114.325 on 1 procs for 1000 steps with 25600 atoms
Performance: 0.756 ns/day, 31.757 hours/ns, 8.747 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 | 27.174 | 27.174 | 27.174 | 0.0 | 23.77
Neigh | 0.82192 | 0.82192 | 0.82192 | 0.0 | 0.72
Comm | 0.12876 | 0.12876 | 0.12876 | 0.0 | 0.11
Output | 0.00077987 | 0.00077987 | 0.00077987 | 0.0 | 0.00
Modify | 86.114 | 86.114 | 86.114 | 0.0 | 75.32
Other | | 0.0853 | | | 0.07
Nlocal: 25600 ave 25600 max 25600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 28247 ave 28247 max 28247 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.59182e+06 ave 1.59182e+06 max 1.59182e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 3.18365e+06 ave 3.18365e+06 max 3.18365e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3183648
Ave neighs/atom = 124.361
Neighbor list builds = 10
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:54

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examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.4 Normal file
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LAMMPS (5 May 2020)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style atomic
read_data data.sigma5
orthogonal box = (-90.272 -4.42719e-07 0) to (90.272 88.5438 17.5)
4 by 1 by 1 MPI processor grid
reading atoms ...
25600 atoms
read_data CPU = 0.0275698 secs
pair_style eam
pair_coeff * * Ni_u3.eam
Reading potential file Ni_u3.eam with DATE: 2007-06-11
timestep 0.001
fix integrator all npt temp 750 750 0.1 iso 0 0 0.1
fix eco all orient/eco 0.08 0.25 3.6 sigma5.ori
thermo 100
thermo_style custom step temp etotal press vol f_eco
velocity all create 750 18527782
#dump save all custom 100 orient_eco.dump xs ys zs f_eco[1] f_eco[2]
#dump_modify save sort id
run 1000
fix orient/eco: cutoff=3.600000 norm_fac=30.012844 neighbors=18
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 54 27 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair eam, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix orient/eco, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 31.41 | 31.5 | 31.6 Mbytes
Step Temp TotEng Press Volume f_eco
0 750 -111027.95 15148.458 279755.85 8.749339e-10
100 422.2681 -110928.91 213.80039 285331.89 -0.89527716
200 388.81794 -110721.17 -481.38349 286440.76 -0.58341827
300 441.89999 -110478.99 -175.70299 286638.58 -0.74804169
400 486.69333 -110212.01 61.917355 287023.71 -0.83525384
500 530.62012 -109924.46 96.49276 287552 -1.7328841
600 569.89036 -109624.5 -78.252217 288224.25 -2.3216775
700 615.71719 -109319.76 -61.072041 288795.44 -3.7080665
800 664.86797 -109021.92 -52.316387 289313.22 -4.603192
900 703.88411 -108742.88 329.87308 289838.93 -8.1835743
1000 734.57012 -108504.44 1032.3825 290208.8 -9.5778417
Loop time of 34.6285 on 4 procs for 1000 steps with 25600 atoms
Performance: 2.495 ns/day, 9.619 hours/ns, 28.878 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.109 | 7.1216 | 7.136 | 0.4 | 20.57
Neigh | 0.21069 | 0.21649 | 0.22302 | 1.1 | 0.63
Comm | 0.15651 | 0.1704 | 0.17919 | 2.1 | 0.49
Output | 0.0003221 | 0.00059247 | 0.0013802 | 0.0 | 0.00
Modify | 27.057 | 27.074 | 27.084 | 0.2 | 78.18
Other | | 0.04514 | | | 0.13
Nlocal: 6400 ave 6429 max 6369 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 9867.75 ave 9885 max 9846 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 397746 ave 401713 max 393565 min
Histogram: 1 1 0 0 0 0 0 0 1 1
FullNghs: 795492 ave 802928 max 788138 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 3181966
Ave neighs/atom = 124.296
Neighbor list builds = 10
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:34

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examples/USER/misc/orient_eco/orient_eco.in
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log log.orient_eco
dimension 3
boundary p p p
units metal
atom_style atomic
read_data examples/USER/misc/orient_eco/sigma5.lammps
pair_style eam
pair_coeff * * potentials/Ni_u3.eam
timestep 0.001
fix integrator all npt temp 750 750 0.1 iso 0 0 0.1
fix eco all orient/eco 0.08 0.25 3.6 examples/USER/misc/orient_eco/sigma5.ori
thermo 100
thermo_style custom step temp etotal press vol f_eco
velocity all create 750 1
dump save all custom 100 orient_eco.dump xs ys zs f_eco[1] f_eco[2]
dump_modify save sort id
run 1000

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examples/USER/misc/orient_eco/sigma5.ori Executable file → Normal file
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