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clean up input and replace log with logs following LAMMPS conventions

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This commit is contained in:
Axel Kohlmeyer
2021-02-09 08:42:31 -05:00
parent 9e25dff8b8
commit 1cbb37b92c
3 changed files with 161 additions and 48 deletions
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26
examples/relres/in.22DMH.relres
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@ -5,17 +5,17 @@ dielectric 1
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/relres 0.675e-9 .725e-9 1.2e-9 1.4e-9
bond_style harmonic
angle_style harmonic
dihedral_style fourier
bond_style harmonic
angle_style harmonic
dihedral_style fourier
read_data Data.22DMH.in.relres
pair_coeff 6 6 1.21585e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 4 4 0.819828e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 5 5 1.00742E-21 0.396E-9 0 0.396E-9
pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9
pair_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9
pair_modify shift yes
pair_coeff 6 6 1.21585e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 4 4 0.819828e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 5 5 1.00742E-21 0.396E-9 0 0.396E-9
pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9
pair_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9
pair_modify shift yes
neighbor 2.0e-10 bin
neigh_modify every 2 delay 4 check yes
@ -26,6 +26,6 @@ fix 2 all nvt temp 290 290 2.0e-13
run 1000
#write_data Data.22DMH.out.relres pair ij
pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11
pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22
pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12
#pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11
#pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22
#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12

66
examples/relres/log.relres → examples/relres/log.09Feb21.22DMH.relres.g++.1
View File

@ -1,5 +1,4 @@
LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
units si
atom_style molecular
@ -10,11 +9,11 @@ special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/relres 0.675e-9 .725e-9 1.2e-9 1.4e-9
bond_style harmonic
angle_style harmonic
dihedral_style fourier
dihedral_style fourier
read_data Data.22DMH.in.relres
Reading data file ...
orthogonal box = (3.7421629e-10 3.7421629e-10 3.7421629e-10) to (6.8257837e-09 6.8257837e-09 6.8257837e-09)
1 by 1 by 2 MPI processor grid
1 by 1 by 1 MPI processor grid
reading atoms ...
8000 atoms
reading velocities ...
@ -38,15 +37,15 @@ Finding 1-2 1-3 1-4 neighbors ...
4 = max # of 1-3 neighbors
5 = max # of 1-4 neighbors
7 = max # of special neighbors
special bonds CPU = 0.003 seconds
read_data CPU = 0.062 seconds
pair_coeff 6 6 1.21585e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 4 4 0.819828e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 5 5 1.00742E-21 0.396E-9 0 0.396E-9
pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9
pair_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9
pair_modify shift yes
special bonds CPU = 0.019 seconds
read_data CPU = 0.168 seconds
pair_coeff 6 6 1.21585e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 4 4 0.819828e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 5 5 1.00742E-21 0.396E-9 0 0.396E-9
pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9
pair_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9
pair_modify shift yes
neighbor 2.0e-10 bin
neigh_modify every 2 delay 4 check yes
@ -68,7 +67,7 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 19.53 | 19.53 | 19.53 Mbytes
Per MPI rank memory allocation (min/avg/max) = 20.39 | 20.39 | 20.39 Mbytes
Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
0 286.85659 -21390710 2.6345656e-17 4.7519899e-17 7.3865555e-17 -3.3260066e-17 5.9605722e-17 2.685318e-25
100 292.25165 10716172 2.5245584e-17 4.841363e-17 7.3659214e-17 -3.2561964e-17 5.7807548e-17 2.685318e-25
@ -81,27 +80,27 @@ Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
800 293.01243 38119194 2.3163674e-17 4.8539659e-17 7.1703333e-17 -3.3641284e-17 5.6804958e-17 2.685318e-25
900 289.1191 32514067 2.3608264e-17 4.7894701e-17 7.1502965e-17 -3.3787865e-17 5.7396129e-17 2.685318e-25
1000 292.45834 -714652.68 2.2885394e-17 4.8447871e-17 7.1333265e-17 -3.3864138e-17 5.6749532e-17 2.685318e-25
Loop time of 7.07676 on 2 procs for 1000 steps with 8000 atoms
Loop time of 20.1906 on 1 procs for 1000 steps with 8000 atoms
99.7% CPU use with 2 MPI tasks x 1 OpenMP threads
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.1275 | 5.1852 | 5.243 | 2.5 | 73.27
Bond | 1.0056 | 1.0072 | 1.0087 | 0.2 | 14.23
Neigh | 0.38261 | 0.38263 | 0.38266 | 0.0 | 5.41
Comm | 0.25513 | 0.31266 | 0.37018 | 10.3 | 4.42
Output | 0.00042391 | 0.00044036 | 0.00045681 | 0.0 | 0.01
Modify | 0.14501 | 0.14643 | 0.14785 | 0.4 | 2.07
Other | | 0.04219 | | | 0.60
Pair | 15.751 | 15.751 | 15.751 | 0.0 | 78.01
Bond | 1.7612 | 1.7612 | 1.7612 | 0.0 | 8.72
Neigh | 1.4937 | 1.4937 | 1.4937 | 0.0 | 7.40
Comm | 0.404 | 0.404 | 0.404 | 0.0 | 2.00
Output | 0.0013139 | 0.0013139 | 0.0013139 | 0.0 | 0.01
Modify | 0.72282 | 0.72282 | 0.72282 | 0.0 | 3.58
Other | | 0.05691 | | | 0.28
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 13887.5 ave 13896 max 13879 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 217142.0 ave 217471 max 216812 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nlocal: 8000.00 ave 8000 max 8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 18912.0 ave 18912 max 18912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 434283.0 ave 434283 max 434283 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 434283
Ave neighs/atom = 54.285375
@ -109,13 +108,10 @@ Ave special neighs/atom = 5.2500000
Neighbor list builds = 13
Dangerous builds = 0
#write_data Data.22DMH.out.relres pair ij
pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11
Creating table file potential.relres with DATE: 2021-02-05
pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22
Appending to table file potential.relres with DATE: 2021-02-05
pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12
Appending to table file potential.relres with DATE: 2021-02-05
#pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11
#pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22
#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:07
Total wall time: 0:00:20

117
examples/relres/log.09Feb21.22DMH.relres.g++.4 Normal file
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@ -0,0 +1,117 @@
LAMMPS (24 Dec 2020)
using 1 OpenMP thread(s) per MPI task
units si
atom_style molecular
boundary p p p
dielectric 1
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/relres 0.675e-9 .725e-9 1.2e-9 1.4e-9
bond_style harmonic
angle_style harmonic
dihedral_style fourier
read_data Data.22DMH.in.relres
Reading data file ...
orthogonal box = (3.7421629e-10 3.7421629e-10 3.7421629e-10) to (6.8257837e-09 6.8257837e-09 6.8257837e-09)
1 by 2 by 2 MPI processor grid
reading atoms ...
8000 atoms
reading velocities ...
8000 velocities
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
3 = max dihedrals/atom
reading bonds ...
7000 bonds
reading angles ...
9000 angles
reading dihedrals ...
5000 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
4 = max # of 1-2 neighbors
4 = max # of 1-3 neighbors
5 = max # of 1-4 neighbors
7 = max # of special neighbors
special bonds CPU = 0.010 seconds
read_data CPU = 0.145 seconds
pair_coeff 6 6 1.21585e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 4 4 0.819828e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9
pair_coeff 5 5 1.00742E-21 0.396E-9 0 0.396E-9
pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9
pair_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9
pair_modify shift yes
neighbor 2.0e-10 bin
neigh_modify every 2 delay 4 check yes
timestep 1.0e-15
thermo 100
thermo_style custom step temp press pe ke etotal epair emol vol
fix 2 all nvt temp 290 290 2.0e-13
run 1000
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.6e-09
ghost atom cutoff = 1.6e-09
binsize = 8e-10, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/relres, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.33 | 10.33 | 10.34 Mbytes
Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume
0 286.85659 -21390710 2.6345656e-17 4.7519899e-17 7.3865555e-17 -3.3260066e-17 5.9605722e-17 2.685318e-25
100 292.25165 10716172 2.5245584e-17 4.841363e-17 7.3659214e-17 -3.2561964e-17 5.7807548e-17 2.685318e-25
200 291.6011 48774461 2.4897987e-17 4.8305863e-17 7.320385e-17 -3.3268705e-17 5.8166692e-17 2.685318e-25
300 291.50656 37655969 2.4389062e-17 4.8290201e-17 7.2679262e-17 -3.3428236e-17 5.7817297e-17 2.685318e-25
400 287.23427 25920755 2.4747225e-17 4.7582464e-17 7.2329689e-17 -3.3065908e-17 5.7813133e-17 2.685318e-25
500 288.56911 -9297451 2.4379025e-17 4.7803591e-17 7.2182615e-17 -3.3515426e-17 5.7894451e-17 2.685318e-25
600 291.82949 20083719 2.3686904e-17 4.8343696e-17 7.2030599e-17 -3.3468666e-17 5.7155569e-17 2.685318e-25
700 290.64445 60535932 2.3704156e-17 4.8147386e-17 7.1851542e-17 -3.3299994e-17 5.700415e-17 2.685318e-25
800 293.01243 38119194 2.3163674e-17 4.8539659e-17 7.1703333e-17 -3.3641284e-17 5.6804958e-17 2.685318e-25
900 289.1191 32514067 2.3608264e-17 4.7894701e-17 7.1502965e-17 -3.3787865e-17 5.7396129e-17 2.685318e-25
1000 292.45834 -714652.68 2.2885394e-17 4.8447871e-17 7.1333265e-17 -3.3864138e-17 5.6749532e-17 2.685318e-25
Loop time of 5.79033 on 4 procs for 1000 steps with 8000 atoms
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.0309 | 4.0713 | 4.1247 | 1.7 | 70.31
Bond | 0.45193 | 0.46562 | 0.49307 | 2.4 | 8.04
Neigh | 0.40834 | 0.40848 | 0.40871 | 0.0 | 7.05
Comm | 0.48313 | 0.56787 | 0.60777 | 6.6 | 9.81
Output | 0.00049329 | 0.0010571 | 0.0020971 | 1.9 | 0.02
Modify | 0.22813 | 0.25523 | 0.27164 | 3.2 | 4.41
Other | | 0.02078 | | | 0.36
Nlocal: 2000.00 ave 2013 max 1987 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 9887.00 ave 9898 max 9865 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 108571.0 ave 110054 max 107417 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 434283
Ave neighs/atom = 54.285375
Ave special neighs/atom = 5.2500000
Neighbor list builds = 13
Dangerous builds = 0
#write_data Data.22DMH.out.relres pair ij
#pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11
#pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22
#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:06