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Merge branch 'atomvec-custom' of github.com:lammps/lammps into atomvec-custom

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Steve Plimpton
2020-05-06 16:25:22 -06:00
parent 25632992f4 8301c7a9c6
commit 8ed5829d32
82 changed files with 7872 additions and 184 deletions
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examples/VISCOSITY/README
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This directory has 5 scripts that compute the viscosity (eta) of a
Lennard-Jones fluid using 5 different methods. See the discussion in
This directory has 6 scripts that compute the viscosity (eta) of fluid
using 6 different methods. 5 of them are for a Lennard-Jones fluid
and the last one is for SPC/E water model. See the discussion in
Section 6.21 of the manual for an overview of the methods and pointers
to doc pages for the commands which implement them. Citations for the
various methods can also be found in the manual.
@ -10,7 +11,7 @@ enough to generate good statistics and highly accurate results.
-------------
These are the 5 methods for computing viscosity. The first 3 are
These are the 5 methods for computing viscosity of a LJ fluid. The first 3 are
non-equilibrium methods; the last 2 are equilibrium methods.
in.wall = move a wall to shear the fluid between two walls
@ -89,3 +90,18 @@ heat/flux doc page - the resulting value prints at the end of the run
and is in the log file
eta = 1.07
-------------
in.cos.1000SPCE is an example script of using cosine periodic perturbation method
to calculate the viscosity of SPC/E water model.
The reciprocal of eta is computed within the script, and printed out as v_invVis
in thermo_style command. The result will converge after hundreds of picoseconds.
Then eta is obtained from the reciprocal of time average of v_invVis.
eta = 0.75 mPa*s
Note that the calculated viscosity by this method decreases with increased acceleration.
It is therefore generally necessary to perform calculation at different accelerations
and extrapolate the viscosity to zero shear.

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# DFF generated Lammps input file
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 10.0
pair_modify mix arithmetic
pair_modify tail yes
kspace_style pppm 1.0e-4
dielectric 1.0
special_bonds amber
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
read_data data.cos.1000SPCE
variable T equal 300
variable P equal 1.0
velocity all create ${T} 12345 mom yes rot yes dist gaussian
timestep 1.0
# Constraint ##################################
fix com all momentum 100 linear 1 1 1
fix rigid all shake 1e-4 20 0 b 1 a 1
# Viscosity ##################################
variable A equal 0.05e-5 # angstrom/fs^2
fix cos all accelerate/cos ${A}
compute cos all viscosity/cos
variable density equal density
variable lz equal lz
variable vMax equal c_cos[7] # velocity of atoms at z=0
variable invVis equal v_vMax/${A}/v_density*39.4784/v_lz/v_lz*100 # reciprocal of viscosity 1/Pa/s
fix npt all npt temp ${T} ${T} 100 iso ${P} ${P} 1000
fix_modify npt temp cos
thermo_style custom step cpu temp press pe density v_vMax v_invVis
thermo_modify temp cos
thermo 100
################################################
dump 1 all custom 10000 dump.lammpstrj id mol type element q xu yu zu
dump_modify 1 sort id element O H
run 2000

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LAMMPS (3 Mar 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# DFF generated Lammps input file
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 10.0
pair_modify mix arithmetic
pair_modify tail yes
kspace_style pppm 1.0e-4
dielectric 1.0
special_bonds amber
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
read_data data.1000SPCE.lmp
orthogonal box = (0 0 0) to (31.043 31.043 31.043)
2 by 2 by 2 MPI processor grid
reading atoms ...
3000 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
2000 bonds
reading angles ...
1000 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.00114917 secs
read_data CPU = 0.00953543 secs
variable T equal 300
variable P equal 1.0
velocity all create ${T} 12345 mom yes rot yes dist gaussian
velocity all create 300 12345 mom yes rot yes dist gaussian
timestep 1.0
# Constraint ##################################
fix com all momentum 100 linear 1 1 1
fix rigid all shake 1e-4 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
1000 = # of frozen angles
find clusters CPU = 0.000442737 secs
# Viscosity ##################################
variable A equal 0.02e-5 # angstrom/fs^2
fix cos all accelerate/cos ${A}
fix cos all accelerate/cos 2e-07
compute cos all viscosity/cos
variable density equal density
variable lz equal lz
variable vMax equal c_cos[7] # velocity of atoms at z=0
variable invVis equal v_vMax/${A}/v_density*39.4784/v_lz/v_lz*100 # reciprocal of viscosity 1/Pa/s
variable invVis equal v_vMax/2e-07/v_density*39.4784/v_lz/v_lz*100
fix npt all npt temp ${T} ${T} 100 iso ${P} ${P} 1000
fix npt all npt temp 300 ${T} 100 iso ${P} ${P} 1000
fix npt all npt temp 300 300 100 iso ${P} ${P} 1000
fix npt all npt temp 300 300 100 iso 1 ${P} 1000
fix npt all npt temp 300 300 100 iso 1 1 1000
fix_modify npt temp cos
thermo_style custom step cpu temp press pe density v_vMax v_invVis
thermo_modify temp cos
thermo 100
################################################
dump 1 all custom 10000 dump.lammpstrj id mol type element q xu yu zu
dump_modify 1 sort id element O H
run 2000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
G vector (1/distance) = 0.263539
grid = 16 16 16
stencil order = 5
estimated absolute RMS force accuracy = 0.0325342
estimated relative force accuracy = 9.79757e-05
using double precision MKL FFT
3d grid and FFT values/proc = 3375 512
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, 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) = 10.14 | 10.14 | 10.14 Mbytes
Step CPU Temp Press PotEng Density v_vMax v_invVis
0 0 450.04468 9838.6886 -7651.736 0.99999331 0.0001293705 2649.9663
100 0.33736925 497.65155 2024.4827 -8342.2499 0.98595028 0.00019602427 4034.2452
200 0.67116638 446.48518 27.075082 -8908.9684 0.9652009 0.00027615455 5723.7907
300 0.99760895 401.79875 -776.99871 -9381.8986 0.95205822 0.00019626685 4086.6103
400 1.3239019 369.65373 -510.5336 -9803.6463 0.94817309 0.00022998514 4795.2142
500 1.6488092 343.35807 -936.31982 -10146.023 0.94840581 0.0001434423 2990.5423
600 1.9826063 319.86131 -1381.3302 -10405.812 0.95459202 6.6411532e-05 1381.5767
700 2.3172637 307.74606 -98.775733 -10643.5 0.96669652 0.00010446317 2164.0664
800 2.6562841 305.14214 -540.57804 -10865.742 0.97808367 5.4381233e-05 1122.1765
900 2.9938415 288.01316 639.00486 -10925.39 0.98686357 0.00010878474 2238.1355
1000 3.327893 295.07773 -226.06503 -11033.826 0.99128496 0.00011935058 2451.8608
1100 3.6618862 299.21578 306.34231 -11049.152 0.99552203 8.9538943e-05 1836.8166
1200 3.9984287 301.82462 85.804646 -11013.564 0.99713434 0.00015912276 3262.51
1300 4.3320735 308.6009 268.08897 -11009.836 0.99695358 0.00026212596 5374.72
1400 4.668875 298.36903 -258.75495 -10962.299 0.99503447 0.00033087355 6788.7027
1500 5.0003694 299.96073 99.512082 -10980.551 0.99315631 0.00033996557 6979.6425
1600 5.3367337 304.18018 -500.65441 -11002.054 0.9914558 0.00039075642 8026.9849
1700 5.6780828 301.63978 -499.07458 -10992.88 0.99234354 0.00038101175 7824.4738
1800 6.0140638 303.25858 640.03432 -11053.335 0.99553958 0.00041336203 8479.7267
1900 6.3532521 301.40882 208.28331 -11119.481 0.99534534 0.00032474734 6662.3144
2000 6.6938104 298.0462 -236.47954 -11162.212 0.99421846 0.00023869721 4898.8129
Loop time of 6.69387 on 8 procs for 2000 steps with 3000 atoms
Performance: 25.815 ns/day, 0.930 hours/ns, 298.781 timesteps/s
99.7% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.36 | 4.4981 | 4.6781 | 5.1 | 67.20
Bond | 0.00074545 | 0.00088463 | 0.0012464 | 0.0 | 0.01
Kspace | 0.86696 | 1.0476 | 1.1863 | 10.5 | 15.65
Neigh | 0.37733 | 0.37785 | 0.3784 | 0.1 | 5.64
Comm | 0.19874 | 0.20168 | 0.20729 | 0.6 | 3.01
Output | 0.0015529 | 0.0015803 | 0.0017546 | 0.2 | 0.02
Modify | 0.54083 | 0.55143 | 0.55445 | 0.6 | 8.24
Other | | 0.01483 | | | 0.22
Nlocal: 375 ave 385 max 361 min
Histogram: 1 1 0 0 1 0 2 0 1 2
Nghost: 5772.25 ave 5789 max 5757 min
Histogram: 1 1 2 0 0 0 2 0 0 2
Neighs: 135285 ave 144189 max 127550 min
Histogram: 1 2 1 1 0 0 0 0 1 2
Total # of neighbors = 1082280
Ave neighs/atom = 360.76
Ave special neighs/atom = 2
Neighbor list builds = 101
Dangerous builds = 1
Total wall time: 0:00:06