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Examples and documentation

This commit is contained in:
Joel Clemmer 2021-01-08 15:27:23 -07:00
parent 50be21902e
commit d5f34f6296
14 changed files with 1604 additions and 23 deletions
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16
doc/src/comm_modify.rst
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@ -66,9 +66,10 @@ For many systems this is an efficient algorithm, but for systems with
widely varying cutoffs for different type pairs, the *multi* mode can
be faster. In this case, each atom type is assigned its own distance
cutoff for communication purposes, and fewer atoms will be
communicated. See the :doc:`neighbor multi <neighbor>` command for a
communicated. See the :doc:`neighbor multi <neighbor>` command for a
neighbor list construction option that may also be beneficial for
simulations of this kind.
simulations of this kind. The *multi* mode is compatable with both the
*multi* and *multi/old* neighbor styles.
The *cutoff* keyword allows you to extend the ghost cutoff distance
for communication mode *single*\ , which is the distance from the borders
@ -95,11 +96,12 @@ using the usual asterisk notation can be given. For granular pair styles,
the default cutoff is set to the sum of the current maximum atomic radii
for each type.
The *cutoff/bytype* option applies to *multi* and automtically sets communication
cutoffs for each particle type based on the largest interaction distance
between two particles of the same type. This method is only compatible
with Newton on and the *bytype* neighbor style. See the :doc:`neighbor bytype <neighbor>`
command for more information.
The *multi/reduce* option applies to *multi* and automatically sets communication
cutoffs for different sized particles based on the largest interaction distance
between two particles in the same multi grouping. This reduces the number of
ghost that need to be communicated This method is only compatible with the
*multi* neighbor style and requires only half neighbor lists and Newton on.
See the :doc:`neighbor multi <neighbor>` command for more information.
These are simulation scenarios in which it may be useful or even
necessary to set a ghost cutoff > neighbor cutoff:

20
doc/src/neigh_modify.rst
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@ -14,7 +14,7 @@ Syntax
.. parsed-literal::
keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize*
keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* or *multi/custom*
*delay* value = N
N = delay building until this many steps since last build
*every* value = M
@ -47,6 +47,9 @@ Syntax
N = max number of neighbors of one atom
*binsize* value = size
size = bin size for neighbor list construction (distance units)
*multi/custom* values = N types
N = number of custom groups
types = N separate types or groups of types (see below)
Examples
""""""""
@ -58,6 +61,7 @@ Examples
neigh_modify exclude group frozen frozen check no
neigh_modify exclude group residue1 chain3
neigh_modify exclude molecule/intra rigid
neigh_modify multi/custom 2 1*2 3*4
Description
"""""""""""
@ -197,6 +201,20 @@ small, the optimal number of atoms is checked, but bin overhead goes
up. If you set the binsize to 0.0, LAMMPS will use the default
binsize of 1/2 the cutoff.
The *multi/custom* option allows you to define custom groups of atom
types for the *multi* neighbor mode. By grouping atom types with
similar cutoffs, one may be able to improve performance by reducing
overhead. You must first specify the number of custom groups N to be
defined followed by N ranges of types. The range can be specified as a
single numeric value, or a wildcard asterisk can be used to specify a range
of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For
example, if N = the number of atom types, then an asterisk with no numeric
values means all types from 1 to N. A leading asterisk means all types
from 1 to n (inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n (inclusive).
Note that any atom types not included in a custom group will be automatically
placed within a new, separate group.
Restrictions
""""""""""""

32
doc/src/neighbor.rst
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@ -11,7 +11,7 @@ Syntax
neighbor skin style
* skin = extra distance beyond force cutoff (distance units)
* style = *bin* or *nsq* or *multi* or *bytype*
* style = *bin* or *nsq* or *multi* or *multi/old*
Examples
""""""""
@ -55,22 +55,24 @@ For the *bin* style, the bin size is set to 1/2 of
the largest cutoff distance between any pair of atom types and a
single set of bins is defined to search over for all atom types. This
can be inefficient if one pair of types has a very long cutoff, but
other type pairs have a much shorter cutoff. For style *multi* the
bin size is set to 1/2 of the shortest cutoff distance and multiple
sets of bins are defined to search over for different atom types.
other type pairs have a much shorter cutoff. The *multi* style uses
different sized bins for groups of different sized particles. Different
sets of bins are then used to construct the neighbor lists as as further
described by Shire, Hanley, and Stratford :ref:`(Shire) <bytype-Shire>`.
This imposes some extra setup overhead, but the searches themselves
may be much faster for the short-cutoff cases.
See the :doc:`comm_modify mode multi <comm_modify>` command for a
communication option that may also be beneficial for simulations of
this kind.
may be much faster. By default, separate groups of particles are defined
for each atom type. For systems with two or more types with similar
cutoffs, one can reduce the extra overhead by defining custom groupings
using the :doc:`neigh_modify <neigh_modify>` command. See the
:doc:`comm_modify mode bytype <comm_modify>` command for compatible
communication options that may be beneficial for simulations of this kind.
The *bytype* style is an extension of the *multi* style that was
presented by Shire, Hanley, and Stratford :ref:`(Shire) <bytype-Shire>`.
For style *bytype*, different bin lists are created for each different
type and separate bin sizes are generated. Whether *bytype* or *multi*
is faster may depend on the specifics of your system. See the
:doc:`comm_modify mode bytype <comm_modify>` command for a compatible
communication option.
An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest
cutoff distance and multiple sets of bins are defined to search over for
different atom types. This algorithm used to be the default *multi*
algorithm in LAMMPS but was found to be significantly slower than the new
approach. Although, there may be instances where the *multi/old* style
could outperform the new style.
The :doc:`neigh_modify <neigh_modify>` command has additional options
that control how often neighbor lists are built and which pairs are

67
examples/multi/in.colloid Normal file
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@ -0,0 +1,67 @@
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.1
region box block 0 60 0 60 -0.5 0.5
create_box 5 box
create_atoms 1 box
#Roughly equally partition atoms between types 1-4
set group all type/fraction 2 0.500 23984
set group all type/fraction 3 0.333 43684
set group all type/fraction 4 0.250 87811
# remove two spheres of small particles and add large particles in the voids
region sphere1 sphere 60.0 60.0 0.0 30.0 units box
region sphere2 sphere 130.0 130.0 0.0 30.0 units box
delete_atoms region sphere1
delete_atoms region sphere2
create_atoms 5 single 60.0 60.0 0.0 units box
create_atoms 5 single 130.0 130.0 0.0 units box
set type 1 mass 400
set type 2 mass 1
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi #multi/old
neigh_modify delay 0 multi/custom 2 1*4 5
comm_modify mode multi multi/reduce
# colloid potential
pair_style colloid 20.0
pair_coeff * * 144.0 1.0 0.0 0.0 3.0
pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 &
mtk no pchain 0 tchain 1
fix 2 all enforce2d
#dump 1 all atom 1000 dump.colloid
#dump 2 all image 1000 image.*.jpg type type &
# zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type &
# zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000

58
examples/multi/in.granular Normal file
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@ -0,0 +1,58 @@
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.5
region box block 0 60 0 60 -0.5 0.5
create_box 2 box
create_atoms 1 box
change_box all triclinic
# remove two spheres of small particles and add large particles in the voids
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
delete_atoms region sphere1
delete_atoms region sphere2
create_atoms 2 single 20.0 20.0 0.0 units box
create_atoms 2 single 60.0 60.0 0.0 units box
set type 2 mass 400
set type 1 mass 1
set type 2 diameter 20
set type 1 diameter 1
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi #multi/old
neigh_modify delay 0
comm_modify mode multi vel yes multi/reduce
# colloid potential
pair_style granular
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
fix 2 all enforce2d
fix 3 all deform 1 xy erate 1e-3
#dump 1 all custom 1000 dump.granular id x y z radius
#dump 2 all image 1000 image.*.jpg type type &
# zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type &
# zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000

183
examples/multi/log.30Nov20.colloid.intel.1 Normal file
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@ -0,0 +1,183 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.1
Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777
region box block 0 60 0 60 -0.5 0.5
create_box 5 box
Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 3600 atoms
create_atoms CPU = 0.001 seconds
#Roughly equally partition atoms between types 1-4
set group all type/fraction 2 0.500 23984
Setting atom values ...
1768 settings made for type/fraction
set group all type/fraction 3 0.333 43684
Setting atom values ...
1255 settings made for type/fraction
set group all type/fraction 4 0.250 87811
Setting atom values ...
927 settings made for type/fraction
# remove two spheres of small particles and add large particles in the voids
region sphere1 sphere 60.0 60.0 0.0 30.0 units box
region sphere2 sphere 130.0 130.0 0.0 30.0 units box
delete_atoms region sphere1
Deleted 289 atoms, new total = 3311
delete_atoms region sphere2
Deleted 287 atoms, new total = 3024
create_atoms 5 single 60.0 60.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
create_atoms 5 single 130.0 130.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
set type 1 mass 400
Setting atom values ...
753 settings made for mass
set type 2 mass 1
Setting atom values ...
722 settings made for mass
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi #/old
neigh_modify delay 0 multi/custom 2 1*4 5
comm_modify mode multi multi/reduce
# colloid potential
pair_style colloid 20.0
pair_coeff * * 144.0 1.0 0.0 0.0 3.0
pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
dump 1 all atom 1000 dump.colloid
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 31
ghost atom cutoff = 31
binsize = 2, bins = 95 95 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair colloid, perpetual
attributes: half, newton on
pair build: half/multi/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 5.538 | 5.538 | 5.538 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395241 0.121 36000
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
2000 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69
3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12
4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299
5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92
6000 2.0797015 -0.086800285 1.992214 0.082095164 78182.702
7000 2.0867886 -0.10960963 1.9764893 0.10103655 63990.386
8000 2.0803886 -0.12736298 1.9523381 0.12561727 52648.372
9000 2.0605661 -0.14572043 1.9141648 0.15154081 44589.764
10000 2.0636909 -0.18556771 1.8774412 0.1604707 38996.941
11000 2.0498344 -0.20303461 1.8461224 0.18295046 34927.993
12000 2.0466611 -0.2217963 1.8241884 0.23031182 31760.363
13000 2.0441824 -0.24716826 1.7963386 0.22167931 29178.226
14000 2.047513 -0.26988172 1.7769547 0.24070752 26991.372
15000 2.0154283 -0.26144354 1.7533187 0.27587713 25247.715
16000 2.0160849 -0.28106984 1.7343488 0.32297139 23703.607
17000 2.0184729 -0.31071368 1.7070922 0.29815613 22300.6
18000 2.0237288 -0.33944941 1.6836106 0.3262795 21098.856
19000 2.0329827 -0.35438937 1.6779215 0.33691952 19989.867
20000 2.021113 -0.37316841 1.6472766 0.39687648 18978.666
21000 2.0352439 -0.40857976 1.6259915 0.38632613 18146.277
22000 2.0158566 -0.41271329 1.6024771 0.41480502 17409.593
23000 2.0170409 -0.42611776 1.5902566 0.40446612 16748.968
24000 2.0108878 -0.43899286 1.5712304 0.42075035 16086.941
25000 2.0218394 -0.47012156 1.5510497 0.46655183 15460.154
26000 2.0100713 -0.47985916 1.5295479 0.45575323 15013.774
27000 2.0251738 -0.5016665 1.5228381 0.50151992 14591.521
28000 2.0062966 -0.50284394 1.5027897 0.5462034 14135.093
29000 2.0146666 -0.53126035 1.4827405 0.60379062 13725.945
30000 2.0036455 -0.53246643 1.4705169 0.56784088 13417.305
31000 2.0127662 -0.54487777 1.4672233 0.6427741 13139.392
32000 2.0221816 -0.5625554 1.4589579 0.60695012 12779.609
33000 2.024983 -0.59515221 1.4291616 0.60005385 12584.572
34000 2.0184045 -0.59033569 1.4274018 0.62519753 12355.49
35000 2.0155635 -0.61190466 1.4029927 0.71044196 12106.819
36000 2.0252503 -0.61581601 1.408765 0.68805882 11728.608
37000 2.0112487 -0.64540754 1.3651765 0.66981639 11475.772
38000 2.0147475 -0.64161981 1.3724619 0.71130901 11285.511
39000 2.0213092 -0.67174661 1.3488946 0.6969697 11044.647
40000 2.0178739 -0.67924699 1.3379601 0.77309897 10824.198
41000 1.9952353 -0.67490899 1.3196669 0.76592358 10646.649
42000 2.002415 -0.70533555 1.2964178 0.81084741 10519.804
43000 2.0211625 -0.71370366 1.3067909 0.77355048 10434.893
44000 2.0252106 -0.72635544 1.2981859 0.83770143 10132.262
45000 2.0126446 -0.75197714 1.2600024 0.88927993 9946.7842
46000 2.0431159 -0.78445975 1.257981 0.84492327 9869.8151
47000 2.0199724 -0.76967899 1.2496259 0.90977181 9653.4334
48000 2.0109636 -0.78968551 1.2206135 0.89458323 9496.7246
49000 2.0131059 -0.79687252 1.2155681 0.91239613 9418.3093
50000 2.0073361 -0.79981468 1.206858 0.98524334 9289.4715
Loop time of 20.4651 on 1 procs for 50000 steps with 3026 atoms
Performance: 1055453.279 tau/day, 2443.179 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.099 | 11.099 | 11.099 | 0.0 | 54.23
Neigh | 2.7536 | 2.7536 | 2.7536 | 0.0 | 13.46
Comm | 0.53353 | 0.53353 | 0.53353 | 0.0 | 2.61
Output | 0.11209 | 0.11209 | 0.11209 | 0.0 | 0.55
Modify | 5.1627 | 5.1627 | 5.1627 | 0.0 | 25.23
Other | | 0.8046 | | | 3.93
Nlocal: 3026.00 ave 3026 max 3026 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 584.000 ave 584 max 584 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 25892.0 ave 25892 max 25892 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 25892
Ave neighs/atom = 8.5565102
Neighbor list builds = 4330
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:20

183
examples/multi/log.30Nov20.colloid.intel.4 Normal file
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@ -0,0 +1,183 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.1
Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777
region box block 0 60 0 60 -0.5 0.5
create_box 5 box
Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3600 atoms
create_atoms CPU = 0.001 seconds
#Roughly equally partition atoms between types 1-4
set group all type/fraction 2 0.500 23984
Setting atom values ...
1768 settings made for type/fraction
set group all type/fraction 3 0.333 43684
Setting atom values ...
1255 settings made for type/fraction
set group all type/fraction 4 0.250 87811
Setting atom values ...
927 settings made for type/fraction
# remove two spheres of small particles and add large particles in the voids
region sphere1 sphere 60.0 60.0 0.0 30.0 units box
region sphere2 sphere 130.0 130.0 0.0 30.0 units box
delete_atoms region sphere1
Deleted 289 atoms, new total = 3311
delete_atoms region sphere2
Deleted 287 atoms, new total = 3024
create_atoms 5 single 60.0 60.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
create_atoms 5 single 130.0 130.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
set type 1 mass 400
Setting atom values ...
753 settings made for mass
set type 2 mass 1
Setting atom values ...
722 settings made for mass
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi #/old
neigh_modify delay 0 multi/custom 2 1*4 5
comm_modify mode multi multi/reduce
# colloid potential
pair_style colloid 20.0
pair_coeff * * 144.0 1.0 0.0 0.0 3.0
pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
dump 1 all atom 1000 dump.colloid
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 31
ghost atom cutoff = 31
binsize = 2, bins = 95 95 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair colloid, perpetual
attributes: half, newton on
pair build: half/multi/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.382 | 5.384 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395241 0.121 36000
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
2000 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688
3000 1.8956738 -0.090814176 1.8042332 0.075557943 77825.289
4000 1.9570462 -0.072505537 1.8838939 0.072824365 90931.708
5000 2.0376745 -0.083247829 1.9537533 0.068496975 90055.295
6000 2.0744887 -0.085395371 1.9884077 0.0821927 78070.648
7000 2.1002183 -0.11654617 1.9829781 0.10523249 63934.448
8000 2.0818325 -0.13271654 1.948428 0.11909162 52636.484
9000 2.0693987 -0.16404154 1.9046733 0.14702552 44539.609
10000 2.0667772 -0.19779488 1.8682993 0.17245383 38822.542
11000 2.0640582 -0.22114917 1.842227 0.18083079 34788.927
12000 2.0308462 -0.20353105 1.8266441 0.20640739 31706.009
13000 2.0395895 -0.24217765 1.7967378 0.21832952 29152.654
14000 2.030848 -0.2586169 1.77156 0.26577748 27068.89
15000 2.0222966 -0.27554585 1.7460825 0.2777169 25272.786
16000 2.0398867 -0.31547563 1.723737 0.27763622 23666.792
17000 2.03026 -0.32453791 1.7050512 0.28099246 22272.809
18000 2.0345512 -0.35026242 1.6836164 0.36600779 21023.172
19000 2.0242864 -0.35813231 1.6654851 0.33415432 19941.244
20000 2.0132465 -0.36563904 1.6469422 0.403365 18979.884
21000 2.0280384 -0.4075867 1.6197815 0.37205362 18152.487
22000 2.0206494 -0.40600336 1.6139782 0.42704594 17370.812
23000 2.0395761 -0.45083258 1.5880695 0.40276343 16700.427
24000 2.017203 -0.44930293 1.5672335 0.43867313 16161.79
25000 2.0191846 -0.4672218 1.5512955 0.47031215 15622.756
26000 2.0131624 -0.46436088 1.5481363 0.51717944 15141.645
27000 2.0322461 -0.50659994 1.5249745 0.49218933 14627.657
28000 2.0169304 -0.50555565 1.5107082 0.55547935 14186.079
29000 2.024656 -0.52258414 1.5014028 0.59125812 13759.99
30000 2.0153725 -0.53585947 1.478847 0.57235811 13384.355
31000 2.0163261 -0.56383766 1.4518221 0.58232057 13098.196
32000 2.0109673 -0.56784395 1.4424588 0.58282178 12831.934
33000 2.0099169 -0.57625621 1.4329964 0.65139601 12479.442
34000 2.0238152 -0.60189607 1.4212503 0.62659152 12210.628
35000 2.0359989 -0.62654733 1.4087787 0.67574446 11972.725
36000 2.0222689 -0.62880837 1.3927923 0.66602146 11690.049
37000 1.9982569 -0.62746376 1.3701328 0.71326589 11433.825
38000 1.9969836 -0.63975181 1.3565719 0.72799891 11285.497
39000 2.0071087 -0.65781805 1.3486274 0.79121297 11107.469
40000 2.0243046 -0.6881221 1.3355135 0.77519099 10943.846
41000 2.0351657 -0.70309175 1.3314014 0.68815156 10742.515
42000 2.0224788 -0.70975664 1.3120538 0.80484619 10505.657
43000 2.0123135 -0.70818545 1.3034631 0.84204556 10353.024
44000 1.999883 -0.70981202 1.2894101 0.94070546 10212.224
45000 2.0127291 -0.73338075 1.2786832 0.82095205 10109.959
46000 2.0109037 -0.75130029 1.2589389 0.88538358 9953.4822
47000 1.9879175 -0.73152019 1.2557404 0.92089629 9832.892
48000 2.0108204 -0.76655178 1.2436041 0.95379465 9633.6453
49000 1.9868193 -0.76613798 1.2200247 0.88790224 9504.2918
50000 2.0141467 -0.80029827 1.2131829 1.0064263 9346.3268
Loop time of 7.28248 on 4 procs for 50000 steps with 3026 atoms
Performance: 2966022.789 tau/day, 6865.793 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1624 | 2.5918 | 2.9227 | 17.4 | 35.59
Neigh | 0.62508 | 0.7436 | 0.83321 | 9.2 | 10.21
Comm | 1.1035 | 1.5265 | 2.0746 | 29.3 | 20.96
Output | 0.050094 | 0.050233 | 0.05062 | 0.1 | 0.69
Modify | 1.8164 | 1.8966 | 1.9583 | 4.2 | 26.04
Other | | 0.4737 | | | 6.50
Nlocal: 756.500 ave 839 max 673 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 292.500 ave 307 max 282 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 6435.25 ave 7367 max 5493 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 25741
Ave neighs/atom = 8.5066094
Neighbor list builds = 4335
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:07

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LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.1
Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777
region box block 0 60 0 60 -0.5 0.5
create_box 5 box
Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 3600 atoms
create_atoms CPU = 0.001 seconds
#Roughly equally partition atoms between types 1-4
set group all type/fraction 2 0.500 23984
Setting atom values ...
1768 settings made for type/fraction
set group all type/fraction 3 0.333 43684
Setting atom values ...
1255 settings made for type/fraction
set group all type/fraction 4 0.250 87811
Setting atom values ...
927 settings made for type/fraction
# remove two spheres of small particles and add large particles in the voids
region sphere1 sphere 60.0 60.0 0.0 30.0 units box
region sphere2 sphere 130.0 130.0 0.0 30.0 units box
delete_atoms region sphere1
Deleted 289 atoms, new total = 3311
delete_atoms region sphere2
Deleted 287 atoms, new total = 3024
create_atoms 5 single 60.0 60.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
create_atoms 5 single 130.0 130.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
set type 1 mass 400
Setting atom values ...
753 settings made for mass
set type 2 mass 1
Setting atom values ...
722 settings made for mass
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi/old
neigh_modify delay 0 #multi/custom 2 1*4 5
comm_modify mode multi #multi/reduce
# colloid potential
pair_style colloid 20.0
pair_coeff * * 144.0 1.0 0.0 0.0 3.0
pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
dump 1 all atom 1000 dump.colloid
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 31
ghost atom cutoff = 31
binsize = 2, bins = 95 95 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair colloid, perpetual
attributes: half, newton on
pair build: half/multi/old/newton
stencil: half/multi/old/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.611 | 5.611 | 5.611 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395241 0.121 36000
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
2000 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69
3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12
4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299
5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92
6000 2.0797015 -0.086800284 1.992214 0.082095164 78182.702
7000 2.086794 -0.10961479 1.9764895 0.10103993 63990.387
8000 2.082863 -0.12779588 1.9543788 0.12672452 52629.802
9000 2.0718275 -0.15189022 1.9192526 0.14728063 44541.722
10000 2.0603856 -0.18054161 1.8791631 0.16715133 38940.135
11000 2.046791 -0.20458359 1.841531 0.19532742 34907.116
12000 2.0406846 -0.2252868 1.8147234 0.2036178 31740.208
13000 2.0369763 -0.23721632 1.7990869 0.25542564 29079.901
14000 2.0376121 -0.26282517 1.7741135 0.24722118 26947.344
15000 2.0312772 -0.2851101 1.7454959 0.2801199 25180.963
16000 2.0080448 -0.28992973 1.7174515 0.30099318 23723.043
17000 2.0234993 -0.30440169 1.7184289 0.3193226 22342.977
18000 2.0216103 -0.32036933 1.7005729 0.3460322 21068.99
19000 2.0493952 -0.37711533 1.6716026 0.33804972 20013.325
20000 2.0307894 -0.38462795 1.6454903 0.37041981 19092.745
21000 2.0328577 -0.39442652 1.6377594 0.36327057 18260.298
22000 2.0325613 -0.40481002 1.6270796 0.42756691 17447.199
23000 2.0199358 -0.42175719 1.5975111 0.40948041 16768.71
24000 2.0149952 -0.43618764 1.5781417 0.45406069 16187.334
25000 2.0153221 -0.45884172 1.5558143 0.52717203 15605.577
26000 2.0099026 -0.47080566 1.5384327 0.49181459 15088.041
27000 2.0128537 -0.49799999 1.5141885 0.53907465 14590.392
28000 2.0287266 -0.53112525 1.4969309 0.59750714 14208.419
29000 2.0143609 -0.53175704 1.4819381 0.56118773 13840.642
30000 2.0235262 -0.53923416 1.4836234 0.52579997 13500.15
31000 2.0390444 -0.57976823 1.4586023 0.5760349 13082.091
32000 2.018046 -0.57797686 1.4394022 0.59127933 12761.726
33000 2.0059068 -0.57185148 1.4333925 0.58992758 12473.866
34000 1.9828456 -0.57147221 1.4107181 0.77593228 12208.869
35000 1.9900097 -0.58349168 1.4058604 0.681968 11937.285
36000 2.0271405 -0.64374859 1.382722 0.63152587 11675.264
37000 2.0032809 -0.63520712 1.3674117 0.71639384 11440.274
38000 2.0000566 -0.63941617 1.3599795 0.74099652 11235.252
39000 1.9872705 -0.64765522 1.3389586 0.7575743 11080.857
40000 2.0224403 -0.6795645 1.3422075 0.82918546 10861.905
41000 2.0137595 -0.69863075 1.3144633 0.80397759 10712.981
42000 1.9950915 -0.68892531 1.3055069 0.77631365 10632.931
43000 2.0080851 -0.70534369 1.3020778 0.82408436 10408.82
44000 2.0239806 -0.73189482 1.2914169 0.83228695 10227.18
45000 2.0019542 -0.72613202 1.2751606 0.9145618 10044.013
46000 2.0173095 -0.75370218 1.2629407 0.99791312 9837.9611
47000 1.9921201 -0.75875076 1.232711 1.0047839 9711.2083
48000 2.0283587 -0.79063641 1.237052 0.83617499 9610.9933
49000 2.0051919 -0.79078067 1.2137485 0.95651813 9411.7165
50000 2.0140985 -0.81796958 1.1954634 0.93791038 9296.069
Loop time of 29.8066 on 1 procs for 50000 steps with 3026 atoms
Performance: 724671.093 tau/day, 1677.479 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.698 | 11.698 | 11.698 | 0.0 | 39.25
Neigh | 10.292 | 10.292 | 10.292 | 0.0 | 34.53
Comm | 1.405 | 1.405 | 1.405 | 0.0 | 4.71
Output | 0.11474 | 0.11474 | 0.11474 | 0.0 | 0.38
Modify | 5.3019 | 5.3019 | 5.3019 | 0.0 | 17.79
Other | | 0.9947 | | | 3.34
Nlocal: 3026.00 ave 3026 max 3026 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2292.00 ave 2292 max 2292 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 25767.0 ave 25767 max 25767 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 25767
Ave neighs/atom = 8.5152016
Neighbor list builds = 4332
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:29

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examples/multi/log.30Nov20.colloid.old.intel.4 Normal file
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LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.1
Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777
region box block 0 60 0 60 -0.5 0.5
create_box 5 box
Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3600 atoms
create_atoms CPU = 0.001 seconds
#Roughly equally partition atoms between types 1-4
set group all type/fraction 2 0.500 23984
Setting atom values ...
1768 settings made for type/fraction
set group all type/fraction 3 0.333 43684
Setting atom values ...
1255 settings made for type/fraction
set group all type/fraction 4 0.250 87811
Setting atom values ...
927 settings made for type/fraction
# remove two spheres of small particles and add large particles in the voids
region sphere1 sphere 60.0 60.0 0.0 30.0 units box
region sphere2 sphere 130.0 130.0 0.0 30.0 units box
delete_atoms region sphere1
Deleted 289 atoms, new total = 3311
delete_atoms region sphere2
Deleted 287 atoms, new total = 3024
create_atoms 5 single 60.0 60.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
create_atoms 5 single 130.0 130.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
set type 1 mass 400
Setting atom values ...
753 settings made for mass
set type 2 mass 1
Setting atom values ...
722 settings made for mass
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi/old
neigh_modify delay 0 #multi/custom 2 1*4 5
comm_modify mode multi #multi/reduce
# colloid potential
pair_style colloid 20.0
pair_coeff * * 144.0 1.0 0.0 0.0 3.0
pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
dump 1 all atom 1000 dump.colloid
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 31
ghost atom cutoff = 31
binsize = 2, bins = 95 95 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair colloid, perpetual
attributes: half, newton on
pair build: half/multi/old/newton
stencil: half/multi/old/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.438 | 5.441 | 5.444 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395241 0.121 36000
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
2000 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688
3000 1.8956738 -0.090814168 1.8042332 0.075557943 77825.289
4000 1.9567884 -0.072243657 1.8838981 0.072836007 90931.521
5000 2.0386455 -0.084279096 1.9536927 0.06867562 90054.581
6000 2.0816461 -0.093158646 1.9877995 0.082802397 78084.994
7000 2.0854943 -0.10553618 1.979269 0.10230351 63886.068
8000 2.0923948 -0.14072173 1.9509816 0.11775174 52590.899
9000 2.0687841 -0.15957251 1.9085279 0.14963059 44575.69
10000 2.0607467 -0.18970216 1.8703636 0.17210861 39016.271
11000 2.0538523 -0.20866031 1.8445133 0.18554787 34992.223
12000 2.0408745 -0.22276635 1.8174337 0.21228473 31794.869
13000 2.0366678 -0.24217764 1.7938171 0.22999314 29186.441
14000 2.0470314 -0.26923854 1.7771164 0.2576977 26941.432
15000 2.0262458 -0.27296827 1.7526079 0.25960813 25184.491
16000 2.0410096 -0.30940081 1.7309343 0.27842776 23619.633
17000 2.027379 -0.32411477 1.7025943 0.32102949 22231.582
18000 2.0338405 -0.34468182 1.6884866 0.3306203 21028.933
19000 2.032206 -0.36558904 1.6659454 0.33926726 19958.945
20000 2.0347643 -0.3915229 1.642569 0.33718716 19054.271
21000 2.0242901 -0.38913219 1.634489 0.38062225 18190.934
22000 2.0207557 -0.41078199 1.6093059 0.40143768 17422.03
23000 2.0069068 -0.42062708 1.5856165 0.40146954 16717.999
24000 2.0300595 -0.4536262 1.5757624 0.49229743 16097.323
25000 2.0347548 -0.47655047 1.5575319 0.46787969 15564.848
26000 2.0180789 -0.46537586 1.5520362 0.48541997 15072.597
27000 2.0150506 -0.4886202 1.5257645 0.53829749 14621.24
28000 2.0175464 -0.50951413 1.5073655 0.50140171 14253.441
29000 2.0186127 -0.53911975 1.4788258 0.52955802 13930.266
30000 2.0006844 -0.52621334 1.4738099 0.60130639 13650.051
31000 2.0179614 -0.54573939 1.4715551 0.58747508 13285.903
32000 2.0333208 -0.57431851 1.4583303 0.62631039 12894.077
33000 2.0017273 -0.57778326 1.4232825 0.61159622 12595.987
34000 2.0063025 -0.58192939 1.4237101 0.66174764 12316.964
35000 2.0174782 -0.60591394 1.4108976 0.63571024 12063.433
36000 2.025112 -0.64319133 1.3812514 0.62829458 11930.246
37000 2.0431268 -0.64342323 1.3990283 0.68038546 11651.664
38000 2.0064271 -0.63716263 1.3686014 0.72167175 11345.421
39000 2.0284014 -0.67236471 1.3553663 0.68693225 11062.293
40000 2.0181711 -0.6962559 1.3212483 0.76033095 10864.176
41000 1.9908152 -0.66607906 1.3240783 0.90250403 10812.599
42000 2.0007084 -0.68853623 1.311511 0.88096905 10627.922
43000 1.998883 -0.69053805 1.3076844 0.81765345 10469.928
44000 2.0197069 -0.72507021 1.2939693 0.87004916 10194.954
45000 2.0112835 -0.72638581 1.284233 0.99236207 9968.2662
46000 2.0195002 -0.75152677 1.2673061 0.92706763 9751.1162
47000 1.983694 -0.75006702 1.2329714 0.8945741 9652.1453
48000 1.9977505 -0.77207122 1.225019 0.92107083 9647.1543
49000 2.0000901 -0.76254934 1.2368798 1.0320945 9536.2823
50000 2.0150929 -0.80463979 1.2097872 0.99556424 9324.0277
Loop time of 11.239 on 4 procs for 50000 steps with 3026 atoms
Performance: 1921872.705 tau/day, 4448.779 timesteps/s
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3936 | 2.7411 | 3.1078 | 16.7 | 24.39
Neigh | 2.2948 | 2.6755 | 3.1013 | 18.5 | 23.81
Comm | 2.522 | 3.3135 | 4.0361 | 31.7 | 29.48
Output | 0.040863 | 0.041031 | 0.041456 | 0.1 | 0.37
Modify | 1.844 | 1.9014 | 1.9701 | 3.4 | 16.92
Other | | 0.5666 | | | 5.04
Nlocal: 756.500 ave 838 max 693 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1282.50 ave 1333 max 1216 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 6426.25 ave 7350 max 5786 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 25705
Ave neighs/atom = 8.4947125
Neighbor list builds = 4326
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:11

175
examples/multi/log.30Nov20.granular.intel.1 Normal file
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LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.5
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
region box block 0 60 0 60 -0.5 0.5
create_box 2 box
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 3600 atoms
create_atoms CPU = 0.001 seconds
change_box all triclinic
Changing box ...
triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)
# remove two spheres of small particles and add large particles in the voids
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
delete_atoms region sphere1
Deleted 154 atoms, new total = 3446
delete_atoms region sphere2
Deleted 158 atoms, new total = 3288
create_atoms 2 single 20.0 20.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
create_atoms 2 single 60.0 60.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
set type 2 mass 400
Setting atom values ...
2 settings made for mass
set type 1 mass 1
Setting atom values ...
3288 settings made for mass
set type 2 diameter 20
Setting atom values ...
2 settings made for diameter
set type 1 diameter 1
Setting atom values ...
3288 settings made for diameter
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi #/old
neigh_modify delay 0
comm_modify mode multi vel yes
# colloid potential
pair_style granular
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
fix 2 all enforce2d
fix 3 all deform 1 xy erate 1e-3
dump 1 all custom 1000 dump.granular id x y z radius
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 21
ghost atom cutoff = 21
binsize = 1, bins = 85 85 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton on, size, history
pair build: half/size/multi/newton/tri
stencil: half/multi/2d/tri
bin: multi
Per MPI rank memory allocation (min/avg/max) = 11.78 | 11.78 | 11.78 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395623 0.66837658 7200
1000 0.32273428 0 0.32263619 0.17174972 7859.8897
2000 0.12441598 0 0.12437817 0.067078155 8212.9946
3000 0.067389284 0 0.067368801 0.040425551 8336.7112
4000 0.044312733 0 0.044299264 0.028220228 8229.0658
5000 0.032702163 0 0.032692223 0.024302012 7931.1298
6000 0.025856 0 0.025848141 0.021241317 7603.5534
7000 0.021437473 0 0.021430957 0.019285494 7243.5757
8000 0.018129567 0 0.018124057 0.020738727 6877.4816
9000 0.016370159 0 0.016365184 0.020261904 6515.3445
10000 0.01500918 0 0.015004618 0.020551803 6160.4475
11000 0.014156551 0 0.014152248 0.021324815 5815.4665
12000 0.013725406 0 0.013721235 0.021159958 5483.6304
13000 0.013215746 0 0.013211729 0.021685712 5165.4758
14000 0.012398153 0 0.012394384 0.024155434 4862.8657
15000 0.011842796 0 0.011839196 0.028503991 4577.9008
16000 0.011433182 0 0.011429706 0.033564839 4309.8792
17000 0.011166574 0 0.01116318 0.040592677 4058.9964
18000 0.01100067 0 0.010997326 0.04899206 3825.155
19000 0.010224474 0 0.010221366 0.063670337 3607.6577
20000 0.0091360559 0 0.0091332789 0.088230111 3408.5658
21000 0.007733647 0 0.0077312964 0.11769368 3227.7002
22000 0.0060202358 0 0.0060184059 0.15272491 3064.3986
23000 0.004670574 0 0.0046691543 0.19450724 2918.0014
24000 0.0040248313 0 0.004023608 0.24161742 2788.4113
25000 0.0032075275 0 0.0032065526 0.2897693 2674.5604
26000 0.0021358024 0 0.0021351532 0.33635617 2574.9564
27000 0.0016902752 0 0.0016897614 0.37624266 2487.2379
28000 0.0014038218 0 0.0014033951 0.41492104 2409.2461
29000 0.00090262506 0 0.0009023507 0.45392905 2340.0308
30000 0.00049466342 0 0.00049451306 0.49295072 2279.2316
31000 0.00056998139 0 0.00056980815 0.53299515 2226.5683
32000 0.00057326945 0 0.0005730952 0.56856537 2181.7092
33000 0.00044845112 0 0.00044831481 0.59623471 2142.7573
34000 0.00059840183 0 0.00059821994 0.61758983 2107.1253
35000 0.00075310993 0 0.00075288103 0.63756827 2072.7217
36000 0.00053774066 0 0.00053757721 0.66026064 2039.1655
37000 0.00030440106 0 0.00030430853 0.69059102 2007.7903
38000 0.00034436264 0 0.00034425797 0.72166344 1980.7137
39000 0.00039693498 0 0.00039681433 0.74680327 1957.9531
40000 0.00035425567 0 0.000354148 0.76604186 1937.3834
41000 0.0003094733 0 0.00030937924 0.78323163 1916.7027
42000 0.00027259246 0 0.0002725096 0.80315535 1895.0714
43000 0.00020659817 0 0.00020653538 0.8274603 1873.5407
44000 0.00016023333 0 0.00016018463 0.85418969 1853.8674
45000 0.00016111931 0 0.00016107034 0.87913944 1837.1141
46000 0.00016130888 0 0.00016125985 0.89921705 1822.7354
47000 0.00015755049 0 0.0001575026 0.91653538 1809.0285
48000 0.00017794781 0 0.00017789372 0.93582908 1794.7041
49000 0.00018878437 0 0.00018872699 0.95775203 1780.032
50000 0.0001778042 0 0.00017775016 0.97893714 1765.9439
Loop time of 77.4487 on 1 procs for 50000 steps with 3290 atoms
Performance: 278894.354 tau/day, 645.589 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 60.017 | 60.017 | 60.017 | 0.0 | 77.49
Neigh | 0.47 | 0.47 | 0.47 | 0.0 | 0.61
Comm | 6.6765 | 6.6765 | 6.6765 | 0.0 | 8.62
Output | 0.24799 | 0.24799 | 0.24799 | 0.0 | 0.32
Modify | 8.8677 | 8.8677 | 8.8677 | 0.0 | 11.45
Other | | 1.17 | | | 1.51
Nlocal: 3290.00 ave 3290 max 3290 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6295.00 ave 6295 max 6295 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 53729.0 ave 53729 max 53729 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 53729
Ave neighs/atom = 16.331003
Neighbor list builds = 348
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:17

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LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.5
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
region box block 0 60 0 60 -0.5 0.5
create_box 2 box
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3600 atoms
create_atoms CPU = 0.001 seconds
change_box all triclinic
Changing box ...
triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)
# remove two spheres of small particles and add large particles in the voids
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
delete_atoms region sphere1
Deleted 154 atoms, new total = 3446
delete_atoms region sphere2
Deleted 158 atoms, new total = 3288
create_atoms 2 single 20.0 20.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
create_atoms 2 single 60.0 60.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
set type 2 mass 400
Setting atom values ...
2 settings made for mass
set type 1 mass 1
Setting atom values ...
3288 settings made for mass
set type 2 diameter 20
Setting atom values ...
2 settings made for diameter
set type 1 diameter 1
Setting atom values ...
3288 settings made for diameter
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi #multi/old
neigh_modify delay 0
comm_modify mode multi vel yes multi/reduce
# colloid potential
pair_style granular
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
fix 2 all enforce2d
fix 3 all deform 1 xy erate 1e-3
dump 1 all custom 1000 dump.granular id x y z radius
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 21
ghost atom cutoff = 21
binsize = 1, bins = 85 85 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton on, size, history
pair build: half/size/multi/newton/tri
stencil: half/multi/2d/tri
bin: multi
Per MPI rank memory allocation (min/avg/max) = 11.33 | 11.33 | 11.33 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395623 0.66837658 7200
1000 0.32273428 0 0.32263619 0.17174972 7859.8897
2000 0.12441598 0 0.12437817 0.067078155 8212.9946
3000 0.067389284 0 0.067368801 0.040425551 8336.7112
4000 0.044312733 0 0.044299264 0.028220228 8229.0658
5000 0.032702163 0 0.032692223 0.024302012 7931.1298
6000 0.025856 0 0.025848141 0.021241317 7603.5534
7000 0.021437473 0 0.021430957 0.019285494 7243.5757
8000 0.018129567 0 0.018124057 0.020738727 6877.4816
9000 0.01637016 0 0.016365184 0.020261904 6515.3445
10000 0.01500918 0 0.015004618 0.020551803 6160.4475
11000 0.014156553 0 0.01415225 0.021324818 5815.4665
12000 0.013725412 0 0.01372124 0.021159958 5483.6304
13000 0.013215733 0 0.013211716 0.021685624 5165.4758
14000 0.012398179 0 0.012394411 0.024155572 4862.8657
15000 0.01184269 0 0.01183909 0.028504106 4577.901
16000 0.01143291 0 0.011429435 0.033564204 4309.88
17000 0.011166204 0 0.01116281 0.040588854 4058.9972
18000 0.011000875 0 0.010997532 0.048998904 3825.1569
19000 0.010225905 0 0.010222797 0.063669586 3607.6622
20000 0.0091390249 0 0.0091362471 0.088165396 3408.567
21000 0.0077382016 0 0.0077358496 0.11770473 3227.6936
22000 0.0060173113 0 0.0060154823 0.15261992 3064.3873
23000 0.0046667554 0 0.004665337 0.19453813 2917.9782
24000 0.0040425764 0 0.0040413476 0.24145834 2788.3897
25000 0.0031933187 0 0.0031923481 0.28989732 2674.5164
26000 0.0021139018 0 0.0021132592 0.33598721 2574.9313
27000 0.0017005052 0 0.0016999884 0.37665029 2487.1628
28000 0.001443434 0 0.0014429952 0.41572112 2409.3271
29000 0.00089885805 0 0.00089858484 0.45343123 2340.2314
30000 0.00048558336 0 0.00048543577 0.49175966 2279.2156
31000 0.00058132898 0 0.00058115228 0.53236819 2226.2347
32000 0.00057751441 0 0.00057733887 0.56915062 2181.2736
33000 0.00044720497 0 0.00044706904 0.59696122 2142.5709
34000 0.00060927898 0 0.00060909379 0.61734988 2107.128
35000 0.00077422577 0 0.00077399045 0.63696024 2072.6004
36000 0.00055753008 0 0.00055736062 0.65981839 2038.8237
37000 0.0003140158 0 0.00031392035 0.69018918 2007.323
38000 0.00034970199 0 0.0003495957 0.72155094 1980.1702
39000 0.00041435514 0 0.00041422919 0.7468053 1957.3837
40000 0.00037229543 0 0.00037218227 0.76581519 1936.8032
41000 0.00031027679 0 0.00031018248 0.78321128 1916.1103
42000 0.00026621832 0 0.00026613741 0.80267694 1894.4646
43000 0.00020544063 0 0.00020537818 0.82714181 1872.768
44000 0.00015635243 0 0.00015630491 0.85496512 1853.0303
45000 0.00014985611 0 0.00014981056 0.87924561 1836.4779
46000 0.00015645346 0 0.00015640591 0.89896131 1822.2004
47000 0.00016007816 0 0.00016002951 0.91662026 1808.4601
48000 0.00017439363 0 0.00017434063 0.93565314 1794.1244
49000 0.00018647711 0 0.00018642043 0.95733125 1779.401
50000 0.00018463414 0 0.00018457802 0.96449755 1765.1506
Loop time of 22.3987 on 4 procs for 50000 steps with 3290 atoms
Performance: 964340.770 tau/day, 2232.270 timesteps/s
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.5158 | 12.318 | 15.836 | 92.1 | 54.99
Neigh | 0.092527 | 0.11392 | 0.13595 | 5.6 | 0.51
Comm | 2.7127 | 6.2337 | 10.096 | 131.0 | 27.83
Output | 0.088027 | 0.088284 | 0.088812 | 0.1 | 0.39
Modify | 2.8544 | 3.0435 | 3.2034 | 9.2 | 13.59
Other | | 0.6017 | | | 2.69
Nlocal: 822.500 ave 859 max 785 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 395.750 ave 424 max 368 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 13439.5 ave 14346 max 12017 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Total # of neighbors = 53758
Ave neighs/atom = 16.339818
Neighbor list builds = 348
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:22

175
examples/multi/log.30Nov20.granular.old.intel.1 Normal file
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LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.5
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
region box block 0 60 0 60 -0.5 0.5
create_box 2 box
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 3600 atoms
create_atoms CPU = 0.001 seconds
change_box all triclinic
Changing box ...
triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)
# remove two spheres of small particles and add large particles in the voids
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
delete_atoms region sphere1
Deleted 154 atoms, new total = 3446
delete_atoms region sphere2
Deleted 158 atoms, new total = 3288
create_atoms 2 single 20.0 20.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
create_atoms 2 single 60.0 60.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
set type 2 mass 400
Setting atom values ...
2 settings made for mass
set type 1 mass 1
Setting atom values ...
3288 settings made for mass
set type 2 diameter 20
Setting atom values ...
2 settings made for diameter
set type 1 diameter 1
Setting atom values ...
3288 settings made for diameter
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi/old
neigh_modify delay 0
comm_modify mode multi vel yes
# colloid potential
pair_style granular
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
fix 2 all enforce2d
fix 3 all deform 1 xy erate 1e-3
dump 1 all custom 1000 dump.granular id x y z radius
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 21
ghost atom cutoff = 21
binsize = 1, bins = 85 85 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton on, size, history
pair build: half/size/multi/old/newton/tri
stencil: half/multi/old/2d/tri
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.75 | 11.75 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395623 0.66837658 7200
1000 0.32273428 0 0.32263619 0.17174972 7859.8897
2000 0.12441598 0 0.12437817 0.067078155 8212.9946
3000 0.067389284 0 0.067368801 0.040425551 8336.7112
4000 0.044312733 0 0.044299264 0.028220228 8229.0658
5000 0.032702163 0 0.032692223 0.024302012 7931.1298
6000 0.025856 0 0.025848141 0.021241317 7603.5534
7000 0.021437473 0 0.021430957 0.019285494 7243.5757
8000 0.018129567 0 0.018124057 0.020738727 6877.4816
9000 0.016370159 0 0.016365184 0.020261904 6515.3445
10000 0.01500918 0 0.015004618 0.020551803 6160.4475
11000 0.014156551 0 0.014152248 0.021324815 5815.4665
12000 0.013725406 0 0.013721235 0.021159958 5483.6304
13000 0.013215746 0 0.013211729 0.021685712 5165.4758
14000 0.012398153 0 0.012394384 0.024155434 4862.8657
15000 0.011842796 0 0.011839196 0.028503991 4577.9008
16000 0.011433182 0 0.011429706 0.033564839 4309.8792
17000 0.011166574 0 0.01116318 0.040592677 4058.9964
18000 0.01100067 0 0.010997326 0.04899206 3825.155
19000 0.010224474 0 0.010221366 0.063670337 3607.6577
20000 0.0091360558 0 0.0091332789 0.088230111 3408.5658
21000 0.0077336471 0 0.0077312964 0.11769368 3227.7002
22000 0.0060202357 0 0.0060184059 0.15272492 3064.3986
23000 0.0046705738 0 0.0046691542 0.19450723 2918.0014
24000 0.0040248311 0 0.0040236078 0.24161743 2788.4113
25000 0.0032075267 0 0.0032065518 0.28976925 2674.5604
26000 0.0021358008 0 0.0021351516 0.33635615 2574.9564
27000 0.0016902771 0 0.0016897633 0.37624261 2487.2379
28000 0.0014038216 0 0.0014033949 0.41492061 2409.2461
29000 0.00090262588 0 0.00090235152 0.45392924 2340.0308
30000 0.00049466445 0 0.0004945141 0.49295063 2279.2316
31000 0.00056998139 0 0.00056980814 0.53299532 2226.5683
32000 0.00057327032 0 0.00057309607 0.56856551 2181.7093
33000 0.00044845449 0 0.00044831818 0.59623461 2142.7574
34000 0.00059840346 0 0.00059822157 0.61758978 2107.1254
35000 0.00075311121 0 0.0007528823 0.63756791 2072.7217
36000 0.00053773653 0 0.00053757309 0.66026022 2039.1654
37000 0.00030439696 0 0.00030430444 0.69059127 2007.7901
38000 0.00034435616 0 0.00034425149 0.72166346 1980.7136
39000 0.00039692535 0 0.0003968047 0.7468036 1957.9531
40000 0.0003542502 0 0.00035414252 0.76604173 1937.3834
41000 0.0003094667 0 0.00030937263 0.78323183 1916.7027
42000 0.00027258976 0 0.0002725069 0.80315572 1895.0714
43000 0.00020659987 0 0.00020653707 0.82746098 1873.5408
44000 0.00016023865 0 0.00016018994 0.85418945 1853.8677
45000 0.00016112731 0 0.00016107833 0.87913874 1837.1144
46000 0.00016131366 0 0.00016126463 0.89921653 1822.7355
47000 0.00015754747 0 0.00015749958 0.91653641 1809.0285
48000 0.00017794764 0 0.00017789356 0.93582953 1794.7043
49000 0.00018879338 0 0.000188736 0.95775166 1780.0323
50000 0.00017781117 0 0.00017775712 0.97893641 1765.9442
Loop time of 80.8597 on 1 procs for 50000 steps with 3290 atoms
Performance: 267129.375 tau/day, 618.355 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 61.524 | 61.524 | 61.524 | 0.0 | 76.09
Neigh | 2.2021 | 2.2021 | 2.2021 | 0.0 | 2.72
Comm | 6.748 | 6.748 | 6.748 | 0.0 | 8.35
Output | 0.25904 | 0.25904 | 0.25904 | 0.0 | 0.32
Modify | 8.9408 | 8.9408 | 8.9408 | 0.0 | 11.06
Other | | 1.186 | | | 1.47
Nlocal: 3290.00 ave 3290 max 3290 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6295.00 ave 6295 max 6295 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 53729.0 ave 53729 max 53729 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 53729
Ave neighs/atom = 16.331003
Neighbor list builds = 348
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:20

175
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LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.5
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
region box block 0 60 0 60 -0.5 0.5
create_box 2 box
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3600 atoms
create_atoms CPU = 0.001 seconds
change_box all triclinic
Changing box ...
triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)
# remove two spheres of small particles and add large particles in the voids
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
delete_atoms region sphere1
Deleted 154 atoms, new total = 3446
delete_atoms region sphere2
Deleted 158 atoms, new total = 3288
create_atoms 2 single 20.0 20.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
create_atoms 2 single 60.0 60.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
set type 2 mass 400
Setting atom values ...
2 settings made for mass
set type 1 mass 1
Setting atom values ...
3288 settings made for mass
set type 2 diameter 20
Setting atom values ...
2 settings made for diameter
set type 1 diameter 1
Setting atom values ...
3288 settings made for diameter
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi/old
neigh_modify delay 0
comm_modify mode multi vel yes #multi/reduce
# colloid potential
pair_style granular
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
fix 2 all enforce2d
fix 3 all deform 1 xy erate 1e-3
dump 1 all custom 1000 dump.granular id x y z radius
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 21
ghost atom cutoff = 21
binsize = 1, bins = 85 85 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton on, size, history
pair build: half/size/multi/old/newton/tri
stencil: half/multi/old/2d/tri
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.48 | 11.48 | 11.49 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395623 0.66837658 7200
1000 0.32273428 0 0.32263619 0.17174972 7859.8897
2000 0.12441598 0 0.12437817 0.067078155 8212.9946
3000 0.067389284 0 0.067368801 0.040425551 8336.7112
4000 0.044312733 0 0.044299264 0.028220228 8229.0658
5000 0.032702163 0 0.032692223 0.024302012 7931.1298
6000 0.025856 0 0.025848141 0.021241317 7603.5534
7000 0.021437473 0 0.021430957 0.019285494 7243.5757
8000 0.018129567 0 0.018124057 0.020738727 6877.4816
9000 0.01637016 0 0.016365184 0.020261904 6515.3445
10000 0.01500918 0 0.015004618 0.020551803 6160.4475
11000 0.014156553 0 0.01415225 0.021324818 5815.4665
12000 0.013725412 0 0.01372124 0.021159958 5483.6304
13000 0.013215733 0 0.013211716 0.021685624 5165.4758
14000 0.012398179 0 0.012394411 0.024155572 4862.8657
15000 0.01184269 0 0.01183909 0.028504106 4577.901
16000 0.01143291 0 0.011429435 0.033564204 4309.88
17000 0.011166204 0 0.01116281 0.040588854 4058.9972
18000 0.011000875 0 0.010997532 0.048998904 3825.1569
19000 0.010225905 0 0.010222797 0.063669588 3607.6622
20000 0.0091390255 0 0.0091362477 0.088165402 3408.567
21000 0.0077382041 0 0.0077358521 0.11770474 3227.6936
22000 0.00601731 0 0.0060154811 0.15261994 3064.3873
23000 0.0046667591 0 0.0046653407 0.19453819 2917.9782
24000 0.0040425749 0 0.0040413461 0.24145833 2788.3897
25000 0.0031933217 0 0.0031923511 0.28989713 2674.5164
26000 0.0021138997 0 0.0021132571 0.33598673 2574.9312
27000 0.001700508 0 0.0016999912 0.37665013 2487.1626
28000 0.0014434246 0 0.0014429859 0.41572163 2409.327
29000 0.00089885063 0 0.00089857742 0.453431 2340.2313
30000 0.00048556478 0 0.00048541719 0.49176025 2279.2155
31000 0.00058130972 0 0.00058113303 0.53236818 2226.2349
32000 0.00057749847 0 0.00057732294 0.5691506 2181.2738
33000 0.00044719326 0 0.00044705733 0.59696179 2142.571
34000 0.00060924828 0 0.0006090631 0.61735036 2107.1282
35000 0.00077419805 0 0.00077396273 0.63696098 2072.6008
36000 0.00055752003 0 0.00055735057 0.65981842 2038.8242
37000 0.00031402452 0 0.00031392907 0.69018949 2007.3235
38000 0.00034969879 0 0.0003495925 0.72155053 1980.1706
39000 0.00041434197 0 0.00041421603 0.74680715 1957.3838
40000 0.00037229243 0 0.00037217927 0.76581686 1936.8034
41000 0.00031028842 0 0.00031019411 0.78321059 1916.1108
42000 0.00026623668 0 0.00026615575 0.80267329 1894.4649
43000 0.00020543723 0 0.00020537479 0.82714001 1872.7672
44000 0.0001563321 0 0.00015628458 0.85496396 1853.0284
45000 0.00014981713 0 0.00014977159 0.87924842 1836.4755
46000 0.00015641585 0 0.00015636831 0.89896936 1822.1989
47000 0.00016004701 0 0.00015999837 0.91661933 1808.4606
48000 0.00017437702 0 0.00017432402 0.93565475 1794.1258
49000 0.00018645903 0 0.00018640235 0.95733183 1779.4032
50000 0.00018469122 0 0.00018463508 0.96446925 1765.1534
Loop time of 30.9351 on 4 procs for 50000 steps with 3290 atoms
Performance: 698235.574 tau/day, 1616.286 timesteps/s
89.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.3702 | 12.796 | 16.045 | 84.3 | 41.36
Neigh | 0.43499 | 0.55158 | 0.64861 | 12.8 | 1.78
Comm | 10.183 | 13.476 | 16.961 | 83.7 | 43.56
Output | 0.088474 | 0.088715 | 0.089272 | 0.1 | 0.29
Modify | 3.0446 | 3.1809 | 3.3227 | 7.4 | 10.28
Other | | 0.8418 | | | 2.72
Nlocal: 822.500 ave 859 max 785 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 3049.75 ave 3089 max 2999 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 13440.5 ave 14459 max 11964 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 53762
Ave neighs/atom = 16.341033
Neighbor list builds = 348
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:30

2
src/comm.cpp
View File

@ -248,6 +248,8 @@ void Comm::init()
error->all(FLERR,"Cannot use multi/reduce communication with Newton off");
if (neighbor->any_full())
error->all(FLERR,"Cannot use multi/reduce communication with a full neighbor list");
if (neighbor->style != Neighbor::MULTI)
error->all(FLERR,"Cannot use multi/reduce communication without multi-style neighbor lists");
}
}