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new fix halt command, other sundry small bug fixes

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This commit is contained in:
Steve Plimpton
2016-10-18 13:11:40 -06:00
parent 713b2af067
commit 2106dce2b3
41 changed files with 118040 additions and 110939 deletions
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4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS Users Manual</TITLE> <TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="12 Oct 2016 version"> <META NAME="docnumber" CONTENT="18 Oct 2016 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD> </HEAD>
@ -21,7 +21,7 @@
<H1></H1> <H1></H1>
LAMMPS Documentation :c,h3 LAMMPS Documentation :c,h3
12 Oct 2016 version :c,h4 18 Oct 2016 version :c,h4
Version info: :h4 Version info: :h4

1
doc/src/Section_commands.txt
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@ -573,6 +573,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"gcmc"_fix_gcmc.html, "gcmc"_fix_gcmc.html,
"gld"_fix_gld.html, "gld"_fix_gld.html,
"gravity (o)"_fix_gravity.html, "gravity (o)"_fix_gravity.html,
"halt"_fix_halt.html,
"heat"_fix_heat.html, "heat"_fix_heat.html,
"indent"_fix_indent.html, "indent"_fix_indent.html,
"langevin (k)"_fix_langevin.html, "langevin (k)"_fix_langevin.html,

16
doc/src/dump_modify.txt
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@ -47,9 +47,9 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o
id = sort per-atom lines by atom ID id = sort per-atom lines by atom ID
N = sort per-atom lines in ascending order by the Nth column N = sort per-atom lines in ascending order by the Nth column
-N = sort per-atom lines in descending order by the Nth column -N = sort per-atom lines in descending order by the Nth column
{thresh} args = attribute operation value {thresh} args = attribute operator value
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
operation = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
value = numeric value to compare to, or LAST value = numeric value to compare to, or LAST
these 3 args can be replaced by the word "none" to turn off thresholding these 3 args can be replaced by the word "none" to turn off thresholding
{unwrap} arg = {yes} or {no} :pre {unwrap} arg = {yes} or {no} :pre
@ -470,7 +470,7 @@ stress of atoms whose energy is above some threshold.
If an atom-style variable is used as the attribute, then it can If an atom-style variable is used as the attribute, then it can
produce continuous numeric values or effective Boolean 0/1 values produce continuous numeric values or effective Boolean 0/1 values
which may be useful for the comparision operation. Boolean values can which may be useful for the comparision operator. Boolean values can
be generated by variable formulas that use comparison or Boolean math be generated by variable formulas that use comparison or Boolean math
operators or special functions like gmask() and rmask() and grmask(). operators or special functions like gmask() and rmask() and grmask().
See the "variable"_variable.html command doc page for details. See the "variable"_variable.html command doc page for details.
@ -503,11 +503,11 @@ less than 1/2 to greater than 1/2 (or vice versa) since the last dump.
E.g. due to reactions and subsequent charge equilibration in a E.g. due to reactions and subsequent charge equilibration in a
reactive force field. reactive force field.
The choice of operations are the usual comparison operators. The XOR The choice of operators listed above are the usual comparison
operation (exclusive or) is also included as "|^". In this context, operators. The XOR operation (exclusive or) is also included as "|^".
XOR means that if either the attribute or value is 0.0 and the other In this context, XOR means that if either the attribute or value is
is non-zero, then the result is "true" and the threshold criterion is 0.0 and the other is non-zero, then the result is "true" and the
met. Otherwise it is not met. threshold criterion is met. Otherwise it is not met.
:line :line

121
doc/src/fix_halt.txt Normal file
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@ -0,0 +1,121 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix halt command :h3
[Syntax:]
fix ID group-ID halt N attribute operator avalue keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
halt = style name of this fix command :l
N = check halt condition every N steps :l
attribute = hstyle or v_name :l
hstyle = {bondmax}
v_name = name of "equal-style variable"_variable.html :pre
operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" :l
avalue = numeric value to compare attribute to :l
string = text string to print with optional variable names :l
zero or more keyword/value pairs may be appended :l
keyword = {error} :l
{error} value = {hard} or {soft} or {continue} :pre
:ule
[Examples:]
fix 10 all halt 1 bondmax > 1.5
fix 10 all print 10 v_myCheck != 0 error soft :pre
[Description:]
Check a condition every N steps during a simulation run. N must be >=
1. If the condition is met, exit the run immediately. In this
context a "run" can be dynamics or minimization iterations, as
specified by the "run"_run.html or "minimize"_minimize.html command.
The specified group-ID is ignored by this fix.
The specified {attribute} can be one of the {hstyle} options listed
above, or an "equal-style variable"_variable.html referenced as
{v_name}, where "name" is the name of a variable that has been defined
previously in the input script.
The only {hstyle} option currently implemented is {bondmax}. This
will loop over all bonds in the system, compute their current
lengths, and set {attribute} to the longest bond distance.
Equal-style variables evaluate to a numeric value. See the
"variable"_variable.html command for a description. They calculate
formulas which can involve mathematical operations, atom properties,
group properties, thermodynamic properties, global values calculated
by a "compute"_compute.html or "fix"_fix.html, or references to other
"variables"_variable.html. Thus they are a very general means of
computing some attribute of the current system. For example, the
following "bondmax" variable will calculate the same quantity as the
hstyle = bondmax option.
compute bdist all bond/local dist
compute bmax all reduce max c_bdist
variable bondmax equal c_bmax :pre
Thus these two versions of a fix halt command will do the same thing:
fix 10 all halt 1 bondmax > 1.5
fix 10 all halt 1 v_bondmax > 1.5 :pre
The version with "bondmax" will just run somewhat faster, due to less
overhead in computing bond lengths and not storing them in a separate
compute.
The choice of operators listed above are the usual comparison
operators. The XOR operation (exclusive or) is also included as "|^".
In this context, XOR means that if either the attribute or avalue is
0.0 and the other is non-zero, then the result is "true". Otherwise
it is "false".
The specified {avalue} must be a numeric value.
:line
The optional {error} keyword determines how the current run is halted.
If its value is {hard}, then LAMMPS will stop with an error message.
If its value is {soft}, LAMMPS will exit the current run, but continue
to execute subsequent commands in the input script. However,
additional "run"_run.html or "minimize"_minimize.html commands will be
skipped. For example, this allows a script to output the current
state of the system, e.g. via a "write_dump"_write_dump.html or
"write_restart"_write_restart.html command.
If its value is {continue}, the behavior is the same as for {soft},
except subsequent subsequent "run"_run.html or
"minimize"_minimize.html commands are executed. This allows your
script to remedy the condition that triggered the halt, if necessary.
Note that you may wish use the "unfix"_unfix.html command on the fix
halt ID, so that the same condition is not immediately triggered in a
subsequent run.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
[Related commands:]
"variable"_variable.html
[Default:]
The option defaults are error = hard.

5
doc/src/minimize.txt
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@ -103,6 +103,11 @@ the line search fails because the step distance backtracks to 0.0
the number of outer iterations or timesteps exceeds {maxiter} the number of outer iterations or timesteps exceeds {maxiter}
the number of total force evaluations exceeds {maxeval} :ul the number of total force evaluations exceeds {maxeval} :ul
NOTE: You can also use the "fix halt"_fix_halt.html command to specify
a general criterion for exiting a minimization, that is a calculation
performed on the state of the current system, as defined by an
"equal-style variable"_variable.html.
For the first criterion, the specified energy tolerance {etol} is For the first criterion, the specified energy tolerance {etol} is
unitless; it is met when the energy change between successive unitless; it is met when the energy change between successive
iterations divided by the energy magnitude is less than or equal to iterations divided by the energy magnitude is less than or equal to

14
doc/src/run.txt
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@ -169,17 +169,17 @@ If the {pre} and {post} options are set to "no" when used with the
run will print the full timing summary, but these operations will be run will print the full timing summary, but these operations will be
skipped for intermediate runs. skipped for intermediate runs.
NOTE: You might hope to specify a command that exits the run by NOTE: You might wish to specify a command that exits the run by
jumping out of the loop, e.g. jumping out of the loop, e.g.
variable t equal temp variable t equal temp
run 10000 every 100 "if '$t < 300.0' then 'jump SELF afterrun'" :pre run 10000 every 100 "if '$t < 300.0' then 'jump SELF afterrun'" :pre
Unfortunately this will not currently work. The run command simply However, this will not work. The run command simply executes each
executes each command one at a time each time it pauses, then command one at a time each time it pauses, then continues the run.
continues the run. You can replace the jump command with a simple
"quit"_quit.html command and cause LAMMPS to exit during the Instead, you should use the "fix halt"_fix_halt.html command, which
middle of a run when the condition is met. has additional options for how to exit the run.
[Restrictions:] [Restrictions:]
@ -198,7 +198,7 @@ successive runs to run a simulation for any number of steps (ok, up to
[Related commands:] [Related commands:]
"minimize"_minimize.html, "run_style"_run_style.html, "minimize"_minimize.html, "run_style"_run_style.html,
"temper"_temper.html "temper"_temper.html, "fix halt"_fix_halt.html
[Default:] [Default:]

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examples/DIFFUSE/log.13Oct16.msd.2d.g++.8 Normal file
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@ -0,0 +1,245 @@
LAMMPS (13 Oct 2016)
# sample LAMMPS input script for diffusion of 2d LJ liquid
# mean-squared displacement via compute msd
# settings
variable x equal 40
variable y equal 40
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
lattice sq2 ${rho}
lattice sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox block 0 $x 0 $y -0.1 0.1
region simbox block 0 40 0 $y -0.1 0.1
region simbox block 0 40 0 40 -0.1 0.1
create_box 1 simbox
Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
4 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3200 atoms
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff * * 1 1
mass * 1.0
velocity all create $t 97287
velocity all create 1 97287
fix 1 all nve
fix 2 all langevin $t $t 0.1 498094
fix 2 all langevin 1 $t 0.1 498094
fix 2 all langevin 1 1 0.1 498094
fix 3 all enforce2d
# equilibration run
thermo 1000
run 5000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 53 53 1
Memory usage per processor = 2.478 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.5652325 -1.5346995
1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
Loop time of 0.554412 on 8 procs for 5000 steps with 3200 atoms
Performance: 3896017.421 tau/day, 9018.559 timesteps/s
98.9% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.23992 | 0.24608 | 0.25161 | 0.7 | 44.39
Neigh | 0.063106 | 0.064417 | 0.066279 | 0.4 | 11.62
Comm | 0.072465 | 0.085066 | 0.094837 | 2.3 | 15.34
Output | 0.00013208 | 0.00013691 | 0.00014591 | 0.0 | 0.02
Modify | 0.11441 | 0.11621 | 0.11769 | 0.3 | 20.96
Other | | 0.04251 | | | 7.67
Nlocal: 400 ave 406 max 394 min
Histogram: 1 1 0 1 0 2 1 0 1 1
Nghost: 202.5 ave 212 max 191 min
Histogram: 1 0 0 0 3 1 0 2 0 1
Neighs: 2800.88 ave 2903 max 2690 min
Histogram: 1 1 0 0 1 2 1 0 1 1
Total # of neighbors = 22407
Ave neighs/atom = 7.00219
Neighbor list builds = 599
Dangerous builds = 0
unfix 2
# data gathering run
reset_timestep 0
# factor of 4 in 2 variables is for 2d
compute msd all msd com yes
variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
fix 9 all vector 10 c_msd[4]
variable fitslope equal slope(f_9)/4/(10*dt)
thermo_style custom step temp c_msd[4] v_twopoint v_fitslope
# only need to run for 10K steps to make a good 100-frame movie
#dump 1 all custom 1 tmp.dump id type vx vy vz
#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
thermo 1000
run 100000
Memory usage per processor = 2.853 Mbytes
Step Temp c_msd[4] v_twopoint v_fitslope
0 0.97069905 0 0 5e+20
1000 0.98138076 4.0484996 0.20242494 0.18046446
2000 0.97606079 9.2121392 0.23030346 0.2091528
3000 0.97924866 14.815034 0.24691721 0.22619184
4000 0.98568451 20.516817 0.25646019 0.23715506
5000 0.97551815 27.33922 0.27339219 0.24709999
6000 0.98482252 34.37734 0.28647782 0.25735178
7000 0.9672559 41.696689 0.29783348 0.26654059
8000 0.9836541 48.340277 0.30212673 0.27440308
9000 0.99087147 56.042692 0.31134828 0.28113047
10000 0.99663166 63.69663 0.31848314 0.28767921
11000 0.97776688 71.144109 0.32338231 0.29344527
12000 0.98246011 78.301774 0.32625739 0.29849471
13000 0.98788732 85.061923 0.32716124 0.3026655
14000 0.96872483 91.1658 0.32559214 0.30601023
15000 0.98955796 97.278388 0.32426129 0.3084275
16000 0.99855196 104.23997 0.3257499 0.31049883
17000 0.98600861 110.66055 0.3254722 0.31220348
18000 0.98696963 116.90111 0.32472531 0.31352676
19000 0.9881192 124.21305 0.32687644 0.31480062
20000 0.98527319 131.09874 0.32774685 0.31596198
21000 0.99015191 137.89263 0.32831579 0.31705324
22000 0.97972418 146.68982 0.33338595 0.31833889
23000 0.98911012 155.1264 0.33723129 0.31979515
24000 0.98810498 162.88634 0.33934653 0.32131187
25000 0.96961962 170.37907 0.34075814 0.32276215
26000 0.99118408 179.26511 0.34474059 0.32427111
27000 0.98515159 185.90764 0.3442734 0.32574529
28000 0.98951677 192.12183 0.34307469 0.32700292
29000 0.9832026 196.99457 0.33964581 0.32799023
30000 0.98449493 203.48475 0.33914124 0.3287171
31000 0.96585993 210.06193 0.33880956 0.32935775
32000 0.98758117 218.94174 0.34209646 0.33001591
33000 0.98875584 225.96489 0.34237104 0.33072947
34000 0.98007229 233.5792 0.34349882 0.3314385
35000 0.98415295 241.98148 0.34568783 0.33216634
36000 0.98101154 250.30876 0.34765106 0.33295272
37000 0.97606878 258.2127 0.34893608 0.33377673
38000 0.97220293 266.40464 0.35053242 0.33459273
39000 0.979783 272.8578 0.34981769 0.33539728
40000 0.98375673 279.87598 0.34984497 0.33609699
41000 0.97506523 288.07676 0.35131312 0.33677708
42000 0.97106749 296.11647 0.3525196 0.33751312
43000 0.97717259 304.46747 0.35403194 0.33823441
44000 0.98541435 312.57228 0.35519578 0.3389771
45000 0.97678287 321.82674 0.35758527 0.33973306
46000 0.98169719 329.78197 0.35845866 0.34051748
47000 0.99471466 337.11283 0.35863066 0.34127239
48000 0.98332437 346.0754 0.3604952 0.34202442
49000 0.98126947 356.11859 0.36338631 0.34282132
50000 0.98809751 365.65248 0.36565248 0.34368171
51000 0.95919516 373.91833 0.36658659 0.34454516
52000 0.98097913 381.26492 0.36660089 0.34538506
53000 0.97774072 388.81031 0.36680218 0.34618232
54000 0.99096915 395.56767 0.36626636 0.3469296
55000 0.97652739 401.72735 0.36520668 0.34760374
56000 0.99185306 407.28834 0.3636503 0.34819906
57000 0.96289342 414.75298 0.3638184 0.34871992
58000 0.97871716 424.69443 0.36611588 0.34927986
59000 0.98637393 433.14205 0.36706953 0.34986296
60000 0.98009845 438.14533 0.36512111 0.35040349
61000 0.99416712 446.08007 0.3656394 0.35088379
62000 0.97612483 450.90846 0.36363585 0.35132647
63000 0.97786531 455.36749 0.36140277 0.35167458
64000 0.99080668 458.04873 0.35785057 0.3519105
65000 0.97952497 461.31241 0.3548557 0.3520506
66000 0.98095955 463.91727 0.35145248 0.35207764
67000 0.98370788 468.93 0.34994776 0.35204043
68000 0.96931818 471.07765 0.34638063 0.35192685
69000 0.98512552 474.59146 0.34390685 0.35174053
70000 0.98065743 478.66071 0.3419005 0.35149002
71000 0.98971283 482.57357 0.33984054 0.35119434
72000 0.99890324 485.32018 0.3370279 0.35084345
73000 0.98649924 490.19497 0.33574998 0.35043722
74000 0.98723422 496.04991 0.33516886 0.35003351
75000 1.0025633 501.6313 0.33442087 0.34962094
76000 0.97859959 505.97813 0.33288035 0.34921013
77000 0.97973006 510.55334 0.33152814 0.3487692
78000 0.9903944 515.06966 0.33017286 0.34830833
79000 0.96847518 518.76483 0.32833217 0.3478214
80000 0.99171112 524.18127 0.32761329 0.34733349
81000 0.97202573 529.09959 0.32660468 0.3468315
82000 0.99368438 535.80271 0.32670897 0.34633058
83000 0.97932483 543.08233 0.32715803 0.34586259
84000 0.99078651 547.57861 0.32593965 0.34540839
85000 0.98973457 552.24581 0.32485048 0.34493584
86000 0.9835873 557.3493 0.32404029 0.34446152
87000 0.97180564 564.93434 0.32467491 0.34400358
88000 0.99743353 571.39837 0.32465817 0.3435667
89000 0.98993437 577.81703 0.32461631 0.3431411
90000 0.9926071 583.39378 0.32410765 0.342724
91000 0.98800458 591.08741 0.3247733 0.34232767
92000 0.98501879 596.10133 0.32396811 0.34193949
93000 0.98810082 604.02652 0.32474544 0.3415681
94000 0.97563748 609.43676 0.32416849 0.341209
95000 0.97283448 615.15754 0.32376713 0.34084828
96000 0.9883071 622.30912 0.32411933 0.34049871
97000 0.97717678 628.84457 0.32414669 0.34016355
98000 0.97190208 634.37377 0.32366009 0.3398341
99000 0.98687379 640.66666 0.32356902 0.33950845
100000 0.97559757 646.96406 0.32348203 0.33919036
Loop time of 9.58779 on 8 procs for 100000 steps with 3200 atoms
Performance: 4505729.040 tau/day, 10429.928 timesteps/s
99.4% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8572 | 4.9363 | 4.9822 | 1.7 | 51.49
Neigh | 1.3583 | 1.376 | 1.3991 | 1.2 | 14.35
Comm | 1.5192 | 1.7079 | 1.8264 | 7.2 | 17.81
Output | 0.0085125 | 0.0086059 | 0.0089455 | 0.1 | 0.09
Modify | 0.77663 | 0.7903 | 0.81378 | 1.3 | 8.24
Other | | 0.7686 | | | 8.02
Nlocal: 400 ave 413 max 391 min
Histogram: 2 1 0 2 0 0 1 1 0 1
Nghost: 204.75 ave 213 max 197 min
Histogram: 1 1 0 1 0 3 0 1 0 1
Neighs: 2800.62 ave 2959 max 2661 min
Histogram: 1 1 1 2 0 0 0 1 1 1
Total # of neighbors = 22405
Ave neighs/atom = 7.00156
Neighbor list builds = 12728
Dangerous builds = 0
Total wall time: 0:00:10

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LAMMPS (13 Oct 2016)
# sample LAMMPS input script for diffusion of 2d LJ liquid
# mean-squared displacement via compute msd
# settings
variable x equal 40
variable y equal 40
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
lattice sq2 ${rho}
lattice sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox block 0 $x 0 $y -0.1 0.1
region simbox block 0 40 0 $y -0.1 0.1
region simbox block 0 40 0 40 -0.1 0.1
create_box 1 simbox
Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
4 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3200 atoms
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff * * 1 1
mass * 1.0
velocity all create $t 97287
velocity all create 1 97287
fix 1 all nve
fix 2 all langevin $t $t 0.1 498094
fix 2 all langevin 1 $t 0.1 498094
fix 2 all langevin 1 1 0.1 498094
fix 3 all enforce2d
# equilibration run
thermo 1000
run 5000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 53 53 1
Memory usage per processor = 2.478 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.5652325 -1.5346995
1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
Loop time of 0.557588 on 8 procs for 5000 steps with 3200 atoms
Performance: 3873826.669 tau/day, 8967.191 timesteps/s
99.1% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.23784 | 0.24683 | 0.25594 | 1.0 | 44.27
Neigh | 0.062975 | 0.06439 | 0.0662 | 0.4 | 11.55
Comm | 0.083826 | 0.092564 | 0.1035 | 2.1 | 16.60
Output | 0.00011778 | 0.00012615 | 0.00014257 | 0.1 | 0.02
Modify | 0.11466 | 0.11648 | 0.1187 | 0.4 | 20.89
Other | | 0.0372 | | | 6.67
Nlocal: 400 ave 406 max 394 min
Histogram: 1 1 0 1 0 2 1 0 1 1
Nghost: 202.5 ave 212 max 191 min
Histogram: 1 0 0 0 3 1 0 2 0 1
Neighs: 2800.88 ave 2903 max 2690 min
Histogram: 1 1 0 0 1 2 1 0 1 1
Total # of neighbors = 22407
Ave neighs/atom = 7.00219
Neighbor list builds = 599
Dangerous builds = 0
unfix 2
# data gathering run
reset_timestep 0
compute vacf all vacf
fix 4 all ave/time 1 1 1 c_vacf[4] #file tmp.vacf
# factor of 0.5 is for 2d
fix 5 all vector 1 c_vacf[4]
variable vacf equal 0.5*dt*trap(f_5)
thermo_style custom step temp c_vacf[4] v_vacf
# only need to run for 10K steps to make a good 100-frame movie
#dump 1 all custom 1 tmp.dump id type vx vy vz
#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
thermo 1000
run 100000
Memory usage per processor = 2.853 Mbytes
Step Temp c_vacf[4] v_vacf
0 0.97069905 1.9407914 0
1000 0.98138076 0.029239763 0.22157396
2000 0.97606079 -0.0015179052 0.23974121
3000 0.97924866 -0.013873067 0.21877575
4000 0.98568451 0.026969065 0.24052934
5000 0.97551815 0.050232557 0.24508207
6000 0.98482252 -0.0018424259 0.25686293
7000 0.9672559 0.018499957 0.27279836
8000 0.9836541 -0.022683127 0.27022734
9000 0.99087147 0.0071767632 0.25267902
10000 0.99663166 -0.011971734 0.2645822
11000 0.97776688 0.01601675 0.27801788
12000 0.98246011 0.0085456779 0.29207728
13000 0.98788732 0.0054252587 0.29148533
14000 0.96872483 0.0087976064 0.29645689
15000 0.98955796 -0.060068996 0.28904116
16000 0.99855196 -0.0066979853 0.24964957
17000 0.98600861 0.021334454 0.23410452
18000 0.98696963 -0.01971883 0.23190572
19000 0.9881192 -0.022828159 0.20882183
20000 0.98527319 -0.0085783561 0.20610922
21000 0.99015191 -0.0061019744 0.20199693
22000 0.97972418 -0.04380952 0.22099864
23000 0.98911012 -0.0031381071 0.19304223
24000 0.98810498 0.023131507 0.18483784
25000 0.96961962 -0.020892151 0.17128259
26000 0.99118408 0.02918818 0.15353531
27000 0.98515159 -0.026417648 0.1457756
28000 0.98951677 0.010372147 0.13321212
29000 0.9832026 0.00058150905 0.13262151
30000 0.98449493 0.0012256712 0.13576655
31000 0.96585993 0.0053021384 0.10734708
32000 0.98758117 -0.011513109 0.11473375
33000 0.98875584 -0.0089140499 0.13003947
34000 0.98007229 0.023423116 0.145185
35000 0.98415295 -0.0078343607 0.16513809
36000 0.98101154 0.025471963 0.1296799
37000 0.97606878 -0.016931612 0.11515595
38000 0.97220293 -0.015288346 0.12046935
39000 0.979783 0.039556949 0.10596988
40000 0.98375673 0.0098704124 0.15651085
41000 0.97506523 -0.029457701 0.14822207
42000 0.97106749 -0.024867475 0.12266294
43000 0.97717259 0.010866403 0.14228602
44000 0.98541435 -0.031545234 0.13017093
45000 0.97678287 -0.011024372 0.11824999
46000 0.98169719 0.011925437 0.1390346
47000 0.99471466 0.0048178625 0.13076123
48000 0.98332437 0.045576305 0.12667585
49000 0.98126947 -0.044123768 0.13582991
50000 0.98809751 0.014296599 0.12323107
51000 0.95919516 -0.0091171161 0.1494511
52000 0.98097913 0.010081012 0.12805794
53000 0.97774072 0.043349117 0.14524942
54000 0.99096915 0.021179196 0.1355801
55000 0.97652739 -0.015118967 0.14955035
56000 0.99185306 0.0018045061 0.16706629
57000 0.96289342 0.0095090659 0.19215008
58000 0.97871716 -0.028989119 0.20370326
59000 0.98637393 0.0067841088 0.21820001
60000 0.98009845 0.011559251 0.24504916
61000 0.99416712 0.0099372548 0.24882366
62000 0.97612483 0.014677063 0.25146482
63000 0.97786531 -0.0047938112 0.26052305
64000 0.99080668 -0.01632121 0.24744267
65000 0.97952497 0.0070583633 0.22323997
66000 0.98095955 0.036296232 0.2151706
67000 0.98370788 -0.0040313363 0.22236193
68000 0.96931818 0.0231486 0.20397659
69000 0.98512552 -0.017450997 0.21854935
70000 0.98065743 0.046916694 0.2080453
71000 0.98971283 0.010974871 0.21628306
72000 0.99890324 -0.023780184 0.23385876
73000 0.98649924 0.012862733 0.23458964
74000 0.98723422 -0.0096252165 0.23873216
75000 1.0025633 -0.070387674 0.2275029
76000 0.97859959 0.0058897922 0.22954358
77000 0.97973006 -0.0082868083 0.25189797
78000 0.9903944 -0.042368536 0.26564349
79000 0.96847518 -0.050630573 0.25344248
80000 0.99171112 0.012126001 0.23257751
81000 0.97202573 -0.029816198 0.27354387
82000 0.99368438 0.030082951 0.27859495
83000 0.97932483 -0.0081664387 0.27409123
84000 0.99078651 0.056610231 0.27593659
85000 0.98973457 0.020424285 0.31002605
86000 0.9835873 -0.0016980943 0.30158255
87000 0.97180564 -0.0051924508 0.27401969
88000 0.99743353 -0.030700753 0.24105471
89000 0.98993437 0.0087866525 0.23913724
90000 0.9926071 -0.014023378 0.24202489
91000 0.98800458 0.033613695 0.2238248
92000 0.98501879 -0.0406599 0.21809043
93000 0.98810082 0.027637634 0.21550897
94000 0.97563748 0.0014112208 0.18954766
95000 0.97283448 0.0093796591 0.17838358
96000 0.9883071 0.033049994 0.18594703
97000 0.97717678 0.01070451 0.19203994
98000 0.97190208 0.015065013 0.20906937
99000 0.98687379 -0.036869401 0.22993959
100000 0.97559757 0.045464091 0.23369283
Loop time of 10.8346 on 8 procs for 100000 steps with 3200 atoms
Performance: 3987213.825 tau/day, 9229.662 timesteps/s
99.5% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8486 | 4.9469 | 5.0248 | 2.8 | 45.66
Neigh | 1.3613 | 1.374 | 1.3916 | 0.8 | 12.68
Comm | 1.8181 | 1.9534 | 2.0665 | 5.7 | 18.03
Output | 0.016565 | 0.016701 | 0.017039 | 0.1 | 0.15
Modify | 1.8395 | 1.9053 | 1.9704 | 2.8 | 17.59
Other | | 0.6383 | | | 5.89
Nlocal: 400 ave 413 max 391 min
Histogram: 2 1 0 2 0 0 1 1 0 1
Nghost: 204.75 ave 213 max 197 min
Histogram: 1 1 0 1 0 3 0 1 0 1
Neighs: 2800.62 ave 2959 max 2661 min
Histogram: 1 1 1 2 0 0 0 1 1 1
Total # of neighbors = 22405
Ave neighs/atom = 7.00156
Neighbor list builds = 12728
Dangerous builds = 0
Total wall time: 0:00:11

223
examples/DIFFUSE/log.1Feb14.msd.2d.g++.8
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@ -1,223 +0,0 @@
LAMMPS (12 Feb 2014)
# sample LAMMPS input script for diffusion of 2d LJ liquid
# mean-squared displacement via compute msd
# settings
variable x equal 40
variable y equal 40
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
lattice sq2 ${rho}
lattice sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox block 0 $x 0 $y -0.1 0.1
region simbox block 0 40 0 $y -0.1 0.1
region simbox block 0 40 0 40 -0.1 0.1
create_box 1 simbox
Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
4 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3200 atoms
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff * * 1 1
mass * 1.0
velocity all create $t 97287
velocity all create 1 97287
fix 1 all nve
fix 2 all langevin $t $t 0.1 498094
fix 2 all langevin 1 $t 0.1 498094
fix 2 all langevin 1 1 0.1 498094
fix 3 all enforce2d
# equilibration run
thermo 1000
run 5000
Memory usage per processor = 2.06238 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.5652325 -1.5346995
1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
5000 0.97069909 -1.5851114 0 -0.61471562 0.90108296
Loop time of 0.548328 on 8 procs for 5000 steps with 3200 atoms
Pair time (%) = 0.242437 (44.2139)
Neigh time (%) = 0.0589295 (10.7471)
Comm time (%) = 0.0797399 (14.5424)
Outpt time (%) = 0.00014773 (0.0269419)
Other time (%) = 0.167074 (30.4697)
Nlocal: 400 ave 406 max 394 min
Histogram: 1 1 0 1 0 2 1 0 1 1
Nghost: 202.5 ave 212 max 191 min
Histogram: 1 0 0 0 3 1 0 2 0 1
Neighs: 2800.88 ave 2903 max 2690 min
Histogram: 1 1 0 0 1 2 1 0 1 1
Total # of neighbors = 22407
Ave neighs/atom = 7.00219
Neighbor list builds = 599
Dangerous builds = 0
unfix 2
# data gathering run
reset_timestep 0
# factor of 4 in 2 variables is for 2d
compute msd all msd com yes
variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
fix 9 all vector 10 c_msd[4]
variable fitslope equal slope(f_9)/4/(10*dt)
thermo_style custom step temp c_msd[4] v_twopoint v_fitslope
# only need to run for 10K steps to make a good 100-frame movie
#dump 1 all custom 1 tmp.dump id type vx vy vz
#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
thermo 1000
run 100000
Memory usage per processor = 2.29126 Mbytes
Step Temp msd[4] twopoint fitslope
0 0.97069909 5.6797985e-31 1.4199496e-25 5e+20
1000 0.98259938 4.018182 0.20090906 0.18018405
2000 0.98866167 9.1771673 0.22942916 0.20819132
3000 0.98066292 14.377973 0.23963287 0.2226381
4000 0.97384109 19.666022 0.24582526 0.23154108
5000 0.97843004 25.570023 0.25570022 0.23873417
6000 0.98703537 31.182236 0.25985196 0.2446473
7000 0.97169186 36.915546 0.26368246 0.24892937
8000 0.9823893 42.723242 0.26702026 0.25284158
9000 0.9998457 49.159596 0.27310886 0.25648405
10000 0.98782869 55.95808 0.27979039 0.26026001
11000 0.99481941 63.387246 0.28812384 0.26436008
12000 0.9760981 70.325901 0.29302458 0.26836823
13000 0.97774297 77.590396 0.2984246 0.2723266
14000 0.96752038 85.055703 0.30377036 0.27627449
15000 0.98697717 92.723433 0.3090781 0.28007928
16000 0.98385955 100.89787 0.31530583 0.28396785
17000 0.9839555 108.44716 0.31896223 0.28772551
18000 0.98000182 115.932 0.32203333 0.29120847
19000 0.96633821 123.99378 0.32629942 0.2945701
20000 0.98641362 131.63233 0.32908082 0.29781576
21000 0.9763779 140.20546 0.33382253 0.30091009
22000 0.97984221 149.3632 0.33946182 0.30410181
23000 0.98384014 157.80278 0.34304952 0.30727461
24000 0.97601102 165.78405 0.34538343 0.31026343
25000 0.99623187 173.8015 0.347603 0.31311142
26000 0.98943691 182.06075 0.35011683 0.31582297
27000 0.98992058 188.30114 0.34870582 0.31827868
28000 0.97957751 196.93202 0.35166432 0.32053702
29000 0.99513582 206.48445 0.35600767 0.32277974
30000 0.99754125 213.2124 0.355354 0.32491307
31000 0.98894929 221.74208 0.35764851 0.32691848
32000 0.973493 229.28872 0.35826363 0.3288054
33000 0.99989261 236.7565 0.35872197 0.33061911
34000 0.97192218 243.57374 0.35819667 0.33225106
35000 0.99711642 250.65118 0.35807311 0.33369124
36000 0.97718259 258.94971 0.35965237 0.33507325
37000 0.98194807 265.83921 0.35924218 0.33634589
38000 0.97195138 272.94984 0.35914453 0.33755459
39000 0.98219017 280.07692 0.35907297 0.33864166
40000 0.98039694 288.4453 0.36055663 0.33967254
41000 0.97621359 295.85108 0.360794 0.3406849
42000 0.97460413 303.13769 0.3608782 0.34161073
43000 0.9799912 312.06356 0.3628646 0.34254857
44000 0.96313376 320.55123 0.36426276 0.34347747
45000 0.97643796 329.68761 0.36631956 0.34443057
46000 0.98641729 338.40463 0.36783111 0.34540729
47000 0.97811939 345.46683 0.3675179 0.34634877
48000 0.99744864 352.87823 0.36758148 0.34720815
49000 0.97480356 362.60002 0.37000002 0.34807624
50000 0.97841509 368.44194 0.36844193 0.34892214
51000 0.97865859 375.44238 0.36808076 0.34966222
52000 0.97415415 382.95453 0.36822551 0.35036495
53000 0.97984491 390.33776 0.36824317 0.35103186
54000 0.99289379 396.4986 0.36712833 0.35162842
55000 0.98606668 403.49336 0.36681214 0.35217399
56000 0.98585489 411.98283 0.36784182 0.35270646
57000 0.98507959 418.14272 0.36679186 0.35321673
58000 0.98030805 423.23791 0.36486026 0.353654
59000 0.98315137 429.40554 0.36390299 0.35400654
60000 0.98762585 437.17376 0.36431146 0.35433653
61000 0.96937507 442.38698 0.36261228 0.3546452
62000 0.97194792 450.91689 0.36364265 0.3549106
63000 0.99877655 460.61733 0.36556931 0.3552122
64000 0.98525211 469.26926 0.36661661 0.35554833
65000 0.9833149 477.52571 0.36732747 0.35589823
66000 0.97191797 485.72618 0.36797438 0.35624251
67000 0.98479592 492.83716 0.36778892 0.35657544
68000 0.98418943 498.90452 0.36684156 0.35688872
69000 0.96953928 507.57013 0.36780444 0.35718476
70000 0.98373337 515.05745 0.36789818 0.35749562
71000 0.98260952 522.33093 0.36783868 0.35778626
72000 0.98906053 527.99215 0.36666121 0.35804724
73000 0.99569597 534.99359 0.36643396 0.35827372
74000 0.97627362 540.94769 0.3655052 0.35847643
75000 0.97276792 546.45533 0.36430355 0.35864641
76000 0.97659072 554.59353 0.36486417 0.35879714
77000 0.9807196 562.96571 0.36556215 0.35896542
78000 0.97398601 571.22804 0.36617182 0.35914269
79000 0.98124212 577.92968 0.36577828 0.35930881
80000 0.98506783 586.73568 0.3667098 0.35948276
81000 0.97926561 596.68206 0.36832226 0.35968089
82000 0.97906184 604.24971 0.36844495 0.35988893
83000 0.96540502 610.7078 0.36789626 0.3600856
84000 0.98726761 619.32703 0.36864704 0.36027536
85000 0.98133061 627.20955 0.36894679 0.3604747
86000 0.99142106 634.68836 0.36900486 0.36067069
87000 0.97917566 641.73186 0.36881141 0.36086497
88000 0.99391197 649.76607 0.36918527 0.36105571
89000 0.98521911 655.50224 0.36825969 0.36123298
90000 0.97419059 664.0397 0.36891095 0.36139717
91000 0.98687774 671.19045 0.36878596 0.36156016
92000 0.97816545 677.37724 0.36813981 0.36171235
93000 0.98734859 684.56734 0.36804696 0.3618463
94000 0.99116168 691.47221 0.36780437 0.36197063
95000 0.99982024 698.01624 0.36737697 0.36208597
96000 0.99232404 703.53179 0.3664228 0.36218818
97000 0.97829693 707.91832 0.36490635 0.36225634
98000 0.99878715 713.77777 0.36417233 0.36230715
99000 0.97026354 717.24468 0.36224478 0.3623226
100000 0.98911409 722.1539 0.36107695 0.36230617
Loop time of 9.28795 on 8 procs for 100000 steps with 3200 atoms
Pair time (%) = 4.87621 (52.5003)
Neigh time (%) = 1.26444 (13.6138)
Comm time (%) = 1.60752 (17.3076)
Outpt time (%) = 0.00843725 (0.0908408)
Other time (%) = 1.53135 (16.4875)
Nlocal: 400 ave 410 max 389 min
Histogram: 1 1 1 0 1 1 0 0 1 2
Nghost: 205.375 ave 216 max 194 min
Histogram: 1 0 0 2 2 0 1 0 0 2
Neighs: 2818 ave 3010 max 2683 min
Histogram: 2 0 2 0 1 1 0 1 0 1
Total # of neighbors = 22544
Ave neighs/atom = 7.045
Neighbor list builds = 12748
Dangerous builds = 0

224
examples/DIFFUSE/log.1Feb14.vacf.2d.g++.8
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@ -1,224 +0,0 @@
LAMMPS (12 Feb 2014)
# sample LAMMPS input script for diffusion of 2d LJ liquid
# mean-squared displacement via compute msd
# settings
variable x equal 40
variable y equal 40
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
lattice sq2 ${rho}
lattice sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox block 0 $x 0 $y -0.1 0.1
region simbox block 0 40 0 $y -0.1 0.1
region simbox block 0 40 0 40 -0.1 0.1
create_box 1 simbox
Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
4 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3200 atoms
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff * * 1 1
mass * 1.0
velocity all create $t 97287
velocity all create 1 97287
fix 1 all nve
fix 2 all langevin $t $t 0.1 498094
fix 2 all langevin 1 $t 0.1 498094
fix 2 all langevin 1 1 0.1 498094
fix 3 all enforce2d
# equilibration run
thermo 1000
run 5000
Memory usage per processor = 2.06238 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.5652325 -1.5346995
1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
5000 0.97069909 -1.5851114 0 -0.61471562 0.90108296
Loop time of 0.556362 on 8 procs for 5000 steps with 3200 atoms
Pair time (%) = 0.242478 (43.5828)
Neigh time (%) = 0.0590148 (10.6073)
Comm time (%) = 0.0862918 (15.51)
Outpt time (%) = 0.000148952 (0.0267725)
Other time (%) = 0.168428 (30.2731)
Nlocal: 400 ave 406 max 394 min
Histogram: 1 1 0 1 0 2 1 0 1 1
Nghost: 202.5 ave 212 max 191 min
Histogram: 1 0 0 0 3 1 0 2 0 1
Neighs: 2800.88 ave 2903 max 2690 min
Histogram: 1 1 0 0 1 2 1 0 1 1
Total # of neighbors = 22407
Ave neighs/atom = 7.00219
Neighbor list builds = 599
Dangerous builds = 0
unfix 2
# data gathering run
reset_timestep 0
compute vacf all vacf
fix 4 all ave/time 1 1 1 c_vacf[4] #file tmp.vacf
# factor of 0.5 is for 2d
fix 5 all vector 1 c_vacf[4]
variable vacf equal 0.5*dt*trap(f_5)
thermo_style custom step temp c_vacf[4] v_vacf
# only need to run for 10K steps to make a good 100-frame movie
#dump 1 all custom 1 tmp.dump id type vx vy vz
#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
thermo 1000
run 100000
Memory usage per processor = 2.29126 Mbytes
Step Temp vacf[4] vacf
0 0.97069909 1.9407915 0
1000 0.98259938 0.068345562 0.21424576
2000 0.98866167 0.028205164 0.24370013
3000 0.98066292 0.008852823 0.27439588
4000 0.97384109 0.011903564 0.3159275
5000 0.97843004 0.019295534 0.33596598
6000 0.98703537 0.01070801 0.34517088
7000 0.97169186 -0.0082938435 0.33784119
8000 0.9823893 0.038402174 0.32756669
9000 0.9998457 0.045317593 0.33379383
10000 0.98782869 0.027148675 0.34751149
11000 0.99481941 0.035783937 0.36009047
12000 0.9760981 -0.0010825507 0.36059769
13000 0.97774297 0.048323885 0.36103752
14000 0.96752038 0.0008189784 0.34988029
15000 0.98697717 -0.0339338 0.35841003
16000 0.98385955 0.03729417 0.36378228
17000 0.9839555 -0.0063931744 0.37486488
18000 0.98000182 0.065439765 0.39975619
19000 0.96633821 0.0034363237 0.39585239
20000 0.98641362 -0.020284 0.39696422
21000 0.9763779 0.013683539 0.36183593
22000 0.97984221 -0.0077108606 0.32642476
23000 0.98384014 -0.030550764 0.32775468
24000 0.97601102 -0.0047287909 0.3294707
25000 0.99623187 0.00653461 0.34586445
26000 0.98943691 -0.05047279 0.3283058
27000 0.98992058 -0.01720223 0.30840611
28000 0.97957751 0.020915942 0.3149002
29000 0.99513582 0.03712206 0.30525251
30000 0.99754125 -0.022509889 0.29511243
31000 0.98894929 0.015289267 0.25586423
32000 0.973493 0.015971435 0.25226411
33000 0.99989261 0.026989142 0.29050941
34000 0.97192218 0.043710515 0.29067058
35000 0.99711642 0.047231436 0.27989734
36000 0.97718259 0.0059969847 0.28843181
37000 0.98194807 0.017440303 0.30325718
38000 0.97195138 -0.040449666 0.29696592
39000 0.98219017 0.0063692991 0.28915832
40000 0.98039694 -0.0038122219 0.24799014
41000 0.97621359 0.012624961 0.2374766
42000 0.97460413 -0.0024187 0.24693474
43000 0.9799912 0.015928618 0.26238505
44000 0.96313376 -0.067284605 0.24397772
45000 0.97643796 -0.0039001998 0.22733962
46000 0.98641729 -0.026949085 0.24167989
47000 0.97811939 -0.050859011 0.2335985
48000 0.99744864 -0.008154229 0.2417371
49000 0.97480356 -0.011051498 0.25474033
50000 0.97841509 -0.00531423 0.25357072
51000 0.97865859 0.067722096 0.25086864
52000 0.97415415 0.015863025 0.2516842
53000 0.97984491 0.021332829 0.28226376
54000 0.99289379 -0.0192578 0.28300764
55000 0.98606668 0.029307891 0.27592186
56000 0.98585489 0.0062922121 0.2687204
57000 0.98507959 -0.0068688582 0.27868708
58000 0.98030805 0.013766115 0.31008116
59000 0.98315137 0.033068034 0.32211415
60000 0.98762585 0.050662295 0.30109082
61000 0.96937507 -0.02797113 0.29968066
62000 0.97194792 -0.0032022157 0.2866526
63000 0.99877655 -0.010154313 0.31701083
64000 0.98525211 -0.020415497 0.31774092
65000 0.9833149 0.0087192442 0.31256891
66000 0.97191797 0.0047184494 0.29880531
67000 0.98479592 -0.010779275 0.294197
68000 0.98418943 -0.035264623 0.29993828
69000 0.96953928 -0.028114432 0.27403611
70000 0.98373337 -0.057363336 0.25554163
71000 0.98260952 0.048742037 0.27102884
72000 0.98906053 0.010799224 0.26908376
73000 0.99569597 -0.0092675754 0.26927752
74000 0.97627362 0.013945821 0.2730712
75000 0.97276792 0.015036012 0.25847255
76000 0.97659072 -0.027078556 0.26783118
77000 0.9807196 -0.044553679 0.25993053
78000 0.97398601 -0.00027444729 0.26127735
79000 0.98124212 -0.012488833 0.27454966
80000 0.98506783 -0.015190822 0.2676633
81000 0.97926561 -0.012755191 0.27046398
82000 0.97906184 0.012564185 0.2835038
83000 0.96540502 -0.007372877 0.29622738
84000 0.98726761 0.021015365 0.32432233
85000 0.98133061 0.020043402 0.3540913
86000 0.99142106 0.025350024 0.36697674
87000 0.97917566 0.0061562414 0.37456288
88000 0.99391197 0.0068565008 0.39150922
89000 0.98521911 0.015500816 0.38121119
90000 0.97419059 0.00037609894 0.34181128
91000 0.98687774 -0.0073221495 0.35316892
92000 0.97816545 0.014057005 0.33181146
93000 0.98734859 0.016570523 0.34546487
94000 0.99116168 -0.0068196043 0.36316635
95000 0.99982024 0.076723346 0.38376316
96000 0.99232404 -0.048534983 0.38369657
97000 0.97829693 0.0041180664 0.38022523
98000 0.99878715 -0.00089133295 0.40289006
99000 0.97026354 -0.0039532716 0.43650647
100000 0.98911409 0.028647976 0.4499919
Loop time of 10.5771 on 8 procs for 100000 steps with 3200 atoms
Pair time (%) = 4.88134 (46.1499)
Neigh time (%) = 1.2657 (11.9664)
Comm time (%) = 1.78371 (16.8638)
Outpt time (%) = 0.0207323 (0.196011)
Other time (%) = 2.62565 (24.8239)
Nlocal: 400 ave 410 max 389 min
Histogram: 1 1 1 0 1 1 0 0 1 2
Nghost: 205.375 ave 216 max 194 min
Histogram: 1 0 0 2 2 0 1 0 0 2
Neighs: 2818 ave 3010 max 2683 min
Histogram: 2 0 2 0 1 1 0 1 0 1
Total # of neighbors = 22544
Ave neighs/atom = 7.045
Neighbor list builds = 12748
Dangerous builds = 0

58
examples/KAPPA/log.7Jun16.ehex.g++.8 → examples/KAPPA/log.13Oct16.ehex.g++.8
View File

@ -1,4 +1,4 @@
LAMMPS (7 Jun 2016) LAMMPS (13 Oct 2016)
# sample LAMMPS input script for thermal conductivity of liquid LJ # sample LAMMPS input script for thermal conductivity of liquid LJ
# use fix ehex to add/subtract energy from 2 regions # use fix ehex to add/subtract energy from 2 regions
@ -79,20 +79,20 @@ Step Temp E_pair E_mol TotEng Press
800 1.3419995 -3.7155648 0 -1.7028172 0.82925676 800 1.3419995 -3.7155648 0 -1.7028172 0.82925676
900 1.3562214 -3.6965609 0 -1.6624831 0.88908117 900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701 1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701
Loop time of 0.878884 on 8 procs for 1000 steps with 8000 atoms Loop time of 0.889114 on 8 procs for 1000 steps with 8000 atoms
Performance: 491532.534 tau/day, 1137.807 timesteps/s Performance: 485876.777 tau/day, 1124.715 timesteps/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads 99.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.48108 | 0.4925 | 0.50422 | 1.0 | 56.04 Pair | 0.48042 | 0.50311 | 0.52772 | 1.9 | 56.59
Neigh | 0.23355 | 0.23565 | 0.23888 | 0.4 | 26.81 Neigh | 0.22997 | 0.23203 | 0.23466 | 0.3 | 26.10
Comm | 0.088565 | 0.10044 | 0.11391 | 2.7 | 11.43 Comm | 0.081187 | 0.10484 | 0.1285 | 4.2 | 11.79
Output | 0.00029421 | 0.00031444 | 0.00041795 | 0.2 | 0.04 Output | 0.00027299 | 0.00028226 | 0.000314 | 0.1 | 0.03
Modify | 0.027427 | 0.032625 | 0.035225 | 1.6 | 3.71 Modify | 0.028298 | 0.032276 | 0.037612 | 2.0 | 3.63
Other | | 0.01735 | | | 1.97 Other | | 0.01658 | | | 1.86
Nlocal: 1000 ave 1020 max 982 min Nlocal: 1000 ave 1020 max 982 min
Histogram: 1 0 2 1 0 1 1 1 0 1 Histogram: 1 0 2 1 0 1 1 1 0 1
@ -121,7 +121,7 @@ thermo_style custom step temp c_Thot c_Tcold
thermo 1000 thermo 1000
run 10000 run 10000
Memory usage per processor = 2.80761 Mbytes Memory usage per processor = 2.80761 Mbytes
Step Temp Thot Tcold Step Temp c_Thot c_Tcold
1000 1.35 1.431295 1.2955644 1000 1.35 1.431295 1.2955644
2000 1.3537291 1.6418772 1.1875127 2000 1.3537291 1.6418772 1.1875127
3000 1.3615152 1.6451299 1.1769094 3000 1.3615152 1.6451299 1.1769094
@ -133,20 +133,20 @@ Step Temp Thot Tcold
9000 1.3701136 1.8238424 1.136342 9000 1.3701136 1.8238424 1.136342
10000 1.3563004 1.8059065 1.1547129 10000 1.3563004 1.8059065 1.1547129
11000 1.3794051 1.692299 1.0515688 11000 1.3794051 1.692299 1.0515688
Loop time of 10.292 on 8 procs for 10000 steps with 8000 atoms Loop time of 10.5555 on 8 procs for 10000 steps with 8000 atoms
Performance: 419743.444 tau/day, 971.628 timesteps/s Performance: 409265.976 tau/day, 947.375 timesteps/s
99.5% CPU use with 8 MPI tasks x no OpenMP threads 99.4% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 4.1797 | 4.902 | 5.5136 | 25.3 | 47.63 Pair | 4.1863 | 5.0134 | 5.8326 | 28.0 | 47.50
Neigh | 2.1913 | 2.4616 | 2.6938 | 14.2 | 23.92 Neigh | 2.1559 | 2.4232 | 2.6516 | 14.2 | 22.96
Comm | 0.87831 | 1.64 | 2.611 | 56.5 | 15.94 Comm | 0.80561 | 1.8126 | 2.8852 | 58.4 | 17.17
Output | 0.00043011 | 0.00063166 | 0.00075626 | 0.5 | 0.01 Output | 0.00044537 | 0.00064856 | 0.00077057 | 0.5 | 0.01
Modify | 0.78531 | 0.92487 | 1.0647 | 10.6 | 8.99 Modify | 0.81915 | 0.94285 | 1.0571 | 9.5 | 8.93
Other | | 0.3628 | | | 3.53 Other | | 0.3628 | | | 3.44
Nlocal: 1000 ave 1105 max 883 min Nlocal: 1000 ave 1105 max 883 min
Histogram: 1 1 2 0 0 0 0 0 2 2 Histogram: 1 1 2 0 0 0 0 0 2 2
@ -174,7 +174,7 @@ thermo_style custom step temp c_Thot c_Tcold v_tdiff f_ave
run 20000 run 20000
Memory usage per processor = 3.0578 Mbytes Memory usage per processor = 3.0578 Mbytes
Step Temp Thot Tcold tdiff ave Step Temp c_Thot c_Tcold v_tdiff f_ave
11000 1.3794051 1.6903393 1.0515688 0 0 11000 1.3794051 1.6903393 1.0515688 0 0
12000 1.3799777 1.8004888 1.1032219 -0.63860014 0 12000 1.3799777 1.8004888 1.1032219 -0.63860014 0
13000 1.3733605 1.7823094 1.0553582 -0.65827891 -0.65827891 13000 1.3733605 1.7823094 1.0553582 -0.65827891 -0.65827891
@ -196,20 +196,20 @@ Step Temp Thot Tcold tdiff ave
29000 1.3819302 1.8619138 1.0495292 -0.78627491 -0.76680973 29000 1.3819302 1.8619138 1.0495292 -0.78627491 -0.76680973
30000 1.3968366 1.883107 1.1004588 -0.83902548 -0.77082172 30000 1.3968366 1.883107 1.1004588 -0.83902548 -0.77082172
31000 1.3822489 1.8220413 1.0322271 -0.7550338 -0.76999077 31000 1.3822489 1.8220413 1.0322271 -0.7550338 -0.76999077
Loop time of 22.3319 on 8 procs for 20000 steps with 8000 atoms Loop time of 22.7579 on 8 procs for 20000 steps with 8000 atoms
Performance: 386890.255 tau/day, 895.579 timesteps/s Performance: 379649.018 tau/day, 878.817 timesteps/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads 99.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 7.4818 | 9.8886 | 12.008 | 66.1 | 44.28 Pair | 7.4811 | 10.102 | 12.63 | 68.7 | 44.39
Neigh | 4.1157 | 5.0693 | 5.9657 | 38.0 | 22.70 Neigh | 4.0495 | 4.9884 | 5.8366 | 37.8 | 21.92
Comm | 1.8343 | 4.6586 | 7.8747 | 129.4 | 20.86 Comm | 1.6695 | 4.9483 | 8.493 | 130.7 | 21.74
Output | 0.00095606 | 0.0017744 | 0.0019104 | 0.7 | 0.01 Output | 0.0010517 | 0.0017769 | 0.0019059 | 0.7 | 0.01
Modify | 1.6812 | 1.9319 | 2.2204 | 13.5 | 8.65 Modify | 1.6903 | 1.9371 | 2.2355 | 14.8 | 8.51
Other | | 0.7817 | | | 3.50 Other | | 0.7799 | | | 3.43
Nlocal: 1000 ave 1121 max 857 min Nlocal: 1000 ave 1121 max 857 min
Histogram: 2 0 1 1 0 0 0 0 1 3 Histogram: 2 0 1 1 0 0 0 0 1 3
@ -222,4 +222,4 @@ Total # of neighbors = 219898
Ave neighs/atom = 27.4872 Ave neighs/atom = 27.4872
Neighbor list builds = 3474 Neighbor list builds = 3474
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:33 Total wall time: 0:00:34

58
examples/KAPPA/log.7Jun16.heat.g++.8 → examples/KAPPA/log.13Oct16.heat.g++.8
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@ -1,4 +1,4 @@
LAMMPS (7 Jun 2016) LAMMPS (13 Oct 2016)
# sample LAMMPS input script for thermal conductivity of liquid LJ # sample LAMMPS input script for thermal conductivity of liquid LJ
# use fix heat to add/subtract energy from 2 regions # use fix heat to add/subtract energy from 2 regions
@ -79,20 +79,20 @@ Step Temp E_pair E_mol TotEng Press
800 1.3419995 -3.7155648 0 -1.7028172 0.82925676 800 1.3419995 -3.7155648 0 -1.7028172 0.82925676
900 1.3562214 -3.6965609 0 -1.6624831 0.88908117 900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701 1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701
Loop time of 0.889036 on 8 procs for 1000 steps with 8000 atoms Loop time of 0.872163 on 8 procs for 1000 steps with 8000 atoms
Performance: 485919.613 tau/day, 1124.814 timesteps/s Performance: 495320.223 tau/day, 1146.575 timesteps/s
99.4% CPU use with 8 MPI tasks x no OpenMP threads 99.5% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.47867 | 0.4928 | 0.5006 | 1.0 | 55.43 Pair | 0.48598 | 0.49768 | 0.50892 | 1.1 | 57.06
Neigh | 0.23302 | 0.23557 | 0.23833 | 0.3 | 26.50 Neigh | 0.22855 | 0.23236 | 0.23463 | 0.5 | 26.64
Comm | 0.1001 | 0.11264 | 0.12817 | 2.6 | 12.67 Comm | 0.082584 | 0.093727 | 0.10748 | 2.9 | 10.75
Output | 0.00032806 | 0.00034043 | 0.00040531 | 0.1 | 0.04 Output | 0.0002718 | 0.00028038 | 0.00031757 | 0.1 | 0.03
Modify | 0.028788 | 0.031511 | 0.033365 | 0.9 | 3.54 Modify | 0.028934 | 0.031425 | 0.03322 | 0.8 | 3.60
Other | | 0.01618 | | | 1.82 Other | | 0.01668 | | | 1.91
Nlocal: 1000 ave 1020 max 982 min Nlocal: 1000 ave 1020 max 982 min
Histogram: 1 0 2 1 0 1 1 1 0 1 Histogram: 1 0 2 1 0 1 1 1 0 1
@ -121,7 +121,7 @@ thermo_style custom step temp c_Thot c_Tcold
thermo 1000 thermo 1000
run 10000 run 10000
Memory usage per processor = 2.55761 Mbytes Memory usage per processor = 2.55761 Mbytes
Step Temp Thot Tcold Step Temp c_Thot c_Tcold
1000 1.35 1.431295 1.2955644 1000 1.35 1.431295 1.2955644
2000 1.3518468 1.5562602 1.154905 2000 1.3518468 1.5562602 1.154905
3000 1.3477229 1.5890075 1.2395414 3000 1.3477229 1.5890075 1.2395414
@ -133,20 +133,20 @@ Step Temp Thot Tcold
9000 1.3739201 1.6846211 1.1138829 9000 1.3739201 1.6846211 1.1138829
10000 1.3751455 1.8039471 1.1500399 10000 1.3751455 1.8039471 1.1500399
11000 1.3716416 1.833336 1.1267278 11000 1.3716416 1.833336 1.1267278
Loop time of 10.488 on 8 procs for 10000 steps with 8000 atoms Loop time of 10.3395 on 8 procs for 10000 steps with 8000 atoms
Performance: 411900.216 tau/day, 953.473 timesteps/s Performance: 417815.278 tau/day, 967.165 timesteps/s
99.5% CPU use with 8 MPI tasks x no OpenMP threads 99.5% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 4.138 | 4.9118 | 5.6168 | 26.2 | 46.83 Pair | 4.2189 | 4.9657 | 5.6225 | 25.3 | 48.03
Neigh | 2.1715 | 2.4541 | 2.7147 | 14.7 | 23.40 Neigh | 2.1359 | 2.4223 | 2.6741 | 14.8 | 23.43
Comm | 0.94395 | 1.8449 | 2.9212 | 55.3 | 17.59 Comm | 0.83801 | 1.6773 | 2.6984 | 57.1 | 16.22
Output | 0.00043416 | 0.00046757 | 0.00054884 | 0.2 | 0.00 Output | 0.00042701 | 0.00046191 | 0.00052905 | 0.1 | 0.00
Modify | 1.0234 | 1.0946 | 1.2539 | 8.7 | 10.44 Modify | 1.0143 | 1.0895 | 1.1846 | 5.7 | 10.54
Other | | 0.1821 | | | 1.74 Other | | 0.1844 | | | 1.78
Nlocal: 1000 ave 1131 max 878 min Nlocal: 1000 ave 1131 max 878 min
Histogram: 3 1 0 0 0 0 0 1 1 2 Histogram: 3 1 0 0 0 0 0 1 1 2
@ -174,7 +174,7 @@ thermo_style custom step temp c_Thot c_Tcold v_tdiff f_ave
run 20000 run 20000
Memory usage per processor = 2.8078 Mbytes Memory usage per processor = 2.8078 Mbytes
Step Temp Thot Tcold tdiff ave Step Temp c_Thot c_Tcold v_tdiff f_ave
11000 1.3716416 1.833336 1.1267278 0 0 11000 1.3716416 1.833336 1.1267278 0 0
12000 1.3703433 1.7829467 1.1194444 -0.66044316 0 12000 1.3703433 1.7829467 1.1194444 -0.66044316 0
13000 1.3686734 1.8334366 1.1193477 -0.71431978 -0.71431978 13000 1.3686734 1.8334366 1.1193477 -0.71431978 -0.71431978
@ -196,20 +196,20 @@ Step Temp Thot Tcold tdiff ave
29000 1.3777555 1.8287284 1.0715132 -0.70375514 -0.74425717 29000 1.3777555 1.8287284 1.0715132 -0.70375514 -0.74425717
30000 1.3821118 1.7382856 1.1078333 -0.79892499 -0.74729427 30000 1.3821118 1.7382856 1.1078333 -0.79892499 -0.74729427
31000 1.3870476 1.8410063 1.1235958 -0.76218423 -0.74807795 31000 1.3870476 1.8410063 1.1235958 -0.76218423 -0.74807795
Loop time of 22.3813 on 8 procs for 20000 steps with 8000 atoms Loop time of 22.4057 on 8 procs for 20000 steps with 8000 atoms
Performance: 386036.860 tau/day, 893.604 timesteps/s Performance: 385616.132 tau/day, 892.630 timesteps/s
99.4% CPU use with 8 MPI tasks x no OpenMP threads 99.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 7.4578 | 9.8912 | 11.96 | 64.5 | 44.19 Pair | 7.6116 | 10.003 | 12.262 | 64.3 | 44.65
Neigh | 4.0721 | 5.0195 | 5.8898 | 36.9 | 22.43 Neigh | 4.038 | 4.9528 | 5.8822 | 37.6 | 22.10
Comm | 1.9554 | 4.7393 | 7.8917 | 125.4 | 21.18 Comm | 1.6649 | 4.7143 | 7.6339 | 124.9 | 21.04
Output | 0.00099301 | 0.0017841 | 0.0019252 | 0.7 | 0.01 Output | 0.00098443 | 0.0017504 | 0.0018921 | 0.7 | 0.01
Modify | 2.2325 | 2.321 | 2.4866 | 6.5 | 10.37 Modify | 2.1819 | 2.3289 | 2.6598 | 12.6 | 10.39
Other | | 0.4085 | | | 1.83 Other | | 0.4047 | | | 1.81
Nlocal: 1000 ave 1134 max 850 min Nlocal: 1000 ave 1134 max 850 min
Histogram: 2 1 0 1 0 0 0 1 0 3 Histogram: 2 1 0 1 0 0 0 1 0 3

230
examples/KAPPA/log.13Oct16.heatflux.g++.8 Normal file
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@ -0,0 +1,230 @@
LAMMPS (13 Oct 2016)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# Green-Kubo method via compute heat/flux and fix ave/correlate
# settings
variable x equal 10
variable y equal 10
variable z equal 10
variable rho equal 0.6
variable t equal 1.35
variable rc equal 2.5
#variable rho equal 0.85
#variable t equal 0.7
#variable rc equal 3.0
variable p equal 200 # correlation length
variable s equal 10 # sample interval
variable d equal $p*$s # dump interval
variable d equal 200*$s
variable d equal 200*10
# setup problem
units lj
atom_style atomic
lattice fcc ${rho}
lattice fcc 0.6
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
region box block 0 $x 0 $y 0 $z
region box block 0 10 0 $y 0 $z
region box block 0 10 0 10 0 $z
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (18.8207 18.8207 18.8207)
2 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
mass 1 1.0
velocity all create $t 87287
velocity all create 1.35 87287
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
# 1st equilibration run
fix 1 all nvt temp $t $t 0.5
fix 1 all nvt temp 1.35 $t 0.5
fix 1 all nvt temp 1.35 1.35 0.5
thermo 100
run 1000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 14 14 14
Memory usage per processor = 2.52285 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.35 -4.1241917 0 -2.0996979 -3.1962625
100 1.1997886 -3.7796264 0 -1.9803934 0.4889458
200 1.271238 -3.7354981 0 -1.8291178 0.6873844
300 1.3346808 -3.6942841 0 -1.6927634 0.84332881
400 1.4020848 -3.7118654 0 -1.6092641 0.87670585
500 1.3723622 -3.6917931 0 -1.6337644 0.92172921
600 1.3451676 -3.7281573 0 -1.7109103 0.76029091
700 1.3021567 -3.6876155 0 -1.7348687 0.82721085
800 1.3489121 -3.7082852 0 -1.6854229 0.86438061
900 1.3708803 -3.6966168 0 -1.6408103 0.921415
1000 1.3640742 -3.7075319 0 -1.6619322 0.86651332
Loop time of 0.457959 on 8 procs for 1000 steps with 4000 atoms
Performance: 943316.262 tau/day, 2183.602 timesteps/s
98.9% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.23307 | 0.24263 | 0.2466 | 1.0 | 52.98
Neigh | 0.10661 | 0.11011 | 0.11166 | 0.5 | 24.04
Comm | 0.069595 | 0.075354 | 0.087444 | 2.2 | 16.45
Output | 0.00028014 | 0.00028831 | 0.00031686 | 0.1 | 0.06
Modify | 0.01694 | 0.01904 | 0.021602 | 1.2 | 4.16
Other | | 0.01053 | | | 2.30
Nlocal: 500 ave 510 max 479 min
Histogram: 1 0 0 0 0 2 1 1 0 3
Nghost: 1519 ave 1539 max 1509 min
Histogram: 2 0 4 0 0 0 0 1 0 1
Neighs: 13553.8 ave 14051 max 12567 min
Histogram: 1 0 0 0 1 0 2 1 1 2
Total # of neighbors = 108430
Ave neighs/atom = 27.1075
Neighbor list builds = 155
Dangerous builds = 0
velocity all scale $t
velocity all scale 1.35
unfix 1
# thermal conductivity calculation
reset_timestep 0
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom NULL virial
compute flux all heat/flux myKE myPE myStress
variable Jx equal c_flux[1]/vol
variable Jy equal c_flux[2]/vol
variable Jz equal c_flux[3]/vol
fix 1 all nve
fix JJ all ave/correlate $s $p $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
fix JJ all ave/correlate 10 $p $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
fix JJ all ave/correlate 10 200 $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
fix JJ all ave/correlate 10 200 2000 c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
variable scale equal $s*dt/$t/$t/vol
variable scale equal 10*dt/$t/$t/vol
variable scale equal 10*dt/1.35/$t/vol
variable scale equal 10*dt/1.35/1.35/vol
variable k11 equal trap(f_JJ[3])*${scale}
variable k11 equal trap(f_JJ[3])*4.11522633744856e-06
variable k22 equal trap(f_JJ[4])*${scale}
variable k22 equal trap(f_JJ[4])*4.11522633744856e-06
variable k33 equal trap(f_JJ[5])*${scale}
variable k33 equal trap(f_JJ[5])*4.11522633744856e-06
thermo $d
thermo 2000
thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
run 100000
Memory usage per processor = 4.39785 Mbytes
Step Temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
0 1.35 0.012561273 -0.087295611 -0.037041124 0.014429409 0.69689289 0.12547278
2000 1.3455113 -0.034571206 -0.17570902 -0.057218308 -1.6110148 7.9287556 8.5035767
4000 1.3477761 -0.029528723 0.018790489 0.056107464 7.698411 1.9459053 9.9605272
6000 1.3411436 -0.20281149 0.2184806 0.036024028 4.6533075 1.6223216 3.7246529
8000 1.3561682 0.12038719 0.034930957 0.12173601 4.6450263 1.9032849 2.7566363
10000 1.3397694 -0.14241489 -0.10956496 0.053088086 6.4191535 3.1582257 2.2786677
12000 1.3410756 0.0033462395 0.14337321 0.16381733 5.9663779 1.6774436 1.7442075
14000 1.3484928 0.0080419803 -0.080232102 0.039035519 4.9483626 1.6210893 1.6103343
16000 1.3414836 -0.11063045 -0.031557643 0.032060333 6.1381241 1.438198 1.5831541
18000 1.3488617 0.15908507 -0.021418806 -0.13992507 5.9198613 1.1016464 1.2905478
20000 1.3535727 0.13217689 0.071933521 -0.028452943 6.3746606 1.003194 1.7007101
22000 1.3408534 -0.078953557 -0.0022323663 -0.22979033 5.0105241 1.1489328 1.720847
24000 1.34722 0.074784199 -0.071218632 0.15238165 4.4835452 0.94086945 3.1603615
26000 1.3539218 0.052534363 0.10419096 0.1866213 4.2233104 1.3973253 3.2802881
28000 1.3510105 0.0080425673 -0.03723976 0.20758595 5.261917 1.1931088 3.498831
30000 1.3410807 -0.043957884 0.065683978 0.015386362 4.3815277 1.5000017 3.2237565
32000 1.34766 -0.060481287 0.17142383 0.034367135 4.0974942 1.1637027 3.3771953
34000 1.3417583 -0.10055844 0.050237668 0.06974988 4.1478021 1.0235517 2.9440249
36000 1.3468728 0.09375756 -0.17875264 -0.063513807 4.4412987 0.71084371 3.4316313
38000 1.3496868 -0.038635804 0.117965 0.018050271 4.962332 0.41701129 3.4690212
40000 1.3403452 -0.092158116 0.14432655 -0.062258229 4.9980486 0.3762815 3.1688552
42000 1.3498661 0.085807945 0.010256385 -0.002956898 4.8200626 0.29278287 3.094633
44000 1.3564084 -0.07415163 -0.051327929 -0.18457986 4.7070907 0.3358167 3.0741797
46000 1.3435866 -0.013911463 0.081813372 0.022628846 4.6043718 0.3682401 2.9956189
48000 1.350611 0.036512747 0.080481423 -0.22973181 4.5648715 0.32728516 3.8573343
50000 1.3421783 0.057665789 0.075597141 0.17377918 4.4278473 0.5383886 3.5866168
52000 1.3473497 -0.11159587 -0.09688769 0.19876168 4.3876613 0.43408155 3.4786305
54000 1.3459495 -0.15341705 0.063996148 -0.0038254597 4.8434026 0.62047297 3.445187
56000 1.3545654 -0.082406034 0.089232864 -0.024355614 4.546051 0.7367607 3.3694561
58000 1.3577504 0.082844384 0.019500036 0.073721698 4.4061886 1.4575694 3.2754066
60000 1.348614 -0.16190321 -0.048576343 0.093820555 4.2946463 1.3416919 3.1159234
62000 1.3551143 0.097443296 -0.04420265 -0.25713945 4.1260882 1.2550603 3.063215
64000 1.346239 0.019198575 -0.095746619 0.18383922 4.5691519 1.2615165 2.9935539
66000 1.3535383 -0.0035547901 -0.1753318 0.014025292 4.5371394 1.0740671 2.9362916
68000 1.3421249 -0.18217113 0.077901408 0.04314081 5.1644747 1.0218342 2.9789097
70000 1.3446114 0.029565781 -0.13771336 0.050328878 5.4811405 1.0430806 2.9748623
72000 1.3692655 0.005711741 0.13966773 -0.062638787 5.3033385 1.1040582 2.7599218
74000 1.3405365 -0.054281977 0.038019086 -0.024980877 5.1246258 2.0782965 2.725331
76000 1.3644178 0.040847675 -0.051968108 -0.12259032 5.1218657 1.8504273 2.6804003
78000 1.353792 -0.093663092 0.018784967 -0.073871437 5.025196 1.7789709 2.5339006
80000 1.3520982 -0.09407101 0.010328039 0.0028841073 5.1410049 1.855057 2.6935895
82000 1.3447597 -0.11935066 -0.2184608 0.073543056 5.2645334 1.7883077 4.2012292
84000 1.3712151 -0.064367612 0.021246872 -0.033571866 5.0479674 1.8947341 4.3856536
86000 1.3453867 -0.029842112 -0.042297039 0.05422886 5.0667777 2.0365983 4.4542311
88000 1.3439543 -0.21625828 -0.028119372 -0.010320332 4.9946428 2.3095763 4.3429587
90000 1.3472579 0.058391002 0.037139373 0.03424008 5.0599004 2.8132794 4.4503426
92000 1.361788 0.028891114 0.072799744 -0.12035229 4.8759851 2.5130025 4.2747068
94000 1.3440566 0.043421348 0.049653856 -0.060444094 4.8884081 2.5072981 4.3105221
96000 1.3537566 0.088733517 -0.11449828 -0.049852036 4.8115085 2.4780963 4.2213579
98000 1.3373399 0.25457663 -0.041723778 0.00084565184 4.7163394 2.4100822 4.485536
100000 1.3487502 0.046333889 0.1247351 0.063467467 4.6563279 2.4049358 4.5742925
Loop time of 49.532 on 8 procs for 100000 steps with 4000 atoms
Performance: 872163.631 tau/day, 2018.897 timesteps/s
99.6% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 27.027 | 27.478 | 28.167 | 6.9 | 55.48
Neigh | 11.257 | 11.369 | 11.491 | 2.3 | 22.95
Comm | 6.6783 | 7.6942 | 8.2758 | 19.3 | 15.53
Output | 0.0075166 | 0.024356 | 0.026799 | 4.1 | 0.05
Modify | 1.7374 | 1.7617 | 1.7845 | 1.0 | 3.56
Other | | 1.205 | | | 2.43
Nlocal: 500 ave 505 max 491 min
Histogram: 1 0 0 1 0 1 0 2 2 1
Nghost: 1529.88 ave 1548 max 1508 min
Histogram: 1 1 0 0 1 1 2 0 0 2
Neighs: 13569.8 ave 13906 max 13235 min
Histogram: 1 1 0 1 1 1 1 1 0 1
Total # of neighbors = 108558
Ave neighs/atom = 27.1395
Neighbor list builds = 16041
Dangerous builds = 0
variable kappa equal (v_k11+v_k22+v_k33)/3.0
print "running average conductivity: ${kappa}"
running average conductivity: 3.8785187495769
Total wall time: 0:00:50

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LAMMPS (13 Oct 2016)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# thermostatting 2 regions via fix langevin
# settings
variable x equal 10
variable y equal 10
variable z equal 20
variable rho equal 0.6
variable t equal 1.35
variable rc equal 2.5
variable tlo equal 1.0
variable thi equal 1.70
#variable rho equal 0.85
#variable t equal 0.7
#variable rc equal 3.0
#variable tlo equal 0.3
#variable thi equal 1.0
# setup problem
units lj
atom_style atomic
lattice fcc ${rho}
lattice fcc 0.6
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
region box block 0 $x 0 $y 0 $z
region box block 0 10 0 $y 0 $z
region box block 0 10 0 10 0 $z
region box block 0 10 0 10 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
2 by 1 by 4 MPI processor grid
create_atoms 1 box
Created 8000 atoms
mass 1 1.0
velocity all create $t 87287
velocity all create 1.35 87287
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
# heat layers
region hot block INF INF INF INF 0 1
region cold block INF INF INF INF 10 11
compute Thot all temp/region hot
compute Tcold all temp/region cold
# 1st equilibration run
fix 1 all nvt temp $t $t 0.5
fix 1 all nvt temp 1.35 $t 0.5
fix 1 all nvt temp 1.35 1.35 0.5
thermo 100
run 1000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 14 14 27
Memory usage per processor = 2.55761 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.35 -4.1241917 0 -2.0994448 -3.1961612
100 1.1819832 -3.7640881 0 -1.991335 0.53985757
200 1.2578365 -3.7395333 0 -1.8530144 0.69591862
300 1.3282971 -3.7215427 0 -1.7293461 0.79036065
400 1.3714367 -3.7043826 0 -1.6474847 0.85873226
500 1.3590952 -3.6707735 0 -1.6323855 0.99602024
600 1.3575117 -3.7118244 0 -1.6758114 0.81454305
700 1.3284444 -3.7075488 0 -1.7151313 0.81136596
800 1.3419995 -3.7155648 0 -1.7028172 0.82925676
900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701
Loop time of 0.876399 on 8 procs for 1000 steps with 8000 atoms
Performance: 492926.111 tau/day, 1141.033 timesteps/s
99.4% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.47963 | 0.4975 | 0.51846 | 1.6 | 56.77
Neigh | 0.22878 | 0.23186 | 0.23458 | 0.4 | 26.46
Comm | 0.081789 | 0.096763 | 0.11865 | 3.6 | 11.04
Output | 0.000247 | 0.00025409 | 0.00028944 | 0.1 | 0.03
Modify | 0.02689 | 0.033982 | 0.042612 | 2.9 | 3.88
Other | | 0.01604 | | | 1.83
Nlocal: 1000 ave 1020 max 982 min
Histogram: 1 0 2 1 0 1 1 1 0 1
Nghost: 2299.5 ave 2331 max 2268 min
Histogram: 1 1 1 1 0 0 0 3 0 1
Neighs: 27122 ave 28382 max 26337 min
Histogram: 2 0 2 1 1 0 0 1 0 1
Total # of neighbors = 216976
Ave neighs/atom = 27.122
Neighbor list builds = 162
Dangerous builds = 0
velocity all scale $t
velocity all scale 1.35
unfix 1
# 2nd equilibration run
fix 1 all nve
fix hot all langevin ${thi} ${thi} 1.0 59804 tally yes
fix hot all langevin 1.7 ${thi} 1.0 59804 tally yes
fix hot all langevin 1.7 1.7 1.0 59804 tally yes
fix cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
fix cold all langevin 1 ${tlo} 1.0 287859 tally yes
fix cold all langevin 1 1 1.0 287859 tally yes
fix_modify hot temp Thot
fix_modify cold temp Tcold
variable tdiff equal c_Thot-c_Tcold
thermo_style custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff
thermo 1000
run 10000
Memory usage per processor = 3.30761 Mbytes
Step Temp c_Thot c_Tcold f_hot f_cold v_tdiff
1000 1.35 1.431295 1.2955644 -0 -0 0.13573065
2000 1.3593243 1.6602094 1.0898701 -0.13903162 0.14234352 0.57033928
3000 1.3412163 1.6308839 1.0677742 -0.2214765 0.25871329 0.56310968
4000 1.3275359 1.5248034 1.0792345 -0.26908328 0.34211202 0.44556887
5000 1.3230922 1.6266046 1.0523802 -0.33175886 0.43533756 0.5742244
6000 1.3037036 1.6021737 1.0408166 -0.3639815 0.49869333 0.56135712
7000 1.2903225 1.5701119 1.0603548 -0.40000421 0.55547714 0.50975712
8000 1.3050677 1.6420218 1.0221774 -0.46368839 0.60293974 0.61984444
9000 1.2950977 1.7153984 1.0583242 -0.51871512 0.66389344 0.65707419
10000 1.3100216 1.6680668 1.0871293 -0.57485359 0.7161839 0.58093752
11000 1.297052 1.6486494 1.088903 -0.60276081 0.75900024 0.55974633
Loop time of 11.5988 on 8 procs for 10000 steps with 8000 atoms
Performance: 372451.299 tau/day, 862.156 timesteps/s
99.4% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.0544 | 4.9719 | 5.8426 | 34.5 | 42.87
Neigh | 2.0735 | 2.3933 | 2.7208 | 18.8 | 20.63
Comm | 0.91559 | 1.9788 | 3.1216 | 70.5 | 17.06
Output | 0.0005753 | 0.00068495 | 0.00080419 | 0.3 | 0.01
Modify | 1.9354 | 1.9837 | 2.0321 | 2.6 | 17.10
Other | | 0.2705 | | | 2.33
Nlocal: 1000 ave 1112 max 841 min
Histogram: 1 1 0 2 0 0 0 0 1 3
Nghost: 2294.38 ave 2506 max 2077 min
Histogram: 2 1 1 0 0 0 0 1 1 2
Neighs: 27441.9 ave 32651 max 19438 min
Histogram: 1 1 0 2 0 0 0 0 0 4
Total # of neighbors = 219535
Ave neighs/atom = 27.4419
Neighbor list builds = 1674
Dangerous builds = 0
# thermal conductivity calculation
# reset langevin thermostats to zero energy accumulation
compute ke all ke/atom
variable temp atom c_ke/1.5
fix hot all langevin ${thi} ${thi} 1.0 59804 tally yes
fix hot all langevin 1.7 ${thi} 1.0 59804 tally yes
fix hot all langevin 1.7 1.7 1.0 59804 tally yes
fix cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
fix cold all langevin 1 ${tlo} 1.0 287859 tally yes
fix cold all langevin 1 1 1.0 287859 tally yes
fix_modify hot temp Thot
fix_modify cold temp Tcold
fix ave all ave/time 10 100 1000 v_tdiff ave running
thermo_style custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.langevin
run 20000
Memory usage per processor = 3.5578 Mbytes
Step Temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave
11000 1.297052 1.6473904 1.088903 -0 -0 0.55848738 0
12000 1.2792808 1.6043738 1.0658375 -0.012256975 0.04611547 0.53853632 0.54492428
13000 1.2787101 1.7035572 1.1159037 -0.073806664 0.099529002 0.58765348 0.5581748
14000 1.289918 1.4642237 1.1073937 -0.11428779 0.13931657 0.35683005 0.56816328
15000 1.2932964 1.5032665 1.0523148 -0.17247717 0.19001309 0.45095174 0.57436291
16000 1.3025037 1.5424316 1.1185175 -0.22598282 0.22640921 0.42391405 0.56973168
17000 1.3009667 1.5582105 1.0745661 -0.27544101 0.26143452 0.48364439 0.5700118
18000 1.2970255 1.5019842 1.0228322 -0.31195285 0.31203237 0.479152 0.56544644
19000 1.2880631 1.5290587 1.0976483 -0.34645573 0.34243366 0.43141047 0.56338309
20000 1.3119675 1.6284144 1.1102294 -0.40922326 0.39217092 0.51818503 0.56614474
21000 1.2838063 1.6670934 0.97721382 -0.43809329 0.46021572 0.68987962 0.5686161
22000 1.2925041 1.7050682 1.0984963 -0.4871305 0.50520177 0.6065719 0.57226368
23000 1.2746463 1.6388503 1.0286701 -0.51212873 0.56478515 0.6101802 0.57290996
24000 1.2745381 1.7085713 1.1362975 -0.54529463 0.58540408 0.57227375 0.57296767
25000 1.2776401 1.5259253 1.0415158 -0.58389862 0.62623289 0.48440948 0.57386374
26000 1.2661888 1.4760829 0.99145001 -0.62638032 0.68155754 0.48463289 0.57021631
27000 1.2923677 1.6070495 1.0300276 -0.70014343 0.70236265 0.5770219 0.57001637
28000 1.2961449 1.7052335 1.0805793 -0.74856241 0.75775659 0.62465427 0.56927907
29000 1.2969474 1.5520176 1.1249649 -0.78900962 0.79539202 0.42705264 0.56986986
30000 1.2900596 1.6556864 1.0302676 -0.84180996 0.87187683 0.6254189 0.57245841
31000 1.2923209 1.6752068 1.0156911 -0.89036148 0.88285227 0.65951571 0.57358134
Loop time of 24.1059 on 8 procs for 20000 steps with 8000 atoms
Performance: 358418.039 tau/day, 829.671 timesteps/s
99.4% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.5967 | 9.9644 | 12.189 | 62.9 | 41.34
Neigh | 3.9305 | 4.7817 | 5.594 | 34.5 | 19.84
Comm | 1.7656 | 4.5624 | 7.6382 | 122.3 | 18.93
Output | 0.0011697 | 0.0018933 | 0.0020008 | 0.6 | 0.01
Modify | 4.1386 | 4.2107 | 4.3622 | 3.8 | 17.47
Other | | 0.5848 | | | 2.43
Nlocal: 1000 ave 1118 max 875 min
Histogram: 2 1 1 0 0 0 0 0 2 2
Nghost: 2298.62 ave 2535 max 2063 min
Histogram: 3 1 0 0 0 0 0 0 1 3
Neighs: 27462.4 ave 32904 max 21333 min
Histogram: 2 2 0 0 0 0 0 0 0 4
Total # of neighbors = 219699
Ave neighs/atom = 27.4624
Neighbor list builds = 3340
Dangerous builds = 0
Total wall time: 0:00:36

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LAMMPS (13 Oct 2016)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# Muller-Plathe method via fix thermal_conductivity
# settings
variable x equal 10
variable y equal 10
variable z equal 20
variable rho equal 0.6
variable t equal 1.35
variable rc equal 2.5
#variable rho equal 0.85
#variable t equal 0.7
#variable rc equal 3.0
# setup problem
units lj
atom_style atomic
lattice fcc ${rho}
lattice fcc 0.6
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
region box block 0 $x 0 $y 0 $z
region box block 0 10 0 $y 0 $z
region box block 0 10 0 10 0 $z
region box block 0 10 0 10 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
2 by 1 by 4 MPI processor grid
create_atoms 1 box
Created 8000 atoms
mass 1 1.0
velocity all create $t 87287
velocity all create 1.35 87287
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
# 1st equilibration run
fix 1 all nvt temp $t $t 0.5
fix 1 all nvt temp 1.35 $t 0.5
fix 1 all nvt temp 1.35 1.35 0.5
thermo 100
run 1000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 14 14 27
Memory usage per processor = 2.55761 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.35 -4.1241917 0 -2.0994448 -3.1961612
100 1.1819832 -3.7640881 0 -1.991335 0.53985757
200 1.2578365 -3.7395333 0 -1.8530144 0.69591862
300 1.3282971 -3.7215427 0 -1.7293461 0.79036065
400 1.3714367 -3.7043826 0 -1.6474847 0.85873226
500 1.3590952 -3.6707735 0 -1.6323855 0.99602024
600 1.3575117 -3.7118244 0 -1.6758114 0.81454305
700 1.3284444 -3.7075488 0 -1.7151313 0.81136596
800 1.3419995 -3.7155648 0 -1.7028172 0.82925676
900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701
Loop time of 0.875524 on 8 procs for 1000 steps with 8000 atoms
Performance: 493418.774 tau/day, 1142.173 timesteps/s
99.5% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.48279 | 0.49681 | 0.51174 | 1.2 | 56.74
Neigh | 0.22868 | 0.23169 | 0.23454 | 0.4 | 26.46
Comm | 0.084792 | 0.098391 | 0.11603 | 3.4 | 11.24
Output | 0.00027204 | 0.00027871 | 0.00031137 | 0.1 | 0.03
Modify | 0.027863 | 0.032316 | 0.039397 | 2.3 | 3.69
Other | | 0.01605 | | | 1.83
Nlocal: 1000 ave 1020 max 982 min
Histogram: 1 0 2 1 0 1 1 1 0 1
Nghost: 2299.5 ave 2331 max 2268 min
Histogram: 1 1 1 1 0 0 0 3 0 1
Neighs: 27122 ave 28382 max 26337 min
Histogram: 2 0 2 1 1 0 0 1 0 1
Total # of neighbors = 216976
Ave neighs/atom = 27.122
Neighbor list builds = 162
Dangerous builds = 0
velocity all scale $t
velocity all scale 1.35
unfix 1
# 2nd equilibration run
compute ke all ke/atom
variable temp atom c_ke/1.5
fix 1 all nve
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.mp
fix 3 all thermal/conductivity 10 z 20
variable tdiff equal f_2[11][3]-f_2[1][3]
thermo_style custom step temp epair etotal f_3 v_tdiff
thermo 1000
run 20000
Memory usage per processor = 2.8078 Mbytes
Step Temp E_pair TotEng f_3 v_tdiff
1000 1.35 -3.7100044 -1.6852575 0 0
2000 1.3572899 -3.7210084 -1.6853282 873.12373 0.26058005
3000 1.359979 -3.7268343 -1.6871208 1750.6998 0.40845169
4000 1.3677509 -3.7394553 -1.6880853 2565.8064 0.63828485
5000 1.3742987 -3.750287 -1.6890966 3373.2897 0.70173279
6000 1.3950535 -3.7827674 -1.6904487 4162.6672 0.83210131
7000 1.3843852 -3.7679238 -1.6916056 4947.5882 0.92719731
8000 1.396125 -3.7861373 -1.6922116 5703.4508 0.92426948
9000 1.4135104 -3.812624 -1.6926234 6465.5676 1.0412501
10000 1.4092351 -3.8065359 -1.6929474 7242.2986 1.0772505
11000 1.3966916 -3.7874302 -1.6926547 8007.3229 1.056805
12000 1.4111272 -3.8089829 -1.6925567 8750.8648 1.097621
13000 1.4091888 -3.8074873 -1.6939684 9514.7196 1.0734167
14000 1.4132159 -3.8134636 -1.6939046 10284.269 1.1643391
15000 1.3991348 -3.7928819 -1.694442 11051.851 1.0716016
16000 1.4055537 -3.8013252 -1.6932583 11836.812 1.1506479
17000 1.4127928 -3.8141054 -1.6951811 12626.124 1.1301728
18000 1.4118868 -3.8119733 -1.6944077 13391.631 1.1521394
19000 1.4209268 -3.826811 -1.6956872 14180.009 1.0929393
20000 1.4093812 -3.8083875 -1.6945801 14969.574 1.2113183
21000 1.4202317 -3.8255696 -1.6954884 15735.893 1.161082
Loop time of 21.0741 on 8 procs for 20000 steps with 8000 atoms
Performance: 409982.223 tau/day, 949.033 timesteps/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.4932 | 10.005 | 12.426 | 70.1 | 47.48
Neigh | 4.0592 | 5.0894 | 6.0544 | 41.7 | 24.15
Comm | 1.7793 | 5.0312 | 8.5027 | 134.6 | 23.87
Output | 0.00058484 | 0.00060964 | 0.0007031 | 0.1 | 0.00
Modify | 0.39735 | 0.4211 | 0.43467 | 2.3 | 2.00
Other | | 0.5269 | | | 2.50
Nlocal: 1000 ave 1188 max 806 min
Histogram: 2 1 1 0 0 0 0 0 2 2
Nghost: 2300.5 ave 2645 max 1963 min
Histogram: 3 1 0 0 0 0 0 0 1 3
Neighs: 27897 ave 37064 max 18367 min
Histogram: 2 2 0 0 0 0 0 0 0 4
Total # of neighbors = 223176
Ave neighs/atom = 27.897
Neighbor list builds = 3537
Dangerous builds = 0
# thermal conductivity calculation
# reset fix thermal/conductivity to zero energy accumulation
fix 3 all thermal/conductivity 10 z 20
fix ave all ave/time 1 1 1000 v_tdiff ave running
thermo_style custom step temp epair etotal f_3 v_tdiff f_ave
run 20000
Memory usage per processor = 3.05853 Mbytes
Step Temp E_pair TotEng f_3 v_tdiff f_ave
21000 1.4202317 -3.8255696 -1.6954884 0 1.161082 1.161082
22000 1.4090517 -3.808543 -1.6952296 745.83128 1.1780376 1.1695598
23000 1.4261394 -3.8350237 -1.696082 1516.9526 1.1393504 1.15949
24000 1.4103907 -3.8098769 -1.6945553 2290.0213 1.1962529 1.1686807
25000 1.4205929 -3.8266444 -1.6960213 3028.2748 1.1355183 1.1620482
26000 1.4148587 -3.8168728 -1.69485 3788.0858 1.1902606 1.1667503
27000 1.4226648 -3.8297832 -1.6960528 4580.4932 1.2378446 1.1769066
28000 1.4167854 -3.8205958 -1.6956834 5328.2357 1.2038835 1.1802787
29000 1.4208636 -3.8267081 -1.6956791 6077.036 1.1970863 1.1821462
30000 1.420575 -3.8256917 -1.6950955 6840.5407 1.1884497 1.1827766
31000 1.4233235 -3.8318045 -1.6970861 7576.9859 1.2088723 1.1851489
32000 1.418912 -3.8229407 -1.6948388 8319.9854 1.1604002 1.1830865
33000 1.4161289 -3.8211375 -1.6972096 9097.8598 1.1381183 1.1796274
34000 1.3982574 -3.7915345 -1.6944106 9819.5817 1.1809721 1.1797235
35000 1.4211314 -3.8267235 -1.6952929 10604.381 1.157812 1.1782627
36000 1.4181668 -3.8217718 -1.6947876 11332.942 1.1843186 1.1786412
37000 1.4092823 -3.8094817 -1.6958226 12068.55 1.1043391 1.1742705
38000 1.4220481 -3.8278441 -1.6950386 12815.406 1.1996255 1.1756791
39000 1.4146432 -3.8175526 -1.6958531 13565.714 1.149226 1.1742868
40000 1.4088356 -3.8079173 -1.694928 14309.801 1.1710565 1.1741253
41000 1.4058693 -3.8043119 -1.6957716 15067.894 1.1839862 1.1745949
Loop time of 22.0429 on 8 procs for 20000 steps with 8000 atoms
Performance: 391962.361 tau/day, 907.320 timesteps/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.8314 | 10.063 | 12.978 | 88.0 | 45.65
Neigh | 3.8802 | 5.2398 | 6.5269 | 52.7 | 23.77
Comm | 1.828 | 5.8112 | 10.14 | 160.2 | 26.36
Output | 0.00050211 | 0.00052819 | 0.00060391 | 0.1 | 0.00
Modify | 0.39313 | 0.41984 | 0.4453 | 3.3 | 1.90
Other | | 0.5084 | | | 2.31
Nlocal: 1000 ave 1188 max 810 min
Histogram: 2 1 1 0 0 0 0 1 1 2
Nghost: 2304.5 ave 2648 max 1970 min
Histogram: 3 1 0 0 0 0 0 0 1 3
Neighs: 27885.2 ave 36431 max 18556 min
Histogram: 2 2 0 0 0 0 0 0 1 3
Total # of neighbors = 223082
Ave neighs/atom = 27.8852
Neighbor list builds = 3626
Dangerous builds = 0
Total wall time: 0:00:44

208
examples/KAPPA/log.1Feb14.heatflux.g++.8
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LAMMPS (1 Feb 2014)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# Green-Kubo method via compute heat/flux and fix ave/correlate
# settings
variable x equal 10
variable y equal 10
variable z equal 10
variable rho equal 0.6
variable t equal 1.35
variable rc equal 2.5
#variable rho equal 0.85
#variable t equal 0.7
#variable rc equal 3.0
variable p equal 200 # correlation length
variable s equal 10 # sample interval
variable d equal $p*$s # dump interval
variable d equal 200*$s
variable d equal 200*10
# setup problem
units lj
atom_style atomic
lattice fcc ${rho}
lattice fcc 0.6
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
region box block 0 $x 0 $y 0 $z
region box block 0 10 0 $y 0 $z
region box block 0 10 0 10 0 $z
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (18.8207 18.8207 18.8207)
2 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
mass 1 1.0
velocity all create $t 87287
velocity all create 1.35 87287
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
# 1st equilibration run
fix 1 all nvt temp $t $t 0.5
fix 1 all nvt temp 1.35 $t 0.5
fix 1 all nvt temp 1.35 1.35 0.5
thermo 100
run 1000
Memory usage per processor = 2.10761 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.35 -4.1241917 0 -2.0996979 -3.1962625
100 1.1997886 -3.7796264 0 -1.9803934 0.4889458
200 1.271238 -3.7354981 0 -1.8291178 0.6873844
300 1.3346808 -3.6942841 0 -1.6927634 0.84332881
400 1.4020848 -3.7118654 0 -1.6092641 0.87670585
500 1.3723622 -3.6917931 0 -1.6337644 0.92172921
600 1.3451676 -3.7281573 0 -1.7109103 0.76029091
700 1.3021567 -3.6876155 0 -1.7348687 0.82721085
800 1.3489121 -3.7082852 0 -1.6854229 0.86438062
900 1.3708803 -3.6966168 0 -1.6408104 0.92141491
1000 1.3640742 -3.7075323 0 -1.6619325 0.86651245
Loop time of 0.464189 on 8 procs for 1000 steps with 4000 atoms
Pair time (%) = 0.235336 (50.6983)
Neigh time (%) = 0.104871 (22.5922)
Comm time (%) = 0.0896717 (19.3179)
Outpt time (%) = 0.000278324 (0.0599591)
Other time (%) = 0.0340324 (7.33158)
Nlocal: 500 ave 510 max 479 min
Histogram: 1 0 0 0 0 2 1 1 0 3
Nghost: 1519 ave 1539 max 1509 min
Histogram: 2 0 4 0 0 0 0 1 0 1
Neighs: 13553.8 ave 14051 max 12567 min
Histogram: 1 0 0 0 1 0 2 1 1 2
Total # of neighbors = 108430
Ave neighs/atom = 27.1075
Neighbor list builds = 155
Dangerous builds = 0
velocity all scale $t
velocity all scale 1.35
unfix 1
# thermal conductivity calculation
reset_timestep 0
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom virial
compute flux all heat/flux myKE myPE myStress
variable Jx equal c_flux[1]/vol
variable Jy equal c_flux[2]/vol
variable Jz equal c_flux[3]/vol
fix 1 all nve
fix JJ all ave/correlate $s $p $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
fix JJ all ave/correlate 10 $p $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
fix JJ all ave/correlate 10 200 $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
fix JJ all ave/correlate 10 200 2000 c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
variable scale equal $s*dt/$t/$t/vol
variable scale equal 10*dt/$t/$t/vol
variable scale equal 10*dt/1.35/$t/vol
variable scale equal 10*dt/1.35/1.35/vol
variable k11 equal trap(f_JJ[3])*${scale}
variable k11 equal trap(f_JJ[3])*4.11522633744856e-06
variable k22 equal trap(f_JJ[4])*${scale}
variable k22 equal trap(f_JJ[4])*4.11522633744856e-06
variable k33 equal trap(f_JJ[5])*${scale}
variable k33 equal trap(f_JJ[5])*4.11522633744856e-06
thermo $d
thermo 2000
thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
run 100000
Memory usage per processor = 3.25202 Mbytes
Step Temp Jx Jy Jz k11 k22 k33
0 1.35 0.012562011 -0.087289131 -0.037038204 0.014431103 0.69678942 0.125453
2000 1.3488448 -0.082686441 -0.05888314 0.15641005 9.6556473 4.8724539 39.132688
4000 1.3506828 0.055310422 -0.038254827 -0.081110393 3.4422239 2.3744865 7.4870977
6000 1.3324005 -0.10634454 -0.011811473 0.024430149 3.6509701 11.111829 2.7413472
8000 1.3465517 -0.13857537 -0.058386681 -0.013220164 6.5578792 6.6188014 3.6355334
10000 1.3454126 -0.044292047 -0.0055045339 -0.051726965 5.6920768 6.5502293 7.8616795
12000 1.3601798 0.18989029 -0.094977713 -0.059726722 5.2989118 8.8331032 7.972481
14000 1.3414287 0.0064865781 0.056749763 0.12775935 4.453589 6.4962925 7.9502167
16000 1.3249032 0.0023833148 0.0074389705 -0.12452498 5.2719354 6.164126 7.9937329
18000 1.3486905 0.24719037 -0.13649854 -0.051766952 3.7849335 5.4803263 6.9701788
20000 1.3572854 0.065005524 0.050772448 0.12768096 3.378611 5.6519702 7.1233623
22000 1.352508 -0.042516792 -0.070285937 -0.03879074 5.4717313 5.4908509 6.7550818
24000 1.3559841 -0.015758535 -0.098318418 0.027238601 6.0025309 5.2571093 6.0763852
26000 1.3442105 -0.047372234 0.036647228 -0.0052159685 6.8263856 4.6880057 6.1674781
28000 1.3522633 0.025172759 -0.016031105 0.12001218 6.3114313 4.1003669 5.7234478
30000 1.3593364 -0.044078855 0.0089521622 0.13278909 5.4296394 3.8944372 5.2946242
32000 1.3412479 -0.013107683 -0.089437735 -0.089978727 5.0171818 4.2838538 6.7869585
34000 1.3490784 -0.069828566 -0.018570411 0.018866428 5.1053455 3.7588109 5.7177159
36000 1.3630314 -0.017768864 0.067999673 0.016212961 5.3345297 3.6547014 5.5137046
38000 1.3564307 0.080792723 0.12705697 0.0023785227 5.1062587 3.6140422 5.5464591
40000 1.3546707 -0.030425013 0.17303248 -0.043210574 4.5874798 3.6033647 5.2304191
42000 1.3549663 0.10109213 -0.056635329 0.047756306 4.1930341 3.4788566 5.3322825
44000 1.3557286 0.0083871709 -0.08039758 0.0060697507 4.8453948 3.7579315 4.9727852
46000 1.3434325 0.048348267 -0.12296683 -0.012320195 4.6106895 3.6890294 4.6654515
48000 1.3520456 0.052909962 0.034221069 0.011730009 4.8097414 3.897061 4.5042484
50000 1.3480467 0.084823081 -0.093901701 0.091139125 4.6836534 3.7687187 4.4227539
52000 1.3473278 -0.12531922 -0.065273509 0.11638381 4.9413341 3.8765808 4.5227649
54000 1.3672128 0.11139848 0.034992201 -0.022009105 4.695476 3.5100821 5.0401349
56000 1.341716 0.12258667 -0.089117615 0.041707151 4.5195052 3.3873269 4.972056
58000 1.359732 0.063106883 -0.026013959 -0.026567969 4.3259743 3.6185582 4.721062
60000 1.3587911 0.05591296 -0.12996822 0.095669495 4.1958916 3.5682633 4.8210022
62000 1.3483527 0.048201166 -0.030400186 -0.018919104 4.0886746 3.7373315 4.8825261
64000 1.3531159 -0.10850158 -0.093503261 0.095145743 3.9415737 3.6946305 4.6787173
66000 1.3534358 0.0070478917 -0.13855333 -0.0028185444 3.989283 3.7940811 4.5848181
68000 1.3509679 -0.17972456 -0.15918151 -0.0092253402 4.1168514 3.689533 4.9348847
70000 1.3496439 0.025102803 -0.12080911 0.0099284856 4.0474517 3.6265752 4.8809921
72000 1.3382578 0.2235088 0.10981254 0.049251118 3.9059236 3.5169408 4.9528845
74000 1.3529223 0.012949328 0.11733173 0.12107899 4.0011677 3.4205986 4.7288624
76000 1.3442459 0.090185942 0.038587691 -0.023131667 3.9854752 3.4013375 4.7967661
78000 1.3423941 0.072006425 -0.009752458 0.058791886 3.87483 3.3898574 5.0306248
80000 1.3501112 -0.041057888 -0.11150244 -0.052369732 3.7648956 3.2969166 4.9549774
82000 1.358605 0.14838249 0.055223984 0.019108344 3.8986959 3.2556248 4.8872754
84000 1.357958 -0.087190849 0.029998974 0.089839797 4.4229469 3.2567955 4.7704664
86000 1.3340187 0.10824995 -0.013149214 0.042146878 3.9867785 3.2596969 4.6510248
88000 1.3428375 -0.033908572 -0.11261352 0.099056349 3.8033502 3.1706434 4.5328732
90000 1.3299574 0.055893064 -0.22127211 -0.042737098 3.7086395 3.118066 4.5709281
92000 1.3488719 0.040126575 0.074080804 0.019410656 3.8714376 3.0342566 4.4798044
94000 1.3621842 -0.087519994 0.028392459 0.047179422 3.7841822 3.1603745 4.3925598
96000 1.3578003 0.081511213 -0.0083540805 0.015204759 3.7117805 3.0610774 4.2886014
98000 1.3477904 -0.13903407 0.1146023 0.059812672 3.7445818 3.284994 4.3000618
100000 1.3583776 0.16015243 0.19139469 0.097636877 3.8265662 3.280556 4.2276263
Loop time of 49.3099 on 8 procs for 100000 steps with 4000 atoms
Pair time (%) = 26.5664 (53.8764)
Neigh time (%) = 10.8228 (21.9485)
Comm time (%) = 8.59585 (17.4323)
Outpt time (%) = 0.0256916 (0.0521023)
Other time (%) = 3.29916 (6.69066)
Nlocal: 500 ave 519 max 493 min
Histogram: 4 1 0 1 0 0 1 0 0 1
Nghost: 1547 ave 1558 max 1523 min
Histogram: 1 0 0 0 0 2 1 0 2 2
Neighs: 13544.8 ave 14633 max 13111 min
Histogram: 2 1 3 1 0 0 0 0 0 1
Total # of neighbors = 108358
Ave neighs/atom = 27.0895
Neighbor list builds = 16041
Dangerous builds = 0
variable kappa equal (v_k11+v_k22+v_k33)/3.0
print "running average conductivity: ${kappa}"
running average conductivity: 3.77824951481468

215
examples/KAPPA/log.1Feb14.langevin.g++.8
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LAMMPS (1 Feb 2014)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# thermostatting 2 regions via fix langevin
# settings
variable x equal 10
variable y equal 10
variable z equal 20
variable rho equal 0.6
variable t equal 1.35
variable rc equal 2.5
variable tlo equal 1.0
variable thi equal 1.70
#variable rho equal 0.85
#variable t equal 0.7
#variable rc equal 3.0
#variable tlo equal 0.3
#variable thi equal 1.0
# setup problem
units lj
atom_style atomic
lattice fcc ${rho}
lattice fcc 0.6
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
region box block 0 $x 0 $y 0 $z
region box block 0 10 0 $y 0 $z
region box block 0 10 0 10 0 $z
region box block 0 10 0 10 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
2 by 1 by 4 MPI processor grid
create_atoms 1 box
Created 8000 atoms
mass 1 1.0
velocity all create $t 87287
velocity all create 1.35 87287
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
# heat layers
region hot block INF INF INF INF 0 1
region cold block INF INF INF INF 10 11
compute Thot all temp/region hot
compute Tcold all temp/region cold
# 1st equilibration run
fix 1 all nvt temp $t $t 0.5
fix 1 all nvt temp 1.35 $t 0.5
fix 1 all nvt temp 1.35 1.35 0.5
thermo 100
run 1000
Memory usage per processor = 2.14238 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.35 -4.1241917 0 -2.0994448 -3.1961612
100 1.1819832 -3.7640881 0 -1.991335 0.53985757
200 1.2578365 -3.7395333 0 -1.8530144 0.69591862
300 1.3282971 -3.7215427 0 -1.7293461 0.79036065
400 1.3714367 -3.7043826 0 -1.6474847 0.85873226
500 1.3590952 -3.6707735 0 -1.6323855 0.99602024
600 1.3575117 -3.7118244 0 -1.6758114 0.81454305
700 1.3284444 -3.7075488 0 -1.7151313 0.81136596
800 1.3419994 -3.7155648 0 -1.7028172 0.82925677
900 1.3562214 -3.6965608 0 -1.662483 0.88908144
1000 1.3732016 -3.7100024 0 -1.6504575 0.83982823
Loop time of 0.862126 on 8 procs for 1000 steps with 8000 atoms
Pair time (%) = 0.482831 (56.0047)
Neigh time (%) = 0.221903 (25.739)
Comm time (%) = 0.104307 (12.0989)
Outpt time (%) = 0.000301003 (0.0349141)
Other time (%) = 0.0527841 (6.12256)
Nlocal: 1000 ave 1020 max 982 min
Histogram: 1 0 2 1 0 1 1 1 0 1
Nghost: 2299.5 ave 2331 max 2268 min
Histogram: 1 1 1 1 0 0 0 3 0 1
Neighs: 27122 ave 28382 max 26337 min
Histogram: 2 0 2 1 1 0 0 1 0 1
Total # of neighbors = 216976
Ave neighs/atom = 27.122
Neighbor list builds = 162
Dangerous builds = 0
velocity all scale $t
velocity all scale 1.35
unfix 1
# 2nd equilibration run
fix 1 all nve
fix hot all langevin ${thi} ${thi} 1.0 59804 tally yes
fix hot all langevin 1.7 ${thi} 1.0 59804 tally yes
fix hot all langevin 1.7 1.7 1.0 59804 tally yes
fix cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
fix cold all langevin 1 ${tlo} 1.0 287859 tally yes
fix cold all langevin 1 1 1.0 287859 tally yes
fix_modify hot temp Thot
fix_modify cold temp Tcold
variable tdiff equal c_Thot-c_Tcold
thermo_style custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff
thermo 1000
run 10000
Memory usage per processor = 2.60014 Mbytes
Step Temp Thot Tcold hot cold tdiff
1000 1.35 1.4312938 1.2955632 0 0 0.13573057
2000 1.360018 1.493833 1.108937 -0.12327246 0.1384129 0.38489598
3000 1.3375537 1.6938591 1.0191771 -0.21101663 0.26135778 0.67468203
4000 1.3233024 1.6026443 1.1480306 -0.26177493 0.34439263 0.45461365
5000 1.3107386 1.711679 1.05711 -0.31795111 0.42339093 0.65456895
6000 1.297964 1.6472939 0.95469459 -0.36994548 0.48890072 0.69259932
7000 1.3062638 1.5806629 1.080306 -0.43385121 0.56448283 0.50035689
8000 1.3062755 1.6415159 1.0407288 -0.48697483 0.62125026 0.60078705
9000 1.2850239 1.6253774 1.0574621 -0.50398307 0.66921986 0.56791525
10000 1.3035594 1.5362476 1.0681602 -0.56218263 0.71574454 0.46808735
11000 1.2973176 1.6350179 1.0433547 -0.61814256 0.75532475 0.59166313
Loop time of 11.3468 on 8 procs for 10000 steps with 8000 atoms
Pair time (%) = 4.81454 (42.4309)
Neigh time (%) = 2.27955 (20.0899)
Comm time (%) = 1.88988 (16.6557)
Outpt time (%) = 0.000712395 (0.00627838)
Other time (%) = 2.36209 (20.8173)
Nlocal: 1000 ave 1135 max 867 min
Histogram: 2 0 2 0 0 0 0 2 1 1
Nghost: 2314.38 ave 2559 max 2067 min
Histogram: 1 1 2 0 0 0 0 2 0 2
Neighs: 27392.4 ave 33962 max 20582 min
Histogram: 2 0 2 0 0 0 0 1 1 2
Total # of neighbors = 219139
Ave neighs/atom = 27.3924
Neighbor list builds = 1666
Dangerous builds = 0
# thermal conductivity calculation
# reset langevin thermostats to zero energy accumulation
compute ke all ke/atom
variable temp atom c_ke/1.5
fix hot all langevin ${thi} ${thi} 1.0 59804 tally yes
fix hot all langevin 1.7 ${thi} 1.0 59804 tally yes
fix hot all langevin 1.7 1.7 1.0 59804 tally yes
fix cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
fix cold all langevin 1 ${tlo} 1.0 287859 tally yes
fix cold all langevin 1 1 1.0 287859 tally yes
fix_modify hot temp Thot
fix_modify cold temp Tcold
fix ave all ave/time 10 100 1000 v_tdiff ave running
thermo_style custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave
fix 2 all ave/spatial 10 100 1000 z lower 0.05 v_temp file profile.langevin units reduced
run 20000
Memory usage per processor = 2.60106 Mbytes
Step Temp Thot Tcold hot cold tdiff ave
11000 1.2973176 1.6350179 1.0433547 0 0 0.59166313 0
12000 1.3039677 1.6419813 1.0477757 -0.046382646 0.056968333 0.5942056 0.59568325
13000 1.3110256 1.5869209 1.0158888 -0.094090387 0.10445821 0.57103213 0.57629599
14000 1.293218 1.6629496 1.1121109 -0.11375822 0.15128701 0.55083862 0.5707904
15000 1.2811676 1.6722435 1.0942864 -0.14415448 0.20239116 0.57795712 0.5695191
16000 1.2791266 1.5765255 1.1007618 -0.2014815 0.2427606 0.47576367 0.56997652
17000 1.2622984 1.6433371 1.0358679 -0.22929967 0.29997963 0.60746917 0.56431552
18000 1.2795857 1.7006846 1.0702476 -0.29495954 0.3304481 0.630437 0.57298103
19000 1.2794851 1.5796065 1.0383562 -0.3325748 0.3825079 0.54125035 0.567257
20000 1.3013271 1.6682287 1.0624636 -0.40206115 0.42100016 0.60576507 0.57276102
21000 1.277446 1.5408233 1.0275158 -0.43012499 0.48360636 0.51330753 0.57340191
22000 1.3031703 1.6370721 1.0356931 -0.51126428 0.52836134 0.60137903 0.57578211
23000 1.2719643 1.4882391 0.98769817 -0.55845167 0.61243478 0.50054093 0.57457152
24000 1.2931956 1.5814171 1.0586513 -0.60691503 0.63563787 0.52276581 0.57294037
25000 1.2846646 1.7006525 1.0209227 -0.64068901 0.67962894 0.67972988 0.57312421
26000 1.2711788 1.6697984 0.99699462 -0.67019827 0.73853772 0.67280381 0.57276936
27000 1.2732777 1.6285951 1.1302554 -0.70566156 0.76748898 0.49833966 0.57255348
28000 1.2831929 1.5938242 1.0977096 -0.75144205 0.81168035 0.49611462 0.57460785
29000 1.2792513 1.4854998 1.0013453 -0.79831201 0.86425474 0.4841545 0.57139895
30000 1.2677402 1.6009684 1.092679 -0.83584426 0.90606945 0.50828948 0.57156924
31000 1.2720929 1.5851445 1.0736744 -0.87730401 0.95644174 0.51147013 0.5717415
Loop time of 23.7017 on 8 procs for 20000 steps with 8000 atoms
Pair time (%) = 9.6584 (40.7498)
Neigh time (%) = 4.57821 (19.3159)
Comm time (%) = 4.45101 (18.7793)
Outpt time (%) = 0.00194073 (0.00818813)
Other time (%) = 5.01215 (21.1468)
Nlocal: 1000 ave 1121 max 880 min
Histogram: 2 2 0 0 0 0 0 0 2 2
Nghost: 2281.5 ave 2471 max 2073 min
Histogram: 3 1 0 0 0 0 0 0 0 4
Neighs: 27428.1 ave 33179 max 21152 min
Histogram: 2 2 0 0 0 0 0 0 1 3
Total # of neighbors = 219425
Ave neighs/atom = 27.4281
Neighbor list builds = 3338
Dangerous builds = 0

200
examples/KAPPA/log.1Feb14.mp.g++.8
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@ -1,200 +0,0 @@
LAMMPS (1 Feb 2014)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# Muller-Plathe method via fix thermal_conductivity
# settings
variable x equal 10
variable y equal 10
variable z equal 20
variable rho equal 0.6
variable t equal 1.35
variable rc equal 2.5
#variable rho equal 0.85
#variable t equal 0.7
#variable rc equal 3.0
# setup problem
units lj
atom_style atomic
lattice fcc ${rho}
lattice fcc 0.6
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
region box block 0 $x 0 $y 0 $z
region box block 0 10 0 $y 0 $z
region box block 0 10 0 10 0 $z
region box block 0 10 0 10 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
2 by 1 by 4 MPI processor grid
create_atoms 1 box
Created 8000 atoms
mass 1 1.0
velocity all create $t 87287
velocity all create 1.35 87287
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
# 1st equilibration run
fix 1 all nvt temp $t $t 0.5
fix 1 all nvt temp 1.35 $t 0.5
fix 1 all nvt temp 1.35 1.35 0.5
thermo 100
run 1000
Memory usage per processor = 2.14238 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.35 -4.1241917 0 -2.0994448 -3.1961612
100 1.1819832 -3.7640881 0 -1.991335 0.53985757
200 1.2578365 -3.7395333 0 -1.8530144 0.69591862
300 1.3282971 -3.7215427 0 -1.7293461 0.79036065
400 1.3714367 -3.7043826 0 -1.6474847 0.85873226
500 1.3590952 -3.6707735 0 -1.6323855 0.99602024
600 1.3575117 -3.7118244 0 -1.6758114 0.81454305
700 1.3284444 -3.7075488 0 -1.7151313 0.81136596
800 1.3419994 -3.7155648 0 -1.7028172 0.82925677
900 1.3562214 -3.6965608 0 -1.662483 0.88908144
1000 1.3732016 -3.7100024 0 -1.6504575 0.83982823
Loop time of 0.862547 on 8 procs for 1000 steps with 8000 atoms
Pair time (%) = 0.478427 (55.4668)
Neigh time (%) = 0.220096 (25.517)
Comm time (%) = 0.10999 (12.7517)
Outpt time (%) = 0.00030601 (0.0354775)
Other time (%) = 0.0537277 (6.22896)
Nlocal: 1000 ave 1020 max 982 min
Histogram: 1 0 2 1 0 1 1 1 0 1
Nghost: 2299.5 ave 2331 max 2268 min
Histogram: 1 1 1 1 0 0 0 3 0 1
Neighs: 27122 ave 28382 max 26337 min
Histogram: 2 0 2 1 1 0 0 1 0 1
Total # of neighbors = 216976
Ave neighs/atom = 27.122
Neighbor list builds = 162
Dangerous builds = 0
velocity all scale $t
velocity all scale 1.35
unfix 1
# 2nd equilibration run
compute ke all ke/atom
variable temp atom c_ke/1.5
fix 1 all nve
fix 2 all ave/spatial 10 100 1000 z lower 0.05 v_temp file profile.mp units reduced
fix 3 all thermal/conductivity 10 z 20
variable tdiff equal f_2[11][3]-f_2[1][3]
thermo_style custom step temp epair etotal f_3 v_tdiff
thermo 1000
run 20000
Memory usage per processor = 2.1433 Mbytes
Step Temp E_pair TotEng 3 tdiff
1000 1.35 -3.7100024 -1.6852556 0 0
2000 1.3488972 -3.708116 -1.6850231 877.52861 0.25969396
3000 1.3658991 -3.735305 -1.6867124 1757.5984 0.40713773
4000 1.3660888 -3.7368211 -1.6879441 2599.882 0.63176318
5000 1.3702365 -3.7439731 -1.6888753 3417.2012 0.68861496
6000 1.3802047 -3.7607288 -1.6906806 4247.6303 0.8258624
7000 1.3981219 -3.7883507 -1.69143 5036.1985 0.90753031
8000 1.3968279 -3.7880683 -1.6930884 5807.0759 0.99392296
9000 1.3960267 -3.7866214 -1.6928431 6584.6398 1.0833481
10000 1.4067029 -3.8038141 -1.6940234 7372.3357 1.0359437
11000 1.4037578 -3.7984096 -1.6930361 8133.4913 1.0506296
12000 1.4112365 -3.8109671 -1.6943769 8908.2356 1.1033313
13000 1.4066326 -3.8036805 -1.6939953 9674.5783 1.1492152
14000 1.4136249 -3.8155288 -1.6953566 10429.951 1.1101441
15000 1.402741 -3.7983064 -1.6944579 11194.927 1.1163151
16000 1.412565 -3.8138997 -1.695317 11931.815 1.2199073
17000 1.4023686 -3.7975376 -1.6942476 12695.415 1.1800489
18000 1.4200941 -3.8257695 -1.6958947 13456.945 1.1583648
19000 1.4016117 -3.7972936 -1.6951388 14216.201 1.1846518
20000 1.4105524 -3.8113272 -1.6957631 14977.184 1.2831156
21000 1.4068217 -3.8054214 -1.6954526 15739.554 1.147926
Loop time of 20.7938 on 8 procs for 20000 steps with 8000 atoms
Pair time (%) = 9.73079 (46.7967)
Neigh time (%) = 4.8843 (23.4893)
Comm time (%) = 5.15718 (24.8016)
Outpt time (%) = 0.000606179 (0.0029152)
Other time (%) = 1.02088 (4.90955)
Nlocal: 1000 ave 1176 max 820 min
Histogram: 2 2 0 0 0 0 0 0 2 2
Nghost: 2318.88 ave 2663 max 1967 min
Histogram: 3 1 0 0 0 0 0 0 2 2
Neighs: 27860.2 ave 36167 max 18992 min
Histogram: 3 1 0 0 0 0 0 0 0 4
Total # of neighbors = 222882
Ave neighs/atom = 27.8603
Neighbor list builds = 3543
Dangerous builds = 0
# thermal conductivity calculation
# reset fix thermal/conductivity to zero energy accumulation
fix 3 all thermal/conductivity 10 z 20
fix ave all ave/time 1 1 1000 v_tdiff ave running
thermo_style custom step temp epair etotal f_3 v_tdiff f_ave
run 20000
Memory usage per processor = 2.33403 Mbytes
Step Temp E_pair TotEng 3 tdiff ave
21000 1.4068217 -3.8054214 -1.6954526 0 1.147926 1.147926
22000 1.3967994 -3.7893902 -1.694453 767.0398 1.1920832 1.1700046
23000 1.4170976 -3.822137 -1.6967564 1517.2987 1.1545977 1.164869
24000 1.4202355 -3.8249732 -1.6948862 2277.7333 1.1750006 1.1674019
25000 1.4205956 -3.8264595 -1.6958326 3028.6456 1.168964 1.1677143
26000 1.4105028 -3.8099425 -1.6944527 3771.4445 1.1535799 1.1653586
27000 1.4121218 -3.8137079 -1.6957899 4524.007 1.1582776 1.164347
28000 1.4073732 -3.8055739 -1.6947781 5297.7257 1.1390419 1.1611839
29000 1.3935065 -3.7848004 -1.6948019 6040.6442 1.106954 1.1551583
30000 1.4126276 -3.8136783 -1.6950018 6777.7617 1.122798 1.1519223
31000 1.4220569 -3.8292934 -1.6964746 7529.6983 1.1517202 1.1519039
32000 1.4157206 -3.8184427 -1.6951273 8293.9624 1.1600224 1.1525805
33000 1.4300672 -3.8403564 -1.6955237 9056.1085 1.1581575 1.1530095
34000 1.4114669 -3.8123726 -1.6954368 9827.2549 1.169357 1.1541771
35000 1.4087756 -3.8085583 -1.695659 10582.235 1.254384 1.1608576
36000 1.4071234 -3.8063392 -1.695918 11335.664 1.1886748 1.1625962
37000 1.4150044 -3.8175559 -1.6953146 12067.647 1.1452763 1.1615774
38000 1.4208299 -3.8269499 -1.6959714 12785.237 1.1689649 1.1619878
39000 1.4132869 -3.8147648 -1.6950995 13548.517 1.1134294 1.1594321
40000 1.4071151 -3.8068479 -1.6964391 14307.339 1.1772366 1.1603223
41000 1.4126121 -3.8153948 -1.6967416 15087.11 1.1408062 1.159393
Loop time of 21.9152 on 8 procs for 20000 steps with 8000 atoms
Pair time (%) = 9.77976 (44.6255)
Neigh time (%) = 5.01423 (22.8802)
Comm time (%) = 6.03064 (27.5181)
Outpt time (%) = 0.000575513 (0.00262609)
Other time (%) = 1.08999 (4.97365)
Nlocal: 1000 ave 1167 max 820 min
Histogram: 3 1 0 0 0 0 0 0 0 4
Nghost: 2292.38 ave 2619 max 1989 min
Histogram: 4 0 0 0 0 0 0 0 2 2
Neighs: 27929.9 ave 37820 max 19105 min
Histogram: 4 0 0 0 0 0 0 0 3 1
Total # of neighbors = 223439
Ave neighs/atom = 27.9299
Neighbor list builds = 3624
Dangerous builds = 0

17965
examples/MC/log.6Jun14.mc.g++.1 → examples/MC/log.13Oct16.mc.g++.1
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436
examples/VISCOSITY/log.13Oct16.einstein.2d.g++.1 Normal file
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LAMMPS (13 Oct 2016)
# sample LAMMPS input script for viscosity of 2d LJ liquid
# Einstein form of Green-Kubo
# settings
variable x equal 20
variable y equal 20
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
variable p equal 400 # correlation length
variable s equal 5 # sample interval
variable d equal $p*$s # dump interval
variable d equal 400*$s
variable d equal 400*5
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
lattice sq2 ${rho}
lattice sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox block 0 $x 0 $y -0.1 0.1
region simbox block 0 20 0 $y -0.1 0.1
region simbox block 0 20 0 20 -0.1 0.1
create_box 1 simbox
Created orthogonal box = (0 0 -0.182574) to (36.5148 36.5148 0.182574)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff * * 1 1
mass * 1.0
velocity all create $t 97287
velocity all create 1 97287
# equilibration run
fix 1 all nve
fix 2 all langevin $t $t 0.1 498094
fix 2 all langevin 1 $t 0.1 498094
fix 2 all langevin 1 1 0.1 498094
fix 3 all enforce2d
thermo $d
thermo 2000
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 27 27 1
Memory usage per processor = 2.47956 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.56617 -1.535262
2000 1.0164992 -1.6006146 0 -0.58538603 0.88642098
4000 1.0955206 -1.6156387 0 -0.52148756 0.94410568
6000 1.0384014 -1.6029223 0 -0.5658189 0.82862123
8000 1.0035814 -1.5749989 0 -0.57267191 1.1514978
10000 1.0149864 -1.5834783 0 -0.56976064 0.94535991
Loop time of 1.69247 on 1 procs for 10000 steps with 800 atoms
Performance: 2552489.906 tau/day, 5908.541 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.93981 | 0.93981 | 0.93981 | 0.0 | 55.53
Neigh | 0.22459 | 0.22459 | 0.22459 | 0.0 | 13.27
Comm | 0.028411 | 0.028411 | 0.028411 | 0.0 | 1.68
Output | 5.6267e-05 | 5.6267e-05 | 5.6267e-05 | 0.0 | 0.00
Modify | 0.4531 | 0.4531 | 0.4531 | 0.0 | 26.77
Other | | 0.04649 | | | 2.75
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 262 ave 262 max 262 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5587 ave 5587 max 5587 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5587
Ave neighs/atom = 6.98375
Neighbor list builds = 1101
Dangerous builds = 0
velocity all scale $t
velocity all scale 1
unfix 2
# Einstein viscosity calculation
reset_timestep 0
# Define distinct components of symmetric traceless stress tensor
variable pxy equal pxy
variable pxx equal pxx-press
fix avstress all ave/time $s $p $d v_pxy v_pxx ave one file einstein.dat
fix avstress all ave/time 5 $p $d v_pxy v_pxx ave one file einstein.dat
fix avstress all ave/time 5 400 $d v_pxy v_pxx ave one file einstein.dat
fix avstress all ave/time 5 400 2000 v_pxy v_pxx ave one file einstein.dat
# Diagonal components of SS are larger by factor 2-2/d,
# which is 4/3 for d=3, but 1 for d=2.
# See Daivis and Evans, J.Chem.Phys, 100, 541-547 (1994)
variable scale equal vol/(2.0*$t*dt*$d)
variable scale equal vol/(2.0*1*dt*$d)
variable scale equal vol/(2.0*1*dt*2000)
variable diagfac equal 2-2/2
variable deltasqxy equal (f_avstress[1]*$d*dt)^2
variable deltasqxy equal (f_avstress[1]*2000*dt)^2
variable deltasqxx equal (f_avstress[2]*$d*dt)^2/${diagfac}
variable deltasqxx equal (f_avstress[2]*2000*dt)^2/${diagfac}
variable deltasqxx equal (f_avstress[2]*2000*dt)^2/1
# compute mean square displacements as running averages
fix avdeltasq all ave/time $d 1 $d v_deltasqxy v_deltasqxx ave running
fix avdeltasq all ave/time 2000 1 $d v_deltasqxy v_deltasqxx ave running
fix avdeltasq all ave/time 2000 1 2000 v_deltasqxy v_deltasqxx ave running
# convert to viscosities
variable vxy equal f_avdeltasq[1]*${scale}
variable vxy equal f_avdeltasq[1]*66.6666666666667
variable vxx equal f_avdeltasq[2]*${scale}
variable vxx equal f_avdeltasq[2]*66.6666666666667
thermo_style custom step temp pe press pxy v_vxy v_vxx
run 500000
Memory usage per processor = 2.47956 Mbytes
Step Temp PotEng Press Pxy v_vxy v_vxx
0 1 -1.5834783 0.93637929 0.013123478 0 0
2000 0.99103273 -1.5739065 0.96182762 0.032871709 0.41926791 0.38581032
4000 1.0416298 -1.6251611 0.9238985 0.02532039 0.35795442 0.29928221
6000 1.0033402 -1.5867776 1.049074 0.056300627 0.29372872 1.5092739
8000 1.0003681 -1.5843096 1.1886635 0.019361031 0.48384709 1.8517115
10000 1.0195921 -1.6022966 0.9009639 -0.075997173 0.67256908 1.5843784
12000 1.0026283 -1.5853941 0.90425907 -0.10655349 0.60161687 1.3594007
14000 1.0062891 -1.5897213 1.120094 0.078261625 0.97450451 1.2282067
16000 0.97921785 -1.5613249 1.056538 -0.27861922 0.87752053 1.1451558
18000 1.012419 -1.5961271 1.0278053 0.022229371 1.5009689 1.0422023
20000 1.0117709 -1.5948272 0.97722275 0.0075466982 1.3698953 0.99945232
22000 1.0008808 -1.5833286 1.0572608 0.087832931 1.3110237 0.93493793
24000 1.0002975 -1.5837822 1.0118667 -0.068081725 1.2215237 0.93661445
26000 0.98509665 -1.5675621 1.1898824 0.21810836 1.3153554 0.87730504
28000 0.9891689 -1.5722635 1.1456688 0.12141752 1.490948 0.90642777
30000 1.0071582 -1.5908732 0.96554132 0.017641823 1.454491 0.95707045
32000 1.0076807 -1.5909133 1.1047186 0.044265263 1.4451215 0.9167669
34000 0.95874174 -1.54087 1.362955 -0.14025695 1.4687664 0.89946229
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470000 0.99238797 -1.5760561 1.0832266 -0.041876018 0.88670298 1.0888446
472000 1.0169724 -1.6006383 0.90761167 -0.12563948 0.89441625 1.0855102
474000 1.0025279 -1.585529 1.0050948 0.043906331 0.89302764 1.0812461
476000 0.99536702 -1.5780191 0.89444096 0.14592241 0.89683614 1.077964
478000 0.98866565 -1.5720704 1.1754384 0.048623957 0.89407347 1.0917047
480000 0.98572668 -1.5687903 0.90601784 -0.26268845 0.89230666 1.087992
482000 1.014423 -1.59804 0.98209159 0.069121411 0.89149689 1.0836584
484000 1.0090002 -1.5916356 0.9957509 -0.09367221 0.9170021 1.1011703
486000 0.99962993 -1.5834522 1.0977267 -0.15748171 0.91654366 1.0989507
488000 0.98394002 -1.5667132 1.0400853 -0.054203925 0.91811726 1.1150492
490000 1.0216626 -1.6057027 0.95663779 -0.076119485 0.91665173 1.1116068
492000 0.98450357 -1.5677506 1.2970783 -0.1684919 0.91932358 1.1071252
494000 1.022591 -1.6056696 0.82845032 -0.10149084 0.91562447 1.1057524
496000 1.0317595 -1.6157971 0.79413446 0.12970065 0.92063013 1.102386
498000 1.0375923 -1.6219641 1.0063299 0.0090318777 0.94925707 1.1005841
500000 1.009533 -1.5922817 0.92939388 0.051496977 0.95185481 1.0969849
Loop time of 70.5997 on 1 procs for 500000 steps with 800 atoms
Performance: 3059502.219 tau/day, 7082.181 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 47.621 | 47.621 | 47.621 | 0.0 | 67.45
Neigh | 12.109 | 12.109 | 12.109 | 0.0 | 17.15
Comm | 1.5187 | 1.5187 | 1.5187 | 0.0 | 2.15
Output | 0.0026052 | 0.0026052 | 0.0026052 | 0.0 | 0.00
Modify | 6.9725 | 6.9725 | 6.9725 | 0.0 | 9.88
Other | | 2.375 | | | 3.36
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 271 ave 271 max 271 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5622 ave 5622 max 5622 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5622
Ave neighs/atom = 7.0275
Neighbor list builds = 59121
Dangerous builds = 0
variable etaxy equal v_vxy
variable etaxx equal v_vxx
variable eta equal 0.5*(${etaxy}+${etaxx})
variable eta equal 0.5*(0.951854813936217+${etaxx})
variable eta equal 0.5*(0.951854813936217+1.09698487634149)
print "running average viscosity: ${eta}"
running average viscosity: 1.02441984513885
Total wall time: 0:01:12

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LAMMPS (13 Oct 2016)
# sample LAMMPS input script for viscosity of 2d LJ liquid
# Green-Kubo method via fix ave/correlate
# settings
variable x equal 20
variable y equal 20
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
variable p equal 400 # correlation length
variable s equal 5 # sample interval
variable d equal $p*$s # dump interval
variable d equal 400*$s
variable d equal 400*5
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
lattice sq2 ${rho}
lattice sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox block 0 $x 0 $y -0.1 0.1
region simbox block 0 20 0 $y -0.1 0.1
region simbox block 0 20 0 20 -0.1 0.1
create_box 1 simbox
Created orthogonal box = (0 0 -0.182574) to (36.5148 36.5148 0.182574)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff * * 1 1
mass * 1.0
velocity all create $t 97287
velocity all create 1 97287
# equilibration run
fix 1 all nve
fix 2 all langevin $t $t 0.1 498094
fix 2 all langevin 1 $t 0.1 498094
fix 2 all langevin 1 1 0.1 498094
fix 3 all enforce2d
thermo $d
thermo 2000
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 27 27 1
Memory usage per processor = 2.47956 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.56617 -1.535262
2000 1.0164992 -1.6006146 0 -0.58538603 0.88642098
4000 1.0955206 -1.6156387 0 -0.52148756 0.94410568
6000 1.0384014 -1.6029223 0 -0.5658189 0.82862123
8000 1.0035814 -1.5749989 0 -0.57267191 1.1514978
10000 1.0149864 -1.5834783 0 -0.56976064 0.94535991
Loop time of 1.68923 on 1 procs for 10000 steps with 800 atoms
Performance: 2557381.154 tau/day, 5919.864 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.93939 | 0.93939 | 0.93939 | 0.0 | 55.61
Neigh | 0.22535 | 0.22535 | 0.22535 | 0.0 | 13.34
Comm | 0.028255 | 0.028255 | 0.028255 | 0.0 | 1.67
Output | 4.6253e-05 | 4.6253e-05 | 4.6253e-05 | 0.0 | 0.00
Modify | 0.44989 | 0.44989 | 0.44989 | 0.0 | 26.63
Other | | 0.0463 | | | 2.74
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 262 ave 262 max 262 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5587 ave 5587 max 5587 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5587
Ave neighs/atom = 6.98375
Neighbor list builds = 1101
Dangerous builds = 0
velocity all scale $t
velocity all scale 1
unfix 2
# Green-Kubo viscosity calculation
reset_timestep 0
# Define distinct components of symmetric traceless stress tensor
variable pxy equal pxy
variable pxx equal pxx-press
fix SS all ave/correlate $s $p $d v_pxy v_pxx type auto file profile.gk.2d ave running
fix SS all ave/correlate 5 $p $d v_pxy v_pxx type auto file profile.gk.2d ave running
fix SS all ave/correlate 5 400 $d v_pxy v_pxx type auto file profile.gk.2d ave running
fix SS all ave/correlate 5 400 2000 v_pxy v_pxx type auto file profile.gk.2d ave running
# Diagonal components of SS are larger by factor 2-2/d,
# which is 4/3 for d=3, but 1 for d=2.
# See Daivis and Evans, J.Chem.Phys, 100, 541-547 (1994)
variable scale equal 1.0/$t*vol*$s*dt
variable scale equal 1.0/1*vol*$s*dt
variable scale equal 1.0/1*vol*5*dt
variable diagfac equal 2-2/2
variable vxy equal trap(f_SS[3])*${scale}
variable vxy equal trap(f_SS[3])*33.3333333333333
variable vxx equal trap(f_SS[4])*${scale}/${diagfac}
variable vxx equal trap(f_SS[4])*33.3333333333333/${diagfac}
variable vxx equal trap(f_SS[4])*33.3333333333333/1
thermo_style custom step temp press pxy v_vxy v_vxx
run 500000
Memory usage per processor = 2.47956 Mbytes
Step Temp Press Pxy v_vxy v_vxx
0 1 0.93637929 0.013123478 0.0028704278 3.6139711e-05
2000 0.99103273 0.96182762 0.032871709 1.0973353 1.7302859
4000 1.0416298 0.9238985 0.02532039 -0.51174928 1.3585307
6000 1.0033402 1.049074 0.056300627 -0.52973835 2.1985256
8000 1.0003681 1.1886635 0.019361031 -0.2525203 1.5354203
10000 1.0195921 0.9009639 -0.075997173 0.77178738 1.9426534
12000 1.0026283 0.90425907 -0.10655349 0.59485093 1.4709129
14000 1.0062891 1.120094 0.078261625 1.3430022 1.4154697
16000 0.97921785 1.056538 -0.27861922 1.1095264 1.2162698
18000 1.012419 1.0278053 0.022229371 1.7339307 1.1123441
20000 1.0117709 0.97722275 0.0075466982 1.7749122 1.0704588
22000 1.0008808 1.0572608 0.087832931 1.6516858 1.0614696
24000 1.0002975 1.0118667 -0.068081725 1.4708723 1.0635481
26000 0.98509665 1.1898824 0.21810836 1.5759129 1.101463
28000 0.9891689 1.1456688 0.12141752 1.7952721 1.1441876
30000 1.0071582 0.96554132 0.017641823 1.5696844 1.207463
32000 1.0076807 1.1047186 0.044265263 1.6946819 1.0605558
34000 0.95874174 1.362955 -0.14025695 1.7962468 1.0166685
36000 0.99528173 1.0970028 -0.016714523 1.6378502 1.0580616
38000 1.0124371 0.99493986 -0.041410673 1.5728087 1.0689583
40000 1.0141237 0.98549019 0.047454345 1.5733219 1.0153622
42000 1.0274867 0.93801507 0.089635945 1.5765417 0.99165386
44000 0.98700259 0.94306661 -0.045695708 1.7023399 0.99608779
46000 1.0080948 1.0304791 -0.0046135743 1.738355 0.87443113
48000 0.97227783 1.1829894 0.042219544 1.6953772 0.82755164
50000 0.99046716 1.0095618 0.018697031 1.6358006 0.79907178
52000 1.0129697 0.88794241 -0.045990748 1.6257284 0.8693729
54000 1.0013276 1.0246693 0.012464296 1.711089 0.85652021
56000 1.0385716 0.75426191 -0.04775685 1.6576515 0.80114077
58000 1.0107757 1.0239619 0.029529278 1.62731 1.01175
60000 1.0177033 0.94723439 -0.16871762 1.6492387 1.3267438
62000 1.0210737 1.0225179 0.079638703 1.5703895 1.3460163
64000 1.0106132 1.0188777 0.02699431 1.5335146 1.3032641
66000 0.98531307 1.1224354 -0.0069578014 1.6159073 1.2791611
68000 0.99450728 1.3016366 0.056607824 1.560555 1.2757996
70000 0.98874589 1.0724556 -0.022405835 1.5275425 1.2439185
72000 1.0108814 0.92375729 -0.12669224 1.5118684 1.2223259
74000 1.0098348 1.0635024 -0.12956833 1.4818607 1.2161456
76000 1.0089021 0.98626851 -0.20311631 1.4768989 1.2153601
78000 1.002405 1.008097 -0.089615503 1.4499417 1.1460696
80000 1.0266582 1.0493411 0.16631226 1.4254227 1.1765198
82000 1.01242 0.81710829 0.18713063 1.3872432 1.1213607
84000 1.0262474 1.1125949 -0.0012088503 1.464111 1.1215723
86000 0.99599827 1.0337621 -0.0056500173 1.4658272 1.1000357
88000 0.98713531 1.0665747 -0.10237303 1.5900602 1.0774497
90000 1.0156011 0.96906164 0.13894564 1.5880395 1.1005107
92000 1.0306883 0.78929887 0.0089544803 1.5445295 1.1172449
94000 0.98455669 1.1917323 0.025629181 1.4984833 1.1347838
96000 0.99528576 1.1055136 0.020277014 1.4904339 1.0982899
98000 1.0504589 0.99135546 -0.051989636 1.455444 1.0661495
100000 0.98210335 1.0867432 0.091525725 1.4218731 1.0813261
102000 1.0316494 1.1350259 0.072311903 1.3978862 1.0946066
104000 1.0292338 0.83829357 -0.04098328 1.3809297 1.1853511
106000 0.98153521 1.0653974 -4.3227008e-05 1.3544205 1.2098378
108000 1.0074159 1.0048635 0.1947269 1.3858614 1.2974418
110000 1.0007684 1.1603181 0.13820163 1.3549744 1.3665589
112000 0.98637814 1.0037644 0.049907343 1.3424521 1.3434275
114000 0.99310586 1.0896413 -0.079352378 1.3189065 1.3424599
116000 0.98829858 0.87861443 0.05118496 1.3323643 1.2973572
118000 1.01049 0.96002545 -0.12320659 1.3042553 1.3143529
120000 1.0218378 0.89637436 0.02750584 1.2880273 1.4129925
122000 1.0263547 0.95854694 0.0034110405 1.2998558 1.4125761
124000 0.9899202 1.0492908 -0.13855042 1.2885462 1.4024599
126000 0.98192121 1.1372352 0.16313842 1.2742073 1.3858109
128000 1.002862 0.97650147 0.048928455 1.3089319 1.4032307
130000 0.99785761 0.93146735 0.026478401 1.2798809 1.4133812
132000 0.98956541 0.96523389 -0.10052306 1.2753991 1.4194387
134000 1.0019397 1.0447894 0.13871691 1.2573725 1.4193379
136000 1.0321449 1.1072168 -0.15369414 1.2214357 1.4798406
138000 1.0239483 0.82920716 -0.011872404 1.1990447 1.4537855
140000 1.0082907 1.0012771 0.027192581 1.2017711 1.488733
142000 1.0007865 1.0399048 -0.096251148 1.2255281 1.4836706
144000 1.0001664 1.0071962 -0.083449668 1.188732 1.4747949
146000 1.0202238 1.0702284 -0.063595518 1.1747017 1.457276
148000 1.0248683 1.0227875 0.069198975 1.1641817 1.4482984
150000 1.0127614 0.80897516 0.0044443031 1.1486331 1.4389959
152000 1.0028044 1.0857002 -0.059930891 1.1448366 1.4107488
154000 1.0149836 0.82631625 0.085962962 1.1469054 1.3899228
156000 0.99818966 1.035248 -0.029178797 1.1381571 1.380388
158000 1.0023756 0.94465038 -0.056571392 1.1308549 1.3564606
160000 0.99847665 1.0656894 -0.022026678 1.1397154 1.4343558
162000 0.98084763 1.2446958 0.097934009 1.1180528 1.3973883
164000 0.98358665 1.1626742 -0.010830507 1.1042107 1.3740411
166000 1.0176133 0.91335665 0.054966014 1.1205556 1.3965323
168000 1.0252828 1.0562376 0.025372153 1.1392262 1.4162518
170000 1.0429701 0.78042973 -0.088860018 1.1624209 1.4180095
172000 1.0167826 0.93307169 -0.0028786839 1.1482597 1.4102599
174000 1.0067129 0.93660255 0.13405338 1.1765833 1.3906822
176000 1.0142368 1.1376546 -0.039887725 1.1490071 1.3803357
178000 1.0337679 0.88782002 -0.013087286 1.1537575 1.4217567
180000 0.96700375 1.2700192 -0.17359042 1.1782075 1.4515137
182000 1.0128669 1.0325786 -0.11340517 1.1601019 1.4525292
184000 1.0016786 1.2423822 -0.04019647 1.1535732 1.4506038
186000 1.0068219 0.91016442 0.12827957 1.140122 1.4814336
188000 1.0111052 0.84190116 0.11675343 1.1385292 1.4872393
190000 1.0428535 0.84579508 0.074521906 1.126706 1.5039655
192000 0.98196941 1.1089098 0.10878744 1.1159363 1.4826447
194000 1.0060461 1.0637631 0.0094883212 1.1126571 1.4825394
196000 1.009729 1.0375371 0.001016821 1.104084 1.4675566
198000 1.0130466 0.94423285 -0.065299989 1.0985735 1.4613693
200000 0.99556457 1.0479236 -0.078093695 1.087735 1.4629234
202000 1.0024053 1.0110919 -0.011771169 1.0789047 1.4423084
204000 1.0487373 0.96913936 0.092389554 1.0752111 1.4428081
206000 1.0040089 0.87055365 -0.0029267837 1.0892902 1.4295861
208000 0.98635833 1.1193994 0.043854107 1.0935635 1.4288422
210000 0.99172336 1.0945983 -0.047827928 1.0845738 1.4610522
212000 0.99572889 1.1375524 -0.19281467 1.0820934 1.4492165
214000 1.0146878 0.93324057 0.023347328 1.0666754 1.4359126
216000 0.99707471 0.96782693 0.083402848 1.0567355 1.4261272
218000 1.0072021 0.8155869 -0.094678429 1.0397772 1.4363021
220000 0.99829642 1.0862336 -0.057344135 1.0264114 1.4261186
222000 1.0214364 1.0020523 -0.081278441 1.0259496 1.4104525
224000 1.0007703 1.1398771 -0.014848249 1.0383859 1.4298639
226000 1.0160887 0.97725713 -0.061995296 1.0437407 1.4241759
228000 1.0094934 1.040651 0.0079530479 1.0393089 1.4155728
230000 0.98902579 1.050377 -0.02091325 1.0338013 1.4183238
232000 0.98365162 1.1795485 0.007265917 1.023983 1.42409
234000 0.98804235 0.99142023 -0.14096873 1.0094423 1.4122007
236000 1.0111715 1.0365441 0.03705863 0.9986353 1.3994269
238000 1.028486 0.77859138 0.03686834 0.99615802 1.4123065
240000 1.0048364 1.0507628 0.177815 0.98769158 1.4053338
242000 1.0612408 0.80528323 -0.065846556 0.96795821 1.3983254
244000 0.99451698 0.90507771 0.0090582429 0.95858362 1.3911554
246000 1.0215777 0.88605366 -0.033084099 0.94891089 1.3837671
248000 1.0346251 1.0266325 0.042180226 0.94589414 1.3805736
250000 0.97725995 0.99997539 0.046921107 0.9413025 1.4054541
252000 1.0045133 1.2089315 -0.20100537 0.93463731 1.3855538
254000 1.0396556 0.8806146 0.16822159 0.92217148 1.3836271
256000 0.99769832 1.0692142 0.03603972 0.90825537 1.37561
258000 0.97543457 1.0623702 0.076387425 0.89703273 1.3792596
260000 0.99005919 1.0412698 -0.19142244 0.8920687 1.3587022
262000 1.0014908 1.0353971 0.10763251 0.88126218 1.346977
264000 1.0392437 1.0236348 -0.19905313 0.87431966 1.3383363
266000 1.0110595 0.943378 -0.055766989 0.86561643 1.3383356
268000 1.0155932 0.84263415 -0.046929409 0.87912277 1.3349971
270000 1.060652 0.75643153 -0.10294749 0.87236853 1.3457342
272000 1.0069743 0.97553062 0.029040039 0.84867311 1.3119881
274000 1.0463214 0.67594148 -0.0069642173 0.83557725 1.3142664
276000 1.0042636 0.98929276 -0.12449786 0.834825 1.3009674
278000 0.97917004 1.1268906 -0.078323442 0.84264211 1.302196
280000 1.0082531 1.0527782 -0.036059017 0.83666146 1.3290452
282000 1.0154843 0.92086705 -0.068530775 0.83838607 1.3283441
284000 1.0098619 1.036216 0.037750753 0.83579051 1.3263873
286000 1.0066095 0.98446812 0.02654871 0.82548297 1.3204648
288000 1.0108484 0.9938665 0.0014634473 0.8212407 1.3432121
290000 1.0084713 0.97267996 -0.16071115 0.81647241 1.3116145
292000 1.0056589 0.84166635 0.11872697 0.80604569 1.2982472
294000 1.0209933 0.9891441 -0.08837825 0.7987701 1.2971225
296000 0.99782768 1.0931691 0.03252435 0.7933436 1.3227693
298000 0.97158829 1.0587163 -0.020509263 0.78826707 1.3403092
300000 0.99635509 1.0508706 -0.13999572 0.80661653 1.3636672
302000 1.0244367 0.98051456 0.078987418 0.79690906 1.3579957
304000 1.0164691 0.92957417 -0.052090111 0.78111523 1.3494573
306000 0.99640652 1.0046382 -0.17696034 0.78527471 1.3388528
308000 0.99001053 1.0661668 -0.040494857 0.78802705 1.3391576
310000 1.0176688 0.88160706 -0.16255132 0.77827469 1.328968
312000 1.0030797 1.1056347 0.2012843 0.77588955 1.3216876
314000 1.0135412 0.89411346 0.14573277 0.76605153 1.3369024
316000 1.0289246 0.95183363 -0.13790235 0.76142201 1.3264365
318000 1.0272076 1.0546778 -0.15570037 0.7550118 1.319986
320000 1.0233555 0.69600824 -0.051301259 0.75973858 1.316099
322000 1.0276771 1.006656 -0.037166444 0.77429945 1.3244899
324000 1.0009085 1.1030988 -0.045003287 0.77270822 1.3241261
326000 0.99820481 0.96157265 0.0051561382 0.77066804 1.313479
328000 1.0034746 0.9828709 0.04098644 0.77299241 1.3168281
330000 0.9855772 1.2748992 0.216881 0.76442667 1.3495639
332000 0.9965209 1.1130749 0.090747874 0.75969604 1.3482028
334000 1.035755 0.88167554 0.02819393 0.75757808 1.3424486
336000 0.99996774 1.0190301 0.063460214 0.75227901 1.3506673
338000 0.99767487 1.0766267 0.17431208 0.84059427 1.3246922
340000 1.0253142 0.95542815 -0.057965391 0.83723497 1.3293585
342000 1.0068098 0.97259996 0.10715327 0.83750839 1.326108
344000 0.99340991 1.0870946 -0.068506912 0.82881344 1.3279886
346000 1.0120696 1.0131809 -0.053688663 0.83810272 1.3174796
348000 1.0309753 0.89960386 -0.060363095 0.82821889 1.3105855
350000 1.0037776 1.0091603 0.02135905 0.82421593 1.3062743
352000 0.98591728 1.1377659 -0.083236455 0.82154361 1.3039211
354000 1.0080397 0.80849869 0.00928565 0.8133737 1.2966239
356000 1.0580451 0.75557573 -0.072592855 0.80584322 1.2906508
358000 1.030585 1.0380857 -0.080811662 0.8014706 1.2924957
360000 1.0095237 1.054976 -0.16712924 0.80086617 1.2972352
362000 1.0310879 0.84077595 0.080477352 0.79545805 1.2769439
364000 1.0000238 1.1775906 0.0031139552 0.79173356 1.2839778
366000 1.0190616 0.92848622 -0.046387272 0.79173254 1.3032921
368000 1.0089574 0.88967276 0.084507509 0.81055496 1.3028473
370000 0.98626285 1.0389475 0.15747394 0.81689831 1.2919537
372000 1.0179928 0.95338149 -0.079240909 0.80533945 1.2877439
374000 1.0036723 0.91169472 0.038159086 0.80466471 1.2811106
376000 1.0059869 0.90711389 -0.093438168 0.80486392 1.27755
378000 1.0376167 0.96969013 -0.11849733 0.79690186 1.2849264
380000 0.98982394 1.1608252 -0.038393364 0.79074513 1.2787152
382000 0.97137184 0.96619112 -0.034678175 0.79040338 1.2750988
384000 0.99272978 1.0509393 0.032343038 0.78854414 1.2713176
386000 1.0100648 0.96303847 -0.0497874 0.78404981 1.2846324
388000 0.99635597 1.016829 -0.04531565 0.7787559 1.306903
390000 1.0128857 1.0168535 0.030123764 0.77822522 1.2950826
392000 1.0414799 0.91612676 0.052204166 0.80240996 1.2882927
394000 0.98112978 1.0438272 -0.068667673 0.79384032 1.2811558
396000 0.97787678 1.0131718 -0.033109536 0.79605418 1.2692971
398000 1.0292431 0.90622851 -0.082576483 0.79540751 1.2680355
400000 1.0026087 1.0275497 0.087158222 0.79029414 1.2644206
402000 1.0163706 0.96588365 -0.029125811 0.78663679 1.2595275
404000 1.0262493 0.79007094 0.0079598958 0.78812507 1.2575526
406000 0.99487107 0.83977277 0.066596384 0.78322554 1.2506377
408000 1.0108518 1.1412871 0.041085191 0.78509472 1.2623544
410000 1.0026966 1.1125145 0.021404009 0.78266826 1.2703102
412000 1.0027426 1.1445941 0.10077025 0.77085701 1.2849866
414000 1.0525169 0.6688189 -0.071885452 0.77565161 1.2911903
416000 0.95514842 1.2198976 -0.020098364 0.76998705 1.2873301
418000 0.99853286 1.040174 -0.043752958 0.78683106 1.2936501
420000 0.96432983 1.2000605 0.0284884 0.78718481 1.312678
422000 1.0110338 0.88925615 -0.0056255993 0.79178119 1.3132659
424000 1.0077925 1.0625448 0.078586775 0.77982291 1.3031021
426000 0.98743189 1.0888581 0.12563331 0.77548305 1.2938035
428000 1.0112301 0.91688673 -0.1605337 0.76902093 1.2909986
430000 1.0283254 0.83233694 0.047589962 0.76791923 1.2841707
432000 0.97982409 1.1875522 -0.060520907 0.7726128 1.2775717
434000 0.9830003 1.2882445 0.026552191 0.77474589 1.2727174
436000 0.98158695 1.2184202 0.10011832 0.76992849 1.2604393
438000 1.0174602 0.98983657 -0.26731543 0.77292394 1.2570614
440000 1.0147922 0.99723521 0.10312258 0.77211658 1.2600691
442000 1.0185438 0.95378608 0.032898335 0.79194152 1.2533085
444000 0.97737381 1.2100163 0.022311362 0.78333762 1.2556328
446000 0.99593648 1.0999746 -0.041825149 0.80441311 1.2459874
448000 1.0259234 0.90080955 -0.057452702 0.80038521 1.2398877
450000 0.98873973 1.0019177 -0.14057947 0.79374658 1.2334462
452000 1.0059102 1.0666545 0.014242262 0.78886902 1.2270249
454000 0.99943215 1.1353551 0.070613563 0.78877577 1.2211064
456000 0.99123683 1.1310395 -0.019958521 0.8212975 1.2153723
458000 0.98476743 1.0628314 -0.024302081 0.84754857 1.2111254
460000 1.0139076 1.0181222 0.089182002 0.8711683 1.2012356
462000 1.0113822 1.1739975 -0.10175863 0.87381822 1.2134671
464000 1.0228404 1.0517714 -0.031783966 0.87936192 1.2110218
466000 1.0126934 0.96656763 -0.015021156 0.87512117 1.205325
468000 1.0070377 1.0378727 -0.0077122994 0.87144073 1.210374
470000 0.99238797 1.0832266 -0.041876018 0.87158524 1.2128182
472000 1.0169724 0.90761167 -0.12563948 0.87563801 1.2031687
474000 1.0025279 1.0050948 0.043906331 0.88508792 1.2034718
476000 0.99536702 0.89444096 0.14592241 0.88559122 1.2006404
478000 0.98866565 1.1754384 0.048623957 0.88245402 1.2048067
480000 0.98572668 0.90601784 -0.26268845 0.8766798 1.1959848
482000 1.014423 0.98209159 0.069121411 0.87638162 1.1900047
484000 1.0090002 0.9957509 -0.09367221 0.91979312 1.2095237
486000 0.99962993 1.0977267 -0.15748171 0.91796166 1.1883856
488000 0.98394002 1.0400853 -0.054203925 0.90840814 1.2065249
490000 1.0216626 0.95663779 -0.076119485 0.89955072 1.213275
492000 0.98450357 1.2970783 -0.1684919 0.9028997 1.2128895
494000 1.022591 0.82845032 -0.10149084 0.90006981 1.2103346
496000 1.0317595 0.79413446 0.12970065 0.91240504 1.2079784
498000 1.0375923 1.0063299 0.0090318777 0.91283445 1.209838
500000 1.009533 0.92939388 0.051496977 0.92195746 1.2070306
Loop time of 70.8372 on 1 procs for 500000 steps with 800 atoms
Performance: 3049246.649 tau/day, 7058.441 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 47.562 | 47.562 | 47.562 | 0.0 | 67.14
Neigh | 12.145 | 12.145 | 12.145 | 0.0 | 17.14
Comm | 1.5125 | 1.5125 | 1.5125 | 0.0 | 2.14
Output | 0.004076 | 0.004076 | 0.004076 | 0.0 | 0.01
Modify | 7.2584 | 7.2584 | 7.2584 | 0.0 | 10.25
Other | | 2.355 | | | 3.32
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 271 ave 271 max 271 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5622 ave 5622 max 5622 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5622
Ave neighs/atom = 7.0275
Neighbor list builds = 59121
Dangerous builds = 0
variable etaxy equal v_vxy
variable etaxx equal v_vxx
variable eta equal 0.5*(${etaxy}+${etaxx})
variable eta equal 0.5*(0.921957460954984+${etaxx})
variable eta equal 0.5*(0.921957460954984+1.20703060474415)
print "running average viscosity: ${eta}"
running average viscosity: 1.06449403284957
Total wall time: 0:01:12

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LAMMPS (13 Oct 2016)
# sample LAMMPS input script for viscosity of 2d LJ liquid
# Muller-Plathe via fix viscosity
# settings
variable x equal 20
variable y equal 20
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
lattice sq2 ${rho}
lattice sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox block 0 $x 0 $y -0.1 0.1
region simbox block 0 20 0 $y -0.1 0.1
region simbox block 0 20 0 20 -0.1 0.1
create_box 1 simbox
Created orthogonal box = (0 0 -0.182574) to (36.5148 36.5148 0.182574)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff * * 1 1
mass * 1.0
velocity all create $t 97287
velocity all create 1 97287
fix 1 all nve
fix 2 all langevin $t $t 0.1 498094
fix 2 all langevin 1 $t 0.1 498094
fix 2 all langevin 1 1 0.1 498094
fix 3 all enforce2d
# equilibration run
thermo 1000
run 5000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 27 27 1
Memory usage per processor = 2.47956 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.56617 -1.535262
1000 0.95906897 -1.571142 0 -0.61327189 0.82593948
2000 1.0164992 -1.6006146 0 -0.58538603 0.88642098
3000 1.0429232 -1.5801639 0 -0.53854441 1.157286
4000 1.0955206 -1.6156387 0 -0.52148756 0.94410568
5000 0.9411767 -1.6155061 0 -0.67550589 0.79353873
Loop time of 0.860626 on 1 procs for 5000 steps with 800 atoms
Performance: 2509801.057 tau/day, 5809.725 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.48372 | 0.48372 | 0.48372 | 0.0 | 56.21
Neigh | 0.11227 | 0.11227 | 0.11227 | 0.0 | 13.05
Comm | 0.014462 | 0.014462 | 0.014462 | 0.0 | 1.68
Output | 4.5061e-05 | 4.5061e-05 | 4.5061e-05 | 0.0 | 0.01
Modify | 0.22682 | 0.22682 | 0.22682 | 0.0 | 26.35
Other | | 0.02332 | | | 2.71
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 256 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5583 ave 5583 max 5583 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5583
Ave neighs/atom = 6.97875
Neighbor list builds = 551
Dangerous builds = 0
unfix 2
# turn on Muller-Plathe driving force and equilibrate some more
velocity all scale $t
velocity all scale 1
fix 4 all viscosity 100 x y 20
compute layers all chunk/atom bin/1d y center 0.05 units reduced
fix 5 all ave/chunk 20 50 1000 layers vx file profile.mp.2d
# equilibration run
variable dVx equal f_5[11][3]-f_5[1][3]
thermo 1000
thermo_style custom step temp epair etotal press f_4 v_dVx
run 20000
Memory usage per processor = 2.72975 Mbytes
Step Temp E_pair TotEng Press f_4 v_dVx
5000 1 -1.6155061 -0.61675613 0.82878859 0 0
6000 0.99205567 -1.6073706 -0.61655497 0.80256133 -40.441513 0.49442509
7000 0.98076638 -1.5968401 -0.6172997 0.93482147 -74.701801 0.81873121
8000 0.99350602 -1.6093282 -0.61706408 1.0032966 -108.00017 1.0369989
9000 1.0130047 -1.6282491 -0.61651065 0.89200717 -133.06372 1.1272589
10000 1.0016704 -1.6170906 -0.61667231 1.0115493 -164.86086 1.1885507
11000 0.99991137 -1.6160496 -0.61738807 0.95811584 -190.62317 1.3389184
12000 0.96344622 -1.5793561 -0.6171142 1.0416296 -221.40727 1.2111221
13000 0.98692912 -1.6022586 -0.61656313 0.9183328 -250.6677 1.4028399
14000 1.0007815 -1.6169097 -0.61737918 0.85210278 -280.3907 1.3446354
15000 0.99742966 -1.6127263 -0.6165434 0.81573578 -308.44839 1.4070968
16000 0.9955551 -1.6105533 -0.61624268 0.88385735 -336.00553 1.3867041
17000 0.98598927 -1.6016934 -0.61693666 1.0601453 -363.09101 1.3716356
18000 0.9827155 -1.5988654 -0.61737831 0.97685532 -391.14488 1.2259196
19000 0.96881647 -1.5839283 -0.6163228 0.9709967 -418.82566 1.2683115
20000 1.0265924 -1.6430234 -0.61771432 0.66156099 -448.12442 1.0964927
21000 1.0001781 -1.6169267 -0.61799878 0.94637366 -477.11852 1.3532793
22000 1.0014617 -1.6170345 -0.61682461 0.89064741 -503.16769 1.2348173
23000 0.98723824 -1.6033256 -0.61732136 0.95636024 -533.04118 1.309259
24000 0.97802015 -1.5945708 -0.61777318 1.1331272 -560.01862 1.3396892
25000 0.98672719 -1.6025172 -0.61702339 1.0225572 -585.97779 1.5256433
Loop time of 2.83606 on 1 procs for 20000 steps with 800 atoms
Performance: 3046484.279 tau/day, 7052.047 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9431 | 1.9431 | 1.9431 | 0.0 | 68.52
Neigh | 0.48329 | 0.48329 | 0.48329 | 0.0 | 17.04
Comm | 0.061027 | 0.061027 | 0.061027 | 0.0 | 2.15
Output | 0.00022459 | 0.00022459 | 0.00022459 | 0.0 | 0.01
Modify | 0.25409 | 0.25409 | 0.25409 | 0.0 | 8.96
Other | | 0.09429 | | | 3.32
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 258 ave 258 max 258 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5583 ave 5583 max 5583 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5583
Ave neighs/atom = 6.97875
Neighbor list builds = 2363
Dangerous builds = 0
# data gathering run
# reset fix viscosity to zero flux accumulation
unfix 4
fix 4 all viscosity 100 x y 20
variable visc equal -(f_4/(2*(step*0.005-125)*lx+1.0e-10))/(v_dVx/(ly/2))
fix vave all ave/time 1000 1 1000 v_visc ave running start 26000
thermo_style custom step temp f_4 v_dVx v_visc f_vave
# only need to run for 10000 steps to make a good 100-frame movie
#dump 1 all custom 100 dump.mp.2d id type x y z vx
#dump 2 all image 100 image.*.jpg vx type zoom 1.6 adiam 1.2
#dump_modify 2 pad 5 amap -0.7 0.7 ca 0.0 2 min blue max red
run 50000
Memory usage per processor = 2.73047 Mbytes
Step Temp f_4 v_dVx v_visc f_vave
25000 0.98672719 0 1.5256433 -0 0
26000 0.98401533 -25.559065 1.3332094 0.95855405 0.47927702
27000 0.99050741 -53.17367 1.3419843 0.99057919 0.64971108
28000 0.98153807 -83.114662 1.1794868 1.1744467 0.78089498
29000 1.0204966 -110.22215 1.3360187 1.0312556 0.83096712
30000 0.99625662 -133.82368 1.5944344 0.83931757 0.83235886
31000 1.0151551 -158.7453 1.5031209 0.88008718 0.83917719
32000 0.98303358 -184.40723 1.4652847 0.89893417 0.84664681
33000 0.99939957 -210.86096 1.3135851 1.0032703 0.86404943
34000 0.96853185 -235.91032 1.3291636 0.98604334 0.87624882
35000 1.0054026 -267.07311 1.4280769 0.93507957 0.88159707
36000 0.97047213 -290.05846 1.4030844 0.93967798 0.88643714
37000 0.99339602 -317.88469 1.3395274 0.98879613 0.89431091
38000 1.0095839 -339.72956 1.5081424 0.86639838 0.89231716
39000 1.033396 -365.46114 1.4202859 0.91898285 0.89409487
40000 1.0069829 -391.35939 1.4315171 0.91129289 0.89516975
41000 1.0145044 -417.94062 1.5126265 0.86344149 0.89330338
42000 0.99701243 -442.43582 1.3830081 0.94090688 0.89594802
43000 1.011832 -466.04588 1.514607 0.8547246 0.89377837
44000 1.016323 -494.28239 1.4459083 0.89960277 0.89406959
45000 1.0048565 -518.02843 1.4397428 0.89951556 0.89432892
46000 0.99726082 -546.29139 1.2399161 1.0490176 0.90136022
47000 0.9817128 -579.0368 1.2816209 1.026819 0.90681495
48000 0.99883406 -606.89944 1.3508577 0.97667325 0.90972571
49000 1.0327324 -639.80418 1.227321 1.0860446 0.91677847
50000 0.99442217 -668.69881 1.1824503 1.1310391 0.92501927
51000 0.99412485 -695.56436 1.3288051 1.0066366 0.92804213
52000 1.0368955 -724.06214 1.2921091 1.0377265 0.93195943
53000 1.02122 -749.03672 1.5201682 0.87988 0.93016359
54000 1.0304794 -772.90678 1.3994802 0.9522092 0.93089844
55000 1.0150735 -800.69744 1.2226831 1.0914486 0.93607748
56000 1.0066993 -830.92913 1.4581021 0.91914572 0.93554836
57000 0.99054006 -858.94251 1.3736656 0.97701919 0.93680505
58000 1.0300499 -881.47715 1.5995216 0.83498179 0.93381025
59000 0.99187983 -909.58612 1.4692824 0.91039454 0.93314123
60000 1.0116153 -936.80603 1.372993 0.9747277 0.93429641
61000 0.98778111 -966.36841 1.3911445 0.9648015 0.93512087
62000 0.97796351 -996.15306 1.2818309 1.0501797 0.93814874
63000 1.0241007 -1026.5146 1.3364909 1.0106145 0.94000683
64000 1.0447876 -1051.1752 1.4339955 0.93979412 0.94000152
65000 1.013822 -1078.5189 1.5730359 0.85703609 0.93797797
66000 1.0003625 -1104.7839 1.4374578 0.93727789 0.9379613
67000 1.0411074 -1132.5569 1.4426372 0.93459539 0.93788302
68000 1.0005746 -1162.5849 1.2729721 1.061958 0.94070291
69000 1.0032978 -1189.5061 1.4109135 0.95803997 0.94108818
70000 1.003145 -1215.7498 1.4255228 0.94760543 0.94122986
71000 1.0216551 -1244.4852 1.1329731 1.1939394 0.94660666
72000 0.96169183 -1272.9346 1.1024076 1.2283893 0.95247713
73000 0.96956712 -1298.3657 1.3689638 0.98794738 0.95320101
74000 1.0081417 -1327.5255 1.3483851 1.0046224 0.95422944
75000 1.0315254 -1357.3275 1.4937254 0.9086861 0.95333643
Loop time of 7.08146 on 1 procs for 50000 steps with 800 atoms
Performance: 3050218.869 tau/day, 7060.692 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8558 | 4.8558 | 4.8558 | 0.0 | 68.57
Neigh | 1.2027 | 1.2027 | 1.2027 | 0.0 | 16.98
Comm | 0.15117 | 0.15117 | 0.15117 | 0.0 | 2.13
Output | 0.00069261 | 0.00069261 | 0.00069261 | 0.0 | 0.01
Modify | 0.63608 | 0.63608 | 0.63608 | 0.0 | 8.98
Other | | 0.235 | | | 3.32
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 273 ave 273 max 273 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5612 ave 5612 max 5612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5612
Ave neighs/atom = 7.015
Neighbor list builds = 5873
Dangerous builds = 0
Total wall time: 0:00:10

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LAMMPS (13 Oct 2016)
# sample LAMMPS input script for viscosity of 2d LJ liquid
# NEMD via fix deform and fix nvt/sllod
# settings
variable x equal 20
variable y equal 20
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
variable srate equal 2.7 # velocity of top edge
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
# problem setup
lattice sq2 ${rho}
lattice sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox prism 0 $x 0 $y -0.1 0.1 0.0 0.0 0.0
region simbox prism 0 20 0 $y -0.1 0.1 0.0 0.0 0.0
region simbox prism 0 20 0 20 -0.1 0.1 0.0 0.0 0.0
create_box 1 simbox
Created triclinic box = (0 0 -0.182574) to (36.5148 36.5148 0.182574) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff * * 1 1
mass * 1.0
velocity all create $t 97287
velocity all create 1 97287
fix 1 all nve
fix 2 all langevin $t $t 0.1 498094
fix 2 all langevin 1 $t 0.1 498094
fix 2 all langevin 1 1 0.1 498094
fix 3 all enforce2d
# equilibration run
thermo 1000
run 5000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 27 27 1
Memory usage per processor = 2.47956 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.56617 -1.535262
1000 0.9455393 -1.573329 0 -0.62897162 0.91884199
2000 1.0359047 -1.6229551 0 -0.58834528 0.96136682
3000 1.0171488 -1.5468681 0 -0.53099077 1.1078235
4000 1.0040221 -1.5977142 0 -0.59494717 0.92428924
5000 0.95883045 -1.6087309 0 -0.651099 0.9201564
Loop time of 0.896852 on 1 procs for 5000 steps with 800 atoms
Performance: 2408424.088 tau/day, 5575.056 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.47349 | 0.47349 | 0.47349 | 0.0 | 52.79
Neigh | 0.15355 | 0.15355 | 0.15355 | 0.0 | 17.12
Comm | 0.017267 | 0.017267 | 0.017267 | 0.0 | 1.93
Output | 4.3392e-05 | 4.3392e-05 | 4.3392e-05 | 0.0 | 0.00
Modify | 0.2278 | 0.2278 | 0.2278 | 0.0 | 25.40
Other | | 0.0247 | | | 2.75
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 266 ave 266 max 266 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5604 ave 5604 max 5604 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5604
Ave neighs/atom = 7.005
Neighbor list builds = 548
Dangerous builds = 0
unfix 1
unfix 2
# turn on NEMD shear and equilibrate some more
velocity all scale $t
velocity all scale 1
# shear rate defined relative to perpendicular dimension
variable xyrate equal ${srate}/ly
variable xyrate equal 2.7/ly
fix 1 all nvt/sllod temp $t $t 0.1
fix 1 all nvt/sllod temp 1 $t 0.1
fix 1 all nvt/sllod temp 1 1 0.1
fix 2 all deform 1 xy erate ${xyrate} remap v
fix 2 all deform 1 xy erate 0.0739425452631974 remap v
compute layers all chunk/atom bin/1d y center 0.05 units reduced
fix 4 all ave/chunk 20 250 5000 layers vx file profile.nemd.2d
compute usual all temp
compute tilt all temp/deform
thermo 1000
thermo_style custom step temp c_usual epair etotal press pxy
thermo_modify temp tilt
run 50000
Memory usage per processor = 2.74501 Mbytes
Step Temp c_usual E_pair TotEng Press Pxy
5000 2.2074694 1 -1.6087309 0.59597914 1.6684033 -0.13173628
6000 0.93152386 1.0817401 -1.6660819 -0.73572242 0.68318536 -0.028129339
7000 1.0014344 1.1738041 -1.7011099 -0.70092725 0.6084685 -0.14709751
8000 1.025345 1.29299 -1.7011316 -0.67706829 0.58584918 -0.13492866
9000 0.98439625 1.3014301 -1.6432929 -0.66012715 0.78568164 0.03166088
10000 0.94167448 1.304837 -1.6809777 -0.74048031 0.6767415 0.004807405
11000 0.98264458 1.3309352 -1.6681636 -0.68674728 0.74844384 -0.043997826
12000 0.99403655 1.3580131 -1.6369662 -0.6441722 0.86251493 -0.05441449
13000 1.0396869 1.4466214 -1.6285376 -0.59015033 0.85584533 -0.077842666
14000 1.0356564 1.4337041 -1.6284938 -0.59413198 0.86325196 0.021727401
15000 0.97016374 1.4146903 -1.6551162 -0.68616512 0.78678055 -0.067107584
16000 0.94805836 1.4367742 -1.6338511 -0.68697777 0.8447822 -0.11723973
17000 0.9784648 1.4621496 -1.6203417 -0.64309998 0.93704401 -0.070556149
18000 1.0180917 1.5223337 -1.6393062 -0.62248714 0.81117394 -0.21773149
19000 1.0186815 1.5716289 -1.6471996 -0.62979147 0.71667451 -0.091605896
20000 0.9743659 1.5914706 -1.6150957 -0.64194775 0.94267754 -0.034378699
21000 1.0482265 1.5882157 -1.6319486 -0.58503242 0.86464563 -0.30608617
22000 1.0372488 1.6614229 -1.618808 -0.58285576 0.9619593 0.030218471
23000 1.02322 1.605947 -1.6128071 -0.5908661 0.89153388 -0.054926254
24000 0.99202826 1.6263761 -1.6309182 -0.64013 0.82035209 -0.15760707
25000 0.96842077 1.6079837 -1.6514188 -0.6842086 0.74289154 -0.15054022
26000 1.0131182 1.6599526 -1.6282941 -0.61644236 0.79717592 -0.17392393
27000 0.99274208 1.6992131 -1.6141775 -0.6226763 0.87559226 -0.025698533
28000 1.0124353 1.682322 -1.6350699 -0.62390012 0.81863458 -0.10578616
29000 1.0159913 1.7444965 -1.670694 -0.65597278 0.77422638 -0.074417391
30000 0.95757504 1.6770477 -1.6100645 -0.65368638 0.84900509 -0.13811335
31000 0.9882106 1.7024812 -1.6135646 -0.62658928 0.8819342 -0.0083109839
32000 0.94243022 1.665312 -1.6173333 -0.67608112 1.0312796 -0.087350514
33000 0.97629132 1.804652 -1.6148954 -0.63982441 0.73933894 -0.010842321
34000 0.96053868 1.768861 -1.6201954 -0.66085743 0.80440002 -0.0098573375
35000 0.96192532 1.7951878 -1.5904258 -0.62970292 0.98930679 0.061382767
36000 1.034984 1.835204 -1.5872923 -0.55360202 1.1673704 -0.086610164
37000 1.0109946 1.8695414 -1.5899371 -0.58020627 1.0247304 -0.081320896
38000 1.0189063 1.9299754 -1.591087 -0.57345437 1.0238951 -0.12903934
39000 0.96964269 1.8518181 -1.5939152 -0.62548456 1.064667 -0.12625393
40000 0.93813023 1.8601846 -1.5808497 -0.64389211 1.0739269 -0.21342957
41000 1.01992 1.9192923 -1.6087202 -0.59007511 0.96050424 -0.3264004
42000 1.0243282 1.9429183 -1.5918401 -0.56879229 1.1845661 -0.062971629
43000 1.0696065 2.0074757 -1.5973264 -0.52905692 0.90524954 -0.12923233
44000 1.0338542 1.9624549 -1.6079246 -0.57536268 1.0536815 0.070524993
45000 0.95583069 1.945773 -1.6279372 -0.67330128 0.74985796 -0.17325375
46000 0.99732695 1.966957 -1.631205 -0.6351247 0.77350616 -0.1852725
47000 1.0135329 2.0107676 -1.6049852 -0.59271924 0.87782961 -0.20632054
48000 0.98735917 1.9771245 -1.6053591 -0.61923413 0.92710662 -0.0002501296
49000 0.99618418 1.9493979 -1.6066882 -0.61174922 0.89595133 -0.20337142
50000 1.0651949 2.0467535 -1.6074294 -0.54356601 0.99645561 -0.099150393
51000 1.0559004 2.0710034 -1.5978367 -0.54325617 0.99030671 -0.1841017
52000 1.0083619 2.0399634 -1.5973313 -0.5902299 1.1130916 -0.0079150985
53000 1.0118925 2.0439094 -1.5896233 -0.57899564 1.1640067 -0.053482574
54000 1.0162238 2.0117062 -1.6173202 -0.60236666 0.92299331 -0.13080758
55000 1.0101742 2.0023882 -1.5870609 -0.57814937 1.0166974 -0.2462163
Loop time of 12.3385 on 1 procs for 50000 steps with 800 atoms
Performance: 1750615.444 tau/day, 4052.351 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.0133 | 5.0133 | 5.0133 | 0.0 | 40.63
Neigh | 3.262 | 3.262 | 3.262 | 0.0 | 26.44
Comm | 0.29422 | 0.29422 | 0.29422 | 0.0 | 2.38
Output | 0.0017447 | 0.0017447 | 0.0017447 | 0.0 | 0.01
Modify | 3.4226 | 3.4226 | 3.4226 | 0.0 | 27.74
Other | | 0.3447 | | | 2.79
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 282 ave 282 max 282 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5602 ave 5602 max 5602 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5602
Ave neighs/atom = 7.0025
Neighbor list builds = 11232
Dangerous builds = 0
# data gathering run
variable visc equal -pxy/(v_srate/ly)
fix vave all ave/time 10 100 1000 v_visc ave running start 56000
thermo_style custom step temp press pxy v_visc f_vave
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690)
thermo_modify temp tilt
# only need to run for 5400 steps to make a good 100-frame movie
# set 54K steps above in equil and 5400 here simply to make good movie
# 54K and 5400 are multiples of box-swap periodicity = 2700 steps
#dump 1 all custom 50 dump.nemd.2d id type x y z vx
#dump 2 all image 50 image.*.jpg vx type zoom 1.2 adiam 1.2
#dump_modify 2 pad 5 amap 0.0 ${srate} ca 0.0 2 min blue max red
run 50000
Memory usage per processor = 2.75392 Mbytes
Step Temp Press Pxy v_visc f_vave
55000 1.0101742 1.0168023 -0.24961054 3.3757364 0
56000 0.95430669 0.99109494 -0.11503816 1.5557777 0.73512854
57000 0.96493583 0.77019161 0.032071381 -0.4337338 0.69832329
58000 1.043882 1.190321 -0.1948503 2.6351582 0.7662455
59000 0.99522262 0.71653967 -0.056810457 0.7683054 0.87054399
60000 1.0147329 1.0803743 -0.13097761 1.7713431 0.8832817
61000 0.93812211 1.0627199 -0.044643317 0.60375683 0.96513251
62000 1.0107288 0.93643991 -0.07289428 0.98582325 0.99515995
63000 1.0516762 1.206755 -0.12107833 1.637465 1.0476529
64000 0.96288473 0.99015782 -0.040632073 0.54950872 1.0857708
65000 0.96981457 1.1393466 0.081769326 -1.1058495 1.0598383
66000 1.0549734 0.9862292 -0.038519333 0.52093599 1.0631279
67000 1.0597179 1.0849355 0.026292892 -0.35558543 1.0560538
68000 1.0260974 0.95293785 0.049285149 -0.66653304 1.0367987
69000 1.0075299 1.0303201 0.041539329 -0.56177846 1.0467854
70000 1.0622593 1.2021547 -0.20731618 2.8037469 1.0667574
71000 0.99847432 1.0509829 -0.15346894 2.075516 1.0655178
72000 0.97453232 0.97670205 -0.22406814 3.0303006 1.0503175
73000 0.9641619 0.89104495 -0.12889334 1.7431553 1.0532335
74000 0.99089222 1.0444418 0.18074575 -2.444408 1.0546561
75000 0.99756998 0.91703128 -0.21829649 2.9522447 1.065423
76000 0.93605182 0.98651769 -0.20794378 2.8122346 1.0798472
77000 0.94258356 0.95471193 -0.14211735 1.9219969 1.0819944
78000 0.9798062 1.2187257 -0.063527885 0.85915199 1.1001509
79000 0.96451401 0.84225692 -0.025071518 0.33906755 1.0969807
80000 0.95011391 1.0570755 -0.11124947 1.5045394 1.1031908
81000 0.99774906 0.96668849 -0.0053084468 0.071791507 1.1312113
82000 0.98889022 0.8762984 0.071585243 -0.96811981 1.1334001
83000 0.93610495 1.0660717 -0.047681336 0.64484304 1.1299719
84000 1.0072593 1.0286446 -0.21827159 2.951908 1.1400137
85000 1.0128434 1.0894592 -0.094017511 1.2714941 1.1421825
86000 1.0193552 0.99088304 -0.057046347 0.77149558 1.1372979
87000 0.92702641 0.88034638 -0.012355342 0.16709381 1.1311508
88000 0.98946493 0.81515436 0.016806513 -0.22729152 1.1379472
89000 0.99799875 1.0151454 -0.084127501 1.1377415 1.1352016
90000 0.99133716 0.86655201 -0.056333485 0.76185483 1.1447978
91000 0.94330916 0.93345911 -0.12219086 1.6525109 1.1417404
92000 0.94909987 1.0726222 -0.26976121 3.6482544 1.1573797
93000 0.99526745 1.0680147 -0.1142234 1.5447588 1.1646702
94000 1.0018217 1.1512259 -0.19659509 2.6587547 1.1604884
95000 0.9686519 1.0577224 -0.055162686 0.74602092 1.1618973
96000 0.97493046 0.96044751 0.050456814 -0.68237864 1.1574483
97000 0.97351913 1.0981546 -0.16357534 2.2121952 1.1677946
98000 1.0157509 0.97339707 -0.13441353 1.8178105 1.1778369
99000 1.0414889 1.0103719 -0.10696881 1.4466477 1.1823616
100000 1.0249428 1.0036886 -0.27447626 3.7120207 1.1792453
101000 0.96960692 0.94692891 -0.053860891 0.72841544 1.1752286
102000 1.0371247 1.0840917 -0.040114754 0.54251249 1.1644228
103000 0.96769028 1.0471324 -0.07971043 1.0780049 1.1657168
104000 0.96896685 1.0326732 -0.23873693 3.2286815 1.162545
105000 1.0122807 0.97927614 -0.068569604 0.92733627 1.1684457
Loop time of 12.8562 on 1 procs for 50000 steps with 800 atoms
Performance: 1680117.354 tau/day, 3889.161 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.0725 | 5.0725 | 5.0725 | 0.0 | 39.46
Neigh | 3.5621 | 3.5621 | 3.5621 | 0.0 | 27.71
Comm | 0.31528 | 0.31528 | 0.31528 | 0.0 | 2.45
Output | 0.00097895 | 0.00097895 | 0.00097895 | 0.0 | 0.01
Modify | 3.5411 | 3.5411 | 3.5411 | 0.0 | 27.54
Other | | 0.3643 | | | 2.83
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 283 ave 283 max 283 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5585 ave 5585 max 5585 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5585
Ave neighs/atom = 6.98125
Neighbor list builds = 12225
Dangerous builds = 0
Total wall time: 0:00:26

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examples/VISCOSITY/log.13Oct16.wall.2d.g++.1 Normal file
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LAMMPS (13 Oct 2016)
# sample LAMMPS input script for viscosity of 2d LJ liquid
# use shearing wall, thermostat via fix langevin
# settings
variable x equal 20
variable y equal 20
variable ylo equal -2.5
variable yhi equal 23
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
variable srate equal 2.7
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
lattice sq2 ${rho}
lattice sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox block 0 $x ${ylo} ${yhi} -0.1 0.1
region simbox block 0 20 ${ylo} ${yhi} -0.1 0.1
region simbox block 0 20 -2.5 ${yhi} -0.1 0.1
region simbox block 0 20 -2.5 23 -0.1 0.1
create_box 3 simbox
Created orthogonal box = (0 -4.56435 -0.182574) to (36.5148 41.9921 0.182574)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 1020 atoms
mass * 1.0
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff * * 1 1
region lower block INF INF INF 0.0 INF INF
region upper block INF INF $y INF INF INF
region upper block INF INF 20 INF INF INF
group lower region lower
120 atoms in group lower
group upper region upper
120 atoms in group upper
set group lower type 2
120 settings made for type
set group upper type 3
120 settings made for type
group wall union lower upper
240 atoms in group wall
group flow subtract all wall
780 atoms in group flow
velocity flow create $t 97287
velocity flow create 1 97287
velocity upper set ${srate} 0.0 0.0 units box
velocity upper set 2.7 0.0 0.0 units box
compute thermal flow temp/partial 0 1 0
compute flow flow temp
fix 1 all nve
fix 2 flow langevin $t $t 0.1 498094
fix 2 flow langevin 1 $t 0.1 498094
fix 2 flow langevin 1 1 0.1 498094
fix_modify 2 temp thermal
fix 3 wall setforce 0.0 0.0 0.0
compute layers all chunk/atom bin/1d y center 0.05 units reduced
fix 4 all ave/chunk 20 500 10000 layers vx file profile.wall.2d
fix 5 all enforce2d
# equilibration run
variable ybox equal $y*ylat
variable ybox equal 20*ylat
compute tilt flow temp/ramp vx 0 ${srate} y 0 ${ybox} units box
compute tilt flow temp/ramp vx 0 2.7 y 0 ${ybox} units box
compute tilt flow temp/ramp vx 0 2.7 y 0 36.5148371670111 units box
thermo 1000
thermo_style custom step temp c_tilt epair etotal press pxy
run 20000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 27 34 1
Memory usage per processor = 2.7306 Mbytes
Step Temp c_tilt E_pair TotEng Press Pxy
0 1.1937193 2.1893943 -1.4419854 -0.24943634 -0.78936698 0.014349737
1000 1.3454512 1.9300306 -1.5968842 -0.25275207 0.66766599 -0.14162185
2000 1.4039195 1.7346977 -1.5342235 -0.13168039 1.0083734 0.018811845
3000 1.3945539 1.6038724 -1.5472166 -0.15402987 0.89714673 -0.21459294
4000 1.4507445 1.5640577 -1.5682837 -0.11896142 0.80780492 -0.11602642
5000 1.5081166 1.5260484 -1.4466585 0.059979546 1.5213379 0.15651364
6000 1.471403 1.3275791 -1.5730732 -0.10311276 0.76780953 -0.028043991
7000 1.5811576 1.3851463 -1.5518076 0.027799848 1.0149281 0.004725238
8000 1.5298095 1.3333038 -1.536974 -0.0086643578 1.2325979 -0.11754624
9000 1.5269137 1.253444 -1.5995915 -0.074174772 0.72678912 0.068344793
10000 1.6201621 1.2415469 -1.4659459 0.15262788 1.4780324 0.12762214
11000 1.6422795 1.2595346 -1.5659612 0.074708257 1.0471534 -0.039697954
12000 1.7111306 1.1978075 -1.5685671 0.14088596 0.97371007 0.099889098
13000 1.6871075 1.1495076 -1.4967158 0.18873768 1.3445558 -0.058891196
14000 1.7237433 1.1976445 -1.5857394 0.13631394 0.96603231 0.082195882
15000 1.7080799 1.1550766 -1.4962561 0.21014912 1.3733324 0.062008565
16000 1.7030363 1.1186642 -1.5735945 0.12777215 1.0071474 -0.12038271
17000 1.7442786 1.1134856 -1.5544631 0.18810536 0.98640596 -0.10793154
18000 1.7433517 1.0565945 -1.4702226 0.27141996 1.5983127 -0.1847178
19000 1.7909641 1.071494 -1.5628363 0.22637195 1.0487763 -0.16215298
20000 1.8291721 1.1152277 -1.4955372 0.33184161 1.4404718 0.13157652
Loop time of 4.60977 on 1 procs for 20000 steps with 1020 atoms
Performance: 1874278.390 tau/day, 4338.607 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2771 | 2.2771 | 2.2771 | 0.0 | 49.40
Neigh | 0.77127 | 0.77127 | 0.77127 | 0.0 | 16.73
Comm | 0.08461 | 0.08461 | 0.08461 | 0.0 | 1.84
Output | 0.00045896 | 0.00045896 | 0.00045896 | 0.0 | 0.01
Modify | 1.3487 | 1.3487 | 1.3487 | 0.0 | 29.26
Other | | 0.1277 | | | 2.77
Nlocal: 1020 ave 1020 max 1020 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 319 ave 319 max 319 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6977 ave 6977 max 6977 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6977
Ave neighs/atom = 6.8402
Neighbor list builds = 3091
Dangerous builds = 0
# data gathering run
variable visc equal -pxy/(v_srate/ly)
fix vave all ave/time 1000 1 1000 v_visc ave running
thermo_style custom step temp pxy v_visc f_vave
thermo_modify temp tilt
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
# only need to run for 5000 steps to make a good 100-frame movie
#dump 1 all custom 50 dump.wall.2d id type x y z vx
#dump 2 all image 50 image.*.jpg vx type zoom 1.6 adiam 1.2
#dump_modify 2 pad 5 amap 0.0 ${srate} ca 0.0 2 min blue max red
run 50000
Memory usage per processor = 2.73133 Mbytes
Step Temp Pxy v_visc f_vave
20000 1.1152277 0.14873839 -2.5647136 -2.5647136
21000 1.0675243 -0.064336523 1.1093622 -0.72767568
22000 1.1044647 -0.092189802 1.5896396 0.044762746
23000 1.0278193 -0.16030404 2.7641414 0.72460741
24000 1.032998 -0.025162118 0.43387337 0.6664606
25000 1.012257 0.15289388 -2.6363671 0.11598931
26000 1.0678095 -0.15317374 2.6411929 0.47673268
27000 0.99951185 -0.013635884 0.23512515 0.44653174
28000 1.0663423 -0.061009474 1.0519935 0.51380527
29000 1.0753719 -0.037018843 0.63832026 0.52625677
30000 1.0749259 -0.0092916614 0.16021721 0.49298044
31000 1.0171594 -0.14103555 2.4318926 0.65455646
32000 1.0811717 -0.22037237 3.7999068 0.89650648
33000 1.0123567 -0.076368085 1.3168239 0.92652915
34000 1.0923478 -0.017551868 0.30264892 0.88493714
35000 1.0252013 0.0042522796 -0.073322558 0.82504591
36000 1.0205412 -0.17942577 3.0938596 0.95850554
37000 1.016861 -0.15185242 2.6184092 1.0507224
38000 1.0156825 -0.058057333 1.0010894 1.0481101
39000 1.0299458 -0.028138186 0.48519005 1.0199641
40000 1.0109947 0.069370747 -1.1961679 0.91443404
41000 0.99255941 -0.20057649 3.4585639 1.0300763
42000 0.93280953 -0.20797609 3.5861562 1.1412102
43000 0.98040039 0.070643632 -1.2181165 1.0429049
44000 1.001795 -0.06620924 1.1416537 1.0468549
45000 0.96231963 0.028026245 -0.48325983 0.98800432
46000 1.0193639 -0.15553891 2.6819757 1.050744
47000 1.0241202 0.0053565438 -0.092363514 1.0099187
48000 0.9736932 0.12643935 -2.1802085 0.89991435
49000 0.96326617 -0.14719163 2.5380426 0.95451862
50000 0.99008772 0.03563038 -0.61437884 0.90390903
51000 1.0689018 -0.11122259 1.9178243 0.93559388
52000 1.0123467 0.021882959 -0.37733044 0.89580829
53000 1.0075671 0.20840798 -3.5936033 0.76376678
54000 0.97454265 -0.027528034 0.47466913 0.75550684
55000 1.0072632 -0.02991098 0.51575854 0.74884717
56000 0.94706748 -0.29624115 5.108121 0.86666538
57000 1.0411989 -0.043160809 0.74422691 0.86344332
58000 1.0040809 0.10858868 -1.8724074 0.7932933
59000 1.0101096 -0.17512944 3.0197775 0.8489554
60000 0.97394086 0.025630293 -0.44194616 0.81747
61000 0.97631407 -0.21776922 3.7550203 0.88741167
62000 0.9650689 -0.036733674 0.63340305 0.88150449
63000 1.0401136 0.11852825 -2.0437965 0.81502038
64000 0.99261276 -0.20362786 3.5111792 0.87493502
65000 1.0397086 -0.056685607 0.97743658 0.87716332
66000 1.0115793 -0.20411863 3.5196415 0.93338626
67000 1.1243059 -0.086897372 1.4983816 0.94515699
68000 1.0005962 0.081847197 -1.4113008 0.89706602
69000 1.0412065 -0.21375629 3.6858249 0.95284119
70000 0.97952466 -0.060208765 1.0381868 0.95451464
Loop time of 11.6259 on 1 procs for 50000 steps with 1020 atoms
Performance: 1857923.682 tau/day, 4300.749 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.6901 | 5.6901 | 5.6901 | 0.0 | 48.94
Neigh | 2.0175 | 2.0175 | 2.0175 | 0.0 | 17.35
Comm | 0.21634 | 0.21634 | 0.21634 | 0.0 | 1.86
Output | 0.00069594 | 0.00069594 | 0.00069594 | 0.0 | 0.01
Modify | 3.3775 | 3.3775 | 3.3775 | 0.0 | 29.05
Other | | 0.3236 | | | 2.78
Nlocal: 1020 ave 1020 max 1020 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 332 ave 332 max 332 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6969 ave 6969 max 6969 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6969
Ave neighs/atom = 6.83235
Neighbor list builds = 8088
Dangerous builds = 0
Total wall time: 0:00:16

386
examples/VISCOSITY/log.1Feb14.gk.2d.g++.1
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@ -1,386 +0,0 @@
LAMMPS (1 Feb 2014)
# sample LAMMPS input script for viscosity of 2d LJ liquid
# Green-Kubo method via fix ave/correlate
# settings
variable x equal 20
variable y equal 20
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
variable p equal 400 # correlation length
variable s equal 5 # sample interval
variable d equal $p*$s # dump interval
variable d equal 400*$s
variable d equal 400*5
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
lattice sq2 ${rho}
lattice sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox block 0 $x 0 $y -0.1 0.1
region simbox block 0 20 0 $y -0.1 0.1
region simbox block 0 20 0 20 -0.1 0.1
create_box 1 simbox
Created orthogonal box = (0 0 -0.182574) to (36.5148 36.5148 0.182574)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff * * 1 1
mass * 1.0
velocity all create $t 97287
velocity all create 1 97287
# equilibration run
fix 1 all nve
fix 2 all langevin $t $t 0.1 498094
fix 2 all langevin 1 $t 0.1 498094
fix 2 all langevin 1 1 0.1 498094
fix 3 all enforce2d
thermo $d
thermo 2000
run 10000
Memory usage per processor = 2.06394 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.56617 -1.535262
2000 1.0164992 -1.6006146 0 -0.58538603 0.88642098
4000 1.0955206 -1.6156387 0 -0.52148756 0.94410568
6000 1.0384043 -1.6029205 0 -0.5658142 0.82862869
8000 1.0288194 -1.5760462 0 -0.54851284 1.1299693
10000 0.97521893 -1.5752855 0 -0.60128557 1.0982639
Loop time of 1.72441 on 1 procs for 10000 steps with 800 atoms
Pair time (%) = 0.929897 (53.9255)
Neigh time (%) = 0.203868 (11.8225)
Comm time (%) = 0.0357857 (2.07524)
Outpt time (%) = 5.60284e-05 (0.00324913)
Other time (%) = 0.554805 (32.1736)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 261 ave 261 max 261 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5617 ave 5617 max 5617 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5617
Ave neighs/atom = 7.02125
Neighbor list builds = 1101
Dangerous builds = 0
velocity all scale $t
velocity all scale 1
unfix 2
# Green-Kubo viscosity calculation
reset_timestep 0
variable pxy equal pxy
fix SS all ave/correlate $s $p $d v_pxy type auto file profile.gk.2d ave running
fix SS all ave/correlate 5 $p $d v_pxy type auto file profile.gk.2d ave running
fix SS all ave/correlate 5 400 $d v_pxy type auto file profile.gk.2d ave running
fix SS all ave/correlate 5 400 2000 v_pxy type auto file profile.gk.2d ave running
variable scale equal 1.0/$t*vol*$s*dt
variable scale equal 1.0/1*vol*$s*dt
variable scale equal 1.0/1*vol*5*dt
variable v11 equal trap(f_SS[3])*${scale}
variable v11 equal trap(f_SS[3])*33.3333333333333
thermo_style custom step temp press pxy v_v11
run 500000
Memory usage per processor = 2.06394 Mbytes
Step Temp Press Pxy v11
0 1 1.1131139 -0.062970733 0.066088554
2000 1.0080895 1.0200888 -0.11243616 -1.2606591
4000 0.99653513 1.0745982 -0.0075361431 -1.2260153
6000 1.015614 1.0288859 -0.045052789 2.2423387
8000 1.0480587 1.0090528 -0.16941968 1.4483022
10000 1.0340413 0.8935734 -0.016265599 1.367264
12000 1.0208142 0.98827028 -0.098494798 0.96391762
14000 1.0063108 1.1900869 0.041555635 0.71920668
16000 1.0104133 1.0341648 -0.08539107 0.87216885
18000 1.0324239 0.78956816 -0.022393354 0.99812938
20000 0.98065939 1.1290253 0.088823616 0.86856675
22000 1.0456522 0.79585972 -0.10649734 1.3811196
24000 1.0120651 1.0552123 0.21725489 1.648588
26000 1.0441983 0.959829 0.0053239549 1.6192642
28000 0.9936521 1.1033308 -0.0013213764 1.4830182
30000 1.0106141 1.0845812 0.048019524 1.3015283
32000 1.0138237 0.96535384 -0.18328359 1.1659494
34000 0.99897229 1.2265577 -0.057168503 1.3064819
36000 0.98508691 1.1289173 -0.18839382 1.5336228
38000 1.0419001 0.79249301 -0.20846158 1.4200528
40000 1.0152017 0.98214979 -0.0067504119 1.3792256
42000 1.0113905 1.0421477 -0.047659129 1.3414456
44000 1.0201365 1.112008 0.01373301 1.3159903
46000 1.018482 0.93142144 -0.10476936 1.3358778
48000 1.0362661 0.77862744 -0.073200405 1.2925615
50000 1.0200063 0.96817572 -0.082635361 1.2477558
52000 1.018602 1.0281262 0.059387055 1.253828
54000 1.0465938 0.78372671 -0.04203004 1.2411918
56000 1.0376258 1.031501 -0.043675881 1.3662686
58000 0.97830162 1.239229 0.033252127 1.2677821
60000 0.99938589 1.2023844 0.05306354 1.191899
62000 1.010291 0.93962979 0.047429505 1.0726624
64000 1.0233048 0.93855809 0.17161686 1.0641676
66000 1.0124208 1.0309115 -0.0040419968 1.0550472
68000 0.98507874 1.0281731 -0.090367158 1.070317
70000 1.0012103 1.0065752 0.11646809 1.2306811
72000 1.0257593 0.94487824 0.047164906 1.2402116
74000 0.99773444 1.0006634 -0.16947105 1.3458531
76000 0.99053502 1.1802621 -0.011315672 1.4050256
78000 1.0266873 0.92896952 0.053862201 1.4183056
80000 1.0181396 1.0028774 -0.1669873 1.3918642
82000 1.0183891 1.0045513 0.12750581 1.3598925
84000 1.0054008 1.1361355 0.11127961 1.3235664
86000 1.0153982 1.0270658 0.032996007 1.244148
88000 1.0089441 0.94065248 -0.14958385 1.2504534
90000 1.0090826 0.96386446 0.04002849 1.19906
92000 0.98701529 1.0170739 0.048669738 1.230085
94000 1.0271895 0.90965645 0.16524668 1.2111807
96000 1.0588564 0.64666046 -0.012052311 1.1865422
98000 1.01362 1.02233 0.015426298 1.198456
100000 0.99253832 1.1498855 -0.11430916 1.1821222
102000 1.0260594 0.8604477 -0.038050842 1.1482599
104000 1.0248424 1.0639555 -0.08295859 1.1390154
106000 1.0069076 1.2491555 0.010334731 1.1352025
108000 1.0350323 0.9938777 0.028015622 1.1395354
110000 1.0090965 1.0811591 -0.069761835 1.1641264
112000 0.98126774 1.2677506 0.03105149 1.1417489
114000 1.0053548 1.05943 -0.053492802 1.1435347
116000 1.0116531 1.1377687 0.08984011 1.1290702
118000 1.0441155 0.94024004 0.069880409 1.1352496
120000 0.99682009 1.1603848 -0.09404725 1.2100588
122000 1.0155742 1.0078645 -0.027651839 1.173532
124000 0.99222072 1.1821546 -0.0308041 1.2037919
126000 1.0405098 1.155637 0.030664374 1.1715576
128000 1.0187941 0.98070733 0.0059064696 1.2064639
130000 1.0399447 0.99686501 0.14875158 1.26474
132000 1.0409005 1.0086593 0.021338889 1.2817848
134000 1.0476219 0.8026445 0.036028195 1.269031
136000 1.0361278 0.82017002 0.12410098 1.2516208
138000 1.0118377 1.017853 -0.051473869 1.2497683
140000 1.0150827 1.0187598 -0.021626098 1.2422255
142000 1.0299632 0.85581133 0.0020789713 1.3028929
144000 1.0299864 0.75409682 0.067708051 1.2807235
146000 1.0300343 0.95486967 -0.12805174 1.2639701
148000 0.99833371 1.0636801 -0.012957113 1.2450247
150000 1.0218031 1.0345594 -0.0076210772 1.238176
152000 1.0166582 1.000406 0.048913573 1.2350809
154000 1.0200436 0.9620376 0.016990704 1.2277908
156000 1.0174714 0.97523697 -0.089095058 1.2333756
158000 1.0057212 0.98373273 0.10571489 1.2207665
160000 1.0116139 1.0531268 0.040970831 1.1908489
162000 1.0141586 0.97503702 -0.12255418 1.1835675
164000 0.96779259 1.1194358 0.17756759 1.1540165
166000 1.0009628 1.1253418 0.050763812 1.141318
168000 0.99014049 1.1155831 -0.14569673 1.1317473
170000 1.0298577 0.98702864 -0.00084160851 1.1904372
172000 1.0202995 0.96163813 0.0045819305 1.1873872
174000 1.0359389 0.89018321 0.011677378 1.1807412
176000 1.0256185 1.0300041 0.02536302 1.1857003
178000 1.0271101 1.0152692 -0.13910986 1.2068771
180000 1.0194759 0.87873048 -0.12169124 1.1850476
182000 1.0319658 1.0033092 -0.095869229 1.1660609
184000 1.0078723 1.2412606 -0.049703306 1.1654829
186000 1.0442603 0.79824994 -0.093218879 1.1463494
188000 1.0004515 0.90810497 -0.048680818 1.1105332
190000 1.000942 0.94373473 0.10613178 1.1009497
192000 1.048449 0.97658358 -0.17712897 1.1263395
194000 1.0290391 0.98531851 -0.012106089 1.0921536
196000 1.0315571 1.1564407 0.057141413 1.0858253
198000 1.0142691 1.0606813 0.029671093 1.0716634
200000 1.0456713 0.84981128 0.11494717 1.0676611
202000 1.0260155 1.0217822 -0.040530429 1.0674862
204000 0.99472169 1.1602851 0.0051321303 1.0579412
206000 1.0014916 1.0461488 0.0060656173 1.0549157
208000 1.0022353 1.0846052 -0.11185825 1.0596996
210000 1.015275 1.0276323 -0.030737448 1.0550317
212000 1.0039546 1.1104646 0.10845813 1.0540841
214000 1.007432 1.024032 -0.11046904 1.0455342
216000 0.99740694 1.140278 -0.065900867 1.048484
218000 1.0237293 0.94527063 -0.20653618 1.0406664
220000 1.0069562 1.1273839 -0.0067054642 1.0387632
222000 1.0342064 1.0131146 0.035157231 1.0296557
224000 1.003096 1.0550729 0.03305911 1.0335
226000 1.0144191 1.0049718 0.042900611 1.0650019
228000 1.0268793 0.90872396 -0.17661877 1.0602896
230000 1.0237908 0.98063448 -0.029475684 1.0685714
232000 1.0069934 1.1044794 0.13426396 1.0662281
234000 0.98863378 0.95248555 -0.024211245 1.0765215
236000 1.0134171 1.0478432 -0.17292923 1.0525098
238000 1.0120921 0.99042234 0.025333354 1.0420108
240000 1.0042316 1.1071855 -0.02061948 1.0468243
242000 1.0086548 1.0773029 -0.10892118 1.0462304
244000 1.0016487 1.0120587 -0.11220572 1.0530018
246000 1.0206702 0.96270397 0.076386758 1.0399964
248000 1.0106322 0.97979007 -0.056885564 1.0285937
250000 1.0521704 0.90240063 -0.098004463 1.0680676
252000 1.0031792 1.1298376 -0.12700293 1.0572962
254000 1.0023361 1.0397687 -0.042138767 1.055246
256000 1.0207399 0.99843942 -0.067694614 1.0678481
258000 0.98874431 1.228494 0.040793426 1.0558317
260000 1.0183455 1.0188006 -0.17725132 1.0629806
262000 1.0018425 0.94317435 0.10076842 1.0548939
264000 1.0166318 0.8436724 -0.056681878 1.0488651
266000 1.0091103 1.0775158 0.028771667 1.0371622
268000 1.0013292 0.95251758 -0.050343862 1.0496861
270000 0.99674492 1.1472622 -0.11346408 1.1092918
272000 1.0049198 1.0673533 -0.064343803 1.0881727
274000 1.0303169 0.97093144 -0.010278759 1.0846913
276000 1.0273615 0.84473644 -0.017151036 1.0688783
278000 1.0127363 1.2089228 -0.039397817 1.0875618
280000 0.98505511 1.1212088 -0.04261016 1.0843387
282000 1.0210332 0.93982023 -0.11219324 1.0790461
284000 1.0157606 1.0203143 0.0002164565 1.0721431
286000 1.0062366 1.0025507 -0.16786234 1.0720064
288000 0.98467873 1.2326624 -0.081203997 1.0660396
290000 1.0099975 0.88882236 -0.031064103 1.0590327
292000 1.0122416 1.0611548 -0.022475529 1.0519549
294000 1.0104116 1.0266518 -0.10512697 1.0414083
296000 1.0034132 1.0427754 -0.014337433 1.0415291
298000 1.0171588 0.92899734 0.10623709 1.0432266
300000 1.0280222 1.0524269 0.079178549 1.0534846
302000 1.035771 0.87031074 0.029223556 1.0548035
304000 0.99817826 0.96586889 -0.092577945 1.051271
306000 0.99961879 1.1082249 -0.079054344 1.0495721
308000 1.0136108 1.0992365 -0.11696242 1.0384906
310000 0.99316114 1.0758087 0.067733542 1.0276102
312000 1.0106481 0.99751609 0.096323719 1.0260196
314000 1.0069421 1.0474061 -0.0071188531 1.0257001
316000 1.0401836 0.81939716 -0.088499972 1.0302389
318000 1.0095707 1.1018438 -0.0069997734 1.0318989
320000 1.0316135 1.003588 0.010687649 1.0262453
322000 1.009186 0.93116391 0.02270494 1.0207195
324000 1.0186856 1.0207355 -0.049273034 1.0315045
326000 1.0496148 0.9479271 -0.019377803 1.0186608
328000 1.0280164 0.83246382 -0.067199824 1.0121899
330000 1.0292958 0.96946051 -0.0067323294 1.0106087
332000 1.0118055 0.94580297 -0.1158678 0.99982007
334000 1.0090884 1.1414243 -0.082638749 0.98931612
336000 0.96668553 1.2041384 0.0042176058 0.98213644
338000 1.0292409 0.91712359 -0.10674714 1.0014886
340000 1.0056353 1.0054878 -0.067790602 0.97639404
342000 1.0105034 1.1000009 -0.065106486 0.98781851
344000 1.0296097 0.97446628 -0.11031518 0.98121512
346000 1.022878 1.0302285 -0.092796664 1.0040982
348000 1.0200294 0.84461432 0.001340607 1.0143357
350000 0.9942428 1.0974217 0.032976965 1.0066948
352000 1.0038173 1.1777572 -0.02105487 0.99841101
354000 1.0363725 1.0742789 -0.068095272 0.99311679
356000 1.0142211 0.93380261 0.011873553 0.98531527
358000 0.99346289 1.2559305 -0.1027067 0.98126142
360000 0.99957906 1.0307272 -0.052751638 1.0043971
362000 1.0196151 1.1349776 -0.09260849 1.0011441
364000 1.0371154 0.88342615 0.12450793 0.99706262
366000 1.014625 1.0304514 -0.027977229 0.9921965
368000 1.0584324 0.83998131 -0.07933342 0.99525213
370000 1.0480268 0.83980605 -0.089536871 0.99539504
372000 1.0124627 1.060244 0.14069432 0.99714731
374000 1.0319035 0.80898054 0.13773298 0.99196179
376000 1.0175987 0.86095756 -0.022196463 0.99034665
378000 1.024277 0.96855584 -0.082372168 0.98711506
380000 1.0309973 0.91266594 -0.0038718874 1.0004437
382000 1.0195474 0.84949163 -0.090011652 0.97877658
384000 1.0127199 0.92573997 -0.047436984 0.99568293
386000 1.0155482 1.0260345 0.058825776 1.0032397
388000 1.0341266 1.0684283 0.042324727 0.9962933
390000 1.015419 1.2043476 -0.065809399 0.98978792
392000 0.99510423 1.0679104 0.1194931 0.98198405
394000 0.99275686 1.1827413 0.064956819 1.0203304
396000 1.0004565 1.1524019 -0.12851079 1.0328568
398000 1.0230487 1.1653679 0.066552948 1.0356753
400000 1.0246668 1.0378562 -0.014987589 1.0388305
402000 0.99713302 0.98996019 -0.12440697 1.0369703
404000 1.0078626 1.0678616 -0.0361031 1.0292353
406000 1.0264278 0.91482461 0.1001659 1.0269674
408000 0.99866487 1.1801482 -0.062540579 1.021615
410000 0.97734309 1.1861242 0.05416943 1.014162
412000 1.0157071 0.9442541 0.22262556 1.0141824
414000 0.98254015 1.2581149 0.015246929 1.0085563
416000 1.0325598 0.90098178 0.041081387 1.0044668
418000 1.0285532 0.82679005 -0.10105529 1.0017654
420000 1.0324223 0.95868597 0.024808094 0.99789922
422000 1.0056928 1.0690554 -0.024850455 1.0197904
424000 0.99482351 1.1228662 0.049501791 1.0272213
426000 1.0222594 0.97941801 -0.11968536 1.0186344
428000 1.0111263 1.1141009 0.1437415 1.0130656
430000 0.98139004 1.0366378 0.067956814 1.0108714
432000 0.98613642 1.0119979 0.041509654 1.0033766
434000 1.0230324 0.86869314 0.055734923 1.0020727
436000 1.0212417 0.8436869 -0.022905431 0.9985587
438000 1.0093302 0.97821341 0.023100883 0.99687144
440000 1.0419272 0.87856473 -0.020071536 0.99762884
442000 1.0172555 0.90164932 0.19704935 0.99904268
444000 1.0399087 1.0051297 -0.022213498 0.99616218
446000 1.0281756 1.0867446 -0.048363674 0.99230925
448000 0.98980118 1.1266212 0.16193455 0.99381525
450000 1.0397066 1.0216642 -0.017946472 1.0119634
452000 1.0148816 1.0709423 -0.072255226 1.0011103
454000 0.97505657 1.1553955 -0.019747328 0.9952685
456000 1.0423127 0.93927199 0.1031593 1.0160711
458000 1.0185738 0.9317795 -0.14238875 1.0212947
460000 1.0254941 0.94237321 0.17279884 1.0176267
462000 1.0331624 0.90556647 -0.17064389 1.0197747
464000 1.0170281 0.98452898 -0.17212408 1.006159
466000 1.0201836 1.0477978 0.0063101913 0.99741201
468000 0.99055758 1.19768 -0.04304958 0.99395064
470000 1.0140337 1.1042576 0.06483947 1.0006513
472000 1.0369845 0.82562513 -0.06621037 1.0320218
474000 1.0149565 0.86550007 0.060011486 1.0723558
476000 1.0056806 0.99384495 -0.069441814 1.0623019
478000 1.0333144 0.91193908 0.0045431056 1.0625281
480000 1.0176402 0.90416174 -0.065787627 1.0534142
482000 0.99406615 1.1281258 0.15969853 1.0526461
484000 1.0119737 1.0284268 -0.020359549 1.0710582
486000 0.98481179 1.08347 0.049797547 1.0738962
488000 1.0444857 0.87660853 0.0011127729 1.0730464
490000 1.0253141 0.92405109 0.070770655 1.0712017
492000 1.0167975 0.88249423 0.12097353 1.0689941
494000 0.96051412 1.3166559 -0.034841104 1.0721439
496000 1.0284614 1.0149666 -0.0055275607 1.0641449
498000 1.0107367 1.0406533 -0.030980028 1.0623882
500000 0.9902026 1.2232023 -0.038731213 1.0606073
Loop time of 70.5579 on 1 procs for 500000 steps with 800 atoms
Pair time (%) = 47.4863 (67.3012)
Neigh time (%) = 11.1177 (15.7568)
Comm time (%) = 1.90226 (2.69603)
Outpt time (%) = 0.00377345 (0.00534802)
Other time (%) = 10.0479 (14.2406)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 260 ave 260 max 260 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5611 ave 5611 max 5611 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5611
Ave neighs/atom = 7.01375
Neighbor list builds = 59311
Dangerous builds = 0
variable eta equal v_v11
print "running average viscosity: ${eta}"
running average viscosity: 1.06060731864499

230
examples/VISCOSITY/log.1Feb14.mp.2d.g++.1
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LAMMPS (1 Feb 2014)
# sample LAMMPS input script for viscosity of 2d LJ liquid
# Muller-Plathe via fix viscosity
# settings
variable x equal 20
variable y equal 20
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
lattice sq2 ${rho}
lattice sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox block 0 $x 0 $y -0.1 0.1
region simbox block 0 20 0 $y -0.1 0.1
region simbox block 0 20 0 20 -0.1 0.1
create_box 1 simbox
Created orthogonal box = (0 0 -0.182574) to (36.5148 36.5148 0.182574)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff * * 1 1
mass * 1.0
velocity all create $t 97287
velocity all create 1 97287
fix 1 all nve
fix 2 all langevin $t $t 0.1 498094
fix 2 all langevin 1 $t 0.1 498094
fix 2 all langevin 1 1 0.1 498094
fix 3 all enforce2d
# equilibration run
thermo 1000
run 5000
Memory usage per processor = 2.06394 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.56617 -1.535262
1000 0.95906897 -1.571142 0 -0.61327189 0.82593948
2000 1.0164992 -1.6006146 0 -0.58538603 0.88642098
3000 1.0429232 -1.5801639 0 -0.53854441 1.157286
4000 1.0955206 -1.6156387 0 -0.52148756 0.94410568
5000 0.94117593 -1.6155055 0 -0.67550602 0.79354126
Loop time of 0.858331 on 1 procs for 5000 steps with 800 atoms
Pair time (%) = 0.46184 (53.8067)
Neigh time (%) = 0.102345 (11.9237)
Comm time (%) = 0.0174992 (2.03875)
Outpt time (%) = 5.10216e-05 (0.00594428)
Other time (%) = 0.276596 (32.2248)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 256 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5583 ave 5583 max 5583 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5583
Ave neighs/atom = 6.97875
Neighbor list builds = 551
Dangerous builds = 0
unfix 2
# turn on Muller-Plathe driving force and equilibrate some more
velocity all scale $t
velocity all scale 1
fix 4 all viscosity 100 x y 20
fix 5 all ave/spatial 20 50 1000 y center 0.05 vx units reduced file profile.mp.2d
# equilibration run
variable dVx equal f_5[11][3]-f_5[1][3]
thermo 1000
thermo_style custom step temp epair etotal press f_4 v_dVx
run 20000
WARNING: Fix viscosity comes before fix ave/spatial (../fix_viscosity.cpp:129)
Memory usage per processor = 2.06486 Mbytes
Step Temp E_pair TotEng Press 4 dVx
5000 1 -1.6155055 -0.61675549 0.82879159 0 0
6000 0.98687509 -1.6019556 -0.6163141 0.81812957 -40.544054 0.48107738
7000 0.99812635 -1.61413 -0.6172513 0.88049928 -72.131982 0.83982485
8000 0.99508548 -1.6108778 -0.61703621 1.0010053 -105.28099 0.80829601
9000 0.94912106 -1.564488 -0.61655333 1.0184324 -141.59349 0.94800981
10000 0.99258056 -1.6078678 -0.61652794 0.94564321 -171.73806 1.1494339
11000 1.0159215 -1.6317434 -0.61709181 0.92235272 -199.00526 1.1830449
12000 1.0126611 -1.6277928 -0.61639754 0.7688915 -227.93583 1.2636885
13000 1.0122947 -1.6285623 -0.61753296 0.88334788 -258.44565 1.217365
14000 1.0175562 -1.6335087 -0.61722444 0.84125493 -282.91095 1.3683789
15000 0.97750561 -1.5930807 -0.61679697 1.1287326 -313.39632 1.2230677
16000 0.98242425 -1.5980008 -0.61680456 0.91325299 -339.83912 1.2882183
17000 1.008242 -1.6242405 -0.61725887 0.87284759 -365.79175 1.4803679
18000 0.99455824 -1.610205 -0.61688999 0.80190574 -391.57365 1.3145093
19000 1.0075504 -1.6245154 -0.61822443 1.1173911 -419.47456 1.2444018
20000 1.0169723 -1.6334224 -0.6177213 0.8584711 -448.67177 1.2101637
21000 0.98967224 -1.6055692 -0.61713404 0.80442505 -476.9284 1.4306147
22000 0.97813764 -1.5935756 -0.61666068 0.99668957 -501.83621 1.5824584
23000 0.98098823 -1.5963749 -0.61661287 1.1169304 -526.25935 1.4837827
24000 1.0002987 -1.6158635 -0.61681517 0.92338935 -554.31346 1.3408732
25000 0.99862734 -1.6139679 -0.61658884 0.87430158 -582.99367 1.2441321
Loop time of 2.75452 on 1 procs for 20000 steps with 800 atoms
Pair time (%) = 1.86056 (67.5458)
Neigh time (%) = 0.440814 (16.0033)
Comm time (%) = 0.0745592 (2.7068)
Outpt time (%) = 0.000242233 (0.00879403)
Other time (%) = 0.378341 (13.7353)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 253 ave 253 max 253 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5598 ave 5598 max 5598 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5598
Ave neighs/atom = 6.9975
Neighbor list builds = 2354
Dangerous builds = 0
# data gathering run
# reset fix viscosity to zero flux accumulation
unfix 4
fix 4 all viscosity 100 x y 20
variable visc equal -(f_4/(2*(step*0.005-125)*lx+1.0e-10))/(v_dVx/(ly/2))
fix vave all ave/time 1000 1 1000 v_visc ave running start 26000
thermo_style custom step temp f_4 v_dVx v_visc f_vave
# only need to run for 10000 steps to make a good 100-frame movie
#dump 1 all custom 100 dump.mp.2d id type x y z vx
#dump 1 all image 100 image.*.jpg vx type zoom 1.6 adiam 1.2
#dump_modify 1 pad 5 amap -0.7 0.7 ca 0.0 2 min blue max red
run 50000
Memory usage per processor = 2.103 Mbytes
Step Temp 4 dVx visc vave
25000 0.99862734 0 1.2441321 0 0
26000 1.006121 -29.834985 1.0067717 1.4817155 0.74085773
27000 1.000685 -57.28656 1.3703643 1.0450973 0.84227093
28000 1.0119383 -82.689969 1.5329066 0.8990542 0.85646674
29000 1.005591 -111.52398 1.3679394 1.0190874 0.88899088
30000 0.9780793 -132.09122 1.4693711 0.89896428 0.89065311
31000 0.98954223 -160.54318 1.4144949 0.94582162 0.89853433
32000 0.98452695 -186.95511 1.3592447 0.9824527 0.90902412
33000 1.0137305 -216.75823 1.1667402 1.1611316 0.93703607
34000 1.004699 -243.79453 1.3554751 0.99921723 0.94325418
35000 0.99279233 -272.99034 1.4414031 0.94696042 0.94359111
36000 0.98601686 -296.44885 1.2290954 1.0963305 0.9563194
37000 0.99960393 -327.77258 1.2754827 1.0707469 0.96512151
38000 1.0232092 -354.20371 1.471032 0.92609943 0.96233422
39000 1.0220897 -380.33308 1.4729611 0.92217809 0.95965714
40000 1.003192 -409.96551 1.1486002 1.189754 0.9740382
41000 1.0339239 -441.2471 1.2766924 1.0800543 0.98027444
42000 0.9707256 -469.29726 1.298219 1.0632151 0.98488226
43000 1.012508 -498.86351 1.3419554 1.0326215 0.98739485
44000 1.0104362 -528.29202 1.2868256 1.0803656 0.99204339
45000 1.0031694 -554.14027 1.3431643 1.0314082 0.9939179
46000 0.98757964 -582.17026 1.3410473 1.0336098 0.99572208
47000 1.0329913 -612.8052 1.0693478 1.3024192 1.0090567
48000 1.0040957 -640.38 1.3648753 1.0199689 1.0095114
49000 1.0213711 -667.39045 1.3779353 1.0090436 1.0094927
50000 1.0028765 -693.00523 1.353182 1.0242602 1.0100607
51000 1.0456929 -723.75516 1.3013825 1.0695063 1.0122624
52000 0.98661701 -753.9132 1.1752559 1.1879417 1.0185366
53000 1.0067127 -785.13019 1.0304513 1.3605866 1.0303315
54000 1.0049746 -814.24066 1.3688029 1.0256138 1.0301742
55000 0.99145341 -839.02294 1.5370182 0.90979505 1.026291
56000 0.99330997 -866.91329 1.4290157 0.9784688 1.0247966
57000 0.97297071 -891.05513 1.3697724 1.016427 1.0245429
58000 1.0055628 -915.32616 1.7035058 0.81411979 1.018354
59000 0.97447836 -940.88078 1.4544592 0.95131452 1.0164386
60000 0.97786144 -970.22273 1.3938314 0.99440472 1.0158266
61000 1.0069781 -996.52024 1.2925348 1.0708074 1.0173125
62000 0.99860063 -1024.4668 1.3677043 1.0122178 1.0171785
63000 1.0160002 -1052.8951 1.2909807 1.0731286 1.0186131
64000 1.0075017 -1081.0833 1.4389443 0.96320906 1.017228
65000 1.0128103 -1110.5507 1.3712762 1.0123332 1.0171086
66000 0.99788687 -1138.143 1.1744686 1.1817934 1.0210297
67000 0.99340723 -1165.3818 1.2141024 1.1427037 1.0238593
68000 0.99891442 -1194.3011 1.1838074 1.1730981 1.0272511
69000 1.010782 -1222.8307 1.2890796 1.0779631 1.028378
70000 1.0084059 -1254.3924 1.3961366 0.99830441 1.0277242
71000 0.98457274 -1285.1565 1.3228471 1.055987 1.0283256
72000 0.98997963 -1309.8959 1.3420552 1.0383376 1.0285342
73000 0.99661456 -1338.2166 1.114478 1.2507878 1.0330699
74000 0.98823959 -1367.5535 1.1382114 1.2260136 1.0369288
75000 0.99114295 -1396.3043 1.181084 1.1822226 1.0397777
Loop time of 6.87975 on 1 procs for 50000 steps with 800 atoms
Pair time (%) = 4.64786 (67.5585)
Neigh time (%) = 1.09953 (15.9821)
Comm time (%) = 0.184543 (2.68241)
Outpt time (%) = 0.000693083 (0.0100742)
Other time (%) = 0.947126 (13.7669)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 257 ave 257 max 257 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5559 ave 5559 max 5559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5559
Ave neighs/atom = 6.94875
Neighbor list builds = 5873
Dangerous builds = 0

271
examples/VISCOSITY/log.1Feb14.nemd.2d.g++.1
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LAMMPS (1 Feb 2014)
# sample LAMMPS input script for viscosity of 2d LJ liquid
# NEMD via fix deform and fix nvt/sllod
# settings
variable x equal 20
variable y equal 20
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
variable srate equal 2.7
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
# problem setup
lattice sq2 ${rho}
lattice sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox prism 0 $y 0 $y -0.1 0.1 0.0 0.0 0.0
region simbox prism 0 20 0 $y -0.1 0.1 0.0 0.0 0.0
region simbox prism 0 20 0 20 -0.1 0.1 0.0 0.0 0.0
create_box 1 simbox
Created triclinic box = (0 0 -0.182574) to (36.5148 36.5148 0.182574) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff * * 1 1
mass * 1.0
velocity all create $t 97287
velocity all create 1 97287
fix 1 all nve
fix 2 all langevin $t $t 0.1 498094
fix 2 all langevin 1 $t 0.1 498094
fix 2 all langevin 1 1 0.1 498094
fix 3 all enforce2d
# equilibration run
thermo 1000
run 5000
Memory usage per processor = 2.06394 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.56617 -1.535262
1000 0.9455393 -1.573329 0 -0.62897162 0.91884199
2000 1.0359047 -1.6229551 0 -0.58834528 0.96136682
3000 1.0171488 -1.5468681 0 -0.53099077 1.1078235
4000 1.0040221 -1.5977142 0 -0.59494717 0.92428924
5000 0.95883045 -1.6087309 0 -0.65109902 0.92015627
Loop time of 0.897984 on 1 procs for 5000 steps with 800 atoms
Pair time (%) = 0.464335 (51.7087)
Neigh time (%) = 0.13359 (14.8767)
Comm time (%) = 0.0208902 (2.32635)
Outpt time (%) = 5.31673e-05 (0.00592074)
Other time (%) = 0.279115 (31.0824)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 266 ave 266 max 266 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5604 ave 5604 max 5604 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5604
Ave neighs/atom = 7.005
Neighbor list builds = 548
Dangerous builds = 0
unfix 1
unfix 2
# turn on NEMD shear and equilibrate some more
velocity all scale $t
velocity all scale 1
variable xyrate equal ${srate}/lx
variable xyrate equal 2.7/lx
fix 1 all nvt/sllod temp $t $t 0.1
fix 1 all nvt/sllod temp 1 $t 0.1
fix 1 all nvt/sllod temp 1 1 0.1
fix 2 all deform 1 xy erate ${xyrate} remap v
fix 2 all deform 1 xy erate 0.0739425452631974 remap v
fix 4 all ave/spatial 20 250 5000 y center 0.05 vx units reduced file profile.nemd.2d
compute usual all temp
compute tilt all temp/deform
thermo 1000
thermo_style custom step temp c_usual epair etotal press pxy
thermo_modify temp tilt
run 50000
Memory usage per processor = 2.06486 Mbytes
Step Temp usual E_pair TotEng Press Pxy
5000 2.2074694 1 -1.6087309 0.59597912 1.6684032 -0.13173614
6000 0.92758142 1.0829648 -1.6587109 -0.732289 0.69434408 -0.040395721
7000 0.95692582 1.2000988 -1.7242343 -0.76850461 0.58119159 -0.078038652
8000 1.0214774 1.223802 -1.6519928 -0.63179227 0.74285068 -0.10278761
9000 1.0293091 1.3122841 -1.6684363 -0.64041383 0.90722071 -0.19178365
10000 1.0445241 1.3788798 -1.6688897 -0.62567124 0.71535783 -0.086951926
11000 1.0023372 1.362187 -1.6622117 -0.66112741 0.71746537 -0.18121663
12000 0.95256804 1.379025 -1.6574208 -0.70604349 0.57745775 -0.040719788
13000 1.0318148 1.4597155 -1.6433202 -0.61279515 0.65027764 -0.093427737
14000 1.0332344 1.4031097 -1.6290961 -0.59715319 0.90536763 0.0020682054
15000 1.0277172 1.5207267 -1.6221988 -0.59576627 0.84609392 -0.0074794989
16000 0.99207101 1.5017016 -1.6247974 -0.63396649 0.92606954 -0.10188984
17000 0.96488503 1.4793873 -1.600228 -0.63654911 0.89923523 -0.14261301
18000 0.99547475 1.5236224 -1.635473 -0.64124255 0.68307708 -0.25098795
19000 1.0323664 1.5855445 -1.6227003 -0.59162439 0.94072356 -0.09360683
20000 1.0180092 1.5842966 -1.6143642 -0.59762743 0.93103828 0.040342848
21000 1.0254077 1.6283785 -1.6301278 -0.60600186 0.87479869 0.044804621
22000 0.97172908 1.5990643 -1.6486056 -0.67809118 0.76887644 0.037405021
23000 0.97049676 1.6076804 -1.6058839 -0.63660024 0.93367017 -0.024871417
24000 1.0026729 1.6776495 -1.622805 -0.62138548 0.8635542 -0.038997148
25000 0.9633361 1.6349825 -1.6404336 -0.67830169 0.76001017 -0.1311218
26000 1.0001388 1.6907443 -1.6004823 -0.60159366 0.81806855 -0.18349721
27000 0.94191819 1.6384271 -1.5965443 -0.65580352 0.95785507 -0.086102432
28000 1.0108584 1.731468 -1.6463325 -0.63673767 0.74516073 -0.19911341
29000 1.0138048 1.7289581 -1.6000006 -0.58746311 0.94740326 0.016609077
30000 1.0050557 1.7572204 -1.599182 -0.59538264 0.8223186 -0.24136602
31000 1.0344558 1.7783254 -1.6122236 -0.57906086 1.1734714 -0.23484979
32000 1.0174318 1.8509241 -1.5854329 -0.56927295 0.81903748 -0.096360108
33000 1.0052704 1.7954794 -1.6076165 -0.60360266 0.98062712 -0.23179974
34000 1.0138726 1.7784382 -1.6535717 -0.64096651 0.79928063 -0.184148
35000 1.0108265 1.7715149 -1.5944308 -0.58486783 0.999611 -0.11864672
36000 0.98516241 1.7509661 -1.6285996 -0.64466861 0.94523235 -0.13010197
37000 0.971965 1.7638125 -1.5746851 -0.60393507 1.2265617 -0.077584507
38000 0.93549343 1.8078749 -1.5840479 -0.64972382 1.0484769 0.031083799
39000 1.0416402 1.8705987 -1.5799828 -0.53964462 0.94816785 -0.0034475262
40000 0.96016973 1.856959 -1.5958952 -0.63692565 0.94610429 -0.18285492
41000 1.0051478 1.8962677 -1.5860155 -0.58212412 1.0946382 -0.068521999
42000 1.0081883 1.8593802 -1.6072469 -0.6003189 0.94320687 -0.041090231
43000 0.98432329 1.8786095 -1.5924866 -0.60939372 1.0486461 -0.12281617
44000 1.0262999 1.9116758 -1.5900042 -0.56498711 1.1223199 0.018952448
45000 0.96577584 1.8870562 -1.6252423 -0.66067367 0.96036779 0.0028994584
46000 1.0245911 1.9444906 -1.613004 -0.58969369 0.99363465 -0.021819492
47000 0.93381748 1.8446233 -1.5772527 -0.64460252 1.0674773 -0.11978723
48000 0.97729437 1.8717878 -1.5711485 -0.59507573 1.1563358 -0.25770589
49000 1.0354354 1.987001 -1.6136701 -0.57952894 0.88244264 0.096378234
50000 1.0094924 1.9808787 -1.612573 -0.60434244 0.94984417 -0.11436064
51000 1.027174 1.9461247 -1.5899623 -0.5640723 1.0198367 0.065037899
52000 1.0281396 2.019881 -1.6005519 -0.57369755 1.0350175 -0.057470252
53000 1.018099 2.0455373 -1.6308565 -0.6140301 0.98344621 -0.095749654
54000 1.0378532 2.0621046 -1.6137201 -0.5771642 0.92484803 -0.20897708
55000 0.94998276 1.9258606 -1.5946282 -0.6458329 1.0304527 -0.061356231
Loop time of 11.8921 on 1 procs for 50000 steps with 800 atoms
Pair time (%) = 4.938 (41.5235)
Neigh time (%) = 2.88697 (24.2764)
Comm time (%) = 0.342039 (2.87619)
Outpt time (%) = 0.00175095 (0.0147236)
Other time (%) = 3.72331 (31.3092)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 286 ave 286 max 286 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5610 ave 5610 max 5610 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5610
Ave neighs/atom = 7.0125
Neighbor list builds = 11310
Dangerous builds = 0
# data gathering run
variable visc equal -pxy/(v_srate/ly)
fix vave all ave/time 10 100 1000 v_visc ave running start 56000
thermo_style custom step temp press pxy v_visc f_vave
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:665)
thermo_modify temp tilt
# only need to run for 5400 steps to make a good 100-frame movie
# set 54K steps above in equil and 5400 here simply to make good movie
# 54K and 5400 are multiples of box-swap periodicity = 2700 steps
#dump 1 all custom 50 dump.nemd.2d id type x y z vx
#dump 1 all image 50 image.*.jpg vx type zoom 1.2 adiam 1.2
#dump_modify 1 pad 5 amap 0.0 ${srate} ca 0.0 2 min blue max red
run 50000
Memory usage per processor = 2.10508 Mbytes
Step Temp Press Pxy visc vave
55000 0.94998276 1.0303592 -0.063500962 0.85878789 0
56000 1.0301515 1.0617767 -0.10024411 1.3557027 1.2310718
57000 1.0250473 1.0794382 -0.32669382 4.4182117 1.2359148
58000 0.98594086 1.1283437 0.0380247 -0.51424657 1.30918
59000 1.0164723 1.0980255 -0.069171978 0.93548279 1.3260744
60000 1.0711985 1.1230358 -0.125773 1.7009558 1.3414067
61000 0.98932053 0.9807511 -0.15097335 2.0417657 1.3671221
62000 0.998341 0.81153573 -0.020326294 0.27489307 1.3670784
63000 1.0718254 1.1974744 -0.1580162 2.1370132 1.3213502
64000 1.0057042 1.0230065 0.034014907 -0.46001807 1.3316618
65000 1.0040774 1.0303633 -0.078600273 1.0629912 1.3072524
66000 1.0382782 0.93946231 -0.043423028 0.58725363 1.2837103
67000 1.0226248 0.98900989 -0.054099059 0.73163642 1.253851
68000 0.96605035 1.2060528 0.011937095 -0.16143744 1.2420174
69000 1.0326968 1.0489439 -0.055891469 0.75587699 1.2551535
70000 0.98367121 0.87910603 -0.16249968 2.1976479 1.2607276
71000 1.02139 1.0729641 0.014510511 -0.19624035 1.2555329
72000 0.95586405 0.82121701 0.016186091 -0.21890092 1.2511372
73000 1.0422537 0.8674772 0.029604958 -0.40037786 1.2700259
74000 1.0249336 1.0985439 -0.13831417 1.8705627 1.2656874
75000 0.98213321 0.88865968 0.045972743 -0.62173601 1.2577007
76000 0.9397546 0.71322157 -0.060283057 0.81526889 1.2699146
77000 1.0063205 1.0310471 -0.065558372 0.88661232 1.2675723
78000 0.96815308 1.1257553 0.025044943 -0.33870816 1.258244
79000 1.039923 1.1557001 -0.16485925 2.2295587 1.2397555
80000 1.0203604 0.88432557 -0.096887682 1.3103103 1.2385055
81000 0.9504362 0.98117588 -0.078463955 1.0611476 1.2476425
82000 0.9959177 1.1195113 -0.013058798 0.17660736 1.2360316
83000 1.0001019 0.90295804 -0.26432373 3.5747177 1.2339827
84000 1.0173461 0.84946561 0.12193823 -1.6490943 1.2473019
85000 1.0325527 1.0523874 0.030626506 -0.41419329 1.2440578
86000 0.94990925 1.0851851 -0.28324305 3.8305829 1.2410903
87000 1.0408269 1.2359016 -0.07443383 1.0066441 1.2404526
88000 1.0006532 0.92603737 -0.20524087 2.7756803 1.2439314
89000 0.99846847 0.94779421 -0.047328236 0.64006771 1.2443818
90000 0.98628639 1.0536216 -0.15876739 2.1471724 1.2354671
91000 0.99478876 1.0885053 -0.17485734 2.3647731 1.2249337
92000 1.0423662 0.95712108 -0.13839217 1.8716176 1.2276722
93000 0.99308815 1.1868657 -0.13322814 1.8017792 1.2254173
94000 0.9835718 0.98339544 -0.10768988 1.4563994 1.224888
95000 0.94438219 0.97622034 -0.068799681 0.93044784 1.2204198
96000 1.0142012 0.9210571 -0.14001612 1.8935799 1.217945
97000 0.99678643 1.2773861 -0.091691808 1.2400413 1.2063637
98000 0.96852646 0.89124039 -0.28173744 3.810221 1.203252
99000 0.97030968 1.0148935 -0.11717859 1.5847249 1.2020913
100000 0.97709835 1.0314408 -0.16108012 2.1784497 1.2019234
101000 0.97653875 1.1948328 -0.085456884 1.1557201 1.2026873
102000 0.97469158 1.0508677 -0.062662919 0.84745418 1.2062227
103000 0.99620509 0.96826158 -0.10181244 1.3769128 1.20325
104000 0.98933536 1.0077017 -0.18015152 2.4363717 1.1999909
105000 0.99627299 0.93278548 -0.099781319 1.3494439 1.2018992
Loop time of 12.3598 on 1 procs for 50000 steps with 800 atoms
Pair time (%) = 5.02156 (40.6281)
Neigh time (%) = 3.14134 (25.4158)
Comm time (%) = 0.36303 (2.93718)
Outpt time (%) = 0.00100946 (0.00816731)
Other time (%) = 3.83288 (31.0108)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 256 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5616 ave 5616 max 5616 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5616
Ave neighs/atom = 7.02
Neighbor list builds = 12247
Dangerous builds = 0

221
examples/VISCOSITY/log.1Feb14.wall.2d.g++.1
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@ -1,221 +0,0 @@
LAMMPS (1 Feb 2014)
# sample LAMMPS input script for viscosity of 2d LJ liquid
# use shearing wall, thermostat via fix langevin
# settings
variable x equal 20
variable y equal 20
variable ylo equal -2.5
variable yhi equal 23
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
variable srate equal 2.7
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
lattice sq2 ${rho}
lattice sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox block 0 $x ${ylo} ${yhi} -0.1 0.1
region simbox block 0 20 ${ylo} ${yhi} -0.1 0.1
region simbox block 0 20 -2.5 ${yhi} -0.1 0.1
region simbox block 0 20 -2.5 23 -0.1 0.1
create_box 3 simbox
Created orthogonal box = (0 -4.56435 -0.182574) to (36.5148 41.9921 0.182574)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 1020 atoms
mass * 1.0
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff * * 1 1
region lower block INF INF INF 0.0 INF INF
region upper block INF INF $y INF INF INF
region upper block INF INF 20 INF INF INF
group lower region lower
120 atoms in group lower
group upper region upper
120 atoms in group upper
set group lower type 2
120 settings made for type
set group upper type 3
120 settings made for type
group wall union lower upper
240 atoms in group wall
group flow subtract all wall
780 atoms in group flow
velocity flow create $t 97287
velocity flow create 1 97287
velocity upper set ${srate} 0.0 0.0 units box
velocity upper set 2.7 0.0 0.0 units box
compute thermal flow temp/partial 0 1 0
compute flow flow temp
fix 1 all nve
fix 2 flow langevin $t $t 0.1 498094
fix 2 flow langevin 1 $t 0.1 498094
fix 2 flow langevin 1 1 0.1 498094
fix_modify 2 temp thermal
fix 3 wall setforce 0.0 0.0 0.0
fix 4 flow ave/spatial 20 500 10000 y center 0.05 vx units reduced file profile.wall.2d
fix 5 all enforce2d
# equilibration run
variable ybox equal $y*ylat
variable ybox equal 20*ylat
compute tilt flow temp/ramp vx 0 ${srate} y 0 ${ybox} units box
compute tilt flow temp/ramp vx 0 2.7 y 0 ${ybox} units box
compute tilt flow temp/ramp vx 0 2.7 y 0 36.5148371670111 units box
thermo 1000
thermo_style custom step temp c_tilt epair etotal press pxy
run 20000
Memory usage per processor = 2.06571 Mbytes
Step Temp tilt E_pair TotEng Press Pxy
0 1.1937193 2.1893943 -1.4419854 -0.24943634 -0.78936698 0.014349737
1000 1.3454512 1.9300306 -1.5968842 -0.25275207 0.66766599 -0.14162185
2000 1.4039346 1.7347137 -1.5342289 -0.13167071 1.008354 0.018819298
3000 1.4366164 1.6062771 -1.5387082 -0.10350032 1.0397303 -0.1707825
4000 1.4109705 1.529146 -1.5813814 -0.1717942 0.8261407 -0.083290587
5000 1.5048218 1.4638099 -1.4771896 0.026156803 1.2811761 0.10617426
6000 1.4732731 1.3291657 -1.5848926 -0.11306394 0.87088047 -0.078205262
7000 1.5878351 1.3674924 -1.5563906 0.029887788 1.0613527 -0.12731515
8000 1.6514036 1.3361332 -1.5283327 0.1214519 1.2440283 -0.22095466
9000 1.6293224 1.1961769 -1.5963023 0.031422811 0.78644571 -0.05204626
10000 1.6942081 1.2257803 -1.4599247 0.23262242 1.4657509 0.1035164
11000 1.7138453 1.1753464 -1.5590901 0.15307494 0.95417101 -0.025106722
12000 1.7266196 1.2007806 -1.5893891 0.13553773 1.0787435 0.098092592
13000 1.7207128 1.1144055 -1.5482322 0.17079356 1.1747293 -0.14991275
14000 1.7945777 1.1420807 -1.5829923 0.20982594 1.0237707 0.022798338
15000 1.8020798 1.0923181 -1.4742089 0.32610413 1.5137094 0.15142119
16000 1.8094386 1.1147657 -1.5756134 0.23205124 1.0384998 0.039411258
17000 1.8504661 1.1454342 -1.6013307 0.24732123 0.99885985 0.064524284
18000 1.8120967 1.0611987 -1.5274247 0.28289545 1.2153993 -0.26659063
19000 1.9125001 1.1489776 -1.5897343 0.32089077 0.92800706 -0.13377604
20000 1.8159111 1.0646767 -1.5138561 0.30027466 1.344041 0.13332455
Loop time of 4.58235 on 1 procs for 20000 steps with 1020 atoms
Pair time (%) = 2.26221 (49.3678)
Neigh time (%) = 0.727145 (15.8684)
Comm time (%) = 0.100413 (2.1913)
Outpt time (%) = 0.000513554 (0.0112072)
Other time (%) = 1.49207 (32.5613)
Nlocal: 1020 ave 1020 max 1020 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 327 ave 327 max 327 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6986 ave 6986 max 6986 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6986
Ave neighs/atom = 6.84902
Neighbor list builds = 3127
Dangerous builds = 0
# data gathering run
variable visc equal -pxy/(v_srate/ly)
fix vave all ave/time 1000 1 1000 v_visc ave running
thermo_style custom step temp pxy v_visc f_vave
thermo_modify temp tilt
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
# only need to run for 5000 steps to make a good 100-frame movie
#dump 1 all custom 50 dump.wall.2d id type x y z vx
#dump 1 all image 50 image.*.jpg vx type zoom 1.6 adiam 1.2
#dump_modify 1 pad 5 amap 0.0 ${srate} ca 0.0 2 min blue max red
run 50000
Memory usage per processor = 2.10386 Mbytes
Step Temp Pxy visc vave
20000 1.0646767 0.15189449 -2.6191346 -2.6191346
21000 1.0786918 -0.10890107 1.877794 -0.3706703
22000 1.0900211 0.13731881 -2.3678043 -1.0363816
23000 1.0651319 -0.28509211 4.9158768 0.45168298
24000 1.0175701 -0.040455765 0.69758351 0.50086309
25000 1.0125344 0.043662601 -0.75287937 0.29190601
26000 1.0857086 -0.19503005 3.3629261 0.73062318
27000 0.99062507 -0.053424367 0.92120263 0.75444561
28000 0.99171297 -0.058537212 1.009364 0.78276988
29000 1.0149672 -0.031160198 0.53729895 0.75822278
30000 1.0485095 0.19756111 -3.4065694 0.37960531
31000 1.0677328 -0.0041714932 0.071929547 0.35396567
32000 1.1082895 -0.056056758 0.96659327 0.40109087
33000 1.0048242 -0.1384997 2.3881667 0.54302485
34000 1.047045 -0.016373106 0.28232339 0.52564476
35000 1.0196427 0.16916051 -2.9168546 0.31048854
36000 1.0362892 -0.20425258 3.5219512 0.49939811
37000 1.0633356 0.10439152 -1.8000353 0.37165181
38000 1.015715 0.058051671 -1.0009918 0.29940741
39000 1.0385941 -0.16716069 2.8823715 0.42855562
40000 1.011397 -0.052797719 0.91039728 0.45150046
41000 0.98609436 -0.1553228 2.6782492 0.55271631
42000 0.96711394 -0.046794703 0.80688657 0.56376719
43000 0.99413772 0.035847044 -0.61811479 0.51452211
44000 1.0240733 0.02187727 -0.37723234 0.47885193
45000 0.97952963 0.097145869 -1.6750976 0.39600772
46000 1.0025347 -0.18830187 3.2469113 0.50159674
47000 1.0256026 -0.018237157 0.31446543 0.49491348
48000 0.98291299 0.179511 -3.0953293 0.371112
49000 1.0402649 -0.11378523 1.9620121 0.424142
50000 1.0049318 0.034725323 -0.59877283 0.39114475
51000 1.0732488 -0.209848 3.6184337 0.49199753
52000 0.97684232 0.00028492106 -0.0049129273 0.47693964
53000 0.92940891 0.11857333 -2.0445739 0.40277747
54000 1.0251118 -0.095039337 1.6387745 0.43809167
55000 0.99517914 0.063163955 -1.0891435 0.39566847
56000 0.99165209 -0.35577322 6.1346395 0.5507758
57000 1.0225405 -0.077905942 1.3433413 0.57163279
58000 1.0021926 0.20894163 -3.602805 0.46459592
59000 0.97414863 -0.21189296 3.6536952 0.5443234
60000 0.99605625 -0.029227184 0.50396777 0.54333912
61000 0.95282293 -0.26403219 4.5527381 0.638801
62000 0.94153456 0.0040018 -0.069003507 0.62234043
63000 1.0511126 -0.012076417 0.20823508 0.61292894
64000 1.0383869 -0.21624175 3.728682 0.6821679
65000 1.0060049 -0.10456568 1.8030384 0.70653465
66000 1.0325485 -0.068797861 1.1862896 0.7167422
67000 1.0362817 -0.13561168 2.3383682 0.75052608
68000 1.0058202 -0.039842193 0.68700361 0.7492297
69000 1.0175259 -0.18169494 3.1329872 0.79690485
70000 1.0369101 -0.16530295 2.8503381 0.83716825
Loop time of 11.5341 on 1 procs for 50000 steps with 1020 atoms
Pair time (%) = 5.65688 (49.0449)
Neigh time (%) = 1.88743 (16.3639)
Comm time (%) = 0.253797 (2.20041)
Outpt time (%) = 0.00080061 (0.00694124)
Other time (%) = 3.73519 (32.3839)
Nlocal: 1020 ave 1020 max 1020 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 318 ave 318 max 318 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6936 ave 6936 max 6936 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6936
Ave neighs/atom = 6.8
Neighbor list builds = 8105
Dangerous builds = 0

252
examples/VISCOSITY/profile.13Oct16.einstein.2d.g++.1 Normal file
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@ -0,0 +1,252 @@
# Time-averaged data for fix avstress
# TimeStep v_pxy v_pxx
2000 0.0112152 -0.0107584
4000 -0.00594131 0.00435131
6000 0.00389329 -0.0277649
8000 0.0136619 0.0219822
10000 0.0155701 0.00609565
12000 0.00513669 -0.00119588
14000 0.0231885 -0.00681743
16000 0.00390478 0.0084919
18000 -0.0326619 -0.00416449
20000 -0.00297889 0.00926245
22000 0.00997575 0.00581308
24000 -0.0047041 -0.0119796
26000 0.0195006 -0.00399279
28000 -0.024339 0.01404
30000 0.0116681 -0.016047
32000 0.0139385 0.00638643
34000 0.0167514 0.00952851
36000 0.00883586 0.010381
38000 0.00536862 -0.0171481
40000 0.0125036 0.00076643
42000 0.00648046 -0.00498005
44000 0.0215778 0.0189297
46000 -0.00252757 -0.00336276
48000 -0.000156431 -0.0066786
50000 -0.0047086 -0.00328836
52000 -0.00605692 0.0195077
54000 0.0247312 -0.0021608
56000 -0.00511857 0.00419997
58000 0.0045804 0.0280795
60000 -0.0191973 0.0153742
62000 0.0020883 -0.00189354
64000 0.00506313 0.010857
66000 0.0233461 -0.0148928
68000 3.57613e-05 0.0189441
70000 0.00079836 -0.000567262
72000 -0.00696381 -0.00396054
74000 -0.00611721 -0.0147648
76000 -0.015906 -0.00662096
78000 -0.00306063 0.00271182
80000 0.0163678 -0.0145694
82000 -0.00632992 0.00675694
84000 -0.0218173 -0.00904426
86000 0.0114677 0.00190344
88000 0.0213114 -0.0122265
90000 0.00854177 -0.0100828
92000 -0.00460807 0.000985539
94000 0.0014285 0.0108011
96000 -0.00529244 -0.00946798
98000 9.68498e-05 0.0108188
100000 0.00243376 0.00430553
102000 -0.00893423 -0.00808788
104000 0.0123899 -0.0229956
106000 0.00212593 -0.0139646
108000 -0.0252742 -0.0226157
110000 0.000788016 -0.0141218
112000 0.000468183 0.00109293
114000 0.00136814 -0.0117171
116000 -0.0177191 0.000832168
118000 0.0129068 -0.0149171
120000 0.00116866 -0.0200124
122000 -0.0130122 0.0130395
124000 -0.000154483 -0.000287707
126000 0.00197866 -0.0127332
128000 0.0193554 -0.0176931
130000 -0.0126289 0.0166008
132000 -0.000262967 0.0108516
134000 -0.00670943 0.0104416
136000 0.00693074 0.0173953
138000 0.00515614 -0.000308274
140000 0.00870144 -0.0235366
142000 -0.0201186 -0.00437381
144000 0.011766 0.0155147
146000 -0.0128676 -0.00650133
148000 0.0116631 -0.00953158
150000 -0.00821172 -0.00548749
152000 0.0104456 0.00704702
154000 -0.0047047 -0.00564389
156000 0.000244375 -0.0059448
158000 -0.00385306 0.00026724
160000 0.0171106 0.0259551
162000 -0.00195837 -0.013138
164000 0.0078954 -0.00129974
166000 0.0200195 -0.0198266
168000 0.0053295 -0.0147863
170000 -0.0196452 -0.0108867
172000 0.00280603 0.0146527
174000 -0.0279518 -0.0118242
176000 0.00119414 -0.00588482
178000 -0.0149993 -0.0240732
180000 -0.0177569 -0.016956
182000 0.0102718 -0.00533898
184000 -0.0118995 0.00695631
186000 0.00928944 0.0144769
188000 0.00497085 0.0136993
190000 -0.000606889 0.0145147
192000 0.00481227 -0.00513361
194000 0.00513961 0.0204281
196000 0.011369 -0.0140078
198000 -0.000724317 -0.00504636
200000 -0.00291217 0.0179881
202000 -0.00133784 -0.0114657
204000 0.00686573 0.0145062
206000 0.0158144 0.00581873
208000 0.00689676 -0.0224338
210000 -0.00664275 -0.0111897
212000 -0.0109287 -0.00066551
214000 0.0115689 0.000995814
216000 -0.00867718 0.000650033
218000 0.00627204 -0.0144768
220000 -0.00521014 0.0121676
222000 -0.00428168 -0.00633152
224000 -0.00654868 0.0265763
226000 0.0177518 0.000124554
228000 0.00583358 -0.00642626
230000 0.0014705 -0.0186267
232000 0.0109219 -0.00549566
234000 -0.00564671 0.0121772
236000 -0.00575428 -0.0196644
238000 0.00136122 -0.0096752
240000 0.00708473 -0.00503572
242000 -0.0026749 -0.00560035
244000 -0.00219854 -0.00726875
246000 0.00174551 0.000231263
248000 0.0111775 0.0116016
250000 -0.00696052 0.0187347
252000 0.00344586 -0.00933347
254000 -0.00268662 -0.0100337
256000 0.00138534 -0.00492126
258000 -0.00702809 0.0173528
260000 -0.00125056 -0.00912894
262000 -0.00114832 0.00337609
264000 -0.00216775 -0.00140793
266000 0.00819513 0.0127788
268000 0.0144847 -0.0161785
270000 -0.0066073 0.0212697
272000 0.00833153 -0.0115414
274000 -0.00107772 -0.014611
276000 -0.00533327 0.00248163
278000 -0.0163776 -0.0113668
280000 0.00555368 -0.0223461
282000 0.00563616 0.0265429
284000 -0.0179494 0.00476518
286000 -0.00771317 -0.0121056
288000 -0.00409544 -0.0215018
290000 0.00726948 0.0134949
292000 -0.00848839 -0.00345347
294000 -0.00111536 0.0121426
296000 0.00877703 0.0209606
298000 -0.000694413 0.0143579
300000 -0.0209555 0.0204249
302000 0.0112983 0.0126598
304000 -0.00525748 0.00433895
306000 0.0132304 -0.0100841
308000 -0.00118392 -0.0134092
310000 -0.00106683 -0.00152728
312000 0.00808451 0.0101688
314000 -0.0163681 0.0227848
316000 -0.00146785 -0.0183972
318000 0.00140947 -0.00273254
320000 -0.0157346 -0.00686335
322000 -0.0151801 0.0215325
324000 0.00148882 0.0001663
326000 -0.00219025 -0.00554906
328000 -0.00587419 0.0198721
330000 0.0029292 0.0219866
332000 0.00304407 -0.00248133
334000 -0.0129756 -0.000139413
336000 0.0100892 0.0233776
338000 0.0452773 -0.0108094
340000 0.0045576 0.0167445
342000 -0.0126063 0.00410148
344000 0.00995452 0.0158463
346000 -0.0186866 -0.00932274
348000 0.00252671 -0.00116703
350000 0.000444441 -0.0120751
352000 -0.0105078 -0.000712541
354000 0.00341219 -0.0146497
356000 0.00196385 0.0151272
358000 0.000779407 0.00821313
360000 -0.00485756 -0.0230288
362000 -0.00340491 0.00761238
364000 0.00194218 -0.0209546
366000 -0.0111596 -0.0183945
368000 -0.0183101 0.00497154
370000 -0.0115596 -0.00260055
372000 -0.00268967 0.0118089
374000 -0.010749 0.000853841
376000 0.00385487 0.0189515
378000 0.00374543 0.00367347
380000 -0.013307 0.0104089
382000 0.0219353 -0.014424
384000 0.00408444 -0.0138134
386000 -0.00454518 -0.0165659
388000 -0.00788435 -0.021046
390000 -0.00481921 -0.0023399
392000 -0.0266187 0.00230699
394000 0.00730945 -0.0060148
396000 -0.0060163 -0.000243301
398000 0.00126518 -0.00946377
400000 -0.00687236 -0.0101298
402000 -0.00451691 -0.00304899
404000 -0.0114194 -0.0102866
406000 -0.00282376 0.00611627
408000 -0.00759005 -0.0303386
410000 0.0110681 -0.00721844
412000 -0.00154634 0.0249071
414000 0.00929146 0.00296884
416000 -0.0125628 -0.0055945
418000 0.0275966 -0.0156531
420000 0.00184817 -0.0180493
422000 -0.0213345 0.0193638
424000 0.00643235 -0.00829116
426000 -0.00799869 0.00585681
428000 0.000798536 0.0150226
430000 0.0122463 0.00421654
432000 -0.00434519 -0.0118032
434000 -0.00564705 0.0218398
436000 0.000705922 -0.00284573
438000 0.0156651 -0.0118715
440000 -0.015039 -0.00869392
442000 -0.0221049 0.00912511
444000 0.0239486 0.0141022
446000 0.0160531 -0.00415558
448000 0.00271719 0.000247656
450000 -0.00740239 -0.000837733
452000 -0.00143208 0.00336615
454000 -0.00227802 -0.000325298
456000 0.0259573 0.00416625
458000 0.0215245 -0.00941907
460000 0.0215742 0.0092169
462000 -0.0254373 0.0243203
464000 -0.0134449 -0.00566257
466000 0.0066995 0.00352812
468000 -0.00983419 0.0125024
470000 0.00482886 0.0152908
472000 -0.0201795 -0.0066922
474000 -0.00919723 0.00325594
476000 -0.0164465 0.00667254
478000 -0.00592193 -0.0256195
480000 0.00838099 0.00543533
482000 0.0102201 -0.0024264
484000 0.0326097 -0.0282995
486000 -0.0109896 0.0091617
488000 0.0139754 -0.0275039
490000 -0.00914545 -0.00634295
492000 -0.0153782 -0.000833631
494000 0.00054007 -0.0107239
496000 0.0180085 -0.00633459
498000 -0.0348081 -0.00988871
500000 -0.0154982 0.00543841

100654
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# Chunk-averaged data for fix 4 and group file
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount vx
10000 20 800
1 0.025 35.66 -0.470575
2 0.075 37.568 -0.225693
3 0.125 39.752 0.00852933
4 0.175 40.656 0.107181
5 0.225 38.78 0.191338
6 0.275 40.436 0.323821
7 0.325 38.78 0.371811
8 0.375 39.124 0.498303
9 0.425 40.352 0.648676
10 0.475 41.204 0.711088
11 0.525 43.06 0.76846
12 0.575 41.772 0.811934
13 0.625 42.56 0.880722
14 0.675 41.036 0.973191
15 0.725 40.46 1.07152
16 0.775 41.288 1.17529
17 0.825 41.8 1.30633
18 0.875 39.692 1.4658
19 0.925 38.848 1.61786
20 0.975 37.172 1.86902
15000 20 800
1 0.025 37.936 -0.523926
2 0.075 38.856 -0.391729
3 0.125 38.392 -0.193245
4 0.175 39.836 -0.0469664
5 0.225 39.044 0.150486
6 0.275 39.6 0.28279
7 0.325 40.148 0.400922
8 0.375 41.86 0.53413
9 0.425 41.532 0.65385
10 0.475 41.156 0.749518
11 0.525 41.404 0.836633
12 0.575 40.464 0.949233
13 0.625 40.696 1.13119
14 0.675 42.232 1.25039
15 0.725 41.8 1.32974
16 0.775 39.792 1.38528
17 0.825 39.468 1.53692
18 0.875 39.096 1.63914
19 0.925 38.968 1.79107
20 0.975 37.72 1.99704
20000 20 800
1 0.025 38.076 -0.589435
2 0.075 37.828 -0.423807
3 0.125 37.44 -0.153006
4 0.175 40.416 0.0590355
5 0.225 41.208 0.220652
6 0.275 39.524 0.285201
7 0.325 40.928 0.366946
8 0.375 41.62 0.568277
9 0.425 40.86 0.732636
10 0.475 40.472 0.824144
11 0.525 40.804 0.994329
12 0.575 41.092 1.11979
13 0.625 40.652 1.28008
14 0.675 40.132 1.29687
15 0.725 40.552 1.42867
16 0.775 40.164 1.51387
17 0.825 40.1 1.61873
18 0.875 40.912 1.74019
19 0.925 38.276 1.85832
20 0.975 38.944 1.98187
25000 20 800
1 0.025 39.92 -0.380869
2 0.075 39.536 -0.160096
3 0.125 37.56 -0.104772
4 0.175 40.376 0.0104117
5 0.225 40.196 0.175219
6 0.275 39.288 0.270334
7 0.325 39.86 0.414566
8 0.375 39.832 0.542404
9 0.425 41.54 0.743595
10 0.475 40.32 0.850959
11 0.525 39.748 0.982747
12 0.575 40.496 1.20059
13 0.625 40.556 1.29414
14 0.675 40.652 1.47912
15 0.725 41.136 1.57179
16 0.775 39.62 1.64292
17 0.825 40.804 1.69484
18 0.875 39.952 1.81386
19 0.925 39.484 1.97894
20 0.975 39.124 2.11318
30000 20 800
1 0.025 38.104 -0.334541
2 0.075 38.928 -0.205184
3 0.125 38.9 -0.0388031
4 0.175 40.88 0.16266
5 0.225 41.32 0.19623
6 0.275 41.356 0.347679
7 0.325 39.692 0.454971
8 0.375 39.808 0.626317
9 0.425 39.984 0.784311
10 0.475 40.236 1.042
11 0.525 40.268 1.08957
12 0.575 40.408 1.15568
13 0.625 39.344 1.25902
14 0.675 40.552 1.41734
15 0.725 39.916 1.60261
16 0.775 40.764 1.65714
17 0.825 41.048 1.8373
18 0.875 39.964 1.90623
19 0.925 39.456 2.01719
20 0.975 39.072 2.20726
35000 20 800
1 0.025 40.312 -0.305842
2 0.075 39.764 -0.121733
3 0.125 39.86 -0.0175595
4 0.175 41.176 0.0613001
5 0.225 40.104 0.248255
6 0.275 40.84 0.399843
7 0.325 39.04 0.563049
8 0.375 38.364 0.70693
9 0.425 38.408 0.821042
10 0.475 39.116 0.950972
11 0.525 38.612 1.08255
12 0.575 41.528 1.2818
13 0.625 40.564 1.43281
14 0.675 38.252 1.50337
15 0.725 40.976 1.56708
16 0.775 38.96 1.69129
17 0.825 40.636 1.86217
18 0.875 41.276 1.99105
19 0.925 41.36 2.19729
20 0.975 40.852 2.27488
40000 20 800
1 0.025 40.748 -0.34792
2 0.075 40.288 -0.209767
3 0.125 39.02 -0.0880769
4 0.175 39.668 0.0965018
5 0.225 38.808 0.248214
6 0.275 41.164 0.456088
7 0.325 41.252 0.545656
8 0.375 39.048 0.698638
9 0.425 38.924 0.832061
10 0.475 39.08 0.972561
11 0.525 38.696 1.16521
12 0.575 39.716 1.39062
13 0.625 40.064 1.51667
14 0.675 41.548 1.63501
15 0.725 39.6 1.7307
16 0.775 38.596 1.88546
17 0.825 38.776 2.0565
18 0.875 40.712 2.1499
19 0.925 42.748 2.18582
20 0.975 41.544 2.20492
45000 20 800
1 0.025 41.832 -0.276046
2 0.075 40.764 -0.188173
3 0.125 40.928 -0.0908881
4 0.175 39.82 0.0951249
5 0.225 38.716 0.283778
6 0.275 40.116 0.465232
7 0.325 40.88 0.581611
8 0.375 40.5 0.743099
9 0.425 39.432 0.965275
10 0.475 38.092 1.1074
11 0.525 38.184 1.27274
12 0.575 38.708 1.46798
13 0.625 39.408 1.57009
14 0.675 39.496 1.5995
15 0.725 41.184 1.72685
16 0.775 39.82 1.87856
17 0.825 40.144 2.04806
18 0.875 41.016 2.21222
19 0.925 41.064 2.33709
20 0.975 39.896 2.3012
50000 20 800
1 0.025 40.892 -0.207683
2 0.075 41.384 -0.0659192
3 0.125 40.86 0.0440943
4 0.175 40.56 0.174286
5 0.225 39.44 0.306898
6 0.275 40.288 0.422548
7 0.325 41.924 0.564891
8 0.375 39.68 0.746744
9 0.425 39.66 0.917907
10 0.475 39.072 1.1111
11 0.525 38.48 1.3334
12 0.575 37.516 1.46033
13 0.625 38.444 1.58782
14 0.675 38.96 1.72852
15 0.725 40.156 1.79322
16 0.775 39.704 1.86805
17 0.825 41.012 2.07201
18 0.875 40.508 2.20185
19 0.925 40.924 2.34159
20 0.975 40.536 2.42783
55000 20 800
1 0.025 41.092 -0.11736
2 0.075 41.48 -0.0527255
3 0.125 40.28 0.125897
4 0.175 39.36 0.228772
5 0.225 39.984 0.342374
6 0.275 38.74 0.504094
7 0.325 39.044 0.674773
8 0.375 39.68 0.81468
9 0.425 39.492 0.953287
10 0.475 39.248 1.14637
11 0.525 38.676 1.30856
12 0.575 39.372 1.42209
13 0.625 40.672 1.52495
14 0.675 39.492 1.61151
15 0.725 39.736 1.79615
16 0.775 40.484 1.96654
17 0.825 40.5 2.06834
18 0.875 40.872 2.17939
19 0.925 41.72 2.3832
20 0.975 40.076 2.50132
60000 20 800
1 0.025 39.176 -0.054677
2 0.075 39.324 0.0941485
3 0.125 40.568 0.164946
4 0.175 40.412 0.332176
5 0.225 40.096 0.446353
6 0.275 38.168 0.683942
7 0.325 40.04 0.792897
8 0.375 40.208 0.884836
9 0.425 40.588 0.99467
10 0.475 42.104 1.09035
11 0.525 40.268 1.21613
12 0.575 40.656 1.34494
13 0.625 40.968 1.41703
14 0.675 40.656 1.5698
15 0.725 39.408 1.71514
16 0.775 39.288 1.94437
17 0.825 38.688 2.1265
18 0.875 39.64 2.2417
19 0.925 39.52 2.3449
20 0.975 40.224 2.46345
65000 20 800
1 0.025 39.644 -0.0205008
2 0.075 38.92 0.093635
3 0.125 40.044 0.184767
4 0.175 41.996 0.369954
5 0.225 41.6 0.568741
6 0.275 40.96 0.744219
7 0.325 39.908 0.756732
8 0.375 40.276 0.845839
9 0.425 39.764 0.985383
10 0.475 40.78 1.09391
11 0.525 40.5 1.16902
12 0.575 40.68 1.32073
13 0.625 39.36 1.45678
14 0.675 38.424 1.62622
15 0.725 39.208 1.75511
16 0.775 39.56 1.90535
17 0.825 39.644 2.08747
18 0.875 40.08 2.28233
19 0.925 38.652 2.37729
20 0.975 40 2.56933
70000 20 800
1 0.025 40.452 -0.00793274
2 0.075 40.864 0.175004
3 0.125 40.536 0.277082
4 0.175 40.968 0.440373
5 0.225 40.492 0.544422
6 0.275 40.2 0.644303
7 0.325 41.524 0.662981
8 0.375 39.284 0.84744
9 0.425 39.444 1.07373
10 0.475 39.564 1.15853
11 0.525 39.516 1.27484
12 0.575 40.536 1.40723
13 0.625 41.564 1.45373
14 0.675 40.572 1.60884
15 0.725 41.332 1.73283
16 0.775 39.352 1.95382
17 0.825 38.296 2.08171
18 0.875 39.064 2.16446
19 0.925 37.76 2.40744
20 0.975 38.68 2.62687
75000 20 800
1 0.025 38.108 -0.05192
2 0.075 37.776 0.076502
3 0.125 38.24 0.281793
4 0.175 39.604 0.457653
5 0.225 40.248 0.566231
6 0.275 38.92 0.629507
7 0.325 40.128 0.777632
8 0.375 40.812 0.936778
9 0.425 41.1 1.0612
10 0.475 41.3 1.16514
11 0.525 39.792 1.27564
12 0.575 41.264 1.39364
13 0.625 41.848 1.57035
14 0.675 41.876 1.72325
15 0.725 41.232 1.78889
16 0.775 42.284 1.96208
17 0.825 39.628 2.12273
18 0.875 39.144 2.26141
19 0.925 37.752 2.35896
20 0.975 38.944 2.42468
80000 20 800
1 0.025 38.812 0.0319443
2 0.075 39.2 0.111841
3 0.125 37.668 0.267422
4 0.175 37.804 0.372523
5 0.225 39.248 0.504566
6 0.275 38.988 0.734804
7 0.325 40.52 0.840295
8 0.375 40.756 0.961573
9 0.425 41.552 1.06823
10 0.475 42.06 1.15877
11 0.525 40.18 1.25104
12 0.575 39.672 1.34817
13 0.625 40.804 1.46558
14 0.675 40.92 1.6829
15 0.725 40.432 1.85785
16 0.775 39.4 2.01498
17 0.825 41.008 2.13502
18 0.875 41.148 2.33356
19 0.925 39.7 2.45562
20 0.975 40.128 2.519
85000 20 800
1 0.025 39.708 0.0675757
2 0.075 38.568 0.155652
3 0.125 39.468 0.257972
4 0.175 39.912 0.381709
5 0.225 39.496 0.540092
6 0.275 38.792 0.663322
7 0.325 40.316 0.778797
8 0.375 40.656 0.930875
9 0.425 40.392 1.0539
10 0.475 40.816 1.11707
11 0.525 39.32 1.26229
12 0.575 40.76 1.39535
13 0.625 39.028 1.58562
14 0.675 40.584 1.71586
15 0.725 39.248 1.8745
16 0.775 40.44 2.07077
17 0.825 40.38 2.18387
18 0.875 42.092 2.32595
19 0.925 39.912 2.47796
20 0.975 40.112 2.62971
90000 20 800
1 0.025 38.612 0.0986624
2 0.075 39.696 0.215871
3 0.125 41.416 0.275936
4 0.175 41.952 0.399801
5 0.225 41.624 0.450175
6 0.275 41.38 0.594899
7 0.325 39.54 0.793344
8 0.375 39.052 0.93
9 0.425 38.8 1.20258
10 0.475 38.46 1.36394
11 0.525 41.188 1.36666
12 0.575 41.524 1.49995
13 0.625 39.676 1.6079
14 0.675 39.436 1.724
15 0.725 40.696 1.84153
16 0.775 39.348 2.00791
17 0.825 40.5 2.11087
18 0.875 39.08 2.20504
19 0.925 39.376 2.42252
20 0.975 38.644 2.55074
95000 20 800
1 0.025 39.896 0.020253
2 0.075 39.888 0.159339
3 0.125 39.884 0.331224
4 0.175 40.108 0.410016
5 0.225 38.672 0.456839
6 0.275 38.076 0.676528
7 0.325 39.308 0.756748
8 0.375 39.112 0.877945
9 0.425 39.436 1.05859
10 0.475 39.9 1.26328
11 0.525 39.036 1.37844
12 0.575 39.428 1.57822
13 0.625 39.852 1.71595
14 0.675 39.956 1.84046
15 0.725 42.6 2.0017
16 0.775 43.268 2.09502
17 0.825 41.86 2.10397
18 0.875 39.688 2.22107
19 0.925 39.82 2.35201
20 0.975 40.212 2.51284
100000 20 800
1 0.025 40.248 0.0342573
2 0.075 39.5 0.194114
3 0.125 39.54 0.288274
4 0.175 41.072 0.479029
5 0.225 40.404 0.511889
6 0.275 40.18 0.632869
7 0.325 38.624 0.786136
8 0.375 39.62 0.931912
9 0.425 38.356 1.04179
10 0.475 40.256 1.26639
11 0.525 39.216 1.45011
12 0.575 39.796 1.53392
13 0.625 42.04 1.67949
14 0.675 41.556 1.77289
15 0.725 40.352 1.89509
16 0.775 39.456 2.03981
17 0.825 39.432 2.15127
18 0.875 39.996 2.30551
19 0.925 40.6 2.47526
20 0.975 39.756 2.56513
105000 20 800
1 0.025 41.732 0.0771493
2 0.075 40.82 0.166641
3 0.125 39.72 0.384061
4 0.175 40.936 0.456062
5 0.225 40.576 0.635406
6 0.275 39.484 0.703436
7 0.325 40.14 0.861474
8 0.375 40.64 0.934846
9 0.425 39.712 1.02313
10 0.475 38.364 1.12357
11 0.525 40.124 1.31844
12 0.575 39.776 1.49364
13 0.625 38.732 1.56976
14 0.675 38.628 1.77318
15 0.725 39.476 1.87792
16 0.775 40.26 2.08435
17 0.825 39.792 2.2232
18 0.875 40.792 2.36756
19 0.925 40.724 2.4943
20 0.975 39.572 2.67398

150
examples/VISCOSITY/profile.13Oct16.wall.2d.g++.1 Normal file
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@ -0,0 +1,150 @@
# Chunk-averaged data for fix 4 and group file
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount vx
10000 20 1020
1 0.025 60 0
2 0.075 60 0
3 0.125 44.684 -0.0148918
4 0.175 53.562 0.0378512
5 0.225 52.13 0.0164067
6 0.275 50.27 0.00901798
7 0.325 49.412 0.0110649
8 0.375 50.71 0.0263262
9 0.425 49.348 0.0973061
10 0.475 49.038 0.155797
11 0.525 51.372 0.222577
12 0.575 51.712 0.272627
13 0.625 52.154 0.374604
14 0.675 51.212 0.626004
15 0.725 51.6 0.884537
16 0.775 50.304 1.28032
17 0.825 50.43 1.91161
18 0.875 42.062 2.58719
19 0.925 60 2.7
20 0.975 40 2.7
20000 20 1020
1 0.025 60 0
2 0.075 60 0
3 0.125 46.672 -0.00692962
4 0.175 52.13 0.050619
5 0.225 51.2 0.0762272
6 0.275 51.062 0.134979
7 0.325 49.312 0.190332
8 0.375 50.808 0.275649
9 0.425 50.444 0.412282
10 0.475 51.124 0.55575
11 0.525 51.994 0.703406
12 0.575 50.494 0.901756
13 0.625 49.454 1.12815
14 0.675 50.336 1.40993
15 0.725 50.162 1.74913
16 0.775 51.636 2.052
17 0.825 49.902 2.3439
18 0.875 43.27 2.64736
19 0.925 60 2.7
20 0.975 40 2.7
30000 20 1020
1 0.025 60 0
2 0.075 60 0
3 0.125 46.784 0.0433334
4 0.175 52.212 0.106243
5 0.225 52.756 0.187486
6 0.275 52.84 0.26382
7 0.325 50.982 0.354413
8 0.375 49.218 0.464784
9 0.425 52.292 0.60338
10 0.475 51.216 0.774681
11 0.525 48.66 1.01585
12 0.575 46.2 1.27722
13 0.625 47.21 1.53339
14 0.675 47.814 1.76302
15 0.725 50.816 2.00443
16 0.775 53.074 2.2387
17 0.825 53.114 2.48323
18 0.875 44.812 2.67883
19 0.925 60 2.7
20 0.975 40 2.7
40000 20 1020
1 0.025 60 0
2 0.075 60 0
3 0.125 45.742 0.0443031
4 0.175 51.798 0.125517
5 0.225 52.432 0.185302
6 0.275 52.118 0.308702
7 0.325 49.756 0.420788
8 0.375 48.446 0.582632
9 0.425 49.994 0.796328
10 0.475 52.324 1.01095
11 0.525 49.63 1.21089
12 0.575 49.492 1.45349
13 0.625 48.072 1.66604
14 0.675 48.694 1.92152
15 0.725 50.884 2.1072
16 0.775 51.718 2.29063
17 0.825 53.018 2.50991
18 0.875 45.882 2.69299
19 0.925 60 2.7
20 0.975 40 2.7
50000 20 1020
1 0.025 60 0
2 0.075 60 0
3 0.125 45.412 0.0648825
4 0.175 51.378 0.172117
5 0.225 51.604 0.340702
6 0.275 53.184 0.466728
7 0.325 50.686 0.613016
8 0.375 50.544 0.769761
9 0.425 48.17 1.03062
10 0.475 51.112 1.24789
11 0.525 50.02 1.39357
12 0.575 50.77 1.56261
13 0.625 52.534 1.73166
14 0.675 51.578 1.97842
15 0.725 49.746 2.15672
16 0.775 50.954 2.31964
17 0.825 49.882 2.52932
18 0.875 42.426 2.68882
19 0.925 60 2.7
20 0.975 40 2.7
60000 20 1020
1 0.025 60 0
2 0.075 60 0
3 0.125 46.822 0.012362
4 0.175 50.92 0.0917424
5 0.225 49.412 0.217361
6 0.275 49.746 0.450329
7 0.325 50.804 0.647831
8 0.375 50.088 0.852854
9 0.425 50.948 1.04219
10 0.475 49.996 1.25129
11 0.525 49.358 1.46107
12 0.575 49.498 1.62029
13 0.625 52.99 1.82195
14 0.675 51.984 1.95183
15 0.725 51.886 2.13791
16 0.775 52.06 2.25464
17 0.825 51.54 2.47603
18 0.875 41.948 2.68352
19 0.925 60 2.7
20 0.975 40 2.7
70000 20 1020
1 0.025 60 0
2 0.075 60 0
3 0.125 44.22 0.0443311
4 0.175 50.19 0.165213
5 0.225 51.914 0.324356
6 0.275 50.208 0.515025
7 0.325 49.374 0.711162
8 0.375 50.164 0.93616
9 0.425 50.216 1.08664
10 0.475 51.04 1.20673
11 0.525 50.354 1.41749
12 0.575 50.08 1.56881
13 0.625 49.406 1.75501
14 0.675 52.444 1.93927
15 0.725 51.878 2.1174
16 0.775 50.846 2.32358
17 0.825 52.45 2.51165
18 0.875 45.216 2.66019
19 0.925 60 2.7
20 0.975 40 2.7

100654
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examples/VISCOSITY/profile.1Feb14.nemd.2d.g++.1
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@ -1,423 +0,0 @@
# Spatial-averaged data for fix 4 and group all
# Timestep Number-of-bins
# Bin Coord Ncount vx
10000 20
1 0.025 35.928 -0.465303
2 0.075 36.856 -0.188969
3 0.125 38.684 -0.0498744
4 0.175 39.568 0.1012
5 0.225 40.596 0.190157
6 0.275 39.924 0.326334
7 0.325 41.024 0.444171
8 0.375 41.32 0.560688
9 0.425 40.784 0.65736
10 0.475 41 0.731622
11 0.525 41.964 0.791196
12 0.575 38.808 0.836052
13 0.625 41.972 0.879215
14 0.675 42.196 0.883648
15 0.725 41.216 0.983798
16 0.775 41.168 1.18281
17 0.825 40.268 1.35084
18 0.875 41.156 1.47257
19 0.925 39.776 1.6245
20 0.975 35.792 1.86027
15000 20
1 0.025 37.372 -0.404754
2 0.075 38.476 -0.280658
3 0.125 38.604 -0.116081
4 0.175 39.1 0.0607617
5 0.225 38.72 0.164968
6 0.275 41.78 0.343067
7 0.325 42.808 0.459161
8 0.375 41.312 0.490663
9 0.425 40.844 0.590049
10 0.475 41.376 0.711643
11 0.525 39.78 0.788457
12 0.575 40.392 0.917817
13 0.625 41.832 1.04955
14 0.675 41.208 1.14763
15 0.725 39.528 1.32995
16 0.775 39.348 1.4926
17 0.825 38.356 1.52117
18 0.875 39.996 1.6647
19 0.925 39.744 1.84739
20 0.975 39.424 2.0051
20000 20
1 0.025 40.028 -0.455513
2 0.075 40.604 -0.307643
3 0.125 41.084 -0.126048
4 0.175 41.712 0.0515925
5 0.225 41.844 0.186159
6 0.275 40.028 0.277703
7 0.325 40.98 0.370102
8 0.375 38.264 0.538244
9 0.425 39.888 0.676071
10 0.475 40.412 0.807649
11 0.525 39.46 1.00087
12 0.575 40.332 1.10485
13 0.625 40.4 1.1685
14 0.675 39.964 1.31712
15 0.725 40.2 1.40366
16 0.775 38.32 1.52802
17 0.825 38.3 1.72349
18 0.875 39.408 1.83911
19 0.925 39.26 2.03208
20 0.975 39.512 2.11142
25000 20
1 0.025 38.228 -0.298243
2 0.075 40.388 -0.158565
3 0.125 39.98 -0.0210132
4 0.175 40.812 0.0740089
5 0.225 40.116 0.105815
6 0.275 40.572 0.201768
7 0.325 40.024 0.290641
8 0.375 38.072 0.455947
9 0.425 40.244 0.714136
10 0.475 39.348 0.856726
11 0.525 40.096 0.966253
12 0.575 40.944 1.16831
13 0.625 41.488 1.34074
14 0.675 41.492 1.50019
15 0.725 40.82 1.60717
16 0.775 39.06 1.72409
17 0.825 39.92 1.77278
18 0.875 40.312 1.89303
19 0.925 39.652 2.02035
20 0.975 38.432 2.17021
30000 20
1 0.025 38.12 -0.280205
2 0.075 38.664 -0.14915
3 0.125 38.8 0.0147312
4 0.175 38.608 0.0434195
5 0.225 39.656 0.163451
6 0.275 41.012 0.317398
7 0.325 40.168 0.500728
8 0.375 39.356 0.672385
9 0.425 40.04 0.828584
10 0.475 40.576 0.950531
11 0.525 40.076 1.07062
12 0.575 39.996 1.24959
13 0.625 40.456 1.30905
14 0.675 39.412 1.36273
15 0.725 40.936 1.60995
16 0.775 41.236 1.70266
17 0.825 40.116 1.84535
18 0.875 41.756 1.9541
19 0.925 40.524 2.09308
20 0.975 40.492 2.20129
35000 20
1 0.025 40.404 -0.159078
2 0.075 38.26 -0.0586985
3 0.125 38.944 0.0176549
4 0.175 39.788 0.048144
5 0.225 40.628 0.22801
6 0.275 41.216 0.449908
7 0.325 41.108 0.549029
8 0.375 41.956 0.66003
9 0.425 40.044 0.776742
10 0.475 39.884 0.916092
11 0.525 39.108 1.08394
12 0.575 38.264 1.19468
13 0.625 38.676 1.32698
14 0.675 39 1.53229
15 0.725 41.184 1.62152
16 0.775 40.8 1.77714
17 0.825 39.944 1.93521
18 0.875 39.752 2.06747
19 0.925 40.956 2.17283
20 0.975 40.084 2.34543
40000 20
1 0.025 41.672 -0.219998
2 0.075 41.052 -0.0690769
3 0.125 39.08 0.00502154
4 0.175 40 0.2124
5 0.225 40.296 0.336344
6 0.275 42.46 0.430182
7 0.325 39.66 0.602977
8 0.375 40.772 0.723553
9 0.425 39.928 0.969229
10 0.475 39.512 1.09986
11 0.525 40.54 1.17274
12 0.575 39.564 1.2647
13 0.625 38.92 1.39656
14 0.675 38.608 1.57314
15 0.725 40.216 1.685
16 0.775 40.12 1.80954
17 0.825 38.384 1.83983
18 0.875 38.96 1.98184
19 0.925 39.768 2.18467
20 0.975 40.488 2.35453
45000 20
1 0.025 39.56 -0.1943
2 0.075 38.916 -0.0403499
3 0.125 39.5 0.0919203
4 0.175 41.036 0.271893
5 0.225 39.304 0.390254
6 0.275 39.352 0.623633
7 0.325 39.896 0.688414
8 0.375 39.92 0.750037
9 0.425 39.612 0.856233
10 0.475 39.492 0.965005
11 0.525 39.312 1.11808
12 0.575 39.58 1.28673
13 0.625 38.884 1.42074
14 0.675 40.54 1.58182
15 0.725 40.54 1.80634
16 0.775 40.888 1.90939
17 0.825 41.768 1.95422
18 0.875 40.3 2.11175
19 0.925 41.428 2.21844
20 0.975 40.172 2.32498
50000 20
1 0.025 40.12 -0.163352
2 0.075 40.588 -0.00168776
3 0.125 40.26 0.136035
4 0.175 39.36 0.249927
5 0.225 40.348 0.380791
6 0.275 41.636 0.554812
7 0.325 41.588 0.703608
8 0.375 38.904 0.894523
9 0.425 39.3 0.987644
10 0.475 38.632 1.03641
11 0.525 38.48 1.14402
12 0.575 39.292 1.28132
13 0.625 40.568 1.48475
14 0.675 41.508 1.63155
15 0.725 41.456 1.75546
16 0.775 40.608 1.89197
17 0.825 39.512 2.01335
18 0.875 39.7 2.13666
19 0.925 38.884 2.28025
20 0.975 39.256 2.38188
55000 20
1 0.025 39.708 -0.108971
2 0.075 39.556 0.0603669
3 0.125 40.964 0.156842
4 0.175 39.84 0.235199
5 0.225 39.832 0.390198
6 0.275 38.92 0.56712
7 0.325 39.4 0.679256
8 0.375 40.108 0.818705
9 0.425 39.288 0.990146
10 0.475 40.04 1.07411
11 0.525 39.168 1.27756
12 0.575 39.312 1.3978
13 0.625 39.324 1.56102
14 0.675 40.928 1.64474
15 0.725 42.08 1.72534
16 0.775 41.556 1.89499
17 0.825 39.592 2.01979
18 0.875 40.488 2.20276
19 0.925 40.408 2.34696
20 0.975 39.488 2.49583
60000 20
1 0.025 39.496 -0.100497
2 0.075 38.604 -0.0102651
3 0.125 39.684 0.178037
4 0.175 39.192 0.341539
5 0.225 38.844 0.439096
6 0.275 40.14 0.486889
7 0.325 39.736 0.664301
8 0.375 41.032 0.815568
9 0.425 40.94 1.00279
10 0.475 40.856 1.16045
11 0.525 40.5 1.31426
12 0.575 40.156 1.40792
13 0.625 39.98 1.51713
14 0.675 40.16 1.70794
15 0.725 40.888 1.81116
16 0.775 40.284 1.88392
17 0.825 40.088 2.08925
18 0.875 39.94 2.32655
19 0.925 39.22 2.45015
20 0.975 40.26 2.50576
65000 20
1 0.025 39.676 -0.0670433
2 0.075 41.028 0.043225
3 0.125 41.004 0.176384
4 0.175 41.996 0.361575
5 0.225 41.088 0.552745
6 0.275 40.812 0.670716
7 0.325 39.744 0.801195
8 0.375 38.808 0.803928
9 0.425 38.584 0.928022
10 0.475 39.976 1.13616
11 0.525 39.796 1.29136
12 0.575 40.972 1.46573
13 0.625 39.92 1.56886
14 0.675 40.084 1.70827
15 0.725 40.048 1.87054
16 0.775 39.976 2.01428
17 0.825 39.7 2.11018
18 0.875 39.988 2.2107
19 0.925 37.956 2.34863
20 0.975 38.844 2.48445
70000 20
1 0.025 39.408 -0.00302681
2 0.075 39.7 0.129197
3 0.125 39.764 0.286801
4 0.175 39.632 0.443646
5 0.225 40.22 0.465482
6 0.275 41.76 0.647897
7 0.325 41.244 0.82129
8 0.375 40.724 0.906752
9 0.425 39.484 1.03096
10 0.475 39.708 1.14897
11 0.525 39.576 1.28366
12 0.575 39.788 1.45256
13 0.625 40.448 1.5882
14 0.675 40.224 1.72367
15 0.725 39.412 1.78116
16 0.775 40.096 1.89053
17 0.825 39.456 2.03298
18 0.875 40.148 2.23227
19 0.925 39.476 2.42699
20 0.975 39.732 2.49355
75000 20
1 0.025 40.948 -0.172942
2 0.075 39.612 0.0368481
3 0.125 38.896 0.252959
4 0.175 40.46 0.45741
5 0.225 41.6 0.540739
6 0.275 40.356 0.623045
7 0.325 41.396 0.71665
8 0.375 40.12 0.942527
9 0.425 38.808 1.05461
10 0.475 40.34 1.18467
11 0.525 39.876 1.29828
12 0.575 39.956 1.3934
13 0.625 38.692 1.63059
14 0.675 37.8 1.80705
15 0.725 40.844 1.92569
16 0.775 40.972 2.07802
17 0.825 40.224 2.18572
18 0.875 39.82 2.31885
19 0.925 39.38 2.39877
20 0.975 39.9 2.45652
80000 20
1 0.025 39.784 -0.0665657
2 0.075 39.884 0.0688813
3 0.125 41.772 0.312162
4 0.175 41.164 0.494595
5 0.225 40.548 0.611019
6 0.275 40.1 0.632487
7 0.325 38.52 0.702356
8 0.375 39.684 0.819079
9 0.425 39.816 0.991753
10 0.475 41.352 1.15255
11 0.525 39.936 1.29366
12 0.575 39.404 1.47041
13 0.625 39.336 1.6785
14 0.675 40.212 1.79326
15 0.725 40.368 1.93652
16 0.775 40.588 2.05911
17 0.825 39.368 2.09269
18 0.875 39.648 2.34305
19 0.925 39.2 2.42405
20 0.975 39.316 2.56819
85000 20
1 0.025 39.408 0.0297935
2 0.075 39.316 0.112095
3 0.125 39.564 0.230359
4 0.175 39.66 0.376766
5 0.225 41.048 0.55746
6 0.275 39.992 0.689822
7 0.325 39.792 0.825437
8 0.375 40.22 0.871438
9 0.425 39.912 1.01581
10 0.475 39.328 1.1664
11 0.525 40.864 1.29245
12 0.575 39.764 1.40137
13 0.625 37.768 1.70767
14 0.675 40.28 1.80284
15 0.725 40.896 1.85025
16 0.775 40.412 1.99244
17 0.825 39.436 2.1574
18 0.875 40.924 2.38627
19 0.925 40.696 2.48128
20 0.975 40.72 2.67178
90000 20
1 0.025 40.28 0.0551947
2 0.075 40.928 0.209965
3 0.125 39.636 0.374114
4 0.175 40.544 0.543279
5 0.225 40.688 0.484909
6 0.275 40.384 0.594895
7 0.325 39.864 0.725557
8 0.375 39.908 0.936843
9 0.425 39.148 1.10227
10 0.475 40.572 1.26264
11 0.525 40.34 1.35539
12 0.575 40.328 1.51105
13 0.625 40.744 1.59789
14 0.675 39.852 1.68812
15 0.725 39.44 1.80735
16 0.775 40.576 1.99386
17 0.825 38.88 2.16786
18 0.875 38.352 2.35497
19 0.925 40.152 2.48042
20 0.975 39.384 2.58549
95000 20
1 0.025 38.652 0.0675057
2 0.075 39.408 0.234276
3 0.125 40.336 0.287062
4 0.175 40.224 0.453603
5 0.225 41.616 0.509951
6 0.275 40.624 0.629072
7 0.325 40.716 0.83863
8 0.375 41.224 0.968013
9 0.425 39.028 1.1245
10 0.475 40.008 1.23591
11 0.525 39.688 1.30079
12 0.575 39.992 1.47726
13 0.625 39.912 1.66047
14 0.675 40.32 1.82563
15 0.725 41.2 1.89419
16 0.775 40.316 1.96269
17 0.825 39.92 2.11759
18 0.875 39.592 2.35149
19 0.925 38.924 2.47
20 0.975 38.3 2.58544
100000 20
1 0.025 40.044 0.0139808
2 0.075 40.56 0.207406
3 0.125 41.612 0.343256
4 0.175 42.06 0.392374
5 0.225 40.02 0.588576
6 0.275 40.484 0.745612
7 0.325 39.08 0.845715
8 0.375 40.672 1.05102
9 0.425 39.408 1.14469
10 0.475 39.396 1.26888
11 0.525 39.448 1.33993
12 0.575 39.476 1.48792
13 0.625 39.684 1.60543
14 0.675 39.264 1.70532
15 0.725 40.08 1.89871
16 0.775 40.328 1.99496
17 0.825 40.236 2.0736
18 0.875 39.636 2.24566
19 0.925 39.72 2.4999
20 0.975 38.792 2.66657
105000 20
1 0.025 40.296 0.0227351
2 0.075 40.9 0.118698
3 0.125 41.388 0.263959
4 0.175 41.256 0.397214
5 0.225 40.548 0.561162
6 0.275 40.48 0.730855
7 0.325 40.244 0.920718
8 0.375 40.236 1.05117
9 0.425 41.08 1.15534
10 0.475 39.896 1.27183
11 0.525 39.272 1.34162
12 0.575 38.768 1.52379
13 0.625 40.492 1.67655
14 0.675 40.436 1.81388
15 0.725 40.568 1.93304
16 0.775 38.672 2.11396
17 0.825 38.956 2.19031
18 0.875 38.472 2.24916
19 0.925 38.928 2.33358
20 0.975 39.112 2.57182

150
examples/VISCOSITY/profile.1Feb14.wall.2d.g++.1
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@ -1,150 +0,0 @@
# Spatial-averaged data for fix 4 and group flow
# Timestep Number-of-bins
# Bin Coord Ncount vx
10000 20
1 0.025 0 0
2 0.075 0 0
3 0.125 45.22 -0.0215999
4 0.175 53.094 0.0239818
5 0.225 52.33 -0.00740041
6 0.275 49.694 -0.0271909
7 0.325 50.596 0.0587613
8 0.375 49.964 0.0596901
9 0.425 49.116 0.0912273
10 0.475 50.838 0.13849
11 0.525 49.87 0.284957
12 0.575 51.146 0.318384
13 0.625 52.088 0.415968
14 0.675 52.014 0.635039
15 0.725 51.34 0.913678
16 0.775 48.69 1.33998
17 0.825 50.52 2.004
18 0.875 23.48 2.50438
19 0.925 0 0
20 0.975 0 0
20000 20
1 0.025 0 0
2 0.075 0 0
3 0.125 46.648 -0.000970018
4 0.175 52.126 0.0890499
5 0.225 51.29 0.0762779
6 0.275 51.024 0.198588
7 0.325 49.542 0.265865
8 0.375 51.258 0.369776
9 0.425 50.178 0.48541
10 0.475 50.856 0.671116
11 0.525 51.596 0.835852
12 0.575 50.138 0.992162
13 0.625 49.724 1.18229
14 0.675 50.102 1.47267
15 0.725 50.662 1.79756
16 0.775 51.142 2.10463
17 0.825 50.304 2.44851
18 0.875 23.41 2.65614
19 0.925 0 0
20 0.975 0 0
30000 20
1 0.025 0 0
2 0.075 0 0
3 0.125 47.21 0.0430345
4 0.175 52.864 0.0974036
5 0.225 52.06 0.168861
6 0.275 52.916 0.271237
7 0.325 51.04 0.410796
8 0.375 50.084 0.557589
9 0.425 51.01 0.713094
10 0.475 51.748 0.833724
11 0.525 47.544 0.956172
12 0.575 46.038 1.16939
13 0.625 47.052 1.53503
14 0.675 49.176 1.83766
15 0.725 51.124 2.04681
16 0.775 51.926 2.25608
17 0.825 53.194 2.47608
18 0.875 25.014 2.63323
19 0.925 0 0
20 0.975 0 0
40000 20
1 0.025 0 0
2 0.075 0 0
3 0.125 45.042 0.0392581
4 0.175 52.554 0.105209
5 0.225 51.922 0.184101
6 0.275 51.04 0.28511
7 0.325 51.492 0.49002
8 0.375 49.406 0.709675
9 0.425 50.496 0.862857
10 0.475 51.344 0.980319
11 0.525 48.514 1.15822
12 0.575 49.578 1.39003
13 0.625 48.378 1.69191
14 0.675 48.596 1.97016
15 0.725 50.052 2.23436
16 0.775 51.374 2.47114
17 0.825 54.178 2.62849
18 0.875 26.034 2.67856
19 0.925 0 0
20 0.975 0 0
50000 20
1 0.025 0 0
2 0.075 0 0
3 0.125 45.894 0.0848964
4 0.175 51.234 0.215681
5 0.225 52.424 0.318127
6 0.275 52.188 0.424113
7 0.325 51.372 0.647998
8 0.375 49.64 0.822176
9 0.425 46.658 0.980504
10 0.475 51.724 1.18072
11 0.525 50.314 1.37386
12 0.575 51.078 1.55686
13 0.625 52.536 1.71776
14 0.675 52.388 1.86494
15 0.725 49.63 2.10648
16 0.775 50.61 2.33368
17 0.825 49.33 2.50284
18 0.875 22.98 2.6457
19 0.925 0 0
20 0.975 0 0
60000 20
1 0.025 0 0
2 0.075 0 0
3 0.125 46.968 0.0408075
4 0.175 51.692 0.204475
5 0.225 48.82 0.358701
6 0.275 49.544 0.547087
7 0.325 49.972 0.685537
8 0.375 49.608 0.827083
9 0.425 51.486 1.04957
10 0.475 50.154 1.2679
11 0.525 49.654 1.43157
12 0.575 50.67 1.59638
13 0.625 51.94 1.72873
14 0.675 52.456 1.8852
15 0.725 51.496 2.06822
16 0.775 51.516 2.27431
17 0.825 51.542 2.44986
18 0.875 22.482 2.63571
19 0.925 0 0
20 0.975 0 0
70000 20
1 0.025 0 0
2 0.075 0 0
3 0.125 45.09 0.0508668
4 0.175 49.42 0.179149
5 0.225 51.216 0.398422
6 0.275 51.022 0.608737
7 0.325 49.168 0.763413
8 0.375 51.53 0.915924
9 0.425 49.268 1.10732
10 0.475 50.228 1.26888
11 0.525 49.894 1.42277
12 0.575 51.222 1.62554
13 0.625 48.75 1.79386
14 0.675 53.434 1.93903
15 0.725 50.482 2.16894
16 0.775 51.518 2.3745
17 0.825 53.188 2.54107
18 0.875 24.57 2.64906
19 0.925 0 0
20 0.975 0 0

25
python/lammps.py
View File

@ -14,15 +14,18 @@
# Python wrappers on LAMMPS library via ctypes # Python wrappers on LAMMPS library via ctypes
# for python3 compatibility # for python3 compatibility
from __future__ import print_function from __future__ import print_function
# imports for simple LAMMPS python wrapper module "lammps" # imports for simple LAMMPS python wrapper module "lammps"
import sys,traceback,types import sys,traceback,types
from ctypes import * from ctypes import *
from os.path import dirname,abspath,join from os.path import dirname,abspath,join
from inspect import getsourcefile from inspect import getsourcefile
# imports for advanced LAMMPS python wrapper modules "PyLammps" and "IPyLammps" # imports for advanced LAMMPS python wrapper modules "PyLammps" and "IPyLammps"
from collections import namedtuple from collections import namedtuple
import os import os
import select import select
@ -38,6 +41,7 @@ class MPIAbortException(Exception):
class lammps(object): class lammps(object):
# detect if Python is using version of mpi4py that can pass a communicator # detect if Python is using version of mpi4py that can pass a communicator
has_mpi4py_v2 = False has_mpi4py_v2 = False
@ -60,23 +64,27 @@ class lammps(object):
modpath = dirname(abspath(getsourcefile(lambda:0))) modpath = dirname(abspath(getsourcefile(lambda:0)))
self.lib = None self.lib = None
# if a pointer to a LAMMPS object is handed in, all symbols should already be available. # if a pointer to a LAMMPS object is handed in,
# all symbols should already be available
try: try:
if ptr: self.lib = CDLL("",RTLD_GLOBAL) if ptr: self.lib = CDLL("",RTLD_GLOBAL)
except: except:
self.lib = None self.lib = None
# load liblammps.so unless name is given. # load liblammps.so unless name is given
# e.g. if name = "g++", load liblammps_g++.so # if name = "g++", load liblammps_g++.so
# try loading the LAMMPS shared object from the location # try loading the LAMMPS shared object from the location
# of lammps.py with an absolute path (so that LD_LIBRARY_PATH # of lammps.py with an absolute path,
# does not need to be set for regular installations. # so that LD_LIBRARY_PATH does not need to be set for regular install
# fall back to loading with a relative path, which typically # fall back to loading with a relative path,
# requires LD_LIBRARY_PATH to be set appropriately. # typically requires LD_LIBRARY_PATH to be set appropriately
if not self.lib: if not self.lib:
try: try:
if not name: self.lib = CDLL(join(modpath,"liblammps.so"),RTLD_GLOBAL) if not name: self.lib = CDLL(join(modpath,"liblammps.so"),RTLD_GLOBAL)
else: self.lib = CDLL(join(modpath,"liblammps_%s.so" % name),RTLD_GLOBAL) else: self.lib = CDLL(join(modpath,"liblammps_%s.so" % name),
RTLD_GLOBAL)
except: except:
if not name: self.lib = CDLL("liblammps.so",RTLD_GLOBAL) if not name: self.lib = CDLL("liblammps.so",RTLD_GLOBAL)
else: self.lib = CDLL("liblammps_%s.so" % name,RTLD_GLOBAL) else: self.lib = CDLL("liblammps_%s.so" % name,RTLD_GLOBAL)
@ -91,6 +99,7 @@ class lammps(object):
# just convert it to ctypes ptr and store in self.lmp # just convert it to ctypes ptr and store in self.lmp
if not ptr: if not ptr:
# with mpi4py v2, can pass MPI communicator to LAMMPS # with mpi4py v2, can pass MPI communicator to LAMMPS
# need to adjust for type of MPI communicator object # need to adjust for type of MPI communicator object
# allow for int (like MPICH) or void* (like OpenMPI) # allow for int (like MPICH) or void* (like OpenMPI)

4
src/dump_custom.cpp
View File

@ -1918,7 +1918,7 @@ int DumpCustom::modify_param(int narg, char **arg)
field2index[nfield+nthresh] = add_custom(suffix,0); field2index[nfield+nthresh] = add_custom(suffix,0);
delete [] suffix; delete [] suffix;
} else error->all(FLERR,"Invalid dump_modify threshold operator"); } else error->all(FLERR,"Invalid dump_modify thresh attribute");
// set operation type of threshold // set operation type of threshold
@ -1929,7 +1929,7 @@ int DumpCustom::modify_param(int narg, char **arg)
else if (strcmp(arg[2],"==") == 0) thresh_op[nthresh] = EQ; else if (strcmp(arg[2],"==") == 0) thresh_op[nthresh] = EQ;
else if (strcmp(arg[2],"!=") == 0) thresh_op[nthresh] = NEQ; else if (strcmp(arg[2],"!=") == 0) thresh_op[nthresh] = NEQ;
else if (strcmp(arg[2],"|^") == 0) thresh_op[nthresh] = XOR; else if (strcmp(arg[2],"|^") == 0) thresh_op[nthresh] = XOR;
else error->all(FLERR,"Invalid dump_modify threshold operator"); else error->all(FLERR,"Invalid dump_modify thresh operator");
// set threshold value as number or special LAST keyword // set threshold value as number or special LAST keyword
// create FixStore to hold LAST values, should work with restart // create FixStore to hold LAST values, should work with restart

9
src/finish.cpp
View File

@ -1,5 +1,5 @@
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMRDS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
@ -246,13 +246,10 @@ void Finish::end(int flag)
if (prdflag) { if (prdflag) {
if (me == 0) { if (me == 0) {
if (screen) fprintf(screen,"\n"); if (screen) fprintf(screen,"\nPRD stats:\n");
if (logfile) fprintf(logfile,"\n"); if (logfile) fprintf(logfile,"\nPRD stats:\n");
} }
if (screen) fprintf(screen,"PRD stats:\n");
if (logfile) fprintf(logfile,"PRD stats:\n");
time = timer->get_wall(Timer::DEPHASE); time = timer->get_wall(Timer::DEPHASE);
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs; time = tmp/nprocs;

2
src/version.h
View File

@ -1 +1 @@
#define LAMMPS_VERSION "12 Oct 2016" #define LAMMPS_VERSION "18 Oct 2016"