new fix halt command, other sundry small bug fixes
This commit is contained in:
Steve Plimpton
@ -1,7 +1,7 @@
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<!-- HTML_ONLY -->
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<HEAD>
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<TITLE>LAMMPS Users Manual</TITLE>
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<META NAME="docnumber" CONTENT="12 Oct 2016 version">
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<META NAME="docnumber" CONTENT="18 Oct 2016 version">
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<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
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<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
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</HEAD>
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@ -21,7 +21,7 @@
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<H1></H1>
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LAMMPS Documentation :c,h3
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12 Oct 2016 version :c,h4
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18 Oct 2016 version :c,h4
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Version info: :h4
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@ -573,6 +573,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
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"gcmc"_fix_gcmc.html,
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"gld"_fix_gld.html,
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"gravity (o)"_fix_gravity.html,
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"halt"_fix_halt.html,
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"heat"_fix_heat.html,
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"indent"_fix_indent.html,
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"langevin (k)"_fix_langevin.html,
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@ -47,9 +47,9 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o
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id = sort per-atom lines by atom ID
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N = sort per-atom lines in ascending order by the Nth column
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-N = sort per-atom lines in descending order by the Nth column
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{thresh} args = attribute operation value
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{thresh} args = attribute operator value
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attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
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operation = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
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operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
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value = numeric value to compare to, or LAST
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these 3 args can be replaced by the word "none" to turn off thresholding
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{unwrap} arg = {yes} or {no} :pre
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@ -470,7 +470,7 @@ stress of atoms whose energy is above some threshold.
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If an atom-style variable is used as the attribute, then it can
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produce continuous numeric values or effective Boolean 0/1 values
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which may be useful for the comparision operation. Boolean values can
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which may be useful for the comparision operator. Boolean values can
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be generated by variable formulas that use comparison or Boolean math
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operators or special functions like gmask() and rmask() and grmask().
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See the "variable"_variable.html command doc page for details.
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@ -503,11 +503,11 @@ less than 1/2 to greater than 1/2 (or vice versa) since the last dump.
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E.g. due to reactions and subsequent charge equilibration in a
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reactive force field.
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The choice of operations are the usual comparison operators. The XOR
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operation (exclusive or) is also included as "|^". In this context,
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XOR means that if either the attribute or value is 0.0 and the other
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is non-zero, then the result is "true" and the threshold criterion is
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met. Otherwise it is not met.
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The choice of operators listed above are the usual comparison
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operators. The XOR operation (exclusive or) is also included as "|^".
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In this context, XOR means that if either the attribute or value is
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0.0 and the other is non-zero, then the result is "true" and the
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threshold criterion is met. Otherwise it is not met.
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:line
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121
doc/src/fix_halt.txt
Normal file
121
doc/src/fix_halt.txt
Normal file
@ -0,0 +1,121 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix halt command :h3
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[Syntax:]
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fix ID group-ID halt N attribute operator avalue keyword value ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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halt = style name of this fix command :l
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N = check halt condition every N steps :l
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attribute = hstyle or v_name :l
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hstyle = {bondmax}
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v_name = name of "equal-style variable"_variable.html :pre
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operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" :l
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avalue = numeric value to compare attribute to :l
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string = text string to print with optional variable names :l
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zero or more keyword/value pairs may be appended :l
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keyword = {error} :l
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{error} value = {hard} or {soft} or {continue} :pre
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:ule
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[Examples:]
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fix 10 all halt 1 bondmax > 1.5
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fix 10 all print 10 v_myCheck != 0 error soft :pre
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[Description:]
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Check a condition every N steps during a simulation run. N must be >=
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1. If the condition is met, exit the run immediately. In this
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context a "run" can be dynamics or minimization iterations, as
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specified by the "run"_run.html or "minimize"_minimize.html command.
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The specified group-ID is ignored by this fix.
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The specified {attribute} can be one of the {hstyle} options listed
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above, or an "equal-style variable"_variable.html referenced as
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{v_name}, where "name" is the name of a variable that has been defined
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previously in the input script.
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The only {hstyle} option currently implemented is {bondmax}. This
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will loop over all bonds in the system, compute their current
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lengths, and set {attribute} to the longest bond distance.
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Equal-style variables evaluate to a numeric value. See the
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"variable"_variable.html command for a description. They calculate
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formulas which can involve mathematical operations, atom properties,
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group properties, thermodynamic properties, global values calculated
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by a "compute"_compute.html or "fix"_fix.html, or references to other
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"variables"_variable.html. Thus they are a very general means of
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computing some attribute of the current system. For example, the
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following "bondmax" variable will calculate the same quantity as the
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hstyle = bondmax option.
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compute bdist all bond/local dist
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compute bmax all reduce max c_bdist
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variable bondmax equal c_bmax :pre
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Thus these two versions of a fix halt command will do the same thing:
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fix 10 all halt 1 bondmax > 1.5
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fix 10 all halt 1 v_bondmax > 1.5 :pre
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The version with "bondmax" will just run somewhat faster, due to less
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overhead in computing bond lengths and not storing them in a separate
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compute.
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The choice of operators listed above are the usual comparison
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operators. The XOR operation (exclusive or) is also included as "|^".
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In this context, XOR means that if either the attribute or avalue is
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0.0 and the other is non-zero, then the result is "true". Otherwise
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it is "false".
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The specified {avalue} must be a numeric value.
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:line
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The optional {error} keyword determines how the current run is halted.
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If its value is {hard}, then LAMMPS will stop with an error message.
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If its value is {soft}, LAMMPS will exit the current run, but continue
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to execute subsequent commands in the input script. However,
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additional "run"_run.html or "minimize"_minimize.html commands will be
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skipped. For example, this allows a script to output the current
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state of the system, e.g. via a "write_dump"_write_dump.html or
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"write_restart"_write_restart.html command.
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If its value is {continue}, the behavior is the same as for {soft},
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except subsequent subsequent "run"_run.html or
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"minimize"_minimize.html commands are executed. This allows your
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script to remedy the condition that triggered the halt, if necessary.
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Note that you may wish use the "unfix"_unfix.html command on the fix
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halt ID, so that the same condition is not immediately triggered in a
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subsequent run.
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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html. None of the "fix_modify"_fix_modify.html options
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various "output
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commands"_Section_howto.html#howto_15. No parameter of this fix can
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be used with the {start/stop} keywords of the "run"_run.html command.
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This fix is not invoked during "energy minimization"_minimize.html.
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[Restrictions:] none
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[Related commands:]
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"variable"_variable.html
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[Default:]
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The option defaults are error = hard.
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@ -103,6 +103,11 @@ the line search fails because the step distance backtracks to 0.0
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the number of outer iterations or timesteps exceeds {maxiter}
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the number of total force evaluations exceeds {maxeval} :ul
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NOTE: You can also use the "fix halt"_fix_halt.html command to specify
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a general criterion for exiting a minimization, that is a calculation
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performed on the state of the current system, as defined by an
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"equal-style variable"_variable.html.
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For the first criterion, the specified energy tolerance {etol} is
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unitless; it is met when the energy change between successive
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iterations divided by the energy magnitude is less than or equal to
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@ -169,17 +169,17 @@ If the {pre} and {post} options are set to "no" when used with the
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run will print the full timing summary, but these operations will be
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skipped for intermediate runs.
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NOTE: You might hope to specify a command that exits the run by
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NOTE: You might wish to specify a command that exits the run by
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jumping out of the loop, e.g.
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variable t equal temp
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run 10000 every 100 "if '$t < 300.0' then 'jump SELF afterrun'" :pre
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Unfortunately this will not currently work. The run command simply
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executes each command one at a time each time it pauses, then
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continues the run. You can replace the jump command with a simple
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"quit"_quit.html command and cause LAMMPS to exit during the
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middle of a run when the condition is met.
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However, this will not work. The run command simply executes each
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command one at a time each time it pauses, then continues the run.
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Instead, you should use the "fix halt"_fix_halt.html command, which
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has additional options for how to exit the run.
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[Restrictions:]
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@ -198,7 +198,7 @@ successive runs to run a simulation for any number of steps (ok, up to
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[Related commands:]
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"minimize"_minimize.html, "run_style"_run_style.html,
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"temper"_temper.html
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"temper"_temper.html, "fix halt"_fix_halt.html
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[Default:]
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245
examples/DIFFUSE/log.13Oct16.msd.2d.g++.8
Normal file
245
examples/DIFFUSE/log.13Oct16.msd.2d.g++.8
Normal file
@ -0,0 +1,245 @@
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LAMMPS (13 Oct 2016)
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# sample LAMMPS input script for diffusion of 2d LJ liquid
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# mean-squared displacement via compute msd
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# settings
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variable x equal 40
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variable y equal 40
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variable rho equal 0.6
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variable t equal 1.0
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variable rc equal 2.5
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# problem setup
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units lj
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dimension 2
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atom_style atomic
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neigh_modify delay 0 every 1
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lattice sq2 ${rho}
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lattice sq2 0.6
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Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
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region simbox block 0 $x 0 $y -0.1 0.1
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region simbox block 0 40 0 $y -0.1 0.1
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region simbox block 0 40 0 40 -0.1 0.1
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create_box 1 simbox
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Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
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4 by 2 by 1 MPI processor grid
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create_atoms 1 box
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Created 3200 atoms
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pair_style lj/cut ${rc}
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pair_style lj/cut 2.5
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pair_coeff * * 1 1
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mass * 1.0
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velocity all create $t 97287
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velocity all create 1 97287
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fix 1 all nve
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fix 2 all langevin $t $t 0.1 498094
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fix 2 all langevin 1 $t 0.1 498094
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fix 2 all langevin 1 1 0.1 498094
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fix 3 all enforce2d
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# equilibration run
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thermo 1000
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run 5000
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4 -> bins = 53 53 1
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Memory usage per processor = 2.478 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1 -1.56492 0 -0.5652325 -1.5346995
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1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
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2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
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3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
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4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
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5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
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Loop time of 0.554412 on 8 procs for 5000 steps with 3200 atoms
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Performance: 3896017.421 tau/day, 9018.559 timesteps/s
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98.9% CPU use with 8 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.23992 | 0.24608 | 0.25161 | 0.7 | 44.39
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Neigh | 0.063106 | 0.064417 | 0.066279 | 0.4 | 11.62
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Comm | 0.072465 | 0.085066 | 0.094837 | 2.3 | 15.34
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Output | 0.00013208 | 0.00013691 | 0.00014591 | 0.0 | 0.02
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Modify | 0.11441 | 0.11621 | 0.11769 | 0.3 | 20.96
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Other | | 0.04251 | | | 7.67
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Nlocal: 400 ave 406 max 394 min
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Histogram: 1 1 0 1 0 2 1 0 1 1
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Nghost: 202.5 ave 212 max 191 min
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Histogram: 1 0 0 0 3 1 0 2 0 1
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Neighs: 2800.88 ave 2903 max 2690 min
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Histogram: 1 1 0 0 1 2 1 0 1 1
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Total # of neighbors = 22407
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Ave neighs/atom = 7.00219
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Neighbor list builds = 599
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Dangerous builds = 0
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unfix 2
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# data gathering run
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reset_timestep 0
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# factor of 4 in 2 variables is for 2d
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compute msd all msd com yes
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variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
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fix 9 all vector 10 c_msd[4]
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variable fitslope equal slope(f_9)/4/(10*dt)
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thermo_style custom step temp c_msd[4] v_twopoint v_fitslope
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# only need to run for 10K steps to make a good 100-frame movie
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#dump 1 all custom 1 tmp.dump id type vx vy vz
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#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
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thermo 1000
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run 100000
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Memory usage per processor = 2.853 Mbytes
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Step Temp c_msd[4] v_twopoint v_fitslope
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0 0.97069905 0 0 5e+20
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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
|
||||
246
examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8
Normal file
246
examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8
Normal file
@ -0,0 +1,246 @@
|
||||
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
|
||||
@ -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
|
||||
@ -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
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (7 Jun 2016)
|
||||
LAMMPS (13 Oct 2016)
|
||||
# sample LAMMPS input script for thermal conductivity of liquid LJ
|
||||
# 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
|
||||
900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
|
||||
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
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.48108 | 0.4925 | 0.50422 | 1.0 | 56.04
|
||||
Neigh | 0.23355 | 0.23565 | 0.23888 | 0.4 | 26.81
|
||||
Comm | 0.088565 | 0.10044 | 0.11391 | 2.7 | 11.43
|
||||
Output | 0.00029421 | 0.00031444 | 0.00041795 | 0.2 | 0.04
|
||||
Modify | 0.027427 | 0.032625 | 0.035225 | 1.6 | 3.71
|
||||
Other | | 0.01735 | | | 1.97
|
||||
Pair | 0.48042 | 0.50311 | 0.52772 | 1.9 | 56.59
|
||||
Neigh | 0.22997 | 0.23203 | 0.23466 | 0.3 | 26.10
|
||||
Comm | 0.081187 | 0.10484 | 0.1285 | 4.2 | 11.79
|
||||
Output | 0.00027299 | 0.00028226 | 0.000314 | 0.1 | 0.03
|
||||
Modify | 0.028298 | 0.032276 | 0.037612 | 2.0 | 3.63
|
||||
Other | | 0.01658 | | | 1.86
|
||||
|
||||
Nlocal: 1000 ave 1020 max 982 min
|
||||
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
|
||||
run 10000
|
||||
Memory usage per processor = 2.80761 Mbytes
|
||||
Step Temp Thot Tcold
|
||||
Step Temp c_Thot c_Tcold
|
||||
1000 1.35 1.431295 1.2955644
|
||||
2000 1.3537291 1.6418772 1.1875127
|
||||
3000 1.3615152 1.6451299 1.1769094
|
||||
@ -133,20 +133,20 @@ Step Temp Thot Tcold
|
||||
9000 1.3701136 1.8238424 1.136342
|
||||
10000 1.3563004 1.8059065 1.1547129
|
||||
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
|
||||
99.5% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
Performance: 409265.976 tau/day, 947.375 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 | 4.1797 | 4.902 | 5.5136 | 25.3 | 47.63
|
||||
Neigh | 2.1913 | 2.4616 | 2.6938 | 14.2 | 23.92
|
||||
Comm | 0.87831 | 1.64 | 2.611 | 56.5 | 15.94
|
||||
Output | 0.00043011 | 0.00063166 | 0.00075626 | 0.5 | 0.01
|
||||
Modify | 0.78531 | 0.92487 | 1.0647 | 10.6 | 8.99
|
||||
Other | | 0.3628 | | | 3.53
|
||||
Pair | 4.1863 | 5.0134 | 5.8326 | 28.0 | 47.50
|
||||
Neigh | 2.1559 | 2.4232 | 2.6516 | 14.2 | 22.96
|
||||
Comm | 0.80561 | 1.8126 | 2.8852 | 58.4 | 17.17
|
||||
Output | 0.00044537 | 0.00064856 | 0.00077057 | 0.5 | 0.01
|
||||
Modify | 0.81915 | 0.94285 | 1.0571 | 9.5 | 8.93
|
||||
Other | | 0.3628 | | | 3.44
|
||||
|
||||
Nlocal: 1000 ave 1105 max 883 min
|
||||
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
|
||||
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
|
||||
12000 1.3799777 1.8004888 1.1032219 -0.63860014 0
|
||||
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
|
||||
30000 1.3968366 1.883107 1.1004588 -0.83902548 -0.77082172
|
||||
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
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.4818 | 9.8886 | 12.008 | 66.1 | 44.28
|
||||
Neigh | 4.1157 | 5.0693 | 5.9657 | 38.0 | 22.70
|
||||
Comm | 1.8343 | 4.6586 | 7.8747 | 129.4 | 20.86
|
||||
Output | 0.00095606 | 0.0017744 | 0.0019104 | 0.7 | 0.01
|
||||
Modify | 1.6812 | 1.9319 | 2.2204 | 13.5 | 8.65
|
||||
Other | | 0.7817 | | | 3.50
|
||||
Pair | 7.4811 | 10.102 | 12.63 | 68.7 | 44.39
|
||||
Neigh | 4.0495 | 4.9884 | 5.8366 | 37.8 | 21.92
|
||||
Comm | 1.6695 | 4.9483 | 8.493 | 130.7 | 21.74
|
||||
Output | 0.0010517 | 0.0017769 | 0.0019059 | 0.7 | 0.01
|
||||
Modify | 1.6903 | 1.9371 | 2.2355 | 14.8 | 8.51
|
||||
Other | | 0.7799 | | | 3.43
|
||||
|
||||
Nlocal: 1000 ave 1121 max 857 min
|
||||
Histogram: 2 0 1 1 0 0 0 0 1 3
|
||||
@ -222,4 +222,4 @@ Total # of neighbors = 219898
|
||||
Ave neighs/atom = 27.4872
|
||||
Neighbor list builds = 3474
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:33
|
||||
Total wall time: 0:00:34
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (7 Jun 2016)
|
||||
LAMMPS (13 Oct 2016)
|
||||
# sample LAMMPS input script for thermal conductivity of liquid LJ
|
||||
# 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
|
||||
900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
|
||||
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
|
||||
99.4% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
Performance: 495320.223 tau/day, 1146.575 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 | 0.47867 | 0.4928 | 0.5006 | 1.0 | 55.43
|
||||
Neigh | 0.23302 | 0.23557 | 0.23833 | 0.3 | 26.50
|
||||
Comm | 0.1001 | 0.11264 | 0.12817 | 2.6 | 12.67
|
||||
Output | 0.00032806 | 0.00034043 | 0.00040531 | 0.1 | 0.04
|
||||
Modify | 0.028788 | 0.031511 | 0.033365 | 0.9 | 3.54
|
||||
Other | | 0.01618 | | | 1.82
|
||||
Pair | 0.48598 | 0.49768 | 0.50892 | 1.1 | 57.06
|
||||
Neigh | 0.22855 | 0.23236 | 0.23463 | 0.5 | 26.64
|
||||
Comm | 0.082584 | 0.093727 | 0.10748 | 2.9 | 10.75
|
||||
Output | 0.0002718 | 0.00028038 | 0.00031757 | 0.1 | 0.03
|
||||
Modify | 0.028934 | 0.031425 | 0.03322 | 0.8 | 3.60
|
||||
Other | | 0.01668 | | | 1.91
|
||||
|
||||
Nlocal: 1000 ave 1020 max 982 min
|
||||
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
|
||||
run 10000
|
||||
Memory usage per processor = 2.55761 Mbytes
|
||||
Step Temp Thot Tcold
|
||||
Step Temp c_Thot c_Tcold
|
||||
1000 1.35 1.431295 1.2955644
|
||||
2000 1.3518468 1.5562602 1.154905
|
||||
3000 1.3477229 1.5890075 1.2395414
|
||||
@ -133,20 +133,20 @@ Step Temp Thot Tcold
|
||||
9000 1.3739201 1.6846211 1.1138829
|
||||
10000 1.3751455 1.8039471 1.1500399
|
||||
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
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.138 | 4.9118 | 5.6168 | 26.2 | 46.83
|
||||
Neigh | 2.1715 | 2.4541 | 2.7147 | 14.7 | 23.40
|
||||
Comm | 0.94395 | 1.8449 | 2.9212 | 55.3 | 17.59
|
||||
Output | 0.00043416 | 0.00046757 | 0.00054884 | 0.2 | 0.00
|
||||
Modify | 1.0234 | 1.0946 | 1.2539 | 8.7 | 10.44
|
||||
Other | | 0.1821 | | | 1.74
|
||||
Pair | 4.2189 | 4.9657 | 5.6225 | 25.3 | 48.03
|
||||
Neigh | 2.1359 | 2.4223 | 2.6741 | 14.8 | 23.43
|
||||
Comm | 0.83801 | 1.6773 | 2.6984 | 57.1 | 16.22
|
||||
Output | 0.00042701 | 0.00046191 | 0.00052905 | 0.1 | 0.00
|
||||
Modify | 1.0143 | 1.0895 | 1.1846 | 5.7 | 10.54
|
||||
Other | | 0.1844 | | | 1.78
|
||||
|
||||
Nlocal: 1000 ave 1131 max 878 min
|
||||
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
|
||||
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
|
||||
12000 1.3703433 1.7829467 1.1194444 -0.66044316 0
|
||||
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
|
||||
30000 1.3821118 1.7382856 1.1078333 -0.79892499 -0.74729427
|
||||
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
|
||||
99.4% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
Performance: 385616.132 tau/day, 892.630 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 | 7.4578 | 9.8912 | 11.96 | 64.5 | 44.19
|
||||
Neigh | 4.0721 | 5.0195 | 5.8898 | 36.9 | 22.43
|
||||
Comm | 1.9554 | 4.7393 | 7.8917 | 125.4 | 21.18
|
||||
Output | 0.00099301 | 0.0017841 | 0.0019252 | 0.7 | 0.01
|
||||
Modify | 2.2325 | 2.321 | 2.4866 | 6.5 | 10.37
|
||||
Other | | 0.4085 | | | 1.83
|
||||
Pair | 7.6116 | 10.003 | 12.262 | 64.3 | 44.65
|
||||
Neigh | 4.038 | 4.9528 | 5.8822 | 37.6 | 22.10
|
||||
Comm | 1.6649 | 4.7143 | 7.6339 | 124.9 | 21.04
|
||||
Output | 0.00098443 | 0.0017504 | 0.0018921 | 0.7 | 0.01
|
||||
Modify | 2.1819 | 2.3289 | 2.6598 | 12.6 | 10.39
|
||||
Other | | 0.4047 | | | 1.81
|
||||
|
||||
Nlocal: 1000 ave 1134 max 850 min
|
||||
Histogram: 2 1 0 1 0 0 0 1 0 3
|
||||
230
examples/KAPPA/log.13Oct16.heatflux.g++.8
Normal file
230
examples/KAPPA/log.13Oct16.heatflux.g++.8
Normal file
@ -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
|
||||
245
examples/KAPPA/log.13Oct16.langevin.g++.8
Normal file
245
examples/KAPPA/log.13Oct16.langevin.g++.8
Normal file
@ -0,0 +1,245 @@
|
||||
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
|
||||
232
examples/KAPPA/log.13Oct16.mp.g++.8
Normal file
232
examples/KAPPA/log.13Oct16.mp.g++.8
Normal file
@ -0,0 +1,232 @@
|
||||
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
|
||||
@ -1,208 +0,0 @@
|
||||
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
|
||||
@ -1,215 +0,0 @@
|
||||
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
|
||||
@ -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
|
||||
File diff suppressed because it is too large
Load Diff
436
examples/VISCOSITY/log.13Oct16.einstein.2d.g++.1
Normal file
436
examples/VISCOSITY/log.13Oct16.einstein.2d.g++.1
Normal file
@ -0,0 +1,436 @@
|
||||
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
|
||||
36000 0.99528173 -1.5791377 1.0970028 -0.016714523 1.4188568 0.88993465
|
||||
38000 1.0124371 -1.5952165 0.99493986 -0.041410673 1.3575213 0.94345659
|
||||
40000 1.0141237 -1.5974959 0.98549019 0.047454345 1.3425092 0.89871657
|
||||
42000 1.0274867 -1.6103177 0.93801507 0.089635945 1.2942122 0.86538125
|
||||
44000 0.98700259 -1.5693265 0.94306661 -0.045695708 1.3728992 0.93162122
|
||||
46000 1.0080948 -1.591735 1.0304791 -0.0046135743 1.3174697 0.89594482
|
||||
48000 0.97227783 -1.5551815 1.1829894 0.042219544 1.2647775 0.87200134
|
||||
50000 0.99046716 -1.5732492 1.0095618 0.018697031 1.221817 0.84123547
|
||||
52000 1.0129697 -1.5965188 0.88794241 -0.045990748 1.1856229 0.9040415
|
||||
54000 1.0013276 -1.5843748 1.0246693 0.012464296 1.2889061 0.87286599
|
||||
56000 1.0385716 -1.6218376 0.75426191 -0.04775685 1.2504841 0.84682228
|
||||
58000 1.0107757 -1.5935394 1.0239619 0.029529278 1.2134635 0.9938075
|
||||
60000 1.0177033 -1.6004904 0.94723439 -0.16871762 1.2535747 1.0125806
|
||||
62000 1.0210737 -1.6038196 1.0225179 0.079638703 1.215309 0.98168447
|
||||
64000 1.0106132 -1.5941352 1.0188777 0.02699431 1.1836603 0.97574934
|
||||
66000 0.98531307 -1.5684662 1.1224354 -0.0069578014 1.2557176 0.99054037
|
||||
68000 0.99450728 -1.5785884 1.3016366 0.056607824 1.2198402 1.0305974
|
||||
70000 0.98874589 -1.5720858 1.0724556 -0.022405835 1.1860738 1.0020293
|
||||
72000 1.0108814 -1.5935405 0.92375729 -0.12669224 1.1627555 0.97777367
|
||||
74000 1.0098348 -1.5932383 1.0635024 -0.12956833 1.1387216 0.99028812
|
||||
76000 1.0089021 -1.5925365 0.98626851 -0.20311631 1.1527717 0.97238965
|
||||
78000 1.002405 -1.5857268 1.008097 -0.089615503 1.1255136 0.94930557
|
||||
80000 1.0266582 -1.6095848 1.0493411 0.16631226 1.1416236 0.96066686
|
||||
82000 1.01242 -1.5953224 0.81710829 0.18713063 1.1208021 0.94504086
|
||||
84000 1.0262474 -1.6102703 1.1125949 -0.0012088503 1.1685343 0.93574513
|
||||
86000 0.99599827 -1.5786216 1.0337621 -0.0056500173 1.1619022 0.91502714
|
||||
88000 0.98713531 -1.5701336 1.0665747 -0.10237303 1.2033676 0.91683937
|
||||
90000 1.0156011 -1.5996767 0.96906164 0.13894564 1.1877816 0.91164181
|
||||
92000 1.0306883 -1.6137656 0.78929887 0.0089544803 1.1655216 0.89238295
|
||||
94000 0.98455669 -1.5668138 1.1917323 0.025629181 1.1415233 0.88999487
|
||||
96000 0.99528576 -1.5779727 1.1055136 0.020277014 1.1220378 0.884028
|
||||
98000 1.0504589 -1.6338024 0.99135546 -0.051989636 1.0995983 0.88195356
|
||||
100000 0.98210335 -1.5653161 1.0867432 0.091525725 1.0788118 0.86708357
|
||||
102000 1.0316494 -1.6156561 1.1350259 0.072311903 1.0682988 0.85879527
|
||||
104000 1.0292338 -1.6126651 0.83829357 -0.04098328 1.0674517 0.90910693
|
||||
106000 0.98153521 -1.5647366 1.0653974 -4.3227008e-05 1.048242 0.91634683
|
||||
108000 1.0074159 -1.5909608 1.0048635 0.1947269 1.1066118 0.96168226
|
||||
110000 1.0007684 -1.5838251 1.1603181 0.13820163 1.0869248 0.96825039
|
||||
112000 0.98637814 -1.5692736 1.0037644 0.049907343 1.0678816 0.95140325
|
||||
114000 0.99310586 -1.574972 1.0896413 -0.079352378 1.049685 0.95078035
|
||||
116000 0.98829858 -1.5705137 0.87861443 0.05118496 1.0673701 0.93474367
|
||||
118000 1.01049 -1.5933529 0.96002545 -0.12320659 1.06809 0.94388888
|
||||
120000 1.0218378 -1.6050064 0.89637436 0.02750584 1.0507296 0.9721852
|
||||
122000 1.0263547 -1.6090242 0.95854694 0.0034110405 1.0519885 0.97478734
|
||||
124000 0.9899202 -1.5732471 1.0492908 -0.13855042 1.0352928 0.95932329
|
||||
126000 0.98192121 -1.5648602 1.1372352 0.16313842 1.0195242 0.96122299
|
||||
128000 1.002862 -1.5860432 0.97650147 0.048928455 1.0422628 0.97854238
|
||||
130000 0.99785761 -1.5808342 0.93146735 0.026478401 1.042581 0.99155317
|
||||
132000 0.98956541 -1.5724182 0.96523389 -0.10052306 1.027027 0.98847097
|
||||
134000 1.0019397 -1.5848811 1.0447894 0.13871691 1.016337 0.9846235
|
||||
136000 1.0321449 -1.6162667 1.1072168 -0.15369414 1.0062486 0.99959003
|
||||
138000 1.0239483 -1.6070861 0.82920716 -0.011872404 0.99440555 0.98531922
|
||||
140000 1.0082907 -1.5911532 1.0012771 0.027192581 0.98750923 1.0234574
|
||||
142000 1.0007865 -1.5839168 1.0399048 -0.096251148 1.0112715 1.0110141
|
||||
144000 1.0001664 -1.5824827 1.0071962 -0.083449668 1.0100611 1.0191469
|
||||
146000 1.0202238 -1.6043224 1.0702284 -0.063595518 1.0113284 1.0091825
|
||||
148000 1.0248683 -1.6088702 1.0227875 0.069198975 1.0099355 1.0038023
|
||||
150000 1.0127614 -1.595093 0.80897516 0.0044443031 1.002562 0.99323586
|
||||
152000 1.0028044 -1.58605 1.0857002 -0.059930891 0.99898861 0.98463631
|
||||
154000 1.0149836 -1.597497 0.82631625 0.085962962 0.98807287 0.97473529
|
||||
156000 0.99818966 -1.5813132 1.035248 -0.029178797 0.97557066 0.9653792
|
||||
158000 1.0023756 -1.5858717 0.94465038 -0.056571392 0.9646132 0.95331791
|
||||
160000 0.99847665 -1.5819798 1.0656894 -0.022026678 0.97680099 0.99699456
|
||||
162000 0.98084763 -1.5637747 1.2446958 0.097934009 0.96520059 0.99886917
|
||||
164000 0.98358665 -1.5664883 1.1626742 -0.010830507 0.95857867 0.98697029
|
||||
166000 1.0176133 -1.6002621 0.91335665 0.054966014 0.97897499 1.0064186
|
||||
168000 1.0252828 -1.6091158 1.0562376 0.025372153 0.96968537 1.0117261
|
||||
170000 1.0429701 -1.6246241 0.78042973 -0.088860018 0.98832737 1.0091494
|
||||
172000 1.0167826 -1.5995939 0.93307169 -0.0028786839 0.97757064 1.0140023
|
||||
174000 1.0067129 -1.5892333 0.93660255 0.13405338 1.0256516 1.0130713
|
||||
176000 1.0142368 -1.5969856 1.1376546 -0.039887725 1.0142342 1.0042825
|
||||
178000 1.0337679 -1.6167973 0.88782002 -0.013087286 1.0196301 1.0360511
|
||||
180000 0.96700375 -1.5494313 1.2700192 -0.17359042 1.0315247 1.0457286
|
||||
182000 1.0128669 -1.5958728 1.0325786 -0.11340517 1.0279582 1.0364275
|
||||
184000 1.0016786 -1.5849657 1.2423822 -0.04019647 1.0270552 1.028752
|
||||
186000 1.0068219 -1.5892056 0.91016442 0.12827957 1.0222492 1.0326718
|
||||
188000 1.0111052 -1.5936203 0.84190116 0.11675343 1.0132227 1.0349714
|
||||
190000 1.0428535 -1.6252876 0.84579508 0.074521906 1.0026939 1.0388207
|
||||
192000 0.98196941 -1.5644931 1.1089098 0.10878744 0.99394843 1.0299225
|
||||
194000 1.0060461 -1.5891845 1.0637631 0.0094883212 0.98560308 1.0478014
|
||||
196000 1.009729 -1.5927481 1.0375371 0.001016821 0.98435144 1.0504309
|
||||
198000 1.0130466 -1.5961561 0.94423285 -0.065299989 0.97454291 1.0416243
|
||||
200000 0.99556457 -1.578527 1.0479236 -0.078093695 0.96545375 1.0526692
|
||||
202000 1.0024053 -1.5849364 1.0110919 -0.011771169 0.9561055 1.0509412
|
||||
204000 1.0487373 -1.6329308 0.96913936 0.092389554 0.94987394 1.0543579
|
||||
206000 1.0040089 -1.5867752 0.87055365 -0.0029267837 0.9567723 1.0463902
|
||||
208000 0.98635833 -1.5695234 1.1193994 0.043854107 0.95068021 1.0683786
|
||||
210000 0.99172336 -1.5744133 1.0945983 -0.047827928 0.94448675 1.0661744
|
||||
212000 0.99572889 -1.5790512 1.1375524 -0.19281467 0.94310134 1.0562378
|
||||
214000 1.0146878 -1.5975136 0.93324057 0.023347328 0.94263065 1.046519
|
||||
216000 0.99707471 -1.5796874 0.96782693 0.083402848 0.93858777 1.0369438
|
||||
218000 1.0072021 -1.5896781 0.8155869 -0.094678429 0.9324393 1.0402187
|
||||
220000 0.99829642 -1.5812727 1.0862336 -0.057344135 0.92566931 1.0397392
|
||||
222000 1.0214364 -1.6037091 1.0020523 -0.081278441 0.91849564 1.032842
|
||||
224000 1.0007703 -1.583861 1.1398771 -0.014848249 0.91289746 1.0653713
|
||||
226000 1.0160887 -1.5986412 0.97725713 -0.061995296 0.92331797 1.0560269
|
||||
228000 1.0094934 -1.5930023 1.040651 0.0079530479 0.91726191 1.0492381
|
||||
230000 0.98902579 -1.5714487 1.050377 -0.02091325 0.90947876 1.0601329
|
||||
232000 0.98365162 -1.5665923 1.1795485 0.007265917 0.90850244 1.0527928
|
||||
234000 0.98804235 -1.5705815 0.99142023 -0.14096873 0.90260469 1.0522485
|
||||
236000 1.0111715 -1.5944579 1.0365441 0.03705863 0.89687478 1.0650694
|
||||
238000 1.028486 -1.6112797 0.77859138 0.03686834 0.88950376 1.0613943
|
||||
240000 1.0048364 -1.5883043 1.0507628 0.177815 0.88491797 1.0540196
|
||||
242000 1.0612408 -1.6455438 0.80528323 -0.065846556 0.87805554 1.047094
|
||||
244000 0.99451698 -1.577672 0.90507771 0.0090582429 0.87117885 1.0414447
|
||||
246000 1.0215777 -1.6050443 0.88605366 -0.033084099 0.86431702 1.0330488
|
||||
248000 1.0346251 -1.6179476 1.0266325 0.042180226 0.8640658 1.0319629
|
||||
250000 0.97725995 -1.5600316 0.99997539 0.046921107 0.85977157 1.0423435
|
||||
252000 1.0045133 -1.5877785 1.2089315 -0.20100537 0.85362501 1.038709
|
||||
254000 1.0396556 -1.6230252 0.8806146 0.16822159 0.847332 1.0358375
|
||||
256000 0.99769832 -1.5808696 1.0692142 0.03603972 0.84086272 1.0290594
|
||||
258000 0.97543457 -1.5580142 1.0623702 0.076387425 0.83692757 1.0365855
|
||||
260000 0.99005919 -1.5729678 1.0412698 -0.19142244 0.8306184 1.0329137
|
||||
262000 1.0014908 -1.5850781 1.0353971 0.10763251 0.82439244 1.0256642
|
||||
264000 1.0392437 -1.6231176 1.0236348 -0.19905313 0.81842954 1.0180519
|
||||
266000 1.0110595 -1.5936149 0.943378 -0.055766989 0.81566316 1.0185788
|
||||
268000 1.0155932 -1.5990965 0.84263415 -0.046929409 0.81998209 1.0239593
|
||||
270000 1.060652 -1.6449021 0.75643153 -0.10294749 0.81609283 1.0386067
|
||||
272000 1.0069743 -1.5895439 0.97553062 0.029040039 0.81351378 1.0375075
|
||||
274000 1.0463214 -1.6293543 0.67594148 -0.0069642173 0.80767486 1.0403024
|
||||
276000 1.0042636 -1.5875148 0.98929276 -0.12449786 0.80322846 1.0331136
|
||||
278000 0.97917004 -1.5627321 1.1268906 -0.078323442 0.8102638 1.0318867
|
||||
280000 1.0082531 -1.5907083 1.0527782 -0.036059017 0.80597557 1.0481782
|
||||
282000 1.0154843 -1.5985096 0.92086705 -0.068530775 0.80179106 1.073873
|
||||
284000 1.0098619 -1.5927428 1.036216 0.037750753 0.8112042 1.067422
|
||||
286000 1.0066095 -1.588402 0.98446812 0.02654871 0.80832515 1.0667938
|
||||
288000 1.0108484 -1.5932756 0.9938665 0.0014634473 0.80352165 1.080693
|
||||
290000 1.0084713 -1.5916424 0.97267996 -0.16071115 0.80043111 1.0816066
|
||||
292000 1.0056589 -1.5888464 0.84166635 0.11872697 0.7982537 1.0747896
|
||||
294000 1.0209933 -1.6049531 0.9891441 -0.08837825 0.79291613 1.0741692
|
||||
296000 0.99782768 -1.5811255 1.0931691 0.03252435 0.79104136 1.0866176
|
||||
298000 0.97158829 -1.5544768 1.0587163 -0.020509263 0.78578918 1.0885357
|
||||
300000 0.99635509 -1.5797521 1.0508706 -0.13999572 0.79997303 1.0997452
|
||||
302000 1.0244367 -1.6074122 0.98051456 0.078987418 0.80030881 1.0995395
|
||||
304000 1.0164691 -1.599263 0.92957417 -0.052090111 0.79628244 1.0931733
|
||||
306000 0.99640652 -1.5798263 1.0046382 -0.17696034 0.79868947 1.0904769
|
||||
308000 0.99001053 -1.5729715 1.0661668 -0.040494857 0.79359692 1.0911752
|
||||
310000 1.0176688 -1.6008189 0.88160706 -0.16255132 0.7885584 1.0842801
|
||||
312000 1.0030797 -1.5862445 1.1056347 0.2012843 0.78631107 1.0817648
|
||||
314000 1.0135412 -1.5963385 0.89411346 0.14573277 0.79263889 1.0968231
|
||||
316000 1.0289246 -1.6116769 0.95183363 -0.13790235 0.78774407 1.104116
|
||||
318000 1.0272076 -1.6108119 1.0546778 -0.15570037 0.78290345 1.0975264
|
||||
320000 1.0233555 -1.605886 0.69600824 -0.051301259 0.78829232 1.09266
|
||||
322000 1.0276771 -1.6115588 1.006656 -0.037166444 0.7929092 1.1049954
|
||||
324000 1.0009085 -1.583632 1.1030988 -0.045003287 0.78813539 1.0982174
|
||||
326000 0.99820481 -1.5808746 0.96157265 0.0051561382 0.78352469 1.0927727
|
||||
328000 1.0034746 -1.5866592 0.9828709 0.04098644 0.78017024 1.1021054
|
||||
330000 0.9855772 -1.5690259 1.2748992 0.216881 0.77581501 1.1148803
|
||||
332000 0.9965209 -1.5793357 1.1130749 0.090747874 0.77153933 1.1084502
|
||||
334000 1.035755 -1.6181093 0.88167554 0.02819393 0.77362798 1.101853
|
||||
336000 0.99996774 -1.582885 1.0190301 0.063460214 0.7730658 1.1168918
|
||||
338000 0.99767487 -1.5806236 1.0766267 0.17431208 0.84891175 1.114904
|
||||
340000 1.0253142 -1.6080987 0.95542815 -0.057965391 0.84475717 1.119315
|
||||
342000 1.0068098 -1.5893898 0.97259996 0.10715327 0.84600544 1.1134594
|
||||
344000 0.99340991 -1.5757393 1.0870946 -0.068506912 0.84493383 1.1166996
|
||||
346000 1.0120696 -1.5950574 1.0131809 -0.053688663 0.85345684 1.1136118
|
||||
348000 1.0309753 -1.6139898 0.89960386 -0.060363095 0.84882315 1.1073002
|
||||
350000 1.0037776 -1.5861394 1.0091603 0.02135905 0.84400778 1.1065317
|
||||
352000 0.98591728 -1.5680629 1.1377659 -0.083236455 0.84339812 1.1002993
|
||||
354000 1.0080397 -1.5904616 0.80849869 0.00928565 0.839096 1.1021557
|
||||
356000 1.0580451 -1.6407084 0.75557573 -0.072592855 0.83455195 1.104521
|
||||
358000 1.030585 -1.6137874 1.0380857 -0.080811662 0.82993805 1.1008832
|
||||
360000 1.0095237 -1.5931114 1.054976 -0.16712924 0.82622185 1.114334
|
||||
362000 1.0310879 -1.614041 0.84077595 0.080477352 0.82210684 1.110334
|
||||
364000 1.0000238 -1.5823394 1.1775906 0.0031139552 0.81775187 1.1202628
|
||||
366000 1.0190616 -1.6010113 0.92848622 -0.046387272 0.81781978 1.1264338
|
||||
368000 1.0089574 -1.591851 0.88967276 0.084507509 0.82548053 1.1212356
|
||||
370000 0.98626285 -1.5690591 1.0389475 0.15747394 0.82583189 1.1154499
|
||||
372000 1.0179928 -1.6012532 0.95338149 -0.079240909 0.82167358 1.1144564
|
||||
374000 1.0036723 -1.5864866 0.91169472 0.038159086 0.82140017 1.1085543
|
||||
376000 1.0059869 -1.5884349 0.90711389 -0.093438168 0.8175783 1.1153576
|
||||
378000 1.0376167 -1.6201331 0.96969013 -0.11849733 0.81376748 1.1099608
|
||||
380000 0.98982394 -1.5727352 1.1608252 -0.038393364 0.81568758 1.1079312
|
||||
382000 0.97137184 -1.5536171 0.96619112 -0.034678175 0.82814609 1.1093848
|
||||
384000 0.99272978 -1.5762779 1.0509393 0.032343038 0.82443143 1.1102277
|
||||
386000 1.0100648 -1.5930531 0.96303847 -0.0497874 0.8208917 1.1139354
|
||||
388000 0.99635597 -1.5791363 1.016829 -0.04531565 0.81880723 1.123366
|
||||
390000 1.0128857 -1.596226 1.0168535 0.030123764 0.8154196 1.1178207
|
||||
392000 1.0414799 -1.6256855 0.91612676 0.052204166 0.83525866 1.1123266
|
||||
394000 0.98112978 -1.5641253 1.0438272 -0.068667673 0.83283911 1.1079269
|
||||
396000 0.97787678 -1.5598426 1.0131718 -0.033109536 0.82986658 1.1023614
|
||||
398000 1.0292431 -1.6119808 0.90622851 -0.082576483 0.8257706 1.0998351
|
||||
400000 1.0026087 -1.585683 1.0275497 0.087158222 0.82322877 1.0977666
|
||||
402000 1.0163706 -1.598545 0.96588365 -0.029125811 0.81982673 1.0926389
|
||||
404000 1.0262493 -1.6102647 0.79007094 0.0079598958 0.82007072 1.0907315
|
||||
406000 0.99487107 -1.5778515 0.83977277 0.066596384 0.81631134 1.0866073
|
||||
408000 1.0108518 -1.5941246 1.1412871 0.041085191 0.81420279 1.1112395
|
||||
410000 1.0026966 -1.5853826 1.1125145 0.021404009 0.81421483 1.1075314
|
||||
412000 1.0027426 -1.5856908 1.1445941 0.10077025 0.81035844 1.1221605
|
||||
414000 1.0525169 -1.6352976 0.6688189 -0.071885452 0.80922951 1.117048
|
||||
416000 0.95514842 -1.5380164 1.2198976 -0.020098364 0.81039185 1.1127016
|
||||
418000 0.99853286 -1.581907 1.040174 -0.043752958 0.83070976 1.1151814
|
||||
420000 0.96432983 -1.5472735 1.2000605 0.0284884 0.82688067 1.1201892
|
||||
422000 1.0110338 -1.5937639 0.88925615 -0.0056255993 0.83729353 1.1266963
|
||||
424000 1.0077925 -1.5914573 1.0625448 0.078586775 0.83465757 1.1235583
|
||||
426000 0.98743189 -1.57002 1.0888581 0.12563331 0.83275041 1.1193766
|
||||
428000 1.0112301 -1.5939984 0.91688673 -0.1605337 0.82889693 1.121168
|
||||
430000 1.0283254 -1.6119787 0.83233694 0.047589962 0.8296882 1.1165262
|
||||
432000 0.97982409 -1.5625913 1.1875522 -0.060520907 0.8264448 1.1156609
|
||||
434000 0.9830003 -1.5662434 1.2882445 0.026552191 0.82362897 1.1251296
|
||||
436000 0.98158695 -1.5642196 1.2184202 0.10011832 0.81988328 1.1202386
|
||||
438000 1.0174602 -1.6006392 0.98983657 -0.26731543 0.82359277 1.1194173
|
||||
440000 1.0147922 -1.5986583 0.99723521 0.10312258 0.82668874 1.1166321
|
||||
442000 1.0185438 -1.6025919 0.95378608 0.032898335 0.8376384 1.1141027
|
||||
444000 0.97737381 -1.5597895 1.2100163 0.022311362 0.85102822 1.1150521
|
||||
446000 0.99593648 -1.5791062 1.0999746 -0.041825149 0.85489871 1.1105882
|
||||
448000 1.0259234 -1.6095208 0.90080955 -0.057452702 0.85131792 1.105654
|
||||
450000 0.98873973 -1.5717826 1.0019177 -0.14057947 0.84916741 1.1007825
|
||||
452000 1.0059102 -1.5895389 1.0666545 0.014242262 0.84548682 1.096266
|
||||
454000 0.99943215 -1.5826409 1.1353551 0.070613563 0.84193028 1.0914609
|
||||
456000 0.99123683 -1.574133 1.1310395 -0.019958521 0.85786896 1.0872
|
||||
458000 0.98476743 -1.5685042 1.0628314 -0.024302081 0.86756819 1.0850446
|
||||
460000 1.0139076 -1.5963225 1.0181222 0.089182002 0.87724533 1.0827991
|
||||
462000 1.0113822 -1.5955924 1.1739975 -0.10175863 0.89205773 1.0951284
|
||||
464000 1.0228404 -1.607263 1.0517714 -0.031783966 0.89340123 1.0913457
|
||||
466000 1.0126934 -1.5964207 0.96656763 -0.015021156 0.89086201 1.0870365
|
||||
468000 1.0070377 -1.5912579 1.0378727 -0.0077122994 0.88981469 1.0868451
|
||||
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
|
||||
423
examples/VISCOSITY/log.13Oct16.gk.2d.g++.1
Normal file
423
examples/VISCOSITY/log.13Oct16.gk.2d.g++.1
Normal file
@ -0,0 +1,423 @@
|
||||
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
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|
||||
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
|
||||
260
examples/VISCOSITY/log.13Oct16.mp.2d.g++.1
Normal file
260
examples/VISCOSITY/log.13Oct16.mp.2d.g++.1
Normal file
@ -0,0 +1,260 @@
|
||||
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
|
||||
304
examples/VISCOSITY/log.13Oct16.nemd.2d.g++.1
Normal file
304
examples/VISCOSITY/log.13Oct16.nemd.2d.g++.1
Normal file
@ -0,0 +1,304 @@
|
||||
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
|
||||
246
examples/VISCOSITY/log.13Oct16.wall.2d.g++.1
Normal file
246
examples/VISCOSITY/log.13Oct16.wall.2d.g++.1
Normal file
@ -0,0 +1,246 @@
|
||||
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
|
||||
@ -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
|
||||
@ -1,230 +0,0 @@
|
||||
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
|
||||
@ -1,271 +0,0 @@
|
||||
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
|
||||
@ -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
252
examples/VISCOSITY/profile.13Oct16.einstein.2d.g++.1
Normal file
@ -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
examples/VISCOSITY/profile.13Oct16.gk.2d.g++.1
Normal file
100654
examples/VISCOSITY/profile.13Oct16.gk.2d.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
1473
examples/VISCOSITY/profile.13Oct16.mp.2d.g++.1
Normal file
1473
examples/VISCOSITY/profile.13Oct16.mp.2d.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
423
examples/VISCOSITY/profile.13Oct16.nemd.2d.g++.1
Normal file
423
examples/VISCOSITY/profile.13Oct16.nemd.2d.g++.1
Normal file
@ -0,0 +1,423 @@
|
||||
# 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
150
examples/VISCOSITY/profile.13Oct16.wall.2d.g++.1
Normal file
@ -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
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -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
|
||||
@ -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
|
||||
@ -14,15 +14,18 @@
|
||||
# Python wrappers on LAMMPS library via ctypes
|
||||
|
||||
# for python3 compatibility
|
||||
|
||||
from __future__ import print_function
|
||||
|
||||
# imports for simple LAMMPS python wrapper module "lammps"
|
||||
|
||||
import sys,traceback,types
|
||||
from ctypes import *
|
||||
from os.path import dirname,abspath,join
|
||||
from inspect import getsourcefile
|
||||
|
||||
# imports for advanced LAMMPS python wrapper modules "PyLammps" and "IPyLammps"
|
||||
|
||||
from collections import namedtuple
|
||||
import os
|
||||
import select
|
||||
@ -38,6 +41,7 @@ class MPIAbortException(Exception):
|
||||
|
||||
|
||||
class lammps(object):
|
||||
|
||||
# detect if Python is using version of mpi4py that can pass a communicator
|
||||
|
||||
has_mpi4py_v2 = False
|
||||
@ -60,23 +64,27 @@ class lammps(object):
|
||||
modpath = dirname(abspath(getsourcefile(lambda:0)))
|
||||
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:
|
||||
if ptr: self.lib = CDLL("",RTLD_GLOBAL)
|
||||
except:
|
||||
self.lib = None
|
||||
|
||||
# load liblammps.so unless name is given.
|
||||
# e.g. if name = "g++", load liblammps_g++.so
|
||||
# load liblammps.so unless name is given
|
||||
# if name = "g++", load liblammps_g++.so
|
||||
# try loading the LAMMPS shared object from the location
|
||||
# of lammps.py with an absolute path (so that LD_LIBRARY_PATH
|
||||
# does not need to be set for regular installations.
|
||||
# fall back to loading with a relative path, which typically
|
||||
# requires LD_LIBRARY_PATH to be set appropriately.
|
||||
# of lammps.py with an absolute path,
|
||||
# so that LD_LIBRARY_PATH does not need to be set for regular install
|
||||
# fall back to loading with a relative path,
|
||||
# typically requires LD_LIBRARY_PATH to be set appropriately
|
||||
|
||||
if not self.lib:
|
||||
try:
|
||||
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:
|
||||
if not name: self.lib = CDLL("liblammps.so",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
|
||||
|
||||
if not ptr:
|
||||
|
||||
# with mpi4py v2, can pass MPI communicator to LAMMPS
|
||||
# need to adjust for type of MPI communicator object
|
||||
# allow for int (like MPICH) or void* (like OpenMPI)
|
||||
|
||||
@ -1918,7 +1918,7 @@ int DumpCustom::modify_param(int narg, char **arg)
|
||||
field2index[nfield+nthresh] = add_custom(suffix,0);
|
||||
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
|
||||
|
||||
@ -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] = NEQ;
|
||||
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
|
||||
// create FixStore to hold LAST values, should work with restart
|
||||
|
||||
@ -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
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -246,13 +246,10 @@ void Finish::end(int flag)
|
||||
|
||||
if (prdflag) {
|
||||
if (me == 0) {
|
||||
if (screen) fprintf(screen,"\n");
|
||||
if (logfile) fprintf(logfile,"\n");
|
||||
if (screen) fprintf(screen,"\nPRD stats:\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);
|
||||
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
time = tmp/nprocs;
|
||||
|
||||
@ -1 +1 @@
|
||||
#define LAMMPS_VERSION "12 Oct 2016"
|
||||
#define LAMMPS_VERSION "18 Oct 2016"
|
||||
|
||||
Reference in New Issue
Block a user