git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3515 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -949,199 +949,212 @@ particles are point masses.
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4.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables) :link(4_15),h4
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Aside from "restart files"_restart.html, there are two basic kinds of
|
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LAMMPS output. The first is "thermodynamic output"_thermo_style.html,
|
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which is a list of quantities printed every few timesteps to the
|
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screen and logfile. The second is "dump files"_dump.html, which
|
||||
contain snapshots of atoms and various per-atom values and are written
|
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at a specified frequency. A simulation prints one set of
|
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thermodynamic output; it may generate any number of dump files. As
|
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discussed below, LAMMPS gives you a variety of ways to determine what
|
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quantities are computed and printed when thermodynamic info or dump
|
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files are output. There are also three fixes which can do their own
|
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output of user-chosen quantities: "fix ave/time"_fix_ave_time.html for
|
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time averaging, "fix ave/spatial"_fix_ave_spatial.html for spatial
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||||
averaging, and "fix print"_fix_print.html. These are also described
|
||||
below. Throughout this discussion, note that users can "add their own
|
||||
computes and fixes to LAMMPS"_Section_modify.html which can then
|
||||
generate values that can be output with these commands.
|
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There are four basic kinds of LAMMPS output:
|
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|
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Thermodynamic output :h5
|
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"Thermodynamic output"_thermo_style.html, which is a list
|
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of quantities printed every few timesteps to the screen and logfile. :ulb,l
|
||||
|
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"Dump files"_dump.html, which contain snapshots of atoms and various
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per-atom values and are written at a specified frequency. :l
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|
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Certain fixes can output user-specified quantities to files: "fix
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ave/time"_fix_ave_time.html for time averaging, "fix
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ave/spatial"_fix_ave_spatial.html for spatial averaging, and "fix
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print"_fix_print.html for single-line output of
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"variables"_variable.html. Fix print can also output to the
|
||||
screen. :l
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|
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"Restart files"_restart.html. :l,ule
|
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|
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A simulation prints one set of thermodynamic output and (optionally)
|
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restart files. It can generate any number of dump files and fix
|
||||
output files, depending on what "dump"_dump.html and "fix"_fix.html
|
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commands you specify.
|
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|
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As discussed below, LAMMPS gives you a variety of ways to determine
|
||||
what quantities are computed and printed when the thermodynamics,
|
||||
dump, or fix commands listed above perform output. Throughout this
|
||||
discussion, note that users can also "add their own computes and fixes
|
||||
to LAMMPS"_Section_modify.html which can then generate values that can
|
||||
then be output with these commands.
|
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|
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The following sub-sections discuss different LAMMPS command related
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to output and the kind of data they operate on and produce:
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"Global/per-atom/local data"_#global
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"Scalar/vector/array data"_#scalar
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"Thermodynamic output"_#thermo
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"Dump file output"_#dump
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"Fixes that write output files"_#fixoutput
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"Computes that process output quantities"_#computeoutput
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"Computes that generate values to output"_#compute
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"Fixes that generate values to output"_#fix
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"Variables that generate values to output"_#variable
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"Summary table of output options and data flow between commands"_#table :ul
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|
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Global/per-atom/local data :h5,link(global)
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Various output-related commands work with three different styles of
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data: global, per-atom, or local. A global datum is one or more
|
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system-wide values, e.g. the temperature of the system. A per-atom
|
||||
datum is one or more values per atom, e.g. the kinetic energy of each
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atom. Local datums are calculated by each processor based on the
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atoms it owns, but there may be zero or more per atom, e.g. a list of
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bond distances.
|
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|
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Scalar/vector/array data :h5,link(scalar)
|
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|
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Global, per-atom, and local datums can each come in three kinds: a
|
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single scalar value, a vector of values, or a 2d array of values. The
|
||||
doc page for a "compute" or "fix" or "variable" that generates data
|
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will specify both the style and kind of data it produces, e.g. a
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per-atom vector.
|
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|
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When a quantity is accessed, as in many of the output commands
|
||||
discussed below, it can be referenced via the following bracket
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notation, where ID in this case is the ID of a compute. The leading
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||||
"c_" would be replaced by "f_" for a fix, or "v_" for a variable:
|
||||
|
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c_ID | entire scalar, vector, or array
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||||
c_ID\[I\] | one element of vector, one column of array
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||||
c_ID\[I\]\[J\] | one element of array :tb(s=|)
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|
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In other words, using one bracket reduces the dimension of the data
|
||||
once (vector -> scalar, array -> vector). Using two brackets reduces
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||||
the dimension twice (array -> scalar). Thus a command that uses
|
||||
scalar values as input can typically also process elements of a vector
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||||
or array.
|
||||
|
||||
Thermodynamic output :h5,link(thermo)
|
||||
|
||||
The frequency and format of thermodynamic output is set by the
|
||||
"thermo"_thermo.html, "thermo_style"_thermo_style.html, and
|
||||
"thermo_modify"_thermo_modify.html commands. The
|
||||
"thermo_style"_thermo_style.html command also specifies what values are
|
||||
calculated and written out. Pre-defined keywords can be specified
|
||||
(e.g. press, etotal, etc). Three additional kinds of keywords can also
|
||||
be specified (c_ID, f_ID, v_name), where a "compute"_compute.html or
|
||||
"fix"_fix.html or "variable"_variable.html provides the value to be
|
||||
output. Each of these are described in turn.
|
||||
"thermo_style"_thermo_style.html command also specifies what values
|
||||
are calculated and written out. Pre-defined keywords can be specified
|
||||
(e.g. press, etotal, etc). Three additional kinds of keywords can
|
||||
also be specified (c_ID, f_ID, v_name), where a "compute"_compute.html
|
||||
or "fix"_fix.html or "variable"_variable.html provides the value to be
|
||||
output. In each case, the compute, fix, or variable must generate
|
||||
global values for input to the "thermo_style custom"_dump.html
|
||||
command.
|
||||
|
||||
In LAMMPS, a "compute"_compute.html comes in two flavors: ones that
|
||||
compute global values (a scalar or a vector, e.g. temperature,
|
||||
6-element pressure tensor) and ones that compute per-atom values.
|
||||
Only global quantities from a compute can be used for thermodynamic
|
||||
output. The user-defined ID of the compute is used along with an
|
||||
optional subscript as part of the "thermo_style"_thermo_style.html
|
||||
command. E.g. c_myTemp outputs the single scalar value generated by
|
||||
the compute; c_myTemp\[2\] outputs the 2nd vector value. Note that
|
||||
there is a "compute reduce"_compute_reduce.html command which can sum
|
||||
per-atom quantities into a global scalar or vector.
|
||||
|
||||
"Fixes"_fix.html can generate global scalar or vector values which can
|
||||
be output with thermodynamic output, e.g. the energy of an indenter's
|
||||
interaction with the simulation atoms. These values are accessed via
|
||||
the same format as a compute's values, as f_ID or f_ID\[N\]. See the
|
||||
doc pages for individual fix commands to see which ones generate
|
||||
global values that can be output with thermodynamic info. The "fix
|
||||
ave/time"_fix_ave_time.html command generates time-averaged global
|
||||
quantities which can be accessed for thermodynamic output, e.g. a
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time-averaged pressure.
|
||||
|
||||
"Variables"_variable.html can be defined in the input script. All
|
||||
styles except the atom-style variable can be used for thermodynamic
|
||||
output, since it generates per-atom values. A variable with the name
|
||||
"abc" is referenced in a thermo_style command as v_abc.
|
||||
|
||||
The formula associated with equal-style variables can contain math
|
||||
operations and functions (x+y,x*y,(),sqrt,exp,etc), atom values
|
||||
(x\[N\],fx\[N\],etc), group functions (mass(),vcm(),etc), references
|
||||
to thermodynamic quantities (temp,press,vol,etc), references to
|
||||
"computes"_compute.html that generate global values, references to
|
||||
"fixes"_fix.html that generate global values, or references to other
|
||||
"variables"_variable.html. Thus an equal-style variable is the most
|
||||
general way to define some quantity to calculate and include with
|
||||
thermodynamic output.
|
||||
|
||||
Dump file output :h5
|
||||
Dump file output :h5,link(dump)
|
||||
|
||||
Dump file output is specified by the "dump"_dump.html and
|
||||
"dump_modify"_dump_modify.html commands. There are several
|
||||
pre-defined formats (dump atom, dump xtc, etc). There is also a "dump
|
||||
custom"_dump.html format where the user specifies what values are
|
||||
output with each atom. Pre-defined keywords can be specified (tag, x,
|
||||
output with each atom. Pre-defined keywords can be specified (id, x,
|
||||
fx, etc). Three additional kinds of keywords can also be specified
|
||||
(c_ID, f_ID, v_name), where a "compute"_compute.html or "fix"_fix.html
|
||||
or "variable"_variable.html provides the value to be output. Each of
|
||||
these are described in turn.
|
||||
or "variable"_variable.html provides the values to be output. In each
|
||||
case, the compute, fix, or variable must generate per-atom values for
|
||||
input to the "dump custom"_dump.html command.
|
||||
|
||||
"Computes"_compute.html that generate one or more per-atom values can
|
||||
be accessed by the dump custom command. These are computes that have
|
||||
the word "atom" in their style name, e.g. ke/atom, stress/atom, etc.
|
||||
The values are accessed as c_myKE for a scalar per-atom quantity or as
|
||||
c_myStress\[2\] for a component of a vector per-atom quantity.
|
||||
Fixes that write output files :h5,link(fixoutput)
|
||||
|
||||
"Fixes"_fix.html can generate per-atom values to output to dump files.
|
||||
For example, the "fix ave/atom"_fix_ave_atom.html command calculates
|
||||
time-averages of per-atom quantities, such as per-atom
|
||||
"computes"_compute.html and atom-style "variables"_variable.html.
|
||||
These per-atom fix values are accessed by the "dump custom"_dump.html
|
||||
command via the same format as a compute's values, as f_myKE or
|
||||
f_myStress\[2\].
|
||||
Three fixes take various quantities as input and can write output
|
||||
files: "fix ave/time"_fix_ave_time.html, "fix
|
||||
ave/spatial"_fix_ave_spatial.html, and "fix print"_fix_print.html.
|
||||
|
||||
"Variables"_variable.html can be defined in the input script. Only
|
||||
atom-style variables can be used for dump custom output, since only
|
||||
they produce per-atom values. A variable with the name "abc" is
|
||||
referenced in a dump custom command as v_abc.
|
||||
|
||||
Just like equal-style variables, the formula associated with
|
||||
atom-style variables can contain math operations and functions
|
||||
(x+y,x*y,(),sqrt,exp,etc), atom values (x\[N\],fx\[N\],etc), group
|
||||
functions (mass(),vcm(),etc), references to thermodynamic quantities
|
||||
(temp,press,vol,etc), references to "computes"_compute.html that
|
||||
generate global values, references to "fixes"_fix.html that generate
|
||||
global values, or references to non atom-style variables that generate
|
||||
global values. In addition, an atom-style variable can reference
|
||||
vectors of atom values (x\[\],fx\[\],etc), "computes"_compute.html
|
||||
that generate per-atom values, "fixes"_fix.html that generate per-atom
|
||||
values, or other atom-style variables. Thus an atom-style variable is
|
||||
the most general way to define some quantity to calculate and output
|
||||
to a dump file.
|
||||
|
||||
Fix output :h5
|
||||
|
||||
Three other fixes are of particular note for output: "fix
|
||||
ave/time"_fix_ave_time.html, "fix ave/spatial"_fix_ave_spatial.html,
|
||||
and "fix print"_fix_print.html.
|
||||
|
||||
The "fix ave/time"_fix_ave_time.html command enables time-averaging of
|
||||
any global quantity, like those output with thermodynamic info. The
|
||||
user specifies one or more quantities to time average. These can be
|
||||
global "compute"_compute.html values, global "fix"_fix.html values, or
|
||||
The "fix ave/time"_fix_ave_time.html command enables direct output to
|
||||
a file and/or time-averaging of any global quantity. The user
|
||||
specifies one or more quantities as input. These can be global
|
||||
"compute"_compute.html values, global "fix"_fix.html values, or
|
||||
"variables"_variable.html of any style except the atom style which
|
||||
produces per-atom values. Since a variable can refer to keywords used
|
||||
by the "thermo_style custom"_thermo_style.html command (like temp or
|
||||
press), any thermodynamic quantity can be time averaged in this way.
|
||||
press) and individual per-atom values, a wide variety of quantities
|
||||
can be time averaged and/or output in this way. The time-averaged
|
||||
output of this fix can also be used as input to other output commands.
|
||||
|
||||
The "fix ave/time"_fix_ave_time.html command offers several options
|
||||
for how it performs time averaging. The results it produces can be
|
||||
used in two ways. First, they can be written directly to a file, one
|
||||
line per timestamp. Note that the averaging parameters can be
|
||||
specified in such a way that averaging is not done at all, in which
|
||||
case this is simply a convenient means of outputting desired
|
||||
quantities directly to a separate file. Like other fixes that produce
|
||||
global quantities, the results of this fix can also be used as input
|
||||
to any command that accesses global quantities, e.g. by the
|
||||
"thermo_style custom"_thermo_style.html command, by a variable, etc.
|
||||
|
||||
The "fix ave/spatial"_fix_ave_spatial.html command enables
|
||||
spatial-averaging of per-atom quantities like those output in dump
|
||||
files, within 1d layers of the simulation box. The per-atom
|
||||
quantities can be atom density (mass or number) or atom attributes
|
||||
such as position, velocity, force. They can also be per-atom
|
||||
quantities calculated by a "compute"_compute.html, by a
|
||||
"fix"_fix.html, or by an atom-style "variable"_variable.html.
|
||||
|
||||
The "fix ave/spatial"_fix_ave_spatial.html command offers several
|
||||
options for how it performs time averaging. The per-layer values it
|
||||
produces can be used in two ways. First, they can be written directly
|
||||
to a file. Note that the averaging parameters can be specified in
|
||||
such a way that time averaging is not done, in which case this is a
|
||||
convenient means of simply outputting desired quantities (summed over
|
||||
atoms within a 1d layer) directly to a separate file. Like other
|
||||
fixes that produce global quantities, the results of this fix can also
|
||||
be used as input by any command that accesses global quantities,
|
||||
e.g. by the "thermo_style custom"_thermo_style.html command, by a
|
||||
variable, etc. See the doc page for "fix
|
||||
ave/spatial"_fix_ave_spatial.html for a description of how these
|
||||
values are indexed.
|
||||
The "fix ave/spatial"_fix_ave_spatial.html command enables direct
|
||||
output to a file of spatial-averaged per-atom quantities like those
|
||||
output in dump files, within 1d layers of the simulation box. The
|
||||
per-atom quantities can be atom density (mass or number) or atom
|
||||
attributes such as position, velocity, force. They can also be
|
||||
per-atom quantities calculated by a "compute"_compute.html, by a
|
||||
"fix"_fix.html, or by an atom-style "variable"_variable.html. The
|
||||
spatial-averaged output of this fix can also be used as input to other
|
||||
output commands.
|
||||
|
||||
The "fix print"_fix_print.html command can generate a line of output
|
||||
written to the screen and log file or to a separate file, periodically
|
||||
during a running simulation. The line can contain one or more
|
||||
"variable"_variable.html values (for any style variable except the
|
||||
atom style), and as explained above, variables themselves can contain
|
||||
"variable"_variable.html values for any style variable except the atom
|
||||
style). As explained above, variables themselves can contain
|
||||
references to global values generated by "thermodynamic
|
||||
keywords"_thermo_style.html, "computes"_compute.html,
|
||||
"fixes"_fix.html, or other "variables"_variable.html. Thus the "fix
|
||||
print"_fix_print.html command is a means to output any desired
|
||||
calculated quantity separate from normal thermodynamic or dump file
|
||||
output.
|
||||
"fixes"_fix.html, or other "variables"_variable.html, or to per-atom
|
||||
values for a specific atom. Thus the "fix print"_fix_print.html
|
||||
command is a means to output a wide variety of quantities separate
|
||||
from normal thermodynamic or dump file output.
|
||||
|
||||
This table summarizes the various output options, specifying what
|
||||
their inputs and outputs are. The frequency with which they are
|
||||
invoked and produce output is also listed. Basically, any two
|
||||
commands can be hooked together so long as one produces output that
|
||||
matches the input needs of the other. A "match" means that the
|
||||
frequencies and global vs per-atom attributes are the same.
|
||||
Computes that process output quantities :h5,link(computeoutput)
|
||||
|
||||
Command: Input: Input Freq: Output: Output Freq
|
||||
thermo_style custom: thermo keyword, global scalar/vector compute, global scalar/vector fix, equal variable: nthermo: screen, log: nthermo
|
||||
dump custom: keyword, per-atom compute, per-atom fix, atom variable: dump freq: file: dump freq
|
||||
global fixes: N/A: N/A: global scalar/vector: 1 or nevery
|
||||
per-atom fixes: N/A: N/A: per-atom vector/array: 1 or nevery
|
||||
fix ave/time: global scalar/vector fix, global scalar/vector compute, equal variable: nevery: global scalar/vector, file: nfreq
|
||||
fix ave/spatial: per-atom fix, per-atom compute, atom vector, atom variable, density mass/number: nevery: global vector: nfreq, file
|
||||
fix ave/atom: per-atom compute, per-atom fix, atom variable, atom vector: nevery: per-atom vector/array: nfreq
|
||||
fix print: any variable: nevery: screen, file: nevery
|
||||
global computes: N/A: N/A: global scalar/vector: N/A
|
||||
per-atom computes: N/A: N/A: per-atom vector/array: N/A
|
||||
compute sum: per-atom compute, per-atom fix, atom variable: N/A: global scalar/vector: N/A
|
||||
variable equal: thermo keywords, atom value vx\[123\], global scalar/vector compute, global scalar/vector fix, non-atom variable: N/A: global scalar: N/A
|
||||
variable atom: thermo keywords, atom value vx\[123\], atom vector vx\[\], global scalar/vector compute, per-atom compute, global fix, per-atom fix, any variable: N/A: per-atom vector: N/A
|
||||
print: any variable: N/A: screen, log: between runs
|
||||
run every: any variable: nevery: screen, log: nevery :tb(s=:)
|
||||
The "compute reduce"_compute_reduce.html and "compute
|
||||
reduce/region"_compute_reduce.html commands take one or more vector
|
||||
quantities as inputs and "reduce" them (sum, min, max, ave) to scalar
|
||||
quantities. These are produced as output values which can be used as
|
||||
input to other output commands.
|
||||
|
||||
Computes that generate values to output :h5,link(compute)
|
||||
|
||||
Every "compute"_compute.html in LAMMPS produces either global or
|
||||
per-atom or local quantities. The quantities can be scalars or
|
||||
vectors or arrays of data. The doc page for each compute command
|
||||
describes what it produces. These values can be output using
|
||||
the other commands described in this section.
|
||||
|
||||
Fixes that generate values to output :h5,link(fix)
|
||||
|
||||
Some "fixes"_fix.html in LAMMPS produces either global or per-atom or
|
||||
local quantities which can be accessed by other commands. The
|
||||
quantities can be scalars or vectors or arrays of data. The doc page
|
||||
for each fix command tells whether it produces any output quantities
|
||||
and describes them. These values can be output using the other
|
||||
commands described in this section.
|
||||
|
||||
Variables that generate values to output :h5,link(variable)
|
||||
|
||||
Every "variables"_variable.html defined in an input script generates
|
||||
either a global scalar value or a per-atom vector (only atom-style
|
||||
variables) when it is accessed. The formulas used to define equal-
|
||||
and atom-style variables can contain references to the thermodynamic
|
||||
keywords and to global and per-atom data generated by computes, fixes,
|
||||
and other variables. The values generated by variables can be output
|
||||
using the other commands described in this section.
|
||||
|
||||
Summary table of output options and data flow between commands :h5,link(table)
|
||||
|
||||
This table summarizes the various commands that can be used for
|
||||
generating output from LAMMPS. Each command produces output data of
|
||||
some kind and/or writes data to a file. Some of the commands take
|
||||
data from other commands as input. Thus you can link many of these
|
||||
commands together in pipeline form, where data produced by one command
|
||||
is used as input to another command and eventually written to the
|
||||
screen or to a file. Note that to hook two commands together the
|
||||
output and input data types must match, e.g. global/per-atom/local
|
||||
data and scalar/vector/array data.
|
||||
|
||||
Also note that, as described above, when a command takes a scalar as
|
||||
input, that could be an element of a vector or array. Likewise a
|
||||
vector input could be a column of an array.
|
||||
|
||||
Command: Input: Output:
|
||||
thermo_style custom: global scalars: screen, log file:
|
||||
dump custom: per-atom vectors: dump file:
|
||||
fix print: global scalar from variable: screen, file:
|
||||
print: global scalar from variable: screen:
|
||||
computes: N/A: global/per-atom/local scalar/vector/array:
|
||||
fixes: N/A: global/per-atom/local scalar/vector/array:
|
||||
variables: global scalars, per-atom vectors: global scalar, per-atom vector:
|
||||
compute reduce: global/per-atom/local vectors: global scalar/vector:
|
||||
fix ave/time: global scalars: global scalar/vector, file:
|
||||
fix ave/spatial: per-atom vectors/arrays: global array, file:
|
||||
fix ave/atom: per-atom vectors: per-atom vector/array:
|
||||
:tb(s=:)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
Reference in New Issue
Block a user