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< title > thermo_modify command — LAMMPS documentation< / title >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_modify.html" > 10. Modifying & extending LAMMPS< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_python.html" > 11. Python interface to LAMMPS< / a > < / li >
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< li > thermo_modify command< / li >
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< a href = "http://lammps.sandia.gov" > Website< / a >
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< span id = "index-0" > < / span > < h1 > thermo_modify command< a class = "headerlink" href = "#thermo-modify-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > thermo_modify keyword value ...
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > one or more keyword/value pairs may be listed< / li >
< / ul >
< pre class = "literal-block" >
keyword = < em > lost< / em > or < em > lost/bond< / em > or < em > norm< / em > or < em > flush< / em > or < em > line< / em > or < em > format< / em > or < em > temp< / em > or < em > press< / em > :l
< em > lost< / em > value = < em > error< / em > or < em > warn< / em > or < em > ignore< / em >
< em > lost/bond< / em > value = < em > error< / em > or < em > warn< / em > or < em > ignore< / em >
< em > norm< / em > value = < em > yes< / em > or < em > no< / em >
< em > flush< / em > value = < em > yes< / em > or < em > no< / em >
< em > line< / em > value = < em > one< / em > or < em > multi< / em >
< em > format< / em > values = < em > int< / em > string or < em > float< / em > string or M string
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M = integer from 1 to N, where N = # of quantities being printed
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string = C-style format string
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< em > temp< / em > value = compute ID that calculates a temperature
< em > press< / em > value = compute ID that calculates a pressure
< / pre >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > thermo_modify lost ignore flush yes
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thermo_modify temp myTemp format 3 %15.8g
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thermo_modify line multi format float %g
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Set options for how thermodynamic information is computed and printed
by LAMMPS.< / p >
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< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
< p class = "last" > These options apply to the currently defined thermo style. When
you specify a < a class = "reference internal" href = "thermo_style.html" > < em > thermo_style< / em > < / a > command, all
thermodynamic settings are restored to their default values, including
those previously reset by a thermo_modify command. Thus if your input
script specifies a thermo_style command, you should use the
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thermo_modify command after it.< / p >
< / div >
< p > The < em > lost< / em > keyword determines whether LAMMPS checks for lost atoms
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each time it computes thermodynamics and what it does if atoms are
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lost. An atom can be “ lost” if it moves across a non-periodic
simulation box < a class = "reference internal" href = "boundary.html" > < em > boundary< / em > < / a > or if it moves more than a box
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length outside the simulation domain (or more than a processor
sub-domain length) before reneighboring occurs. The latter case is
typically due to bad dynamics, e.g. too large a timestep or huge
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forces and velocities. If the value is < em > ignore< / em > , LAMMPS does not
check for lost atoms. If the value is < em > error< / em > or < em > warn< / em > , LAMMPS
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checks and either issues an error or warning. The code will exit with
an error and continue with a warning. A warning will only be issued
once, the first time an atom is lost. This can be a useful debugging
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option.< / p >
< p > The < em > lost/bond< / em > keyword determines whether LAMMPS throws an error or
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not if an atom in a bonded interaction (bond, angle, etc) cannot be
found when it creates bonded neighbor lists. By default this is a
fatal error. However in some scenarios it may be desirable to only
issue a warning or ignore it and skip the computation of the missing
bond, angle, etc. An example would be when gas molecules in a vapor
are drifting out of the box through a fixed boundary condition (see
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the < a class = "reference internal" href = "boundary.html" > < em > boundary< / em > < / a > command). In this case one atom may be
deleted before the rest of the molecule is, on a later timestep.< / p >
< p > The < em > norm< / em > keyword determines whether various thermodynamic output
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values are normalized by the number of atoms or not, depending on
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whether it is set to < em > yes< / em > or < em > no< / em > . Different unit styles have
different defaults for this setting (see below). Even if < em > norm< / em > is
set to < em > yes< / em > , a value is only normalized if it is an “ extensive”
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quantity, meaning that it scales with the number of atoms in the
system. For the thermo keywords described by the doc page for the
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< a class = "reference internal" href = "thermo_style.html" > < em > thermo_style< / em > < / a > command, all energy-related keywords
are extensive, such as < em > pe< / em > or < em > ebond< / em > or < em > enthalpy< / em > . Other keywords
such as < em > temp< / em > or < em > press< / em > are “ intensive” meaning their value is
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independent (in a statistical sense) of the number of atoms in the
system and thus are never normalized. For thermodynamic output values
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extracted from fixes and computes in a < a class = "reference internal" href = "thermo_style.html" > < em > thermo_style custom< / em > < / a > command, the doc page for the individual
< a class = "reference internal" href = "fix.html" > < em > fix< / em > < / a > or < a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > lists whether the value is
“ extensive” or “ intensive” and thus whether it is normalized.
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Thermodynamic output values calculated by a variable formula are
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assumed to be “ intensive” and thus are never normalized. You can
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always include a divide by the number of atoms in the variable formula
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if this is not the case.< / p >
< p > The < em > flush< / em > keyword invokes a flush operation after thermodynamic info
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is written to the log file. This insures the output in that file is
current (no buffering by the OS), even if LAMMPS halts before the
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simulation completes.< / p >
< p > The < em > line< / em > keyword determines whether thermodynamics will be printed
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as a series of numeric values on one line or in a multi-line format
with 3 quantities with text strings per line and a dashed-line header
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containing the timestep and CPU time. This modify option overrides
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the < em > one< / em > and < em > multi< / em > thermo_style settings.< / p >
< p > The < em > format< / em > keyword sets the numeric format of individual printed
quantities. The < em > int< / em > and < em > float< / em > keywords set the format for all
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integer or floating-point quantities printed. The setting with a
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numeric value M (e.g. format 5 %10.4g) sets the format of the Mth
value printed in each output line, e.g. the 5th column of output in
this case. If the format for a specific column has been set, it will
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take precedent over the < em > int< / em > or < em > float< / em > setting.< / p >
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< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
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< p class = "last" > The thermo output values < em > step< / em > and < em > atoms< / em > are stored
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internally as 8-byte signed integers, rather than the usual 4-byte
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signed integers. When specifying the “ format int” keyword you can use
a “ %d” -style format identifier in the format string and LAMMPS will
convert this to the corresponding “ %lu” form when it is applied to
those keywords. However, when specifying the “ format M string”
keyword for < em > step< / em > and < em > natoms< / em > , you should specify a string
appropriate for an 8-byte signed integer, e.g. one with “ %ld” .< / p >
< / div >
< p > The < em > temp< / em > keyword is used to determine how thermodynamic temperature
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is calculated, which is used by all thermo quantities that require a
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temperature (“ temp” , “ press” , “ ke” , “ etotal” , “ enthalpy” , “ pxx” , etc).
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The specified compute ID must have been previously defined by the user
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via the < a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > command and it must be a style of
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compute that calculates a temperature. As described in the
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< a class = "reference internal" href = "thermo_style.html" > < em > thermo_style< / em > < / a > command, thermo output uses a default
compute for temperature with ID = < em > thermo_temp< / em > . This option allows
the user to override the default.< / p >
< p > The < em > press< / em > keyword is used to determine how thermodynamic pressure is
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calculated, which is used by all thermo quantities that require a
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pressure (“ press” , “ enthalpy” , “ pxx” , etc). The specified compute ID
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must have been previously defined by the user via the
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< a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > command and it must be a style of compute that
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calculates a pressure. As described in the
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< a class = "reference internal" href = "thermo_style.html" > < em > thermo_style< / em > < / a > command, thermo output uses a default
compute for pressure with ID = < em > thermo_press< / em > . This option allows the
user to override the default.< / p >
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< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
< p class = "last" > If both the < em > temp< / em > and < em > press< / em > keywords are used in a single
thermo_modify command (or in two separate commands), then the order in
which the keywords are specified is important. Note that a < a class = "reference internal" href = "compute_pressure.html" > < em > pressure compute< / em > < / a > defines its own temperature compute as
an argument when it is specified. The < em > temp< / em > keyword will override
this (for the pressure compute being used by thermodynamics), but only
if the < em > temp< / em > keyword comes after the < em > press< / em > keyword. If the < em > temp< / em >
keyword comes before the < em > press< / em > keyword, then the new pressure
compute specified by the < em > press< / em > keyword will be unaffected by the
< em > temp< / em > setting.< / p >
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< / div >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< blockquote >
< div > none< / div > < / blockquote >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "thermo.html" > < em > thermo< / em > < / a > , < a class = "reference internal" href = "thermo_style.html" > < em > thermo_style< / em > < / a > < / p >
< / div >
< div class = "section" id = "default" >
< h2 > Default< a class = "headerlink" href = "#default" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > The option defaults are lost = error, norm = yes for unit style of
< em > lj< / em > , norm = no for unit style of < em > real< / em > and < em > metal< / em > , flush = no,
and temp/press = compute IDs defined by thermo_style.< / p >
< p > The defaults for the line and format options depend on the thermo
style. For styles “ one” and “ custom” , the line and format defaults
are “ one” , “ %8d” , and “ %12.8g” . For style “ multi” , the line and
format defaults are “ multi” , “ %8d” , and “ %14.4f” .< / p >
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© Copyright 2013 Sandia Corporation.
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