2006-09-22 00:22:34 +08:00
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>thermo_modify command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>thermo_modify keyword value ...
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</PRE>
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<UL><LI>one or more keyword/value pairs may be listed
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2013-12-17 22:13:04 +08:00
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<PRE>keyword = <I>lost</I> or <I>lost/bond</I> or <I>norm</I> or <I>flush</I> or <I>line</I> or <I>format</I> or <I>temp</I> or <I>press</I>:l
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2012-06-08 22:49:44 +08:00
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<I>lost</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I>
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2013-12-17 22:13:04 +08:00
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<I>lost/bond</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I>
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2006-09-22 00:22:34 +08:00
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<I>norm</I> value = <I>yes</I> or <I>no</I>
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<I>flush</I> value = <I>yes</I> or <I>no</I>
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<I>line</I> value = <I>one</I> or <I>multi</I>
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2007-04-07 02:03:05 +08:00
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<I>format</I> values = <I>int</I> string or <I>float</I> string or M string
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M = integer from 1 to N, where N = # of quantities being printed
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2006-09-22 00:22:34 +08:00
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string = C-style format string
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2007-04-07 01:59:59 +08:00
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<I>temp</I> value = compute ID that calculates a temperature
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2012-08-31 22:56:40 +08:00
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<I>press</I> value = compute ID that calculates a pressure
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</PRE>
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2006-09-22 00:22:34 +08:00
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</UL>
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<P><B>Examples:</B>
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</P>
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2007-06-20 20:56:17 +08:00
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<PRE>thermo_modify lost ignore flush yes
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2007-04-07 02:03:05 +08:00
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thermo_modify temp myTemp format 3 %15.8g
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thermo_modify line multi format float %g
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2006-09-22 00:22:34 +08:00
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</PRE>
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<P><B>Description:</B>
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</P>
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2007-02-10 05:37:30 +08:00
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<P>Set options for how thermodynamic information is computed and printed
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by LAMMPS.
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2006-09-22 00:22:34 +08:00
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</P>
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2007-06-20 20:56:17 +08:00
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<P>IMPORTANT NOTE: These options apply to the currently defined thermo
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2007-06-25 22:36:36 +08:00
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style. When you specify a <A HREF = "thermo_style.html">thermo_style</A> command,
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all thermodynamic settings are restored to their default values,
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2009-03-19 02:15:38 +08:00
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including those previously reset by a thermo_modify command. Thus if
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2007-06-25 22:36:36 +08:00
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your input script specifies a thermo_style command, you should use the
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thermo_modify command after it.
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2007-06-20 20:56:17 +08:00
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</P>
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2007-02-10 05:37:30 +08:00
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<P>The <I>lost</I> 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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2010-06-03 04:38:41 +08:00
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lost. An atom can be "lost" if it moves across a non-periodic
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simulation box <A HREF = "boundary.html">boundary</A> or if it moves more than a box
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length outside the simulation domain (or more than a processor
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sub-domain length) before reneighboring occurs. The latter case is
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typically due to bad dynamics, e.g. too large a timestep or huge
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forces and velocities. If the value is <I>ignore</I>, LAMMPS does not
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check for lost atoms. If the value is <I>error</I> or <I>warn</I>, LAMMPS
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checks and either issues an error or warning. The code will exit with
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an error and continue with a warning. A warning will only be issued
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once, the first time an atom is lost. This can be a useful debugging
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option.
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2006-09-22 00:22:34 +08:00
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</P>
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2013-12-17 22:13:04 +08:00
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<P>The <I>lost/bond</I> 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
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found when it creates bonded neighbor lists. By default this is a
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fatal error. However in some scenarios it may be desirable to only
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issue a warning or ignore it and skip the computation of the missing
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bond, angle, etc. An example would be when gas molecules in a vapor
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are drifting out of the box through a fixed boundary condition (see
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the <A HREF = "boundary.html">boundary</A> command). In this case one atom may be
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deleted before the rest of the molecule is, on a later timestep.
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</P>
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2009-01-06 07:48:45 +08:00
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<P>The <I>norm</I> 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 <I>yes</I> or <I>no</I>. Different unit styles have
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different defaults for this setting (see below). Even if <I>norm</I> is
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set to <I>yes</I>, 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
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system. For the thermo keywords described by the doc page for the
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<A HREF = "thermo_style.html">thermo_style</A> command, all energy-related keywords
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are extensive, such as <I>pe</I> or <I>ebond</I> or <I>enthalpy</I>. Other keywords
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such as <I>temp</I> or <I>press</I> are "intensive" meaning their value is
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independent (in a statistical sense) of the number of atoms in the
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system and thus are never normalized. For thermodynamic output values
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extracted from fixes and computes in a <A HREF = "thermo_style.html">thermo_style
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custom</A> command, the doc page for the individual
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<A HREF = "fix.html">fix</A> or <A HREF = "compute.html">compute</A> lists whether the value is
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"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.
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2006-09-22 00:22:34 +08:00
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</P>
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2007-02-10 05:37:30 +08:00
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<P>The <I>flush</I> keyword invokes a flush operation after thermodynamic info
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2006-09-22 00:22:34 +08:00
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is written to the log file. This insures the output in that file is
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current (no buffering by the OS), even if LAMMPS halts before the
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simulation completes.
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</P>
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2007-02-10 05:37:30 +08:00
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<P>The <I>line</I> 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
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with 3 quantities with text strings per line and a dashed-line header
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2006-09-22 00:22:34 +08:00
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containing the timestep and CPU time. This modify option overrides
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the <I>one</I> and <I>multi</I> thermo_style settings.
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</P>
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2007-02-10 05:37:30 +08:00
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<P>The <I>format</I> keyword sets the numeric format of individual printed
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2007-04-07 02:03:05 +08:00
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quantities. The <I>int</I> and <I>float</I> keywords set the format for all
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2006-09-22 00:22:34 +08:00
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integer or floating-point quantities printed. The setting with a
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2011-01-05 03:00:12 +08:00
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numeric value M (e.g. format 5 %10.4g) sets the format of the Mth
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value printed in each output line, e.g. the 5th column of output in
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this case. If the format for a specific column has been set, it will
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take precedent over the <I>int</I> or <I>float</I> setting.
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</P>
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<P>IMPORTANT NOTE: The thermo output values <I>step</I> and <I>atoms</I> 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
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a "%d"-style format identifier in the format string and LAMMPS will
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convert this to the corresponding "%lu" form when it is applied to
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those keywords. However, when specifying the "format M string"
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keyword for <I>step</I> and <I>natoms</I>, you should specify a string
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2011-12-22 23:33:47 +08:00
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appropriate for an 8-byte signed integer, e.g. one with "%ld".
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2006-09-22 00:22:34 +08:00
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</P>
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2007-02-10 05:37:30 +08:00
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<P>The <I>temp</I> 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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2008-02-13 22:59:22 +08:00
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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 HREF = "compute.html">compute</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 HREF = "thermo_style.html">thermo_style</A> command, thermo output uses a default
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compute for temperature with ID = <I>thermo_temp</I>. This option allows
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the user to override the default.
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2007-02-10 05:37:30 +08:00
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</P>
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<P>The <I>press</I> 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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2008-02-13 22:59:22 +08:00
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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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2007-02-10 05:37:30 +08:00
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<A HREF = "compute.html">compute</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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2007-06-20 20:56:17 +08:00
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<A HREF = "thermo_style.html">thermo_style</A> command, thermo output uses a default
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2008-01-18 07:46:30 +08:00
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compute for pressure with ID = <I>thermo_press</I>. This option allows the
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user to override the default.
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2007-02-10 05:37:30 +08:00
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</P>
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2008-03-11 01:48:22 +08:00
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<P>IMPORTANT NOTE: If both the <I>temp</I> and <I>press</I> keywords are used in a
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2008-03-12 00:37:01 +08:00
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single thermo_modify command (or in two separate commands), then the
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order in which the keywords are specified is important. Note that a
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<A HREF = "compute_pressure.html">pressure compute</A> defines its own temperature
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compute as an argument when it is specified. The <I>temp</I> keyword will
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override this (for the pressure compute being used by thermodynamics),
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but only if the <I>temp</I> keyword comes after the <I>press</I> keyword. If
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the <I>temp</I> keyword comes before the <I>press</I> keyword, then the new
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pressure compute specified by the <I>press</I> keyword will be unaffected
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by the <I>temp</I> setting.
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2008-03-11 01:48:22 +08:00
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</P>
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2006-09-22 00:22:34 +08:00
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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2007-03-22 04:37:22 +08:00
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<P><A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_style.html">thermo_style</A>
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2006-09-22 00:22:34 +08:00
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</P>
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<P><B>Default:</B>
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</P>
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2007-02-10 05:37:30 +08:00
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<P>The option defaults are lost = error, norm = yes for unit style of
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<I>lj</I>, norm = no for unit style of <I>real</I> and <I>metal</I>, flush = no,
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2012-06-08 22:49:44 +08:00
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and temp/press = compute IDs defined by thermo_style.
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2007-02-10 05:37:30 +08:00
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</P>
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<P>The defaults for the line and format options depend on the thermo
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2011-01-05 03:00:12 +08:00
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style. For styles "one" and "custom", the line and format defaults
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2008-03-18 07:43:56 +08:00
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are "one", "%8d", and "%12.8g". For style "multi", the line and
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format defaults are "multi", "%8d", and "%14.4f".
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2006-09-22 00:22:34 +08:00
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</P>
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</HTML>
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