forked from lijiext/lammps
156 lines
7.2 KiB
Plaintext
156 lines
7.2 KiB
Plaintext
"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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thermo_modify command :h3
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[Syntax:]
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thermo_modify keyword value ... :pre
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one or more keyword/value pairs may be listed :ulb,l
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keyword = {lost} or {norm} or {flush} or {line} or {format} or {temp} or {press}:l
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{lost} value = {error} or {warn} or {ignore}
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{norm} value = {yes} or {no}
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{flush} value = {yes} or {no}
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{line} value = {one} or {multi}
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{format} values = {int} string or {float} 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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{temp} value = compute ID that calculates a temperature
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{press} value = compute ID that calculates a pressure :pre
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:ule
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[Examples:]
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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
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[Description:]
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Set options for how thermodynamic information is computed and printed
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by LAMMPS.
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IMPORTANT NOTE: These options apply to the currently defined thermo
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style. When you specify a "thermo_style"_thermo_style.html command,
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all thermodynamic settings are restored to their default values,
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including those previously reset by a thermo_modify command. Thus if
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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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The {lost} 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
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simulation box "boundary"_boundary.html 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 {ignore}, LAMMPS does not
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check for lost atoms. If the value is {error} or {warn}, 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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The {norm} 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 {yes} or {no}. Different unit styles have
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different defaults for this setting (see below). Even if {norm} is
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set to {yes}, 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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"thermo_style"_thermo_style.html command, all energy-related keywords
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are extensive, such as {pe} or {ebond} or {enthalpy}. Other keywords
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such as {temp} or {press} 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 "thermo_style
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custom"_thermo_style.html command, the doc page for the individual
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"fix"_fix.html or "compute"_compute.html 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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The {flush} 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
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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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The {line} 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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containing the timestep and CPU time. This modify option overrides
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the {one} and {multi} thermo_style settings.
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The {format} keyword sets the numeric format of individual printed
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quantities. The {int} and {float} 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
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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 {int} or {float} setting.
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IMPORTANT NOTE: The thermo output values {step} and {atoms} 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 {step} and {natoms}, you should specify a string
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appropriate for an 8-byte signed integer, e.g. one with "%ld".
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The {temp} 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 "compute"_compute.html 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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"thermo_style"_thermo_style.html command, thermo output uses a default
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compute for temperature with ID = {thermo_temp}. This option allows
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the user to override the default.
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The {press} 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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"compute"_compute.html 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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"thermo_style"_thermo_style.html command, thermo output uses a default
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compute for pressure with ID = {thermo_press}. This option allows the
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user to override the default.
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IMPORTANT NOTE: If both the {temp} and {press} keywords are used in a
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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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"pressure compute"_compute_pressure.html defines its own temperature
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compute as an argument when it is specified. The {temp} keyword will
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override this (for the pressure compute being used by thermodynamics),
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but only if the {temp} keyword comes after the {press} keyword. If
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the {temp} keyword comes before the {press} keyword, then the new
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pressure compute specified by the {press} keyword will be unaffected
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by the {temp} setting.
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[Restrictions:] none
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[Related commands:]
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"thermo"_thermo.html, "thermo_style"_thermo_style.html
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[Default:]
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The option defaults are lost = error, norm = yes for unit style of
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{lj}, norm = no for unit style of {real} and {metal}, flush = no,
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and temp/press = compute IDs defined by thermo_style.
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The defaults for the line and format options depend on the thermo
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style. For styles "one" and "custom", the line and format defaults
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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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