thermo_modify command

Syntax

thermo_modify keyword value ...
  • one or more keyword/value pairs may be listed

    keyword = lost or lost/bond or norm or flush or line or format or temp or press:l
      lost value = error or warn or ignore
      lost/bond value = error or warn or ignore
      norm value = yes or no
      flush value = yes or no
      line value = one or multi
      format values = line string, int string, float string, M string, or none
        string = C-style format string
        M = integer from 1 to N, where N = # of quantities being output
      temp value = compute ID that calculates a temperature
      press value = compute ID that calculates a pressure

Examples

thermo_modify lost ignore flush yes
thermo_modify temp myTemp format 3 %15.8g
thermo_modify temp myTemp format line "%ld %g %g %15.8g"
thermo_modify line multi format float %g

Description

Set options for how thermodynamic information is computed and printed by LAMMPS.

Note

These options apply to the currently defined thermo style. When you specify a thermo_style 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 thermo_modify command after it.

The lost keyword determines whether LAMMPS checks for lost atoms each time it computes thermodynamics and what it does if atoms are lost. An atom can be “lost” if it moves across a non-periodic simulation box boundary or if it moves more than a box 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 forces and velocities. If the value is ignore, LAMMPS does not check for lost atoms. If the value is error or warn, LAMMPS 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 option.

The lost/bond keyword determines whether LAMMPS throws an error or 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 the boundary command). In this case one atom may be deleted before the rest of the molecule is, on a later timestep.

The norm keyword determines whether various thermodynamic output values are normalized by the number of atoms or not, depending on whether it is set to yes or no. Different unit styles have different defaults for this setting (see below). Even if norm is set to yes, a value is only normalized if it is an “extensive” quantity, meaning that it scales with the number of atoms in the system. For the thermo keywords described by the doc page for the thermo_style command, all energy-related keywords are extensive, such as pe or ebond or enthalpy. Other keywords such as temp or press are “intensive” meaning their value is independent (in a statistical sense) of the number of atoms in the system and thus are never normalized. For thermodynamic output values extracted from fixes and computes in a thermo_style custom command, the doc page for the individual fix or compute lists whether the value is “extensive” or “intensive” and thus whether it is normalized. Thermodynamic output values calculated by a variable formula are assumed to be “intensive” and thus are never normalized. You can always include a divide by the number of atoms in the variable formula if this is not the case.

The flush keyword invokes a flush operation after thermodynamic info 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 simulation completes.

The line keyword determines whether thermodynamics will be output 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 containing the timestep and CPU time. This modify option overrides the one and multi thermo_style settings.

The format keyword can be used to change the default numeric format of any of quantities the thermo_style command outputs. All the specified format strings are C-style formats, e.g. as used by the C/C++ printf() command. The line keyword takes a single argument which is the format string for the entire line of thermo output, with N fields, which you must enclose in quotes if it is more than one field. The int and float keywords take a single format argument and are applied to all integer or floating-point quantities output. The setting for M string also takes a single format argument which is used for the Mth value output in each line, e.g. the fifth column is output in high precision for “format 5 %20.15g”.

The format keyword can be used multiple times. The precedence is that for each value in a line of output, the M format (if specified) is used, else the int or float setting (if specified) is used, else the line setting (if specified) for that value is used, else the default setting is used. A setting of none clears all previous settings, reverting all values to their default format.

Note

The thermo output values step and atoms are stored internally as 8-byte signed integers, rather than the usual 4-byte signed integers. When specifying the format int option you can use a “%d”-style format identifier in the format string and LAMMPS will convert this to the corresponding 8-byte form when it is applied to those keywords. However, when specifying the line option or format M string option for step and natoms, you should specify a format string appropriate for an 8-byte signed integer, e.g. one with “%ld”.

The temp keyword is used to determine how thermodynamic temperature is calculated, which is used by all thermo quantities that require a temperature (“temp”, “press”, “ke”, “etotal”, “enthalpy”, “pxx”, etc). The specified compute ID must have been previously defined by the user via the compute command and it must be a style of compute that calculates a temperature. As described in the thermo_style command, thermo output uses a default compute for temperature with ID = thermo_temp. This option allows the user to override the default.

The press keyword is used to determine how thermodynamic pressure is calculated, which is used by all thermo quantities that require a pressure (“press”, “enthalpy”, “pxx”, etc). The specified compute ID must have been previously defined by the user via the compute command and it must be a style of compute that calculates a pressure. As described in the thermo_style command, thermo output uses a default compute for pressure with ID = thermo_press. This option allows the user to override the default.

Note

If both the temp and press 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 pressure compute defines its own temperature compute as an argument when it is specified. The temp keyword will override this (for the pressure compute being used by thermodynamics), but only if the temp keyword comes after the press keyword. If the temp keyword comes before the press keyword, then the new pressure compute specified by the press keyword will be unaffected by the temp setting.

Restrictions

none

Default

The option defaults are lost = error, norm = yes for unit style of lj, norm = no for unit style of real and metal, flush = no, and temp/press = compute IDs defined by thermo_style.

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”.