thermo_modify command — LAMMPS documentation

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# thermo_modify command

## Syntax

    thermo_modify keyword value ...

- one or more keyword/value pairs may be listed

- keyword = lost or lost/bond or warn or norm or flush or line or colname or format or temp or press or triclinic/general

      lost value = error or warn or ignore
      lost/bond value = error or warn or ignore
      warn value = ignore or reset or default or a number
      norm value = yes or no
      flush value = yes or no
      line value = one or multi or yaml
      colname values =  ID string, or default
        string = new column header name
        ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
             or a thermo keyword or reference to compute, fix, property or variable.
      format values = line string, int string, float string, ID string, or none
        string = C-style format string
        ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
             or an integer range such as 2*6 (negative values are not allowed)
             or a thermo keyword or reference to compute, fix, property or variable.
      temp value = compute ID that calculates a temperature
      press value = compute ID that calculates a pressure
      triclinic/general arg = yes or no

## 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
    thermo_modify line yaml format none
    thermo_modify colname 1 Timestep colname -2 Pressure colname f_1[1] AvgDensity

## 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 subdomain length) before reneighboring occurs. The latter case is typically due to bad dynamics (e.g., too large a time step and/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 simulation 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 warn keyword allows you to control whether LAMMPS will print warning messages and how many of them. Most warning messages are only printed by MPI rank 0. They are usually pointing out important issues that should be investigated, but LAMMPS cannot determine for certain whether they are an indication of an error.

Some warning messages are printed during a run (or immediately before) each time a specific MPI rank encounters the issue (e.g., bonds that are stretched too far or dihedrals in extreme configurations). These number of these can quickly blow up the size of the log file and screen output. Thus, a limit of 100 warning messages is applied by default. The warning count is applied to the entire input unless reset with a `thermo_modify warn reset` command. If there are more warnings than the limit, LAMMPS will print one final warning that it will not print any additional warning messages.

Note

The warning limit is enforced on either the per-processor count or the total count across all processors. For efficiency reasons, however, the total count is only updated at steps with thermodynamic output. Thus when running on a large number of processors in parallel, the total number of warnings printed can be significantly larger than the given limit.

Any number after the keyword warn will change the warning limit accordingly. With the value ignore all warnings will be suppressed, with the value always no limit will be applied and warnings will always be printed, with the value reset the internal warning counter will be reset to zero, and with the value default, the counter is reset and the limit set to 100. An example usage of either reset or default would be to re-enable warnings that were disabled or have reached the limit during equilibration, where the warnings would be acceptable while the system is still adjusting, but then change to all warnings for the production run, where they would indicate problems that would require a closer look at what is causing them.

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 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 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 screen and log file. This ensures the output is updated and not buffered (by the application) even if LAMMPS halts before the simulation completes. Please note that this does not affect buffering by the OS or devices, so you may still lose data in case the simulation stops due to a hardware failure.

The line keyword determines whether thermodynamics will be output as a series of numeric values on one line (“one”), in a multi-line format with 3 quantities with text strings per line and a dashed-line header containing the timestep and CPU time (“multi”), or in a YAML format block (“yaml”). This modify option overrides the one, multi, or yaml thermo_style settings.

Added in version 4May2022.

The colname keyword can be used to change the default header keyword for a column or field of thermodynamic output. The setting for ID string replaces the default text with the provided string. ID can be a positive integer when it represents the column number counting from the left, a negative integer when it represents the column number from the right (i.e., \(-1\) is the last column/keyword), or a thermo keyword (or compute, fix, property, or variable reference) and then it replaces the string for that specific thermo keyword.

The colname keyword can be used multiple times. If multiple colname settings refer to the same keyword, the last setting has precedence. A setting of default clears all previous settings, reverting all values to their default values.

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 (i.e., 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 ID string also takes a single format argument that is used for the indexed value in each line. The interpretation is the same as for colname (i.e., a positive integer is the n-th value corresponding to the n-th thermo keyword, a negative integer is counting backwards, and a string matches the entry with the thermo keyword). For example, the fifth column is output in high precision for “format 5 %20.15g”, and the pair energy for “format epair %20.15g”. The ID field can be a range, such as “3*6”, “*”, “2*”, or “*3”; in such cases, all fields in the range (inclusive) are set to the specified format string. Ranges containing negative numbers are not supported.

The format keyword can be used multiple times. The precedence is that for each value in a line of output, the ID 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 ID string option for step and natoms, you should specify a format string appropriate for an 8-byte signed integer (i.e., one with “%ld” or “%lld”, depending on the platform).

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.

The triclinic/general keyword can only be used with a value of yes if the simulation box was created as a general triclinic box. See the Howto_triclinic doc page for a detailed explanation of orthogonal, restricted triclinic, and general triclinic simulation boxes.

If this keyword is yes, the output of the simulation box edge vectors and the pressure tensor components for the system are affected. These are specified by the avec,bvec,cvec and pxx,pyy,pzz,pxy,pxz,pyz keywords of the thermo_style command. See the thermo_style doc page for details.

## Restrictions

none

## Related commands

thermo, thermo_style

## Default

The option defaults are lost = error, warn = 100, norm = yes for unit style of lj, norm = no for unit style of real and metal, flush = no, temp/press = compute IDs defined by thermo_style, and triclinic/general = no.

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”, “%10d”, and “%14.8g”. For style “multi”, the line and format defaults are “multi”, “%14d”, and “%14.4f”. For style “yaml”, the line and format defaults are “%d” and “%.15g”.