4.5. File formats used by LAMMPS — LAMMPS documentation

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# 4.5. File formats used by LAMMPS

This page provides a general overview of the kinds of files and file formats that LAMMPS is reading and writing.

## 4.5.1. Character Encoding

For processing text files, the LAMMPS source code assumes ASCII character encoding which represents the digits 0 to 9, the lower and upper case letters a to z, some common punctuation and other symbols and a few whitespace characters including a regular “space character”, “line feed”, “carriage return”, “tabulator”. These characters are all represented by single bytes with a value smaller than 128 and only 95 of those 128 values represent printable characters. This list is sufficient to represent most English text, but misses accented characters or umlauts or Greek symbols and more.

Modern text often uses UTF-8 character encoding instead. This encoding is a way to represent many more different characters as defined by the Unicode standard. UFT-8 is compatible with ASCII, since the first 128 values are identical with the ASCII encoding. It is important to note, however, that there are Unicode characters that look similar to ASCII characters, but have a different binary representation. As a general rule, these characters may not be correctly recognized by LAMMPS. For some parts of LAMMPS’ text processing, translation tables with known “lookalike” characters are used. The tables are used to substitute non-ASCII characters with their ASCII equivalents. Non-ASCII lookalike characters are often used by web browsers or PDF viewers to improve the readability of text. Thus, when using copy and paste to transfer text from such an application to your input file, you may unintentionally create text that is not exclusively using ASCII encoding and may cause errors when LAMMPS is trying to read it.

Lines with non-printable and non-ASCII characters in text files can be detected for example with a (Linux) command like the following:

    env LC_ALL=C grep -n '[^ -~]' some_file.txt

## 4.5.2. Number Formatting

Different countries and languages have different conventions to format numbers. While in some regions commas are used for fractions and points to indicate thousand, million and so on, this is reversed in other regions. Modern operating systems have facilities to adjust input and output accordingly that are collectively referred to as “native language support” (NLS). The exact rules are often applied according to the value of the `$LANG` environment variable (e.g. “en_US.utf8” for English text in UTF-8 encoding).

For the sake of simplicity of the implementation and transferability of results, LAMMPS does not support this and instead expects numbers being formatted in the generic or “C” locale. The “C” locale has no punctuation for thousand, million and so on and uses a decimal point for fractions. One thousand would be represented as “1000.0” and not as “1,000.0” nor as “1.000,0”. Having native language support enabled for a locale other than “C” will result in different behavior when converting or formatting numbers that can trigger unexpected errors.

LAMMPS also only accepts integer numbers when an integer is required, so using floating point equivalents like “1.0” are not accepted; you must use “1” instead.

For floating point numbers in scientific notation, the Fortran double precision notation “1.1d3” is not accepted; you have to use “1100”, “1100.0” or “1.1e3”.

## 4.5.3. Input file

A LAMMPS input file is a text file with commands. It is read line-by-line and each line is processed immediately. Before looking for commands and executing them, there is a pre-processing step where comments (non-quoted text starting with a pound sign ‘#’) are removed, `${variable}` and `$(expression)` constructs are expanded or evaluated, and lines that end in the ampersand character ‘&’ are combined with the next line (similar to Fortran 90 free-format source code). After the pre-processing, lines are split into “words” and evaluated. The first word must be a command and all following words are arguments. Below are some example lines:

    # full line comment

    # some global settings
    units           lj
    atom_style      atomic
    # ^^ command    ^^ argument(s)

    variable        x index 1       # may be overridden from command line with -var x <value>
    variable        xx equal 20*$x  # variable "xx" is always 20 times "x"

    lattice         fcc 0.8442

    # example of a command written across multiple lines
    # the "region" command uses spacing from "lattice" command, unless "units box" is specified
    region          box block 0.0 ${xx} &
                              0.0 40.0  &
                              0.0 30.0
    # create simulation box and fill with atoms according to lattice setting
    create_box      1 box
    create_atoms    1 box

    # set force field and parameters
    mass            1 1.0
    pair_style      lj/cut 2.5
    pair_coeff      1 1 1.0 1.0 2.5

    # run simulation
    fix             1 all nve
    run             1000

The pivotal command in this example input is the create_box command. It defines the simulation system and many parameters that go with it: units, atom style, number of atom types (and other types) and more. Those settings are locked in after the box is created. Commands that change these kind of settings are only allowed before a simulation box is created and many other commands are only allowed after the simulation box is defined (e.g. pair_coeff). Very few commands (e.g. pair_style) may be used in either part of the input. The read_data and read_restart commands also create the system box and thus have a similar pivotal function.

The LAMMPS input syntax has minimal support for conditionals and loops, but if more complex operations are required, it is recommended to use the library interface, e.g. from Python using the LAMMPS Python module.

There is a frequent misconception about the if command: this is a command for conditional execution outside a run or minimization. To trigger actions on specific conditions during a run is a non-trivial operation that usually requires adopting one of the available “fix” commands or creating a new “fix” command.

LAMMPS commands change the internal state and thus the order of commands matters and reordering them can produce different results. For example, the region defined by the region command in the example above depends on the lattice setting and thus its dimensions will be different depending on the order of the two commands.

Each line must have an “end-of-line” character (line feed or carriage return plus line feed). Some text editors do not automatically insert one which may cause LAMMPS to ignore the last command. It is thus recommended to always have an empty line at the end of an input file.

The specific details describing how LAMMPS input is processed and parsed are explained in Parsing rules for input scripts.

## 4.5.4. Data file

A LAMMPS data file contains a description of a system suitable for reading with the read_data command. Data files are commonly used for setting up complex molecular systems that can be difficult to achieve with the commands create_box and create_atoms alone. Also, data files can be used as a portable alternatives to a binary restart file. A restart file can be converted into a data file from the command line.

Data files have a header section at the very beginning of the file and multiple titled sections such as “Atoms”, Masses”, “Pair Coeffs”, and so on. Header keywords can only be used before the first title section.

The data file always starts with a “title” line, which will be ignored by LAMMPS. Omitting the title line can lead to unexpected behavior because a line of the header with an actual setting may be ignored. In this case, the mistakenly ignored line often contains the “atoms” keyword, which results in LAMMPS assuming that there are no atoms in the data file and thus throwing an error on the contents of the “Atoms” section. The title line may contain some keywords that can be used by external programs to convey information about the system (included as comments), that is not required and not read by LAMMPS.

The line following a section title is also ignored. An error will occur if an empty line is not placed after a section title. The number of lines in titled sections depends on header keywords, like the number of atom types, the number of atoms, the number of bond types, the number of bonds, and so on. The data in those sections has to be complete. A special case are the “Pair Coeffs” and “PairIJ Coeffs” sections; the former is for force fields and pair styles that use mixing of non-bonded potential parameters, the latter for pair styles and force fields requiring explicit coefficients. Thus with N being the number of atom types, the “Pair Coeffs” section has N entries while “PairIJ Coeffs” has \(N \cdot (N-1)\) entries. Internally, these sections will be converted to pair_coeff commands. Thus the corresponding pair style must have been set before the read_data command reads the data file.

Data files may contain comments, which start with the pound sign ‘#’. There must be at least one blank between a valid keyword and the pound sign. Below is a simple example case of a data file for atom style full.

    LAMMPS Title line (ignored)
    # full line comment

            10  atoms # comment
             4  atom types

     -36.840194 64.211560 xlo xhi
     -41.013691 68.385058 ylo yhi
     -29.768095 57.139462 zlo zhi

    Masses

      1 12.0110
      2 12.0110
      3 15.9990
      4  1.0080

    Pair Coeffs  # this section is optional

      1    0.110000    3.563595    0.110000    3.563595
      2    0.080000    3.670503    0.010000    3.385415
      3    0.120000    3.029056    0.120000    2.494516
      4    0.022000    2.351973    0.022000    2.351973

    Atoms # full

          1      1       1       0.560   43.99993  58.52678  36.78550   0   0   0
          2      1       2      -0.270   45.10395  58.23499  35.86693   0   0   0
          3      1       3      -0.510   43.81519  59.54928  37.43995   0   0   0
          4      1       4       0.090   45.71714  57.34797  36.13434   0   0   0
          5      1       4       0.090   45.72261  59.13657  35.67007   0   0   0
          6      1       4       0.090   44.66624  58.09539  34.85538   0   0   0
          7      1       3      -0.470   43.28193  57.47427  36.91953   0   0   0
          8      1       4       0.070   42.07157  57.45486  37.62418   0   0   0
          9      1       1       0.510   42.19985  57.57789  39.12163   0   0   0
         10      1       1       0.510   41.88641  58.62251  39.70398   0   0   0
    #  ^^atomID ^^molID ^^type  ^^charge ^^xcoord  ^^ycoord  ^^ycoord  ^^image^^flags (optional)

    Velocities # this section is optional

          1  0.0050731  -0.00398928  0.00391473
          2 -0.0175184   0.0173484  -0.00489207
          3  0.00597225 -0.00202006  0.00166454
          4 -0.010395   -0.0082582   0.00316419
          5 -0.00390877  0.00470331 -0.00226911
          6 -0.00111157 -0.00374545 -0.0169374
          7  0.00209054 -0.00594936 -0.000124563
          8  0.00635002 -0.0120093  -0.0110999
          9 -0.004955   -0.0123375   0.000403422
         10  0.00265028 -0.00189329 -0.00293198

The common problem is processing the “Atoms” section, since its format depends on the atom style used, and that setting must be done in the input file before reading the data file. To assist with detecting incompatible data files, a comment is appended to the “Atoms” title indicating the atom style used (or intended) when writing the data file. For example, below is an “Atoms” section for atom style charge, which omits the molecule ID column.

    Atoms # charge

          1      1       0.560   43.99993  58.52678  36.78550
          2      2      -0.270   45.10395  58.23499  35.86693
          3      3      -0.510   43.81519  59.54928  37.43995
          4      4       0.090   45.71714  57.34797  36.13434
          5      4       0.090   45.72261  59.13657  35.67007
          6      4       0.090   44.66624  58.09539  34.85538
          7      3      -0.470   43.28193  57.47427  36.91953
          8      4       0.070   42.07157  57.45486  37.62418
          9      1       0.510   42.19985  57.57789  39.12163
         10      1       0.510   41.88641  58.62251  39.70398
    #  ^^atomID ^^type  ^^charge ^^xcoord  ^^ycoord  ^^ycoord

Another source of confusion about the “Atoms” section format is the ordering of columns. The three atom style variants atom_style full, atom_style hybrid charge molecular, and atom_style hybrid molecular charge all carry the same per-atom information. However, in data files, the Atoms section has the columns ‘Atom-ID Molecule-ID Atom-type Charge X Y Z’ for atom style full, but for hybrid atom styles the first columns are always ‘Atom-ID Atom-type X Y Z’ followed by any additional data added by the hybrid styles, for example, ‘Charge Molecule-ID’ for the first hybrid style and ‘Molecule-ID Charge’ in the second hybrid style variant. Finally, an alternative to a hybrid atom style is to use fix property/atom, e.g. to add molecule IDs to atom style charge. In this case the “Atoms” section is formatted according to atom style charge and a new section, “Molecules” is added that contains lines with ‘Atom-ID Molecule-ID’, one for each atom in the system. For adding charges to atom style molecular with fix property/atom, the “Atoms” section is now formatted according to the atom style and a “Charges” section is added.

## 4.5.5. Molecule file

Molecule files for use with the molecule command look quite similar to data files but they do not have a compatible format, i.e., one cannot use a data file as molecule file and vice versa. Below is a simple example for a water molecule (SPC/E model). Same as a data file, there is an ignored title line and you can use comments. However, there is no information about the number of types or the box dimensions. These parameters are set when the simulation box is created. Thus the header only has the count of atoms, bonds, and so on.

Molecule files have a header followed by sections (just as in data files), but the section names are different than those of a data file. There is no “Atoms” section and the section formats in molecule files is independent of the atom style. Its information is split across multiple sections, like “Coords”, “Types”, and “Charges”. Note that no “Masses” section is needed here. The atom masses are by default tied to the atom type and set with a data file or the mass command. A “Masses” section would only be required for atom styles with per-atom masses, e.g. atom style sphere, where in data files you would provide the density and the diameter instead of the mass.

Since the entire file is a ‘molecule’, LAMMPS will assign a new molecule-ID (if supported by the atom style) when atoms are instantiated from a molecule file, e.g. with the create_atoms command. It is possible to include a “Molecules” section to indicate that the atoms belong to multiple ‘molecules’. Atom-IDs and molecule-IDs in the molecule file are relative for the file (i.e. starting from 1) and will be translated into actual atom-IDs also when the atoms from the molecule are created.

    # Water molecule. SPC/E model.

    3 atoms
    2 bonds
    1 angles

    Coords

    1    1.12456   0.09298   1.27452
    2    1.53683   0.75606   1.89928
    3    0.49482   0.56390   0.65678

    Types

    1        1
    2        2
    3        2

    Charges

    1       -0.8472
    2        0.4236
    3        0.4236

    Bonds

    1   1      1      2
    2   1      1      3

    Angles

    1   1      2      1      3

There are also optional sections, e.g. about SHAKE and special bonds. Those sections are only needed if the molecule command is issued before the simulation box is defined. Otherwise, the molecule command can derive the required settings internally.

## 4.5.6. Restart file

LAMMPS restart files are binary files and not available in text format. They can be identified by the first few bytes that contain the (C-style) string `LammpS RestartT` as magic string. This string is followed by a 16-bit integer of the number 1 used for detecting whether the computer writing the restart has the same endianness as the computer reading it. If not, the file cannot be read correctly. This integer is followed by a 32-bit integer indicating the file format revision (currently 3), which can be used to implement backward compatibility for reading older revisions.

This information has been added to the Unix “file” command’s <https://www.darwinsys.com/file/> “magic” file so that restart files can be identified without opening them. If you have a fairly recent version, it should already be included. If you have an older version, the LAMMPS source package contains a file with the necessary additions.

The rest of the file is organized in sections of a 32-bit signed integer constant indicating the kind of content and the corresponding value (or values). If those values are arrays (including C-style strings), then the integer constant is followed by a 32-bit integer indicating the length of the array. This mechanism will read the data regardless of the ordering of the sections. Symbolic names of the section constants are in the `lmprestart.h` header file.

LAMMPS restart files are not expected to be portable between platforms or LAMMPS versions, but changes to the file format are rare.