2.4. The lammps Python module — LAMMPS documentation

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# 2.4. The `lammps` Python module

The LAMMPS Python interface is implemented as a module called `lammps` which is defined in the `lammps` package in the `python` folder of the LAMMPS source code distribution. After compilation of LAMMPS, the module can be installed into a Python system folder or a user folder with `make install-python`. Components of the module can then loaded into a Python session with the `import` command.

There are multiple Python interface classes in the `lammps` module:

- the `lammps` class. This is a wrapper around the C-library interface and its member functions try to replicate the C-library API closely. This is the most feature-complete Python API.

- the `PyLammps` class. This is a more high-level and more Python style class implemented on top of the `lammps` class.

- the `IPyLammps` class is derived from `PyLammps` and adds embedded graphics features to conveniently include LAMMPS into Jupyter notebooks.

Version check

The `lammps` module stores the version number of the LAMMPS version it is installed from. When initializing the `lammps` class, this version is checked to be the same as the result from `lammps.version()`, the version of the LAMMPS shared library that the module interfaces to. If the they are not the same an AttributeError exception is raised since a mismatch of versions (e.g. due to incorrect use of the `LD_LIBRARY_PATH` or `PYTHONPATH` environment variables can lead to crashes or data corruption and otherwise incorrect behavior.

LAMMPS module global members:

lammps.__version__

  Numerical representation of the LAMMPS version this module was taken from. Has the same format as the result of `lammps.version()`.

## 2.4.1. The `lammps` class API

The `lammps` class is the core of the LAMMPS Python interfaces. It is a wrapper around the LAMMPS C library API using the Python ctypes module and a shared library compiled from the LAMMPS sources code. The individual methods in this class try to closely follow the corresponding C functions. The handle argument that needs to be passed to the C functions is stored internally in the class and automatically added when calling the C library functions. Below is a detailed documentation of the API.

class lammps.lammps(name='', cmdargs=None, ptr=None, comm=None)

  Create an instance of the LAMMPS Python class.

  This is a Python wrapper class that exposes the LAMMPS C-library interface to Python. It either requires that LAMMPS has been compiled as shared library which is then dynamically loaded via the ctypes Python module or that this module called from a Python function that is called from a Python interpreter embedded into a LAMMPS executable, for example through the python invoke command. When the class is instantiated it calls the `lammps_open()` function of the LAMMPS C-library interface, which in turn will create an instance of the `LAMMPS` C++ class. The handle to this C++ class is stored internally and automatically passed to the calls to the C library interface.

  Parameters:

    - name (string) – “machine” name of the shared LAMMPS library (“mpi” loads `liblammps_mpi.so`, “” loads `liblammps.so`)

    - cmdargs (list) – list of command line arguments to be passed to the `lammps_open()` function. The executable name is automatically added.

    - ptr (pointer) – pointer to a LAMMPS C++ class instance when called from an embedded Python interpreter. None means load symbols from shared library.

    - comm (MPI_Comm) – MPI communicator (as provided by mpi4py). `None` means use `MPI_COMM_WORLD` implicitly.

  property numpy

    Return object to access numpy versions of API

    It provides alternative implementations of API functions that return numpy arrays instead of ctypes pointers. If numpy is not installed, accessing this property will lead to an ImportError.

    Returns:

      instance of numpy wrapper object

    Return type:

      numpy_wrapper

  close()

    Explicitly delete a LAMMPS instance through the C-library interface.

    This is a wrapper around the `lammps_close()` function of the C-library interface.

  finalize()

    Shut down the MPI communication and Kokkos environment (if active) through the library interface by calling `lammps_mpi_finalize()` and `lammps_kokkos_finalize()`.

    You cannot create or use any LAMMPS instances after this function is called unless LAMMPS was compiled without MPI and without Kokkos support.

  error(error_type, error_text)

    Forward error to the LAMMPS Error class.

    New in version 3Nov2022.

    This is a wrapper around the `lammps_error()` function of the C-library interface.

    Parameters:

      - error_type (int) –

      - error_text (string) –

  version()

    Return a numerical representation of the LAMMPS version in use.

    This is a wrapper around the `lammps_version()` function of the C-library interface.

    Returns:

      version number

    Return type:

      int

  get_os_info()

    Return a string with information about the OS and compiler runtime

    This is a wrapper around the `lammps_get_os_info()` function of the C-library interface.

    Returns:

      OS info string

    Return type:

      string

  get_mpi_comm()

    Get the MPI communicator in use by the current LAMMPS instance

    This is a wrapper around the `lammps_get_mpi_comm()` function of the C-library interface. It will return `None` if either the LAMMPS library was compiled without MPI support or the mpi4py Python module is not available.

    Returns:

      MPI communicator

    Return type:

      MPI_Comm

  file(path)

    Read LAMMPS commands from a file.

    This is a wrapper around the `lammps_file()` function of the C-library interface. It will open the file with the name/path file and process the LAMMPS commands line by line until the end. The function will return when the end of the file is reached.

    Parameters:

      path (string) – Name of the file/path with LAMMPS commands

  command(cmd)

    Process a single LAMMPS input command from a string.

    This is a wrapper around the `lammps_command()` function of the C-library interface.

    Parameters:

      cmd (string) – a single lammps command

  commands_list(cmdlist)

    Process multiple LAMMPS input commands from a list of strings.

    This is a wrapper around the `lammps_commands_list()` function of the C-library interface.

    Parameters:

      cmdlist (list of strings) – a single lammps command

  commands_string(multicmd)

    Process a block of LAMMPS input commands from a string.

    This is a wrapper around the `lammps_commands_string()` function of the C-library interface.

    Parameters:

      multicmd (string) – text block of lammps commands

  get_natoms()

    Get the total number of atoms in the LAMMPS instance.

    Will be precise up to 53-bit signed integer due to the underlying `lammps_get_natoms()` function returning a double.

    Returns:

      number of atoms

    Return type:

      int

  extract_box()

    Extract simulation box parameters

    This is a wrapper around the `lammps_extract_box()` function of the C-library interface. Unlike in the C function, the result is returned as a list.

    Returns:

      list of the extracted data: boxlo, boxhi, xy, yz, xz, periodicity, box_change

    Return type:

      [ 3*double, 3*double, double, double, 3*int, int]

  reset_box(boxlo, boxhi, xy, yz, xz)

    Reset simulation box parameters

    This is a wrapper around the `lammps_reset_box()` function of the C-library interface.

    Parameters:

      - boxlo (list of 3 floating point numbers) – new lower box boundaries

      - boxhi (list of 3 floating point numbers) – new upper box boundaries

      - xy (float) – xy tilt factor

      - yz (float) – yz tilt factor

      - xz (float) – xz tilt factor

  get_thermo(name)

    Get current value of a thermo keyword

    This is a wrapper around the `lammps_get_thermo()` function of the C-library interface.

    Parameters:

      name (string) – name of thermo keyword

    Returns:

      value of thermo keyword

    Return type:

      double or None

  property last_thermo_step

    Get the last timestep where thermodynamic data was computed

    Returns:

      the timestep or a negative number if there has not been any thermo output yet

    Return type:

      int

  last_thermo()

    Get a dictionary of the last thermodynamic output

    This is a wrapper around the `lammps_last_thermo()` function of the C-library interface. It collects the cached thermo data from the last timestep into a dictionary. The return value is None, if there has not been any thermo output yet.

    Returns:

      a dictionary containing the last computed thermo output values

    Return type:

      dict or None

  extract_setting(name)

    Query LAMMPS about global settings that can be expressed as an integer.

    This is a wrapper around the `lammps_extract_setting()` function of the C-library interface. Its documentation includes a list of the supported keywords.

    Parameters:

      name (string) – name of the setting

    Returns:

      value of the setting

    Return type:

      int

  extract_global_datatype(name)

    Retrieve global property datatype from LAMMPS

    This is a wrapper around the `lammps_extract_global_datatype()` function of the C-library interface. Its documentation includes a list of the supported keywords. This function returns `None` if the keyword is not recognized. Otherwise it will return a positive integer value that corresponds to one of the data type constants define in the `lammps` module.

    Parameters:

      name (string) – name of the property

    Returns:

      data type of global property, see Data Types

    Return type:

      int

  extract_global(name, dtype=None)

    Query LAMMPS about global settings of different types.

    This is a wrapper around the `lammps_extract_global()` function of the C-library interface. Since there are no pointers in Python, this method will - unlike the C function - return the value or a list of values. The `lammps_extract_global()` documentation includes a list of the supported keywords and their data types. Since Python needs to know the data type to be able to interpret the result, by default, this function will try to auto-detect the data type by asking the library. You can also force a specific data type. For that purpose the `lammps` module contains data type constants. This function returns `None` if either the keyword is not recognized, or an invalid data type constant is used.

    Parameters:

      - name (string) – name of the property

      - dtype (int, optional) – data type of the returned data (see Data Types)

    Returns:

      value of the property or list of values or None

    Return type:

      int, float, list, or NoneType

  extract_atom_datatype(name)

    Retrieve per-atom property datatype from LAMMPS

    This is a wrapper around the `lammps_extract_atom_datatype()` function of the C-library interface. Its documentation includes a list of the supported keywords. This function returns `None` if the keyword is not recognized. Otherwise it will return an integer value that corresponds to one of the data type constants defined in the `lammps` module.

    Parameters:

      name (string) – name of the property

    Returns:

      data type of per-atom property (see Data Types)

    Return type:

      int

  extract_atom(name, dtype=None)

    Retrieve per-atom properties from LAMMPS

    This is a wrapper around the `lammps_extract_atom()` function of the C-library interface. Its documentation includes a list of the supported keywords and their data types. Since Python needs to know the data type to be able to interpret the result, by default, this function will try to auto-detect the data type by asking the library. You can also force a specific data type by setting `dtype` to one of the data type constants defined in the `lammps` module. This function returns `None` if either the keyword is not recognized, or an invalid data type constant is used.

    Note

    While the returned arrays of per-atom data are dimensioned for the range [0:nmax] - as is the underlying storage - the data is usually only valid for the range of [0:nlocal], unless the property of interest is also updated for ghost atoms. In some cases, this depends on a LAMMPS setting, see for example comm_modify vel yes.

    Parameters:

      - name (string) – name of the property

      - dtype (int, optional) – data type of the returned data (see Data Types)

    Returns:

      requested data or `None`

    Return type:

      ctypes.POINTER(ctypes.c_int32), ctypes.POINTER(ctypes.POINTER(ctypes.c_int32)), ctypes.POINTER(ctypes.c_int64), ctypes.POINTER(ctypes.POINTER(ctypes.c_int64)), ctypes.POINTER(ctypes.c_double), ctypes.POINTER(ctypes.POINTER(ctypes.c_double)), or NoneType

  extract_compute(cid, cstyle, ctype)

    Retrieve data from a LAMMPS compute

    This is a wrapper around the `lammps_extract_compute()` function of the C-library interface. This function returns `None` if either the compute id is not recognized, or an invalid combination of cstyle and ctype constants is used. The names and functionality of the constants are the same as for the corresponding C-library function. For requests to return a scalar or a size, the value is returned, otherwise a pointer.

    Parameters:

      - cid (string) – compute ID

      - cstyle (int) – style of the data retrieve (global, atom, or local), see Style Constants

      - ctype (int) – type or size of the returned data (scalar, vector, or array), see Type Constants

    Returns:

      requested data as scalar, pointer to 1d or 2d double array, or None

    Return type:

      c_double, ctypes.POINTER(c_double), ctypes.POINTER(ctypes.POINTER(c_double)), or NoneType

  extract_fix(fid, fstyle, ftype, nrow=0, ncol=0)

    Retrieve data from a LAMMPS fix

    This is a wrapper around the `lammps_extract_fix()` function of the C-library interface. This function returns `None` if either the fix id is not recognized, or an invalid combination of fstyle and ftype constants is used. The names and functionality of the constants are the same as for the corresponding C-library function. For requests to return a scalar or a size, the value is returned, also when accessing global vectors or arrays, otherwise a pointer.

    Parameters:

      - fid (string) – fix ID

      - fstyle (int) – style of the data retrieve (global, atom, or local), see Style Constants

      - ftype (int) – type or size of the returned data (scalar, vector, or array), see Type Constants

      - nrow (int) – index of global vector element or row index of global array element

      - ncol (int) – column index of global array element

    Returns:

      requested data or None

    Return type:

      c_double, ctypes.POINTER(c_double), ctypes.POINTER(ctypes.POINTER(c_double)), or NoneType

  extract_variable(name, group=None, vartype=None)

    Evaluate a LAMMPS variable and return its data

    This function is a wrapper around the function `lammps_extract_variable()` of the C library interface, evaluates variable name and returns a copy of the computed data. The memory temporarily allocated by the C-interface is deleted after the data is copied to a Python variable or list. The variable must be either an equal-style (or equivalent) variable or an atom-style variable. The variable type can be provided as the `vartype` parameter, which may be one of several constants: `LMP_VAR_EQUAL`, `LMP_VAR_ATOM`, `LMP_VAR_VECTOR`, or `LMP_VAR_STRING`. If omitted or `None`, LAMMPS will determine its value for you based on a call to `lammps_extract_variable_datatype()` from the C library interface. The group parameter is only used for atom-style variables and defaults to the group “all”.

    Parameters:

      - name (string) – name of the variable to execute

      - group (string, only for atom-style variables) – name of group for atom-style variable

      - vartype (int) – type of variable, see Variable Type Constants

    Returns:

      the requested data

    Return type:

      c_double, (c_double), or NoneType

  flush_buffers()

    Flush output buffers

    This is a wrapper around the `lammps_flush_buffers()` function of the C-library interface.

  set_variable(name, value)

    Set a new value for a LAMMPS string style variable

    This is a wrapper around the `lammps_set_variable()` function of the C-library interface.

    Parameters:

      - name (string) – name of the variable

      - value (any. will be converted to a string) – new variable value

    Returns:

      either 0 on success or -1 on failure

    Return type:

      int

  gather_bonds()

    Retrieve global list of bonds

    New in version 28Jul2021.

    This is a wrapper around the `lammps_gather_bonds()` function of the C-library interface.

    This function returns a tuple with the number of bonds and a flat list of ctypes integer values with the bond type, bond atom1, bond atom2 for each bond.

    Returns:

      a tuple with the number of bonds and a list of c_int or c_long

    Return type:

      (int, 3*nbonds*c_tagint)

  gather_angles()

    Retrieve global list of angles

    New in version 8Feb2023.

    This is a wrapper around the `lammps_gather_angles()` function of the C-library interface.

    This function returns a tuple with the number of angles and a flat list of ctypes integer values with the angle type, angle atom1, angle atom2, angle atom3 for each angle.

    Returns:

      a tuple with the number of angles and a list of c_int or c_long

    Return type:

      (int, 4*nangles*c_tagint)

  gather_dihedrals()

    Retrieve global list of dihedrals

    New in version 8Feb2023.

    This is a wrapper around the `lammps_gather_dihedrals()` function of the C-library interface.

    This function returns a tuple with the number of dihedrals and a flat list of ctypes integer values with the dihedral type, dihedral atom1, dihedral atom2, dihedral atom3, dihedral atom4 for each dihedral.

    Returns:

      a tuple with the number of dihedrals and a list of c_int or c_long

    Return type:

      (int, 5*ndihedrals*c_tagint)

  gather_impropers()

    Retrieve global list of impropers

    New in version 8Feb2023.

    This is a wrapper around the `lammps_gather_impropers()` function of the C-library interface.

    This function returns a tuple with the number of impropers and a flat list of ctypes integer values with the improper type, improper atom1, improper atom2, improper atom3, improper atom4 for each improper.

    Returns:

      a tuple with the number of impropers and a list of c_int or c_long

    Return type:

      (int, 5*nimpropers*c_tagint)

  encode_image_flags(ix, iy, iz)

    convert 3 integers with image flags for x-, y-, and z-direction into a single integer like it is used internally in LAMMPS

    This method is a wrapper around the `lammps_encode_image_flags()` function of library interface.

    Parameters:

      - ix (int) – x-direction image flag

      - iy (int) – y-direction image flag

      - iz (int) – z-direction image flag

    Returns:

      encoded image flags

    Return type:

      lammps.c_imageint

  decode_image_flags(image)

    Convert encoded image flag integer into list of three regular integers.

    This method is a wrapper around the `lammps_decode_image_flags()` function of library interface.

    Parameters:

      image (lammps.c_imageint) – encoded image flags

    Returns:

      list of three image flags in x-, y-, and z- direction

    Return type:

      list of 3 int

  create_atoms(n, id, type, x, v=None, image=None, shrinkexceed=False)

    Create N atoms from list of coordinates and properties

    This function is a wrapper around the `lammps_create_atoms()` function of the C-library interface, and the behavior is similar except that the v, image, and shrinkexceed arguments are optional and default to None, None, and False, respectively. With None being equivalent to a `NULL` pointer in C.

    The lists of coordinates, types, atom IDs, velocities, image flags can be provided in any format that may be converted into the required internal data types. Also the list may contain more than N entries, but not fewer. In the latter case, the function will return without attempting to create atoms. You may use the `encode_image_flags` method to properly combine three integers with image flags into a single integer.

    Parameters:

      - n (int) – number of atoms for which data is provided

      - id (list of lammps.tagint) – list of atom IDs with at least n elements or None

      - type (list of int) – list of atom types

      - x (list of float) – list of coordinates for x-, y-, and z (flat list of 3n entries)

      - v (list of float) – list of velocities for x-, y-, and z (flat list of 3n entries) or None (optional)

      - image (list of lammps.imageint) – list of encoded image flags (optional)

      - shrinkexceed (bool) – whether to expand shrink-wrap boundaries if atoms are outside the box (optional)

    Returns:

      number of atoms created. 0 if insufficient or invalid data

    Return type:

      int

  property has_mpi_support

    Report whether the LAMMPS shared library was compiled with a real MPI library or in serial.

    This is a wrapper around the `lammps_config_has_mpi_support()` function of the library interface.

    Returns:

      False when compiled with MPI STUBS, otherwise True

    Return type:

      bool

  property is_running

    Report whether being called from a function during a run or a minimization

    New in version 9Oct2020.

    Various LAMMPS commands must not be called during an ongoing run or minimization. This property allows to check for that. This is a wrapper around the `lammps_is_running()` function of the library interface.

    Returns:

      True when called during a run otherwise false

    Return type:

      bool

  force_timeout()

    Trigger an immediate timeout, i.e. a “soft stop” of a run.

    New in version 9Oct2020.

    This function allows to cleanly stop an ongoing run or minimization at the next loop iteration. This is a wrapper around the `lammps_force_timeout()` function of the library interface.

  property has_exceptions

    Report whether the LAMMPS shared library was compiled with C++ exceptions handling enabled

    This is a wrapper around the `lammps_config_has_exceptions()` function of the library interface.

    Returns:

      state of C++ exception support

    Return type:

      bool

  property has_gzip_support

    Report whether the LAMMPS shared library was compiled with support for reading and writing compressed files through `gzip`.

    This is a wrapper around the `lammps_config_has_gzip_support()` function of the library interface.

    Returns:

      state of gzip support

    Return type:

      bool

  property has_png_support

    Report whether the LAMMPS shared library was compiled with support for writing images in PNG format.

    This is a wrapper around the `lammps_config_has_png_support()` function of the library interface.

    Returns:

      state of PNG support

    Return type:

      bool

  property has_jpeg_support

    Report whether the LAMMPS shared library was compiled with support for writing images in JPEG format.

    This is a wrapper around the `lammps_config_has_jpeg_support()` function of the library interface.

    Returns:

      state of JPEG support

    Return type:

      bool

  property has_ffmpeg_support

    State of support for writing movies with `ffmpeg` in the LAMMPS shared library

    This is a wrapper around the `lammps_config_has_ffmpeg_support()` function of the library interface.

    Returns:

      state of ffmpeg support

    Return type:

      bool

  has_package(name)

    Report if the named package has been enabled in the LAMMPS shared library.

    New in version 3Nov2022.

    This is a wrapper around the `lammps_config_has_package()` function of the library interface.

    Parameters:

      name (string) – name of the package

    Returns:

      state of package availability

    Return type:

      bool

  property accelerator_config

    Return table with available accelerator configuration settings.

    This is a wrapper around the `lammps_config_accelerator()` function of the library interface which loops over all known packages and categories and returns enabled features as a nested dictionary with all enabled settings as list of strings.

    Returns:

      nested dictionary with all known enabled settings as list of strings

    Return type:

      dictionary

  property has_gpu_device

    Availability of GPU package compatible device

    This is a wrapper around the `lammps_has_gpu_device()` function of the C library interface.

    Returns:

      True if a GPU package compatible device is present, otherwise False

    Return type:

      bool

  get_gpu_device_info()

    Return a string with detailed information about any devices that are usable by the GPU package.

    This is a wrapper around the `lammps_get_gpu_device_info()` function of the C-library interface.

    Returns:

      GPU device info string

    Return type:

      string

  property installed_packages

    List of the names of enabled packages in the LAMMPS shared library

    This is a wrapper around the functions `lammps_config_package_count()` and :cpp:func`lammps_config_package_name` of the library interface.

    :return

  has_style(category, name)

    Returns whether a given style name is available in a given category

    This is a wrapper around the function `lammps_has_style()` of the library interface.

    Parameters:

      - category (string) – name of category

      - name (string) – name of the style

    Returns:

      true if style is available in given category

    Return type:

      bool

  available_styles(category)

    Returns a list of styles available for a given category

    This is a wrapper around the functions `lammps_style_count()` and `lammps_style_name()` of the library interface.

    Parameters:

      category (string) – name of category

    Returns:

      list of style names in given category

    Return type:

      list

  has_id(category, name)

    Returns whether a given ID name is available in a given category

    New in version 9Oct2020.

    This is a wrapper around the function `lammps_has_id()` of the library interface.

    Parameters:

      - category (string) – name of category

      - name (string) – name of the ID

    Returns:

      true if ID is available in given category

    Return type:

      bool

  available_ids(category)

    Returns a list of IDs available for a given category

    New in version 9Oct2020.

    This is a wrapper around the functions `lammps_id_count()` and `lammps_id_name()` of the library interface.

    Parameters:

      category (string) – name of category

    Returns:

      list of id names in given category

    Return type:

      list

  available_plugins(category)

    Returns a list of plugins available for a given category

    New in version 10Mar2021.

    This is a wrapper around the functions `lammps_plugin_count()` and `lammps_plugin_name()` of the library interface.

    Returns:

      list of style/name pairs of loaded plugins

    Return type:

      list

  set_fix_external_callback(fix_id, callback, caller=None)

    Set the callback function for a fix external instance with a given fix ID.

    Optionally also set a reference to the calling object.

    This is a wrapper around the `lammps_set_fix_external_callback()` function of the C-library interface. However this is set up to call a Python function with the following arguments.

    - object is the value of the “caller” argument

    - ntimestep is the current timestep

    - nlocal is the number of local atoms on the current MPI process

    - tag is a 1d NumPy array of integers representing the atom IDs of the local atoms

    - x is a 2d NumPy array of doubles of the coordinates of the local atoms

    - f is a 2d NumPy array of doubles of the forces on the local atoms that will be added

    Changed in version 28Jul2021.

    Parameters:

      - fix_id – Fix-ID of a fix external instance

      - callback – Python function that will be called from fix external

      - caller – reference to some object passed to the callback function

    Type:

      string

    Type:

      function

    Type:

      object, optional

  fix_external_get_force(fix_id)

    Get access to the array with per-atom forces of a fix external instance with a given fix ID.

    New in version 28Jul2021.

    This is a wrapper around the `lammps_fix_external_get_force()` function of the C-library interface.

    Parameters:

      fix_id – Fix-ID of a fix external instance

    Type:

      string

    Returns:

      requested data

    Return type:

      ctypes.POINTER(ctypes.POINTER(ctypes.double))

  fix_external_set_energy_global(fix_id, eng)

    Set the global energy contribution for a fix external instance with the given ID.

    New in version 28Jul2021.

    This is a wrapper around the `lammps_fix_external_set_energy_global()` function of the C-library interface.

    Parameters:

      - fix_id – Fix-ID of a fix external instance

      - eng – potential energy value to be added by fix external

    Type:

      string

    Type:

      float

  fix_external_set_virial_global(fix_id, virial)

    Set the global virial contribution for a fix external instance with the given ID.

    New in version 28Jul2021.

    This is a wrapper around the `lammps_fix_external_set_virial_global()` function of the C-library interface.

    Parameters:

      - fix_id – Fix-ID of a fix external instance

      - eng – list of 6 floating point numbers with the virial to be added by fix external

    Type:

      string

    Type:

      float

  fix_external_set_energy_peratom(fix_id, eatom)

    Set the per-atom energy contribution for a fix external instance with the given ID.

    New in version 28Jul2021.

    This is a wrapper around the `lammps_fix_external_set_energy_peratom()` function of the C-library interface.

    Parameters:

      - fix_id – Fix-ID of a fix external instance

      - eatom – list of potential energy values for local atoms to be added by fix external

    Type:

      string

    Type:

      float

  fix_external_set_virial_peratom(fix_id, vatom)

    Set the per-atom virial contribution for a fix external instance with the given ID.

    New in version 28Jul2021.

    This is a wrapper around the `lammps_fix_external_set_virial_peratom()` function of the C-library interface.

    Parameters:

      - fix_id – Fix-ID of a fix external instance

      - vatom – list of natoms lists with 6 floating point numbers to be added by fix external

    Type:

      string

    Type:

      float

  fix_external_set_vector_length(fix_id, length)

    Set the vector length for a global vector stored with fix external for analysis

    New in version 28Jul2021.

    This is a wrapper around the `lammps_fix_external_set_vector_length()` function of the C-library interface.

    Parameters:

      - fix_id – Fix-ID of a fix external instance

      - length – length of the global vector

    Type:

      string

    Type:

      int

  fix_external_set_vector(fix_id, idx, val)

    Store a global vector value for a fix external instance with the given ID.

    New in version 28Jul2021.

    This is a wrapper around the `lammps_fix_external_set_vector()` function of the C-library interface.

    Parameters:

      - fix_id – Fix-ID of a fix external instance

      - idx – 1-based index of the value in the global vector

      - val – value to be stored in the global vector

    Type:

      string

    Type:

      int

    Type:

      float

  get_neighlist(idx)

    Returns an instance of `NeighList` which wraps access to the neighbor list with the given index

    See `lammps.numpy.get_neighlist()` if you want to use NumPy arrays instead of `c_int` pointers.

    Parameters:

      idx (int) – index of neighbor list

    Returns:

      an instance of `NeighList` wrapping access to neighbor list data

    Return type:

      NeighList

  get_neighlist_size(idx)

    Return the number of elements in neighbor list with the given index

    Parameters:

      idx (int) – neighbor list index

    Returns:

      number of elements in neighbor list with index idx

    Return type:

      int

  get_neighlist_element_neighbors(idx, element)

    Return data of neighbor list entry

    Parameters:

      - element (int) – neighbor list index

      - element – neighbor list element index

    Returns:

      tuple with atom local index, number of neighbors and array of neighbor local atom indices

    Return type:

      (int, int, POINTER(c_int))

  find_pair_neighlist(style, exact=True, nsub=0, reqid=0)

    Find neighbor list index of pair style neighbor list

    Search for a neighbor list requested by a pair style instance that matches “style”. If exact is True, the pair style name must match exactly. If exact is False, the pair style name is matched against “style” as regular expression or sub-string. If the pair style is a hybrid pair style, the style is instead matched against the hybrid sub-styles. If the same pair style is used as sub-style multiple types, you must set nsub to a value n > 0 which indicates the nth instance of that sub-style to be used (same as for the pair_coeff command). The default value of 0 will fail to match in that case.

    Once the pair style instance has been identified, it may have requested multiple neighbor lists. Those are uniquely identified by a request ID > 0 as set by the pair style. Otherwise the request ID is 0.

    Parameters:

      - style (string) – name of pair style that should be searched for

      - exact (bool, optional) – controls whether style should match exactly or only must be contained in pair style name, defaults to True

      - nsub (int, optional) – match nsub-th hybrid sub-style, defaults to 0

      - reqid (int, optional) – list request id, > 0 in case there are more than one, defaults to 0

    Returns:

      neighbor list index if found, otherwise -1

    Return type:

      int

  find_fix_neighlist(fixid, reqid=0)

    Find neighbor list index of fix neighbor list

    The fix instance requesting the neighbor list is uniquely identified by the fix ID. In case the fix has requested multiple neighbor lists, those are uniquely identified by a request ID > 0 as set by the fix. Otherwise the request ID is 0 (the default).

    Parameters:

      - fixid (string) – name of fix

      - reqid (int, optional) – id of neighbor list request, in case there are more than one request, defaults to 0

    Returns:

      neighbor list index if found, otherwise -1

    Return type:

      int

  find_compute_neighlist(computeid, reqid=0)

    Find neighbor list index of compute neighbor list

    The compute instance requesting the neighbor list is uniquely identified by the compute ID. In case the compute has requested multiple neighbor lists, those are uniquely identified by a request ID > 0 as set by the compute. Otherwise the request ID is 0 (the default).

    Parameters:

      - computeid (string) – name of compute

      - reqid (int, optional) – index of neighbor list request, in case there are more than one request, defaults to 0

    Returns:

      neighbor list index if found, otherwise -1

    Return type:

      int

class lammps.numpy_wrapper.numpy_wrapper(lmp)

  lammps API NumPy Wrapper

  This is a wrapper class that provides additional methods on top of an existing `lammps` instance. The methods transform raw ctypes pointers into NumPy arrays, which give direct access to the original data while protecting against out-of-bounds accesses.

  There is no need to explicitly instantiate this class. Each instance of `lammps` has a `numpy` property that returns an instance.

  Parameters:

    lmp (lammps) – instance of the `lammps` class

  extract_atom(name, dtype=None, nelem=None, dim=None)

    Retrieve per-atom properties from LAMMPS as NumPy arrays

    This is a wrapper around the `lammps.extract_atom()` method. It behaves the same as the original method, but returns NumPy arrays instead of `ctypes` pointers.

    Note

    The returned arrays of per-atom data are by default dimensioned for the range [0:nlocal] since that data is always valid. The underlying storage for the data, however, is typically allocated for the range of [0:nmax]. Whether there is valid data in the range [nlocal:nlocal+nghost] depends on whether the property of interest is also updated for ghost atoms. This is not often the case. In some cases, it depends on a LAMMPS setting, see for example comm_modify vel yes. By using the optional nelem parameter the size of the returned NumPy can be overridden. There is no check whether the number of elements chosen is valid.

    Parameters:

      - name (string) – name of the property

      - dtype (int, optional) – type of the returned data (see Data Types)

      - nelem (int, optional) – number of elements in array

      - dim (int, optional) – dimension of each element

    Returns:

      requested data as NumPy array with direct access to C data or None

    Return type:

      numpy.array or NoneType

  extract_compute(cid, cstyle, ctype)

    Retrieve data from a LAMMPS compute

    This is a wrapper around the `lammps.extract_compute()` method. It behaves the same as the original method, but returns NumPy arrays instead of `ctypes` pointers.

    Parameters:

      - cid (string) – compute ID

      - cstyle (int) – style of the data retrieve (global, atom, or local), see Style Constants

      - ctype (int) – type of the returned data (scalar, vector, or array), see Type Constants

    Returns:

      requested data either as float, as NumPy array with direct access to C data, or None

    Return type:

      float, numpy.array, or NoneType

  extract_fix(fid, fstyle, ftype, nrow=0, ncol=0)

    Retrieve data from a LAMMPS fix

    This is a wrapper around the `lammps.extract_fix()` method. It behaves the same as the original method, but returns NumPy arrays instead of `ctypes` pointers.

    Parameters:

      - fid (string) – fix ID

      - fstyle (int) – style of the data retrieve (global, atom, or local), see Style Constants

      - ftype (int) – type or size of the returned data (scalar, vector, or array), see Type Constants

      - nrow (int) – index of global vector element or row index of global array element

      - ncol (int) – column index of global array element

    Returns:

      requested data

    Return type:

      integer or double value, pointer to 1d or 2d double array or None

  extract_variable(name, group=None, vartype=0)

    Evaluate a LAMMPS variable and return its data

    This function is a wrapper around the function `lammps.extract_variable()` method. It behaves the same as the original method, but returns NumPy arrays instead of `ctypes` pointers.

    Parameters:

      - name (string) – name of the variable to execute

      - group (string) – name of group for atom-style variable (ignored for equal-style variables)

      - vartype (int) – type of variable, see Variable Type Constants

    Returns:

      the requested data or None

    Return type:

      c_double, numpy.array, or NoneType

  gather_bonds()

    Retrieve global list of bonds as NumPy array

    New in version 28Jul2021.

    This is a wrapper around `lammps.gather_bonds()` It behaves the same as the original method, but returns a NumPy array instead of a `ctypes` list.

    Returns:

      the requested data as a 2d-integer numpy array

    Return type:

      numpy.array(nbonds,3)

  gather_angles()

    Retrieve global list of angles as NumPy array

    New in version 8Feb2023.

    This is a wrapper around `lammps.gather_angles()` It behaves the same as the original method, but returns a NumPy array instead of a `ctypes` list.

    Returns:

      the requested data as a 2d-integer numpy array

    Return type:

      numpy.array(nangles,4)

  gather_dihedrals()

    Retrieve global list of dihedrals as NumPy array

    New in version 8Feb2023.

    This is a wrapper around `lammps.gather_dihedrals()` It behaves the same as the original method, but returns a NumPy array instead of a `ctypes` list.

    Returns:

      the requested data as a 2d-integer numpy array

    Return type:

      numpy.array(ndihedrals,5)

  gather_impropers()

    Retrieve global list of impropers as NumPy array

    New in version 8Feb2023.

    This is a wrapper around `lammps.gather_impropers()` It behaves the same as the original method, but returns a NumPy array instead of a `ctypes` list.

    Returns:

      the requested data as a 2d-integer numpy array

    Return type:

      numpy.array(nimpropers,5)

  fix_external_get_force(fix_id)

    Get access to the array with per-atom forces of a fix external instance with a given fix ID.

    Changed in version 28Jul2021.

    This function is a wrapper around the `lammps.fix_external_get_force()` method. It behaves the same as the original method, but returns a NumPy array instead of a `ctypes` pointer.

    Parameters:

      fix_id – Fix-ID of a fix external instance

    Type:

      string

    Returns:

      requested data

    Return type:

      numpy.array

  fix_external_set_energy_peratom(fix_id, eatom)

    Set the per-atom energy contribution for a fix external instance with the given ID.

    New in version 28Jul2021.

    This function is an alternative to `lammps.fix_external_set_energy_peratom()` method. It behaves the same as the original method, but accepts a NumPy array instead of a list as argument.

    Parameters:

      - fix_id – Fix-ID of a fix external instance

      - eatom – per-atom potential energy

    Type:

      string

    Type:

      numpy.array

  fix_external_set_virial_peratom(fix_id, vatom)

    Set the per-atom virial contribution for a fix external instance with the given ID.

    New in version 28Jul2021.

    This function is an alternative to `lammps.fix_external_set_virial_peratom()` method. It behaves the same as the original method, but accepts a NumPy array instead of a list as argument.

    Parameters:

      - fix_id – Fix-ID of a fix external instance

      - eatom – per-atom potential energy

    Type:

      string

    Type:

      numpy.array

  get_neighlist(idx)

    Returns an instance of `NumPyNeighList` which wraps access to the neighbor list with the given index

    Parameters:

      idx (int) – index of neighbor list

    Returns:

      an instance of `NumPyNeighList` wrapping access to neighbor list data

    Return type:

      NumPyNeighList

  get_neighlist_element_neighbors(idx, element)

    Return data of neighbor list entry

    This function is a wrapper around the function `lammps.get_neighlist_element_neighbors()` method. It behaves the same as the original method, but returns a NumPy array containing the neighbors instead of a `ctypes` pointer.

    Parameters:

      - element (int) – neighbor list index

      - element – neighbor list element index

    Returns:

      tuple with atom local index and numpy array of neighbor local atom indices

    Return type:

      (int, numpy.array)

## 2.4.2. The `PyLammps` class API

The `PyLammps` class is a wrapper that creates a simpler, more “Pythonic” interface to common LAMMPS functionality. LAMMPS data structures are exposed through objects and properties. This makes Python scripts shorter and more concise. See the PyLammps Tutorial for an introduction on how to use this interface.

class lammps.PyLammps(name='', cmdargs=None, ptr=None, comm=None, verbose=False)

  This is a Python wrapper class around the lower-level `lammps` class, exposing a more Python-like, object-oriented interface for prototyping system inside of IPython and Jupyter notebooks.

  It either creates its own instance of `lammps` or can be initialized with an existing instance. The arguments are the same of the lower-level interface. The original interface can still be accessed via `PyLammps.lmp`.

  Parameters:

    - name (string) – “machine” name of the shared LAMMPS library (“mpi” loads `liblammps_mpi.so`, “” loads `liblammps.so`)

    - cmdargs (list) – list of command line arguments to be passed to the `lammps_open()` function. The executable name is automatically added.

    - ptr (pointer) – pointer to a LAMMPS C++ class instance when called from an embedded Python interpreter. None means load symbols from shared library.

    - comm (MPI_Comm) – MPI communicator (as provided by mpi4py). `None` means use `MPI_COMM_WORLD` implicitly.

    - verbose (bool) – print all LAMMPS output to stdout

  Variables:

    - lmp (`lammps`) – instance of original LAMMPS Python interface

    - runs – list of completed runs, each storing the thermo output

  close()

    Explicitly delete a LAMMPS instance

    This is a wrapper around the `lammps.close()` of the Python interface.

  version()

    Return a numerical representation of the LAMMPS version in use.

    This is a wrapper around the `lammps.version()` function of the Python interface.

    Returns:

      version number

    Return type:

      int

  file(file)

    Read LAMMPS commands from a file.

    This is a wrapper around the `lammps.file()` function of the Python interface.

    Parameters:

      path (string) – Name of the file/path with LAMMPS commands

  property enable_cmd_history
    Getter:

      Return whether command history is saved

    Setter:

      Set if command history should be saved

    Type:

      bool

  write_script(filepath)

    Write LAMMPS script file containing all commands executed up until now

    Parameters:

      filepath (string) – path to script file that should be written

  clear_cmd_history()

    Clear LAMMPS command history up to this point

  command(cmd)

    Execute LAMMPS command

    If `PyLammps.enable_cmd_history` is set to `True`, commands executed will be recorded. The entire command history can be written to a file using `PyLammps.write_script()`. To clear the command history, use `PyLammps.clear_cmd_history()`.

    Parameters:

      cmd – command string that should be executed

    Type:

      cmd: string

  run(*args, **kwargs)

    Execute LAMMPS run command with given arguments

    Thermo data of the run is recorded and saved as new entry in `PyLammps.runs`. The latest run can be retrieved by `PyLammps.last_run`.

    Note, for recording of all thermo steps during a run, the PYTHON package needs to be enabled in LAMMPS. Otherwise, it will only capture the final timestep.

  property last_run

    Return data produced of last completed run command

    Getter:

      Returns an object containing information about the last run command

    Type:

      dict

  property atoms

    All atoms of this LAMMPS instance

    Getter:

      Returns a list of atoms currently in the system

    Type:

      AtomList

  property system

    The system state of this LAMMPS instance

    Getter:

      Returns an object with properties storing the current system state

    Type:

      namedtuple

  property communication

    The communication state of this LAMMPS instance

    Getter:

      Returns an object with properties storing the current communication state

    Type:

      namedtuple

  property computes

    The list of active computes of this LAMMPS instance

    Getter:

      Returns a list of computes that are currently active in this LAMMPS instance

    Type:

      list

  property dumps

    The list of active dumps of this LAMMPS instance

    Getter:

      Returns a list of dumps that are currently active in this LAMMPS instance

    Type:

      list

  property fixes

    The list of active fixes of this LAMMPS instance

    Getter:

      Returns a list of fixes that are currently active in this LAMMPS instance

    Type:

      list

  property groups

    The list of active atom groups of this LAMMPS instance

    Getter:

      Returns a list of atom groups that are currently active in this LAMMPS instance

    Type:

      list

  property variables

    Returns a dictionary of all variables defined in the current LAMMPS instance

    Getter:

      Returns a dictionary of all variables that are defined in this LAMMPS instance

    Type:

      dict

  eval(expr)

    Evaluate expression

    Parameters:

      expr (string) – the expression string that should be evaluated inside of LAMMPS

    Returns:

      the value of the evaluated expression

    Return type:

      float if numeric, string otherwise

  lmp_print(s)

    needed for Python2 compatibility, since print is a reserved keyword

class lammps.AtomList(pylammps_instance)

  A dynamic list of atoms that returns either an `Atom` or `Atom2D` instance for each atom. Instances are only allocated when accessed.

  Variables:

    - natoms – total number of atoms

    - dimensions – number of dimensions in system

class lammps.Atom(pylammps_instance, index)

  A wrapper class then represents a single atom inside of LAMMPS

  It provides access to properties of the atom and allows you to change some of them.

  property id

    Return the atom ID

    Type:

      int

  property type

    Return the atom type

    Type:

      int

  property mol

    Return the atom molecule index

    Type:

      int

  property mass

    Return the atom mass

    Type:

      float

  property radius

    Return the particle radius

    Type:

      float

  property position
    Getter:

      Return position of atom

    Setter:

      Set position of atom

    Type:

      numpy.array (float, float, float)

  property velocity
    Getter:

      Return velocity of atom

    Setter:

      Set velocity of atom

    Type:

      numpy.array (float, float, float)

  property force

    Return the total force acting on the atom

    Type:

      numpy.array (float, float, float)

  property omega

    Return the rotational velocity of the particle

    Type:

      numpy.array (float, float, float)

  property torque

    Return the total torque acting on the particle

    Type:

      numpy.array (float, float, float)

  property angular_momentum

    Return the angular momentum of the particle

    Type:

      numpy.array (float, float, float)

  property charge

    Return the atom charge

    Type:

      float

class lammps.Atom2D(pylammps_instance, index)

  A wrapper class then represents a single 2D atom inside of LAMMPS

  Inherits all properties from the `Atom` class, but returns 2D versions of position, velocity, and force.

  It provides access to properties of the atom and allows you to change some of them.

  property position

    Access to coordinates of an atom

    Getter:

      Return position of atom

    Setter:

      Set position of atom

    Type:

      numpy.array (float, float)

  property velocity

    Access to velocity of an atom :getter: Return velocity of atom :setter: Set velocity of atom :type: numpy.array (float, float)

  property force

    Access to force of an atom :getter: Return force of atom :setter: Set force of atom :type: numpy.array (float, float)

## 2.4.3. The `IPyLammps` class API

The `IPyLammps` class is an extension of `PyLammps`, adding additional functions to quickly display visualizations such as images and videos inside of IPython. See the PyLammps Tutorial for examples.

class lammps.IPyLammps(name='', cmdargs=None, ptr=None, comm=None)

  IPython wrapper for LAMMPS which adds embedded graphics capabilities to PyLammmps interface

  It either creates its own instance of `lammps` or can be initialized with an existing instance. The arguments are the same of the lower-level interface. The original interface can still be accessed via `PyLammps.lmp`.

  Parameters:

    - name (string) – “machine” name of the shared LAMMPS library (“mpi” loads `liblammps_mpi.so`, “” loads `liblammps.so`)

    - cmdargs (list) – list of command line arguments to be passed to the `lammps_open()` function. The executable name is automatically added.

    - ptr (pointer) – pointer to a LAMMPS C++ class instance when called from an embedded Python interpreter. None means load symbols from shared library.

    - comm (MPI_Comm) – MPI communicator (as provided by mpi4py). `None` means use `MPI_COMM_WORLD` implicitly.

  image(filename='snapshot.png', group='all', color='type', diameter='type', size=None, view=None, center=None, up=None, zoom=1.0, background_color='white')

    Generate image using write_dump command and display it

    See dump image for more information.

    Parameters:

      - filename (string) – Name of the image file that should be generated. The extension determines whether it is PNG or JPEG

      - group (string) – the group of atoms write_image should use

      - color (string) – name of property used to determine color

      - diameter (string) – name of property used to determine atom diameter

      - size (tuple (width, height)) – dimensions of image

      - view (tuple (theta, phi)) – view parameters

      - center (tuple (flag, center_x, center_y, center_z)) – center parameters

      - up (tuple (up_x, up_y, up_z)) – vector pointing to up direction

      - zoom (float) – zoom factor

      - background_color (string) – background color of scene

    Returns:

      Image instance used to display image in notebook

    Return type:

      `IPython.core.display.Image`

  video(filename)

    Load video from file

    Can be used to visualize videos from dump movie.

    Parameters:

      filename (string) – Path to video file

    Returns:

      HTML Video Tag used by notebook to embed a video

    Return type:

      `IPython.display.HTML`

## 2.4.4. Additional components of the `lammps` module

The `lammps` module additionally contains several constants and the `NeighList` class:

### Data Types

LAMMPS_INT, LAMMPS_INT_2D, LAMMPS_DOUBLE, LAMMPS_DOUBLE_2D, LAMMPS_INT64, LAMMPS_INT64_2D, LAMMPS_STRING

  Constants in the `lammps` module to indicate how to cast data when the C library function returns a void pointer. Used in `lammps.extract_global()` and `lammps.extract_atom()`. See `_LMP_DATATYPE_CONST` for the equivalent constants in the C library interface.

### Style Constants

LMP_STYLE_GLOBAL, LMP_STYLE_ATOM, LMP_STYLE_LOCAL

  Constants in the `lammps` module to select what style of data to request from computes or fixes. See `_LMP_STYLE_CONST` for the equivalent constants in the C library interface. Used in `lammps.extract_compute()`, `lammps.extract_fix()`, and their NumPy variants `lammps.numpy.extract_compute()` and `lammps.numpy.extract_fix()`.

### Type Constants

LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS

  Constants in the `lammps` module to select what type of data to request from computes or fixes. See `_LMP_TYPE_CONST` for the equivalent constants in the C library interface. Used in `lammps.extract_compute()`, `lammps.extract_fix()`, and their NumPy variants `lammps.numpy.extract_compute()` and `lammps.numpy.extract_fix()`.

### Variable Type Constants

LMP_VAR_EQUAL, LMP_VAR_ATOM

  Constants in the `lammps` module to select what type of variable to query when calling `lammps.extract_variable()`. See also: variable command.

### Classes representing internal objects

class lammps.NeighList(lmp, idx)

  This is a wrapper class that exposes the contents of a neighbor list.

  It can be used like a regular Python list. Each element is a tuple of:

  - the atom local index

  - its number of neighbors

  - and a pointer to an c_int array containing local atom indices of its neighbors

  Internally it uses the lower-level LAMMPS C-library interface.

  Parameters:

    - lmp (lammps) – reference to instance of `lammps`

    - idx (int) – neighbor list index

  property size
    Returns:

      number of elements in neighbor list

  get(element)

    Access a specific neighbor list entry. “element” must be a number from 0 to the size-1 of the list

    Returns:

      tuple with atom local index, number of neighbors and ctypes pointer to neighbor’s local atom indices

    Return type:

      (int, int, ctypes.POINTER(c_int))

  find(iatom)

    Find the neighbor list for a specific (local) atom iatom. If there is no list for iatom, (-1, None) is returned.

    Returns:

      tuple with number of neighbors and ctypes pointer to neighbor’s local atom indices

    Return type:

      (int, ctypes.POINTER(c_int))

class lammps.numpy_wrapper.NumPyNeighList(lmp, idx)

  This is a wrapper class that exposes the contents of a neighbor list.

  It can be used like a regular Python list. Each element is a tuple of:

  - the atom local index

  - a NumPy array containing the local atom indices of its neighbors

  Internally it uses the lower-level LAMMPS C-library interface.

  Parameters:

    - lmp (lammps) – reference to instance of `lammps`

    - idx (int) – neighbor list index

  get(element)

    Access a specific neighbor list entry. “element” must be a number from 0 to the size-1 of the list

    Returns:

      tuple with atom local index, numpy array of neighbor local atom indices

    Return type:

      (int, numpy.array)

  find(iatom)

    Find the neighbor list for a specific (local) atom iatom. If there is no list for iatom, None is returned.

    Returns:

      numpy array of neighbor local atom indices

    Return type:

      numpy.array or None