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.

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

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=0)¶

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 has to provided as vartype parameter which may be one of two constants: LMP_VAR_EQUAL or LMP_VAR_ATOM; it defaults to equal-style variables. The group parameter is only used for atom-style variables and defaults to the group “all” if set to None, which is the default.

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

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

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.

New in version 28Jul2021.

Returns: a tuple with the number of bonds and a list of c_int or c_long
Return type: (int, 3*nbonds*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

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.

New in version 9Oct2020.

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.

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.

New in version 9Oct2020.

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

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

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

New in version 9Oct2020.

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

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

New in version 9Oct2020.

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

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

New in version 10Mar2021.

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.

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

New in version 28Jul2021.

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.

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

New in version 28Jul2021.

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.

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

New in version 28Jul2021.

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.

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

New in version 28Jul2021.

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.

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

New in version 28Jul2021.

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

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

New in version 28Jul2021.

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.

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

New in version 28Jul2021.

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

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) – 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

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.

New in version 28Jul2021.

Returns: the requested data as a 2d-integer numpy array
Return type: numpy.array(nbonds,3)

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.

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.

Changed in version 28Jul2021.

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.

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.

New in version 28Jul2021.

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.

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.

New in version 28Jul2021.

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)¶

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.

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

All thermo output during the run is captured and saved as new entry in PyLammps.runs. The latest run can be retrieved by PyLammps.last_run.

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 position¶

Getter: Return position of atom
Setter: Set position of atom
Type: tuple (float, float, float)

property force¶

Return the total force acting on the atom

Type: tuple (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: tuple (float, float)

property velocity¶: Access to velocity of an atom :getter: Return velocity of atom :setter: Set velocity of atom :type: tuple (float, float)

property force¶

Access to force of an atom

Type: tuple (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

2.4. The lammps Python module¶

2.4.1. The lammps class API¶

2.4.2. The PyLammps class API¶

2.4.3. The IPyLammps class API¶

2.4.4. Additional components of the lammps module¶

Data Types¶

Style Constants¶

Type Constants¶

Variable Type Constants¶

Classes representing internal objects¶

2.4. The `lammps` Python module¶

2.4.1. The `lammps` class API¶

2.4.2. The `PyLammps` class API¶

2.4.3. The `IPyLammps` class API¶

2.4.4. Additional components of the `lammps` module¶