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.. _particles-input:

Input

The present section describes in details the different operators used for simulation's setup, post-analysis, visualization and I/O operations in Molecular Dynamics simulations using exaStamp.

.. code-block:: yaml

input_data: - domain - init_rcb_grid - particle_regions - lattice

.. _builtin-particles:

Built-in particle creation

.. _input-lattice:

Lattice generator

.. _input-bulk-lattice:

Bulk lattice generator

.. _external-readers:

Reading external files

.. _input-read-dump-atoms:

Readers of restart files for atomic systems

.. _input-read-dump-mol:

Readers of restart files for flexible molecules systems

.. _input-read-dump-rigidmol:

Readers of restart files for rigid molecules systems

.. _input-read-xyz-xform:

Readers of xyz File

  • Name: read_xyz
  • Description: This operator reads a file written according to the xyz format.
  • Parameters:
  • bounds_mode : default mode corresponde to ReadBoundsSelectionMode.
  • enlarge_bounds : Define a layer around the volume size in the xyz file. Default size is 0.
  • file : File name, this parameter is required.
  • pbc_adjust_xform : Ajust the form.

Reading external file formats

.. warning:: Only supported for atomic systems

.. warning:: If multiple structures are present in the file, the operator will always read the first one.

In addition to :ref:builtin-particles creation <builtin-particles> and :ref:restart files<input-read-dump-atoms>, ExaStamp can read external file formats though the read_external_file_format operator.

.. code-block:: yaml

read_external_file_format: file: /path/to/example-file.xyz.gz format: xyz compression: gz units_style: metal style_style: full

.. list-table:: :widths: 10 40 10 :header-rows: 1

    • Property
    • Description
    • Data Type
    • file
    • File name
    • string
    • format
    • File format extension (see :ref:supported format<input-supported-ext-format>)
    • string
    • compression
    • File compression extension (gz , bz2 , xz)
    • string
    • units_style
    • LAMMPS units style (only used for LAMMPS format)
    • string
    • atom_style
    • LAMMPS atom style (only used for LAMMPS format)
    • string

Only the file parameters is required. By default, format and compression are deduced from the file's extension. The units_style and atom_style parametyers are used only with LAMMPS format to define the unit system and the atom style.

.. _input-supported-ext-format:

Supported file formats

Currently ExaStamp support the following external file formats:

.. list-table:: :widths: 40 40 40 :header-rows: 1

    • Name
    • Description
    • Extension
    • LAMMPS data
    • File format used by LAMMPS <https://docs.lammps.org/Run_formats.html#input-file>_
    • lmp, lmp-data, data
    • LAMMPS Dump
    • File format used by LAMMPS <https://docs.lammps.org/Run_formats.html#input-file>_
    • dump, lmp-dump
    • XYZ
    • Extended XYZ <https://github.com/libAtoms/extxyz?tab=readme-ov-file#xyz-file>_ format.
    • xyz