lammpsparser 0.0.1__tar.gz

lammpsparser-0.0.1/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2023, pyiron
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

lammpsparser-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: lammpsparser
+Version: 0.0.1
+Summary: Vector-oriented LAMMPS interface to rapidly iterate over series of atomistic structures or interatomic potentials.
+Project-URL: Homepage, https://github.com/pyiron/lammpsparser
+Project-URL: Documentation, https://github.com/pyiron/lammpsparser
+Project-URL: Repository, https://github.com/pyiron/lammpsparser
+Author-email: Jan Janssen <janssen@mpie.de>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2023, pyiron
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        * Redistributions of source code must retain the above copyright notice, this
+          list of conditions and the following disclaimer.
+        
+        * Redistributions in binary form must reproduce the above copyright notice,
+          this list of conditions and the following disclaimer in the documentation
+          and/or other materials provided with the distribution.
+        
+        * Neither the name of the copyright holder nor the names of its
+          contributors may be used to endorse or promote products derived from
+          this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+License-File: LICENSE
+Keywords: pyiron
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: <3.15,>=3.9
+Requires-Dist: ase<=3.27.0,>=3.22.1
+Requires-Dist: numpy<=2.4.2,>=1.26.0
+Requires-Dist: pandas<=3.0.0,>=2.0.3
+Requires-Dist: scipy<=1.17.0,>=1.11.1
+Provides-Extra: h5md
+Requires-Dist: h5py<=3.15.1,>=3.9.0; extra == 'h5md'
+Description-Content-Type: text/markdown
+
+# lammpsparser
+
+[![Pipeline](https://github.com/pyiron/lammpsparser/actions/workflows/pipeline.yml/badge.svg)](https://github.com/pyiron/lammpsparser/actions/workflows/pipeline.yml)
+[![codecov](https://codecov.io/gh/pyiron/lammpsparser/graph/badge.svg?token=OeZVIJ9vyW)](https://codecov.io/gh/pyiron/lammpsparser)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pyiron/lammpsparser/main?urlpath=%2Fdoc%2Ftree%2Fnotebooks%2Fexample.ipynb)
+
+The `lammpsparser` packages provides primarily two functions. A `write_lammps_structure()` function to write an `ase.atoms.Atoms`
+structure to an LAMMPS data file and a `parse_lammps_output_files()` function to parse the `log.lammps`, `dump.out` and
+`dump.h5` files from the LAMMPS `thermo` and `dump` commands. 
+
+## Installation 
+The `lammpsparser` package is distributed via both [pypi](https://pypi.org/project/lammpsparser/):
+```
+pip install lammpsparser
+```
+and [conda-forge](https://anaconda.org/conda-forge/lammpsparser):
+```
+conda install -c conda-forge lammpsparser
+```
+
+## Write LAMMPS structure 
+The `write_lammps_structure()` function is designed to write an `ase.atoms.Atoms` structure to an LAMMPS data file:
+```python
+from lammpsparser import write_lammps_structure
+
+write_lammps_structure(
+    structure,
+    potential_elements,
+    units="metal",
+    file_name="lammps.data",
+    working_directory=None,
+)
+```
+The `structure` parameter refers to the `ase.atoms.Atoms` structure and the `potential_elements` refers to the list of 
+elements implemented in the specific interatomic potential. For example the [NiAlH_jea.eam.alloy](https://github.com/lammps/lammps/blob/develop/potentials/NiAlH_jea.eam.alloy)
+potential implements the elements `Ni`, `Al` and `H`, so when writing a structure for a simulation with this potential 
+the `potential_elements=["Ni", "Al", "H"]`. It is important to maintain the order of the elements as LAMMPS internally 
+references the elements based on their index, starting from one. The `units` parameter refers to the LAMMPS internal 
+[units](https://docs.lammps.org/units.html) to convert the `ase.atoms.Atoms` object which is defined in Angstrom to the 
+length scale of the LAMMPS simulation. Finally, `file_name` parameter and the current working directory `working_directory` 
+parameter are designed to select the location where the LAMMPS structure should be written. With the default parameters 
+the LAMMPS structure is written in the `lammps.data` file in the current directory. 
+
+## Parse LAMMPS output
+In addition to writing the LAMMPS input structure `lammpsparser` also provide the `parse_lammps_output_files()` function
+to parse the LAMMPS output files, namely the `log.lammps`, `dump.out` and `dump.h5` files:
+```python
+from lammpsparser import parse_lammps_output_files
+
+parse_lammps_output_files(
+    working_directory,
+    structure,
+    potential_elements,
+    units="metal",
+    dump_h5_file_name="dump.h5",
+    dump_out_file_name="dump.out",
+    log_lammps_file_name="log.lammps",
+)
+```
+In analogy to the `write_lammps_structure()` function the `working_directory` parameter refers to the directory which 
+contains the output files. The `structure` parameter reefers to the `ase.atoms.Atoms` object which should be used as 
+template to parse the structure from the dump files. This structure is again required as LAMMPS internally references 
+elements only by an index, so the template structure is required to map the elements from the interatomic potential back
+to the elements of the `ase.atoms.Atoms` object. In the same way the `potential_elements` refers to the list of 
+elements implemented in the specific interatomic potential. The `units` parameter refers to the LAMMPS internal 
+[units](https://docs.lammps.org/units.html) to convert the `ase.atoms.Atoms` object which is defined in Angstrom to the 
+length scale of the LAMMPS simulation. Finally, the parameters `dump_h5_file_name`, `dump_out_file_name` and `log_lammps_file_name`
+refer to the output file names. 
+
+For the `dump.out` file the following LAMMPS `dump` command should be added to the LAMMPS input file:
+```
+dump 1 all custom 100 dump.out id type xsu ysu zsu fx fy fz vx vy vz
+dump_modify 1 sort id format line "%d %d %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g"
+```
+
+For the `log.lammps` file the following LAMMPS `thermo` command should be added to the LAMMPS input file:
+```
+thermo_style custom step temp pe etotal pxx pxy pxz pyy pyz pzz vol
+thermo_modify format float %20.15g
+thermo 100
+```
+
+## Usage 
+Currently, the `lammpsparser` parser is primarily used in the [pyiron_atomistics](https://github.com/pyiron/pyiron_atomistics) 
+package and its successor the [atomistics](https://github.com/pyiron/atomistics) package to provide a simple LAMMPS 
+parser. It only depends on `ase`, `numpy`, `pandas` and `scipy` and has an optional dependency on `h5py` to parse the 
+LAMMPS [h5md](https://docs.lammps.org/dump_h5md.html) format. 

lammpsparser-0.0.1/README.md

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+# lammpsparser
+
+[![Pipeline](https://github.com/pyiron/lammpsparser/actions/workflows/pipeline.yml/badge.svg)](https://github.com/pyiron/lammpsparser/actions/workflows/pipeline.yml)
+[![codecov](https://codecov.io/gh/pyiron/lammpsparser/graph/badge.svg?token=OeZVIJ9vyW)](https://codecov.io/gh/pyiron/lammpsparser)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pyiron/lammpsparser/main?urlpath=%2Fdoc%2Ftree%2Fnotebooks%2Fexample.ipynb)
+
+The `lammpsparser` packages provides primarily two functions. A `write_lammps_structure()` function to write an `ase.atoms.Atoms`
+structure to an LAMMPS data file and a `parse_lammps_output_files()` function to parse the `log.lammps`, `dump.out` and
+`dump.h5` files from the LAMMPS `thermo` and `dump` commands. 
+
+## Installation 
+The `lammpsparser` package is distributed via both [pypi](https://pypi.org/project/lammpsparser/):
+```
+pip install lammpsparser
+```
+and [conda-forge](https://anaconda.org/conda-forge/lammpsparser):
+```
+conda install -c conda-forge lammpsparser
+```
+
+## Write LAMMPS structure 
+The `write_lammps_structure()` function is designed to write an `ase.atoms.Atoms` structure to an LAMMPS data file:
+```python
+from lammpsparser import write_lammps_structure
+
+write_lammps_structure(
+    structure,
+    potential_elements,
+    units="metal",
+    file_name="lammps.data",
+    working_directory=None,
+)
+```
+The `structure` parameter refers to the `ase.atoms.Atoms` structure and the `potential_elements` refers to the list of 
+elements implemented in the specific interatomic potential. For example the [NiAlH_jea.eam.alloy](https://github.com/lammps/lammps/blob/develop/potentials/NiAlH_jea.eam.alloy)
+potential implements the elements `Ni`, `Al` and `H`, so when writing a structure for a simulation with this potential 
+the `potential_elements=["Ni", "Al", "H"]`. It is important to maintain the order of the elements as LAMMPS internally 
+references the elements based on their index, starting from one. The `units` parameter refers to the LAMMPS internal 
+[units](https://docs.lammps.org/units.html) to convert the `ase.atoms.Atoms` object which is defined in Angstrom to the 
+length scale of the LAMMPS simulation. Finally, `file_name` parameter and the current working directory `working_directory` 
+parameter are designed to select the location where the LAMMPS structure should be written. With the default parameters 
+the LAMMPS structure is written in the `lammps.data` file in the current directory. 
+
+## Parse LAMMPS output
+In addition to writing the LAMMPS input structure `lammpsparser` also provide the `parse_lammps_output_files()` function
+to parse the LAMMPS output files, namely the `log.lammps`, `dump.out` and `dump.h5` files:
+```python
+from lammpsparser import parse_lammps_output_files
+
+parse_lammps_output_files(
+    working_directory,
+    structure,
+    potential_elements,
+    units="metal",
+    dump_h5_file_name="dump.h5",
+    dump_out_file_name="dump.out",
+    log_lammps_file_name="log.lammps",
+)
+```
+In analogy to the `write_lammps_structure()` function the `working_directory` parameter refers to the directory which 
+contains the output files. The `structure` parameter reefers to the `ase.atoms.Atoms` object which should be used as 
+template to parse the structure from the dump files. This structure is again required as LAMMPS internally references 
+elements only by an index, so the template structure is required to map the elements from the interatomic potential back
+to the elements of the `ase.atoms.Atoms` object. In the same way the `potential_elements` refers to the list of 
+elements implemented in the specific interatomic potential. The `units` parameter refers to the LAMMPS internal 
+[units](https://docs.lammps.org/units.html) to convert the `ase.atoms.Atoms` object which is defined in Angstrom to the 
+length scale of the LAMMPS simulation. Finally, the parameters `dump_h5_file_name`, `dump_out_file_name` and `log_lammps_file_name`
+refer to the output file names. 
+
+For the `dump.out` file the following LAMMPS `dump` command should be added to the LAMMPS input file:
+```
+dump 1 all custom 100 dump.out id type xsu ysu zsu fx fy fz vx vy vz
+dump_modify 1 sort id format line "%d %d %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g"
+```
+
+For the `log.lammps` file the following LAMMPS `thermo` command should be added to the LAMMPS input file:
+```
+thermo_style custom step temp pe etotal pxx pxy pxz pyy pyz pzz vol
+thermo_modify format float %20.15g
+thermo 100
+```
+
+## Usage 
+Currently, the `lammpsparser` parser is primarily used in the [pyiron_atomistics](https://github.com/pyiron/pyiron_atomistics) 
+package and its successor the [atomistics](https://github.com/pyiron/atomistics) package to provide a simple LAMMPS 
+parser. It only depends on `ase`, `numpy`, `pandas` and `scipy` and has an optional dependency on `h5py` to parse the 
+LAMMPS [h5md](https://docs.lammps.org/dump_h5md.html) format. 

lammpsparser-0.0.1/pyproject.toml

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+[build-system]
+requires = [
+    "ase", 
+    "numpy", 
+    "h5py", 
+    "pandas", 
+    "scipy", 
+    "hatchling==1.28.0",
+    "hatch-vcs==0.5.0",
+]
+build-backend = "hatchling.build"
+
+[project]
+name = "lammpsparser"
+description = "Vector-oriented LAMMPS interface to rapidly iterate over series of atomistic structures or interatomic potentials."
+authors = [
+    { name = "Jan Janssen", email = "janssen@mpie.de" },
+]
+readme = "README.md"
+license = { file = "LICENSE" }
+keywords = ["pyiron"]
+requires-python = ">=3.9, <3.15"
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Topic :: Scientific/Engineering :: Physics",
+    "License :: OSI Approved :: BSD License",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+]
+dependencies = [
+    "ase>=3.22.1,<=3.27.0",
+    "numpy>=1.26.0,<=2.4.2",
+    "pandas>=2.0.3,<=3.0.0",
+    "scipy>=1.11.1,<=1.17.0",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/pyiron/lammpsparser"
+Documentation = "https://github.com/pyiron/lammpsparser"
+Repository = "https://github.com/pyiron/lammpsparser"
+
+[project.optional-dependencies]
+h5md = ["h5py>=3.9.0,<=3.15.1"]
+
+[tool.hatch.build]
+include = [
+    "src/lammpsparser"
+]
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/lammpsparser/_version.py"
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "src/lammpsparser"
+]
+
+[tool.hatch.build.targets.wheel]
+packages = [
+    "src/lammpsparser"
+]
+
+[tool.hatch.version]
+source = "vcs"
+path = "src/lammpsparser/_version.py"
+
+[tool.coverage.run]
+source = ["lammpsparser"]
+command_line = "-m unittest discover tests"

lammpsparser-0.0.1/src/lammpsparser/__init__.py

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+import lammpsparser._version
+from lammpsparser.compatibility.calculate import calc_md, calc_minimize, calc_static
+from lammpsparser.compatibility.file import (
+    lammps_file_initialization,
+    lammps_file_interface_function,
+)
+from lammpsparser.output import parse_lammps_output as parse_lammps_output_files
+from lammpsparser.potential import (
+    get_potential_by_name,
+    get_potential_dataframe,
+    validate_potential_dataframe,
+)
+from lammpsparser.structure import write_lammps_datafile as write_lammps_structure
+
+DUMP_COMMANDS = [
+    "dump 1 all custom 100 dump.out id type xsu ysu zsu fx fy fz vx vy vz\n",
+    'dump_modify 1 sort id format line "%d %d %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g"\n',
+]
+
+THERMO_COMMANDS = [
+    "thermo_style custom step temp pe etotal pxx pxy pxz pyy pyz pzz vol\n",
+    "thermo_modify format float %20.15g\n",
+    "thermo 100\n",
+]
+
+__version__ = lammpsparser._version.__version__
+__all__ = [
+    "calc_md",
+    "calc_minimize",
+    "calc_static",
+    "get_potential_by_name",
+    "get_potential_dataframe",
+    "lammps_file_initialization",
+    "lammps_file_interface_function",
+    "parse_lammps_output_files",
+    "validate_potential_dataframe",
+    "write_lammps_structure",
+]

lammpsparser-0.0.1/src/lammpsparser/_version.py

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+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '0.0.1'
+__version_tuple__ = version_tuple = (0, 0, 1)
+
+__commit_id__ = commit_id = None