lammpsparser 0.0.1__py3-none-any.whl

lammpsparser/units.py

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+# coding: utf-8
+# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
+# Distributed under the terms of "New BSD License", see the LICENSE file.
+
+from __future__ import annotations
+
+import warnings
+from typing import Any, Dict, List, Union
+
+import numpy as np
+import scipy.constants as spc
+
+__author__ = "Joerg Neugebauer, Sudarsan Surendralal, Jan Janssen"
+__copyright__ = (
+    "Copyright 2021, Max-Planck-Institut für Eisenforschung GmbH - "
+    "Computational Materials Design (CM) Department"
+)
+
+
+# Conversion factors for transfroming pyiron units to Lammps units (alphabetical)
+
+AMU_TO_G = spc.atomic_mass * spc.kilo
+AMU_TO_KG = spc.atomic_mass
+ANG_PER_FS_TO_ANG_PER_PS = spc.pico / spc.femto
+ANG_PER_FS_TO_BOHR_PER_FS = spc.angstrom / spc.physical_constants["Bohr radius"][0]
+ANG_PER_FS_TO_CM_PER_S = (spc.angstrom / spc.femto) / spc.centi
+ANG_PER_FS_TO_M_PER_S = spc.angstrom / spc.femto
+ANG_TO_BOHR = spc.angstrom / spc.physical_constants["Bohr radius"][0]
+ANG_TO_CM = spc.angstrom / spc.centi
+ANG_TO_M = spc.angstrom
+EL_TO_COUL = spc.elementary_charge
+EV_PER_ANG_TO_DYNE = (spc.electron_volt / spc.angstrom) / spc.dyne
+EV_PER_ANG_TO_HA_PER_BOHR = (
+    spc.physical_constants["electron volt-hartree relationship"][0]
+    * spc.physical_constants["Bohr radius"][0]
+    / spc.angstrom
+)
+EV_PER_ANG_TO_KCAL_PER_MOL_ANG = spc.eV / (spc.kilo * spc.calorie / spc.N_A)
+EV_PER_ANG_TO_N = spc.electron_volt / spc.angstrom
+EV_TO_ERG = spc.electron_volt / spc.erg
+EV_TO_HA = spc.physical_constants["electron volt-hartree relationship"][0]
+EV_TO_J = spc.electron_volt
+EV_TO_KCAL_PER_MOL = spc.eV / (spc.kilo * spc.calorie / spc.N_A)
+FS_TO_PS = spc.femto / spc.pico
+FS_TO_S = spc.femto
+GPA_TO_ATM = spc.giga / spc.atm
+GPA_TO_BAR = spc.giga / spc.bar
+GPA_TO_BARYE = spc.giga / (spc.micro * spc.bar)  # "barye" = 1e-6 bar
+GPA_TO_PA = spc.giga
+
+# Conversions for most of the Lammps units to Pyiron units
+# Lammps units source doc: https://lammps.sandia.gov/doc/units.html
+# Pyrion units source doc: https://pyiron.readthedocs.io/en/latest/source/faq.html
+# At time of writing, not all these conversion factors are used, but may be helpful later.
+
+LAMMPS_UNIT_CONVERSIONS: Dict[str, Dict[str, float]] = {
+    "metal": {
+        "mass": 1.0,
+        "distance": 1.0,
+        "time": FS_TO_PS,
+        "energy": 1.0,
+        "velocity": ANG_PER_FS_TO_ANG_PER_PS,
+        "force": 1.0,
+        "temperature": 1.0,
+        "pressure": GPA_TO_BAR,
+        "charge": 1.0,
+        "natoms": 1,
+    },
+    "si": {
+        "mass": AMU_TO_KG,
+        "distance": ANG_TO_M,
+        "time": FS_TO_S,
+        "energy": EV_TO_J,
+        "velocity": ANG_PER_FS_TO_M_PER_S,
+        "force": EV_PER_ANG_TO_N,
+        "temperature": 1.0,
+        "pressure": GPA_TO_PA,
+        "charge": EL_TO_COUL,
+        "natoms": 1,
+    },
+    "cgs": {
+        "mass": AMU_TO_G,
+        "distance": ANG_TO_CM,
+        "time": FS_TO_S,
+        "energy": EV_TO_ERG,
+        "velocity": ANG_PER_FS_TO_CM_PER_S,
+        "force": EV_PER_ANG_TO_DYNE,
+        "temperature": 1.0,
+        "pressure": GPA_TO_BARYE,
+        "charge": 4.8032044e-10,  # In statCoulombs, but these are deprecated and thus not in scipt.constants
+        "natoms": 1,
+    },
+    "real": {
+        "mass": 1.0,
+        "distance": 1.0,
+        "time": 1.0,
+        "energy": EV_TO_KCAL_PER_MOL,
+        "velocity": 1.0,
+        "force": EV_PER_ANG_TO_KCAL_PER_MOL_ANG,
+        "temperature": 1.0,
+        "pressure": GPA_TO_ATM,
+        "charge": 1.0,
+        "natoms": 1,
+    },
+    "electron": {
+        "mass": 1.0,
+        "distance": ANG_TO_BOHR,
+        "time": 1.0,
+        "energy": EV_TO_HA,
+        "velocity": ANG_PER_FS_TO_BOHR_PER_FS,
+        "force": EV_PER_ANG_TO_HA_PER_BOHR,
+        "temperature": 1.0,
+        "pressure": GPA_TO_PA,
+        "charge": 1.0,
+        "natoms": 1,
+    },
+}
+
+# Define conversion for volumes based on distances
+for values in LAMMPS_UNIT_CONVERSIONS.values():
+    values["volume"] = values["distance"] ** 3
+    values["dimensionless_integer_quantity"] = 1
+
+
+# Hard coded list of all quantities we store in pyiron and the type of quantity it stores (Expand if necessary)
+_conversion_dict: Dict[str, List[str]] = dict()
+_conversion_dict["distance"] = [
+    "positions",
+    "cells",
+    "unwrapped_positions",
+    "mean_unwrapped_positions",
+]
+_conversion_dict["volume"] = ["volume", "volumes"]
+_conversion_dict["pressure"] = ["pressure", "pressures", "mean_pressures"]
+_conversion_dict["time"] = ["time"]
+_conversion_dict["energy"] = [
+    "energy_tot",
+    "energy_pot",
+    "energy_pot_per_atom",
+    "energy_kin_per_atom",
+    "mean_energy_pot",
+]
+_conversion_dict["temperature"] = ["temperature", "temperatures"]
+_conversion_dict["velocity"] = ["velocity", "velocities", "mean_velocities"]
+_conversion_dict["mass"] = ["mass"]
+_conversion_dict["charge"] = ["charges", "charge"]
+_conversion_dict["force"] = ["forces", "force", "mean_forces"]
+_conversion_dict["dimensionless_integer_quantity"] = ["steps", "indices"]
+_conversion_dict["natoms"] = ["natoms"]
+
+# Reverse _conversion_dict
+quantity_dict: Dict[str, str] = dict()
+for key, val in _conversion_dict.items():
+    for v in val:
+        quantity_dict[v] = key
+
+# Data type dict to ensure that the units are converted to the proper units
+dtype_dict: Dict[str, Any] = dict()
+for key, val in _conversion_dict.items():
+    for v in val:
+        # Everything except dimensionless integer quantities are stored as floats
+        if key in ["dimensionless_integer_quantity"]:
+            dtype_dict[v] = int
+        else:
+            dtype_dict[v] = np.float64
+
+
+class UnitConverter:
+    """This is a class to aid conversion of physical quantities between LAMMPS and pyiron units."""
+
+    def __init__(self, units: str):
+        """
+        Initialize the class by specifiying the type of lammps units used
+
+        Args:
+            units (str): The type of LAMMPS units used (eg. metal, real, cgs, lj, etc.)
+
+        """
+        self._units = units
+        self._dict: Dict[str, float] = LAMMPS_UNIT_CONVERSIONS[self._units]
+
+    def __getitem__(self, quantity: str) -> float:
+        """
+        Get quantity from `_dict`
+
+        Args:
+            quantity (str): The physical quantity
+
+        Returns:
+            float: The conversion factor
+        """
+        return self._dict[quantity]
+
+    def lammps_to_pyiron(self, quantity: str) -> float:
+        """
+        Get the conversion factor for a given physical quantity to be converted from LAMMPS to pyiron units
+
+        Args:
+            quantity (str): The physical quantity (must be a key in the dictionary `_conversion_dict`)
+
+        Returns:
+
+            float: The conversion factor
+
+        """
+        return 1.0 / self[quantity]
+
+    def pyiron_to_lammps(self, quantity: str) -> float:
+        """
+        Get the conversion factor for a given physical quantity to be converted from pyiron to LAMMPS units
+
+        Args:
+            quantity (str): The physical quantity (must be a key in the dictionary `_conversion_dict`)
+
+        Returns:
+
+            float: The conversion factor
+
+        """
+        return self[quantity]
+
+    def convert_array_to_pyiron_units(
+        self, array: Union[np.ndarray, list], label: str
+    ) -> np.ndarray:
+        """
+        Convert a labelled numpy array into pyiron units based on the physical quantity the label corresponds to
+
+        Args:
+            array (numpy.ndarray/list): The array to be converted
+            label (str): The label of the quantity (must be a key in the dictionary `quantity_dict`)
+
+        Returns:
+            ndarray: The array after conversion
+
+        """
+        if label in quantity_dict.keys():
+            return np.array(
+                np.array(array) * self.lammps_to_pyiron(quantity_dict[label]),
+                dtype=dtype_dict[label],
+            )
+        else:
+            warnings.warn(
+                message="Warning: Couldn't determine the LAMMPS to pyiron unit conversion type of quantity "
+                f"{label}. Returning un-normalized quantity"
+            )
+            return np.array(array)

lammpsparser-0.0.1.dist-info/METADATA

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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.dist-info/RECORD

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lammpsparser-0.0.1.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: hatchling 1.28.0
+Root-Is-Purelib: true
+Tag: py3-none-any

lammpsparser-0.0.1.dist-info/licenses/LICENSE

@@ -0,0 +1,29 @@
+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.