├── .github └── workflows │ ├── main.yml │ └── pythonpackage.yml ├── .gitignore ├── LICENSE ├── README.md ├── docs ├── Makefile ├── about.rst ├── api_reference │ └── index.rst ├── conf.py ├── getting_started │ ├── index.rst │ └── python │ │ └── getting_started.py ├── index.rst ├── installation.rst └── requirements.txt ├── examples ├── logfiles │ └── crack_log.lammps └── plot_logdata.py ├── lammps_logfile ├── File.py ├── __init__.py ├── cmd_interface.py └── utils.py ├── setup.py └── tests ├── __init__.py ├── data ├── in.crack └── log.lammps └── test_File.py /.github/workflows/main.yml: -------------------------------------------------------------------------------- 1 | name: build docs 2 | on: 3 | push: 4 | branches: 5 | - master 6 | 7 | jobs: 8 | deploy: 9 | runs-on: ubuntu-22.04 10 | steps: 11 | - uses: actions/checkout@v2 12 | 13 | - name: Setup Python 14 | uses: actions/setup-python@v2 15 | with: 16 | python-version: '3.10' 17 | 18 | - name: Upgrade pip 19 | run: | 20 | # install pip=>20.1 to use "pip cache dir" 21 | python3 -m pip install --upgrade pip 22 | - name: Get pip cache dir 23 | id: pip-cache 24 | run: echo "::set-output name=dir::$(pip cache dir)" 25 | 26 | - name: Cache dependencies 27 | uses: actions/cache@v1 28 | with: 29 | path: ${{ steps.pip-cache.outputs.dir }} 30 | key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} 31 | restore-keys: | 32 | ${{ runner.os }}-pip- 33 | - name: Install dependencies 34 | run: | 35 | python3 -m pip install -r ./docs/requirements.txt 36 | python3 -m pip install . 37 | 38 | - name: Build 39 | run: | 40 | cd docs && make examples && make html 41 | 42 | - name: Deploy 43 | uses: peaceiris/actions-gh-pages@v3 44 | with: 45 | github_token: ${{ secrets.GITHUB_TOKEN }} 46 | force_orphan: true 47 | publish_dir: ./docs/_build/html 48 | -------------------------------------------------------------------------------- /.github/workflows/pythonpackage.yml: -------------------------------------------------------------------------------- 1 | name: Install and tests 2 | 3 | on: [push] 4 | 5 | jobs: 6 | build: 7 | 8 | runs-on: ubuntu-latest 9 | strategy: 10 | max-parallel: 4 11 | matrix: 12 | python-version: [3.10.15] 13 | 14 | steps: 15 | - uses: actions/checkout@v1 16 | - name: Set up Python ${{ matrix.python-version }} 17 | uses: actions/setup-python@v1 18 | with: 19 | python-version: ${{ matrix.python-version }} 20 | - name: Install dependencies 21 | run: | 22 | python -m pip install --upgrade pip 23 | 24 | - name: setup 25 | run: | 26 | pip install . 27 | - name: Test with pytest 28 | run: | 29 | pip install pytest 30 | pytest 31 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | build/ 12 | develop-eggs/ 13 | dist/ 14 | downloads/ 15 | eggs/ 16 | .eggs/ 17 | lib/ 18 | lib64/ 19 | parts/ 20 | sdist/ 21 | var/ 22 | wheels/ 23 | *.egg-info/ 24 | .installed.cfg 25 | *.egg 26 | MANIFEST 27 | 28 | # PyInstaller 29 | # Usually these files are written by a python script from a template 30 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 31 | *.manifest 32 | *.spec 33 | 34 | # Installer logs 35 | pip-log.txt 36 | pip-delete-this-directory.txt 37 | 38 | # Unit test / coverage reports 39 | htmlcov/ 40 | .tox/ 41 | .coverage 42 | .coverage.* 43 | .cache 44 | nosetests.xml 45 | coverage.xml 46 | *.cover 47 | .hypothesis/ 48 | .pytest_cache/ 49 | 50 | # Translations 51 | *.mo 52 | *.pot 53 | 54 | # Django stuff: 55 | *.log 56 | local_settings.py 57 | db.sqlite3 58 | 59 | # Flask stuff: 60 | instance/ 61 | .webassets-cache 62 | 63 | # Scrapy stuff: 64 | .scrapy 65 | 66 | # Sphinx documentation 67 | docs/_build/ 68 | 69 | # PyBuilder 70 | target/ 71 | 72 | # Jupyter Notebook 73 | .ipynb_checkpoints 74 | 75 | # pyenv 76 | .python-version 77 | 78 | # celery beat schedule file 79 | celerybeat-schedule 80 | 81 | # SageMath parsed files 82 | *.sage.py 83 | 84 | # Environments 85 | .env 86 | .venv 87 | env/ 88 | venv/ 89 | ENV/ 90 | env.bak/ 91 | venv.bak/ 92 | 93 | # Spyder project settings 94 | .spyderproject 95 | .spyproject 96 | 97 | # Rope project settings 98 | .ropeproject 99 | 100 | # mkdocs documentation 101 | /site 102 | 103 | # mypy 104 | .mypy_cache/ 105 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | ![](https://github.com/henriasv/lammps-logfile/workflows/Install%20and%20tests/badge.svg) 2 | # LAMMPS logfile reader 3 | Tool to read a logfile produced by [LAMMPS](https://lammps.sandia.gov) into a simple python data structure with a `get()`-function providing the log data. 4 | 5 | ## Installation 6 | From pypi (preferred/stable) 7 | ``` 8 | pip install lammps-logfile 9 | ``` 10 | Depending on your python installation, you may have to use `pip3` instead of `pip`. This is usualy the case if you need to run `python3` rather than `python` to run python version 3. 11 | 12 | Install using pip directly from github to get the latest (possibly unstable) version: 13 | ``` 14 | pip install git+https://github.com/henriasv/lammps-logfile.git 15 | ``` 16 | Or by cloning the repository: 17 | ``` 18 | git clone https://github.com/henriasv/lammps-logfile.git 19 | cd lammps-logfile 20 | pip3 install . 21 | ``` 22 | 23 | ## Basic usage 24 | 25 | ``` 26 | import lammps_logfile 27 | 28 | log = lammps_logfile.File("path/to/logfile") 29 | 30 | x = log.get("Time") 31 | y = log.get("Temp") 32 | 33 | import matplotlib.pyplot as plt 34 | plt.plot(x, y) 35 | plt.show() 36 | ``` 37 | This will give the concatenated log entries of all the runs where the style of the thermo output didn't change with respect to the last run. I.e. if the entries in the `thermo_style` was not changed between runs it will contain the log data for all the timesteps. If the `thermo_style` *was* changed, `x` and `y` will contain the data from all the timesteps after the `thermo_style` was changed for the last time. 38 | 39 | ## Multiple runs in the same log file 40 | If multiple run statements have been made in a simulation, these can be retrieved bu supplying the `run_num` keyword to the `get()`-function 41 | 42 | ``` 43 | import lammps_logfile 44 | 45 | log = lammps_logfile.File("path/to/logfile") 46 | 47 | x = log.get("Time", run_num=N) 48 | y = log.get("Temp", run_num=N) 49 | 50 | import matplotlib.pyplot as plt 51 | plt.plot(x, y) 52 | plt.show() 53 | ``` 54 | In this case, `x` and `y` will contain the log data from the `N`'th `run` command in LAMMPS, counting from 0. 55 | 56 | Any invalid call to the `get()`-function will result in the function returning `None`. This happes if the user asks for a thermo propery that does not exist in the log file, or if the user asks for a `run_num` larger than the number of runs in the logfile. 57 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line, and also 5 | # from the environment for the first two. 6 | SPHINXOPTS ?= 7 | SPHINXBUILD ?= sphinx-build 8 | SOURCEDIR = . 9 | BUILDDIR = _build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | .PHONY: examples 18 | examples: 19 | cd getting_started/python && python3 getting_started.py > output.txt && cd ../.. 20 | # Catch-all target: route all unknown targets to Sphinx using the new 21 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 22 | %: Makefile 23 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 24 | 25 | -------------------------------------------------------------------------------- /docs/about.rst: -------------------------------------------------------------------------------- 1 | About lammps-logfile 2 | ======================== 3 | :code:`lammps-logfile` is a lightweight package for reading time-series data from LAMMPS log files. 4 | 5 | Basic usage to get and plot the temperature in a simulation as a function of time is: 6 | 7 | .. code-block:: python 8 | 9 | import lammps_logfile 10 | 11 | log = lammps_logfile.File("log.lammps") 12 | 13 | x = log.get("Time") 14 | y = log.get("Temp") 15 | 16 | import matplotlib.pyplot as plt 17 | plt.plot(x, y) 18 | plt.show() 19 | 20 | 21 | -------------------------------------------------------------------------------- /docs/api_reference/index.rst: -------------------------------------------------------------------------------- 1 | API Reference 2 | ========================= 3 | 4 | File 5 | -------------------------- 6 | .. automodule:: lammps_logfile.File 7 | :members: 8 | 9 | 10 | Utilities 11 | -------------------------- 12 | .. automodule:: lammps_logfile.utils 13 | :members: 14 | 15 | Command line interface 16 | -------------------------- 17 | .. argparse:: 18 | :ref: lammps_logfile.cmd_interface.get_parser 19 | :prog: lammps_logplotter 20 | 21 | Indices and tables 22 | ------------------------ 23 | 24 | * :ref:`genindex` 25 | * :ref:`modindex` 26 | * :ref:`search` -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- 1 | # Configuration file for the Sphinx documentation builder. 2 | # 3 | # This file only contains a selection of the most common options. For a full 4 | # list see the documentation: 5 | # https://www.sphinx-doc.org/en/master/usage/configuration.html 6 | 7 | # -- Path setup -------------------------------------------------------------- 8 | 9 | # If extensions (or modules to document with autodoc) are in another directory, 10 | # add these directories to sys.path here. If the directory is relative to the 11 | # documentation root, use os.path.abspath to make it absolute, like shown here. 12 | # 13 | import sphinx_rtd_theme 14 | import os 15 | import sys 16 | sys.path.insert(0, os.path.abspath('..')) 17 | 18 | 19 | # -- Project information ----------------------------------------------------- 20 | 21 | project = 'lammps-logfile' 22 | copyright = '2020, Henrik Andersen Sveinsson' 23 | author = 'Henrik Andersen Sveinsson' 24 | 25 | 26 | # -- General configuration --------------------------------------------------- 27 | 28 | # Add any Sphinx extension module names here, as strings. They can be 29 | # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom 30 | # ones. 31 | extensions = [ "sphinx.ext.autodoc", 32 | "sphinx.ext.doctest", 33 | "recommonmark", 34 | "sphinxarg.ext"] 35 | add_module_names = False 36 | 37 | # Add any paths that contain templates here, relative to this directory. 38 | templates_path = ['_templates'] 39 | 40 | # List of patterns, relative to source directory, that match files and 41 | # directories to ignore when looking for source files. 42 | # This pattern also affects html_static_path and html_extra_path. 43 | exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] 44 | 45 | 46 | # -- Options for HTML output ------------------------------------------------- 47 | 48 | # The theme to use for HTML and HTML Help pages. See the documentation for 49 | # a list of builtin themes. 50 | # 51 | html_theme = 'sphinx_rtd_theme' 52 | 53 | # Add any paths that contain custom static files (such as style sheets) here, 54 | # relative to this directory. They are copied after the builtin static files, 55 | # so a file named "default.css" will overwrite the builtin "default.css". 56 | #html_static_path = ['_static'] -------------------------------------------------------------------------------- /docs/getting_started/index.rst: -------------------------------------------------------------------------------- 1 | Getting started 2 | ================== 3 | 4 | Getting log data 5 | ----------------- 6 | 7 | .. literalinclude:: python/getting_started.py 8 | :lines: 1-6 9 | 10 | Now the arrays :code:`t` and :code:`temp` contain the log data corresponding to the :code:`Time` and :code:`Temp` columns in the log file. 11 | 12 | Plotting log data 13 | ----------------- 14 | 15 | .. literalinclude:: python/getting_started.py 16 | :lines: 8-14 17 | 18 | To make the plot pop up in a window rather than being saved to a file, run `plt.show()` rather than `plt.savefig(...)`. 19 | 20 | .. figure:: python/time_temp.png 21 | :scale: 100 % 22 | :alt: Plot of temperature vs. time 23 | 24 | Plot of temperature vs. time 25 | 26 | 27 | Running average 28 | ---------------- 29 | .. literalinclude:: python/getting_started.py 30 | :lines: 16-24 31 | 32 | .. figure:: python/time_temp_avg.png 33 | :scale: 100 % 34 | :alt: Plot of temperature vs. time 35 | 36 | Plot of temperature vs. time. The blue curve is the raw output, whereas in the orange curve the temperature has been smoothed over a 100 log entries wide averaging window. 37 | 38 | What data are available in the log file? 39 | ---------------------------------------- 40 | To inspect what columns are available, you can run the `get_keywords`-method on the `File` object: 41 | 42 | .. code-block:: python 43 | 44 | print(log.get_keywords()) 45 | 46 | This command yields an output like the one below, which shows what columns we may :code:`get` from the :code:`File` object: 47 | 48 | .. literalinclude:: python/output.txt 49 | 50 | Command line tool 51 | ------------------ 52 | The following is the help message from the command line tool `lammps_logplotter` that comes with lammps-logplotter. This tool is meant to quicky inspect lammps log files without having to write a python script. 53 | 54 | .. code-block:: bash 55 | 56 | usage: lammps_logplotter [-h] [-x X] [-y Y [Y ...]] [-a RUNNING_AVERAGE] input_file 57 | 58 | Plot contents from lammps log files 59 | 60 | positional arguments: 61 | input_file Lammps log file containing thermo output from lammps simulation. 62 | 63 | optional arguments: 64 | -h, --help show this help message and exit 65 | -x X Data to plot on the first axis 66 | -y Y [Y ...] Data to plot on the second axis. You can supply several names to get several plot lines in the same figure. 67 | -a RUNNING_AVERAGE, --running_average RUNNING_AVERAGE 68 | Optionally average over this many log entries with a running average. Some thermo properties fluctuate wildly, and often we are interested in te 69 | running average of properties like temperature and pressure. -------------------------------------------------------------------------------- /docs/getting_started/python/getting_started.py: -------------------------------------------------------------------------------- 1 | from lammps_logfile import File 2 | 3 | log = File("../../../examples/logfiles/crack_log.lammps") 4 | 5 | t = log.get("Time") 6 | temp = log.get("Temp") 7 | 8 | import matplotlib.pyplot as plt 9 | 10 | plt.plot(t, temp) 11 | plt.xlabel("Time (ps)") 12 | plt.ylabel("Temperature (K)") 13 | plt.ylim([215, 225]) 14 | plt.savefig("time_temp.png") 15 | 16 | from lammps_logfile import running_mean 17 | 18 | temp_avg = running_mean(temp, 100) 19 | 20 | plt.plot(t, temp_avg) 21 | plt.xlabel("Time (ps)") 22 | plt.ylabel("Temperature (K)") 23 | plt.ylim([215, 225]) 24 | plt.savefig("time_temp_avg.png") 25 | 26 | print(log.get_keywords()) 27 | 28 | -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- 1 | Welcome to lammps-logfile's documentation 2 | ========================================= 3 | 4 | .. toctree:: 5 | :maxdepth: 2 6 | 7 | about 8 | installation 9 | getting_started/index 10 | api_reference/index -------------------------------------------------------------------------------- /docs/installation.rst: -------------------------------------------------------------------------------- 1 | Installation 2 | ====================== 3 | 4 | Install using pip 5 | 6 | .. code-block:: bash 7 | 8 | pip install lammps-logfile 9 | 10 | or manually 11 | 12 | .. code-block:: bash 13 | 14 | git clone https://github.com/henriasv/lammps-logfile 15 | cd lammps-logfile 16 | python setup.py 17 | 18 | -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- 1 | sphinx 2 | sphinx_rtd_theme 3 | recommonmark 4 | sphinx.argparse -------------------------------------------------------------------------------- /examples/plot_logdata.py: -------------------------------------------------------------------------------- 1 | import os 2 | import matplotlib.pyplot as plt 3 | 4 | import lammps_logfile 5 | 6 | log = lammps_logfile.File(os.path.join(os.path.dirname(__file__), "logfiles", "crack_log.lammps")) 7 | 8 | print("Log keywords: ", log.get_keywords()) 9 | 10 | x = log.get("Time") 11 | y = log.get("Pyy") 12 | 13 | plt.figure(figsize=(6,6)) 14 | plt.subplot(221) 15 | plt.plot(x, y) 16 | plt.xlabel("$t$") 17 | plt.ylabel("$p_{yy}$") 18 | 19 | plt.subplot(222) 20 | for i in range(log.get_num_partial_logs()): 21 | x = log.get("Time", run_num=i) 22 | y = log.get("Pyy", run_num=i) 23 | plt.plot(x, y) 24 | plt.xlabel("$t$") 25 | plt.ylabel("$p_{yy}$") 26 | 27 | plt.subplot(223) 28 | x = log.get("Time") 29 | y = log.get("Temp") 30 | plt.plot(x, y) 31 | plt.xlabel("$t$") 32 | plt.ylabel("$T$") 33 | 34 | plt.subplot(224) 35 | for i in range(log.get_num_partial_logs()): 36 | x = log.get("Time", run_num=i) 37 | y = log.get("Temp", run_num=i) 38 | plt.plot(x, y) 39 | plt.xlabel("$t$") 40 | plt.ylabel("$T$") 41 | plt.tight_layout() 42 | plt.show() 43 | 44 | -------------------------------------------------------------------------------- /lammps_logfile/File.py: -------------------------------------------------------------------------------- 1 | from io import BytesIO, StringIO 2 | 3 | import numpy as np 4 | import pandas as pd 5 | 6 | 7 | class File: 8 | """Class for handling lammps log files. 9 | 10 | Parameters 11 | ---------------------- 12 | :param ifile: path to lammps log file 13 | :type ifile: string or file 14 | 15 | """ 16 | def __init__(self, ifile): 17 | # Identifiers for places in the log file 18 | self.start_thermo_strings = ["Memory usage per processor", "Per MPI rank memory allocation"] 19 | self.stop_thermo_strings = ["Loop time", "ERROR", "Fix halt condition"] 20 | self.data_dict = {} 21 | self.keywords = [] 22 | self.output_before_first_run = "" 23 | self.partial_logs = [] 24 | if hasattr(ifile, "read"): 25 | self.logfile = ifile 26 | else: 27 | self.logfile = open(ifile, 'r') 28 | self.read_file_to_dict() 29 | 30 | def read_file_to_dict(self): 31 | contents = self.logfile.readlines() 32 | keyword_flag = False 33 | before_first_run_flag = True 34 | i = 0 35 | while i < len(contents): 36 | line = contents[i] 37 | if before_first_run_flag: 38 | self.output_before_first_run += line 39 | 40 | if keyword_flag: 41 | keywords = line.split() 42 | tmpString = "" 43 | # Check wheter any of the thermo stop strings are in the present line 44 | while not sum([string in line for string in self.stop_thermo_strings]) >= 1: 45 | if "\n" in line: 46 | tmpString+=line 47 | i+=1 48 | if i= 1: 68 | keyword_flag = True 69 | before_first_run_flag = False 70 | i += 1 71 | 72 | def flush_dict_and_set_new_keyword(self, keywords): 73 | self.data_dict = {} 74 | for entry in keywords: 75 | self.data_dict[entry] = np.asarray([]) 76 | self.keywords = keywords 77 | 78 | def get(self, entry_name, run_num=-1): 79 | """Get time-series from log file by name. 80 | 81 | Paramerers 82 | -------------------- 83 | :param entry_name: Name of the entry, for example "Temp" 84 | :type entry_name: str 85 | :param run_num: Lammps simulations commonly involve several run-commands. Here you may choose what run you want the log data from. Default of :code:`-1` returns data from all runs concatenated 86 | :type run_num: int 87 | 88 | If the rows in the log file changes between runs, the logs are being flushed. 89 | """ 90 | 91 | if run_num == -1: 92 | if entry_name in self.data_dict.keys(): 93 | return self.data_dict[entry_name] 94 | else: 95 | return None 96 | else: 97 | if len(self.partial_logs) > run_num: 98 | partial_log = self.partial_logs[run_num] 99 | if entry_name in partial_log.keys(): 100 | return partial_log[entry_name] 101 | else: 102 | return None 103 | else: 104 | return None 105 | 106 | def get_keywords(self, run_num=-1): 107 | """Return list of available data columns in the log file.""" 108 | if run_num == -1: 109 | return sorted(self.keywords) 110 | else: 111 | if len(self.partial_logs) > run_num: 112 | return sorted(list(self.partial_logs[run_num].keys())) 113 | else: 114 | return None 115 | 116 | def to_exdir_group(self, name, exdirfile): 117 | group = exdirfile.require_group(name) 118 | for i, log in enumerate(self.partial_logs): 119 | subgroup = group.require_group(str(i)) 120 | for key, value in log.items(): 121 | key = key.replace("/", ".") 122 | subgroup.create_dataset(key, data=value) 123 | 124 | def to_dataframe(self, run_num=-1): 125 | return pd.DataFrame(self.partial_logs[run_num]) 126 | 127 | 128 | def get_num_partial_logs(self): 129 | return len(self.partial_logs) 130 | 131 | @property 132 | def names(self): 133 | """Exposes the keywords returned by get_keywords.""" 134 | return self.get_keywords() 135 | -------------------------------------------------------------------------------- /lammps_logfile/__init__.py: -------------------------------------------------------------------------------- 1 | from .File import File 2 | from .utils import running_mean, get_color_value, get_matlab_color 3 | from .cmd_interface import run -------------------------------------------------------------------------------- /lammps_logfile/cmd_interface.py: -------------------------------------------------------------------------------- 1 | from lammps_logfile import File 2 | from lammps_logfile import running_mean 3 | import argparse 4 | import matplotlib.pyplot as plt 5 | 6 | def get_parser(): 7 | parser = argparse.ArgumentParser(description="Plot contents from lammps log files. Input file argument comes before keyword arguments. ") 8 | parser.add_argument("-x", type=str, default="Time", help="Data to plot on the first axis") 9 | parser.add_argument("-y", type=str, nargs="+", help="Data to plot on the second axis. You can supply several names to get several plot lines in the same figure.") 10 | parser.add_argument("-a", "--running_average", type=int, default=1, help="Optionally average over this many log entries with a running average. Some thermo properties fluctuate wildly, and often we are interested in te running average of properties like temperature and pressure.") 11 | parser.add_argument("input_file", metavar='INPUT_FILE', type=str, help="Lammps log file containing thermo output from lammps simulation.") 12 | parser.add_argument("-o", type=str, dest='fout', default='', help='Save the figure to this file; the format must be supported by matplotlib.') 13 | parser.add_argument("-c", "--columns", action='store_true', default=False, help='Print columns of the lammps logfile') 14 | 15 | return parser 16 | 17 | def run(): 18 | args = get_parser().parse_args() 19 | log = File(args.input_file) 20 | 21 | if args.columns: 22 | print(f"Columns available in log file:\n{' '.join(log.get_keywords())}") 23 | if args.y is None: 24 | exit(0) 25 | 26 | x = log.get(args.x) 27 | if args.running_average >= 2: 28 | x = running_mean(x, args.running_average) 29 | for y in args.y: 30 | data = log.get(y) 31 | if args.running_average >= 2: 32 | data = running_mean(data, args.running_average) 33 | 34 | plt.plot(x, data, label=y) 35 | plt.legend() 36 | plt.show() 37 | if args.fout != '': 38 | plt.savefig(args.fout, dpi=300) 39 | 40 | -------------------------------------------------------------------------------- /lammps_logfile/utils.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import matplotlib 3 | 4 | def running_mean(data, N): 5 | """Calculate running mean of an array-like dataset. 6 | 7 | Parameters 8 | -------------------- 9 | :param data: The array 10 | :type data: 1d array-like 11 | :param N: Width of the averaging window 12 | :type N: int 13 | 14 | """ 15 | 16 | data = np.asarray(data) 17 | if N == 1: 18 | return data 19 | else: 20 | retArray = np.zeros(data.size)*np.nan 21 | padL = int(N/2) 22 | padR = N-padL-1 23 | retArray[padL:-padR] = np.convolve(data, np.ones((N,))/N, mode='valid') 24 | return retArray 25 | 26 | def get_color_value(value, minValue, maxValue, cmap='viridis'): 27 | """Get color from colormap. 28 | 29 | Parameters 30 | ----------------- 31 | :param value: Value used tpo get color from colormap 32 | :param minValue: Minimum value in colormap. Values below this value will saturate on the lower color of the colormap. 33 | :param maxValue: Maximum value in colormap. Values above this value will saturate on the upper color of the colormap. 34 | 35 | :returns: 4-vector containing colormap values. 36 | 37 | This is useful if you are plotting data from several simulations, and want to color them based on some parameters changing between the simulations. For example, you may want the color to gradually change along a clormap as the temperature increases. 38 | 39 | """ 40 | diff = maxValue-minValue 41 | cmap = matplotlib.cm.get_cmap(cmap) 42 | rgba = cmap((value-minValue)/diff) 43 | return rgba 44 | 45 | def get_matlab_color(i): 46 | """Get colors from matlabs standard color order. 47 | 48 | Parameters 49 | ------------- 50 | :param i: Index. Cycles with a period of 7, so calling with 1 returns the same color as calling with 8. 51 | :type i: int 52 | 53 | :returns: color as 3-vector 54 | 55 | """ 56 | colors = np.asarray([ [0, 0.447000000000000, 0.741000000000000], 57 | [0.850000000000000, 0.325000000000000, 0.098000000000000], 58 | [0.929000000000000, 0.694000000000000, 0.125000000000000], 59 | [0.494000000000000, 0.184000000000000, 0.556000000000000], 60 | [0.466000000000000, 0.674000000000000, 0.188000000000000], 61 | [0.301000000000000, 0.745000000000000, 0.933000000000000], 62 | [0.635000000000000, 0.078000000000000, 0.184000000000000]]) 63 | return colors[ i%len(colors) ] 64 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | import setuptools 2 | from setuptools import setup 3 | 4 | with open("README.md", "r") as fh: 5 | long_description = fh.read() 6 | 7 | setup(name='lammps-logfile', 8 | version='1.0.2', 9 | description='Tool to read lammps log files into python data structure', 10 | long_description=long_description, 11 | long_description_content_type="text/markdown", 12 | url='http://github.com/henriasv/lammps-logfile', 13 | author='Henrik Andersen Sveinsson', 14 | author_email='henrik.sveinsson@me.com', 15 | license='GNU GPL v3.0', 16 | packages=setuptools.find_packages(), 17 | test_suite='nose.collector', 18 | tests_require=['nose'], 19 | install_requires=['pandas', 'numpy', 'matplotlib'], 20 | entry_points={ 21 | 'console_scripts': [ 22 | 'lammps_logplotter=lammps_logfile.cmd_interface:run' 23 | ] 24 | }, 25 | zip_safe=False) 26 | -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/henriasv/lammps-logfile/d31b1fb0ae9896507c00877dfca48b05bfdc534e/tests/__init__.py -------------------------------------------------------------------------------- /tests/data/in.crack: -------------------------------------------------------------------------------- 1 | # 2d LJ crack simulation 2 | 3 | dimension 2 4 | boundary s s p 5 | 6 | atom_style atomic 7 | neighbor 0.3 bin 8 | neigh_modify delay 5 9 | 10 | # create geometry 11 | 12 | lattice hex 0.93 13 | region box block 0 100 0 40 -0.25 0.25 14 | create_box 5 box 15 | create_atoms 1 box 16 | 17 | mass 1 1.0 18 | mass 2 1.0 19 | mass 3 1.0 20 | mass 4 1.0 21 | mass 5 1.0 22 | 23 | # LJ potentials 24 | 25 | pair_style lj/cut 2.5 26 | pair_coeff * * 1.0 1.0 2.5 27 | 28 | # define groups 29 | 30 | region 1 block INF INF INF 1.25 INF INF 31 | group lower region 1 32 | region 2 block INF INF 38.75 INF INF INF 33 | group upper region 2 34 | group boundary union lower upper 35 | group mobile subtract all boundary 36 | 37 | region leftupper block INF 20 20 INF INF INF 38 | region leftlower block INF 20 INF 20 INF INF 39 | group leftupper region leftupper 40 | group leftlower region leftlower 41 | 42 | set group leftupper type 2 43 | set group leftlower type 3 44 | set group lower type 4 45 | set group upper type 5 46 | 47 | # initial velocities 48 | 49 | compute new mobile temp 50 | velocity mobile create 0.01 887723 temp new 51 | velocity upper set 0.0 0.3 0.0 52 | velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes 53 | 54 | # fixes 55 | 56 | fix 1 all nve 57 | fix 2 boundary setforce NULL 0.0 0.0 58 | 59 | # run 60 | 61 | timestep 0.003 62 | thermo 100 63 | thermo_style custom step time temp pxx pyy cpuremain 64 | 65 | neigh_modify exclude type 2 3 66 | 67 | run 5000 68 | 69 | thermo_style custom step time temp pxx pyy press cpuremain 70 | 71 | run 5000 72 | 73 | thermo_style custom step temp pxx pyy cpuremain 74 | 75 | run 400 -------------------------------------------------------------------------------- /tests/data/log.lammps: -------------------------------------------------------------------------------- 1 | LAMMPS (22 Jun 2018) 2 | OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:87) 3 | using 1 OpenMP thread(s) per MPI task 4 | # 2d LJ crack simulation 5 | 6 | dimension 2 7 | boundary s s p 8 | 9 | atom_style atomic 10 | neighbor 0.3 bin 11 | neigh_modify delay 5 12 | 13 | # create geometry 14 | 15 | lattice hex 0.93 16 | Lattice spacing in x,y,z = 1.11428 1.92998 1.11428 17 | region box block 0 100 0 40 -0.25 0.25 18 | create_box 5 box 19 | Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569) 20 | 1 by 1 by 1 MPI processor grid 21 | create_atoms 1 box 22 | Created 8141 atoms 23 | Time spent = 0.00101018 secs 24 | 25 | mass 1 1.0 26 | mass 2 1.0 27 | mass 3 1.0 28 | mass 4 1.0 29 | mass 5 1.0 30 | 31 | # LJ potentials 32 | 33 | pair_style lj/cut 2.5 34 | pair_coeff * * 1.0 1.0 2.5 35 | 36 | # define groups 37 | 38 | region 1 block INF INF INF 1.25 INF INF 39 | group lower region 1 40 | 302 atoms in group lower 41 | region 2 block INF INF 38.75 INF INF INF 42 | group upper region 2 43 | 302 atoms in group upper 44 | group boundary union lower upper 45 | 604 atoms in group boundary 46 | group mobile subtract all boundary 47 | 7537 atoms in group mobile 48 | 49 | region leftupper block INF 20 20 INF INF INF 50 | region leftlower block INF 20 INF 20 INF INF 51 | group leftupper region leftupper 52 | 841 atoms in group leftupper 53 | group leftlower region leftlower 54 | 841 atoms in group leftlower 55 | 56 | set group leftupper type 2 57 | 841 settings made for type 58 | set group leftlower type 3 59 | 841 settings made for type 60 | set group lower type 4 61 | 302 settings made for type 62 | set group upper type 5 63 | 302 settings made for type 64 | 65 | # initial velocities 66 | 67 | compute new mobile temp 68 | velocity mobile create 0.01 887723 temp new 69 | velocity upper set 0.0 0.3 0.0 70 | velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes 71 | 72 | # fixes 73 | 74 | fix 1 all nve 75 | fix 2 boundary setforce NULL 0.0 0.0 76 | 77 | # run 78 | 79 | timestep 0.003 80 | thermo 100 81 | thermo_style custom step time temp pxx pyy cpuremain 82 | 83 | neigh_modify exclude type 2 3 84 | 85 | run 5000 86 | Neighbor list info ... 87 | update every 1 steps, delay 5 steps, check yes 88 | max neighbors/atom: 2000, page size: 100000 89 | master list distance cutoff = 2.8 90 | ghost atom cutoff = 2.8 91 | binsize = 1.4, bins = 80 56 1 92 | 1 neighbor lists, perpetual/occasional/extra = 1 0 0 93 | (1) pair lj/cut, perpetual 94 | attributes: half, newton on 95 | pair build: half/bin/atomonly/newton 96 | stencil: half/bin/2d/newton 97 | bin: standard 98 | Per MPI rank memory allocation (min/avg/max) = 3.112 | 3.112 | 3.112 Mbytes 99 | Step Time Temp Pxx Pyy CPULeft 100 | 0 0 0.066999022 -0.08406601 0.023352245 0 101 | 100 0.3 0.062586901 -0.11310916 -0.12882594 4.0526512 102 | 200 0.6 0.061882589 -0.15947586 -0.29123755 3.9601936 103 | 300 0.9 0.062212437 -0.20547907 -0.45464633 3.8933103 104 | 400 1.2 0.062324688 -0.24426358 -0.60503271 3.8236127 105 | 500 1.5 0.062352633 -0.27815189 -0.74875218 3.7779129 106 | 600 1.8 0.062615145 -0.31014555 -0.88379594 3.6933088 107 | 700 2.1 0.06288345 -0.33133642 -1.0125663 3.6005621 108 | 800 2.4 0.06341206 -0.35037809 -1.1344373 3.52275 109 | 900 2.7 0.063615289 -0.36733706 -1.2505378 3.4798663 110 | 1000 3 0.064084368 -0.37838922 -1.3583945 3.4124527 111 | 1100 3.3 0.064762835 -0.38621191 -1.4615187 3.3192973 112 | 1200 3.6 0.065321008 -0.39091417 -1.5578001 3.2478472 113 | 1300 3.9 0.066159989 -0.3939606 -1.6518818 3.3870026 114 | 1400 4.2 0.066915292 -0.39096277 -1.7364292 3.486163 115 | 1500 4.5 0.067935205 -0.38911792 -1.8224931 3.3925409 116 | 1600 4.8 0.068950603 -0.38173567 -1.8978622 3.3557195 117 | 1700 5.1 0.069647678 -0.36882884 -1.9719961 3.3213802 118 | 1800 5.4 0.070589688 -0.35355604 -2.038963 3.2253121 119 | 1900 5.7 0.071376824 -0.33506745 -2.1008265 3.1103899 120 | 2000 6 0.072218214 -0.31363701 -2.1606285 2.9923156 121 | 2100 6.3 0.073139872 -0.29218486 -2.2124962 2.8702529 122 | 2200 6.6 0.074092142 -0.26797305 -2.2605065 2.7532846 123 | 2300 6.9 0.075078297 -0.24243601 -2.3024656 2.640411 124 | 2400 7.2 0.076021461 -0.21236784 -2.3419383 2.5274417 125 | 2500 7.5 0.07677898 -0.17776117 -2.3745273 2.4174831 126 | 2600 7.8 0.077802484 -0.1431674 -2.4033595 2.312941 127 | 2700 8.1 0.078773028 -0.10947863 -2.4268424 2.2132354 128 | 2800 8.4 0.0795636 -0.075949648 -2.4439372 2.1139918 129 | 2900 8.7 0.08053241 -0.040620709 -2.4583448 2.0170037 130 | 3000 9 0.081509075 -0.0066445715 -2.4693983 1.9186533 131 | 3100 9.3 0.082590961 0.026296862 -2.4745466 1.8241662 132 | 3200 9.6 0.083747868 0.058053159 -2.4750398 1.7243286 133 | 3300 9.9 0.084896121 0.089586381 -2.4800392 1.6260691 134 | 3400 10.2 0.085918049 0.1227962 -2.4785809 1.5281092 135 | 3500 10.5 0.08669673 0.15909307 -2.4774432 1.4290658 136 | 3600 10.8 0.087672157 0.19877206 -2.4736765 1.3308412 137 | 3700 11.1 0.088566473 0.23131529 -2.4672682 1.2317458 138 | 3800 11.4 0.089161561 0.26596102 -2.4542366 1.1360173 139 | 3900 11.7 0.089763483 0.29277009 -2.4428439 1.0402159 140 | 4000 12 0.08985281 0.31122192 -2.4251574 0.94414878 141 | 4100 12.3 0.088138682 0.32632891 -2.406837 0.84869343 142 | 4200 12.6 0.086254998 0.33387816 -2.3979692 0.75338155 143 | 4300 12.9 0.085723564 0.34342733 -2.3952074 0.65787515 144 | 4400 13.2 0.086494787 0.34461302 -2.3906185 0.56331614 145 | 4500 13.5 0.08682319 0.33886131 -2.3786501 0.46870711 146 | 4600 13.8 0.087008602 0.32460744 -2.3547476 0.37420783 147 | 4700 14.1 0.087520366 0.29442151 -2.3239268 0.28058808 148 | 4800 14.4 0.088731576 0.25391148 -2.2960552 0.18685521 149 | 4900 14.7 0.089962836 0.21900237 -2.2574458 0.093313777 150 | 5000 15 0.090608908 0.18841703 -2.2179781 0 151 | Loop time of 4.65965 on 1 procs for 5000 steps with 8141 atoms 152 | 153 | Performance: 278132.601 tau/day, 1073.042 timesteps/s 154 | 97.5% CPU use with 1 MPI tasks x 1 OpenMP threads 155 | 156 | MPI task timing breakdown: 157 | Section | min time | avg time | max time |%varavg| %total 158 | --------------------------------------------------------------- 159 | Pair | 3.9478 | 3.9478 | 3.9478 | 0.0 | 84.72 160 | Neigh | 0.19429 | 0.19429 | 0.19429 | 0.0 | 4.17 161 | Comm | 0.0036759 | 0.0036759 | 0.0036759 | 0.0 | 0.08 162 | Output | 0.0041168 | 0.0041168 | 0.0041168 | 0.0 | 0.09 163 | Modify | 0.38046 | 0.38046 | 0.38046 | 0.0 | 8.16 164 | Other | | 0.1293 | | | 2.77 165 | 166 | Nlocal: 8141 ave 8141 max 8141 min 167 | Histogram: 1 0 0 0 0 0 0 0 0 0 168 | Nghost: 0 ave 0 max 0 min 169 | Histogram: 1 0 0 0 0 0 0 0 0 0 170 | Neighs: 71389 ave 71389 max 71389 min 171 | Histogram: 1 0 0 0 0 0 0 0 0 0 172 | 173 | Total # of neighbors = 71389 174 | Ave neighs/atom = 8.76907 175 | Neighbor list builds = 100 176 | Dangerous builds = 0 177 | 178 | thermo_style custom step time temp pxx pyy press cpuremain 179 | 180 | run 5000 181 | Per MPI rank memory allocation (min/avg/max) = 3.114 | 3.114 | 3.114 Mbytes 182 | Step Time Temp Pxx Pyy Press CPULeft 183 | 5000 15 0.090608908 0.18837991 -2.2175412 -1.0145806 0 184 | 5100 15.3 0.091245887 0.14407923 -2.1711508 -1.0135358 4.4449849 185 | 5200 15.6 0.091839804 0.091121561 -2.0998723 -1.0043754 4.3448181 186 | 5300 15.9 0.094453238 0.014115988 -2.021764 -1.003824 4.2634337 187 | 5400 16.2 0.096707467 -0.090196664 -1.9160294 -1.003113 4.1779729 188 | 5500 16.5 0.10033942 -0.21809813 -1.7938504 -1.0059743 4.1051702 189 | 5600 16.8 0.10621254 -0.3489582 -1.6504528 -0.99970551 4.0361934 190 | 5700 17.1 0.11294739 -0.46604782 -1.4626835 -0.96436566 3.9937672 191 | 5800 17.4 0.11606476 -0.52859387 -1.2515736 -0.89008373 3.9104784 192 | 5900 17.7 0.12036583 -0.54743406 -1.067752 -0.80759303 3.8190275 193 | 6000 18 0.12319937 -0.52864435 -0.91180314 -0.72022375 3.7308521 194 | 6100 18.3 0.12750402 -0.48741571 -0.7664699 -0.6269428 3.6385232 195 | 6200 18.6 0.13138215 -0.40723012 -0.6355442 -0.52138716 3.5447954 196 | 6300 18.9 0.13547924 -0.33527477 -0.54607801 -0.44067639 3.4510812 197 | 6400 19.2 0.13787406 -0.28779527 -0.47130925 -0.37955226 3.360955 198 | 6500 19.5 0.14098059 -0.23394595 -0.44459574 -0.33927084 3.2724419 199 | 6600 19.8 0.14427435 -0.2046593 -0.44273376 -0.32369653 3.1779037 200 | 6700 20.1 0.14402616 -0.15224598 -0.40945993 -0.28085295 3.100527 201 | 6800 20.4 0.14650767 -0.13052827 -0.41706736 -0.27379781 3.0109762 202 | 6900 20.7 0.15169782 -0.12366203 -0.41010956 -0.26688579 2.9211366 203 | 7000 21 0.15378158 -0.07576874 -0.40276577 -0.23926725 2.8384817 204 | 7100 21.3 0.15648546 -0.042006532 -0.39284705 -0.21742679 2.7480278 205 | 7200 21.6 0.1586544 -0.015158462 -0.39615573 -0.2056571 2.6563434 206 | 7300 21.9 0.16021716 0.02084344 -0.40989747 -0.19452701 2.5576256 207 | 7400 22.2 0.16305481 0.027777436 -0.45547888 -0.21385072 2.4610896 208 | 7500 22.5 0.16284144 0.079005006 -0.47705735 -0.19902617 2.364706 209 | 7600 22.8 0.16426335 0.07728209 -0.47217063 -0.19744427 2.2714654 210 | 7700 23.1 0.16554325 0.070668071 -0.45276681 -0.19104937 2.1746407 211 | 7800 23.4 0.16829508 0.056401348 -0.42215026 -0.18287445 2.0809541 212 | 7900 23.7 0.17000245 0.082559769 -0.37151525 -0.14447774 1.9876522 213 | 8000 24 0.17149488 0.10974507 -0.35277134 -0.12151313 1.8950588 214 | 8100 24.3 0.17313528 0.10325942 -0.31901721 -0.1078789 1.8009028 215 | 8200 24.6 0.17267217 0.1318115 -0.2919738 -0.080081147 1.70855 216 | 8300 24.9 0.17391638 0.12915917 -0.31054187 -0.090691346 1.6136714 217 | 8400 25.2 0.17382715 0.11504449 -0.32285694 -0.10390622 1.5196391 218 | 8500 25.5 0.17441655 0.10977096 -0.32785489 -0.10904197 1.423041 219 | 8600 25.8 0.17552551 0.10950002 -0.30515982 -0.097829901 1.3278802 220 | 8700 26.1 0.17565159 0.12382868 -0.32804391 -0.10210762 1.2330269 221 | 8800 26.4 0.17832953 0.081307133 -0.31380308 -0.11624797 1.1381309 222 | 8900 26.7 0.17801754 0.10200027 -0.27974562 -0.088872672 1.042844 223 | 9000 27 0.17788921 0.1300792 -0.27419009 -0.072055444 0.94771475 224 | 9100 27.3 0.17860872 0.11537032 -0.2803544 -0.082492039 0.85234547 225 | 9200 27.6 0.17841788 0.12414385 -0.25380882 -0.064832486 0.75768498 226 | 9300 27.9 0.17625963 0.13723586 -0.21105379 -0.036908965 0.6636656 227 | 9400 28.2 0.17801505 0.12331144 -0.21061868 -0.043653619 0.56854242 228 | 9500 28.5 0.17714527 0.15181865 -0.2079837 -0.028082526 0.47324755 229 | 9600 28.8 0.17967835 0.13556573 -0.1990823 -0.03175828 0.3783334 230 | 9700 29.1 0.17705493 0.15394524 -0.17111212 -0.0085834388 0.28408232 231 | 9800 29.4 0.17817334 0.17353827 -0.18089706 -0.003679395 0.19037521 232 | 9900 29.7 0.17661448 0.17217651 -0.15407839 0.0090490616 0.095067632 233 | 10000 30 0.17731223 0.19355368 -0.1423432 0.02560524 0 234 | Loop time of 4.74984 on 1 procs for 5000 steps with 8141 atoms 235 | 236 | Performance: 272851.240 tau/day, 1052.667 timesteps/s 237 | 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads 238 | 239 | MPI task timing breakdown: 240 | Section | min time | avg time | max time |%varavg| %total 241 | --------------------------------------------------------------- 242 | Pair | 3.8358 | 3.8358 | 3.8358 | 0.0 | 80.76 243 | Neigh | 0.4183 | 0.4183 | 0.4183 | 0.0 | 8.81 244 | Comm | 0.0051625 | 0.0051625 | 0.0051625 | 0.0 | 0.11 245 | Output | 0.0040231 | 0.0040231 | 0.0040231 | 0.0 | 0.08 246 | Modify | 0.36433 | 0.36433 | 0.36433 | 0.0 | 7.67 247 | Other | | 0.1222 | | | 2.57 248 | 249 | Nlocal: 8141 ave 8141 max 8141 min 250 | Histogram: 1 0 0 0 0 0 0 0 0 0 251 | Nghost: 0 ave 0 max 0 min 252 | Histogram: 1 0 0 0 0 0 0 0 0 0 253 | Neighs: 69249 ave 69249 max 69249 min 254 | Histogram: 1 0 0 0 0 0 0 0 0 0 255 | 256 | Total # of neighbors = 69249 257 | Ave neighs/atom = 8.5062 258 | Neighbor list builds = 185 259 | Dangerous builds = 0 260 | 261 | thermo_style custom step temp pxx pyy cpuremain 262 | 263 | run 400 264 | Per MPI rank memory allocation (min/avg/max) = 3.116 | 3.116 | 3.116 Mbytes 265 | Step Temp Pxx Pyy CPULeft 266 | 10000 0.17731223 0.19351318 -0.14231342 0 267 | 10100 0.17832333 0.20504646 -0.11497251 0.26945114 268 | 10200 0.17837879 0.23324545 -0.06602532 0.18344402 269 | 10300 0.17835133 0.24793925 -0.074760067 0.092408021 270 | 10400 0.17897071 0.24298626 -0.082191499 0 271 | Loop time of 0.369093 on 1 procs for 400 steps with 8141 atoms 272 | 273 | Performance: 280904.857 tau/day, 1083.738 timesteps/s 274 | 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads 275 | 276 | MPI task timing breakdown: 277 | Section | min time | avg time | max time |%varavg| %total 278 | --------------------------------------------------------------- 279 | Pair | 0.29446 | 0.29446 | 0.29446 | 0.0 | 79.78 280 | Neigh | 0.036822 | 0.036822 | 0.036822 | 0.0 | 9.98 281 | Comm | 0.0004859 | 0.0004859 | 0.0004859 | 0.0 | 0.13 282 | Output | 0.00031304 | 0.00031304 | 0.00031304 | 0.0 | 0.08 283 | Modify | 0.027533 | 0.027533 | 0.027533 | 0.0 | 7.46 284 | Other | | 0.009483 | | | 2.57 285 | 286 | Nlocal: 8141 ave 8141 max 8141 min 287 | Histogram: 1 0 0 0 0 0 0 0 0 0 288 | Nghost: 0 ave 0 max 0 min 289 | Histogram: 1 0 0 0 0 0 0 0 0 0 290 | Neighs: 69164 ave 69164 max 69164 min 291 | Histogram: 1 0 0 0 0 0 0 0 0 0 292 | 293 | Total # of neighbors = 69164 294 | Ave neighs/atom = 8.49576 295 | Neighbor list builds = 16 296 | Dangerous builds = 0 297 | Total wall time: 0:00:09 298 | -------------------------------------------------------------------------------- /tests/test_File.py: -------------------------------------------------------------------------------- 1 | from unittest import TestCase 2 | import numpy as np 3 | import os 4 | 5 | import lammps_logfile 6 | 7 | class TestFileWithLogFile(TestCase): 8 | """Test whether the readings from a supplied log file are correct. Requires the supplied file log.lammps. 9 | """ 10 | def setUp(self): 11 | self.log = lammps_logfile.File(os.path.join(os.path.dirname(__file__), "data", "log.lammps")) 12 | 13 | def test_num_entries(self): 14 | self.assertEqual(self.log.get_num_partial_logs(), 3) 15 | 16 | def test_len_partial_logs(self): 17 | step = self.log.get("Step", -1) 18 | self.assertEqual(len(step), 5) 19 | step = self.log.get("Step", 0) 20 | self.assertEqual(len(step), 51) 21 | step = self.log.get("Step", 1) 22 | self.assertEqual(len(step), 51) 23 | step = self.log.get("Step", 2) 24 | self.assertEqual(len(step), 5) 25 | 26 | def test_keyword_partial_logs(self): 27 | keyword0 = ["Step", "Time", "Temp", "Pxx", "Pyy", "CPULeft"] 28 | for keyword in keyword0: 29 | self.assertIsNotNone(self.log.get(keyword, 0)) 30 | self.assertIsNone(self.log.get("Press", 0)) 31 | 32 | keyword1 = ["Step", "Time", "Temp", "Pxx", "Pyy", "Press", "CPULeft"] 33 | for keyword in keyword1: 34 | self.assertIsNotNone(self.log.get(keyword, 1)) 35 | 36 | keyword2 = ["Step", "Temp", "Pxx", "Pyy", "CPULeft"] 37 | for keyword in keyword2: 38 | self.assertIsNotNone(self.log.get(keyword, 2)) 39 | self.assertIsNone(self.log.get("Press", 2)) 40 | self.assertIsNone(self.log.get("Time", 2)) 41 | 42 | def test_step_entries_contents(self): 43 | np.testing.assert_equal(self.log.get("Step", 0), np.arange(0,5001, 100)) 44 | np.testing.assert_equal(self.log.get("Step", 1), np.arange(5000,10001, 100)) 45 | np.testing.assert_equal(self.log.get("Step", 2), np.arange(10000,10401, 100)) 46 | 47 | def test_get_keywords(self): 48 | self.assertListEqual(self.log.get_keywords(), sorted(["Step", "Temp", "Pxx", "Pyy", "CPULeft"])) 49 | self.assertListEqual(self.log.get_keywords(run_num=0), sorted(["Step", "Time", "Temp", "Pxx", "Pyy", "CPULeft"])) 50 | self.assertListEqual(self.log.get_keywords(run_num=1), sorted(["Step", "Time", "Temp", "Pxx", "Pyy", "Press", "CPULeft"])) 51 | self.assertListEqual(self.log.get_keywords(run_num=2), sorted(["Step", "Temp", "Pxx", "Pyy", "CPULeft"])) --------------------------------------------------------------------------------