Add section about how to output YAML or JSON
This commit is contained in:
Richard Berger
@ -54,6 +54,7 @@ Analysis howto
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Howto_kappa
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Howto_viscosity
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Howto_diffusion
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Howto_structured_data
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Force fields howto
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==================
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154
doc/src/Howto_structured_data.rst
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154
doc/src/Howto_structured_data.rst
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@ -0,0 +1,154 @@
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Output structured data from LAMMPS
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##################################
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LAMMPS can output structured data with the :doc:`print <print>` and :doc:`fix
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print <fix_print>` command. This gives you flexibility since you can build
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custom data formats that contain system properties, thermo data, and variables
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values. This output can be directed to the screen and/or to a file for post
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processing.
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Writing the current system state, thermo data, variable values
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==============================================================
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Use the :doc:`print <print>` command to output the current system state, which
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can include system properties, thermo data and variable values.
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YAML
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----
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.. code-block:: LAMMPS
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print """---
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timestep: $(step)
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pe: $(pe)
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ke: $(ke)""" file current_state.yaml screen no
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.. code-block:: yaml
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:caption: current_state.yaml
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---
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timestep: 250
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pe: -4.7774327356321810711
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ke: 2.4962152903997174569
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JSON
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----
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.. code-block:: LAMMPS
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print """{
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"timestep": $(step),
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"pe": $(pe),
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"ke": $(ke)
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}""" file current_state.json screen no
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.. code-block:: JSON
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:caption: current_state.json
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{
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"timestep": 250,
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"pe": -4.7774327356321810711,
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"ke": 2.4962152903997174569
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}
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Writing continuous data during a simulation
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===========================================
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The :doc:`fix print <fix_print>` command allows you to output an arbitrary string at defined times during a simulation run.
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YAML
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----
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.. code-block:: LAMMPS
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fix extra all print 50 """
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- timestep: $(step)
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pe: $(pe)
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ke: $(ke)""" file output.yaml screen no
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.. code-block:: yaml
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:caption: output.yaml
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# Fix print output for fix extra
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- timestep: 0
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pe: -6.77336805325924729
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ke: 4.4988750000000026219
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- timestep: 50
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pe: -4.8082494418323200591
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ke: 2.5257981827119797558
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- timestep: 100
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pe: -4.7875608875581505686
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ke: 2.5062598821985102582
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- timestep: 150
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pe: -4.7471033686005483787
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ke: 2.466095925545450207
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- timestep: 200
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pe: -4.7509052858544134068
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ke: 2.4701136792591693592
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- timestep: 250
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pe: -4.7774327356321810711
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ke: 2.4962152903997174569
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Post-processing of YAML files can be easily be done with Python and other
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scripting languages. In case of Python the `yaml` package allows you to load the
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data files and obtain a list of dictionaries.
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.. code-block:: python
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import yaml
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with open("output.yaml") as f:
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data = yaml.load(f, Loader=yaml.FullLoader)
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print(data)
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.. code-block::
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[{'timestep': 0, 'pe': -6.773368053259247, 'ke': 4.498875000000003}, {'timestep': 50, 'pe': -4.80824944183232, 'ke': 2.5257981827119798}, {'timestep': 100, 'pe': -4.787560887558151, 'ke': 2.5062598821985103}, {'timestep': 150, 'pe': -4.747103368600548, 'ke': 2.46609592554545}, {'timestep': 200, 'pe': -4.750905285854413, 'ke': 2.4701136792591694}, {'timestep': 250, 'pe': -4.777432735632181, 'ke': 2.4962152903997175}]
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Line Delimited JSON (LD-JSON)
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-----------------------------
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The JSON format itself is very strict when it comes to delimiters. For continous
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output/streaming data it is beneficial use the *line delimited JSON* format.
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Each line represents one JSON object.
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.. code-block:: LAMMPS
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fix extra all print 50 """{"timestep": $(step), "pe": $(pe), "ke": $(ke)}""" title "" file output.json screen no
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.. code-block:: json
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:caption: output.json
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{"timestep": 0, "pe": -6.77336805325924729, "ke": 4.4988750000000026219}
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{"timestep": 50, "pe": -4.8082494418323200591, "ke": 2.5257981827119797558}
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{"timestep": 100, "pe": -4.7875608875581505686, "ke": 2.5062598821985102582}
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{"timestep": 150, "pe": -4.7471033686005483787, "ke": 2.466095925545450207}
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{"timestep": 200, "pe": -4.7509052858544134068, "ke": 2.4701136792591693592}
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{"timestep": 250, "pe": -4.7774327356321810711, "ke": 2.4962152903997174569}
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One simple way to load this data into a Python script is to use the `pandas`
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package. It can directly load these files into a data frame:
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.. code-block:: python
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import pandas as pd
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data = pd.read_json('output.json', lines=True)
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print(data)
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.. code-block:: bash
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timestep pe ke
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0 0 -6.773368 4.498875
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1 50 -4.808249 2.525798
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2 100 -4.787561 2.506260
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3 150 -4.747103 2.466096
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4 200 -4.750905 2.470114
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5 250 -4.777433 2.496215
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