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