Viscosity examples #62
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corrected
modified
lorisercole
requested changes
Jul 7, 2022
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Thanks for this PR @cesaremalosso! Very neat. 👍
Here a couple of requests to finalize it.
examples/06_example_cepstrum_viscosity_h2o.ipynb- To be consistent with the other examples, could you please use the
i_omodule to load the data file? Like this:
- To be consistent with the other examples, could you please use the
jfile = st.i_o.TableFile('./data/h2o/h2o.dat')
jfile.read_datalines()
DT_FS = 1 # time step [fs]
TEMPERATURE = np.mean(jfile.data['Temp']) # temperature [K] (983.173 K)
VOLUME = 1918.4149658 # volume [A^3]
print(DT_FS, TEMPERATURE, VOLUME)
j = st.StressCurrent(np.column_stack([jfile.data['s_xy'], jfile.data['s_xz'], jfile.data['s_yz']]),
UNITS='real', DT_FS=DT_FS, TEMPERATURE=TEMPERATURE, VOLUME=VOLUME)
- There is a typo in the first line of
examples/data/h2o/lammps/h2o.in. It should be:
Temp s_xy s_xz s_yz
- Could you also try to setup a test? For reference, to see how it works, you can check the silica case in test_notebooks.py (you will need to add a function in that file, and the results of cepstral analysis in the
tests/test_notebookfolder. - If you feel brave, you could even setup another test alongside those in test_as_example.py. But I can help you out on this!
| @@ -10,7 +10,8 @@ The `data` folder contains the trajectories, obtained from classical NVE molecul | |||
| These examples show how to use the `sportran` package in a Python script, step by step, to analyse a time series and perform cepstral analysis. Some of the tools and plot functions of the code are presented. | |||
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| * [01 - Silica (single component)](01_example_cepstrum_singlecomp_silica.ipynb): analysis of solid amorphous silica, a one-component system. | |||
| * [02 - Liquid NaCl (multi-component)](02_example_cepstrum_doublecomp_NaCl.ipynb): analysis of molten NaCl, a two-component system. | |||
| * [02 - Liquid NaCl (multi-)](02_example_cepstrum_doublecomp_NaCl.ipynb): analysis of molten NaCl, a two-component system. | |||
| * [06 - Liquid h2o (viscosity)](06_example_cesptrum_viscosity_h2o.ipynb) : computation of the shear viscosity of liquid water. | |||
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Suggested change
| * [06 - Liquid h2o (viscosity)](06_example_cesptrum_viscosity_h2o.ipynb) : computation of the shear viscosity of liquid water. | |
| * [06 - Liquid H2O (viscosity)](06_example_cesptrum_viscosity_h2o.ipynb) : computation of the shear viscosity of liquid water. |
| @@ -10,7 +10,8 @@ The `data` folder contains the trajectories, obtained from classical NVE molecul | |||
| These examples show how to use the `sportran` package in a Python script, step by step, to analyse a time series and perform cepstral analysis. Some of the tools and plot functions of the code are presented. | |||
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| * [01 - Silica (single component)](01_example_cepstrum_singlecomp_silica.ipynb): analysis of solid amorphous silica, a one-component system. | |||
| * [02 - Liquid NaCl (multi-component)](02_example_cepstrum_doublecomp_NaCl.ipynb): analysis of molten NaCl, a two-component system. | |||
| * [02 - Liquid NaCl (multi-)](02_example_cepstrum_doublecomp_NaCl.ipynb): analysis of molten NaCl, a two-component system. | |||
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Suggested change
| * [02 - Liquid NaCl (multi-)](02_example_cepstrum_doublecomp_NaCl.ipynb): analysis of molten NaCl, a two-component system. | |
| * [02 - Liquid NaCl (multi-component)](02_example_cepstrum_doublecomp_NaCl.ipynb): analysis of molten NaCl, a two-component system. |
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| ####################################### | ||
| ### Read Structure | ||
| ####################################### |
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You can remove the lines
#######################################
### Read Structure
#######################################
or move read_data "h2o_64.init" under it, if it works for LAMMPS.
| ######################################################################### | ||
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| thermo ${thermo_print_interval} | ||
| thermo_style custom temp c_thermo_press[4] c_thermo_press[5] c_thermo_press[6] |
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I do not see where you defined a compute thermo_press. Maybe that line got lost?
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Added examples for the computation of viscosity