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Viscosity example #72

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Viscosity example #72

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8448a83
added the example for viscosity
DavideTisi Dec 8, 2023
d16eb37
notebook works
DavideTisi Dec 8, 2023
1a14e32
added tests for viscosity in h2o
DavideTisi Dec 10, 2023
8f28791
added numba to "tests" requirements
DavideTisi Feb 5, 2024
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793 changes: 793 additions & 0 deletions examples/06_example_cepstrum_viscosity_h2o.ipynb
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100,001 changes: 100,001 additions & 0 deletions examples/data/h2o/h2o.dat
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3 changes: 2 additions & 1 deletion setup.json
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,8 @@
"pytest-regressions>=2.4.2",
"pandas>=1.1.0",
"testbook",
"ipykernel"
"ipykernel",
"numba"
],
"doc": [
"sphinx==4.2.0",
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14 changes: 14 additions & 0 deletions tests/conftest.py
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Expand Up @@ -56,6 +56,20 @@ def data_SiO2(data_SiO2_path):
print('T = {:f} K'.format(TEMPERATURE))
return jfile, DT_FS, TEMPERATURE, VOLUME

@pytest.fixture(scope='session')
def data_h2o(data_h2o_path):
import sportran as st
import numpy as np

jfile = st.i_o.TableFile(data_h2o_path, group_vectors=True)
jfile.read_datalines()
DT_FS = 1.0 # time step [fs]
TEMPERATURE = np.mean(jfile.data['Temp']) # temperature [K] (983.173 K)
VOLUME = 1918.4149658 # volume [A^3]
print('T = {:f} K'.format(TEMPERATURE))
print('V = {:f} A^3'.format(VOLUME))
return jfile, DT_FS, TEMPERATURE, VOLUME


@pytest.fixture
def check_reg(num_regression, data_regression):
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12 changes: 12 additions & 0 deletions tests/test_as_example.py
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Expand Up @@ -41,6 +41,18 @@ def test_example_SiO2_fixed_K(data_SiO2, check_reg):
jf.cepstral_analysis(manual_cutoffK=42)
print(jf.cepstral_log)
check_reg(jf)

def test_example_viscosity_h2o(data_h2o, check_reg):
import sportran as st

jfile, DT_FS, TEMPERATURE, VOLUME = data_h2o
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)
print(j.Nyquist_f_THz)
FSTAR_THZ = 25.0
jf = j.resample(fstar_THz=FSTAR_THZ, plot=False, freq_units='thz')
jf.cepstral_analysis()
print(jf.cepstral_log)


if __name__ == '__main__':
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112 changes: 75 additions & 37 deletions tests/test_as_example/regenerate_results.py
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Expand Up @@ -2,6 +2,7 @@
import sportran as st
import numpy as np
import yaml, pandas as pd
import argparse


def write_results(jf, filename):
Expand All @@ -24,48 +25,85 @@ def write_results(jf, filename):
with open(filename + '.yml', 'w') as f:
f.write(yaml.dump(d))

def main(inputs):
if (inputs == 'all' or inputs == 'NaCl' ):
# NaCl
jfile = st.i_o.TableFile('../data/NaCl/NaCl.dat', group_vectors=True)
jfile.read_datalines(start_step=0, NSTEPS=0, select_ckeys=['Temp', 'flux', 'vcm[1]'])
DT_FS = 5.0 # time step [fs]
TEMPERATURE = np.mean(jfile.data['Temp']) # temperature [K]
VOLUME = 40.21**3 # volume [A^3]
print('T = {:f} K'.format(TEMPERATURE))
print('V = {:f} A^3'.format(VOLUME))

# NaCl
jfile = st.i_o.TableFile('../data/NaCl/NaCl.dat', group_vectors=True)
jfile.read_datalines(start_step=0, NSTEPS=0, select_ckeys=['Temp', 'flux', 'vcm[1]'])
DT_FS = 5.0 # time step [fs]
TEMPERATURE = np.mean(jfile.data['Temp']) # temperature [K]
VOLUME = 40.21**3 # volume [A^3]
print('T = {:f} K'.format(TEMPERATURE))
print('V = {:f} A^3'.format(VOLUME))
j = st.HeatCurrent([jfile.data['flux'], jfile.data['vcm[1]']], DT_FS=DT_FS, UNITS='metal', TEMPERATURE=TEMPERATURE,
VOLUME=VOLUME)
print(j.Nyquist_f_THz)
FSTAR_THZ = 14.0
jf = j.resample(fstar_THz=FSTAR_THZ, plot=False, freq_units='thz')
jf.cepstral_analysis()
print(jf.cepstral_log)

j = st.HeatCurrent([jfile.data['flux'], jfile.data['vcm[1]']], DT_FS=DT_FS, UNITS='metal', TEMPERATURE=TEMPERATURE,
VOLUME=VOLUME)
print(j.Nyquist_f_THz)
FSTAR_THZ = 14.0
jf = j.resample(fstar_THz=FSTAR_THZ, plot=False, freq_units='thz')
jf.cepstral_analysis()
print(jf.cepstral_log)
write_results(jf, 'test_example_NaCl')

if (inputs == 'all' or inputs == 'SiO2' ):
# SiO2
jfile = st.i_o.TableFile('../data/Silica/Silica.dat', group_vectors=True)
jfile.read_datalines(start_step=0, NSTEPS=0, select_ckeys=['flux1', 'Temp'])
DT_FS = 1.0 # time step [fs]
TEMPERATURE = np.mean(jfile.data['Temp']) # temperature [K]
VOLUME = 3130.431110818 # volume [A^3]
print('T = {:f} K'.format(TEMPERATURE))

write_results(jf, 'test_example_NaCl')
j = st.HeatCurrent(jfile.data['flux1'], DT_FS=DT_FS, UNITS='metal', TEMPERATURE=TEMPERATURE, VOLUME=VOLUME)
print(j.Nyquist_f_THz)
FSTAR_THZ = 28.0
jf = j.resample(fstar_THz=FSTAR_THZ, plot=False, freq_units='thz')
jf.cepstral_analysis()
print(jf.cepstral_log)

# SiO2
jfile = st.i_o.TableFile('../data/Silica/Silica.dat', group_vectors=True)
jfile.read_datalines(start_step=0, NSTEPS=0, select_ckeys=['flux1', 'Temp'])
DT_FS = 1.0 # time step [fs]
TEMPERATURE = np.mean(jfile.data['Temp']) # temperature [K]
VOLUME = 3130.431110818 # volume [A^3]
print('T = {:f} K'.format(TEMPERATURE))
write_results(jf, 'test_example_SiO2')

j = st.HeatCurrent(jfile.data['flux1'], DT_FS=DT_FS, UNITS='metal', TEMPERATURE=TEMPERATURE, VOLUME=VOLUME)
print(j.Nyquist_f_THz)
FSTAR_THZ = 28.0
jf = j.resample(fstar_THz=FSTAR_THZ, plot=False, freq_units='thz')
jf.cepstral_analysis()
print(jf.cepstral_log)
j = st.HeatCurrent(jfile.data['flux1'], DT_FS=DT_FS, UNITS='metal', TEMPERATURE=TEMPERATURE, VOLUME=VOLUME)
print(j.Nyquist_f_THz)
FSTAR_THZ = 28.0
jf = j.resample(fstar_THz=FSTAR_THZ, plot=False, freq_units='thz')
jf.cepstral_analysis(manual_cutoffK=42)
print(jf.cepstral_log)

write_results(jf, 'test_example_SiO2')
write_results(jf, 'test_example_SiO2_fixed_K')

if (inputs == 'all' or inputs == 'h2o' ):
# Viscosity H2O
jfile = st.i_o.TableFile('../data/h2o/h2o.dat', group_vectors=True)
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('T = {:f} K'.format(TEMPERATURE))
print('V = {:f} A^3'.format(VOLUME))

j = st.HeatCurrent(jfile.data['flux1'], DT_FS=DT_FS, UNITS='metal', TEMPERATURE=TEMPERATURE, VOLUME=VOLUME)
print(j.Nyquist_f_THz)
FSTAR_THZ = 28.0
jf = j.resample(fstar_THz=FSTAR_THZ, plot=False, freq_units='thz')
jf.cepstral_analysis(manual_cutoffK=42)
print(jf.cepstral_log)
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)
print(j.Nyquist_f_THz)
FSTAR_THZ = 25.0
jf = j.resample(fstar_THz=FSTAR_THZ, plot=False, freq_units='thz')
jf.cepstral_analysis()
print(jf.cepstral_log)

write_results(jf, 'test_example_SiO2_fixed_K')
write_results(jf, 'test_example_viscosity_h2o')


if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Regenerate data for the test.')
parser.add_argument('-i', type=str,
help='''what data do you want to regenerate?
Valid options "all", "NaCl", "SiO2", "h2o".
Combinations can be done adding "_", e.g. "NaCl_SiO2"''')

inputs = parser.parse_args().i.split('_')
for i in inputs:
if i not in ["all", "NaCl", "SiO2", "h2o"]:
print('input values not valid use "-h" to get help')
else:
main(i)
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