Error in executing randomization of modulus reduction and damping ratio curves

[AniketSanjayDesai]

Hello.
I have been using PYSTRATA for a long time and it worked very well. However, I just downloaded the latest version of PYSTRATA and Python both. During an equivalent linear analysis based on one of your examples, I executed the following command to implement the randomization of modulus reduction and damping ratio curves:

var_soiltypes = pystrata.variation.DarendeliVariation(-0.5)
count = 4
for geopsy_profile in iter_geopsy_profiles(fname):
for profile in pystrata.variation.iter_varied_profiles(
profile,
count,
var_thickness=None,
var_velocity=None,
var_soiltypes=var_soiltypes
):
calc(ts, profile, profile.location('outcrop', index=-1))
outputs(calc)

In earlier versions, it used to show only this message:
C:\Users\ADMIN\anaconda3\lib\site-packages\pystrata\site.py:741: RuntimeWarning: divide by zero encountered in divide
err = 100.0 * np.max((self.previous - self.value) / self.value)
C:\Users\ADMIN\anaconda3\lib\site-packages\pystrata\site.py:741: RuntimeWarning: invalid value encountered in divide
err = 100.0 * np.max((self.previous - self.value) / self.value)

But, it used to work well and provided the results properly.

However, with the latest version, It showed this message:
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\site.py:804: RuntimeWarning: divide by zero encountered in divide
err = 100.0 * np.max((self.previous - self.value) / self.value)
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\site.py:804: RuntimeWarning: invalid value encountered in divide
err = 100.0 * np.max((self.previous - self.value) / self.value)
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:327: RuntimeWarning: overflow encountered in multiply
waves_a[i + 1, :] = 0.5 * waves_a[i] * (1 + cimped) * np.exp(
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:327: RuntimeWarning: invalid value encountered in multiply
waves_a[i + 1, :] = 0.5 * waves_a[i] * (1 + cimped) * np.exp(
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:329: RuntimeWarning: overflow encountered in multiply
) + 0.5 * waves_b[i] * (1 - cimped) * np.exp(-cterm)
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:327: RuntimeWarning: invalid value encountered in add
waves_a[i + 1, :] = 0.5 * waves_a[i] * (1 + cimped) * np.exp(
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:330: RuntimeWarning: overflow encountered in multiply
waves_b[i + 1, :] = 0.5 * waves_a[i] * (1 - cimped) * np.exp(
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:330: RuntimeWarning: invalid value encountered in multiply
waves_b[i + 1, :] = 0.5 * waves_a[i] * (1 - cimped) * np.exp(
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:332: RuntimeWarning: overflow encountered in multiply
) + 0.5 * waves_b[i] * (1 + cimped) * np.exp(-cterm)
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:330: RuntimeWarning: invalid value encountered in add
waves_b[i + 1, :] = 0.5 * waves_a[i] * (1 - cimped) * np.exp(
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:369: RuntimeWarning: overflow encountered in multiply
return 2 * self._waves_a[l.index] * np.exp(cterm)
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:369: RuntimeWarning: invalid value encountered in multiply
return 2 * self._waves_a[l.index] * np.exp(cterm)
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:455: RuntimeWarning: overflow encountered in multiply
denom = -(ang_freqs2) * self.wave_at_location(lin)
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:455: RuntimeWarning: invalid value encountered in multiply
denom = -(ang_freqs2) * self.wave_at_location(lin)
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:461: RuntimeWarning: invalid value encountered in divide
tf[mask] = GRAVITY * numer[mask] / denom[mask]
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:461: RuntimeWarning: overflow encountered in multiply
tf[mask] = GRAVITY * numer[mask] / denom[mask]
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:309: RuntimeWarning: invalid value encountered in divide
wave_nums[i, :] = angular_freqs / l.comp_shear_vel
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:329: RuntimeWarning: invalid value encountered in multiply
) + 0.5 * waves_b[i] * (1 - cimped) * np.exp(-cterm)
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:332: RuntimeWarning: invalid value encountered in multiply
) + 0.5 * waves_b[i] * (1 + cimped) * np.exp(-cterm)
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:451: RuntimeWarning: overflow encountered in multiply
self._waves_a[lout.index, :] * np.exp(cterm)
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:451: RuntimeWarning: invalid value encountered in multiply
self._waves_a[lout.index, :] * np.exp(cterm)
C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:452: RuntimeWarning: invalid value encountered in multiply

• self._waves_b[lout.index, :] * np.exp(-cterm)
  C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:448: RuntimeWarning: overflow encountered in multiply
  1j
  C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:461: RuntimeWarning: invalid value encountered in multiply
  tf[mask] = GRAVITY * numer[mask] / denom[mask]
  C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:327: RuntimeWarning: overflow encountered in exp
  waves_a[i + 1, :] = 0.5 * waves_a[i] * (1 + cimped) * np.exp(
  C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:330: RuntimeWarning: overflow encountered in exp
  waves_b[i + 1, :] = 0.5 * waves_a[i] * (1 - cimped) * np.exp(
  C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:448: RuntimeWarning: invalid value encountered in multiply
  1j
  C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:451: RuntimeWarning: invalid value encountered in subtract
  self._waves_a[lout.index, :] * np.exp(cterm)
  C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:451: RuntimeWarning: overflow encountered in subtract
  self._waves_a[lout.index, :] * np.exp(cterm)
  C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:309: RuntimeWarning: divide by zero encountered in divide
  wave_nums[i, :] = angular_freqs / l.comp_shear_vel
  C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:362: RuntimeWarning: invalid value encountered in multiply
  cterm = 1j * self._wave_nums[l.index] * l.depth_within
  C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\site.py:804: RuntimeWarning: divide by zero encountered in double_scalars
  err = 100.0 * np.max((self.previous - self.value) / self.value)
  C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:387: RuntimeWarning: invalid value encountered in divide
  tf = self.wave_at_location(lout) / self.wave_at_location(lin)
  C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\propagation.py:561: RuntimeWarning: divide by zero encountered in double_scalars
  l.strain = self._motion.pgv / l.initial_shear_vel
  C:\Users\ADMIN\miniconda3\lib\site-packages\pystrata\site.py:804: RuntimeWarning: invalid value encountered in double_scalars
  err = 100.0 * np.max((self.previous - self.value) / self.value)

After that, it generated results, but in the output, the majority of the values are shown as 'NaN' and therefore, in the plots also, very few output curves are shown (Figure attached(Previous version and current)). I request you to kindly let me know how to rectify this error.

[arkottke]

Can you provide the complete script that causes this problem?

[AniketSanjayDesai]

Sure Here is the script:

import numba
import re
import matplotlib.pyplot as plt
import numpy as np
import pystrata
%matplotlib inline

Increased figure sizes

plt.rcParams['figure.dpi'] = 120

def iter_geopsy_profiles(fname):
"""Read a Geopsy formatted text file created by gpdcreport."""
with open(fname) as fp:
next(fp)
while True:
try:
line = next(fp)
except StopIteration:
break

        m = re.search(r'Layered model (\d+): value=([0-9.]+)', line)
        id, score = m.groups()
        count = int(next(fp))
        d = {
            'id': id,
            'score': score,
            'layers': [],
        }
        cols = ['thickness', 'vel_comp', 'vel_shear', 'density']
        for _ in range(count):
            values = [float(p) for p in next(fp).split()]
            d['layers'].append(dict(zip(cols, values)))
        yield d

fname = 'data/ChamoliAftershock.AT2'
ts = pystrata.motion.TimeSeriesMotion.load_at2_file(fname)
ts.accels

calc = pystrata.propagation.EquivalentLinearCalculator()

freqs = np.logspace(-1, 2, num=500)

outputs = pystrata.output.OutputCollection([
pystrata.output.ResponseSpectrumOutput(
# Frequency
freqs,
# Location of the output
pystrata.output.OutputLocation('outcrop', index=0),
# Damping
0.05),
pystrata.output.ResponseSpectrumRatioOutput(
# Frequency
freqs,
# Location in (denominator),
pystrata.output.OutputLocation('outcrop', index=-1),
# Location out (numerator)
pystrata.output.OutputLocation('outcrop', index=0),
# Damping
0.05),
pystrata.output.FourierAmplitudeSpectrumOutput(
# Frequency
freqs,
# Location of the output
pystrata.output.OutputLocation('outcrop', index=0),
# Bandwidth for Konno-Omachi smoothing window
ko_bandwidth=30),
pystrata.output.AccelTransferFunctionOutput(
# Frequency
freqs,
# Location in (denominator),
pystrata.output.OutputLocation('outcrop', index=-1),
# Location out (numerator)
pystrata.output.OutputLocation('outcrop', index=0)
)
])

fname = 'data/EQD_NoAPAll.txt'
for geopsy_profile in iter_geopsy_profiles(fname):
profile = pystrata.site.Profile([
pystrata.site.Layer(
pystrata.site.DarendeliSoilType(
l['density'] * 9.81/1000, plas_index=0, ocr=1, stress_mean=200),
l['thickness'], l['vel_shear'])
for i, l in enumerate(geopsy_profile['layers'])
])
profile[-1].soil_type.damping = 0.02

var_soiltypes = pystrata.variation.DarendeliVariation(-0.5)
count = 4
for geopsy_profile in iter_geopsy_profiles(fname):
for profile in pystrata.variation.iter_varied_profiles(
profile,
count,
var_thickness=None,
var_velocity=None,
var_soiltypes=var_soiltypes
):
calc(ts, profile, profile.location('outcrop', index=-1))
outputs(calc)

for o in outputs:
fig, ax = plt.subplots()
ax.plot(o.refs, o.values)
ax.set(xlabel=o.xlabel, xscale='log', ylabel=o.ylabel)
fig.tight_layout();

The required input files are attached herewith.
data.zip

[arkottke]

Please attach the actual file as the formatting is lost when you just paste the code as a comment.

[AniketSanjayDesai]

Ex6_MRDR_final-Copy5.zip

[arkottke]

A few comments.

In this cell:

var_soiltypes = pystrata.variation.DarendeliVariation(-0.5)
count = 4
for geopsy_profile in iter_geopsy_profiles(fname):
    for profile in pystrata.variation.iter_varied_profiles(
            profile,
            count,
            var_thickness=None,
            var_velocity=None,
            var_soiltypes=var_soiltypes
        ):
            calc(ts, profile, profile.location('outcrop', index=-1))
            outputs(calc)

You are only varying the last created profile. The for loop that loop[s over iter_geopsy_profile(fname) is never used.
More importantly, you are using the variable named profile multiple times and they are overwriting each other. It works if you change it to something like this:

var_soiltypes = pystrata.variation.DarendeliVariation(-0.5)
count = 4
for geopsy_profile in iter_geopsy_profiles(fname):
    for p in pystrata.variation.iter_varied_profiles(
            profile,
            count,
            var_thickness=None,
            var_velocity=None,
            var_soiltypes=var_soiltypes
        ):
            calc(ts, p, p.location('outcrop', index=-1))
            outputs(calc)

[AniketSanjayDesai]

It is working now.
Thanks a lot!