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!