_calc_damping_min and _calc_strain_ref functions are using _stress_mean in kPa! This value must be converted to ATM: change _stress_mean for (_stress_mean * KPA_TO_ATM)

It seems to run twice! The first with correct values but the second (unnecessary) time with incorrect input values (like self._stress_mean = None)

I got this error while running the example 6 given in PYSRA:

Traceback (most recent call last):
File "", line 1, in
File "", line 20, in iter_geopsy_profiles
File "", line 20, in
NameError: name 'floa4t' is not defined

It was shown when executing this command:

fname = 'data/best100_GM_linux.txt'

for geopsy_profile in iter_geopsy_profiles(fname):
profile = pysra.site.Profile([
pysra.site.Layer(
pysra.site.SoilType(
'soil-%d' % i, l['density'] / pysra.site.GRAVITY,
damping=0.05), l['thickness'], l['vel_shear'])
for i, l in enumerate(geopsy_profile['layers'])
])
# Use 1% damping for the half-space
profile[-1].soil_type.damping = 0.01
# Compute the waves from the last layer
calc(ts, profile, profile.location('outcrop', index=-1))
# Compute the site amplification
outputs(calc)

The above was while running in python.

While running in Jupyter notebook, below error was shown:
TypeError Traceback (most recent call last)
in
18 pysra.output.OutputLocation('outcrop', index=0),
19 # Damping
---> 20 0.05
21 ),
22

TypeError: init() takes 2 positional arguments but 3 were given

This was while executing the commands given in In[12] in the example 6.

Installing pystrata on my various machines has resulted in several issues. The most common one is that it says pyexcel is needed when importing pystrata.

This is what I've found to be the most successful way of installing pystrata
conda create --name pystrata python=3.9 spyder-kernels=2.1.0 pandas pyexcel
pip install pystrata

This allows pystrata to be successfully imported, but when launching spyder in the environment there are a handful of matplotlib warnings that can be solved by also running this in the environment
pip3 install PyQt5

I have been able to reproduce the nonlinear EQL examples given on the website using pystrata.site.DarendeliSoilType layers. However, I have not been successful with using other published models included with pystrata. Here is an example layer, which the calculator cannot use:

model = [pystrata.site.Layer(
                pystrata.site.SoilType(name="Soil",
                                       unit_wt=18,
                                       mod_reduc="Seed & Idriss, Sand Mean",
                                       damping="Seed & Idriss, Sand Mean"),
                30, 400)]

I underlay this layer with rock:

    bedrock = pystrata.site.Layer(pystrata.site.SoilType("Rock", rho_br*9.8067, None, 1/2/Qs_br), 0, Vs_br)
    model.append(bedrock)

    # Create the profile object:
    ps_profile = pystrata.site.Profile(model)

Then attempt to calculate the EQL response using a time-history of my own. However, calculation fails producing the following errors:

  File "P:\Projects\Seismic\SHA\JPR_scenario\ReelfootFault\pySTRATA\bin\process_sta_trial.py", line 191, in calc_resp
    calc(ts, profile, profile.location("outcrop", index=-1))
  File "C:\Users\nvca223\Anaconda3\envs\pystrata\Lib\site-packages\pystrata\propagation.py", line 505, in __call__
    super().__call__(motion, profile, loc_input)
  File "C:\Users\nvca223\Anaconda3\envs\pystrata\Lib\site-packages\pystrata\propagation.py", line 288, in __call__
    self._calc_waves(motion.angular_freqs, profile)
  File "C:\Users\nvca223\Anaconda3\envs\pystrata\Lib\site-packages\pystrata\propagation.py", line 305, in _calc_waves
    wave_nums[i, :] = angular_freqs / l.comp_shear_vel
                                      ^^^^^^^^^^^^^^^^
  File "C:\Users\nvca223\Anaconda3\envs\pystrata\Lib\site-packages\pystrata\site.py", line 916, in comp_shear_vel
    return np.sqrt(self.comp_shear_mod / self.density)
                   ^^^^^^^^^^^^^^^^^^^
  File "C:\Users\nvca223\Anaconda3\envs\pystrata\Lib\site-packages\pystrata\site.py", line 907, in comp_shear_mod
    comp_factor = np.sqrt(1 - 4 * damping**2) + 2j * damping
                                  ~~~~~~~^^~
TypeError: unsupported operand type(s) for ** or pow(): 'str' and 'int'

It seems that pystrata is not obtaining nonlinear damping values from the "Seed & Idriss, Sand Mean" nonlinear curve as I expect.

Can you please describe what I am doing wrong or instruct me how to use the published nonlinear models?

Thanks!

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.

In the manifest file please change:
include HISTORY.rst
include README.rst

to:
include HISTORY.md
include README.md

Hi, I am working through some of the examples and came across a problem with example 15. Here's what I ran:

import pystrata

pystrata.site._load_published_curves()

And this is what was returned:

Traceback (most recent call last):
  File "P:\Projects\Seismic\SHA\JPR_scenario\ReelfootFault\pySTRATA\bin\nonlinear_work.py", line 3, in <module>
    pystrata.site._load_published_curves()
  File "C:\Users\nvca223\Anaconda3\envs\pystrata\Lib\site-packages\pystrata\site.py", line 56, in _load_published_curves
    models = tomli.load(fp)["models"]
             ^^^^^^^^^^^^^^
  File "C:\Users\nvca223\Anaconda3\envs\pystrata\Lib\site-packages\tomli\_parser.py", line 66, in load
    return loads(s, parse_float=parse_float)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\nvca223\Anaconda3\envs\pystrata\Lib\site-packages\tomli\_parser.py", line 116, in loads
    raise suffixed_err(src, pos, "Invalid statement")
tomli.TOMLDecodeError: Invalid statement (at line 1, column 1)

The published_curves.toml file was not apparently included in my original download, so I downloaded it from github and installed it at ...\Anaconda3\envs\pystrata\Lib\site-packages\pystrata\data. I had to create the "data" folder shown in that path.

I would appreciate any help sorting out this issue.

New packages are not in the install requires list on setup.py. Causes build failure.

Hello, I just installled pystrata and when running the first example as a jupyter threw teh following error, suggesting the pyrvt module is missing. I installed all the dependencies listed (cmake, qt, gsl, qwt, and fftw). How can I fix this?

`import matplotlib.pyplot as plt
import numpy as np

import pystrata

%matplotlib inline

ModuleNotFoundError Traceback (most recent call last)
Cell In[7], line 4
1 import matplotlib.pyplot as plt
2 import numpy as np
----> 4 import pystrata
6 get_ipython().run_line_magic('matplotlib', 'inline')

File ~\Anaconda3\envs\pystrata\Lib\site-packages\pystrata_init_.py:23
1 # -- coding: utf-8 --
2 # The MIT License (MIT)
3 #
(...)
21 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
22 # SOFTWARE.
---> 23 from . import motion
24 from . import output
25 from . import propagation

File ~\Anaconda3\envs\pystrata\Lib\site-packages\pystrata\motion.py:27
24 import re
26 import numpy as np
---> 27 import pyrvt
28 from scipy.constants import g as GRAVITY
30 # Gravity in m/sec²

ModuleNotFoundError: No module named 'pyrvt'`

Dear sir,
While running a site response analysis, I came across the following problem.

Error:
The maximum shear strain profile estimated in MaxStrainProfile class for a layer is returning Array of strain values.

Possible reason:
Line 437, output.py:
values = [0] + [l.strain for l in calc.profile[:-1]]

The above line can be modified as
values = [0] + [l.strain_max for l in calc.profile[:-1]]
to obtain correct results..

Kindly confirm whether the above fix is ok...

I am trying to install pysra from requirements.txt it doesn't build unless I first manually install Cython.

See error message below:

Collecting cyko (from pySRA->-r requirements.txt (line 8))
Downloading https://files.pythonhosted.org/packages/06/10/7401c797e805c04ddce76aec75ee100c4894fe97b3c5af078f678a4fdcd5/cyko-0.2.5.2.tar.gz (54kB)
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "", line 1, in
File "/tmp/pip-install-a64yu20q/cyko/setup.py", line 3, in
from Cython.Build import cythonize
ModuleNotFoundError: No module named 'Cython'

I noticed this error occurring in python 3.7 but not in python 3.6. The error occurs when all the soil layers are added (i.e., when I execute this: "pysra.site.Profile(layers)"). Below is some information on where this error occurs.

File "/home1/04482/marafi/anaconda3/lib/python3.7/site-packages/pysra/site.py", line 833, in init
self.update_layers()
File "/home1/04482/marafi/anaconda3/lib/python3.7/site-packages/pysra/site.py", line 845, in update_layers
for layer in self[start_layer:]:
File "/home1/04482/marafi/anaconda3/lib/python3.7/collections/init.py", line 1096, in getitem
return self.class(self.data[i])
RecursionError: maximum recursion depth exceeded while calling a Python object
self.update_layers()

Let me know if you need more information. If you are unable to recreate this error, try using a large number of soil layers (>100).