pyStrata 0.5.0__tar.gz → 0.5.2__tar.gz

{pyStrata-0.5.0 → pystrata-0.5.2}/HISTORY.rst

@@ -1,6 +1,18 @@
 History
 =======
 
+v0.5.2 (2023-01-18)
+-------------------
+- Fixed: Providing unsmoothed transfer function output
+- Fixed: MenqSoilType
+
+v0.5.1 (2022-09-22)
+-------------------
+- Fixed: Correlation model from Toro. Previously used rho_0 instead of d_0, and the
+  wrong depth
+- Renamed: BedrockDepthVariation to HalfSpaceDepthVariation
+- Fixed: HalfSpaceDepthVariation was removing the last layer
+
 v0.5.0 (2022-06-14)
 -------------------
 - Renamed to `pyStrata`.

{pyStrata-0.5.0 → pystrata-0.5.2}/PKG-INFO

@@ -1,23 +1,11 @@
 Metadata-Version: 2.1
-Name: pyStrata
-Version: 0.5.0
-Summary: Site Response Analysis with Python
-Home-page: http://github.com/arkottke/pystrata
-Author: Albert Kottke
+Name: pystrata
+Version: 0.5.2
+Summary: Site response analysis with Python
+Home-page: https://github.com/arkottke/pystrata
+Author: Albert R. Kottke
 Author-email: albert.kottke@gmail.com
 License: MIT
-Keywords: site response
-Classifier: Development Status :: 4 - Beta
-Classifier: Environment :: Console
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Natural Language :: English
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Topic :: Scientific/Engineering
-Classifier: Intended Audience :: Science/Research
-Description-Content-Type: text/x-rst
-Provides-Extra: dataframe
 License-File: LICENSE
 License-File: AUTHORS.rst
 
@@ -40,9 +28,20 @@ Strata_. These features include:
     - equivalent-linear with frequency dependent properties
     - quarter wavelength
 - Nonlinear curve models:
-    - Darendeli (2001)
-    - Menq (2004)
-    - Kishida (2012)
+    - Predictive models:
+        - Darendeli (2001)
+        - Menq (2004)
+        - Kishida (2012)
+    - Curves:
+        - Vucetic & Dobry (1991)
+        - EPRI (1993)
+        - GEI (1983)
+        - GeoMatrix (1990)
+        - Idriss (1990)
+        - Imperial Valley Soils
+        - Iwasaki
+        - Peninsular Range
+        - Seed & Idriss
 - Site and soil property uncertainty:
     - Toro (1994) Vs correlation model
     - G/Gmax and D uncertainty:
@@ -78,28 +77,40 @@ directory`_. An interactive Jupyter interface of these examples is available on
 
 .. _Strata: https://github.com/arkottke/strata
 .. _DOI: https://zenodo.org/badge/latestdoi/8959678
-.. _`examples directory`: https://github.com/arkottke/pystrata/tree/master/examples
+.. _`examples directory`: https://github.com/arkottke/pystrata/tree/main/examples
 
 .. |PyPi Cheese Shop| image:: https://img.shields.io/pypi/v/pystrata.svg
    :target: https://pypi.python.org/pypi/pystrata
-.. |Build Status| image:: https://img.shields.io/travis/arkottke/pystrata.svg
-   :target: https://travis-ci.org/arkottke/pystrata
+.. |Build Status| image:: https://img.shields.io/github/workflow/status/arkottke/pystrata/Python%20application
+   :alt: GitHub Workflow Status
+   :target: https://github.com/arkottke/pystrata/actions/workflows/python-app.yml
 .. |Documentation Status| image:: https://readthedocs.org/projects/pystrata/badge/?version=latest&style=flat
    :target: https://pystrata.readthedocs.org
-.. |Code Quality| image:: https://api.codacy.com/project/badge/Grade/6dbbb3a4279744d697b9bfe08af19ded
-   :target: https://www.codacy.com/app/arkottke/pystrata
-.. |Test Coverage| image:: https://api.codacy.com/project/badge/Coverage/6dbbb3a4279744d697b9bfe08af19ded
-   :target: https://www.codacy.com/app/arkottke/pystrata
+.. |Code Quality| image:: https://app.codacy.com/project/badge/Grade/6dbbb3a4279744d697b9bfe08af19ded
+   :target: https://www.codacy.com/gh/arkottke/pystrata/dashboard
+.. |Test Coverage| image:: https://app.codacy.com/project/badge/Coverage/6dbbb3a4279744d697b9bfe08af19ded
+   :target: https://www.codacy.com/gh/arkottke/pystrata/dashboard
 .. |License| image:: https://img.shields.io/badge/license-MIT-blue.svg
 .. |Zenodo| image:: https://zenodo.org/badge/8959678.svg
    :target: https://zenodo.org/badge/latestdoi/8959678
 .. |MyBinder| image:: https://mybinder.org/badge_logo.svg
-   :target: https://mybinder.org/v2/gh/arkottke/pystrata/master?filepath=examples
-
+   :target: https://mybinder.org/v2/gh/arkottke/pystrata/main?filepath=examples
 
 History
 =======
 
+v0.5.2 (2023-01-18)
+-------------------
+- Fixed: Providing unsmoothed transfer function output
+- Fixed: MenqSoilType
+
+v0.5.1 (2022-09-22)
+-------------------
+- Fixed: Correlation model from Toro. Previously used rho_0 instead of d_0, and the
+  wrong depth
+- Renamed: BedrockDepthVariation to HalfSpaceDepthVariation
+- Fixed: HalfSpaceDepthVariation was removing the last layer
+
 v0.5.0 (2022-06-14)
 -------------------
 - Renamed to `pyStrata`.

{pyStrata-0.5.0 → pystrata-0.5.2}/README.rst

@@ -17,9 +17,20 @@ Strata_. These features include:
     - equivalent-linear with frequency dependent properties
     - quarter wavelength
 - Nonlinear curve models:
-    - Darendeli (2001)
-    - Menq (2004)
-    - Kishida (2012)
+    - Predictive models:
+        - Darendeli (2001)
+        - Menq (2004)
+        - Kishida (2012)
+    - Curves:
+        - Vucetic & Dobry (1991)
+        - EPRI (1993)
+        - GEI (1983)
+        - GeoMatrix (1990)
+        - Idriss (1990)
+        - Imperial Valley Soils
+        - Iwasaki
+        - Peninsular Range
+        - Seed & Idriss
 - Site and soil property uncertainty:
     - Toro (1994) Vs correlation model
     - G/Gmax and D uncertainty:
@@ -55,20 +66,21 @@ directory`_. An interactive Jupyter interface of these examples is available on
 
 .. _Strata: https://github.com/arkottke/strata
 .. _DOI: https://zenodo.org/badge/latestdoi/8959678
-.. _`examples directory`: https://github.com/arkottke/pystrata/tree/master/examples
+.. _`examples directory`: https://github.com/arkottke/pystrata/tree/main/examples
 
 .. |PyPi Cheese Shop| image:: https://img.shields.io/pypi/v/pystrata.svg
    :target: https://pypi.python.org/pypi/pystrata
-.. |Build Status| image:: https://img.shields.io/travis/arkottke/pystrata.svg
-   :target: https://travis-ci.org/arkottke/pystrata
+.. |Build Status| image:: https://img.shields.io/github/workflow/status/arkottke/pystrata/Python%20application
+   :alt: GitHub Workflow Status
+   :target: https://github.com/arkottke/pystrata/actions/workflows/python-app.yml
 .. |Documentation Status| image:: https://readthedocs.org/projects/pystrata/badge/?version=latest&style=flat
    :target: https://pystrata.readthedocs.org
-.. |Code Quality| image:: https://api.codacy.com/project/badge/Grade/6dbbb3a4279744d697b9bfe08af19ded
-   :target: https://www.codacy.com/app/arkottke/pystrata
-.. |Test Coverage| image:: https://api.codacy.com/project/badge/Coverage/6dbbb3a4279744d697b9bfe08af19ded
-   :target: https://www.codacy.com/app/arkottke/pystrata
+.. |Code Quality| image:: https://app.codacy.com/project/badge/Grade/6dbbb3a4279744d697b9bfe08af19ded
+   :target: https://www.codacy.com/gh/arkottke/pystrata/dashboard
+.. |Test Coverage| image:: https://app.codacy.com/project/badge/Coverage/6dbbb3a4279744d697b9bfe08af19ded
+   :target: https://www.codacy.com/gh/arkottke/pystrata/dashboard
 .. |License| image:: https://img.shields.io/badge/license-MIT-blue.svg
 .. |Zenodo| image:: https://zenodo.org/badge/8959678.svg
    :target: https://zenodo.org/badge/latestdoi/8959678
 .. |MyBinder| image:: https://mybinder.org/badge_logo.svg
-   :target: https://mybinder.org/v2/gh/arkottke/pystrata/master?filepath=examples
+   :target: https://mybinder.org/v2/gh/arkottke/pystrata/main?filepath=examples

{pyStrata-0.5.0 → pystrata-0.5.2}/pystrata/__init__.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 # The MIT License (MIT)
 #
 # Copyright (c) 2016-2022 Albert Kottke
@@ -19,9 +20,6 @@
 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
-
-from pkg_resources import get_distribution
-
 from . import motion
 from . import output
 from . import propagation
@@ -35,4 +33,4 @@ __author__ = "Albert Kottke"
 __copyright__ = "Copyright 2016-2022 Albert Kottke"
 __license__ = "MIT"
 __title__ = "pyStrata"
-__version__ = get_distribution("pyStrata").version
+__version__ = "0.5.2"

{pyStrata-0.5.0 → pystrata-0.5.2}/pystrata/motion.py

@@ -200,7 +200,7 @@ class TimeSeriesMotion(Motion):
         tf : :class:`numpy.ndarray`
             Complex-valued transfer function with length equal to `self.freq`.
         """
-        return -(osc_freq ** 2.0) / (
+        return -(osc_freq**2.0) / (
             np.square(self.freqs)
             - np.square(osc_freq)
             - 2.0j * damping * osc_freq * self.freqs

{pyStrata-0.5.0 → pystrata-0.5.2}/pystrata/output.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 # The MIT License (MIT)
 #
 # Copyright (c) 2016-2021 Albert Kottke
@@ -406,7 +407,7 @@ class AriasIntensityTSOutput(AccelerationTSOutput):
 
     def _modify_values(self, calc, location, values):
         time_step = calc.motion.time_step
-        values = scipy.integrate.cumtrapz(values ** 2, dx=time_step)
+        values = scipy.integrate.cumtrapz(values**2, dx=time_step)
         values *= GRAVITY * np.pi / 2
         return values
 
@@ -486,15 +487,17 @@ class FourierAmplitudeSpectrumOutput(LocationBasedOutput):
         loc = self._get_location(calc)
         tf = calc.calc_accel_tf(calc.loc_input, loc)
 
-        if self.ko_bandwidth:
-            smoothed = pykooh.smooth(
+        if self._ko_bandwidth is None:
+            tf = np.interp(self.freqs, calc.motion.freqs, tf)
+        else:
+            tf = pykooh.smooth(
                 self.freqs,
                 calc.motion.freqs,
                 np.abs(tf * calc.motion.fourier_amps),
                 self.ko_bandwidth,
             )
 
-        self._add_values(smoothed)
+        self._add_values(tf)
 
 
 class ResponseSpectrumOutput(LocationBasedOutput):

{pyStrata-0.5.0 → pystrata-0.5.2}/pystrata/propagation.py

@@ -452,7 +452,7 @@ class LinearElasticCalculator(AbstractCalculator):
                 - self._waves_b[lout.index, :] * np.exp(-cterm)
             )
         )
-        denom = -(ang_freqs ** 2) * self.wave_at_location(lin)
+        denom = -(ang_freqs**2) * self.wave_at_location(lin)
 
         # Only compute transfer function for non-zero frequencies
         mask = ~np.isclose(ang_freqs, 0)

{pyStrata-0.5.0 → pystrata-0.5.2}/pystrata/site.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 # The MIT License (MIT)
 #
 # Copyright (c) 2016-2018 Albert Kottke
@@ -22,7 +23,10 @@
 from __future__ import annotations
 
 import collections
+import warnings
 from dataclasses import dataclass
+from pathlib import Path
+from typing import List
 from typing import Optional
 from typing import Tuple
 
@@ -30,6 +34,7 @@ import matplotlib.pyplot as plt
 import numpy as np
 import numpy.typing as npt
 import scipy.constants
+import tomli
 from scipy.interpolate import interp1d
 
 from .motion import GRAVITY
@@ -39,6 +44,32 @@ COMP_MODULUS_MODEL = "dormieux"
 
 KPA_TO_ATM = scipy.constants.kilo / scipy.constants.atm
 
+PUBLISHED_CURVES = None
+
+
+def _load_published_curves():
+    """Load published nonlinear curves."""
+    global PUBLISHED_CURVES
+
+    fpath = Path(__file__).parent / "data" / "published_curves.toml"
+    with fpath.open("rb") as fp:
+        models = tomli.load(fp)["models"]
+
+    # Count to make sure there aren't repeated names
+    counts = collections.Counter([m["name"] for m in models])
+    if max(counts.values()) > 1:
+        names = ", ".join([k for k, v in counts.items() if v > 1])
+        warnings.warn(f"Repeated names in {fpath}: " + names)
+
+    PUBLISHED_CURVES = {m["name"]: m for m in models}
+
+
+def known_published_curves() -> List[dict]:
+    """List of published curves in the database."""
+    if not PUBLISHED_CURVES:
+        _load_published_curves()
+    return list(PUBLISHED_CURVES.keys())
+
 
 class NonlinearProperty(object):
     """Class for nonlinear property with a method for log-linear interpolation.
@@ -76,6 +107,18 @@ class NonlinearProperty(object):
 
         self._update()
 
+    @classmethod
+    def from_published(cls, name, param):
+        assert param in cls.PARAMS
+        if not PUBLISHED_CURVES:
+            _load_published_curves()
+
+        selected = PUBLISHED_CURVES[name][param]
+
+        return cls(
+            name, strains=selected["strains"], values=selected["values"], param=param
+        )
+
     def __call__(self, strains):
         """Return the nonlinear property at a specific strain.
 
@@ -192,6 +235,21 @@ class SoilType(object):
         self.mod_reduc = mod_reduc
         self.damping = damping
 
+    @classmethod
+    def from_published(cls, name, unit_wt, *args):
+        if not PUBLISHED_CURVES:
+            _load_published_curves()
+
+        model_mr = args[0]
+        model_d = args[1] if len(args) > 1 else args[0]
+
+        return cls(
+            name,
+            unit_wt=unit_wt,
+            mod_reduc=NonlinearProperty.from_published(model_mr, "mod_reduc"),
+            damping=NonlinearProperty.from_published(model_d, "damping"),
+        )
+
     def copy(self):
         return SoilType(self.name, self.unit_wt, self.mod_reduc, self.damping)
 
@@ -227,7 +285,7 @@ class SoilType(object):
         # return all(
         #     getattr(self, attr) == getattr(other, attr)
         #     for attr in ['name', 'unit_wt', 'mod_reduc', 'damping'])
-        return self.__dict__ == other.__dict__
+        return (type(self) == type(other)) and (self.__dict__ == other.__dict__)
 
     def __hash__(self):
         return hash(self.__dict__.values())
@@ -269,22 +327,22 @@ class ModifiedHyperbolicSoilType(SoilType):
                 - strain_ref_percent
                 * np.log((strains_percent + strain_ref_percent) / strain_ref_percent)
             )
-            / (strains_percent ** 2 / (strains_percent + strain_ref_percent))
+            / (strains_percent**2 / (strains_percent + strain_ref_percent))
             - 2.0
         )
         # Correction between perfect hyperbolic strain model and modified
         # model [%].
-        c1 = -1.1143 * self.curvature ** 2 + 1.8618 * self.curvature + 0.2523
-        c2 = 0.0805 * self.curvature ** 2 - 0.0710 * self.curvature - 0.0095
-        c3 = -0.0005 * self.curvature ** 2 + 0.0002 * self.curvature + 0.0003
+        c1 = -1.1143 * self.curvature**2 + 1.8618 * self.curvature + 0.2523
+        c2 = 0.0805 * self.curvature**2 - 0.0710 * self.curvature - 0.0095
+        c3 = -0.0005 * self.curvature**2 + 0.0002 * self.curvature + 0.0003
         damping_masing = (
             c1 * damping_masing_a1
-            + c2 * damping_masing_a1 ** 2
-            + c3 * damping_masing_a1 ** 3
+            + c2 * damping_masing_a1**2
+            + c3 * damping_masing_a1**3
         )
 
         # Compute the damping correction in percent
-        d_correction = self.masing_scaling * damping_masing * mod_reduc ** 0.1
+        d_correction = self.masing_scaling * damping_masing * mod_reduc**0.1
 
         # Prevent the damping from reducing as it can at large strains
         damping = np.maximum.accumulate(d_correction / 100.0)
@@ -371,14 +429,14 @@ class TwoParamModifiedHyperbolicSoilType(SoilType):
         stress_mean_atm = stress_mean * KPA_TO_ATM
 
         # Convert from percent to decimal strain
-        strain_mr = C.g1 * stress_mean_atm ** C.g2 / 100
+        strain_mr = C.g1 * stress_mean_atm**C.g2 / 100
         b = C.b1 + C.b2 * stress_mean_atm
         values_mr = 1 / ((1 + (strains / strain_mr) ** C.a)) ** b
         mod_reduc = NonlinearProperty(name, strains, values_mr)
 
-        d_min = C.d0 * stress_mean_atm ** C.d1
+        d_min = C.d0 * stress_mean_atm**C.d1
         # Convert from percent to decimal strain
-        strain_dr = (C.gd1 * stress_mean_atm ** C.gd2) / 100
+        strain_dr = (C.gd1 * stress_mean_atm**C.gd2) / 100
         term = (strains / strain_dr) ** C.c
         # Convert to damping in decimal
         values_d = (C.d * term + d_min) / (term + 1) / 100
@@ -437,7 +495,7 @@ class DarendeliSoilType(ModifiedHyperbolicSoilType):
     def _calc_damping_min(self):
         """minimum damping [decimal]"""
         return (
-            (0.8005 + 0.0129 * self._plas_index * self._ocr ** -0.1069)
+            (0.8005 + 0.0129 * self._plas_index * self._ocr**-0.1069)
             * (self._stress_mean * KPA_TO_ATM) ** -0.2889
             * (1 + 0.2919 * np.log(self._freq))
         ) / 100
@@ -451,7 +509,7 @@ class DarendeliSoilType(ModifiedHyperbolicSoilType):
     def strain_ref(self):
         """reference strain [decimal]"""
         return (
-            (0.0352 + 0.0010 * self._plas_index * self._ocr ** 0.3246)
+            (0.0352 + 0.0010 * self._plas_index * self._ocr**0.3246)
             * (self._stress_mean * KPA_TO_ATM) ** 0.3483
         ) / 100
 
@@ -464,7 +522,7 @@ class DarendeliSoilType(ModifiedHyperbolicSoilType):
         return fmt.format(self._plas_index, self._ocr, self._stress_mean)
 
 
-class MenqSoilType(DarendeliSoilType):
+class MenqSoilType(ModifiedHyperbolicSoilType):
     """
     Menq SoilType for gravelly soils.
 
@@ -510,18 +568,23 @@ class MenqSoilType(DarendeliSoilType):
     def _calc_damping_min(self):
         return (
             0.55
-            * self._uniformity_coeff ** 0.1
-            * self._diam_mean ** -0.3
+            * self._uniformity_coeff**0.1
+            * self._diam_mean**-0.3
             * (self._stress_mean * KPA_TO_ATM) ** -0.08
         ) / 100
 
+    @property
+    def masing_scaling(self):
+        # Masing correction factor
+        return 0.6329 - 0.00566 * np.log(self._num_cycles)
+
     @property
     def strain_ref(self):
         return (
             0.12
-            * self._uniformity_coeff ** -0.6
+            * self._uniformity_coeff**-0.6
             * (self._stress_mean * KPA_TO_ATM)
-            ** (0.5 * self._uniformity_coeff ** -0.15)
+            ** (0.5 * self._uniformity_coeff**-0.15)
         ) / 100
 
     @property
@@ -758,13 +821,7 @@ class Layer(object):
 
         self._soil_type = soil_type
         self._thickness = thickness
-        self._initial_shear_vel = shear_vel
-
-        self._damping = None
-        self._shear_mod = None
-        self._strain = None
-        self.strain_max = None
-        self.reset()
+        self.initial_shear_vel = shear_vel
 
         self._depth = 0
         self._stress_vert = 0
@@ -781,6 +838,20 @@ class Layer(object):
             f"soil_type={st_name})>"
         )
 
+    def __eq__(self, other):
+        attrs = ["_soil_type", "_thickness", "initial_shear_vel"]
+        return (type(self) == type(other)) and all(
+            [getattr(self, a) == getattr(other, a) for a in attrs]
+        )
+
+    def __hash__(self):
+        return hash(self.__dict__.values())
+
+    @classmethod
+    def copy_of(cls, other):
+        """Return a copy of the Layer instance with previously defined SoilType."""
+        return cls(other.soil_type, other.thickness, other.shear_vel)
+
     @property
     def depth(self):
         """Depth to the top of the layer [m]."""
@@ -796,11 +867,6 @@ class Layer(object):
         """Depth to the base of the layer [m]."""
         return self._depth + self._thickness
 
-    @classmethod
-    def duplicate(cls, other):
-        """Create a copy of the layer."""
-        return cls(other.soil_type, other.thickness, other.shear_vel)
-
     @property
     def density(self):
         """Density of soil in [kg/m³]."""
@@ -818,13 +884,21 @@ class Layer(object):
     @property
     def initial_shear_mod(self):
         """Initial (small-strain) shear modulus [kN/m²]."""
-        return self.density * self.initial_shear_vel ** 2
+        return self.density * self.initial_shear_vel**2
 
     @property
     def initial_shear_vel(self):
         """Initial (small-strain) shear-wave velocity [m/s]."""
         return self._initial_shear_vel
 
+    @initial_shear_vel.setter
+    def initial_shear_vel(self, value: float):
+        """Set initial (small-strain) shear-wave velocity [m/s]."""
+
+        self._initial_shear_vel = value
+        # Reset the iterated values
+        self.reset()
+
     @property
     def comp_shear_mod(self):
         """Strain-compatible complex shear modulus [kN/m²]."""
@@ -838,12 +912,12 @@ class Layer(object):
             # Simplifed shear modulus (Kramer, 1996)
             # Correct dissipated energy
             # Incorrect shear modulus: G * \sqrt{1 + 2 \beta^2 + \beta^4 }
-            comp_factor = 1 - damping ** 2 + 2j * damping
+            comp_factor = 1 - damping**2 + 2j * damping
         elif COMP_MODULUS_MODEL == "dormieux":
             # Dormieux and Canou (1990)
             # Correct dissipated energy
             # Correct shear modulus:
-            comp_factor = np.sqrt(1 - 4 * damping ** 2) + 2j * damping
+            comp_factor = np.sqrt(1 - 4 * damping**2) + 2j * damping
         else:
             raise NotImplementedError
         comp_shear_mod = self.shear_mod * comp_factor
@@ -864,6 +938,8 @@ class Layer(object):
         # Use a small initial value
         self._strain = IterativeValue(1e-6)
 
+        self.strain_max = None
+
     @property
     def shear_mod(self):
         """Strain-compatible shear modulus [kN//m²]."""
@@ -933,7 +1009,7 @@ class Layer(object):
     @thickness.setter
     def thickness(self, thickness):
         self._thickness = thickness
-        self._profile.update_layers(self, self._profile.index(self) + 1)
+        self._profile.update_layers(self._profile.index(self) + 1)
 
     @property
     def travel_time(self):
@@ -1050,6 +1126,11 @@ class Profile(collections.abc.Container):
     def __getitem__(self, key):
         return self.layers[key]
 
+    @classmethod
+    def copy_of(cls, other):
+        """Return a copy of the profile with new Layer instances."""
+        return cls([Layer.copy_of(layer) for layer in other], other.wt_depth)
+
     def index(self, layer):
         return self.layers.index(layer)
 
@@ -1259,7 +1340,7 @@ class Profile(collections.abc.Container):
         depths_mid = self.depth_mid
         shear_vels = self.initial_shear_vel
 
-        mode_incr = depths_mid * thicks / shear_vels ** 2
+        mode_incr = depths_mid * thicks / shear_vels**2
         # Mode shape is computed as the sumation from the base of
         # the profile. Need to append a 0 for the roll performed in the next
         # step
@@ -1269,7 +1350,7 @@ class Profile(collections.abc.Container):
         # can be calculated for two adjacent layers
         freq_fund = np.sqrt(
             4
-            * np.sum(thicks * depths_mid ** 2 / shear_vels ** 2)
+            * np.sum(thicks * depths_mid**2 / shear_vels**2)
             / np.sum(
                 thicks * np.sum(np.c_[shape, np.roll(shape, -1)], axis=1)[:-1] ** 2
             )

{pyStrata-0.5.0 → pystrata-0.5.2}/pystrata/variation.py

@@ -20,6 +20,7 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 import copy
+from abc import abstractmethod
 from typing import Dict
 from typing import List
 from typing import Optional
@@ -241,24 +242,47 @@ class ToroThicknessVariation(object):
         return varied
 
 
-class BedrockDepthVariation(object):
-    def __init__(
-        self,
-        dist: stats.rv_continuous,
-        discretize_kwds: Optional[Dict[str, float]] = None,
-    ):
+class HalfSpaceDepthVariation(object):
+    def __init__(self, dist: stats.rv_continuous):
         self._dist = dist
-        self._discretize_kwds = discretize_kwds or dict(max_freq=50, wave_frac=2)
 
     def __call__(self, profile: site.Profile) -> site.Profile:
+        # Update the distribution with the central value of the profile
         varied_depth = self._dist.rvs()
 
+        # Find the layer
         index, depth_within = profile.lookup_depth(varied_depth)
 
-        _profile = site.Profile([layer for layer in profile[: (index + 1)]])
-        _profile[-1].thickness = depth_within
+        print(varied_depth, profile[-1].depth, index, depth_within)
+
+        half_space = profile[-1]
+
+        if index < (len(profile) - 1):
+            # Variation is within the layers
+            layers = [site.Layer.copy_of(layer) for layer in profile[: (index + 1)]]
+            # Reduce the thickness of the layer above the half-space
+            layers[-1]._thickness = depth_within
+        else:
+            # Variation extends past the depth of the model
+            orig_thick = profile[-2].thickness
+            total_thick = orig_thick + depth_within
+            count = np.ceil(total_thick // orig_thick).astype(int)
+
+            thick = total_thick / count
 
-        return _profile.auto_discretize(**self._discretize_kwds)
+            print(count, thick)
+
+            # Don't copy half-space
+            layers = [site.Layer.copy_of(layer) for layer in profile[:-1]]
+            # Don't call the setter function as it needs a profile defined
+            layers[-1]._thickness = thick
+            parent = layers[-1]
+            for _ in range(count - 1):
+                layers.append(site.Layer.copy_of(parent))
+
+        layers.append(half_space)
+
+        return site.Profile(layers, profile.wt_depth)
 
 
 class LayerThicknessVariation(object):
@@ -302,17 +326,12 @@ class VelocityVariation(object):
         ln_vel = np.clip(ln_vel_rand, mean - offset, mean + offset)
         vel = np.exp(ln_vel)
 
-        # Create the new layers
+        varied = site.Profile.copy_of(profile)
+        # Update the velocities
         end = None if self.vary_bedrock else -1
-        # FIXME: Can we use .copy()?
-        layers = [
-            site.Layer(l.soil_type, l.thickness, vel[i])
-            for i, l in enumerate(profile[:end])
-        ]
-        if not self.vary_bedrock:
-            layers.append(profile[-1])
+        for i, v in enumerate(vel[:end]):
+            varied[i].initial_shear_vel = v
 
-        varied = site.Profile(layers, profile.wt_depth)
         return varied
 
     def _calc_covar_matrix(self, profile):
@@ -341,6 +360,7 @@ class VelocityVariation(object):
 
         return mat
 
+    @abstractmethod
     def _calc_corr(self, profile):
         """Compute the adjacent-layer correlations.
 
@@ -356,6 +376,7 @@ class VelocityVariation(object):
         """
         raise NotImplementedError
 
+    @abstractmethod
     def _calc_ln_std(self, profile):
         """Compute the standard deviation for each layer.
 
@@ -497,13 +518,20 @@ class ToroVelocityVariation(VelocityVariation):
         corr : :class:`numpy.array`
             Adjacent-layer correlations
         """
-        depth = profile.depth_mid[:-1]
+
+        # Toro defines the depth as the average midpoint depths of layers i and i-1.
+        depths_mid = np.array(profile.depth_mid)
+        depth = np.mean(np.c_[depths_mid[:-1], depths_mid[1:]], axis=1)
+
+        # t variable from Toro; defined as the difference of the midpoint depths
         thick = np.diff(depth)
-        depth = depth[1:]
+        # Remove the depth associated with the final layer. We will set that it is
+        # perfectly correlated later.
+        depth = depth[:-1]
 
         # Depth dependent correlation
         corr_depth = self.rho_200 * np.power(
-            (depth + self.rho_0) / (200 + self.rho_0), self.b
+            (depth + self.h_0) / (200 + self.h_0), self.b
         )
         corr_depth[depth > 200] = self.rho_200
 
@@ -627,7 +655,7 @@ class DepthDependToroVelVariation(ToroVelocityVariation):
         rho_200: float,
         h_0: float,
         b: float,
-        ln_std_map=Optional[Dict[str,float]],
+        ln_std_map=Optional[Dict[str, float]],
         vary_bedrock=False,
     ):
         """Initialize the model."""
@@ -875,9 +903,9 @@ def iter_varied_profiles(
     var_velocity: VelocityVariation = None,
     var_soiltypes: SoilTypeVariation = None,
 ):
-    for i in range(count):
+    for _ in range(count):
         # Copy the profile to form the realization
-        p = profile
+        p = site.Profile.copy_of(profile)
 
         if var_thickness:
             p = var_thickness(p)

{pyStrata-0.5.0/pyStrata.egg-info → pystrata-0.5.2/pystrata.egg-info}/PKG-INFO

@@ -1,23 +1,11 @@
 Metadata-Version: 2.1
-Name: pyStrata
-Version: 0.5.0
-Summary: Site Response Analysis with Python
-Home-page: http://github.com/arkottke/pystrata
-Author: Albert Kottke
+Name: pystrata
+Version: 0.5.2
+Summary: Site response analysis with Python
+Home-page: https://github.com/arkottke/pystrata
+Author: Albert R. Kottke
 Author-email: albert.kottke@gmail.com
 License: MIT
-Keywords: site response
-Classifier: Development Status :: 4 - Beta
-Classifier: Environment :: Console
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Natural Language :: English
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Topic :: Scientific/Engineering
-Classifier: Intended Audience :: Science/Research
-Description-Content-Type: text/x-rst
-Provides-Extra: dataframe
 License-File: LICENSE
 License-File: AUTHORS.rst
 
@@ -40,9 +28,20 @@ Strata_. These features include:
     - equivalent-linear with frequency dependent properties
     - quarter wavelength
 - Nonlinear curve models:
-    - Darendeli (2001)
-    - Menq (2004)
-    - Kishida (2012)
+    - Predictive models:
+        - Darendeli (2001)
+        - Menq (2004)
+        - Kishida (2012)
+    - Curves:
+        - Vucetic & Dobry (1991)
+        - EPRI (1993)
+        - GEI (1983)
+        - GeoMatrix (1990)
+        - Idriss (1990)
+        - Imperial Valley Soils
+        - Iwasaki
+        - Peninsular Range
+        - Seed & Idriss
 - Site and soil property uncertainty:
     - Toro (1994) Vs correlation model
     - G/Gmax and D uncertainty:
@@ -78,28 +77,40 @@ directory`_. An interactive Jupyter interface of these examples is available on
 
 .. _Strata: https://github.com/arkottke/strata
 .. _DOI: https://zenodo.org/badge/latestdoi/8959678
-.. _`examples directory`: https://github.com/arkottke/pystrata/tree/master/examples
+.. _`examples directory`: https://github.com/arkottke/pystrata/tree/main/examples
 
 .. |PyPi Cheese Shop| image:: https://img.shields.io/pypi/v/pystrata.svg
    :target: https://pypi.python.org/pypi/pystrata
-.. |Build Status| image:: https://img.shields.io/travis/arkottke/pystrata.svg
-   :target: https://travis-ci.org/arkottke/pystrata
+.. |Build Status| image:: https://img.shields.io/github/workflow/status/arkottke/pystrata/Python%20application
+   :alt: GitHub Workflow Status
+   :target: https://github.com/arkottke/pystrata/actions/workflows/python-app.yml
 .. |Documentation Status| image:: https://readthedocs.org/projects/pystrata/badge/?version=latest&style=flat
    :target: https://pystrata.readthedocs.org
-.. |Code Quality| image:: https://api.codacy.com/project/badge/Grade/6dbbb3a4279744d697b9bfe08af19ded
-   :target: https://www.codacy.com/app/arkottke/pystrata
-.. |Test Coverage| image:: https://api.codacy.com/project/badge/Coverage/6dbbb3a4279744d697b9bfe08af19ded
-   :target: https://www.codacy.com/app/arkottke/pystrata
+.. |Code Quality| image:: https://app.codacy.com/project/badge/Grade/6dbbb3a4279744d697b9bfe08af19ded
+   :target: https://www.codacy.com/gh/arkottke/pystrata/dashboard
+.. |Test Coverage| image:: https://app.codacy.com/project/badge/Coverage/6dbbb3a4279744d697b9bfe08af19ded
+   :target: https://www.codacy.com/gh/arkottke/pystrata/dashboard
 .. |License| image:: https://img.shields.io/badge/license-MIT-blue.svg
 .. |Zenodo| image:: https://zenodo.org/badge/8959678.svg
    :target: https://zenodo.org/badge/latestdoi/8959678
 .. |MyBinder| image:: https://mybinder.org/badge_logo.svg
-   :target: https://mybinder.org/v2/gh/arkottke/pystrata/master?filepath=examples
-
+   :target: https://mybinder.org/v2/gh/arkottke/pystrata/main?filepath=examples
 
 History
 =======
 
+v0.5.2 (2023-01-18)
+-------------------
+- Fixed: Providing unsmoothed transfer function output
+- Fixed: MenqSoilType
+
+v0.5.1 (2022-09-22)
+-------------------
+- Fixed: Correlation model from Toro. Previously used rho_0 instead of d_0, and the
+  wrong depth
+- Renamed: BedrockDepthVariation to HalfSpaceDepthVariation
+- Fixed: HalfSpaceDepthVariation was removing the last layer
+
 v0.5.0 (2022-06-14)
 -------------------
 - Renamed to `pyStrata`.

pystrata-0.5.2/pystrata.egg-info/SOURCES.txt

@@ -0,0 +1,26 @@
+AUTHORS.rst
+HISTORY.rst
+LICENSE
+MANIFEST.in
+README.rst
+requirements.txt
+setup.cfg
+setup.py
+pystrata/__init__.py
+pystrata/motion.py
+pystrata/output.py
+pystrata/propagation.py
+pystrata/site.py
+pystrata/tools.py
+pystrata/variation.py
+pystrata.egg-info/PKG-INFO
+pystrata.egg-info/SOURCES.txt
+pystrata.egg-info/dependency_links.txt
+pystrata.egg-info/top_level.txt
+tests/__init__.py
+tests/motion_test.py
+tests/notebooks_test.py
+tests/output_test.py
+tests/propagation_test.py
+tests/site_test.py
+tests/variation_test.py

{pyStrata-0.5.0 → pystrata-0.5.2}/requirements.txt

@@ -1,11 +1,13 @@
 --index-url https://pypi.python.org/simple/
 
 matplotlib
-numpy
 numba
+numpy
+pandas
 pyexcel
 pyexcel-xlsx
 pykooh
 pyrvt
 scipy
 setuptools
+tomli

pystrata-0.5.2/setup.cfg

@@ -0,0 +1,37 @@
+[metadata]
+name = pystrata
+version = attr: pystrata.__version__
+description = Site response analysis with Python
+description_file = README.rst
+long_description = file: README.rst, HISTORY.rst
+author = Albert R. Kottke
+author_email = albert.kottke@gmail.com
+license = MIT
+url = https://github.com/arkottke/pystrata
+
+[options]
+packages = find:
+
+[aliases]
+test = pytest
+
+[flake8]
+exclude = docs/
+
+[yapf]
+based_on_style = pep8
+spaces_around_power_operator = true
+
+[tool:test]
+addopts = --flake8
+
+[wheel]
+universal = 1
+
+[pydocstyle]
+ignore = D100,D101,D102,D103,D104,W503
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

pystrata-0.5.2/setup.py

@@ -0,0 +1,6 @@
+#!/usr/bin/python3
+# -*- coding: utf-8 -*-
+from setuptools import setup
+
+if __name__ == "__main__":
+    setup()

pyStrata-0.5.0/tests/test_motion.py → pystrata-0.5.2/tests/motion_test.py

@@ -77,7 +77,7 @@ def test_ts_fft_with_tf(tsm):
 def test_ts_fa_normalize(tsm):
     """Test the normalization of the Fourier amplitudes with Parsevla's theorem."""
     assert_allclose(
-        trapz(tsm.accels ** 2, dx=tsm.time_step),
+        trapz(tsm.accels**2, dx=tsm.time_step),
         2 * trapz(np.abs(tsm.fourier_amps) ** 2, tsm.freqs),
     )
 

pyStrata-0.5.0/tests/test_notebooks.py → pystrata-0.5.2/tests/notebooks_test.py

@@ -38,7 +38,7 @@ def test_notebook(fpath):
     with fpath.open() as fp:
         nb = nbformat.read(fp, as_version=4)
 
-    ep = ExecutePreprocessor(timeout=600)
+    ep = ExecutePreprocessor(timeout=600, kernel_name="python3")
 
     try:
         ep.preprocess(nb, {"metadata": {"path": fpath.parent}})

pyStrata-0.5.0/tests/test_output.py → pystrata-0.5.2/tests/output_test.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 # encoding: utf-8
-
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation; either version 2 of the License, or
@@ -16,10 +15,8 @@
 # Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
 #
 # Copyright (C) Albert Kottke, 2013-2016
-
 import numpy as np
 import pytest
-
 from numpy.testing import assert_allclose
 
 import pystrata

pyStrata-0.5.0/tests/test_propagation.py → pystrata-0.5.2/tests/propagation_test.py

@@ -294,7 +294,9 @@ class TestExample02LE(DeepSoilComparison):
                 pystrata.site.SoilType("Soil", 20.0, mod_reduc=None, damping=0), 20, 500
             ),
             pystrata.site.Layer(
-                pystrata.site.SoilType("Rock", 25.0, mod_reduc=None, damping=0.02), 0, 760
+                pystrata.site.SoilType("Rock", 25.0, mod_reduc=None, damping=0.02),
+                0,
+                760,
             ),
         ]
     )
@@ -310,7 +312,9 @@ class TestExample02EL(DeepSoilComparison):
                 pystrata.site.SoilType("Soil", 20.0, mod_reduc=None, damping=0), 20, 500
             ),
             pystrata.site.Layer(
-                pystrata.site.SoilType("Rock", 25.0, mod_reduc=None, damping=0.02), 0, 760
+                pystrata.site.SoilType("Rock", 25.0, mod_reduc=None, damping=0.02),
+                0,
+                760,
             ),
         ]
     )
@@ -322,10 +326,14 @@ class TestExample04EL(DeepSoilComparison):
     profile = pystrata.site.Profile(
         [
             pystrata.site.Layer(
-                pystrata.site.SoilType("Soil", 20.0, mod_reduc=None, damping=0.05), 20, 500
+                pystrata.site.SoilType("Soil", 20.0, mod_reduc=None, damping=0.05),
+                20,
+                500,
             ),
             pystrata.site.Layer(
-                pystrata.site.SoilType("Rock", 25.0, mod_reduc=None, damping=0.02), 0, 760
+                pystrata.site.SoilType("Rock", 25.0, mod_reduc=None, damping=0.02),
+                0,
+                760,
             ),
         ]
     )

pyStrata-0.5.0/tests/test_site.py → pystrata-0.5.2/tests/site_test.py

@@ -27,6 +27,26 @@ from . import FPATH_DATA
 from pystrata import site
 
 
+def test_published_nonlinear_property():
+    site.NonlinearProperty.from_published("Vucetic & Dobry (91), PI=0", "damping")
+
+
+def test_published_soiltype_same():
+    model = "Vucetic & Dobry (91), PI=0"
+
+    st = site.SoilType.from_published("test", 14, model)
+    assert st.mod_reduc.name == model
+
+
+def test_published_soiltype_same():
+    model_mr = "Vucetic & Dobry (91), PI=0"
+    model_d = "Vucetic & Dobry (91), PI=15"
+
+    st = site.SoilType.from_published("test", 14, model_mr, model_d)
+    assert st.mod_reduc.name == model_mr
+    assert st.damping.name == model_d
+
+
 @pytest.fixture
 def nlp():
     """Create an example NonlinearProperty."""

pyStrata-0.5.0/tests/test_variation.py → pystrata-0.5.2/tests/variation_test.py

@@ -16,7 +16,10 @@
 #
 # Copyright (C) Albert Kottke, 2013-2016
 import numpy as np
+import pytest
 from numpy.testing import assert_allclose
+from scipy.stats import lognorm
+from scipy.stats import norm
 from scipy.stats import pearsonr
 
 from pystrata import motion
@@ -144,17 +147,26 @@ class TestSpidVariation:
         )
 
 
-def test_iter_variations():
-    m = motion.SourceTheoryRvtMotion(6.0, 30, "wna")
-    m.calc_fourier_amps()
-
-    profile = site.Profile(
+@pytest.fixture
+def profile():
+    """Simple profile for tests."""
+    return site.Profile(
         [
+            site.Layer(
+                site.DarendeliSoilType(18.0, plas_index=0, ocr=1, stress_mean=200),
+                10,
+                300,
+            ),
             site.Layer(
                 site.DarendeliSoilType(18.0, plas_index=0, ocr=1, stress_mean=200),
                 10,
                 400,
             ),
+            site.Layer(
+                site.DarendeliSoilType(18.0, plas_index=0, ocr=1, stress_mean=200),
+                10,
+                500,
+            ),
             site.Layer(
                 site.DarendeliSoilType(18.0, plas_index=0, ocr=1, stress_mean=200),
                 20,
@@ -164,6 +176,32 @@ def test_iter_variations():
         ]
     )
 
+
+@pytest.mark.parametrize("dist", [norm(scale=2, loc=50), lognorm(s=0.2, scale=50)])
+def test_halfspace_depth_variation(dist, profile):
+    varier = variation.HalfSpaceDepthVariation(dist)
+    count = 500
+
+    varied = varier(profile)
+    # Check the surface and bedrock is the same
+    assert profile[0] == varied[0]
+    assert profile[-1] == varied[-1]
+
+    for _ in range(10):
+        v = varier(profile)
+        assert all(layer.thickness >= 0 for layer in v)
+
+    # Sample to the half-space from the varied profiles
+    depths = [varier(profile)[-1].depth for _ in range(count)]
+
+    assert_allclose(dist.mean(), np.mean(depths), rtol=0.2)
+    assert_allclose(dist.std(), np.std(depths), rtol=0.2)
+
+
+def test_iter_variations(profile):
+    m = motion.SourceTheoryRvtMotion(6.0, 30, "wna")
+    m.calc_fourier_amps()
+
     calc = propagation.EquivalentLinearCalculator()
     var_thickness = variation.ToroThicknessVariation()
     var_velocity = variation.ToroVelocityVariation.generic_model("USGS C")

pyStrata-0.5.0/pyStrata.egg-info/SOURCES.txt

@@ -1,27 +0,0 @@
-AUTHORS.rst
-HISTORY.rst
-LICENSE
-MANIFEST.in
-README.rst
-requirements.txt
-setup.cfg
-setup.py
-pyStrata.egg-info/PKG-INFO
-pyStrata.egg-info/SOURCES.txt
-pyStrata.egg-info/dependency_links.txt
-pyStrata.egg-info/requires.txt
-pyStrata.egg-info/top_level.txt
-pystrata/__init__.py
-pystrata/motion.py
-pystrata/output.py
-pystrata/propagation.py
-pystrata/site.py
-pystrata/tools.py
-pystrata/variation.py
-tests/__init__.py
-tests/test_motion.py
-tests/test_notebooks.py
-tests/test_output.py
-tests/test_propagation.py
-tests/test_site.py
-tests/test_variation.py

pyStrata-0.5.0/pyStrata.egg-info/requires.txt

@@ -1,10 +0,0 @@
-matplotlib
-numpy
-pyrvt
-pykooh
-scipy
-setuptools
-typing
-
-[dataframe]
-pandas

pyStrata-0.5.0/setup.cfg

@@ -1,26 +0,0 @@
-[aliases]
-test = pytest
-
-[flake8]
-exclude = docs/
-
-[metadata]
-description-file = README.rst
-
-[yapf]
-based_on_style = pep8
-spaces_around_power_operator = true
-
-[tool:test]
-addopts = --flake8
-
-[wheel]
-universal = 1
-
-[pydocstyle]
-ignore = D100,D101,D102,D103,D104,W503
-
-[egg_info]
-tag_build = 
-tag_date = 0
-

pyStrata-0.5.0/setup.py

@@ -1,48 +0,0 @@
-#!/usr/bin/python3
-# -*- coding: utf-8 -*-
-from setuptools import find_packages
-from setuptools import setup
-
-with open("README.rst") as fp:
-    readme = fp.read()
-
-with open("HISTORY.rst") as fp:
-    history = fp.read()
-
-setup(
-    name="pyStrata",
-    version="0.5.0",
-    description="Site Response Analysis with Python",
-    long_description=readme + "\n\n" + history,
-    long_description_content_type='text/x-rst',
-    author="Albert Kottke",
-    author_email="albert.kottke@gmail.com",
-    url="http://github.com/arkottke/pystrata",
-    packages=find_packages(),
-    install_requires=[
-        "matplotlib",
-        "numpy",
-        "pyrvt",
-        "pykooh",
-        "scipy",
-        "setuptools",
-        "typing",
-    ],
-    extras_require={
-        "dataframe": ["pandas"],
-    },
-    keywords="site response",
-    license="MIT",
-    classifiers=[
-        "Development Status :: 4 - Beta",
-        "Environment :: Console",
-        "License :: OSI Approved :: MIT License",
-        "Natural Language :: English",
-        "Operating System :: OS Independent",
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 3.6",
-        "Topic :: Scientific/Engineering",
-        "Intended Audience :: Science/Research",
-    ],
-    test_suite="tests",
-)