dyncfs 2.0.2__tar.gz → 2.1.0__tar.gz

{dyncfs-2.0.2 → dyncfs-2.1.0}/MANIFEST.in

@@ -3,7 +3,7 @@ include LICENSE
 recursive-include fortran_src_codes  *.f *.for *.f90 *.F *.F90
 recursive-include fortran_src_codes  *.inc *.INC *.par *.PAR *.dat *.DAT *.txt *.cfg *.in *.h *.H
 recursive-include dyncfs/exec *.jar
-exclude dyncfs/exec/*.bin
-exclude dyncfs/exec/*.exe
+#exclude dyncfs/exec/*.bin
+#exclude dyncfs/exec/*.exe
 exclude dyncfs/exec/*.out
 exclude dyncfs/exec/*.o

{dyncfs-2.0.2/dyncfs.egg-info → dyncfs-2.1.0}/PKG-INFO

@@ -1,92 +1,45 @@
 Metadata-Version: 2.4
 Name: dyncfs
-Version: 2.0.2
+Version: 2.1.0
 Summary: A Python library for computing Coulomb Failure Stress Change.
 Author-email: Zhou Jiangcheng <zhoujcpku@outlook.com>
-License: MIT License
-        
-        Copyright (c) 2024 Zhou Jiangcheng
-        
-        Permission is hereby granted, free of charge, to any person obtaining a copy
-        of this software and associated documentation files (the "Software"), to deal
-        in the Software without restriction, including without limitation the rights
-        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-        copies of the Software, and to permit persons to whom the Software is
-        furnished to do so, subject to the following conditions:
-        
-        The above copyright notice and this permission notice shall be included in all
-        copies or substantial portions of the Software.
-        
-        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-        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.
+License-Expression: MIT
 Project-URL: Homepage, https://github.com/Zhou-Jiangcheng/dyncfs
-Requires-Python: >=3.11
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy>=2.3.3
+Requires-Dist: pygrnwang>=2.1.0
 Requires-Dist: matplotlib>=3.9.2
-Requires-Dist: scipy>=1.16.2
-Requires-Dist: pandas>=2.2.3
-Requires-Dist: jpype1>=1.5.2
-Requires-Dist: tqdm>=4.67.1
 Dynamic: license-file
 
 # Introduction
 
-This Python package serves as the frontend for calculating and building a Green's function library for synthetic seismograms and then compute the static/dynamic Coulomb Failure Stress Change. The backend consists of Wang Rongjiang's program for calculating synthetic seismograms, including EDGRN/EDCMP, [QSEIS_2006_STRESS](https://github.com/Zhou-Jiangcheng/QSEIS_2006_STRESS) and QSSP.  Traveling time is calculated using [TAUP](https://github.com/crotwell/TauP). Some geographic coordinate transformations use code from [obspy](https://github.com/obspy/obspy).
-
-References:
-Wang, R. (1999). A simple orthonormalization method for stable and efficient computation of Green’s functions.  *Bulletin of the Seismological Society of America* ,  *89* (3), 733–741. [https://doi.org/10.1785/BSSA0890030733](https://doi.org/10.1785/BSSA0890030733)
-
-Wang, R. (2003). Computation of deformation induced by earthquakes in a multi-layered elastic crust—FORTRAN programs EDGRN/EDCMP. Computers & Geosciences, 29(2), 195–207. https://doi.org/10.1016/S0098-3004(02)00111-5
-
-Wang, R., & Wang, H. (2007). A fast converging and anti-aliasing algorithm for green’s functions in terms of spherical or cylindrical harmonics. Geophysical Journal International, 170(1), 239–248. https://doi.org/10.1111/j.1365-246X.2007.03385.x
-
-Wang, R., Heimann, S., Zhang, Y., Wang, H., & Dahm, T. (2017). Complete synthetic seismograms based on a spherical self-gravitating earth model with an atmosphere–ocean–mantle–core structure. Geophysical Journal International, 210(3), 1739–1764. https://doi.org/10.1093/gji/ggx259
+This Python package serves as the frontend for computing static and dynamic Coulomb Failure Stress changes in layerd media. The backend relies on programs developed by Rongjiang Wang and modified by Jiangcheng Zhou for calculating synthetic seismograms, specifically EDGRN/EDCMP, [QSEIS_2006_STRESS](https://github.com/Zhou-Jiangcheng/QSEIS_2006_STRESS), and QSSP. The generation and retrieval of Green's function libraries are handled by the [pygrnwang](https://github.com/Zhou-Jiangcheng/pygrnwang) package, while travel-time calculations and geographic coordinate transformations are implemented using [obspy](https://github.com/obspy/obspy).
 
 # Installation
 
-1. Install the requirments by conda (conda 24.11.3)
+1. For user mode
 
 ```
-conda create -n cfs python=3.11
-conda activate cfs
-conda install openjdk jpype1 gfortran numpy scipy pandas matplotlib tqdm -c conda-forge
-conda install geographiclib mpi4py -c conda-forge # optional
-```
-
-or install the requirments using system package manager, such as apt (Debian 12)
-
-```
-sudo apt install openjdk gfortran
-sudo apt install openmpi-common # optional
+pip install dyncfs
 ```
 
-2. Download this reposity and install by pip.
+2. For developer mode.
 
 ```
+conda create -n cfs python=3.13
+conda activate cfs
+conda install gfortran obspy tqdm -c conda-forge
+conda install geographiclib mpi4py -c conda-forge # optional
+git clone https://github.com/Zhou-Jiangcheng/pygrnwang
+cd pygrnwang
+pip install -e .
+cd ..
 git clone https://github.com/Zhou-Jiangcheng/dyncfs.git
 cd dyncfs
-pip install .
-```
-
-For code modification and debugging, use editable mode:
-
-```
 pip install -e .
 ```
 
-or install from pypi
-
-```
-pip install dyncfs
-```
-
 # Usage
 
 Fill in all parameters in the .ini file, and prepare the input files as described in `example.ini`, including `source_plane[m].csv` and `obs_plane[n].csv` under the input directory, as well as `model.nd` representing the Earth model.
@@ -140,3 +93,14 @@ if __name__ == "__main__":
     create_dynamic_lib(config)
     compute_dynamic_cfs_parallel(config)
 ```
+
+# References:
+Wang, R. (1999). A simple orthonormalization method for stable and efficient computation of Green’s functions.  *Bulletin of the Seismological Society of America* ,  *89* (3), 733–741. https://doi.org/10.1785/BSSA0890030733
+
+Wang, R. (2003). Computation of deformation induced by earthquakes in a multi-layered elastic crust—FORTRAN programs EDGRN/EDCMP. Computers & Geosciences, 29(2), 195–207. https://doi.org/10.1016/S0098-3004(02)00111-5
+
+Wang, R., & Wang, H. (2007). A fast converging and anti-aliasing algorithm for green’s functions in terms of spherical or cylindrical harmonics. Geophysical Journal International, 170(1), 239–248. https://doi.org/10.1111/j.1365-246X.2007.03385.x
+
+Wang, R., Heimann, S., Zhang, Y., Wang, H., & Dahm, T. (2017). Complete synthetic seismograms based on a spherical self-gravitating earth model with an atmosphere–ocean–mantle–core structure. Geophysical Journal International, 210(3), 1739–1764. https://doi.org/10.1093/gji/ggx259
+
+Zhou, J., Wang, R., & Zhang, Y. (2026). DynCFS: a program for modeling dynamic coulomb failure stress changes in layered elastic media. Geophysical Journal International, ggaf534. https://doi.org/10.1093/gji/ggaf534

{dyncfs-2.0.2 → dyncfs-2.1.0}/README.md

@@ -1,54 +1,31 @@
 # Introduction
 
-This Python package serves as the frontend for calculating and building a Green's function library for synthetic seismograms and then compute the static/dynamic Coulomb Failure Stress Change. The backend consists of Wang Rongjiang's program for calculating synthetic seismograms, including EDGRN/EDCMP, [QSEIS_2006_STRESS](https://github.com/Zhou-Jiangcheng/QSEIS_2006_STRESS) and QSSP.  Traveling time is calculated using [TAUP](https://github.com/crotwell/TauP). Some geographic coordinate transformations use code from [obspy](https://github.com/obspy/obspy).
-
-References:
-Wang, R. (1999). A simple orthonormalization method for stable and efficient computation of Green’s functions.  *Bulletin of the Seismological Society of America* ,  *89* (3), 733–741. [https://doi.org/10.1785/BSSA0890030733](https://doi.org/10.1785/BSSA0890030733)
-
-Wang, R. (2003). Computation of deformation induced by earthquakes in a multi-layered elastic crust—FORTRAN programs EDGRN/EDCMP. Computers & Geosciences, 29(2), 195–207. https://doi.org/10.1016/S0098-3004(02)00111-5
-
-Wang, R., & Wang, H. (2007). A fast converging and anti-aliasing algorithm for green’s functions in terms of spherical or cylindrical harmonics. Geophysical Journal International, 170(1), 239–248. https://doi.org/10.1111/j.1365-246X.2007.03385.x
-
-Wang, R., Heimann, S., Zhang, Y., Wang, H., & Dahm, T. (2017). Complete synthetic seismograms based on a spherical self-gravitating earth model with an atmosphere–ocean–mantle–core structure. Geophysical Journal International, 210(3), 1739–1764. https://doi.org/10.1093/gji/ggx259
+This Python package serves as the frontend for computing static and dynamic Coulomb Failure Stress changes in layerd media. The backend relies on programs developed by Rongjiang Wang and modified by Jiangcheng Zhou for calculating synthetic seismograms, specifically EDGRN/EDCMP, [QSEIS_2006_STRESS](https://github.com/Zhou-Jiangcheng/QSEIS_2006_STRESS), and QSSP. The generation and retrieval of Green's function libraries are handled by the [pygrnwang](https://github.com/Zhou-Jiangcheng/pygrnwang) package, while travel-time calculations and geographic coordinate transformations are implemented using [obspy](https://github.com/obspy/obspy).
 
 # Installation
 
-1. Install the requirments by conda (conda 24.11.3)
+1. For user mode
 
 ```
-conda create -n cfs python=3.11
-conda activate cfs
-conda install openjdk jpype1 gfortran numpy scipy pandas matplotlib tqdm -c conda-forge
-conda install geographiclib mpi4py -c conda-forge # optional
-```
-
-or install the requirments using system package manager, such as apt (Debian 12)
-
-```
-sudo apt install openjdk gfortran
-sudo apt install openmpi-common # optional
+pip install dyncfs
 ```
 
-2. Download this reposity and install by pip.
+2. For developer mode.
 
 ```
+conda create -n cfs python=3.13
+conda activate cfs
+conda install gfortran obspy tqdm -c conda-forge
+conda install geographiclib mpi4py -c conda-forge # optional
+git clone https://github.com/Zhou-Jiangcheng/pygrnwang
+cd pygrnwang
+pip install -e .
+cd ..
 git clone https://github.com/Zhou-Jiangcheng/dyncfs.git
 cd dyncfs
-pip install .
-```
-
-For code modification and debugging, use editable mode:
-
-```
 pip install -e .
 ```
 
-or install from pypi
-
-```
-pip install dyncfs
-```
-
 # Usage
 
 Fill in all parameters in the .ini file, and prepare the input files as described in `example.ini`, including `source_plane[m].csv` and `obs_plane[n].csv` under the input directory, as well as `model.nd` representing the Earth model.
@@ -102,3 +79,14 @@ if __name__ == "__main__":
     create_dynamic_lib(config)
     compute_dynamic_cfs_parallel(config)
 ```
+
+# References:
+Wang, R. (1999). A simple orthonormalization method for stable and efficient computation of Green’s functions.  *Bulletin of the Seismological Society of America* ,  *89* (3), 733–741. https://doi.org/10.1785/BSSA0890030733
+
+Wang, R. (2003). Computation of deformation induced by earthquakes in a multi-layered elastic crust—FORTRAN programs EDGRN/EDCMP. Computers & Geosciences, 29(2), 195–207. https://doi.org/10.1016/S0098-3004(02)00111-5
+
+Wang, R., & Wang, H. (2007). A fast converging and anti-aliasing algorithm for green’s functions in terms of spherical or cylindrical harmonics. Geophysical Journal International, 170(1), 239–248. https://doi.org/10.1111/j.1365-246X.2007.03385.x
+
+Wang, R., Heimann, S., Zhang, Y., Wang, H., & Dahm, T. (2017). Complete synthetic seismograms based on a spherical self-gravitating earth model with an atmosphere–ocean–mantle–core structure. Geophysical Journal International, 210(3), 1739–1764. https://doi.org/10.1093/gji/ggx259
+
+Zhou, J., Wang, R., & Zhang, Y. (2026). DynCFS: a program for modeling dynamic coulomb failure stress changes in layered elastic media. Geophysical Journal International, ggaf534. https://doi.org/10.1093/gji/ggaf534

{dyncfs-2.0.2 → dyncfs-2.1.0}/dyncfs/cfs_dynamic.py

@@ -13,21 +13,22 @@ import numpy as np
 import pandas as pd
 from scipy import signal
 from tqdm import tqdm
-
-from .configuration import CfsConfig
-from .obspy_geo import gps2dist_azimuth
-from .create_qssp2020_bulk import (
+from obspy.geodetics import gps2dist_azimuth
+from pygrnwang.create_qssp2020_bulk import (
     pre_process_qssp2020,
     create_grnlib_qssp2020_parallel,
 )
-from .read_qssp2020 import seek_qssp2020
-from .create_qseis2025_bulk import (
+from pygrnwang.read_qssp2020 import seek_qssp2020
+from pygrnwang.create_qseis2025_bulk import (
     pre_process_qseis2025,
     create_grnlib_qseis2025_parallel,
 )
-from .read_qseis2025 import seek_qseis2025
-from .focal_mechanism import plane2nd, check_convert_fm, mt2plane
-from .signal_process import resample, correct_zero_frequency
+from pygrnwang.read_qseis2025 import seek_qseis2025
+from pygrnwang.focal_mechanism import plane2nd, check_convert_fm, mt2plane
+from pygrnwang.signal_process import resample
+
+from .configuration import CfsConfig
+from .signal_process import correct_zero_frequency
 from .cfs_static import (
     cal_coulomb_failure_stress,
     cal_coulomb_failure_stress_poroelasticity,
@@ -48,7 +49,6 @@ def create_dynamic_lib(config: CfsConfig):
         pre_process_qssp2020(
             processes_num=config.processes_num,
             path_green=config.path_green_dynamic,
-            path_bin=config.path_bin_qssp,
             event_depth_list=config.event_depth_list,
             receiver_depth_list=config.receiver_depth_list,
             spec_time_window=config.spec_time_window,
@@ -88,7 +88,6 @@ def create_dynamic_lib(config: CfsConfig):
         pre_process_qseis2025(
             processes_num=config.processes_num,
             path_green=config.path_green_dynamic,
-            path_bin=config.path_bin_qseis,
             event_depth_list=config.event_depth_list,
             receiver_depth_list=config.receiver_depth_list,
             dist_range=config.grn_dist_range,
@@ -140,8 +139,7 @@ def synthesize_dynamic_stress(
                         stf_array(dimensionless)]
                         The stf at the end will be normalized by m0.
     :param obs_array_single_point: 1D numpy array,
-                        [lat(deg), lon(deg), depth(km),
-                        strike(deg), dip(deg), rake(deg)]
+                        [lat(deg), lon(deg), depth(km)]
     :param srate_stf: Sampling rate of stf in Hz.
     :param static_stress: Static stress tensor used for correcting zero-frequency values.
     :param max_slowness: Seismograms after dist(km)*max_slowness(s/km) will be set to 0.
@@ -208,6 +206,7 @@ def synthesize_dynamic_stress(
                 output_type="stress",
                 model_name=green_info["path_nd_without_Q"],
                 green_info=green_info,
+                interpolate_type=1
             )
         else:
             (
@@ -234,6 +233,7 @@ def synthesize_dynamic_stress(
                 output_type="stress",
                 model_name=green_info["path_nd_without_Q"],
                 green_info=green_info,
+                interpolate_type=1
             )
         tp_i = tpts_table["p_onset"]
         tp_ic = max(1, round((tp_i - 1) * srate_cfs))
@@ -407,10 +407,10 @@ def cal_cfs_dynamic_single_point_fm(
     sigma_vector = cal_stress_vector_ned_dynamic(stress_ned, n)
     sigma = np.dot(sigma_vector, n).flatten()
     tau = np.dot(sigma_vector, d).flatten()
-    mean_stress = (stress_ned[:, 0] + stress_ned[:, 3] + stress_ned[:, 5]) / 3
-    if B_pore != 0:
+    if B_pore == 0:
         cfs = cal_coulomb_failure_stress(norm_stress=sigma, shear_stress=tau, mu_f=mu_f)
     else:
+        mean_stress = (stress_ned[:, 0] + stress_ned[:, 3] + stress_ned[:, 5]) / 3
         cfs = cal_coulomb_failure_stress_poroelasticity(
             norm_stress=sigma,
             shear_stress=tau,
@@ -594,7 +594,7 @@ def cal_cfs_dynamic_single_point_opt_rake(
     # Shear stress scalar with optimal rake: tau = |s|
     tau = s_norm  # (N,)
 
-    if B_pore != 0:
+    if B_pore == 0:
         cfs = cal_coulomb_failure_stress(
             norm_stress=sigma_n, shear_stress=tau, mu_f=mu_f
         )
@@ -689,8 +689,7 @@ def cal_cfs_dynamic_single_point_oop(
                         stf_array(dimensionless)]
                         The stf at the end will be normalized by m0.
     :param obs_array_single_point: 1D numpy array,
-                        [lat(deg), lon(deg), depth(km),
-                        strike(deg), dip(deg), rake(deg)]
+                        [lat(deg), lon(deg), depth(km)]
     :param srate_stf: Sampling rate of stf in Hz.
     :param tectonic_stress_type: 1 for stress, 2 for orientations
     :param tectonic_stress:
@@ -842,7 +841,7 @@ def cal_cfs_dynamic_single_point_oop(
     sigma2 = np.einsum("ni,ni->n", sigvec2, n2)
     tau2 = np.einsum("ni,ni->n", sigvec2, d2)
 
-    if B_pore != 0:
+    if B_pore == 0:
         cfs = cal_coulomb_failure_stress(
             norm_stress=sigma2, shear_stress=tau2, mu_f=mu_f
         )