QDYN release 2.0.0

User features:
- Microphysically-based friction model: Chen-Niemeijer-Spiers (CNS) model
- Thermal pressurization
- Faults surrounded by damaged zone
- Runge-Kutta solver
- Free surface in 2D simulations
- Python wrapper
- Windows 10 compatibility

Developer features:
- Testing suite
- SCEC2018 benchmark results
- Code clean-up and re-structuring
- Versioning and version control policy

README.md

@@ -5,6 +5,8 @@
 
 ## News 
 
+*11 December 2018* | QDYN version 2.0 has been released!
+
 *6 December 2018* | Results of QDYN earthquake cycle simulations on faults surrounded by damaged zones were presented at:  
 * the AGU Fall Meeting 2017 (San Francisco, 11-15 December 2017): B. Idini and J. P. Ampuero, *Rupture complexity promoted by damaged fault zones in earthquake cycle models* (doi:10.1002/essoar.10500080.1, [poster](https://www.essoar.org/doi/abs/10.1002/essoar.10500080.1))  
 * the [10th ACES International Workshop](http://quaketm.bosai.go.jp/~shiqing/ACES2018/index_aces.html) (Japan, September 25-28, 2018), J. P. Ampuero et al., *Rupture complexity promoted by damaged fault zones in earthquake cycle models* ([slides](http://quaketm.bosai.go.jp/~shiqing/ACES2018/abstracts/aces_abstract_ampuero.pdf)) 
@@ -109,18 +111,17 @@ Questions, feedback or suggestions can be submitted via our [issue tracking syst
 ------------------------
 ## Developers
 
-[Yingdi Luo](https://science.jpl.nasa.gov/people/YLuo/) (NASA JPL, USA)
+[Yingdi Luo](https://science.jpl.nasa.gov/people/YLuo/) (UCLA / NASA JPL, USA)
 
-[Jean-Paul Ampuero](http://www.seismolab.caltech.edu/ampuero_jp.html) (Caltech Seismolab, USA and IRD / UCA, Geoazur, France)
+[Jean-Paul Ampuero](http://www.seismolab.caltech.edu/ampuero_jp.html) (Caltech Seismolab, USA and IRD / UCA, Géoazur, France)
 
-[Percy Galvez](https://smi.kaust.edu.sa/Pages/People-Galvez.aspx) (KAUT, Saudi Arabia)
+[Percy Galvez](https://smi.kaust.edu.sa/Pages/People-Galvez.aspx) (KAUST, Saudi Arabia; AECOM, Switzerland)
 
-[Martijn van den Ende](https://www.linkedin.com/in/martijnvandenende) (Universite Cote d'Azur, Geoazur, France)
+[Martijn van den Ende](https://www.linkedin.com/in/martijnvandenende) (Université Côte d'Azur, Géoazur, France)
 
 [Benjamin Idini](http://www.seismolab.caltech.edu/idini_b.html) (Caltech Seismolab, USA)
 
 
-
 -------------------------
 
 ## Suggested References

examples/CNS/stick-slip/stick-slip.py

@@ -0,0 +1,97 @@
+# Importing some required modules
+import gzip
+import os
+import pickle
+import sys
+
+import matplotlib.pyplot as plt
+
+# Go up in the directory tree
+upup = [os.pardir]*4
+qdyn_dir = os.path.join(*upup)
+# Get QDYN src directory
+src_dir = os.path.abspath(
+    os.path.join(
+        os.path.join(__file__, qdyn_dir), "src")
+)
+# Append src directory to Python path
+sys.path.append(src_dir)
+# Import QDYN wrapper
+from pyqdyn import qdyn
+from numpy.testing import assert_allclose
+
+# QDYN class object
+p = qdyn()
+
+# Python dictionary with general settings
+set_dict = {
+    "FRICTION_MODEL": "CNS",
+    "ACC": 1e-10,
+    "SOLVER": 2,
+    "MU": 2e10,
+    "TMAX": 1e4,
+    "DTTRY": 1e-6,
+    "MESHDIM": 0,
+    "NTOUT": 10000,
+    "SIGMA": 5e6,
+    "V_PL": 1e-6,
+    "L": 1e1,
+}
+
+# Python dictionary with CNS parameters
+set_dict_CNS = {
+    "A": [1e-10],
+    "N": [1],
+    "M": [1],
+    "A_TILDE": 0.02,
+    "MU_TILDE_STAR": 0.4,
+    "Y_GR_STAR": 1e-6,
+    "PHI_INI": 0.25,
+    "THICKNESS": 1e-4,
+    "TAU": 3e6,
+}
+
+# Add CNS dictionary to QDYN dictionary
+set_dict["SET_DICT_CNS"] = set_dict_CNS
+
+p.settings(set_dict)
+p.render_mesh()
+
+# Write input file
+p.write_input()
+
+# Run simulation
+p.run()
+
+# Get our results
+p.read_output()
+
+# Plot results
+plt.subplot(211)
+plt.plot(p.ot["t"], p.ot["tau"] / p.set_dict["SIGMA"])
+plt.ylabel("friction [-]")
+plt.subplot(212)
+plt.plot(p.ot["t"], p.ot["theta"] * 100)
+plt.ylabel("porosity [%]")
+plt.xlabel("time [s]")
+plt.tight_layout()
+plt.show()
+
+with gzip.GzipFile("benchmark.tar.gz", "r") as f:
+    benchmark = pickle.load(f)
+
+print("Performing benchmark comparison")
+
+plt.figure(2)
+plt.plot(p.ot["t"], p.ot["tau"]*1e-6, label="Current")
+plt.plot(benchmark["t"], benchmark["tau"]*1e-6, "k--", label="Benchmark")
+plt.xlabel("time [s]")
+plt.ylabel("shear stress [MPa]")
+plt.legend(loc=4, ncol=2)
+plt.tight_layout()
+plt.show()
+
+assert_allclose(benchmark["t"], p.ot["t"], rtol=1e-4)
+assert_allclose(benchmark["tau"], p.ot["tau"], rtol=1e-4)
+assert_allclose(benchmark["phi"], p.ot["theta"], rtol=1e-4)
+print("Benchmark comparison OK")

examples/CNS/velocity-step/v-step.py

@@ -1,29 +1,30 @@
-# Path where QDYN executable and wrapper are located
-qdyn_path = "/home/martijn/QDyn/src"
-
 # Importing some required modules
-import numpy as np
-import matplotlib.pyplot as plt
+import gzip
+import os
+import pickle
 import sys
-sys.path.append(qdyn_path)
-from pyqdyn import qdyn
 
-# CNS kinetic parameters
+import matplotlib.pyplot as plt
+import numpy as np
 
-d = 10e-6			# Nominal grain size
-O = 2.69e-5			# Molar volume
-R = 8.3144			# Universal gas constant
-T = 293				# Absolute temperature
-DCS0 = 2.79e-15		# Kinetic pre-factor
-dH = 2.45e4			# Activation energy
-DCS = DCS0*np.exp(-dH/(R*T))			# Kinetic parameter at T
-Z_ps = (24/np.pi)*DCS*O/(R*T*d**3)		# Combined (lumped) kinetic constant
+# Go up in the directory tree
+upup = [os.pardir]*4
+qdyn_dir = os.path.join(*upup)
+# Get QDYN src directory
+src_dir = os.path.abspath(
+    os.path.join(
+        os.path.join(__file__, qdyn_dir), "src")
+)
+# Append src directory to Python path
+sys.path.append(src_dir)
+# Import QDYN wrapper
+from pyqdyn import qdyn
+from numpy.testing import assert_allclose
 
 # QDYN class object
 p = qdyn()
 
-# Define where the QDYN executable is located
-p.qdyn_path = qdyn_path
+Z_ps = 1e-10
 
 # Python dictionary with general settings
 set_dict = {
@@ -41,7 +42,9 @@
 
 # Python dictionary with CNS parameters
 set_dict_CNS = {
-    "IPS_CONST_DIFF": Z_ps,
+    "A": [0.5*Z_ps, 0.5*Z_ps, 0.0*Z_ps],
+    "N": [1, 1, 1],
+    "M": [1, 1, 1],
     "A_TILDE": 0.02,
     "MU_TILDE_STAR": 0.4,
     "Y_GR_STAR": 1e-6,
@@ -64,6 +67,10 @@
 # Total slip distance per simulation
 x_ss = 500e-6
 
+t_all = np.array([])
+tau_all = np.array([])
+phi_all = np.array([])
+
 # Loop over all velocity steps
 for i, V in enumerate(Vs):
     # Set load-point velocity
@@ -93,6 +100,10 @@
     plt.subplot(212)
     plt.plot(p.ot["t"]-p.ot["t"].iloc[0]+t_final, p.ot["theta"]*100)
 
+    t_all = np.hstack([t_all, p.ot["t"]-p.ot["t"].iloc[0]+t_final])
+    tau_all = np.hstack([tau_all, p.ot["tau"]])
+    phi_all = np.hstack([phi_all, p.ot["theta"]])
+
     # Set starting point for next simulation
     tau_final = p.ot["tau"].values[-1]
     phi_final = p.ot["theta"].values[-1]
@@ -106,3 +117,20 @@
 plt.tight_layout()
 plt.show()
 
+with gzip.GzipFile("benchmark.tar.gz", "r") as f:
+    benchmark = pickle.load(f)
+
+plt.figure(2)
+plt.plot(t_all, tau_all*1e-6, label="Current")
+plt.plot(benchmark["t"], benchmark["tau"]*1e-6, "k--", label="Benchmark")
+plt.xlabel("time [s]")
+plt.ylabel("shear stress [MPa]")
+plt.legend(loc=4, ncol=2)
+plt.tight_layout()
+plt.show()
+
+print("Performing benchmark comparison")
+assert_allclose(benchmark["t"], t_all, rtol=1e-6)
+assert_allclose(benchmark["tau"], tau_all, rtol=1e-6)
+assert_allclose(benchmark["phi"], phi_all, rtol=1e-6)
+print("Benchmark comparison OK")

examples/PyQDYN/Tse+Rice/tse_rice.py

@@ -4,25 +4,29 @@
 # Omit the run argument to execute script file without
 # re-running the simulation (e.g. for plotting data)
 
-# Path where QDYN executable and wrapper are located
-from __future__ import print_function
-
-qdyn_path = "/home/martijn/QDyn/src"
-
 # Importing some required modules
+import os
 import sys
-import numpy as np
-sys.path.append(qdyn_path)
-from pyqdyn import qdyn
+
 import matplotlib.pyplot as plt
+import numpy as np
 
+# Go up in the directory tree
+upup = [os.pardir]*4
+qdyn_dir = os.path.join(*upup)
+# Get QDYN src directory
+src_dir = os.path.abspath(
+    os.path.join(
+        os.path.join(__file__, qdyn_dir), "src")
+)
+# Append src directory to Python path
+sys.path.append(src_dir)
+# Import QDYN wrapper
+from pyqdyn import qdyn
 
 # QDYN class object
 p = qdyn()
 
-# Define where the QDYN executable is located
-p.qdyn_path = qdyn_path
-
 # Number of fault segments
 N = np.power(2, 11)
 

examples/single_asperity/single_asperity.m

@@ -45,6 +45,7 @@
   %p.V_0 = 1.01*p.V_SS ;
   p.V_0 = ( 1.+0.01*exp( -(p.X/Lasp*2).^6 ) )*p.V_SS ;
   p.V_0 = p.V_0/mean(p.V_0)*p.V_SS;
+
   [p,ot1,ox1] = qdyn('run',p) ;
 
 

src/Makefile

@@ -17,8 +17,8 @@ OPT = -O3 -Wall
 #OPT = -O3 -Wall -fopenmp
 #OPT = -O2 -w
 #-- Intel Fortran --
-#F90 = ifort
-#OPT = -O3 -ip -ipo
+# F90 = ifort
+# OPT = -O3 -ip -ipo
 # For parallel runs with OpenMP:
 #OPT = -O3 -ip -ipo -parallel -openmp -par-threshold:50
 #-no-inline-factor
@@ -43,11 +43,11 @@ OPT = -O3 -Wall
 
 # 3. Set the compiler option that enables preprocessing in your compiler
 # ifort
-#PREPROC = -fpp
+# PREPROC = -fpp
 # gfortran
 PREPROC = -cpp
 #PG, KAUST server
-CFLAGS = -B/usr/lib/x86_64-linux-gnu
+# CFLAGS = -B/usr/lib/x86_64-linux-gnu
 #CFLAGS = '' 
 
 #== END USER SETTINGS =============================================

src/Makefile.depend

@@ -1,13 +1,14 @@
 derivs_all.o: diffusion_solver.o fault_stress.o friction.o friction_cns.o \
-	problem_class.o
+	problem_class.o utils.o
 diffusion_solver.o: constants.o mesh.o problem_class.o
-fault_stress.o: constants.o fftsg.o mesh.o okada.o parallel.o utils.o
+fault_stress.o: constants.o fftsg.o mesh.o okada.o parallel.o
 friction.o: friction_cns.o problem_class.o
 friction_cns.o: constants.o problem_class.o
 initialize.o: constants.o diffusion_solver.o fault_stress.o friction.o mesh.o \
 	output.o parallel.o problem_class.o solver.o
 input.o: constants.o mesh.o output.o parallel.o problem_class.o
-main.o: derivs_all.o initialize.o input.o parallel.o problem_class.o solver.o
+main.o: derivs_all.o initialize.o input.o parallel.o problem_class.o solver.o \
+	unittests.o
 mesh.o: constants.o parallel.o
 ode_bs.o: derivs_all.o parallel.o problem_class.o
 ode_rk45.o: derivs_all.o
@@ -17,4 +18,10 @@ parallel.o: constants.o
 problem_class.o: fault_stress.o mesh.o
 solver.o: constants.o derivs_all.o diffusion_solver.o friction.o \
 	friction_cns.o ode_bs.o ode_rk45.o output.o parallel.o \
-	problem_class.o
+	problem_class.o utils.o
+unittests.o: constants.o fault_stress.o friction.o mesh.o problem_class.o \
+	solver.o unittests_rsf.o
+unittests_aux.o: constants.o problem_class.o solver.o
+unittests_rsf.o: constants.o fault_stress.o friction.o mesh.o problem_class.o \
+	solver.o unittests_aux.o
+utils.o: problem_class.o

src/constants.f90

@@ -56,6 +56,6 @@ module constants
 ! Which ODE solver to use:
 !   1 : Bulirsch-Stoer
 !   2 : Runge-Kutta-Fehlberg
-integer :: SOLVER = 0
+integer :: SOLVER_TYPE = 0
 
 end module constants