Merge pull request #128 from kwschultz/master

Preparing for next Release, version 2.1.0

CMakeLists.txt

@@ -23,7 +23,7 @@ LIST(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/quakelib/cmake/)
 
 # Set the version number
 SET(VQ_VERSION_MAJOR 2)
-SET(VQ_VERSION_MINOR 0)
+SET(VQ_VERSION_MINOR 1)
 SET(VQ_VERSION_SUBMINOR 0)
 SET(VQ_VERSION_STR "${VQ_VERSION_MAJOR}.${VQ_VERSION_MINOR}.${VQ_VERSION_SUBMINOR}")
 

PyVQ/pyvq/pyvq.py

@@ -151,11 +151,11 @@ def trace_plot(self, model_file):
             model_file = model_file.split("/")[-1]
         return "traces_"+model_file.split(".")[0]+".png"
 
-    def element_plot(self, model_file,type):
+    def distribution_plot(self, model_file, type):
         # Remove any folders in front of model_file name
         if len(model_file.split("/")) > 1:
             model_file = model_file.split("/")[-1]
-        return "block_"+type+"_hist_"+model_file.split(".")[0]+".png"
+        return type+"_"+model_file.split(".")[0]+".png"
 
     def diagnostic_plot(self, event_file, plot_type, min_year=None, max_year=None, min_mag=None, combine=None):
         # Add tags to convey the subsets/cuts being made
@@ -1874,7 +1874,7 @@ def create_plot(self, fig, color_index, plot_type, log_y, x_data, y_data, plot_t
             if len(x_data) > 200: BINS=100
             elif len(x_data) < 60: BINS=20
             else: BINS=100
-            ax.hist(x_data, bins=BINS, color = STAT_COLOR_CYCLE[color_index%len(STAT_COLOR_CYCLE)], histtype='stepfilled')
+            ax.hist(x_data, bins=BINS, color = STAT_COLOR_CYCLE[color_index%len(STAT_COLOR_CYCLE)], histtype='stepfilled', log=log_y)
         plt.gca().get_xaxis().get_major_formatter().set_useOffset(False)
         #plt.savefig(filename,dpi=100)
         #sys.stdout.write("Plot saved: {}\n".format(filename))
@@ -2877,7 +2877,7 @@ def leonard_2010(self, type, min_mag, max_mag, num=5):
             if args.reference: 
                 areas = [area/args.reference for area in areas]
                 units = "{:.5f}".format(args.reference)+units
-            filename = SaveFile().element_plot(model_file, "area")
+            filename = SaveFile().distribution_plot(model_file, "area_hist")
             if len(model_file.split("/")) > 1:
                 model_file = model_file.split("/")[-1]
             BasePlotter().create_plot(fig, 0, "hist", False, areas, None, model_file, "element area ["+units+"]", "", filename)
@@ -2895,7 +2895,7 @@ def leonard_2010(self, type, min_mag, max_mag, num=5):
             if args.reference: 
                 lengths = [length/args.reference for length in lengths]
                 units = "{:.5f}".format(args.reference)+units
-            filename = SaveFile().element_plot(model_file, "fault_length_hist")
+            filename = SaveFile().distribution_plot(model_file, "fault_length_hist")
             if len(model_file.split("/")) > 1:
                 model_file = model_file.split("/")[-1]
             BasePlotter().create_plot(fig, 0, "hist", False, lengths, None, model_file, "fault length ["+units+"]", "", filename)
@@ -2918,7 +2918,7 @@ def leonard_2010(self, type, min_mag, max_mag, num=5):
             for size in sorted(cum_len.iterkeys()):
                 lens_x.append(size)
                 lens_y.append(cum_len[size])
-            filename = SaveFile().element_plot(model_file, "fault_length_distrib")
+            filename = SaveFile().distribution_plot(model_file, "fault_length_distrib")
             if len(model_file.split("/")) > 1:
                 model_file = model_file.split("/")[-1]
             BasePlotter().create_plot(fig, 0, "line", True, lens_x, lens_y, model_file, "fault length L ["+units+"]", "Cumulative faults with length L or larger", filename)
@@ -2933,7 +2933,7 @@ def leonard_2010(self, type, min_mag, max_mag, num=5):
             fig = plt.figure()
             model_file = args.model_file
             fractions = [geometry.model.element(elem_num).aseismic() for elem_num in range(geometry.model.num_elements())]
-            filename = SaveFile().element_plot(model_file, "aseismic")
+            filename = SaveFile().distribution_plot(model_file, "aseismic_hist")
             if len(model_file.split("/")) > 1:
                 model_file = model_file.split("/")[-1]
             BasePlotter().create_plot(fig, 0, "hist", False, fractions, None, model_file, units, "", filename)
@@ -2951,7 +2951,7 @@ def leonard_2010(self, type, min_mag, max_mag, num=5):
             if args.reference: 
                 lengths = [length/args.reference for length in lengths]
                 units = "{:.5f}".format(args.reference)+units
-            filename = SaveFile().element_plot(model_file, "length")
+            filename = SaveFile().distribution_plot(model_file, "length_hist")
             if len(model_file.split("/")) > 1:
                 model_file = model_file.split("/")[-1]
             BasePlotter().create_plot(fig, 0, "hist", False, lengths, None, model_file, "element length ["+units+"]", "", filename)
@@ -2970,7 +2970,7 @@ def leonard_2010(self, type, min_mag, max_mag, num=5):
             if args.reference: 
                 areas = [area/args.reference for area in areas]
                 units = "{:.5f}".format(args.reference)+units
-            filename = SaveFile().element_plot(model_file, "stress drop")
+            filename = SaveFile().distribution_plot(model_file, "stress_drop_hist")
             if len(model_file.split("/")) > 1:
                 model_file = model_file.split("/")[-1]
             BasePlotter().create_plot(fig, 0, "hist", False, drops, None, model_file, "element stress drop ["+units+"], stress drop factor = {}".format(factor), "", filename)

doc/vq.tex

@@ -41,8 +41,8 @@
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%% Lyx Title Page
 \title{Virtual Quake User Manual}
-\author{Kasey W. Schultz\\Eric M. Heien\\Michael K. Sachs\\Mark R. Yoder\\John B. Rundle\\Donald L. Turcotte\\\\ \copyright University of California, Davis\\
-Version 2.0.0}
+\author{Kasey W. Schultz\\Eric M. Heien\\Michael K. Sachs\\Mark R. Yoder\\John M. Wilson\\John B. Rundle\\Donald L. Turcotte\\\\ \copyright University of California, Davis\\
+Version 2.1.0}
 %\date{\noindent \today}
 
 
@@ -117,7 +117,7 @@
 % FILL: author list
 % e.g. Author One\\Author Two\\Author Three\\
 % be sure to have a newline (\\) after the final author
-Kasey W. Schultz~~~Eric M. Heien~~~Michael K. Sachs\\Mark R. Yoder~~~John B. Rundle~~~Donald L. Turcotte\\
+Kasey W. Schultz~~~Eric M. Heien~~~Michael K. Sachs~~~John M. Wilson\\Mark R. Yoder~~~John B. Rundle~~~Donald L. Turcotte\\
 }
 {\fontfamily{\sfdefault}\selectfont www.geodynamics.org}
 
@@ -207,7 +207,7 @@ \section*{Citation}
 
 And to cite the manual:
 \begin{itemize}
-\item K. W. Schultz, E. M. Heien, M. K. Sachs, M. R. Yoder, J. B. Rundle, D. L. Turcotte (2015), Virtual Quake User Manual, Version 2.0.0. Davis, California, USA: Computational Infrastructure for Geodynamics. URL:  \href{http://geodynamics.org/cig/software/github/vq/v2.0.0/vq_manual_2.0.0.pdf}{geodynamics.org/cig/software/github/vq/v2.0.0/vq\_manual\_2.0.0.pdf}
+\item K. W. Schultz, E. M. Heien, M. K. Sachs, M. R. Yoder, J. M. Wilson,  J. B. Rundle, D. L. Turcotte (2015), Virtual Quake User Manual, Version 2.1.0. Davis, California, USA: Computational Infrastructure for Geodynamics. URL:  \href{http://geodynamics.org/cig/software/github/vq/v2.1.0/vq_manual_2.1.0.pdf}{geodynamics.org/cig/software/github/vq/v2.1.0/vq\_manual\_2.1.0.pdf}
 \end{itemize}
 
 The developers also request that in your oral presentations and in
@@ -2312,6 +2312,12 @@ \subsection{\noindent Geometry/Model Plotting Parameters}
 \hline
 \texttt{\small{--block\_length\_hist}} & Create and save a histogram of fault element lengths (square root of area). To present numbers relative to a reference value, must specify --reference .\tabularnewline
 \hline
+\texttt{\small{--block\_aseismic\_hist}} & Create and save a histogram of fault element aseismic fractions (percent of fault slip that is aseismic).\tabularnewline
+\hline
+\texttt{\small{--fault\_length\_hist}} & Create and save a histogram of fault lengths . To present numbers relative to a reference value, must specify --reference .\tabularnewline
+\hline
+\texttt{\small{--fault\_length\_distribution}} & Create and save the cumulative distribution of fault lengths.\tabularnewline
+\hline
 \texttt{\small{--reference}} & A reference number or unit value for \texttt{\small{--block\_length\_hist}} or \texttt{\small{--block\_area\_hist}} plots.\tabularnewline
 \hline
 \texttt{\small{--traces}} & Plot the fault traces on a simple map.\tabularnewline

quakelib/src/QuakeLibIO.cpp

@@ -892,8 +892,14 @@ void quakelib::ModelWorld::compute_stress_drops(const double &stress_drop_factor
 
         eit->second.set_stress_drop(stress_drop);
 
-        //////////////////////
-        //std::cout << eit->second.stress_drop() << std::endl;
+
+        /////
+        // TEMPORARY ASEISMIC CUT OFF, anything less than 0.13 gets set to 0
+        /////
+        //        if (eit->second.aseismic() <= 0.13 ) {
+        //            eit->second.set_aseismic(0.0);
+        //        }
+
     }
 
 }
@@ -1024,6 +1030,10 @@ void quakelib::ModelWorld::clear(void) {
     _vertices.clear();
 }
 
+void quakelib::ModelWorld::clear_faults(void) {
+    _faults.clear();
+}
+
 int quakelib::ModelWorld::read_file_ascii(const std::string &file_name) {
     std::ifstream       in_file;
     unsigned int        i, num_sections, num_elements, num_vertices, num_faults;

quakelib/src/QuakeLibIO.h

@@ -1377,6 +1377,7 @@ namespace quakelib {
                                                     const UIndex &start_vertex_index) const;
             ModelRemapping remove_duplicate_vertices_remap(void) const;
             void clear(void);
+            void clear_faults(void);
 
             void reset_base_coord(const LatLonDepth &new_base);
 

src/core/Simulation.cpp

@@ -50,8 +50,6 @@ Simulation::Simulation(int argc, char **argv) : SimFramework(argc, argv) {
 
     // Check validity of parameters
     // TODO: add more checks here
-    //assertThrow(!getVersion().compare("2.0"),
-    //            "sim.version: Parameter file version must be 2.0");
     assertThrow(getSimStart()>=0,
                 "sim.start_year: Start year must be at least 0.");
     assertThrow(getSimStart() < getSimDuration(),