Merge pull request #131 from kwschultz/master

Ready for new version release

PyVQ/pyvq/pyvq.py

@@ -1986,16 +1986,16 @@ def scatter_and_error_polygon(self, fig, log_y, x_data, y_data, err_x, err_y, y_
         widths = [x_bounds[i][1] - x_bounds[i][0]for i in range(len(x_bounds))]
         heigths = [y_bounds[i][1] - y_bounds[i][0]for i in range(len(y_bounds))]
         for i in range(len(x_bounds)):
-            if i==0: ax.add_patch(mpatches.Rectangle(x0_y0[i], widths[i], heigths[i], alpha=0.55, facecolor='r', label='{} 95% confidence bounds'.format(err_label)))
-            else: ax.add_patch(mpatches.Rectangle(x0_y0[i], widths[i], heigths[i], alpha=0.55, facecolor='r'))
+            if i==0: ax.add_patch(mpatches.Rectangle(x0_y0[i], widths[i], heigths[i], alpha=0.4, facecolor='r', label='{} 95% confidence bounds'.format(err_label)))
+            else: ax.add_patch(mpatches.Rectangle(x0_y0[i], widths[i], heigths[i], alpha=0.4, facecolor='r'))
 
         ax.scatter(x_data, y_data, label=label, alpha=SCATTER_ALPHA, color=STAT_COLOR_CYCLE[0], s=SCATTER_SIZE, zorder=10)
         if add_x is not None:
             if log_y: ax.semilogy(add_x, add_y, label = add_label, c = 'r', zorder=5)
             if not log_y: ax.plot(add_x, add_y, label = add_label, c = 'r', zorder=5)
         plt.gca().get_xaxis().get_major_formatter().set_useOffset(False)
-        #if args.max_magnitude is None:
-        #    plt.xlim(plt.xlim()[0], max(x_data))
+        if args.max_magnitude is None:
+            plt.xlim(plt.xlim()[0], max(max(x_data),8.05))
         #ax.legend(loc = "best")
         #plt.savefig(filename,dpi=100)
         #sys.stdout.write("Plot saved: {}\n".format(filename))
@@ -3034,7 +3034,8 @@ def leonard_2010(self, type, min_mag, max_mag, num=5):
             raise BaseException("Must specify a fault model with --model_file.")
         else:
             units = "Pa"
-            if float(args.reference) == 1e6: units = "MPa"
+            if args.reference is not None: 
+                if float(args.reference) == 1e6: units = "MPa"
             fig = plt.figure()
             model_file = args.model_file
             drops = geometry.get_stress_drops()

doc/vq.tex

@@ -42,7 +42,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%% Lyx Title Page
 \title{Virtual Quake User Manual}
 \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}
+Version 2.1.1}
 %\date{\noindent \today}
 
 
@@ -107,7 +107,7 @@
 \hfill{\Huge \fontfamily{\sfdefault}\selectfont User Manual \\
 % FILL: manual version
 % e.g. 1.0
-\raggedleft \huge \fontfamily{\sfdefault}\selectfont Version {2.1.0}\\}
+\raggedleft \huge \fontfamily{\sfdefault}\selectfont Version {2.1.1}\\}
 
 %AUTHOR(S) & WEBSITE%
 \null
@@ -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. 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}
+\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 2.1.1. Davis, California, USA: Computational Infrastructure for Geodynamics. URL:  \href{http://geodynamics.org/cig/software/github/vq/v2.1.1/vq_manual_2.1.1.pdf}{geodynamics.org/cig/software/github/vq/v2.1.1/vq\_manual\_2.1.1.pdf}
 \end{itemize}
 
 The developers also request that in your oral presentations and in

quakelib/src/QuakeLibIO.cpp

@@ -2204,7 +2204,7 @@ int quakelib::ModelWorld::read_files_eqsim(const std::string &geom_file_name, co
         for (it=sit->second.rectangles.begin(); it!=sit->second.rectangles.end(); ++it) {
             quakelib::ModelElement   new_element;
             unsigned int             i;
-            
+
             // Initialize fault slip rate tapering data structures
             section_taper_flow[sit->second.sid()] = 0.0;
             section_taper_full[sit->second.sid()] = 0.0;

src/mesher.cpp

@@ -204,7 +204,7 @@ int main (int argc, char **argv) {
     std::string                 eqsim_geom_out_file, eqsim_fric_out_file, eqsim_cond_out_file;
     std::string                 stat_out_file;
     std::vector<std::string>    files[2], types[2];
-    std::string    				taper_fault_method;
+    std::string                 taper_fault_method;
     std::vector<double>         trace_element_sizes;
     double                      stress_drop_factor = 0.3;  // default value is a reasonable 0.3
     int                         ch, res;
@@ -329,11 +329,11 @@ int main (int argc, char **argv) {
     }
 
     // Check that the taper methods are valid
-	if (taper_fault_method != "none" && taper_fault_method != "taper"
-		&& taper_fault_method != "taper_full" && taper_fault_method != "taper_renorm") {
-		std::cerr << "ERROR: Taper method " << taper_fault_method << " must be one of: none, taper, taper_full, taper_renorm." << std::endl;
-		arg_error = true;
-	}
+    if (taper_fault_method != "none" && taper_fault_method != "taper"
+        && taper_fault_method != "taper_full" && taper_fault_method != "taper_renorm") {
+        std::cerr << "ERROR: Taper method " << taper_fault_method << " must be one of: none, taper, taper_full, taper_renorm." << std::endl;
+        arg_error = true;
+    }
 
     if (!(compute_stress_drops) && (eqsim_fric_in_file.empty() || eqsim_geom_in_file.empty() )) {
         std::cerr << "ERROR: If not computing stress drops, must specify EQSim geometry and EQSim friction file. EQSim friction should contain stress drops." << std::endl;

src/simulation/UpdateBlockStress.cpp

@@ -116,7 +116,7 @@ void UpdateBlockStress::init(SimFramework *_sim) {
 
         sim->setDynamicVal(gid, sim->getDynamic());
         sim->setFailed(gid, false);
-        
+
         // Set stresses to their specified initial values
         sim->setShearStress(gid, sim->getInitShearStress(gid));
         sim->setNormalStress(gid, sim->getInitNormalStress(gid));