gs2crmod 0.11.24 → 0.11.26

data/VERSION

@@ -1 +1 @@
-0.11.24
+0.11.26

data/ext/extconf.rb

@@ -1,6 +1,9 @@
 require 'mkmf'
 
-$CFLAGS = " -Wall -I../include "
+#Need to link with C GSL libraries to use in C extensions
+gsl_inc = `gsl-config --cflags`
+
+$CFLAGS = " -Wall -I../include #{gsl_inc}"
 
 srcs = Dir.glob("*.c")
                                                                                                          

data/ext/gs2crmod_ext.c

@@ -2,7 +2,6 @@
 #include <math.h>
 #include <string.h>
 #include <gsl/gsl_spline.h>
-#include <gsl/gsl_spline.h>
 
 VALUE gs2crmod_tensor_complexes_field_gsl_tensor_complex_2(VALUE self, VALUE options)
 {
@@ -409,9 +408,9 @@ VALUE gs2crmod_tensor_field_correlation_gsl_tensor(VALUE self, VALUE options)
     //Write some as floats to avoid flooring to wrong (lower) number later
     float *lx_bin, *ly_bin, *lz_bin, *lt_bin;
     float lxmin, lxmax, lymin, lymax, lzmin, lzmax, ltmin, ltmax, lx, ly, lz, *lt;
-    double *x, *y, *z, *t, *field, *coarray, *corr_norm, amin;
+    double *x, *y, *z, *t, *field, *coarray, *corr_norm;
     int *c_shape, tot_size, ith, ix, iy, it, t_size, first=1;
-    int index, i, i2, i3, i4, tot_bins, *count;
+    int index, i2, i3, i4, tot_bins, *count;
     long int i1;
 
     printf("Starting correlation analysis\n");
@@ -427,12 +426,6 @@ VALUE gs2crmod_tensor_field_correlation_gsl_tensor(VALUE self, VALUE options)
         t[it] = NUM2DBL(CR_TELMT_R1(t_gsl_vector, it));
     }
 
-    //Read from options
-	  if(RTEST(CR_HKS(options, "amin")))
-        amin = NUM2DBL(CR_HKS(options, "amin"));
-    else
-        amin = 1.0;
-
     VALUE nbins_array=CR_HKS(options, "nbins_array");
     int *nbins;
 	  if(RTEST(nbins_array) && RTEST(rb_obj_is_kind_of(nbins_array, RGET_CLASS_TOP("Array")))){
@@ -471,6 +464,7 @@ VALUE gs2crmod_tensor_field_correlation_gsl_tensor(VALUE self, VALUE options)
 
         if(first)
         {
+            //ALLOC_N is used since it works correctly with ruby garbage collector
             tot_size = c_shape[0]*c_shape[1]*c_shape[2]*t_size; 
             x = ALLOC_N(double, tot_size);
             y = ALLOC_N(double, tot_size);
@@ -496,8 +490,8 @@ VALUE gs2crmod_tensor_field_correlation_gsl_tensor(VALUE self, VALUE options)
     
 
     /******************************
-     * GSL Interpolation of field *
-     *        in time             *
+     *    GSL Interpolation of    *
+     *       field in time        *
      *****************************/
     //Read t interp from options (default is 100)
     int nt_reg;
@@ -508,7 +502,6 @@ VALUE gs2crmod_tensor_field_correlation_gsl_tensor(VALUE self, VALUE options)
     int idx, ti;
     double *x_reg, *y_reg, *z_reg, *t_reg, *field_reg, delta_t_reg, *y1;
     tot_size = c_shape[0]*c_shape[1]*c_shape[2]*nt_reg; 
-    //printf("Start interpolation, %d, %d, %d, %d, %d\n", c_shape[0], c_shape[1], c_shape[2], nt_reg, tot_size);
     delta_t_reg = (t[t_size-1]-t[0])/(nt_reg-1);
 
     y1 = ALLOC_N(double, t_size);
@@ -520,11 +513,9 @@ VALUE gs2crmod_tensor_field_correlation_gsl_tensor(VALUE self, VALUE options)
 
     for(i1=0; i1<c_shape[0]*c_shape[1]*c_shape[2]*t_size; i1+=t_size)
     {
-        //printf("%d, %d\n", i1, c_shape[0]*c_shape[1]*c_shape[2]*t_size);
         for (i2 = 0; i2 < t_size; i2++)
         {
             y1[i2] = field[i1+i2];
-            //printf ("%d, %lf %lf\n", i2, t[i2], y1[i2]);
         }
 
         gsl_interp_accel *acc 
@@ -534,7 +525,6 @@ VALUE gs2crmod_tensor_field_correlation_gsl_tensor(VALUE self, VALUE options)
 
         gsl_spline_init (spline, t, y1, t_size);
 
-        //printf("Interpolated:\n");
         for (ti = 0; ti < nt_reg; ti++)
         {
             t_reg[ti] = t[0]+ti*delta_t_reg;
@@ -549,7 +539,7 @@ VALUE gs2crmod_tensor_field_correlation_gsl_tensor(VALUE self, VALUE options)
 
     }
     
-    //Can now free the original pointers
+    //Can now free the original pointers since redefined variables on a regular grid
     free(x); x=0;
     free(y); y=0;
     free(z); z=0;
@@ -567,7 +557,6 @@ VALUE gs2crmod_tensor_field_correlation_gsl_tensor(VALUE self, VALUE options)
      * since the binning will be done at each step since there is too much*
      * info to store.                                                     *
      * ********************************************************************/
-    double lx_pos_min=20;
     i3=0;
     lxmin=0; lymin=0; lzmin=0;
     for(i1=0; i1<tot_size; i1+=nt_reg){

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.11.24"
+  s.version = "0.11.26"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2014-03-12"
+  s.date = "2014-03-14"
   s.description = "GS2 is a gyrokinetic flux tube initial value turbulence code which can be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated running and analysis of large simulations. This module allows GS2 (and its sister code AstroGK) to harness the power of the CodeRunner framework."
   s.email = "edmundhighcock@sourceforge.net"
   s.extensions = ["ext/extconf.rb"]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.11.24
+  version: 0.11.26
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-12 00:00:00.000000000 Z
+date: 2014-03-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
-  requirement: &16185280 !ruby/object:Gem::Requirement
+  requirement: &10326280 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
         version: 0.14.10
   type: :runtime
   prerelease: false
-  version_requirements: *16185280
+  version_requirements: *10326280
 - !ruby/object:Gem::Dependency
   name: rubyhacks
-  requirement: &16184640 !ruby/object:Gem::Requirement
+  requirement: &10325680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *16184640
+  version_requirements: *10325680
 - !ruby/object:Gem::Dependency
   name: ruby-netcdf-updated
-  requirement: &16184000 !ruby/object:Gem::Requirement
+  requirement: &10325060 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: 0.6.6.1
   type: :runtime
   prerelease: false
-  version_requirements: *16184000
+  version_requirements: *10325060
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &16183340 !ruby/object:Gem::Requirement
+  requirement: &10324220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *16183340
+  version_requirements: *10324220
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &16182800 !ruby/object:Gem::Requirement
+  requirement: &10323080 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *16182800
+  version_requirements: *10323080
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &16182300 !ruby/object:Gem::Requirement
+  requirement: &10322500 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -77,10 +77,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *16182300
+  version_requirements: *10322500
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &16181760 !ruby/object:Gem::Requirement
+  requirement: &10321640 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,7 +88,7 @@ dependencies:
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: *16181760
+  version_requirements: *10321640
 description: GS2 is a gyrokinetic flux tube initial value turbulence code which can
   be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated
   running and analysis of large simulations. This module allows GS2 (and its sister