gs2crmod 0.11.26 → 0.11.27
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- data/VERSION +1 -1
- data/gs2crmod.gemspec +2 -2
- data/lib/gs2crmod/graphs.rb +8 -8
- data/lib/gs2crmod/gsl_data.rb +62 -41
- data/lib/gs2crmod/gsl_tools.rb +16 -0
- metadata +51 -16
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
0.11.
|
1
|
+
0.11.27
|
data/gs2crmod.gemspec
CHANGED
@@ -5,7 +5,7 @@
|
|
5
5
|
|
6
6
|
Gem::Specification.new do |s|
|
7
7
|
s.name = "gs2crmod"
|
8
|
-
s.version = "0.11.
|
8
|
+
s.version = "0.11.27"
|
9
9
|
|
10
10
|
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
11
11
|
s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
|
@@ -84,7 +84,7 @@ Gem::Specification.new do |s|
|
|
84
84
|
s.licenses = ["GSLv3"]
|
85
85
|
s.require_paths = ["lib"]
|
86
86
|
s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
|
87
|
-
s.rubygems_version = "1.8.
|
87
|
+
s.rubygems_version = "1.8.23"
|
88
88
|
s.summary = "Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes."
|
89
89
|
|
90
90
|
if s.respond_to? :specification_version then
|
data/lib/gs2crmod/graphs.rb
CHANGED
@@ -50,7 +50,8 @@ def auto_axiskits(name, options)
|
|
50
50
|
'spectrum_over_kpar' => ["Spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 1],
|
51
51
|
'spectrum_over_ky_over_kx' => ["Spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 2],
|
52
52
|
'spectrum_over_ky_over_kpar' => ["Spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 2],
|
53
|
-
'phi0_over_x_over_y' => ["Phi at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 2],
|
53
|
+
#'phi0_over_x_over_y' => ["Phi at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 2],
|
54
|
+
'phi0_over_x_over_y' => ["Phi at theta = 0", '', 2],
|
54
55
|
'es_mom_flux_over_time' => ["#{species_type((options[:species_index] or 1)).capitalize} Momentum Flux", '', 1]
|
55
56
|
|
56
57
|
|
@@ -1852,20 +1853,19 @@ module GraphKits
|
|
1852
1853
|
when :help
|
1853
1854
|
return "The potential at the outboard midplane"
|
1854
1855
|
when :options
|
1855
|
-
return [:rgbformulae, :limit]
|
1856
|
+
return [:rgbformulae, :limit, :xres, :x_resolution, :yres, :y_resolution, :no_zonal, :t_index]
|
1856
1857
|
else
|
1857
1858
|
zaxis = axiskit('phi0_over_x_over_y', options)
|
1858
1859
|
zaxis.data = zaxis.data.transpose
|
1859
1860
|
shape = zaxis.data.shape
|
1860
|
-
kit = GraphKit.autocreate({x: GraphKit::AxisKit.autocreate({data: (GSL::Vector.alloc((0...shape[0]).to_a)/shape[0] - 0.5) * (@x0 or @y0 * @
|
1861
|
-
# kit.xrange = [0,shape[0]]
|
1862
|
-
# kit.yrange = [0,shape[1]]
|
1861
|
+
kit = GraphKit.autocreate({x: GraphKit::AxisKit.autocreate({data: (GSL::Vector.alloc((0...shape[0]).to_a)/shape[0] - 0.5) * 2*Math::PI * (@x0 or @y0 * @jtwist / 2 / Math::PI / @shat), title: "x", units: "rho_#{species_letter}"}), y: AxisKit.autocreate({data: (GSL::Vector.alloc((0...shape[1]).to_a)/shape[1] - 0.5) * 2*Math::PI * @y0, title: "y", units: "rho_#{species_letter}"}), z: zaxis})
|
1863
1862
|
kit.zrange = options[:limit] if options[:limit]
|
1864
1863
|
kit.title = "Spectrum"
|
1865
1864
|
kit.palette = "rgbformulae #{(options[:rgbformulae] or "-3,3,0")}"
|
1866
|
-
kit.view = "map"
|
1867
|
-
kit.style = "data pm3d"
|
1868
|
-
|
1865
|
+
kit.gp.view = "map"
|
1866
|
+
kit.gp.style = "data pm3d"
|
1867
|
+
kit.gp.size = "ratio #{@y0 / (@x0 or @y0 * @jtwist / 2 / Math::PI / @shat)}"
|
1868
|
+
kit.title = "Phi at theta = 0, t = #{sprintf("%.3f" ,list(:t)[options[:t_index]])}"
|
1869
1869
|
# kit.data[0].with = (options[:with] or 'pm3d palette')
|
1870
1870
|
kit.file_name = options[:graphkit_name]
|
1871
1871
|
kit
|
data/lib/gs2crmod/gsl_data.rb
CHANGED
@@ -1175,11 +1175,10 @@ module GSLMatrices
|
|
1175
1175
|
def phi0_over_x_over_y_gsl_matrix(options)
|
1176
1176
|
Dir.chdir(@directory) do
|
1177
1177
|
|
1178
|
-
options.convert_to_index(:t) if options[:t] or options[:t_element]
|
1178
|
+
#options.convert_to_index(:t) if options[:t] or options[:t_element]
|
1179
|
+
options.convert_to_index(self, :t) if options[:t] or options[:t_element]
|
1179
1180
|
options[:t_index] ||= list(:t).keys.max
|
1180
|
-
#phi2_by_mode index order (in Fortran) is kx, ky, t
|
1181
1181
|
phi_re_narray = netcdf_file.var("phi0").get('start' => [0, 0, 0, options[:t_index] - 1], 'end' => [0, -1, -1, options[:t_index] - 1])
|
1182
|
-
# ep phi_re_narray.shape
|
1183
1182
|
phi_re_narray.reshape!(*phi_re_narray.shape.slice(1..2))
|
1184
1183
|
# The narray has index order ky, kx, but we want kx, ky for historical reasons, hence the transpose.
|
1185
1184
|
gm_re = phi_re_narray.to_gm
|
@@ -1188,60 +1187,82 @@ module GSLMatrices
|
|
1188
1187
|
# The narray has index order ky, kx, but we want kx, ky for historical imasons, hence the transpose.
|
1189
1188
|
gm_im = phi_im_narray.to_gm
|
1190
1189
|
gm = GSL::Matrix::Complex.re_im(gm_re, gm_im)
|
1191
|
-
# ep gm.shape
|
1192
1190
|
|
1193
|
-
|
1194
|
-
|
1191
|
+
ntheta0_temp = gm.shape[1]
|
1192
|
+
naky_temp = gm.shape[0]
|
1193
|
+
|
1194
|
+
|
1195
|
+
# Due to a strange GS2 convention, non zonal modes must be divided by 2:
|
1196
|
+
for i in 1...naky_temp
|
1197
|
+
for j in 0...ntheta0_temp
|
1198
|
+
gm[i,j] = gm[i,j]/2.0
|
1199
|
+
end
|
1200
|
+
end
|
1201
|
+
|
1202
|
+
if options[:no_zonal]
|
1195
1203
|
for i in 0...gm.shape[1]
|
1196
1204
|
gm[0,i] = GSL::Complex.alloc([0,0])
|
1197
1205
|
end
|
1198
1206
|
end
|
1199
1207
|
if xres = (options[:xres] or options[:x_resolution])
|
1200
|
-
|
1201
|
-
|
1202
|
-
|
1203
|
-
|
1204
|
-
|
1205
|
-
|
1206
|
-
mat[i, j+extra] = gm[i,-j] unless j==0
|
1207
|
-
end
|
1208
|
-
end
|
1209
|
-
gm = mat
|
1210
|
-
|
1211
|
-
|
1212
|
-
# gm = mat.vertcat(gm).vertcat(mat)
|
1208
|
+
if xres < nx
|
1209
|
+
puts "Warning: xres should be at least nx. Using nx instead of the xres you specified."
|
1210
|
+
xres = nx
|
1211
|
+
end
|
1212
|
+
else
|
1213
|
+
xres = nx
|
1213
1214
|
end
|
1214
1215
|
if yres = (options[:yres] or options[:y_resolution])
|
1215
|
-
|
1216
|
-
|
1217
|
-
|
1218
|
-
|
1219
|
-
|
1220
|
-
|
1221
|
-
# mat[i, j+extra] = gm[i,-j] unless j==0
|
1222
|
-
end
|
1223
|
-
end
|
1224
|
-
gm = mat
|
1225
|
-
|
1226
|
-
|
1227
|
-
# gm = mat.vertcat(gm).vertcat(mat)
|
1216
|
+
if yres < ny
|
1217
|
+
puts "Warning: yres should be at least ny. Using ny instead of the yres you specified."
|
1218
|
+
yres = ny
|
1219
|
+
end
|
1220
|
+
else
|
1221
|
+
yres = ny
|
1228
1222
|
end
|
1229
|
-
|
1230
|
-
#
|
1231
|
-
|
1232
|
-
#
|
1233
|
-
|
1234
|
-
|
1235
|
-
|
1223
|
+
|
1224
|
+
# Next, pad with 0's:
|
1225
|
+
padded = GSL::Matrix::Complex.calloc(yres, xres)
|
1226
|
+
# Zonal modes first:
|
1227
|
+
for ix in 0...((ntheta0_temp+1)/2)
|
1228
|
+
padded[0, ix] = gm[0, ix]
|
1229
|
+
end
|
1230
|
+
for ix in ((ntheta0_temp+1)/2)...ntheta0_temp
|
1231
|
+
padded[0, ix+xres-ntheta0_temp] = gm[0, ix]
|
1232
|
+
end
|
1233
|
+
# Now include the non-zonal modes in the padded matrix mat:
|
1234
|
+
for iy in 1...naky_temp
|
1235
|
+
for ix in 0...((ntheta0_temp + 1)/2)
|
1236
|
+
padded[iy, ix] = gm[iy, ix]
|
1237
|
+
end
|
1238
|
+
for ix in ((ntheta0_temp+1)/2)...ntheta0_temp
|
1239
|
+
padded[iy, ix+xres-ntheta0_temp] = gm[iy, ix]
|
1240
|
+
end
|
1241
|
+
padded[yres-iy, 0] = gm[iy,0].conj
|
1242
|
+
for ix in 1...xres
|
1243
|
+
padded[yres-iy, ix] = padded[iy, xres-ix].conj
|
1244
|
+
end
|
1245
|
+
end
|
1246
|
+
gm = padded
|
1247
|
+
|
1248
|
+
gm = gm.backward_cols_c2c(false).backward_rows_c2c(false)
|
1249
|
+
# At this point, gm should be purely real (within machine precision), but let's check to be sure:
|
1250
|
+
should_be_zero = gm.imag.abs.max
|
1251
|
+
if should_be_zero > 1.0e-10
|
1252
|
+
puts "should_be_zero = #{should_be_zero}"
|
1253
|
+
raise "Something went wrong - reconstructed phi is not purely real."
|
1254
|
+
end
|
1255
|
+
|
1256
|
+
gm = gm.real
|
1257
|
+
|
1236
1258
|
if options[:limit]
|
1237
1259
|
for i in 0...gm.shape[0]
|
1238
1260
|
for j in 0...gm.shape[1]
|
1239
|
-
# j+= extra if
|
1240
1261
|
gm[i, j] = [[gm[i,j], options[:limit][0]].max, options[:limit][1]].min
|
1241
|
-
# mat[i, j+extra] = gm[i,-j] unless j==0
|
1242
1262
|
end
|
1243
1263
|
end
|
1244
1264
|
end
|
1265
|
+
|
1245
1266
|
return gm
|
1246
1267
|
end
|
1247
1268
|
end
|
data/lib/gs2crmod/gsl_tools.rb
CHANGED
@@ -85,6 +85,22 @@ class GSL::Matrix::Complex
|
|
85
85
|
gm
|
86
86
|
end
|
87
87
|
|
88
|
+
def backward_rows_c2c(normalise = false)
|
89
|
+
gm = self.dup
|
90
|
+
rows, cols = gm.shape
|
91
|
+
table = GSL.cache[[:fft_table, :complex, cols]] ||= GSL::FFT::ComplexWavetable.alloc(cols)
|
92
|
+
work = GSL.cache[[:fft_work, :complex, cols]] ||= GSL::FFT::ComplexWorkspace.alloc(cols)
|
93
|
+
for i in 0...rows
|
94
|
+
vec = gm.row(i)
|
95
|
+
vec.backward!(table, work)
|
96
|
+
for j in 0...cols
|
97
|
+
gm[i,j] = vec[j]
|
98
|
+
end
|
99
|
+
end
|
100
|
+
gm = gm / cols if normalise
|
101
|
+
gm
|
102
|
+
end
|
103
|
+
|
88
104
|
def forward_cols_c2c
|
89
105
|
gm = self.dup
|
90
106
|
rows, cols = gm.shape
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: gs2crmod
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.11.
|
4
|
+
version: 0.11.27
|
5
5
|
prerelease:
|
6
6
|
platform: ruby
|
7
7
|
authors:
|
@@ -14,7 +14,7 @@ date: 2014-03-14 00:00:00.000000000 Z
|
|
14
14
|
dependencies:
|
15
15
|
- !ruby/object:Gem::Dependency
|
16
16
|
name: coderunner
|
17
|
-
requirement:
|
17
|
+
requirement: !ruby/object:Gem::Requirement
|
18
18
|
none: false
|
19
19
|
requirements:
|
20
20
|
- - ! '>='
|
@@ -22,10 +22,15 @@ dependencies:
|
|
22
22
|
version: 0.14.10
|
23
23
|
type: :runtime
|
24
24
|
prerelease: false
|
25
|
-
version_requirements:
|
25
|
+
version_requirements: !ruby/object:Gem::Requirement
|
26
|
+
none: false
|
27
|
+
requirements:
|
28
|
+
- - ! '>='
|
29
|
+
- !ruby/object:Gem::Version
|
30
|
+
version: 0.14.10
|
26
31
|
- !ruby/object:Gem::Dependency
|
27
32
|
name: rubyhacks
|
28
|
-
requirement:
|
33
|
+
requirement: !ruby/object:Gem::Requirement
|
29
34
|
none: false
|
30
35
|
requirements:
|
31
36
|
- - ! '>='
|
@@ -33,10 +38,15 @@ dependencies:
|
|
33
38
|
version: 0.1.2
|
34
39
|
type: :runtime
|
35
40
|
prerelease: false
|
36
|
-
version_requirements:
|
41
|
+
version_requirements: !ruby/object:Gem::Requirement
|
42
|
+
none: false
|
43
|
+
requirements:
|
44
|
+
- - ! '>='
|
45
|
+
- !ruby/object:Gem::Version
|
46
|
+
version: 0.1.2
|
37
47
|
- !ruby/object:Gem::Dependency
|
38
48
|
name: ruby-netcdf-updated
|
39
|
-
requirement:
|
49
|
+
requirement: !ruby/object:Gem::Requirement
|
40
50
|
none: false
|
41
51
|
requirements:
|
42
52
|
- - ! '>='
|
@@ -44,10 +54,15 @@ dependencies:
|
|
44
54
|
version: 0.6.6.1
|
45
55
|
type: :runtime
|
46
56
|
prerelease: false
|
47
|
-
version_requirements:
|
57
|
+
version_requirements: !ruby/object:Gem::Requirement
|
58
|
+
none: false
|
59
|
+
requirements:
|
60
|
+
- - ! '>='
|
61
|
+
- !ruby/object:Gem::Version
|
62
|
+
version: 0.6.6.1
|
48
63
|
- !ruby/object:Gem::Dependency
|
49
64
|
name: shoulda
|
50
|
-
requirement:
|
65
|
+
requirement: !ruby/object:Gem::Requirement
|
51
66
|
none: false
|
52
67
|
requirements:
|
53
68
|
- - ! '>='
|
@@ -55,10 +70,15 @@ dependencies:
|
|
55
70
|
version: '0'
|
56
71
|
type: :development
|
57
72
|
prerelease: false
|
58
|
-
version_requirements:
|
73
|
+
version_requirements: !ruby/object:Gem::Requirement
|
74
|
+
none: false
|
75
|
+
requirements:
|
76
|
+
- - ! '>='
|
77
|
+
- !ruby/object:Gem::Version
|
78
|
+
version: '0'
|
59
79
|
- !ruby/object:Gem::Dependency
|
60
80
|
name: rdoc
|
61
|
-
requirement:
|
81
|
+
requirement: !ruby/object:Gem::Requirement
|
62
82
|
none: false
|
63
83
|
requirements:
|
64
84
|
- - ~>
|
@@ -66,10 +86,15 @@ dependencies:
|
|
66
86
|
version: '3.12'
|
67
87
|
type: :development
|
68
88
|
prerelease: false
|
69
|
-
version_requirements:
|
89
|
+
version_requirements: !ruby/object:Gem::Requirement
|
90
|
+
none: false
|
91
|
+
requirements:
|
92
|
+
- - ~>
|
93
|
+
- !ruby/object:Gem::Version
|
94
|
+
version: '3.12'
|
70
95
|
- !ruby/object:Gem::Dependency
|
71
96
|
name: bundler
|
72
|
-
requirement:
|
97
|
+
requirement: !ruby/object:Gem::Requirement
|
73
98
|
none: false
|
74
99
|
requirements:
|
75
100
|
- - ! '>'
|
@@ -77,10 +102,15 @@ dependencies:
|
|
77
102
|
version: 1.0.0
|
78
103
|
type: :development
|
79
104
|
prerelease: false
|
80
|
-
version_requirements:
|
105
|
+
version_requirements: !ruby/object:Gem::Requirement
|
106
|
+
none: false
|
107
|
+
requirements:
|
108
|
+
- - ! '>'
|
109
|
+
- !ruby/object:Gem::Version
|
110
|
+
version: 1.0.0
|
81
111
|
- !ruby/object:Gem::Dependency
|
82
112
|
name: jeweler
|
83
|
-
requirement:
|
113
|
+
requirement: !ruby/object:Gem::Requirement
|
84
114
|
none: false
|
85
115
|
requirements:
|
86
116
|
- - ! '>='
|
@@ -88,7 +118,12 @@ dependencies:
|
|
88
118
|
version: 1.8.4
|
89
119
|
type: :development
|
90
120
|
prerelease: false
|
91
|
-
version_requirements:
|
121
|
+
version_requirements: !ruby/object:Gem::Requirement
|
122
|
+
none: false
|
123
|
+
requirements:
|
124
|
+
- - ! '>='
|
125
|
+
- !ruby/object:Gem::Version
|
126
|
+
version: 1.8.4
|
92
127
|
description: GS2 is a gyrokinetic flux tube initial value turbulence code which can
|
93
128
|
be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated
|
94
129
|
running and analysis of large simulations. This module allows GS2 (and its sister
|
@@ -183,7 +218,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
183
218
|
version: '0'
|
184
219
|
requirements: []
|
185
220
|
rubyforge_project:
|
186
|
-
rubygems_version: 1.8.
|
221
|
+
rubygems_version: 1.8.23
|
187
222
|
signing_key:
|
188
223
|
specification_version: 3
|
189
224
|
summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.
|