gs2crmod 0.11.35 → 0.11.36
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/VERSION +1 -1
- data/gs2crmod.gemspec +7 -5
- data/lib/gs2crmod/gs2.rb +5 -0
- data/lib/gs2crmod/read_netcdf.rb +96 -0
- metadata +57 -38
checksums.yaml
ADDED
@@ -0,0 +1,7 @@
|
|
1
|
+
---
|
2
|
+
SHA1:
|
3
|
+
metadata.gz: f661dc2bf1a80c9e9f7b18ab69761e427ef70c5f
|
4
|
+
data.tar.gz: a6b052352a440b0b0618e409d9d7ad82a2b41dff
|
5
|
+
SHA512:
|
6
|
+
metadata.gz: d81a214c19e7ffa023f532f6952e2dd3897922e65ddc83dcca56f0c7f6d3b4ec4a5e4c61d235faf19aed1e6d3d92cf5d305c3595cc27b3f0ef3e5a217e3cf63f
|
7
|
+
data.tar.gz: e8505a545ebb2080c7584444435669973d129a30bfb61a8c872c48fdf7d178ea917a1480a79872b4ddcaf96e0a2b755d17b05adf4eba42decb85c47c59fb6059
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
0.11.
|
1
|
+
0.11.36
|
data/gs2crmod.gemspec
CHANGED
@@ -2,14 +2,17 @@
|
|
2
2
|
# DO NOT EDIT THIS FILE DIRECTLY
|
3
3
|
# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
|
4
4
|
# -*- encoding: utf-8 -*-
|
5
|
+
# stub: gs2crmod 0.11.36 ruby lib
|
6
|
+
# stub: ext/extconf.rb
|
5
7
|
|
6
8
|
Gem::Specification.new do |s|
|
7
9
|
s.name = "gs2crmod"
|
8
|
-
s.version = "0.11.
|
10
|
+
s.version = "0.11.36"
|
9
11
|
|
10
12
|
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
13
|
+
s.require_paths = ["lib"]
|
11
14
|
s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
|
12
|
-
s.date = "2014-03-
|
15
|
+
s.date = "2014-03-27"
|
13
16
|
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."
|
14
17
|
s.email = "edmundhighcock@sourceforge.net"
|
15
18
|
s.extensions = ["ext/extconf.rb"]
|
@@ -82,13 +85,12 @@ Gem::Specification.new do |s|
|
|
82
85
|
]
|
83
86
|
s.homepage = "http://gs2crmod.sourceforge.net"
|
84
87
|
s.licenses = ["GSLv3"]
|
85
|
-
s.require_paths = ["lib"]
|
86
88
|
s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
|
87
|
-
s.rubygems_version = "
|
89
|
+
s.rubygems_version = "2.2.1"
|
88
90
|
s.summary = "Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes."
|
89
91
|
|
90
92
|
if s.respond_to? :specification_version then
|
91
|
-
s.specification_version =
|
93
|
+
s.specification_version = 4
|
92
94
|
|
93
95
|
if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
|
94
96
|
s.add_runtime_dependency(%q<coderunner>, [">= 0.14.10"])
|
data/lib/gs2crmod/gs2.rb
CHANGED
data/lib/gs2crmod/read_netcdf.rb
CHANGED
@@ -47,8 +47,21 @@ class NetcdfSmartReader
|
|
47
47
|
end
|
48
48
|
def read_variable(varname, options)
|
49
49
|
#start = get_start(dims, options)
|
50
|
+
if varname == 's' # dummy response for species index
|
51
|
+
return NArray.float(@nspec||1)
|
52
|
+
end
|
50
53
|
dims = dimensions(varname)
|
51
54
|
narray = @file.var(varname).get('start'=>starts(dims, options), 'end'=>ends(dims, options))
|
55
|
+
if options[:modify_variable]
|
56
|
+
dimhash = dims.inject({}){|hash, dim|
|
57
|
+
opts = options.dup
|
58
|
+
opts[:modify_variable] = nil
|
59
|
+
dimval = read_variable(dimension_variable_name(dim.name), opts)
|
60
|
+
hash[dim.name] = dimval
|
61
|
+
hash
|
62
|
+
}
|
63
|
+
narray = options[:modify_variable].call(varname, narray, hash)
|
64
|
+
end
|
52
65
|
shape = narray.shape
|
53
66
|
shape.delete_if{|i| i==1}
|
54
67
|
#p 'shape', shape; STDIN.gets
|
@@ -108,6 +121,8 @@ class NetcdfSmartReader
|
|
108
121
|
'hermite'
|
109
122
|
when 'p'
|
110
123
|
'hankel'
|
124
|
+
when 's'
|
125
|
+
's'
|
111
126
|
else
|
112
127
|
raise "Unknown dimension #{n}"
|
113
128
|
end
|
@@ -177,4 +192,85 @@ def old_smart_graphkit(options)
|
|
177
192
|
end
|
178
193
|
end
|
179
194
|
|
195
|
+
def hyperviscosity_graphkit(options)
|
196
|
+
raise "This only works for spectrogk" unless spectrogk?
|
197
|
+
options[:modify_variable] = Proc.new do |varname, narray, dimhash|
|
198
|
+
#dimnames = dimhash.keys
|
199
|
+
ky = gsl_vector('ky')
|
200
|
+
kx = gsl_vector('kx').to_box_order
|
201
|
+
shape = narray.shape
|
202
|
+
if varname == "gnew2_ta"
|
203
|
+
shape = narray.shape
|
204
|
+
for ig in 0...shape[0]
|
205
|
+
for ik in 0...shape[1]
|
206
|
+
for it in 0...shape[2]
|
207
|
+
for il in 0...shape[3]
|
208
|
+
for ie in 0...shape[4]
|
209
|
+
for is in 0...shape[5]
|
210
|
+
narray[ig,ik,it,il,ie,is]*=(ky(ik)**2.0 + kx(it)**2.0)*@d_hypervsic
|
211
|
+
end
|
212
|
+
end
|
213
|
+
end
|
214
|
+
end
|
215
|
+
end
|
216
|
+
end
|
217
|
+
end
|
218
|
+
narray
|
219
|
+
end
|
220
|
+
options[:graphkit_name] = 'cdf_gnew2_ta'
|
221
|
+
kit = smart_graphkit(options)
|
222
|
+
end
|
223
|
+
def hypercoll_graphkit(options)
|
224
|
+
raise "This only works for spectrogk" unless spectrogk?
|
225
|
+
options[:modify_variable] = Proc.new do |varname, narray, dimhash|
|
226
|
+
#dimnames = dimhash.keys
|
227
|
+
if varname == "gnew2_ta"
|
228
|
+
shape = narray.shape
|
229
|
+
p 'shape',shape
|
230
|
+
for ig in 0...shape[0]
|
231
|
+
for ik in 0...shape[1]
|
232
|
+
for it in 0...shape[2]
|
233
|
+
for il in 0...shape[3]
|
234
|
+
for ie in 0...shape[4]
|
235
|
+
for is in 0...shape[5]
|
236
|
+
narray[ig,ik,it,il,ie,is]*=send(:nu_h_ + (is+1).to_sym)*(il/(shape[3]-1))**send(:nexp_h_ + (is+1).to_sym)
|
237
|
+
end
|
238
|
+
end
|
239
|
+
end
|
240
|
+
end
|
241
|
+
end
|
242
|
+
end
|
243
|
+
end
|
244
|
+
narray
|
245
|
+
end
|
246
|
+
options[:graphkit_name] = 'cdf_gnew2_ta'
|
247
|
+
kit = smart_graphkit(options)
|
248
|
+
end
|
249
|
+
def lenardbern_graphkit(options)
|
250
|
+
raise "This only works for spectrogk" unless spectrogk?
|
251
|
+
options[:modify_variable] = Proc.new do |varname, narray, dimhash|
|
252
|
+
#dimnames = dimhash.keys
|
253
|
+
if varname == "gnew2_ta"
|
254
|
+
shape = narray.shape
|
255
|
+
for ig in 0...shape[0]
|
256
|
+
for ik in 0...shape[1]
|
257
|
+
for it in 0...shape[2]
|
258
|
+
for il in 0...shape[3]
|
259
|
+
for ie in 0...shape[4]
|
260
|
+
for is in 0...shape[5]
|
261
|
+
narray[ik,it,il,ie,is]*=send(:nu_ + (is+1).to_sym)*il
|
262
|
+
end
|
263
|
+
end
|
264
|
+
end
|
265
|
+
end
|
266
|
+
end
|
267
|
+
end
|
268
|
+
end
|
269
|
+
narray
|
270
|
+
end
|
271
|
+
options[:graphkit_name] = 'cdf_gnew2_ta'
|
272
|
+
kit = smart_graphkit(options)
|
273
|
+
end
|
274
|
+
|
275
|
+
|
180
276
|
end
|
metadata
CHANGED
@@ -1,8 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: gs2crmod
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.11.
|
5
|
-
prerelease:
|
4
|
+
version: 0.11.36
|
6
5
|
platform: ruby
|
7
6
|
authors:
|
8
7
|
- Edmund Highcock
|
@@ -10,85 +9,106 @@ authors:
|
|
10
9
|
autorequire:
|
11
10
|
bindir: bin
|
12
11
|
cert_chain: []
|
13
|
-
date: 2014-03-
|
12
|
+
date: 2014-03-27 00:00:00.000000000 Z
|
14
13
|
dependencies:
|
15
14
|
- !ruby/object:Gem::Dependency
|
16
15
|
name: coderunner
|
17
|
-
requirement:
|
18
|
-
none: false
|
16
|
+
requirement: !ruby/object:Gem::Requirement
|
19
17
|
requirements:
|
20
|
-
- -
|
18
|
+
- - ">="
|
21
19
|
- !ruby/object:Gem::Version
|
22
20
|
version: 0.14.10
|
23
21
|
type: :runtime
|
24
22
|
prerelease: false
|
25
|
-
version_requirements:
|
23
|
+
version_requirements: !ruby/object:Gem::Requirement
|
24
|
+
requirements:
|
25
|
+
- - ">="
|
26
|
+
- !ruby/object:Gem::Version
|
27
|
+
version: 0.14.10
|
26
28
|
- !ruby/object:Gem::Dependency
|
27
29
|
name: rubyhacks
|
28
|
-
requirement:
|
29
|
-
none: false
|
30
|
+
requirement: !ruby/object:Gem::Requirement
|
30
31
|
requirements:
|
31
|
-
- -
|
32
|
+
- - ">="
|
32
33
|
- !ruby/object:Gem::Version
|
33
34
|
version: 0.1.2
|
34
35
|
type: :runtime
|
35
36
|
prerelease: false
|
36
|
-
version_requirements:
|
37
|
+
version_requirements: !ruby/object:Gem::Requirement
|
38
|
+
requirements:
|
39
|
+
- - ">="
|
40
|
+
- !ruby/object:Gem::Version
|
41
|
+
version: 0.1.2
|
37
42
|
- !ruby/object:Gem::Dependency
|
38
43
|
name: ruby-netcdf-updated
|
39
|
-
requirement:
|
40
|
-
none: false
|
44
|
+
requirement: !ruby/object:Gem::Requirement
|
41
45
|
requirements:
|
42
|
-
- -
|
46
|
+
- - ">="
|
43
47
|
- !ruby/object:Gem::Version
|
44
48
|
version: 0.6.6.1
|
45
49
|
type: :runtime
|
46
50
|
prerelease: false
|
47
|
-
version_requirements:
|
51
|
+
version_requirements: !ruby/object:Gem::Requirement
|
52
|
+
requirements:
|
53
|
+
- - ">="
|
54
|
+
- !ruby/object:Gem::Version
|
55
|
+
version: 0.6.6.1
|
48
56
|
- !ruby/object:Gem::Dependency
|
49
57
|
name: shoulda
|
50
|
-
requirement:
|
51
|
-
none: false
|
58
|
+
requirement: !ruby/object:Gem::Requirement
|
52
59
|
requirements:
|
53
|
-
- -
|
60
|
+
- - ">="
|
54
61
|
- !ruby/object:Gem::Version
|
55
62
|
version: '0'
|
56
63
|
type: :development
|
57
64
|
prerelease: false
|
58
|
-
version_requirements:
|
65
|
+
version_requirements: !ruby/object:Gem::Requirement
|
66
|
+
requirements:
|
67
|
+
- - ">="
|
68
|
+
- !ruby/object:Gem::Version
|
69
|
+
version: '0'
|
59
70
|
- !ruby/object:Gem::Dependency
|
60
71
|
name: rdoc
|
61
|
-
requirement:
|
62
|
-
none: false
|
72
|
+
requirement: !ruby/object:Gem::Requirement
|
63
73
|
requirements:
|
64
|
-
- - ~>
|
74
|
+
- - "~>"
|
65
75
|
- !ruby/object:Gem::Version
|
66
76
|
version: '3.12'
|
67
77
|
type: :development
|
68
78
|
prerelease: false
|
69
|
-
version_requirements:
|
79
|
+
version_requirements: !ruby/object:Gem::Requirement
|
80
|
+
requirements:
|
81
|
+
- - "~>"
|
82
|
+
- !ruby/object:Gem::Version
|
83
|
+
version: '3.12'
|
70
84
|
- !ruby/object:Gem::Dependency
|
71
85
|
name: bundler
|
72
|
-
requirement:
|
73
|
-
none: false
|
86
|
+
requirement: !ruby/object:Gem::Requirement
|
74
87
|
requirements:
|
75
|
-
- -
|
88
|
+
- - ">"
|
76
89
|
- !ruby/object:Gem::Version
|
77
90
|
version: 1.0.0
|
78
91
|
type: :development
|
79
92
|
prerelease: false
|
80
|
-
version_requirements:
|
93
|
+
version_requirements: !ruby/object:Gem::Requirement
|
94
|
+
requirements:
|
95
|
+
- - ">"
|
96
|
+
- !ruby/object:Gem::Version
|
97
|
+
version: 1.0.0
|
81
98
|
- !ruby/object:Gem::Dependency
|
82
99
|
name: jeweler
|
83
|
-
requirement:
|
84
|
-
none: false
|
100
|
+
requirement: !ruby/object:Gem::Requirement
|
85
101
|
requirements:
|
86
|
-
- -
|
102
|
+
- - ">="
|
87
103
|
- !ruby/object:Gem::Version
|
88
104
|
version: 1.8.4
|
89
105
|
type: :development
|
90
106
|
prerelease: false
|
91
|
-
version_requirements:
|
107
|
+
version_requirements: !ruby/object:Gem::Requirement
|
108
|
+
requirements:
|
109
|
+
- - ">="
|
110
|
+
- !ruby/object:Gem::Version
|
111
|
+
version: 1.8.4
|
92
112
|
description: GS2 is a gyrokinetic flux tube initial value turbulence code which can
|
93
113
|
be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated
|
94
114
|
running and analysis of large simulations. This module allows GS2 (and its sister
|
@@ -102,7 +122,7 @@ extra_rdoc_files:
|
|
102
122
|
- README.md
|
103
123
|
- README.rdoc
|
104
124
|
files:
|
105
|
-
- .document
|
125
|
+
- ".document"
|
106
126
|
- Gemfile
|
107
127
|
- LICENSE.txt
|
108
128
|
- README.md
|
@@ -165,26 +185,25 @@ files:
|
|
165
185
|
homepage: http://gs2crmod.sourceforge.net
|
166
186
|
licenses:
|
167
187
|
- GSLv3
|
188
|
+
metadata: {}
|
168
189
|
post_install_message:
|
169
190
|
rdoc_options: []
|
170
191
|
require_paths:
|
171
192
|
- lib
|
172
193
|
required_ruby_version: !ruby/object:Gem::Requirement
|
173
|
-
none: false
|
174
194
|
requirements:
|
175
|
-
- -
|
195
|
+
- - ">="
|
176
196
|
- !ruby/object:Gem::Version
|
177
197
|
version: 1.9.1
|
178
198
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
179
|
-
none: false
|
180
199
|
requirements:
|
181
|
-
- -
|
200
|
+
- - ">="
|
182
201
|
- !ruby/object:Gem::Version
|
183
202
|
version: '0'
|
184
203
|
requirements: []
|
185
204
|
rubyforge_project:
|
186
|
-
rubygems_version:
|
205
|
+
rubygems_version: 2.2.1
|
187
206
|
signing_key:
|
188
|
-
specification_version:
|
207
|
+
specification_version: 4
|
189
208
|
summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.
|
190
209
|
test_files: []
|