trinitycrmod 0.8.5 → 0.8.7
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/lib/trinitycrmod/namelists.rb +84 -7
- data/lib/trinitycrmod/read_netcdf.rb +1 -1
- data/lib/trinitycrmod/trinity.rb +4 -4
- data/trinitycrmod.gemspec +3 -3
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: d7f6043bbbf9d711cc6e96336a98c5287662128e
|
4
|
+
data.tar.gz: fb380727728f5a141c35828cbcc331cb28da77b3
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: af0622605eea593634f0e9816d720ef3803ae9b790af1002d854c788e46758d4b854b274f55b3a023abd55b18bacb14d79b76d3488237872e72322b065d512c2
|
7
|
+
data.tar.gz: fb295f132ca8402d63b0a634c3a2192887a2b04ebb9c493d053cbae8b6f40f24d995662001534e80cfc9bf731d064843fa61ffe73b4cde37f00180ce48f85c8b
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
0.8.
|
1
|
+
0.8.7
|
@@ -180,9 +180,9 @@
|
|
180
180
|
:phia_in=>
|
181
181
|
{:should_include=>"true",
|
182
182
|
:description=>
|
183
|
-
" if phia_in > 0.0 and overwrite_db_input=T, set
|
183
|
+
" if phia_in > 0.0 and overwrite_db_input=T, set psitor_a = phia_in (psitor_a is sqrt(tor flux) at separatrix)",
|
184
184
|
:help=>
|
185
|
-
" if phia_in > 0.0 and overwrite_db_input=T, set
|
185
|
+
" if phia_in > 0.0 and overwrite_db_input=T, set psitor_a = phia_in (psitor_a is sqrt(tor flux) at separatrix)",
|
186
186
|
:code_name=>:phia_in,
|
187
187
|
:must_pass=>
|
188
188
|
[{:test=>"kind_of? Numeric",
|
@@ -251,6 +251,27 @@
|
|
251
251
|
:explanation=>
|
252
252
|
"This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
|
253
253
|
:type=>:Float,
|
254
|
+
:autoscanned_defaults=>[-1.0]},
|
255
|
+
:nrad_netcdf=>
|
256
|
+
{:should_include=>"true",
|
257
|
+
:description=>" # of radial points in netcdf output (=nrad if <0)",
|
258
|
+
:help=>" # of radial points in netcdf output (=nrad if <0)",
|
259
|
+
:code_name=>:nrad_netcdf,
|
260
|
+
:must_pass=>
|
261
|
+
[{:test=>"kind_of? Integer",
|
262
|
+
:explanation=>"This variable must be an integer."}],
|
263
|
+
:type=>:Integer,
|
264
|
+
:autoscanned_defaults=>[-1]},
|
265
|
+
:rad_out_netcdf=>
|
266
|
+
{:should_include=>"true",
|
267
|
+
:description=>" outer radial boundary (=rad_out if < 0)",
|
268
|
+
:help=>" outer radial boundary (=rad_out if < 0)",
|
269
|
+
:code_name=>:rad_out_netcdf,
|
270
|
+
:must_pass=>
|
271
|
+
[{:test=>"kind_of? Numeric",
|
272
|
+
:explanation=>
|
273
|
+
"This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
|
274
|
+
:type=>:Float,
|
254
275
|
:autoscanned_defaults=>[-1.0]}}},
|
255
276
|
:species=>
|
256
277
|
{:description=>"",
|
@@ -762,7 +783,7 @@
|
|
762
783
|
:explanation=>
|
763
784
|
"This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
|
764
785
|
:type=>:Float,
|
765
|
-
:autoscanned_defaults=>[2.0]},
|
786
|
+
:autoscanned_defaults=>[2, 2.0]},
|
766
787
|
:ddens=>
|
767
788
|
{:should_include=>"true",
|
768
789
|
:description=>" step size for density is -density * ddens",
|
@@ -994,7 +1015,63 @@
|
|
994
1015
|
:explanation=>
|
995
1016
|
"This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
|
996
1017
|
:type=>:Float,
|
997
|
-
:autoscanned_defaults=>[0.2]}
|
1018
|
+
:autoscanned_defaults=>[0.2]},
|
1019
|
+
:single_radius=>
|
1020
|
+
{:should_include=>"true",
|
1021
|
+
:description=>
|
1022
|
+
" If > 0 then run single flux tube at cc_grid(single_radius). All the rest of the fluxes will be the matched fluxes",
|
1023
|
+
:help=>
|
1024
|
+
" If > 0 then run single flux tube at cc_grid(single_radius). All the rest of the fluxes will be the matched fluxes",
|
1025
|
+
:code_name=>:single_radius,
|
1026
|
+
:must_pass=>
|
1027
|
+
[{:test=>"kind_of? Integer",
|
1028
|
+
:explanation=>"This variable must be an integer."}],
|
1029
|
+
:type=>:Integer,
|
1030
|
+
:autoscanned_defaults=>[-1]},
|
1031
|
+
:flux_driver=>
|
1032
|
+
{:should_include=>"true",
|
1033
|
+
:description=>" If true, run flux simulations for the cell centres then quit ",
|
1034
|
+
:help=>" If true, run flux simulations for the cell centres then quit",
|
1035
|
+
:code_name=>:flux_driver,
|
1036
|
+
:must_pass=>
|
1037
|
+
[{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
|
1038
|
+
:explanation=>
|
1039
|
+
"This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
|
1040
|
+
:type=>:Fortran_Bool,
|
1041
|
+
:autoscanned_defaults=>[".true."]},
|
1042
|
+
:ifspppl_bmag=>
|
1043
|
+
{:should_include=>"true",
|
1044
|
+
:description=>
|
1045
|
+
" Specify which magnetic field to use with ifspppl. Set to 'trinity' unless you know what you are doing. Other choices are: 'bunit'",
|
1046
|
+
:help=>
|
1047
|
+
" Specify which magnetic field to use with ifspppl. Set to 'trinity' unless you know what you are doing. Other choices are: 'bunit'",
|
1048
|
+
:code_name=>:ifspppl_bmag,
|
1049
|
+
:must_pass=>
|
1050
|
+
[{:test=>"kind_of? String",
|
1051
|
+
:explanation=>"This variable must be a string."}],
|
1052
|
+
:type=>:String,
|
1053
|
+
:autoscanned_defaults=>["trinity"]},
|
1054
|
+
:override_collisionality=>
|
1055
|
+
{:should_include=>"true",
|
1056
|
+
:description=>nil,
|
1057
|
+
:help=>nil,
|
1058
|
+
:code_name=>:override_collisionality,
|
1059
|
+
:must_pass=>
|
1060
|
+
[{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
|
1061
|
+
:explanation=>
|
1062
|
+
"This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
|
1063
|
+
:type=>:Fortran_Bool,
|
1064
|
+
:autoscanned_defaults=>[]},
|
1065
|
+
:flux_driver=>
|
1066
|
+
{:should_include=>"true",
|
1067
|
+
:description=>"",
|
1068
|
+
:help=>"",
|
1069
|
+
:code_name=>:flux_driver,
|
1070
|
+
:must_pass=>
|
1071
|
+
[{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
|
1072
|
+
:explanation=>
|
1073
|
+
"This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
|
1074
|
+
:type=>:Fortran_Bool}}},
|
998
1075
|
:init=>
|
999
1076
|
{:description=>"",
|
1000
1077
|
:should_include=>"true",
|
@@ -1167,7 +1244,7 @@
|
|
1167
1244
|
:explanation=>
|
1168
1245
|
"This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
|
1169
1246
|
:type=>:Fortran_Bool,
|
1170
|
-
:autoscanned_defaults=>[".false."]},
|
1247
|
+
:autoscanned_defaults=>[".false.", ".true."]},
|
1171
1248
|
:flux_groups=>
|
1172
1249
|
{:should_include=>"true",
|
1173
1250
|
:description=>" The number of processors for each flux calculation",
|
@@ -1612,7 +1689,7 @@
|
|
1612
1689
|
:explanation=>
|
1613
1690
|
"This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
|
1614
1691
|
:type=>:Fortran_Bool,
|
1615
|
-
:autoscanned_defaults=>[".true."]},
|
1692
|
+
:autoscanned_defaults=>[".false.", ".true."]},
|
1616
1693
|
:evolve_temperature=>
|
1617
1694
|
{:should_include=>"true",
|
1618
1695
|
:description=>" if true, evolve temperature profile(s)",
|
@@ -1623,7 +1700,7 @@
|
|
1623
1700
|
:explanation=>
|
1624
1701
|
"This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
|
1625
1702
|
:type=>:Fortran_Bool,
|
1626
|
-
:autoscanned_defaults=>[".true."]},
|
1703
|
+
:autoscanned_defaults=>[".false.", ".true."]},
|
1627
1704
|
:evolve_flow=>
|
1628
1705
|
{:should_include=>"true",
|
1629
1706
|
:description=>" if true, evolve toroidal angular momentum",
|
@@ -104,7 +104,7 @@ class NetcdfSmartReader
|
|
104
104
|
when 'mrow', 'mcol', 'ivar', 'tspec', 'iter', 'jac', 'grad', 'eval'
|
105
105
|
return GraphKit::AxisKit.autocreate(data: GSL::Vector.linspace(1, sz=@file.dim(variable).length, sz), title: variable)
|
106
106
|
end
|
107
|
-
GraphKit::AxisKit.autocreate(data: read_variable(variable, options), units: @file.var(variable).att('units').get, title: @file.var(variable).att('description').get.sub(/(,|summed|average).*$/, '').sub(/[vV]alues of (the )?/, '').sub(/ coordinate/, ''))
|
107
|
+
GraphKit::AxisKit.autocreate(data: read_variable(variable, options), units: @file.var(variable).att('units').get, title: @file.var(variable).att('description').get.sub(/(,|summed|average).*$/, '').sub(/[vV]alues of (the )?/, '').sub(/ coordinate/, '').sub(/.*rho.*The definition.*/, 'rho'))
|
108
108
|
end
|
109
109
|
def dimension_variable_name(n)
|
110
110
|
case n
|
data/lib/trinitycrmod/trinity.rb
CHANGED
@@ -381,13 +381,13 @@ class CodeRunner
|
|
381
381
|
|
382
382
|
def generate_component_runs
|
383
383
|
#puts "HERE"
|
384
|
-
@
|
385
|
-
|
386
|
-
if
|
387
|
-
@component_runs = existing.sort_by{|r| -r.id}
|
384
|
+
if (existing = @runner.component_run_list.values.find_all{|r| r.real_id==@id}).size > 0
|
385
|
+
@component_runs = existing.sort_by{|r| -r.id}
|
386
|
+
if @running
|
388
387
|
return
|
389
388
|
end
|
390
389
|
end
|
390
|
+
@component_runs ||= []
|
391
391
|
if flux_gryfx? or flux_gs2?
|
392
392
|
fclass = flux_class
|
393
393
|
|
data/trinitycrmod.gemspec
CHANGED
@@ -2,16 +2,16 @@
|
|
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: trinitycrmod 0.8.
|
5
|
+
# stub: trinitycrmod 0.8.7 ruby lib
|
6
6
|
|
7
7
|
Gem::Specification.new do |s|
|
8
8
|
s.name = "trinitycrmod"
|
9
|
-
s.version = "0.8.
|
9
|
+
s.version = "0.8.7"
|
10
10
|
|
11
11
|
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
12
12
|
s.require_paths = ["lib"]
|
13
13
|
s.authors = ["Edmund Highcock"]
|
14
|
-
s.date = "2015-
|
14
|
+
s.date = "2015-12-22"
|
15
15
|
s.description = "This module allows Trinity, the Multiscale Gyrokinetic Turbulent Transport solver for Fusion Reactors, to harness the power of CodeRunner, a framework for the automated running and analysis of simulations."
|
16
16
|
s.email = "edmundhighcock@sourceforge.net"
|
17
17
|
s.extra_rdoc_files = [
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: trinitycrmod
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.8.
|
4
|
+
version: 0.8.7
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Edmund Highcock
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2015-
|
11
|
+
date: 2015-12-22 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: coderunner
|