cronoscrmod 0.1.1 → 0.1.2

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: ac201c7e381fe074df24db61e63e60df5c17151a
+  data.tar.gz: 32b3cfde01015ce590dbdf152297d66496c74c31
+SHA512:
+  metadata.gz: 4ab19a83935902bce67fcceb114b70bdc78d8b5c83438e6193b4372f9268b90a81d659bdb2580dc58e01a8ed4900267e8f4253d40f661c0b46eb1e93a3895d8b
+  data.tar.gz: 939ca19f7861e41e1f909852c20eda13b305a953abaa311c378efa290d11a0969000cf8e1fdb89e2dfe18229125756a848768302003f262456f63588e56022a0

data/Gemfile

@@ -2,15 +2,14 @@ source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
 #   gem "activesupport", ">= 2.3.5"
-   gem "coderunner", ">= 0.13.18"
+gem "coderunner", ">= 1.0"
    #gem "matlab-ruby", "> 2.0.0"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "shoulda", ">= 0"
+  gem "shoulda", "~> 3.5"
   gem "rdoc", "~> 3.12"
-  gem "bundler", "> 1.0.0"
-  gem "jeweler", ">= 1.8.4"
-  #gem "rcov", ">= 0"
+  #gem "bundler", "> 1.0.0"
+  gem "jeweler", "~> 2.3"
 end

data/VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

data/cronoscrmod.gemspec

@@ -2,16 +2,18 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+# stub: cronoscrmod 0.1.2 ruby lib
 
 Gem::Specification.new do |s|
-  s.name = "cronoscrmod"
-  s.version = "0.1.1"
+  s.name = "cronoscrmod".freeze
+  s.version = "0.1.2"
 
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Edmund Highcock"]
-  s.date = "2013-10-17"
-  s.description = "A module to allow CodeRunner to run the integrated tokamak modelling suite Cronos. Requires matlab and matlab-ruby (Cronos also requires Matlab)."
-  s.email = "edmundhighcock@users.sourceforge.net"
+  s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib".freeze]
+  s.authors = ["Edmund Highcock".freeze]
+  s.date = "2017-01-16"
+  s.description = "A module to allow CodeRunner to run the integrated tokamak modelling suite Cronos. Requires matlab and matlab-ruby (Cronos also requires Matlab).".freeze
+  s.email = "edmundhighcock@users.sourceforge.net".freeze
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.md",
@@ -30,37 +32,36 @@ Gem::Specification.new do |s|
     "lib/cronoscrmod.rb",
     "lib/cronoscrmod/cronos.rb",
     "lib/cronoscrmod/defaults_files/cronos_defaults.rb",
+    "lib/cronoscrmod/matlab/cronos_eqdsk.m",
+    "lib/cronoscrmod/matlab/eqdsk_jc.m",
+    "lib/cronoscrmod/matlab/output_ogyropsi.m",
     "test/helper.rb",
     "test/test_cronoscrmod.rb"
   ]
-  s.homepage = "http://github.com/edmundhighcock/cronoscrmod"
-  s.licenses = ["MIT"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.23"
-  s.summary = "A module to allow CodeRunner to run the integrated tokamak modelling suite Cronos"
+  s.homepage = "http://github.com/edmundhighcock/cronoscrmod".freeze
+  s.licenses = ["MIT".freeze]
+  s.rubygems_version = "2.6.8".freeze
+  s.summary = "A module to allow CodeRunner to run the integrated tokamak modelling suite Cronos".freeze
 
   if s.respond_to? :specification_version then
-    s.specification_version = 3
+    s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<coderunner>, [">= 0.13.18"])
-      s.add_development_dependency(%q<shoulda>, [">= 0"])
-      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_development_dependency(%q<bundler>, ["> 1.0.0"])
-      s.add_development_dependency(%q<jeweler>, [">= 1.8.4"])
+      s.add_runtime_dependency(%q<coderunner>.freeze, [">= 1.0"])
+      s.add_development_dependency(%q<shoulda>.freeze, ["~> 3.5"])
+      s.add_development_dependency(%q<rdoc>.freeze, ["~> 3.12"])
+      s.add_development_dependency(%q<jeweler>.freeze, ["~> 2.3"])
     else
-      s.add_dependency(%q<coderunner>, [">= 0.13.18"])
-      s.add_dependency(%q<shoulda>, [">= 0"])
-      s.add_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_dependency(%q<bundler>, ["> 1.0.0"])
-      s.add_dependency(%q<jeweler>, [">= 1.8.4"])
+      s.add_dependency(%q<coderunner>.freeze, [">= 1.0"])
+      s.add_dependency(%q<shoulda>.freeze, ["~> 3.5"])
+      s.add_dependency(%q<rdoc>.freeze, ["~> 3.12"])
+      s.add_dependency(%q<jeweler>.freeze, ["~> 2.3"])
     end
   else
-    s.add_dependency(%q<coderunner>, [">= 0.13.18"])
-    s.add_dependency(%q<shoulda>, [">= 0"])
-    s.add_dependency(%q<rdoc>, ["~> 3.12"])
-    s.add_dependency(%q<bundler>, ["> 1.0.0"])
-    s.add_dependency(%q<jeweler>, [">= 1.8.4"])
+    s.add_dependency(%q<coderunner>.freeze, [">= 1.0"])
+    s.add_dependency(%q<shoulda>.freeze, ["~> 3.5"])
+    s.add_dependency(%q<rdoc>.freeze, ["~> 3.12"])
+    s.add_dependency(%q<jeweler>.freeze, ["~> 2.3"])
   end
 end
 

data/lib/cronoscrmod/cronos.rb

@@ -38,7 +38,12 @@ class CodeRunner
 			def cronos(*args)
 				if args.size > 0
 					args.each do |com|
-					CodeRunner::Cronos.rcp.engine_handler.cronos.puts(com)
+						begin
+							CodeRunner::Cronos.rcp.engine_handler.cronos.puts(com)
+						rescue Errno::EPIPE
+							CodeRunner::Cronos.rcp.engine_handler.restart_cronos(@r.executable.sub(/cronos$/, ""))
+							retry
+						end
 					end
 				end
 			end
@@ -58,8 +63,13 @@ class CodeRunner
 				return if @cronos_started
 				raise "cronos not found in #{path}" unless FileTest.exist?("#{path}/cronos.m")
 				@cronos = IO.popen("#{path}/cronos 3>&2 2>&1 1>&3 | grep -v 'Time Machine' 3>&2 2>&1 1>&3 ",  'w')
+				@cronos.puts("addpath('#{CodeRunner::Cronos.rcp.code_module_folder}/matlab')")
 				@cronos_started = true
 			end
+			def restart_cronos(path)
+				@cronos_started = false
+				start_cronos(path)
+			end
 			def new_file
 				@cronos.puts("zuicreate")
 			end
@@ -181,6 +191,11 @@ class CodeRunner
 			refresh_gui
 		end
 
+		def load_result
+			cronos.puts("zuiload('#@directory/#{@run_name}_resultat.mat')")
+			refresh_gui
+		end
+
 		def cronos
 			set_cronos_path
 			rcp.engine_handler.cronos

data/lib/cronoscrmod/matlab/cronos_eqdsk.m

@@ -0,0 +1,276 @@
+function no_results = cronos_eqdsk(data, fname, tavg, resofactor)
+%CREATES A EFIT EQDSK G FILE AND MATLABSTRUCTURE FROM CRONOS DATA.EQUI DATA. USED FOR CREATING 
+%GEOMETRY INPUT FILES FOR GENE. ALSO CREATES CONVENIENT MATLAB STRUCTURE WITH KEY INFORMATION
+%
+%A CRONOS DATA FILE NEEDS TO BE IN THE BACKGROUND WHEN RUNNING THIS ROUTINE
+%J.Citrin 20.05.2013
+
+
+%%%%%%%%%%%%INPUT PARAMETERS%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%fname='JET75225_Ptotred'; %choose a name for the output geometry file
+%tavg=[46 47]; %choose a time window for averaging of CRONOS data
+printflag=0; %flag to plot or not (=1) or not to plot (anything else) a figure of the 2D flux surfaces
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+bleed=0.02; %space around limits of R,Z points to define the rectangular grid
+
+ind=round(interp1(data.gene.temps,1:length(data.gene.temps),tavg)); ind=ind(1):ind(2); %find the indexes in data.gene.temps of the desired time window
+x=linspace(0,1,101); 
+
+%obtain R,Z, and psi from data.equi. Note that the normalized radial coordinate below is from equi.rhoRZ./equi.rhoRZ(end) and not the uniform x!
+R=squeeze(mean(data.equi.R(ind,:,:))); R=double(R); 
+Z=squeeze(mean(data.equi.Z(ind,:,:))); Z=double(Z);
+psiequi=-mean(data.equi.psiRZ(ind,:)); psiequi=(double(psiequi)); %the minus sign is there since eqdsk expects flipped psi profiles
+resotheta=length(R(1,:)); %finds the theta resolution from the CRONOS simulation
+
+%JC 15.5.13
+%TO BE CONSISTENT WITH THE CHEASE EQDSK DATA, PSIEQUI IS SHIFTED SUCH THAT PSIEQUI(1)=0
+%FEEL FREE TO CHANGE THIS, IT IS TRIVIAL TO DO SO
+psiequi=psiequi-psiequi(1);
+%psiequi=psiequi-psiequi(end);
+xrho=mean(data.equi.rhoRZ(ind,:)); xrho=xrho./xrho(end);
+psix=interp1(xrho,psiequi,x);
+rho1=mean(data.equi.rhomax(ind));
+
+%set the resolution of the rectangular box (for now kept the same as the theta resolution from cronos)
+resoR=resotheta*resofactor; 
+resoZ=resotheta*resofactor;
+resopsi=resotheta*resofactor;
+
+%resoR=100; 
+%resoZ=100;
+%resopsi=65;
+
+%interpolate equi.psi onto the uniform toroidal flux grid and create 
+%the normalized poloidal flux coordinate to interpolate the q, P, P', F, FF' profiles
+xrho=mean(data.equi.rhoRZ(ind,:)); xrho=xrho./xrho(end); xrho=double(xrho);
+psix=interp1(xrho,psiequi,x, 'splines');
+psinormx=(psix-psix(1))./(psix(end)-psix(1));
+psinormequi = (psiequi-psiequi(1))./(psiequi(end) - psiequi(1));
+dvdrho=mean(data.equi.vpr(ind,:));
+%create desired uniform normalized poloidal flux grid
+xpsi=linspace(0,1,resopsi);
+
+
+
+%define boundaries of rectangular grid
+maxR=max(max(R))+bleed;
+minR=min(min(R))-bleed;
+maxZ=max(max(Z))+bleed;
+minZ=min(min(Z))-bleed;
+
+maxxZ = max([maxZ, -minZ]);
+maxZ = maxxZ;
+minZ = -maxxZ;
+
+%create rectangular grid
+xR=linspace(minR,maxR,resoR); 
+% EGH Z is defined from - to plus, and it must also be symmetric
+yR=linspace(minZ,maxZ,resoZ);
+[xnodes,ynodes] = meshgrid(xR,yR); %xnodes, ynodes are matrices defining the x and y (R and Z) coordinates
+
+%Create a 2D array for psi corresponding to x,theta (is a flux function, so same at every theta and tmp is discarded)
+%This 2D array, which fits the x,theta arrays of R,Z, are interpolated onto the rectangular grid with coordinates xnodes,ynodes
+[psibig,tmp]=meshgrid(psiequi,1:resotheta); psibig=psibig';
+zefit1 = griddata(R,Z,psibig,xnodes,ynodes,'cubic');
+
+%define psi quantities for all points in rectangular grid that lay outside of separatrix (became NaN in interpolation)
+zefit1(isnan(zefit1))=psiequi(end)*1.05;
+
+%grab necessary profiles and interpolate onto normalized poloidal flux grid
+qraw=mean(data.equi.q(ind,:)); qraw=double(qraw);
+s=mean(data.equi.shear(ind,:)); 
+F=mean(data.equi.F(ind,:));
+P=mean(data.prof.ptot(ind,:));
+%FFprime=gradient(F,-psiequi); %the minus sign on psiequi defines the gradient to the ORIGINAL psi (i.e. the unflipped one)
+% EGH Bugfix
+% F and P are on grids of x not rho, so need to take gradient wrt psix
+FFprime=gradient(F,psix); %the minus sign on psiequi defines the gradient to the ORIGINAL psi (i.e. the unflipped one)
+Pprime=gradient(P,psix);
+
+% Values of psi on the output grid of xpsi
+psixpsi = interp1(psinormequi, psiequi, xpsi);
+
+q=interp1(psinormx,qraw,xpsi);
+F=interp1(psinormx,F,xpsi, 'spline');
+FFprime=interp1(psinormx,FFprime,xpsi).*F; %FFprime(1) = 0.0; 
+%FFprime = gradient(F, psixpsi).*F;
+%FFprime = interp1(psinormequi, mean(squeeze(data.equi.df2RZ(ind, :)))*pi, xpsi);
+%FFprime(1)=(FFprime(1)+FFprime(2))/2.0; 
+FFprime(3) = FFprime(4);
+FFprime(2) = FFprime(3);
+FFprime(1) = FFprime(2);
+%FFprime(1) = 0.0;
+P=interp1(psinormx,P,xpsi, 'spline');
+Pprime=interp1(psinormx,Pprime,xpsi); %Pprime(1) = 0.0; 
+%Pprime = interp1(psinormequi, mean(squeeze(data.equi.dprRZ(ind, :)))*-300000, xpsi);
+%Pprime=gradient(P, psixpsi);
+%Pprime(1)=(Pprime(1)+Pprime(2))/2.0; 
+%Pprime(1)=Pprime(2)/2.0;
+Pprime(3)=Pprime(4);
+Pprime(2)=Pprime(3);
+Pprime(1)=Pprime(2);
+%Pprime(1) = 0.0;
+
+%define header quantities for eqdsk file
+boxw=maxR-minR; 
+boxh=maxZ-minZ; 
+rmaj=(maxR+minR)/2; 
+rleft=minR;
+
+zmid=(maxZ+minZ)/2; 
+zmaxis=Z(1,1);
+
+
+%ZMID AND ZMAXIS SWITCHED TO ZERO TO BE CONSISTENT WITH THE CHEASE EQDSK INFO
+%zmid=0; 
+%zmaxis=0;
+
+
+%IT IS RECOMMENDED TO LEAVE RMAXIS AS IS, SINCE THIS PROVIDES INFORMATION ON THE SHAFRANOV SHIFT
+rmaxis1=R(1,1);  
+psiAxis=psiequi(1); 
+%psiSep=psi(end)/1.05; %TEMP FIX
+psiSep=psiequi(end);
+B=mean(data.geo.b0(ind));
+Ip=mean(data.gene.ip(ind))/1e6;
+Ip=mean(data.gene.ip(ind));
+
+fid1 = fopen(fname, 'w');
+
+%write header quantities
+%fprintf(fid1, '     JET    EFIT  TRACER                           %d  %d  %d\n',0,resoR,resoZ);
+fprintf(fid1, '   JET    EFIT   FILE   FROM    CRONOS            %d%4d%4d\n',0,resoR,resoZ);
+fprintf(fid1,'% 16.9E% 16.9E% 16.9E% 16.9E% 16.9E\n% 16.9E% 16.9E% 16.9E% 16.9E% 16.9E\n% 16.9E% 16.9E% 16.9E% 16.9E% 16.9E\n% 16.9E% 16.9E% 16.9E% 16.9E% 16.9E\n',...
+boxw,boxh,rmaj,rleft,zmid,rmaxis1,zmaxis,psiAxis,psiSep,B,Ip,psiAxis,0,rmaxis1,0,zmaxis,0,psiSep,0,0);;
+
+%write F, FF', P, P' quantities 
+for k=1:resopsi
+	fprintf(fid1,'% 16.9E',F(k));
+	if mod(k,5)==0
+		fprintf(fid1,'\n');
+	end
+end
+
+for k=1:resopsi
+	fprintf(fid1,'% 16.9E',P(k));
+	if mod(k,5)==0
+		fprintf(fid1,'\n');
+	end
+end
+
+for k=1:resopsi
+	fprintf(fid1,'% 16.9E',FFprime(k));
+	if mod(k,5)==0
+		fprintf(fid1,'\n');
+	end
+end
+
+for k=1:resopsi
+	fprintf(fid1,'% 16.9E',Pprime(k));
+	if mod(k,5)==0
+		fprintf(fid1,'\n');
+	end
+end
+
+%write poloidal flux onto rectangular grid
+for j=1:resoZ
+	for k=1:resoR
+		fprintf(fid1,'% 16.9E',zefit1(j,k));
+		if mod(k,5)==0
+			fprintf(fid1,'\n');
+		end
+	end
+end
+
+%write the q-profile
+for k=1:resopsi
+	fprintf(fid1,'% 16.9E',q(k));
+	if mod(k,5)==0
+		fprintf(fid1,'\n');
+	end
+end
+
+fprintf(fid1, ' %d %d \n', resotheta-1, 1);
+j = 1
+for k=1:(resotheta-1)
+	fprintf(fid1, '% 16.9E', R(end, k));
+	if mod(j,5)==0
+		fprintf(fid1, '\n');
+	end
+	j = j + 1;
+	fprintf(fid1, '% 16.9E', Z(end, k));
+	if mod(j,5)==0
+		fprintf(fid1, '\n');
+	end
+	j = j + 1;
+end
+	if mod(j-1,5)~=0
+		fprintf(fid1, '\n');
+	end
+
+fprintf(fid1, ' %16.9E  %16.9E \n', 0.0, 0.0);
+	
+
+
+fclose(fid1);
+
+
+%%%PLOT FLUX SURFACES FROM JUST MADE EQDSK FILE
+
+fid=fopen(fname);
+fseek(fid, 60, 'bof');
+p=fscanf(fid,'%f');
+fclose(fid);
+pars=p(1:20);
+p(1:20)=[];
+p(1:resopsi*4)=[];
+xefit=linspace(0,1,resopsi);
+qefit=p(resoR*resoZ+1:end);
+for j=1:resoZ
+	for k=1:resoR
+		psiefit(j,k)=p(resoR*(j-1)+k,1);
+			
+	end
+end
+
+%2D poloidal flux on R,Z grid
+eval([fname,'.psi2D=psiefit;']);
+
+%poloidal flux on the magnetic axis and the last-closed-flux surface 
+eval([fname,'.psiaxis=psiequi(1);']);
+eval([fname,'.psiedge=psiequi(end);']);
+
+%major radius
+eval([fname,'.r0=rmaj;']);
+
+%radius of the magnetic axis (difference between raxis and r0 is the Shafranov shift)
+eval([fname,'.raxis=rmaxis1;']);
+
+%z location of the geometric and magnetic axis center. If they are not the same it just means that the magnetic geometry is not up-down symmetric (which is common)
+eval([fname,'.zmid=zmid;']);
+eval([fname,'.zaxis=zmaxis;']);
+
+%R and Z grids for the 2D psi
+eval([fname,'.rmesh=xnodes(1,:)'';']);
+eval([fname,'.zmesh=ynodes(:,1);']);
+
+%Normalized toroidal flux coordinate grid
+eval([fname,'.rhonorm=linspace(0,1,101);']);
+
+%Toroidal flux on the last-closed-flux surface
+eval([fname,'.rhoedge=rho1;']);
+
+%1D psi on the toroidal flux grid
+eval([fname,'.psi1D=psix;']);
+
+%dvdrho on the toroidal flux grid
+eval([fname,'.dvdrho=dvdrho;']);
+
+eval(['save(''',fname,''');']);
+
+%quick automatic contour plot of 2D flux surfaces
+if printflag==1
+	figure; contour(xnodes,ynodes,psiefit,40); axis equal
+end

data/lib/cronoscrmod/matlab/eqdsk_jc.m

@@ -0,0 +1,226 @@
+function no_results = eqdsk_jc(data, fname, tavg, resofactor)
+%CREATES A EFIT EQDSK G FILE AND MATLAB STRUCTURE FROM CRONOS DATA.EQUI DATA. USED FOR CREATING 
+%GEOMETRY INPUT FILES FOR GENE. ALSO CREATES CONVENIENT MATLAB STRUCTURE WITH KEY INFORMATION
+%
+%A CRONOS DATA FILE NEEDS TO BE IN THE BACKGROUND WHEN RUNNING THIS ROUTINE
+%J.Citrin 20.05.2013
+
+disp('Version 2.2');
+
+
+%%%%%%%%%%%%INPUT PARAMETERS%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%fname='JET75225_Ptotred'; %choose a name for the output geometry file
+%tavg=[46 47]; %choose a time window for averaging of CRONOS data
+printflag=1; %flag to plot or not (=1) or not to plot (anything else) a figure of the 2D flux surfaces
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+bleed=0.02; %space around limits of R,Z points to define the rectangular grid
+
+ind=round(interp1(data.gene.temps,1:length(data.gene.temps),tavg)); ind=ind(1):ind(2); %find the indexes in data.gene.temps of the desired time window
+x=linspace(0,1,101); 
+
+%obtain R,Z, and psi from data.equi. Note that the normalized radial coordinate below is from equi.rhoRZ./equi.rhoRZ(end) and not the uniform x!
+R=squeeze(mean(data.equi.R(ind,:,:))); R=double(R); 
+Z=squeeze(mean(data.equi.Z(ind,:,:))); Z=double(Z);
+psiequi=-mean(data.equi.psiRZ(ind,:)); psiequi=(double(psiequi)); %the minus sign is there since eqdsk expects flipped psi profiles
+resotheta=length(R(1,:)); %finds the theta resolution from the CRONOS simulation
+
+%JC 15.5.13
+%TO BE CONSISTENT WITH THE CHEASE EQDSK DATA, PSIEQUI IS SHIFTED SUCH THAT PSIEQUI(1)=0
+%FEEL FREE TO CHANGE THIS, IT IS TRIVIAL TO DO SO
+%psiequi=psiequi-psiequi(1);
+%psiequi=psiequi-psiequi(end);
+xrho=mean(data.equi.rhoRZ(ind,:)); xrho=xrho./xrho(end);
+psix=interp1(xrho,psiequi,x);
+rho1=mean(data.equi.rhomax(ind));
+
+%set the resolution of the rectangular box (for now kept the same as the theta resolution from cronos)
+resoR=resotheta; 
+resoZ=resotheta;
+resopsi=resotheta;
+
+%resoR=100; 
+%resoZ=100;
+%resopsi=65;
+
+%interpolate equi.psi onto the uniform toroidal flux grid and create 
+%the normalized poloidal flux coordinate to interpolate the q, P, P', F, FF' profiles
+xrho=mean(data.equi.rhoRZ(ind,:)); xrho=xrho./xrho(end); xrho=double(xrho);
+psix=interp1(xrho,psiequi,x);
+psinormx=(psix-psix(1))./(psix(end)-psix(1));
+dvdrho=mean(data.equi.vpr(ind,:));
+%create desired uniform normalized poloidal flux grid
+xpsi=linspace(0,1,resopsi);
+
+
+%define boundaries of rectangular grid
+maxR=max(max(R))+bleed;
+minR=min(min(R))-bleed;
+maxZ=max(max(Z))+bleed;
+minZ=min(min(Z))-bleed;
+
+%create rectangular grid
+xR=linspace(minR,maxR,resoR); yR=linspace(maxZ,minZ,resoZ);
+[xnodes,ynodes] = meshgrid(xR,yR); %xnodes, ynodes are matrices defining the x and y (R and Z) coordinates
+
+%Create a 2D array for psi corresponding to x,theta (is a flux function, so same at every theta and tmp is discarded)
+%This 2D array, which fits the x,theta arrays of R,Z, are interpolated onto the rectangular grid with coordinates xnodes,ynodes
+[psibig,tmp]=meshgrid(psiequi,1:resotheta); psibig=psibig';
+zefit1 = griddata(R,Z,psibig,xnodes,ynodes,'cubic');
+
+%define psi quantities for all points in rectangular grid that lay outside of separatrix (became NaN in interpolation)
+zefit1(isnan(zefit1))=psiequi(end)*1.05;
+
+%grab necessary profiles and interpolate onto normalized poloidal flux grid
+qraw=mean(data.equi.q(ind,:)); qraw=double(qraw);
+s=mean(data.equi.shear(ind,:)); 
+F=mean(data.equi.F(ind,:));
+P=mean(data.prof.ptot(ind,:));
+%FFprime=-gradient(F,-psiequi).*F; %the minus sign on psiequi defines the gradient to the ORIGINAL psi (i.e. the unflipped one)
+FFprime=gradient(F,-psiequi); %the minus sign on psiequi defines the gradient to the ORIGINAL psi (i.e. the unflipped one)
+Pprime=gradient(F,-psiequi);
+%Pprime=-gradient(P,-psiequi);
+
+q=interp1(psinormx,qraw,xpsi);
+F=interp1(psinormx,F,xpsi);
+FFprime=interp1(psinormx,FFprime,xpsi); FFprime(1)=FFprime(2); 
+P=interp1(psinormx,P,xpsi);
+Pprime=interp1(psinormx,Pprime,xpsi); Pprime(1)=Pprime(2); 
+
+%define header quantities for eqdsk file
+boxw=maxR-minR; 
+boxh=maxZ-minZ; 
+rmaj=(maxR+minR)/2; 
+rleft=minR;
+
+zmid=(maxZ+minZ)/2; 
+zmaxis=Z(1,1);
+
+%ZMID AND ZMAXIS SWITCHED TO ZERO TO BE CONSISTENT WITH THE CHEASE EQDSK INFO
+%zmid=0; 
+%zmaxis=0;
+
+
+%IT IS RECOMMENDED TO LEAVE RMAXIS AS IS, SINCE THIS PROVIDES INFORMATION ON THE SHAFRANOV SHIFT
+rmaxis1=R(1,1);  
+psiAxis=psiequi(1); 
+%psiSep=psi(end)/1.05; %TEMP FIX
+psiSep=psiequi(end);
+B=mean(data.geo.b0(ind));
+Ip=mean(data.gene.ip(ind))/1e6;
+
+fid1 = fopen(fname, 'w');
+
+%write header quantities
+fprintf(fid1, '     JET    EFIT  TRACER                           %d  %d  %d\n',0,resoR,resoZ);
+fprintf(fid1,'% 16.9E% 16.9E% 16.9E% 16.9E% 16.9E\n% 16.9E% 16.9E% 16.9E% 16.9E% 16.9E\n% 16.9E% 16.9E% 16.9E% 16.9E% 16.9E\n% 16.9E% 16.9E% 16.9E% 16.9E% 16.9E\n',...
+boxw,boxh,rmaj,rleft,zmid,rmaxis1,zmaxis,psiAxis,psiSep,B,0,psiAxis,0,rmaxis1,0,zmaxis,0,psiSep,0,0);;
+
+%write F, FF', P, P' quantities 
+for k=1:resopsi
+	fprintf(fid1,'% 16.9E',F(k));
+	if mod(k,5)==0
+		fprintf(fid1,'\n');
+	end
+end
+
+for k=1:resopsi
+	fprintf(fid1,'% 16.9E',P(k));
+	if mod(k,5)==0
+		fprintf(fid1,'\n');
+	end
+end
+
+for k=1:resopsi
+	fprintf(fid1,'% 16.9E',FFprime(k));
+	if mod(k,5)==0
+		fprintf(fid1,'\n');
+	end
+end
+
+for k=1:resopsi
+	fprintf(fid1,'% 16.9E',Pprime(k));
+	if mod(k,5)==0
+		fprintf(fid1,'\n');
+	end
+end
+
+%write poloidal flux onto rectangular grid
+for j=1:resoZ
+	for k=1:resoR
+		fprintf(fid1,'% 16.9E',zefit1(j,k));
+		if mod(k,5)==0
+			fprintf(fid1,'\n');
+		end
+	end
+end
+
+%write the q-profile
+for k=1:resopsi
+	fprintf(fid1,'% 16.9E',q(k));
+	if mod(k,5)==0
+		fprintf(fid1,'\n');
+	end
+end
+
+fclose(fid1);
+
+
+%%%PLOT FLUX SURFACES FROM JUST MADE EQDSK FILE
+
+fid=fopen(fname);
+fseek(fid, 60, 'bof');
+p=fscanf(fid,'%f');
+fclose(fid);
+pars=p(1:20);
+p(1:20)=[];
+p(1:resopsi*4)=[];
+xefit=linspace(0,1,resopsi);
+qefit=p(resoR*resoZ+1:end);
+for j=1:resoZ
+	for k=1:resoR
+		psiefit(j,k)=p(resoR*(j-1)+k,1);
+			
+	end
+end
+
+%2D poloidal flux on R,Z grid
+eval([fname,'.psi2D=psiefit;']);
+
+%poloidal flux on the magnetic axis and the last-closed-flux surface 
+eval([fname,'.psiaxis=psiequi(1);']);
+eval([fname,'.psiedge=psiequi(end);']);
+
+%major radius
+eval([fname,'.r0=rmaj;']);
+
+%radius of the magnetic axis (difference between raxis and r0 is the Shafranov shift)
+eval([fname,'.raxis=rmaxis1;']);
+
+%z location of the geometric and magnetic axis center. If they are not the same it just means that the magnetic geometry is not up-down symmetric (which is common)
+eval([fname,'.zmid=zmid;']);
+eval([fname,'.zaxis=zmaxis;']);
+
+%R and Z grids for the 2D psi
+eval([fname,'.rmesh=xnodes(1,:)'';']);
+eval([fname,'.zmesh=ynodes(:,1);']);
+
+%Normalized toroidal flux coordinate grid
+eval([fname,'.rhonorm=linspace(0,1,101);']);
+
+%Toroidal flux on the last-closed-flux surface
+eval([fname,'.rhoedge=rho1;']);
+
+%1D psi on the toroidal flux grid
+eval([fname,'.psi1D=psix;']);
+
+%dvdrho on the toroidal flux grid
+eval([fname,'.dvdrho=dvdrho;']);
+
+eval(['save(''',fname,''');']);
+
+%quick automatic contour plot of 2D flux surfaces
+if printflag==1
+	figure; contour(xnodes,ynodes,psiefit,40); axis equal
+end

data/lib/cronoscrmod/matlab/output_ogyropsi.m

@@ -0,0 +1,159 @@
+function no_results = output_ogyropsi(data, tavg)
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% The ogyropsi CHEASE output file 
+% consists of MKSA quantities on a
+% flux surface grid. Not sure yet
+% what the spacing of the grid is
+% set by.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% This file is currently incomplete:
+% It outputs zeros for a lot of quantities
+% and skips some altogether. It is intended
+% to output quantities to compare to a CHEASE
+% run which uses an EQDSK file from the same
+% Cronos run as input
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% data is the cronos data structure
+% and t avg is an a time window given
+% as an array of two values... quanitities
+% are averaged over that time window.
+% e.g. output_ogyropsi(data, [45.2 46]);
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+ind=round(interp1(data.gene.temps,1:length(data.gene.temps),tavg)); ind=ind(1):ind(2); %find the indexes in data.gene.temps of the desired time window
+npsi = size(data.equi.R, 2);
+nchi = size(data.equi.R, 3) - 1; % ogyropsi doesn't have the 2pi point
+
+x=linspace(0,1,npsi); 
+% xrho is the values of x on the grid used for some equi quantities like psiRZ
+xrho=mean(data.equi.rhoRZ(ind,:)); xrho=xrho./xrho(end); xrho=double(xrho);
+
+outfile = fopen('ogyropsi.dat', 'w');
+
+fprintf(outfile, 'NPSI\n %d\nNCHI\n %d\n', npsi, nchi);
+R = squeeze(mean(data.equi.R(ind, :, :)));
+Z = squeeze(mean(data.equi.Z(ind, :, :)));
+% R and Z are not on the uniform toroidal flux grid
+for i=1:(nchi+1)
+	R(:,i) = interp1(xrho, R(:,i), x);
+	Z(:,i) = interp1(xrho, Z(:,i), x);
+end
+
+
+B=mean(data.geo.b0(ind));
+fprintf(outfile, 'R0EXP\n %16.9E\nB0EXP\n %16.9E\n', R(1,1), B);
+
+
+psiequi=mean(data.equi.psiRZ(ind,:)); psiequi=(double(psiequi)); %the minus sign is there since eqdsk expects flipped psi profiles
+psiequi=-psiequi + psiequi(1);
+psix=interp1(xrho,psiequi,x);
+%fprintf(outfile, 'PSI\n'); fprintf(outfile, form, psix);
+write_array(outfile, 'PSI', psix);
+
+chi = linspace(0.0, 2*pi, nchi+1);
+chi = chi(1:nchi);
+write_array(outfile, 'CHI', chi);
+
+%%% MAJOR AND MINOR RADII
+Rgeom = (R(:,1)+R(:,(nchi)/2))/2;
+write_array(outfile, 'Rgeom', Rgeom);
+ageom = (R(:,1)-R(:,(nchi)/2));
+write_array(outfile, 'ageom', ageom);
+
+%%% SAFETY FACTOR
+q=mean(data.equi.q(ind,:)); q=double(q);
+write_array(outfile, 'q', q);
+dqdpsi = gradient(q, psix);
+write_array(outfile, 'dqdpsi', dqdpsi);
+d2qdpsi2 = gradient(dqdpsi, psix);
+write_array(outfile, 'd2qdpsi2', d2qdpsi2);
+
+%%% PRESSURE
+p=mean(data.prof.ptot(ind,:));
+write_array(outfile, 'p', p);
+dpdpsi = gradient(p, psix);
+write_array(outfile, 'dpdpsi', dpdpsi);
+
+%%% TOROIDAL FIELD CURRENT FUNCTION
+f=mean(data.equi.F(ind,:));
+write_array(outfile, 'f', f);
+fdfdpsi = gradient(f, psix).*f;
+write_array(outfile, 'fdfdpsi', fdfdpsi);
+
+%%% FLUX SURFACE VOLUME 
+v=mean(data.equi.volume(ind,:));
+% The above gives NaNs.... don't know why
+v = q*0.0;
+write_array(outfile, 'V', v);
+
+
+% SQRT TOROIDAL FLUX
+rhox = interp1(xrho, mean(data.equi.rhoRZ(ind,:)), x);
+write_array(outfile, 'rho_t', rhox);
+
+%%% MAGNETIC SHEAR
+shear=mean(data.equi.shear(ind,:)); shear=double(shear);
+write_array(outfile, 'shear', shear);
+dsheardpsi = gradient(shear, psix);
+write_array(outfile, 'dsheardpsi', dsheardpsi);
+
+dummy_array = shear*0.0;
+write_array(outfile, 'kappa', dummy_array);
+write_array(outfile, 'delta_lower', dummy_array);
+write_array(outfile, 'delta_upper', dummy_array);
+write_array(outfile, 'dVdpsi', dummy_array);
+write_array(outfile, 'dpsidrhotor', dummy_array);
+write_array(outfile, 'GDPSI_av', dummy_array);
+write_array(outfile, 'radius_av', dummy_array);
+write_array(outfile, 'R_av', dummy_array);
+
+%%% ELECTRON PROFILES
+te=mean(data.prof.te(ind,:));
+write_array(outfile, 'TE', te);
+dtedpsi = gradient(te, psix);
+write_array(outfile, 'DTEDPSI', dtedpsi);
+
+ne=mean(data.prof.ne(ind,:));
+write_array(outfile, 'NE', ne);
+dnedpsi = gradient(ne, psix);
+write_array(outfile, 'DNEDPSI', dnedpsi);
+
+%%% ION PROFILES
+ti=mean(data.prof.ti(ind,:));
+write_array(outfile, 'TI', ti);
+dtidpsi = gradient(ti, psix);
+write_array(outfile, 'DTIDPSI', dtidpsi);
+
+ni=mean(data.prof.ni(ind,:));
+write_array(outfile, 'NI', ni);
+dnidpsi = gradient(ni, psix);
+write_array(outfile, 'DNIDPSI', dnidpsi);
+
+%%% ZEFF
+zeff=mean(data.prof.zeff(ind,:));
+write_array(outfile, 'ZEFF', zeff);
+
+%%% MAJOR RADIUS OF FLUX SURFACES
+write_array(outfile, 'R', R(:, 1:nchi));
+
+
+%%% HEIGHT Z OF FLUX SURFACES
+write_array(outfile, 'Z', Z(:, 1:nchi));
+
+fclose(outfile);
+
+function write_array(outfile, name, array)
+
+form = ' %16.9E %16.9E %16.9E %16.9E %16.9E\n';
+fprintf(outfile, '%s\n', name); 
+fprintf(outfile, form, array);
+if mod(size(array),5) ~= 0
+	fprintf(outfile, '\n');
+end
+
+

metadata

@@ -1,96 +1,71 @@
 --- !ruby/object:Gem::Specification
 name: cronoscrmod
 version: !ruby/object:Gem::Version
-  version: 0.1.1
-  prerelease: 
+  version: 0.1.2
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-17 00:00:00.000000000 Z
+date: 2017-01-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 0.13.18
+        version: '1.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 0.13.18
+        version: '1.0'
 - !ruby/object:Gem::Dependency
   name: shoulda
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '3.5'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '3.5'
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.12'
-- !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>'
-      - !ruby/object:Gem::Version
-        version: 1.0.0
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>'
-      - !ruby/object:Gem::Version
-        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.8.4
+        version: '2.3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.8.4
+        version: '2.3'
 description: A module to allow CodeRunner to run the integrated tokamak modelling
   suite Cronos. Requires matlab and matlab-ruby (Cronos also requires Matlab).
 email: edmundhighcock@users.sourceforge.net
@@ -102,10 +77,11 @@ extra_rdoc_files:
 - README.md.orig
 - README.rdoc
 files:
-- .document
+- ".document"
 - Gemfile
 - LICENSE.txt
 - README.md
+- README.md.orig
 - README.rdoc
 - Rakefile
 - VERSION
@@ -113,36 +89,34 @@ files:
 - lib/cronoscrmod.rb
 - lib/cronoscrmod/cronos.rb
 - lib/cronoscrmod/defaults_files/cronos_defaults.rb
+- lib/cronoscrmod/matlab/cronos_eqdsk.m
+- lib/cronoscrmod/matlab/eqdsk_jc.m
+- lib/cronoscrmod/matlab/output_ogyropsi.m
 - test/helper.rb
 - test/test_cronoscrmod.rb
-- README.md.orig
 homepage: http://github.com/edmundhighcock/cronoscrmod
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: 2607351872289710569
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.23
+rubygems_version: 2.6.8
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: A module to allow CodeRunner to run the integrated tokamak modelling suite
   Cronos
 test_files: []