PrincetonUniversity
Lconstraint=-2, and pyspec higher derivatives of magnetic field
This branch contains three changes:
-
the implementation by Elizabeth Paul of Lconstraint=-2 (toroidal flux is adjusted until specified linking current is achieved), extended to work with the new Zernike version of SPEC.
-
possibility to specify non-zero normal component of the magnetic field in single-volume fixed-boundary calculations (through Vns/Vnc), toggled with inputlist flag Lbdybnzero (by default =.true., i.e. Bsups=0).
-
py_spec feature: derivatives of the magnetic field with respect to s, zeta and theta can now be obtained.
Hi Richard,
Thanks for putting together this PR. A few comments:
- At the moment, Lconstraint = -2 allows one to both a) impose the normal field in a 1 volume calculation and 2) use the toroidal flux to fix the poloidal linking current. Maybe it would make sense to use a separate input variable for each of these options?
- It looks like some of the documentation needs to be updated: https://github.com/PrincetonUniversity/SPEC/blob/ad9f86d569c9330a8084ce9f240e6703e1a3563e/ma02aa.f90#L376-L385 https://github.com/PrincetonUniversity/SPEC/blob/ad9f86d569c9330a8084ce9f240e6703e1a3563e/mp00ac.f90#L65-L68
- There are a few leftover print statements: https://github.com/PrincetonUniversity/SPEC/blob/ad9f86d569c9330a8084ce9f240e6703e1a3563e/ma02aa.f90#L494 https://github.com/PrincetonUniversity/SPEC/blob/ad9f86d569c9330a8084ce9f240e6703e1a3563e/ma02aa.f90#L556 https://github.com/PrincetonUniversity/SPEC/blob/ad9f86d569c9330a8084ce9f240e6703e1a3563e/mp00ac.f90#L226-L228 https://github.com/PrincetonUniversity/SPEC/blob/ad9f86d569c9330a8084ce9f240e6703e1a3563e/mp00ac.f90#L621-L624 https://github.com/PrincetonUniversity/SPEC/blob/ad9f86d569c9330a8084ce9f240e6703e1a3563e/mp00ac.f90#L792
- At the moment, Lconstraint = -2 only applies to the "plasma" volumes and not the "vacuum" volume. It also appears that we have assumed a single-volume calculation. Can you make sure that the relevant input parameters match these assumptions in global.f90: https://github.com/PrincetonUniversity/SPEC/blob/ad9f86d569c9330a8084ce9f240e6703e1a3563e/global.f90#L1078
Hi Elizabeth,
At the moment, Lconstraint = -2 allows one to both a) impose the normal field in a 1 volume calculation and 2) use the toroidal flux to fix the poloidal linking current. Maybe it would make sense to use a separate input variable for each of these options?
I think the way it is implemented, the normal field can be imposed in a fixed-boundary calculation for any Lconstraint: the change is in preset.f90, where the reading Vns/Vnc is now outside of if(Lfreebound). Am I missing something?
Hi Elizabeth,
At the moment, Lconstraint = -2 allows one to both a) impose the normal field in a 1 volume calculation and 2) use the toroidal flux to fix the poloidal linking current. Maybe it would make sense to use a separate input variable for each of these options?
I think the way it is implemented, the normal field can be imposed in a fixed-boundary calculation for any Lconstraint: the change is in preset.f90, where the reading Vns/Vnc is now outside of if(Lfreebound). Am I missing something?
Yes, I agree. I guess at the moment Vns/Vnc are read regardless of the input flags but are defaulted to zero. This seems sensible to me. I would just be careful that there are no other places where Bsups is assumed to be zero. For example,
https://github.com/PrincetonUniversity/SPEC/blob/0030936b7236185168e392205d2dd0e27362807e/src/curent.f90#L124-L140
I would just be careful that there are no other places where Bsups is assumed to be zero.
Good catch, thanks for pointing that out. Of course, I could just remove "if(Lconstraint .eq. -2)" and always compute Bsups, but explicitly setting it to zero seems cleaner for those cases where we want the boundary to be a flux surface. Would this be motivation enough to introduce another input variable for the case when the normal BC is non-zero?
Do you (or someone else) perhaps also know how I can check the Doxygen documentation for the branch with the changes I added? I'd like to make sure the formatting worked out.
Thanks, Richard
@richardnies
Do you (or someone else) perhaps also know how I can check the Doxygen documentation for the branch with the changes I added? I'd like to make sure the formatting worked out.
You can run doxygen locally on any branch you like. On GitHub, you only get the documentation from the master branch.
Just type doxygen in the main folder (i.e., where the Doxyfile resides) and you should get a docs folder.
In there, there is html(the website part; examine it by opening index.html in your browser) and latex for the PDF documentation. In the latex folder, you have to do a separate make to get the LaTeX version of the documentation to build. The resulting file should be refman.pdf.
Hope this helps :-)
Would this be motivation enough to introduce another input variable for the case when the normal BC is non-zero?
I would be ok either way. Does anyone else have an opinion on this?
I am not going to test (yet) this branch on our machines since I see that you are probably going to make some more changes.
Also, it seems to me that one should really split the "imposing the toroidal flux" option with the "imposiing a non-zero normal field on the boundary" option. The former may be called Lconstraint=-2, and the latter may simply be a flag like Lfreeboundary, e.g. Lboundarybnzero=T by default, and set to false if one wants Vns to be read and imposed at the boundary. Then, if your Lconstraint=-2 option needs to use that always, then a simple "if(Lconstraint=-2) then Lboundarybnzero=F" would suffice. What do you think?
@richardnies
Do you (or someone else) perhaps also know how I can check the Doxygen documentation for the branch with the changes I added? I'd like to make sure the formatting worked out.
You can run doxygen locally on any branch you like. On GitHub, you only get the documentation from the master branch. Just type
doxygenin the main folder (i.e., where theDoxyfileresides) and you should get adocsfolder. In there, there ishtml(the website part; examine it by openingindex.htmlin your browser) andlatexfor the PDF documentation. In thelatexfolder, you have to do a separatemaketo get the LaTeX version of the documentation to build. The resulting file should berefman.pdf.Hope this helps :-)
Thanks Jonathan! That was very helpful indeed.
I am not going to test (yet) this branch on our machines since I see that you are probably going to make some more changes.
Also, it seems to me that one should really split the "imposing the toroidal flux" option with the "imposiing a non-zero normal field on the boundary" option. The former may be called Lconstraint=-2, and the latter may simply be a flag like Lfreeboundary, e.g. Lboundarybnzero=T by default, and set to false if one wants Vns to be read and imposed at the boundary. Then, if your Lconstraint=-2 option needs to use that always, then a simple "if(Lconstraint=-2) then Lboundarybnzero=F" would suffice. What do you think?
I think you're right, the additional Lboundarybnzero flag is the best way to go. I will implement that now and hopefully we can get this merged then.
Sorry I did not see this earlier - I somehow did not receive any notification. I am satisfied with this PR, but I think @jloizu should also give his review.
Sorry I did not review this yet, I will test compilation/execution tomorrow on our machines. Could you add (e.g. on the folder with test cases) an input file where these new options are used?
@jloizu I have now added the test case in InputFiles/TestCases/G3V01Lm2Fi.info and .sp Thanks for reviewing!
It looks like the "py_spec build" check now fails, although I only added two new test case files. Can this be caused by changes I made locally?
Compilation works well on our machines.
However, when testing this case, G2V32L1Fi.001.sp, it does not retrieve the converged equilibrium (force balance ~1e-11) as before. Can you check?
Regarding pyspec build, I have no idea, you need to ask @zhucaoxiang or @mbkumar I guess...
Compilation works well on our machines. However, when testing this case,
G2V32L1Fi.001.sp,it does not retrieve the converged equilibrium (force balance ~1e-11) as before. Can you check? Regarding pyspec build, I have no idea, you need to ask @zhucaoxiang or @mbkumar I guess...
Hi @jloizu , how does the lack of force balance manifest itself? I ran the case you quoted with the master and Lconstraint=-2 executables and got very similar outputs, see file attached.
For example when I run G3V02L1Fi.001.sp, I get this
xspech : : version = 3.10
: compiled : date = Thu Oct 21 14:21:54 CEST 2021 ;
: : srcdir = /home/loizu/Sandboxes/SPEC ;
: : macros = src/macros ;
: : fc = mpif90 ;
: : flags = -r8 -DIFORT -O2 -ip -no-prec-div -xHost -fPIC -
DOPENMP -fopenmp ;
xspech : :
xspech : 0.00 : date=2021/10/22 , 13:32:52 ; machine precision= 1.11E-16 ; vsmall= 1.11E-14 ; small= 1.11E-12 ;
xspech : :
xspech : 0.00 : parallelism : ncpu= 1 ; nthreads= 8 ;
rdcmdl : :
rdcmdl : 0.00 : ext = G3V02L1Fi.001
xspech : :
xspech : 0.00 : begin execution ; calling global:readin ;
readin : :
readin : 0.01 : Igeometry= 3 ; Istellsym= 1 ; Lreflect= 0 ; Lbdybnzero= T ;
readin : : Lfreebound= 0 ; phiedge= 2.000000000000000E+00 ; curtor= 1.038123580200000E-09 ; curpol= 0.000000000000000E+00 ;
readin : : gamma= 0.000000000000000E+00 ;
readin : : Nfp= 5 ; Nvol= 2 ; Mvol= 2 ; Mpol= 4 ; Ntor= 4 ;
readin : : pscale= 1.00000E-03 ; Ladiabatic= 0 ; Lconstraint= 1 ; mupf: tol,its= 1.00E-12 , 128 ;
readin : : Lrad = 8, 4,
readin : :
readin : 0.01 : Linitialize= 0 ;LautoinitBn= 1 ; Lzerovac= 0 ; Ndiscrete= 2 ;
readin : : Nquad= -1 ; iMpol= -4 ; iNtor= -4 ;
readin : : Lsparse= 0 ; Lsvdiota= 0 ; imethod= 3 ; iorder= 2 ; iprecon= 1 ; iotatol= -1.00000E+00 ;
readin : : Lextrap= 0 ; Mregular= -1 ; Lrzaxis= 1 ; Ntoraxis= 3 ;
readin : :
readin : 0.01 : LBeltrami= 4 ; Linitgues= 1 ; Lmatsolver= 3 ; LGMRESprec= 1 ; NiterGMRES= 200 ; epsGMRES= 1.00000E-14 ; epsILU= 1.00000E-12 ;
readin : :
readin : 0.01 : Lfindzero= 2 ;
readin : : escale= 0.00000E+00 ; opsilon= 1.00000E+00 ; pcondense= 4.000 ; epsilon= 1.00000E+00 ; wpoloidal= 1.0000 ; upsilon= 1.00000E+00 ;
readin : : forcetol= 1.00000E-12 ; c05xmax= 1.00000E-06 ; c05xtol= 1.00000E-12 ; c05factor= 1.00000E-04 ; LreadGF= F ;
readin : : mfreeits= 0 ; gBntol= 1.00000E-06 ; gBnbld= 6.66000E-01 ;
readin : : vcasingeps= 1.00000E-12 ; vcasingtol= 1.00000E-08 ; vcasingits= 8 ; vcasingper= 1 ;
readin : :
readin : 0.01 : odetol= 1.00E-07 ; nPpts= 0 ;
readin : : LHevalues= F ; LHevectors= F ; LHmatrix= F ; Lperturbed= 0 ; dpp= -1 ; dqq= -1 ; dRZ= 1.00000000E-05 ; Lcheck= 0 ; Ltiming= F ;
readin : :
readin : : myid= 0 ; Rscale= 1.000000000000000E+01 ;
preset : : myid= 0 ; Mrad= 8 : Lrad= 8, 4,
preset : 0.01 : LBsequad= F , LBnewton= F , LBlinear= T ;
preset : :
preset : 0.01 : Nquad= -1 ; mn= 41 ; NGdof= 81 ; NAdof= 361, 370,
preset : :
preset : 0.01 : Nt= 32 ; Nz= 32 ; Ntz= 1024 ;
mp00ac : 0.10 : myid= 0 ; lvol= 1 ; ideriv= 0 ; GMRES ierr= -3 ; solver internal break down ;
mp00ac : 0.15 : myid= 0 ; lvol= 1 ; ideriv= 0 ; GMRES ierr= -3 ; solver internal break down ;
mp00ac : 0.15 : myid= 0 ; lvol= 1 ; ideriv= 1 ; GMRES ierr= -3 ; solver internal break down ;
mp00ac : 0.15 : myid= 0 ; lvol= 1 ; ideriv= 0 ; GMRES ierr= -3 ; solver internal break down ;
tr00ab : 0.15 ; myid= 0 ; lvol= 1 ; innout= 1 ; jderiv= 2 ; idgesvx= 1 ; time= 0.0001 ; singular ;
tr00ab : fatal : myid= 0 ; idgesvx.ne.0 ; failed to construct straight-fieldline angle using dgesvx ;
while with an older version I get this
xspech : : version = 3.01
: compiled : date = Fri Jun 25 12:03:54 CEST 2021 ;
: : srcdir = /home/loizu/Sandboxes/SPEC ;
: : macros = macros ;
: : fc = mpif90 ;
: : flags = -r8 -O2 -ip -no-prec-div -xHost -fPIC -DOPENMP
-fopenmp ;
xspech : :
xspech : 0.00 : begin execution ; ncpu= 1 ; omp_threads= 8; calling global:readin ;
readin : :
readin : 0.00 : date=2021/10/22 , 13:32:30 ; machine precision= 1.11E-16 ; vsmall= 1.11E-14 ; small= 1.11E-12 ;
readin : :
readin : 0.00 : ext = G3V02L1Fi.001
readin : :
readin : :
readin : 0.00 : Igeometry= 3 ; Istellsym= 1 ; Lreflect= 0 ;
readin : : Lfreebound= 0 ; phiedge= 2.000000000000000E+00 ; curtor= 1.038123580200000E-09 ; curpol= 0.000000000000000E+00 ;
readin : : gamma= 0.000000000000000E+00 ;
readin : : Nfp= 5 ; Nvol= 2 ; Mvol= 2 ; Mpol= 4 ; Ntor= 4 ;
readin : : pscale= 1.00000E-03 ; Ladiabatic= 0 ; Lconstraint= 1 ; mupf: tol,its= 1.00E-12 , 128 ;
readin : : Lrad = 8, 4,
readin : :
readin : 0.00 : Linitialize= 0 ;LautoinitBn= 1 ; Lzerovac= 0 ; Ndiscrete= 2 ;
readin : : Nquad= -1 ; iMpol= -4 ; iNtor= -4 ;
readin : : Lsparse= 0 ; Lsvdiota= 0 ; imethod= 3 ; iorder= 2 ; iprecon= 1 ; iotatol= -1.00000E+00 ;
readin : : Lextrap= 0 ; Mregular= -1 ; Lrzaxis= 1 ; Ntoraxis= 3 ;
readin : :
readin : 0.00 : LBeltrami= 4 ; Linitgues= 1 ; Lmatsolver= 3 ; LGMRESprec= 1 ; NiterGMRES= 200 ; epsGMRES= 1.00000E-14 ; epsILU= 1.00000E-12 ;
readin : :
readin : 0.00 : Lfindzero= 2 ;
readin : : escale= 0.00000E+00 ; opsilon= 1.00000E+00 ; pcondense= 4.000 ; epsilon= 1.00000E+00 ; wpoloidal= 1.0000 ; upsilon= 1.00000E+00 ;
readin : : forcetol= 1.00000E-12 ; c05xmax= 1.00000E-06 ; c05xtol= 1.00000E-12 ; c05factor= 1.00000E-04 ; LreadGF= F ;
readin : : mfreeits= 0 ; gBntol= 1.00000E-06 ; gBnbld= 6.66000E-01 ;
readin : : vcasingeps= 1.00000E-12 ; vcasingtol= 1.00000E-08 ; vcasingits= 8 ; vcasingper= 1 ;
readin : : dxdesc= 1.00000E-03 ; ftoldesc= 1.00000E-10 ; maxitdesc= 15000 ; Lwritedesc= 1 ; nwritedesc= 100 ; Manderson= 1 ;
readin : :
readin : 0.00 : odetol= 1.00E-07 ; nPpts= 0 ;
readin : : LHevalues= F ; LHevectors= F ; LHmatrix= F ; Lperturbed= 0 ; dpp= -1 ; dqq= -1 ; dRZ= 1.00000000E-05 ; Lcheck= 0 ; Ltiming= F ;
readin : :
readin : : myid= 0 ; Rscale= 1.000000000000000E+01 ;
preset : : myid= 0 ; Mrad= 8 : Lrad= 8, 4,
preset : 0.00 : LBsequad= F , LBnewton= F , LBlinear= T ;
preset : :
preset : 0.00 : Nquad= -1 ; mn= 41 ; NGdof= 81 ; NAdof= 361, 370,
preset : :
preset : 0.00 : Nt= 32 ; Nz= 32 ; Ntz= 1024 ;
newton : 0.07 : 0 0 ; |f|= 1.48437E-02 ; time= 0.06s ; log|BB|e= -4.66
newton : : ; ; log|II|o= -2.42
fcn2 : 0.57 : 1 1 ; |f|= 1.48437E-02 ; time= 0.56s ; log|BB|e= -4.66
fcn2 : : ; ; log|II|o= -2.42
fcn2 : 0.61 : 2 1 ; |f|= 1.46506E-02 ; time= 0.04s ; log|BB|e= -4.74
fcn2 : : ; ; log|II|o= -2.42
fcn2 : 0.65 : 3 1 ; |f|= 1.42655E-02 ; time= 0.04s ; log|BB|e= -4.96
fcn2 : : ; ; log|II|o= -2.44
fcn2 : 0.69 : 4 1 ; |f|= 1.35002E-02 ; time= 0.04s ; log|BB|e= -4.65
fcn2 : : ; ; log|II|o= -2.47
fcn2 : 0.73 : 5 1 ; |f|= 1.19909E-02 ; time= 0.04s ; log|BB|e= -4.15
fcn2 : : ; ; log|II|o= -2.53
fcn2 : 0.77 : 6 1 ; |f|= 9.08607E-03 ; time= 0.04s ; log|BB|e= -3.81
fcn2 : : ; ; log|II|o= -2.64
fcn2 : 0.81 : 7 1 ; |f|= 4.32438E-03 ; time= 0.04s ; log|BB|e= -3.57
fcn2 : : ; ; log|II|o= -2.85
fcn2 : 0.85 : 8 1 ; |f|= 1.21257E-03 ; time= 0.04s ; log|BB|e= -4.24
fcn2 : : ; ; log|II|o= -3.25
fcn2 : 0.91 : 9 1 ; |f|= 2.55751E-03 ; time= 0.06s ; log|BB|e= -4.65
fcn2 : : ; ; log|II|o= -2.91
fcn2 : 0.96 : 10 1 ; |f|= 7.31985E-04 ; time= 0.05s ; log|BB|e= -4.45
fcn2 : : ; ; log|II|o= -3.41
fcn2 : 1.02 : 11 1 ; |f|= 1.44780E-03 ; time= 0.06s ; log|BB|e= -4.47
fcn2 : : ; ; log|II|o= -3.03
fcn2 : 1.07 : 12 1 ; |f|= 5.42314E-04 ; time= 0.05s ; log|BB|e= -4.66
fcn2 : : ; ; log|II|o= -3.48
fcn2 : 1.12 : 13 1 ; |f|= 4.39564E-04 ; time= 0.05s ; log|BB|e= -4.79
fcn2 : : ; ; log|II|o= -3.53
fcn2 : 1.27 : 14 1 ; |f|= 8.33093E-05 ; time= 0.16s ; log|BB|e= -5.29
fcn2 : : ; ; log|II|o= -4.29
fcn2 : 1.35 : 15 1 ; |f|= 6.10494E-05 ; time= 0.07s ; log|BB|e= -5.52
fcn2 : : ; ; log|II|o= -4.39
fcn2 : 1.39 : 16 1 ; |f|= 1.33442E-05 ; time= 0.05s ; log|BB|e= -6.18
fcn2 : : ; ; log|II|o= -5.06
fcn2 : 1.44 : 17 1 ; |f|= 7.78188E-06 ; time= 0.04s ; log|BB|e= -6.70
fcn2 : : ; ; log|II|o= -5.30
fcn2 : 1.48 : 18 1 ; |f|= 4.16587E-06 ; time= 0.04s ; log|BB|e= -6.63
fcn2 : : ; ; log|II|o= -5.69
fcn2 : 1.51 : 19 1 ; |f|= 2.58076E-06 ; time= 0.04s ; log|BB|e= -6.85
fcn2 : : ; ; log|II|o= -5.89
fcn2 : 1.55 : 20 1 ; |f|= 8.29873E-08 ; time= 0.04s ; log|BB|e= -8.33
fcn2 : : ; ; log|II|o= -7.30
fcn2 : 1.58 : 21 1 ; |f|= 1.95748E-08 ; time= 0.03s ; log|BB|e= -8.95
fcn2 : : ; ; log|II|o= -7.94
fcn2 : 1.61 : 22 1 ; |f|= 5.43977E-10 ; time= 0.03s ; log|BB|e=-10.51
fcn2 : : ; ; log|II|o= -9.43
fcn2 : 1.64 : 23 1 ; |f|= 7.17071E-11 ; time= 0.03s ; log|BB|e=-11.38
fcn2 : : ; ; log|II|o=-10.27
fcn2 : 1.66 : 24 1 ; |f|= 9.22314E-12 ; time= 0.02s ; log|BB|e=-12.28
fcn2 : : ; ; log|II|o=-11.09
fcn2 : 1.68 : 25 1 ; |f|= 3.25930E-12 ; time= 0.02s ; log|BB|e=-12.72
fcn2 : : ; ; log|II|o=-11.55
fcn2 : 1.71 : 26 1 ; |f|= 1.34467E-13 ; time= 0.02s ; log|BB|e=-14.03
fcn2 : : ; ; log|II|o=-12.93
fcn2 : 1.72 : 27 1 ; |f|= 2.85433E-14 ; time= 0.02s ; log|BB|e=-14.80
fcn2 : : ; ; log|II|o=-13.64
fcn2 : 1.74 : 28 1 ; |f|= 9.64711E-15 ; time= 0.02s ; log|BB|e=-15.12
fcn2 : : ; ; log|II|o=-14.06
fcn2 : 1.75 : 29 1 ; |f|= 2.39385E-15 ; time= 0.01s ; log|BB|e=-15.61
fcn2 : : ; ; log|II|o=-14.75
newton : :
newton : 1.75 : finished ; success ; ic05p*f= 1 ; its= 29 , 1 ;
xspech : 1.76 : #freeits= 0 ; |f|= 2.39385E-15 ; time= 0.01s ; log|BB|e=-15.61
xspech : : ; ; log|II|o=-14.75
xspech : :
xspech : 1.79 : myid= 0 : time= 0.03m = 0.00h = 0.00d ;
ending : :
ending : 1.79 : myid= 0 ; completion ; time= 1.79s = 0.03m = 0.00h = 0.00d ; date= 2021/10/22 ; time= 13:32:32 ; ext = G3V02L1Fi.001
ending : :
Hi @jloizu , are you able to run that same case G3V02L1Fi.001.sp with a new xspec from the master branch? I can't run this case (on master or Lconstraint_-2 branches) due to the error "volume : fatal : myid= 0 ; vflag.eq.0 .and. vvolume(lvol).lt.small ; volume cannot be zero or negative", which I've encountered for other cases before.
Indeed there seems to be something already screwed up in the master branch...this is not good.
I don't even understand how the previous versions passed the CI tests, since I just tried running some of them with the master branch and the code does not find equilibria...We should open an issue on this!
So my guess is that your changes and branch are all fine, but there is some other more general issue...
@jloizu @richardnies The problem volume : fatal : myid= 0 ; vflag.eq.0 .and. vvolume(lvol).lt.small ; volume cannot be zero or negative arises on my machine if I build SPEC using the CMake setup. When built using the traditional Makefile, it works.
The problem seems to be that in the current CMake setup the NSCREENLIST macro is not expanded.
Thus in G3V02L1Fi.001.sp reading the screenlist fails since Wpp00aa is not member of the namelist screenlist.
@mbkumar Could you please fix the expansion of NSCREENLIST in the CMake setup?
I added a few checks on the master branch in global.f90:read_inputlists_from_file() to help debug further problems like this.
@jloizu
I don't even understand how the previous versions passed the CI tests, since I just tried running some of them with the master branch and the code does not find equilibria...We should open an issue on this!
I think this could be because in the CI on GitLab Actions we still build SPEC using the Makefile setup, but @richardnies probably uses the CMake setup (as preferred these days)?
Thanks Jon for debugging it. I'll work on fixing the CMake setup.
Bharat Medasani
Engineer Princeton Plasma Physics Lab (PPPL)
On Mon, Oct 25, 2021 at 6:09 AM Jonathan Schilling @.***> wrote:
@jloizu https://github.com/jloizu @richardnies https://github.com/richardnies The problem volume : fatal : myid= 0 ; vflag.eq.0 .and. vvolume(lvol).lt.small ; volume cannot be zero or negative arises on my machine if I build SPEC using the CMake setup. When built using the traditional Makefile, it works. The problem seems to be that in the current CMake setup the NSCREENLIST macro is not expanded. Thus in G3V02L1Fi.001.sp reading the screenlist fails since Wpp00aa is not member of the namelist screenlist.
@mbkumar https://github.com/mbkumar Could you please fix the expansion of NSCREENLIST in the CMake setup?
I added a few checks on the master branch in global.f90:read_inputlists_from_file() to help debug further problems like this.
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@jonathanschilling
@jloizu
I don't even understand how the previous versions passed the CI tests, since I just tried running some of them with the master branch and the code does not find equilibria...We should open an issue on this!
I think this could be because in the CI on GitLab Actions we still build SPEC using the Makefile setup, but @richardnies probably uses the CMake setup (as preferred these days)?
Actually I use the Makefile setup as well. With gfortran, if that helps.
EDIT: I just saw you updated the master branch, the test runs fine now. Thanks!
NSCREENLIST awk processing step is commented out in Makefile as well. I introduced that change in the makefile. I need to better understand how NSCREENLIST is used in the code.
Bharat Medasani
Engineer Princeton Plasma Physics Lab (PPPL)
On Tue, Oct 26, 2021 at 6:58 AM Richard Nies @.***> wrote:
@jonathanschilling https://github.com/jonathanschilling
@jloizu https://github.com/jloizu
I don't even understand how the previous versions passed the CI tests, since I just tried running some of them with the master branch and the code does not find equilibria...We should open an issue on this!
I think this could be because in the CI on GitLab Actions we still build SPEC using the Makefile setup, but @richardnies https://github.com/richardnies probably uses the CMake setup (as preferred these days)?
Actually I use the Makefile setup as well. With gfortran, if that helps.
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@ejpaul @richardnies
EDIT: I just saw you updated the master branch, the test runs fine now. Thanks!
I re-ran the suggested test case just now and they still seem to work. I guess we can merge this then?
@jonathanschilling Sorry for not getting back to you earlier. One change that happened since the code changes were reviewed is that I implemented FFT's to obtain the B-field in py_spec. Should that be reviewed by someone?
Apart from that, it is ready to merge on my side.
@richardnies No worries :-)
I like the implementation of FFTs and I would be happy to test this.
Could you maybe include an example script in the repository, which shows how to use these new routines along with some plots/... of expected results?