Lconstraint=-2, and pyspec higher derivatives of magnetic field #153

richardnies · 2021-09-09T19:37:07Z

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.

ejpaul · 2021-09-12T18:22:31Z

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:

SPEC/ma02aa.f90

Lines 376 to 385 in ad9f86d

    
           !> <li> The function \f${\bf f}(\boldsymbol{\mu})\f$, which is computed by mp00ac(), is defined by the input parameter \c Lconstraint: 
        
           !> <ul> 
        
           !> <li> If \c Lconstraint = -1, 0, then \f$\boldsymbol{\mu}\f$       is *not* varied and \c Nxdof=0. </li> 
        
           !> <li> If \c Lconstraint =  1,    then \f$\boldsymbol{\mu}\f$       is       varied to satisfy the transform constraints; 
        
           !>      and \c Nxdof=1 in the simple torus and \c Nxdof=2 in the annular regions. 
        
           !>      (Note that in the "simple-torus" region, the enclosed poloidal flux \f$\Delta\psi_p\f$ is not well-defined, 
        
           !>      and only \f$\mu=\boldsymbol{\mu}_1\f$ is varied in order to satisfy the transform constraint on the "outer" interface of that volume.) </li> 
        
           !> <li> \todo If \c Lconstraint =  2,    then \f$\mu=\boldsymbol{\mu}_1\f$ is       varied in order to satisfy the helicity constraint, 
        
           !>      and \f$\Delta\psi_p=\boldsymbol{\mu}_2\f$ is *not* varied, and \c Nxdof=1. 
        
           !>      (under re-construction)

SPEC/mp00ac.f90

Lines 65 to 68 in ad9f86d

    
           !> (&                                            0&,&                                 0&)^T, & \textrm{if }\texttt{Lconstraint} &=& -1 \\ 
        
           !> (&                                            0&,&                                 0&)^T, & \textrm{if }\texttt{Lconstraint} &=&  0 \\ 
        
           !> (&{{\,\iota\!\!\!}-}(+1)-\texttt{iota (lvol  )}&,&                                 0&)^T, & \textrm{if }\texttt{Lconstraint} &=&  1 \\ 
        
           !> (&                                            ?&,&                                 ?&)^T, & \textrm{if }\texttt{Lconstraint} &=&  2

There are a few leftover print statements:

SPEC/ma02aa.f90

Line 494 in ad9f86d

print *,"dtflux(lvol): ", dtflux(lvol)

SPEC/ma02aa.f90

Line 556 in ad9f86d

print *,"End of ma02aa.f90- dtflux(lvol): ", dtflux(lvol)

SPEC/mp00ac.f90

Lines 226 to 228 in ad9f86d

    
           print *,"dtf: ", dtf 
        
           print *,"dpf: ", dpf 
        
           print *,"lmu: ", lmu

SPEC/mp00ac.f90

Lines 621 to 624 in ad9f86d

    
           print *,"curtor (computed): ", dItGpdxtp(0,0,lvol) 
        
           print *,"curpol (computed): ", dItGpdxtp(1,0,lvol) 
        
           print *,"curpol (requested): ", curpol 
        
           print *,"Fdof: ", Fdof(1)

SPEC/mp00ac.f90

Line 792 in ad9f86d

print *,"mu(lvol): ", mu(lvol)

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:

SPEC/global.f90

Line 1078 in ad9f86d

FATAL( readin, Lconstraint.lt.-2 .or. Lconstraint.gt.3, illegal Lconstraint )

richardnies · 2021-09-29T15:13:19Z

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?

ejpaul · 2021-09-30T14:55:49Z

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,

SPEC/src/curent.f90

Lines 124 to 140 in 0030936

    
           if (Lconstraint .eq. -2) then 
        
                call build_vector_potential(lvol, innout, ideriv, 0) 
        
                do ii = 1, mn ! loop over Fourier harmonics; 17 May 21; 
        
                    efmn(ii) = -in(ii)*efmn(ii) ! zeta  derivative of Ate 
        
                    ofmn(ii) =  in(ii)*ofmn(ii) ! zeta  derivative of Ato 
        
                    cfmn(ii) = -im(ii)*cfmn(ii) ! theta derivative of Aze 
        
                    sfmn(ii) =  im(ii)*sfmn(ii) ! theta derivative of Azo 
        
                enddo ! end of do ii;  
        
                call invfft( mn, im(1:mn), in(1:mn), ofmn(1:mn), cfmn(1:mn), sfmn(1:mn), efmn(1:mn), & 
        
                        Nt, Nz, Bsups(1:Ntz,ideriv), Bsups_2(1:Ntz,ideriv)) 
        
                Bsups(1:Ntz,ideriv) = Bsups(1:Ntz,ideriv) + Bsups_2(1:ntz,ideriv) 
        
           else 
        
                Bsups = zero 
        
           end if

richardnies · 2021-09-30T18:31:55Z

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

jonathanschilling · 2021-10-04T10:12:10Z

@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 :-)

ejpaul · 2021-10-04T11:52:45Z

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?

jloizu · 2021-10-11T07:48:32Z

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 · 2021-10-11T11:11:12Z

@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 :-)

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.

… new option inputlist (Lbdybnzero)

…zero=false

… single-volume

…o only allowed with Lconstraint=-2 and Lfreebound=0; and Lconstraint=-2 only allowed with Nvol=1).

richardnies · 2021-10-12T22:12:21Z

@jloizu @ejpaul I think this PR is now ready.
Thanks,
Richard

ejpaul · 2021-10-19T19:39:09Z

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.

jloizu · 2021-10-19T19:44:36Z

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?

richardnies · 2021-10-20T23:09:09Z

@jloizu I have now added the test case in InputFiles/TestCases/G3V01Lm2Fi.info and .sp
Thanks for reviewing!

richardnies · 2021-10-21T09:16:07Z

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?

jloizu · 2021-10-21T12:35:40Z

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...

richardnies · 2021-10-22T10:20:32Z

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.

diff_log_G2V32L1Fi.001.txt

jloizu · 2021-10-22T12:00:03Z

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 :            :

richardnies · 2021-10-22T14:00:27Z

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.

jloizu · 2021-10-22T14:29:48Z

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...

jonathanschilling · 2021-10-25T10:08:53Z

@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.

jonathanschilling · 2021-10-25T10:10:29Z

@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)?

mbkumar · 2021-10-25T12:21:31Z

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. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#153 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA62VEBNLH2BNXF2KDRJU6DUIUUEBANCNFSM5DX24OWA> .

richardnies · 2021-10-26T10:57:56Z

@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!

mbkumar · 2021-10-26T11:27:58Z

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. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#153 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA62VECU362UMVZ2NGNIMZLUI2CT7ANCNFSM5DX24OWA> .

…tonUniversity/SPEC into Lconstraint_-2_and_pyspec_Zernike

jonathanschilling · 2022-02-16T14:47:13Z

@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?

richardnies · 2022-02-22T14:53:20Z

@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.

jonathanschilling · 2022-02-22T16:43:34Z

@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?

ejpaul and others added 10 commits September 9, 2020 07:22

Initial commit.

0cb35b3

Resolved merge conflicts between Lconstraint=-2 and new Zernike changes

9c19a2b

Changes in SPEC + further merge conflict resolutions.

b5d0e89

Normal field B.C. now correctly read in.

9352b8c

NUMBA accelerated Zernike construction.

abb700b

More effective reading in of magnetic field.

f01ecaa

Clean-up of py_spec processing.

4dea0f4

Merge branch 'master' into Lconstraint_-2_and_pyspec_Zernike

84362d5

minor clean-ups

aefcc77

Further minor clean-ups.

ad9f86d

richardnies requested review from ejpaul and zhisong September 9, 2021 19:37

richardnies added 3 commits September 27, 2021 19:50

Removed print statements, added checks of inputs.

9d03364

Added documentation.

eccc082

Merge branch 'master' into Lconstraint_-2_and_pyspec_Zernike

0aca587

Corrected documentation.

0030936

richardnies requested a review from jloizu September 29, 2021 17:59

richardnies added 5 commits October 11, 2021 16:33

Changes to documentation + added Bn!=zero option in fixed-boundary as…

101ae5b

… new option inputlist (Lbdybnzero)

Removed fossil comment + corrected check of Nvol must be 1 for Lbdybn…

501a652

…zero=false

Two checks for Lbdybnzero=.false.: must be fixed-boundary and must be…

21fd292

… single-volume

Checks for testing purpose.

4257f89

Merge branch 'master' into Lconstraint_-2_and_pyspec_Zernike

bc4ace6

Cleaned up comments. Corrected checks of consistent inputs (Lbdybnzer…

eed9ff7

…o only allowed with Lconstraint=-2 and Lfreebound=0; and Lconstraint=-2 only allowed with Nvol=1).

Added test case.

ef4aa39

jonathanschilling mentioned this pull request Oct 25, 2021

Problem running tests on master branch #156

Closed

Merge branch 'master' into Lconstraint_-2_and_pyspec_Zernike

55197bb

Merge branch 'master' into Lconstraint_-2_and_pyspec_Zernike

9003cd6

jonathanschilling and others added 6 commits October 26, 2021 14:42

SCREENLIST awk preprocessing removed from traditional Makefile

3a75635

Merge branch 'Lconstraint_-2_and_pyspec_Zernike' of github.com:Prince…

77b5721

…tonUniversity/SPEC into Lconstraint_-2_and_pyspec_Zernike

FFT to read B field and derivatives.

8184075

Removed numba package.

44a88bd

Merge branch 'master' into Lconstraint_-2_and_pyspec_Zernike

cf4512c

Merge branch 'master' into Lconstraint_-2_and_pyspec_Zernike

44627e6

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