Fix logical errors and typos in Spec equilibrium object

[missing-user]

There were a few bugs in the Spec equilibrium object that I spotted:

• Many error checks were written, but the raise clause was omitted, so they didn't take effect
• The RHS of the assignments to si.iota[0:self.nvol+1] and si.oita[0:self.nvol+1] had the wrong shape
• array shape check in as_spec compared tuple to list and always raised

[missing-user]

nvol+1 is the correct size here, compare to:

https://github.com/missing-user/SPEC/blob/6a231606a626968fc1b83eed7dfa01c234842905/InputFiles/Verification/forcefree/solovev/generate_spec_nl_from_vmec.m#L167

I think the other iota sizes in spec wrapper must be adjusted.

[missing-user]

I noticed, that parts of the codebase assume all profiles to be the same size (mvol), in this example according to the error message local_full_x = self.mvol

simsopt/src/simsopt/mhd/profiles.py

Lines 93 to 98 in 9fc2c36

	# Check that volume index is within bounds
	if (lvol < 0).any():
	raise ValueError('lvol should be larger or equal than zero')
	if (lvol >= self.local_full_x.size).any():
	raise ValueError('lvol should be smaller than Mvol')

or here, where volume_current_profile is simply overwritten in the vacuum region for freeboundary runs, so although nvol elements are used, the profile has to be at least mvol in size:

simsopt/src/simsopt/mhd/spec.py

Lines 1001 to 1019 in 9fc2c36

	if self.volume_current_profile is not None:
	# Volume current is a cumulative profile; special care is required
	# when a dofs is changed in order to keep fixed dofs fixed!
	old_ivolume = copy.copy(si.ivolume)
	for lvol in range(0, self.mvol):
	if self.volume_current_profile.is_fixed(lvol):
	if lvol != 0:
	si.ivolume[lvol] = si.ivolume[lvol] - \
	old_ivolume[lvol - 1] + si.ivolume[lvol - 1]
	self.set_profile(
	'volume_current', lvol=lvol, value=si.ivolume[lvol])
	else:
	si.ivolume[lvol] = self.get_profile('volume_current', lvol)
	if si.lfreebound:
	si.ivolume[self.nvol] = si.ivolume[self.nvol - 1]
	self.volume_current_profile.set(
	key=self.mvol - 1, new_val=si.ivolume[self.nvol - 1])

while other parts create different sizes for different profiles.

simsopt/src/simsopt/mhd/spec.py

Lines 766 to 781 in 9fc2c36

	profile_dict = {
	'pressure': {'specname': 'pressure', 'cumulative': False, 'length': self.nvol},
	'volume_current': {'specname': 'ivolume', 'cumulative': True, 'length': self.nvol},
	'interface_current': {'specname': 'isurf', 'cumulative': False, 'length': self.nvol-1},
	'helicity': {'specname': 'helicity', 'cumulative': False, 'length': self.mvol},
	'iota': {'specname': 'iota', 'cumulative': False, 'length': self.mvol},
	'oita': {'specname': 'oita', 'cumulative': False, 'length': self.mvol},
	'mu': {'specname': 'mu', 'cumulative': False, 'length': self.mvol},
	'pflux': {'specname': 'pflux', 'cumulative': True, 'length': self.mvol},
	'tflux': {'specname': 'tflux', 'cumulative': True, 'length': self.mvol}
	}
	profile_data = self.inputlist.__getattribute__(profile_dict[longname]['specname'])[0:profile_dict[longname]['length']]
	profile = ProfileSpec(profile_data, cumulative=profile_dict[longname]['cumulative'], psi_edge=self.inputlist.phiedge)
	profile.unfix_all()
	self.__setattr__(longname + '_profile', profile)

What is the intended design @smiet ? I think variable size will result in stricter error handling, whereas having all profiles the same size makes them easier to switch out, iterate over, etc. On the other hand, having the same size might confuse users about which elements actually affect the result.

[missing-user]

Also @smiet , shouldn't iota profiles be nvol+1 elements and not mvol? How can the vacuum computational boundary have a prescribed iota?
#457 (comment)