bugs related to boundarychk, electron energy vars, and scr fixed among others #4
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… here we have specific things from the ebysus code
…a similar format as in IDL, i.e., assign snapshot number while calling the variable and not when we define the object. We store the variables in the structure and cleans when we read new snapshot. Any other features.
… here we have specific things from the ebysus code
…ear and a minor bug when reading entropy
…ther, although I think it can be improved
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I am unable to merge this as is. It is based on an older version of the repository and there are several conflicts. I will have to go through the changes manually and put in the new parts in the current master. |
helita/sim/bifrost.py
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| 'get composite variable %s. Note that' | ||
| 'simple_var available variables are: %s' % (var,repr(self.simple_vars)))) | ||
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| def do_mesh(self, x=None, y=None, z=None, nx=None, ny=None, nz=None, |
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This function is not generic. It has values hardcoded. It does not belong here!
helita/sim/cstagger.pyx
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| ctypedef fused FLOAT_t: |
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This should not be removed. Now cstagger.pyx uses fused types.
helita/sim/cstagger.pyx
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| ------- | ||
| None. Results saved in cstagger.zupc, cstagger.zdnc. | ||
| ''' | ||
| def init_stagger(int mz, FLOAT_t dx, FLOAT_t dy, np.ndarray[FLOAT_t, ndim=1] z, np.ndarray[FLOAT_t, ndim=1] zdn, np.ndarray[FLOAT_t, ndim=1] dzup, np.ndarray[FLOAT_t, ndim=1] dzdn): |
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Again, this is replacing previously updated code with an old version.
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On Sep 11, 2017, at 8:41 AM, Tiago M. D. Pereira ***@***.***> wrote:
@tiagopereira commented on this pull request.
In helita/sim/bifrost.py <#4 (comment)>:
> else:
raise ValueError(('_get_composite_var: do not know (yet) how to'
- 'get composite variable %s.' % var))
+ 'get composite variable %s. Note that'
+ 'simple_var available variables are: %s' % (var,repr(self.simple_vars))))
+
+ def do_mesh(self, x=None, y=None, z=None, nx=None, ny=None, nz=None,
This function is not generic. It has values hardcoded. It does not belong here!
I asked where do you want to have the do_mesh (BTW, this do_mesh is 3 times shorter than
the idl version!). I want to add code that allows me to create snapshots, mesh and tables (also for ebysus
that I have already partially done).
In helita/sim/cstagger.pyx <#4 (comment)>:
>
-ctypedef fused FLOAT_t:
This should not be removed. Now cstagger.pyx uses fused types.
Ups, something I did wrong here. I though I had this as you had. I wonder if I deleted
some version that I had and I shouldn’t… Do you want me to go through this?
In helita/sim/cstagger.pyx <#4 (comment)>:
> - From init_stagger.c and init_stagger.pro
-
- Parameters
- ----------
- mz - integer
- Number of z points
- z - 1-D ndarray, float
- z scale
- zdn - 1-D ndarray, float
- z scale derivative
-
- Returns
- -------
- None. Results saved in cstagger.zupc, cstagger.zdnc.
- '''
+def init_stagger(int mz, FLOAT_t dx, FLOAT_t dy, np.ndarray[FLOAT_t, ndim=1] z, np.ndarray[FLOAT_t, ndim=1] zdn, np.ndarray[FLOAT_t, ndim=1] dzup, np.ndarray[FLOAT_t, ndim=1] dzdn):
Again, this is replacing previously updated code with an old version.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub <#4 (review)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ANp4BDbMbuuFBXQj2yv591lSEDQmuX2cks5shVSlgaJpZM4PNbnQ>.
I am not sure what is wrong there. Note that the version above is ready to do derivative and xdn and ydn etc.
J
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helita/sim/bifrost.py
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| @@ -329,44 +360,196 @@ def _get_simple_var_xy(self, var, order='F', mode='r'): | |||
| return np.memmap(filename, dtype=self.dtype, order=order, offset=offset, | |||
| mode=mode, shape=(self.nx, self.ny)) | |||
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| def _get_composite_var(self, var): | |||
| def boundcut(self, name,var): | |||
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This function should only be called when params['boundarychk'] = 1, but right now it is called all the time. Besides, it should not even exist. You are getting these problems because you called init_cstagger with self.nz, but you should have used self.nzb, which includes the additional boundary points.
helita/sim/bifrost.py
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| else: # will call xdn, ydn, or zdn to get r at cell faces | ||
| return p / getattr(cstagger, var[1] + 'dn')(self.r) | ||
| rdt = self.r.dtype | ||
| cs.init_stagger(self.nz, self.dx, self.dy, self.z.astype(rdt), self.zdn.astype(rdt), self.dzidzup.astype(rdt), self.dzidzdn.astype(rdt)) |
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Always call init_cstagger with self.nzb instead of self.nz to avoid boundary problems.
helita/sim/bifrost.py
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| return result | ||
| elif (len(var) > 2): | ||
| if var in ['ixc', 'iyc', 'izc'] or var in ['exc', 'eyc', 'ezc']: | ||
| p = self.variables[var[0:2] +'c'] = self.get_var(var[0:2],self.snap) |
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There must be another way for this. Calling self.get_var from inside self._get_composite_var could result in an infinite loop. Please don't do it.
…F code as well as atomic info
…from diper to ebysus atom file format, and minor bugs fixed
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Most of this was fixed by 51549f3, minus the conflicts. Closing. |
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Does this mean that I should do the new fork now?
On Sep 26, 2017 4:03 AM, "Tiago M. D. Pereira" <notifications@github.com> wrote:
Closed #4 <#4>.
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Reply to this email directly, view it on GitHub
<#4 (comment)>, or mute the
thread
<https://github.com/notifications/unsubscribe-auth/ANp4BClqV_NvDj3AUxpn05nASpKY_YK-ks5smNnkgaJpZM4PNbnQ>
.
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Yes. But be careful not to lose any files that are not updated in the master. |
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I'm pretty sure I'll do stupid things.... :😁
…On Sep 26, 2017 8:51 AM, "Tiago M. D. Pereira" ***@***.***> wrote:
Yes. But be careful not to lose any files that are not updated in the
master.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#4 (comment)>, or mute
the thread
<https://github.com/notifications/unsubscribe-auth/ANp4BFq66BG0FBlYfjDk9G63suHrzNdkks5smR1kgaJpZM4PNbnQ>
.
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