Mailman 3 October 2017 - yt-users

Problem with making SlicePlot and ProjectionPlot from new derived field
by tazkera haque Oct. 6, 2017

Oct. 6, 2017

Dear yt people, I am working on a tipsy output file from a n-body simulation. My file contains some scaled units for fields like density, coordinates, mass etc. To make a physical sense of the data, I had to convert those fields units to some physical units (c.g.s) and I derived new fields having cgs unit. for example: *dd = ds.all_data()# derive a new domain width with conversion factor (6Mpc*current_time/hubble_constant) def _NewDomainWidth(field, data): return ds.domain_width*((3.086e18*6e6*0.909090893796)/(0.7))ds.add_field(('gas', 'PhysicalDomainWidth'), function=_NewDomainWidth, units="code_length")* *# derive a new domain center with conversion factor (6Mpc*current_time/hubble_constant) def _NewDomainCenter(field, data): return ds.domain_center*((3.086e18*6e6*0.909090893796)/(0.7))ds.add_field(('gas', 'PhysicalDomainCenter'), function=_NewDomainCenter, units="code_length")* note that here "code_length" is actually in "cm". but I could not just do dd["Gas",'Coordinates'].in_units('cm'), because this conversion does not take into account some constant corrections and returns the wrong length magnitude. My goal was to make sliceplot and projectionplot of a newly derived field : *# derive a new electron pressure fielddef _ElectronPressure(field, data): return data['Gas','Density']*(5.49e-7)*data['Gas','Temperature']ds.add_field(('gas', 'ElectronPressure'), function=_ElectronPressure, units="(code_mass*K)/(code_length**3)")* *# integration of pressure field along line of sight* *yt.ProjectionPlot(ds, 'z', ('gas', 'ElectronPressure'), width = dd['gas', 'PhysicalDomainWidth'], center = dd['gas', 'PhysicalDomainCenter'] )* *and it is returning me * ValueError Traceback (most recent call last)<ipython-input-8-fa351b6c09d1> in <module>() 1 yt.ProjectionPlot(ds, 'z', ('gas', 'ElectronPressure'), width = dd['gas', 'PhysicalDomainWidth'], ----> 2 center = dd['gas', 'PhysicalDomainCenter'] ) ValueError: operands could not be broadcast together with shapes (39678,) (54608,) Now I cannot use width =ds.domain_width and center = ds.domain_center for the same unit error. I was wondering how I can make the projectionplot for my newly derived field and newly derived domain width and domain center. Your suggestion is most welcome Best Tazkera

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Plotting SFRs
by Ashley Jarvis Oct. 5, 2017

Oct. 5, 2017

Hi all, I’m attempting to adapt the example script for plotting star formation rates (found at http://yt-project.org/doc/analyzing/analysis_modules/star_analysis.html#sta… <http://yt-project.org/doc/analyzing/analysis_modules/star_analysis.html#sta…>) to work with output data from a simulation run using Enzo. However, when I attempt to run the script, I get the following error: ——————————————————— File "PlotSFR.py", line 26, in <module> sfr = StarFormationRate(data, star_mass=mass_old, star_creation_time=ct_old, volume=sp.volume()) File "/usr/local/anaconda/lib/python2.7/site-packages/yt/analysis_modules/star_analysis/sfr_spectrum.py", line 115, in __init__ self._ds.quan(1.0, 'Mpccm**3').units File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/yt_array.py", line 1355, in __new__ dtype=dtype, bypass_validation=bypass_validation) File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/yt_array.py", line 430, in __new__ units = Unit(input_units, registry=registry) File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/unit_object.py", line 257, in __new__ unit_data = _get_unit_data_from_expr(unit_expr, registry.lut) File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/unit_object.py", line 572, in _get_unit_data_from_expr unit_data = _get_unit_data_from_expr(unit_expr.args[0], unit_symbol_lut) File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/unit_object.py", line 566, in _get_unit_data_from_expr return _lookup_unit_symbol(str(unit_expr), unit_symbol_lut) File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/unit_object.py", line 657, in _lookup_unit_symbol "symbols." % symbol_str) yt.units.unit_registry.UnitParseError: Could not find unit symbol 'Mpccm' in the provided symbols. ——————————————————— I am using version 3.3.5 of yt. Does anyone know how I can resolve this? Any suggestions would be greatly appreciated. Thanks, Ashley

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Re: [yt-users] defining derived field only for Gas particles
by Ari Maller Oct. 4, 2017

Oct. 4, 2017

It is a little unclear why you are trying to do what you are doing. To convert unit systems in yt there are a bunch of unit commands. For example dd[“Gas’,’Mass’].in_units(‘g’) would return the masses in grams. I think what is going wrong in your derived field is that you set the units to grams and then add your conversion factor to that, but you wanted to use your conversion factor on the code masses. If you just want Physical mass to be in grams and no extra conversion then you could set the units to grams and do nothing to the array. The first question is whether yt internal unit conversion is working correctly for you or not. Gadget does not output Tipsy files, so it is possible the frontend is doing something wrong since your data sounds very unusual. If you need some extra conversion then you can see what the values of your Masses are in the units of your choice and then add derived field in those units that makes the extra conversion. Ari > On Oct 3, 2017, at 11:53 PM, yt-users-request(a)lists.spacepope.org wrote: > > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. defining derived field only for Gas particles (tazkera haque) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 3 Oct 2017 23:29:31 -0400 > From: tazkera haque <h.tazkera(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: [yt-users] defining derived field only for Gas particles > Message-ID: > <CAFj_7zyiZYPOWuFPsPtbGtNVDvXF9G3Z+1srY_TvDKrFM8oRkg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear yt community, > > I am analyzing some Tipsy data output from Gadget 3. I have three different > particles, Gas, Star and Dark Matter. I want to derive a new field > 'PhysicalMass', that will make a unit conversion of code_mass to some > physical mass units. My code so far looks like this: > > > > > > > > > > *import ytfrom yt import derived_field@derived_field(name="PhysicalMass", > units="g")def _PhysicalMass(field, data): M = > data['Gas','Mass']*((5995.*(1e10)*(1.98855e33))/(0.7)) return Mds = > yt.load('snap_p6n36fof_031.bin', n_ref=64)dd= ds.all_data* > > > My default ('Gas', 'Mass') array looks like this: > *dd['Gas','Mass']* > > YTArray([ 9.64448986e-07, 9.64448986e-07, 9.64448986e-07, ..., > 9.64448986e-07, 9.64448986e-07, 9.64448986e-07]) code_mass > > But when I call the new derived field, it takes some values which does > not correspond to the conversion constants I have multiplied with: > > dd['PhysicalMass'] > YTArray([ 3.26598467e+74, 3.26598467e+74, 3.26598467e+74, ..., > 3.26598467e+74, 3.26598467e+74, 3.26598467e+74]) g > > I can directly multiply the ('Gas', 'Mass') array with some conversion > factors to get accurate values, but I need to define a new field for > later calls: > dd['Gas','Mass']*((5995.*(1e10)*(1.98855e33))/(0.7)) > > > > So my question is how do I get a new field which will only contain > PhysicalMass from Gas particles. it seems dd['Gas', 'PhysicalMass'] does > not exist. > > > Thanks very much for your time. > > Best > Tazkera > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201…> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 116, Issue 1 > ****************************************

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defining derived field only for Gas particles
by tazkera haque Oct. 4, 2017

Oct. 4, 2017

Dear yt community, I am analyzing some Tipsy data output from Gadget 3. I have three different particles, Gas, Star and Dark Matter. I want to derive a new field 'PhysicalMass', that will make a unit conversion of code_mass to some physical mass units. My code so far looks like this: *import ytfrom yt import derived_field@derived_field(name="PhysicalMass", units="g")def _PhysicalMass(field, data): M = data['Gas','Mass']*((5995.*(1e10)*(1.98855e33))/(0.7)) return Mds = yt.load('snap_p6n36fof_031.bin', n_ref=64)dd= ds.all_data* My default ('Gas', 'Mass') array looks like this: *dd['Gas','Mass']* YTArray([ 9.64448986e-07, 9.64448986e-07, 9.64448986e-07, ..., 9.64448986e-07, 9.64448986e-07, 9.64448986e-07]) code_mass But when I call the new derived field, it takes some values which does not correspond to the conversion constants I have multiplied with: dd['PhysicalMass'] YTArray([ 3.26598467e+74, 3.26598467e+74, 3.26598467e+74, ..., 3.26598467e+74, 3.26598467e+74, 3.26598467e+74]) g I can directly multiply the ('Gas', 'Mass') array with some conversion factors to get accurate values, but I need to define a new field for later calls: dd['Gas','Mass']*((5995.*(1e10)*(1.98855e33))/(0.7)) So my question is how do I get a new field which will only contain PhysicalMass from Gas particles. it seems dd['Gas', 'PhysicalMass'] does not exist. Thanks very much for your time. Best Tazkera

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