[yt-svn] commit/yt: 3 new changesets

Thu Jul 31 10:05:10 PDT 2014

3 new commits in yt:

https://bitbucket.org/yt_analysis/yt/commits/cd82cf32b4e4/
Changeset:   cd82cf32b4e4
Branch:      yt-3.0
User:        MatthewTurk
Date:        2014-07-31 16:31:12
Summary:     Adding deposited and smoothed field info.
Affected #:  1 file

diff -r 61f020440f1a983b9d0e4875f16773b5a3419e69 -r cd82cf32b4e4b595e82a1a6f269e228c957b74e5 doc/source/analyzing/fields.rst

--- a/doc/source/analyzing/fields.rst
+++ b/doc/source/analyzing/fields.rst
@@ -206,6 +206,41 @@
 that tracks the position and velocity (respectively) in code units.
 
 
+.. _deposited-particle-fields:
+
+Deposited Particle Fields
++++++++++++++++++++++++++
+
+In order to turn particle (discrete) fields into fields that are deposited in
+some regular, space-filling way (even if that space is empty, it is defined
+everywhere.)  These are in the special field-type space ``deposit``, and are
+typically of the form ``("deposit", "particletype_depositiontype")`` where
+``depositiontype`` is the mechanism by which the field is deposited, and
+``particletype`` is the particle type of the particles being deposited.  If you
+are attempting to examine the cloud-in-cell (``cic``) deposition of the ``all``
+particle type, you would access the field ``("deposit", "all_cic")``.
+
+yt defines a few particular types of deposition internally, and creating new
+ones can be done by modifying the files ``yt/geometry/particle_deposit.pyx``
+and ``yt/fields/particle_fields.py``, although that is an advanced topic
+somewhat outside the scope of this section.
+
+ * ``count`` - this field counts the total number of particles of a given type
+   in a given mesh zone.  Note that because, in general, the mesh for particle
+   datasets is defined by the number of particles in a region, this may not be
+   the most useful metric.
+ * ``density`` - this field takes the total sum of ``particle_mass`` in a given
+   mesh field and divides by the volume.
+ * ``mass`` - this field takes the total sum of ``particle_mass`` in each mesh
+   zone.
+ * ``cic`` - this field performs cloud-in-cell interpolation (see `Section 2.2
+   <http://ta.twi.tudelft.nl/dv/users/Lemmens/MThesis.TTH/chapter4.html>`_ for more
+   information) of the density of particles in a given mesh zone.
+ * ``smoothed`` - this is a special deposition type.  See discussion below for
+   more information, in :ref:`sph-fields`.
+
+.. _sph-fields:
+
 SPH Fields
 ++++++++++
 
@@ -213,3 +248,31 @@
 a field for the smoothing length ``h``, which is roughly equivalent to 
 ``(m/\rho)^{1/3}``, where ``m`` and ``rho`` are the particle mass and density 
 respectively.  This can be useful for doing neighbour finding.
+
+As a note, SPH fields are special cases of the "deposited" particle fields.
+They contain an additional piece of information about what is being examined,
+and any fields that are recognized as being identical to intrinsic yt fields
+will be aliased.  For example, in a Gadget dataset, the smoothed density of
+``Gas`` particles will be aliased to the mesh field ``("gas", "density")`` so
+that operations conducted on the mesh field ``density`` (which are frequent
+occurrences) will operate on the smoothed gas density from the SPH particles.
+
+The special deposition types based on smoothing (``smoothed``) are defined in
+the file ``yt/geometry/particle_smooth.pyx``, and they require non-local
+operations defined on a variable number of neighbors.  The default smoothing
+type utilizes a cubic spline kernel and uses 64 nearest neighbors, providing a
+volume-normalized smoothing.  Other types are possible, and yt provides
+functionality for many different types of non-local correlation between
+particles.  (For instance, a friends-of-friends grouper has been built on this
+same infrastructure.)
+
+Every particle field on a smoothed particle type is the source for a smoothed
+field; this is not always useful, but it errs on the side of extra fields,
+rather than too few fields.  (For instance, it may be unlikely that the
+smoothed angular momentum field will be useful.)  The naming scheme is an
+extension of the scheme described in :ref:`deposited-particle-fields`, and is
+defined as such: ``("deposit", "particletype_smoothed_fieldname")``, where 
+``fieldname`` is the name of the field being smoothed.  For example, smoothed
+``Temperature`` of the ``Gas`` particle type would be ``("deposit",
+"Gas_smoothed_Temperature")``, which in most cases would be aliased to the
+field ``("gas", "temperature")`` for convenience.


https://bitbucket.org/yt_analysis/yt/commits/bd7b752446fa/
Changeset:   bd7b752446fa
Branch:      yt-3.0
User:        MatthewTurk
Date:        2014-07-31 17:28:01
Summary:     Update for comments.
Affected #:  1 file

diff -r cd82cf32b4e4b595e82a1a6f269e228c957b74e5 -r bd7b752446fa8ce28f8d4e1bc5c545e3a6eda286 doc/source/analyzing/fields.rst
--- a/doc/source/analyzing/fields.rst
+++ b/doc/source/analyzing/fields.rst
@@ -213,22 +213,25 @@
 
 In order to turn particle (discrete) fields into fields that are deposited in
 some regular, space-filling way (even if that space is empty, it is defined
-everywhere.)  These are in the special field-type space ``deposit``, and are
-typically of the form ``("deposit", "particletype_depositiontype")`` where
-``depositiontype`` is the mechanism by which the field is deposited, and
-``particletype`` is the particle type of the particles being deposited.  If you
-are attempting to examine the cloud-in-cell (``cic``) deposition of the ``all``
-particle type, you would access the field ``("deposit", "all_cic")``.
+everywhere) yt provides mechanisms for depositing particles onto a mesh.  These
+are in the special field-type space ``deposit``, and are typically of the form
+``("deposit", "particletype_depositiontype")`` where ``depositiontype`` is the
+mechanism by which the field is deposited, and ``particletype`` is the particle
+type of the particles being deposited.  If you are attempting to examine the
+cloud-in-cell (``cic``) deposition of the ``all`` particle type, you would
+access the field ``("deposit", "all_cic")``.
 
 yt defines a few particular types of deposition internally, and creating new
 ones can be done by modifying the files ``yt/geometry/particle_deposit.pyx``
 and ``yt/fields/particle_fields.py``, although that is an advanced topic
-somewhat outside the scope of this section.
+somewhat outside the scope of this section.  The default deposition types
+available are:
 
  * ``count`` - this field counts the total number of particles of a given type
    in a given mesh zone.  Note that because, in general, the mesh for particle
    datasets is defined by the number of particles in a region, this may not be
-   the most useful metric.
+   the most useful metric.  This may be made more useful by depositing particle
+   data onto an :ref:`arbitrary-grid`.
  * ``density`` - this field takes the total sum of ``particle_mass`` in a given
    mesh field and divides by the volume.
  * ``mass`` - this field takes the total sum of ``particle_mass`` in each mesh


https://bitbucket.org/yt_analysis/yt/commits/01738d3373b2/
Changeset:   01738d3373b2
Branch:      yt-3.0
User:        ngoldbaum
Date:        2014-07-31 19:05:02
Summary:     Merged in MatthewTurk/yt/yt-3.0 (pull request #1114)

Adding deposited and smoothed field info.
Affected #:  1 file

diff -r a8dd15c035af1ff44b6c08f33db2f1e71a9ce20f -r 01738d3373b2f648be72f2a0ae0ca48040d75a1a doc/source/analyzing/fields.rst
--- a/doc/source/analyzing/fields.rst
+++ b/doc/source/analyzing/fields.rst
@@ -248,6 +248,44 @@
 that tracks the position and velocity (respectively) in code units.
 
 
+.. _deposited-particle-fields:
+
+Deposited Particle Fields
++++++++++++++++++++++++++
+
+In order to turn particle (discrete) fields into fields that are deposited in
+some regular, space-filling way (even if that space is empty, it is defined
+everywhere) yt provides mechanisms for depositing particles onto a mesh.  These
+are in the special field-type space ``deposit``, and are typically of the form
+``("deposit", "particletype_depositiontype")`` where ``depositiontype`` is the
+mechanism by which the field is deposited, and ``particletype`` is the particle
+type of the particles being deposited.  If you are attempting to examine the
+cloud-in-cell (``cic``) deposition of the ``all`` particle type, you would
+access the field ``("deposit", "all_cic")``.
+
+yt defines a few particular types of deposition internally, and creating new
+ones can be done by modifying the files ``yt/geometry/particle_deposit.pyx``
+and ``yt/fields/particle_fields.py``, although that is an advanced topic
+somewhat outside the scope of this section.  The default deposition types
+available are:
+
+ * ``count`` - this field counts the total number of particles of a given type
+   in a given mesh zone.  Note that because, in general, the mesh for particle
+   datasets is defined by the number of particles in a region, this may not be
+   the most useful metric.  This may be made more useful by depositing particle
+   data onto an :ref:`arbitrary-grid`.
+ * ``density`` - this field takes the total sum of ``particle_mass`` in a given
+   mesh field and divides by the volume.
+ * ``mass`` - this field takes the total sum of ``particle_mass`` in each mesh
+   zone.
+ * ``cic`` - this field performs cloud-in-cell interpolation (see `Section 2.2
+   <http://ta.twi.tudelft.nl/dv/users/Lemmens/MThesis.TTH/chapter4.html>`_ for more
+   information) of the density of particles in a given mesh zone.
+ * ``smoothed`` - this is a special deposition type.  See discussion below for
+   more information, in :ref:`sph-fields`.
+
+.. _sph-fields:
+
 SPH Fields
 ++++++++++
 
@@ -255,3 +293,31 @@
 a field for the smoothing length ``h``, which is roughly equivalent to 
 ``(m/\rho)^{1/3}``, where ``m`` and ``rho`` are the particle mass and density 
 respectively.  This can be useful for doing neighbour finding.
+
+As a note, SPH fields are special cases of the "deposited" particle fields.
+They contain an additional piece of information about what is being examined,
+and any fields that are recognized as being identical to intrinsic yt fields
+will be aliased.  For example, in a Gadget dataset, the smoothed density of
+``Gas`` particles will be aliased to the mesh field ``("gas", "density")`` so
+that operations conducted on the mesh field ``density`` (which are frequent
+occurrences) will operate on the smoothed gas density from the SPH particles.
+
+The special deposition types based on smoothing (``smoothed``) are defined in
+the file ``yt/geometry/particle_smooth.pyx``, and they require non-local
+operations defined on a variable number of neighbors.  The default smoothing
+type utilizes a cubic spline kernel and uses 64 nearest neighbors, providing a
+volume-normalized smoothing.  Other types are possible, and yt provides
+functionality for many different types of non-local correlation between
+particles.  (For instance, a friends-of-friends grouper has been built on this
+same infrastructure.)
+
+Every particle field on a smoothed particle type is the source for a smoothed
+field; this is not always useful, but it errs on the side of extra fields,
+rather than too few fields.  (For instance, it may be unlikely that the
+smoothed angular momentum field will be useful.)  The naming scheme is an
+extension of the scheme described in :ref:`deposited-particle-fields`, and is
+defined as such: ``("deposit", "particletype_smoothed_fieldname")``, where 
+``fieldname`` is the name of the field being smoothed.  For example, smoothed
+``Temperature`` of the ``Gas`` particle type would be ``("deposit",
+"Gas_smoothed_Temperature")``, which in most cases would be aliased to the
+field ``("gas", "temperature")`` for convenience.

Repository URL: https://bitbucket.org/yt_analysis/yt/

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