Merged in prabhuramachandran/pysph/clean-parallel-tests (pull request #…

…162)

Cleanup parallel tests

MANIFEST.in

@@ -1,6 +1,5 @@
-include MANIFEST.in Makefile *.py *.txt pip_requirements.txt README.md
-include build_zoltan.sh shippable.yml
-recursive-include examples *.py
-recursive-include docs *.* *
-recursive-include pysph *.pxd *.h *.c *.src
-recursive-include pyzoltan *.pxd *.h *.c *.src
+include MANIFEST.in Makefile *.bat *.py *.rst *.sh *.txt *.yml
+recursive-include examples *.py *.vtk.gz
+recursive-include docs *.*
+recursive-include pysph *.pxd *.src *.txt.gz
+recursive-include pyzoltan *.pxd *.h *.src *.txt

README.rst

@@ -0,0 +1,126 @@
+PySPH: a Python-based SPH framework
+-----------------------------------
+
+|Shippable Status| |Drone Status|
+
+PySPH is an open source framework for Smoothed Particle Hydrodynamics
+(SPH) simulations. It is implemented in
+`Python <http://www.python.org>`__ and the performance critical parts
+are implemented in `Cython <http://www.cython.org>`__.
+
+PySPH allows users to write their high-level code in pure Python.  This Python
+code is automatically converted to high-performance Cython which is compiled
+and executed.  PySPH can also work with OpenMP and MPI for larger scale
+computing.
+
+The latest documentation for PySPH is available at
+`pysph.readthedocs.org <http://pysph.readthedocs.org>`__.
+
+.. |Shippable Status| image:: https://api.shippable.com/projects/540e849c3479c5ea8f9f030e/badge?branchName=master
+   :target: https://app.shippable.com/projects/540e849c3479c5ea8f9f030e/builds/latest
+.. |Drone Status| image:: https://drone.io/bitbucket.org/pysph/pysph/status.png
+   :target: https://drone.io/bitbucket.org/pysph/pysph/latest
+
+Features
+--------
+
+-  Solver framework to add arbitrary collection of particles.
+-  Flexibility to define arbitrary SPH equations operating on particles
+   in pure Python.
+-  Any kind of user-defined multi-step integrator.
+-  Seamless parallel integration using
+   `Zoltan <http://www.cs.sandia.gov/zoltan/>`__.
+-  High-performance: our performance is comparable to hand-written
+   solvers implemented in FORTRAN.
+
+Solvers
+-------
+
+Currently, PySPH has numerous examples to solve a variety of problems.  The
+features of the implementation are:
+
+-  `Weakly Compressible SPH
+   (WCSPH) <http://www.tandfonline.com/doi/abs/10.1080/00221686.2010.9641250>`__
+   for free-surface flows (Gesteira et al. 2010, Journal of Hydraulic
+   Research, 48, pp. 6--27)
+-  `Transport Velocity
+   Formulation <http://dx.doi.org/10.1016/j.jcp.2013.01.043>`__ for
+   incompressilbe fluids (Adami et al. 2013, JCP, 241, pp. 292--307)
+-  `SPH for elastic
+   dynamics <http://dx.doi.org/10.1016/S0045-7825(01)00254-7>`__ (Gray
+   et al. 2001, CMAME, Vol. 190, pp 6641--6662)
+-  `Compressible SPH <http://dx.doi.org/10.1016/j.jcp.2013.08.060>`__
+   (Puri et al. 2014, JCP, Vol. 256, pp 308--333)
+
+Installation
+============
+
+Up-to-date details on how to install PySPH on Linux/OS X and Windows are
+available from
+`here <http://pysph.readthedocs.org/en/latest/installation.html>`__.
+
+If you wish to see a working build/test script please see our
+`shippable.yml <https://bitbucket.org/pysph/pysph/src/master/shippable.yml>`__.
+Or you could see the `build
+script <https://drone.io/bitbucket.org/pysph/pysph/admin>`__ hosted at
+`drone.io <http://drone.io>`__.
+
+Running the examples
+--------------------
+
+You can verify the installation by exploring some examples. A fairly
+quick running example (taking about 5-10 minutes) would be the
+following::
+
+    $ cd examples
+    $ python dam_break.py
+
+The solution can be viewed live by running::
+
+    $ pysph_viewer
+
+This requires that Mayavi be installed. The saved output data can be
+viewed by running::
+
+    $ pysph_viewer dam_break_output/
+
+A 3D version of the dam-break problem is also available, and may be run
+as::
+
+    $ python dam_break3D.py
+
+This runs the 3D dam-break problem which is also a SPHERIC benchmark
+`Test 2 <https://wiki.manchester.ac.uk/spheric/index.php/Test2>`__
+
+.. figure:: https://bitbucket.org/pysph/pysph/raw/master/docs/Images/db3d.png
+   :alt: IMAGE
+
+PySPH is more than a tool for wave-body interactions:::
+
+    $ cd examples/transport_velocity
+    $ python cavity.py
+
+This runs the driven cavity problem using the transport velocity
+formulation of Adami et al. You can verify the results for this problem
+using the helper script
+``examples/transport_velocity/ldcavity_results.py`` to plot, for example
+the streamlines:
+
+.. figure:: https://bitbucket.org/pysph/pysph/raw/master/docs/Images/ldc-streamlines.png
+   :alt: IMAGE
+
+If you want to use PySPH for elastic dynamics, you can try some of the
+examples from the directory ``examples/solid_mech``::
+
+    $ cd examples/solid_mech
+    $ python rings.py
+
+Which runs the problem of the collision of two elastic rings:
+
+.. figure:: https://bitbucket.org/pysph/pysph/raw/master/docs/Images/rings-collision.png
+   :alt: IMAGE
+
+The auto-generated code for the example resides in the directory
+``~/.pysph/source``. A note of caution however, it's not for the faint
+hearted.
+

examples/transport_velocity/cavity.py

@@ -120,9 +120,9 @@ def create_particles(**kwargs):
 
     # set the output arrays
     fluid.set_output_arrays( ['x', 'y', 'u', 'v', 'vmag2', 'rho', 'p',
-                              'V', 'm', 'h'] )
+                              'V', 'm', 'h', 'gid'] )
 
-    solid.set_output_arrays( ['x', 'y', 'u', 'rho', 'p'] )
+    solid.set_output_arrays( ['x', 'y', 'u', 'rho', 'p', 'gid'] )
 
     return [fluid, solid]
 

pysph/__init__.py

@@ -1,3 +1,7 @@
+# See PEP 440 for more on suitable version numbers.
+__version__ = '1.0a1.dev'
+
+
 # Conditional Imports for Parallel stuff
 
 # Check for MPI

pysph/base/nnps.pxd

@@ -122,8 +122,6 @@ cdef class NNPS:
     ##########################################################################
     # Data Attributes
     ##########################################################################
-    cdef public bint warn             # Flag to warn when extending lists
-    cdef public bint trace            # Flag for timing and debugging
     cdef public list particles        # list of particle arrays
     cdef public list pa_wrappers      # list of particle array wrappers
     cdef public int narrays           # Number of particle arrays
@@ -142,6 +140,7 @@ cdef class NNPS:
     cdef public double radius_scale   # Radius scale for kernel
     cdef IntArray cell_shifts         # cell shifts
     cdef public int n_cells           # number of cells
+    cdef public bint sort_gids        # Sort neighbors by their gids.
 
     ##########################################################################
     # Member functions
@@ -155,6 +154,9 @@ cdef class NNPS:
     # assumed to be of type unsigned int and local to the NNPS object
     cpdef _bin(self, int pa_index, UIntArray indices)
 
+    cdef void _sort_neighbors(self, unsigned int* nbrs, size_t length,
+                              unsigned int *gids) nogil
+
     # compute the min and max for the particle coordinates
     cdef _compute_bounds(self)