removed _tmpx,_tmpy,_tmpz properties and added appropriate num_output…

…s to funcs

stepping,gradient functions now only set the appropriate dimension properties instead of all 3
*Reverted* pickling of particle_array to pickle all properties since it broke parallel runs (elliptical_drop)

Makefile

@@ -73,10 +73,10 @@ epydoc :
 doc :
 	cd docs; make html
 
-develop : $(DIRS)
+develop :
 	python setup.py develop
 
-install : $(DIRS)
+install :
 	python setup.py install
 
 clang :

source/pysph/base/particle_array.pyx

@@ -202,13 +202,12 @@ cdef class ParticleArray:
         default_values = {}
 
         for prop, arr in self.properties.iteritems():
-            if not prop.startswith('_'):
-                pinfo = {}
-                pinfo['name'] = prop            
-                pinfo['type'] = arr.get_c_type()
-                pinfo['data'] = arr.get_npy_array()
-                pinfo['default'] = self.default_values[prop]
-                props[prop] = pinfo
+            pinfo = {}
+            pinfo['name'] = prop            
+            pinfo['type'] = arr.get_c_type()
+            pinfo['data'] = arr.get_npy_array()
+            pinfo['default'] = self.default_values[prop]
+            props[prop] = pinfo
 
         d['properties'] = props
 

source/pysph/base/particles.py

@@ -312,8 +312,7 @@ def get_particle_array(cl_precision="double", **props):
 
     default_props = {'x':0.0, 'y':0.0, 'z':0.0, 'u':0.0, 'v':0.0 ,
                      'w':0.0, 'm':1.0, 'h':1.0, 'p':0.0,'e':0.0,
-                     'rho':1.0, 'cs':0.0, '_tmpx':0.0,
-                     '_tmpy':0.0, '_tmpz':0.0}
+                     'rho':1.0, 'cs':0.0}
 
     #Add the properties requested
 

source/pysph/parallel/tests/test_particle_array_pickling.py → source/pysph/parallel/tests/particle_array_pickling.py

@@ -32,9 +32,6 @@
     # make sure the sending data defines the underscored variables
     assert pa.properties.has_key('_rho')
     assert pa.properties.has_key('_p')
-    assert pa.properties.has_key('_tmpx')
-    assert pa.properties.has_key('_tmpy')
-    assert pa.properties.has_key('_tmpz')
 
     comm.send(obj=pa, dest=1)
 
@@ -45,9 +42,6 @@
     # make sure that the underscored variables are not there
     assert not pa2.properties.has_key('_rho')
     assert not pa2.properties.has_key('_p')
-    assert not pa2.properties.has_key('_tmpx')
-    assert not pa2.properties.has_key('_tmpy')
-    assert not pa2.properties.has_key('_tmpz')
 
     # now append the received array to the local array
     pa.append_parray(pa2)

source/pysph/parallel/tests/test_parallel_runs.py

@@ -84,6 +84,10 @@ def test_parallel_cell_check3(self):
     def test_share_data(self):
         for i in range(1,6):
             run_mpi_script('share_data.py', i)
+
+    def test_particle_array_pickling(self):
+        for i in range(2,3):
+            run_mpi_script('particle_array_pickling.py', i)
 
 
 #for filename in tests:

source/pysph/solver/fluid_solver.py

@@ -75,7 +75,7 @@ def setup_solver(self):
         self.add_operation(SPHIntegration(
             sph.MomentumEquation.withargs(alpha=0.01, beta=0.0, hks=False),
             from_types=[Fluids], on_types=[Fluids], 
-            updates=['u','v'], 
+            updates=['u','v','w'], 
             id='mom')
                            )
 

source/pysph/solver/integrator.py

@@ -222,8 +222,6 @@ def __init__(self, particles=None, calcs=[], pcalcs = []):
 
         self.rupdate_list = []
 
-        self.step_props = '_tmpx', '_tmpy', '_tmpz'
-
     def set_rupdate_list(self):
         for i in range(len(self.particles.arrays)):
             self.rupdate_list.append([])

source/pysph/solver/solver.py

@@ -141,8 +141,8 @@ def add_operation_step(self, types, xsph=False, eps=0.5):
         id = 'step'
 
         self.add_operation(SPHIntegration(
-            sph.PositionStepping, on_types=types, updates=updates, id=id,
-            kernel=kernel)
+                sph.PositionStepping.withargs(dim=self.dim), on_types=types,
+                updates=updates, id=id, kernel=kernel)
                            )
 
     def add_operation_xsph(self, eps, hks=False):
@@ -171,13 +171,12 @@ def add_operation_xsph(self, eps, hks=False):
         assert self.operation_dict.has_key('step'), err
 
         types = self.operation_dict['step'].on_types
-        from_types = self.operation_dict['step'].from_types
         updates = self.operation_dict['step'].updates
 
 
         self.add_operation(SPHIntegration(
 
-            sph.XSPHCorrection.withargs(eps=eps, hks=hks), from_types=from_types,
+            sph.XSPHCorrection.withargs(eps=eps, hks=hks, dim=self.dim), from_types=types,
             on_types=types, updates=updates, id=id, kernel=self.default_kernel)
 
                            )        

source/pysph/sph/funcs/adke_funcs.pyx

@@ -27,6 +27,7 @@ cdef class ADKEPilotRho(CSPHFunctionParticle):
 
         self.cl_kernel_src_file = "adke_funcs.cl"
         self.cl_kernel_function_name = "ADKEPilotRho"
+        self.num_outputs = 1
 
     def set_src_dst_reads(self):
 
@@ -94,6 +95,7 @@ cdef class ADKESmoothingUpdate(SPHFunction):
 
         self.cl_kernel_src_file = "adke_funcs.cl"
         self.cl_kernel_function_name = "ADKESmoothingUpdate"
+        self.num_outputs = 1
 
     cpdef setup_arrays(self):
         """
@@ -237,6 +239,7 @@ cdef class ADKEConductionCoeffUpdate(SPHFunction):
         self.cl_kernel_src_file = "adke_funcs.cl"
 
         self.cl_kernel_function_name = "ADKEConductionCoeffUpdate"
+        self.num_outputs = 1
 
     def set_src_dst_reads(self):
         self.src_reads = []

source/pysph/sph/funcs/arithmetic_funcs.pxd

@@ -9,13 +9,15 @@ cdef class PropertyGet(SPHFunction):
 cdef class PropertyAdd(SPHFunction):
     cdef list prop_names, d_props
     cdef int num_props
+    cdef public double constant
 
 cdef class PropertyNeg(SPHFunction):
     cdef list prop_names, d_props
 
 cdef class PropertyMul(SPHFunction):
     cdef list prop_names, d_props
     cdef int num_props
+    cdef public double constant
 
 cdef class PropertyInv(SPHFunction):
     cdef list prop_names, d_props

source/pysph/sph/funcs/arithmetic_funcs.pyx

@@ -37,16 +37,18 @@ cdef class PropertyGet(SPHFunction):
 cdef class PropertyAdd(SPHFunction):
     """ function to add property arrays (any number of arrays) """
     def __init__(self, ParticleArray source, ParticleArray dest=None,
-                 prop_names=['rho'], **kwargs):
+                 prop_names=['rho'], constant=0.0, **kwargs):
         """ Constructor for SPH
 
         Parameters:
         -----------
         source -- The source particle array
         dest -- The destination particle array
         prop_names -- The properties to get the sum of
+        constant -- a constant value to add to the result
         """
         self.prop_names = prop_names
+        self.constant = constant
         SPHFunction.__init__(self, source, dest, setup_arrays=True)
         self.num_outputs = 1
         self.id = 'property_add'
@@ -55,7 +57,7 @@ cdef class PropertyAdd(SPHFunction):
         #Setup the basic properties like m, x rho etc.
         SPHFunction.setup_arrays(self)
         self.d_props = [self.dest.get_carray(i) for i in self.prop_names]
-        self.num_props = len(self.prop_names)
+        self.num_props = len(self.d_props)
 
     cpdef eval(self, KernelBase kernel, DoubleArray output1,
                DoubleArray output2, DoubleArray output3):
@@ -67,7 +69,7 @@ cdef class PropertyAdd(SPHFunction):
         for n in range(1, self.num_props):
             arr = self.d_props[n]
             for i in range(np):
-                output1.data[i] += arr.data[i]
+                output1.data[i] += arr.data[i] + self.constant
 
 cdef class PropertyNeg(SPHFunction):
     """ function to return the negative of upto 3 particle arrays """
@@ -105,16 +107,18 @@ cdef class PropertyNeg(SPHFunction):
 cdef class PropertyMul(SPHFunction):
     """ function to get product of property arrays (any number of arrays) """
     def __init__(self, ParticleArray source, ParticleArray dest=None,
-                 prop_names=['rho'], **kwargs):
+                 prop_names=['rho'], constant=0.0, **kwargs):
         """ Constructor for SPH
 
         Parameters:
         -----------
         source -- The source particle array.
         dest -- The destination particle array.
         prop_names -- The properties to get product of
+        constant -- a constant value to multiply to the result
         """
         self.prop_names = prop_names
+        self.constant = constant
         SPHFunction.__init__(self, source, dest, setup_arrays=True)
         self.num_outputs = 1
         self.id = 'property_mul'
@@ -123,7 +127,7 @@ cdef class PropertyMul(SPHFunction):
         #Setup the basic properties like m, x rho etc.
         SPHFunction.setup_arrays(self)
         self.d_props = [self.dest.get_carray(i) for i in self.prop_names]
-        self.num_props = len(self.prop_names)
+        self.num_props = len(self.d_props)
 
     cpdef eval(self, KernelBase kernel, DoubleArray output1,
                DoubleArray output2, DoubleArray output3):
@@ -135,7 +139,7 @@ cdef class PropertyMul(SPHFunction):
         for n in range(1, self.num_props):
             arr = self.d_props[n]
             for i in range(np):
-                output1.data[i] *= arr.data[i]
+                output1.data[i] *= arr.data[i] * self.constant
 
 cdef class PropertyInv(SPHFunction):
     """ function to return the inverse of upto 3 particle arrays """

source/pysph/sph/funcs/basic_funcs.pyx

@@ -32,6 +32,7 @@ cdef class SPH(CSPHFunctionParticle):
 
         self.cl_kernel_src_file = "basic_funcs.clt"
         self.cl_kernel_function_name = "SPH"
+        self.num_outputs = 1
 
     def set_src_dst_reads(self):
         self.src_reads = []
@@ -337,6 +338,7 @@ cdef class SPHLaplacian(SPHFunctionParticle):
 
         self.cl_kernel_src_file = "basic_funcs.cl"
         self.cl_kernel_function_name = "SPHLaplacian"
+        self.num_outputs = 1
 
     def set_src_dst_reads(self):
         self.src_reads = []

source/pysph/sph/funcs/density_funcs.pyx

@@ -26,6 +26,7 @@ cdef class SPHRho(CSPHFunctionParticle):
 
         self.cl_kernel_src_file = "density_funcs.clt"
         self.cl_kernel_function_name = "SPHRho"
+        self.num_outputs = 1
 
     def set_src_dst_reads(self):
         self.src_reads = []
@@ -98,6 +99,7 @@ cdef class SPHDensityRate(SPHFunctionParticle):
 
         self.cl_kernel_src_file = "density_funcs.cl"
         self.cl_kernel_function_name = "SPHDensityRate"
+        self.num_outputs = 1
 
     def set_src_dst_reads(self):
         self.src_reads = []

source/pysph/sph/funcs/energy_funcs.pyx

@@ -23,6 +23,7 @@ cdef class EnergyEquationNoVisc(SPHFunctionParticle):
 
         self.cl_kernel_src_file = "energy_funcs.cl"
         self.cl_kernel_function_name = "EnergyEquationNoVisc"
+        self.num_outputs = 1
 
     def set_src_dst_reads(self):
         self.src_reads = []
@@ -128,6 +129,7 @@ cdef class EnergyEquationAVisc(SPHFunctionParticle):
 
         self.cl_kernel_src_file = "energy_funcs.cl"
         self.cl_kernel_function_name = "EnergyEquationAVisc"
+        self.num_outputs = 1
 
     def set_src_dst_reads(self):
         self.src_reads = []
@@ -251,6 +253,7 @@ cdef class EnergyEquation(SPHFunctionParticle):
 
         self.cl_kernel_src_file = "energy_funcs.cl"
         self.cl_kernel_function_name = "EnergyEquationWithVisc"
+        self.num_outputs = 1
 
     def set_src_dst_reads(self):
         self.src_reads = []
@@ -400,6 +403,7 @@ cdef class ArtificialHeat(SPHFunctionParticle):
 
         self.cl_kernel_src_file = "energy_funcs.cl"
         self.cl_kernel_function_name = "ArtificialHeat"
+        self.num_outputs = 1
 
     def set_src_dst_reads(self):
         self.src_reads = ['x','y','z','h','m','rho','e,','u','v','w','cs','q']

source/pysph/sph/funcs/eos_funcs.pyx

@@ -24,6 +24,7 @@ cdef class IdealGasEquation(SPHFunction):
 
         self.cl_kernel_src_file = "eos_funcs.cl"
         self.cl_kernel_function_name = "IdealGasEquation"
+        self.num_outputs = 2
 
     def set_src_dst_reads(self):
         self.src_reads = []
@@ -93,6 +94,7 @@ cdef class TaitEquation(SPHFunction):
         self.tag = "state"
 
         self.cl_kernel_src_file = "eos_funcs.cl"
+        self.num_outputs = 2
 
     def set_src_dst_reads(self):
         self.src_reads = []

source/pysph/sph/funcs/external_force.pyx

@@ -109,6 +109,7 @@ cdef class MoveCircleX(SPHFunction):
 
         self.id = 'circlex'
         self.tag = "position"
+        self.num_outputs = 2
 
     def set_src_dst_reads(self):
         pass        
@@ -144,6 +145,7 @@ cdef class MoveCircleY(SPHFunction):
 
         self.id = 'circley'
         self.tag = "position"
+        self.num_outputs = 2
 
     def set_src_dst_reads(self):
         pass        

source/pysph/sph/funcs/position_funcs.pyx

@@ -12,7 +12,7 @@ cdef class PositionStepping(SPHFunction):
 
     #Defined in the .pxd file
     def __init__(self, ParticleArray source, ParticleArray dest, 
-                 bint setup_arrays=True):
+                 bint setup_arrays=True, int dim=3):
 
         SPHFunction.__init__(self, source, dest, setup_arrays)
 
@@ -21,12 +21,13 @@ cdef class PositionStepping(SPHFunction):
 
         self.cl_kernel_src_file = "position_funcs.clt"
         self.cl_kernel_function_name = "PositionStepping"
+        self.num_outputs = dim
 
     def set_src_dst_reads(self):
         self.src_reads = []
         self.dst_reads = []
 
-        self.dst_reads.extend( ['u','v','w'] )        
+        self.dst_reads.extend( ['u','v','w'][:self.num_outputs] )
 
     cpdef eval(self, KernelBase kernel, DoubleArray output1,
                DoubleArray output2, DoubleArray output3):
@@ -35,14 +36,29 @@ cdef class PositionStepping(SPHFunction):
 
         self.setup_iter_data()
         cdef size_t np = self.dest.get_number_of_particles()
-
-        for i in range(np):
-            if tag_arr.data[i] == LocalReal:
-                output1[i] = self.d_u.data[i]
-                output2[i] = self.d_v.data[i]
-                output3[i] = self.d_w.data[i]
-            else:
-                output1[i] = output2[i] = output3[i] = 0
+
+        if self.num_outputs == 3:
+            for i in range(np):
+                if tag_arr.data[i] == LocalReal:
+                    output1.data[i] += self.d_u.data[i]
+                    output2.data[i] += self.d_v.data[i]
+                    output3.data[i] += self.d_w.data[i]
+                else:
+                    output1.data[i] = output2.data[i] = output3.data[i] = 0
+        elif self.num_outputs == 2:
+            for i in range(np):
+                if tag_arr.data[i] == LocalReal:
+                    output1.data[i] += self.d_u.data[i]
+                    output2.data[i] += self.d_v.data[i]
+                else:
+                    output1.data[i] = output2.data[i] = 0
+        elif self.num_outputs == 1:
+            for i in range(np):
+                if tag_arr.data[i] == LocalReal:
+                    output1.data[i] += self.d_u.data[i]
+                else:
+                    output1.data[i] = 0
+
 
     def _set_extra_cl_args(self):
         pass