Adding SPHFunction read requirements as a class defined function.

Each function defines it's read and write requirements separately.

source/pysph/sph/funcs/adke_funcs.pyx

@@ -85,6 +85,14 @@ cdef class ADKESmoothingUpdate(ADKEPilotRho):
         self.cl_kernel_src_file = "adke_funcs.cl"
         self.cl_kernel_function_name = "ADKESmoothingUpdate"
 
+    def set_src_dst_reads(self):
+
+        self.src_reads = []
+        self.dst_reads = []
+
+        self.src_reads.extend( ['x','y','z','m','rho'] )
+        self.dst_reads.extend( ['x','y','z','tag'] )
+
     cpdef eval(self, KernelBase kernel, DoubleArray output1,
                DoubleArray output2, DoubleArray output3):
         """ Evaluate the store the results in the output arrays """
@@ -147,12 +155,16 @@ cdef class SPHVelocityDivergence(SPHFunctionParticle):
         self.id = "vdivergence"
         self.tag = "vdivergence"
 
-        self.src_reads.extend( ['u','v','w'] )
-        self.dst_reads.extend( ['u','v','w'] )
-
         self.cl_kernel_src_file = "adke_funcs.cl"
         self.cl_kernel_function_name = "SPHVelocityDivergence"
 
+    def set_src_dst_reads(self):
+        self.src_reads = []
+        self.dst_reads = []
+
+        self.src_reads.extend( ['x','y','z','h','u','v','w','m'] )
+        self.dst_reads.extend( ['x','y','z','h','u','v','w','rho','tag'] )
+
     cdef void eval_nbr(self, size_t source_pid, size_t dest_pid,
                        KernelBase kernel, double *nr):
         """ Compute the contribution from source_pid on dest_pid.
@@ -166,7 +178,6 @@ cdef class SPHVelocityDivergence(SPHFunctionParticle):
 
 
         """
-
         cdef double ha = self.d_h.data[dest_pid]
         cdef double hb = self.s_h.data[source_pid]
 
@@ -232,6 +243,13 @@ cdef class ADKEConductionCoeffUpdate(SPHVelocityDivergence):
 
         self.cl_kernel_function_name = "ADKEConductionCoeffUpdate"
 
+    def set_src_dst_reads(self):
+        self.src_reads = []
+        self.dst_reads = []
+
+        self.src_reads.extend( ['x','y','z','h','u','v','w','m'] )
+        self.dst_reads.extend( ['x','y','z','h','u','v','w','rho','cs','tag'] )
+
     cpdef eval(self, KernelBase kernel, DoubleArray output1,
                DoubleArray output2, DoubleArray output3):
         """ Evaluate the store the results in the output arrays Note

source/pysph/sph/funcs/basic_funcs.pyx

@@ -33,6 +33,13 @@ cdef class SPH(CSPHFunctionParticle):
         self.cl_kernel_src_file = "basic_funcs.clt"
         self.cl_kernel_function_name = "SPH"
 
+    def set_src_dst_reads(self):
+        self.src_reads = []
+        self.dst_reads = []
+
+        self.src_reads.extend( ['x','y','z','h','m','rho',self.prop_name] )
+        self.dst_reads.extend( ['x','y','z','h','tag'] )
+
     cpdef setup_arrays(self):
         """ Setup the arrays required to read data from source and dest. """
 
@@ -129,6 +136,13 @@ cdef class SPHSimpleGradient(SPHFunctionParticle):
         self.cl_kernel_src_file = "basic_funcs.cl"
         self.cl_kernel_function_name = "SPHSimpleGradient"
 
+    def set_src_dst_reads(self):
+        self.src_reads = []
+        self.dst_reads = []
+
+        self.src_reads.extend( ['x','y','z','h','m','rho',self.prop_name] )
+        self.dst_reads.extend( ['x','y','z','h','tag'] )
+
     cpdef setup_arrays(self):
         """ Setup the arrays required to read data from source and dest. """
 
@@ -138,9 +152,6 @@ cdef class SPHSimpleGradient(SPHFunctionParticle):
         self.d_prop = self.dest.get_carray(self.prop_name)
         self.s_prop = self.source.get_carray(self.prop_name)
 
-        self.src_reads.append(self.prop_name)
-        self.dst_reads.append(self.prop_name)
-
     cdef void eval_nbr(self, size_t source_pid, size_t dest_pid,
                        KernelBase kernel, double *nr):
         """ 
@@ -227,6 +238,13 @@ cdef class SPHGradient(SPHFunctionParticle):
         self.cl_kernel_src_file = "basic_funcs.cl"
         self.cl_kernel_function_name = "SPHGradient"
 
+    def set_src_dst_reads(self):
+        self.src_reads = []
+        self.dst_reads = []
+
+        self.src_reads.extend( ['x','y','z','h','m','rho',self.prop_name] )
+        self.dst_reads.extend( ['x','y','z','h','tag'] )
+
     cpdef setup_arrays(self):
         """ Setup the arrays required to read data from source and dest. """
 
@@ -236,9 +254,6 @@ cdef class SPHGradient(SPHFunctionParticle):
         self.d_prop = self.dest.get_carray(self.prop_name)
         self.s_prop = self.source.get_carray(self.prop_name)
 
-        self.src_reads.append(self.prop_name)
-        self.dst_reads.append(self.prop_name)
-
     cdef void eval_nbr(self, size_t source_pid, size_t dest_pid, 
                        KernelBase kernel, double *nr):
         """ Perform an SPH interpolation of the property `prop_name` 
@@ -323,6 +338,13 @@ cdef class SPHLaplacian(SPHFunctionParticle):
         self.cl_kernel_src_file = "basic_funcs.cl"
         self.cl_kernel_function_name = "SPHLaplacian"
 
+    def set_src_dst_reads(self):
+        self.src_reads = []
+        self.dst_reads = []
+
+        self.src_reads.extend( ['x','y','z','h','m','rho',self.prop_name] )
+        self.dst_reads.extend( ['x','y','z','h','tag',self.prop_name] )        
+
     cpdef setup_arrays(self):
         """ Setup the arrays required to read data from source and dest. """
 
@@ -331,9 +353,6 @@ cdef class SPHLaplacian(SPHFunctionParticle):
         self.s_prop = self.source.get_carray(self.prop_name)
         self.d_prop = self.dest.get_carray(self.prop_name)
 
-        self.src_reads.append(self.prop_name)
-        self.dst_reads.append(self.prop_name)
-
     cdef void eval_nbr(self, size_t source_pid, size_t dest_pid, 
                        KernelBase kernel, double *nr):
         """ 
@@ -411,6 +430,9 @@ cdef class CountNeighbors(SPHFunctionParticle):
         SPHFunctionParticle.__init__(self, source, dest, setup_arrays = True)
         self.id = 'nbrs'
 
+    def set_src_dst_reads(self):
+        pass
+
     cdef void eval_single(self, size_t dest_pid,
                           KernelBase kernel, double *result):
         result[0] += self.nbr_locator.get_nearest_particles(dest_pid).length

source/pysph/sph/funcs/boundary_funcs.pyx

@@ -40,8 +40,17 @@ cdef class MonaghanBoundaryForce(SPHFunctionParticle):
         self.s_ny = self.source.get_carray("ny")
         self.s_nz = self.source.get_carray("nz")
 
+
+
+    def set_src_dst_reads(self):
+        self.src_reads = []
+        self.dst_reads = []
+
+        self.src_reads.extend( ['x','y','z','h','m','rho'] )
         self.src_reads.extend( ['tx','ty','tz','nx','ny','nz','cs'] )
 
+        self.dst_reads.extend( ['x','y','z','h','m','cs','tag'] )
+
     cdef void eval_nbr(self, size_t source_pid, size_t dest_pid, 
                        KernelBase kernel, double *nr):
         """ Perform the boundary force computation """
@@ -61,10 +70,12 @@ cdef class MonaghanBoundaryForce(SPHFunctionParticle):
         self._dst.y = self.d_y.data[dest_pid]
         self._dst.z = self.d_z.data[dest_pid]
 
-        cdef cPoint norm = cPoint(self.s_nx.data[source_pid], self.s_ny.data[source_pid],
+        cdef cPoint norm = cPoint(self.s_nx.data[source_pid],
+                                  self.s_ny.data[source_pid],
                                   self.s_nz.data[source_pid])
 
-        cdef cPoint tang = cPoint(self.s_tx.data[source_pid], self.s_ty.data[source_pid],
+        cdef cPoint tang = cPoint(self.s_tx.data[source_pid],
+                                  self.s_ty.data[source_pid],
                                   self.s_tz.data[source_pid])
 
         cs = self.d_cs.data[dest_pid]
@@ -125,6 +136,9 @@ cdef class BeckerBoundaryForce(SPHFunctionParticle):
         self.cl_kernel_src_file = "boundary_funcs.cl"
         self.cl_kernel_function_name = "BeckerBoundaryForce"
 
+    def set_src_dst_reads(self):
+        pass
+
     cdef void eval_nbr(self, size_t source_pid, size_t dest_pid, 
                        KernelBase kernel, double *nr):
         """
@@ -213,6 +227,9 @@ cdef class LennardJonesForce(SPHFunctionParticle):
         self.cl_kernel_src_file = "boundary_funcs.cl"
         self.cl_kernel_function_name = "LennardJonesForce"
 
+    def set_src_dst_reads(self):
+        pass
+
     cdef void eval_nbr(self, size_t source_pid, size_t dest_pid, 
                        KernelBase kernel, double *nr):
         """

source/pysph/sph/funcs/density_funcs.pyx

@@ -27,6 +27,13 @@ cdef class SPHRho(CSPHFunctionParticle):
         self.cl_kernel_src_file = "density_funcs.clt"
         self.cl_kernel_function_name = "SPHRho"
 
+    def set_src_dst_reads(self):
+        self.src_reads = []
+        self.dst_reads = []
+
+        self.src_reads.extend( ['x','y','z','h','m'] )
+        self.dst_reads.extend( ['x','y','z','h','tag'] )
+
     cdef void eval_nbr_csph(self, size_t source_pid, size_t dest_pid,
                             KernelBase kernel, double *nr, double *dnr):
         """ Compute the contribution from source_pid on dest_pid. """
@@ -89,12 +96,19 @@ cdef class SPHDensityRate(SPHFunctionParticle):
         self.id = 'densityrate'
         self.tag = "density"
 
-        self.src_reads.extend( ['u','v','w'] )
-        self.dst_reads.extend( ['u','v','w'] )
-
         self.cl_kernel_src_file = "density_funcs.cl"
         self.cl_kernel_function_name = "SPHDensityRate"
 
+    def set_src_dst_reads(self):
+        self.src_reads = []
+        self.dst_reads = []
+
+        self.src_reads.extend( ['x','y','z','h','m'] )
+        self.dst_reads.extend( ['x','y','z','h','tag'] )
+
+        self.src_reads.extend( ['u','v','w'] )
+        self.dst_reads.extend( ['u','v','w'] )
+
     cdef void eval_nbr(self, size_t source_pid, size_t dest_pid, 
                        KernelBase kernel, double *nr):
         """ Compute the contribution of particle at source_pid on particle at

source/pysph/sph/funcs/energy_funcs.pyx

@@ -19,11 +19,18 @@ cdef class EnergyEquationNoVisc(SPHFunctionParticle):
         self.id = 'energyeqn'
         self.tag = "energy"
 
-        self.src_reads.extend( ['u','v','w','p'] )
-        self.dst_reads.extend( ['u','v','w','p'] )
-
         self.cl_kernel_src_file = "energy_funcs.cl"
         self.cl_kernel_function_name = "EnergyEquationNoVisc"
+
+    def set_src_dst_reads(self):
+        self.src_reads = []
+        self.dst_reads = []
+
+        self.src_reads.extend( ['x','y','z','h','m','rho'] )
+        self.dst_reads.extend( ['x','y','z','h','rho','tag'] )
+
+        self.src_reads.extend( ['u','v','w','p'] )
+        self.dst_reads.extend( ['u','v','w','p'] )
 
     cdef void eval_nbr(self, size_t source_pid, size_t dest_pid, 
                        KernelBase kernel, double *nr):
@@ -107,11 +114,18 @@ cdef class EnergyEquationAVisc(SPHFunctionParticle):
         self.id = 'energyavisc'
         self.tag = "energy"
 
-        self.src_reads.extend( ['u','v','w','p','cs'] )
-        self.dst_reads.extend( ['u','v','w','p','cs'] )
-
         self.cl_kernel_src_file = "energy_funcs.cl"
         self.cl_kernel_function_name = "EnergyEquationAVisc"
+
+    def set_src_dst_reads(self):
+        self.src_reads = []
+        self.dst_reads = []
+
+        self.src_reads.extend( ['x','y','z','h','m','rho'] )
+        self.dst_reads.extend( ['x','y','z','h','rho','tag'] )
+
+        self.src_reads.extend( ['u','v','w','p','cs'] )
+        self.dst_reads.extend( ['u','v','w','p','cs'] )
 
     cdef void eval_nbr(self, size_t source_pid, size_t dest_pid, 
                        KernelBase kernel, double *nr):
@@ -222,15 +236,21 @@ cdef class EnergyEquation(SPHFunctionParticle):
         self.id = 'energyequation'
         self.tag = "energy"
 
-        self.src_reads.extend( ['u','v','w','p','cs'] )
-        self.dst_reads.extend( ['u','v','w','p','cs'] )
-
         self.cl_kernel_src_file = "energy_funcs.cl"
         self.cl_kernel_function_name = "EnergyEquation"
+
+    def set_src_dst_reads(self):
+        self.src_reads = []
+        self.dst_reads = []
+
+        self.src_reads.extend( ['x','y','z','h','m','rho'] )
+        self.dst_reads.extend( ['x','y','z','h','rho','tag'] )
+
+        self.src_reads.extend( ['u','v','w','p','cs'] )
+        self.dst_reads.extend( ['u','v','w','p','cs'] )        
 
     cdef void eval_nbr(self, size_t source_pid, size_t dest_pid, 
-                       KernelBase kernel, double *nr):
-
+                       KernelBase kernel, double *nr):    
 
         cdef cPoint vab, rab
         cdef double Pa, Pb, rhoa, rhob, rhoab, mb

source/pysph/sph/funcs/eos_funcs.pyx

@@ -20,14 +20,17 @@ cdef class IdealGasEquation(SPHFunction):
         self.id = 'idealgas'
         self.tag = "state"
 
-        self.dst_reads.extend( ['e','rho', 'p'] )
-
         self.cl_kernel_src_file = "eos_funcs.cl"
 
+    def set_src_dst_reads(self):
+        self.src_reads = []
+        self.dst_reads = []
+
+        self.dst_reads.extend( ['e','rho'] )
+
     cdef void eval_single(self, size_t dest_pid, KernelBase kernel,
                           double* result):
 
-        cdef double Pa = self.d_p.data[dest_pid]
         cdef double ea = self.d_e.data[dest_pid]
         cdef double rhoa = self.d_rho.data[dest_pid]
         cdef double gamma = self.gamma
@@ -75,10 +78,14 @@ cdef class TaitEquation(SPHFunction):
         self.id = 'tait'
         self.tag = "state"
 
-        self.dst_reads.append('rho')
-
         self.cl_kernel_src_file = "eos_funcs.cl"
 
+    def set_src_dst_reads(self):
+        self.src_reads = []
+        self.dst_reads = []
+
+        self.dst_reads.extend( ['rho'] )
+
     cdef void eval_single(self, size_t dest_pid, KernelBase kernel,
                           double* result):
 

source/pysph/sph/funcs/external_force.clt

@@ -28,7 +28,7 @@ __kernel void NBodyForce(%(kernel_args)s)
 
     // The term `dest_id` will be suitably defined at this point.
 
-    REAL4 pa = (REAL4)( d_x[dest_id],d_y[dest_id], d_z[dest_id], d_h[dest_id] );
+    REAL4 pa = (REAL4)( d_x[dest_id],d_y[dest_id], d_z[dest_id], 0.0F );
     REAL4 rba;
     REAL invr, force_mag;
 
@@ -37,7 +37,7 @@ __kernel void NBodyForce(%(kernel_args)s)
         // SPH innermost loop code goes here.  The index `src_id` will
         // be available and looped over, this index.
 
-        REAL4 pb = (REAL4)( s_x[src_id],s_y[src_id],s_z[src_id],s_h[src_id] );
+        REAL4 pb = (REAL4)( s_x[src_id],s_y[src_id],s_z[src_id], 0.0F );
         rba = pb - pa;
 
         invr = 1.0F/( length(rba) + eps );