This document puts together all the essential information on how to write equations. We assume that you have already read the section The PySPH framework. Some information is repeated from there as well.
The PySPH equations are written in a very restricted way. The reason for this is that if you do follow the suggestions and the conventions below you will benefit from:
- a high-performance serial implementation.
- support for using your equations with OpenMP.
- support for running on a GPU.
These are the main motivations for the severe restrictions we impose when you write your equations.
PySPH takes the equations you write and converts them on the fly to a high-performance implementation suitable for the particular backend you request.
It is important to understand the overall structure of how the equations are
used when the high-performance code is generated. Let us look at the different
methods of a typical
class YourEquation(Equation): def __init__(self, dest, sources): # Overload this only if you need to pass additional constants # Otherwise, no need to override __init__ def py_initialize(self, dst, t, dt): # Called once per destination array before initialize. # This is a pure Python function and is not translated. def initialize(self, d_idx, ...): # Called once per destination particle before loop. def initialize_pair(self, d_idx, d_*, s_*): # Called once per destination particle for each source. # Can access all source arrays. Does not have # access to neighbor information. def loop_all(self, d_idx, ..., NBRS, N_NBRS, ...): # Called once before the loop and can be used # for non-pairwise interactions as one can pass the neighbors # for particle d_idx. def loop(self, d_idx, s_idx, ...): # loop over neighbors for all sources, # called once for each pair of particles! def post_loop(self, d_idx ...): # called after all looping is done. def reduce(self, dst, t, dt): # Called once for the destination array. # Any Python code can go here. def converged(self): # return > 0 for convergence < 0 for lack of convergence
It is easier to understand this if we take a specific example. Let us say, we
have a case where we have two particle arrays
'fluid', 'solid'. Let us say
the equation is used as
'solid']). Now given this context, let us see what happens when this
equation is used. What happens is as follows:
- for each destination particle array (
'fluid'in this case), the
py_initializemethod is called and is passed the destination particle array,
reduce). This function is a pure Python function so you can do what you want here, including importing any Python code and run anything you want. The code is NOT transpiled into C/OpenCL/CUDA.
- for each fluid particle, the
initializemethod is called with the required arrays.
- for each fluid particle, the
initialize_pairmethod is called while having access to all the fluid arrays.
- the fluid neighbors for each fluid particle are found for each particle
and can be passed en-masse to the
loop_allmethod. One can pass
NBRSwhich is an array of unsigned ints with indices to the neighbors in the source particles.
N_NBRSis the number of neighbors (an integer). This method is ideal for any non-pairwise computations or more complex computations.
- the fluid neighbors for each fluid particle are found and for each pair,
loopmethod is called with the required properties/values.
- for each fluid particle, the
initialize_pairmethod is called while having access to all the solid arrays.
- the solid neighbors for each fluid particle are found and for each pair,
loopmethod is called with the required properties/values.
- for each fluid particle, the
post_loopmethod is called with the required properties.
- If a reduce method exists, it is called for the destination (only once, not once per particle). It is passed the destination particle array and the time and timestep. It is transpiled when you are using Cython but is a pure Python function when you run this via OpenCL or CUDA.
initialize, initialize_pair, loop_all, loop, post_loop methods all may
be called in separate threads (both on CPU/GPU) depending on the
implementation of the backend.
It is possible to set a scalar value in the equation as an instance attribute,
i.e. by setting
self.something = value but remember that this is just one
value for the equation. This value must also be initialized in the
__init__ method. Also make sure that the attributes are public and not
private (i.e. do not start with an underscore). There is only one equation
instance used in the code, not one equation per thread or particle. So if you
wish to calculate a temporary quantity for each particle, you should create a
separate property for it and use that instead of assuming that the initialize
and loop functions run in serial. They do not run in serial when you use
OpenMP or OpenCL. So do not create temporary arrays inside the equation for
these sort of things. In general if you need a constant per destination array,
add it as a constant to the particle array. Also note that you can add
properties that have strides (see Learning the ropes and look for
Now, if the group containing the equation has
iterate set to True, then
the group will be iterated until convergence is attained for all the equations
(or sub-groups) contained by it. The
converged method is called once and
not once per particle.
If you wish to compute something like a convergence condition, like the maximum error or the average error, you should do it in the reduce method.
The reduce function is called only once every time the accelerations are
evaluated. As such you may write any Python code there. The only caveat is
that when using the CPU, one will have to declare any variables used a little
carefully – ideally declare any variables used in this as
declare('object'). On the GPU, this function is not called via OpenCL and
is a pure Python function.
Understanding Groups a bit more¶
Equations can be grouped together and it is important to understand how
exactly this works. Let us take a simple example of a
two equations. We illustrate two simple equations with pseudo-code:
class Eq1(Equation): def initialize(self, ...): # ... def loop(...): # ... def post_loop(...): # ...
Let us say that
Eq2 has a similar structure with respect to its methods.
Let us say we have a group defined as:
Group( equations=[ Eq1(dest='fluid', sources=['fluid', 'solid']), Eq2(dest='fluid', sources=['fluid', 'solid']), ] )
When this is expanded out and used inside PySPH, this is what happens in terms of pseudo-code:
# Instances of the Eq1, and Eq2. eq1 = Eq1(...) eq2 = Eq2(...) for d_idx in range(n_destinations): eq1.initialize(...) eq2.initialize(...) # Sources from 'fluid' for d_idx in range(n_destinations): for s_idx in NEIGHBORS('fluid', d_idx): eq1.loop(...) eq2.loop(...) # Sources from 'solid' for d_idx in range(n_destinations): for s_idx in NEIGHBORS('solid', d_idx): eq1.loop(...) eq2.loop(...) for d_idx in range(n_destinations): eq1.post_loop(...) eq2.post_loop(...)
That is, all the initialization is done for each equation in sequence,
followed by the loops for each set of sources, fluid and solid in this case.
In the end, the
post_loop is called for the destinations. The equations
are therefore merged inside a group and entirely completed before the next
group is taken up. Note that the order of the equations will be exactly as
specified in the group.
real=False is used, then the non-local destination particles
are also iterated over.
real=True by default, which means that only
destination particles whose
tag property is local or equal to 0 are
operated on. Otherwise, when
real=False, remote and ghost particles are
also operated on. It is important to note that this does not affect the source
particles. That is, ALL source particles influence the destinations
whether the sources are local, remote or ghost particles. The
argument only affects the destination particles and not the sources.
Note that if you have different destinations in the same group, they are
internally split up into different sets of loops for each destination and that
these are done separately. I.e. one destination is fully processed and then
the next is considered. So if we had for example, both
destinations, they would be processed separately. For example lets say you had
Group( equations=[ Eq1(dest='fluid', sources=['fluid', 'solid']), Eq1(dest='solid', sources=['fluid', 'solid']), Eq2(dest='fluid', sources=['fluid', 'solid']), Eq2(dest='solid', sources=['fluid', 'solid']), ] )
This would internally be equivalent to the following:
[ Group( equations=[ Eq1(dest='fluid', sources=['fluid', 'solid']), Eq2(dest='fluid', sources=['fluid', 'solid']), ] ), Group( equations=[ Eq1(dest='solid', sources=['fluid', 'solid']), Eq2(dest='solid', sources=['fluid', 'solid']), ] ) ]
Note that basically the fluids are done first and then the solid particles are done. Obviously the first form is a lot more compact.
While it may appear that the PySPH equations and groups are fairly complex, they actually do a lot of work for you and allow you to express the interactions in a rather compact form.
When debugging it sometimes helps to look at the generated log file which will also print out the exact equations and groups that are being used.
There are a few important conventions that are to be followed when writing the
equations. When passing arguments to the
initialize, loop, post_loop
d_*indicates a destination array.
s_*indicates a source array.
s_idxrepresent the destination and source index respectively.
- Each function can take any number of arguments as required, these are automatically supplied internally when the application runs.
- All the standard math symbols from
math.hare also available.
The following precomputed quantites are available and may be passed into any equation:
HIJ = 0.5*(d_h[d_idx] + s_h[s_idx]).
XIJ = d_x[d_idx] - s_x[s_idx],
XIJ = d_y[d_idx] - s_y[s_idx],
XIJ = d_z[d_idx] - s_z[s_idx]
R2IJ = XIJ*XIJ + XIJ*XIJ + XIJ*XIJ
RIJ = sqrt(R2IJ)
WIJ = KERNEL(XIJ, RIJ, HIJ)
WJ = KERNEL(XIJ, RIJ, s_h[s_idx])
RHOIJ = 0.5*(d_rho[d_idx] + s_rho[s_idx])
WI = KERNEL(XIJ, RIJ, d_h[d_idx])
RHOIJ1 = 1.0/RHOIJ
GRADIENT(XIJ, RIJ, HIJ, DWIJ)
GRADIENT(XIJ, RIJ, s_h[s_idx], DWJ)
GRADIENT(XIJ, RIJ, d_h[d_idx], DWI)
VIJ = d_u[d_idx] - s_u[s_idx]
VIJ = d_v[d_idx] - s_v[s_idx]
VIJ = d_w[d_idx] - s_w[s_idx]
EPS = 0.01 * HIJ * HIJ
SPH_KERNEL: the kernel being used and one can call the kernel as
SPH_KERNEL.kernel(xij, rij, h)the gradient as
SPH_KERNEL.gradient_h(...)etc. The kernel is any one of the instances of the kernel classes defined in
In addition if one requires the current time or the timestep in an equation, the following may be passed into any of the methods of an equation:
t: is the current time.
dt: the current time step.
loop_all method and the
loop method, one may also pass the
NBRS: an array of unsigned ints with neighbor indices.
N_NBRS: an integer denoting the number of neighbors for the current destination particle with index,
Note that all standard functions and constants in
math.h are available
for use in the equations. The value of \(\pi\) is available as
M_PI. Please avoid using functions from
numpy as these are Python
functions and are slow. They also will not allow PySPH to be run with
OpenMP. Similarly, do not use functions or constants from
other libraries inside the equation methods as these will significantly
slow down your code.
In addition, these constants from the math library are available:
M_E: value of e
M_LOG2E: value of log2e
M_LOG10E: value of log10e
M_LN2: value of loge2
M_LN10: value of loge10
M_PI: value of pi
M_PI_2: value of pi / 2
M_PI_4: value of pi / 4
M_1_PI: value of 1 / pi
M_2_PI: value of 2 / pi
M_2_SQRTPI: value of 2 / (square root of pi)
M_SQRT2: value of square root of 2
M_SQRT1_2: value of square root of 1/2
In an equation, any undeclared variables are automatically declared to be
doubles in the high-performance Cython code that is generated. In addition
one may declare a temporary variable to be a
matrix or a
vec, vec1 = declare("matrix(3)", 2) mat = declare("matrix((3,3))") i, j = declare('int')
When the Cython code is generated, this gets translated to:
cdef double vec, vec1 cdef double mat cdef int i, j
One can also declare any valid c-type using the same approach, for example if
one desires a
long data type, one may use
i = declare("long").
Note that the additional (optional) argument in the declare specifies the
number of variables. While this is ignored during transpilation, this is
useful when writing functions in pure Python, the
compyle.api.declare() function provides a pure Python
implementation of this so that the code works both when compiled as well as
when run from pure Python. For example:
i, j = declare("int", 2)
In this case, the declare function call returns two integers so that the code runs correctly in pure Python also. The second argument is optional and defaults to 1. If we defined a matrix, then this returns two NumPy arrays of the appropriate shape.
>>> declare("matrix(2)", 2) (array([ 0., 0.]), array([ 0., 0.]))
Thus the code one writes can be used in pure Python and can also be safely transpiled into other languages.
Writing the reduce method¶
One may also perform any reductions on properties. Consider a trivial example
of calculating the total mass and the maximum
u velocity in the following
class FindMaxU(Equation): def reduce(self, dst, t, dt): m = serial_reduce_array(dst.m, 'sum') max_u = serial_reduce_array(dst.u, 'max') dst.total_mass = parallel_reduce_array(m, 'sum') dst.max_u = parallel_reduce_array(u, 'max')
dst: refers to a destination
t, dt: are the current time and timestep respectively.
serial_reduce_array: is a special function provided that performs reductions correctly in serial. It currently supports
sum, prod, maxand
pysph.base.reduce_array.serial_reduce_array(). There is also a
pysph.base.reduce_array.parallel_reduce_array()which is to be used to reduce an array across processors. Using
parallel_reduce_arrayis expensive as it is an all-to-all communication. One can reduce these by using a single array and use that to reduce the communication.
We recommend that for any kind of reductions one always use the
serial_reduce_array function and the
parallel_reduce_array inside a
reduce method. One should not worry about parallel/serial modes in this
case as this is automatically taken care of by the code generator. In serial,
the parallel reduction does nothing.
With this machinery, we are able to write complex equations to solve almost any SPH problem. A user can easily define a new equation and instantiate the equation in the list of equations to be passed to the application. It is often easiest to look at the many existing equations in PySPH and learn the general patterns.
There are a couple of ways to use adaptive timesteps. The first is to compute
a required timestep directly per-particle in a particle array property called
dt_adapt. The minimum value of this array across all particle arrays is
used to set the timestep directly. This is the easiest way to set the adaptive
dt_adapt parameter is not set one may also use standard velocity,
force, and viscosity based parameters. The integrator uses information from
dt_visc in each of the particle
arrays to determine the most suitable time step. This is done using the
following approach. The minimum smoothing parameter
h is found as
hmin. Let the CFL number be given as
cfl. For the velocity criterion,
the maximum value of
dt_cfl is found and then a suitable timestep is found
dt_min_vel = hmin/max(dt_cfl)
For the force based criterion we use the following:
dt_min_force = sqrt(hmin/sqrt(max(dt_force)))
for the viscosity we have:
dt_min_visc = hmin/max(dt_visc_fac)
Then the correct timestep is found as:
dt = cfl*min(dt_min_vel, dt_min_force, dt_min_visc)
cfl is set to 0.3 by default. One may pass
--cfl to the
application to change the CFL. Note that when the
dt_adapt property is
used the CFL has no effect as we assume that the user will compute a suitable
value based on their requirements.
pysph.sph.integrator.Integrator class code may be instructive
to look at if you are wondering about any particular details.
Illustration of the
loop_all is a powerful method we show how we can use the above to
perform what the
loop method usually does ourselves.
class LoopAllEquation(Equation): def initialize(self, d_idx, d_rho): d_rho[d_idx] = 0.0 def loop_all(self, d_idx, d_x, d_y, d_z, d_rho, d_h, s_m, s_x, s_y, s_z, s_h, SPH_KERNEL, NBRS, N_NBRS): i = declare('int') s_idx = declare('long') xij = declare('matrix(3)') rij = 0.0 sum = 0.0 for i in range(N_NBRS): s_idx = NBRS[i] xij = d_x[d_idx] - s_x[s_idx] xij = d_y[d_idx] - s_y[s_idx] xij = d_z[d_idx] - s_z[s_idx] rij = sqrt(xij*xij + xij*xij + xij*xij) sum += s_m[s_idx]*SPH_KERNEL.kernel(xij, rij, 0.5*(s_h[s_idx] + d_h[d_idx])) d_rho[d_idx] += sum
This seems a bit complex but let us look at what is being done.
is called once per particle and each of their densities is set to zero. Then
loop_all is called it is called once per destination particle (unlike
loop which is called pairwise for each destination and source particle).
loop_all is passed arrays as is typical of most equations but is also
SPH_KERNEL itself, the list of neighbors, and the number of
The code first declares the variables,
i, s_idx as an integer and long,
x_ij as a 3-element array. These are important for performance in
the generated code. The code then loops over all neighbors and computes the
summation density. Notice how the kernel is computed using
SPH_KERNEL.kernel(...). Notice also how the source index,
s_idx is found
from the neighbors.
loop_all code does exactly what the following single line of
def loop(self, d_idx, d_rho, s_m, s_idx, WIJ): d_rho[d_idx] += s_m[s_idx]*WIJ
loop is only called pairwise and there are times when we want to
do more with the neighbors. For example if we wish to setup a matrix and solve
it per particle, we could do it in
loop_all efficiently. This is also very
useful for non-pairwise interactions which are common in other particle
methods like molecular dynamics.
Calling user-defined functions from equations¶
Sometimes we may want to call a user-defined function from the equations. Any pure Python function defined using the same conventions as listed above (with suitable type hints) can be called from the equations. Here is a simple example from one of the tests in PySPH.
def helper(x=1.0): return x*1.5 class SillyEquation(Equation): def initialize(self, d_idx, d_au, d_m): d_au[d_idx] += helper(d_m[d_idx]) def _get_helpers_(self): return [helper]
initialize is calling the
helper function defined above.
The helper function has a default argument to indicate to our code generation
that x is a floating point number. We could have also set the default argument
to a list and this would then be passed an array of values. The
_get_helpers_ method returns a list of functions and these functions are
automatically transpiled into high-performance C or OpenCL/CUDA code and can
be called from your equations.
Here is a more complex helper function.
def trace(x=[1.0, 1.0], nx=1): i = declare('int') result = 0.0 for i in range(nx): result += x[i] return result class SillyEquation(Equation): def loop(self, d_idx, d_au, d_m, XIJ): d_au[d_idx] += trace(XIJ, 3) def _get_helpers_(self): return [trace]
The trace function effectively is converted into a function with signature
double trace(double* x, int nx) and thus can be called with any
Calling arbitrary Python functions from a Group¶
Sometimes, you may need to implement something that is hard to write (at least
initially) with the constraints that PySPH places. For example if you need to
implement an algorithm that requires more complex data structures and you want
to do it easily in Python. There are ways to call arbitrary Python code from
the application already but sometimes you need to do this during every
acceleration evaluation. To support this the
Group class supports
two additional keyword arguments called
post. These can be any
Python callable that take no arguments. Any callable passed as
pre will be
called before any equation related code is executed and
post will be
executed after the entire group is finished. If the group is iterated, it
should call those functions repeatedly.
Now these functions are pure Python functions so you may choose to do anything in them. These are not called within an OpenMP context and if you are using the OpenCL or CUDA backends again this will simply be a Python function call that has nothing to do with the particular backend. However, since it is arbitrary Python, you can choose to implement the code using any approach you choose to do. This should be flexible enough to customize PySPH greatly.
Conditional execution of groups¶
Group takes a keyword argument called
condition which can be
any Python callable (function/method). This callable is passed the values of
t, dt. If the function returns
True then the group is executed,
otherwise it is not. This is useful in situations when you say want to run a
specific set of equations only every 20 iterations. Or you want to move an
object only at a specified time. Here is a quick pseudo-example, we define the
Group as below:
def check_time(t, dt): if int(t/dt) % 20 == 0: return True else: return False equations = [ Group( ... ), Group( equations=[ ShepardDensityFilter(dest='fluid', sources=['fluid']) ], condition=check_time ) ]
In the above pseudo-code the idea is that only when the
True will the density filter group be executed. You can also pass a method
instead of a function. The only condition is that it should accept the two
Controlling the looping over destination particles¶
Sometimes (this is pretty rare) you may want to only iterate over a subset of the particles. Usually, the iterations over the destinations are performed roughly like the following pure Python code:
for d_idx in range(n_destinations): # ...
Group class also takes a
start_idx argument which defaults
to 0 and a
stop_idx which defaults to the total number of particles. One
can pass either a number or a string with a property/constant whose first item
will be used as the number. For example you could have this:
Group( equations=[ SimpleEquation(dest='fluid', sources=['fluid']) ], start_idx=10, stop_idx=20 )
This would iterate from the index number 10 to the index number 19, i.e.
similar to using a
range(10, 20). You could also do:
Group( equations=[ SimpleEquation(dest='fluid', sources=['fluid']) ], stop_idx='n_body' )
'n_body' is a constant available in the destination particle array.
Another instance where this could be useful is when you want to run an
equation only on the ghost particles, i.e. when
real is False. In this
case, let us say there are 5000 real particles, we could simply pass
start_idx=5000, real=False and it will only iterate over the non-real
Similar rules apply when writing an
IntegratorStep. One can create
a multi-stage integrator as follows:
class MyStepper(IntegratorStep): def initialize(self, d_idx, d_x): # ... def py_stage1(self, dst, t, dt): # ... def stage1(self, d_idx, d_x, d_ax): # ... def py_stage2(self, dst, t, dt): # ... def stage2(self, d_idx, d_x, d_ax): # ...
In this case, the
initialize, stage1, stage2, methods are transpiled and
called but the
py_stage1, py_stage2 are pure Python functions called
before the respective
stage functions are called. Defining the
py_stage2 methods are optional. If you have defined them,
they will be called automatically. They are passed the destination particle
array, the current time, and current timestep.
Different equations for different stages¶
By default, when one creates equations the implicit assumption is that the
same right-hand-side is evaluated at each stage of the integrator. However,
some schemes require that one solve different equations for different
integrator stages. PySPH does support this but to do this when one creates
equations in the application, one should return an instance of
pysph.sph.equation.MultiStageEquations. For example:
def create_equations(self): # ... eqs = [ [Eq1(dest='fluid', sources=['fluid'])], [Eq2(dest='fluid', sources=['fluid'])] ] from pysph.sph.equation import MultiStageEquations return MultiStageEquations(eqs)
In the above, note that each element of
eqs is a list, it could have also
been a group. Each item of the given equations is treated as a separate
collection of equations which is to be used. The use of the
pysph.sph.equation.MultiStageEquations tells PySPH that multiple
equation sets are being used.
Now that we have this, how do we call the right accelerations at the right
times? We do this by sub-classing the
pysph.sph.integrator.Integrator. We show a simple example from our
test suite to illustrate this:
from pysph.sph.integrator import Integrator class MyIntegrator(Integrator): def one_timestep(self, t, dt): self.compute_accelerations(0) # Equivalent to self.compute_accelerations() self.stage1() self.do_post_stage(dt, 1) self.compute_accelerations(1, update_nnps=False) self.stage2() self.update_domain() self.do_post_stage(dt, 2)
Note that the
compute_accelerations method takes two arguments, the
index (which defaults to zero) and
update_nnps which defaults to
True. A simple integrator with a single RHS would simply call
self.compute_accelerations(). However, in the above, the first set of
equations is called first, and then for the second stage the second set of
equations is evaluated but without updating the NNPS (handy if the particles
do not move in stage1). Note the call
self.update_domain() after the
second stage, this sets up any ghost particles for periodicity when particles
have been moved, it also updates the neighbor finder to use an appropriate
neighbor length based on the current smoothing length. If you do not need to
do this for your particular integrator you may choose not to add this. In the
above case, the domain is not updated after the first stage as the particles
have not moved.
The above illustrates how one can create more complex integrators that employ different accelerations in each stage.
Examples to study¶
The following equations provide good examples for how one could use/write the
pysph.sph.gas_dynamics.basic.SummationDensityADKE: relatively simple.
pysph.sph.rigid_body.RigidBodyMoments: this is pretty complex.
pysph.sph.iisph.PressureSolve: relatively straight-forward.
The equations that demonstrate the
converged method are:
Some equations that demonstrate using matrices and solving systems of equations are: