Writing equations

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.

Overview

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 Equation subclass:

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 YourEquation(dest='fluid', sources=['fluid', '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_initialize method is called and is passed the destination particle array, t and dt (similar to 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 initialize method is called with the required arrays.
  • for each fluid particle, the initialize_pair method 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_all method. One can pass NBRS which is an array of unsigned ints with indices to the neighbors in the source particles. N_NBRS is 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, the loop method is called with the required properties/values.
  • for each fluid particle, the initialize_pair method is called while having access to all the solid arrays.
  • the solid neighbors for each fluid particle are found and for each pair, the loop method is called with the required properties/values.
  • for each fluid particle, the post_loop method 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.

The 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 “stride”).

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 Group with 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.

When the 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 real keyword 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 fluid and solid destinations, they would be processed separately. For example lets say you had this:

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.

Conventions followed

There are a few important conventions that are to be followed when writing the equations. When passing arguments to the initialize, loop, post_loop methods,

  • d_* indicates a destination array.
  • s_* indicates a source array.
  • d_idx and s_idx represent 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.h are 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[0] = d_x[d_idx] - s_x[s_idx], XIJ[1] = d_y[d_idx] - s_y[s_idx], XIJ[2] = d_z[d_idx] - s_z[s_idx]
  • R2IJ = XIJ[0]*XIJ[0] + XIJ[1]*XIJ[1] + XIJ[2]*XIJ[2]
  • 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
  • DWIJ: GRADIENT(XIJ, RIJ, HIJ, DWIJ)
  • DWJ: GRADIENT(XIJ, RIJ, s_h[s_idx], DWJ)
  • DWI: GRADIENT(XIJ, RIJ, d_h[d_idx], DWI)
  • VIJ[0] = d_u[d_idx] - s_u[s_idx] VIJ[1] = d_v[d_idx] - s_v[s_idx] VIJ[2] = 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(...), SPH_KERNEL.gradient_h(...) etc. The kernel is any one of the instances of the kernel classes defined in pysph.base.kernels

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.

For the loop_all method and the loop method, one may also pass the following:

  • 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, d_idx.

Note

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 sympy and 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 cPoint by writing:

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[3], vec1[3]
cdef double mat[3][3]
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 equation:

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[0] = parallel_reduce_array(m, 'sum')
        dst.max_u[0] = parallel_reduce_array(u, 'max')

where:

  • dst: refers to a destination ParticleArray.
  • 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, max and min operations. See 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_array is 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.

Adaptive timesteps

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 timestep.

If the dt_adapt parameter is not set one may also use standard velocity, force, and viscosity based parameters. The integrator uses information from the arrays dt_cfl, dt_force, and 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 as:

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)

The 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.

The 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 method

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[0] = d_x[d_idx] - s_x[s_idx]
            xij[1] = d_y[d_idx] - s_y[s_idx]
            xij[2] = d_z[d_idx] - s_z[s_idx]
            rij = sqrt(xij[0]*xij[0] + xij[1]*xij[1] + xij[2]*xij[2])
            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. initialize is called once per particle and each of their densities is set to zero. Then when loop_all is called it is called once per destination particle (unlike loop which is called pairwise for each destination and source particle). The loop_all is passed arrays as is typical of most equations but is also passed the SPH_KERNEL itself, the list of neighbors, and the number of neighbors.

The code first declares the variables, i, s_idx as an integer and long, and then 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.

This above loop_all code does exactly what the following single line of code does.

def loop(self, d_idx, d_rho, s_m, s_idx, WIJ):
    d_rho[d_idx] += s_m[s_idx]*WIJ

However, 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]

Notice that 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 one-dimensional array.

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 pre and 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.

Writing integrators

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_stage1 or 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 reduce method:

The equations that demonstrate the converged method are:

Some equations that demonstrate using matrices and solving systems of equations are: