Source code for pysph.solver.solver

""" An implementation of a general solver base class """

# System library imports.
import os
import numpy

# PySPH imports
from pysph.base.kernels import CubicSpline
from pysph.sph.acceleration_eval import AccelerationEval
from pysph.sph.sph_compiler import SPHCompiler

from pysph.solver.utils import FloatPBar, load, dump

import logging
logger = logging.getLogger(__name__)

EPSILON = numpy.finfo(float).eps*2

[docs]class Solver(object): """Base class for all PySPH Solvers """ def __init__(self, dim=2, integrator=None, kernel=None, n_damp=0, tf=1.0, dt=1e-3, adaptive_timestep=False, cfl=0.3, output_at_times=(), fixed_h=False, **kwargs): """**Constructor** Any additional keyword args are used to set the values of any of the attributes. Parameters ---------- dim : int Dimension of the problem integrator : pysph.sph.integrator.Integrator Integrator to use kernel : pysph.base.kernels.Kernel SPH kernel to use n_damp : int Number of timesteps for which the initial damping is required. This is used to improve stability for problems with strong discontinuity in initial condition. Setting it to zero will disable damping of the timesteps. dt : double Suggested initial time step for integration tf : double Final time for integration adaptive_timestep : bint Flag to use adaptive time steps cfl : double CFL number for adaptive time stepping pfreq : int Output files dumping frequency. output_at_times : list/array Optional list of output times to force dump the output file fixed_h : bint Flag for constant smoothing lengths `h` Example ------- >>> integrator = PECIntegrator(fluid=WCSPHStep()) >>> kernel = CubicSpline(dim=2) >>> solver = Solver(dim=2, integrator=integrator, kernel=kernel, ... n_damp=50, tf=1.0, dt=1e-3, adaptive_timestep=True, ... pfreq=100, cfl=0.5, output_at_times=[1e-1, 1.0]) """ self.integrator = integrator self.dim = dim if kernel is not None: self.kernel = kernel else: self.kernel = CubicSpline(dim) # set the particles to None self.particles = None # Set the AccelerationEval instance to None. self.acceleration_eval = None # solver time and iteration count self.t = 0 self.count = 0 self.execute_commands = None # list of functions to be called before and after an integration step self.pre_step_callbacks = [] self.post_step_callbacks = [] # List of functions to be called after each stage of the integrator. self.post_stage_callbacks = [] # default output printing frequency self.pfreq = 100 # Compress generated files. self.compress_output = False self.disable_output = False # the process id for parallel runs self.pid = None # set the default rank to 0 self.rank = 0 # set the default comm to None. self.comm = None # set the default mode to serial self.in_parallel = False # arrays to print output self.arrays_to_print = [] # the default parallel output mode self.parallel_output_mode = "collected" # flag to print all arrays self.detailed_output = False # flag to save Remote arrays self.output_only_real = True # output filename self.fname = self.__class__.__name__ # output drectory self.output_directory = self.fname+'_output' # solution damping to avoid impulsive starts self.n_damp = n_damp # Use adaptive time steps and cfl number self.adaptive_timestep = adaptive_timestep self.cfl = cfl # list of output times self.output_at_times = numpy.asarray(output_at_times) self.force_output = False # default time step constants self.tf = tf self.dt = dt self.max_steps = 1 << 31 self._prev_dt = None self._damping_factor = 1.0 self._epsilon = EPSILON*tf # flag for constant smoothing lengths self.fixed_h = fixed_h # Set all extra keyword arguments for attr, value in kwargs.items(): if hasattr(self, attr): setattr(self, attr, value) else: msg = 'Unknown keyword arg "%s" passed to constructor'%attr raise TypeError(msg) ########################################################################## # Public interface. ##########################################################################
[docs] def setup(self, particles, equations, nnps, kernel=None, fixed_h=False): """ Setup the solver. The solver's processor id is set if the in_parallel flag is set to true. The order of the integrating calcs is determined by the solver's order attribute. This is usually called at the start of a PySPH simulation. """ self.particles = particles if kernel is not None: self.kernel = kernel mode = 'mpi' if self.in_parallel else 'serial' self.acceleration_eval = AccelerationEval( particles, equations, self.kernel, mode ) sep = '-'*70 eqn_info = '[\n' + ',\n'.join([str(e) for e in equations]) + '\n]' logger.info('Using equations:\n%s\n%s\n%s'%(sep, eqn_info, sep)) logger.info( 'Using integrator:\n%s\n %s\n%s'%(sep, self.integrator, sep) ) sph_compiler = SPHCompiler( self.acceleration_eval, self.integrator ) sph_compiler.compile() # Set the nnps for all concerned objects. self.acceleration_eval.set_nnps(nnps) self.integrator.set_nnps(nnps) # set the parallel manager for the integrator self.integrator.set_parallel_manager(self.pm) # Set the post_stage_callback. self.integrator.set_post_stage_callback(self._post_stage_callback) # set integrator option for constant smoothing length self.fixed_h = fixed_h self.integrator.set_fixed_h( fixed_h ) logger.debug("Solver setup complete.")
[docs] def add_post_stage_callback(self, callback): """These callbacks are called *after* each integrator stage. The callbacks are passed (current_time, dt, stage). See the the `Integrator.one_timestep` methods for examples of how this is called. Example ------- >>> def post_stage_callback_function(t, dt, stage): >>> # This function is called after every stage of integrator. >>> print t, dt, stage >>> # Do something >>> solver.add_post_stage_callback(post_stage_callback_function) """ self.post_stage_callbacks.append(callback)
[docs] def add_post_step_callback(self, callback): """These callbacks are called *after* each timestep is performed. The callbacks are passed the solver instance (i.e. self). Example ------- >>> def post_step_callback_function(solver): >>> # This function is called after every time step. >>> print solver.t, solver.dt >>> # Do something >>> solver.add_post_step_callback(post_step_callback_function) """ self.post_step_callbacks.append(callback)
[docs] def add_pre_step_callback(self, callback): """These callbacks are called *before* each timestep is performed. The callbacks are passed the solver instance (i.e. self). Example ------- >>> def pre_step_callback_function(solver): >>> # This function is called before every time step. >>> print solver.t, solver.dt >>> # Do something >>> solver.add_pre_step_callback(pre_step_callback_function) """ self.pre_step_callbacks.append(callback)
[docs] def append_particle_arrrays(self, arrays): """ Append the particle arrays to the existing particle arrays """ if not self.particles: print('Warning! Particles not defined.') return for array in self.particles: array_name = array.name for arr in arrays: if array_name == arr.name: array.append_parray(arr) self.setup(self.particles)
[docs] def set_adaptive_timestep(self, value): """Set it to True to use adaptive timestepping based on cfl, viscous and force factor. Look at pysph.sph.integrator.compute_time_step for more details. """ self.adaptive_timestep = value
[docs] def set_cfl(self, value): 'Set the CFL number for adaptive time stepping' self.cfl = value
[docs] def set_final_time(self, tf): """ Set the final time for the simulation """ self.tf = tf self._epsilon = EPSILON*tf
[docs] def set_n_damp(self, ndamp): """Set the number of timesteps for which the timestep should be initially damped. """ self.n_damp = ndamp
[docs] def set_time_step(self, dt): """ Set the time step to use """ self.dt = dt
[docs] def set_print_freq(self, n): """ Set the output print frequency """ self.pfreq = n
[docs] def set_disable_output(self, value): """Disable file output. """ self.disable_output = value
[docs] def set_arrays_to_print(self, array_names=None): """Only print the arrays with the given names. """ available_arrays = [array.name for array in self.particles] if array_names: for name in array_names: if not name in available_arrays: raise RuntimeError("Array %s not availabe"%(name)) for arr in self.particles: if arr.name == name: array = arr break self.arrays_to_print.append(array) else: self.arrays_to_print = self.particles
[docs] def set_output_fname(self, fname): """ Set the output file name """ self.fname = fname
[docs] def set_output_printing_level(self, detailed_output): """ Set the output printing level """ self.detailed_output = detailed_output
[docs] def set_output_only_real(self, output_only_real): """ Set the flag to save out only real particles """ self.output_only_real = output_only_real
[docs] def set_output_directory(self, path): """ Set the output directory """ self.output_directory = path
[docs] def set_output_at_times(self, output_at_times): """ Set a list of output times """ self.output_at_times = numpy.asarray(output_at_times)
[docs] def set_max_steps(self, max_steps): """Set the maximum number of iterations to perform. """ self.max_steps = max_steps
[docs] def set_compress_output(self, compress): """Compress the dumped output files. """ self.compress_output = compress
[docs] def set_parallel_output_mode(self, mode="collected"): """Set the default solver dump mode in parallel. The available modes are: collected : Collect array data from all processors on root and dump a single file. distributed : Each processor dumps a file locally. """ assert mode in ("collected", "distributed") self.parallel_output_mode = mode
[docs] def set_command_handler(self, callable, command_interval=1): """ set the `callable` to be called at every `command_interval` iteration the `callable` is called with the solver instance as an argument """ self.execute_commands = callable self.command_interval = command_interval
def set_parallel_manager(self, pm): self.pm = pm def barrier(self): if self.comm: self.comm.barrier()
[docs] def solve(self, show_progress=True): """ Solve the system Notes ----- Pre-stepping functions are those that need to be called before the integrator is called. Similarly, post step functions are those that are called after the stepping within the integrator. """ if self.in_parallel: show = False else: show = show_progress bar = FloatPBar(self.t, self.tf, show=show) self._epsilon = EPSILON*self.tf # Initial solution self.dump_output() self.barrier() # everybody waits for this to complete # Compute the accelerations once for the predictor corrector # integrator to work correctly at the first time step. self.acceleration_eval.compute(self.t, self.dt) # Now get a suitable adaptive (if requested) and damped timestep to # integrate with. self.dt = self._get_timestep() while (self.tf - self.t) > self._epsilon and \ (self.count < self.max_steps): # perform any pre step functions for callback in self.pre_step_callbacks: callback(self) if self.rank == 0: logger.debug( "Iteration=%d, time=%f, timestep=%f" % \ (self.count, self.t, self.dt) ) # perform the integration and update the time. #print 'Solver Iteration', self.count, self.dt, self.t self.integrator.step(self.t, self.dt) # perform any post step functions for callback in self.post_step_callbacks: callback(self) # update time and iteration counters if successfully # integrated self.t += self.dt self.count += 1 self._epsilon = EPSILON*self.tf*self.count # Compute the next timestep. self.dt = self._get_timestep() # Note: this may adjust dt to land at a desired time. self._dump_output_if_needed() # update progress bar bar.update(self.t) # update the time for all arrays self.update_particle_time() if self.execute_commands is not None: if self.count % self.command_interval == 0: self.execute_commands(self) # close the progress bar bar.finish() # final output save self.dump_output()
def update_particle_time(self): for array in self.particles: array.set_time(self.t)
[docs] def dump_output(self): """Dump the simulation results to file The arrays used for printing are determined by the particle array's `output_property_arrays` data attribute. For debugging it is sometimes nice to have all the arrays (including accelerations) saved. This can be chosen from using the command line option `--detailed-output` Output data Format: A single file named as: <fname>_<rank>_<iteration_count>.npz The data is saved as a Python dictionary with two keys: `solver_data` : Solver meta data like time, dt and iteration number `arrays` : A dictionary keyed on particle array names and with particle properties as value. Example: You can load the data output by PySPH like so: >>> from pysph.solver.utils import load >>> data = load('output_directory/filename_x_xxx.npz') >>> solver_data = data['solver_data'] >>> arrays = data['arrays'] >>> fluid = arrays['fluid'] >>> ... In the above example, it is assumed that the output file contained an array named fluid. """ if self.disable_output: return if self.rank == 0: msg = 'Writing output at time %g, iteration %d, dt = %g'%( self.t, self.count, self.dt) logger.info(msg) fname = os.path.join(self.output_directory, self.fname + '_' + str(self.count)) comm = None if self.parallel_output_mode == "collected" and self.in_parallel: comm = self.comm dump(fname, self.particles, self._get_solver_data(), detailed_output=self.detailed_output, only_real=self.output_only_real, mpi_comm=comm, compress=self.compress_output)
[docs] def load_output(self, count): """Load particle data from dumped output file. Parameters ---------- count : str The iteration time from which to load the data. If time is '?' then list of available data files is returned else the latest available data file is used Notes ----- Data is loaded from the :py:attr:`output_directory` using the same format as stored by the :py:meth:`dump_output` method. Proper functioning required that all the relevant properties of arrays be dumped. """ # get the list of available files available_files = [i.rsplit('_',1)[1][:-4] for i in os.listdir(self.output_directory) if i.startswith(self.fname) and i.endswith('.npz')] if count == '?': return sorted(set(available_files), key=int) else: if not count in available_files: msg = "File with iteration count `%s` does not exist"%(count) msg += "\nValid iteration counts are %s"%(sorted(set(available_files), key=int)) #print msg raise IOError(msg) array_names = [pa.name for pa in self.particles] # load the output file data = load(os.path.join(self.output_directory, self.fname+'_'+str(count)+'.npz')) arrays = [ data["arrays"][i] for i in array_names ] # set the Particle's arrays self.particles = arrays solver_data = data['solver_data'] self.t = float(solver_data['t']) self.dt = float(solver_data['dt']) self.count = int(solver_data['count'])
[docs] def get_options(self, arg_parser): """ Implement this to add additional options for the application """ pass
[docs] def setup_solver(self, options=None): """ Implement the basic solvers here All subclasses of Solver may implement this function to add the necessary operations for the problem at hand. Parameters ---------- options : dict options set by the user using commandline (there is no guarantee of existence of any key) """ pass
########################################################################## # Non-public interface. ########################################################################## def _compute_timestep(self): undamped_dt = self._get_undamped_timestep() if self.adaptive_timestep: # locally stable time step dt = self.integrator.compute_time_step(undamped_dt, self.cfl) # set the globally stable time step across all processors if self.in_parallel: if dt is None: # For some reason this processor does not have an adaptive # timestep constraint so we set it to a large number so the # timestep is determined by the other processors. dt = 1e20 dt = self.pm.update_time_steps(dt) else: if dt is None: dt = undamped_dt else: dt = undamped_dt return dt def _damp_timestep(self, dt): """Damp the timestep initially to prevent transient errors at startup. This basically damps the initial timesteps by the factor 0.5 (sin(pi*(-0.5 + count/n_damp)) + 1) Where n_damp is the number of iterations to damp the timestep for and count is the number of iterations. """ n_damp = self.n_damp if self.count < n_damp and n_damp > 0: iter_fraction = (self.count+1)/float(n_damp) fac = 0.5*(numpy.sin(numpy.pi*(-0.5 + iter_fraction)) + 1.0) self._damping_factor = fac else: self._damping_factor = 1.0 return dt*self._damping_factor def _dump_output_if_needed(self): """Dump output if needed while solve is running. This is called by `solve`. Warning ------- This will adjust `dt` if the user has asked for output at a non-integral multiple of dt. """ if abs(self.t - self.tf) < self._epsilon: return # dump output if the iteration number is a multiple of the printing # frequency. dump = self.count % self.pfreq == 0 # Consider the other cases if user has requested output at a specified # time. output_at_times = self.output_at_times dt = self.dt # adjust dt to land on specific output times or dump output if we have # reached a desired time. if len(output_at_times) > 0: tdiff = output_at_times - self.t if numpy.any(numpy.abs(tdiff) < self._epsilon): dump = True # Our next step may exceed a required timestep so we adjust the # timestep. timestep_too_big = (tdiff > 0.0) & (tdiff < dt) if numpy.any(timestep_too_big): index = numpy.where(timestep_too_big)[0] output_time = output_at_times[index] if abs(output_time - self.t) > self._epsilon: # It sometimes happens that the current time is just # shy of the requested output time which results in a # ridiculously small dt so we skip that case. # Compute the new time-step to fall on the specified output # time instant and save the previous dt value. self._prev_dt = dt self.dt = float(output_time - self.t) if dump: self.dump_output() self.barrier() def _get_solver_data(self): if self._prev_dt is not None: dt = self._prev_dt/self._damping_factor else: dt = self._get_undamped_timestep() return {'dt': dt, 't': self.t, 'count': self.count} def _get_timestep(self): if abs(self.tf - self.t) < self._epsilon: # We have reached the end, so no need to adjust the timestep # anymore. return self.dt if self._prev_dt is not None and \ abs(self._prev_dt - self.dt) > self._epsilon: # if the _prev_dt was set then we need to use it as the current dt # was set to print at an intermediate time. self.dt = self._prev_dt self._prev_dt = None dt = self._compute_timestep() dt = self._damp_timestep(dt) # adjust dt to land exactly on final time if (self.t + dt) > (self.tf - self._epsilon): dt = self.tf - self.t return dt def _get_undamped_timestep(self): return self.dt/self._damping_factor def _post_stage_callback(self, time, dt, stage): for callback in self.post_stage_callbacks: callback(time, dt, stage)
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