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Experimental: indexed/flat particle backends #73

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c85ec0b
CPU fastpath: cheaper stencils, fewer allocations
rogeriojorge Mar 14, 2026
5184a38
Aggressive CPU fast modes: fewer ops, opt-in extreme
rogeriojorge Mar 14, 2026
6bdbbf9
Add indexed/flat particle backends for physics-preserving refactor
rogeriojorge Mar 14, 2026
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456 changes: 374 additions & 82 deletions PyPIC3D/J.py
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201 changes: 174 additions & 27 deletions PyPIC3D/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
import os
import time
import jax
from jax import block_until_ready
from jax import block_until_ready, lax
import jax.numpy as jnp
from tqdm import tqdm

Expand All @@ -23,10 +23,6 @@
write_openpmd_particles, write_openpmd_fields
)

from PyPIC3D.diagnostics.vtk import (
plot_field_slice_vtk, plot_vectorfield_slice_vtk, plot_vtk_particles
)

from PyPIC3D.utils import (
dump_parameters_to_toml, load_config_file, compute_energy,
setup_pmd_files
Expand All @@ -50,11 +46,41 @@
def run_PyPIC3D(config_file):
##################################### INITIALIZE SIMULATION ################################################

loop, particles, fields, world, simulation_parameters, constants, plotting_parameters, plasma_parameters, solver, electrostatic, verbose, GPUs, Nt, curl_func, J_func, relativistic = initialize_simulation(config_file)
cfg = config_file
if isinstance(cfg, dict):
sim = cfg.setdefault("simulation_parameters", {})
fast_mode = sim.get("fast_mode", "off")
if fast_mode not in ("off", "fp32", "aggressive", "extreme"):
raise ValueError("simulation_parameters.fast_mode must be one of: off, fp32, aggressive, extreme")

if fast_mode in ("fp32", "aggressive", "extreme"):
sim["enable_x64"] = False

if fast_mode in ("aggressive", "extreme"):
sim["shape_factor"] = 1
sim["filter_j"] = "none"

plot = cfg.setdefault("plotting", {})
for key in (
"plot_phasespace",
"plot_vtk_particles",
"plot_vtk_scalars",
"plot_vtk_vectors",
"plot_openpmd_particles",
"plot_openpmd_fields",
"dump_particles",
"dump_fields",
):
plot[key] = False
plot["plotting_interval"] = 10**9

if fast_mode == "extreme":
# opt-in physics approximation for maximum throughput
sim["relativistic"] = False

loop, particles, fields, world, simulation_parameters, constants, plotting_parameters, plasma_parameters, solver, electrostatic, verbose, GPUs, Nt, curl_func, J_func, relativistic = initialize_simulation(cfg)
# initialize the simulation

jit_loop = jax.jit(loop, static_argnames=('curl_func', 'J_func', 'solver', 'relativistic'))

dt = world['dt']
output_dir = simulation_parameters['output_dir']
vertex_grid = world['grids']['vertex']
Expand All @@ -77,12 +103,88 @@ def run_PyPIC3D(config_file):

###################################################### SIMULATION LOOP #####################################

for t in tqdm(range(Nt)):
scan_chunk = int(simulation_parameters.get("scan_chunk", 1))
plotting_interval = int(plotting_parameters["plotting_interval"])
fast_mode = str(simulation_parameters.get("fast_mode", "off"))
advance_impl = str(simulation_parameters.get("advance_impl", "fori"))
scan_unroll = int(simulation_parameters.get("scan_unroll", 1))

if scan_chunk < 1:
raise ValueError("simulation_parameters.scan_chunk must be >= 1")

if scan_chunk > 1 and (plotting_interval % scan_chunk) != 0:
raise ValueError(
f"scan_chunk={scan_chunk} requires plotting_interval to be a multiple of scan_chunk "
f"(got plotting_interval={plotting_interval})."
)

def make_advance(n_steps):
def advance(particles, fields, world, constants, curl_func, J_func, solver, relativistic=True):
if fast_mode == "aggressive" and advance_impl == "scan":
def scan_body(carry, _):
p, f = carry
return loop(p, f, world, constants, curl_func, J_func, solver, relativistic=relativistic), None

(particles, fields), _ = lax.scan(
scan_body,
(particles, fields),
xs=None,
length=n_steps,
unroll=scan_unroll,
)
return particles, fields

def body(_, state):
p, f = state
return loop(p, f, world, constants, curl_func, J_func, solver, relativistic=relativistic)

return lax.fori_loop(0, n_steps, body, (particles, fields))

return jax.jit(
advance,
static_argnames=("curl_func", "J_func", "solver", "relativistic"),
donate_argnums=(0, 1),
)

advance_full = make_advance(scan_chunk) if scan_chunk > 1 else None
tail = Nt % scan_chunk
advance_tail = make_advance(tail) if (scan_chunk > 1 and tail) else None

outputs_enabled = any(
plotting_parameters.get(k, False)
for k in (
"plot_phasespace",
"plot_vtk_scalars",
"plot_vtk_vectors",
"plot_vtk_particles",
"plot_openpmd_particles",
"plot_openpmd_fields",
"dump_particles",
"dump_fields",
)
)

if (not outputs_enabled) and plotting_interval > Nt:
advance_all = make_advance(Nt)
particles, fields = advance_all(
particles,
fields,
world,
constants,
curl_func,
J_func,
solver,
relativistic=relativistic,
)
return Nt, plotting_parameters, simulation_parameters, plasma_parameters, constants, particles, fields, world

step_iter = range(0, Nt, scan_chunk) if scan_chunk > 1 else range(Nt)
for t in tqdm(step_iter):

# plot the data
if t % plotting_parameters['plotting_interval'] == 0:
if t % plotting_interval == 0:

plot_num = t // plotting_parameters['plotting_interval']
plot_num = t // plotting_interval
# determine the plot number

E, B, J, rho, *rest = fields
Expand Down Expand Up @@ -111,6 +213,11 @@ def run_PyPIC3D(config_file):


if plotting_parameters['plot_vtk_scalars']:
try:
from PyPIC3D.diagnostics.vtk import plot_field_slice_vtk
except ModuleNotFoundError as e:
raise ModuleNotFoundError("VTK diagnostics requested but 'vtk' is not installed.") from e

rho = compute_rho(particles, rho, world, constants)
# calculate the charge density based on the particle positions
mass_density = compute_mass_density(particles, rho, world)
Expand All @@ -122,13 +229,23 @@ def run_PyPIC3D(config_file):


if plotting_parameters['plot_vtk_vectors']:
try:
from PyPIC3D.diagnostics.vtk import plot_vectorfield_slice_vtk
except ModuleNotFoundError as e:
raise ModuleNotFoundError("VTK diagnostics requested but 'vtk' is not installed.") from e

vector_field_slices = [ [E[0][:,world['Ny']//2,:], E[1][:,world['Ny']//2,:], E[2][:,world['Ny']//2,:]],
[B[0][:,world['Ny']//2,:], B[1][:,world['Ny']//2,:], B[2][:,world['Ny']//2,:]],
[J[0][:,world['Ny']//2,:], J[1][:,world['Ny']//2,:], J[2][:,world['Ny']//2,:]]]
plot_vectorfield_slice_vtk(vector_field_slices, vector_field_names, 1, vertex_grid, t, 'vector_field', output_dir, world)
# Plot the vector fields in VTK format

if plotting_parameters['plot_vtk_particles']:
try:
from PyPIC3D.diagnostics.vtk import plot_vtk_particles
except ModuleNotFoundError as e:
raise ModuleNotFoundError("VTK diagnostics requested but 'vtk' is not installed.") from e

plot_vtk_particles(particles, plot_num, output_dir)
# Plot the particles in VTK format

Expand All @@ -143,35 +260,65 @@ def run_PyPIC3D(config_file):
fields = (E, B, J, rho, *rest)
# repack the fields

particles, fields = jit_loop(
particles,
fields,
world,
constants,
curl_func,
J_func,
solver,
relativistic=relativistic,
)
# time loop to update the particles and fields
if scan_chunk == 1:
particles, fields = loop(
particles,
fields,
world,
constants,
curl_func,
J_func,
solver,
relativistic=relativistic,
)
else:
if (t + scan_chunk) <= Nt:
particles, fields = advance_full(
particles,
fields,
world,
constants,
curl_func,
J_func,
solver,
relativistic=relativistic,
)
else:
particles, fields = advance_tail(
particles,
fields,
world,
constants,
curl_func,
J_func,
solver,
relativistic=relativistic,
)
# advance the particles and fields


return Nt, plotting_parameters, simulation_parameters, plasma_parameters, constants, particles, fields, world

def main():
###################### JAX SETTINGS ########################################################################
jax.config.update("jax_enable_x64", True)
# set Jax to use 64 bit precision
toml_file = load_config_file()
# load the configuration file

sim = toml_file.get("simulation_parameters", {}) if isinstance(toml_file, dict) else {}
fast_mode = sim.get("fast_mode", "off")
enable_x64 = bool(sim.get("enable_x64", True))
if fast_mode in ("fp32", "aggressive", "extreme"):
enable_x64 = False
jax.config.update("jax_enable_x64", enable_x64)
# set Jax precision (default preserves legacy behavior)

# jax.config.update("jax_debug_nans", True)
# debugging for nans
jax.config.update('jax_platform_name', 'cpu')
# set Jax to use CPUs
#jax.config.update("jax_disable_jit", True)
############################################################################################################

toml_file = load_config_file()
# load the configuration file

start = time.time()
# start the timer

Expand Down
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