Genesis4 Particles¶
This shows examples of the various ways to input particle data into Genesis4.
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import logging
import os
from math import pi, sqrt
import matplotlib.pyplot as plt
import numpy as np
from scipy.constants import c
import genesis.version4 as g4
logging.basicConfig()
# logging.getLogger("genesis").setLevel("DEBUG")
%config InlineBackend.figure_format = 'retina'
import logging
import os
from math import pi, sqrt
import matplotlib.pyplot as plt
import numpy as np
from scipy.constants import c
import genesis.version4 as g4
logging.basicConfig()
# logging.getLogger("genesis").setLevel("DEBUG")
%config InlineBackend.figure_format = 'retina'
Lattice¶
Create a simple drift lattice
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D1 = g4.Drift(L=1)
lattice = g4.Lattice(elements={"D1": D1, "LAT": g4.Line(elements=[D1])})
D1 = g4.Drift(L=1)
lattice = g4.Lattice(elements={"D1": D1, "LAT": g4.Line(elements=[D1])})
profile_gauss¶
This profile will make a Gaussian distribition. Here we do some calculations to make the correct bunch length for a given bunch charge to provide a peak current.
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PEAK_CURRENT = 1000
BUNCH_CHARGE = 100e-12
SIGMA_T = BUNCH_CHARGE / (sqrt(2 * pi) * PEAK_CURRENT)
SIGMA_Z = SIGMA_T * c
SLEN = 6 * SIGMA_Z
S0 = 3 * SIGMA_Z
SIGMA_T, SIGMA_Z, SLEN
PEAK_CURRENT = 1000
BUNCH_CHARGE = 100e-12
SIGMA_T = BUNCH_CHARGE / (sqrt(2 * pi) * PEAK_CURRENT)
SIGMA_Z = SIGMA_T * c
SLEN = 6 * SIGMA_Z
S0 = 3 * SIGMA_Z
SIGMA_T, SIGMA_Z, SLEN
Out[3]:
(3.989422804014327e-14, 1.1959988684167075e-05, 7.175993210500245e-05)
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main = g4.MainInput(
namelists=[
g4.Setup(
rootname="drift_test",
# lattice="LATFILE",
beamline="LAT",
gamma0=1000,
lambda0=1e-07,
delz=0.026,
seed=123456,
npart=128,
),
g4.Time(slen=SLEN),
g4.ProfileGauss(
label="beamcurrent",
c0=PEAK_CURRENT,
s0=S0,
sig=SIGMA_Z,
),
g4.Beam(
gamma=1000,
delgam=1,
current="beamcurrent",
),
g4.Track(zstop=1),
g4.Write(beam="end"),
],
)
G = g4.Genesis4(main, lattice, verbose=True)
output = G.run()
main = g4.MainInput(
namelists=[
g4.Setup(
rootname="drift_test",
# lattice="LATFILE",
beamline="LAT",
gamma0=1000,
lambda0=1e-07,
delz=0.026,
seed=123456,
npart=128,
),
g4.Time(slen=SLEN),
g4.ProfileGauss(
label="beamcurrent",
c0=PEAK_CURRENT,
s0=S0,
sig=SIGMA_Z,
),
g4.Beam(
gamma=1000,
delgam=1,
current="beamcurrent",
),
g4.Track(zstop=1),
g4.Write(beam="end"),
],
)
G = g4.Genesis4(main, lattice, verbose=True)
output = G.run()
Configured to run in: /tmp/tmp513pys1t Running Genesis4 in /tmp/tmp513pys1t /home/runner/miniconda3/envs/lume-genesis-dev/bin/genesis4 -l genesis.lat genesis4.in
--------------------------------------------- GENESIS - Version 4.6.7 has started... Compile info: Compiled by conda at 2025-05-20 22:47:32 [UTC] from Git Commit ID: 88f9e172efe23614bf17667bbec6774b723d37cd Starting Time: Mon Jun 2 16:37:51 2025 MPI-Comm Size: 1 node Opened input file genesis4.in Parsing lattice file genesis.lat ... Setting up time window of 71.8 microns with 718 sample points... Adding profile with label: beamcurrent Generating input particle distribution... Running Core Simulation... Time-dependent run with 718 slices for a time window of 71.8 microns Initial analysis of electron beam and radiation field... Calculation: 0% done Writing output file... Core Simulation done. End of Track Writing particle distribution to file: end.par.h5 ...
Program is terminating... Ending Time: Mon Jun 2 16:37:51 2025 Total Wall Clock Time: 0.282958 seconds ------------------------------------- Success - execution took 1.46s.
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G.input.main.setup.delz
G.input.main.setup.delz
Out[5]:
0.026
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print(G.output.run.output_log)
print(G.output.run.output_log)
--------------------------------------------- GENESIS - Version 4.6.7 has started... Compile info: Compiled by conda at 2025-05-20 22:47:32 [UTC] from Git Commit ID: 88f9e172efe23614bf17667bbec6774b723d37cd Starting Time: Mon Jun 2 16:37:51 2025 MPI-Comm Size: 1 node Opened input file genesis4.in Parsing lattice file genesis.lat ... Setting up time window of 71.8 microns with 718 sample points... Adding profile with label: beamcurrent Generating input particle distribution... Running Core Simulation... Time-dependent run with 718 slices for a time window of 71.8 microns Initial analysis of electron beam and radiation field... Calculation: 0% done Writing output file... Core Simulation done. End of Track Writing particle distribution to file: end.par.h5 ... Program is terminating... Ending Time: Mon Jun 2 16:37:51 2025 Total Wall Clock Time: 0.282958 seconds -------------------------------------
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output.load_particles()
P1 = output.particles["end"]
P1.drift_to_z()
P1.plot("t", "energy")
P1
output.load_particles()
P1 = output.particles["end"]
P1.drift_to_z()
P1.plot("t", "energy")
P1
Out[7]:
<ParticleGroup with 91904 particles at 0x7f890d9bb8c0>
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output.particles["end"]
output.particles["end"]
Out[8]:
<ParticleGroup with 91904 particles at 0x7f890d9bb8c0>
Check the charge
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P1.charge
P1.charge
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np.float64(9.973150081144012e-11)
profile_file¶
LUME-Genesis automatically makes an HDF5 file with ProfileArray.
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NPTS = 100
SLEN = 100e-6
S = np.linspace(0, SLEN, NPTS)
CURRENT = np.linspace(1, 1000.0, NPTS)
plt.plot(S, CURRENT)
NPTS = 100
SLEN = 100e-6
S = np.linspace(0, SLEN, NPTS)
CURRENT = np.linspace(1, 1000.0, NPTS)
plt.plot(S, CURRENT)
Out[10]:
[<matplotlib.lines.Line2D at 0x7f890d38a5d0>]
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main = g4.MainInput(
namelists=[
g4.Setup(
rootname="drift_test",
# lattice=lattice,
beamline="LAT",
gamma0=1000,
lambda0=1e-07,
delz=0.026,
seed=123456,
npart=128,
),
g4.Time(slen=SLEN),
g4.ProfileArray(label="beamcurrent", xdata=S, ydata=CURRENT),
g4.Beam(
gamma=1000,
delgam=1,
current="beamcurrent",
ex=1e-06,
ey=1e-06,
betax=7.910909406464387,
betay=16.881178621346898,
alphax=-0.7393217413918415,
alphay=1.3870723536888105,
),
g4.Track(zstop=1),
g4.Write(beam="end"),
]
)
G = g4.Genesis4(main, lattice, verbose=True)
output = G.run()
main = g4.MainInput(
namelists=[
g4.Setup(
rootname="drift_test",
# lattice=lattice,
beamline="LAT",
gamma0=1000,
lambda0=1e-07,
delz=0.026,
seed=123456,
npart=128,
),
g4.Time(slen=SLEN),
g4.ProfileArray(label="beamcurrent", xdata=S, ydata=CURRENT),
g4.Beam(
gamma=1000,
delgam=1,
current="beamcurrent",
ex=1e-06,
ey=1e-06,
betax=7.910909406464387,
betay=16.881178621346898,
alphax=-0.7393217413918415,
alphay=1.3870723536888105,
),
g4.Track(zstop=1),
g4.Write(beam="end"),
]
)
G = g4.Genesis4(main, lattice, verbose=True)
output = G.run()
Configured to run in: /tmp/tmpou6b6xgh Running Genesis4 in /tmp/tmpou6b6xgh /home/runner/miniconda3/envs/lume-genesis-dev/bin/genesis4 -l genesis.lat genesis4.in
--------------------------------------------- GENESIS - Version 4.6.7 has started... Compile info: Compiled by conda at 2025-05-20 22:47:32 [UTC] from Git Commit ID: 88f9e172efe23614bf17667bbec6774b723d37cd Starting Time: Mon Jun 2 16:37:54 2025 MPI-Comm Size: 1 node Opened input file genesis4.in Parsing lattice file genesis.lat ... Setting up time window of 100 microns with 1000 sample points... Adding profile with label: beamcurrent Generating input particle distribution... Running Core Simulation... Time-dependent run with 1000 slices for a time window of 100 microns Initial analysis of electron beam and radiation field... Calculation: 0% done Writing output file... Core Simulation done. End of Track Writing particle distribution to file: end.par.h5 ...
Program is terminating... Ending Time: Mon Jun 2 16:37:54 2025 Total Wall Clock Time: 0.377004 seconds ------------------------------------- Success - execution took 1.56s.
Inspect the input and output¶
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print(main.to_genesis())
print(main.to_genesis())
&setup rootname = drift_test lattice = genesis.lat beamline = LAT gamma0 = 1000.0 lambda0 = 1e-07 delz = 0.026 seed = 123456 npart = 128 &end &time slen = 0.0001 &end &profile_file label = beamcurrent xdata = ProfileArray_0.h5/x ydata = ProfileArray_0.h5/y &end &beam gamma = 1000.0 delgam = 1.0 current = @beamcurrent ex = 1e-06 ey = 1e-06 betax = 7.910909406464387 betay = 16.881178621346898 alphax = -0.7393217413918415 alphay = 1.3870723536888105 &end &track zstop = 1.0 &end &write beam = end &end
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print(lattice.to_genesis())
print(lattice.to_genesis())
D1: drift = {l=1.0};
LAT: LINE = {D1};
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print(output.run.output_log)
print(output.run.output_log)
--------------------------------------------- GENESIS - Version 4.6.7 has started... Compile info: Compiled by conda at 2025-05-20 22:47:32 [UTC] from Git Commit ID: 88f9e172efe23614bf17667bbec6774b723d37cd Starting Time: Mon Jun 2 16:37:54 2025 MPI-Comm Size: 1 node Opened input file genesis4.in Parsing lattice file genesis.lat ... Setting up time window of 100 microns with 1000 sample points... Adding profile with label: beamcurrent Generating input particle distribution... Running Core Simulation... Time-dependent run with 1000 slices for a time window of 100 microns Initial analysis of electron beam and radiation field... Calculation: 0% done Writing output file... Core Simulation done. End of Track Writing particle distribution to file: end.par.h5 ... Program is terminating... Ending Time: Mon Jun 2 16:37:54 2025 Total Wall Clock Time: 0.377004 seconds -------------------------------------
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output.meta
output.meta
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OutputMeta(
extra={},
beamdumps=OutputMetaDumps(extra={}, filenames={}, intstep=array([], dtype=float64)),
fielddumps=OutputMetaDumps(extra={}, filenames={}, intstep=array([], dtype=float64)),
host='Undefined',
input_file='&setup\n rootname = drift_test\n lattice = genesis.lat\n beamline = LAT\n gamma0 = 1000.0\n lambda0 = 1e-07\n delz = 0.026\n seed...
lattice_file='D1: drift = {l=1.0};\nLAT: LINE = {D1};\n',
time_stamp='Mon Jun 2 16:37:54 2025\n',
user='runner',
version=OutputMetaVersion(
extra={},
build_info='Compiled by conda at 2025-05-20 22:47:32 [UTC] from Git Commit ID: 88f9e172efe23614bf17667bbec6774b723d37cd',
major=4.0,
minor=6.0,
revision=7.0,
),
cwd='/tmp/tmpou6b6xgh',
mpisize=1.0,
)
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output.load_particles()
P1 = output.particles["end"]
P1.drift_to_z()
P1.plot("t", "energy")
P1
output.load_particles()
P1 = output.particles["end"]
P1.drift_to_z()
P1.plot("t", "energy")
P1
Out[16]:
<ParticleGroup with 128000 particles at 0x7f890d3d5a90>
Resample particles for equal weights. This is neccessary when reading from a distribution file.
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NSAMPLE = len(P1)
P1r = P1.resample(NSAMPLE)
P1r.plot("t", "energy")
P1r
NSAMPLE = len(P1)
P1r = P1.resample(NSAMPLE)
P1r.plot("t", "energy")
P1r
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<ParticleGroup with 128000 particles at 0x7f890147bed0>
Make a more interesting distribution from this:
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P1r.pz[0 : len(P1) // 2] *= 1.1
P1r.plot("t", "energy")
P1r.pz[0 : len(P1) // 2] *= 1.1
P1r.plot("t", "energy")
ParticleGroup can write to a file for Genesis4.
Please note that LUME-Genesis will write the distribution for you prior to running Genesis4, so this step is not necessary.
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DIST_FILE = "genesis4_distribution.h5"
P1r.write_genesis4_distribution(DIST_FILE, verbose=True)
DIST_FILE = "genesis4_distribution.h5"
P1r.write_genesis4_distribution(DIST_FILE, verbose=True)
Resampling 128000 weighted particles
Datasets x, xp, y, yp, t, p written to: genesis4_distribution.h5
ParticleGroup¶
Genesis4Input directly supports OpenPMD-beamphysics ParticleGroup instances.
When using the MainInput.initial_particles property setter, LUME-Genesis will ensure the namelist is added before the first "Track" or "Write" namelist in the main input.
It will implicitly set the import_distribution charge and the time.slen to the calculated time window from the particles, equivalent to the following:
import_distribution.charge = particles.charge
main.time.slen = max(
c_light * np.ptp(particles.t),
np.ptp(particles.z),
)
Additionally, the appropriate input file for Genesis4 will be written automatically when Genesis4 is executed.
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main = g4.MainInput(
namelists=[
g4.Setup(
rootname="drift_test",
# lattice=full_path(LATFILE),
beamline="LAT",
gamma0=1000,
lambda0=1e-07,
delz=0.026,
seed=123456,
npart=512,
),
g4.Time(slen=0), # This will change slen to span all particles
g4.Track(zstop=1),
g4.Write(beam="end"),
],
)
G1 = g4.Genesis4(main, lattice, verbose=True, initial_particles=P1r)
output = G1.run()
main = g4.MainInput(
namelists=[
g4.Setup(
rootname="drift_test",
# lattice=full_path(LATFILE),
beamline="LAT",
gamma0=1000,
lambda0=1e-07,
delz=0.026,
seed=123456,
npart=512,
),
g4.Time(slen=0), # This will change slen to span all particles
g4.Track(zstop=1),
g4.Write(beam="end"),
],
)
G1 = g4.Genesis4(main, lattice, verbose=True, initial_particles=P1r)
output = G1.run()
WARNING:genesis.version4.input.core:Updating time namelist slen: 0.000100 (was 0.000000) to span all particles
Configured to run in: /tmp/tmptm2sxd8s Running Genesis4 in /tmp/tmptm2sxd8s /home/runner/miniconda3/envs/lume-genesis-dev/bin/genesis4 -l genesis.lat genesis4.in
--------------------------------------------- GENESIS - Version 4.6.7 has started... Compile info: Compiled by conda at 2025-05-20 22:47:32 [UTC] from Git Commit ID: 88f9e172efe23614bf17667bbec6774b723d37cd Starting Time: Mon Jun 2 16:38:33 2025 MPI-Comm Size: 1 node Opened input file genesis4.in Parsing lattice file genesis.lat ... Setting up time window of 100 microns with 1000 sample points... Importing distribution file... Charge of external distribution: 1.66782e-10 Particles in external distribution: 128000 Analysing external distribution... Analysis of the imported distribution Total Bunch Length (microns): 99.5548 Length for Matching (microns): 99.5548 Energy (MeV): 536.475 Norm. Emittance in x (micron): 1.00634 Norm. Emittance in y (micron): 1.00625 Beta Function in x (m): 10.0386 Beta Function in y (m): 14.8975 Alpha Function in x : -0.9364 Alpha Function in y : 1.2109 Beam center in x (micron): -0.549456 Beam center in y (micron): 0.0593406 Beam center in px : -6.02225e-08 Beam center in py : 3.4135e-08 Sorting external distribution... Global Sorting: Slicelength: 0 - Send backwards for theta < 4.97774e-07 - Send forward for theta > 9.94022e-05 *** Non-matching PArticle Transfar: Rank: 0 Deleted: 0 Forward: 395 Backward: 6 Generating internal particle distribution...
Running Core Simulation... Time-dependent run with 1000 slices for a time window of 100 microns Initial analysis of electron beam and radiation field... Calculation: 0% done Writing output file... Core Simulation done. End of Track Writing particle distribution to file: end.par.h5 ...
Program is terminating... Ending Time: Mon Jun 2 16:38:34 2025 Total Wall Clock Time: 1.01766 seconds ------------------------------------- Success - execution took 15.16s.
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output.run
output.run
Out[21]:
RunInfo( error_reason='', run_script='/home/runner/miniconda3/envs/lume-genesis-dev/bin/genesis4 -l genesis.lat genesis4.in', run_time=15.160122841999964, )
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output.load_particles()
P2 = output.particles["end"]
P2.z
output.load_particles()
P2 = output.particles["end"]
P2.z
Out[22]:
array([1.37818754e-08, 4.49490871e-08, 7.63733781e-08, ...,
9.99259177e-05, 9.99504745e-05, 9.99753343e-05], shape=(512000,))
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P2.drift_to_z()
P2.plot("t", "energy")
P2
P2.drift_to_z()
P2.plot("t", "energy")
P2
Out[23]:
<ParticleGroup with 512000 particles at 0x7f890d46c5f0>
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P2.plot("weight", bins=100)
P2.plot("weight", bins=100)
Notice that importdistribution is filled in:
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print(G1.input.to_genesis())
print(G1.input.to_genesis())
# Main input
&setup
rootname = drift_test
lattice = genesis.lat
beamline = LAT
gamma0 = 1000.0
lambda0 = 1e-07
delz = 0.026
seed = 123456
npart = 512
&end
&time
slen = 9.999850899316347e-05
&end
&importdistribution
file = initial_particles.h5
charge = 1.667822143811236e-10
&end
&track
zstop = 1.0
&end
&write
beam = end
&end
# Lattice
D1: drift = {l=1.0};
LAT: LINE = {D1};
Cleanup¶
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G1.input.initial_particles
G1.input.initial_particles
Out[26]:
<ParticleGroup with 128000 particles at 0x7f890147bed0>
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os.remove(DIST_FILE)
os.remove(DIST_FILE)