Merge branch 'develop'

SmileiPIC · Oct 29, 2024 · a314517 · a314517
2 parents 60be162 + 538f721
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diff --git a/.gitignore b/.gitignore
@@ -33,3 +33,4 @@ exec_script.sh.*
 .DS_Store
 tables/*
 *.stats*
+.venv*
diff --git a/benchmarks/collisions/ionization_multiple.py b/benchmarks/collisions/ionization_multiple.py
@@ -22,7 +22,7 @@
 
 		timestep2 = int(np.double(S2.namelist.Main.timestep))
 		D += [
-			S2.ParticleBinning(0,sum={"ekin":[0,1]}, linestyle="", marker=".", color=color )
+			S2.ParticleBinning(0,sum={"ekin":[0,1]}, linestyle="", marker=".", color=color, label=elm )
 		]
 
 

diff --git a/benchmarks/tst_collisions3_AM_uniformity.py b/benchmarks/tst_collisions3_AM_uniformity.py
@@ -0,0 +1,87 @@
+# ---------------------------------------------
+# SIMULATION PARAMETERS FOR THE PIC-CODE SMILEI
+# ---------------------------------------------
+
+import math
+L0 = 2.*math.pi # conversion from normalization length to wavelength
+
+
+Main(
+	geometry = "AMcylindrical",
+
+	number_of_patches = [ 4, 4 ],
+
+	interpolation_order = 2,
+        number_of_AM = 1,
+
+	timestep = 1 * L0,
+	simulation_time = 10 * L0,
+
+	time_fields_frozen = 100000000000.,
+
+	cell_length = [L0, L0],
+	grid_length = [64.*L0, 64*L0],
+
+	EM_boundary_conditions = [ ["periodic", "periodic"], ["silver-muller", "buneman"] ],
+
+	solve_poisson = False,
+
+	reference_angular_frequency_SI = L0 * 3e8 /1.e-6,
+)
+
+
+ion = "ion"
+eon = "eon"
+
+Species(
+	name = eon,
+	position_initialization = "random",
+	momentum_initialization = "cold",
+	particles_per_cell= 100,
+	mass = 1.0,
+	charge = -1.0,
+	charge_density = 1.,
+	mean_velocity = [0.8, 0., 0.],
+	temperature = [0.]*3,
+	time_frozen = 100000000.0,
+	boundary_conditions = [
+		["periodic", "periodic"],
+		["remove", "remove"],
+	],
+)
+
+Species(
+	name = ion,
+	position_initialization = "random",
+	momentum_initialization = "cold",
+	particles_per_cell= 100,
+	mass = 1836.0*13.,
+	charge = 3.0,
+	charge_density = 1.,
+	mean_velocity = [0., 0., 0.],
+	temperature = [0.]*3,
+	time_frozen = 100000000.0,
+	boundary_conditions = [
+		["periodic", "periodic"],
+		["remove", "reflective"],
+	],
+	atomic_number = 13
+)
+
+Collisions(
+	species1 = [eon],
+	species2 = [ion],
+	coulomb_log = 3,
+)
+
+def radius(particles): return np.sqrt(particles.y**2 + particles.z**2)
+
+DiagParticleBinning(
+	deposited_quantity = "weight_vy_py",
+	every = 4,
+	species = [ion],
+	axes = [
+		 ["x",       0,    Main.grid_length[0],   64],
+		 [radius,    0,    Main.grid_length[1],   64]
+	]
+)
diff --git a/doc/Sphinx/Overview/material.rst b/doc/Sphinx/Overview/material.rst
@@ -30,7 +30,7 @@ Papers involving Smilei
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
 Only papers published in peer-reviewed journals are listed (for the complete list of citing papers see `Google Scholar <https://scholar.google.com/scholar?hl=fr&as_sdt=2005&sciodt=0,5&cites=17416460455672944837&scipsc=&q=&scisbd=1>`_).
-As of May 2024, at least 192 papers have been published covering a broad range of topics:
+As of October 2024, at least 211 papers have been published covering a broad range of topics:
 
 * laser-plasma interaction (LPI) / inertial fusion (FCI)
 * ultra-high intensity (UHI) applications
@@ -51,6 +51,127 @@ Following is the distribution of these topics in the listed publications up to N
    You can count the number of papers in the list with the vim command :%s/.. \[//gn. 
 
 
+.. [Jirka2024]
+
+    M. Jirka and S. V. Bulanov,
+    `Effects of Colliding Laser Pulses Polarization on e- e+ Cascade Development in Extreme Focusing`,
+    `Physical Review Letters 133, 125001 (2024) <http://dx.doi.org/10.1103/PhysRevLett.133.125001>`_
+
+.. [Plotnikov2024]
+
+    I. Plotnikov, A. J. van Marle, C. Guépin, A. Marcowith and Pierrick Martin,
+    `Kinetic simulations of electron–positron induced streaming instability in the context of gamma-ray halos around pulsars`,
+    `Astronomy & Astrophysics 688, A134 (2024) <http://dx.doi.org/10.1051/0004-6361/202449661>`_
+
+.. [Mukherjee2024]
+
+    A. Mukherjee and Daniel Seipt,
+    `Laser polarization control of ionization-injected electron beams and x-ray radiation in laser wakefield accelerators`,
+    `Plasma Physics and Controlled Fusion 66, 085001 (2024) <http://dx.doi.org/10.1088/1361-6587/ad5379>`_
+
+.. [Yao2024]
+
+    W. Yao, R. Lelièvre, T. Waltenspiel, I. Cohen, A. Allaoua, P. Antici, A. Beck, E. Cohen, X. Davoine, E. d’Humières, Q. Ducasse, E. Filippov, C. Gautier, L. Gremillet, P. Koseoglou, D. Michaeli, D. Papadopoulos, S. Pikuz, I. Pomerantz, F. Trompier, Y. Yuan, F. Mathieu and Julien Fuchs,
+    `Enhanced Energy, Conversion Efficiency and Collimation of Protons Driven by High-Contrast and Ultrashort Laser Pulses`,
+    `Applied Sciences 14, 6101 (2024) <http://dx.doi.org/10.3390/app14146101>`_
+
+.. [Dmitriev2024]
+
+    E. Dmitriev and Ph. Korneev,
+    `Angular momentum gain by electrons under the action of intense structured light`,
+    `Physical Review A 110, 013514 (2024) <http://dx.doi.org/10.1103/PhysRevA.110.013514>`_
+
+.. [Yu2024]
+
+    H. Yu, Q. Xia and Jun Fang,
+    `Nonthermal Acceleration of Electrons, Positrons, and Protons at a Nonrelativistic Quasi-parallel Collisionless Shock`,
+    `The Astrophysical Journal 969, 13 (2024) <http://dx.doi.org/10.3847/1538-4357/ad5181>`_
+
+
+.. [Liu2024]
+
+    B. Liu, B. Lei, Y. Gao, M. Wen, and K. Zhu,
+    `Plasma opacity induced by laser-driven movement of background ions`,
+    `Plasma Physics and Controlled Fusion 66, 115004  (2024) <https://doi.org/10.1088/1361-6587/ad797f>`_
+
+.. [Martin2024]
+
+    H. Martin, R. W. Paddock, M. W. von der Leyen, V. Eliseev, R. T. Ruskov, R. Timmis, J. J. Lee, A. James, and P. A. Norreys,
+    `Electrothermal filamentation of igniting plasmas`,
+    `Physical Review E 110, 035205 (2024) <https://doi.org/10.1103/PhysRevE.110.035205>`_
+
+.. [Horny2024]
+
+    V. Horný, P. G. Bleotu, D. Ursescu, V. Malka, and P. Tomassini,
+    `Efficient laser wakefield accelerator in pump depletion dominated bubble regime`,
+    `Physical Review E 110, 035202 (2024) <https://doi.org/10.1103/PhysRevE.110.035202>`_
+       
+.. [DeAndres2024]
+
+    A. De Andres, S. Bhadoria, J. T. Marmolejo, A. Muschet, P. Fischer, H. R. Barzegar, T. Blackburn, A. Gonoskov, D. Hanstorp, M. Marklund and L. Veisz,
+    `Unforeseen advantage of looser focusing in vacuum laser acceleration`,
+    `Nature Communications Physics 7, 293 (2024) <https://doi.org/10.1038/s42005-024-01781-9>`_
+
+.. [Yoon2024]
+
+    Y. D. Yoon, M. Laishram, T. E. Moore, and G. S. Yun,
+    `Non-equilibrium formation and relaxation of magnetic flux ropes at kinetic scales`,
+    `Nature Communications Physics 7, 297 (2024) <https://doi.org/10.1038/s42005-024-01784-6>`_
+
+.. [Laishram2024]
+
+    M. Laishram, G. S. Yun, and Y. D. Yoon,
+    `Magnetogenesis via the canonical battery effect`,
+    `Physical Review Research 6, L032052 (2024) <https://doi.org/10.1103/PhysRevResearch.6.L032052>`_
+
+.. [Kang2024]
+
+    H. L. Kang, Y. D. Yoon, M.-H. Cho and G. S. Yun,
+    `Fast nonlinear scattering of runaway electron beams through resonant interactions with plasma waves`,
+    `Nuclear Fusion 64, 10 (2024) <https://doi.org/10.1088/1741-4326/ad6ce6>`_
+       
+.. [Gonzalez-Izquierdo2024]
+
+    B. Gonzalez-Izquierdo, P. Fischer, M. Touati, J. Hartmann, M. Speicher, V. Scutelnic, G. Bodini, A. Fazzini, M. M. Guenther, A. K. Haerle, K. Kenney, E. Schork, S. Bruce, M. Spinks, H. J. Quevedo, A. Helal, M. Medina, E. Gaul, H. Ruhl, M. Schollmeier, S. Steinke, and G. Korn,
+    `Efficient laser-driven proton acceleration from a petawatt contrast-enhanced second harmonic mixed-glass laser system`,
+    `Physics of Plasmas 31, 083105 (2024) <https://doi.org/10.1063/5.0191366>`_
+       
+.. [Ma2024]
+
+    Z. Ma, Y. Wang, Y. Yang, Y. Wang, K. Zhao, Y. Li, C. Fu, W. He, Y. Ma,
+    `Simulation of nuclear isomer production in laser-induced plasma`,
+    `Matter and Radiation at Extremes 9, 055201 (2024) <https://doi.org/10.1063/5.0212163>`_
+       
+.. [Kleij2024]
+
+    P. S. Kleij, S. Marini, M. Caetano de Sousa, M. Grech, C. Riconda, M. Raynaud,
+    `Photon emission and radiation reaction effects in surface plasma waves in ultra-high intensities`,
+    `Physics of Plasmas 31, 072111 (2024) <https://doi.org/10.1063/5.0209316>`_
+       
+.. [Ghizzo2024]
+
+    A. Ghizzo, D. Del Sarto, H. Betar,
+    `Collisionless heating in Vlasov plasma and turbulence-driven filamentation aspects`,
+    `Physics of Plasmas 31, 072109 (2024) <https://doi.org/10.1063/5.0205253>`_
+
+.. [Gelfer2024]
+
+    E. G. Gelfer, A. M. Fedotov, O. Klimo, and S. Weber,
+    `Coherent radiation of an electron bunch colliding with an intense laser pulse`,
+    `Physical Review Research 6, L032013 (2024) <https://doi.org/10.1103/PhysRevResearch.6.L032013>`_
+
+.. [Zagidullin2024]
+
+    R. Zagidullin, V. Zorina, J. W. Wang, S. G. Rykovanov,
+    `Polarization control of attosecond pulses from laser-nanofoil interactions using an external magnetic field`,
+    `Physics of Plasmas 31, 073303 (2024) <https://doi.org/10.1063/5.0213592>`_
+
+.. [Marini2024]
+
+    S. Marini, D. F. G. Minenna, F. Massimo, L. Batista, V. Bencini, A. Chancé, N. Chauvin, S. Doebert, J. Farmer, E. Gschwendtner, I. Moulanier, P. Muggli, D. Uriot, B. Cros, and P. A. P. Nghiem,
+    `Beam physics studies for a high charge and high beam quality laser-plasma accelerator`,
+    `Physical Review Accelerators and Beams 27, 063401 (2024) <https://doi.org/10.1103/PhysRevAccelBeams.27.063401>`_
+
 .. [Sikorski2024]
 
     P. Sikorski, A. G. R. Thomas, S. S. Bulanov, M. Zepf and D. Seipt,
@@ -385,7 +506,7 @@ Following is the distribution of these topics in the listed publications up to N
 
   V. Istokskaia, M. Tosca, L. Giuffrida, J. Psikal, F. Grepl, V. Kantarelou, S. Stancek, S. Di Siena, A. Hadjikyriacou, A. McIlvenny, Y. Levy, J. Huynh, M. Cimrman, P. Pleskunov, D. Nikitin, A. Choukourov, F. Belloni, A. Picciotto, S. Kar, M. Borghesi, A. Lucianetti, T. Mocek and D. Margarone,
   `A multi-MeV alpha particle source via proton-boron fusion driven by a 10-GW tabletop laser`,
-  `Communications Physics 6, 27 (2023) <http://dx.doi.org/10.1038/s42005-023-01135-x>`_
+  `Nature Communications Physics 6, 27 (2023) <http://dx.doi.org/10.1038/s42005-023-01135-x>`_
 
 .. [Yoon2023]
 
@@ -428,6 +549,12 @@ Following is the distribution of these topics in the listed publications up to N
     S. Marini, M. Grech, P. S. Kleij, M. Raynaud and C. Riconda,
     `Electron acceleration by laser plasma wedge interaction`,
     `Physical Review Research 5, 013115 (2023) <http://dx.doi.org/10.1103/PhysRevResearch.5.013115>`_
+  
+.. [Miloshevsky2023] 
+
+    G. Miloshevsky,
+    `Particle-in-Cell Modeling of Omega Experiments on Ablation of Plasmas`,
+    `IEEE Transactions on Plasma Science 51, 4 (2023) <https://doi.org/10.1109/TPS.2022.3220184>`_
 
 .. [Blackman2022]
 
@@ -507,7 +634,7 @@ Following is the distribution of these topics in the listed publications up to N
      `Injection of electron beams into two laser wakefields and generation of electron rings`,
      `Physical Review E 106, 055202 (2022) <https://doi.org/10.1103/PhysRevE.106.055202>`_
 
-.. [Kumar2022b]
+.. [Ku2022]
 
     S. Ku., R. Dhawan, D.K. Singh and H. K. Malik,
     `Diagnostic of laser wakefield acceleration with ultra – Short laser pulse by using SMILEI PIC code`,
@@ -519,12 +646,6 @@ Following is the distribution of these topics in the listed publications up to N
     `Comparative study of ultrashort single-pulse and multi-pulse driven laser wakefield acceleration`,
     `Laser Physics Letters 20, 026001 (2022) <http://dx.doi.org/10.1088/1612-202X/aca978>`_
 
-.. [Miloshevsky2022]
-
-    G. Miloshevsky,
-    `Pic Modeling of Omega Experiments on Ablation of Plasmas`,
-    `2022 IEEE International Conference on Plasma Science (ICOPS), ICOPS45751.2022.9813047 (2022) <http://dx.doi.org/10.1109/ICOPS45751.2022.9813047>`_
-
 .. [Zhang2022b]
 
     Y. Zhang, F. Wang, J. Liu and J. Sun,
@@ -628,12 +749,6 @@ Following is the distribution of these topics in the listed publications up to N
   `Subcycle terahertz field waveforms clocked by attosecond high-harmonic pulses from relativistic laser plasmas`,
   `Journal of Applied Physics 131, 103104 (2022) <http://dx.doi.org/10.1063/5.0070670>`_
 
-.. [Umstadter2022]
-
-   D. Umstadter
-   `Controlled Injection of Electrons for Improved Performance of Laser-Wakefield Acceleration`,
-   `United States Department of Energy Technical Report (2022) <http://dx.doi.org/10.2172/1838680>`_
-
 .. [Massimo2022]
 
   F. Massimo, M. Lobet, J. Derouillat, A. Beck, G. Bouchard, M. Grech, F. Pérez, T. Vinci,
@@ -880,7 +995,7 @@ Following is the distribution of these topics in the listed publications up to N
 
   W. Yao, A. Fazzini, S. N. Chen, K. Burdonov, P. Antici, J. Béard, S. Bolaños, A. Ciardi, R. Diab, E. D. Filippov, S. Kisyov, V. Lelasseux, M. Miceli, Q. Moreno, V. Nastasa, S. Orlando, S. Pikuz, D. C. Popescu, G. Revet, X. Ribeyre, E. d’Humières and J. Fuchs,
   `Laboratory evidence for proton energization by collisionless shock surfing`,
-  `Nat. Phys. 17, 1177-1182 (2021) <http://dx.doi.org/10.1038/s41567-021-01325-w>`_
+  `Nature Physics 17, 1177-1182 (2021) <http://dx.doi.org/10.1038/s41567-021-01325-w>`_
 
 .. [Gelfer2021]
 

diff --git a/doc/Sphinx/Overview/releases.rst b/doc/Sphinx/Overview/releases.rst
@@ -28,12 +28,14 @@ Changes made in the repository (not released)
   * Prescribed fields in AM geometry.
   * Particle reflective boundary conditions at Rmax in AM geometry.
   * 1st order Ruyten shape function in AM geometry.
+  * Support for collisions in single mode AM geometry.
 
 * **Bug fixes**:
 
   * Tunnel ionization was wrong in some cases for high atomic numbers.
   * Custom functions in ``ParticleBinning`` crashed with python 3.12.
   * Species-specific diagnostics in AM geometry with vectorization.
+  * Frozen particles in AM geometry with adaptive vectorization.
   * Happi's ``average`` argument would sometimes be missing the last bin.
   * 1D projector on GPU without diagnostics
 

diff --git a/doc/Sphinx/Understand/collisions.rst b/doc/Sphinx/Understand/collisions.rst
@@ -309,21 +309,38 @@ the ion:
   \sum\limits_{p=0}^{k-1} R^{i+k}_{i+p} \left(\bar{P}^{i+k} - \bar{P}^{i+p}\right)
   \prod\limits_{j=0,j\ne p}^{k-1} R^{i+p}_{i+j}
   &
-  \quad\mathrm{if}\quad 0<k<k_\mathrm{max}
+  \quad\mathrm{if}\quad 0<k<Z-Z^\star
+  \end{array}
+  \right.
+
+..
   \\
   \sum\limits_{p=0}^{k-1} \left[ 1+R^{i+k}_{i+p}\left(\frac{W_{i+k}}{W_{i+p}}\bar{P}^{i+p} - \bar{P}^{i+k}\right) \right]
   \prod\limits_{j=0,j\ne p}^{k-1} R^{i+p}_{i+j}
   &
   \quad\mathrm{if}\quad k=k_\mathrm{max}
-  \end{array}
-  \right.
 
-where :math:`k_\mathrm{max} = Z-Z^\star`.
+
+To simplify the calculation of :math:`P^i_k` (in particular the second case in the
+equation above) we use the following equivalent expression:
+
+.. math::
+  
+  P^i_k = A_{k-1} \sum\limits_{p=0}^{k-1}  \left(\bar{P}^{i+k} - \bar{P}^{i+p}\right)
+  / B_k^p
+  \quad\mathrm{if}\quad 0<k<Z-Z^\star
+
+where :math:`A_k = \prod\limits_{j=0}^{k} W_{i+j}` and
+:math:`B_k^p = \prod\limits_{j=0,j\ne p}^{k} (W_{i+j}-W_{i+p})`.
+These two quantities can be computed recursively for each :math:`k`.
+
 
 The cumulative probability :math:`F^i_k = \sum_{j=0}^{k} P^i_j` provides an efficient
 way to pick when the ionization stops: we pick a random number :math:`U\in [0,1]` and
 loop from :math:`k=0` to :math:`k_\mathrm{max}`. We stop ionizing when :math:`F^i_k>U`.
 
+
+
 ----
 
 Test cases for ionization

diff --git a/doc/Sphinx/Use/namelist.rst b/doc/Sphinx/Use/namelist.rst
@@ -1390,8 +1390,8 @@ Lasers
 ^^^^^^
 
 A laser consists in applying oscillating boundary conditions for the magnetic
-field on one of the box sides. The only boundary condition that supports lasers
-is ``"silver-muller"`` (see :py:data:`EM_boundary_conditions`).
+field on one of the box sides. The only boundary conditions that support lasers
+are ``"silver-muller"`` and ``"PML"`` (see :py:data:`EM_boundary_conditions`).
 There are several syntaxes to introduce a laser in :program:`Smilei`:
 
 .. note::
@@ -1440,10 +1440,10 @@ There are several syntaxes to introduce a laser in :program:`Smilei`:
 
 .. py:data:: space_time_profile_AM
 
-    :type: A list of maximum 2 x ``number_of_AM`` *python* functions.
+    :type: A list of maximum 2 x ``number_of_AM`` complex valued *python* functions.
 
-    These profiles define the first modes of :math:`B_r` and :math:`B_\theta` in the
-    order shown in the above example. Undefined modes are considered zero.
+    These profiles define the first modes of :math:`B_r` and :math:`B_\theta` of the laser in the
+    order shown in the above example. Higher undefined modes are considered zero.
     This can be used only in ``AMcylindrical`` geometry. In this
     geometry a two-dimensional :math:`(x,r)` grid is used and the laser is injected from a
     :math:`x` boundary, thus the provided profiles must be a function of :math:`(r,t)`.