Merge branch 'development' into add_particle_boundary_none

.github/workflows/cuda.yml

@@ -115,7 +115,7 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach d857968968ae2cdf18f39ee50df96529e326ff39 && cd -
+        cd ../amrex && git checkout --detach 7ca419ebb90da60fefc01d8c1816846fff8638a5 && cd -
         make COMP=gcc QED=FALSE USE_MPI=TRUE USE_GPU=TRUE USE_OMP=FALSE USE_PSATD=TRUE USE_CCACHE=TRUE -j 4
 
         ccache -s

CMakeLists.txt

@@ -1,7 +1,7 @@
 # Preamble ####################################################################
 #
 cmake_minimum_required(VERSION 3.20.0)
-project(WarpX VERSION 24.04)
+project(WarpX VERSION 24.05)
 
 include(${WarpX_SOURCE_DIR}/cmake/WarpXFunctions.cmake)
 

Docs/source/conf.py

@@ -103,9 +103,9 @@ def __init__(self, *args, **kwargs):
 # built documents.
 #
 # The short X.Y version.
-version = u'24.04'
+version = u'24.05'
 # The full version, including alpha/beta/rc tags.
-release = u'24.04'
+release = u'24.05'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

Examples/Tests/nuclear_fusion/analysis_proton_boron_fusion.py

@@ -40,8 +40,8 @@
 ## the initial number of protons and borons.
 ##
 ## The third test corresponds to a Maxwellian plasma with a 44 keV temperature. The alpha yield is
-## directly compared to the analytical fits of W.M. Nevins and R. Swain, Nuclear Fusion, 40, 865
-## (2000) for a thermal plasma.
+## directly compared to the analytical fits of A. Tentori and F. Belloni, Nuclear Fusion, 63, 086001
+## (2023) for a thermal plasma.
 ##
 ## The fourth test corresponds to a plasma with an extremely small boron density, so that all boron
 ## macroparticles should have disappeared by the end of the simulation, which we verify.
@@ -259,10 +259,10 @@ def check_isotropy(data, relative_tolerance):
 def astrophysical_factor_lowE(E):
     ## E is in keV
     ## Returns astrophysical factor in MeV b using the low energy fit in the range E < 400 keV
-    ## described in equation (2) of W.M. Nevins and R. Swain, Nuclear Fusion, 40, 865 (2000)
+    ## described in equation (3) of A. Tentori and F. Belloni, Nuclear Fusion, 63, 086001 (2023)
     C0 = 197.
-    C1 = 0.24
-    C2 = 2.31e-4
+    C1 = 0.269
+    C2 = 2.54e-4
     AL = 1.82e4
     EL = 148.
     dEL = 2.35
@@ -271,12 +271,12 @@ def astrophysical_factor_lowE(E):
 def astrophysical_factor_midE(E):
     ## E is in keV
     ## Returns astrophysical factor in MeV b using the mid energy fit in the range
-    ## 400 keV < E < 642 keV described in equation (3) of W.M. Nevins and R. Swain,
-    ## Nuclear Fusion, 40, 865 (2000)
-    D0 = 330.
-    D1 = 66.1
-    D2 = -20.3
-    D5 = -1.58
+    ## 400 keV < E < 668 keV described in equation (4) of A. Tentori and F. Belloni,
+    ## Nuclear Fusion, 63, 086001 (2023)
+    D0 = 346.
+    D1 = 150.
+    D2 = -59.9
+    D5 = -0.460
     E_400 = 400.
     E_100 = 100.
     E_norm = (E - E_400)/E_100
@@ -285,29 +285,29 @@ def astrophysical_factor_midE(E):
 def astrophysical_factor_highE(E):
     ## E is in keV
     ## Returns astrophysical factor in MeV b using the high energy fit in the range
-    ## 642 keV < E < 3500 keV described in equation (4) of W.M. Nevins and R. Swain,
-    ## Nuclear Fusion, 40, 865 (2000)
-    A0 = 2.57e6
-    A1 = 5.67e5
-    A2 = 1.34e5
-    A3 = 5.68e5
-    E0 = 581.3
-    E1 = 1083.
-    E2 = 2405.
-    E3 = 3344.
-    dE0 = 85.7
-    dE1 = 234.
-    dE2 = 138.
-    dE3 = 309.
-    B = 4.38
+    ## 668 keV < E < 9760 keV described in equation (5) of A. Tentori and F. Belloni,
+    ## Nuclear Fusion, 63, 086001 (2023)
+    A0 = 1.98e6
+    A1 = 3.89e6
+    A2 = 1.36e6
+    A3 = 3.71e6
+    E0 = 640.9
+    E1 = 1211.
+    E2 = 2340.
+    E3 = 3294.
+    dE0 = 85.5
+    dE1 = 414.
+    dE2 = 221.
+    dE3 = 351.
+    B = 0.381
     return A0/((E-E0)**2 + dE0**2) + A1/((E-E1)**2 + dE1**2) + \
            A2/((E-E2)**2 + dE2**2) + A3/((E-E3)**2 + dE3**2) + B
 
 def astrophysical_factor(E):
     ## E is in keV
-    ## Returns astrophysical factor in MeV b using the fits described in W.M. Nevins
-    ## and R. Swain, Nuclear Fusion, 40, 865 (2000)
-    conditions = [E <= 400, E <= 642, E > 642]
+    ## Returns astrophysical factor in MeV b using the fits described in A. Tentori
+    ## and F. Belloni, Nuclear Fusion, 63, 086001 (2023)
+    conditions = [E <= 400, E <= 668, E > 668]
     choices = [astrophysical_factor_lowE(E),
                astrophysical_factor_midE(E),
                astrophysical_factor_highE(E)]
@@ -316,20 +316,20 @@ def astrophysical_factor(E):
 def pb_cross_section_buck_fit(E):
     ## E is in MeV
     ## Returns cross section in b using a power law fit of the data presented in Buck et al.,
-    ## Nuclear Physics A, 398(2), 189-202 (1983) in the range E > 3.5 MeV.
-    E_start_fit = 3.5
+    ## Nuclear Physics A, 398(2), 189-202 (1983) in the range E > 9.76 MeV.
+    E_start_fit = 9.76
     ## Cross section at E = E_start_fit = 3.5 MeV
-    cross_section_start_fit = 0.2168440845211521
+    cross_section_start_fit = 0.01277998
     slope_fit = -2.661840717596765
     return cross_section_start_fit*(E/E_start_fit)**slope_fit
 
 def pb_cross_section(E):
     ## E is in keV
-    ## Returns cross section in b using the fits described in W.M. Nevins and R. Swain,
-    ## Nuclear Fusion, 40, 865 (2000) for E < 3.5 MeV and a power law fit of the data presented in
-    ## Buck et al., Nuclear Physics A, 398(2), 189-202 (1983) for E > 3.5 MeV.
+    ## Returns cross section in b using the fits described in A. Tentori and F. Belloni,
+    ## Nucl. Fusion, 63, 086001 (2023) for E < 9.76 MeV otherwise returns a power law fit
+    ## of the data in Buck et al., Nuclear Physics A, 398(2), 189-202 (1983)
     E_MeV = E/1.e3
-    conditions = [E <= 3500, E > 3500]
+    conditions = [E <= 9760, E > 9760]
     choices = [astrophysical_factor(E)/E_MeV * np.exp(-np.sqrt(E_Gamow_MeV / E_MeV)),
                pb_cross_section_buck_fit(E_MeV)]
     return np.select(conditions, choices)
@@ -598,13 +598,13 @@ def check_xy_isotropy(data):
 def sigmav_thermal_fit_lowE_nonresonant(T):
     ## Temperature T is in keV
     ## Returns the nonresonant average of cross section multiplied by relative velocity in m^3/s,
-    ## in the range T <= 70 keV, as described by equation 9 of W.M. Nevins and R. Swain,
-    ## Nuclear Fusion, 40, 865 (2000).
+    ## in the range T <= 70 keV, as described by equations 10-14 of A. Tentori and F. Belloni,
+    ## Nuclear Fusion, 63, 086001 (2023).
     E0 = (E_Gamow_keV/4.)**(1./3.) * T**(2./3.)
     DE0 = 4.*np.sqrt(T*E0/3.)
     C0 = 197.*1.e3
-    C1 = 0.24*1.e3
-    C2 = 2.31e-4*1.e3
+    C1 = 0.269*1.e3
+    C2 = 2.54e-4*1.e3
     tau = 3.*E0/T
     Seff = C0*(1.+5./(12.*tau)) + C1*(E0+35./36.*T) + C2*(E0**2 + 89./36.*E0*T)
     ## nonresonant sigma times vrel, in barn meter per second
@@ -615,21 +615,21 @@ def sigmav_thermal_fit_lowE_nonresonant(T):
 def sigmav_thermal_fit_lowE_resonant(T):
     ## Temperature T is in keV
     ## Returns the resonant average of cross section multiplied by relative velocity in m^3/s,
-    ## in the range T <= 70 keV, as described by equation 11 of W.M. Nevins and R. Swain,
-    ## Nuclear Fusion, 40, 865 (2000).
+    ## in the range T <= 70 keV, as described by equation 15 of A. Tentori and F. Belloni,
+    ## Nuclear Fusion, 63, 086001 (2023).
     return 5.41e-21 * np.exp(-148./T) / T**(3./2.)
 
 def sigmav_thermal_fit_lowE(T):
     ## Temperature T is in keV
     ## Returns the average of cross section multiplied by relative velocity in m^3/s, using the
-    ## fits described in section 3.1 of W.M. Nevins and R. Swain, Nuclear Fusion, 40, 865 (2000).
+    ## fits described in section 2.2 of A. Tentori and F. Belloni, Nuclear Fusion, 63, 086001 (2023).
     ## The fits are valid for T <= 70 keV.
     return sigmav_thermal_fit_lowE_nonresonant(T) + sigmav_thermal_fit_lowE_resonant(T)
 
 def expected_alpha_thermal(T, proton_density, boron_density, dV, dt):
     ## Computes the expected number of produced alpha particles when the protons and borons follow
     ## a Maxwellian distribution with a temperature T, in keV. This uses the thermal fits described
-    ## in W.M. Nevins and R. Swain, Nuclear Fusion, 40, 865 (2000).
+    ## in A. Tentori and F. Belloni, Nuclear Fusion, 63, 086001 (2023).
 
     ## The fit used here is only valid in the range T <= 70 keV.
     assert((T >=0) and (T<=70))

Examples/Tests/scraping/analysis_rz.py

@@ -60,6 +60,14 @@ def n_scraped_particles( iteration ):
 n_total = n_remaining[0]
 assert np.all( n_scraped+n_remaining == n_total)
 
+# Check that the particle IDs match between the initial iteration
+# (all particles in the simulation domain) and the finall iteration (particles are either scraped or still in simulation box)
+id_initial, = ts_full.get_particle(['id'], iteration=0)
+id_final_scrape, = ts_scraping.get_particle(['id'], iteration=ts_scraping.iterations[0])
+id_final_box, = ts_full.get_particle(['id'], iteration=ts_full.iterations[-1])
+id_final = np.concatenate( (id_final_scrape, id_final_box))
+assert np.all( np.sort(id_initial) == np.sort(id_final) ) # Sort because particles may not be in the same order
+
 # Checksum test
 test_name = os.path.split(os.getcwd())[1]
 checksumAPI.evaluate_checksum(test_name, fn, do_particles=False)

LICENSE.txt

@@ -1,16 +1,44 @@
-WarpX Copyright (c) 2018, The Regents of the University of California, through Lawrence Berkeley National Laboratory, and Lawrence Livermore National Security, LLC, for the operation of Lawrence Livermore National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.
-
-
-Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-
-
-(1) Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
-
-(2) Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
-
-(3) Neither the name of the University of California, Lawrence Berkeley National Laboratory, Lawrence Livermore National Security, LLC, Lawrence Livermore National Laboratory, U.S. Dept. of Energy, nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-You are under no obligation whatsoever to provide any bug fixes, patches, or upgrades to the features, functionality or performance of the source code ("Enhancements") to anyone; however, if you choose to make your Enhancements available either publicly, or directly to Lawrence Berkeley National Laboratory, without imposing a separate written license agreement for such Enhancements, then you hereby grant the following license: a non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into other computer software, distribute, and sublicense such enhancements or derivative works thereof, in binary and source code form.
+WarpX Copyright (c) 2018, The Regents of the University of California,
+through Lawrence Berkeley National Laboratory, and Lawrence Livermore National
+Security, LLC, for the operation of Lawrence Livermore National Laboratory
+(subject to receipt of any required approvals from the U.S. Dept. of Energy).
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+(1) Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+
+(2) Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+(3) Neither the name of the University of California, Lawrence Berkeley
+National Laboratory, U.S. Dept. of Energy nor the names of its contributors
+may be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+
+You are under no obligation whatsoever to provide any bug fixes, patches,
+or upgrades to the features, functionality or performance of the source
+code ("Enhancements") to anyone; however, if you choose to make your
+Enhancements available either publicly, or directly to Lawrence Berkeley
+National Laboratory, without imposing a separate written license agreement
+for such Enhancements, then you hereby grant the following license: a
+non-exclusive, royalty-free perpetual license to install, use, modify,
+prepare derivative works, incorporate into other computer software,
+distribute, and sublicense such enhancements or derivative works thereof,
+in binary and source code form.

Python/setup.py

@@ -54,7 +54,7 @@
     package_data = {}
 
 setup(name = 'pywarpx',
-      version = '24.04',
+      version = '24.05',
       packages = ['pywarpx'],
       package_dir = {'pywarpx': 'pywarpx'},
       description = """Wrapper of WarpX""",