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-rw-r--r--Source/Utils/IonizationEnergiesTable.H6
-rw-r--r--Source/Utils/NCIGodfreyTables.H6
-rw-r--r--Source/Utils/WarpXAlgorithmSelection.H7
-rw-r--r--Source/Utils/WarpXAlgorithmSelection.cpp8
-rw-r--r--Source/Utils/WarpXConst.H7
-rw-r--r--Source/Utils/WarpXMovingWindow.cpp129
-rw-r--r--Source/Utils/WarpXTagging.cpp7
-rw-r--r--Source/Utils/WarpXUtil.H117
-rw-r--r--Source/Utils/WarpXUtil.cpp50
-rw-r--r--Source/Utils/WarpX_Complex.H21
-rw-r--r--Source/Utils/atomic_data.txt6
-rw-r--r--Source/Utils/utils_ES.F906
-rw-r--r--Source/Utils/write_atomic_data_cpp.py8
13 files changed, 336 insertions, 42 deletions
diff --git a/Source/Utils/IonizationEnergiesTable.H b/Source/Utils/IonizationEnergiesTable.H
index 47b71e4f1..f910fa4fe 100644
--- a/Source/Utils/IonizationEnergiesTable.H
+++ b/Source/Utils/IonizationEnergiesTable.H
@@ -1,3 +1,9 @@
+/* Copyright 2019 Axel Huebl, Maxence Thevenet
+ *
+ * This file is part of WarpX.
+ *
+ * License: BSD-3-Clause-LBNL
+ */
// This script was automatically generated!
// Edit dev/Source/Utils/write_atomic_data_cpp.py instead!
#ifndef WARPX_IONIZATION_TABLE_H_
diff --git a/Source/Utils/NCIGodfreyTables.H b/Source/Utils/NCIGodfreyTables.H
index 708215c77..0403b10c3 100644
--- a/Source/Utils/NCIGodfreyTables.H
+++ b/Source/Utils/NCIGodfreyTables.H
@@ -1,3 +1,9 @@
+/* Copyright 2019 Maxence Thevenet
+ *
+ * This file is part of WarpX.
+ *
+ * License: BSD-3-Clause-LBNL
+ */
#include <AMReX_AmrCore.H>
#ifndef WARPX_GODFREY_COEFF_TABLE_H_
diff --git a/Source/Utils/WarpXAlgorithmSelection.H b/Source/Utils/WarpXAlgorithmSelection.H
index 7d26e7af5..919428704 100644
--- a/Source/Utils/WarpXAlgorithmSelection.H
+++ b/Source/Utils/WarpXAlgorithmSelection.H
@@ -1,3 +1,10 @@
+/* Copyright 2019 David Grote, Luca Fedeli, Remi Lehe
+ * Yinjian Zhao
+ *
+ * This file is part of WarpX.
+ *
+ * License: BSD-3-Clause-LBNL
+ */
#ifndef UTILS_WARPXALGORITHMSELECTION_H_
#define UTILS_WARPXALGORITHMSELECTION_H_
diff --git a/Source/Utils/WarpXAlgorithmSelection.cpp b/Source/Utils/WarpXAlgorithmSelection.cpp
index 08272089e..f6e2405a9 100644
--- a/Source/Utils/WarpXAlgorithmSelection.cpp
+++ b/Source/Utils/WarpXAlgorithmSelection.cpp
@@ -1,3 +1,11 @@
+/* Copyright 2019-2020 Axel Huebl, David Grote, Luca Fedeli
+ * Remi Lehe, Weiqun Zhang, Yinjian Zhao
+ *
+ *
+ * This file is part of WarpX.
+ *
+ * License: BSD-3-Clause-LBNL
+ */
#include <WarpXAlgorithmSelection.H>
#include <map>
diff --git a/Source/Utils/WarpXConst.H b/Source/Utils/WarpXConst.H
index 70436cb72..34e08118d 100644
--- a/Source/Utils/WarpXConst.H
+++ b/Source/Utils/WarpXConst.H
@@ -1,3 +1,10 @@
+/* Copyright 2019 Andrew Myers, Luca Fedeli, Maxence Thevenet
+ * Weiqun Zhang
+ *
+ * This file is part of WarpX.
+ *
+ * License: BSD-3-Clause-LBNL
+ */
#ifndef WARPX_CONST_H_
#define WARPX_CONST_H_
diff --git a/Source/Utils/WarpXMovingWindow.cpp b/Source/Utils/WarpXMovingWindow.cpp
index c577da7f3..f6cd6de20 100644
--- a/Source/Utils/WarpXMovingWindow.cpp
+++ b/Source/Utils/WarpXMovingWindow.cpp
@@ -1,4 +1,14 @@
+/* Copyright 2019-2020 Andrew Myers, Axel Huebl, Maxence Thevenet
+ * Remi Lehe, Revathi Jambunathan, Weiqun Zhang
+ *
+ *
+ * This file is part of WarpX.
+ *
+ * License: BSD-3-Clause-LBNL
+ */
+#include "GuardCellManager.H"
#include <WarpX.H>
+#include <WarpXUtil.H>
#include <WarpXConst.H>
using namespace amrex;
@@ -28,6 +38,9 @@ WarpX::MoveWindow (bool move_j)
{
if (do_moving_window == 0) return 0;
+ IntVect ng_extra = guard_cells.ng_Extra;
+ IntVect ng_zero = IntVect::TheZeroVector();
+
// Update the continuous position of the moving window,
// and of the plasma injection
moving_window_x += moving_window_v * dt[0];
@@ -97,34 +110,49 @@ WarpX::MoveWindow (bool move_j)
// Shift each component of vector fields (E, B, j)
for (int dim = 0; dim < 3; ++dim) {
-
// Fine grid
- shiftMF(*Bfield_fp[lev][dim], geom[lev], num_shift, dir, B_external_grid[dim]);
- shiftMF(*Efield_fp[lev][dim], geom[lev], num_shift, dir, E_external_grid[dim]);
+ ParserWrapper *Bfield_parser;
+ ParserWrapper *Efield_parser;
+ bool use_Bparser = false;
+ bool use_Eparser = false;
+ if (B_ext_grid_s == "parse_b_ext_grid_function") {
+ use_Bparser = true;
+ if (dim == 0) Bfield_parser = Bxfield_parser.get();
+ if (dim == 1) Bfield_parser = Byfield_parser.get();
+ if (dim == 2) Bfield_parser = Bzfield_parser.get();
+ }
+ if (E_ext_grid_s == "parse_e_ext_grid_function") {
+ use_Eparser = true;
+ if (dim == 0) Efield_parser = Exfield_parser.get();
+ if (dim == 1) Efield_parser = Eyfield_parser.get();
+ if (dim == 2) Efield_parser = Ezfield_parser.get();
+ }
+ shiftMF(*Bfield_fp[lev][dim], geom[lev], num_shift, dir, ng_extra, B_external_grid[dim], use_Bparser, Bfield_parser);
+ shiftMF(*Efield_fp[lev][dim], geom[lev], num_shift, dir, ng_extra, E_external_grid[dim], use_Eparser, Efield_parser);
if (move_j) {
- shiftMF(*current_fp[lev][dim], geom[lev], num_shift, dir);
+ shiftMF(*current_fp[lev][dim], geom[lev], num_shift, dir, ng_zero);
}
if (do_pml && pml[lev]->ok()) {
const std::array<MultiFab*, 3>& pml_B = pml[lev]->GetB_fp();
const std::array<MultiFab*, 3>& pml_E = pml[lev]->GetE_fp();
- shiftMF(*pml_B[dim], geom[lev], num_shift, dir);
- shiftMF(*pml_E[dim], geom[lev], num_shift, dir);
+ shiftMF(*pml_B[dim], geom[lev], num_shift, dir, ng_extra);
+ shiftMF(*pml_E[dim], geom[lev], num_shift, dir, ng_extra);
}
if (lev > 0) {
- // Coarse grid
- shiftMF(*Bfield_cp[lev][dim], geom[lev-1], num_shift_crse, dir, B_external_grid[dim]);
- shiftMF(*Efield_cp[lev][dim], geom[lev-1], num_shift_crse, dir, E_external_grid[dim]);
- shiftMF(*Bfield_aux[lev][dim], geom[lev], num_shift, dir);
- shiftMF(*Efield_aux[lev][dim], geom[lev], num_shift, dir);
+ // coarse grid
+ shiftMF(*Bfield_cp[lev][dim], geom[lev-1], num_shift_crse, dir, ng_zero, B_external_grid[dim], use_Bparser, Bfield_parser);
+ shiftMF(*Efield_cp[lev][dim], geom[lev-1], num_shift_crse, dir, ng_zero, E_external_grid[dim], use_Eparser, Efield_parser);
+ shiftMF(*Bfield_aux[lev][dim], geom[lev], num_shift, dir, ng_zero);
+ shiftMF(*Efield_aux[lev][dim], geom[lev], num_shift, dir, ng_zero);
if (move_j) {
- shiftMF(*current_cp[lev][dim], geom[lev-1], num_shift_crse, dir);
+ shiftMF(*current_cp[lev][dim], geom[lev-1], num_shift_crse, dir, ng_zero);
}
if (do_pml && pml[lev]->ok()) {
const std::array<MultiFab*, 3>& pml_B = pml[lev]->GetB_cp();
const std::array<MultiFab*, 3>& pml_E = pml[lev]->GetE_cp();
- shiftMF(*pml_B[dim], geom[lev-1], num_shift_crse, dir);
- shiftMF(*pml_E[dim], geom[lev-1], num_shift_crse, dir);
+ shiftMF(*pml_B[dim], geom[lev-1], num_shift_crse, dir, ng_extra);
+ shiftMF(*pml_E[dim], geom[lev-1], num_shift_crse, dir, ng_extra);
}
}
}
@@ -132,19 +160,19 @@ WarpX::MoveWindow (bool move_j)
// Shift scalar component F for dive cleaning
if (do_dive_cleaning) {
// Fine grid
- shiftMF(*F_fp[lev], geom[lev], num_shift, dir);
+ shiftMF(*F_fp[lev], geom[lev], num_shift, dir, ng_zero);
if (do_pml && pml[lev]->ok()) {
MultiFab* pml_F = pml[lev]->GetF_fp();
- shiftMF(*pml_F, geom[lev], num_shift, dir);
+ shiftMF(*pml_F, geom[lev], num_shift, dir, ng_extra);
}
if (lev > 0) {
// Coarse grid
- shiftMF(*F_cp[lev], geom[lev-1], num_shift_crse, dir);
+ shiftMF(*F_cp[lev], geom[lev-1], num_shift_crse, dir, ng_zero);
if (do_pml && pml[lev]->ok()) {
MultiFab* pml_F = pml[lev]->GetF_cp();
- shiftMF(*pml_F, geom[lev-1], num_shift_crse, dir);
+ shiftMF(*pml_F, geom[lev-1], num_shift_crse, dir, ng_zero);
}
- shiftMF(*rho_cp[lev], geom[lev-1], num_shift_crse, dir);
+ shiftMF(*rho_cp[lev], geom[lev-1], num_shift_crse, dir, ng_zero);
}
}
@@ -152,10 +180,10 @@ WarpX::MoveWindow (bool move_j)
if (move_j) {
if (rho_fp[lev]){
// Fine grid
- shiftMF(*rho_fp[lev], geom[lev], num_shift, dir);
+ shiftMF(*rho_fp[lev], geom[lev], num_shift, dir, ng_zero);
if (lev > 0){
// Coarse grid
- shiftMF(*rho_cp[lev], geom[lev-1], num_shift_crse, dir);
+ shiftMF(*rho_cp[lev], geom[lev-1], num_shift_crse, dir, ng_zero);
}
}
}
@@ -204,7 +232,8 @@ WarpX::MoveWindow (bool move_j)
void
WarpX::shiftMF (MultiFab& mf, const Geometry& geom, int num_shift, int dir,
- amrex::Real external_field)
+ IntVect ng_extra, amrex::Real external_field, bool useparser,
+ ParserWrapper *field_parser)
{
BL_PROFILE("WarpX::shiftMF()");
const BoxArray& ba = mf.boxArray();
@@ -216,7 +245,16 @@ WarpX::shiftMF (MultiFab& mf, const Geometry& geom, int num_shift, int dir,
MultiFab tmpmf(ba, dm, nc, ng);
MultiFab::Copy(tmpmf, mf, 0, 0, nc, ng);
- tmpmf.FillBoundary(geom.periodicity());
+
+ IntVect ng_mw = IntVect::TheUnitVector();
+ // Enough guard cells in the MW direction
+ ng_mw[dir] = num_shift;
+ // Add the extra cell (if momentum-conserving gather with staggered field solve)
+ ng_mw += ng_extra;
+ // Make sure we don't exceed number of guard cells allocated
+ ng_mw = ng_mw.min(ng);
+ // Fill guard cells.
+ tmpmf.FillBoundary(ng_mw, geom.periodicity());
// Make a box that covers the region that the window moved into
const IndexType& typ = ba.ixType();
@@ -246,20 +284,57 @@ WarpX::shiftMF (MultiFab& mf, const Geometry& geom, int num_shift, int dir,
shiftiv[dir] = num_shift;
Dim3 shift = shiftiv.dim3();
+ const RealBox& real_box = geom.ProbDomain();
+ const auto dx = geom.CellSizeArray();
+
#ifdef _OPENMP
#pragma omp parallel if (Gpu::notInLaunchRegion())
#endif
+
+
for (MFIter mfi(tmpmf); mfi.isValid(); ++mfi )
{
auto const& dstfab = mf.array(mfi);
auto const& srcfab = tmpmf.array(mfi);
const Box& outbox = mfi.fabbox() & adjBox;
+
if (outbox.ok()) {
- AMREX_PARALLEL_FOR_4D ( outbox, nc, i, j, k, n,
- {
- srcfab(i,j,k,n) = external_field;
- });
+ if (useparser == false) {
+ AMREX_PARALLEL_FOR_4D ( outbox, nc, i, j, k, n,
+ {
+ srcfab(i,j,k,n) = external_field;
+ });
+ } else if (useparser == true) {
+ // index type of the src mf
+ auto const& mf_IndexType = (tmpmf).ixType();
+ IntVect mf_type(AMREX_D_DECL(0,0,0));
+ for (int idim = 0; idim < AMREX_SPACEDIM; ++idim) {
+ mf_type[idim] = mf_IndexType.nodeCentered(idim);
+ }
+
+ amrex::ParallelFor (outbox, nc,
+ [=] AMREX_GPU_DEVICE (int i, int j, int k, int n) noexcept
+ {
+ // Compute x,y,z co-ordinates based on index type of mf
+ Real fac_x = (1.0 - mf_type[0]) * dx[0]*0.5;
+ Real x = i*dx[0] + real_box.lo(0) + fac_x;
+#if (AMREX_SPACEDIM==2)
+ Real y = 0.0;
+ Real fac_z = (1.0 - mf_type[1]) * dx[1]*0.5;
+ Real z = j*dx[1] + real_box.lo(1) + fac_z;
+#else
+ Real fac_y = (1.0 - mf_type[1]) * dx[1]*0.5;
+ Real y = j*dx[1] + real_box.lo(1) + fac_y;
+ Real fac_z = (1.0 - mf_type[2]) * dx[2]*0.5;
+ Real z = k*dx[2] + real_box.lo(2) + fac_z;
+#endif
+ srcfab(i,j,k,n) = field_parser->getField(x,y,z);
+ }
+ , amrex::Gpu::numThreadsPerBlockParallelFor() * sizeof(double)*4
+ );
+ }
+
}
Box dstBox = mf[mfi].box();
diff --git a/Source/Utils/WarpXTagging.cpp b/Source/Utils/WarpXTagging.cpp
index 91bb802e8..b2ac48e40 100644
--- a/Source/Utils/WarpXTagging.cpp
+++ b/Source/Utils/WarpXTagging.cpp
@@ -1,3 +1,10 @@
+/* Copyright 2019 Axel Huebl, Maxence Thevenet, Weiqun Zhang
+ *
+ *
+ * This file is part of WarpX.
+ *
+ * License: BSD-3-Clause-LBNL
+ */
#include <WarpX.H>
#include <AMReX_BoxIterator.H>
diff --git a/Source/Utils/WarpXUtil.H b/Source/Utils/WarpXUtil.H
index 195e309cf..9231fa60a 100644
--- a/Source/Utils/WarpXUtil.H
+++ b/Source/Utils/WarpXUtil.H
@@ -1,9 +1,18 @@
+/* Copyright 2019-2020 Andrew Myers, Luca Fedeli, Maxence Thevenet
+ * Revathi Jambunathan, Revathi Jambunathan
+ *
+ * This file is part of WarpX.
+ *
+ * License: BSD-3-Clause-LBNL
+ */
#ifndef WARPX_UTILS_H_
#define WARPX_UTILS_H_
#include <AMReX_REAL.H>
#include <AMReX_Vector.H>
#include <AMReX_MultiFab.H>
+#include <AMReX_ParmParse.H>
+#include <WarpXParser.H>
#include <string>
@@ -15,14 +24,108 @@ void ConvertLabParamsToBoost();
void NullifyMF(amrex::MultiFab& mf, int lev, amrex::Real zmin,
amrex::Real zmax);
+/**
+ * \brief Parse a string (typically a mathematical expression) from the
+ * input file and store it into a variable.
+ *
+ * \param ParmParse pp used to read the query_string pp.<function>=string
+ * \param parmparse_string String used to initialize ParmParse
+ * \param query_string ParmParse.query will look for this string
+ * \param stored_string variable in which the string to parse is stored
+ */
+void Store_parserString(amrex::ParmParse &pp, std::string query_string,
+ std::string& stored_string);
+
namespace WarpXUtilIO{
- /**
- * A helper function to write binary data on disk.
- * @param[in] filename where to write
- * @param[in] data Vector containing binary data to write on disk
- * return true if it succeeds, false otherwise
- */
- bool WriteBinaryDataOnFile(std::string filename, const amrex::Vector<char>& data);
+/**
+ * A helper function to write binary data on disk.
+ * @param[in] filename where to write
+ * @param[in] data Vector containing binary data to write on disk
+ * return true if it succeeds, false otherwise
+ */
+bool WriteBinaryDataOnFile(std::string filename, const amrex::Vector<char>& data);
+}
+
+namespace WarpXUtilAlgo{
+
+/** \brief Returns a pointer to the first element in the range [first, last) that is greater than val
+ *
+ * A re-implementation of the upper_bound algorithm suitable for GPU kernels.
+ *
+ * @param first: pointer to left limit of the range to consider
+ * @param last: pointer to right limit of the range to consider
+ * @param val: value to compare the elements of [first, last) to
+ */
+template<typename T> AMREX_GPU_DEVICE AMREX_FORCE_INLINE
+const T* upper_bound(const T* first, const T* last, const T& val)
+{
+ const T* it;
+ size_t count, step;
+ count = last-first;
+ while(count>0){
+ it = first;
+ step = count/2;
+ it += step;
+ if (!(val<*it)){
+ first = ++it;
+ count -= step + 1;
+ }
+ else{
+ count = step;
+ }
+ }
+ return first;
}
+/** \brief Performs a linear interpolation
+ *
+ * Performs a linear interpolation at x given the 2 points
+ * (x0, f0) and (x1, f1)
+ */
+template<typename T> AMREX_GPU_DEVICE AMREX_FORCE_INLINE
+T linear_interp(T x0, T x1, T f0, T f1, T x)
+{
+ return ((x1-x)*f0 + (x-x0)*f1)/(x1-x0);
+}
+
+/** \brief Performs a bilinear interpolation
+ *
+ * Performs a bilinear interpolation at (x,y) given the 4 points
+ * (x0, y0, f00), (x0, y1, f01), (x1, y0, f10), (x1, y1, f11).
+ */
+template<typename T> AMREX_GPU_DEVICE AMREX_FORCE_INLINE
+T bilinear_interp(T x0, T x1, T y0, T y1, T f00, T f01, T f10, T f11, T x, T y)
+{
+ const T fx0 = linear_interp(x0, x1, f00, f10, x);
+ const T fx1 = linear_interp(x0, x1, f01, f11, x);
+ return linear_interp(y0, y1, fx0, fx1, y);
+}
+
+/** \brief Performs a trilinear interpolation
+ *
+ * Performs a trilinear interpolation at (x,y,z) given the 8 points
+ * (x0, y0, z0, f000), (x0, y0, z1, f001), (x0, y1, z0, f010), (x0, y1, z1, f011),
+ * (x1, y0, z0, f100), (x1, y0, z1, f101), (x1, y1, z0, f110), (x1, y1, z1, f111)
+ */
+template<typename T> AMREX_GPU_DEVICE AMREX_FORCE_INLINE
+T trilinear_interp(T x0, T x1,T y0, T y1, T z0, T z1,
+ T f000, T f001, T f010, T f011, T f100, T f101, T f110, T f111,
+ T x, T y, T z)
+{
+ const T fxy0 = bilinear_interp(
+ x0, x1, y0, y1, f000, f010, f100, f110, x, y);
+ const T fxy1 = bilinear_interp(
+ x0, x1, y0, y1, f001, f011, f101, f111, x, y);
+ return linear_interp(z0, z1, fxy0, fxy1, z);
+}
+
+}
+
+/**
+* \brief Initialize a WarpXParser object from a string containing a math expression
+*
+* \param parse_function String to read to initialize the parser.
+*/
+WarpXParser makeParser (std::string const& parse_function);
+
#endif //WARPX_UTILS_H_
diff --git a/Source/Utils/WarpXUtil.cpp b/Source/Utils/WarpXUtil.cpp
index 8764a09c6..983654aed 100644
--- a/Source/Utils/WarpXUtil.cpp
+++ b/Source/Utils/WarpXUtil.cpp
@@ -1,3 +1,11 @@
+/* Copyright 2019-2020 Andrew Myers, Burlen Loring, Luca Fedeli
+ * Maxence Thevenet, Remi Lehe, Revathi Jambunathan
+ * Revathi Jambunathan
+ *
+ * This file is part of WarpX.
+ *
+ * License: BSD-3-Clause-LBNL
+ */
#include <WarpXUtil.H>
#include <WarpXConst.H>
#include <AMReX_ParmParse.H>
@@ -164,3 +172,45 @@ namespace WarpXUtilIO{
}
}
+void Store_parserString(amrex::ParmParse& pp, std::string query_string,
+ std::string& stored_string)
+{
+
+ char cstr[query_string.size()+1];
+ strcpy(cstr, query_string.c_str());
+
+ std::vector<std::string> f;
+ pp.getarr(cstr, f);
+ stored_string.clear();
+ for (auto const& s : f) {
+ stored_string += s;
+ }
+ f.clear();
+
+}
+
+
+WarpXParser makeParser (std::string const& parse_function)
+{
+ WarpXParser parser(parse_function);
+ parser.registerVariables({"x","y","z","t"});
+ ParmParse pp("my_constants");
+ std::set<std::string> symbols = parser.symbols();
+ symbols.erase("x");
+ symbols.erase("y");
+ symbols.erase("z");
+ symbols.erase("t");
+ for (auto it = symbols.begin(); it != symbols.end(); ) {
+ Real v;
+ if (pp.query(it->c_str(), v)) {
+ parser.setConstant(*it, v);
+ it = symbols.erase(it);
+ } else {
+ ++it;
+ }
+ }
+ for (auto const& s : symbols) {
+ amrex::Abort("makeParser::Unknown symbol "+s);
+ }
+ return parser;
+}
diff --git a/Source/Utils/WarpX_Complex.H b/Source/Utils/WarpX_Complex.H
index 25ed1a53a..cda4204a8 100644
--- a/Source/Utils/WarpX_Complex.H
+++ b/Source/Utils/WarpX_Complex.H
@@ -1,15 +1,23 @@
+/* Copyright 2019-2020 Andrew Myers, David Grote, Maxence Thevenet
+ * Remi Lehe
+ *
+ * This file is part of WarpX.
+ *
+ * License: BSD-3-Clause-LBNL
+ */
#ifndef WARPX_COMPLEX_H_
#define WARPX_COMPLEX_H_
#include <AMReX_REAL.H>
#include <AMReX_Gpu.H>
+#include <AMReX_GpuComplex.H>
+
+#include <complex>
// Define complex type on GPU/CPU
#ifdef AMREX_USE_GPU
-#include <thrust/complex.h>
-
-using Complex = thrust::complex<amrex::Real>;
+using Complex = amrex::GpuComplex<amrex::Real>;
#ifdef WARPX_USE_PSATD
#include <cufft.h>
@@ -19,7 +27,6 @@ static_assert( sizeof(Complex) == sizeof(cuDoubleComplex),
#else
-#include <complex>
using Complex = std::complex<amrex::Real>;
#ifdef WARPX_USE_PSATD
@@ -39,7 +46,7 @@ namespace MathFunc
template<typename T>
AMREX_GPU_HOST_DEVICE T exp (const T& val){
#ifdef AMREX_USE_GPU
- return thrust::exp(val);
+ return amrex::exp(val);
#else
return std::exp(val);
#endif
@@ -49,7 +56,7 @@ namespace MathFunc
template<typename T>
AMREX_GPU_HOST_DEVICE T sqrt (const T& val){
#ifdef AMREX_USE_GPU
- return thrust::sqrt(val);
+ return amrex::sqrt(val);
#else
return std::sqrt(val);
#endif
@@ -59,7 +66,7 @@ namespace MathFunc
template<typename T1, typename T2>
AMREX_GPU_HOST_DEVICE T1 pow (const T1& val, const T2& power){
#ifdef AMREX_USE_GPU
- return thrust::pow(val, power);
+ return amrex::pow(val, power);
#else
return std::pow(val, power);
#endif
diff --git a/Source/Utils/atomic_data.txt b/Source/Utils/atomic_data.txt
index 140f5a26a..cd58e076a 100644
--- a/Source/Utils/atomic_data.txt
+++ b/Source/Utils/atomic_data.txt
@@ -1,3 +1,9 @@
+# Copyright 2019 Maxence Thevenet
+#
+# This file is part of WarpX.
+#
+# License: BSD-3-Clause-LBNL
+
# Reference:
# Kramida, A., Ralchenko, Yu., Reader, J., and NIST ASD Team (2014).
# NIST Atomic Spectra Database (ver. 5.2), [Online].
diff --git a/Source/Utils/utils_ES.F90 b/Source/Utils/utils_ES.F90
index baadeb7af..c11e849eb 100644
--- a/Source/Utils/utils_ES.F90
+++ b/Source/Utils/utils_ES.F90
@@ -1,3 +1,9 @@
+! Copyright 2019 Maxence Thevenet, Remi Lehe
+!
+! This file is part of WarpX.
+!
+! License: BSD-3-Clause-LBNL
+
module warpx_ES_utils
use iso_c_binding
diff --git a/Source/Utils/write_atomic_data_cpp.py b/Source/Utils/write_atomic_data_cpp.py
index 35baf2cdf..12cafad0c 100644
--- a/Source/Utils/write_atomic_data_cpp.py
+++ b/Source/Utils/write_atomic_data_cpp.py
@@ -1,3 +1,10 @@
+# Copyright 2019-2020 Axel Huebl, Luca Fedeli, Maxence Thevenet
+#
+#
+# This file is part of WarpX.
+#
+# License: BSD-3-Clause-LBNL
+
'''
This python script reads ionization tables in atomic_data.txt (generated from
the NIST website) and extracts ionization levels into C++ file
@@ -6,7 +13,6 @@ IonizationEnergiesTable.H, which contains tables + metadata.
import re, os
import numpy as np
-from scipy.constants import e
filename = os.path.join( '.', 'atomic_data.txt' )
with open(filename) as f:
generated by cgit v1.2.3 (git 2.46.0) at 2025-08-20 01:35:16 +0000