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commit 443f00a Author: Maxim Yurkin <yurkin@gmail.com> Date: Tue Mar 29 13:34:30 2022 +0700 Minor changes in figure spacing commit 581bec6 Author: stefaniagl <stefgluhova@gmail.com> Date: Tue Mar 29 00:03:24 2022 +0700 Bessel 0 (adda-team#315) Tests and examples for Bessel beams: - test using equivalent command line strings `tests/equiv/bb_equiv.py` - simple examples `examples/bessel` - scripts to reproduce 4 figures in a recent paper (submitted) Fixes a bug in TML type of Bessel beams. commit d7e6169 Author: Maxim Yurkin <yurkin@gmail.com> Date: Mon Feb 21 23:35:49 2022 +0700 Makes the test for inconsistencies in the input shape format more sensitive. Detects extra number present in a line for ADDA formats (both single- and multi-domain). The formats themselves are now defines instead of static strings. commit 887a63c Author: Maxim Yurkin <yurkin@gmail.com> Date: Mon Feb 21 14:48:46 2022 +0700 - All math constants are now given to 35 significant digits (was 32 in most places) - This includes the LDR constants (for which a separate calculation procedure was performed) - Improves a few related comments commit a993a91 Author: Maxim Yurkin <yurkin@gmail.com> Date: Tue Feb 15 10:21:53 2022 +0700 - renames find_adda.sh into find_adda (and sets executable flag) - this script now returns ADDA path to stdout, hence does not need to be sourced (was a bad idea due to potential variables collision) - updates all calling scripts commit c8ea4ed Author: Maxim Yurkin <yurkin@gmail.com> Date: Mon Jan 31 14:52:02 2022 +0700 minor formatting changes commit a6be5f4 Author: Maxim Yurkin <yurkin@gmail.com> Date: Mon Jan 31 14:31:10 2022 +0700 - adds a special script to locate ADDA binaries (to be used by various examples). - updates existing examples in `examples/papers/2021_WKBr/` and `misc/near_field/` accordingly - other minor changes to `examples/papers/2021_WKBr/calc.sh` commit 2896575 Author: inzhevatkin <51568160+inzhevatkin@users.noreply.github.com> Date: Sun Jan 30 11:40:56 2022 +0700 WKBr scripts (adda-team#311) * Adds scripts to reproduce Figs.15 and 16 from paper (Inzhevatkin & Yurkin, 2022) * Includes general-purpose scripts to generate internal field in a sphere in the framework of the WKBr approximation (two modifications). * Also includes interface with Mie-theory calculations. Co-authored-by: Maxim Yurkin <yurkin@gmail.com> commit 6c0b401 Merge: 49e6c23 deebdbf Author: Maxim Yurkin <yurkin@gmail.com> Date: Tue Jan 11 19:11:38 2022 +0700 Merge branch 'master' of github.com:adda-team/adda commit 49e6c23 Author: Maxim Yurkin <yurkin@gmail.com> Date: Tue Jan 11 19:09:51 2022 +0700 Updates extracting of gcc version in Makefile to be compatible with all possible configurations of gcc. commit deebdbf Author: stefaniagl <stefgluhova@gmail.com> Date: Fri Jan 7 17:44:39 2022 +0700 Changes in tests (adda-team#310) - updates ignores in `comp2exec` so that all tests pass (after recent adda-team#304) - adds -beam_center to various lines in test suites * Corrections in `GenerateB.c`: - removes redundant EOL in multi-line beam descriptions - fixes incorrect calculation of incident plane wave for grazing incidence in surface mode (when prop_z is on the order of 1e-16). For that the code was completely rewritten to specifically calculate potentially small quantities (e.g., expm1 instead of exp and rcp1=rc+1 instead of rc). - removes duplicate initialization of `prIncRefl` - mentions `vorticity` in instructions for adding new beam - in several places (when accounting for `beam_center`) `LinComb()` was replaced by `vSubtr()`. * Other changes: - adds functions `imExpM1()` and `cExpM1()` to `cmplx.h` - definitions of `prIncRelf` and `prIncTran` are now semi-global (only in `GenerateB.c` and `param.c`) - updates copyright year in `param.c` Co-authored-by: Maxim Yurkin <yurkin@gmail.com> commit 6a9ec2e Author: Maxim Yurkin <yurkin@gmail.com> Date: Mon Jan 3 00:02:33 2022 +0700 adds ignoring of errors when getting commit hash (i.e. when compiling from downloaded source code, not from git repository)
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| Various examples of using ADDA. Mostly these are tutorial examples, which illustrate certain features of ADDA and should not consume too much computational time. The only exception is subfolder `papers/`, which additionally aims to reproduce specific published simulations (thus, may require a large cluster). All examples are designed to be run out of the box assuming that compiled binaries are available (either by default compilation or pre-compiled for Windows). Some only run ADDA with proper command lines, others - also plot or post-process the obtained results. See further details inside corresponding folders: | ||
| * `bessel/` – examples involving excitation by Bessel beams (will be added after #209) | ||
| * `bessel/` – examples involving excitation by Bessel beams | ||
| * `eels/` – examples involving excitation by a fast electron (will be added after #155) | ||
| * `papers/` – examples reproducing published results | ||
| * `find_adda.sh` - common script to locate ADDA binaries and set corresponding environmenal variables |
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| /option*/ | ||
| /saved/ |
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| This python code "bb_examples" represents the comparison of scattering intensities calculated with DDA (ADDA code) | ||
| for the scattering of Bessel beam of 2 options by choice (option_1 and option_2). | ||
| The python code `bb_examples.py` performs the comparison of scattering intensities calculated with ADDA for two different Bessel beams. By default, they are LE and LM beams of order 2 scattered by a wavelength-sized sphere, but it can be easily modified inside the script. | ||
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| Other folders (produced by the script): | ||
| * `option_1/` - contains raw ADDA results (log file, mueller matrix, incident field, and cross sections by default) for the 1st command line option | ||
| * `option_2/` - the same for the 2nd option | ||
| * `saved/` - final figures in PDF format |
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| #!/bin/bash | ||
| # Copyright (C) ADDA contributors | ||
| # GNU General Public License version 3 | ||
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| # Finds adda binary and returns its path to stdout. If the variable ADDA_SEQ, ADDA_MPI, or ADDA_OCL is already defined, | ||
| # returns its value, but first tests that the file exist. Otherwise, first checks if the binary is directly available | ||
| # (on the PATH), then looks at the corresponding compilation folder, and finally (on Windows only) looks for precompiled | ||
| # binary in win64/ | ||
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| # A single optional argument is the mode (seq, mpi, or ocl), which binary to search. 'seq' is the default one. | ||
| # The script must not be moved from this folder (searches for a few places relative to its position), | ||
| # but can be executed from anywhere. | ||
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| # The minimal test example is the following (note the test for exit value) | ||
| #ADDA_SEQ=$(./find_adda) | ||
| #if [ $? -ne 0 ]; then | ||
| # exit 1 | ||
| #fi | ||
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| mode=${1:-seq} | ||
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| # We do not add .exe for Windows, since all Bash interpreters for Windows seem to work fine without it | ||
| if [ $mode == "seq" ]; then | ||
| var=ADDA_SEQ | ||
| bin=adda | ||
| elif [ $mode == "mpi" ]; then | ||
| var=ADDA_MPI | ||
| bin=adda_mpi | ||
| elif [ $mode == "ocl" ]; then | ||
| var=ADDA_OCL | ||
| bin=adda_ocl | ||
| else | ||
| echo "ERROR: unkwnown mode '$mode'" >&2 | ||
| exit 1 | ||
| fi | ||
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| if [ -z "${!var}" ]; then | ||
| # Locates root path for ADDA (relative to script's location), https://stackoverflow.com/a/246128/2633728 | ||
| top=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")/../" &> /dev/null && pwd) | ||
| if command -v $bin &> /dev/null; then | ||
| path="$bin" | ||
| elif [ -f "$top/src/$mode/$bin" ]; then | ||
| path="$top/src/$mode/$bin" | ||
| elif [[ ("$OSTYPE" == "msys" || "$OSTYPE" == "cygwin" || "$OSTYPE" == "win32" || "$OSTYPE" == "win64" ) && -f "$top/win64/$bin" ]]; then | ||
| path="$top/win64/$bin" | ||
| else | ||
| echo "ERROR: No $bin binary found (and variable $var is not defined)" >&2 | ||
| exit 1 | ||
| fi | ||
| elif [ ! -f "${!var}" ]; then | ||
| echo "ERROR: No $bin binary found (path given by $var='${!var}' does not exist)" >&2 | ||
| exit 1 | ||
| else | ||
| path="${!var}" | ||
| fi | ||
| echo "$path" |
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| /*/__pycache__ | ||
| /*/*.dat | ||
| /Mie_solution/work/* | ||
| /run* | ||
| /ExpCount |
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| The script `exact-script.sh` calculates the exact internal electric field using either [`Bhfield`](https://scattport.org/index.php/light-scattering-software/mie-type-codes/list/521-bhfield) or [`Scattnlay`](https://github.com/ovidiopr/scattnlay) (to be obtained separately). The `toADDA.py` script changes Bhfield / Scattnlay grid so that it matches the ADDA one. | ||
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| After setting the required parameters and paths to scripts, execute: | ||
| ``` | ||
| sh exact-script.sh | ||
| python toADDA.py | ||
| ``` | ||
| The scripts can also accept parameters through the command line - see the comments inside. |
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| #!/bin/bash | ||
| # The script calculates the exact internal electric field using either Bhfield or Scattnlay. | ||
| # You need to obtain the required executables (Bhfield or Scattnlay) separately and specify the path to the corresponding | ||
| # executables below (or copy them in work/ subfolder) | ||
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| # SET YOUR PARAMETERS (either here or in command line): | ||
| size=${1:-10} | ||
| m=${2:-1.1} | ||
| grid=${3:-16} | ||
| type=${4:-scattnlay} # program type: [bhfield, scattnlay] | ||
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| # SET YOUR PATHS: | ||
| # Path to the working folder (for temporary files, only for bhfield) and for placing output (both must exist) | ||
| workpath="$(pwd)/work" | ||
| outpath="$(pwd)" | ||
| # Executables (with full path) to be used for actual computation | ||
| BHFIELD="$workpath/bhfield-std" | ||
| # The name of the executable can also be fieldnlay or fieldnlay-mp, depending on installation. | ||
| # We tested on the Scattnlay version dated June 7, 2021. | ||
| FIELDNLAY="$workpath/fieldnlay-dp" | ||
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| # Calculating the required variables: | ||
| # simple workaround for float computations using awk | ||
| calc() { awk "BEGIN{print $*}"; } | ||
| radius=$(calc $size/2) | ||
| rb=$(calc $radius - $radius/$grid) | ||
| lb=-$rb; | ||
| if [ "$type" == "bhfield" ]; then | ||
| cd $workpath | ||
| "$BHFIELD" 6.28318530718 $radius $radius $grid $lb $rb $grid $lb $rb $grid $lb $rb other 0 1 $m 0 $m 0 | ||
| cp V_0Ereim.dat "$outpath/bhfield-$size-$m-$grid.dat" | ||
| elif [ "$type" == "scattnlay" ]; then | ||
| "$FIELDNLAY" -l 1 $radius $m 0 -p $lb $rb $grid $lb $rb $grid $lb $rb $grid > "$outpath/scattnlay-$size-$m-$grid.dat" | ||
| fi |
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