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use local copy of x3dom
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2 changes: 1 addition & 1 deletion README.Rmd
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Expand Up @@ -126,7 +126,7 @@ When running the stand-alone executable, main input parameters are read from a p
If you use TERMS, please cite the following user guide, as well as other publications listed below if relevant:

<div style="display: none;">
[@Schebarchov:2022wc], [@Schebarchov:2021ut], [@Somerville:2016aa], [@schebarchov2019mind], [@Lee:2020aa], [@Fazel-Najafabadi:2021uq], [@Fazel-Najafabadi:2022ud], [@Fazel-Najafabadi:2022aa]
[@Schebarchov:2022wc], [@Schebarchov:2021ut], [@Somerville:2016aa], [@schebarchov2019mind], [@Lee:2020aa], [@Fazel-Najafabadi:2021uq], [@Fazel-Najafabadi:2022ud], [@Fazel-Najafabadi:2022vx], [@Glukhova:2023aa]
</div>


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156 changes: 84 additions & 72 deletions README.md
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Expand Up @@ -29,47 +29,47 @@ to simulate particles and systems of particles in random orientation.

The possible computations are divided into three main modes:

- Far-field quantities (absorption, scattering, extinction, circular
dichroism) for multiple wavelengths and angles of incidence, as well
as orientation-averages
- Near-field calculations for multiple wavelengths and incident
angles, also computing the local degree of chirality, as well as
orientation-averages
- Stokes parameters and differential scattering cross-sections for
multiple incidence or scattering angles
- Far-field quantities (absorption, scattering, extinction, circular
dichroism) for multiple wavelengths and angles of incidence, as well
as orientation-averages
- Near-field calculations for multiple wavelengths and incident angles,
also computing the local degree of chirality, as well as
orientation-averages
- Stokes parameters and differential scattering cross-sections for
multiple incidence or scattering angles

The computational cost scales with the size of the linear system,
proportional to the number of particles Np, and to the square of the
maximum multipolar order Nmax. On a typical PC we may treat up to \~500
particles with Nmax=1, and a dimer with Nmax up to \~60.
maximum multipolar order Nmax. On a typical PC we may treat up to ~500
particles with Nmax=1, and a dimer with Nmax up to ~60.

Notable features of TERMS include:

- Incident plane waves along arbitrary directions, with linear or
circular polarisation
- Built-in calculation of individual *T*-matrices for coated spheres;
import of general *T*-matrices from other programs
(e.g. [SMARTIES](https://www.victoria.ac.nz/scps/research/research-groups/raman-lab/numerical-tools/smarties))
- Built-in dielectric functions for common materials such as Au, Ag,
Al, Cr, Pt, Pd, Si, and Water, or from tabulated values
- Per-layer absorption in layered spheres
- Orientation-averaging of far-field cross-sections, as well as linear
and circular dichroism
- Near-field maps of electric and magnetic field components, E^2, E^4,
local degree of chirality
- Calculation of the global cluster *T*-matrix
- “Masking” of specific multipolar orders
- Calculation of Stokes parameters, phase matrix, differential
scattering
- Plain text or HDF5 I/O format
- Possible compilation in quad-precision
- Incident plane waves along arbitrary directions, with linear or
circular polarisation
- Built-in calculation of individual *T*-matrices for coated spheres;
import of general *T*-matrices from other programs
(e.g. [SMARTIES](https://www.victoria.ac.nz/scps/research/research-groups/raman-lab/numerical-tools/smarties))
- Built-in dielectric functions for common materials such as Au, Ag, Al,
Cr, Pt, Pd, Si, and Water, or from tabulated values
- Per-layer absorption in layered spheres
- Orientation-averaging of far-field cross-sections, as well as linear
and circular dichroism
- Near-field maps of electric and magnetic field components, E^2, E^4,
local degree of chirality
- Calculation of the global cluster *T*-matrix
- “Masking” of specific multipolar orders
- Calculation of Stokes parameters, phase matrix, differential
scattering
- Plain text or HDF5 I/O format
- Possible compilation in quad-precision

### System requirements

- Fortran 90 compiler
- Cmake
- (optional) HDF5 library
- (optional) LAPACK
- Fortran 90 compiler
- Cmake
- (optional) HDF5 library
- (optional) LAPACK

The electromagnetic field is expanded in the basis of vector spherical
waves, with the Bessel/Hankel functions computed using
Expand Down Expand Up @@ -110,7 +110,7 @@ Edit ‘buildTERMS.sh’ to specify a compiler other than

We recommend downloading the [latest release
here](https://github.com/nano-optics/terms/releases)
\[`terms_code_1.0.0(.zip|.tar)`\]. You can also browse/clone/fork the
\[`terms_code_1.0.2(.zip|.tar)`\]. You can also browse/clone/fork the
[entire repository](https://github.com/nano-optics/terms), but note that
it contains many files used to generate the website, which are not
relevant for using TERMS.
Expand Down Expand Up @@ -183,90 +183,102 @@ publications listed below if relevant:

<div style="display: none;">

<sup>1</sup>,,<sup>2</sup>,<sup>3</sup>,<sup>4</sup>,<sup>5</sup>,<sup>6</sup>,<sup>7</sup><sup>8</sup>
<sup>1</sup>,<sup>2</sup>,<sup>3</sup>,<sup>4</sup>,<sup>5</sup>,<sup>6</sup>,<sup>7</sup>,<sup>8</sup>,<sup>9</sup>

</div>

<div id="refs" class="references csl-bib-body">
<div id="refs" class="references csl-bib-body" entry-spacing="0">

<div id="ref-Schebarchov:2022wc" class="csl-entry">

<span class="csl-left-margin">(1) </span><span
class="csl-right-inline">Schebarchov, D.; Fazel-Najafabadi, A.; Le Ru,
E. C.; Auguié, B. Multiple Scattering of Light in Nanoparticle
Assemblies: User Guide for the Terms Program. *Journal of Quantitative
Spectroscopy and Radiative Transfer* **2022**, 108131.
https://doi.org/<https://doi.org/10.1016/j.jqsrt.2022.108131>.</span>
<span class="csl-left-margin">(1)
</span><span class="csl-right-inline">Schebarchov, D.; Fazel-Najafabadi,
A.; Le Ru, E. C.; Auguié, B. Multiple Scattering of Light in
Nanoparticle Assemblies: User Guide for the Terms Program. *Journal of
Quantitative Spectroscopy and Radiative Transfer* **2022**, 108131.
<https://doi.org/10.1016/j.jqsrt.2022.108131>.</span>

</div>

<div id="ref-Schebarchov:2021ut" class="csl-entry">

<span class="csl-left-margin">(2) </span><span
class="csl-right-inline">Schebarchov, D.; Fazel-Najafabadi, A.; Le Ru,
E. C.; Auguié, B. *TERMS Website*; 2021.
<span class="csl-left-margin">(2)
</span><span class="csl-right-inline">Schebarchov, D.; Fazel-Najafabadi,
A.; Le Ru, E. C.; Auguié, B. *TERMS Website*; 2021.
<https://doi.org/10.5281/zenodo.5703291>.</span>

</div>

<div id="ref-Somerville:2016aa" class="csl-entry">

<span class="csl-left-margin">(3) </span><span
class="csl-right-inline">Somerville, W. R. C.; Auguié, B.; Le Ru, E. C.
SMARTIES: User-Friendly Codes for Fast and Accurate Calculations of
Light Scattering by Spheroids. *J. Quant. Spectrosc. Ra.* **2016**,
*174*, 39–55. <https://doi.org/10.1016/j.jqsrt.2016.01.005>.</span>
<span class="csl-left-margin">(3)
</span><span class="csl-right-inline">Somerville, W. R. C.; Auguié, B.;
Le Ru, E. C. SMARTIES: User-Friendly Codes for Fast and Accurate
Calculations of Light Scattering by Spheroids. *J. Quant. Spectrosc.
Ra.* **2016**, *174*, 39–55.
<https://doi.org/10.1016/j.jqsrt.2016.01.005>.</span>

</div>

<div id="ref-schebarchov2019mind" class="csl-entry">

<span class="csl-left-margin">(4) </span><span
class="csl-right-inline">Schebarchov, D.; Le Ru, E. C.; Grand, J.;
Auguié, B. Mind the Gap: Testing the Rayleigh Hypothesis in *T*-Matrix
Calculations with Adjacent Spheroids. *Optics express* **2019**, *27*
(24), 35750–35760. <https://doi.org/10.1364/OE.27.035750>.</span>
<span class="csl-left-margin">(4)
</span><span class="csl-right-inline">Schebarchov, D.; Le Ru, E. C.;
Grand, J.; Auguié, B. Mind the Gap: Testing the Rayleigh Hypothesis in
$T$-Matrix Calculations with Adjacent Spheroids. *Optics express*
**2019**, *27* (24), 35750–35760.
<https://doi.org/10.1364/OE.27.035750>.</span>

</div>

<div id="ref-Lee:2020aa" class="csl-entry">

<span class="csl-left-margin">(5) </span><span
class="csl-right-inline">Lee, S.; Hwang, H.; Lee, W.; Schebarchov, D.;
Wy, Y.; Grand, J.; Augui’e, B.; Wi, D. H.; Cort’es, E.; Han, S. W.
Core–Shell Bimetallic Nanoparticle Trimers for Efficient
<span class="csl-left-margin">(5)
</span><span class="csl-right-inline">Lee, S.; Hwang, H.; Lee, W.;
Schebarchov, D.; Wy, Y.; Grand, J.; Auguié, B.; Wi, D. H.; Cort’es, E.;
Han, S. W. Core–Shell Bimetallic Nanoparticle Trimers for Efficient
Light-to-Chemical Energy Conversion. *ACS Energy Letters* **2020**, *5*
(12), 3881–3890. <https://doi.org/10.1021/acsenergylett.0c02110>.</span>

</div>

<div id="ref-Fazel-Najafabadi:2021uq" class="csl-entry">

<span class="csl-left-margin">(6) </span><span
class="csl-right-inline">Fazel-Najafabadi, A.; Schuster, S.; Auguié, B.
Orientation Averaging of Optical Chirality Near Nanoparticles and
Aggregates. *Physical Review B* **2021**, *103* (11), 115405.
<https://doi.org/10.1103/PhysRevB.103.115405>.</span>
<span class="csl-left-margin">(6)
</span><span class="csl-right-inline">Fazel-Najafabadi, A.; Schuster,
S.; Auguié, B. Orientation Averaging of Optical Chirality Near
Nanoparticles and Aggregates. *Physical Review B* **2021**, *103* (11),
115405. <https://doi.org/10.1103/PhysRevB.103.115405>.</span>

</div>

<div id="ref-Fazel-Najafabadi:2022ud" class="csl-entry">

<span class="csl-left-margin">(7) </span><span
class="csl-right-inline">Fazel-Najafabadi, A.; Auguié, B. Orientation
Dependence of Optical Activity in Light Scattering by Nanoparticle
Clusters. *Mater. Adv.* **2022**, –.
<span class="csl-left-margin">(7)
</span><span class="csl-right-inline">Fazel-Najafabadi, A.; Auguié, B.
Orientation Dependence of Optical Activity in Light Scattering by
Nanoparticle Clusters. *Mater. Adv.* **2022**, –.
<https://doi.org/10.1039/D1MA00869B>.</span>

</div>

<div id="ref-Fazel-Najafabadi:2022aa" class="csl-entry">
<div id="ref-Fazel-Najafabadi:2022vx" class="csl-entry">

<span class="csl-left-margin">(8) </span><span
class="csl-right-inline">Fazel-Najafabadi, A.; Auguié, B.
<span class="csl-left-margin">(8)
</span><span class="csl-right-inline">Fazel-Najafabadi, A.; Auguié, B.
Orientation-Averaged Light Scattering by Nanoparticle Clusters:
Far-Field and Near-Field Benchmarks of Numerical Cubature Methods,
2022.</span>
Far-Field and Near-Field Benchmarks of Numerical Cubature Methods. *J.
Quant. Spectrosc. Radiat. Transf.* **2022**.
<https://doi.org/10.1016/j.jqsrt.2022.108197>.</span>

</div>

<div id="ref-Glukhova:2023aa" class="csl-entry">

<span class="csl-left-margin">(9)
</span><span class="csl-right-inline">Glukhova, S.; Le Ru, E.; Auguié,
B. Generalised Coupled-Dipole Model for Core-Satellite Nanostructures.
*Nanoscale* **2023**, –. <https://doi.org/10.1039/D3NR05238A>.</span>

</div>

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