From ecee71af8f77bc0360b3c5d8bc85592802652eb0 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Fri, 10 May 2024 18:55:37 +0200 Subject: [PATCH] Build website that demonstrates model computations (#25) * DOC: create HTML pages from Markdown documents * DX: activate format-on-save * DX: add Ruff as Python linter and formatter * DX: add pre-commit hooks for Python * MAINT: move markdown files to `docs/` directory * DOC: host documentation on GitHub * FIX: install Julia with `juliaup` * DOC: add example notebooks for Python and Julia * DX: define `doclive` job * DOC: import Julia example https://github.com/mmikhasenko/ThreeBodyDecaysIO.jl/blob/d12b999/builders/Lc2pKpi_read.jl * DOC: shorten titles * DOC: remove environment activation cell * DX: cache Julia and `jupyter-cache` caches * DOC: show output of package installation * TEMP: print whether kernel is alive * DX: switch to Quarto as builder * MAINT: switch to `pixi.toml` file * DOC: add links to homepage and repo * FIX: cache correct `.jupyter_cache` paths * FIX: set output path to `docs/_build/html` * DX: activate html preview extension * FIX: import model from mmikhasenko/ThreeBodyDecaysIO.jl@d12b999 * DOC: improve code rendering * MAINT: move models to `models/` * DOC: remove hard-coded JSON example * DX: hide `pixi.lock` from VSCode search * FIX: use correct syntax for Python minimum version * DOC: add dark mode * FIX: remove format-on-save for notebooks * DOC: improve print statement * FIX: remove redundant pre-commit hooks * DOC: add links to GitHub * DX: rename Documentation job Looks better in the Actions overview * FIX: update links to `models/` * add text to the Lc2pKpi page * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add new julia deps * MAINT: update `pixi.lock` --------- Co-authored-by: Mikhail Mikhasenko Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .github/workflows/docs.yml | 58 + .gitignore | 2 + .pre-commit-config.yaml | 2 + .taplo.toml | 6 + .vscode/extensions.json | 3 + .vscode/settings.json | 13 +- README.md | 1016 +------ docs/.gitignore | 3 + HS3.md => docs/HS3.md | 4 +- docs/_images/favicon.ico | Bin 0 -> 15406 bytes docs/_quarto.yml | 40 + description.md => docs/description.md | 16 +- docs/index.md | 153 + docs/julia/Manifest.toml | 1301 +++++++++ docs/julia/Project.toml | 10 + docs/julia/lc2pkpi.qmd | 213 ++ docs/python/lc2pkpi.qmd | 9 + HS3_base.json => models/HS3_base.json | 0 HS3_extended.json => models/HS3_extended.json | 0 Lc2ppiK.json => models/Lc2ppiK.json | 0 pixi.lock | 2583 +++++++++++++++-- pixi.toml | 26 +- 22 files changed, 4177 insertions(+), 1281 deletions(-) create mode 100644 .github/workflows/docs.yml create mode 100644 docs/.gitignore rename HS3.md => docs/HS3.md (76%) create mode 100644 docs/_images/favicon.ico create mode 100644 docs/_quarto.yml rename description.md => docs/description.md (98%) create mode 100644 docs/index.md create mode 100644 docs/julia/Manifest.toml create mode 100644 docs/julia/Project.toml create mode 100644 docs/julia/lc2pkpi.qmd create mode 100644 docs/python/lc2pkpi.qmd rename HS3_base.json => models/HS3_base.json (100%) rename HS3_extended.json => models/HS3_extended.json (100%) rename Lc2ppiK.json => models/Lc2ppiK.json (100%) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 0000000..658e9ff --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,58 @@ +name: Documentation + +on: + pull_request: + branches: + - main + push: + branches: + - main + +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Julia cache + uses: actions/cache@v4 + with: + key: | + julia-${{hashFiles('Manifest.toml')}}-${{hashFiles('**/*.jl')}} + restore-keys: | + julia-${{hashFiles('Manifest.toml')}} + julia + path: | + ~/.julia/ + - uses: prefix-dev/setup-pixi@v0.6.0 + with: + cache: true + - name: Jupyter cache + uses: actions/cache@v4 + with: + key: | + jupyter-cache-${{hashFiles('pixi.lock')}}-${{hashFiles('docs/*/*.md')}} + restore-keys: | + jupyter-cache-${{hashFiles('pixi.lock')}} + jupyter-cache + path: | + **/.jupyter_cache + - run: pixi run doc + - if: always() + uses: actions/upload-pages-artifact@v3 + with: + path: docs/_build/html + + deploy: + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + if: >- + github.event_name == 'push' && github.ref == format('refs/heads/{0}', github.event.repository.default_branch) + needs: build + permissions: + pages: write + id-token: write + runs-on: ubuntu-latest + steps: + - id: deployment + uses: actions/deploy-pages@v4 diff --git a/.gitignore b/.gitignore index 40efc6e..031edf5 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,5 @@ *.egg-info/ +.ipynb_checkpoints/ .pixi/ +_build/ node_modules/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0166aa2..a1ef9e3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -14,6 +14,7 @@ repos: - id: check-case-conflict - id: check-json - id: check-merge-conflict + - id: check-toml - id: check-yaml - id: end-of-file-fixer - id: mixed-line-ending @@ -35,3 +36,4 @@ repos: - id: toml-sort args: - --in-place + exclude: (?x)^(.*/Manifest\.toml|.*/Project\.toml)$ diff --git a/.taplo.toml b/.taplo.toml index 0db1df7..aff6843 100644 --- a/.taplo.toml +++ b/.taplo.toml @@ -1,3 +1,9 @@ +exclude = [ + "**/Manifest.toml", + "**/Project.toml", + ".pixi/**", +] + [formatting] align_comments = false align_entries = false diff --git a/.vscode/extensions.json b/.vscode/extensions.json index c2c3cc0..9ced585 100644 --- a/.vscode/extensions.json +++ b/.vscode/extensions.json @@ -6,6 +6,9 @@ "github.vscode-pull-request-github", "julialang.language-julia", "ms-python.python", + "ms-toolsai.jupyter", + "ms-vscode.live-server", + "quarto.quarto", "tamasfe.even-better-toml", "yzhang.markdown-all-in-one" ] diff --git a/.vscode/settings.json b/.vscode/settings.json index 6b4ac22..5bb57cf 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -8,7 +8,18 @@ "[markdown]": { "editor.defaultFormatter": "esbenp.prettier-vscode" }, + "[yaml]": { + "editor.defaultFormatter": "esbenp.prettier-vscode" + }, "editor.formatOnSave": true, "julia.executablePath": "${workspaceFolder}/.pixi/envs/default/bin/julia", - "python.defaultInterpreterPath": ".pixi/envs/default/bin/python" + "livePreview.defaultPreviewPath": "docs/_build/html", + "python.defaultInterpreterPath": ".pixi/envs/default/bin/python", + "quarto.path": ".pixi/envs/default/bin/quarto", + "search.exclude": { + "**/*.code-search": true, + "**/bower_components": true, + "**/node_modules": true, + "**/pixi.lock": true + } } diff --git a/README.md b/README.md index 20ce841..f5f30fa 100644 --- a/README.md +++ b/README.md @@ -1,1015 +1,3 @@ -# Cascade amplitude models in json format +# Cascade amplitude models in JSON format -The zero version of the model tries to keep the structures as flatt as possible for readability purpose. - -Any value in the dictionary can be replaced by string, that corresponds to a key translated later in the file. -It enables keeping consistent numerical values for masses, and lineshape parametrizations. - -- [Detailed description of the format!](description.md) -- Notes on [HS3](HS3.md) - -## Example - -A realistic decay description for Lc2pKpi amplitude is produced with [`ThreeBodyDecayIO.jl`](https://github.com/mmikhasenko/ThreeBodyDecaysIO.jl) using the default model of the Lc2ppiK decays, -[`Lc2ppiKSemileptonicModelLHCb.jl`](https://github.com/mmikhasenko/Lc2ppiKSemileptonicModelLHCb.jl). - -For a description of a three body decay amplitude, one must provide several mandatory section at the root of the object, -`"kinematics"`, `"chains"`, `"reference_topology"`, and `"validation"` sections. - -### Kinematics Overview - -The `kinematics` section details the particle states involved in decay processes: - -- `initial_state`: Specifies the decaying particle at the start of the process. Contains keys for `index` (unique identifier), `name` (label), `spin` (quantum spin number), and `mass` (in GeV/c²). -- `final_state`: An array detailing each resulting particle from the decay. Each entry includes the same keys as `initial_state`, defining the properties of these particles. - -For example, the kinematics of the decay Lc2pKpi would look like, - -```json -"kinematics": { - "initial_state" : { - "index" : 0, - "name" : "Lc", - "spin" : "1/2", - "mass" : 2.28646 - }, - "final_state" : [ - { - "index" : 1, - "name" : "p", - "spin" : "1/2", - "mass" : 0.938272046 - }, - { - "index" : 2, - "name" : "pi", - "spin" : "0", - "mass" : 0.13957018 - }, - { - "index" : 3, - "name" : "K", - "spin" : "0", - "mass" : 0.493677 - }] -} -``` - -The `index` field serves as the primary identifier for particles. -The `name` field gives an label, which is not identifiers, it does not have to be unique. -The index zero is reserved for the decay particle in the initial state. -Spins are presented in conventional notation (e.g., "1/2") for familiarity. Most of implementations use Integers to store twice the value of the spin. - -### Decay chains - -Each decay chain is described by a JSON object containing five mandatory fields: - -- `"topology"`: defines nodes and edges of the decay graph, order of particles, -- `"propagators"`: for every decay node(!) describes parametrization of the decay particle -- `"vertices"`: for every node, describes parametrization of the coupling and form-factor -- `"weight"`: complex coefficient multiplying the chain -- `"name"`: name of the chain - -### Topology - -Tolopogy of a decay is a tree of intermediate decays given in a compact form using brackets. -In this notation, each pair of brackets indicate the node and it's children. -The name of the node is simply given by its decay in the same bracket notations. - -```json - "topology": [[1, 2], 3], -``` - -Here the 3-body decay process described by the notation `[[1,2],3]`, - -``` - 0 - | - [[1,2],3] - / \ - / 3 - [1,2] - / \ - / 2 -1 -``` - -- The innermost pair `[1,2]` represents the decay of a parent particle into particles 1 and 2. -- The next level `[[1,2],3]` indicates that the products of the first decay, along with particle 3 are combined into a new node. -- The starting node is also associated with the initial state decay particle. - -Nodes of this example topology are `[1,2]` and `[[1,2],3]`. -They are referenced when describing the decay vertices and propagators. -The order matters, i.e. `[[1,2],3] != [[2,1],3] != [3,[2,1]]`. - -Spins of the final state particles are quantized in the frames defined by the `"reference_topology"`, -i.e. there are no Wigner rotations for particles in the reference topology, while for the chains with different topology, -quantization axes must be adjusted by using appropriate wigner rotations. - -### Appendix - -The `appendix` gives definition to the text keys used elsewhere in the desciption. These definions are inserted recursively, while processing the json file. - -### Complex numbers - -The use of strings for complex numbers follows physics conventions for ease of reading. - -```json - "appendix": { - "BlattWeisskopf(resonance)": { - "type": "BlattWeisskopf", - "radius": 1.5 - }, - "L(1405)_Flatte": { - "type": "Flatte1405{@NamedTuple{m::Float64, Γ::Float64}}", - "mass": 1.4051, - "width": 0.0505 - }, - "L(1690)_BW": { - "l": 2, - "mb": 0.938272046, - "type": "BreitWigner", - "mass": 1.69, - "ma": 0.493677, - "width": 0.07 - }, - } -``` - -The string values that are not expanded in the `"appendix"` should be identifiers declared in the serialization document. - -### Validation Block - -The last block `validation` provides reference values of the amplitude for every chain at a single kinematic point. -This section acts as a model integrity check, providing reference amplitudes for comparison against calculated values. - -
- See the full example - -```json -{ - "kinematics": { - "spins": ["1/2", "0", "0", "1/2"], - "indices": [1, 2, 3, 0], - "names": ["p", "pi", "K", "Lc"], - "masses": [0.938272046, 0.13957018, 0.493677, 2.28646] - }, - "reference_topology": [[1, 2], 3], - "chains": [ - { - "propagators": [ - { - "spin": "1/2", - "node": [1, 2], - "parametrization": "L(1405)_Flatte" - } - ], - "weight": "7.38649400481717 + 1.971018433257411i", - "vertices": [ - { - "type": "helicity", - "helicities": ["1/2", "0"], - "node": [[1, 2], 3], - "formfactor": "" - }, - { - "type": "parity", - "helicities": ["0", "1/2"], - "parity_factor": "+", - "node": [1, 2], - "formfactor": "" - } - ], - "topology": [[1, 2], 3], - "name": "L(1405)" - }, - { - "propagators": [ - { - "spin": "1/2", - "node": [1, 2], - "parametrization": "L(1405)_Flatte" - } - ], - "weight": "-3.2332358574805515 + 2.2557724553615772i", - "vertices": [ - { - "type": "helicity", - "helicities": ["-1/2", "0"], - "node": [[1, 2], 3], - "formfactor": "" - }, - { - "type": "parity", - "helicities": ["0", "1/2"], - "parity_factor": "+", - "node": [1, 2], - "formfactor": "" - } - ], - "topology": [[1, 2], 3], - "name": "L(1405)" - }, - { - "propagators": [ - { - "spin": "3/2", - "node": [1, 2], - "parametrization": "L(1520)_BW" - } - ], - "weight": "0.146999 + 0.022162i", - "vertices": [ - { - "type": "helicity", - "helicities": ["-1/2", "0"], - "node": [[1, 2], 3], - "formfactor": "BlattWeisskopf(resonance)" - }, - { - "type": "parity", - "helicities": ["0", "1/2"], - "parity_factor": "-", - "node": [1, 2], - "formfactor": "BlattWeisskopf(b-decay)" - } - ], - "topology": [[1, 2], 3], - "name": "L(1520)" - }, - { - "propagators": [ - { - "spin": "3/2", - "node": [1, 2], - "parametrization": "L(1520)_BW" - } - ], - "weight": "-0.0803435 + 0.7494165i", - "vertices": [ - { - "type": "helicity", - "helicities": ["1/2", "0"], - "node": [[1, 2], 3], - "formfactor": "BlattWeisskopf(resonance)" - }, - { - "type": "parity", - "helicities": ["0", "1/2"], - "parity_factor": "-", - "node": [1, 2], - "formfactor": "BlattWeisskopf(b-decay)" - } - ], - "topology": [[1, 2], 3], - "name": "L(1520)" - }, - { - "propagators": [ - { - "spin": "1/2", - "node": [1, 2], - "parametrization": "L(1600)_BW" - } - ], - "weight": "4.929406127531439 - 0.5956915012088891i", - "vertices": [ - { - "type": "helicity", - "helicities": ["1/2", "0"], - "node": [[1, 2], 3], - "formfactor": "BlattWeisskopf(resonance)" - }, - { - "type": "parity", - "helicities": ["0", "1/2"], - "parity_factor": "-", - "node": [1, 2], - "formfactor": "BlattWeisskopf(b-decay)" - } - ], - "topology": [[1, 2], 3], - "name": "L(1600)" - }, - { - "propagators": [ - { - "spin": "1/2", - "node": [1, 2], - "parametrization": "L(1600)_BW" - } - ], - "weight": "-3.4228557332438796 - 2.179858885546952i", - "vertices": [ - { - "type": "helicity", - "helicities": ["-1/2", "0"], - "node": [[1, 2], 3], - "formfactor": "BlattWeisskopf(resonance)" - }, - { - "type": "parity", - "helicities": ["0", "1/2"], - 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"mass": 0.8955, - "ma": 0.13957018, - "width": 0.047299999999999995 - }, - "K(700)_BuggBW": { - "gamma": 0.94106, - "type": "BuggBreitWignerMinL{@NamedTuple{m::Float64, Γ::Float64, γ::Float64}}", - "mass": 0.824, - "width": 0.478 - }, - "K(1430)_BuggBW": { - "gamma": 0.020981, - "type": "BuggBreitWignerMinL{@NamedTuple{m::Float64, Γ::Float64, γ::Float64}}", - "mass": 1.375, - "width": 0.19 - }, - "L(1670)_BW": { - "l": 0, - "mb": 0.938272046, - "type": "BreitWigner", - "mass": 1.67, - "ma": 0.493677, - "width": 0.03 - } - }, - "validation": { - "kinematic_point": { - "masses_angles": { - "kinematic_point": [ - { - "theta": 0.0, - "phi": 0.0, - "mass": 2.28646, - "node": [[1, 2], 3] - }, - { - "theta": 0.23678498926410071, - "phi": 0.0, - "mass": 1.7058127512193626, - "node": [1, 2] - } - ] - }, - "spin_projections": ["-1/2", "0", "0", "1/2"] - }, - "chains_values": [ - "0.09389266961789793 - 0.04444705194077252i", - "1.8571303475689018 - 0.8791311329744668i", - "3.495920386153536 - 1.6621763488223895i", - "1.777402925980676 - 0.8450870670837528i", - "0.12310500032232206 + 0.45678965772531055i", - "0.7791574963528171 + 2.891118030471891i", - "-5.823582950121089 - 1.1382638760343922i", - "-0.2944283101312339 - 0.05754826751411962i", - "-1.268163307415927 - 0.18551935112595022i", - "-0.6447621582430986 - 0.09432212438913892i", - "-0.04778942695357844 - 0.007824626304773727i", - "-0.9452409378665694 - 0.15476555335062303i", - "-0.07018362000955466 + 0.056344615892922126i", - "0.40521434793619865 - 0.3253130400748459i", - "-0.055066194114012104 + 0.1403939638292559i", - "0.31793190402831634 - 0.8105829893001436i", - "0.03312110072401607 - 0.4254498634584363i", - "-0.05865524970987039 + 0.7534431958684904i", - "-0.0 + 0.0i", - "1.9607019086003359 - 2.284190639309832i", - "-0.0 + 0.0i", - "-0.0 + 0.0i", - "10.6954516256848 - 6.211539520339878i", - "-0.0 + 0.0i", - "0.0 + 0.0i", - "-0.9942263897808797 - 0.10224685775008081i" - ] - } -} -``` - -
+See **[rub-ep1.github.io/amplitude-serialization](https://rub-ep1.github.io/amplitude-serialization)**. diff --git a/docs/.gitignore b/docs/.gitignore new file mode 100644 index 0000000..a2237fc --- /dev/null +++ b/docs/.gitignore @@ -0,0 +1,3 @@ +.jupyter_cache/ +*.ipynb +/.quarto/ diff --git a/HS3.md b/docs/HS3.md similarity index 76% rename from HS3.md rename to docs/HS3.md index eb0c62d..e340d5e 100644 --- a/HS3.md +++ b/docs/HS3.md @@ -16,7 +16,7 @@ In parallel to development of the model description format, compatibility with H ## Example of HS3 file -- [HS3_base.json](HS3_base.json) give description of basic interfaces of the model variables and parameters consistently with HS3. It sets default value of variable, and describes a validation point in HS3 consistent way. -- [HS3_extended.json](HS3_extended.json) prototypes +- [HS3_base.json](../models/HS3_base.json) give description of basic interfaces of the model variables and parameters consistently with HS3. 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It is computed by contracting the transition amplitude and its complex conjugate with the polarization matrix ($\rho$). This process involves summing over the final helicities while keeping the initial helicity states ($\lambda_0, \lambda_0'$) explicit in the calculation: - $$I_\text{polarized}(\tau | \text{pars}) = \sum_{\text{final\_helicities}} A^*_{\lambda_0, \text{final\_helicities}}(\tau | \text{pars}) \times \rho_{\lambda_0,\lambda_0'} \times A_{\lambda_0', \text{final\_helicities}}(\tau | \text{pars})$$ + $$ + I_\text{polarized}(\tau | \text{pars}) = \sum_{\text{final\_helicities}} A^*_{\lambda_0, \text{final\_helicities}}(\tau | \text{pars}) \times \rho_{\lambda_0,\lambda_0'} \times A_{\lambda_0', \text{final\_helicities}}(\tau | \text{pars}) + $$ Here, $A^*_{\lambda_0', \text{final\_helicities}}$ represents the complex conjugate of the amplitude for initial helicity $\lambda_0'$ and a sum over final helicities. The polarization matrix $\rho_{\lambda_0,\lambda_0'}$ encapsulates the initial polarization states of the system, allowing for a detailed analysis of how polarization affects the transition probabilities. -```jsonc +```json { "distributions" : [] { @@ -132,13 +136,13 @@ As as example, let's look into an application of the conventional helicity forma In the given topology, the decay amplitude calculation involves a series of Wigner D-functions, each corresponding to rotations and boosts that define the helicity states of the particles: -```math +$$ \begin{align} A &= n_{j_0} D_{\tau, \lambda_2}^{j_0}(\text{angles}_{[[3,1],4]}) \\ &\quad \cdot n_{j_{[[3,1],4]}} D_{\nu, \lambda_4}^{j_{[[3,1],4]}}(\text{angles}_{[3,1]}) \\ &\quad \cdot n_{j_{[3,1]}} D_{\lambda_3, \lambda_1}^{j_{[3,1]}}(\text{angles}_3) \end{align} -``` +$$ - $D_{\tau, \lambda_2}^{j_0}(\text{angles}_{[[3,1],4]})$: This function describes the transformation for particle 2's helicity (`λ2`) in the overall rest frame of the system (comprising particles 3, 1, 4, and 2). Here, particle 2's helicity is defined relative to the frame where all other particles are considered, emphasizing its position in the decay sequence. @@ -164,7 +168,7 @@ Vertices define the nodes in the decay graphs, where one particle transits into Three types are defined: `ls`, `parity`, and `helicity`. These reflect different ways of relating combinations of the helicity indices to a real-valued factor, the recoupling coefficient. - ```math + $$ \begin{align} H^\text{helicity}(\lambda_a,\lambda_b|\lambda_a^0,\lambda_b^0) &= \delta_{\lambda_a,\lambda_a^0}\delta_{\lambda_b,\lambda_b^0}\,, \\ H^\text{parity}(\lambda_a,\lambda_b|\lambda_a^0,\lambda_b^0, f) &= @@ -173,7 +177,7 @@ Vertices define the nodes in the decay graphs, where one particle transits into \left\langle j_a,\lambda_a; j_b,-\lambda_b|s,\lambda_a-\lambda_b\right\rangle \left\langle l,0; s,\lambda_a-\lambda_b|j,\lambda_a-\lambda_b\right\rangle\,. \end{align} - ``` + $$ The `helicity` indicated no recoupling, the factor is $1$ for a pair of selected helicities ($\lambda_a^0$ and $\lambda_b^0$) and zero for other combinations. The `ParityRecoupling` is controlled by the controlled by the `parity factor`, $f$, and gives non-zero value for two combination of the helicity pair, the selected one and the opposite. Finally, the `RecouplingLS` computes the value of the recoupling functions from Clebsch–Gordan coefficients. For spin-half particles, this recoupling is equivalent to `ParityRecoupling`, with $f = (-1)^l$. diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..33c53e1 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,153 @@ +# Cascade amplitude models in json format + +The zero version of the model tries to keep the structures as flatt as possible for readability purpose. + +Any value in the dictionary can be replaced by string, that corresponds to a key translated later in the file. +It enables keeping consistent numerical values for masses, and lineshape parametrizations. + +- [Detailed description of the format!](description.md) +- Notes on [HS3](HS3.md) + +## Example + +A realistic decay description for Lc2pKpi amplitude is produced with [`ThreeBodyDecayIO.jl`](https://github.com/mmikhasenko/ThreeBodyDecaysIO.jl) using the default model of the Lc2ppiK decays, +[`Lc2ppiKSemileptonicModelLHCb.jl`](https://github.com/mmikhasenko/Lc2ppiKSemileptonicModelLHCb.jl). + +For a description of a three body decay amplitude, one must provide several mandatory section at the root of the object, +`"kinematics"`, `"chains"`, `"reference_topology"`, and `"validation"` sections. + +### Kinematics Overview + +The `kinematics` section details the particle states involved in decay processes: + +- `initial_state`: Specifies the decaying particle at the start of the process. Contains keys for `index` (unique identifier), `name` (label), `spin` (quantum spin number), and `mass` (in GeV/c²). +- `final_state`: An array detailing each resulting particle from the decay. Each entry includes the same keys as `initial_state`, defining the properties of these particles. + +For example, the kinematics of the decay Lc2pKpi would look like, + +```json +"kinematics": { + "initial_state" : { + "index" : 0, + "name" : "Lc", + "spin" : "1/2", + "mass" : 2.28646 + }, + "final_state" : [ + { + "index" : 1, + "name" : "p", + "spin" : "1/2", + "mass" : 0.938272046 + }, + { + "index" : 2, + "name" : "pi", + "spin" : "0", + "mass" : 0.13957018 + }, + { + "index" : 3, + "name" : "K", + "spin" : "0", + "mass" : 0.493677 + }] +} +``` + +The `index` field serves as the primary identifier for particles. +The `name` field gives an label, which is not identifiers, it does not have to be unique. +The index zero is reserved for the decay particle in the initial state. +Spins are presented in conventional notation (e.g., "1/2") for familiarity. Most of implementations use Integers to store twice the value of the spin. + +### Decay chains + +Each decay chain is described by a JSON object containing five mandatory fields: + +- `"topology"`: defines nodes and edges of the decay graph, order of particles, +- `"propagators"`: for every decay node(!) describes parametrization of the decay particle +- `"vertices"`: for every node, describes parametrization of the coupling and form-factor +- `"weight"`: complex coefficient multiplying the chain +- `"name"`: name of the chain + +### Topology + +Tolopogy of a decay is a tree of intermediate decays given in a compact form using brackets. +In this notation, each pair of brackets indicate the node and it's children. +The name of the node is simply given by its decay in the same bracket notations. + +```json + "topology": [[1, 2], 3], +``` + +Here the 3-body decay process described by the notation `[[1,2],3]`, + +``` + 0 + | + [[1,2],3] + / \ + / 3 + [1,2] + / \ + / 2 +1 +``` + +- The innermost pair `[1,2]` represents the decay of a parent particle into particles 1 and 2. +- The next level `[[1,2],3]` indicates that the products of the first decay, along with particle 3 are combined into a new node. +- The starting node is also associated with the initial state decay particle. + +Nodes of this example topology are `[1,2]` and `[[1,2],3]`. +They are referenced when describing the decay vertices and propagators. +The order matters, i.e. `[[1,2],3] != [[2,1],3] != [3,[2,1]]`. + +Spins of the final state particles are quantized in the frames defined by the `"reference_topology"`, +i.e. there are no Wigner rotations for particles in the reference topology, while for the chains with different topology, +quantization axes must be adjusted by using appropriate wigner rotations. + +### Appendix + +The `appendix` gives definition to the text keys used elsewhere in the desciption. These definions are inserted recursively, while processing the json file. + +### Complex numbers + +The use of strings for complex numbers follows physics conventions for ease of reading. + +```json + "appendix": { + "BlattWeisskopf(resonance)": { + "type": "BlattWeisskopf", + "radius": 1.5 + }, + "L(1405)_Flatte": { + "type": "Flatte1405{@NamedTuple{m::Float64, Γ::Float64}}", + "mass": 1.4051, + "width": 0.0505 + }, + "L(1690)_BW": { + "l": 2, + "mb": 0.938272046, + "type": "BreitWigner", + "mass": 1.69, + "ma": 0.493677, + "width": 0.07 + }, + } +``` + +The string values that are not expanded in the `"appendix"` should be identifiers declared in the serialization document. + +### Validation Block + +The last block `validation` provides reference values of the amplitude for every chain at a single kinematic point. +This section acts as a model integrity check, providing reference amplitudes for comparison against calculated values. + +
+ See the full example + +```json +{{< include ../models/Lc2ppiK.json >}} +``` + +
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"a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +HadronicLineshapes = "49c9d978-1f9d-4e96-a984-0a9783c0b9bf" +JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" +Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" +Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" +Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +ThreeBodyDecaysIO = "418e7ecf-680e-4cb5-ad61-5e2f006aefac" diff --git a/docs/julia/lc2pkpi.qmd b/docs/julia/lc2pkpi.qmd new file mode 100644 index 0000000..daaf14d --- /dev/null +++ b/docs/julia/lc2pkpi.qmd @@ -0,0 +1,213 @@ +--- +jupyter: julia-amplitude-serialization-1.10 +--- + +# $\Lambda_c^+ \to p K^- \pi^+$ + +This page demostrates deserialization and evaluation of an amplitude model for the decay $\Lambda_c^+ \to p K^- \pi^+$. The amplitude analysis is performed based on roughly half a millon of $\Lambda_c^{\pm}$ decay candidates by the LHCb collaboration, [INSPIRE-HEP 2683025](https://inspirehep.net/literature/2683025). Detains on the mapped of the ampltude model onto the standard helicity formalism can be found in appendix of [INSPIRE-HEP 2623821](https://inspirehep.net/literature/2623821). + +```{julia} +#| code-fold: true +#| code-summary: Activate environment +#| output: false +import Pkg +Pkg.activate(@__DIR__) +Pkg.instantiate() + +using ThreeBodyDecaysIO +using ThreeBodyDecaysIO.ThreeBodyDecays +using ThreeBodyDecaysIO.HadronicLineshapes +using ThreeBodyDecaysIO.Parameters +using ThreeBodyDecaysIO.DataFrames +using ThreeBodyDecaysIO.JSON +using Measurements +using Statistics +using QuadGK +using Plots + +theme(:wong2, frame=:box, grid=false, minorticks=true, + guidefontvalign=:top, guidefonthalign=:right, + foreground_color_legend=nothing, + xlim=(:auto, :auto), ylim=(:auto, :auto), + lab="") +``` + +## Function definitions + +Non-standard lineshapes are used to model resonances that do not conform to a simple `BreitWigner` distributions, or a `MultichannelBreitWigner` has to be defined explicitly. +The code below defines a new lineshape, and its deserialization method. + +```{julia} +struct BreitWignerWidthExpLikeBugg <: HadronicLineshapes.AbstractFlexFunc + m::Float64 + Γ::Float64 + γ::Float64 +end +function (BW::BreitWignerWidthExpLikeBugg)(σ) + mK = 0.493677 + mπ = 0.13957018 + σA = mK^2 - mπ^2 / 2 + @unpack m, Γ, γ = BW + Γt = (σ - σA) / (m^2 - σA) * Γ * exp(-γ * σ) + 1 / (m^2 - σ - 1im * m * Γt) +end +function ThreeBodyDecaysIO.dict2instance(::Type{BreitWignerWidthExpLikeBugg}, dict) + @unpack mass, width, slope = dict + return BreitWignerWidthExpLikeBugg(mass, width, slope) +end +``` + +## Deserialization of Objects to a Workspace + +Model components are deserialized from a JSON file into computational objects within a workspace for further manipulation. First, functions representing lineshapes and formfactors are built. Following this, distributions are processed and added to the workspace. + +```{julia} +input = open(joinpath(@__DIR__, "..", "..", "models", "Lc2ppiK.json")) do io + JSON.parse(io) +end + +workspace = Dict{String,Any}() + +@unpack functions = input +for fn in functions + @unpack name, type = fn + instance_type = eval(Symbol(type)) + workspace[name] = dict2instance(instance_type, fn) +end + +@unpack distributions = input +for dist in distributions + @unpack name, type = dist + instance_type = eval(Symbol(type)) + workspace[name] = dict2instance(instance_type, distributions[1]; workspace) +end +``` + +## Validation + +The integrity of the model is checked by validating the value of distributions at a few phase space points. +The table lists the validation checkes and their status ("🟢" or "🔴"). + +```{julia} +#| code-fold: true +#| code-summary: A loop over validation points +let + @unpack misc, parameter_points = input + @unpack amplitude_model_checksums = misc + + map(amplitude_model_checksums) do check_point_info + @unpack name, value, distribution = check_point_info + # + # pull distribution + dist = workspace[distribution] + + # pull correct parameter point + parameter_points_dict = array2dict(parameter_points; key="name") + # find the point in the list of points + parameter_point = parameter_points_dict[name] + # compute, compare + _parameters = array2dict(parameter_point["parameters"]; + key="name", apply=v -> v["value"]) + # + # @assert value ≈ dist(_parameters) "Check-point validation failed with $distribution 🥕" + status = (value ≈ dist(_parameters)) ? "🟢" : "🔴" + (; Distribution=distribution, + Point=name, Status=status) + end |> DataFrame +end +``` + +## Visualization + +The model descibing the decay is fetched from the workspace + +```{julia} +model_dist = [v for (k, v) in workspace if v isa HadronicUnpolarizedIntensity] |> first; +``` + +### Dalitz plot + +The Dalitz plot shows the probability distribution across two dimensional phase space of the decay. + +```{julia} +#| code-fold: true +#| code-summary: Dalitz plot plotting +let iσx = 2, iσy = 1 + xlab = ((i, j) = ij_from_k(iσx); + "m²($i$j) [GeV²]") + ylab = ((i, j) = ij_from_k(iσy); + "m²($i$j) [GeV²]") + model = model_dist.model + + plot(masses(model), Base.Fix1(unpolarized_intensity, model); + iσx, iσy, xlab, ylab) +end +``` + + +c +The projection of the model onto a mass variable is shown by black line. +Contributions from individual resonances are shown by the colored lines. + +```{julia} +#| code-fold: true +#| code-summary: Computation of projections +let k = 2 + i, j = ij_from_k(k) + xlab = "m($i$j) [GeV]" + model = model_dist.model + # + mlims = sqrt.(lims(k, masses(model))) + mv = range(mlims..., 150) |> shift_by_half + # + plot() + plot!(mv, lab="Total") do m + I = Base.Fix1(unpolarized_intensity, model) + m * quadgk(projection_integrand(I, masses(model), m^2; k), 0, 1)[1] + end + chain_names = Set(model.names) |> collect |> sort + for name in chain_names + _model = model[model.names.==name] + plot!(mv, lab=name) do m + I = Base.Fix1(unpolarized_intensity, _model) + m * quadgk(projection_integrand(I, masses(_model), m^2; k), 0, 1)[1] + end + end + plot!(; xlab) +end +``` + +## Fit Fractions + +The contribution of different resonances to the overall decay process is quantitatively assessed using numerical evaluation on a finite-size sample. Statistical uncertainty in the reported values only reflects the precision of these calculations. For a understanding of model uncertainties, refer to the original publications. + +```{julia} +#| code-fold: true +#| code-summary: Computation of fit fractions +#| output: true +let + model = model_dist.model + ms = masses(model) + # + x2 = rand(10000, 2) + data = map(eachslice(x2; dims=1)) do (x, y) + σ1 = lims1(ms)[1] + x * diff(lims1(ms) |> collect)[1] + σ2 = lims2(ms)[1] + y * diff(lims2(ms) |> collect)[1] + σs = Invariants(ms; σ1, σ2) + end + filter!(data) do σs + Kibble(σs, ms^2) < 0 + end + # + chain_names = Set(model.names) |> collect |> sort + _int_i = map(chain_names) do name + _calv = unpolarized_intensity.(model[model.names.==name] |> Ref, data) + _value = mean(_calv) + _err = sqrt(cov(_calv, _calv) / length(data)) + _value ± _err + end + _int0 = sum(unpolarized_intensity.(model |> Ref, data)) / length(data) + ff = round.(_int_i ./ _int0 .* 100; digits=2) + DataFrame("Resonance" => chain_names, "Fit Franction [%]" => ff) +end +``` diff --git a/docs/python/lc2pkpi.qmd b/docs/python/lc2pkpi.qmd new file mode 100644 index 0000000..b99a9b9 --- /dev/null +++ b/docs/python/lc2pkpi.qmd @@ -0,0 +1,9 @@ +--- +jupyter: python3 +--- + +# Test + +```{python} +print("Test to see if Python kernel is alive") +``` diff --git a/HS3_base.json b/models/HS3_base.json similarity index 100% rename from HS3_base.json rename to models/HS3_base.json diff --git a/HS3_extended.json b/models/HS3_extended.json similarity index 100% rename from HS3_extended.json rename to models/HS3_extended.json diff --git a/Lc2ppiK.json b/models/Lc2ppiK.json similarity index 100% rename from Lc2ppiK.json rename to models/Lc2ppiK.json diff --git a/pixi.lock b/pixi.lock index d928810..5284fa8 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3,92 +3,288 @@ environments: default: channels: - 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