Merge pull request #11 from shareloqs/master

Update doc-writing with latest modifs of master

.github/workflows/docs.yml

@@ -3,7 +3,7 @@ name: Documentation
 on:
   push:
     branches:
-      - doc-writing
+      - master
     tags: '*'
   pull_request:
 

CITATION.cff

@@ -0,0 +1,63 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: MPSDynamics.jl
+message: >-
+  If you use this software, please cite it
+type: software
+authors:
+  - given-names: Angus J.
+    family-names: Dunnett
+    orcid: 'https://orcid.org/0000-0002-8579-7826'
+  - given-names: Thibaut
+    family-names: Lacroix
+    orcid: 'https://orcid.org/0000-0002-5190-040X'
+  - given-names: Angela
+    family-names: Riva
+    orcid: 'https://orcid.org/0009-0005-8509-9162'
+  - given-names: Brieuc
+    family-names: Le Dé
+    orcid: 'https://orcid.org/0000-0001-6004-0758'
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.5106434
+    description: Zenodo Repository
+  - type: doi
+    value: 10.1063/5.0223107
+    description: J. Chem. Phys. Paper
+url: 'https://github.com/shareloqs/MPSDynamics'
+abstract: >-
+  Tensor network simulations for finite temperature, open
+  quantum system dynamics
+license: GPL-3.0
+preferred-citation:
+  type: article
+  authors:
+  - given-names: Thibaut
+    family-names: Lacroix
+    orcid: 'https://orcid.org/0000-0002-5190-040X'
+    affiliation: Institute of Theoretical Physics, Ulm University
+  - given-names: Brieuc
+    family-names: Le Dé
+    orcid: 'https://orcid.org/0000-0001-6004-0758'
+    affiliation: Sorbonne Université, CNRS, Institut des NanoSciences de Paris
+  - given-names: Angela
+    family-names: Riva
+    orcid: 'https://orcid.org/0009-0005-8509-9162'
+    affiliation: LPENS, Département de Physique, École Normale Supérieure, Centre Automatique et Systèmes (CAS), MINES ParisTech, Université PSL, Sorbonne Université, CNRS, Inria
+  - given-names: Angus J.
+    family-names: Dunnett
+    orcid: 'https://orcid.org/0000-0002-8579-7826'
+    affiliation: Multiverse Computing
+  - given-names: Alex W.
+    family-names: Chin
+    orcid: 'https://orcid.org/0000-0001-7741-5915'
+    affiliation: Sorbonne Université, CNRS, Institut des NanoSciences de Paris
+  doi: "10.1063/5.0223107"
+  journal: "The Journal of Chemical Physics"
+  month: 8
+  title: "MPSDynamics.jl: Tensor network simulations for finite-temperature (non-Markovian) open quantum system dynamics"
+  issue: 8
+  volume: 161
+  year: 2024

ChainOhmT/gauss.jl

@@ -1,16 +1,11 @@
 using LinearAlgebra
 
-""" GAUSS Gauss quadrature rule.
+""" 
+    gauss(N,ab)
 
-    Given a weight function w encoded by the nx2 array ab of the
-    first n recurrence coefficients for the associated orthogonal
-    polynomials, the first column of ab containing the n alpha-
-    coefficients and the second column the n beta-coefficients,
-    the call xw = GAUSS(n,ab) generates the nodes and weights xw of
-    the n-point Gauss quadrature rule for the weight function w.
-    The nodes, in increasing order, are stored in the first
-    column, the n corresponding weights in the second column, of
-    the nx2 array xw.
+Gauss quadrature rule for `N` sites on an interval `ab`. Given a weight function w encoded by the `N`x2 array `ab` of the first `N` recurrence coefficients for the associated orthogonal
+polynomials, the first column of `ab` containing the `N` alpha-coefficients and the second column the `N` beta-coefficients, the call xw = gauss(N,ab) generates the nodes and weights xw of the `N`-point Gauss quadrature rule for the weight function w.
+The nodes, in increasing order, are stored in the first column, the n corresponding weights in the second column, of the `N`x2 array xw.
 """
 function gauss(N,ab)
     N0 = size(ab,1)

ChainOhmT/lanczos.jl

@@ -1,17 +1,9 @@
-""" LANCZOS Lanczos algorithm.
+""" 
+    lanczos(N,xw)
 
-    Given the discrete inner product whose nodes are contained
-    in the first column, and whose weights are contained in the
-    second column, of the nx2 array xw, the call ab=LANCZOS(n,xw)
-    generates the first n recurrence coefficients ab of the
-    corresponding discrete orthogonal polynomials. The n alpha-
-    coefficients are stored in the first column, the n beta-
-    coefficients in the second column, of the nx2 array ab.
+Given the discrete inner product whose nodes are contained in the first column, and whose weights are contained in the second column, of the `N`x2 array `xw`, the call ab=lanczos(N,xw) generates the first `N` recurrence coefficients ab of the corresponding discrete orthogonal polynomials. The `N` alpha-coefficients are stored in the first column, the `N` beta-coefficients in the second column, of the `N`x2 array ab.
 
-    The script is adapted from the routine RKPW in
-    W.B. Gragg and W.J. Harrod, ``The numerically stable
-    reconstruction of Jacobi matrices from spectral data'',
-    Numer. Math. 44 (1984), 317-335.
+The script is adapted from the routine RKPW in W.B. Gragg and W.J. Harrod, ``The numerically stable reconstruction of Jacobi matrices from spectral data'', Numer. Math. 44 (1984), 317-335.
 """
 function lanczos(N,xw) #return ab
     Ncap = size(xw,1)

ChainOhmT/stieltjes.jl

@@ -1,12 +1,7 @@
-""" STIELTJES Discretized Stieltjes procedure.
+""" 
+    stieltjes(N,xw)
 
-    Given the discrete inner product whose nodes are contained
-    in the first column, and whose weights are contained in the
-    second column, of the nx2 array xw, the call ab=STIELTJES(n,xw)
-    generates the first n recurrence coefficients ab of the
-    corresponding discrete orthogonal polynomials. The n alpha-
-    coefficients are stored in the first column, the n beta-
-    coefficients in the second column, of the nx2 array ab.
+Discretized Stieltjes procedure. Given the discrete inner product whose nodes are contained in the first column, and whose weights are contained in the second column, of the `N`x2 array `xw`, the call ab=stieltjes(N,xw) generates the first `N` recurrence coefficients ab of the corresponding discrete orthogonal polynomials. The `N` alpha- coefficients are stored in the first column, the `N` beta-coefficients in the second column, of the `N`x2 array ab.
 """
 function stieltjes(N,xw) #return ab
     #tiny = 10*realmin

Project.toml

@@ -1,7 +1,7 @@
 name = "MPSDynamics"
 uuid = "8fc8f346-e1eb-498f-94db-02ffe92d8134"
 authors = ["angus-dunnett <[email protected]>", "Thibaut Lacroix <[email protected]>"]
-version = "1.0.0"
+version = "1.1.0"
 
 [deps]
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
@@ -25,5 +25,6 @@ SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 TensorOperations = "6aa20fa7-93e2-5fca-9bc0-fbd0db3c71a2"
 
 [compat]
+ITensors = "0.6"
 TensorOperations = "4.0.7"
 julia = "1.7"

README.md

@@ -3,7 +3,9 @@
 # MPSDynamics.jl
 *Tensor network simulations for finite temperature, open quantum system dynamics.*
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5106435.svg)](https://doi.org/10.5281/zenodo.5106435) [![license](https://img.shields.io/badge/License-GPL_3.0-orange.svg)](https://github.com/angusdunnett/MPSDynamics/blob/master/LICENSE) [![documentation workflow](https://github.com/angusdunnett/MPSDynamics/actions/workflows/docs.yml/badge.svg)](https://angusdunnett.github.io/MPSDynamics/)
+
+
+[![J. Chem. Phys.](https://img.shields.io/badge/J.%20Chem.%20Phys.%20-%2010.1063%2F5.0223107%20-%20navy)](https://doi.org/10.1063/5.0223107) [![ArXiv](https://img.shields.io/badge/arXiv-2406.07052-B31B1B.svg)](https://arxiv.org/abs/2406.07052) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11400776.svg)](https://doi.org/10.5281/zenodo.11400776) [![license](https://img.shields.io/badge/License-GPL_3.0-orange.svg)](https://github.com/shareloqs/MPSDynamics/blob/master/LICENSE) [![documentation workflow](https://github.com/shareloqs/MPSDynamics/actions/workflows/docs.yml/badge.svg)](https://shareloqs.github.io/MPSDynamics/)
 
 
 This package is intended to provide an easy to use interface for performing tensor network simulations on Matrix Product
@@ -152,16 +154,37 @@ Import["~/MPSDynamics/XXXXX/dat_XXXXX.jld",{"HDF5","Datasets","/data/sz"}]
 
 # Publications
 Publications which make use of MPSDynamics:
+* Lacroix et al. Making Quantum Collision Models Exact, *arXiv e-print*, November 2024
+    * [https://doi.org/10.48550/arXiv.2411.13166](https://doi.org/10.48550/arXiv.2411.13166)
+
+* Le Dé et al. Extending Non-Perturbative Simulation Techniques for Open-Quantum Systems to Excited-State Proton Transfer and Ultrafast Non-Adiabatic Dynamics, *J. Chem. Theory Comput.*, October 2024
+    * [https://doi.org/10.1021/acs.jctc.4c00666](https://doi.org/10.1021/acs.jctc.4c00666)
+
+* Lambertson et al. Computing Linear Optical Spectra in the Presence of Nonadiabatic Effects on Graphics Processing Units Using Molecular Dynamics and Tensor-Network Approaches, *J. Chem. Phys.*, 161, 114101, September 2024
+    * [https://doi.org/10.1063/5.0224316](https://doi.org/10.1063/5.0224316)
+
+* Lacroix et al. Connectivity Matters: Impact of Bath Modes Ordering and Geometry in Open Quantum System Simulation with Matrix Product States, *arXiv e-print*, September 2024
+    * [https://doi.org/10.48550/arXiv.2409.04145](https://doi.org/10.48550/arXiv.2409.04145)
+
+* Lacroix et al. MPSDynamics.jl: Tensor network simulations for finite-temperature (non-Markovian) open quantum system dynamics, *J. Chem. Phys.*, 161, 084116, August 2024
+    * [https://doi.org/10.1063/5.0223107](https://doi.org/10.1063/5.0223107)
+
+* Le Dé et al. Managing Temperature in Open Quantum Systems Strongly Coupled with Structured Environments, *J. Chem. Phys.* 160, 244102, June 2024
+    * [https://doi.org/10.1063/5.0214051](https://doi.org/10.1063/5.0214051)
+
+* Hunter et al. Environmentally Driven Symmetry Breaking Quenches Dual Fluorescence in Proflavine. *J.Phys. Chem. Lett.* 15, 4623−4632, April 2024
+  * [https://doi.org/10.1021/acs.jpclett.4c00677](https://doi.org/10.1021/acs.jpclett.4c00677)
+
 * Lacroix et al. From Non-Markovian Dissipation to Spatiotemporal Control of Quantum Nanodevices. *Quantum* 8, 1305, April 2024
     * [https://doi.org/10.22331/q-2024-04-03-1305](https://doi.org/10.22331/q-2024-04-03-1305)
+
 * Riva et al. Thermal cycle and polaron formation in structured bosonic environments. *Phys. Rev. B*  108(19):195138, November 2023
     * [https://doi.org/10.1103/PhysRevB.108.195138](https://doi.org/10.1103/PhysRevB.108.195138)
 
 * Lacroix et al. Unveiling non-Markovian spacetime signaling in open quantum systems with long-range tensor network dynamics. *Phys. Rev. A* 104(5):052204, November 2021
      * [https://link.aps.org/doi/10.1103/PhysRevA.104.052204](https://link.aps.org/doi/10.1103/PhysRevA.104.052204)
 
 * Dunnett et al. Influence of non-adiabatic effects on linear absorption spectra in the condensed phase: Methylene blue. *J. Chem. Phys.* 155(14):144112, October 2021
-
      * [http://aip.scitation.org/doi/10.1063/5.0062950](http://aip.scitation.org/doi/10.1063/5.0062950)
 
 * Dunnett and Chin. Simulating quantum vibronic dynamics at finite temperatures with many body wave functions at 0K. *Front. Chem.* 8, January 2021
@@ -179,15 +202,45 @@ Publications which make use of MPSDynamics:
      * [10.5281/zenodo.4352728](https://doi.org/10.5281/zenodo.4352728)
 
 # Citation
-
-If you use this package in your research, please cite it:
-* Dunnett, A. (2021). angusdunnett/MPSDynamics: (v1.0). Zenodo. https://doi.org/10.5281/zenodo.5106435
+If you use the package in your research, please consider citing it.
+You can add the Zenodo record and the software paper to your BibTex file:
+
+```tex
+@misc{mpsdynamics_zenodo,
+	title = {shareloqs/{MPSDynamics}: v1.1},
+	shorttitle = {{MPSDynamics}.jl: v1.1},
+	url = {https://doi.org/10.5281/zenodo.11400776},
+	abstract = {Tensor network simulations for finite temperature, open quantum system dynamics},
+	publisher = {Zenodo},
+	author = {Dunnett, Angus J. and Lacroix, Thibaut and Riva, Angela and Le Dé, Brieuc},
+	month = may,
+	year = {2024},
+	doi = {10.5281/zenodo.11400776},
+}
+
+@article{mpsdynamicsjl_2024,
+	title = {{MPSDynamics}.jl: {Tensor} network simulations for finite-temperature (non-{Markovian}) open quantum system dynamics},
+	volume = {161},
+	issn = {0021-9606},
+	shorttitle = {{MPSDynamics}.jl},
+	url = {https://doi.org/10.1063/5.0223107},
+	doi = {10.1063/5.0223107},
+	number = {8},
+	journal = {The Journal of Chemical Physics},
+	author = {Lacroix, Thibaut and Le Dé, Brieuc and Riva, Angela and Dunnett, Angus J. and Chin, Alex W.},
+	month = aug,
+	year = {2024},
+	pages = {084116},
+}
+```
 
 # How to Contribute
 Contributions are welcome! Don't hesitate to contact us if you
 * found a bug;
 * have a suggestion on how to improve the code and/or documentation;
 * would like to get involved in writing code and/or documentation.
+
+Feel free to open an [issue](https://github.com/shareloqs/MPSDynamics/issues) on Github :)
 
 # References
 

docs/Project.toml

@@ -2,4 +2,4 @@
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 
 [compat]
-Documenter = "0.26"
+Documenter = "1.4"

docs/make.jl

@@ -7,12 +7,12 @@ makedocs(
     modules = [MPSDynamics],
     highlightsig = true,
     sitename = "MPSDynamics.jl",
-    authors = "Angus Dunnett, Thibaut Lacroix, Brieuc Le Dé, Angela Riva",
+    authors = "Angus J. Dunnett, Thibaut Lacroix, Brieuc Le Dé, Angela Riva",
     pages = [
         "index.md",
         "user-guide.md",
         "nutshell.md",
-        "Examples" => ["./examples/sbm.md", "./examples/puredephasing.md", "./examples/timedep.md", "./examples/anderson-model.md", "./examples/bath-observables.md"],
+        "Examples" => ["./examples/sbm.md", "./examples/puredephasing.md", "./examples/timedep.md", "./examples/anderson-model.md", "./examples/bath-observables.md", "./examples/protontransfer.md"],
         "theory.md",
         "Methods" => "methods.md",
         "dev.md"
@@ -24,5 +24,5 @@ makedocs(
 deploydocs(
     repo = "github.com/shareloqs/MPSDynamics.git",
     devurl = "docs",
-    devbranch = "doc-writing"
+    devbranch = "master"
 )