# Chemistry

**URL:** https://discourse.julialang.org/c/domain/chemistry/53.md

[Latest](https://discourse.julialang.org/latest.md) · [Categories](https://discourse.julialang.org/categories.md) · [Tags](https://discourse.julialang.org/tags.md)

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## [About the Chemistry category](https://discourse.julialang.org/t/about-the-chemistry-category/51271)

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**Author:** [@vchuravy](https://discourse.julialang.org/u/vchuravy)\
**Replies:** 0\
**Last updated:** [December 4, 2020, 7:47pm UTC](https://discourse.julialang.org/t/about-the-chemistry-category/51271 "2020-12-04T19:47:46Z")

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Discussion and questions concerning Chemistry in Julia. Current Git Resources for Chemistry in Julia : Julia.jl/Chemistry.md at master · svaksha/Julia.jl (github.com) Discussions about Julia’s usage for Chemistry, c…

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## [How to get dipole moments for a molecule in Atomic Orbital basis within the Julia ecosystem?](https://discourse.julialang.org/t/how-to-get-dipole-moments-for-a-molecule-in-atomic-orbital-basis-within-the-julia-ecosystem/130436)

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**Author:** [@Uranium238](https://discourse.julialang.org/u/Uranium238)\
**Replies:** 1\
**Last updated:** [July 6, 2025, 6:33am UTC](https://discourse.julialang.org/t/how-to-get-dipole-moments-for-a-molecule-in-atomic-orbital-basis-within-the-julia-ecosystem/130436 "2025-07-06T06:33:33Z")

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I am trying to develop an implementation of a certain electronic structure method within Julia aimed at modelling strong light-matter interactions. The method is closely related to the widely popular Hartree-Fock method.…

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## [Time-plotting the derivative of a species (reaction velocity) in catalyst](https://discourse.julialang.org/t/time-plotting-the-derivative-of-a-species-reaction-velocity-in-catalyst/129927)

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**Author:** [@Andre\_Renard](https://discourse.julialang.org/u/Andre_Renard)\
**Replies:** 1\
**Last updated:** [June 16, 2025, 9:37pm UTC](https://discourse.julialang.org/t/time-plotting-the-derivative-of-a-species-reaction-velocity-in-catalyst/129927 "2025-06-16T21:37:32Z")

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Hello, I can’t find an easy way to time-plot a derivative of a species, although I’m sure data are stored somewhere. Thanks for help. Andre

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## [Using Catalyst ODEproblem and algebraic equations](https://discourse.julialang.org/t/using-catalyst-odeproblem-and-algebraic-equations/128375)

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**Author:** [@AnthonySoive](https://discourse.julialang.org/u/AnthonySoive)\
**Replies:** 4\
**Last updated:** [April 25, 2025, 12:50pm UTC](https://discourse.julialang.org/t/using-catalyst-odeproblem-and-algebraic-equations/128375 "2025-04-25T12:50:33Z")

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Dear all, I am trying to add algebraic equations to a Catalyst reaction system. I read old post on this subject where It was not possible to do with ODEproblem function. Is it still the case? For example, I’ve tried thi…

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## [Time dependent inputs to reaction network in Catalyst](https://discourse.julialang.org/t/time-dependent-inputs-to-reaction-network-in-catalyst/121078)

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**Author:** [@contejuz](https://discourse.julialang.org/u/contejuz)\
**Replies:** 5\
**Last updated:** [February 11, 2025, 3:20pm UTC](https://discourse.julialang.org/t/time-dependent-inputs-to-reaction-network-in-catalyst/121078 "2025-02-11T15:20:25Z")

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I’m trying to create a simple reaction network that takes external input. Here is one example (adapted from the docs): # Create model. model = @reaction\_network begin kB\*I(t), S + E --\> SE kD, SE --\> S + E k…

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## [JuliaMolSim community](https://discourse.julialang.org/t/juliamolsim-community/125362)

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**Author:** [@rkurchin](https://discourse.julialang.org/u/rkurchin)\
**Replies:** 0\
**Last updated:** [January 29, 2025, 8:46pm UTC](https://discourse.julialang.org/t/juliamolsim-community/125362 "2025-01-29T20:46:16Z")

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Hey everyone! I want to make a plug for the JuliaMolSim community – a home for anyone engaged in molecular and materials modeling in Julia! We maintain some community interface packages (GH) like AtomsBase and AtomsCalcu…

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## [How to solve the non linear Coupled Cluster equations using Inexact Newton with DIIS?](https://discourse.julialang.org/t/how-to-solve-the-non-linear-coupled-cluster-equations-using-inexact-newton-with-diis/115291)

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**Author:** [@Uranium238](https://discourse.julialang.org/u/Uranium238)\
**Replies:** 1\
**Last updated:** [June 16, 2024, 12:02pm UTC](https://discourse.julialang.org/t/how-to-solve-the-non-linear-coupled-cluster-equations-using-inexact-newton-with-diis/115291 "2024-06-16T12:02:09Z")

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I have been trying to solve the Coupled Cluster Amplitude Equations which are a set of non-linear equations using Julia. The aim is to find cluster amplitudes tensor T2 such that the residual tensor (defined below) is ze…

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## [Zero Order Extinction Reaction](https://discourse.julialang.org/t/zero-order-extinction-reaction/108749)

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**Author:** [@kkakosim](https://discourse.julialang.org/u/kkakosim)\
**Replies:** 21\
**Last updated:** [March 27, 2024, 3:25pm UTC](https://discourse.julialang.org/t/zero-order-extinction-reaction/108749 "2024-03-27T15:25:57Z")

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Is there any way to achieve the positive\_domain effect with the Catalyst.jl syntax? In my example (decomposition of CaC2 yielding Calcium gas and solid Carbon): CaC2 → Ca(g) + 2C(s) I am looking for a way to “remove” …

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## [@unpack from Catalyst reaction system and unused variables](https://discourse.julialang.org/t/unpack-from-catalyst-reaction-system-and-unused-variables/110766)

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**Author:** [@johannesnauta](https://discourse.julialang.org/u/johannesnauta)\
**Replies:** 9\
**Last updated:** [February 26, 2024, 3:26pm UTC](https://discourse.julialang.org/t/unpack-from-catalyst-reaction-system-and-unused-variables/110766 "2024-02-26T15:26:27Z")

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Hi all. I have happily been using Catalyst.jl (and of course related packages, such as ModelingToolkit.jl and DifferentialEquations.jl), but when remaking problems while using EnsembleProblem I encountered some odd behav…

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## [Failed to use OpenSmiles](https://discourse.julialang.org/t/failed-to-use-opensmiles/109408)

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**Author:** [@Kirill\_Vostrecov](https://discourse.julialang.org/u/Kirill_Vostrecov)\
**Replies:** 0\
**Last updated:** [January 29, 2024, 5:06pm UTC](https://discourse.julialang.org/t/failed-to-use-opensmiles/109408 "2024-01-29T17:06:18Z")

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Hi all! Tried to use OpenSmiles like using OpenSMILES OpenSMILES.ParseSMILES(“C1CC12CC2”) just for test and got error ERROR: LoadError: MethodError: no method matching add\_vertex!(::SimpleWeightedGraphs.SimpleWeight…

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## [Combining Catalyst DSL models and ModelingToolkit explicit ODE models](https://discourse.julialang.org/t/combining-catalyst-dsl-models-and-modelingtoolkit-explicit-ode-models/54418)

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**Author:** [@conradh](https://discourse.julialang.org/u/conradh)\
**Replies:** 18\
**Last updated:** [November 28, 2023, 6:49pm UTC](https://discourse.julialang.org/t/combining-catalyst-dsl-models-and-modelingtoolkit-explicit-ode-models/54418 "2023-11-28T18:49:02Z")

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I’d like to connect a model defined via explicit ODEs using ModelingToolkit.jl with a model defined using the reaction DSL provided by Catalyst.jl. Specifically, I’d like to use an output of my ODE model as a forcing fun…

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## [AIP has a call for papers for software in Chemical Physics](https://discourse.julialang.org/t/aip-has-a-call-for-papers-for-software-in-chemical-physics/105063)

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**Author:** [@Knud\_Sorensen](https://discourse.julialang.org/u/Knud_Sorensen)\
**Replies:** 1\
**Last updated:** [October 17, 2023, 2:38pm UTC](https://discourse.julialang.org/t/aip-has-a-call-for-papers-for-software-in-chemical-physics/105063 "2023-10-17T14:38:44Z")

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Maybe a chance to show some julia code.

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## [Calling Cantera using PyCall from within DifferentialEquations function](https://discourse.julialang.org/t/calling-cantera-using-pycall-from-within-differentialequations-function/104942)

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**Author:** [@NikoBiele](https://discourse.julialang.org/u/NikoBiele)\
**Replies:** 2\
**Last updated:** [October 14, 2023, 6:14am UTC](https://discourse.julialang.org/t/calling-cantera-using-pycall-from-within-differentialequations-function/104942 "2023-10-14T06:14:27Z")

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Hi, I’m trying to simulate the combustion of hydrogen using Cantera from Julia via PyCall. But I’m having trouble using PyCall from within my DifferentialEquations function. I have translated this (custom.py | Cantera) …

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## [Any crystallography and material structure package suggestions?](https://discourse.julialang.org/t/any-crystallography-and-material-structure-package-suggestions/63028)

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**Author:** [@wujinq](https://discourse.julialang.org/u/wujinq)\
**Replies:** 7\
**Last updated:** [July 18, 2023, 5:10am UTC](https://discourse.julialang.org/t/any-crystallography-and-material-structure-package-suggestions/63028 "2023-07-18T05:10:15Z")

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Is there any existing package that helps user read crystal structure from, say, VASP POSCAR or CONTCAR files and determin crystallography data like the space group and the point group?

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## [ElementaryChemistry.jl](https://discourse.julialang.org/t/elementarychemistry-jl/63373)

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**Author:** [@Baobab\_The\_fruit](https://discourse.julialang.org/u/Baobab_The_fruit)\
**Replies:** 3\
**Last updated:** [January 30, 2023, 4:46pm UTC](https://discourse.julialang.org/t/elementarychemistry-jl/63373 "2023-01-30T16:46:27Z")

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Both an announcement and topic that would fit in here this is my package should be added to the general registry tomorrow. I would love suggestions, ideas on what formulas, ideas, or concepts to add to the project. bao…

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## [Computing titration curves](https://discourse.julialang.org/t/computing-titration-curves/81415)

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**Author:** [@tp2750](https://discourse.julialang.org/u/tp2750)\
**Replies:** 12\
**Last updated:** [December 11, 2022, 1:35pm UTC](https://discourse.julialang.org/t/computing-titration-curves/81415 "2022-12-11T13:35:17Z")

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Is there a Julia package for computing titration curves? I’ll like to simulate a titration experiment where a weak acid with several pKa values is titrated by a strong base. Something similar to figure 17.3.5 here: 17.3…

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## [CAS Common Chemistry](https://discourse.julialang.org/t/cas-common-chemistry/76429)

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**Author:** [@tp2750](https://discourse.julialang.org/u/tp2750)\
**Replies:** 3\
**Last updated:** [October 1, 2022, 9:14pm UTC](https://discourse.julialang.org/t/cas-common-chemistry/76429 "2022-10-01T21:14:33Z")

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Is there a Julia package for accessing the CAS Common Chemistry database?

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## [How to convert a molecule(s) to bitvector to matrix](https://discourse.julialang.org/t/how-to-convert-a-molecule-s-to-bitvector-to-matrix/87738)

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**Author:** [@nick\_m](https://discourse.julialang.org/u/nick_m)\
**Replies:** 7\
**Last updated:** [September 24, 2022, 1:53pm UTC](https://discourse.julialang.org/t/how-to-convert-a-molecule-s-to-bitvector-to-matrix/87738 "2022-09-24T13:53:25Z")

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I am new to Julia and trying to convert a list of molecules to a matrix. I am using rdkit, so far I’ve got mol = RDKitMinimalLib.get\_mol("CC(=O)Oc1ccccc1C(=O)O") fp\_details = Dict{String, Any}("nBits" =\> 512, "radius" =\>…

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## [How to model a chemical reaction network with changing parameters? (Catalyst.jl)](https://discourse.julialang.org/t/how-to-model-a-chemical-reaction-network-with-changing-parameters-catalyst-jl/79489)

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**Author:** [@govissers](https://discourse.julialang.org/u/govissers)\
**Replies:** 5\
**Last updated:** [April 14, 2022, 5:38pm UTC](https://discourse.julialang.org/t/how-to-model-a-chemical-reaction-network-with-changing-parameters-catalyst-jl/79489 "2022-04-14T17:38:12Z")

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Hello, I am hoping to model a chemical reaction network within a cell, where an organism may change the rate of a reaction given an external stimulus at time t. Is it possible to model a CRN wherea reaction constant, sp…

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## [Is there a direct link function for chemical process simulator like Aspen plus in Julia like in Matlab or python through COM technology?](https://discourse.julialang.org/t/is-there-a-direct-link-function-for-chemical-process-simulator-like-aspen-plus-in-julia-like-in-matlab-or-python-through-com-technology/79133)

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**Author:** [@JackaChou](https://discourse.julialang.org/u/JackaChou)\
**Replies:** 4\
**Last updated:** [April 7, 2022, 6:55am UTC](https://discourse.julialang.org/t/is-there-a-direct-link-function-for-chemical-process-simulator-like-aspen-plus-in-julia-like-in-matlab-or-python-through-com-technology/79133 "2022-04-07T06:55:50Z")

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Something like Aspen Plus - Matlab Link - File Exchange - MATLAB Central

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## [How to convert a String to a Reaction/ReactionSystem type (Catalyst.jl)?](https://discourse.julialang.org/t/how-to-convert-a-string-to-a-reaction-reactionsystem-type-catalyst-jl/75377)

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**Author:** [@Leticia-maria](https://discourse.julialang.org/u/Leticia-maria)\
**Replies:** 1\
**Last updated:** [January 29, 2022, 2:58pm UTC](https://discourse.julialang.org/t/how-to-convert-a-string-to-a-reaction-reactionsystem-type-catalyst-jl/75377 "2022-01-29T14:58:18Z")

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Hey you all, I wanna use Strings to add reactions to a @reaction\_network in Catalyst.jl. For example: julia\> example = @reaction\_network empty julia\> addreaction!(example, "k, A --\> B") or julia\> addreaction!(example,…

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## [How does ModelingToolkit substitute the u0map?](https://discourse.julialang.org/t/how-does-modelingtoolkit-substitute-the-u0map/72688)

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**Author:** [@cjwyett](https://discourse.julialang.org/u/cjwyett)\
**Replies:** 2\
**Last updated:** [December 7, 2021, 3:48am UTC](https://discourse.julialang.org/t/how-does-modelingtoolkit-substitute-the-u0map/72688 "2021-12-07T03:48:10Z")

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Hi there, I’m trying to port some code over to use Catalyst. using Catalyst, Symbolics rs = @reaction\_network begin 1, 2A --\> B 2, B + C --\> 0 end v = Catalyst.oderatelaw.(reactions(rs)) u0 = \[1,1,1\] Now if i…

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## [Solving chemical systems of equations with both equilibrium and kinetic species](https://discourse.julialang.org/t/solving-chemical-systems-of-equations-with-both-equilibrium-and-kinetic-species/68755)

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**Author:** [@gagnonaa10](https://discourse.julialang.org/u/gagnonaa10)\
**Replies:** 1\
**Last updated:** [September 25, 2021, 5:52pm UTC](https://discourse.julialang.org/t/solving-chemical-systems-of-equations-with-both-equilibrium-and-kinetic-species/68755 "2021-09-25T17:52:41Z")

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This is building on a different discourse post I made previously: https://discourse.julialang.org/t/constraints-in-catalyst-jl-for-weak-acids-and-ph-equilibrium/68037/2 And on Github: https://github.com/SciML/Catalyst…

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## [Constraints in Catalyst.jl for weak acids and pH equilibrium](https://discourse.julialang.org/t/constraints-in-catalyst-jl-for-weak-acids-and-ph-equilibrium/68037)

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**Author:** [@gagnonaa10](https://discourse.julialang.org/u/gagnonaa10)\
**Replies:** 2\
**Last updated:** [September 12, 2021, 12:09pm UTC](https://discourse.julialang.org/t/constraints-in-catalyst-jl-for-weak-acids-and-ph-equilibrium/68037 "2021-09-12T12:09:27Z")

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Hello Everyone, I was hoping for some guidance on how to incorporate constraints for pH equilibriums constants into a disinfection model I am building in Julia. A simplified version of the reaction network is here: us…

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## [Error when calculating RHS of reaction ode "no method matching Float64(::Num)"](https://discourse.julialang.org/t/error-when-calculating-rhs-of-reaction-ode-no-method-matching-float64-num/64420)

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**Author:** [@SA8416](https://discourse.julialang.org/u/SA8416)\
**Replies:** 4\
**Last updated:** [July 10, 2021, 8:59pm UTC](https://discourse.julialang.org/t/error-when-calculating-rhs-of-reaction-ode-no-method-matching-float64-num/64420 "2021-07-10T20:59:44Z")

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I have some code that uses a function to calculate some changes in concentration, but I get an error of: ERROR: LoadError: MethodError: no method matching Float64(::Num) Closest candidates are: (::Type{T})(::Real, ::R…

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## [Rdkit in Julia](https://discourse.julialang.org/t/rdkit-in-julia/60582)

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**Author:** [@Modatu](https://discourse.julialang.org/u/Modatu)\
**Replies:** 0\
**Last updated:** [May 5, 2021, 2:02pm UTC](https://discourse.julialang.org/t/rdkit-in-julia/60582 "2021-05-05T14:02:23Z")

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Hey Julia-Chemistry community, this could be of interest to all of us: P.S.: I am not the author, I just found the article.

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## [Trying to use textbook with ChemEquations.jl package](https://discourse.julialang.org/t/trying-to-use-textbook-with-chemequations-jl-package/55356)

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**Author:** [@22natarajank](https://discourse.julialang.org/u/22natarajank)\
**Replies:** 2\
**Last updated:** [February 17, 2021, 2:07pm UTC](https://discourse.julialang.org/t/trying-to-use-textbook-with-chemequations-jl-package/55356 "2021-02-17T14:07:19Z")

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I have been learning Julia along side my AP chemistry class and was trying the ChemEquations.jl. It uses keyword ce to define a chemical Equations like this. balance(ce"Al{3} + Cl{-1} = AlCl3") What is ce above as a la…

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## [Brusselator and Catalyst](https://discourse.julialang.org/t/brusselator-and-catalyst/54222)

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**Author:** [@aquarelleX332](https://discourse.julialang.org/u/aquarelleX332)\
**Replies:** 3\
**Last updated:** [January 30, 2021, 1:38pm UTC](https://discourse.julialang.org/t/brusselator-and-catalyst/54222 "2021-01-30T13:38:27Z")

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Good evening to all, I recently solved the ODEs system for the brusselator: A -\> X (k1) 2X + Y -\> 3X (k2) B + X -\> Y + D (k3) X -\> E (k4) where A, B, etc are chemical species and k represents kinetics coefficients. B…

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## [Chemfiles -- contains](https://discourse.julialang.org/t/chemfiles-contains/53493)

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**Author:** [@aquarelleX332](https://discourse.julialang.org/u/aquarelleX332)\
**Replies:** 2\
**Last updated:** [January 17, 2021, 6:34pm UTC](https://discourse.julialang.org/t/chemfiles-contains/53493 "2021-01-17T18:34:36Z")

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Hello dear all, I tried to install Chemfiles.jl. During the test: julia\> Pkg.test("Chemfiles") I obtained an error: Test Summary: | Pass Total Generics | 1 1 Test Summary: | Pass Total Atom |…

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## [Packages used to create animated reaction systems](https://discourse.julialang.org/t/packages-used-to-create-animated-reaction-systems/52664)

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**Author:** [@22natarajank](https://discourse.julialang.org/u/22natarajank)\
**Replies:** 2\
**Last updated:** [December 31, 2020, 4:35pm UTC](https://discourse.julialang.org/t/packages-used-to-create-animated-reaction-systems/52664 "2020-12-31T16:35:53Z")

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Hello! I am working on a Pluto notebook where I am trying to simulate how reaction systems will naturally move back to equilibrium, even after making changes to concentrations of the species, the addition of catalysts, o…

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