{"id":16352068,"url":"https://github.com/kneth/kc","last_synced_at":"2025-11-12T01:39:21.548Z","repository":{"id":147478821,"uuid":"316905761","full_name":"kneth/kc","owner":"kneth","description":"Kinetic Compiler - simulation of chemical reactions","archived":false,"fork":false,"pushed_at":"2021-08-28T09:34:26.000Z","size":673,"stargazers_count":7,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-10-26T02:39:27.587Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/kneth.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-11-29T08:19:21.000Z","updated_at":"2024-10-13T19:18:10.000Z","dependencies_parsed_at":null,"dependency_job_id":"c6d06023-1b5c-4e94-859f-c2a900f2a698","html_url":"https://github.com/kneth/kc","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/kneth/kc","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kneth%2Fkc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kneth%2Fkc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kneth%2Fkc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kneth%2Fkc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kneth","download_url":"https://codeload.github.com/kneth/kc/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kneth%2Fkc/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":283961755,"owners_count":26923662,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-11-11T02:00:06.610Z","response_time":65,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-11T01:24:53.059Z","updated_at":"2025-11-12T01:39:21.542Z","avatar_url":"https://github.com/kneth.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"# kc - A Kinetic Compiler\n\nSource code, test files, and documentation in this repository go back\nto mid-1990s. With only a few modifications, the files are left as\nthey were. The authors' addresses have been removed since they have\nchanged. Moreover, the license has changed from GNU General Public\nLicense v2 to GNU General Public License v3. Furthermore this preamble\nhas been added.\n\nRecently (November 2020) the source code has been compiled on MacOS\nv10.15 using GCC.\n\nThe publication of kc has been a wish for some time. We hope it can be\nuseful to some, and asumement for others.\n\n## Introduction\n\nThis is the README file for the kc project. The kc program is a\n\"kinetic compiler\". This means it is able to transform chemical\nequations into simulation programs.\n\nThe motivation of the compiler and the use is documented in one of the\nauthors' master thesis (_Chemical waves in reaction-diffusion systems:\na numerical study_, K. Geisshirt, University of Copenhagen, May 1994).\n\nThe newest edition of the user's manual can be founded in\n`docs/kc-man.tex`, and the programmer's manual in `docs/kc.tex`. For\nusers who do not have LaTeX, please write to the author to obtain\neither a hard-copy or a postscript version.\n\nIn addition to the user's manual there exists a directory with\nexamples of input to kc. The directory is named `test` (some of our test\nexamples are found here).\n\nNo program is bug free, and the known bugs in kc are documented in the\nfile `KnownBugs.md`. Furthermore, the program is not complete (which\nprogram is?), and a list of future enchancement is found in the file\n`TODO.md`.\n\n\n## The history of kc\n*  April 1995: Version 1.05 released. A number of bugs were \n   discovered in version 1.0 and they have been fixed. Some\n   cleaning up has been done.\n\n   This version was developed at KIKU and RUC.\n\n*  December 1994: Version 1.00 released. The compiler is now running\n   very fine. It works very well together with a backend which is \n   solving ordinary differential equations. The following code \n   generators are supported in this version:\n     1. Waves (dymanical simulations of reaction-diffusion systems).\n     2. Eigen (computing various properties of a given system of ODEs).\n     3. KNcont (continuation program written in Pascal).\n     4. KCI (numerical solution of ODEs/dynamical simulation of \n        homogenous chemical reactions).\n\n*  July 1994: Version 0.99 released (only for internal use). A number\n   of bugs have been fixed. A solver of ordinary differential\n   equations called KGode has been developed. The solver is written in\n   ANSI C and have been ported to at least to four platforms: HP-UX,\n   ConvexOS, Linux, and MS-DOS. There exists an automatic steplength\n   controller. The solver implements three numerical schemes:\n     1. 4th order Runge-Kutta [1]. \n     2. Calahan's method [2].\n     3. Generalised Runge-Kutta [1, 3].\n\n   Various modes have been developed and old ones have been extended.\n   But in total, the following modes are supported now:\n     1. Kin (dynamical simulations - requires a Pascal compiler).\n     2. Waves (dynamical simulations of reaction-diffusion systems,\n        simulation programs written by K. Geisshirt).\n     3. KNcont (continuations - require a Pascal compiler).\n     4. Eigen (calculation of eigenvalues and -vectors of the Jacobian\n        matrix). \n     5. KGode (dynamical simulations).\n     6. Stoc (dynamical simulations using a stochastic approach [5]).\n     7. IScont (also called CONT - a continuation package in\n        Fortran-77). \n\n   The grammar has been extended a little so now it is possible of\n   read and store string constants. The grammar for expressions has\n   been modified a bit in order to fix a major bug. \n\n   This version has been developed at KIKU.\n\n*  December 1993: Version 0.50 released. It mainly fixes of a number of bugs.\n\n*  September 1993: Version 0.25 released. Only the following modes are\n   supported in this version:\n     1. Kin\n     2. Waves\n     3. KNcont\n     4. Eigen\n   Other modes in previous versions were never used, and therefore the\n   author stopped supporting them.\n\n   A lot of cleaning up has been done. K. Nielsen has done a lot of\n   testing, which has discovered many minor bugs and some major ones.\n   These errors had been corrected. \n\n*  May 1993: Version 0.20 released. Autocatalytic reactions can be\n   used, and the code generators are supporting parameters. Bugs in\n   version 0.10 have been corrected. This version is developed at KIKU\n   in Copenhagen. The grammar is changed, so the following features\n   are supported: \n     1. parameters\n\n   The following code generators have been added:\n     1. Waves (A PDE solver by O. Jensen et al.).\n     2. Keld Nielsen's continuation program (KNcont).\n     3. A mode which calculates the Jacoby matrix, its eigenvalues and\n   eigenvectors. \n\n   The code generator to CONT is now full operative, i.e. it supports\n   the use of parameters. \n\n*  October 1992: Version 0.10 released. This version supports KIN,\n   CONT, and Dalimil Snita's Chemical Meta Language. This version is\n   developed at KIKU in Copenhagen. The grammar is now supporting \n     1. ordinary differential equations\n     2. constraints \n\n   The program is now not using so much memory as previous version.\n\n*  September 1992: Version 0.00 released. This version only supports\n   KIN and CONT. This version is the initial guess of the system. It\n   was developed at VSCHT in Prague.\n\n\n## Installation and running\n\nThe installation is very easy! There exists a small script called\nkc-inst which does most of the job. The script must be supplied with\ntwo arguments, namely a directory name and a platform. The directory\nname is a prefix to the directories which you want kc to \"live\". The\nplatform is at the moment one of the following: \n\n* Generic GNU C-compiler\n* Linux \n* DECstations running Ultrix \n* Silicon Graphics \n* Convex running ConvexOS \n* HP-UX v7 \n* IBM RS/6000 running AIX v3.2\n\nRun the script with no arguments and you will get some help. The\nscript will generate a script called kci, which is a front-end to the\nkci-mode. \n\nAn example: If you want to install the system on a Linux machine \nin the directories /usr/local you should type:\n\n```sh\nkc-inst /usr/local LINUX\n```\n\nIn order to use the DOS version, you have to have an Intel 80386 (or\nhigher) computer. You also have to install the djgpp package, and this\npackage is surposed to be used during all your simulations. The\nmakefile you should used is `src/Makefile.DOS`, and the file\n`Scripts/kci.bat` is a front-end to the `kci-mode`.\n\nThere can be a problem with newer Unices, because they have support\nfor your natioonal language. Therefore, check the enviroment variable\ncalled `LANG` to see if it is set to `C`.\n\nAnother thing is that you should create a new directories before\ninstalling. Let us assume you want to use the directory `DIR` as prefix\n(as mentioned above). You should them create the directories `DIR/num`\nand `DIR/bin`.\n\n## Legal issues\n\nThe program is copyrighted in the sense of GNU General Public License\nv3. The authors cannot be responsible for any looses the programs in\nthis package may produce.\n\nIf the program is used to published scientific results, authors are\nasked to make a footnote or better a reference to kc. A the moment the\nbest reference is [4], but this may change in the future.\n\nThe package comes under the GNU General Public License v3 (GPLv3), and GPLv3\nis supplied in form of the file `LICENSE`. Please read this file.\n\n\n## Support\n\nThe program is NOT supported by the authors, but you are welcome to\ncreate an issue.\n\n\n## Acknowledgements\n\nThe authors wish to thank the following people:\n\n* M. Marek - ideas to the first version.\n* P.G. Sorensen - do. and advices.\n* F. Hynne - same as P.G. Sorensen.\n* and the first users (J. Wang, A. Nagy, etc.).\n\n## Abbreviations\n\n* VSCHT:  Prague Institute for Chemical Engineering.\n* KIKU: Institute of Chemistry, University of Copenhagen.\n* KIN: KINetic compiler and simulator (by P.G. Sorensen).\n* CONT: CONTinuation program (by I. Screiber).\n* EIGEN: Mode calculating the jacoby matrix and its eigenvectors and eigenvalues.\n* KNcont: Keld Nielsen's continuation programs.\n* KGode: An ODE solver written by Keld Nielsen and Kenneth Geisshirt.\n* Stoc: A dynamical simulator using a stochastic scheme.\n* GPL: GNU General Public License.\n* RUC: Roskilde University\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkneth%2Fkc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkneth%2Fkc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkneth%2Fkc/lists"}