{"id":33175297,"url":"https://github.com/thynnine/pysic","last_synced_at":"2025-11-20T20:02:33.641Z","repository":{"id":50745790,"uuid":"4558987","full_name":"thynnine/pysic","owner":"thynnine","description":"Python library for advanced atomistic simulations","archived":false,"fork":false,"pushed_at":"2017-09-21T06:55:38.000Z","size":18063,"stargazers_count":23,"open_issues_count":3,"forks_count":4,"subscribers_count":6,"default_branch":"master","last_synced_at":"2024-02-15T11:36:03.584Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://thynnine.github.com/pysic/","language":"Fortran","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"lgpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/thynnine.png","metadata":{"files":{"readme":"readme.txt","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}},"created_at":"2012-06-05T11:31:21.000Z","updated_at":"2022-08-01T08:51:24.000Z","dependencies_parsed_at":"2022-09-24T19:04:21.326Z","dependency_job_id":null,"html_url":"https://github.com/thynnine/pysic","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/thynnine/pysic","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/thynnine%2Fpysic","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/thynnine%2Fpysic/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/thynnine%2Fpysic/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/thynnine%2Fpysic/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/thynnine","download_url":"https://codeload.github.com/thynnine/pysic/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/thynnine%2Fpysic/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":285503668,"owners_count":27182913,"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":"2025-11-20T02:00:05.334Z","response_time":54,"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":"2025-11-16T02:00:37.344Z","updated_at":"2025-11-20T20:02:33.629Z","avatar_url":"https://github.com/thynnine.png","language":"Fortran","funding_links":[],"categories":["Simulations"],"sub_categories":[],"readme":"\nWelcome to Pysic\n----------------\n\nPysic is a calculator incorporating various empirical pair and many-body potentials in an object-based Python environment and user interface while implementing an efficient numeric core written in Fortran. The immediate aim of the Pysic project is to implement advanced variable charge potentials.\n\nThe code is developed as part of the EU FP7 Mordred project.\n\nPysic is open source, available at http://github.com/thynnine/pysic/\nThe official documentation is found at http://thynnine.github.com/pysic/\n\n\nContents of the Pysic repository\n--------------------------------\n\nWhen you download Pysic, you should receive a package containing three directories [doc], [fortran], and [pysic]. The directory [doc] contains the source reStructuredText used for generating the documentation (with Sphinx). For readability, check the online version. The directories [fortran] and [pysic] contain the Fortran and Python source code, respectively. In addition to these folders, there should be a readme.txt file containing installation instructions and a Makefile for compiling with make.\n\n\nRequirements\n------------\n\nTo compile and run Pysic you need:\n\n- Python 2.x\n- Numpy (which includes f2py)\n- ASE\n\nPysic is designed to interface with the Atomic Simulation Environment package \n(ASE, developed by CAMd, DTU), and although in theory ASE is not a prerequisite\nfor running Pysic, in practice you need it to do anything interesting.\n\n\nQuick compilation\n-----------------\n\nTo compile Pysic, go to the directory where you have the Makefile and folders *fortran* and \n*pysic*, and enter the command ``make \u003ctarget\u003e`` on command line, where ``\u003ctarget\u003e`` is for instance \n``serial`` or ``parallel``. A list of available targets are shown with the command ``make help``.\n\nThe default compilers listed in the Makefile are ``gfortran`` and ``mpif90``. \nYou may need to edit the names of the compilers to match those available on your system.\n\nBy default, make creates the pysic Python module as a folder named *pysic* (or *pysic_debug* etc., \ndepending on the type of compilation) in the folder *build*. To run Pysic, copy the folder *pysic* \nto whereever you wish to run your simulations and import it in Python with ``import pysic``.\n\n\nCompilation under the hood\n--------------------------\n\nThe Python part of Pysic does not have to be compiled separately, but the Fortran core must be.\nIn order to link the Fortran and Python sides together, you need to compile the code with the\n*f2py* tool, which is part of the *Numpy* package.\n\nThe Fortran part is compiled with the commands::\n\n  f2py -m pysic_fortran -h pysic_fortran.pyf PyInterface.F90\n  f2py -c --fcompiler=gfortran --f90exec=mpif90 --f90flags=\"-D MPI\" \\\n  pysic_fortran.pyf Mersenne.F90 MPI.F90 Quaternions.F90 Utility.F90 \\\n  Geometry.F90 Potentials.F90 Core.F90 PyInterface.F90\n\nThe first run creates the interface file ``pysic_fortran.pyf`` from the Fortran source file \n``PyInterface.F90``. The second run compiles the rest of the code in a native Fortran mode and\ncreates the Python accessible binary file ``pysic_fortran.so``. \nFrom this file, the subroutines of ``PyInterface.F90`` are callable as Python functions.\n\nThe created ``pysic_fortran.so`` appears in Python as a module ``pysic_fortran.pysic_interface``.\nThe package structure of pysic expects to find it at ``pysic.pysic_fortran.pysic_interface``, i.e.,\nthe ``.so`` file should be in the folder ``pysic`` (the root folder of the Python package).\nThe Makefile should take care of putting it in the right place, but if you decide to compile the\nFortran part manually, keep in mind that the file needs to be moved there.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fthynnine%2Fpysic","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fthynnine%2Fpysic","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fthynnine%2Fpysic/lists"}