From nobody Tue Jan 21 15:18:25 2025 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4YcrSd2rDqz5lDCp; Tue, 21 Jan 2025 15:18:25 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4YcrSd2GgNz489V; Tue, 21 Jan 2025 15:18:25 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1737472705; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=2RXY7pUT2IX4p2WEGhhdTAWExP6/iEKGPKTTt1PRqDw=; b=ucuPIeC8CMwPtE/23XUtiJvUJGJqW8DXOpa5S0QzeGGvI6anWNAXJhtO1tvjb3jtI0zZDF V9WfsbRt8gjnHL85Fh4kkleRD5Jb0zQkr0XEk/juwa9eFCZXz4r2y7ne6ThVvNdT3GT5HB eDLf8m6POtvY4ml8ZH1HxL+XaDVMKGORiOlI+gx1dTpQSonPKAxe2eriPrlIJFLkMIgFPf OcONO971+gv/yP0l7Vm8rgES51hipoguLv27FnB9/YfFeJYi10t4wINdsfN8+gUfFjvyLh G+4fMwSvGlJgmMTqCW2gmYraFZpLLst8uif0qoqebwH8oOvRCDi7HelcNmf1kg== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1737472705; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=2RXY7pUT2IX4p2WEGhhdTAWExP6/iEKGPKTTt1PRqDw=; b=oxOoKR7wDT/oBINppt/wZCA9mwyO3aWh83jyM9cGtaSfDJ5aebeI8Tpzck/7cIjS/QhH4j psGoQcyF1rPfb4rQyNGQ13tyq2r/x6LU4wI0KTscC9OoX/kpnJLwxRSEdaAl9QZq7bEbWw Hrw3n2+hTE07Geok75uojdS1PSJI9sFTe8GRWsIjo+fC8VJ+78W9lL/VJjpxYJBLRp2mTu a3U82NU/HpNv8yIESwpgmjczAqKXF2gnh6qx8J7JFmRlfoMYCkQnGeVh1Zqdd+t6VgM0D9 QaYDuSax3aBjaV/R+aDxIg8LYj49DmcKcK6OPIhbj+aQRbKkn/lIieQPY73mcg== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1737472705; a=rsa-sha256; cv=none; b=qHeYEyNlJuGmpcjZLHuXMNWiJLTfAo0NnvqDVWlpDzbvE7ftO/fJMa4KuRHyBQRnb4BHiS qxiHNKKXoz08IKyII+ljByjW4+rKXlqjX7Ao9jSt0FtRSRBtxP7p3yk1Ai3oneJ8mht2mM 4Zketl+Uy3yontGzBSoS4kk54Yaf0eZdLEqM0CthOZuZ4qDJ4l8U3jdORLivt7iLhRbB0s wBxQ9nTK6RWW4LgVZBelM3vtCWD6gzsXGmrN7eHVAAcPo8znyhV8LnyMta5Eb8S/lVWGZv ViiYZuTly7tUsvnEdKkiMt2u76yvUS6MoxMQusj9TtCEFjeS40WzvCqeJ8y3iw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4YcrSd1knFz1B4k; Tue, 21 Jan 2025 15:18:25 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 50LFIPZe079317; Tue, 21 Jan 2025 15:18:25 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 50LFIPdV079314; Tue, 21 Jan 2025 15:18:25 GMT (envelope-from git) Date: Tue, 21 Jan 2025 15:18:25 GMT Message-Id: <202501211518.50LFIPdV079314@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 88365ea6e44a - main - science/packmol: Update to 20.15.3 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 88365ea6e44a43d62f9fab2dee873eac5a680cb9 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=88365ea6e44a43d62f9fab2dee873eac5a680cb9 commit 88365ea6e44a43d62f9fab2dee873eac5a680cb9 Author: Jason W. Bacon AuthorDate: 2025-01-21 15:14:48 +0000 Commit: Jason W. Bacon CommitDate: 2025-01-21 15:14:48 +0000 science/packmol: Update to 20.15.3 Numerous fixes and improvements since 18.169 Changes: https://github.com/m3g/packmol/releases Release maintainership to ports@ PR: 283265 Reported by: alster@vinterdalen.se --- science/packmol/Makefile | 13 +++++++------ science/packmol/distinfo | 6 +++--- science/packmol/pkg-descr | 15 ++++++++++++--- science/packmol/pkg-message | 10 ---------- 4 files changed, 22 insertions(+), 22 deletions(-) diff --git a/science/packmol/Makefile b/science/packmol/Makefile index a591f8ec2a4b..1fa6a80a6993 100644 --- a/science/packmol/Makefile +++ b/science/packmol/Makefile @@ -1,18 +1,19 @@ PORTNAME= packmol -DISTVERSION= 18.169 -PORTREVISION= 1 +DISTVERSIONPREFIX= v +DISTVERSION= 20.15.3 CATEGORIES= science -MAINTAINER= jwb@FreeBSD.org -COMMENT= Pack molecules in defined regions of space -WWW= http://m3g.iqm.unicamp.br/packmol/home.shtml +MAINTAINER= ports@FreeBSD.org +COMMENT= Creates Initial Configurations for Molecular Dynamics Simulations +WWW= https://m3g.github.io/packmol/ \ + https://github.com/m3g/packmol/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE USES= cmake:noninja fortran USE_GITHUB= yes -GH_ACCOUNT= mcubeg +GH_ACCOUNT= m3g PLIST_FILES= bin/packmol diff --git a/science/packmol/distinfo b/science/packmol/distinfo index a598b7f167d4..08b9aca28e9e 100644 --- a/science/packmol/distinfo +++ b/science/packmol/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1563043114 -SHA256 (mcubeg-packmol-18.169_GH0.tar.gz) = 8acf2cbc742a609e763eb00cae55aecd09af2edb4cc4e931706e2f06ac380de9 -SIZE (mcubeg-packmol-18.169_GH0.tar.gz) = 169840 +TIMESTAMP = 1733943120 +SHA256 (m3g-packmol-v20.15.3_GH0.tar.gz) = a7e63208251c9e404437e3c58c976afc2e747d545c6c42dcfbf0e3e29c2c3d14 +SIZE (m3g-packmol-v20.15.3_GH0.tar.gz) = 629639 diff --git a/science/packmol/pkg-descr b/science/packmol/pkg-descr index acb1d3600884..20acf4963f80 100644 --- a/science/packmol/pkg-descr +++ b/science/packmol/pkg-descr @@ -1,3 +1,12 @@ -PACKMOL creates an initial point for molecular dynamics simulations by packing -molecules in defined regions of space. The packing guarantees that short range -repulsive interactions do not disrupt the simulations. +PACKMOL creates an initial point for molecular dynamics simulations by +packing molecules in defined regions of space. The packing guarantees +that short range repulsive interactions do not disrupt the +simulations. + +The package is compatible with input files of PDB, TINKER, XYZ and +MOLDY formats. + +See also: ComplexMixtures.jl: A powerful package to understand +solvation structures in complex solutions. CellListMap.jl: Efficient +and customizable cell list data structure for molecular simulations +and customizable simulation analysis. diff --git a/science/packmol/pkg-message b/science/packmol/pkg-message deleted file mode 100644 index 8ffd9e822894..000000000000 --- a/science/packmol/pkg-message +++ /dev/null @@ -1,10 +0,0 @@ -[ -{ type: install - message: <