From owner-svn-ports-head@freebsd.org Sun Jun 9 03:26:17 2019 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 7F01B15BB43F; Sun, 9 Jun 2019 03:26:17 +0000 (UTC) (envelope-from yuri@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) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 1DD0B8596C; Sun, 9 Jun 2019 03:26:17 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 0B4FA25078; Sun, 9 Jun 2019 03:26:17 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id x593QGt6051185; Sun, 9 Jun 2019 03:26:16 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id x593QGGw051178; Sun, 9 Jun 2019 03:26:16 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201906090326.x593QGGw051178@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Sun, 9 Jun 2019 03:26:16 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r503774 - in head/science: . smoldyn X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/science: . smoldyn X-SVN-Commit-Revision: 503774 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: 1DD0B8596C X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.97 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-0.998,0]; NEURAL_HAM_SHORT(-0.97)[-0.972,0]; NEURAL_HAM_LONG(-1.00)[-1.000,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US] X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 09 Jun 2019 03:26:17 -0000 Author: yuri Date: Sun Jun 9 03:26:15 2019 New Revision: 503774 URL: https://svnweb.freebsd.org/changeset/ports/503774 Log: New port: science/smoldyn: Biochemical simulator for molecular diffusion, surface interactions Added: head/science/smoldyn/ head/science/smoldyn/Makefile (contents, props changed) head/science/smoldyn/distinfo (contents, props changed) head/science/smoldyn/pkg-descr (contents, props changed) Modified: head/science/Makefile Modified: head/science/Makefile ============================================================================== --- head/science/Makefile Sun Jun 9 03:24:40 2019 (r503773) +++ head/science/Makefile Sun Jun 9 03:26:15 2019 (r503774) @@ -308,6 +308,7 @@ SUBDIR += simint SUBDIR += simlib SUBDIR += simsmith + SUBDIR += smoldyn SUBDIR += sparta SUBDIR += spglib SUBDIR += step Added: head/science/smoldyn/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/smoldyn/Makefile Sun Jun 9 03:26:15 2019 (r503774) @@ -0,0 +1,22 @@ +# $FreeBSD$ + +PORTNAME= smoldyn +DISTVERSION= 2.60 +CATEGORIES= science +MASTER_SITES= http://www.smoldyn.org/ + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Biochemical simulator for molecular diffusion, surface interactions + +LICENSE= LGPL3 +LICENSE_FILE= ${WRKSRC}/License.txt + +LIB_DEPENDS= libtiff.so:graphics/tiff + +USES= cmake gl tar:tgz +USE_GL= gl glu glut +USE_XORG= xi xmu + +PLIST_FILES= bin/${PORTNAME} + +.include Added: head/science/smoldyn/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/smoldyn/distinfo Sun Jun 9 03:26:15 2019 (r503774) @@ -0,0 +1,3 @@ +TIMESTAMP = 1560034820 +SHA256 (smoldyn-2.60.tgz) = 912cfbd2d165070fe7c36542b1c312a8dec100d4979223e63feafc6a201833af +SIZE (smoldyn-2.60.tgz) = 44801998 Added: head/science/smoldyn/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/smoldyn/pkg-descr Sun Jun 9 03:26:15 2019 (r503774) @@ -0,0 +1,15 @@ +Smoldyn is a computer program for cell-scale biochemical simulations. It +simulates each molecule of interest individually to capture natural +stochasticity and to yield nanometer-scale spatial resolution. It treats other +molecules implicitly, enabling it to simulate hundreds of thousands of molecules +over several minutes of real time. Simulated molecules diffuse, react, are +confined by surfaces, and bind to membranes much as they would in a real +biological system. + +Smoldyn is easy to use and easy to install. It is more accurate and faster than +other particle-based simulators. Smoldyn's unique features include: +a "virtual experimenter" who can manipulate or measure the simulated system, +support for spatial compartments, molecules with excluded volume, and +simulations in 1, 2, or 3 dimensions. + +WWW: http://www.smoldyn.org/