From MAILER-DAEMON Mon Jun 17 05:13:28 2013 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1UoVVA-0003To-0H for mharc-espressomd-devel@gnu.org; Mon, 17 Jun 2013 05:13:28 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:44816) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1UoVV4-0003SC-Cs for espressomd-devel@nongnu.org; Mon, 17 Jun 2013 05:13:27 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1UoVUz-0002bp-QU for espressomd-devel@nongnu.org; Mon, 17 Jun 2013 05:13:22 -0400 Received: from savannah.gnu.org ([140.186.70.70]:57978 helo=frontend.savannah.gnu.org) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1UoVUz-0002bi-LZ for espressomd-devel@nongnu.org; Mon, 17 Jun 2013 05:13:17 -0400 Received: from www-data by frontend.savannah.gnu.org with local (Exim 4.72) (envelope-from ) id 1UoVUy-0001Aa-KE; Mon, 17 Jun 2013 09:13:16 +0000 Date: Mon, 17 Jun 2013 09:13:16 +0000 To: Rudolf Weeber , espressomd-devel@nongnu.org X-PHP-Originating-Script: 0:sendmail.php From: Rudolf Weeber X-Savane-Server: savannah.nongnu.org:443 [140.186.70.71] MIME-Version: 1.0 Content-Type: text/plain;charset=UTF-8 X-Savane-Project: espressomd X-Savane-Tracker: bugs X-Savane-Item-ID: 39264 User-Agent: ELinks/0.12~pre5-3.2ubuntu1 (textmode; Ubuntu; Linux 3.0.0-32-server x86_64; 120x37-2) X-Apparently-From: 88.67.16.90 (Savane authenticated user rudolfweeber) Message-Id: <20130617-111315.sv80910.94297@savannah.nongnu.org> References: In-Reply-To: X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 140.186.70.70 Subject: [ESPResSo-devel] [bug #39264] Tcl output of quatu broken X-BeenThere: espressomd-devel@nongnu.org X-Mailman-Version: 2.1.14 Precedence: list List-Id: ESPResSo developers' discussions List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 17 Jun 2013 09:13:27 -0000 URL: Summary: Tcl output of quatu broken Project: ESPResSo Submitted by: rudolfweeber Submitted on: Mon 17 Jun 2013 11:13:15 AM CEST Category: None Severity: 3 - Normal Status: None Assigned to: None Open/Closed: Open Discussion Lock: Any Release: None Fixed Release: None _______________________________________________________ Details: part print quatu returned nonsense. Fix can be found on my github. _______________________________________________________ Reply to this item at: _______________________________________________ Message sent via/by Savannah http://savannah.nongnu.org/ From MAILER-DAEMON Mon Jun 17 05:17:15 2013 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1UoVYp-0004Si-3C for mharc-espressomd-devel@gnu.org; Mon, 17 Jun 2013 05:17:15 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:45778) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1UoVYk-0004QS-Is for espressomd-devel@nongnu.org; Mon, 17 Jun 2013 05:17:12 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1UoVYj-0004Mh-7G for espressomd-devel@nongnu.org; Mon, 17 Jun 2013 05:17:10 -0400 Received: from savannah.gnu.org ([140.186.70.70]:56978 helo=frontend.savannah.gnu.org) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1UoVYj-0004Mb-48 for espressomd-devel@nongnu.org; Mon, 17 Jun 2013 05:17:09 -0400 Received: from www-data by frontend.savannah.gnu.org with local (Exim 4.72) (envelope-from ) id 1UoVYi-0001HG-T8; Mon, 17 Jun 2013 09:17:08 +0000 Date: Mon, 17 Jun 2013 09:17:08 +0000 To: Rudolf Weeber , espressomd-devel@nongnu.org X-PHP-Originating-Script: 0:sendmail.php From: Rudolf Weeber X-Savane-Server: savannah.nongnu.org:443 [140.186.70.71] MIME-Version: 1.0 Content-Type: text/plain;charset=UTF-8 X-Savane-Project: espressomd X-Savane-Tracker: bugs X-Savane-Item-ID: 39265 User-Agent: ELinks/0.12~pre5-3.2ubuntu1 (textmode; Ubuntu; Linux 3.0.0-32-server x86_64; 120x37-2) X-Apparently-From: 88.67.16.90 (Savane authenticated user rudolfweeber) Message-Id: <20130617-111707.sv80910.20717@savannah.nongnu.org> References: In-Reply-To: X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 140.186.70.70 Subject: [ESPResSo-devel] [bug #39265] Pressure contribution for rigid bodies using vs_relative missing X-BeenThere: espressomd-devel@nongnu.org X-Mailman-Version: 2.1.14 Precedence: list List-Id: ESPResSo developers' discussions List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 17 Jun 2013 09:17:13 -0000 URL: Summary: Pressure contribution for rigid bodies using vs_relative missing Project: ESPResSo Submitted by: rudolfweeber Submitted on: Mon 17 Jun 2013 11:17:07 AM CEST Category: Simulation core Severity: 3 - Normal Status: None Assigned to: None Open/Closed: Open Discussion Lock: Any Release: None Fixed Release: None _______________________________________________________ Details: There needs to be a pressure contribution for rigid bodies. For each virtual site: P += where F_i is the force on virtual site i and d_i is the vector from virtual site to center of mass of the rigid body. _______________________________________________________ Reply to this item at: _______________________________________________ Message sent via/by Savannah http://savannah.nongnu.org/ From MAILER-DAEMON Mon Jun 24 05:46:25 2013 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1Ur3Lt-0007a5-AI for mharc-espressomd-devel@gnu.org; Mon, 24 Jun 2013 05:46:25 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:55699) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Ur3Lq-0007ZE-Fq for espressomd-devel@nongnu.org; Mon, 24 Jun 2013 05:46:23 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Ur3Lp-0002AN-8v for espressomd-devel@nongnu.org; Mon, 24 Jun 2013 05:46:22 -0400 Received: from mail-wg0-x231.google.com ([2a00:1450:400c:c00::231]:60746) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Ur3Lp-0002A6-1T for espressomd-devel@nongnu.org; Mon, 24 Jun 2013 05:46:21 -0400 Received: by mail-wg0-f49.google.com with SMTP id a12so8009382wgh.28 for ; Mon, 24 Jun 2013 02:46:19 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:date:message-id:subject:from:to:content-type; bh=4IVwf+JwXD4eGS94TEFzYrqPKlP66YsoqrEZ+PznZJQ=; b=a4AEboJyRDCwPtx/VlsJoesWqKrUuxj4AEB8/LsaL3gqNbsV/QRy08R9Z7wKQaJhNi N8zNnZ38sGpTcHoourpdx0W2LPuwGXRti8qpa7fLYIM0u+6v6J9bQ8Udxw5yHsoF3pUJ OkfM22SVBt9CHE2QBR3sD4hAOZwutJe34jVumBGTXW0A/HiR++ImScTsDAIHLNNr1gGe bneuZMjbo4JCLGdw6tStgwX9YW+aDX90ImEFvGkPkkQw1YcVwXUPGEucLQs/WpsL+3J8 PMt8m48W0czqtC6yDQIDF4PFQuGr7NopiNyS8w/Lv7JLcp4gxY2TNgIfwkbvV304H6TD BNRA== MIME-Version: 1.0 X-Received: by 10.195.12.202 with SMTP id es10mr16133385wjd.17.1372067179478; Mon, 24 Jun 2013 02:46:19 -0700 (PDT) Received: by 10.194.164.129 with HTTP; Mon, 24 Jun 2013 02:46:19 -0700 (PDT) Date: Mon, 24 Jun 2013 11:46:19 +0200 Message-ID: From: Josh Berryman To: espressomd-devel@nongnu.org Content-Type: multipart/alternative; boundary=047d7bb04b40d743d904dfe34890 X-detected-operating-system: by eggs.gnu.org: Error: Malformed IPv6 address (bad octet value). X-Received-From: 2a00:1450:400c:c00::231 Subject: [ESPResSo-devel] Pressure virials changes X-BeenThere: espressomd-devel@nongnu.org X-Mailman-Version: 2.1.14 Precedence: list List-Id: ESPResSo developers' discussions List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 24 Jun 2013 09:46:24 -0000 --047d7bb04b40d743d904dfe34890 Content-Type: text/plain; charset=ISO-8859-1 Hello, I'm trying to merge down the main branch with some local code, partly with a view to submitting (maybe, eventually) but mainly just to consolidate and check work that has been done here by Anwar and not kept up to date. .....I've come across a change in the pressure calculation on the main branch, fairly recent: Rudolf Weeber (Hi Rudolf!) commit 464f2bf67f82a79b56134fe39c4b3a85467df592 - #ifdef ROTATION - virials.data.e[0] /= (6.0*volume*time_step*time_step); - #else virials.data.e[0] /= (3.0*volume*time_step*time_step); - #endif ....as you might expect, this means that my merged code (if ROTATION is defined) gives half the ideal contribution to the pressure that the old code did, which is a fairly big behaviour change. Have I messed up my merging, or is there something meaningful happening here which I need to understand? Josh --047d7bb04b40d743d904dfe34890 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hello, I'm trying to merge down the main branch with s= ome local code, partly with a view to submitting (maybe, eventually) =A0but= mainly just to consolidate and check work that has been done here by Anwar= and not kept up to date.

.....I've come across a change in the pressure calculati= on on the main branch, fairly recent:


Rudolf Weeber (Hi Rudolf!)
commit 464f2bf67f82a79b56134fe39c4b= 3a85467df592

- #ifdef ROTATION
- =A0virials.dat= a.e[0] /=3D (6.0*volume*time_step*time_step);
- #else
= =A0=A0 virials.data.e[0] /=3D (3.0*volume*time_step*time_step);
=
- #endif

....as you might expect, this means that my merged code= (if ROTATION is defined) gives half the ideal contribution to the pressure= that the old code did, which is a fairly big behaviour change.

Have I messed up my merging, or is there something meaningfu= l happening here which I need to understand?=A0

Jo= sh
--047d7bb04b40d743d904dfe34890-- From MAILER-DAEMON Mon Jun 24 09:19:38 2013 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1Ur6gE-0002ZF-IB for mharc-espressomd-devel@gnu.org; Mon, 24 Jun 2013 09:19:38 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:58879) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Ur6g8-0002RF-FW for espressomd-devel@nongnu.org; Mon, 24 Jun 2013 09:19:37 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Ur6g3-0003fU-NW for espressomd-devel@nongnu.org; Mon, 24 Jun 2013 09:19:32 -0400 Received: from medousa.rus.uni-stuttgart.de ([129.69.1.57]:44238) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Ur6g3-0003f3-HU for espressomd-devel@nongnu.org; Mon, 24 Jun 2013 09:19:27 -0400 Received: from localhost (localhost [127.0.0.1]) by medousa.rus.uni-stuttgart.de (Postfix) with ESMTP id E333837EC0; Mon, 24 Jun 2013 15:19:23 +0200 (CEST) X-Virus-Scanned: by amavisd-new at medousa.rus.uni-stuttgart.de Received: from medousa.rus.uni-stuttgart.de ([IPv6:::1]) by localhost (medousa.rus.uni-stuttgart.de [IPv6:::1]) (amavisd-new, port 10024) with ESMTP id o6oyWfkTMjnr; Mon, 24 Jun 2013 15:19:23 +0200 (CEST) Received: from anoa.icp.uni-stuttgart.de (smtp.icp.uni-stuttgart.de [129.69.120.76]) by medousa.rus.uni-stuttgart.de (Postfix) with ESMTP; Mon, 24 Jun 2013 15:19:23 +0200 (CEST) Received: from argali.icp.uni-stuttgart.de (argali.icp.uni-stuttgart.de [129.69.120.92]) by anoa.icp.uni-stuttgart.de (Postfix) with ESMTP id 00322A40DC; Mon, 24 Jun 2013 15:19:22 +0200 (CEST) Received: by argali.icp.uni-stuttgart.de (Postfix, from userid 1085) id CB55E1FB; Mon, 24 Jun 2013 15:19:22 +0200 (CEST) Date: Mon, 24 Jun 2013 15:19:22 +0200 From: Rudolf Weeber To: Josh Berryman Message-ID: <20130624131922.GA18928@argali.icp.uni-stuttgart.de> References: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.5.21 (2010-09-15) X-detected-operating-system: by eggs.gnu.org: GNU/Linux 3.x X-Received-From: 129.69.1.57 Cc: espressomd-devel@nongnu.org Subject: Re: [ESPResSo-devel] Pressure virials changes X-BeenThere: espressomd-devel@nongnu.org X-Mailman-Version: 2.1.14 Precedence: list List-Id: ESPResSo developers' discussions List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 24 Jun 2013 13:19:37 -0000 Hi Josh, On Mon, Jun 24, 2013 at 11:46:19AM +0200, Josh Berryman wrote: > .....I've come across a change in the pressure calculation on the main > branch, fairly recent: > > > Rudolf Weeber (Hi Rudolf!) > commit 464f2bf67f82a79b56134fe39c4b3a85467df592 > > - #ifdef ROTATION > - virials.data.e[0] /= (6.0*volume*time_step*time_step); > - #else > virials.data.e[0] /= (3.0*volume*time_step*time_step); > - #endif > > ....as you might expect, this means that my merged code (if ROTATION is > defined) gives half the ideal contribution to the pressure that the old > code did, which is a fairly big behaviour change. > > Have I messed up my merging, or is there something meaningful happening > here which I need to understand? So, this change was already made in May 2011. It removes the contribution of the rotational kinetic energy from the pressure. See commit a46afe for the original. The physical reasoning is that the amount of momentum transferred, when a particle runs into the wall does not depend on how fast the particle is rotating. So, to my understanding, the current version should be correct. The change does two things: * Don't add contribution like viriaul += 1/2 J omega^2 (in add_kinetic_virials()) * Divide only by number of translational degrees of freedom (hence 3 instead of 6). In most cases, the simulation result will not change either way, because every degree of freedom carries 1/2kT. So if I have twice as many degrees of freedom and divide by 6 instead of 3, the result is the same. It's strange, that the changes appear again in the commits merging the "rotation per particle" feature, though. Hope that helps, Regards, Rudolf