From MAILER-DAEMON Tue Dec 06 05:51:21 2022 Received: from list by lists.gnu.org with archive (Exim 4.90_1) id 1p2VXk-0002Zp-4m for mharc-espressomd-users@gnu.org; Tue, 06 Dec 2022 05:51:20 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p2VXg-0002ZY-EU for espressomd-users@nongnu.org; Tue, 06 Dec 2022 05:51:17 -0500 Received: from mx4.rus.uni-stuttgart.de ([2001:7c0:2041:25::a:4]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p2VXd-00079W-Rr for espressomd-users@nongnu.org; Tue, 06 Dec 2022 05:51:16 -0500 Received: from localhost (localhost [127.0.0.1]) by mx4.rus.uni-stuttgart.de (Postfix) with ESMTP id D70D524 for ; Tue, 6 Dec 2022 11:50:51 +0100 (CET) X-Virus-Scanned: USTUTT mailrelay AV services at mx4.rus.uni-stuttgart.de Received: from mx4.rus.uni-stuttgart.de ([127.0.0.1]) by localhost (mx4.rus.uni-stuttgart.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id EYn5f9N2ifEw for ; Tue, 6 Dec 2022 11:50:49 +0100 (CET) Received: from eland.icp.uni-stuttgart.de (eland.ica1.uni-stuttgart.de [129.69.120.40]) by mx4.rus.uni-stuttgart.de (Postfix) with ESMTP for ; Tue, 6 Dec 2022 11:50:49 +0100 (CET) Received: from www2.icp.uni-stuttgart.de (elk.icp.uni-stuttgart.de [129.69.120.50]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (Client did not present a certificate) by eland.icp.uni-stuttgart.de (Postfix) with ESMTPSA id 62055206A5A for ; Tue, 6 Dec 2022 11:50:49 +0100 (CET) MIME-Version: 1.0 Date: Tue, 06 Dec 2022 11:50:49 +0100 From: =?UTF-8?Q?Jean-No=C3=ABl_Grad?= To: Espressomd Users Subject: Build system changes in the python branch User-Agent: Roundcube Webmail/1.4.13 Message-ID: <0e2290a6e28694b660f3d552126bc61f@icp.uni-stuttgart.de> X-Sender: jgrad@icp.uni-stuttgart.de Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2001:7c0:2041:25::a:4; envelope-from=jgrad@icp.uni-stuttgart.de; helo=mx4.rus.uni-stuttgart.de X-Spam_score_int: -18 X-Spam_score: -1.9 X-Spam_bar: - X-Spam_report: (-1.9 / 5.0 requ) BAYES_00=-1.9, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: espressomd-users@nongnu.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: General discussions about ESPResSo List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 06 Dec 2022 10:51:18 -0000 Dear users, We would like to share with you some important changes to the way the development version of ESPResSo is configured and built. As discussed in the community call from October 13, 2022, we are working on integrating more external libraries into ESPResSo, such as waLBerla for hydrodynamics and librepa+kdpart for MD load balancing. We opted for the CMake FetchContent method, which allows us to finely tune the way these libraries are compiled and integrated within our codebase. In the process of doing so, we noticed imperfections in our build system that made it difficult to integrate new libraries [1], or to use ESPResSo as a library in a parent project. In particular, CMake flags such as WITH_FFTW were inherited by included projects, which could cause them to build components that were not needed in ESPResSo. This behavior would unnecessarily increase the build time, and in a few cases, force users to install extra dependencies to complete the build. The latter is problematic for clusters users, who typically have access to a restricted set of dependencies and cannot easily install new packages. CMake options name conflicts are commonly resolved by adding a unique, project-specific prefix on all CMake options. While we worked with external libraries maintainers to rename their CMake options, we obviously needed to rename ESPResSo CMake options too. As such, on the python branch of ESPResSo, a prefix `ESPRESSO_BUILD_` was added to all options that control compilation, and a prefix `ESPRESSO_` was added to the other options [2]. The new option names can be found in the user guide, section 2.4.4. "Options and Variables" [3]. If you accidentally use the old options when building the development branch of ESPResSo, or the new options when building older ESPResSo releases, CMake will print a warning and list which options were not recognized. We also took this opportunity to modernize the ESPResSo codebase by requiring C++17 and CUDA 11, as well as enforcing minimal versions for compilers and MPI libraries. These changes helped us simplify the CMake logic and the C++ core greatly, and we expect that contributing new features to ESPResSo will lead to a smoother experience for first-time contributors. We will continue supporting C++14 and CUDA 10 in the 4.2 line of ESPResSo, and a bugfix release is currently in preparation [4]. Best regards, Jean-Noël Grad Links: [1] https://github.com/espressomd/espresso/issues/4618 [2] https://github.com/espressomd/espresso/pull/4612 [3] https://espressomd.github.io/doc/installation.html#options-and-variables [4] https://github.com/espressomd/espresso/wiki/es-421-release-notes From MAILER-DAEMON Thu Dec 22 03:41:53 2022 Received: from list by lists.gnu.org with archive (Exim 4.90_1) id 1p8H9F-0005F6-BE for mharc-espressomd-users@gnu.org; Thu, 22 Dec 2022 03:41:53 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p8H9D-0005Ei-SQ for espressomd-users@nongnu.org; Thu, 22 Dec 2022 03:41:51 -0500 Received: from mail-oi1-x22a.google.com ([2607:f8b0:4864:20::22a]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p8H9C-0002ND-Du for espressomd-users@nongnu.org; Thu, 22 Dec 2022 03:41:51 -0500 Received: by mail-oi1-x22a.google.com with SMTP id c129so1357034oia.0 for ; Thu, 22 Dec 2022 00:41:49 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=to:subject:message-id:date:from:mime-version:from:to:cc:subject :date:message-id:reply-to; bh=l4ip8YRH/n6twP3P6sQINxviJt/hvKw3rG/KDg3Dl14=; b=cLaTlIpSeoMykHA/UvTgXDeuNUlBGPEyG/0CZLKzP1OpguxG6ZbpudpKujh2QDE0Ly 0zF+hN8HU+Nhg4nOcj3XSXhg6OsKog4L0FIB/u0W+6dXmaN0s7+LvxPS9nB99dwrKTmB sYcr+4VwBIaarxtlZqxAVF7H2bJV4zmLT4zpdx9nuBtjP9/khMXEEtSFWktUEgIRjOno wl+OVWsaR2Pu2WqLipcyH4wL5GzYHvrYXUJ3GlFPO53ZyA4IT6MQKLDJkaTdBUUMJxj0 4ceCg3yvu6kPpRivJMB79ocv35sjdVdCoCwe7DLS56nZhyj8tMVJ0K6hWuuKXI/OdAJu DsVg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=to:subject:message-id:date:from:mime-version:x-gm-message-state :from:to:cc:subject:date:message-id:reply-to; bh=l4ip8YRH/n6twP3P6sQINxviJt/hvKw3rG/KDg3Dl14=; b=FIhOep2B0tFqpoLwyHlye5bfSOhxEYXhbq8w/thon9XYKB03pn4c5XHXnTudQ7TFyQ 66jhaoM0kj7HaV72YW8EFNbEBhEB+ed172AN8UZdCUWETVl5OEbPsNleOophZKHe+j3n JnO8QNiEvkJ1NLys8S2Vq6SqufuvvGjnqLCg4F8ATssgNQQZXHTeE2p1e3NTwiJy+0K8 XVyo++iZcLKc9cS/vIxhqEP041lj89Q/a/ebY0rYigjacARS3gh60iidvMknAZTVlXlX /MCAhv+n5d9SClYVRnjrHLolo3mtzYbIxcwwlN0I2p151zgQSzN4PwaECEywuK4Yi92g g+nw== X-Gm-Message-State: AFqh2krvoGh4odFSL0ekHpJGeJwYyieaIUuQ98H2uAmajwVERCJSzWhB Igb1pdBg9Zjd5TKEaDrYdMFXV9Z0bdkSILpaYZaRxtap3aotDQ== X-Google-Smtp-Source: AMrXdXspB9BePpJKG/j8Kxdjdmqqt3eR+MQKsCvfR+98flZqjvcw9WGsGY3MJLOuskvwFInUoh3Zwram4XGLVKUhguU= X-Received: by 2002:aca:1118:0:b0:35b:dfbb:a9b with SMTP id 24-20020aca1118000000b0035bdfbb0a9bmr129106oir.68.1671698508494; Thu, 22 Dec 2022 00:41:48 -0800 (PST) MIME-Version: 1.0 From: AmirMahdi Jafary Date: Thu, 22 Dec 2022 12:11:36 +0330 Message-ID: Subject: Using customized boundary for LBBOUNDARY To: espressomd-users@nongnu.org Content-Type: multipart/alternative; boundary="000000000000c53d8305f066a3fb" Received-SPF: pass client-ip=2607:f8b0:4864:20::22a; envelope-from=jafary.am@gmail.com; helo=mail-oi1-x22a.google.com X-Spam_score_int: -6 X-Spam_score: -0.7 X-Spam_bar: / X-Spam_report: (-0.7 / 5.0 requ) BAYES_05=-0.5, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, HTML_MESSAGE=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: espressomd-users@nongnu.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: General discussions about ESPResSo List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 22 Dec 2022 08:41:52 -0000 --000000000000c53d8305f066a3fb Content-Type: text/plain; charset="UTF-8" Hi I'm a new user of espressomd package and I really appreciate the well-coded libraries for fluid-particle interactions that you have developed in this package. The problem that I've come across is that I don't know how to define my microchannel geometry which is customized and not found in the library of shapes in LBfluid or LBboundaries. I would really appreciate if you could help me with a way to introduce my own geometry to LBBOUNDARIES. SINCERELY, Amir --000000000000c53d8305f066a3fb Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi
I'm a new user of espressomd pack= age and I really appreciate the well-coded libraries for fluid-particle int= eractions that you have developed in this package.=C2=A0

The problem that I've come across is t= hat I don't know how to define my microchannel geometry which is custom= ized and not found in the library of shapes in LBfluid or LBboundaries.

I would really appreciate i= f you could help me
with a way to introduce my own g= eometry to LBBOUNDARIES.

SINCERELY, Amir
--000000000000c53d8305f066a3fb-- From MAILER-DAEMON Thu Dec 22 05:37:35 2022 Received: from list by lists.gnu.org with archive (Exim 4.90_1) id 1p8IxC-0006p7-3A for mharc-espressomd-users@gnu.org; Thu, 22 Dec 2022 05:37:35 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p8IxB-0006or-2E for espressomd-users@nongnu.org; Thu, 22 Dec 2022 05:37:33 -0500 Received: from mx4.rus.uni-stuttgart.de ([129.69.192.4]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p8Ix7-0004mP-Jh for espressomd-users@nongnu.org; Thu, 22 Dec 2022 05:37:31 -0500 Received: from localhost (localhost [127.0.0.1]) by mx4.rus.uni-stuttgart.de (Postfix) with ESMTP id B6A0923; Thu, 22 Dec 2022 11:37:13 +0100 (CET) X-Virus-Scanned: USTUTT mailrelay AV services at mx4.rus.uni-stuttgart.de Received: from mx4.rus.uni-stuttgart.de ([127.0.0.1]) by localhost (mx4.rus.uni-stuttgart.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id ch3NbG_oBxny; Thu, 22 Dec 2022 11:37:11 +0100 (CET) Received: from eland.icp.uni-stuttgart.de (smtp.icp.uni-stuttgart.de [129.69.120.40]) by mx4.rus.uni-stuttgart.de (Postfix) with ESMTP; Thu, 22 Dec 2022 11:37:11 +0100 (CET) Received: from sheep.icp.uni-stuttgart.de (sheep.icp.uni-stuttgart.de [129.69.120.102]) by eland.icp.uni-stuttgart.de (Postfix) with ESMTP id 6D49920A8BB; Thu, 22 Dec 2022 11:37:11 +0100 (CET) Received: by sheep.icp.uni-stuttgart.de (Postfix, from userid 1085) id 6725E9F6AB; Thu, 22 Dec 2022 11:37:11 +0100 (CET) Date: Thu, 22 Dec 2022 11:37:11 +0100 From: Rudolf Weeber To: AmirMahdi Jafary Cc: espressomd-users@nongnu.org Subject: Re: Using customized boundary for LBBOUNDARY Message-ID: <20221222103711.GA857157@icp.uni-stuttgart.de> References: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: Received-SPF: pass client-ip=129.69.192.4; envelope-from=weeber@icp.uni-stuttgart.de; helo=mx4.rus.uni-stuttgart.de X-Spam_score_int: -41 X-Spam_score: -4.2 X-Spam_bar: ---- X-Spam_report: (-4.2 / 5.0 requ) BAYES_00=-1.9, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: espressomd-users@nongnu.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: General discussions about ESPResSo List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 22 Dec 2022 10:37:33 -0000 Hi Amir, > The problem that I've come across is that I don't know how to define my > microchannel geometry which is customized and not found in the library of > shapes in LBfluid or LBboundaries. For the release version (4.2) you have the option of assembling your channel by overlapping several shapes. More fine-grained control is available in the experimental version of Espresso which uses the Walberla library for LB. This version will become the "official" development verison of Espresso soon. In this version, you can control the velocity boundary condition per lattice site. See sampels/lb_circualr_couette.py for an example. For the particles, you can use https://espressomd.github.io/doc/constraints.html#external-fields You can find this version at github.com/RudolfWeeber/espresso in the `walberla` branch. git clone https://github.com/RduolfWeeber/espresso --branch walberla Regards, Rudolf From MAILER-DAEMON Fri Dec 23 18:28:26 2022 Received: from list by lists.gnu.org with archive (Exim 4.90_1) id 1p8rSk-0007An-L2 for mharc-espressomd-users@gnu.org; Fri, 23 Dec 2022 18:28:26 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p8rSi-00079H-Kk for espressomd-users@nongnu.org; Fri, 23 Dec 2022 18:28:24 -0500 Received: from mx2.rus.uni-stuttgart.de ([129.69.192.2]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p8rSg-0000EW-JL for espressomd-users@nongnu.org; Fri, 23 Dec 2022 18:28:24 -0500 Received: from localhost (localhost [127.0.0.1]) by mx2.rus.uni-stuttgart.de (Postfix) with ESMTP id 551E3200C3 for ; Sat, 24 Dec 2022 00:28:06 +0100 (CET) X-Virus-Scanned: USTUTT mailrelay AV services at mx2.rus.uni-stuttgart.de Received: from mx2.rus.uni-stuttgart.de ([127.0.0.1]) by localhost (mx2.rus.uni-stuttgart.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 5oorH_LtWbI3 for ; Sat, 24 Dec 2022 00:28:04 +0100 (CET) Received: from eland.icp.uni-stuttgart.de (smtp.icp.uni-stuttgart.de [129.69.120.40]) by mx2.rus.uni-stuttgart.de (Postfix) with ESMTP for ; Sat, 24 Dec 2022 00:28:04 +0100 (CET) Received: from www2.icp.uni-stuttgart.de (elk.icp.uni-stuttgart.de [129.69.120.50]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (Client did not present a certificate) by eland.icp.uni-stuttgart.de (Postfix) with ESMTPSA id 17CAF20AD06 for ; Sat, 24 Dec 2022 00:28:04 +0100 (CET) MIME-Version: 1.0 Date: Sat, 24 Dec 2022 00:28:03 +0100 From: =?UTF-8?Q?Jean-No=C3=ABl_Grad?= To: espressomd-users@nongnu.org Subject: Bug in 4.2.0 checkpointing code User-Agent: Roundcube Webmail/1.4.13 Message-ID: <986f2b89ee780704ac8c3c10cc0d36dd@icp.uni-stuttgart.de> X-Sender: jgrad@icp.uni-stuttgart.de Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=129.69.192.2; envelope-from=jgrad@icp.uni-stuttgart.de; helo=mx2.rus.uni-stuttgart.de X-Spam_score_int: -41 X-Spam_score: -4.2 X-Spam_bar: ---- X-Spam_report: (-4.2 / 5.0 requ) BAYES_00=-1.9, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: espressomd-users@nongnu.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: General discussions about ESPResSo List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 23 Dec 2022 23:28:24 -0000 Dear ESPResSo users, It has come to our attention that the checkpointing mechanism was broken in release 4.2.0. When reloading the state of the system from a checkpoint file, if the DIPOLES feature is part of the myconfig file, the magnetic dipole moment overwrites the particle director, which causes non-magnetic particles to be all aligned along the z-axis. This bug breaks momentum conservation and can lead to nonphysical forces being applied in simulations where the particle director plays a role (ex: relative virtual sites, Gay-Berne potential, anisotropic particles, active particles, etc.). Since the default myconfig file contains DIPOLES, most ESPResSo users are affected. In addition, when reloading from a checkpoint file, the particle angular velocity in the body frame is sometimes calculated using a default-constructed quaternion instead of the particle quaternion. These issues have been fixed in the python branch of ESPResSo (PR #4637) and will be fixed in the upcoming 4.2.1 bugfix release (PR #4611). If you are using 4.2.0 and need checkpointing for simulations with the ROTATION feature, you can update ESPResSo 4.2.0 locally with the following git commands: ```sh git remote add upstream https://github.com/espressomd/espresso.git git fetch upstream pull/4611/head:pr-4611 git cherry-pick 992f093ce947b ``` We are sorry for the inconvenience. Best regards, Jean-Noël Grad