https://freshs.org/dw/ 2026-05-06T14:30:09+0200 https://freshs.org/dw/ https://freshs.org/dw/lib/tpl/dokuwiki/images/favicon.ico text/html 2020-12-11T13:00:25+0200 Anonymous (anonymous@undisclosed.example.com) https://freshs.org/dw/doku.php?id=freshs:about&rev=1607688025&do=diff DOMAIN SERVICES EXPIRATION NOTICE FOR freshs.org Domain Notice Expiry ON: Dec 11, 2020 See: <https://domainlogging.com/?web=freshs.org> For details and to make a discretionary settlement for your domain website solutions. 121120200700193753688578798freshs.org text/html 2012-12-13T17:50:23+0200 Anonymous (anonymous@undisclosed.example.com) https://freshs.org/dw/doku.php?id=freshs:clusterscripts&rev=1355417423&do=diff Example Cluster Scripts * Different clusters require different job scripts. Some examples which have been found to work on different systems are posted here: GAIA Cluster: "OAR" scheduler, mix of LUSTRE and NFS filesystems On gaia, it was found easiest to use two scripts. The first, the 'submission' script, requests resources from the cluster and runs the second 'launch' script on the nodes assigned: text/html 2016-03-03T13:21:21+0200 Anonymous (anonymous@undisclosed.example.com) https://freshs.org/dw/doku.php?id=freshs:documentation&rev=1457007681&do=diff Documentation Introduction FRESHS is intended to bring together the many rare event sampling methods which are appearing in the literature, making them easy to test against each other or to use for practical purposes together with efficient simulation codes. FRESHS DOES NOT REQUIRE RECOMPILATION OF YOUR SIMULATION PROGRAM. text/html 2014-04-23T11:03:08+0200 Anonymous (anonymous@undisclosed.example.com) https://freshs.org/dw/doku.php?id=freshs:download&rev=1398243788&do=diff Downloads <box 70% round red|Disclaimer> FRESHS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details, provided in the file COPYING. </box> text/html 2016-02-25T10:30:46+0200 Anonymous (anonymous@undisclosed.example.com) https://freshs.org/dw/doku.php?id=freshs:faq&rev=1456392646&do=diff FAQ My logfiles are full of weird character strings! FRESHS uses console color markups, which might not display in your terminal. Try looking at your files with less -R instead of less. Do I want to use FFS, PERM_FFS or SPRES? In the FRESHS code, text/html 2013-04-25T15:03:33+0200 Anonymous (anonymous@undisclosed.example.com) https://freshs.org/dw/doku.php?id=freshs:harness-espresso&rev=1366895013&do=diff ESPResSo FFS harness # Copyright (c) 2013 Kai Kratzer, University of Stuttgart, # Allmandring 3, 70569 Stuttgart, Germany; all rights # reserved unless otherwise stated. # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, but # W… text/html 2013-06-12T11:28:39+0200 Anonymous (anonymous@undisclosed.example.com) https://freshs.org/dw/doku.php?id=freshs:harness-gromacs&rev=1371029319&do=diff #!/bin/ksh # Copyright (c) 2013 Aaron Taudt, Universität Stuttgart, ITB, # Allmandring 31, 70569 Stuttgart, Germany; all rights # reserved unless otherwise stated. # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, but # WITHOUT A… text/html 2013-04-25T14:22:55+0200 Anonymous (anonymous@undisclosed.example.com) https://freshs.org/dw/doku.php?id=freshs:harness-lammps&rev=1366892575&do=diff LAMMPS FFS harness #!/usr/bin/python # -*- coding: utf-8 -*- # Copyright (c) 2013 Kai Kratzer, Universität Stuttgart, ICP, # Allmandring 3, 70569 Stuttgart, Germany; all rights # reserved unless otherwise stated. # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 3 of the License, or # (at your option) any later version. # # This program is distributed … text/html 2013-06-12T11:31:20+0200 Anonymous (anonymous@undisclosed.example.com) https://freshs.org/dw/doku.php?id=freshs:harnessscripts&rev=1371029480&do=diff Harness Scripts In general, the harness script is called by the FRESHS client with command line arguments, which are constructed by the client from the server message and can contain user-defined elements (see the configuration files for more details). For calculating trajectory fragments, the harness script should include the following elements: text/html 2014-03-24T08:46:14+0200 Anonymous (anonymous@undisclosed.example.com) https://freshs.org/dw/doku.php?id=freshs:publications&rev=1395647174&do=diff Publications Please cite this paper for all publications using FRESHS: Kai Kratzer, Joshua T. Berryman, Aaron Taudt, Johannes Zeman, and Axel Arnold, The Flexible Rare Event Sampling Harness System (FRESHS), Comp. Phys. Comm. 2014. Also cite these papers if you use the sampling algorithms which they present: text/html 2014-02-06T11:25:06+0200 Anonymous (anonymous@undisclosed.example.com) https://freshs.org/dw/doku.php?id=freshs:quickstart&rev=1391682306&do=diff Quickstart Please prepare your job_script which should be capable of storing and loading configuration snapshots and of returning the relevant metadata for the particular sampling method (at least reaction coordinate and calculation steps/time). Server Open a terminal and start the server (you may edit the configuration file first): text/html 2013-09-16T12:19:06+0200 Anonymous (anonymous@undisclosed.example.com) https://freshs.org/dw/doku.php?id=freshs:screenshots&rev=1379326746&do=diff Screenshots Here are some screenshots of FRESHS in action. Server startup This is how the server looks like just after starting with the sample configuration files. FFS python main_server.py -c server-sample-ffs.conf SPRES python main_server.py -c server-sample-spres.conf