Software

Introduction to LimeSurvey Online surveys can be used for any type of data collection, not just for marketing purposes. Possible uses of surveys are sign-up forms for conferences, questionnaires for research projects, order forms, etc. For students and employees of the beta-faculty, C&CZ offers a survey service based on LimeSurvey. LimeSurvey is an open source web application. It currently offers: Sending of invitations, reminders and tokens by email Multilingual surveys Conditions for questions depending on earlier answers (Skip Logic / Branching) Integration of pictures and movies into a survey Logging in The admin login page is located at: ...

Matlab, a “matrix laboratory” for interactive scientific calculations of The Mathworks Inc. is an integrated software package, it combines numeric calculations, data visualization and a programming language. License A number of departments in the university have bought shares in the network license that C&CZ has arranged for the use of Matlab. When one has bought a share, one can get the software and installation/licensing keys of Matlab for either Linux, Mac or MS-Windows, also for older versions of Matlab, from C&CZ system administration. ...

NBGrader is a system for assigning and grading Jupyter notebooks. Student Interface Using the assignment list extension within the JupyterHub, students may conveniently view, fetch, submit, and validate their assignments. For details see: https://nbgrader.readthedocs.io/en/stable/user_guide/highlights.html#student-interface Instructor Interface The NBGrader services guide the instructor and teaching assistants through assignment and grading tasks using the familiar JupyterHub environment. For details see: https://nbgrader.readthedocs.io/en/stable/user_guide/highlights.html#instructor-interface

License servers For several software packages there is a license server, that allows use of the software on all PCs while making sure that the total number of licenses in use does not exceed what has been bought. Most of these license servers use FlexNet by Flexera. Science software licences negotiated by C&CZ All info can be found on the Science licenses pages. Questions: please contact C&CZ. Most software can be found on the install share. On a PC with MS-Windows (or a Linux “Samba client”), one can connect to the service: ...

Prerequisities Same as for gaussian set-up environment (check gaussian) General topics General topics like queue handling, queues and similar are covered in the gaussian wiki entry. Submitting jobs Basic syntax of crest submission script is following: cnorris@lilo7:~$ Crest structure.xyz where structure.xyz is the structure which you want to submit. More advanced syntax looks like this: cnorris@lilo7:~$ Crest structure.xyz -chrg 1 -uhf 0 -quick Here I’ve added quick keyword which makes the screening less in-depth but it goes much quicker. I also added chrg keyword to define charge and uhf keyword to define spin state. For more detailed description and full list of keywords, please refer to crest command line arguments documentation. ...

General Account The procedure below only works for employees with an U-number. For access with an E-number account please contact labservant@science.ru.nl All employees and guests who need to access to labservant can obtain an account using the following steps: Request labservant access via the secretariat of your department, they can grand labservant access via RBS. After labservant access is granted in RBS, login to labservant using your RU account (https://labservant.science.ru.nl) During your first logon an account is created based on your personal data in RBS After a successful login (you should see the Labservant home screen), the lab-manager of your department can grant you the authorizations needed. When the message “Logged in but no verified check” is displayed after logon, try to login again using a capital letter in your user name (U-number). If the message persists the most probable cause is that labservant access was not granted in RBS by your department’s secretariat. ...

Starting December 2022 the ChemOffice+ license is being replaced by a ChemDraw Prime campus license. ChemDraw Prime is a complete “entry-level” drawing program that provides all the tools you need to quickly create chemically intelligent, publication-ready chemical structures and reactions, laboratory notes and experiment write-ups. As well as a full set of chemical structure essentials such as rings, bonds, chains, atoms and functional groups, ChemDraw Prime includes chemical and lab equipment templates and handy TLC and Gel Electrophoresis Plate drawing tools. ...

The latest version of Matlab, R2022a, is available for departments that have licenses. The software and license codes can be obtained through a mail to postmaster for those entitled to it. The software can also be found on the install-disc. All C&CZ-managed Linux machines have this version installed, an older version (/opt/matlab-R2021a/bin/matlab) is still available temporarily. The C&CZ-managed Windows machines will not receive a new version during the semester to prevent problems with version dependencies in current lectures.

C&CZ administers the licenses for the use of LabVIEW within FNWI. LabVIEW by NI is a graphical programming environment engineers use to develop automated research, validation, and production test systems. From version 2022Q3 LabVIEW no longer works standalone and unlimited in terms of time. C&CZ manages a LabVIEW license server with a small number of licenses that have to be renewed every year. Users of this license must be registered on the license server.

Prerequisities Science (CNCZ) account. Being member of the qm, qmorgchem or qmteaching and gaussian groups (ask Jan for access). Vpn (when working from home). SSH client (linux usually has OpenSSH, windows - for instance MobaXterm or Putty). X11 client (linux usually has OpenSSH, windows - for instance MobaXterm (optional) WinSCP Video guides GUIDE how to setup environment for Gaussian calculations in windows. Setting-up the environment (to be done once) To submit calculations easily you need to set-up the environment first. ...