Embedded Files
ORCA is the quantum chemistry code used in this course. Like almost all quantum chemistry codes it is completely command-line based (i.e. input and output is text) and to use the code you need to learn how to use the Unix command line.
ORCA is already installed on Sól, the Linux computing cluster that we use. It is also possible to download the code for your Mac/Windows/Linux laptop/desktop computer and run the program there (still command-line based).
When we want ORCA to calculate a specific molecule we have to tell ORCA the elements involved but also the initial Cartesian (or internal) coordinates of a molecule (that specify where the atoms are in relation to each other). To create molecular coordinates and to later visualize results (molecular geometries, molecular orbitals etc.) we use the Chemcraft program (150 day trial version) that needs to be installed on each Mac/Windows/Linux laptop.
To connect to Sól we use the SSH (Secure Shell) and SFTP (Secure File Transfer Protocol) protocols that requires installing some programs below.
Installing Chemcraft on Windows, Mac and Linux
Windows
Installing Chemcraft on Windows is straightforward. Download one of the versions on this site. Choosing the version that is not 64bit usually works best.
Mac
There is no Mac version of Chemcraft available sadly but using Windows Chemcraft via the Wine emulation environment actually works quite well.
1. First install a Wine program. Winebottler usually works quite well. Other options are PlayOnMac and Wineskin. If the Wine program complains about the lack of X11/Xquartz on your computer you need to first install Xquartz from this site.
2a. It is probably best to download the standalone Chemcraft program ("WinZip archive without installer, 18 MB.") from the Chemcraft download site and then just try opening the Chemcraft.exe file. The Winebottler program will start and will ask whether you want to run the program or install it. Choosing simply to run it should work well. It may take some time in the beginning.
2b. Other option is to download the installer ("Self-installing executable, 14 MB.") from the Chemcraft download site and open the Installer exe file via the Winebottler program and have Winebottler install it and create a Mac application.
Linux
You can try the Linux version that is available on the download site. If it does not work it is recommended to install the Windows version using Wine.
First install a Wine program e.g. from WineHQ or perhaps even easier using PlayOnLinux.
Then download the Chemcraft Windows version (either the installer or the standalone program) and run via Wine.
Installing an SSH client to connect to Sól
Windows
Unlike Mac and Linux, Windows is not built on Unix and does not have a command-line Unix/Linux interface that can be used to connect to a Linux cluster immediately but requires one to set up an SSH client to connect to Sól. There are many clients available: Bitvise, Putty etc.
Bitvise is an advanced client that also seems to be one of the nicest ones to use and it also includes a good SFTP program.
1. Download the Bitvise SSH Client from this page.
2. Install the program. Should be straightforward.
3. Open the program.
4. To connect to Sól, in the main window you type "sol.raunvis.hi.is" in the Host field, change 22 to 1047 in the Port field, you type your Sól username in the Username field and then click Login. Disable "Enable obfuscation" if ticked. Accept the hostkey ("Accept and Save") if asked. Type in your Sól password when asked that you should have been given.
5. If password was correct, you should be logged in to Sól and 2 windows should have appeared.
One window is your command line (or shell) window (probably black). This one you use to type in commands on the cluster, e.g. change directory (cd), list files (ls), create a directory (mkdir), submit an ORCA calculation (suborca). All the commands you can type in the command line windows is explained in the next tutorial.
The other window is an SFTP client window. You can use this window to copy-paste files between you laptop and your user directory on Sól. You will use this window to e.g. copy ORCA outputfiles created on Sól back to your laptop so that you can open them with Chemcraft.
Mac
Mac OS X has a Unix background and comes with a command-line interface already. If you go to the Utilities directory inside /Applications, you will find the Terminal program. An alternative free program is iTerm2 that I prefer but both programs behave pretty much the same.
To connect to Sól, all you need to do is to to type the correct SSH command in the Terminal/iTerm window (and press Enter):
ssh -p 1047 username@sol.raunvis.hi.is
If connecting works, it will ask for a password that you type in (it will not show the characters when you type, that is normal). Once connected you should be greeted by a Sól welcome message in the shell.
In this window you will type in commands on the cluster, e.g. change directory (cd), list files (ls), create a directory (mkdir), submit an ORCA calculation (suborca). All the commands you can type in the command line windows is explained in the next tutorial.
To disconnect from Sól, you can either type the exit command or simply close the window.
Linux
Linux also has a built-in shell that you can use immediately. Connect to Sól like this:
ssh -p 1047 username@sol.raunvis.hi.is
If connecting works, it will ask for a password that you type in (it will not show the characters when you type, that is normal). Once connected you should be greeted by a Sól welcome message in the shell.
In this window you will type in commands on the cluster, e.g. change directory (cd), list files (ls), create a directory (mkdir), submit an ORCA calculation (suborca). All the commands you can type in the command line windows is explained in the next tutorial.
To disconnect from Sól, you can either type the exit command or simply close the window.
Advanced Mac/Linux tip:
It's also possible to set up an alias for the SSH command in your Mac/Linux computer shell so you don't have to type the whole command every time.
Put:
alias sol='ssh -p 1047 username@sol.raunvis.hi.is'
as a single line to your .bash_profile on your Mac/Linux computer (not on Sól).
To avoid typing in the password each time you can set up SSH keys.
SFTP program to copy files between your computer and Sól
Windows laptop:
The Bitvise program is both an SSH Shell client and an SFTP program so you don't need to setup another SFTP program. Filezilla is another option if you prefer and there are many others.
Mac laptop:
It's convenient to have a GUI-like program to exchange files betweeen your Mac and Sól. Filezilla is a free FTP & SFTP client and works well. Other options are Captain FTP, Transmit. When downloading Filezilla, try to avoid the installer as it contains adware.
Installing Filezilla on Mac for use with Sól is quite easy:
1. Download the installer from here.
2. Launch the installer and start installation. Ignore everything (close windows) concerning Zipcloud that you don't need.
3. Open the program.
4. Open the Site Manager. File -> Site Manager (Command+S). Add a New Site and change the name from "New Site" to "Sól". In the "Host:" field type sol.raunvis.hi.is, in "Port:" add 1047. Change Protocol from FTP to SFTP. Change "Logon Type:" from Anonymous to Normal and then fill in your username and password to Sól that you have been given.
5. Connect to the Server by clicking Connect. Say yes to trusting the Host if asked. You should now be connected to Sól.
6. You can now easily drag and drop files between your computer (left side) and Sól (the remote computer) on the right.
Note that it is always best to go to the Site Manager to connect File -> Site Manager (Command+S) and double-click the Sól entry you previously created. Typing in the hostname in the main window when you want to connect to Sól, will not work, unless you add "sftp://sol.raunvis.hi.is" in the "Host:" field.
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