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--- exercises:2018_uzh_acpc2:installation [2018/04/16 15:10] – gtocci
+++ exercises:2018_uzh_acpc2:installation [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 36: / Line 36: @@
 ===== 0.1b Installation of XCode and XQuartz  on Mac OSX =====
-You need to use an X11 server. Download and install [[https://www.xquartz.org/|XQuartz]] unless you already have it on your machine.
+If you are running on a Mac OS X you need to install XCode and XQuartz.
+Download and install [[https://www.xquartz.org/|XQuartz]] unless you already have it on your machine.
 Also, you need to install XCode from the apple store or from the following link: [[https://developer.apple.com/xcode/|XCode]].
@@ Line 114: / Line 116: @@
 ===== 0.2b CP2K Installation on Mac OS X =====
-Visit [[http://sourceforge.net/projects/cp2k/files/|sourceforge CP2K project page]] and download any of ''cp2k-2.6.2.tar.bz2''.\\
+Visit [[http://sourceforge.net/projects/cp2k/files/|sourceforge CP2K project page]] and download ''cp2k-2.6.2.tar.bz2''.\\
 Unpack the compressed ''tar.bz2'' file by using the following command from the Apple terminal:\\
 <code>
@@ Line 148: / Line 150: @@
 If you find ''cp2k.sopt'' in ''cp2k-2.6.2/exe'' directory, then compilation is successfully done.
-===== First CP2K simulation =====
+===== 0.3 First CP2K simulation =====
-It is possible to run cp2k from any directory your own machine by adding a line to your ''.bashrc'' file, without having to specify the location of the binary.
+It is possible to run cp2k from any directory on your own machine by adding a line to your ''.bashrc'' file, without having to specify the location of the ''cp2k.sopt'' file.
-To do this go to the directory where the binary is located and type ''pwd''. Copy the output of this command and edit the ''.bashrc'' file located on your home directory:
+To do this change to the directory where the ''cp2k.sopt'' binary is located and type ''pwd''. Copy the output of this command and edit the ''.bashrc'' file located on your home directory:
 To edit the ''.bashrc'' file type
 <code>
@@ Line 212: / Line 214: @@
 You just ran a short Molecular Dynamics trajectory of liquid argon.
-===== Visualization with VMD =====
+===== 0.4 Visualization with VMD =====
 We will visualize this trajectory with VMD, a molecular visualization program. First of all, download and install VMD for your operating system as indicated [[http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD|here]].
@@ Line 227: / Line 230: @@
 {{:exercises:2018_uzh_acpc2:argon_liq_first_sim.png?400 |}}
-===== Plotting tools =====
+===== 0.5 Plotting tools =====
 Throughout the course you will also need to plot some graphs. You can use any tool you like for that. ''gnuplot'' and ''Xmgrace'' are two programmes often used in Linux environments that are rather easy to use, but you can also use ''MS Office'', ''Numbers'', the plotting library of python ''Matplotlib'', etc. Take care to install any of these software on your machine as needed.