exercises:2018_uzh_acpc2:installation
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exercises:2018_uzh_acpc2:installation [2018/04/16 14:17] – gtocci | exercises:2018_uzh_acpc2:installation [2018/04/16 15:18] – [0.3 First CP2K simulation] gtocci | ||
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</ | </ | ||
- | + | ===== 0.1a Installation of Cygwin | |
- | ===== Installation of XCode and XQuartz | + | |
- | + | ||
- | You need to use an X11 server. Download and install [[https:// | + | |
- | + | ||
- | Also, you need to install XCode from the apple store or from the following link: [[https:// | + | |
- | + | ||
- | ===== Installation of required software | + | |
If your machine is running windows you will need to install Cygwin. [[http:// | If your machine is running windows you will need to install Cygwin. [[http:// | ||
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For 32 bit Windows execute | For 32 bit Windows execute | ||
- | For 64 bit Windows[[http:// | + | For 64 bit Windows [[http:// |
When installing Cygwin make sure you install the following additional packages:\\ | When installing Cygwin make sure you install the following additional packages:\\ | ||
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Please operate according to the wizard to finish the Cygwin installation.\\ | Please operate according to the wizard to finish the Cygwin installation.\\ | ||
+ | ===== 0.1b Installation of XCode and XQuartz | ||
- | ===== Using the terminal ===== | + | If you are running on a Mac OS X you need to install XCode and XQuartz. |
+ | |||
+ | Download and install [[https:// | ||
+ | |||
+ | Also, you need to install XCode from the apple store or from the following link: [[https:// | ||
+ | |||
+ | |||
+ | ===== 0.2 Using the terminal ===== | ||
Throughout this course you will need to use the terminal or command line. Below there' | Throughout this course you will need to use the terminal or command line. Below there' | ||
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- | ===== CP2K Installation on Windows ===== | + | ===== 0.2a CP2K Installation on Windows ===== |
- | Visit [[http:// | + | Visit [[http:// |
Unpack the compressed '' | Unpack the compressed '' | ||
< | < | ||
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Change directory to '' | Change directory to '' | ||
- | An example CP2K ARCH file for a serial build of CP2K on Cygwin | + | Copy the following lines and paste into the newly opened '' |
< | < | ||
CC = cc | CC = cc | ||
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If you find '' | If you find '' | ||
- | ===== CP2K Installation on Mac OS X ===== | + | ===== 0.2b CP2K Installation on Mac OS X ===== |
- | [[https://www.cp2k.org/howto: | + | Visit [[http://sourceforge.net/ |
- | ===== First CP2K simulation ===== | + | Unpack the compressed '' |
- | It is possible to run cp2k from any directory your own machine by adding a line to your '' | + | < |
+ | tar -xvf cp2k-2.6.2.tar.bz2 | ||
+ | </ | ||
+ | |||
+ | After the code has been extracted you will find it in the directory '' | ||
+ | |||
+ | In order to compile cp2k one has to specify an arch file to indicate which compilers and libraries to use. | ||
+ | Change directory to '' | ||
+ | |||
+ | < | ||
+ | CC = gcc | ||
+ | CPP | ||
+ | FC = gfortran | ||
+ | LD = gfortran | ||
+ | AR = ar -r | ||
+ | RANLIB | ||
+ | DFLAGS | ||
+ | FCFLAGS | ||
+ | | ||
+ | LDFLAGS | ||
+ | LIBS = -framework Accelerate | ||
+ | |||
+ | </ | ||
+ | Save it as '' | ||
+ | Launch the Terminal and change the working directory to '' | ||
+ | < | ||
+ | make ARCH=Darwin-IntelMacintosh-gfortran VERSION=sopt | ||
+ | </ | ||
+ | It may take quite a while until a compilation is completed. | ||
+ | |||
+ | If you find '' | ||
+ | |||
+ | ===== 0.3 First CP2K simulation ===== | ||
+ | It is possible to run cp2k from any directory | ||
- | To do this go to the directory where the binary is located and type '' | + | To do this change |
To edit the '' | To edit the '' | ||
< | < | ||
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You just ran a short Molecular Dynamics trajectory of liquid argon. | 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:// | 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:// | ||
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{{: | {{: | ||
+ | |||
+ | |||
+ | ===== 0.5 Plotting tools ===== | ||
+ | |||
+ | Throughout the course you will also need to plot some graphs. You can use any tool you like for that. '' | ||
exercises/2018_uzh_acpc2/installation.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1