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--- exercises:2018_uzh_cmest:stm [2018/09/17 12:52] – external edit 127.0.0.1
+++ exercises:2018_uzh_cmest:stm [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 8: / Line 8: @@
 ===== Preparation =====
-  * On the server is a package for you to unpack (hohoho ;-)), containing a number of input files. Run the following in a new and empty directory: <code>tar xf /users/tiziano/CHE437_ex7.tar.gz</code>
+  * On the server is a package for you to unpack, containing a number of input files. Run the following in a new and empty directory: <code>tar xf /users/tiziano/CHE437_ex7.tar.gz</code>
-  * The scripts are contained in yet another python package: <code>pip install --user https://github.com/ltalirz/asetk/archive/master.zip</code>... and since you have setup the path variable in [[exercises:2017_uzh_cmest:phonon_calculation|a previous exercise]], you should now have the following new commands available: ''stm.py'', ''cube-plot.py'', ''cp2k-sumbias.py''. If the installation fails, make sure that you do **not** have the CP2K module loaded: ''module list'' should return an empty list. To explicitly unload the CP2K module, run ''module unload cp2k''.
+  * The scripts are contained in yet another python package: <code>pip2 install --user https://github.com/ltalirz/asetk/archive/master.zip</code>... and since you have setup the path variable in [[exercises:2017_uzh_cmest:phonon_calculation|a previous exercise]], you should now have the following new commands available: ''stm.py'', ''cube-plot.py'', ''cp2k-sumbias.py''. If the installation fails, make sure that you do **not** have the CP2K module loaded: ''module list'' should return an empty list. To explicitly unload the CP2K module, run ''module unload cp2k''.
 ===== Geometry optimization =====
-First take a look at the complete geometry in ''all.xyz'' using ''vmd''. As you can see, this is a much larger geometry than what we had before and would therefore take a lot longer to optimize. This is why some tricks are used in ''geo_opt.inp'': For the nanoribbon (''mol.xyz''), we use the Density Functional based Tight-Binding (DFTB) method instead of GPW and couple the systems together by Force Fields (''FIST''). Look at the CP2K input file ''geo_opt.inp'' to get an idea how that looks like and then run the simulation.
+First take a look at the complete geometry in ''all.xyz'' using ''vmd''. As you can see, this is a much larger geometry than what we had before and would therefore take a lot longer to optimize. This is why some tricks are used in ''nanoribbon-geo_opt.inp'': For the nanoribbon (''mol.xyz''), we use the Density Functional based Tight-Binding (DFTB) method instead of GPW and couple the systems together by Force Fields (''FIST''). Look at the CP2K input file ''nanoribbon-geo_opt.inp'' to get an idea how that looks like and then run the simulation.
 Like with the geometry optimization in the previous examples, you now should have a file ''nanoribbon-geo_opt-pos-1.xyz''.