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--- exercises:2017_uzh_cmest:basic_electronic_structure [2017/09/27 11:04] – created tmueller
+++ exercises:2017_uzh_cmest:basic_electronic_structure [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
 ======= Basic electronic structure calculation =======
-In this exercise, you will perform a first basic electronic structure calculation to obtain the molecular orbitals (**MO**s) of Ethene: Your calculations will produce a list of occupied and non occupied MOs and a series of ''*.cube'' files, that allow the visualization of the orbitals with VMD.
+In this exercise, you will perform a first basic electronic structure calculation to obtain the molecular orbitals (**MO**s) of Ethene: Your calculations will produce a list of occupied and non occupied MOs and a series of ''*.cube'' files, that allow the visualization of the orbitals with //VMD//.
+It is recommended to install and run //VMD// on your local machine. //VMD// can be [[http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD|downloaded free of charge]] after registering with your name and email address. To load and render the ''*.cube'' files on your local //VMD// you first have to transfer them from the server to your machine by using one of the transfer tools recommended on the [[exercises:2017_uzh_cmest:login|First Login]] page.
 ===== 1. Step: Run the calculation =====
-Create a new directory for this exercise and run a CP2K calculation with the following (commented) input file:
+Create a new directory for this exercise and run a CP2K calculation with the following (commented) input file (look at the [[exercises:2017_uzh_cmest:first_simulation_run|first exercise again to figure out how to run a simulation]]):
 <code - ethene.inp >
@@ Line 43: / Line 44: @@
     &END SCF
-    &XC                        ! Parametes needed to compute the electronic exchange potential
+    &XC                        ! Parameters needed to compute the electronic exchange potential
       &XC_FUNCTIONAL NONE      ! No xc functional
       &END XC_FUNCTIONAL
@@ Line 57: / Line 58: @@
     &CELL
       ABC 10 10 10
-      PERIODIC NONE              ! Non periodic calculations. That's why the POISSON section is needed
+      PERIODIC NONE              ! Non-periodic calculations. That's why the POISSON section is needed
     &END CELL
     &TOPOLOGY                    ! Section used to center the atomic coordinates in the given box. Useful for big molecules
@@ Line 135: / Line 136: @@
 Use VMD to visualize the cube-files:
-  - To run: ''$ vmd ethene-WFN_00008_1-1_0.cube''
+  - Open one ''.cube'' file at a time in //VMD//
   - To visualize the molecule (sometimes it's not visible by default):\\ go to **Graphics > Representations > Draw style** and set **Drawing Method** to **CPK**
   - Add a second representation by clicking on **Create Rep**
@@ Line 157: / Line 158: @@
   - The eigenvalues are given in Hartree (//Eh//) while the band-gap is stated directly in electronvolt
   - Lookup the molecular orbital diagram of Ethen to identify which MOs and therefore which cube files you need to open.
-  - Use the [[http://cccbdb.nist.gov/|Computational Chemistry Comparison and Benchmark DataBase]] to lookup the calculated geometry for Propene (CH2CHCH3), use the geometry made using a Hartree-Fock calculation and the ''6-311+G(3df,2pd)'' basis set.
+  - Use the [[http://cccbdb.nist.gov/|Computational Chemistry Comparison and Benchmark DataBase]] to lookup the calculated geometry for Propene (CH2CHCH3), use the geometry optimized using a Hartree-Fock calculation and the ''6-311+G(3df,2pd)'' basis set.
 </note>