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--- exercises:2019_conexs_newcastle:ex1 [2019/09/10 12:41] – [Part 3: Geometry optimization] abussy
+++ exercises:2019_conexs_newcastle:ex1 [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 114: / Line 114: @@
 &END COORD
 </code>
-sets up our simulation cell and atomic coordinates respectively. In the &KIND sections,
+sets up our simulation cell and atomic coordinates respectively. By default, CP2K will run your calculations with periodic boundary conditions but since we are using a large simulation box, the molecule does not interact with its own copies and we are effectively looking at it in gas phase. In the &KIND sections,
 <code>
 &KIND H
@@ Line 137: / Line 137: @@
 or
 <code>
-./cp2k.sopt water.inp | tee water.out
+sbatch cp2k.sh
 </code>
-if you want to follow the output as it runs. When the program is finished, you will have two new files in your working directory:
+if you are logged in to the cluster and have modified the //cp2k.sh// accordingly. When the program is finished, you will have two new files in your working directory:
 <code>
 water.out
@@ Line 326: / Line 326: @@
 Here we can see that the bond angle is now 102.8°, which is better but still quite far from the accepted 104.45°. Also comparing the final total energy to our first single-point calculation, we can see that our new geometry is more energetically stable.
+=====Part 4: Computing PDOS=====
+Now that we have obtained a more reasonable geometry, we will know attempt to compute the eigenvalues of our Kohn-Sham orbitals and compare the energy levels to the attached experimental spectra. We will also use this opportunity to try out the option to restart a calculation.
+-0.316280
+To restart our calculation from the previous geometry optimization, we need to copy two files from the old working directory, e.g.
+    h2o_opt-RESTART.wfn
+    h2o_opt-1.restart
+to our current working directory. To make the code read these files, we have to add a section
+<code>
+&EXT_RESTART
+  RESTART_FILE_NAME h2o_opt-1.restart
+&END EXT_RESTART
+</code>
+as well as adding
+<code>
+SCF_GUESS RESTART
+RESTART_FILE_NAME h2o_opt-RESTART.wfn
+</code>
+to the &SCF and &DFT sections respectively. To print the PDOS, we also need to add the &PDOS section under &DFT
+<code>
+&PRINT
+  &PDOS
+     FILENAME ./pdos
+     NLUMO 2
+  &END
+&END
+</code>
+and specify the spectra file names for example if we want to include unoccupied virtual orbitals. The final input can e.g. look like this:
+<code>
+&DFT
+  BASIS_SET_FILE_NAME GTH_BASIS_SETS
+  POTENTIAL_FILE_NAME GTH_POTENTIALS
+  LSD 0
+  RESTART_FILE_NAME h2o_opt-RESTART.wfn
+  &QS
+    METHOD GPW
+    EPS_DEFAULT 1.0E-10
+  &END QS
+  &SCF
+    MAX_SCF    300
+    EPS_SCF    1.0E-06
+    SCF_GUESS RESTART
+    &MIXING
+      METHOD DIRECT_P_MIXING
+      ALPHA   0.6
+    &END MIXING
+    &DIAGONALIZATION
+      ALGORITHM STANDARD
+    &END DIAGONALIZATION
+  &END SCF
+  &MGRID
+    NGRIDS 4
+    CUTOFF 300
+    REL_CUTOFF 60
+  &END
+  &XC
+    &XC_FUNCTIONAL BLYP
+    &END XC_FUNCTIONAL
+  &END XC
+  &PRINT
+    &PDOS
+      FILENAME ./h2o
+      NLUMO 2
+    &END
+  &END
+&END DFT
+</code>
+When the calculation is done, open the file
+    *h2o-k1-1.pdos
+and compare your calculated energies to the experimental measurements reported in the attached paper, e.g. Fig. 1. As a reminder, one 1 a.u. = 27.212 eV. Look in particular on the energy differences between the three valence states.
+{{:exercises:2019_conexs_newcastle:h2o_pes.pdf | Water PES}}
+----
+=====Part 5: (Optional) Testing your parameters=====
+If you followed this exercise closely, chances are that the computed orbital energies in your PDOS files are quite similar to the experimental ones, given an ad hoc shift of the energies. However, the 1b2 orbital will be slightly off. Can we do better by tweaking our input, or can we get as good results with a faster method? In this exercise, we will investigate and try to get a feel for how different parameters affect the accuracy and time consumption of your calculation. Go back to Part 3 and Part 4 and redo the calculation while changing the following parameters
+<code>
+&XC_FUNCTIONAL  {PADE BLYP B3LYP}
+CUTOFF          {100 300 600}
+BASIS_SET       {SZV-GTH DZVP-GTH TZVP-GTH}
+EPS_SCF         {1.0E-04 1.0E-06 1.0E-0.8}
+</code>
+(choose one of the suggested in the brackets). The suggestions are given from less accurate to more accurate. When you feel comfortable, feel free to experiment with other keywords!   Note that using e.g. a larger basis set will make the calculation take longer, so you might want to do something else in the mean time.