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--- exercises:2016_uzh_cmest:geometry_optimization [2016/10/12 08:54] – [1. Step: Setting up a calculation] tmueller
+++ exercises:2016_uzh_cmest:geometry_optimization [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 62: / Line 62: @@
       MAX_SCF 300
     &END SCF
-    &XC                        ! Parametes needed to compute the electronic exchange potential
+    &XC                        ! Parameters needed to compute the electronic exchange potential
       &XC_FUNCTIONAL PBE
       &END XC_FUNCTIONAL
@@ Line 98: / Line 98: @@
 ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.):              -14.746153797151329
 </code>
+You can also directly open a XYZ file in VMD:
+<code>
+$ vmd ethane1.xyz
+</code>
+===== 2. Step: Optimizing the geometry =====
+The only thing you have to change to get a geometry optimization instead of a single point energy calculation is the following:
+<code - ethane1_opt.inp >
+&GLOBAL
+  PROJECT ethane1_opt
+  RUN_TYPE GEO_OPT
+  PRINT_LEVEL MEDIUM
+&END GLOBAL
+[...]
+</code>
+Note the different ''RUN_TYPE'' and the changed ''PROJECT'' name. The latter is not strictly necessary but recommended, since CP2K automatically creates additional files using this project name as a prefix.
+After running this, you will have the following files:
+<code>
+$ ls ethane1_opt*
+ethane1_opt-1.restart        ethane1_opt-1.restart.bak-3  ethane1_opt.out          ethane1_opt-RESTART.wfn.bak-1
+ethane1_opt-1.restart.bak-1  ethane1_opt-BFGS.Hessian     ethane1_opt-pos-1.xyz    ethane1_opt-RESTART.wfn.bak-2
+ethane1_opt-1.restart.bak-2  ethane1_opt.inp              ethane1_opt-RESTART.wfn  ethane1_opt-RESTART.wfn.bak-3
+</code>
+Take a look at the output file, especially the following section (repeated the number of cycles it took to reach convergence):
+<code>
+ --------  Informations at step =     1 ------------
+  Optimization Method        =                 BFGS
+  Total Energy               =       -14.9417142787
+  Real energy change         =        -0.1955604816
+  Predicted change in energy =        -0.1885432833
+  Scaling factor             =         0.0000000000
+  Step size                  =         0.2677976891
+  Trust radius               =         0.4724315332
+  Decrease in energy         =                  YES
+  Used time                  =               19.018
+  Convergence check :
+  Max. step size             =         0.2677976891
+  Conv. limit for step size  =         0.0030000000
+  Convergence in step size   =                   NO
+  RMS step size              =         0.1458070233
+  Conv. limit for RMS step   =         0.0015000000
+  Convergence in RMS step    =                   NO
+  Max. gradient              =         0.0287243359
+  Conv. limit for gradients  =         0.0004500000
+  Conv. for gradients        =                   NO
+  RMS gradient               =         0.0180771987
+  Conv. limit for RMS grad.  =         0.0003000000
+  Conv. for gradients        =                   NO
+ ---------------------------------------------------
+</code>
+For each convergence criterion you see the value which is used to check whether convergence is reached and convergence is only reached if all of them are satisfied simultaneously.
+From the output file, extract the following data and generate 3 plots with the values vs the iteration number:
+  * ''Total FORCE_EVAL ( QS ) energy''
+  * ''Max. gradient'' .. the maximal force (seen over all atoms)
+  * ''Max. step size'' .. the maximal displacement (seen over all atoms)
+===== 3. Step: Optimizing the geometry with an alternative geometry =====
+Now change the used coordinate file to ''ethane2.xyz'' and update the ''PROJECT'' name to not overwrite the results from the previous simulation and run it again.
+  * Compare the final energy reached for both structures and the total number of optimization steps required
+  * Open the two output XYZ files (''<PROJECT>-pos-1.xyz'') in VMD and compare them. Is there a difference? What is it?
+  * Which one is likely to be more stable and why?
+===== 4. Step: Visualize the geometry optimization =====
+Append the following section to your input file (does not matter for which structure) and run the simulation again.
+<code>
+&MOTION
+  &PRINT
+    &TRAJECTORY
+      LOG_PRINT_KEY T
+      FORMAT XYZ
+      ADD_LAST NUMERIC
+    &END TRAJECTORY
+  &END PRINT
+&END MOTION
+</code>
+If you check the output XYZ file now (''<PROJECT>-pos-1.xyz'') and compare it to the input structure, you will notice that the same molecule is now specified multiple times as so-called //frames//. Checking the CP2K output file you will also notice the following entry:
+<code>
+[...]
+ Writing TRAJECTORY 1_1 to ethane2_opt_traj-pos-1.xyz
+[...]
+</code>
+Open this new XYZ file again with VMD, choose an appropriate drawing method (//Licorice// or //CPK//), hit the play button and enjoy:
+{{ vmd_play.png |}}