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--- exercises:2021_uzh_acpc2:ex01 [2021/04/26 07:32] – [Part III: Radial distribution functions] mrossmannek
+++ exercises:2021_uzh_acpc2:ex01 [2021/05/17 11:35] (current) – [Part III: Radial distribution function] Fix type mrossmannek
@@ Line 442: / Line 442: @@
 .2150    1.1041
 .2831    1.0977
-.3512    1~0904
+.3512    1.0904
 .4193    1.0835
 .4874    1.0774
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 </code>
-===== Part IV:  Ensembles  =====
+===== Part IV: Other Ensembles  =====
-In previous section, you have already run NVE ensemble molecular dynamics for Ar liquid. In this section, we will focus on the NVT, NPT ensembles.
+In the previous sections, you have already run NVE ensemble molecular dynamics calculations for liquid Ar. In this section, we will focus on the NVT and NPT ensembles.
-Step up NVT calculation, change the setting in &MD section.
+To set up an NVT calculation, change the settings in the &MD section as shown below:
@@ Line 476: / Line 476: @@
-Step up NPT calculation, change the setting in &MD section.
+To set up an NPT calculation, change the settings in the &MD section as shown below:
   &FORCE_EVAL
@@ Line 503: / Line 503: @@
 <note>
 **TASK**
-   *Run calculation using NVT at 300K, check the temperature, and energy of the whole system, and compare the result to NVE (300K), and rationalize the difference.
+   *Run a calculation using the NVT ensemble at 300K. Check the temperature and energy of the whole system, and compare the result to an NVE ensemble (300K). Rationalize and discuss the difference.
-   *Run calculation using NVT (300K) until the system is equilibrated then run NVE, check the temperature, and energy of the whole system, and  compare to previous NVE simulation.
+   *Run a calculation using the NVT ensemble (300K) until the system is equilibrated, then run an NVE ensemble calculation. Check the temperature and energy of the whole system, and compare to the previous NVE simulation. Discuss your observations.
-   *Remove some atoms and run NPT simulation then check the size of the simulation box.
+   *Remove some atoms and run an NPT ensemble simulation. Then, check the size of the simulation box. Discuss your observations.
+</note>
+<note tip>
+You have multiple options on how to restart a CP2K calculation off of a previous one. What all approaches have in common, is that you need to make use of the RESTART-files which are automatically written by CP2K (unless you explicitly disable them).
+For the purposes of this example, you should see a file called ''ar108-1.restart'' (at least for Part 1 of this exercise). //Note:// there will also be multiple backup files (''.bak-#'' suffixes) which you do not need to care about.
+These files are nothing but another input file. However, their parameters are set such that they continue a CP2K calculation from the last step of the simulation which generated the RESTART file.
+Here are two options for how you can use these RESTART-files:
+. Directly using the RESTART as an input.
+   - You can copy the RESTART file to a new input file: <code>cp ar108-1.restart argon_follow_up.inp</code>
+   - Now you can change the input to your liking (e.g. change the ensemble, etc.)
+   - And finally simply run CP2K with the new input file: <code>cp2k -i argon_followup.inp -o argon_followup.out</code>
+. You can also tell CP2K to load a specific RESTART-file.
+   - Write a new input file as usual: <code>argon_followup.inp</code>
+   - Add an [[https://manual.cp2k.org/trunk/CP2K_INPUT/EXT_RESTART.html|EXT_RESTART]] section:
+      <code>
+&EXT_RESTART
+  RESTART_FILE_NAME ar108-1.restart
+&END EXT_RESTART</code>
+   - And now, again, simply run CP2K:  <code>cp2k -i argon_followup.inp -o argon_followup.out</code>
 </note>