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--- exercises:2016_uzh_cmest:faq [2016/11/30 12:24] – created tmueller
+++ exercises:2016_uzh_cmest:faq [2016/12/07 13:15] – [How do I build a slab model for a surface?] scaravati
@@ Line 5: / Line 5: @@
 In some cases (for example for tin) there is only a short-range basis set available, called ''DZVP-MOLOPT-SR-GTH''.
-You can find all available MOLOPT basis sets in ''BASIS_MOLOPT'' which is located in the folder ''$CP2K_DATA_DIR'' (after loading the CP2K module).
+You can find all available MOLOPT basis sets in ''BASIS_MOLOPT'', which is located in the folder ''$CP2K_DATA_DIR'' (after loading the CP2K module).
+===== How do I run CP2K in parallel? =====
+The command ''cp2k.sopt'' is the single-process variant of CP2K.
+To run CP2K in parallel, you have to use a different executable named ''cp2k.popt'' and prefix that with ''mpirun -n 8'' to run it on 8 CPUs in parallel. So, a complete command line to run CP2K on 8 CPUs would then be:
+<code>
+$ mpirun -n 8 cp2k.popt -i yourinput.inp -o youroutput.out
+</code>
+===== How do I obtain a charge density difference? =====
+In [[exercises:2016_uzh_cmest:basic_electronic_structure|Exercise 2]] a series of ''*.cube'' files was already produced for MOs.
+To obtain the electronic charge density in a ''*.cube'', file the following snippet of input file can be used (see also the [[https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/DFT/PRINT/E_DENSITY_CUBE.html|reference manual]]):
+<code>
+&FORCE_EVAL
+  &DFT
+    &PRINT
+      &E_DENSITY_CUBE
+      &END E_DENSITY_CUBE
+      ...
+    &END PRINT
+    ... ...
+  &END DFT
+&END FORCE_EVAL
+</code>
+The [[tools:cubecruncher|cubecruncher]] tool can be used to obtain charge density differences. A precompiled executable is available on the server ''tcopt3'', its path being ''/users/scaravat/bin/cubecruncher.x''.
+The basic usage to obtain a charge density difference is:
+<code>
+$ /users/scaravat/bin/cubecruncher.x -i input.cube -o output.cube -subtract subsystem.cube
+</code>
+===== How do I build a slab model for a surface? =====
+E.g. by using [[http://jp-minerals.org/vesta/en/|VESTA]].
+A tutorial is available [[http://hjklol.mit.edu/content/building-slab-geometries-catalysis-vesta|here]].
+Vesta comes preinstalled on ''tcopt3'', provided that you load the proper module.
+<code>
+$ module load vesta
+</code>
+===== How do I obtain the stress tensor? =====
+You have to add the following snippet to the input file:
+<code>
+&FORCE_EVAL
+  ...
+  STRESS_TENSOR ANALYTICAL
+  &PRINT
+    &STRESS_TENSOR
+    &END STRESS_TENSOR
+  &END PRINT
+  ...
+&END FORCE_EVAL
+</code>
+<note tip>Your calculation should be set up in such a way that forces are being calculated:
+e.g. ''RUN_TYPE'' set to ''GEO_OPT'' or ''ENERGY_FORCE''; instead ''RUN_TYPE ENERGY'' won't work!</note>
+===== How do I restart a calculation? =====
+There are two restart files usually produced by a run:
+  * a binary file, typically ''//<PROJECT>//-RESTART.wfn'', which contains the WFs coefficients.
+  * a ASCII file, typically ''//<PROJECT>//-1.restart'', which has the same structure as the input file with all the keyword specified (in case with the default values).
+To employ the WFs restart file it's enough to change in the input file ''SCF_GUESS ATOMIC'' or ''SCF_GUESS RANDOM''
+into ''SCF_GUESS RESTART'' (see the [[https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/DFT/SCF.html#SCF_GUESS|manual]]).
+Instead, to restart e.g. the positions of the atoms along a GEO_OPT run, you should add
+a [[https://manual.cp2k.org/trunk/CP2K_INPUT/EXT_RESTART.html|new section]] to the input file:
+<code>
+&EXT_RESTART
+    RESTART_FILE_NAME <PROJECT>-1.restart
+&END EXT_RESTART
+</code>
+where you should replace ''//<PROJECT>//'' with the content of your ''PROJECT_NAME'' (eventually aliased to ''PROJECT'') keyword in section ''&GLOBAL''.