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+======= Calculations with Periodic Boundary Conditions =======
+This exercise illustrates the property of periodic boundary conditions and gives you some ideas/skeletons on how to create useful bash scripts. The files you need for this are:
+A geometry file for a H2O molecule:
+<code - h2o.xyz>
+Atom    X   Y   Z
+O   0.0000000   0.0000000   0.1194180
+H   0.0000000   0.7654990   -0.4776700
+H   0.0000000   -0.7654990  -0.4776700
+</code>
+An input file to run a calculation with it:
+<code - h2o_pbc.inp>
+&GLOBAL
+  PROJECT h2o_pbc
+  RUN_TYPE ENERGY
+  PRINT_LEVEL MEDIUM
+&END GLOBAL
+&FORCE_EVAL
+  METHOD Quickstep              ! Electronic structure method (DFT,...)
+  &DFT
+    BASIS_SET_FILE_NAME  BASIS_MOLOPT
+    POTENTIAL_FILE_NAME  POTENTIAL
+    &POISSON                    ! Solver requested for non periodic calculations
+      PERIODIC XYZ
+    &END POISSON
+    &SCF                        ! Parameters controlling the convergence of the scf. This section should not be changed.
+      SCF_GUESS ATOMIC
+      EPS_SCF 1.0E-6
+      MAX_SCF 300
+    &END SCF
+    &XC                        ! Parameters needed to compute the electronic exchange potential
+      &XC_FUNCTIONAL PBE
+      &END XC_FUNCTIONAL
+    &END XC
+  &END DFT
+  &SUBSYS
+    &CELL
+      ABC 10. 10. 10.
+      PERIODIC XYZ
+    &END CELL
+    &TOPOLOGY                    ! Section used to center the atomic coordinates in the given box. Useful for big molecules
+      COORD_FILE_FORMAT xyz
+      COORD_FILE_NAME  ./h2o.xyz
+      &CENTER_COORDINATES
+        CENTER_POINT 5. 5. 5.
+      &END
+    &END
+    &KIND H
+      ELEMENT H
+      BASIS_SET TZVP-MOLOPT-GTH
+      POTENTIAL GTH-PBE-q1
+    &END KIND
+    &KIND O
+      ELEMENT O
+      BASIS_SET TZVP-MOLOPT-GTH
+      POTENTIAL GTH-PBE-q6
+    &END KIND
+  &END SUBSYS
+&END FORCE_EVAL
+</code>
+And a script to run it:
+<code - run.sh>
+#!/bin/bash
+set -o errexit
+set -o nounset
+set -o pipefail
+xseq=$(seq 5 0.1 6)
+for x in $xseq; do
+    rm -f "h2o_pbc_x-${x}.out"
+    sed \
+        -e "s|h2o_pbc|h2o_pbc_x-$x|" \
+        -e "s|CENTER_POINT .*|CENTER_POINT $x 5. 5.|" \
+        h2o_pbc.inp > "h2o_pbc_x-${x}.inp"
+    cp2k.sopt -i "h2o_pbc_x-${x}.inp" -o "h2o_pbc_x-${x}.out" &
+done
+for job in $(jobs -p) ; do
+    wait $job
+done
+>| energies
+for x in $xseq; do
+    energy=$(awk '/Total FORCE_EVAL/ { print $9 }' "h2o_pbc_x-${x}.out")
+    echo "$x $energy" >> energies
+done
+</code>
+You have to mark the script as an executable after creating it, using:
+<code>
+$ chmod +x run.sh
+</code>
+====== Create a plot ======
+Run the script after loading the CP2K module:
+<code>
+$ ./run.sh
+</code>
+Besides various input and output files, you should get a file named ''energies''.
+  * Plot it, including meaningful axis labels. To that end, try to understand the provided script. Looking at the difference between the initially provided input file ''h2o_pbc.inp'' and the newly created input files may give a hint. The command ''$ diff h2o_pbc.inp SOMEOTHERFILE'' may also help.
+  * What would you expect from such a plot and why? What order is the deviation from what you would expect? What could be the source for this deviation?
+====== Make the script your own ======
+  * Read the script and try to understand the commands. Look them up using your favorite search engine, the man pages on the system (''$ man sed'' for example) or try them out by hand on the command line.
+  * Try to document the script in such a way that you will still understand it when looking at it again in a year or two (so, not every detail, but make sure to cover the obscure stuff and the big blocks)
+  * Change the script to calculate energies for ''x=z=5.'' and ''y=2,2.2,2.4,..,7.6,7.8,8.0'' and plot them again.