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--- exercises:2016_uzh_cmest:band_structure_calculation [2016/11/06 15:04] – tmueller
+++ exercises:2016_uzh_cmest:band_structure_calculation [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 97: / Line 97: @@
   * By specifying the ''KPOINT'' section you are enabling the K-Point calculation.
   * While you could specify the K-Points directly, we are using the Monkhorst-Pack scheme [(http://journals.aps.org/prb/abstract/10.1103/PhysRevB.13.5188)] to generate them. The numbers following the keyword ''MONKHORST-PACK'' specify the tiling of the brillouin zone.
-  * After the basic calculation, CP2K calculates the energies along certain lines, denoted as ''KPOINT_SET'' (when you check [https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/DFT/KPOINTS/BAND_STRUCTURE/KPOINT_SET.html|the documentation] you will note that this section can be repeated).
+  * After the basic calculation, CP2K calculates the energies along certain lines, denoted as ''KPOINT_SET'' (when you check [[https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/DFT/KPOINTS/BAND_STRUCTURE/KPOINT_SET.html|the documentation]] you will note that this section can be repeated).
   * The keyword ''NPOINTS'' specifies how many points (in the addition to the starting point) should be sampled between two special points.
   * The ''SPECIAL_POINT'' keyword is used to specify the start-, mid- and endpoints of the line. Those points usually denote special points in the reciprocal lattice/unit cell, like the $\Gamma$, $M$ or $K$ point. You can find the definition for these in the appendix section of [[http://www.sciencedirect.com/science/article/pii/S0927025610002697|this paper]]. This keyword can also be specified multiple times, making it possible to directly get the band structure for a complete //path//.
@@ Line 123: / Line 123: @@
 Your tasks:
-  * Lookup the special points for the $\Gamma$, $M$, $K$ points in the mentioned paper (make sure you choose the right lattice). Calculate and plot the band structure for graphene from $\Gamma$ over $M$, $K$ back to $\Gamma$ (you are free to decide whether to use multiple K-Point sets are multiple special points in a single set). Mark the special points.
+  * Lookup the special points for the $\Gamma$, $M$, $K$ points in the mentioned paper (make sure you choose the right lattice). Calculate and plot the band structure for graphene from $\Gamma$ over $M$, $K$ back to $\Gamma$ (you are free to decide whether to use multiple K-Point sets are multiple special points in a single set). Mark the special points. Choose an appropriate number of interpolation points to get a smooth plot.
   * Compare your plot with plots from literature. What is different?
   * Why do you get 8 orbital energies? Try to change the input to get more unoccupied orbitals.
-To convert the band structure file to a file which can be loaded directly into MATLAB for example, you can use the script ''/users/tiziano/bin/cp2k_bs2csv.py'' which when passed a band structure file ''graphene.bs'' as an argument will write files ''graphene.bs-setN.csv'' for each set containing the K-Point coordinates and the energies in one line.
+To convert the band structure file to a file which can be loaded directly into MATLAB for example, you can use the script ''cp2k_bs2csv.py'' from below, which when passed a band structure file ''graphene.bs'' as an argument will write files ''graphene.bs-setN.csv'' for each set containing the K-Point coordinates and the energies in one line.
+<file python cp2k_bs2csv.py>
+#!/usr/bin/env python
+"""
+Convert the CP2K band structure output to CSV files
+"""
+import re
+import argparse
+SET_MATCH = re.compile(r'''
+[ ]*
+  SET: [ ]* (?P<setnr>\d+) [ ]*
+  TOTAL [ ] POINTS: [ ]* (?P<totalpoints>\d+) [ ]*
+  \n
+(?P<content>
+  [\s\S]*?(?=\n.*?[ ] SET|$)  # match everything until next 'SET' or EOL
+)
+''', re.VERBOSE)
+SPOINTS_MATCH = re.compile(r'''
+[ ]*
+  POINT [ ]+ (?P<pointnr>\d+) [ ]+ (?P<a>\S+) [ ]+ (?P<b>\S+) [ ]+ (?P<c>\S+)
+''', re.VERBOSE)
+POINTS_MATCH = re.compile(r'''
+[ ]*
+  Nr\. [ ]+ (?P<nr>\d+) [ ]+
+  Spin [ ]+ (?P<spin>\d+) [ ]+
+  K-Point [ ]+ (?P<a>\S+) [ ]+ (?P<b>\S+) [ ]+ (?P<c>\S+) [ ]*
+  \n
+[ ]* (?P<npoints>\d+) [ ]* \n
+(?P<values>
+  [\s\S]*?(?=\n.*?[ ] Nr|$)  # match everything until next 'Nr.' or EOL
+)
+''', re.VERBOSE)
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument('bsfilename', metavar='bandstructure-file', type=str,
+                        help="the band structure file generated by CP2K")
+    args = parser.parse_args()
+    with open(args.bsfilename, 'r') as fhandle:
+        for kpoint_set in SET_MATCH.finditer(fhandle.read()):
+            filename = "{}.set-{}.csv".format(args.bsfilename,
+                                              kpoint_set.group('setnr'))
+            set_content = kpoint_set.group('content')
+            with open(filename, 'w') as csvout:
+                print(("writing point set {}"
+                       " (total number of k-points: {totalpoints})"
+                       .format(filename, **kpoint_set.groupdict())))
+                print("  with the following special points:")
+                for point in SPOINTS_MATCH.finditer(set_content):
+                    print("  {pointnr}: {a}/{b}/{c}".format(
+                        **point.groupdict()))
+                for point in POINTS_MATCH.finditer(set_content):
+                    results = point.groupdict()
+                    results['values'] = " ".join(results['values'].split())
+                    csvout.write("{a} {b} {c} {values}\n".format(**results))
+</file>