[CP2K:7381] Re: Velocity DCD file broken

Krack Matthias (PSI) matthia... at psi.ch
Thu Jan 28 12:21:34 CET 2016


Hi Norman,

for such purpose (post-processing of CP2K pos and vel files) you may employ the dumpdcd.f90 code in the cp2k/tools folder which I mentioned already in my first email. It performs also the simple task of just changing “VEL” to “CORD”. Please check the examples listed using the –h flag. For example check the last examples which are mostly related to VMD specifically like:


-          dumpdcd -o new.dcd -of dcd -vel2cord old.dcd         (dump old.dcd as new.dcd and change only the DCD id string from VEL to CORD)

This is fixes the issue we are discussing here. I am also reluctant in changing VEL to CORD for CP2K vel files, because one would loose the information about the type of that file.

Please note, that dumpdcd.f90 provides even more advanced functionalities for conversion which sometimes might make the use of VMD for such purposes dispensable,  like


-          Output of an “atomic temperature”

-          Application of periodic boundary conditions (PBC), i.e. “folding back” atoms to the original cell)

-          Extraction of a subset of configurations (frames): scope by first and last frame, optionally with a stride

-          Concatenation of several DCD files

-          Dump in XMOL format

-          List of atoms leaving the box (given a threshold value)

-          Displacement of the atoms w.r.t. the first (original) configuration

Here is the full list of examples available with the –h flag:
  dumpdcd UO2-2x2x2-pos-1.dcd (without atomic labels from XYZ file)
  dumpdcd -xyz UO2-2x2x2.xyz UO2-2x2x2-pos-1.dcd (single DCD file)
  dumpdcd -xyz UO2-2x2x2.xyz UO2-2x2x2-pos-1.dcd UO2-2x2x2-pos-2.dcd ... (multiple DCD files are dumped consecutively)
  dumpdcd -info -xyz UO2-2x2x2.xyz UO2-2x2x2-pos-1.dcd UO2-2x2x2-pos-2.dcd (print additional information)
  dumpdcd -debug -xyz UO2-2x2x2.xyz UO2-2x2x2-pos-1.dcd UO2-2x2x2-pos-2.dcd (print debug information)
  dumpdcd -ekin -d -xyz UO2-2x2x2.xyz UO2-2x2x2-vel-1.dcd (print the "temperature" of each atom)
  dumpdcd -ekin -xyz UO2-2x2x2.xyz UO2-2x2x2-vel-1.dcd (print just the temperature of each atom)
  dumpdcd -first_frame 5 -last_frame 10 UO2-2x2x2-pos-1.dcd (just dump frame 5 to 10, ie. 6 frames in total)
  dumpdcd -o outfile.xyz UO2-2x2x2-pos-1.dcd (write output to the file "outfile.xyz" instead of stdout)
  dumpdcd -o test.xyz -output_format xmol -xyz ref.xyz -first 10 -last 10 test.dcd (dump 10th frame in XMOL format)
  dumpdcd -of dcd -ff 10 -lf 20 test.dcd (dump the frames 10 to 20 in DCD format to the default output file output.dcd)
  dumpdcd -o part.dcd -of dcd -ff 1 -lf 3 test.dcd (dump the frames 1 to 3 in DCD format to the output file part.dcd)
  dumpdcd -o part.dcd -of dcd -first 10 -lf 100 -stride 10 test.dcd (dump the frames 10, 20, ..., 100 to the file part.dcd)
  dumpdcd -output new.dcd -output_format dcd -pbc old.dcd (dump all frames applying PBC to the output file new.dcd)
  dumpdcd -o new.dcd -of dcd -pbc -trace_atoms 0.02 old.dcd (all atoms more than 2% out of the box are listed)
  dumpdcd -o new.dcd -e out_of_box.log -of dcd -pbc -trace_atoms 0.1 old.dcd (atoms more than 10% out of the box are listed)
  dumpdcd -o new.dcd -of dcd -vel2cord old.dcd (dump old.dcd as new.dcd and change only the DCD id string from VEL to CORD)
  dumpdcd -i -disp UO2-2x2x2-pos-1.dcd (dump the displacements of all atoms w.r.t. their positions in the first frame)
  dumpdcd -i -of dcd -disp UO2-2x2x2-pos-1.dcd (dump the atomic displacements as x-coordinates of a DCD CORD file)
  dumpdcd -i -of dcd -ekin -v2c -xyz UO2-2x2x2.xyz UO2-2x2x2-vel-1.dcd (dump the atomic temperatures as x-coordinates of a
                                                                        DCD CORD file -> hack for VMD)

HTH,

Matthias


From: cp... at googlegroups.com [mailto:cp... at googlegroups.com] On Behalf Of NORMAN GEIST
Sent: Donnerstag, 28. Januar 2016 11:10
To: cp2k
Subject: Re: [CP2K:7381] Re: Velocity DCD file broken

Hey Matthias,

IMHO I wouldn't expect any DCD code out there to accept something else to be the magic string than "CORD", therefore the greatest benefit might just be, being able to load the files without trouble.
In VMD in particular, one don't want to actually visualize the data like coordinates, but use VMD mechanisms of file and trajectory processing for analysation purpose, e.g temperature distributions along various atom types /elements.

Best wishes

Norman Geist
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