[CP2K:9772] Re: RAMAN spectrum from AIMD
ION SUCH
ion.... at gcloud.ua.es
Tue Dec 5 07:51:59 UTC 2017
Dear Juerg Hutter,
Thank you for taking the time to answer.
>From your replies I gather that I may be using the wrong trajectory file as
I am using the ions+centres file and that of course means there are
different number of particles in the topology file and the trajectory file.
This probably should be addressed in the Travis tutorial in the cp2k web
page as it appears is not clear for newbies. Maybe seeing this thread some
other people will avoid hitting the same stone.
Ion
El martes, 5 de diciembre de 2017, 7:32:44 (UTC+1), jgh escribió:
>
> Hi
>
> I am not a TRAVIS user, but looking at your files it seems to
> me that you have used the wrong 'trajectory' file.
> CP2K writes a trajectory file during MD that is usually call
> ....pos-x.xyz. This file contains the coordinates of all particles.
> If you calculate Wannier functions during a MD you can also request
> a file ions+wannier-centers. This last file should only be used for
> analysis, not as a REFTRAJ! as it contains Wannier center information.
>
> If this distinction is not clear from the TRAVIS documentation,
> tell the TRAVIS developers to upgrade the manual.
>
> regards
>
> Juerg
> --------------------------------------------------------------
> Juerg Hutter Phone : ++41 44 635 4491
> Institut für Chemie C FAX : ++41 44 635 6838
> Universität Zürich E-mail: hut... at chem.uzh.ch
> <javascript:>
> Winterthurerstrasse 190
> CH-8057 Zürich, Switzerland
> ---------------------------------------------------------------
>
> -----cp... at googlegroups.com <javascript:> wrote: -----
> To: cp2k <cp... at googlegroups.com <javascript:>>
> From: nju... at gmail.com <javascript:>
> Sent by: cp... at googlegroups.com <javascript:>
> Date: 12/04/2017 04:06PM
> Subject: [CP2K:9772] Re: RAMAN spectrum from AIMD
>
> Dear developers and users,
>
>
> I’m plaguing with the same problem and it’s outputting the same error.
> Could anyone give some advice?
>
>
> Thank you very much.
>
> 在 2017年11月17日星期五 UTC+8下午7:33:13，ION SUCH写道：
> Dear users and developers,
>
> My name is Ion Such and I am a recent CP2K user. I am interested in
> getting raman spectra of adsorbed molecules.
> As an exercise I am following one of the HOWTOs on the cp2k web: "How to
> calculate infrared and Raman spectra from MD with CP2K and TRAVIS". In my
> case I am simulating a molecule of para-nitroaniline in a box.
> At the time of writing I have made the first Molecular Dynamics run and
> have obtained the infrared spectrum and a cp2k input file for the
> calculation of the polarizabilities by using TRAVIS but I run into an error
> when trying to execute the polarizabilities calculation that I don't
> understand and need some help to go ahead.
>
> The error in the output file reads
>
> MD| Molecular Dynamics Protocol
> MD| Ensemble Type
> REFTRAJ
> MD| Number of Time Steps
> 2000
> MD| Time Step [fs]
> 0.50
> MD| Temperature [K]
> 300.00
> MD| Temperature tolerance [K]
> 0.00
> MD| Print MD information every 1
> step(s)
> MD| File type Print frequency[steps] File
> names
> MD| Coordinates 1
> polarizability-pos-1.xyz
> MD| Velocities 1
> polarizability-vel-1.xyz
> MD| Energies 1
> polarizability-1.ener
> MD| Dump 1
> polarizability-1.restart
>
> ROT| Rotational Analysis Info
> ROT| Principal axes and moments of inertia in atomic units:
> ROT| 1 2 3
> ROT| EIGENVALUES 0.853999142E+06 0.406672822E+07
> 0.491400783E+07
> ROT| X -0.022761946 -0.821027156
> -0.570435187
> ROT| Y 0.067435865 0.568022568
> -0.820245552
> ROT| Z 0.997463933 -0.057138175
> 0.042437378
> ROT| Numer of Rotovibrational vectors: 6
>
> Calculation of degrees of freedom
> Number of atoms:
> 16
> Number of Intramolecular constraints:
> 0
> Number of Intermolecular constraints:
> 0
> Invariants(translation + rotations):
> 3
> Degrees of freedom:
> 45
>
>
> Restraints Information
> Number of Intramolecular restraints:
> 0
> Number of Intermolecular restraints:
> 0
> ************************** Velocities initialization
> **************************
> Initial Temperature
> 300.00 K
> COM velocity: 0.000000000000 -0.000000000000
> 0.000000000000
> *******************************************************************************
>
>
>
> *******************************************************************************
>
> * ___
> *
> * / \
> *
> * [ABORT]
> *
> * \___/ CPASSERT failed
> *
> * |
> *
> * O/|
> *
> * /| |
> *
> * / \
> motion/integrator.F:1541 *
> *******************************************************************************
>
>
>
> ===== Routine Calling Stack =====
>
> 3 velocity_verlet
> 2 qs_mol_dyn_low
> 1 CP2K
>
>
>
>
> The relevant part of the TRAVIS generated input is the following:
>
> &MOTION
> &MD
> ENSEMBLE REFTRAJ
> STEPS 2000
> TIMESTEP 0.500000
> &REFTRAJ
> EVAL_ENERGY_FORCES
> TRAJ_FILE_NAME polarizability_reftraj.xyz
> LAST_SNAPSHOT 2001
> STRIDE 1
> &END REFTRAJ
> &END MD
> &PRINT
> &RESTART
> &EACH
> MD 1
> &END EACH
> &END RESTART
> &END PRINT
> &END MOTION
>
> THANKS
>
> Ion
>
>
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