[CP2K:9772] Re: RAMAN spectrum from AIMD

hut... at chem.uzh.ch hut... at chem.uzh.ch
Tue Dec 5 06:32:37 UTC 2017


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.


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
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland

-----cp... at googlegroups.com wrote: -----
To: cp2k <cp... at googlegroups.com>
From: nju... at gmail.com
Sent by: cp... at googlegroups.com
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: 

  STEPS 2000
  TIMESTEP 0.500000
   TRAJ_FILE_NAME polarizability_reftraj.xyz
    STRIDE 1
    MD 1



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