RAMAN spectrum from AIMD

ION SUCH

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Nov 17, 2017, 6:33:13 AM11/17/17

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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

nju...@gmail.com

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Dec 4, 2017, 10:06:36 AM12/4/17

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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：

hut...@chem.uzh.ch

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Dec 4, 2017, 10:17:28 AM12/4/17

to cp...@googlegroups.com

Hi

the code stops because the number of particles in the input
file and the number of particles read from the reference
trajectory are not the same (line 1541 in motion/integrator.F)

Please check your settings (input file and reference trajectory).
For further help we would need more information on the different
steps of your simulation.

regards

Juerg
--------------------------------------------------------------
Juerg Hutter Phone : ++41 44 635 4491
Institut für Chemie C FAX : ++41 44 635 6838
Universität Zürich E-mail: hut...@chem.uzh.ch
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
---------------------------------------------------------------

-----cp...@googlegroups.com wrote: -----To: cp2k <cp...@googlegroups.com>
From: nju...@gmail.com
Sent by: cp...@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:
&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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hut...@chem.uzh.ch

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Dec 5, 2017, 1:32:44 AM12/5/17

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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...@chem.uzh.ch
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
---------------------------------------------------------------

-----cp...@googlegroups.com wrote: -----
To: cp2k <cp...@googlegroups.com>
From: nju...@gmail.com
Sent by: cp...@googlegroups.com
Date: 12/04/2017 04:06PM
Subject: [CP2K:9772] Re: RAMAN spectrum from AIMD

ION SUCH

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Dec 5, 2017, 2:52:00 AM12/5/17

to cp2k

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

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