Using DTFD3(BJ) for molecular dynamics

Richard Edwards

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Aug 10, 2016, 3:08:20 PM8/10/16

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Hello,

I have been working with small (20-40 atom) quantum dots and am trying to see at what temperature the conformation is stable. Without including dispersion forces the structures were stable above 300K but with DFTD3 the structure began to break at much lower temperatures ~125K. To get a more accurate idea of the working temperature I attempted to use DFTD3(BJ) however when I used the parameters retrieved from the cp2k manual site and the following input code section:

&XC_FUNCTIONAL PBE

&END XC_FUNCTIONAL

&VDW_POTENTIAL

POTENTIAL_TYPE PAIR_POTENTIAL

&PAIR_POTENTIAL

TYPE DFTD3(BJ)

REFERENCE_FUNCTIONAL PBE

PARAMETER_FILE_NAME /bg01/homescinet/i/ihamilto/edwa3980/DFTD3BJ_Parameters/reference.dat

R_CUTOFF 15

&END

I got the following output file:

*****************************************************************************

*** 14:56:52 ERRORL2 in input_enumeration_types:enum_c2i :: invalid value ***

*** for enumeration:DFTD3(BJ) ***

*****************************************************************************

*** 14:56:52 ERRORL2 in input_enumeration_types:enum_c2i :: invalid value ***

*** for enumeration2:DFTD3(BJ) ***

*****************************************************************************

Looking for words in the input similar to the unknown:

'DFTD3(BJ)'

enum DFTD2 in section %__ROOT__%FORCE_EVAL%DFT%TDDFPT%XC%VDW_POTENTIAL%PAIR_POTENTIAL for keyword TYPE

enum DFTD3 in section %__ROOT__%FORCE_EVAL%DFT%TDDFPT%XC%VDW_POTENTIAL%PAIR_POTENTIAL for keyword TYPE

enum DFTD2 in section %__ROOT__%FORCE_EVAL%DFT%XC%VDW_POTENTIAL%PAIR_POTENTIAL for keyword TYPE

enum DFTD3 in section %__ROOT__%FORCE_EVAL%DFT%XC%VDW_POTENTIAL%PAIR_POTENTIAL for keyword TYPE

enum DFTD2 in section %__ROOT__%FORCE_EVAL%PROPERTIES%LINRES%EPR%PRINT%G_TENSOR%XC%VDW_POTENTIAL%PAIR_POTENTIAL for keyword TYPE

enum DFTD3 in section %__ROOT__%FORCE_EVAL%PROPERTIES%LINRES%EPR%PRINT%G_TENSOR%XC%VDW_POTENTIAL%PAIR_POTENTIAL for keyword TYPE

enum DFTD2 in section %__ROOT__%ATOM%METHOD%XC%VDW_POTENTIAL%PAIR_POTENTIAL for keyword TYPE

enum DFTD3 in section %__ROOT__%ATOM%METHOD%XC%VDW_POTENTIAL%PAIR_POTENTIAL for keyword TYPE

subsection DFT in section %__ROOT__%FORCE_EVAL

enum DFTB in section %__ROOT__%FORCE_EVAL%DFT%QS for keyword METHOD

subsection DFTB in section %__ROOT__%FORCE_EVAL%DFT%QS

CP2K failed to parse the input file.

A full description of the input for this CP2K version

can be generated using:

cp2k.sopt --html-manual

The manual for the latest version of CP2K is online available:

http://manual.cp2k.org/trunk

If this input was an input of a previous version

of CP2K, you can try to convert it with --permissive-echo.

However, this will just ignore the unknown keywords ...

CP2K| Abnormal program termination, stopped by process number 0

Does anyone know why it does not seem to recognize the DFTD3BJ type command? Or has anyone set up these calculations that can provide any insight to help me run these.

Thanks, Richard Edwards

Iain Bethune

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Aug 11, 2016, 1:41:14 AM8/11/16

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The DFTD3(BJ) option was added in CP2K 2.6 - which version are you using?

- Iain

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Email: ibet...@epcc.ed.ac.uk
Twitter: @IainBethune @PrimeGrid @CP2Kproject
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Richard Edwards

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Aug 11, 2016, 10:49:09 AM8/11/16

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Yes thank you. The server I was using had the default set to use version 2.4 but 3.0 is available to use with some permissions. I will try to use this and post again if I have an issues.

Thanks again, Richard Edwards

Richard Edwards

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Aug 24, 2016, 10:16:49 AM8/24/16

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Hello,

There was some problems regarding having cp2k version 3 working however now I am having different problems running the dtfd3bj jobs. I have download the files from http://www.thch.uni-bonn.de/tc/downloads/DFT-D3/functionalsbj.html to use these parameters however I am not sure what to put in the code as the actual parameter_file_name as the download is a zip file containing many coord files and a reference.dat that is a fortram program. When I attempted to use the reference file as the parameter file an error that the file could not be found.

Does anyone who's used bj damping know how this parameter file works or has an alternate parameter file I could use with the PBE functional?

Thanks, Richard Edwards

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hut...@chem.uzh.ch

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Aug 24, 2016, 10:38:26 AM8/24/16

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Hi

you can used the same data file for both types of damping,
original and BJ. The file is provided with the CP2K distribution
in the data directoty.

&vdW_POTENTIAL
DISPERSION_FUNCTIONAL PAIR_POTENTIAL
&PAIR_POTENTIAL
TYPE DFTD3(BJ)
CALCULATE_C9_TERM .TRUE.
REFERENCE_C9_TERM .TRUE.
LONG_RANGE_CORRECTION .TRUE.
PARAMETER_FILE_NAME dftd3.dat
REFERENCE_FUNCTIONAL PBE
R_CUTOFF 15.
&END PAIR_POTENTIAL
&END vdW_POTENTIAL

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: cp...@googlegroups.com
From: Richard Edwards
Sent by: cp...@googlegroups.com
Date: 08/24/2016 04:16PM
Subject: Re: [CP2K:8094] Re: Using DTFD3(BJ) for molecular dynamics

Hello,
There was some problems regarding having cp2k version 3 working however now I am having different problems running the dtfd3bj jobs. I have download the files from http://www.thch.uni-bonn.de/tc/downloads/DFT-D3/functionalsbj.html to use these parameters however I am not sure what to put in the code as the actual parameter_file_name as the download is a zip file containing many coord files and a reference.dat that is a fortram program. When I attempted to use the reference file as the parameter file an error that the file could not be found.
Does anyone who's used bj damping know how this parameter file works or has an alternate parameter file I could use with the PBE functional?
Thanks, Richard Edwards
On Thu, Aug 11, 2016 at 10:49 AM, Richard Edwards <edwa...@gmail.com> wrote:
Yes thank you. The server I was using had the default set to use version 2.4 but 3.0 is available to use with some permissions. I will try to use this and post again if I have an issues.
Thanks again, Richard Edwards

On Wednesday, August 10, 2016 at 3:08:20 PM UTC-4, Richard Edwards wrote:Hello,
I have been working with small (20-40 atom) quantum dots and am trying to see at what temperature the conformation is stable. Without including dispersion forces the structures were stable above 300K but with DFTD3 the structure began to break at much lower temperatures ~125K. To get a more accurate idea of the working temperature I attempted to use DFTD3(BJ) however when I used the parameters retrieved from the cp2k manual site and the following input code section:

&XC_FUNCTIONAL PBE &END XC_FUNCTIONAL &VDW_POTENTIAL POTENTIAL_TYPE PAIR_POTENTIAL &PAIR_POTENTIAL TYPE DFTD3(BJ) REFERENCE_FUNCTIONAL PBE PARAMETER_FILE_NAME /bg01/homescinet/i/ihamilto/edwa3980/DFTD3BJ_Parameters/reference.dat R_CUTOFF 15 &END &ENDI got the following output file:

***************************************************************************** *** 14:56:52 ERRORL2 in input_enumeration_types:enum_c2i :: invalid value *** *** for enumeration:DFTD3(BJ) *** *****************************************************************************

***************************************************************************** *** 14:56:52 ERRORL2 in input_enumeration_types:enum_c2i :: invalid value *** *** for enumeration2:DFTD3(BJ) *** *****************************************************************************
Looking for words in the input similar to the unknown: 'DFTD3(BJ)' enum DFTD2 in section %__ROOT__%FORCE_EVAL%DFT%TDDFPT%XC%VDW_POTENTIAL%PAIR_POTENTIAL for keyword TYPE enum DFTD3 in section %__ROOT__%FORCE_EVAL%DFT%TDDFPT%XC%VDW_POTENTIAL%PAIR_POTENTIAL for keyword TYPE enum DFTD2 in section %__ROOT__%FORCE_EVAL%DFT%XC%VDW_POTENTIAL%PAIR_POTENTIAL for keyword TYPE enum DFTD3 in section %__ROOT__%FORCE_EVAL%DFT%XC%VDW_POTENTIAL%PAIR_POTENTIAL for keyword TYPE enum DFTD2 in section %__ROOT__%FORCE_EVAL%PROPERTIES%LINRES%EPR%PRINT%G_TENSOR%XC%VDW_POTENTIAL%PAIR_POTENTIAL for keyword TYPE enum DFTD3 in section %__ROOT__%FORCE_EVAL%PROPERTIES%LINRES%EPR%PRINT%G_TENSOR%XC%VDW_POTENTIAL%PAIR_POTENTIAL for keyword TYPE enum DFTD2 in section %__ROOT__%ATOM%METHOD%XC%VDW_POTENTIAL%PAIR_POTENTIAL for keyword TYPE enum DFTD3 in section %__ROOT__%ATOM%METHOD%XC%VDW_POTENTIAL%PAIR_POTENTIAL for keyword TYPE subsection DFT in section %__ROOT__%FORCE_EVAL enum DFTB in section %__ROOT__%FORCE_EVAL%DFT%QS for keyword METHOD subsection DFTB in section %__ROOT__%FORCE_EVAL%DFT%QS CP2K failed to parse the input file. A full description of the input for this CP2K version can be generated using: cp2k.sopt --html-manual The manual for the latest version of CP2K is online available: http://manual.cp2k.org/trunk If this input was an input of a previous version of CP2K, you can try to convert it with --permissive-echo. However, this will just ignore the unknown keywords ... CP2K| Abnormal program termination, stopped by process number 0
Does anyone know why it does not seem to recognize the DFTD3BJ type command? Or has anyone set up these calculations that can provide any insight to help me run these.
Thanks, Richard Edwards

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Richard Edwards

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Aug 30, 2016, 1:45:30 PM8/30/16

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Hello,

Sorry I just noticed I did not reply. It is working perfefctly now. Thank you very much for your help.

Richard Edwards

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