Hi Christoph, I have moved my <lammps> block inside the <bond> block. But again, i am getting the following error.
ERROR:
#
# csg_get_interaction_property: Could not get 'max' for interaction with
name 'bond-AB' from bond.xml and no default was found in
/usr/share/votca/xml/csg_defaults.xml #
# Details can be found above
And, if i am setting the min, max, and step value, as shown in my bond.xml
file, THEN the <lammps> block is not read again, and i am getting the
following error.
ERROR:
#
# do_external: subscript
#
# /usr/share/votca/scripts/inverse/table_to_tab.pl --header lammps --type
bond input_bond-AB.pot.shift.dq5Vy input_bond-AB.pot.deriv.JWRcY
./table/table_AB.xvg #
# (from tags convert_potential tab) failed
#
# Details can be found above
I am attaching all my files here for your reference.
On Friday, September 9, 2022 at 10:42:55 PM UTC-4 Christoph Junghans wrote:
> On Fri, Sep 9, 2022 at 7:01 PM Sanjeet Singh <[email protected]> wrote:
>
>> Hi Christoph,
>>
>> Thank you for your prompt response. Actually, i am not able to understand
>> the following lines:
>>
>> csg_get_interaction_property: No value for 'inverse.lammps.table_bins'
>> found in bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
>> csg_get_interaction_property: returning emtpy value for
>> 'inverse.lammps.table_bins'
>> csg_get_interaction_property: No value for 'inverse.lammps.table_begin'
>> found in bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
>> csg_get_interaction_property: returning emtpy value for
>> 'inverse.lammps.table_begin'
>>
>
>
>>
>> I have given the values of table_bins, table_begin, in my bond.xml file.
>> But, i don't think csg_call is reading these values from there. And same is
>> the case for lammps.scale and lammps.y_scale. Why csg_call is taking the
>> default values, if the values for these parameters are already given in
>> bond.xml file.
>>
>
> The table properties etc are an per-interaction property (hence the line
> with csg_get_interaction_property instead of csg_get_property)
> So for VOTCA to read it you will have to move that part of the <lammps>
> block inside the <bond> block, e.g.
> <bond>
> <name>foo</name>
> <lammps>
> <table_bins>0.01</table_bins>
> </lammps>
> </bond>
>
>
>
>>
>> And furthermore, what is the meaning of scriptpath in the following lines.
>>
>> csg_get_property: No value for 'cg.inverse.scriptpath' found in bond.xml,
>> trying /usr/share/votca/xml/csg_defaults.xml
>> csg_get_property: returning emtpy value for 'cg.inverse.scriptpath'
>>
> VOTCA has the option to use user-provided scripts, e.g. you can use your
> own custom interpolation script, and the script path would be the place
> where you would put them.
> For standard usage, this is ok to be empty.
>
> Christoph
>
>>
>> Thank you.
>>
>> Sanjeet
>>
>>
>>
>> On Fri, Sep 9, 2022 at 6:34 PM Christoph Junghans <[email protected]>
>> wrote:
>>
>>> On Fri, Sep 9, 2022 at 1:06 PM Sanjeet Singh <[email protected]> wrote:
>>> >
>>> > Hi Christoph,
>>> >
>>> > I am trying to convert the bonded potential to LAMMPS table. For this,
>>> i am using the following command:
>>> >
>>> > csg_call --ia-type bond --ia-name bond-AB --options bond.xml
>>> convert_potential lammps --clean input_bond-AB.pot table_AB.xvg
>>> >
>>> > I am able to get the final output file table_AB.xvg.
>>> >
>>> > But, i am not able to understand the following lines on TERMINAL.
>>> >
>>> > csg_get_property: No value for 'cg.inverse.scriptpath' found in
>>> bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
>>> > csg_get_property: returning emtpy value for 'cg.inverse.scriptpath'
>>> > We are using Sim Program: lammps
>>> > Running subscript 'potential_to_lammps.sh --clean input_bond-AB.pot
>>> ./TABLE/table_AB.xvg' (from tags convert_potential lammps) dir
>>> /usr/share/votca/scripts/inverse
>>> > Convert input_bond-AB.pot to ./TABLE/table_AB.xvg
>>> > csg_get_interaction_property: No value for 'inverse.lammps.table_bins'
>>> found in bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
>>> > csg_get_interaction_property: returning emtpy value for
>>> 'inverse.lammps.table_bins'
>>> > csg_get_interaction_property: No value for
>>> 'inverse.lammps.table_begin' found in bond.xml, trying
>>> /usr/share/votca/xml/csg_defaults.xml
>>> > csg_get_interaction_property: returning emtpy value for
>>> 'inverse.lammps.table_begin'
>>> > csg_get_interaction_property: No value for 'inverse.lammps.table_end'
>>> found in bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
>>> > csg_get_interaction_property: returning emtpy value for
>>> 'inverse.lammps.table_end'
>>> > csg_get_interaction_property: No value for 'inverse.lammps.scale'
>>> found in bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
>>> > csg_get_interaction_property: value for 'inverse.lammps.scale' from
>>> /usr/share/votca/xml/csg_defaults.xml: 1
>>> > csg_get_interaction_property: No value for 'inverse.lammps.y_scale'
>>> found in bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
>>> > csg_get_interaction_property: value for 'inverse.lammps.y_scale' from
>>> /usr/share/votca/xml/csg_defaults.xml: 1
>>> > Running critical command 'mktemp input_bond-AB.pot.smooth.XXXXX'
>>> > Running critical command 'csg_resample --in input_bond-AB.pot --out
>>> input_bond-AB.pot.smooth.I7rqa --grid 0:0.001:1.0'
>>> > Running critical command 'mktemp input_bond-AB.pot.extrapol.XXXXX'
>>> > csg_get_interaction_property: No value for
>>> 'inverse.lammps.table_left_extrapolation' found in bond.xml, trying
>>> /usr/share/votca/xml/csg_defaults.xml
>>> > csg_get_interaction_property: returning emtpy value for
>>> 'inverse.lammps.table_left_extrapolation'
>>> > csg_get_interaction_property: No value for
>>> 'inverse.lammps.table_right_extrapolation' found in bond.xml, trying
>>> /usr/share/votca/xml/csg_defaults.xml
>>> > csg_get_interaction_property: returning emtpy value for
>>> 'inverse.lammps.table_right_extrapolation'
>>> > Running subscript 'potential_extrapolate.sh --clean --type bond
>>> input_bond-AB.pot.smooth.I7rqa input_bond-AB.pot.extrapol.IjNh9' (from tags
>>> potential extrapolate) dir /usr/share/votca/scripts/inverse
>>> > Extrapolate input_bond-AB.pot.smooth.I7rqa to
>>> input_bond-AB.pot.extrapol.IjNh9
>>> > Running critical command 'mktemp
>>> input_bond-AB.pot.smooth.I7rqa.onlyleft.XXXXX'
>>> > Running subscript 'table_extrapolate.pl --function linear --avgpoints
>>> 3 --region left input_bond-AB.pot.smooth.I7rqa
>>> input_bond-AB.pot.smooth.I7rqa.onlyleft.FDhHj' (from tags table
>>> extrapolate) dir /usr/share/votca/scripts/inverse
>>> > table_extrapolate.pl: extrapolating the left using linear with
>>> gradient -2509.86163466666
>>> > Running subscript 'table_extrapolate.pl --function linear --avgpoints
>>> 3 --region right input_bond-AB.pot.smooth.I7rqa.onlyleft.FDhHj
>>> input_bond-AB.pot.extrapol.IjNh9' (from tags table extrapolate) dir
>>> /usr/share/votca/scripts/inverse
>>> > table_extrapolate.pl: extrapolating the right using linear with
>>> gradient 2241.54540033333
>>> > Running critical command 'mktemp input_bond-AB.pot.interpol.XXXXX'
>>> > Running critical command 'mktemp input_bond-AB.pot.deriv.XXXXX'
>>> > Running critical command 'csg_resample --in
>>> input_bond-AB.pot.extrapol.IjNh9 --out input_bond-AB.pot.interpol.LyEum
>>> --grid 0:0.001:1.0 --der input_bond-AB.pot.deriv.TAbSL --comment Created on
>>> Fri Sep 9 03:02:09 PM EDT 2022 by sanjeetsingh@fedora
>>> > called from potential_to_lammps.sh, version 2022-dev
>>> > settings file:
>>> '/home/sanjeetsingh/Documents/SANJEET-PEO/PEO-TRIAL/MAPPING-TRIAL/RDF-GENERATION/BONDED-POTENTIAL/bond.xml'
>>> > working directory:
>>> /home/sanjeetsingh/Documents/SANJEET-PEO/PEO-TRIAL/MAPPING-TRIAL/RDF-GENERATION/BONDED-POTENTIAL'
>>> > Running critical command 'mktemp input_bond-AB.pot.shift.XXXXX'
>>> > Running subscript 'potential_shift.pl --type bond
>>> input_bond-AB.pot.interpol.LyEum input_bond-AB.pot.shift.moz4C' (from tags
>>> potential shift) dir /usr/share/votca/scripts/inverse
>>> > Running subscript 'table_to_tab.pl --header lammps --type bond
>>> input_bond-AB.pot.shift.moz4C input_bond-AB.pot.deriv.TAbSL
>>> ./TABLE/table_AB.xvg' (from tags convert_potential tab) dir
>>> /usr/share/votca/scripts/inverse
>>> >
>>> > I mean, am i doing any mistake?
>>> Is there an error? I don't see any error message above.
>>> Just have a look at table_AB.xvg. The output above is mainly, so you
>>> can see all the sub steps that have done.
>>>
>>> In short lines starting with "csg_get_interaction_property" read
>>> values from your xml file (or use the default if empty)
>>> Line with "Running subscript .." run a sub step e.g. interpolation,
>>> extrapolation
>>>
>>> Christoph
>>>
>>> >
>>> > I am attaching my bond.xml file here.
>>> >
>>> > Can you please help me with this.
>>> >
>>> > Thank you.
>>> >
>>> > Sanjeet
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
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>>> .
>>>
>>>
>>>
>>> --
>>> Christoph Junghans
>>> Web: http://www.compphys.de
>>>
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>>> .
>>>
>>
>>
>> --
>> *Sanjeet Kumar Singh*
>>
>> *Postdoctoral Fellow*
>>
>> *LPCM Lab.*
>> *University De Sherbrooke*
>> *Sherbrooke, Canada.*
>>
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> To view this discussion on the web visit
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>>
>> <https://groups.google.com/d/msgid/votca/CABgeOec4V5xTeZ0vwNvzLNdKYp-SDzoCH-XEcgML729As5-NnA%40mail.gmail.com?utm_medium=email&utm_source=footer>
>> .
>>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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<cg>
<bonded>
<!-- name of the interaction -->
<name>bond-AB</name>
<min>0.20</min>
<max>0.361</max>
<step>0.001</step>
<lammps>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.20</table_begin>
<table_end>0.361</table_end>
<table_bins>0.001</table_bins>
</lammps>
</bonded>
<inverse>
<program> lammps </program>
<lammps>
<!-- name of the table for lammps run -->
<table>CG-BOND-AB.pot</table>
</lammps>
</inverse>
</cg>
input_bond-AB.pot
Description: MS-Powerpoint presentation
