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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>
--
Christoph Junghans
Web: http://www.compphys.de
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