On Sat, Sep 10, 2022 at 10:23 AM Sanjeet Singh <[email protected]> wrote:
> Hi,
>
> Can you please check my bond.xml file? if everything is correct there.
>
Sorry the entry VOTCA is looking for inverse.lammps.table_bins, and you
(and I in my example) missed the <inverse> indentation of the block, try:
<bond>
<name>foo</name>
<inverse>
<lammps>
<table_bins>0.01</table_bins>
</lammps>
</inverse>
</bond>
Also if you set table_begin, table_bins and table_end to the same values as
min, step and max respectively, it is kind of pointless to set them.
Christoph
>
> On Saturday, September 10, 2022 at 12:13:56 PM UTC-4 Sanjeet Singh wrote:
>
>> 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
>>>>>
>>>>> --
>>>>> Join us on Slack: https://join.slack.com/t/votca/signup
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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
>>>> https://groups.google.com/d/msgid/votca/CABgeOec4V5xTeZ0vwNvzLNdKYp-SDzoCH-XEcgML729As5-NnA%40mail.gmail.com
>>>> <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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--
Christoph Junghans
Web: http://www.compphys.de
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