Hi, Can you please check my bond.xml file? if everything is correct there.
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 >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > -- >>>> > Join us on Slack: https://join.slack.com/t/votca/signup >>>> > --- >>>> > You received this message because you are subscribed to the Google >>>> Groups "votca" group. >>>> > To unsubscribe from this group and stop receiving emails from it, >>>> send an email to [email protected]. >>>> > To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/votca/f13d79c3-fcf7-4f7d-b608-01546106f1b2n%40googlegroups.com >>>> . >>>> >>>> >>>> >>>> -- >>>> Christoph Junghans >>>> Web: http://www.compphys.de >>>> >>>> -- >>>> Join us on Slack: https://join.slack.com/t/votca/signup >>>> --- >>>> You received this message because you are subscribed to the Google >>>> Groups "votca" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/votca/CAHG27e4TebU%3D%3DCC9CcWuTs_B-Tt7-c83P9F5nagM%2BiX5cAU3fA%40mail.gmail.com >>>> . >>>> >>> >>> >>> -- >>> *Sanjeet Kumar Singh* >>> >>> *Postdoctoral Fellow* >>> >>> *LPCM Lab.* >>> *University De Sherbrooke* >>> *Sherbrooke, Canada.* >>> >>> -- >>> Join us on Slack: https://join.slack.com/t/votca/signup >>> --- >>> You received this message because you are subscribed to the Google >>> Groups "votca" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> >> 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 >> > -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. 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