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.
