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?
I am attaching my bond.xml file here.
Can you please help me with this.
Thank you.
Sanjeet
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<cg>
<bonded>
<!-- name of the interaction -->
<name>bond-AB</name>
<min>0</min>
<max>1.0</max>
<step>0.001</step>
</bonded>
<inverse>
<program> lammps </program>
<lammps>
<!-- name of the table for lammps run -->
<table>CG-BOND-AB.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.20</table_begin>
<table_bins>0.001</table_bins>
</lammps>
</inverse>
</cg>
