Hello Christoph,
I hope you are doing well!
I have a query regarding the Iterative Boltzmann Inversion Method.
Actually, I am trying to perform IBI for a polymer for non-bonded
interactions only. I have already got my bonded potential using Simple
Boltzmann Inversion. So here when I am running the following command:
csg_inverse --options settings.xml
I am getting the following error:
ERROR:
# do_external: subscript
# /usr/share/votca/scripts/inverse/run_genericsim.sh
# (from tags run lammps) failed
# For details see the logfile
/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/inverse.log #
Can you please help me with this?
I am also attaching the inverse.log and settings.xml file for your
reference.
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For a more verbose log see: inverse.log
csg_get_property: No value for 'cg.inverse.mpi.tasks' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.mpi.tasks'
csg_get_property: No value for 'cg.inverse.mpi.cmd' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.mpi.cmd'
csg_get_property: No value for 'cg.inverse.parallel.tasks' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.parallel.tasks'
csg_get_property: No value for 'cg.inverse.parallel.cmd' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.parallel.cmd'
csg_get_property: No value for 'cg.inverse.gromacs.mdrun.bin' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.gromacs.mdrun.bin'
csg_get_property: No value for 'cg.inverse.espresso.bin' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.espresso.bin'
csg_get_property: No value for 'cg.inverse.scriptdir' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.scriptdir'
csg_get_property: No value for 'cg.inverse.gromacs.grompp.topol' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.gromacs.grompp.topol'
csg_get_property: No value for 'cg.inverse.gromacs.grompp.index' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.gromacs.grompp.index'
csg_get_property: No value for 'cg.inverse.gromacs.g_rdf.topol' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.gromacs.g_rdf.topol'
csg_get_property: No value for 'cg.inverse.convergence_check' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.convergence_check'
csg_get_property: No value for 'cg.inverse.convergence_check_options.name_glob' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.convergence_check_options.name_glob'
csg_get_property: No value for 'cg.inverse.convergence_check_options.limit' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.convergence_check_options.limit'
csg_get_property: No value for 'cg.inverse.espresso.table_end' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.espresso.table_end'
csg_get_property: No value for 'cg.inverse.gromacs.traj_type' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.gromacs.traj_type'
csg_get_property: No value for 'cg.inverse.gromacs.topol_out' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.gromacs.topol_out'
csg_get_property: No value for 'cg.inverse.espresso.blockfile' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.espresso.blockfile'
csg_get_property: No value for 'cg.inverse.espresso.blockfile_out' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.espresso.blockfile_out'
csg_get_property: No value for 'cg.inverse.espresso.n_steps' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.espresso.n_steps'
csg_get_property: No value for 'cg.inverse.espresso.exclusions' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.espresso.exclusions'
csg_get_property: No value for 'cg.inverse.espresso.debug' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.espresso.debug'
csg_get_property: No value for 'cg.inverse.espresso.n_snapshots' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.espresso.n_snapshots'
csg_get_property: No value for 'cg.non-bonded.inverse.espresso.index1' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.inverse.espresso.index1'
csg_get_property: No value for 'cg.non-bonded.inverse.espresso.index2' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.inverse.espresso.index2'
csg_get_property: No value for 'cg.inverse.espresso.success' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.espresso.success'
csg_get_property: No value for 'cg.inverse.espresso.scriptdir' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.espresso.scriptdir'
csg_get_property: No value for 'cg.non-bonded.inverse.post_update_options.kbibi.type' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.inverse.post_update_options.kbibi.type'
csg_get_property: No value for 'cg.inverse.imc.numpy.bin' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.imc.numpy.bin'
csg_get_property: No value for 'cg.inverse.imc.octave.bin' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.imc.octave.bin'
csg_get_property: No value for 'cg.inverse.imc.matlab.bin' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.imc.matlab.bin'
csg_get_property: No value for 'cg.inverse.imc.solver' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.imc.solver'
csg_get_property: No value for 'cg.non-bonded.inverse.imc.reg' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.inverse.imc.reg'
Sim started Fri Oct 28 12:17:57 PM EDT 2022
We are doing Method: ibi
csg_get_property: No value for 'cg.inverse.scriptpath' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.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
#The order in which scripts get called
#CSGSHARE is /usr/share/votca/scripts/inverse
#From: /usr/share/votca/scripts/inverse/csg_table
tag file tag_file.sh
dummy dummy dummy.sh
functions common functions_common.sh
csg master inverse.sh
prepare ibi prepare_generic.sh
prepare iie prepare_iie.sh
prepare imc prepare_imc.sh
prepare generic prepare_generic.sh
prepare optimizer prepare_optimizer.sh
prepare re prepare_re.sh
prepare_single ibi prepare_generic_single.sh
prepare_single imc prepare_generic_single.sh
prepare_single generic prepare_generic_single.sh
prepare_single optimizer prepare_optimizer_single.sh
initstep ibi initialize_step_generic.sh
initstep iie initialize_step_generic.sh
initstep imc initialize_step_generic.sh
initstep optimizer initialize_step_optimizer.sh
initstep re initialize_step_re.sh
add_pot ibi add_pot_generic.sh
add_pot iie add_pot_generic.sh
add_pot imc add_pot_generic.sh
add_pot optimizer dummy.sh
add_pot re dummy.sh
pre_update ibi dummy.sh
pre_update iie dummy.sh
pre_update imc dummy.sh
pre_update optimizer dummy.sh
pre_update re pre_update_re.sh
post_update ibi post_update_generic.sh
post_update iie post_update_generic.sh
post_update imc post_update_generic.sh
post_update optimizer dummy.sh
post_update re post_update_generic.sh
post_update_single ibi post_update_generic_single.sh
post_update_single iie post_update_generic_single.sh
post_update_single imc post_update_generic_single.sh
post_update_single re post_update_re_single.sh
postupd scale postupd_scale.sh
postupd pressure postupd_pressure.sh
postupd lj postupd_addlj.sh
postupd splinesmooth postupd_splinesmooth.sh
postupd smooth postupd_smooth.sh
postupd shift postadd_shift.sh
postupd dummy postadd_dummy.sh
postupd tag tag_file.sh
postupd extrapolate postupd_extrapolate.sh
postupd kbibi postupd_kbibi_correction.sh
postupd cibi postupd_cibi_correction.sh
postupd ibi postupd_ibi.sh
post add post_add.sh
post add_single post_add_single.sh
postadd tag tag_file.sh
postadd dummy postadd_dummy.sh
postadd copyback postadd_copyback.sh
postadd compress postadd_compress.sh
postadd convergence postadd_convergence.sh
postadd acc_convergence postadd_acc_convergence.sh
postadd shift postadd_shift.sh
postadd overwrite postadd_overwrite.sh
postadd plot postadd_plot.sh
postadd average postadd_average.sh
postadd smooth_at_cut_off postadd_smooth_at_cut_off.sh
convergence_check default convergence_check_default.sh
resample target resample_target.sh
update ibi update_ibi.sh
update ibi_single update_ibi_single.sh
update ibi_pot update_ibi_pot.pl
update iie update_iie.sh
update iie_pot iie.py
dist invert_iie iie.py
rdf_incl_intra generic calc_rdf_generic.sh
update imc update_imc.sh
update imc_single update_imc_single.sh
optimizer prepare_state optimizer_prepare_state.sh
optimizer parameters_to_potential optimizer_parameters_to_potential.sh
optimizer state_to_potentials optimizer_state_to_potentials.sh
optimizer state_to_mapping optimizer_state_to_mapping.sh
update optimizer update_optimizer.sh
update optimizer_single update_optimizer_single.sh
optimizer_target rdf optimizer_target_rdf.sh
optimizer_target density optimizer_target_density.sh
optimizer_target pressure optimizer_target_pressure.sh
simplex precede_state simplex_downhill_processor.pl
cma precede_state cma_processor.py
update re update_re.sh
calc target_rdf calc_target_rdf_generic.sh
pressure_cor simple pressure_cor_simple.pl
pressure_cor wjk pressure_cor_wjk.pl
compute_lj 12_6 lj_126.pl
kbibi ramp_correction kbibi_ramp_correction.pl
calc kbint calc_kbint.sh
table add add_POT.pl
table integrate table_integrate.pl
table extrapolate table_extrapolate.pl
table merge merge_tables.pl
table smooth table_smooth.pl
table smooth_at_cut_off table_smooth_at_cut_off.py
table linearop table_linearop.pl
table dummy table_dummy.sh
table get_value table_get_value.pl
table switch_border table_switch_border.pl
table compare table_combine.pl --die --op =
table combine table_combine.pl
table average table_average.sh
table scale table_scale.pl
table change_flag table_change_flag.sh
table functional table_functional.sh
potential extrapolate potential_extrapolate.sh
potential shift potential_shift.pl
convert_potential tab table_to_tab.pl
dist adjust dist_adjust.pl
dist invert dist_boltzmann_invert.pl
tables jackknife tables_jackknife.pl
initstep gromacs initialize_step_genericsim.sh
run gromacs run_gromacs.sh
clean gromacs clean_generic.sh
presimulation gromacs run_gromacs.sh --pre
pressure gromacs calc_pressure_gromacs.sh
pressure lammps calc_pressure_lammps.sh
rdf gromacs calc_rdf_generic.sh
imc_stat gromacs imc_stat_generic.sh
density gromacs calc_density_generic.sh
convert_potential gromacs potential_to_gromacs.sh
convert_potentials gromacs potentials_to_generic.sh
convert_potential xvg table_to_xvg.pl
functions gromacs functions_gromacs.sh
initstep espresso initialize_step_genericsim.sh
run espresso run_genericsim.sh
clean espresso clean_generic.sh
rdf espresso calc_rdf_generic.sh
imc_stat espresso imc_stat_generic.sh
density espresso calc_density_generic.sh
convert_potential espresso potential_to_generic.sh
convert_potentials espresso potentials_to_generic.sh
functions espresso functions_genericsim.sh
convert_potential lammps potential_to_lammps.sh
convert_potentials lammps potentials_to_generic.sh
initstep lammps initialize_step_genericsim.sh
run lammps run_genericsim.sh
clean lammps clean_generic.sh
rdf lammps calc_rdf_generic.sh
imc_stat lammps imc_stat_generic.sh
density lammps calc_density_generic.sh
functions lammps functions_genericsim.sh
convert_potential espressopp potential_to_generic.sh
convert_potentials espressopp potentials_to_generic.sh
initstep espressopp initialize_step_genericsim.sh
run espressopp run_genericsim.sh
clean espressopp clean_generic.sh
rdf espressopp calc_rdf_generic.sh
imc_stat espressopp imc_stat_generic.sh
density espressopp calc_density_generic.sh
functions espressopp functions_genericsim.sh
initstep dlpoly initialize_step_genericsim.sh
run dlpoly run_genericsim.sh
clean dlpoly clean_generic.sh
rdf dlpoly calc_rdf_generic.sh
imc_stat dlpoly imc_stat_generic.sh
density dlpoly calc_density_generic.sh
functions dlpoly functions_dlpoly.sh
convert_potential dlpoly potential_to_dlpoly.sh
convert_potentials dlpoly potentials_to_dlpoly.sh
convert_potential hoomd-blue potential_to_generic.sh
convert_potentials hoomd-blue potentials_to_generic.sh
initstep hoomd-blue initialize_step_genericsim.sh
run hoomd-blue run_genericsim.sh
clean hoomd-blue clean_generic.sh
rdf hoomd-blue calc_rdf_generic.sh
imc_stat hoomd-blue imc_stat_generic.sh
density hoomd-blue calc_density_generic.sh
functions hoomd-blue functions_genericsim.sh
------------------------
Prepare (dir step_000)
------------------------
Running critical command 'pushd /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT'
~/PEO-CH3_END-572-COORDINATES-19OCT ~/PEO-CH3_END-572-COORDINATES-19OCT/step_000
cp_from_main_dir: 'PEO-CG-TOPOLOGY.data MY.in BOND-AB.pot BOND-BB.pot BOND-BC.pot ANGLE-ABB.pot ANGLE-BBB.pot ANGLE-BBC.pot DIHEDRAL-ABBB.pot DIHEDRAL-BBBB.pot DIHEDRAL-BBBC.pot'
Running critical command 'cp PEO-CG-TOPOLOGY.data MY.in BOND-AB.pot BOND-BB.pot BOND-BC.pot ANGLE-ABB.pot ANGLE-BBB.pot ANGLE-BBC.pot DIHEDRAL-ABBB.pot DIHEDRAL-BBBB.pot DIHEDRAL-BBBC.pot /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'popd'
~/PEO-CH3_END-572-COORDINATES-19OCT/step_000
Running subscript 'prepare_generic.sh' (from tags prepare ibi) dir /usr/share/votca/scripts/inverse
csg_get_property: No value for 'cg.bonded.name' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.bonded.name'
csg_get_property: No value for 'cg.bonded.min' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.bonded.min'
For all bonded
csg_get_property: No value for 'cg.bonded.name' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.bonded.name'
For all non-bonded
for_all: run 'do_external prepare_single ibi' for interaction named 'A-A'
Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi) dir /usr/share/votca/scripts/inverse
Using initial guess from dist A-A.dist.tgt for A-A
Running subscript 'resample_target.sh A-A.dist.tgt A-A.dist.tgt' (from tags resample target) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp A-A.dist.tgt_smooth.XXXXX'
Running critical command 'csg_resample --in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/A-A.dist.tgt --out A-A.dist.tgt_smooth.px9AG --grid 0.336:0.002:0.75 --comment Created on Fri Oct 28 12:17:57 PM EDT 2022 by sanjeetsingh@fedora
called from resample_target.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp A-A.dist.tgt_extrapolated.XXXXX'
Running critical command 'mktemp A-A.dist.tgt_extrapolated_left.XXXXX'
Running subscript 'table_extrapolate.pl --function linear --avgpoints 1 --region left A-A.dist.tgt_smooth.px9AG A-A.dist.tgt_extrapolated_left.QsxlT' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient -0.0295531490000001
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right A-A.dist.tgt_extrapolated_left.QsxlT A-A.dist.tgt_extrapolated.lhB4k' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running subscript 'dist_adjust.pl A-A.dist.tgt_extrapolated.lhB4k A-A.dist.tgt' (from tags dist adjust) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp A-A.pot.new.raw.XXX'
csg_get_property: No value for 'cg.inverse.dist_min' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.dist_min' from /usr/share/votca/xml/csg_defaults.xml: 1e-10
Running subscript 'dist_boltzmann_invert.pl --type non-bonded --kbT 2.49435 --min 1e-10 A-A.dist.tgt A-A.pot.new.raw.RjF' (from tags dist invert) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp A-A.pot.new.smooth.XXX'
Running critical command 'csg_resample --in A-A.pot.new.raw.RjF --out A-A.pot.new.smooth.OBL --grid 0.336:0.002:0.75 --comment Created on Fri Oct 28 12:17:57 PM EDT 2022 by sanjeetsingh@fedora
called from prepare_generic_single.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp A-A.pot.new.extrapolate.XXX'
Running subscript 'potential_extrapolate.sh --type non-bonded A-A.pot.new.smooth.OBL A-A.pot.new.extrapolate.OGS' (from tags potential extrapolate) dir /usr/share/votca/scripts/inverse
Extrapolate A-A.pot.new.smooth.OBL to A-A.pot.new.extrapolate.OGS
Running critical command 'mktemp A-A.pot.new.smooth.OBL.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left A-A.pot.new.smooth.OBL A-A.pot.new.smooth.OBL.onlyleft.wWDgn' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient 14.7162716666666
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right A-A.pot.new.smooth.OBL.onlyleft.wWDgn A-A.pot.new.extrapolate.OGS' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running critical command 'mktemp A-A.pot.new.shifted.XXX'
Running subscript 'potential_shift.pl --type non-bonded A-A.pot.new.extrapolate.OGS A-A.pot.new.shifted.lTF' (from tags potential shift) dir /usr/share/votca/scripts/inverse
Running subscript 'table_change_flag.sh A-A.pot.new.shifted.lTF A-A.pot.new' (from tags table change_flag) dir /usr/share/votca/scripts/inverse
Running critical command 'sed -e s/o$/i/ A-A.pot.new.shifted.lTF'
for_all: run 'do_external prepare_single ibi' for interaction named 'B-B'
Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi) dir /usr/share/votca/scripts/inverse
Using initial guess from dist B-B.dist.tgt for B-B
Running subscript 'resample_target.sh B-B.dist.tgt B-B.dist.tgt' (from tags resample target) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp B-B.dist.tgt_smooth.XXXXX'
Running critical command 'csg_resample --in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/B-B.dist.tgt --out B-B.dist.tgt_smooth.hcEhI --grid 0.3:0.002:0.75 --comment Created on Fri Oct 28 12:17:58 PM EDT 2022 by sanjeetsingh@fedora
called from resample_target.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp B-B.dist.tgt_extrapolated.XXXXX'
Running critical command 'mktemp B-B.dist.tgt_extrapolated_left.XXXXX'
Running subscript 'table_extrapolate.pl --function linear --avgpoints 1 --region left B-B.dist.tgt_smooth.hcEhI B-B.dist.tgt_extrapolated_left.dxHyD' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient 0.03771767325
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right B-B.dist.tgt_extrapolated_left.dxHyD B-B.dist.tgt_extrapolated.pUYnv' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running subscript 'dist_adjust.pl B-B.dist.tgt_extrapolated.pUYnv B-B.dist.tgt' (from tags dist adjust) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp B-B.pot.new.raw.XXX'
csg_get_property: No value for 'cg.inverse.dist_min' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.dist_min' from /usr/share/votca/xml/csg_defaults.xml: 1e-10
Running subscript 'dist_boltzmann_invert.pl --type non-bonded --kbT 2.49435 --min 1e-10 B-B.dist.tgt B-B.pot.new.raw.300' (from tags dist invert) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp B-B.pot.new.smooth.XXX'
Running critical command 'csg_resample --in B-B.pot.new.raw.300 --out B-B.pot.new.smooth.cIA --grid 0.3:0.002:0.75 --comment Created on Fri Oct 28 12:17:58 PM EDT 2022 by sanjeetsingh@fedora
called from prepare_generic_single.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp B-B.pot.new.extrapolate.XXX'
Running subscript 'potential_extrapolate.sh --type non-bonded B-B.pot.new.smooth.cIA B-B.pot.new.extrapolate.2s7' (from tags potential extrapolate) dir /usr/share/votca/scripts/inverse
Extrapolate B-B.pot.new.smooth.cIA to B-B.pot.new.extrapolate.2s7
Running critical command 'mktemp B-B.pot.new.smooth.cIA.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left B-B.pot.new.smooth.cIA B-B.pot.new.smooth.cIA.onlyleft.p2VNQ' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient -364.46013
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right B-B.pot.new.smooth.cIA.onlyleft.p2VNQ B-B.pot.new.extrapolate.2s7' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running critical command 'mktemp B-B.pot.new.shifted.XXX'
Running subscript 'potential_shift.pl --type non-bonded B-B.pot.new.extrapolate.2s7 B-B.pot.new.shifted.6U8' (from tags potential shift) dir /usr/share/votca/scripts/inverse
Running subscript 'table_change_flag.sh B-B.pot.new.shifted.6U8 B-B.pot.new' (from tags table change_flag) dir /usr/share/votca/scripts/inverse
Running critical command 'sed -e s/o$/i/ B-B.pot.new.shifted.6U8'
for_all: run 'do_external prepare_single ibi' for interaction named 'C-C'
Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi) dir /usr/share/votca/scripts/inverse
Using initial guess from dist C-C.dist.tgt for C-C
Running subscript 'resample_target.sh C-C.dist.tgt C-C.dist.tgt' (from tags resample target) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp C-C.dist.tgt_smooth.XXXXX'
Running critical command 'csg_resample --in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/C-C.dist.tgt --out C-C.dist.tgt_smooth.lgrK6 --grid 0.332:0.002:0.75 --comment Created on Fri Oct 28 12:17:58 PM EDT 2022 by sanjeetsingh@fedora
called from resample_target.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp C-C.dist.tgt_extrapolated.XXXXX'
Running critical command 'mktemp C-C.dist.tgt_extrapolated_left.XXXXX'
Running subscript 'table_extrapolate.pl --function linear --avgpoints 1 --region left C-C.dist.tgt_smooth.lgrK6 C-C.dist.tgt_extrapolated_left.1aEa7' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient -0.0245047840000002
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right C-C.dist.tgt_extrapolated_left.1aEa7 C-C.dist.tgt_extrapolated.jWZEI' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running subscript 'dist_adjust.pl C-C.dist.tgt_extrapolated.jWZEI C-C.dist.tgt' (from tags dist adjust) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp C-C.pot.new.raw.XXX'
csg_get_property: No value for 'cg.inverse.dist_min' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.dist_min' from /usr/share/votca/xml/csg_defaults.xml: 1e-10
Running subscript 'dist_boltzmann_invert.pl --type non-bonded --kbT 2.49435 --min 1e-10 C-C.dist.tgt C-C.pot.new.raw.NL1' (from tags dist invert) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp C-C.pot.new.smooth.XXX'
Running critical command 'csg_resample --in C-C.pot.new.raw.NL1 --out C-C.pot.new.smooth.cy6 --grid 0.332:0.002:0.75 --comment Created on Fri Oct 28 12:17:58 PM EDT 2022 by sanjeetsingh@fedora
called from prepare_generic_single.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp C-C.pot.new.extrapolate.XXX'
Running subscript 'potential_extrapolate.sh --type non-bonded C-C.pot.new.smooth.cy6 C-C.pot.new.extrapolate.rVq' (from tags potential extrapolate) dir /usr/share/votca/scripts/inverse
Extrapolate C-C.pot.new.smooth.cy6 to C-C.pot.new.extrapolate.rVq
Running critical command 'mktemp C-C.pot.new.smooth.cy6.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left C-C.pot.new.smooth.cy6 C-C.pot.new.smooth.cy6.onlyleft.xPvAA' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient -153.669986666667
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right C-C.pot.new.smooth.cy6.onlyleft.xPvAA C-C.pot.new.extrapolate.rVq' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running critical command 'mktemp C-C.pot.new.shifted.XXX'
Running subscript 'potential_shift.pl --type non-bonded C-C.pot.new.extrapolate.rVq C-C.pot.new.shifted.GLc' (from tags potential shift) dir /usr/share/votca/scripts/inverse
Running subscript 'table_change_flag.sh C-C.pot.new.shifted.GLc C-C.pot.new' (from tags table change_flag) dir /usr/share/votca/scripts/inverse
Running critical command 'sed -e s/o$/i/ C-C.pot.new.shifted.GLc'
for_all: run 'do_external prepare_single ibi' for interaction named 'A-B'
Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi) dir /usr/share/votca/scripts/inverse
Using initial guess from dist A-B.dist.tgt for A-B
Running subscript 'resample_target.sh A-B.dist.tgt A-B.dist.tgt' (from tags resample target) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp A-B.dist.tgt_smooth.XXXXX'
Running critical command 'csg_resample --in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/A-B.dist.tgt --out A-B.dist.tgt_smooth.RzG5R --grid 0.32:0.002:0.75 --comment Created on Fri Oct 28 12:17:59 PM EDT 2022 by sanjeetsingh@fedora
called from resample_target.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp A-B.dist.tgt_extrapolated.XXXXX'
Running critical command 'mktemp A-B.dist.tgt_extrapolated_left.XXXXX'
Running subscript 'table_extrapolate.pl --function linear --avgpoints 1 --region left A-B.dist.tgt_smooth.RzG5R A-B.dist.tgt_extrapolated_left.fvHm1' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient 0.666408923499999
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right A-B.dist.tgt_extrapolated_left.fvHm1 A-B.dist.tgt_extrapolated.urIdf' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running subscript 'dist_adjust.pl A-B.dist.tgt_extrapolated.urIdf A-B.dist.tgt' (from tags dist adjust) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp A-B.pot.new.raw.XXX'
csg_get_property: No value for 'cg.inverse.dist_min' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.dist_min' from /usr/share/votca/xml/csg_defaults.xml: 1e-10
Running subscript 'dist_boltzmann_invert.pl --type non-bonded --kbT 2.49435 --min 1e-10 A-B.dist.tgt A-B.pot.new.raw.Uqx' (from tags dist invert) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp A-B.pot.new.smooth.XXX'
Running critical command 'csg_resample --in A-B.pot.new.raw.Uqx --out A-B.pot.new.smooth.JqP --grid 0.32:0.002:0.75 --comment Created on Fri Oct 28 12:17:59 PM EDT 2022 by sanjeetsingh@fedora
called from prepare_generic_single.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp A-B.pot.new.extrapolate.XXX'
Running subscript 'potential_extrapolate.sh --type non-bonded A-B.pot.new.smooth.JqP A-B.pot.new.extrapolate.N9z' (from tags potential extrapolate) dir /usr/share/votca/scripts/inverse
Extrapolate A-B.pot.new.smooth.JqP to A-B.pot.new.extrapolate.N9z
Running critical command 'mktemp A-B.pot.new.smooth.JqP.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left A-B.pot.new.smooth.JqP A-B.pot.new.smooth.JqP.onlyleft.axeuh' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient -360.834658333333
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right A-B.pot.new.smooth.JqP.onlyleft.axeuh A-B.pot.new.extrapolate.N9z' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running critical command 'mktemp A-B.pot.new.shifted.XXX'
Running subscript 'potential_shift.pl --type non-bonded A-B.pot.new.extrapolate.N9z A-B.pot.new.shifted.JJb' (from tags potential shift) dir /usr/share/votca/scripts/inverse
Running subscript 'table_change_flag.sh A-B.pot.new.shifted.JJb A-B.pot.new' (from tags table change_flag) dir /usr/share/votca/scripts/inverse
Running critical command 'sed -e s/o$/i/ A-B.pot.new.shifted.JJb'
for_all: run 'do_external prepare_single ibi' for interaction named 'B-C'
Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi) dir /usr/share/votca/scripts/inverse
Using initial guess from dist B-C.dist.tgt for B-C
Running subscript 'resample_target.sh B-C.dist.tgt B-C.dist.tgt' (from tags resample target) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp B-C.dist.tgt_smooth.XXXXX'
Running critical command 'csg_resample --in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/B-C.dist.tgt --out B-C.dist.tgt_smooth.wNnmI --grid 0.31:0.002:0.75 --comment Created on Fri Oct 28 12:17:59 PM EDT 2022 by sanjeetsingh@fedora
called from resample_target.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp B-C.dist.tgt_extrapolated.XXXXX'
Running critical command 'mktemp B-C.dist.tgt_extrapolated_left.XXXXX'
Running subscript 'table_extrapolate.pl --function linear --avgpoints 1 --region left B-C.dist.tgt_smooth.wNnmI B-C.dist.tgt_extrapolated_left.37cKZ' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient 0.0330199305
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right B-C.dist.tgt_extrapolated_left.37cKZ B-C.dist.tgt_extrapolated.XU9sk' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running subscript 'dist_adjust.pl B-C.dist.tgt_extrapolated.XU9sk B-C.dist.tgt' (from tags dist adjust) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp B-C.pot.new.raw.XXX'
csg_get_property: No value for 'cg.inverse.dist_min' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.dist_min' from /usr/share/votca/xml/csg_defaults.xml: 1e-10
Running subscript 'dist_boltzmann_invert.pl --type non-bonded --kbT 2.49435 --min 1e-10 B-C.dist.tgt B-C.pot.new.raw.yGj' (from tags dist invert) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp B-C.pot.new.smooth.XXX'
Running critical command 'csg_resample --in B-C.pot.new.raw.yGj --out B-C.pot.new.smooth.tWu --grid 0.31:0.002:0.75 --comment Created on Fri Oct 28 12:17:59 PM EDT 2022 by sanjeetsingh@fedora
called from prepare_generic_single.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp B-C.pot.new.extrapolate.XXX'
Running subscript 'potential_extrapolate.sh --type non-bonded B-C.pot.new.smooth.tWu B-C.pot.new.extrapolate.lXJ' (from tags potential extrapolate) dir /usr/share/votca/scripts/inverse
Extrapolate B-C.pot.new.smooth.tWu to B-C.pot.new.extrapolate.lXJ
Running critical command 'mktemp B-C.pot.new.smooth.tWu.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left B-C.pot.new.smooth.tWu B-C.pot.new.smooth.tWu.onlyleft.uHB3j' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient -460.121353333333
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right B-C.pot.new.smooth.tWu.onlyleft.uHB3j B-C.pot.new.extrapolate.lXJ' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running critical command 'mktemp B-C.pot.new.shifted.XXX'
Running subscript 'potential_shift.pl --type non-bonded B-C.pot.new.extrapolate.lXJ B-C.pot.new.shifted.cOj' (from tags potential shift) dir /usr/share/votca/scripts/inverse
Running subscript 'table_change_flag.sh B-C.pot.new.shifted.cOj B-C.pot.new' (from tags table change_flag) dir /usr/share/votca/scripts/inverse
Running critical command 'sed -e s/o$/i/ B-C.pot.new.shifted.cOj'
for_all: run 'do_external prepare_single ibi' for interaction named 'A-C'
Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi) dir /usr/share/votca/scripts/inverse
Using initial guess from dist A-C.dist.tgt for A-C
Running subscript 'resample_target.sh A-C.dist.tgt A-C.dist.tgt' (from tags resample target) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp A-C.dist.tgt_smooth.XXXXX'
Running critical command 'csg_resample --in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/A-C.dist.tgt --out A-C.dist.tgt_smooth.wQyNb --grid 0.318:0.002:0.75 --comment Created on Fri Oct 28 12:18:00 PM EDT 2022 by sanjeetsingh@fedora
called from resample_target.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp A-C.dist.tgt_extrapolated.XXXXX'
Running critical command 'mktemp A-C.dist.tgt_extrapolated_left.XXXXX'
Running subscript 'table_extrapolate.pl --function linear --avgpoints 1 --region left A-C.dist.tgt_smooth.wQyNb A-C.dist.tgt_extrapolated_left.J0CCP' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient 1.0906167065
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right A-C.dist.tgt_extrapolated_left.J0CCP A-C.dist.tgt_extrapolated.cD5jp' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running subscript 'dist_adjust.pl A-C.dist.tgt_extrapolated.cD5jp A-C.dist.tgt' (from tags dist adjust) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp A-C.pot.new.raw.XXX'
csg_get_property: No value for 'cg.inverse.dist_min' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.dist_min' from /usr/share/votca/xml/csg_defaults.xml: 1e-10
Running subscript 'dist_boltzmann_invert.pl --type non-bonded --kbT 2.49435 --min 1e-10 A-C.dist.tgt A-C.pot.new.raw.8BO' (from tags dist invert) dir /usr/share/votca/scripts/inverse
Running critical command 'mktemp A-C.pot.new.smooth.XXX'
Running critical command 'csg_resample --in A-C.pot.new.raw.8BO --out A-C.pot.new.smooth.Fdt --grid 0.318:0.002:0.75 --comment Created on Fri Oct 28 12:18:00 PM EDT 2022 by sanjeetsingh@fedora
called from prepare_generic_single.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp A-C.pot.new.extrapolate.XXX'
Running subscript 'potential_extrapolate.sh --type non-bonded A-C.pot.new.smooth.Fdt A-C.pot.new.extrapolate.rLD' (from tags potential extrapolate) dir /usr/share/votca/scripts/inverse
Extrapolate A-C.pot.new.smooth.Fdt to A-C.pot.new.extrapolate.rLD
Running critical command 'mktemp A-C.pot.new.smooth.Fdt.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left A-C.pot.new.smooth.Fdt A-C.pot.new.smooth.Fdt.onlyleft.MVpxP' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient -217.10475
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right A-C.pot.new.smooth.Fdt.onlyleft.MVpxP A-C.pot.new.extrapolate.rLD' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running critical command 'mktemp A-C.pot.new.shifted.XXX'
Running subscript 'potential_shift.pl --type non-bonded A-C.pot.new.extrapolate.rLD A-C.pot.new.shifted.2eu' (from tags potential shift) dir /usr/share/votca/scripts/inverse
Running subscript 'table_change_flag.sh A-C.pot.new.shifted.2eu A-C.pot.new' (from tags table change_flag) dir /usr/share/votca/scripts/inverse
Running critical command 'sed -e s/o$/i/ A-C.pot.new.shifted.2eu'
csg_get_property: No value for 'cg.bonded.name' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.bonded.name'
csg_get_property: No value for 'cg.bonded.min' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.bonded.min'
For all dihedral
csg_get_property: No value for 'cg.bonded.name' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.bonded.name'
step 0 done
We are doing 1 of 300 iterations (0=inf).
-------------------------------
Doing iteration 1 (dir step_001)
-------------------------------
Step 1 started at Fri Oct 28 12:18:01 PM EDT 2022
Running critical command 'pushd /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT'
~/PEO-CH3_END-572-COORDINATES-19OCT ~/PEO-CH3_END-572-COORDINATES-19OCT/step_001
cp_from_main_dir: 'PEO-CG-TOPOLOGY.data MY.in BOND-AB.pot BOND-BB.pot BOND-BC.pot ANGLE-ABB.pot ANGLE-BBB.pot ANGLE-BBC.pot DIHEDRAL-ABBB.pot DIHEDRAL-BBBB.pot DIHEDRAL-BBBC.pot'
Running critical command 'cp PEO-CG-TOPOLOGY.data MY.in BOND-AB.pot BOND-BB.pot BOND-BC.pot ANGLE-ABB.pot ANGLE-BBB.pot ANGLE-BBC.pot DIHEDRAL-ABBB.pot DIHEDRAL-BBBB.pot DIHEDRAL-BBBC.pot /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001'
Running critical command 'popd'
~/PEO-CH3_END-572-COORDINATES-19OCT/step_001
Running subscript 'initialize_step_generic.sh' (from tags initstep ibi) dir /usr/share/votca/scripts/inverse
csg_get_property: No value for 'cg.bonded.name' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.bonded.name'
csg_get_property: No value for 'cg.bonded.min' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.bonded.min'
For all non-bonded
for_all: run 'cp_from_last_step --rename $(csg_get_interaction_property name).pot.new $(csg_get_interaction_property name).pot.cur' for interaction named 'A-A'
cp_from_last_step: 'A-A.pot.new' to 'A-A.pot.cur'
Running critical command 'pushd /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
~/PEO-CH3_END-572-COORDINATES-19OCT/step_000 ~/PEO-CH3_END-572-COORDINATES-19OCT/step_001
Running critical command 'cp A-A.pot.new /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001/A-A.pot.cur'
Running critical command 'popd'
~/PEO-CH3_END-572-COORDINATES-19OCT/step_001
for_all: run 'cp_from_last_step --rename $(csg_get_interaction_property name).pot.new $(csg_get_interaction_property name).pot.cur' for interaction named 'B-B'
cp_from_last_step: 'B-B.pot.new' to 'B-B.pot.cur'
Running critical command 'pushd /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
~/PEO-CH3_END-572-COORDINATES-19OCT/step_000 ~/PEO-CH3_END-572-COORDINATES-19OCT/step_001
Running critical command 'cp B-B.pot.new /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001/B-B.pot.cur'
Running critical command 'popd'
~/PEO-CH3_END-572-COORDINATES-19OCT/step_001
for_all: run 'cp_from_last_step --rename $(csg_get_interaction_property name).pot.new $(csg_get_interaction_property name).pot.cur' for interaction named 'C-C'
cp_from_last_step: 'C-C.pot.new' to 'C-C.pot.cur'
Running critical command 'pushd /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
~/PEO-CH3_END-572-COORDINATES-19OCT/step_000 ~/PEO-CH3_END-572-COORDINATES-19OCT/step_001
Running critical command 'cp C-C.pot.new /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001/C-C.pot.cur'
Running critical command 'popd'
~/PEO-CH3_END-572-COORDINATES-19OCT/step_001
for_all: run 'cp_from_last_step --rename $(csg_get_interaction_property name).pot.new $(csg_get_interaction_property name).pot.cur' for interaction named 'A-B'
cp_from_last_step: 'A-B.pot.new' to 'A-B.pot.cur'
Running critical command 'pushd /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
~/PEO-CH3_END-572-COORDINATES-19OCT/step_000 ~/PEO-CH3_END-572-COORDINATES-19OCT/step_001
Running critical command 'cp A-B.pot.new /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001/A-B.pot.cur'
Running critical command 'popd'
~/PEO-CH3_END-572-COORDINATES-19OCT/step_001
for_all: run 'cp_from_last_step --rename $(csg_get_interaction_property name).pot.new $(csg_get_interaction_property name).pot.cur' for interaction named 'B-C'
cp_from_last_step: 'B-C.pot.new' to 'B-C.pot.cur'
Running critical command 'pushd /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
~/PEO-CH3_END-572-COORDINATES-19OCT/step_000 ~/PEO-CH3_END-572-COORDINATES-19OCT/step_001
Running critical command 'cp B-C.pot.new /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001/B-C.pot.cur'
Running critical command 'popd'
~/PEO-CH3_END-572-COORDINATES-19OCT/step_001
for_all: run 'cp_from_last_step --rename $(csg_get_interaction_property name).pot.new $(csg_get_interaction_property name).pot.cur' for interaction named 'A-C'
cp_from_last_step: 'A-C.pot.new' to 'A-C.pot.cur'
Running critical command 'pushd /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
~/PEO-CH3_END-572-COORDINATES-19OCT/step_000 ~/PEO-CH3_END-572-COORDINATES-19OCT/step_001
Running critical command 'cp A-C.pot.new /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001/A-C.pot.cur'
Running critical command 'popd'
~/PEO-CH3_END-572-COORDINATES-19OCT/step_001
For all bonded
csg_get_property: No value for 'cg.bonded.name' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.bonded.name'
Running subscript 'initialize_step_genericsim.sh' (from tags initstep lammps) dir /usr/share/votca/scripts/inverse
csg_get_property: No value for 'cg.inverse.lammps.conf' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.lammps.conf'
Using intial configuration from maindir
Option cg.inverse.lammps.conf was empty, so I assume lammps needs no conf or you have added it to cg.inverse.filelist.
Running subscript 'potentials_to_generic.sh' (from tags convert_potentials lammps) dir /usr/share/votca/scripts/inverse
csg_get_property: No value for 'cg.bonded.name' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.bonded.name'
csg_get_property: No value for 'cg.bonded.min' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.bonded.min'
For all non-bonded
for_all: run 'do_external convert_potential lammps $(csg_get_interaction_property name).pot.cur $(csg_get_interaction_property inverse.lammps.table)' for interaction named 'A-A'
Running subscript 'potential_to_lammps.sh A-A.pot.cur A-A.pot' (from tags convert_potential lammps) dir /usr/share/votca/scripts/inverse
Convert A-A.pot.cur to A-A.pot
Running critical command 'mktemp A-A.pot.scale.XXXXX'
Running subscript 'table_linearop.pl --on-x A-A.pot.cur A-A.pot.scale.sIKD6 10 0' (from tags table linearop) dir /usr/share/votca/scripts/inverse
table_linearop.pl: A-A.pot.cur to A-A.pot.scale.sIKD6 with x' = 10*x + 0
Running critical command 'mktemp A-A.pot.yscale.XXXXX'
Running subscript 'table_linearop.pl A-A.pot.scale.sIKD6 A-A.pot.yscale.9OOXo 0.239006 0' (from tags table linearop) dir /usr/share/votca/scripts/inverse
table_linearop.pl: A-A.pot.scale.sIKD6 to A-A.pot.yscale.9OOXo with y' = 0.239006*y + 0
Running critical command 'mktemp A-A.pot.smooth.XXXXX'
Running critical command 'csg_resample --in A-A.pot.yscale.9OOXo --out A-A.pot.smooth.JeXUr --grid 1:0.02:7.6'
Running critical command 'mktemp A-A.pot.extrapol.XXXXX'
csg_get_interaction_property: No value for 'inverse.lammps.table_left_extrapolation' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.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 /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.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 --type non-bonded A-A.pot.smooth.JeXUr A-A.pot.extrapol.RgdsI' (from tags potential extrapolate) dir /usr/share/votca/scripts/inverse
Extrapolate A-A.pot.smooth.JeXUr to A-A.pot.extrapol.RgdsI
Running critical command 'mktemp A-A.pot.smooth.JeXUr.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left A-A.pot.smooth.JeXUr A-A.pot.smooth.JeXUr.onlyleft.dKe08' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient 0.351727733333332
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right A-A.pot.smooth.JeXUr.onlyleft.dKe08 A-A.pot.extrapol.RgdsI' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running critical command 'mktemp A-A.pot.interpol.XXXXX'
Running critical command 'mktemp A-A.pot.deriv.XXXXX'
Running critical command 'csg_resample --in A-A.pot.extrapol.RgdsI --out A-A.pot.interpol.bBf98 --grid 1:0.002:7.6 --der A-A.pot.deriv.rpyyF --comment Created on Fri Oct 28 12:18:01 PM EDT 2022 by sanjeetsingh@fedora
called from potential_to_lammps.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001
Comments from /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001/A-A.pot.cur:\nCreated on Fri Oct 28 12:17:57 PM EDT 2022 by sanjeetsingh@fedora
called from prepare_generic_single.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp A-A.pot.shift.XXXXX'
Running subscript 'potential_shift.pl --type non-bonded A-A.pot.interpol.bBf98 A-A.pot.shift.CHgWI' (from tags potential shift) dir /usr/share/votca/scripts/inverse
Running subscript 'table_to_tab.pl --header lammps --type non-bonded A-A.pot.shift.CHgWI A-A.pot.deriv.rpyyF A-A.pot' (from tags convert_potential tab) dir /usr/share/votca/scripts/inverse
for_all: run 'do_external convert_potential lammps $(csg_get_interaction_property name).pot.cur $(csg_get_interaction_property inverse.lammps.table)' for interaction named 'B-B'
Running subscript 'potential_to_lammps.sh B-B.pot.cur B-B.pot' (from tags convert_potential lammps) dir /usr/share/votca/scripts/inverse
Convert B-B.pot.cur to B-B.pot
Running critical command 'mktemp B-B.pot.scale.XXXXX'
Running subscript 'table_linearop.pl --on-x B-B.pot.cur B-B.pot.scale.ZDanp 10 0' (from tags table linearop) dir /usr/share/votca/scripts/inverse
table_linearop.pl: B-B.pot.cur to B-B.pot.scale.ZDanp with x' = 10*x + 0
Running critical command 'mktemp B-B.pot.yscale.XXXXX'
Running subscript 'table_linearop.pl B-B.pot.scale.ZDanp B-B.pot.yscale.MRrYF 0.239006 0' (from tags table linearop) dir /usr/share/votca/scripts/inverse
table_linearop.pl: B-B.pot.scale.ZDanp to B-B.pot.yscale.MRrYF with y' = 0.239006*y + 0
Running critical command 'mktemp B-B.pot.smooth.XXXXX'
Running critical command 'csg_resample --in B-B.pot.yscale.MRrYF --out B-B.pot.smooth.tHrDj --grid 1:0.02:7.6'
Running critical command 'mktemp B-B.pot.extrapol.XXXXX'
csg_get_interaction_property: No value for 'inverse.lammps.table_left_extrapolation' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.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 /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.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 --type non-bonded B-B.pot.smooth.tHrDj B-B.pot.extrapol.JOjHK' (from tags potential extrapolate) dir /usr/share/votca/scripts/inverse
Extrapolate B-B.pot.smooth.tHrDj to B-B.pot.extrapol.JOjHK
Running critical command 'mktemp B-B.pot.smooth.tHrDj.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left B-B.pot.smooth.tHrDj B-B.pot.smooth.tHrDj.onlyleft.yF0Mn' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient -8.71081578333332
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right B-B.pot.smooth.tHrDj.onlyleft.yF0Mn B-B.pot.extrapol.JOjHK' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running critical command 'mktemp B-B.pot.interpol.XXXXX'
Running critical command 'mktemp B-B.pot.deriv.XXXXX'
Running critical command 'csg_resample --in B-B.pot.extrapol.JOjHK --out B-B.pot.interpol.K9Wg8 --grid 1:0.002:7.6 --der B-B.pot.deriv.sQQa6 --comment Created on Fri Oct 28 12:18:02 PM EDT 2022 by sanjeetsingh@fedora
called from potential_to_lammps.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001
Comments from /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001/B-B.pot.cur:\nCreated on Fri Oct 28 12:17:58 PM EDT 2022 by sanjeetsingh@fedora
called from prepare_generic_single.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp B-B.pot.shift.XXXXX'
Running subscript 'potential_shift.pl --type non-bonded B-B.pot.interpol.K9Wg8 B-B.pot.shift.z0cwo' (from tags potential shift) dir /usr/share/votca/scripts/inverse
Running subscript 'table_to_tab.pl --header lammps --type non-bonded B-B.pot.shift.z0cwo B-B.pot.deriv.sQQa6 B-B.pot' (from tags convert_potential tab) dir /usr/share/votca/scripts/inverse
for_all: run 'do_external convert_potential lammps $(csg_get_interaction_property name).pot.cur $(csg_get_interaction_property inverse.lammps.table)' for interaction named 'C-C'
Running subscript 'potential_to_lammps.sh C-C.pot.cur C-C.pot' (from tags convert_potential lammps) dir /usr/share/votca/scripts/inverse
Convert C-C.pot.cur to C-C.pot
Running critical command 'mktemp C-C.pot.scale.XXXXX'
Running subscript 'table_linearop.pl --on-x C-C.pot.cur C-C.pot.scale.6Z53H 10 0' (from tags table linearop) dir /usr/share/votca/scripts/inverse
table_linearop.pl: C-C.pot.cur to C-C.pot.scale.6Z53H with x' = 10*x + 0
Running critical command 'mktemp C-C.pot.yscale.XXXXX'
Running subscript 'table_linearop.pl C-C.pot.scale.6Z53H C-C.pot.yscale.QbILK 0.239006 0' (from tags table linearop) dir /usr/share/votca/scripts/inverse
table_linearop.pl: C-C.pot.scale.6Z53H to C-C.pot.yscale.QbILK with y' = 0.239006*y + 0
Running critical command 'mktemp C-C.pot.smooth.XXXXX'
Running critical command 'csg_resample --in C-C.pot.yscale.QbILK --out C-C.pot.smooth.vScmn --grid 1:0.02:7.6'
Running critical command 'mktemp C-C.pot.extrapol.XXXXX'
csg_get_interaction_property: No value for 'inverse.lammps.table_left_extrapolation' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.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 /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.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 --type non-bonded C-C.pot.smooth.vScmn C-C.pot.extrapol.1mpR1' (from tags potential extrapolate) dir /usr/share/votca/scripts/inverse
Extrapolate C-C.pot.smooth.vScmn to C-C.pot.extrapol.1mpR1
Running critical command 'mktemp C-C.pot.smooth.vScmn.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left C-C.pot.smooth.vScmn C-C.pot.smooth.vScmn.onlyleft.vyUy0' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient -3.67280488333333
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right C-C.pot.smooth.vScmn.onlyleft.vyUy0 C-C.pot.extrapol.1mpR1' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running critical command 'mktemp C-C.pot.interpol.XXXXX'
Running critical command 'mktemp C-C.pot.deriv.XXXXX'
Running critical command 'csg_resample --in C-C.pot.extrapol.1mpR1 --out C-C.pot.interpol.beqZP --grid 1:0.002:7.6 --der C-C.pot.deriv.QRws4 --comment Created on Fri Oct 28 12:18:02 PM EDT 2022 by sanjeetsingh@fedora
called from potential_to_lammps.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001
Comments from /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001/C-C.pot.cur:\nCreated on Fri Oct 28 12:17:58 PM EDT 2022 by sanjeetsingh@fedora
called from prepare_generic_single.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp C-C.pot.shift.XXXXX'
Running subscript 'potential_shift.pl --type non-bonded C-C.pot.interpol.beqZP C-C.pot.shift.Wz06x' (from tags potential shift) dir /usr/share/votca/scripts/inverse
Running subscript 'table_to_tab.pl --header lammps --type non-bonded C-C.pot.shift.Wz06x C-C.pot.deriv.QRws4 C-C.pot' (from tags convert_potential tab) dir /usr/share/votca/scripts/inverse
for_all: run 'do_external convert_potential lammps $(csg_get_interaction_property name).pot.cur $(csg_get_interaction_property inverse.lammps.table)' for interaction named 'A-B'
Running subscript 'potential_to_lammps.sh A-B.pot.cur A-B.pot' (from tags convert_potential lammps) dir /usr/share/votca/scripts/inverse
Convert A-B.pot.cur to A-B.pot
Running critical command 'mktemp A-B.pot.scale.XXXXX'
Running subscript 'table_linearop.pl --on-x A-B.pot.cur A-B.pot.scale.W7q9Y 10 0' (from tags table linearop) dir /usr/share/votca/scripts/inverse
table_linearop.pl: A-B.pot.cur to A-B.pot.scale.W7q9Y with x' = 10*x + 0
Running critical command 'mktemp A-B.pot.yscale.XXXXX'
Running subscript 'table_linearop.pl A-B.pot.scale.W7q9Y A-B.pot.yscale.hysx7 0.239006 0' (from tags table linearop) dir /usr/share/votca/scripts/inverse
table_linearop.pl: A-B.pot.scale.W7q9Y to A-B.pot.yscale.hysx7 with y' = 0.239006*y + 0
Running critical command 'mktemp A-B.pot.smooth.XXXXX'
Running critical command 'csg_resample --in A-B.pot.yscale.hysx7 --out A-B.pot.smooth.DAGaM --grid 1:0.02:7.6'
Running critical command 'mktemp A-B.pot.extrapol.XXXXX'
csg_get_interaction_property: No value for 'inverse.lammps.table_left_extrapolation' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.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 /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.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 --type non-bonded A-B.pot.smooth.DAGaM A-B.pot.extrapol.jTqxC' (from tags potential extrapolate) dir /usr/share/votca/scripts/inverse
Extrapolate A-B.pot.smooth.DAGaM to A-B.pot.extrapol.jTqxC
Running critical command 'mktemp A-B.pot.smooth.DAGaM.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left A-B.pot.smooth.DAGaM A-B.pot.smooth.DAGaM.onlyleft.ppH2C' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient -8.62416483333339
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right A-B.pot.smooth.DAGaM.onlyleft.ppH2C A-B.pot.extrapol.jTqxC' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running critical command 'mktemp A-B.pot.interpol.XXXXX'
Running critical command 'mktemp A-B.pot.deriv.XXXXX'
Running critical command 'csg_resample --in A-B.pot.extrapol.jTqxC --out A-B.pot.interpol.9S0cn --grid 1:0.002:7.6 --der A-B.pot.deriv.uomzw --comment Created on Fri Oct 28 12:18:03 PM EDT 2022 by sanjeetsingh@fedora
called from potential_to_lammps.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001
Comments from /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001/A-B.pot.cur:\nCreated on Fri Oct 28 12:17:59 PM EDT 2022 by sanjeetsingh@fedora
called from prepare_generic_single.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp A-B.pot.shift.XXXXX'
Running subscript 'potential_shift.pl --type non-bonded A-B.pot.interpol.9S0cn A-B.pot.shift.9CSvh' (from tags potential shift) dir /usr/share/votca/scripts/inverse
Running subscript 'table_to_tab.pl --header lammps --type non-bonded A-B.pot.shift.9CSvh A-B.pot.deriv.uomzw A-B.pot' (from tags convert_potential tab) dir /usr/share/votca/scripts/inverse
for_all: run 'do_external convert_potential lammps $(csg_get_interaction_property name).pot.cur $(csg_get_interaction_property inverse.lammps.table)' for interaction named 'B-C'
Running subscript 'potential_to_lammps.sh B-C.pot.cur B-C.pot' (from tags convert_potential lammps) dir /usr/share/votca/scripts/inverse
Convert B-C.pot.cur to B-C.pot
Running critical command 'mktemp B-C.pot.scale.XXXXX'
Running subscript 'table_linearop.pl --on-x B-C.pot.cur B-C.pot.scale.2ojb3 10 0' (from tags table linearop) dir /usr/share/votca/scripts/inverse
table_linearop.pl: B-C.pot.cur to B-C.pot.scale.2ojb3 with x' = 10*x + 0
Running critical command 'mktemp B-C.pot.yscale.XXXXX'
Running subscript 'table_linearop.pl B-C.pot.scale.2ojb3 B-C.pot.yscale.3ASxk 0.239006 0' (from tags table linearop) dir /usr/share/votca/scripts/inverse
table_linearop.pl: B-C.pot.scale.2ojb3 to B-C.pot.yscale.3ASxk with y' = 0.239006*y + 0
Running critical command 'mktemp B-C.pot.smooth.XXXXX'
Running critical command 'csg_resample --in B-C.pot.yscale.3ASxk --out B-C.pot.smooth.96mDt --grid 1:0.02:7.6'
Running critical command 'mktemp B-C.pot.extrapol.XXXXX'
csg_get_interaction_property: No value for 'inverse.lammps.table_left_extrapolation' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.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 /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.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 --type non-bonded B-C.pot.smooth.96mDt B-C.pot.extrapol.BblSP' (from tags potential extrapolate) dir /usr/share/votca/scripts/inverse
Extrapolate B-C.pot.smooth.96mDt to B-C.pot.extrapol.BblSP
Running critical command 'mktemp B-C.pot.smooth.96mDt.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left B-C.pot.smooth.96mDt B-C.pot.smooth.96mDt.onlyleft.6x5JM' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient -10.9971764166667
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right B-C.pot.smooth.96mDt.onlyleft.6x5JM B-C.pot.extrapol.BblSP' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running critical command 'mktemp B-C.pot.interpol.XXXXX'
Running critical command 'mktemp B-C.pot.deriv.XXXXX'
Running critical command 'csg_resample --in B-C.pot.extrapol.BblSP --out B-C.pot.interpol.iIi3K --grid 1:0.002:7.6 --der B-C.pot.deriv.pQ63Z --comment Created on Fri Oct 28 12:18:03 PM EDT 2022 by sanjeetsingh@fedora
called from potential_to_lammps.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001
Comments from /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001/B-C.pot.cur:\nCreated on Fri Oct 28 12:17:59 PM EDT 2022 by sanjeetsingh@fedora
called from prepare_generic_single.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp B-C.pot.shift.XXXXX'
Running subscript 'potential_shift.pl --type non-bonded B-C.pot.interpol.iIi3K B-C.pot.shift.65nok' (from tags potential shift) dir /usr/share/votca/scripts/inverse
Running subscript 'table_to_tab.pl --header lammps --type non-bonded B-C.pot.shift.65nok B-C.pot.deriv.pQ63Z B-C.pot' (from tags convert_potential tab) dir /usr/share/votca/scripts/inverse
for_all: run 'do_external convert_potential lammps $(csg_get_interaction_property name).pot.cur $(csg_get_interaction_property inverse.lammps.table)' for interaction named 'A-C'
Running subscript 'potential_to_lammps.sh A-C.pot.cur A-C.pot' (from tags convert_potential lammps) dir /usr/share/votca/scripts/inverse
Convert A-C.pot.cur to A-C.pot
Running critical command 'mktemp A-C.pot.scale.XXXXX'
Running subscript 'table_linearop.pl --on-x A-C.pot.cur A-C.pot.scale.dxNEm 10 0' (from tags table linearop) dir /usr/share/votca/scripts/inverse
table_linearop.pl: A-C.pot.cur to A-C.pot.scale.dxNEm with x' = 10*x + 0
Running critical command 'mktemp A-C.pot.yscale.XXXXX'
Running subscript 'table_linearop.pl A-C.pot.scale.dxNEm A-C.pot.yscale.p8CXd 0.239006 0' (from tags table linearop) dir /usr/share/votca/scripts/inverse
table_linearop.pl: A-C.pot.scale.dxNEm to A-C.pot.yscale.p8CXd with y' = 0.239006*y + 0
Running critical command 'mktemp A-C.pot.smooth.XXXXX'
Running critical command 'csg_resample --in A-C.pot.yscale.p8CXd --out A-C.pot.smooth.v2xcu --grid 1:0.02:7.6'
Running critical command 'mktemp A-C.pot.extrapol.XXXXX'
csg_get_interaction_property: No value for 'inverse.lammps.table_left_extrapolation' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.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 /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.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 --type non-bonded A-C.pot.smooth.v2xcu A-C.pot.extrapol.lgxpf' (from tags potential extrapolate) dir /usr/share/votca/scripts/inverse
Extrapolate A-C.pot.smooth.v2xcu to A-C.pot.extrapol.lgxpf
Running critical command 'mktemp A-C.pot.smooth.v2xcu.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left A-C.pot.smooth.v2xcu A-C.pot.smooth.v2xcu.onlyleft.Mtssw' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient -5.18893378333333
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right A-C.pot.smooth.v2xcu.onlyleft.Mtssw A-C.pot.extrapol.lgxpf' (from tags table extrapolate) dir /usr/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running critical command 'mktemp A-C.pot.interpol.XXXXX'
Running critical command 'mktemp A-C.pot.deriv.XXXXX'
Running critical command 'csg_resample --in A-C.pot.extrapol.lgxpf --out A-C.pot.interpol.jB047 --grid 1:0.002:7.6 --der A-C.pot.deriv.nTGQq --comment Created on Fri Oct 28 12:18:04 PM EDT 2022 by sanjeetsingh@fedora
called from potential_to_lammps.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001
Comments from /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_001/A-C.pot.cur:\nCreated on Fri Oct 28 12:18:00 PM EDT 2022 by sanjeetsingh@fedora
called from prepare_generic_single.sh, version 2022-dev
settings file: '/home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml'
working directory: /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/step_000'
Running critical command 'mktemp A-C.pot.shift.XXXXX'
Running subscript 'potential_shift.pl --type non-bonded A-C.pot.interpol.jB047 A-C.pot.shift.EoYc2' (from tags potential shift) dir /usr/share/votca/scripts/inverse
Running subscript 'table_to_tab.pl --header lammps --type non-bonded A-C.pot.shift.EoYc2 A-C.pot.deriv.nTGQq A-C.pot' (from tags convert_potential tab) dir /usr/share/votca/scripts/inverse
For all bonded
csg_get_property: No value for 'cg.bonded.name' found in /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/settings1.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.bonded.name'
Simulation with lammps
Running subscript 'run_genericsim.sh' (from tags run lammps) dir /usr/share/votca/scripts/inverse
Running critical command 'lmp -in MY.in'
LAMMPS (29 Sep 2021 - Update 2)
using 4 OpenMP thread(s) per MPI task
Reading data file ...
orthogonal box = (0.21847600 -0.039426000 0.82776900) to (15.478230 15.220328 16.087523)
1 by 1 by 1 MPI processor grid
reading atoms ...
50 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
scanning dihedrals ...
1 = max dihedrals/atom
reading bonds ...
45 bonds
reading angles ...
40 angles
reading dihedrals ...
35 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.011 seconds
WARNING: 142 of 3301 force values in table VOTCA are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 162 of 3301 force values in table VOTCA are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 148 of 3301 force values in table VOTCA are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 147 of 3301 force values in table VOTCA are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 149 of 3301 force values in table VOTCA are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 162 of 3301 force values in table VOTCA are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 1556 of 2501 force values in table are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/MOLECULE/bond_table.cpp:380)
WARNING: 686 of 2501 force values in table are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/MOLECULE/bond_table.cpp:380)
WARNING: 869 of 2501 force values in table are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/MOLECULE/bond_table.cpp:380)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9.6
ghost atom cutoff = 9.6
binsize = 4.8, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 5
WARNING: Communication cutoff 9.6 is shorter than a bond length based estimate of 10.39475. This may lead to errors. (src/comm.cpp:730)
WARNING: Inconsistent image flags (src/domain.cpp:814)
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:935)
Per MPI rank memory allocation (min/avg/max) = 9.666 | 9.666 | 9.666 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -80.749372 519.0741 482.14264 1747.2598
10000 407.23799 -86.200358 60.403024 33.683721 6229.8801
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:935)
Loop time of 0.0984972 on 4 procs for 10000 steps with 50 atoms
Performance: 43859.136 ns/day, 0.001 hours/ns, 101525.778 timesteps/s
399.9% CPU use with 1 MPI tasks x 4 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.038154 | 0.038154 | 0.038154 | 0.0 | 38.74
Bond | 0.036719 | 0.036719 | 0.036719 | 0.0 | 37.28
Neigh | 0.0061769 | 0.0061769 | 0.0061769 | 0.0 | 6.27
Comm | 0.010166 | 0.010166 | 0.010166 | 0.0 | 10.32
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.01
Modify | 0.0054588 | 0.0054588 | 0.0054588 | 0.0 | 5.54
Other | | 0.001817 | | | 1.85
Nlocal: 50.0000 ave 50 max 50 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 532.000 ave 532 max 532 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1196.00 ave 1196 max 1196 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1196
Ave neighs/atom = 23.920000
Ave special neighs/atom = 4.8000000
Neighbor list builds = 128
Dangerous builds = 0
Total wall time: 0:00:00
Callstack:
/usr/share/votca/scripts/inverse/inverse.sh - linenumber 246
do_external - linenumber 179 in /usr/share/votca/scripts/inverse/functions_common.sh
die - linenumber 110 in /usr/share/votca/scripts/inverse/functions_common.sh
################################################################################################
# #
# ERROR: #
# do_external: subscript #
# /usr/share/votca/scripts/inverse/run_genericsim.sh #
# (from tags run lammps) failed #
# For details see the logfile /home/sanjeetsingh/PEO-CH3_END-572-COORDINATES-19OCT/inverse.log #
# #
################################################################################################
die: (called from 266178) CSG_MASTER_PID is 266178
die: pids to kill: 266178
<cg>
<!-- FIRST TYPE OF NON-BONDED -->
<non-bonded>
<name>A-A</name>
<!-- types involved in this interaction -->
<type1>A</type1>
<type2>A</type2>
<min>0.336</min>
<max>0.75</max>
<step>0.002</step>
<inverse>
<target>A-A.dist.tgt</target>
<do_potential>1 0 0</do_potential> <!-- 1 0 0 WILL UPDATE THE POTENTIAL AT 1st STEP AND WILL NOT UPDATE IN THE SECOND AND 3RD STEP, AND THE CYCLE WILL CONTINUE-->
<post_update>smooth</post_update>
<post_update_options>
<smooth> <!-- POST UPDATE SMOOTH OPERATIONS OF POTENTIAL UPDATE -->
<iterations>3</iterations> <!-- NUMBER OF TRIANGULAR SMOOTH ITERATIONS TO BE PERFORMED ON POTENTIAL UPDATE-->
</smooth>
<scale>0.1</scale> <!--SCALE FACTOR FOR THE UPDATE-->
</post_update_options>
<post_add>convergence</post_add>
<lammps>
<!-- name of the table for lammps run -->
<table>A-A.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.1</table_begin>
<table_end>0.76</table_end>
<table_bins>0.002</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- SECOND TYPE OF NON-BONDED -->
<non-bonded>
<name>B-B</name>
<type1>B</type1>
<type2>B</type2>
<min>0.3</min>
<max>0.75</max>
<step>0.002</step>
<inverse>
<target>B-B.dist.tgt</target>
<do_potential>1 0 0</do_potential> <!-- 1 0 0 WILL UPDATE THE POTENTIAL AT 1st STEP AND WILL NOT UPDATE IN THE SECOND AND 3RD STEP, AND THE CYCLE WILL CONTINUE-->
<post_update>smooth</post_update>
<post_update_options>
<smooth> <!-- POST UPDATE SMOOTH OPERATIONS OF POTENTIAL UPDATE -->
<iterations>3</iterations> <!-- NUMBER OF TRIANGULAR SMOOTH ITERATIONS TO BE PERFORMED ON POTENTIAL UPDATE-->
</smooth>
<scale>0.1</scale> <!--SCALE FACTOR FOR THE UPDATE-->
</post_update_options>
<post_add>convergence</post_add>
<lammps>
<!-- name of the table for lammps run -->
<table>B-B.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.1</table_begin>
<table_end>0.76</table_end>
<table_bins>0.002</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- THIRD TYPE OF NON-BONDED -->
<non-bonded>
<name>C-C</name>
<type1>C</type1>
<type2>C</type2>
<min>0.332</min>
<max>0.75</max>
<step>0.002</step>
<inverse>
<target>C-C.dist.tgt</target>
<do_potential>1 0 0</do_potential> <!-- 1 0 0 WILL UPDATE THE POTENTIAL AT 1st STEP AND WILL NOT UPDATE IN THE SECOND AND 3RD STEP, AND THE CYCLE WILL CONTINUE-->
<post_update>smooth</post_update>
<post_update_options>
<smooth> <!-- POST UPDATE SMOOTH OPERATIONS OF POTENTIAL UPDATE -->
<iterations>3</iterations> <!-- NUMBER OF TRIANGULAR SMOOTH ITERATIONS TO BE PERFORMED ON POTENTIAL UPDATE-->
</smooth>
<scale>0.1</scale> <!--SCALE FACTOR FOR THE UPDATE-->
</post_update_options>
<post_add>convergence</post_add>
<lammps>
<!-- name of the table for lammps run -->
<table>C-C.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.1</table_begin>
<table_end>0.76</table_end>
<table_bins>0.002</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- FOURTH TYPE OF NON-BONDED -->
<non-bonded>
<name>A-B</name>
<type1>A</type1>
<type2>B</type2>
<min>0.32</min>
<max>0.75</max>
<step>0.002</step>
<inverse>
<target>A-B.dist.tgt</target>
<do_potential>1 0 0</do_potential> <!-- 1 0 0 WILL UPDATE THE POTENTIAL AT 1st STEP AND WILL NOT UPDATE IN THE SECOND AND 3RD STEP, AND THE CYCLE WILL CONTINUE-->
<post_update>smooth</post_update>
<post_update_options>
<smooth> <!-- POST UPDATE SMOOTH OPERATIONS OF POTENTIAL UPDATE -->
<iterations>3</iterations> <!-- NUMBER OF TRIANGULAR SMOOTH ITERATIONS TO BE PERFORMED ON POTENTIAL UPDATE-->
</smooth>
<scale>0.1</scale> <!--SCALE FACTOR FOR THE UPDATE-->
</post_update_options>
<post_add>convergence</post_add>
<lammps>
<!-- name of the table for lammps run -->
<table>A-B.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.1</table_begin>
<table_end>0.76</table_end>
<table_bins>0.002</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- FIFTH TYPE OF NON-BONDED -->
<non-bonded>
<name>B-C</name>
<type1>B</type1>
<type2>C</type2>
<min>0.31</min>
<max>0.75</max>
<step>0.002</step>
<inverse>
<target>B-C.dist.tgt</target>
<do_potential>1 0 0</do_potential> <!-- 1 0 0 WILL UPDATE THE POTENTIAL AT 1st STEP AND WILL NOT UPDATE IN THE SECOND AND 3RD STEP, AND THE CYCLE WILL CONTINUE-->
<post_update>smooth</post_update>
<post_update_options>
<smooth> <!-- POST UPDATE SMOOTH OPERATIONS OF POTENTIAL UPDATE -->
<iterations>3</iterations> <!-- NUMBER OF TRIANGULAR SMOOTH ITERATIONS TO BE PERFORMED ON POTENTIAL UPDATE-->
</smooth>
<scale>0.1</scale> <!--SCALE FACTOR FOR THE UPDATE-->
</post_update_options>
<post_add>convergence</post_add>
<lammps>
<!-- name of the table for lammps run -->
<table>B-C.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.1</table_begin>
<table_end>0.76</table_end>
<table_bins>0.002</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- SIXTH TYPE OF NON-BONDED -->
<non-bonded>
<name>A-C</name>
<type1>A</type1>
<type2>C</type2>
<min>0.318</min>
<max>0.75</max>
<step>0.002</step>
<inverse>
<target>A-C.dist.tgt</target>
<do_potential>1 0 0</do_potential> <!-- 1 0 0 WILL UPDATE THE POTENTIAL AT 1st STEP AND WILL NOT UPDATE IN THE SECOND AND 3RD STEP, AND THE CYCLE WILL CONTINUE-->
<post_update>smooth</post_update>
<post_update_options>
<smooth> <!-- POST UPDATE SMOOTH OPERATIONS OF POTENTIAL UPDATE -->
<iterations>3</iterations> <!-- NUMBER OF TRIANGULAR SMOOTH ITERATIONS TO BE PERFORMED ON POTENTIAL UPDATE-->
</smooth>
<scale>0.1</scale> <!--SCALE FACTOR FOR THE UPDATE-->
</post_update_options>
<post_add>convergence</post_add>
<lammps>
<!-- name of the table for lammps run -->
<table>A-C.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.1</table_begin>
<table_end>0.76</table_end>
<table_bins>0.002</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- general options for inverse script -->
<inverse>
<!-- votca units 300*0.00831451 kJ/mol -->
<kBT>2.49435</kBT> <!--THIS IS CORRECT. I HAVE CHECKED FROM SPCE IBI_LAMMPS TUTORIAL-->
<!-- use lammps as simulation program -->
<program>lammps</program>
<!-- lammps specific options -->
<lammps>
<command>lmp</command>
<opts>-in ${script}</opts>
<tasks>4</tasks>
<!-- lammps script to run !-->
<script>MY.in</script>
<!-- topology to be used by csg_stat !-->
<topol>PEO-CG-TOPOLOGY.data</topol>
<!-- traj file created by lammps !-->
<traj>traj.dump</traj>
</lammps>
<initial_configuration>maindir</initial_configuration>
<!-- these files are copied for each new run -->
<filelist>PEO-CG-TOPOLOGY.data MY.in BOND-AB.pot BOND-BB.pot BOND-BC.pot ANGLE-ABB.pot ANGLE-BBB.pot ANGLE-BBC.pot DIHEDRAL-ABBB.pot DIHEDRAL-BBBB.pot DIHEDRAL-BBBC.pot</filelist>
<!-- do so many iterations -->
<iterations_max>300</iterations_max>
<convergence_check>
<type>default</type>
<limit>0.001</limit>
</convergence_check>
<!-- ibi: inverse biltzmann imc: inverse monte carlo -->
<method>ibi</method>
<log_file>inverse.log</log_file>
<restart_file>restart.log</restart_file>
</inverse>
</cg>
