Dear Votca Users,
I am trying to run ibi with my own polymer system to derive non-bonded
potentials.
I am trying to look at inverse.log file but I do not figure out what the
problem is. Would you please give me some advice?
I set for A and D beads interaction in setting.xml file below, and my A-D
target rdf from 0 to 2 obtained from csg_stat command. Step size is 0.01
and the rdf looks fine for me.
<non-bonded>
<!-- name of the interaction -->
<name>A-D</name>
<!-- types involved in this interaction -->
<type1>A</type1>
<type2>D</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>2.0</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>CG-CG.A-D.dist.tgt</target>
<!-- update cycles -->
<do_potential>0 0 0 0 0 0 1</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_update></post_update>
<!-- additional post processing of U after dU added to potential -->
<post_add>convergence</post_add>
<!-- inverse monte carlo specific stuff -->
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_A_D.xvg</table>
</gromacs>
</inverse>
</non-bonded>
The error message inverse.log is attached. In short, it says that
Running subscript 'dist_boltzmann_invert.pl --type non-bonded --kbT 2.49435
--min 1e-10 A-D.dist.tgt A-D.pot.new.raw.R6h' (from tags dist invert) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
Only 3 points are valid after Boltzmann inversion from file 'A-D.dist.tgt',
please check if your distribution is a valid dist.
Callstack:
/home/chang/PACKAGE/votca/share/votca/scripts/inverse/inverse.sh -
linenumber 156
do_external - linenumber 176 in
/home/chang/PACKAGE/votca/share/votca/scripts/inverse/functions_common.sh
/home/chang/PACKAGE/votca/share/votca/scripts/inverse/prepare_generic.sh -
linenumber 31
for_all - linenumber 22 (see 'csg_call --cat function for_all')
do_external - linenumber 19 (see 'csg_call --cat
function do_external')
/home/chang/PACKAGE/votca/share/votca/scripts/inverse/prepare_generic_single.sh
- linenumber 64
do_external - linenumber 22 (see 'csg_call
--cat function do_external')
die - linenumber 2 (see 'csg_call --cat
function die')
###############################################################################################################################################################
#
#
#
ERROR:
#
# do_external:
subscript
#
# /home/chang/PACKAGE/votca/share/votca/scripts/inverse/
dist_boltzmann_invert.pl --type non-bonded --kbT 2.49435 --min 1e-10
A-D.dist.tgt A-D.pot.new.raw.R6h #
# (from tags dist invert)
failed
#
# For details see the logfile
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/inverse.log
#
#
#
###############################################################################################################################################################
Thank you very much.
Best regards,
Changwoon Jang,
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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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.espresso.scriptdir'
Sim started Mon Jan 25 11:03:04 EST 2016
We are doing Method: ibi
csg_get_property: No value for 'cg.inverse.scriptpath' found in
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.scriptpath'
We are using Sim Program: gromacs
csg_get_property: No value for 'cg.inverse.gromacs.gmxrc' found in
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.gromacs.gmxrc'
#The order in which scripts get called
#CSGSHARE is /home/chang/PACKAGE/votca/share/votca/scripts/inverse
#From: /home/chang/PACKAGE/votca/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 imc prepare_imc.sh
prepare generic prepare_generic.sh
prepare tf 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 tf prepare_generic_single.sh
prepare_single optimizer prepare_optimizer_single.sh
initstep ibi initialize_step_generic.sh
initstep imc initialize_step_generic.sh
initstep tf initialize_step_generic.sh
initstep optimizer initialize_step_optimizer.sh
initstep re initialize_step_re.sh
prepare ibm prepare_ibm.sh
update ibm update_ibm.sh
add_pot ibi add_pot_generic.sh
add_pot imc add_pot_generic.sh
add_pot tf add_pot_generic.sh
add_pot optimizer dummy.sh
add_pot re dummy.sh
pre_update ibi dummy.sh
pre_update imc dummy.sh
pre_update tf dummy.sh
pre_update optimizer dummy.sh
pre_update re pre_update_re.sh
post_update ibi post_update_generic.sh
post_update imc post_update_generic.sh
post_update tf 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 imc post_update_generic_single.sh
post_update_single tf 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 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
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
convergence_check default convergence_check_default.sh
resample target resample_target.sh
dpot crop dpot_crop.pl
update ibi update_ibi.sh
update ibi_single update_ibi_single.sh
update ibi_pot update_ibi_pot.pl
update imc update_imc.sh
imcsolver matlab solve_matlab.sh
solve matlab linsolve.m
imcsolver octave solve_octave.sh
solve octave linsolve.octave
imcsolver numpy solve_numpy.sh
solve numpy linsolve.py
imc purify imc_purify.sh
update tf update_tf.sh
update tf_single update_tf_single.sh
calc thermforce calc_thermforce.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 get cma_get.sh
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
kbibi ramp_correction kbibi_ramp_correction.pl
calc kbint calc_kbint.sh
density symmetrize density_symmetrize.py
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 linearop table_linearop.pl
table dummy table_dummy.sh
table get_value table_get_value.pl
table getsubset table_getsubset.py
table smooth_borders table_smooth_borders.py
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
configuration compare configuration_compare.py
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
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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI'
~/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI
~/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/step_000
cp_from_main_dir: 'grompp.mdp topol.top table.xvg ABAangle.xvg CDCangle.xvg
ABbond.xvg CDbond.xvg index.ndx'
Running critical command 'cp grompp.mdp topol.top table.xvg ABAangle.xvg
CDCangle.xvg ABbond.xvg CDbond.xvg index.ndx
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/step_000'
Running critical command 'popd'
~/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/step_000
Running subscript 'prepare_generic.sh' (from tags prepare ibi) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
csg_get_property: No value for 'cg.bonded.name' found in
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/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 /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Using initial guess from dist CG-CG.A-A.dist.tgt for A-A
Running subscript 'resample_target.sh CG-CG.A-A.dist.tgt A-A.dist.tgt' (from
tags resample target) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running critical command 'mktemp A-A.dist.tgt_smooth.XXXXX'
Running critical command 'csg_resample --in
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/CG-CG.A-A.dist.tgt
--out A-A.dist.tgt_smooth.hrPtL --grid 0:0.01:2.0 --comment Created on Mon Jan
25 11:03:04 EST 2016 by chang@chang
called from resample_target.sh, version 1.4-dev gitid: fb9f982
settings file:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml
working directory:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/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.hrPtL A-A.dist.tgt_extrapolated_left.X1Rb6'
(from tags table extrapolate) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient 0
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1
--region right A-A.dist.tgt_extrapolated_left.X1Rb6
A-A.dist.tgt_extrapolated.HKYuv' (from tags table extrapolate) dir
/home/chang/PACKAGE/votca/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.HKYuv A-A.dist.tgt'
(from tags dist adjust) dir
/home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.dist_min' from
/home/chang/PACKAGE/votca/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.wKp' (from tags dist invert) dir
/home/chang/PACKAGE/votca/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.wKp --out
A-A.pot.new.smooth.GHw --grid 0:0.01:2.0 --comment Created on Mon Jan 25
11:03:04 EST 2016 by chang@chang
called from prepare_generic_single.sh, version 1.4-dev gitid: fb9f982
settings file:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml
working directory:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/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.GHw A-A.pot.new.extrapolate.Sxn' (from tags potential
extrapolate) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Extrapolate A-A.pot.new.smooth.GHw to A-A.pot.new.extrapolate.Sxn
Running critical command 'mktemp A-A.pot.new.smooth.GHw.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3
--region left A-A.pot.new.smooth.GHw A-A.pot.new.smooth.GHw.onlyleft.adZt2'
(from tags table extrapolate) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient
-403.704397
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1
--region right A-A.pot.new.smooth.GHw.onlyleft.adZt2
A-A.pot.new.extrapolate.Sxn' (from tags table extrapolate) dir
/home/chang/PACKAGE/votca/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.Sxn A-A.pot.new.shifted.At0' (from tags potential
shift) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running subscript 'table_change_flag.sh A-A.pot.new.shifted.At0 A-A.pot.new'
(from tags table change_flag) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running critical command 'sed -e s/o$/i/ A-A.pot.new.shifted.At0'
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 /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Using initial guess from dist CG-CG.B-B.dist.tgt for B-B
Running subscript 'resample_target.sh CG-CG.B-B.dist.tgt B-B.dist.tgt' (from
tags resample target) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running critical command 'mktemp B-B.dist.tgt_smooth.XXXXX'
Running critical command 'csg_resample --in
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/CG-CG.B-B.dist.tgt
--out B-B.dist.tgt_smooth.SGTPD --grid 0:0.01:2.0 --comment Created on Mon Jan
25 11:03:05 EST 2016 by chang@chang
called from resample_target.sh, version 1.4-dev gitid: fb9f982
settings file:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml
working directory:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/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.SGTPD B-B.dist.tgt_extrapolated_left.fJoME'
(from tags table extrapolate) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient 0
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1
--region right B-B.dist.tgt_extrapolated_left.fJoME
B-B.dist.tgt_extrapolated.12y9h' (from tags table extrapolate) dir
/home/chang/PACKAGE/votca/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.12y9h B-B.dist.tgt'
(from tags dist adjust) dir
/home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.dist_min' from
/home/chang/PACKAGE/votca/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.GP5' (from tags dist invert) dir
/home/chang/PACKAGE/votca/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.GP5 --out
B-B.pot.new.smooth.ZQm --grid 0:0.01:2.0 --comment Created on Mon Jan 25
11:03:05 EST 2016 by chang@chang
called from prepare_generic_single.sh, version 1.4-dev gitid: fb9f982
settings file:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml
working directory:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/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.ZQm B-B.pot.new.extrapolate.p46' (from tags potential
extrapolate) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Extrapolate B-B.pot.new.smooth.ZQm to B-B.pot.new.extrapolate.p46
Running critical command 'mktemp B-B.pot.new.smooth.ZQm.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3
--region left B-B.pot.new.smooth.ZQm B-B.pot.new.smooth.ZQm.onlyleft.07iX2'
(from tags table extrapolate) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient
-581.320321533333
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1
--region right B-B.pot.new.smooth.ZQm.onlyleft.07iX2
B-B.pot.new.extrapolate.p46' (from tags table extrapolate) dir
/home/chang/PACKAGE/votca/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.p46 B-B.pot.new.shifted.491' (from tags potential
shift) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running subscript 'table_change_flag.sh B-B.pot.new.shifted.491 B-B.pot.new'
(from tags table change_flag) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running critical command 'sed -e s/o$/i/ B-B.pot.new.shifted.491'
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 /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Using initial guess from dist CG-CG.C-C.dist.tgt for C-C
Running subscript 'resample_target.sh CG-CG.C-C.dist.tgt C-C.dist.tgt' (from
tags resample target) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running critical command 'mktemp C-C.dist.tgt_smooth.XXXXX'
Running critical command 'csg_resample --in
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/CG-CG.C-C.dist.tgt
--out C-C.dist.tgt_smooth.zvjea --grid 0:0.01:2.0 --comment Created on Mon Jan
25 11:03:05 EST 2016 by chang@chang
called from resample_target.sh, version 1.4-dev gitid: fb9f982
settings file:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml
working directory:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/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.zvjea C-C.dist.tgt_extrapolated_left.lCvic'
(from tags table extrapolate) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient 0
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1
--region right C-C.dist.tgt_extrapolated_left.lCvic
C-C.dist.tgt_extrapolated.pkNmh' (from tags table extrapolate) dir
/home/chang/PACKAGE/votca/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.pkNmh C-C.dist.tgt'
(from tags dist adjust) dir
/home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.dist_min' from
/home/chang/PACKAGE/votca/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.gEL' (from tags dist invert) dir
/home/chang/PACKAGE/votca/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.gEL --out
C-C.pot.new.smooth.QTD --grid 0:0.01:2.0 --comment Created on Mon Jan 25
11:03:05 EST 2016 by chang@chang
called from prepare_generic_single.sh, version 1.4-dev gitid: fb9f982
settings file:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml
working directory:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/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.QTD C-C.pot.new.extrapolate.iF8' (from tags potential
extrapolate) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Extrapolate C-C.pot.new.smooth.QTD to C-C.pot.new.extrapolate.iF8
Running critical command 'mktemp C-C.pot.new.smooth.QTD.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3
--region left C-C.pot.new.smooth.QTD C-C.pot.new.smooth.QTD.onlyleft.l63b8'
(from tags table extrapolate) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient
-392.306050333333
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1
--region right C-C.pot.new.smooth.QTD.onlyleft.l63b8
C-C.pot.new.extrapolate.iF8' (from tags table extrapolate) dir
/home/chang/PACKAGE/votca/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.iF8 C-C.pot.new.shifted.5Dw' (from tags potential
shift) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running subscript 'table_change_flag.sh C-C.pot.new.shifted.5Dw C-C.pot.new'
(from tags table change_flag) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running critical command 'sed -e s/o$/i/ C-C.pot.new.shifted.5Dw'
for_all: run 'do_external prepare_single ibi' for interaction named 'D-D'
Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi)
dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Using initial guess from dist CG-CG.D-D.dist.tgt for D-D
Running subscript 'resample_target.sh CG-CG.D-D.dist.tgt D-D.dist.tgt' (from
tags resample target) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running critical command 'mktemp D-D.dist.tgt_smooth.XXXXX'
Running critical command 'csg_resample --in
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/CG-CG.D-D.dist.tgt
--out D-D.dist.tgt_smooth.n61aO --grid 0:0.01:2.0 --comment Created on Mon Jan
25 11:03:06 EST 2016 by chang@chang
called from resample_target.sh, version 1.4-dev gitid: fb9f982
settings file:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml
working directory:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/step_000'
Running critical command 'mktemp D-D.dist.tgt_extrapolated.XXXXX'
Running critical command 'mktemp D-D.dist.tgt_extrapolated_left.XXXXX'
Running subscript 'table_extrapolate.pl --function linear --avgpoints 1
--region left D-D.dist.tgt_smooth.n61aO D-D.dist.tgt_extrapolated_left.iBDgg'
(from tags table extrapolate) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient 0
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1
--region right D-D.dist.tgt_extrapolated_left.iBDgg
D-D.dist.tgt_extrapolated.IRotT' (from tags table extrapolate) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running subscript 'dist_adjust.pl D-D.dist.tgt_extrapolated.IRotT D-D.dist.tgt'
(from tags dist adjust) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running critical command 'mktemp D-D.pot.new.raw.XXX'
csg_get_property: No value for 'cg.inverse.dist_min' found in
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.dist_min' from
/home/chang/PACKAGE/votca/share/votca/xml/csg_defaults.xml: 1e-10
Running subscript 'dist_boltzmann_invert.pl --type non-bonded --kbT 2.49435
--min 1e-10 D-D.dist.tgt D-D.pot.new.raw.lXs' (from tags dist invert) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running critical command 'mktemp D-D.pot.new.smooth.XXX'
Running critical command 'csg_resample --in D-D.pot.new.raw.lXs --out
D-D.pot.new.smooth.Gtl --grid 0:0.01:2.0 --comment Created on Mon Jan 25
11:03:06 EST 2016 by chang@chang
called from prepare_generic_single.sh, version 1.4-dev gitid: fb9f982
settings file:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml
working directory:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/step_000'
Running critical command 'mktemp D-D.pot.new.extrapolate.XXX'
Running subscript 'potential_extrapolate.sh --type non-bonded
D-D.pot.new.smooth.Gtl D-D.pot.new.extrapolate.ypM' (from tags potential
extrapolate) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Extrapolate D-D.pot.new.smooth.Gtl to D-D.pot.new.extrapolate.ypM
Running critical command 'mktemp D-D.pot.new.smooth.Gtl.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3
--region left D-D.pot.new.smooth.Gtl D-D.pot.new.smooth.Gtl.onlyleft.NIH3b'
(from tags table extrapolate) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient
-330.6566117
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1
--region right D-D.pot.new.smooth.Gtl.onlyleft.NIH3b
D-D.pot.new.extrapolate.ypM' (from tags table extrapolate) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running critical command 'mktemp D-D.pot.new.shifted.XXX'
Running subscript 'potential_shift.pl --type non-bonded
D-D.pot.new.extrapolate.ypM D-D.pot.new.shifted.wzW' (from tags potential
shift) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running subscript 'table_change_flag.sh D-D.pot.new.shifted.wzW D-D.pot.new'
(from tags table change_flag) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running critical command 'sed -e s/o$/i/ D-D.pot.new.shifted.wzW'
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 /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Using initial guess from dist CG-CG.A-B.dist.tgt for A-B
Running subscript 'resample_target.sh CG-CG.A-B.dist.tgt A-B.dist.tgt' (from
tags resample target) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running critical command 'mktemp A-B.dist.tgt_smooth.XXXXX'
Running critical command 'csg_resample --in
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/CG-CG.A-B.dist.tgt
--out A-B.dist.tgt_smooth.kDt7j --grid 0:0.01:2.0 --comment Created on Mon Jan
25 11:03:06 EST 2016 by chang@chang
called from resample_target.sh, version 1.4-dev gitid: fb9f982
settings file:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml
working directory:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/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.kDt7j A-B.dist.tgt_extrapolated_left.BygAo'
(from tags table extrapolate) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient 0
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1
--region right A-B.dist.tgt_extrapolated_left.BygAo
A-B.dist.tgt_extrapolated.n3UnZ' (from tags table extrapolate) dir
/home/chang/PACKAGE/votca/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.n3UnZ A-B.dist.tgt'
(from tags dist adjust) dir
/home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.dist_min' from
/home/chang/PACKAGE/votca/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.DZO' (from tags dist invert) dir
/home/chang/PACKAGE/votca/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.DZO --out
A-B.pot.new.smooth.pbn --grid 0:0.01:2.0 --comment Created on Mon Jan 25
11:03:06 EST 2016 by chang@chang
called from prepare_generic_single.sh, version 1.4-dev gitid: fb9f982
settings file:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml
working directory:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/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.pbn A-B.pot.new.extrapolate.KYX' (from tags potential
extrapolate) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Extrapolate A-B.pot.new.smooth.pbn to A-B.pot.new.extrapolate.KYX
Running critical command 'mktemp A-B.pot.new.smooth.pbn.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3
--region left A-B.pot.new.smooth.pbn A-B.pot.new.smooth.pbn.onlyleft.fWvq4'
(from tags table extrapolate) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient
-436.222277
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1
--region right A-B.pot.new.smooth.pbn.onlyleft.fWvq4
A-B.pot.new.extrapolate.KYX' (from tags table extrapolate) dir
/home/chang/PACKAGE/votca/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.KYX A-B.pot.new.shifted.ak1' (from tags potential
shift) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running subscript 'table_change_flag.sh A-B.pot.new.shifted.ak1 A-B.pot.new'
(from tags table change_flag) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running critical command 'sed -e s/o$/i/ A-B.pot.new.shifted.ak1'
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 /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Using initial guess from dist CG-CG.A-C.dist.tgt for A-C
Running subscript 'resample_target.sh CG-CG.A-C.dist.tgt A-C.dist.tgt' (from
tags resample target) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running critical command 'mktemp A-C.dist.tgt_smooth.XXXXX'
Running critical command 'csg_resample --in
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/CG-CG.A-C.dist.tgt
--out A-C.dist.tgt_smooth.0YtcC --grid 0:0.01:2.0 --comment Created on Mon Jan
25 11:03:07 EST 2016 by chang@chang
called from resample_target.sh, version 1.4-dev gitid: fb9f982
settings file:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml
working directory:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/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.0YtcC A-C.dist.tgt_extrapolated_left.44NL8'
(from tags table extrapolate) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient 0
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1
--region right A-C.dist.tgt_extrapolated_left.44NL8
A-C.dist.tgt_extrapolated.TQ7KW' (from tags table extrapolate) dir
/home/chang/PACKAGE/votca/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.TQ7KW A-C.dist.tgt'
(from tags dist adjust) dir
/home/chang/PACKAGE/votca/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/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.dist_min' from
/home/chang/PACKAGE/votca/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.4zj' (from tags dist invert) dir
/home/chang/PACKAGE/votca/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.4zj --out
A-C.pot.new.smooth.VC9 --grid 0:0.01:2.0 --comment Created on Mon Jan 25
11:03:07 EST 2016 by chang@chang
called from prepare_generic_single.sh, version 1.4-dev gitid: fb9f982
settings file:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml
working directory:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/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.VC9 A-C.pot.new.extrapolate.gba' (from tags potential
extrapolate) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Extrapolate A-C.pot.new.smooth.VC9 to A-C.pot.new.extrapolate.gba
Running critical command 'mktemp A-C.pot.new.smooth.VC9.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3
--region left A-C.pot.new.smooth.VC9 A-C.pot.new.smooth.VC9.onlyleft.k7jOf'
(from tags table extrapolate) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using exponential with gradient
-469.665632666667
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1
--region right A-C.pot.new.smooth.VC9.onlyleft.k7jOf
A-C.pot.new.extrapolate.gba' (from tags table extrapolate) dir
/home/chang/PACKAGE/votca/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.gba A-C.pot.new.shifted.Rup' (from tags potential
shift) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running subscript 'table_change_flag.sh A-C.pot.new.shifted.Rup A-C.pot.new'
(from tags table change_flag) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running critical command 'sed -e s/o$/i/ A-C.pot.new.shifted.Rup'
for_all: run 'do_external prepare_single ibi' for interaction named 'A-D'
Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi)
dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Using initial guess from dist CG-CG.A-D.dist.tgt for A-D
Running subscript 'resample_target.sh CG-CG.A-D.dist.tgt A-D.dist.tgt' (from
tags resample target) dir /home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running critical command 'mktemp A-D.dist.tgt_smooth.XXXXX'
Running critical command 'csg_resample --in
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/CG-CG.A-D.dist.tgt
--out A-D.dist.tgt_smooth.TeGcr --grid 0:0.01:2.0 --comment Created on Mon Jan
25 11:03:07 EST 2016 by chang@chang
called from resample_target.sh, version 1.4-dev gitid: fb9f982
settings file:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml
working directory:
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/step_000'
Running critical command 'mktemp A-D.dist.tgt_extrapolated.XXXXX'
Running critical command 'mktemp A-D.dist.tgt_extrapolated_left.XXXXX'
Running subscript 'table_extrapolate.pl --function linear --avgpoints 1
--region left A-D.dist.tgt_smooth.TeGcr A-D.dist.tgt_extrapolated_left.bBzZv'
(from tags table extrapolate) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient 0
Running subscript 'table_extrapolate.pl --function constant --avgpoints 1
--region right A-D.dist.tgt_extrapolated_left.bBzZv
A-D.dist.tgt_extrapolated.DVbto' (from tags table extrapolate) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using constant with gradient 0
Running subscript 'dist_adjust.pl A-D.dist.tgt_extrapolated.DVbto A-D.dist.tgt'
(from tags dist adjust) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
Running critical command 'mktemp A-D.pot.new.raw.XXX'
csg_get_property: No value for 'cg.inverse.dist_min' found in
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/settings.xml,
trying /home/chang/PACKAGE/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.dist_min' from
/home/chang/PACKAGE/votca/share/votca/xml/csg_defaults.xml: 1e-10
Running subscript 'dist_boltzmann_invert.pl --type non-bonded --kbT 2.49435
--min 1e-10 A-D.dist.tgt A-D.pot.new.raw.R6h' (from tags dist invert) dir
/home/chang/PACKAGE/votca/share/votca/scripts/inverse
Only 3 points are valid after Boltzmann inversion from file 'A-D.dist.tgt',
please check if your distribution is a valid dist.
Callstack:
/home/chang/PACKAGE/votca/share/votca/scripts/inverse/inverse.sh - linenumber
156
do_external - linenumber 176 in
/home/chang/PACKAGE/votca/share/votca/scripts/inverse/functions_common.sh
/home/chang/PACKAGE/votca/share/votca/scripts/inverse/prepare_generic.sh -
linenumber 31
for_all - linenumber 22 (see 'csg_call --cat function for_all')
do_external - linenumber 19 (see 'csg_call --cat function
do_external')
/home/chang/PACKAGE/votca/share/votca/scripts/inverse/prepare_generic_single.sh
- linenumber 64
do_external - linenumber 22 (see 'csg_call --cat
function do_external')
die - linenumber 2 (see 'csg_call --cat
function die')
###############################################################################################################################################################
#
#
# ERROR:
#
# do_external: subscript
#
#
/home/chang/PACKAGE/votca/share/votca/scripts/inverse/dist_boltzmann_invert.pl
--type non-bonded --kbT 2.49435 --min 1e-10 A-D.dist.tgt A-D.pot.new.raw.R6h #
# (from tags dist invert) failed
#
# For details see the logfile
/home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/inverse.log
#
#
#
###############################################################################################################################################################
die: (called from 9951) CSG_MASTER_PID is 6991
die: pids to kill: 0
