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.plcma get cma_get.sh
cma precede_state cma_processor.py
calc target_rdf calc_target_rdf_generic.sh
pressure_cor simple
pressure_cor_simple.plpressure_cor wjk
pressure_cor_wjk.plkbibi ramp_correction
kbibi_ramp_correction.plcalc kbint calc_kbint.sh
density symmetrize density_symmetrize.py
table add add_POT.pl
table integrate
table_integrate.pltable extrapolate
table_extrapolate.pltable merge
merge_tables.pltable smooth
table_smooth.pltable linearop
table_linearop.pltable dummy table_dummy.sh
table get_value
table_get_value.pltable getsubset table_getsubset.py
table smooth_borders table_smooth_borders.py
table compare
table_combine.pl --die --op =
table combine
table_combine.pltable average table_average.sh
table scale
table_scale.pltable change_flag table_change_flag.sh
table functional table_functional.sh
potential extrapolate potential_extrapolate.sh
configuration compare configuration_compare.py
tables jackknife
tables_jackknife.plrun gromacs run_gromacs.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_gromacs.sh
prepare_generic gromacs prepare_generic_gromacs.sh
initstep_generic gromacs initialize_step_generic_gromacs.sh
prepare_generic espresso prepare_generic_espresso.sh
initstep_generic espresso initialize_step_generic_espresso.sh
convert_potential gromacs potential_to_gromacs.sh
convert_potential xvg
table_to_xvg.plfunctions gromacs functions_gromacs.sh
run espresso run_espresso.sh
pressure espresso calc_pressure_espresso.sh
rdf espresso calc_rdf_espresso.sh
convert_potential espresso potential_to_espresso.sh
convert_potential tab
table_to_tab.plfunctions espresso functions_espresso.sh
------------------------
Prepare (dir step_000)
------------------------
cp_from_main_dir: 'grompp.mdp topol.top table_C_C.xvg table_a1.xvg table_b1.xvg table_d1.xvg index.ndx'
Running critical command 'pushd /home/valentina/CG'
~/CG ~/CG/step_000
Running critical command 'cp grompp.mdp topol.top table_C_C.xvg table_a1.xvg table_b1.xvg table_d1.xvg index.ndx /home/valentina/CG/step_000'
Running critical command 'popd'
~/CG/step_000
Running subscript 'prepare_generic.sh' (from tags prepare ibi) dir /share/apps/votca/share/votca/scripts/inverse
For all bonded
for_all: run 'do_external prepare_single ibi'
Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi) dir /share/apps/votca/share/votca/scripts/inverse
Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) .*/\1/p'
Running critical command 'mktemp CC.pot.in.smooth.XXX'
Converting /home/valentina/CG/
CC.pot.in to CC.pot.new
Running critical command 'csg_resample --in /home/valentina/CG/
CC.pot.in --out CC.pot.in.smooth.sU6 --grid 0:0.01:4 --comment Created on Wed Oct 17 17:42:27 BST 2012 by vale...@compute-0-4.local
called from prepare_generic_single.sh, version 1.3-dev hgid: cae513aba385
settings file: /home/valentina/CG/settings.xml
working directory: /home/valentina/CG/step_000'
Running critical command 'mktemp CC.pot.in.extrapolate.XXX'
Running subscript 'potential_extrapolate.sh --type CC.pot.in.smooth.sU6 CC.pot.in.extrapolate.YdY' (from tags potential extrapolate) dir /share/apps/votca/share/votca/scripts/inverse
Callstack:
/share/apps/votca/share/votca/scripts/inverse/inverse.sh - linenumber 166
do_external - linenumber 170 in /share/apps/votca/share/votca/scripts/inverse/functions_common.sh
/share/apps/votca/share/votca/scripts/inverse/prepare_generic.sh - linenumber 31
for_all - linenumber 17 (see 'csg_call --cat function for_all')
do_external - linenumber 18 (see 'csg_call --cat function do_external')
/share/apps/votca/share/votca/scripts/inverse/prepare_generic_single.sh - linenumber 43
do_external - linenumber 18 (see 'csg_call --cat function do_external')
/share/apps/votca/share/votca/scripts/inverse/potential_extrapolate.sh - linenumber 64
die - linenumber 2 (see 'csg_call --cat function die')
################################################################################################################################
# #
# ERROR: #
# potential_extrapolate.sh: please specify add potential type (--type options) from: non-bonded bond thermforce angle dihedral #
# For details see the logfile /home/valentina/CG/inverse.log #
# #
################################################################################################################################
die: (called from 591) CSG_MASTER_PID is 32479
die: pids to kill: 0
On Friday, September 28, 2012 2:07:44 PM UTC+1, Valentina wrote: