votca-csg-scripts 1.3.0-3 / usr / share / votca / scripts / inverse / csg_table

#
# Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#

#general scripts
tag file tag_file.sh
dummy dummy dummy.sh

#only here for building the manual (not actually used)
functions common functions_common.sh
csg master inverse.sh

# BEGIN: these scripts have to be defined for each method
# method initialization
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

#this is just to warn users from old versions
prepare ibm prepare_ibm.sh
update ibm update_ibm.sh

# the update step

# add up the potential
# TODO: think about name add_pot, is other name maybe better
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

# END: these scripts have to be defined for each method

# pre update
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
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

#post update scripts
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 post_add.sh
post add_single post_add_single.sh

# post add scripts
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 checks
convergence_check default convergence_check_default.sh

# table preparation
resample target resample_target.sh
dpot crop dpot_crop.pl

# ibi specific stuff
update ibi update_ibi.sh
update ibi_single update_ibi_single.sh
update ibi_pot update_ibi_pot.pl

# imc specific stuff
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

# tf specific stuff
update tf update_tf.sh
update tf_single update_tf_single.sh
calc thermforce calc_thermforce.sh

# optimzer(generic) stuff
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 specific stuff
simplex precede_state simplex_downhill_processor.pl

# cma specific stuff
cma get cma_get.sh
cma precede_state cma_processor.py

# relative entroy (re) specific stuff
update re update_re.sh

# recalculate reference
calc target_rdf calc_target_rdf_generic.sh

# pressure correction
pressure_cor simple pressure_cor_simple.pl
pressure_cor wjk pressure_cor_wjk.pl

# kirkwood-buff correction
kbibi ramp_correction kbibi_ramp_correction.pl
calc kbint calc_kbint.sh

#density correction
density symmetrize density_symmetrize.py 

# generic table manipulation
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
#do not use table functional here as it needs gnuplot
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

# generic potential manipulation
potential extrapolate potential_extrapolate.sh
potential shift potential_shift.pl
convert_potential tab table_to_tab.pl

# generic distribution manipulation
dist adjust dist_adjust.pl
dist invert dist_boltzmann_invert.pl


# tools needed for (atom/molecule) configuration handling
configuration compare configuration_compare.py

# error analysis
tables jackknife tables_jackknife.pl

# BEGIN: these scripts have to be defined for each simulation program
# interface to gromacs
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

# gromacs scripts specific stuff
convert_potential gromacs potential_to_gromacs.sh
convert_potentials gromacs potentials_to_generic.sh
convert_potential xvg table_to_xvg.pl

#function for gromacs
functions gromacs functions_gromacs.sh

# Interface to ESPResSo
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

# ESPResSo scripts
convert_potential espresso potential_to_generic.sh
convert_potentials espresso potentials_to_generic.sh

# function for ESPResSo
functions espresso functions_genericsim.sh

# lammps scripts
convert_potential lammps potential_to_lammps.sh
convert_potentials lammps potentials_to_generic.sh

# interface to lammps
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

# function for lammps
functions lammps functions_genericsim.sh

# espressopp scripts
convert_potential espressopp potential_to_generic.sh
convert_potentials espressopp potentials_to_generic.sh

# interface to espressopp
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

# function for espressopp
functions espressopp functions_genericsim.sh

# interface to dlpoly
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

# function for dlpoly
functions dlpoly functions_dlpoly.sh

# dlpoly scripts
convert_potential dlpoly potential_to_dlpoly.sh
convert_potentials dlpoly potentials_to_dlpoly.sh

# hoomd-blue scripts
convert_potential hoomd-blue potential_to_generic.sh
convert_potentials hoomd-blue potentials_to_generic.sh

# interface to hoomd-blue
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

# function for hoomd-blue
functions hoomd-blue functions_genericsim.sh

# END: these scripts have to be defined for each simulation program