
add_POT.pl
^^^^^^^^^^

.. include:: scripts/add_POT.pl.rst

add_pot_generic.sh
^^^^^^^^^^^^^^^^^^

.. include:: scripts/add_pot_generic.sh.rst

calc_density_generic.sh
^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/calc_density_generic.sh.rst

calc_kbint.sh
^^^^^^^^^^^^^

.. include:: scripts/calc_kbint.sh.rst

calc_pressure_gromacs.sh
^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/calc_pressure_gromacs.sh.rst

calc_pressure_lammps.sh
^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/calc_pressure_lammps.sh.rst

calc_rdf_generic.sh
^^^^^^^^^^^^^^^^^^^

.. include:: scripts/calc_rdf_generic.sh.rst

calc_target_rdf_generic.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/calc_target_rdf_generic.sh.rst

check_csg_xml.py
^^^^^^^^^^^^^^^^

.. include:: scripts/check_csg_xml.py.rst

clean_generic.sh
^^^^^^^^^^^^^^^^

.. include:: scripts/clean_generic.sh.rst

cma_processor.py
^^^^^^^^^^^^^^^^

.. include:: scripts/cma_processor.py.rst

convergence_check_default.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/convergence_check_default.sh.rst

dist_adjust.pl
^^^^^^^^^^^^^^

.. include:: scripts/dist_adjust.pl.rst

dist_boltzmann_invert.pl
^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/dist_boltzmann_invert.pl.rst

dummy.sh
^^^^^^^^

.. include:: scripts/dummy.sh.rst

functions_common.sh
^^^^^^^^^^^^^^^^^^^

.. include:: scripts/functions_common.sh.rst

functions_dlpoly.sh
^^^^^^^^^^^^^^^^^^^

.. include:: scripts/functions_dlpoly.sh.rst

functions_genericsim.sh
^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/functions_genericsim.sh.rst

functions_gromacs.sh
^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/functions_gromacs.sh.rst

iie.py
^^^^^^

.. include:: scripts/iie.py.rst

imc_stat_generic.sh
^^^^^^^^^^^^^^^^^^^

.. include:: scripts/imc_stat_generic.sh.rst

initialize_step_generic.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/initialize_step_generic.sh.rst

initialize_step_genericsim.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/initialize_step_genericsim.sh.rst

initialize_step_optimizer.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/initialize_step_optimizer.sh.rst

initialize_step_re.sh
^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/initialize_step_re.sh.rst

inverse.sh
^^^^^^^^^^

.. include:: scripts/inverse.sh.rst

kbibi_ramp_correction.pl
^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/kbibi_ramp_correction.pl.rst

lj_126.pl
^^^^^^^^^

.. include:: scripts/lj_126.pl.rst

merge_tables.pl
^^^^^^^^^^^^^^^

.. include:: scripts/merge_tables.pl.rst

optimizer_parameters_to_potential.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/optimizer_parameters_to_potential.sh.rst

optimizer_prepare_state.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/optimizer_prepare_state.sh.rst

optimizer_state_to_mapping.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/optimizer_state_to_mapping.sh.rst

optimizer_state_to_potentials.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/optimizer_state_to_potentials.sh.rst

optimizer_target_density.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/optimizer_target_density.sh.rst

optimizer_target_pressure.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/optimizer_target_pressure.sh.rst

optimizer_target_rdf.sh
^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/optimizer_target_rdf.sh.rst

post_add.sh
^^^^^^^^^^^

.. include:: scripts/post_add.sh.rst

post_add_single.sh
^^^^^^^^^^^^^^^^^^

.. include:: scripts/post_add_single.sh.rst

post_update_generic.sh
^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/post_update_generic.sh.rst

post_update_generic_single.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/post_update_generic_single.sh.rst

post_update_re_single.sh
^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/post_update_re_single.sh.rst

postadd_acc_convergence.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/postadd_acc_convergence.sh.rst

postadd_average.sh
^^^^^^^^^^^^^^^^^^

.. include:: scripts/postadd_average.sh.rst

postadd_compress.sh
^^^^^^^^^^^^^^^^^^^

.. include:: scripts/postadd_compress.sh.rst

postadd_convergence.sh
^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/postadd_convergence.sh.rst

postadd_copyback.sh
^^^^^^^^^^^^^^^^^^^

.. include:: scripts/postadd_copyback.sh.rst

postadd_dummy.sh
^^^^^^^^^^^^^^^^

.. include:: scripts/postadd_dummy.sh.rst

postadd_overwrite.sh
^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/postadd_overwrite.sh.rst

postadd_plot.sh
^^^^^^^^^^^^^^^

.. include:: scripts/postadd_plot.sh.rst

postadd_shift.sh
^^^^^^^^^^^^^^^^

.. include:: scripts/postadd_shift.sh.rst

postadd_smooth_at_cut_off.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/postadd_smooth_at_cut_off.sh.rst

postupd_addlj.sh
^^^^^^^^^^^^^^^^

.. include:: scripts/postupd_addlj.sh.rst

postupd_cibi_correction.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/postupd_cibi_correction.sh.rst

postupd_extrapolate.sh
^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/postupd_extrapolate.sh.rst

postupd_ibi.sh
^^^^^^^^^^^^^^

.. include:: scripts/postupd_ibi.sh.rst

postupd_kbibi_correction.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/postupd_kbibi_correction.sh.rst

postupd_pressure.sh
^^^^^^^^^^^^^^^^^^^

.. include:: scripts/postupd_pressure.sh.rst

postupd_scale.sh
^^^^^^^^^^^^^^^^

.. include:: scripts/postupd_scale.sh.rst

postupd_smooth.sh
^^^^^^^^^^^^^^^^^

.. include:: scripts/postupd_smooth.sh.rst

postupd_splinesmooth.sh
^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/postupd_splinesmooth.sh.rst

potential_extrapolate.sh
^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/potential_extrapolate.sh.rst

potential_shift.pl
^^^^^^^^^^^^^^^^^^

.. include:: scripts/potential_shift.pl.rst

potential_to_dlpoly.sh
^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/potential_to_dlpoly.sh.rst

potential_to_generic.sh
^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/potential_to_generic.sh.rst

potential_to_gromacs.sh
^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/potential_to_gromacs.sh.rst

potential_to_lammps.sh
^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/potential_to_lammps.sh.rst

potentials_to_dlpoly.sh
^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/potentials_to_dlpoly.sh.rst

potentials_to_generic.sh
^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/potentials_to_generic.sh.rst

pre_update_re.sh
^^^^^^^^^^^^^^^^

.. include:: scripts/pre_update_re.sh.rst

prepare_generic.sh
^^^^^^^^^^^^^^^^^^

.. include:: scripts/prepare_generic.sh.rst

prepare_generic_single.sh
^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/prepare_generic_single.sh.rst

prepare_iie.sh
^^^^^^^^^^^^^^

.. include:: scripts/prepare_iie.sh.rst

prepare_imc.sh
^^^^^^^^^^^^^^

.. include:: scripts/prepare_imc.sh.rst

prepare_optimizer.sh
^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/prepare_optimizer.sh.rst

prepare_optimizer_single.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/prepare_optimizer_single.sh.rst

prepare_re.sh
^^^^^^^^^^^^^

.. include:: scripts/prepare_re.sh.rst

pressure_cor_simple.pl
^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/pressure_cor_simple.pl.rst

pressure_cor_wjk.pl
^^^^^^^^^^^^^^^^^^^

.. include:: scripts/pressure_cor_wjk.pl.rst

resample_target.sh
^^^^^^^^^^^^^^^^^^

.. include:: scripts/resample_target.sh.rst

run_genericsim.sh
^^^^^^^^^^^^^^^^^

.. include:: scripts/run_genericsim.sh.rst

run_gromacs.sh
^^^^^^^^^^^^^^

.. include:: scripts/run_gromacs.sh.rst

simplex_downhill_processor.pl
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/simplex_downhill_processor.pl.rst

table_average.sh
^^^^^^^^^^^^^^^^

.. include:: scripts/table_average.sh.rst

table_change_flag.sh
^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/table_change_flag.sh.rst

table_combine.pl
^^^^^^^^^^^^^^^^

.. include:: scripts/table_combine.pl.rst

table_dummy.sh
^^^^^^^^^^^^^^

.. include:: scripts/table_dummy.sh.rst

table_extrapolate.pl
^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/table_extrapolate.pl.rst

table_functional.sh
^^^^^^^^^^^^^^^^^^^

.. include:: scripts/table_functional.sh.rst

table_get_value.pl
^^^^^^^^^^^^^^^^^^

.. include:: scripts/table_get_value.pl.rst

table_integrate.pl
^^^^^^^^^^^^^^^^^^

.. include:: scripts/table_integrate.pl.rst

table_linearop.pl
^^^^^^^^^^^^^^^^^

.. include:: scripts/table_linearop.pl.rst

table_scale.pl
^^^^^^^^^^^^^^

.. include:: scripts/table_scale.pl.rst

table_smooth.pl
^^^^^^^^^^^^^^^

.. include:: scripts/table_smooth.pl.rst

table_smooth_at_cut_off.py
^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/table_smooth_at_cut_off.py.rst

table_switch_border.pl
^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/table_switch_border.pl.rst

table_to_tab.pl
^^^^^^^^^^^^^^^

.. include:: scripts/table_to_tab.pl.rst

table_to_xvg.pl
^^^^^^^^^^^^^^^

.. include:: scripts/table_to_xvg.pl.rst

tables_jackknife.pl
^^^^^^^^^^^^^^^^^^^

.. include:: scripts/tables_jackknife.pl.rst

tag_file.sh
^^^^^^^^^^^

.. include:: scripts/tag_file.sh.rst

update_ibi.sh
^^^^^^^^^^^^^

.. include:: scripts/update_ibi.sh.rst

update_ibi_pot.pl
^^^^^^^^^^^^^^^^^

.. include:: scripts/update_ibi_pot.pl.rst

update_ibi_single.sh
^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/update_ibi_single.sh.rst

update_iie.sh
^^^^^^^^^^^^^

.. include:: scripts/update_iie.sh.rst

update_imc.sh
^^^^^^^^^^^^^

.. include:: scripts/update_imc.sh.rst

update_imc_single.sh
^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/update_imc_single.sh.rst

update_optimizer.sh
^^^^^^^^^^^^^^^^^^^

.. include:: scripts/update_optimizer.sh.rst

update_optimizer_single.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: scripts/update_optimizer_single.sh.rst

update_re.sh
^^^^^^^^^^^^

.. include:: scripts/update_re.sh.rst

