Documentation‎ > ‎Coarse-graining‎ > ‎

scripts

Key1 Key2 Scriptname
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_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
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
rdf pot RDF_to_POT.pl
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_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
postupd scale postupd_scale.sh
postupd pressure postupd_pressure.sh
postupd splinesmooth postupd_splinesmooth.sh
postupd smooth postupd_smooth.sh
postupd shift dpot_shift_nb.pl
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 convergence postadd_convergence.sh
postadd acc_convergence postadd_acc_convergence.sh
postadd shift dpot_shift_nb.pl
postadd overwrite postadd_overwrite.sh
postadd plot postadd_plot.sh
convergence_check default convergence_check_default.sh
dpot shift_nonbonded dpot_shift_nb.pl
pot shift_nonbonded dpot_shift_nb.pl
dpot shift_bonded dpot_shift_bo.pl
pot shift_bonded dpot_shift_bo.pl
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
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
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
configuration compare configuration_compare.py
tables jackknife tables_jackknife.pl
run gromacs run_gromacs.sh
presimulation gromacs run_gromacs.sh
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.pl
functions 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.pl
functions espresso functions_espresso.sh

add_pot_generic.sh

This script adds up the tables

Usage: csg_call [OPTIONS] add_pot ibi

Used xml options:

  • cg.non-bonded.name

add_POT.pl

This script adds up two potentials In addition, it does some magic tricks:

  1. order of infiles MATTERS !!!!
  2. if infile2 contains an undefined value, it uses the value from infile1
  3. if value for infile1 and infile2 are both invalid, the result is also invalid

Usage: csg_call [OPTIONS] table add infile1 infile2 outfile

calc_density_gromacs.sh

This script calcs the density for gromacs

Usage: csg_call [OPTIONS] density gromacs outputfile csg_density_options

Used xml options:

  • cg.inverse.gromacs.density.block_length
  • cg.inverse.gromacs.density.with_errors
  • cg.inverse.gromacs.equi_time
  • cg.inverse.gromacs.first_frame
  • cg.inverse.gromacs.topol_out
  • cg.inverse.gromacs.traj_type
  • cg.inverse.program
  • cg.non-bonded.name

calc_kbint.sh

This script calculates the Kirkwood-Buff integral out of the rdf

Usage: csg_call [OPTIONS] calc kbint [options] infile outfile

Allowed options:

  • --help show this help
  • --clean remove all intermediate temp files

calc_pressure_espresso.sh

This script calcs the pressure for espresso and writes it to outfile

Usage: csg_call [OPTIONS] pressure espresso outfile

Used external packages: espresso

Used xml options:

  • cg.inverse.espresso.blockfile
  • cg.inverse.espresso.pressure_command

calc_pressure_gromacs.sh

This script calcs the pressure for gromacs and writes it to outfile

Usage: csg_call [OPTIONS] pressure gromacs outfile

Used external packages: gromacs

Used xml options:

  • cg.inverse.gromacs.g_energy.bin
  • cg.inverse.gromacs.g_energy.opts (optional)
  • cg.inverse.gromacs.g_energy.pressure.allow_nan
  • cg.inverse.gromacs.g_energy.topol (optional)
  • cg.inverse.gromacs.topol_out

calc_rdf_espresso.sh

This script calcs the rdf for espresso

Usage: csg_call [OPTIONS] rdf espresso

Used external packages: espresso

Used xml options:

  • cg.inverse.espresso.blockfile
  • cg.inverse.espresso.first_frame
  • cg.inverse.espresso.rdf_command
  • cg.inverse.espresso.traj
  • cg.non-bonded.inverse.espresso.index1
  • cg.non-bonded.inverse.espresso.index2
  • cg.non-bonded.max
  • cg.non-bonded.min
  • cg.non-bonded.name
  • cg.non-bonded.step
  • cg.non-bonded.type1
  • cg.non-bonded.type2

calc_rdf_generic.sh

This script implemtents statistical analysis for the iterative Boltzmann inversion using generic csg tools (csg_stat)

Usage: csg_call [OPTIONS] rdf gromacs

Used xml options:

  • cg.bonded.name (optional)
  • cg.inverse.gromacs.equi_time
  • cg.inverse.gromacs.first_frame
  • cg.inverse.gromacs.rdf.block_length
  • cg.inverse.gromacs.rdf.map (optional)
  • cg.inverse.gromacs.rdf.topol (optional)
  • cg.inverse.gromacs.rdf.with_errors
  • cg.inverse.gromacs.topol_out
  • cg.inverse.gromacs.traj_type
  • cg.inverse.map (optional)
  • cg.inverse.program
  • cg.non-bonded.name

calc_target_rdf_generic.sh

This script calculated reference rdf using generic csg_stat

Usage: csg_call [OPTIONS] calc target_rdf

Used xml options:

  • cg.inverse.gromacs.ref.equi_time
  • cg.inverse.gromacs.ref.first_frame
  • cg.inverse.gromacs.ref.mapping
  • cg.inverse.gromacs.ref.rdf.opts (optional)
  • cg.inverse.gromacs.ref.topol
  • cg.inverse.gromacs.ref.traj
  • cg.inverse.program

calc_thermforce.sh

This script calcs the thermoforce out of gromacs density for the AdResS therm force

Usage: csg_call [OPTIONS] calc thermforce infile outfile

Used xml options:

  • cg.inverse.gromacs.mdp
  • cg.non-bonded.inverse.tf.cg_prefactor (optional)
  • cg.non-bonded.inverse.tf.prefactor
  • cg.non-bonded.inverse.tf.spline_end
  • cg.non-bonded.inverse.tf.spline_start
  • cg.non-bonded.inverse.tf.spline_step
  • cg.non-bonded.max
  • cg.non-bonded.min
  • cg.non-bonded.name
  • cg.non-bonded.step

cma_get.sh

Will download cma python module and put it in CSGSHARE

Usage: csg_call [OPTIONS] cma get

cma_processor.py

Could not import matplotlib.pylab, therefore cma.plot() etc. is not available

Usage: csg_call [OPTIONS] cma precede_state [options] statefile-in statefile-out

Options:

  • -h, --help show this help message and exit
  • --eps=EPS tolerance for initialization

configuration_compare.py

Usage: csg_call [OPTIONS] configuration compare [options] conf1 conf2

Options:

  • -h, --help show this help message and exit
  • --eps=EPS tolerance for mismatch

convergence_check_default.sh

Calculated the sum of all convergence files and create a file 'stop' if the sum is bigger than a given limit

Usage: csg_call [OPTIONS] convergence_check default

Used xml options:

  • cg.inverse.convergence_check.limit
  • cg.non-bonded.name

density_symmetrize.py

This script symmetrizes the density around --adressc for thermodynamic force iteration

Usage: csg_call [OPTIONS] density symmetrize

Allowed options:

  • --adressc X.X center of the adress zone (x-value)
  • --infile FILE input file
  • --outfile FILE output file

dpot_crop.pl

crop the potential update at poorly sampled ends

Usage: csg_call [OPTIONS] dpot crop [OPTIONS] <file> <a> <b>

Allowed options:

  • -h, --help Show this help message

Examples:

  • dpot_crop.pl tmp.dpot.cur tmp.dpot.new

dpot_shift_bo.pl

This script shifts the whole potential to minimum, like it is normally done for bonded potentials.

Usage: csg_call [OPTIONS] dpot shift_bonded infile outfile

dpot_shift_nb.pl

This script shifts the whole potential to the last value, like it is normally done for non-bonded potentials.

Usage: csg_call [OPTIONS] postupd shift infile outfile

dummy.sh

dummy script (does nothing), useful to overwrite default by nothing

Usage: csg_call [OPTIONS] dummy dummy

functions_common.sh

This file defines some commonly used functions:

  • msg -- echos a msg on the screen and send it to the logfile if logging is enabled
  • show_callstack -- show the current callstack
  • die -- make the iterative frame work stopp
  • cat_external -- takes a two tags and shows content of the according script
  • do_external -- takes two tags, find the according script and excute it
  • critical -- executes arguments as command and calls die if not succesful
  • csg_get_interaction_property -- gets an interaction property from the xml file, should only be called from inside a for_all loop or with --all option
  • csg_get_property -- get an property from the xml file
  • trim_all -- make multiple lines into one and strip white space from beginning and the end, reads from stdin
  • mark_done -- mark a task (1st argument) as done in the restart file
  • is_done -- checks if something is already do in the restart file
  • is_int -- checks if all arguments are integers
  • to_int -- convert all given numbers to int using awk's int function
  • is_part -- checks if 1st argument is part of the set given by other arguments
  • has_duplicate -- check if one of the argument is double
  • is_num -- checks if all arguments are numbers
  • get_stepname -- get the dir name of a certain step number (1st argument)
  • get_current_step_dir -- print the directory of the current step
  • get_last_step_dir -- print the directory of the last step
  • get_main_dir -- print the main directory
  • get_current_step_nr -- print the main directory
  • get_step_nr -- print the number of a certain step directory (1st argument)
  • cp_from_main_dir -- copy something from the main directory
  • cp_from_last_step -- copy something from the last step
  • get_time -- gives back current time in sec from 1970
  • get_number_tasks -- get the number of possible tasks from the xml file or determine it automatically under some systems
  • get_table_comment -- get comment lines from a table and add common information, which include the hgid and other information
  • csg_inverse_clean -- clean out the main directory
  • check_path_variable -- check if a variable contains only valid paths
  • add_to_csgshare -- added an directory to the csg internal search directories
  • globalize_dir -- convert a local directory to a global one
  • globalize_file -- convert a local file name to a global one
  • source_function -- source an extra function file
  • csg_banner -- print a big banner
  • csg_calc -- simple calculator, a + b, ...
  • show_csg_tables -- show all concatinated csg tables
  • get_command_from_csg_tables -- print the name of script belonging to certain tags (1st, 2nd argument)
  • source_wrapper -- print the full name of a script belonging to two tags (1st, 2nd argument)
  • find_in_csgshare -- find a script in csg script search path
  • enable_logging -- enables the logging to a certain file (1st argument) or the logfile taken from the xml file
  • get_restart_file -- print the name of the restart file to use
  • check_for_obsolete_xml_options -- check xml file for obsolete options
  • command_not_found_handle -- print and error message if a command or a function was not found

Used xml options:

  • cg.inverse.log_file
  • cg.inverse.map (optional)
  • cg.inverse.method (optional)
  • cg.inverse.restart_file
  • cg.inverse.simulation.tasks
  • cg.non-bonded.min
  • cg.non-bonded.name

functions_espresso.sh

Useful functions for espresso:

  • simulation_finish -- checks if simulation is finished
  • checkpoint_exist -- check if a checkpoint exists
  • get_simulation_setting -- gets parameter a parameter from the settings file (1st argument) from simulation setting file

Used external packages: espresso

Used xml options:

  • cg.inverse.espresso.blockfile_out
  • cg.inverse.espresso.scriptdir (optional)
  • cg.inverse.espresso.success
  • cg.inverse.espresso.traj

functions_gromacs.sh

Useful functions for gromacs:

  • get_simulation_setting -- gets a parameter (1st argument) from gromacs mdp file (default 2nd parameter)
  • check_cutoff -- compared current interactions cutoff vs rvdw,
  • check_temp -- compares k_B T in xml with temp in mpd file
  • simulation_finish -- checks if simulation is finished
  • checkpoint_exist -- check if a checkpoint exists
  • calc_begin_time -- return the max of dt*frames and eqtime
  • calc_end_time -- return dt * nsteps
  • gromacs_log -- redirect stdin to a separate gromacs log file, 1st argument can be the name of the command to echo if redirection takes place

Used external packages: gromacs

Used xml options:

  • cg.inverse.gromacs.conf_out
  • cg.inverse.gromacs.cutoff_check
  • cg.inverse.gromacs.equi_time
  • cg.inverse.gromacs.first_frame
  • cg.inverse.gromacs.gmxrc (optional)
  • cg.inverse.gromacs.log (optional)
  • cg.inverse.gromacs.mdp
  • cg.inverse.gromacs.mdrun.checkpoint
  • cg.inverse.gromacs.pre_simulation
  • cg.inverse.gromacs.temp_check
  • cg.inverse.gromacs.traj_type
  • cg.inverse.kBT
  • cg.inverse.log_file
  • cg.non-bonded.max

imc_purify.sh

This scripts cleans up the dpot tables for each interaction when using IMC

Usage: csg_call [OPTIONS] imc purify

Used xml options:

  • cg.inverse.kBT
  • cg.non-bonded.inverse.do_potential
  • cg.non-bonded.max
  • cg.non-bonded.min
  • cg.non-bonded.name
  • cg.non-bonded.step

imc_stat_generic.sh

This script implemtents statistical analysis for the Inverse Monte Carlo Method using generic csg tools (csg_stat)

Usage: csg_call [OPTIONS] imc_stat gromacs

Used xml options:

  • cg.inverse.gromacs.equi_time
  • cg.inverse.gromacs.first_frame
  • cg.inverse.gromacs.topol_out
  • cg.inverse.gromacs.traj_type
  • cg.inverse.program
  • cg.non-bonded.inverse.target
  • cg.non-bonded.name

initialize_step_generic_espresso.sh

This script initializes an espresso simulation

Usage: csg_call [OPTIONS] initstep_generic espresso

Used xml options:

  • cg.inverse.espresso.blockfile
  • cg.inverse.espresso.blockfile_out
  • cg.inverse.initial_configuration

initialize_step_generic_gromacs.sh

This script implemtents the function initialize

Usage: csg_call [OPTIONS] initstep_generic gromacs

Used external packages: gromacs

Used xml options:

  • cg.inverse.gromacs.conf
  • cg.inverse.gromacs.conf_out
  • cg.inverse.initial_configuration
  • cg.inverse.method

initialize_step_generic.sh

This script implements the initialization for every step in a generic way

Usage: csg_call [OPTIONS] initstep ibi

Used xml options:

  • cg.inverse.program
  • cg.non-bonded.name

initialize_step_optimizer.sh

This script implements the initialization for every step in a generic way

Usage: csg_call [OPTIONS] initstep optimizer

Used xml options:

  • cg.inverse.optimizer.type
  • cg.inverse.program
  • cg.non-bonded.name

inverse.sh

Start the script to run ibi, imc, etc. or clean out current dir

Usage: csg_call [OPTIONS] csg master [OPTIONS] --options settings.xml [clean]

Allowed options:

  • -h, --help show this help
  • -N, --do-iterations N only do N iterations
  • --wall-time SEK Set wall clock time
  • --options FILE Specify the options xml file to use
  • --debug enable debug mode with a lot of information
  • --nocolor disable colors

Examples:

  • inverse.sh --options cg.xml
  • inverse.sh -6 --options cg.xml

Used xml options:

  • cg.inverse.cleanlist (optional)
  • cg.inverse.convergence_check.type
  • cg.inverse.filelist (optional)
  • cg.inverse.iterations_max
  • cg.inverse.method
  • cg.inverse.program
  • cg.inverse.scriptpath (optional)
  • cg.inverse.simulation.background

kbibi_ramp_correction.pl

This script calculates Kirkwood-Buff correction as described in P. Ganguly, D. Mukherji, C. Junghans, N. F. A. van der Vegt, Kirkwood-Buff coarse-grained force fields for aqueous solutions, J. Chem. Theo. Comp., in press (2012), doi:10.1021/ct3000958

Usage: csg_call [OPTIONS] kbibi ramp_correction [OPTIONS] kbint target_kbint outfile

Allowed options:

  • -h, --help Show this help message

Used xml options:

  • cg.inverse.kBT
  • cg.non-bonded.inverse.post_update_options.kbibi.factor
  • cg.non-bonded.inverse.post_update_options.kbibi.r_ramp (optional)
  • cg.non-bonded.inverse.post_update_options.kbibi.start
  • cg.non-bonded.inverse.post_update_options.kbibi.stop
  • cg.non-bonded.max
  • cg.non-bonded.min
  • cg.non-bonded.step

linsolve.m

This script has no help

linsolve.octave

This script has no help

linsolve.py

This script has no help

merge_tables.pl

Merge two tables

Usage: csg_call [OPTIONS] table merge [OPTIONS] <source> <dest> <out>

Allowed options:

  • -v, --version Print version
  • -h, --help Show this help message
  • --withflag only change entries with specific flag in src
  • --noflags don't copy flags
  • --novalues don't copy values

Examples:

  • merge_tables.pl intable intable2 outtable

optimizer_parameters_to_potential.sh

This script generates a single potential (.pot.new) out a parameter value string (1st argument)

Usage: csg_call [OPTIONS] optimizer parameters_to_potential parametervalues

Used xml options:

  • cg.non-bonded.inverse.optimizer.function
  • cg.non-bonded.inverse.optimizer.functionfile (optional)
  • cg.non-bonded.inverse.optimizer.parameters
  • cg.non-bonded.max
  • cg.non-bonded.min
  • cg.non-bonded.name
  • cg.non-bonded.step

optimizer_prepare_state.sh

This script generates the initial state file and puts all in-file together

Usage: csg_call [OPTIONS] optimizer prepare_state outputfile

Used xml options:

  • cg.inverse.optimizer.cma.eps
  • cg.inverse.optimizer.type
  • cg.non-bonded.inverse.optimizer.parameters
  • cg.non-bonded.name

optimizer_state_to_mapping.sh

This script generates a mapping for the reference mapping from the parameters of the active in input state using the mapping template

Usage: csg_call [OPTIONS] optimizer state_to_mapping input

Used xml options:

  • cg.non-bonded.inverse.optimizer.mapping.change
  • cg.non-bonded.inverse.optimizer.mapping.output
  • cg.non-bonded.inverse.optimizer.mapping.template
  • cg.non-bonded.inverse.optimizer.parameters
  • cg.non-bonded.name

optimizer_state_to_potentials.sh

This script generates potential (.pot.new) for all interactions out the first pending line in the input state file and flags this line active in output state

Usage: csg_call [OPTIONS] optimizer state_to_potentials input output

optimizer_target_density.sh

Calculated the difference between rdf

Usage: csg_call [OPTIONS] optimizer_target density

Used xml options:

  • cg.inverse.program
  • cg.non-bonded.inverse.optimizer.density.axis
  • cg.non-bonded.inverse.optimizer.density.max
  • cg.non-bonded.inverse.optimizer.density.min
  • cg.non-bonded.inverse.optimizer.density.molname
  • cg.non-bonded.inverse.optimizer.density.step
  • cg.non-bonded.inverse.optimizer.density.target
  • cg.non-bonded.name

optimizer_target_pressure.sh

Calculates the difference current and target pressure

Usage: csg_call [OPTIONS] optimizer_target pressure

Used xml options:

  • cg.inverse.program
  • cg.non-bonded.inverse.optimizer.pressure.undef (optional)
  • cg.non-bonded.inverse.p_target
  • cg.non-bonded.name

optimizer_target_rdf.sh

Calculated the difference between rdf

Usage: csg_call [OPTIONS] optimizer_target rdf

Used xml options:

  • cg.inverse.optimizer.type
  • cg.inverse.program
  • cg.non-bonded.inverse.optimizer.mapping.change
  • cg.non-bonded.inverse.optimizer.rdf.target
  • cg.non-bonded.inverse.optimizer.rdf.weight (optional)
  • cg.non-bonded.inverse.optimizer.rdf.weightfile (optional)
  • cg.non-bonded.max
  • cg.non-bonded.min
  • cg.non-bonded.name
  • cg.non-bonded.step

postadd_acc_convergence.sh

postadd accumulate convergence script: accumulate ${name}.conv of all steps

Usage: csg_call [OPTIONS] postadd acc_convergence infile outfile

Used xml options:

  • cg.non-bonded.name

postadd_convergence.sh

postadd convergence script, calcs the sum of |${name}.DIST.tgt-${name}.DIST.new| and saves it to ${name}.conv. DIST stands for 'dist', but can be changed by onvergence.what option

usage: postadd_convergence.sh infile outfile

Used xml options:

  • cg.inverse.method
  • cg.non-bonded.inverse.post_add_options.convergence.weight
  • cg.non-bonded.inverse.post_add_options.convergence.what
  • cg.non-bonded.inverse.target
  • cg.non-bonded.max
  • cg.non-bonded.min
  • cg.non-bonded.name
  • cg.non-bonded.step

postadd_copyback.sh

postadd copyback script, copies files back to the maindir

Usage: csg_call [OPTIONS] postadd copyback infile outfile

Used xml options:

  • cg.non-bonded.inverse.post_add_options.copyback.filelist

postadd_dummy.sh

postadd dummy script (does nothing), useful to overwrite default by nothing

Usage: csg_call [OPTIONS] postupd dummy infile outfile

postadd_overwrite.sh

postadd overwrite script, overwrites potential of all other interactions with this one

Usage: csg_call [OPTIONS] postadd overwrite infile outfile

Used xml options:

  • cg.non-bonded.inverse.post_add
  • cg.non-bonded.inverse.post_add_options.overwrite.do
  • cg.non-bonded.name

postadd_plot.sh

postadd plot script, send a certain plot script to gnuplot

Usage: csg_call [OPTIONS] postadd plot infile outfile

Used external packages: gnuplot

Used xml options:

  • cg.inverse.gnuplot.bin
  • cg.non-bonded.inverse.post_add_options.plot.fd
  • cg.non-bonded.inverse.post_add_options.plot.gnuplot_opts (optional)
  • cg.non-bonded.inverse.post_add_options.plot.kill (optional)
  • cg.non-bonded.inverse.post_add_options.plot.script

post_add.sh

This script makes all the post update

Usage: csg_call [OPTIONS] post add

post_add_single.sh

This script makes all the post update with backup for single pairs

Usage: csg_call [OPTIONS] post add_single

Used xml options:

  • cg.non-bonded.inverse.post_add (optional)
  • cg.non-bonded.name

post_update_generic.sh

This script makes all the post update

Usage: csg_call [OPTIONS] post_update ibi

Used xml options:

  • cg.inverse.method

post_update_generic_single.sh

This script makes all the post update with backup for single pairs incl. backups

Usage: csg_call [OPTIONS] post_update_single ibi

Used xml options:

  • cg.non-bonded.inverse.post_update (optional)
  • cg.non-bonded.name

postupd_extrapolate.sh

This script implements extrapolation undefined region of the potential update (.dpot)

Usage: csg_call [OPTIONS] postupd extrapolate infile outfile

Used xml options:

  • cg.non-bonded.bondtype
  • cg.non-bonded.inverse.post_update_options.extrapolate.points
  • cg.non-bonded.name

postupd_kbibi_correction.sh

This script implemtents the post update routine for the various Kirkwood-Buff corrections

Usage: csg_call [OPTIONS] postupd kbibi

Used xml options:

  • cg.inverse.program
  • cg.non-bonded.bondtype
  • cg.non-bonded.inverse.post_update_options.kbibi.do
  • cg.non-bonded.inverse.post_update_options.kbibi.kbint_with_errors
  • cg.non-bonded.inverse.post_update_options.kbibi.type
  • cg.non-bonded.inverse.target
  • cg.non-bonded.max
  • cg.non-bonded.min
  • cg.non-bonded.name
  • cg.non-bonded.step

postupd_pressure.sh

This script implements the pressure update

Usage: csg_call [OPTIONS] postupd pressure infile outfile

Used xml options:

  • cg.inverse.program
  • cg.non-bonded.bondtype
  • cg.non-bonded.inverse.post_update_options.pressure.do
  • cg.non-bonded.inverse.post_update_options.pressure.type
  • cg.non-bonded.max
  • cg.non-bonded.min
  • cg.non-bonded.name
  • cg.non-bonded.step

postupd_scale.sh

This script implements scaling of the potential update (.dpot)

Usage: csg_call [OPTIONS] postupd scale infile outfile

Used xml options:

  • cg.non-bonded.inverse.post_update_options.scale
  • cg.non-bonded.name

postupd_smooth.sh

This script implements smoothing of the potential update (.dpot)

Usage: csg_call [OPTIONS] postupd smooth infile outfile

Used xml options:

  • cg.non-bonded.inverse.post_update_options.smooth.iterations
  • cg.non-bonded.name

postupd_splinesmooth.sh

This script implements smoothing of the potential update (.dpot)

Usage: csg_call [OPTIONS] postupd splinesmooth infile outfile

Used xml options:

  • cg.non-bonded.inverse.post_update_options.splinesmooth.step
  • cg.non-bonded.max
  • cg.non-bonded.min
  • cg.non-bonded.name
  • cg.non-bonded.step

potential_extrapolate.sh

This script extrapolates a potential in the correct way depending on its type.

Usage: csg_call [OPTIONS] potential extrapolate [options] input output

Allowed options:

  • --help show this help
  • --clean remove all intermediate temp files
  • --type TYPE type of the potential possible: non-bonded bond thermforce angle dihedral
  • --avg-point INT number of average points default: 5

potential_to_espresso.sh

This script is a wrapper to convert a potential to espresso

Usage: csg_call [OPTIONS] convert_potential espresso

Used xml options:

  • cg.inverse.espresso.table_bins
  • cg.non-bonded.inverse.espresso.table
  • cg.non-bonded.max
  • cg.non-bonded.name

potential_to_gromacs.sh

This script is a wrapper to convert a potential to gromacs

Usage: csg_call [OPTIONS] convert_potential gromacs [options] input output

Allowed options:

  • --help show this help
  • --clean remove all intermediate temp files
  • --r2d converts rad to degree (scale x axis with 180/3.1415) for angle and dihedral Note: VOTCA calcs in rad, but gromacs in degree
  • --no-shift do not shift the potential

Used xml options:

  • cg.inverse.gromacs.mdp
  • cg.inverse.gromacs.pot_max (optional)
  • cg.inverse.gromacs.table_bins
  • cg.inverse.gromacs.table_end
  • cg.inverse.gromacs.table_end (optional)
  • cg.non-bonded.bondtype
  • cg.non-bonded.inverse.gromacs.table
  • cg.non-bonded.name

prepare_generic_espresso.sh

This script implements the prepare step for espresso

Usage: csg_call [OPTIONS] prepare_generic espresso

Used xml options:

  • cg.inverse.espresso.blockfile
  • cg.inverse.espresso.blockfile_out

prepare_generic_gromacs.sh

This script does the prepare step for gromacs

Usage: csg_call [OPTIONS] prepare_generic gromacs

Used xml options:

  • cg.inverse.gromacs.conf
  • cg.inverse.gromacs.conf_out

prepare_generic.sh

This script prepares potentials in a generic way

Usage: csg_call [OPTIONS] prepare ibi

Used xml options:

  • cg.inverse.method
  • cg.inverse.program

prepare_generic_single.sh

This script implements the prepares the potential in step 0, using pot.in or by resampling the target distribution

Usage: csg_call [OPTIONS] prepare_single ibi

Used xml options:

  • cg.non-bonded.bondtype
  • cg.non-bonded.inverse.target
  • cg.non-bonded.max
  • cg.non-bonded.min
  • cg.non-bonded.name
  • cg.non-bonded.step

prepare_ibm.sh

Informs users that ibm was renamed to ibi.

Usage: csg_call [OPTIONS] prepare ibm

prepare_imc.sh

This script initializes potentials for imc

Usage: csg_call [OPTIONS] prepare imc

Used xml options:

  • cg.bonded.name (optional)

prepare_optimizer.sh

This script initizalizes potentials for optimizer methods

Usage: csg_call [OPTIONS] prepare optimizer

Used xml options:

  • cg.inverse.optimizer.type
  • cg.inverse.program
  • cg.non-bonded.inverse.optimizer.parameters

prepare_optimizer_single.sh

This script

  • reads sinple interaction optimizer infile
  • checks if the number of values are enough

Usage: csg_call [OPTIONS] prepare_single optimizer N

where N is the total number of parameters

Used xml options:

  • cg.inverse.optimizer.type
  • cg.non-bonded.inverse.optimizer.parameters
  • cg.non-bonded.name

pressure_cor_simple.pl

This script calls the pressure corrections $dU=A*(1-r/r_c)$, where $A=-0.1k_B T * \max(1,|p_cur-p_target|*scale) * \sign(p_cur-p_target)$

Usage: csg_call [OPTIONS] pressure_cor simple p_cur outfile

Used xml options:

  • cg.inverse.kBT
  • cg.non-bonded.inverse.post_update_options.pressure.simple.scale
  • cg.non-bonded.inverse.p_target
  • cg.non-bonded.max
  • cg.non-bonded.min
  • cg.non-bonded.step

pressure_cor_wjk.pl

This script calls the pressure corrections like in Wan, Junghans & Kremer, Euro. Phys. J. E 28, 221 (2009) Basically dU=A*(1-r/r_c) with A= -max(0.1k_B T, Int ) * sign(p_cur-p_target) and Int is the integral from Eq. 7 in the paper.

Usage: csg_call [OPTIONS] pressure_cor wjk p_cur outfile

Used xml options:

  • cg.inverse.kBT
  • cg.non-bonded.inverse.particle_dens
  • cg.non-bonded.inverse.post_update_options.pressure.wjk.scale
  • cg.non-bonded.inverse.p_target
  • cg.non-bonded.max
  • cg.non-bonded.min
  • cg.non-bonded.name
  • cg.non-bonded.step

RDF_to_POT.pl

This script converts rdf to pot of mean force ($F(r)=-k_B T\ln g(r)$)

In addtion, it does some magic tricks:

  • do not crash when calc log(0)
  • extrapolate the beginning of pot
  • the maximum to interpolate is pot_max (see xml)
  • bigger value will be set to that max
  • shift the potential, so that it is zero at the cutoff
  • set all values to zero after the cutoff

Usage: csg_call [OPTIONS] rdf pot infile outfile

Used xml options:

  • cg.inverse.kBT
  • cg.non-bonded.max

resample_target.sh

This script resamples distribution to grid spacing of the setting xml file and extrapolates if needed

Usage: csg_call [OPTIONS] resample target input output

Used xml options:

  • cg.non-bonded.bondtype
  • cg.non-bonded.max
  • cg.non-bonded.min
  • cg.non-bonded.name
  • cg.non-bonded.step

run_espresso.sh

This script runs espresso for the Inverse Boltzmann Method

Usage: csg_call [OPTIONS] run espresso

Used external packages: espresso

Used xml options:

  • cg.inverse.espresso.blockfile
  • cg.inverse.espresso.blockfile_out
  • cg.inverse.espresso.command
  • cg.inverse.espresso.debug
  • cg.inverse.espresso.exclusions
  • cg.inverse.espresso.n_snapshots
  • cg.inverse.espresso.n_steps
  • cg.inverse.espresso.success
  • cg.inverse.espresso.traj
  • cg.inverse.method
  • cg.non-bonded.inverse.espresso.index1
  • cg.non-bonded.inverse.espresso.index2

run_gromacs.sh

This script runs a gromacs simulation or pre-simulation

Usage: csg_call [OPTIONS] run gromacs [--pre]

Used external packages: gromacs

Used xml options:

  • cg.inverse.gromacs.conf
  • cg.inverse.gromacs.conf_out
  • cg.inverse.gromacs.grompp.bin
  • cg.inverse.gromacs.grompp.opts (optional)
  • cg.inverse.gromacs.index
  • cg.inverse.gromacs.mdp
  • cg.inverse.gromacs.mdrun.checkpoint
  • cg.inverse.gromacs.mdrun.command
  • cg.inverse.gromacs.mdrun.opts (optional)
  • cg.inverse.gromacs.pre_simulation
  • cg.inverse.gromacs.topol_in
  • cg.inverse.gromacs.topol_out
  • cg.inverse.gromacs.traj_type

simplex_downhill_processor.pl

Changes a simplex state according to the current state using the Nelder–Mead method or downhill simplex algorithm.

Usage: csg_call [OPTIONS] simplex precede_state current_state new_state

solve_matlab.sh

This script solves a linear equation system from imc using matlab

Usage: csg_call [OPTIONS] imcsolver matlab <group> <outfile>

Used external packages: matlab

Used xml options:

  • cg.inverse.imc.matlab.bin

solve_numpy.sh

This script solves a linear equation system from imc using numpy

Usage: csg_call [OPTIONS] imcsolver numpy <group> <outfile>

Used external packages: numpy

Used xml options:

  • cg.inverse.imc.numpy.bin

solve_octave.sh

This script solves a linear equation system from imc using octave

Usage: csg_call [OPTIONS] imcsolver octave <group> <outfile>

Used external packages: octave

Used xml options:

  • cg.inverse.imc.octave.bin

table_average.sh

This script creates averages tables and also calculates the error.

Usage: csg_call [OPTIONS] table average [options] table1 table2 table3 ....

Allowed options:

  • -h, --help show this help
  • -o, --output NANE output file name
  • --cols NUM Number of columns per file Default: 3
  • --col-y NUM y-data column Default: 2
  • --col-x NUM x-data column Default: 1
  • ``--clean `` Clean intermediate files

Examples:

  • table_average.sh --output CG-CG.dist.new CG-CG*.dist.new

table_change_flag.sh

This script changes the flags (col 3) of a table

Usage: csg_call [OPTIONS] table change_flag input outfile

table_combine.pl

This script combines two tables with a certain operation

Usage: table_combine.pl [OPTIONS] <in> <in2> <out>

Allowed options:

  • --error ERR Relative error Default: 1e-05
  • --op OP Operation to perform Possible: =,+,-,,/,d,d2,x d = |y1-y2|, d2 = (y1-y2)^2, x=* (to avoid shell trouble)
  • --sum Output the sum instead of a new table
  • --die Die if op '=' fails
  • --no-flags Do not check for the flags
  • --scale XXX Scale output/sum with this number Default 1
  • --withflag FL only operate on entries with specific flag in src
  • -h, --help Show this help message

table_dummy.sh

This script creates a zero table with grid min:step:max

Usage: csg_call [OPTIONS] table dummy min:step:max outfile

table_extrapolate.pl

This script extrapolates a table

Usage: csg_call [OPTIONS] table extrapolate [OPTIONS] <in> <out>

Allowed options:

  • --avgpoints A average over the given number of points to extrapolate: default is 3
  • --function constant, linear, quadratic or exponential, sasha: default is quadratic
  • --no-flagupdate do not update the flag of the extrapolated values
  • --region left, right, or leftright: default is leftright
  • --curvature C curvature of the quadratic function: default is 10000, makes sense only for quadratic extrapolation, ignored for other cases
  • -h, --help Show this help message

Extrapolation methods: always $m = dy/dx= (y[i+A]-y[i])/(x[i+A]-x[i])$

  • constant: $y = y0$
  • linear: $y = ax + b\;\;b = - m*x_0 + y_0;;a = m$
  • sasha: $y = a*(x-b)^2\;\;b = (x0 - 2y_0/m)\;\; a = m^2/(4*y_0)$
  • exponential: $y = a*\exp(b*x)\;\;a = y0*\exp(-m*x0/y0)\;\;b = m/y_0$
  • quadratic: $y = C*(x+a)^2 + b\;\;a = m/(2*C) - x0\;\; b = y_0 - m^2/(4*C)$

table_functional.sh

This script creates a table with grid min:step:max for the a functional form

Usage: csg_call [OPTIONS] table functional [options] output

Allowed options:

  • -h, --help show this help
  • --grid XX:XX:XX Output grid of the table
  • --var X=Y Set a variable used in the function
  • --fct FCT functional form of the table
  • --headerfile XXX Extra headerfile for the plot script (useful for complicated functions)
  • --gnuplot CMD Gnuplot command to use Default: gnuplot
  • ``--clean `` Clean intermediate files

Used external packages: gnuplot

Examples:

  • table_functional.sh --grid 0:0.1:1 --fct x**2 CG-CG.tab.new

table_getsubset.py

This script get the a subset of a table

Usage: csg_call [OPTIONS] table getsubset

Allowed options:

  • --xstart X.X x value where the subset starts
  • --xstop X.X x value where the subset stops
  • --infile FILE input file
  • --outfile FILE output file

table_get_value.pl

This script print the y value of x, which is closest to X.

Usage: csg_call [OPTIONS] table get_value [OPTIONS] X infile

Allowed options:

  • -h, --help Show this help message

table_integrate.pl

This script calculates the integral of a table. Please note the force is the NEGATIVE integral of the potential (use 'table linearop' and multiply the table with -1)

Usage: csg_call [OPTIONS] table integrate [OPTIONS] <in> <out>

Allowed options:

  • --with-errors calculate error
  • --with-S Add entropic contribution to force $2k_B T/r$
  • --kbT NUMBER use NUMBER as $k_B*T$ for the entropic part
  • --from Integrate from left or right (to define the zero point) Default: right
  • --sphere Add spherical volume term ($r^2$)
  • -h, --help Show this help message

Examples:

  • table_integrate.pl --with-S --kbT 2.49435 tmp.force tmp.dpot

table_linearop.pl

This script performs a linear operation on the y values: $y_{new} = a*y_{old} + b$

Usage: csg_call [OPTIONS] table linearop [OPTIONS] <in> <out> <a> <b>

Allowed options:

  • -h, --help Show this help message
  • --withflag FL only change entries with specific flag in src
  • --with-errors also read and calculate errors
  • --on-x work on x values instead of y values

Examples:

  • table_linearop.pl tmp.dpot.cur tmp.dpot.new 1.0 0.0

table_scale.pl

This script applies a prefactor to infile. The prefactor is is interpolated lines between the prefactor1 and prefactor2.

Usage: csg_call [OPTIONS] table scale [OPTIONS] infile outfile prefactor1 prefactor2

Allowed options:

  • -h, --help Show this help message

tables_jackknife.pl

This script has no help

table_smooth_borders.py

This script smooths the border for thermodynamic force iteration

Usage: csg_call [OPTIONS] table smooth_borders

Allowed options:

  • --xstart X.X where the smoothing starts
  • --xstop X.X where the smoothing stops
  • --infile FILE input file
  • --outfile FILE output file

table_smooth.pl

This script smoothes a table

Usage: csg_call [OPTIONS] table smooth infile outfile

table_to_tab.pl

This script converts csg potential files to the tab format (as read by espresso). Potential is copied in the C12 column.

In addition, it does some magic tricks:

  • shift the potential, so that it is zero at the cutoff
  • set all values to zero after the cutoff

Usage: csg_call [OPTIONS] convert_potential tab in_pot in_deriv_pot outfile

Used xml options:

  • cg.inverse.espresso.table_bins
  • cg.inverse.espresso.table_end

table_to_xvg.pl

This script converts csg potential files to the xvg format.

Allowed options:

  • -v, --version print version
  • -h, --help show this help message
  • --type XXX change the type of xvg table Default: non-bonded
  • --max MAX Replace all pot value bigger MAX by MAX

Possible types: non-bonded (=C12), bond, thermforce, C12, C6, CB, angle, dihedral

Examples:

  • table_to_xvg.pl --type bond table.in table_b0.xvg

tag_file.sh

Add table_comment to the head of a file

Usage: csg_call [OPTIONS] tag file input output

update_ibi_pot.pl

This script calcs dU out of two rdfs with the rules of inverse boltzmann

In addition, it does some magic tricks:

  • do not update if one of the two rdf is undefined

Usage: csg_call [OPTIONS] update ibi_pot target_rdf new_rdf cur_pot outfile

Used xml options:

  • cg.inverse.kBT

update_ibi.sh

This script implements the function update for the Inverse Boltzmann Method

Usage: csg_call [OPTIONS] update ibi

Used xml options:

  • cg.inverse.program

update_ibi_single.sh

This script implemtents the function update for a single pair for the Inverse Boltzmann Method

Usage: csg_call [OPTIONS] update ibi_single

Used xml options:

  • cg.non-bonded.bondtype
  • cg.non-bonded.inverse.do_potential
  • cg.non-bonded.inverse.target
  • cg.non-bonded.max
  • cg.non-bonded.min
  • cg.non-bonded.name
  • cg.non-bonded.step

update_ibm.sh

Informs users that ibm was renamed to ibi.

Usage: csg_call [OPTIONS] update ibm

update_imc.sh

This script implements the function update for the Inverse Monte Carlo Method

Usage: csg_call [OPTIONS] update imc

Used xml options:

  • cg.inverse.imc.solver
  • cg.inverse.program
  • cg.non-bonded.inverse.imc.group

update_optimizer.sh

This script:

  • implements the update function for each non-bonded interaction
  • performs optimizer algorithm if no pending parameter sets present
  • continues with next parameter set in table if otherwise

Usage: csg_call [OPTIONS] update optimizer

Used xml options:

  • cg.inverse.optimizer.type
  • cg.non-bonded.name

update_optimizer_single.sh

This script:

  • calculates the new property
  • compares it to the target property and calculates the target function accordingly

Usage: csg_call [OPTIONS] update optimizer_single

Used xml options:

  • cg.inverse.program
  • cg.non-bonded.inverse.optimizer.targets
  • cg.non-bonded.inverse.optimizer.target_weights
  • cg.non-bonded.inverse.post_update (optional)
  • cg.non-bonded.name

update_tf.sh

This script implements the function update for the thermodynamic force interation

Usage: csg_call [OPTIONS] update tf

update_tf_single.sh

This script implemtents the function update of a single interaction for the thermodynamics force iteration

Usage: csg_call [OPTIONS] update tf_single

Used xml options:

  • cg.inverse.program
  • cg.non-bonded.inverse.do_potential
  • cg.non-bonded.inverse.tf.molname
  • cg.non-bonded.inverse.tf.spline_end
  • cg.non-bonded.max
  • cg.non-bonded.min
  • cg.non-bonded.name
  • cg.non-bonded.step