add_POT.pl¶
NAME¶
csg_call table add - Part of the VOTCA package
SYNOPSIS¶
csg_call table add [OPTIONS]
csg_call table add [–help]
Usage: csg_call [OPTIONS] table add infile1 infile2 outfile
DESCRIPTION¶
This script adds up two potentials In addition, it does some magic tricks: + order of infiles MATTERS !!!! + if infile2 contains an undefined value, it uses the value from infile1 + if value for infile1 and infile2 are both invalid, the result is also invalid
add_pot_generic.sh¶
NAME¶
csg_call add_pot ibi - Part of the VOTCA package
SYNOPSIS¶
csg_call add_pot ibi [OPTIONS]
csg_call add_pot ibi [–help]
Usage: csg_call [OPTIONS] add_pot ibi
DESCRIPTION¶
This script adds up the tables
calc_density_generic.sh¶
NAME¶
csg_call density gromacs - Part of the VOTCA package
SYNOPSIS¶
csg_call density gromacs [OPTIONS]
csg_call density gromacs [–help]
Usage: csg_call [OPTIONS] density gromacs outputfile csg_density_options
DESCRIPTION¶
This script calcs the density using csg_density
calc_kbint.sh¶
NAME¶
csg_call calc kbint - Part of the VOTCA package
SYNOPSIS¶
csg_call calc kbint [OPTIONS]
csg_call calc kbint [–help]
Usage: csg_call [OPTIONS] calc kbint [options] infile outfile
DESCRIPTION¶
This script calculates the Kirkwood-Buff integral out of the rdf
OPTIONS¶
Allowed options:
--help show this help
--clean remove all intermediate temp files
calc_pressure_gromacs.sh¶
NAME¶
csg_call pressure gromacs - Part of the VOTCA package
SYNOPSIS¶
csg_call pressure gromacs [OPTIONS]
csg_call pressure gromacs [–help]
Usage: csg_call [OPTIONS] pressure gromacs outfile
DESCRIPTION¶
This script calcs the pressure for gromacs and writes it to outfile
Used external packages: gromacs
calc_pressure_lammps.sh¶
NAME¶
csg_call pressure lammps - Part of the VOTCA package
SYNOPSIS¶
csg_call pressure lammps [OPTIONS]
csg_call pressure lammps [–help]
Usage: csg_call [OPTIONS] pressure lammps outfile
DESCRIPTION¶
This script calcs the pressure for lammps and writes it to outfile
Used external packages: lammps
calc_rdf_generic.sh¶
NAME¶
csg_call rdf_incl_intra generic - Part of the VOTCA package
SYNOPSIS¶
csg_call rdf_incl_intra generic [OPTIONS]
csg_call rdf_incl_intra generic [–help]
Usage: csg_call [OPTIONS] rdf_incl_intra generic [–help] [–include-intra]
DESCRIPTION¶
using generic csg tools (csg_stat)
With –include-intra intramolecular interactions are included and the distributions are saved as .dist-incl.new.
calc_target_rdf_generic.sh¶
NAME¶
csg_call calc target_rdf - Part of the VOTCA package
SYNOPSIS¶
csg_call calc target_rdf [OPTIONS]
csg_call calc target_rdf [–help]
Usage: csg_call [OPTIONS] calc target_rdf
DESCRIPTION¶
This script calculated reference rdf using generic csg_stat
clean_generic.sh¶
NAME¶
csg_call clean gromacs - Part of the VOTCA package
SYNOPSIS¶
csg_call clean gromacs [OPTIONS]
csg_call clean gromacs [–help]
Usage: csg_call [OPTIONS] clean gromacs
DESCRIPTION¶
This script cleans up after a simulation step
cma_processor.py¶
NAME¶
csg_call cma precede_state - Part of the VOTCA package
SYNOPSIS¶
csg_call cma precede_state [OPTIONS]
csg_call cma precede_state [–help]
Usage: cma_processor.py [-h] [–eps EPS]
%prog [options] statefile-in statefile-out
DESCRIPTION¶
OPTIONS¶
options:
-h, --help show this help message and exit
--eps EPS tolerance for initialization
convergence_check_default.sh¶
NAME¶
csg_call convergence_check default - Part of the VOTCA package
SYNOPSIS¶
csg_call convergence_check default [OPTIONS]
csg_call convergence_check default [–help]
Usage: csg_call [OPTIONS] convergence_check default
DESCRIPTION¶
Calculated the sum of all convergence files and create a file ‘stop’ if the sum is bigger than a given limit
dist_adjust.pl¶
NAME¶
csg_call dist adjust - Part of the VOTCA package
SYNOPSIS¶
csg_call dist adjust [OPTIONS]
csg_call dist adjust [–help]
Usage: csg_call [OPTIONS] dist adjust [OPTIONS] <in> <out>
DESCRIPTION¶
This script adjusts a distribution in such a way that value smaller 0 will be replaces with 0.
EXAMPLES¶
* dist_adjust.pl CG-CG.dist.tmp CG-CG.dist.new
OPTIONS¶
Allowed options:
-h, --help Show this help message
dist_boltzmann_invert.pl¶
NAME¶
csg_call dist invert - Part of the VOTCA package
SYNOPSIS¶
csg_call dist invert [OPTIONS]
csg_call dist invert [–help]
Usage: csg_call [OPTIONS] dist invert [OPTIONS] <in> <out>
DESCRIPTION¶
Boltzmann inverts a distribution (‘’$F(x)=-k_B T\ln g(x)$’’)
In addtion, it does some magic tricks: - do not crash when calc log(0) - choose the right normalization depending on the type of interaction - input dist should be unnormalized (like csg_stat calcs it)
EXAMPLES¶
* dist_boltzmann_invert.pl --kbT 2.49435 --min 0.001 tmp.dist tmp.pot
OPTIONS¶
Allowed options:
--kbT NUMBER use NUMBER as ''$k_B*T$'' for the entropic part
--type XXX change the type of interaction
Default: non-bonded
--min XXX minimum value to consider
Default: 1e-10
-h, --help Show this help message
Possible types: non-bonded, bond, angle, dihedral
dummy.sh¶
NAME¶
csg_call dummy dummy - Part of the VOTCA package
SYNOPSIS¶
csg_call dummy dummy [OPTIONS]
csg_call dummy dummy [–help]
Usage: csg_call [OPTIONS] dummy dummy
DESCRIPTION¶
dummy script (does nothing), useful to overwrite default by nothing
functions_common.sh¶
NAME¶
csg_call functions common - Part of the VOTCA package
SYNOPSIS¶
csg_call functions common [OPTIONS]
csg_call functions common [–help]
DESCRIPTION¶
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 arguments is double
remove_duplicate – remove duplicates list of arguments
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 git id 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
functions_dlpoly.sh¶
NAME¶
csg_call functions dlpoly - Part of the VOTCA package
SYNOPSIS¶
csg_call functions dlpoly [OPTIONS]
csg_call functions dlpoly [–help]
DESCRIPTION¶
Useful functions for the generic simulation program: * simulation_finish – checks if simulation is finished * checkpoint_exist – check if a checkpoint exists (REVIVE _and_ REVCON - both are needed!) * get_simulation_setting – gets parameter a parameter from the settings file (1st argument) from simulation setting file (not implemented)
functions_genericsim.sh¶
NAME¶
csg_call functions espresso - Part of the VOTCA package
SYNOPSIS¶
csg_call functions espresso [OPTIONS]
csg_call functions espresso [–help]
DESCRIPTION¶
Useful functions for the generic simulation program: * simulation_finish – checks if simulation is finished * checkpoint_exist – check if a checkpoint exists (not implemented) * get_simulation_setting – gets parameter a parameter from the settings file (1st argument) from simulation setting file (not implemented)
functions_gromacs.sh¶
NAME¶
csg_call functions gromacs - Part of the VOTCA package
SYNOPSIS¶
csg_call functions gromacs [OPTIONS]
csg_call functions gromacs [–help]
DESCRIPTION¶
Useful functions for gromacs: * get_simulation_setting – gets a parameter (1st argument) from gromacs mdp file (default 2nd parameter) * 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
iie.py¶
NAME¶
csg_call update iie_pot - Part of the VOTCA package
SYNOPSIS¶
csg_call update iie_pot [OPTIONS]
csg_call update iie_pot [–help]
Usage: iie.py [-h] {potential_guess,newton,newton-mod,gauss-newton} …
Calculate U or ΔU with Integral Equations.
DESCRIPTION¶
OPTIONS¶
positional arguments:
{potential_guess,newton,newton-mod,gauss-newton}
potential_guess potential guess from inverting integral equation
newton potential update using Newton method
newton-mod potential update using a modified Newton method
gauss-newton potential update using Gauss-Newton method
options:
-h, --help show this help message and exit
imc_stat_generic.sh¶
NAME¶
csg_call imc_stat gromacs - Part of the VOTCA package
SYNOPSIS¶
csg_call imc_stat gromacs [OPTIONS]
csg_call imc_stat gromacs [–help]
Usage: csg_call [OPTIONS] imc_stat gromacs
DESCRIPTION¶
This script implemtents statistical analysis for the Inverse Monte Carlo Method using generic csg tools (csg_stat)
initialize_step_generic.sh¶
NAME¶
csg_call initstep ibi - Part of the VOTCA package
SYNOPSIS¶
csg_call initstep ibi [OPTIONS]
csg_call initstep ibi [–help]
Usage: csg_call [OPTIONS] initstep ibi
DESCRIPTION¶
This script implements the initialization for every step in a generic way
initialize_step_genericsim.sh¶
NAME¶
csg_call initstep gromacs - Part of the VOTCA package
SYNOPSIS¶
csg_call initstep gromacs [OPTIONS]
csg_call initstep gromacs [–help]
Usage: csg_call [OPTIONS] initstep gromacs
DESCRIPTION¶
This script initializes an iteration for the generic simulation program
initialize_step_optimizer.sh¶
NAME¶
csg_call initstep optimizer - Part of the VOTCA package
SYNOPSIS¶
csg_call initstep optimizer [OPTIONS]
csg_call initstep optimizer [–help]
Usage: csg_call [OPTIONS] initstep optimizer
DESCRIPTION¶
This script implements the initialization for every step in a generic way
initialize_step_re.sh¶
NAME¶
csg_call initstep re - Part of the VOTCA package
SYNOPSIS¶
csg_call initstep re [OPTIONS]
csg_call initstep re [–help]
Usage: csg_call [OPTIONS] initstep re
DESCRIPTION¶
This script implements the initialization for every step of relative entropy method by csg_reupdate program
inverse.sh¶
NAME¶
csg_call csg master - Part of the VOTCA package
SYNOPSIS¶
csg_call csg master [OPTIONS]
csg_call csg master [–help]
Usage: csg_call [OPTIONS] csg master [OPTIONS] –options settings.xml [clean]
DESCRIPTION¶
Start the script to run ibi, imc, etc. or clean out current dir
EXAMPLES¶
* inverse.sh --options cg.xml
* inverse.sh -6 --options cg.xml
OPTIONS¶
Allowed options:
-h, --help show this help
-N, --do-iterations N only do N iterations (ignoring settings.xml)
--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
kbibi_ramp_correction.pl¶
NAME¶
csg_call kbibi ramp_correction - Part of the VOTCA package
SYNOPSIS¶
csg_call kbibi ramp_correction [OPTIONS]
csg_call kbibi ramp_correction [–help]
Usage: csg_call [OPTIONS] kbibi ramp_correction [OPTIONS] kbint target_kbint outfile kBT min:step:max int_start:int_end ramp_factor
DESCRIPTION¶
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., 8, 1802 (2012), doi:10.1021/ct3000958
OPTIONS¶
Allowed options:
-h, --help Show this help message
lj_126.pl¶
NAME¶
csg_call compute_lj 12_6 - Part of the VOTCA package
SYNOPSIS¶
csg_call compute_lj 12_6 [OPTIONS]
csg_call compute_lj 12_6 [–help]
Usage: csg_call [OPTIONS] compute_lj 12_6 outfile min:step:max C6 C12
DESCRIPTION¶
This script calculates the LJ 12-6 potential ‘’$U=C12/r^12 - C6/r^6$’’
merge_tables.pl¶
NAME¶
csg_call table merge - Part of the VOTCA package
SYNOPSIS¶
csg_call table merge [OPTIONS]
csg_call table merge [–help]
Usage: csg_call [OPTIONS] table merge [OPTIONS] <source> <dest> <out>
DESCRIPTION¶
Merge two tables
EXAMPLES¶
* merge_tables.pl intable intable2 outtable
OPTIONS¶
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
optimizer_parameters_to_potential.sh¶
NAME¶
csg_call optimizer parameters_to_potential - Part of the VOTCA package
SYNOPSIS¶
csg_call optimizer parameters_to_potential [OPTIONS]
csg_call optimizer parameters_to_potential [–help]
Usage: csg_call [OPTIONS] optimizer parameters_to_potential parametervalues
DESCRIPTION¶
This script generates a single potential (.pot.new) out a parameter value string (1st argument)
optimizer_prepare_state.sh¶
NAME¶
csg_call optimizer prepare_state - Part of the VOTCA package
SYNOPSIS¶
csg_call optimizer prepare_state [OPTIONS]
csg_call optimizer prepare_state [–help]
Usage: csg_call [OPTIONS] optimizer prepare_state outputfile
DESCRIPTION¶
This script generates the initial state file and puts all in-file together
optimizer_state_to_mapping.sh¶
NAME¶
csg_call optimizer state_to_mapping - Part of the VOTCA package
SYNOPSIS¶
csg_call optimizer state_to_mapping [OPTIONS]
csg_call optimizer state_to_mapping [–help]
Usage: csg_call [OPTIONS] optimizer state_to_mapping input
DESCRIPTION¶
This script generates a mapping for the reference mapping from the parameters of the active in input state using the mapping template
optimizer_state_to_potentials.sh¶
NAME¶
csg_call optimizer state_to_potentials - Part of the VOTCA package
SYNOPSIS¶
csg_call optimizer state_to_potentials [OPTIONS]
csg_call optimizer state_to_potentials [–help]
Usage: csg_call [OPTIONS] optimizer state_to_potentials input output
DESCRIPTION¶
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
optimizer_target_density.sh¶
NAME¶
csg_call optimizer_target density - Part of the VOTCA package
SYNOPSIS¶
csg_call optimizer_target density [OPTIONS]
csg_call optimizer_target density [–help]
Usage: csg_call [OPTIONS] optimizer_target density
DESCRIPTION¶
Calculated the difference between rdf
optimizer_target_pressure.sh¶
NAME¶
csg_call optimizer_target pressure - Part of the VOTCA package
SYNOPSIS¶
csg_call optimizer_target pressure [OPTIONS]
csg_call optimizer_target pressure [–help]
Usage: csg_call [OPTIONS] optimizer_target pressure
DESCRIPTION¶
Calculates the difference current and target pressure
optimizer_target_rdf.sh¶
NAME¶
csg_call optimizer_target rdf - Part of the VOTCA package
SYNOPSIS¶
csg_call optimizer_target rdf [OPTIONS]
csg_call optimizer_target rdf [–help]
Usage: csg_call [OPTIONS] optimizer_target rdf
DESCRIPTION¶
Calculated the difference between rdf
post_add.sh¶
NAME¶
csg_call post add - Part of the VOTCA package
SYNOPSIS¶
csg_call post add [OPTIONS]
csg_call post add [–help]
Usage: csg_call [OPTIONS] post add
DESCRIPTION¶
This script makes all the post update
post_add_single.sh¶
NAME¶
csg_call post add_single - Part of the VOTCA package
SYNOPSIS¶
csg_call post add_single [OPTIONS]
csg_call post add_single [–help]
Usage: csg_call [OPTIONS] post add_single
DESCRIPTION¶
This script makes all the post update with backup for single pairs
post_update_generic.sh¶
NAME¶
csg_call post_update ibi - Part of the VOTCA package
SYNOPSIS¶
csg_call post_update ibi [OPTIONS]
csg_call post_update ibi [–help]
Usage: csg_call [OPTIONS] post_update ibi
DESCRIPTION¶
This script makes all the post update
post_update_generic_single.sh¶
NAME¶
csg_call post_update_single ibi - Part of the VOTCA package
SYNOPSIS¶
csg_call post_update_single ibi [OPTIONS]
csg_call post_update_single ibi [–help]
Usage: csg_call [OPTIONS] post_update_single ibi
DESCRIPTION¶
This script makes all the post update with backup for single pairs incl. backups
post_update_re_single.sh¶
NAME¶
csg_call post_update_single re - Part of the VOTCA package
SYNOPSIS¶
csg_call post_update_single re [OPTIONS]
csg_call post_update_single re [–help]
Usage: csg_call [OPTIONS] post_update_single re
DESCRIPTION¶
This script makes all the post update with backup for single pairs incl. backups
postadd_acc_convergence.sh¶
NAME¶
csg_call postadd acc_convergence - Part of the VOTCA package
SYNOPSIS¶
csg_call postadd acc_convergence [OPTIONS]
csg_call postadd acc_convergence [–help]
Usage: csg_call [OPTIONS] postadd acc_convergence infile outfile
DESCRIPTION¶
postadd accumulate convergence script: accumulate ${name}.conv of all steps
postadd_average.sh¶
NAME¶
csg_call postadd average - Part of the VOTCA package
SYNOPSIS¶
csg_call postadd average [OPTIONS]
csg_call postadd average [–help]
Usage: postadd_average.sh
DESCRIPTION¶
postadd average script, calcs averages of (${name}.DIST.cur) for the past few steps and saves it to ${name}.DIST.avg DIST can be specified by average.what option
postadd_compress.sh¶
NAME¶
csg_call postadd compress - Part of the VOTCA package
SYNOPSIS¶
csg_call postadd compress [OPTIONS]
csg_call postadd compress [–help]
Usage: csg_call [OPTIONS] postadd compress
DESCRIPTION¶
postadd compress script, compresses files
postadd_convergence.sh¶
NAME¶
csg_call postadd convergence - Part of the VOTCA package
SYNOPSIS¶
csg_call postadd convergence [OPTIONS]
csg_call postadd convergence [–help]
Usage: postadd_convergence.sh
DESCRIPTION¶
postadd convergence script, calcs norm of error (${name}.DIST.BASE-${name}.DIST.new) and saves it to ${name}.conv. DIST stands for ‘dist’, but can be changed by onvergence.what option
postadd_copyback.sh¶
NAME¶
csg_call postadd copyback - Part of the VOTCA package
SYNOPSIS¶
csg_call postadd copyback [OPTIONS]
csg_call postadd copyback [–help]
Usage: csg_call [OPTIONS] postadd copyback
DESCRIPTION¶
postadd copyback script, copies files back to the maindir
postadd_dummy.sh¶
NAME¶
csg_call postupd dummy - Part of the VOTCA package
SYNOPSIS¶
csg_call postupd dummy [OPTIONS]
csg_call postupd dummy [–help]
Usage: csg_call [OPTIONS] postupd dummy infile outfile
DESCRIPTION¶
postadd dummy script (cp infile to outfile), useful to overwrite default by nothing
postadd_overwrite.sh¶
NAME¶
csg_call postadd overwrite - Part of the VOTCA package
SYNOPSIS¶
csg_call postadd overwrite [OPTIONS]
csg_call postadd overwrite [–help]
Usage: csg_call [OPTIONS] postadd overwrite infile outfile
DESCRIPTION¶
postadd overwrite script, overwrites potential of all other interactions with this one
postadd_plot.sh¶
NAME¶
csg_call postadd plot - Part of the VOTCA package
SYNOPSIS¶
csg_call postadd plot [OPTIONS]
csg_call postadd plot [–help]
Usage: csg_call [OPTIONS] postadd plot
DESCRIPTION¶
postadd plot script, send a certain plot script to gnuplot
Used external packages: gnuplot
postadd_shift.sh¶
NAME¶
csg_call postupd shift - Part of the VOTCA package
SYNOPSIS¶
csg_call postupd shift [OPTIONS]
csg_call postupd shift [–help]
Usage: csg_call [OPTIONS] postupd shift infile outfile
DESCRIPTION¶
postadd shift script, shift pot and dpot
postadd_smooth_at_cut_off.sh¶
NAME¶
csg_call postadd smooth_at_cut_off - Part of the VOTCA package
SYNOPSIS¶
csg_call postadd smooth_at_cut_off [OPTIONS]
csg_call postadd smooth_at_cut_off [–help]
Usage: csg_call [OPTIONS] postadd smooth_at_cut_off infile outfile
DESCRIPTION¶
This script implements smoothing of the potential (.pot) at the cut off
postupd_addlj.sh¶
NAME¶
csg_call postupd lj - Part of the VOTCA package
SYNOPSIS¶
csg_call postupd lj [OPTIONS]
csg_call postupd lj [–help]
Usage: csg_call [OPTIONS] postupd lj infile outfile
DESCRIPTION¶
This script adds LJ 12-6 component to the CG potential
postupd_cibi_correction.sh¶
NAME¶
csg_call postupd cibi - Part of the VOTCA package
SYNOPSIS¶
csg_call postupd cibi [OPTIONS]
csg_call postupd cibi [–help]
Usage: csg_call [OPTIONS] postupd cibi infile outfile
DESCRIPTION¶
This script implemtents the post update routine for the integral Kirkwood-Buff corrections described in: T. E. de Oliveira, P. A. Netz, K. Kremer, C. Junghans, and D. Mukherji, C-IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids, J. Chem. Phys. (in press).
postupd_extrapolate.sh¶
NAME¶
csg_call postupd extrapolate - Part of the VOTCA package
SYNOPSIS¶
csg_call postupd extrapolate [OPTIONS]
csg_call postupd extrapolate [–help]
Usage: csg_call [OPTIONS] postupd extrapolate infile outfile
DESCRIPTION¶
This script implements extrapolation undefined region of the potential update (.dpot)
postupd_ibi.sh¶
NAME¶
csg_call postupd ibi - Part of the VOTCA package
SYNOPSIS¶
csg_call postupd ibi [OPTIONS]
csg_call postupd ibi [–help]
Usage: csg_call [OPTIONS] postupd ibi infile outfile
DESCRIPTION¶
This script implemtents the function post update with the Inverse Boltzmann Method. This one is not like other post update methods in that the infile is ignored.
postupd_kbibi_correction.sh¶
NAME¶
csg_call postupd kbibi - Part of the VOTCA package
SYNOPSIS¶
csg_call postupd kbibi [OPTIONS]
csg_call postupd kbibi [–help]
Usage: csg_call [OPTIONS] postupd kbibi infile outfile
DESCRIPTION¶
This script implemtents the post update routine for the ramp Kirkwood-Buff corrections 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., 8, 1802 (2012), doi:10.1021/ct3000958
postupd_pressure.sh¶
NAME¶
csg_call postupd pressure - Part of the VOTCA package
SYNOPSIS¶
csg_call postupd pressure [OPTIONS]
csg_call postupd pressure [–help]
Usage: csg_call [OPTIONS] postupd pressure infile outfile
DESCRIPTION¶
This script implements the pressure update
postupd_scale.sh¶
NAME¶
csg_call postupd scale - Part of the VOTCA package
SYNOPSIS¶
csg_call postupd scale [OPTIONS]
csg_call postupd scale [–help]
Usage: csg_call [OPTIONS] postupd scale infile outfile
DESCRIPTION¶
This script implements scaling of the potential update (.dpot)
postupd_smooth.sh¶
NAME¶
csg_call postupd smooth - Part of the VOTCA package
SYNOPSIS¶
csg_call postupd smooth [OPTIONS]
csg_call postupd smooth [–help]
Usage: csg_call [OPTIONS] postupd smooth infile outfile
DESCRIPTION¶
This script implements smoothing of the potential update (.dpot)
postupd_splinesmooth.sh¶
NAME¶
csg_call postupd splinesmooth - Part of the VOTCA package
SYNOPSIS¶
csg_call postupd splinesmooth [OPTIONS]
csg_call postupd splinesmooth [–help]
Usage: csg_call [OPTIONS] postupd splinesmooth infile outfile
DESCRIPTION¶
This script implements smoothing of the potential update (.dpot)
potential_extrapolate.sh¶
NAME¶
csg_call potential extrapolate - Part of the VOTCA package
SYNOPSIS¶
csg_call potential extrapolate [OPTIONS]
csg_call potential extrapolate [–help]
Usage: csg_call [OPTIONS] potential extrapolate [options] input output
DESCRIPTION¶
This script extrapolates a potential in the correct way depending on its type.
OPTIONS¶
Allowed options:
--help show this help
--clean remove all intermediate temp files
--type TYPE type of the potential
possible: non-bonded bond angle dihedral
--lfct FCT type of the left extrapolation function
possible:
default: exponential(non-bonded), linear (bonded)
--rfct FCT type of the right extrapolation function
possible: constant linear quadratic exponential sasha
default: constant(non-bonded), periodic(dihedral), linear (bonded)
--avg-points INT number of average points
default: 3
potential_shift.pl¶
NAME¶
csg_call potential shift - Part of the VOTCA package
SYNOPSIS¶
csg_call potential shift [OPTIONS]
csg_call potential shift [–help]
Usage: csg_call [OPTIONS] potential shift [OPTIONS] <in> <out>
DESCRIPTION¶
This script shifts the whole potential by minimum (bonded potentials) or last value (non-bonded potentials).
EXAMPLES¶
* potential_shift.pl --type bond table.in table.out
OPTIONS¶
Allowed options:
-h, --help show this help message
--type XXX change the type of potential
Default: non-bonded
Possible types: non-bonded, bond, angle, dihedral, bonded
potential_to_dlpoly.sh¶
NAME¶
csg_call convert_potential dlpoly - Part of the VOTCA package
SYNOPSIS¶
csg_call convert_potential dlpoly [OPTIONS]
csg_call convert_potential dlpoly [–help]
Usage: csg_call [OPTIONS] convert_potential dlpoly
DESCRIPTION¶
This script is a high class wrapper to convert a potential to the dlpoly format
potential_to_generic.sh¶
NAME¶
csg_call convert_potential espresso - Part of the VOTCA package
SYNOPSIS¶
csg_call convert_potential espresso [OPTIONS]
csg_call convert_potential espresso [–help]
Usage: csg_call [OPTIONS] convert_potential espresso
DESCRIPTION¶
This script is a high class wrapper to convert a potential to the generic 3 column tab format used by espresso and espressopp
potential_to_gromacs.sh¶
NAME¶
csg_call convert_potential gromacs - Part of the VOTCA package
SYNOPSIS¶
csg_call convert_potential gromacs [OPTIONS]
csg_call convert_potential gromacs [–help]
Usage: csg_call [OPTIONS] convert_potential gromacs [options] input output
DESCRIPTION¶
This script is a wrapper to convert a potential to gromacs
OPTIONS¶
Allowed options:
--help show this help
--clean remove all intermediate temp files
--no-r2d do not 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
--step XXX use XXX as step for the interaction
potential_to_lammps.sh¶
NAME¶
csg_call convert_potential lammps - Part of the VOTCA package
SYNOPSIS¶
csg_call convert_potential lammps [OPTIONS]
csg_call convert_potential lammps [–help]
Usage: csg_call [OPTIONS] convert_potential lammps [options] input output
DESCRIPTION¶
This script is a high class wrapper to convert a potential to the lammps format
OPTIONS¶
Allowed options:
--help show this help
--clean remove all intermediate temp files
--no-r2d do not converts rad to degree (scale x axis with 180/3.1415)
for angle interactions
Note: VOTCA calcs in rad, but lammps uses degrees for angle
--no-shift do not shift the potential
potentials_to_dlpoly.sh¶
NAME¶
csg_call convert_potentials dlpoly - Part of the VOTCA package
SYNOPSIS¶
csg_call convert_potentials dlpoly [OPTIONS]
csg_call convert_potentials dlpoly [–help]
Usage: csg_call [OPTIONS] convert_potentials dlpoly
DESCRIPTION¶
This script converts all potentials to the format needed by dlpoly
potentials_to_generic.sh¶
NAME¶
csg_call convert_potentials gromacs - Part of the VOTCA package
SYNOPSIS¶
csg_call convert_potentials gromacs [OPTIONS]
csg_call convert_potentials gromacs [–help]
Usage: csg_call [OPTIONS] convert_potentials gromacs
DESCRIPTION¶
This script converts all potentials to the format needed by the simulation program
pre_update_re.sh¶
NAME¶
csg_call pre_update re - Part of the VOTCA package
SYNOPSIS¶
csg_call pre_update re [OPTIONS]
csg_call pre_update re [–help]
Usage: csg_call [OPTIONS] pre_update re
DESCRIPTION¶
This script implements the pre update tasks for the Relative Entropy Method
prepare_generic.sh¶
NAME¶
csg_call prepare ibi - Part of the VOTCA package
SYNOPSIS¶
csg_call prepare ibi [OPTIONS]
csg_call prepare ibi [–help]
Usage: csg_call [OPTIONS] prepare ibi
DESCRIPTION¶
This script prepares potentials in a generic way
prepare_generic_single.sh¶
NAME¶
csg_call prepare_single ibi - Part of the VOTCA package
SYNOPSIS¶
csg_call prepare_single ibi [OPTIONS]
csg_call prepare_single ibi [–help]
Usage: csg_call [OPTIONS] prepare_single ibi [–help] [–use-table|–use-bi]”
DESCRIPTION¶
This script prepares the potential in step 0, using pot.in or by resampling and inverting the target distribution
Use –use-table or –use-bi to enforce the method. Otherwise it will use .pot.in if present and BI if not.
prepare_iie.sh¶
NAME¶
csg_call prepare iie - Part of the VOTCA package
SYNOPSIS¶
csg_call prepare iie [OPTIONS]
csg_call prepare iie [–help]
Usage: csg_call [OPTIONS] prepare iie
DESCRIPTION¶
This script prepares potentials in a generic way
prepare_imc.sh¶
NAME¶
csg_call prepare imc - Part of the VOTCA package
SYNOPSIS¶
csg_call prepare imc [OPTIONS]
csg_call prepare imc [–help]
Usage: csg_call [OPTIONS] prepare imc
DESCRIPTION¶
This script initializes potentials for imc
prepare_optimizer.sh¶
NAME¶
csg_call prepare optimizer - Part of the VOTCA package
SYNOPSIS¶
csg_call prepare optimizer [OPTIONS]
csg_call prepare optimizer [–help]
Usage: csg_call [OPTIONS] prepare optimizer
DESCRIPTION¶
This script initizalizes potentials for optimizer methods
prepare_optimizer_single.sh¶
NAME¶
csg_call prepare_single optimizer - Part of the VOTCA package
SYNOPSIS¶
csg_call prepare_single optimizer [OPTIONS]
csg_call prepare_single optimizer [–help]
Usage: csg_call [OPTIONS] prepare_single optimizer N
where N is the total number of parameters
DESCRIPTION¶
This script - reads sinple interaction optimizer infile - checks if the number of values are enough
prepare_re.sh¶
NAME¶
csg_call prepare re - Part of the VOTCA package
SYNOPSIS¶
csg_call prepare re [OPTIONS]
csg_call prepare re [–help]
Usage: csg_call [OPTIONS] prepare re
DESCRIPTION¶
This script implements the preparation of the relative entropy method iteration
pressure_cor_simple.pl¶
NAME¶
csg_call pressure_cor simple - Part of the VOTCA package
SYNOPSIS¶
csg_call pressure_cor simple [OPTIONS]
csg_call pressure_cor simple [–help]
Usage: csg_call [OPTIONS] pressure_cor simple p_cur outfile kBT min:step:max scale p_target
DESCRIPTION¶
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)$’’
pressure_cor_wjk.pl¶
NAME¶
csg_call pressure_cor wjk - Part of the VOTCA package
SYNOPSIS¶
csg_call pressure_cor wjk [OPTIONS]
csg_call pressure_cor wjk [–help]
Usage: csg_call [OPTIONS] pressure_cor wjk p_cur outfile kBT min:step:max scale p_target particle_dens rdf_file
DESCRIPTION¶
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.
resample_target.sh¶
NAME¶
csg_call resample target - Part of the VOTCA package
SYNOPSIS¶
csg_call resample target [OPTIONS]
csg_call resample target [–help]
Usage: csg_call [OPTIONS] resample target input output
DESCRIPTION¶
This script resamples distribution to grid spacing of the setting xml file and extrapolates if needed
run_genericsim.sh¶
NAME¶
csg_call run espresso - Part of the VOTCA package
SYNOPSIS¶
csg_call run espresso [OPTIONS]
csg_call run espresso [–help]
Usage: csg_call [OPTIONS] run espresso
DESCRIPTION¶
This script runs a generic simulation program
run_gromacs.sh¶
NAME¶
csg_call run gromacs - Part of the VOTCA package
SYNOPSIS¶
csg_call run gromacs [OPTIONS]
csg_call run gromacs [–help]
Usage: csg_call [OPTIONS] run gromacs [–pre]
DESCRIPTION¶
This script runs a gromacs simulation or pre-simulation
Used external packages: gromacs
simplex_downhill_processor.pl¶
NAME¶
csg_call simplex precede_state - Part of the VOTCA package
SYNOPSIS¶
csg_call simplex precede_state [OPTIONS]
csg_call simplex precede_state [–help]
Usage: csg_call [OPTIONS] simplex precede_state current_state new_state
DESCRIPTION¶
Changes a simplex state according to the current state using the Nelder–Mead method or downhill simplex algorithm.
table_average.sh¶
NAME¶
csg_call table average - Part of the VOTCA package
SYNOPSIS¶
csg_call table average [OPTIONS]
csg_call table average [–help]
Usage: csg_call [OPTIONS] table average [options] table1 table2 table3 ….
DESCRIPTION¶
This script creates averages tables and also calculates the error.
EXAMPLES¶
* table_average.sh --output CG-CG.dist.new CG-CG*.dist.new
OPTIONS¶
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
table_change_flag.sh¶
NAME¶
csg_call table change_flag - Part of the VOTCA package
SYNOPSIS¶
csg_call table change_flag [OPTIONS]
csg_call table change_flag [–help]
Usage: csg_call [OPTIONS] table change_flag input outfile
DESCRIPTION¶
This script changes the flags (col 3) of a table
table_combine.pl¶
NAME¶
csg_call table compare - Part of the VOTCA package
SYNOPSIS¶
csg_call table compare [OPTIONS]
csg_call table compare [–help]
Usage: table_combine.pl [OPTIONS] <in> <in2> <out>
DESCRIPTION¶
This script combines two tables with a certain operation
OPTIONS¶
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¶
NAME¶
csg_call table dummy - Part of the VOTCA package
SYNOPSIS¶
csg_call table dummy [OPTIONS]
csg_call table dummy [–help]
Usage: csg_call [OPTIONS] table dummy [options] min:step:max outfile
DESCRIPTION¶
This script creates a zero table with grid min:step:max using linear interpolation
OPTIONS¶
Allowed options:
--y1 X.X using X.X instead of 0 for the 1st y-value
this creates a linear instead of a constant table
--y2 X.X using X.X instead of 0 for the 2nd y-value
this creates a linear instead of a constant table
--help show this help
--clean remove all intermediate temp files
table_extrapolate.pl¶
NAME¶
csg_call table extrapolate - Part of the VOTCA package
SYNOPSIS¶
csg_call table extrapolate [OPTIONS]
csg_call table extrapolate [–help]
Usage: csg_call [OPTIONS] table extrapolate [OPTIONS] <in> <out>
DESCRIPTION¶
This script extrapolates a table
OPTIONS¶
Allowed options:
--avgpoints A average over the given number of points to extrapolate: default is 3
--function constant, linear, quadratic or exponential, sasha, periodic: 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)$''
- periodic same as linear, but extrapolates right side to end at first point of left side
table_functional.sh¶
NAME¶
csg_call table functional - Part of the VOTCA package
SYNOPSIS¶
csg_call table functional [OPTIONS]
csg_call table functional [–help]
Usage: csg_call [OPTIONS] table functional [options] output
DESCRIPTION¶
This script creates a table with grid min:step:max for the a functional form
EXAMPLES¶
* table_functional.sh --grid 0:0.1:1 --fct x**2 CG-CG.tab.new
OPTIONS¶
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
table_get_value.pl¶
NAME¶
csg_call table get_value - Part of the VOTCA package
SYNOPSIS¶
csg_call table get_value [OPTIONS]
csg_call table get_value [–help]
Usage: csg_call [OPTIONS] table get_value [OPTIONS] X infile
DESCRIPTION¶
This script print the y value of x, which is closest to X.
OPTIONS¶
Allowed options:
-h, --help Show this help message
table_integrate.pl¶
NAME¶
csg_call table integrate - Part of the VOTCA package
SYNOPSIS¶
csg_call table integrate [OPTIONS]
csg_call table integrate [–help]
Usage: csg_call [OPTIONS] table integrate [OPTIONS] <in> <out>
DESCRIPTION¶
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)
EXAMPLES¶
* table_integrate.pl --with-S --kbT 2.49435 tmp.force tmp.dpot
OPTIONS¶
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
table_linearop.pl¶
NAME¶
csg_call table linearop - Part of the VOTCA package
SYNOPSIS¶
csg_call table linearop [OPTIONS]
csg_call table linearop [–help]
Usage: csg_call [OPTIONS] table linearop [OPTIONS] <in> <out> <a> <b>
DESCRIPTION¶
This script performs a linear operation on the y values: ‘’$y_{new} = a*y_{old} + b$’’
EXAMPLES¶
* table_linearop.pl tmp.dpot.cur tmp.dpot.new 1.0 0.0
OPTIONS¶
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
table_scale.pl¶
NAME¶
csg_call table scale - Part of the VOTCA package
SYNOPSIS¶
csg_call table scale [OPTIONS]
csg_call table scale [–help]
Usage: csg_call [OPTIONS] table scale [OPTIONS] infile outfile prefactor1 prefactor2
DESCRIPTION¶
This script applies a prefactor to infile. The prefactor is is interpolated lines between the prefactor1 and prefactor2.
OPTIONS¶
Allowed options:
-h, --help Show this help message
table_smooth.pl¶
NAME¶
csg_call table smooth - Part of the VOTCA package
SYNOPSIS¶
csg_call table smooth [OPTIONS]
csg_call table smooth [–help]
Usage: csg_call [OPTIONS] table smooth infile outfile
DESCRIPTION¶
This script smoothes a table
table_smooth_at_cut_off.py¶
NAME¶
csg_call table smooth_at_cut_off - Part of the VOTCA package
SYNOPSIS¶
csg_call table smooth_at_cut_off [OPTIONS]
csg_call table smooth_at_cut_off [–help]
Usage: table_smooth_at_cut_off.py [-h] –cut-off CUT_OFF input output
Smooth the potential close to the cut-off.
DESCRIPTION¶
OPTIONS¶
positional arguments:
input potential input
output potential output
options:
-h, --help show this help message and exit
--cut-off CUT_OFF cut-off
table_switch_border.pl¶
NAME¶
csg_call table switch_border - Part of the VOTCA package
SYNOPSIS¶
csg_call table switch_border [OPTIONS]
csg_call table switch_border [–help]
Usage: csg_call [OPTIONS] table switch_border infile outfile <x_switch>
DESCRIPTION¶
This script applies a switching function to the end of the table to switch it smoothly to zero by y = y*cos( pi*(x-x_switch)/(2*(x_end-x_switch)) )
table_to_tab.pl¶
NAME¶
csg_call convert_potential tab - Part of the VOTCA package
SYNOPSIS¶
csg_call convert_potential tab [OPTIONS]
csg_call convert_potential tab [–help]
Usage: csg_call [OPTIONS] convert_potential tab [OPTIONS] <in> <derivatives_in> <out>
DESCRIPTION¶
This script converts csg potential files to the tab format (as read by espresso or lammps or dlpoly).
In addition, it does some magic tricks: - shift the potential, so that it is zero at the cutoff
EXAMPLES¶
* table_to_tab.pl --type non-bonded table.in table_b0.xvg
OPTIONS¶
Allowed options:
-h, --help show this help message
--type XXX change the type of xvg table
Default: non-bonded
--header XXX Write a special simulation programm header
table_to_xvg.pl¶
NAME¶
csg_call convert_potential xvg - Part of the VOTCA package
SYNOPSIS¶
csg_call convert_potential xvg [OPTIONS]
csg_call convert_potential xvg [–help]
Usage: csg_call [OPTIONS] convert_potential xvg [OPTIONS] <in> <out>
DESCRIPTION¶
This script converts csg potential files to the xvg format.
EXAMPLES¶
* table_to_xvg.pl --type bond table.in table_b0.xvg
OPTIONS¶
Allowed options:
-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, C12, C6, CB, angle, dihedral
tables_jackknife.pl¶
NAME¶
csg_call tables jackknife - Part of the VOTCA package
SYNOPSIS¶
csg_call tables jackknife [OPTIONS]
csg_call tables jackknife [–help]
Usage: csg_call [OPTIONS] tables jackknife out full block1 block2 …
DESCRIPTION¶
This script calculates the jackknife error from existing tables * full = table calculated with full dataset * blocks = tables calculated with 1 block missing * outfile = file to write results
tag_file.sh¶
NAME¶
csg_call tag file - Part of the VOTCA package
SYNOPSIS¶
csg_call tag file [OPTIONS]
csg_call tag file [–help]
Usage: csg_call [OPTIONS] tag file input output
DESCRIPTION¶
Add table_comment to the head of a file
update_ibi.sh¶
NAME¶
csg_call update ibi - Part of the VOTCA package
SYNOPSIS¶
csg_call update ibi [OPTIONS]
csg_call update ibi [–help]
Usage: csg_call [OPTIONS] update ibi
DESCRIPTION¶
This script implements the function update for the Inverse Boltzmann Method
update_ibi_pot.pl¶
NAME¶
csg_call update ibi_pot - Part of the VOTCA package
SYNOPSIS¶
csg_call update ibi_pot [OPTIONS]
csg_call update ibi_pot [–help]
Usage: csg_call [OPTIONS] update ibi_pot target_rdf new_rdf cur_pot outfile kBT
DESCRIPTION¶
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
update_ibi_single.sh¶
NAME¶
csg_call update ibi_single - Part of the VOTCA package
SYNOPSIS¶
csg_call update ibi_single [OPTIONS]
csg_call update ibi_single [–help]
Usage: csg_call [OPTIONS] update ibi_single
DESCRIPTION¶
This script implemtents the function update for a single pair for the Inverse Boltzmann Method
update_iie.sh¶
NAME¶
csg_call update iie - Part of the VOTCA package
SYNOPSIS¶
csg_call update iie [OPTIONS]
csg_call update iie [–help]
Usage: csg_call [OPTIONS] update iie
DESCRIPTION¶
This script implements the function update for the HNC methods
There is not support for not doing potential updates on some interactions yet. Also no support for per interaction extrapolation.
update_imc.sh¶
NAME¶
csg_call update imc - Part of the VOTCA package
SYNOPSIS¶
csg_call update imc [OPTIONS]
csg_call update imc [–help]
Usage: csg_call [OPTIONS] update imc
DESCRIPTION¶
This script implements the function update for the Inverse Monte Carlo Method
update_imc_single.sh¶
NAME¶
csg_call update imc_single - Part of the VOTCA package
SYNOPSIS¶
csg_call update imc_single [OPTIONS]
csg_call update imc_single [–help]
Usage: csg_call [OPTIONS] update imc_single
DESCRIPTION¶
This scripts multiplies the dpot tables for each interaction when using IMC by kBT and handles potential update schemes
update_optimizer.sh¶
NAME¶
csg_call update optimizer - Part of the VOTCA package
SYNOPSIS¶
csg_call update optimizer [OPTIONS]
csg_call update optimizer [–help]
Usage: csg_call [OPTIONS] update optimizer
DESCRIPTION¶
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
update_optimizer_single.sh¶
NAME¶
csg_call update optimizer_single - Part of the VOTCA package
SYNOPSIS¶
csg_call update optimizer_single [OPTIONS]
csg_call update optimizer_single [–help]
Usage: csg_call [OPTIONS] update optimizer_single
DESCRIPTION¶
This script: - calculates the new property - compares it to the target property and calculates the target function accordingly
update_re.sh¶
NAME¶
csg_call update re - Part of the VOTCA package
SYNOPSIS¶
csg_call update re [OPTIONS]
csg_call update re [–help]
Usage: csg_call [OPTIONS] update re
DESCRIPTION¶
This script implements update step of relative entropy method by csg_reupdate program