| Key1 |
Key2 |
Scriptname |
| tag |
file |
tag_file.sh |
| dummy |
dummy |
dummy.sh |
| function |
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_single |
ibi |
prepare_generic_single.sh |
| prepare_single |
imc |
prepare_generic_single.sh |
| prepare_single |
tf |
prepare_generic_single.sh |
| initstep |
ibi |
initialize_step_generic.sh |
| initstep |
imc |
initialize_step_generic.sh |
| initstep |
tf |
initialize_step_generic.sh |
| prepare |
ibm |
prepare_ibm.sh |
| update |
ibm |
update_ibm.sh |
| update |
ibi |
update_ibi.sh |
| update |
imc |
update_imc.sh |
| add_pot |
ibi |
add_pot_generic.sh |
| add_pot |
imc |
add_pot_generic.sh |
| add_pot |
tf |
add_pot_generic.sh |
| rdf |
pot |
RDF_to_POT.pl |
| post_update |
ibi |
post_update_generic.sh |
| post_update |
imc |
post_update_generic.sh |
| post_update |
tf |
dummy.sh |
| post_update_single |
ibi |
post_update_generic_single.sh |
| post_update_single |
imc |
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 |
| 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 |
| pot |
shift_bonded |
dpot_shift_bo.pl |
| resample |
target |
resample_target.sh |
| dpot |
crop |
dpot_crop.pl |
| update |
ibi_single |
update_ibi_single.sh |
| update |
ibi_pot |
update_ibi_pot.pl |
| imcsolver |
matlab |
solve_matlab.sh |
| solve |
matlab |
linsolve.m |
| imcsolver |
octave |
solve_octave.sh |
| solve |
octave |
linsolve.octave |
| imc |
purify |
imc_purify.sh |
| update |
tf |
update_tf.sh |
| update |
tf_single |
update_tf_single.sh |
| calc |
thermforce |
calc_thermforce.sh |
| tf |
apply_prefactor |
apply_prefactor.pl |
| pressure_cor |
simple |
pressure_cor_simple.pl |
| pressure_cor |
wjk |
pressure_cor_wjk.pl |
| 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_compare.pl |
| tables |
jackknife |
tables_jackknife.pl |
| run |
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: add_pot_generic.sh
Used xml options:
add_POT.pl
This script adds up two potentials
In addition, it does some magic tricks:
- order of infiles MATTER !!!!
- 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
Usage: add_POT.pl infile1 infile2 outfile
apply_prefactor.pl
This script calculates the integral of a table
Usage: apply_prefactor.pl [OPTIONS] <in> <out>
Allowed options:
-h, --help Show this help message
calc_density_gromacs.sh
This script calcs the density for gromacs for the AdResS therm force
Usage: calc_density_gromacs.sh
Used xml options:
- cg.inverse.gromacs.topol (default: topol.tpr)
- cg.inverse.gromacs.traj_type (default: xtc)
- cg.inverse.program
- cg.inverse.$sim_prog.equi_time (default: 0)
- cg.inverse.$sim_prog.first_frame (default: 0)
- name
- step
- tf.molname (default: *)
- tf.spline_end
calc_pressure_espresso.sh
This script calcs the pressure for espresso and writes it to outfile
Usage: calc_pressure_espresso.sh outfile
Used external packages: espresso
Used xml options:
- cg.inverse.espresso.blockfile (default: conf.esp.gz)
- cg.inverse.espresso.pressure_command (default: Espresso_bin)
calc_pressure_gromacs.sh
This script calcs the pressure for gromacs and writes it to outfile
Usage: calc_pressure_gromacs.sh outfile
Used external packages: gromacs
Used xml options:
- cg.inverse.gromacs.g_energy.bin (default: g_energy)
- cg.inverse.gromacs.g_energy.opts (default: empty)
- cg.inverse.gromacs.g_energy.topol (default: topol.tpr)
calc_rdf_espresso.sh
This script calcs the rdf for espresso
Usage: calc_rdf_espresso.sh
Used external packages: espresso
Used xml options:
- cg.inverse.espresso.blockfile (default: conf.esp.gz)
- cg.inverse.espresso.first_frame (default: 0)
- cg.inverse.espresso.rdf_command (default: Espresso_bin)
- cg.inverse.espresso.traj (default: top_traj.esp)
- inverse.espresso.index1
- inverse.espresso.index2
- max
- min
- name
- step
- type1
- type2
calc_rdf_generic.sh
This script implemtents statistical analysis for the iterative Boltzmann inversion
using generic csg tools (csg_stat)
Usage: calc_rdf_generic.sh
Used xml options:
- cg.inverse.gromacs.rdf.topol (default: topol.tpr)
- cg.inverse.gromacs.traj_type (default: xtc)
- cg.inverse.program
- cg.inverse.$sim_prog.equi_time (default: 0)
- cg.inverse.$sim_prog.first_frame (default: 0)
calc_thermforce.sh
This script calcs the thermoforce out of gromacs density for the AdResS therm force
Usage: calc_thermforce.sh infile outfile
Used xml options:
- cg.inverse.gromacs.mdp (default: grompp.mdp)
- max
- min
- name
- step
- tf.cg_prefactor (default: empty)
- tf.prefactor
- tf.spline_end
- tf.spline_start
- tf.spline_step
convergence_check_default.sh
dummy script (does nothing), useful to overwrite default by nothing
Usage: convergence_check_default.sh
Used xml options:
- cg.inverse.convergence_check_options.limit
- cg.inverse.convergence_check_options.name_glob (default: *.conv)
density_symmetrize.py
This script symmetrizes the density around --adressc for thermodynamic force iteration
Usage: density_symmetrize.py
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: dpot_crop.pl [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: dpot_shift_bo.pl 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: dpot_shift_nb.pl infile outfile
dummy.sh
dummy script (does nothing), useful to overwrite default by nothing
Usage: dummy.sh
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
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
check_for_duplicated_interactions -- checks for duplicated interactions
csg_get_interaction_property -- gets an interaction property from the xml file, should only be called from inside a for_all loop
csg_get_property -- get an property from the xml file
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
int_check -- checks if 1st argument is a integer or calls die with error message (2nd argument)
num_check -- checks if 1st argument is a number or calls die with error message (2nd argument)
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_number_tasks -- get the number of possible tasks from the xml file or determine it automatically under linux
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
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 (default: inverse.log)
- cg.inverse.restart_file (default: restart_points.log)
- cg.inverse.simulation.tasks (default: auto)
- cg.non-bonded.name
- 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 -- check if a checkpoint exists
Used external packages: espresso
Used xml options:
- cg.inverse.espresso.blockfile_out (default: confout.esp.gz)
- cg.inverse.espresso.scriptdir (default: empty)
- cg.inverse.espresso.success (default: success.esp)
- cg.inverse.espresso.traj (default: top_traj.esp)
functions_gromacs.sh
Useful functions for gromacs:
get_simulation_setting -- gets a parameter (1st argument) from gromacs mdp file (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
Used external packages: gromacs
Used xml options:
- cg.inverse.gromacs.conf_out (default: confout.gro)
- cg.inverse.gromacs.cutoff_check (default: yes)
- cg.inverse.gromacs.equi_time (default: 0)
- cg.inverse.gromacs.first_frame (default: 0)
- cg.inverse.gromacs.gmxrc (default: empty)
- cg.inverse.gromacs.mdp (default: grompp.mdp)
- cg.inverse.gromacs.mdrun.checkpoint (default: state.cpt)
- cg.inverse.gromacs.temp_check (default: yes)
- cg.inverse.gromacs.traj_type (default: xtc)
- cg.inverse.kBT
- max
imc_purify.sh
This scripts cleans up the dpot tables for each interaction when using IMC
Usage: imc_purify.sh
Used xml options:
- cg.inverse.kBT
- inverse.do_potential (default: 1)
- max
- min
- name
- step
imc_stat_generic.sh
This script implemtents statistical analysis for the Inverse Monte Carlo Method
using generic csg tools (csg_stat)
Usage: imc_stat_generic.sh
Used xml options:
- cg.inverse.gromacs.topol (default: topol.tpr)
- cg.inverse.gromacs.traj_type (default: xtc)
- cg.inverse.program
- cg.inverse.$sim_prog.equi_time (default: 0)
- cg.inverse.$sim_prog.first_frame (default: 0)
initialize_step_generic_espresso.sh
This script initializes an espresso simulation
Usage: initialize_step_generic_espresso.sh
Used xml options:
- cg.inverse.espresso.blockfile (default: conf.esp.gz)
- cg.inverse.espresso.blockfile_out (default: confout.esp.gz)
- cg.inverse.initial_configuration (default: laststep)
initialize_step_generic_gromacs.sh
This script implemtents the function initialize
Usage: initialize_step_generic_gromacs.sh
Used external packages: gromacs
Used xml options:
- cg.inverse.gromacs.conf (default: conf.gro)
- cg.inverse.gromacs.conf_out (default: confout.gro)
- cg.inverse.initial_configuration (default: laststep)
initialize_step_generic.sh
This script implements the initialization for every step in a generic way
Usage: initialize_step_generic.sh
Used xml options:
- cg.inverse.method
- cg.inverse.program
- name
inverse.sh
Start the script to run ibi, imc, etc. or clean out current dir
Usage: inverse.sh [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 (default: empty)
- cg.inverse.convergence_check (default: none)
- cg.inverse.filelist (default: empty)
- cg.inverse.iterations_max
- cg.inverse.method
- cg.inverse.program
- cg.inverse.scriptdir (default: empty)
- cg.inverse.simulation.background (default: no)
linsolve.m
\nThis script has no help
linsolve.octave
\nThis script has no help
merge_tables.pl
Merge two tables
Usage: merge_tables.pl [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
postadd_acc_convergence.sh
postadd accumulate convergence script: accumulate ${name}.conv of all steps
Usage: postadd_acc_convergence.sh infile outfile
Used xml options:
postadd_convergence.sh
postadd convergence script, calcs int of (${name}.DIST.tgt-${name}.DIST.new)**2
and saves it to ${name}.conv.
DIST is dist, but changed by onvergence.what option
usage: postadd_convergence.sh infile outfile
Used xml options:
- inverse.post_add_options.convergence.weight (default: 1)
- inverse.post_add_options.convergence.what (default: dist)
- name
- step
postadd_copyback.sh
postadd copyback script, copies files back to the maindir,
use ${name} in filename as replacement for the interaction name
Usage: postadd_copyback.sh infile outfile
Used xml options:
- inverse.post_add_options.copyback.filelist (default: empty)
- name
postadd_dummy.sh
postadd dummy script (does nothing), useful to overwrite default by nothing
Usage: postadd_dummy.sh infile outfile
postadd_overwrite.sh
postadd copyback script, copys files back to the maindir
use ${name} in filename, as replacement for the interaction name
Usage: postadd_overwrite.sh infile outfile
Used xml options:
- inverse.post_add
- inverse.post_add_options.overwrite.do (default: 1)
- name
postadd_plot.sh
postadd plot script, send a certain plot script to gnuplot
Usage: postadd_plot.sh infile outfile
Used external packages: gnuplot
Used xml options:
- inverse.post_add_options.plot.fd (default: 8)
- inverse.post_add_options.plot.gnuplot_bin (default: gnuplot)
- inverse.post_add_options.plot.gnuplot_opts (default: empty)
- inverse.post_add_options.plot.kill (default: empty)
- inverse.post_add_options.plot.script
post_add.sh
This script makes all the post update
Usage: post_add.sh
post_add_single.sh
This script makes all the post update with backup for single pairs
Usage: post_add_single.sh
Used xml options:
- inverse.post_add (default: empty)
- name
post_update_generic.sh
This script makes all the post update
Usage: post_update_generic.sh
Used xml options:
post_update_generic_single.sh
This script makes all the post update with backup for single pairs incl. backups
Usage: post_update_generic_single.sh
Used xml options:
- inverse.post_update (default: empty)
- name
postupd_pressure.sh
This script implements the pressure update
Usage: postupd_pressure.sh infile outfile
Used xml options:
- cg.inverse.program
- inverse.post_update_options.pressure.do (default: 1)
- inverse.post_update_options.pressure.type (default: simple)
- max
- min
- name
- step
postupd_scale.sh
This script implements scaling of the potential update (.dpot)
Usage: postupd_scale.sh infile outfile
Used xml options:
- inverse.post_update_options.scale (default: 1.0)
- name
postupd_smooth.sh
This script implements smoothing of the potential update (.dpot)
Usage: postupd_smooth.sh infile outfile
Used xml options:
- inverse.post_update_options.smooth.iterations (default: 1)
- name
postupd_splinesmooth.sh
This script implements smoothing of the potential update (.dpot)
Usage: postupd_splinesmooth.sh infile outfile
Used xml options:
- inverse.post_update_options.splinesmooth.step
- max
- min
- name
- step
potential_to_espresso.sh
This script is a wrapper to convert a potential to espresso
Usage: potential_to_espresso.sh
Used xml options:
- cg.inverse.espresso.table_bins
- inverse.espresso.table
- max
- name
potential_to_gromacs.sh
This script is a wrapper to convert a potential to gromacs
Usage: potential_to_gromacs.sh [input] [output]
Used xml options:
- cg.inverse.gromacs.mdp (default: grompp.mdp)
- cg.inverse.gromacs.pot_max (default: empty)
- cg.inverse.gromacs.table_bins
- cg.inverse.gromacs.table_end
- cg.inverse.gromacs.table_end (default: empty)
- cg.inverse.method (default: empty)
- bondtype
- inverse.gromacs.table
- name
prepare_generic_espresso.sh
This script implements the prepare step for espresso
Usage: prepare_generic_espresso.sh
Used xml options:
- cg.inverse.espresso.blockfile (default: conf.esp.gz)
- cg.inverse.espresso.blockfile_out (default: confout.esp.gz)
prepare_generic_gromacs.sh
This script does the prepare step for gromacs
Usage: prepare_generic_gromacs.sh
Used xml options:
- cg.inverse.gromacs.conf (default: conf.gro)
- cg.inverse.gromacs.conf_out (default: confout.gro)
prepare_generic.sh
This script prepares potentials in a generic way
Usage: prepare_generic.sh
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: prepare_generic_single.sh
Used xml options:
- cg.inverse.method
- inverse.target
- max
- min
- name
- step
prepare_ibm.sh
Informs users that ibm was renamed to ibi.
Usage: prepare_ibm.sh
prepare_imc.sh
This script initializes potentials for imc
Usage: prepare_imc.sh
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: pressure_cor_simple.pl p_cur outfile
Used xml options:
- cg.inverse.kBT
- inverse.post_update_options.pressure.simple.scale
- inverse.p_target
- max
- min
- 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: pressure_cor_wjk.pl p_cur outfile
Used xml options:
- cg.inverse.kBT
- inverse.particle_dens
- inverse.post_update_options.pressure.wjk.scale (default: 1.0)
- inverse.p_target
- max
- min
- name
- 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: RDF_to_POT.pl infile outfile
Used xml options:
resample_target.sh
This script resamples target distribution to grid spacing of the setting xml file
Usage: resample_target.sh
Used xml options:
- inverse.target
- max
- min
- name
- step
run_espresso.sh
This script runs espresso for the Inverse Boltzmann Method
Usage: run_espresso.sh
Used external packages: espresso
Used xml options:
- cg.inverse.espresso.blockfile (default: conf.esp.gz)
- cg.inverse.espresso.blockfile_out (default: confout.esp.gz)
- cg.inverse.espresso.command (default: Espresso_bin)
- cg.inverse.espresso.debug (default: no)
- cg.inverse.espresso.exclusions (default: 0)
- cg.inverse.espresso.n_snapshots
- cg.inverse.espresso.n_steps
- cg.inverse.espresso.success (default: success.esp)
- cg.inverse.espresso.traj (default: top_traj.esp)
- cg.inverse.method
- cg.non-bonded.inverse.espresso.index1
- cg.non-bonded.inverse.espresso.index2
run_gromacs.sh
This script runs a gromacs simulation
Usage: run_gromacs.sh
Used external packages: gromacs
Used xml options:
- cg.inverse.gromacs.conf (default: conf.gro)
- cg.inverse.gromacs.conf_out (default: confout.gro)
- cg.inverse.gromacs.grompp.bin (default: grompp)
- cg.inverse.gromacs.grompp.index (default: index.ndx)
- cg.inverse.gromacs.grompp.opts (default: empty)
- cg.inverse.gromacs.grompp.topol (default: topol.top)
- cg.inverse.gromacs.mdp (default: grompp.mdp)
- cg.inverse.gromacs.mdrun.checkpoint (default: state.cpt)
- cg.inverse.gromacs.mdrun.command (default: mdrun)
- cg.inverse.gromacs.mdrun.opts (default: empty)
- cg.inverse.gromacs.topol (default: topol.tpr)
solve_matlab.sh
This script solves a linear equation system from imc using matlab
Usage: solve_matlab.sh <group> <outfile>
Used external packages: matlab
Used xml options:
- cg.inverse.imc.matlab.bin (default: matlab)
solve_octave.sh
This script solves a linear equation system from imc using octave
Usage: solve_octave.sh <group> <outfile>
Used external packages: octave
Used xml options:
- cg.inverse.imc.octave.bin (default: octave)
table_compare.pl
This script compares two tables
Usage: table_compare.pl infile outfile
table_dummy.sh
This script creates a dummy table with grid min:step:max
Usage: table_dummy.sh min:step:max outfile
table_extrapolate.pl
This script extrapolates a table
Usage: table_extrapolate.pl [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
--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_getsubset.py
This script get the a subset of a table
Usage: table_getsubset.py
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: table_get_value.pl [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: table_integrate.pl [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
-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: table_linearop.pl [OPTIONS] <in> <out> <a> <b>
Allowed options:
-h, --help Show this help message
--withflag only change entries with specific flag in src
--with-errors also read and calculate errors
Examples:
table_linearop.pl tmp.dpot.cur tmp.dpot.new 1.0 0.0
tables_jackknife.pl
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
Usage: tables_jackknife.pl out full block1 block2 ...
table_smooth_borders.py
This script smooths the border for thermodynamic force iteration
Usage: table_smooth_borders.py
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: table_smooth.pl 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: table_to_tab.pl 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, thermoforce, C12, C6
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: tag_file.sh 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: update_ibi_pot.pl new_rdf target_rdf cur_pot outfile
Used xml options:
update_ibi.sh
This script implements the function update for the Inverse Boltzmann Method
Usage: update_ibi.sh
Used xml options:
update_ibi_single.sh
This script implemtents the function update for a single pair
for the Inverse Boltzmann Method
Usage: update_ibi_single.sh
Used xml options:
- inverse.do_potential (default: 1)
- max
- min
- name
- step
update_ibm.sh
Informs users that ibm was renamed to ibi.
Usage: update_ibm.sh
update_imc.sh
This script implements the function update
for the Inverse Monte Carlo Method
Usage: update_imc.sh
Used xml options:
- cg.inverse.imc.solver
- cg.inverse.program
- cg.non-bonded.inverse.imc.group
update_tf.sh
This script implements the function update for the thermodynamic force interation
Usage: update_tf.sh
update_tf_single.sh
This script implemtents the function update of a single interaction
for the thermodynamics force iteration
Usage: update_tf_single.sh
Used xml options:
- cg.inverse.program
- inverse.do_potential (default: 1)
- max
- min
- name
- step
