Reference¶
Programs¶
csg_boltzmann¶
NAME¶
csg_boltzmann - Part of the VOTCA package
SYNOPSIS¶
csg_boltzmann [OPTIONS]
csg_boltzmann [–help]
DESCRIPTION¶
Performs tasks that are needed for simple boltzmann inversion in an interactive environment.
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
Mapping options:
--cg arg coarse graining mapping and bond definitions
(xml-file)
--map-ignore arg list of molecules to ignore separated by ;
--no-map disable mapping and act on original trajectory
Special options:
--excl arg write atomistic exclusion list to file
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_call¶
NAME¶
csg_call - Part of the VOTCA package
SYNOPSIS¶
csg_call [OPTIONS]
csg_call [–help]
Usage: csg_call [OPTIONS] key1 key2 [SCRIPT OPTIONS]
DESCRIPTION¶
This script calls scripts and functions for the iterative framework. Function can be executed or shows if key1=’function’.
EXAMPLES¶
* csg_call table smooth [ARGUMENTS]
* csg_call --show run gromacs
OPTIONS¶
Allowed options:
-l, --list Show list of all script
--cat Show the content of the script
--show Show the path to the script
--show-share Shows the used VOTCASHARE dir and exits
--scriptdir DIR Set the user script dir
(Used if no options xml file is given)
Default: empty
--options FILE Specify the options xml file to use
--log FILE Specify the log file to use
Default: stdout
--ia-type type Specify the interaction type to use
--ia-name name Specify the interaction name to use
--nocolor Disable colors
--sloppy-tables Allow tables without flags
--debug Enable debug mode with a lot of information
-h, --help Show this help
csg_density¶
NAME¶
csg_density - Part of the VOTCA package
SYNOPSIS¶
csg_density [OPTIONS]
csg_density [–help]
DESCRIPTION¶
Calculates the mass density distribution along a box axis or radial density profile from reference point
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
Mapping options:
--cg arg [OPTIONAL] coarse graining mapping and bond
definitions
(xml-file). If no file is given, program acts on
original trajectory
--map-ignore arg list of molecules to ignore if mapping is done
separated by ;
Specific options::
--type arg (=mass) density type: mass or number
--axis arg (=r) [x|y|z|r] density axis (r=spherical)
--step arg (=0.01) spacing of density
--block-length arg write blocks of this length, the averages are
cleared after every write
--out arg Output file
--rmax arg rmax (default for [r] =min of all box vectors/2, else
l )
--scale arg (=1) scale factor for the density
--molname arg (=*) molname
--filter arg (=*) filter bead names
--ref arg reference zero point
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_dlptopol¶
NAME¶
csg_dlptopol - Part of the VOTCA package
SYNOPSIS¶
csg_dlptopol [OPTIONS]
csg_dlptopol [–help]
DESCRIPTION¶
Create a dlpoly topology template based on an existing (atomistic) topology and a mapping xml-file. The created template file needs to be inspected and amended by the user!
EXAMPLES¶
* csg_dlptopol --top .dlpf --out .dlpf --cg cg-map.xml
convert FIELD to FIELD_CGV using cg-map.xml
* csg_dlptopol --top FA-dlpoly.dlpf --out CG-dlpoly.dlpf --cg cg-map.xml
* csg_dlptopol --top FA-gromacs.tpr --out FA-dlpoly.dlpf --no-map
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
--out arg output topology in dlpoly format
Mapping options:
--cg arg coarse graining mapping and bond definitions
(xml-file)
--map-ignore arg list of molecules to ignore separated by ;
--no-map disable mapping and act on original trajectory
csg_dump¶
NAME¶
csg_dump - Part of the VOTCA package
SYNOPSIS¶
csg_dump [OPTIONS]
csg_dump [–help]
DESCRIPTION¶
Print atoms that are read from topology file to help debugging atom naming.
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
Mapping options:
--cg arg [OPTIONAL] coarse graining mapping and bond
definitions
(xml-file). If no file is given, program acts on
original trajectory
--map-ignore arg list of molecules to ignore if mapping is done
separated by ;
Specific options:
--excl display exclusion list instead of molecule list
csg_fmatch¶
NAME¶
csg_fmatch - Part of the VOTCA package
SYNOPSIS¶
csg_fmatch [OPTIONS]
csg_fmatch [–help]
DESCRIPTION¶
Perform force matching (also called multiscale coarse-graining)
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
--options arg options file for coarse graining
--trj-force arg coarse-grained trajectory containing forces of
already known interactions
Mapping options:
--cg arg coarse graining mapping and bond definitions
(xml-file)
--map-ignore arg list of molecules to ignore separated by ;
--no-map disable mapping and act on original trajectory
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_gmxtopol¶
NAME¶
csg_gmxtopol - Part of the VOTCA package
SYNOPSIS¶
csg_gmxtopol [OPTIONS]
csg_gmxtopol [–help]
DESCRIPTION¶
Create skeleton for gromacs topology based on atomistic topology and a mapping file. File still needs to be modified by the user.
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
--out arg output topology (will create .top and in future also
.itp)
Mapping options:
--cg arg coarse graining mapping and bond definitions
(xml-file)
--map-ignore arg list of molecules to ignore separated by ;
--no-map disable mapping and act on original trajectory
csg_imc_solve¶
NAME¶
csg_imc_solve - Part of the VOTCA package
SYNOPSIS¶
csg_imc_solve [OPTIONS]
csg_imc_solve [–help]
DESCRIPTION¶
Solves the linear system for IMCs
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
-r [ --regularization ] arg (=0) regularization factor
-i [ --imcfile ] arg imc statefile
-g [ --gmcfile ] arg gmc statefile
-n [ --idxfile ] arg idx statefile
csg_inverse¶
NAME¶
csg_inverse - Part of the VOTCA package
SYNOPSIS¶
csg_inverse [OPTIONS]
csg_inverse [–help]
Usage: csg_inverse [OPTIONS] –options settings.xml [clean]
DESCRIPTION¶
Start the script to run ibi, imc, etc. or clean out current dir
EXAMPLES¶
* csg_inverse --options cg.xml
* csg_inverse -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
csg_map¶
NAME¶
csg_map - Part of the VOTCA package
SYNOPSIS¶
csg_map [OPTIONS]
csg_map [–help]
DESCRIPTION¶
Convert a reference atomistic trajectory or configuration into a coarse-grained one based on a mapping xml-file. The mapping can be applied to either an entire trajectory or a selected set of frames only (see options).
EXAMPLES¶
* csg_map --top FA-topol.tpr --trj FA-traj.trr --out CG-traj.xtc --cg cg-map.xml
* csg_map --top FA-topol.tpr --trj FA-conf.gro --out CG-conf.gro --cg cg-map.xml
* csg_map --top FA-topol.tpr --trj FA-traj.xtc --out FA-history.dlph --no-map
* csg_map --top FA-field.dlpf --trj FA-history.dlph --out CG-history.dlph --cg cg-map.xml
* csg_map --top .dlpf --trj .dlph --out .dlph --cg cg-map.xml convert HISTORY to HISTORY_CGV
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
--out arg output file for coarse-grained trajectory
--vel Write mapped velocities (if available)
--force Write mapped forces (if available)
--hybrid Create hybrid trajectory containing both atomistic
and coarse-grained
Mapping options:
--cg arg coarse graining mapping and bond definitions
(xml-file)
--map-ignore arg list of molecules to ignore separated by ;
--no-map disable mapping and act on original trajectory
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_property¶
NAME¶
csg_property - Part of the VOTCA package
SYNOPSIS¶
csg_property [OPTIONS]
csg_property [–help]
DESCRIPTION¶
Helper program called by inverse scripts to parse xml file.
OPTIONS¶
Allowed options:
--help produce this help message
--path arg path to part of the xml file to print
--filter arg list option values that match given criteria
--print arg (=.) specifies which children or root to print
--file arg xml file to parse
--short short version of output
--with-path include path of node in output
csg_resample¶
NAME¶
csg_resample - Part of the VOTCA package
SYNOPSIS¶
csg_resample [OPTIONS]
csg_resample [–help]
DESCRIPTION¶
Change grid and interval of any sort of table files. Mainly called internally by inverse script, can also be used to manually prepare input files for coarse-grained simulations.
OPTIONS¶
Allowed options:
--help produce this help message
--in arg table to read
--out arg table to write
--derivative arg table to write
--grid arg new grid spacing (min:step:max). If 'grid' is specified
only, interpolation is performed.
--type arg (=akima) [cubic|akima|linear]. If option is not specified, the
default type 'akima' is assumed.
--fitgrid arg specify fit grid (min:step:max). If 'grid' and
'fitgrid' are specified, a fit is performed.
--nocut Option for fitgrid: Normally, values out of fitgrid
boundaries are cut off. If they shouldn't, choose
--nocut.
--comment arg store a comment in the output table
--boundaries arg (natural|periodic|derivativezero) sets boundary
conditions
csg_reupdate¶
NAME¶
csg_reupdate - Part of the VOTCA package
SYNOPSIS¶
csg_reupdate [OPTIONS]
csg_reupdate [–help]
DESCRIPTION¶
computes relative entropy update.
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file (only needed for
RE update)
RE Specific options:
--options arg options file for coarse graining
--gentable arg (=0) only generate potential tables from given
parameters, NO RE update!
--interaction arg [OPTIONAL] generate potential tables only
for the specified interactions,
only valid when 'gentable' is true
--param-in-ext arg (=param.cur) Extension of the input parameter tables
--param-out-ext arg (=param.new) Extension of the output parameter tables
--pot-out-ext arg (=pot.new) Extension of the output potential tables
--hessian-check arg (=1) Disable the hessian check (mostly for
testing)
Threading options:
--nt arg (=1) number of threads
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works
for Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_stat¶
NAME¶
csg_stat - Part of the VOTCA package
SYNOPSIS¶
csg_stat [OPTIONS]
csg_stat [–help]
DESCRIPTION¶
Calculate all distributions (bonded and non-bonded) specified in options file. Optionally calculates update Eigen::Matrix3d for invere Monte Carlo. This program is called inside the inverse scripts. Unlike csg_boltzmann, big systems can be treated as well as non-bonded interactions can be evaluated.
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
Mapping options:
--cg arg [OPTIONAL] coarse graining mapping and bond
definitions
(xml-file). If no file is given, program acts on
original trajectory
--map-ignore arg list of molecules to ignore if mapping is done
separated by ;
Specific options:
--options arg options file for coarse graining
--do-imc write out additional Inverse Monte Carlo data
--include-intra do not exclude intramolecular neighbors
--block-length arg write blocks of this length, the averages are
cleared after every write
--ext arg (=dist.new) Extension of the output
Threading options:
--nt arg (=1) number of threads
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
Mapping file¶
The root node always has to be cg_molecule. It can contain the following keywords:
The following table contains the input options for CSG,
Property Name |
Default Value |
Description |
|---|---|---|
ident |
Molecule name in reference topology. |
|
topology |
Section defining coarse grained beads of molecule. |
|
topology.cg_beads |
Section defining coarse grained beads of molecule. |
|
topology.cg_beads.cg_bead |
Definition of a coarse grained bead. |
|
topology.cg_beads.cg_bead.name |
Name of coarse grained bead. |
|
topology.cg_beads.cg_bead.type |
Type of coarse grained bead. |
|
topology.cg_beads.cg_bead.mapping |
Mapping scheme to be used for this bead (specified in
section mapping) to map from reference system.
|
|
topology.cg_beads.cg_bead.beads |
The beads section lists all atoms of the reference system
that are mapped to this particular coarse grained bead.
The syntax is RESID:RESNAME:ATOMNAME, the beads are separated
by spaces.
|
|
topology.cg_bonded |
The cg_bonded section contains all bonded interaction
of the molecule. Those can be bond, angle or dihedral.
An entry for each group of bonded interaction can be specified,
e.g. several groups (types) of bonds can be specified.
A specific bonded interaction can be later on addressed
by MOLECULE:NAME:NUMBER, where MOLECULE is the molecule
ID in the whole topology, NAME the name of the interaction
group and NUMBER addresses the interaction in the group.
|
|
topology.cg_bonded.bond |
Definition of a group of bonds. |
|
topology.cg_bonded.bond.name |
Name of the bond. |
|
topology.cg_bonded.bond.beads |
List of pair of beads that define a bond. Names specified
in cg_beads
|
|
topology.cg_bonded.angle |
Definition of a group of angles. |
|
topology.cg_bonded.angle.name |
Name of the angle |
|
topology.cg_bonded.angle.beads |
List of triples of beads that define a bond. Names specified
in cg_beads
|
|
topology.cg_bonded.dihedral |
Definition of a group of dihedrals. Since the exact functional
form does not matter, this combines proper as well as
improper dihedrals.
|
|
topology.cg_bonded.dihedral.name |
Name of the dihedral |
|
topology.cg_bonded.dihedral.beads |
List of quadruples of beads that define a bond. Names
specified in cg_beads
|
|
maps |
Section containing definitions of mapping schemes. |
|
maps.map |
Section for a mapping for 1 bead. |
|
maps.map.name |
Name of the mapping |
|
maps.map.weights |
Weights of the mapping matrix. Entries are normalized
to 1, number of entries must match the number of reference
beads in a coarse-grained bead.
|
Topology file¶
The XMLtopology file
The XML topology root element, the base for the topology can be defined by the “name” attribute The following table contains the input options for CSG,
Property Name |
Default Value |
Description |
|---|---|---|
h5md_particle_group |
Attribute name holds the name of particles group in H5MD
file
|
|
molecules |
The the molecules in the trajectory or other operation
on the molecules.
|
|
molecules.molecule |
Definition of the molecule, with attributes: name, nmols
and nbeads. The name defines residue name, nmols tells
how many times this molecule has to be replicated to match
with trajectory file and nbeads defines number of beads
in every molecule.
|
|
molecules.molecule.bead |
Define the bead in the molecule. Attributes are: name
- the name of bead, type - the type of bead, mass - the
mass of bead, q - the value of charge and resid - the
id of the residue the bead belongs to (>=1).
|
|
molecules.clear |
Clear the information about the molecules |
|
molecules.rename |
Rename the molecules; attributes: “name” - the new name,
“range” - the range where the new name will be set in
the format start_range:end_range
|
|
molecules.define |
Define the molecules; attributes: “name” - the name of
molecule, “first” - the id of first molecule, “nbeads”
- the number of beads in the molecule, “nmols” - the number
of molecules
|
|
bonded |
This section defines the topology of the molecules, it
is used to generate proper exclusions for calculating
rdfs
|
|
bonded.bond |
Describes the bond |
|
bonded.bond.name |
The name of the bond |
|
bonded.bond.beads |
The pair of the beads in the format MOLECULE_NAME:BEAD_NAME
|
|
bonded.angle |
Describes the angle |
|
bonded.angle.name |
The name of the angle |
|
bonded.angle.beads |
The triplet of the beads in the format MOLECULE_NAME:BEAD_NAME
|
|
bonded.dihedral |
Describes the dihedrals |
|
bonded.dihedral.name |
The name of the dihedral |
|
bonded.dihedral.beads |
The quadruplet of the beads in the format MOLECULE_NAME:BEAD_NAME
|
|
beadtypes |
Allows defining bead types |
|
beadtypes.rename |
Rename the bead type; attributes: “name” - the old name,
“newname” - the new name
|
|
beadtypes.mass |
Define the mass of the bead type; attributes: “name” -
the bead type name, “value” - the new mass
|
Settings file¶
All options for the iterative script are stored in an xml file.
Section containing the all coarse-graining options The following table contains the input options for CSG,
Property Name |
Default Value |
Description |
|---|---|---|
fmatch |
Force matching options |
|
fmatch.constrainedLS |
boolean variable: false - simple least squares, true -
constrained least squares. For details see the VOTCA paper.
Practically, both algorithms give the same results, but
simple least squares is faster. If you are a mathematician
and you think that a spline can only then be called a
spline if it has continuous first and second derivatives,
use constrained least squares.
|
|
fmatch.dist |
1e-5 |
Accuracy for evaluating the difference in bead positions.
Default is 1e-5
|
fmatch.frames_per_block |
number of frames, being used for block averaging. Atomistic
trajectory, specified with –trj option, is divided into
blocks and the force matching equations are solved separately
for each block. Coarse-grained force-field, which one
gets on the output is averaged over those blocks.
|
|
inverse |
general options for inverse script |
|
inverse.cleanlist |
these files are removed after each iteration |
|
inverse.convergence_check |
||
inverse.convergence_check.limit |
0 |
lower convergency limit to stop |
inverse.convergence_check.type |
none |
type of convergence check to do |
inverse.dlpoly |
general dlpoly specific options |
|
inverse.dlpoly.command |
DLPOLY.Z |
command to run dlpoly (name or absolute path or ‘mpirun
dlpoly’ or such)
|
inverse.dlpoly.topol |
.dlpf |
Name of dlpoly topology file |
inverse.dlpoly.traj |
.dlph |
Name of the output dlpoly trajectory file |
inverse.dlpoly.checkpoint |
REVIVE REVCON |
Names of the dlpoly checkpoint files |
inverse.dlpoly.table_end |
dlpoly internal grid end point for tabulated non-bonded
potentials (applied to all non-bonded)
|
|
inverse.dlpoly.table_grid |
dlpoly internal grid number for tabulated non-bonded potentials
(applied to all non-bonded)
|
|
inverse.dlpoly.bonds |
dlpoly specs for tabulated bonded potentials (applied
to all bonds)
|
|
inverse.dlpoly.bonds.table_end |
dlpoly internal grid end point for tabulated potentials |
|
inverse.dlpoly.bonds.table_grid |
dlpoly internal grid number for tabulated potentials |
|
inverse.dlpoly.angles |
dlpoly specs for tabulated bonded potentials (applied
to all angles)
|
|
inverse.dlpoly.angles.table_grid |
dlpoly internal grid number for tabulated potentials |
|
inverse.dlpoly.dihedrals |
dlpoly specs for tabulated bonded potentials (applied
to all dihedrals)
|
|
inverse.dlpoly.dihedrals.table_grid |
dlpoly internal grid number for tabulated potentials |
|
inverse.espresso |
||
inverse.espresso.command |
python3 |
Command to run espresso (name or absolute path or mpirun
espresso..)
|
inverse.espresso.opts |
${script} |
option to be given to espresso program, use ${script}
in there
|
inverse.espresso.first_frame |
0 |
trash the given number of frames at the beginning of trajectory
|
inverse.espresso.table_bins |
espresso internal grid for tabulated potentials |
|
inverse.espresso.traj |
Name of the output Espresso trajectory file |
|
inverse.espressopp |
||
inverse.espressopp.command |
python3 |
Command to run espresso (name or absolute path or mpirun
espresso..)
|
inverse.espressopp.opts |
${script} |
option to be given to espresso program, use ${script}
in there
|
inverse.espressopp.first_frame |
0 |
trash the given number of frames at the beginning of trajectory
|
inverse.filelist |
these files are copied to each iteration step |
|
inverse.gnuplot |
||
inverse.gnuplot.bin |
gnuplot |
gnuplot binary to use |
inverse.gromacs |
gromacs specific options |
|
inverse.gromacs.conf |
conf.gro |
Name of the coordinate file read by grompp |
inverse.gromacs.conf_out |
confout.gro |
Name of the original outcome coordinate written by mdrun |
inverse.gromacs.density |
||
inverse.gromacs.density.block_length |
Length of the block for the error analysis |
|
inverse.gromacs.density.with_errors |
no |
calculate error on the density: yes/no |
inverse.gromacs.equi_time |
0 |
begin analysis after this time when using gromacs (max
of this and first_frame is used)
|
inverse.gromacs.first_frame |
0 |
trash the given number of frames at the beginning of trajectory
(max of this and first_frame is used)
|
inverse.gromacs.g_energy |
||
inverse.gromacs.g_energy.bin |
/usr/bin/gmx_d energy |
Name (or absolute path) of the g_energy binary |
inverse.gromacs.g_energy.opts |
Additional options to Gromacs g_energy (e.g. -P 1) |
|
inverse.gromacs.g_energy.pressure |
options for pressure calculation using g_energy |
|
inverse.gromacs.g_energy.pressure.allow_nan |
no |
is nan an allowed result: yes/no |
inverse.gromacs.g_energy.topol |
Gromacs binary topol (tpr) file to use by g_energy |
|
inverse.gromacs.gmxrc |
GMXRC to source at the startup |
|
inverse.gromacs.grompp |
||
inverse.gromacs.grompp.bin |
/usr/bin/gmx_d grompp |
Name (or absolute path) of the grompp binary |
inverse.gromacs.grompp.opts |
Additional options to Gromacs grompp (e.g. -maxwarn 1) |
|
inverse.gromacs.index |
index.ndx |
Gromacs grompp index file to used by grompp |
inverse.gromacs.log |
Separate log file for gromacs programs (useful with mdrun
-v)
|
|
inverse.gromacs.mdp |
grompp.mdp |
Gromacs mdp file to be used by grompp |
inverse.gromacs.mdrun |
||
inverse.gromacs.mdrun.checkpoint |
state.cpt |
Name of the checkpint to use in case of restarted simulation |
inverse.gromacs.mdrun.command |
/usr/bin/gmx_d mdrun |
Command to run mdrun (name or absolute path or mpirun
mdrun..)
|
inverse.gromacs.mdrun.multidir |
List of directories for multidir simulations |
|
inverse.gromacs.mdrun.opts |
Additional options to Gromacs mdrun (e.g. -nosum) |
|
inverse.gromacs.pot_max |
1000000 |
cut the potential at this value (gromacs bug) |
inverse.gromacs.pre_simulation |
no |
A pre simulation (e.g. minimization / equilibration )
is a simulation with a different mdp/topol/index
|
inverse.gromacs.pre_simulation.index |
Gromacs grompp index file to used by grompp in the pre
simulation
|
|
inverse.gromacs.pre_simulation.mdp |
Gromacs mdp file to be used by grompp in the pre simulation |
|
inverse.gromacs.pre_simulation.topol_in |
Gromacs text topol (top) file to use by grompp in the
pre simulation
|
|
inverse.gromacs.ref |
Options for the case that calculation of reference system
is needed
|
|
inverse.gromacs.ref.equi_time |
0 |
begin analysis after this time when using gromacs (max
of this and first_frame is used)
|
inverse.gromacs.ref.first_frame |
0 |
trash the given number of frames at the beginning of trajectory
(max of this and first_frame is used)
|
inverse.gromacs.ref.mapping |
Mapping to apply on the coarse-grained topology, use autogenerated
ones (cg.inverse.optimizer.mapping.output) and given ones
(map other components)
|
|
inverse.gromacs.ref.rdf |
Contains options for Reference rdf calculation |
|
inverse.gromacs.ref.rdf.opts |
Extra options to give to csg_stat (e.g. –nframes 100) |
|
inverse.gromacs.ref.topol |
Reference binary topology(global or local path) |
|
inverse.gromacs.ref.traj |
Reference trajectory(global or local path) |
|
inverse.gromacs.rdf |
||
inverse.gromacs.rdf.block_length |
Length of the block for the error analysis |
|
inverse.gromacs.rdf.map |
Space separated list of special mapping file(s) for rdf
calculations needed for bonded interactions
|
|
inverse.gromacs.rdf.with_errors |
no |
calculate error on the rdf: yes/no |
inverse.gromacs.table_bins |
0.002 |
grid for gromacs xvg table |
inverse.gromacs.table_end |
extend the gromacs xvg tables to this value |
|
inverse.gromacs.temp_check |
yes |
check kBT against t_ref in mdp file: yes/no |
inverse.gromacs.topol_in |
topol.top |
Gromacs text topology (top) file read by grompp |
inverse.gromacs.topol |
topol.tpr |
Gromacs binary topology (tpr) file to be written by grompp
and used for the simlation
|
inverse.gromacs.traj |
traj.xtc |
Gromacs trajectory file to use |
inverse.gromacs.trjcat |
||
inverse.gromacs.trjcat.bin |
/usr/bin/gmx_d trjcat |
Name (or absolute path) of the trjcat binary |
inverse.hoomd-blue |
||
inverse.hoomd-blue.command |
hoomd |
Command to run hoomd-blue (name or absolute path or mpirun
..)
|
inverse.hoomd-blue.opts |
${script} |
option to be given to hoomd-blue program, use ${script}
in there
|
inverse.imc |
general imc specific options |
|
inverse.imc.default_reg |
0 |
default magnitude for regularization parameter if not
given for the group explicitly, default =0
|
inverse.lammps |
general lammps specific options |
|
inverse.lammps.command |
/usr/bin/lmp |
command to run lammps (name or absolute path or mpirun
lammps..)
|
inverse.lammps.script |
lammps script to run |
|
inverse.lammps.opts |
-in ${script} |
option to be given to lammps program, use ${script} in
there
|
inverse.lammps.traj |
trajectory file to be created by lammps, use a format
like xyz, which can be read by csg_stat
|
|
inverse.lammps.pressure_file |
pressure file generated by lammps, use “fix print” in
lammps input (e.g., “fix pressure all print 50 “${mypress}”
file lammps.pressure screen no title “LAMMPS_PRESSURE”
“ ; pressure_file would be lammps.pressure in this example).
The title can be anything as VOTCA skips over this line
as a header when parsing
|
|
inverse.sim_prog |
options, which apply to all simulation programs |
|
inverse.sim_prog.command |
Command to run for the simulation (name or absolute path
or mpirun XXX ..)
|
|
inverse.sim_prog.conf |
Name of the coordinate file read by the simulation program
(if needed)
|
|
inverse.sim_prog.conf_out |
Name of the original outcome coordinate written by simulation
program (if any)
|
|
inverse.sim_prog.equi_time |
0 |
begin analysis after this time (max of this and first_frame
is used)
|
inverse.sim_prog.density |
||
inverse.sim_prog.density.block_length |
Length of the block for the error analysis |
|
inverse.sim_prog.density.with_errors |
no |
calculate error on the density: yes/no |
inverse.sim_prog.first_frame |
0 |
trash the given number of frames at the beginning of trajectory
(max of this and first_frame is used)
|
inverse.sim_prog.imc |
||
inverse.sim_prog.imc.topol |
Special topology file to be used for csg_stat used in imc |
|
inverse.sim_prog.imc.traj |
Special trajectory file to be used for csg_stat used in imc |
|
inverse.sim_prog.re |
||
inverse.sim_prog.re.topol |
Special topology file to be used for csg_reupdate |
|
inverse.sim_prog.re.traj |
Special trajectory file to be used for csg_reupdate |
|
inverse.sim_prog.rdf |
||
inverse.sim_prog.rdf.block_length |
Length of the block for the error analysis |
|
inverse.sim_prog.rdf.map |
Space separated list of special mapping file(s) for rdf
calculations needed for bonded interactions
|
|
inverse.sim_prog.rdf.topol |
Special topology file to be used for csg_stat |
|
inverse.sim_prog.rdf.traj |
Special trajectory file to be used for csg_stat |
|
inverse.sim_prog.rdf.with_errors |
n |
calculate error on the rdf: yes/no |
inverse.sim_prog.topol |
General topology file to be use if no special one is specified
|
|
inverse.sim_prog.traj |
trajectory file to be created by the simulation program |
|
inverse.sim_prog.script |
simulation script to run (if any) |
|
inverse.sim_prog.opts |
option to be given to simulation program, use ${script}
in there
|
|
inverse.re |
general options for realtive entropy method |
|
inverse.re.csg_reupdate |
||
inverse.re.csg_reupdate.opts |
options for the csg_reupdate command |
|
inverse.average |
||
inverse.average.steps |
1 |
number of steps to be used for average computation. For
relative entropy method, these many last iteration steps
are used to compute average CG potentials or parameters
or both.
|
inverse.initial_configuration |
maindir |
what initial configuration to use in every step: maindir/laststep/nowhere.
|
inverse.iterations_max |
do the given number of iterations (-1=inf, 0=only step_000) |
|
inverse.kBT |
kBT in KJ/mol (i.e. XXX K * 0.00831451) |
|
inverse.log_file |
inverse.log |
name of the log file |
inverse.map |
Special mapping file(s) for rdf calculations needed for
bonded interactions
|
|
inverse.method |
method to be performed: ibi/iie/imc/ft/optimizer |
|
inverse.iie |
general options for the IIE schemes (hncgn/ihnc/hncn/pygn/ipy/pyn)
|
|
inverse.iie.initial_guess |
Settings for the initial guess |
|
inverse.iie.initial_guess.method |
ie |
Method for the initial potential guess: table/bi/ie |
inverse.iie.initial_guess.closure |
OZ equation closure in case of method=ie: hnc/py |
|
inverse.iie.initial_guess.ignore_intramolecular_correlation |
false |
If true, the initial guess will ignore the presence of
intramolecular correlation in the CG molecule.
|
inverse.iie.method |
gauss-newton |
Update method to use: gauss-newton/newton/newton-mod.
For example closure=hnc + method=gauss-newton will result
in the HNCGN method. newton_mod is a modified newton scheme
that results in an IBI like expression e.g. IHNC.
|
inverse.iie.closure |
hnc |
OZ equation closure for the IIE update: hnc/py |
inverse.iie.ignore_intramolecular_correlation |
false |
If true, the IIE updates (not the initial guess) will
ignore the presence of intramolecular correlation in the
CG molecule.
|
inverse.iie.cut_off |
Cut-off used for non-bonded potenitals in MD. Potential
will be set to zero beyond this point.
|
|
inverse.iie.g_extrap_factor |
1.0 |
Lenght factor by which RDF will be extrapolated |
inverse.iie.cut_jacobian |
true |
Wether to cut the Jacobian before multiplying with Δg.
Only for Newton methods
|
inverse.iie.densities |
List of densities of the beads, sorted by bead name. TODO:
replace by automatic calculation.
|
|
inverse.iie.n_intra |
List of n_intra, the number of equal beads, sorted by
bead name. TODO: replace by automatic calculation.
|
|
inverse.iie.pressure_constraint |
none |
Apply pressure constraint. Only for hncgn/pygn |
inverse.iie.extrap_near_core |
power |
Method for extrapolation in and close to core region.
Valid values are: power (default), constant, none
|
inverse.iie.fix_near_cut_off |
full-deriv |
Method for fixing discontinuity at end of potential. Valid
values are: full-deriv (default), none
|
inverse.iie.verbose |
true |
Print some info and dump compressed numpy arrays. Valid
values are: true (default), false
|
inverse.optimizer |
||
inverse.optimizer.cma |
general options for the cma optimizer |
|
inverse.optimizer.cma.eps |
standard epsilon, in which the best solution is searched |
|
inverse.optimizer.type |
Type of optimizer to be used |
|
inverse.program |
gromacs |
simulation package to be used (gromacs/espresso/lammps) |
inverse.restart_file |
restart_points.log |
Name of the restart file in case a step has to be resumed |
inverse.dist_min |
1e-10 |
minimal value for the rdf to consider for initial guess
of the potential)
|
inverse.scriptpath |
list of directories for user scripts (e.g. $PWD) separated
by a colon (like PATH)
|
|
inverse.simulation |
simulation options |
|
inverse.simulation.background |
no |
tells csg_inverse that simulation was send to the backgroud |
inverse.simulation.tasks |
auto |
number of threads to use for csg_stat |
inverse.scale |
update scaling factor for the relative entropy update |
|
nbsearch |
grid |
Grid search algorithm, simple (N square search) or grid |
bonded |
Interaction specific option for bonded interactions, see
the cg.non-bonded section for all options
|
|
bonded.dlpoly |
||
bonded.dlpoly.header |
Header of the interaction in dlpoly TABBND or TABANG file.
The header should be a unique set of the interaction-site
names, and these should match the corresponding names
specified in the mapping file.
|
|
bonded.name |
Name of the bonded interaction. The name can be arbitrary
but should be unique. For bonded interactions, this should
match the name specified in the mapping file.
|
|
bonded.periodic |
0 |
set to 1 when calculating bond dihedral potentials with
csg_fmatch -> enforces periodicity of potential. (default
is 0)
|
non-bonded |
Interaction specific option for non-bonded interactions |
|
non-bonded.dlpoly |
||
non-bonded.dlpoly.header |
Header of the interaction in dlpoly TABLE file. The header
should be a unique pair of the interaction-site names,
and these should match the corresponding names specified
in the mapping file.
|
|
non-bonded.name |
Name of the interaction. The name can be arbitrary but
should be unique. For bonded interactions, this should
match the name specified in the mapping file.
|
|
non-bonded.type1 |
Bead type 1 of non-bonded interaction. |
|
non-bonded.type2 |
Bead type 2 of non-bonded interaction. |
|
non-bonded.bondtype |
Internal alias for “non-bonded” or “bonded”, set automatically
|
|
non-bonded.min |
Lower bound of interval for potential table in which calculations
are performed. Should be set based on reference distributions.
|
|
non-bonded.max |
Upper bound of interval for potential table in which calculations
are performed. Should be set based on reference distributions.
|
|
non-bonded.step |
Step size of interval for potential table in which calculations
are performed. If step site is too small, lots of statistics
is needed ( long runs ). If it’s too big, features in
the distribtuion/potentials might get lost.
|
|
non-bonded.fmatch |
Force matching options |
|
non-bonded.fmatch.min |
Minimum value of interval for distribution sampled in
atomistic MD simulation. One can get this number by looking
at the distribution function for this interaction. For
non-bonded interactions it’s the distance to the rdf start.
For CG bonds and angles the variable has the similar meaning
( note, that for angles it is specified in radians ).
|
|
non-bonded.fmatch.max |
Maximum value of interval for distribution sampled in
atomistic MD simulation. One can get this number by looking
at the distribution function for this interaction. For
non-bonded interactions it’s the cut-off of the interaction.
|
|
non-bonded.fmatch.step |
grid spacing for the spline, which represents the interaction.
This parameter should not be too big, otherwise you might
lose some features of the interaction potential, and not
too small either, otherwise you will have unsampled bins
which result in an ill-defined equation system and NaNs
in the output.
|
|
non-bonded.fmatch.out_step |
Grid spacing for the output grid. Normally, one wants
to have this parameter smaller than fmatch.step, to have
a smooth curve, without additional spline interpolation.
As a rule of thumb we normally use fmatch.out_step which
is approximately 5 times smaller than fmatch.step.
|
|
non-bonded.re |
Relative entropy options |
|
non-bonded.re.function |
Functional form for the potential. Available functional
forms: lj126 (Lennard-Jones 12-6), ljg (Lennard-Jones
12-6 plus Gaussian), and cbspl (uniform cubic B-splines).
|
|
non-bonded.re.cbspl |
options specific to cbspl function form |
|
non-bonded.re.cbspl.nknots |
Number of knot values to be used for the cbspl functional
form. Uniform grid size of the CBSPL depends on this parameter;
for fixed potential range more the nknots smaller the
grid spacing. Make sure grid spacing is sufficiently large
and enough CG simulation steps are performed such that
the bins at distance greater than the minimum distance
are sampled sufficiently otherwise ill-defined system
of equation would give NaNs in the output.
|
|
non-bonded.inverse |
Contains all information relevant to iterative process |
|
non-bonded.inverse.target |
target distribution (e.g. rdf) which is tried to match
during iterations to match
|
|
non-bonded.inverse.p_target |
pressure contribution of this interaction |
|
non-bonded.inverse.particle_dens |
particle density of this species (for wjk pressure correction)
|
|
non-bonded.inverse.do_potential |
1 |
Update cycle for the potential update. 1 means update,
0 don’t update. 1 1 0 means update 2 iterations, then
don’t one iteration update, then repeat.
|
non-bonded.inverse.espresso |
Espresso specific options for this interations |
|
non-bonded.inverse.espresso.table |
Name of file for tabulated potential of this interaction.
This fill will be created from the internal tabulated
potential format in every step. Note, though, that the
original espresso script needs to contain the name of
that table as the tabulated interaction (see tutorial
methanol ibi_espresso for details).
|
|
non-bonded.inverse.espressopp |
Espresso++ specific options for this interations |
|
non-bonded.inverse.hoomd-blue |
HOOMD-blue specific options for this interations |
|
non-bonded.inverse.gromacs |
Gromacs specific options for this interations |
|
non-bonded.inverse.gromacs.table |
Name of file for tabulated potential of this interaction.
This fill will be created from the internal tabulated
potential format in every step.
|
|
non-bonded.inverse.sim_prog |
interaction specific options, which apply to all simulation
programs
|
|
non-bonded.inverse.sim_prog.table |
Name of file for tabulated potential of this interaction.
This fill will be created from the internal tabulated
potential format in every step. Note, though, that the
original simulation script needs to contain the name of
that table as the tabulated interaction (see tutorial
methanol ibi_espresso for details).
|
|
non-bonded.inverse.sim_prog.table_begin |
Start of the tabulated potential of this interaction.
(Automatic for gromacs)
|
|
non-bonded.inverse.sim_prog.table_end |
End of the tabulated potential of this interaction. (Automatic
for gromacs)
|
|
non-bonded.inverse.sim_prog.table_left_extrapolation |
Extrapolation function to use on the left. Default: exponential(non-bonded),
linear (bonded), Options: constant linear quadratic exponential
sasha
|
|
non-bonded.inverse.sim_prog.table_right_extrapolation |
Extrapolation function to use on the right. Default: constant(non-bonded),
linear (bonded), Options: constant linear quadratic exponential
sasha
|
|
non-bonded.inverse.sim_prog.table_bins |
Binszie of the tabulated potential of this interaction.
(gromacs uses a non interaction specific option)
|
|
non-bonded.inverse.imc |
section containing inverse monte carlo specific options. |
|
non-bonded.inverse.imc.group |
Group of interaction. Cross-correlations of all members
of a group are taken into account for calculating the
update. If no cross correlations should be calculated,
interactions have to be put into different groups. Group
‘none’ is completely ignored and update_potential needs
to be zero for the respective interactions.
|
|
non-bonded.inverse.lammps |
lammps specific options for this interations |
|
non-bonded.inverse.lammps.scale |
1 |
x-axis scaling factor for the potential output, can be
used to convert VOTCA units, nm, to other units, e.g.
angstroms
|
non-bonded.inverse.lammps.table |
Name of file for tabulated potential of this interaction.
This fill will be created from the internal tabulated
potential format in every step. Note, though, that the
lammps script needs to contain the name of that table
as the tabulated interaction and the interaction is stored
in the VOTCA section of the file..
|
|
non-bonded.inverse.lammps.y_scale |
1 |
y-axis scaling factor for the potential output, can be
used to convert VOTCA units, kJ/mol, to other units, e.g.
kcal/mol
|
non-bonded.inverse.post_add |
Additional post processing of U after dU added to potential.
This is a list of scripts separated by spaces which are
called. See section on iterative framework for details.
|
|
non-bonded.inverse.post_add_options |
Contains all options of post add scripts |
|
non-bonded.inverse.post_add_options.compress |
Contains all options of the postadd compress sripts |
|
non-bonded.inverse.post_add_options.compress.filelist |
Files to be compressed |
|
non-bonded.inverse.post_add_options.compress.program_opts |
-9 |
Option to give to the compression command |
non-bonded.inverse.post_add_options.compress.program |
gzip |
Compression command to run |
non-bonded.inverse.post_add_options.convergence |
||
non-bonded.inverse.post_add_options.convergence.weight |
1 |
weight factors for the convergence of this interaction,
should be a list of same length as inverse.post_add_options.convergence.what
|
non-bonded.inverse.post_add_options.convergence.what |
dist |
list from what to calc the convergence: dist pot, .. |
non-bonded.inverse.post_add_options.convergence.base |
tgt |
what base values to be used to compute convergene error:
tgt, cur, ..
|
non-bonded.inverse.post_add_options.convergence.norm |
1 |
which norm to use to compute error: 1 first norm, 2 second
norm
|
non-bonded.inverse.post_add_options.copyback |
Contains all options of the postadd copyback sripts |
|
non-bonded.inverse.post_add_options.copyback.filelist |
File to be copied to back to maindir |
|
non-bonded.inverse.post_add_options.overwrite |
Contains all options of the overwrite postadd scripts |
|
non-bonded.inverse.post_add_options.overwrite.do |
1 |
Cycle for overwrite postadd script (1 do, 0 do not) like
do_potential.
|
non-bonded.inverse.post_add_options.plot |
Contains all options of the plot postadd scripts |
|
non-bonded.inverse.post_add_options.plot.fd |
8 |
file descriptor to use, make it unique if you want to
plot multiple things
|
non-bonded.inverse.post_add_options.plot.gnuplot_opts |
extra options to give to gnuplot_bin like -persist or
-geometry
|
|
non-bonded.inverse.post_add_options.plot.kill |
kill all processes with that name before ploting (e.g.
gnuplot_x11), this is more reliable than using named pipes
|
|
non-bonded.inverse.post_add_options.plot.script |
plot script to give to gnuplot |
|
non-bonded.inverse.post_add_options.average |
||
non-bonded.inverse.post_add_options.average.what |
list for which averages of last few steps are to computed:
param, pot, … For relative entropy method, specify param
before pot.
|
|
non-bonded.inverse.post_update |
Additional post-processing of dU before added to potential.
This is a list of scripts separated by spaces which are
called. See section on iterative framework for details.
|
|
non-bonded.inverse.post_update_options |
Contains all options of post update scripts |
|
non-bonded.inverse.post_update_options.cibi |
Contains all options of the Kirkwood-Buff integral corrections
scripts
|
|
non-bonded.inverse.post_update_options.cibi.do |
1 |
Update cycle for the Kirkwood-Buff integral correction
(1 do, 0 do not). To do the correction every third step
specify “0 0 1”, similar to do_potential
|
non-bonded.inverse.post_update_options.cibi.kbint_with_errors |
no |
calculate errors on the Kirkwood-Buff integral: yes/no |
non-bonded.inverse.post_update_options.extrapolate |
||
non-bonded.inverse.post_update_options.extrapolate.points |
5 |
Number of point to calculate the average from for the
extrapolation
|
non-bonded.inverse.post_update_options.ibi |
Contains all options of the IBI post-update script |
|
non-bonded.inverse.post_update_options.ibi.do |
1 |
Update cycle for the IBI post-update (1 do, 0 do not).
To do the post-update every third step specify “0 0 1”,
similar to do_potential
|
non-bonded.inverse.post_update_options.kbibi |
Contains all options of the Kirkwood-Buff ramp corrections
scripts
|
|
non-bonded.inverse.post_update_options.kbibi.do |
1 |
Update cycle for the Kirkwood-Buff ramp correction (1
do, 0 do not). To do the correction every third step specify
“0 0 1”, similar to do_potential
|
non-bonded.inverse.post_update_options.kbibi.factor |
scaling factor for the ramp correction |
|
non-bonded.inverse.post_update_options.kbibi.kbint_with_errors |
no |
calculate errors on the Kirkwood-Buff integral: yes/no |
non-bonded.inverse.post_update_options.kbibi.r_ramp |
cutoff of the ramp |
|
non-bonded.inverse.post_update_options.kbibi.start |
Where to start averaging the Kirkwood-Buff integral for
the ramp
|
|
non-bonded.inverse.post_update_options.kbibi.stop |
Where to stop averaging the Kirkwood-Buff integral for
the ramp
|
|
non-bonded.inverse.post_update_options.lj |
Contains all options of the Lennard-Jones potential update |
|
non-bonded.inverse.post_update_options.lj.c6 |
The c6 value for the extra LJ potential |
|
non-bonded.inverse.post_update_options.lj.c12 |
The c12 value for the extra LJ potential |
|
non-bonded.inverse.post_update_options.pressure |
Contains all options of the pressure correction scripts |
|
non-bonded.inverse.post_update_options.pressure.do |
1 |
Update cycle for the pressure correction (1 do, 0 do not).
To do pressure correction every third step specify “0
0 1”, similar to do_potential
|
non-bonded.inverse.post_update_options.pressure.simple |
Contains all options of the simple pressure correction |
|
non-bonded.inverse.post_update_options.pressure.simple.max_A |
0.1 |
maximum prefactor in units of kBT |
non-bonded.inverse.post_update_options.pressure.simple.scale |
slope of the simple pressure correction |
|
non-bonded.inverse.post_update_options.pressure.ptype |
Generic Pressure correction options |
|
non-bonded.inverse.post_update_options.pressure.ptype.max_A |
maximum prefactor in units of kBT |
|
non-bonded.inverse.post_update_options.pressure.ptype.scale |
slope of the pressure correction |
|
non-bonded.inverse.post_update_options.pressure.type |
simple |
Pressure correction type, can be simple or wjk |
non-bonded.inverse.post_update_options.pressure.wjk |
Contains all options of the wjk pressure correction |
|
non-bonded.inverse.post_update_options.pressure.wjk.max_A |
0.1 |
maximum prefactor in units of kBT |
non-bonded.inverse.post_update_options.pressure.wjk.scale |
1.0 |
extra scaling factor of pressure wjk correction |
non-bonded.inverse.post_update_options.scale |
1.0 |
scale factor for the update |
non-bonded.inverse.post_update_options.smooth |
Contains all options of the post_update smooth script |
|
non-bonded.inverse.post_update_options.smooth.iterations |
1 |
number of triangular smooth to be performed |
non-bonded.inverse.post_update_options.splinesmooth |
Contains all options of the post_update spline smooth script |
|
non-bonded.inverse.post_update_options.splinesmooth.step |
grid spacing for spline fit when doing spline smoothing |
|
non-bonded.inverse.optimizer |
||
non-bonded.inverse.optimizer.density |
Contains all options for the density calculation of the
optimizer
|
|
non-bonded.inverse.optimizer.density.axis |
x |
Axis along which the density is calculated |
non-bonded.inverse.optimizer.density.min |
Lower bound of interval in which density calculation is
performed.
|
|
non-bonded.inverse.optimizer.density.max |
Upper bound of interval in which density calculation is
performed.
|
|
non-bonded.inverse.optimizer.density.step |
Step size of interval in which density calculation is
performed.
|
|
non-bonded.inverse.optimizer.density.scale |
1.0 |
Scaling factor for density |
non-bonded.inverse.optimizer.density.molname |
The molname of this interaction |
|
non-bonded.inverse.optimizer.density.target |
Filename of the target denstiy distribution in the maindir |
|
non-bonded.inverse.optimizer.function |
Functional form of the interaction, using parameters in here |
|
non-bonded.inverse.optimizer.functionfile |
If the function is very complicated it can be defined
in this files, which is used as an header
|
|
non-bonded.inverse.optimizer.mapping |
option related to mapping changes |
|
non-bonded.inverse.optimizer.mapping.change |
no |
Does the mapping change in optimization: yes/no |
non-bonded.inverse.optimizer.mapping.output |
no |
Output file name for mapping |
non-bonded.inverse.optimizer.mapping.template |
template for the mapping optimization |
|
non-bonded.inverse.optimizer.parameters |
Parameters to be fitted by the optimizer for this interaction.
Note that the parameter names are global
|
|
non-bonded.inverse.optimizer.pressure |
Contains all options for the pressure calculation of the
optimizer
|
|
non-bonded.inverse.optimizer.pressure.undef |
Pressure to use if pressure from the simulation was nan
(use a big number)
|
|
non-bonded.inverse.optimizer.rdf |
Contains all options for the rdf calculation of the optimizer
|
|
non-bonded.inverse.optimizer.rdf.target |
Filename of the target rdf in the maindir |
|
non-bonded.inverse.optimizer.rdf.weight |
Weighting function for calculating the convergency of
the rdf
|
|
non-bonded.inverse.optimizer.rdf.weightfile |
File with the weighting function definition calculating
the rdf
|
|
non-bonded.inverse.optimizer.targets |
rdf |
Targets to be fitted by the optimizer |
non-bonded.inverse.optimizer.target_weights |
1 |
Weight of the targets, amount has to be the same as of
targets
|
Scripts¶
Scripts are used by csg_call and csg_inverse. The script table commonly used (compare
csg_call –list):
Script calls can be overwritten by adding a similar line with the 3rd column
changed from the original csg_table in directory list in the
<scriptdir> property of the settings xml file.
List of the default scripts:
Key1 |
Key2 |
Scriptname |
|---|---|---|
tag |
file |
tag_file.sh |
dummy |
dummy |
dummy.sh |
functions |
common |
functions_common.sh |
csg |
master |
inverse.sh |
check |
csg_xml |
check_csg_xml.py |
prepare |
ibi |
prepare_generic.sh |
prepare |
iie |
prepare_iie.sh |
prepare |
imc |
prepare_imc.sh |
prepare |
generic |
prepare_generic.sh |
prepare |
optimizer |
prepare_optimizer.sh |
prepare |
re |
prepare_re.sh |
prepare_single |
ibi |
prepare_generic_single.sh |
prepare_single |
imc |
prepare_generic_single.sh |
prepare_single |
generic |
prepare_generic_single.sh |
prepare_single |
optimizer |
prepare_optimizer_single.sh |
initstep |
ibi |
initialize_step_generic.sh |
initstep |
iie |
initialize_step_generic.sh |
initstep |
imc |
initialize_step_generic.sh |
initstep |
optimizer |
initialize_step_optimizer.sh |
initstep |
re |
initialize_step_re.sh |
add_pot |
ibi |
add_pot_generic.sh |
add_pot |
iie |
add_pot_generic.sh |
add_pot |
imc |
add_pot_generic.sh |
add_pot |
optimizer |
dummy.sh |
add_pot |
re |
dummy.sh |
pre_update |
ibi |
dummy.sh |
pre_update |
iie |
dummy.sh |
pre_update |
imc |
dummy.sh |
pre_update |
optimizer |
dummy.sh |
pre_update |
re |
pre_update_re.sh |
post_update |
ibi |
post_update_generic.sh |
post_update |
iie |
post_update_generic.sh |
post_update |
imc |
post_update_generic.sh |
post_update |
optimizer |
dummy.sh |
post_update |
re |
post_update_generic.sh |
post_update_single |
ibi |
post_update_generic_single.sh |
post_update_single |
iie |
post_update_generic_single.sh |
post_update_single |
imc |
post_update_generic_single.sh |
post_update_single |
re |
post_update_re_single.sh |
postupd |
scale |
postupd_scale.sh |
postupd |
pressure |
postupd_pressure.sh |
postupd |
lj |
postupd_addlj.sh |
postupd |
splinesmooth |
postupd_splinesmooth.sh |
postupd |
smooth |
postupd_smooth.sh |
postupd |
shift |
postadd_shift.sh |
postupd |
dummy |
postadd_dummy.sh |
postupd |
tag |
tag_file.sh |
postupd |
extrapolate |
postupd_extrapolate.sh |
postupd |
kbibi |
postupd_kbibi_correction.sh |
postupd |
cibi |
postupd_cibi_correction.sh |
postupd |
ibi |
postupd_ibi.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 |
compress |
postadd_compress.sh |
postadd |
convergence |
postadd_convergence.sh |
postadd |
acc_convergence |
postadd_acc_convergence.sh |
postadd |
shift |
postadd_shift.sh |
postadd |
overwrite |
postadd_overwrite.sh |
postadd |
plot |
postadd_plot.sh |
postadd |
average |
postadd_average.sh |
postadd |
smooth_at_cut_off |
postadd_smooth_at_cut_off.sh |
convergence_check |
default |
convergence_check_default.sh |
resample |
target |
resample_target.sh |
update |
ibi |
update_ibi.sh |
update |
ibi_single |
update_ibi_single.sh |
update |
ibi_pot |
update_ibi_pot.pl |
update |
iie |
update_iie.sh |
update |
iie_pot |
iie.py |
dist |
invert_iie |
iie.py |
rdf_incl_intra |
generic |
calc_rdf_generic.sh |
update |
imc |
update_imc.sh |
update |
imc_single |
update_imc_single.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 |
precede_state |
cma_processor.py |
update |
re |
update_re.sh |
calc |
target_rdf |
calc_target_rdf_generic.sh |
pressure_cor |
simple |
pressure_cor_simple.pl |
pressure_cor |
wjk |
pressure_cor_wjk.pl |
compute_lj |
12_6 |
lj_126.pl |
kbibi |
ramp_correction |
kbibi_ramp_correction.pl |
calc |
kbint |
calc_kbint.sh |
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 |
smooth_at_cut_off |
table_smooth_at_cut_off.py |
table |
linearop |
table_linearop.pl |
table |
dummy |
table_dummy.sh |
table |
get_value |
table_get_value.pl |
table |
switch_border |
table_switch_border.pl |
table |
compare |
table_combine.pl –die –op = |
table |
combine |
table_combine.pl |
table |
average |
table_average.sh |
table |
scale |
table_scale.pl |
table |
change_flag |
table_change_flag.sh |
table |
functional |
table_functional.sh |
potential |
extrapolate |
potential_extrapolate.sh |
potential |
shift |
potential_shift.pl |
convert_potential |
tab |
table_to_tab.pl |
dist |
adjust |
dist_adjust.pl |
dist |
invert |
dist_boltzmann_invert.pl |
tables |
jackknife |
tables_jackknife.pl |
initstep |
gromacs |
initialize_step_genericsim.sh |
run |
gromacs |
run_gromacs.sh |
clean |
gromacs |
clean_generic.sh |
presimulation |
gromacs |
run_gromacs.sh –pre |
pressure |
gromacs |
calc_pressure_gromacs.sh |
pressure |
lammps |
calc_pressure_lammps.sh |
rdf |
gromacs |
calc_rdf_generic.sh |
imc_stat |
gromacs |
imc_stat_generic.sh |
density |
gromacs |
calc_density_generic.sh |
convert_potential |
gromacs |
potential_to_gromacs.sh |
convert_potentials |
gromacs |
potentials_to_generic.sh |
convert_potential |
xvg |
table_to_xvg.pl |
functions |
gromacs |
functions_gromacs.sh |
initstep |
espresso |
initialize_step_genericsim.sh |
run |
espresso |
run_genericsim.sh |
clean |
espresso |
clean_generic.sh |
rdf |
espresso |
calc_rdf_generic.sh |
imc_stat |
espresso |
imc_stat_generic.sh |
density |
espresso |
calc_density_generic.sh |
convert_potential |
espresso |
potential_to_generic.sh |
convert_potentials |
espresso |
potentials_to_generic.sh |
functions |
espresso |
functions_genericsim.sh |
convert_potential |
lammps |
potential_to_lammps.sh |
convert_potentials |
lammps |
potentials_to_generic.sh |
initstep |
lammps |
initialize_step_genericsim.sh |
run |
lammps |
run_genericsim.sh |
clean |
lammps |
clean_generic.sh |
rdf |
lammps |
calc_rdf_generic.sh |
imc_stat |
lammps |
imc_stat_generic.sh |
density |
lammps |
calc_density_generic.sh |
functions |
lammps |
functions_genericsim.sh |
convert_potential |
espressopp |
potential_to_generic.sh |
convert_potentials |
espressopp |
potentials_to_generic.sh |
initstep |
espressopp |
initialize_step_genericsim.sh |
run |
espressopp |
run_genericsim.sh |
clean |
espressopp |
clean_generic.sh |
rdf |
espressopp |
calc_rdf_generic.sh |
imc_stat |
espressopp |
imc_stat_generic.sh |
density |
espressopp |
calc_density_generic.sh |
functions |
espressopp |
functions_genericsim.sh |
initstep |
dlpoly |
initialize_step_genericsim.sh |
run |
dlpoly |
run_genericsim.sh |
clean |
dlpoly |
clean_generic.sh |
rdf |
dlpoly |
calc_rdf_generic.sh |
imc_stat |
dlpoly |
imc_stat_generic.sh |
density |
dlpoly |
calc_density_generic.sh |
functions |
dlpoly |
functions_dlpoly.sh |
convert_potential |
dlpoly |
potential_to_dlpoly.sh |
convert_potentials |
dlpoly |
potentials_to_dlpoly.sh |
convert_potential |
hoomd-blue |
potential_to_generic.sh |
convert_potentials |
hoomd-blue |
potentials_to_generic.sh |
initstep |
hoomd-blue |
initialize_step_genericsim.sh |
run |
hoomd-blue |
run_genericsim.sh |
clean |
hoomd-blue |
clean_generic.sh |
rdf |
hoomd-blue |
calc_rdf_generic.sh |
imc_stat |
hoomd-blue |
imc_stat_generic.sh |
density |
hoomd-blue |
calc_density_generic.sh |
functions |
hoomd-blue |
functions_genericsim.sh |
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
check_csg_xml.py¶
NAME¶
csg_call check csg_xml - Part of the VOTCA package
SYNOPSIS¶
csg_call check csg_xml [OPTIONS]
csg_call check csg_xml [–help]
Usage: check_csg_xml.py [-h] csg_xml_file csg_xml_defaults_file
Check the csg XML file for invalid tags. It works by comparing to the tags in the default XML file.
DESCRIPTION¶
OPTIONS¶
positional arguments:
csg_xml_file csg XML file
csg_xml_defaults_file
csg XML defaults file
options:
-h, --help show this help message and exit
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
csgapps¶
Extra user-contibuted applications based on the csg application class, that aren’t needed for the normal workflows. Installable with -DINSTALL_CSGAPPS=ON.
csg_fluctuations¶
NAME¶
csg_fluctuations - Part of the VOTCA package
SYNOPSIS¶
csg_fluctuations [OPTIONS]
csg_fluctuations [–help]
DESCRIPTION¶
calculate density fluctuations in subvolumes of the simulation box.Subolumes can be either cubic slabs in dimensions (x|y|z) or sphericalslabs with respect to either the center of box or a reference molecule
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
Fluctuation options:
--filter arg (=*) filter molecule names
--rmax arg maximal distance to be considered
--rmin arg (=0) minimal distance to be considered
--refmol arg Reference molecule
--nbin arg (=100) Number of bins
--geometry arg (sphere|x|y|z) Take radial or x, y, z
slabs from rmin to rmax
--outfile arg (=fluctuations.dat) Output file
Mapping options:
--cg arg coarse graining mapping and bond
definitions (xml-file)
--map-ignore arg list of molecules to ignore separated by
;
--no-map disable mapping and act on original
trajectory
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works
for Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_orientcorr¶
NAME¶
csg_orientcorr - Part of the VOTCA package
SYNOPSIS¶
csg_orientcorr [OPTIONS]
csg_orientcorr [–help]
DESCRIPTION¶
Calculates the orientational correlation function <3/2*u(0)*u(r) - 1/2> for a polymer melt, where u is the vector pointing along a bond and r the distance between bond segments (centered on middle of bond).
The output is correlation.dat (with intra-molecular contributions) and correlation_excl.dat, where inter-molecular contributions are excluded.
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
Neighbor search options:
-c [ --cutoff ] arg (=1) cutoff for the neighbor search
--nbins arg (=40) number of bins for the grid
--nbmethod arg (=grid) neighbor search algorithm (simple or grid)
Threading options:
--nt arg (=1) number of threads
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_part_dist¶
NAME¶
csg_part_dist - Part of the VOTCA package
SYNOPSIS¶
csg_part_dist [OPTIONS]
csg_part_dist [–help]
DESCRIPTION¶
This program reads a topology and (set of) trajectory(ies). For every binned value of a chosen coordinate, it outputs the time-averaged number of particles, listed by particle types.
OPTIONS¶
Allowed options:
--top arg topology file
--trj arg trajectory file
--grid arg output grid spacing (min:step:max)
--out arg output particle distribution table
--ptypes arg particle types to include in the analysis
arg: file - particle types separated by space
default: all particle types
--first_frame arg first frame considered for analysis
--last_frame arg last frame considered for analysis
--coord arg coordinate analyzed ('x', 'y', or 'z' (default))
--shift_com shift center of mass to zero
--comment arg store a comment in the output table
--help produce this help message
csg_partial_rdf¶
NAME¶
csg_partial_rdf - Part of the VOTCA package
SYNOPSIS¶
csg_partial_rdf [OPTIONS]
csg_partial_rdf [–help]
DESCRIPTION¶
Calculate spatially confined rdfs
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
Mapping options:
--cg arg [OPTIONAL] coarse graining mapping and bond
definitions
(xml-file). If no file is given, program acts on
original trajectory
--map-ignore arg list of molecules to ignore if mapping is done
separated by ;
Specific options:
--options arg options file defining the rdfs
--subvolume_radius arg Rdf calc. in spherical subvolume of this radius (from
center of box)
--do-vol-corr Correct for subvolume truncation in rdf
--write-every arg (UNIMPLEMENTED) write after every block of this
length, if --blocking is set, the averages are
cleared after every output
--do-blocks write output for blocking analysis
Threading options:
--nt arg (=1) number of threads
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_radii¶
NAME¶
csg_radii - Part of the VOTCA package
SYNOPSIS¶
csg_radii [OPTIONS]
csg_radii [–help]
DESCRIPTION¶
calculate gyration- and hydrodynamic radius for a specific molecule or molecule type
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
Molecule filter options:
--mol arg molecule number
--molname arg (=*) pattern for molecule name
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_sphericalorder¶
NAME¶
csg_sphericalorder - Part of the VOTCA package
SYNOPSIS¶
csg_sphericalorder [OPTIONS]
csg_sphericalorder [–help]
DESCRIPTION¶
- !! EXPERIMENTAL !! Calculate spherical order parameter.
Needs non-spherical beads in mapping.
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
--filter arg (=*) filter molecule names
--radialcut arg (=0) radial cutoff: distance from center where bead is
considered
--minrad arg (=0) minimal distance a parcle has to be apart from center
to be considerd
--refmol arg Reference molecule
--rbinw arg (=0) Do multiple r_bins multiple histograms
Mapping options:
--cg arg coarse graining mapping and bond definitions
(xml-file)
--map-ignore arg list of molecules to ignore separated by ;
--no-map disable mapping and act on original trajectory
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_traj_force¶
NAME¶
csg_traj_force - Part of the VOTCA package
SYNOPSIS¶
csg_traj_force [OPTIONS]
csg_traj_force [–help]
DESCRIPTION¶
Adds/subtracts forces from given atomistic trajectories
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
--scale arg (=-1) scaling factor for trajectory forces
--trj-force arg atomistic reference trajectory containing forces to
add/subtract
--out arg output trajectory file with resultant forces
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames