GalaTackle

Usage

The “galaTackle” is a plugin of GALAMOST to analyze some important properties by reading the generated configuration files. The “galaTackle” can be found in the installed “bin” folder. You can use this tool to analyze one or more files by running the following commands.

Examples:

galaTackle particle.xml
galaTackle particle0.xml particle1.xml
galaTackle *.xml

After pressing enter, a menu of function options will be listed. You can choose one or more functions by the number indexes separated by blank. The parameters for a function can be input after “:” and seperated by “|”.

Such as:

4:npot=1000 3:gpu=0|rmax=2.0

The “galaTackle” also can be called and passed parameters in Shell script.

Such as:

echo -e "18:gpu=1|rmax=3.0" | galaTackle particles.*.xml

The “galaTackle” plugin supports the configuration files with XML and DCD formats. The XML files can be tackled independently. However, a DCD trajectory file has to be tackled along with a XML file for particles attributes and topological information.

Examples:

galaTackle particle.xml trajectory.dcd

For the help about the parameters, you could input “function number:h” after the function list shown.

Examples:

14:h

Functions

Function list:

-------------------------------------------------------------
1  Rg^2              2  Ed^2             3  RDF
4  bond_distri       5  angle_distri     6  dihedral_distri
7  stress tensor     8  density          9  unwrapping
10 MSD               11 RDF-CM           12 MSD-CM
13 ents              14 strfac           15 domain size
16 dynamic strfac    17 config check     18 RDF between types
19 XML conversion
-------------------------------------------------------------

1 Rg^2:

Description:
To calculate the mean square of gyration radius and output result to rg2.log.
\begin{eqnarray*} R{_{g}^{2}}&=&\frac{1}{N}\sum\limits_{i=1}^{N}{{{({{{\vec{R}}}_{i}}-{{{\vec{R}}}_{cm}})}^{2}}} \\ {{\vec{R}}_{cm}}&=&\frac{1}{N}\sum\limits_{i=1}^{N}{{{{\vec{R}}}_{i}}} \end{eqnarray*}

Coefficients:

  • \({\vec{R}}_{i}\) - monomer position vector

2 Ed^2:

Description:
To calculate the mean square of end to end distance and output result to ed2.log.
\begin{eqnarray*} E{_{d}^{2}}={( {{{\vec{R}}}_{0}}-{{{\vec{R}}}_{N-1}} )}^{2} \end{eqnarray*}

Coefficients:

  • \({\vec{R}}_{i}\) - monomer position vector

3 RDF:

Description:
To calculate the radial distribution function of all particles and output result to *.rdf and rdf.log.
Parameters:
:maxbin=100|gpu=0|rmax=Lx/2|bondex=false|angleex=false|molex=false

4 bond_distri:

Description:
To calculate the distribution of bond lengths and output result to bond_distr.log.
\begin{eqnarray*} bond\_distri(i \cdot dr)=N(i)/(N \cdot dr) \end{eqnarray*}

Coefficients:

  • \(dr\) - the space of bond length L/(2npot), where L is the box size
  • \(N(i)\) - the number of bonds in the range of idr < r < (i+1)dr, where i is an integer
  • \(N\) - the total number of bonds
Parameters:
:npot=2001

5 angle_distri:

Description:
To calculate the distribution of angle degrees and output result to angle_distr.log.
\begin{eqnarray*} angle\_distri(i \cdot da)=N(i)/(N \cdot da) \end{eqnarray*}

Coefficients:

  • \(da\) - the space of angle radian pi/npot
  • \(N(i)\) - the number of angles in the range of ida < angle < (i+1)da, where i is an integer
  • \(N\) - the total number of angles
Parameters:
:npot=2001

6 dihedral_distri:

Description:
To calculate the distribution of dihedral degrees and output result to dihedral_distr.log.
\begin{eqnarray*} dihedral\_distri(i \cdot da)=N(i)/(N \cdot da) \end{eqnarray*}

Coefficients:

  • \(da\) - the space of dihedral angle radian 2pi/npot
  • \(N(i)\) - the number of dihedrals in the range of ida < dihedral angle < (i+1)da, where i is an integer
  • \(N\) - the total number of dihedrals
Parameters:
:npot=2001

7 stress tensor:

Description:
To calculate the stress tensor by inputing the parameters of force calculation and output result to stress_tensor.log.
Parameters:
:bondex=true|bodyex=true|diameter=true

8 density:

Description:
To calculate the real density (g/cm^3) with basic units [amu] and [nm] and output result to density.log.

9 unwrapping:

Description:
To unwrap or shift molecules by changing the image information
Parameters:
:unwrap_molecule=true|label_free_particle=particle type|molecule_center_in_box=false| shiftx=0.0|shifty=0.0|shiftz=0.0|remove_image=false|convert_constraint_to_bond=false| remove_bond_cross_box=false

10 MSD:

Description:
To compute mean square displacement of all particles and output result to msd.log.
Parameters:
:direction=XYZ (candidates are X,Y,Z,XY,YZ,XZ,XYZ)

11 RDF-CM:

Description:
To calculate the radial distribution function of the mass center of molecules and output result to rdf_cm.log.
Parameters:
:maxbin=100|gpu=0|rmax=Lx/2

12 MSD-CM:

Description:
To compute mean square displacement of the mass center of molecules and output result to msd_cm.log.
Parameters:
:direction=XYZ (candidates are X,Y,Z,XY,YZ,XZ,XYZ)

13 ents:

Description:
To analyze the entanglements of polymers and output result to ents.log.

14 strfac:

Description:
To calculate the structure factor of particles and output result to *.strf and strf.log.
Parameters:
:qmax=160pi/Lmin|gpu=0|deltaq=2pi/Lmin|direction=XYZ|2D=false

15 domain size:

Description:
To calculate the domain size of components in mixtures and output result to domsize.log.
Parameters:
:kmax=20|qc=0.4690|gpu=0

16 dynamic strfac:

Description:

Dynamic structure factor (incoherent intermediate) measures the decorrelation of the positions of individual monomers with the time on length scale \(1/q\), where \(q=2\pi\sqrt{x^2+y^2+z^2}/L\), and \(L\) is cubic box length. \(\mbox{kmax}\) limits the space in which the \(q\) with possible combinations of x, y, z will be generated.

The results will be output to dstrf.log.

Parameters:
:kmax=int(L)|q=7.0

Maintainer: Shu-Jia Li

17 config check:

Description:
To check the configuration including the minimum distance of particles, and the Maximum and minimum length of bonds, etc. and output result to config_check.log.
Parameters:
:bondex=true|angleex=true|dihedralex=true|bodyex=true|rcut=2.0

18 RDF between types:

Description:
To compute the radial distribution function between types and output result to *.type.rdf and rdf_by_type.log.
Parameters:
:maxbin=100|gpu=0|rmax=Lx/2|bondex=false|angleex=false|molex=false

19 XML conversion:

Description:
To convert XML files into other formats
Parameters:
:lammps=false|gromacs=false