dataTackle

Load dataTackle

The dataTackle can be loaded by the command “from poetry import dataTackle” in Python3. Then you can use dataTackle locally by the command “./dataTackle”.

Usage

The dataTackle is a plugin of PYGAMD to analyze some important properties by reading the generated configuration files. The dataTackle can be compiled and installed by “sh compile.sh”. You can use this tool to analyze one or more files at a time.

Examples for running:

./dataTackle particle.mst
./dataTackle particle0.mst particle1.mst
./dataTackle *.mst

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 dataTackle also can be called and passed parameters in a Shell script.

Such as:

echo -e "18:gpu=1|rmax=3.0" | dataTackle particles.*.mst

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

Examples:

dataTackle particle.mst 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 MST conversion    20 patch/spot display 21 SSF
22 ADF               23 CND                24 MSAD
25 RMSAD             26 ISF                27 OACF
28 Q4Q6              29 VORONOI            30 NGP
31 RNGP              32 VHF                33 RVHF
34 fpSus             35 RfpSus             36 OvlaF
37 CISF              38 CAGEISF            39 CAGEMSD
40 RMSD              41 P2P4               42 CRYSTALLINITY
43 G6_3D             44 W4W6
-------------------------------------------------------------

1 Rg^2:

Description:

The mean square of gyration radius is calculated and output 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:

The mean square of end-to-end distance is calculated and output 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:

The radial distribution function of all particles is calculated and output to filename.rdf. Averaged value among files will be output to rdf.log.

Parameters:

:maxbin=100|gpu=0|rmax=Lx/2|bondex=false|angleex=false|molex=false

4 bond_distri:

Description:

The distribution of bond lengths is calculated and output 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:

The distribution of angle degrees is calculated and output 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:

The distribution of dihedral degrees is calculated and output 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:

Stress tensor is calculated by inputing the parameters for force calculation. Result will be output to stress_tensor.log.

Parameters:

:bondex=true|bodyex=true|diameter=true

8 density:

Description:

Real density (g/cm^3) with basic units [amu] and [nm] is calculated and output to density.log.

9 unwrapping:

Description:

This function would unwrap or shift molecules by changing image or position of particles. New configuration will be output to filename.reimage.mst

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|add_image_to_pos=true| remove_bond_cross_box=false|body_keep=false

10 MSD:

Description:

The mean square displacement of all particles is calculated and output to msd.log.

Parameters:

:direction=XYZ (candidates are X,Y,Z,XY,YZ,XZ,XYZ)

11 RDF-CM:

Description:

The radial distribution function of the mass center of molecules is calculated and output to rdf_cm.log.

Parameters:

:maxbin=100|gpu=0|rmax=Lx/2

12 MSD-CM:

Description:

The mean square displacement of the mass center of molecules is calculated and output to msd_cm.log.

Parameters:

:direction=XYZ (candidates are X,Y,Z,XY,YZ,XZ,XYZ)

13 ents:

Description:

This function would analyze the entanglements of polymers. Result will be output to ents.log.

14 strfac:

Description:

The structure factor of particles is calculated and output to filename.strf. The averaged value among files is output to strf.log.

Parameters:

:qmax=160pi/Lmin|gpu=0|deltaq=2pi/Lmin|direction=XYZ|2D=false

15 domain size:

Description:

The domain size of components in mixtures is calculated and output 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.

Results will be output to dstrf.log.

Parameters:

:kmax=int(L)|q=7.0

Maintainer: Shu-Jia Li

17 config check:

Description:

This function would check the configuration including the minimum distance of particles, and the maximum and minimum length of bonds, etc. Result will be output to config_check.log.

Parameters:

:bondex=true|angleex=true|dihedralex=true|bodyex=true|rcut=2.0

18 RDF between types:

Description:

The radial distribution function between types is calculated and output to filename.type.rdf. The averaged value among files will be output to rdf_by_type.log.

Parameters:

:maxbin=100|gpu=0|rmax=Lx/2|bondex=false|angleex=false|molex=false

19 MST conversion:

Description:

This function would convert MST files into new files with another format.

Parameters:

:lammps=false|gromacs=false|xml=false