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 tordf.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 tostrf.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 tordf_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