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``. .. math:: :nowrap: \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: - :math:`{\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``. .. math:: :nowrap: \begin{eqnarray*} E{_{d}^{2}}={( {{{\vec{R}}}_{0}}-{{{\vec{R}}}_{N-1}} )}^{2} \end{eqnarray*} Coefficients: - :math:`{\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``. .. math:: :nowrap: \begin{eqnarray*} bond\_distri(i \cdot dr)=N(i)/(N \cdot dr) \end{eqnarray*} Coefficients: - :math:`dr` - the space of bond length `L/(2npot)`, where `L` is the box size - :math:`N(i)` - the number of bonds in the range of `idr < r < (i+1)dr`, where `i` is an integer - :math:`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``. .. math:: :nowrap: \begin{eqnarray*} angle\_distri(i \cdot da)=N(i)/(N \cdot da) \end{eqnarray*} Coefficients: - :math:`da` - the space of angle radian `pi/npot` - :math:`N(i)` - the number of angles in the range of `ida < angle < (i+1)da`, where `i` is an integer - :math:`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``. .. math:: :nowrap: \begin{eqnarray*} dihedral\_distri(i \cdot da)=N(i)/(N \cdot da) \end{eqnarray*} Coefficients: - :math:`da` - the space of dihedral angle radian `2pi/npot` - :math:`N(i)` - the number of dihedrals in the range of `ida < dihedral angle < (i+1)da`, where `i` is an integer - :math:`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 :math:`1/q`, where :math:`q=2\pi\sqrt{x^2+y^2+z^2}/L`, and :math:`L` is cubic box length. :math:`\mbox{kmax}` limits the space in which the :math:`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