PolyLib

Polymer generating libraries and a few other functions.

Documentation

Dependencies

C++ 9.0 and above
make

Installation

1. Download the tar file. Extract to install location.
   tar -xf Polylib.tar
   OR
   git clone https://github.com/SerpentByte/PolyLib.git
2. mv Polylib
3. cd /Polylib
4. make
5. echo "export PATH=\$PATH:<install location>/Polylib/bin" >> ~/.bashrc
6. source ~/.bashrc

Example

1. pwd /home/user/Downloads
2. tar -xf Polylib.tar
3. mv Polylib /home/user/programs
4. cd /home/user/programs/Polylib
5. make
6. echo "export PATH=\$PATH:/home/user/programs/Polylib/bin" >> ~/.bashrc
7. source ~/.bashrc

Usage

If you type the command without any options, usage will be shown.

1. rnd rnd -beads <integer> -sig <float>
   

   Essential flags
   -beads	<number of beads in the polymer>
   -sig	<size of one bead>

   Optional flags
   -o <output>	Output file name [default = out.gro]
   -bond <value>	Manual bond distance [default = sigma]
   -c	Center polymer inside box (overrides -centre)
   -box <a> <b> <c>	(a,b,c) are box side lengths [default = (0,0,0)]
   -centre <x> <y> <z>	Define center [default (0,0,0)]
   -avoid <true/false>	Self avoiding beads [default true]
   -nt	[default 1]
   -v	Verbose. Print parameters.

2. box box -beads <integer> -sig <float> -box <float> <float> <float>
   

   Essential flags
   -beads	<number of beads in the polymer>
   -sig	<size of one bead>
   -box	<a> <b> <c> (a, b, c are box side lengths)

   Optional flags
   -o <output>	Output file name [default = out.gro]
   -bond <value>	Manual bond distance [default = sigma]
   -c	Center polymer inside box (overrides -centre)
   -box <a> <b> <c>	(a,b,c) are box side lengths [default = (0,0,0)]
   -centre <x> <y> <z>	Define center [default (0,0,0)]
   -avoid <true/false>	Self avoiding beads [default true]
   -nt	[default 1]
   -v	Verbose. Print parameters.

3. sph sph -beads <integer> -sig <float> -r <float>
   

   Essential flags
   -beads	<number of beads in the polymer>
   -sig	<size of one bead>
   -r	<r> (radius of the sphere)

   Optional flags
   -o <output>	Output file name [default = out.gro]
   -bond <value>	Manual bond distance [default = sigma]
   -c	Center polymer inside box (overrides -centre)
   -centre <x> <y> <z>	Define center [default (0,0,0)]
   -avoid <true/false>	Self avoiding beads [default true]
   -nt	[default 1]
   -v	Verbose. Print parameters.

   Box is set to (2r, 2r, 2r) by default.

4. spcl sph -beads <integer> -sig <float> -r <float> -l <float>
   

   Essential flags
   -beads	<number of beads in the polymer>
   -sig	<size of one bead>
   -r	<r> (radius of the sphere)
   -l	<length of cylinder including end-caps>

   Optional flags
   -o <output>	Output file name [default = out.gro]
   -bond <value>	Manual bond distance [default = sigma]
   -c	Center polymer inside box (overrides -centre)
   -centre <x> <y> <z>	Define center [default (0,0,0)]
   -avoid <true/false>	Self avoiding beads [default true]
   -nt	[default 1]
   -v	Verbose. Print parameters.

   Box is set to (2r, 2r, l) by default.

5. re re -f

Uninstallation

1. rm -rf /Polylib
   
2. edit .bashrc and remove the line
   export PATH=$PATH:<install location>/Polylib/bin

example

1. rm -rf /home/user/programs/Polylib
   
2. edit .bashrc in your home using any text editor and remove the following line
   export PATH=$PATH:/home/user/programs/Polylib/bin