ELMA-BraCat

ELMA - Extensions of the LeMonADE library BraCat - Branched Catalysis related to the paper

Installation

Clone and Install LeMonADE v2.2.2, see LeMonADE v2.2.2
Install cmake (minimum version 2.8)
Just do for standard compilation of the ELMA-BraCat project:

    # generates the projects
    mkdir build
    cd build
    cmake -DLEMONADE_INCLUDE_DIR=/path/to/LeMonADE-library/include/ -DLEMONADE_LIBRARY_DIR=/path/to/LeMonADE-library/lib/ ..
    make

    cmake -S. -Bbuild -DCMAKE_BUILD_TYPE=Release -DLEMONADE_INCLUDE_DIR=/path/to/LeMonADE-library/include/ -DLEMONADE_LIBRARY_DIR=/path/to/LeMonADE-library/lib/
    cmake --build build/

The executables can be found in the build/projects folder.

Environment

tested with g++ version GNU 11.1.1
LeMonADE v2.2.2 or LeMonADE v2.2.2 on Zenodo
cmake version 3.20.4

Run

Create branched structures with Chain Walking (CW) approach

Creates an excluded volume CW structure with 500 monomers, walking rate $w=1/p=1/0.5=2$ in $L=256$ box:

    ./CreatorChainWalkingTertiaryBondWalking -f out.bfm -n 500 -p 0.5 -t 1.0 -b 256

Evaluates the creation properties (distance between reaction events) of an excluded volume CW structure with 500 monomers, walking rate $w=1/p=1/0.5=2$ in $L=256$ box using 10 samples:

    ./CreatorChainWalkingTertiaryBondWalking_CreationProperties -f out.bfm -n 500 -p 0.5 -b 256 -s 10

Evaluates the topological properties (number vertices from topological center) of an excluded volume CW structure with 500 monomers, walking rate $w=1/p=1/0.5=2$ in $L=256$ box using 10 samples:

    ./CreatorChainWalkingTertiaryBondWalking_TopologicalProperties -f out.bfm -n 500 -p 0.5 -b 256 -s 10

Evaluates the eigenvalues of the Rouse matrix of an excluded volume CW structure with 500 monomers, walking rate $w=1/p=1/0.5=2$ in $L=256$ box using 10 samples:

    ./CreatorChainWalkingTertiaryBondWalking_RouseMatrix -f out.bfm -n 500 -p 0.5 -b 256 -s 10

Simulation of a BFM structure under excluded volume condition for 1000MCS with dump every 100MCS:

    ./SimpleSimulatorStandard -i in.bfm -o out.bfm -m 1000 -s 100

Creates an excluded volume Barabasi-Albert structure with restricted node functionality $f <= 3$ with 500 monomers, $m_0=2$, and $m=1$ in $L=256$ box:

    ./CreatorBarabasiAlbertRestrictedF3_Creator -f out.bfm -n 500 -b 256

Evaluates the eigenvalues of the Rouse matrix of an excluded volume Barabasi-Albert structure with restricted node functionality $f <= 3$ with 500 monomers, $m_0=2$, and $m=1$ in $L=256$ box using 10 samples:

    ./CreatorBarabasiAlbertRestrictedF3_RouseMatrix -f out.bfm -n 500 -b 256 -s 10

Evaluates the creation properties (distance between reaction events) of ideal BGRW structure (no excluded volume) with 500 monomers, walking rate $w=1/p=1/0.5=2$ in $L=256$ box using 10 samples:

    ./CreatorBGRWTertiaryBondWalking_CreationProperties -f out.bfm -n 500 -p 0.5 -b 256 -s 10

Evaluates the eigenvalues of the Rouse matrix of ideal BGRW structure (no excluded volume) with 500 monomers, walking rate $w=1/p=1/0.5=2$ in $L=256$ box using 10 samples:

    ./CreatorBGRWTertiaryBondWalking_RouseMatrix -f out.bfm -n 500 -p 0.5 -b 256 -s 10

Creates an ideal Barabasi-Albert structure (no excluded volume) with 500 monomers, $m_0=2$, and $m=1$ in $L=256$ box:

    ./CreatorBarabasiAlbert_Creator -f out.bfm -n 500 -b 256

Evaluates the eigenvalues of the Rouse matrix of an ideal Barabasi-Albert structure (no excluded volume) with 500 monomers, $m_0=2$, and $m=1$ in $L=256$ box using 10 samples:

    ./CreatorBarabasiAlbert_RouseMatrix -f out.bfm -n 500 -b 256 -s 10

Evaluates the time average of the radius of gyration $Rg2$ of any structure:

    ./ChainWalking_Analyzer_RG2 -f out.bfm

Evaluates the eigenvalues of the Rouse matrix of an excluded volume Slow Growth structure with restricted node functionality $f <= 3$ with 500 monomers in $L=256$ box using 10 samples:

    ./CreatorSlowGrowth_RouseMatrix -f out.bfm -n 500 -b 256 -s 10

Creates a perfect dendrimer structure under excluded volume condition with functionality $f <= 3$, generation $G=4$, and spacer length $S=2$ in $L=256$ box:

    ./CreateDendrimerGeneral_FGS -o out.bfm -f 3 -g 4 -s 2 -x 256 -y 256 -z 256

Evaluates the eigenvalues of the Rouse matrix of an perfect "hyperstar" structure (no excluded volume - $2^(-f)$ node distribution) with generation $G=7$ in $L=256$ box:

    ./CreatorHyperstar_RouseMatrix -f out.bfm -g 7 -b 512

License

See the LICENSE in the root directory.

How to cite

The development of the code is mainly funded by academic research grants.
If you find the source code useful please cite the related paper:

[1] A. Jurjiu, R. Dockhorn, O. Mironova, J.-U. Sommer,
"Two universality classes for random hyperbranched polymers", Soft Matter 2014, 10, 4935-4946
[2] R. Dockhorn, L. Plüschke, M. Geisler, J. Zessin, P. Lindner, R. Mundil, J. Merna, J.-U. Sommer, A. Lederer,
"Polyolefins Formed by Chain Walking Catalysis-A Matter of Branching Density Only?", J. Am. Chem. Soc. 2019, 141 (31), 15586-15596
[3] R. Dockhorn, J.-U. Sommer,
"Theory of Chain Walking Catalysis: From Disordered Dendrimers to Dendritic Bottle-Brushes", 2022

Bondoki / ELMA-BraCat