This software package calculates the Phantom modulus for the following systems:
- linear chains mixed with cross linkers
This project needs the LeMonADE-library installed. The configure file helps to set the correct path and options. Execute in a shell
./configure -DLEMONADE_DIR=/path/to/installation/lemonade_install -DBUILDDIR=./build -DLEMONADE_TESTS=OFF/ON -DCMAKE_BUILD_TYPE=Release/DebugThis will run cmake and create the build directory. Now type in make which compiles the executables and runs the test if this option was given.
The main program reads in a .bfm file and a data file. It is expected that the bfm file contains the following flags
#!number_of_linear_chains=value
#!number_of_crosslinkers=value
#!chainLength=value
#!functionality=value
#!nMonomersPerCrossLink=value
!reactivity
1-1:1/2
...
Moreover, it is expected that in the bfm file first all chains and afterwards all cross-links are given. The data file should be created during the connection process and needs to contain:
Time ChainID MonID1 P1X P1Y P1Z MonID2 P2X P2Y P2Z
where MonID1 and MonID2 are the cross-link ID starting at 0. ChainID starts at 0 as well. For the calculations only the ChainID and MonID1 is needed. The remaining fields are arbitrary for a correct calculation of the positions of the cross links in a force equilibrium. (The format was given from a previous simulation.)
For the force equilibrium only active chains are of interest. Therefore, there exist two programs extracting the active gel structure from the total system.
There are programs specialized on tendomers. They read the tendomer specific tag and can use a custom force extension relation (e.g. numerical solution of the tendomer) to calculate the forces between cross-links.
These systems are tendomer specific. A star is created and a monomer along the chain with a distance to the center according to the tendomer distribution of the number of elastic segments is marked as fixed in space. In a second system a double star is simulated.
Find the information about active developers, former contributors, and people who contributed in the AUTHORS file.
See the LICENSE in the root directory.