fix topoII

Inside each of the folders in this directory you will find the files fix_topo2.cpp and fix_topo2.h. These files contain the implementation of the new fix. In order to add the implementation to the LAMMPS executable you need to simply:

1.- Download the most recent version of LAMMPS (currently this has been tested using the **29-Oct-2020** version).
2.- Unzip the tar file containing the LAMMPS distribution.
3.- Copy and paste the files "fix_topo2.cpp" and  "fix_topo2.h" into the folder "src/" (this folder is part of the standard directories of the lammps distribution).
4.- Make sure that the **MOLECULE** package is installed.
5.- Compile the LAMMPS executable as usual (make mpi or make serial). We renamed the mpi and serial executable as: "lmp_mpi_29Oct2020_fixtopo2" and "lmp_serial_29Oct2020_fixtopo2".
6.- Move the executables to your home directory (~).

Please be aware that the .cpp and .h files inside the folder testing are slightly different than the ones inside running. This is because the files in the former case allow to print the position of the topo2 every time the fix topo II is called, and in this way we can test if the fix is doing what we expect. In the latter case (running) this information is not printed.

Syntax

fix ID group-ID topoII keyword values ...

• ID, group-ID are documented in fix command
• topoII = style name of this fix command
• Only one keyword can be used at a time
• keyword = static or randjump or jump2maxdens or jump2maxcurv

static values: n, l, topotype, seed, t

​ n = the number of topoII in the system. Currently it only accepts 1. ​ l = the length in beads of each topoII in the system. ​ topotype = the topoII particle type. ​ seed = random seed to generate the random position of the topoII ​ t' = timestep at which the topoII is simulated into the system.

randjump, jump2maxdens and jump2maxcurv have the same values: n, l, topotype, seed, freq, prob, intertype.

​ n = the number of topoII in the system. Currently it only accepts 1. ​ l = the length in beads of each topoII in the system. ​ topotype = the topoII particle type. ​ seed = random seed to generate the random position of the topoII (it only has a meaning for randjump, in the other cases is ignored). ​ freq = how often the fix is called. ​ prob = probability that the topoII changes position each time the fix is called. ​ intertype: intermediate type assigned to atoms from a section where topoII is jumping from.

Examples

fix 0 all topoII static 1 50 4 336644 1000 fix 0 all topoII randjump 1 50 4 336644 1000 0.1 5 fix 0 all topoII jump2maxdens 1 50 4 336644 1000 0.1 5 fix 0 all topoII jump2maxcurv 1 50 4 336644 1000 0.1 5

Description

This fix changes the atom type of selected beads according to an specific criteria:

• static: at timestep t' a bead in the polymer is selected randomly. Then this bead and the (l-1) beads "behind it" change type to topotype. After this, there is no change in the atom type during the course of the simulation.
• randjump: The fix is called every freq time-steps. Every time the fix is called there is a probabiliti (prob, between 0 and 1) that certain beads change type. When this happens, three type of beads are defined in the simulation: (i) intertype (type 5 in the example), for beads in the region that the topoII is moving from; (ii) topotype (type 4 in the example) for beads in the region where the topoII is moving to; (iii) type 1, for the rest of the beads representing regions of the polymer free of topoII. The beads that change type to topotype are selected in the same way as in the static case.
• jump2maxdens: The fix is called every freq time-steps. Every time the fix is called there is a probabiliti (prob, between 0 and 1) that certain beads change type. When this happens, three type of beads are defined in the simulation: (i) intertype (type 5 in the example), for beads in the region that the topoII is moving from; (ii) topotype (type 4 in the example) for beads in the region where the topoII is moving to; (iii) type 1, for the rest of the beads representing regions of the polymer free of topoII. The beads that change type to topotype are selected in the following way: the bead with maximum number of neighbors, i.e., the one with maximum density, is chosen. Then this bead and the (l-1) beads "behind it" change type.
• jump2maxcurv: The fix is called every freq time-steps. Every time the fix is called there is a probabiliti (prob, between 0 and 1) that certain beads change type. When this happens, three type of beads are defined in the simulation: (i) intertype (type 5 in the example), for beads in the region that the topoII is moving from; (ii) topotype (type 4 in the example) for beads in the region where the topoII is moving to; (iii) type 1, for the rest of the beads representing regions of the polymer free of topoII. The beads that change type to topotype are selected in the following way: the bead with maximum curvature is chosen. Then this bead and the (l-1) beads "behind it" change type.

Testing

We have tested that the serial and mpi executables. Inside testing you will find eight folders corresponding to eight different tests we carried out to check that everything is working as expected. Inside each folder there is a README.md file with a description of the test. Each test is run by typing ./bash.run.sh in a terminal. After the test has finished you should see a success :) legend in the terminal, indicating that the test has been passed.