@@ -13,6 +13,6 @@ The position of the TopoII-bound segment can be either:
A brief explanation of the implementation in each of these cases and the scripts to run these simulations are provided inside the corresponding folders in this repository. All the LAMMPS scripts have been tested using the current stable-version of LAMMPS (29-October-2020). To built the LAMMPS executables please make sure that the MOLECULE package is installed. This is a standard package that come with LAMMPS, and can be enabled before compiling, e.g. with the command: make yes-molecule.
In addition, we provide in **4.FixTopoII** the implementation of the same system using a new fix (**fix topoII**) written for LAMMPS. We have checked that when running in serial, this fix provides a 30%-35% speed up in comparison with the simulation using the external code. Also, this new fix reduces considerably the hard drive space needed to store the output from simulations. Just to give an example, running 32 replicas of a system that consists of 1000 beads, for 300 000 000 time-steps and dumping data every 100 000 time-steps; The external program requires 288 GB of space, while with the fixtopo2 only 14.5 GB are required. This is because when running with the external program, every time LAMMPS reads a file (generated by the external programm), it dumps all the atom information to the *log.lammps* file. Creating in this way huge log.lammps files.
In addition, we provide in **4.FixTopoII** the implementation of the same system using a new fix (**fix topoII**) written for LAMMPS. We have checked that when running in serial, this fix provides a 30%-35% speed up in comparison with the simulation using the external code. Also, this new fix reduces considerably the hard drive space needed to store the output from simulations. Just to give an example, running 32 replicas of a system that consists of 1000 beads, for 300 000 000 time-steps and dumping data every 100 000 time-steps; the external program requires 288 GB of space, while the fixtopo2 only requires 14.5 GB. This is because when running with the external program, every time LAMMPS reads a file (generated by the external programm), it dumps all the atom information to the *log.lammps* file. Creating in this way huge log.lammps files.
Please note that we refer to the executable with the standard packages as *lmp_mpi_29Oct2020*. This will be necessary to run the scripts with the external code (in folder 1 to 3). The simulations inside folder 4 require the custom fix. Further instructions on how to compile the corresponding LAMMPS executables (*lmp_mpi_29Oct2020_fixtopo2* and *lmp_serial_29Oct2020_fixtopo2*) can be found in the README files inside folder 4.
