Quick start guide for RMC_POT
Here is described, how to start RMC_POT quickly. It is however recommended to read the manual to have an understanding of how RMC works, and how to use the various options efficiently.
Which code should I use?
RMC_POT can be compiled for either standard consecutive or for parallel execution. Parallelism achieved by using the POSIX-based threads, and can speed up the program on shared-memory multi-processor (or hyper-threading) computers depending on the simulated system. POSIX is a Linux standard and usually installed with LInux, but a interface for Windows exists, and can be downloaded from the download page. So compile the code for multi-threading, if possible, and only use the consecutive compilation, if you have just one processor. The code compiled for parallel execution can be used to handle only one thread, if necessary, but use as many threads, as the number of free processors, if possible.
The result will be the same regardless parallel oor consecutive execution if no potential is calculated, if it is, then there can be slight differences due to the rounding errors accumulating differently..
RMC_POT is suitable of the simulations of disordered materials, as fluids and amorphous solid materials. The systems can be treated the following way, depending on the requirements of the given material, and simulation requirements:
· atomic systems using atomic moves using 1 or more moved atoms with or without non-bonded potential;
· molecular systems, where molecules are kept together by FNC constraint, but atomic moves are applied, using 1 or more moved atoms;
· molecular systems, where molecules are kept together by FNC constraint, molecular move is used, which means, that a whole molecule is moved together the way it is described in the makemovecus.cpp file specially designed for this molecules, and the code has to be compiled with this makemovecus.cpp replacing the one given in the distribution. The same makemovecus.cpp can be used for both RMC_new and for RMC_multi beginning with version 1.6.1, but not before that! The *.cus file containing the adjustable parameters has to be given for the makemovecus.cpp files given in the source code package, its structure depends on the parameters required by the makemovecus.cpp file. Some ideas, how it could look like can be learned from the ccl4_mol.cus file in the test_run/CCl4_mol directory of the example validation suite.
· molecular systems, where molecules are kept together with flexible bonded potential interactions (bonds, angles, dihedrals), with or without non-bonded potential.
RMC needs the following files to run
· experimental data files, if needed, their name should appear in the *.dat file. RMC can be run actually without any experimental data, moving around the atoms, like hard-core balls
· *.fnc (only needed, if molecules are handled with FNC constarint, both in case of atomic and molecular RMC);
· *.top (*.itp) if potential is present to describe the molecule;
· *.cus (only needed, if molecular RMC is used), code has to be compiled using the makemovecus.cpp file designed for the given molecule;
· sfactorcube file, if rmax>Ö2 (do not change the content)
* denotes the same name to be used for the files
The validation suite contains five directories with five examples, read the readme.txt file of the validation suite to learn about them, they can be started easily with the name of the executable followed by the filename (without any extension). For example, if we have my.cfg and my.dat for a simple run, then start it with executable my.
If you want to start your own simulations:
· Create your own *.dat file using an appropriate example dat file in one of the directories of the validation suite.
· Create the *.cfg file according to the one in the same directory of the validation suite, see the manual and the auxiliary program section of the download page.
· If molecules are handled, which should be kept together with FNC during the simulation, regardless atomic or molecular RMC is used, a *.fnc file describing the constraints holding together the molecules has to be created, (see the fnc file in the CCl4_at or CCl4_mol directories of the validation suite) and the manual how to create it and the auxiliary program section of the download page.
· You will need some experimental data, (see formats in the dummy directory of the validation suite), or you can run a hard-core RMC without it.
· In case of molecular RMC use the makemovecus.cpp file describing the move of your molecule. CCl4 is the default given in the distribution beginning with version 1.6.1, and C2Cl4 and water can also be found in the source package makemovecus directory along with their *.cus files. If something else is needed, you have to write it yourself using the CCl4 and C2Cl4 makemovecus.cpp file, as examples.
· In case of molecules kept flexibly together by bonded potential and/or if in case of non-bonded potential you will need the *.top (*.itp) file for describing the molecular topology (or simply the binding of the potential parameters to the RMC configuration). See the manual and the GROMACS manual for this, but it is NOT RECOMMENDED to start with this kind of systems, if you are new to RMC, first master the usage of RMC through the simpler systems!
Last change by Orsolya