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Quick start guide for RMC_POT |
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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.
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Which code
should I use? |
The capability of the exe file depends on what compiler options were used
during the compilation. Presently the standard compilation compiled without any
specific compiler options and using the free format *.dat file is capable of multi-threading,
handling bonded and non-bonded potential, all the data sets, the standard
(average and normal coordination, cosine distribution of bond angle)
constraints and swapping atoms.
For additional features (as the advanced geometric constraints, local
invariance, vibrational amplitude calculation, non-periodic
boundary conditions) new compilations are needed with the appropriate compiler
options. See the manual for the details.
System
RMC_POT is suitable of the simulations of
disordered materials, as fluids, glasses and amorphous solids. 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,
only in case of fixed format *.dat file, discontinued) 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 (same
as above) 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 *.cus file containing the adjustable parameters has to be
given additionally to the fixed format *.dat file, if free format data input is used, then the
parameters can be given there. These additional parameters depend on the
system, described in the given 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. This approach was abandoned.
·
molecular systems, where molecules are kept together
with flexible, bonded potential interactions (bonds, angles, dihedrals), with
or without non-bonded potential. To select the suitable potential and create
appropriate staring configuration molecular dynamics (MD) simulations has to be
run previously.
Parallelization
RMC_POT is parallelized to increase speed on shared-memory
multi-processor (or hyper-threading) computers the efficiency depending on the
simulated system. As RMC is not as well parallelizable as MD, usage of very
many threads does not increase speed significantly. In a usual system size of
10000-20000 molecules and few hundred data point containing data sets 4-8
threads are ideal. Of course it can run consecutively (no threading) if the
number of threads is set to 1 in the *.dat file.
The result
will be mostly the same regardless parallel or consecutive execution were used,
if no potential is calculated, no local invariance or BVS constraint is used.
If it is, then there can be slight differences due to the rounding errors
accumulating differently.
Input data
The earlier
RMC versions used the fixed format *.dat file input inherited from RMCA and amended with more and more additional parameters for the
new features. It became increasingly difficult to include additional data
in this rigid format, so a totally new approach, the free format data input was
developed by László Temleitner. Obviously this is not entirely ‘free’, it has
its rules (see the manual), and it is very flexible and
easy to accommodate more new data for the new features. In the same time lot of
the parameters were given a default value, which made it possible not to be
necessary to include them into the free format *.dat file. Although for the downward
compatibility the program can work with the old fixed format *.dat, it is
recommended to use the free format data input. To facilitate the change to the
new format, the program automatically creates several free format *.dat files
for a simulation. The *.free file contains
all the parameters (those as well, where default values were used), the *.freer file lists only the non-default
values of the simulation, and in some cases the *.freers file is created as well, where
the non-default parameters are given, but those, which should be determined by
calculation are given with their new, calculated value (for example the actual
value of the sigma parameters, if scalable sigma were used).
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Starting RMC |
RMC needs the following files to run.
·
*.cfg
·
*.dat
·
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 constraint, 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;
* 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.
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Starting your
own simulation |
·
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, the papers on this subject on
the references page 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!
Good
Luck!
Last modified 04/03/2023) by Orsolya Gereben
(comments welcome!)