Rmpcdmd_ simulations of colloids with coarse-grained hydrodynamics, chemical reactions and external fields


RMPCDMD is implemented in Fortran, following the 2008 version of the standard, and uses OpenMP for multi-core execution. Iqd to usd Trajectories are stored in the H5MD file format [ 9], and Python programs are provided to illustrate data analysis. Amazon international shipping rates The module fortran_h5md [ 10] provides helper routines to write H5MD files from Fortran.

Verizon modem setup H5MD files are HDF5 files ( https://www.hdfgroup.org/HDF5/) with an internal organization tailored for molecular simulations [ 9].

In designing RMPCDMD, we tried to adopt practices for scientific computing that help to deliver reproducible results and facilitate the extension of the code and its maintenance. Inr to usd exchange rate We also made special efforts on the usability of the software. Mortgage meaning in tagalog The design choices are the results of the authors’ experience on scientific programming, with further motivation by the article on “Best Practices for Scientific Computing” by Wilson et al [ 11]:

• The algorithms are implemented in Fortran modules in the src/ directory and shared between the simulations found in programs/. Python dictionary Table 1 summarizes their content.

• The build procedure and partial testing are automatically executed on the Travis CI platform ( https://travis-ci.org/pdebuyl-lab/RMPCDMD) for continuous integration.

CMake is used to build RMPCDMD and run automated test programs in test/ that cover some of the base algorithms such as particle sorting or the histogram routine. Binary addition overflow For spatial sorting, for instance, the compact Hilbert index of the particles is re-computed after sorting to check the consistency of the sorted list. Stock superstock The Fortran module fortran_tester [ 13] provide convenience routines for testing (e.g. Euro news today equality assertions). Conversion from inr to usd All programs in test/ whose filename starts with test_ are executed automatically by Travis CI when the code repository is updated. Eur usd chart investing Users can also execute the make test command on their machine after having compiled RMPCDMD.

Automated testing using actual simulations is difficult and very much time intensive, and we rely on it only for a small part of the code. Binary to octal conversion In simulations without a thermostat or wall interactions, the total momentum and energy of the system must be conserved. Currency converter xpf to usd This is verified for a short run of the single_dimer_pbc simulation as part of the continuous integration testing: A Python program test/dimer_test.py reads the simulation output and validates, to a set accuracy, these conservation laws. Binary hexadecimal chart This also insures that the common foundation of RMPCDMD, such as the force computation, neighbor listing, particle sorting, etc., fulfil their role.

Further validation of the code is done via comparison of physical results. Currency converter aud to usd For pure solvent simulations in equilibrium, one can verify that the velocity distribution of the solvent particles is a Boltzmann distribution at the set temperature. Convert us dollars to pounds sterling The Poiseuille flow simulations allows one to verify the viscosity, via the velocity profile. Usd canadian exchange rate For colloids, one can check the diffusion coefficient against the literature results [ 14]. Swiss market index futures These validations must be performed by the user. Euro to usd conversion The presence of analysis programs in Python in the experiments/ directory gives a good starting point for this work.

The prototypical use of the MPCD algorithm to study chemically active particles is the dimer nanomotor, whose model was introduced by Rückner and Kapral [ 5]. Dollar pound conversion rate It consists of two rigidly linked spheres evolving in a solvent. Gender definition sociology Chemical reactions are catalyzed by one of the spheres and create a local concentration gradient, effectively propelling the dimer along its symmetry axis. Taux de change euro dollar australien This simulation is implemented in the program single_dimer_pbc.

To facilitate usage of RMPCDMD by newcomers, ready-made simulation “experiments” are provided in experiments/. Venezuela money to us dollars There, makefiles allow the user to simply type make simulation

to start a simulation. Asian stock market futures The terminology that we have chosen reflects our opinion that computer simulations can be viewed as numerical experiments in which one prepares a setup and conducts a study to understand a certain physical phenomenon. Binary to english translator The ability to modify a given experimental choice (i.e. Hex editor windows 10 thermostating or not, surface properties, etc.) to assess its effect is therefore critical. Rate gbp to usd By providing several chemical models and collision rules, RMPCDMD provides such a framework.

Four programs are provided to analyze the data of the first experiment 01-single-dimer. Javascript print command plot_velocity.py displays the laboratory reference frame velocity or the directed velocity of the dimer (with the option –directed). Binary music plot_histogram.py displays the cylindrical shell histogram of the reaction product concentration. 1 usd to krw plot_msd.py displays the mean-squared displacement of the dimer’s center-of-mass position. Usd nzd chart This quantity is a practical interest in comparison to experimental studies [ 31]. Dollar euro exchange rate today view_last_simulation_frame.py displays a 3D representation of the dimer motor using the Mayavi visualization library [ 19], either with its full trajectory as a line (with option –unwrap) or with the product solvent particles B (with option –show-B). The fx firm The two first analysis programs are modeled after the results by Rückner and Kapral [ 5]. Binary code translater Their output is shown in Figures 1 and 2 for a simulation of the “experiment” 01-single-dimer. Html code reader 1

The tree-dimensional visualization of view_last_simulation_frame.py is shown in Figure 3. 1 usd to bgn The assessment of the correctness for a simulation, discussed in section quality control, can be started by using the provided plotting tool to observe the conservation of the center of mass velocity ( rmpcdmd plot dimer.h5 –obs center_of_mass_velocity) or of the internal energy ( rmpcdmd plot dimer.h5 –obs internal_energy).

RMPCDMD’s most valuable content consists in the collection of algorithms in src/, many of which are not available widely, and the simulation protocols implemented in programs/. Usd brl exchange rate All steps of a simulation appear in the body of the corresponding program, including calls to the force computation, RATTLE, neighbor listing, etc, so that following the full execution of the code is explicit.

There are two directions to modify RMPCDMD. Funny quotes about friendship The first one is to add an application, or a virtual experiment, via an additional program in programs/, using the closest existing program as a basis. Yahoo news canada The second one is to implement a new algorithm or feature in an existing or new module under src/, ideally with dedicated tests in test/. Us futures market hours Ideas for further extensions include alternative chemical schemes and geometries, performance tuning for many-motor simulations, more efficient rigid-body implementation, etc.

Given the scarcity of open-source nanomotor simulation code, we briefly compare RMPCDMD to nano-dimer [ 30] (by Peter Colberg, available under the MIT license), these two being the only open-source softwares to provide support for chemically-powered nanomotor simulation. Euro to pound exchange rate today RMPCDMD has, in addition to nano-dimer, support for external fields or rigid-body dynamics for assemblies larger than the dimer. Usd cad nano-dimer, on the other hand, is based on OpenCL C and on the Message Passing Interface for distributed parallel execution, and is able to handle many-motors simulations that are out of reach of RMPCDMD for performance reasons.

Given the research activity on the topic of active colloids, we believe that providing a reference implementation of a chemically active MPCD fluid can serve both as a tool to reproduce earlier results from the literature and as a starting point for further modeling, by us or by other groups. Gender identity quiz RMPCMD has not been used for published work yet. Aud usd graph It is in use for ongoing research projects at the Instituut voor Theoretische Fysica of the KU Leuven.

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