This repository contains extra information and code for the article Mesoscopic simulations of anisotropic chemically-powered nanomotors by Pierre de Buyl.
The preprint should be available on the author's arXiv profile: https://arxiv.org/a/debuyl_p_1.html
The license for the code in this repository is the 3-clause BSD, found in the file LICENSE.
The mesoscopic simulations are performed with the code RMPCDMD that is implemented in Fortran 2008 with a C extension.
The simulations were run at the supercomputer ThinKing operated jointly by the KU Leuven and Hasselt University.
The hardware specifications are summarized with the following command-line programs:
user@hpc-p-login-2:~$ uname -mosv
Linux #1 SMP Mon Oct 24 10:22:33 EDT 2016 x86_64 GNU/Linux
user@hpc-p-login-2:~$ grep -E '(^model name|^vendor_id|^flags)' /proc/cpuinfo | sort | uniq
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms
model name : Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz
vendor_id : GenuineIntel
The compilers used are, for C:
user@hpc-p-login-2:~$ icc --version
icc (ICC) 18.0.1 20171018
Copyright (C) 1985-2017 Intel Corporation. All rights reserved.
with flags -std=c99 -O3.
For Fortran:
user@hpc-p-login-2:~$ ifort --version
ifort (IFORT) 18.0.1 20171018
Copyright (C) 1985-2017 Intel Corporation. All rights reserved.
with flags -openmp -stand f08 -O3.
The analysis was run with Python 3.5.2 using the interpreter and libraries listed below:
Platform: linux
Python: 3.5.2 (default, Nov 17 2016, 17:05:23)
[GCC 5.4.0 20160609]
Machine and architecture x86_64 64bit ELF
NumPy: 1.15.1
SciPy: 1.0.0
matplotlib: 2.1.0
h5py: 2.6.0
The Python code is provided in Jupyter notebooks.
To reproduce the simulations of the paper, you need to install the software
RMPCDMD. After installation of RMPCDMD, with
the rmpcdmd command-line program available in your terminal, run simulations
using the parameter and datafiles provided in the directory parameter_files.
The notebooks enable the reproduction of all the figures from the article.
For information, the whole simulation set required about 700 core days.