lorenzo-rovigatti/ashell

ashell

ashell is a proof-of-concept code I am developing to learn modern c++ and to practice object-oriented programming. Its design has been inspired by HOOMD-blue's architecture.

Building the executable

Requirements

• CMake >= 2.8
• make
• A c++14-compliant compiler (tested with GCC 5.4)
• A few Boost modules:
  • Boost Python (libboost-python-dev on debian-derived distros)
  • Boost Log (libboost-log-dev)
  • Boost Signals2 (libboost-signals-dev)

Compilation

Extract the ashell archive (or download the nightly build via git) and compile it with the following commands:

cd ashell		# enter the ashell folder
mkdir build 	# create a new build folder. It is good practice to compile out-of-source
cd build
cmake ..		# here you can specify additional options, see next section
make -j4		# compile ashell. The -jX make option makes it compile the code in parallel by using X threads.

At the end of the compilation the final executable (ashell) will be placed in the build/bin folder.

cmake options

Here is a list of options that can be passed to cmake during the pre-compilation stage:

• -DPython=On Enables Python bindings
• -DDebug=ON Compiles with debug symbols and without optimisation flags
• -DG=ON Compiles with debug symbols + optimisation flags
• -DINTEL=ON Uses INTEL's compiler suite

Usage

Initial configuration

• If the input file contains no configuration_file key, ashell will attempt to generate a random configuration using the initial_N and initial_box keys as initial number of particles and box size, respectively.
• Use the utilities/generate.py script to set up a configuration of a spherical triangulated mesh. The script, which takes as argument the number of points that will compose the sphere, produces an initial configuration and a topology file.

Potentials

• lennard_jones_force, parameters:
  1. rc
  2. sigma
• FENE_force, parameters:
  1. k
  2. r0
• Harmonic force, parameters:
  1. k
  2. r0
• force_triangulated_mesh, parameters:
  1. kv force constant associated to the relative change of the total volume
  2. ka force constant associated to the relative change of the total area
  3. V0_from_conf boolean, if true V0 will be initialised by using the volume of the starting configuration
  4. V0 used only if V0_from_initial_conf is absent or set to false
  5. A0_from_conf boolean, if true A0 will be initialised by using the area of the starting configuration
  6. A0 used only if A0_from_initial_conf is absent or set to false
• force_dihedral, parameters:
  1. kb
  2. theta0

Acknowledgements

• The structure of ashell has been inspired by HOOMD-blue
• Eigen 3.3.4 is included in the source tree
• Some utility classes have been taken (and subsequently modified) from oxDNA