Nanoparticle Shape Lab

Install instructions on BigRed3

• First, git clone the project: git clone https://github.com/softmaterialslab/np-shape-lab.git
• Then, load the required modules using following command: module swap PrgEnv-intel PrgEnv-gnu && module load boost/gnu && module load gsl
• Next, go to the root directory: cd np-shape-lab
• Then, install the project: make cluster-install
• Finally, submit the job: make cluster-submit
• All outputs from the simulation will be stored in the bin folder when the simulation is completed.
• Check and compare files (ex: energy_nanomembrane.dat) inside the bin/outfiles directory.
• Clean the datafiles if desired: make dataclean

Install instructions on Local computer

• Load the necessary modules: module load gsl && module load openmpi/3.0.1 && module load boost/1_67_0
• Next, go to the root directory: cd np-shape-lab
• Then, install the project: make all
• This should create np_shape_lab executable in the bin directory

Testing

Homogeneously-charged Disc Formation:

• A reference set of parameters for testing homogeneously charged disc formation are provided below in the complete executable command: time ./np_shape_lab -R 10 -q 600 -c 0.005 -t 1 -v 1 -b 40 -s 40 -S 25000 -D 4 -F n
• Respectively, these are the (radius (in nm), net charge (in e), salt concentration (in Molar), surface tension (in dyn/cm), volume tension (in atm/nm^3), bending rigidity (in kBT), stretching rigidity (in kBT), net number of steps, and discretization parameter).
• After a few (3 - 10) minutes, this should produce a disc of final reduced area (A = 15.675), local potential (U = 2620.98 kB T), and conserved total energy (E = 2699.97 kB T).
• Note that minor changes on order of a percent are expected due to shuffling of the initial charge distributions dependent on different machines' random seed.
• For testing a higher resolution grid (D = 8), use: time ./np_shape_lab -R 10 -q 600 -c 0.005 -t 1 -v 1 -b 40 -s 40 -S 25000 -D 8 -F n

Homogeneously-charged Rod Formation:

• Simply increasing the salt concentration (c) allows for testing homogeneously charged rod formation using the command below: time ./np_shape_lab -R 10 -q 600 -c 0.01 -t 1 -v 1 -b 40 -s 40 -S 25000 -D 4 -F n
• After a few minutes, this should produce a rod of final reduced area (A = 13.259), local potential (U = 1919.14 kB T), and conserved total energy (E = 1939.96 kB T).

Inhomogeneously-charged Hemisphere Formation:

• The same parameters as in the disc example above may be used to test hemisphere formation, with two added parameters (N) and (p): time ./np_shape_lab -R 10 -q 600 -N 2 -p 0.5 -c 0.005 -t 1 -v 1 -b 40 -s 40 -S 25000 -D 4 -F n
• Respectively, the new parameters specify the collective number of stripes (N) and the fractional area of the charged patch (p), such that (p = 0.5) is a standard Janus particle. The charge (q) now specifies the charge were it homogeneously charged, effectively specifying a charge density in the charged region.
• After a few minutes, this should produce a hemisphere of unchanged final reduced area (A = 12.53), local potential (U = 1224 kB T), and conserved total energy (E = 1437).

Uncharged, Icosahedrally Buckled Control:

• The above three examples use the default setting that does not induce spontaneous elastic buckling.: time ./np_shape_lab -R 10 -q 0 -c 0.005 -t 0 -v 0 -b 1 -s 1000 -S 25000 -D 4 -F n -B y
• The added parameter is a buckling flag ("-B").
• After a few (3 - 10) minutes, this should produce an icosahedron of final reduced area (A = 12.3795), local potential (U = 26.86 kB T), and conserved total energy (E = 127.69 kB T).

Yin-yang Patterns:

• The same parameters as in the Inhomogeneously-charged Hemisphere example, with one additional parameter (H): time ./np_shape_lab -R 10 -q 600 -N 2 -p 0.5 -c 0.005 -t 1 -v 1 -b 40 -s 40 -S 25000 -D 4 -F n -H y
• The added parameter is a function flag ("-H")£¬argument 'y' means yin-yang pattern.
• After a few minutes, this should produce an yinyang-sphere of unchanged final reduced area (A = 12.5099), local potential (U = 1218.48 kB T), and conserved total energy (E = 1433.25 kB T).

Inhomogeneously-charged Cube Formation:

• The same parameters as in the disc example, with one additional function parameter (H): time ./np_shape_lab -R 10 -q 600 -c 0.005 -t 1 -v 1 -b 80 -s 40 -S 25000 -D 4 -F n -H c
• In function flag "-H", argument 'c' means cube formation.
• After a few minutes, this should produce a cube of unchanged final reduced area (A = 12.712), local potential (U = 2852.72 kB T), and conserved total energy (E = 3626.28 kB T).

more resources:

• nanoHUB tool: https://nanohub.org/tools/npshapelab
• nanoBIO workshop talk: https://www.youtube.com/watch?v=C4jvU6TuXao&list=PLnC9T36tFWrDnTt4yex5asWW624ceP9Jd&index=5
• Louis Stokes workshop: https://www.youtube.com/watch?v=mGhCOmNg6FI&list=PLnC9T36tFWrBy5xGsn99IQEWo6BmHxUq7&index=5
• Updated with travis integration testing