- 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/outfilesdirectory. - Clean the datafiles if desired:
make dataclean
- 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
- 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
- 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).
- 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).
- 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).
- 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).
- 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).
- 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