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).
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