def make_cubes(loop,F=[10],T=[1.2],P=10000000,A=27,B=27,r=3.0,r2=3.0,
gr=4.5,make_rigid=False,noskip=True,exalted=False,
L=False, no_linker=False,delta=20,small_linker=False):
"""# Creates a dna.xml file for set parameters
loop should be dictionary that contains three arrrays
loop = {'allsp':[x,x,x],'allphi':[x,x,x],'ndna':[x,x,x]}
T = array of values for temperature
P = runtime
A/B equal number of A and B nanoparticles to make
F is energy between nucleotides"""
for spacer in loop['allsp']:
for phi in loop['allphi']:
for num_dna in loop['ndna']:
tolerance = 1.8
n_sphere=60
#sigma of nucleotide
sig=0.45
#linker end beads
li1 = ['A','C','K']
li2 = ['F','G','T']
if small_linker:
li1 = ['A','C']
li2 = ['G','T']
# number of dna linker in chain
linker = len(li1)
N_sphere= A+B #number of nanoparticles
#tot:wal number of particles that make up dna tethered nanoparticle
rows = (linker*2+spacer)*num_dna+n_sphere+1
#sphere
#L=box_size(N_sphere,r,phi,gr)
#cube
if L == False:
L=packing_size_cube(N_sphere,r,phi,linker+spacer,139)
#Decrease Box Size incrementally(50000 time steps to do so)
#This will be used later to set the volume fraction in the simulation
Lx = '(2e5,%f)'%(L)
Runs1 = {'sig':sig,'F':F,'n_s':spacer,'n_l':linker,
'num_dna':num_dna,'phi':phi,'n_sphere':n_sphere,'N_linker':0,
'T':T,'P':P,'Lx':Lx,'r':r,'L':L,'total':rows,'N_sphere':N_sphere}
Runs2 = {'sig':sig,'F':F,'n_s':spacer,'n_l':linker,
'num_dna':num_dna,'phi':phi,'n_sphere':n_sphere,'N_linker':0,
'T':T,'P':P,'Lx':Lx,'r':r2,'L':L,'total':rows,'N_sphere':N_sphere}
###########################
#cube MAKE Initial Configuration
###########################
print( "Making NPA"
NPA = makeNP_cube(Runs1, li1, 'V', make_rigid,x_length=r,
no_linker = no_linker)
print( "Making NPB"
NPB = makeNP_cube(Runs2, li2, 'W', make_rigid,x_length=r,
no_linker = no_linker)
NPA.grow()
NPB.grow()
xmp.nanoparticle(NPA, 'nanoparticle1.xyz')
xmp.nanoparticle(NPB, 'nanoparticle2.xyz')
xmp.dnaxml([L,L,L],[[NPA,1]],read='nanoparticle1.xyz',save='npa1.xml')
xmp.dnaxml([L,L,L],[[NPB,1]],read='nanoparticle2.xyz',save='npa2.xml')
#write a packmol input script
xmp.packdna(L+L*2/3., [A,B])
###########################
#run packmol
##############################
import pack_shapes as pshapes
pshapes.pack_shape([NPA.ssDNA,NPB.ssDNA],[A,B],delta=delta)
#os.system('ppackmol 4 dna.inp')
print( '\n#############################\n file written to dna.xyz'
####################
# Write XML file
####################
Lstart=points.inside_box(L/2.0,open('dna.xyz','r'))
print( Lstart,L
Runs1['Lx'] = '(0,%f),(2e5,%f)'%(max(Lstart)+2,L)
#read input script and parce it into an xml file
#numsphere is +1 because there is a point in the middle
xmp.dnaxml(Lstart,[[NPA,A],[NPB,B]])
print(_vars(Runs1)
# Build Files
if no_linker ==True:
Runs1['n_l'] = 0
Runs1['n_s'] += 1
subj(Runs1)
no_linker = no_linker)
Poly = make_polymer(Runs2)
NPA.grow()
Poly.grow()
xmp.nanoparticle(NPA, 'nanoparticle1.xyz')
xmp.nanoparticle(Poly, 'nanoparticle2.xyz')
xmp.dnaxml([L,L,L],[[NPA,1]],read='nanoparticle1.xyz',save='npa1.xml')
xmp.dnaxml([L,L,L],[[NPB,1]],read='nanoparticle2.xyz',save='npa2.xml')
#write a packmol input script
xmp.packdna(L+L*2/3., [A,B])
###########################
#run packmol
##############################
import pack_shapes as pshapes
pshapes.pack_shape([NPA.ssDNA,Poly.ssDNA],[A,B],delta=15)
#os.system('ppackmol 4 dna.inp')
print( '\n#############################\n file written to dna.xyz'
####################
# Write XML file
####################
Lstart=points.inside_box(L/2.0,open('dna.xyz','r'))
print( Lstart,L
Runs1['Lx'] = '(0,%f),(2e5,%f)'%(Lstart[0],L)
#read input script and parce it into an xml file
#numsphere is +1 because there is a point in the middle
xmp.dnaxml(Lstart,[[NPA,A],[Poly,B]])
print(_vars(Runs1)
###################