def GetNNStatsMany(main_id, min, max):
folder = './dat/' + main_id + '/'
fname = main_id + 'stats_NN.csv'
fout = folder + fname
ensure_dir(fout)
with open(fout,'w') as f:
for i in range(min, max):
curr_id = main_id + str(i)
[n_s, n_c, r_c, coords] = read(curr_id)
stats = GetNNStatsIndiv(curr_id, n_s, n_c, r_c, coords)
for s in stats:
print s
f.write(str(s))
f.write(',')
f.write('\n')
f.close()
def Download(res, curr_id):
print 'running tm.download...'
[n_s, n_c, r_c, coords] = readcenters.read(curr_id)
down_folder = './dat/' + curr_id + '/Download/'
ensure_dir(down_folder)
cmd = 'scp ' + '[email protected]:/home/chaneyl/' + curr_id + '/out/* ' + down_folder
os.system(cmd)
def PlotSk(curr_id):
[n_s, n_c, r_c, coords] = readcenters.read(curr_id)
print 'plotting Sk...'
plt.figure(figsize=(12.0,4.0))
for i in range(0,n_s):
fname = './dat/' + curr_id + '/Sk/' + curr_id + '_Sk_' + str(i) + '.txt'
[k, Sk] = ReadSk(fname)
axes_indiv = plt.subplot(1, n_s + 2, i+1)
FormatPlotSk(axes_indiv, 'species {:d}'.format(i))
[popt, pcov, fit_k, fit_Sk] = FitSk(k,Sk)
PlotSkFit(popt, pcov, fit_k, fit_Sk, axes_indiv)
plt.loglog(k,Sk)
# run for all
fname = './dat/' + curr_id + '/Sk/' + curr_id + '_Sk_T.txt'
[k, Sk] = ReadSk(fname)
axes_combined = plt.subplot(1, n_s + 2, n_s+1)
FormatPlotSk(axes_combined, 'all species')
[popt, pcov, fit_k, fit_Sk] = FitSk(k,Sk)
PlotSkFit(popt, pcov, fit_k, fit_Sk, axes_combined)
plt.loglog(k,Sk)
# run for delaunay
fname = './dat/' + curr_id + '/Sk/' + curr_id + '_Sk_del.txt'
[k, Sk] = ReadSk(fname)
axes_delaunay = plt.subplot(1, n_s + 2, n_s+2)
FormatPlotSk(axes_delaunay, 'delaunay')
[popt, pcov, fit_k, fit_Sk] = FitSk(k,Sk)
PlotSkFit(popt, pcov, fit_k, fit_Sk, axes_delaunay)
plt.loglog(k,Sk)
fname = curr_id + '_Sk.eps'
fout = './dat/' + curr_id + '/Plots/' + fname
ensure_dir(fout)
plt.suptitle('structure factor, S(k)', fontsize=12)
plt.savefig(fout, bbox_inches=0, dpi = 300)
def Upload(curr_id, numbands):
print "running TE.upload..."
[n_s, n_c, r_c, coords] = readcenters.read(curr_id)
[N, walls] = getWallsNonDel(curr_id, n_s, coords)
N1 = 300
rad = MakeRad(1)
for r in rad:
fname_make = CreateMakeFile(curr_id, r, N)
fname_define = CreateDefineFile(curr_id, N1, r, walls)
fname_param = CreateFileParam(curr_id, numbands, N1, r, fname_make, fname_define)
fname_run = CreateFileRun(curr_id, numbands, r, fname_param)
def MakePlots(curr_id, opt):
[n_s, n_c, r_c, coords] = readcenters.read(curr_id)
N = 0
for i in range(0,n_s):
N += n_c[i]
delaunaymap.RunDelMap(curr_id, n_s, coords)
#GetNN(curr_id, n_s, n_c, r_c, coords)
GetNN(curr_id, n_s, n_c, r_c, coords)
PlotCenters(curr_id, n_s, n_c, r_c, coords)
#PlotSk(curr_id, n_s)
# elif opt==2:
#subbands = [97, 98, 99, 100, 101, 102, 103, 198, 199, 200, 201, 202, 203, 297, 298, 299, 300, 301, 302, 303]
subbands = [97, 98, 99, 100, 101, 102, 298, 299, 300, 301, 302]
def Upload(res, curr_id, numbands, N_part):
print 'running tm.upload...'
[n_s, n_c, r_c, coords] = readcenters.read(curr_id)
N = 0
for i in range(0,n_s):
N += n_c[i]
rad = MakeRad(res, n_s)
for r in rad:
fname_make = CreateMakeFile(curr_id, N, n_s, r)
fname_define = CreateDefineFile(curr_id, N, n_s, n_c, r, coords, N_part)
fname_param = CreateFileParam(curr_id, n_s, r, numbands, N, fname_make, fname_define, N_part)
fname_run = CreateFileRun(curr_id, n_s, r, numbands, fname_param)
MakeQsub(curr_id, res, n_s, rad)
def CalcSk(curr_id):
fout_Sk = './dat/' + curr_id + '/Sk/' + curr_id + '_Sk_'
ensure_dir(fout_Sk)
[n_s, n_c, r_c, coords] = readcenters.read(curr_id)
N = 0
for i in range(0,n_s):
N += n_c[i]
total_in = [maxx, maxy, N]
for i in range(0,n_s):
inputs = [maxx, maxy, n_c[i]]
for j in range(0,n_c[i]):
tmpx = coords[i][j][0]
tmpy = coords[i][j][1]
inputs.extend( [ tmpx, tmpy ] )
total_in.extend( [ tmpx, tmpy ] )
outname = fout_Sk + str(i) + '.txt'
RunSk(inputs, outname)
outname = fout_Sk + 'T.txt'
RunSk(total_in, outname)
del_fin = './dat/' + curr_id + '/Del/' + curr_id + '_del_T.txt'
del_data = list(csv.reader( open(del_fin, 'rb') , delimiter = '\t' ))
del_in = [maxx, maxy, len(del_data)]
for i in range( len(del_data) ):
tmpx = float(del_data[i][0])
tmpy = float(del_data[i][1])
del_in.extend( [tmpx, tmpy] )
outname = fout_Sk + 'del.txt'
RunSk(del_in,outname)