def animate_beads(frames=[0,1]):
#print out directory
M=MD.ReadCord()
Lx = M.box_length
Ly = M.box_length_y
Lz = M.box_length_z
L = M.box_volume()
last = M.frames
try:
VW = util.pickle_load('VW.pkl')
npType = M.get_type(['V','W'])
except:
VW=M.cord_auto(['V','W'])
npType = M.get_type(['V','W'])
util.pickle_dump(VW,'VW.pkl')
#for binary systems use this A
for k in frames:
fid = open('animate/Color%i.tcl'%k,'w')
fid.write('%i\n\n'%VW.shape[1])
V = Average(VW,L,k-5,5)
A = read_color_index(frame=k)
for i in range(VW.shape[1]):
x = V[i][0]
y = V[i][1]
z = V[i][2]
color = ['B','R','G','O','P']
fid.write('%c %.2f %.2f %.2f\n'%(color[int(A[i])],x,y,z))
fid.close()
def structure_factor(VW, L, n_frames=10, n_start=1,
filters=0.05, dh=0.05,save='sf'):
import MD.analysis.sfactor as sf
#Find Structure Factor
stmp,qx = sf.sfactor(VW[n_start:n_start+n_frames],L=L,l=20)
S,Q,primitive_vectors = sf.sort_sfpeaks(stmp,qx)
#Plot the graph
xlabel = '$|\\vec{q}$ $|$'
ylabel = '$S(\\vec{q}$ $)$ '
pyplot.plot(Q, S, linestyle='', marker='x',
xlabel=xlabel, ylabel=ylabel, save=save)
util.pickle_dump(Q,'Vsfx%i.pkl'%n_start)
util.pickle_dump(S,'Vsfy%i.pkl'%n_start)
#if len(QQ)>500:
# bars,height = sf.sf_max(QQ,qpeaks=8)
# db_x,db_y = sf.dbfactor(msdr=5)
# pyplot.plot_bar(bars, height, xlabel=xlabel, ylabel=ylabel,
# save=save)
# pyplot.plot(db_x, db_y, linestyle='--', xlabel=xlabel, ylabel=ylabel,
# save=save)
# #return q, s, bars, height, db_x, db_y
# return Q, S, primitive_vectors
#filter out the noise
Q, S, primitive_vectors = sf.sf_filter(Q, S, primitive_vectors,
filters=filters, save = 'sf%i'%n_start)
return Q, S, primitive_vectors
def ipy_single():
dirname = os.getcwd().partition('/')[-1]
print "Starting:",dirname.split('/')[-1]
#initial file
dirname = os.getcwd().partition('/')[-1]
print "Starting:",dirname.split('/')[-1]
delta = 10
M=MD.ReadCord()
Lx = M.box_length
Ly = M.box_length_y
Lz = M.box_length_z
L = np.array([Lx, Ly, Lz])
L_cont = M.box_volume()
L_cont[-1] = L_cont[-2]
util.print_box_volume(L_cont,delta=delta)
last = M.frames
#V_index = M.get_index(['V'])
#W_index = M.get_index(['W'])
try:
VW = util.pickle_load('VW.pkl')
except:
VW=M.cord_auto(['V','W'])
#VW,Z,W = drift_remove_all(VW,Z,VW,L)
util.pickle_dump(VW,'VW.pkl')
#L_last = L_cont[0][0]
#for i,j in enumerate(L_cont):
# if j[0] != L_last:
# L_last = j[0]
# if i - 5 > 0:
# x.append(i-5)
x = range(0,last)
index = M.get_index(['C','G'])
ndna = len(index)/VW.shape[1]
return [M,VW,L_cont,x,ndna]
def _connections(M):
try:
con = util.pickle_load('conn.pkl')
except:
fid = open('conn_who.dat','r')
c_index = M.get_index(['C'])
g_index = M.get_index(['G'])
con = []
count = 0
for line in fid.readlines():
print count
con_K = []
con_T = []
#linker alternates between c g and cc gg
line = line.replace('}','')
for i in line.split('{')[1].split():
#translate connections
try:
con_K.append(c_index.index(int(i)))
except:
print 'error connection was not in list'
for i in line.split('{')[2].split():
#translate connections
try:
con_T.append(g_index.index(int(i)))
except:
print 'error connection was not in list'
con.append([con_K,con_T])
count += 1
del con[-1]
util.pickle_dump(con,'conn.pkl')
return con
def species_mixing(V,W,L,n_finish=1,n_start=0,delta=100,rcut=False):
#The total number of frames we are going to look at
if rcut == False:
rcut=min_particle_distance(V[-1:],W[-1:],L)+6
print rcut
#rcut = 19
rcut = 22
n_frames = (n_finish-n_start)/delta
x = np.arange(n_start,n_finish,delta)
s = []
o = []
for k in x:
Same = 0
Other = 0
print k
for i in range(V[k].shape[0]):
Same += len(nearest_neighbors_point(V[k],V[k][i],L,rcut)[0])
Same += len(nearest_neighbors_point(W[k],W[k][i],L,rcut)[0])
Other += len(nearest_neighbors_point(W[k],V[k][i],L,rcut)[0])
Other += len(nearest_neighbors_point(V[k],W[k][i],L,rcut)[0])
s.append(float(Same)/(W[k].shape[0]+V[k].shape[0]))
o.append(float(Other)/(V[k].shape[0]+W[k].shape[0]))
print s
print o
util.pickle_dump([x,s,o],'mix.pkl')
pyplot.plot2(x, s, x, o, label1='Same',
label2='other', save=('mixing_avg_cut%.1f'%rcut), showleg=True)
def msd(VW,L,step=1):
from MD.analysis.msd import msd
#Find the msd of the system
x,msd=msd(VW,L,step=step)
print x
print msd
pyplot.plot(x,msd,xlabel='time',ylabel='msd',save='MSDtime')
util.pickle_dump(msd,'msd.pkl')
def msd_index(VW,L):
k=100
time = 500
surface = util.pickle_load('surface.pkl')
DV = util.pickle_load('DV_s.pkl')
DW = util.pickle_load('DW_s.pkl')
CV = util.pickle_load('CV.pkl')
CW = util.pickle_load('CW.pkl')
defects = []
print DV.shape
print DW.shape
for i in range(DV[k].shape[0]):
if DV[k][i] == -1:
index, d = close_neighbors_point(VW[k],CV[i],L)
defects.append(index)
for i in range(DW[k].shape[0]):
if DW[k][i] == -1:
index, d = close_neighbors_point(VW[k],CW[i],L)
defects.append(index)
print len(defects)
fid = open('large.xyz','r')
M = readxyz.ReadCord(trajectory = 'large.xyz',frames = 777)
crystal = M.cord_auto(['V','W'])
bcc = np.zeros((777,432,1))
for frame in range(bcc.shape[0]):
for i in range(bcc.shape[1]):
if crystal[frame][i][0] > L[0]:
bcc[frame][i]=0
else:
bcc[frame][i]=1
s = []
for i in range(len(bcc[k])):
if surface[k][i]:
s.append(i)
gel = []
for i in range(len(bcc[k])):
if bcc[k][i] ==0 and surface[k][i] == 0:
gel.append(i)
crystal = []
for i in range(len(bcc[k])):
if bcc[k][i] == 1:
crystal.append(i)
#diffuse.index_msd(VW,s,L,time,save='msd_index_%i_surface_%i'%(k,len(s)))
x,msd=diffuse.index_msd(VW,gel,L,time,save='msd_index_%i_gel_%i'%(k,len(gel)))
x2,msd2=diffuse.index_msd(VW,crystal,L,time,save='msd_index_%i_solid_%i'%(k,len(crystal)))
util.pickle_dump([x,msd,x2,msd2],'msd_index.pkl')
#diffuse.index_msd(VW,defects,L,time,save='msd_index_%i_defects_%i'%(k,len(defects)))
#r = list(set(s)-set(defects))
#diffuse.index_msd(VW,r,L,time,save='msd_index_%i_nodefect%i'%(k,len(r)))
#print len(defects)
#print len(s)
import MD.plot.pyplot_eps as pyplot_eps
pyplot_eps.plot2(x,msd,x2,msd2,xlabel='t',ylabel='msd',label1='gel',label2='solid',save='msdgelsolid')
def run_blah2():
dirname = os.getcwd().partition('/')[-1]
print "Starting:",dirname.split('/')[-1]
M=MD.ReadCord()
Lx = M.box_length
Ly = M.box_length_y
Lz = M.box_length_z
L = np.array([Lx, Ly, Lz])
surface = util.pickle_load('surface.pkl')
fid = open('large.xyz','r')
M = readxyz.ReadCord(trajectory = 'large.xyz',frames = 777)
crystal = M.cord_auto(['V','W'])
###########################
bcc = np.zeros((777,432,1))
for k in range(bcc.shape[0]):
for i in range(bcc.shape[1]):
if crystal[k][i][0] > L[0]:
bcc[k][i]=0
else:
bcc[k][i]=1
crystal = []
for k in range(len(bcc)):
c=[]
for i in range(len(bcc[k])):
if bcc[k][i] == 1:
c.append(i)
crystal.append(len(c))
s = []
for k in range(len(surface)):
surf = []
for i in range(len(surface[k])):
if surface[k][i]:
surf.append(i)
s.append(surf)
util.pickle_dump(s,'surface_diffusion.pkl')
util.pickle_dump(crystal,'crystal_diffusion.pkl')
lamda=4
D=0.05
ns = []
dt = 10
dmdt = []
C = lamda**2/(D*24)
start = 100
finish = 350
for k in range(start,finish,dt):
n = 0
for i in range(dt):
n += len(s[i+k])
ns.append(n/dt)
count = 0
for i in range(start,finish,dt):
dm = crystal[i]-crystal[i-dt]
dmdt.append(C*dm/ns[count])
count += 1
x = np.arange(start,finish,dt)
pyplot.plot(x,dmdt,save='diffusion')
def self_intermediate_scattering(VW, L, x, n_start=1,
filters=0.05, dh=0.05,save='sf',l=5,delta=5,calc=True):
import MD.analysis.sfactor as sf
#Find Structure Factor
if calc:
import time
from MD.canalysis.int_scattering import int_scatter
F = []
for i in range(delta):
print i
print "caculating Average"
print VW.shape
print "Structure Factor"
A = VW[n_start+i]
stmp,qx = sf.sfactor(np.array([A]),L=L[n_start],l=l)
S,Q,primitive_vectors = sf.sort_sfpeaks(stmp,qx)
S,Q,primitive_vectors = sf.sf_filter_max(S,Q,primitive_vectors,filters=0.5)
index = S.index(max(S))
k = primitive_vectors[S.index(max(S))]
#take the average over different starting configurations
print "Calculating Int Scattering"
start = time.clock()
scat_c = int_scatter(VW[n_start+i:],np.array(L[0]),np.array(k),
np.array(x[:-(n_start+i)]))
end = time.clock()
print 'cython runtime'
print end-start
F.append(scat_c)
F_avg = np.zeros((len(F[-1])))
for i in F:
for j in range(len(F[-1])):
F_avg[j] += i[j]
F_avg /= delta
#reset the zero of x so that the plot starts at the correct time
x = range(len(F[-1]))
util.pickle_dump([x,F_avg],'si_scat.pkl')
xlabel = 't'
ylabel = 'F(q,t)'
save = 'int_scatter'
A = util.pickle_load('si_scat.pkl')
x = A[0]
F_avg = A[1]
#Kohlraush-Williams-Watts function
# A exp[-(t/tau_b)^beta]
beta = 1.4
tau_a = 6
K = []
K_x = []
fid = open('self_scat.dat','w')
for i in range(len(A[0])):
fid.write('%i %.4f\n'%(A[0][i],A[1][i]))
fid.close()
for i in np.arange(1,len(x),0.1):
K.append(F_avg[1] * math.exp(-(i/tau_a)**beta))
K_x.append(i)
def structure_factor(VW, L, n_frames=10, n_start=1,
filters=0.05, dh=0.05,save='sf',l=10):
import MD.analysis.sfactor as sf
#Find Structure Factor
A = Average(VW,L,n_start,n_frames)
#A = VW[n_start]
stmp,qx = sf.sfactor(np.array([A]),L=L[n_start],l=l)
S,Q,primitive_vectors = sf.sort_sfpeaks(stmp,qx)
fid = open('sftotal.txt','w')
fid.write('S Q\n')
for i in range(len(S)):
fid.write('%.5f %.5f\n'%(S[i],Q[i]))
fid.close()
#Plot the graph
xlabel = '$|\\vec{q}$ $|$'
ylabel = '$S(\\vec{q}$ $)$ '
#sp4 = 0.634698
#sp12 = 0.530493
#sc 1.121997
#pyplot_eps.plot_sf(Q, S,0.552381, linestyle='', marker='x',
#xlabel=xlabel, ylabel=ylabel, save=save,xlen=20)
pyplot.plot_sf(Q, S,0.552381, linestyle='', marker='x',
xlabel=xlabel, ylabel=ylabel, save=save,xlen=20)
util.pickle_dump(Q,'Vsfx%i.pkl'%n_start)
util.pickle_dump(S,'Vsfy%i.pkl'%n_start)
print 'finished reconstruction'
#if len(QQ)>500:
# bars,height = sf.sf_max(QQ,qpeaks=8)
# db_x,db_y = sf.dbfactor(msdr=5)
# pyplot.plot_bar(bars, height, xlabel=xlabel, ylabel=ylabel,
# save=save)
# pyplot.plot(db_x, db_y, linestyle='--', xlabel=xlabel, ylabel=ylabel,
# save=save)
# #return q, s, bars, height, db_x, db_y
# return Q, S, primitive_vectors
#filter out the noise
Q, S, primitive_vectors = sf.sf_filter(Q, S, primitive_vectors,
filters=filters,save=save)
import MD.analysis.reconstruct_lattice as rl
import MD.unit.make_bcc as mb
con = True
while con:
a1,a2,a3 = rl.reconstruct_lattice(Q,primitive_vectors,save+'recipricol.txt')
print a1,a2,a3
mb.make_bcc(a1,a2,a3,A[0],L[n_start])
if raw_input('Reselect? (y)/N') == 'N':
con = False
return Q, S, primitive_vectors
def msd(VW,L,step=1,save='MSD_time',time_scale=1):
from MD.analysis.msd import msd_no_drift #Find the msd of the system x,msd=msd_no_drift(VW,L,step=step)
D=0.1
D2=0.03
tau=10
try:
M = util.pickle_load('msd.pkl')
x = M[0][0]
msd = M[1][0]
except:
x, msd = msd_no_drift(VW,L)
x = x*time_scale
util.pickle_dump([[x],[msd]],'msd.pkl')
#msd_fit
fit = []
for i in x:
fit.append((2*3*D2*(i) - tau*(1-math.e**(-i/tau)))**0.5)
msd2 = (6*D*x)**0.5
pyplot.plot(x,msd,xlabel='Time',ylabel='msd',save=save)
def structure_factor(VW, L, n_frames=10, n_start=1,
filters=0.05, dh=0.05,save='sf',l=10):
import MD.analysis.sfactor as sf
#Find Structure Factor
#Average_position
stmp,qx = sf.sfactor(np.array([VW]),L=L,l=l)
S,Q,primitive_vectors = sf.sort_sfpeaks(stmp,qx)
#Plot the graph
xlabel = '$|\\vec{q}$ $|$'
ylabel = '$S(\\vec{q}$ $)$ '
pyplot.plot(Q, S, linestyle='', marker='x',
xlabel=xlabel, ylabel=ylabel, save=save)
util.pickle_dump(Q,'Vsfx%i.pkl'%n_start)
util.pickle_dump(S,'Vsfy%i.pkl'%n_start)
print 'finished reconstruction'
Q, S, primitive_vectors = sf.sf_filter(Q, S, primitive_vectors,
filters=filters,save=save)
print 'sorting peaks'
return Q, S, primitive_vectors
def vac_msd(DV,DW,CV,CW,L):
vacancies = np.zeros((DV.shape[0],1,3))
for k in range(len(DW)):
print k
#find the points that are nearest neighbor that are different
index = np.where(DW[k] == 0)[0]
if len(index) > 0:
if len(index) > 1:
index = index[1]
vacancies[k][0] = CW[index]
else:
index = np.where(DV[k] == 0)[0]
if len(index) > 1:
index = index[1]
vacancies[k][0] = CV[index]
from MD.analysis.msd import msd_no_drift as msd
#Find the msd of the system
x, msd = msd(vacancies, L)
msd = msd**0.5
util.pickle_dump([x,msd],'msd_vac.pkl')
pyplot.plot(x,msd,xlabel='time',ylabel='msd',save='MSD_vacancey')
def get_crystals():
dirname = os.getcwd().partition('/')[-1]
print "Starting:",dirname.split('/')[-1]
#initial file
dirname = os.getcwd().partition('/')[-1]
print "Starting:",dirname.split('/')[-1]
delta = 10
M=MD.ReadCord()
Lx = M.box_length
Ly = M.box_length_y
Lz = M.box_length_z
L = np.array([Lx, Ly, Lz])
L_cont = M.box_volume()
L_cont[-1] = L_cont[-2]
last = M.frames
try:
VW = util.pickle_load('VW.pkl')
except:
VW=M.cord_auto(['V','W','A0','A1'])
util.pickle_dump(VW,'VW.pkl')
#######################################
delta = 1
x = range(0,last-2*delta,delta)
C = np.zeros((len(x),VW.shape[1]),dtype=int)
os.mkdir('imd_trajectory')
os.chdir('imd_trajectory')
for i,k in enumerate(x):
A = Average(VW,L_cont,k,delta)
util.print_imd(np.array([A]),L_cont,k)
ovitojs(k)
os.system('ovito --script ovito.js --nogui')
name = 'data'+'%i'%(k)+'.dump'
fid = open(name,'r')
for j in range(9):
fid.readline()
for j, line in enumerate(fid.readlines()):
C[i][j] = int(line.split()[0])
fid.close()
os.chdir('../')
crystal_count(C,delta)
def solid_particles(VW, L, VW_names, x, avg=1, step=5e4, bcc = True, sc = False, GenLattice = False):
solid_particles = []
solid_crystals = []
try:
solid_crystals = util.pickle_load('spcrystal.pkl')
solid_particles = util.pickle_load('solidp.pkl')
except:
for k in x:
print 'step', k
A = av.average_position(VW,k,avg,L)
if bcc:
num, crystals = (bond_order.solid_particles(A,
L[k],c_cut=0.15, count=8,l=6,crystal=7))
if sc:
num, crystals = (bond_order.solid_particles(VW[k],
L[k],c_cut=0.175, count=6,l=4,crystal=5))
solid_crystals.append(crystals)
solid_particles.append(num)
util.pickle_dump(solid_crystals,'spcrystal.pkl')
util.pickle_dump(solid_particles,'solidp.pkl')
fid = open('solidpart.txt','w')
for i in range(len(x)):
fid.write('%i %i %.2f\n'%(x[i], solid_particles[i], L[x[i]][0]))
fid.close()
if GenLattice:
# make an xyz file of the crystals and there locations
f = open('solidpcrystals.xyz','w')
count=0
for k in x:
f.write(('%i \n\n')%(VW.shape[1]))
for i in range((len(solid_crystals[count]))):
if solid_crystals[count][i] == 1:
f.write(('%c %.2f %.2f %.2f \n')%('V',VW[k][i][0],VW[k][i][1],VW[k][i][2]))
else:
f.write(('%c %.2f %.2f %.2f\n')%('W',4*L[k][0],4*L[k][0],4*L[k][0]))
count += 1
f.close()
return x, solid_particles
def msd_jump(VW,L):
reload(diffuse)
fid = open('large.xyz','r')
M = readxyz.ReadCord(trajectory = 'large.xyz',frames = 777)
crystal = M.cord_auto(['V','W'])
bcc = np.zeros((777,432,1))
x = range(50,500,50)
delta = 50
for frame in range(bcc.shape[0]):
for i in range(bcc.shape[1]):
if crystal[frame][i][0] > L[0]:
bcc[frame][i]=0
else:
bcc[frame][i]=1
jumps = []
for i in x:
jumps.extend(diffuse.crystal_jump(VW,bcc,L,i,delta))
print len(jumps)
import MD.plot.pyplot_eps as pyplot_eps
util.pickle_dump(jumps,'jump.pkl')
hist_s,xs=histogram_reg(jumps,bins=20)
pyplot_eps.plot_bar(xs,hist_s,xlabel=r'$\sigma$',ylabel='count',save='jump_hist')
def msd_jump_average(VW,L):
reload(diffuse)
try:
jump_d = util.pickle_load('jump_d.pkl')
jump_t = util.pickle_load('jump_t.pkl')
except:
fid = open('large.xyz','r')
M = readxyz.ReadCord(trajectory = 'large.xyz',frames = 777)
crystal = M.cord_auto(['V','W'])
bcc = np.zeros((777,432,1))
for frame in range(bcc.shape[0]):
for i in range(bcc.shape[1]):
if crystal[frame][i][0] > L[0]:
bcc[frame][i]=0
else:
bcc[frame][i]=1
jump_d, jump_t = diffuse.crystal_jump(VW,bcc,L)
util.pickle_dump(jump_d,'jump_d.pkl')
util.pickle_dump(jump_t,'jump_t.pkl')
pyplot.plot(jump_t,jump_d,'','s',xlabel='time',ylabel='jump distance',save='msd_jump')
hist_s,xs,max_hist=histogram(jump_d,bins=20)
pyplot.plot(xs,hist_s,xlabel='distance',ylabel='count',save='jump_hist')
def run_defect():
#setup
#print out directory
dirname = os.getcwd().partition('/')[-1]
print "Starting:",dirname.split('/')[-1]
try:
var = MD.util.get_path_variables()
except:
var = {'ndna':60}
print var
M=MD.ReadCord()
L = M.box_length
last = M.frames
try:
V = util.pickle_load('V.pkl')
W = util.pickle_load('W.pkl')
R = util.pickle_load('R.pkl')
VW = util.pickle_load('VW.pkl')
except:
V=M.cord_auto(['V'])
W=M.cord_auto(['W'])
R=M.cord_auto(['R'])
VW=M.cord_auto(['V','W'])
VW,V,W = drift_remove_all(VW,V,W,L)
R = drift_remove(R,L)
util.pickle_dump(V,'V.pkl')
util.pickle_dump(W,'W.pkl')
util.pickle_dump(VW,'VW.pkl')
util.pickle_dump(R,'R.pkl')
x = range(0,last,last/5)
#mylog()
#plt.close()
solid_particles_vmd(VW,V,W,L,var,skip=100)
plt.close()
#species_mixing(V,W,L,n_finish=last)
#plt.close()
#species_mixing_fcc(VW,L,n_finish=last)
#plt.close()
for i in x:
#print "finding s(q)"
structure_factor(VW, L, var, n_start=i,save='sf'+str(i))
print "finding g(s)"
distance_distribution(V,W,L,n_start=i)
plt.close()
msd(VW,L)
plt.close()
msd(R,L,save='msd_R')
plt.close()
def find_networks(M, VW, L,x,ndna=25):
import MD.canalysis.connections as con
import MD.analysis.connections as conn
import MD.analysis.graph as graph
#plot total number of connections
connections = _connections(M)
num_connections=conn.num_connections(connections,VW.shape[1])
con_all = []
for i in range(len(connections)):
con_all.append(len(connections[i][0]))
print len(x),len(num_connections)
pyplot.plot(x,num_connections,xlabel='Time',
ylabel='hyrbid. density', save='connections')
pyplot.plot(x,con_all,xlabel='Time',
ylabel='hyrbid', save='connections_all')
plt.close()
#get the info
networks, num_networks, deg, neighbors, num_n, gr = graph.grapher(connections,VW.shape[1],ndna)
util.pickle_dump(networks,'net.pkl')
#plot the number of neighbors at each timesteps
pyplot.plot(x,num_n,xlabel='Time',
ylabel='num neighbors', save='neighbors')
plt.close()
print 'making plot'
net = []
for i in networks:
net.append(len(i))
pyplot.plot(x,net,xlabel='t',ylabel='networks',save='net')
label = ['networks','1','2','3','4','5','6','7','8','9']
x = [x for i in range(len(deg))]
#pyplot.plot(x,num_networks,xlabel='t',ylabel='Networks',save='net')
#pyplot.plot_multi(x[:4],deg[:4],label,xlabel='time',ylabel='number',save='con_net')
plt.close()
return networks, num_networks, deg, neighbors, num_n, gr
#pyplot.plot_multi(x[:4],deg[:4],label,xlabel='time',ylabel='number',save='con_net')
plt.close()
return networks, num_networks, deg, neighbors, num_n, gr
def run_test():
#print out directory dirname = os.getcwd().partition('/')[-1]
dirname = os.getcwd().partition('/')[-1]
print "Starting:",dirname.split('/')[-1]
M=MD.ReadCord()
Lx = M.box_length
Ly = M.box_length_y
Lz = M.box_length_z
L = np.array([Lx, Ly, Lz])
print L
last = M.frames
delta = 25
try:
V = util.pickle_load('V.pkl')
W = util.pickle_load('W.pkl')
VW = util.pickle_load('VW.pkl')
except:
#V=M.cord_range(['V'],delta=delta)
#W=M.cord_range(['W'],delta=delta)
#VW=M.cord_range(['V','W'],delta=delta)
V=M.cord_auto(['V'])
W=M.cord_auto(['W'])
VW=M.cord_auto(['V','W'])
VW_index=M.get_names(['V','W'])
VW,V,W = drift_remove_all(VW,V,W,L,VW_index)
util.pickle_dump(V,'V.pkl')
util.pickle_dump(W,'W.pkl')
util.pickle_dump(VW,'VW.pkl')
if V.shape[0]>5:
x = range(0,V.shape[0],V.shape[0]/3)
else:
x = range(V.shape[0])
delta = 1
#step,temp = mylog(row = 2)
#plt.close()
mylog_average(row = 1,delta=20)
msd(VW,L,time_scale=delta)
print V
#msd_phases(VW,L)
#msd_jump(VW,L)
#sd_index(VW,L)
#jump_lattice(VW,L)
#solid_particles_vmd(VW,V,W,L,M,skip=25)
#solid_particles_vmd(VW[1000:],V[1000:],W[1000:],L,var,skip=10)
#plt.close()
#species_mixing(V,W,L,n_finish=last)
#plt.close()
#end_end(V,W,M,L)
##plt.close()
for i in x:
print "finding s(q)"
structure_factor(VW, L, n_start=i,save='sf'+str(i))
#structure_factor(V, L, n_start=i,save='sfV'+str(i))
#structure_factor(W, L, n_start=i,save='sfW'+str(i))
print "finding g(s)"
distance_distribution(V,W,L,n_start=i)
plt.close()
def find_networks(M, VW, L, n_finish=1, n_start=0, delta=30, rcut=1.0, ndna=25):
#The total number of frames we are going to look at
x=np.arange(n_start,n_finish,delta)
print len(x)
#Find the number of connections at specific points x
import MD.canalysis.connections as con
import MD.analysis.connections as conn
import MD.analysis.graph as graph
try:
connections = util.pickle_load('con.pkl')
except:
try:
C = util.pickle_load('C.pkl')
G = util.pickle_load('G.pkl')
except:
G=M.cord_auto(['G'])
C=M.cord_auto(['C'])
util.pickle_dump(C,'C.pkl')
util.pickle_dump(G,'G.pkl')
connections = con.connections(C[x],G[x],L,rcut=rcut)
util.pickle_dump(connections,'con.pkl')
#plot total number of connections
num_connections=conn.num_connections(connections,VW.shape[1])
con_all = []
for i in range(len(connections)):
con_all.append(len(connections[i])/2.)
pyplot.plot(x,num_connections,xlabel='Time',
ylabel='hyrbid. density', save='connections')
pyplot.plot(x,con_all,xlabel='Time',
ylabel='hyrbid', save='connections_all')
plt.close()
#get the info
networks, num_networks, deg, neighbors, num_n, gr = graph.grapher(connections,VW.shape[1],ndna)
util.pickle_dump(networks,'net.pkl')
#plot the number of neighbors at each timesteps
pyplot_eps.plot(x,num_n,xlabel='Time',
ylabel='num neighbors', save='neighbors')
plt.close()
print 'making plot'
net = []
for i in networks:
net.append(len(i))
pyplot_eps.plot(x,net,xlabel='t',ylabel='networks',save='net')
label = ['networks','1','2','3','4','5','6','7','8','9']
pyplot_eps.plot(x,networks,xlabel='t',ylabel='Networks',save='net')
pyplot.plot_multi(x,deg,label,xlabel='time',ylabel='number',save='con_net')
return x, networks, connections
def find_lifetime(M,L,steps,temp,step_range=30,delta=4,rcut=1.0,step=5e4):
import MD.analysis.lifetime as life
try:
C = util.pickle_load('C.pkl')
G = util.pickle_load('G.pkl')
except:
C=M.cord_auto(['C'])
G=M.cord_auto(['G'])
util.pickle_dump(C,'C.pkl')
util.pickle_dump(G,'G.pkl')
#The total number of frames we are going to look at
for i in steps:
try:
print 'Frame',i,'Temp',temp[i]
except:
print i
x=np.arange(i,step_range+i,delta)
#Find he number of connections at specific points x
remain = life.lifetime(C[x],G[x],L)
x=np.arange(i,step_range+i,delta)*50000
print remain
pyplot_eps.plot(x,remain,xlabel='time', ylabel='remaining connections',
save='lifetime%i'%i)
plt.close()
def animate_binary(frames=[0,1]):
#print out directory
M=MD.ReadCord()
Lx = M.box_length
Ly = M.box_length_y
Lz = M.box_length_z
L = M.box_volume()
last = M.frames
try:
Z = util.pickle_load('Z.pkl')
VW = util.pickle_load('VW.pkl')
npType = M.get_type(['V','W'])
except:
Z=M.cord_auto(['Z'])
VW=M.cord_auto(['V','W'])
npType = M.get_type(['V','W'])
util.pickle_dump(Z,'Z.pkl')
util.pickle_dump(VW,'VW.pkl')
for k in frames:
#apply boundary conditions to move particle
for i in range(VW.shape[1]):
for j in range(i*6,i*6+6):
Z[k][j] = boundary(Z[k][j],VW[k][i],L[k])
util.pickle_dump(Z,'Zbound.pkl')
animate_script = open('animate/animate.tcl','w')
#for binary systems use this A
#fid = open('sc_num.txt','r')
#crystal = []
#for line in fid.readlines():
# crystal.append(float(line.split()[0]))
#fid.close()
A = []
for i in range(VW.shape[1]):
if npType[i] == 'V':
A.append(0)
else:
A.append(1)
for k in frames:
fid = open('animate/square%i.tcl'%k,'w')
for i in range(VW.shape[1]):
c = VW[k][i]
#v1 = Z[k][i*6] - c
#v2 = Z[k][i*6+2] - c
#v3 = Z[k][i*6+4] - c
v1 = Z[k][i*6] - c
v2 = Z[k][i*6+1] - c
v3 = Z[k][i*6+5] - c
#v1,v2,v3 = allign(v1,v2,v3)
color = ['blue','red','green','orange','purple']
dw.draw_cube(fid,c,v1,v2,v3,color[int(A[i])])
cub.gaussmap_color(VW,Z,L,k,A)
animate_script.write('\nsource square%i.tcl\n display update ui\n'%k)
animate_script.write('\nafter 1000\ndraw delete all\n display update ui\n')
fid.close()
def animate(frames=[0,1]):
#print out directory
M=MD.ReadCord()
Lx = M.box_length
Ly = M.box_length_y
Lz = M.box_length_z
L = M.box_volume()
last = M.frames
try:
Z = util.pickle_load('Z.pkl')
VW = util.pickle_load('VW.pkl')
except:
Z=M.cord_auto(['Z'])
VW=M.cord_auto(['V','W'])
util.pickle_dump(Z,'Z.pkl')
util.pickle_dump(VW,'VW.pkl')
cubic_order_animate(VW,Z,L,frames)
for k in frames:
#apply boundary conditions to move particle
for i in range(VW.shape[1]):
for j in range(i*6,i*6+6):
Z[k][j] = boundary(Z[k][j],VW[k][i],L[k])
util.pickle_dump(Z,'Zbound.pkl')
animate_script = open('animate/animate.tcl','w')
#for binary systems use this A
#A = []
#for i in range(VW.shape[1]):
# if i < VW.shape[1]/2:
# A.append(0)
# else:
# A.append(1)
#for k in range(len(VW.shape[0])):
for k in frames:
fid = open('animate/square%i.tcl'%k,'w')
fid2= open('animate/square%i.txt'%k,'w')
A = read_color_index(frame=k)
for i in range(VW.shape[1]):
c = VW[k][i]
v1 = Z[k][i*6] - c
v2 = Z[k][i*6+2] - c
v3 = Z[k][i*6+4] - c
#v1 = Z[k][i*6] - c
#v2 = Z[k][i*6+1] - c
#v3 = Z[k][i*6+5] - c
#v1,v2,v3 = allign(v1,v2,v3)
color = ['blue','red','green','orange','purple']
dw.draw_cube(fid,fid2,c,v1,v2,v3,color[int(A[i])])
cub.gaussmap_color(VW,Z,L,k,A)
animate_script.write('\nsource square%i.tcl\n display update ui\n'%k)
animate_script.write('\nafter 1000\ndraw delete all\n display update ui\n')
fid.close()
def end_end_connected(M,L): #find the length of the polymer
## \brief end to end distance of hybridized vs nonhybridized polymers
#
# \returns average distance from start to end of polymer
# for hybridizations and free polymer
#
# \param M - ReadCord Class
# \param L
#
# V ----- A C k
# W ----- F G T
import MD.analysis.connections as con
try:
K=util.pickle_load('K.pkl')
T=util.pickle_load('T.pkl')
S=util.pickle_load('S.pkl')
except:
K=M.cord_auto(['K'])
T=M.cord_auto(['T'])
S=M.cord_auto(['M'])
util.pickle_dump(K,'K.pkl')
util.pickle_dump(T,'T.pkl')
util.pickle_dump(S,'S.pkl')
#get connections
con = _connections(M)
h_sum = []
f_sum = []
for k in range(len(con)):
print k
hybrid = []
free = []
#get the points that are not connected
for i in range(K.shape[1]):
if i in con[k][0]:
hybrid.append(points.dist(K[k][i],S[k][i],L[k])[0]+0.5)
else:
free.append(points.dist(K[k][i],S[k][i],L[k])[0]+0.5)
for i in range(T.shape[1]):
if i in con[k][1]:
hybrid.append(points.dist(T[k][i],S[k][i+K.shape[1]],L[k])[0]+0.5)
else:
free.append(points.dist(T[k][i],S[k][i+K.shape[1]],L[k])[0]+0.5)
print hybrid
h_sum.append(sum(hybrid)/len(hybrid))
f_sum.append(sum(free)/len(free))
f_sum[-1]= f_sum[-2]
h_sum[-1]= h_sum[-2]
x = range(S.shape[0])
pyplot.plot2(x,h_sum,x,f_sum,xlabel='timestep',ylabel='sigma',label1='hybridizations',
label2='free',save='free_hybrid_end_end_connections',showleg='true')
def find_lattice(MD,VW,L,n_finish=1,n_start=0,delta=20,filters=0.2):
# Identify the bcc lattice as a grid and find the recipricol lattice
#Find Structure Factor
#print VW.shape
redo = True
while redo == True:
stmp,qx = sf.sfactor(VW[-10:-1],L=L,l=10)
S,Q,primitive_vectors = sf.sort_sfpeaks(stmp,qx)
print np.array(Q)
Q, S, primitive_vectors = sf.sf_filter(Q, S, primitive_vectors,
filters=filters, save = 'sffilter')
a,b = MD.analysis.sfactor.recipricol(Q,primitive_vectors)
#Find the best fit for the qlattice at a particular frame by looking
#for the lowest value of the msdr
x = np.arange(n_start,n_finish,delta)
defects = np.zeros((len(x),15))
lowest=10000
for k in x:
for i in range(10):
crystal, c = make.make_bcc(a[0], a[1], a[2], VW[k][i], L[0]+5)
msdr_x = msdr.msd_r(VW[k], crystal, L)
if lowest > msdr_x:
lowest = msdr_x
index = i
frame = k
crystal, cword = make.make_bcc(a[0], a[1], a[2], VW[frame][index], L[0]+5)
print np.array(b)
print np.array(a)
if raw_input('Do you want to retry?[no]/yes ') == 'yes':
redo = True
else:
redo = False
util.pickle_dump(cword,'cword.pkl')
util.pickle_dump(crystal,'ccrystal.pkl')
#filter out the comensurate crystal
C = []
for i in crystal:
#make sure there aren't two that are close due to pbc
if rcut_neighbors_point(np.array(C),i,L,rcut=6) == 0:
C.append(i)
#write out the lattice
fid = open('testlattice.xyz','w')
fid.write(('%i\n')%(len(C)))
fid.write('Atoms\n')
for i in range(len(C)):
fid.write(('%c %f %f %f\n')%('A',C[i][0],C[i][1], C[i][2]))
fid.close()
util.pickle_dump(C,'C.pkl')
return crystal, C
def run_binary():
#print out directory dirname = os.getcwd().partition('/')[-1]
dirname = os.getcwd().partition('/')[-1]
print "Starting:",dirname.split('/')[-1]
M=MD.ReadCord()
Lx = M.box_length
Ly = M.box_length_y
Lz = M.box_length_z
L = np.array([Lx, Ly, Lz])
print L
last = M.frames
L_cont = M.box_volume()
try:
V = util.pickle_load('V.pkl')
W = util.pickle_load('W.pkl')
VW = util.pickle_load('VW.pkl')
except:
#delta = 25
#V=M.cord_range(['V'],delta=delta)
#W=M.cord_range(['W'],delta=delta)
#VW=M.cord_range(['V','W'],delta=delta)
V=M.cord_auto(['V'])
W=M.cord_auto(['W'])
VW=M.cord_auto(['V','W'])
VW_index=M.get_names(['V','W'])
#VW,V,W = drift_remove_all(VW,V,W,L,VW_index)
util.pickle_dump(V,'V.pkl')
util.pickle_dump(W,'W.pkl')
util.pickle_dump(VW,'VW.pkl')
delta = 30
x = range(0,V.shape[0],delta)
print V.shape[0]
print x
#plt.close()
msd(VW,L,time_scale=delta)
type_ordering(VW,L_cont)
def run_():
#setp
dirname = os.getcwd().partition('/')[-1]
print "Starting:",dirname.split('/')[-1]
M=MD.ReadCord()
Lx = M.box_length
Ly = M.box_length_y
Lz = M.box_length_z
L = np.array([Lx, Ly, Lz])
L_cont = M.box_volume()
L_cont[-1] =L_cont[-2]
last = M.frames
new = False
try:
V = util.pickle_load('V.pkl')
if V.shape[0] != last:
print 'generating new pickle'
asdf
#Z = util.pickle_load('Z.pkl')
except:
#V=M.cord_auto(['V','W'])
new = True
V=M.cord_auto(['V'])
if V.shape[1] < 1:
V=M.cord_auto(['A','A0','A1'])
#Z=M.cord_auto(['Z'])
#VW_index=M.get_names(['V','W'])
#Z_index=M.get_names(['Z'])
#V = drift_remove(V,L,VW_index)
#Z = drift_remove(Z,L,Z_index)
#dump_xyz(V)
#dump_xyz(Z)
util.pickle_dump(V,'V.pkl')
#util.pickle_dump(Z,'Z.pkl')
# if (os.path.isfile('msd.pkl') is False):
# msd(V,L)
print V
asdf
x, xcount = util.get_box_size_steps(L_cont)
print x
x_set = []
n_frames = []
print xcount
print x
#F = filter(lambda x: x > 10, xcount)
for i in range(len(xcount)):
if xcount[i] > 10:
x_set.append(x[i])
n_frames.append(xcount[i]-10)
print n_frames
print x_set
f = h5py.File('../pmf_dist.hdf5','w')
for j,i in enumerate(x_set):
if i + n_frames[j] <= V.shape[0]:
if L_cont[i] == L_cont[i+n_frames[j]]:
print "L = ",L_cont[i][0]
print "rho = ",V.shape[1]/L_cont[i][0]**3
print "frame = ", i
print "n_frame", n_frames[j]
PMF(f, V,L_cont[i],n_start=i,n_frames=n_frames[j])
else:
print "L is not the same reduce the n_frames"
f.close()
import MD
from MD.dna_scripts.square import drift_remove_all
print 'MD.L is '
M=readxyz.ReadCord(trajectory = 'surface.xyz',frames=777)
last = 777
MD.L = [103.85,103.85,103.84]
MD.last = last
try:
MD.V = util.pickle_load('Vs.pkl')
MD.W = util.pickle_load('Ws.pkl')
MD.VW = util.pickle_load('VWs.pkl')
except:
MD.V = M.cord_auto(['V'])
MD.W = M.cord_auto(['W'])
MD.VW = M.cord_auto(['V','W'])
util.pickle_dump(MD.V,'Vs.pkl')
util.pickle_dump(MD.W,'Ws.pkl')
util.pickle_dump(MD.VW,'VWs.pkl')
CV = util.pickle_load('CV.pkl')
CW = util.pickle_load('CW.pkl')
try:
print 'attempting to load DW, DV'
DV = util.pickle_load('DV_s.pkl')
DW = util.pickle_load('DW_s.pkl')
plot_def = util.pickle_load('plot_def_s.pkl')
except:
print 'finding the defects'
DV, DW, plot_def = find_defects_mod(CW,CV,MD.VW,MD.V,MD.W,MD.L,n_finish=MD.last-1,n_start=0,delta=1)
plots = util.pickle_load('plot_def.pkl')
for index,k in enumerate(x):
Vn = []
def find_defects_mod(CV,CW,VW,V,W,L,n_finish=1,n_start=0,delta=20,filters=0.2):
from MD.analysis.nearest_neighbor import ws_neighbors_point
from MD.analysis.nearest_neighbor import close_neighbors_point
#######
debug = False
x = np.arange(n_start,n_finish,delta)
lattice = []
for i in range(CV.shape[0]):
lattice.append(int(points.dist(CV[0],CV[i],L)[0]))
for i in range(CW.shape[0]):
lattice.append(int(points.dist(CV[0],CW[i],L)[0]))
points.unique(lattice)
lattice.sort()
print lattice
rmin = lattice[1] / 2.0
rmax = lattice[2] / 2.0 +1
#for interstitial
s = min(W.shape[1],V.shape[1])
#for vacancy
#s = max(W.shape[1],V.shape[1])
DW = np.zeros((len(x),CW.shape[0]))
DV = np.zeros((len(x),CV.shape[0]))
vac_count = np.zeros((len(x),1))
int_count = np.zeros((len(x),1))
fid = open('defects.txt','w')
master = [[],[]]
particle_frame = []
for index,k in enumerate(x):
print 'frame',k
# Identify the points on the bcc Lattice which belong to A and B type
#lets look at one point first
# Assign each point to its place on the lattice
#find the closest point
#####################
N = []
N_V = []
N_W = []
Vn = []
Wn = []
for i in V[k]:
if abs(i[0]) < L[0]:
Vn.append(i)
for i in W[k]:
if abs(i[0]) < L[0]:
Wn.append(i)
print 'Wn',len(Wn)
print 'Vn',len(Vn)
particle_frame.append(len(Wn)+len(Vn))
Wn = np.array(Wn)
Vn = np.array(Vn)
for i in range(CV.shape[0]):
N = ws_neighbors_point(Vn,CV[i],L,i,rmin=rmin,rmax=rmax)[0]
N_V.extend(N)
num = len(N)
if num == 0:
N2 = ws_neighbors_point(Wn,CV[i],L,i,rmin=rmin,rmax=rmax)[0]
N_W.extend(N2)
num = -len(N2)
DV[index][i] = num
###########################
for i in range(CW.shape[0]):
N = ws_neighbors_point(Wn,CW[i],L,i+W.shape[1],rmin=rmin,rmax=rmax)[0]
N_W.extend(N)
num = len(N)
if num == 0:
N2 = ws_neighbors_point(Vn,CW[i],L,i+V.shape[1],rmin=rmin,rmax=rmax)[0]
N_V.extend(N2)
num = -len(N2)
DW[index][i] = num
#find the atoms that haven't been placed on the lattice yet
IV = points.difference(range(Vn.shape[0]),N_V)
IW = points.difference(range(Wn.shape[0]),N_W)
##
if debug:
print 'atoms not added listed after first sorting'
print IV, IW
print DW[index]
print DV[index]
for i in IV:
#find closest lattice point
nw, dw = close_neighbors_point(CW,Vn[i],L)
nv, dv = close_neighbors_point(CV,Vn[i],L)
if dw <= dv:
#check to see if there is already an atom at that point
if DW[index][nw] == 1 or DW[index][nw] == -1:
if DV[index][nv] == 0:
DV[index][nv] = 1
N_V.extend([i])
else:
DW[index][nw] = -2
N_V.extend([i])
if DW[index][nw] == 0:
DW[index][nw] = -1
N_V.extend([i])
#check to see if there is already an atom at that point
else:
if DV[index][nv] == 1 or DV[index][nv] == -1:
#if there isn't one at the other point add it
if DW[index][nw] == 0:
DW[index][nw] = -1
N_V.extend([i])
else:
if DV[index][nv] == 1:
DV[index][nv] = 2
if DV[index][nv] == -1:
DV[index][nv] = -2
N_V.extend([i])
if DV[index][nv] == 0:
DV[index][nv] = 1
N_V.extend([i])
for i in IW:
nw, dw = close_neighbors_point(CW,Wn[i],L)
nv, dv = close_neighbors_point(CV,Wn[i],L)
if dv <= dw:
if DV[index][nv] == 1 or DV[index][nv] == -1:
if DW[index][nw] == 0:
DW[index][nw] = 1
N_W.extend([i])
else:
DV[index][nv] = -2
N_W.extend([i])
if DV[index][nv] == 0:
DV[index][nv] = -1
N_W.extend([i])
else:
if DW[index][nw] == 1 or DW[index][nw] == -1:
if DV[index][nv] == 0:
DV[index][nv] = -1
N_W.extend([i])
else:
DW[index][nw] = 2
N_W.extend([i])
if DW[index][nw] == 0:
DW[index][nw] = 1
N_W.extend([i])
#find the atoms that haven't been placed on the lattice yet
IV = points.difference(range(Vn.shape[0]),N_V)
IW = points.difference(range(Wn.shape[0]),N_W)
##
if debug:
print 'atoms not added list for debugging'
print IV, IW
print DW[index]
print DV[index]
print 'Defect list for lattice'
#print out the vacency, substitutions
def out_defect(A, index, fid, def_list, C=0):
for i in range(A.shape[1]):
if A[index][i] == 0:
pr = 'vacecy at '+ str(i+C)+ '\n'
try:
def_list[0].extend(i+C)
except:
def_list[0].append(i+C)
if debug:
print pr
fid.write(pr)
if A[index][i] == -1:
pr = 'substitution ' + str(i+C)+ '\n'
if debug:
print pr
fid.write(pr)
if A[index][i] == -2:
pr = 'interstitial ' + str(i + C)+ '\n'
try:
def_list[1].extend(i+C)
except:
def_list[1].append(i+C)
if debug:
print pr
fid.write(pr)
if A[index][i] == 2:
pr = 'interstitial ' + str(i + C)+ '\n'
try:
def_list[1].extend(i+C)
except:
def_list[1].append(i+C)
if debug:
print pr
fid.write(pr)
frame = 'Frame ' + str(k) + '\n'
fid.write(frame)
def_list = [[],[]]
out_defect(DV, index, fid, def_list)
out_defect(DW, index, fid, def_list, C = DV.shape[1])
if len(points.difference(def_list[0], master[0])) != 0:
vac_count[index] += len(points.difference(def_list[1],master[1]))
master[0] = def_list[0]
if len(points.difference(def_list[1],master[1])) != 0:
int_count[index] += len(points.difference(def_list[1],master[1]))
master[1] = def_list[1]
#find the atoms that haven't been placed on the lattice yet
IV = points.difference(range(V.shape[1]),N_V)
IW = points.difference(range(W.shape[1]),N_W)
# Identify the defects surrounding each point
#The total number of frames we are going to look at
# Find the number of defects in each frame
count = 0
substitutions = []
vacancies = []
intersticial = []
def count_def(A,check):
count = 0
for i in A:
if i == check:
count +=1
return count
def count_ldef(A,check):
count = 0
for i in A:
if i < check:
count +=1
return count
def count_adef(A,check):
count = 0
for i in A:
if abs(i) == check:
count +=1
return count
for k in range(DW.shape[0]):
#find the points that are nearest neighbor that are different
substitutions.append(count_ldef(DW[k],0)+count_ldef(DV[k],0))
vacancies.append(count_def(DW[k],0)+count_def(DV[k],0))
intersticial.append(count_adef(DW[k],2.0)+count_adef(DV[k],2.0))
print 'substitions'
print substitutions
print 'vacancies'
print vacancies
print 'interstitials'
print intersticial
util.pickle_dump(DV,'DV_s.pkl')
util.pickle_dump(DW,'DW_s.pkl')
util.pickle_dump([substitutions, vacancies, intersticial, x],'plot_def_s.pkl')
pyplot.plot3(x, substitutions, x, particle_frame, x, intersticial,
label1='substitutions',label2='number of particles',label3='intersticial',
save='defects_per_frame_surface',showleg=True)
#pyplot.plot(x, vac_count, save='defect_vac_diffusion_count')
#pyplot.plot(x, int_count, save='defect_int_diffusion_count')
return DV, DW, [substitutions, vacancies, intersticial, x]