def animate():
##FROM DCD
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()
Z = util.pickle_load('Zbound.pkl')
VW = util.pickle_load('VW.pkl')
animate_script = open('animate/animate.tcl','w')
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 range(50,100):
fid = open('animate/square%i.tcl'%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,c,v1,v2,v3,color[int(A[i])])
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_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 run_colored(frame=1):
##FROM DCD
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
#V_index = M.get_index(['V'])
#W_index = M.get_index(['W'])
##
#Z = util.pickle_load('Z.pkl')
#VW = util.pickle_load('VW.pkl')
##
#k = last
#FROM XYZ
VW,Z,VW_name = read_xyz()
fid = open('square%i.tcl'%frame,'w')
#set x to be the particles you wish to choose
#x = np.array([47190, 77220, 72215, 80795, 42185, 17875, 72930, 52910,
# 67925])
#index 47190 77220 72215 80795 42185 17875 72930 52910 67925
#x = x/715
#print x
#x = [1,2,3,4,5]
#for i in x:
A = read_color_index()
for i in range(len(VW)):
c = VW[i]
v1 = Z[i*6] - c
v2 = Z[i*6+2] - c
v3 = Z[i*6+4] - c
#v1 = Z[i*6] - c
#v2 = Z[i*6+1] - c
#v3 = Z[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[A[i]])
fid.close()
