def atomicMobility():
multip = 1
fnameOptions = 'options/' + systemName + '.json'
o = options(fnameOptions)
uo = universalOptions()
folder = o.props['folders'][0][:-6:1]
pdStart = parseData(folder + 'co.' + str(50000) + '.data')
pdFinish = parseData(folder + 'co.' + str(2500000) + '.data')
masses = pdStart.masses
atomsFullStart = pdStart.atomsFull
atomsFullFinish = pdFinish.atomsFull
lx = pdStart.xhi - pdStart.xlo
ly = pdStart.yhi - pdStart.ylo
lz = pdStart.zhi - pdStart.zlo
mobilityProfile = [[0, 0] for i in range(300 * multip)]
for i in range(len(atomsFullStart)):
if masses[atomsFullStart[i][2] - 1] < 5:
continue
z = int(100 + multip * atomsFullStart[i][6])
dx = min(abs(atomsFullFinish[i][4] - atomsFullStart[i][4]),
lx - abs(atomsFullFinish[i][4] - atomsFullStart[i][4]))
dy = min(abs(atomsFullFinish[i][5] - atomsFullStart[i][5]),
ly - abs(atomsFullFinish[i][5] - atomsFullStart[i][5]))
dz = min(abs(atomsFullFinish[i][6] - atomsFullStart[i][6]),
lz - abs(atomsFullFinish[i][6] - atomsFullStart[i][6]))
mobilityProfile[z][0] += 1
mobilityProfile[z][1] += (dx**2 + dy**2 + dz**2)**0.5
f = open('log', 'w')
for i in range(len(mobilityProfile)):
if mobilityProfile[i][0] != 0:
f.write(
str((i - 100) / multip) + ' ' + str(mobilityProfile[i][0]) +
' ' + str(mobilityProfile[i][1] / mobilityProfile[i][0]) +
'\n')
def main1A7L():
step = 100
filesNum = int(2500000 / step) + 1
fnameOptions = 'options/' + systemName + '.json'
o = options(fnameOptions)
uo = universalOptions()
folder = o.props['folders'][folderNum]
f = open('log', 'w')
f.write(folder + '\n')
f.write('LayerNum Period Magnitude Error\n')
lx = o.props['xhi'] - o.props['xlo']
ly = o.props['yhi'] - o.props['ylo']
lz = o.props['zhi'] - o.props['zlo']
pressOneStep = [0 for j in range(uo.multip * uo.bigNumber)]
pressures = []
for i in range(filesNum):
print(i)
fname = folder + 'ALLstress.' + str(i * step)
pd = parseDump(fname)
stp = stressToPressure(pd.stresses, lx, ly, lz)
stp.pres1A()
pressOneStep7L = [0 for i in range(500)]
for i in range(59, len(pressOneStep)):
pressOneStep7L[int((i - 59) / 4.5)] += stp.pressOneStep[i]
pressures.append(pressOneStep7L)
for k in range(15):
period = len(pressures)
for layerNum in range(len(pressures[0])):
press = []
for step in range(len(pressures)):
press.append(pressures[step][layerNum] / 4.5)
pressTmp = []
for step in range(len(press)):
pressTmp.append(press[step])
a = appro(pressTmp)
a.error()
if a.magnitude != 0:
f.write(
str(layerNum) + ' ' + str(period) + ' ' +
str(a.magnitude) + ' +- ' + str(a.error) + '\n')
for step in range(len(pressures) - 1):
for layer in range(len(pressures[step])):
pressures[step][layer] += pressures[step + 1][layer]
pressures[step][layer] /= 2
firstelement = pressures[0]
endelement = pressures[-1]
pressures = pressures[1:-2:2]
pressures.insert(0, firstelement)
pressures.append(endelement)
k += 1
def modifierDistribution(systemName='mixed'):
"""Change systemName, ParentFolders and Folders and start and end"""
segregatedParentFolder = (
"/media/anton/Seagate Expansion Drive/Article-MMT/" +
"Cluster calculations for article/1st conf/" + "segregated/500K/")
segregatedFolders = [
"1332494 - 2.5ns/", "1338014 - 2.5ns more/", "1343289 - 2.5ns more/",
"1352547 - 2.5 ns more/", "1388142 - 2.5 ns more/", "1404644/"
]
mixedParentFolder = ("/media/anton/Seagate Expansion Drive/Article-MMT/" +
"Cluster calculations for article/1st conf/" +
"mixed ok/500K/")
mixedFolders = [
"all/", "1388141/", "1393565/", "1397381/", "1400005/", "1404643/"
]
fnameOptions = 'options/' + systemName + '.json'
o = options(fnameOptions)
uo = universalOptions()
folder = o.props['folders'][len(o.props['folders']) - 1][:-6:1]
[top, bottom] = returnCalyRanges(systemName)
filenum = 0
f = open('log', 'w')
for j in range(len(mixedFolders)):
end = 51
start = 1
if j == 0:
end = 24
if j == 2:
end = 50
for i in range(start, end):
filenum += 1
fname = (mixedParentFolder + mixedFolders[j] + 'co.' +
str(i * 50000) + '.data')
pd = parseData(fname)
lz = pd.zhi - pd.zlo
atomsFull = pd.atomsFull
distanceSum = 0
atomsNum = 0
for atom in atomsFull:
if definePhase(atom[0], systemName) == 2:
atomsNum += 1
distance = min((atom[6] - top)**2,
(lz + bottom - atom[6])**2)
distanceSum += distance
f.write(
str(filenum) + ' ' + str((distanceSum / atomsNum)**0.5) + '\n')
def densityProfileMass(folderNum=1, systemName="mixed"):
"""Define the folder number, range for files"""
fnameOptions = 'options/' + systemName + '.json'
o = options(fnameOptions)
uo = universalOptions()
uo.multip = 10
folder = ('/media/anton/Seagate Expansion Drive/Article-MMT/Cluster' +
' calculations for article/1st conf/mixed ok/300K/' +
'npt after 6th cycle/1440224/')
densityProfile = [[0, 0, 0, 0] for i in range(uo.multip * uo.bigNumber)]
for i in range(1, 51):
print(i)
fname = folder + 'co.' + str(i * 50000) + '.data'
pd = parseData(fname)
masses = pd.masses
atomsFull = pd.atomsFull
lx = pd.xhi - pd.xlo
ly = pd.yhi - pd.ylo
for atom in atomsFull:
atomNumber = atom[0]
#z = int(9 + (atom[6] - int(pd.zlo)) * uo.multip)
z = int((atom[6] + 150) * uo.multip)
atomType = atom[2]
mass = masses[atomType - 1]
phase = definePhase(atomNumber, systemName)
densityProfile[z][
0] += mass * 1.66 # coefficient from units conversion
densityProfile[z][phase] += mass * 1.66
f = open('log', 'w')
for i in range(len(densityProfile)):
if (densityProfile[i][0] > 0):
f.write(
str(i / uo.multip - 150) + ' ' +
str(densityProfile[i][0] / 50 / (lx * ly) * uo.multip) + ' ' +
str(densityProfile[i][1] / 50 / (lx * ly) * uo.multip) + ' ' +
str(densityProfile[i][2] / 50 / (lx * ly) * uo.multip) + ' ' +
str(densityProfile[i][3] / 50 / (lx * ly) * uo.multip) + '\n')
def __init__(self, stresses, lx, ly, lz):
self.uo = universalOptions()
self.stresses = stresses
self.lx = lx
self.ly = ly
self.lz = lz
def rgyr(folderNum=6, systemName="10x20"):
fnameOptions = 'options/' + systemName + '.json'
o = options(fnameOptions)
uo = universalOptions()
r_xVSz = [[0, 0] for i in range(1500)]
r_yVSz = [[0, 0] for i in range(1500)]
r_zVSz = [[0, 0] for i in range(1500)]
for i in range(len(o.props['folders'])):
print(i)
folder = o.props['folders'][i][:-6:1]
fname = folder + 'co.' + str(1 * 50000) + '.data'
pd = parseData(fname)
masses = pd.masses
atomsFull = pd.atomsFull
lx = pd.xhi - pd.xlo
ly = pd.yhi - pd.ylo
lz = pd.zhi - pd.zlo
for chainNum in range(int(o.props['polymerChainsNum'])):
(moleculeStart,
moleculeEnd) = computeChainRange(chainNum, systemName)
groupOfAtoms = copy.deepcopy(
atomsFull[moleculeStart:moleculeEnd:1])
groupOfAtoms = makeMolecule(groupOfAtoms, lx, ly, lz)
(rx, ry, rz) = computeCM(groupOfAtoms)
outputXYZ(groupOfAtoms,
'pics/' + systemName + str(chainNum) + '.xyz')
(rGyr_x, rGyr_y, rGyr_z, ex, ey, ez) = computeRgyr(groupOfAtoms)
z = int((550 + rz) * uo.multip)
r_xVSz[z][0] += 1
r_xVSz[z][1] += rGyr_x
r_yVSz[z][0] += 1
r_yVSz[z][1] += rGyr_y
r_zVSz[z][0] += 1
r_zVSz[z][1] += rGyr_z
f = open('log', 'w')
for i in range(len(r_zVSz)):
if r_zVSz[i][0] != 0:
f.write(
str(i / uo.multip - 150) + ' ' +
str(r_zVSz[i][1] / r_zVSz[i][0]) + '\n')
r_x_mean = 0
valuesNum = 0
for i in range(len(r_xVSz)):
if r_xVSz[i][0] != 0:
r_x_mean += r_xVSz[i][1]
valuesNum += r_xVSz[i][0]
print(r_x_mean / valuesNum)
r_y_mean = 0
valuesNum = 0
for i in range(len(r_yVSz)):
if r_yVSz[i][0] != 0:
r_y_mean += r_yVSz[i][1]
valuesNum += r_yVSz[i][0]
print(r_y_mean / valuesNum)
r_z_mean = 0
valuesNum = 0
for i in range(len(r_zVSz)):
if r_zVSz[i][0] != 0:
r_z_mean += r_zVSz[i][1]
valuesNum += r_zVSz[i][0]
print(r_z_mean / valuesNum)
print(valuesNum)
def anglesOrientation(systemName="10x20"):
multip = 1
fnameOptions = 'options/' + systemName + '.json'
o = options(fnameOptions)
uo = universalOptions()
folder = o.props['folders'][0][:-6:1]
orientations = [[0, 0] for i in range(500)]
end = 51
if systemName == '5x20':
end = 50
if systemName == '10x20':
end = 51
for i in range(1, end):
pd = parseData(folder + 'co.' + str(i * 50000) + '.data')
lx = pd.xhi - pd.xlo
ly = pd.yhi - pd.ylo
lz = pd.zhi - pd.zlo
atomsFull = pd.atomsFull
angles = pd.angles
for angle in angles:
if systemName == 'mixed':
if angle[1] not in [
1, 2, 3, 7, 9, 10, 16, 19, 20, 21, 22, 25, 26, 28, 29
]:
continue
elif systemName == 'segregated':
if angle[1] not in [
1, 2, 3, 7, 9, 10, 16, 19, 20, 21, 22, 25, 26, 28, 29
]:
continue
elif systemName == 'long':
if angle[1] not in [
1, 2, 5, 7, 8, 9, 10, 13, 14, 16, 20, 22, 23, 24, 26
]:
continue
elif systemName == '5x20':
if angle[1] not in [
1, 2, 3, 7, 9, 10, 16, 19, 20, 21, 22, 25, 26, 28, 29
]:
continue
elif systemName == '10x20':
if angle[1] not in [
1, 2, 3, 7, 9, 10, 16, 19, 20, 21, 22, 25, 26, 28, 29
]:
continue
atomOne = atomsFull[angle[2] - 1]
atomMid = atomsFull[angle[3] - 1]
atomTwo = atomsFull[angle[4] - 1]
bondx = min(abs(atomOne[4] - atomTwo[4]),
lx - abs(atomOne[4] - atomTwo[4]))
bondy = min(abs(atomOne[5] - atomTwo[5]),
lx - abs(atomOne[5] - atomTwo[5]))
bondz = min(abs(atomOne[6] - atomTwo[6]),
lx - abs(atomOne[6] - atomTwo[6]))
cosTheta = bondz / (bondx**2 + bondy**2 + bondz**2)**0.5
parameter = (3 * cosTheta**2 - 1) / 2
z = int((100 + atomMid[6]) * multip)
orientations[z][0] += 1
orientations[z][1] += parameter
f = open('log', 'w')
for i in range(len(orientations)):
if orientations[i][0] != 0:
f.write(
str(i / multip - 100) + ' ' +
str(orientations[i][1] / orientations[i][0]) + ' ' +
str(orientations[i][0]) + '\n')
def bondsOrientation(systemName="mixed"):
multip = 1
fnameOptions = 'options/' + systemName + '.json'
o = options(fnameOptions)
uo = universalOptions()
orientations = [[0, 0] for i in range(1500)]
end = 51
if systemName == '5x20':
end = 50
if systemName == '10x20':
end = 51
if systemName == 'long':
folder = (
'/media/anton/Seagate Expansion Drive/Article-MMT/Cluster' +
' calculations for article/BiggerSystems/Comp/1chain (long)/' +
'1845502 - wiggle1/')
elif systemName == 'mixed':
folder = ('/media/anton/Seagate Expansion Drive/Article-MMT/Cluster' +
' calculations for article/1st conf/mixed ok/300K/' +
'npt after 6th cycle/1440224/')
for i in range(1, 51):
print(i)
pd = parseData(folder + 'co.' + str(i * 50000) + '.data')
lx = pd.xhi - pd.xlo
ly = pd.yhi - pd.ylo
lz = pd.zhi - pd.zlo
atomsFull = pd.atomsFull
bonds = pd.bonds
for bond in bonds:
if systemName == 'mixed':
if bond[1] not in [3, 4, 5, 7, 8, 11, 12, 13, 14, 16]:
#if bond[1] not in [5, 8]:
continue
elif systemName == 'segregated':
if bond[1] not in [3, 4, 5, 7, 8, 11, 12, 13, 14, 16]:
continue
elif systemName == 'long':
if bond[1] not in [4, 5, 6, 7, 8, 9, 11, 12, 14, 15]:
continue
elif systemName == '5x20':
if bond[1] not in [3, 4, 5, 7, 8, 11, 12, 13, 14, 16]:
continue
elif systemName == '10x20':
if bond[1] not in [3, 4, 5, 7, 8, 11, 12, 13, 14, 16]:
continue
atomOne = atomsFull[bond[2] - 1]
atomTwo = atomsFull[bond[3] - 1]
bondx = min(abs(atomOne[4] - atomTwo[4]),
abs(lx - abs(atomOne[4] - atomTwo[4])))
bondy = min(abs(atomOne[5] - atomTwo[5]),
abs(ly - abs(atomOne[5] - atomTwo[5])))
bondz = min(abs(atomOne[6] - atomTwo[6]),
abs(lz - abs(atomOne[6] - atomTwo[6])))
if bondx >= 3 or bondy >= 3 or bondz >= 3:
print("Long bond ", bondx, bondy, bondz)
cosTheta = bondz / ((bondx**2 + bondy**2 + bondz**2)**0.5)
parameter = (3 * cosTheta**2 - 1) / 2
z = int((250 + atomOne[6]) * multip)
orientations[z][0] += 1
orientations[z][1] += parameter
f = open('log', 'w')
for i in range(len(orientations)):
if orientations[i][0] != 0:
f.write(
str(i / multip - 250) + ' ' +
str(orientations[i][1] / orientations[i][0]) + ' ' +
str(orientations[i][0]) + '\n')
def polymerChainsMobility():
fnameOptions = 'options/' + systemName + '.json'
o = options(fnameOptions)
uo = universalOptions()
folder = o.props['folders'][len(o.props['folders']) - 1][:-6:1]
cms = [[] for i in range(int(o.props['polymerChainsNum']))]
#cms[molecule][filenum] = [x, y, z]
for i in range(1, 51):
print(i)
fname = folder + 'co.' + str(i * 50000) + '.data'
pd = parseData(fname)
masses = pd.masses
atomsFull = pd.atomsFull
lx = pd.xhi - pd.xlo
ly = pd.yhi - pd.ylo
lz = pd.zhi - pd.zlo
for chainNum in range(int(o.props['polymerChainsNum'])):
(moleculeStart,
moleculeEnd) = computeChainRange(chainNum, systemName)
groupOfAtoms = copy.deepcopy(
atomsFull[moleculeStart:moleculeEnd:1])
groupOfAtoms = makeMolecule(groupOfAtoms, lx, ly, lz)
(x_cm, y_cm, z_cm) = computeCM(groupOfAtoms)
cms[chainNum].append([x_cm, y_cm, z_cm])
for i in range(49):
xOld = cms[1][i][0]
yOld = cms[1][i][1]
zOld = cms[1][i][2]
xNew = cms[1][i + 1][0]
yNew = cms[1][i + 1][1]
zNew = cms[1][i + 1][2]
xMin = 0
yMin = 0
zMin = 0
rMin = 10000
for x in [-1, 0, 1]:
xNewTmp = xNew + x * lx
r = xNewTmp - xOld
if r < rMin:
rMin = r
xMin = x
rMin = 10000
for y in [-1, 0, 1]:
yNewTmp = yNew + y * ly
r = yNewTmp - yOld
if r < rMin:
rMin = r
yMin = y
rMin = 10000
for z in [-1, 0, 1]:
zNewTmp = zNew + z * lz
r = zNewTmp - zOld
if r < rMin:
rMin = r
zMin = z
xNew += x * lx
yNew += y * ly
zNew += z * lz
deltaCM = 0
for i in range(int(o.props['polymerChainsNum'])):
deltaCM += (cms[i][49][0] - cms[i][0][0])**2
deltaCM += (cms[i][49][1] - cms[i][0][1])**2
deltaCM += (cms[i][49][2] - cms[i][0][2])**2
deltaCM = deltaCM**0.5
deltaCM /= int(o.props['polymerChainsNum'])
print(deltaCM)