def createXYZFile(fp, model, atomsIndexes, xyzFile, options):
"""
Function utilizes frames, model and atomsIndexes to create xyzFile
"""
startTime = time()
while True: # loop over trajectory
xyzFrame = XYZFrame()
xyzFrame.comment = "%.3f,%.3f,%.3f" % (
model.box[0][0], model.box[1][1], model.box[2][2])
#comment = boxSize
frame = readXTCFrame(fp)
if not frame:
break # end of trajectory or error
model.update(frame) # update the model data with coords, box
for atomIndex in atomsIndexes:
model.atoms[atomIndex - 1].x[2] = 0.
xyzAtom = XYZAtom(model.atoms[atomIndex - 1].resname,
*model.atoms[atomIndex - 1].x)
xyzFrame.atoms.append(xyzAtom)
xyzFile.addFrame(xyzFrame)
if options.verbose:
delLine()
print "time = %g step = %g" % (frame['time'], frame['step']),
xyzFile.save()
print "Done. Execution time=%f" % (time() - startTime)
def main(argv = None):
options = parseCommandLine()
xyzFile, datFile = openFiles(options)
frame = xyzFile.nextFrame()
frameCounter= 1
binSize = 0.02
boxSize = max([vectorLength(v) for v in frame.boxVectors])
hist = calcHist(frame, propagateThroughPBC(frame.atoms, frame.boxVectors), binSize, boxSize, options)
frame = xyzFile.nextFrame()
startTime = time()
while not frame is None:
if options.verbose:
delLine()
print frameCounter,
newHist = calcHist(frame, propagateThroughPBC(frame.atoms, frame.boxVectors), binSize, boxSize, options)
for i in range(len(hist)):
hist[i] += newHist[i]
frameCounter += 1
frame = xyzFile.nextFrame()
for i in range(len(hist)):
datFile.write('%f %f\n' %(i * binSize, hist[i] / float(frameCounter)))
datFile.close()
print time() - startTime
def createXYZFile(fp, model, atomsIndexes, xyzFile, options):
"""
Function utilizes frames, model and atomsIndexes to create xyzFile
"""
startTime = time()
while True: # loop over trajectory
xyzFrame = XYZFrame()
xyzFrame.comment = "%.3f,%.3f,%.3f" % (model.box[0][0],
model.box[1][1], model.box[2][2])
#comment = boxSize
frame = readXTCFrame(fp)
if not frame:
break # end of trajectory or error
model.update(frame) # update the model data with coords, box
for atomIndex in atomsIndexes:
model.atoms[atomIndex - 1].x[2] = 0.
xyzAtom = XYZAtom(model.atoms[atomIndex - 1].resname,
*model.atoms[atomIndex - 1].x)
xyzFrame.atoms.append(xyzAtom)
xyzFile.addFrame(xyzFrame)
if options.verbose:
delLine()
print "time = %g step = %g" % (frame['time'],frame['step']),
xyzFile.save()
print "Done. Execution time=%f" % (time() - startTime)
def main(argv=None):
options = parseCommandLine()
xyzFile, datFile = openFiles(options)
frame = xyzFile.nextFrame()
frameCounter = 1
binSize = 0.02
boxSize = max([vectorLength(v) for v in frame.boxVectors])
hist = calcHist(frame, propagateThroughPBC(frame.atoms, frame.boxVectors),
binSize, boxSize, options)
frame = xyzFile.nextFrame()
startTime = time()
while not frame is None:
if options.verbose:
delLine()
print frameCounter,
newHist = calcHist(frame,
propagateThroughPBC(frame.atoms, frame.boxVectors),
binSize, boxSize, options)
for i in range(len(hist)):
hist[i] += newHist[i]
frameCounter += 1
frame = xyzFile.nextFrame()
for i in range(len(hist)):
datFile.write('%f %f\n' % (i * binSize, hist[i] / float(frameCounter)))
datFile.close()
print time() - startTime
def main():
options = parseCommandLine()
avgArea = getAvgSize(options.inXyzFilename)
print avgArea
lattBoxSize = ((2 * avgArea) / (3**(1/2.)) )**(1/2.) #area of parallelogram
print lattBoxSize
inFile = XYZFile(options.inXyzFilename)
latt = HexLattice(int(options.lattSize), (0,0), (lattBoxSize, lattBoxSize))
lattProj = NearestNeighborLatticeProj(inFile, latt)
clearFile(options.outXyzFilename)
outFile = XYZFile(options.outXyzFilename)
i = 0
startTime = time()
errors = []
#lattProj = LatticeProjectorSimple(inFile, latt)
while True:
if options.verbose:
delLine()
if i > 0: midTime = (time() - startTime) / i
else: midTime = 0
print i, "Avg time per frame: ", midTime,
sys.stdout.flush()
projLattice = lattProj.next()
if projLattice is None:
break
frame = projLattice.frame
if options.reference:
frame.atoms.extend(projLattice.refFrame.atoms)
symb = "DOPC"
length = len(frame.atoms)
num = 0
for atom in frame.atoms:
if atom.symbol == symb: num += 1
for j in range(15000 - num):
frame.atoms.append(XYZAtom("DOPC", -10., 0., 0.))
for j in range(15000 - (length - num)):
frame.atoms.append(XYZAtom("DPPC", -10., 0., 0.))
atoms = sorted(frame.atoms, key=lambda w: w.symbol)
frame.atoms = atoms
#frame.atoms = []#sorted(frame.atoms, key=lambda w: w.symbol)
i += 1
err = (i, max(projLattice.errors), sum(projLattice.errors) / len(projLattice.errors))
errors.append("{0} {1} {2}".format(*err))
outFile.addFrame(frame)
if i > 10: break
if not options.errFile is None:
with open(options.errFile, 'w') as errFile:
errFile.write('\n'.join(errors))
outFile.save()
if options.verbose:
print "Done. Execution time=%f" % (time() - startTime)
def main(argv=None):
global options
options = parseCommandLine()
xyzFile, xyzOutputFile = openFiles(options)
frame = xyzFile.nextFrame()
startTime = time()
frameCounter = 0
neighborPairs = {}
while not frame is None:
findNeighborPairs( frame, frameCounter, neighborPairs )
clustered = findClusteredAtoms( neighborPairs, frameCounter, int( options.framesThr ) )
if options.verbose:
delLine()
print frameCounter,
#l = neighborPairs.keys()
#l.sort()
#print "Neighbor pairs", [ (str(i) + ":" + str(neighborPairs[i])) for i in l ]
#print "Clusters", identifyClusters( neighborPairs, frameCounter, 1, frame )
#print "Clustered atoms", findClusteredAtoms( neighborPairs, frameCounter, 1 )
frameCounter += 1
newFrame = XYZFrame()
clusteredAtoms = []
interAtoms = []
nonClustAtoms = []
if ( len(clustered["clustered"]) + len(clustered["interchanging"]) > 0
):
print frameCounter, ( len(clustered["clustered"]) +
len(clustered["interchanging"])) / float(len(frame.atoms))
for atomInd in range( len( frame.atoms ) ):
if atomInd in clustered['clustered']:
clusteredAtoms.append( XYZAtom( "Clustered", *frame.atoms[atomInd].x0 ) )
elif atomInd in clustered['interchanging']:
interAtoms.append( XYZAtom( "Inter", *frame.atoms[atomInd].x0 ) )
else:
nonClustAtoms.append( XYZAtom( "NonCl", *frame.atoms[atomInd].x0 ) )
maxNum = 0
for i in range( maxNum - len( clusteredAtoms ) ):
clusteredAtoms.append( XYZAtom( "Clustered", 0, 0, 0, ) )
for i in range( maxNum - len( interAtoms ) ):
interAtoms.append( XYZAtom( "Inter", 0, 0, 0, ) )
for i in range( maxNum - len( nonClustAtoms ) ):
nonClustAtoms.append( XYZAtom( "Clustered", 0, 0, 0, ) )
newFrame.atoms = clusteredAtoms + interAtoms + nonClustAtoms
xyzOutputFile.addFrame( newFrame )
frame = xyzFile.nextFrame()
if options.verbose:
print "Execution time", time() - startTime
xyzOutputFile.save()
def main(argv=None):
options = parseCommandLine()
startTime = time()
begin = int( options.begin )
end = int( options.end )
clearFile( options.datFilename )
with open( options.datFilename, 'w' ) as output:
try:
interval = int( options.interval )
for frameCounter in range( begin, end, interval ):
if options.verbose:
delLine()
print frameCounter,
stdout.flush()
path = options.Filename + str( frameCounter ) + ".png" #TODO: png should be configurable
im = Image.open( path )
width, height = im.size
correctionFactor = ( float( width - height ) / height )
pixMap = im.load()
correction = correctionFactor
neighbors = [ ( 1, 0 ), ( 0, 1 ), ( -1, 0 ), ( 0, -1 ) ]
allPixelsCount = 0
similarPixelsCount = 0
for h in range( 1, height - 1 ):
for w in range( 1, height - 1 ):
neighbor = neighbors[ randint( 0, len( neighbors ) - 1 ) ]
x = int( w + correction )
y = h
nX = x + neighbor[ 0 ]
nY = y + neighbor[ 1 ]
if pixMap[ x, y ] - pixMap[ nX, nY ] < 35:
similarPixelsCount += 1
allPixelsCount += 1
correction += correctionFactor
fraction = float( similarPixelsCount ) / allPixelsCount
output.write( str( frameCounter ) + " " + str( fraction ) + "\n" )
except:
pass
if options.verbose:
print "Execution time", time() - startTime
def main():
options = parseCommandLine()
inFile = XYZFile(options.inXyzFilename)
clearFile(options.outDatFilename)
outFile = open(options.outDatFilename, 'w')
i = 0
startTime = time()
omegas = []
sumOmegas = 0L
calc = EnergyCalculator(inFile, R, T)
while True:
i += 1
if options.verbose:
delLine()
print i,
omega = calc.getNextEnergy(options.symbol)
if omega is None:
break
omega , sim, diff = omega
if omega > -10**4 and omega < 10**10:
omegas.append(omega)
sumOmegas += omega
outFile.write("%d %f %f %f \n" % (i, omega, sim, diff))
outFile.close()
if options.verbose:
print "Done. Execution time=%f" % (time() - startTime)
print "omegas" ,sumOmegas, (sum(omegas))
lenOmegas = len(omegas)
midOmega = (sum(omegas)/len(omegas))
print "Result omegaAB = %f" % midOmega
sd = 0
for omega in omegas:
sd += (midOmega - omega)**2
sd /= len(omegas)
sd **= (1./2.)
print "Standard deviation = %f" % sd
def main():
options = parseCommandLine()
inFile = XYZFile(options.inXyzFilename)
clearFile(options.outDatFilename)
outFile = open(options.outDatFilename, 'w')
i = 0
startTime = time()
omegas = []
sumOmegas = 0L
calc = EnergyCalculator(inFile, R, T)
while True:
i += 1
if options.verbose:
delLine()
print i,
omega = calc.getNextEnergy(options.symbol)
if omega is None:
break
omega, sim, diff = omega
if omega > -10**4 and omega < 10**10:
omegas.append(omega)
sumOmegas += omega
outFile.write("%d %f %f %f \n" % (i, omega, sim, diff))
outFile.close()
if options.verbose:
print "Done. Execution time=%f" % (time() - startTime)
print "omegas", sumOmegas, (sum(omegas))
lenOmegas = len(omegas)
midOmega = (sum(omegas) / len(omegas))
print "Result omegaAB = %f" % midOmega
sd = 0
for omega in omegas:
sd += (midOmega - omega)**2
sd /= len(omegas)
sd **= (1. / 2.)
print "Standard deviation = %f" % sd
def main():
options = parseCommandLine()
inFile = XYZFile(options.inXyzFilename)
clearFile(options.outDatFilename)
outXYZ = XYZFile(options.outDatFilename)
i = 0
startTime = time()
dist = 1
num = int(options.number)
while True:
frame = inFile.nextFrame()
if i == 0:
x, y = [], []
for atom in frame.atoms:
x.append(atom.x)
y.append(atom.y)
fieldX = ( max(x) - min(x) ) / 1.73
fieldY = max(y) - min(y)
newFrame = XYZFrame()
if frame is None:
break
for atom in frame.atoms:
newFrame.atoms.append(atom)
for k in range(num):
x0 = atom.x0
for coord in range(len(x0)):
x0[coord] += (random() - 0.4) * dist * 2
newFrame.atoms.append(XYZAtom(atom.symbol, *x0))
newFrame.comment = "%s, %s, 0.00" % (fieldX, fieldY)
outXYZ.addFrame(newFrame)
i += 1
if options.verbose:
delLine()
print i,
if options.verbose:
print "Done. Execution time=%f" % (time() - startTime)
def main():
options = parseCommandLine()
inFile = XYZFile(options.inXyzFilename)
clearFile(options.outDatFilename)
outXYZ = XYZFile(options.outDatFilename)
i = 0
startTime = time()
dist = 1
num = int(options.number)
while True:
frame = inFile.nextFrame()
if i == 0:
x, y = [], []
for atom in frame.atoms:
x.append(atom.x)
y.append(atom.y)
fieldX = (max(x) - min(x)) / 1.73
fieldY = max(y) - min(y)
newFrame = XYZFrame()
if frame is None:
break
for atom in frame.atoms:
newFrame.atoms.append(atom)
for k in range(num):
x0 = atom.x0
for coord in range(len(x0)):
x0[coord] += (random() - 0.4) * dist * 2
newFrame.atoms.append(XYZAtom(atom.symbol, *x0))
newFrame.comment = "%s, %s, 0.00" % (fieldX, fieldY)
outXYZ.addFrame(newFrame)
i += 1
if options.verbose:
delLine()
print i,
if options.verbose:
print "Done. Execution time=%f" % (time() - startTime)
def main():
options = parseCommandLine()
avgArea = getAvgSize(options.inXyzFilename)
print avgArea
lattBoxSize = ((2 * avgArea) / (3**(1 / 2.)))**(1 / 2.
) #area of parallelogram
print lattBoxSize
inFile = XYZFile(options.inXyzFilename)
latt = HexLattice(int(options.lattSize), (0, 0),
(lattBoxSize, lattBoxSize))
lattProj = NearestNeighborLatticeProj(inFile, latt)
clearFile(options.outXyzFilename)
outFile = XYZFile(options.outXyzFilename)
i = 0
startTime = time()
errors = []
#lattProj = LatticeProjectorSimple(inFile, latt)
while True:
if options.verbose:
delLine()
if i > 0: midTime = (time() - startTime) / i
else: midTime = 0
print i, "Avg time per frame: ", midTime,
sys.stdout.flush()
projLattice = lattProj.next()
if projLattice is None:
break
frame = projLattice.frame
if options.reference:
frame.atoms.extend(projLattice.refFrame.atoms)
symb = "DOPC"
length = len(frame.atoms)
num = 0
for atom in frame.atoms:
if atom.symbol == symb: num += 1
for j in range(15000 - num):
frame.atoms.append(XYZAtom("DOPC", -10., 0., 0.))
for j in range(15000 - (length - num)):
frame.atoms.append(XYZAtom("DPPC", -10., 0., 0.))
atoms = sorted(frame.atoms, key=lambda w: w.symbol)
frame.atoms = atoms
#frame.atoms = []#sorted(frame.atoms, key=lambda w: w.symbol)
i += 1
err = (i, max(projLattice.errors),
sum(projLattice.errors) / len(projLattice.errors))
errors.append("{0} {1} {2}".format(*err))
outFile.addFrame(frame)
if i > 10: break
if not options.errFile is None:
with open(options.errFile, 'w') as errFile:
errFile.write('\n'.join(errors))
outFile.save()
if options.verbose:
print "Done. Execution time=%f" % (time() - startTime)
def stdoutStep( options, i ):
""" Outputs progress information if options.verbose is set"""
if options.verbose:
delLine()
print i,
sys.stdout.flush()
def stdoutStep(options, i):
""" Outputs progress information if options.verbose is set"""
if options.verbose:
delLine()
print i,
sys.stdout.flush()