def main(argv=None):
options = parseCommandLine()
#===========================================================================
# opening files and so on
#===========================================================================
try:
model = Model().read(options.groFilename)
fp = openXTC(options.xtcFilename)
clearFile(options.xyzFilename)
xyzFile = XYZFile(options.xyzFilename)
except:
raise (InputError(options.xyzFilename,
"error while opening gro, xtc or xyz file"))
if not options.ndxFilename is None:
try:
ndxFile = IndexFile(fname=options.ndxFilename)
except:
raise (InputError("error while opening ndx file"))
atomsIndexes = []
for (_, atomList) in ndxFile.dic.items():
atomsIndexes += atomList
else:
atomsIndexes = range(1, len(model.atoms) + 1)
createXYZFile(fp, model, atomsIndexes, xyzFile, options)
def main(argv = None):
options = parseCommandLine()
#===========================================================================
# opening files and so on
#===========================================================================
try:
model = Model().read(options.groFilename)
fp = openXTC(options.xtcFilename)
clearFile(options.xyzFilename)
xyzFile = XYZFile(options.xyzFilename)
except:
raise(InputError(options.xyzFilename, "error while opening gro, xtc or xyz file"))
if not options.ndxFilename is None:
try:
ndxFile = IndexFile(fname = options.ndxFilename)
except:
raise(InputError("error while opening ndx file"))
atomsIndexes = []
for (_, atomList) in ndxFile.dic.items():
atomsIndexes += atomList
else:
atomsIndexes = range(1, len(model.atoms) + 1)
createXYZFile(fp, model, atomsIndexes, xyzFile, options)
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():
options = parseCommandLine()
symbols, atomNum = identifyAtomTypes(options.inXyzFilename, options)
print symbols
inFile = XYZFile(options.inXyzFilename)
clearFile(options.outPngFileTemp)
i = 0
startTime = time()
frame = inFile.nextFrame()
colours = [
(255, 255, 255) #white
,
(150, 150, 150) # grey
,
(0, 0, 0) # black
,
(150, 0, 0) # blue
,
(0, 150, 0) # green
]
sizeX, sizeY = 500, 500
countX, countY = 100, 100
while not frame is None:
stdoutStep(options, i)
i += 1
#prepare image
im = Image.new("RGBA", (countX, countY))
pix = im.load()
rescaleFrameToImage(frame, countX, countY)
for coords in product(range(countX), range(countY)):
pix[coords[0], coords[1]] = colours[symbols.index(
findClosestAtom(frame, coords))]
#print findClosestAtom( frame, coords), coords
#for atom in frame.atoms:
# print atom.x, atom.y
# pix[ int( atom.x ), int( atom.y )] = colours[-1]
im = im.resize((sizeX, sizeY), Image.ANTIALIAS)
im = im.transpose(Image.FLIP_TOP_BOTTOM)
#im.show()
im.save(options.outPngFileTemp + str(i) + ".png")
frame = inFile.nextFrame()
if options.verbose:
print "Done. Execution time=%f" % (time() - startTime)
def main():
options = parseCommandLine()
symbols, atomNum = identifyAtomTypes( options.inXyzFilename, options )
print symbols
inFile = XYZFile( options.inXyzFilename )
clearFile( options.outPngFileTemp )
i = 0
startTime = time()
frame = inFile.nextFrame()
colours = [
( 255, 255, 255 ) #white
, ( 150, 150, 150 ) # grey
, ( 0, 0, 0 ) # black
, ( 150, 0, 0) # blue
, ( 0, 150, 0 ) # green
]
sizeX, sizeY = 500, 500
countX, countY = 100, 100
while not frame is None:
stdoutStep( options, i )
i += 1
#prepare image
im = Image.new( "RGBA", ( countX, countY ) )
pix = im.load()
rescaleFrameToImage( frame, countX, countY )
for coords in product( range( countX ), range( countY ) ):
pix[coords[0], coords[1]] = colours[symbols.index( findClosestAtom( frame,
coords ) )]
#print findClosestAtom( frame, coords), coords
#for atom in frame.atoms:
# print atom.x, atom.y
# pix[ int( atom.x ), int( atom.y )] = colours[-1]
im = im.resize( ( sizeX, sizeY ), Image.ANTIALIAS )
im = im.transpose( Image.FLIP_TOP_BOTTOM )
#im.show()
im.save( options.outPngFileTemp + str(i) + ".png" )
frame = inFile.nextFrame()
if options.verbose:
print "Done. Execution time=%f" % (time() - startTime)
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 openFiles(options):
xyzFile = XYZFile(options.xyzFilename)
clearFile( options.xyzOutput )
outFile = XYZFile( options.xyzOutput )
return xyzFile, outFile