def repeteANI(ANIinfile, XVinfile, outfile, rep=[1, 1, 1]):
"""Generates a new ANI-file with cell repetitions"""
GeomList, Energy = SIO.ReadANIFile(ANIinfile)
initGeom = Geom(XVinfile)
newGeomList = []
for i in range(len(GeomList)):
geom = copy.deepcopy(GeomList[i])
geom.pbc = N.zeros((3, 3), N.float)
for i in range(3):
geom.repeteGeom(initGeom.pbc[i], rep=rep[i])
geom.pbc[i] = [rep[i] * x for x in initGeom.pbc[i]]
newGeomList.append(geom)
SIO.WriteANIFile(outfile, newGeomList, Energy)
def runNEB():
global general, steps, savedData
# Restarting?
fns=glob.glob('NEB_*/CGrun')
if len(fns)==0:
restart = False
elif len(fns)!=general.NNEB:
sys.exit('Number of NEB_??? directories %i does not match number of steps %i'%(len(fns), general.NNEB))
else:
restart=True
fns = ["NEB_%i/CGrun"%ii for ii in range(general.NNEB)]
fns = [general.initial+"/CGrun"]+fns+[general.final+"/CGrun"]
i, f = step(fns[0], False, 0), step(fns[general.NNEB+1], False, general.NNEB+1)
checkConst(i, f)
if restart:
try:
savedData.E, savedData.F, savedData.Fmax, savedData.geom, savedData.v=pickle.load(open('NEB_%i/savedData.pickle'%0, 'r'))
except:
savedData.E = []
savedData.F = []
savedData.geom = []
savedData.Fmax = []
savedData.v = N.zeros((general.NNEB+2, len(i.XVgeom.xyz), 3), N.float)
else:
savedData.E = []
savedData.F = []
savedData.geom = []
savedData.Fmax = []
savedData.v = N.zeros((general.NNEB+2, len(i.XVgeom.xyz), 3), N.float)
steps = [step(fn, restart, ii, initial=i, final=f) for ii, fn in enumerate(fns)]
done=False
while not done:
# Start calculations
for ii in steps:
ii.run()
nextstep=False
while not nextstep:
for ii in steps:
if not ii.checkDone():
break
else:
nextstep=True
if not nextstep:
time.sleep(30)
savedData.E += [[SIO.GetTotalEnergy(ii.dir+'/RUN.out') for ii in steps]]
savedData.geom += [[copy.copy(ii.XVgeom) for ii in steps]]
oldgeom = [copy.deepcopy(ii.XVgeom) for ii in steps]
for ii, jj in enumerate(steps[1:-1]):
jj.update(oldgeom[ii], oldgeom[ii+2])
# Write status
savedData.F += [[ii.Ftot for ii in steps]]
savedData.Fmax += [[ii.Fmax for ii in steps]]
for ii in range(1, len(steps)-1):
geoms = [savedData.geom[jj][ii] for jj in range(len(savedData.geom))]
Ftots = [savedData.Fmax[jj][ii] for jj in range(len(savedData.geom))]
Fs = [savedData.F[jj][ii] for jj in range(len(savedData.geom))]
SIO.WriteANIFile('NEB_%i/Steps.ANI'%(ii-1), geoms, Ftots)
SIO.WriteAXSFFiles('NEB_%i/Steps.XASF'%(ii-1), geoms, forces=Fs)
geoms = [ii.XVgeom for ii in steps]
Fmax = [ii.Fmax for ii in steps]
Ftot = [ii.Ftot for ii in steps]
SIO.WriteANIFile('NEB_%i/NextStep.ANI'%0, geoms, Fmax)
SIO.WriteAXSFFiles('NEB_%i/NextStep.XASF'%0, geoms, forces=Ftot)
done = True
for ii in steps:
done = done and ii.converged
pickle.dump((savedData.E, savedData.F, savedData.Fmax, savedData.geom, savedData.v),\
open('NEB_%i/savedData.pickle'%0, 'w'))
def runNEB():
global opts, steps, savedData
# Restarting?
fns = glob.glob('NEB_*/CGrun')
if len(fns) == 0:
restart = False
elif len(fns) != opts.NNEB:
sys.exit(
'Number of NEB_??? directories %i does not match number of steps %i'
% (len(fns), opts.NNEB))
else:
if opts.onlyInit:
sys.exit('NEB_* directories already exist, exititng.')
else:
restart = True
fns = ["NEB_%i/CGrun" % ii for ii in range(opts.NNEB)]
fns = [opts.initial + "/CGrun"] + fns + [opts.final + "/CGrun"]
i, f = step(fns[0], False, 0), step(fns[opts.NNEB + 1], False,
opts.NNEB + 1)
if restart:
try:
savedData.E, savedData.F, savedData.Fmax, \
savedData.FmaxWOspring, savedData.geom = pickle.load(open('NEB_0/savedData.pickle', 'r'))
except:
savedData.E = []
savedData.F = []
savedData.geom = []
savedData.Fmax = []
else:
savedData.E = []
savedData.F = []
savedData.geom = []
savedData.Fmax = []
steps = [
step(fn, restart, ii, initial=i, final=f) for ii, fn in enumerate(fns)
]
checkConst(i, f)
if restart:
for ii in range(len(steps) - 1):
checkConst(steps[ii], steps[ii + 1])
done = opts.onlyInit
while not done:
# Start calculations
for ii in steps:
ii.run()
nextstep = False
while not nextstep:
for ii in steps:
if not ii.checkDone(): # Reads forces!
break
else:
nextstep = True
if not nextstep:
time.sleep(10)
savedData.E += [[
SIO.GetTotalEnergy(ii.dirr + '/RUN.out') for ii in steps
]]
savedData.geom += [[copy.deepcopy(ii.XVgeom) for ii in steps]]
overShoot = False
for ii, jj in enumerate(steps[:-1]):
if ii != 0: # Skip first and last
overShoot = overShoot or jj.shootOver(
savedData.geom[-1][ii - 1], savedData.geom[-1][ii + 1])
if overShoot: # Kill speed if one image overshoot ... otherwise kinks will appear
for ii in steps:
ii.v = ii.v * 0
for ii, jj in enumerate(steps[:-1]):
if ii != 0: # Skip first and last
jj.update(savedData.geom[-1][ii - 1],
savedData.geom[-1][ii + 1])
# Write status
savedData.F += [[ii.F for ii in steps]]
savedData.Fmax += [[ii.Fmax for ii in steps]]
for ii in range(1, len(steps) - 1):
geoms = [
savedData.geom[jj][ii] for jj in range(len(savedData.geom))
]
Fmax = [
savedData.Fmax[jj][ii] for jj in range(len(savedData.geom))
]
Fs = [savedData.F[jj][ii] for jj in range(len(savedData.geom))]
SIO.WriteANIFile('NEB_%i/Steps.ANI' % (ii - 1), geoms, Fmax)
SIO.WriteAXSFFiles('NEB_%i/Steps.XASF' % (ii - 1),
geoms,
forces=Fs)
geoms = [ii.XVgeom for ii in steps]
Fmax = [ii.Fmax for ii in steps]
F = [ii.F for ii in steps]
SIO.WriteANIFile('NextStep.ANI', geoms, \
[ii-savedData.E[-1][0] for ii in savedData.E[-1]])
SIO.WriteAXSFFiles('NextStep.XASF', geoms, forces=F)
done = True
for ii in steps:
done = done and ii.converged
pickle.dump((savedData.E, savedData.F, savedData.Fmax, savedData.geom),\
open('NEB_%i/savedData.pickle'%0, 'w'))
f = open('Convergence', 'a')
f.write(('####### Iteration %i #######\n#Fmax '+('%2.3f '*(opts.NNEB+2))+'\n')%\
tuple([len(savedData.Fmax), ]+savedData.Fmax[-1]))
f.write(('#step length '+(('%2.4f ')*(opts.NNEB+2))+'\n')%\
tuple([LA.norm(ii.v) for ii in steps]))
f.write('# Barrier [meV]:\n')
f.write((('%4.1f '*(opts.NNEB+2))+'\n')%tuple([1000*(savedData.E[-1][ii]-savedData.E[-1][0])\
for ii in range(opts.NNEB+2)]))
f.write('# delta E compared to start/restart [meV]:\n')
f.write((('%4.1f '*(opts.NNEB+2))+'\n')%tuple([1000*(savedData.E[0][ii]-savedData.E[-1][ii])\
for ii in range(opts.NNEB+2)]))
f.close()