def main(filename = 'mp-1368.mson', beta = 1.0, initial_temp = 1.0, precomputed_structure = False):
def temperature(phi_, beta_, initial_temp_):
#cooling profile. returns a temperature according to initial_temp*exp(-beta*phi), where phi is the current packing fraction, and beta is a free parameter
return initial_temp_*np.exp(-beta_*phi_)
#Filename of starting structure
#Cutoff for tetrahedron distortion -- higher numbers will accept more distorted tetrahedra
std_dev_cutoff = 0.50
#Initial factor for increasing all axes
initial_increase_factor = 2.5
#Compression increment -- compress by fixed percentage:
compression_factor = -0.01
#Tetrahedra become distorted due compounding numerical error. Re-regularize every n steps:
normalization_frequency = 1
#Save structure every n steps:
save_frequency = 1
#Controls how much tetrahedra can jostle during packing
temp = 1.
#How many tries to fit a tetrahedra before skipping
resolution_max = 5000
#How far a tet can travel randomly
distance_max = 1.0
#Initialize sturcture and tetrahedra
print '\nLoading initial structure...',
sys.stdout.flush()
initial_structure = pm.read_structure(filename)
if not precomputed_structure:
path = initial_structure.composition.alphabetical_formula.replace(' ', '') + '_beta_' + str(beta) + '_T_' + str(initial_temp)
if not os.path.exists(path):
os.mkdir(path)
print initial_structure.composition.alphabetical_formula + ' loaded.'
print '\nExtracting tetrahedra...',
sys.stdout.flush()
tet_str, tet_reg = tetpack.tetrahedra_from_structure(initial_structure, stdcutoff=std_dev_cutoff)
print str(len(tet_reg)) + ' initial tetrahedra extracted.'
#Expand structure initally
print '\nExpanding cell axes by factor of ' + str(initial_increase_factor) + '...',
sys.stdout.flush()
current_tet_str = tetpack.adjust_axes(tet_str, initial_increase_factor)
current_tet_reg = map(tetpack.tetrahedron, [current_tet_str[5*i:5*i+5] for i in range(len(current_tet_str)/5)])
print 'done: \na = ' + str(current_tet_str.lattice.a) + '\nb = ' + str(current_tet_str.lattice.b) + '\nc = ' + str(current_tet_str.lattice.c)
phi = tetpack.packing_density(current_tet_str)
print '\nRelaxing structure via Ewald summation...'
sys.stdout.flush()
current_tet_str = tetpack.ewald_relaxation(current_tet_str, max_steps = 1, motion_factor = temperature(phi, beta, initial_temp))
else:
path = filename.rstrip('.mson') + '_beta_' + str(beta) + '_T_' + str(initial_temp)
if not os.path.exists(path):
os.mkdir(path)
current_tet_str = initial_structure
current_tet_reg = map(tetpack.tetrahedron, [current_tet_str[5*i:5*i+5] for i in range(len(current_tet_str)/5)])
print '\nBeginning compression loop:'
#Loop until collision
collision = False
step = 0
while(not collision):
phi = tetpack.packing_density(current_tet_str)
if np.mod(step, normalization_frequency) == 0:
print 'Normalizing tetrahedra...',
sys.stdout.flush()
[tet.regularize() for tet in current_tet_reg]
print 'done.'
current_tet_str, current_tet_reg = compress(current_tet_str, current_tet_reg, temperature(phi, beta, initial_temp)*compression_factor)
print 'Step '+ str(step) + ' packing fraction: ' + str(phi) + ' T:' + str(temperature(phi, beta, initial_temp)) + '...',
sys.stdout.flush()
failed = check_and_resolve_collisions(current_tet_str, current_tet_reg, temperature(phi, beta, initial_temp), distance_max, int(1./temperature(phi, beta, initial_temp)*resolution_max))
if failed:
print 'Relaxing structure...',
sys.stdout.flush()
current_tet_str, current_tet_reg = compress(current_tet_str, current_tet_reg, -1.5* temperature(phi, beta, initial_temp)* compression_factor)
phi = tetpack.packing_density(current_tet_str)
print 'done. Packing fraction: ' + str(phi)
print 'Single-step Ewald relaxation...'
sys.stdout.flush()
current_tet_str = tetpack.ewald_relaxation(current_tet_str, max_steps = 1, motion_factor = temperature(phi, beta, initial_temp))
print 'done.'
failed = False
else:
if np.mod(step, save_frequency) == 0:
print 'Writing structure...',
sys.stdout.flush()
pm.write_structure(current_tet_str, os.path.join(path, str(step) + '.cif'))
tetpack.to_challenge_output(current_tet_str, os.path.join(path, str(step) + '.csv'))
print 'done.'
step += 1
def main(filename='mp-1368.mson',
beta=1.0,
initial_temp=1.0,
precomputed_structure=False):
def temperature(phi_, beta_, initial_temp_):
#cooling profile. returns a temperature according to initial_temp*exp(-beta*phi), where phi is the current packing fraction, and beta is a free parameter
return initial_temp_ * np.exp(-beta_ * phi_)
#Filename of starting structure
#Cutoff for tetrahedron distortion -- higher numbers will accept more distorted tetrahedra
std_dev_cutoff = 0.50
#Initial factor for increasing all axes
initial_increase_factor = 2.5
#Compression increment -- compress by fixed percentage:
compression_factor = -0.01
#Tetrahedra become distorted due compounding numerical error. Re-regularize every n steps:
normalization_frequency = 1
#Save structure every n steps:
save_frequency = 1
#Controls how much tetrahedra can jostle during packing
temp = 1.
#How many tries to fit a tetrahedra before skipping
resolution_max = 5000
#How far a tet can travel randomly
distance_max = 1.0
#Initialize sturcture and tetrahedra
print '\nLoading initial structure...',
sys.stdout.flush()
initial_structure = pm.read_structure(filename)
if not precomputed_structure:
path = initial_structure.composition.alphabetical_formula.replace(
' ', '') + '_beta_' + str(beta) + '_T_' + str(initial_temp)
if not os.path.exists(path):
os.mkdir(path)
print initial_structure.composition.alphabetical_formula + ' loaded.'
print '\nExtracting tetrahedra...',
sys.stdout.flush()
tet_str, tet_reg = tetpack.tetrahedra_from_structure(
initial_structure, stdcutoff=std_dev_cutoff)
print str(len(tet_reg)) + ' initial tetrahedra extracted.'
#Expand structure initally
print '\nExpanding cell axes by factor of ' + str(
initial_increase_factor) + '...',
sys.stdout.flush()
current_tet_str = tetpack.adjust_axes(tet_str, initial_increase_factor)
current_tet_reg = map(tetpack.tetrahedron, [
current_tet_str[5 * i:5 * i + 5]
for i in range(len(current_tet_str) / 5)
])
print 'done: \na = ' + str(current_tet_str.lattice.a) + '\nb = ' + str(
current_tet_str.lattice.b) + '\nc = ' + str(
current_tet_str.lattice.c)
phi = tetpack.packing_density(current_tet_str)
print '\nRelaxing structure via Ewald summation...'
sys.stdout.flush()
current_tet_str = tetpack.ewald_relaxation(current_tet_str,
max_steps=1,
motion_factor=temperature(
phi, beta,
initial_temp))
else:
path = filename.rstrip('.mson') + '_beta_' + str(beta) + '_T_' + str(
initial_temp)
if not os.path.exists(path):
os.mkdir(path)
current_tet_str = initial_structure
current_tet_reg = map(tetpack.tetrahedron, [
current_tet_str[5 * i:5 * i + 5]
for i in range(len(current_tet_str) / 5)
])
print '\nBeginning compression loop:'
#Loop until collision
collision = False
step = 0
while (not collision):
phi = tetpack.packing_density(current_tet_str)
if np.mod(step, normalization_frequency) == 0:
print 'Normalizing tetrahedra...',
sys.stdout.flush()
[tet.regularize() for tet in current_tet_reg]
print 'done.'
current_tet_str, current_tet_reg = compress(
current_tet_str, current_tet_reg,
temperature(phi, beta, initial_temp) * compression_factor)
print 'Step ' + str(step) + ' packing fraction: ' + str(
phi) + ' T:' + str(temperature(phi, beta, initial_temp)) + '...',
sys.stdout.flush()
failed = check_and_resolve_collisions(
current_tet_str, current_tet_reg,
temperature(phi, beta, initial_temp), distance_max,
int(1. / temperature(phi, beta, initial_temp) * resolution_max))
if failed:
print 'Relaxing structure...',
sys.stdout.flush()
current_tet_str, current_tet_reg = compress(
current_tet_str, current_tet_reg, -1.5 *
temperature(phi, beta, initial_temp) * compression_factor)
phi = tetpack.packing_density(current_tet_str)
print 'done. Packing fraction: ' + str(phi)
print 'Single-step Ewald relaxation...'
sys.stdout.flush()
current_tet_str = tetpack.ewald_relaxation(
current_tet_str,
max_steps=1,
motion_factor=temperature(phi, beta, initial_temp))
print 'done.'
failed = False
else:
if np.mod(step, save_frequency) == 0:
print 'Writing structure...',
sys.stdout.flush()
pm.write_structure(current_tet_str,
os.path.join(path,
str(step) + '.cif'))
tetpack.to_challenge_output(
current_tet_str, os.path.join(path,
str(step) + '.csv'))
print 'done.'
step += 1
def compress(current_str, current_tet, compression_factor):
compressed_str = tetpack.adjust_axes(current_str, compression_factor)
compressed_tet = map(tetpack.tetrahedron, [current_str[5*i:5*i+5] for i in range(len(current_str)/5)])
return compressed_str, compressed_tet
def compress(current_str, current_tet, compression_factor):
compressed_str = tetpack.adjust_axes(current_str, compression_factor)
compressed_tet = map(
tetpack.tetrahedron,
[current_str[5 * i:5 * i + 5] for i in range(len(current_str) / 5)])
return compressed_str, compressed_tet