def _molecular_dynamics(self, resume=None):
"""Performs a molecular dynamics simulation, until mdmin is
exceeded. If resuming, the file number (md%05i) is expected."""
self._log('msg', 'Molecular dynamics: md%05i' % self._counter)
mincount = 0
energies, oldpositions = [], []
thermalized = False
if resume:
self._log('msg', 'Resuming MD from md%05i.traj' % resume)
if os.path.getsize('md%05i.traj' % resume) == 0:
self._log(
'msg', 'md%05i.traj is empty. Resuming from '
'qn%05i.traj.' % (resume, resume - 1))
atoms = io.read('qn%05i.traj' % (resume - 1), index=-1)
else:
images = io.Trajectory('md%05i.traj' % resume, 'r')
for atoms in images:
energies.append(atoms.get_potential_energy())
oldpositions.append(atoms.positions.copy())
passedmin = self._passedminimum(energies)
if passedmin:
mincount += 1
self._atoms.set_momenta(atoms.get_momenta())
thermalized = True
self._atoms.positions = atoms.get_positions()
self._log('msg',
'Starting MD with %i existing energies.' % len(energies))
if not thermalized:
MaxwellBoltzmannDistribution(self._atoms,
temp=self._temperature * units.kB,
force_temp=True)
traj = io.Trajectory('md%05i.traj' % self._counter, 'a', self._atoms)
self._constrain()
dyn = NPT(self._atoms,
timestep=self._timestep * units.fs,
temperature=self._temperature * units.kB,
externalstress=self._externalstress,
ttime=self._ttime * units.fs,
pfactor=self._pfactor * units.fs**2)
# dyn = NPTber(self._atoms, timestep=self._timestep * units.fs, temperature=self._temperature, fixcm=True, pressure=self._pressure, taut=self._taut * units.fs, taup=self._taup * units.fs, compressibility=self._compressibility)
log = MDLogger(dyn,
self._atoms,
'md%05i.log' % self._counter,
header=True,
stress=False,
peratom=False)
dyn.attach(log, interval=1)
dyn.attach(traj, interval=1)
while mincount < self._mdmin:
# self._constrain()
dyn.run(1)
# del self._atoms.constraints
energies.append(self._atoms.get_potential_energy())
passedmin = self._passedminimum(energies)
if passedmin:
mincount += 1
oldpositions.append(self._atoms.positions.copy())
# Reset atoms to minimum point.
self._atoms.positions = oldpositions[passedmin[0]]
def read_evaluation_data(
filename,
MLIP_cache_dir='MLIP_cache',
struct_types=['known', 'polymorphD3', 'random'],
dyn_types=['md', 'relax', 'sp', 'ce', 'dimer'],
use_forces=True,
remove_force_drift=True,
bad_data_traj_list=[],
):
with open(filename, 'r') as fid:
lines = fid.readlines()
image_pairs = []
for line in lines:
if '#' not in line:
sline = line.split()
struct_type = sline[-3]
dyn_type = sline[-2]
if dyn_type in dyn_types and struct_type in struct_types:
data_file = sline[-1]
im_index = int(sline[-4])
if data_file in bad_data_traj_list:
print('%s[%i] in bad_data_traj_list, skipping...' %
(data_file, im_index))
else:
dirlist = data_file.split('/')
cache_path = MLIP_cache_dir + '/' + dirlist[
-4] + '/' + dirlist[-3] + '/' + dirlist[-2] + '/'
cache_file = cache_path + '%i.traj' % im_index
data_traj = io.Trajectory(data_file, 'r')
cache_traj = io.Trajectory(cache_file, 'r')
data_im = data_traj[im_index]
cache_im = cache_traj[0]
if use_forces:
if remove_force_drift:
cancel_net_force(cache_im)
cancel_net_force(data_im)
image_pairs.append((cache_im, data_im, cache_path))
data_traj.close()
cache_traj.close()
return image_pairs
def _molecular_dynamics(self, N, resume=None):
"""Performs a molecular dynamics simulation, until mdmin is
exceeded. If resuming, the file number (md%05i) is expected."""
self._log('msg', 'Molecular dynamics: md%05i' % self._counter)
mincount = 0
energies, oldpositions = [], []
thermalized = False
if resume:
self._log('msg', 'Resuming MD from md%05i.traj' % resume)
if os.path.getsize('md.traj') == 0:
self._log('msg', 'md%05i.traj is empty. Resuming from '
'qn%05i.traj.' % (resume, resume - 1))
atoms = io.read('qn.traj', index=-1)
else:
images = io.Trajectory('md.traj' % resume, 'r')
for atoms in images:
energies.append(atoms.get_potential_energy())
oldpositions.append(atoms.positions.copy())
passedmin = self._passedminimum(energies)
if passedmin:
mincount += 1
self._atoms.set_momenta(atoms.get_momenta())
thermalized = True
self._atoms.positions = atoms.get_positions()
self._log('msg', 'Starting MD with %i existing energies.' %
len(energies))
if not thermalized:
self.MaxwellBoltzmannDistribution(self._atoms,
N,
temp=self._temperature * units.kB,
force_temp=True)
if (self._counter > 1):
os.remove('md.log')
os.remove('md.traj')
traj = io.Trajectory('md.traj', 'a', self._atoms)
dyn = VelocityVerlet(self._atoms, dt=self._timestep * units.fs)
log = MDLogger(dyn, self._atoms, 'md.log',
header=True, stress=False, peratom=False)
dyn.attach(log, interval=1)
dyn.attach(traj, interval=1)
while mincount < self._mdmin:
dyn.run(1)
energies.append(self._atoms.get_potential_energy())
passedmin = self._passedminimum(energies)
if passedmin:
mincount += 1
oldpositions.append(self._atoms.positions.copy())
# Reset atoms to minimum point.
self._atoms.positions = oldpositions[passedmin[0]]
def _molecular_dynamics(self, step, N):
"""Performs a molecular dynamics simulation, until mdmin is
exceeded. If resuming, the file number (md%05i) is expected."""
mincount = 0
energies, oldpositions = [], []
thermalized = False
if not thermalized:
self.MaxwellBoltzmannDistribution(N,
temp=self.temperature * kB,
force_temp=True)
traj = io.Trajectory('md.traj', 'a', self.atoms)
dyn = VelocityVerlet(self.atoms, dt=self.timestep * units.fs)
log = MDLogger(dyn, self.atoms, 'md.log',
header=True, stress=False, peratom=False)
dyn.attach(log, interval=1)
dyn.attach(traj, interval=1)
os.remove('md.log')
os.remove('md.traj')
while mincount < self.mdmin:
dyn.run(1)
energies.append(self.atoms.get_potential_energy())
passedmin = self.passedminimum(energies)
if passedmin:
mincount += 1
oldpositions.append(self.atoms.positions.copy())
# Reset atoms to minimum point.
self.atoms.positions = oldpositions[passedmin[0]]
def makePDFs(trajs, n_images, output):
"""Creates PDFs of each band in the trajectory files, assuming n_images
images per band. Then concatenates them all into a single pdf called
<output>.pdf and deletes the source files."""
if n_images == -1:
n_images = guess_nimages(ase.io.read(trajs[0], index=':'))
count = 0
filenames = []
tmpd = mkdtemp() # temporary directory
for file in trajs:
print('Analyzing: %s' % file)
traj = io.Trajectory(file, 'r')
assert (len(traj) % n_images) == 0
steps = len(traj) // n_images
for step in range(steps):
filenames.append(os.path.join(tmpd, 'neb_plot%04i.pdf' % count))
indices = range(step * n_images, step * n_images + n_images)
print('%i/%i %s: %s' % (step + 1, steps, filenames[-1], indices))
images = [traj[index] for index in indices]
fig = get_NEB_plot(images)
fig.savefig(filenames[-1])
pyplot.close(fig) # garbage collection
count += 1
command = 'pdftk ' + ('%s ' * len(filenames)) + 'cat output %s.pdf'
command = command % tuple(filenames + [output])
print('Combining pdfs with pdftk to %s.' % output)
os.system(command)
shutil.rmtree(tmpd)
def read_energy_radius_traj(file_name):
traj = io.Trajectory(os.path.abspath(file_name),'r')
#data = [ (im.get_volume()/len(im), im.get_potential_energy(force_consistent = True)/len(im)) for im in traj]
data = [ (np.linalg.norm(im[0].position - im[1].position),
im.get_potential_energy()/len(im)) for im in traj]
traj.close()
data = np.asarray(data).T
smap = np.argsort(data[0])
return np.array([data[0][smap],data[1][smap]] )
def read_energy_volume_traj(file_name):
'''Returns [V/atom,E/atom] sorted by volume/atom from traj file'''
from ase import io
traj = io.Trajectory(os.path.abspath(file_name), 'r')
#data = [ (im.get_volume()/len(im), im.get_potential_energy(force_consistent = True)/len(im)) for im in traj]
data = [(im.get_volume() / len(im), im.get_potential_energy() / len(im))
for im in traj]
traj.close()
data = np.asarray(data).T
smap = np.argsort(data[0])
return np.array([data[0][smap], data[1][smap]])
def hash_images(images, Gs, log=None, ordered=False):
""" Converts input images -- which may be a list, a trajectory file, or
a database -- into a dictionary indexed by their hashes.
Returns this dictionary. If ordered is True, returns an OrderedDict. When
duplicate images are encountered (based on encountering an identical hash),
a warning is written to the logfile. The number of duplicates of each image
can be accessed by examinging dict_images.metadata['duplicates'], where
dict_images is the returned dictionary.
"""
if log is None:
log = Logger(None)
if images is None:
return
elif hasattr(images, "keys"):
log(" %i unique images after hashing." % len(images))
return images # Apparently already hashed.
else:
# Need to be hashed, and possibly read from file.
if isinstance(images, str):
log("Attempting to read images from file %s." % images)
extension = os.path.splitext(images)[1]
from ase import io
if extension == ".traj":
images = io.Trajectory(images, "r")
elif extension == ".db":
images = [
row.toatoms() for row in connect(images, "db").select(None)
]
# images converted to dictionary form; key is hash of image.
log("Hashing images...", tic="hash")
dict_images = MetaDict()
dict_images.metadata["duplicates"] = {}
dup = dict_images.metadata["duplicates"]
if ordered is True:
from collections import OrderedDict
dict_images = OrderedDict()
for image in images:
hash = get_hash(image, Gs)
if hash in dict_images.keys():
log("Warning: Duplicate image (based on identical hash)."
" Was this expected? Hash: %s" % hash)
if hash in dup.keys():
dup[hash] += 1
else:
dup[hash] = 2
dict_images[hash] = image
log(" %i unique images after hashing." % len(dict_images))
log("...hashing completed.", toc="hash")
return dict_images
def _read_minima(self):
"""Reads in the list of minima from the minima file."""
exists = os.path.exists(self._minima_traj)
if exists:
empty = os.path.getsize(self._minima_traj) == 0
if not empty:
traj = io.Trajectory(self._minima_traj, 'r')
self._minima = [atoms for atoms in traj]
else:
self._minima = []
return True
else:
self._minima = []
return False
def test():
# Generate atomic system to create test data.
atoms = fcc110('Cu', (2, 2, 2), vacuum=7.)
adsorbate = Atoms([
Atom('H', atoms[7].position + (0., 0., 2.)),
Atom('H', atoms[7].position + (0., 0., 5.))
])
atoms.extend(adsorbate)
atoms.set_constraint(FixAtoms(indices=[0, 2]))
calc = EMT() # cheap calculator
atoms.set_calculator(calc)
# Run some molecular dynamics to generate data.
trajectory = io.Trajectory('data.traj', 'w', atoms=atoms)
MaxwellBoltzmannDistribution(atoms, temp=300. * units.kB)
dynamics = VelocityVerlet(atoms, dt=1. * units.fs)
dynamics.attach(trajectory)
for step in range(50):
dynamics.run(5)
trajectory.close()
# Train the calculator.
train_images, test_images = randomize_images('data.traj')
calc = Amp(descriptor=Behler(), regression=NeuralNetwork())
calc.train(train_images, energy_goal=0.001, force_goal=None)
# Plot and test the predictions.
import matplotlib
matplotlib.use('Agg')
from matplotlib import pyplot
fig, ax = pyplot.subplots()
for image in train_images:
actual_energy = image.get_potential_energy()
predicted_energy = calc.get_potential_energy(image)
ax.plot(actual_energy, predicted_energy, 'b.')
for image in test_images:
actual_energy = image.get_potential_energy()
predicted_energy = calc.get_potential_energy(image)
ax.plot(actual_energy, predicted_energy, 'r.')
ax.set_xlabel('Actual energy, eV')
ax.set_ylabel('Amp energy, eV')
fig.savefig('parityplot.png')
def _plot_qn(self, index, line):
"""Plots a dashed vertical line for the optimization."""
if line[1] == 'performing MD':
return
file = os.path.join(self._rundirectory, 'qn%05i.traj' % index)
if os.path.getsize(file) == 0:
return
traj = io.Trajectory(file, 'r')
energies = [traj[0].get_potential_energy(),
traj[-1].get_potential_energy()]
if index > 0:
file = os.path.join(self._rundirectory, 'md%05i.traj' % index)
atoms = io.read(file, index=-3)
energies[0] = atoms.get_potential_energy()
self._ax.plot([index + 0.25] * 2, energies, ':k')
def _plot_md(self, step, line):
"""Adds a curved plot of molecular dynamics trajectory."""
if step == 0:
return
energies = [self._data[step - 1][0]]
file = os.path.join(self._rundirectory, 'md%05i.traj' % step)
traj = io.Trajectory(file, 'r')
for atoms in traj:
energies.append(atoms.get_potential_energy())
xi = step - 1 + .5
if len(energies) > 2:
xf = xi + (step + 0.25 - xi) * len(energies) / (len(energies) - 2.)
else:
xf = step
if xf > (step + .75):
xf = step
self._ax.plot(np.linspace(xi, xf, num=len(energies)), energies, '-k')
def generate_data(count, filename='cmd.traj'):
"""Generates test or training data with a simple MD simulation."""
if os.path.exists(filename):
return
traj = io.Trajectory(filename, 'w')
atoms = io.read('2.xyz')
atoms.set_calculator(Amp.load('sio2.amp'))
atoms.get_potential_energy()
traj.write(atoms)
mb(atoms, 300. * units.kB)
# dyn = vv(atoms, dt=1. * units.fs, logfile='cmd.log')
dyn = NVTB(atoms,
timestep=0.5 * units.fs,
temperature=300,
taut=2.0 * units.fs,
logfile='cmd.log')
for step in range(count - 1):
dyn.run(1)
traj.write(atoms)
def randomize_images(images, fraction=0.8):
"""Randomly assigns 'fraction' of the images to a training set and (1
- 'fraction') to a test set. Returns two lists of ASE images.
Parameters
----------
images : list or str
List of ASE atoms objects in ASE format. This can also be the path to
an ASE trajectory (.traj) or database (.db) file.
fraction : float
Portion of train_images to all images.
Returns
-------
train_images, test_images : list
Lists of train and test images.
"""
file_opened = False
if type(images) == str:
extension = os.path.splitext(images)[1]
if extension == '.traj':
images = aseio.Trajectory(images, 'r')
elif extension == '.db':
images = aseio.read(images)
file_opened = True
trainingsize = int(fraction * len(images))
testsize = len(images) - trainingsize
testindices = []
while len(testindices) < testsize:
next = np.random.randint(len(images))
if next not in testindices:
testindices.append(next)
testindices.sort()
trainindices = [
index for index in range(len(images)) if index not in testindices
]
train_images = [images[index] for index in trainindices]
test_images = [images[index] for index in testindices]
if file_opened:
images.close()
return train_images, test_images
def main(argv):
tr = io.Trajectory(argv)
return tr
def _record_minimum(self):
"""Adds the current atoms configuration to the minima list."""
traj = io.Trajectory(self._minima_traj, 'a')
traj.write(self._atoms)
self._read_minima()
self._log('msg', 'Recorded minima #%i.' % (len(self._minima) - 1))
mpirun = spawn.find_executable('mpirun')
vasp = '/home/mmm0007/vasp/vasp.5.4.1/bin/vasp_std'
vasp_client = VaspClient(client_id=0,
npj=96,
ppn=1,
exe=vasp,
mpirun=mpirun,
parmode='mpi',
ibrion=13,
nsw=1000000,
npar=4,
**vasp_args)
if not args.no_relax:
traj = io.Trajectory('relaxation.traj', 'a', gam_cell)
qm_pot = SocketCalculator(vasp_client)
gam_cell.set_calculator(qm_pot)
opt = PreconLBFGS(gam_cell)
opt.attach(traj.write, interval=1)
opt.run(fmax=args.fmax)
traj.close()
qm_pot.shutdown()
#remove defect atom with symbol
del gam_cell[[atom.symbol == args.symbol for atom in gam_cell]]
defect_cell = gam_cell.copy()
defect_cell.write('no_impurity.xyz')
#Need accurate forces
vasp_args['ediff'] = 1e-5
while iframe >= 2000 and iframe % 2 == 0:
print(nAtoms, file=xyz)
print(
'Lattice="%5.3f 0.0 0.0 %5.3f %5.3f 0.0 0.0 0.0 %5.3f" Properties=species:S:1:pos:R:3 energy=%15.8f pbc="T T T"'
% (ax, bx, by, cz, float(out[iframe])),
file=xyz)
for i in range(nAtoms):
tmp = lines[i + 1].split()
u = float(tmp[0])
v = float(tmp[1])
w = float(tmp[2])
frac_coor = np.array([[u], [v], [w]])
cart_coor = (lattice_vector.T).dot(frac_coor)
if i < num_ele1:
print('%-4s %15.8f %15.8f %15.8f' %
(ele1, cart_coor[0], cart_coor[1], cart_coor[2]),
file=xyz)
else:
print('%-4s %15.8f %15.8f %15.8f' %
(ele2, cart_coor[0], cart_coor[1], cart_coor[2]),
file=xyz)
break
xyz.close()
aseTrj = io.Trajectory(dirName + aseTrajFileName, 'w')
exyz = io.read(dirName + exyzFileName, index=':')
for atoms in exyz:
atoms.set_pbc((1, 1, 1))
aseTrj.write(atoms)
return atoms
else:
if verbose:
print("Stucture expanded to %ix%ix%i" % tuple(cells_needed) +
" super cell to fit rcut = %f" % rcut)
return super_cell(
atoms,
cells_needed,
use_initial_magnetic_moments=use_initial_magnetic_moments)
if __name__ == "__main__":
from ase import io
traj = io.Trajectory('test_structures/AFM_Cr.traj', 'r')
Cr_atoms = traj[0]
traj.close()
ZrO2_atoms = io.read('test_structures/ZrO2.OUTCAR')
#tlins_atoms = io.read('test_structures/TlInS2_mp-632539_primitive.cif')
tests = [Cr_atoms, ZrO2_atoms]
for atoms in tests:
super_cell(atoms, [1, 1, 2])
#calc = atoms.get_calculator()
#print(calc)
#if calc != None:
"""
Imports a pdb
"""
filen = open(file_name, 'r')
orig = np.identity(3)
trans = np.zeros(3)
for line in filen.readlines():
if line.startswith('ATOM') or line.startswith('HETATM'):
try:
# Only dealing with H, C, O and N so single letter for symbol
symbol = line[13].strip().lower().capitalize()
words = line[30:55].split()
position = np.array(
[float(words[0]),
float(words[1]),
float(words[2])])
position = np.dot(orig, position) + trans
atoms.append(Atom(symbol, position))
except:
pass
return (atom_col)
traj = io.Trajectory(filename='./common/kr_geoms.traj', mode='w')
for i in range(1, 71):
atoms = Atoms()
atoms = import_pdb(atoms, '../common/{}-as.pdb'.format(i))
traj.write(atoms=atoms)
from ase import io
from ase.neb import NEB
from ase.optimize import MDMin, BFGS
from ase.calculators.dftb import Dftb
import copy
calc = Dftb(label='neb_path1',
Hamiltonian_MaxAngularMomentum_='',
Hamiltonian_MaxAngularMomentum_O='"p"',
Hamiltonian_MaxAngularMomentum_H='"s"',
Hamiltonian_MaxAngularMomentum_C='"p"',
Hamiltonian_MaxAngularMomentum_N='"p"')
all = io.Trajectory('../common/kr_geoms.traj')
initial = all[0]
final = all[6]
#initial.set_calculator(calc=calc)
#final.set_calculator(calc=calc)
#print(len(all))
#print(initial.get_positions())
#print(final.get_positions())
#images = [all[0]]
#for i in range(1,7):
# images += [all[i]]
images = [initial]
images += [copy.deepcopy(initial) for i in range(3)]
images += [final]
neb = NEB(images, k=0.01)
args = parser.parse_args()
from os import listdir
def list_of_files(dir_name, suffix):
return [f for f in listdir(dir_name) if f.endswith('.' + suffix)]
args = parser.parse_args()
ftraj = list_of_files(args.lm, 'traj')
minima = []
for i in range(len(ftraj)):
empty = os.path.getsize(args.lm + "/" + ftraj[i]) == 0
if not empty:
traj = io.Trajectory(args.lm + "/" + ftraj[i], 'r')
mini = [atoms for atoms in traj]
mini = [mini[-1:]]
else:
print('no minima founded in ', ftraj[i])
mini = []
minima = minima + mini
nminima = len(minima)
# load minima
nminima = len(minima)
print('# minima: ', nminima)
sep = math.floor(nminima / args.nmin)
minima = minima[-1::-sep]
def hash_images(images, log=None, ordered=False, list_seq=False):
""" Converts input images -- which may be a list, a trajectory file, or
a database -- into a dictionary indexed by their hashes.
Returns this dictionary. If ordered is True, returns an OrderedDict. When
duplicate images are encountered (based on encountering an identical hash),
a warning is written to the logfile. The number of duplicates of each image
can be accessed by examinging dict_images.metadata['duplicates'], where
dict_images is the returned dictionary.
"""
if log is None:
log = Logger(None)
if images is None:
return
############# images alread have keys
elif hasattr(images, 'keys'):
log(' %i unique images after hashing.' % len(images))
return images # Apparently already hashed.
############ else
else:
########## Need to be hashed, and possibly read from file.
if isinstance(images, str):
log('Attempting to read images from file %s.' % images)
extension = os.path.splitext(images)[1]
from ase import io
if extension == '.traj':
images = io.Trajectory(images, 'r')
elif extension == '.db':
images = [
row.toatoms() for row in connect(images, 'db').select(None)
]
####### images converted to dictionary form;
######### key is hash of image.
####### i.e. hash is keys for images
log('Hashing images...', tic='hash')
dict_images = MetaDict()
dict_images.metadata['duplicates'] = {}
dup = dict_images.metadata['duplicates']
if ordered is True:
from collections import OrderedDict
dict_images = OrderedDict()
if list_seq:
seq_list = []
for image in images:
########### get_hash make hash for an atom object
hash = get_hash(image)
if list_seq:
seq_list.append(hash)
if hash in dict_images.keys():
log('Warning: Duplicate image (based on identical hash).'
' Was this expected? Hash: %s' % hash)
if hash in dup.keys():
dup[hash] += 1
else:
dup[hash] = 2
dict_images[hash] = image
log(' %i unique images after hashing.' % len(dict_images))
log('...hashing completed.', toc='hash')
if list_seq:
return dict_images, seq_list
else:
return dict_images
def get_traj_file_list(basedirs=[''],
traj_skip=1,
traj_skip_offset=0,
traj_offset=0,
struct_types=['random', 'known', 'polymorphD3'],
dyn_types=['md', 'relax', 'sp', 'ce', 'dimer'],
return_image_and_atom_counts=False):
from ase import io
from glob import glob
import time
import os
import numpy as np
def composition_str(sorted_elements, counts):
comp_format = '( '
for el, cnt in zip(sorted_elements, counts):
comp_format = comp_format + el + '_%i ' % cnt
comp_format = comp_format + ')'
return comp_format
#def remove_force_drift(atoms):
# forces = atoms.calc.results['forces']
# drift = np.sum(forces, axis = 0)/len(atoms)
# atoms.calc.results['forces'] = forces-drift
# #return drift
element_set = set()
traj_file_list = []
image_and_atom_counts = []
total = 0
total_atoms = 0
time1 = time.time()
for basedir in basedirs:
for struct_type in struct_types:
for dyn_type in dyn_types:
top_direct = os.path.abspath(
basedir) + ('/%s_%s/') % (struct_type, dyn_type)
#print(top_direct)
if os.path.isdir(top_direct):
print(top_direct)
sub_total = 0
sub_dirs = sorted(glob(top_direct + '*/'))
#file_list.sort()
sub_dirs.sort(key=lambda x: len(x))
for sub_dir in sub_dirs:
name = sub_dir.split('/')[-2]
if name.isdigit():
if int(name) >= traj_offset and int(
name) % traj_skip == traj_skip_offset:
traj = io.Trajectory(filename=sub_dir +
'images.traj',
mode='r') #trying a read
traj_file_list.append(sub_dir + 'images.traj')
if True: #we'll need a conditional here related to un needed parsing for making this general
print(sub_dir.ljust(22), end='')
# for printing the compositions
symbols = traj[0].get_chemical_symbols()
element_set.update(symbols)
sorted_elements = sorted(list(element_set))
comp = [
symbols.count(el)
for el in sorted_elements
]
comp_format = composition_str(
sorted_elements, comp)
image_and_atom_counts.append(
(len(traj), len(traj[0])))
subsub_total = len(traj)
total_atoms += len(traj) * len(traj[0])
print( (' atoms %i'%len(traj[0])).ljust(12) + \
('images found %i '%subsub_total).ljust(24) + \
comp_format )
sub_total += len(traj)
traj.close()
# subtotal for this struct+dyn_type
print('sub_total: %i \n' % sub_total)
total += sub_total
print('Total Number of Images:', total)
print('Total Atoms: %i' % total_atoms)
print('Time for file parsing is: {:.3f} sec.'.format(time.time() - time1))
if return_image_and_atom_counts:
return traj_file_list, np.array(image_and_atom_counts)
else:
return traj_file_list
def get_image_list(basedirs=[''],
image_skip=2,
image_skip_offset=0,
traj_skip=1,
traj_skip_offset=0,
image_offset=0,
traj_offset=0,
struct_types=['random', 'known', 'polymorphD3'],
dyn_types=['md', 'relax', 'sp', 'ce', 'dimer'],
max_energy_per_atom=None,
max_force_on_atom=None,
max_energy_deviation_per_atom=None,
remove_force_drift_in_training_data=True,
return_file_paths=False):
from ase import io
from glob import glob
import time
import os
import numpy as np
def composition_str(sorted_elements, counts):
comp_format = '( '
for el, cnt in zip(sorted_elements, counts):
comp_format = comp_format + el + '_%i ' % cnt
comp_format = comp_format + ')'
return comp_format
def remove_force_drift(atoms):
forces = atoms.calc.results['forces']
drift = np.sum(forces, axis=0) / len(atoms)
atoms.calc.results['forces'] = forces - drift
#return drift
element_set = set()
image_list = []
file_path_list = []
total = 0
time1 = time.time()
for basedir in basedirs:
for struct_type in struct_types:
for dyn_type in dyn_types:
top_direct = os.path.abspath(
basedir) + ('/%s_%s/') % (struct_type, dyn_type)
#if dyn_type == 'ce':
#print(top_direct)
if os.path.isdir(top_direct):
print(top_direct)
sub_total = 0
sub_dirs = sorted(glob(top_direct + '*/'))
#file_list.sort()
sub_dirs.sort(key=lambda x: len(x))
for sub_dir in sub_dirs:
name = sub_dir.split('/')[-2]
if name.isdigit():
if int(name) >= traj_offset and int(
name) % traj_skip == traj_skip_offset:
traj = io.Trajectory(filename=sub_dir +
'images.traj',
mode='r')
subsub_total = 0
if dyn_type == 'ce':
ce_data = np.loadtxt(sub_dir + 'ce.log',
skiprows=2).T
ce_endev = ce_data[-1]
print(sub_dir.ljust(22), end='')
# for printing the compositions
symbols = traj[0].get_chemical_symbols()
element_set.update(symbols)
sorted_elements = sorted(list(element_set))
comp = [
symbols.count(el) for el in sorted_elements
]
comp_format = composition_str(
sorted_elements, comp)
for image_index in range(len(traj)):
image = traj[image_index]
#if image.get_potential_energy()/len(image) <= max_energy_per_atom:
training_image = False
if struct_type == 'known':
training_image = True
#if (int(name)%trajskip) == trajskip_offset:
if image_index >= image_offset and (
(image_index) %
image_skip) == image_skip_offset:
training_image = True
if training_image:
## now we test for unreasonably high energies/forces
## if thought we'd include the structure
if max_energy_per_atom is not None:
energy_per_atom = image.get_potential_energy(
) / len(image)
if energy_per_atom > max_energy_per_atom:
training_image = False
print('image', image_index,
'Energy too high:',
energy_per_atom)
if max_force_on_atom is not None:
max_force = np.linalg.norm(
image.get_forces(),
axis=1).max()
if max_force > max_force_on_atom:
training_image = False
print('image', image_index,
'Max Force too high:',
max_force)
if dyn_type == 'ce' and max_energy_deviation_per_atom is not None:
if abs(
ce_endev[image_index]
) > max_energy_deviation_per_atom:
training_image = False
print(
'image', image_index,
'CE energy deviation too high:',
ce_endev[image_index])
#if (int(name) in bad_polymorphs) and struct_type == 'polymorphD3' :
# training_image = False
if training_image:
#print ('adding image no', image_index)
if remove_force_drift_in_training_data:
remove_force_drift(image)
image_list.append(image)
file_path_list.append([
image_index, struct_type, dyn_type,
sub_dir + 'images.traj'
])
subsub_total += 1
sub_total += 1
total += 1
print( (' atoms %i'%len(traj[0])).ljust(12) +\
('images loaded %i/%i '%(subsub_total, len(traj))).ljust(24) +comp_format )
traj.close()
# subtotal for this struct+dyn_type
print('sub_total: %i \n' % sub_total)
sum_total_atoms = 0
for image in image_list:
sum_total_atoms += len(image)
print('Total Number of Images:', total)
print('Total Atoms: %i' % sum_total_atoms)
print('Time for file parsing is: {:.3f} sec.'.format(time.time() - time1))
if return_file_paths:
return image_list, file_path_list
else:
return image_list
}, #convergence parameters
dipole={'status':
True}, #dipole correction to account for periodicity in z
output={
'avoidio': False,
'removewf': True,
'wf_collect': False
},
spinpol=False,
parflags='-npool 2',
outdir='calcdir') #output directory for Quantum Espresso files
#calc.calculation_required = lambda x, y: True
slab.set_calculator(calc)
slab.get_potential_energy()
traj = io.Trajectory('opt.traj', 'w')
traj.write(slab)
#qn=QuasiNewton(slab,trajectory='opt.traj',logfile='opt.log')
#qn.run(fmax=0.03)
calc.save_flev_chg('efchg.tgz')
potential = calc.extract_total_potential()
potential_file = open('potential.pickle', 'w')
pickle.dump(potential, potential_file)
potential_file.close()
posin = io.read('opt.traj')
p = posin.copy()
p.calc = calc
p.calc.load_flev_chg('efchg.tgz')
dos = calc.calc_pdos(nscf=True,
image_list = []
total = 0
time1 = time.time()
for struct_type in struct_types:
for dyn_type in dyn_types:
top_direct = ('%s_%s/') % (struct_type, dyn_type)
if path.isdir(top_direct):
print(top_direct)
sub_total = 0
sub_dirs = sorted(glob(top_direct + '*/'))
for sub_dir in sub_dirs:
name = sub_dir.split('/')[-2]
if name.isdigit():
traj = io.Trajectory(filename=sub_dir + 'images.traj',
mode='r')
image_index = -1
image = traj[image_index]
verbose = False
# im = super_cell_if_needed(image, cut_off_radius, verbose=verbose)
im = image
print(
sub_dir.ljust(22) +
('atoms %i' % len(traj[0])).ljust(12) +
'images loaded %i/%i' % (1, len(traj)))
DFT_e = image.get_potential_energy() / len(image)
NN_e = MLIP.get_potential_energy(im) / len(im)
def plot_error(load,
images,
plot_forces=True,
plotfile='errorplot.pdf',
color='b.',
overwrite=False):
"""
Makes a plot of deviations in per atom energies and forces versus real
energies and forces.
:param load: Path for loading an existing parameters of Amp calculator.
:type load: str
:param images: List of ASE atoms objects with positions, symbols, energies,
and forces in ASE format. This is the training set of data.
This can also be the path to an ASE trajectory (.traj) or
database (.db) file. Energies can be obtained from any
reference, e.g. DFT calculations.
:type images: list or str
:param plot_forces: Determines whether or not forces should be plotted as
well.
:type plot_forces: bool
:param plotfile: File for plots.
:type plotfile: Object
:param color: Plot color.
:type color: str
:param overwrite: If a plot or an script containing values found overwrite
it.
:type overwrite: bool
"""
base_filename = os.path.splitext(plotfile)[0]
energyscript = os.path.join('energy-' + base_filename + '.json')
if (not overwrite) and os.path.exists(plotfile):
raise IOError('File exists: %s.\nIf you want to overwrite,'
' set overwrite=True or manually delete.' % plotfile)
if plot_forces is not None:
forcescript = os.path.join('force-' + base_filename + '.json')
from . import Amp
from utilities import hash_image
from matplotlib import rc
# activate latex text rendering
rc('text', usetex=True)
calc = Amp(load=load)
if isinstance(images, str):
extension = os.path.splitext(images)[1]
if extension == '.traj':
images = io.Trajectory(images, 'r')
elif extension == '.db':
images = io.read(images)
# Images is converted to dictionary form; key is hash of image.
dict_images = {}
for image in images:
hash = hash_image(image)
dict_images[hash] = image
images = dict_images.copy()
del dict_images
hashs = sorted(images.keys())
no_of_images = len(hashs)
energy_data = {}
# Reading energy script
try:
fp = paropen(energyscript, 'rb')
data = json.load(fp)
except IOError:
pass
else:
for hash in data.keys():
energy_data[hash] = data[hash]
# calculating errors for images if json is not found
if len(energy_data.keys()) == 0:
count = 0
while count < no_of_images:
hash = hashs[count]
atoms = images[hash]
no_of_atoms = len(atoms)
act_energy = atoms.get_potential_energy(apply_constraint=False)
amp_energy = calc.get_potential_energy(atoms)
energy_error = abs(amp_energy - act_energy) / no_of_atoms
act_energy_per_atom = act_energy / no_of_atoms
energy_data[hash] = [act_energy_per_atom, energy_error]
count += 1
# saving energy script
try:
json.dump(energy_data, energyscript)
energyscript.flush()
return
except AttributeError:
with paropen(energyscript, 'wb') as outfile:
json.dump(energy_data, outfile)
# calculating energy per atom rmse
energy_square_error = 0.
count = 0
while count < no_of_images:
hash = hashs[count]
energy_square_error += energy_data[hash][1]**2.
count += 1
del hash
energy_per_atom_rmse = np.sqrt(energy_square_error / no_of_images)
min_act_energy = min([energy_data[hash][0] for hash in hashs])
max_act_energy = max([energy_data[hash][0] for hash in hashs])
if plot_forces is None:
fig = pyplot.figure(figsize=(5., 5.))
ax = fig.add_subplot(111)
else:
fig = pyplot.figure(figsize=(5., 10.))
ax = fig.add_subplot(211)
# energy plot
count = 0
while count < no_of_images:
hash = hashs[count]
ax.plot(energy_data[hash][0], energy_data[hash][1], color)
count += 1
# draw horizontal line for rmse
ax.plot(
[min_act_energy, max_act_energy],
[energy_per_atom_rmse, energy_per_atom_rmse],
color='black',
linestyle='dashed',
lw=1,
)
ax.text(max_act_energy,
energy_per_atom_rmse,
'energy rmse = %6.5f' % energy_per_atom_rmse,
ha='right',
va='bottom',
color='black')
ax.set_xlabel(r"\textit{ab initio} energy (eV) per atom")
ax.set_ylabel(
r"$|$\textit{ab initio} energy - \textit{Amp} energy$|$ / number of atoms"
)
ax.set_title("Energies")
if plot_forces:
force_data = {}
# Reading force script
try:
fp = paropen(forcescript, 'rb')
data = json.load(fp)
except IOError:
pass
else:
hashs = data.keys()
no_of_images = len(hashs)
count0 = 0
while count0 < no_of_images:
hash = hashs[count0]
force_data[hash] = {}
indices = data[hash].keys()
len_of_indices = len(indices)
count1 = 0
while count1 < len_of_indices:
index = indices[count1]
force_data[hash][int(index)] = {}
ks = data[hash][index].keys()
len_of_ks = len(ks)
count2 = 0
while count2 < len_of_ks:
k = ks[count2]
force_data[hash][int(index)][int(k)] = \
data[hash][index][k]
count2 += 1
count1 += 1
count0 += 1
# calculating errors for images if json is not found
if len(force_data.keys()) == 0:
count = 0
while count < no_of_images:
hash = hashs[count]
atoms = images[hash]
no_of_atoms = len(atoms)
force_data[hash] = {}
act_force = atoms.get_forces(apply_constraint=False)
atoms.set_calculator(calc)
amp_force = calc.get_forces(atoms)
index = 0
while index < no_of_atoms:
force_data[hash][index] = {}
k = 0
while k < 3:
force_data[hash][index][k] = \
[act_force[index][k],
abs(amp_force[index][k] - act_force[index][k])]
k += 1
index += 1
count += 1
# saving force script
try:
json.dump(force_data, forcescript)
forcescript.flush()
return
except AttributeError:
with paropen(forcescript, 'wb') as outfile:
json.dump(force_data, outfile)
# calculating force rmse
force_square_error = 0.
count = 0
while count < no_of_images:
hash = hashs[count]
atoms = images[hash]
no_of_atoms = len(atoms)
index = 0
while index < no_of_atoms:
k = 0
while k < 3:
force_square_error += \
((1.0 / 3.0) * force_data[hash][index][k][1] ** 2.) / \
no_of_atoms
k += 1
index += 1
count += 1
del hash, index, k
force_rmse = np.sqrt(force_square_error / no_of_images)
min_act_force = min([
force_data[hash][index][k][0] for hash in hashs
for index in range(len(images[hash])) for k in range(3)
])
max_act_force = max([
force_data[hash][index][k][0] for hash in hashs
for index in range(len(images[hash])) for k in range(3)
])
##############################################################
# force plot
ax = fig.add_subplot(212)
count = 0
while count < no_of_images:
hash = hashs[count]
atoms = images[hash]
no_of_atoms = len(atoms)
index = 0
while index < no_of_atoms:
k = 0
while k < 3:
ax.plot(force_data[hash][index][k][0],
force_data[hash][index][k][1], color)
k += 1
index += 1
count += 1
# draw horizontal line for rmse
ax.plot(
[min_act_force, max_act_force],
[force_rmse, force_rmse],
color='black',
linestyle='dashed',
lw=1,
)
ax.text(
max_act_force,
force_rmse,
'force rmse = %5.4f' % force_rmse,
ha='right',
va='bottom',
color='black',
)
ax.set_xlabel(r"\textit{ab initio} force, eV/\AA")
ax.set_ylabel(r"$|$\textit{ab initio} force - \textit{Amp} force$|$")
ax.set_title(r"Forces")
##############################################################
fig.savefig(plotfile)
total = 0
#time1 = time.time()
for struct_type in struct_types:
for dyn_type in dyn_types:
top_direct = ('%s_%s/') % (struct_type, dyn_type)
if os.path.isdir(top_direct):
print(top_direct)
sub_total = 0
sub_dirs = sorted(glob(top_direct + '*/'))
for sub_dir in sub_dirs:
name = sub_dir.split('/')[-2]
if name.isdigit():
#print()
traj = io.Trajectory(filename=sub_dir +
'images_supercell.traj',
mode='r')
subsub_total = 0
#for image in traj:
for image_index in range(len(traj)):
image = traj[image_index]
if int(name) % 2 == 0:
#if image_index >= 0 and image_index%1 == 0:
train_images.append(image)
elif struct_type == 'known':
train_images.append(image)
else:
test_images.append(image)
subsub_total += 1
print(
width = 0.01 # Fermi width
nbands = 6 # bands in GS calculation
nconv = 4 # bands in GS calculation to converge
R = 2.99 # starting distance
iex = 1 # excited state index
d = 0.01 # step for numerical force evaluation
exc = 'LDA' # xc for the linear response TDDFT kernel
s = Cluster([Atom('Na'), Atom('Na', [0, 0, R])])
s.minimal_box(box, h=h)
c = GPAW(h=h,
nbands=nbands,
eigensolver='cg',
occupations=FermiDirac(width=width),
setups={'Na': '1'},
convergence={'bands': nconv})
c.calculate(s)
lr = LrTDDFT(c, xc=exc, eps=0.1, jend=nconv - 1)
ex = ExcitedState(lr, iex, d=d)
s.set_calculator(ex)
ftraj = 'relax_ex' + str(iex)
ftraj += '_box' + str(box) + '_h' + str(h)
ftraj += '_d' + str(d) + '.traj'
traj = io.Trajectory(ftraj, 'w', s)
dyn = optimize.FIRE(s)
dyn.attach(traj.write)
dyn.run(fmax=0.05)
