def plot_history(abinitfile, dataset=""):
history = get_history(abinitfile, dataset)
av = InputVariables(abinitfile.get_input_filename())
if dataset == "":
filep = abinitfile.basedir + "/" + abinitfile.files['tmpout'] + ".pdf"
else:
filep = abinitfile.basedir + "/" + abinitfile.files['tmpout'] + "_DS" + str(dataset) + ".pdf"
xcart = history.variables['xcart'][:]
fcart = history.variables['fcart'][:]
# rprimd = history.variables['rprimd'][:]
etotal = history.variables['etotal'][:]
if 'ekin' in history.variables:
ekin = history.variables['ekin'][:]
if max(history.variables['ekin'][:]) == 0.0:
ekin = None
else:
ekin = None
# Getting Labels of atoms
labels = [av.atom_name(i) for i in range(av.get_value('natom', dataset))]
znucl = av.get_value('znucl', idtset=dataset)
typat = av.get_value('typat', idtset=dataset)
bonds = compute_bonds(typat, xcart, znucl)
# natom = len(xcart[0])
# ComputeAngles(bonds,natom)
plot_history_energy(etotal, ekin, fcart, labels, bonds, filep)
def plot_history(abinitfile, dataset=""):
history = get_history(abinitfile, dataset)
av = InputVariables(abinitfile.get_input_filename())
if dataset == "":
filep = abinitfile.basedir + "/" + abinitfile.files['tmpout'] + ".pdf"
else:
filep = abinitfile.basedir + "/" + abinitfile.files[
'tmpout'] + "_DS" + str(dataset) + ".pdf"
xcart = history.variables['xcart'][:]
fcart = history.variables['fcart'][:]
# rprimd = history.variables['rprimd'][:]
etotal = history.variables['etotal'][:]
if 'ekin' in history.variables:
ekin = history.variables['ekin'][:]
if max(history.variables['ekin'][:]) == 0.0:
ekin = None
else:
ekin = None
# Getting Labels of atoms
labels = [av.atom_name(i) for i in range(av.get_value('natom', dataset))]
znucl = av.get_value('znucl', idtset=dataset)
typat = av.get_value('typat', idtset=dataset)
bonds = compute_bonds(typat, xcart, znucl)
# natom = len(xcart[0])
# ComputeAngles(bonds,natom)
plot_history_energy(etotal, ekin, fcart, labels, bonds, filep)
def structure_from_file(structure_file):
st = None
if not os.path.isfile(structure_file):
print("ERROR: Could not open file '%s'" % structure_file)
sys.exit(1)
if structure_file[-4:].lower() == 'json':
st = Structure.load_json(structure_file)
elif structure_file[-3:].lower() == 'cif' and HAS_PYMATGEN:
import pychemia.external.pymatgen
st = pychemia.external.pymatgen.cif2structure(structure_file)[0]
elif structure_file[-6:].lower() == 'poscar':
st = read_poscar(structure_file)
elif structure_file[-6:].lower() == 'contcar':
st = read_poscar(structure_file)
elif structure_file[-6:].lower() == 'abinit.in':
av = InputVariables(structure_file)
av.get_structure()
else:
try:
st = read_poscar(structure_file)
except ValueError:
print("ERROR: Could not extract structure from file '%s'" %
structure_file)
exit(1)
return st
def __init__(self, name, abinit_input='abinit.in', natpawu=None, oxidations=None):
Population.__init__(self, name, 'global')
if not os.path.isfile(abinit_input):
print("Abinit input not found")
raise ValueError
self.input = InputVariables(abinit_input)
self.structure = self.input.get_structure()
self.maxlpawu = max(self.input.get_value('lpawu'))
if natpawu is None:
spinat = self.input.get_value('spinat')
if spinat is None:
print('I could not determine the number of atoms playing a role in the DFT+U calculation')
raise ValueError('Could not determine natpawu')
else:
spinat = np.array(spinat).reshape((-1, 3))
self.natpawu = np.sum(np.apply_along_axis(np.linalg.norm, 1, spinat) != 0)
else:
self.natpawu = natpawu
if self.input.has_variable('nsppol'):
self.nsppol = self.input.get_value('nsppol')
else:
self.nsppol = 1
if self.input.has_variable('nspinor'):
self.nspinor = self.input.get_value('nspinor')
else:
self.nspinor = 1
self.oxidations = oxidations
self.connection = [1, -1, -1, 1]
def test_abinit_input():
"""
Tests (pychemia.code.abinit) [input] :
"""
if pychemia.HAS_SCIPY and pychemia.HAS_SCIENTIFIC:
from pychemia.code.abinit import AbiFiles, InputVariables
filename = "pychemia/test/data/abinit_01/abinit.files"
abf = AbiFiles(filename)
inp = InputVariables(abf)
print(inp)
print(len(inp))
assert len(inp) == 31
assert inp.get_value('ecut') == 10
assert len(inp.get_dtsets_keys()) == 12
assert inp.get_value('ntime', 41) == 10
assert inp.get_value('acell', 41)[0] == 14
def prepare_folder(self, entry_id, workdir='.', source_dir='.'):
"""
Prepare directories for abinit execution
:param entry_id: bson.ObjectID of the entry that will be used for preparing the folder
:param source_dir: (str) is the directory where 'abinit.files' and 'batch.pbs' should be present
those directories will be symbolically linked inside the individual work directories
:param workdir: (str) Base work directory for abinit executions. Inside this directory, a set of subdirectories
will be created using the mongo ID as name.
"""
# Individual workdir
iworkdir = workdir + os.sep + str(entry_id)
if not os.path.isdir(iworkdir):
os.mkdir(iworkdir)
if os.path.lexists(iworkdir + os.sep + 'abinit.files'):
os.remove(iworkdir + os.sep + 'abinit.files')
if not os.path.isfile(source_dir + os.sep + 'abinit.files'):
print(
'WARNIG: The file %s should be present on %s, symbolic links will be created pointing '
'to that location' % ('abinit.files', source_dir))
os.symlink(os.path.abspath(source_dir + os.sep + 'abinit.files'),
iworkdir + os.sep + 'abinit.files')
abiinput = InputVariables(self.input_path)
params = self.get_correlation_params(entry_id, final=False)
dmatpawu = params2dmatpawu(params)
abiinput['dmatpawu'] = list(dmatpawu.flatten())
abiinput.write(iworkdir + os.sep + 'abinit.in')
d_abiinput = InputVariables(iworkdir + os.sep + 'abinit.in')
d_dmatpawu = d_abiinput['dmatpawu']
assert (d_dmatpawu is not None)
d_params = dmatpawu2params(d_dmatpawu, self.ndim)
if not np.all(
np.sum(d_params['occupations'], axis=1) == np.array(
self.num_electrons_dftu)):
print(
'ERROR: Inconsistent number of DFT+U electrons for correlated orbitals: %s'
% entry_id)
print('From the population: %s ' % self.num_electrons_dftu)
print('From "abinit.in": %s ' % d_params['occupations'])
def plot_bonds(listabifile, listidtset):
pp = PdfPages("bonds.pdf")
plt.ioff()
if not listidtset:
allbonds = get_all_bonds(listabifile)
else:
allbonds = get_all_bonds(listabifile, listidtset)
plt.figure(figsize=(32, 20), dpi=100)
plt.subplots_adjust(left=0.05,
bottom=0.05,
right=0.95,
top=0.95,
wspace=None,
hspace=None)
abivar = InputVariables(listabifile[0].get_input_filename())
nbond = len(allbonds[0])
n = 0
for ibond in allbonds:
if len(ibond) != nbond:
print('ERROR: Number of bonds changed')
if not listidtset:
print(
(listabifile[n].basedir, 'contains', len(ibond), 'bonds'))
else:
print(
(listabifile[n].filename + ':' + listidtset[n], 'contains',
len(ibond), 'bonds'))
n += 1
iplot = 1
for ibond in range(nbond):
plt.subplot(5, 4, iplot)
y = [bohr_angstrom * seti[ibond][2] for seti in allbonds]
label = abivar.atom_name(seti[ibond][0]) + ' ' + abivar.atom_name(
seti[ibond][1])
plt.plot(y, label=label)
plt.plot(y, 'ro')
iplot += 1
plt.legend()
pp.savefig()
plt.clf()
for ibond in range(nbond):
y = [bohr_angstrom * seti[ibond][2] for seti in allbonds]
label = abivar.atom_name(seti[ibond][0]) + ' ' + abivar.atom_name(
seti[ibond][1])
plt.plot(y, label=label)
plt.plot(y, 'ro')
plt.text(0.09, y[0] + 0.001, label, size='small')
iplot += 1
plt.legend()
pp.savefig()
pp.close()
def __init__(self,
name,
abinit_input='abinit.in',
natpawu=None,
oxidations=None):
Population.__init__(self, name, 'global')
if not os.path.isfile(abinit_input):
print("Abinit input not found")
raise ValueError
self.input = InputVariables(abinit_input)
self.structure = self.input.get_structure()
self.maxlpawu = max(self.input.get_value('lpawu'))
if natpawu is None:
spinat = self.input.get_value('spinat')
if spinat is None:
print(
'I could not determine the number of atoms playing a role in the DFT+U calculation'
)
raise ValueError('Could not determine natpawu')
else:
spinat = np.array(spinat).reshape((-1, 3))
self.natpawu = np.sum(
np.apply_along_axis(np.linalg.norm, 1, spinat) != 0)
else:
self.natpawu = natpawu
if self.input.has_variable('nsppol'):
self.nsppol = self.input.get_value('nsppol')
else:
self.nsppol = 1
if self.input.has_variable('nspinor'):
self.nspinor = self.input.get_value('nspinor')
else:
self.nspinor = 1
self.oxidations = oxidations
self.connection = [1, -1, -1, 1]
def get_all_bonds(abinitfile, dtset=''):
allbonds = []
index = 0
for abf in abinitfile:
if dtset == '':
idt = ''
else:
idt = int(dtset[index])
index += 1
filep = abf.basedir + "/" + abf.files['tmpout'] + "_OUT.nc"
out = InputVariables(filep)
xcart = out.get_value('xcart', idtset=idt)
znucl = out.get_value('znucl', idtset=idt)
typat = out.get_value('typat', idtset=idt)
bonds = compute_bonds(typat, xcart, znucl)
allbonds.append(bonds)
abivar = InputVariables(abinitfile[0].get_input_filename())
save_bonds(allbonds, abivar)
return allbonds
def structure_from_file(structure_file):
st = None
if not os.path.isfile(structure_file):
print("ERROR: Could not open file '%s'" % structure_file)
sys.exit(1)
if structure_file[-4:].lower() == 'json':
st = Structure.load_json(structure_file)
elif structure_file[-3:].lower() == 'cif' and HAS_PYMATGEN:
import pychemia.external.pymatgen
st = pychemia.external.pymatgen.cif2structure(structure_file)[0]
elif structure_file[-6:].lower() == 'poscar':
st = read_poscar(structure_file)
elif structure_file[-6:].lower() == 'contcar':
st = read_poscar(structure_file)
elif structure_file[-6:].lower() == 'abinit.in':
av = InputVariables(structure_file)
av.get_structure()
else:
try:
st = read_poscar(structure_file)
except ValueError:
print("ERROR: Could not extract structure from file '%s'" % structure_file)
exit(1)
return st
def test_abinit_input():
"""
Tests (pychemia.code.abinit) [input] :
"""
if pychemia.HAS_SCIPY and pychemia.HAS_SCIENTIFIC:
from pychemia.code.abinit import AbiFiles, InputVariables
filename = "pychemia/test/data/abinit_01/abinit.files"
abf = AbiFiles(filename)
inp = InputVariables(abf)
print(inp)
print(len(inp))
assert len(inp) == 31
assert inp.get_value('ecut') == 10
assert len(inp.get_dtsets_keys()) == 12
assert inp.get_value('ntime', 41) == 10
assert inp.get_value('acell', 41)[0] == 14
def __init__(self,
name,
input_path='abinit.in',
num_electrons_dftu=None,
num_indep_matrices=None,
connections=None):
"""
This population is created with the purpose of global optimization of correlated orbitals 'd'
and 'f'.
The population is basically a collection of ABINIT inputs, the candidates have the same structure and
uses the same input variables with exception of 'dmatpawu', the purpose of the
population is to use global-population searchers to find the correlation matrices
'dmatpawu' that minimizes the energy.
The variable 'dmatpawu' is a list of numbers that can be arranged into N matrices.
The matrices are 5x5 for 'd' orbitals and 7x7 for 'f' orbitals.
:param name: The name of the 'PyChemiaDB' database created to stored the different
set of variables and the resulting output from abinit.
When using databases protected with username and password, the database
should be created independently and the database object must be use
as the 'name' argument
:param input_path: The abinit input file, all the variables will be preserve for all new candidates, except
for 'dmatpawu' the only variable that changes.
:param num_electrons_dftu: Example [5, 1, 5, 1]
"""
# Call the parent class initializer to link the PyChemiaDB that will be used
Population.__init__(self, name, 'global', distance_tolerance=0.1)
# Checking for existence of 'abinit.in'
if not os.path.isfile(input_path):
raise ValueError("Abinit input not found")
# Reading the input variables and getting the structure
self.input_path = input_path
self.input = InputVariables(input_path)
if 'dmatpawu' not in self.input.variables:
raise ValueError(
"Abinit input file does not contain 'dmatpawu' variable")
self.structure = self.input.get_structure()
print('Orbital population:')
print('Species [znucl]: %s' % self.input['znucl'])
self.natpawu = 0
print('Orbitals corrected:')
for i in range(self.input['ntypat']):
if self.input['lpawu'][i] == -1:
print("%3s : False" % self.input['znucl'][i])
else:
print("%3s : True (l=%d)" %
(self.input['znucl'][i], self.input['lpawu'][i]))
self.natpawu += sum(
[1 for x in self.input['typat'] if x == i + 1])
print('Number of atoms where DFT+U is applied: %d' % self.natpawu)
# Computing the orbital that will be corrected
# 2 (d-orbitals) or 3 (f-orbitals)
self.maxlpawu = max(self.input['lpawu'])
if self.maxlpawu == 2:
print("Correlation of 'd' orbitals")
elif self.maxlpawu == 3:
print("Correlation of 'f' orbitals")
# nsppol is the number of independent spin polarisations. Can take the values 1 or 2
if self.input.has_variable('nsppol'):
self.nsppol = self.input.get_value('nsppol')
else:
# Default from ABINIT
self.nsppol = 1
# nspinor it the umber of spinorial components of the wavefunctions
if self.input.has_variable('nspinor'):
self.nspinor = self.input.get_value('nspinor')
else:
self.nspinor = 1
# nspden is the number of spin-density components
if self.input.has_variable('nspden'):
self.nspden = self.input.get_value('nspden')
else:
self.nspden = self.nsppol
if self.nsppol == 1 and self.nspinor == 1 and self.nspden == 1:
# Non-magnetic system (nsppol=1, nspinor=1, nspden=1):
# One (2lpawu+1)x(2lpawu+1) dmatpawu matrix is given for each atom on which +U is applied.
# It contains the "spin-up" occupations.
self.nmatrices = self.natpawu
elif self.nsppol == 2 and self.nspinor == 1 and self.nspden == 2:
# Ferromagnetic spin-polarized (collinear) system (nsppol=2, nspinor=1, nspden=2):
# Two (2lpawu+1)x(2lpawu+1) dmatpawu matrices are given for each atom on which +U is applied.
# They contain the "spin-up" and "spin-down" occupations.
self.nmatrices = 2 * self.natpawu
elif self.nsppol == 1 and self.nspinor == 1 and self.nspden == 2:
# Anti-ferromagnetic spin-polarized(collinear) system(nsppol=1, nspinor=1, nspden=2):
# One(2lpawu + 1)x(2lpawu + 1) dmatpawu matrix is given for each atom on which +U is applied.
# It contains the "spin-up" occupations.
self.nmatrices = self.natpawu
elif self.nsppol == 1 and self.nspinor == 2 and self.nspden == 4:
# Non-collinear magnetic system (nsppol=1, nspinor=2, nspden=4):
# Two (2lpawu+1)x(2lpawu+1) dmatpawu matrices are given for each atom on which +U is applied.
# They contains the "spin-up" and "spin-down" occupations (defined as n_up=(n+|m|)/2 and n_dn=(n-|m|)/2),
# where m is the integrated magnetization vector).
self.nmatrices = 2 * self.natpawu
elif self.nsppol == 1 and self.nspinor == 2 and self.nspden == 1:
# Non-collinear magnetic system with zero magnetization (nsppol=1, nspinor=2, nspden=1):
# Two (2lpawu+1)x(2lpawu+1) dmatpawu matrices are given for each atom on which +U is applied.
# They contain the "spin-up" and "spin-down" occupations;
self.nmatrices = 2 * self.natpawu
print('Variables controling the total number of matrices')
print('nsppol : %d' % self.nsppol)
print('nspinor: %d' % self.nspinor)
print('nspden : %d' % self.nspden)
print('Total number of matrices expected on dmatpawu: %d' %
self.nmatrices)
if num_electrons_dftu is None:
abiinput = InputVariables(input_path)
dmatpawu = np.array(abiinput['dmatpawu']).reshape(
-1, self.ndim, self.ndim)
params = dmatpawu2params(dmatpawu, 5)
self.num_electrons_dftu = np.apply_along_axis(
sum, 1, params['occupations'])
else:
self.num_electrons_dftu = np.array(num_electrons_dftu)
print('Number of electrons for each correlation matrix: %s' %
self.num_electrons_dftu)
if num_indep_matrices is not None:
self.num_indep_matrices = num_indep_matrices
else:
self.num_indep_matrices = self.nmatrices
self.num_electrons_dftu = [int(x) for x in self.num_electrons_dftu]
print('Number of independent matrices: %d' % self.num_indep_matrices)
if connections is not None:
self.connections = list(connections)
if len(self.connections) != self.nmatrices:
raise ValueError(
'Number of connections between matrices is not consistent with the number of matrices '
'defined on dmatpawu')
print('Connections: %s' % self.connections)
else:
self.connections = list(range(self.nmatrices))
class OrbitalDFTU(Population):
def __init__(self,
name,
input_path='abinit.in',
num_electrons_dftu=None,
num_indep_matrices=None,
connections=None):
"""
This population is created with the purpose of global optimization of correlated orbitals 'd'
and 'f'.
The population is basically a collection of ABINIT inputs, the candidates have the same structure and
uses the same input variables with exception of 'dmatpawu', the purpose of the
population is to use global-population searchers to find the correlation matrices
'dmatpawu' that minimizes the energy.
The variable 'dmatpawu' is a list of numbers that can be arranged into N matrices.
The matrices are 5x5 for 'd' orbitals and 7x7 for 'f' orbitals.
:param name: The name of the 'PyChemiaDB' database created to stored the different
set of variables and the resulting output from abinit.
When using databases protected with username and password, the database
should be created independently and the database object must be use
as the 'name' argument
:param input_path: The abinit input file, all the variables will be preserve for all new candidates, except
for 'dmatpawu' the only variable that changes.
:param num_electrons_dftu: Example [5, 1, 5, 1]
"""
# Call the parent class initializer to link the PyChemiaDB that will be used
Population.__init__(self, name, 'global', distance_tolerance=0.1)
# Checking for existence of 'abinit.in'
if not os.path.isfile(input_path):
raise ValueError("Abinit input not found")
# Reading the input variables and getting the structure
self.input_path = input_path
self.input = InputVariables(input_path)
if 'dmatpawu' not in self.input.variables:
raise ValueError(
"Abinit input file does not contain 'dmatpawu' variable")
self.structure = self.input.get_structure()
print('Orbital population:')
print('Species [znucl]: %s' % self.input['znucl'])
self.natpawu = 0
print('Orbitals corrected:')
for i in range(self.input['ntypat']):
if self.input['lpawu'][i] == -1:
print("%3s : False" % self.input['znucl'][i])
else:
print("%3s : True (l=%d)" %
(self.input['znucl'][i], self.input['lpawu'][i]))
self.natpawu += sum(
[1 for x in self.input['typat'] if x == i + 1])
print('Number of atoms where DFT+U is applied: %d' % self.natpawu)
# Computing the orbital that will be corrected
# 2 (d-orbitals) or 3 (f-orbitals)
self.maxlpawu = max(self.input['lpawu'])
if self.maxlpawu == 2:
print("Correlation of 'd' orbitals")
elif self.maxlpawu == 3:
print("Correlation of 'f' orbitals")
# nsppol is the number of independent spin polarisations. Can take the values 1 or 2
if self.input.has_variable('nsppol'):
self.nsppol = self.input.get_value('nsppol')
else:
# Default from ABINIT
self.nsppol = 1
# nspinor it the umber of spinorial components of the wavefunctions
if self.input.has_variable('nspinor'):
self.nspinor = self.input.get_value('nspinor')
else:
self.nspinor = 1
# nspden is the number of spin-density components
if self.input.has_variable('nspden'):
self.nspden = self.input.get_value('nspden')
else:
self.nspden = self.nsppol
if self.nsppol == 1 and self.nspinor == 1 and self.nspden == 1:
# Non-magnetic system (nsppol=1, nspinor=1, nspden=1):
# One (2lpawu+1)x(2lpawu+1) dmatpawu matrix is given for each atom on which +U is applied.
# It contains the "spin-up" occupations.
self.nmatrices = self.natpawu
elif self.nsppol == 2 and self.nspinor == 1 and self.nspden == 2:
# Ferromagnetic spin-polarized (collinear) system (nsppol=2, nspinor=1, nspden=2):
# Two (2lpawu+1)x(2lpawu+1) dmatpawu matrices are given for each atom on which +U is applied.
# They contain the "spin-up" and "spin-down" occupations.
self.nmatrices = 2 * self.natpawu
elif self.nsppol == 1 and self.nspinor == 1 and self.nspden == 2:
# Anti-ferromagnetic spin-polarized(collinear) system(nsppol=1, nspinor=1, nspden=2):
# One(2lpawu + 1)x(2lpawu + 1) dmatpawu matrix is given for each atom on which +U is applied.
# It contains the "spin-up" occupations.
self.nmatrices = self.natpawu
elif self.nsppol == 1 and self.nspinor == 2 and self.nspden == 4:
# Non-collinear magnetic system (nsppol=1, nspinor=2, nspden=4):
# Two (2lpawu+1)x(2lpawu+1) dmatpawu matrices are given for each atom on which +U is applied.
# They contains the "spin-up" and "spin-down" occupations (defined as n_up=(n+|m|)/2 and n_dn=(n-|m|)/2),
# where m is the integrated magnetization vector).
self.nmatrices = 2 * self.natpawu
elif self.nsppol == 1 and self.nspinor == 2 and self.nspden == 1:
# Non-collinear magnetic system with zero magnetization (nsppol=1, nspinor=2, nspden=1):
# Two (2lpawu+1)x(2lpawu+1) dmatpawu matrices are given for each atom on which +U is applied.
# They contain the "spin-up" and "spin-down" occupations;
self.nmatrices = 2 * self.natpawu
print('Variables controling the total number of matrices')
print('nsppol : %d' % self.nsppol)
print('nspinor: %d' % self.nspinor)
print('nspden : %d' % self.nspden)
print('Total number of matrices expected on dmatpawu: %d' %
self.nmatrices)
if num_electrons_dftu is None:
abiinput = InputVariables(input_path)
dmatpawu = np.array(abiinput['dmatpawu']).reshape(
-1, self.ndim, self.ndim)
params = dmatpawu2params(dmatpawu, 5)
self.num_electrons_dftu = np.apply_along_axis(
sum, 1, params['occupations'])
else:
self.num_electrons_dftu = np.array(num_electrons_dftu)
print('Number of electrons for each correlation matrix: %s' %
self.num_electrons_dftu)
if num_indep_matrices is not None:
self.num_indep_matrices = num_indep_matrices
else:
self.num_indep_matrices = self.nmatrices
self.num_electrons_dftu = [int(x) for x in self.num_electrons_dftu]
print('Number of independent matrices: %d' % self.num_indep_matrices)
if connections is not None:
self.connections = list(connections)
if len(self.connections) != self.nmatrices:
raise ValueError(
'Number of connections between matrices is not consistent with the number of matrices '
'defined on dmatpawu')
print('Connections: %s' % self.connections)
else:
self.connections = list(range(self.nmatrices))
def __str__(self):
ret = ' Population LDA+U\n\n'
ret += ' Name: %s\n' % self.name
ret += ' Tag: %s\n' % self.tag
ret += ' Formula: %s\n' % self.structure.formula
ret += ' natpawu: %d\n' % self.natpawu
ret += ' nmatrices: %d\n' % self.nmatrices
ret += ' maxlpawu: %d\n' % self.maxlpawu
ret += ' num_indep_matrices: %s\n' % self.num_indep_matrices
ret += ' connections: %s\n' % self.connections
ret += ' Members: %d\n' % len(self.members)
ret += ' Actives: %d\n' % len(self.actives)
ret += ' Evaluated: %d\n' % len(self.evaluated)
return ret
@property
def ndim(self):
"""
Dimension of the matrices defined on dmatpawu, for 'd' orbitals is 5 for 'f' orbitals is 7
:return:
"""
return 2 * self.maxlpawu + 1
@property
def to_dict(self):
ret = super(self.__class__, self).to_dict
ret['input_path'] = self.input_path
ret['num_electrons_dftu'] = list(self.num_electrons_dftu)
ret['num_indep_matrices'] = self.num_indep_matrices
ret['connections'] = list(self.connections)
return ret
def add_random(self):
"""
Creates a new set of variables to reconstruct the dmatpawu
matrix_i (integers) is a matrix natpawu x ndim with entries are 0 or 1
matrix_d (deltas) is a matrix natpawu x ndim with entries are [0, 0.5)
P (matrices) is a set of matrices natpawu x ndim x ndim
Those three matrices allow to reconstruct the variable 'dmatpawu' used by ABINIT
:return:
"""
matrices_defined = []
matrix_i = self.num_indep_matrices * [None]
matrix_d = self.num_indep_matrices * [None]
euler = self.num_indep_matrices * [None]
for i in range(self.num_indep_matrices):
nelect = self.num_electrons_dftu[i]
val = [
x for x in list(
itertools.product(list(range(2)), repeat=self.ndim))
if sum(x) == nelect
]
ii = val[np.random.randint(len(val))]
dd = np.zeros(self.ndim)
matrix_i[i] = list(ii)
matrix_d[i] = list(dd)
matrices_defined.append(self.connections[i])
p = gram_smith_qr(self.ndim)
euler[i] = gea_all_angles(p)
data = {
'euler_angles': euler,
'occupations': matrix_i,
'deltas': matrix_d,
'num_matrices': self.num_indep_matrices,
'ndim': self.ndim
}
return self.new_entry(data), None
def cross(self, ids):
"""
Crossing algorithm used notably by GA to mix the information from several candidates
This crossing algorithm is mixing the angles of two correlation matrices preserving the
ordering of the atoms where the angles are applied. The occupations and deltas are also
mixed independently of the euler angles.
:param ids:
:return:
"""
assert len(ids) == 2
properties1 = self.get_correlation_params(ids[0])
properties2 = self.get_correlation_params(ids[1])
euler_angles1 = properties1['euler_angles']
euler_angles2 = properties2['euler_angles']
occupations1 = properties1['occupations']
occupations2 = properties2['occupations']
deltas1 = properties1['deltas']
deltas2 = properties2['deltas']
newdata1 = {
'euler_angles': [],
'occupations': [],
'deltas': [],
'num_matrices': self.num_indep_matrices,
'ndim': self.ndim
}
newdata2 = {
'euler_angles': [],
'occupations': [],
'deltas': [],
'num_matrices': self.num_indep_matrices,
'ndim': self.ndim
}
for i in range(self.num_indep_matrices):
rnd = random.randint(0, 1)
if rnd == 0:
newdata1['euler_angles'].append(euler_angles1[i])
newdata2['euler_angles'].append(euler_angles2[i])
else:
newdata1['euler_angles'].append(euler_angles2[i])
newdata2['euler_angles'].append(euler_angles1[i])
rnd = random.randint(0, 1)
if rnd == 0:
newdata1['occupations'].append(occupations1[i])
newdata2['occupations'].append(occupations2[i])
newdata1['deltas'].append(deltas1[i])
newdata2['deltas'].append(deltas2[i])
else:
newdata1['occupations'].append(occupations2[i])
newdata2['occupations'].append(occupations1[i])
newdata1['deltas'].append(deltas2[i])
newdata2['deltas'].append(deltas1[i])
entry_id = self.new_entry(newdata1)
entry_jd = self.new_entry(newdata2)
return entry_id, entry_jd
def collect_data(self, entry_id, workdir, filename='abinit.out'):
if os.path.isfile(workdir + os.sep + filename):
ao = AbinitOutput(workdir + os.sep + filename)
dmatpawu = get_final_dmatpawu(workdir + os.sep + filename)
dmat = dmatpawu2params(dmatpawu, self.ndim)
if 'etot' in ao.get_energetics():
etot = ao.get_energetics()['etot'][-1]
nres2 = ao.get_energetics()['nres2'][-1]
print('Uploading energy data for %s' % entry_id)
self.set_final_results(entry_id, dmat, etot, nres2)
return True
else:
return False
else:
return False
def set_final_results(self, entry_id, dmat, etot, nres2):
self.pcdb.db.pychemia_entries.update({'_id': entry_id}, {
'$set': {
'properties.final_dmat': dmat,
'properties.etot': etot,
'properties.nres2': nres2
}
})
def collect(self, entry_id, workdir='.'):
idir = workdir + os.sep + str(entry_id)
abinitout = self.get_final_abinit_out(idir)
if self.get_entry(
entry_id) is not None and not self.is_evaluated(entry_id):
print("%s Setting final dmat" % entry_id)
self.set_final_dmat(entry_id, abinitout)
elif self.get_entry(entry_id) is None:
print("%s Is not in database" % entry_id)
elif self.is_evaluated(entry_id):
print("%s Is already evaluated" % entry_id)
def distance(self, entry_id, entry_jd):
"""
Measure of distance for two entries with identifiers 'entry_id' and 'entry_jd'
:param entry_id: Identifier of first entry
:param entry_jd: Identifier of second entry
:return:
"""
dmat1 = self.get_correlation_params(entry_id)
dmat2 = self.get_correlation_params(entry_jd)
euler_angles1 = dmat1['euler_angles']
euler_angles2 = dmat2['euler_angles']
uvect1 = unit_vector(
np.concatenate(
(np.cos(euler_angles1), np.sin(euler_angles1))).flatten())
uvect2 = unit_vector(
np.concatenate(
(np.cos(euler_angles2), np.sin(euler_angles2))).flatten())
dist_euler = 1 - np.dot(uvect1, uvect2)
return dist_euler
def evaluate_entry(self, entry_id):
"""
Evaluation externalized, no implemented
:param entry_id:
:return:
"""
pass
def evaluator(self,
username,
basedir,
queue,
walltime,
ppn,
features=None):
while True:
# 1. Get actives no evaluated
ane = self.actives_no_evaluated
if len(ane) > 0:
print("Candidates to be evaluated: %d" % len(ane))
else:
print("No candidates to be evaluated")
# 2. Get jobs in queue
jobs = get_jobs(username)
jobnames = [jobs[x]['Job_Name'] for x in jobs]
check = False
for entry_id in ane:
if str(entry_id) not in jobnames:
check = True
else:
jobids = [
jobs[x]['Job_Id'] for x in jobs
if jobs[x]['Job_Name'] == str(entry_id)
]
for jobid in jobids:
check = True
if jobs[jobid]['job_state'] != 'C':
check = False
break
to_submit = False
if check:
to_submit = True
if not os.path.isdir(basedir + os.sep + str(entry_id)):
self.prepare_folder(entry_id,
workdir=basedir,
source_dir=basedir)
elif os.path.isfile(basedir + os.sep + str(entry_id) +
os.sep + 'COMPLETE'):
abinitout = self.get_final_abinit_out(basedir +
os.sep +
str(entry_id))
if abinitout is not None:
abo = AbinitOutput(abinitout)
# check if finished
if abo.is_finished:
# Collect results
self.collect(entry_id, basedir)
to_submit = False
if to_submit:
self.submit(entry_id, basedir, queue, walltime, ppn,
features)
print('Sleeping for 10 minutes')
time.sleep(600)
def from_dict(self, population_dict):
return self.__init__(
name=self.name,
input_path=population_dict['input_path'],
num_electrons_dftu=population_dict['num_electrons_dftu'],
connections=population_dict['connections'],
num_indep_matrices=population_dict['num_indep_matrices'])
def get_correlation_params(self, entry_id, final=True):
if final:
key = 'final_dmat'
else:
key = 'initial_dmat'
entry = self.get_entry(entry_id, {'properties.' + key: 1},
with_id=False)
if entry is not None:
ret = entry['properties'][key]
else:
ret = None
return ret
@staticmethod
def get_final_abinit_out(path):
outputfile = None
if not os.path.isfile(path + os.sep + 'abinit.in'):
raise ValueError('ERROR: No abinit.in at %s' % path)
for i in np.arange(10, -1, -1):
filename = path + os.sep + 'abinit_%d.out' % i
if os.path.isfile(filename):
outputfile = filename
break
return outputfile
def get_final_properties(self, path):
outputfile = self.get_final_abinit_out(path)
if outputfile is None:
raise ValueError("Not such dir: %s" % path)
# Reading the OUTPUT
dmatpawu = get_final_dmatpawu(outputfile)
odmatpawu = np.array(dmatpawu).reshape(-1, self.ndim, self.ndim)
oparams = dmatpawu2params(odmatpawu, self.ndim)
abo = AbinitOutput(outputfile)
if not abo.is_finished:
print('This output is not finished')
return None, None
data = abo.get_energetics()
nres2 = data['nres2'][-1]
etot = data['etot'][-1]
final_properties = None
if etot is not None and oparams is not None:
final_properties = {
'etot': etot,
'nres2': nres2,
'final_dmat': gs(oparams)
}
return final_properties, etot
def is_evaluated(self, entry_id):
"""
One candidate is considered evaluated if it contains any finite value of energy on the properties.energy field
:param entry_id:
:return:
"""
entry = self.get_entry(entry_id, {'_id': 0, 'properties': 1})
if entry['properties']['etot'] is not None:
return True
else:
return False
def move_random(self, entry_id, factor=0.2, in_place=False, kind='move'):
"""
Move one candidate with identifier 'entry_id' randomly with a factor
given by 'factor'
:param entry_id: Identifier of entry
:param factor: Factor use to scale the randomness of change
:param in_place: If True the candidate is changed keeping the identifier unchanged
:param kind: Use when several algorithms are used for movement. One implemented here
:return:
"""
if self.is_evaluated(entry_id):
dmat = self.get_correlation_params(entry_id)
else:
dmat = self.get_correlation_params(entry_id, final=False)
newdata = dict(dmat)
for i in range(self.num_indep_matrices):
for j in range(self.ndim):
perturbation = dmat['euler_angles'][i][j] + 2 * np.random.rand(
) * factor - factor
if np.pi / 2.0 > perturbation > -np.pi / 2.0:
newdata['euler_angles'][i][j] = perturbation
if in_place:
return self.update_dmat_inplace(entry_id, newdata)
else:
return self.new_entry(newdata, active=False)
def move(self, entry_id, entry_jd, factor=0.2, in_place=False):
"""
Move one candidate with identifier 'entry_id' in the direction of another candidate 'entry_jd'
:param entry_id: Identifier of first entry (Origin)
:param entry_jd: Identifier of second entry (Target)
:param factor: Scale factor for change, 0 scale is the 'Origin' candidate, 1 is the 'Target' candidate
Intermediate values will change candidates accordingly
:param in_place: If True the candidate is changed keeping the identifier unchanged
:return:
"""
if self.is_evaluated(entry_id):
dmat1 = self.get_correlation_params(entry_id)
else:
dmat1 = self.get_correlation_params(entry_id, final=False)
if self.is_evaluated(entry_id):
dmat2 = self.get_correlation_params(entry_jd)
else:
dmat2 = self.get_correlation_params(entry_jd, final=False)
euler_angles1 = dmat1['euler_angles']
euler_angles2 = dmat2['euler_angles']
euler_angles_new = np.zeros(
(self.num_indep_matrices, int(self.ndim * (self.ndim - 1) / 2)))
for i in range(self.num_indep_matrices):
for j in range(int(self.ndim * (self.ndim - 1) / 2)):
angle1 = euler_angles1[i][j]
angle2 = euler_angles2[i][j]
if angle1 < angle2:
if angle2 - angle1 < angle1 - angle2 + 2 * np.pi:
direction = 1 # Forward
angle = angle2 - angle1
else:
direction = -1 # Backward
angle = angle1 - angle2 + 2 * np.pi
else:
if angle1 - angle2 < angle2 - angle1 + 2 * np.pi:
direction = -1 # Backward
angle = angle1 - angle2
else:
direction = 1
angle = angle2 - angle1 + 2 * np.pi
euler_angles_new[i, j] = angle1 + direction * factor * angle
if euler_angles_new[i, j] > np.pi:
euler_angles_new[i, j] -= -2 * np.pi
if euler_angles_new[i, j] < -np.pi:
euler_angles_new[i, j] += -2 * np.pi
newdata = dict(dmat1)
newdata['euler_angles'] = gs(euler_angles_new)
if in_place:
return self.update_dmat_inplace(entry_id, newdata)
else:
return self.new_entry(newdata, active=False)
def new_entry(self, dmat, active=True):
"""
Creates a new entry on the population database from given data.
:param dmat: density matrix params, a dictionrary with 'deltas' for deltas, 'occupations' for the integers
and 'euler_angles' for angles needed to recreate the rotation matrix applied to the orbitals
:param active: if True, the entry is enabled on the DB to be evaluated.
:return:
"""
assert 'euler_angles' in dmat
assert 'occupations' in dmat
assert 'deltas' in dmat
assert 'ndim' in dmat
assert 'num_matrices' in dmat
status = {self.tag: active}
properties = {
'etot': None,
'initial_dmat': dmat,
'nres2': None,
'final_dmat': None
}
entry = {
'structure': self.structure.to_dict,
'properties': properties,
'status': status
}
entry_id = self.insert_entry(entry)
pcm_log.debug('Added new entry: %s with tag=%s: %s' %
(str(entry_id), self.tag, str(active)))
return entry_id
def plot_distance_matrix(self, filename=None, ids=None):
import matplotlib.pyplot as plt
if ids is None:
ids = self.members
if filename is None:
filename = self.name + '.pdf'
else:
if filename[-3:] not in ['pdf', 'png', 'jpg']:
raise ValueError(
"Filename should have extension such as pdf, png or jpg")
m = self.distance_matrix(self.ids_sorted(ids))
fig = plt.figure()
ax = fig.add_axes()
ax.imshow(m)
ax.colorbar()
fig.savefig(filename)
fig.clf()
def prepare_folder(self, entry_id, workdir='.', source_dir='.'):
"""
Prepare directories for abinit execution
:param entry_id: bson.ObjectID of the entry that will be used for preparing the folder
:param source_dir: (str) is the directory where 'abinit.files' and 'batch.pbs' should be present
those directories will be symbolically linked inside the individual work directories
:param workdir: (str) Base work directory for abinit executions. Inside this directory, a set of subdirectories
will be created using the mongo ID as name.
"""
# Individual workdir
iworkdir = workdir + os.sep + str(entry_id)
if not os.path.isdir(iworkdir):
os.mkdir(iworkdir)
if os.path.lexists(iworkdir + os.sep + 'abinit.files'):
os.remove(iworkdir + os.sep + 'abinit.files')
if not os.path.isfile(source_dir + os.sep + 'abinit.files'):
print(
'WARNIG: The file %s should be present on %s, symbolic links will be created pointing '
'to that location' % ('abinit.files', source_dir))
os.symlink(os.path.abspath(source_dir + os.sep + 'abinit.files'),
iworkdir + os.sep + 'abinit.files')
abiinput = InputVariables(self.input_path)
params = self.get_correlation_params(entry_id, final=False)
dmatpawu = params2dmatpawu(params)
abiinput['dmatpawu'] = list(dmatpawu.flatten())
abiinput.write(iworkdir + os.sep + 'abinit.in')
d_abiinput = InputVariables(iworkdir + os.sep + 'abinit.in')
d_dmatpawu = d_abiinput['dmatpawu']
assert (d_dmatpawu is not None)
d_params = dmatpawu2params(d_dmatpawu, self.ndim)
if not np.all(
np.sum(d_params['occupations'], axis=1) == np.array(
self.num_electrons_dftu)):
print(
'ERROR: Inconsistent number of DFT+U electrons for correlated orbitals: %s'
% entry_id)
print('From the population: %s ' % self.num_electrons_dftu)
print('From "abinit.in": %s ' % d_params['occupations'])
def recover(self):
pass
def set_final_dmat(self, entry_id, abinitout):
abo = AbinitOutput(abinitout)
if not abo.is_finished:
return None
dmatpawu = get_final_dmatpawu(abinitout)
if dmatpawu is None:
return None
odmatpawu = np.array(dmatpawu).reshape(-1, self.ndim, self.ndim)
oparams = dmatpawu2params(odmatpawu, self.ndim)
data = abo.get_energetics()
if data is None:
return None
nres2 = data['nres2'][-1]
etot = data['etot'][-1]
if not np.all(
np.sum(oparams['occupations'], axis=1) == np.array(
self.num_electrons_dftu)):
print(
'ERROR: Inconsistent number of DFT+U electrons for correlated orbitals: %s'
% entry_id)
print('From the population : %s ' % self.num_electrons_dftu)
print('From %20s : %s ' % (abinitout, oparams['occupations']))
return self.pcdb.db.pychemia_entries.update({'_id': entry_id}, {
'$set': {
'properties.etot': etot,
'properties.nres2': nres2,
'properties.final_dmat': gs(oparams)
}
})
def str_entry(self, entry_id):
entry = self.get_entry(entry_id, projection={'properties': 1})
ret = "%s etot: %7.3f nres2: %9.3e" % (entry_id,
entry['properties']['etot'],
entry['properties']['nres2'])
return ret
@staticmethod
def submit(entry_id, workdir, queue, walltime, ppn, features):
idir = str(entry_id)
workdir = os.path.abspath(workdir)
path = workdir + os.sep + idir
outputs = [x for x in os.listdir(path) if x[-4:] == '.out']
for ifile in outputs:
os.remove(path + os.sep + ifile)
cwd = os.getcwd()
os.chdir(path)
if os.path.lexists('batch.pbs'):
os.remove('batch.pbs')
pbs = PBSRunner(path)
pbs.initialize(nodes=1,
ppn=ppn,
walltime=walltime,
message='ae',
queue=queue,
features=features)
pbs.set_template('../template')
pbs.write_pbs()
output = subprocess.check_output('qsub batch.pbs', shell=True).strip()
print("Entry: %s Job: %s" % (entry_id, output))
os.chdir(cwd)
def update_dmat_inplace(self, entry_id, dmat):
return self.pcdb.db.pychemia_entries.update({'_id': entry_id}, {
'$set': {
'properties.initial_dmat': dmat,
'properties.etot': None,
'properties.nres2': None,
'properties.final_dmat': dmat
}
})
def value(self, entry_id):
"""
Return the energy value associated to the candidate with identifier 'entry_id'
:param entry_id:
:return:
"""
entry = self.get_entry(entry_id, {'properties.etot': 1})
return entry['properties']['etot']
class OrbitalDFTU(Population):
def __init__(self,
name,
abinit_input='abinit.in',
natpawu=None,
oxidations=None):
Population.__init__(self, name, 'global')
if not os.path.isfile(abinit_input):
print("Abinit input not found")
raise ValueError
self.input = InputVariables(abinit_input)
self.structure = self.input.get_structure()
self.maxlpawu = max(self.input.get_value('lpawu'))
if natpawu is None:
spinat = self.input.get_value('spinat')
if spinat is None:
print(
'I could not determine the number of atoms playing a role in the DFT+U calculation'
)
raise ValueError('Could not determine natpawu')
else:
spinat = np.array(spinat).reshape((-1, 3))
self.natpawu = np.sum(
np.apply_along_axis(np.linalg.norm, 1, spinat) != 0)
else:
self.natpawu = natpawu
if self.input.has_variable('nsppol'):
self.nsppol = self.input.get_value('nsppol')
else:
self.nsppol = 1
if self.input.has_variable('nspinor'):
self.nspinor = self.input.get_value('nspinor')
else:
self.nspinor = 1
self.oxidations = oxidations
self.connection = [1, -1, -1, 1]
@property
def ndim(self):
return 2 * self.maxlpawu + 1
def __str__(self):
ret = ' Population LDA+U\n\n'
ret += ' Name: %s\n' % self.name
ret += ' Tag: %s\n' % self.tag
ret += ' Formula: %s\n' % self.structure.formula
ret += ' natpawu: %d\n' % self.natpawu
ret += ' connection: %s\n' % self.connection
ret += ' Members: %d\n' % len(self.members)
ret += ' Actives: %d\n' % len(self.actives)
ret += ' Evaluated: %d\n' % len(self.evaluated)
return ret
def add_random(self):
"""
Creates a new set of variables to reconstruct the dmatpawu
I (integers) is a matrix natpawu x ndim with entries are 0 or 1
D (deltas) is a matrix natpawu x ndim with entries are [0, 0.5)
P (matrices) is a set of matrices natpawu x ndim x ndim
Those three matrices allow to reconstruct the variable 'dmatpawu' used by ABINIT
:return:
"""
I = np.zeros((self.natpawu, self.ndim), dtype=int)
D = np.zeros((self.natpawu, self.ndim))
eigvec = np.zeros((self.natpawu, self.ndim, self.ndim))
# I and D for atoms 0 and 3
if self.oxidations[0] < 0:
nelect = self.ndim + self.oxidations[0]
else:
nelect = self.oxidations[0]
val = [
x for x in list(itertools.product(range(2), repeat=self.ndim))
if sum(x) == nelect
]
ii = val[np.random.randint(len(val))]
dd = 0.0 * np.random.random_sample((self.ndim, ))
I[0] = ii
D[0] = dd
I[3] = ii
D[3] = dd
# I and D for atoms 1 and 2
if self.oxidations[1] < 0:
nelect = self.ndim + self.oxidations[1]
else:
nelect = self.oxidations[1]
val = [
x for x in list(itertools.product(range(2), repeat=self.ndim))
if sum(x) == nelect
]
ii = val[np.random.randint(len(val))]
dd = 0.0 * np.random.random_sample((self.ndim, ))
I[1] = ii
D[1] = dd
I[2] = ii
D[2] = dd
p = gram_smith_qr(self.ndim)
eigvec[0] = p
eigvec[4] = np.dot(np.diag(self.connection), p)
p = gram_smith_qr(self.ndim)
eigvec[1] = p
eigvec[2] = np.dot(np.diag(self.connection), p)
data = {'eigvec': eigvec, 'I': I, 'D': D}
return self.new_entry(data), None
def cross(self, ids):
pass
def from_dict(self, population_dict):
pass
def new_entry(self, data, active=True):
properties = {
'eigvec': list(data['eigvec'].flatten()),
'D': list(data['D'].flatten()),
'I': list(data['I'].flatten())
}
status = {self.tag: active}
entry = {
'structure': self.structure.to_dict,
'properties': properties,
'status': status
}
entry_id = self.insert_entry(entry)
pcm_log.debug('Added new entry: %s with tag=%s: %s' %
(str(entry_id), self.tag, str(active)))
return entry_id
def is_evaluated(self, entry_id):
pass
def check_duplicates(self, ids):
ret = {}
for i in range(len(ids)):
entry_i = self.get_entry(ids[i])
for j in range(i + 1, len(ids)):
entry_j = self.get_entry(ids[j])
if self.distance(ids[i], ids[j]) < 1E-3:
if entry_i in ret:
ret[entry_i].append(entry_j)
else:
ret[entry_i] = [entry_j]
def distance(self, entry_id, entry_jd):
entry_i = self.get_entry(entry_id)
entry_j = self.get_entry(entry_jd)
dmat_i = entry_i['properties']['P']
dmat_j = entry_j['properties']['P']
dist_P = np.linalg.norm(dmat_j - dmat_i)
dmat_i = entry_i['properties']['d']
dmat_j = entry_j['properties']['d']
dist_d = np.linalg.norm(dmat_j - dmat_i)
return dist_d + dist_P
def move_random(self, entry_id, factor=0.2, in_place=False, kind='move'):
pass
# entry_i = self.get_entry(entry_id)
# dmat_i = entry_i['properties']['dmatpawu']
# dmat_i += factor*np.random.random_sample(len(dmat_i))
# self.pcdb.db.pychemia_entries.update({'_id': entry_id}, {'$set': {'properties.dmatpawu': list(dmat_i)}})
def move(self, entry_id, entry_jd, factor=0.2, in_place=False):
entry_i = self.get_entry(entry_id)
dmat_i = np.array(entry_i['properties']['P'])
entry_j = self.get_entry(entry_jd)
dmat_j = np.array(entry_j['properties']['P'])
dmat_i += factor * (dmat_j - dmat_i)
def recover(self):
pass
def value(self, entry_id):
pass
def str_entry(self, entry_id):
entry = self.get_entry(entry_id)
print(entry['properties']['P'], entry['properties']['d'])
def get_duplicates(self, ids):
return None
class OrbitalDFTU(Population):
def evaluate_entry(self, entry_id):
pass
def __init__(self, name, abinit_input='abinit.in', natpawu=None, oxidations=None):
Population.__init__(self, name, 'global')
if not os.path.isfile(abinit_input):
print("Abinit input not found")
raise ValueError
self.input = InputVariables(abinit_input)
self.structure = self.input.get_structure()
self.maxlpawu = max(self.input.get_value('lpawu'))
if natpawu is None:
spinat = self.input.get_value('spinat')
if spinat is None:
print('I could not determine the number of atoms playing a role in the DFT+U calculation')
raise ValueError('Could not determine natpawu')
else:
spinat = np.array(spinat).reshape((-1, 3))
self.natpawu = np.sum(np.apply_along_axis(np.linalg.norm, 1, spinat) != 0)
else:
self.natpawu = natpawu
if self.input.has_variable('nsppol'):
self.nsppol = self.input.get_value('nsppol')
else:
self.nsppol = 1
if self.input.has_variable('nspinor'):
self.nspinor = self.input.get_value('nspinor')
else:
self.nspinor = 1
self.oxidations = oxidations
self.connection = [1, -1, -1, 1]
@property
def ndim(self):
return 2 * self.maxlpawu + 1
def __str__(self):
ret = ' Population LDA+U\n\n'
ret += ' Name: %s\n' % self.name
ret += ' Tag: %s\n' % self.tag
ret += ' Formula: %s\n' % self.structure.formula
ret += ' natpawu: %d\n' % self.natpawu
ret += ' connection: %s\n' % self.connection
ret += ' Members: %d\n' % len(self.members)
ret += ' Actives: %d\n' % len(self.actives)
ret += ' Evaluated: %d\n' % len(self.evaluated)
return ret
def add_random(self):
"""
Creates a new set of variables to reconstruct the dmatpawu
I (integers) is a matrix natpawu x ndim with entries are 0 or 1
D (deltas) is a matrix natpawu x ndim with entries are [0, 0.5)
P (matrices) is a set of matrices natpawu x ndim x ndim
Those three matrices allow to reconstruct the variable 'dmatpawu' used by ABINIT
:return:
"""
I = np.zeros((self.natpawu, self.ndim), dtype=int)
D = np.zeros((self.natpawu, self.ndim))
eigvec = np.zeros((self.natpawu, self.ndim, self.ndim))
# I and D for atoms 0 and 3
if self.oxidations[0] < 0:
nelect = self.ndim + self.oxidations[0]
else:
nelect = self.oxidations[0]
val = [x for x in list(itertools.product(range(2), repeat=self.ndim)) if sum(x) == nelect]
ii = val[np.random.randint(len(val))]
dd = 0.0 * np.random.random_sample((self.ndim,))
I[0] = ii
D[0] = dd
I[3] = ii
D[3] = dd
# I and D for atoms 1 and 2
if self.oxidations[1] < 0:
nelect = self.ndim + self.oxidations[1]
else:
nelect = self.oxidations[1]
val = [x for x in list(itertools.product(range(2), repeat=self.ndim)) if sum(x) == nelect]
ii = val[np.random.randint(len(val))]
dd = 0.0 * np.random.random_sample((self.ndim,))
I[1] = ii
D[1] = dd
I[2] = ii
D[2] = dd
p = gram_smith_qr(self.ndim)
eigvec[0] = p
eigvec[4] = np.dot(np.diag(self.connection), p)
p = gram_smith_qr(self.ndim)
eigvec[1] = p
eigvec[2] = np.dot(np.diag(self.connection), p)
data = {'eigvec': eigvec, 'I': I, 'D': D}
return self.new_entry(data), None
def cross(self, ids):
pass
def from_dict(self, population_dict):
pass
def new_entry(self, data, active=True):
properties = {'eigvec': list(data['eigvec'].flatten()),
'D': list(data['D'].flatten()),
'I': list(data['I'].flatten())}
status = {self.tag: active}
entry = {'structure': self.structure.to_dict, 'properties': properties, 'status': status}
entry_id = self.insert_entry(entry)
pcm_log.debug('Added new entry: %s with tag=%s: %s' % (str(entry_id), self.tag, str(active)))
return entry_id
def is_evaluated(self, entry_id):
pass
def check_duplicates(self, ids):
ret = {}
for i in range(len(ids)):
entry_i = self.get_entry(ids[i])
for j in range(i + 1, len(ids)):
entry_j = self.get_entry(ids[j])
if self.distance(ids[i], ids[j]) < 1E-3:
if entry_i in ret:
ret[entry_i].append(entry_j)
else:
ret[entry_i] = [entry_j]
def distance(self, entry_id, entry_jd):
entry_i = self.get_entry(entry_id)
entry_j = self.get_entry(entry_jd)
dmat_i = entry_i['properties']['P']
dmat_j = entry_j['properties']['P']
dist_P = np.linalg.norm(dmat_j - dmat_i)
dmat_i = entry_i['properties']['d']
dmat_j = entry_j['properties']['d']
dist_d = np.linalg.norm(dmat_j - dmat_i)
return dist_d + dist_P
def move_random(self, entry_id, factor=0.2, in_place=False, kind='move'):
pass
# entry_i = self.get_entry(entry_id)
# dmat_i = entry_i['properties']['dmatpawu']
# dmat_i += factor*np.random.random_sample(len(dmat_i))
# self.pcdb.db.pychemia_entries.update({'_id': entry_id}, {'$set': {'properties.dmatpawu': list(dmat_i)}})
def move(self, entry_id, entry_jd, factor=0.2, in_place=False):
entry_i = self.get_entry(entry_id)
dmat_i = np.array(entry_i['properties']['P'])
entry_j = self.get_entry(entry_jd)
dmat_j = np.array(entry_j['properties']['P'])
dmat_i += factor * (dmat_j - dmat_i)
def recover(self):
pass
def value(self, entry_id):
pass
def str_entry(self, entry_id):
entry = self.get_entry(entry_id)
print(entry['properties']['P'], entry['properties']['d'])
def get_duplicates(self, ids):
return None
if __name__ == '__main__':
narg = len(sys.argv) - 1
list_abifile = []
list_idtset = []
dtsetall = False
for i in range(narg):
filename = sys.argv[i + 1]
if ':' in filename:
idtset = filename.split(':')[1]
if idtset == 'all':
dtsetall = True
else:
list_idtset.append(idtset)
filename = filename.split(':')[0]
abifile = AbiFiles(filename)
if dtsetall:
av = InputVariables(abifile.get_input_filename())
keys = av.get_dtsets_keys()
for j in keys:
list_abifile.append(abifile)
list_idtset.append(str(j))
else:
list_abifile.append(abifile)
plot_bonds(list_abifile, list_idtset)
def __init__(self, name, abinit_input='abinit.in', num_electrons_dftu=None, num_indep_matrices=None, connections=None):
"""
This population is created with the purpose of global optimization of correlated orbitals 'd'
and 'f'.
The population is basically a collection of ABINIT inputs, the candidates have the same structure and
uses the same input variables with exception of 'dmatpawu', the purpose of the
population is to use global-population searchers to find the correlation matrices
'dmatpawu' that minimizes the energy.
The variable 'dmatpawu' is a list of numbers that can be arranged into N matrices.
The matrices are 5x5 for 'd' orbitals and 7x7 for 'f' orbitals.
:param name: The name of the 'PyChemiaDB' database created to stored the different
set of variables and the resulting output from abinit.
When using databases protected with username and password, the database
should be created independently and the database object must be use
as the 'name' argument
:param abinit_input: The abinit input file, all the variables will be preserve for all new candidates, except
for 'dmatpawu' the only variable that changes.
"""
# Call the parent class initializer to link the PychemiaDB that will be used
Population.__init__(self, name, 'global')
# Checking for existence of 'abinit.in'
if not os.path.isfile(abinit_input):
print("Abinit input not found")
raise ValueError
# Reading the input variables and getting the structure
self.input = InputVariables(abinit_input)
self.structure = self.input.get_structure()
print('Orbital population:')
print('Species [znucl]: %s' % self.input['znucl'])
self.natpawu = 0
print('Orbitals corrected:')
for i in range(self.input['ntypat']):
if self.input['lpawu'][i] == -1:
print("%3s : False" % self.input['znucl'][i])
else:
print("%3s : True (l=%d)" % (self.input['znucl'][i], self.input['lpawu'][i]))
self.natpawu += sum([1 for x in self.input['typat'] if x == i+1])
print('Number of atoms where DFT+U is applied: %d' % self.natpawu)
# Computing the orbital that will be corrected
# 2 (d-orbitals) or 3 (f-orbitals)
self.maxlpawu = max(self.input['lpawu'])
if self.maxlpawu == 2:
print("Correlation of 'd' orbitals")
elif self.maxlpawu == 3:
print("Correlation of 'f' orbitals")
# nsppol is the number of independent spin polarisations. Can take the values 1 or 2
if self.input.has_variable('nsppol'):
self.nsppol = self.input.get_value('nsppol')
else:
# Default from ABINIT
self.nsppol = 1
# nspinor it the umber of spinorial components of the wavefunctions
if self.input.has_variable('nspinor'):
self.nspinor = self.input.get_value('nspinor')
else:
self.nspinor = 1
# nspden is the number of spin-density components
if self.input.has_variable('nspden'):
self.nspden = self.input.get_value('nspden')
else:
self.nspden = self.nsppol
if self.nsppol == 1 and self.nspinor == 1 and self.nspden == 1:
# Non-magnetic system (nsppol=1, nspinor=1, nspden=1):
# One (2lpawu+1)x(2lpawu+1) dmatpawu matrix is given for each atom on which +U is applied.
# It contains the "spin-up" occupations.
self.nmatrices = self.natpawu
elif self.nsppol == 2 and self.nspinor == 1 and self.nspden == 2:
# Ferromagnetic spin-polarized (collinear) system (nsppol=2, nspinor=1, nspden=2):
# Two (2lpawu+1)x(2lpawu+1) dmatpawu matrices are given for each atom on which +U is applied.
# They contain the "spin-up" and "spin-down" occupations.
self.nmatrices = 2*self.natpawu
elif self.nsppol == 1 and self.nspinor == 1 and self.nspden == 2:
# Anti-ferromagnetic spin-polarized(collinear) system(nsppol=1, nspinor=1, nspden=2):
# One(2lpawu + 1)x(2lpawu + 1) dmatpawu matrix is given for each atom on which +U is applied.
# It contains the "spin-up" occupations.
self.nmatrices = self.natpawu
elif self.nsppol == 1 and self.nspinor == 2 and self.nspden == 4:
# Non-collinear magnetic system (nsppol=1, nspinor=2, nspden=4):
# Two (2lpawu+1)x(2lpawu+1) dmatpawu matrices are given for each atom on which +U is applied.
# They contains the "spin-up" and "spin-down" occupations (defined as n_up=(n+|m|)/2 and n_dn=(n-|m|)/2),
# where m is the integrated magnetization vector).
self.nmatrices = 2*self.natpawu
elif self.nsppol == 1 and self.nspinor == 2 and self.nspden == 1:
# Non-collinear magnetic system with zero magnetization (nsppol=1, nspinor=2, nspden=1):
# Two (2lpawu+1)x(2lpawu+1) dmatpawu matrices are given for each atom on which +U is applied.
# They contain the "spin-up" and "spin-down" occupations;
self.nmatrices = 2*self.natpawu
print('Variables controling the total number of matrices')
print('nsppol : %d' % self.nsppol)
print('nspinor: %d' % self.nspinor)
print('nspden : %d' % self.nspden)
print('Total number of matrices expected on dmatpawu: %d' % self.nmatrices )
self.num_electrons_dftu = list(num_electrons_dftu)
if num_indep_matrices is not None:
self.num_indep_matrices = list(num_indep_matrices)
else:
self.num_indep_matrices = self.nmatrices
print('Number of independent matrices: %d' % self.num_indep_matrices)
if connections is not None:
self.connections = list(connections)
if len(self.connections) != self.nmatrices:
raise ValueError('Number of connections between matrices is not consistent with the number of matrices '
'defined on dmatpawu')
print('Connections: %s' % self.connections)
else:
self.connections = range(self.nmatrices)
class OrbitalDFTU(Population):
def __init__(self, name, abinit_input='abinit.in', num_electrons_dftu=None, num_indep_matrices=None, connections=None):
"""
This population is created with the purpose of global optimization of correlated orbitals 'd'
and 'f'.
The population is basically a collection of ABINIT inputs, the candidates have the same structure and
uses the same input variables with exception of 'dmatpawu', the purpose of the
population is to use global-population searchers to find the correlation matrices
'dmatpawu' that minimizes the energy.
The variable 'dmatpawu' is a list of numbers that can be arranged into N matrices.
The matrices are 5x5 for 'd' orbitals and 7x7 for 'f' orbitals.
:param name: The name of the 'PyChemiaDB' database created to stored the different
set of variables and the resulting output from abinit.
When using databases protected with username and password, the database
should be created independently and the database object must be use
as the 'name' argument
:param abinit_input: The abinit input file, all the variables will be preserve for all new candidates, except
for 'dmatpawu' the only variable that changes.
"""
# Call the parent class initializer to link the PychemiaDB that will be used
Population.__init__(self, name, 'global')
# Checking for existence of 'abinit.in'
if not os.path.isfile(abinit_input):
print("Abinit input not found")
raise ValueError
# Reading the input variables and getting the structure
self.input = InputVariables(abinit_input)
self.structure = self.input.get_structure()
print('Orbital population:')
print('Species [znucl]: %s' % self.input['znucl'])
self.natpawu = 0
print('Orbitals corrected:')
for i in range(self.input['ntypat']):
if self.input['lpawu'][i] == -1:
print("%3s : False" % self.input['znucl'][i])
else:
print("%3s : True (l=%d)" % (self.input['znucl'][i], self.input['lpawu'][i]))
self.natpawu += sum([1 for x in self.input['typat'] if x == i+1])
print('Number of atoms where DFT+U is applied: %d' % self.natpawu)
# Computing the orbital that will be corrected
# 2 (d-orbitals) or 3 (f-orbitals)
self.maxlpawu = max(self.input['lpawu'])
if self.maxlpawu == 2:
print("Correlation of 'd' orbitals")
elif self.maxlpawu == 3:
print("Correlation of 'f' orbitals")
# nsppol is the number of independent spin polarisations. Can take the values 1 or 2
if self.input.has_variable('nsppol'):
self.nsppol = self.input.get_value('nsppol')
else:
# Default from ABINIT
self.nsppol = 1
# nspinor it the umber of spinorial components of the wavefunctions
if self.input.has_variable('nspinor'):
self.nspinor = self.input.get_value('nspinor')
else:
self.nspinor = 1
# nspden is the number of spin-density components
if self.input.has_variable('nspden'):
self.nspden = self.input.get_value('nspden')
else:
self.nspden = self.nsppol
if self.nsppol == 1 and self.nspinor == 1 and self.nspden == 1:
# Non-magnetic system (nsppol=1, nspinor=1, nspden=1):
# One (2lpawu+1)x(2lpawu+1) dmatpawu matrix is given for each atom on which +U is applied.
# It contains the "spin-up" occupations.
self.nmatrices = self.natpawu
elif self.nsppol == 2 and self.nspinor == 1 and self.nspden == 2:
# Ferromagnetic spin-polarized (collinear) system (nsppol=2, nspinor=1, nspden=2):
# Two (2lpawu+1)x(2lpawu+1) dmatpawu matrices are given for each atom on which +U is applied.
# They contain the "spin-up" and "spin-down" occupations.
self.nmatrices = 2*self.natpawu
elif self.nsppol == 1 and self.nspinor == 1 and self.nspden == 2:
# Anti-ferromagnetic spin-polarized(collinear) system(nsppol=1, nspinor=1, nspden=2):
# One(2lpawu + 1)x(2lpawu + 1) dmatpawu matrix is given for each atom on which +U is applied.
# It contains the "spin-up" occupations.
self.nmatrices = self.natpawu
elif self.nsppol == 1 and self.nspinor == 2 and self.nspden == 4:
# Non-collinear magnetic system (nsppol=1, nspinor=2, nspden=4):
# Two (2lpawu+1)x(2lpawu+1) dmatpawu matrices are given for each atom on which +U is applied.
# They contains the "spin-up" and "spin-down" occupations (defined as n_up=(n+|m|)/2 and n_dn=(n-|m|)/2),
# where m is the integrated magnetization vector).
self.nmatrices = 2*self.natpawu
elif self.nsppol == 1 and self.nspinor == 2 and self.nspden == 1:
# Non-collinear magnetic system with zero magnetization (nsppol=1, nspinor=2, nspden=1):
# Two (2lpawu+1)x(2lpawu+1) dmatpawu matrices are given for each atom on which +U is applied.
# They contain the "spin-up" and "spin-down" occupations;
self.nmatrices = 2*self.natpawu
print('Variables controling the total number of matrices')
print('nsppol : %d' % self.nsppol)
print('nspinor: %d' % self.nspinor)
print('nspden : %d' % self.nspden)
print('Total number of matrices expected on dmatpawu: %d' % self.nmatrices )
self.num_electrons_dftu = list(num_electrons_dftu)
if num_indep_matrices is not None:
self.num_indep_matrices = list(num_indep_matrices)
else:
self.num_indep_matrices = self.nmatrices
print('Number of independent matrices: %d' % self.num_indep_matrices)
if connections is not None:
self.connections = list(connections)
if len(self.connections) != self.nmatrices:
raise ValueError('Number of connections between matrices is not consistent with the number of matrices '
'defined on dmatpawu')
print('Connections: %s' % self.connections)
else:
self.connections = range(self.nmatrices)
def __str__(self):
ret = ' Population LDA+U\n\n'
ret += ' Name: %s\n' % self.name
ret += ' Tag: %s\n' % self.tag
ret += ' Formula: %s\n' % self.structure.formula
ret += ' natpawu: %d\n' % self.natpawu
ret += ' nmatrices: %d\n' % self.nmatrices
ret += ' maxlpawu: %d\n' % self.maxlpawu
ret += ' num_indep_matrices: %s\n' % self.num_indep_matrices
ret += ' connections: %s\n' % self.connections
ret += ' Members: %d\n' % len(self.members)
ret += ' Actives: %d\n' % len(self.actives)
ret += ' Evaluated: %d\n' % len(self.evaluated)
return ret
@property
def ndim(self):
"""
Dimension of the matrices defined on dmatpawu, for 'd' orbitals is 5 for 'f' orbitals is 7
:return:
"""
return 2 * self.maxlpawu + 1
def add_random(self):
"""
Creates a new set of variables to reconstruct the dmatpawu
matrix_i (integers) is a matrix natpawu x ndim with entries are 0 or 1
matrix_d (deltas) is a matrix natpawu x ndim with entries are [0, 0.5)
P (matrices) is a set of matrices natpawu x ndim x ndim
Those three matrices allow to reconstruct the variable 'dmatpawu' used by ABINIT
:return:
"""
matrices_defined = []
matrix_i = self.num_indep_matrices*[None]
matrix_d = self.num_indep_matrices*[None]
euler = self.num_indep_matrices*[None]
for i in range(self.num_indep_matrices):
nelect = self.num_electrons_dftu[i]
val = [x for x in list(itertools.product(range(2), repeat=self.ndim)) if sum(x) == nelect]
ii = val[np.random.randint(len(val))]
dd = np.zeros(self.ndim)
matrix_i[i] = list(ii)
matrix_d[i] = list(dd)
matrices_defined.append(self.connections[i])
p = gram_smith_qr(self.ndim)
euler[i] = gea_all_angles(p)
data = {'E': euler, 'O': matrix_i, 'D': matrix_d}
return self.new_entry(data), None
def cross(self, ids):
"""
Crossing algorithm used notably by GA to mix the information from several candidates
Not implemented
:param ids:
:return:
"""
pass
def evaluate_entry(self, entry_id):
"""
Evaluation externalized, no implemented
:param entry_id:
:return:
"""
pass
def from_dict(self, population_dict):
pass
def new_entry(self, data, active=True):
"""
Creates a new entry on the population database from given data.
:param data: dictionary with 3 keys 'D' for deltas, 'I' for the integers
and eigen for the rotation matrix applied to the orbitals
:param active: if True, the entry is enabled on the DB to be evaluated.
:return:
"""
properties = {'R': list(data['R'].flatten()),
'D': list(data['D'].flatten()),
'O': list(data['O'].flatten())}
status = {self.tag: active}
entry = {'structure': self.structure.to_dict, 'properties': properties, 'status': status}
entry_id = self.insert_entry(entry)
pcm_log.debug('Added new entry: %s with tag=%s: %s' % (str(entry_id), self.tag, str(active)))
return entry_id
def is_evaluated(self, entry_id):
pass
def check_duplicates(self, ids):
"""
For a given list of identifiers 'ids' checks the values for the function 'distance' and return a dictionary
where each key is the identifier of a unique candidate and the value is a list of identifiers considered
equivalents to it.
:param ids: List of identifiers for wich the check will be performed
:return:
"""
ret = {}
for i in range(len(ids)):
entry_i = self.get_entry(ids[i])
for j in range(i + 1, len(ids)):
entry_j = self.get_entry(ids[j])
if self.distance(ids[i], ids[j]) < 1E-3:
if entry_i in ret:
ret[entry_i].append(entry_j)
else:
ret[entry_i] = [entry_j]
def distance(self, entry_id, entry_jd):
"""
Measure of distance for two entries with identifiers 'entry_id' and 'entry_jd'
TODO: The definition must be changed and compare the resulting dmatpawu instead of
individual components
:param entry_id: Identifier of first entry
:param entry_jd: Identifier of second entry
:return:
"""
entry_i = self.get_entry(entry_id)
entry_j = self.get_entry(entry_jd)
dmat_i = entry_i['properties']['P']
dmat_j = entry_j['properties']['P']
dist_p = np.linalg.norm(dmat_j - dmat_i)
dmat_i = entry_i['properties']['d']
dmat_j = entry_j['properties']['d']
dist_d = np.linalg.norm(dmat_j - dmat_i)
return dist_d + dist_p
def move_random(self, entry_id, factor=0.2, in_place=False, kind='move'):
"""
Move one candidate with identifier 'entry_id' randomly with a factor
given by 'factor'
:param entry_id: Identifier of entry
:param factor: Factor use to scale the randomness of change
:param in_place: If True the candidate is changed keeping the identifier unchanged
:param kind: Use when several algorithms are used for movement. One implemented here
:return:
"""
pass
# entry_i = self.get_entry(entry_id)
# dmat_i = entry_i['properties']['dmatpawu']
# dmat_i += factor*np.random.random_sample(len(dmat_i))
# self.pcdb.db.pychemia_entries.update({'_id': entry_id}, {'$set': {'properties.dmatpawu': list(dmat_i)}})
def move(self, entry_id, entry_jd, factor=0.2, in_place=False):
"""
Move one candidate with identifier 'entry_id' in the direction of another candidate 'entry_jd'
:param entry_id: Identifier of first entry (Origin)
:param entry_jd: Identifier of second entry (Target)
:param factor: Scale factor for change, 0 scale is the 'Origin' candidate, 1 is the 'Target' candidate
Intermediate values will change candidates accordingly
:param in_place: If True the candidate is changed keeping the identifier unchanged
:return:
"""
entry_i = self.get_entry(entry_id)
dmat_i = np.array(entry_i['properties']['P'])
entry_j = self.get_entry(entry_jd)
dmat_j = np.array(entry_j['properties']['P'])
dmat_i += factor * (dmat_j - dmat_i)
def recover(self):
pass
def value(self, entry_id):
pass
def str_entry(self, entry_id):
entry = self.get_entry(entry_id)
print(entry['properties']['P'], entry['properties']['d'])
def get_duplicates(self, ids):
return None