def principalAxes(self, **kwargs):
weight = [qtk.n2m(elem) for elem in self.type_list]
center = self.getCenterOfMass()
self.center(center)
inertia = np.zeros([3,3])
I0 = 0
for i in range(3):
I0 = I0 + sum(self.R[:,i]**2 * weight)
for i in range(3):
coord_i = self.R[:,i]
inertia[i,i] = I0 - sum(coord_i**2 * weight)
for j in range(i+1,3):
coord_j = self.R[:,j]
inertia[i,j] = -sum(coord_i*coord_j*weight)
inertia[j,i] = inertia[i,j]
I, U = np.linalg.eigh(inertia)
self.shift(center)
#return sorted(I,reverse=True), U[I.argsort()[::-1]]
return I, U
def principalAxes(self, order='ascent', **kwargs):
weight = [qtk.n2m(elem) for elem in self.type_list]
center = self.getCenterOfMass()
self.center(center)
inertia = np.zeros([3,3])
I0 = 0
for i in range(3):
I0 = I0 + sum(self.R[:,i]**2 * weight)
for i in range(3):
coord_i = self.R[:,i]
inertia[i,i] = I0 - sum(coord_i**2 * weight)
for j in range(i+1,3):
coord_j = self.R[:,j]
inertia[i,j] = -sum(coord_i*coord_j*weight)
inertia[j,i] = inertia[i,j]
I, U = np.linalg.eigh(inertia)
self.shift(center)
if order == 'ascent':
return I, U
else:
return sorted(I,reverse=True), U[I.argsort()[::-1]]
def writeInp(name=None, **setting):
inp, molecule = \
PlanewaveInput.write(self, name, **setting)
molecule.sort()
type_index = molecule.index
type_list = molecule.type_list
pp_files = []
self.content['system']['nat'] = molecule.N
self.content['system']['ntyp'] = len(type_index) - 1
if setting['full_kmesh']:
self.content['system']['nosym'] = True
self.content['system']['noinv'] = True
if 'restart' in setting and setting['restart']:
self.content['control']['restart_mode'] = 'restart'
if 'save_density' in setting and setting['save_density']:
self.content['control']['wf_collect'] = True
if 'save_wf' in setting and setting['save_wf']:
self.content['control']['wf_collect'] = True
if 'print_force' not in setting or not setting['print_force']:
self.content['control']['tprnfor'] = True
if not setting['periodic']:
self.content['system']['assume_isolated'] = 'mt'
if 'exx' in setting and setting['exx'] == 'anisotropic':
self.content['system']['exxdiv_treatment'] = 'vcut_ws'
self.content['system']['ecutvcut'] = 0.7
self.content['system']['x_gamma_extrapolation'] = False
if molecule.charge != 0:
self.content['system']['tot_charge'] = molecule.charge
if molecule.multiplicity != 1:
self.content['system']['nspin'] = 2
diff = molecule.multiplicity - 1
self.content['system']['tot_magnetization'] = diff
if 'theory' in setting:
if self.setting['theory'] in dft_dict:
self.content['system']['input_dft'] = \
dft_dict[self.setting['theory']]
else:
self.content['system']['input_dft'] = self.setting['theory']
if 'scf_step' in setting:
self.content['electrons']['electron_maxstep'] =\
setting['scf_step']
if 'ks_states' in setting and setting['ks_states']:
vs = int(round(self.molecule.getValenceElectrons() / 2.0))
self.content['system']['nbnd'] = setting['ks_states'] + vs
if 'd_shell' in setting:
for a in molecule.type_list:
if a in setting['d_shell'] and qtk.n2ve(a) < 10:
self.content['system']['nbnd'] += 5
if 'symmetry' in setting:
if setting['symmetry'] == 'fcc':
self.content['system']['ibrav'] = 2
setting['fractional_coordinate'] = True
dm = ['A', 'B', 'C', 'cosBC', 'cosAC', 'cosAB']
for i in range(6):
self.content['system'][dm[i]] = float(self
.molecule.celldm[i])
for section_key in self.content.iterkeys():
section = '&' + section_key + '\n'
inp.write(section)
for key, value in self.content[section_key].iteritems():
if type(value) is str:
entry = " %s = '%s',\n" % (key, value)
elif type(value) is int:
entry = ' %s = %d,\n' % (key, value)
elif type(value) is float:
entry = ' %s = %14.8E,\n' % (key, value)
elif type(value) is bool:
if value:
entry = ' %s = .true.,\n' % key
else:
entry = ' %s = .false.,\n' % key
inp.write(entry)
inp.write('/\n')
inp.write("ATOMIC_SPECIES\n")
for a in range(len(type_index)-1):
type_n = type_index[a+1] - type_index[a]
PPStr = PPString(self, molecule,
type_index[a], type_n, inp)
stem, ext = os.path.splitext(PPStr)
if ext != '.UPF':
PPStr = PPStr + '.UPF'
mass = qtk.n2m(type_list[type_index[a]])
inp.write(' %-3s % 6.3f %s\n' % \
(type_list[type_index[a]], mass, PPStr))
pp_files.append(PPStr)
inp.write("\n")
inp.write("ATOMIC_POSITIONS ")
if self.content['system']['ibrav'] == 0:
if not setting['fractional_coordinate']:
inp.write("angstrom\n")
R = molecule.R
else:
inp.write("crystal\n")
R = molecule.R_scale
else:
inp.write("\n")
R = molecule.R_scale
for a in range(len(type_list)):
inp.write(' %-3s' % type_list[a])
for i in range(3):
inp.write(' % 12.8f' % R[a, i])
inp.write("\n")
inp.write("\n")
if 'kmesh' in setting and setting['kmesh']:
inp.write("K_POINTS automatic\n")
for k in setting['kmesh']:
inp.write(" %d" % k)
for s in range(3):
inp.write(" 0")
inp.write('\n\n')
if 'save_restart' in setting and setting['save_restart']:
inp.write("ALCHEMY reference\n\n")
if 'restart' in setting and setting['restart']:
if 'scf_step' in setting and setting['scf_step'] == 1:
inp.write("ALCHEMY prediction\n\n")
if self.content['system']['ibrav'] == 0:
inp.write("CELL_PARAMETERS angstrom\n")
if 'lattice' not in self.setting:
self.celldm2lattice()
lattice_vec = self.setting['lattice']
for vec in lattice_vec:
for component in vec:
inp.write(' % 11.6f' % component)
inp.write('\n')
for pp in pp_files:
pp_file = os.path.join(qtk.setting.espresso_pp, pp)
if pp not in inp.dependent_files:
inp.dependent_files.append(pp_file)
if 'no_cleanup' in setting and setting['no_cleanup']:
inp.close(no_cleanup=True)
else:
inp.close()
return inp
def writeInp(name=None, **setting):
inp, molecule = \
PlanewaveInput.write(self, name, **setting)
molecule.sort()
type_index = molecule.index
type_list = molecule.type_list
pp_files = []
self.content['system']['nat'] = molecule.N
self.content['system']['ntyp'] = len(type_index) - 1
if setting['full_kmesh']:
self.content['system']['nosym'] = True
self.content['system']['noinv'] = True
if 'restart' in setting and setting['restart']:
self.content['control']['restart_mode'] = 'restart'
if 'save_density' in setting and setting['save_density']:
self.content['control']['wf_collect'] = True
if 'save_wf' in setting and setting['save_wf']:
self.content['control']['wf_collect'] = True
if 'print_force' not in setting or not setting['print_force']:
self.content['control']['tprnfor'] = True
if not setting['periodic']:
self.content['system']['assume_isolated'] = 'mt'
if 'exx' in setting and setting['exx'] == 'anisotropic':
self.content['system']['exxdiv_treatment'] = 'vcut_ws'
self.content['system']['ecutvcut'] = 0.7
self.content['system']['x_gamma_extrapolation'] = False
if molecule.charge != 0:
self.content['system']['tot_charge'] = molecule.charge
if molecule.multiplicity != 1:
self.content['system']['nspin'] = 2
diff = molecule.multiplicity - 1
self.content['system']['tot_magnetization'] = diff
if 'theory' in setting:
if self.setting['theory'] in dft_dict:
self.content['system']['input_dft'] = \
dft_dict[self.setting['theory']]
else:
self.content['system']['input_dft'] = self.setting[
'theory']
if 'scf_step' in setting:
self.content['electrons']['electron_maxstep'] =\
setting['scf_step']
if 'ks_states' in setting and setting['ks_states']:
vs = int(round(self.molecule.getValenceElectrons() / 2.0))
self.content['system']['nbnd'] = setting['ks_states'] + vs
if 'd_shell' in setting:
for a in molecule.type_list:
if a in setting['d_shell'] and qtk.n2ve(a) < 10:
self.content['system']['nbnd'] += 5
if 'symmetry' in setting:
if setting['symmetry'] == 'fcc':
self.content['system']['ibrav'] = 2
setting['fractional_coordinate'] = True
dm = ['A', 'B', 'C', 'cosBC', 'cosAC', 'cosAB']
for i in range(6):
self.content['system'][dm[i]] = float(
self.molecule.celldm[i])
for section_key in self.content.iterkeys():
section = '&' + section_key + '\n'
inp.write(section)
for key, value in self.content[section_key].iteritems():
if type(value) is str:
entry = " %s = '%s',\n" % (key, value)
elif type(value) is int:
entry = ' %s = %d,\n' % (key, value)
elif type(value) is float:
entry = ' %s = %14.8E,\n' % (key, value)
elif type(value) is bool:
if value:
entry = ' %s = .true.,\n' % key
else:
entry = ' %s = .false.,\n' % key
inp.write(entry)
inp.write('/\n')
inp.write("ATOMIC_SPECIES\n")
for a in range(len(type_index) - 1):
type_n = type_index[a + 1] - type_index[a]
PPStr = PPString(self, molecule, type_index[a], type_n, inp)
stem, ext = os.path.splitext(PPStr)
if ext != '.UPF':
PPStr = PPStr + '.UPF'
mass = qtk.n2m(type_list[type_index[a]])
inp.write(' %-3s % 6.3f %s\n' % \
(type_list[type_index[a]], mass, PPStr))
pp_files.append(PPStr)
inp.write("\n")
inp.write("ATOMIC_POSITIONS ")
if self.content['system']['ibrav'] == 0:
if not setting['fractional_coordinate']:
inp.write("angstrom\n")
R = molecule.R
else:
inp.write("crystal\n")
R = molecule.R_scale
else:
inp.write("\n")
R = molecule.R_scale
for a in range(len(type_list)):
inp.write(' %-3s' % type_list[a])
for i in range(3):
inp.write(' % 12.8f' % R[a, i])
inp.write("\n")
inp.write("\n")
if 'kmesh' in setting and setting['kmesh']:
inp.write("K_POINTS automatic\n")
for k in setting['kmesh']:
inp.write(" %d" % k)
for s in range(3):
inp.write(" 0")
inp.write('\n\n')
if 'save_restart' in setting and setting['save_restart']:
inp.write("ALCHEMY reference\n\n")
if 'restart' in setting and setting['restart']:
if 'scf_step' in setting:
if setting['scf_step'] != 1:
qtk.warning('alchemy with optimization...')
inp.write("ALCHEMY prediction\n\n")
if self.content['system']['ibrav'] == 0:
inp.write("CELL_PARAMETERS angstrom\n")
if 'lattice' not in self.setting:
self.celldm2lattice()
lattice_vec = self.setting['lattice']
for vec in lattice_vec:
for component in vec:
inp.write(' % 11.6f' % component)
inp.write('\n')
for pp in pp_files:
pp_file = os.path.join(qtk.setting.espresso_pp, pp)
if pp not in inp.dependent_files:
inp.dependent_files.append(pp_file)
if 'no_cleanup' in setting and setting['no_cleanup']:
inp.close(no_cleanup=True)
else:
inp.close()
return inp
def getCenterOfMass(self): mass_list = [qtk.n2m(elem) for elem in self.type_list] weighted = self.R * np.array(mass_list).reshape([self.N,1]) return np.sum(weighted, axis=0)/float(sum(mass_list))
def getCenterOfMass(self): mass_list = [qtk.n2m(elem) for elem in self.type_list] weighted = self.R * np.array(mass_list).reshape([self.N,1]) return np.sum(weighted, axis=0)/float(sum(mass_list))