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):
setting['no_update'] = True
inp, molecule = PlanewaveInput.write(self, name, **setting)
if 'ks_states' in setting and 'ks_states':
setting['mode'] = 'ks_states'
if 'big_memory' not in setting:
if qtk.setting.memory > 16:
setting['big_memory'] = True
# if molecule.scale:
# molecule.R = molecule.R_scale
# setting['scale'] = molecule.scale
inp.write('&INFO\n')
inp.write(' ' + setting['info'] + '\n')
inp.write('&END\n\n')
inp.write('&CPMD\n MIRROR\n')
if 'save_restart' not in setting\
or not setting['save_restart']:
inp.write(' BENCHMARK\n')
inp.write(' 1 0 0 0 0 0 0 0 0 0\n')
if 'init_random' in setting\
and setting['init_random']:
inp.write(' INITIALIZE WAVEFUNCTION RANDOM\n')
if setting['mode'].lower() == 'single_point':
inp.write(' OPTIMIZE WAVEFUNCTION\n')
elif setting['mode'].lower() == 'geopt':
inp.write(' OPTIMIZE GEOMETRY\n')
elif setting['mode'].lower() == 'ks_states':
if not setting['restart']:
setting['restart'] = True
inp.write(' KOHN-SHAM ENERGIES\n %d\n'\
% setting['ks_states'])
#inp.write(' LANCZOS PARAMETER N=5\n')
#inp.write(' 1000 16 20 1.D-9\n')
#inp.write(' 0.05 1.D-11\n')
#inp.write(' 0.01 1.D-13\n')
#inp.write(' 0.0025 1.D-16\n')
#inp.write(' 0.001 1.D-18\n')
elif setting['mode'].lower() == 'md':
inp.write(' MOLECULAR DYNAMICS BO\n')
if re.match(setting['mode'], 'md'):
inp.write(' TRAJECTORY SAMPLE XYZ\n %d\n'\
% setting['sample_period'])
inp.write(' TEMPERATURE\n')
inp.write(' %.1f\n' % setting['T'])
if setting['thermostat'].lower() == 'nose-hoover':
inp.write(' NOSE IONS\n %.1f %.1f\n' % \
(setting['T'], setting['T_tolerance']))
if 'geometry_convergence' in setting:
inp.write(' CONVERGENCE GEOMETRY\n %.2E\n' %\
setting['geometry_convergence'])
if 'md_step' in setting:
inp.write(' MAXSTEP\n %d\n' % setting['md_step'])
if 'wf_convergence' in setting:
inp.write(' CONVERGENCE ORBITAL\n %.2E\n' %\
setting['wf_convergence'])
if 'scf_step' in setting:
inp.write(' MAXITER\n %d\n' % setting['scf_step'])
if 'restart' in setting and setting['restart']:
inp.write(' RESTART WAVEFUNCTION\n')
if 'fix_molecule' in setting\
and setting['fix_molecule']:
inp.write(' CENTER MOLECULE OFF\n')
if ('save_density' in setting and setting['save_density'])\
or ('save_wf' in setting and setting['save_wf']):
inp.write(' RHOOUT')
if setting['save_wf']:
inp.write(' BANDS\n %d\n ' % len(setting['save_wf']))
for i in setting['save_wf']:
inp.write(' %d' % i)
inp.write('\n')
if molecule.multiplicity != 1:
inp.write(' LOCAL SPIN DENSITY\n')
if 'big_memory' in setting and setting['big_memory']:
inp.write(' MEMORY BIG\n')
inp.write('&END\n\n')
inp.write('&DFT\n FUNCTIONAL %s\n&END\n\n' % \
setting['theory'].upper())
inp.write('&SYSTEM\n')
if setting['periodic']:
inp.write(' CELL VECTORS\n')
lattice_vec = self.setting['lattice']
for vec in lattice_vec:
inp.write(' ')
for component in vec:
inp.write(' % 11.6f' % component)
inp.write('\n')
else:
inp.write(' SYMMETRY\n')
inp.write(' ISOLATED\n')
if setting['isolation'] == 'mt':
inp.write(' POISSON SOLVER TUCKERMAN\n')
inp.write(' CELL ABSOLUTE\n ')
for d in setting['celldm']:
inp.write(' %6.3f'% float(d))
inp.write('\n')
if setting['unit'].lower() == 'angstrom':
inp.write(' ANGSTROM\n')
inp.write(' CUTOFF\n %.1f\n' % setting['cutoff'])
if 'kmesh' in setting and setting['kmesh']:
inp.write(' KPOINTS MONKHORST-PACK\n %d %d %d\n' %\
(setting['kmesh'][0],
setting['kmesh'][1],
setting['kmesh'][2]))
if 'mesh' in setting:
inp.write(' MESH\n %d %d %d\n' %\
(setting['mesh'][0],
setting['mesh'][1],
setting['mesh'][2]))
if molecule.charge != 0:
inp.write(' CHARGE\n %d\n' % molecule.charge)
if molecule.multiplicity != 1:
inp.write(' MULTIPLICITY\n %d\n' % molecule.multiplicity)
inp.write('&END\n\n')
inp.write('&ATOMS\n')
molecule.sort()
type_index = molecule.index
type_list = molecule.type_list
# loop through sorted atom type indices
for atom_type in xrange(0,len(type_index)-1):
# number of each atom type
type_n = type_index[atom_type+1] - type_index[atom_type]
PPString(self, molecule, type_index[atom_type], type_n, inp)
for I in\
xrange(type_index[atom_type],type_index[atom_type+1]):
inp.write(' ')
for i in range(3):
inp.write(' % 8.4f' % molecule.R[I,i])
inp.write('\n')
inp.write('&END\n')
for pp in self.pp_files:
pp_file = os.path.join(qtk.setting.cpmd_pp, pp)
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 writeInp(name=None, **setting):
setting['no_update'] = True
inp, molecule = PlanewaveInput.write(self, name, **setting)
if 'ks_states' in setting and 'ks_states':
setting['mode'] = 'ks_states'
if 'big_memory' not in setting:
if qtk.setting.memory > 16:
setting['big_memory'] = True
# if molecule.scale:
# molecule.R = molecule.R_scale
# setting['scale'] = molecule.scale
inp.write('&INFO\n')
inp.write(' ' + setting['info'] + '\n')
inp.write('&END\n\n')
inp.write('&CPMD\n MIRROR\n')
if 'save_restart' not in setting\
or not setting['save_restart']:
inp.write(' BENCHMARK\n')
inp.write(' 1 0 0 0 0 0 0 0 0 0\n')
if 'init_random' in setting\
and setting['init_random']:
inp.write(' INITIALIZE WAVEFUNCTION RANDOM\n')
if setting['mode'].lower() == 'single_point':
inp.write(' OPTIMIZE WAVEFUNCTION\n')
elif setting['mode'].lower() == 'geopt':
inp.write(' OPTIMIZE GEOMETRY\n')
elif setting['mode'].lower() == 'ks_states':
if not setting['restart']:
setting['restart'] = True
inp.write(' KOHN-SHAM ENERGIES\n %d\n'\
% setting['ks_states'])
#inp.write(' LANCZOS PARAMETER N=5\n')
#inp.write(' 1000 16 20 1.D-9\n')
#inp.write(' 0.05 1.D-11\n')
#inp.write(' 0.01 1.D-13\n')
#inp.write(' 0.0025 1.D-16\n')
#inp.write(' 0.001 1.D-18\n')
elif setting['mode'].lower() == 'md':
inp.write(' MOLECULAR DYNAMICS BO\n')
if re.match(setting['mode'], 'md'):
inp.write(' TRAJECTORY SAMPLE XYZ\n %d\n'\
% setting['sample_period'])
inp.write(' TEMPERATURE\n')
inp.write(' %.1f\n' % setting['T'])
if setting['thermostat'].lower() == 'nose-hoover':
inp.write(' NOSE IONS\n %.1f %.1f\n' % \
(setting['T'], setting['T_tolerance']))
if 'geometry_convergence' in setting:
inp.write(' CONVERGENCE GEOMETRY\n %.2E\n' %\
setting['geometry_convergence'])
if 'md_step' in setting:
inp.write(' MAXSTEP\n %d\n' % setting['md_step'])
if 'wf_convergence' in setting:
inp.write(' CONVERGENCE ORBITAL\n %.2E\n' %\
setting['wf_convergence'])
if 'scf_step' in setting:
inp.write(' MAXITER\n %d\n' % setting['scf_step'])
if 'restart' in setting and setting['restart']:
inp.write(' RESTART WAVEFUNCTION\n')
if 'restart_wavefunction_file' in setting:
if os.path.exists(setting['restart_wavefunction_file']):
inp.dependent_files.append(
[setting['restart_wavefunction_file'], 'RESTART']
)
else:
qtk.warning('%s not found' % setting['restart_wavefunction_file'])
if 'fix_molecule' in setting\
and setting['fix_molecule']:
inp.write(' CENTER MOLECULE OFF\n')
if ('save_density' in setting and setting['save_density'])\
or ('save_wf' in setting and setting['save_wf']):
inp.write(' RHOOUT')
if setting['save_wf']:
inp.write(' BANDS\n %d\n ' % len(setting['save_wf']))
for i in setting['save_wf']:
inp.write(' %d' % i)
inp.write('\n')
if molecule.multiplicity != 1:
inp.write(' LOCAL SPIN DENSITY\n')
if 'big_memory' in setting and setting['big_memory']:
inp.write(' MEMORY BIG\n')
inp.write('&END\n\n')
inp.write('&DFT\n FUNCTIONAL %s\n&END\n\n' % \
setting['theory'].upper())
inp.write('&SYSTEM\n')
if setting['periodic']:
inp.write(' CELL VECTORS\n')
lattice_vec = self.setting['lattice']
for vec in lattice_vec:
inp.write(' ')
for component in vec:
inp.write(' % 11.6f' % component)
inp.write('\n')
else:
inp.write(' SYMMETRY\n')
inp.write(' ISOLATED\n')
if setting['isolation'] == 'mt':
inp.write(' POISSON SOLVER TUCKERMAN\n')
inp.write(' CELL ABSOLUTE\n ')
for d in setting['celldm']:
inp.write(' %6.3f'% float(d))
inp.write('\n')
if setting['unit'].lower() == 'angstrom':
inp.write(' ANGSTROM\n')
inp.write(' CUTOFF\n %.1f\n' % setting['cutoff'])
if 'kmesh' in setting and setting['kmesh']:
inp.write(' KPOINTS MONKHORST-PACK\n %d %d %d\n' %\
(setting['kmesh'][0],
setting['kmesh'][1],
setting['kmesh'][2]))
if 'mesh' in setting:
inp.write(' MESH\n %d %d %d\n' %\
(setting['mesh'][0],
setting['mesh'][1],
setting['mesh'][2]))
if molecule.charge != 0:
inp.write(' CHARGE\n %d\n' % molecule.charge)
if molecule.multiplicity != 1:
inp.write(' MULTIPLICITY\n %d\n' % molecule.multiplicity)
inp.write('&END\n\n')
inp.write('&ATOMS\n')
molecule.sort()
type_index = molecule.index
type_list = molecule.type_list
# loop through sorted atom type indices
for atom_type in xrange(0,len(type_index)-1):
# number of each atom type
type_n = type_index[atom_type+1] - type_index[atom_type]
PPString(self, molecule, type_index[atom_type], type_n, inp)
for I in\
xrange(type_index[atom_type],type_index[atom_type+1]):
inp.write(' ')
for i in range(3):
inp.write(' % 8.4f' % molecule.R[I,i])
inp.write('\n')
inp.write('&END\n')
for pp in self.pp_files:
pp_file = os.path.join(qtk.setting.cpmd_pp, pp)
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