bugged stringlengths 4 228k | fixed stringlengths 0 96.3M | __index_level_0__ int64 0 481k |
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def parprint(*args, **kwargs): """MPI save print - prints only from master. Tries to adopt python 3 behaviour. """ if rank > 0: return defaults = { 'end' : '\n', 'file' : sys.stdout } for key in defaults: if not key in kwargs: kwargs[key] = defaults[key] for arg in args[:-1]: print >> kwargs['file'], arg, if len(args... | def parprint(*args, **kwargs): """MPI-safe print - prints only from master. Tries to adopt python 3 behaviour. """ if rank > 0: return defaults = { 'end' : '\n', 'file' : sys.stdout } for key in defaults: if not key in kwargs: kwargs[key] = defaults[key] for arg in args[:-1]: print >> kwargs['file'], arg, if len(args... | 448,000 |
def parprint(*args, **kwargs): """MPI save print - prints only from master. Tries to adopt python 3 behaviour. """ if rank > 0: return defaults = { 'end' : '\n', 'file' : sys.stdout } for key in defaults: if not key in kwargs: kwargs[key] = defaults[key] for arg in args[:-1]: print >> kwargs['file'], arg, if len(args... | def parprint(*args, **kwargs): """MPI save print - prints only from master. Tries to adopt python 3 behaviour. """ if rank > 0: return defaults = {'end': '\n', 'file': sys.stdout } for key in defaults: if not key in kwargs: kwargs[key] = defaults[key] for arg in args[:-1]: print >> kwargs['file'], arg, if len(args): ... | 448,001 |
def __init__(self, nc='out.nc', outnc=None, debug=logging.WARN, stay_alive=False, **kwargs): ''' Initialize the Jacapo calculator | def __init__(self, nc='out.nc', outnc=None, debug=logging.WARN, stay_alive=False, **kwargs): ''' Initialize the Jacapo calculator | 448,002 |
def set_nc(self, nc='out.nc'): ''' set filename for the netcdf and text output for this calculation | def set_nc(self, nc='out.nc'): ''' set filename for the netcdf and text output for this calculation | 448,003 |
def set_electronic_minimization(self, method, diagsperband=None): '''set the eigensolver method | def set_electronic_minimization(self, method='eigsolve', diagsperband=2): '''set the eigensolver method | 448,004 |
def get_dipole_moment(self): ''' return dipole moment of unit cell | def get_dipole_moment(self,atoms=None): ''' return dipole moment of unit cell | 448,005 |
def get_dipole_moment(self): ''' return dipole moment of unit cell | def get_dipole_moment(self): ''' return dipole moment of unit cell | 448,006 |
def set_attributes(self, *args): self.param = {} self.param["xc"] = self.xc.get_active_text() self.param["prec"] = self.prec.get_active_text() self.param["kpts"] = (int(self.kpts[0].value), int(self.kpts[1].value), int(self.kpts[2].value)) self.param["encut"] = self.encut.value self.param["ediff"] = self.ediff.value se... | def set_attributes(self, *args): self.param = {} self.param["xc"] = self.xc.get_active_text() self.param["prec"] = self.prec.get_active_text() self.param["kpts"] = (int(self.kpts[0].value), int(self.kpts[1].value), int(self.kpts[2].value)) self.param["encut"] = self.encut.value self.param["ediff"] = self.ediff.value se... | 448,007 |
def run(self): """Run the vibration calculations. | def run(self): """Run the vibration calculations. | 448,008 |
def run(self): """Run the vibration calculations. | def run(self): """Run the vibration calculations. | 448,009 |
def run(self): """Run the vibration calculations. | def run(self): """Run the vibration calculations. | 448,010 |
def kpts_changed(calc, x): ''' check if kpt grid has changed. we have to take care to generate teh right k-points from x if needed. if a user provides (4,4,4) we need to generate the MP grid, etc... Since i changed the MP code in set_kpts, there is some incompatibility with old jacapo calculations and their MP grids.... | def kpts_changed(calc, x): ''' check if kpt grid has changed. we have to take care to generate teh right k-points from x if needed. if a user provides (4,4,4) we need to generate the MP grid, etc... Since i changed the MP code in set_kpts, there is some incompatibility with old jacapo calculations and their MP grids.... | 448,011 |
def rotate_vectors(v1i, v2i, angle): """Rotate vectors *v1i* and *v2i* by *angle*""" cAng = cos(angle) sAng = sin(angle) v1o = v1i * cAng + v2i * sAng v2o = v2i * cAng - v1i * sAng # Ensure the length of the input and output vectors is equal return normalize(v1o) * norm(v1i), normalize(v2o) * norm(v2i) | def rotate_vectors(v1i, v2i, angle): """Rotate vectors *v1i* and *v2i* by *angle*""" cAng = cos(angle) sAng = sin(angle) v1o = v1i * cAng + v2i * sAng v2o = v2i * cAng - v1i * sAng # Ensure the length of the input and output vectors is equal return normalize(v1o) * norm(v1i), normalize(v2o) * norm(v2i) | 448,012 |
def rotate_vectors(v1i, v2i, angle): """Rotate vectors *v1i* and *v2i* by *angle*""" cAng = cos(angle) sAng = sin(angle) v1o = v1i * cAng + v2i * sAng v2o = v2i * cAng - v1i * sAng # Ensure the length of the input and output vectors is equal return normalize(v1o) * norm(v1i), normalize(v2o) * norm(v2i) | def rotate_vectors(v1i, v2i, angle): """Rotate vectors *v1i* and *v2i* by *angle*""" cAng = cos(angle) sAng = sin(angle) v1o = v1i * cAng + v2i * sAng v2o = v2i * cAng - v1i * sAng # Ensure the length of the input and output vectors is equal return normalize(v1o) * norm(v1i), normalize(v2o) * norm(v2i) | 448,013 |
def rotate_vectors(v1i, v2i, angle): """Rotate vectors *v1i* and *v2i* by *angle*""" cAng = cos(angle) sAng = sin(angle) v1o = v1i * cAng + v2i * sAng v2o = v2i * cAng - v1i * sAng # Ensure the length of the input and output vectors is equal return normalize(v1o) * norm(v1i), normalize(v2o) * norm(v2i) | def rotate_vectors(v1i, v2i, angle): """Rotate vectors *v1i* and *v2i* by *angle*""" cAng = cos(angle) sAng = sin(angle) v1o = v1i * cAng + v2i * sAng v2o = v2i * cAng - v1i * sAng # Ensure the length of the input and output vectors is equal return normalize(v1o) * norm(v1i), normalize(v2o) * norm(v2i) | 448,014 |
def rotate_vectors(v1i, v2i, angle): """Rotate vectors *v1i* and *v2i* by *angle*""" cAng = cos(angle) sAng = sin(angle) v1o = v1i * cAng + v2i * sAng v2o = v2i * cAng - v1i * sAng # Ensure the length of the input and output vectors is equal return normalize(v1o) * norm(v1i), normalize(v2o) * norm(v2i) | def rotate_vectors(v1i, v2i, angle): """Rotate vectors *v1i* and *v2i* by *angle*""" cAng = cos(angle) sAng = sin(angle) v1o = v1i * cAng + v2i * sAng v2o = v2i * cAng - v1i * sAng # Ensure the length of the input and output vectors is equal return normalize(v1o) * norm(v1i), normalize(v2o) * norm(v2i) | 448,015 |
def reset_all_counters(self): """Reset all counters.""" for key in self.counters.keys(): self.counters[key] = 0 | def reset_all_counters(self): """Reset all counters.""" for key in self.counters.keys(): self.counters[key] = 0 | 448,016 |
def reset_all_counters(self): """Reset all counters.""" for key in self.counters.keys(): self.counters[key] = 0 | def reset_all_counters(self): """Reset all counters.""" for key in self.counters.keys(): self.counters[key] = 0 | 448,017 |
def log(self, parameter=None): """Log the parameters of the eigenmode search.""" if self.logfile is not None: if parameter is not None: l = 'DIM:CONTROL: Updated Parameter: %s = %s\n' % (parameter, str(self.get_parameter(parameter))) else: l = 'MINMODE:METHOD: Dimer\n' l += 'DIM:CONTROL: Search Parameters:\n' l += 'DIM... | def log(self, parameter=None): """Log the parameters of the eigenmode search.""" if self.logfile is not None: if parameter is not None: l = 'DIM:CONTROL: Updated Parameter: %s = %s\n' % (parameter, str(self.get_parameter(parameter))) else: l = 'MINMODE:METHOD: Dimer\n' l += 'DIM:CONTROL: Search Parameters:\n' l += 'DIM... | 448,018 |
def log(self, parameter=None): """Log the parameters of the eigenmode search.""" if self.logfile is not None: if parameter is not None: l = 'DIM:CONTROL: Updated Parameter: %s = %s\n' % (parameter, str(self.get_parameter(parameter))) else: l = 'MINMODE:METHOD: Dimer\n' l += 'DIM:CONTROL: Search Parameters:\n' l += 'DIM... | def log(self, parameter=None): """Log the parameters of the eigenmode search.""" if self.logfile is not None: if parameter is not None: l = 'DIM:CONTROL: Updated Parameter: %s = %s\n' % (parameter, str(self.get_parameter(parameter))) else: l = 'MINMODE:METHOD: Dimer\n' l += 'DIM:CONTROL: Search Parameters:\n' l += 'DIM... | 448,019 |
def log(self, parameter=None): """Log the parameters of the eigenmode search.""" if self.logfile is not None: if parameter is not None: l = 'DIM:CONTROL: Updated Parameter: %s = %s\n' % (parameter, str(self.get_parameter(parameter))) else: l = 'MINMODE:METHOD: Dimer\n' l += 'DIM:CONTROL: Search Parameters:\n' l += 'DIM... | def log(self, parameter=None): """Log the parameters of the eigenmode search.""" if self.logfile is not None: if parameter is not None: l = 'DIM:CONTROL: Updated Parameter: %s = %s\n' % (parameter, str(self.get_parameter(parameter))) else: l = 'MINMODE:METHOD: Dimer\n' l += 'DIM:CONTROL: Search Parameters:\n' l += 'DIM... | 448,020 |
def log(self, parameter=None): """Log the parameters of the eigenmode search.""" if self.logfile is not None: if parameter is not None: l = 'DIM:CONTROL: Updated Parameter: %s = %s\n' % (parameter, str(self.get_parameter(parameter))) else: l = 'MINMODE:METHOD: Dimer\n' l += 'DIM:CONTROL: Search Parameters:\n' l += 'DIM... | def log(self, parameter=None): """Log the parameters of the eigenmode search.""" if self.logfile is not None: if parameter is not None: l = 'DIM:CONTROL: Updated Parameter: %s = %s\n' % (parameter, str(self.get_parameter(parameter))) else: l = 'MINMODE:METHOD: Dimer\n' l += 'DIM:CONTROL: Search Parameters:\n' l += 'DIM... | 448,021 |
def _set_frame_number(self, frame=None): '''set framenumber in the netcdf file | def _set_frame_number(self, frame=None): '''set framenumber in the netcdf file | 448,022 |
def _set_frame_number(self, frame=None): '''set framenumber in the netcdf file | def _set_frame_number(self, frame=None): '''set framenumber in the netcdf file | 448,023 |
def restart_load(self): """Method which is called upon restart.""" # Try to read sorting file if os.path.isfile('ase-sort.dat'): self.sort = [] self.resort = [] file = open('ase-sort.dat', 'r') lines = file.readlines() file.close() for line in lines: data = line.split() self.sort.append(int(data[0])) self.resort.appen... | def restart_load(self): """Method which is called upon restart.""" # Try to read sorting file if os.path.isfile('ase-sort.dat'): self.sort = [] self.resort = [] file = open('ase-sort.dat', 'r') lines = file.readlines() file.close() for line in lines: data = line.split() self.sort.append(int(data[0])) self.resort.appen... | 448,024 |
def convert(self): lines = open(self.xdatcar).readlines() | def convert(self): lines = open(self.xdatcar).readlines() | 448,025 |
def set_nbands(self, nbands=None): '''Set the number of bands. a few unoccupied bands are recommended. | def set_nbands(self, nbands=None): '''Set the number of bands. a few unoccupied bands are recommended. | 448,026 |
def set_kpts(self, kpts): ''' set the kpt grid. | def set_kpts(self, kpts): ''' set the kpt grid. | 448,027 |
def atoms_are_equal(self,atoms): ''' comparison of atoms to self.atoms using tolerances to account for float/double differences and float math. ''' TOL = 1.0e-6 #angstroms | def atoms_are_equal(self,atoms): ''' comparison of atoms to self.atoms using tolerances to account for float/double differences and float math. ''' TOL = 1.0e-6 #angstroms | 448,028 |
def set_nc(self,nc='out.nc'): ''' set filename for the netcdf and text output for this calculation | def set_nc(self,nc='out.nc'): ''' set filename for the netcdf and text output for this calculation | 448,029 |
def get_symmetry(self): '''return the type of symmetry used''' nc = netCDF(self.nc,'r') if 'UseSymmetry' in nc.variables: sym = string.join(nc.variables['UseSymmetry'][:],'').strip() else: sym = None nc.close() return sym | def get_symmetry(self): '''return the type of symmetry used''' nc = netCDF(self.nc,'r') if 'UseSymmetry' in nc.variables: sym = string.join(nc.variables['UseSymmetry'][:],'').strip() else: sym = None nc.close() return sym | 448,030 |
def set_fftgrid(self,soft=None,hard=None): ''' sets the dimensions of the FFT grid to be used | def set_fftgrid(self,soft=None,hard=None): ''' sets the dimensions of the FFT grid to be used | 448,031 |
def set_fftgrid(self,soft=None,hard=None): ''' sets the dimensions of the FFT grid to be used | def set_fftgrid(self,soft=None,hard=None): ''' sets the dimensions of the FFT grid to be used | 448,032 |
def get_external_dipole(self): var = 'ExternalDipolePotential' nc = netCDF(self.get_nc(),'r') if var in nc.variables: v = nc.variables[var] value = v.getValue() if hasattr(v,'DipoleLayerPosition'): position = v.DipoleLayerPosition else: position = None else: value,position = None,None nc.close() return {'value':value,'... | def get_external_dipole(self): var = 'ExternalDipolePotential' nc = netCDF(self.get_nc(),'r') if var in nc.variables: v = nc.variables[var] value = v.getValue() if hasattr(v,'DipoleLayerPosition'): position = v.DipoleLayerPosition else: position = None else: value,position = None,None nc.close() return {'value':value,'... | 448,033 |
def delete_ncattdimvar(self,ncf,ncattrs=[],ncdims=[],ncvars=[]): ''' helper function to delete attributes, dimensions and variables in a netcdffile | def delete_ncattdimvar(self,ncf,ncattrs=[],ncdims=[],ncvars=[]): ''' helper function to delete attributes, dimensions and variables in a netcdffile | 448,034 |
def valid_kpts(self, x): if isinstance(x,str): return x in ['cc-6-1x1', 'cc-12-2x3', 'cc-18-sq3xsq3', 'cc-18-1x1', 'cc-54-sq3xsq3', 'cc-54-1x1', 'cc-162-1x1'] x = np.array(x) #empty arg is no good if x.shape == (): return False #monkhorst-pack elif x.shape == (3,) and ((x.dtype == 'int32') or (x.dtype == 'int64')): ret... | def valid_kpts(self, x): if isinstance(x,str): return x in ['cc-6-1x1', 'cc-12-2x3', 'cc-18-sq3xsq3', 'cc-18-1x1', 'cc-54-sq3xsq3', 'cc-54-1x1', 'cc-162-1x1'] x = np.array(x) #empty arg is no good if x.shape == (): return False #monkhorst-pack elif x.shape == (3,) and ((x.dtype == 'int32') or (x.dtype == 'int64')): ret... | 448,035 |
def electronic_minimization_changed(self, x): print 'checking if em changed' myx = self.get_electronic_minimization() print myx print x return False | def electronic_minimization_changed(self, x): myx = self.get_electronic_minimization() print myx print x return False | 448,036 |
def electronic_minimization_changed(self, x): print 'checking if em changed' myx = self.get_electronic_minimization() print myx print x return False | def electronic_minimization_changed(self, x): print 'checking if em changed' myx = self.get_electronic_minimization() for key in myx: if myx[key] != x[key]: print key, myx[key],' changed to ',x[key] return True return False | 448,037 |
def symmetry_changed(self,x): if x != self.get_symmetry: return True else: return False | def symmetry_changed(self,x): if x != self.get_symmetry(): return True else: return False | 448,038 |
def save(self, action): chooser = gtk.FileChooserDialog( _('Save ...'), None, gtk.FILE_CHOOSER_ACTION_SAVE, (gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_SAVE, gtk.RESPONSE_OK)) | def save(self, action): chooser = gtk.FileChooserDialog( _('Save ...'), None, gtk.FILE_CHOOSER_ACTION_SAVE, (gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_SAVE, gtk.RESPONSE_OK)) | 448,039 |
def valid_int(x): return isinstance(x, int) | def valid_int(x): if (isinstance(x, int) or isinstance(x,np.int32)): return True | 448,040 |
def valid_int_or_float(x): return (isinstance(x, int) or isinstance(x, float)) | def valid_int_or_float(x): return ((isinstance(x, int) or isinstance(x,np.int32)) or isinstance(x, float)) | 448,041 |
def valid_kpts(x): if isinstance(x, str): return x in ['cc-6-1x1', 'cc-12-2x3', 'cc-18-sq3xsq3', 'cc-18-1x1', 'cc-54-sq3xsq3', 'cc-54-1x1', 'cc-162-1x1'] x = np.array(x) #empty arg is no good if x.shape == (): return False #monkhorst-pack elif x.shape == (3,) and ((x.dtype == 'int32') or (x.dtype == 'int64')): return T... | def valid_kpts(x): if isinstance(x, str): return x in ['cc6_1x1', 'cc12_2x3', 'cc18_sq3xsq3', 'cc18_1x1', 'cc54_sq3xsq3', 'cc54_1x1', 'cc162_sq3xsq3', 'cc162_1x1'] x = np.array(x) #empty arg is no good if x.shape == (): return False #monkhorst-pack elif x.shape == (3,) and ((x.dtype == 'int32') or (x.dtype == 'int64'))... | 448,042 |
def summary(self, method='standard', direction='central'): hnu = self.get_energies(method, direction) s = 0.01 * units._e / units._c / units._hplanck parprint('-------------------------------------') parprint(' Mode Frequency Intensity') parprint(' # meV cm^-1 (D/Å)^2 amu^-1') parprint('------------... | def summary(self, method='standard', direction='central'): hnu = self.get_energies(method, direction) s = 0.01 * units._e / units._c / units._hplanck parprint('-------------------------------------') parprint(' Mode Frequency Intensity') parprint(' # meV cm^-1 (D/Å)^2 amu^-1') parprint('------------... | 448,043 |
def build(): p = OptionParser(usage='%prog [options] [ads@]surf [output file]', version='%prog 0.1', description='Example ads/surf: CO@2x2Ru0001') p.add_option('-l', '--layers', type='int', default=4, help='Number of layers.') p.add_option('-v', '--vacuum', type='float', default=5.0, help='Vacuum.') p.add_option('-x',... | def build(): p = OptionParser(usage='%prog [options] [ads@]surf [output file]', version='%prog 0.1', description='Example ads/surf: CO@2x2Ru0001') p.add_option('-l', '--layers', type='int', default=4, help='Number of layers.') p.add_option('-v', '--vacuum', type='float', default=5.0, help='Vacuum.') p.add_option('-x',... | 448,044 |
def build(): p = OptionParser(usage='%prog [options] [ads@]surf [output file]', version='%prog 0.1', description='Example ads/surf: CO@2x2Ru0001') p.add_option('-l', '--layers', type='int', default=4, help='Number of layers.') p.add_option('-v', '--vacuum', type='float', default=5.0, help='Vacuum.') p.add_option('-x',... | def build(): p = OptionParser(usage='%prog [options] [ads@]surf [output file]', version='%prog 0.1', description='Example ads/surf: CO@2x2Ru0001') p.add_option('-l', '--layers', type='int', default=4, help='Number of layers.') p.add_option('-v', '--vacuum', type='float', default=5.0, help='Vacuum.') p.add_option('-x',... | 448,045 |
def build(): p = OptionParser(usage='%prog [options] [ads@]surf [output file]', version='%prog 0.1', description='Example ads/surf: CO@2x2Ru0001') p.add_option('-l', '--layers', type='int', default=4, help='Number of layers.') p.add_option('-v', '--vacuum', type='float', default=5.0, help='Vacuum.') p.add_option('-x',... | def build(): p = OptionParser(usage='%prog [options] [ads@]surf [output file]', version='%prog 0.1', description='Example ads/surf: CO@2x2Ru0001') p.add_option('-l', '--layers', type='int', default=4, help='Number of layers.') p.add_option('-v', '--vacuum', type='float', default=5.0, help='Vacuum.') p.add_option('-x',... | 448,046 |
def build(): p = OptionParser(usage='%prog [options] [ads@]surf [output file]', version='%prog 0.1', description='Example ads/surf: CO@2x2Ru0001') p.add_option('-l', '--layers', type='int', default=4, help='Number of layers.') p.add_option('-v', '--vacuum', type='float', default=5.0, help='Vacuum.') p.add_option('-x',... | def build(): p = OptionParser(usage='%prog [options] [ads@]surf [output file]', version='%prog 0.1', description='Example ads/surf: CO@2x2Ru0001') p.add_option('-l', '--layers', type='int', default=4, help='Number of layers.') p.add_option('-v', '--vacuum', type='float', default=5.0, help='Vacuum.') p.add_option('-x',... | 448,047 |
def scroll(self, window, event): from copy import copy CTRL = event.state == gtk.gdk.CONTROL_MASK SHIFT = event.state == gtk.gdk.SHIFT_MASK dxdydz = {gtk.keysyms.KP_Add: ('zoom', 1.2, 0), gtk.keysyms.KP_Subtract: ('zoom', 1 / 1.2), gtk.keysyms.Up: ( 0, -1 + CTRL, +CTRL), gtk.keysyms.Down: ( 0, +1 - CTRL, -CTRL), gt... | def scroll(self, window, event): from copy import copy CTRL = event.state == gtk.gdk.CONTROL_MASK SHIFT = event.state == gtk.gdk.SHIFT_MASK dxdydz = {gtk.keysyms.KP_Add: ('zoom', 1.2, 0), gtk.keysyms.KP_Subtract: ('zoom', 1 / 1.2), gtk.keysyms.Up: ( 0, -1 + CTRL, +CTRL), gtk.keysyms.Down: ( 0, +1 - CTRL, -CTRL), gt... | 448,048 |
def __imul__(self, m): if len(self._constraints) > 0: raise RuntimeError('Remove constraint before modifying atoms.') if isinstance(m, int): m = (m, m, m) M = np.product(m) n = len(self) for name, a in self.arrays.items(): self.arrays[name] = np.tile(a, (M,) + (1,) * (len(a.shape) - 1)) | def __imul__(self, m): if len(self._constraints) > 0: from ase.constraints import FixAtoms fixed_only = True fixed_atoms = [False for a in self] have_constraints = True for con in self.constraints: if isinstance(con, FixAtoms): for i in con.index: fixed_atoms[i] = True else: fixed_only = False if not fixed_only: raise ... | 448,049 |
def get_spectrum(self, start=800, end=4000, npts=None, width=4, type='Gaussian', method='standard', direction='central'): """Get infrared spectrum. | def get_spectrum(self, start=800, end=4000, npts=None, width=4, type='Gaussian', method='standard', direction='central'): """Get infrared spectrum. | 448,050 |
def save(self, action): chooser = gtk.FileChooserDialog( _('Save ...'), None, gtk.FILE_CHOOSER_ACTION_SAVE, (gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_SAVE, gtk.RESPONSE_OK)) | def save(self, action): chooser = gtk.FileChooserDialog( _('Save ...'), None, gtk.FILE_CHOOSER_ACTION_SAVE, (gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_SAVE, gtk.RESPONSE_OK)) | 448,051 |
def ados_changed(self,x): ados = self.get_ados() | def ados_changed(self,x): ados = self.get_ados() | 448,052 |
def ados_changed(self,x): ados = self.get_ados() | def ados_changed(self,x): ados = self.get_ados() | 448,053 |
def ados_changed(self,x): ados = self.get_ados() | defelif ados is not None and x is None: return True ados_changed(self,x):elif ados is not None and x is None: return True adoselif ados is not None and x is None: return True =elif ados is not None and x is None: return True self.get_ados() | 448,054 |
def kpts_changed(calc, x): ''' check if kpt grid has changed. we have to take care to generate teh right k-points from x if needed. if a user provides (4,4,4) we need to generate the MP grid, etc... Since i changed the MP code in set_kpts, there is some incompatibility with old jacapo calculations and their MP grids.... | def kpts_changed(calc, x): ''' check if kpt grid has changed. we have to take care to generate teh right k-points from x if needed. if a user provides (4,4,4) we need to generate the MP grid, etc... Since i changed the MP code in set_kpts, there is some incompatibility with old jacapo calculations and their MP grids.... | 448,055 |
def kpts_changed(calc, x): ''' check if kpt grid has changed. we have to take care to generate teh right k-points from x if needed. if a user provides (4,4,4) we need to generate the MP grid, etc... Since i changed the MP code in set_kpts, there is some incompatibility with old jacapo calculations and their MP grids.... | def kpts_changed(calc, x): ''' check if kpt grid has changed. we have to take care to generate teh right k-points from x if needed. if a user provides (4,4,4) we need to generate the MP grid, etc... Since i changed the MP code in set_kpts, there is some incompatibility with old jacapo calculations and their MP grids.... | 448,056 |
def read_ldau(self): ldau_luj = None ldauprint = None ldau = None ldautype = None atomtypes = [] # read ldau parameters from outcar for line in open('OUTCAR'): if line.find('TITEL') != -1: # What atoms are present atomtypes.append(line.split()[3].split('_')[0].split('.')[0]) if line.find('LDAUTYPE') != -1: # Is this... | def read_ldau(self): ldau_luj = None ldauprint = None ldau = None ldautype = None atomtypes = [] # read ldau parameters from outcar for line in open('OUTCAR'): if line.find('TITEL') != -1: # What atoms are present atomtypes.append(line.split()[3].split('_')[0].split('.')[0]) if line.find('LDAUTYPE') != -1: # Is this... | 448,057 |
def __init__(self, gui): Simulation.__init__(self, gui) self.set_title("Homogeneous scaling") vbox = gtk.VBox() self.packtext(vbox, "XXXX Bla bla bla.") self.packimageselection(vbox) pack(vbox, gtk.Label("")) | def __init__(self, gui): Simulation.__init__(self, gui) self.set_title("Homogeneous scaling") vbox = gtk.VBox() self.packtext(vbox, "XXXX Bla bla bla.") self.packimageselection(vbox) pack(vbox, gtk.Label("")) | 448,058 |
def choose_possible_deformations(self): """Turn on sensible radio buttons. | def choose_possible_deformations(self, first=False): """Turn on sensible radio buttons. | 448,059 |
def get_deformation_axes(self): """Return which axes the user wants to deform along.""" for but, deform in self.deformtable: if but.get_active() and but.get_sensitive(): return np.array(deform) # No deformation chosen! oops("No deformation chosen: Please choose a deformation mode.") return False | def get_deformation_axes(self): """Return which axes the user wants to deform along.""" for but, deform in self.deformtable: if but.get_active(): return np.array(deform) # No deformation chosen! oops("No deformation chosen: Please choose a deformation mode.") return False | 448,060 |
def __init__(self, gui): Simulation.__init__(self, gui) self.set_title("Homogeneous scaling") vbox = gtk.VBox() self.packtext(vbox, "XXXX Bla bla bla.") self.packimageselection(vbox, txt1="", txt2="") self.start_radio_nth.set_active(True) pack(vbox, gtk.Label("")) | def __init__(self, gui): Simulation.__init__(self, gui) self.set_title("Homogeneous scaling") vbox = gtk.VBox() self.packtext(vbox, scaling_txt) self.packimageselection(vbox, txt1="", txt2="") self.start_radio_nth.set_active(True) pack(vbox, gtk.Label("")) | 448,061 |
framedef = gtk.Frame("Deformation:") | framedef = gtk.Frame("Deformation:") | 448,062 |
def step(self,f): atoms = self.atoms if self.v is None: self.v = np.zeros((len(atoms), 3)) else: vf = np.vdot(f, self.v) if vf > 0.0: self.v = (1.0 - self.a) * self.v + self.a * f / np.sqrt( np.vdot(f, f)) * np.sqrt(np.vdot(self.v, self.v)) if self.Nsteps > self.Nmin: self.dt = min(self.dt * self.finc, self.dtmax) self... | def step(self,f): atoms = self.atoms if self.v is None: self.v = np.zeros((len(atoms), 3)) else: vf = np.vdot(f, self.v) if vf > 0.0: self.v = (1.0 - self.a) * self.v + self.a * f / np.sqrt( np.vdot(f, f)) * np.sqrt(np.vdot(self.v, self.v)) if self.Nsteps > self.Nmin: self.dt = min(self.dt * self.finc, self.dtmax) self... | 448,063 |
def step(self,f): atoms = self.atoms if self.v is None: self.v = np.zeros((len(atoms), 3)) else: vf = np.vdot(f, self.v) if vf > 0.0: self.v = (1.0 - self.a) * self.v + self.a * f / np.sqrt( np.vdot(f, f)) * np.sqrt(np.vdot(self.v, self.v)) if self.Nsteps > self.Nmin: self.dt = min(self.dt * self.finc, self.dtmax) self... | def step(self,f): atoms = self.atoms if self.v is None: self.v = np.zeros((len(atoms), 3)) else: vf = np.vdot(f, self.v) if vf > 0.0: self.v = (1.0 - self.a) * self.v + self.a * f / np.sqrt( np.vdot(f, f)) * np.sqrt(np.vdot(self.v, self.v)) if self.Nsteps > self.Nmin: self.dt = min(self.dt * self.finc, self.dtmax) self... | 448,064 |
def set_frame(self, frame=None, focus=False, init=False): if frame is None: frame = self.frame | def set_frame(self, frame=None, focus=False, init=False): if frame is None: frame = self.frame | 448,065 |
def __repr__(self): return 'FixedMode(%d, %s)' % (ints2string(self.index), self.mode.tolist()) | def __repr__(self): return 'FixedMode(%d, %s)' % (ints2string(self.index), self.mode.tolist()) | 448,066 |
def build(): p = OptionParser(usage='%prog [options] [ads@]surf [output file]', version='%prog 0.1', description='Example ads/surf: CO@2x2Ru0001') p.add_option('-l', '--layers', type='int', default=4, help='Number of layers.') p.add_option('-v', '--vacuum', type='float', default=5.0, help='Vacuum.') p.add_option('-x',... | def build(): p = OptionParser(usage='%prog [options] [ads@]surf [output file]', version='%prog 0.1', description='Example ads/surf: CO@2x2Ru0001') p.add_option('-l', '--layers', type='int', default=4, help='Number of layers.') p.add_option('-v', '--vacuum', type='float', default=5.0, help='Vacuum.') p.add_option('-x',... | 448,067 |
def read(ncfile): '''return atoms and calculator from ncfile >>> atoms, calc = read('co.nc') ''' calc = Jacapo(ncfile) atoms = calc.get_atoms() #this returns a copy return (atoms, calc) | def read(ncfile): '''return atoms and calculator from ncfile >>> atoms, calc = read('co.nc') ''' calc = Jacapo(ncfile) atoms = calc.get_atoms() #this returns a copy return (atoms, calc) | 448,068 |
def __init__(self, nc='out.nc', outnc=None, debug=logging.WARN, stay_alive=False, **kwargs): ''' Initialize the Jacapo calculator | def __init__(self, nc='out.nc', outnc=None, debug=logging.WARN, stay_alive=False, **kwargs): ''' Initialize the Jacapo calculator | 448,069 |
def __init__(self, nc='out.nc', outnc=None, debug=logging.WARN, stay_alive=False, **kwargs): ''' Initialize the Jacapo calculator | def __init__(self, nc='out.nc', outnc=None, debug=logging.WARN, stay_alive=False, **kwargs): ''' Initialize the Jacapo calculator | 448,070 |
def initnc(self, ncfile=None): '''create an ncfile with minimal dimensions in it | def initnc(self, ncfile=None): '''create an ncfile with minimal dimensions in it | 448,071 |
def __str__(self): ''' pretty-print the calculator and atoms. | def __str__(self): ''' pretty-print the calculator and atoms. | 448,072 |
def _set_frame_number(self, frame=None): 'set framenumber in the netcdf file' if frame is None: nc = netCDF(self.nc, 'r') if 'TotalEnergy' in nc.variables: frame = nc.variables['TotalEnergy'].shape[0] # make sure the last energy is reasonable. Sometime # the field is empty if the calculation ran out of # walltime for ... | def _set_frame_number(self, frame=None): '''set framenumber in the netcdf file this is equal to the number of ionic steps dimension''' if frame is None: nc = netCDF(self.nc, 'r') if 'TotalEnergy' in nc.variables: frame = nc.variables['TotalEnergy'].shape[0] # make sure the last energy is reasonable. Sometime # the fi... | 448,073 |
def _set_frame_number(self, frame=None): 'set framenumber in the netcdf file' if frame is None: nc = netCDF(self.nc, 'r') if 'TotalEnergy' in nc.variables: frame = nc.variables['TotalEnergy'].shape[0] # make sure the last energy is reasonable. Sometime # the field is empty if the calculation ran out of # walltime for ... | def _set_frame_number(self, frame=None): 'set framenumber in the netcdf file' if frame is None: nc = netCDF(self.nc, 'r') if 'TotalEnergy' in nc.variables: frame = nc.variables['TotalEnergy'].shape[0] # make sure the last energy is reasonable. Sometime # the field is empty if the calculation ran out of # walltime for ... | 448,074 |
def _set_frame_number(self, frame=None): 'set framenumber in the netcdf file' if frame is None: nc = netCDF(self.nc, 'r') if 'TotalEnergy' in nc.variables: frame = nc.variables['TotalEnergy'].shape[0] # make sure the last energy is reasonable. Sometime # the field is empty if the calculation ran out of # walltime for ... | def _set_frame_number(self, frame=None): 'set framenumber in the netcdf file' if frame is None: nc = netCDF(self.nc, 'r') if 'TotalEnergy' in nc.variables: frame = nc.variables['TotalEnergy'].shape[0] # make sure the last energy is reasonable. Sometime # the field is empty if the calculation ran out of # walltime for ... | 448,075 |
def cut(atoms, a=(1,0,0), b=(0,1,0), c=(0,0,1), origo=(0,0,0), nlayers=None, extend=1.0, tolerance=0.001): """Cuts out a cell defined by *a*, *b*, *c* and *origo* from a sufficiently repeated copy of *atoms*. Typically, this function is used to create slabs of different sizes and orientations. The vectors *a*, *b* and... | def>>> cut(atoms,>>> a=(1,0,0),>>> b=(0,1,0),>>> c=(0,0,1),>>> origo=(0,0,0),>>> nlayers=None,>>> extend=1.0,>>> tolerance=0.001):>>> """Cuts>>> out>>> a>>> cell>>> defined>>> by>>> *a*,>>> *b*,>>> *c*>>> and>>> *origo*>>> from>>> a>>> sufficiently>>> repeated>>> copy>>> of>>> *atoms*.>>> >>> Typically,>>> this>>> func... | 448,076 |
def cut(atoms, a=(1,0,0), b=(0,1,0), c=(0,0,1), origo=(0,0,0), nlayers=None, extend=1.0, tolerance=0.001): """Cuts out a cell defined by *a*, *b*, *c* and *origo* from a sufficiently repeated copy of *atoms*. Typically, this function is used to create slabs of different sizes and orientations. The vectors *a*, *b* and... | def>>> cut(atoms,>>> a=(1,0,0),>>> b=(0,1,0),>>> c=(0,0,1),>>> origo=(0,0,0),>>> nlayers=None,>>> extend=1.0,>>> tolerance=0.001):>>> """Cuts>>> out>>> a>>> cell>>> defined>>> by>>> *a*,>>> *b*,>>> *c*>>> and>>> *origo*>>> from>>> a>>> sufficiently>>> repeated>>> copy>>> of>>> *atoms*.>>> >>> Typically,>>> this>>> func... | 448,077 |
def cut(atoms, a=(1,0,0), b=(0,1,0), c=(0,0,1), origo=(0,0,0), nlayers=None, extend=1.0, tolerance=0.001): """Cuts out a cell defined by *a*, *b*, *c* and *origo* from a sufficiently repeated copy of *atoms*. Typically, this function is used to create slabs of different sizes and orientations. The vectors *a*, *b* and... | def>>> cut(atoms,>>> a=(1,0,0),>>> b=(0,1,0),>>> c=(0,0,1),>>> origo=(0,0,0),>>> nlayers=None,>>> extend=1.0,>>> tolerance=0.001):>>> """Cuts>>> out>>> a>>> cell>>> defined>>> by>>> *a*,>>> *b*,>>> *c*>>> and>>> *origo*>>> from>>> a>>> sufficiently>>> repeated>>> copy>>> of>>> *atoms*.>>> >>> Typically,>>> this>>> func... | 448,078 |
def cut(atoms, a=(1,0,0), b=(0,1,0), c=(0,0,1), origo=(0,0,0), nlayers=None, extend=1.0, tolerance=0.001): """Cuts out a cell defined by *a*, *b*, *c* and *origo* from a sufficiently repeated copy of *atoms*. Typically, this function is used to create slabs of different sizes and orientations. The vectors *a*, *b* and... | def>>> cut(atoms,>>> a=(1,0,0),>>> b=(0,1,0),>>> c=(0,0,1),>>> origo=(0,0,0),>>> nlayers=None,>>> extend=1.0,>>> tolerance=0.001):>>> """Cuts>>> out>>> a>>> cell>>> defined>>> by>>> *a*,>>> *b*,>>> *c*>>> and>>> *origo*>>> from>>> a>>> sufficiently>>> repeated>>> copy>>> of>>> *atoms*.>>> >>> Typically,>>> this>>> func... | 448,079 |
def stack(atoms1, atoms2, axis=2, cell=None, fix=0.5, maxstrain=0.5, distance=None): """Return a new Atoms instance with *atoms2* added to atoms1 along the given axis. Periodicity in all directions is ensured. The size of the final cell is determined by *cell*, except that the length alongh *axis* will be the sum of *... | def>>> stack(atoms1,>>> atoms2,>>> axis=2,>>> cell=None,>>> fix=0.5,>>> maxstrain=0.5,>>> distance=None):>>> """Return>>> a>>> new>>> Atoms>>> instance>>> with>>> *atoms2*>>> added>>> to>>> atoms1>>> along>>> the>>> given>>> axis.>>> Periodicity>>> in>>> all>>> directions>>> is>>> ensured.>>> >>> The>>> size>>> of>>> t... | 448,080 |
def stack(atoms1, atoms2, axis=2, cell=None, fix=0.5, maxstrain=0.5, distance=None): """Return a new Atoms instance with *atoms2* added to atoms1 along the given axis. Periodicity in all directions is ensured. The size of the final cell is determined by *cell*, except that the length alongh *axis* will be the sum of *... | def>>> stack(atoms1,>>> atoms2,>>> axis=2,>>> cell=None,>>> fix=0.5,>>> maxstrain=0.5,>>> distance=None):>>> """Return>>> a>>> new>>> Atoms>>> instance>>> with>>> *atoms2*>>> added>>> to>>> atoms1>>> along>>> the>>> given>>> axis.>>> Periodicity>>> in>>> all>>> directions>>> is>>> ensured.>>> >>> The>>> size>>> of>>> t... | 448,081 |
def stack(atoms1, atoms2, axis=2, cell=None, fix=0.5, maxstrain=0.5, distance=None): """Return a new Atoms instance with *atoms2* added to atoms1 along the given axis. Periodicity in all directions is ensured. The size of the final cell is determined by *cell*, except that the length alongh *axis* will be the sum of *... | def>>> stack(atoms1,>>> atoms2,>>> axis=2,>>> cell=None,>>> fix=0.5,>>> maxstrain=0.5,>>> distance=None):>>> """Return>>> a>>> new>>> Atoms>>> instance>>> with>>> *atoms2*>>> added>>> to>>> atoms1>>> along>>> the>>> given>>> axis.>>> Periodicity>>> in>>> all>>> directions>>> is>>> ensured.>>> >>> The>>> size>>> of>>> t... | 448,082 |
def stack(atoms1, atoms2, axis=2, cell=None, fix=0.5, maxstrain=0.5, distance=None): """Return a new Atoms instance with *atoms2* added to atoms1 along the given axis. Periodicity in all directions is ensured. The size of the final cell is determined by *cell*, except that the length alongh *axis* will be the sum of *... | def>>> stack(atoms1,>>> atoms2,>>> axis=2,>>> cell=None,>>> fix=0.5,>>> maxstrain=0.5,>>> distance=None):>>> """Return>>> a>>> new>>> Atoms>>> instance>>> with>>> *atoms2*>>> added>>> to>>> atoms1>>> along>>> the>>> given>>> axis.>>> Periodicity>>> in>>> all>>> directions>>> is>>> ensured.>>> >>> The>>> size>>> of>>> t... | 448,083 |
def read_aims_output(filename, index = -1): """ Import FHI-aims output files with all data available, i.e. relaxations, MD information, force information etc etc etc. """ from ase import Atoms, Atom from ase.calculators.singlepoint import SinglePointCalculator from ase.units import Ang, fs molecular_dynamics = False f... | def read_aims_output(filename, index = -1): """ Import FHI-aims output files with all data available, i.e. relaxations, MD information, force information etc etc etc. """ from ase import Atoms, Atom from ase.calculators.singlepoint import SinglePointCalculator from ase.units import Ang, fs molecular_dynamics = False f... | 448,084 |
def __init__(self, stpmin=1e-8, xtol=1e-14): | def __init__(self, stpmin=1e-8, xtol=1e-14): | 448,085 |
def __init__(self, stpmin=1e-8, xtol=1e-14): | def __init__(self, stpmin=1e-8, xtol=1e-14): | 448,086 |
def _line_search(self, func, myfprime, xk, pk, gfk, old_fval, old_old_fval, maxstep=.2, c1=.23, c2=0.46, xtrapl=1.1, xtrapu=4., stpmax=50., args=()): | def _line_search(self, func, myfprime, xk, pk, gfk, old_fval, old_old_fval, maxstep=.2, c1=.23, c2=0.46, xtrapl=1.1, xtrapu=4., stpmax=50., args=()): | 448,087 |
def _line_search(self, func, myfprime, xk, pk, gfk, old_fval, old_old_fval, maxstep=.2, c1=.23, c2=0.46, xtrapl=1.1, xtrapu=4., stpmax=50., args=()): | def _line_search(self, func, myfprime, xk, pk, gfk, old_fval, old_old_fval, maxstep=.2, c1=.23, c2=0.46, xtrapl=1.1, xtrapu=4., stpmax=50., args=()): | 448,088 |
def _line_search(self, func, myfprime, xk, pk, gfk, old_fval, old_old_fval, maxstep=.2, c1=.23, c2=0.46, xtrapl=1.1, xtrapu=4., stpmax=50., args=()): | def _line_search(self, func, myfprime, xk, pk, gfk, old_fval, old_old_fval, maxstep=.2, c1=.23, c2=0.46, xtrapl=1.1, xtrapu=4., stpmax=50., args=()): | 448,089 |
def step(self, stp, f, g, c1, c2, xtol, isave, dsave): if self.task[:5] == 'START': | def step(self, stp, f, g, c1, c2, xtol, isave, dsave): if self.task[:5] == 'START': | 448,090 |
def step(self, stp, f, g, c1, c2, xtol, isave, dsave): if self.task[:5] == 'START': | def step(self, stp, f, g, c1, c2, xtol, isave, dsave): if self.task[:5] == 'START': | 448,091 |
def step(self, stp, f, g, c1, c2, xtol, isave, dsave): if self.task[:5] == 'START': | def step(self, stp, f, g, c1, c2, xtol, isave, dsave): if self.task[:5] == 'START': | 448,092 |
def step(self, stp, f, g, c1, c2, xtol, isave, dsave): if self.task[:5] == 'START': | def step(self, stp, f, g, c1, c2, xtol, isave, dsave): if self.task[:5] == 'START': | 448,093 |
def step(self, stp, f, g, c1, c2, xtol, isave, dsave): if self.task[:5] == 'START': | def step(self, stp, f, g, c1, c2, xtol, isave, dsave): if self.task[:5] == 'START': | 448,094 |
def step(self, stp, f, g, c1, c2, xtol, isave, dsave): if self.task[:5] == 'START': | def step(self, stp, f, g, c1, c2, xtol, isave, dsave): if self.task[:5] == 'START': | 448,095 |
def get_mass(self): return self._get('mass') | def get_mass(self): return self._get('mass') | 448,096 |
def set_mass(self, mass): self._set('mass', mass) | def set_mass(self, mass): self._set('mass', mass) | 448,097 |
def open(self, button=None, filenames=None): if filenames == None: chooser = gtk.FileChooserDialog( _('Open ...'), None, gtk.FILE_CHOOSER_ACTION_OPEN, (gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_OPEN, gtk.RESPONSE_OK)) ok = chooser.run() if ok == gtk.RESPONSE_OK: filenames = [chooser.get_filename()] chooser.destr... | def open(self, button=None, filenames=None): if filenames == None: chooser = gtk.FileChooserDialog( _('Open ...'), None, gtk.FILE_CHOOSER_ACTION_OPEN, (gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_OPEN, gtk.RESPONSE_OK)) ok = chooser.run() == gtk.RESPONSE_OK if ok: filenames = [chooser.get_filename()] chooser.destr... | 448,098 |
def read_aims_output(filename, index = -1): """ Import FHI-aims output files with all data available, i.e. relaxations, MD information, force information etc etc etc. """ from ase import Atoms, Atom from ase.calculators.singlepoint import SinglePointCalculator molecular_dynamics = False fd = open(filename, 'r') cell =... | def read_aims_output(filename, index = -1): """ Import FHI-aims output files with all data available, i.e. relaxations, MD information, force information etc etc etc. """ from ase import Atoms, Atom from ase.calculators.singlepoint import SinglePointCalculator molecular_dynamics = False fd = open(filename, 'r') cell =... | 448,099 |
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