seminar:jacapo_object
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| seminar:jacapo_object [2020/08/18 13:26] – 作成 kimi | seminar:jacapo_object [2022/08/23 13:34] (現在) – 外部編集 127.0.0.1 | ||
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| - | <html>< | + | <code> |
| - | </ | + | |
| + | ase.calculators.jacapo.jacapo | ||
| + | index | ||
| + | /usr/ | ||
| + | python module for ASE2-free and Numeric-free dacapo
U{John Kitchin<mailto: | ||
| + | |||
| + | Modules | ||
| + | |||
| + | |||
| + | ase.calculators.jacapo.changed | ||
| + | exceptions | ||
| + | glob | ||
| + | logging | ||
| + | numpy | ||
| + | os | ||
| + | pickle | ||
| + | subprocess | ||
| + | string | ||
| + | sys | ||
| + | ase.calculators.jacapo.validate | ||
| + | |||
| + | Classes | ||
| + | |||
| + | |||
| + | Jacapo | ||
| + | exceptions.Exception(exceptions.BaseException) | ||
| + | DacapoAbnormalTermination | ||
| + | DacapoAborted | ||
| + | DacapoDryrun | ||
| + | DacapoInput | ||
| + | DacapoRunning | ||
| + | |||
| + | class DacapoAbnormalTermination(exceptions.Exception) | ||
| + | |||
| + | Raised when text file does not end correctly | ||
| + | |||
| + | |||
| + | Method resolution order: | ||
| + | DacapoAbnormalTermination | ||
| + | exceptions.Exception | ||
| + | exceptions.BaseException | ||
| + | __builtin__.object | ||
| - | <table width=" | + | Data descriptors defined here: |
| - | <tr bgcolor="# | + | __weakref__ |
| - | <td valign=bottom>& | + | list of weak references to the object (if defined) |
| - | <font color="# | + | |
| - | ><td align=right valign=bottom | + | |
| - | >< | + | |
| - | < | + | |
| - | & | + | |
| - | U{John& | + | |
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| - | This& | + | |
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| - | see& | + | |
| - | documentation</ | + | |
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| - | <tr bgcolor="# | + | |
| - | <td colspan=2>< | + | |
| - | < | + | |
| - | <td width=" | + | |
| - | < | + | |
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| - | </ | + | |
| - | < | + | |
| - | Data descriptors defined here:<br> | + | |
| - | < | + | |
| - | < | + | |
| - | </ | + | |
| - | < | + | |
| - | Methods inherited from <a href=" | + | |
| - | < | + | |
| - | < | + | Methods |
| - | Data and other attributes | + | __init__(...) |
| - | < | + | x.__init__(...) initializes x; see help(type(x)) for signature |
| - | < | + | Data and other attributes |
| - | Methods | + | __new__ = <built-in method __new__ of type object> |
| - | <dl>< | + | T.__new__(S, ...) -> |
| - | <dl>< | + | Methods inherited from exceptions.BaseException: |
| + | __delattr__(...) | ||
| + | x.__delattr__(' | ||
| + | __getattribute__(...) | ||
| + | x.__getattribute__(' | ||
| + | __getitem__(...) | ||
| + | x.__getitem__(y) <==> x[y] | ||
| + | __getslice__(...) | ||
| + | x.__getslice__(i, | ||
| + | |||
| + | Use of negative indices is not supported. | ||
| + | __reduce__(...) | ||
| + | __repr__(...) | ||
| + | x.__repr__() <==> repr(x) | ||
| + | __setattr__(...) | ||
| + | x.__setattr__(' | ||
| + | __setstate__(...) | ||
| + | __str__(...) | ||
| + | x.__str__() <==> str(x) | ||
| + | __unicode__(...) | ||
| - | < | + | Data descriptors inherited from exceptions.BaseException: |
| + | __dict__ | ||
| + | args | ||
| + | message | ||
| + | |||
| + | class DacapoAborted(exceptions.Exception) | ||
| + | |||
| + | Raised when ncfile.status = ' | ||
| + | |||
| + | |||
| + | Method resolution order: | ||
| + | DacapoAborted | ||
| + | exceptions.Exception | ||
| + | exceptions.BaseException | ||
| + | __builtin__.object | ||
| - | < | + | Data descriptors defined here: |
| - | & | + | __weakref__ |
| - | Use& | + | list of weak references to the object (if defined) |
| - | < | + | Methods inherited from exceptions.Exception: |
| + | __init__(...) | ||
| + | x.__init__(...) initializes x; | ||
| - | <dl>< | + | Data and other attributes inherited from exceptions.Exception: |
| + | __new__ = <built-in method __new__ of type object> | ||
| + | T.__new__(S, ...) -> | ||
| - | <dl><dt><a name=" | + | Methods inherited from exceptions.BaseException: |
| + | __delattr__(...) | ||
| + | x.__delattr__(' | ||
| + | __getattribute__(...) | ||
| + | x.__getattribute__(' | ||
| + | __getitem__(...) | ||
| + | x.__getitem__(y) < | ||
| + | __getslice__(...) | ||
| + | x.__getslice__(i, | ||
| + | |||
| + | Use of negative indices is not supported. | ||
| + | __reduce__(...) | ||
| + | __repr__(...) | ||
| + | x.__repr__() <==> repr(x) | ||
| + | __setattr__(...) | ||
| + | x.__setattr__(' | ||
| + | __setstate__(...) | ||
| + | __str__(...) | ||
| + | x.__str__() <==> str(x) | ||
| + | __unicode__(...) | ||
| - | < | + | Data descriptors inherited from exceptions.BaseException: |
| + | __dict__ | ||
| + | args | ||
| + | message | ||
| + | |||
| + | class DacapoDryrun(exceptions.Exception) | ||
| + | |||
| + | Raised when text file does not end correctly | ||
| + | |||
| + | |||
| + | Method resolution order: | ||
| + | DacapoDryrun | ||
| + | exceptions.Exception | ||
| + | exceptions.BaseException | ||
| + | __builtin__.object | ||
| - | < | + | Data descriptors defined here: |
| + | __weakref__ | ||
| + | list of weak references to the object (if defined) | ||
| - | < | + | Methods inherited from exceptions.Exception: |
| + | __init__(...) | ||
| + | x.__init__(...) initializes x; | ||
| - | < | + | Data and other attributes |
| - | Data descriptors | + | __new__ |
| - | < | + | T.__new__(S, ...) -> |
| - | </ | + | |
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| - | </ | + | |
| - | < | + | |
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| - | </ | + | |
| - | <table width=" | + | |
| - | <tr bgcolor="# | + | |
| - | <td colspan=3 valign=bottom>& | + | |
| - | <font color="# | + | |
| - | + | ||
| - | <tr bgcolor="# | + | |
| - | <td colspan=2>< | + | |
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| - | Data descriptors defined here:< | + | |
| - | < | + | |
| - | < | + | |
| - | </ | + | |
| - | < | + | |
| - | Methods inherited from <a href=" | + | |
| - | < | + | |
| - | < | + | Methods |
| - | Data and other attributes | + | __delattr__(...) |
| - | <dl><dt>< | + | x.__delattr__(' |
| + | __getattribute__(...) | ||
| + | x.__getattribute__(' | ||
| + | __getitem__(...) | ||
| + | x.__getitem__(y) <==> x[y] | ||
| + | __getslice__(...) | ||
| + | x.__getslice__(i, | ||
| + | |||
| + | Use of negative indices is not supported. | ||
| + | __reduce__(...) | ||
| + | __repr__(...) | ||
| + | x.__repr__() <==> repr(x) | ||
| + | __setattr__(...) | ||
| + | x.__setattr__(' | ||
| + | __setstate__(...) | ||
| + | __str__(...) | ||
| + | x.__str__() <==> str(x) | ||
| + | __unicode__(...) | ||
| - | < | + | Data descriptors |
| - | Methods | + | __dict__ |
| - | < | + | args |
| + | message | ||
| + | |||
| + | class DacapoInput(exceptions.Exception) | ||
| + | |||
| + | raised for bad input variables | ||
| + | |||
| + | |||
| + | Method resolution order: | ||
| + | DacapoInput | ||
| + | exceptions.Exception | ||
| + | exceptions.BaseException | ||
| + | __builtin__.object | ||
| - | < | + | Data descriptors defined here: |
| + | __weakref__ | ||
| + | list of weak references to the object (if defined) | ||
| - | < | + | Methods inherited from exceptions.Exception: |
| + | __init__(...) | ||
| + | x.__init__(...) initializes x; see help(type(x)) for signature | ||
| - | <dl>< | + | Data and other attributes inherited from exceptions.Exception: |
| - | & | + | __new__ = <built-in method __new__ of type object> |
| - | Use& | + | T.__new__(S, ...) -> |
| - | <dl><dt><a name=" | + | Methods inherited from exceptions.BaseException: |
| + | __delattr__(...) | ||
| + | x.__delattr__(' | ||
| + | __getattribute__(...) | ||
| + | x.__getattribute__(' | ||
| + | __getitem__(...) | ||
| + | x.__getitem__(y) < | ||
| + | __getslice__(...) | ||
| + | x.__getslice__(i, | ||
| + | |||
| + | Use of negative indices is not supported. | ||
| + | __reduce__(...) | ||
| + | __repr__(...) | ||
| + | x.__repr__() <==> repr(x) | ||
| + | __setattr__(...) | ||
| + | x.__setattr__(' | ||
| + | __setstate__(...) | ||
| + | __str__(...) | ||
| + | x.__str__() <==> str(x) | ||
| + | __unicode__(...) | ||
| - | < | + | Data descriptors inherited from exceptions.BaseException: |
| + | __dict__ | ||
| + | args | ||
| + | message | ||
| + | |||
| + | class DacapoRunning(exceptions.Exception) | ||
| + | |||
| + | Raised when ncfile.status = ' | ||
| + | |||
| + | |||
| + | Method resolution order: | ||
| + | DacapoRunning | ||
| + | exceptions.Exception | ||
| + | exceptions.BaseException | ||
| + | __builtin__.object | ||
| - | < | + | Data descriptors defined here: |
| + | __weakref__ | ||
| + | list of weak references to the object (if defined) | ||
| - | < | + | Methods inherited from exceptions.Exception: |
| + | __init__(...) | ||
| + | x.__init__(...) initializes x; | ||
| - | <dl>< | + | Data and other attributes inherited from exceptions.Exception: |
| + | __new__ = <built-in method __new__ of type object> | ||
| + | T.__new__(S, ...) -> | ||
| - | <dl><dt><a name=" | + | Methods inherited from exceptions.BaseException: |
| + | __delattr__(...) | ||
| + | x.__delattr__(' | ||
| + | __getattribute__(...) | ||
| + | x.__getattribute__(' | ||
| + | __getitem__(...) | ||
| + | x.__getitem__(y) < | ||
| + | __getslice__(...) | ||
| + | x.__getslice__(i, | ||
| + | |||
| + | Use of negative indices is not supported. | ||
| + | __reduce__(...) | ||
| + | __repr__(...) | ||
| + | x.__repr__() <==> repr(x) | ||
| + | __setattr__(...) | ||
| + | x.__setattr__(' | ||
| + | __setstate__(...) | ||
| + | __str__(...) | ||
| + | x.__str__() <==> str(x) | ||
| + | __unicode__(...) | ||
| - | < | + | Data descriptors inherited from exceptions.BaseException: |
| - | Data descriptors inherited from <a href="exceptions.html#BaseException"> | + | __dict__ |
| - | <dl><dt>< | + | args |
| - | </dl> | + | message |
| - | <dl><dt>< | + | |
| - | </dl> | + | class Jacapo |
| - | <dl><dt>< | + | |
| - | </dl> | + | Python interface to the Fortran DACAPO code |
| - | </td></tr></ | + | |
| - | <table width=" | + | |
| - | <tr bgcolor="#ffc8d8"> | + | Methods defined here: |
| - | <td colspan=3 valign=bottom>& | + | __del__(self) |
| - | <font color="#000000" | + | If calculator is deleted try to stop dacapo program |
| - | + | __init__(self, | |
| - | <tr bgcolor="#ffc8d8">< | + | Initialize the Jacapo calculator |
| - | <td colspan=2>< | + | |
| - | < | + | :Parameters: |
| - | <td width="100%">< | + | |
| - | < | + | nc : |
| - | <dd><a href="exceptions.html# | + | output netcdf file, |
| - | < | + | |
| - | < | + | outnc : |
| - | </dl> | + | output file. by default equal to nc |
| - | <hr> | + | |
| - | Data descriptors defined here:<br> | + | deletenc : |
| - | <dl><dt>< | + | determines whether the ncfile is deleted on initialization |
| - | <dd><tt>list of weak | + | so a fresh run occurs. If True, |
| - | </dl> | + | it exists. |
| - | <hr> | + | |
| - | Methods inherited from <a href=" | + | debug : |
| - | < | + | logging debug level. |
| + | |||
| + | Valid kwargs: | ||
| + | |||
| + | atoms : | ||
| + | atoms is an ase.Atoms object that will be attached | ||
| + | to this calculator. | ||
| + | |||
| + | pw : | ||
| + | sets planewave cutoff | ||
| + | |||
| + | dw : | ||
| + | sets density cutoff | ||
| + | |||
| + | kpts : | ||
| + | set chadi-cohen, | ||
| + | e.g. kpts = (2, | ||
| + | |||
| + | spinpol : | ||
| + | sets whether spin-polarization is used or not. | ||
| + | |||
| + | fixmagmom : | ||
| + | set the magnetic moment of the unit cell. only used | ||
| + | in spin polarize calculations | ||
| + | |||
| + | ft : | ||
| + | set the Fermi temperature used in occupation smearing | ||
| + | |||
| + | xc : | ||
| + | set the exchange-correlation functional. | ||
| + | one of [' | ||
| + | |||
| + | dipole | ||
| + | boolean | ||
| + | turn the dipole correction on (True) or off (False) | ||
| + | |||
| + | or: | ||
| + | dictionary of parameters to fine-tune behavior | ||
| + | {' | ||
| + | ' | ||
| + | ' | ||
| + | ' | ||
| + | ' | ||
| + | |||
| + | nbands : | ||
| + | set the number of bands | ||
| + | |||
| + | symmetry : | ||
| + | Turn symmetry reduction on (True) or off (False) | ||
| + | |||
| + | stress : | ||
| + | Turn stress calculation on (True) or off (False) | ||
| + | |||
| + | debug : | ||
| + | could be something like | ||
| + | logging.DEBUG or an integer 0-50. The higher the integer, | ||
| + | the less information you see set debug level (0 = off, | ||
| + | extreme) | ||
| + | |||
| + | Modification of the nc file only occurs at calculate time if needed | ||
| + | |||
| + | >>> | ||
| + | |||
| + | reads the calculator from CO.nc if it exists or | ||
| + | minimally initializes CO.nc with dimensions if it does not exist. | ||
| + | |||
| + | >>> | ||
| + | |||
| + | reads the calculator from CO.nc or initializes it if | ||
| + | it does not exist and changes the planewave cutoff energy to | ||
| + | 300eV | ||
| + | |||
| + | >>> | ||
| + | |||
| + | returns the atoms in the netcdffile CO.nc, | ||
| + | attached to it. | ||
| + | |||
| + | >>> | ||
| + | __str__(self) | ||
| + | pretty-print the calculator and atoms. | ||
| + | |||
| + | we read everything directly from the ncfile to prevent | ||
| + | triggering any calculations | ||
| + | atoms_are_equal(self, | ||
| + | comparison of atoms to self.atoms using tolerances to account | ||
| + | for float/ | ||
| + | attach_child(self, | ||
| + | calculate(self) | ||
| + | run a calculation. | ||
| + | |||
| + | you have to be a little careful with code in here. Use the | ||
| + | calculation_required function to tell if a calculation is | ||
| + | required. It is assumed here that if you call this, | ||
| + | it. | ||
| + | calculation_required(self, | ||
| + | determines if a calculation is needed. | ||
| + | |||
| + | return True if a calculation is needed to get up to date data. | ||
| + | return False if no calculation is needed. | ||
| + | |||
| + | quantities is here because of the ase interface. | ||
| + | delete_ncattdimvar(self, | ||
| + | helper function to delete attributes, | ||
| + | dimensions and variables in a netcdffile | ||
| + | |||
| + | this functionality is not implemented for some reason in | ||
| + | netcdf, | ||
| + | attributes, | ||
| + | the ones you want to delete and then rename the new file. | ||
| + | |||
| + | if you delete a dimension, | ||
| + | are also deleted. | ||
| + | execute_external_dynamics(self, | ||
| + | Implementation of the stay alive functionality with socket | ||
| + | communication between dacapo and python. Known limitations: | ||
| + | It is not possible to start 2 independent Dacapo calculators | ||
| + | from the same python process, | ||
| + | identifier for the script[PID].py file. | ||
| + | execute_parent_calculation(self) | ||
| + | Implementation of an extra level of parallelization, | ||
| + | dacapo.run processes. This is used for NEBs parallelized over images. | ||
| + | get(self, *args) | ||
| + | get values for args. | ||
| + | |||
| + | e.g. calc.get(' | ||
| + | get_ados(self, | ||
| + | attempt at maintaining backward compatibility with get_ados | ||
| + | returning data | ||
| + | |||
| + | Now when we call calc.get_ados() it will return settings, | ||
| + | |||
| + | and calc.get_ados(atoms=[], | ||
| + | get_ados_data(self, | ||
| + | get atom projected data | ||
| + | |||
| + | : | ||
| + | |||
| + | atoms | ||
| + | list of atom indices (integers) | ||
| + | |||
| + | orbitals | ||
| + | list of strings | ||
| + | [' | ||
| + | [' | ||
| + | [' | ||
| + | |||
| + | cutoff : | ||
| + | cutoff radius you want the results for ' | ||
| + | |||
| + | spin | ||
| + | : | ||
| + | spin you want the results for | ||
| + | [0] or [1] or [0, | ||
| + | |||
| + | returns (egrid, | ||
| + | egrid has the fermi level at 0 eV | ||
| + | get_all_eigenvalues(self, | ||
| + | return all the eigenvalues at all the kpoints for a spin. | ||
| + | |||
| + | : | ||
| + | |||
| + | spin : | ||
| + | which spin the eigenvalues are for | ||
| + | get_ascii_debug(self) | ||
| + | Return the debug settings in Dacapo | ||
| + | get_atoms(self) | ||
| + | return the atoms attached to a calculator() | ||
| + | get_bz_k_points(self) | ||
| + | return list of kpoints in the Brillouin zone | ||
| + | get_calculate_stress(self) | ||
| + | return whether stress is calculated or not | ||
| + | get_cd = get_charge_density(self, | ||
| + | get_charge_density(self, | ||
| + | return x, | ||
| + | |||
| + | x, | ||
| + | cd is the charge density data | ||
| + | |||
| + | netcdf documentation:: | ||
| + | |||
| + | ChargeDensity(number_of_spin, | ||
| + | hardgrid_dim3, | ||
| + | hardgrid_dim2, | ||
| + | hardgrid_dim1) | ||
| + | ChargeDensity: | ||
| + | ChargeDensity: | ||
| + | get_charge_mixing(self) | ||
| + | return charge mixing parameters | ||
| + | get_convergence(self) | ||
| + | return convergence settings for Dacapo | ||
| + | get_debug(self) | ||
| + | Return the python logging level | ||
| + | get_decoupling(self) | ||
| + | return the electrostatic decoupling parameters | ||
| + | get_dipole(self) | ||
| + | return dictionary of parameters if the DipoleCorrection was used | ||
| + | get_dipole_moment(self, | ||
| + | return dipole moment of unit cell | ||
| + | |||
| + | Defined by the vector connecting the center of electron charge | ||
| + | density to the center of nuclear charge density. | ||
| + | |||
| + | Units = eV*angstrom | ||
| + | |||
| + | 1 Debye = 0.208194 eV*angstrom | ||
| + | get_dw(self) | ||
| + | return the density wave cutoff | ||
| + | get_ef = get_fermi_level(self) | ||
| + | get_effective_potential(self, | ||
| + | returns the realspace local effective potential for the spin. | ||
| + | the units of the potential are eV | ||
| + | |||
| + | : | ||
| + | |||
| + | spin : | ||
| + | specify which spin you want, | ||
| + | get_eigenvalues(self, | ||
| + | return the eigenvalues for a kpt and spin | ||
| + | |||
| + | : | ||
| + | |||
| + | kpt : | ||
| + | index of the IBZ kpoint | ||
| + | |||
| + | spin : | ||
| + | which spin the eigenvalues are for | ||
| + | get_electronic_minimization(self) | ||
| + | get method and diagonalizations per band for electronic | ||
| + | minimization algorithms | ||
| + | get_electronic_temperature = get_ft(self) | ||
| + | get_electrostatic_potential(self, | ||
| + | get electrostatic potential | ||
| + | |||
| + | Netcdf documentation:: | ||
| + | |||
| + | double ElectrostaticPotential(number_of_spin, | ||
| + | hardgrid_dim3, | ||
| + | hardgrid_dim2, | ||
| + | hardgrid_dim1) ; | ||
| + | ElectrostaticPotential: | ||
| + | Description = "realspace local effective potential" ; | ||
| + | unit = "eV" ; | ||
| + | get_ensemble_coefficients(self) | ||
| + | returns exchange correlation ensemble coefficients | ||
| + | get_esp | ||
| + | get_external_dipole(self) | ||
| + | return the External dipole settings | ||
| + | get_extpot(self) | ||
| + | return the external potential set in teh calculator | ||
| + | get_extracharge(self) | ||
| + | Return the extra charge set in teh calculator | ||
| + | get_fermi_level(self) | ||
| + | return Fermi level | ||
| + | get_fftgrid(self) | ||
| + | return soft and hard fft grids | ||
| + | get_fixmagmom(self) | ||
| + | returns the value of FixedMagneticMoment | ||
| + | get_forces(self, | ||
| + | Calculate atomic forces | ||
| + | get_ft(self) | ||
| + | return the FermiTemperature used in the calculation | ||
| + | get_ibz_k_points = get_ibz_kpoints(self) | ||
| + | get_ibz_kpoints(self) | ||
| + | return list of kpoints in the irreducible brillouin zone | ||
| + | get_k_point_weights(self) | ||
| + | return the weights on the IBZ kpoints | ||
| + | get_kpts(self) | ||
| + | return the BZ kpts | ||
| + | get_kpts_type(self) | ||
| + | return the kpt grid type | ||
| + | get_magnetic_moment(self, | ||
| + | calculates the magnetic moment (Bohr-magnetons) of the supercell | ||
| + | get_magnetic_moments(self, | ||
| + | return magnetic moments on each atom after the calculation is | ||
| + | run | ||
| + | get_mdos(self) | ||
| + | return multicentered projected dos parameters | ||
| + | get_mdos_data(self, | ||
| + | returns data from multicentered projection | ||
| + | |||
| + | |||
| + | returns (mdos, | ||
| + | |||
| + | the rotation matrices are retrieved from the text file. I am | ||
| + | not sure what you would do with these, | ||
| + | about them in the old documentation so I put the code to | ||
| + | retrieve them here. the syntax for the return value is: | ||
| + | rotmat[atom#][label] returns the rotation matrix for the | ||
| + | center on the atom# | ||
| + | label refers to. | ||
| + | get_nbands(self) | ||
| + | return the number of bands used in the calculation | ||
| + | get_nc(self) | ||
| + | return the ncfile used for output | ||
| + | get_ncoutput(self) | ||
| + | returns the control variables for the ncfile | ||
| + | get_number_of_bands | ||
| + | get_number_of_electrons = get_valence(self, | ||
| + | get_number_of_grid_points(self) | ||
| + | return soft fft grid | ||
| + | get_number_of_iterations(self) | ||
| + | get_number_of_spins(self) | ||
| + | if spin-polarized returns 2, | ||
| + | get_occ = get_occupation_numbers(self, | ||
| + | get_occupation_numbers(self, | ||
| + | return occupancies of eigenstates for a kpt and spin | ||
| + | |||
| + | : | ||
| + | |||
| + | kpt : | ||
| + | index of the IBZ kpoint you want the occupation of | ||
| + | |||
| + | spin : | ||
| + | 0 or 1 | ||
| + | get_occupationstatistics(self) | ||
| + | return occupation statistics method | ||
| + | get_potential_energy(self, | ||
| + | return the potential energy. | ||
| + | get_pseudo_wave_function(self, | ||
| + | return the pseudo wavefunction | ||
| + | get_pseudopotentials(self) | ||
| + | get pseudopotentials set for atoms attached to calculator | ||
| + | get_psp(self, | ||
| + | get the pseudopotential filename from the psp database | ||
| + | |||
| + | : | ||
| + | |||
| + | sym : | ||
| + | the chemical symbol of the species | ||
| + | |||
| + | z : | ||
| + | the atomic number of the species | ||
| + | |||
| + | |||
| + | you can only specify sym or z. Returns the pseudopotential | ||
| + | filename, | ||
| + | get_psp_nuclear_charge(self, | ||
| + | get the nuclear charge of the atom from teh psp-file. | ||
| + | |||
| + | This is not the same as the atomic number, | ||
| + | necessarily the negative of the number of valence electrons, | ||
| + | since a psp may be an ion. this function is needed to compute | ||
| + | centers of ion charge for the dipole moment calculation. | ||
| + | |||
| + | We read in the valence ion configuration from the psp file and | ||
| + | add up the charges in each shell. | ||
| + | get_psp_valence(self, | ||
| + | get the psp valence charge on an atom from the pspfile. | ||
| + | get_pw(self) | ||
| + | return the planewave cutoff used | ||
| + | get_reciprocal_bloch_function(self, | ||
| + | return the reciprocal bloch function. Need for Jacapo | ||
| + | Wannier class. | ||
| + | get_reciprocal_fft_index(self, | ||
| + | return the Wave Function FFT Index | ||
| + | get_scratch(self) | ||
| + | finds an appropriate scratch directory for the calculation | ||
| + | get_spin_polarized(self) | ||
| + | Return True if calculate is spin-polarized or False if not | ||
| + | get_spinpol(self) | ||
| + | Returns the spin polarization setting, | ||
| + | get_status(self) | ||
| + | get status of calculation from ncfile. usually one of: | ||
| + | ' | ||
| + | ' | ||
| + | ' | ||
| + | ' | ||
| + | None | ||
| + | get_stay_alive(self) | ||
| + | return the stay alive settings | ||
| + | get_stress(self, | ||
| + | get stress on the atoms. | ||
| + | |||
| + | you should have set up the calculation | ||
| + | to calculate stress first. | ||
| + | |||
| + | returns [sxx, | ||
| + | get_symmetry(self) | ||
| + | return the type of symmetry used | ||
| + | get_txt(self) | ||
| + | return the txt file used for output | ||
| + | get_ucgrid(self, | ||
| + | Return X, | ||
| + | |||
| + | dims = (n0, | ||
| + | |||
| + | n0 points along unitcell vector 0 | ||
| + | n1 points along unitcell vector 1 | ||
| + | n2 points along unitcell vector 2 | ||
| + | get_valence(self, | ||
| + | return the total number of valence electrons for the | ||
| + | atoms. valence electrons are read directly from the | ||
| + | pseudopotentials. | ||
| + | |||
| + | the psp filenames are stored in the ncfile. They may be just | ||
| + | the name of the file, | ||
| + | same directory as the ncfile, | ||
| + | may be defined by an absolute or relative path. This function | ||
| + | deals with all these possibilities. | ||
| + | get_wannier_localization_matrix(self, | ||
| + | return wannier localization matrix | ||
| + | get_wave_function(self, | ||
| + | return the wave function. This is the pseudo wave function | ||
| + | divided by volume. | ||
| + | get_wf = get_wave_function(self, | ||
| + | get_xc(self) | ||
| + | return the self-consistent exchange-correlation functional used | ||
| + | |||
| + | returns a string | ||
| + | get_xc_energies(self, | ||
| + | Get energies for different functionals self-consistent and | ||
| + | non-self-consistent. | ||
| + | |||
| + | : | ||
| + | |||
| + | functional : | ||
| + | some set of ' | ||
| + | |||
| + | This function returns the self-consistent energy and/ | ||
| + | energies associated with various functionals. | ||
| + | The functionals are currently PZ, | ||
| + | The different energies may be useful for calculating improved | ||
| + | adsorption energies as in B. Hammer, | ||
| + | J.K. Norskov, | ||
| + | Examples: | ||
| + | get_xcenergies() #returns all the energies | ||
| + | get_xcenergies(' | ||
| + | get_xcenergies(' | ||
| + | # | ||
| + | initial_wannier(self, | ||
| + | return initial wannier | ||
| + | initnc(self, | ||
| + | create an ncfile with minimal dimensions in it | ||
| + | |||
| + | this makes sure the dimensions needed for other set functions | ||
| + | exist when needed. | ||
| + | read_only_atoms(self, | ||
| + | read only the atoms from an existing netcdf file. Used to | ||
| + | initialize a calculator from a ncfilename. | ||
| + | |||
| + | : | ||
| + | |||
| + | ncfile : | ||
| + | name of file to read from. | ||
| + | |||
| + | return ASE.Atoms with no calculator attached or None if no | ||
| + | atoms found | ||
| + | restart(self) | ||
| + | Restart the calculator by deleting nc dimensions that will | ||
| + | be rewritten on the next calculation. This is sometimes required | ||
| + | when certain dimensions change related to unitcell size changes | ||
| + | planewave/densitywave cutoffs and kpt changes. These can cause | ||
| + | fortran netcdf errors if the data does not match the pre-defined | ||
| + | dimension sizes. | ||
| + | |||
| + | also delete all the output from previous calculation. | ||
| + | set(self, **kwargs) | ||
| + | set a parameter | ||
| + | |||
| + | parameter is stored in dictionary that is processed later if a | ||
| + | calculation is need. | ||
| + | set_ados(self, | ||
| + | setup calculation of atom-projected density of states | ||
| + | |||
| + | : | ||
| + | |||
| + | energywindow : | ||
| + | sets (emin, | ||
| + | |||
| + | energywidth : | ||
| + | the gaussian used in smearing | ||
| + | |||
| + | npoints : | ||
| + | the number of points to sample the DOS at | ||
| + | |||
| + | cutoff : | ||
| + | the cutoff radius in angstroms for the integration. | ||
| + | set_ascii_debug(self, | ||
| + | set the debug level for Dacapo | ||
| + | |||
| + | : | ||
| + | |||
| + | level : | ||
| + | one of ' | ||
| + | set_atoms(self, | ||
| + | attach an atoms to the calculator and update the ncfile | ||
| + | |||
| + | : | ||
| + | |||
| + | atoms | ||
| + | ASE.Atoms instance | ||
| + | set_calculate_stress(self, | ||
| + | Turn on stress calculation | ||
| + | |||
| + | : | ||
| + | |||
| + | stress : | ||
| + | set_calculate_stress(True) calculates stress | ||
| + | set_calculate_stress(False) do not calculate stress | ||
| + | set_charge_mixing(self, | ||
| + | set density mixing method and parameters | ||
| + | |||
| + | : | ||
| + | |||
| + | method : | ||
| + | ' | ||
| + | |||
| + | mixinghistory : | ||
| + | number of iterations to mix | ||
| + | Number of charge residual vectors stored for generating | ||
| + | the Pulay estimate on the self-consistent charge density, | ||
| + | see Sec. 4.2 in Kresse/Furthmuller: | ||
| + | Comp. Mat. Sci. 6 (1996) p34ff | ||
| + | |||
| + | mixingcoeff : | ||
| + | Mixing coefficient for Pulay charge mixing, | ||
| + | to A in G$^1$ in Sec. 4.2 in Kresse/Furthmuller: | ||
| + | Comp. Mat. Sci. 6 (1996) p34ff | ||
| + | |||
| + | precondition : | ||
| + | ' | ||
| + | |||
| + | * "Yes" : Kerker preconditiong is used, | ||
| + | i.e. q$_0$ is different from zero, | ||
| + | in Kresse/Furthmuller: | ||
| + | The value of q$_0$ is fix to give a damping of 20 | ||
| + | of the lowest q vector. | ||
| + | |||
| + | * "No" | ||
| + | |||
| + | updatecharge : | ||
| + | ' | ||
| + | |||
| + | * " | ||
| + | ChargeMixing: | ||
| + | |||
| + | * " | ||
| + | This setting is useful when evaluating the Harris-Foulkes | ||
| + | density functional | ||
| + | set_convergence(self, | ||
| + | set convergence criteria for stopping the dacapo calculator. | ||
| + | |||
| + | : | ||
| + | |||
| + | energy : | ||
| + | set total energy change (eV) required for stopping | ||
| + | |||
| + | density : | ||
| + | set density change required for stopping | ||
| + | |||
| + | occupation : | ||
| + | set occupation change required for stopping | ||
| + | |||
| + | maxsteps : | ||
| + | specify maximum number of steps to take | ||
| + | |||
| + | maxtime : | ||
| + | specify maximum number of hours to run. | ||
| + | |||
| + | Autopilot not supported here. | ||
| + | set_debug(self, | ||
| + | set debug level for python logging | ||
| + | |||
| + | debug should be an integer from 0-100 or one of the logging | ||
| + | constants like logging.DEBUG, | ||
| + | set_decoupling(self, | ||
| + | Decoupling activates the three dimensional electrostatic | ||
| + | decoupling. Based on paper by Peter E. Bloechl: | ||
| + | page7422 (1995). | ||
| + | |||
| + | : | ||
| + | |||
| + | ngaussians : | ||
| + | The number of gaussian functions per atom | ||
| + | used for constructing the model charge of the system | ||
| + | |||
| + | ecutoff : | ||
| + | The cut off energy (eV) of system charge density in | ||
| + | g-space used when mapping constructing the model change of | ||
| + | the system, | ||
| + | ECutoff enters when constructing the model change. | ||
| + | |||
| + | gausswidth : | ||
| + | The width of the Gaussians defined by | ||
| + | $widthofgaussian*1.5^(n-1)$ $n$=(1 to numberofgaussians) | ||
| + | set_dipole(self, | ||
| + | turn on and set dipole correction scheme | ||
| + | |||
| + | : | ||
| + | |||
| + | status : | ||
| + | True turns dipole on. False turns Dipole off | ||
| + | |||
| + | mixpar : | ||
| + | Mixing Parameter for the the dipole correction field | ||
| + | during the electronic minimization process. If instabilities | ||
| + | occur during electronic minimization, | ||
| + | decreased. | ||
| + | |||
| + | initval : | ||
| + | initial value to start at | ||
| + | |||
| + | adddipfield : | ||
| + | additional dipole field to add | ||
| + | units : | ||
| + | External additive, | ||
| + | third unit cell vector, | ||
| + | dipole layer. The field discontinuity follows the position | ||
| + | of the dynamical dipole correction, | ||
| + | DipoleCorrection: | ||
| + | discontinuity is at this value, | ||
| + | vacuum position farthest from any other atoms on both | ||
| + | sides of the slab. | ||
| + | |||
| + | position : | ||
| + | scaled coordinates along third unit cell direction. | ||
| + | If this attribute is set, | ||
| + | compensation dipole layer plane in at the provided value. | ||
| + | If this attribute is not set, | ||
| + | dipole layer plane in the vacuum position farthest from any | ||
| + | other atoms on both sides of the slab. Do not set this to | ||
| + | 0.0 | ||
| + | |||
| + | |||
| + | calling set_dipole() sets all default values. | ||
| + | set_dw(self, | ||
| + | set the density wave cutoff energy. | ||
| + | |||
| + | : | ||
| + | |||
| + | dw : | ||
| + | the density wave cutoff | ||
| + | |||
| + | The function checks to make sure it is not less than the | ||
| + | planewave cutoff. | ||
| + | |||
| + | Density_WaveCutoff describes the kinetic energy neccesary to | ||
| + | represent a wavefunction associated with the total density, | ||
| + | i.e. G-vectors for which $ ert G ert^2$ $<$ | ||
| + | 4*Density_WaveCutoff will be used to describe the total | ||
| + | density (including augmentation charge and partial core | ||
| + | density). If Density_WaveCutoff is equal to PlaneWaveCutoff | ||
| + | this implies that the total density is as soft as the | ||
| + | wavefunctions described by the kinetic energy cutoff | ||
| + | PlaneWaveCutoff. If a value of Density_WaveCutoff is specified | ||
| + | (must be larger than or equal to PlaneWaveCutoff) the program | ||
| + | will run using two grids, | ||
| + | wavefunction density (softgrid_dim) and one representing the | ||
| + | total density (hardgrid_dim). If the density can be | ||
| + | reprensented on the same grid as the wavefunction density | ||
| + | Density_WaveCutoff can be chosen equal to PlaneWaveCutoff | ||
| + | (default). | ||
| + | set_electronic_minimization(self, | ||
| + | set the eigensolver method | ||
| + | |||
| + | Selector for which subroutine to use for electronic | ||
| + | minimization | ||
| + | |||
| + | Recognized options : | ||
| + | |||
| + | * "resmin" | ||
| + | k-point parallization. | ||
| + | |||
| + | * "eigsolve : | ||
| + | (Claus Bendtsen et al). | ||
| + | |||
| + | * "rmm-diis : | ||
| + | method (RMM), | ||
| + | subspace) The implementaion follows closely the algorithm | ||
| + | outlined in Kresse and Furthmuller, | ||
| + | |||
| + | : | ||
| + | |||
| + | method : | ||
| + | should be ' | ||
| + | |||
| + | diagsperband : | ||
| + | The number of diagonalizations per band for | ||
| + | electronic minimization algorithms (maps onto internal | ||
| + | variable ndiapb). Applies for both | ||
| + | ElectronicMinimization: | ||
| + | default value = 2 | ||
| + | set_external_dipole(self, | ||
| + | Externally imposed dipole potential. This option overwrites | ||
| + | DipoleCorrection if set. | ||
| + | |||
| + | : | ||
| + | |||
| + | value : | ||
| + | units of volts | ||
| + | |||
| + | position : | ||
| + | scaled coordinates along third unit cell direction. | ||
| + | if None, | ||
| + | vacuum position farthest from any other atoms on both | ||
| + | sides of the slab. Do not set to 0.0. | ||
| + | set_extpot(self, | ||
| + | add external potential of value | ||
| + | |||
| + | see this link before using this | ||
| + | https://listserv.fysik.dtu.dk/pipermail/ | ||
| + | |||
| + | :Parameters: | ||
| + | |||
| + | potgrid : | ||
| + | the shape must be the same as the fft soft grid | ||
| + | the value of the potential to add | ||
| + | |||
| + | |||
| + | you have to know both of the fft grid dimensions ahead of time! | ||
| + | if you know what you are doing, | ||
| + | before hand with: | ||
| + | calc.set_fftgrid((n1, | ||
| + | set_extracharge(self, | ||
| + | add extra charge to unit cell | ||
| + | |||
| + | : | ||
| + | |||
| + | val : | ||
| + | extra electrons to add or subtract from the unit cell | ||
| + | |||
| + | Fixed extra charge in the unit cell (i.e. deviation from | ||
| + | charge neutrality). This assumes a compensating, | ||
| + | constant backgound charge (jellium) to forge overall charge | ||
| + | neutrality. | ||
| + | set_fftgrid(self, | ||
| + | sets the dimensions of the FFT grid to be used | ||
| + | |||
| + | : | ||
| + | |||
| + | soft : | ||
| + | make a n1 x n2 x n3 grid | ||
| + | |||
| + | hard : | ||
| + | make a n1 x n2 x n3 grid | ||
| + | |||
| + | |||
| + | >>> | ||
| + | sets the soft and hard grid dimensions to 42, | ||
| + | |||
| + | >>> | ||
| + | sets the soft grid dimensions to 42, | ||
| + | grid dimensions to 80, | ||
| + | |||
| + | These are the fast FFt grid numbers listed in fftdimensions.F | ||
| + | |||
| + | data list_of_fft / | ||
| + | 22, | ||
| + | 56, | ||
| + | 96, | ||
| + | 160, | ||
| + | 216, | ||
| + | 450, | ||
| + | |||
| + | otherwise you will get some errors from mis-dimensioned variables. | ||
| + | |||
| + | this is usually automatically set by Dacapo. | ||
| + | set_fixmagmom(self, fixmagmom=None) | ||
| + | set a fixed magnetic moment for a spin polarized calculation | ||
| + | |||
| + | : | ||
| + | |||
| + | fixmagmom : | ||
| + | the magnetic moment of the cell in Bohr magnetons | ||
| + | set_ft(self, | ||
| + | set the Fermi temperature for occupation smearing | ||
| + | |||
| + | : | ||
| + | |||
| + | ft : | ||
| + | Fermi temperature in kT (eV) | ||
| + | |||
| + | Electronic temperature, | ||
| + | statistics. Device used to stabilize the convergence towards | ||
| + | the electronic ground state. Higher values stabilizes the | ||
| + | convergence. Values in the range 0.1-1.0 eV are recommended, | ||
| + | depending on the complexity of the Fermi surface (low values | ||
| + | for d-metals and narrow gap semiconducters, | ||
| + | electron-like metals). | ||
| + | set_kpts(self, | ||
| + | set the kpt grid. | ||
| + | |||
| + | Parameters: | ||
| + | |||
| + | kpts: | ||
| + | chadi-cohen sets: | ||
| + | |||
| + | * cc6_1x1 | ||
| + | * cc12_2x3 | ||
| + | * cc18_sq3xsq3 | ||
| + | * cc18_1x1 | ||
| + | * cc54_sq3xsq3 | ||
| + | * cc54_1x1 | ||
| + | * cc162_sq3xsq3 | ||
| + | * cc162_1x1 | ||
| + | |||
| + | (n1, | ||
| + | [k1, | ||
| + | defined in k1, | ||
| + | |||
| + | There is also a possibility to have Dacapo (fortran) create | ||
| + | the Kpoints in chadi-cohen or monkhorst-pack form. To do this | ||
| + | you need to set the KpointSetup.gridtype attribute, | ||
| + | KpointSetup. | ||
| + | |||
| + | KpointSetup = [3,0,0] | ||
| + | KpointSetup.gridtype = ' | ||
| + | |||
| + | KpointSetup(1) Chadi-Cohen k-point set | ||
| + | 1 6 k-points 1x1 | ||
| + | 2 18-kpoints sqrt(3)*sqrt(3) | ||
| + | 3 18-kpoints 1x1 | ||
| + | 4 54-kpoints sqrt(3)*sqrt(3) | ||
| + | 5 54-kpoints 1x1 | ||
| + | 6 162-kpoints 1x1 | ||
| + | 7 12-kpoints 2x3 | ||
| + | 8 162-kpoints 3xsqrt 3 | ||
| + | |||
| + | or | ||
| + | KpointSetup = [4, | ||
| + | KpointSetup.gridtype = ' | ||
| + | we do not use this functionality. | ||
| + | set_mdos(self, | ||
| + | Setup multicentered projected DOS. | ||
| + | |||
| + | mcenters | ||
| + | a list of tuples containing (atom#, | ||
| + | (0, | ||
| + | on atom 0 | ||
| + | |||
| + | (1, | ||
| + | with m = +1 on atom 0 | ||
| + | |||
| + | l=0 s-orbital | ||
| + | l=1 p-orbital | ||
| + | l=2 d-orbital | ||
| + | |||
| + | m in range of ( -l ... 0 ... +l ) | ||
| + | |||
| + | The direction cosines for which the spherical harmonics are | ||
| + | set up are using the next different atom in the list | ||
| + | (cyclic) as direction pointer, | ||
| + | along the direction to this next atom. At the moment the | ||
| + | rotation matrices is only given in the text file, | ||
| + | use grep' | ||
| + | |||
| + | adapated from old MultiCenterProjectedDOS.py | ||
| + | set_nbands(self, | ||
| + | Set the number of bands. a few unoccupied bands are | ||
| + | recommended. | ||
| + | |||
| + | : | ||
| + | |||
| + | nbands : | ||
| + | the number of bands. | ||
| + | |||
| + | if nbands = None the function returns with nothing done. At | ||
| + | calculate time, | ||
| + | by: | ||
| + | |||
| + | the number of bands is calculated as | ||
| + | $nbands=nvalence*0.65 + 4$ | ||
| + | set_nc(self, | ||
| + | set filename for the netcdf and text output for this calculation | ||
| + | |||
| + | : | ||
| + | |||
| + | nc : | ||
| + | filename for netcdf file | ||
| + | |||
| + | if the ncfile attached to the calculator is changing, | ||
| + | file will be copied to the new file if it doesn not exist so | ||
| + | that all the calculator details are preserved. Otherwise, | ||
| + | |||
| + | if the ncfile does not exist, | ||
| + | |||
| + | the text file will have the same basename as the ncfile, | ||
| + | with a .txt extension. | ||
| + | set_ncoutput(self, | ||
| + | set the output of large variables in the netcdf output file | ||
| + | |||
| + | : | ||
| + | |||
| + | wf : | ||
| + | controls output of wavefunction. values can | ||
| + | be ' | ||
| + | |||
| + | cd : | ||
| + | controls output of charge density. values can | ||
| + | be ' | ||
| + | |||
| + | efp : | ||
| + | controls output of effective potential. values can | ||
| + | be ' | ||
| + | |||
| + | esp : | ||
| + | controls output of electrostatic potential. values can | ||
| + | be ' | ||
| + | set_occupationstatistics(self, | ||
| + | set the method used for smearing the occupations. | ||
| + | |||
| + | : | ||
| + | |||
| + | method : | ||
| + | one of ' | ||
| + | Currently, | ||
| + | is implemented to 1th order (which is recommemded by most authors). | ||
| + | ' | ||
| + | set_parent(self, | ||
| + | set_pseudopotentials(self, | ||
| + | Set all the pseudopotentials from a dictionary. | ||
| + | |||
| + | The dictionary should have this form:: | ||
| + | |||
| + | {symbol1: | ||
| + | symbol2: | ||
| + | set_psp(self, | ||
| + | set the pseudopotential file for a species or an atomic number. | ||
| + | |||
| + | : | ||
| + | |||
| + | sym : | ||
| + | chemical symbol of the species | ||
| + | |||
| + | z : | ||
| + | the atomic number of the species | ||
| + | |||
| + | psp : | ||
| + | filename of the pseudopotential | ||
| + | |||
| + | |||
| + | you can only set sym or z. | ||
| + | |||
| + | examples:: | ||
| + | |||
| + | set_psp(' | ||
| + | set_psp(z=6, | ||
| + | set_psp_database(self, | ||
| + | get the xc-dependent psp database | ||
| + | |||
| + | : | ||
| + | |||
| + | xc : | ||
| + | one of ' | ||
| + | |||
| + | |||
| + | not all the databases are complete, | ||
| + | some psp do not exist. | ||
| + | |||
| + | note: | ||
| + | imported now. Changing the xc at this point results in loading | ||
| + | a nearly empty database, | ||
| + | resolve that | ||
| + | set_pw(self, | ||
| + | set the planewave cutoff. | ||
| + | |||
| + | : | ||
| + | |||
| + | pw : | ||
| + | the planewave cutoff in eV | ||
| + | |||
| + | this function checks to make sure the density wave cutoff is | ||
| + | greater than or equal to the planewave cutoff. | ||
| + | set_spinpol(self, | ||
| + | set Spin polarization. | ||
| + | |||
| + | : | ||
| + | |||
| + | spinpol : | ||
| + | set_spinpol(True) spin-polarized. | ||
| + | set_spinpol(False) no spin polarization, | ||
| + | |||
| + | Specify whether to perform a spin polarized or unpolarized | ||
| + | calculation. | ||
| + | set_status(self, | ||
| + | set the status flag in the netcdf file | ||
| + | |||
| + | : | ||
| + | |||
| + | status : | ||
| + | status flag, | ||
| + | set_stay_alive(self, | ||
| + | set the stay alive setting | ||
| + | set_symmetry(self, | ||
| + | set how symmetry is used to reduce k-points | ||
| + | |||
| + | : | ||
| + | |||
| + | val : | ||
| + | set_sym(True) Maximum symmetry is used | ||
| + | set_sym(False) No symmetry is used | ||
| + | |||
| + | This variable controls the if and how DACAPO should attempt | ||
| + | using symmetry in the calculation. Imposing symmetry generally | ||
| + | speeds up the calculation and reduces numerical noise to some | ||
| + | extent. Symmetry should always be applied to the maximum | ||
| + | extent, | ||
| + | the symmetry of the equilibrium state may be lower than the | ||
| + | initial state. Such an equilibrium state with lower symmetry | ||
| + | is missed, | ||
| + | algorithms for ionic propagation will generally not break the | ||
| + | symmetry of the initial state, | ||
| + | BFGS may break the symmetry of the initial state. Recognized | ||
| + | options: | ||
| + | |||
| + | "Off": | ||
| + | symmetry in recipical space. This is utilized to reduce the | ||
| + | k-point sampling set for Brillouin zone integration and has no | ||
| + | influence on the ionic forces/motion. | ||
| + | |||
| + | " | ||
| + | atomic structure and extract the highest possible symmetry | ||
| + | group. During the calculation, | ||
| + | spatial symmetry on ionic forces and electronic structure, | ||
| + | i.e. the symmetry will be conserved during the calculation. | ||
| + | set_xc(self, | ||
| + | Set the self-consistent exchange-correlation functional | ||
| + | |||
| + | : | ||
| + | |||
| + | xc : | ||
| + | Must be one of ' | ||
| + | |||
| + | Selects which density functional to use for | ||
| + | exchange-correlation when performing electronic minimization | ||
| + | (the electronic energy is minimized with respect to this | ||
| + | selected functional) Notice that the electronic energy is also | ||
| + | evaluated non-selfconsistently by DACAPO for other | ||
| + | exchange-correlation functionals Recognized options : | ||
| + | |||
| + | * " | ||
| + | * " | ||
| + | * " | ||
| + | * " | ||
| + | * " | ||
| + | * " | ||
| + | |||
| + | option " | ||
| + | calculation; | ||
| + | strip(self) | ||
| + | remove all large memory nc variables not needed for | ||
| + | anything I use very often. | ||
| + | update_input_parameters(self) | ||
| + | read in all the input parameters from the netcdfile | ||
| + | write(self, new=False) | ||
| + | write out everything to the ncfile : | ||
| + | |||
| + | new determines whether to delete any existing ncfile, | ||
| + | write_input(self) | ||
| + | write out input parameters as needed | ||
| + | |||
| + | you must define a self._set_keyword function that does all the | ||
| + | actual writing. | ||
| + | write_nc(self, | ||
| + | write out atoms to a netcdffile. | ||
| + | |||
| + | This does not write out the calculation parameters! | ||
| + | |||
| + | : | ||
| + | |||
| + | nc : | ||
| + | ncfilename to write to. this file will get clobbered | ||
| + | if it already exists. | ||
| + | |||
| + | atoms : | ||
| + | atoms to write. if None use the attached atoms | ||
| + | if no atoms are attached only the calculator is | ||
| + | written out. | ||
| + | |||
| + | the ncfile is always opened in ' | ||
| + | |||
| + | note: | ||
| + | sure that the geometry you mean gets written! Otherwise, | ||
| + | atoms in the calculator is used, | ||
| + | the external copy of the atoms. | ||
| - | <hr> | + | Static methods defined here: |
| - | Data and other attributes inherited from <a href=" | + | read_atoms(filename) |
| - | <dl><dt>< | + | read atoms and calculator from an existing netcdf file. |
| + | |||
| + | : | ||
| + | |||
| + | filename : | ||
| + | name of file to read from. | ||
| + | |||
| + | static method | ||
| + | |||
| + | example:: | ||
| + | |||
| + | >>> | ||
| + | >>> | ||
| + | |||
| + | this method is here for legacy purposes. I used to use it alot. | ||
| - | <hr> | + | Data and other attributes defined here: |
| - | Methods inherited from <a href=" | + | __version__ |
| - | < | + | default_input |
| + | |||
| + | Functions | ||
| + | |||
| + | |||
| + | read(ncfile) | ||
| + | return atoms and calculator from ncfile | ||
| + | |||
| + | >>> | ||
| + | |||
| + | Data | ||
| + | |||
| + | |||
| + | __docformat__ | ||
| + | formatstring = ' | ||
| + | formatter | ||
| + | handler = <logging.StreamHandler object> | ||
| + | log = <logging.Logger object> | ||
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seminar/jacapo_object.1597724780.txt.gz · 最終更新: (外部編集)