Dalton files (`chemistry_files.dalton`)

Note

About DALTON.PROP:

NORD = 0    energy (ground or excited)
       1    exp. value
       2    Linear response function
       3    Quadratic response function
       4    Cubic response function
      -1    ground - excited  transition matrix element, <0|x|i>
      -2    excited - excited transition matrix element, |<i|x|f>|
      -11   First order excited state property, <i|x|i>
      -20   <0|x|i><i|y|0>
      -21   w*<0|x|i><i|y|0>
      -22   (w_f - w_i)*|<i|x|f>|^2
      -30   D_pa
      -31   D_pe
      -32   D_pc
      -33   w1w2D_pa
      -34   w1w2D_pe
      -35   w1w2D_pc
       400  oscillator strength
       401  chemical shielding isotropic
       402  chemical shielding tensor

qcip_tools.chemistry_files.dalton.ALLOWED_LEVEL_0_MODULES = ['**DALTON', '**INTEGRAL', '**WAVE F', '**START', '**EACH S', '**PROPERTIES', '**RESPONSE']: Name of the allowed modules in dalton (according to documentation)

class qcip_tools.chemistry_files.dalton.ArchiveOutput

Archive output of Dalton. Contains lots of information for who can extract them.

self.molecule: the molecule (qcip_tools.molecule.Molecule)
self.tar_file: pipe to the tar file (tarfile.TarFile)

classmethod attempt_identification(f): A dalton archive does contain a lot of files name “DALTON”

file_type = 'DALTON_ARCHIVE': The identifier

classmethod from_molecule(molecule, *args, **kwargs)

Create an object out of a molecule

Parameters:: molecule (qcip_tools.molecule.Molecule) – the molecule
Return type:: WithMoleculeMixin

get_file(name)

Get a io.BufferedReader from a filename, if exists. Note that you get bytes out of that kind of objects, so you need to decode() them.

Parameters:: name (str) – file name
Return type:: io.BufferedReader

classmethod possible_file_extensions()

Return the common extention of this kind of files

Return type:: list

read(f)

Expects f to be open on binary mode.

Note

In Dalton archive, the molecule is given in a old, weird format, called “molplt”. Information about it is given in this webpage.

Parameters:: f (file) – File

class qcip_tools.chemistry_files.dalton.Input

Dalton dal input file.

Does NOT contain a molecule!

Note

Since Dalton only interpret the 7 first characters of any module (** included), the storage key is reduced to 5 characters.

self.module: modules (collections.OrderedDict of InputModule)

classmethod attempt_identification(f): Very specific beginning (**DALTON INPUT) and end ('*END OF INPUT)

file_type = 'DALTON_DAL': The identifier

classmethod possible_file_extensions()

Return the common extention of this kind of files

Return type:: list

read(f)

Parameters:: f (file) – File

update(r)

Update the content from a given piece of string

Parameters:: r (str|Input) – string

class qcip_tools.chemistry_files.dalton.InputCard(name=None, parameters=None)

Dalton input card

Parameters:

name (str) – name of the module
parameters (list) – the parameters

exception qcip_tools.chemistry_files.dalton.InputFormatError

class qcip_tools.chemistry_files.dalton.InputModule(level=1, name=None, input_cards=None, submodules=None)

The dalton (sub)modules, with level indicating it they are module (level=0) or submodule (level=1)

Note

Since Dalton only interpret the 7 first characters of any input card or module (* or . included), the storage key is reduced to that.

Parameters:

level (int) – level of the module (either 0 if principal or 1 if submodule)
name (str) – name of the module
input_cards (collections.OrderedDict) – The eventual input cards
submodules (collections.OrderedDict) – The eventual sub modules

set_input_card(input_card, force=True)

Set an input card

Parameters:

input_card (InputCard) – module
force (bool) – force replacing the card if exists

set_submodule(submodule, force=False)

Set up a submodule

Parameters:

submodule (qcip_tools.chemistry_files.dalton.InputModule) – module
force (bool) – force replacing the submodule if exists

update(r)

Update a module with respect to another

Parameters:: r (InputModule) – source module

exception qcip_tools.chemistry_files.dalton.InputModuleError

class qcip_tools.chemistry_files.dalton.MoleculeInput

Dalton mol input file.

Warning

Multiplicity seems to be given in the .dal file, so it may be wrong!!

self.molecule: the molecule (qcip_tools.molecule.Molecule)
self.title: the title (str)
self.basis_set: the basis set (str)

classmethod attempt_identification(f): A dalton molecule is quite unique (“charge=”)

file_type = 'DALTON_MOL': The identifier

classmethod from_molecule(molecule, title='', basis_set='', *args, **kwargs)

Create a file from molecule

Parameters:

molecule (qcip_tools.molecule.Molecule) – the molecule
title (str) – title of the run
basis_set (str) – the basis set

Return type:

qcip_tools.chemistry_files.dalton.MoleculeInput

classmethod possible_file_extensions()

Return the common extention of this kind of files

Return type:: list

read(f)

Parameters:: f (file) – File

to_string(in_angstrom=True, nosym=False, group_atoms=False)

Parameters:

in_angstrom – gives the atomic coordinates in angstrom
nosym (bool) – specify “nosymmetry”
group_atoms (bool) – group of the same type together (the order may be lost)

Type:

in_angstrom: bool

Return type:

str

write(f, in_angstrom=True, nosym=False, group_atoms=False)

Parameters:

f (file) – File
in_angstrom – gives the atomic coordinates in angstrom
nosym (bool) – specify “nosymmetry”
group_atoms (bool) – group of the same type together (the order may be lost)

Type:

in_angstrom: bool

class qcip_tools.chemistry_files.dalton.Output

Output of Dalton.

self.molecule: the molecule (qcip_tools.molecule.Molecule)
self.lines: the lines of the file (list of str)
self.sections: the different sections (list of OutputSection)

classmethod attempt_identification(f): A dalton output … Does contains a lot of (european) countries and universities name at some point (and a little bit of “Dalton” as well)

file_type = 'DALTON_LOG': The identifier

get_inputs()

Fetch the inputs from the log file

Return type:: tuple

read(f)

Parameters:: f (file) – File

exception qcip_tools.chemistry_files.dalton.OutputFormatError

class qcip_tools.chemistry_files.dalton.OutputSection(section, line_start, line_end)

Remind when a section is entered and exited

Parameters:: section (str) – name of the section

exception qcip_tools.chemistry_files.dalton.WrongNumberOfData(n, p)

qcip_tools.chemistry_files.dalton.check_module(name)

Check if the module name is allowed

Parameters:: name (str) – name of the module
Return type:: bool

qcip_tools.chemistry_files.dalton.dalton__archive_output__property__computed_energies(obj, *args, **kwargs)

Get the energies. Returns only the energy found on top of DALTON.PROP as the total energy (+labeled)

Parameters:: obj (qcip_tools.chemistry_files.dalton.ArchiveOutput) – object
Return type:: dict

qcip_tools.chemistry_files.dalton.dalton__archive_output__property__electrical_derivatives(obj, *args, **kwargs)

Get electrical derivatives in Dalton archives. Returns a dictionary of dictionaries:

+ "F"
    + static : ElectricDipole
+ "FF":
    + static : PolarizabilityTensor
+ "FD":
    + 0.042 : PolarizabilityTensor
    + ...
+ "FDD":
    + static : FirstHyperpolarizabilityTensor
    + ...
+ ...

Note

CC response calculations in Dalton are nice, since it allows form many order of response at the same time (thought it takes some memory) and it gives all the responses in one single file: DALTON.PROP.

On the other hand, the **RESPONSE module of dalton does not allows for many order at the same time, and is f***g inconsistent:

dipole moment is in DALTON.PROP
alpha is in DALTON.PROP, but only the non-zero components (and you need to assume permutation)
beta is in RESULTS.RSP, because why not. You need to assume Kleinman condition for SHG, and optical rectification is assumed to be the same as EOP, just permuted (and I’m not entirely sure of the validity of what I did there).
If you use the patched version of Dalton (see installation part), results are then available in DALTON.PROP (but you still need to assume permutation).
gamma is in DALTON.PROP (main source, but only non-zero components that contribute to \(\gamma_{||}\)) and also in RESULTS.RSP. You need to use an hidden option, .GAMALL to get all components of the gamma tensor (otherwise only the one contributing to :math:`gamma_{||}` are computed). The rest of the components are obtained from RESULT.RSP (when symmetry is assumed) if .GAMALL is used. Note that the first frequency is non-null for dc-Kerr, while it is the last one with CC response module (so it is dDFF in with RESPONSE and dFFD with CC).
If you use the patched version, everything (!) is in DALTON.PROP.

Parameters:: obj (qcip_tools.chemistry_files.dalton.ArchiveOutput) – object
Return type:: dict

qcip_tools.chemistry_files.dalton.dalton__archive_output__property__excitations(obj, *args, **kwargs)

Get excitations in Dalton archives. Returns a dictionary of tensor

Warning

The excitations are NOT sorted by energy (since Dalton groups them by symmetry)

Parameters:: obj (qcip_tools.chemistry_files.dalton.ArchiveOutput) – object
Return type:: dict

qcip_tools.chemistry_files.dalton.dalton__archive_output__property__geometrical_derivatives(obj, *args, **kwargs)

Get geometrical derivatives in Dalton archives. Returns a dictionary of tensor

Note

Only return geometrical hessian

Parameters:: obj (qcip_tools.chemistry_files.dalton.ArchiveOutput) – object
Return type:: dict

qcip_tools.chemistry_files.dalton.dalton__output__computed_energies(obj, *args, **kwargs)

Get the energies. Find the SCF/DFT energy, as well as the CCx one (which is given with MP2).

Note

Not (yet?) CI, CASCI or MCSCF
Probably wrong on geometry optimization.

Parameters:: obj (qcip_tools.chemistry_files.dalton.Output) – object
Return type:: dict

qcip_tools.chemistry_files.dalton.dalton__output__get_geometrical_derivatives(obj, *args, **kwargs)

Get the cartesian gradient out of a dalton calculation output

Parameters:: obj (qcip_tools.chemistry_files.dalton.Output) – object
Return type:: dict

Dalton files (chemistry_files.dalton)

Dalton files (`chemistry_files.dalton`)