Comments (8)
I'll make a list of additional name/API changes w.r.t #1:
Name changes
-
numbers
->atnums
(atomic numbers) -
pseudo_numbers
->atcorenums
(effective core charges, zero for ghost atoms) -
coordinates
->atcoords
(atomic Cartesian coordinates) -
polar
->polarizability_tensor
, shape(3, 3)
(dipolar polarizability matrix) -
cell
orrvecs
->cellvecs
(matrix whose rows are cell vectors, shape(nvec, 3)
-
ms2=1+abs(nalpha-nbeta)
will be replaced byspinpol=abs(nalpha-nbeta)
(spin polarization)
Behavior changes
- Include ghost atoms in the
at*
attributes. Elements corresponding to ghost atoms inatcorenums
must be zero.
Consolidation of ever-growing number of attributes
-
mulliken_charges
,npa_charges
,esp_charges
->atcharges
is a dictionary where the key is a string describing the type of atomic charge and the value is a corresponding array of atomic charges. Keys should be specific and somewhat self-explaining, e.g.'mulliken'
,'natural'
,'lowdin'
,'hly'
,'msk'
, etc. -
one_mo
,kin
,na
,olp
->one_ints
is a dictionary where the key is any of'core'
,'kin'
,'na'
,'olp'
, followed by a suffix'_ao'
or'_mo'
. With this change the class attributeIOData.two_index_names
can also be removed. -
two_mo
,er
->two_ints
is a dictionary where the key is any of'er'
,'two'
, followed by a suffix'_ao'
or'_mo'
-
dm_*
->one_rdms
is a dictionary with various types of 1-particle reduced density matrices. Standard keys are'scf'
,'post_scf'
,'scf_spin'
,'post_scf_spin'
. These are always stored in the AO basis. -
extra
in which everything is stored for which IOData does not define standard names. For nowgaussian_command
, -
dipole_moment
,quadrupole_moments
->moments
dictionary with (angmom, kind) keys or something similar (to be decided).
Things to be removed because they are not needed at this stage or in the near future
-
links
-
permutation
andsigns
(See #42)
New attributes for IOData
for generating QC & MM input files, keeping QM/MM in mind
-
run_type
:'energy'
,'opt'
,'freq'
, ... -
obasis_name
, e.g.'6-31g'
, or'sto-3g'
-
lot
level of theory. -
extcharges
, array with values of external charges, with shape(nextcharge, 4)
. First three columns for Cartesian X, Y and Z coordinates, last column for the actual charge. -
charge
, the net charge (should not be a new attribute, but something that is coupled tonelec
). -
bonds
, an integer array with shape(nbond, 3)
. Each row represents one bond. One row consists of three integers: first atom index (starting from zero), second atom index & an optional bond type (0: not known, 1: single, 2: double, 3: triple, 4: conjugated)
New attributes for IOData
for reading useful properties out of QM or MM calculations, and other popular file formats
-
atforces
, forces in Cartesian coordinates, shape(natom, 3)
-
athessian
, hessian in Cartesian coordinates, shape(3*natom, 3*natom)
-
atmasses
, vector with atomic masses -
atfrozen
, boolean flags, True for atoms whose positions were not optimized, or for which no Hessian matrix elements were computed. (Does not affect the size of the Hessian.) -
g_rot
the rotational symmetry number of the molecule, a.k.a. the degeneracy of the rotational partition function. -
two_rdms
is a dictionary of two-particle reduced density matrices, standard keys'post_scf'
and'post_scf_spin'
plus a suffix'_mo'
or'_ao'
should be used to specify the basis in which these matrices are stored. -
'atffparams'
is a dictionary with arrays of atomic force field parameters (typically non-bonded). Keys include'charges'
,'vdw_radii'
,'sigmas'
,'epsilons'
,'alphas'
(atomic polarizabilities),'c6s'
,'c8s'
,'c10s'
,'buck_as'
,'buck_bs'
,'lj_as'
,'core_charges'
,'valence_charges'
,'valence_widths'
, ... Not all of them have to be present, depending on the use case. -
basisdef
is a basis set definition. This can be a dictionary whose keys are symbols (of chemical elements), atomic numbers (similar to previous,str
to make distinction with following) or an atom index (integer referring to a specific atom in a molecule). With this attribute we can easily load and dump basis set definitions from EMSL and derive molecular basis sets from them (see #42).
Other API changes
from iodata.
I've edited the plan to include an extra
attributes where everything must be stored for which we do not have standard names. This makes it possible to add more attributes to the IOData
class in future without breaking any code that uses IOData. All allowed attributes should be put in __slots__
, either manually or with the attr
package. See https://docs.python.org/3/reference/datamodel.html#slots
from iodata.
I've merged extcoords
and extcharges
into one array. One is never used without the other, so putting them into one array would save us from checking the consistency of the sizes of these arrays.
I've also removed (some time ago) the atghost attribute. Ghost atoms can be identified with atcorenums == 0.0
.
from iodata.
@FarnazH I'll take care of this one soon.
from iodata.
Small change of plan after brief chat with @PaulWAyers : spinpol=abs(nalpha-nbeta)
will replace spinmult=1+abs(nalpha+nbeta)
because spin multiplicity is in several cases not a very accurate name.
from iodata.
Small change of plan. one_ints
and two_ints
instead of one_body_integrals
and two_body_integrals
, similar to one_rdms
and two_rdms
.
from iodata.
Small changes: added lot
and moments
.
from iodata.
I've renamed runtype
to run_type
in the second comment.
from iodata.
Related Issues (20)
- Support different types of normalization of the primitives in `iodata.basis` HOT 1
- Fix `dump_one` and `dump_many` for SDF file format HOT 6
- Support *.mol files HOT 3
- CFOUR molden files HOT 4
- Extract some information from results of `opt` and `scrf` Gaussian jobs HOT 4
- 2-electron reduced density matrices HOT 14
- PDB load_one issue with atom type CL HOT 5
- Compute electronic energy/gradient(force) in IOData
- Input writers for other quantum chemistry software HOT 2
- Install issue on Windows HOT 2
- Can I trust IOData for handling molden files generated from PySCF HOT 2
- Rename some fields read from PDB, to be more in line with PDB conventions HOT 3
- AttributeError: module 'numpy' has no attribute 'int'
- Scipy Factorial2 change HOT 4
- Issues related to factorial2 function HOT 1
- Can't install on macos with M1 HOT 3
- Computing Center of Mass HOT 3
- Support GPAW HOT 2
- Python 3.9 Numpy 1.20 Depreciation: np.int, np.float HOT 7
- Fix Factorial2 HOT 4
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from iodata.