GauChkParser package
Submodules
GauChkParser.ChkReader module
- class GauChkParser.ChkReader.ChkReader(fname: str)
Bases:
objectA class for reading .chk file generaged by Gaussian 09/16 x64 version
- property ilsw: List[int]
Return ILSW array (size=100)
- property rlsw: List[float]
Return RLSW array (size=ilsw[57])
- write_gjf(fname: str)
Write a gjf file based on the information of .chk
- Parameters:
fname – the output gjf file name
- write_fchk(fname: str)
Write a formatted checkpoint file based on the partial information of .chk
Note
The generated .fchk file is not as complete as one created using formchk. However, it contains enough information to be used by [Multiwfn](http://sobereva.com/multiwfn).
- Parameters:
fname – the output fchk file name
GauChkParser.Constants module
- GauChkParser.Constants.Bohr2Ang = 0.529177249
Bohr to Angstrom constant in 1986, the value used in GaussView 6.0
- GauChkParser.Constants.Bohr2Ang1998 = 0.5291772083
Borh to Angstrom constant in 1998, the value used in Gaussian 03
- GauChkParser.Constants.Bohr2Ang2006 = 0.52917720859
Borh to Angstrom constant in 2006, the value used in Gaussian 09
- GauChkParser.Constants.Bohr2Ang2010 = 0.52917721092
Borh to Angstrom constant in 2010, the value used in Gaussian 16
https://physics.nist.gov/cuu/Constants/Preprints/lsa2010.pdf
GauChkParser.Types module
- class GauChkParser.Types.GenDef(value)
Bases:
IntEnumGen Array index in enum type, such as use genarr[GenDef.VirialRatio]
- VirialRatio = 0
Virial ratio.
- ElecX = 1
X Component of applied electric field
- ElecY = 2
Y Component of applied electric field
- ElecZ = 3
Z Component of applied electric field
- Scf2E = 4
2e SCF energy
- ScrfGf = 5
SCRF g-factor
- ScrfA0 = 6
SCRF a0
- ThermalEne = 7
Thermal Energy
- ECiCcQciBd = 8
E(CI/CC/QCI/BD)
- Eccd = 9
E(CCD+ST4(CCD)/QCISD(T)/BD(T)/CI+Davidson)
- Evar1 = 10
E(VAR1)
- ZeroPointEne = 11
Zero-point energy
- MultiStepEne = 12
Multi-step (G1, G2, etc.) energy
- NimagFreq = 13
Number of imaginary frequencies.
- Dpuhf = 14
D(PUHF)
- Epuhf = 15
EPUHF
- Ecbs2 = 16
ECBS2
- Ecbsi = 17
ECBSI
- Epmp20 = 18
EPMP2-0
- Epmp30 = 19
EPMP3-0
- Rmsdopt = 20
ROOT-MEAN-SQUARED FORCE OF OPTIMIZED PARAMETERS
- EcisMP2 = 21
E(CIS-MP2)
- RmsError = 22
RMS ERROR IN DENSITY MATRIX
- S2 = 23
S**2 after annihilation of first contaminant.
- CisEne = 24
CIS energy
- Ump4d = 25
UMP4D (=UMP4DQ - E4(R+Q))
- RefBdEne = 26
Reference energy for BD
- MP5 = 27
MP5
- S4SD = 28
S4SD, computed in ANNIL in L502, used by PSCF spin projection routines
- ForzenEne = 29
Frozen-core part of total energy
- Tau = 30
‘TAU’ FROM SCFDM
- ScfEne = 31
SCF ENERGY.
- UMP2Ene = 32
UMP2 ENERGY.
- UMP3Ene = 33
UMP3 ENERGY.
- UMP4Ene = 34
UMP4(SDTQ) ENERGY.
- CbsOIii = 35
CBS OIii
- TotEneRF = 36
Total energy with RF from L116
- MP4EDQEne = 37
MP4DQ ENERGY
- MP4SDQEne = 38
MP4SDQ ENERGY
- L116 = 39
Set in L116 for some reason
- NucRepEne = 40
NUCLEAR REPULSION ENERGY
- LenRefDet = 41
T (LENGTH OF CORRECTION OF REFERENCE DETERMINANT)
- UpdateEne = 42
UPDATED ENERGY FOR OPTIMIZATIONS
- S2Scf = 43
<S**2> OF SCF WAVE FUNCTION
- S2FirstOrder = 44
<S**2> CORRECTED TO FIRST ORDER (AFTER DOUBAR)
- S2Doubles = 45
<S**2> CORRECTED FOR DOUBLES (NOT IMPLEMENTED)
- A0 = 46
A0
- Dummy = 47
Unused in G16
- TempTher = 48
Temperature for thermochemistry
- PressTher = 49
Pressure for thermochemistry
- ScalFactorFreqTher = 50
Scale factor for frequencies in thermochemistry
- NucRep = 51
Nuclear repulsion contribution from inactive atom pairs
- SingE2ToRomp2 = 52
Singles contribution to E2 in ROMP2
- E2 = 53
E(2) with current orbitals for extrapolation
- NucRF = 54
Nuclear term in the reaction field energy
- ElecRF = 55
Electronic term in the reaction field energy
- CurProFreq = 56
Curvature from projected frequency jobs
- ReacCoord = 57
Reaction coordinate for single-points along IRCs
- FlagExt = 58
Flag for status from external programs; see RunExt
- ScfEneFirstIter = 59
SCF energy at first iteration
- JobStat = 60
Job status, -1 = in progress, 0 = undefined/old chk file, 1 = finished successfully, 2 = step in mult i-step job completed successfully, 3 = job terminated with error
- HighestOrder = 61
Highest order of nuclear coordinate derivatives available
- NIterMostRecSCF = 62
Number of iterations in most recent SCF
- NucRepEneNoExf = 63
Nuclear repulsion energy without external field contribution
- class GauChkParser.Types.DensDef(value)
Bases:
IntEnumDensity matrix definition in enum type, such as use totdens[DensDef.DensSCF], return empty list if not exists
- DensSCF = 0
SCF Density
- DensPSI = 1
Psi(1) Density
- DensMP2 = 2
MP2 Density
- DensMP3 = 3
MP3 Density
- DensMP4 = 4
MP4 Density
- DensCIRho = 5
CI Rho(1) Density
- DensCI = 6
CI Density
- DensCC = 7
CC Density
- Dens2ndOrder = 8
2nd Order Density
- class GauChkParser.Types.Mol(natoms: int = 0, totchg: int = 0, ne: int = 0, nae: int = 0, nbe: int = 0, nbasis: int = 0, nbsuse: int = 0, ndim: int = 0, multiplicity: int = 0, maxbond: int = 0, nbond: ~typing.List[str] = <factory>, ibond: ~typing.List[str] = <factory>, rbond: ~typing.List[str] = <factory>, names: ~typing.List[str] = <factory>, atomicnums: ~typing.List[int] = <factory>, coords: ~numpy.ndarray = <factory>, gradient: ~typing.List[float] = <factory>, hessian: ~numpy.ndarray = <factory>, aoene: ~typing.List[float] = <factory>, boene: ~typing.List[float] = <factory>, amocoeff: ~typing.List[float] = <factory>, bmocoeff: ~typing.List[float] = <factory>, orthbasis: ~typing.List[float] = <factory>, cell: ~numpy.ndarray = <factory>, primexp: ~typing.List[float] = <factory>, concoeff: ~typing.List[float] = <factory>, spconcoeff: ~typing.List[float] = <factory>, cshell: ~numpy.ndarray = <factory>, nucchg: ~typing.List[float] = <factory>, shelltypes: ~typing.List[int] = <factory>, shellnprim: ~typing.List[int] = <factory>, shell2map: ~typing.List[int] = <factory>, orblabels: ~typing.List[str] = <factory>, totdens: ~typing.List[~typing.List[float]] = <factory>, spindens: ~typing.List[~typing.List[float]] = <factory>)
Bases:
objectA mol dataclass for storing molecule data
- natoms
number of atoms
- Type:
int
- totchg
total charge
- Type:
int
- ne
number of electrons
- Type:
int
- nae
number of alpha electrons
- Type:
int
- nbe
number of beta electrons
- Type:
int
- nbasis
number of basis functions
- Type:
int
- nbsuse
number of independent functions
- Type:
int
- ndim
number of translation vectors (0-3 dim)
- Type:
int
- multiplicity
multiplicity
- Type:
int
- maxbond
The max connect bonds
- Type:
int
- nbond
The number of bonds for each atom, length= natoms
- Type:
List[str]
- ibond
The atom index(0 means no) for all bonds, length= maxbond*natoms
- Type:
List[str]
- rbond
The bond order for all bonds, length= maxbond*natoms
- Type:
List[str]
- names
atom element name
- Type:
List[str]
- coords
atomic coords (N*3), unit is Angstrom
- Type:
numpy.ndarray
- hessian
hessian matrix (3N*3N)
- Type:
numpy.ndarray
- gradient
cartesian gradient (N*3 list)
- Type:
List[float]
- aoene
alpha orbital energies
- Type:
List[float]
- boene
beta orbital energies
- Type:
List[float]
- amocoeff
alpha MO coefficients
- Type:
List[float]
- bmocoeff
beta MO coefficients
- Type:
List[float]
- orthbasis
orthogonal basis
- Type:
List[float]
- cell
cell size (3*3) of molecule, unit is Angstrom
- Type:
numpy.ndarray
- primexp
primitives exponents
- Type:
List[float]
- concoeff
contraction coefficients
- Type:
List[float]
- spconcoeff
P(S=P) Contraction coefficients
- Type:
List[float]
- cshell
Coordinates of each shell, unit is Angstrom
- Type:
numpy.ndarray
- nucchg
nuclear charges
- Type:
List[float]
- shelltypes
shell types
- Type:
List[int]
- shellnprim
number of primitives in each shell
- Type:
List[int]
- shell2map
shell to map
- Type:
List[int]
- orblabels
each atom orbital labels
- Type:
List[str]
- totdens
total density matrix, nine types see DensDef, such as Total SCF Density
- Type:
List[List[float]]
- spindens
spin density matrix, nine types see DensDef, such as Spin SCF Density
- Type:
List[List[float]]
- class GauChkParser.Types.ChkParams(mol: ~GauChkParser.Types.Mol = <factory>, route: str = None, gauver: str = None, title: str = None, jobtype: str = None, method: str = None, baset: str = None, viratio: float = 0, scfene: float = 0, totene: float = 0, info1_9: ~typing.List[int] = <factory>, genarr: ~typing.List[float] = <factory>)
Bases:
objectA chk parameters dataclass
- mol
The mol structure dataclass
- Type:
- route
The route string
- Type:
str
- gauver
The gaussian version description
- Type:
str
- title
The title section description
- Type:
str
- jobtype
job type, such as SP, Freq, etc.
- Type:
str
- method
method, such as RHF, MP4, etc.
- Type:
str
- baset
basis set, such as def2SVP, 6-31G, etc
- Type:
str
- viratio
virtual ratio
- Type:
float
- scfene
scf energy
- Type:
float
- totene
total energy
- Type:
float
- info1_9
The scalar data of Info1-9, size=9
- Type:
List[int]
- genarr
The scalar data of the calculation (Gen array), size=1000
- Type:
List[float]