QChem performs a number of standard wave function analyses by default. Switching the $rem variable WAVEFUNCTION_ANALYSIS to FALSE will prevent the calculation of all wave function analysis features (described in this section). Alternatively, each wave function analysis feature may be controlled by its $rem variable. (The NBO program, which is interfaced with QChem, is capable of performing more sophisticated analyses. See Section 10.3 of this manual, along with the NBO manual, for more details.
WAVEFUNCTION_ANALYSIS
Controls the running of the default wave function analysis tasks.
TYPE:
LOGICAL
DEFAULT:
TRUE
OPTIONS:
TRUE
Perform default wave function analysis.
FALSE
Do not perform default wave function analysis.
RECOMMENDATION:
None
Note: WAVEFUNCTION_ANALYSIS has no effect on NBO, solvent models or vibrational analyses.
The oneelectron charge density, usually written as
(10.1) 
represents the probability of finding an electron at the point , but implies little regarding the number of electrons associated with a given nucleus in a molecule. However, since the number of electrons is related to the occupied orbitals by
(10.2) 
We can substitute the atomic orbital (AO) basis expansion of into Eq. (10.2) to obtain
(10.3) 
where we interpret as the number of electrons associated with . If the basis functions are atomcentered, the number of electrons associated with a given atom can be obtained by summing over all the basis functions. This leads to the Mulliken formula for the net charge of the atom :
(10.4) 
where is the atom’s nuclear charge. This is called a Mulliken population analysis [10]. QChem performs a Mulliken population analysis by default.
POP_MULLIKEN
Controls running of Mulliken population analysis.
TYPE:
LOGICAL/INTEGER
DEFAULT:
TRUE (or 1)
OPTIONS:
FALSE (or 0)
Do not calculate Mulliken populations.
TRUE (or 1)
Calculate Mulliken populations.
2
Also calculate shell populations for each occupied orbital.
Calculate Mulliken charges for both the ground state and any CIS,
RPA, or TDDFT excited states.
RECOMMENDATION:
Leave as TRUE, unless excitedstate charges are desired. Mulliken analysis is a trivial additional calculation, for ground or excited states.
LOWDIN_POPULATION
Run a Löwdin population analysis instead of a Mulliken.
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
FALSE
Do not calculate Löwdin populations.
TRUE
Run Löwdin Population analyses instead of Mulliken.
RECOMMENDATION:
None
Although conceptually simple, Mulliken population analyses suffer from a heavy dependence on the basis set used, as well as the possibility of producing unphysical negative numbers of electrons. An alternative is that of Löwdin Population analysis [518], which uses the Löwdin symmetrically orthogonalized basis set (which is still atomtagged) to assign the electron density. This shows a reduced basis set dependence, but maintains the same essential features.
While Mulliken and Löwdin population analyses are commonly employed, and can be used to produce information about changes in electron density and also localized spin polarizations, they should not be interpreted as oxidation states of the atoms in the system. For such information we would recommend a bonding analysis technique (LOBA or NBO).
A more stable alternative to Mulliken or Löwdin charges are the socalled “CHELPG” charges (“Charges from the Electrostatic Potential on a Grid”) [519]. These are the atomcentered charges that provide the best fit to the molecular electrostatic potential, evaluated on a realspace grid outside of the van der Waals region and subject to the constraint that the sum of the CHELPG charges must equal the molecular charge. QChem’s implementation of the CHELPG algorithm differs slightly from the one originally algorithm described by Breneman and Wiberg [519], in that QChem weights the grid points with a smoothing function to ensure that the CHELPG charges vary continuously as the nuclei are displaced [520]. (For any particular geometry, however, numerical values of the charges are quite similar to those obtained using the original algorithm.) Note, however, that the BrenemanWiberg approach uses a Cartesian grid and becomes expensive for large systems. (It is especially expensive when CHELPG charges are used in QM/MMEwald calculations [521].) For that reason, an alternative procedure based on atomcentered Lebedev grids is also available [521], which provides very similar charges using far fewer grid points. In order to use the Lebedev grid implementation the $rem variables CHELPG_H and CHELPG_HA must be set, which specify the number of Lebedev grid points for the hydrogen atoms and the heavy atoms, respectively.
CHELPG
Controls the calculation of CHELPG charges.
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
FALSE
Do not calculate CHELPG charges.
TRUE
Compute CHELPG charges.
RECOMMENDATION:
Set to TRUE if desired. For large molecules, there is some overhead associated with computing CHELPG charges, especially if the number of grid points is large.
CHELPG_HEAD
Sets the “head space” [519] (radial extent) of the CHELPG grid.
TYPE:
INTEGER
DEFAULT:
30
OPTIONS:
Corresponding to a head space of , in .
RECOMMENDATION:
Use the default, which is the value recommended by Breneman and Wiberg [519].
CHELPG_DX
Sets the rectangular grid spacing for the traditional Cartesian CHELPG grid or the spacing between concentric Lebedev shells (when the variables CHELPG_HA and CHELPG_H are specified as well).
TYPE:
INTEGER
DEFAULT:
6
OPTIONS:
Corresponding to a grid space of , in .
RECOMMENDATION:
Use the default (which corresponds to the “dense grid” of Breneman and Wiberg [519]), unless the cost is prohibitive, in which case a larger value can be selected. Note that this default value is set with the Cartesian grid in mind and not the Lebedev grid. In the Lebedev case, a larger value can typically be used.
CHELPG_H
Sets the Lebedev grid to use for hydrogen atoms.
TYPE:
INTEGER
DEFAULT:
NONE
OPTIONS:
Corresponding to a number of points in a Lebedev grid.
RECOMMENDATION:
CHELPG_H must always be less than or equal to CHELPG_HA. If it is greater, it will automatically be set to the value of CHELPG_HA.
CHELPG_HA
Sets the Lebedev grid to use for nonhydrogen atoms.
TYPE:
INTEGER
DEFAULT:
NONE
OPTIONS:
Corresponding to a number of points in a Lebedev grid (see Section 4.4.5.1.
RECOMMENDATION:
None.
Finally, Hirschfeld population analysis [522] provides yet another definition of atomic charges in molecules via a Stockholder prescription. The charge on atom , , is defined by
(10.5) 
where is the nuclear charge of , is the isolated groundstate atomic density of atom , and is the molecular density. The sum goes over all atoms in the molecule. Thus computing Hirshfeld charges requires a selfconsistent calculation of the isolated atomic densities (the promolecule) as well as the total molecule. Following SCF completion, the Hirshfeld analysis proceeds by running another SCF calculation to obtain the atomic densities. Next numerical quadrature is used to evaluate the integral in Eq. (10.5). Neutral groundstate atoms are used, and the choice of appropriate reference for a charged molecule is ambiguous (such jobs will crash). As numerical integration (with default quadrature grid) is used, charges may not sum precisely to zero. A larger XC_GRID may be used to improve the accuracy of the integration.
The charges (and corresponding molecular dipole moments) obtained using Hirshfeld charges are typically underestimated as compared to other charge schemes or experimental data. To correct this, Marenich et al. [523] introduced “Charge Model 5” (CM5), which employs a single set of parameters to map the Hirshfeld charges onto a more reasonable representation of the electrostatic potential. CM5 charges generally lead to more accurate dipole moments as compared to the original Hirshfeld charges, at negligible additional cost. CM5 is available for molecules composed of elements H–Ca, Zn, Ge–Br, and I.
The use of neutral groundstate atoms to define the promolecular density in Hirshfeld scheme has no strict theoretical basis and there is no unique way to construct the promolecular densities. For example, LiF, LiF, or LiF could each be used to construct the promolecular densities for LiF. Furthermore, the choice of appropriate reference for a charged molecule is ambiguous, and for this reason Hirshfeld analysis is disable in QChem for any molecule with a net charge. A solution for charged molecules is to use the iterative “HirshfeldI” partitioning scheme proposed by Bultinck et al. [524, 525], in which the reference state is not predefined but rather determined selfconsistently, thus eliminating the arbitrariness. The final selfconsistent reference state for HirshfeldI partitioning usually consists of noninteger atomic populations.
In the first iteration, the HirshfeldI method uses neutral atomic densities (as in the original Hirshfeld scheme), with electronic population . This affords charges
(10.6) 
on the first iteration. The new electronic population (number of electrons) for atom is , and is derived from the promolecular populations . One then computes new isolated atomic densities with and uses them to construct the promolecular densities in the next iteration. In general, the new weighting function for atom in the th iteration is
(10.7) 
The atomic densities with corresponding fractional electron numbers are obtained by linear interpolation between and of the same atom [524, 526]:
(10.8) 
where and denote the integers that bracket The two atomic densities on the right side of Eq. eq:interpolate are obtained from densities that are computed in advance. (That is, the method uses the neutral atomic density along with the densities for the singly and doublycharged cations and anions of the element in equation.) The HirshfeldI iterations are converged once the atomic populations change insignificantly between iterations, say [524, 527].
The iterative Hirshfeld scheme generally affords more reasonable charges as compared to the original Hirshfeld scheme. In LiF, for example, the original Hirshfeld scheme predicts atomic charges of 0.57 while the iterative scheme increases these charges to 0.93. The integral in Eq. eq:hirshc is evaluated by numerical quadrature, and the cost of each iteration of HirshfeldI is equal to the cost of computing the original Hirshfeld charges. Within QChem, HirshfeldI charges are available for molecules containing only H, Li, C, N, O, F, S, and Cl. The $rem variable SYM_IGNORE must be set to TRUE for HirshfeldI analysis.
HIRSHFELD
Controls running of Hirshfeld population analysis.
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
TRUE
Calculate Hirshfeld populations.
FALSE
Do not calculate Hirshfeld populations.
RECOMMENDATION:
None
HIRSHFELD_READ
Switch to force reading in of isolated atomic densities.
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
TRUE
Read in isolated atomic densities from previous Hirshfeld calculation from disk.
FALSE
Generate new isolated atomic densities.
RECOMMENDATION:
Use the default unless system is large. Note, atoms should be in the same order with same basis set used as in the previous Hirshfeld calculation (although coordinates can change). The previous calculation should be run with the save switch.
HIRSHFELD_SPHAVG
Controls whether atomic densities should be spherically averaged in promolecule.
TYPE:
LOGICAL
DEFAULT:
TRUE
OPTIONS:
TRUE
Spherically average atomic densities.
FALSE
Do not spherically average.
RECOMMENDATION:
Use the default.
CM5
Controls running of CM5 population analysis.
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
TRUE
Calculate CM5 populations.
FALSE
Do not calculate CM5 populations.
RECOMMENDATION:
None
HIRSHITER
Controls running of iterative Hirshfeld population analysis.
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
TRUE
Calculate iterative Hirshfeld populations.
FALSE
Do not calculate iterative Hirshfeld populations.
RECOMMENDATION:
None
HIRSHITER_THRESH
Controls the convergence criterion of iterative Hirshfeld population analysis.
TYPE:
INTEGER
DEFAULT:
5
OPTIONS:
Corresponding to the convergence criterion of , in .
RECOMMENDATION:
Use the default, which is the value recommended in Ref. Bultinck:2007
The iterative Hirshfeld population analysis for .
$molecule 1 1 O 1.197566 0.108087 0.000000 H 1.415397 0.827014 0.000000 H 0.134830 0.084378 0.000000 F 1.236389 0.012239 0.000000 $end $rem sym_ignore true method B3LYP basis 631G* hirshiter true $end
The next section discusses how to compute arbitrary electrostatic multipole moments for an entire molecule, including both ground and excitedstate electron densities. Occasionally, however, it is useful to decompose the electronic part of the multipole moments into contributions from individual MOs. This decomposition is especially useful for systems containing unpaired electrons [528], where the firstorder moments , , and characterize the centroid (mean position) of the halffilled MO, and the secondorder moments determine its radius of gyration, , which characterizes the size of the MO. Upon setting PRINT_RADII_GYRE = TRUE, QChem will print out centroids and radii of gyration for each occupied MO and for the overall electron density. If CIS or TDDFT excited states are requested, then this keyword will also print out the centroids and radii of gyration for each excitedstate electron density.
PRINT_RADII_GYRE
Controls printing of MO centroids and radii of gyration.
TYPE:
LOGICAL/INTEGER
DEFAULT:
FALSE
OPTIONS:
TRUE (or 1)
Print the centroid and radius of gyration for each occupied MO and each density.
2
Print centroids and radii of gyration for the virtual MOs as well.
FALSE (or 0)
Do not calculate these quantities.
RECOMMENDATION:
None
QChem can compute Cartesian multipole moments of the charge density to arbitrary order, both for the ground state and for excited states calculated using the CIS or TDDFT methods.
MULTIPOLE_ORDER
Determines highest order of multipole moments to print if wave function analysis requested.
TYPE:
INTEGER
DEFAULT:
4
OPTIONS:
Calculate moments to th order.
RECOMMENDATION:
Use the default unless higher multipoles are required.
CIS_MOMENTS
Controls calculation of excitedstate (CIS or TDDFT) multipole moments
TYPE:
LOGICAL/INTEGER
DEFAULT:
FALSE (or 0)
OPTIONS:
FALSE (or 0)
Do not calculate excitedstate moments.
TRUE (or 1)
Calculate moments for each excited state.
RECOMMENDATION:
Set to TRUE if excitedstate moments are desired. (This is a trivial additional calculation.) The MULTIPOLE_ORDER controls how many multipole moments are printed.
QChem’s default is to write the SCF wave function molecular orbital symmetries and energies to the output file. If requested, a symmetry decomposition of the kinetic and nuclear attraction energies can also be calculated.
SYMMETRY_DECOMPOSITION
Determines symmetry decompositions to calculate.
TYPE:
INTEGER
DEFAULT:
1
OPTIONS:
0
No symmetry decomposition.
1
Calculate MO eigenvalues and symmetry (if available).
2
Perform symmetry decomposition of kinetic energy and nuclear attraction
matrices.
RECOMMENDATION:
None
Localized Orbital Bonding Analysis (LOBA) [365] is a technique developed by Dr. Alex Thom and Eric Sundstrom at Berkeley with Prof. Martin HeadGordon. Inspired by the work of Rhee and HeadGordon [529], it makes use of the fact that the postSCF localized occupied orbitals of a system provide a large amount of information about the bonding in the system.
While the canonical Molecular Orbitals can provide information about local reactivity and ionization energies, their delocalized nature makes them rather uninformative when looking at the bonding in larger molecules. Localized orbitals in contrast provide a convenient way to visualize and account for electrons. Transformations of the orbitals within the occupied subspace do not alter the resultant density; if a density can be represented as orbitals localized on individual atoms, then those orbitals can be regarded as nonbonding. If a maximally localized set of orbitals still requires some to be delocalized between atoms, these can be regarded as bonding electrons. A simple example is that of He versus H. In the former, the delocalized and canonical orbitals may be transformed into 1s orbitals on each He atom, and there is no bond between them. This is not possible for the H molecule, and so we can regard there being a bond between the atoms. In cases of multiple bonding, multiple delocalized orbitals are required.
While there are no absolute definitions of bonding and oxidation state, it has been shown that the localized orbitals match the chemically intuitive notions of core, nonbonded, single and doublebonded electrons, etc.. By combining these localized orbitals with population analyses, LOBA allows the nature of the bonding within a molecule to be quickly determined.
In addition, it has been found that by counting localized electrons, the oxidation states of transition metals can be easily found. Owing to polarization caused by ligands, an upper threshold is applied, populations above which are regarded as “localized” on an atom, which has been calibrated to a range of transition metals, recovering standard oxidation states ranging from II to VII.
LOBA
Specifies the methods to use for LOBA
TYPE:
INTEGER
DEFAULT:
00
OPTIONS:
specifies the localization method
0 Perform Boys localization.
1 Perform PM localization.
2 Perform ER localization.
specifies the population analysis method
0 Do not perform LOBA. This is the default.
1 Use Mulliken population analysis.
2 Use Löwdin population analysis.
RECOMMENDATION:
Boys Localization is the fastest. ER will require an auxiliary basis set.
LOBA 12 provides a reasonable speed/accuracy compromise.
LOBA_THRESH
Specifies the thresholds to use for LOBA
TYPE:
INTEGER
DEFAULT:
6015
OPTIONS:
specifies the threshold to use for localization
specifies the threshold to use for occupation
Both are measured in %
RECOMMENDATION:
Decrease to see the smaller contributions to orbitals. Values of between 40 and 75 have been shown to given meaningful results.
On a technical note, LOBA can function of both Restricted and Unrestricted SCF calculations. The figures printed in the bonding analysis count the number of electrons on each atom from that orbital (i.e., up to 1 for Unrestricted or singly occupied Restricted orbitals, and up to 2 for double occupied Restricted.)
For CIS, TDHF, and TDDFT excitedstate calculations, we have already mentioned that Mulliken population analysis of the excitedstate electron densities may be requested by setting POP_MULLIKEN = , and multipole moments of the excitedstate densities will be generated if CIS_MOMENTS = TRUE. Another useful decomposition for excited states is to separate the excitation into “particle” and “hole” components, which can then be analyzed separately [160]. To do this, we define a density matrix for the excited electron,
(10.9) 
and a density matrix for the hole that is left behind in the occupied space:
(10.10) 
The quantities and are the transition density matrices, i.e., the components of the TDDFT eigenvector [530]. The indices and denote MOs that occupied in the ground state, whereas and index virtual MOs. Note also that , the difference between the ground and excitedstate density matrices.
Upon transforming and into the AO basis, one can write
(10.11) 
where is the total charge that is transferred from the occupied space to the virtual space. For a CIS calculation, or for TDDFT within the TammDancoff approximation [419], . For full TDDFT calculations, may be slightly different than .
Comparison of Eq. () to Eq. (10.3) suggests that the quantities and are amenable to to population analyses of precisely the same sort used to analyze the groundstate density matrix. In particular, represents the th AO’s contribution to the excited electron, while is a contribution to the hole. The sum of these quantities,
(10.12) 
represents the contribution to arising from the th AO. For the particle/hole density matrices, both Mulliken and Löwdin population analyses available, and are requested by setting CIS_MULLIKEN = TRUE.
CIS_MULLIKEN
Controls Mulliken and Löwdin population analyses for excitedstate particle and hole density matrices.
TYPE:
LOGICAL/INTEGER
DEFAULT:
FALSE
OPTIONS:
FALSE (or 0)
Do not perform particle/hole population analysis.
TRUE (or 1)
Perform both Mulliken and Löwdin analysis of the particle and hole
density matrices for each excited state.
RECOMMENDATION:
Set to TRUE if desired. This represents a trivial additional calculation.
Although the excitedstate analysis features described in this section require very little computational effort, they are turned off by default, because they can generate a large amount of output, especially if a large number of excited states are requested. They can be turned on individually, or collectively by setting CIS_AMPL_ANAL = TRUE. This collective option also requests the calculation of natural transition orbitals (NTOs), which were introduced in Section 6.12.2. (NTOs can also be requested without excitedstate population analysis. Some practical aspects of calculating and visualizing NTOs are discussed below, in Section 10.5.2.)
CIS_AMPL_ANAL
Perform additional analysis of CIS and TDDFT excitation amplitudes, including generation of natural transition orbitals, excitedstate multipole moments, and Mulliken analysis of the excited state densities and particle/hole density matrices.
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
TRUE
Perform additional amplitude analysis.
FALSE
Do not perform additional analysis.
RECOMMENDATION:
None
QChem features a new module for extended excitedstate analysis, which is interfaced to the ADC, CC/EOMCC, CIS and TDDFT methods [531, 450, 451, 532, 533, 534]. These analyses are based on the state, transition and difference density matrices of the excited states; the theoretical background for such analysis is given in Chapter 6.12.
Descriptor 
Explanation 
Leading SVs 
Largest NTO occupation numbers 
Sum of SVs 
Sum of NTO occupation numbers 
PR_NTO 
NTO participation ratio 
omega 
Norm of the 1TDM , singleexc. character 
<r_h> [Ang] 
Mean position of hole 
<r_e> [Ang] 
Mean position of electron 
<r_e  r_h> [Ang] 
Linear e/h distance 
Hole size [Ang] 
RMS hole size: 
Electron size [Ang] 
RMS elec. size: 
RMS electronhole separation [Ang] 

Covariance(r_h, r_e) [Ang^2] 

Correlation coefficient 

Descriptor 
Explanation 
n_u 
Number of unpaired electrons 
n_u,nl 
Number of unpaired electrons 
PR_NO 
NO participation ratio 
p_D and p_A 
Promotion number and 
PR_D and PR_A 
D/A participation ratio and 
<r_h> [Ang] 
Mean position of detachment density 
<r_e> [Ang] 
Mean position of attachment density 
<r_e  r_h> [Ang] 
Linear D/A distance 
Hole size [Ang] 
RMS size of detachment density 
Electron size [Ang] 
RMS size of attachment density 
The transitiondensity (1TDM) based analyses comprise the construction and export of natural transition orbitals (NTO) [449], as well as electron and hole densities, the evaluation of charge transfer numbers [531], and an analysis of exciton multipole moments [532, 533, 534]. Furthermore, the formation and export of stateaveraged NTOs, and the decomposition of the excited states into transitions of stateaveraged NTOs are implemented [450]. The difference and/or state densities can be exported themselves, as well as employed to construct and export natural orbitals, natural difference orbitals, and attachment and detachment densities [351]. Furthermore, two measures of unpaired electrons are computed [535]. In addition, a Mulliken or Löwdin population analysis and an exciton analysis can be performed based on the difference/state densities. The main descriptors of the various analyses that are printed for each excited state are given in Tables 10.1 and 10.2. For a detailed description with illustrative examples, see Refs. Plasser:2014a and Plasser:2014b.
To activate any excitedstate analysis STATE_ANALYSIS has to be set to TRUE. For individual analyses there is currently only a limited amount of fine grained control. The construction and export of any type of orbitals is controlled by MOLDEN_FORMAT to export the orbitals as MolDen files, and NTO_PAIRS which specifies the number of important orbitals to print. Setting MAKE_CUBE_FILES to TRUE triggers the construction and export of densities in “cube file” format [536] (see Section 10.5.4 for details). Activating transition densities in $plots will generate cube files for the transition density, the electron density, and the hole density of the respective excited states, while activating state densities or attachment/detachment densities will generate cube files for the state density, the difference density, the attachment density and the detachment density. Setting GUI=2 will export data to the “.fchk” file and switches off the generation of cube files. The population analyses are controlled by POP_MULLIKEN and LOWDIN_POPULATION. Setting the latter to TRUE will enforce Löwdin population analysis to be employed, while by default the Mulliken population analysis is used.
Any MolDen or cube files generated by the excited state analyses can be found in the directory plots in the job’s scratch directory. Their names always start with a unique identifier of the excited state (the exact form of this human readable identifier varies with the excited state method). The names of MolDen files are then followed by either _no.mo, _ndo.mo, or _nto.mo depending on the type of orbitals they contain. In case of cube files the state identifier is followed by _dens, _diff, _trans, _attach, _detach, _elec, or _hole for state, difference, transition, attachment, detachment, electron, or hole densities, respectively. All cube files have the suffice .cube. In unrestricted calculations an additional part is added to the file name before .cube which indicates (_a) or (_b) spin. The only exception is the state density for which _tot or _sd are added indicating the total or spindensity parts of the state density.
The _ctnum_atomic.om files created in the main directory serve as input for a charge transfer number analysis, as explained, e.g., in Refs. [531, 537]. These files are processed by the external TheoDORE program (http://theodoreqc.sourceforge.net) to create electron/hole correlation plots and to compute fragment based descriptors.