The simplest way to visualize the charge densities and molecular orbitals that Q-Chem evaluates is via a graphical user interface, such as those described in the preceding section. An alternative procedure, which is often useful for generating high-quality images for publication, is to evaluate certain densities and orbitals on a user-specified grid of points. This is accomplished by invoking the $plots option, which is itself enabled by requesting IANLTY = 200.
The format of the $plots input is documented below. It permits plotting of molecular orbitals, the SCF ground-state density, and excited-state densities obtained from CIS, RPA or TDDFT/TDA, or TDDFT calculations. Also in connection with excited states, either transition densities, attachment/detachment densities, or natural transition orbitals (at the same levels of theory given above) can be plotted as well.
By default, the output from the $plots command is one (or several) ASCII files in the working directory, named plot.mo, etc.. The results then must be visualized with a third-party program capable of making 3-D plots. (Some suggestions are given in Section 10.5.4.)
An example of the use of the $plots option is the following input deck:
$molecule 0 1 H 0.0 0.0 0.35 H 0.0 0.0 -0.35 $end $rem METHOD hf BASIS 6-31g** IANLTY 200 $end $plots Plot the HOMO and the LUMO on a line 1 0.0 0.0 1 0.0 0.0 15 -3.0 3.0 2 0 0 0 1 2 $end
General format for the $plots section of the Q-Chem input deck.
$plots
One comment line
Specification of the 3-D mesh of points on 3 lines:
${N}_{x}\mathit{\hspace{1em}}{x}_{\mathrm{min}}\mathit{\hspace{1em}}{x}_{\mathrm{max}}$
${N}_{y}\mathit{\hspace{1em}}{y}_{\mathrm{min}}\mathit{\hspace{1em}}{y}_{\mathrm{max}}$
${N}_{z}\mathit{\hspace{1em}}{z}_{\mathrm{min}}\mathit{\hspace{1em}}{z}_{\mathrm{max}}$
A line with 4 integers indicating how many things to plot:
${N}_{\mathrm{MO}}\mathit{\hspace{1em}}{N}_{\mathrm{Rho}}\mathit{\hspace{1em}}{N}_{\mathrm{Trans}}\mathit{\hspace{1em}}{N}_{\mathrm{DA}}$
An optional line with the integer list of MO’s to evaluate (only if ${N}_{\mathrm{MO}}>0$)
MO(1) MO(2) $\mathrm{\dots}$ MO(${N}_{\mathrm{MO}}$)
An optional line with the integer list of densities to evaluate (only if ${N}_{\mathrm{Rho}}>0$)
Rho(1) Rho(2) $\mathrm{\dots}$ Rho(${N}_{\mathrm{Rho}}$)
An optional line with the integer list of transition densities (only if ${N}_{\mathrm{Trans}}>0$)
Trans(1) Trans(2) $\mathrm{\dots}$ Trans(${N}_{\mathrm{Trans}}$)
An optional line with states for detachment/attachment densities (if ${N}_{\mathrm{DA}}>0$)
DA(1) DA(2) $\mathrm{\dots}$ DA(${N}_{\mathrm{DA}}$)
$end
Line 1 of the $plots keyword section is reserved for comments. Lines 2–4 list the number of one dimension points and the range of the grid (note that coordinate ranges are in Ångstroms if INPUT_BOHR is not set, while all output is in atomic units). Line 5 must contain 4 non-negative integers indicating the number of: molecular orbitals (${N}_{\mathrm{MO}}$), electron densities (${N}_{\mathrm{Rho}}$), transition densities and attach/detach densities (${N}_{\mathrm{DA}}$), to have mesh values calculated.
The final lines specify which MOs, electron densities, transition densities and CIS attach/detach states are to be plotted (the line can be left blank, or removed, if the number of items to plot is zero). Molecular orbitals are numbered $1\mathrm{\dots}{N}_{\alpha},{N}_{\alpha}+1\mathrm{\dots}{N}_{\alpha}+{N}_{\beta}$; electron densities numbered where 0= ground state, 1 = first excited state, 2 = second excited state, etc.; and attach/detach specified from state $1\to {N}_{\mathrm{DA}}$.
By default, all output data are printed to files in the working directory, overwriting any existing file of the same name.
Molecular orbital data is printed to a file called plot.mo
Densities are plotted to plots.hf
Restricted unrelaxed attachment/detachment analysis is sent to plot.attach.alpha and plot.detach.alpha;
Unrestricted unrelaxed attachment/detachment analysis is sent to plot.attach.alpha, plot.detach.alpha, plot.attach.beta and plot.detach.beta
Restricted relaxed attachments/detachment analysis is plotted in plot.attach.rlx.alpha and plot.detach.rlx.alpha;
Unrestricted relaxed attachment/detachment analysis is sent to plot.attach.rlx.alpha, plot.detach.rlx.alpha, plot.attach.rlx.beta and plot.detach.rlx.beta.
Output is printed in atomic units, with coordinates first followed by item value, as shown below:
x1 y1 z1 a1 a2 ... aN x2 y1 z1 b1 b2 ... bN ...
Instead of a standard one-, two-, or three-dimensional Cartesian grid, a user may wish to plot orbitals or densities on a set of grid points of his or her choosing. Such points are specified using a $grid input section whose format is simply the Cartesian coordinates of all user-specified grid points:
x1 y1 z1 x2 y2 z2 ...
The $plots section must still be specified as described above, but if the $grid input section is present, then these user-specified grid points will override the ones specified in the $plots section.
The Q-Chem $plots utility allows the user to plot transition densities and detachment/attachment densities directly from amplitudes saved from a previous calculation, without having to solve the post-SCF (CIS, RPA, TDA, or TDDFT) equations again. To take advantage of this feature, the same Q-Chem scratch directory must be used, and the SKIP_CIS_RPA $rem variable must be set to TRUE. To further reduce computational time, the SCF_GUESS $rem can be set to READ.
SKIP_CIS_RPA
Skips the solution of the CIS, RPA, TDA or TDDFT equations for wave function
analysis.
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
TRUE / FALSE
RECOMMENDATION:
Set to true to speed up the generation of plot data if the same calculation
has been run previously with the scratch files saved.
New format for the $plots section provides readable and friendly input for generation of volumetric data. The input section can be divided into three parts. The first part contains basic plot options which define the 3-D mesh of points. The second part contains the selection of densities or orbitals. The advanced options are included in the last part.
With new plot format, there are multiple ways to define 3-D mesh points. If no plot option is given, the boundaries of the mesh box are the maximum/minimum molecular coordinates $\pm 3.0$ Å. The default box can be simply enlarged or reduced by setting grid_range to a value larger or smaller than $3.0$ (negative number is accepted), respectively. To customize the mesh box, set grid_range to desired boundaries:
$plots grid_range (-1,1) (-1,1) (-1,1) $end
This defines a 2$\times $2$\times $2 mesh box centered at the molecular coordinate origin. Note that there is no space in the parentheses.
The number of one dimension points is the value of the box length divided by grid_spacing. The default grid point spacing is $0.3$ Å. To override the usage of grid_spacing and customize the number of 3-D points, set grid_points to desired values.
To generate cube file (Section 10.5.4) using new plot format, just set MAKE_CUBE_FILES to TRUE in $rem section. The new plot format is enabled by requesting PLOTS = 1.
Option | Explanation |
---|---|
Basic plot options | |
grid_range | boundaries${}^{\u2020}$ of the mesh box or increment/decrement in the default boundaries${}^{\u2020\u2020}$ in Å |
grid_spacing | grid point spacing${}^{\u2020\u2020\u2020}$ in Å |
grid_points | ${N}_{x}$ ${N}_{y}$ ${N}_{z}$ |
Density/orbital selection${}^{\mathrm{\star}}$ | |
alpha_molecular_orbital | an integer range of alpha MO’s to evaluate |
beta_molecular_orbital | an integer range of beta MO’s to evaluate |
total_density | an integer range of total densities to evaluate |
spin_density | an integer range of spin densities to evaluate |
transition_density | an integer range of transition densities to evaluate |
natural_transition_orbitals | an integer range of excited states whose NTOs are evaluated |
attachment_detachment_density | an integer range of det.-att. densities to evaluate |
natural_bond_orbitals | an integer range of NBOs for each state to evaluate |
nbo_state | an integer range of states whose NBOs are evaluated |
Advanced options | |
reduced_density_gradient | invoke non-covalent interaction (NCI) plot |
orbital_laplacians | evaluate orbital Laplacians |
average_local_ionization | evaluate average local ionization energies^{883} with a given contour value of the electron density. The default is $0.0135e/{\text{\xc5}}^{3}$ ($\approx 0.002e/{a}_{0}^{3}$). |
elf | invoke electron localization function (ELF) plots |
${}^{\u2020}$the format: $({x}_{\mathrm{min}},{x}_{\mathrm{max}})({y}_{\mathrm{min}},{y}_{\mathrm{max}})({z}_{\mathrm{min}},{z}_{\mathrm{max}})$ | |
${}^{\u2020\u2020}$the default is $3.0$ Å increment in the boundaries derived from the molecular coordinates | |
${}^{\u2020\u2020\u2020}$the default is $0.3$ Å; it can be overridden by option ’grid_points’ | |
${}^{\star}$input format: n-m or n, indicating n-th oribtal or state; use $0$ for the ground-state |
$molecule 0 1 C 0.0000000 -0.0000000 -0.6133791 O -0.0000000 0.0000000 0.6060734 H 0.0000000 0.9391300 -1.1555819 H 0.0000000 -0.9391300 -1.1555819 $end $rem METHOD cis BASIS 6-31+G* CIS_N_ROOTS 4 CIS_TRIPLETS false MAKE_CUBE_FILES true ! triggers writing of cube files PLOTS true $end $plots grid_range (-8,8) (-8,8) (-8,8) grid_points 40 40 40 total_density 0-2 transition_density 1-2 attachment_detachment_density 1-2 alpha_molecular_orbital 28-31 $end
$molecule 0 1 H -2.952725 -0.026758 0.000000 C -1.871492 -0.010683 0.000000 C -1.172124 -0.001127 -1.197270 H -1.709244 -0.009471 -2.137819 C 0.211522 0.017487 -1.202676 H 0.754733 0.024328 -2.137945 C 0.916518 0.025234 0.000000 N 2.357874 0.119819 0.000000 H 2.747183 -0.346427 -0.829920 H 2.747183 -0.346427 0.829920 C 0.211522 0.017487 1.202676 H 0.754733 0.024328 2.137945 C -1.172124 -0.001127 1.197270 H -1.709244 -0.009471 2.137819 $end $rem EXCHANGE hf BASIS 6-31g* MAKE_CUBE_FILES true PLOTS true $end $plots grid_spacing 0.1 total_density 0 average_local_ionization $end