Dropping The Drop Boxes: Current “Best Set” Keywords For Solid-State Terahertz DMol3 Calculations

Of the few discussions I’ve had with fellow theoreticians, the general consensus is that employing drop boxes for defining parameters in quantum chemistry programs is methodologically akin to using solvents and starting materials as purchased from a chemical company “as is.” Certainly good enough to get something decent to happen because, of course, the companies providing the product need to stay in business, but certainly not ideal and, by their removal of the background steps and understanding of the generation methods, somehow lacking, neglecting the efforts of researchers “behind the scenes” that made the (pardon) gross simplification of “hitting the dirt running” possible.

The subject of this post is the Materials Studio (graphical interface) implementation of DMol3 (DOS/shell) and the settings available via the MS interface (coarse, medium, fine in many cases, with the actual values associated with these general settings varying slightly with the properties of the crystal cell). Are the standard options available for setting job parameters good enough to get a workable result out? In the case of “fine”, yes, with very few instances noted here of calculations behaving badly. Can one do better? Definitely. For terahertz spectroscopy studies alone, the parameter options provided by the Materials Studio interface are good enough to get something out to aid in assignments, and certainly good enough to convince anyone that ISOLATED-MOLECULE CALCULATIONS ARE ENTIRELY INAPPROPRIATE TO USE FOR THE ASSIGNMENT OF SOLID-STATE TERAHERTZ SPECTRA. At this point in the game, however, I would not consider them rigorously publication-quality results (I would not argue if agreement was good and the spectra clean, but I would certainly check the level of theory carefully), given that agreement can be improved and a better overall assignment achieved by tweaking the keyword list.

It is with that in mind (and Matt Hudson’s reminder) that I’m posting a keyword set that, over the course of a few hundred DMol3 calculations or so, has been found to provide a decent balance of time (longer than the menu options but only by %15 – %20 or so) and interpretive power (or predictive power if no one’s taken the Terahertz spectrum). Note that the “#” is the “comment/ignore” character, so much of the content below is ignored by DMol3.

####################################################################
#
# Input cheat-sheet for THz DMol3 solid-state calculations
# Quests, comms, complaints, Damian Allis, damian@somewhereville.com
#
# Definitely works with DMol3 version 3.2
#
####################################################################
###   Optimization Properties   ####################################
####################################################################
Calculate                    optimize
###   Optimize the structure
###
Opt_energy_convergence       5.0000e-007
###   Energy convergence (dE step to finish)
###
Opt_gradient_convergence     1.0000e-004 A
###   Conv when largest grad vector comp < this
###
Opt_displacement_convergence 1.0000e-004 A
###   Conv when largest atom disp < this
###
Opt_iterations               100
###   Steps to opt (large value for tight conv)
###
Opt_max_displacement         0.3000 A
###   Max length geom update vector
###
####################################################################
###   Electronic Structure Descriptions   ##########################
####################################################################
Spin_polarization            restricted
###   un/restricted wavefunction description
###
Charge                       0
###   System charge
###
###   Basis set approx's are not direct comparisons
Basis                        dnp
###   Basis     dnp    Gaussian approx 6-31G(d,p) basis set
###   Basis     dnd    Gaussian approx 6-31G(d) basis set
###   Basis     dn     Gaussian approx 6-31G basis set
###   Basis     min    Gaussian approx 3-21G basis set
###
Pseudopotential              none
###   Consider for transition metal systems
###
###   GGA Functionals - Gen Grad Approx: density and gradient
Functional                   bp
###   So far, bp is the best all-around THz freq functional
###   Functional                 blyp            ###
###   Functional                 bop             ###
###   Functional                 gga(p91)        ###
###   Functional                 hcth407         ###
###   Functional                 vwn-bp
###   So far, vwn-bp is the 2nd best THz freq functional
###   Functional                 rpbe            ###
###   Functional                 pbe             ###
###
###   LDA Functionals - Local Den Approx: density at position
###   Functional                 pwc             ###
###   Functional                 vwn             ###
###
####################################################################
###   Additional Electronic Structure Parameters   #################
####################################################################
###
###   Integration_grid - mesh points for numerical integr procedure
###                    value       ipa iomax iomin thres   rmaxp sp
###   Integration_grid xcoarse ###  6    3     1   0.01     10.0 1.0
###   Integration_grid coarse  ###  6    4     1   0.001    10.0 1.0
###   Integration_grid medium  ###  6    6     1   0.0001   10.0 1.0
Integration_grid   fine        ###  6    6     1   0.00001  12.0 1.2
###   Integration_grid xfine   ###  6    7     1   0.000001 15.0 1.5
###
Aux_density                  octupole
###   Max ang momentum multipolar fit funcs
###
Occupation                   fermi
###   Converger aid.  See manual for more
###
Cutoff_Global                4.0000 angstrom
###   Atom-centered basis set cut-off distance
###
Scf_density_convergence      1.0000e-008
###   Conv when density conv < this
###
Scf_charge_mixing            0.2000
###   Init charge density mix coeff restrict
###
Scf_iterations               100
###   Max iters for SCF (large b/c conv’rs)
###
Scf_diis                     6 pulay
###   Max size of DIIS subspace for SCF calc
###
###   Kpoint -> defined for each a,b,c lattice vector
###   General protocol (appropr of selections is theological):
###   If a,b,c    < 5        set kpoint to 5
###   If a,b,c  5 < X < 10   set kpoint to 4
###   If a,b,c 10 < X < 15   set kpoint to 3
###   If a,b,c 15 < X < 20   set kpoint to 2
###   If a,b,c    < 20       set kpoint to 1
###                                     a b c
Kpoints                      on     5 5 5
###   Max set here.  Adjust as approp
###
###   Print options
Print                        vib_hess
###   amount of printout.  Read manual.
###
####################################################################
###   Terahertz Vibrational Analysis   #############################
####################################################################
###
Symmetry                     on
###   Recalc symm after opt for use in freq
###
Mulliken_analysis            charge
###   Mulliken charges.  MS 4.2 broke this (!)
###
Hirshfeld_analysis           charge
###   Hirshfeld charges.
###
Frequency_analysis           on
###   Perform normal mode analysis
###

Either copy+paste the above, or download DMol3_THz_complete.input.

For those a bit overcome by what Frank Zappa would refer to as the “statistical density” of the content above, the whole file reduces down to the following (the selection of Kpoints being the only keyword one has to think about below).

Calculate                    optimize
Opt_energy_convergence       5.0000e-007
Opt_gradient_convergence     1.0000e-004 A
Opt_displacement_convergence 1.0000e-004 A
Opt_iterations               100
Opt_max_displacement         0.3000 A
Spin_polarization            restricted
Charge                       0
Basis                        dnp
Functional                   bp
Integration_grid             fine
Aux_density                  octupole
Occupation                   fermi
Cutoff_Global                4.0000 angstrom
Scf_density_convergence      1.0000e-008
Scf_charge_mixing            0.2000
Scf_iterations               100
Scf_diis                     6 pulay
Kpoints                      on     5 5 5
Print                        vib_hess
Symmetry                     on
Mulliken_analysis            charge
Hirshfeld_analysis           charge
Frequency_analysis           on

Either copy+paste the above, or download DMol3_THz_min.input.

Yes, I am aware that I am recommending the replacement of one “standard” set of keywords (Accelrys) with another “standard” set (mine). Further, it must be noted that these above keywords are very much terahertz-specific, where the lowest-energy, largest-amplitude, most neighboring molecule-dependent solid-state properties are considered. This is NOT the “be all, end all” keyword set for every system (certainly not even for general inelastic neutron scattering spectroscopy use, where the agreement between theory and experiment is very dependent on the choice of density functional (blyp and bop seem to be the best in the 500 to 1500 cm-1 region, by the way)). And, far from trying to use this post to complain about theory, program, and parameters, I note that DMol3 has been the mainstay of my solid-state terahertz theoretical work to date and I’ve spoken quite favorably of it in the past. Any program with keywords and input parameters should be expected to have optimal settings for different tasks, a point in no way lost on researchers familiar with the variety of empirically-derived functionals in density functional theory. We don’t refer to the computational chemistry implementations of quantum theory as the “approximate methods” for nothing.

Since it is just a text file, settings above may undergo further refinement at a more rapid pace than a commercial interface. That said, if your goal is reasonable terahertz simulation with as standard a set of keywords as possible, the set above will (so far, anyway) bring you quite close to your destination.

It is probably far less interesting to list my explanations for each choice (like the Kpoints settings, functional choice, the super-tight convergence criteria) than reading any comments you (the reader) might make, so I invite/encourage questions in the comment section that will keep record of choices, my reasons, and the logic of others.

en.wikipedia.org/wiki/Quantum_chemistry
www.accelrys.com/products/mstudio
www.accelrys.com/products/mstudio/modeling/quantumandcatalysis/dmol3.html
en.wikipedia.org/wiki/Time_domain_terahertz_spectroscopy
en.wikipedia.org/wiki/Frank_Zappa
www.zappa.com
en.wikipedia.org/wiki/The_Black_Page
www.accelrys.com
en.wikipedia.org/wiki/Inelastic_neutron_scattering
www.accelrys.com/reference/cases/studies/korter.pdf
en.wikipedia.org/wiki/Density_functional_theory

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