Gaussian16 (g16) input files are plain text files that end in .com or .gjf. They can be generated using a molecular modeling program like GaussView or Avogadro or in a simple text editor (provided one has the atomic coordinates already). The general format of a Gaussian input file is given below accompanied by a short description of each section.
Link 0 commands ! Specifies memory, CPU, and other job information
Routing information ! Specifies job parameters
<<<BLANK LINE>>>
Title line ! Free-format comment line
<<<BLANK LINE>>>
Charge and Multiplicity ! Space delimited
Molecule specification(s) ! Cartesian, Z-matrix, or Redundant Internals
<<<BLANK LINE>>>
Job/option specific input ! See g16 manual
<<<BLANK LINE>>>
<<<BLANK LINE>>>
Formatting and syntax
In general, Gaussian input files follow simple and flexible syntax and grammar rules:1
- Inputs are case-insensitive i.e., opt, OPT, and oPt request the same optimization job
- Comments are made using the exclamation point (
!) - External files can be read into an input using the syntax:
@path/to/file - Keywords and keyword options can be specified using the following options:
- keyword=option
- keyword(option)
- keyword=(option1, option2, …)
- keyword(option1, option2, …)
Link 0
Link 0 command lines begin with the percent % symbol and set program control options such as resource limits, whether to save and what to name scratch files, where to access old scratch files, etc… The link 0 commands are detailed here.2 Each link 0 command requires its own line. Every link 0 option can also be called as a command line flag in your shell script or passed to Gaussian as an environmental variable. Equivalent commands and the corresponding precedence are detailed under the “Equivalencies” tab in the link above.
This section (and everything else in the input file) is an instruction to Gaussian , not SLURM. The memory and CPU allocations specified in the input file should, ideally, be equal to those requested from SLURM (so that there is no “wasted” computing power), but must not be greater than those requested from SLURM, otherwise Gaussian will attempt to allocate more resources than has been made available to it which will lead to job failure.
The .chk file
A common link 0 command is %chk, used to save the checkpoint file from the calculation (typically deleted with other scratch files when the job is completed). Every iteration of a calculation Gaussian saves an image of job in the checkpoint file (like a savepoint) allowing the user to go back and restart a failed job. In addition to various savepoints, the checkpoint file also allows the user to view the molecular orbitals in GaussView. Additionally, specifications (e.g. basis set, functional, molecular geometries, etc…) can be read from the checkpoint file for future jobs; however, this means the .chk file can get very large (on the order of 100s of mb). Saving .chk files indiscriminately is unadvisable unless you have ample storage space.
Routing information
The routing line of the Gaussian job file begins with the pound/hash # symbol. The letter following the # determines the level of output. The options are #P, #N, & #T which provide verbose, normal, and terse levels of description in the job’s output file. The default option is #N (which can shortened to #). The options that follow are referred to by Gaussian as “keywords” and are responsible for setting up the requested calculation.3
The routing line continues with a method and basis set declaration in single-slash notation. If no options are specified the default method is a Hartree-Fock calculation (HF) using the minimal Slater-type orbital basis functions (STO-3G), given as HF/STO-3G. g16’s built in DFT methods and basis sets are available in the documentation. The choice of functional and basis set are discussed further in a later section.4,5
With the advancement of computational chemistry and the availability of computing resources there is no reason to perform the default HF/STO-3G computation. The most commonly used theory/basis combination in computational organic chemistry is the infamous Becke, 3-parameter, Lee-Yang-Parr (B3LYP) hybrid-exchange correlated functional used in combination with the 6-31g* basis set.
The final required keyword in the routing line is the type of calculation. Typical calculations include geometry optimizations (Opt), vibrational frequency analysis (Freq), single-point molecular energy calculations (SP), NMR shift calculations (NMR), etc… A full list of g16’s computational capabilities can be found here.6 These job keywords can be specified on their own or with various options.
A calculation minimally requires a functional, basis set, and the type of calculation; however, it is usually necessary to specify customizable options such as implicit solvation, temperature (for frequency analysis), initial guesses, counterpoise correction, empirical dispersion correction, extra basis functions, effective core potentials (i.e., pseudopotentials), etc… These options are specified from the routing line using their respective keyword options.3 The full list of Gaussian keywords and their availbe options can be found in the g16 documentation.7
Keywords can be specified in any order. The routing section is fully reproduced in the output file and terminated by a blank line.
Integration grid size
All DFT methods implemented in Gaussian involve a grid-based numerical integration of the functional (or its derivatives). Consequently, the accuracy of a DFT calculation is dependent on the resolution of the integration grid. In Gaussian16 the default integration for all DFT functionals is calculated over a pruned grid with 99 radial shells and 590 angular points, denoted (99,590), and specified by the keyword Integral(grid=ultrafine). This is sufficient for the vast majority of all calculations. Using a smaller grid, while faster, is not recommended for most DFT calculations. Lastly, energy comparisons must be done using the same grid size.4
Job title
The title/comment line is plaintext that is reproduced in the Gaussian output file and terminated by a blank line.
Charge and multiplicity
The charge and multiplicity of the system is given before the molecule specification in standard convention separated by a space. For example, -1 1 describes an anionic singlet state.
Molecule specification
The molecule specification can be given in either standard cartesian (xyz) or internal (Z-matrix) coordinates. Note that specification in one coordinate system or another will not dictate what coordinates will be used to perform the optimization itself which defaults to Gaussian’s redundant internal coordinates, but can be changed by specifying an option in the Opt keyword.
This section may be omitted altogether if reading the start geometry from a pre-existing file (such as a checkpoint (.chk) file) using the geom=checkpoint option.
The molecule specification is terminated by a blank line.
Job/keyword options
Some keyword options require additional input (such as specifying ECPs or additional basis functions). This additional information is placed after the molecule specification and each individual keyword’s specifications are terminated by blank lines.
The input file is terminated by two blank lines.
A simple g16 input file
Below is a fully functional Gaussian input file for a single point molecular energy calculation. Copy + paste it into a text editor and save it as coolMolecule.com and see if you can figure out what we’re trying to do in the next section. (Hint: open it up in your favorite molecular editor/viewer)
%NPROCSHARED=16 ! run on 16 parallel cores
%MEM=28GB ! run with 28 gb memory
%Chk=coolMolecule.chk ! save a checkpoint file
#N M062X/def2tzvp SP ! calculate single-point energy
My cool molecule
0 1 ! neutral singlet
C ! starting geometry for
C 1 B1 ! a molecule specified in
C 2 B2 1 A1 ! gaussian internal coordinates
C 3 B3 2 A2 1 D1 0
C 4 B4 3 A3 2 D2 0 ! to save space bond lengths,
C 1 B5 2 A4 3 D3 0 ! angles, and dihedrals are all
H 3 B6 2 A5 1 D4 0 ! specified as variables
H 2 B7 1 A6 6 D5 0
H 1 B8 6 A7 5 D6 0
H 1 B9 6 A8 5 D7 0
H 4 B10 3 A9 2 D8 0
H 4 B11 3 A10 2 D9 0
H 5 B12 4 A11 3 D10 0 ! g16 doesn't support comments
H 5 B13 4 A12 3 D11 0 ! in the molecule specification
H 6 B14 1 A13 2 D12 0 ! so get rid of these comments
H 6 B15 1 A14 2 D13 0 ! before you try to run this job
H 3 B16 2 A15 1 D14 0
C 2 B17 1 A16 6 D15 0
H 18 B18 2 A17 1 D16 0
H 18 B19 2 A18 1 D17 0
H 18 B20 2 A19 1 D18 0
B1 1.51510600
B2 1.51517951
B3 1.51543497
B4 1.51512522
B5 1.51498514
B6 1.12087116
B7 1.12176819
B8 1.12177478
B9 1.12093060
B10 1.12176062
B11 1.12091101
B12 1.12095758
B13 1.12181557
B14 1.12176019
B15 1.12097986
B16 1.12168148
B17 1.54000000
B18 1.07000000
B19 1.07000000
B20 1.07000000
A1 111.36252447
A2 111.24127560
A3 111.26574203
A4 111.30936835
A5 109.59001104
A6 109.39681635
A7 109.40740597
A8 109.57492433
A9 109.41106707
A10 109.58676541
A11 109.55885178
A12 109.38713435
A13 109.41082787
A14 109.56859847
A15 109.42519797
A16 109.55953690
A17 109.47120255
A18 109.47120255
A19 109.47123134
D1 55.25714299
D2 -55.23663791
D3 -55.19282652
D4 176.59526965
D5 65.84971766
D6 -65.94975705
D7 176.44368868
D8 65.79362957
D9 -176.57422515
D10 176.61579480
D11 -65.80639557
D12 -65.96332262
D13 176.42532586
D14 -65.75731388
D15 -176.56184324
D16 -178.76723016
D17 -58.76721537
D18 61.23277724
SLURM Basics |
My First Gaussian Job |
References
(1) Gaussian input file syntax
(2) Link 0 commands
(3) Gaussian keyword list
(4) DFT methods
(5) Basis sets
(6) Gaussian capabilities
(7) Gaussian16 documentation