The AutoTS Output File
The output file (jobname.out) prints various messages about the program flow as well as useful data. It is the first place to look to find out exactly what happened during the calculation. The bottom of the output file of a complete calculation either contains an error message or summarizes the transition states found. If the calculation was fully successful there is a table that summarizes the individual reactions in a possibly multi-step process. This table contains energetic information as well as whether or not the connection between reactant-TS-product was verified by an IRC calculation. Following this is a diagram that visually summarizes the results. Examples of these tables and diagrams are given at the end of this topic.
The output file of a successful AutoTS calculation is described and discussed in detail below.
At the top of the file there is a table summarizing the launch of the calculation. This allows you to quickly establish how and where this calculation was run and with what executable.
============================================================================
AutoTS
============================================================================
Version: 2015-4
Start time: Wed Jul 8 22:33:27 2015
$SCHRODINGER: /nfs/working/builds/NB/2015-4/2015-07-08
Launch Host: nyc-desk-l48.schrodinger.com
Launch Directory: /scr/jacobson/sample
Running on Host: bob-0-110.local
Run Directory: /scr/jacobson/sample
Command Line: $SCHRODINGER/jaguar run AutoTS.py -jobname sample -PARALLEL 4
============================================================================
Following this, there is some text indicating that the code is preparing the reaction complexes. Once the atoms have been renumbered and complexes formed, an optimization of the reactant and product complexes is typically performed (controlled by the keyword optimize_inputs). The output file logs some details of the calculations.
JobId: nyc-desk-l48-0-559da508 Processing the following subjobs: (1) jaguar run -TPP 2 sample.in (2) jaguar run -TPP 2 sample.in Timer (optimization) : 24335.458484 s
Since optimization sometimes significantly alters the geometry of the reactants and products, the internal geometries are then aligned in an attempt to remove motion that is unimportant for the reaction to occur. Once aligned, either a linear interpolation between reactants and products is performed, or a TS geometry is guessed using a template. Either way, the initial TS guess is optimized, and following this a TS vetting analysis is performed. This analysis ensures that the optimized TS geometry is reasonable in that the geometry contains at least one active bond (breaking or forming) at an intermediate distance, possesses one imaginary vibrational frequency, and the corresponding transition vector involves active atoms.
Optimizing TS guess ================================================== Executing 1 distributed subjobs: --------------------------------- No more than 4 cpu(s) will be used simultaneously. Processing the following subjobs: (1) jaguar run sample_qst.in -TPP 4 Timer (distribute subjobs) : 18189.23 secs Inspecting quality of TS frequencies ================================================== Number of Negative Frequencies 1 Frequency 1 = -85.10 Vibrational mode has been vetted
If this step is unsuccessful there is a terse statement about an attempt to improve the guess followed by additional TS search calculations. If the QST and vetting analysis were successful then a TS geometry has been found and verified. Next, an IRC calculation is performed to find the minimum energy geometries at the bottom of the potential energy hill on both sides of the TS. The geometries at the minima (endpoints) are compared to the input geometries and a brief statement about which structures are the same is printed.
Run IRC job JobId: nyc-desk-l48-0-559da50c Processing the following subjobs: (1) jaguar run -TPP 4 sample_irc.in Timer (irc) : 50222.457886 secs IRC matched both reactant and product
At this point, if there are additional calculations (because the IRC endpoints failed to match at least one of the endpoints) a new path is constructed in order to find additional transition states. This process is repeated until all structures are connected by a TS or the program fails to find a connection. If no additional matches are found, a few energy corrections are performed and the results are printed. By default the program estimates the energy of the critical points (reactant, product, TS and intermediates) along the reaction at infinite separation as well as the complex energy. This latter energy is that of the reaction complexes. To estimate the energy at infinite separation, each individual molecule is extracted from the reaction and product complexes and separate optimizations are performed. In order to do this the charge and multiplicity for each molecule must be set separately. To define these values, a search in the input structures is done for the properties i_j_Molecular_charge and i_j_Spin_multiplicity. If these properties exist and the extracted molecules are conformers of the input, these settings are used. Otherwise, Mulliken charges from the calculations are used. If Mulliken charges are not available, an xTB calculation is run to determine charge and spin populations. If none of these methods succeed, the properties are guessed.
When free energy calculations are requested, the standard state for the reported Gibbs free energies depends on the solvent model. For calculations using an implicit solvent model, free energies are reported at standard concentration (1 M). For gas-phase calculations, free energies are reported at standard pressure (1 atm). Kinetics tables always use standard concentration free energies regardless of the solvent model.
Finally the results are summarized in tables. Below is an example of a very complex summary table for a multi-step reaction.
----------------------------------------------------------------------------------------------------
Final Reaction Results
Complex Energy (kcal/mol)
----------------------------------------------------------------------------------------------------
Rxn Er Ep Ets Rxn E Act E frequency Confirmed by IRC? Path number
1 0.00 33.89 52.11 33.89 52.11 -791.41 True 1
2 33.89 64.08 82.18 30.19 48.29 -381.61 True 3
3 64.08 23.95 None None None None Unconnected None
4 23.95 23.77 24.26 -0.18 0.31 -596.70 True 0
5 23.77 -5.86 None None None None Unconnected None
----------------------------------------------------------------------------------------------------
Each entry in this table is a reaction and the energetics are given. Additionally if a TS is available for the reaction the frequency is given as well as whether or not it is connected and which path it is associated with. The calculations for this TS will be found in the directory jobname_path_path-number. If a TS does not appear then AutoTS was unable to find a TS connecting the two minima appearing in that row. After these tables are printed an ASCII diagram is printed which visually presents these data. Below is an example of a two step reaction (not the one in the table above).
11.82
/-------\
/
\
/
/ 6.13
\ /-------\
/
/ \
/ \
/ \
/
/ \
0.00 \
-------/
/ \
\ / \
/ \
\
/ \
/ -8.10
\-------
-9.41
\-------/
If a connection was not made the minima are still printed but no lines connect them to a TS.
The AutoTS HTML Report
In addition to the output file, AutoTS writes an HTML report named jobname_report.html. This report complements the output file by summarizing the key results on a single page. You can open the report in any web browser. You can also open it from Maestro by choosing View AutoTS Results from the Workflow Action Menu for the entry, as described in AutoTS: Perform Calculations Panel.
The report contains the following information:
- A summary of the calculation, including the job name, the user, the date, the software release, the host, the wall time, the completion status, and the command line used to run the job.
- The level of theory, such as the functional and basis set, the machine learning force field, or the semiempirical method used, together with whether the calculation was run in the gas phase or in solution.
- A reaction energy profile that plots the energy along the reaction path, with 2D structures of the reactants, products, and intermediates, and an accompanying table of the energies. You can choose which type of energy to plot.
- The imaginary vibrational modes of each transition state. Both the number of imaginary modes and their frequencies are reported. A well-behaved transition state has a single imaginary mode, but additional small imaginary modes are sometimes present.
- Rate constants for each reaction step, reported when free energies are computed.
- The input and output files for the calculation, embedded in the report so that it is self-contained.