Templating in ESIgen¶

Builtin templates¶

Some templates are included with ESIgen for your convenience:

default.md. Uses an interactive 3D viewer in the web interface and static images on the command line. A table of magnitudes is provided, together with the coordinates and, if available, first 10 frequencies.
TD.md. Same as default, but listing the excitation energies of TD calculations.
simple.md. Dummy example to help illustrate easy templating.
chemshell.md. Shows experimental support for some ChemShell QM/MM jobs.
checks.md. Day-to-day analysis tasks for Gaussian jobs.

However, you might want to modify them or create your own from scratch. Keep reading for further details.

Syntax¶

ESIgen templates are written using **Markdown** (a subset of HTML designed to be highly readable) syntax on top of the wonderful **Jinja2** engine, which allows easy keyword replacing. For example:

# {{ name }}

- Stoichiometry: {{ stoichiometry }}
- Electronic Energy (eV): {{ electronic_energy }}

, which results in something like this:

heme_fe2singlet_fe3doublet¶

Stoichiometry: C34H30FeN4O4(1-,2)
Electronic Energy (eV): -1957.86428957

As you see, you just write normal Markdown (syntax is described here) and then insert the desired variables between double curly braces, like this {{ energy }}. Jinja2 also supports for loops, if conditionals and so on, but you won’t probably need it. However, one of the advanced features might be helpful: filters, which allow you to post-process some values (ie, centering with respect to a fixed width with {{ value|center(20) }}).

Data Fields¶

All fields provided by cclib parsers are available. Simply refer to the official documentation on Parsed Data and Parsed Data Notes to check the full list and the compatibility matrix across different programs.

Additionally, ESIgen provides some more fields and methods you can use during the templating:

Features
- {{ name }}: Extracted from the filename, without the extension.
- {{ filename }}: Filename, with extension.
- {{ filepath }}: Full path to the file.
- {{ stoichiometry }}. Self-explanatory.
- {{ imaginary_freqs }}: Number of negative frequencies.
- {{ mean_of_electrons }}: Mean of alphaelectrons and betaelectrons.
- {{ metadata['route'] }}: First of Gaussian route sections. For other programs, check metadata.
- {{ nsteps }}: Number of optimization steps. Extracted from scfenergies size.
- {{ solvent }}. Solvent chosen, if applicable. (Gaussian only).
- ModRedundant scans (Gaussian only, might change anytime; see checks.md for an example):
  - {{ modredvars }}: List of variables being scanned (R83, A21, D125…).
  - {{ modreddefs }}: Atomic definition of those variables (2 atoms for R, 3 for A, 4 for D)
  - {{ modredvalues }}: (m, n) array for variable values (distance in A, angle in degrees), where m is the number of cycles and n the number of variables.
  - {{ modredenergies }}: (j, k, l) array of -dE/dx values, where j is the number of cycles, k the number of iteration at each cycle and l the number of variables being scanned.
Magnitudes (Gaussian only)
- {{ electronic_energy }}. Last of scfenergies, Eh.
- {{ thermalenergy }}: Sum of electronic and thermal energies, Eh.
- {{ zeropointenergy }}: Sum of electronic and zero-point energies, Eh.
Structural info
- {{ viewer3d }}: Insert interactive 3D depiction of the structure. Only available in web UI.
- {{ image }}: Static depiction of the structure. Requires PyMol (not available on public demo!)
- {{ cartesians }}: Molecule structure exported in XYZ format.
Functions
- {{ convertor(value, from_unit, to_unit) }} can be used to change units in most cases. Check here for supported constants. If not, you can always use normal math inside the curly braces ({{ (10+value)**2 }}).
Experimental support for QM/MM jobs in ChemShell (might change anytime; see chemshell.md template for an example)
- {{ scfenergies }}: Lists “QM/MM energy” entries.
- {{ mmenergies }}: List of dicts which detail MM energy decomposition for each cycle.
- {{ energycontributions }}: List of dicts which detail QM/MM energy decomposition for each cycle.
- {{ optdone }}: True if optimization converged (only available with Turbomole backend).

Note

Depending on the software used to create the output file, some fields might not be available. When in doubt, you can check the JSON dump of the files by appending /json to the report URL (a link is also available in the bottom of the page). This will list all the attributes available for each file. (JSON dumps are best viewed in Firefox 57+).

Missing Values¶

An additional flag missing is passed to the template to control what to report when the requested field is missing in the file. By default, in the WebUI, maximum length is restricted to 10 chars.

In the default.md template, missing is checked in every row to control if the row should be written or not. If missing is set to the empty string '' (default value) and the value is not present in the file, the row won’t be written; if missing is set to any other string (for example, N/A) and the value is not present, the row will be written but the value will be reported as N/A.

For example, if stoichiometry is not available in the file:

Case A: missing = ''

# TDNI_GGCMPW

__Requested operations__

`p td=(nstates=30) MPW1PW91 scrf=(solvent=water) geom=connectivity def2tzvp`

__Relevant magnitudes__

| Datum                                            | Value                     |
|:-------------------------------------------------|--------------------------:|
| Charge                                           |             -2            |
| Multiplicity                                     |             1             |
| Stoichiometry                                    |      C7H9N3NiO4S(2-)      |
| Number of Basis Functions                        |            570            |
| Electronic Energy (eV)                           |    -2644.5302088499993    |
| Mean of alpha and beta Electrons                 |             75            |

Case B: missing = 'N/A', default

# TDNI_GGCMPW

__Requested operations__

`p td=(nstates=30) MPW1PW91 scrf=(solvent=water) geom=connectivity def2tzvp`

__Relevant magnitudes__

| Datum                                            | Value                     |
|:-------------------------------------------------|--------------------------:|
| Charge                                           |             -2            |
| Multiplicity                                     |             1             |
| Stoichiometry                                    |      C7H9N3NiO4S(2-)      |
| Number of Basis Functions                        |            570            |
| Electronic Energy (Eh)                           |    -2644.5302088499993    |
| Sum of electronic and zero-point Energies (Eh)   |            N/A            |
| Sum of electronic and thermal Energies (Eh)      |            N/A            |
| Sum of electronic and thermal Enthalpies (Eh)    |            N/A            |
| Sum of electronic and thermal Free Energies (Eh) |            N/A            |
| Number of Imaginary Frequencies                  |            N/A            |
| Mean of alpha and beta Electrons                 |             75            |