Examples
This page shows compact, current input patterns. Use them as starting points, then adapt levels of theory, software routing, and server settings to your site.
Minimal Species Thermochemistry
project: ethanol_thermo
species:
- label: ethanol
smiles: CCO
level_of_theory: wb97xd/def2svp
ess_settings:
gaussian: local
This asks ARC to use the default job types, which include conformer optimization, optimization, fine-grid optimization, frequency, single-point, rotor, and IRC where applicable.
Several Species and Coordinate Formats
project: species_inputs
ess_settings:
gaussian:
- local
- server1
orca: local
job_types:
conf_opt: true
opt: true
fine: true
freq: true
sp: true
rotors: true
level_of_theory: CCSD(T)-F12/cc-pVTZ-F12//wb97xd/def2tzvp
species:
- label: propane
smiles: CCC
- label: propanol
inchi: InChI=1S/C3H8O/c1-2-3-4/h4H,2-3H2,1H3
- label: vinoxy
xyz: |
O 1.35170118 -1.00275231 -0.48283333
C -0.67437022 0.01989281 0.16029161
C 0.62797113 -0.03193934 -0.15151370
H -1.14812497 0.95492850 0.42742905
H -1.27300665 -0.88397696 0.14797321
H 1.11582953 0.94384729 -0.10134685
Reaction with a TS Guess
This is a reaction-definition fragment. Add level_of_theory and
ess_settings for the ESS you intend to use before running it.
project: reaction_demo
species:
- label: N2H4
smiles: NN
- label: NH
smiles: '[NH]'
- label: N2H3
smiles: N[NH]
- label: NH2
smiles: '[NH2]'
reactions:
- label: N2H4 + NH <=> N2H3 + NH2
ts_xyz_guess:
- |
N -0.4465194713 0.6830090994 -0.0932618217
H -0.4573825998 1.1483344874 0.8104886823
H 0.6773598975 0.3820642106 -0.2197000290
N -1.2239012380 -0.4695695875 -0.0069891203
H -1.8039356973 -0.5112019151 0.8166872835
H -1.7837217777 -0.5685801608 -0.8405154279
N 1.9039017235 -0.1568337145 -0.0766247796
H 1.7333130781 -0.8468572038 0.6711695415
Transition-State Species
Use is_ts: true when the species entry itself is a transition state:
This example is a fragment; add ess_settings for your configured ESS before
running it.
project: ts_opt
level_of_theory: apfd/def2TZVPP
freq_scale_factor: 0.992
species:
- label: TS1
is_ts: true
multiplicity: 2
xyz:
- TS1/guess_1.gjf
- TS1/guess_2.gjf
- TS1/guess_3.gjf
ARC can read coordinate guesses from multiline XYZ strings, XYZ files, Gaussian input files, and supported ESS output files.
Python API
from arc import ARC
from arc.species import ARCSpecies
from arc.reaction import ARCReaction
n2h4 = ARCSpecies(label='N2H4', smiles='NN')
nh = ARCSpecies(label='NH', smiles='[NH]')
n2h3 = ARCSpecies(label='N2H3', smiles='N[NH]')
nh2 = ARCSpecies(label='NH2', smiles='[NH2]')
reaction = ARCReaction(
label='N2H4 + NH <=> N2H3 + NH2',
r_species=[n2h4, nh],
p_species=[n2h3, nh2],
)
arc = ARC(
project='api_reaction_demo',
species=[n2h4, nh, n2h3, nh2],
reactions=[reaction],
job_types={
'conf_opt': True,
'opt': True,
'fine': True,
'freq': True,
'sp': True,
'rotors': True,
},
level_of_theory='wb97xd/def2svp',
ess_settings={'gaussian': 'local'},
)
arc.execute()
Use ARCSpecies for species definitions, ARCReaction for reactions, and
ARC for project execution. The same keyword names used in YAML are generally
accepted by the Python API.
Job-Type Shortcuts
To run only one job family, use specific_job_type:
This example is a fragment; add level_of_theory and ess_settings before
running it.
project: bde_demo
specific_job_type: bde
species:
- label: ethanol
smiles: CCO
For BDE workflows, ARC automatically enables the supporting optimization, fine-grid, frequency, and single-point jobs required by the workflow.
Where to Find More Inputs
The repository includes more examples and fixtures:
examples- maintained YAML examples for minimal, stationary-species, reaction, BDE, TS, and developer/mock workflows;ipython/Demo- tutorial notebooks and YAML examples;ipython/Tools- notebook tools that exercise ARC utilities;arc/testing/yml_testing- YAML fixtures used by tests;arc/testing/restart- restart-file examples.