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KinBot
https://github.com/zadorlab/kinbot
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Automated reaction pathway search for gas-phase molecules
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### KinBot Fireworks Configuration File Examples Source: https://github.com/zadorlab/kinbot/wiki/Computational-Environment Examples of configuration files used when KinBot integrates with the Fireworks workflow management system. These include `my_qadapter.yaml` for defining queue submission parameters, `my_launchpad.yaml` for MongoDB connection details, and `my_fworker.yaml` for worker setup. ```YAML _fw_name: CommonAdapter _fw_q_type: SLURM rocket_launch: srun -n 8 rlaunch rapidfire --nlaunches infinite nodes: 4 ntasks: 32 cpus_per_task: 1 ntasks_per_node: 8 walltime: '48:00:00' qos: regular job_name: KB_FW pre_rocket: "conda activate kinbot\nmodule load qchem" post_rocket: null ``` ```YAML authsource: KinBot host: mongodb07 logdir: null mongoclient_kwargs: {} name: KinBot password: ************* port: 27017 ssl: false ssl_ca_certs: null ssl_certfile: null ssl_keyfile: null ssl_pem_passphrase: null strm_lvl: WARNING uri_mode: false user_indices: [] username: KinBot_admin wf_user_indices: [] ``` ```YAML ``` -------------------------------- ### Install KinBot using pip Source: https://github.com/zadorlab/kinbot/wiki/Setting-Up-KinBot-on-Your-System This command installs the KinBot package and its required Python dependencies using pip, the Python package installer. It is crucial to have Python 3.8 or higher installed on your system before executing this command for KinBot to function correctly. ```Shell pip install kinbot ``` -------------------------------- ### Install KinBot via PyPI Source: https://github.com/zadorlab/kinbot/blob/master/README.md Install the KinBot package using pip from the Python Package Index. This method requires Python version 3.10 or higher to be installed on your system. ```bash pip install kinbot ``` -------------------------------- ### Install KinBot from GitHub Source Source: https://github.com/zadorlab/kinbot/blob/master/README.md Clone the KinBot project repository from GitHub to obtain the very latest version or to prepare for local modifications. After cloning, navigate into the KinBot directory and install it in editable mode using pip. ```bash git clone git@github.com:zadorlab/KinBot.git ``` ```bash pip install -e . ``` -------------------------------- ### Install KinBot via Conda Source: https://github.com/zadorlab/kinbot/blob/master/README.md Install the KinBot package using the Conda package manager. This command fetches KinBot from the conda-forge channel, ensuring all dependencies are managed automatically. ```bash conda install -c conda-forge kinbot ``` -------------------------------- ### Example KinBot Input Configuration JSON Source: https://github.com/zadorlab/kinbot/wiki/Input-and-Keywords This JSON file serves as the primary input for KinBot, defining all necessary options and parameters for a computational run. It specifies details such as the calculation title, queuing system, charge, multiplicity, quantum chemistry methods (e.g., B3LYP, 6-31+G*), and flags for various search types (e.g., conformer search, reaction search, PES). The 'username' field is a mandatory, user-specific parameter. ```JSON { "title":"pentyl_pes", "queuing" : "slurm", "queue_name" : "normal", "charge" : 0, "mult" : 2, "method" : "b3lyp", "basis" : "6-31+g*", "qc" : "gauss", "conformer_search" : 0, "reaction_search" : 1, "rotor_scan" : 0, "high_level" : 0, "pes" : 1, "barrier_threshold" : 50.0, "ppn" : 4, "username" : "user", "single_point_command" : "molpro -d /scratch/ --mpp -n 4", "single_point_ppn" : 4, "smiles" : "[CH2]CCCC" } ``` -------------------------------- ### Run pes to explore a full Potential Energy Surface (PES) Source: https://github.com/zadorlab/kinbot/wiki/Modes-of-Running:-Kinbot-and-pes This command initiates the exploration of a full Potential Energy Surface (PES) using the 'pes' tool, taking an input JSON file as an argument. When executed, it creates separate subdirectories for each well and runs KinBot within each. If wells have been previously explored, 'pes' should be started from the parent directory, and existing well directories must be renamed to their corresponding chemid. ```Shell pes input.json ``` -------------------------------- ### Visualize All Reactions from a Specific Well Source: https://github.com/zadorlab/kinbot/wiki/The-no-kinbot-mode Displays all reactions originating from a single specified chemical well. This helps in understanding the branching and progression of reactions from a particular starting point in the reaction network. ```Shell pes input.json no-kinbot well [chemid1] ``` -------------------------------- ### KinBot Configuration Parameters Reference Source: https://github.com/zadorlab/kinbot/wiki/Computational-Environment Reference table for KinBot's input parameters, detailing their purpose, default values, and accepted options. These parameters control job submission, resource allocation, file handling, and integration with queuing systems like PBS, SLURM, and Fireworks. ```APIDOC parameter: queuing default: pbs description: 'pbs' or 'slurm' or 'fireworks' or 'local' parameter: scratch default: '' description: Scratch directory of the calculations parameter: username default: '' description: User name, required. parameter: queue_name default: 'medium' description: Queue name where the calculations are submitted to. parameter: queue_template default: '' description: The user can supply a queue submission script. The parameter is the name of the file. For details see below this table. When queuing is set to 'fireworks' a [Fireworks Queue Adapter .yaml file](https://materialsproject.github.io/fireworks/queue_tutorial.html) is expected. parameter: slurm_feature default: '' description: The SLURM feature defined after the -C, see [here](https://slurm.schedmd.com/sbatch.html). parameter: ppn default: 1 description: Number of cores per quantum chemistry calculation, e.g., in Gaussian the number after %nprocshared. parameter: single_point_ppn default: 4 description: Number of cores to run the single-point calculations on. parameter: zf default: 4 description: Number of characters in file numbers. parameter: delete_intermediate_files default: 0 description: Delete chk, py and pbs or sbatch files. Can be useful is disk space is limited. However, care must be taken. If for instance the barrier_threshold is increased, the deleted chk files will prevent the IRC calculations to proceed. Use this keyword wisely. parameter: queue_job_limit default: -1 description: If set to a positive number, no more than queue_job_limit jobs from user username are submitted to the queue. This counts jobs from other KinBot jobs or any other application from the user and it is checked every 30 seconds. In fireworks mode this is the number of jobs submitted to the queue at the beginning of the simulation. parameter: lpad_file default: my_launchpad.yaml description: Only when using Fireworks. File with the necessary configuration to access the MongoDB server to manage FireWorks tasks. See examples below. parameter: fworker_file default: my_fworker.yaml description: Only when using Fireworks. File with the necessary configuration to set up a worker carrying out the FireWorks tasks. See examples below. ``` -------------------------------- ### Run KinBot for Single-Well Exploration Source: https://github.com/zadorlab/kinbot/blob/master/README.md Execute KinBot to perform a single-well exploration. This command requires an input JSON file (e.g., input.json) that defines the parameters for the exploration. ```bash kinbot input.json ``` -------------------------------- ### Run PESViewer with Input File Source: https://github.com/zadorlab/kinbot/wiki/Output This command executes the PESViewer application, using the generated 'pesviewer.inp' file as input. It visualizes the reaction graph, including reactants, products, barrier heights, and energy levels, allowing for interactive manipulation of stationary points and molecule figures. ```Shell pesviewer pesviewer.inp ``` -------------------------------- ### Default KinBot Job Submission Queue Templates Source: https://github.com/zadorlab/kinbot/wiki/Computational-Environment KinBot provides default job submission script templates for PBS and SLURM queuing systems. These templates include directives for job naming, resource allocation (nodes, ppn), queue selection, and output/error file redirection. Users can customize these templates by providing their own file via the `queue_template` keyword, ensuring system-specific commands and environment activations are included. ```Bash #! /bin/bash -f #PBS -N {name} #PBS -l nodes=1:ppn={ppn} #PBS -q {queue_name} #PBS -o {errdir}/$PBS_JOBNAME.stdout #PBS -e {errdir}/$PBS_JOBNAME.err #PBS -m n ``` ```Bash #! /bin/bash -f #SBATCH -N 1 #SBATCH -c {ppn} #SBATCH -q {queue_name} #SBATCH -o {errdir}/{name}.stdout #SBATCH -e {errdir}/{name}.err {slurm_feature} ``` -------------------------------- ### KinBot Internal Molpro Template Source: https://github.com/zadorlab/kinbot/wiki/Quantum-Chemistry This code block shows KinBot's default internal Molpro template used for single-point (L3) energy calculations. It sets up memory, geometry input from XYZ coordinates, defines a UHF wavefunction, specifies basis sets (cc-pvdz-f12 and cc-pvtz-f12), performs CCSD(T)-F12 calculations, and extracts energies into variables. ```Molpro ***,{name} memory,1600,M geomtyp=xyz geometry={{ {natom} {name} {geom} }} {{uhf;wf,{nelectron},1,{spin},{charge}}} basis=cc-pvdz-f12 rhf CCSD(T)-F12 myena(1) = energy(1) myenb(1) = energy(2) basis=cc-pvtz-f12 rhf CCSD(T)-F12 myenergy(2) = energy(1) myenb(2) = energy(2) --- ``` -------------------------------- ### KinBot Quantum Chemistry Input Parameters Source: https://github.com/zadorlab/kinbot/wiki/Quantum-Chemistry This section details the configurable parameters for quantum chemistry calculations within KinBot. Each parameter includes its default value, a description of its purpose, and the quantum chemistry software or calculation type it applies to. Parameters marked with an asterisk (*) cannot be changed upon restart without compromising calculations. ```APIDOC Parameters: - name: qc type: string default: "gauss" description: The quantum chemistry package to use: available ones are 'gauss' for Gaussian, "nwchem" for NWChem and "qchem" for Q-Chem, but currently only Gaussian is supported. applies_to: all - name: methodclass type: string default: "dft" description: Class of methods used, other available values are "mp2" or "scf". applies_to: NWChem - name: qc_command type: string default: "g16" description: Command to run the quantum chemistry code. applies_to: all - name: method type: string default: "b3lyp" description: Low-level (L1) method for reaction and conformational searches. applies_to: all - name: basis type: string default: "6-31G" description: Low-level (L1) basis set for reaction and conformational searches. applies_to: all - name: barrierless_saddle_method type: string default: "b3lyp" description: Low-level (L1) method for the barrierless_saddle family reaction and conformational searches. applies_to: all - name: barrierless_saddle_basis type: string default: "6-31G" description: Low-level (L1) basis set for the barrierless_saddle family reaction and conformational searches. applies_to: all - name: calcall_ts type: number default: 1 description: '1: Use CalcAll in the final optimization of saddle points at the L1 level. It is quite crucial in certain cases to use this setting. 0: do not' applies_to: all - name: high_level_method type: string default: "M062X" description: High-level (L2) method for energy and frequency calculations. applies_to: all - name: high_level_basis type: string default: "6-311++G(d,p)" description: High-level (L2) basis set for energy and frequency calculations. Can be extended with additional keywords like 'EmpiricalDispersion=GD2'. applies_to: all - name: barrierless_saddle_method_high type: string default: "b3lyp" description: High-level (L2) basis set for energy and frequency calculations for the barrierless_saddle family. applies_to: all - name: barrierless_saddle_basis_high type: string default: "6-31G" description: High-level (L2) basis set for energy and frequency calculations for the barrierless_saddle family. applies_to: all - name: integral type: string default: "" description: Integral grid, only used for the high-level (L2) calculations. applies_to: Gaussian - name: opt type: string default: "" description: Convergence threshold in L2 calculations, as in Opt=VeryTight. applies_to: Gaussian - name: irc_maxsteps type: number default: 30 description: Maximum number of steps in IRC calculations. applies_to: all - name: irc_stepsize type: number default: 20 description: Step size in IRC calculations in units of 0.01 Bohr. applies_to: all - name: L3_calc type: number default: 0 description: Turn on or off the generation of L3 input files and the reading of the L3 output files. applies_to: all - name: single_point_qc type: string default: "molpro" description: Code to use for single-point (L3) energies. applies_to: all - name: single_point_template type: string default: "" description: If not specified, the default template is used. The user can specify a path to a modified file. An example is shown below this table. applies_to: all - name: barrierless_saddle_single_point_template type: string default: "" description: Molpro template for the barrierless_saddle family's L3 calculation. The user needs to provide this template, typically a CASPT2 calculation. applies_to: all - name: barrierless_saddle_norbital type: number default: 0 description: Number of active orbitals for the L3 barrierless_saddle calculation. applies_to: all - name: barrierless_saddle_nelectron type: number default: 0 description: Number of electrons in the active orbitals for the L3 barrierless_saddle calculation. applies_to: all - name: barrierless_saddle_nstate type: number default: 0 description: Number of states for the L3 barrierless_saddle calculation. applies_to: all - name: single_point_command type: string default: "" description: Command line string to run Molpro. User should always define this parameter if running single point calculations. If -n option for Molpro is used, the value (i.e. -n 4) should match the single_point_ppn value defined below. applies_to: Molpro - name: single_point_key type: string default: "" description: String to parse when searching for the energy in output. User should always define. applies_to: Molpro - name: barrierless_saddle_single_point_key type: string default: "" description: String to parse when searching for the energy in output for the L3 barrierless_saddle calculation. User should always define. applies_to: Molpro ``` -------------------------------- ### CoriNode YAML Configuration Source: https://github.com/zadorlab/kinbot/wiki/Computational-Environment Defines the core properties for a CoriNode using YAML syntax. It includes the node's unique name, an empty string for its category, and an empty JSON object for any associated queries. ```YAML name: CoriNode category: '' query: '{}' ``` -------------------------------- ### KinBot Input Parameters Reference Source: https://github.com/zadorlab/kinbot/wiki/General Defines the configuration parameters for a KinBot run, specifying their types, default values, and descriptions. It also notes which parameters cannot be altered during a restart without compromising the calculation integrity. ```APIDOC KinBot Configuration Parameters: title: type: string default: N/A description: Title of the KinBot run. Required. restart_changeable: No (implied by 'Required' and core identifier nature) verbose: type: integer default: 0 description: Print verbose information to the log file. restart_changeable: Yes Note: While KinBot is fully restartable, some parameters cannot be changed upon restart without compromising the calculations. These are marked with an asterisk (*). ``` -------------------------------- ### Run KinBot for Full Potential Energy Surface (PES) Search Source: https://github.com/zadorlab/kinbot/blob/master/README.md Execute KinBot to perform a full potential energy surface (PES) search. Similar to single-well exploration, this command also requires a properly formatted input JSON file. ```bash pes input.json ``` -------------------------------- ### MESS Phase Space Theory (PST) Core Definition Source: https://github.com/zadorlab/kinbot/blob/master/kinbot/tpl/readme.txt Configures the core parameters for a Phase Space Theory calculation. This involves defining the geometries of two fragments, a symmetry factor, and potential energy prefactor and exponent. ```APIDOC Core PhaseSpaceTheory FragmentGeometry {natom1} {geom1} FragmentGeometry {natom2} {geom2} SymmetryFactor {symm} PotentialPrefactor[au] {prefact} PotentialPowerExponent {exponent} End ! Core ``` -------------------------------- ### Cite KinBot in Scientific Publications (BibTeX) Source: https://github.com/zadorlab/kinbot/blob/master/README.md BibTeX entries for citing the KinBot software in scientific publications. The first entry is for the 2019/2020 publication on automated stationary point search, and the second for the 2023 publication on automated reaction kinetics. ```BibTeX @article{Vijver2020, author = {Van de Vijver, Ruben and Z\'ador, Judit}, title = {KinBot: Automated stationary point search on potential energy surfaces}, journal = {Comput. Phys. Commun.}, volume = {248}, pages = {106947}, year = {2020}, type = {Journal Article} } ``` ```BibTeX @article{Zador2022, author = {Z\'ador, Judit and Mart\'i, Carles and Van de Vijver, Ruben and Johansen, Sommer L. and Yang, Yoona and Michelsen, Hope A. and Najm, Habib N.}, title = {Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces}, journal = {J. Phys. Chem. A}, volume = {127}, pages = {565-588}, year = {2023}, type = {Journal Article} } ``` -------------------------------- ### KinBot Calculation Parameters Source: https://github.com/zadorlab/kinbot/wiki/Reactant This section outlines the key parameters used to define the initial state and properties for KinBot calculations. Parameters marked with an asterisk (*) are critical and cannot be altered upon restarting a calculation without potentially compromising its integrity. ```APIDOC Parameter: smiles Default: N/A Description: SMILES (Simplified molecular-input line-entry system) of the starting well. Required if no structure is given. Required: Yes Parameter: structure Default: N/A Description: Required if no smiles is given. Structure of the starting well written in one vector in which each atom occupies four consecutive elements: the atom symbol followed by the x, the y and the z Cartesian coordinates of the atom. Required: Yes Parameter: charge Default: 0 Description: Charge of the PES (Potential Energy Surface). Required: Yes Parameter: mult Default: N/A Description: Multiplicity of the PES. 1 is singlet, 2 is doublet, etc. Required: Yes Parameter: bimol Default: 0 Description: Whether or not the starting point is a bimolecular reaction. (under development) Required: Yes Note: While KinBot is fully restartable, some parameters cannot be changed upon restart without compromising the calculations. These are marked with an asterisk (*). ``` -------------------------------- ### KinBot Configuration Parameters Source: https://github.com/zadorlab/kinbot/wiki/Conformational-Search Detailed description of parameters controlling KinBot's computational chemistry functionalities, including conformational analysis, reaction pathway searches, and master equation calculations. Parameters marked with an asterisk (*) cannot be changed upon restart without compromising calculations. ```APIDOC KinBot Parameters: - conformer_search: default: 0 description: '1: perform conformational search, 0: do not.' - conf_grid: default: 3 description: 'The angular grid for dihedrals in the conformational search, angle = 360 / grid.' restart_restricted: true - semi_emp_conformer_search: default: 0 description: 'Whether to carry out a semiempirical optimization prior to L1.' - rotor_scan: default: 0 description: '1: perform 1D hindered rotor scans, 0: do not.' - nrotation: default: 12 description: 'Number of energy evaluations along a 1D hindered rotor scan.' restart_restricted: true - free_rotor_thrs: default: 0.1 description: 'Threshold to consider a rotor free. This is the maximum barrier in kcal/mol.' - plot_hir_profiles: default: 0 description: 'Make figures of the HIR profiles' - me: default: 0 description: '1: automatically run the master equation calculations, 0: do not.' - rotation_restart: default: 3 description: 'Number of hindered internal rotor calculation restarts in case a lower energy point is found along a scan.' - max_dihed: default: 5 description: 'Maximum number of diherals for which exhaustive conformation search is done.' restart_restricted: true - random_conf: default: 500 description: 'Number of random conformers in case no exhaustive search is done.' restart_restricted: true - flat_ring_dih_angle: default: 5.0 description: 'If the dihedral angle between four atoms in a ring are smaller than this value (in degrees), then that section of the ring is considered flat, and is not considered in the ring conformer search algorithm.' restart_restricted: true - multi_conf_tst: default: 0 description: 'Set up a multi-conformer TST calculation, useful for low-temperature, e.g., atmospheric chemistry.' - multi_conf_tst_temp: default: 300 description: 'Temperature (in K) for which the conformers are considered if multi_conf_tst is active.' - multi_conf_tst_boltz: default: 0.05 description: 'Fractional abundance as in exp(-E/RT), where T is multi_conf_tst_temp, above which a conformer is discarded.' - print_conf: default: 0 description: 'If set to 1, KinBot prints the list of unique conformers into the log file. Can take longer on restarts in case of many conformers. If multi_conf_tst is 1, it is always printed. Note that in that case only the ones determined by multi_conf_tst_temp and multi_conf_tst_boltz are considered.' - min_bond_break: default: 2 description: 'In the combinatorial reaction search, this parameter specifies the minimum number of bonds to be broken per reaction.' - max_bond_break: default: 3 description: 'In the combinatorial reaction search, this parameter specifies the maximum number of bonds to be broken per reaction.' - comb_molec: default: 1 description: 'In the combinatorial reaction search, allow for molecular pathways.' - comb_rad: default: 1 description: 'In the combinatorial reaction search, allow for radical pathways.' - comb_lone: default: 1 description: 'In the combinatorial reaction search, allow for reactions involving lone electron pairs.' - comb_pi: default: 1 description: 'In the combinatorial reaction search, allow for reactions involving pi-electrons.' - break_valence: default: 1 description: 'In the combinatorial reaction search, allow for atom valences to be altered.' - one_reaction_comb: default: 0 description: 'Search for a specific reaction using the combinatorial algorithm.' - one_reaction_fam: default: 0 description: 'Search for a specific reactions using the reaction family algorithm.' - ringrange: default: '[3, 9]' description: 'For cyclic transition states search for cycle sizes within this range.' - barrierless_saddle: default: '{}' description: 'Prescribe which bonds to be broken for which species to search for the barrierless_saddle channel in the following form: {chemid1: [[atom1, atom2], [atom3, atom4], ...], [chemid2: [..]]}. In this case for species 1 defined by the chemid two barrierless channels are searched for, the breaking of the atom1 -- atom2 and atom3 -- atom4 bonds. For species 2 further requests can be provided. Note that the family can only be requested once the chemids and the atom numbers are known, such as on a restart.' - barrierless_saddle_start: default: 2.0 description: 'The starting distance for the scan in the barrierless_saddle family in Angstrom.' - imagfreq_threshold: default: 50. description: 'The largest imaginary frequency (need a positive number) that is still accepted as valid for minima. In the master equation the frequency is flipped, and a warning is given in the log file.' ``` -------------------------------- ### KinBot Master Equation Code Configuration Parameters Source: https://github.com/zadorlab/kinbot/wiki/Master-Equation-Calculations This section details the configuration parameters available in KinBot for integrating and controlling master equation codes such as MESS and MESMER. It includes parameters for thermodynamic conditions, energy calculations, and Lennard-Jones potential definitions. Note that some parameters, though not explicitly marked with an asterisk in this table, might be critical for restartability and should not be changed upon restart. ```APIDOC KinBot Master Equation Code Parameters: me_code: string default: "mess" description: Name of the master equation code. Options are 'mess' for MESS and 'mesmer' for MESMER. mess_command: string default: "mess" description: Command to run MESS. (Used with MESS) TemperatureList: number default: 1000 description: List of temperatures. Refer to the MESS manual for details. (Used with MESS) PressureList: number default: 760 description: List of pressures. Refer to the MESS manual for details. (Used with MESS) EnergyStepOverTemperature: number default: 0.2 description: Energy step over temperature. Refer to the MESS manual for details. (Used with MESS) ExcessEnergyOverTemperature: number default: 30 description: Excess energy over temperature. Refer to the MESS manual for details. (Used with MESS) ModelEnergyLimit: number default: 400 description: Model energy limit. Refer to the MESS manual for details. (Used with MESS) CalculationMethod: string default: "direct" description: Calculation method. Refer to the MESS manual for details. (Used with MESS) ChemicalEigenvalueMax: number default: 0.2 description: Maximum chemical eigenvalue. Refer to the MESS manual for details. (Used with MESS) EnergyRelaxationFactor: number default: 200 description: Energy relaxation factor. Refer to the MESS manual for details. (Used with MESS) EnergyRelaxationPower: number default: 0.85 description: Energy relaxation power. Refer to the MESS manual for details. (Used with MESS) EnergyRelaxationExponentCutoff: number default: 15 description: Energy relaxation exponent cutoff. Refer to the MESS manual for details. (Used with MESS) epsilon: number default: 0.0 description: The epsilon parameter from the Lennard-Jones potential in units of epsilon_unit. (Used with MESS) epsilon_unit: string default: "K" description: Unit of the epsilon in the Lennard-Jones potential. Can be 'K', 'cm-1', or 'J/mol'. (Used with MESS) sigma: number default: 0.0 description: The sigma parameter from the Lennard-Jones potential in Angstrom. (Used with MESS) collider: string default: "He" description: The symbol for the collider. Options include 'He', 'N2', 'Ar', 'O2', or 'H2O'. (Used with MESS) mesmer_command: string default: "mesmer" description: Command to run MESMER. (Used with MESMER) ``` -------------------------------- ### Highlight All Pathways Between Two Species Source: https://github.com/zadorlab/kinbot/wiki/The-no-kinbot-mode Identifies and highlights all possible reaction pathways between two specified chemical species (wells or products) identified by their 'chemid's. The output is the 'pesviewer.inp' file, which can be visualized with the PESViewer code. ```Shell pes input.json no-kinbot allpaths [chemid1] [chemid2] ``` -------------------------------- ### Run KinBot for single well exploration Source: https://github.com/zadorlab/kinbot/wiki/Modes-of-Running:-Kinbot-and-pes This command executes the KinBot program. It requires an input JSON file (e.g., input.json) as an argument. The command must be run from the directory where the specified input file is located. ```Shell kinbot input.json ``` -------------------------------- ### Korcek Step 2 Reaction Source: https://github.com/zadorlab/kinbot/wiki/Reaction-Types This describes a generalized Korcek step. The 4-membered ring (2,2 cycloaddition) is not considered as it involves no H shift. The 5-membered ring proceeds through a 6-membered transition state, including a 1,2 H migration. Only the forward direction is included. ```APIDOC --O--O-- | | HO-C---C----C-R ==> RCOOH + R3CC(R)O | / \ | R R R R ``` -------------------------------- ### KinBot Configuration Parameters Source: https://github.com/zadorlab/kinbot/wiki/Request-Actions Defines the various input parameters that control the behavior of KinBot, including reaction search strategies, family selections, bond manipulation, and energy thresholds for reaction termination. Parameters marked with an asterisk (*) cannot be changed upon restart. ```APIDOC KinBot Configuration Parameters:\n parameter: reaction_search\n default: 1\n description: 1: search for reactions, 0: do not.\n parameter: families\n default: ["all"]\n description: List of the reaction types to be used in the reaction search. If ‘all’ is put in the list, all of the families are used. Otherwise it is possible to choose any number from the list underneath this section. Additionally, it is possible to supply 'combinatorial' which searches for reactions in a combinatorial fashion. This leads to a very large number of reaction searches.\n parameter: bimol_families\n default: ["all"]\n description: List of the reaction types to use in the reaction search if the initial species is a bimolecular reaction. If ‘all’ is put in the list, all of the families are used. Otherwise it is possible to choose any number from the list underneath this section. Additionally, it is possible to supply 'combinatorial' which searches for reactions in a combinatorial fashion. This leads to a very large number of reaction searches..\n parameter: skip_families\n default: ["none"]\n description: List of reaction families to skip during a kinbot run.\n parameter: skip_chemids\n default: ["none"]\n description: List of chemids to skip KinBot runs of during PES calculations. If 'none' is put in the list then all of the chemids generated during a PES calculation for KinBot runs will be submitted. Skipped chemids should be entered as strings, e.g., ["842282702691721350181", "842282832261801180571"].\n parameter: keep_chemids\n default: ["none"]\n description: List of chemids to keep and run KinBot for during PES calculations. If 'none' is put in the list then all of the chemids generated during a PES calculation for KinBot runs will be submitted. The selected chemids should be entered as strings, e.g., ["842282702691721350181", "842282832261801180571"]. This mode of calculations is meaningful and useful when an L1 PES is completed, but it is desired to run further calculations on a subset of these wells only.\n parameter: variational\n default: 0\n description: Whether to perform variational calculations for the homolytic scissions.\n parameter: barrierless_saddle\n default: {}\n description: Only break specific bonds in the homolytic search. This is a dictionary written as {chemid1: [[atom1, atom2], [atom3, atom4], ...], [chemid2: [..]]}\n parameter: barrierless_saddle_start *\n default: 2.0\n description: Starting distance for barrierless_saddle search.\n parameter: barrierless_saddle_step *\n default: 0.2\n description: Step size for barrierless_saddle search.\n parameter: homolytic_bonds\n default: {}\n description: For species sp include homolytic scission between atoms a and b (zero-indexed), the syntax is {"chemid of sp": [[a, b]]}. Several species and several bonds per species can be included.\n parameter: specific_reaction\n default: 0\n description: Search for specific reaction in which user defined bonds are broken or formed based on the 'break_bonds' and 'form_bonds' parameters below. Feature is in testing/development.\n parameter: break_bonds\n default: []\n description: Bond between atoms listed will be broken. (ex: [2,5] breaks the bond between atoms 2 and 5.) Atom numbering begins at index 0.\n parameter: form_bonds\n default: []\n description: Bond between atoms listed will be formed. (ex: [3,4] forms the bond between atoms 3 and 4.) Atom numbering begins at index 0.\n parameter: barrier_threshold\n default: none\n description: Maximum electronic energy (i.e., no ZPE is included) in kcal mol<sup>-1</sup> at L1 above which barriers are neglected and the search for products is terminated. One of barrier_threshold or barrier_threshold_L2 needs to be set.\n parameter: barrier_threshold_L2\n default: none\n description: Maximum electronic energy (i.e., no ZPE is included) in kcal mol<sup>-1</sup> at L2 above which barriers are neglected and the search for products is terminated. One of barrier_threshold or barrier_threshold_L2 needs to be set.\n parameter: barrier_threshold_add\n default: 10.\n description: Additional threshold allowance for L1 relative to L2 when barrier_threshold_L2 is set to avoid excluding channels due to L1 uncertainties.\n parameter: hom_sci_threshold_add\n default: 5.0\n description: Additional energy over barrier_threshold specific to barrierless reactions.\n parameter: scan_step\n default: 30\n description: Number of scan points for reaction families where no geometry template is given but rather the TS is searched for via scanning the energy as a function of the bond length of two atoms.\n parameter: pes *\n default: 0\n description: 0: search only for the reactions of the starting well, 1: explore the full multiwell PES.\n parameter: simultaneous_kinbot\n default: 5\n description: Maximum number of simultaneous kinbot runs during a full pes search.\n parameter: high_level\n default: 0\n description: 1: run high-level (L2) optimizations and frequency calculations, 0: the low-level (L1) results are used.\n parameter: calc_aie\n default: 0\n description: 1: run calculations of ionic counterparts to compute Adiabatic Ionization energies, 0: Do not run them. ``` -------------------------------- ### MESS Eckart Tunneling Model Parameters Source: https://github.com/zadorlab/kinbot/blob/master/kinbot/tpl/readme.txt Sets the parameters for the Eckart tunneling correction model. This includes the cutoff energy, the imaginary frequency of the transition state, and the well depths on both sides of the barrier. ```APIDOC Tunneling Eckart CutoffEnergy[kcal/mol] {cutoff} ImaginaryFrequency[1/cm] {imfreq} WellDepth[kcal/mol] {welldepth1} WellDepth[kcal/mol] {welldepth2} End ! Tunneling ``` -------------------------------- ### KinBot Configuration Parameters for VRC-TST and RotdPy Source: https://github.com/zadorlab/kinbot/wiki/Variable-reaction-coordinate-transition-state-theory-(VRC‐TST)-calculations This section details the configuration parameters available in KinBot for controlling Variational Reaction Coordinate Transition State Theory (VRC-TST) calculations, rotdPy inputs, and pivot point procedures. Each parameter's purpose, default value, and expected data type are described. Parameters marked with an asterisk (*) cannot be changed upon restart. ```APIDOC Parameter: vrc_tst_scan Default: {} Description: A dictionary describing the rections to be considered for VRC-TST. The keys are the chemids of the wells for which scans to be made, and the value is a list. Each element of the list is the name of the reaction. E.g., "vrc_tst_scan": {"1022904475485954882032": ["1022904475485954882032_hom_sci_3_14", "1022904475485954882032_hom_sci_5_6"]}. Triggers the automatic calculation of a 1D correction. ``` ```APIDOC Parameter: vrc_tst_noscan Default: {} Description: Same as vrc_tst_scan except that it does not trigger the calculation of a 1D correction. Only optimize fragments at the sampling level and calculate the asymptotic energy before creating a rotdPy input. ``` ```APIDOC Parameter: vrc_tst_scan_method Default: "ub3lyp" Description: Level of theory for optimizing the separated fragments and the geometries along the scan coordinate. ``` ```APIDOC Parameter: vrc_tst_scan_basis Default: "6-31+G(d)" Description: Basis set for optimizing the separated fragments and the geometries along the scan coordinate. ``` ```APIDOC Parameter: vrc_tst_active_space Default: "minimal" Description: Active space for CAS calculation, can be "minimal", '"automatic"' or the user can provide a list of two values, the number of active electrons and orbitals, respectively. ``` ```APIDOC Parameter: vrc_tst_scan_points Default: [[2.5, 20.0, 0.2]] Description: List of distances in units of Angstrom for the scan. Distances can be provided as an explicit flat list, or as a nested list, where each element defines the start, end, and stepsize. If more than one elements are present in the nested list, their union is used. ``` ```APIDOC Parameter: vrc_tst_scan_molpro_key Default: [] Description: The list of keys to read the Molpro results. ``` ```APIDOC Parameter: vrc_tst_scan_molpro_tpl Default: "" Description: Molpro template for the correction potential. ``` ```APIDOC Parameter: vrc_tst_scan_deviation Default: 100.0 Description: RMSD value to prevent too sudden reorientation along scanned bond. ``` ```APIDOC Parameter: vts_ang_dev Default: 10 Description: Maximum change (in degree) in inter-fragment angles and dihedrals across two points along the 1D correction. ``` ```APIDOC Parameter: rotdPy_inputs Default: None Description: Creates the RotdPy inputs for barrierless reactions. The argument must be a dictionary. Key: Chemid of the KinBot well. Value: List containing two strings. The first string is the name of a reaction instance (or TS name), while the second is the name of the bimolecular product (as found in the KinBot summary file). ``` ```APIDOC Parameter: rotdPy_mem Default: 300 Description: Amount (Mb) of memory to use in rotdPy for each job during the sampling. ``` ```APIDOC Parameter: rotdpy_dist Default: [2.2,2.4,...12.8, 13.0, 13.5, ...,15.5, 16.0] Description: List of distances used for the VRC TST surfaces in rotdPy. ``` ```APIDOC Parameter: pp_oriented Default: [1.5, 6] Description: Bracket of distances (Angstrom) for which to use the internal pp_oriented procedure. Geometric placement of pivot points is automatic and depends on the valence of the reactive atoms. ``` ```APIDOC Parameter: pp_length Default: {"H": [0.1], "O": [0.1], "N": [0.1], "C":[0.1]} Description: Distances (in Bohr) between the pivot point and the atom used to define the reaction coordinate during the pp_oriented procedure. ``` ```APIDOC Parameter: pp_on_atom Default: [5.0, 12.0] Description: Bracket of distances (Angstrom) for which to use the internal pp_on_atom procedure. Should overlap with pp_oriented distances. ``` ```APIDOC Parameter: pp_on_COM Default: 10.0 Description: Minimum distance (in Angstrom) from which to place a single pivot point on the center of mass of each fragment. Should overlap with pp_on_atom distances. ``` -------------------------------- ### MESS Two-Transition State (2TS) Method Definition Source: https://github.com/zadorlab/kinbot/blob/master/kinbot/tpl/readme.txt Specifies a statistical Two-Transition State method. It references an outer transition state, which can be defined using either the RRHO or Phase Space Theory models, potentially without tunneling. ```APIDOC 2TSMethod statistical {outerts} ==> can be mess_rrho (repeated if needed, but no tunneling) or mess_phasespacetheory ``` -------------------------------- ### MESS Input Parameters for Uncertainty Analysis and Barrierless Reactions Source: https://github.com/zadorlab/kinbot/wiki/Uncertainty-Quantification This table lists KinBot input parameters used to configure Uncertainty Analysis and barrierless reaction channels for MESS calculations. Parameters marked with an asterisk (*) cannot be changed upon restart without compromising calculations. ```APIDOC | parameter | default | description | use with... | |---|---|---|---| |`uq` |0 | Turns on (0)/ off (1) Uncertainty Analysis feature. |MESS | |`uq_n` |100 |Number of MESS input files generated/number of iterations of MESS calculations |MESS | |`uq_max_runs`|5|Maximum number of MESS calculations submitted to the queue at once|MESS| |`well_uq`|0.5|Uncertainty in stable intermediate energy, +/- 0.5 kcal/mol|MESS| |`barrier_uq`|1.0|Uncertainty in saddle point (TS) energy, +/- 1.0 kcal/mol|MESS| |`freq_uq`|1.2|Uncertainty harmonic positive frequencies, factor of 1.2 corresponds to values ranging from 0.833 to 1.2 times the original frequency. Scaling is exact for 100 1/cm, and is larger for smaller and smaller for larger frequencies. Same quantity is used for the hindered rotor uncertainties.|MESS| |`imagfreq_uq`|1.1|Uncertainty in imaginary frequency, factor of 1.1 corresponds to values ranging from 0.909 to 1.1 times the original frequency.|MESS| |`epsilon_uq`|1.2|Multiplicative uncertainty factor of the epsilon Lennard-Jones parameter.|MESS| |`sigma_uq`|1.2|Multiplicative uncertainty factor of the sigma Lennard-Jones parameter.|MESS| |`erelfact_uq`|1.2|Multiplicative uncertainty factor of the energy relaxation preexponential factor.|MESS| |`enrelpow_uq`|1.2|Multiplicative uncertainty factor of the energy relaxation power.|MESS| |`barrierless_rxn`|0|Whether or not you want to include barrierless channels in your MESS input file|MESS| |`barrierless_template`|''|Name of the barrierless template file, which holds the barrierless block needed for MESS. See the `barrierless_mess.tpl` file in the `tpl` directory.|MESS| |`barrierless_prod_template`|''|Name of the barrierless product template file, which holds the barrierless product block needed for MESS. See the `barrierless_prod_mess.tpl` file in the `tpl` directory.|MESS| |`barrierless_energy`|0.|Energy of the barrierless step of the reaction.|MESS| |`barrierless_states_file`|''|Name of the barrierless states file, which holds the state information for the barrierless step. See the `mc_flux.out` file in the `tpl` directory.|MESS| ``` -------------------------------- ### Intra R Migration Source: https://github.com/zadorlab/kinbot/wiki/Reaction-Types This class covers several RMG classes. R cannot be an H, as that is handled by intra_H_migration. Currently, it only moves atoms to radical sites. ```APIDOC Description of R migration to radical sites. ``` -------------------------------- ### 12_shift_S_R Source: https://github.com/zadorlab/kinbot/wiki/Reaction-Types This is an RMG class. TODO: why not forward?? ```APIDOC C-S-R* <== *S-R-C ``` -------------------------------- ### Filter Pathways by Branching Fraction at Temperature Source: https://github.com/zadorlab/kinbot/wiki/The-no-kinbot-mode Selects reaction pathways with a branching fraction of 1% or more for a particular well at a given temperature (in Kelvin). The search iteratively expands the network based on sufficient branching fractions from the previous iteration. ```Shell pes input.json no-kinbot temperature [temperature] ``` -------------------------------- ### R_Addition_MultipleBond Source: https://github.com/zadorlab/kinbot/wiki/Reaction-Types This is an RMG class. Note: only the reverse direction is available. ```APIDOC R=R + R* <== R*-R-R ``` -------------------------------- ### Intra OH Migration Source: https://github.com/zadorlab/kinbot/wiki/Reaction-Types This is an RMG class. It finds all unique cases for ring sizes between 3 and 9. ```APIDOC R*~~~~~~~O-OH <==> HOR~~~~~~~O* ``` -------------------------------- ### MESS Core Rigid Rotor Parameters Source: https://github.com/zadorlab/kinbot/blob/master/kinbot/tpl/readme.txt Defines the core parameters for a Rigid Rotor model within MESS. Its primary function is to specify the symmetry factor for the molecular system. ```APIDOC Core RigidRotor SymmetryFactor {symm} End ! Core ``` -------------------------------- ### r14_cyclic_birad_scission_R Source: https://github.com/zadorlab/kinbot/wiki/Reaction-Types This is an RMG class. TODO forward? ```APIDOC R1-R*~~~~~~R*-R2 <== R1=R~~~~~~R=R2 |______________| ``` -------------------------------- ### Cyclic Ether Formation Source: https://github.com/zadorlab/kinbot/wiki/Reaction-Types This is an RMG class. It finds all unique cases for ring sizes between 3 and 9. The OR groups are not counted in the cycle size but must be present. Only the forward direction is included. ```APIDOC R*~~~~~~~O-OR ==> R~~~~~~~O + OR |_______| ``` -------------------------------- ### barrierless_saddle Source: https://github.com/zadorlab/kinbot/wiki/Reaction-Types This is not an RMG class. Attempts to find a saddle point for a nominally barrierless reaction. ```APIDOC R - R ==> R + R ``` -------------------------------- ### R_Addition_COm3_R Source: https://github.com/zadorlab/kinbot/wiki/Reaction-Types This is an RMG class. Note: only the reverse direction is available. ```APIDOC C#O + R* <== R-C*=O ```
