HRG:HuntResearchGRoup

Hunt Research Group Wiki

Report and Paper Writing

1. procedures link
2. advice link
3. report components link
4. files to provide when writing a paper link

Data Base

1. File naming on the database link
2. Database xlsx instructions and template link
3. Database CREST and xlsx instructions and template link

Methodology

1. Preferred Methodology link
2. Basis sets link

Key Papers

1. Best-Practice Protocols for choosing method and basis doi
2. Status and Challenges of Density Functional Theory doi
3. Meta study on DFT functionals doi
4. Molecular Geometry is relatively insensitive to basis set doi
5. Scale factors for vibrational frequencies DFT doi and MP2 doi
6. M06 suite of DFT functionals doi
7. SMD for ILs doi
8. Box size for MD simulations of ILs doi

HPC Resources

1. Getting started and introduction to the HPC: link
2. Running jobs on the HPC Raapoi: link
3. Running jobs on the HPC Raapoi with sub script (Muhammad): link
4. Running jobs on the HPC NeSI: link
5. How much memory (and disk) to use: link
6. How to start an interactive session: link
7. How to set-up access from your desktop to the hpc link
8. How to use cloud storage resources link

Using Windows PCs

1. use MobaXTerm link
2. use Putty link
3. very basic using a Terminal on a Windows PC external link
4. install a Linux distribution link
5. How to fix Windows files under UNIX link

Tips and Tricks

1. Tired of entering your password all the time: set up a SSH keypair link
2. How to make ssh more comfortable link
3. How to comfortably search through old BASH commands link
4. A terminal emulator capable of splitting into multiple screens link
5. module command not working or giving error "bad argument" link

Gaussian General

1. We are starting a database of common errors encountered when running Gaussian jobs link
2. Here is an already existing database of common errors link
3. beginners starting from a chemdraw structure link
4. optimisation errors and problems link
5. partial optimisations and scans link
6. general procedure for locating transition state structures link
7. problems with scf convergence link
8. Population and charge analysis link

Gaussian Advanced

1. basic ONIOM (Mechanical Embedding) link
2. how to run at a higher temperature link
3. correcting the entropy due to low modes link
4. generating natural transition orbitals link
5. computing excited state polarisabilities link
6. dipoles in Gaussian link
7. molecules in an electric field link
8. computing deuterated and/or anharmonic spectra link
9. for NMR calculations look here: Chemical Shift Repository
10. old:systematic conformational scan for ion-pair dimers link
11. old: optimisation of charged molecules in an electric field link
12. old: multidimensional Scans of Internal Coordinates link

Solvation

1. Atomic radii link
2. Using the SMD model link
3. Molecular volume calculations link
4. The cavity link
5. How to download and use GeomView to visualise solvation cavities link
6. Surfaces (Solvent-Accessible and Connolly) in Jmol link
7. Using SMD on ILs link
8. Troublesome optimisations in SMD link

QC Visualisation

1. Using AIMALL: density based visualisation
   1. download AIMALL
   2. once downloaded and installed you need to send tricia your aimall-serialnumber.txt file, and she will arrange for a aimallpro.lic or license file for you
   3. basic instructions link
   4. AimAll volume / surface area calculations link
   5. AimAll with pseudo potentials link
   6. AIMAll 19.10.12 on iMacs link
2. FCHK and CUBE files and manipulation
   1. creating formatted checkpoint files link
   2. generating and manipulating cube files link
   3. Format of cube files link
3. ESPs files and analysis
   1. Instructions for visualizing electrostatic potentials (Gaussview)link
   2. Electrostatic Potentials II (Molden) link
   3. Using A. Stone's distributed multipole analysis link
   4. Finding sigma hole (Vs,max and Vs,min values) using Multiwfn link
4. NCI Plots
   1. How to install NCIPlot on your mac link
   2. Using NCIPlot link
5. Using Multiwfn: density based visualisation
   1. Download Multiwfn link
   2. Installation of Multiwfn on Mac link
   3. Using MP2 Densities in Multiwfn Surface Analysis link
   4. Generate BCPs link
6. Jmol Visualisations
   1. Jmol basics link
   2. Visualising MOs using Jmol link
   3. Visualising vibrations using Jmol link
   4. Using Jmol to make a structure animation link
   5. Jmol movie script link
   6. Using Jmol to overlap structures link
7. VMD: a molecular dynamics visualisation package
   1. VMD can be installed from the VMD downloads page
   2. Quick reminder link
   3. Colour in VMD link
   4. Changing the graphical representation of your structures link
   5. VMD indexing link
   6. Using scripts in VMD link
   7. Instructions for how to extract geometry and charges (ESP) into a .pdb file for visualising in VMD, especially if you want a blue-red colour variation rather than gaussviews red-greeen link
   8. Dealing with periodic boundaries and bonding (under construction) link
   9. Dealing with bonding (under construction) link
   10. How to turn a Gaussian optimization into a VMD movie link
   11. Overlapping two structures link

ORCA

1. This section is about using ORCA 6.1 on the HPC (Raapoi) link
2. Installing on a mac link
3. Running ORCA link
4. Using different basis sets and pseudopotentials for heavy elements in ORCA link
5. Plotting MOs with ORCA in GaussView format link
6. Visualize ORCA output files in GaussView link
7. Using Custom Solvent Parameters in ORCA link
8. Memory Specification in ORCA link
9. Using GOAT for global minimum and/or conformer search link

Other Programes

1. CREST link
2. ABCluster conformational search of atomic and molecular clusters link
3. MD programs and instructions link
4. ADF Submission script link
5. POLYRATE how to install link
6. Psi4 and running SAPT calculations link
7. LDdecomposition (London Dispersion decomposition) link
8. SpectroIBIS WINDOWS spectral data processing https://github.com/bbulcock/SpectroIBIS
9. MultiWfn WINDOWS density/ESP analysis http://sobereva.com/multiwfn/

Coding

1. installing Xcode and other programming environments
   1. to use many programs you will need a compiler, this is not installed by default on your mac
   2. How to install Xcode on your mac link
   3. using MacPorts as code for managing other codes on your mac link
   4. HomeBrew and Fink are other options (HomeBrew is not advised for us)
   5. Runing windows codes using wine link
   6. gfortran on your mac link
   7. using python on your mac link
2. Ling's EMO Code link
3. Jan's charge based analysis Code link
4. Oxana's visualisation of ESPs Code link
5. Richard M's Calculate pDoS/XP spectra code link
6. Becky's script to extract frequency data from gaussian .log files and generate vibrational spectra link

Python scripts

Intro

• note: scripts with "D" in front are those made to run on groups of files

they can be for when you have a large number of files from a crest run

they can be for use within a single directory, running on all files in that directory

made to be used with a set of specific gaussian log files, Tricia's ones are made to work on files with a structured naming sequence, for example struc_xx_B3LYP_D3BJ_6311pGdp_opt.log where xx is the individual number

for set-up and running

1. sumbit.py script to submit G16 jobs: Code to auto-create a batch script link
2. Dsumbit.py script: Code to auto-create a batch script for ALL the com files in a partucluar directory and submit them to the que link
3. suborca.py script to submit Orca jobs: Code to auto-create a batch script link
4. Dsuborca.py script: Code to auto-create a batch script for a specified number of jobs with input files of the form base_xx.inp link
5. get_energy.py script: Check a job while it is running, plot energy, find lowest force link
6. tlog.py script: Check a G16 job while it is running by using tail, printing Max force, Max displacement, Energy and saving a version to your home directory link
7. Dgetorca.py script: Check an orca job while it is running, or has finished link
8. ocheck.py script: Check an orca job while it is running, or has finished link
9. Dcreate_EEF_coms.py script: Creates a set of .com files with varying field strengths based on a provided template (Laura) link
10. Dsubmit_EEF.py script: Code to auto-create a batch script for .com files created using Dcreate_EEF_coms (Laura) link

to extract structures

1. extract_structure.py script: Extract last Standard Orientation structure of gaussian log file link
2. Dextract_structure.py script: Extract last Standard Orientation structure of multiple gaussian log files of the form struc_xx_B3LYP_D3BJ_6311pGdp_opt.log link
3. extract_geom.py script: Extract Optimized Geometry Gaussian/ORCA log file into an .xyz or .com file link
4. extract_steps.py script: Extract each optimised step from a scan into xyz coordinate file link
5. extract_crest_conf.py script: Extract given structure from a CREST conformer file and save to a *.xyz file (useful for using with Jmol) link
6. extract_GOAT_conformer_to_com.py script: Extract user-specified structures from the finalensemble.xyz output of a GOAT job to Gaussian input .com files. link

to build new files from data or existing files

1. build_freq.py script: Build a frequency file from an optimisation file ready to submit, this will require editing for your particular job link
2. Dbuild_freq.py script: Extract last structure of gaussian optimisation and build a freq com file for multiple gaussian log files of the form struc_xx_B3LYP_D3BJ_6311pGdp_opt.log link
3. symb_zmat.py script: Generate a symbolic z-matrix, requires you to use extract_structure.py and form a *.inp file with the xyz coords and a set of command words link
4. pos_zmat.py script: Orientate the molecule along a specific axis, rotate by a defined angle and or fix a particular atom as the origin. Requires you to use extract_structure.py and form a *.inp file with the xyz coords and a set of command words, generates a symbolic z-matrix link
5. pos_restartzmat.py script: This script restarts a symbolic z-matrix job (used for electric fields). Requires you to use extract_structure.py and form a *.inp file with the xyz coords, generates a symbolic z-matrix file to continue an optimisation link

to extract Thermochem data

1. getdata.py script: Extract thermodynamic data and low frequencies from a single log file into a formatted line to copy and paste into an excel files for the database link
2. Dgetdata.py script: Extract thermodynamic data and low frequencies from all the log files in a directory into a csv file for the database (Tricia) link
3. Dget_frequencies_data.py script: Extract thermodynamic data and low frequencies from all the log files in a directory to a csv file for the database (Muhammad) link
4. extract_vib.py script: for G16, extract vibrational data and make a plot link
5. orca_vib.py script: for orca, extract vibrational data and make a plot link

to extract NMR data

1. Dboltzmann_NMR_of_conformers.py script: Extract NMR data from all conformed log files into an excel file (csv) for with individual shielding tensors, Boltzmann averaged tensors, Boltzmann factor etc. (Muhammad) link

to extract charges and calculate dipole moment / charge arm

1. extract_charges.py script: Extract ESP and NBO charges link
2. dipole_moment.py code to extract multiple charges and evaluate the dipole moment (Irelie) link
3. center-of-mass_calculation.py code to calculate center of mass (CoM) from an XYZ or log file (Muhammad) link
4. calculate_dipole_wrt_CoIR_CoP_g16.py code to calculate dipole moment w.r.t center of imidazolium ring from g16 log file (Muhammad) link
5. calculate_dipole_wrt_atom_or_coordinate_g16.py code to calculate dipole moment w.r.t any atom or coordinate from g16 log file (Muhammad) link
6. charge_diff_pdb.py code to compute charge differences between 2 .pdb files (Laura) link

Other quantities

1. extract_aim.py script: Extract volume data from AIMALL sumviz files link
2. get_MOenergy.py script: Extract the MO orbital energies and convert to eV link
3. plot_PES.py script: Plot a potential energy surface (Laura) link

Historical codes

1. CArm.py script: Extract charges from *.fck and calculate the charge arm link
2. freq.py historical python2 script" Extract thermodynamic data and low frequencies from log files link
3. Codes to visualise data matrices (correlation matrices/heatmaps)link
4. Python toolkit currently focussed towards gaussian analysis link
5. Extract E2 Values (From NBO Calculations) link

Admin Stuff

1. Not used to writing a wiki, make your test runs on this page
2. How to set-up gaussian and gaussview on macs link
3. Mac user admin basics link
4. Moving large files and directories around link
5. How to launch on a Mac a Gaussview installed on a HPC link

Old Imperial

1. Old Imperial HPC information link
2. Old Imperial use gaussview directly on the HPC link
3. Old Imperial How to connect to HPC directory on desktop for file transfers link
4. Old Imperial How to run jobs interactively link
5. Old Imperial Computing resources available in the chemistry department link
6. Old Imperial New gf script (more convenient job submitting) link
7. Old Imperial How to make qsub more comfortable (gfunc) link
8. Old Imperial How to use a slimmed down terminal on your IPhone link