Basic Q- Chem Calcula/ons using IQmol

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Alan Shawn Goodwin
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1 Basic Q- Chem Calcula/ons using IQmol

2 Outline IQmol: ge7ng started; Hartree- Fock, DFT, MP2, CCSD calcula/ons; Geometry op/miza/on and vibra/onal analysis; Visualiza/on of molecular orbitals and densi/es; Exercises.

3 WriQen by Dr. Andrew Gilbert IQmol iqmol.org (forum, tutorials); also see webinar from Q- Chem website Molecular builder, hierarchical input generator, job manager, local/remote submission, visualizer

4 IQmol basics How to get started: 1. Install IQmol. 2. Configure IQmol for local and/or remote job submission (need to know where Q- Chem is installed). 3. Use builder to build a molecule (or read in geometries). 4. Setup Q- Chem calcula/on. 5. Hit the submit buqon.

5 Install IQmol hqp://iqmol.org/

6 IQmol: Server setup

7 IQmol: Server setup

8 IQmol: Server setup This is a setup for USC HPCC cluster, but with small modifica/ons it can be used for other clusters running pbs (such as fluffy). Username: your USC account name used for the USC e- mail Password (will be asked when you test connec/on): your password for the USC account.

9 IQmol: Server setup Copy from next slide!

10 IQmol: Server setup #!/bin/bash #PBS - q ${QUEUE} #PBS - l walltime=${walltime} #PBS - l ncpus=${ncpus} source /usr/usc/intel/default/setup.sh source /usr/usc/openmpi/1.8.1/gnu/setup.sh export QC=/home/rcf- proj/ak/ikaliman/qchem/trunk export QCAUX=/home/rcf- proj/ak/ikaliman/qchem/qcaux export QCPLATFORM=LINUX_Ix86_64 export QCRSH=ssh export PATH=$QC/bin:$PATH export QCSCRATCH=$TMPDIR cd $PBS_O_WORKDIR qchem - nt ${NCPUS} ${JOB_NAME}.inp ${JOB_NAME}.out

11 IQmol: Submit job

12 IQmol: Submit job - Use default queue on HPCC; - Leave the rest of se7ngs unchanged. default queue! For advanced users: - To run Q- Chem in parallel (openmp), change the number in CPUs (consult the manual to see which types of jobs are openmp- parallelized); - for MPI- parallel, you will need to tweak the se7ngs in the previous page; - Memory and scratch se7ngs are not important here, but for op/mal performance you may need to tweak these se7ngs in the Q- Chem input file, especially for advanced calcula/ons. Consult the manual before doing so!

13 IQmol: Check job status

14 Exercises Formaldehyde: build molecule, clean- up (force- field opt- n), check symmetry (symmetrize molecule) op/mize wb97x- D/6-31+G* Play with changing the view of the molecule, move it around, zoom Use Select feature to measure bonds and angles Look at MOs: HOMO, HOMO- 1; LUMO Run FREQ job, look at vibra/ons (click versus double- click) Advanced: Run NBO analysis, look at NBO charges and bond orders Sample geometry on the next slide (formaldehyde.xyz)

15 Formaldehyde geometry 4 C O H H #omegab97x/6-31+g* op/mized This is formaldehyde geometry in XYX format (JMol or Avogadro format). You can save it in fomaldehyde.xyz file and open by using Open File buqon in IQmol. Alterna/vely, you can cut and paste the coordinates into the $molecule sec/on in the Q- Chem input (need to add mul/plicity/charge line).

16 Troubleshoo/ng Known problems and glitches: 1. When configuring servers, follow the instruc/ons precisely. If you get crashes when configuring the server, delete the configura/on and start over again. 2. Symmetrize func/on some/mes causes IQmol to crash. 3. If IQmol stops working (warnings like cannot create a directory ) RESTART IQmol and try again. 4. If connec/on is poor, IQmol may show the running job as failed. In this case, or IQmol crashed, or your job is too long, you can copy the output and checkpoint files manually (by sup) to your laptop and then open them by IQmol (may need to rename checkpoint files).

17 Troubleshoo/ng Known problems and glitches: 5. The job name is assigned when you select a working directory on the server. Auer the job finishes, IQmol will ask your permission to copy the files from the server. The name of the directory on your laptop should match the name of the directory on the server (i.e., the job name) precisely. If they do not match, you will get no valid data found in error message. The files are actually OK and are copied to you laptop. You can open them individually with Open command.

18 Troubleshoo/ng

19 More about IQmol - IQmol has many advanced features for a seasoned user; - IQmol is being ac/vely developed to incorporate new features and to address users feedback; See iqmol.org (forum, tutorials) for detailed descrip/on of all features; also watch a webinar from Q- Chem website.

Introduc)ontoIQmol:PartI* ShirinFaraji,IlyaKaliman,andAnnaKrylov*

Introduc)on*to*IQmol:*Part*I* Shirin*Faraji,*Ilya*Kaliman,*and*Anna*Krylov* 1 Resources Written by Dr. Andrew Gilbert Keep yourself up to date with IQmol website: http://iqmol.org IQmol Youtube channel: