HowTo:nwchem

From CAC Wiki
Revision as of 17:39, 27 May 2016 by Hasch (Talk | contribs) (→‎NWChem)

Jump to: navigation, search

NWChem

This is a short help file on using the parallel electronic-structure code "NWChem" on systems at the Centre for Advanced Computing. This software uses MPI as a message-passing system and is (in principle) able to run on an arbitrary number of processors. Its ability to perform a very broad spectrum of molecular-structure calculations, ranging from CI to ab-initio molecular dynamics, makes it an interesting alternative to the standard electronic structure code Gaussian.

Features

NWChem is an electronic-structure code that is suitable to perform complex calculations on molecular structure. It was specifically designed to perform well on high-performance parallel computers. The installation on the SunFire cluster of HPCVL employs the MPI message passing package for parallel execution.

NWChem allows, among others, the following calculations to be performed:

  • Hartree-Fock (e.g. RHF, UHF, ROHF etc.)
  • DFT including spin-orbit DFT, with many exchange and correlation functionals.
  • Complete Active Space SCF (CAS-SCF)
  • Coupled-Cluster (CCSD, CCSD+T, etc.)
  • limited CI (eg, CISD) with perturbative corrections
  • MP2 (2nd-order Mollar-Plesset Perturbation Theory)
  • In general: single-point calculations, geometry optimizations, vibrational analysis.
  • Static one-electron properties, densities, electrostatic potentials.
  • ONIOM model for multi-level calculations on larger systems
  • Relativistic corrections (Douglas-Kroll, Dyall-Dirac, spin-orbit)
  • Ab-initio molecular dynamics (Carr-Parinello)
  • Extended (solid-state) systems DFT
  • Classical force-fields (Molecular Mechanics: AMBER, CHARMM, etc.)

For a more complete list, see the official NWChem homepage and click on "capabilities".

Location of the program and setup

The NWChem program is located in the directory /opt/nwchem/bin. To access it, you have to use the usepackage command 

use nwchem

which will set you up automatically.

Running NWChem from a command line

Like other electronic-structure programs, NWChem is run by supplying an input file that defines the system on which to perform a calculation (usually a molecule, or a group of molecules), and the method to use (i.e., the level of calculation, such as "Hartree-Fock", the basis set, and other details of the computation).

The variety of possible calculations is great, and so is the complexity of systems. It is impossible for us here to explain the format that a NWChem input file needs to have. This is explained in the User's Manual which is available online.

Here, we provide a simple sample input file which should be given the file extension .nw. 

start h2o

title "H2O, cc-pVDZ basis, SCF optimized geometry"

geometry units au
H       0.0000000000   1.4140780900  -1.1031626600
H       0.0000000000  -1.4140780900  -1.1031626600
O       0.0000000000   0.0000000000  -0.0080100000
end

basis
H library cc-pVDZ
O library cc-pVDZ
end

scf
   thresh 1.0e-8
end

task scf

This extension may be omitted when calling the program. NWChem creates typically a whole array of output files that are documented in the User's Manual. A general log is displayed on the console, and may be saved in a file by redirecting the standard output: 

nwchem sample > sample.log

where we assume that your input file is called sample.nw and you want to save the log to a file sample.log.

Note that this is just the basic syntax of the program call. In practise you will use a parallel environment to execute the program (see next section). In fact, executing NWChem by just typing the above line will run it in serial mode.

Parallel Runs

NWChem is inherently parallelized and designed to scale well on a multi-processor machine or a cluster. The underlying parallel system is MPI (Message Passing Interface) which is a commonly available standard that runs on many platforms. Consult our HowTo:mpi MPI help file and follow some of the links in there if you want to have more information about MPI. Even if you want to use only one processor for your NWChem run (which sometimes is the best solution, particularly for smaller computations), you have to submit the program to a parallel environment. On our clusters, the relevant command is mpirun: 

mpirun -np 8 nwchem sample > sample.log

This will run your sample.nw input file on eight processors. Note that you are only allowed to run NWChem this way for small test systems! For any production jobs, you have to submit the task to the scheduler (see next section.).

Submitting (parallel) Gaussian jobs

If you want to run Gaussian on several processors on our machines, you have to include a line in your input file: 

%nproc=8

where we assume that you want to use 8 processors (cores, threads).

It is mandatory to submit a Gaussian job script through our scheduling software (see our Scheduler Help File for details).

Here is a "bare bones" sample of a Gaussian submission script: 

#! /bin/bash
#$ -S /bin/bash
#$ -q abaqus.q
#$ -l qname=abaqus.q
#$ -cwd
#$ -V
#$ -M hpcXXXX@localhost
#$ -m be
#$ -o STD.out
#$ -e STD.err
#$ -pe shm.pe 8
g09 < sample.g09 > sample.log
  • The first 6 lines of the script make sure the right shell is used, the program executes on the correct cluster, and all necessary setup is done.
  • An email address for notifications is specified in the #$ -M line. We suggest "hpcXXXX@localhost" (hpcXXXX stands for the username). Place a file .forward containing your actual email address into your home directory.
  • The -o and -e lines are used to tell the system where to write "standard output" and "standard error", i.e. the screen output.
  • The #$ -pe gaussian.pe 8 line specifies the number of processors the scheduler will allocate (8 in this example). It is crucial to choose the same number as specified in the %nrocs= line of the input file.

The script (let's call it g09.sh) is submitted by the qsub command: 

qsub g09.sh

This must be done from the working directory, i.e. the directory that contains the input file and is supposed to contain the output. Also make sure that you have set up gaussian (use g09) before you submit a job.

Licensing

Gaussian is a licensed program. The license held by the Centre for Advanced Computing is limited to our computers at our main site. That means that any of our users can use the program on our machines (but nowhere else), whether they are located at Queen's or not.

We require users of Gaussian to sign a statement in which they state that they are informed about the terms of the license to be included in the Gaussian user group named "g98". Please fax the completed statement to (613) 533-2015 or scan/email to cac.admin@queensu.ca.

Where can I get more detailed information ?

Retrieved from ‘https://info.cac.queensu.ca/wiki/index.php?title=HowTo:nwchem&oldid=525’