HowTo:cpmd

Car-Parinello Molecular Dynamics (CPMD)

This is an introduction to the usage of the Ab Initio Molecular Dynamics code "CPMD" on our clusters. It is meant as an initial pointer to more detailed information, and to get started. It doesn't replace the study of the manual.

Features The CPMD code is a parallelized plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio Molecular Dynamics simulation as described by Car and Parinello (R. Car and M. Parrinello, Phys. Rev. Lett. 55, 2471 (1985)) and is distributed free of charge to non-profit organizations. CPMD runs on many different computer architectures and it is well parallelized. CPMD performs many Quantum-Chemical and Molecular-Dynamics calculations, including: Wavefunction optimization: direct minimization and diagonalization Geometry optimization: local optimization and simulated annealing Molecular dynamics: NVE, NVT, NPT ensembles. Path integral MD, free-energy path-sampling methods Response functions and many electronic structure properties Time-dependent DFT (excitations, molecular dynamics in excited states) LDA, LSD and many popular gradient correction schemes Isolated systems and system with periodic boundary conditions; k-points Hybrid quantum mechanical / molecular mechanics calculations (QM/MM) Coarse-grained non-Markovian meta-dynamics Works with norm conserving or ultra-soft pseudopotentials For a complete list of capabilities of CPMD, consult the CPMD online manual (note: this refers to a newer version), or check an extensive database of related publications. Location and Setup The program resides in /opt/cpmd and is called cpmd.x. You also find some test examples in this directory, which are useful to get an idea of the input format for the program. You are not allowed to copy the executable or any part of the distribution onto your local machine. However you can easily obtain the program yourself. See the CPMD download page. Note that you will need a valid password to download the code. Unlike other programs, no special setup is needed to run CPMD. However, it is a good idea to put the directory with the CPMD program into the path, which can be done by "usepackage": use cpmd

Running from a command line Before you can access the CPMD executables and run the program, you have to read our license agreement. You also have to sign a statement that you have done so, and return it to us (see last section for more information). To run CPMD, you need to specify the executable, an input file, and (optionally) an output file. Assuming that the CPMD home is in your path, all you need to do is type cpmd_serial.x input_name >output_name where input_name is the name of the input file (file extension is recommended to be.inp). If no output file output_name is specified, then the output is sent to the terminal screen. Parallel Runs The above command line is for the serial version of the program. For larger runs, it is recommentded to use the parallel version. Then the command line is: mpirun -np 8 cpmd_ct8.x input_name >output_name if 8 processes are to be used in the parallel run. Because CPMD uses the Messageg Passing Interface MPI for parallelism, a runtime environment needs to be used to start the program, which is the reason for the mpirun command. In this case, we are using OpenMPI. -np 1 boils down to a serial run. Like most programs, CPMD requires an input (.inp) file that describes the system for which the calculation will be performed, specifies the level of calculation, and provides other necessary information. The format of the input is described in detail in the CPMD documentation and cannot be explained here. In addition to the input file you may need other auxiliary files which can be obtained from the CPMD directory. In most cases, you will have provide pseudo-potential files which usually have the file extension .psp. A collection of these may be found in directories below /opt/cpmd/3.13. Once all input is prepared, you will have to make the decision how many processes you want to use. This involves a trade-off between availability of CPU's on our systems, and the efficiency of additional processes, i.e. scaling. We suggest you perform test calculations of the same type as your production calculation, rerun several times with a varying number of processors. Comparing the timings lets you determine the maximum number of processors that yield acceptable scaling for your production calculation. Batch Jobs CPMD, like all production software, has to be run through our scheduler, which submits batch jobs to low-load processors on the cluster. Click here to learn more. A CPMD job must be submitted to the Grid Engine in the form of an execution script. The calculation is set up by editing the execution script. #!/bin/bash #$ -S /bin/bash #$ -q abaqus.q #$ -l qname=abaqus.q #$ -V #$ -cwd #$ -pe shm.pe 12 #$ -m be #$ -M hpcXXXX@localhost #$ -o STD.out #$ -e STD.err fluent 3ddp -t$NSLOTS -g -i example.flin In the template, just replace all entries enclosed in by the proper values. The lines starting with "#$ -o" and "#$ -e" define the standard output and standard error files, respectively. Note that all lines starting with "#$" are directives for the Grid Engine, and will be interpreted when the script is submitted to that program. The "#$ -V" and "#$ -cwd" instruct the executing shell of the script to inherit the environment of the calling shell (for instance the path), and set the starting directory to the current working directory, repsectively. You also need to specify the name of the input file just like in an interactive run. The input file and the necessary pseudo-potential files are supposed to reside in the same directory as the Grid Engine script. The number of processes is specified in the "#$ -pe" line, which instructs the Grid Engine to allocate the proper number of CPUs for your run. You do not have to specify it separately in the cpmdcommand line, because Grid Engine sets the environment variable $NSLOTS properly. We assume your Grid Engine script is called cpmd.sh. The script is submitted to GridEngine by typing qsub cpmd.csh No further specification of the output is necessary, since this is done inside the script and handled by GridEngine.

Licensing ADF 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 ADF 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 "adf". Please fax the completed statement to (613) 533-2015 or scan/email to cac.admin@queensu.ca. Help To learn the basics about Gaussian input and output, refer to the ADF 2016 Manual. For templates, and to get many examples, check out https://www.scm.com/documentation/ADF/Examples/Examples/. The Gaussian web page contains a lot of information. Send to cac.help@queensu.ca. We're happy to help.