General Overview of ADINA

ADINA (Automatic Dynamic Incremental Non-linear Analysis) is a general-purpose finite element program for advanced engineering analysis in the fields of Structural Mechanics, Fluid Mechanics, Fluid-Structure Interactions, Heat Transfer, and Themomechanical Coupling.

The ADINA system consists of various programs that come with different tools and utilities that can be used independently or at once. In particular:

• 0ADINA (adina8.5) for processing and analysis
• ADINA User Interface (aui8.5) for pre-processing and post-processing (including geometry, mesh generation and analysis).

The present version of ADINA program in HPCVL machines is: ADINA 8.5.2

ADINA system

ADINA can run indiferently from the command line in interactive or batch mode, or through the AUI graphic interface.

Adina program has a large number of features and also Parallel Processing capabilities; as showed in this list of most important features:

Problems Solved

• Linear and Nonlinear structural analysis
• Dynamic analysis
• Thermal analysis of structures
• Buckling of structure
• Frequency analysis of structures
• Structural materials
• Heat Transfer
• Coupled Problems
• Multiphysics
• CFD including CFD Boundary conditions, and CFD Material models.

For more details check the information provided at the end of this document.

Solvers

• Frequency
  • Sparse solver
• Large Models
  • Iterative conjugate-gradient procedure with preconditioning
  • GMRES with preconditioning
• Fluid Flows
  • Iterative conjugate-gradient procedure
  • Iterative procedures
  • Bi-conjugate-gradient technique
• Multigrid
• Direct Skyline
• Explicit
  • For ADINA-F only

For more details check the information provided at the end of this document.

Parallel Processing

ADINA also allows Parallel Processing (at the solver level only for SUN)

• Parallelization for:
  • Calculation
  • Assemblage of the element matrices
  • Solution of the equations
  • Calculation of the elements results
• NO pre-and post-processing with SUN Sparc architectures
• DDM is performed automatically
• Parallelization for:
  • ADINA-F does not have paralellized assembly.
  • ADINA and ADINA-T have paralellized assembly.
  • 64-bit Equation solver(for problems demanding large size memory)
  • 32-bit Porthole file.

For more details check the information provided at the end of this document.

Available tools

Moreover the adina and aui binaries, the ADINA system provides a set of shell scripts and utilities that allow the user to handle all aspects of running ADINA applications (located under $ADINAHOME/tools)

The most important ones are:

• adina8.5 Shell script program that controls most of ADINA programs.
• aui8.5 Run the GUI and all demo examples.

And, the list of applications (programs) is:

• ADINA Structural Analysis $ADINAHOME/bin/adinat8.5
• ADINA-F Incompressible and fully compressible flows $ADINAHOME/bin/adina8.5
• ADINA-T Heat Transfer and field problems $ADINAHOME/adinat8.5
• ADINA-FSI Fluid flows with structural interactions $ADINAHOME/adfsi8.5
• ADINA-TMC Thermomechanical Coupling $ADINAHOME/adtmc8.5
• ADINA-M ADINA User interface with solid Modeling $ADINAHOME/aui8.5
• AUI ADINA User interface $ADINAHOME/aui8.5

Running ADF from a command line

The following instructions assume that you are a member of the Unix group "adf". The instructions in this section are only useful if you need to run test jobs of a short duration. If you want to run a production job, please refer to to instructions on how to start a ADF batch job.

Once program usage is set up through the "use" command, the program(s) can be run:

adf <in >out 

Instructions about the job are read from standard input, which has been redirected from a file in in the above command lines. Commonly an input file will be constructed to specify what calculation is to be run. The output of the program(s) goes to "standard output" and has been redirected to an output file out above. Note that the output of these programs is commonly thousands of lines long and should therefore be redirected in any case.

The construction of a proper input file for ADF is an involved process, and is outside the scope of this help file. Detailed instructions can be found in the ADF User's Guide, which should be studied before the program can be used properly. As an initial hint, here is a sample input file:

title benzene BP/SZ bondorders tol=0.05

define
 cc=1.38476576
 ccc=120.0
 dih=0.0
 hc=1.07212846
 hcc= 120.0
 dih2=180.0
end

atoms Z-matrix
 C  0 0 0
 C  1 0 0  cc
 C  2 1 0  cc ccc
 C  3 2 1  cc ccc dih
 C  4 3 2  cc ccc dih
 C  5 4 3  cc ccc dih
 H  2 1 3  hc hcc dih2
 H  3 2 4  hc hcc dih2
 H  4 3 5  hc hcc dih2
 H  5 4 3  hc hcc dih2
 H  6 5 4  hc hcc dih2
 H  1 2 3  hc hcc dih2
end

basis
 Type SZ
 Core None
end

symmetry NOSYM

xc
  gga becke perdew
end

bondorder tol=0.05 printall

noprint sfo

The input consists of several units, separated by blank lines, starting with a keyword, and ending with the statement END. For instance, the atoms in a molecules may be specified by issuing the keyword atoms, followed by one line with the atom name and "Z-matrix" relative coordinates for each atom, and closing with end (case insensitive).

Note: It is absolutely essential to have a good idea about the size and complexity of your calculations before you start a ADF job. Many of the methods have terrible scaling properties, i.e. the computational cost grows very quickly with the number of electrons, degrees of freedom, or number of basis functions used. We suggest you start with a small basis set and a cheap method, and then slowly increase those parameters.

Submitting (parallel) ADF jobs

In most cases, you will run ADF in batch mode.

Production jobs are submitted to our systems via the Grid Engine, which is a load-balancing software. To obtain details, read our Grid Engine FAQ. For an ADF batch job, this means that rather than issuing the above commands directly, you wrap them into a Grid Engine batch script. Here is an example for such a batch script:

#! /bin/bash
#$ -S /bin/bash
#$ -V
#$ -cwd
#$ -M MyEmailAdress@whatever.com
#$ -m be
#$ -o STD.out
#$ -e STD.err
#$ -pe shm.pe 12
adf -n $NSLOTS <sample.adf >sample.log

This script needs to be altered by replacing all the relevant items. It sets all the necessary environment variables (make sure you issued a "use adf" statement before using this), and then starts the program. The lines in the script that start with #$ are interpreted the Grid Engine load balancing software as directives for the execution of the program.

For instance the line "#$ -m be" tells the Grid Engine to notify the user via email when the job has started and when it is finished, while the line beginning with "#$ -M" tells the Grid Engine about the email address of the user.

The -o and -e lines determine whence the standard input and the standard error are to be redirected. Since the job is going to be executed in batch, no terminal is available as a default for these.

The ADF package is able to execute on several processors simultaneously in a distributed-memory fashion. This means that some tasks such as the calculation of a large number of matrix elements, or numerical integrations may be done in a fraction of the time it takes to execute on a single CPU. For this, the processors on the cluster need to be able to communicate. To this end ADF uses the MPI (Message Passing Interface), a well-established communication system.

Because ADF uses a specific version of the parallel system MPI (ClusterTools 7), executing the use adf command will also cause the system to "switch" to that version, which might have an impact on jobs that you are running from the same shell later. To undo this effect, you need to type use ct8 when you are finished using ADF and want to return to the production version of MPI (ClusterTools 8).

ADF parallel jobs that are to be submitted to Grid Engine will use the MPI parallel environment and queues already defined for the user.

Our sample script contains a line that determines the number of parallel processes to be used by ADF. The Grid Engine will start the MPI parallel environment (PE) with a given number of slots that you specify by modifying that line:

#$ -pe shm.pe ''number of processes''

where number of processes must be replaced (for instance, by 12 in our example above). It then determines the value of the environment variable NSLOTS which is used in the "adf" line of the sample script. This way, the system allocates exactly the number of processors that are used for the adf run, and no mismatch can occur.

Once properly modified, the script (let's call it "adf.sh") can be submitted to the Grid Engine by typing

qsub adf.sh

The advantage to submit jobs via a load balancing software is that the software will automatically find the resources required and put the job onto a node that has a low load. This will help executing the job faster. Note that the usage of Grid Engine for all production jobs on HPCVL clusters is mandatory. Production jobs that are submitted outside of the load balancing software will be terminated by the system administrator.

Luckily, there is an easier way to do all this: We are supplying a small perl script called that can be called directly, and will ask a few basic questions, such as the name for the job to be submitted and the number of processes to be used in the job. Simply type

ADFSubmit

and answer the questions. The script expects a ADF input file with "file extension" .adf to be present and will do everything else automatically. This is meant for simple ADF job submissions. More complex job submissions are better done manually.

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.