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MEMS Proportional Pneumatic Valve

Abstract: 
<h4>MEMS Proportional Pneumatic Valve</h4><p><span style="color: rgb(51, 51, 51); font-size: 14px; background-color: rgb(255, 255, 255); line-height: 1.5;">This project involves designing a new type of generic pneumatic valve based on micro-electrical-mechanical-systems (MEMS) technology. The valve utilizes an array of micro-actuators positioned over a matching array of micro-orifices. Several benefits are realized by using this scheme instead of a single large actuator acting on a single large orifice. The three most notable are very low actuation power requirements, very fast response and potentially very low cost. The potential cost benefits are realized by exploiting MEMS batch fabrication technologies. MSI resources are utilized to do computational mechanics flow modeling for the valve</span>.</p><p>A bibliography of this group&rsquo;s publications is attached.</p><p><span style="font-size: 14px; line-height: 1.5;">Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/ec4e80ff741b2de9a4cac84a77662606/10208">main page</a>.</span></p><p>&nbsp;</p>
Group name: 
chasetr
Attachment: 

AMBER

Software Description: 

AMBER. Assisted Model Building with Energy Refinement. AMBER refers to two things: a molecular mechanical force field for the simulation of biomolecules (which is in general use in a variety of simulation programs)- and a package of molecular simulation programs which includes source code and demos.

Software Support Level: 
Secondary Support
Itasca Documentation: 
Amber 11 is available on Itasca. Calling the sander.MPI binary on more than one node (8 cores) requires the amber module to be loaded in your .bashrc file. If you are running pmemd.MPI this step is not necessary. A sample job script is below.
#!/bin/bash -l
#PBS -l walltime=8:00:00,pmem=1000mb,nodes=8:ppn=8
#PBS -m abe

module load amber/11

cd $PBS_O_WORKDIR

mpirun -np 64 -hostfile $PBS_NODEFILE `which pmemd.MPI` \
  -O -i mdin -c eq200.x -o cellulose.sander.log

Additional Documentation

Software Access Level: 
Open Access
PBS Example: 

An example PBS script for submitting AMBER jobs to the queue is shown below.

#!/bin/bash -l 
#PBS -l walltime=24:00:00,mem=16gb,nodes=2:ppn=8 
#PBS -m abe 

module load amber 

cd $PBS_O_WORKDIR 

mpirun sander.MPI -O -i AMP2md39.in -o AMP2md39.out -p \
  AMP2_wat.prmtop -c AMP2md38.rst -r AMP2md39.rst -x \
  AMP2md39.mdcrd
Software Interactive/GUI: 
No
General Linux Documentation: 

To run this software interactively in a Linux environment run the command:

module avail amber

and choose the most recent version of the software applicable to your research. The exact name of the module will vary from machine to machine, and over time with new updates so be sure to study the list printed with the 'module avail' command demonstrated above. For example,

module load amber/11
The amber module requires and will automatically load several other modules. Pay attention to any error messages or warnings that result from loading the module as conflicts with other packages already loaded in your environment are a common source of error. An example submission script is below. Note that the #PBS lines need to be tuned for each cluster's policies. You may not need to run short jobs through the queue, so the program can be used interactively by loading the module and running the executable directly at the command prompt.
#!/bin/bash -l 
#PBS -l walltime=24:00:00,mem=16gb,nodes=2:ppn=8 
#PBS -m abe 

module load amber 

cd $PBS_O_WORKDIR 

mpirun sander.MPI -O -i AMP2md39.in -o AMP2md39.out -p \
  AMP2_wat.prmtop -c AMP2md38.rst -r AMP2md39.rst -x \
  AMP2md39.mdcrd

Additional Documentation

Utilization and Account Sharing

Utilization The facilities and resources of the Minnesota Supercomputing Institute are provided to support the research and scholarship of our Principal Investigators and their coworkers and students. Under no circumstances may MSI systems be used for any other purpose than to support University-...

Matlab

Software Description: 

Matlab is a high level technical computing language and interactive environment for data visualization, data analysis, numerical computation, and algorithm development.

Software Support Level: 
Primary Support
Software Access Level: 
Limited Licenses
PBS Example: 

Matlab programs can be submitted to a queue using PBS script such as the one below. 

#PBS -l nodes=1:ppn=1,mem=1gb,walltime=4:00:00
#PBS -m abe
cd /location/of/the/script
module load matlab
matlab -nodisplay -r "maxNumCompThreads(1)" < my.m

where maxNumCompThreads(1) sets one thread (or one core) for running my.m (the matlab job). The number of threads can have a value up to the number of cores in that node.   The variable maxNumCompThreads must be specified. Otherwise, the job will request twice as many cores as there are available on a computing node. This can cause problems for all jobs running on the same node.

Software Interactive/GUI: 
No
General Linux Documentation: 

To run this software interactively in a Linux environment run the commands:

module load matlab
matlab

Several versions of Matlab are available, but the versions may be different on different platforms.To list all versions of Matlab available on the machine, type

module avail matlab

When running on the elmob nodes use this module instead:

module load matlab/R2010b
matlab

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