Micro and Nano Mechanics Group - User contributions [en]

ParaDiS Manuals

2015-11-18T23:32:09Z

Amin1:

<UL>

<LI> [[Overview of ParaDiS 2.2]]

<LI> [[Before You Start: Known Bugs in ParaDiS]]

<LI> [[M01 How to Obtain and Run ParaDiS]]

<LI> [[M02 Straight dislocations]]

<LI> [[M03 Frank-Read Source]]

<LI> [[M04 Binary Junction]]

<LI> [[M05 ParaDiS Flowchart]]

<LI> [[Create Straight Dislocations for ParaDiS Input]]

<LI> [[Programming tips for ParaDiS]]

<LI> [[ParaDiS FAQs]]

<LI> [[ Cross-slip in ParaDiS]]

<LI> [[ParaDiS Manual Updated]]

<LI> [[Parallel Cluster Guides]]

</UL>

ParaDiS Manuals

2015-11-18T23:31:39Z

Amin1:

<UL>

<LI> [[Overview of ParaDiS 2.2]]

<LI> [[Before You Start: Known Bugs in ParaDiS]]

<LI> [[M01 How to Obtain and Run ParaDiS]]

<LI> [[M02 Straight dislocations]]

<LI> [[M03 Frank-Read Source]]

<LI> [[M04 Binary Junction]]

<LI> [[M05 ParaDiS Flowchart]] [[Media:ParaDiS Flowchart.pdf]]

<LI> [[Create Straight Dislocations for ParaDiS Input]]

<LI> [[Programming tips for ParaDiS]]

<LI> [[ParaDiS FAQs]]

<LI> [[ Cross-slip in ParaDiS]]

<LI> [[ParaDiS Manual Updated]]

<LI> [[Parallel Cluster Guides]]

</UL>

M05 ParaDiS Flowchart

2015-11-18T23:31:01Z

Amin1:

[[Media:ParaDiS Flowchart.pdf]]

ParaDiS Flowchart.pdf

2015-11-18T23:30:18Z

Amin1: Created page with "Media:ParaDiS Flowchart.pdf"

[[Media:ParaDiS Flowchart.pdf]]

M05 ParaDiS Flowchart

2015-11-18T23:27:51Z

Amin1:

[[ParaDiS Flowchart.pdf]]

File:ParaDiS Flowchart.pdf

2015-11-18T23:25:56Z

Amin1:

M05 ParaDiS Flowchart

2015-11-18T23:25:44Z

Amin1:

[[File:ParaDiS Flowchart.pdf]]

M05 ParaDiS Flowchart

2015-11-18T23:24:27Z

Amin1: Created page with "File:Example.jpg"

[[File:Example.jpg]]

ParaDiS Manuals

2015-11-18T23:23:57Z

Amin1:

Running Hybrid MPI/OpenMP Simulations

2015-11-07T14:47:09Z

Amin1: /* References */

=Running Hybrid MPI/OpenMP Simulations=
This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed on both MC2 and WCR clusters. In this page we assume the code is already written in the hybrid fashion, e.g. both MPI and OpenMP headers are included in the code and you are able to compile and run your code.

==Assigning the number of CPUs==
Suppose you have 16 CPUs and want to have two MPI processors, each with 8 OpenMP threads.
*Assigning OpenMP threads:
export OMP_NUM_THREADS=8
*Running:
mpirun -np 2 a.out
where a.out is name of the executable.

==OpenMP setting==
One of the crucial settings that we need be careful about is the "processor affinity". By default, multi-threading affinity is not set in mvapich2. That means, by default, all your OpenMP threading will be bound to a single processor (if you have compiled it through mvapich2 wrappers such as mpicc, mpic++ or mpif90). This is because mvapich2 gives priority to MPI processors and does not allow OpenMP to use more than one CPU (even if there are available cpus for OpenMP threads). This setting can be changed through MV2_ENABLE_AFFINITY variable. In your terminal or PBS file type in the following command to enable OpenMP threads to run on different cores:

export MV2_ENABLE_AFFINITY=0

==Binding MPI runs to different nodes==
By default, mvapich2 tries to put all MPI processors on adjacent cores (not nodes). For example if you request 2 nodes and 8 cores through your PBS file and use "mpirun -np 2 a.out" both MPI processors will be assigned to the first node and the second node will be empty. In order to reserve the cores for OpenMP and put MPI processors on different nodes, you must use a modified nodefile as following:

sed -n "1~${PBS_NUM_PPN}p" $PBS_NODEFILE > my_nodefile
mpirun -f my_nodefile -np $PBS_NUM_NODES my_program

==References==
*https://www.cct.lsu.edu/~estrabd/intro-hybrid-mpi-openmp.pdf
*https://wikis.nyu.edu/display/NYUHPC/Running+jobs+-+MPI
*https://www.mir.wustl.edu/Portals/0/Documents/Uploads/CHPC/WashU_7_mvapich.pdf

Running Hybrid MPI/OpenMP Simulations

2015-11-04T22:08:43Z

Amin1: /* OpenMP setting */

=Running Hybrid MPI/OpenMP Simulations=
This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed on both MC2 and WCR clusters. In this page we assume the code is already written in the hybrid fashion, e.g. both MPI and OpenMP headers are included in the code and you are able to compile and run your code.

==Assigning the number of CPUs==
Suppose you have 16 CPUs and want to have two MPI processors, each with 8 OpenMP threads.
*Assigning OpenMP threads:
export OMP_NUM_THREADS=8
*Running:
mpirun -np 2 a.out
where a.out is name of the executable.

==OpenMP setting==
One of the crucial settings that we need be careful about is the "processor affinity". By default, multi-threading affinity is not set in mvapich2. That means, by default, all your OpenMP threading will be bound to a single processor (if you have compiled it through mvapich2 wrappers such as mpicc, mpic++ or mpif90). This is because mvapich2 gives priority to MPI processors and does not allow OpenMP to use more than one CPU (even if there are available cpus for OpenMP threads). This setting can be changed through MV2_ENABLE_AFFINITY variable. In your terminal or PBS file type in the following command to enable OpenMP threads to run on different cores:

export MV2_ENABLE_AFFINITY=0

==Binding MPI runs to different nodes==
By default, mvapich2 tries to put all MPI processors on adjacent cores (not nodes). For example if you request 2 nodes and 8 cores through your PBS file and use "mpirun -np 2 a.out" both MPI processors will be assigned to the first node and the second node will be empty. In order to reserve the cores for OpenMP and put MPI processors on different nodes, you must use a modified nodefile as following:

sed -n "1~${PBS_NUM_PPN}p" $PBS_NODEFILE > my_nodefile
mpirun -f my_nodefile -np $PBS_NUM_NODES my_program

==References==
https://www.cct.lsu.edu/~estrabd/intro-hybrid-mpi-openmp.pdf
https://wikis.nyu.edu/display/NYUHPC/Running+jobs+-+MPI
https://www.mir.wustl.edu/Portals/0/Documents/Uploads/CHPC/WashU_7_mvapich.pdf

Running Hybrid MPI/OpenMP Simulations

2015-11-04T22:06:02Z

Amin1: /* OpenMP setting */

=Running Hybrid MPI/OpenMP Simulations=
This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed on both MC2 and WCR clusters. In this page we assume the code is already written in the hybrid fashion, e.g. both MPI and OpenMP headers are included in the code and you are able to compile and run your code.

==Assigning the number of CPUs==
Suppose you have 16 CPUs and want to have two MPI processors, each with 8 OpenMP threads.
*Assigning OpenMP threads:
export OMP_NUM_THREADS=8
*Running:
mpirun -np 2 a.out
where a.out is name of the executable.

==OpenMP setting==
One of the crucial settings that we need be careful about is the "processor affinity". By default, multi-threading affinity is not set in mvapich2. That means all your OpenMP threading will be bound to a single processor if you have not changed this setting (and if you have compiled it through mpicc, mpic++ or mpif90). This is because mvapich2 gives priority to MPI processors and does not allow OpenMP to use more than one CPU (even if there are available cpus for OpenMP threads). This setting can be changed through MV2_ENABLE_AFFINITY variable. In your terminal or PBS file type in the following command to enable OpenMP threads to run on different cores:

export MV2_ENABLE_AFFINITY=0

==Binding MPI runs to different nodes==
By default, mvapich2 tries to put all MPI processors on adjacent cores (not nodes). For example if you request 2 nodes and 8 cores through your PBS file and use "mpirun -np 2 a.out" both MPI processors will be assigned to the first node and the second node will be empty. In order to reserve the cores for OpenMP and put MPI processors on different nodes, you must use a modified nodefile as following:

sed -n "1~${PBS_NUM_PPN}p" $PBS_NODEFILE > my_nodefile
mpirun -f my_nodefile -np $PBS_NUM_NODES my_program

==References==
https://www.cct.lsu.edu/~estrabd/intro-hybrid-mpi-openmp.pdf
https://wikis.nyu.edu/display/NYUHPC/Running+jobs+-+MPI
https://www.mir.wustl.edu/Portals/0/Documents/Uploads/CHPC/WashU_7_mvapich.pdf

Running Hybrid MPI/OpenMP Simulations

2015-11-04T22:05:17Z

Amin1: /* Running Hybrid MPI/OpenMP Simulations */

=Running Hybrid MPI/OpenMP Simulations=
This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed on both MC2 and WCR clusters. In this page we assume the code is already written in the hybrid fashion, e.g. both MPI and OpenMP headers are included in the code and you are able to compile and run your code.

==Assigning the number of CPUs==
Suppose you have 16 CPUs and want to have two MPI processors, each with 8 OpenMP threads.
*Assigning OpenMP threads:
export OMP_NUM_THREADS=8
*Running:
mpirun -np 2 a.out
where a.out is name of the executable.

==OpenMP setting==
One of the main settings that we need be careful about is the "processor affinity". By default, multi-threading affinity is not set in mvapich2. That means all your OpenMP threading will be bound to a single processor if you have not changed this setting (and if you have compiled it through mpicc, mpic++ or mpif90). This is because mvapich2 gives priority to MPI processors and does not allow OpenMP to use more than one CPU (even if there are available cpus for OpenMP threads). This setting can be changed through MV2_ENABLE_AFFINITY variable. In your terminal or PBS file type in the following command to enable OpenMP threads to run on different cores:

export MV2_ENABLE_AFFINITY=0

==Binding MPI runs to different nodes==
By default, mvapich2 tries to put all MPI processors on adjacent cores (not nodes). For example if you request 2 nodes and 8 cores through your PBS file and use "mpirun -np 2 a.out" both MPI processors will be assigned to the first node and the second node will be empty. In order to reserve the cores for OpenMP and put MPI processors on different nodes, you must use a modified nodefile as following:

sed -n "1~${PBS_NUM_PPN}p" $PBS_NODEFILE > my_nodefile
mpirun -f my_nodefile -np $PBS_NUM_NODES my_program

==References==
https://www.cct.lsu.edu/~estrabd/intro-hybrid-mpi-openmp.pdf
https://wikis.nyu.edu/display/NYUHPC/Running+jobs+-+MPI
https://www.mir.wustl.edu/Portals/0/Documents/Uploads/CHPC/WashU_7_mvapich.pdf

Running Hybrid MPI/OpenMP Simulations

2015-11-04T06:21:35Z

Amin1: /* Assigning the number of CPUs */

=Running Hybrid MPI/OpenMP Simulations=
This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed on both MC2 and WCR clusters. In this page we assume the code is already written in the hybrid fashion, e.g. both MPI and OpenMP headers are included in the code and you are able to compile and run your code using either MPI or OpenMP.

==Assigning the number of CPUs==
Suppose you have 16 CPUs and want to have two MPI processors, each with 8 OpenMP threads.
*Assigning OpenMP threads:
export OMP_NUM_THREADS=8
*Running:
mpirun -np 2 a.out
where a.out is name of the executable.

==OpenMP setting==
One of the main settings that we need be careful about is the "processor affinity". By default, multi-threading affinity is not set in mvapich2. That means all your OpenMP threading will be bound to a single processor if you have not changed this setting (and if you have compiled it through mpicc, mpic++ or mpif90). This is because mvapich2 gives priority to MPI processors and does not allow OpenMP to use more than one CPU (even if there are available cpus for OpenMP threads). This setting can be changed through MV2_ENABLE_AFFINITY variable. In your terminal or PBS file type in the following command to enable OpenMP threads to run on different cores:

export MV2_ENABLE_AFFINITY=0

==Binding MPI runs to different nodes==
By default, mvapich2 tries to put all MPI processors on adjacent cores (not nodes). For example if you request 2 nodes and 8 cores through your PBS file and use "mpirun -np 2 a.out" both MPI processors will be assigned to the first node and the second node will be empty. In order to reserve the cores for OpenMP and put MPI processors on different nodes, you must use a modified nodefile as following:

sed -n "1~${PBS_NUM_PPN}p" $PBS_NODEFILE > my_nodefile
mpirun -f my_nodefile -np $PBS_NUM_NODES my_program

==References==
https://www.cct.lsu.edu/~estrabd/intro-hybrid-mpi-openmp.pdf
https://wikis.nyu.edu/display/NYUHPC/Running+jobs+-+MPI
https://www.mir.wustl.edu/Portals/0/Documents/Uploads/CHPC/WashU_7_mvapich.pdf

Running Hybrid MPI/OpenMP Simulations

2015-11-04T06:21:09Z

Amin1: /* Assigning the number of CPUs */

=Running Hybrid MPI/OpenMP Simulations=
This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed on both MC2 and WCR clusters. In this page we assume the code is already written in the hybrid fashion, e.g. both MPI and OpenMP headers are included in the code and you are able to compile and run your code using either MPI or OpenMP.

==Assigning the number of CPUs==
Suppose you have 16 CPUs and want to have two MPI processors, each with 8 OpenMP threads.
*Assigning OpenMP threads: export
export OMP_NUM_THREADS=8
*Running:
mpirun -np 2 a.out
where a.out is name of the executable.

==OpenMP setting==
One of the main settings that we need be careful about is the "processor affinity". By default, multi-threading affinity is not set in mvapich2. That means all your OpenMP threading will be bound to a single processor if you have not changed this setting (and if you have compiled it through mpicc, mpic++ or mpif90). This is because mvapich2 gives priority to MPI processors and does not allow OpenMP to use more than one CPU (even if there are available cpus for OpenMP threads). This setting can be changed through MV2_ENABLE_AFFINITY variable. In your terminal or PBS file type in the following command to enable OpenMP threads to run on different cores:

export MV2_ENABLE_AFFINITY=0

==Binding MPI runs to different nodes==
By default, mvapich2 tries to put all MPI processors on adjacent cores (not nodes). For example if you request 2 nodes and 8 cores through your PBS file and use "mpirun -np 2 a.out" both MPI processors will be assigned to the first node and the second node will be empty. In order to reserve the cores for OpenMP and put MPI processors on different nodes, you must use a modified nodefile as following:

sed -n "1~${PBS_NUM_PPN}p" $PBS_NODEFILE > my_nodefile
mpirun -f my_nodefile -np $PBS_NUM_NODES my_program

==References==
https://www.cct.lsu.edu/~estrabd/intro-hybrid-mpi-openmp.pdf
https://wikis.nyu.edu/display/NYUHPC/Running+jobs+-+MPI
https://www.mir.wustl.edu/Portals/0/Documents/Uploads/CHPC/WashU_7_mvapich.pdf

Running Hybrid MPI/OpenMP Simulations

2015-11-04T06:20:32Z

Amin1: /* OpenMP setting */

=Running Hybrid MPI/OpenMP Simulations=
This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed on both MC2 and WCR clusters. In this page we assume the code is already written in the hybrid fashion, e.g. both MPI and OpenMP headers are included in the code and you are able to compile and run your code using either MPI or OpenMP.

==Assigning the number of CPUs==
Suppose you have 16 CPUs and want to have two MPI processors, each with 8 OpenMP threads.
*Assigning OpenMP threads: export
OMP_NUM_THREADS=8
*Running:
mpirun -np 2 a.out
where a.out is name of the executable.

==OpenMP setting==
One of the main settings that we need be careful about is the "processor affinity". By default, multi-threading affinity is not set in mvapich2. That means all your OpenMP threading will be bound to a single processor if you have not changed this setting (and if you have compiled it through mpicc, mpic++ or mpif90). This is because mvapich2 gives priority to MPI processors and does not allow OpenMP to use more than one CPU (even if there are available cpus for OpenMP threads). This setting can be changed through MV2_ENABLE_AFFINITY variable. In your terminal or PBS file type in the following command to enable OpenMP threads to run on different cores:

export MV2_ENABLE_AFFINITY=0

==Binding MPI runs to different nodes==
By default, mvapich2 tries to put all MPI processors on adjacent cores (not nodes). For example if you request 2 nodes and 8 cores through your PBS file and use "mpirun -np 2 a.out" both MPI processors will be assigned to the first node and the second node will be empty. In order to reserve the cores for OpenMP and put MPI processors on different nodes, you must use a modified nodefile as following:

sed -n "1~${PBS_NUM_PPN}p" $PBS_NODEFILE > my_nodefile
mpirun -f my_nodefile -np $PBS_NUM_NODES my_program

==References==
https://www.cct.lsu.edu/~estrabd/intro-hybrid-mpi-openmp.pdf
https://wikis.nyu.edu/display/NYUHPC/Running+jobs+-+MPI
https://www.mir.wustl.edu/Portals/0/Documents/Uploads/CHPC/WashU_7_mvapich.pdf

Running Hybrid MPI/OpenMP Simulations

2015-11-04T06:19:26Z

Amin1: /* References */

=Running Hybrid MPI/OpenMP Simulations=
This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed on both MC2 and WCR clusters. In this page we assume the code is already written in the hybrid fashion, e.g. both MPI and OpenMP headers are included in the code and you are able to compile and run your code using either MPI or OpenMP.

==Assigning the number of CPUs==
Suppose you have 16 CPUs and want to have two MPI processors, each with 8 OpenMP threads.
*Assigning OpenMP threads: export
OMP_NUM_THREADS=8
*Running:
mpirun -np 2 a.out
where a.out is name of the executable.

==OpenMP setting==
One of the main settings that we need be careful about is the "processor affinity". By default, multi-threading affinity is not set in mvapich2. That means all your OpenMP threading will be bound to a single processor if you have not changed this setting (and if you have compiled it through mpicc, mpic++ or mpif90). This is because mvapich2 gives priority to MPI threads and does not allow OpenMP to use more than one CPU (even if there are available cpus for OpenMP threads). This setting can be changed through MV2_ENABLE_AFFINITY variable. In your terminal or PBS file type in the following command to enable OpenMP threads to run on different cores:

export MV2_ENABLE_AFFINITY=0

==Binding MPI runs to different nodes==
By default, mvapich2 tries to put all MPI processors on adjacent cores (not nodes). For example if you request 2 nodes and 8 cores through your PBS file and use "mpirun -np 2 a.out" both MPI processors will be assigned to the first node and the second node will be empty. In order to reserve the cores for OpenMP and put MPI processors on different nodes, you must use a modified nodefile as following:

sed -n "1~${PBS_NUM_PPN}p" $PBS_NODEFILE > my_nodefile
mpirun -f my_nodefile -np $PBS_NUM_NODES my_program

==References==
https://www.cct.lsu.edu/~estrabd/intro-hybrid-mpi-openmp.pdf
https://wikis.nyu.edu/display/NYUHPC/Running+jobs+-+MPI
https://www.mir.wustl.edu/Portals/0/Documents/Uploads/CHPC/WashU_7_mvapich.pdf

Running Hybrid MPI/OpenMP Simulations

2015-11-04T06:15:24Z

Amin1: /* Running Hybrid MPI/OpenMP Simulations */

=Running Hybrid MPI/OpenMP Simulations=
This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed on both MC2 and WCR clusters. In this page we assume the code is already written in the hybrid fashion, e.g. both MPI and OpenMP headers are included in the code and you are able to compile and run your code using either MPI or OpenMP.

==Assigning the number of CPUs==
Suppose you have 16 CPUs and want to have two MPI processors, each with 8 OpenMP threads.
*Assigning OpenMP threads: export
OMP_NUM_THREADS=8
*Running:
mpirun -np 2 a.out
where a.out is name of the executable.

==OpenMP setting==
One of the main settings that we need be careful about is the "processor affinity". By default, multi-threading affinity is not set in mvapich2. That means all your OpenMP threading will be bound to a single processor if you have not changed this setting (and if you have compiled it through mpicc, mpic++ or mpif90). This is because mvapich2 gives priority to MPI threads and does not allow OpenMP to use more than one CPU (even if there are available cpus for OpenMP threads). This setting can be changed through MV2_ENABLE_AFFINITY variable. In your terminal or PBS file type in the following command to enable OpenMP threads to run on different cores:

export MV2_ENABLE_AFFINITY=0

==Binding MPI runs to different nodes==
By default, mvapich2 tries to put all MPI processors on adjacent cores (not nodes). For example if you request 2 nodes and 8 cores through your PBS file and use "mpirun -np 2 a.out" both MPI processors will be assigned to the first node and the second node will be empty. In order to reserve the cores for OpenMP and put MPI processors on different nodes, you must use a modified nodefile as following:

sed -n "1~${PBS_NUM_PPN}p" $PBS_NODEFILE > my_nodefile
mpirun -f my_nodefile -np $PBS_NUM_NODES my_program

==References==
https://www.cct.lsu.edu/~estrabd/intro-hybrid-mpi-openmp.pdf
https://wikis.nyu.edu/display/NYUHPC/Running+jobs+-+MPI

Running Hybrid MPI/OpenMP Simulations

2015-11-04T06:14:07Z

Amin1: /* Binding MPI runs to different nodes */

=Running Hybrid MPI/OpenMP Simulations=
This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed on both MC2 and WCR clusters. In this page we assume the code is already written in the hybrid fashion, e.g. both MPI and OpenMP headers are included in the code and you are able to compile and run your code using either MPI or OpenMP.

==Assigning the number of CPUs==
Suppose you have 16 CPUs and want to have two MPI processors, each with 8 OpenMP threads.
*Assigning OpenMP threads: export
OMP_NUM_THREADS=8
*Running:
mpirun -np 2 a.out
where a.out is name of the executable.

==OpenMP setting==
One of the main settings that we need be careful about is the "processor affinity". By default, multi-threading affinity is not set in mvapich2. That means all your OpenMP threading will be bound to a single processor if you have not changed this setting (and if you have compiled it through mpicc, mpic++ or mpif90). This is because mvapich2 gives priority to MPI threads and does not allow OpenMP to use more than one CPU (even if there are available cpus for OpenMP threads). This setting can be changed through MV2_ENABLE_AFFINITY variable. In your terminal or PBS file type in the following command to enable OpenMP threads to run on different cores:

export MV2_ENABLE_AFFINITY=0

==Binding MPI runs to different nodes==
By default, mvapich2 tries to put all MPI processors on adjacent cores (not nodes). For example if you request 2 nodes and 8 cores through your PBS file and use "mpirun -np 2 a.out" both MPI processors will be assigned to the first node and the second node will be empty. In order to reserve the cores for OpenMP and put MPI processors on different nodes, you must use a modified nodefile as following:

sed -n "1~${PBS_NUM_PPN}p" $PBS_NODEFILE > my_nodefile
mpirun -f my_nodefile -np $PBS_NUM_NODES my_program

Running Hybrid MPI/OpenMP Simulations

2015-11-04T06:13:18Z

Amin1: /* Assigning the number of CPUs */

=Running Hybrid MPI/OpenMP Simulations=
This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed on both MC2 and WCR clusters. In this page we assume the code is already written in the hybrid fashion, e.g. both MPI and OpenMP headers are included in the code and you are able to compile and run your code using either MPI or OpenMP.

==Assigning the number of CPUs==
Suppose you have 16 CPUs and want to have two MPI processors, each with 8 OpenMP threads.
*Assigning OpenMP threads: export
OMP_NUM_THREADS=8
*Running:
mpirun -np 2 a.out
where a.out is name of the executable.

==OpenMP setting==
One of the main settings that we need be careful about is the "processor affinity". By default, multi-threading affinity is not set in mvapich2. That means all your OpenMP threading will be bound to a single processor if you have not changed this setting (and if you have compiled it through mpicc, mpic++ or mpif90). This is because mvapich2 gives priority to MPI threads and does not allow OpenMP to use more than one CPU (even if there are available cpus for OpenMP threads). This setting can be changed through MV2_ENABLE_AFFINITY variable. In your terminal or PBS file type in the following command to enable OpenMP threads to run on different cores:

export MV2_ENABLE_AFFINITY=0

==Binding MPI runs to different nodes==
By default, mvapich2 tries to put all MPI threads on adjacent cores (not nodes). For example if you request 2 nodes and 8 cores through your PBS file and use "mpirun -np 2 a.out" both MPI processors will be assigned to the first node and the second node will be empty. In order to reserve the cores for OpenMP and put MPI processors on different nodes, you must use a modified nodefile as following:

sed -n "1~${PBS_NUM_PPN}p" $PBS_NODEFILE > my_nodefile
mpirun -f my_nodefile -np $PBS_NUM_NODES my_program

Running Hybrid MPI/OpenMP Simulations

2015-11-04T06:13:03Z

Amin1: /* Assigning the number of CPUs */

=Running Hybrid MPI/OpenMP Simulations=
This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed on both MC2 and WCR clusters. In this page we assume the code is already written in the hybrid fashion, e.g. both MPI and OpenMP headers are included in the code and you are able to compile and run your code using either MPI or OpenMP.

==Assigning the number of CPUs==
Suppose you have 16 CPUs and want to have two MPI processors, each with 8 OpenMP threads.
*Assigning OpenMP threads: export
OMP_NUM_THREADS=8
*Running: mpirun -np 2 a.out
where a.out is name of the executable.

==OpenMP setting==
One of the main settings that we need be careful about is the "processor affinity". By default, multi-threading affinity is not set in mvapich2. That means all your OpenMP threading will be bound to a single processor if you have not changed this setting (and if you have compiled it through mpicc, mpic++ or mpif90). This is because mvapich2 gives priority to MPI threads and does not allow OpenMP to use more than one CPU (even if there are available cpus for OpenMP threads). This setting can be changed through MV2_ENABLE_AFFINITY variable. In your terminal or PBS file type in the following command to enable OpenMP threads to run on different cores:

export MV2_ENABLE_AFFINITY=0

==Binding MPI runs to different nodes==
By default, mvapich2 tries to put all MPI threads on adjacent cores (not nodes). For example if you request 2 nodes and 8 cores through your PBS file and use "mpirun -np 2 a.out" both MPI processors will be assigned to the first node and the second node will be empty. In order to reserve the cores for OpenMP and put MPI processors on different nodes, you must use a modified nodefile as following:

sed -n "1~${PBS_NUM_PPN}p" $PBS_NODEFILE > my_nodefile
mpirun -f my_nodefile -np $PBS_NUM_NODES my_program

Running Hybrid MPI/OpenMP Simulations

2015-11-04T06:12:33Z

Amin1: /* Binding MPI runs to different nodes */

=Running Hybrid MPI/OpenMP Simulations=
This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed on both MC2 and WCR clusters. In this page we assume the code is already written in the hybrid fashion, e.g. both MPI and OpenMP headers are included in the code and you are able to compile and run your code using either MPI or OpenMP.

==Assigning the number of CPUs==
Suppose you have 16 CPUs and want to have two MPI processors, each with 8 OpenMP threads.
*Assigning OpenMP threads: export OMP_NUM_THREADS=8
*Running: mpirun -np 2 a.out
where a.out is name of the executable.

==OpenMP setting==
One of the main settings that we need be careful about is the "processor affinity". By default, multi-threading affinity is not set in mvapich2. That means all your OpenMP threading will be bound to a single processor if you have not changed this setting (and if you have compiled it through mpicc, mpic++ or mpif90). This is because mvapich2 gives priority to MPI threads and does not allow OpenMP to use more than one CPU (even if there are available cpus for OpenMP threads). This setting can be changed through MV2_ENABLE_AFFINITY variable. In your terminal or PBS file type in the following command to enable OpenMP threads to run on different cores:

export MV2_ENABLE_AFFINITY=0

==Binding MPI runs to different nodes==
By default, mvapich2 tries to put all MPI threads on adjacent cores (not nodes). For example if you request 2 nodes and 8 cores through your PBS file and use "mpirun -np 2 a.out" both MPI processors will be assigned to the first node and the second node will be empty. In order to reserve the cores for OpenMP and put MPI processors on different nodes, you must use a modified nodefile as following:

sed -n "1~${PBS_NUM_PPN}p" $PBS_NODEFILE > my_nodefile
mpirun -f my_nodefile -np $PBS_NUM_NODES my_program

Running Hybrid MPI/OpenMP Simulations

2015-11-04T06:12:18Z

Amin1: /* OpenMP setting */

=Running Hybrid MPI/OpenMP Simulations=
This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed on both MC2 and WCR clusters. In this page we assume the code is already written in the hybrid fashion, e.g. both MPI and OpenMP headers are included in the code and you are able to compile and run your code using either MPI or OpenMP.

==Assigning the number of CPUs==
Suppose you have 16 CPUs and want to have two MPI processors, each with 8 OpenMP threads.
*Assigning OpenMP threads: export OMP_NUM_THREADS=8
*Running: mpirun -np 2 a.out
where a.out is name of the executable.

==OpenMP setting==
One of the main settings that we need be careful about is the "processor affinity". By default, multi-threading affinity is not set in mvapich2. That means all your OpenMP threading will be bound to a single processor if you have not changed this setting (and if you have compiled it through mpicc, mpic++ or mpif90). This is because mvapich2 gives priority to MPI threads and does not allow OpenMP to use more than one CPU (even if there are available cpus for OpenMP threads). This setting can be changed through MV2_ENABLE_AFFINITY variable. In your terminal or PBS file type in the following command to enable OpenMP threads to run on different cores:

export MV2_ENABLE_AFFINITY=0

==Binding MPI runs to different nodes==
By default, mvapich2 tries to put all MPI threads on adjacent cores (not nodes). For example if you request 2 nodes and 8 cores through your PBS file and use "mpirun -np 2 a.out" both MPI processors will be assigned to the first node and the second node will be empty. In order to reserve the cores for OpenMP and put MPI processors on different nodes, you must use a modified nodefile as following:

sed -n "1~${PBS_NUM_PPN}p" $PBS_NODEFILE > my_nodefile

mpirun -f my_nodefile -np $PBS_NUM_NODES my_program

Running Hybrid MPI/OpenMP Simulations

2015-11-04T06:10:30Z

Amin1: /* Binding MPI runs to different nodes */

=Running Hybrid MPI/OpenMP Simulations=
This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed on both MC2 and WCR clusters. In this page we assume the code is already written in the hybrid fashion, e.g. both MPI and OpenMP headers are included in the code and you are able to compile and run your code using either MPI or OpenMP.

==Assigning the number of CPUs==
Suppose you have 16 CPUs and want to have two MPI processors, each with 8 OpenMP threads.
*Assigning OpenMP threads: export OMP_NUM_THREADS=8
*Running: mpirun -np 2 a.out
where a.out is name of the executable.

==OpenMP setting==
One of the main settings that we need be careful about is the "processor affinity". By default, multi-threading affinity is not set in mvapich2. That means all your OpenMP threading will be bound to a single processor if you have not changed this setting (and if you have compiled it through mpicc, mpic++ or mpif90). This is because mvapich2 gives priority to MPI threads and does not allow OpenMP to use more than one CPU (even if there are available cpus for OpenMP threads). This setting can be changed through MV2_ENABLE_AFFINITY variable. In your terminal or PBS file type in the following command to enable OpenMP threads to run on different cores:

*export MV2_ENABLE_AFFINITY=0

==Binding MPI runs to different nodes==
By default, mvapich2 tries to put all MPI threads on adjacent cores (not nodes). For example if you request 2 nodes and 8 cores through your PBS file and use "mpirun -np 2 a.out" both MPI processors will be assigned to the first node and the second node will be empty. In order to reserve the cores for OpenMP and put MPI processors on different nodes, you must use a modified nodefile as following:

sed -n "1~${PBS_NUM_PPN}p" $PBS_NODEFILE > my_nodefile

mpirun -f my_nodefile -np $PBS_NUM_NODES my_program

Running Hybrid MPI/OpenMP Simulations

2015-11-04T06:09:47Z

Amin1: /* Running Hybrid MPI/OpenMP Simulations */

=Running Hybrid MPI/OpenMP Simulations=
This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed on both MC2 and WCR clusters. In this page we assume the code is already written in the hybrid fashion, e.g. both MPI and OpenMP headers are included in the code and you are able to compile and run your code using either MPI or OpenMP.

==Assigning the number of CPUs==
Suppose you have 16 CPUs and want to have two MPI processors, each with 8 OpenMP threads.
*Assigning OpenMP threads: export OMP_NUM_THREADS=8
*Running: mpirun -np 2 a.out
where a.out is name of the executable.

==OpenMP setting==
One of the main settings that we need be careful about is the "processor affinity". By default, multi-threading affinity is not set in mvapich2. That means all your OpenMP threading will be bound to a single processor if you have not changed this setting (and if you have compiled it through mpicc, mpic++ or mpif90). This is because mvapich2 gives priority to MPI threads and does not allow OpenMP to use more than one CPU (even if there are available cpus for OpenMP threads). This setting can be changed through MV2_ENABLE_AFFINITY variable. In your terminal or PBS file type in the following command to enable OpenMP threads to run on different cores:

*export MV2_ENABLE_AFFINITY=0

==Binding MPI runs to different nodes==
By default, mvapich2 tries to put all MPI threads on adjacent cores (not nodes). For example if you request 2 nodes and 8 cores through your PBS file and use "mpirun -np 2 a.out" both MPI processors will be assigned to the first node and the second node will be empty. In order to reserve the cores for OpenMP and put MPI processors on different nodes, you must use a modified nodefile as following:

sed -n "1~${PBS_NUM_PPN}p" $PBS_NODEFILE > my_nodefile
mpirun -f my_nodefile -np $PBS_NUM_NODES my_program

Running Hybrid MPI/OpenMP Simulations

2015-11-04T05:26:17Z

Amin1: /* OpenMP setting */

Running Hybrid MPI/OpenMP Simulations

2015-11-04T05:25:23Z

Amin1: /* OpenMP setting */

Running Hybrid MPI/OpenMP Simulations

2015-11-04T05:24:07Z

Amin1: /* OpenMP setting */

Running Hybrid MPI/OpenMP Simulations

2015-11-04T05:10:05Z

Amin1: Created page with "=Running Hybrid MPI/OpenMP Simulations= This tutorial explains how to run a multi-threaded hybrid MPI/OpenMP simulation using mvapich2 library. mvapich2 is currently installed..."

Tutorials

2015-11-04T04:53:58Z

Amin1: /* Computers */

== Simulation Codes ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[MD++ Manuals]]
!width="200" | [[ParaDiS Manuals]]
!width="300" | [[ParaDiS Workshop Notes]]
|-
!width="200" | [[DDLab Manuals]]
!width="200" | [[VASP Manuals]]
!width="300" | [[How to compile Qbox]]
|-
!width="200" |
!width="200" | [[How to compile LAMMPS]]
!width="300" | [[How to compile pimc++]]
|}

== Computers ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[Unix Basics]]
!width="200" | [[Computer Setup]]
!width="200" | [[Computing Clusters | Parallel Clusters]]
|-
!width="200" | [[Install Ubuntu]]
!width="200" | [[Install FFTW3]]
!width="200" | [[Install HDF5]]
|-
!width="200" | [[Install GSL]]
!width="200" | [[Standard Tcl Library | Tcl Library]]
!width="200" | [[Install the GNU Compiler Collection (GCC)]]
|-
!width="200" | [[Running Hybrid MPI/OpenMP Simulations]]
|}

== Scientific Background ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[Dislocations]]
|}

== Science Outreach ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [http://www.youtube.com/watch?v=SgM-Xes16Sw Outreach interview]
!width="200" | [[How to install MD++ in Ubuntu | Install MD++ in Ubuntu]]
!width="200" | [[Introduction to Molecular Dynamics Simulations of Fullerenes | MD of Fullerenes]]
|-
!width="200" | [[Images of Fullerenes]]
!width="200" | [[Android Applications and Information]]
|

|}

<br> <br>

== [[Tutorial:Members_Only | Members Only]] ==

Amin Aghaei

2014-01-10T23:47:14Z

Amin1: /* Publications */

=Amin Aghaei=
Amin is a Postdoctoral researcher in the Micro and Nano-Mechanical group.

===Education===
*PhD in Computational Mechanics (2009-2013), Carnegie Mellon university<br/>
*Master of Science in Computational Mechanics (2012), Carnegie Mellon university<br/>
*Master of Science in Structural engineering (2006-2008), Sharif University of Technology, Iran<br/>
*Bachelor of Science in Civil engineering (2002-2006), University of Tehran, Iran.

===Publications===
* '''A. Aghaei''', K. Dayal, R.S. Elliott, “''Symmetry-Adapted Phonon Analysis of Nanotubes''”, Journal of the Mechanics and Physics of Solids, 61 (2013) 557–578.

* '''A. Aghaei''', K. Dayal, R.S. Elliott, “''Anomalous Phonon Behavior of Carbon Nanotubes: First-Order Influence of External Load''”, Journal of Applied Physics (2013) 113:023503.

* '''A. Aghaei''', K. Dayal, “''Tension-and-Twist of Chiral Nanotubes: Torsional Buckling, Mechanical Response, and Indicators of Failure''”, Modeling and Simulation in Material Science Engineering, 20:085001 (2012).

* '''A. Aghaei''', K. Dayal, “''Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading''”, Journal of Applied Physics (2011) 109:123501.

* M.J. Abdolhosseini Qomi, '''A. Aghaei''', A.R. Khoei, “''Multiscale Modeling of Surface Effect via Boundary Cauchy-Born Method''”, International Journal for Numerical Methods in Engineering, 45 (2011) 827–846.

* '''A. Aghaei''', M.J. Abdolhosseini and A.R. Khoei, “''Stability and Size-Dependency of Cauchy-Born Hypothesis in Three- Dimensional Applications''”, International Journal of Solids and Structures, (2009) 1925.

* A.R. Khoei, M.T. Kazemi, M.J. Abdolhosseini and '''A. Aghaei''', “''An Investigation on the Validity of Cauchy-Born Hypothesis Using Sutton-Chen Many-Body Potential''”, Computational Material Science, 44 (2009) 999.

===Awards===
*2012-13 Dowd-ICES Fellowship, Carnegie Mellon University, 2012 – 2013.
*Dean Fellowship, Carnegie Mellon University, 2009 – 2012.
*USNCCM12 Travel Award, US Association for Computational Mechanics, 2013.
*Fenves Travel Grant, Carnegie Mellon University, 2011, 2012.
*GSA Conference Funding Award, Carnegie Mellon University, 2010, 2012.
*SES2011 travel scholarship, 48’th Annual Technical Meeting of Society of Engineering Sciences.
*USNCTAM2010 scholarship, 16th U.S. National Congress of Theoretical and Applied Mechanics.
*Tavakoli prize for conducting original researches, Sharif University of Technology, 2009.
*Ranked 3’rd in the nationwide Iranian entrance exam for M.Sc. degree in civil eng. among around 16,000 examinees, 2006.

===Contact Information===
Office: Durand 204 <br/>
<table>
<tr><td>Address: <td/><td>Amin Aghaei<td/><tr/>
<tr><td><td/><td>Mechanics and Computation Group<td/><tr/>
<td><td/><td>Durand Bldg. Rm. 204<td/><tr/>
<tr><td><td/><td>496 Lomita Mall<td/><tr/>
<tr><td><td/><td>Stanford, CA 94305<td/><tr/>
</table>
Email: amin1@stanford.edu

Amin Aghaei

2014-01-10T23:46:14Z

Amin1: /* Publications */

=Amin Aghaei=
Amin is a Postdoctoral researcher in the Micro and Nano-Mechanical group.

===Education===
*PhD in Computational Mechanics (2009-2013), Carnegie Mellon university<br/>
*Master of Science in Computational Mechanics (2012), Carnegie Mellon university<br/>
*Master of Science in Structural engineering (2006-2008), Sharif University of Technology, Iran<br/>
*Bachelor of Science in Civil engineering (2002-2006), University of Tehran, Iran.

===Publications===
* '''A. Aghaei''', K. Dayal, R.S. Elliott, “Symmetry-Adapted Phonon Analysis of Nanotubes”, Journal of the Mechanics and Physics of Solids, 61 (2013) 557–578.

* A. Aghaei, K. Dayal, R.S. Elliott, “Anomalous Phonon Behavior of Carbon Nanotubes: First-Order Influence of External Load”, Journal of Applied Physics (2013) 113:023503.

* A. Aghaei, K. Dayal, “Tension-and-Twist of Chiral Nanotubes: Torsional Buckling, Mechanical Response, and Indicators of Failure”, Modeling and Simulation in Material Science Engineering, 20:085001 (2012).

* A. Aghaei, K. Dayal, “Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading”, Journal of Applied Physics (2011) 109:123501.

* M.J. Abdolhosseini Qomi, A. Aghaei, A.R. Khoei, “Multiscale Modeling of Surface Effect via Boundary Cauchy-Born Method”, International Journal for Numerical Methods in Engineering, 45 (2011) 827–846.

* A. Aghaei, M.J. Abdolhosseini and A.R. Khoei, “Stability and Size-Dependency of Cauchy-Born Hypothesis in Three- Dimensional Applications”, International Journal of Solids and Structures, (2009) 1925.

* A.R. Khoei, M.T. Kazemi, M.J. Abdolhosseini and A. Aghaei, “An Investigation on the Validity of Cauchy-Born Hypothesis Using Sutton-Chen Many-Body Potential”, Computational Material Science, 44 (2009) 999.

===Awards===
*2012-13 Dowd-ICES Fellowship, Carnegie Mellon University, 2012 – 2013.
*Dean Fellowship, Carnegie Mellon University, 2009 – 2012.
*USNCCM12 Travel Award, US Association for Computational Mechanics, 2013.
*Fenves Travel Grant, Carnegie Mellon University, 2011, 2012.
*GSA Conference Funding Award, Carnegie Mellon University, 2010, 2012.
*SES2011 travel scholarship, 48’th Annual Technical Meeting of Society of Engineering Sciences.
*USNCTAM2010 scholarship, 16th U.S. National Congress of Theoretical and Applied Mechanics.
*Tavakoli prize for conducting original researches, Sharif University of Technology, 2009.
*Ranked 3’rd in the nationwide Iranian entrance exam for M.Sc. degree in civil eng. among around 16,000 examinees, 2006.

===Contact Information===
Office: Durand 204 <br/>
<table>
<tr><td>Address: <td/><td>Amin Aghaei<td/><tr/>
<tr><td><td/><td>Mechanics and Computation Group<td/><tr/>
<td><td/><td>Durand Bldg. Rm. 204<td/><tr/>
<tr><td><td/><td>496 Lomita Mall<td/><tr/>
<tr><td><td/><td>Stanford, CA 94305<td/><tr/>
</table>
Email: amin1@stanford.edu

Amin Aghaei

2014-01-10T23:45:25Z

Amin1: /* Publications */

=Amin Aghaei=
Amin is a Postdoctoral researcher in the Micro and Nano-Mechanical group.

===Education===
*PhD in Computational Mechanics (2009-2013), Carnegie Mellon university<br/>
*Master of Science in Computational Mechanics (2012), Carnegie Mellon university<br/>
*Master of Science in Structural engineering (2006-2008), Sharif University of Technology, Iran<br/>
*Bachelor of Science in Civil engineering (2002-2006), University of Tehran, Iran.

===Publications===
* ""A. Aghaei"", K. Dayal, R.S. Elliott, “Symmetry-Adapted Phonon Analysis of Nanotubes”, Journal of the Mechanics and Physics of Solids, 61 (2013) 557–578.

* A. Aghaei, K. Dayal, R.S. Elliott, “Anomalous Phonon Behavior of Carbon Nanotubes: First-Order Influence of External Load”, Journal of Applied Physics (2013) 113:023503.

* A. Aghaei, K. Dayal, “Tension-and-Twist of Chiral Nanotubes: Torsional Buckling, Mechanical Response, and Indicators of Failure”, Modeling and Simulation in Material Science Engineering, 20:085001 (2012).

* A. Aghaei, K. Dayal, “Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading”, Journal of Applied Physics (2011) 109:123501.

* M.J. Abdolhosseini Qomi, A. Aghaei, A.R. Khoei, “Multiscale Modeling of Surface Effect via Boundary Cauchy-Born Method”, International Journal for Numerical Methods in Engineering, 45 (2011) 827–846.

* A. Aghaei, M.J. Abdolhosseini and A.R. Khoei, “Stability and Size-Dependency of Cauchy-Born Hypothesis in Three- Dimensional Applications”, International Journal of Solids and Structures, (2009) 1925.

* A.R. Khoei, M.T. Kazemi, M.J. Abdolhosseini and A. Aghaei, “An Investigation on the Validity of Cauchy-Born Hypothesis Using Sutton-Chen Many-Body Potential”, Computational Material Science, 44 (2009) 999.

===Awards===
*2012-13 Dowd-ICES Fellowship, Carnegie Mellon University, 2012 – 2013.
*Dean Fellowship, Carnegie Mellon University, 2009 – 2012.
*USNCCM12 Travel Award, US Association for Computational Mechanics, 2013.
*Fenves Travel Grant, Carnegie Mellon University, 2011, 2012.
*GSA Conference Funding Award, Carnegie Mellon University, 2010, 2012.
*SES2011 travel scholarship, 48’th Annual Technical Meeting of Society of Engineering Sciences.
*USNCTAM2010 scholarship, 16th U.S. National Congress of Theoretical and Applied Mechanics.
*Tavakoli prize for conducting original researches, Sharif University of Technology, 2009.
*Ranked 3’rd in the nationwide Iranian entrance exam for M.Sc. degree in civil eng. among around 16,000 examinees, 2006.

===Contact Information===
Office: Durand 204 <br/>
<table>
<tr><td>Address: <td/><td>Amin Aghaei<td/><tr/>
<tr><td><td/><td>Mechanics and Computation Group<td/><tr/>
<td><td/><td>Durand Bldg. Rm. 204<td/><tr/>
<tr><td><td/><td>496 Lomita Mall<td/><tr/>
<tr><td><td/><td>Stanford, CA 94305<td/><tr/>
</table>
Email: amin1@stanford.edu

Amin Aghaei

2014-01-10T23:45:13Z

Amin1: /* Publications */

=Amin Aghaei=
Amin is a Postdoctoral researcher in the Micro and Nano-Mechanical group.

===Education===
*PhD in Computational Mechanics (2009-2013), Carnegie Mellon university<br/>
*Master of Science in Computational Mechanics (2012), Carnegie Mellon university<br/>
*Master of Science in Structural engineering (2006-2008), Sharif University of Technology, Iran<br/>
*Bachelor of Science in Civil engineering (2002-2006), University of Tehran, Iran.

===Publications===
* A. Aghaei, K. Dayal, R.S. Elliott, “Symmetry-Adapted Phonon Analysis of Nanotubes”, Journal of the Mechanics and Physics of Solids, 61 (2013) 557–578.

* A. Aghaei, K. Dayal, R.S. Elliott, “Anomalous Phonon Behavior of Carbon Nanotubes: First-Order Influence of External Load”, Journal of Applied Physics (2013) 113:023503.

* A. Aghaei, K. Dayal, “Tension-and-Twist of Chiral Nanotubes: Torsional Buckling, Mechanical Response, and Indicators of Failure”, Modeling and Simulation in Material Science Engineering, 20:085001 (2012).

* A. Aghaei, K. Dayal, “Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading”, Journal of Applied Physics (2011) 109:123501.

* M.J. Abdolhosseini Qomi, A. Aghaei, A.R. Khoei, “Multiscale Modeling of Surface Effect via Boundary Cauchy-Born Method”, International Journal for Numerical Methods in Engineering, 45 (2011) 827–846.

* A. Aghaei, M.J. Abdolhosseini and A.R. Khoei, “Stability and Size-Dependency of Cauchy-Born Hypothesis in Three- Dimensional Applications”, International Journal of Solids and Structures, (2009) 1925.

* A.R. Khoei, M.T. Kazemi, M.J. Abdolhosseini and A. Aghaei, “An Investigation on the Validity of Cauchy-Born Hypothesis Using Sutton-Chen Many-Body Potential”, Computational Material Science, 44 (2009) 999.

===Awards===
*2012-13 Dowd-ICES Fellowship, Carnegie Mellon University, 2012 – 2013.
*Dean Fellowship, Carnegie Mellon University, 2009 – 2012.
*USNCCM12 Travel Award, US Association for Computational Mechanics, 2013.
*Fenves Travel Grant, Carnegie Mellon University, 2011, 2012.
*GSA Conference Funding Award, Carnegie Mellon University, 2010, 2012.
*SES2011 travel scholarship, 48’th Annual Technical Meeting of Society of Engineering Sciences.
*USNCTAM2010 scholarship, 16th U.S. National Congress of Theoretical and Applied Mechanics.
*Tavakoli prize for conducting original researches, Sharif University of Technology, 2009.
*Ranked 3’rd in the nationwide Iranian entrance exam for M.Sc. degree in civil eng. among around 16,000 examinees, 2006.

===Contact Information===
Office: Durand 204 <br/>
<table>
<tr><td>Address: <td/><td>Amin Aghaei<td/><tr/>
<tr><td><td/><td>Mechanics and Computation Group<td/><tr/>
<td><td/><td>Durand Bldg. Rm. 204<td/><tr/>
<tr><td><td/><td>496 Lomita Mall<td/><tr/>
<tr><td><td/><td>Stanford, CA 94305<td/><tr/>
</table>
Email: amin1@stanford.edu

Amin Aghaei

2014-01-10T23:42:23Z

Amin1: /* Publications */

=Amin Aghaei=
Amin is a Postdoctoral researcher in the Micro and Nano-Mechanical group.

===Education===
*PhD in Computational Mechanics (2009-2013), Carnegie Mellon university<br/>
*Master of Science in Computational Mechanics (2012), Carnegie Mellon university<br/>
*Master of Science in Structural engineering (2006-2008), Sharif University of Technology, Iran<br/>
*Bachelor of Science in Civil engineering (2002-2006), University of Tehran, Iran.

===Publications===
* A. Aghaei, K. Dayal, R.S. Elliott, “Symmetry-Adapted Phonon Analysis of Nanotubes”, Journal of the Mechanics and Physics of Solids, 61 (2013) 557–578. <a href="http://www.sciencedirect.com/science/article/pii/S0022509612002013/">pdf</a>

<a href="http://www.w3schools.com/">Visit W3Schools</a>

* A. Aghaei, K. Dayal, R.S. Elliott, “Anomalous Phonon Behavior of Carbon Nanotubes: First-Order Influence of External Load”, Journal of Applied Physics (2013) 113:023503.

* A. Aghaei, K. Dayal, “Tension-and-Twist of Chiral Nanotubes: Torsional Buckling, Mechanical Response, and Indicators of Failure”, Modeling and Simulation in Material Science Engineering, 20:085001 (2012).

* A. Aghaei, K. Dayal, “Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading”, Journal of Applied Physics (2011) 109:123501.

* M.J. Abdolhosseini Qomi, A. Aghaei, A.R. Khoei, “Multiscale Modeling of Surface Effect via Boundary Cauchy-Born Method”, International Journal for Numerical Methods in Engineering, 45 (2011) 827–846.

* A. Aghaei, M.J. Abdolhosseini and A.R. Khoei, “Stability and Size-Dependency of Cauchy-Born Hypothesis in Three- Dimensional Applications”, International Journal of Solids and Structures, (2009) 1925.

* A.R. Khoei, M.T. Kazemi, M.J. Abdolhosseini and A. Aghaei, “An Investigation on the Validity of Cauchy-Born Hypothesis Using Sutton-Chen Many-Body Potential”, Computational Material Science, 44 (2009) 999.

===Awards===
*2012-13 Dowd-ICES Fellowship, Carnegie Mellon University, 2012 – 2013.
*Dean Fellowship, Carnegie Mellon University, 2009 – 2012.
*USNCCM12 Travel Award, US Association for Computational Mechanics, 2013.
*Fenves Travel Grant, Carnegie Mellon University, 2011, 2012.
*GSA Conference Funding Award, Carnegie Mellon University, 2010, 2012.
*SES2011 travel scholarship, 48’th Annual Technical Meeting of Society of Engineering Sciences.
*USNCTAM2010 scholarship, 16th U.S. National Congress of Theoretical and Applied Mechanics.
*Tavakoli prize for conducting original researches, Sharif University of Technology, 2009.
*Ranked 3’rd in the nationwide Iranian entrance exam for M.Sc. degree in civil eng. among around 16,000 examinees, 2006.

===Contact Information===
Office: Durand 204 <br/>
<table>
<tr><td>Address: <td/><td>Amin Aghaei<td/><tr/>
<tr><td><td/><td>Mechanics and Computation Group<td/><tr/>
<td><td/><td>Durand Bldg. Rm. 204<td/><tr/>
<tr><td><td/><td>496 Lomita Mall<td/><tr/>
<tr><td><td/><td>Stanford, CA 94305<td/><tr/>
</table>
Email: amin1@stanford.edu

Amin Aghaei

2014-01-10T23:41:57Z

Amin1: /* Publications */

=Amin Aghaei=
Amin is a Postdoctoral researcher in the Micro and Nano-Mechanical group.

===Education===
*PhD in Computational Mechanics (2009-2013), Carnegie Mellon university<br/>
*Master of Science in Computational Mechanics (2012), Carnegie Mellon university<br/>
*Master of Science in Structural engineering (2006-2008), Sharif University of Technology, Iran<br/>
*Bachelor of Science in Civil engineering (2002-2006), University of Tehran, Iran.

===Publications===
* A. Aghaei, K. Dayal, R.S. Elliott, “Symmetry-Adapted Phonon Analysis of Nanotubes”, Journal of the Mechanics and Physics of Solids, 61 (2013) 557–578. <a href="http://www.sciencedirect.com/science/article/pii/S0022509612002013/">pdf</a>

* A. Aghaei, K. Dayal, R.S. Elliott, “Anomalous Phonon Behavior of Carbon Nanotubes: First-Order Influence of External Load”, Journal of Applied Physics (2013) 113:023503.

* A. Aghaei, K. Dayal, “Tension-and-Twist of Chiral Nanotubes: Torsional Buckling, Mechanical Response, and Indicators of Failure”, Modeling and Simulation in Material Science Engineering, 20:085001 (2012).

* A. Aghaei, K. Dayal, “Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading”, Journal of Applied Physics (2011) 109:123501.

* M.J. Abdolhosseini Qomi, A. Aghaei, A.R. Khoei, “Multiscale Modeling of Surface Effect via Boundary Cauchy-Born Method”, International Journal for Numerical Methods in Engineering, 45 (2011) 827–846.

* A. Aghaei, M.J. Abdolhosseini and A.R. Khoei, “Stability and Size-Dependency of Cauchy-Born Hypothesis in Three- Dimensional Applications”, International Journal of Solids and Structures, (2009) 1925.

* A.R. Khoei, M.T. Kazemi, M.J. Abdolhosseini and A. Aghaei, “An Investigation on the Validity of Cauchy-Born Hypothesis Using Sutton-Chen Many-Body Potential”, Computational Material Science, 44 (2009) 999.

===Awards===
*2012-13 Dowd-ICES Fellowship, Carnegie Mellon University, 2012 – 2013.
*Dean Fellowship, Carnegie Mellon University, 2009 – 2012.
*USNCCM12 Travel Award, US Association for Computational Mechanics, 2013.
*Fenves Travel Grant, Carnegie Mellon University, 2011, 2012.
*GSA Conference Funding Award, Carnegie Mellon University, 2010, 2012.
*SES2011 travel scholarship, 48’th Annual Technical Meeting of Society of Engineering Sciences.
*USNCTAM2010 scholarship, 16th U.S. National Congress of Theoretical and Applied Mechanics.
*Tavakoli prize for conducting original researches, Sharif University of Technology, 2009.
*Ranked 3’rd in the nationwide Iranian entrance exam for M.Sc. degree in civil eng. among around 16,000 examinees, 2006.

===Contact Information===
Office: Durand 204 <br/>
<table>
<tr><td>Address: <td/><td>Amin Aghaei<td/><tr/>
<tr><td><td/><td>Mechanics and Computation Group<td/><tr/>
<td><td/><td>Durand Bldg. Rm. 204<td/><tr/>
<tr><td><td/><td>496 Lomita Mall<td/><tr/>
<tr><td><td/><td>Stanford, CA 94305<td/><tr/>
</table>
Email: amin1@stanford.edu

Amin Aghaei

2014-01-10T23:41:21Z

Amin1: /* Publications */

=Amin Aghaei=
Amin is a Postdoctoral researcher in the Micro and Nano-Mechanical group.

===Education===
*PhD in Computational Mechanics (2009-2013), Carnegie Mellon university<br/>
*Master of Science in Computational Mechanics (2012), Carnegie Mellon university<br/>
*Master of Science in Structural engineering (2006-2008), Sharif University of Technology, Iran<br/>
*Bachelor of Science in Civil engineering (2002-2006), University of Tehran, Iran.

===Publications===
* A. Aghaei, K. Dayal, R.S. Elliott, “Symmetry-Adapted Phonon Analysis of Nanotubes”, Journal of the Mechanics and Physics of Solids, 61 (2013) 557–578. <a href="http://www.sciencedirect.com/science/article/pii/S0022509612002013">pdf</a>

* A. Aghaei, K. Dayal, R.S. Elliott, “Anomalous Phonon Behavior of Carbon Nanotubes: First-Order Influence of External Load”, Journal of Applied Physics (2013) 113:023503.

* A. Aghaei, K. Dayal, “Tension-and-Twist of Chiral Nanotubes: Torsional Buckling, Mechanical Response, and Indicators of Failure”, Modeling and Simulation in Material Science Engineering, 20:085001 (2012).

* A. Aghaei, K. Dayal, “Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading”, Journal of Applied Physics (2011) 109:123501.

* M.J. Abdolhosseini Qomi, A. Aghaei, A.R. Khoei, “Multiscale Modeling of Surface Effect via Boundary Cauchy-Born Method”, International Journal for Numerical Methods in Engineering, 45 (2011) 827–846.

* A. Aghaei, M.J. Abdolhosseini and A.R. Khoei, “Stability and Size-Dependency of Cauchy-Born Hypothesis in Three- Dimensional Applications”, International Journal of Solids and Structures, (2009) 1925.

* A.R. Khoei, M.T. Kazemi, M.J. Abdolhosseini and A. Aghaei, “An Investigation on the Validity of Cauchy-Born Hypothesis Using Sutton-Chen Many-Body Potential”, Computational Material Science, 44 (2009) 999.

===Awards===
*2012-13 Dowd-ICES Fellowship, Carnegie Mellon University, 2012 – 2013.
*Dean Fellowship, Carnegie Mellon University, 2009 – 2012.
*USNCCM12 Travel Award, US Association for Computational Mechanics, 2013.
*Fenves Travel Grant, Carnegie Mellon University, 2011, 2012.
*GSA Conference Funding Award, Carnegie Mellon University, 2010, 2012.
*SES2011 travel scholarship, 48’th Annual Technical Meeting of Society of Engineering Sciences.
*USNCTAM2010 scholarship, 16th U.S. National Congress of Theoretical and Applied Mechanics.
*Tavakoli prize for conducting original researches, Sharif University of Technology, 2009.
*Ranked 3’rd in the nationwide Iranian entrance exam for M.Sc. degree in civil eng. among around 16,000 examinees, 2006.

===Contact Information===
Office: Durand 204 <br/>
<table>
<tr><td>Address: <td/><td>Amin Aghaei<td/><tr/>
<tr><td><td/><td>Mechanics and Computation Group<td/><tr/>
<td><td/><td>Durand Bldg. Rm. 204<td/><tr/>
<tr><td><td/><td>496 Lomita Mall<td/><tr/>
<tr><td><td/><td>Stanford, CA 94305<td/><tr/>
</table>
Email: amin1@stanford.edu

Amin Aghaei

2014-01-10T23:39:02Z

Amin1: /* Publications */

=Amin Aghaei=
Amin is a Postdoctoral researcher in the Micro and Nano-Mechanical group.

===Education===
*PhD in Computational Mechanics (2009-2013), Carnegie Mellon university<br/>
*Master of Science in Computational Mechanics (2012), Carnegie Mellon university<br/>
*Master of Science in Structural engineering (2006-2008), Sharif University of Technology, Iran<br/>
*Bachelor of Science in Civil engineering (2002-2006), University of Tehran, Iran.

===Publications===
* A. Aghaei, K. Dayal, R.S. Elliott, “Symmetry-Adapted Phonon Analysis of Nanotubes”, Journal of the Mechanics and Physics of Solids, 61 (2013) 557–578.

* A. Aghaei, K. Dayal, R.S. Elliott, “Anomalous Phonon Behavior of Carbon Nanotubes: First-Order Influence of External Load”, Journal of Applied Physics (2013) 113:023503.

* A. Aghaei, K. Dayal, “Tension-and-Twist of Chiral Nanotubes: Torsional Buckling, Mechanical Response, and Indicators of Failure”, Modeling and Simulation in Material Science Engineering, 20:085001 (2012).

* A. Aghaei, K. Dayal, “Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading”, Journal of Applied Physics (2011) 109:123501.

* M.J. Abdolhosseini Qomi, A. Aghaei, A.R. Khoei, “Multiscale Modeling of Surface Effect via Boundary Cauchy-Born Method”, International Journal for Numerical Methods in Engineering, 45 (2011) 827–846.

* A. Aghaei, M.J. Abdolhosseini and A.R. Khoei, “Stability and Size-Dependency of Cauchy-Born Hypothesis in Three- Dimensional Applications”, International Journal of Solids and Structures, (2009) 1925.

* A.R. Khoei, M.T. Kazemi, M.J. Abdolhosseini and A. Aghaei, “An Investigation on the Validity of Cauchy-Born Hypothesis Using Sutton-Chen Many-Body Potential”, Computational Material Science, 44 (2009) 999.

===Awards===
*2012-13 Dowd-ICES Fellowship, Carnegie Mellon University, 2012 – 2013.
*Dean Fellowship, Carnegie Mellon University, 2009 – 2012.
*USNCCM12 Travel Award, US Association for Computational Mechanics, 2013.
*Fenves Travel Grant, Carnegie Mellon University, 2011, 2012.
*GSA Conference Funding Award, Carnegie Mellon University, 2010, 2012.
*SES2011 travel scholarship, 48’th Annual Technical Meeting of Society of Engineering Sciences.
*USNCTAM2010 scholarship, 16th U.S. National Congress of Theoretical and Applied Mechanics.
*Tavakoli prize for conducting original researches, Sharif University of Technology, 2009.
*Ranked 3’rd in the nationwide Iranian entrance exam for M.Sc. degree in civil eng. among around 16,000 examinees, 2006.

===Contact Information===
Office: Durand 204 <br/>
<table>
<tr><td>Address: <td/><td>Amin Aghaei<td/><tr/>
<tr><td><td/><td>Mechanics and Computation Group<td/><tr/>
<td><td/><td>Durand Bldg. Rm. 204<td/><tr/>
<tr><td><td/><td>496 Lomita Mall<td/><tr/>
<tr><td><td/><td>Stanford, CA 94305<td/><tr/>
</table>
Email: amin1@stanford.edu

Amin Aghaei

2014-01-10T23:38:44Z

Amin1: /* Publications */

=Amin Aghaei=
Amin is a Postdoctoral researcher in the Micro and Nano-Mechanical group.

===Education===
*PhD in Computational Mechanics (2009-2013), Carnegie Mellon university<br/>
*Master of Science in Computational Mechanics (2012), Carnegie Mellon university<br/>
*Master of Science in Structural engineering (2006-2008), Sharif University of Technology, Iran<br/>
*Bachelor of Science in Civil engineering (2002-2006), University of Tehran, Iran.

===Publications===
* A. Aghaei, K. Dayal, R.S. Elliott, “Symmetry-Adapted Phonon Analysis of Nanotubes”, Journal of the Mechanics and Physics of Solids, 61 (2013) 557–578.

* A. Aghaei, K. Dayal, R.S. Elliott, “Anomalous Phonon Behavior of Carbon Nanotubes: First-Order Influence of External Load”, Journal of Applied Physics (2013) 113:023503.

* A. Aghaei, K. Dayal, “Tension-and-Twist of Chiral Nanotubes: Torsional Buckling, Mechanical Response, and Indicators of Failure”, Modeling and Simulation in Material Science Engineering, 20:085001 (2012).

* A. Aghaei, K. Dayal, “Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading”, Journal of Applied Physics (2011) 109:123501.

* M.J. Abdolhosseini Qomi, A. Aghaei, A.R. Khoei, “Multiscale Modeling of Surface Effect via Boundary Cauchy-Born Method”, International Journal for Numerical Methods in Engineering, 45 (2011) 827–846.

* A. Aghaei, M.J. Abdolhosseini and A.R. Khoei, “Stability and Size-Dependency of Cauchy-Born Hypothesis in Three- Dimensional Applications”, International Journal of Solids and Structures, (2009) 1925.

* A.R. Khoei, M.T. Kazemi, M.J. Abdolhosseini and A. Aghaei, “An Investigation on the Validity of Cauchy-Born
Hypothesis Using Sutton-Chen Many-Body Potential”, Computational Material Science, 44 (2009) 999.

===Awards===
*2012-13 Dowd-ICES Fellowship, Carnegie Mellon University, 2012 – 2013.
*Dean Fellowship, Carnegie Mellon University, 2009 – 2012.
*USNCCM12 Travel Award, US Association for Computational Mechanics, 2013.
*Fenves Travel Grant, Carnegie Mellon University, 2011, 2012.
*GSA Conference Funding Award, Carnegie Mellon University, 2010, 2012.
*SES2011 travel scholarship, 48’th Annual Technical Meeting of Society of Engineering Sciences.
*USNCTAM2010 scholarship, 16th U.S. National Congress of Theoretical and Applied Mechanics.
*Tavakoli prize for conducting original researches, Sharif University of Technology, 2009.
*Ranked 3’rd in the nationwide Iranian entrance exam for M.Sc. degree in civil eng. among around 16,000 examinees, 2006.

===Contact Information===
Office: Durand 204 <br/>
<table>
<tr><td>Address: <td/><td>Amin Aghaei<td/><tr/>
<tr><td><td/><td>Mechanics and Computation Group<td/><tr/>
<td><td/><td>Durand Bldg. Rm. 204<td/><tr/>
<tr><td><td/><td>496 Lomita Mall<td/><tr/>
<tr><td><td/><td>Stanford, CA 94305<td/><tr/>
</table>
Email: amin1@stanford.edu

Amin Aghaei

2014-01-10T23:38:26Z

Amin1: /* Publications */

=Amin Aghaei=
Amin is a Postdoctoral researcher in the Micro and Nano-Mechanical group.

===Education===
*PhD in Computational Mechanics (2009-2013), Carnegie Mellon university<br/>
*Master of Science in Computational Mechanics (2012), Carnegie Mellon university<br/>
*Master of Science in Structural engineering (2006-2008), Sharif University of Technology, Iran<br/>
*Bachelor of Science in Civil engineering (2002-2006), University of Tehran, Iran.

===Publications===
* A. Aghaei, K. Dayal, R.S. Elliott, “Symmetry-Adapted Phonon Analysis of Nanotubes”, Journal of the Mechanics and Physics of Solids, 61 (2013) 557–578.

* A. Aghaei, K. Dayal, R.S. Elliott, “Anomalous Phonon Behavior of Carbon Nanotubes: First-Order Influence of External Load”, Journal of Applied Physics (2013) 113:023503.
* A. Aghaei, K. Dayal, “Tension-and-Twist of Chiral Nanotubes: Torsional Buckling, Mechanical Response, and Indicators of Failure”, Modeling and Simulation in Material Science Engineering, 20:085001 (2012).
* A. Aghaei, K. Dayal, “Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading”, Journal of Applied Physics (2011) 109:123501.
* M.J. Abdolhosseini Qomi, A. Aghaei, A.R. Khoei, “Multiscale Modeling of Surface Effect via Boundary Cauchy-Born Method”, International Journal for Numerical Methods in Engineering, 45 (2011) 827–846.
* A. Aghaei, M.J. Abdolhosseini and A.R. Khoei, “Stability and Size-Dependency of Cauchy-Born Hypothesis in Three- Dimensional Applications”, International Journal of Solids and Structures, (2009) 1925.
* A.R. Khoei, M.T. Kazemi, M.J. Abdolhosseini and A. Aghaei, “An Investigation on the Validity of Cauchy-Born
Hypothesis Using Sutton-Chen Many-Body Potential”, Computational Material Science, 44 (2009) 999.

===Awards===
*2012-13 Dowd-ICES Fellowship, Carnegie Mellon University, 2012 – 2013.
*Dean Fellowship, Carnegie Mellon University, 2009 – 2012.
*USNCCM12 Travel Award, US Association for Computational Mechanics, 2013.
*Fenves Travel Grant, Carnegie Mellon University, 2011, 2012.
*GSA Conference Funding Award, Carnegie Mellon University, 2010, 2012.
*SES2011 travel scholarship, 48’th Annual Technical Meeting of Society of Engineering Sciences.
*USNCTAM2010 scholarship, 16th U.S. National Congress of Theoretical and Applied Mechanics.
*Tavakoli prize for conducting original researches, Sharif University of Technology, 2009.
*Ranked 3’rd in the nationwide Iranian entrance exam for M.Sc. degree in civil eng. among around 16,000 examinees, 2006.

===Contact Information===
Office: Durand 204 <br/>
<table>
<tr><td>Address: <td/><td>Amin Aghaei<td/><tr/>
<tr><td><td/><td>Mechanics and Computation Group<td/><tr/>
<td><td/><td>Durand Bldg. Rm. 204<td/><tr/>
<tr><td><td/><td>496 Lomita Mall<td/><tr/>
<tr><td><td/><td>Stanford, CA 94305<td/><tr/>
</table>
Email: amin1@stanford.edu

Amin Aghaei

2014-01-10T23:38:08Z

Amin1: /* Publications */

=Amin Aghaei=
Amin is a Postdoctoral researcher in the Micro and Nano-Mechanical group.

===Education===
*PhD in Computational Mechanics (2009-2013), Carnegie Mellon university<br/>
*Master of Science in Computational Mechanics (2012), Carnegie Mellon university<br/>
*Master of Science in Structural engineering (2006-2008), Sharif University of Technology, Iran<br/>
*Bachelor of Science in Civil engineering (2002-2006), University of Tehran, Iran.

===Publications===
*1. A. Aghaei, K. Dayal, R.S. Elliott, “Symmetry-Adapted Phonon Analysis of Nanotubes”, Journal of the Mechanics and Physics of Solids, 61 (2013) 557–578.

*2. A. Aghaei, K. Dayal, R.S. Elliott, “Anomalous Phonon Behavior of Carbon Nanotubes: First-Order Influence of External Load”, Journal of Applied Physics (2013) 113:023503.
*3. A. Aghaei, K. Dayal, “Tension-and-Twist of Chiral Nanotubes: Torsional Buckling, Mechanical Response, and Indicators of Failure”, Modeling and Simulation in Material Science Engineering, 20:085001 (2012).
*4. A. Aghaei, K. Dayal, “Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading”, Journal of Applied Physics (2011) 109:123501.
*5. M.J. Abdolhosseini Qomi, A. Aghaei, A.R. Khoei, “Multiscale Modeling of Surface Effect via Boundary Cauchy-Born Method”, International Journal for Numerical Methods in Engineering, 45 (2011) 827–846.
*6. A. Aghaei, M.J. Abdolhosseini and A.R. Khoei, “Stability and Size-Dependency of Cauchy-Born Hypothesis in Three- Dimensional Applications”, International Journal of Solids and Structures, (2009) 1925.
*7. A.R. Khoei, M.T. Kazemi, M.J. Abdolhosseini and A. Aghaei, “An Investigation on the Validity of Cauchy-Born
Hypothesis Using Sutton-Chen Many-Body Potential”, Computational Material Science, 44 (2009) 999.

===Awards===
*2012-13 Dowd-ICES Fellowship, Carnegie Mellon University, 2012 – 2013.
*Dean Fellowship, Carnegie Mellon University, 2009 – 2012.
*USNCCM12 Travel Award, US Association for Computational Mechanics, 2013.
*Fenves Travel Grant, Carnegie Mellon University, 2011, 2012.
*GSA Conference Funding Award, Carnegie Mellon University, 2010, 2012.
*SES2011 travel scholarship, 48’th Annual Technical Meeting of Society of Engineering Sciences.
*USNCTAM2010 scholarship, 16th U.S. National Congress of Theoretical and Applied Mechanics.
*Tavakoli prize for conducting original researches, Sharif University of Technology, 2009.
*Ranked 3’rd in the nationwide Iranian entrance exam for M.Sc. degree in civil eng. among around 16,000 examinees, 2006.

===Contact Information===
Office: Durand 204 <br/>
<table>
<tr><td>Address: <td/><td>Amin Aghaei<td/><tr/>
<tr><td><td/><td>Mechanics and Computation Group<td/><tr/>
<td><td/><td>Durand Bldg. Rm. 204<td/><tr/>
<tr><td><td/><td>496 Lomita Mall<td/><tr/>
<tr><td><td/><td>Stanford, CA 94305<td/><tr/>
</table>
Email: amin1@stanford.edu

Amin Aghaei

2014-01-10T23:37:59Z

Amin1: /* Publications */

=Amin Aghaei=
Amin is a Postdoctoral researcher in the Micro and Nano-Mechanical group.

===Education===
*PhD in Computational Mechanics (2009-2013), Carnegie Mellon university<br/>
*Master of Science in Computational Mechanics (2012), Carnegie Mellon university<br/>
*Master of Science in Structural engineering (2006-2008), Sharif University of Technology, Iran<br/>
*Bachelor of Science in Civil engineering (2002-2006), University of Tehran, Iran.

===Publications===
*1. A. Aghaei, K. Dayal, R.S. Elliott, “Symmetry-Adapted Phonon Analysis of Nanotubes”, Journal of the Mechanics and Physics of Solids, 61 (2013) 557–578.
*2. A. Aghaei, K. Dayal, R.S. Elliott, “Anomalous Phonon Behavior of Carbon Nanotubes: First-Order Influence of External Load”, Journal of Applied Physics (2013) 113:023503.
*3. A. Aghaei, K. Dayal, “Tension-and-Twist of Chiral Nanotubes: Torsional Buckling, Mechanical Response, and Indicators of Failure”, Modeling and Simulation in Material Science Engineering, 20:085001 (2012).
*4. A. Aghaei, K. Dayal, “Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading”, Journal of Applied Physics (2011) 109:123501.
*5. M.J. Abdolhosseini Qomi, A. Aghaei, A.R. Khoei, “Multiscale Modeling of Surface Effect via Boundary Cauchy-Born Method”, International Journal for Numerical Methods in Engineering, 45 (2011) 827–846.
*6. A. Aghaei, M.J. Abdolhosseini and A.R. Khoei, “Stability and Size-Dependency of Cauchy-Born Hypothesis in Three- Dimensional Applications”, International Journal of Solids and Structures, (2009) 1925.
*7. A.R. Khoei, M.T. Kazemi, M.J. Abdolhosseini and A. Aghaei, “An Investigation on the Validity of Cauchy-Born
Hypothesis Using Sutton-Chen Many-Body Potential”, Computational Material Science, 44 (2009) 999.

===Awards===
*2012-13 Dowd-ICES Fellowship, Carnegie Mellon University, 2012 – 2013.
*Dean Fellowship, Carnegie Mellon University, 2009 – 2012.
*USNCCM12 Travel Award, US Association for Computational Mechanics, 2013.
*Fenves Travel Grant, Carnegie Mellon University, 2011, 2012.
*GSA Conference Funding Award, Carnegie Mellon University, 2010, 2012.
*SES2011 travel scholarship, 48’th Annual Technical Meeting of Society of Engineering Sciences.
*USNCTAM2010 scholarship, 16th U.S. National Congress of Theoretical and Applied Mechanics.
*Tavakoli prize for conducting original researches, Sharif University of Technology, 2009.
*Ranked 3’rd in the nationwide Iranian entrance exam for M.Sc. degree in civil eng. among around 16,000 examinees, 2006.

===Contact Information===
Office: Durand 204 <br/>
<table>
<tr><td>Address: <td/><td>Amin Aghaei<td/><tr/>
<tr><td><td/><td>Mechanics and Computation Group<td/><tr/>
<td><td/><td>Durand Bldg. Rm. 204<td/><tr/>
<tr><td><td/><td>496 Lomita Mall<td/><tr/>
<tr><td><td/><td>Stanford, CA 94305<td/><tr/>
</table>
Email: amin1@stanford.edu

Amin Aghaei

2014-01-10T23:37:29Z

Amin1: /* Amin Aghaei */

=Amin Aghaei=
Amin is a Postdoctoral researcher in the Micro and Nano-Mechanical group.

===Education===
*PhD in Computational Mechanics (2009-2013), Carnegie Mellon university<br/>
*Master of Science in Computational Mechanics (2012), Carnegie Mellon university<br/>
*Master of Science in Structural engineering (2006-2008), Sharif University of Technology, Iran<br/>
*Bachelor of Science in Civil engineering (2002-2006), University of Tehran, Iran.

===Publications===
Journal Papers:
1. A. Aghaei, K. Dayal, R.S. Elliott, “Symmetry-Adapted Phonon Analysis of Nanotubes”, Journal of the Mechanics and Physics of Solids, 61 (2013) 557–578.
2. A. Aghaei, K. Dayal, R.S. Elliott, “Anomalous Phonon Behavior of Carbon Nanotubes: First-Order Influence of External Load”, Journal of Applied Physics (2013) 113:023503.
3. A. Aghaei, K. Dayal, “Tension-and-Twist of Chiral Nanotubes: Torsional Buckling, Mechanical Response, and Indicators of Failure”, Modeling and Simulation in Material Science Engineering, 20:085001 (2012).
4. A. Aghaei, K. Dayal, “Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading”, Journal of Applied Physics (2011) 109:123501.
5. M.J. Abdolhosseini Qomi, A. Aghaei, A.R. Khoei, “Multiscale Modeling of Surface Effect via Boundary Cauchy-Born Method”, International Journal for Numerical Methods in Engineering, 45 (2011) 827–846.
6. A. Aghaei, M.J. Abdolhosseini and A.R. Khoei, “Stability and Size-Dependency of Cauchy-Born Hypothesis in Three- Dimensional Applications”, International Journal of Solids and Structures, (2009) 1925.
7. A.R. Khoei, M.T. Kazemi, M.J. Abdolhosseini and A. Aghaei, “An Investigation on the Validity of Cauchy-Born
Hypothesis Using Sutton-Chen Many-Body Potential”, Computational Material Science, 44 (2009) 999.

===Awards===
*2012-13 Dowd-ICES Fellowship, Carnegie Mellon University, 2012 – 2013.
*Dean Fellowship, Carnegie Mellon University, 2009 – 2012.
*USNCCM12 Travel Award, US Association for Computational Mechanics, 2013.
*Fenves Travel Grant, Carnegie Mellon University, 2011, 2012.
*GSA Conference Funding Award, Carnegie Mellon University, 2010, 2012.
*SES2011 travel scholarship, 48’th Annual Technical Meeting of Society of Engineering Sciences.
*USNCTAM2010 scholarship, 16th U.S. National Congress of Theoretical and Applied Mechanics.
*Tavakoli prize for conducting original researches, Sharif University of Technology, 2009.
*Ranked 3’rd in the nationwide Iranian entrance exam for M.Sc. degree in civil eng. among around 16,000 examinees, 2006.

===Contact Information===
Office: Durand 204 <br/>
<table>
<tr><td>Address: <td/><td>Amin Aghaei<td/><tr/>
<tr><td><td/><td>Mechanics and Computation Group<td/><tr/>
<td><td/><td>Durand Bldg. Rm. 204<td/><tr/>
<tr><td><td/><td>496 Lomita Mall<td/><tr/>
<tr><td><td/><td>Stanford, CA 94305<td/><tr/>
</table>
Email: amin1@stanford.edu

Group Members

2014-01-10T23:35:32Z

Amin1: /* Graduate Students */

__NOTOC__
===Professor===
:[[Wei Cai]]

===Graduate Students===
:[[William Kuykendall]]
:[[Yanming Wang]]
:[[Ryan Sills]]
:[[Amin Aghaei]]

===Former Members===
:[[William Cash | William Cash (former PhD student)]]
:[[Hark Lee | Hark Lee (former PhD student)]]
:[[Ill Ryu | Ill Ryu (former PhD student)]]
:[[Jie Yin | Jie Yin (former PhD student)]]
:[[Seunghwa Ryu | Seunghwa Ryu (former PhD student) ]]
:[[Seokwoo Lee | Seokwoo Lee (former PhD student) ]]
:[[Haneesh Kesari | Haneesh Kesari (former PhD student)]]
:[[Chris Weinberger | Chris Weinberger (former PhD student)]]
:[[William Fong | William Fong (guest)]]
:[[Alfredo Correa | Alfredo Correa (former postdoc)]]
:[[Keonwook Kang | Keonwook Kang (former PhD student)]]
:[[Eunseok Lee | Eunseok Lee (former PhD student)]]
:[[Sylvie Aubry | Sylvie Aubry (former Research Associate)]]

===Outreach Collaborator===
:[[Alfonso Garcia | Alfonso Garcia (high school teacher)]]

Amin Aghaei

2014-01-10T23:35:19Z

Amin1:

Group Members

2014-01-10T23:33:49Z

Amin1: /* Graduate Students */

__NOTOC__
===Professor===
:[[Wei Cai]]

===Graduate Students===
:[[William Kuykendall]]
:[[Yanming Wang]]
:[[Ryan Sills]]
:[[Amin Aghaei]]
:[[Amin]]
:[[Amin Aghaei]]

===Former Members===
:[[William Cash | William Cash (former PhD student)]]
:[[Hark Lee | Hark Lee (former PhD student)]]
:[[Ill Ryu | Ill Ryu (former PhD student)]]
:[[Jie Yin | Jie Yin (former PhD student)]]
:[[Seunghwa Ryu | Seunghwa Ryu (former PhD student) ]]
:[[Seokwoo Lee | Seokwoo Lee (former PhD student) ]]
:[[Haneesh Kesari | Haneesh Kesari (former PhD student)]]
:[[Chris Weinberger | Chris Weinberger (former PhD student)]]
:[[William Fong | William Fong (guest)]]
:[[Alfredo Correa | Alfredo Correa (former postdoc)]]
:[[Keonwook Kang | Keonwook Kang (former PhD student)]]
:[[Eunseok Lee | Eunseok Lee (former PhD student)]]
:[[Sylvie Aubry | Sylvie Aubry (former Research Associate)]]

===Outreach Collaborator===
:[[Alfonso Garcia | Alfonso Garcia (high school teacher)]]

Group Members

2014-01-10T23:33:29Z

Amin1: /* Graduate Students */

__NOTOC__
===Professor===
:[[Wei Cai]]

===Graduate Students===
:[[William Kuykendall]]
:[[Yanming Wang]]
:[[Ryan Sills]]
:[[Amin Aghaei]]
:[[Amin]]

===Former Members===
:[[William Cash | William Cash (former PhD student)]]
:[[Hark Lee | Hark Lee (former PhD student)]]
:[[Ill Ryu | Ill Ryu (former PhD student)]]
:[[Jie Yin | Jie Yin (former PhD student)]]
:[[Seunghwa Ryu | Seunghwa Ryu (former PhD student) ]]
:[[Seokwoo Lee | Seokwoo Lee (former PhD student) ]]
:[[Haneesh Kesari | Haneesh Kesari (former PhD student)]]
:[[Chris Weinberger | Chris Weinberger (former PhD student)]]
:[[William Fong | William Fong (guest)]]
:[[Alfredo Correa | Alfredo Correa (former postdoc)]]
:[[Keonwook Kang | Keonwook Kang (former PhD student)]]
:[[Eunseok Lee | Eunseok Lee (former PhD student)]]
:[[Sylvie Aubry | Sylvie Aubry (former Research Associate)]]

===Outreach Collaborator===
:[[Alfonso Garcia | Alfonso Garcia (high school teacher)]]

Amin

2014-01-10T23:25:11Z

Amin1: /* Contact Information */

Amin

2014-01-10T23:23:58Z

Amin1: /* Amin Aghaei */

Amin

2014-01-10T23:23:34Z

Amin1: /* Awards */