AENET_tutorial_e/example - 第一原理分子動力学プログラム STATE Senri Wiki

Running the TiO2 example †

Having compiled AENET executables (*.x), let us run them by using the example provided at the AENET web page (see the download section).

In the AENET directory (~/AENET), create the example directory as

$ cd ~/AENET
$ mkdir examples

and change the directory

$ cd examples

Download the example file

$ wget http://ann.atomistic.net/files/aenet-example-01-TiO2.tar.bz2

and expand it

$ tar jxvf aenet-example-01-TiO2.tar.bz2

to get

aenet-example-01-TiO2/

In this directory, we can find the following directories:

01-generate/  02-train/  03-predict/  04-MD-ASE/  LICENSE  README  xsf/

I prepared sample job scripts for AENET to be used in our smith cluster system, which are located in

~ikutaro/AENET/example/scripts

and those for generation, training, and prediction are respectively,

Go to the 01-generate/ directory and execute

$ ~/AENET/src/aenet-2.0.3/bin/generate.x-2.0.3-ifort_intelmpi generate.in > generate.out

NOTE: generate.x is not parallelized with MPI or OpenMP, and the number of cores used should be 1 when submitting the job using the queueing system.

Or using a job script:

$ qsub qsub_generate.sh

In this example, the file "TiO2.train" is generated, and will be used in the training.

Go to the 02-train/ directory and execute the following (for example, depending on your system)

$ mpirun -np 8 ~/AENET/src/aenet-2.0.3/bin/train.x-2.0.3-ifort_intelmpi train.in > train.out

Using a job script:

$ qsub qsub_train.sh

When the training is finished, we obtain the following potentials

which will be used in the prediction.

Go to the 03-predict/ directory and execute the following (for example, depending on your system)

$ mpirun -np 8 ~/AENET/src/aenet-2.0.3/bin/predict.x-2.0.3-ifort_intelmpi predict.in > predict.out

Make sure that there are ANN potentials generated in the previous step. Using a job script:

$ qsub qsub_predict.sh