Remotely Accessing a Linux Machine via Secure Shell (SSH)
Linux and Mac Users
Open your terminal and enter ssh username@hostname
Refer my github page for few useful scripts for vasp output analysis. https://github.com/princego
Atomistic Modeling for getting started with basic DFT calculations and linux basics.
Bilbao Crystallographic Server for database for space groups and wyckoff positions information
Materials Project | NOMAD Encyclopedia | AFLOW
Open your terminal and enter ssh username@hostname
In your local computer (for linx and mac users only), type ssh-keygen, then type ssh-copy-id username@hostname
Once you login, you’ll be taken to your home directory (folder). Always press Enter key after entering a command. If the directory name is too long, you need not type in full directory name, instead type first few letters then press tab key. Directory name will be auto filled.
| Decription | Command |
|---|---|
| List contents in the directory | ls |
| Present working directory | pwd |
| Create a new directory | mkdir directoryname Don't use space in between for long directories, use _ instead |
| Go inside a directory | cd directoryname |
| Switch to home directory from any directory | cd or cd ~/ |
| Go back to previous directory | cd .. |
| Go back to two directories | cd ../.. |
| Go to subdirectory | cd directory/subdirectory/ |
| Rename a directory | mv old_name new_name |
| Delete a file | rm filename |
| Delete a directory/folder | rm -r directoryname |
| Move directory to a new location | mv directoryname path_to_new_location |
| Check total disk space occupied | df -h |
| Search for a directory starts with dir | find . -type d | grep dir* |
Here I am showing the commands for inbuild vi editor. You can use the favourite editor of your choice.
| Decription | Command |
|---|---|
| Create a new file | vi filename |
| To start editing the new file or old file | i then you'll go to insert mode. i.e., you can start editing. |
| Write changes to the file | :w |
| To quit the file | :q |
| To write changes to the file and quit | :wq |
| Save file without making changes | :q! |
| Delete a file | rm filename |
| Go to the last line | G |
| Go to first line | :1 or gg |
| Jump to line 25 | :25 or 25G |
| Move to end of a line | $ |
| Move one page forward | ctrl+f |
| Move one page backward | ctrl+b |
| Delete 10 lines from the current line | 10dd |
| Delete 1 to 10 lines/rows | :1,10d |
| Delete from line 10 to the end | :10,$d |
| Open multiple files | vi -O file1 file 2 |
| Switch between multiple files opened [to move to the file on right side] | Ctrl+w rightarrow |
| Search for a file starts with fil | find . -type f | grep fil* |
| Compress an individual file to .gz | gzip filename |
| Search and compress a specific filename to .gz | find . -type f -name "FILENAME" -exec gzip -f {} \; |
| unzip a .gz file | gzip -d filename.gz |
| view the contents in a tar.gz file without extracting | tar -tf filename.tar.gz |
| Remove lines from file1_big which are in file2_small | grep -v -x -f file2_small file1_big > file3_available |
| print a sequence of 1 to 10 numbers | seq 10 > sysNum |
| Print only col2 and 3 from a csv file | awk -F "," '{print $2","$3}' file.csv > file_new.csv |
| Sum of column of numbers in a file | paste -sd+ int_freq | bc |
If you are tranferring files, after scp, -r is not required. To know the path, type pwd in your terminal
| Copy directories from local to remote computer | scp -r fullpath/ user@hostname:/fullpath/ |
| Copy directories from remote to local computer | scp -r user@hostname:/fullpath/ /fullpath_in_local_computer |
| Copy directories from remote computer to another remote computer | scp -r user1@hostname1:/fullpath/ user2@hostname2:/fullpath/ |
Go to connect to server and type sftp://username@servername. Now you can drag and drop the files. Alternatively, you can use Filezilla.
Use Forklift from App Store or use Filezilla.
Open MobaXterm software, go to Session, go to SFTP and login. Alternatively, you can use Filezilla.
#!/bin/bash
#PBS -o out
## Merge output and error files
#PBS -j oe
#PBS -k eod
#PBS -l walltime=00:59:59
## Select n nodes, each with n CPUs
#PBS -l select=1:ncpus=12
tpdir=`echo $PBS_JOBID | cut -f 1 -d .`
tempdir=$HOME/scratch/job$tpdir
mkdir -p $tempdir
cd $tempdir
cp -R $PBS_O_WORKDIR/* .
mpirun -n 12 vasp_std > log
echo "`date '+%m/%d/%y %H:%M:%S' ` $PBS_O_WORKDIR" >> ~/joblog.txt
mv ../job$tpdir $PBS_O_WORKDIR/.
grep command helps us to print the line when it finds the character you have entered. The syntax is grep character filename. If you are looking for long words, which has space in between, use " "
grep ! log
grep "total energy" log
4-read, 2-write, 1-execute. For example, chmod 755 filename has three digits 7(4+2+1), 5(4+1), 5(4+1). The first digit corresponds to the user, second and third corresponds to the group and others. 755 means the user can read, write, and execute, group and others can only read and execute a file.
| Print 5th column | awk '{print $5}' filename |
| Comma seperated values (csv) for 1st three columns | awk '{print $1","$2","$3}' filename >file.csv |
| Print last row | awk 'END{print}' filename |
| Adds 0.5 0.5 0.5 to line 5 of the file POSCAR | sed -i '5i 0.5 0.5 0.5' POSCAR |
| Deactivate python base environemnt on login | conda config --set auto_activate_base false |
| Exporting figure in tiff format with 600 dpi resolution | exportgraphics(gcf,'eigenval.tiff', 'Resolution', 600) |
| Exporting figure as pdf | exportgraphics(gcf,'figure.pdf') |
| Deletes every 25th row from a matrix | A(25:25:end,:) = [] |
(2*pi)/(a*kpoints along a), where a is the lattice distance.
To create FCC supercell along (111) plane, enter the below values in the transformation matrix vertically,
a1=[-0.5 0.5 0], b1=[-0.5 -0.5 1], c1=[1 1 1]
Now the new directions are will be a=[1 1 0], b=[1 1 2] and c=[1 1 1]