FEFF input files generator is a cli application for generating input files for FEFF9 program. Input files are generated for atom-doped samples in a crystal structure with defects such as
- substitutions,
- implants,
- antisites,
- substitutionsetc.
- Automatic generation of project folders.
- Automatic start of the calculation using the generated SLURM script.
- Do calculation on the remote host by using ssh protocol.
- Wide possibilities of choosing the way of placing the wanted atom / atoms in the target crystal structure.
- Ability to filter atoms by tag / ipot / coordinates / distance.
- Separate configuration file
- WebUI menu for changing base config options.
Additional information on https://www.python.org/downloads/ and Creation of virtual environments
or simple way to create subfolder venv (with python packages) inside the current directory:
$ python -m venv venv
$ mkdir feff_generate_input_files && cd feff_generate_input_files
$ git clone https://github.com/xyz-man/feff_generate_input_files.git
or
$ git clone -b develop https://github.com/xyz-man/feff_generate_input_files.git
$ pip install -r requirements.txt
On your localhost execute the next command to generate a pair of authentication keys. Do not enter a passphrase:
$ ssh-keygen -t rsa
Generating public/private rsa key pair.
Enter file in which to save the key (/home/a/.ssh/id_rsa):
Created directory '/home/a/.ssh'.
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/a/.ssh/id_rsa.
Your public key has been saved in /home/a/.ssh/id_rsa.pub.
Then copy id_rsa.pub to remote host by using certain User Login and IP-address
In example remote host has 10.88.0.245 ip-address and the remote host user login is: wien2k
$ ssh-copy-id -i ~/.ssh/id_rsa.pub wien2k@10.88.0.245
/usr/bin/ssh-copy-id: INFO: Source of key(s) to be installed: "/home/localhostuser/.ssh/id_rsa.pub"
The authenticity of host '10.88.0.245 (10.88.0.245)' can't be established.
ECDSA key fingerprint is SHA256:WZ34iul54wKqqS5XhBG8N/sfthtH26q5GoPOjcdgOFw.
Are you sure you want to continue connecting (yes/no)? yes
/usr/bin/ssh-copy-id: INFO: attempting to log in with the new key(s), to filter out any that are already installed
/usr/bin/ssh-copy-id: INFO: 1 key(s) remain to be installed -- if you are prompted now it is to install the new keys
wien2k@10.88.0.245's password:
Number of key(s) added: 1
Now try logging into the machine, with: "ssh 'wien2k@10.88.0.245'"
and check to make sure that only the key(s) you wanted were added.
On your localhost and remote host install nfs client service:
$apt-get install nfs-common
On the NFS server, edit /etc/exports and add the local and remote host access permission
by changing the 10.88.0.1/24 IP pool:
$ cat /etc/exports
# /etc/exports: the access control list for filesystems which may be exported
# to NFS clients. See exports(5).
#
# Example for NFSv2 and NFSv3:
# /srv/homes hostname1(rw,sync,no_subtree_check) hostname2(ro,sync,no_subtree_check)
#
# Example for NFSv4:
# /srv/nfs4 gss/krb5i(rw,sync,fsid=0,crossmnt,no_subtree_check)
# /srv/nfs4/homes gss/krb5i(rw,sync,no_subtree_check)
#
/mnt/nfsv4/nfs_share 10.88.0.1/24(rw,no_root_squash,no_subtree_check,crossmnt,fsid=0)
On NFS-client machine (localhost or remote host)
print the nfs mount folders exported by NFS-server (Ex.: nfs server ip-address is 10.88.0.251):
$# showmount -e 10.88.0.251
Export list for 10.88.0.251:
/mnt/nfsv4/nfs_share 10.88.0.1/24
edit /etc/fstab and write line with mount NFS share options:
$ #10.88.0.251:/mnt/nfsv4/nfs_share /mnt/nfsv4/abel_share nfs4 soft,intr,rsize=8192,wsize=8192 0 0
10.88.0.251:/ /mnt/nfsv4/abel_share nfs4 soft,intr,rsize=8192,wsize=8192 0 0
or execute mount command:
$ mount.nfs4 10.88.0.251:/ /mnt/nfsv4/abel_share -o rw
directory /mnt/nfsv4/abel_share was created earlier on localhost and remote host by using:
$ mkdir -p /mnt/nfsv4/abel_share
You can use another folder name.
If NFS is configured correctly on client hosts, the mount command shows that you have mounted an NFS share::
$ /home/wien2k# mount
sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime)
proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
udev on /dev type devtmpfs (rw,relatime,size=10240k,nr_inodes=2315885,mode=755)
.....
10.88.0.251:/ on /mnt/nfsv4/abel_share type nfs4 (rw,relatime,vers=4,rsize=8192,wsize=81
92,namlen=255,soft,proto=tcp,timeo=600,retrans=2,sec=sys,clientaddr=10.88.0.245,minorver
sion=0,local_lock=none,addr=10.88.0.251)
Open cfg/config.py file and edit needed variables.
FEFF input files generator has been created under the GNU GPLv3 license