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# Clp
## Introduction
Clp (Coin-or linear programming) is an open-source linear programming solver written in C++. It is primarily meant to be used as a callable library, but a basic, stand-alone executable version is also available.
Clp ([projects.coin-or.org/Clp](https://projects.coin-or.org/Clp)) is a part of the COIN-OR (The Computational Infrastracture for Operations Research) project ([projects.coin-or.org/](https://projects.coin-or.org/)).
## Modules
Clp, version 1.16.10 is available on Salomon via module Clp:
```console
$ ml Clp
```
The module sets up environment variables required for linking and running applications using Clp. This particular command loads the default module Clp/1.16.10-intel-2017a, Intel module intel/2017a and other related modules.
## Compiling and Linking
!!! note
Link with -lClp
Load the Clp module. Link using -lClp switch to link your code against Clp.
```console
$ ml Clp
$ icc myprog.c -o myprog.x -Wl,-rpath=$LIBRARY_PATH -lClp
```
## Example
An example of Clp enabled application follows. In this example, the library solves linear programming problem loaded from file.
```cpp
#include "coin/ClpSimplex.hpp"
int main (int argc, const char *argv[])
{
ClpSimplex model;
int status;
if (argc<2)
status=model.readMps("/apps/all/Clp/1.16.10-intel-2017a/lib/p0033.mps");
else
status=model.readMps(argv[1]);
if (!status) {
model.primal();
}
return 0;
}
```
### Load Modules and Compile:
```console
ml Clp
icc lp.c -o lp.x -Wl,-rpath=$LIBRARY_PATH -lClp
```
In this example, the lp.c code is compiled using the Intel compiler and linked with Clp. To run the code, the Intel module has to be loaded.
# LMGC90
## Introduction
LMGC90 is a free and open source software dedicated to multiple physics simulation of discrete material and structures.
## Modules
The LMGC90, version 2017.rc1 is available on Salomon via module `LMGC90`:
```sh
$ ml LMGC90
```
The module sets up environment variables and loads some other modules, required for running LMGC90 python scripts. This particular command loads the default module, which is `LMGC90/2017.rc1-GCC-6.3.0-2.27`, and modules:
```console
GCCcore/6.3.0
binutils/2.27-GCCcore-6.3.0
GCC/6.3.0-2.27
bzip2/1.0.6
zlib/1.2.8
ncurses/6.0
libreadline/6.3
Tcl/8.6.3
SQLite/3.8.8.1
Python/2.7.9
```
## Running Generic Example
LMGC90 software main API is a Python module. It comes with a pre-processor written in Python. There are several examples that you can copy from the `examples` directory which is in `/apps/all/LMGC90/2017.rc1-GCC-6.3.0-2.27` folder. Follow the next steps to run one of them.
First choose an example and open a terminal in the directory of the copied example.
### Generation
To have more information on the pre-processor open in a web navigator the file [docs/pre_lmgc/index.html][pre_lmgc].
To run an example, if there is no `DATBOX` directory or it is empty, run the Python generation script which is mostly called `gen_sample.py` with the command:
```console
$ python gen_sample.py
```
You should now have a `DATBOX` directory containing all needed `.DAT` and `.INI` files.
### Computation
Now run the command script usually called `command.py`:
```console
$ python command.py
```
To get more information on the structure on command scripts read the documentation opening the file [docs/chipy/index.html][chipy] in a web browser.
Once the computation is done, you should get the directory `OUTBOX` containing ASCII output files, and a `DISPLAY` directory with output file readable by paraview.
### Postprocessing and Visualization
The ASCII files in `POSTPRO` directory result from the commands in the `DATBOX/POSTPRO.DAT` file. To have more information on how to use these features read the documents [manuals/LMGC90_Postpro.pdf][LMGC90_Postpro.pdf].
The files inside the `DISPLAY` directory can be visualized with paraview. It is advised to read the `.pvd` files which ensure time consistency. The different output files are:
- tacts: contactors of rigid objects
- rigids: center of mass of rigid objects
- inter: interactions
- mecafe: mechanical mesh
- therfe: thermal mesh
- porofe: porous mechanical mesh
- multife: multi-phasic fluid in porous media mesh
[Welcome](http://www.lmgc.univ-montp2.fr/~dubois/LMGC90/Web/Welcome_!.html)
[pre_lmgc](http://www.lmgc.univ-montp2.fr/%7Edubois/LMGC90/UserDoc/pre/index.html)
[chipy](http://www.lmgc.univ-montp2.fr/%7Edubois/LMGC90/UserDoc/chipy/index.html)
[LMGC90_Postpro.pdf](https://git-xen.lmgc.univ-montp2.fr/lmgc90/lmgc90_user/blob/2017.rc1/manuals/LMGC90_Postpro.pdf)
# PragTic
## Introduction
PragTic is a freeware tool for an automated fatigue damage calculation based on a FE-solution or done at an isolated point with no relation to FEA. More details of PragTic are available on its [website][Welcome]. Here is HPC version which was parallelized using MPI library.
## Modules
The PragTic, version 0.1 is available on Salomon via module PragTic:
```sh
$ ml PragTic
```
The module sets up environment variables and loads some other modules, required for running PragTic simulations. This particular command loads the default module, which is PragTic/0.1-GCC-5.3.0-2.25, and modules:
```console
GCCcore/5.3.0
binutils/2.25-GCCcore-5.3.0
GCC/5.3.0-2.25
MPICH/3.2-GCC-5.3.0-2.25.
```
## Running
Follow the next step to compute simulations sequentially:
```sh
pragtic DATABASE ANSET SET_OF_POINTS LOAD_REGIME METHOD RESULT_FILE
```
and this step to compute it in parallel:
```sh
mpirun -np NP pragtic DATABASE ANSET SET_OF_POINTS LOAD_REGIME METHOD RESULT_FILE
```
where
| Parameter | Description |
| --------------- | -------------------------------------------- |
| *NP* | number of processes |
| *DATABASE* | .fdb database specially prepared for PragTic |
| *ANSET* | analyse setup name |
| *SET_OF_POINTS* | set of points name |
| *LOAD_REGIME* | load regime name |
| *METHOD* | method name |
| *RESULT_FILE* | file where results will be saved |
## Results
After computation newly created result file *RESULT_FILE* in the current directory should contain results. More detailed result informations then should be found in the file *res.txt* which is in every single randomly named folder created by PragTic in the very same current directory.
[Welcome](http://www.pragtic.com/)
# Storage
## Introduction
There are two main shared file systems on Salomon cluster, the [HOME](#home) and [SCRATCH](#shared-filesystems).
All login and compute nodes may access same data on shared file systems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp file systems.
## Policy (In a Nutshell)
!!! note
\* Use [HOME](#home) for your most valuable data and programs.
\* Use [WORK](#work) for your large project files.
\* Use [TEMP](#temp) for large scratch data.
!!! warning
Do not use for [archiving](#archiving)!
## Archiving
Please don't use shared file systems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use [CESNET storage service](#cesnet-data-storage), which is available via SSHFS.
## Shared File Systems
Salomon computer provides two main shared file systems, the [HOME file system](#home-filesystem) and the [SCRATCH file system](#scratch-filesystem). The SCRATCH file system is partitioned to [WORK and TEMP workspaces](#shared-workspaces). The HOME file system is realized as a tiered NFS disk storage. The SCRATCH file system is realized as a parallel Lustre file system. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both HOME/SCRATCH file systems for the purpose of sharing data with other users using fine-grained control.
### HOME File System
The HOME file system is realized as a Tiered file system, exported via NFS. The first tier has capacity 100 TB, second tier has capacity 400 TB. The file system is available on all login and computational nodes. The Home file system hosts the [HOME workspace](#home).
### SCRATCH File System
The architecture of Lustre on Salomon is composed of two metadata servers (MDS) and six data/object storage servers (OSS). Accessible capacity is 1.69 PB, shared among all users. The SCRATCH file system hosts the [WORK and TEMP workspaces](#shared-workspaces).
Configuration of the SCRATCH Lustre storage
* SCRATCH Lustre object storage
* Disk array SFA12KX
* 540 x 4 TB SAS 7.2krpm disk
* 54 x OST of 10 disks in RAID6 (8+2)
* 15 x hot-spare disk
* 4 x 400 GB SSD cache
* SCRATCH Lustre metadata storage
* Disk array EF3015
* 12 x 600 GB SAS 15 krpm disk
### Understanding the Lustre File Systems
[http://www.nas.nasa.gov](http://www.nas.nasa.gov)
A user file on the Lustre file system can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing.
When a client (a compute node from your job) needs to create or access a file, the client queries the metadata server ( MDS) and the metadata target ( MDT) for the layout and location of the [file's stripes](http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping). Once the file is opened and the client obtains the striping information, the MDS is no longer involved in the file I/O process. The client interacts directly with the object storage servers (OSSes) and OSTs to perform I/O operations such as locking, disk allocation, storage, and retrieval.
If multiple clients try to read and write the same part of a file at the same time, the Lustre distributed lock manager enforces coherency so that all clients see consistent results.
There is default stripe configuration for Salomon Lustre file systems. However, users can set the following stripe parameters for their own directories or files to get optimum I/O performance:
1. stripe_size: the size of the chunk in bytes; specify with k, m, or g to use units of KB, MB, or GB, respectively; the size must be an even multiple of 65,536 bytes; default is 1MB for all Salomon Lustre file systems
1. stripe_count the number of OSTs to stripe across; default is 1 for Salomon Lustre file systems one can specify -1 to use all OSTs in the file system.
1. stripe_offset The index of the OST where the first stripe is to be placed; default is -1 which results in random selection; using a non-default value is NOT recommended.
!!! note
Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.
Use the lfs getstripe for getting the stripe parameters. Use the lfs setstripe command for setting the stripe parameters to get optimal I/O performance The correct stripe setting depends on your needs and file access patterns.
```console
$ lfs getstripe dir | filename
$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir | filename
```
Example:
```console
$ lfs getstripe /scratch/work/user/username
/scratch/work/user/username
stripe_count: 1 stripe_size: 1048576 stripe_offset: -1
$ lfs setstripe -c -1 /scratch/work/user/username/
$ lfs getstripe /scratch/work/user/username/
/scratch/work/user/username/
stripe_count: -1 stripe_size: 1048576 stripe_offset: -1
```
In this example, we view current stripe setting of the /scratch/username/ directory. The stripe count is changed to all OSTs, and verified. All files written to this directory will be striped over all (54) OSTs
Use lfs check OSTs to see the number and status of active OSTs for each file system on Salomon. Learn more by reading the man page
```console
$ lfs check osts
$ man lfs
```
### Hints on Lustre Stripping
!!! note
Increase the stripe_count for parallel I/O to the same file.
When multiple processes are writing blocks of data to the same file in parallel, the I/O performance for large files will improve when the stripe_count is set to a larger value. The stripe count sets the number of OSTs the file will be written to. By default, the stripe count is set to 1. While this default setting provides for efficient access of metadata (for example to support the ls -l command), large files should use stripe counts of greater than 1. This will increase the aggregate I/O bandwidth by using multiple OSTs in parallel instead of just one. A rule of thumb is to use a stripe count approximately equal to the number of gigabytes in the file.
Another good practice is to make the stripe count be an integral factor of the number of processes performing the write in parallel, so that you achieve load balance among the OSTs. For example, set the stripe count to 16 instead of 15 when you have 64 processes performing the writes.
!!! note
Using a large stripe size can improve performance when accessing very large files
Large stripe size allows each client to have exclusive access to its own part of a file. However, it can be counterproductive in some cases if it does not match your I/O pattern. The choice of stripe size has no effect on a single-stripe file.
Read more on [http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html](http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html)
## Disk Usage and Quota Commands
Disk usage and user quotas can be checked and reviewed using following command:
```console
$ it4i-disk-usage
```
Example:
```console
$ it4i-disk-usage -h
# Using human-readable format
# Using power of 1024 for space
# Using power of 1000 for entries
Filesystem: /home
Space used: 110G
Space limit: 238G
Entries: 40k
Entries limit: 500k
# based on filesystem quota
Filesystem: /scratch
Space used: 377G
Space limit: 93T
Entries: 14k
Entries limit: 0
# based on Lustre quota
Filesystem: /scratch
Space used: 377G
Entries: 14k
# based on Robinhood
Filesystem: /scratch/work
Space used: 377G
Entries: 14k
# based on Robinhood
Filesystem: /scratch/temp
Space used: 12K
Entries: 6
# based on Robinhood
```
In this example, we view current size limits and space occupied on the /home and /scratch filesystem, for a particular user executing the command.
Note that limits are imposed also on number of objects (files, directories, links, etc...) that are allowed to create.
To have a better understanding of where the space is exactly used, you can use following command to find out.
```console
$ du -hs dir
```
Example for your HOME directory:
```console
$ cd /home
$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr
258M cuda-samples
15M .cache
13M .mozilla
5,5M .eclipse
2,7M .idb_13.0_linux_intel64_app
```
This will list all directories which are having MegaBytes or GigaBytes of consumed space in your actual (in this example HOME) directory. List is sorted in descending order from largest to smallest files/directories.
To have a better understanding of previous commands, you can read manpages.
```console
$ man lfs
```
```console
$ man du
```
## Extended Access Control List (ACL)
Extended ACLs provide another security mechanism beside the standard POSIX ACLs which are defined by three entries (for owner/group/others). Extended ACLs have more than the three basic entries. In addition, they also contain a mask entry and may contain any number of named user and named group entries.
ACLs on a Lustre file system work exactly like ACLs on any Linux file system. They are manipulated with the standard tools in the standard manner. Below, we create a directory and allow a specific user access.
```console
[vop999@login1.salomon ~]$ umask 027
[vop999@login1.salomon ~]$ mkdir test
[vop999@login1.salomon ~]$ ls -ld test
drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.salomon ~]$ getfacl test
# file: test
# owner: vop999
# group: vop999
user::rwx
group::r-x
other::---
[vop999@login1.salomon ~]$ setfacl -m user:johnsm:rwx test
[vop999@login1.salomon ~]$ ls -ld test
drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.salomon ~]$ getfacl test
# file: test
# owner: vop999
# group: vop999
user::rwx
user:johnsm:rwx
group::r-x
mask::rwx
other::---
```
Default ACL mechanism can be used to replace setuid/setgid permissions on directories. Setting a default ACL on a directory (-d flag to setfacl) will cause the ACL permissions to be inherited by any newly created file or subdirectory within the directory. Refer to this page for more information on Linux ACL:
[redhat guide](https://access.redhat.com/documentation/en-US/Red_Hat_Storage/2.0/html/Administration_Guide/ch09s05.html)
## Shared Workspaces
### Home
Users home directories /home/username reside on HOME file system. Accessible capacity is 0.5 PB, shared among all users. Individual users are restricted by file system usage quotas, set to 250 GB per user. If 250 GB should prove as insufficient for particular user, contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
!!! note
The HOME file system is intended for preparation, evaluation, processing and storage of data generated by active Projects.
The HOME should not be used to archive data of past Projects or other unrelated data.
The files on HOME will not be deleted until end of the [users lifecycle](/general/obtaining-login-credentials/obtaining-login-credentials/).
The workspace is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files.
| HOME workspace | |
| -------------- | -------------- |
| Accesspoint | /home/username |
| Capacity | 0.5 PB |
| Throughput | 6 GB/s |
| User quota | 250 GB |
| Protocol | NFS, 2-Tier |
### Work
The WORK workspace resides on SCRATCH file system. Users may create subdirectories and files in directories **/scratch/work/user/username** and **/scratch/work/project/projectid. **The /scratch/work/user/username is private to user, much like the home directory. The /scratch/work/project/projectid is accessible to all users involved in project projectid.
!!! note
The WORK workspace is intended to store users project data as well as for high performance access to input and output files. All project data should be removed once the project is finished. The data on the WORK workspace are not backed up.
Files on the WORK file system are **persistent** (not automatically deleted) throughout duration of the project.
The WORK workspace is hosted on SCRATCH file system. The SCRATCH is realized as Lustre parallel file system and is available from all login and computational nodes. Default stripe size is 1 MB, stripe count is 1. There are 54 OSTs dedicated for the SCRATCH file system.
!!! note
Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.
| WORK workspace | |
| -------------------- | --------------------------------------------------------- |
| Accesspoints | /scratch/work/user/username, /scratch/work/user/projectid |
| Capacity | 1.6 PB |
| Throughput | 30 GB/s |
| User quota | 100 TB |
| Default stripe size | 1 MB |
| Default stripe count | 1 |
| Number of OSTs | 54 |
| Protocol | Lustre |
### Temp
The TEMP workspace resides on SCRATCH file system. The TEMP workspace accesspoint is /scratch/temp. Users may freely create subdirectories and files on the workspace. Accessible capacity is 1.6 PB, shared among all users on TEMP and WORK. Individual users are restricted by file system usage quotas, set to 100 TB per user. The purpose of this quota is to prevent runaway programs from filling the entire file system and deny service to other users. >If 100 TB should prove as insufficient for particular user, contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
!!! note
The TEMP workspace is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs must use the TEMP workspace as their working directory.
Users are advised to save the necessary data from the TEMP workspace to HOME or WORK after the calculations and clean up the scratch files.
!!! warning
Files on the TEMP file system that are **not accessed for more than 90 days** will be automatically **deleted**.
The TEMP workspace is hosted on SCRATCH file system. The SCRATCH is realized as Lustre parallel file system and is available from all login and computational nodes. Default stripe size is 1 MB, stripe count is 1. There are 54 OSTs dedicated for the SCRATCH file system.
!!! note
Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.
| TEMP workspace | |
| -------------------- | ------------- |
| Accesspoint | /scratch/temp |
| Capacity | 1.6 PB |
| Throughput | 30 GB/s |
| User quota | 100 TB |
| Default stripe size | 1 MB |
| Default stripe count | 1 |
| Number of OSTs | 54 |
| Protocol | Lustre |
## RAM Disk
### Local RAM Disk
Every computational node is equipped with file system realized in memory, so called RAM disk.
The local RAM disk is mounted as /ramdisk and is accessible to user at /ramdisk/$PBS_JOBID directory.
The RAM disk is private to a job and local to node, created when the job starts and deleted at the job end.
!!! note
The local RAM disk directory /ramdisk/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.
The local RAM disk file system is intended for temporary scratch data generated during the calculation as well as
for high-performance access to input and output files. Size of RAM disk file system is limited.
It is not recommended to allocate large amount of memory and use large amount of data in RAM disk file system at the same time.
!!! warning
Be very careful, use of RAM disk file system is at the expense of operational memory.
| Local RAM disk | |
| ----------- | ------------------------------------------------------------------------------------------------------- |
| Mountpoint | /ramdisk |
| Accesspoint | /ramdisk/$PBS_JOBID |
| Capacity | 110 GB |
| Throughput | over 1.5 GB/s write, over 5 GB/s read, single thread, over 10 GB/s write, over 50 GB/s read, 16 threads |
| User quota | none |
### Global RAM Disk
The Global RAM disk spans the local RAM disks of all the nodes within a single job.
![Global RAM disk](../img/global_ramdisk.png)
The Global RAM disk deploys
BeeGFS On Demand parallel filesystem, using local RAM disks as a storage backend.
The Global RAM disk is mounted at /mnt/global_ramdisk.
!!! note
The global RAM disk is on-demand. It has to be activated by **global_ramdisk=true** in the qsub command.
```console
$ qsub -q qprod -l select=4,global_ramdisk=true ./jobscript
```
This command would submit 4 node job in qprod queue, once running a 440GB RAM disk shared across the 4 nodes will be created.
The RAM disk will be accessible at /mnt/global_ramdisk, files written to this RAM disk will be visible on all 4 nodes.
The file system is private to a job and shared among the nodes, created when the job starts and deleted at the job end.
!!! note
The Global RAM disk will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.
The files on the Global RAM disk will be equally striped across all the nodes, using 512k stripe size.
Check the Global RAM disk status:
```console
$ beegfs-df -p /mnt/global_ramdisk
$ beegfs-ctl --mount=/mnt/global_ramdisk --getentryinfo /mnt/global_ramdisk
```
Use Global RAM disk in case you need very large RAM disk space. The Global RAM disk allows for high performance sharing of data among compute nodes
within a job.
!!! warning
Be very careful, use of Global RAM disk file system is at the expense of operational memory.
| Global RAM disk | |
| ------------------ | --------------------------------------------------------------------------|
| Mountpoint | /mnt/global_ramdisk |
| Accesspoint | /mnt/global_ramdisk |
| Capacity | N*110 GB |
| Throughput | 3*(N+1) GB/s, 2GB/s single POSIX thread |
| User quota | none |
N = number of compute nodes in the job.
## Summary
| Mountpoint | Usage | Protocol | Net Capacity| Throughput | Limitations | Access | Service |
| ------------------- | ------------------------------ | ----------- | ------------| -------------- | ------------ | --------------------------- | --------------------------- |
| /home | home directory | NFS, 2-Tier | 0.5 PB | 6 GB/s | Quota 250GB | Compute and login nodes | backed up |
| /scratch/work | large project files | Lustre | 1.69 PB | 30 GB/s | Quota | Compute and login nodes | none |
| /scratch/temp | job temporary data | Lustre | 1.69 PB | 30 GB/s | Quota 100 TB | Compute and login nodes | files older 90 days removed |
| /ramdisk | job temporary data, node local | tmpfs | 110GB | 90 GB/s | none | Compute nodes, node local | purged after job ends |
| /mnt/global_ramdisk | job temporary data | BeeGFS | N*110GB | 3*(N+1) GB/s | none | Compute nodes, job shared | purged after job ends |
N = number of compute nodes in the job.
## CESNET Data Storage
Do not use shared file systems at IT4Innovations as a backup for large amount of data or long-term archiving purposes.
!!! note
The IT4Innovations does not provide storage capacity for data archiving. Academic staff and students of research institutions in the Czech Republic can use [CESNET Storage service](https://du.cesnet.cz/).
The CESNET Storage service can be used for research purposes, mainly by academic staff and students of research institutions in the Czech Republic.
User of data storage CESNET (DU) association can become organizations or an individual person who is either in the current employment relationship (employees) or the current study relationship (students) to a legal entity (organization) that meets the “Principles for access to CESNET Large infrastructure (Access Policy)”.
User may only use data storage CESNET for data transfer and storage which are associated with activities in science, research, development, the spread of education, culture and prosperity. In detail see “Acceptable Use Policy CESNET Large Infrastructure (Acceptable Use Policy, AUP)”.
The service is documented [here](https://du.cesnet.cz/en/start). For special requirements contact directly CESNET Storage Department via e-mail [du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
The procedure to obtain the CESNET access is quick and trouble-free.
(source [https://du.cesnet.cz/](https://du.cesnet.cz/wiki/doku.php/en/start "CESNET Data Storage"))
## CESNET Storage Access
### Understanding CESNET Storage
!!! note
It is very important to understand the CESNET storage before uploading data. [Please read](https://du.cesnet.cz/en/navody/home-migrace-plzen/start) first.
Once registered for CESNET Storage, you may [access the storage](https://du.cesnet.cz/en/navody/faq/start) in number of ways. We recommend the SSHFS and RSYNC methods.
### SSHFS Access
!!! note
SSHFS: The storage will be mounted like a local hard drive
The SSHFS provides a very convenient way to access the CESNET Storage. The storage will be mounted onto a local directory, exposing the vast CESNET Storage as if it was a local removable hard drive. Files can be than copied in and out in a usual fashion.
First, create the mount point
```console
$ mkdir cesnet
```
Mount the storage. Note that you can choose among the ssh.du1.cesnet.cz (Plzen), ssh.du2.cesnet.cz (Jihlava), ssh.du3.cesnet.cz (Brno) Mount tier1_home **(only 5120M !)**:
```console
$ sshfs username@ssh.du1.cesnet.cz:. cesnet/
```
For easy future access from Anselm, install your public key
```console
$ cp .ssh/id_rsa.pub cesnet/.ssh/authorized_keys
```
Mount tier1_cache_tape for the Storage VO:
```console
$ sshfs username@ssh.du1.cesnet.cz:/cache_tape/VO_storage/home/username cesnet/
```
View the archive, copy the files and directories in and out
```console
$ ls cesnet/
$ cp -a mydir cesnet/.
$ cp cesnet/myfile .
```
Once done, remember to unmount the storage
```console
$ fusermount -u cesnet
```
### Rsync Access
!!! note
Rsync provides delta transfer for best performance, can resume interrupted transfers
Rsync is a fast and extraordinarily versatile file copying tool. It is famous for its delta-transfer algorithm, which reduces the amount of data sent over the network by sending only the differences between the source files and the existing files in the destination. Rsync is widely used for backups and mirroring and as an improved copy command for everyday use.
Rsync finds files that need to be transferred using a "quick check" algorithm (by default) that looks for files that have changed in size or in last-modified time. Any changes in the other preserved attributes (as requested by options) are made on the destination file directly when the quick check indicates that the file's data does not need to be updated.
More about Rsync at [here](https://du.cesnet.cz/en/navody/rsync/start#pro_bezne_uzivatele)
Transfer large files to/from CESNET storage, assuming membership in the Storage VO
```console
$ rsync --progress datafile username@ssh.du1.cesnet.cz:VO_storage-cache_tape/.
$ rsync --progress username@ssh.du1.cesnet.cz:VO_storage-cache_tape/datafile .
```
Transfer large directories to/from CESNET storage, assuming membership in the Storage VO
```console
$ rsync --progress -av datafolder username@ssh.du1.cesnet.cz:VO_storage-cache_tape/.
$ rsync --progress -av username@ssh.du1.cesnet.cz:VO_storage-cache_tape/datafolder .
```
Transfer rates of about 28 MB/s can be expected.
# Visualization Servers
Remote visualization with NICE DCV software is availabe on two nodes.
| Node | Count | Processor | Cores | Memory | GPU Accelerator |
|---------------|-------|-----------------------------------|-------|--------|------------------------------|
| visualization | 2 | 2 x Intel Xeon E5-2695v3, 2.3 GHz | 28 | 512 GB | NVIDIA QUADRO K5000 4 GB |
## Resource Allocation Policy
| queue | active project | project resources | nodes | min ncpus | priority | authorization | walltime |
|-------|----------------|-------------------|-------|-----------|----------|---------------|----------|
| qviz Visualization queue | yes | none required | 2 (with NVIDIA Quadro K5000) | 4 | 150 | no | 1h/8h |
## References
* [Graphical User Interface](/salomon/shell-and-data-access/#graphical-user-interface)
* [VPN Access](/salomon/shell-and-data-access/#vpn-access)
## Install and Run
**Install NICE DCV 2016** (user-computer)
* [Overview](https://www.nice-software.com/download/nice-dcv-2016)
* [Linux download](http://www.nice-software.com/storage/nice-dcv/2016.0/endstation/linux/nice-dcv-endstation-2016.0-17066.run)
* [Windows download](http://www.nice-software.com/storage/nice-dcv/2016.0/endstation/win/nice-dcv-endstation-2016.0-17066-Release.msi)
**Install VPN client** [VPN Access](/general/accessing-the-clusters/vpn-access/) (user-computer)
!!! note
Visualisation server is a compute node. You are not able to SSH with your private key. There are two solutions available to solve login issue.
### Windows Users
**Solution 1 - Add the public fingerprint**
* Generate public fingerprint for your private key with PuTTYgen
![](../img/puttygen.png)
* Add this key to `~/.ssh/authorized_keys` on the cluster
![](../img/addsshkey.png)
* Use your standard SSH key to connect to visualization server
**Solution 2 - Copy private key from the cluster**
* Install WinSCP client (user-computer) [Download WinSCP installer](https://winscp.net/download/WinSCP-5.13.3-Setup.exe)
* Add credentials
![](../img/viz1-win.png)
* Add path to key file
![](../img/viz2-win.png)
* Save
* Copy `~/.ssh/id_rsa` to your computer
* Convert key to PuTTY format with PuTTYgen
![](../img/puttygenconvert.png)
* Use this new ssh key to connect to visualization server
**Install PuTTY**
* [Overview](https://docs.it4i.cz/general/accessing-the-clusters/shell-access-and-data-transfer/putty/)
* [Download PuTTY installer](https://the.earth.li/~sgtatham/putty/latest/w64/putty-64bit-0.70-installer.msi)
* Configure PuTTY
![](../img/viz3-win.png)
* Add credentials and key file (create 3x sessions: **vizserv1.salomon.it4i.cz**, **vizserv2.salomon.it4i.cz**, **login1.salomon.it4i.cz**)
* Config SSH tunnels (user-computer) (for sessions vizserv1 and vizserv2 only) - ports: **5901**, **5902**, **7300-7305**
![](../img/viz4-win.png)
* Save
**Run VPN client** [VPN IT4Innovations](https://vpn.it4i.cz/user) (user-computer)
**Login to Salomon via PuTTY** (user-computer)
```console
$ ssh salomon.it4i.cz
```
**Remove ~/.vnc/xstartup**
**Run job**
```console
$ qsub -I -q qviz -A OPEN-XX-XX -l select=1:ncpus=4:host=vizserv1,walltime=04:00:00 -N Vizserver1
$ qsub -I -q qviz -A OPEN-XX-XX -l select=1:ncpus=4:host=vizserv2,walltime=04:00:00 -N Vizserver2
```
**Run vncserver on vizservX**
* check existing vncservers in /tmp/.X11-unix/X\* (rm /tmp/.X11-unix/X1 /tmp/.X11-unix/X2)
* vizserv1: vncserver :1 -geometry 2540x1380 -depth 24
* vizserv2: vncserver :2 -geometry 2540x1380 -depth 24
* set password for vncserver
**Login to vizservX via PuTTY (vizserv1/vizserv2) with tunnels** (user-computer)
**Run NICE DCV 2016** (user-computer)
* vizserv1: localhost:5901
* vizserv2: localhost:5902
* fill password
![](../img/viz5-win.png)
![](../img/viz6-win.png)
**Check DCV status (Salomon-vizservX) in VNC window**
**Run glxgears (Salomon-vizservX)**
![](../img/viz7-win.png)
**LOGOUT FROM MENU: System->Logout**
### Linux Users
**Config SSH tunnels (user-computer)**
* ports: 5901, 5902, 7300-7305
* vizserv1
```console
$ ssh -i ~/salomon_key -TN -f user@vizserv1.salomon.it4i.cz -L 5901:localhost:5901 -L 7300:localhost:7300 -L 7301:localhost:7301 -L 7302:localhost:7302 -L 7303:localhost:7303 -L 7304:localhost:7304 -L 7305:localhost:7305
```
* vizserv2
```console
$ ssh -i ~/salomon_key -TN -f user@vizserv2.salomon.it4i.cz -L 5902:localhost:5902 -L 7300:localhost:7300 -L 7301:localhost:7301 -L 7302:localhost:7302 -L 7303:localhost:7303 -L 7304:localhost:7304 -L 7305:localhost:7305
```
**Run VPN client** [VPN IT4Innovations](https://vpn.it4i.cz/user) (user-computer)
**Login to Salomon** (user-computer)
```console
$ ssh salomon.it4i.cz
```
**Remove ~/.vnc/xstartup**
**Run job**
```console
$ qsub -I -q qviz -A OPEN-XX-XX -l select=1:ncpus=4:host=vizserv1,walltime=04:00:00 -N Vizserver1
$ qsub -I -q qviz -A OPEN-XX-XX -l select=1:ncpus=4:host=vizserv2,walltime=04:00:00 -N Vizserver2
```
**Run vncserver on vizservX**
* check existing vncservers in /tmp/.X11-unix/X\* (rm /tmp/.X11-unix/X1 /tmp/.X11-unix/X2)
* vizserv1: vncserver :1 -geometry 2540x1380 -depth 24
* vizserv2: vncserver :2 -geometry 2540x1380 -depth 24
* set password for vncserver
**Run SSH (vizserv1/vizserv2) with tunnels** (user-computer)
**Run NICE DCV 2016** (user-computer)
* vizserv1: localhost:5901
* vizserv2: localhost:5902
* fill password
![](../img/viz1.png)
![](../img/viz2.png)
**Check DCV status in VNC window**
**Run glxgears**
![](../img/viz3.png)
**LOGOUT FROM MENU: System->Logout**
$$
MAX\_FAIRSHARE * ( 1 - \frac{usage_{Project}}{usage_{Total}} )
$$
$$
1000*queue\_priority + \frac{fairshare\_priority}{1000} + \frac{eligible\_time}{864000}
$$
<script type="text/x-mathjax-config">
MathJax.Hub.Config({
config: ["MMLorHTML.js"],
jax: ["input/TeX", "output/HTML-CSS", "output/NativeMML"],
extensions: ["tex2jax.js", "MathMenu.js", "MathZoom.js"],
tex2jax: {
inlineMath: [ ["\\(","\\)"] ],
displayMath: [ ["\\[","\\]"] ]
},
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TagSide: "right",
TagIndent: ".8em",
MultLineWidth: "85%",
equationNumbers: {
autoNumber: "AMS",
}
},
displayAlign: 'left',
showProcessingMessages: false,
messageStyle: 'none'
});
</script>
<script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.1.1/jquery.slim.min.js" integrity="sha256-/SIrNqv8h6QGKDuNoLGA4iret+kyesCkHGzVUUV0shc=" crossorigin="anonymous"></script>
<script>
// override to case insensitive search
$.expr[":"].contains = $.expr.createPseudo(function(arg) {
return function( elem ) {
return $(elem).text().toUpperCase().indexOf(arg.toUpperCase()) >= 0;
};
});
$("#searchInput").keyup(function () {
//split the current value of searchInput
var data = this.value.split(" ");
//create a jquery object of the rows
var jo = $("tbody").find("tr");
if (this.value == "") {
jo.show();
return;
}
//hide all the rows
jo.hide();
//Recusively filter the jquery object to get results.
jo.filter(function (i, v) {
var $t = $(this);
for (var d = 0; d < data.length; ++d) {
if ($t.is(":contains('" + data[d] + "')")) {
return true;
}
}
return false;
})
//show the rows that match.
.show();
}).focus(function () {
this.value = "";
$(this).css({
"color": "black"
});
}).css({
"color": "#C0C0C0"
});
</script>
# Resource Accounting Policy
## Wall-Clock Core-Hours WCH
The wall-clock core-hours (WCH) are the basic metric of computer utilization time.
1 wall-clock core-hour is defined as 1 processor core allocated for 1 hour of wall-clock time. Allocating a full node (16 cores Anselm, 24 cores Salomon)
for 1 hour amounts to 16 wall-clock core-hours (Anselm) or 24 wall-clock core-hours (Salomon).
## Normalized Core-Hours NCH
The resources subject to accounting are the normalized core-hours (NCH).
The normalized core-hours are obtained from WCH by applying a normalization factor:
$$
NCH = F*WCH
$$
All jobs are accounted in normalized core-hours, using factor F valid at the time of the execution:
| System | F | Validity |
| ------------------------------- | - | -------- |
| Salomon | 1.00 | 2017-09-11 to 2019-03-01 |
| Anselm | 0.65 | 2017-09-11 to 2019-03-01 |
The accounting runs whenever the computational cores are allocated via the PBS Pro workload manager (the qsub command), regardless of whether
the cores are actually used for any calculation.
!!! note
**The allocations are requested/granted in normalized core-hours NCH.**
!!! warning
Whenever the term core-hour is used in this documentation, we mean the normalized core-hour, NCH.
The normalized core-hours were introduced to treat systems of different age on equal footing.
Normalized core-hour is an accounting tool to discount the legacy systems. The past (before 2017-09-11) F factors are all 1.0.
In future, the factors F will be updated, as new systems are installed. Factors F are expected to only decrease in time.
See examples in the [Job submission and execution](job-submission-and-execution/) section.
## Consumed Resources
Check how many core-hours have been consumed. The command it4ifree is available on cluster login nodes.
```console
$ it4ifree
Projects I am participating in
==============================
PID Days left Total Used WCHs Used NCHs WCHs by me NCHs by me Free
---------- ----------- ------- ----------- ----------- ------------ ------------ -------
OPEN-XX-XX 323 0 5169947 5169947 50001 50001 1292555
Projects I am Primarily Investigating
=====================================
PID Login Used WCHs Used NCHs
---------- ---------- ----------- -----------
OPEN-XX-XX user1 376670 376670
user2 4793277 4793277
Legend
======
WCH = Wall-clock Core Hour
NCH = Normalized Core Hour
```
The **it4ifree** command is a part of it4i.portal.clients package, located here: <https://pypi.python.org/pypi/it4i.portal.clients>
# Bioinformatics Applications
## Introduction
In addition to the many applications available through modules (deployed through EasyBuild packaging system) we provide an alternative source of applications on our clusters inferred from [Gentoo Linux](https://www.gentoo.org/). The user's environment is setup through a script which returns a bash instance to the user (you can think of it a starting a whole virtual machine but inside your current namespace) . The applications were optimized by gcc compiler for the SandyBridge and IvyBridge platforms. The binaries use paths from /apps/gentoo prefix to find the required runtime dependencies, config files, etc. The Gentoo Linux is a standalone installation not even relying on the glibc provided by host operating system (Redhat). The trick which allowed us to install Gentoo Linux on the host Redhat system is called Gentoo::RAP and uses a modified loader with a hardcoded path ([links](https://wiki.gentoo.org/wiki/Prefix/libc)).
## Starting the Environment
```console
mmokrejs@login2~$ /apps/gentoo/startprefix
```
## Starting PBS Jobs Using the Applications
Create a template file which can be used and an argument to qsub command. Notably, the 'PBS -S' line specifies full PATH to the Bourne shell of the Gentoo Linux environment.
```console
mmokrejs@login2~$ cat myjob.pbs
#PBS -S /apps/gentoo/bin/sh
#PBS -l nodes=1:ppn=16,walltime=12:00:00
#PBS -q qfree
#PBS -M my_email@foo.bar
#PBS -m ea
#PBS -N sample22
#PBS -A DD-13-5
#source ~/.bashrc
cd $PBS_O_WORKDIR || exit 255
myscript.sh foo 1>myjob.log 2>&1
$ head -n 1 myscript.sh
#! /apps/gentoo/bin/sh
$ qsub myjob.pbs
$ qstat
```
## Reading Manual Pages for Installed Applications
```console
mmokrejs@login2~$ man -M /apps/gentoo/usr/share/man bwa
mmokrejs@login2~$ man -M /apps/gentoo/usr/share/man samtools
```
## Listing of Bioinformatics Applications
```console
mmokrejs@login2~$ grep biology /scratch/mmokrejs/gentoo_rap/installed.txt
sci-biology/ANGLE-bin-20080813-r1
sci-biology/AlignGraph-9999
sci-biology/Atlas-Link-0.01-r1
sci-biology/BRANCH-9999
sci-biology/EBARDenovo-1.2.2
sci-biology/FLASH-1.2.9
sci-biology/GAL-0.2.2
sci-biology/Gambit-0.4.145
sci-biology/HTSeq-0.6.1
sci-biology/InterMine-0.98
sci-biology/MochiView-1.45
sci-biology/MuSeqBox-5.4
sci-biology/ONTO-PERL-1.41
sci-biology/ORFcor-20130507
sci-biology/Rcorrector-9999
sci-biology/SSAKE-3.8.2
sci-biology/STAR-9999
sci-biology/YASRA-2.33
sci-biology/abacas-1.3.1
sci-biology/align_to_scf-1.06
sci-biology/assembly-stats-9999
sci-biology/bambus-2.33
sci-biology/bamtools-9999
sci-biology/bcftools-1.2
sci-biology/bedtools-2.22.1
sci-biology/bfast-0.7.0a
sci-biology/biobambam2-9999
sci-biology/bismark-0.13.0
sci-biology/blat-34-r1
sci-biology/blue-1.1.3
sci-biology/bowtie-2.2.9
sci-biology/brat-1.2.4
sci-biology/bwa-0.7.13
sci-biology/bx-python-9999
sci-biology/cast-bin-20080813
sci-biology/cd-hit-4.6.5
sci-biology/cdbfasta-0.1
sci-biology/clover-2011.10.24
sci-biology/clustalw-2.1
sci-biology/cnrun-2.0.3
sci-biology/codonw-1.4.4-r2
sci-biology/conform-gt-1174
sci-biology/conifer-0.2.2
sci-biology/coral-1.4
sci-biology/cross_genome-20140822
sci-biology/cutadapt-9999
sci-biology/dawg-1.1.2
sci-biology/dna2pep-1.1
sci-biology/edena-3.131028
sci-biology/epga-9999
sci-biology/erpin-5.5b
sci-biology/estscan-3.0.3
sci-biology/eugene-4.1d
sci-biology/exonerate-gff3-9999
sci-biology/fastx_toolkit-0.0.14
sci-biology/gemini-9999
sci-biology/geneid-1.4.4
sci-biology/genepop-4.2.1
sci-biology/glimmerhmm-3.0.1-r1
sci-biology/gmap-2015.12.31.5
sci-biology/hexamer-19990330
sci-biology/hts-python-9999
sci-biology/jellyfish-2.1.4
sci-biology/jigsaw-3.2.10
sci-biology/kallisto-9999
sci-biology/karect-1.0.0
sci-biology/lastz-1.03.66
sci-biology/libgtextutils-0.6.1
sci-biology/lucy-1.20
sci-biology/megahit-9999
sci-biology/merlin-1.1.2
sci-biology/miranda-3.3a
sci-biology/mreps-2.5
sci-biology/mrfast-2.6.0.1
sci-biology/mummer-3.22-r1
sci-biology/muscle-3.8.31
sci-biology/nrcl-110625
sci-biology/nwalign-0.3.1
sci-biology/oases-9999
sci-biology/parafly-20130121
sci-biology/phrap-1.080812-r1
sci-biology/phred-071220
sci-biology/phylip-3.696-r1
sci-biology/plinkseq-0.10
sci-biology/primer3-2.3.7
sci-biology/prinseq-lite-0.20.4
sci-biology/proda-1.0
sci-biology/pybedtools-0.6.9
sci-biology/pysam-0.9.0
sci-biology/pysamstats-0.24.2
sci-biology/quast-2.3
sci-biology/quorum-1.0.0
sci-biology/reaper-15348
sci-biology/repeatmasker-libraries-20150807
sci-biology/reptile-1.1
sci-biology/samstat-20130708
sci-biology/samtools-0.1.20-r2
sci-biology/samtools-1.3-r1
sci-biology/scaffold_builder-20131122-r1
sci-biology/scan_for_matches-20121220
sci-biology/screed-0.7.1
sci-biology/scythe-0.992
sci-biology/seqan-2.1.1
sci-biology/seqtools-4.34.5
sci-biology/sff_dump-1.04
sci-biology/sgp2-1.1
sci-biology/shrimp-2.2.3
sci-biology/sickle-9999
sci-biology/smalt-0.7.6
sci-biology/snpomatic-9999
sci-biology/ssaha2-bin-2.5.5
sci-biology/stampy-1.0.28
sci-biology/stringtie-1.2.2
sci-biology/subread-1.4.6
sci-biology/swissknife-1.72
sci-biology/tagdust-20101028
sci-biology/tclust-110625
sci-biology/tigr-foundation-libs-2.0-r1
sci-biology/trans-abyss-1.4.8
sci-biology/trf-4.07b
sci-biology/uchime-4.2.40
sci-biology/velvet-1.2.10
sci-biology/velvetk-20120606
sci-biology/zmsort-110625
```
```console
mmokrejs@login2~$ grep sci-libs /scratch/mmokrejs/gentoo_rap/installed.txt
sci-libs/amd-2.3.1
sci-libs/blas-reference-20151113-r1
sci-libs/camd-2.3.1
sci-libs/cbflib-0.9.3.3
sci-libs/ccolamd-2.8.0
sci-libs/cholmod-2.1.2
sci-libs/coinor-cbc-2.8.9
sci-libs/coinor-cgl-0.58.6
sci-libs/coinor-clp-1.15.6-r1
sci-libs/coinor-dylp-1.9.4
sci-libs/coinor-osi-0.106.6
sci-libs/coinor-utils-2.9.11
sci-libs/coinor-vol-1.4.4
sci-libs/colamd-2.8.0
sci-libs/cxsparse-3.1.2
sci-libs/dcmtk-3.6.0
sci-libs/gsl-2.1
sci-libs/hdf5-1.8.15_p1
sci-libs/htslib-1.3
sci-libs/io_lib-1.14.7
sci-libs/lapack-reference-3.6.0-r1
sci-libs/lemon-1.3-r2
sci-libs/libmaus2-9999
sci-libs/qrupdate-1.1.2-r1
sci-libs/scikits-0.1-r1
sci-libs/suitesparseconfig-4.2.1
sci-libs/umfpack-5.6.2
```
## Classification of Applications
| Applications for bioinformatics at IT4I | |
| --------------------------------------- | ------ |
| error-correctors | 6 |
| aligners | 20 |
| clusterers | 5 |
| assemblers | 9 |
| scaffolders | 6 |
| motif searching | 6 |
| ORF/gene prediction/genome annotation | 13 |
| genotype/haplotype/popullation genetics | 3 |
| phylogenetics | 1 |
| transcriptome analysis | 2 |
| utilities | 15 |
| GUI | 3 |
| libraries | 4 |
| **Total** | **93** |
![graphs](../../img/bio-graphs.png)
## Other Applications Available Through Gentoo Linux
Gentoo Linux is a allows compilation of its applications from source code while using compiler and optimize flags set to user's wish. This facilitates creation of optimized binaries for the host platform. Users maybe also use several versions of gcc, python and other tools.
```console
mmokrejs@login2~$ gcc-config -l
mmokrejs@login2~$ java-config -L
mmokrejs@login2~$ eselect
```
# Diagnostic Component (TEAM)
## Access
TEAM is available at the [following address](http://omics.it4i.cz/team/)
!!! note
The address is accessible only via VPN.
## Diagnostic Component
VCF files are scanned by this diagnostic tool for known diagnostic disease-associated variants. When no diagnostic mutation is found, the file can be sent to the disease-causing gene discovery tool to see whether new disease associated variants can be found.
TEAM (27) is an intuitive and easy-to-use web tool that fills the gap between the predicted mutations and the final diagnostic in targeted enrichment sequencing analysis. The tool searches for known diagnostic mutations, corresponding to a disease panel, among the predicted patient’s variants. Diagnostic variants for the disease are taken from four databases of disease-related variants (HGMD, HUMSAVAR , ClinVar and COSMIC) If no primary diagnostic variant is found, then a list of secondary findings that can help to establish a diagnostic is produced. TEAM also provides with an interface for the definition of and customization of panels, by means of which, genes and mutations can be added or discarded to adjust panel definitions.
![Interface of the application. Panels for defining targeted regions of interest can be set up by just drag and drop known disease genes or disease definitions from the lists. Thus, virtual panels can be interactively improved as the knowledge of the disease increases.](../../../img/fig5.png)
** Figure 5. **Interface of the application. Panels for defining targeted regions of interest can be set up by just drag and drop known disease genes or disease definitions from the lists. Thus, virtual panels can be interactively improved as the knowledge of the disease increases.
# Overview
The human NGS data processing solution
## Introduction
The scope of this OMICS MASTER solution is restricted to human genomics research (disease causing gene discovery in whole human genome or exome) or diagnosis (panel sequencing), although it could be extended in the future to other usages.
The pipeline inputs the raw data produced by the sequencing machines and undergoes a processing procedure that consists on a quality control, the mapping and variant calling steps that result in a file containing the set of variants in the sample. From this point, the prioritization component or the diagnostic component can be launched.
![OMICS MASTER solution overview. Data is produced in the external labs and comes to IT4I (represented by the blue dashed line). The data pre-processor converts raw data into a list of variants and annotations for each sequenced patient. These lists files together with primary and secondary (alignment) data files are stored in IT4I sequence DB and uploaded to the discovery (candidate priorization) or diagnostic component where they can be analysed directly by the user that produced
them, depending of the experimental design carried out.](../../../img/fig1.png)
Figure 1. OMICS MASTER solution overview. Data is produced in the external labs and comes to IT4I (represented by the blue dashed line). The data pre-processor converts raw data into a list of variants and annotations for each sequenced patient. These lists files together with primary and secondary (alignment) data files are stored in IT4I sequence DB and uploaded to the discovery (candidate prioritization) or diagnostic component where they can be analyzed directly by the user that produced them, depending of the experimental design carried out.
Typical genomics pipelines are composed by several components that need to be launched manually. The advantage of OMICS MASTER pipeline is that all these components are invoked sequentially in an automated way.
OMICS MASTER pipeline inputs a FASTQ file and outputs an enriched VCF file. This pipeline is able to queue all the jobs to PBS by only launching a process taking all the necessary input files and creates the intermediate and final folders
Let’s see each of the OMICS MASTER solution components:
## Components
### Processing
This component is composed by a set of programs that carry out quality controls, alignment, realignment, variant calling and variant annotation. It turns raw data from the sequencing machine into files containing lists of variants (VCF) that once annotated, can be used by the following components (discovery and diagnosis).
We distinguish three types of sequencing instruments: bench sequencers (MySeq, IonTorrent, and Roche Junior, although this last one is about being discontinued), which produce relatively Genomes in the clinic
low throughput (tens of million reads), and high end sequencers, which produce high throughput (hundreds of million reads) among which we have Illumina HiSeq 2000 (and new models) and SOLiD. All of them but SOLiD produce data in sequence format. SOLiD produces data in a special format called colour space that require of specific software for the mapping process. Once the mapping has been done, the rest of the pipeline is identical. Anyway, SOLiD is a technology which is also about being discontinued by the manufacturer so, this type of data will be scarce in the future.
#### Quality Control, Preprocessing and Statistics for FASTQ
FastQC& FastQC.
These steps are carried out over the original FASTQ file with optimized scripts and includes the following steps: sequence cleansing, estimation of base quality scores, elimination of duplicates and statistics.
Input: FASTQ file.
Output: FASTQ file plus an HTML file containing statistics on the data.
FASTQ format It represents the nucleotide sequence and its corresponding quality scores.
![FASTQ file.](../../../img/fig2.png)
Figure 2.FASTQ file.
#### Mapping
Component: Hpg-aligner.
Sequence reads are mapped over the human reference genome. SOLiD reads are not covered by this solution; they should be mapped with specific software (among the few available options, SHRiMP seems to be the best one). For the rest of NGS machine outputs we use HPG Aligner. HPG-Aligner is an innovative solution, based on a combination of mapping with BWT and local alignment with Smith-Waterman (SW), that drastically increases mapping accuracy (97% versus 62-70% by current mappers, in the most common scenarios). This proposal provides a simple and fast solution that maps almost all the reads, even those containing a high number of mismatches or indels.
Input: FASTQ file.
Output: Aligned file in BAM format.
#### Sequence Alignment/Map (SAM)
It is a human readable tab-delimited format in which each read and its alignment is represented on a single line. The format can represent unmapped reads, reads that are mapped to unique locations, and reads that are mapped to multiple locations.
The SAM format (1) consists of one header section and one alignment section. The lines in the header section start with character ‘@’, and lines in the alignment section do not. All lines are TAB delimited.
In SAM, each alignment line has 11 mandatory fields and a variable number of optional fields. The mandatory fields are briefly described in Table 1. They must be present but their value can be a ‘\’ or a zero (depending on the field) if the
corresponding information is unavailable.
| No. | Name | Description |
| --------- | ---------- | ----------------------------------------------------- |
| 1 | QNAME | Query NAME of the read or the read pai |
| 2 | FLAG | Bitwise FLAG (pairing,strand,mate strand,etc.) |
| 3 | RNAME | Reference sequence NAME |
| 4 | POS | 1-Based leftmost POSition of clipped alignment |
| 5 | MAPQ | MAPping Quality (Phred-scaled) |
| 6 | CIGAR | Extended CIGAR string (operations:MIDNSHP) |
| 7 | MRNM | Mate REference NaMe ('=' if same RNAME) |
| 8 | MPOS | 1-Based leftmost Mate POSition |
| 9 | ISIZE | Inferred Insert SIZE |
| 10 | SEQ | Query SEQuence on the same strand as the reference |
| 11 | QUAL | Query QUALity (ASCII-33=Phred base quality) |
Table 1 . Mandatory fields in the SAM format.
The standard CIGAR description of pairwise alignment defines three operations: ‘M’ for match/mismatch, ‘I’ for insertion compared with the reference and ‘D’ for deletion. The extended CIGAR proposed in SAM added four more operations: ‘N’ for skipped bases on the reference, ‘S’ for soft clipping, ‘H’ for hard clipping and ‘P’ for padding. These support splicing, clipping, multi-part and padded alignments. Figure 3 shows examples of CIGAR strings for different types of alignments.
![SAM format file. The ‘@SQ’ line in the header section gives the order of reference sequences. Notably, r001 is the name of a read pair. According to FLAG 163 (=1+2+32+128), the read mapped to position 7 is the second read in the pair (128) and regarded as properly paired (1 + 2); its mate is mapped to 37 on the reverse strand (32). Read r002 has three soft-clipped (unaligned) bases. The coordinate shown in SAM is the position of the first aligned base. The CIGAR string for this alignment contains a P (padding) operation which correctly aligns the inserted sequences. Padding operations can be absent when an aligner does not support multiple sequence alignment. The last six bases of read r003 map to position 9, and the first five to position 29 on the reverse strand. The hard clipping operation H indicates that the clipped sequence is not present in the sequence field. The NM tag gives the number of mismatches. Read r004 is aligned across an intron, indicated by the N operation.](../../../img/fig3.png)
Figure 3 . SAM format file. The ‘@SQ’ line in the header section gives the order of reference sequences. Notably, r001 is the name of a read pair. According to FLAG 163 (=1+2+32+128), the read mapped to position 7 is the second read in the pair (128) and regarded as properly paired (1 + 2); its mate is mapped to 37 on the reverse strand (32). Read r002 has three soft-clipped (unaligned) bases. The coordinate shown in SAM is the position of the first aligned base. The CIGAR string for this alignment contains a P (padding) operation which correctly aligns the inserted sequences. Padding operations can be absent when an aligner does not support multiple sequence alignment. The last six bases of read r003 map to position 9, and the first five to position 29 on the reverse strand. The hard clipping operation H indicates that the clipped sequence is not present in the sequence field. The NM tag gives the number of mismatches. Read r004 is aligned across an intron, indicated by the N operation.
##### Binary Alignment/Map (BAM)
BAM is the binary representation of SAM and keeps exactly the same information as SAM. BAM uses lossless compression to reduce the size of the data by about 75% and provides an indexing system that allows reads that overlap a region of the genome to be retrieved and rapidly traversed.
#### Quality Control, Preprocessing and Statistics for BAM
Component: Hpg-Fastq & FastQC.
Some features
Quality control
reads with N errors
reads with multiple mappings
strand bias
paired-end insert
Filtering: by number of errors, number of hits
Comparator: stats, intersection, ...
Input: BAM file.
Output: BAM file plus an HTML file containing statistics.
#### Variant Calling
Component: GATK.
Identification of single nucleotide variants and indels on the alignments is performed using the Genome Analysis Toolkit (GATK). GATK (2) is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.
Input: BAM
Output:VCF
Variant Call Format (VCF)
VCF (3) is a standardized format for storing the most prevalent types of sequence variation, including SNPs, indels and larger structural variants, together with rich annotations. The format was developed with the primary intention to represent human genetic variation, but its use is not restricted to diploid genomes and can be used in different contexts as well. Its flexibility and user extensibility allows representation of a wide variety of genomic variation with respect to a single reference sequence.
A VCF file consists of a header section and a data section. The header contains an arbitrary number of metainformation lines, each starting with characters ‘##’, and a TAB delimited field definition line, starting with a single ‘#’ character. The meta-information header lines provide a standardized description of tags and annotations used in the data section. The use of meta-information allows the information stored within a VCF file to be tailored to the dataset in question. It can be also used to provide information about the means of file creation, date of creation, version of the reference sequence, software used and any other information relevant to the history of the file. The field definition line names eight mandatory columns, corresponding to data columns representing the chromosome (CHROM), a 1-based position of the start of the variant (POS), unique identifiers of the variant (ID), the reference allele (REF), a comma separated list of alternate non-reference alleles (ALT), a phred-scaled quality score (QUAL), site filtering information (FILTER) and a semicolon separated list of additional, user extensible annotation (INFO). In addition, if samples are present in the file, the mandatory header columns are followed by a FORMAT column and an arbitrary number of sample IDs that define the samples included in the VCF file. The FORMAT column is used to define the information contained within each subsequent genotype column, which consists of a colon separated list of fields. For example, the FORMAT field GT:GQ:DP in the fourth data entry of Figure 1a indicates that the subsequent entries contain information regarding the genotype, genotype quality and read depth for each sample. All data lines are TAB delimited and the number of fields in each data line must match the number of fields in the header line. It is strongly recommended that all annotation tags used are declared in the VCF header section.
![a) Example of valid VCF. The header lines ##fileformat and #CHROM are mandatory, the rest is optional but strongly recommended. Each line of the body describes variants present in the sampled population at one genomic position or region. All alternate alleles are listed in the ALT column and referenced from the genotype fields as 1-based indexes to this list; the reference haplotype is designated as 0. For multiploid data, the separator indicates whether the data are phased (|) or unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in this figure occur on the same chromosome in SAMPLE1. The first data line shows an example of a deletion (present in SAMPLE1) and a replacement of two bases by another base (SAMPLE2); the second line shows a SNP and an insertion; the third a SNP; the fourth a large structural variant described by the annotation in the INFO column, the coordinate is that of the base before the variant. (b–f ) Alignments and VCF representations of different sequence variants: SNP, insertion, deletion, replacement, and a large deletion. The REF columns shows the reference bases replaced by the haplotype in the ALT column. The coordinate refers to the first reference base. (g) Users are advised to use simplest representation possible and lowest coordinate in cases where the position is ambiguous.](../../../img/fig4.png)
Figure 4 . (a) Example of valid VCF. The header lines ##fileformat and #CHROM are mandatory, the rest is optional but strongly recommended. Each line of the body describes variants present in the sampled population at one genomic position or region. All alternate alleles are listed in the ALT column and referenced from the genotype fields as 1-based indexes to this list; the reference haplotype is designated as 0. For multiploid data, the separator indicates whether the data are phased (|) or unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in this figure occur on the same chromosome in SAMPLE1. The first data line shows an example of a deletion (present in SAMPLE1) and a replacement of two bases by another base (SAMPLE2); the second line shows a SNP and an insertion; the third a SNP; the fourth a large structural variant described by the annotation in the INFO column, the coordinate is that of the base before the variant. (b–f ) Alignments and VCF representations of different sequence variants: SNP, insertion, deletion, replacement, and a large deletion. The REF columns shows the reference bases replaced by the haplotype in the ALT column. The coordinate refers to the first reference base. (g) Users are advised to use simplest representation possible and lowest coordinate in cases where the position is ambiguous.
### Annotating
Component: HPG-Variant
The functional consequences of every variant found are then annotated using the HPG-Variant software, which extracts from CellBase, the Knowledge database, all the information relevant on the predicted pathologic effect of the variants.
VARIANT (VARIant Analysis Tool) (4) reports information on the variants found that include consequence type and annotations taken from different databases and repositories (SNPs and variants from dbSNP and 1000 genomes, and disease-related variants from the Genome-Wide Association Study (GWAS) catalog, Online Mendelian Inheritance in Man (OMIM), Catalog of Somatic Mutations in Cancer (COSMIC) mutations, etc. VARIANT also produces a rich variety of annotations that include information on the regulatory (transcription factor or miRNAbinding sites, etc.) or structural roles, or on the selective pressures on the sites affected by the variation. This information allows extending the conventional reports beyond the coding regions and expands the knowledge on the contribution of non-coding or synonymous variants to the phenotype studied.
Input: VCF
Output: The output of this step is the Variant Calling Format (VCF) file, which contains changes with respect to the reference genome with the corresponding QC and functional annotations.
#### CellBase
CellBase(5) is a relational database integrates biological information from different sources and includes:
Core features
We took genome sequences, genes, transcripts, exons, cytobands or cross references (xrefs) identifiers (IDs) from Ensembl (6). Protein information including sequences, xrefs or protein features (natural variants, mutagenesis sites, post-translational modifications, etc.) were imported from UniProt (7).
Regulatory
CellBase imports miRNA from miRBase (8); curated and non-curated miRNA targets from miRecords (9), miRTarBase (10),
TargetScan(11) and microRNA.org (12) and CpG islands and conserved regions from the UCSC database (13).
Functional annotation
OBO Foundry (14) develops many biomedical ontologies that are implemented in OBO format. We designed a SQL schema to store these OBO ontologies and 30 ontologies were imported. OBO ontology term annotations were taken from Ensembl (6). InterPro (15) annotations were also imported.
Variation
CellBase includes SNPs from dbSNP (16)^; SNP population frequencies from HapMap (17), 1000 genomes project (18) and Ensembl (6); phenotypically annotated SNPs were imported from NHRI GWAS Catalog (19),HGMD (20), Open Access GWAS Database (21), UniProt (7) and OMIM (22); mutations from COSMIC (23) and structural variations from Ensembl (6).
Systems biology
We also import systems biology information like interactome information from IntAct (24). Reactome (25) stores pathway and interaction information in BioPAX (26) format. BioPAX data exchange format enables the integration of diverse pathway
resources. We successfully solved the problem of storing data released in BioPAX format into a SQL relational schema, which allowed us importing Reactome in CellBase.
### [Diagnostic Component (TEAM)](/software/bio/omics-master/diagnostic-component-team/)
### [Priorization Component (BiERApp)](/software/bio/omics-master/priorization-component-bierapp/)
## Usage
First of all, we should load ngsPipeline module:
```console
$ ml ngsPipeline
```
This command will load python/2.7.5 module and all the required modules (hpg-aligner, gatk, etc)
If we launch ngsPipeline with ‘-h’, we will get the usage help:
```console
$ ngsPipeline -h
Usage: ngsPipeline.py [-h] -i INPUT -o OUTPUT -p PED --project PROJECT --queue
QUEUE [--stages-path STAGES_PATH] [--email EMAIL]
[--prefix PREFIX] [-s START] [-e END] --log
Python pipeline
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
-o OUTPUT, --output OUTPUT
Output Data directory
-p PED, --ped PED Ped file with all individuals
--project PROJECT Project Id
--queue QUEUE Queue Id
--stages-path STAGES_PATH
Custom Stages path
--email EMAIL Email
--prefix PREFIX Prefix name for Queue Jobs name
-s START, --start START
Initial stage
-e END, --end END Final stage
--log Log to file
```
Let us see a brief description of the arguments:
```console
-h --help. Show the help.
-i, --input. The input data directory. This directory must to have a special structure. We have to create one folder per sample (with the same name). These folders will host the fastq files. These fastq files must have the following pattern “sampleName” + “_” + “1 or 2” + “.fq”. 1 for the first pair (in paired-end sequences), and 2 for the
second one.
-o , --output. The output folder. This folder will contain all the intermediate and final folders. When the pipeline will be executed completely, we could remove the intermediate folders and keep only the final one (with the VCF file containing all the variants)
-p , --ped. The ped file with the pedigree. This file contains all the sample names. These names must coincide with the names of the input folders. If our input folder contains more samples than the .ped file, the pipeline will use only the samples from the .ped file.
--email. Email for PBS notifications.
--prefix. Prefix for PBS Job names.
-s, --start & -e, --end. Initial and final stage. If we want to launch the pipeline in a specific stage we must use -s. If we want to end the pipeline in a specific stage we must use -e.
--log. Using log argument NGSpipeline will prompt all the logs to this file.
--project>. Project ID of your supercomputer allocation.
--queue. [Queue](../../salomon/resources-allocation-policy/) to run the jobs in.
```
Input, output and ped arguments are mandatory. If the output folder does not exist, the pipeline will create it.
## Examples
This is an example usage of NGSpipeline:
We have a folder with the following structure in
```console
/apps/bio/omics/1.0/sample_data/ >:
/apps/bio/omics/1.0/sample_data
└── data
├── file.ped
├── sample1
│ ├── sample1_1.fq
│ └── sample1_2.fq
└── sample2
├── sample2_1.fq
└── sample2_2.fq
```
The ped file ( file.ped) contains the following info:
```console
#family_ID sample_ID parental_ID maternal_ID sex phenotype
FAM sample_A 0 0 1 1
FAM sample_B 0 0 2 2
```
Now, lets load the NGSPipeline module and copy the sample data to a [scratch directory](/salomon/storage/):
```console
$ ml ngsPipeline
$ mkdir -p /scratch/$USER/omics/results
$ cp -r /apps/bio/omics/1.0/sample_data /scratch/$USER/omics/
```
Now, we can launch the pipeline (replace OPEN-0-0 with your Project ID):
```console
$ ngsPipeline -i /scratch/$USER/omics/sample_data/data -o /scratch/$USER/omics/results -p /scratch/$USER/omics/sample_data/data/file.ped --project OPEN-0-0 --queue qprod
```
This command submits the processing [jobs to the queue](/salomon/job-submission-and-execution/).
If we want to re-launch the pipeline from stage 4 until stage 20 we should use the next command:
```console
$ ngsPipeline -i /scratch/$USER/omics/sample_data/data -o /scratch/$USER/omics/results -p /scratch/$USER/omics/sample_data/data/file.ped -s 4 -e 20 --project OPEN-0-0 --queue qprod
```
## Details on the Pipeline
The pipeline calls the following tools
[fastqc](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), quality control tool for high throughput sequence data.
[gatk](https://www.broadinstitute.org/gatk/), The Genome Analysis Toolkit or GATK is a software package developed at
the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
[hpg-aligner](https://github.com/opencb-hpg/hpg-aligner), HPG Aligner has been designed to align short and long reads with high sensitivity, therefore any number of mismatches or indels are allowed. HPG Aligner implements and combines two well known algorithms: _Burrows-Wheeler Transform_ (BWT) to speed-up mapping high-quality reads, and _Smith-Waterman_> (SW) to increase sensitivity when reads cannot be mapped using BWT.
[hpg-fastq](http://docs.bioinfo.cipf.es/projects/fastqhpc/wiki), a quality control tool for high throughput sequence data.
[hpg-variant](http://docs.bioinfo.cipf.es/projects/hpg-variant/wiki), The HPG Variant suite is an ambitious project aimed to provide a complete suite of tools to work with genomic variation data, from VCF tools to variant profiling or genomic statistics. It is being implemented using High Performance Computing technologies to provide the best performance possible.
[picard](http://picard.sourceforge.net/), Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (HTSJDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.
[samtools](http://samtools.sourceforge.net/samtools-c.shtml), SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
[snpEff](http://snpeff.sourceforge.net/), Genetic variant annotation and effect prediction toolbox.
This listing show which tools are used in each step of the pipeline
stage-00: fastqc
stage-01: hpg_fastq
stage-02: fastqc
stage-03: hpg_aligner and samtools
stage-04: samtools
stage-05: samtools
stage-06: fastqc
stage-07: picard
stage-08: fastqc
stage-09: picard
stage-10: gatk
stage-11: gatk
stage-12: gatk
stage-13: gatk
stage-14: gatk
stage-15: gatk
stage-16: samtools
stage-17: samtools
stage-18: fastqc
stage-19: gatk
stage-20: gatk
stage-21: gatk
stage-22: gatk
stage-23: gatk
stage-24: hpg-variant
stage-25: hpg-variant
stage-26: snpEff
stage-27: snpEff
stage-28: hpg-variant
## Interpretation
The output folder contains all the subfolders with the intermediate data. This folder contains the final VCF with all the variants. This file can be uploaded into [TEAM](diagnostic-component-team/) by using the VCF file button. It is important to note here that the entire management of the VCF file is local: no patient’s sequence data is sent over the Internet thus avoiding any problem of data privacy or confidentiality.
![TEAM upload panel. Once the file has been uploaded, a panel must be chosen from the Panel list. Then, pressing the Run button the diagnostic process starts.]\((../../img/fig7.png)
Figure 7. _TEAM upload panel._ _Once the file has been uploaded, a panel must be chosen from the Panel_ list. Then, pressing the Run button the diagnostic process starts.
Once the file has been uploaded, a panel must be chosen from the Panel list. Then, pressing the Run button the diagnostic process starts. TEAM searches first for known diagnostic mutation(s) taken from four databases: HGMD-public (20), [HUMSAVAR](http://www.uniprot.org/docs/humsavar), ClinVar (29) and COSMIC (23).
![The panel manager. The elements used to define a panel are (A) disease terms, (B) diagnostic mutations and (C) genes. Arrows represent actions that can be taken in the panel manager. Panels can be defined by using the known mutations and genes of a particular disease. This can be done by dragging them to the Primary Diagnostic box (action D). This action, in addition to defining the diseases in the Primary Diagnostic box, automatically adds the corresponding genes to the Genes box. The panels can be customized by adding new genes (action F) or removing undesired genes (action G). New disease mutations can be added independently or associated to an already existing disease term (action E). Disease terms can be removed by simply dragging themback (action H).](../../../img/fig7x.png)
Figure 7. The panel manager. The elements used to define a panel are ( A ) disease terms, ( B ) diagnostic mutations and ( C ) genes. Arrows represent actions that can be taken in the panel manager. Panels can be defined by using the known mutations and genes of a particular disease. This can be done by dragging them to the Primary Diagnostic box (action D ). This action, in addition to defining the diseases in the Primary Diagnostic box, automatically adds the corresponding genes to the Genes box. The panels can be customized by adding new genes (action F ) or removing undesired genes (action G). New disease mutations can be added independently or associated to an already existing disease term (action E ). Disease terms can be removed by simply dragging them back (action H ).
For variant discovering/filtering we should upload the VCF file into BierApp by using the following form:
![BierApp VCF upload panel. It is recommended to choose a name for the job as well as a description.](../../../img/fig8.png)\
Figure 8 . \BierApp VCF upload panel. It is recommended to choose a name for the job as well as a description \\.
Each prioritization (‘job’) has three associated screens that facilitate the filtering steps. The first one, the ‘Summary’ tab, displays a statistic of the data set analyzed, containing the samples analyzed, the number and types of variants found and its distribution according to consequence types. The second screen, in the ‘Variants and effect’ tab, is the actual filtering tool, and the third one, the ‘Genome view’ tab, offers a representation of the selected variants within the genomic context provided by an embedded version of the Genome Maps Tool (30).
![This picture shows all the information associated to the variants. If a variant has an associated phenotype we could see it in the last column. In this case, the variant 7:132481242 CT is associated to the phenotype: large intestine tumor.](../../../img/fig9.png)
Figure 9 . This picture shows all the information associated to the variants. If a variant has an associated phenotype we could see it in the last column. In this case, the variant 7:132481242 CT is associated to the phenotype: large intestine tumor.
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1. Altshuler,D.M., Gibbs,R.A., Peltonen,L., Dermitzakis,E., Schaffner,S.F., Yu,F., Bonnen,P.E., de Bakker,P.I., Deloukas,P., Gabriel,S.B. et al. (2010) Integrating common and rare genetic variation in diverse human populations. Nature, 467, 52–58.
1. 1000 Genomes Project Consortium. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061–1073.
1. Hindorff,L.A., Sethupathy,P., Junkins,H.A., Ramos,E.M., Mehta,J.P., Collins,F.S. and Manolio,T.A. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA, 106, 9362–9367.
1. Stenson,P.D., Ball,E.V., Mort,M., Phillips,A.D., Shiel,J.A., Thomas,N.S., Abeysinghe,S., Krawczak,M. and Cooper,D.N. (2003) Human gene mutation database (HGMD): 2003 update. Hum. Mutat., 21, 577–581.
1. Johnson,A.D. and O’Donnell,C.J. (2009) An open access database of genome-wide association results. BMC Med. Genet, 10, 6.
1. McKusick,V. (1998) A Catalog of Human Genes and Genetic Disorders, 12th edn. John Hopkins University Press,Baltimore, MD.
1. Forbes,S.A., Bindal,N., Bamford,S., Cole,C., Kok,C.Y., Beare,D., Jia,M., Shepherd,R., Leung,K., Menzies,A. et al. (2011) COSMIC: mining complete cancer genomes in the catalogue of somatic mutations in cancer. Nucleic Acids Res., 39, D945–D950.
1. Kerrien,S., Aranda,B., Breuza,L., Bridge,A., Broackes-Carter,F., Chen,C., Duesbury,M., Dumousseau,M., Feuermann,M., Hinz,U. et al. (2012) The Intact molecular interaction database in 2012. Nucleic Acids Res., 40, D841–D846.
1. Croft,D., O’Kelly,G., Wu,G., Haw,R., Gillespie,M., Matthews,L., Caudy,M., Garapati,P., Gopinath,G., Jassal,B. et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res., 39, D691–D697.
1. Demir,E., Cary,M.P., Paley,S., Fukuda,K., Lemer,C., Vastrik,I.,Wu,G., D’Eustachio,P., Schaefer,C., Luciano,J. et al. (2010) The BioPAX community standard for pathway data sharing. Nature Biotechnol., 28, 935–942.
1. Alemán Z, García-García F, Medina I, Dopazo J (2014): A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications. Nucleic Acids Res 42: W83-7.
1. [Alemán A](http://www.ncbi.nlm.nih.gov/pubmed?term=Alem%C3%A1n%20A%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Garcia-Garcia F](http://www.ncbi.nlm.nih.gov/pubmed?term=Garcia-Garcia%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Salavert F](http://www.ncbi.nlm.nih.gov/pubmed?term=Salavert%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Medina I](http://www.ncbi.nlm.nih.gov/pubmed?term=Medina%20I%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Dopazo J](http://www.ncbi.nlm.nih.gov/pubmed?term=Dopazo%20J%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)> (2014). A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. [Nucleic Acids Res.](http://www.ncbi.nlm.nih.gov/pubmed/?term=BiERapp "Nucleic acids research.")>42 :W88-93.
1. Landrum,M.J., Lee,J.M., Riley,G.R., Jang,W., Rubinstein,W.S., Church,D.M. and Maglott,D.R. (2014) ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res., 42, D980–D985.
1. Medina I, Salavert F, Sanchez R, de Maria A, Alonso R, Escobar P, Bleda M, Dopazo J: Genome Maps, a new generation genome browser. Nucleic Acids Res 2013, 41:W41-46.
# Prioritization Component (BiERapp)
## Access
BiERapp is available at the [following address](http://omics.it4i.cz/bierapp/)
!!! note
The address is accessible only via VPN.
## BiERapp
** This tool is aimed to discover new disease genes or variants by studying affected families or cases and controls. It carries out a filtering process to sequentially remove: (i) variants which are not no compatible with the disease because are not expected to have impact on the protein function; (ii) variants that exist at frequencies incompatible with the disease; (iii) variants that do not segregate with the disease. The result is a reduced set of disease gene candidates that should be further validated experimentally. **
BiERapp (28) efficiently helps in the identification of causative variants in family and sporadic genetic diseases. The program reads lists of predicted variants (nucleotide substitutions and indels) in affected individuals or tumor samples and controls. In family studies, different modes of inheritance can easily be defined to filter out variants that do not segregate with the disease along the family. Moreover, BiERapp integrates additional information such as allelic frequencies in the general population and the most popular damaging scores to further narrow down the number of putative variants in successive filtering steps. BiERapp provides an interactive and user-friendly interface that implements the filtering strategy used in the context of a large-scale genomic project carried out by the Spanish Network for Research, in Rare Diseases (CIBERER) and the Medical Genome Project. in which more than 800 exomes have been analyzed.
![Web interface to the prioritization tool. This figure shows the interface of the web tool for candidate gene prioritization with the filters available. The tool includes a genomic viewer (Genome Maps 30) that enables the representation of the variants in the corresponding genomic coordinates.](../../../img/fig6.png)
** Figure 6 **. Web interface to the prioritization tool. This figure shows the interface of the web tool for candidate gene
prioritization with the filters available. The tool includes a genomic viewer (Genome Maps 30) that enables the representation of the variants in the corresponding genomic coordinates.
# COMSOL Multiphysics
## Introduction
[COMSOL](http://www.comsol.com) is a powerful environment for modelling and solving various engineering and scientific problems based on partial differential equations. COMSOL is designed to solve coupled or multiphysics phenomena. For many standard engineering problems COMSOL provides add-on products such as electrical, mechanical, fluid flow, and chemical applications.
* [Structural Mechanics Module](http://www.comsol.com/structural-mechanics-module),
* [Heat Transfer Module](http://www.comsol.com/heat-transfer-module),
* [CFD Module](http://www.comsol.com/cfd-module),
* [Acoustics Module](http://www.comsol.com/acoustics-module),
* and [many others](http://www.comsol.com/products)
COMSOL also allows an interface support for equation-based modelling of partial differential equations.
## Execution
On the clusters COMSOL is available in the latest stable version. There are two variants of the release:
* **Non commercial** or so called **EDU variant**, which can be used for research and educational purposes.
* **Commercial** or so called **COM variant**, which can used also for commercial activities. **COM variant** has only subset of features compared to the **EDU variant** available. More about licensing [here](/software/cae/comsol/licensing-and-available-versions/).
To load the of COMSOL load the module
```console
$ ml COMSOL
```
By default the **EDU variant** will be loaded. If user needs other version or variant, load the particular version. To obtain the list of available versions use
```console
$ ml av COMSOL
```
If user needs to prepare COMSOL jobs in the interactive mode it is recommend to use COMSOL on the compute nodes via PBS Pro scheduler. In order run the COMSOL Desktop GUI on Windows is recommended to use the [Virtual Network Computing (VNC)](/general/accessing-the-clusters/graphical-user-interface/x-window-system/).
Example for Salomon:
```console
$ xhost +
$ qsub -I -X -A PROJECT_ID -q qprod -l select=1:ppn=24
$ ml COMSOL
$ comsol
```
To run COMSOL in batch mode, without the COMSOL Desktop GUI environment, user can utilized the default (comsol.pbs) job script and execute it via the qsub command.
```bash
#!/bin/bash
#PBS -l select=3:ppn=24
#PBS -q qprod
#PBS -N JOB_NAME
#PBS -A PROJECT_ID
cd /scratch/work/user/$USER/ || exit # on Anselm use: /scratch/$USER
echo Time is `date`
echo Directory is `pwd`
echo '**PBS_NODEFILE***START*******'
cat $PBS_NODEFILE
echo '**PBS_NODEFILE***END*********'
text_nodes < cat $PBS_NODEFILE
ml COMSOL
# ml COMSOL/51-EDU
ntask=$(wc -l $PBS_NODEFILE)
comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/.../$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log
```
Working directory has to be created before sending the (comsol.pbs) job script into the queue. Input file (name_input_f.mph) has to be in working directory or full path to input file has to be specified. The appropriate path to the temp directory of the job has to be set by command option (-tmpdir).
## LiveLink for MATLAB
COMSOL is the software package for the numerical solution of the partial differential equations. LiveLink for MATLAB allows connection to the COMSOL API (Application Programming Interface) with the benefits of the programming language and computing environment of the MATLAB.
LiveLink for MATLAB is available in both **EDU** and **COM** **variant** of the COMSOL release. On the clusters 1 commercial (**COM**) license and the 5 educational (**EDU**) licenses of LiveLink for MATLAB (see the [ISV Licenses](/software/isv_licenses/)) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode (on Anselm use 16 threads).
```console
$ xhost +
$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ppn=24
$ ml MATLAB
$ ml COMSOL
$ comsol server MATLAB
```
At the first time to launch the LiveLink for MATLAB (client-MATLAB/server-COMSOL connection) the login and password is requested and this information is not requested again.
To run LiveLink for MATLAB in batch mode with (comsol_matlab.pbs) job script you can utilize/modify the following script and execute it via the qsub command.
```bash
#!/bin/bash
#PBS -l select=3:ppn=24
#PBS -q qprod
#PBS -N JOB_NAME
#PBS -A PROJECT_ID
cd /scratch/work/user/$USER || exit # on Anselm use: /scratch/$USER
echo Time is `date`
echo Directory is `pwd`
echo '**PBS_NODEFILE***START*******'
cat $PBS_NODEFILE
echo '**PBS_NODEFILE***END*********'
text_nodes < cat $PBS_NODEFILE
ml MATLAB
ml COMSOL/51-EDU
ntask=$(wc -l $PBS_NODEFILE)
comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/work/user/$USER/work &
cd /apps/cae/COMSOL/51/mli
matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/work/user/$USER/work; test_job"
```
This example shows how to run LiveLink for MATLAB with following configuration: 3 nodes and 16 cores per node. Working directory has to be created before submitting (comsol_matlab.pbs) job script into the queue. Input file (test_job.m) has to be in working directory or full path to input file has to be specified. The Matlab command option (-r ”mphstart”) created a connection with a COMSOL server using the default port number.
# Licensing and Available Versions
## Comsol License Can Be Used By:
* all persons in the carrying out of the CE IT4Innovations Project (In addition to the primary licensee, which is VSB - Technical University of Ostrava, users are CE IT4Innovations third parties - CE IT4Innovations project partners, particularly the University of Ostrava, the Brno University of Technology - Faculty of Informatics, the Silesian University in Opava, Institute of Geonics AS CR.)
* all persons who have a valid license
* students of the Technical University
## Comsol EDU Network Licence
The licence intended to be used for science and research, publications, students’ projects, teaching (academic licence).
## Comsol COM Network Licence
The licence intended to be used for science and research, publications, students’ projects, commercial research with no commercial use restrictions. Enables the solution of at least one job by one user in one program start.
## Available Versions
* ver. 51
PREC = Accurate
IBRION = -1
ENCUT = 500
EDIFF = 1.0e-08
ISMEAR = 0
SIGMA = 0.01
IALGO = 38
LREAL = .FALSE.
ADDGRID = .TRUE.
LWAVE = .FALSE.
LCHARG = .FALSE.
NCORE = 8
KPAR = 8
Automatic mesh
0
Monkhorst Pack
3 3 3
0.5 0.5 0.5
Si
1.0
5.4335600309153529 0.0000000000000000 0.0000000000000000
0.0000000000000000 5.4335600309153529 0.0000000000000000
0.0000000000000000 0.0000000000000000 5.4335600309153529
Si
8
Direct
0.8750000000000000 0.8750000000000000 0.8750000000000000
0.8750000000000000 0.3750000000000000 0.3750000000000000
0.3750000000000000 0.8750000000000000 0.3750000000000000
0.3750000000000000 0.3750000000000000 0.8750000000000000
0.1250000000000000 0.1250000000000000 0.1250000000000000
0.1250000000000000 0.6250000000000000 0.6250000000000000
0.6250000000000000 0.1250000000000000 0.6250000000000000
0.6250000000000000 0.6250000000000000 0.1250000000000000
PAW_PBE Si 05Jan2001
4.00000000000000
parameters from PSCTR are:
VRHFIN =Si: s2p2
LEXCH = PE
EATOM = 103.0669 eV, 7.5752 Ry
TITEL = PAW_PBE Si 05Jan2001
LULTRA = F use ultrasoft PP ?
IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no
RPACOR = 1.500 partial core radius
POMASS = 28.085; ZVAL = 4.000 mass and valenz
RCORE = 1.900 outmost cutoff radius
RWIGS = 2.480; RWIGS = 1.312 wigner-seitz radius (au A)
ENMAX = 245.345; ENMIN = 184.009 eV
ICORE = 2 local potential
LCOR = T correct aug charges
LPAW = T paw PP
EAUG = 322.069
DEXC = 0.000
RMAX = 1.950 core radius for proj-oper
RAUG = 1.300 factor for augmentation sphere
RDEP = 1.993 radius for radial grids
RDEPT = 1.837 core radius for aug-charge
Atomic configuration
6 entries
n l j E occ.
1 0 0.50 -1785.8828 2.0000
2 0 0.50 -139.4969 2.0000
2 1 1.50 -95.5546 6.0000
3 0 0.50 -10.8127 2.0000
3 1 0.50 -4.0811 2.0000
3 2 1.50 -4.0817 0.0000
Description
l E TYP RCUT TYP RCUT
0 -10.8127223 23 1.900
0 -7.6451159 23 1.900
1 -4.0811372 23 1.900
1 2.4879257 23 1.900
2 -4.0817478 7 1.900
Error from kinetic energy argument (eV)
NDATA = 100
STEP = 20.000 1.050
10.1 9.04 8.56 7.65 7.23 6.44 5.73 5.40
4.79 4.25 4.00 3.54 3.13 2.77 2.45 2.16
1.91 1.69 1.50 1.24 1.10 0.975 0.812 0.718
0.636 0.529 0.440 0.388 0.322 0.266 0.219 0.180
0.148 0.121 0.986E-01 0.804E-01 0.614E-01 0.504E-01 0.392E-01 0.328E-01
0.265E-01 0.220E-01 0.189E-01 0.166E-01 0.149E-01 0.135E-01 0.123E-01 0.109E-01
0.977E-02 0.840E-02 0.707E-02 0.605E-02 0.488E-02 0.387E-02 0.290E-02 0.229E-02
0.185E-02 0.152E-02 0.134E-02 0.125E-02 0.121E-02 0.117E-02 0.112E-02 0.102E-02
0.915E-03 0.776E-03 0.640E-03 0.524E-03 0.425E-03 0.369E-03 0.331E-03 0.310E-03
0.294E-03 0.273E-03 0.242E-03 0.210E-03 0.175E-03 0.146E-03 0.124E-03 0.113E-03
0.105E-03 0.973E-04 0.879E-04 0.755E-04 0.633E-04 0.539E-04 0.478E-04 0.438E-04
0.404E-04 0.362E-04 0.308E-04 0.264E-04 0.229E-04 0.209E-04 0.192E-04 0.170E-04
0.145E-04 0.126E-04 0.112E-04 0.103E-04
END of PSCTR-controll parameters
local part
98.2657514061040
0.84157827E+01 0.84210738E+01 0.84276982E+01 0.84387529E+01 0.84542581E+01
0.84742396E+01 0.84987267E+01 0.85277503E+01 0.85613408E+01 0.85995259E+01
0.86423293E+01 0.86897698E+01 0.87418601E+01 0.87986073E+01 0.88600119E+01
0.89260684E+01 0.89967646E+01 0.90720817E+01 0.91519931E+01 0.92364635E+01
0.93254478E+01 0.94188892E+01 0.95167180E+01 0.96188495E+01 0.97251831E+01
0.98356006E+01 0.99499656E+01 0.10068122E+02 0.10189896E+02 0.10315092E+02
0.10443494E+02 0.10574869E+02 0.10708960E+02 0.10845494E+02 0.10984175E+02
0.11124688E+02 0.11266699E+02 0.11409854E+02 0.11553782E+02 0.11698093E+02
0.11842379E+02 0.11986220E+02 0.12129179E+02 0.12270807E+02 0.12410647E+02
0.12548229E+02 0.12683078E+02 0.12814715E+02 0.12942655E+02 0.13066413E+02
0.13185507E+02 0.13299453E+02 0.13407778E+02 0.13510011E+02 0.13605696E+02
0.13694386E+02 0.13775649E+02 0.13849071E+02 0.13914257E+02 0.13970832E+02
0.14018447E+02 0.14056776E+02 0.14085521E+02 0.14104413E+02 0.14113214E+02
0.14111717E+02 0.14099750E+02 0.14077174E+02 0.14043887E+02 0.13999823E+02
0.13944953E+02 0.13879287E+02 0.13802871E+02 0.13715791E+02 0.13618172E+02
0.13510174E+02 0.13391995E+02 0.13263871E+02 0.13126072E+02 0.12978902E+02
0.12822701E+02 0.12657837E+02 0.12484712E+02 0.12303752E+02 0.12115414E+02
0.11920177E+02 0.11718542E+02 0.11511032E+02 0.11298186E+02 0.11080557E+02
0.10858712E+02 0.10633228E+02 0.10404687E+02 0.10173679E+02 0.99407916E+01
0.97066145E+01 0.94717325E+01 0.92367246E+01 0.90021610E+01 0.87686002E+01
0.85365875E+01 0.83066515E+01 0.80793028E+01 0.78550311E+01 0.76343038E+01
0.74175639E+01 0.72052283E+01 0.69976864E+01 0.67952987E+01 0.65983955E+01
0.64072761E+01 0.62222079E+01 0.60434255E+01 0.58711305E+01 0.57054914E+01
0.55466428E+01 0.53946864E+01 0.52496904E+01 0.51116908E+01 0.49806913E+01
0.48566647E+01 0.47395535E+01 0.46292714E+01 0.45257040E+01 0.44287107E+01
0.43381259E+01 0.42537609E+01 0.41754051E+01 0.41028283E+01 0.40357824E+01
0.39740032E+01 0.39172126E+01 0.38651205E+01 0.38174269E+01 0.37738239E+01
0.37339980E+01 0.36976316E+01 0.36644057E+01 0.36340010E+01 0.36061008E+01
0.35803917E+01 0.35565662E+01 0.35343243E+01 0.35133744E+01 0.34934356E+01
0.34742386E+01 0.34555273E+01 0.34370594E+01 0.34186082E+01 0.33999625E+01
0.33809283E+01 0.33613289E+01 0.33410051E+01 0.33198163E+01 0.32976400E+01
0.32743723E+01 0.32499276E+01 0.32242386E+01 0.31972561E+01 0.31689481E+01
0.31393000E+01 0.31083133E+01 0.30760055E+01 0.30424088E+01 0.30075693E+01
0.29715464E+01 0.29344112E+01 0.28962459E+01 0.28571426E+01 0.28172018E+01
0.27765317E+01 0.27352466E+01 0.26934661E+01 0.26513137E+01 0.26089155E+01
0.25663991E+01 0.25238926E+01 0.24815235E+01 0.24394172E+01 0.23976965E+01
0.23564804E+01 0.23158831E+01 0.22760134E+01 0.22369739E+01 0.21988601E+01
0.21617599E+01 0.21257533E+01 0.20909117E+01 0.20572975E+01 0.20249639E+01
0.19939549E+01 0.19643047E+01 0.19360380E+01 0.19091702E+01 0.18837070E+01
0.18596451E+01 0.18369721E+01 0.18156671E+01 0.17957010E+01 0.17770369E+01
0.17596305E+01 0.17434311E+01 0.17283815E+01 0.17144192E+01 0.17014767E+01
0.16894823E+01 0.16783606E+01 0.16680337E+01 0.16584212E+01 0.16494414E+01
0.16410120E+01 0.16330503E+01 0.16254746E+01 0.16182040E+01 0.16111597E+01
0.16042653E+01 0.15974473E+01 0.15906355E+01 0.15837638E+01 0.15767703E+01
0.15695978E+01 0.15621942E+01 0.15545124E+01 0.15465111E+01 0.15381545E+01
0.15294125E+01 0.15202610E+01 0.15106817E+01 0.15006618E+01 0.14901946E+01
0.14792787E+01 0.14679181E+01 0.14561220E+01 0.14439045E+01 0.14312843E+01
0.14182845E+01 0.14049320E+01 0.13912573E+01 0.13772941E+01 0.13630790E+01
0.13486508E+01 0.13340503E+01 0.13193195E+01 0.13045019E+01 0.12896413E+01
0.12747816E+01 0.12599667E+01 0.12452398E+01 0.12306429E+01 0.12162169E+01
0.12020007E+01 0.11880315E+01 0.11743438E+01 0.11609698E+01 0.11479386E+01
0.11352766E+01 0.11230067E+01 0.11111486E+01 0.10997185E+01 0.10887293E+01
0.10781901E+01 0.10681067E+01 0.10584812E+01 0.10493126E+01 0.10405963E+01
0.10323245E+01 0.10244864E+01 0.10170684E+01 0.10100541E+01 0.10034245E+01
0.99715842E+00 0.99123278E+00 0.98562260E+00 0.98030147E+00 0.97524176E+00
0.97041492E+00 0.96579177E+00 0.96134272E+00 0.95703813E+00 0.95284851E+00
0.94874481E+00 0.94469866E+00 0.94068261E+00 0.93667036E+00 0.93263699E+00
0.92855911E+00 0.92441506E+00 0.92018508E+00 0.91585139E+00 0.91139837E+00
0.90681257E+00 0.90208284E+00 0.89720031E+00 0.89215846E+00 0.88695307E+00
0.88158221E+00 0.87604623E+00 0.87034764E+00 0.86449105E+00 0.85848310E+00
0.85233228E+00 0.84604885E+00 0.83964467E+00 0.83313304E+00 0.82652853E+00
0.81984678E+00 0.81310436E+00 0.80631854E+00 0.79950711E+00 0.79268821E+00
0.78588011E+00 0.77910103E+00 0.77236900E+00 0.76570163E+00 0.75911595E+00
0.75262828E+00 0.74625406E+00 0.74000769E+00 0.73390245E+00 0.72795034E+00
0.72216201E+00 0.71654666E+00 0.71111201E+00 0.70586419E+00 0.70080779E+00
0.69594576E+00 0.69127948E+00 0.68680873E+00 0.68253171E+00 0.67844512E+00
0.67454419E+00 0.67082277E+00 0.66727336E+00 0.66388728E+00 0.66065470E+00
0.65756482E+00 0.65460595E+00 0.65176565E+00 0.64903085E+00 0.64638804E+00
0.64382333E+00 0.64132264E+00 0.63887182E+00 0.63645681E+00 0.63406371E+00
0.63167898E+00 0.62928953E+00 0.62688282E+00 0.62444703E+00 0.62197109E+00
0.61944485E+00 0.61685909E+00 0.61420564E+00 0.61147745E+00 0.60866857E+00
0.60577426E+00 0.60279097E+00 0.59971637E+00 0.59654936E+00 0.59329001E+00
0.58993961E+00 0.58650059E+00 0.58297648E+00 0.57937187E+00 0.57569237E+00
0.57194448E+00 0.56813556E+00 0.56427372E+00 0.56036773E+00 0.55642691E+00
0.55246106E+00 0.54848032E+00 0.54449508E+00 0.54051586E+00 0.53655323E+00
0.53261770E+00 0.52871958E+00 0.52486894E+00 0.52107546E+00 0.51734836E+00
0.51369633E+00 0.51012743E+00 0.50664899E+00 0.50326761E+00 0.49998904E+00
0.49681819E+00 0.49375905E+00 0.49081466E+00 0.48798714E+00 0.48527765E+00
0.48268635E+00 0.48021249E+00 0.47785436E+00 0.47560937E+00 0.47347400E+00
0.47144395E+00 0.46951410E+00 0.46767862E+00 0.46593101E+00 0.46426418E+00
0.46267051E+00 0.46114196E+00 0.45967012E+00 0.45824631E+00 0.45686165E+00
0.45550718E+00 0.45417389E+00 0.45285284E+00 0.45153526E+00 0.45021257E+00
0.44887651E+00 0.44751921E+00 0.44613322E+00 0.44471163E+00 0.44324809E+00
0.44173687E+00 0.44017292E+00 0.43855189E+00 0.43687018E+00 0.43512494E+00
0.43331410E+00 0.43143638E+00 0.42949128E+00 0.42747908E+00 0.42540083E+00
0.42325834E+00 0.42105410E+00 0.41879135E+00 0.41647393E+00 0.41410629E+00
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0.30157850E+00 0.29989478E+00 0.29821295E+00 0.29653774E+00 0.29487384E+00
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0.27847372E+00 0.27723499E+00 0.27604598E+00 0.27490705E+00 0.27381811E+00
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0.26170380E+00 0.26112078E+00 0.26053582E+00 0.25994525E+00 0.25934552E+00
0.25873328E+00 0.25810539E+00 0.25745897E+00 0.25679138E+00 0.25610030E+00
0.25538370E+00 0.25463989E+00 0.25386749E+00 0.25306548E+00 0.25223319E+00
0.25137030E+00 0.25047681E+00 0.24955311E+00 0.24859991E+00 0.24761822E+00
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0.22456503E+00 0.22358838E+00 0.22264133E+00 0.22172517E+00 0.22084090E+00
0.21998924E+00 0.21917062E+00 0.21838518E+00 0.21763278E+00 0.21691298E+00
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0.12704568E+00 0.12663761E+00 0.12624221E+00 0.12585997E+00 0.12549131E+00
0.12513650E+00 0.12479568E+00 0.12446890E+00 0.12415605E+00 0.12385692E+00
0.12357117E+00 0.12329835E+00 0.12303789E+00 0.12278912E+00 0.12255128E+00
0.12232351E+00 0.12210488E+00 0.12189437E+00 0.12169094E+00 0.12149345E+00
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0.11681676E+00 0.11650590E+00 0.11618540E+00 0.11585569E+00 0.11551727E+00
0.11517075E+00 0.11481682E+00 0.11445624E+00 0.11408986E+00 0.11371856E+00
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0.10649150E+00 0.10623816E+00 0.10599560E+00 0.10576362E+00 0.10554191E+00
0.10533006E+00 0.10512760E+00 0.10493397E+00 0.10474853E+00 0.10457057E+00
0.10439934E+00 0.10423403E+00 0.10407377E+00 0.10391769E+00 0.10376486E+00
0.10361436E+00 0.10346525E+00 0.10331660E+00 0.10316749E+00 0.10301700E+00
0.10286427E+00 0.10270845E+00 0.10254875E+00 0.10238443E+00 0.10221481E+00
0.10203926E+00 0.10185725E+00 0.10166830E+00 0.10147204E+00 0.10126815E+00
0.10105642E+00 0.10083671E+00 0.10060898E+00 0.10037327E+00 0.10012971E+00
0.99878499E-01 0.99619941E-01 0.99354403E-01 0.99082329E-01 0.98804234E-01
0.98520694E-01 0.98232343E-01 0.97939865E-01 0.97643987E-01 0.97345468E-01
0.97045098E-01 0.96743682E-01 0.96442039E-01 0.96140988E-01 0.95841346E-01
0.95543917E-01 0.95249483E-01 0.94958801E-01 0.94672589E-01 0.94391526E-01
0.94116241E-01 0.93847307E-01 0.93585238E-01 0.93330481E-01 0.93083416E-01
0.92844349E-01 0.92613514E-01 0.92391067E-01 0.92177088E-01 0.91971582E-01
0.91774473E-01 0.91585615E-01 0.91404784E-01 0.91231686E-01 0.91065960E-01
0.90907179E-01 0.90754858E-01 0.90608455E-01 0.90467383E-01 0.90331010E-01
0.90198671E-01 0.90069670E-01 0.89943293E-01 0.89818810E-01 0.89695483E-01
0.89572578E-01 0.89449363E-01 0.89325125E-01 0.89199170E-01 0.89070830E-01
0.88939475E-01 0.88804513E-01 0.88665401E-01 0.88521645E-01 0.88372809E-01
0.88218518E-01 0.88058459E-01 0.87892386E-01 0.87720120E-01 0.87541552E-01
0.87356640E-01 0.87165411E-01 0.86967963E-01 0.86764459E-01 0.86555125E-01
0.86340254E-01 0.86120194E-01 0.85895352E-01 0.85666183E-01 0.85433191E-01
0.85196919E-01 0.84957943E-01 0.84716871E-01 0.84474330E-01 0.84230965E-01
0.83987427E-01 0.83744375E-01 0.83502460E-01 0.83262325E-01 0.83024599E-01
0.82789886E-01 0.82558766E-01 0.82331783E-01 0.82109442E-01 0.81892206E-01
0.81680487E-01 0.81474646E-01 0.81274989E-01 0.81081762E-01 0.80895153E-01
0.80715285E-01 0.80542223E-01 0.80375965E-01 0.80216452E-01 0.80063558E-01
0.79917102E-01 0.79776842E-01 0.79642482E-01 0.79513673E-01 0.79390016E-01
0.79271070E-01 0.79156353E-01 0.79045348E-01 0.78937510E-01 0.78832270E-01
0.78729044E-01 0.78627233E-01 0.78526236E-01 0.78425450E-01 0.78324279E-01
0.78222140E-01 0.78118466E-01 0.78012713E-01 0.77904366E-01 0.77792943E-01
0.77678000E-01 0.77559135E-01 0.77435994E-01 0.77308271E-01 0.77175713E-01
0.77038121E-01 0.76895353E-01 0.76747321E-01 0.76593998E-01 0.76435410E-01
0.76271640E-01 0.76102829E-01 0.75929167E-01 0.75750899E-01 0.75568317E-01
gradient corrections used for XC
5
core charge-density (partial)
0.13681949E+01 0.13676959E+01 0.13662000E+01 0.13637104E+01 0.13602324E+01
0.13557734E+01 0.13503428E+01 0.13439523E+01 0.13366153E+01 0.13283472E+01
0.13191654E+01 0.13090891E+01 0.12981392E+01 0.12863383E+01 0.12737106E+01
0.12602819E+01 0.12460793E+01 0.12311313E+01 0.12154677E+01 0.11991193E+01
0.11821181E+01 0.11644969E+01 0.11462894E+01 0.11275300E+01 0.11082538E+01
0.10884961E+01 0.10682931E+01 0.10476808E+01 0.10266956E+01 0.10053741E+01
0.98375262E+00 0.96186755E+00 0.93975498E+00 0.91745072E+00 0.89499016E+00
0.87240821E+00 0.84973922E+00 0.82701686E+00 0.80427411E+00 0.78154316E+00
0.75885532E+00 0.73624100E+00 0.71372964E+00 0.69134965E+00 0.66912839E+00
0.64709210E+00 0.62526589E+00 0.60367368E+00 0.58233822E+00 0.56128101E+00
0.54052235E+00 0.52008128E+00 0.49997557E+00 0.48022176E+00 0.46083511E+00
0.44182966E+00 0.42321818E+00 0.40501223E+00 0.38722214E+00 0.36985705E+00
0.35292494E+00 0.33643261E+00 0.32038576E+00 0.30478900E+00 0.28964586E+00
0.27495885E+00 0.26072948E+00 0.24695831E+00 0.23364497E+00 0.22078821E+00
0.20838595E+00 0.19643529E+00 0.18493257E+00 0.17387344E+00 0.16325283E+00
0.15306506E+00 0.14330386E+00 0.13396239E+00 0.12503331E+00 0.11650882E+00
0.10838067E+00 0.10064023E+00 0.93278518E-01 0.86286246E-01 0.79653843E-01
0.73371502E-01 0.67429213E-01 0.61816795E-01 0.56523931E-01 0.51540200E-01
0.46855106E-01 0.42458107E-01 0.38338646E-01 0.34486172E-01 0.30890172E-01
0.27540190E-01 0.24425849E-01 0.21536878E-01 0.18863124E-01 0.16394576E-01
0.14121382E-01 0.12033859E-01 0.10122515E-01 0.83780585E-02 0.67914089E-02
0.53537106E-02 0.40563407E-02 0.28909176E-02 0.18493085E-02 0.92363542E-03
0.10628041E-03 -0.61011040E-03 -0.12326236E-02 -0.17680763E-02 -0.22230145E-02
-0.26037132E-02 -0.29161761E-02 -0.31661366E-02 -0.33590602E-02 -0.35001461E-02
-0.35943308E-02 -0.36462914E-02 -0.36604499E-02 -0.36409778E-02 -0.35918010E-02
-0.35166057E-02 -0.34188437E-02 -0.33017394E-02 -0.31682955E-02 -0.30213003E-02
-0.28633343E-02 -0.26967779E-02 -0.25238181E-02 -0.23464567E-02 -0.21665170E-02
-0.19856524E-02 -0.18053531E-02 -0.16269545E-02 -0.14516446E-02 -0.12804716E-02
-0.11143515E-02 -0.95407586E-03 -0.80031865E-03 -0.65364404E-03 -0.51451333E-03
-0.38329200E-03 -0.26025655E-03 -0.14560117E-03 -0.39444206E-04 0.58165511E-04
0.14724262E-03 0.22785936E-03 0.30013988E-03 0.36425486E-03 0.42041628E-03
0.46887249E-03 0.50990345E-03 0.54381626E-03 0.57094089E-03 0.59162618E-03
0.60623606E-03 0.61514598E-03 0.61873965E-03 0.61740590E-03 0.61153586E-03
0.60152029E-03 0.58774720E-03 0.57059962E-03 0.55045360E-03 0.52767638E-03
0.50262483E-03 0.47564398E-03 0.44706578E-03 0.41720804E-03 0.38637349E-03
0.35484905E-03 0.32290520E-03 0.29079554E-03 0.25875640E-03 0.22700668E-03
0.19574774E-03 0.16516339E-03 0.13542003E-03 0.10666685E-03 0.79036085E-04
0.52643449E-04 0.27588516E-04 0.39552468E-05 -0.18187463E-04 -0.38785176E-04
-0.57797261E-04 -0.75196218E-04 -0.90966955E-04 -0.10510606E-03 -0.11762103E-03
-0.12852953E-03 -0.13785857E-03 -0.14564378E-03 -0.15192857E-03 -0.15676342E-03
-0.16020506E-03 -0.16231574E-03 -0.16316249E-03 -0.16281640E-03 -0.16135194E-03
-0.15884627E-03 -0.15537858E-03 -0.15102952E-03 -0.14588055E-03 -0.14001345E-03
-0.13350974E-03 -0.12645021E-03 -0.11891448E-03 -0.11098055E-03 -0.10272444E-03
-0.94219805E-04 -0.85537640E-04 -0.76745997E-04 -0.67909725E-04 -0.59090261E-04
-0.50345444E-04 -0.41729365E-04 -0.33292246E-04 -0.25080348E-04 -0.17135911E-04
-0.94971158E-05 -0.21980783E-05 0.47311370E-05 0.11264478E-04 0.17379845E-04
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kinetic energy density (partial)
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atomic pseudo charge-density
0.40000000E+01 0.39865777E+01 0.39466377E+01 0.38811433E+01 0.37916420E+01
0.36801845E+01 0.35492225E+01 0.34014950E+01 0.32399100E+01 0.30674335E+01
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0.19554911E+01 0.17779180E+01 0.16068237E+01 0.14431992E+01 0.12877965E+01
0.11411517E+01 0.10036103E+01 0.87535141E+00 0.75641221E+00 0.64671002E+00
0.54606322E+00 0.45420995E+00 0.37082491E+00 0.29553413E+00 0.22792794E+00
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0.18555189E-05 0.17120850E-05 0.15565060E-05 0.13905063E-05 0.12158623E-05
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0.39492396E-06 0.43477660E-06 0.46977849E-06 0.49969185E-06 0.52433087E-06
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0.24553519E-07 0.25451815E-07 0.26099624E-07 0.26493423E-07 0.26632132E-07
0.26517089E-07 0.26152020E-07 0.25542974E-07 0.24698245E-07 0.23628266E-07
0.22345494E-07 0.20864267E-07 0.19200649E-07 0.17372264E-07 0.15398111E-07
0.13298372E-07 0.11094206E-07 0.88075432E-08 0.64608682E-08 0.40770010E-08
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0.12754986E-07 0.14133267E-07 0.15364369E-07 0.16438116E-07 0.17345916E-07
0.18080829E-07 0.18637614E-07 0.19012761E-07 0.19204509E-07 0.19212846E-07
0.19039488E-07 0.18687849E-07 0.18162994E-07 0.17471570E-07 0.16621732E-07
0.15623051E-07 0.14486408E-07 0.13223881E-07 0.11848618E-07 0.10374701E-07
0.88170072E-08 0.71910591E-08 0.55128719E-08 0.37987983E-08 0.20653706E-08
0.32914233E-09 -0.13934677E-08 -0.30863295E-08 -0.47337509E-08 -0.63206208E-08
-0.78325462E-08 -0.92559808E-08 -0.10578344E-07 -0.11788132E-07 -0.12875014E-07
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-0.15130034E-07 -0.14440317E-07 -0.13620840E-07 -0.12680557E-07 -0.11629478E-07
19.8421228800787 T
Non local Part
0 2 1.03170241276447
8.48191517218165 11.7757836767903 11.7757836767903
16.3515625171536
Reciprocal Space Part
0.59618802E+02 0.58728804E+02 0.56074024E+02 0.51699804E+02 0.45680746E+02
0.38119274E+02 0.29143671E+02 0.18905623E+02 0.75773282E+01 -0.46517683E+01
-0.17578547E+02 -0.30990019E+02 -0.44667277E+02 -0.58389527E+02 -0.71938095E+02
-0.85100345E+02 -0.97673425E+02 -0.10946776E+03 -0.12031025E+03 -0.13004704E+03
-0.13854596E+03 -0.14569837E+03 -0.15142064E+03 -0.15565502E+03 -0.15837002E+03
-0.15956027E+03 -0.15924591E+03 -0.15747139E+03 -0.15430398E+03 -0.14983176E+03
-0.14416132E+03 -0.13741514E+03 -0.12972880E+03 -0.12124795E+03 -0.11212524E+03
-0.10251722E+03 -0.92581277E+02 -0.82472653E+02 -0.72341667E+02 -0.62331121E+02
-0.52573985E+02 -0.43191382E+02 -0.34290898E+02 -0.25965259E+02 -0.18291368E+02
-0.11329718E+02 -0.51241765E+01 0.29787571E+00 0.49250688E+01 0.87612564E+01
0.11824451E+02 0.14145521E+02 0.15766686E+02 0.16739863E+02 0.17124899E+02
0.16987748E+02 0.16398621E+02 0.15430172E+02 0.14155746E+02 0.12647730E+02
0.10976046E+02 0.92067952E+01 0.74011008E+01 0.56141435E+01 0.38944113E+01
0.22831646E+01 0.81411644E+00 -0.48667978E+00 -0.16007453E+01 -0.25169103E+01
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-0.18363896E+01 -0.12917960E+01 -0.76044515E+00 -0.25934295E+00 0.19722322E+00
0.59787806E+00 0.93424642E+00 0.12009418E+01 0.13954638E+01 0.15180138E+01
0.15712429E+01 0.15599426E+01 0.14906942E+01 0.13714899E+01 0.12113407E+01
0.10198828E+01 0.80699697E+00 0.58245003E+00 0.35557023E+00 0.13496271E+00
Real Space Part
-0.87257185E+03 -0.87217325E+03 -0.87097758E+03 -0.86898535E+03 -0.86619740E+03
-0.86261493E+03 -0.85823952E+03 -0.85307319E+03 -0.84711839E+03 -0.84037811E+03
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-0.63111840E+03 -0.61230331E+03 -0.59292512E+03 -0.57301089E+03 -0.55258976E+03
-0.53169298E+03 -0.51035396E+03 -0.48860832E+03 -0.46649386E+03 -0.44405060E+03
-0.42132076E+03 -0.39834870E+03 -0.37518093E+03 -0.35186599E+03 -0.32845440E+03
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0.84646067E+02 0.95915987E+02 0.10609024E+03 0.11514887E+03 0.12307763E+03
0.12986821E+03 0.13551849E+03 0.14003271E+03 0.14342163E+03 0.14570263E+03
0.14689971E+03 0.14704353E+03 0.14617130E+03 0.14432667E+03 0.14155957E+03
0.13792593E+03 0.13348743E+03 0.12831116E+03 0.12246922E+03 0.11603831E+03
0.10909924E+03 0.10173648E+03 0.94037578E+02 0.86092680E+02 0.77993902E+02
0.69834817E+02 0.61709839E+02 0.53713688E+02 0.45940793E+02 0.38484762E+02
0.31437841E+02 0.24890391E+02 0.18930406E+02 0.13643042E+02 0.91101706E+01
0.54100403E+01 0.26168332E+01 0.79835325E+00 0.23427012E-01 0.00000000E+00
Reciprocal Space Part
-0.36489549E+02 -0.35864156E+02 -0.33998755E+02 -0.30925471E+02 -0.26697153E+02
-0.21386360E+02 -0.15083959E+02 -0.78973858E+01 0.51413298E-01 0.86282977E+01
0.17689472E+02 0.27084188E+02 0.36657552E+02 0.46253383E+02 0.55717063E+02
0.64898313E+02 0.73653855E+02 0.81849887E+02 0.89364344E+02 0.96088881E+02
0.10193057E+03 0.10681323E+03 0.11067846E+03 0.11348624E+03 0.11521523E+03
0.11586261E+03 0.11544365E+03 0.11399089E+03 0.11155304E+03 0.10819353E+03
0.10398888E+03 0.99026864E+02 0.93404459E+02 0.87225735E+02 0.80599650E+02
0.73637846E+02 0.66452460E+02 0.59154022E+02 0.51849465E+02 0.44640290E+02
0.37620922E+02 0.30877278E+02 0.24485577E+02 0.18511398E+02 0.13009009E+02
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0.23202264E+01 0.26864349E+01 0.29148468E+01 0.30144856E+01 0.29972475E+01
0.28772789E+01 0.26703472E+01 0.23932227E+01 0.20630867E+01 0.16969795E+01
0.13113025E+01 0.92138094E+00 0.54109837E+00 0.18260423E+00 -0.14390035E+00
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-0.72874294E+00 -0.57630417E+00 -0.41558297E+00 -0.25324963E+00 -0.95455204E-01
Real Space Part
0.63319797E+03 0.63291041E+03 0.63204781E+03 0.63061056E+03 0.62859924E+03
0.62601473E+03 0.62285817E+03 0.61913101E+03 0.61483503E+03 0.60997237E+03
0.60454559E+03 0.59855767E+03 0.59201211E+03 0.58491291E+03 0.57726472E+03
0.56907280E+03 0.56034314E+03 0.55108251E+03 0.54129849E+03 0.53099960E+03
0.52019530E+03 0.50889609E+03 0.49711358E+03 0.48486054E+03 0.47215095E+03
0.45900011E+03 0.44542463E+03 0.43144254E+03 0.41707331E+03 0.40233788E+03
0.38725874E+03 0.37185991E+03 0.35616701E+03 0.34020723E+03 0.32400934E+03
0.30760369E+03 0.29102220E+03 0.27429832E+03 0.25746694E+03 0.24056440E+03
0.22362837E+03 0.20669777E+03 0.18981266E+03 0.17301414E+03 0.15634416E+03
0.13984541E+03 0.12356113E+03 0.10753493E+03 0.91810566E+02 0.76431735E+02
0.61441833E+02 0.46883707E+02 0.32799393E+02 0.19229849E+02 0.62146659E+01
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-0.38656440E+01 -0.18700414E+01 -0.57059033E+00 -0.16714955E-01 0.00000000E+00
Non local Part
1 2 1.03170241276447
2.65859946877321 4.88238126795342 4.88238126795342
8.98435195357541
Reciprocal Space Part
0.00000000E+00 0.38861820E+01 0.76566506E+01 0.11198191E+02 0.14402530E+02
0.17168669E+02 0.19405054E+02 0.21031535E+02 0.21981079E+02 0.22201184E+02
0.21654974E+02 0.20321960E+02 0.18198431E+02 0.15297488E+02 0.11648712E+02
0.72974833E+01 0.23039596E+01 -0.32582469E+01 -0.93036735E+01 -0.15736848E+02
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0.72043400E+01 0.80031754E+01 0.84492707E+01 0.85780039E+01 0.84279913E+01
0.80399981E+01 0.74558696E+01 0.67175093E+01 0.58659233E+01 0.49403528E+01
0.39775094E+01 0.30109262E+01 0.20704331E+01 0.11817624E+01 0.36628567E+00
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0.81250966E+00 0.91645487E+00 0.97612004E+00 0.99335246E+00 0.97132649E+00
Real Space Part
0.00000000E+00 -0.22186814E+02 -0.44301839E+02 -0.66273522E+02 -0.88030777E+02
-0.10950322E+03 -0.13062140E+03 -0.15131703E+03 -0.17152321E+03 -0.19117468E+03
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0.97823113E+02 0.96490698E+02 0.94358601E+02 0.91483927E+02 0.87929701E+02
0.83764422E+02 0.79061549E+02 0.73898935E+02 0.68358280E+02 0.62524490E+02
0.56485105E+02 0.50329625E+02 0.44148922E+02 0.38034576E+02 0.32078283E+02
0.26371234E+02 0.21003526E+02 0.16063609E+02 0.11637728E+02 0.78094126E+01
0.46590409E+01 0.22633368E+01 0.69369210E+00 0.17747648E-01 0.00000000E+00
Reciprocal Space Part
0.00000000E+00 -0.17868362E+01 -0.35144269E+01 -0.51248277E+01 -0.65626676E+01
-0.77763629E+01 -0.87192468E+01 -0.93505888E+01 -0.96364809E+01 -0.95505728E+01
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0.15123488E+02 0.18752190E+02 0.22396628E+02 0.25997448E+02 0.29496018E+02
0.32835608E+02 0.35962514E+02 0.38827099E+02 0.41384736E+02 0.43596618E+02
0.45430445E+02 0.46860950E+02 0.47870266E+02 0.48448142E+02 0.48591976E+02
0.48306705E+02 0.47604523E+02 0.46504469E+02 0.45031872E+02 0.43217686E+02
0.41097721E+02 0.38711805E+02 0.36102874E+02 0.33316045E+02 0.30397658E+02
0.27394336E+02 0.24352070E+02 0.21315355E+02 0.18326389E+02 0.15424354E+02
0.12644790E+02 0.10019079E+02 0.75740326E+01 0.53316035E+01 0.33087123E+01
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0.12600861E+01 0.12958921E+01 0.12811875E+01 0.12220191E+01 0.11252269E+01
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0.16889148E+00 0.11242749E-01 -0.13113830E+00 -0.25464171E+00 -0.35664077E+00
-0.43549155E+00 -0.49050126E+00 -0.52186870E+00 -0.53060095E+00 -0.51841055E+00
Real Space Part
0.00000000E+00 0.12161252E+02 0.24283469E+02 0.36327742E+02 0.48255417E+02
0.60028220E+02 0.71608383E+02 0.82958767E+02 0.94042991E+02 0.10482555E+03
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0.41175622E+02 0.32585400E+02 0.24246514E+02 0.16198468E+02 0.84788075E+01
0.11228377E+01 -0.58366451E+01 -0.12369614E+02 -0.18449055E+02 -0.24051197E+02
-0.29155721E+02 -0.33745943E+02 -0.37808973E+02 -0.41335852E+02 -0.44321651E+02
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-0.24784108E+01 -0.12044157E+01 -0.36926989E+00 -0.93979993E-02 0.00000000E+00
PAW radial sets
351 0.989218471734280
(5E20.12)
augmentation charges (non sperical)
-0.118612820244E+00 -0.166184190184E+00 -0.532145144881E-01 -0.101222164724E+00 -0.166184190184E+00
-0.232848406670E+00 -0.743582353105E-01 -0.141431561143E+00 -0.532145144881E-01 -0.743582353105E-01
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-0.655142723317E-01
uccopancies in atom
0.200000000235E+01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
0.666666668254E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
0.000000000000E+00
grid
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aepotential
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-0.163629117637E+02 -0.177712183098E+02 -0.191824857852E+02 -0.205912204531E+02 -0.219910948777E+02
-0.233748286767E+02 -0.247341319073E+02 -0.260597523206E+02 -0.273417023275E+02 -0.285696934068E+02
-0.297338412853E+02 -0.308256304858E+02 -0.318391158428E+02 -0.327722938273E+02 -0.336286100568E+02
-0.344184456425E+02 -0.351602597585E+02 -0.358801414497E+02 -0.366068311139E+02 -0.373574865876E+02
-0.381118852062E+02 -0.387867275622E+02 -0.392441858557E+02 -0.393634905455E+02 -0.391349287148E+02
-0.386756213346E+02 -0.381417405135E+02 -0.376357899161E+02 -0.371876084550E+02 -0.367857306580E+02
-0.364089018964E+02 -0.360404071207E+02 -0.356705439437E+02 -0.352947736228E+02 -0.349113814513E+02
-0.345198082255E+02 -0.341197553652E+02 -0.337108267652E+02 -0.332925072698E+02 -0.328642387355E+02
-0.324255741088E+02 -0.319762374262E+02 -0.315162189773E+02 -0.310457677673E+02 -0.305653859428E+02
-0.300757994671E+02 -0.295778859655E+02 -0.290726427811E+02 -0.285611001088E+02 -0.280442533230E+02
-0.275230192225E+02 -0.269981679715E+02 -0.264702980396E+02 -0.259398216884E+02 -0.254069826533E+02
-0.248718994035E+02 -0.243346314120E+02 -0.237952586509E+02 -0.232539624826E+02 -0.227110955590E+02
-0.221672327097E+02 -0.216231877485E+02 -0.210800244667E+02 -0.205390174919E+02 -0.200016158604E+02
-0.194693867508E+02
core charge-density
0.566100408154E-04 0.603274793074E-04 0.642889044283E-04 0.685103166568E-04 0.730087644875E-04
0.778024129493E-04 0.829106165872E-04 0.883539971990E-04 0.941545266560E-04 0.100335615085E-03
0.106922204822E-03 0.113940870473E-03 0.121419925474E-03 0.129389535603E-03 0.137881839861E-03
0.146931079213E-03 0.156573733698E-03 0.166848668447E-03 0.177797289174E-03 0.189463707768E-03
0.201894918628E-03 0.215140986428E-03 0.229255246056E-03 0.244294515512E-03 0.260319322588E-03
0.277394146221E-03 0.295587673465E-03 0.314973073077E-03 0.335628286780E-03 0.357636339348E-03
0.381085668699E-03 0.406070477287E-03 0.432691106152E-03 0.461054433064E-03 0.491274296314E-03
0.523471945761E-03 0.557776522887E-03 0.594325571702E-03 0.633265582435E-03 0.674752570119E-03
0.718952690251E-03 0.766042893893E-03 0.816211624674E-03 0.869659560374E-03 0.926600401855E-03
0.987261712339E-03 0.105188581019E-02 0.112073071853E-02 0.119407117529E-02 0.127219970739E-02
0.135542777315E-02 0.144408697705E-02 0.153853036146E-02 0.163913378001E-02 0.174629735768E-02
0.186044704296E-02 0.198203625776E-02 0.211154765105E-02 0.224949496259E-02 0.239642500343E-02
0.255291976042E-02 0.271959863213E-02 0.289712080418E-02 0.308618777247E-02 0.328754602307E-02
0.350198987838E-02 0.373036451926E-02 0.397356919385E-02 0.423256062398E-02 0.450835662100E-02
0.480203992329E-02 0.511476226845E-02 0.544774871395E-02 0.580230222061E-02 0.617980851421E-02
0.658174124108E-02 0.700966743491E-02 0.746525331166E-02 0.795027041269E-02 0.846660211345E-02
0.901625052094E-02 0.960134377894E-02 0.102241438053E-01 0.108870544842E-01 0.115926303386E-01
0.123435857075E-01 0.131428044576E-01 0.139933502544E-01 0.148984774251E-01 0.158616424421E-01
0.168865160593E-01 0.179769961364E-01 0.191372211820E-01 0.203715846550E-01 0.216847500588E-01
0.230816668678E-01 0.245675873256E-01 0.261480841549E-01 0.278290692218E-01 0.296168131969E-01
0.315179662576E-01 0.335395798759E-01 0.356891297379E-01 0.379745398409E-01 0.404042078155E-01
0.429870315194E-01 0.457324369501E-01 0.486504075246E-01 0.517515147717E-01 0.550469504838E-01
0.585485603728E-01 0.622688792735E-01 0.662211679360E-01 0.704194514465E-01 0.748785593126E-01
0.796141672432E-01 0.846428406544E-01 0.899820799218E-01 0.956503673943E-01 0.101667216183E+00
0.108053220723E+00 0.114830109098E+00 0.122020797119E+00 0.129649444112E+00 0.137741510382E+00
0.146323816290E+00 0.155424602864E+00 0.165073593849E+00 0.175302059090E+00 0.186142879083E+00
0.197630610560E+00 0.209801552888E+00 0.222693815062E+00 0.236347383047E+00 0.250804187144E+00
0.266108169064E+00 0.282305348315E+00 0.299443887476E+00 0.317574155859E+00 0.336748791043E+00
0.357022757646E+00 0.378453402702E+00 0.401100506871E+00 0.425026330694E+00 0.450295654993E+00
0.476975814429E+00 0.505136723178E+00 0.534850891530E+00 0.566193432183E+00 0.599242054859E+00
0.634077047765E+00 0.670781244335E+00 0.709439973560E+00 0.750140992075E+00 0.792974396116E+00
0.838032511244E+00 0.885409757763E+00 0.935202489441E+00 0.987508803254E+00 0.104242831757E+01
0.110006191624E+01 0.116051145584E+01 0.122387943346E+01 0.129026861193E+01 0.135978160000E+01
0.143252038425E+01 0.150858581009E+01 0.158807700896E+01 0.167109076893E+01 0.175772084621E+01
0.184805721494E+01 0.194218525332E+01 0.204018486382E+01 0.214212952620E+01 0.224808528199E+01
0.235810964998E+01 0.247225047259E+01 0.259054469391E+01 0.271301707089E+01 0.283967882006E+01
0.297052620347E+01 0.310553905827E+01 0.324467927606E+01 0.338788923929E+01 0.353509022378E+01
0.368618077801E+01 0.384103509149E+01 0.399950136699E+01 0.416140021288E+01 0.432652307442E+01
0.449463072490E+01 0.466545184006E+01 0.483868168119E+01 0.501398091525E+01 0.519097460207E+01
0.536925138135E+01 0.554836289419E+01 0.572782347558E+01 0.590711015619E+01 0.608566301289E+01
0.626288590845E+01 0.643814766086E+01 0.661078368325E+01 0.678009813289E+01 0.694536660815E+01
0.710583942709E+01 0.726074551989E+01 0.740929696058E+01 0.755069415923E+01 0.768413172658E+01
0.780880501609E+01 0.792391733716E+01 0.802868782233E+01 0.812235991814E+01 0.820421045514E+01
0.827355923749E+01 0.832977907498E+01 0.837230616406E+01 0.840065070529E+01 0.841440762640E+01
0.841326726196E+01 0.839702582182E+01 0.836559546387E+01 0.831901377096E+01 0.825745241774E+01
0.818122480318E+01 0.809079241634E+01 0.798676970036E+01 0.786992718088E+01 0.774119263277E+01
0.760165007160E+01 0.745253637713E+01 0.729523538244E+01 0.713126929714E+01 0.696228737445E+01
0.679005178084E+01 0.661642068236E+01 0.644332862226E+01 0.627276433103E+01 0.610674617685E+01
0.594729553438E+01 0.579640841756E+01 0.565602577058E+01 0.552800288253E+01 0.541407841905E+01
0.531584356652E+01 0.523471181475E+01 0.517188988547E+01 0.512835031200E+01 0.510480618875E+01
0.510168864942E+01 0.511912769994E+01 0.515693711116E+01 0.521460413879E+01 0.529128484590E+01
0.538580571386E+01 0.549667199677E+01 0.562208291152E+01 0.575995334559E+01 0.590794145701E+01
0.606348143532E+01 0.622382075557E+01 0.638606135679E+01 0.654720421042E+01 0.670419668250E+01
0.685398197262E+01 0.699354974359E+01 0.711998698134E+01 0.723052801287E+01 0.732260261476E+01
0.739388115435E+01 0.744231577198E+01 0.746617668668E+01 0.746408283670E+01 0.743502617611E+01
0.737838909120E+01 0.729395456103E+01 0.718190882688E+01 0.704283651135E+01 0.687770827554E+01
0.668786127413E+01 0.647497281612E+01 0.624102777379E+01 0.598828043165E+01 0.571921157955E+01
0.543648173800E+01 0.514288151879E+01 0.484128016393E+01 0.453457335746E+01 0.422563144517E+01
0.391724918675E+01 0.361209817668E+01 0.331268302840E+01 0.302130238260E+01 0.274001574527E+01
0.247061699977E+01 0.221461533156E+01 0.197322403846E+01 0.174735751206E+01 0.153763599448E+01
0.134439801278E+01 0.116771925944E+01 0.100743683521E+01 0.863177139249E+00 0.734385165797E+00
0.620352459116E+00 0.520241286779E+00 0.433104991178E+00 0.357908936157E+00 0.293558957004E+00
0.238939321053E+00 0.192952592630E+00 0.154550553295E+00 0.122752018839E+00 0.966509407173E-01
0.754197350591E-01 0.583105682925E-01 0.446553131657E-01 0.338641471811E-01 0.254227490621E-01
0.188882113068E-01 0.138839137385E-01 0.100936590292E-01 0.725537509450E-02 0.515466309716E-02
0.361842930266E-02 0.250879268147E-02 0.171741309607E-02 0.116033964584E-02 0.773437417305E-03
0.508414784907E-03 0.329443540380E-03 0.210340978410E-03 0.132266603092E-03 0.818759218551E-04
0.498690344207E-04 0.298714443437E-04 0.175875916060E-04 0.101729842592E-04 0.577752330293E-05
0.321986957660E-05 0.175987680434E-05 0.942778890139E-06 0.494707936977E-06 0.254108048780E-06
0.127681574306E-06 0.627159654587E-07 0.300924318689E-07 0.140943050873E-07 0.643877401768E-08
0.286674509825E-08
kinetic energy-density
0.667225310700E+01 0.673712425060E+01 0.680446712075E+01 0.687435266836E+01 0.694687887984E+01
0.702214082218E+01 0.710025487509E+01 0.718131997169E+01 0.726545491156E+01 0.735279351610E+01
0.744345621126E+01 0.753759398662E+01 0.763534237524E+01 0.773686628737E+01 0.784232168333E+01
0.795188785384E+01 0.806574492238E+01 0.818408265740E+01 0.830710733444E+01 0.843502925423E+01
0.856807463323E+01 0.870648022710E+01 0.885049499152E+01 0.900038141274E+01 0.915641556867E+01
0.931888763846E+01 0.948810409274E+01 0.966438660997E+01 0.984807420966E+01 0.100395236808E+02
0.102391106259E+02 0.104472306217E+02 0.106643002129E+02 0.108907581658E+02 0.111270667128E+02
0.113737129173E+02 0.116312100590E+02 0.119000995563E+02 0.121809512045E+02 0.124743676751E+02
0.127809824020E+02 0.131014661587E+02 0.134365246352E+02 0.137869037259E+02 0.141533910827E+02
0.145368181700E+02 0.149380606607E+02 0.153580481103E+02 0.157977592006E+02 0.162582301660E+02
0.167405536651E+02 0.172458849260E+02 0.177754489910E+02 0.183305360512E+02 0.189125147524E+02
0.195228293783E+02 0.201630086713E+02 0.208346731063E+02 0.215395302738E+02 0.222793960940E+02
0.230561817871E+02 0.238719218157E+02 0.247287599035E+02 0.256289715181E+02 0.265749638623E+02
0.275692850611E+02 0.286146340209E+02 0.297138695051E+02 0.308700182642E+02 0.320862867047E+02
0.333660717388E+02 0.347129698754E+02 0.361307926843E+02 0.376235764044E+02 0.391956004794E+02
0.408513960801E+02 0.425957666062E+02 0.444337942387E+02 0.463708781148E+02 0.484127240612E+02
0.505653883328E+02 0.528352819288E+02 0.552292043731E+02 0.577543512402E+02 0.604183612533E+02
0.632293138540E+02 0.661957773286E+02 0.693268340532E+02 0.726320939962E+02 0.761217542966E+02
0.798066090433E+02 0.836980910427E+02 0.878083249418E+02 0.921501355979E+02 0.967371238079E+02
0.101583684198E+03 0.106705064907E+03 0.112117414382E+03 0.117837828166E+03 0.123884409252E+03
0.130276320038E+03 0.137033846315E+03 0.144178456681E+03 0.151732871301E+03 0.159721130996E+03
0.168168668145E+03 0.177102387622E+03 0.186550741797E+03 0.196543819667E+03 0.207113432275E+03
0.218293201433E+03 0.230118672341E+03 0.242627385569E+03 0.255859010707E+03 0.269855440106E+03
0.284660908978E+03 0.300322108546E+03 0.316888318424E+03 0.334411529406E+03 0.352946573140E+03
0.372551274533E+03 0.393286576958E+03 0.415216695313E+03 0.438409280187E+03 0.462935557123E+03
0.488870494758E+03 0.516292978425E+03 0.545285959475E+03 0.575936645981E+03 0.608336673183E+03
0.642582272764E+03 0.678774465893E+03 0.717019234895E+03 0.757427713585E+03 0.800116365041E+03
0.845207163513E+03 0.892827774214E+03 0.943111730250E+03 0.996198604607E+03 0.105223417127E+04
0.111137056935E+04 0.117376644321E+04 0.123958708989E+04 0.130900456745E+04 0.138219781473E+04
0.145935272609E+04 0.154066222765E+04 0.162632630841E+04 0.171655203448E+04 0.181155353272E+04
0.191155192916E+04 0.201677522893E+04 0.212745822677E+04 0.224384225326E+04 0.236617496487E+04
0.249470999554E+04 0.262970664059E+04 0.277142932316E+04 0.292014710882E+04 0.307613311454E+04
0.323966371690E+04 0.341101780179E+04 0.359047581918E+04 0.377831874540E+04 0.397482689787E+04
0.418027868224E+04 0.439494910623E+04 0.461910823060E+04 0.485301940433E+04 0.509693739042E+04
0.535110624785E+04 0.561575714459E+04 0.589110587709E+04 0.617735029231E+04 0.647466747894E+04
0.678321077715E+04 0.710310660594E+04 0.743445110603E+04 0.777730657840E+04 0.813169778138E+04
0.849760803098E+04 0.887497515215E+04 0.926368732206E+04 0.966357873788E+04 0.100744252544E+05
0.104959398994E+05 0.109277683923E+05 0.113694846547E+05 0.118205863594E+05 0.122804905999E+05
0.127485296775E+05 0.132239471319E+05 0.137058940235E+05 0.141934255844E+05 0.146854982713E+05
0.151809673402E+05 0.156785850245E+05 0.161769993384E+05 0.166747537999E+05 0.171702877851E+05
0.176619381795E+05 0.181479417092E+05 0.186264388693E+05 0.190954787135E+05 0.195530252077E+05
0.199969649781E+05 0.204251165206E+05 0.208352408440E+05 0.212250539761E+05 0.215922406971E+05
0.219344702466E+05 0.222494132725E+05 0.225347605700E+05 0.227882431008E+05 0.230076533887E+05
0.231908681093E+05 0.233358716618E+05 0.234407805422E+05 0.235038681649E+05 0.235235900533E+05
0.234986087273E+05 0.234278183452E+05 0.233103682573E+05 0.231456854657E+05 0.229334951930E+05
0.226738393464E+05 0.223670922687E+05 0.220139733481E+05 0.216155560262E+05 0.211732727643E+05
0.206889155309E+05 0.201646315262E+05 0.196029137234E+05 0.190065861750E+05 0.183787838063E+05
0.177229268159E+05 0.170426897439E+05 0.163419655306E+05 0.156248249789E+05 0.148954722996E+05
0.141581974366E+05 0.134173260145E+05 0.126771691922E+05 0.119419712654E+05 0.112158605109E+05
0.105028006708E+05 0.980654494715E+04 0.913059233055E+04 0.847814609089E+04 0.785207437181E+04
0.725487344241E+04 0.668863511465E+04 0.615502070274E+04 0.565524418908E+04 0.519006674861E+04
0.475980360345E+04 0.436434269355E+04 0.400317323797E+04 0.367542134980E+04 0.337988976738E+04
0.311509951930E+04 0.287933230868E+04 0.267067322820E+04 0.248705367813E+04 0.232629416860E+04
0.218614663490E+04 0.206433550064E+04 0.195859682514E+04 0.186671473352E+04 0.178655448544E+04
0.171609162157E+04 0.165343661643E+04 0.159685503183E+04 0.154478263373E+04 0.149583588863E+04
0.144881771439E+04 0.140271881257E+04 0.135671510542E+04 0.131016154370E+04 0.126258277404E+04
0.121366142449E+04 0.116322423992E+04 0.111122677010E+04 0.105773711321E+04 0.100291904396E+04
0.947015115197E+03 0.890329984746E+03 0.833214293651E+03 0.776049439334E+03 0.719233318915E+03
0.663167296841E+03 0.608244410857E+03 0.554838974842E+03 0.503297365412E+03 0.453930342998E+03
0.407006607762E+03 0.362747812430E+03 0.321325009274E+03 0.282856892955E+03 0.247409239962E+03
0.214996579478E+03 0.185585236387E+03 0.159098170048E+03 0.135421626809E+03 0.114413852193E+03
0.959157052909E+02 0.797613940556E+02 0.657850483488E+02 0.538188496239E+02 0.436847852099E+02
0.351899899383E+02 0.281331189963E+02 0.223174718914E+02 0.175614959268E+02 0.137029350510E+02
0.105987314150E+02 0.812353702200E+01 0.616817828814E+01 0.463832179287E+01 0.345324799301E+01
0.254463529365E+01 0.185531917238E+01 0.133803581425E+01 0.954179117826E+00 0.672602600260E+00
0.468493246228E+00 0.322336920783E+00 0.218987948819E+00 0.146848889647E+00 0.971612490355E-01
0.634035384763E-01 0.407898120808E-01 0.258595430908E-01 0.161483043720E-01 0.992815188083E-02
0.600670032098E-02 0.357447468542E-02 0.209108518893E-02 0.120193474515E-02 0.678419162901E-03
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0.317114132527E-06
mkinetic energy-density pseudized
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0.317114132527E-06
local pseudopotential core
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pspotential valence only
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-0.194693867508E+02
core charge-density (pseudized)
0.158850899689E-07 0.169349736624E-07 0.180542466866E-07 0.192474951488E-07 0.205196082630E-07
0.218757983829E-07 0.233216223594E-07 0.248630043089E-07 0.265062598867E-07 0.282581221651E-07
0.301257692211E-07 0.321168535480E-07 0.342395334107E-07 0.365025062734E-07 0.389150444365E-07
0.414870330287E-07 0.442290105108E-07 0.471522118554E-07 0.502686145814E-07 0.535909878306E-07
0.571329446878E-07 0.609089979589E-07 0.649346196361E-07 0.692263042922E-07 0.738016366658E-07
0.786793637127E-07 0.838794714198E-07 0.894232666954E-07 0.953334646720E-07 0.101634281779E-06
0.108351534969E-06 0.115512747495E-06 0.123147261690E-06 0.131286359191E-06 0.139963389111E-06
0.149213904686E-06 0.159075808951E-06 0.169589510039E-06 0.180798086755E-06 0.192747465083E-06
0.205486606363E-06 0.219067707906E-06 0.233546416867E-06 0.248982058249E-06 0.265437877988E-06
0.282981302089E-06 0.301684212902E-06 0.321623243648E-06 0.342880092415E-06 0.365541856912E-06
0.389701391334E-06 0.415457686827E-06 0.442916277090E-06 0.472189670789E-06 0.503397812546E-06
0.536668574398E-06 0.572138279738E-06 0.609952261885E-06 0.650265459564E-06 0.693243051754E-06
0.739061134484E-06 0.787907442368E-06 0.839982117817E-06 0.895498531103E-06 0.954684154611E-06
0.101778149488E-05 0.108504908622E-05 0.115676255007E-05 0.123321572426E-05 0.131472186699E-05
0.140161494038E-05 0.149425097881E-05 0.159300954771E-05 0.169829529876E-05 0.181053962793E-05
0.193020244302E-05 0.205777404804E-05 0.219377715217E-05 0.233876901146E-05 0.249334371211E-05
0.265813460454E-05 0.283381689853E-05 0.302111042968E-05 0.322078260881E-05 0.343365156625E-05
0.366058950397E-05 0.390252626918E-05 0.416045316422E-05 0.443542700810E-05 0.472857446660E-05
0.504109666844E-05 0.537427412660E-05 0.572947198482E-05 0.610814561085E-05 0.651184655941E-05
0.694222892908E-05 0.740105613948E-05 0.789020815618E-05 0.841168919314E-05 0.896763592422E-05
0.956032623723E-05 0.101921885666E-04 0.108658118429E-04 0.115839560993E-04 0.123495637799E-04
0.131657717945E-04 0.140359243703E-04 0.149635867530E-04 0.159525598129E-04 0.170068956168E-04
0.181309140281E-04 0.193292204042E-04 0.206067244636E-04 0.219686603991E-04 0.234206083207E-04
0.249685171141E-04 0.266187288110E-04 0.283780045687E-04 0.302535523666E-04 0.322530565318E-04
0.343847092167E-04 0.366572439552E-04 0.390799714357E-04 0.416628176384E-04 0.444163644905E-04
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0.652091431015E-04 0.695188524752E-04 0.741133845867E-04 0.790115618292E-04 0.842334503093E-04
0.898004420053E-04 0.957353423503E-04 0.102062463597E-03 0.108807724347E-03 0.115998755648E-03
0.123665014094E-03 0.131837902394E-03 0.140550897889E-03 0.149839689558E-03 0.159742324059E-03
0.170299361400E-03 0.181554040889E-03 0.193552458017E-03 0.206343753015E-03 0.219980311839E-03
0.234517980402E-03 0.250016292931E-03 0.266538715372E-03 0.284152904832E-03 0.302930986106E-03
0.322949846427E-03 0.344291449616E-03 0.367043170908E-03 0.391298153825E-03 0.417155690514E-03
0.444721627115E-03 0.474108795766E-03 0.505437475018E-03 0.538835880487E-03 0.574440687740E-03
0.612397589507E-03 0.652861889451E-03 0.695999134887E-03 0.741985790982E-03 0.791009959124E-03
0.843272142330E-03 0.898986060746E-03 0.958379520474E-03 0.102169533918E-02 0.108919233216E-02
0.116114636271E-02 0.123785146100E-02 0.131962101582E-02 0.140678904387E-02 0.149971154154E-02
0.159876792447E-02 0.170436256045E-02 0.181692640162E-02 0.193691872220E-02 0.206482896848E-02
0.220117872808E-02 0.234652382591E-02 0.250145655494E-02 0.266660804989E-02 0.284265081290E-02
0.303030140045E-02 0.323032328145E-02 0.344352987696E-02 0.367078779245E-02 0.391302025435E-02
0.417121076298E-02 0.444640697483E-02 0.473972482752E-02 0.505235292185E-02 0.538555717557E-02
0.574068576454E-02 0.611917436752E-02 0.652255173154E-02 0.695244557544E-02 0.741058885008E-02
0.789882637401E-02 0.841912186447E-02 0.897356538393E-02 0.956438122282E-02 0.101939362401E-01
0.108647486828E-01 0.115794975075E-01 0.123410322246E-01 0.131523832881E-01 0.140167730542E-01
0.149376273269E-01 0.159185875152E-01 0.169635234187E-01 0.180765466621E-01 0.192620247931E-01
0.205245960596E-01 0.218691848759E-01 0.233010179867E-01 0.248256413302E-01 0.264489375990E-01
0.281771444893E-01 0.300168736216E-01 0.319751301066E-01 0.340593327208E-01 0.362773346404E-01
0.386374446716E-01 0.411484488953E-01 0.438196326246E-01 0.466608025533E-01 0.496823089450E-01
0.528950676826E-01 0.563105819652E-01 0.599409633995E-01 0.637989521880E-01 0.678979360665E-01
0.722519675861E-01 0.768757792715E-01 0.817847961130E-01 0.869951447703E-01 0.925236587738E-01
0.983878789095E-01 0.104606047856E+00 0.111197098026E+00 0.118180631410E+00 0.125576890089E+00
0.133406715896E+00 0.141691497534E+00 0.150453103263E+00 0.159713797041E+00 0.169496135792E+00
0.179822845227E+00 0.190716671374E+00 0.202200204726E+00 0.214295673644E+00 0.227024703349E+00
0.240408036607E+00 0.254465211927E+00 0.269214194858E+00 0.284670957798E+00 0.300849003557E+00
0.317758827869E+00 0.335407316081E+00 0.353797069410E+00 0.372925656495E+00 0.392784786538E+00
0.413359401140E+00 0.434626683071E+00 0.456554981802E+00 0.479102657604E+00 0.502216848651E+00
0.525832168810E+00 0.549869347839E+00 0.574233830650E+00 0.598814358233E+00 0.623481559867E+00
0.648086594575E+00 0.672459889336E+00 0.696410032536E+00 0.719722893489E+00 0.742161052417E+00
0.763463640029E+00 0.783346701288E+00 0.801504213699E+00 0.817609905660E+00 0.831320034071E+00
0.842277290994E+00 0.850116014825E+00 0.854468879722E+00 0.854975224885E+00 0.851291158898E+00
0.843101529429E+00 0.830133779791E+00 0.812173615663E+00 0.789082271343E+00 0.760814989247E+00
0.727440103218E+00 0.689157841522E+00 0.646317637620E+00 0.599432358703E+00 0.549187442962E+00
0.496442495144E+00 0.442222457189E+00 0.387695093883E+00 0.334131279817E+00 0.282844534494E+00
0.235106544671E+00 0.192036181160E+00 0.154460929685E+00 0.122751894914E+00 0.966509407173E-01
0.754197350591E-01 0.583105682925E-01 0.446553131657E-01 0.338641471811E-01 0.254227490621E-01
0.188882113068E-01 0.138839137385E-01 0.100936590292E-01 0.725537509450E-02 0.515466309716E-02
0.361842930266E-02 0.250879268147E-02 0.171741309607E-02 0.116033964584E-02 0.773437417305E-03
0.508414784907E-03 0.329443540380E-03 0.210340978410E-03 0.132266603092E-03 0.818759218551E-04
0.498690344207E-04 0.298714443437E-04 0.175875916060E-04 0.101729842592E-04 0.577752330293E-05
0.321986957660E-05 0.175987680434E-05 0.942778890139E-06 0.494707936977E-06 0.254108048780E-06
0.127681574306E-06 0.627159654587E-07 0.300924318689E-07 0.140943050873E-07 0.643877401768E-08
0.286674509825E-08
pseudo wavefunction
0.575355347414E-04 0.594064467959E-04 0.613381962429E-04 0.633327613625E-04 0.653921847638E-04
0.675185754763E-04 0.697141111098E-04 0.719810400846E-04 0.743216839340E-04 0.767384396819E-04
0.792337822973E-04 0.818102672291E-04 0.844705330228E-04 0.872173040230E-04 0.900533931633E-04
0.929817048467E-04 0.960052379201E-04 0.991270887455E-04 0.102350454371E-03 0.105678635804E-03
0.109115041394E-03 0.112663190320E-03 0.116326716196E-03 0.120109370793E-03 0.124015027879E-03
0.128047687189E-03 0.132211478517E-03 0.136510665951E-03 0.140949652232E-03 0.145532983271E-03
0.150265352799E-03 0.155151607175E-03 0.160196750351E-03 0.165405948993E-03 0.170784537776E-03
0.176338024845E-03 0.182072097454E-03 0.187992627794E-03 0.194105679006E-03 0.200417511387E-03
0.206934588804E-03 0.213663585314E-03 0.220611391995E-03 0.227785124008E-03 0.235192127880E-03
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0.162160440109E+00
ae wavefunction
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0.162160440109E+00
pseudo wavefunction
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0.956971426101E-04 0.988089749485E-04 0.102021996311E-03 0.105339497112E-03 0.108764874763E-03
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0.293297788203E-03 0.302835100467E-03 0.312682542321E-03 0.322850198405E-03 0.333348481284E-03
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0.107038344193E+01 0.109540473587E+01 0.112019002089E+01 0.114462060011E+01 0.116856306300E+01
0.119186802024E+01 0.121436881520E+01 0.123588023556E+01 0.125619725611E+01 0.127509385139E+01
0.129232192750E+01 0.130761043238E+01 0.132066471690E+01 0.133116623170E+01 0.133877265895E+01
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0.130177973302E+01 0.127788310298E+01 0.124791979347E+01 0.121195594119E+01 0.117012955700E+01
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
0.000000000000E+00
ae wavefunction
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0.117714963085E-02 0.121517864012E-02 0.125443472469E-02 0.129495738219E-02 0.133678737526E-02
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0.161767387661E-02 0.166991159220E-02 0.172383337419E-02 0.177949333353E-02 0.183694730789E-02
0.189625291594E-02 0.195746961331E-02 0.202065875021E-02 0.208588363083E-02 0.215320957455E-02
0.222270397899E-02 0.229443638492E-02 0.236847854317E-02 0.244490448353E-02 0.252379058570E-02
0.260521565239E-02 0.268926098453E-02 0.277601045878E-02 0.286555060725E-02 0.295797069967E-02
0.305336282787E-02 0.315182199281E-02 0.325344619405E-02 0.335833652195E-02 0.346659725239E-02
0.357833594433E-02 0.369366354008E-02 0.381269446850E-02 0.393554675108E-02 0.406234211102E-02
0.419320608539E-02 0.432826814042E-02 0.446766179001E-02 0.461152471742E-02 0.475999890040E-02
0.491323073976E-02 0.507137119125E-02 0.523457590114E-02 0.540300534538E-02 0.557682497239E-02
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0.920451321506E-01 0.947157026489E-01 0.974532859865E-01 0.100258855501E+00 0.103133345273E+00
0.106077644955E+00 0.109092594252E+00 0.112178977021E+00 0.115337514994E+00 0.118568861090E+00
0.121873592304E+00 0.125252202151E+00 0.128705092655E+00 0.132232565851E+00 0.135834814797E+00
0.139511914062E+00 0.143263809684E+00 0.147090308573E+00 0.150991067341E+00 0.154965580557E+00
0.159013168383E+00 0.163132963604E+00 0.167323898026E+00 0.171584688232E+00 0.175913820679E+00
0.180309536147E+00 0.184769813516E+00 0.189292352876E+00 0.193874557970E+00 0.198513517983E+00
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0.252080821818E+00 0.257031750433E+00 0.261963596859E+00 0.266866819394E+00 0.271731229666E+00
0.276545969613E+00 0.281299489013E+00 0.285979523755E+00 0.290573075042E+00 0.295066389746E+00
0.299444942160E+00 0.303693417394E+00 0.307795696707E+00 0.311734845064E+00 0.315493101250E+00
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0.121138806437E+01 0.124520914300E+01 0.127414049534E+01 0.129788344230E+01 0.131617463165E+01
0.132879041294E+01 0.133554760128E+01 0.133630339312E+01 0.133095550857E+01 0.131944261315E+01
0.130174470424E+01 0.127788310298E+01 0.124791979347E+01 0.121195594119E+01 0.117012955700E+01
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
0.000000000000E+00
pseudo wavefunction
0.291401325933E-08 0.310660738532E-08 0.331193051905E-08 0.353082395115E-08 0.376418457520E-08
0.401296856259E-08 0.427819528042E-08 0.456095146815E-08 0.486239569049E-08 0.518376308447E-08
0.552637042028E-08 0.589162149659E-08 0.628101289253E-08 0.669614009969E-08 0.713870405956E-08
0.761051813289E-08 0.811351552983E-08 0.864975723099E-08 0.922144043214E-08 0.983090754699E-08
0.104806558050E-07 0.111733474834E-07 0.119118208158E-07 0.126991016216E-07 0.135384157035E-07
0.144332020655E-07 0.153871270036E-07 0.164040991280E-07 0.174882853783E-07 0.186441280971E-07
0.198763632322E-07 0.211900397413E-07 0.225905402799E-07 0.240836032562E-07 0.256753463434E-07
0.273722915463E-07 0.291813919246E-07 0.311100600826E-07 0.331661985409E-07 0.353582321169E-07
0.376951424442E-07 0.401865047739E-07 0.428425272086E-07 0.456740925285E-07 0.486928027827E-07
0.519110268276E-07 0.553419510066E-07 0.589996331800E-07 0.628990603257E-07 0.670562099465E-07
0.714881155364E-07 0.762129363737E-07 0.812500319263E-07 0.866200411755E-07 0.923449671818E-07
0.984482672403E-07 0.104954948994E-06 0.111891672901E-06 0.119286861471E-06 0.127170815725E-06
0.135575839351E-06 0.144536371063E-06 0.154089125712E-06 0.164273244717E-06 0.175130456449E-06
0.186705247203E-06 0.199045043477E-06 0.212200406300E-06 0.226225238396E-06 0.241177005044E-06
0.257116969541E-06 0.274110444214E-06 0.292227058035E-06 0.311541041917E-06 0.332131532864E-06
0.354082898227E-06 0.377485081388E-06 0.402433970297E-06 0.429031790352E-06 0.457387523265E-06
0.487617353594E-06 0.519845144797E-06 0.554202946748E-06 0.590831536791E-06 0.629880996560E-06
0.671511326916E-06 0.715893103531E-06 0.763208175796E-06 0.813650411926E-06 0.867426493305E-06
0.924756761334E-06 0.985876120248E-06 0.105103499960E-05 0.112050038036E-05 0.119455688881E-05
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0.241518195837E-05 0.257480689749E-05 0.274498180033E-05 0.292640393503E-05 0.311981665323E-05
0.332601243583E-05 0.354583613993E-05 0.378018846037E-05 0.403002962015E-05 0.429638330457E-05
0.458034085547E-05 0.488306574269E-05 0.520579833094E-05 0.554986096174E-05 0.591666337125E-05
0.630770846606E-05 0.672459848077E-05 0.716904154238E-05 0.764285866862E-05 0.814799122864E-05
0.868650889678E-05 0.926061813200E-05 0.987267121753E-05 0.105251758980E-04 0.112208056533E-04
0.119624106514E-04 0.127530294250E-04 0.135959013195E-04 0.144944797639E-04 0.154524464180E-04
0.164737262553E-04 0.175625036414E-04 0.187232394758E-04 0.199606894654E-04 0.212799236061E-04
0.226863469507E-04 0.241857217502E-04 0.257841910562E-04 0.274883038842E-04 0.293050420377E-04
0.312418487062E-04 0.333066589503E-04 0.355079322021E-04 0.378546869117E-04 0.403565374822E-04
0.430237336441E-04 0.458672024310E-04 0.488985929263E-04 0.521303239658E-04 0.555756349902E-04
0.592486402555E-04 0.631643866225E-04 0.673389151628E-04 0.717893268303E-04 0.765338524702E-04
0.815919274473E-04 0.869842712009E-04 0.927329720510E-04 0.988615775995E-04 0.105395191097E-03
0.112360574171E-03 0.119786256323E-03 0.127702651659E-03 0.136142183310E-03 0.145139416064E-03
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ae wavefunction
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pseudo wavefunction
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End of Dataset