Shell commands

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All commands described here allow -h parameter that will display a help message containing a wider description of its usage.

Basic parameters

Command Description
source start-rep-shell Connect to repository
lspro List current path contents
pwdpro Print current path (similar to pwd)
exit-rep Disconnect from repository


Project related commands

Command Description
catpro Display project information
cdpro Change to project
cpro Create a new project
mpro Modify a project
dpro Delete a project
findpro Find project by it’s name (regex allowed)


Calculation related commands

Command Description
viewcalc View calculation information
dcalc Delete calculation from repository
loadcalc Load calculation into repository
Calculation type specific commands
loadgauss Load Gaussian calculation
loadadf Load ADF calculation
loadturbo Load Turbomole calculation
loadorca Load Orca calculation
loadvasp Load Vasp calculation


Basic parameters

start-rep-shell

Used to connect to the repository, it must be always preceded by source or . (dot), otherwise neither connection nor commands will work.

Examples
user$ source start-rep-shell Connect to repository using long format
user$ . start-rep-shell Connect to repository using short format

lspro

Displays content of current path: projects and calculations. Otherwise we can define a path to list its content.

Parameters Description
-n path Relative or absolute path project (optional)
-f Display long format in listing (optional)
-o order Order by. Possible values n->name, o->owner, g->group,t->time,c->concept,s->state (optional)


Examples:
user$ lspro Sample listing in current path
user$ lspro -n /db/username/hexenol: Lists by name the content of hexenol project (absolute path)
user$ lspro -o Sc2C82 Lists by owner the content of hexenol project (relative to current path)

pwdpro

Displays the current path, similar to pwd (print working directory) but lists current position inside the project's hierarchy.

Examples
user$ pwdpro Prints current path

exit-rep

Disconnects from the repository and ends current session. All repository commands are disabled after this command is executed.

Examples
user$ exit-rep Disconnects from repository


Project related commands

catpro

Displays project information.

Parameters Description
-n path Relative or absolute project path (mandatory)


Examples:
user$ catpro -n hexenol Prints project information using relative path
user$ catpro -n /db/username/hexenol Print project information using absolute path

cdpro

Changes path by navigating to parent / child project or an absolute path.

Parameters Description
-n path Relative or absolute project path (mandatory except on ..)


Examples:
user$ cdpro .. Changes path to parent project
user$ cdpro -n metanol Navigates to child project called metanol
user$ cdpro -n /db/username/metanol/freq Navigates to project using full path

cpro

Creates new project in current path. If name or description parameters contains blank spaces, they must be enclosed in double quotes.

Parameters Description
-n Name of the project (mandatory)
-d Description of the project (mandatory)
-cg Concept Group of the project (optional)


Examples:
user$ cpro -n metanol -d metanol Creates metanol project with metanol description
user$ cpro -n metanol -d metanol -cg FRQ Creates project with description and concept group
user$ cpro -n metanol -d "This is the metanol project description" Creates metanol project with a long description


mpro

Modifies the selected project properties, name, description or even moves it to another project (as a nested project).

Parameters Description
-n path Relative or absolute project path (mandatory)
-p permissions Permissions of the project. Ex: '110100' (optional)
-o owner Owner of the project (optional)
-g group Group owner of the project (optional)
-cg concept_group Concept Group of the project (optional)
-nn name New Name of the project (optional)
-np path New Parent project (absolute path) (optional)
-d description Description of the project (optional)


Examples
user$ mpro -n /db/username/hexenol -nn hexenolMod Replaces project name by hexenolMod
user$ mpro -n /db/username/hexenol -np /db/user/alcohols Moves selected project to another parent project
user$ mpro -n /db/username/hexenol -d "Replaced description" Replaces description on selected project

dpro

Deletes a project by defining its path, all child projects and calculations will also be removed from Create.

Parameters Description
-n path Relative or absolute project path (mandatory)
Examples
user$ dpro -n metanol Deletes metanol project using relative path, our path must be at the level of this project
user$ dpro -n /db/username/alcohols/metanol Deletes metanol project using absolute path, current path position is not relevant here

findpro

Find project by it’s name (regex allowed)

Parameters Description
-n name Regular expression to find in the name field of project (optional)
-d description Regular expression to find in the description field of project (optional)
-p path Regular expression to find in the path field of project (optional)


Examples
findpro -n metan* Finds projects which name match regular expression metan*
findpro -d "alco* " Finds projects which description match regular expression alco*


Calculation related commands

viewcalc

This comands displays the most relevant information about a calculation.

Parameters Description
-n path Relative or absolute project path (mandatory)
-f If present shows full contents. (optional)


dcalc

This comands deletes a calculation given its name.

Parameters Description
-n path Relative or absolute calculation path (mandatory)

Using full calculation path:

$ dcalc -n  /db/user/metOH-oxidation/freq1    #Will delete calculation freq1 inside metOH-oxidation project

Navigating to parent project and using calculation name:

$ cdpro metOH-oxidation             #Move to parent project
$ dcalc -n freq1                    #Will delete calculation freq1

loadcalc

Uploads a calculation into the Create module on the current project path. It is not allowed to upload calculations to the base path (/db/username), you must always upload calculations into a project.
This is a generic command that will allow us to upload multiple files and formats, some parameters will be shared by more than one format so they will behave differently depending on the format, so please read the command help (-h parameter) carefully.

Common parameters for all calculations

Parameters Description
-n name Name of the calculation inside Create. (mandatory)
-d desc Description of the calculation. (mandatory)
-i filename Input file (mandatory)
-o filename Output file (OUTCAR on VASP, job.last on Turbomole).(mandatory)
-a filename Additional file loading for calculation. (optional)

Note: Two calculations with the same name and in the same project are not allowed, otherwise upload process will fail.

Additional parameters for Turbomole

Parameters Description
-oc filename Turbomole coords file. (optional)
-oe filename Turbomole energy file. (optional)
-ob filename Turbomole basis file. (optional)

Additional parameters for VASP

Parameters Description
-dc filename VASP DOSCAR file. (optional)
-kp filename VASP KPOINTS file (optional)


Examples
user$ loadcalc -i ESR_TiF3.run -o ESR_TiF3.run.o33132 -n ESR_TiF3 -d "Sample description" Upload ADF calculation and set its name to ESR_TiF3
user$ loadcalc -i control -o job.last -oc coords -oe energy -ob basis -n Fe_Bipy -d Fe_Bipy Upload Turbomole calculation and set its name to Fe_Bipy
user$ loadcalc -i INCAR -o OUTCAR -n NO_dim -d NO_dim Upload VASP calculation and set its name to NO_dim

To leverage the usage of this command we have developed a group of helper Linux scripts to simplify shell upload

Script Function
loadadf Upload ADF calculation
loadgauss Upload Gaussian calculation
loadturbo Upload Turbomole calculation
loadvasp Upload Vasp calculations (Nudge Elastic Band and Dimmer are also included)