Shell commands

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

Warning

It is not allowed to upload calculations to the base path (/db/username), you must always upload calculations into a project.

Warning

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

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
mcalc	Modify a calculation
dcalc	Delete calculation from repository
getxyz	Retrieve calculation geometry as XYZ
Calculation type specific commands
loadadf	Load ADF calculation
loadams	Load AMS calculation
loadamber	Load Amber calculation
loadcastep	Load CASTEP calculation
loadgauss	Load Gaussian calculation
loadgromacs	Load GROMACS calculation
loadgronor	Load GronOR calculation
loadgrrm	Load GRRM calculation
loadlammps	Load LAMMPS calculation
loadmolcas	Load Molcas calculation
loadmopac	Load Mopac calculation
loadorca	Load Orca calculation
loadqespresso	Load QuantumESPRESSO calculation
loadturbo	Load Turbomole calculation
loadsiesta	Load SIESTA calculation
loadvasp	Load Vasp calculation

Basic parameters explained

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:

$ source start-rep-shell   #Connect to repository using long format
$ . 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 ->groupt->time,

c->concept,

s->state

Examples:

$ lspro                               #Sample listing in current path
$ lspro -n /db/username/hexenol       #Lists by name the content of hexenol project (absolute path)
$ 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:

$ 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:

$ exit-rep     #Disconnects from repository

Project related commands

catpro

Displays project information.

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

Examples:

$ catpro -n hexenol                 # Prints project information using relative path
$ 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:

$ cdpro ..                               # Changes path to parent project
$ cdpro -n metanol                       # Navigates to child project called metanol
$ 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:

$ cpro -n metanol -d metanol                 # Creates metanol project with metanol description
$ cpro -n metanol -d metanol -cg FRQ         # Creates project with description and concept group
$ 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: ‘rw—-’ (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:

$ mpro -n /db/username/hexenol -nn hexenolMod             # Replaces project name by hexenolMod
$ mpro -n /db/username/hexenol -np /db/user/alcohols      # Moves selected project to another parent project
$ 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:

$ dpro -n metanol                          # Deletes metanol project using relative path, our path must be at the level of this project
$ 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 and retrieves its files.

Parameters	Description
-n path	Relative or absolute project path (mandatory)
-f [filename]	Download single calculation file, all if filename not specified. Requires -dcp parameter. (optional)
-dcp path	Full path where to store the files. It is mandatory to set also -f parameter. (optional)

Examples:

$ viewcalc -n calc1                      # Display calculation on current project with name calc1
$ viewcalc -n /db/user1/project/calc1    # Display calculation providing is fullpath
$ viewcalc -n calc1 -f output.cml -dcp /home/user/tmp/calc1  # Display calculation information and store output.cml file on the provided folder
$ viewcalc -n calc1 -f -dcp /home/user/tmp/calc1  # Display calculation information and store its files on the provided folder

mcalc

Modifies the selected calculation properties, name, description or even moves it to another project.

Parameters	Description
-n path	Relative or absolute calculation path (mandatory)
-nn name	New Name of the calculation (optional)
-np path	New Parent project (absolute path) (optional)
-d description	New description of the calculation (optional)

Examples:

$ mcalc -n /db/user/metOH-oxidation/freq1 -nn freq2                  # Replaces calculation name by freq2
$ mcalc -n /db/user/metOH-oxidation/freq1 -np /db/user/alcohols      # Moves selected calculation to another project
$ mcalc -n /db/user/metOH-oxidation/freq1 -d "Another description"   # Replaces description on selected calculation

dcalc

This command 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

getxyz

This command retrieves the geometry of a calculation given its id.

Parameters	Description
-n id	Calculation number id (mandatory)
-o filename	Output to file instead of stdout (optional)

$ getxyz -n 14837                   # Retrieve geometry of calculation with ID 14837 and display on stdout
$ getxyz -n 14837 -o geom.xyz       # Retrieve geometry of calculation with ID 14837 and store it in geom.xyz file

There is a group of helper Linux scripts that simplify the process of uploading calculations:

Script	Function
loadadf	Upload ADF calculation
loadams	Upload AMS calculation
loadamber	Upload Amber calculation
loadcastep	Upload CASTEP calculation
loadgauss	Upload Gaussian calculation
loadgromacs	Upload GROMACS calculation
loadgronor	Upload GronOR calculation
loadgrrm	Upload GRRM calculation
loadlammps	Upload LAMMPS calculation
loadmolcas	Upload Molcas calculation
loadmopac	Upload Mopac calculation
loadorca	Upload Orca calculation
loadqespresso	Upload QuantumEspresso calculation
loadturbo	Upload Turbomole calculation
loadsiesta	Upload SIESTA calculation
loadvasp	Upload Vasp calculations (Nudge Elastic Band and Dimmer are also included)