Shell commands

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

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: ‘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:

$ 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 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)

Warning

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:

$ 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
$ 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
$ loadcalc -i INCAR -o OUTCAR -n NO_dim -d NO_dim                                       # Upload **VASP** calculation and set its name to NO_dim

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

Script Function
loadadf Upload ADF calculation
loadamber Upload Amber calculation
loadgauss Upload Gaussian calculation
loadgromacs Upload GROMACS calculation
loadgronor Upload GronOR 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
loadvasp Upload Vasp calculations (Nudge Elastic Band and Dimmer are also included)