Shell automated scripts

All ioChem-BD shell client commands can be shell-scripted to ease upload files into the Create Module in an automated way. Find herein few helper scripts that will assist you when uploading calculations.

By using scripts, uploading data automatically is just a trivial exercise.

All our shell commands are contained within the shell client, which is downloadable from your Create web page. Feel free to customize these scripts to fit your needs, or turn them into new ones. Set the -v parameter (verbose) on these scripts to display more information about each script mechanism.

Per file type

loadadf

Loads an ADF calculation into the Create module (until AMS2020).

Parameters	Description
-i filename	Input file, if not defined will use script defined name
-o filename	Output file, if not defined will use script defined name
-a filename	Append additional file (optional)
-n name	Name of the calculation in the data base (optional), if not defined will use parent folder name
-d desc	Description of the calculation in the data base (optional), if not defined will use parent folder name
--auto	Autogenerate current path into Create module (optional). Refer to -auto parameter section.

If parameters -i and -o are not set, this script will look for input.in and output.out files. If that info is missing, the upload process will be aborted. If you wish to use another naming convention just edit the loadadf script file and replace default filenames.

bash

# Default static file names, change them in order to fit your naming conventions
INPUT_DEFAULT_FILENAME="input.in"
OUTPUT_DEFAULT_FILENAME="output.out"

If parameters -n and -d are not defined, the scripts will use the parent folder's name as calculation name and description.

Examples

Upload calculation a-pw12 using a-pw12.opt.in and a-pw12.opt.out files

bash

$ loadadf -i a-pw12.opt.in -o a-pw12.opt.out -n "a-pw12" -d "Optimization a-pw12"

Upload calculation named metane using me-mp2.in and me-mp2.out files; name and description are picked from the parent folder name.

bash

$ pwd
/home/user/Desktop/methane
$ loadadf -i me-mp2.in -o me-mo2.out

Upload calculation named a-pw12.opt and attach additional file report.pdf

bash

$ loadadf -i a-pw12.opt.in -o a-pw12.opt.out -a report.pdf -n a-pw12.opt -d "Optimization a-pw12"

Upload calculation and automatically build its parent folder. calculation name and description will be same as parent folder

bash

$ loadadf -i irc_ts2_09.in -o irc_ts2_09.out --auto

loadams

Loads an AMS ADF calculation into the Create module (since AMS2020).

Parameters	Description
-i filename	Input file, if not defined will use script defined name
-rkf1 filename	ams.rkf binary file, if not defined will use script defined name
-rkf2 filename	adf.rkf binary file, if not defined will use script defined name
-o filename	Output file, if not defined will use script defined name
-a filename	Append additional file (optional)
-n name	Name of the calculation in the data base (optional), if not defined will use parent folder name
-d desc	Description of the calculation in the data base (optional), if not defined will use parent folder name
--auto	Autogenerate current path into Create module (optional). Refer to -auto parameter section.

If parameters -i, -rkf1, -rkf2 and -o are not set, this script will look for input.in, ams.rkf, adf.rkf and output.out files. If that info is missing, the upload process will be aborted. If you wish to use another naming convention just edit the loadams script file and replace default filenames.

bash

# Default static file names, change them in order to fit your naming conventions
INPUT_DEFAULT_FILENAME="input.in"
OUTPUT_DEFAULT_FILENAME="output.out"
AMS_DEFAULT_FILENAME="ams.rkf"
ADF_DEFAULT_FILENAME="adf.rkf"

If parameters -n and -d are not defined, the scripts will use the parent folder's name as calculation name and description.

Examples

Upload calculation a-pw12 with its files:

bash

$ loadams -i a-pw12.opt.in -o a-pw12.opt.out -rkf1 Test.results/ams.rkf -rkf2 Test.results/adf.rkf -n "a-pw12" -d "Optimization a-pw12"

Upload calculation named a-pw12.opt and attach additional file report.pdf

bash

$ loadams -i a-pw12.opt.in -o a-pw12.opt.out -rkf1 Test.results/ams.rkf -rkf2 Test.results/adf.rkf -a report.pdf -n a-pw12.opt -d "Optimization a-pw12"

Upload calculation and automatically build its parent folder. calculation name and description will be same as parent folder

bash

$ loadams -i irc_ts2_09.in -o irc_ts2_09.out -rkf1 Test.results/ams.rkf -rkf2 Test.results/adf.rkf --auto

loadamber

Loads a Amber calculation into the Create module.

Parameters	Description
-i filename	Input file, if not defined will use script defined name
-o filename	Output file, if not defined will use script defined name
-p filename	Parameter/topology file specification (.prmtop), if not defined will use script defined name
-ir filename	Initial coordinates file (.inpcrd) or intial restart file (.ncrst) used, if not defined will use script defined name
-r filename	Final restart file (.ncrst), if not defined will use script defined name
-t filename	Trajectory file (.nc), if not defined will use script defined name
-a filename	Append additional file (optional)
-n name	Name of the calculation in the data base (optional), if not defined will use parent folder name
-d desc	Description of the calculation in the data base (optional), if not defined will use parent folder name
--auto	Autogenerate current path into Create module (optional). Refer to -auto parameter section.

If parameters -i, -o, -p, -ir, -r and/or -t are not set, this script will look for input.in, output.out, topology.prmtop, coords.inpcrd, restartnc.ncrst and trajectory.nc files. If that info is missing, the upload process will be aborted. If you wish to use another naming convention just edit the loadamber script file and replace default filenames.

bash

# Default static file names, change them in order to fit your naming conventions
INPUT_DEFAULT_FILENAME="input.in"
OUTPUT_DEFAULT_FILENAME="output.out"
TOPOLOGY_DEFAULT_FILENAME="topology.prmtop"
COORDINATES_DEFAULT_FILENAME="coords.inpcrd"
RESTART_DEFAULT_FILENAME="restartnc.ncrst"
TRAJECTORY_DEFAUL_FILENAME="trajectory.nc"

If parameters -n and -d are not defined, the scripts will use the parent folder's name as calculation name and description.

Examples

This command will set upload calculation name and description equals to parent folder and upload all files that match by name.

bash

$ loadamber

This command will upload all matching files in directory, set calculation name as "Au-CoO-H2O" and description as "Sample upload".

bash

$ loadamber -n Au-CoO-H2O -d "Sample upload"

This command will behave the same as previous one but will upload different files rather than default.

bash

$ loadamber -n Au-CoO-H2O -d "Sample upload" -i step1.in -o step1.out -p Au-CoO-H2O.prmtop -ir Au-CoO-H2O.inpcrd -r Au-CoO-H2O.ncrst -t Au-CoO-H2O.nc

loadcastep

Loads a CASTEP calculation into the Create module.

More about the format capture restrictions on the following page.

Parameters	Description
-i filename	Input parameters file (.param), if not defined will use script defined name
-o filename	Output resume file (.castep), if not defined will use script defined name
-oc filename	Cell file (.cell), if not defined will use script defined name
-xcd filename	Graph file (.xcd), can be repeated to add multiple files (optional)
-og filename	Geometry steps file (.geom), it is mandatory only on geometry optimization calculations.
-a filename	Append additional file, can be repeated to add multiple files (optional)
-n name	Name of the calculation in the data base (optional), if not defined will use parent folder name
-d desc	Description of the calculation in the data base (optional), if not defined will use parent folder name
--auto	Autogenerate current path into Create module (optional). Refer to -auto parameter section

                 |                                                                                                              |

If parameters -i, -o and -oc are not set, this script will look for calc.param, calc.castep, calc.cell files. If that files are missing, the upload process will be aborted.

If you wish to use another naming convention set the parameters to override default values or edit the loadcastep script file and replace default filenames.

bash

# Default static file names, change them in order to fit your naming conventions
INPUT_DEFAULT_FILENAME="calc.param"
OUTPUT_DEFAULT_FILENAME="calc.castep"
CELL_DEFAULT_FILENAME="calc.cell"

If parameters -n and -d are not defined, the scripts will use the parent folder's name as calculation name and description.

Additional files, like trajectories (.trj), can be attached to the uploaded calculation using the -a additional file parameter.

Examples

bash

$ loadcastep

This command will set upload calculation name and description equals to parent folder and upload all required files if they match by name.

bash

$ loadcastep -n Si_51688 -d "Sample upload"

This command will upload required matching files in directory, set calculation name as "Si_51688" and description as "Sample upload".

bash

$ loadcastep -n Si_51688 -d "Sample upload" -i Si_51688.param -o Si_51688.castep -oc Si_51688.cell -xcd Si_51688_Energies.xcd -xcd Si_51688_Convergence.xcd

This command will use different filenames and also upload two additional graph files.

bash

$ loadcastep -n Si_51688 -d "Sample upload" -i Si_51688.param -o Si_51688.castep -oc Si_51688.cell -geom Si_51688.geom

This command will add the .geom file due to it's an optimization calculation.

bash

$ loadcastep -n Si_51688 -d "Sample upload" -i Si_51688.param -o Si_51688.castep -oc Si_51688.cell -a Si_51688.trj

This command will upload the calculation adding a trajectory file as an additional file.

loadgauss

Same parameters and functionalities than the loadadf script.

WARNING

It is advised to use #p flag in Gaussian calculations. Link information helps ioChem-BD to capture some more extra information such as basis sets used.

loadgromacs

Loads a GROMACS calculation into the Create module.

Parameters	Description
-i filename	Molecular dynamics parameters (.mdp) as the Input file, if not defined will use script defined name
-o filename	Logfile (.log) as the Output file, if not defined will use script defined name
-oc filename	Molecular structure in Gromos87 format. (.gro), if not defined will use script defined name
-t filename	Trajectory file (.xtc), if not defined will use script defined name
-a filename	Append additional file (optional)
-n name	Name of the calculation in the data base (optional), if not defined will use parent folder name
-d desc	Description of the calculation in the data base (optional), if not defined will use parent folder name
--auto	Autogenerate current path into Create module (optional). Refer to -auto parameter section.

If parameters -i, -o, -oc and/or -t are not set, this script will look for input.mdp, output.log, geometry.gro and trajectory.xtc files. If that info is missing, the upload process will be aborted. If you wish to use another naming convention just edit the loadgromacs script file and replace default filenames.

bash

# Default static file names, change them in order to fit your naming conventions
INPUT_DEFAULT_FILENAME="input.mdp"
OUTPUT_DEFAULT_FILENAME="output.log"
GEOMETRY_DEFAULT_FILENAME="geometry.gro"
TRAJECTORY_DEFAULT_FILENAME="trajectory.xtc"

If parameters -n and -d are not defined, the scripts will use the parent folder's name as calculation name and description.

Examples

Upload calculation LIN24_LI192 using required files

bash

$ loadgromacs -i npt.mdp -o LIN24_LI192.log -oc LIN24_LI192.gro -t  LIN24_LI192.xtc -n "LIN24_LI192" -d "LIN24 LI192 SOL25208 40000ps NPT 300K calculation"

Upload same calculation but name and description are picked from the parent folder name.

bash

$ pwd
/home/user/Desktop/LIN24_LI192
$ loadgromacs -i npt.mdp -o LIN24_LI192.log -oc LIN24_LI192.gro -t  LIN24_LI192.xtc

Upload calculation and automatically build its parent folder. calculation name and description will be same as parent folder

bash

$ loadgromacs -i npt.mdp -o LIN24_LI192.log -oc LIN24_LI192.gro -t  LIN24_LI192.xtc --auto

loadgronor

Loads an GronOR calculation into the Create module.

Parameters	Description
-i filename	Input file (optional)
-o filename	Output file in CML format, if not defined will use script defined name
-a filename	Append additional file (optional)
-n name	Name of the calculation in the data base (optional), if not defined will use parent folder name
-d desc	Description of the calculation in the data base (optional), if not defined will use parent folder name
--auto	Autogenerate current path into Create module (optional). Refer to -auto parameter section.

If parameter -o are not set, this script will look for output.out files. If that info is missing, the upload process will be aborted. If you wish to use another naming convention just edit the loadgronor script file and replace default filenames.

bash

# Default static file names, change them in order to fit your naming conventions
OUTPUT_DEFAULT_FILENAME="output.cml"

If parameters -n and -d are not defined, the scripts will use the parent folder's name as calculation name and description.

Examples

This command will set upload calculation name and description equals to parent folder and upload all files that match by name.

bash

$ loadgronor

This command will upload all matching files in directory, set calculation name as "Sc2C82" and description as "Sample upload".

bash

$ loadgronor -n Sc2C82 -d "Sample upload"

This command will behave the same as previous one but will upload different files rather than default.

bash

$ loadgronor -n Sc2C82 -d "Sample upload" -i input2.in -o dimmer.cml

loadgrrm

Same parameters and functionalities than the loadadf script.

WARNING

Reaction path searches are not yet supported (AFIR, etc).

loadlammps

Loads a LAMMPS calculation into the Create module.

Read more about LAMMPS format capture restricitions on the following page.

Parameters	Description
-i filename	User defined input file, if not provided will use script defined name
-p filename	Data file used on the read_data command, if not defined will use script defined name
-o filename	Output file, called by default log.lammps, if not defined will use script defined name
-t filename	Trajectory file, it can be compressed in .zip or .tar.gz, if not defined will use script defined name
-a filename	Append additional file (optional)
-n name	Name of the calculation in the data base (optional), if not defined will use parent folder name
-d desc	Description of the calculation in the data base (optional), if not defined will use parent folder name
--auto	Autogenerate current path into Create module (optional). Refer to -auto parameter section.

If parameters -i, -o, -p and/or -t are not set, this script will look for input.in, log.lammps, lammps.dat and trajectory.zip files. If that info is missing, the upload process will be aborted. If you wish to use another naming convention just edit the loadlammps script file and replace default filenames.

bash

# Default static file names, change them in order to fit your naming conventions
INPUT_DEFAULT_FILENAME="input.in"
OUTPUT_DEFAULT_FILENAME="log.lammps"
DATAFILE_DEFAULT_FILENAME="lammps.dat"
TRAJECTORY_DEFAULT_FILENAME="trajectory.zip"

If parameters -n and -d are not defined, the scripts will use the parent folder's name as calculation name and description.

Examples

Upload calculation LIN24_LI192 using required files

bash

$ loadlammps -i lammps.lmp -p lammps.dat -o log.lammps -t trajectory.zip -n "LIN24_LI192" -d "LIN24 LI192 SOL25208 40000ps NPT 300K calculation"

Upload same calculation but name and description are picked from the parent folder name.

bash

$ pwd
/home/user/Desktop/LIN24_LI192
$ loadlammps -i lammps.lmp -p lammps.dat -o log.lammps -t trajectory.zip

Upload calculation and automatically build its parent folder. calculation name and description will be same as parent folder

bash

$ loadlammps -i lammps.lmp -p lammps.dat -o log.lammps -t trajectory.zip --auto

loadmolcas

Same parameters and functionalities than the loadadf script.

loadmopac

Same parameters and functionalities than the loadadf script.

loadorca

Loads an ORCA calculation into the Create module, it can be used standalone as other shell client commands or it can be attached to a job script to be automatically uploaded after the calculation has finished.

Parameters	Description
-i filename	Input file, (optional), if not defined will use script defined name
-o filename	Output file (optional), if not defined will use script defined name
-a filename	Append additional file (optional)
-n name	Name of the calculation in the data base (optional), if not defined will use parent folder name
-d desc	Description of the calculation in the data base (optional), if not defined will use parent folder name
--molden	Build molden file with calculation molecular orbitals from output file. Will use orca_m2kl script to do such conversion. Please read --molden section for further configuration.
--auto	Autogenerate current path into Create module (optional). Refer to -auto parameter section.

If parameters -i and -o are not set, it will look for input.in and 'output.out' files, if they are missing, the upload will be aborted. If we use another naming convention just edit the loadorca script file and replace default file names.

bash

# Default static file names, change them in order to fit your naming conventions
INPUT_DEFAULT_FILENAME="input.in"
OUTPUT_DEFAULT_FILENAME="output.out"

If parameters -n and -d are not defined, the loadorca script will use the parent folder's name as calculation name and description. If a parameter value contains multiple words and blank spaces (like description), they must be enclosed inside double quotes.

loadqespresso

Loads a QuantumESPRESSO calculation into the Create module.

Options like -b, -dos, -pi or -.po are restricted to specificic calculation types described below.

Parameters	Description
-i filename	Input file, if not defined will use script defined name.
-o filename	Output file, if not defined will use script defined name.
-as filename	Absorption spectra data file, see Absorption spectra section below for further details (optional).
-b filename	Reordered band data file, see Band structure section below for further details (optional).
-dos filename	PDOS atom file(s) (optional).
-pi filename	Input used on the phonon matdyn.x tool, contains k-points and labels (optional).
-po filename	Output file containing the phonon frequencies. (optional)
-a filename	Append additional file (optional).
-n name	Name of the calculation in the data base (optional), if not defined will use parent folder name.
-d desc	Description of the calculation in the data base (optional), if not defined will use parent folder name.
--auto	Autogenerate current path into Create module (optional). Refer to -auto parameter section.

If parameters -i and -o are not set, this script will look for input.in and output.out files. If any of that files don't exist, the upload process will be aborted. If you wish to use another naming convention just edit the loadqespresso script file and replace default filenames.

bash

# Default static file names, change them in order to fit your naming conventions
INPUT_DEFAULT_FILENAME="input.in"
OUTPUT_DEFAULT_FILENAME="output.out"

If parameters -n and -d are not defined, the scripts will use the parent folder's name as calculation name and description.

Examples

Upload calculation a-pw12 using a-pw12.opt.in and a-pw12.opt.in files

bash

$ loadqespresso -i a-pw12.opt.in -o a-pw12.opt.out -n "a-pw12" -d "Optimization a-pw12"

Upload calculation named bencene using pw_scf.in and pw_scf.out files; name and description are picked from the parent folder name.

bash

$ pwd
/home/user/Desktop/bencene
$ loadqespresso -i pw_scf.in -o pw_scf.out

Upload calculation and automatically build its parent folder. calculation name and description will be same as parent folder

bash

$ loadqespresso -i irc_ts2_09.in -o irc_ts2_09.out --auto

Absorption spectra calculations

ioChem-BD can process and display absorption spectrum data coming from time-dependent density functional theory calculations (TDDFT).

Sample absorption spectra plot

The required file is generated by the combination of the following QuantumEspresso tools:

pw.x -> turbo_lanczos.x -> turbo_spectrum.x
SCF -> TDDF calculation -> Spectrum creation

Once the spectrum data file is generated, it can be uploaded along with the calculation using the -as parameter.

Example

Upload calculation named a-pw12.opt and attach spectra file plot_chi.dat

bash

$ loadqespresso -i pw_scf.in -o pw_scf.out -as plot_chi.dat -n a-pw12.opt -d "Bencene calculation"

Band structure calculations

ioChem-BD can process and display band dispersion data on its HTML report.

Sample band structure plot

The following QuantumEspresso tool workflow will generate the required files:

pw.x -> pw.x (bands) -> bands.x
SCF -> Band path calculation -> Band dispersion calculation

Once the bands dispersion file is generated, it must be uploaded along with the calculation using the -b parameter. When having spin up/down band files, please provide two -b parameters, being the spin up band file the first and the down file the second.

The provided input file must be the band path calculation file from 2nd step, which contains kpoint band path.

The provided output files must be the SCF output file from the 1st step and the band path calculation file from 2nd step, so two -o parameters should be provided, the order must be kept the same as described here.

WARNING

The first output file (SCF) is optional but if not provided the generated graph won't center its energies on fermi energy value.

Examples

Upload calculation named Ce_bands and attach band structure information file bands.out:

bash

$ loadqespresso -i ce_nscf.in -o ce_scf.out -o ce_nscf.out -b bands.out -n Ce_bands -d "Bands for Ce atom"

Same calculation but with spin up/down band files:

bash

$ loadqespresso -i ce_nscf.in -o ce_scf.out -o ce_nscf.out -b bands_up.out -b bands_down.out -n Ce_bands -d "Bands for Ce atom"

Projected Density of States calculations

ioChem-BD can process and display the projected density of states information on its HTML report.

PDOS plot per atom and orbital type, both spins

The following QuantumEspresso tool workflow will generate the required files:

pw.x -> pw.x -> projwfc.x
SCF -> NSCF -> Projects wavefunctions onto orthogonalized atomic wavefunctions.

We need first a self-consistent field calculation and then a non-self-consistent field calculation with denser k-points. Then we prepare the input file for the tool projwfc.x.

The tool generates all the PDOS values files following this naming template:

text

.*.pdos_atm#XXX(YYY)_wfc#AAA(BBB)

Being the first two parameters (in uppercase) the id and element symbol of the atom and the last two the id and number of the atomic orbital.

All the atom pdos files must be uploaded along with the calculation using the -dos parameter on each file, the totals dos file is not required because it is calculated from the individual values.

The provided output files must be the SCF output file from the 1st step and the NSCF output file from the 2nd step, so two -o parameters should be provided, the order must be kept the same as described here.

WARNING

Review the section DATA CONVERSION -> From CML to HTML -> QuantumEspresso to check the used file format.

Example

Upload calculation named CeO2_pdos and attach the pdos files:

bash

$ loadqespresso -i ceo2_nscf.in -o ceo2_scf.out -o ceo2_nscf.out -n CeO2_pdos -d 'Cerium dioxide PDOS' -dos 'pwscf.pdos_atm#1(Fe)_wfc#1(s) '-dos pwscf.pdos_atm#1\(Fe\)_wfc#2\(p\) -dos 'pwscf.pdos_atm#1(Fe)_wfc#3(d)'

On calculation with spin up/down files we will upload all PDOS files as on the previous example.

WARNING

The PDOS filename contain symbols that can break the upload process if they are not escaped or enclosed between single quotes, please review last the command for both examples.

Phonon dispersion

ioChem-BD can process and display phonon dispersion data on its HTML report.

Sample phonon dispersion plot

The following QuantumEspresso tool workflow will generate the required files:

pw.x -> ph.x -> matdyn.x
Structure optimization -> PHonon -> Phonon dispersion calculation

Once the structure is relaxed, the dynamical matrix is calculated on the on 2nd step to finally get the phonon dispersion on the 3rd calculation.

The provided input -i and output file -o must be the optimization ones from 1st step.

The provided phonon input file -pi will contain the kpoint definition, weights and labels. Finally the -po will be the data file containing the phonon frequency level on each kpoint.

WARNING

Review the section DATA CONVERSION -> From CML to HTML-> QuantumEspresso to check the used file format.

Example

Upload calculation named Ce_phonon and attach phonon dispersion information file matdyn.freq:

bash

$ loadqespresso -i ce_opt.in -o ce_opt.out -pi qe_matdyn_phdisp.pwi -po matdyn.freq -n Ce_phonon -d "Phonon dispersion for Ce atom"

Phonon DOS

ioChem-BD can process and display phonon density of states data on its HTML report.

Sample phonon DOS plot

Will use the same tool workflow that the previous Phonon dispersion example but on the 3rd step will request matdyn.x tool to generate Phonon DOS data.

The uploaded files will be the same except that, in this case, the -pi file won't be required, just the the -po with the data file containing the phonon dos energies.

Example

Upload calculation named Ce_phonon_dos and attach phonon dispersion information file matdyn.dos:

bash

$ loadqespresso -i ce_opt.in -o ce_opt.out -po matdyn.dos -n Ce_phonon_dos -d "Phonon DOS for Ce atom"

loadturbo

Loads a Turbomole calculation into the Create Module. It can be used standalone as other shell client commands, or it can be attached to a job script to be automatically uploaded after the calculation has finished.

Parameters	Description
-i control	Input file (optional) , if not defined it will look for control file on current folder
-o job.last	Output file (optional) , if not defined it will look for job.last file on current folder
-oe energy	Energy file (optional), if not defined it will look for energy file on current folder
-ob basis	Basis file (optional) , if not defined it will look for basis file on current folder
-oc coord	Coord file (optional), if not defined it will look for coord file on current folder
-a file	Append an additional file (optional)
-n	Name of the calculation in the data base (optional), if not defined it will use the parent folder's name
-d desc	Description of the calculation in the data base (optional), if not defined it will use parent folder's name
--auto	Autogenerate current path into the Create module (optional). Refer to -auto parameter section.

If parameters -i and -o are not set, it will look by default for control and job.last files on current folders, if they are missing the upload will be aborted. If we use another naming convention just edit loadturbo script file and replace the default file names.

bash

# Default static file names, change them in order to fit your naming conventions
CONTROL_DEFAULT_FILENAME="control"
ENERGY_DEFAULT_FILENAME="energy"
BASIS_DEFAULT_FILENAME="basis"
COORD_DEFAULT_FILENAME="coord"
JOB_LAST_DEFAULT_FILENAME="job.last"

If parameters -n and -d are not defined, the loadturbo script will use the parent folder's name as calculation name and description. If a parameter value contains multiple words and blank spaces (like description), they have to be enclosed inside double quotes.

Multiple step calculation

On calculations that generate multiple output files like dscf, escf, we can upload them as a unique file by joining its output files into one. We do so by repeating the -o parameter with the name of each output file. Must be defined in the same order as they were generated. Example:

bash

$ loadturbo -i control -o dscf.out -o escf.out

The output of freeh (the free enthalpy module), can also be appended also using the -o parameter. HTML Report will then display thermochemistry values and energy corrections.

bash

$ loadturbo -i control -o job.last -o freeh.out

WARNING

The freeh module processing is only valid for single temperature and pressure values, it will not work for ranges.

Examples

Upload calculation flourophenol using control. job.last, energy, basis and coord files. Set name as flourophenol.

bash

$ loadturbo -i control -o job.last  -n "flourophenol" -d "Population analysis" -oe energy -ob basis -oc coord

We can omit multiple parameters if they are named the same as default script names, so the last command can be the same than this one:

bash

$ loadturbo -n "flourophenol" -d "Population analysis"

If no parameter is set, name and description fields will come from parent folder.

bash

$ pwd
/home/user/Desktop/flourophenol
$ loadturbo

loadsiesta

Loads a SIESTA calculation into the Create module.

For this chemical format, the provided output file must not be the textual one, it must be the XML one. It is generated by declaring the following flag on the input file:

text

XML.Write .true.

Parameters	Description
-i filename(s)	Input file(s), if not defined will use script defined name
-o filename	Output file, if not defined will use script defined name
-a filename	Append additional file (optional)
-n name	Name of the calculation in the data base (optional), if not defined will use parent folder name
-d desc	Description of the calculation in the data base (optional), if not defined will use parent folder name
--auto	Autogenerate current path into Create module (optional). Refer to -auto parameter section.

SIESTA can combine multiple input files to bundle the final input file, in this case, you can set multiple -i parameters, one for each partial input file.

If parameters -i and -o are not set, this script will look for input.fdf and output.xml files. If that info is missing, the upload process will be aborted. If you wish to use another naming convention just edit the loadsiesta script file and replace default filenames.

bash

# Default static file names, change them in order to fit your naming conventions
INPUT_DEFAULT_FILENAME="input.fdf"
OUTPUT_DEFAULT_FILENAME="output.xml"

If parameters -n and -d are not defined, the scripts will use the parent folder's name as calculation name and description.

Examples

Upload h2o calculation, that contains two input files and a output .xml file:

bash

$ loadsiesta -n h2o -d \"Sample upload\" -i h2o.fdf -i Default.fdf  -o h2o.xml

loadvasp

Loads a VASP calculation into the Create module, it can be used standalone as other shell client commands or it can be attached to a job script to be automatically uploaded after the calculation has finished.

Parameters	Description
-i INCAR	Input file (optional), if not defined it will look for INCAR file on current folder
-o OUTCAR	Output file (optional) , set to OUTCAR by default
-dc DOSCAR	Attach DOSCAR file information to resulting uploaded calculation (optional), it will extract Density of states coefficients.
-kp KPOINTS	Attach KPOINTS file information to resulting uploaded calculation (optional), it will extract KPOINT generation data
-a filename	Coord file (optional), if not defined it will look for the coord file from the current folder
-n	Name of the calculation in the data base (optional), if not defined the calculations' output file name will be used
-d desc	Description of the calculation in the data base (optional), if not defined the calculations' file name will used.
--auto	Autogenerate current path into Create module (optional). Refer to the -auto parameter section.
-neb	Upload Nudged Elastic Band calculation, see more at: Uploading NEB/DIM calculations section
-dim	Upload Dimmer calculation, see more at: Uploading NEB/DIM calculations section

Examples

Uploads a calculation and sets identical name and description as the parent folder. It will capture INCAR and OUTCAR files by default

bash

$ loadvasp

Automatically generates parent folder structure and uploads calculation and sets identical name and description as the parent folder. It will capture INCAR and OUTCAR files by default, and will attach report.pdf file to calculation.

bash

$ loadvasp -a report.pdf --auto

Uploads calculation and associates its KPOINTS and DOSCAR files, sets name and description to opt1. It will capture INCAR and OUTCAR files by default

bash

$  loadvasp -n opt1 -d opt1 -kp KPOINTS -dc DOSCAR

Upload calculation set name and description to opt2. Will capture INCAR2 and OUTCAR2 files, because we set -i and -o parameters.

bash

$  loadvasp -i INCAR2 -o OUTCAR2 -n opt2 -d opt2 -kp KPOINTS -dc DOSCAR

Uploading VASP NEB/DIM calculation

NEB

The nudged elastic band (NEB) is a method for finding saddle points and minimum energy paths between known reactants and products. The method works by optimizing a number of intermediate images along the reaction path.1 This kind of calculation generates multiple output files (images) inside a collection of numbered subfolders. To upload this kind of calculations we will set -neb parameter on base folder. loadvasp script will expect at last this file structure, it will iterate all XX folders and concatenate all outcar files.

text

   .
   ├── 00
   │   └── OUTCAR
   ├── 01
   │   └── OUTCAR
   ├── 02
   │   └── OUTCAR
   ├── 03
   │   └── OUTCAR
   ├── 04
   │   └── OUTCAR
   ├── 05
   │   └── OUTCAR
   ├── 06
   │   └── OUTCAR
   └── INCAR

Example of a NEB calculation upload: Upload NEB, attach KPOINTS file information and set NEB-1 as name and description.

bash

$ loadvasp -neb -kp KPOINTS -n NEB-1-2 -d NEB-1-2

DIM

The dimer method is one of the min-mode following methods that allows the user to start from any initial configuration and search for a nearby saddle point. This method can also be used to start from a minimum basin and search in random directions for saddle points.2 We can just upload calculation as a normal single calculation or we can use -dim parameter if we already have initial and final state calculations, so we must set a folder structure like this:

text

   .
   ├── IS
   │   └── OUTCAR
   ├── TS
   │   ├── INCAR
   │   └── OUTCAR
   └── FS
       └── OUTCAR

Example of a DIM calculation upload: Upload Dimmer, attach KPOINTS and DOSCAR information and set NO_dim as name and description.

bash

   $ loadvasp -dim -kp KPOINTS -dc TS/DOSCAR -n NO_dim -d NO_dim

Molden orbitals file generation

Along with input, output and additional files. This script allows generating a molden-format file that contains calculation molecular orbitals. If we use this flag, uploaded calculations will also display molecular orbitals on JSmol viewer. To generate such file, we must first edit the loadorca script file that resides on the shell client folder. First lines define multiple orca_2mkl_X_X_X variables.

bash

orca_2mkl_2_8="/opt/ORCA2_8/orca_x86_64_exe_r2131/orca_2mkl"
orca_2mkl_2_9_0="/opt/ORCA2_9/orca_x86_64_exe_r2131/orca_2mkl"
orca_2mkl_3_0_0=
orca_2mkl_3_0_1=

We must set the correct path to this script file to match your file system configuration. orca_2mkl is installed along with Orca software. Be careful to define as much variables and paths for each installed Orca version on yous system. If you use -molden parameter on a Orca v2.8 output file and its parameter is undefined, wrong or points a different version (2.9, 3.0, ...), it will fail to work.

Examples

Upload calculation ete using ete.inp and ete.out files

bash

$ loadorca -i ete.inp -o ete.out -n "ete optimization" -d "Optimization ete"

Upload calculation named ncs2 using ncs2.inp and ncs2.out files, name and description came from parent folder, then build molden molecular orbital files and upload it.

bash

$ pwd
/home/user/Desktop/ncs2
$ loadorca -i ncs2.inp -o ncs2.out -molden

Upload calculation and automatically build its parent folder, calculation name and description will be same as parent folder

bash

$ loadorca -i ete.inp -o ete.out --auto

Additional commands

--auto parameter

In some situations our calculations lay inside a complex folder structure, under a high number of nested subfolders. Such project structure can be generated via the Create web interface or using the Create shell client commands, like cpro, cdpro and pwdpro. This can be a time-consuming process, so we can use the -auto parameter to generate such structure for us. Imagine that we want to upload a calculation inside a path from a folder mounted like this:

text

/home/user/mnt_cluster/metOH-oxidation/MoO2/metOH/TS1_NEB/02/reopt/freq

Generating such project hierarchy via shell commands (excluding $HOME) will be like this

bash

$  cpro -n metOH-oxidation -d metOH-oxidation    
$  cdpro metOH-oxidation    
$  cpro -n MoO2 -d MoO2    
$  cdpro MoO2    
$  cpro -n metOH -d metOH    
$  cdpro metOH    
$  cpro -n TS1_NEB -d TS1_NEB    
$  cdpro TS1_NEB    
$  cpro -n 02 -d 02    
$  cdpro 02    
$  cpro -n reopt -d reopt    
$  cdpro reopt
$  cpro -n freq -d freq    
$  cdpro freq    
$  loadgauss -i input.in -o output -n freq1 -d freq1

Using -auto parameter can be as simple as this

bash

$  cd /home/user/mnt_cluster/metOH-oxidation/MoO2/metOH/TS1_NEB/02/reopt/freq
$  loadgauss -i input.in -o output -n freq1 -d freq1 **-auto**

Generated projects path will generate also mnt_cluster project, because -auto parameter excludes $HOME. If we want to exclude mnt_cluster folder or our folder is mounted in another path that does not contain a $HOME path like /mnt/cluster/... we can edit our upload script loadXXXX:

bash

#On auto mode we will generate a project path, navigate inside and then upload calculation
if [ $auto -gt 0 ]; then
    moveBasePath
    full_path="$(cd "$(dirname "$output")"; pwd)"   #Will use 'output' file parent folders
    home_path="$(cd $HOME_PATH/mnt_cluster; pwd)"   #Set this home_path if uploading from /home/user/mnt_cluster
    home_path="$(cd /mnt/cluster; pwd)"             #Set this home_path if uploading from /mnt/cluster


    partial_path="${full_path/$home_path/''}"         #Remove user home folder
    partial_path="${partial_path//[-@\$\%\& \"]/_}"   #Replace special characters and blank spaces by underscore
    if [ $verbose -gt 0 ]; then
        echo "Generating path : "$partial_path
    fi
    projects=$(echo $partial_path | tr "/" "\n")
    for project in $projects
    do
        if [ $project = "''" -o $project = "" ]; then
          continue
        fi
        project="${project//[-@\$\%\&\"\' ]/_}"
        createpro="cpro -n "$project" -d "$project
        changepro="cdpro "$project
        executeRepCommand "$REP_SCRIPTS/exe-rep-command $changepro" ""     #Try cdpro to project, if it fails, we'll create this project
        if [ ! $retval -eq  0 ]; then
        executeRepCommand "$REP_SCRIPTS/exe-rep-command $createpro" ""
            executeRepCommand "$REP_SCRIPTS/exe-rep-command $changepro" ""
        fi
    done
fi

getproject

This script is an example of how the shell client tools can be used in order to retrieve, query or manipulate content that is inside Create module.

It retrieves a complete project content using the shell client commands. Project names will be prepended with p_ and calculations with c_ to ease its grouping and reading.

Must be run using the source command to be effective. The project full path must be provided as parameter, user must be the owner of that project or at least have read rights on it.

bash

$  source getproject /db/username/hexenol

To execute it outside the shell client folder, append the path to the shell client to your PATH environment variable.

Shell upload automation

We can attach these lines to our calculation job scripts, so after the calculation software finishes its processing, it gets uploaded automatically into ioChem-BD, making this step totally unattended.

Consider adding more verification steps inside upload scripts to avoid uploading erroneous calculations like premature exits, program crashes, not converged optimizations, etc.

In these examples, we consider that the shell client resides on $HOME/shell:

Gaussian job submit file example

bash

#!/bin/bash 
#\` -pe smp\* 12
#\$ -N test
#\$ -cwd
input=input.in 
output=output.out

/home/programs/bin/gaussian09.sh C01 $input $output
. $HOME/shell/start-rep-shell
loadgauss -i $input -o $output -n $output -d $output --auto
exit-rep

Numbered lines do:

Connect to Create
Upload calculation using Gaussian script and $input and $output parameters (builds path automatically)
Disconnect from Create

Turbomole job submit file example

bash

#!/bin/bash

#$ -pe smp* 1-
#$ -cwd
#$ -q mag14.q

. /home/programs/bin/turbomole.sh 6.6

export TURBOTMPDIR=$TMPDIR

cp HILL/* .
/usr/bin/time -o time_output dscf

output=$(basename $SGE_STDOUT_PATH)
. $HOME/shell/start-rep-shell
loadturbo -o $output --auto
exit-rep

Numbered lines do:

Connect to Create
Upload calculation using turbomole script and $output parameters
Disconnect from Create

Recursive upload

We can take advantage of shell scripting to automate calculation upload of multiple nested folders and subfolders.

One calculation per folder

This is an example script that uploads a group of ADF calculations starting from current folder.
Restrictions:

There must be only one input and ouput file inside each folder,
Uploaded calculations will have its name same as its parent folder name.

We can customize which input and output files are captured setting wildcards *.in and *.out.

bash

#!/bin/bash
. start-rep-shell                           # <---Please append full path to start-rep-shell command
 for folder in $(find  `pwd` -type d); do
     echo "Processing folder :" $folder
     inputfile="$(find  $folder -maxdepth 1  -name '*.in' -printf "%f\n")"
     outputfile="$(find $folder -maxdepth 1  -name '*.out' -printf "%f\n")"
     if [ -z $inputfile ]; then
    echo "  Not matching files"
     else
       echo "   Input file "$inputfile
       echo "   Output file "$outputfile
       cd $folder
       loadadf --auto -i $inputfile -o $outputfile
     fi
done
exit-rep

We can derive previous script into more sophisticated versions.

Multiple calculations per folder

The following script navigates inside all child folders, it search for all input and output files inside each folder and then uploads them. This script allows setting file extensions for input and output files.
Restrictions:

Input and output files of the same calculation must have same name (and different extension)
Uploaded calculation will be named as input file (to avoid name collisions)

bash

#!/bin/bash
#Replace this variables to suit your naming convention
INPUT_FILE_EXTENSION=in
OUTPUT_FILE_EXTENSION=out
. start-rep-shell                         # <--- Please append full path to start-rep-shell command
 for folder in $(find  `pwd` -type d); do
    echo "Processing folder :" $folder
    for inputfile in $(find  $folder -maxdepth 1  -name "*.$INPUT_FILE_EXTENSION" -printf "%f\n"); do
        filename=$(echo $inputfile | sed "s/\.$INPUT_FILE_EXTENSION//")
        outputfile="$filename.$OUTPUT_FILE_EXTENSION"
        if [ -z $outputfile ]; then
            echo "  Not matching output file "$outputfile
        else
            cd $folder
            loadgauss --auto -i $inputfile -o $outputfile -n $filename -d $filename
        fi
    done
done
exit-rep

Using the shell client

Shell automated scripts ​

Per file type ​

loadadf ​

Examples ​

loadams ​

Examples ​

loadamber ​

Examples ​

loadcastep ​

Examples ​

loadgauss ​

loadgromacs ​

Examples ​

loadgronor ​

Examples ​

loadgrrm ​

loadlammps ​

Examples ​

loadmolcas ​

loadmopac ​

loadorca ​

loadqespresso ​

Examples ​

Absorption spectra calculations ​

Example ​

Band structure calculations ​

Examples ​

Projected Density of States calculations ​

Example ​

Phonon dispersion ​

Example ​

Phonon DOS ​

Example ​

loadturbo ​

Multiple step calculation ​

Examples ​

loadsiesta ​

Examples ​

loadvasp ​

Examples ​

Uploading VASP NEB/DIM calculation ​

NEB ​

DIM ​

Molden orbitals file generation ​

Examples ​

Additional commands ​

--auto parameter ​

getproject ​

Shell upload automation ​

Gaussian job submit file example ​

Turbomole job submit file example ​

Recursive upload ​

One calculation per folder ​

Multiple calculations per folder ​

Shell automated scripts

Per file type

loadadf

Examples

loadams

Examples

loadamber

Examples

loadcastep

Examples

loadgauss

loadgromacs

Examples

loadgronor

Examples

loadgrrm

loadlammps

Examples

loadmolcas

loadmopac

loadorca

loadqespresso

Examples

Absorption spectra calculations

Example

Band structure calculations

Examples

Projected Density of States calculations

Example

Phonon dispersion

Example

Phonon DOS

Example

loadturbo

Multiple step calculation

Examples

loadsiesta

Examples

loadvasp

Examples

Uploading VASP NEB/DIM calculation

NEB

DIM

Molden orbitals file generation

Examples

Additional commands

--auto parameter

getproject

Shell upload automation

Gaussian job submit file example

Turbomole job submit file example

Recursive upload

One calculation per folder

Multiple calculations per folder