### Input text example for calculation.setup Source: https://docs.iochem-bd.org/data/codes/xtb/calculation.setup-d3e54022.html Example input text showing the calculation setup section from an xtb log file, including program call, coordinate file, and omp threads. ```text ------------------------------------------------- | Calculation Setup | ------------------------------------------------- program call : xtb water.xyz --input water.inp coordinate file : water.xyz omp threads : 8 ``` -------------------------------- ### Install libcap-progs and run postinstall.sh Source: https://docs.iochem-bd.org/doc/guides/installation/installation.html Install the libcap-progs package using zypper and then run the postinstall script again as root. ```bash root# zypper install libcap-progs root# BASEPATH/postinstall.sh ``` -------------------------------- ### Run the ioChem-BD installer script Source: https://docs.iochem-bd.org/doc/guides/installation/installation.html Execute the visual installer by moving to the BASE_PATH directory and running init.sh as the iochembd user. ```bash iochembd$ cd *BASEPATH* iochembd$ ./init.sh ``` -------------------------------- ### Example handle input Source: https://docs.iochem-bd.org/doc/faqs/admin/unpublish-collection.html Example of providing the handle identifier when prompted by the script. ```bash Handle (example: 100/300) : 100/1234 ``` -------------------------------- ### Example collection URL Source: https://docs.iochem-bd.org/doc/faqs/admin/unpublish-collection.html Example URL showing the handle identifier as the last part after /handle/. ```text https://your-domain.com/handle/100/1234 ``` -------------------------------- ### Pagination example request Source: https://docs.iochem-bd.org/api/browse.html Example GET request using pagination parameters limit and offset to retrieve items from a collection. ```http GET https://iochem-bd.iciq.es/rest/collections/19/items?limit=5&offset=10 ``` -------------------------------- ### Start the web service Source: https://docs.iochem-bd.org/doc/guides/other-operations/replace-https-certificate/with-existing-certificate.html Starts the Apache Tomcat service using the startup script after a successful certificate replacement. ```bash iochembd$ BASE_PATH/apache-tomcat/bin/startup.sh ``` -------------------------------- ### Private key file example (.key) Source: https://docs.iochem-bd.org/doc/guides/other-operations/replace-https-certificate/with-existing-certificate.html Example of a private key file in unencrypted PKCS#8 PEM format with .key extension. The content is truncated with '...' in the source. ```console -----BEGIN PRIVATE KEY----- MHcCAQEEIBdVHnnzZmJm+Z1HAYYOZlvnB8Dj8kVx9XBH+6UCWlGUoAoGCCqGSM49 AwEHoUQDQgAEThPp/xgEov0mKg2s0GII76VkZAcCc//3quAqzg+PuFKXgruaF7K ... -----END PRIVATE KEY----- ``` -------------------------------- ### Start ioChem-BD web service Source: https://docs.iochem-bd.org/doc/guides/other-operations/replace-https-certificate/validate-domain-owner.html Starts the ioChem-BD web service again after copying the file and editing the configuration. ```bash iochembd$ BASE_PATH/apache-tomcat/bin/startup.sh ``` -------------------------------- ### Start and stop the web service with Tomcat scripts Source: https://docs.iochem-bd.org/doc/guides/installation/installation.html Use these commands to start and stop the ioChem-BD web service. Replace BASE_PATH with the actual path. After starting, check BASE_PATH/apache-tomcat/logs/catalina.out for startup errors. ```console iochembd$ BASE_PATH/apache-tomcat/bin/startup.sh # to start service iochembd$ BASE_PATH/apache-tomcat/bin/shutdown.sh -force # to stop service ``` -------------------------------- ### Hard limit example with 2GB and 100MB Source: https://docs.iochem-bd.org/doc/faqs/admin/setup-upload-limits.html Example setting hard limits: 2GB for uploaded files, 100MB for output files, and assigning to users jdoe and dzavala. ```bash upload.max.file.size.hard = 2147483648 upload.max.output.file.size.hard = 104857600 upload.restriction.users.hard = jdoe:dzavala ``` -------------------------------- ### Intermediate certificates bundle example (.bundle) Source: https://docs.iochem-bd.org/doc/guides/other-operations/replace-https-certificate/with-existing-certificate.html Example of a bundle file containing three intermediate certificates in X.509 PEM format, ordered from most local to most global. The content is truncated with '....' in the source. ```console -----BEGIN CERTIFICATE----- .... -----END CERTIFICATE----- -----BEGIN CERTIFICATE----- .... -----END CERTIFICATE----- -----BEGIN CERTIFICATE----- .... -----END CERTIFICATE----- ``` -------------------------------- ### Start ioChem-BD web service Source: https://docs.iochem-bd.org/doc/guides/installation/migration-guide.html Run as the iochembd user to start the Apache Tomcat service. ```bash iochembd$ BASE_PATH/apache-tomcat/bin/startup.sh ``` -------------------------------- ### getxyz examples Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/shell-commands.html Examples of the getxyz command to retrieve the geometry of a calculation by ID, either to stdout or to a file. ```console $ 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 ``` -------------------------------- ### Initialize PostgreSQL database (initdb) Source: https://docs.iochem-bd.org/doc/guides/installation/installation.html Run as root to initialize the PostgreSQL database after installing the server and postgresql-contrib package. ```bash root# /sbin/service postgresql initdb ``` -------------------------------- ### Soft limit example with 500MB and 25MB Source: https://docs.iochem-bd.org/doc/faqs/admin/setup-upload-limits.html Example setting soft limits: 500MB for uploaded files and 25MB for output files. ```bash upload.max.file.size.soft = 524288000 # 500*1024*1024 in bytes upload.max.output.file.size.soft = 26214400 # 25*1024*1024 in bytes ``` -------------------------------- ### viewcalc examples Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/shell-commands.html Examples of the viewcalc command to display calculation information and optionally download files. The -f parameter requires -dcp to specify the download path. ```console $ 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 ``` -------------------------------- ### Update process log output Source: https://docs.iochem-bd.org/doc/faqs/admin/update-current-distribution.html Example output from the updater script showing successful update. The server starts automatically after the update completes. If the update fails, copy this output and send it to contact@iochem-bd.org. ```bash 17:01:09.543 [main] INFO update.UpdatePatch - Task: Running Ant target : update 17:03:42.600 [main] INFO utils.SqlRunner - Running update vxxx.SetCalculationOrdering 17:03:43.073 [main] INFO update.UpdatePatch - Task: Updating Browse dspace.cfg file 17:03:43.120 [main] INFO update.TomcatManager - Starting Apache Tomcat... <== Server started 17:03:43.128 [main] INFO utils.Utils - Running command:[/home/iochembd/iochem-bd/apache-tomcat/bin/startup.sh] 17:03:43.128 [main] INFO update.UpdateProcess - ioChem-BD updated to latest version. Update process finished. ``` -------------------------------- ### Install Ubuntu 24.04 via WSL Source: https://docs.iochem-bd.org/shell-client.html Install Ubuntu 24.04 from PowerShell. Follow the prompts to set up your Ubuntu username and password. ```powershell wsl --install -d Ubuntu-24.04 ``` -------------------------------- ### Install required software packages Source: https://docs.iochem-bd.org/doc/guides/installation/migration-guide.html Commands to install Java JDK 17, PostgreSQL (version 11 or newer), and libcap for privileged port access on the new machine. Includes alternatives for CentOS/Fedora/Rocky and Debian/Ubuntu distributions. ```bash # Install Java JDK 17 root# dnf install java-17-openjdk.x86_64 # For CentOS/Fedora/Rocky # or root# apt install openjdk-17-jdk # For Debian/Ubuntu # Install PostgreSQL (version 11 or newer) root# yum install postgresql-server postgresql # For CentOS/Fedora/Rocky # or root# apt-get install postgresql # For Debian/Ubuntu # Install libcap for privileged port access root# yum install libcap # For CentOS/Fedora/Rocky # or root# apt-get install libcap2-bin # For Debian/Ubuntu ``` -------------------------------- ### Public certificate file example (.crt) Source: https://docs.iochem-bd.org/doc/guides/other-operations/replace-https-certificate/with-existing-certificate.html Example of a public certificate file in X.509 PEM format with .crt extension. The content is truncated with '...' in the source. ```console -----BEGIN CERTIFICATE----- MIIE/zCCBGgCAg4CMA0GCSqGSIb3DQEBBQUAMIGbMQswCQYDVQQGEwJKUDEOMAwG A1UECBMFVG9reW8xEDAOBgNVBAcTB0NodW8ta3UxETAPBgNVBAoTCEZyYW5rNERE ... 3V1dbLU5id63lVD8sUEULyfWFGk3L+Uka5oiSsxwZhdIb/Q= -----END CERTIFICATE---- ``` -------------------------------- ### Start server manually Source: https://docs.iochem-bd.org/doc/faqs/admin/update-current-distribution.html Starts the Apache Tomcat server manually if the update process did not start it automatically. Use this only if the update did not end successfully. ```bash iochembd$ cd BASE_PATH/apache-tomcat/bin iochembd$ ./startup.sh ``` -------------------------------- ### Output XML for calculation.setup Source: https://docs.iochem-bd.org/data/codes/xtb/calculation.setup-d3e54022.html Example output XML generated by the template, showing the extracted parameters as scalar elements with dictRef attributes. ```xml program call xtb water.xyz --opt hostname p038 coordinate file water.xyz omp threads 24 ``` -------------------------------- ### Example news.html for Create module welcome page Source: https://docs.iochem-bd.org/doc/guides/other-operations/customizing-system-interface.html HTML file loaded as an independent file in the Create module welcome panel. Must be valid and well-formed. Contains commented maintenance alert that can be uncommented to notify users. ```html

Current version 1.1.0

View changelog
``` -------------------------------- ### sharepro command example with output Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/shell-commands.html Shows the sharepro command and its output listing shared projects with project ID, path, group, and permission. ```console $ sharepro Shared Projects: ================ Project_id Path Group Permission ------------------------------------------------------------------------ 449 /db/kpotts/turbomole fock_group WRITE 584 /db/slester/adf fock_group WRITE 628 /db/slester/turbomole/fetz fock_group FULLACCESS 635 /db/slester/turbomole/fluorophenol fock_group WRITE ``` -------------------------------- ### Initialize and configure PostgreSQL Source: https://docs.iochem-bd.org/doc/guides/installation/migration-guide.html Initialize PostgreSQL databases (only necessary on CentOS/Fedora/Rocky/RHEL), enable the service to start on boot, and edit pg_hba.conf to allow password authentication. The file path may vary by version and OS; create the file if it doesn't exist. ```bash # Initialize PostgreSQL databases (if not already done), only necessary on CentOS/Fedora/Rocky/RHEL root# postgresql-setup initdb # Configure PostgreSQL to start on boot root# systemctl enable postgresql # Edit pg_hba.conf to allow password authentication, folder names can vary depending on your version and OS # If file doesn't exist, just create it. root# vi /var/lib/postgresql/16/main/pg_hba.conf ``` -------------------------------- ### Check openssl version Source: https://docs.iochem-bd.org/doc/guides/other-operations/replace-https-certificate/with-existing-certificate.html Verify that openssl is installed and accessible in the PATH. Run this command as the same user that runs ioChem-BD. The output shows the installed version. ```bash iochembd$ openssl version OpenSSL 1.0.2h 3 May 2016 (or another version) ``` -------------------------------- ### xTB command-line input Source: https://docs.iochem-bd.org/data/codes/xtb/xtb.input-d3e65226.html Example of invoking xTB with a molecule file and options for charge, spin, GFN method, solvent, and Hessian calculation. ```bash xtb molecule.xyz --chrg -1 --uhf 2 --gfn 1 --alpb toluene --ohess ``` -------------------------------- ### ORCA input file example (run.inp) Source: https://docs.iochem-bd.org/data/codes/orca/input-d3e39394.html Example ORCA input file named run.inp, showing a Hartree-Fock calculation with def2-SVP basis, TightSCF, geometry optimization, a geometry constraint, and a custom basis for oxygen. ```orca ================================================================================ INPUT FILE ================================================================================ NAME = run.inp | 1> %PAL NPROCS 1 END | 2> ! HF def2-SVP TightSCF Opt | 3> | 4> %geom Constraints | 5> { A 1 0 2 90.0 C} | 6> end | 7> end | 8> | 9> %basis basis SV | 10> newGTO O "6-31G" end | 11> end | 12> | 13> * xyzfile 0 1 h2o.xyz | 14> | 15> | 16> | 17> | 18> ****END OF INPUT**** ================================================================================ ``` -------------------------------- ### loadgronor upload with custom input and output files Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/using-shell-client/shell-automated-scripts.html Behaves the same as the previous example but uploads different files rather than the default ones. ```bash $ loadgronor -n Sc2C82 -d "Sample upload" -i input2.in -o dimmer.cml ``` -------------------------------- ### Example base URL for URV university Source: https://docs.iochem-bd.org/api/create.html Example REST API base URL for the Create module at URV. ```text https://iochem-bd.urv.es/create/rest ``` -------------------------------- ### Spin density XML output example Source: https://docs.iochem-bd.org/data/codes/adf/multipole-d3e3977.html Example output for the spin density template, showing the XML structure with arrays for serial numbers, element types, and multipole moments (mdcm, mdcd, mdcq). ```xml 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 W W W W W W W W V W O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O -0.095556 -0.095556 -0.118334 -0.118334 -0.095556 -0.095556 -0.118334 -0.118334 0.026743 0.017092 0.001171 8.86E-4 0.009845 0.009845 0.009845 0.009845 0.018074 0.018074 0.018074 0.018074 -0.065793 -0.065793 -0.045436 -0.045436 0.018945 0.018945 -0.065793 -0.065793 -0.045436 -0.045436 0.018945 0.018945 0.007884 0.007884 0.008961 0.008961 -9.38E-4 6.87E-4 0.007884 0.007884 0.008961 0.008961 -0.079659 -0.079659 -0.096979 -0.096979 -0.079659 -0.079659 -0.096979 -0.096979 0.020389 0.011044 0.001927 7.46E-4 0.003208 0.003208 0.003208 0.003208 0.010174 0.010174 0.010174 0.010174 -0.05465 -0.05465 -0.040162 -0.040162 -0.002407 -0.002407 -0.05465 -0.05465 -0.040162 -0.040162 -0.002407 -0.002407 0.001339 0.001339 0.001586 0.001586 -0.002912 -9.96E-4 0.001339 0.001339 0.001586 0.001586 -0.0788 -0.0788 -0.097869 -0.097869 -0.0788 -0.0788 -0.097869 -0.097869 0.02355 0.014337 0.004075 0.006227 -1.7E-4 -1.7E-4 -1.7E-4 -1.7E-4 0.005147 0.005147 0.005147 0.005147 -0.055226 -0.055226 -0.039869 -0.039869 -6.52E-4 -6.52E-4 -0.055226 -0.055226 -0.039869 -0.039869 -6.52E-4 -6.52E-4 0.001951 0.001951 0.003487 0.003487 -5.85E-4 4.01E-4 0.001951 0.001951 0.003487 0.003487 ``` -------------------------------- ### Enable PostgreSQL service on boot Source: https://docs.iochem-bd.org/doc/guides/installation/installation.html Set PostgreSQL to start on server restart. Older versions use chkconfig, newer versions use systemctl. ```bash root# chkconfig --level 345 postgresql on # Older versions or root# systemctl enable --now postgresql # Newer versions ``` -------------------------------- ### loadamber with custom file names Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/using-shell-client/shell-automated-scripts.html Uploads custom files instead of the defaults, while setting the calculation name and description as in the previous example. ```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 ``` -------------------------------- ### Create administrator with dspace create-administrator Source: https://docs.iochem-bd.org/doc/faqs/admin/add-administrator.html Run this command from the browse/bin subfolder of the ioChem-BD installation. It prompts for email, name, and password, then confirms the account creation. ```bash $ cd browse/bin $ ./dspace create-administrator Creating an initial administrator account E-mail address: user@institution.org First name: Michael Last name: Knight Password will not display on screen. Password: ***** Again to confirm: ***** Is the above data correct? (y or n): y Administrator account created ``` -------------------------------- ### Run the Shell Client in WSL Source: https://docs.iochem-bd.org/shell-client.html Open your WSL Ubuntu terminal and run these commands to navigate and start the shell client. ```bash # Navigate to the directory cd # Navigate to the directory cd shell # Run the shell client . ./start-rep-shell ``` -------------------------------- ### ORCA input file example (ch2.inp) Source: https://docs.iochem-bd.org/data/codes/orca/input-d3e39394.html Example ORCA input file named ch2.inp, showing a multi-job input with two jobs using TZVPP basis, TightSCF, MR-DDC(3) method, and CASSCF with NEVPT2 correction. ```orca ================================================================================ INPUT FILE ================================================================================ NAME = ch2.inp | 1> ! TZVPP TightSCF mrddci3 | 2> * xyz 0 3 | 3> C 0 0 0 | 4> H 0.7 0.5 0 | 5> H -0.7 0.5 0 | 6> * | 7> | 8> %CASSCF nel 2 | 9> norb 2 | 10> nevpt2 true | 11> end | 12> | 13> $new_job | 14> ! TZVPP TightSCF mrddci3 | 15> * xyz 0 1 | 16> C 0 0 0 | 17> H 0.7 0.5 0 | 18> H -0.7 0.5 0 | 19> * | 20> | 21> %CASSCF nel 2 | 22> norb 2 | 23> nevpt2 true | 24> end | 25> | 26> | 27> | 28> | 29> ****END OF INPUT**** ================================================================================ ``` -------------------------------- ### Pagination example: GET /rest/collections?limit=5&offset=10 Source: https://docs.iochem-bd.org/api/find.html Shows how to paginate results from endpoints that return arrays by adding the limit and offset query parameters. The default limit is 100 and the default offset is 0. ```http GET https://www.iochem-bd.org/rest/collections?limit=5&offset=10 ``` -------------------------------- ### Connect to repository with start-rep-shell Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/shell-commands.html Use 'source start-rep-shell' or '. start-rep-shell' to connect to the repository. Must be preceded by 'source' or '.' to work. ```console $ source start-rep-shell #Connect to repository using long format $ . start-rep-shell #Connect to repository using short format ``` -------------------------------- ### Quantum Espresso input file for spin-polarized DFT+U calculation Source: https://docs.iochem-bd.org/data/codes/quantumespresso/qespresso.input-d3e63562.html Full example input for a Quantum Espresso calculation with relaxation, spin polarization, and Hubbard U corrections. Includes CONTROL, SYSTEM, ELECTRONS, IONS namelists, plus ATOMIC_SPECIES and ATOMIC_POSITIONS sections. Note the comments about Hubbard_J0 being ignored and lda_plus_u_kind=0. ```fortran &CONTROL calculation = 'relax' , restart_mode = 'from_scratch' , wf_collect = .true. , prefix = 'Fe.USPP.001_2x2_145_vaccum' , verbosity = 'high' , etot_conv_thr = 1.0D-9 , forc_conv_thr = 1.0D-5 , tstress = .true. , tprnfor = .true. , dipfield = .true. , / &SYSTEM ibrav = 14, A = 10.2304 , B = 10.2304 , C = 28.3548 , cosAB = -0.5 , cosAC = 0 , cosBC = 0 , nat = 120 , ntyp = 3, ecutwfc = 40.0 , ecutrho = 320.0 , input_dft = 'PBE' , occupations = 'smearing' , degauss = 0.02 , smearing = 'gaussian' , nspin = 2 , starting_magnetization(1) = 1.0, starting_magnetization(2) = -1.0, starting_magnetization(3) = 0.0, lda_plus_u = .true. , lda_plus_u_kind = 0 , !type 2 not implemented, ignores J Hubbard_U(1) = 4.2, Hubbard_U(2) = 4.2, Hubbard_J0(1) = 0.0, !Is ignored! Hubbard_J0(2) = 0.0, !Is ignored! / &ELECTRONS electron_maxstep = 800, conv_thr_init = 1e-4 , conv_thr = 1e-9 , startingpot = 'atomic' , startingwfc = 'random' , adaptive_thr = .true. , mixing_beta = 0.14, diagonalization = 'cg' , / &IONS ion_dynamics = 'bfgs' , trust_radius_min = 1.D-5 , / ATOMIC_SPECIES Fe1 55.84500 Fe.pbe-sp-van_ak.UPF Fe2 55.84500 Fe.pbe-sp-van_ak.UPF O 15.99990 O.pbe-van_ak.UPF ATOMIC_POSITIONS crystal Fe2 0.166663898 0.333337143 0.409451359 Fe1 -0.000002447 0.000003614 0.451051249 Fe2 0.166660000 0.333340000 0.061240000 0 0 0 Fe1 0.333340000 0.166670000 0.000000000 0 0 0 Fe2 0.000000000 0.000000000 0.081950000 0 0 0 Fe1 0.333340000 0.166670000 0.143190000 0 0 0 Fe2 -0.000005343 0.000005009 0.225538724 Fe1 0.166660000 0.333340000 0.163900000 0 0 0 Fe2 0.333327346 0.166671997 0.246584781 Fe1 0.166662601 0.333338569 0.308651469 Fe2 0.333330456 0.166670754 0.396298854 Fe1 -0.000003950 0.000004548 0.328137387 O 0.152380000 0.000000000 0.030620000 0 0 0 O 0.000000000 0.152380000 0.030620000 0 0 0 O 0.493114653 0.320585686 0.442431216 O 0.327462379 0.006886637 0.442431019 O 0.179415420 0.172539124 0.442431172 O 0.347620000 0.347620000 0.030620000 0 0 0 O 0.485638190 0.166610684 0.194910500 O 0.333389960 0.319042226 0.194910254 O 0.319050000 0.485720000 0.112570000 0 0 0 O 0.166660000 0.180960000 0.112570000 0 0 0 O 0.014280000 0.333340000 0.112570000 0 0 0 O 0.180958728 0.014363721 0.194910054 O 0.321788281 0.333225075 0.360556075 O 0.166775360 0.488574984 0.360556183 O 0.152375882 0.153125384 0.277338078 O 0.000735347 0.347624423 0.277338029 O 0.346875072 -0.000734132 0.277338119 O 0.011425967 0.178212850 0.360556085 Fe2 0.666663975 0.333337151 0.409451269 Fe1 0.499997414 0.000003470 0.451051255 Fe2 0.666660000 0.333340000 0.061240000 0 0 0 Fe1 0.833330000 0.166670000 0.000000000 0 0 0 Fe2 0.500000000 0.000000000 0.081950000 0 0 0 Fe1 0.833330000 0.166670000 0.143190000 0 0 0 Fe2 0.499993955 0.000003637 0.225539296 Fe1 0.666660000 0.333340000 0.163900000 0 0 0 Fe2 0.833328682 0.166672502 0.246584853 Fe1 0.666662589 0.333338201 0.308651364 Fe2 0.833330375 0.166670545 0.396298876 Fe1 0.499996285 0.000004543 0.328137528 O 0.652380000 0.000000000 0.030620000 0 0 0 ``` -------------------------------- ### start-rep-shell Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/shell-commands.html Connects to the repository. Must be preceded by 'source' or '.' to work. ```APIDOC ## start-rep-shell ### Description Connects to the repository. Must be preceded by `source` or `.` (dot) to work. ### Usage ``` $ source start-rep-shell #Connect to repository using long format $ . start-rep-shell #Connect to repository using short format ``` ``` -------------------------------- ### findpro command examples Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/shell-commands.html Shows usage of findpro with -n and -d parameters for case-insensitive substring search. At least one parameter is required, each at least 3 characters long. ```console $ findpro -n metanol # Finds projects containing "metanol" in their name $ findpro -d alcohol # Finds projects containing "alcohol" in their description $ findpro -n freq -d opt # Finds projects matching both name and description criteria ``` -------------------------------- ### ORCA input file example with CASSCF and multiple jobs Source: https://docs.iochem-bd.org/data/codes/orca/input-d3e40560.html Example ORCA input file (ch2.inp) showing two jobs: the first with a triplet state and CASSCF(2,2) with NEVPT2, and a second job using $new_job with a singlet state and the same CASSCF settings. The input is terminated by the '****END OF INPUT****' marker. ```orca ================================================================================ INPUT FILE ================================================================================ NAME = ch2.inp | 1> ! TZVPP TightSCF mrddci3 | 2> * xyz 0 3 | 3> C 0 0 0 | 4> H 0.7 0.5 0 | 5> H -0.7 0.5 0 | 6> * | 7> | 8> %CASSCF nel 2 | 9> norb 2 | 10> nevpt2 true | 11> end | 12> | 13> $new_job | 14> ! TZVPP TightSCF mrddci3 | 15> * xyz 0 1 | 16> C 0 0 0 | 17> H 0.7 0.5 0 | 18> H -0.7 0.5 0 | 19> * | 20> | 21> %CASSCF nel 2 | 22> norb 2 | 23> nevpt2 true | 24> end | 25> | 26> | 27> | 28> | 29> ****END OF INPUT**** ================================================================================ ``` -------------------------------- ### Example output for steps template Source: https://docs.iochem-bd.org/data/codes/lammps/steps-d3e32946.html Shows the CML output structure for the steps template, containing arrays for step, time, cpu, potential energy, kinetic energy, total energy, enthalpy, temperature, pressure, volume, density, and cell parameters. ```xml 0 100 200 300 400 500 600 700 800 900 1000 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0 10.095992 20.191317 30.431144 40.396035 50.500032 60.471975 70.601622 80.577136 90.683058 100.6761 -251712.73 -251781.03 -251712.1 -251580.75 -251671.5 -251625.13 -251680.41 -251695.4 -251726.63 -251658.44 -251714.12 0 252.98733 292.144 280.09057 331.92131 303.80671 305.6443 318.9768 292.77818 317.04192 306.74721 -251712.73 -251528.04 -251419.96 -251300.66 -251339.58 -251321.32 -251374.77 -251376.42 -251433.85 -251341.4 -251407.37 -249625.61 -250233.15 -251705.83 -251269.69 -251553.22 -251326.68 -251371.43 -251297.31 -251324.23 -251443.23 -251592.69 0 318.60575 367.91867 352.73888 418.01318 382.60638 384.9206 401.71121 368.71733 399.27446 386.30957 41011.594 24605.457 -5323.8838 577.41271 -3972.446 -100.16461 62.366674 1482.807 2051.9063 -1900.723 -3454.2197 81536.298 84316.37 86029.812 85939.533 86165.151 85679.38 85592.738 85479.476 85596.807 85834.957 85958.138 11.26254 10.891192 10.674274 10.685488 10.657508 10.717932 10.728782 10.742998 10.728272 10.698506 10.683175 43.362768 43.865149 44.159056 44.136137 44.204662 44.176884 44.146663 44.092644 44.104736 44.151242 44.163795 43.362768 43.843403 44.12428 44.151916 44.229721 44.122329 44.018522 44.000189 44.072441 44.128413 44.161229 43.362768 43.841909 44.153099 44.104355 44.075904 43.962795 44.050933 44.064688 44.041728 44.062526 44.080492 90 90.083248 90.295318 90.523589 90.692058 90.810811 90.757753 90.778967 90.879925 90.945548 90.94757 90 89.926643 89.924338 89.911426 89.940226 89.987609 90.043298 90.127865 90.224179 90.276751 90.31916 90 89.904346 89.771092 89.545686 89.451883 89.464337 89.54896 89.643866 89.733529 89.811958 89.881871 ``` -------------------------------- ### xTB xcontrol file input Source: https://docs.iochem-bd.org/data/codes/xtb/xtb.input-d3e65226.html Example of an xcontrol file specifying charge, spin, and GFN method settings. ```plaintext $chrg 0 $spin 1 $gfn method=2 $end ``` -------------------------------- ### STARTTLS SMTP configuration in dspace.cfg Source: https://docs.iochem-bd.org/doc/faqs/admin/configure-email.html Set mail.server.port to 587 and configure mail.extraproperties with STARTTLS enabled and required. If this setup doesn't work, try also setting the SSL protocol as shown in the second block. ```bash mail.server.port = 587 mail.extraproperties = mail.smtp.starttls.enable=true, \ mail.smtp.socketFactory.port=587, \ mail.smtp.starttls.required=true ``` ```bash mail.server.port = 587 mail.extraproperties = mail.smtp.starttls.enable=true, \ mail.smtp.socketFactory.port=587, \ mail.smtp.ssl.protocols=TLSv1.2, \ mail.smtp.starttls.required=true ``` -------------------------------- ### source start-rep-shell Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/shell-commands.html Connects to the repository. ```APIDOC ## source start-rep-shell ### Description Connects to the repository. ### Command `source start-rep-shell` ### Parameters - `-h` (flag) - Optional - Displays help message with wider description of usage. ``` -------------------------------- ### loadamber with name and description Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/using-shell-client/shell-automated-scripts.html Uploads all matching files in the directory, setting the calculation name to "Au-CoO-H2O" and description to "Sample upload". ```bash $ loadamber -n Au-CoO-H2O -d "Sample upload" ``` -------------------------------- ### GET /create/rest/project/descendant Source: https://docs.iochem-bd.org/api/create.html Gets children of a project based on type and depth parameters. Requires bearer authentication. ```APIDOC ## GET /create/rest/project/descendant ### Description Gets children of a project. Handles hierarchy based on type and depth parameters. ### Method GET ### Endpoint /create/rest/project/descendant ### Parameters #### Query Parameters - **id** (integer) - Required - id - **type** (string) - Optional - type of search ( calculation, project ) - **depth** (string) - Optional - depth of search ( 1, 2 ... or all ) ### Response #### Success Response (200) Successful operation #### Error Responses - **400** - Invalid ID supplied - **404** - Project not found ### Security - bearerAuth ``` -------------------------------- ### loadxtb with name and description Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/using-shell-client/shell-automated-scripts.html Uploads matching files and sets calculation name to 'water' and description to 'Water geometry optimization'. ```bash $ loadxtb -n water -d "Water geometry optimization" ``` -------------------------------- ### Upload band structure calculation with spin up/down files Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/using-shell-client/shell-automated-scripts.html Uploads a band structure calculation with separate spin up and down band files. Provide two -b parameters, spin up first, spin down second. The input and output files follow the same order as the single-band example. ```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" ``` -------------------------------- ### Example custom upload error message Source: https://docs.iochem-bd.org/doc/faqs/admin/setup-upload-limits.html Example message instructing users to contact admin for extended limit. ```bash upload.max.file.size.message = Please contact with admin1@iochem-bd.org to request an extended upload limit. ``` -------------------------------- ### DIM upload command with loadvasp Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/using-shell-client/shell-automated-scripts.html Example command to upload a DIM calculation using the -dim parameter, attach KPOINTS and DOSCAR (from TS/DOSCAR) files, and set name and description to 'NO_dim'. ```bash $ loadvasp -dim -kp KPOINTS -dc TS/DOSCAR -n NO_dim -d NO_dim ``` -------------------------------- ### loadsiesta upload example Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/using-shell-client/shell-automated-scripts.html Uploads a SIESTA calculation with two input files and an XML output file, specifying name and description. ```bash $ loadsiesta -n h2o -d "Sample upload" -i h2o.fdf -i Default.fdf -o h2o.xml ``` -------------------------------- ### Source start-rep-shell Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/using-shell-client.html Use the source command to load the shell client commands into the current shell. ```console $ source start-rep-shell ```