CENSO 2.1.2

• Fixed some bugs from version 2.1.1

Full Changelog: v2.1.1...v2.1.2

CENSO 2.1.1

Added some minor fixes as well as a refactor of the whole part/ensembledata/results structure.

• Results are no longer stored in the MoleculeData objects but saved in CensoPart instances, which are created upon running a part. References to these instances are then appended to the EnsembleData object.
• In case you used custom scripts for running CENSO, you will have to revise them for the new version.
• Json outputs now contain more information and are structured slightly differently than before. Results can be found under the "results" key.
• It is now finally possible to use the --loglevel flag correctly.
• The omp setting was removed from the general settings section and can instead be found in Config.OMP from the params module. Nothing changes for the command line version.

What's Changed

• censo 2.1.1 by @lmseidler in #63

Full Changelog: v2.1.0...v2.1.1

CENSO 2.1.0

Release of CENSO version 2.1. Added TURBOMOLE implementation + COSMO-RS ontop of the already existing ORCA implementation. Also added capability to reload data from previous runs using the --reload cml option or the EnsembleData.read_output method, respectively. Furthermore, the logger's loglevel can now be set using --loglevel. Some bugfixes carried over from updates of CENSO 2.0.

What's Changed

• CENSO 2.1 by @lmseidler in #60

Full Changelog: v2.0.1...v2.1.0

CENSO in version 1.2.0

• new command-line flags: ⚠️ a new censorc should be created because of the renaming of arguments
  -part2_P_threshold (formerly part2_threshold): Sets the Boltzmann threshold in percent (between 1 and 100) up to which all remaining conformers are considered further in the following parts (i.e., high-level free energy (part3), NMR (part4) or OR (part5)).
  -part2_threshold (formerly opt_limit): The intermediate threshold in kcal/mol applied during the geometry optimization in part2 below which conformers are optimized.
  -prog2opt choose the QM-Code used for the geometry optimization of structures in part2 independently of the QM-Code used for single-point and or solvation contribution calculation in part2. For example, optimize with r2scan-3c/SMD in ORCA but calculate single-point and solvation contribution with TURBOMOLE and COSMO-RS. This requires the functional func to be available in both QM programs!
  -consider_unconverged When the geometry optimization (part2) is restarted and unconverged conformers should be included in the restart, this option considers the previously sorted out conformers again. (Useful if the threshold part2_threshold is increased).
• A new file censo_ORCA_editable.dat is introduced to the directory ~/.censo_assets/ and will be created upon the next start of censo. It contains ORCA keywords which will be added to every ORCA-input generated by CENSO, therefore it can only contain global information independent of specific calculation types. There exists no check for misspelling so typos will lead to crashes. The intention is to enable the user to specify additional input like for example "NOTRAH". This feature is considered to be an expert user option. The file looks like this:

! smallprint printgap noloewdin
! NOSOSCF
%MaxCore 8000
%output
      print[P_BondOrder_M] 1
      print[P_Mayer] 1
      print[P_basis] 2
end

• Censo is now checking if the home directory of the user is read-only, in which case censo will not create user-editable files. These can however be copied manually to the directory ~/.censo_assets/ and are available in the (github) folder censo_assets. Concerns: censo_nmr_ref.json, censo_solvents.json and censo_ORCA_editable.dat.
• added information for the functional revtpss-novdw, available functionals can be listed by using censo -tutorial.
• added information for the solvents chbr3 and dibromoethane
• removed the redundant charge and uhf information in the file enso.json, as the charge and number of unpaired electrons can only be set globally.
• For large ensembles during the geometry optimization (part2) CENSO now saves information on converged results in between optimization cycles to the file enso.json. This ensures that data will not be lost if CENSO should be terminated for any reason.
• Added error handling concerning python OSError during execution in order to keep the python instance alive, if there is some IOError i.e., the hard drive has no space left or related errors
• improved the creation of new .censorc global configuration files. This does now ask for the main QM program and sets defaults accordingly.

An existing .censorc has been found in /home/USER/.censorc
Do you want to copy existing program path information to the new remote configuration file?
Please type 'yes' or 'no':
yes

Please chose your QM code applied in parts 0-2 either TURBOMOLE (TM) or ORCA (ORCA) or decide later (later):
tm

A new ensorc was written into the current directory file: censorc_new!
You have to adjust the settings to your needs and it is mandatory to correctly set the program paths!
Additionally move the file to the correct filename: '.censorc'
and place it either in your /home/$USER/ or current directory.

All done!

• better error output for TURBOMOLE input generation, i.e., cefine.out is written if cefine should crash.
• improved tracking which QM codes are required to perform the requested calculation

CENSO in version 1.1.2

• Updated the input generation for ORCA5.0.1
◇ it is necessary to provide the ORCA version number to the censorc (otherwise the old input generation is choosen!)

ORCA: /tmp1/orca_5_0_1_linux_x86-64_openmpi411
ORCA version: 5.0.1

◇ r2SCAN-3c is supported by ORCA >= 5.0.0
◇ usage of the new DEFGRIDS (please check if the grid settings are appropriate for your study)
• Fix in .anmrrc generation for gas-phase calculations
• Fix in xtb-driver orcapath

CENSO in version 1.1.1

improved solvent handling (#15)


    - added solvents dichloroethane and octane to solvents list
    - print clearer warning if solvent is not parameterized for the respective solvent model (and a replacement solvent is employed)
    - improved the automated SI generation (e.g. ALPB information)
    - improved the printout of the available density functionals in the tutorial option crenso -tutorial
    - added an option for the calculation of vapor_pressure in combination with crenso 1.0.4 and COSMO-RS

* vapor pressure calculation possible for COSMO-RS file same_solvents.json contains information on other needed solvent parameters
  e.g.
          {
          "same":{
            "cosmors": ["same", "same"],
            "dcosmors": [null, "thf"],
            "xtb": [null, "thf"],
            "cpcm": [null, null],
            "smd": [null, null],
            "DC": 7.8
          }
        }

CENSO in version 1.1.0

⚠️This release introduces new handling of density functional names. Therefore a new .censorc and ~/.censo_assets/censo_nmr_ref.json should be created.

• new density functional name handling, which also enables use of different dispersion corrections
for information on the available functionals call censo -tutorial and then choose functionals in the tutorial menu.
• fix for pyinstaller created binaries on some suse systems concerning LD_LIBRARY_PATH
• improved automated supporting information creation
• restart at different temperature possible if other temperatures have been calculated before (get Boltzmann factors at different temperatures), be aware that the sorting of an ensemble within CENSO is threshold dependent and that for higher temperatures larger thresholds are required
• gbsa_gsolv, alpb_gsolv, smd_gsolv from now on can be used at different temperatures, but they do not have a temperature dependence!
• updated nmr_ref data (shielding constants) to include the basisS information
• printout number of structures in part4/ part5
• more precise error output

CENSO in version 1.0.9

devel (#12)

• work in progress: automatic supporting information (SI) generation (with bib entries)
• new printout showing the number of conformers within an energy window
• symmetry number correction (for part1) because of (DFT) unoptimized geometries
• the configuration file location information is saved and automatically reloaded on restart
• printing command line argument call at program startup
• experimental “read only” feature to fill the enso.json information by only reading the output of previous calculations (the program input arguments have to be exactly the same!)
• fixed NMR shielding constant calculations and MORead
• NMR new printout of min and max calculated shielding constants per investigated nuclei
• OR new printout of min and max OR value and corresponding conformers
• fixed balance option and wrong xtb call
• improved restarting of optical rotation calculations
• tutorial option has details on solvents and naming within CENSO, and information on functionals for OR is updated
• improved optimization routine

CENSO in version 1.0.8

symmetry in G_mRRHO (#10)

• better time printout, which also includes restarts
• symmetry in the G_mRRHO contribution is always detected, but its contribution to S_rot can be switched on and off by CENSO -consider_sym without the need to recalculate
• if new censorc remote configuration files are created and an existing .censorc is found the program paths can be copied to the new censorc
• printout of OR data to file
• printout of NMR data to file
• new option to creat a censo.inp file from all settings set by command line

CENSO in version 1.0.7

cleanup includes amat.tmp files (#9)

* cleanup_all removes amat.tmp files which can be quiet large (several Mb)
* update README