[pull] main from grimme-lab:main #8
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* consider_unconverged option implemented and introduce prog2opt * option for reconsidering conformers that were removed during geometry optimization based on the energy threshold * using a different QM code only for the geometry optimization imposes the condition that the functional func is available in both QM programs * updated tm_job concerning cefine/define error printout * rename of opt_limit --> part2_threshold and part2_threshold --> part2_P_threshold * added environment in all subprocess calls * added better printout to parallelization * avoid error if user/home/ is read-only; add revTPSS for NMR; printout for nmrprop.dat * better tracking of which external codes are required * fix output for unchecked basis sets * removed .chrg .uhf per conformer redundant information .censorc now tm or orca dependent saving info on converged optimizations in case of crashes for large ensembles * removed crash because of None-type when COSMO-RS is requested, but no cefine for TM is available * Catch OSError which is related to system-related errors, including I/O failures such as “file not found” or “disk full” to keep the python instance alive * created user-editable ORCA input which will be added to every ORCA input and used as provided by the USER without any checks (version or correct spelling) * added files to censo_assets * update in tutorials and small corrections * better printout * added bromoform and 1,2-dibromoethane * improved -h help page
* temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * temp commit * include commit hash * commit hash fix * startup description fix * version tagging etc * updated setup * stderr output as text hopefully * censo callable via 'censo' + possible to set logging level * censo callable fix + info on rcfile * nmr/uvvis uses ensembleopt energies, tpssh added * autoaux for orcaproc * typo fix * popen fix * autoaux fixed * version centering * introducing orca optimization * typo fix * formatting fix 2 * formatting fix 3 * formatting fix 4 * orca optimization actually usable * orca optimization actually usable 2 * orca optimization fix * implemented fromxyz * fromxyz fixed * optimization fix * orca input parsing fix * orca input parsing fix 2 * typo fix * removed conformer ids * results mismatch fix * results mismatch fix2 * orca optlevel mapping * small fix * typo fix * ordering optimized for orca optimization * screening now also prints boltzmann weight * removed md5 + optimization small fix * fixed removal of unconverged conformers in optimization * optimization maxiter fix * optimization prep fix * added r2scan * orca 6 fix + autobalance fix * cml args rename + maxcores to part run function signature * updated readme
* prepare reload capability * reload capability * tm proc basic setup * tm proc basic setup * tm prep almost done * sm/prog compatibility check * settings case insensitive * tm solvation cosmo + dcosmors done, cosmors basics * optimization additional sort * cosmors gsolv calculation basics * tm gsolv sp calls * change on how to copy mo * turbomole single-point * cosmors done * tm xtb_opt done * tm nmr done * property calculations boilerplate class * cosmors gsolv calculation done * property boilerplate * hopefully removed all faulty format strings * fixed missing tm import * next try * next try 2 * fixed cml parser * parallel call fix * loglevel setting cml * proper environment variable setting (no strings allowed) * fixed missing cefine call * fixed outdated code? * fixed usage of 'solvent' * fixed solvation in tm prep * tm cefine prep change * formatting * formatting again * log level adjustable via cml * cefine fix? * added basis lookup for turbomole * tm encoding * cefine proper error handling * subprocess error reraise + removed tm file encoding * coord file generation order fix * turbomole gcp + d4 bug avoided * turbomole gcp + d4 bug avoided for real now * r2scan-3c turbomole grid fix * tm solv prep missing newlines fix * tm copy mo moved before prep * tm xtbopt fixed * new handling for solvent and dfa availability check * small fix 1 * small fix 2 * small fix 3 * small fix 4 * small fix 5 * small fix 6 * small fix 7 * 'legacy' load balancing for using tm * part json dump contains part name * read_output reads new jsons correctly * read_output error fixed * small fix * small fix 2 * improved _set_energy for property_calculator * tm nmr prep fix * tm nmr nucsel fix * tm gcp+d4 bug switching disp/gcp off decision * typo fix * nmr grid settings fix * cosmors redone * copy_mo/prep order never violated (hopefully) * write_results for screening fixed when using gsolv * screening fixes * better check for explicit gsolv inclusion * screening refienement writeresults final fix * small fix * fixed dummy functionality + not available for tm * tm nmr fconly * finalized basic tm implementation * small fix
* prepare reload capability * reload capability * tm proc basic setup * tm proc basic setup * tm prep almost done * sm/prog compatibility check * settings case insensitive * tm solvation cosmo + dcosmors done, cosmors basics * optimization additional sort * cosmors gsolv calculation basics * tm gsolv sp calls * change on how to copy mo * turbomole single-point * cosmors done * tm xtb_opt done * tm nmr done * property calculations boilerplate class * cosmors gsolv calculation done * property boilerplate * hopefully removed all faulty format strings * fixed missing tm import * next try * next try 2 * fixed cml parser * parallel call fix * loglevel setting cml * proper environment variable setting (no strings allowed) * fixed missing cefine call * fixed outdated code? * fixed usage of 'solvent' * fixed solvation in tm prep * tm cefine prep change * formatting * formatting again * log level adjustable via cml * cefine fix? * added basis lookup for turbomole * tm encoding * cefine proper error handling * subprocess error reraise + removed tm file encoding * coord file generation order fix * turbomole gcp + d4 bug avoided * turbomole gcp + d4 bug avoided for real now * r2scan-3c turbomole grid fix * tm solv prep missing newlines fix * tm copy mo moved before prep * tm xtbopt fixed * new handling for solvent and dfa availability check * small fix 1 * small fix 2 * small fix 3 * small fix 4 * small fix 5 * small fix 6 * small fix 7 * 'legacy' load balancing for using tm * part json dump contains part name * read_output reads new jsons correctly * read_output error fixed * small fix * small fix 2 * improved _set_energy for property_calculator * tm nmr prep fix * tm nmr nucsel fix * tm gcp+d4 bug switching disp/gcp off decision * typo fix * nmr grid settings fix * cosmors redone * copy_mo/prep order never violated (hopefully) * write_results for screening fixed when using gsolv * screening fixes * better check for explicit gsolv inclusion * screening refienement writeresults final fix * small fix * fixed dummy functionality + not available for tm * tm nmr fconly * finalized basic tm implementation * small fix * setting up tests * refactoring and restructuring part architecture 1 * some dfa modifications + part_no references fixed * some changes to code structure for less clutter * small fix * small fix 2 * small fix 3 * small fix 4 * small fix 5 * small fix 6 * small fix 7 * some fixes w.r.t. part execution * refactoring and restructuring part architecture 2 * small fixes * small fix * small fix 2 * Revert "small fix 2" This reverts commit dd8bcae. * Revert "small fix" This reverts commit 19297b6. * Revert "small fixes" This reverts commit 1df8332. * Revert "refactoring and restructuring part architecture 2" This reverts commit a059dc0. * Revert "some fixes w.r.t. part execution" This reverts commit 10305b8. * Revert "small fix 6" This reverts commit fa4cb55. * Revert "small fix 5" This reverts commit 1b7394f. * Revert "small fix 4" This reverts commit b9a2610. * Revert "small fix 3" This reverts commit 1b40624. * Revert "small fix 2" This reverts commit 24c0870. * Revert "small fix" This reverts commit 22a77b6. * Revert "some changes to code structure for less clutter" This reverts commit 916fd4f. * big part/results refactor try 1 * big refactor stragglers * big refactor stragglers 2 * big refactor stragglers 3 * setup conformers fix * calc boltzmannweights fix * print comparison fix * ensemble cutting fix * some small fixes * optimization key error fix * orca proc fix * small fix * small fix 2 * optimization key error fix * print_comparison fix * moved _write_results call and fixed results appending to ensemble * small fix * moving around xtb energies etc * small fix * small fix 2 * small fix 3 * output writing/printing refactor * small fixes * small fix * small print_comparison fix * small fix * small fix 2 * small fix 3 * small fix 4 * small fix 5 * small fix 6 * properties calculator fix * small fix * some changes to read_input * ensembledata read_input fix
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