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ReactionMechanismGenerator / ARC

ARC - Automatic Rate Calculator
https://reactionmechanismgenerator.github.io/ARC/index.html
MIT License
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ARC conda environment is too stiff to be created #707

Open wangdu817 opened 11 months ago

wangdu817 commented 11 months ago

I tried to install dependencies of ARC through "conda env create -f environment.yml" , but the dependency is too stiff to be solved, I can not create it correctly. Conda will get stuck in "Solving environment", is there any alternative way to install the dependencies?

calvinp0 commented 11 months ago

Hi @wangdu817, we suggest you either change the solver for Conda to libmamba, as described here or you can utilize mamabaforge

wangdu817 commented 11 months ago

Hi @calvinp0 ,thank you so much, it works! But after I installed the dependencies, ARC could not run, and gave the following information, do you have any ideal how to fix it?

ERROR:root:Unable to find specified property fr_Al_COO ERROR:root:Unable to find specified property fr_Al_OH ERROR:root:Unable to find specified property fr_Al_OH_noTert ERROR:root:Unable to find specified property fr_ArN ERROR:root:Unable to find specified property fr_Ar_COO ERROR:root:Unable to find specified property fr_Ar_N ERROR:root:Unable to find specified property fr_Ar_NH ERROR:root:Unable to find specified property fr_Ar_OH ERROR:root:Unable to find specified property fr_COO ERROR:root:Unable to find specified property fr_COO2 ERROR:root:Unable to find specified property fr_C_O ERROR:root:Unable to find specified property fr_C_O_noCOO ERROR:root:Unable to find specified property fr_C_S ERROR:root:Unable to find specified property fr_HOCCN ERROR:root:Unable to find specified property fr_Imine ERROR:root:Unable to find specified property fr_NH0 ERROR:root:Unable to find specified property fr_NH1 ERROR:root:Unable to find specified property fr_NH2 ERROR:root:Unable to find specified property fr_N_O ERROR:root:Unable to find specified property fr_Ndealkylation1 ERROR:root:Unable to find specified property fr_Ndealkylation2 ERROR:root:Unable to find specified property fr_Nhpyrrole ERROR:root:Unable to find specified property fr_SH ERROR:root:Unable to find specified property fr_aldehyde ERROR:root:Unable to find specified property fr_alkyl_carbamate ERROR:root:Unable to find specified property fr_alkyl_halide ERROR:root:Unable to find specified property fr_allylic_oxid ERROR:root:Unable to find specified property fr_amide ERROR:root:Unable to find specified property fr_amidine ERROR:root:Unable to find specified property fr_aniline ERROR:root:Unable to find specified property fr_aryl_methyl ERROR:root:Unable to find specified property fr_azide ERROR:root:Unable to find specified property fr_azo ERROR:root:Unable to find specified property fr_barbitur ERROR:root:Unable to find specified property fr_benzene ERROR:root:Unable to find specified property fr_benzodiazepine ERROR:root:Unable to find specified property fr_bicyclic ERROR:root:Unable to find specified property fr_diazo ERROR:root:Unable to find specified property fr_dihydropyridine ERROR:root:Unable to find specified property fr_epoxide ERROR:root:Unable to find specified property fr_ester ERROR:root:Unable to find specified property fr_ether ERROR:root:Unable to find specified property fr_furan ERROR:root:Unable to find specified property fr_guanido ERROR:root:Unable to find specified property fr_halogen ERROR:root:Unable to find specified property fr_hdrzine ERROR:root:Unable to find specified property fr_hdrzone ERROR:root:Unable to find specified property fr_imidazole ERROR:root:Unable to find specified property fr_imide ERROR:root:Unable to find specified property fr_isocyan ERROR:root:Unable to find specified property fr_isothiocyan ERROR:root:Unable to find specified property fr_ketone ERROR:root:Unable to find specified property fr_ketone_Topliss ERROR:root:Unable to find specified property fr_lactam ERROR:root:Unable to find specified property fr_lactone ERROR:root:Unable to find specified property fr_methoxy ERROR:root:Unable to find specified property fr_morpholine ERROR:root:Unable to find specified property fr_nitrile ERROR:root:Unable to find specified property fr_nitro ERROR:root:Unable to find specified property fr_nitro_arom ERROR:root:Unable to find specified property fr_nitro_arom_nonortho ERROR:root:Unable to find specified property fr_nitroso ERROR:root:Unable to find specified property fr_oxazole ERROR:root:Unable to find specified property fr_oxime ERROR:root:Unable to find specified property fr_para_hydroxylation ERROR:root:Unable to find specified property fr_phenol ERROR:root:Unable to find specified property fr_phenol_noOrthoHbond ERROR:root:Unable to find specified property fr_phos_acid ERROR:root:Unable to find specified property fr_phos_ester ERROR:root:Unable to find specified property fr_piperdine ERROR:root:Unable to find specified property fr_piperzine ERROR:root:Unable to find specified property fr_priamide ERROR:root:Unable to find specified property fr_prisulfonamd ERROR:root:Unable to find specified property fr_pyridine ERROR:root:Unable to find specified property fr_quatN ERROR:root:Unable to find specified property fr_sulfide ERROR:root:Unable to find specified property fr_sulfonamd ERROR:root:Unable to find specified property fr_sulfone ERROR:root:Unable to find specified property fr_term_acetylene ERROR:root:Unable to find specified property fr_tetrazole ERROR:root:Unable to find specified property fr_thiazole ERROR:root:Unable to find specified property fr_thiocyan ERROR:root:Unable to find specified property fr_thiophene ERROR:root:Unable to find specified property fr_unbrch_alkane ERROR:root:Unable to find specified property fr_urea ERROR:root:Unable to make new descriptors, descriptor generator not installed ERROR:root:Unable to find specified property fr_Al_COO ERROR:root:Unable to find specified property fr_Al_OH ERROR:root:Unable to find specified property fr_Al_OH_noTert ERROR:root:Unable to find specified property fr_ArN ERROR:root:Unable to find specified property fr_Ar_COO ERROR:root:Unable to find specified property fr_Ar_N ERROR:root:Unable to find specified property fr_Ar_NH ERROR:root:Unable to find specified property fr_Ar_OH ERROR:root:Unable to find specified property fr_COO ERROR:root:Unable to find specified property fr_COO2 ERROR:root:Unable to find specified property fr_C_O ERROR:root:Unable to find specified property fr_C_O_noCOO ERROR:root:Unable to find specified property fr_C_S ERROR:root:Unable to find specified property fr_HOCCN ERROR:root:Unable to find specified property fr_Imine ERROR:root:Unable to find specified property fr_NH0 ERROR:root:Unable to find specified property fr_NH1 ERROR:root:Unable to find specified property fr_NH2 ERROR:root:Unable to find specified property fr_N_O ERROR:root:Unable to find specified property fr_Ndealkylation1 ERROR:root:Unable to find specified property fr_Ndealkylation2 ERROR:root:Unable to find specified property fr_Nhpyrrole ERROR:root:Unable to find specified property fr_SH ERROR:root:Unable to find specified property fr_aldehyde ERROR:root:Unable to find specified property fr_alkyl_carbamate ERROR:root:Unable to find specified property fr_alkyl_halide ERROR:root:Unable to find specified property fr_allylic_oxid ERROR:root:Unable to find specified property fr_amide ERROR:root:Unable to find specified property fr_amidine ERROR:root:Unable to find specified property fr_aniline ERROR:root:Unable to find specified property fr_aryl_methyl ERROR:root:Unable to find specified property fr_azide ERROR:root:Unable to find specified property fr_azo ERROR:root:Unable to find specified property fr_barbitur ERROR:root:Unable to find specified property fr_benzene ERROR:root:Unable to find specified property fr_benzodiazepine ERROR:root:Unable to find specified property fr_bicyclic ERROR:root:Unable to find specified property fr_diazo ERROR:root:Unable to find specified property fr_dihydropyridine ERROR:root:Unable to find specified property fr_epoxide ERROR:root:Unable to find specified property fr_ester ERROR:root:Unable to find specified property fr_ether ERROR:root:Unable to find specified property fr_furan ERROR:root:Unable to find specified property fr_guanido ERROR:root:Unable to find specified property fr_halogen ERROR:root:Unable to find specified property fr_hdrzine ERROR:root:Unable to find specified property fr_hdrzone ERROR:root:Unable to find specified property fr_imidazole ERROR:root:Unable to find specified property fr_imide ERROR:root:Unable to find specified property fr_isocyan ERROR:root:Unable to find specified property fr_isothiocyan ERROR:root:Unable to find specified property fr_ketone ERROR:root:Unable to find specified property fr_ketone_Topliss ERROR:root:Unable to find specified property fr_lactam ERROR:root:Unable to find specified property fr_lactone ERROR:root:Unable to find specified property fr_methoxy ERROR:root:Unable to find specified property fr_morpholine ERROR:root:Unable to find specified property fr_nitrile ERROR:root:Unable to find specified property fr_nitro ERROR:root:Unable to find specified property fr_nitro_arom ERROR:root:Unable to find specified property fr_nitro_arom_nonortho ERROR:root:Unable to find specified property fr_nitroso ERROR:root:Unable to find specified property fr_oxazole ERROR:root:Unable to find specified property fr_oxime ERROR:root:Unable to find specified property fr_para_hydroxylation ERROR:root:Unable to find specified property fr_phenol ERROR:root:Unable to find specified property fr_phenol_noOrthoHbond ERROR:root:Unable to find specified property fr_phos_acid ERROR:root:Unable to find specified property fr_phos_ester ERROR:root:Unable to find specified property fr_piperdine ERROR:root:Unable to find specified property fr_piperzine ERROR:root:Unable to find specified property fr_priamide ERROR:root:Unable to find specified property fr_prisulfonamd ERROR:root:Unable to find specified property fr_pyridine ERROR:root:Unable to find specified property fr_quatN ERROR:root:Unable to find specified property fr_sulfide ERROR:root:Unable to find specified property fr_sulfonamd ERROR:root:Unable to find specified property fr_sulfone ERROR:root:Unable to find specified property fr_term_acetylene ERROR:root:Unable to find specified property fr_tetrazole ERROR:root:Unable to find specified property fr_thiazole ERROR:root:Unable to find specified property fr_thiocyan ERROR:root:Unable to find specified property fr_thiophene ERROR:root:Unable to find specified property fr_unbrch_alkane ERROR:root:Unable to find specified property fr_urea Traceback (most recent call last): File "/home/test/ARC_NEW/ARC.py", line 12, in from arc.common import read_yaml_file File "/home/test/ARC_NEW/arc/init.py", line 2, in import arc.main File "/home/test/ARC_NEW/arc/main.py", line 21, in from arkane.encorr.corr import assign_frequency_scale_factor File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/arkane/i nit.py", line 34, in from arkane.common import ArkaneSpecies File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/arkane/com mon.py", line 62, in from arkane.pdep import PressureDependenceJob File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/arkane/pde p.py", line 43, in from rmgpy.chemkin import write_kinetics_entry File "rmgpy/chemkin.pyx", line 52, in init rmgpy.chemkin File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/rmgpy/rmg/ pdep.py", line 48, in from rmgpy.rmg.react import react_species File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/rmgpy/rmg/ react.py", line 36, in from rmgpy.data.rmg import get_db File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/rmgpy/data /rmg.py", line 42, in from rmgpy.data.thermo import ThermoDatabase File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/rmgpy/data /thermo.py", line 47, in from rmgpy.ml.estimator import MLEstimator File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/rmgpy/ml/e stimator.py", line 36, in import chemprop File "", line 983, in _find_and_load File "", line 967, in _find_and_load_unlocked File "", line 668, in _load_unlocked File "", line 638, in _load_backward_compatible File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/chemprop-0 .0.1-py3.7.egg/chemprop/init.py", line 1, in

-- coding: utf-8 --

File "", line 983, in _find_and_load File "", line 967, in _find_and_load_unlocked File "", line 668, in _load_unlocked File "", line 638, in _load_backward_compatible File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/chemprop-0 .0.1-py3.7.egg/chemprop/data/init.py", line 1, in

-- coding: utf-8 --

File "", line 983, in _find_and_load File "", line 967, in _find_and_load_unlocked File "", line 668, in _load_unlocked File "", line 638, in _load_backward_compatible File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/chemprop-0 .0.1-py3.7.egg/chemprop/data/data.py", line 10, in File "", line 983, in _find_and_load File "", line 967, in _find_and_load_unlocked File "", line 668, in _load_unlocked File "", line 638, in _load_backward_compatible File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/chemprop-0 .0.1-py3.7.egg/chemprop/features/init.py", line 1, in

-- coding: utf-8 --

File "", line 983, in _find_and_load File "", line 967, in _find_and_load_unlocked File "", line 668, in _load_unlocked File "", line 638, in _load_backward_compatible File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/chemprop-0 .0.1-py3.7.egg/chemprop/features/features_generators.py", line 95, in File "", line 983, in _find_and_load File "", line 967, in _find_and_load_unlocked File "", line 668, in _load_unlocked File "", line 638, in _load_backward_compatible File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/descriptas torus-2.0.0.32-py3.7.egg/descriptastorus/descriptors/init.py", line 3, in File "", line 983, in _find_and_load File "", line 967, in _find_and_load_unlocked File "", line 668, in _load_unlocked File "", line 638, in _load_backward_compatible File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/descriptas torus-2.0.0.32-py3.7.egg/descriptastorus/descriptors/rdDescriptors.py", line 278 , in File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/descriptas torus-2.0.0.32-py3.7.egg/descriptastorus/descriptors/rdDescriptors.py", line 271 , in init ValueError: RDKit2D: Failed to initialize: unable to find specified properties: fr_Al_COO fr_Al_OH fr_Al_OH_noTert fr_ArN fr_Ar_COO fr_Ar_N fr_Ar_NH fr_Ar_OH fr_COO fr_COO2 fr_C_O fr_C_O_noCOO fr_C_S fr_HOCCN fr_Imine fr_NH0 fr_NH1 fr_NH2 fr_N_O fr_Ndealkylation1 fr_Ndealkylation2 fr_Nhpyrrole fr_SH fr_aldehyde fr_alkyl_carbamate fr_alkyl_halide fr_allylic_oxid fr_amide fr_amidine fr_aniline fr_aryl_methyl fr_azide fr_azo fr_barbitur fr_benzene fr_benzodiazepine fr_bicyclic fr_diazo fr_dihydropyridine fr_epoxide fr_ester fr_ether fr_furan fr_guanido fr_halogen fr_hdrzine fr_hdrzone fr_imidazole fr_imide fr_isocyan fr_isothiocyan fr_ketone fr_ketone_Topliss fr_lactam fr_lactone fr_methoxy fr_morpholine fr_nitrile fr_nitro fr_nitro_arom fr_nitro_arom_nonortho fr_nitroso fr_oxazole fr_oxime fr_para_hydroxylation fr_phenol fr_phenol_noOrthoHbond fr_phos_acid fr_phos_ester fr_piperdine fr_piperzine fr_priamide fr_prisulfonamd fr_pyridine fr_quatN fr_sulfide fr_sulfonamd fr_sulfone fr_term_acetylene fr_tetrazole fr_thiazole fr_thiocyan fr_thiophene fr_unbrch_alkane fr_urea