Skip to content

Fix problems manually #7

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
danieleongari wants to merge 4 commits into
base: master
Choose a base branch
from
Open

Fix problems manually #7

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
83dea26
Use atomic symbols only for XYZ files
danieleongari Jun 25, 2021
ae5f5a1
fix some wrong natoms, partly as suggested by kylebystrom
danieleongari Jun 28, 2021
ee1dfd4
fix for missing geometries
danieleongari Jun 28, 2021
f9f587e
use suffix _ALL only if the database is a collection of the others in…
danieleongari Jun 28, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
0 Databases/GMTKN/MB08-165/MB08-165_ALL.list → Databases/GMTKN/MB08-165/MB08-165.list
View file
Open in desktop
File renamed without changes.
6 changes: 3 additions & 3 deletions Databases/MetalsEE/MOR41/DatasetEval.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,8 @@ MOR41_33,-1,MOR41_ED33,-1,MOR41_PhOH,1,MOR41_PR33,1,MOR41_C2H4,-0.017051548
MOR41_34,-1,MOR41_ED33,-1,MOR41_PhSH,1,MOR41_PR34,1,MOR41_C2H4,-0.040796228
MOR41_35,-1,MOR41_ED33,-1,MOR41_PhSeH,1,MOR41_PR35,1,MOR41_C2H4,-0.049242322
MOR41_36,-1,MOR41_ED36,-1,MOR41_I2,1,MOR41_PR36,1,MOR41_C2H4,-0.063425385
MOR41_37,-1,MOR41_ED37,-3,MOR41_MeCN,1,MOR41_PR37,1,Bz,-0.022310437
MOR41_38,-1,MOR41_ED37,-3,MOR41_PMe3,1,MOR41_PR38,1,Bz,-0.10262801
MOR41_37,-1,MOR41_ED37,-3,MOR41_MeCN,1,MOR41_PR37,1,MOR41_Bz,-0.022310437
MOR41_38,-1,MOR41_ED37,-3,MOR41_PMe3,1,MOR41_PR38,1,MOR41_Bz,-0.10262801
MOR41_39,-2,MOR41_ED39,1,MOR41_PR39,-0.101831209
MOR41_40,-1,MOR41_ED40a,-1,MOR41_ED40b,1,MOR41_PR40,-0.104859054
MOR41_41,-1,MOR41_ED41,1,MOR41_PR41,-0.005099528
MOR41_41,-1,MOR41_EDPR41,1,MOR41_PR41,-0.005099528
0 Databases/MetalsEE/Por21/MetalsEE_Por21.list → ...es/MetalsEE/Por21/MetalsEE_Por21_ALL.list
View file
Open in desktop
File renamed without changes.
4 changes: 2 additions & 2 deletions Databases/SSSS/MB13/DatasetEval.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
MB13_1,-2,MB08-165_048,-2,MB08-165_166_h,2,MB08-165_176_al,2,MB08-165_170_c,1,172_o,0.15350552741
MB13_1,-2,MB08-165_048,-2,MB08-165_166_h,2,MB08-165_176_al,2,MB08-165_170_c,1,MB08-165_172_o,0.15350552741
MB13_2,-2,MB08-165_050,2,MB08-165_176_al,1,MB08-165_180_cl,3,MB08-165_166_h,0.09979442526
MB13_3,-2,MB08-165_070,-1,MB08-165_166_h,2,MB08-165_168_be,2,MB08-165_170_c,1,173_f,0.09974964503
MB13_3,-2,MB08-165_070,-1,MB08-165_166_h,2,MB08-165_168_be,2,MB08-165_170_c,1,MB08-165_173_f,0.09974964503
MB13_4,-1,MB08-165_076,1,MB08-165_169_b,1,MB08-165_167_li,1,MB08-165_166_h,0.10437539541
MB13_5,-2,MB08-165_088,-9,MB08-165_166_h,6,MB08-165_170_c,1,MB08-165_171_n,1,MB08-165_179_s,-0.62929137271
MB13_6,-2,MB08-165_096,-3,MB08-165_166_h,4,MB08-165_170_c,1,MB08-165_178_p,-0.13983703819
Expand Down
28 changes: 14 additions & 14 deletions Geometries/00_As1_4pIsoE4.xyz
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,16 +1,16 @@
14
0 1
6 -2.223403000 1.195100000 0.002932000
6 -0.836543000 1.210443000 -0.000078000
6 -0.117983000 0.017432000 -0.002729000
6 -0.812803000 -1.188683000 -0.009937000
6 -2.200965000 -1.204445000 0.002393000
6 -2.908374000 -0.012220000 0.007603000
1 -2.771222000 2.130266000 0.003278000
1 -0.312275000 2.158987000 0.001898000
1 -0.268569000 -2.126948000 -0.028692000
1 -2.728959000 -2.150793000 0.000786000
1 -3.991782000 -0.022372000 0.011152000
33 1.836641000 -0.055102000 -0.027990000
1 2.031763000 0.343568000 1.431293000
1 2.032333000 1.379912000 -0.497135000
C -2.223403000 1.195100000 0.002932000
C -0.836543000 1.210443000 -0.000078000
C -0.117983000 0.017432000 -0.002729000
C -0.812803000 -1.188683000 -0.009937000
C -2.200965000 -1.204445000 0.002393000
C -2.908374000 -0.012220000 0.007603000
H -2.771222000 2.130266000 0.003278000
H -0.312275000 2.158987000 0.001898000
H -0.268569000 -2.126948000 -0.028692000
H -2.728959000 -2.150793000 0.000786000
H -3.991782000 -0.022372000 0.011152000
As 1.836641000 -0.055102000 -0.027990000
H 2.031763000 0.343568000 1.431293000
H 2.032333000 1.379912000 -0.497135000
34 changes: 17 additions & 17 deletions Geometries/00_C1_2pIsoE4.xyz
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,19 +1,19 @@
17
0 1
6 0.881444000 0.881444000 0.881444000
1 0.274833000 1.524471000 1.524471000
1 1.524471000 0.274833000 1.524471000
1 1.524471000 1.524471000 0.274833000
6 -0.881444000 -0.881444000 0.881444000
1 -1.524471000 -0.274833000 1.524471000
1 -1.524471000 -1.524471000 0.274833000
1 -0.274833000 -1.524471000 1.524471000
6 0.881444000 -0.881444000 -0.881444000
1 0.274833000 -1.524471000 -1.524471000
1 1.524471000 -0.274833000 -1.524471000
1 1.524471000 -1.524471000 -0.274833000
6 -0.881444000 0.881444000 -0.881444000
1 -0.274833000 1.524471000 -1.524471000
1 -1.524471000 0.274833000 -1.524471000
1 -1.524471000 1.524471000 -0.274833000
6 0.000000000 0.000000000 0.000000000
C 0.881444000 0.881444000 0.881444000
H 0.274833000 1.524471000 1.524471000
H 1.524471000 0.274833000 1.524471000
H 1.524471000 1.524471000 0.274833000
C -0.881444000 -0.881444000 0.881444000
H -1.524471000 -0.274833000 1.524471000
H -1.524471000 -1.524471000 0.274833000
H -0.274833000 -1.524471000 1.524471000
C 0.881444000 -0.881444000 -0.881444000
H 0.274833000 -1.524471000 -1.524471000
H 1.524471000 -0.274833000 -1.524471000
H 1.524471000 -1.524471000 -0.274833000
C -0.881444000 0.881444000 -0.881444000
H -0.274833000 1.524471000 -1.524471000
H -1.524471000 0.274833000 -1.524471000
H -1.524471000 1.524471000 -0.274833000
C 0.000000000 0.000000000 0.000000000
28 changes: 14 additions & 14 deletions Geometries/01_As2_4pIsoE4.xyz
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,16 +1,16 @@
14
0 1
6 1.577764000 -0.468793000 0.666443000
6 0.368771000 0.269170000 1.215339000
6 0.368771000 0.269170000 -1.215339000
6 1.577764000 -0.468793000 -0.666443000
1 2.333761000 -0.909686000 1.302078000
1 2.333761000 -0.909686000 -1.302078000
6 0.368771000 1.679051000 0.664577000
1 0.412983000 2.551867000 1.302311000
6 0.368771000 1.679051000 -0.664577000
1 0.412983000 2.551867000 -1.302311000
1 0.204164000 0.169568000 2.284224000
1 0.204164000 0.169568000 -2.284224000
33 -0.958479000 -0.660436000 0.000000000
1 -2.055670000 0.417748000 0.000000000
C 1.577764000 -0.468793000 0.666443000
C 0.368771000 0.269170000 1.215339000
C 0.368771000 0.269170000 -1.215339000
C 1.577764000 -0.468793000 -0.666443000
H 2.333761000 -0.909686000 1.302078000
H 2.333761000 -0.909686000 -1.302078000
C 0.368771000 1.679051000 0.664577000
H 0.412983000 2.551867000 1.302311000
C 0.368771000 1.679051000 -0.664577000
H 0.412983000 2.551867000 -1.302311000
H 0.204164000 0.169568000 2.284224000
H 0.204164000 0.169568000 -2.284224000
As -0.958479000 -0.660436000 0.000000000
H -2.055670000 0.417748000 0.000000000
34 changes: 17 additions & 17 deletions Geometries/01_C2_2pIsoE4.xyz
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,19 +1,19 @@
17
0 1
6 -2.534797000 -0.323313000 -0.000075000
6 -1.271840000 0.521299000 0.000122000
1 -3.434668000 0.294930000 -0.001199000
1 -2.574611000 -0.969714000 -0.880678000
1 -2.575864000 -0.968328000 0.881480000
6 -0.000061000 -0.311378000 0.000042000
1 -1.269420000 1.181298000 -0.874393000
1 -1.269502000 1.180915000 0.874929000
6 1.271857000 0.521255000 -0.000122000
1 -0.000073000 -0.972802000 0.875181000
1 -0.000264000 -0.972885000 -0.875032000
1 1.269368000 1.180984000 -0.874848000
1 1.269384000 1.181326000 0.874346000
6 2.534871000 -0.323274000 0.000032000
1 2.575355000 -0.969364000 -0.881175000
1 3.434712000 0.295070000 -0.000130000
1 2.575402000 -0.968968000 0.881523000
C -2.534797000 -0.323313000 -0.000075000
C -1.271840000 0.521299000 0.000122000
H -3.434668000 0.294930000 -0.001199000
H -2.574611000 -0.969714000 -0.880678000
H -2.575864000 -0.968328000 0.881480000
C -0.000061000 -0.311378000 0.000042000
H -1.269420000 1.181298000 -0.874393000
H -1.269502000 1.180915000 0.874929000
C 1.271857000 0.521255000 -0.000122000
H -0.000073000 -0.972802000 0.875181000
H -0.000264000 -0.972885000 -0.875032000
H 1.269368000 1.180984000 -0.874848000
H 1.269384000 1.181326000 0.874346000
C 2.534871000 -0.323274000 0.000032000
H 2.575355000 -0.969364000 -0.881175000
H 3.434712000 0.295070000 -0.000130000
H 2.575402000 -0.968968000 0.881523000
22 changes: 11 additions & 11 deletions Geometries/02_Br1_4pIsoE4.xyz
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
11
0 1
6 0.038809000 0.302544000 0.000000000
6 0.603932000 1.712514000 0.000000000
1 0.187809000 2.210755000 0.879276000
1 0.187809000 2.210755000 -0.879276000
6 2.117357000 1.812271000 0.000000000
1 2.547641000 1.341880000 0.884204000
1 2.547641000 1.341880000 -0.884204000
1 2.406975000 2.863905000 0.000000000
35 0.603932000 -0.674483000 -1.585999000
35 0.603932000 -0.674483000 1.585999000
35 -1.906106000 0.408020000 0.000000000
C 0.038809000 0.302544000 0.000000000
C 0.603932000 1.712514000 0.000000000
H 0.187809000 2.210755000 0.879276000
H 0.187809000 2.210755000 -0.879276000
C 2.117357000 1.812271000 0.000000000
H 2.547641000 1.341880000 0.884204000
H 2.547641000 1.341880000 -0.884204000
H 2.406975000 2.863905000 0.000000000
Br 0.603932000 -0.674483000 -1.585999000
Br 0.603932000 -0.674483000 1.585999000
Br -1.906106000 0.408020000 0.000000000
22 changes: 11 additions & 11 deletions Geometries/02_F1_2pIsoE4.xyz
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
11
0 1
6 0.371363000 0.246436000 0.000000000
6 -1.131949000 0.257852000 0.000000000
1 -1.440478000 0.824768000 -0.880227000
1 -1.440478000 0.824768000 0.880227000
6 -1.730362000 -1.137149000 0.000000000
1 -1.421370000 -1.696828000 -0.883292000
1 -1.421370000 -1.696828000 0.883292000
1 -2.818808000 -1.079695000 0.000000000
9 0.869933000 -0.377963000 -1.078403000
9 0.869933000 1.491590000 0.000000000
9 0.869933000 -0.377963000 1.078403000
C 0.371363000 0.246436000 0.000000000
C -1.131949000 0.257852000 0.000000000
H -1.440478000 0.824768000 -0.880227000
H -1.440478000 0.824768000 0.880227000
C -1.730362000 -1.137149000 0.000000000
H -1.421370000 -1.696828000 -0.883292000
H -1.421370000 -1.696828000 0.883292000
H -2.818808000 -1.079695000 0.000000000
F 0.869933000 -0.377963000 -1.078403000
F 0.869933000 1.491590000 0.000000000
F 0.869933000 -0.377963000 1.078403000
22 changes: 11 additions & 11 deletions Geometries/03_Br2_4pIsoE4.xyz
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
11
0 1
6 -0.583305000 1.003580000 1.233936000
6 -0.311213000 0.169388000 0.000000000
1 0.157589000 1.790829000 1.356869000
1 -1.577666000 1.445123000 1.167169000
6 -0.583305000 1.003580000 -1.233936000
1 -0.929561000 -0.726774000 0.000000000
1 -1.577666000 1.445123000 -1.167169000
1 0.157589000 1.790829000 -1.356869000
35 -0.583305000 -0.031553000 2.869641000
35 1.527657000 -0.474164000 0.000000000
35 -0.583305000 -0.031553000 -2.869641000
C -0.583305000 1.003580000 1.233936000
C -0.311213000 0.169388000 0.000000000
H 0.157589000 1.790829000 1.356869000
H -1.577666000 1.445123000 1.167169000
C -0.583305000 1.003580000 -1.233936000
H -0.929561000 -0.726774000 0.000000000
H -1.577666000 1.445123000 -1.167169000
H 0.157589000 1.790829000 -1.356869000
Br -0.583305000 -0.031553000 2.869641000
Br 1.527657000 -0.474164000 0.000000000
Br -0.583305000 -0.031553000 -2.869641000
22 changes: 11 additions & 11 deletions Geometries/03_F2_2pIsoE4.xyz
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
11
0 1
6 -0.274124000 0.617475000 1.248676000
6 -0.074906000 -0.202482000 0.000000000
1 0.536634000 1.343404000 1.359604000
1 -1.233212000 1.142792000 1.210311000
6 -0.274124000 0.617475000 -1.248676000
1 -0.770947000 -1.048099000 0.000000000
1 -1.233212000 1.142792000 -1.210311000
1 0.536634000 1.343404000 -1.359604000
9 1.204139000 -0.722148000 0.000000000
9 -0.274124000 -0.201098000 -2.353577000
9 -0.274124000 -0.201098000 2.353577000
C -0.274124000 0.617475000 1.248676000
C -0.074906000 -0.202482000 0.000000000
H 0.536634000 1.343404000 1.359604000
H -1.233212000 1.142792000 1.210311000
C -0.274124000 0.617475000 -1.248676000
H -0.770947000 -1.048099000 0.000000000
H -1.233212000 1.142792000 -1.210311000
H 0.536634000 1.343404000 -1.359604000
F 1.204139000 -0.722148000 0.000000000
F -0.274124000 -0.201098000 -2.353577000
F -0.274124000 -0.201098000 2.353577000
34 changes: 17 additions & 17 deletions Geometries/04_Ge1_4pIsoE4.xyz
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,19 +1,19 @@
17
0 1
6 1.130984000 1.130984000 1.130984000
1 0.518959000 1.769944000 1.769944000
1 1.769944000 0.518959000 1.769944000
1 1.769944000 1.769944000 0.518959000
6 -1.130984000 -1.130984000 1.130984000
1 -1.769944000 -0.518959000 1.769944000
1 -1.769944000 -1.769944000 0.518959000
1 -0.518959000 -1.769944000 1.769944000
6 1.130984000 -1.130984000 -1.130984000
1 0.518959000 -1.769944000 -1.769944000
1 1.769944000 -0.518959000 -1.769944000
1 1.769944000 -1.769944000 -0.518959000
6 -1.130984000 1.130984000 -1.130984000
1 -0.518959000 1.769944000 -1.769944000
1 -1.769944000 0.518959000 -1.769944000
1 -1.769944000 1.769944000 -0.518959000
32 0.000000000 0.000000000 0.000000000
C 1.130984000 1.130984000 1.130984000
H 0.518959000 1.769944000 1.769944000
H 1.769944000 0.518959000 1.769944000
H 1.769944000 1.769944000 0.518959000
C -1.130984000 -1.130984000 1.130984000
H -1.769944000 -0.518959000 1.769944000
H -1.769944000 -1.769944000 0.518959000
H -0.518959000 -1.769944000 1.769944000
C 1.130984000 -1.130984000 -1.130984000
H 0.518959000 -1.769944000 -1.769944000
H 1.769944000 -0.518959000 -1.769944000
H 1.769944000 -1.769944000 -0.518959000
C -1.130984000 1.130984000 -1.130984000
H -0.518959000 1.769944000 -1.769944000
H -1.769944000 0.518959000 -1.769944000
H -1.769944000 1.769944000 -0.518959000
Ge 0.000000000 0.000000000 0.000000000
28 changes: 14 additions & 14 deletions Geometries/04_N1_2pIsoE4.xyz
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,16 +1,16 @@
14
0 1
6 1.164320000 -1.194671000 0.003402000
6 -0.220167000 -1.200183000 -0.004942000
6 -0.934402000 -0.000111000 -0.008653000
6 -0.220120000 1.200196000 -0.004948000
6 1.164154000 1.194771000 0.003409000
6 1.870449000 -0.000026000 0.007664000
1 1.696626000 -2.138894000 0.007499000
1 -0.759175000 -2.141784000 -0.012811000
1 -0.759445000 2.141613000 -0.013195000
1 1.696669000 2.138876000 0.007740000
1 2.952946000 0.000166000 0.014915000
1 -2.767302000 -0.834784000 0.265559000
1 -2.767154000 0.834766000 0.265925000
7 -2.319796000 0.000027000 -0.073032000
C 1.164320000 -1.194671000 0.003402000
C -0.220167000 -1.200183000 -0.004942000
C -0.934402000 -0.000111000 -0.008653000
C -0.220120000 1.200196000 -0.004948000
C 1.164154000 1.194771000 0.003409000
C 1.870449000 -0.000026000 0.007664000
H 1.696626000 -2.138894000 0.007499000
H -0.759175000 -2.141784000 -0.012811000
H -0.759445000 2.141613000 -0.013195000
H 1.696669000 2.138876000 0.007740000
H 2.952946000 0.000166000 0.014915000
H -2.767302000 -0.834784000 0.265559000
H -2.767154000 0.834766000 0.265925000
N -2.319796000 0.000027000 -0.073032000
34 changes: 17 additions & 17 deletions Geometries/05_Ge2_4pIsoE4.xyz
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,19 +1,19 @@
17
0 1
6 -3.677143000 -0.466829000 0.000037000
6 -2.507571000 0.502878000 -0.000031000
1 -4.634828000 0.057177000 0.000053000
1 -3.651936000 -1.113025000 -0.881203000
1 -3.651872000 -1.112968000 0.881317000
6 -1.156355000 -0.198710000 -0.000053000
1 -2.569370000 1.159041000 -0.875041000
1 -2.569305000 1.159089000 0.874951000
6 0.019740000 0.768828000 0.000028000
1 -1.097530000 -0.857363000 0.874367000
1 -1.097489000 -0.857254000 -0.874553000
1 -0.023853000 1.422073000 -0.876472000
1 -0.023882000 1.421957000 0.876614000
32 1.766425000 -0.119006000 0.000003000
1 1.907159000 -1.010198000 -1.248105000
1 2.908141000 0.912938000 0.000048000
1 1.907141000 -1.010291000 1.248046000
C -3.677143000 -0.466829000 0.000037000
C -2.507571000 0.502878000 -0.000031000
H -4.634828000 0.057177000 0.000053000
H -3.651936000 -1.113025000 -0.881203000
H -3.651872000 -1.112968000 0.881317000
C -1.156355000 -0.198710000 -0.000053000
H -2.569370000 1.159041000 -0.875041000
H -2.569305000 1.159089000 0.874951000
C 0.019740000 0.768828000 0.000028000
H -1.097530000 -0.857363000 0.874367000
H -1.097489000 -0.857254000 -0.874553000
H -0.023853000 1.422073000 -0.876472000
H -0.023882000 1.421957000 0.876614000
Ge 1.766425000 -0.119006000 0.000003000
H 1.907159000 -1.010198000 -1.248105000
H 2.908141000 0.912938000 0.000048000
H 1.907141000 -1.010291000 1.248046000
28 changes: 14 additions & 14 deletions Geometries/05_N2_2pIsoE4.xyz
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,16 +1,16 @@
14
0 1
6 -1.108617000 0.751835000 0.662203000
6 0.253847000 0.182117000 1.077100000
6 0.253847000 0.182117000 -1.077100000
6 -1.108617000 0.751835000 -0.662203000
1 -1.894476000 1.036001000 1.345581000
1 -1.894476000 1.036001000 -1.345581000
6 0.253847000 -1.305587000 0.663542000
1 0.177595000 -2.144622000 1.340107000
6 0.253847000 -1.305587000 -0.663542000
1 0.177595000 -2.144622000 -1.340107000
1 0.590606000 0.411976000 2.085297000
1 0.590606000 0.411976000 -2.085297000
1 1.979630000 0.334342000 0.000000000
7 1.069142000 0.788367000 0.000000000
C -1.108617000 0.751835000 0.662203000
C 0.253847000 0.182117000 1.077100000
C 0.253847000 0.182117000 -1.077100000
C -1.108617000 0.751835000 -0.662203000
H -1.894476000 1.036001000 1.345581000
H -1.894476000 1.036001000 -1.345581000
C 0.253847000 -1.305587000 0.663542000
H 0.177595000 -2.144622000 1.340107000
C 0.253847000 -1.305587000 -0.663542000
H 0.177595000 -2.144622000 -1.340107000
H 0.590606000 0.411976000 2.085297000
H 0.590606000 0.411976000 -2.085297000
H 1.979630000 0.334342000 0.000000000
N 1.069142000 0.788367000 0.000000000
Loading