I wonder if someone can help me to avoid confusion as to description of geometry in the NWChem output file. I am trying to optimize the structure written in the input file in Ångström units (default) as
geometry
Pu 0.008547019 2.933383261 2.986384046
N 0.009654496 -0.032791895 0.293844380
C 2.572480214 1.454386961 2.986409478
O 2.572346177 2.748527262 2.989962104
O 0.009450326 2.932316787 4.810599807
Pu 2.571033451 1.440081288 8.489384815
N 0.006584110 -0.026140729 5.796313302
C 0.006777342 2.918379143 8.489760372
O 1.451993511 0.807212883 2.989282884
O 3.693327546 0.807662857 2.990294578
O 0.006541468 1.624196772 8.491251265
O 1.127488934 3.565211620 8.494433082
O -1.113793318 3.565472718 8.494010288
O 2.571082316 1.438834994 10.313648031
O 2.571097957 1.441372668 6.700643159
O 0.008873510 2.934236490 1.197610670
H 0.009483442 -0.036775051 1.323988073
H 0.861777112 0.451642673 -0.040413879
H -0.834912873 0.463878834 -0.041618463
H 2.565987245 3.426770424 -0.041059330
H 0.000880720 -0.026881372 6.826494007
H 0.854441646 -0.518674850 5.463555377
H 0.013578370 0.953597543 5.460918201
H 1.720335461 3.927747003 5.458936925
end
The NWChem input module reads this input and writes the following in the output file:
Geometry "geometry" -> ""
-------------------------
Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)
No. Tag Charge X Y Z
---- ---------------- ---------- -------------- -------------- --------------
1 Pu 94.0000 -0.55205158 2.90304600 0.18630258
2 N 7.0000 2.01127150 5.00875572 -2.05943283
3 C 6.0000 2.22001068 1.90102915 0.45614801
4 O 8.0000 1.49277471 2.08371763 1.51092975
5 O 8.0000 -1.15958151 1.18693731 0.06949750
6 Pu 94.0000 0.39038020 -3.27613680 0.09234965
7 N 7.0000 0.16882422 -0.16442221 -2.40704764
8 C 6.0000 -2.38166873 -2.27449804 -0.17827666
9 O 8.0000 1.73320756 2.15031658 -0.71654611
10 O 8.0000 3.43064439 1.45932064 0.57372995
11 O 8.0000 -1.65637263 -2.46182211 -1.23362756
12 O 8.0000 -1.89702205 -2.53100094 0.99378666
13 O 8.0000 -3.59501507 -1.84047261 -0.29591746
14 O 8.0000 -0.21771202 -4.99205289 -0.02509682
15 O 8.0000 0.98667807 -1.59365722 0.20763048
16 O 8.0000 0.04470114 4.58541179 0.30137900
17 H 1.0000 1.66957681 4.03938446 -2.12854166
18 H 1.0000 2.49664789 5.13037751 -1.15271552
19 H 1.0000 1.20477958 5.65568159 -2.11917296
20 H 1.0000 2.11906730 5.03382944 2.25372383
21 H 1.0000 -0.17889298 -1.13165887 -2.47669935
22 H 1.0000 1.19849986 -0.18330413 -2.29938309
23 H 1.0000 -0.26352719 0.28966768 -1.58285076
24 H 1.0000 -0.63818363 0.19345115 1.82434216
As one can see, the coordinates are quite different from those in input. Is that a result of centering? While the NWChem manual states that the input coordinates are converted to a.u. by the program, it is not clear in what units these coordinates are.
When the optimization procedure is complete, I find two sets of coordinates at the end of the output file:
DFT ENERGY GRADIENTS
atom coordinates gradient
x y z x y z
1 Pu 1.511604 6.403050 1.484433 -0.000127 -0.000228 -0.000320
2 N 2.035427 5.298519 -3.279268 -0.000011 -0.000012 -0.000374
3 C 7.151896 6.784079 2.672360 0.000170 0.000175 -0.000245
4 O 5.354999 7.314594 4.338294 -0.000164 0.000099 -0.000040
5 O 0.037237 2.521073 2.492718 0.000647 0.000419 0.000228
6 Pu -1.724758 -7.969039 -1.739139 0.000113 -0.000041 -0.000093
7 N 0.957320 -0.071036 -2.264304 -0.000000 0.000211 -0.000078
8 C -5.014802 -3.516208 -2.590188 -0.000006 0.000029 -0.000067
9 O 6.418702 6.202535 0.354063 -0.000164 -0.000212 -0.000021
10 O 9.513264 6.808400 3.302178 -0.000028 0.000039 0.000193
11 O -2.797113 -3.626641 -3.829258 0.000343 0.000019 -0.000065
12 O -5.250514 -4.958466 -0.574034 0.000023 0.000015 -0.000028
13 O -6.803738 -2.095383 -3.449250 -0.000039 -0.000048 0.000045
14 O -3.919151 -9.826207 -3.810404 -0.000161 -0.000118 0.000340
15 O 0.674719 -6.342050 0.319266 0.000049 0.000125 -0.000012
16 O -0.257142 10.071078 0.636371 -0.000737 -0.000260 -0.000456
17 H 3.915298 5.649612 -3.616033 0.000072 -0.000039 0.000234
18 H 0.922063 6.298538 -4.506356 0.000180 -0.000051 0.000211
19 H 1.655875 3.351265 -3.376414 -0.000035 0.000036 -0.000017
20 H -0.458131 11.880324 0.283306 0.000544 0.000340 0.000245
21 H -0.455764 -0.994184 -3.240645 -0.000299 -0.000052 0.000071
22 H 2.613861 -1.061645 -2.209790 0.000071 -0.000148 0.000165
23 H 0.429470 0.636912 -0.507390 -0.000122 -0.000143 -0.000001
24 H -0.207885 1.249973 3.823906 -0.000318 -0.000158 0.000086
and
Geometry "geometry" -> "geometry"
---------------------------------
Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)
No. Tag Charge X Y Z
---- ---------------- ---------- -------------- -------------- --------------
1 Pu 94.0000 0.79990634 3.38834834 0.78552815
2 N 7.0000 1.07710143 2.80385559 -1.73531400
3 C 6.0000 3.78462060 3.58998023 1.41415192
4 O 8.0000 2.83374384 3.87071695 2.29572641
5 O 8.0000 0.01970474 1.33409437 1.31908958
6 Pu 94.0000 -0.91270257 -4.21703419 -0.92031276
7 N 7.0000 0.50659196 -0.03759068 -1.19821803
8 C 6.0000 -2.65371891 -1.86069719 -1.37066865
9 O 8.0000 3.39663109 3.28224047 0.18736200
10 O 8.0000 5.03420301 3.60285046 1.74743737
11 O 8.0000 -1.48016846 -1.91913609 -2.02635607
12 O 8.0000 -2.77845270 -2.62390732 -0.30376555
13 O 8.0000 -3.60038316 -1.10882914 -1.82526475
14 O 8.0000 -2.07392566 -5.19980519 -2.01637912
15 O 8.0000 0.35704578 -3.35606879 0.16894831
16 O 8.0000 -0.13607346 5.32938528 0.33675313
17 H 1.0000 2.07188653 2.98964587 -1.91352235
18 H 1.0000 0.48793460 3.33304300 -2.38466097
19 H 1.0000 0.87625112 1.77341304 -1.78672151
20 H 1.0000 -0.24243264 6.28679718 0.14991934
21 H 1.0000 -0.24118011 -0.52609968 -1.71487556
22 H 1.0000 1.38319577 -0.56179828 -1.16937066
23 H 1.0000 0.22726562 0.33703951 -0.26849907
24 H 1.0000 -0.11000825 0.66145712 2.02352396
It is again confusing: what is what and which set is best to use.
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