error with specified geometry

Basudha Deb

unread,

Sep 8, 2023, 9:18:14 AM9/8/23

to NWChem Forum

Respected sir,

This is my input file and i am encountering error while running it. ( I am using NWchem version 7.2.0)

charge 0
basis spherical
* library 6-311++G**
end
geometry units angstrom
C 2.435028 -0.243686 0.10618
C 1.347148 0.768536 -0.141410
C 0.035405 0.572354 -0.277425
H -0.586154 1.432788 -0.413740
C -0.702476 -0.666546 -0.270767
C -2.817882 0.058251 0.076032
O 1.922828 1.977577 -0.205101
F 3.235729 -0.341866 -0.984272
F 1.937943 -1.471669 0.376805
F 3.198425 0.132158 1.159359
O -0.600236 -1.815574 -0.423212
H 1.362584 2.728791 -0.377277
F -3.721334 -0.568420 -0.723502
F -2.877256 1.405776 -0.210313
F -3.233562 -0.088318 1.366574

end
geometry adjust
zcoord
bond 5 6 2.262712 cc constant
end
end
mcscf
multiplicity 3
end
scf
maxiter 500000
end
dft
xc b3lyp
end

task dft optimize
task dft freq numerical

This is the error i am getting.

Variables with the same non-blank name are constrained to be equal

Number of frozen variables = 1
Frozen variables = 9

!!! You are using internal coordinates for the optimization but applying
!!! constraints on the Cartesian coordinates by only computing gradients
!!! for a subset of the atoms (via geometry:actlist). This does not
!!! currently work. Either,
!!!
!!! 1) Retain the Cartesian constraints and perform the optimization
!!! entirely in Cartesians by specifying the coordinates in
!!! cartesians and using the NOAUTOZ keyword on the GEOMETRY directive
!!!
!!! or
!!!
!!! 2) Remove the Cartesian constraints and perform the optimization
!!! in redundant internal coordinates. To remove the Cartesian
!!! constraints remove the "set geometry:actlist ..." directive from
!!! startup jobs, or use "unset geometry:actlist" in restart jobs.

------------------------------------------------------------------------
driver: cartesian constraints+internals 0
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
38: task dft optimize
------------------------------------------------------------------------
------------------------------------------------------------------------
There is an error related to the specified geometry
------------------------------------------------------------------------
For more information see the NWChem manual at https://nwchemgit.github.io

For further details see manual section:

Edoardo Aprà

unread,

Sep 8, 2023, 8:04:16 PM9/8/23

to NWChem Forum

This is not what I see.

Have a look what happens with the 7.2.0 Docker image that you could try, too

$ docker run --shm-size 256m -u `id -u` --rm -v `pwd`:/data ghcr.io/nwchemgit/nwchem-720 /data/basusep.nw
Unable to find image 'ghcr.io/nwchemgit/nwchem-720:latest' locally
latest: Pulling from nwchemgit/nwchem-720
846c0b181fff: Already exists
a8e8f4525eb2: Pull complete
99cac80d6782: Pull complete
9b78e3e1cf7a: Pull complete
931237d27a34: Pull complete
Digest: sha256:fbe14da63da7f56fcc4c938c4d5b0beb0a47b148993df4446acc057b1ba1200b
Status: Downloaded newer image for ghcr.io/nwchemgit/nwchem-720:latest
argument 1 = /data/basusep.nw
NWChem w/ OpenMP: maximum threads = 1

============================== echo of input deck ==============================
echo
start
charge 0

geometry units angstrom
C 2.435028 -0.243686 0.10618
C 1.347148 0.768536 -0.141410
C 0.035405 0.572354 -0.277425
H -0.586154 1.432788 -0.413740
C -0.702476 -0.666546 -0.270767
C -2.817882 0.058251 0.076032
O 1.922828 1.977577 -0.205101
F 3.235729 -0.341866 -0.984272
F 1.937943 -1.471669 0.376805
F 3.198425 0.132158 1.159359
O -0.600236 -1.815574 -0.423212
H 1.362584 2.728791 -0.377277
F -3.721334 -0.568420 -0.723502
F -2.877256 1.405776 -0.210313
F -3.233562 -0.088318 1.366574

end
geometry adjust
zcoord
bond 5 6 2.262712 cc constant
end
end

eof
================================================================================

Northwest Computational Chemistry Package (NWChem) 7.2.0
--------------------------------------------------------

Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory
Richland, WA 99352

Copyright (c) 1994-2022
Pacific Northwest National Laboratory
Battelle Memorial Institute

NWChem is an open-source computational chemistry package
distributed under the terms of the
Educational Community License (ECL) 2.0
A copy of the license is included with this distribution
in the LICENSE.TXT file

ACKNOWLEDGMENT
--------------

This software and its documentation were developed at the
EMSL at Pacific Northwest National Laboratory, a multiprogram
national laboratory, operated for the U.S. Department of Energy
by Battelle under Contract Number DE-AC05-76RL01830. Support
for this work was provided by the Department of Energy Office
of Biological and Environmental Research, Office of Basic
Energy Sciences, and the Office of Advanced Scientific Computing.

Job information
---------------

hostname = b14a0cba3d14
program = nwchem
date = Sat Sep 9 00:01:24 2023

compiled = Fri_Jul_21_18:11:07_2023
source = /opt/nwchem
nwchem branch = 7.2.0
nwchem revision = N/A
ga revision = 5.8.0
use scalapack = T
input = /data/basusep.nw
prefix = basusep.
data base = ./basusep.db
status = startup
nproc = 1
time left = -1s

Memory information
------------------

heap = 123668504 doubles = 943.5 Mbytes
stack = 123668505 doubles = 943.5 Mbytes
global = 70667719 doubles = 539.2 Mbytes (distinct from heap & stack)
total = 318004728 doubles = 2426.2 Mbytes
verify = yes
hardfail = no

Directory information
---------------------

0 permanent = .
0 scratch = .

NWChem Input Module
-------------------

Scaling coordinates for geometry "geometry" by 1.889725989
(inverse scale = 0.529177249)

C1 symmetry detected

------
auto-z
------
autoz: The atoms group into disjoint clusters
cluster 1: 1 2 3 4 5 7 8 9 10 11 12

cluster 2: 6 13 14 15
Connecting clusters 1 2 via atoms 5 6 r = 2.26
autoz: regenerating connections with new bonds
no constraints, skipping 0.0000000000000000
no constraints, skipping 0.0000000000000000

Geometry "geometry" -> ""
-------------------------

Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)

No. Tag Charge X Y Z
---- ---------------- ---------- -------------- -------------- --------------
1 C 6.0000 -0.22468979 -2.43676897 0.10811793
2 C 6.0000 0.77652233 -1.34148178 -0.15129934
3 C 6.0000 0.56918203 -0.03115419 -0.28437368
4 H 1.0000 1.42335981 0.59668491 -0.43087427
5 C 6.0000 -0.67487085 0.69770350 -0.26235517
6 C 6.0000 0.03870773 2.81820581 0.07649340
7 O 8.0000 1.98884827 -1.90834096 -0.22991621
8 F 9.0000 -0.33029845 -3.23780379 -0.98139434
9 F 9.0000 -1.45287020 -1.94870834 0.39385090
10 F 9.0000 0.16945939 -3.19776108 1.15633410
11 O 8.0000 -1.82489401 0.58716769 -0.40087014
12 H 1.0000 2.73382639 -1.34259702 -0.41097362
13 F 9.0000 -0.60417767 3.71734340 -0.71499042
14 F 9.0000 1.38218651 2.88746319 -0.22617892
15 F 9.0000 -0.09518059 3.23238576 1.36889422

Atomic Mass
-----------

C 12.000000
H 1.007825
O 15.994910
F 18.998400

Effective nuclear repulsion energy (a.u.) 850.7444519393

Nuclear Dipole moment (a.u.)
----------------------------
X Y Z
---------------- ---------------- ----------------
0.0000000000 0.0000000000 0.0000000000

Z-matrix (autoz)
--------

Units are Angstrom for bonds and degrees for angles

Type Name I J K L M Value
----------- -------- ----- ----- ----- ----- ----- ----------
1 Stretch 1 2 1.50645
2 Stretch 1 8 1.35641
3 Stretch 1 9 1.35214
4 Stretch 1 10 1.35396
5 Stretch 2 3 1.33329
6 Stretch 2 7 1.34061
7 Stretch 3 4 1.07017
8 Stretch 3 5 1.44201
9 Stretch 5 6 2.26286
10 Stretch 5 11 1.16360
11 Stretch 6 13 1.35948
12 Stretch 6 14 1.37889
13 Stretch 6 15 1.36373
14 Stretch 7 12 0.95281
15 Bend 1 2 3 128.93063
16 Bend 1 2 7 107.67925
17 Bend 2 1 8 110.04752
18 Bend 2 1 9 112.18770
19 Bend 2 1 10 110.39491
20 Bend 2 3 4 117.78200
21 Bend 2 3 5 129.00444
22 Bend 2 7 12 117.84852
23 Bend 3 2 7 123.38967
24 Bend 3 5 6 101.76399
25 Bend 3 5 11 143.40085
26 Bend 4 3 5 113.21350
27 Bend 5 6 13 112.54885
28 Bend 5 6 14 108.75018
29 Bend 5 6 15 113.30056
30 Bend 6 5 11 114.74049
31 Bend 8 1 9 108.19074
32 Bend 8 1 10 108.21564
33 Bend 9 1 10 107.67962
34 Bend 13 6 14 107.44147
35 Bend 13 6 15 107.72482
36 Bend 14 6 15 106.76364
37 Torsion 1 2 3 4 177.76051
38 Torsion 1 2 3 5 -2.33567
39 Torsion 1 2 7 12 178.72464
40 Torsion 2 3 5 6 163.28963
41 Torsion 2 3 5 11 -20.81895
42 Torsion 3 2 1 8 111.91100
43 Torsion 3 2 1 9 -8.60094
44 Torsion 3 2 1 10 -128.70353
45 Torsion 3 2 7 12 -1.49966
46 Torsion 3 5 6 13 136.43954
47 Torsion 3 5 6 14 17.51366
48 Torsion 3 5 6 15 -101.03038
49 Torsion 4 3 2 7 -1.96477
50 Torsion 4 3 5 6 -16.80296
51 Torsion 4 3 5 11 159.08845
52 Torsion 5 3 2 7 177.93904
53 Torsion 7 2 1 8 -68.32974
54 Torsion 7 2 1 9 171.15832
55 Torsion 7 2 1 10 51.05573
56 Torsion 11 5 6 13 -40.86462
57 Torsion 11 5 6 14 -159.79050
58 Torsion 11 5 6 15 81.66546

XYZ format geometry
-------------------
15
geometry
C -0.22468979 -2.43676897 0.10811793
C 0.77652233 -1.34148178 -0.15129934
C 0.56918203 -0.03115419 -0.28437368
H 1.42335981 0.59668491 -0.43087427
C -0.67487085 0.69770350 -0.26235517
C 0.03870773 2.81820581 0.07649340
O 1.98884827 -1.90834096 -0.22991621
F -0.33029845 -3.23780379 -0.98139434
F -1.45287020 -1.94870834 0.39385090
F 0.16945939 -3.19776108 1.15633410
O -1.82489401 0.58716769 -0.40087014
H 2.73382639 -1.34259702 -0.41097362
F -0.60417767 3.71734340 -0.71499042
F 1.38218651 2.88746319 -0.22617892
F -0.09518059 3.23238576 1.36889422

==============================================================================
internuclear distances
------------------------------------------------------------------------------
center one | center two | atomic units | angstroms
------------------------------------------------------------------------------
2 C | 1 C | 2.84677 | 1.50645
3 C | 2 C | 2.51955 | 1.33329
4 H | 3 C | 2.02233 | 1.07017
5 C | 3 C | 2.72500 | 1.44201
7 O | 2 C | 2.53339 | 1.34061
8 F | 1 C | 2.56324 | 1.35641
9 F | 1 C | 2.55517 | 1.35214
10 F | 1 C | 2.55862 | 1.35396
11 O | 5 C | 2.19888 | 1.16360
12 H | 7 O | 1.80054 | 0.95281
13 F | 6 C | 2.56905 | 1.35948
14 F | 6 C | 2.60573 | 1.37889
15 F | 6 C | 2.57708 | 1.36373
------------------------------------------------------------------------------
number of included internuclear distances: 13
==============================================================================

==============================================================================
internuclear angles
------------------------------------------------------------------------------
center 1 | center 2 | center 3 | degrees
------------------------------------------------------------------------------
2 C | 1 C | 8 F | 110.05
2 C | 1 C | 9 F | 112.19
2 C | 1 C | 10 F | 110.39
8 F | 1 C | 9 F | 108.19
8 F | 1 C | 10 F | 108.22
9 F | 1 C | 10 F | 107.68
1 C | 2 C | 3 C | 128.93
1 C | 2 C | 7 O | 107.68
3 C | 2 C | 7 O | 123.39
2 C | 3 C | 4 H | 117.78
2 C | 3 C | 5 C | 129.00
4 H | 3 C | 5 C | 113.21
3 C | 5 C | 11 O | 143.40
13 F | 6 C | 14 F | 107.44
13 F | 6 C | 15 F | 107.72
14 F | 6 C | 15 F | 106.76
2 C | 7 O | 12 H | 117.85
------------------------------------------------------------------------------
number of included internuclear angles: 17
==============================================================================

Adjusting existing geometry named geometry

User specification of redundant internal variables
--------------------------------------------------

i j k l value name frz
--- --- --- --- ------------ -------- ---
5 6 2.262712 cc T

C1 symmetry detected

------
auto-z
------

Geometry "geometry" -> "geometry"
---------------------------------

Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)

No. Tag Charge X Y Z
---- ---------------- ---------- -------------- -------------- --------------
1 C 6.0000 -0.22469239 -2.43672883 0.10811930
2 C 6.0000 0.77652651 -1.34144755 -0.15129681
3 C 6.0000 0.56919453 -0.03111834 -0.28436803
4 H 1.0000 1.42337620 0.59671555 -0.43086830
5 C 6.0000 -0.67485359 0.69774737 -0.26234637
6 C 6.0000 0.03869195 2.81810409 0.07648354
7 O 8.0000 1.98884868 -1.90831442 -0.22991643
8 F 9.0000 -0.33030758 -3.23776058 -0.98139459
9 F 9.0000 -1.45286928 -1.94866087 0.39385487
10 F 9.0000 0.16945317 -3.19772579 1.15633332
11 O 8.0000 -1.82487765 0.58721931 -0.40086016
12 H 1.0000 2.73383024 -1.34257491 -0.41097352
13 F 9.0000 -0.60418860 3.71724757 -0.71499751
14 F 9.0000 1.38217080 2.88735343 -0.22619030
15 F 9.0000 -0.09519208 3.23228208 1.36888544

Atomic Mass
-----------

C 12.000000
H 1.007825
O 15.994910
F 18.998400

Effective nuclear repulsion energy (a.u.) 850.7527932649

Nuclear Dipole moment (a.u.)
----------------------------
X Y Z
---------------- ---------------- ----------------
-0.0004258537 -0.0012421454 -0.0001582855

Z-matrix (autoz)
--------

Units are Angstrom for bonds and degrees for angles

Constants are marked with an asterisk (*).

Type Name I J K L M Value
----------- -------- ----- ----- ----- ----- ----- ----------
1 Stretch 1 2 1.50645
2 Stretch 1 8 1.35641
3 Stretch 1 9 1.35214
4 Stretch 1 10 1.35396
5 Stretch 2 3 1.33329
6 Stretch 2 7 1.34061
7 Stretch 3 4 1.07017
8 Stretch 3 5 1.44201
9*Stretch cc 5 6 2.26271
10 Stretch 5 11 1.16360
11 Stretch 6 13 1.35948
12 Stretch 6 14 1.37889
13 Stretch 6 15 1.36373
14 Stretch 7 12 0.95281
15 Bend 1 2 3 128.93063
16 Bend 1 2 7 107.67925
17 Bend 2 1 8 110.04752
18 Bend 2 1 9 112.18770
19 Bend 2 1 10 110.39491
20 Bend 2 3 4 117.78200
21 Bend 2 3 5 129.00444
22 Bend 2 7 12 117.84852
23 Bend 3 2 7 123.38967
24 Bend 3 5 6 101.76399
25 Bend 3 5 11 143.40085
26 Bend 4 3 5 113.21350
27 Bend 5 6 13 112.54885
28 Bend 5 6 14 108.75018
29 Bend 5 6 15 113.30056
30 Bend 6 5 11 114.74049
31 Bend 8 1 9 108.19074
32 Bend 8 1 10 108.21564
33 Bend 9 1 10 107.67962
34 Bend 13 6 14 107.44147
35 Bend 13 6 15 107.72482
36 Bend 14 6 15 106.76364
37 Torsion 1 2 3 4 177.76051
38 Torsion 1 2 3 5 -2.33567
39 Torsion 1 2 7 12 178.72464
40 Torsion 2 3 5 6 163.28963
41 Torsion 2 3 5 11 -20.81895
42 Torsion 3 2 1 8 111.91100
43 Torsion 3 2 1 9 -8.60094
44 Torsion 3 2 1 10 -128.70353
45 Torsion 3 2 7 12 -1.49966
46 Torsion 3 5 6 13 136.43954
47 Torsion 3 5 6 14 17.51366
48 Torsion 3 5 6 15 -101.03038
49 Torsion 4 3 2 7 -1.96477
50 Torsion 4 3 5 6 -16.80296
51 Torsion 4 3 5 11 159.08845
52 Torsion 5 3 2 7 177.93904
53 Torsion 7 2 1 8 -68.32974
54 Torsion 7 2 1 9 171.15832
55 Torsion 7 2 1 10 51.05573
56 Torsion 11 5 6 13 -40.86462
57 Torsion 11 5 6 14 -159.79050
58 Torsion 11 5 6 15 81.66546

XYZ format geometry
-------------------
15
geometry
C -0.22469239 -2.43672883 0.10811930
C 0.77652651 -1.34144755 -0.15129681
C 0.56919453 -0.03111834 -0.28436803
H 1.42337620 0.59671555 -0.43086830
C -0.67485359 0.69774737 -0.26234637
C 0.03869195 2.81810409 0.07648354
O 1.98884868 -1.90831442 -0.22991643
F -0.33030758 -3.23776058 -0.98139459
F -1.45286928 -1.94866087 0.39385487
F 0.16945317 -3.19772579 1.15633332
O -1.82487765 0.58721931 -0.40086016
H 2.73383024 -1.34257491 -0.41097352
F -0.60418860 3.71724757 -0.71499751
F 1.38217080 2.88735343 -0.22619030
F -0.09519208 3.23228208 1.36888544

==============================================================================
internuclear distances
------------------------------------------------------------------------------
center one | center two | atomic units | angstroms
------------------------------------------------------------------------------
2 C | 1 C | 2.84677 | 1.50645
3 C | 2 C | 2.51955 | 1.33329
4 H | 3 C | 2.02233 | 1.07017
5 C | 3 C | 2.72500 | 1.44201
7 O | 2 C | 2.53339 | 1.34061
8 F | 1 C | 2.56324 | 1.35641
9 F | 1 C | 2.55517 | 1.35214
10 F | 1 C | 2.55862 | 1.35396
11 O | 5 C | 2.19888 | 1.16360
12 H | 7 O | 1.80054 | 0.95281
13 F | 6 C | 2.56905 | 1.35948
14 F | 6 C | 2.60573 | 1.37889
15 F | 6 C | 2.57708 | 1.36373
------------------------------------------------------------------------------
number of included internuclear distances: 13
==============================================================================

==============================================================================
internuclear angles
------------------------------------------------------------------------------
center 1 | center 2 | center 3 | degrees
------------------------------------------------------------------------------
2 C | 1 C | 8 F | 110.05
2 C | 1 C | 9 F | 112.19
2 C | 1 C | 10 F | 110.39
8 F | 1 C | 9 F | 108.19
8 F | 1 C | 10 F | 108.22
9 F | 1 C | 10 F | 107.68
1 C | 2 C | 3 C | 128.93
1 C | 2 C | 7 O | 107.68
3 C | 2 C | 7 O | 123.39
2 C | 3 C | 4 H | 117.78
2 C | 3 C | 5 C | 129.00
4 H | 3 C | 5 C | 113.21
3 C | 5 C | 11 O | 143.40
13 F | 6 C | 14 F | 107.44
13 F | 6 C | 15 F | 107.72
14 F | 6 C | 15 F | 106.76
2 C | 7 O | 12 H | 117.85
------------------------------------------------------------------------------
number of included internuclear angles: 17
==============================================================================

Summary of allocated global arrays
-----------------------------------
No active global arrays

MA_summarize_allocated_blocks: starting scan ...
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
MA usage statistics:

allocation statistics:
heap stack
---- -----
current number of blocks 0 0
maximum number of blocks 0 6
current total bytes 0 0
maximum total bytes 0 103144
maximum total K-bytes 0 104
maximum total M-bytes 0 1

Total times cpu: 0.1s wall: 0.1s

Basudha Deb

unread,

Sep 9, 2023, 11:01:37 AM9/9/23

to NWChem Forum

Thankyou sir,

It is working now.

Reply all

Reply to author

Forward