Hi All,
I am running a TD-DFT calculation to get the absorption spectrum but i am getting following error.
write_file_entry: failed to position file
rtdb_seq_put: put failed for "dft:converged" in ./molecule.db
------------------------------------------------------------------------
dft_scfcvg: rtdb_put failed 1
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
51: task tddft energy
------------------------------------------------------------------------
------------------------------------------------------------------------
An error occured in the Runtime Database.
Please help me. I am attaching my input and output.
Input:
start molecule
title "Title"
charge 0
geometry units angstroms print xyz nocenter noautoz noautosym
C -0.89037 -0.89037 -0.89037
C 0.00000 0.00000 -1.77693
C 0.89037 0.89037 -0.89037
C 0.00000 1.77693 0.00000
C -0.89037 0.89037 0.89037
C -1.77693 0.00000 0.00000
C 0.00000 0.00000 1.77693
C 0.00000 -1.77693 0.00000
C 1.77693 0.00000 0.00000
C 0.89037 -0.89037 0.89037
H -2.42917 -0.62203 0.62203
H -0.62203 0.62203 -2.42917
H 0.62203 -0.62203 -2.42917
H 1.52224 1.52224 -1.52224
H 0.62203 2.42917 0.62203
H -0.62203 2.42917 -0.62203
H -1.52224 1.52224 1.52224
H -2.42917 0.62203 -0.62203
H -0.62203 -0.62203 2.42917
H 0.62203 0.62203 2.42917
H -0.62203 -2.42917 0.62203
H 0.62203 -2.42917 -0.62203
H 2.42917 0.62203 0.62203
H 2.42917 -0.62203 -0.62203
H 1.52224 -1.52224 1.52224
H -1.52224 -1.52224 -1.52224
end
basis
* library 6-31G**
end
dft
xc xcamb88 1.00 lyp 0.81 vwn_5 0.19 hfexch 1.00
cam 0.33 cam_alpha 0.19 cam_beta 0.46
direct
mult 1
end
TDDFT
RPA
NROOTS 10
end
task tddft energy
Output
echo
start molecule
title "Title"
charge 0
geometry units angstroms print xyz nocenter noautoz noautosym
C -0.89037 -0.89037 -0.89037
C 0.00000 0.00000 -1.77693
C 0.89037 0.89037 -0.89037
C 0.00000 1.77693 0.00000
C -0.89037 0.89037 0.89037
C -1.77693 0.00000 0.00000
C 0.00000 0.00000 1.77693
C 0.00000 -1.77693 0.00000
C 1.77693 0.00000 0.00000
C 0.89037 -0.89037 0.89037
H -2.42917 -0.62203 0.62203
H -0.62203 0.62203 -2.42917
H 0.62203 -0.62203 -2.42917
H 1.52224 1.52224 -1.52224
H 0.62203 2.42917 0.62203
H -0.62203 2.42917 -0.62203
H -1.52224 1.52224 1.52224
H -2.42917 0.62203 -0.62203
H -0.62203 -0.62203 2.42917
H 0.62203 0.62203 2.42917
H -0.62203 -2.42917 0.62203
H 0.62203 -2.42917 -0.62203
H 2.42917 0.62203 0.62203
H 2.42917 -0.62203 -0.62203
H 1.52224 -1.52224 1.52224
H -1.52224 -1.52224 -1.52224
end
basis
* library 6-31G**
end
dft
xc xcamb88 1.00 lyp 0.81 vwn_5 0.19 hfexch 1.00
cam 0.33 cam_alpha 0.19 cam_beta 0.46
direct
mult 1
end
TDDFT
RPA
NROOTS 10
end
task tddft energy
====================================================================
Northwest Computational Chemistry Package (NWChem) 6.6
------------------------------------------------------
Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory
Richland, WA 99352
Copyright (c) 1994-2015
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 = compute-1-16.local
program = /share/apps/NWChem/6.6/bin/nwchem
date = Wed Jul 26 12:32:56 2017
compiled = Tue_Jan_19_16:15:08_2016
source = /share/apps/NWChem/nwchem-6.6
nwchem branch = 6.6
nwchem revision = 27746
ga revision = 10594
input = ada_opt_b3lyp_tzvp_Td1.nw
prefix = molecule.
data base = ./molecule.db
status = startup
nproc = 2
time left = -1s
Memory information
------------------
heap = 13107196 doubles = 100.0 Mbytes
stack = 13107201 doubles = 100.0 Mbytes
global = 26214400 doubles = 200.0 Mbytes (distinct from heap & stack)
total = 52428797 doubles = 400.0 Mbytes
verify = yes
hardfail = no
Directory information
---------------------
0 permanent = .
0 scratch = .
NWChem Input Module
-------------------
Title
-----
Scaling coordinates for geometry "geometry" by 1.889725989
(inverse scale = 0.529177249)
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 -0.89037000 -0.89037000 -0.89037000
2 C 6.0000 0.00000000 0.00000000 -1.77693000
3 C 6.0000 0.89037000 0.89037000 -0.89037000
4 C 6.0000 0.00000000 1.77693000 0.00000000
5 C 6.0000 -0.89037000 0.89037000 0.89037000
6 C 6.0000 -1.77693000 0.00000000 0.00000000
7 C 6.0000 0.00000000 0.00000000 1.77693000
8 C 6.0000 0.00000000 -1.77693000 0.00000000
9 C 6.0000 1.77693000 0.00000000 0.00000000
10 C 6.0000 0.89037000 -0.89037000 0.89037000
11 H 1.0000 -2.42917000 -0.62203000 0.62203000
12 H 1.0000 -0.62203000 0.62203000 -2.42917000
13 H 1.0000 0.62203000 -0.62203000 -2.42917000
14 H 1.0000 1.52224000 1.52224000 -1.52224000
15 H 1.0000 0.62203000 2.42917000 0.62203000
16 H 1.0000 -0.62203000 2.42917000 -0.62203000
17 H 1.0000 -1.52224000 1.52224000 1.52224000
18 H 1.0000 -2.42917000 0.62203000 -0.62203000
19 H 1.0000 -0.62203000 -0.62203000 2.42917000
20 H 1.0000 0.62203000 0.62203000 2.42917000
21 H 1.0000 -0.62203000 -2.42917000 0.62203000
22 H 1.0000 0.62203000 -2.42917000 -0.62203000
23 H 1.0000 2.42917000 0.62203000 0.62203000
24 H 1.0000 2.42917000 -0.62203000 -0.62203000
25 H 1.0000 1.52224000 -1.52224000 1.52224000
26 H 1.0000 -1.52224000 -1.52224000 -1.52224000
Atomic Mass
-----------
C 12.000000
H 1.007825
Effective nuclear repulsion energy (a.u.) 596.5781673563
Nuclear Dipole moment (a.u.)
----------------------------
X Y Z
---------------- ---------------- ----------------
0.0000000000 0.0000000000 -0.0000000000
XYZ format geometry
-------------------
26
geometry
C -0.89037000 -0.89037000 -0.89037000
C 0.00000000 0.00000000 -1.77693000
C 0.89037000 0.89037000 -0.89037000
C 0.00000000 1.77693000 0.00000000
C -0.89037000 0.89037000 0.89037000
C -1.77693000 0.00000000 0.00000000
C 0.00000000 0.00000000 1.77693000
C 0.00000000 -1.77693000 0.00000000
C 1.77693000 0.00000000 0.00000000
C 0.89037000 -0.89037000 0.89037000
H -2.42917000 -0.62203000 0.62203000
H -0.62203000 0.62203000 -2.42917000
H 0.62203000 -0.62203000 -2.42917000
H 1.52224000 1.52224000 -1.52224000
H 0.62203000 2.42917000 0.62203000
H -0.62203000 2.42917000 -0.62203000
H -1.52224000 1.52224000 1.52224000
H -2.42917000 0.62203000 -0.62203000
H -0.62203000 -0.62203000 2.42917000
H 0.62203000 0.62203000 2.42917000
H -0.62203000 -2.42917000 0.62203000
H 0.62203000 -2.42917000 -0.62203000
H 2.42917000 0.62203000 0.62203000
H 2.42917000 -0.62203000 -0.62203000
H 1.52224000 -1.52224000 1.52224000
H -1.52224000 -1.52224000 -1.52224000
==============================================================================
internuclear distances
------------------------------------------------------------------------------
center one | center two | atomic units | angstroms
------------------------------------------------------------------------------
2 C | 1 C | 2.91012 | 1.53997
3 C | 2 C | 2.91012 | 1.53997
4 C | 3 C | 2.91012 | 1.53997
5 C | 4 C | 2.91012 | 1.53997
6 C | 1 C | 2.91012 | 1.53997
6 C | 5 C | 2.91012 | 1.53997
7 C | 5 C | 2.91012 | 1.53997
8 C | 1 C | 2.91012 | 1.53997
9 C | 3 C | 2.91012 | 1.53997
10 C | 7 C | 2.91012 | 1.53997
10 C | 8 C | 2.91012 | 1.53997
10 C | 9 C | 2.91012 | 1.53997
11 H | 6 C | 2.06945 | 1.09511
12 H | 2 C | 2.06945 | 1.09511
13 H | 2 C | 2.06945 | 1.09511
14 H | 3 C | 2.06817 | 1.09443
15 H | 4 C | 2.06945 | 1.09511
16 H | 4 C | 2.06945 | 1.09511
17 H | 5 C | 2.06817 | 1.09443
18 H | 6 C | 2.06945 | 1.09511
19 H | 7 C | 2.06945 | 1.09511
20 H | 7 C | 2.06945 | 1.09511
21 H | 8 C | 2.06945 | 1.09511
22 H | 8 C | 2.06945 | 1.09511
23 H | 9 C | 2.06945 | 1.09511
24 H | 9 C | 2.06945 | 1.09511
25 H | 10 C | 2.06817 | 1.09443
26 H | 1 C | 2.06817 | 1.09443
------------------------------------------------------------------------------
number of included internuclear distances: 28
==============================================================================
==============================================================================
internuclear angles
------------------------------------------------------------------------------
center 1 | center 2 | center 3 | degrees
------------------------------------------------------------------------------
2 C | 1 C | 6 C | 109.36
2 C | 1 C | 8 C | 109.36
2 C | 1 C | 26 H | 109.59
6 C | 1 C | 8 C | 109.36
6 C | 1 C | 26 H | 109.59
8 C | 1 C | 26 H | 109.59
1 C | 2 C | 3 C | 109.70
1 C | 2 C | 12 H | 110.05
1 C | 2 C | 13 H | 110.05
3 C | 2 C | 12 H | 110.05
3 C | 2 C | 13 H | 110.05
12 H | 2 C | 13 H | 106.89
2 C | 3 C | 4 C | 109.36
2 C | 3 C | 9 C | 109.36
2 C | 3 C | 14 H | 109.59
4 C | 3 C | 9 C | 109.36
4 C | 3 C | 14 H | 109.59
9 C | 3 C | 14 H | 109.59
3 C | 4 C | 5 C | 109.70
3 C | 4 C | 15 H | 110.05
3 C | 4 C | 16 H | 110.05
5 C | 4 C | 15 H | 110.05
5 C | 4 C | 16 H | 110.05
15 H | 4 C | 16 H | 106.89
4 C | 5 C | 6 C | 109.36
4 C | 5 C | 7 C | 109.36
4 C | 5 C | 17 H | 109.59
6 C | 5 C | 7 C | 109.36
6 C | 5 C | 17 H | 109.59
7 C | 5 C | 17 H | 109.59
1 C | 6 C | 5 C | 109.70
1 C | 6 C | 11 H | 110.05
1 C | 6 C | 18 H | 110.05
5 C | 6 C | 11 H | 110.05
5 C | 6 C | 18 H | 110.05
11 H | 6 C | 18 H | 106.89
5 C | 7 C | 10 C | 109.70
5 C | 7 C | 19 H | 110.05
5 C | 7 C | 20 H | 110.05
10 C | 7 C | 19 H | 110.05
10 C | 7 C | 20 H | 110.05
19 H | 7 C | 20 H | 106.89
1 C | 8 C | 10 C | 109.70
1 C | 8 C | 21 H | 110.05
1 C | 8 C | 22 H | 110.05
10 C | 8 C | 21 H | 110.05
10 C | 8 C | 22 H | 110.05
21 H | 8 C | 22 H | 106.89
3 C | 9 C | 10 C | 109.70
3 C | 9 C | 23 H | 110.05
3 C | 9 C | 24 H | 110.05
10 C | 9 C | 23 H | 110.05
10 C | 9 C | 24 H | 110.05
23 H | 9 C | 24 H | 106.89
7 C | 10 C | 8 C | 109.36
7 C | 10 C | 9 C | 109.36
7 C | 10 C | 25 H | 109.59
8 C | 10 C | 9 C | 109.36
8 C | 10 C | 25 H | 109.59
9 C | 10 C | 25 H | 109.59
------------------------------------------------------------------------------
number of included internuclear angles: 60
==============================================================================
Summary of "ao basis" -> "" (cartesian)
------------------------------------------------------------------------------
Tag Description Shells Functions and Types
---------------- ------------------------------ ------ ---------------------
* 6-31G** on all atoms
NWChem DFT Module
-----------------
Title
Basis "ao basis" -> "ao basis" (cartesian)
-----
C (Carbon)
----------
Exponent Coefficients
-------------- ---------------------------------------------------------
1 S 3.04752490E+03 0.001835
1 S 4.57369510E+02 0.014037
1 S 1.03948690E+02 0.068843
1 S 2.92101550E+01 0.232184
1 S 9.28666300E+00 0.467941
1 S 3.16392700E+00 0.362312
2 S 7.86827240E+00 -0.119332
2 S 1.88128850E+00 -0.160854
2 S 5.44249300E-01 1.143456
3 P 7.86827240E+00 0.068999
3 P 1.88128850E+00 0.316424
3 P 5.44249300E-01 0.744308
4 S 1.68714400E-01 1.000000
5 P 1.68714400E-01 1.000000
6 D 8.00000000E-01 1.000000
H (Hydrogen)
------------
Exponent Coefficients
-------------- ---------------------------------------------------------
1 S 1.87311370E+01 0.033495
1 S 2.82539370E+00 0.234727
1 S 6.40121700E-01 0.813757
2 S 1.61277800E-01 1.000000
3 P 1.10000000E+00 1.000000
Summary of "ao basis" -> "ao basis" (cartesian)
------------------------------------------------------------------------------
Tag Description Shells Functions and Types
---------------- ------------------------------ ------ ---------------------
C 6-31G** 6 15 3s2p1d
H 6-31G** 3 5 2s1p
Summary of "ao basis" -> "ao basis" (cartesian)
------------------------------------------------------------------------------
Tag Description Shells Functions and Types
---------------- ------------------------------ ------ ---------------------
C 6-31G** 6 15 3s2p1d
H 6-31G** 3 5 2s1p
int_init: cando_txs set to always be F
Caching 1-el integrals
General Information
-------------------
SCF calculation type: DFT
Wavefunction type: closed shell.
No. of atoms : 26
No. of electrons : 76
Alpha electrons : 38
Beta electrons : 38
Charge : 0
Spin multiplicity: 1
Use of symmetry is: off; symmetry adaption is: off
Maximum number of iterations: 30
This is a Direct SCF calculation.
AO basis - number of functions: 230
number of shells: 108
Convergence on energy requested: 1.00D-06
Convergence on density requested: 1.00D-05
Convergence on gradient requested: 5.00D-04
XC Information
--------------
Hartree-Fock (Exact) Exchange 1.000
CAM-Becke88 Exchange Functional 1.000
VWN V Correlation Functional 0.190 local
Lee-Yang-Parr Correlation Functional 0.810
Range-Separation Parameters
---------------------------
Alpha : 0.19
Beta : 0.46
Gamma : 0.33
Short-Range HF : F
Grid Information
----------------
Grid used for XC integration: medium
Radial quadrature: Mura-Knowles
Angular quadrature: Lebedev.
Tag B.-S. Rad. Rad. Pts. Rad. Cut. Ang. Pts.
--- ---------- --------- --------- ---------
C 0.70 49 11.0 434
H 0.35 45 12.0 434
Grid pruning is: on
Number of quadrature shells: 1210
Spatial weights used: Erf1
Convergence Information
-----------------------
Convergence aids based upon iterative change in
total energy or number of iterations.
Levelshifting, if invoked, occurs when the
HOMO/LUMO gap drops below (HL_TOL): 1.00D-02
DIIS, if invoked, will attempt to extrapolate
using up to (NFOCK): 10 stored Fock matrices.
Damping( 0%) Levelshifting(0.5) DIIS
--------------- ------------------- ---------------
dE on: start ASAP start
dE off: 2 iters 30 iters 30 iters
Screening Tolerance Information
-------------------------------
Density screening/tol_rho: 1.00D-10
AO Gaussian exp screening on grid/accAOfunc: 14
CD Gaussian exp screening on grid/accCDfunc: 20
XC Gaussian exp screening on grid/accXCfunc: 20
Schwarz screening/accCoul: 1.00D-08
Superposition of Atomic Density Guess
-------------------------------------
Sum of atomic energies: -384.57426211
Non-variational initial energy
------------------------------
Total energy = -392.531829
1-e energy = -1699.991452
2-e energy = 710.881455
HOMO = -0.307028
LUMO = 0.101159
Time after variat. SCF: 7.9
Time prior to 1st pass: 7.9
Grid_pts file = ./molecule.gridpts.0
Record size in doubles = 12289 No. of grid_pts per rec = 3070
Max. records in memory = 96 Max. recs in file = 3537147
Grid integrated density: 76.002782842685
Requested integration accuracy: 0.10E-05
Memory utilization after 1st SCF pass:
Heap Space remaining (MW): 11.93 11925764
Stack Space remaining (MW): 13.11 13105108
convergence iter energy DeltaE RMS-Dens Diis-err time
---------------- ----- ----------------- --------- --------- --------- ------
d= 0,ls=0.0,diis 1 -390.4104093064 -9.87D+02 3.75D-03 1.04D+00 117.5
Grid integrated density: 76.002350701752
Requested integration accuracy: 0.10E-05
d= 0,ls=0.0,diis 2 -390.5116748345 -1.01D-01 6.40D-04 1.52D-02 229.3
Grid integrated density: 76.002362417630
Requested integration accuracy: 0.10E-05
d= 0,ls=0.0,diis 3 -390.5135415405 -1.87D-03 2.38D-04 5.12D-03 340.4
Grid integrated density: 76.002355614791
Requested integration accuracy: 0.10E-05
d= 0,ls=0.0,diis 4 -390.5141345326 -5.93D-04 8.86D-05 4.77D-04 470.4
Grid integrated density: 76.002351173539
Requested integration accuracy: 0.10E-05
d= 0,ls=0.0,diis 5 -390.5141849091 -5.04D-05 2.87D-05 3.89D-05 600.5
Grid integrated density: 76.002352537601
Requested integration accuracy: 0.10E-05
Resetting Diis
d= 0,ls=0.0,diis 6 -390.5141889428 -4.03D-06 6.27D-06 3.57D-06 730.7
Grid integrated density: 76.002352637716
Requested integration accuracy: 0.10E-05
d= 0,ls=0.0,diis 7 -390.5141893807 -4.38D-07 8.86D-07 1.29D-08 859.6
hdbm_fseek: Stale file handle
write_file_entry: failed to position file
rtdb_seq_put: put failed for "dft:converged" in ./molecule.db
------------------------------------------------------------------------
dft_scfcvg: rtdb_put failed 1
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
51: task tddft energy
------------------------------------------------------------------------
------------------------------------------------------------------------
An error occured in the Runtime Database
------------------------------------------------------------------------
For more information see the NWChem manual at http://nwchemgit.github.io/index.php/NWChem_Documentation
For further details see manual section:
0:dft_scfcvg: rtdb_put failed:Received an Error in Communication
dft_scfcvg: rtdb_put failed 1
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
0:
------------------------------------------------------------------------
------------------------------------------------------------------------
An error occured in the Runtime Database
------------------------------------------------------------------------
For more information see the NWChem manual at http://nwchemgit.github.io/index.php/NWChem_Documentation
For further details see manual section:
1:dft_scfcvg: rtdb_put failed:Received an Error in Communication
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM 0
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
MPI_ABORT was invoked on rank 1 in communicator MPI COMMUNICATOR 3 DUP FROM 0
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
srun: error: compute-1-16: tasks 0-1: Exited with exit code 1
|