Question regarding frequency analysis
Jörg Saßmannshausen
jorg.sassm... at strath.ac.uk
Mon Mar 9 11:34:26 UTC 2009
Dear all,
I am fairly new to cp2k and after the workshop in Zurich I am beginning
slowly to find my way around the program. I thought I started off a bit
simple and run a geometry optimisation of 2 molecules in one box which I
have done before using a different program. After successful convergence
of that run, I decided to run the frequency calculation to see whether
or not I actually reached a minimum (global or local does not matter
here right now). So I had a look at the regtest files, picked out one
which has a frequency calculation in it, amended my input file so it is
using the restart files as an input. Judging from the output, it was
reading the new geometry as I got that warning in the logfile:
*** 18:44:39 WARNING in atoms_input:read_atoms_input err=-300
***
*** Overwriting coordinates. Active coordinates read from &COORD
section. ***
*** Active coordinates READ from &COORD section atoms_input.F line
130 ***
I assume that was ok?
I am somehow confused about the output. As it is rather long, I only
copy the confusing bits in here. The run finished without any errors.
After the calculation of the Hessian I get:
VIB| Cartesian Low frequencies --- -15.825 -13.679 -12.802
-2.2949
VIB| Cartesian Low frequencies --- -1.3729 -0.44402 -0.38034
-0.21622
VIB| Cartesian Low frequencies ----0.15963
VIB| Frequencies after removal of the rotations and translations
*) VIB| Internal Low frequencies --- -13.696 -12.335 -9.2308
-1.6738
VIB| Internal Low frequencies ----0.86027 -0.37350 -0.23108E-01
0.80471E-02
VIB| Internal Low frequencies --- 0.45472E-01 0.13125 0.27273
0.33375
VIB| Internal Low frequencies --- 0.37453 0.42756 0.49331
0.55433
VIB| Internal Low frequencies --- 0.65046 0.85933 1.1011
1.1978
Ok, I am aware that the first 6 frequencies can be dumped as they are
usually due to rotation and translation of the molecule. That is what
the program did for me, fine, that makes sense.
So from the next line onwards, which I marked with a *), I should get
the frequencies which matter in my case. Surprise, surprise, I get
negative ones, so I am not really in the miniumum but somewhere else.
However, further down in the logfile I will find that:
VIB| NORMAL MODES - CARTESIAN DISPLACEMENTS
VIB|
VIB| 1 2 3
VIB|Frequency (cm^-1) -812.246483 -770.814156 -666.811278
VIB|Intensities 0.000000 0.000000 0.000000
VIB|Red.Masses (a.u.) 13.143487 15.458038 10.885859
VIB|Frc consts (a.u.) -0.014647 -0.013971 -0.005510
[...]
VIB| 4 5 6
VIB|Frequency (cm^-1) -283.949590 -203.564861 -134.130900
VIB|Intensities 0.000000 0.000000 0.000000
VIB|Red.Masses (a.u.) 2.055003 2.986810 2.007608
VIB|Frc consts (a.u.) -0.000034 -0.000013 -0.000002
[...]
VIB| 7 8 9
VIB|Frequency (cm^-1) -33.363199 19.688092 46.801179
VIB|Intensities 0.000000 0.000000 0.000000
VIB|Red.Masses (a.u.) 3.570177 3.101716 2.496785
VIB|Frc consts (a.u.) 0.000000 0.000000 0.000000
Ok, doing the same as I did above, ignoring the first 6 ones would still
leave me with the first one I am interested in. As I wanted to have the
output in the molden-format so I can actually find out which part of the
molecule is causing the negative frequency, I opened that file in
molden, only to find out that I am having the 19.68 as the lowest
frequency but not the -33.36.
So, now I am completly confused. Apparently, my molecule has not
converged to a minimum as I got negative frequencies, but they are not
in the molden file so how can I find out which part of the molecule is
causing the negative frequency?
Is there something I did wrong here?
I have attached input files (input, forceeval and subsys) at the end of
this email. I took the liberty to omit the coordinates and cut out some
part of the subsys.inc as they are not part of the problem. As I said,
the program runs ok, so there is more a confusion or a problem in the
input file. I can, if requested, provide them of cause.
Many thanks for you help!
Best wishes from Glasgow!
Jörg
input-file:
! Possibly restart (if explicitly requested)
@IF 1
&EXT_RESTART ON
RESTART_DEFAULT F
RESTART_FILE_NAME FLUORGEOM-1.restart
RESTART_POS T
RESTART_COUNTERS T
&END EXT_RESTART
@ENDIF
&GLOBAL
PROJECT FLUORGEOM
RUN_TYPE NORMAL_MODES
PRINT_LEVEL LOW
&END GLOBAL
&VIBRATIONAL_ANALYSIS
NPROC_REP 4
DX 0.001
! INTENSITIES
&PRINT
&PROGRAM_RUN_INFO ON
&END
&MOLDEN_VIB
FILENAME=frequencies.mol
&END
&END
&END
@INCLUDE 'force_eval.inc'
force_eval.inc file:
@SET SCF_CONV 1.0E-6
@SET CUTOFF 450
@SET FUNCTIONAL BLYP
@SET DECOUPLING MT
@SET CHARGE 1
&FORCE_EVAL
&PRINT
&FORCES OFF
&END
&END
&MIXED
&PRINT
&DIPOLE
&END
&END
&END
METHOD QS
&DFT
CHARGE ${CHARGE}
&MGRID
CUTOFF ${CUTOFF}
NGRIDS 5
&END MGRID
&QS
EPS_DEFAULT 1.0E-12
&END QS
&SCF
SCF_GUESS ATOMIC
EPS_SCF ${SCF_CONV}
MAX_SCF 30
&PRINT
&RESTART
LOG_PRINT_KEY T
FILENAME =./WFN_restart.wfn
&EACH
QS_SCF 0
&END EACH
ADD_LAST NUMERIC
COMMON_ITERATION_LEVELS 1
&END RESTART
&END PRINT
&OT ON
MINIMIZER DIIS
! MINIMIZER CG
! PRECONDITIONER FULL_ALL
! PRECONDITIONER FULL_KINETIC
PRECONDITIONER FULL_SINGLE_INVERSE
!ENERGY_GAP 0.001
&END OT
&OUTER_SCF
EPS_SCF ${SCF_CONV}
MAX_SCF 5
&END OUTER_SCF
&END SCF
&XC
&XC_FUNCTIONAL ${FUNCTIONAL}
&END XC_FUNCTIONAL
&END XC
@IF ( ${DECOUPLING} == NONE )
&POISSON
&END
@ENDIF
@IF ( ${DECOUPLING} == MT )
&POISSON
POISSON_SOLVER MT
PERIODIC NONE
&MT
&END
&END
@ENDIF
@IF ( ${DECOUPLING} == WAVELET )
&POISSON
POISSON_SOLVER WAVELET
PERIODIC NONE
&WAVELET
SCF_TYPE 60
&END
&END
@ENDIF
&END DFT
! Include subsys
@INCLUDE 'subsys.inc'
&END FORCE_EVAL
subsys.inc file:
&SUBSYS
&CELL
# ABC [angstrom] 23 15 10.0
ABC [angstrom] 25 17 12
PERIODIC NONE
&END CELL
&TOPOLOGY
CONNECTIVITY OFF
COORDINATE XYZ
COORD_FILE_NAME fluor.xyz
CENTER_COORDINATES
&END TOPOLOGY
&KIND C
POTENTIAL GTH
&POTENTIAL
# C GTH-BLYP-q4
2 2
0.33806609 2 -9.13626871 1.42925956
2
0.30232223 1 9.66551228
0.28637912 0
&END POTENTIAL
&BASIS
# C DZVP-GTH-BLYP
2
2 0 1 4 2 2
4.3451975957 0.1511172750 0.0000000000 -0.0883417890
0.0000000000
1.2765552224 -0.0330272512 0.0000000000 -0.2797032766
0.0000000000
0.4047139801 -0.6994401873 0.0000000000 -0.4686400677
0.0000000000
0.1166096360 -0.3842706677 1.0000000000 -0.4085514115
1.0000000000
3 2 2 1 1
0.6000000000 1.0000000000
&END BASIS
&END KIND
&KIND F
POTENTIAL GTH
&POTENTIAL
# F GTH-BLYP-q7
2 5
0.21384014 2 -21.90241518 3.27597572
2
0.19459028 1 23.79658295
0.18786326 0
&END POTENTIAL
&BASIS
# F DZVP-GTH-BLYP
2
2 0 1 4 2 2
10.7284760684 0.1539953252 0.0000000000 -0.1034591141
0.0000000000
3.1496622427 -0.0503062083 0.0000000000 -0.3116781877
0.0000000000
0.9671794608 -0.7107682323 0.0000000000 -0.4776960745
0.0000000000
0.2640315133 -0.3648266470 1.0000000000 -0.3688578623
1.0000000000
3 2 2 1 1
1.0000000000 1.0000000000
&END BASIS
&END KIND
&KIND H
POTENTIAL GTH
&POTENTIAL
# H GTH-BLYP-q1
1
0.20000000 2 -4.19596147 0.73049821
0
&END POTENTIAL
&BASIS
# H DZV-GTH-BLYP
[...]
&END BASIS
&END KIND
&END SUBSYS
--
*************************************************************
Jörg Saßmannshausen
Research Fellow
University of Strathclyde
Department of Pure and Applied Chemistry
295 Cathedral St.
Glasgow
G1 1XL
email: jorg.sassm... at strath.ac.uk
web: http://sassy.formativ.net
Please avoid sending me Word or PowerPoint attachments.
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