[molpro-user] isotope vibrational frequencies
Kirk Peterson
kipeters at wsu.edu
Tue Dec 9 16:32:28 GMT 2008
Jeremy,
ummm, this seems like a bit of a bug. The only way I could get the
2nd frequency job to accept the new masses was to restart the
calculation from file 2:
***,HCl
memory,100,M
FILE,2,HCl.WFU
gprint,distance=1,angle=1
geometry={X,Y,ANGSTROM
H,
Cl, H, R1}
R1 = 1.27
basis=VDZ
! mass,iso,H=2.0141018,Cl=34.96885271
! {HF}
! {OPTG}
! {Frequencies}
mass,iso,H=1.00794,Cl=34.96885271
{Frequencies}
-Kirk
On Dec 9, 2008, at 6:57 AM, Jeremy Merritt wrote:
> Dr. Peterson,
> Thankyou for your reply. However this still doesn't fully work for
> me. My output file is below. The calculation does correctly
> redefine the mass for the 1st freq. calculation, but then I get the
> same answer for the second freq. calc. I even tried to recalculate
> the hessian with {frequencies,new} for the second freq. calc and it
> still gives the vibrational freq. of DCl.
>
> Any suggestions?
> Thanks,
> Jeremy
>
>
> ***,HCl
> FILE,2,HCl.WFU,NEW
> memory,200,M
> gprint,distance=1,angle=1
> geometry={X,Y,ANGSTROM
> H,
> Cl, H, R1}
> R1 = 1.27
> basis=VDZ
> mass,iso,H=2.0141018,Cl=34.96885271
> {HF}
> {OPTG}
> {Frequencies}
> mass,iso,H=1.00794,Cl=34.96885271
> {Frequencies}
>
> Variables initialized (599), CPU time= 0.01 sec
> Commands initialized (355), CPU time= 0.02 sec, 460 directives.
> Default parameters read. Elapsed time= 0.09 sec
> Checking input...
> Passed
> 1
>
>
> *** PROGRAM SYSTEM MOLPRO ***
> Copyright, University College Cardiff
> Consultants Limited, 2004
>
> Version 2008.1 linked 25 Aug 2008
> 15:17:21
>
>
> **********************************************************************************************************************************
> LABEL * HCl
> Linux-2.6.4-52-smp/f23(x86_64) 64 bit
> version DATE: 9-
> Dec-08 TIME: 09:18:52
> **********************************************************************************************************************************
>
> Patch level: 3
> **********************************************************************************************************************************
>
> Variable memory set to 8000000 words, buffer space 230000 words
>
>
>
> Permanent file 2 hcl.wfu assigned. Implementation=df
>
>
> **********************************************************************************************************************************
> DATASETS * FILE NREC LENGTH (MB) RECORD NAMES
> 2 1 0.03
> 500 VAR
> PROGRAMS * TOTAL FILE
> CPU TIMES * 0.28 0.00
> REAL TIME * 0.34 SEC
> DISK USED * 0.03 MB
> **********************************************************************************************************************************
>
> SETTING R1 = 1.27000000
> Variable memory set to 200000000 words, buffer space 230000 words
>
> SETTING BASIS = VDZ
>
> SETTING MASS FOR H (Z= 1) TO 2.014
> SETTING MASS FOR CL (Z= 17) TO 34.969
>
>
> Recomputing integrals since basis changed
>
>
> Using spherical harmonics
>
> Library entry H S cc-pVDZ selected for orbital
> group 1
> Library entry H P cc-pVDZ selected for orbital
> group 1
> Library entry CL S cc-pVDZ selected for orbital
> group 2
> Library entry CL P cc-pVDZ selected for orbital
> group 2
> Library entry CL D cc-pVDZ selected for orbital
> group 2
>
> 1PROGRAM * SEWARD (Integral evaluation for generally contracted
> gaussian basis sets) Author: Roland Lindh, 1990
>
> Geometry written to block 1 of record 700
>
> Orientation using atomic masses Molecule type: Linear
> User-specified symmetry elements: X,Y
> Symmetry elements: X,Y
> Rotational constants: 164.5313064 164.5313064 0.0000000
> GHz
>
> Point group C2v
>
>
>
> ATOMIC COORDINATES
>
> NR ATOM CHARGE X Y Z
>
> 1 H 1.00 0.000000000 0.000000000 -2.269250136
> 2 CL 17.00 0.000000000 0.000000000 0.130702051
>
> Bond lengths in Bohr (Angstrom)
>
> 1-2 2.399952187
> (1.270000000)
>
> NUCLEAR CHARGE: 18
> NUMBER OF PRIMITIVE AOS: 49
> NUMBER OF SYMMETRY AOS: 48
> NUMBER OF CONTRACTIONS: 23 ( 12A1 + 5B1 + 5B2
> + 1A2 )
> NUMBER OF CORE ORBITALS: 5 ( 3A1 + 1B1 + 1B2
> + 0A2 )
> NUMBER OF VALENCE ORBITALS: 5 ( 3A1 + 1B1 + 1B2
> + 0A2 )
>
>
> NUCLEAR REPULSION ENERGY 7.08347445
>
> EXTRA SYMMETRY OF AOS IN SYMMETRY 1: 1 1 1 1 1 1 1 1 1 1 1 2
>
> Eigenvalues of metric
>
> 1 0.209E-01 0.656E-01 0.103E+00 0.165E+00 0.927E+00 0.100E+01
> 0.100E+01 0.100E+01
> 2 0.124E+00 0.651E+00 0.100E+01 0.123E+01 0.199E+01
> 3 0.124E+00 0.651E+00 0.100E+01 0.123E+01 0.199E+01
> 4 0.100E+01
>
>
> Contracted 2-electron integrals neglected if value below 1.0D-11
> AO integral compression algorithm 1 Integral accuracy 1.0D-11
>
> 0.262 MB (compressed) written to integral file (100.0%)
>
>
> NUMBER OF SORTED TWO-ELECTRON INTEGRALS: 12241. BUFFER
> LENGTH: 32768
> NUMBER OF SEGMENTS: 1 SEGMENT LENGTH: 12241 RECORD
> LENGTH: 524288
>
> Memory used in sort: 0.57 MW
>
> SORT1 READ 16495. AND WROTE 9376. INTEGRALS IN 1
> RECORDS. CPU TIME: 0.00 SEC, REAL TIME: 0.01 SEC
> SORT2 READ 9376. AND WROTE 12241. INTEGRALS IN 1
> RECORDS. CPU TIME: 0.00 SEC, REAL TIME: 0.02 SEC
>
> FILE SIZES: FILE 1: 2.3 MBYTE, FILE 4: 4.2 MBYTE,
> TOTAL: 6.6 MBYTE
>
> OPERATOR DM FOR CENTER 0 COORDINATES: 0.000000
> 0.000000 0.000000
>
>
> **********************************************************************************************************************************
> DATASETS * FILE NREC LENGTH (MB) RECORD NAMES
> 1 19 2.13 500 610 700
> 900 950 970 1000 129 960
> 1100 VAR BASINP
> GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S
> 1400 1410 1200
> 1210 1080 1600 1650 1300
> 1700 T V
> H0 H01 AOSYM SMH MOLCAS ERIS OPER
> 2 4 1.11 500 610 700
> 1000 VAR BASINP
> GEOM BASIS
> PROGRAMS * TOTAL INT FILE
> CPU TIMES * 0.40 0.09 0.00
> REAL TIME * 0.53 SEC
> DISK USED * 7.90 MB
> **********************************************************************************************************************************
>
> 1PROGRAM * RHF-SCF (CLOSED SHELL) Authors: W. Meyer, H.-J.
> Werner
>
>
> NUMBER OF ELECTRONS: 9+ 9-
> CONVERGENCE THRESHOLDS: 1.00E-06 (Density) 1.00E-07 (Energy)
> MAX. NUMBER OF ITERATIONS: 60
> INTERPOLATION TYPE: DIIS
> INTERPOLATION STEPS: 2 (START) 1 (STEP)
> LEVEL SHIFTS: 0.00 (CLOSED) 0.00 (OPEN)
>
>
>
> Orbital guess generated from atomic densities. Occupancy: 6
> 2 2 0
>
> Molecular orbital dump at record 2100.2
>
> ITERATION DDIFF GRAD ENERGY 2-
> EL.EN. DIPOLE MOMENTS DIIS
> 1 0.000D+00 0.000D+00 -460.07344612 366.700881
> 0.000000 0.000000 -0.981778 0
> 2 0.000D+00 0.195D-01 -460.08804901 365.127719
> 0.000000 0.000000 -0.501179 1
> 3 0.478D-01 0.619D-02 -460.08927421 365.611507
> 0.000000 0.000000 -0.575282 2
> 4 0.909D-02 0.141D-02 -460.08940947 365.565954
> 0.000000 0.000000 -0.558117 3
> 5 0.327D-02 0.277D-03 -460.08941449 365.576206
> 0.000000 0.000000 -0.555003 4
> 6 0.611D-03 0.412D-04 -460.08941458 365.572539
> 0.000000 0.000000 -0.554803 5
> 7 0.858D-04 0.930D-05 -460.08941459 365.573051
> 0.000000 0.000000 -0.554676 6
> 8 0.321D-04 0.106D-05 -460.08941459 365.573013
> 0.000000 0.000000 -0.554658 6
> 9 0.319D-05 0.191D-06 -460.08941459 365.573014
> 0.000000 0.000000 -0.554655 5
> 10 0.639D-06 0.125D-07 -460.08941459 365.573014
> 0.000000 0.000000 -0.554654 0
>
> Final occupancy: 5 2 2 0
>
> !RHF STATE 1.1 Energy -460.089414586984
> Nuclear energy 7.08347445
> One-electron energy -649.95939593
> Two-electron energy 182.78650689
> Virial quotient -0.99998596
> !RHF STATE 1.1 Dipole moment 0.00000000 0.00000000
> -0.55465432
> Dipole moment /Debye 0.00000000 0.00000000
> -1.40969832
>
> Orbital energies:
>
> 1.1 2.1 3.1 4.1
> 5.1 6.1 7.1
> -104.843011 -10.568600 -8.036591 -1.114522 -0.621678
> 0.150193 0.494246
>
> 1.2 2.2 3.2 4.2
> -8.032814 -0.471580 0.750907 0.879037
>
> 1.3 2.3 3.3 4.3
> -8.032814 -0.471580 0.750907 0.879037
>
> 1.4
> 0.981016
>
>
> **********************************************************************************************************************************
> DATASETS * FILE NREC LENGTH (MB) RECORD NAMES
> 1 19 2.13 500 610 700
> 900 950 970 1000 129 960
> 1100 VAR BASINP
> GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S
> 1400 1410 1200
> 1210 1080 1600 1650 1300
> 1700 T V
> H0 H01 AOSYM SMH MOLCAS ERIS OPER
> 2 5 1.14 500 610 700
> 1000 2100 VAR
> BASINP GEOM BASIS RHF
> PROGRAMS * TOTAL HF INT FILE
> CPU TIMES * 0.42 0.01 0.09 0.00
> REAL TIME * 0.58 SEC
> DISK USED * 7.90 MB
> **********************************************************************************************************************************
>
>
> PROGRAM * OPT (Geometry optimization) Authors: F. Eckert and H.-
> J. Werner
>
>
> *** Long output written to logfile /fire/heaven/merrit/MOLPOOL/BeOBe/
> BeOBe-iso.log ***
>
>
> Geometry optimization using default procedure for command HF-SCF
>
> Geometry written to block 1 of record 700
>
> Making model hessian for Z-matrix coordinates
>
> Quadratic Steepest Descent - Minimum Search
>
> Optimization point 1
>
> Variable Last Current
> Next Gradient Hessian
>
> E(HF-SCF000) / Hartree 0.00000000 -460.08941459 0.00000000
> R1 / ANGSTROM 0.00000000 1.27000000
> 1.27471876 -0.00976772 2.06997840
> Convergence: 0.00000000 (line search)
> 0.00891716 0.00516886 (total)
>
> Optimization point 2
>
> Variable Last Current
> Next Gradient Hessian
>
> E(HF-SCF000) / Hartree -460.08941459 -460.08944561 0.00000000
> R1 / ANGSTROM 1.27000000 1.27471876
> 1.27724501 -0.00340590 1.34820007
> Convergence: 0.00000000 (line search)
> 0.00477393 0.00180232 (total)
>
> Optimization point 3
>
> Variable Last Current
> Next Gradient Hessian
>
> E(HF-SCF000) / Hartree -460.08944561 -460.08944998 0.00000000
> R1 / ANGSTROM 1.27471876 1.27724501
> 1.27729469 -0.00006569 1.32219818
> Convergence: 0.00000000 (line search)
> 0.00009388 0.00003476 (total)
>
> END OF GEOMETRY OPTIMIZATION. TOTAL CPU: 7.3 SEC
>
> ITER. ENERGY(OLD) ENERGY(NEW) DE GRADMAX
> GRADNORM GRADRMS STEPMAX STEPLEN STEPRMS
> 1 -460.08941459 -460.08944561 -0.00003102 0.00516886
> 0.00516886 0.00516886 0.00891716 0.00891716 0.00891716
> 2 -460.08944561 -460.08944998 -0.00000438 0.00180232
> 0.00180232 0.00180232 0.00477393 0.00477393 0.00477393
> 3 -460.08944998 -460.08944998 0.00000000 0.00003476
> 0.00003476 0.00003476 0.00009388 0.00009388 0.00009388
>
> Geometry written to block 1 of record 700
>
>
> **********************************************************************************************************************************
> DATASETS * FILE NREC LENGTH (MB) RECORD NAMES
> 1 19 2.13 500 610 700
> 900 950 970 1000 129 960
> 1100 VAR BASINP
> GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S
> 1400 1410 1200
> 1210 1080 1600 1650 1300
> 1700 T V
> H0 H01 AOSYM SMH MOLCAS ERIS OPER
> 2 5 1.14 500 610 700
> 1000 2100 VAR
> BASINP GEOM BASIS RHF
> PROGRAMS * TOTAL OPTG HF INT FILE
> CPU TIMES * 7.69 7.26 0.01 0.09 0.00
> REAL TIME * 9.44 SEC
> DISK USED * 7.93 MB
> **********************************************************************************************************************************
>
>
> PROGRAM * HESSIAN
>
> Computing numerical hessian using default procedure for command HF-SCF
>
> Symmetry elements for unique displacements: X Y
> Using no symmetry in wavefunction calculations
>
> Running default procedure: HF-SCF000
>
>
> Numerically approximating hessian using central gradient differences
>
> Task list generated. Total number of displacements: 8
>
> 5 tasks completed, CPU= 12.54 sec, Elapsed= 13.78 sec
>
> Numerical HF-SCF000 hessian completed. CPU-time: 20.08 sec,
> Elapsed: 21.46 sec
>
> HF-SCF hessian saved to record 5300.2
>
> FREQUENCIES * CALCULATION OF HARMONIC VIBRATIONAL SPECTRA FOR HF-SCF
>
>
> Permanent Dipole Moment [debye]
> 1- 3 0.000000 0.000000 -1.417564
>
> Dipole Moment Norm 1.4175641 [debye]
>
> Dipole Moment Derivatives [debye/ang]
> 1 2 3
> 4 5 6
> 1 1.1098250 0.0000000 0.0000000 -1.1098210
> 0.0000000 0.0000000
> 2 0.0000000 1.1098250 0.0000000 0.0000000
> -1.1098210 0.0000000
> 3 0.0000000 0.0000000 1.0777493 0.0000000
> 0.0000000 -1.0777532
>
> Projecting out rotations and translations
>
> Low Vibration Wavenumber
> Nr [1/cm]
> 1 0.00
> 2 0.00
> 3 0.00
> 4 0.00
> 5 0.00
>
> Vibration Wavenumber
> Nr [1/cm]
> 1 2258.72
>
> FREQUENCIES * CALCULATION OF NORMAL MODES FOR HF-SCF
>
>
> Atomic Coordinates
>
> Nr Atom Charge X Y Z
>
> 1 H 1.00 0.000000000 0.000000000 -2.282284369
> 2 CL 17.00 0.000000000 0.000000000 0.131452784
>
> Frequencies dumped to record 5400.2
>
> Gradient norm at reference geometry: 0.65687D-04
>
> Normal Modes
>
> 1 A1
> Wavenumbers [cm-1] 2258.72
> Intensities [km/mol] 25.78
> Intensities [relative] 100.00
> HX1 0.00000
> HY1 0.00000
> HZ1 0.68517
> CLX2 0.00000
> CLY2 0.00000
> CLZ2 -0.03946
>
>
> Normal Modes of low/zero frequencies
>
> 1 2 3
> 4 5
> Wavenumbers [cm-1] 0.00 0.00 0.00
> 0.00 0.00
> Intensities [km/mol] 0.00 0.00 0.00
> 0.00 0.00
> Intensities [relative] 0.00 0.00 0.00
> 0.00 0.00
> HX1 0.00000 0.00000 -0.07488
> 0.70064 0.00000
> HY1 0.67032 0.00000 0.00000
> 0.00000 0.21718
> HZ1 -0.05068 0.00000 0.00000
> 0.00000 0.15643
> CLX2 0.00000 -0.00015 0.16815
> 0.01797 0.00000
> CLY2 0.00000 0.16911 0.00014
> 0.00002 0.00000
> CLZ2 -0.05068 0.00000 0.00000
> 0.00000 0.15643
>
>
> Zero point energy: 0.00514573 [H] 1129.36 [1/CM] 13.51
> [KJ/MOL]
> Frequency information read from record 5400.2
>
> Recomputing wavefunction at initial geometry
>
>
> **********************************************************************************************************************************
> DATASETS * FILE NREC LENGTH (MB) RECORD NAMES
> 1 19 2.13 500 610 700
> 900 950 970 1000 129 960
> 1100 VAR BASINP
> GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S
> 1400 1410 1200
> 1210 1080 1600 1650 1300
> 1700 T V
> H0 H01 AOSYM SMH MOLCAS ERIS OPER
> 2 8 1.15 500 610 700
> 1000 2100 5300 5400
> 5450 VAR BASINP
> GEOM BASIS RHF HESS FREQ NMOD
> PROGRAMS * TOTAL FREQ OPTG HF
> INT FILE
> CPU TIMES * 27.64 19.93 7.26 0.01
> 0.09 0.00
> REAL TIME * 31.13 SEC
> DISK USED * 9.16 MB
> **********************************************************************************************************************************
>
> SETTING MASS FOR H (Z= 1) TO 1.008
> SETTING MASS FOR CL (Z= 17) TO 34.969
>
>
> PROGRAM * HESSIAN
>
> HF-SCF hessian read from record 5300.2
>
> FREQUENCIES * CALCULATION OF HARMONIC VIBRATIONAL SPECTRA FOR HF-SCF
>
>
> Permanent Dipole Moment [debye]
> 1- 3 0.000000 0.000000 -1.417564
>
> Dipole Moment Norm 1.4175641 [debye]
>
> Dipole Moment Derivatives [debye/ang]
> 1 2 3
> 4 5 6
> 1 1.1098250 0.0000000 0.0000000 -1.1098210
> 0.0000000 0.0000000
> 2 0.0000000 1.1098250 0.0000000 0.0000000
> -1.1098210 0.0000000
> 3 0.0000000 0.0000000 1.0777493 0.0000000
> 0.0000000 -1.0777532
>
> Projecting out rotations and translations
>
> Low Vibration Wavenumber
> Nr [1/cm]
> 1 0.00
> 2 0.00
> 3 0.00
> 4 0.00
> 5 0.00
>
> Vibration Wavenumber
> Nr [1/cm]
> 1 2258.72
>
> FREQUENCIES * CALCULATION OF NORMAL MODES FOR HF-SCF
>
>
> Atomic Coordinates
>
> Nr Atom Charge X Y Z
>
> 1 H 1.00 0.000000000 0.000000000 -2.282284369
> 2 CL 17.00 0.000000000 0.000000000 0.131452784
>
> Frequencies dumped to record 5401.2
>
> Gradient norm at reference geometry: 0.65687D-04
>
> Normal Modes
>
> 1 A1
> Wavenumbers [cm-1] 2258.72
> Intensities [km/mol] 25.78
> Intensities [relative] 100.00
> HX1A 0.00000
> HY1A 0.00000
> HZ1A 0.68517
> CLX2A 0.00000
> CLY2A 0.00000
> CLZ2A -0.03946
>
>
> Normal Modes of low/zero frequencies
>
> 1 2 3
> 4 5
> Wavenumbers [cm-1] 0.00 0.00 0.00
> 0.00 0.00
> Intensities [km/mol] 0.00 0.00 0.00
> 0.00 0.00
> Intensities [relative] 0.00 0.00 0.00
> 0.00 0.00
> HX1A 0.00000 0.00000 -0.07488
> 0.70064 0.00000
> HY1A 0.67032 0.00000 0.00000
> 0.00000 0.21718
> HZ1A -0.05068 0.00000 0.00000
> 0.00000 0.15643
> CLX2A 0.00000 -0.00015 0.16815
> 0.01797 0.00000
> CLY2A 0.00000 0.16911 0.00014
> 0.00002 0.00000
> CLZ2A -0.05068 0.00000 0.00000
> 0.00000 0.15643
>
>
> Zero point energy: 0.00514573 [H] 1129.36 [1/CM] 13.51
> [KJ/MOL]
> Frequency information read from record 5401.2
>
>
> **********************************************************************************************************************************
> DATASETS * FILE NREC LENGTH (MB) RECORD NAMES
> 1 20 2.14 500 610 700
> 900 950 970 1000 129 960
> 1100 VAR BASINP
> GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S
> 1400 1410 1200
> 1210 1080 1600 1650 1300 1700
> 701 T V
> H0 H01 AOSYM SMH MOLCAS ERIS OPER GEOM
> 2 11 1.35 500 610 700
> 1000 2100 5300 5400 5450 701
> 5401 VAR BASINP
> GEOM BASIS RHF HESS FREQ NMOD GEOM
> FREQ
> 5451 NMOD
> PROGRAMS * TOTAL FREQ FREQ OPTG
> HF INT FILE
> CPU TIMES * 27.67 0.01 19.93 7.26
> 0.01 0.09 0.00
> REAL TIME * 31.18 SEC
> DISK USED * 9.16 MB
> **********************************************************************************************************************************
>
> OPTG(HF) HF-SCF -460.08944998 -460.08941459
> **********************************************************************************************************************************
>
> --
> Jeremy Merritt, PhD
> Department of Chemistry
> CB 212 Atwood Hall
> Emory University
> Atlanta, Ga 30322
> Voice: 404-727-0029
> Fax: 404-727-6586
> Email: jeremy.merritt at emory.edu
>
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