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标题: 用甲醛分子和氧气分子生成碳酸分子，在用Dmol3寻找过渡态时出现报错，请问怎么解决？ [打印本页]

作者
Author: 快车奥斯卡 时间: 2025-4-26 11:23
标题: 用甲醛分子和氧气分子生成碳酸分子，在用Dmol3寻找过渡态时出现报错，请问怎么解决？

   ===============================================================
   Materials Studio DMol^3 version 2023
   compiled on Oct 26 2022 20:49:04
   ===============================================================

   ===============================================================
   Density Functional Theory Electronic Structure Program
   Copyright (c) 2022, Dassault Systemes, all rights reserved.
   Cite work using this program as:
   B. Delley, J. Chem. Phys. 92,  508  (1990).
   B. Delley, J. Chem. Phys. 113, 7756 (2000).
   DMol^3 is available as part of Materials Studio.
   ===============================================================

DATE:    Apr 26 11:03:02 2025

Job started on host MS

This run uses 8 processors

Message: License checkout of MS_dmol successful

Message:  Using user-supplied basis set file: basfile_v4.4
Basis set is read from file: basfile_v4.4

parallel run with 8 processors

no INCOOR file: try ZMAT
no ZMAT file: try CAR

Geometry is read from file: TS.car

INCOOR, atomic coordinates in au (for archive):
______________________________________________________________________>8

$coordinates
C          -3.04363662706693 0.11490174134309 1.89559131521089
O          -3.04451635693908 1.89954030235045 3.31608776830569
H          -1.56640337505630 -0.13408374085636 0.40597879994722
H          -4.52000359082735 -1.39349170551998 1.98640488960376
O          -4.06122938051511 -2.61853659174999 0.41910757015540
O          -2.15424728377211 -1.87084945042006 -0.63613246589190
$end
______________________________________________________________________>8

N_atoms = 6    N_atom_types =  3

INPUT_DMOL keywords (for archive):
______________________________________________________________________>8

                                                                                                                                 <--
# Task parameters                                                                                                                <--
Calculate                   lstqst                                                                                              <--
Opt_ts_cg_steps             20                                                                                                 <--
Opt_ts_qst_cycles          5                                                                                                    <--
Opt_ts_gradtol             2.0000e-03 A                                                                                        <--
Symmetry                   off                                                                                                 <--
Max_memory                   2048                                                                                                 <--
File_usage                   smart                                                                                              <--
Scf_density_convergence    1.000000e-06                                                                                        <--
Scf_charge_mixing          1.000000e-01                                                                                        <--
Scf_diis                   10 pulay                                                                                           <--
Scf_iterations             500                                                                                                 <--
                                                                                                                                 <--
# Electronic parameters                                                                                                          <--
Spin_polarization          restricted                                                                                           <--
Charge                      0                                                                                                    <--
Basis                      dnp                                                                                                 <--
basis_version                basfile_v4.4                                                                                        <--
Pseudopotential             none                                                                                                 <--
Functional                   pwc                                                                                                 <--
Harris                      off                                                                                                 <--
Aux_density                hexadecapole                                                                                        <--
Dftd                         OBS                                                                                                 <--
Integration_grid             fine                                                                                                 <--
Occupation                   fermi                                                                                              <--
Cutoff_Global                3.7000 angstrom                                                                                     <--
                                                                                                                                 <--
# Calculated properties                                                                                                          <--
Frequency_analysis          on                                                                                                 <--
Raman                      on                                                                                                 <--
______________________________________________________________________>8

Publications of specific relevance to this calculation:

Density functional:
local functional PWC: Perdew Wang: Phys. Rev. B 45, 13244 (1992)

+---------------------------------------------------+
|                                                 |
|  Using DFT-SEDC - the DFT Semi-Empirical       |
|  Dispersion interaction Correction module       |
|  Copyright (c) 2008 Erik McNellis and Joerg Meyer |
|  Fritz-Haber-Institut der MPG. Distributed under  |
|  the GNU Lesser General Public License (LGPL). |
|                                                 |
| Please cite the following publication in all    |
| work arising from your use of DMol3 SEDC:       |
|                                                 |
| Erik R. McNellis, Joerg Meyer, and Karsten Reuter |
| Phys. Rev. B 80, 205414 (2009)                   |
|                                                 |
+---------------------------------------------------+

The Generation and Use of Delocalized Internal Coordinates in Geometry optimization;
Baker Kessi Delley: J. Chem. Phys., 105, 192 (1996)
Andzelm Fitzgerald King-Smith: Chem. Phys. Lett., 335, 321 (2001)

Parallel eigenvalue solution:
Parallel solution of partial symmetric eigenvalue problems from electronic structure calculations:
Auckenthaler, Blum, Bungartz, et al.: Parallel Computing 37, 783 (2011)

Warning: SYMDEC file generation reset to off

Calculation is Spin_restricted

Message: No symmetry used in transition state runs

Warning: no SYM file, no symmetry used in vibrational analysis
Warning: at least C1 SYM file should be there for optgeom
Hydrogen    nbas=  1, z= 1, nrfn=  5, rcut=  6.99, e_ref= -0.035020 Ha
                              rcore=  0.00  zval= 1.00 1.00
n=1  L=0  occ= 1.00 e=    -0.225630Ha       -6.1397eV
n=1  L=0  occ= 0.00 e=    -0.844913Ha    -22.9913eV
n=2  L=1  occ= 0.00 e=    -1.999991Ha    -54.4226eV
n=1  L=0  occ= 0.00 e=    -0.104745Ha       -2.8503eV  eliminated
n=2  L=1  occ= 0.00 e=    -0.090477Ha       -2.4620eV  eliminated
Carbon    nbas=  2, z= 6, nrfn=  9, rcut=  6.99, e_ref= -0.049184 Ha
                              rcore=  0.00  zval= 6.00 6.00
n=1  L=0  occ= 2.00 e=    -9.928371Ha    -270.1648eV
n=2  L=0  occ= 2.00 e=    -0.488446Ha    -13.2913eV
n=2  L=1  occ= 2.00 e=    -0.184959Ha       -5.0330eV
n=2  L=0  occ= 0.00 e=    -1.475475Ha    -40.1497eV
n=2  L=1  occ= 0.00 e=    -1.170309Ha    -31.8457eV
n=3  L=2  occ= 0.00 e=    -1.999885Ha    -54.4197eV
n=1  L=0  occ= 0.00 e=    -0.104745Ha       -2.8503eV  eliminated
n=2  L=1  occ= 0.00 e=    -0.090477Ha       -2.4620eV  eliminated
n=3  L=2  occ= 0.00 e=    -0.468386Ha    -12.7454eV  eliminated
Oxygen    nbas=  3, z= 8, nrfn=  9, rcut=  6.99, e_ref= -0.055405 Ha
                              rcore=  0.00  zval= 8.00 8.00
n=1  L=0  occ= 2.00 e=    -18.752869Ha    -510.2917eV
n=2  L=0  occ= 2.00 e=    -0.867475Ha    -23.6052eV
n=2  L=1  occ= 4.00 e=    -0.334304Ha       -9.0969eV
n=2  L=0  occ= 0.00 e=    -2.130064Ha    -57.9620eV
n=2  L=1  occ= 0.00 e=    -1.593460Ha    -43.3603eV
n=3  L=2  occ= 0.00 e=    -1.999885Ha    -54.4197eV
n=1  L=0  occ= 0.00 e=    -0.104745Ha       -2.8503eV  eliminated
n=2  L=1  occ= 0.00 e=    -0.090477Ha       -2.4620eV  eliminated
n=3  L=2  occ= 0.00 e=    -0.468386Ha    -12.7454eV  eliminated

Symmetry orbitals C1
n  norb representation
1 66       a
  total number of valence orbitals:    66

molecule charge=    0.0 active electron number=    32.0
(without charge=          32.0)

preparation workspace 6p has max memory requirements    5.2 MB

real array elements, matrices vectors etc:    1.6 MB
integer arrays                         :    0.1 MB
min recommended for all-incl workspace :    2.5 MB
Total memory allocated for arrays       :    4.9 MB
Memory for temporary file storage on disk :    0.8 MB
Total memory allocated                   :    5.6 MB
Max memory requested                   : 2048.0 MB

+++ Entering Transition State Search Section +++

This is a molecular system
Maximum number of conjugate gradient steps requested = 11
No symmetry used in transition state calculations!

Message: Found reactant structure file
TS_reac.car

Message: Found product structure file
TS_prod.car

            p-vector (au)
            x       y       z
   C    0.003896  -0.647077  -0.511662    0
   O    0.034402  -0.656158  -0.487177    0
   H    1.340127 0.646843  -0.815618    0
   H    -1.462844  -0.513433 0.691913    0
   O    -0.701618 0.242969 0.947455    0
   O    0.786036 0.926856 0.175089    0
Message: Linear synchronous transit method

Checking fixed coordinate information

Found OPT file
TS.opt
Number of fixed atoms 0

Calculate P vector

P vector
0.003895899 -0.647076745 -0.511661745
0.034402281 -0.656158324 -0.487176711
1.340126958 0.646842933 -0.815617869
-1.462843785 -0.513432891 0.691912619
-0.701617536 0.242968698 0.947454871
0.786036185 0.926856329 0.175088832
No coordinate superposition requested

RMS deviation of structures :          1.2954

Resetting SCF cycle automatically

Symmetry orbitals C1
n  norb representation
1 66       a
  total number of valence orbitals:    66

molecule charge=    0.0 active electron number=    32.0
(without charge=          32.0)

preparation workspace 6p has max memory requirements    5.2 MB

real array elements, matrices vectors etc:    1.6 MB
integer arrays                         :    0.1 MB
min recommended for all-incl workspace :    2.5 MB
Total memory allocated for arrays       :    4.9 MB
Memory for temporary file storage on disk :    0.8 MB
Total memory allocated                   :    5.6 MB
Max memory requested                   : 2048.0 MB

         Total Energy          Binding E    Cnvgnce    Time Iter
Ef       -262.848652Ha       -0.8508996Ha    1.66E-01    0.0m    1
Ef       -262.823419Ha       -0.8256666Ha    1.39E-01    0.0m    2
Ef       -262.778226Ha       -0.7804742Ha    6.21E-02    0.0m    3
Ef       -262.772131Ha       -0.7743785Ha    2.58E-02    0.0m    4
Ef       -262.771427Ha       -0.7736746Ha    1.24E-02    0.0m    5
Ef       -262.770836Ha       -0.7730842Ha    6.92E-03    0.0m    6
Ef       -262.770683Ha       -0.7729305Ha    1.95E-03    0.0m    7
Ef       -262.770656Ha       -0.7729037Ha    6.45E-04    0.0m    8
Ef       -262.770652Ha       -0.7728997Ha    3.10E-04    0.0m    9
Ef       -262.770651Ha       -0.7728988Ha    5.41E-05    0.0m    10
Ef       -262.770651Ha       -0.7728989Ha    3.68E-05    0.0m    11
Ef       -262.770651Ha       -0.7728988Ha    2.32E-05    0.0m    12
Ef       -262.770651Ha       -0.7728987Ha    4.71E-06    0.0m    13
Ef       -262.770651Ha       -0.7728987Ha    3.87E-06    0.0m    14
Ef       -262.770651Ha       -0.7728987Ha    1.53E-06    0.0m    15
Ef       -262.770651Ha       -0.7728987Ha    1.11E-06    0.0m    16
Ef       -262.770651Ha       -0.7728987Ha    5.28E-07    0.0m    17
Message: SCF converged

Energy of Highest Occupied Molecular Orbital:  -0.19677Ha -5.354eV
Energy of Lowest Unoccupied Molecular Orbital:  -0.12873Ha -3.503eV

  HOMO is orbital number 16
  LUMO is orbital number 17

DFT-D corrected derivatives:

df             ATOMIC  COORDINATES (au)                DERIVATIVES (au)
df          x       y       z          x       y       z
df C -3.043637 0.114902 1.895591 -0.021529  -0.311943  -0.253563
df O -3.044516 1.899540 3.316088    0.005811 0.036011 0.031039
df H -1.566403  -0.134084 0.405979 -0.033901  -0.016202 0.009340
df H -4.520004  -1.393492 1.986405    0.032831 0.009863  -0.030506
df O -4.061229  -2.618537 0.419108    0.144131 0.201812 0.054866
df O -2.154247  -1.870849  -0.636132 -0.127344 0.080459 0.188825
df  binding energy    -0.7773207Ha    -21.15198eV       -487.786kcal/mol

Energy components:
Sum of atomic energies =    -261.9977522Ha
               Kinetic =    -2.3302526Ha
         Electrostatic =       0.8248385Ha
   Exchange-correlation =       0.4470764Ha
      Spin polarization =       0.2854390Ha
      DFT-D correction =    -0.0044220Ha
   =====================
   Total DFT-D energy =    -262.7750730Ha

         Total Energy          Binding E                Time Iter
Ef       -262.775073Ha       -0.7773207Ha                0.0m    18
TS Search Status: Type, Search #, reaction coord, Energy
LST    0    0.000000          -0.77732074
Message: Reactant structure complete

Reactant Structure
------------------

Reactant: Energy:       -0.7773207 Ha

Reactant: Geometry (Angs)
-1.610623141 0.060803383 1.003103725
-1.611088674 1.005193439 1.754798076
-0.828904969 -0.070954060 0.214834729
-2.391882893 -0.737404054 1.051160199
-2.149110036 -1.385669890 0.221782175
-1.139978569 -0.990010894 -0.336626804

Reactant: Gradient
-0.021528688 -0.311942741 -0.253563454
0.005811253 0.036010669 0.031038808
-0.033900735 -0.016202084 0.009340056
0.032831372 0.009863453 -0.030505844
0.144131262 0.201811565 0.054865771
-0.127344464 0.080459137 0.188824662

Resetting SCF cycle automatically

Symmetry orbitals C1
n  norb representation
1 66       a
  total number of valence orbitals:    66

molecule charge=    0.0 active electron number=    32.0
(without charge=          32.0)

preparation workspace 6p has max memory requirements    5.2 MB

real array elements, matrices vectors etc:    1.6 MB
integer arrays                         :    0.1 MB
min recommended for all-incl workspace :    2.5 MB
Total memory allocated for arrays       :    4.9 MB
Memory for temporary file storage on disk :    0.8 MB
Total memory allocated                   :    5.6 MB
Max memory requested                   : 2048.0 MB

         Total Energy          Binding E    Cnvgnce    Time Iter
Ef       -263.313522Ha       -1.3157698Ha    1.84E-01    0.0m    1
Ef       -263.259438Ha       -1.2616853Ha    1.40E-01    0.0m    2
Ef       -263.197032Ha       -1.1992793Ha    6.60E-02    0.0m    3
Ef       -263.191525Ha       -1.1937724Ha    2.71E-02    0.0m    4
Ef       -263.190678Ha       -1.1929258Ha    2.21E-02    0.0m    5
Ef       -263.189116Ha       -1.1913634Ha    5.83E-03    0.0m    6
Ef       -263.188986Ha       -1.1912342Ha    2.00E-03    0.0m    7
Ef       -263.188976Ha       -1.1912239Ha    1.08E-03    0.0m    8
Ef       -263.188963Ha       -1.1912111Ha    2.35E-04    0.0m    9
Ef       -263.188964Ha       -1.1912122Ha    1.89E-04    0.0m    10
Ef       -263.188963Ha       -1.1912109Ha    2.93E-05    0.0m    11
Ef       -263.188963Ha       -1.1912108Ha    2.57E-05    0.0m    12
Ef       -263.188963Ha       -1.1912108Ha    3.16E-06    0.0m    13
Ef       -263.188963Ha       -1.1912108Ha    2.61E-06    0.0m    14
Ef       -263.188963Ha       -1.1912108Ha    3.79E-07    0.0m    15
Message: SCF converged

Energy of Highest Occupied Molecular Orbital:  -0.26202Ha -7.130eV
Energy of Lowest Unoccupied Molecular Orbital:  -0.02214Ha -0.603eV

  HOMO is orbital number 16
  LUMO is orbital number 17

DFT-D corrected derivatives:

df             ATOMIC  COORDINATES (au)                DERIVATIVES (au)
df          x       y       z          x       y       z
df C -3.039741  -0.532175 1.383930    0.000711  -0.001714 0.000282
df O -3.010114 1.243382 2.828911    0.000229  -0.000483  -0.000254
df H -0.226276 0.512759  -0.409639 -0.000543 0.000998  -0.000735
df H -5.982847  -1.906925 2.678318 -0.001066 0.000905  -0.000678
df O -4.762847  -2.375568 1.366562    0.000245 0.000002 0.000861
df O -1.368211  -0.943993  -0.461044    0.000424 0.000292 0.000524
df  binding energy    -1.1934616Ha    -32.47575eV       -748.923kcal/mol

Energy components:
Sum of atomic energies =    -261.9977522Ha
               Kinetic =    -1.8392244Ha
         Electrostatic =    -0.0695911Ha
   Exchange-correlation =       0.4321657Ha
      Spin polarization =       0.2854390Ha
      DFT-D correction =    -0.0022507Ha
   =====================
   Total DFT-D energy =    -263.1912138Ha

         Total Energy          Binding E                Time Iter
Ef       -263.191214Ha       -1.1934616Ha                0.0m    16
TS Search Status: Type, Search #, reaction coord, Energy
LST    0    1.000000          -1.19346155
Message: Product structure complete

Product Structure
-----------------

Product: Energy:       -1.1934616 Ha

Product: Geometry (Angs)
-1.608561520 -0.281614884 0.732343990
-1.592883771 0.657969407 1.496995263
-0.119740323 0.271340479 -0.216771660
-3.165986487 -1.009101039 1.417304589
-2.520390047 -1.257096392 0.723153701
-0.724026133 -0.499539647 -0.243973784

Product: Gradient
0.000711280 -0.001714318 0.000281792
0.000228543 -0.000482802 -0.000254357
-0.000543135 0.000997956 -0.000734768
-0.001065541 0.000904878 -0.000678014
0.000244862 0.000002489 0.000860953
0.000423990 0.000291797 0.000524395
Message: Commencing LST maximum bracketing

Bracketing from reactant
Bracket size    :          0.2000
Bracket tolerance :          0.0068
Message: Commencing bracketing from reactant

Resetting SCF cycle automatically

Symmetry orbitals C1
n  norb representation
1 66       a
  total number of valence orbitals:    66

molecule charge=    0.0 active electron number=    32.0
(without charge=          32.0)

preparation workspace 6p has max memory requirements    5.2 MB

real array elements, matrices vectors etc:    1.6 MB
integer arrays                         :    0.1 MB
min recommended for all-incl workspace :    2.5 MB
Total memory allocated for arrays       :    4.9 MB
Memory for temporary file storage on disk :    0.8 MB
Total memory allocated                   :    5.6 MB
Max memory requested                   : 2048.0 MB

         Total Energy          Binding E    Cnvgnce    Time Iter
Ef       -262.792709Ha       -0.7949571Ha    1.65E-01    0.0m    1
Ef       -262.766485Ha       -0.7687331Ha    1.36E-01    0.0m    2
Ef       -262.727846Ha       -0.7300936Ha    7.27E-02    0.0m    3
Ef       -262.720321Ha       -0.7225683Ha    3.54E-02    0.0m    4
Ef       -262.718851Ha       -0.7210983Ha    1.98E-02    0.0m    5
Ef       -262.718206Ha       -0.7204535Ha    8.15E-03    0.0m    6
Ef       -262.717982Ha       -0.7202301Ha    3.94E-03    0.0m    7
Ef       -262.717928Ha       -0.7201756Ha    1.30E-03    0.0m    8
Ef       -262.717920Ha       -0.7201674Ha    8.24E-04    0.1m    9
Ef       -262.717916Ha       -0.7201641Ha    3.17E-04    0.1m    10
Ef       -262.717916Ha       -0.7201636Ha    9.55E-05    0.1m    11
Ef       -262.717916Ha       -0.7201636Ha    5.49E-05    0.1m    12
Ef       -262.717916Ha       -0.7201635Ha    1.36E-05    0.1m    13
Ef       -262.717916Ha       -0.7201635Ha    1.14E-05    0.1m    14
Ef       -262.717916Ha       -0.7201635Ha    3.31E-06    0.1m    15
Ef       -262.717916Ha       -0.7201635Ha    2.18E-06    0.1m    16
Ef       -262.717916Ha       -0.7201635Ha    7.05E-07    0.1m    17
Message: SCF converged

Energy of Highest Occupied Molecular Orbital:  -0.17806Ha -4.845eV
Energy of Lowest Unoccupied Molecular Orbital:  -0.10626Ha -2.891eV

  HOMO is orbital number 16
  LUMO is orbital number 17

DFT-D corrected derivatives:

df             ATOMIC  COORDINATES (au)                DERIVATIVES (au)
df          x       y       z          x       y       z
df C -3.041099 0.019696 1.822155 -0.029696  -0.330745  -0.274347
df O -3.037288 1.801777 3.245182    0.009762 0.025501 0.023585
df H -1.268459 0.005382 0.225657    0.005517  -0.003266  -0.012650
df H -4.842017  -1.513087 2.137980 -0.001554  -0.006379  -0.010251
df O -4.201779  -2.599422 0.582637    0.029743 0.167534 0.127297
df O -1.999395  -1.716865  -0.626574 -0.013772 0.147356 0.146365
df  binding energy    -0.7232051Ha    -19.67942eV       -453.827kcal/mol

Energy components:
Sum of atomic energies =    -261.9977522Ha
               Kinetic =    -2.0753293Ha
         Electrostatic =       0.6722483Ha
   Exchange-correlation =       0.3974785Ha
      Spin polarization =       0.2854390Ha
      DFT-D correction =    -0.0030415Ha
   =====================
   Total DFT-D energy =    -262.7209573Ha

         Total Energy          Binding E                Time Iter
Ef       -262.720957Ha       -0.7232051Ha                0.1m    18
TS Search Status: Type, Search #, reaction coord, Energy
LST    0    0.200080          -0.72320505

Resetting SCF cycle automatically

Symmetry orbitals C1
n  norb representation
1 66       a
  total number of valence orbitals:    66

molecule charge=    0.0 active electron number=    32.0
(without charge=          32.0)

preparation workspace 6p has max memory requirements    5.2 MB

real array elements, matrices vectors etc:    1.6 MB
integer arrays                         :    0.1 MB
min recommended for all-incl workspace :    2.5 MB
Total memory allocated for arrays       :    4.9 MB
Memory for temporary file storage on disk :    0.8 MB
Total memory allocated                   :    5.6 MB
Max memory requested                   : 2048.0 MB

         Total Energy          Binding E    Cnvgnce    Time Iter
Ef       -262.894823Ha       -0.8970712Ha    1.93E-01    0.1m    1
Ef       -262.830705Ha       -0.8329532Ha    1.37E-01    0.1m    2
Ef       -262.790095Ha       -0.7923426Ha    8.10E-02    0.1m    3
Ef       -262.793539Ha       -0.7957868Ha    6.58E-02    0.1m    4
Ef       -262.785553Ha       -0.7878010Ha    4.36E-02    0.1m    5
Ef       -262.780510Ha       -0.7827579Ha    1.67E-02    0.1m    6
Ef       -262.779671Ha       -0.7819187Ha    5.40E-03    0.1m    7
Ef       -262.779578Ha       -0.7818253Ha    1.75E-03    0.1m    8
Ef       -262.779564Ha       -0.7818115Ha    4.73E-04    0.1m    9
Ef       -262.779564Ha       -0.7818119Ha    3.47E-04    0.1m    10
Ef       -262.779565Ha       -0.7818125Ha    1.24E-04    0.1m    11
Ef       -262.779565Ha       -0.7818130Ha    4.35E-05    0.1m    12
Ef       -262.779565Ha       -0.7818129Ha    2.82E-05    0.1m    13
Ef       -262.779565Ha       -0.7818129Ha    3.96E-06    0.1m    14
Ef       -262.779565Ha       -0.7818129Ha    2.59E-06    0.1m    15
Ef       -262.779565Ha       -0.7818129Ha    8.17E-07    0.1m    16
Message: SCF converged

Energy of Highest Occupied Molecular Orbital:  -0.17260Ha -4.697eV
Energy of Lowest Unoccupied Molecular Orbital:  -0.12844Ha -3.495eV

  HOMO is orbital number 16
  LUMO is orbital number 17

DFT-D corrected derivatives:

df             ATOMIC  COORDINATES (au)                DERIVATIVES (au)
df          x       y       z          x       y       z
df C -3.038932  -0.091785 1.736386    0.002526 0.112385 0.099784
df O -3.029852 1.687382 3.161430 -0.000141 0.042234 0.031816
df H -0.986350 0.140585 0.053221 -0.066227 0.016658 0.075031
df H -5.149428  -1.623010 2.281789    0.079549 0.072103  -0.008191
df O -4.342878  -2.567253 0.759331    0.267694  -0.008606  -0.249061
df O -1.842596  -1.548438  -0.605119 -0.283401  -0.234774 0.050621
df  binding energy    -0.7843263Ha    -21.34261eV       -492.182kcal/mol

Energy components:
Sum of atomic energies =    -261.9977522Ha
               Kinetic =    -2.1521321Ha
         Electrostatic =       0.7067569Ha
   Exchange-correlation =       0.3781234Ha
      Spin polarization =       0.2854390Ha
      DFT-D correction =    -0.0025135Ha
   =====================
   Total DFT-D energy =    -262.7820785Ha

         Total Energy          Binding E                Time Iter
Ef       -262.782079Ha       -0.7843263Ha                0.1m    17
TS Search Status: Type, Search #, reaction coord, Energy
LST    0    0.397999          -0.78432631

LST maximum bracketing from reactant successful
Cumulative number of energy/gradient calls :                4
Message: Bracketing from reactant successful

Message: Commencing maximum search

Brent Tolerance :          0.0068

Resetting SCF cycle automatically

Symmetry orbitals C1
n  norb representation
1 66       a
  total number of valence orbitals:    66

molecule charge=    0.0 active electron number=    32.0
(without charge=          32.0)

preparation workspace 6p has max memory requirements    5.2 MB

real array elements, matrices vectors etc:    1.6 MB
integer arrays                         :    0.1 MB
min recommended for all-incl workspace :    2.5 MB
Total memory allocated for arrays       :    4.9 MB
Memory for temporary file storage on disk :    0.8 MB
Total memory allocated                   :    5.6 MB
Max memory requested                   : 2048.0 MB

         Total Energy          Binding E    Cnvgnce    Time Iter
Ef       -262.795992Ha       -0.7982394Ha    1.65E-01    0.1m    1
Ef       -262.769874Ha       -0.7721221Ha    1.36E-01    0.1m    2
Ef       -262.731134Ha       -0.7333823Ha    7.22E-02    0.1m    3
Ef       -262.723678Ha       -0.7259255Ha    3.50E-02    0.1m    4
Ef       -262.722211Ha       -0.7244585Ha    1.93E-02    0.1m    5
Ef       -262.721602Ha       -0.7238500Ha    8.15E-03    0.1m    6
Ef       -262.721375Ha       -0.7236224Ha    3.83E-03    0.1m    7
Ef       -262.721323Ha       -0.7235711Ha    1.29E-03    0.1m    8
Ef       -262.721315Ha       -0.7235629Ha    8.18E-04    0.1m    9
Ef       -262.721312Ha       -0.7235597Ha    3.14E-04    0.1m    10
Ef       -262.721311Ha       -0.7235592Ha    9.00E-05    0.1m    11
Ef       -262.721311Ha       -0.7235592Ha    5.31E-05    0.1m    12
Ef       -262.721311Ha       -0.7235591Ha    1.33E-05    0.1m    13
Ef       -262.721311Ha       -0.7235591Ha    1.12E-05    0.1m    14
Ef       -262.721311Ha       -0.7235591Ha    3.30E-06    0.1m    15
Ef       -262.721311Ha       -0.7235591Ha    2.07E-06    0.1m    16
Ef       -262.721311Ha       -0.7235591Ha    9.09E-07    0.1m    17
Message: SCF converged

Energy of Highest Occupied Molecular Orbital:  -0.18067Ha -4.916eV
Energy of Lowest Unoccupied Molecular Orbital:  -0.10708Ha -2.914eV

  HOMO is orbital number 16
  LUMO is orbital number 17

DFT-D corrected derivatives:

df             ATOMIC  COORDINATES (au)                DERIVATIVES (au)
df          x       y       z          x       y       z
df C -3.041196 0.023280 1.824905 -0.029485  -0.329655  -0.273145
df O -3.037540 1.805447 3.247859    0.009621 0.025947 0.023883
df H -1.278400 0.000640 0.231700    0.004755  -0.003435  -0.012164
df H -4.831218  -1.509174 2.132919 -0.000899  -0.006068  -0.010662
df O -4.196992  -2.600327 0.576808    0.031227 0.167554 0.125967
df O -2.004691  -1.722385  -0.627152 -0.015219 0.145658 0.146122
df  binding energy    -0.7266350Ha    -19.77275eV       -455.979kcal/mol

Energy components:
Sum of atomic energies =    -261.9977522Ha
               Kinetic =    -2.0798699Ha
         Electrostatic =       0.6721426Ha
   Exchange-correlation =       0.3987291Ha
      Spin polarization =       0.2854390Ha
      DFT-D correction =    -0.0030759Ha
   =====================
   Total DFT-D energy =    -262.7243872Ha

         Total Energy          Binding E                Time Iter
Ef       -262.724387Ha       -0.7266350Ha                0.1m    18
TS Search Status: Type, Search #, reaction coord, Energy
LST    0    0.193266          -0.72663497
Message: SCF not converging. Choose "Use Smearing" on DMol3 SCF panel
or set "Occupation  Thermal" in the input file.
You may also need to change spin or use symmetry.
Resubmit DMol3.
Message: DMol3 job failed
Error: DMol3 exiting
Message: License checkin of MS_dmol successful
Error: SCF iterations not converged in  500 iterations
DELTE = 1.000000000000000E-008
Errors from parallel task 2:
Error: SCF iterations not converged in  500 iterations
DELTE = 1.000000000000000E-008
Errors from parallel task 3:
Error: SCF iterations not converged in  500 iterations
DELTE = 1.000000000000000E-008
Errors from parallel task 4:
Error: SCF iterations not converged in  500 iterations
DELTE = 1.000000000000000E-008
Errors from parallel task 5:
Error: SCF iterations not converged in  500 iterations
DELTE = 1.000000000000000E-008
Errors from parallel task 6:
Error: SCF iterations not converged in  500 iterations
DELTE = 1.000000000000000E-008
Errors from parallel task 7:
Error: SCF iterations not converged in  500 iterations
DELTE = 1.000000000000000E-008
Errors from parallel task 8:
Error: SCF iterations not converged in  500 iterations
DELTE = 1.000000000000000E-008

DMol3.pl message: DMol3 job finished in 0 hr 0 min 30 sec.

作者
Author: 快车奥斯卡 时间: 2025-4-26 11:24
报错问题在这里

作者
Author: Uus/pMeC6H4-/キ 时间: 2025-4-26 12:02
啊？？你觉得能写出一个形式上的“H2CO + O2 → H2CO3”反应方程式，就一定存在对应的俩分子直接碰撞获得产物的微观过程，还试图按单步基元反应寻找过渡态？？这是我至今看到的化学上最离谱的想法，相比之下M$都是次要的槽点了……不会是打算对比“H2CO + O2 → H2CO3”在气相直接反应和在催化剂表面反应的难易程度之类的吧，不妨描述一下实际研究体系的特征和计算要说明的问题。

作者
Author: 快车奥斯卡 时间: 2025-4-26 14:17

Uus/pMeC6H4-/キ发表于 2025-4-26 12:02
啊？？你觉得能写出一个形式上的“H2CO + O2 → H2CO3”反应方程式，就一定存在对应的俩分子直接碰撞获得产 ...

我实际研究就是负载型催化剂催化氧化甲醛成碳酸。关键我只知道反应物是氧气和甲醛，产物是碳酸。所以我想试一下能不能找到中间的过渡态。

作者
Author: Uus/pMeC6H4-/キ 时间: 2025-4-26 14:36

快车奥斯卡发表于 2025-4-26 14:17
我实际研究就是负载型催化剂催化氧化甲醛成碳酸。关键我只知道反应物是氧气和甲醛，产物是碳酸。所以我想 ...

那显然不能抛开负载催化剂不谈嘛，当前两分子碰撞的模型相当于气相环境反应，完全没体现催化剂的作用。真实的反应历程应该是反应物分子吸附到催化剂表面，经过一系列吸附态的中间体得到产物，最后又从表面脱附的样子。研究类似催化反应的文献多了去了，都是先从构建一个负载催化剂表面的合理模型开始的，哪有上来就当孤立小分子反应硬找过渡态的。

计算软件这点，建议参考http://sobereva.com/706的第4个投票换更好的。

作者
Author: 快车奥斯卡 时间: 2025-4-26 14:41

Uus/pMeC6H4-/キ发表于 2025-4-26 14:36
那显然不能抛开负载催化剂不谈嘛，当前两分子碰撞的模型相当于气相环境反应，完全没体现催化剂的作用。真 ...

是的，我也知道这个反应需要催化剂的参与，但是我的催化剂是配位化合物吸附到石墨烯上，然后吸附甲醛和氧气发生氧化，这个过程我知道，但是如何模拟就蒙了。

作者
Author: Uus/pMeC6H4-/キ 时间: 2025-4-26 14:57

快车奥斯卡发表于 2025-4-26 14:41
是的，我也知道这个反应需要催化剂的参与，但是我的催化剂是配位化合物吸附到石墨烯上，然后吸附甲醛和氧 ...

具体是什么配位化合物，怎么吸附到石墨烯上的？请按http://sobereva.com/620来详细描述，每个帖子都尽量把信息提供完整了才可能提供帮助。

另外也不要忽视我说的软件的问题，参考http://sobereva.com/508的评论。

作者
Author: 快车奥斯卡 时间: 2025-4-26 15:04

Uus/pMeC6H4-/キ发表于 2025-4-26 14:57
具体是什么配位化合物，怎么吸附到石墨烯上的？请按http://sobereva.com/620来详细描述，每个帖子都尽量 ...

配位化合物是四磺酸单核酞菁钴，是因为本身是活性炭（用石墨烯结构代替），石墨烯表面上有亲水基团（手动添加）组成复合型结构催化剂。

作者
Author: 快车奥斯卡 时间: 2025-4-26 15:38
解决了，调整了一下方程，打开SCF中的smearing

作者
Author: Uus/pMeC6H4-/キ 时间: 2025-4-26 16:13

快车奥斯卡发表于 2025-4-26 15:38
解决了，调整了一下方程，打开SCF中的smearing

解决了啥呀，别再试图找“H2CO + O2 → H2CO3”的无催化剂气相双分子单步协同反应过渡态了，这种错误的建模既没有化学意义也无关你的实际体系。我不信既往研究没有类似的活性炭吸附配合物催化氧化反应可供参考，退一步讲不说吸附如何，有机钴配合物的催化反应总能找到吧。

由于缺少相应反馈，无法确定我说的每一点是否都把信息传达到位了，我不再跟进此帖。

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