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如图所示，当吸附分子和吸附表面太近的时候就会报错，距离大概小于等于2.1艾;
请问问题的原因是什么，怎么解决？报错文件如下：
===============================================================
Materials Studio DMol^3 version 2020
compiled on Oct 17 2019 19:55:04
===============================================================
===============================================================
Density Functional Theory Electronic Structure Program
Copyright (c) 2019, 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: May 24 11:10:09 2024
Job started on host DESKTOP-40G7NI3
This run uses 8 processors
Message: License checkout of MS_dmol successful
Message: License checkout of MS_dsolid successful
Basis set is read from file:
D:\MS2020\Materials Studio 20.1 x64 Server\share\Resources\Quantum\DMol3\BASFILE_v3.5
parallel run with 8 processors
no INCOOR file: try ZMAT
no ZMAT file: try CAR
Geometry is read from file: CuO__1_1_1_.car
INCOOR, atomic coordinates in au (for archive):
______________________________________________________________________>8
$cell vectors
16.35198913218203 0.00000000000000 0.00000000000000
-7.57230239468089 33.98462000162537 0.00000000000000
0.00000000000000 0.00000000000000 38.61315185721902
$coordinates
Cu 2.10579681297190 9.91979001526571 9.50176277319008
Cu 3.01131937936432 9.95017535248704 0.76551210394641
Cu 1.72629872820668 1.43881667324439 5.13363743856824
Cu 4.27337361633790 4.28606467873238 0.76551210394641
Cu 0.46424448934338 7.10292734699905 5.13363743856824
Cu 3.36785104994548 4.25567933962133 9.50176277319008
O 3.15306407560059 4.76452599345384 5.89914954251465
O -0.65606504950421 7.58138866172050 10.26727487713649
O 1.51151175386179 1.94766332518717 1.53102420978254
O 3.22610635370921 9.44132870054426 4.36812533462184
O 1.94108570255157 0.92997001941188 8.73625066735395
O 1.58455403008069 6.62446603227759 0.00000000000000
Cu 7.55647825981549 9.91979001526571 9.50176277319008
Cu 8.46200082620791 9.95017535248704 0.76551210394641
Cu 7.17698017505027 1.43881667324439 5.13363743856824
Cu 9.72405506507122 4.28606467873238 0.76551210394641
Cu 5.91492593807670 7.10292734699905 5.13363743856824
Cu 8.81853249867880 4.25567933962133 9.50176277319008
O 8.60374552433391 4.76452599345384 5.89914954251465
O 4.79461639733938 7.58138866172050 10.26727487713649
O 6.96219320070538 1.94766332518717 1.53102420978254
O 8.67678780055281 9.44132870054426 4.36812533462184
O 7.39176714939516 0.92997001941188 8.73625066735395
O 7.03523547881401 6.62446603227759 0.00000000000000
Cu 13.00715970854881 9.91979001526571 9.50176277319008
Cu 13.91268227494123 9.95017535248704 0.76551210394641
Cu 12.62766162378359 1.43881667324439 5.13363743856824
Cu 15.17473651191481 4.28606467873238 0.76551210394641
Cu 11.36560738681001 7.10292734699905 5.13363743856824
Cu 14.26921394552239 4.25567933962133 9.50176277319008
O 14.05442697117750 4.76452599345384 5.89914954251465
O 10.24529784607270 7.58138866172050 10.26727487713649
O 12.41287464943870 1.94766332518717 1.53102420978254
O 14.12746924928612 9.44132870054426 4.36812533462184
O 12.84244859812848 0.92997001941188 8.73625066735395
O 12.48591692754733 6.62446603227759 0.00000000000000
Cu -0.41831166286498 21.24801136466476 9.50176277319008
Cu 0.48721090352744 21.27839670188609 0.76551210394641
Cu -0.79780974763020 12.76703802075371 5.13363743856824
Cu 1.74926514050102 15.61428602813143 0.76551210394641
Cu -2.05986398460378 18.43114869639809 5.13363743856824
Cu 0.84374257599832 15.58390068902037 9.50176277319008
O 0.62895560165343 16.09274734096316 5.89914954251465
O -3.18017352534109 18.90961000922982 10.26727487713649
O -1.01259672197509 13.27588467269649 1.53102420978254
O 0.70199787787233 20.76955004994331 4.36812533462184
O -0.58302277328531 12.25819136881092 8.73625066735395
O -0.93955444386646 17.95268738167664 0.00000000000000
Cu 5.03236978586834 21.24801136466476 9.50176277319008
Cu 5.93789235226076 21.27839670188609 0.76551210394641
Cu 4.65287170110312 12.76703802075371 5.13363743856824
Cu 7.19994658923434 15.61428602813143 0.76551210394641
Cu 3.39081746412954 18.43114869639809 5.13363743856824
Cu 6.29442402284191 15.58390068902037 9.50176277319008
O 6.07963704849703 16.09274734096316 5.89914954251465
O 2.27050792339223 18.90961000922982 10.26727487713649
O 4.43808472675823 13.27588467269649 1.53102420978254
O 6.15267932660565 20.76955004994331 4.36812533462184
O 4.86765867544801 12.25819136881092 8.73625066735395
O 4.51112700486685 17.95268738167664 0.00000000000000
Cu 10.48305123460165 21.24801136466476 9.50176277319008
Cu 11.38857380099408 21.27839670188609 0.76551210394641
Cu 10.10355314983644 12.76703802075371 5.13363743856824
Cu 12.65062803796766 15.61428602813143 0.76551210394641
Cu 8.84149891286286 18.43114869639809 5.13363743856824
Cu 11.74510547157523 15.58390068902037 9.50176277319008
O 11.53031849723034 16.09274734096316 5.89914954251465
O 7.72118937212555 18.90961000922982 10.26727487713649
O 9.88876617549155 13.27588467269649 1.53102420978254
O 11.60336077533897 20.76955004994331 4.36812533462184
O 10.31834012418133 12.25819136881092 8.73625066735395
O 9.96180845171045 17.95268738167664 0.00000000000000
Cu -2.94242013681213 32.57623271217408 9.50176277319008
Cu -2.03689757041971 32.60661805128514 0.76551210394641
Cu -3.32191822157735 24.09525937015275 5.13363743856824
Cu -0.77484333344613 26.94250737753048 0.76551210394641
Cu -4.58397245855093 29.75937004390742 5.13363743856824
Cu -1.68036589983856 26.91212203841942 9.50176277319008
O -1.89515287418345 27.42096869036220 5.89914954251465
O -5.70428199928824 30.23783135862887 10.26727487713649
O -3.53670519592224 24.60410602209554 1.53102420978254
O -1.82211059607482 32.09777139934236 4.36812533462184
O -3.10713124723246 23.58641271820997 8.73625066735395
O -3.46366291781362 29.28090873107569 0.00000000000000
Cu 2.50826131192118 32.57623271217408 9.50176277319008
Cu 3.41378387831360 32.60661805128514 0.76551210394641
Cu 2.12876322715596 24.09525937015275 5.13363743856824
Cu 4.67583811528718 26.94250737753048 0.76551210394641
Cu 0.86670898829266 29.75937004390742 5.13363743856824
Cu 3.77031554889476 26.91212203841942 9.50176277319008
O 3.55552857454987 27.42096869036220 5.89914954251465
O -0.25360055055493 30.23783135862887 10.26727487713649
O 1.91397625281107 24.60410602209554 1.53102420978254
O 3.62857085265849 32.09777139934236 4.36812533462184
O 2.34355020150085 23.58641271820997 8.73625066735395
O 1.98701852902997 29.28090873107569 0.00000000000000
Cu 7.95894276065450 32.57623271217408 9.50176277319008
Cu 8.86446532515720 32.60661805128514 0.76551210394641
Cu 7.57944467399956 24.09525937015275 5.13363743856824
Cu 10.12651956402050 26.94250737753048 0.76551210394641
Cu 6.31739043702598 29.75937004390742 5.13363743856824
Cu 9.22099699762808 26.91212203841942 9.50176277319008
O 9.00621002328319 27.42096869036220 5.89914954251465
O 5.19708089628867 30.23783135862887 10.26727487713649
O 7.36465769965467 24.60410602209554 1.53102420978254
O 9.07925229950209 32.09777139934236 4.36812533462184
O 7.79423164834445 23.58641271820997 8.73625066735395
O 7.43769997776329 29.28090873107569 0.00000000000000
C -2.19022923010576 -15.26887455108828 16.00278656595542
C -4.79923057374413 -16.50467669761564 15.74705159052930
C -2.44696409363969 -12.40925937092527 16.39798722413161
C -0.69682168746939 -16.47200971451963 18.17573272941859
H -1.13731035032698 -15.59163956158786 14.22858906115237
H -4.65639100042666 -18.55554445580822 15.43205013242040
H -5.89179313539705 -15.68770328648476 14.17716334129028
H -5.89590457284295 -16.21400771402985 17.49097454519483
H -3.49104900834101 -12.02703007255051 18.15646299936996
H -3.48859955856587 -11.50361925222952 14.84219187770056
H -0.59276395430141 -11.48056006572080 16.55656543439342
H 1.19526943165936 -15.63126986798049 18.37279952835036
H -0.46516403763471 -18.52217022570239 17.91331276656708
H -1.70177906308281 -16.18061040280913 19.97395315459794
$end
______________________________________________________________________>8
N_atoms = 122 N_atom_types = 4
INPUT_DMOL keywords (for archive):
______________________________________________________________________>8
#Warning: no global confinement specs in BASFILE
<--
# Task parameters <--
Calculate optimize <--
Opt_energy_convergence 2.0000e-05 <--
Opt_gradient_convergence 4.0000e-03 A <--
Opt_displacement_convergence 5.0000e-03 A <--
Opt_iterations 1000 <--
Opt_max_displacement 0.3000 A <--
Opt_coordinate_system cartesian <--
<--
# Cartesian constraints <--
Opt_fixed <--
2 XYZ
4 XYZ
9 XYZ
12 XYZ
14 XYZ
16 XYZ
21 XYZ
24 XYZ
26 XYZ
28 XYZ
33 XYZ
36 XYZ
38 XYZ
40 XYZ
45 XYZ
48 XYZ
50 XYZ
52 XYZ
57 XYZ
60 XYZ
62 XYZ
64 XYZ
69 XYZ
72 XYZ
74 XYZ
76 XYZ
81 XYZ
84 XYZ
86 XYZ
88 XYZ
93 XYZ
96 XYZ
98 XYZ
100 XYZ
105 XYZ
108 XYZ
Symmetry off <--
Max_memory 2048 <--
File_usage smart <--
Scf_density_convergence 1.000000e-05 <--
Scf_charge_mixing 2.000000e-01 <--
Scf_diis 10 pulay <--
Scf_iterations 5000 <--
<--
# Electronic parameters <--
Spin_polarization restricted <--
Charge 0 <--
Basis dnd <--
Pseudopotential dspp <--
Functional pbe <--
Aux_density hexadecapole <--
Integration_grid medium <--
Occupation thermal 0.0050 <--
Cutoff_Global 4.0000 angstrom <--
Kpoints off <--
<--
# Calculated properties <--
Mulliken_analysis charge <--
Hirshfeld_analysis charge <--
______________________________________________________________________>8
Publications of specific relevance to this calculation:
Density functional:
PBE functional: Perdew Burke Ernzerhof: Phys. Rev. Lett. 77, 3865 (1996)
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)
Hardness conserving semilocal pseudopotentials; Delley: Phys. Rev. B 66, 155125 (2002)
Fractional occupations and density functional energies and forces; Weinert Davenport: Phys. Rev. B 45, 13709 (1992)
Fractional occupations, iterative stability:
Delley in; Modern Density Functional Theory vol 2 pg 221 ff (1995),
Elsevier, Seminario Politzer eds.
Fast Calculation of Electrostatics in Crystals and Large Molecules;
Delley: J. Phys. Chem. 100, 6107 (1996)
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: dspp takes precedence over using symmetrized basis
Warning: Existing Hessian file deleted.
Calculation is Spin_restricted
Lattice:
translation vector [a0] 1 16.351989132 0.000000000 0.000000000
translation vector [a0] 2 -7.572302395 33.984620002 0.000000000
translation vector [a0] 3 0.000000000 0.000000000 38.613151857
Cell volume 21457.952 a0^3
Warning: at least C1 SYM file should be there for optgeom
Hydrogen nbas= 1, z= 1, nrfn= 3, rcut= 7.56, e_ref= -0.042108 Ha
rcore= 0.00 zval= 1.00 1.00
n=1 L=0 occ= 1.00 e= -0.234111Ha -6.3705eV
n=1 L=0 occ= 0.00 e= -0.844967Ha -22.9927eV
n=2 L=1 occ= 0.00 e= -1.999998Ha -54.4227eV eliminated
Carbon nbas= 2, z= 6, nrfn= 7, rcut= 7.56, e_ref= -0.048580 Ha
rcore= 0.00 zval= 6.00 6.00
n=1 L=0 occ= 2.00 e= -10.029631Ha -272.9203eV
n=2 L=0 occ= 2.00 e= -0.496729Ha -13.5167eV
n=2 L=1 occ= 2.00 e= -0.185150Ha -5.0382eV
n=2 L=0 occ= 0.00 e= -1.483211Ha -40.3602eV
n=2 L=1 occ= 0.00 e= -1.167392Ha -31.7664eV
n=3 L=2 occ= 0.00 e= -2.722219Ha -74.0754eV
n=3 L=2 occ= 0.00 e= -1.388515Ha -37.7834eV eliminated
Oxygen nbas= 3, z= 8, nrfn= 7, rcut= 7.56, e_ref= -0.056429 Ha
rcore= 0.00 zval= 8.00 8.00
n=1 L=0 occ= 2.00 e= -18.895620Ha -514.1762eV
n=2 L=0 occ= 2.00 e= -0.876655Ha -23.8550eV
n=2 L=1 occ= 4.00 e= -0.329847Ha -8.9756eV
n=2 L=0 occ= 0.00 e= -2.141939Ha -58.2852eV
n=2 L=1 occ= 0.00 e= -1.589268Ha -43.2462eV
n=3 L=2 occ= 0.00 e= -2.722219Ha -74.0754eV
n=3 L=2 occ= 0.00 e= -1.388515Ha -37.7834eV eliminated
Copper nbas= 4, z= 29, nrfn= 7, rcut= 7.56, e_ref= -0.017921 Ha
DSPP: PWC_PBE s 01d21 release rcore= 0.59 zval= 19.00 29.00
n=3 L=0 occ= 2.00 e= -4.297815Ha -116.9496eV
n=3 L=1 occ= 6.00 e= -2.746007Ha -74.7227eV
n=3 L=2 occ=10.00 e= -0.165762Ha -4.5106eV
n=4 L=0 occ= 1.00 e= -0.147704Ha -4.0192eV
n=3 L=2 occ= 0.00 e= -1.089072Ha -29.6352eV
n=4 L=0 occ= 0.00 e= -0.819300Ha -22.2943eV
n=4 L=1 occ= 0.00 e= -0.559370Ha -15.2212eV
Note: calculation of reference xc derivative is turned on
for pseudopotential with core density correction
Symmetry orbitals C1
n norb representation
1 1858 a
total number of valence orbitals: 1858
cell charge= 0.000000 active electron number 1492.0
(without charge= 1492.0 )
electron temperature= 0.005_Ha 0.14_eV 1579._K
Errors from parallel task 2:
Error: failed allocating memory in section 6_p 3856431 7722576
... Calling mpi_abort ...
Errors from parallel task 4:
Error: failed allocating memory in section 6_p 3856431 7722576
... Calling mpi_abort ...
Errors from parallel task 5:
Error: failed allocating memory in section 6_p 3856431 7722576
Errors from parallel task 6:
Error: failed allocating memory in section 6_p 3856431 7722576
... Calling mpi_abort ...
Errors from parallel task 7:
Error: failed allocating memory in section 6_p 3856431 7722576
Errors from parallel task 8:
Error: failed allocating memory in section 6_p 3856431 7722576
... Calling mpi_abort ...
DMol3.pl message: DMol3 job finished in 0 hr 0 min 2 sec.
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吸附构型
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发表于 Post on 2024-5-24 11:16:56
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