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标题: 求助：Dmol计算晶胞表面能的任务无法开启 [打印本页]

作者
Author: 冰皮麻薯麻 时间: 2023-4-3 17:05
标题: 求助：Dmol计算晶胞表面能的任务无法开启
在得到Hg在石墨烯表面的吸附的几何优化结构后，我删除了Hg原子并对剩下的石墨烯表面进行表面能计算。然后在程序的启动阶段报错了无法启动。我试过其他的同类模型（汞在其他位点的吸附）都是可以正常运行的。报错如下：
(, 下载次数 Times of downloads: 10)
outmol错误报警内容如下：
Errors from parallel task 2:
Error: failed establishing atom transformations
... Calling mpi_abort ...

具体outmol文件内容如下：

   ===============================================================
   Materials Studio DMol^3 version 2018
   compiled on Nov 21 2017 23:05:02
   ===============================================================

   ===============================================================
   Density Functional Theory Electronic Structure Program
   Copyright (c) 2017, 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  3 16:44:11 2023

Job started on host DESKTOP-OUB0DOA

This run uses 6 processors

Message: License checkout of MS_dmol successful
Message: License checkout of MS_dsolid successful

Basis set is read from file:
C:\Program Files (x86)\BIOVIA\Materials Studio 18.1 x64 Server\share\Resources\Quantum\DMol3\BASFILE_v3.5

parallel run with 6 processors

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

Geometry is read from file: sub_2.car

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

$cell vectors
         23.28803990135850 0.00000000000000 0.00000000000000
         -11.64401995067925 20.16803415892212 0.00000000000000
            0.00000000000000 0.00000000000000 37.79452249987180
$coordinates
C          -0.00002554342803 -0.00031920308840 0.89897076686432
C          2.32880399013585 1.34498760429235 0.89739689901249
C          4.65763352369973 -0.00031920308840 0.89897076686432
C          6.98643112656128 1.34489231107305 0.89811152729255
C          9.31519680438967 -0.00035670092390 0.89811152729255
C          11.64399440725122 1.34485481323755 0.89897076686432
C          13.97282394081510 -0.00045199414321 0.89739689901249
C          16.30165347437898 1.34485481323755 0.89897076686432
C          18.63045107724053 -0.00035670092390 0.89811152729255
C          20.95921675506893 1.34489231107305 0.89811152729255
C          -2.32892103977203 4.03314962821902 0.90179805415007
C          -0.00004893823746 5.37842362806452 0.90111981065682
C          2.32880399013585 4.03321284333736 0.89670162719713
C          4.65765691850916 5.37842362806452 0.90111981065682
C          6.98652902004373 4.03314962821902 0.90179805415007
C          9.31520142099060 5.37846592013520 0.90858143205588
C          11.64405200988296 4.03315573014468 0.90722811791955
C          13.97282394081510 5.37852211492098 0.91226595769343
C          16.30159587174724 4.03315573014468 0.90722811791955
C          18.63044646063961 5.37846592013520 0.90858143205588
C          -4.65786119034437 8.06669290339742 0.91908658777034
C          -2.32901611756256 9.41195451608817 0.91565677831718
C          -0.00080000988584 8.06600191181173 0.90251738028927
C          2.32880399013585 9.41172142403983 0.88891317388530
C          4.65840799015754 8.06600191181173 0.90251738028927
C          6.98662409783426 9.41195451608817 0.91565677831718
C          9.31546917061607 8.06669290339742 0.91908658777034
C          11.64403059361679 9.41214146102453 0.92393499572828
C          13.97282394081510 8.06686433557203 0.92260343044992
C          16.30161728801341 9.41214146102453 0.92393499572828
C          -6.98642261334509 12.10042830892067 0.92393499572828
C          -4.65786119034437 13.44587686654778 0.91908658777034
C          -2.32901611756256 12.10061525385703 0.91565677831718
C          -0.00080000988584 13.44656785813347 0.90251738028927
C          2.32880399013585 12.10084834590537 0.88891317388530
C          4.65840799015754 13.44656785813347 0.90251738028927
C          6.98662409783426 12.10061525385703 0.91565677831718
C          9.31546917061607 13.44587686654778 0.91908658777034
C          11.64403059361679 12.10042830892067 0.92393499572828
C          13.97282394081510 13.44570543437318 0.92260343044992
C          -9.31521596054340 16.13404765313450 0.91226595769343
C          -6.98644402961126 17.47941403980052 0.90722811791955
C          -4.65759344071889 16.13410384981000 0.90858143205588
C          -2.32892103977203 17.47942014172618 0.90179805415007
C          -0.00004893823746 16.13414614188068 0.90111981065682
C          2.32880399013585 17.47935692471812 0.89670162719713
C          4.65765691850916 16.13414614188068 0.90111981065682
C          6.98652902004373 17.47942014172618 0.90179805415007
C          9.31520142099060 16.13410384981000 0.90858143205588
C          11.64405200988296 17.47941403980052 0.90722811791955
$end
______________________________________________________________________>8

N_atoms = 50    N_atom_types =  1

INPUT_DMOL keywords (for archive):
______________________________________________________________________>8

#Warning: no global confinement specs in BASFILE
                                                                                                                                 <--
# Task parameters                                                                                                                <--
Calculate                   energy                                                                                              <--
Symmetry                   on                                                                                                 <--
Max_memory                   2048                                                                                                 <--
File_usage                   smart                                                                                              <--
Scf_density_convergence    1.000000e-004                                                                                        <--
Scf_charge_mixing          2.000000e-001                                                                                        <--
Scf_diis                   6 pulay                                                                                              <--
Scf_iterations             50                                                                                                 <--
                                                                                                                                 <--
# Electronic parameters                                                                                                          <--
Spin_polarization          restricted                                                                                           <--
Charge                      0                                                                                                    <--
Basis                      dnp                                                                                                 <--
Pseudopotential             none                                                                                                 <--
Functional                   pbe                                                                                                 <--
Aux_density                hexadecapole                                                                                        <--
Integration_grid             coarse                                                                                              <--
Occupation                   thermal 0.0500                                                                                     <--
Cutoff_Global                5.0000 angstrom                                                                                     <--
                                                                                                                                 <--
# Kpoint definition file (intervals/offset):                                                                                     <--
Kpoints                      file    5 5 1 0.0000 0.0000 0.0000                                                                <--
sub_2.kpoints
                                                                                                                                 <--
# Calculated properties                                                                                                          <--
______________________________________________________________________>8

Publications of specific relevance to this calculation:

Density functional:
PBE functional: Perdew Burke Ernzerhof: Phys. Rev. Lett. 77, 3865 (1996)

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)

Thermal smearing overrode tetrahedra Bloechl correction

Calculation is Spin_restricted

The point group of the crystal is:
full hexagonal group
with inversion symmetry

Note: C3 point group operation found: mesh 3

Errors from parallel task 2:
Error: failed establishing atom transformations
... Calling mpi_abort ...

DMol3.pl message: DMol3 job finished in 0 hr 0 min 3 sec.

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