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flymice金虫 (著名写手)
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[求助]
求问为什么使用DMOL3模块优化石墨烯结构的时候没有能量曲线？
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如题，我建石墨烯的方法是： 导入石墨结构，make p1,把上面的一层删掉，然后将下面的一层移动到中间。 Dmol3中出了计算任务选择了结构优化，其他全部采用默认设置，但是计算结构里面没有convergence和energy两个文件，不知道怎么回事？求高手解答。 |
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2楼2012-04-24 20:11:58
mengfc
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3楼2012-04-24 22:01:41
flymice
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4楼2012-04-25 09:54:53
flymice
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5楼2012-04-25 09:55:24
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6楼2012-04-25 14:42:34
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7楼2012-04-25 15:08:45
flymice
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我换了种方法成功了，建模方法在下面地址 http://muchong.com/bbs/viewthread.php?tid=3191417&page=1 这是输出结果 =============================================================== Materials Studio DMol^3 version 5.0 compiled on Oct 22 2009 07:07:30 =============================================================== =============================================================== Density Functional Theory Electronic Structure Program Copyright (c) 2009, Accelrys Inc. 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 25 16:14:15 2012 Message: License checkout of MS_dmol successful Message: License checkout of MS_dsolid successful Basis set is read from file: C:\PROGRA~2\Accelrys\MATERI~1.0\etc\Gateway\..\..\share\Resources\Quantum\DMol3\BASFILE_v3.5 no INCOOR file: try ZMAT no ZMAT file: try CAR Geometry is read from file: graphite__0_0_1___2_.car INCOOR, atomic coordinates in au (for archive): ______________________________________________________________________>8 $cell vectors 9.29745253496846 0.00000000000000 0.00000000000000 4.64872626748423 8.05183008576271 0.00000000000000 0.00000000000000 0.00000000000000 18.89726124993590 $coordinates C 0.00000000000000 0.00000000000000 0.00000000000000 C 2.32436211329001 1.34197109117081 0.00000000000000 C 4.64872626748423 0.00000000000000 0.00000000000000 C 6.97308838077424 1.34197109117081 0.00000000000000 C 2.32436313374212 4.02591504229607 0.00000000000000 C 4.64872524703212 5.36788613346688 0.00000000000000 C 6.97308940122635 4.02591504229607 0.00000000000000 C 9.29745151451635 5.36788613346688 0.00000000000000 $end ______________________________________________________________________>8 N_atoms = 8 N_atom_types = 1 INPUT_DMOL keywords (for archive): ______________________________________________________________________>8 #Warning: no global confinement specs in BASFILE <-- # Task parameters <-- Calculate optimize <-- Opt_energy_convergence 2.0000e-005 <-- Opt_gradient_convergence 4.0000e-003 A <-- Opt_displacement_convergence 5.0000e-003 A <-- Opt_iterations 50 <-- Opt_max_displacement 0.3000 A <-- Symmetry on <-- Max_memory 2048 <-- <-- # Electronic parameters <-- Spin_polarization restricted <-- Charge 0 <-- Basis dnd <-- Pseudopotential none <-- Functional pwc <-- Harris off <-- Aux_density octupole <-- Integration_grid medium <-- Occupation fermi <-- Cutoff_Global 3.3000 angstrom <-- Scf_density_convergence 1.0000e-005 <-- Scf_charge_mixing 0.2000 <-- Scf_iterations 50 <-- Scf_diis 6 pulay <-- <-- # Kpoint definition file (intervals/offset): <-- Kpoints file 5 5 2 0.0000 0.0000 0.0000 <-- graphite__0_0_1___2_.kpoints <-- # Calculated properties <-- ______________________________________________________________________>8 Publications of specific relevance to this calculation: Density functional: local functional PWC: Perdew Wang: Phys. Rev. B 45, 13244 (1992) 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) Fast Calculation of Electrostatics in Crystals and Large Molecules; Delley: J. Phys. Chem. 100, 6107 (1996) Calculation is Spin_restricted Note: C3 point group operation found: mesh 3 Note: this cell has 4 times the volume of the primitive cell Lattice: translation vector [a0] 1 9.297452535 0.000000000 0.000000000 translation vector [a0] 2 4.648726267 8.051830086 0.000000000 translation vector [a0] 3 0.000000000 0.000000000 18.897261250 Cell volume 1414.677 a0^3 ** GEOMETRY OPTIMIZATION IN DELOCALIZED COORDINATES ** Searching for a Minimum Input Coordinates (Angstroms) ---------------------------------------------------------------------- ATOM X Y Z 1 C 0.000000 0.000000 0.000000 2 C 1.229999 0.710141 0.000000 3 C 2.460000 0.000000 0.000000 4 C 3.689999 0.710141 0.000000 5 C 1.230000 2.130422 0.000000 6 C 2.459999 2.840563 0.000000 7 C 3.690000 2.130422 0.000000 8 C 4.919999 2.840563 0.000000 ---------------------------------------------------------------------- Crystal symmetry: full hexagonal group with inversion symmetry Crystal symmetry: full hexagonal group with inversion symmetry Message: Generating delocalized internals MDF file does not exist. Generating automatic internal coordinates. *** OPTIMIZATION USES DELOCALIZED INTERNALS *** The preliminary size of active space is : 21 There are : 21 degrees of freedom There are likely: 84 primitive internals Message: Generation of delocalized internals is successful Carbon nbas= 1, z= 6, nrfn= 7, rcut= 6.24, e_ref= -0.055391 Ha rcore= 0.00 zval= 6.00 6.00 n=1 L=0 occ= 2.00 e= -9.911120Ha -269.6954eV n=2 L=0 occ= 2.00 e= -0.477695Ha -12.9988eV n=2 L=1 occ= 2.00 e= -0.172177Ha -4.6852eV n=2 L=0 occ= 0.00 e= -1.475201Ha -40.1423eV n=2 L=1 occ= 0.00 e= -1.169933Ha -31.8355eV n=3 L=2 occ= 0.00 e= -2.722144Ha -74.0733eV n=3 L=2 occ= 0.00 e= -1.385417Ha -37.6991eV eliminated Kpoints mesh: 5 5 2 0 0 0 0 1 50 Parameters for generating k-points: 5 5 2 0.00 0.00 0.00 50 Total number of symmetry-unique k points: 5 Total number of symmetry-unique tetrahedra: 15 Symmetry orbitals C1 n norb representation 1 112 a total number of valence orbitals: 112 cell charge= 0.000000 active electron number 48.0 (without charge= 48.0 ) Integration in 3d (fixed mesh): ipa= 6 f3= T npri,iomax,iomin, thres, rmaxp, sp 0 6 1 0.00010 10.00 1.00 Integration points, checksum 42488 48.001371 real array elements, matrices vectors etc: 11.2 MB integer arrays : 0.8 MB min recommended for all-incl workspace : 13.4 MB Total memory allocated for arrays : 26.2 MB Total Energy Binding E Cnvgnce Time Iter Ef -302.476521Ha -2.7553370Ha 1.50E-01 0.0m 1 Ef -302.407964Ha -2.6867798Ha 1.13E-01 0.0m 2 Ef -302.342766Ha -2.6215822Ha 2.55E-02 0.0m 3 Ef -302.340753Ha -2.6195693Ha 4.74E-03 0.0m 4 Ef -302.340481Ha -2.6192970Ha 7.54E-04 0.0m 5 Ef -302.340444Ha -2.6192598Ha 1.02E-05 0.0m 6 Ef -302.340443Ha -2.6192595Ha 9.62E-06 0.0m 7 Message: SCF converged Fermi Energy -0.170628 Ha -4.643 eV within the k-points mesh accuracy this solid is an insulator or semiconductor DFT energy gap: 2.06 eV direct valence band edge at 0.600 0.400 0.250 in fractional units of recip conduction band edge at 0.600 0.400 0.250 df ATOMIC COORDINATES (au) DERIVATIVES (au) df x y z x y z df C 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 df C 2.324362 1.341971 0.000000 0.000000 0.000000 0.000000 df C 4.648726 0.000000 0.000000 0.000000 0.000000 0.000000 df C -2.324364 1.341971 0.000000 0.000000 0.000000 0.000000 df C 2.324363 4.025915 0.000000 0.000000 0.000000 0.000000 df C -0.000001 -2.683944 0.000000 0.000000 0.000000 0.000000 df C 6.973089 4.025915 0.000000 0.000000 0.000000 0.000000 df C -4.648727 -2.683944 0.000000 0.000000 0.000000 0.000000 df binding energy -2.6192595Ha -71.27371eV -1643.643kcal/mol Total Energy Binding E Time Iter Ef -302.340443Ha -2.6192595Ha 0.0m 8 Energy components: Sum of atomic energies = -299.7211839Ha Kinetic = -4.5243759Ha Electrostatic = 0.6068696Ha Exchange-correlation = 0.8551185Ha Spin polarization = 0.4431283Ha ** GEOMETRY OPTIMIZATION IN DELOCALIZED COORDINATES ** Searching for a Minimum Input Coordinates (Angstroms) ---------------------------------------------------------------------- ATOM X Y Z 1 C 0.000000 0.000000 0.000000 2 C 1.229999 0.710141 0.000000 3 C 2.460000 0.000000 0.000000 4 C 3.689999 0.710141 0.000000 5 C 1.230000 2.130422 0.000000 6 C 2.459999 2.840563 0.000000 7 C 3.690000 2.130422 0.000000 8 C 4.919999 2.840563 0.000000 ---------------------------------------------------------------------- Message: Gradients are very small. RMS cartesian gradient: 0.3E-07 Message: Geometry is converged +++ Entering Properties Section +++ Message: License checkin of MS_dmol successful Message: License checkin of MS_dsolid successful Message: DMol3 job finished successfully time all done 0.00m 0.02s DMol3.pl message: DMol3 job finished in 0 hr 0 min 21 sec. 下面是结构图  |
8楼2012-04-25 16:28:02
9楼2012-05-27 15:03:31
来去无风6988
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10楼2012-05-29 15:41:32
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