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feiyunxts

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虫号: 718480
注册: 2009-03-09
专业: 原子和分子物理

[求助] 关于siesta动力学问题

用siesta做PbSe动力学，一个PbSe分子自洽场收敛，但三个PbSe分子就不收敛，本人刚用siesta，望各位多多指教，下面是我的.fdf文件：
**********************************************************
# FDF file for  pbse

# General System descriptors

SystemName pbse Molecular # Descriptive name of the system
SystemLabel          pbse          # Short name for naming files

NumberOfAtoms          6          # Number of atoms
NumberOfSpecies       2          # Number of species

%block Chemical_Species_Label
1  34  Se    # Species index, atomic number, species label
2  82  Pb
%endblock Chemical_Species_Label
PAO.BasisType split
%block PAO.Basis                # Define Basis set
Se                   3  -0.739          # Label, l-shells, ionic net charge
n=4 0 2                      # n, l, Nzeta
5.801    3.944
1.000    1.000
n=4 1 2                      # n, l, Nzeta
4.971    3.847
1.000    1.000
n=4 2 1                      # n, l, Nzeta
4.888
1.000
Pb                   3 1.263          # Label, l-shells, ionic net charge
n=6 0 2                      # n, l, Nzeta
5.992    3.944
1.000    1.000
n=6 1 2                      # n, l, Nzeta
6.145    4.434
1.000    1.000
n=6 2 1                      # n, l, Nzeta
3.505
1.000
%endblock PAO.Basis

#%block kgrid_Monkhorst_Pack
#  4 0 0 0.5
#  0 4 0 0.5
#  0 0 4 0.5
#%endblock kgrid_Monkhorst_Pack

# Lattice, coordinates, k-sampling

AtomicCoordinatesFormat Ang # Format for coordinates
AtomicCoorFormatOut    Ang

%block AtomicCoordinatesAndAtomicSpecies
10.2779072 10.2779072 10.2779072  1
10.5864658 11.4565565 12.2545855  1
9.1235465    9.1258796    9.1254856 1
12.4458954 15.0215668 13.1256565  2
11.2779069 11.2779069 11.2779069  2
14.0213566 16.0214589 14.0213563  2
%endblock AtomicCoordinatesAndAtomicSpecies

LatticeConstant  1.00  Ang

#%block LatticeParameters
# 4.330 4.330 4.330  60. 60. 60.
#%endblock LatticeParameters
%block LatticeVectors
20.000000 0.0000000 0.0000000
0.0000000  20.0000000 0.0000000
0.0000000 0.0000000  20.0000000
%endblock LatticeVectors
kgrid_cutoff       7. Ang

# DFT, Grid, SCF

XC.functional          GGA       # Exchange-correlation functional type
XC.authors             PBE    # Particular parametrization of xc func
SpinPolarized          .false.    # Spin unpolarized calculation
MeshCutoff             200. Ry    # Equivalent planewave cutoff for the grid
MaxSCFIterations       100       # Maximum number of SCF iterations per step
DM.MixingWeight       0.3       # New DM amount for next SCF cycle
DM.Tolerance          1.d-4    # Tolerance in maximum difference
                                 # between input and output DM
DM.NumberPulay       3          # Number of SCF steps between pulay mixing

# Eigenvalue problem: order-N or diagonalization

SolutionMethod       diagon    # OrderN or Diagon
ElectronicTemperature 5 K       # Temp. for Fermi smearing

# Molecular dynamics and relaxations

# Output options

WriteCoorInitial
WriteCoorStep
WriteForces
WriteKpoints          .false.
WriteEigenvalues       .false.
WriteKbands          .false.
WriteBands             .false.
WriteMullikenPop       1          # Write Mulliken Population Analysis
WriteMDhistory       .false.
WriteCoorXmol             T
# Options for saving/reading information
PAO.EnergyShift    70 meV

DM.UseSaveDM                      # Use DM Continuation files
MD.UseSaveXV          T    # Use stored positions and velocities
MD.UseSaveCG          T    # Use stored positions and velocities
#SaveRho                            # Write valence pseudocharge at the mesh
#SaveDeltaRho                      # Write RHOscf-RHOatm at the mesh
#SaveElectrostaticPotential .false. # Write the total elect. pot. at the mesh
#SaveTotalPotential    T    # Write the total pot. at the mesh
#WriteSiestaDim       T    # Write minimum dim to siesta.h and stop
#WriteDenchar                      # Write information for DENCHAR

MD.TypeOfRun       Verlet
MD.NumVerletsteps       100
MD.InitialTimeStep    1
MD.FinalTimeStep       100
MD.LenghTimeStep       1.0 fs
MD.InitialTemperature 2000 k
MD.MaxForceTol       0.01 eV/Ang
*****************************************************

基组是我自己优化的，不知道问题出在呢，算六个原子时候能量就在跳动

* Maximum dynamic memory allocated = 228 MB

siesta:                ==============================
                        Begin MD step =    24
                     ==============================

outcoor: Atomic coordinates (Ang):
10.45509635 10.05264256 10.21606736 1    1  Se
9.77621935 11.88324222 13.63281076 1    2  Se
9.09885123 8.96546340 8.91861146 1    3  Se
12.13358260 14.84222738 12.98919191 2    4  Pb
11.58034012 11.21672808 10.69083138 2    5  Pb
14.28159461 16.24783399 14.32300934 2    6  Pb

outcell: Unit cell vectors (Ang):
   20.000000 0.000000 0.000000
      0.000000 20.000000 0.000000
      0.000000 0.000000 20.000000

outcell: Cell vector modules (Ang) : 20.000000 20.000000 20.000000
outcell: Cell angles (23,13,12) (deg):    90.0000    90.0000    90.0000
outcell: Cell volume (Ang**3)       : 8000.0000
New_DM. Step: 24
Re-using DM from previous geometry...
Extrapolating Density Matrix...

siesta: iscf Eharris(eV)    E_KS(eV) FreeEng(eV) dDmax  Ef(eV)
siesta: 1 -6523.1808 -6391.7257 -6391.7268  1.1943-16.9715
siesta: 2 -7863.2689 -6021.2781 -6021.2781  6.1972-20.0659
siesta: 3 -6597.3824 -6373.5952 -6373.5952  1.3095-16.8452
siesta: 4 -6482.1489 -6396.0876 -6396.0876  1.1505-15.8880
siesta: 5 -6596.1925 -6386.9402 -6386.9402  1.2520-14.5525
siesta: 6 -6449.5342 -6400.0936 -6400.0936  1.1046-15.7057
siesta: 7 -6424.9559 -6401.7500 -6401.7500  1.0285-16.8837
siesta: 8 -6580.8532 -6389.2100 -6389.2100  1.2667-18.5420
siesta: 9 -6474.3629 -6403.5998 -6403.5998  1.0870-16.6360
siesta: 10 -6466.1174 -6404.0260 -6404.0260  1.1922-15.8651
siesta: 11 -6507.7729 -6401.6928 -6401.6928  1.2916-14.7086
siesta: 12 -6469.5706 -6405.5066 -6405.5066  1.1486-16.5515
siesta: 13 -6476.4370 -6404.4300 -6404.4300  1.1787-17.3792
siesta: 14 -6468.3152 -6405.9718 -6405.9718  1.1180-12.6934
siesta: 15 -6519.2248 -6403.1768 -6403.1768  1.4044-16.2424
siesta: 16 -6462.8296 -6403.5238 -6403.5246  1.1140-16.4565
siesta: 17 -6478.9239 -6402.5692 -6402.5692  1.1963-16.6896
siesta: 18 -6439.7391 -6406.1912 -6406.1912  1.0734-15.2156
siesta: 19 -6473.5417 -6406.3545 -6406.3545  1.2866-16.1422
siesta: 20 -6522.9718 -6399.1185 -6399.1185  1.2962-18.5459
siesta: 21 -6460.8589 -6405.7340 -6405.7340  1.0877-15.3274
siesta: 22 -6455.9165 -6405.6944 -6405.6945  1.0786-16.2317
siesta: 23 -6497.9210 -6404.9917 -6404.9917  1.3688-18.0443
siesta: 24 -6476.2342 -6403.0544 -6403.0544  1.1666-18.0503
siesta: 25 -6469.0556 -6405.2461 -6405.2461  1.1241-14.1203
siesta: 26 -6467.9829 -6402.8779 -6402.8779  1.0799-17.5551
siesta: 27 -6503.3981 -6404.0033 -6404.0033  1.3338-16.7269
siesta: 28 -6455.8193 -6404.4824 -6404.4824  1.0965-16.0490
siesta: 29 -6453.5310 -6405.6983 -6405.6983  1.0559-13.3146
siesta: 30 -6453.8245 -6405.7218 -6405.7218  1.0749-16.6353
siesta: 31 -6513.7181 -6404.1251 -6404.1251  1.4187-17.4377
siesta: 32 -6485.6262 -6402.9036 -6402.9036  1.1824-16.8319
siesta: 33 -6456.4487 -6405.8565 -6405.8565  1.1169-13.1927
siesta: 34 -6462.6221 -6403.3116 -6403.3116  1.0731-17.0234
siesta: 35 -6513.9138 -6403.4287 -6403.4287  1.4265-16.8760
siesta: 36 -6474.7561 -6402.3595 -6402.3595  1.1073-15.8377
siesta: 37 -6446.4162 -6405.4064 -6405.4064  1.0896-13.3745
siesta: 38 -6463.4651 -6402.4831 -6402.4831  1.0702-16.7524
siesta: 39 -6527.8657 -6402.0344 -6402.0344  1.4349-16.5939
siesta: 40 -6471.9765 -6401.8044 -6401.8044  1.0886-15.5861
siesta: 41 -6438.6053 -6405.2816 -6405.2816  0.9995-13.7189
siesta: 42 -6469.4875 -6402.8409 -6402.8409  1.0736-17.5412
siesta: 43 -6511.9132 -6403.3302 -6403.3302  1.3803-16.6417
siesta: 44 -6468.3385 -6404.5087 -6404.5087  1.1351-15.9266
siesta: 45 -6447.1657 -6406.0478 -6406.0478  1.0506-13.4848
siesta: 46 -6455.7496 -6406.1575 -6406.1584  1.0790-16.4855
siesta: 47 -6493.7368 -6405.5682 -6405.5682  1.3878-17.4775
siesta: 48 -6512.6331 -6400.5700 -6400.5700  1.2325-18.0375
siesta: 49 -6472.9243 -6405.1503 -6405.1503  1.1450-13.6589
siesta: 50 -6456.5702 -6403.8601 -6403.8601  1.0581-17.6460
siesta: 51 -6492.7700 -6404.2691 -6404.2691  1.3668-16.9855
siesta: 52 -6475.8983 -6403.3928 -6403.3928  1.1065-15.2945
siesta: 53 -6433.1762 -6406.9014 -6406.9014  1.0824-14.9806
siesta: 54 -6561.1902 -6394.8041 -6394.8050  1.2308-17.6666
siesta: 55 -6471.7145 -6405.9974 -6405.9974  1.2885-15.7839
siesta: 56 -6437.6745 -6406.5006 -6406.5006  1.0698-16.9832
siesta: 57 -6502.4497 -6403.3326 -6403.3326  1.1403-15.5341
siesta: 58 -6455.0907 -6404.3636 -6404.3636  1.0735-16.3082
siesta: 59 -6453.4083 -6406.5751 -6406.5751  1.2735-16.5671
siesta: 60 -6449.5329 -6405.0184 -6405.0186  1.0602-15.6619
siesta: 61 -6497.4620 -6403.7463 -6403.7463  1.2255-14.1030

*************************************************************

算一个PbSe分子的结果如下机组都一样

****siesta:                ==============================
                        Begin MD step =    1
                     ==============================

outcoor: Atomic coordinates (Ang):
10.27790720 10.27790720 10.27790720 1    1  Se
11.27790690 11.27790690 11.27790690 2    2  Pb

outcell: Unit cell vectors (Ang):
   20.000000 0.000000 0.000000
      0.000000 20.000000 0.000000
      0.000000 0.000000 20.000000

outcell: Cell vector modules (Ang) : 20.000000 20.000000 20.000000
outcell: Cell angles (23,13,12) (deg):    90.0000    90.0000    90.0000
outcell: Cell volume (Ang**3)       : 8000.0000
New_DM. Step:    1
Initializing Density Matrix...

InitMesh: MESH = 180 x 180 x 180 =    5832000
InitMesh: Mesh cutoff (required, used) = 200.000 223.865 Ry

* Maximum dynamic memory allocated = 207 MB

stepf: Fermi-Dirac step function

siesta: Program's energy decomposition (eV):
siesta: Eions =    1652.849803
siesta: Ena    =       97.470241
siesta: Ekin =    121.233987
siesta: Enl    =       -9.321532
siesta: DEna =       -0.000000
siesta: DUscf =       0.000000
siesta: DUext =       0.000000
siesta: Exc    =    -551.300261
siesta: eta*DQ  =       0.000000
siesta: Emadel  =       0.000000
siesta: Emeta =       0.000000
siesta: Emolmec =       0.000000
siesta: Ekinion =       0.000000
siesta: Eharris =    -2377.653320
siesta: Etot =    -1994.767369
siesta: FreeEng =    -1994.767369

siesta: iscf Eharris(eV)    E_KS(eV) FreeEng(eV) dDmax  Ef(eV)
siesta: 1 -2377.6533 -1994.7674 -1994.7674  2.0247-47.0728
timer: Routine,Calls,Time,% = IterSCF       1    6.420  87.04
elaps: Routine,Calls,Wall,% = IterSCF       1    6.432  87.02
siesta: 2 -2485.2656 -2032.6617 -2032.6617 28.5395 -3.7215
siesta: 3 -2201.6240 -2080.6059 -2080.6059  1.6440-28.0872
siesta: 4 -2266.1698 -2104.1888 -2104.1888  3.3302 -5.3165
siesta: 5 -2165.6644 -2109.7116 -2109.7116  0.8744-17.6820
siesta: 6 -2163.7805 -2123.9590 -2123.9602  0.7239-17.7512
siesta: 7 -2162.0157 -2147.1562 -2147.1574  0.5897-15.0849
siesta: 8 -2161.9164 -2156.7185 -2156.7197  0.4753-14.5905
siesta: 9 -2161.9324 -2157.3961 -2157.3961  0.4748-14.8787
siesta: 10 -2162.0008 -2166.7425 -2166.7425  0.4204-13.7599
siesta: 11 -2161.9813 -2165.4353 -2165.4355  0.4488-14.5985
siesta: 12 -2161.9161 -2165.3212 -2165.3212  0.3737-14.3286
siesta: 13 -2161.9214 -2164.6483 -2164.6488  0.4396-14.5059
siesta: 14 -2161.9104 -2164.0639 -2164.0640  0.4320-14.5033
siesta: 15 -2161.9026 -2164.0083 -2164.0083  0.2417-14.3379
siesta: 16 -2161.9235 -2162.8467 -2162.8476  0.4426-14.7411
siesta: 17 -2161.8971 -2163.0768 -2163.0768  0.1824-14.4467
siesta: 18 -2161.8964 -2163.0211 -2163.0222  0.0538-14.4973
siesta: 19 -2161.8961 -2162.7034 -2162.7046  0.1485-14.5239
siesta: 20 -2161.8958 -2162.6412 -2162.6423  0.0198-14.5016
siesta: 21 -2161.8957 -2162.4806 -2162.4818  0.0815-14.5302
siesta: 22 -2161.8956 -2162.4089 -2162.4101  0.0174-14.5387
siesta: 23 -2161.8956 -2162.2558 -2162.2570  0.0565-14.5388
siesta: 24 -2161.8956 -2162.2598 -2162.2610  0.0179-14.5392
siesta: 25 -2161.8956 -2162.1675 -2162.1687  0.0315-14.5505
siesta: 26 -2161.8956 -2162.1417 -2162.1429  0.0101-14.5529
siesta: 27 -2161.8956 -2162.0694 -2162.0706  0.0213-14.5539
siesta: 28 -2161.8956 -2162.0718 -2162.0730  0.0109-14.5539
siesta: 29 -2161.8956 -2162.0235 -2162.0247  0.0113-14.5588
siesta: 30 -2161.8956 -2162.0137 -2162.0149  0.0083-14.5594
siesta: 31 -2161.8956 -2161.9795 -2161.9807  0.0070-14.5602
siesta: 32 -2161.8956 -2161.9807 -2161.9819  0.0094-14.5602
siesta: 33 -2161.8956 -2161.9567 -2161.9579  0.0053-14.5622
siesta: 34 -2161.8956 -2161.9519 -2161.9531  0.0047-14.5624
siesta: 35 -2161.8956 -2161.9364 -2161.9376  0.0029-14.5629
siesta: 36 -2161.8956 -2161.9361 -2161.9373  0.0063-14.5629
siesta: 37 -2161.8957 -2161.9250 -2161.9262  0.0021-14.5637
siesta: 38 -2161.8957 -2161.9224 -2161.9236  0.0033-14.5638
siesta: 39 -2161.8957 -2161.9154 -2161.9166  0.0012-14.5640
siesta: 40 -2161.8957 -2161.9146 -2161.9158  0.0049-14.5641
siesta: 41 -2161.8957 -2161.9098 -2161.9110  0.0011-14.5644
siesta: 42 -2161.8957 -2161.9083 -2161.9095  0.0018-14.5644
siesta: 43 -2161.8957 -2161.9052 -2161.9064  0.0006-14.5645
siesta: 44 -2161.8957 -2161.9041 -2161.9053  0.0028-14.5646
siesta: 45 -2161.8957 -2161.9025 -2161.9037  0.0005-14.5647
siesta: 46 -2161.8957 -2161.9017 -2161.9029  0.0011-14.5647
siesta: 47 -2161.8957 -2161.9003 -2161.9015  0.0003-14.5648
siesta: 48 -2161.8957 -2161.8995 -2161.9007  0.0012-14.5648
siesta: 49 -2161.8957 -2161.8989 -2161.9001  0.0002-14.5648
siesta: 50 -2161.8957 -2161.8985 -2161.8997  0.0006-14.5649
siesta: 51 -2161.8957 -2161.8979 -2161.8991  0.0002-14.5649
siesta: 52 -2161.8957 -2161.8974 -2161.8986  0.0006-14.5649
siesta: 53 -2161.8957 -2161.8972 -2161.8984  0.0001-14.5649
siesta: 54 -2161.8957 -2161.8970 -2161.8981  0.0003-14.5649
siesta: 55 -2161.8957 -2161.8967 -2161.8979  0.0001-14.5649
siesta: 56 -2161.8957 -2161.8965 -2161.8977  0.0002-14.5649
siesta: 57 -2161.8957 -2161.8964 -2161.8976  0.0001-14.5649
siesta: 58 -2161.8957 -2161.8963 -2161.8975  0.0001-14.5649

siesta: E_KS(eV) =          -2161.8961

siesta: E_KS - E_eggbox =    -2161.8961

siesta: Atomic forces (eV/Ang):
   1 8.665684 8.665684 8.665684
   2 -8.663728 -8.663726 -8.663729
----------------------------------------
Tot 0.001955 0.001958 0.001955
----------------------------------------
Max 8.665684
Res 8.664706 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 8.665684 constrained

Stress-tensor-Voigt (kbar):       1.72       1.67       1.74       1.78       1.75       1.72
(Free)E + p*V (eV/cell) -2170.4341
Target enthalpy (eV/cell) -2161.8973

siesta: Stress tensor (static) (eV/Ang**3):
      0.001088 0.001081 0.001081
      0.001081 0.001088 0.001081
      0.001081 0.001081 0.001088

siesta: Pressure (static):       -1.74395318  kBar

siesta: Stress tensor (total) (eV/Ang**3):
      0.001073 0.001108 0.001075
      0.001108 0.001043 0.001092
      0.001075 0.001092 0.001086

siesta: Pressure (total):       -1.70968682  kBar

mulliken: Atomic and Orbital Populations:

Species: Se
Atom  Qatom  Qorb
            4s    4s    4py    4pz    4px    4py    4pz    4px
            4dxy 4dyz 4dz2 4dxz 4dx2-y2
1  3.627 1.085 0.768 0.299 0.299 0.299 0.276 0.276 0.276
            0.007 0.007 0.014 0.007 0.014

Species: Pb
Atom  Qatom  Qorb
            6s    6s    6py    6pz    6px    6py    6pz    6px
            6dxy 6dyz 6dz2 6dxz 6dx2-y2
2  6.373 0.032  -0.008  -0.005  -0.005  -0.005 0.015 0.015 0.015
            1.213 1.213 1.339 1.213 1.339

mulliken: Qtot =    10.000

siesta: Temp_ion = 2000.000 K
*********************************************************
本人新手金币不多望各位见谅

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1楼 2011-05-08 14:32:47

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

wangsong1016

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gzqdyouxia(金币+2): 谢谢详细指导 2011-05-20 15:53:13

引用回帖:

Originally posted by feiyunxts at 2011-05-08 14:32:47:
用siesta做PbSe动力学，一个PbSe分子自洽场收敛，但三个PbSe分子就不收敛，本人刚用siesta，望各位多多指教，下面是我的.fdf文件：
**********************************************************
# FDF file fo ...

你的程序我没有跑，不过目前看出来一些问题，你尝试修改一下，看看有没有帮助。
首先MD.ForceTol 0.01eV/Ang 这个选项只适用于MD.TypeofRun CG or broyden，你这里采用的是Verlet算法，这一项没用。
第二，latticeparameter 和latticevector模块都是用来划分体系的元胞，如果两个都在输出文件中出现，就会有优先级，其中一个有效，一个无效。具体哪个有效我也不清楚了。不过可能跟你享有的元胞参数是不符的。
ElectronicTemperature 5 K这个选项温度是不是太低了，我自己没用过，不过见到过有人计算采用300k，说是跟收敛有关的。
你输入的原子坐标自己验证过吗？我把原子坐标取出来之后没有看明白到底是什么结构，你应该再确认一下。
还有MD的温度是2000K，这个在体系中引起的震动还是比较大的，不知道这里有没有必要选取如此大的数值。
对于这么一个小体系，K点却没有取值，应该不合理，尝试一下多去一点k点吧。

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2楼2011-05-20 13:24:16

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

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