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yoghurt117

木虫 (正式写手)

应助: 3 (幼儿园)
金币: 8018.3
散金: 56
红花: 8
帖子: 576
在线: 134.9小时
虫号: 761174
注册: 2009-05-01
性别: GG
专业: 理论和计算化学

[求助] 盒子，盒子：（

最近看cpmd官网的教程，其中一个bulk系统的动力学计算，其输入文件是：
&INFO
md at T=300K with thermostats
&END
&CPMD
MOLECULAR DYNAMICS
RESTART WAVEFUNCTIONS COORDINATES VELOCITIES LATEST

TRAJECTORY SAMPLE XYZ
  10

RESCALE OLD VELOCITIES
NOSE IONS
   400.0d0 3000.0d0
NOSE ELECTRONS
0.0080d0  10000.0d0
MAXSTEP
  5000
TIMESTEP
  4.0
EMASS
  400.0
MEMORY BIG
&END

&SYSTEM
SYMMETRY
  1
ANGSTROM
CELL
  9.95991 1.0 1.0  0.0  0.0  0.0
DUAL
  5.0
CUTOFF
  25.0
CHARGE
  1
&END
&DFT
FUNCTIONAL BLYP
GC-CUTOFF
  5.0d-6
&END
&ATOMS
ISOTOPES
16.00
  2.016
*O_VDB_BLYP.psp FORMATTED
LMAX=P
  33
   0.7327 -4.2440  2.1886
-0.8347 -4.7227  4.3691
   2.6518 -1.5714 -0.1309
   3.2623 -4.4641  2.6462
-4.7361  4.8510 -2.0459
-2.3920  0.3963  3.9231
-0.5493 -4.5740 -2.0499
   2.2782 -3.3931 -4.3667
-3.5142 -4.3400  2.4342
-3.8442  0.5428 -2.4979
   2.6625  2.2735  2.5634
   4.0301  2.4810 -3.1204
-1.3385 -0.8110 -0.2060
   3.3646 -4.3723 -0.2574
   0.7415 -0.6233 -1.8793
   4.5585  3.6260  4.3279
   1.4453  3.8230 -1.3437
   0.7650  1.2950  4.2396
-2.5713  3.1043 -4.8839
-4.1207  3.2564  1.0086
   0.4496  3.1128  1.4121
   4.0998  0.0228  4.2341
-0.5407 -2.4217 -3.9645
-4.5374 -1.1430 -0.2440
-1.6032  1.7664  0.5732
-3.1993 -1.5826 -4.4357
   0.5592 -1.4779  1.7951
-1.8413  2.8694 -2.0738
   0.9314  1.6635 -3.0237
   4.8851  0.6455  1.8791
-4.7775 -3.9950 -4.5931
-2.9360 -3.2201 -0.0728
   1.8651 -1.3161  4.1881
*H_VDB_BLYP.psp FORMATTED
LMAX=P
  67
   0.1804 -4.3091  3.0196
   0.4583 -3.4352  1.6684
-0.8907 -3.8505  4.8551
-1.4470 -5.3849  4.8012
   2.6813 -2.5699 -0.0836
   3.5705 -1.2189 -0.3089
   2.2641 -4.5114  2.6070
   3.6143 -5.2567  3.1440
-5.2043  3.9908 -2.2480
-5.2257  5.3344 -1.3202
-2.8338  0.3816  3.0261
-2.6987 -0.3905  4.4587
   0.2035 -5.0868 -1.6374
-1.2460 -5.2114 -2.3791
   3.1464 -3.8096 -4.0969
   1.5234 -3.8864 -3.9344
-4.2719 -3.7659  2.7445
-2.7608 -4.2804  3.0891
-3.5930 -0.0389 -3.2716
-3.0803  1.1482 -2.2743
   3.3247  1.5747  2.2926
   3.0265  2.7969  3.3338
   4.7065  1.8430 -2.7522
   3.1319  2.0416 -3.1370
-1.9556 -1.5794 -0.0367
-1.7355  0.0251  0.1726
   3.1616 -4.3000  0.7191
   2.7360 -5.0244 -0.6811
   1.5443 -1.0463 -1.4591
-0.0408 -0.7072 -1.2621
   5.5462  3.4712  4.3092
   4.1734  3.2213  5.1573
   1.3289  3.2796 -0.5124
   1.3588  3.2301 -2.1443
   1.2158  1.6650  3.4272
-0.2192  1.4615  4.1796
-2.3393  2.1786 -5.1828
-2.3958  3.1917 -3.9033
-4.0469  3.9980  1.6755
-4.8820  3.4416  0.3872
   1.3081  2.8588  1.8577
   0.2815  4.0896  1.5449
   4.4722  0.2911  3.3456
   4.8505 -0.1433  4.8736
-0.5906 -3.0520 -3.1897
-0.0056 -1.6175 -3.7060
-4.2505 -0.6992 -1.0929
-3.9724 -1.9523 -0.0834
-2.3879  2.3426  0.8019
-0.7686  2.1804  0.9365
-3.8725 -2.3207 -4.3898
-2.2782 -1.9717 -4.4453
   1.3775 -1.3132  1.2443
-0.2523 -1.2143  1.2736
-1.1466  2.2371 -2.4168
-2.0815  2.6232 -1.1348
   1.0048  0.8099 -2.5081
   0.8075  1.4570 -3.9943
   5.3467  1.4906  1.6095
   4.9527 -0.0223  1.1379
-4.4389 -4.2859 -3.6983
-5.0180 -4.7996 -5.1361
-2.9873 -3.6787  0.8143
-2.9264 -3.9045 -0.8018
   1.8677 -2.1810  4.7284
   2.7693 -0.8629  4.0578
   1.2248 -1.2816  3.3950
&END

我把原子和坐标部分做成了xyz格式的文件
100
O 0.7327 -4.2440  2.1886
O -0.8347 -4.7227  4.3691
O 2.6518 -1.5714 -0.1309
O 3.2623 -4.4641  2.6462
O -4.7361  4.8510 -2.0459
O -2.3920  0.3963  3.9231
O -0.5493 -4.5740 -2.0499
O    2.2782 -3.3931 -4.3667
O -3.5142 -4.3400  2.4342
O -3.8442  0.5428 -2.4979
O    2.6625  2.2735  2.5634
O 4.0301  2.4810 -3.1204
O -1.3385 -0.8110 -0.2060
O 3.3646 -4.3723 -0.2574
O    0.7415 -0.6233 -1.8793
O    4.5585  3.6260  4.3279
O    1.4453  3.8230 -1.3437
O    0.7650  1.2950  4.2396
O -2.5713  3.1043 -4.8839
O -4.1207  3.2564  1.0086
O    0.4496  3.1128  1.4121
O    4.0998  0.0228  4.2341
O -0.5407 -2.4217 -3.9645
O -4.5374 -1.1430 -0.2440
O -1.6032  1.7664  0.5732
O -3.1993 -1.5826 -4.4357
O    0.5592 -1.4779  1.7951
O -1.8413  2.8694 -2.0738
O    0.9314  1.6635 -3.0237
O    4.8851  0.6455  1.8791
O -4.7775 -3.9950 -4.5931
O -2.9360 -3.2201 -0.0728
O    1.8651 -1.3161  4.1881
H    0.1804 -4.3091  3.0196
H    0.4583 -3.4352  1.6684
H -0.8907 -3.8505  4.8551
H -1.4470 -5.3849  4.8012
H    2.6813 -2.5699 -0.0836
H    3.5705 -1.2189 -0.3089
H    2.2641 -4.5114  2.6070
H    3.6143 -5.2567  3.1440
H -5.2043  3.9908 -2.2480
H -5.2257  5.3344 -1.3202
H -2.8338  0.3816  3.0261
H -2.6987 -0.3905  4.4587
H    0.2035 -5.0868 -1.6374
H -1.2460 -5.2114 -2.3791
H    3.1464 -3.8096 -4.0969
H    1.5234 -3.8864 -3.9344
H -4.2719 -3.7659  2.7445
H -2.7608 -4.2804  3.0891
H -3.5930 -0.0389 -3.2716
H -3.0803  1.1482 -2.2743
H    3.3247  1.5747  2.2926
H    3.0265  2.7969  3.3338
H    4.7065  1.8430 -2.7522
H    3.1319  2.0416 -3.1370
H -1.9556 -1.5794 -0.0367
H -1.7355  0.0251  0.1726
H    3.1616 -4.3000  0.7191
H    2.7360 -5.0244 -0.6811
H    1.5443 -1.0463 -1.4591
H -0.0408 -0.7072 -1.2621
H    5.5462  3.4712  4.3092
H    4.1734  3.2213  5.1573
H    1.3289  3.2796 -0.5124
H    1.3588  3.2301 -2.1443
H    1.2158  1.6650  3.4272
H -0.2192  1.4615  4.1796
H -2.3393  2.1786 -5.1828
H -2.3958  3.1917 -3.9033
H -4.0469  3.9980  1.6755
H -4.8820  3.4416  0.3872
H    1.3081  2.8588  1.8577
H    0.2815  4.0896  1.5449
H    4.4722  0.2911  3.3456
H    4.8505 -0.1433  4.8736
H -0.5906 -3.0520 -3.1897
H -0.0056 -1.6175 -3.7060
H -4.2505 -0.6992 -1.0929
H -3.9724 -1.9523 -0.0834
H -2.3879  2.3426  0.8019
H -0.7686  2.1804  0.9365
H -3.8725 -2.3207 -4.3898
H -2.2782 -1.9717 -4.4453
H    1.3775 -1.3132  1.2443
H -0.2523 -1.2143  1.2736
H -1.1466  2.2371 -2.4168
H -2.0815  2.6232 -1.1348
H    1.0048  0.8099 -2.5081
H    0.8075  1.4570 -3.9943
H    5.3467  1.4906  1.6095
H    4.9527 -0.0223  1.1379
H -4.4389 -4.2859 -3.6983
H -5.0180 -4.7996 -5.1361
H -2.9873 -3.6787  0.8143
H -2.9264 -3.9045 -0.8018
H    1.8677 -2.1810  4.7284
H    2.7693 -0.8629  4.0578
H    1.2248 -1.2816  3.3950

然后转化成mol用gaussview量了一下，这个系统各个方向上平均10个多埃，最大的有16埃，不知道symmetry部分的
CELL
  9.95991 1.0 1.0  0.0  0.0  0.0
里面的9.995991×9.995991×9.995991埃这样的格子怎么放下的，初学不太明白，请教一下，谢谢。

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