3.1. OUT文件¶
OUT文件是一个日志文件，它包含了计算过程的各种信息。它的开始部分会给出版本信息、计算的开始时间、并行设置等信息（称为共有信息），后续会根据不同的计算任务给出不同的信息。
OUT文件分为不同的块，每个大块的开头和结尾以=作为分隔，大块中的每个小块以-作为分隔。
3.1.1. 共有信息¶
OUT文件的开头部分均为如下形式，这部分包括3个大块，分别是Hylanemos的版本信息部分（HYLANEMOS Version）、并行信息部分（parallel info）、初始化信息部分（initialization）。 右侧#后的文字为说明。
================================================================================
| HYLANEMOS Version: 1.0.0 | #版本信息
| Calculated at: 2022-12-08 10:32:20 | #计算开始时间
================================================================================
================================================================================
| parallel info | #并行信息
--------------------------------------------------------------------------------
FFT mesh decomposition (1, 1)
HYLANEMOS starts with kgroups=1 npfft=1 nt=1 #k点和fft的并行信息
G vector decomposition: total max min #G点的并行信息
wave function: 411 411 411
dense grid: 3383 3383 3383
================================================================================
================================================================================
| initialization | #初始化信息
--------------------------------------------------------------------------------
Time spent until now is 1.694 seconds #初始化用时
================================================================================
3.1.2. scf计算¶
scf计算的OUT文件在共有信息之后有两个部分，分别是scf主循环部分（Main part of scf calculation）和scf结果部分（scf result）。
================================================================================
| Main part of scf calculation | #scf主循环
--------------------------------------------------------------------------------
iteration 1 begins #第几个电子步迭代开始
E(Ha) dE(Ha) estimated scf_diff(Ha) #E：体系能量；dE：当前电子步与上一个电子步之间的能量差；estimated scf_diff：两步scf之间的误差的预估，用于和scf_conv_thr比较判断电子步是否收敛。
-178.18006358 0.00000000 1.79540636
Energy by parts: #不同部分对体系总能量的贡献
one_electron contribution = -65.24907601 Ha / -1775.51780756 eV
hartree contribution = 45.03834947 Ha / 1225.55592196 eV
xc contribution = -29.06702338 Ha / -790.95399925 eV
ewald contribution = -130.02699089 Ha / -3538.21466755 eV
smearing contribution = -0.00000000 Ha / -0.00000000 eV
iteration 1 ends, not converged yet.
--------------------------------------------------------------------------------
#中间省略
convergence achieved in 27 iterations #scf在多少步达到收敛，在最后一个电子步会输出。
Time spent until now is 16.259 seconds
================================================================================
================================================================================
| scf result | #scf结果
--------------------------------------------------------------------------------
Electron Step Finish
Total Energy: -179.09698121 Ha / -4873.47712576 eV #scf计算结束后的体系总能量和费米能级。
Fermi level: 11.21408010 eV
#后续的部分与之前的scf主循环中的相同。
Energy by parts:
one_electron contribution = -65.29724621 Ha / -1776.82858548 eV
hartree contribution = 44.51479212 Ha / 1211.30920063 eV
xc contribution = -28.61982408 Ha / -778.78508636 eV
ewald contribution = -130.02699089 Ha / -3538.21466755 eV
hubbard contribution = 0.33228785 Ha / 9.04201300 eV
smearing contribution = -0.00000000 Ha / -0.00000000 eV
Time spent until now is 16.26 seconds
3.1.3. 结构优化计算¶
结构优化计算的OUT文件在共有信息之后有结构优化信息部分（Structure optimization information）， 结构优化信息部分又分别包括scf主循环部分（Main part of scf calculation）、scf结果部分（scf result）、 受力计算部分（Force calculation）、应力计算部分（Stress calculation）、离子步结果部分。
其中scf主循环部分（Main part of scf calculation）和scf结果部分（scf result）与scf计算中相同，这里不再进行说明。 应力计算部分（Stress calculation）仅在变晶格结构优化计算中有。
================================================================================
| Force calculation | #受力计算部分
--------------------------------------------------------------------------------
local contribution: #不同部分对每个原子在x/y/z方向上的受力的贡献
0.00000383 0.00000022 -0.00000192
-0.00000277 0.00000018 0.00000193
ewald contribution:
-0.00000000 -0.00000000 0.00000000
0.00000000 0.00000000 -0.00000000
non-local contribution:
0.00000042 0.00000163 -0.00000220
0.00000202 0.00000018 0.00000124
non-linear core correction contribution:
0.00000001 -0.00000005 0.00000008
-0.00000004 0.00000003 -0.00000007
hubbard contribution:
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
dispersion contribution:
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
contribution due to not exact scf convergence:
-0.00000184 -0.00000063 0.00000223
0.00000168 0.00000028 -0.00000263
total force after symmetrization: #每个原子在x/y/z方向上的总受力
0.00000076 0.00000025 -0.00000114
-0.00000076 -0.00000025 0.00000114
Time spent until now is 14.775 seconds
================================================================================
================================================================================
| Stress calculation | #应力计算部分
--------------------------------------------------------------------------------
local contribution: #不同部分对晶胞在各个方向上受到的应力的贡献
0.00104147 -0.00000002 0.00000000
-0.00000002 0.00104138 0.00000002
0.00000000 0.00000002 0.00104136
hartree contribution:
-0.00137425 0.00000000 -0.00000000
0.00000000 -0.00137425 0.00000000
-0.00000000 0.00000000 -0.00137425
exchange correlation contribution:
0.00111761 -0.00000000 0.00000000
-0.00000000 0.00111761 0.00000000
0.00000000 0.00000000 0.00111761
non-linear core correction contribution:
0.00523706 0.00000000 -0.00000000
0.00000000 0.00523705 0.00000000
-0.00000000 0.00000000 0.00523705
ewald contribution:
0.02015016 -0.00000000 -0.00000000
-0.00000000 0.02015016 -0.00000000
-0.00000000 -0.00000000 0.02015016
dispersion contribution:
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
kinetic contribution:
-0.01481014 0.00000000 -0.00000001
0.00000000 -0.01481013 -0.00000001
-0.00000001 -0.00000001 -0.01481011
non-local contribution:
-0.01140188 -0.00000000 0.00000000
-0.00000000 -0.01140184 -0.00000001
0.00000000 -0.00000001 -0.01140183
hubbard contribution:
-0.00000000 -0.00000000 -0.00000000
-0.00000000 -0.00000000 -0.00000000
-0.00000000 -0.00000000 -0.00000000
total stress after symmetrization: #晶胞在各个方向上受到的总的应力
-0.00003998 -0.00000001 -0.00000001
-0.00000001 -0.00004002 0.00000001
-0.00000001 0.00000001 -0.00004002
in kbar units:
-5.88194947 -0.00188522 -0.00081451
-0.00188522 -5.88695903 0.00087894
-0.00081451 0.00087894 -5.88653513
Time spent until now is 15.969 seconds
================================================================================
================================================================================
================================================================================
Iteration 1 structure optimization finished #每个离子步完成后输出
Structure optimization convergence informmation: #当前体系的原子受力、能量变化、（原子位移）、（应力）的值，对应的收敛标准和是否达到收敛
Term | Converged | Value | Tolerance | Units
Energy | yes | / | 0.00004000 | eV
Force | yes | 0.00003587 | 0.05000000 | eV/A
Total energy of 1 iteration: #当前体系的总能量
total energy = -8.45582656 Ha / -230.09476229 eV
Lattice (A): #当前体系的晶胞参数
3.34889861 0.00000000 1.93348751
1.11629954 3.15737189 1.93348751
0.00000000 0.00000000 3.86697503
Lattice (bohr):
6.32850119 0.00000000 3.65376186
2.10950040 5.96656814 3.65376186
0.00000000 0.00000000 7.30752373
Lattice constants(A and degree):
3.86697503 3.86697503 3.86697503
60.00000004 60.00000004 60.00000000
Atom positions (fractional coordinates): #当前体系的原子位置
Si 0.00000000 0.00000000 0.00000000
Si 0.75000000 0.75000000 0.75000000
External pressure(kbar) #当前体系受到的压强
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
Volume of cell: 275.92795687 #当前体系的体积
Structure optimization completed successfully in 2 iterations
final frequency unchanged from initial value
final bulk modulus unchanged from initial value
================================================================================
3.1.4. 能带和态密度计算¶
能带和态密度计算都属于非自洽计算，它们的OUT文件在共有信息之后有两个部分，分别是k点计算部分和nscf结果部分（nscf result）。
Calculation of k point 1 / 28 finished. #当前计算到第几个k点，所用的时间
Time spent until now is 4.373 seconds
--------------------------------------------------------------------------------
Calculation of k point 2 / 28 finished.
Time spent until now is 5.474 seconds
--------------------------------------------------------------------------------
#中间省略
--------------------------------------------------------------------------------
Calculation of k point 28 / 28 finished.
Time spent until now is 34.91 seconds
--------------------------------------------------------------------------------
================================================================================
| nscf result | #nscf结果部分
--------------------------------------------------------------------------------
Electron Step Finish #体系的总能量、Ewald能和费米能级
Total Energy: -4857.56015512 eV
Ewald Energy: -3538.21466755 eV
Fermi level: 10.73411679 eV
3.1.5. 分子动力学计算¶
分子动力学计算的OUT文件在共有信息之后有分子动力学部分， 分子动力学部分又分别包括scf主循环部分（Main part of scf calculation）、scf结果部分（scf result）、受力计算部分（Force calculation）。
其中scf主循环部分（Main part of scf calculation）和scf结果部分（scf result）与scf计算中相同，这里不再进行说明。 受力计算部分（Force calculation）与结构优化计算中相同，这里不再进行说明。
3.1.6. 过渡态计算¶
对于过渡态计算，在scf主循环部分（Main part of scf calculation）、scf结果部分（scf result）、等这些部分会在原有基础上增加属于哪个iamge和对应的image的原子位置信息。
================================================================================
do_scf idx 1 positions [0.0 0.0 0.16667 0.5 0.6666666666666665 3.533949646070574e-17 0.16667000000000007 0.5 0.6666666666666666; 0.0 0.0 0.3333333333333333 0.0 0.3333333333333333 0.5 0.83333 0.5 0.83333; 0.29779 0.17000000000000004 0.17000000000000004 0.17000000000000004 0.17000000000000004 0.17000000000000004 0.17000000000000004 0.17000000000000004 0.17000000000000004] #第一个image的scf，后面是原子的坐标
================================================================================
| initialization |
--------------------------------------------------------------------------------
Time spent until now is 4.106 seconds
================================================================================
================================================================================
| Main part of scf calculation |
--------------------------------------------------------------------------------
3.1.7. 自旋极化计算¶
对于自旋极化计算，在scf主循环部分（Main part of scf calculation）、scf结果部分（scf result）、等这些部分会在原有基础上增加自旋和磁矩相关的信息。
================================================================================
| Main part of scf calculation |
--------------------------------------------------------------------------------
iteration 1 begins
E(Ha) dE(Ha) estimated scf_diff(Ha)
-178.18006358 0.00000000 1.79540636
Energy by parts:
one_electron contribution = -65.24907601 Ha / -1775.51780756 eV
hartree contribution = 45.03834947 Ha / 1225.55592196 eV
xc contribution = -29.06702338 Ha / -790.95399925 eV
ewald contribution = -130.02699089 Ha / -3538.21466755 eV
smearing contribution = -0.00000000 Ha / -0.00000000 eV
Magnetizations: #在自旋极化计算中，不同原子的电荷量和磁矩的信息
Element index charge magnet
Ti 1 7.8016 0.3139
Ti 2 7.8055 0.3148
O 3 5.6615 -0.0470
O 4 5.6629 -0.0461
O 5 5.6619 -0.0460
O 6 5.6629 -0.0458
total magnetization = 0.72 #体系的总磁矩，正负互相抵消
absolute magnetization = 1.11 #体系的磁矩绝对值，所有原子的磁矩的绝对值之和
3.1.8. DFT+U计算¶
对于自旋极化计算，在scf主循环部分（Main part of scf calculation）、scf结果部分（scf result）、 受力计算部分（Force calculation）、应力计算部分（Stress calculation）等这些部分会在原有基础上增加DFT+U相关的信息。
================================================================================
| Main part of scf calculation |
--------------------------------------------------------------------------------
iteration 1 begins
E(Ha) dE(Ha) estimated scf_diff(Ha)
-178.33348695 0.00000000 1.59867740
Energy by parts:
one_electron contribution = -65.35764253 Ha / -1778.47205318 eV
hartree contribution = 44.97200141 Ha / 1223.75049933 eV
xc contribution = -29.01578196 Ha / -789.55964936 eV
ewald contribution = -130.02699089 Ha / -3538.21466755 eV
hubbard contribution = 0.30312464 Ha / 8.24844177 eV #Hubbard项对能量的贡献
smearing contribution = -0.00000000 Ha / -0.00000000 eV
Hubbard occupation matrix #Hubbard占据数矩阵
Atom[1]: Ti
Spin=1
0.443204 0.000225 -0.000142 -0.000180 -0.069906
0.000225 0.177962 -0.164039 -0.000255 0.000117
-0.000142 -0.164039 0.177785 0.000298 -0.000098
-0.000180 -0.000255 0.000298 0.281660 0.000297
-0.069906 0.000117 -0.000098 0.000297 0.178811
Atom[2]: Ti
Spin=1
0.443666 0.000253 0.000267 -0.000466 0.069952
0.000253 0.178039 0.164136 -0.000222 0.000269
0.000267 0.164136 0.177883 -0.000065 0.000201
-0.000466 -0.000222 -0.000065 0.281936 -0.000106
0.069952 0.000269 0.000201 -0.000106 0.178574
iteration 1 ends, not converged yet.
--------------------------------------------------------------------------------
================================================================================
| scf result |
--------------------------------------------------------------------------------
Electron Step Finish
Total Energy: -179.09698153 Ha / -4873.47713452 eV
Fermi level: 11.20892629 eV
Energy by parts:
one_electron contribution = -65.29712312 Ha / -1776.82523595 eV
hartree contribution = 44.51452983 Ha / 1211.30206347 eV
xc contribution = -28.61969375 Ha / -778.78154013 eV
ewald contribution = -130.02699089 Ha / -3538.21466755 eV
hubbard contribution = 0.33229640 Ha / 9.04224564 eV
smearing contribution = -0.00000000 Ha / -0.00000000 eV
Hubbard occupation matrix
Atom[1]: Ti
Spin=1
0.592185 0.000001 -0.000001 -0.000003 -0.085285
0.000001 0.251063 -0.237966 0.000001 0.000000
-0.000001 -0.237966 0.251065 -0.000001 -0.000000
-0.000003 0.000001 -0.000001 0.524681 -0.000004
-0.085285 0.000000 -0.000000 -0.000004 0.208561
Atom[2]: Ti
Spin=1
0.592179 -0.000001 -0.000002 0.000001 0.085277
-0.000001 0.251137 0.238036 -0.000015 0.000000
-0.000002 0.238036 0.251133 0.000013 0.000001
0.000001 -0.000015 0.000013 0.524684 0.000000
0.085277 0.000000 0.000001 0.000000 0.208580
Time spent until now is 5.184 seconds
================================================================================
================================================================================
| Force calculation |
--------------------------------------------------------------------------------
local contribution:
0.00012392 0.00005813 0.00005127
-0.00010663 0.00001557 -0.00003812
4.10663072 4.10672823 -0.00006103
-4.10562151 4.10558013 -0.00002588
-4.10669328 -4.10670286 0.00003500
4.10564812 -4.10563323 0.00001951
ewald contribution:
0.00000000 0.00000000 0.00000000
-0.00000000 0.00000000 0.00000000
-3.85506692 -3.85506692 0.00000000
3.85506692 -3.85506692 -0.00000000
3.85506692 3.85506692 0.00000000
-3.85506692 3.85506692 -0.00000000
non-local contribution:
0.00000823 0.00000584 0.00000622
0.00001548 0.00001170 -0.00000602
-0.22963669 -0.22964926 0.00004367
0.22752999 -0.22749918 0.00000499
0.22958144 0.22957210 0.00000606
-0.22750544 0.22752776 -0.00000552
non-linear core correction contribution:
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
hubbard contribution: #Hubbard项对原子受力的贡献
-0.00000020 -0.00000061 0.00000034
-0.00000052 0.00000145 -0.00000026
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
dispersion contribution:
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
contribution due to not exact scf convergence:
-0.00011792 -0.00003930 -0.00006153
0.00011060 -0.00000085 0.00004418
-0.00015167 -0.00023952 0.00003330
-0.00018942 0.00019497 0.00002360
0.00023898 0.00025280 -0.00004411
0.00014976 -0.00020175 -0.00000363
total force after symmetrization:
0.00001170 0.00002705 -0.00000737
0.00001660 0.00003085 -0.00000390
0.02177311 0.02177551 0.00001227
-0.02321635 0.02321198 -0.00000096
-0.02180827 -0.02180806 -0.00000673
0.02322320 -0.02323733 0.00000669
Time spent until now is 6.176 seconds
================================================================================
3.1.9. 色散修正计算¶
对于使用了色散修正的计算，在scf主循环部分（Main part of scf calculation）、scf结果部分（scf result）、 受力计算部分（Force calculation）、应力计算部分（Stress calculation）等这些部分会在原有基础上增加与色散修正相关的信息。
================================================================================
| scf result |
--------------------------------------------------------------------------------
Electron Step Finish
Total Energy: -22.76226167 Ha / -619.39269358 eV
Fermi level: -0.45903063 eV
Energy by parts:
one_electron contribution = -204.63410957 Ha / -5568.37778850 eV
hartree contribution = 104.11901789 Ha / 2833.22280828 eV
xc contribution = -7.01257081 Ha / -190.82177264 eV
ewald contribution = 84.77733180 Ha / 2306.90871806 eV
smearing contribution = -0.00228828 Ha / -0.06226723 eV
dispersion contribution = -0.00965333 Ha / -0.26268051 eV #色散修正的能量贡献
================================================================================
| Force calculation |
--------------------------------------------------------------------------------
local contribution:
0.00000035 0.00000054 11.76014844
-0.00000135 -0.00000054 -11.76943977
-0.00000208 -0.00000107 11.76038683
-0.00000004 -0.00000007 -11.76967475
ewald contribution:
0.00000010 -0.00000005 -11.76483814
-0.00000010 0.00000005 11.76483814
-0.00000010 0.00000005 -11.76456410
0.00000010 -0.00000005 11.76456410
non-local contribution:
-0.00000072 -0.00000483 0.00091123
-0.00000069 0.00000098 -0.00176336
0.00000273 0.00000154 -0.00082698
0.00000140 -0.00000028 -0.00002676
non-linear core correction contribution:
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
hubbard contribution:
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
dispersion contribution: #色散修正对受力的贡献
-0.00018673 -0.00037345 0.00123840
-0.00116313 -0.00232626 0.00004546
-0.00138018 -0.00276037 0.00043691
-0.00114668 -0.00229336 -0.00086421
contribution due to not exact scf convergence:
-0.00000089 0.00000049 0.00000202
0.00000095 -0.00000024 0.00020082
0.00000038 0.00000006 0.00000043
-0.00000014 -0.00000003 0.00019831
total force after symmetrization:
0.00078132 0.00156192 0.00221870
-0.00019512 -0.00038679 -0.00136197
-0.00041005 -0.00082057 0.00018983
-0.00017616 -0.00035456 -0.00104657
Time spent until now is 43.135 seconds
================================================================================
3.1.10. 加电场计算¶
对于加电场的计算，在scf主循环部分（Main part of scf calculation）、 受力计算部分（Force calculation）、应力计算部分（Stress calculation）等这些部分会在原有基础上增加与电场相关的信息。
================================================================================
| scf result |
--------------------------------------------------------------------------------
Electron Step Finish
Total Energy: -525.83598512 Ha / -14308.72607749 eV
Fermi level: -0.61312805 eV
Energy by parts:
one_electron contribution = -3755.21355904 Ha / -102184.56647910 eV
hartree contribution = 1878.44497477 Ha / 51115.09169414 eV
xc contribution = -70.41652824 Ha / -1916.13134589 eV
ewald contribution = 1421.34485496 Ha / 38676.76379457 eV
smearing contribution = 0.00402082 Ha / 0.10941206 eV
efield contribution = 0.00025161 Ha / 0.00684672 eV #电场的贡献
Time spent until now is 132.675 seconds
================================================================================
================================================================================
| Force calculation |
--------------------------------------------------------------------------------
local contribution:
0.16030531 0.04896427 -54.62215538
0.03523412 -0.41132382 -97.87584273
-0.38758851 1.01253514 -135.53510375
0.25678839 -1.08227780 55.56580251
-0.06350667 0.51269621 234.27379701
ewald contribution:
-0.15099321 -0.07534604 54.08867183
-0.04753036 0.51554136 100.29427067
0.39391493 -1.01114363 135.29155447
-0.25728886 1.08506476 -55.67412613
0.06189751 -0.51411644 -234.00037084
non-local contribution:
-0.01422215 0.02872250 0.56962671
0.01264702 -0.11005052 -2.57174192
-0.00018107 -0.00261254 0.18633866
-0.00236251 0.00237788 0.00895015
0.00206337 -0.00159507 -0.33954645
non-linear core correction contribution:
0.00075952 0.00043473 0.01218072
-0.00022831 0.00237401 0.05524727
0.00036468 -0.00019125 -0.01572425
0.00004337 -0.00011331 0.00534673
-0.00009357 0.00006077 0.00468505
hubbard contribution:
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
dispersion contribution:
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000
contribution due to not exact scf convergence:
0.00000000 -0.00000001 -0.00000066
-0.00000000 -0.00000000 -0.00000042
-0.00000001 -0.00000002 -0.00000044
-0.00000000 -0.00000003 0.00000205
0.00000000 0.00000004 0.00000206
slab contribution: #电场的贡献
0.00000000 0.00000000 0.01738373
0.00000000 0.00000000 0.02607560
0.00000000 0.00000000 0.07822679
0.00000000 0.00000000 0.07822679
0.00000000 0.00000000 0.07822679
total force after symmetrization:
-0.00415512 0.00277522 0.06570642
0.00011788 -0.00345921 -0.07199204
0.00650542 -0.00141253 0.00529095
-0.00282422 0.00505125 -0.01579842
0.00035604 -0.00295473 0.01679310
Time spent until now is 133.839 seconds
================================================================================