bulk计算,直译为“体相计算”,指的是模拟理想的三维无限大晶体(无表面、界面或缺陷,不模拟则体系太大算不动),利用 周期性边界条件 描述材料的体相性质,主要用于研究材料的本征物理化学性质(如晶格结构、电子能带、热力学稳定性等)

准备POSCAR

打开materials studio-File-Import-Structures-Metals-pure metals-Cu.xsd,然后export为cif文件

用vesta打开Cu.cif文件,再export data,导出保存为POSCAR文件

准备KPOINTS

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KPOINTS for Cu-concentional-cell-bulk-calc
0
Gamma
13 13 13
0 0 0

准备INCAR

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SYSTEM = Cu-conventional-cell-bulk-calculation
ISMEAR = 0
SIGMA = 0.1
ENCUT = 700
ISIF = 3
NSW = 200
NELM = 200
IBRION = 2
POTIM = 0.1
EDIFFG = -0.01
ALGO = Normal
EDIFF = 1E-6

提交任务

第一次使用超算平台,还算顺利,稍微折腾了一下终于能成功提交任务了

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[ctan@baifq-hpc141 Cu-statistic]$ sbatch vasp  #vasp is the script
[ctan@baifq-hpc141 Cu-statistic]$ grep accuracy OUTCAR
reached required accuracy - stopping structural energy minimisation #calculation finished normally

优化后的结构CONTCAR如下

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Cu
1.00000000000000
3.6346781666386048 0.0000000000000000 0.0000000000000000
0.0000000000000000 3.6346781666386048 0.0000000000000000
-0.0000000000000000 0.0000000000000000 3.6346781666386048
Cu/0e71e558f37
4
Direct
0.0000000000000000 0.0000000000000000 -0.0000000000000000
-0.0000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.5000000000000000
0.5000000000000000 0.5000000000000000 0.0000000000000000

0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00

其他信息:

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[ctan@baifq-hpc141 bulk-calc]$ cat OSZICAR
N E dE d eps ncg rms rms(c)
DAV: 1 0.103476848532E+03 0.10348E+03 -0.27847E+04 6720 0.246E+03
DAV: 2 -0.180387697818E+02 -0.12152E+03 -0.12091E+03 7280 0.155E+02
DAV: 3 -0.185227503579E+02 -0.48398E+00 -0.48396E+00 10160 0.132E+01
DAV: 4 -0.185240376489E+02 -0.12873E-02 -0.12873E-02 8200 0.464E-01
DAV: 5 -0.185240414620E+02 -0.38131E-05 -0.38134E-05 10480 0.143E-02 0.154E+01
DAV: 6 -0.164394189736E+02 0.20846E+01 -0.72731E+01 6800 0.881E+01 0.783E+00
DAV: 7 -0.149577606472E+02 0.14817E+01 -0.11165E+01 6720 0.344E+01 0.111E+00
DAV: 8 -0.149148685722E+02 0.42892E-01 -0.18431E-02 7280 0.139E+00 0.620E-01
DAV: 9 -0.149081819010E+02 0.66867E-02 -0.51836E-02 8440 0.220E+00 0.636E-02
DAV: 10 -0.149081753161E+02 0.65849E-05 -0.22202E-04 9000 0.149E-01 0.115E-02
DAV: 11 -0.149081715196E+02 0.37964E-05 -0.16862E-06 8520 0.968E-03 0.844E-04
DAV: 12 -0.149081716052E+02 -0.85577E-07 -0.88627E-08 4640 0.248E-03
1 F= -.14908172E+02 E0= -.14905377E+02 d E =-.149082E+02
N E dE d eps ncg rms rms(c)
DAV: 1 -0.149363274123E+02 -0.28156E-01 -0.51946E-01 6720 0.830E+00 0.131E+00
DAV: 2 -0.149199449776E+02 0.16382E-01 -0.41291E-01 6720 0.646E+00 0.538E-01
DAV: 3 -0.149119014518E+02 0.80435E-02 -0.68998E-02 6720 0.271E+00 0.192E-01
DAV: 4 -0.149112107699E+02 0.69068E-03 -0.11896E-03 9800 0.216E-01 0.117E-02
DAV: 5 -0.149112123403E+02 -0.15704E-05 -0.80430E-06 7320 0.267E-02 0.594E-03
DAV: 6 -0.149112142891E+02 -0.19488E-05 -0.13229E-06 4760 0.997E-03 0.128E-04
DAV: 7 -0.149112142406E+02 0.48522E-07 -0.22610E-08 3560 0.101E-03
2 F= -.14911214E+02 E0= -.14908447E+02 d E =-.304264E-02
N E dE d eps ncg rms rms(c)
DAV: 1 -0.150389301673E+02 -0.12772E+00 -0.26022E+00 6720 0.187E+01 0.290E+00
DAV: 2 -0.149566578541E+02 0.82272E-01 -0.20265E+00 6720 0.143E+01 0.119E+00
DAV: 3 -0.149175257623E+02 0.39132E-01 -0.34317E-01 6720 0.604E+00 0.437E-01
DAV: 4 -0.149140056079E+02 0.35202E-02 -0.72028E-03 10080 0.565E-01 0.378E-02
DAV: 5 -0.149139977907E+02 0.78172E-05 -0.11528E-04 7840 0.108E-01 0.134E-02
DAV: 6 -0.149140005388E+02 -0.27480E-05 -0.66656E-06 7680 0.220E-02 0.371E-04
DAV: 7 -0.149140005655E+02 -0.26792E-07 -0.64306E-08 3960 0.196E-03
3 F= -.14914001E+02 E0= -.14911298E+02 d E =-.582896E-02
[ctan@baifq-hpc141 bulk-calc]$ grep accuracy OUTCAR
reached required accuracy - stopping structural energy minimisation
[ctan@baifq-hpc141 bulk-calc]$ grep ' without' OUTCAR
energy without entropy= -14.90258332 energy(sigma->0) = -14.90537746
energy without entropy= -14.90568039 energy(sigma->0) = -14.90844732
energy without entropy= -14.90859467 energy(sigma->0) = -14.91129762

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乙醇分子的结构优化

INCAR

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SYSTEM = ethanol
ISMEAR = 0 #Gaussian ismear, for insulator
SIGMA = 0.01
NSW = 200

IBRION = 2 #Optimizarion
POTIM = 0.01 #a little conservative step

KPOINTS

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K-POINTS
0
Gamma
1 1 1
0 0 0

POSCAR

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Title
1.0
4.8082499504 0.0000000000 0.0000000000
0.0000000000 4.8082499504 0.0000000000
0.0000000000 0.0000000000 4.8082499504
O C H
1 2 6
Direct
0.747990456 0.438959082 0.500000000
0.508714210 0.577741385 0.500000000
0.269437963 0.438959082 0.500000000
0.900000025 0.568403268 0.500000000
0.508714210 0.689008479 0.307289552
0.508714210 0.689008479 0.692710448
0.100000016 0.583231948 0.500000000
0.257895302 0.310991525 0.318291476
0.257895302 0.310991525 0.681708524

分子结构可以使用ChemDraw绘制,也可以去RSC的网站上下载https://www.chemspider.com/、

但是不管是下载的mol结构还是ChemDraw导出的mol结构,导入进Vesta里面发现都少了氢原子,笨比博主(😭)至今没找到解决方案,只能笨拙地把mol结构导入到GaussView里面,GaussView会自动补加上氢原子,然后再导入到Vesta中,再导出为POSCAR文件,当然理论上可以手动改POSCAR,不一定要使用可视化软件

POTCAR

使用基础的不带后缀的PBE赝势

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cat ..potpaw_PBE.64/O/POTCAR ..potpaw_PBE.64/C/POTCAR ..potpaw_PBE.64/H/POTCAR >> POTCAR

对比优化前后

简单对比一下键长吧

  • 优化前
    • C-C bond: 1.33001(0) Å
    • O-H bond: 0.96000(0) Å
O-H bond
C-C bond
  • 优化后
    • C-C bond: 1.53893(0) Å
    • O-H bond: 0.96454(0) Å
O-H bond
C-C bond

频率计算

频率计算的作用:

  • 确定结构是否稳定
  • 看振动方式和大小,用来和实验对比
  • 反应热,反应能垒,吸附能等的零点能矫正
  • 确认过渡态(有一个振动的虚频)
  • 热力学中计算entropy,用于计算化学势,微观动力学中的指前因子和反应能垒。

POSCAR

使用先前优化的CONTCAR作为POSCAR

INCAR

修改一下IBRION,计算频率(IBRION = 5)而非结构优化(IBRION = 2)

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SYSTEM = ethanol
ISMEAR = 0 #Gaussian ismear, for insulator
SIGMA = 0.01
NSW = 1
IBRION = 5 #freq calculation
POTIM = 0.01 #a little conservative step
EDIFF = 1E-8
NFREE = 2

Jmol分析频率

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jmol OUTCAR

Tools-AtomSetChooser-Frequencies

Jmol分析频率

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Rocks could save the world (Yes, rocks)

The Canary Islands are home to Mount Teide, one of the world’s largest active volcanoes.

Capable of ==spewing== tens of millions of cubic meters of lava in a single eruption, Teide’s destructive power ==is nothing to scoff at== .

But there may be a way to use the ==basalt== rock inside Teide to save humanity.

That’s right—blowing up this volcano could offset Earth’s emissions for the foreseeable future.

Obviously, destroying an ancient volcano is not a good idea.

The ecological ==fallout== would be catastrophic and unpredictable.

But even if we harvested some of that basalt, could we really use it to stop climate change?

This theoretical scheme is a dramatic way to enhance one of Earth’s least dramatic natural processes: rock weathering.

Rock weathering occurs whenever it rains.

As falling rainwater mixes with atmospheric carbon dioxide, it becomes a weak acid that can ==eat away at== minerals called silicates.

And since silicates are in over 90% of Earth’s exposed rock, this happens pretty much anywhere rain hits stone.

As this acid reacts with the stone, the dissolved carbon dioxide in the rainwater turns into a new form called bicarbonate, which trickles downstream alongside the rain to the ocean.

Here, marine ==critters== use it to create structures like shells.

And when they die, those shells sink to the ==seafloor== , trapping that carbon dioxide in the ocean for ==millennia== .

This process has a massive impact on Earth’s climate.

When it’s warm and wet, the rock weathering speeds up, ==tempering== greenhouse warming.

When it’s cold and dry, the process slows down, building up atmospheric carbon dioxide.

But these effects take time—natural rock weathering balances Earth’s climate over millions of years.

Thankfully, experts working to sequester atmospheric carbon have plans to speed things up.

Two major factors determine the pace of this process: the types of rock exposed to weather and the amount of rock that’s exposed.

Silicates that form at higher temperatures tend to weather faster due to their chemical composition.

These rocks include those from Earth’s deep ==mantle== and volcanic rocks like basalt.

But piled up in a mountain, not very much rock is exposed.

So, some climate experts believe we should harvest that fast-weathering rock, ==crush== it, and spread it out to weather more rock in less time.

This sped-up process is called enhanced rock weathering, and it’s among the most practical plans we have for drawing down carbon.

Rather than needing to invent all-new technology, we can rely on existing systems for mining and processing rock.

And since agricultural communities have long known that volcanic rocks and soils can improve crop yield, farmlands could be the perfect ==dispersal== sites.

But for this approach to have impact, it needs to be deployed globally.

And even without ==demolishing== any volcanoes, large-scale solutions always come with large-scale problems.

First off, rock weathering—enhanced or otherwise—runs through the entire global water cycle.

Since this open system has more variables than we could ever account for, it’s difficult to measure enhanced rock weathering’s precise impact.

Second, despite existing mining technology, it would be a massive ecological and engineering challenge to ==quarry== , crush, transport, and spread this much rock.

The logistical difficulty of distributing this material would be similarly demanding.

And unless the energy used for both tasks came from mostly clean sources, it would undermine the project’s net carbon impact.

Finally, any endeavor that impacts Earth’s natural systems at this scale might have unpredictable side effects.

For example, quarried rocks might contain dangerous heavy metals or other unknown elements.

But these challenges aren’t reasons to abandon enhanced rock weathering—they’re just the first obstacles to implementing this promising strategy.

Simulations suggest a global enhanced rock weathering program that spreads 10 tons of basalt dust on every hectare of global farmland could ==sequester== over 200 ==gigatons== of CO₂ over a 75-year period.

Those are remarkable figures for an approach this cheap and practical, and they prove you don’t need to blow up a mountain to have a big impact.

Vocabulary, Phrases and Sentences

Words Chinese Definition Phonetic Symbol
spew 喷出;涌出;呕吐 /spjuː/
be nothing to scoff at 没什么可嘲笑的 /biː ˈnʌθɪŋ tuː skɒf æt/
basalt 玄武岩 /ˈbæslæt/
fallout 沉降物;附带结果 /ˈfɔːlaʊt/
eat away at 侵蚀;消耗 /ˈiːt əˈweɪ æt/
critter 生物;动物 /ˈkrɪtə(r)/
seafloor 海底 /ˈsiːflɔː(r)/
millennia 千年;千年期 /mɪˈleniə/
temper 脾气;情绪;回火 /ˈtempə(r)/
mantle 地幔;覆盖物 /ˈmæntl/
crush 压碎;挤压;碾碎 /ˈkrʌʃ/
dispersal 分散;传播 /ˈdɪspɜːsl/
demolish 拆除;摧毁 /ˈdeməlɪʃ/
quarry 采石场;猎物;费力地找 /ˈkwɒri/
sequester 使隔绝;使隐退;扣押 /ˈsiːkwestə(r)/
gigaton 十亿吨 /ˈdʒɪɡəˌtʌn/

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What staying up all night does to your brain

You’re just one Roman Empire history final away from a relaxing spring break.

But you still have so much to study!

So you decide to follow in the footsteps of many students before you and pull an all-nighter.

When you stay up all night, you’re fighting against your body’s natural circadian rhythms.

These are the cyclical changes that virtually all living things experience over the course of a 24-hour period—such as sleeping and waking—and they’re heavily influenced by light.

But for the moment, you’re alert and powering through the rule of Julius Caesar.

As the sun sets, your eyes send signals about the dwindling light to a part of your brain called the suprachiasmatic nucleus.

This is basically your circadian rhythm’s clock.

It alerts your pineal gland to start producing melatonin.

That’s the hormone that helps prepare your body for sleep, and levels start to rise about two hours before your normal bedtime.

At the same time, neurons in the hypothalamus and brain stem release a compound called GABA.

This slows down activity in your brain and can have a calming effect.

You’re approaching your normal bedtime.

Since the brain needs to cool down before sleep, your core body temperature starts to drop.

Huh, that map kind of looks like a face.

Uh-oh, your attention has started to drift.

Throughout the day, your brain has been releasing a waste product called adenosine.

The more adenosine latching onto receptors in your brain, the more tired and inattentive you become.

Time for a cup of coffee.

Caffeine blocks adenosine from binding to receptors, which can give you a boost of energy.

However, it might also make you jittery and increase your anxiety.

You’re acing these flashcards!

Right now these dates and names are being stored in an area of the brain called the hippocampus.

Normally when you go to sleep, memories like these are consolidated and slotted into long-term storage in your brain’s neocortex.

So it’s a good thing you only need to remember this information through tomorrow.

Microsleeps are unpredictable periods of sleep that last for only a few seconds and are triggered by sleep deprivation.

You stretch in an attempt to stay awake.

But at this point your motor skills have also taken a hit.

Studies have found that people who have been awake for 19 hours have similar coordination and reaction times as those who have been drinking.

As the sun rises, your pineal gland stops releasing melatonin.

You feel a “second wind” come on.

And despite everything, you leave for school in a really good mood.

Sleep deprivation can briefly induce euphoria.

It’s caused by a temporary boost in dopamine levels, which can unfortunately also lead to poor choices.

The final starts off well.

It’s all multiple choice!

But then you get to the essay portion.

It’s thought that during sleep, our brains process ideas and draw connections between new memories and old ones.

So your sleepless brain might be able to regurgitate facts, but you’re finding it more difficult to find patterns or problem solve.

You stare at the blank page, defeated.

You head up to your room, anxious and irritable.

Your amygdala, the part of the brain involved with processing emotion, is going haywire.

Your prefrontal cortex usually keeps your amygdala in check, but it still isn’t firing on all cylinders.

Your bed has never felt so sweet.

After one sleepless night, your body and brain bounce back pretty quickly.

Which is a good thing since we can’t always control how much sleep we get.

But going for long periods without a good night’s sleep or constantly changing your bedtime can take its toll.

Regularly getting less than seven hours of sleep each night is linked to all sorts of health issues, from diabetes to stroke to chronic pain.

It also leaves you more vulnerable to developing mental health issues like depression.

Your sleep schedule can even affect your grades.

Studies have shown that college students who keep regular sleep hours have, on average, a higher GPA than students who don’t.

So the next time you’re thinking of pulling an all-nighter, remember that Rome wasn’t built in a day, or for that matter, one night.

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单点能计算又叫做静态计算,计算时不会优化结构

INCAR

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SYSTEM = O
ISMEAR = 0 #绝缘体系ISMEAR = 0
SIGMA = 0.01
ISPIN = 2 #氧气是顺磁性分子,ISPIN = 2开启自旋
MAGMON = 2*2 #设置磁矩

#IBRION = 2 确定计算过程中晶体结构如何变化的参数,不设置使默认IBRION = -1,IBRION =2为共轭梯度算法
#NSW = 10 离子步10步

POSCAR

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O
1.0
7.5 0.0 0.0
0.0 8.0 0.0
0.0 0.0 8.9 #三斜的格子打破对称性,symmetry broken solution!!!
O
2
Cartesian
0.0 0.0 0.0
0.0 0.0 1.2074

KPOINTS

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K-POINTS
0
Gamma
1 1 1
0 0 0

运行mpirun -n 8 vasp,正常结束,OUTCAR的部分信息如下,显然,单点计算的结果并不可靠

α电子部分

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spin component 1

k-point 1 : 0.0000 0.0000 0.0000
band No. band energies occupation
1 -32.9044 1.00000 #1σ轨道
2 -20.2474 1.00000 #2σ轨道
3 -13.3174 1.00000 #3σ轨道,能量应比1π和2π轨道更低,不合理
4 -13.3171 1.00000 #1π轨道
5 -13.2940 1.00000 #2π轨道,能量应与1π轨道相同,不合理
6 -6.5560 1.00000 #3π轨道
7 -6.5524 1.00000 #4π轨道
8 -0.3909 0.00000
9 1.1220 0.00000
10 1.5493 0.00000
11 1.7604 0.00000
12 2.0536 0.00000
13 2.0592 0.00000
14 2.4672 0.00000
15 3.1984 0.00000
16 3.6244 0.00000
Fermi energy: -6.4848556277

β电子,正常

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spin component 2

k-point 1 : 0.0000 0.0000 0.0000
band No. band energies occupation
1 -31.6977 1.00000
2 -18.4541 1.00000
3 -12.3485 1.00000
4 -11.4763 1.00000
5 -11.4760 1.00000
6 -4.2772 0.00000
7 -4.2742 0.00000
8 -0.2440 0.00000
9 1.4049 0.00000
10 1.6215 0.00000
11 1.9473 0.00000
12 2.1710 0.00000
13 2.2499 0.00000
14 2.5860 0.00000
15 3.5816 0.00000
16 3.8831 0.00000
Molecule orbital of oxygen

对氧气进行结构优化,更改INCAR

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SYSTEM = O
ISMEAR = 0 #绝缘体系ISMEAR = 0
SIGMA = 0.01
ISPIN = 2 #氧气是顺磁性分子,ISPIN = 2开启自旋
MAGMON = 2*2 #设置磁矩

IBRION = 2 #确定计算过程中晶体结构如何变化的参数,不设置使默认IBRION = -1,IBRION =2为共轭梯度算法
NSW = 10 #离子步10步

计算后发现α电子部分已经修正

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spin component 1

k-point 1 : 0.0000 0.0000 0.0000
band No. band energies occupation
1 -32.2878 1.00000 #1σ轨道
2 -20.4859 1.00000 #2σ轨道
3 -13.2238 1.00000 #3σ轨道,能量合理
4 -13.0591 1.00000
5 -13.0588 1.00000
6 -6.7814 1.00000
7 -6.7778 1.00000
8 -0.3857 0.00000
9 1.0213 0.00000
10 1.6177 0.00000
11 1.7818 0.00000
12 2.0634 0.00000
13 2.0746 0.00000
14 2.4643 0.00000
15 2.8035 0.00000
16 3.6409 0.00000
Fermi energy: -6.7122607632

用VESTA打开优化好的结构(CONTCAR)可以查看键长

优化完的氧气分子的键长

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2025年4月AMD平台下VASP的编译安装

WSL2安装

本次安装选择的Ubuntu作为发行版,使用人数较多,解决方案较多

Ubuntu 24.04.1 on AMD 7840HS

更新源

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安装编译器

AOCC

下载aocc-compiler-5.0.0.tar,解压

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tar -xvf aocc-compiler-5.0.0.tar #解压
cd aocc-compiler-3.2.0 #进入目录
install.sh #如果没有可执行权限请赋予可执行权限, chmod +x install.sh
source .setenv_AOCC.sh #这一行可以写入~/.bashrc,然后source ~/.bashrc,刷新一下环境变量

AOCL

下载AOCL 5.0 binary packages compiled with AOCC 5.0

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tar -zxvf XXX.tar.gz #解压tar.gz包,如果报错请查询Linux下的解压命令,up记不太清了、、、  
cd XXX
install.sh -t /home/XXX #安装,可以指定安装目录,up安装在/home目录下的某个文件夹里的,这样不需要管理员权限、

安装OpenMPI

在安装OpenMPI之前请确保AOCC、AOCL以及必备的依赖已安装完全

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which clang #检查clang
which clang++ #检查clang++
which flang #检查flang
以上三个来自于AOCC和AOCL
which c #检查有没有C
which c++ #检查有没有C++
sudo apt install g++
sudo apt install gcc

下载OpenMPI的稳定版本,然后解压,进入目录

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configure CC=clang CXX=clang++ FC=flang --prefix=/xxxx #可以手动指定/xxx目录
make -j4 #以4核心编译,大小可调,比如16核处理器就改成make -j16
make install #编译安装

OpenMPI安装时报错很可能是由于依赖问题造成的,建议安装之前sudo apt install g++ cmake gcc

~/.bashrc中添加环境变量

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MPI_HOME=/xxx/; make #这一步容易出错,记得添加对目录
export PATH=${MPI_HOME}/bin:$PATH
export LD_LIBRARY_PATH=${MPI_HOME}/lib:$LD_LIBRARY_PATH
export MANPATH=${MPI_HOME}/share/man:$MANPATH

安装完后检查一下which mpirun

编译VASP

不提供源码包,可以尝试去各种论坛,微信公众号搜索,仅供学习使用

本次使用的源码包是vasp.6.4.2.tgz

编译之前首先要选择模板,也就是makefile.include,将/vasp.x.x.x/arch文件夹下的makefile.include.aocc_ompi_aocl复制一份到/vasp.x.x.x根目录,因为本次平台是AMD ZEN4,安装了AOCC,AOCL和OpenMPI,所以选择此模板,接下来修改模板

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# Default precompiler options
CPP_OPTIONS = -DHOST=\"LinuxGNU\" \
-DMPI -DMPI_BLOCK=8000 -Duse_collective \
-DscaLAPACK \
-DCACHE_SIZE=4000 \
-Davoidalloc \
-Dvasp6 \
-Duse_bse_te \
-Dtbdyn \
-Dfock_dblbuf

CPP = flang -E -ffree-form -C -w $*$(FUFFIX) >$*$(SUFFIX) $(CPP_OPTIONS)

FC = mpif90
FCL = mpif90

FREE = -ffree-form -ffree-line-length-none

FFLAGS = -w -fno-fortran-main -Mbackslash

OFLAG = -O2
OFLAG_IN = $(OFLAG)
DEBUG = -O0

OBJECTS = fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o
OBJECTS_O1 += fftw3d.o fftmpi.o fftmpiw.o
OBJECTS_O2 += fft3dlib.o

# For what used to be vasp.5.lib
CPP_LIB = $(CPP)
FC_LIB = $(FC)
CC_LIB = clang
CFLAGS_LIB = -O
FFLAGS_LIB = -O1
FREE_LIB = $(FREE)

OBJECTS_LIB = linpack_double.o

# For the parser library
CXX_PARS = clang++
LLIBS = -lstdc++

##
## Customize as of this point! Of course you may change the preceding
## part of this file as well if you like, but it should rarely be
## necessary ...
##

# When compiling on the target machine itself, change this to the
# relevant target when cross-compiling for another architecture
VASP_TARGET_CPU ?= -march=znver4 #7840HS belongs to ZEN4 platform
FFLAGS += $(VASP_TARGET_CPU)

# BLAS (mandatory)
AMDBLIS_ROOT ?= /home/storm/AOCL_INSTALL/5.0.0/aocc #Installation category of AOCL
BLAS = -L${AMDBLIS_ROOT}/lib -lblis

# LAPACK (mandatory)
AMDLIBFLAME_ROOT ?= /home/storm/AOCL_INSTALL/5.0.0/aocc #Installation category of AOCL
LAPACK = -L${AMDLIBFLAME_ROOT}/lib -lflame

# scaLAPACK (mandatory)
AMDSCALAPACK_ROOT ?= /home/storm/AOCL_INSTALL/5.0.0/aocc #Installation category of AOCL
SCALAPACK = -L${AMDSCALAPACK_ROOT}/lib -lscalapack

LLIBS += $(SCALAPACK) $(LAPACK) $(BLAS)

# FFTW (mandatory)
AMDFFTW_ROOT ?= /home/storm/AOCL_INSTALL/5.0.0/aocc #Installation category of AOCL
LLIBS += -L$(AMDFFTW_ROOT)/lib -lfftw3
INCS += -I$(AMDFFTW_ROOT)/include

# HDF5-support (optional but strongly recommended)
#CPP_OPTIONS+= -DVASP_HDF5
#HDF5_ROOT ?= /path/to/your/hdf5/installation
#LLIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran
#INCS += -I$(HDF5_ROOT)/include

# For the VASP-2-Wannier90 interface (optional)
#CPP_OPTIONS += -DVASP2WANNIER90
#WANNIER90_ROOT ?= /path/to/your/wannier90/installation
#LLIBS += -L$(WANNIER90_ROOT)/lib -lwannier

然后运行make all即可,官网给的命令是并行安装make DEPS=1 -Jn <target>,我自己尝试并行安装后测试make test会报错,所以make all,这样去测试全部通过不报错

测试安装

为了测试是否正确安装,可以进行测试

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make test

添加到环境变量

官方提供的是源码包,通过编译,我们得到了CPU可执行的二进制包,再二进制包的目录下(bin/目录下),我可以同在终端中直接输入二进制包的名字来直接执行(VASP编译会产生三个二进制包:vasp_std, vasp_gam, vasp_ncl),比如在bin/目录下直接输入vasp_std就可以看到VASP的标志,但是为了随时随地在任意目录下也能执行计算,因此需要将bin/目录添加到环境变量里(前提是make test不报错)

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export PATH=$PATH:/path/to/vasp.x.x.x/bin
source ~/.bashrc

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Mild Waterfall

in 沉思录

这几天高强度学习VASP第一性原理计算,越来越上头了,尽管还不能figure out每一个参数的含义,但是大概已经弄懂一些简单算例的思路了。

上午终于也是向老师交流完实验室的事,有一种如释重负的感觉。

中午意外地抢到了五一去北京的票,终于能和老同学相见了~😜

下午又是、、、仪器分析实验,D A M N! 极度缺乏ATP的大脑拖着我,稀里糊涂的弄完高效液相色谱实验,回到图书馆美美地睡了一觉,起床又继续学VASP😇

春日宴,绿酒一杯歌一遍~

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THE ERA OF MIGHT MAKES RIGHT

In the MAGA vision of the national interest, America will be more like Russia, China, and Iran. (BY GEORGE PACKER)

The best way to ==dismantle== the federal government, then ==repurpose== it as a tool of personal power and ideological warfare, is to start with the soft targets. Entitlements and defense, which comprise more than half of federal spending and a large share of its fraud and waste, enjoy too much support for Elon Musk to ==roll them up== easily. But nothing is less popular than sending taxpayers’ money to unknown people in poor, faraway countries that might ==be rife with corruption== . Americans dislike foreign aid so much that they wrongly believe it consumes at least a quarter of the budget (in the previous fiscal year, aid constituted barely 1 percent). President John F. Kennedy understood the problem, and after creating the United States Agency for International Development, in 1961, he told his advisers: “We hope we can tie this whole concept of aid to the safety of the United States. That is the reason we give aid. The test is whether it will serve the United States. Aid is not a good word. Perhaps we can describe it better as ‘Mutual Assistance.’ ” At another meeting, Kennedy suggested “International Security.”

USAID continued for the next six decades because leaders of both parties believed that ending ==polio== , preventing famine, stabilizing poor countries, strengthening democracies, and opening new markets served the United States. But on January 20, within hours of his inauguration, President Donald Trump signed an executive order that froze foreign aid. USAID was instructed to stop nearly all work. Its Washington headquarters was occupied and sensitive data were ==seized== by ==whiz== kids from Musk’s Department of Government Efficiency, or DOGE. One of their elder members, a 25-yearold software engineer and Matt Gaetz fan named Gavin Kliger, acquired an official email address to instruct the staff of USAID to stay home.

Contractors were fired and employees ==were placed on indefinite leave== ; those on overseas missions were given 30 days to return to the States with their families. Under orders to remain silent, they used ==pseudonyms== on encrypted chats to inform the outside world of what was going on. When I spoke on Signal with government employees, they sounded as if they were in Moscow or Tehran. “It felt like it went very ==authoritarian== very quickly,” one ==civil servant== told me. “You have to watch everything you say and do in a way that is gross.”

The website usaid.gov vanished, then ==reappeared== with a ==bare-bones== announcement of the organization’s ==dismemberment== , followed by the message “Thank you for your service.” A ==veteran== USAID official called it “ ==brutal== — from some 20-yearold idiot who doesn’t know anything. What the fuck do you know about my service?” ==A curtain fell over the public information== that could have served to challenge the ==outpouring== of lies and ==distortions== from the White House and from Musk, who called USAID “a criminal organization” and “evil.” If you looked into the charges, nearly all turned out to be ==outright== ==falsehoods== , highly misleading, or isolated examples of the kind of stupid, wasteful programs that exist in any organization.

A ==grant== for hundreds of ethnic-minority students from Myanmar to attend universities throughout Southeast Asia became a propaganda tool in the hands of the ==wrecking crew== because it went under the name “Diversity and ==Inclusion== Scholar ship Program”—as if the money were going to a “woke” bureaucracy, not to Rohingya refugees from the military regime’s ==genocide== . The ==orthodoxy== of a previous administration required the ==terminology== ; the orthodoxy of the new one has ended the students’ education and forced them to return to the country that ==oppressed== them. One of Trump’s executive orders is called “Defending Women Against Gender Ideology Extremism and Restoring Biological Truth to the Federal Government”; meanwhile, the administration suspended the online education of nearly 1,000 women in Afghanistan who had been studying undetected by the Taliban with funding from the State Department.

But hardly anyone in this country knows these things. ==Contesting== Musk’s algorithmically boosted lies on X with the tools of a reporter is like fighting a wildfire with a garden hose.

With no workforce or funding, USAID’s efforts around the world—vaccine campaigns in Nepal, HIV-drug distribution in Nigeria, nutrition for starving children in Sudanese refugee camps—were forced to end. Secretary of State Marco Rubio (who ==championed== USAID as a senator and now, as the agency’s acting head, is its ==executioner== ) issued a ==waiver== for lifesaving programs. But it proved almost meaningless, because the people needed to run the programs were locked out of their computers, had no way to communicate, and feared punishment if they kept working.

The ==heedlessness== of the aid ==wreckers== recalls Nick Carraway’s description in The Great Gatsby of Tom and Daisy Buchanan: “They were careless people, Tom and Daisy—they smashed up things and creatures and then retreated back into their money or their vast carelessness, or whatever it was that kept them together, and let other people clean up the mess they had made.” An agency of 10,000 employees is shrinking to about 300 and, despite its ==statutory== independence, being dissolved into the State Department. The veteran USAID official I spoke with foresaw a ==skeletal== operation reduced to health and food assistance, with everything else—education, the environment, governance, economic development—gone.

But even basic ==humanitarian== programs will be nearly impossible to sustain with the numbers that the administration ==envisions== —for example, 12 staff members for all of Africa.

“This is the infrastructure and architecture that has given us a doubling of the human lifespan,” Atul Gawande, the writer and surgeon who was the most recent, and perhaps last, head of the agency’s Bureau for Global Health, told me. “Taking it down kills people.”

Trump and Musk’s destruction of USAID was a trial ==blitzkrieg== : Send tanks and ==bombers== into ==defenseless== Poland to see what works before turning on the Western powers. The ==assault== provided a model for ==eviscerating== the rest of the federal bureaucracy. It also demonstrated the radicalism of Trump’s view of America’s role in the world.

Every president from Franklin D. Roosevelt to Barack Obama understood that American power was enhanced, not threatened, by attaching it to alliances, institutions, and values that the American people support, such as freedom, ==pluralism== , and humanitarianism. This was the common idea behind Harry Truman’s Marshall Plan for ==postwar== Europe, Kennedy’s establishment of USAID, Jimmy Carter’s creation of the U.S. refugee program, and George W. Bush’s Emergency Plan for AIDS Relief. These weren’t simple acts of generosity. They were designed to prevent chaos and misery from overwhelming other countries and, eventually, harming our own. They expanded American influence by attraction rather than ==coercion== , showing people around the world that the ==Leviathan== could benefit them, too. Political scientists call this “soft power.”

Every president betrayed these ideas in one way or another, making U.S. foreign policy ==a fat target== for criticism at home and abroad, by the left and the right. Kennedy used foreign aid to ==wage== a bloody ==counterinsurgency== in South Vietnam; Carter put human rights at the center of his policy and then ==toasted the repressive== ==shah== of Iran; Bush, claiming to be spreading democracy to the Middle East, seriously damaged America’s global legitimacy. USAID ==antagonized== host governments and local populations with its ==arrogance== and ==bloat== . “We had a hand in our own destruction,” one longtime official told me. “We threw money in areas we didn’t need to.”

But the alternative to the ==hypocrisies== of soft power and the postwar liberal order was never going to be a ==chastened== , ==humbler== American foreign policy— neither the left’s fantasy of ==a plus-size Norway== nor the right’s of a return to the ==isolationist== 1920s. The U.S. is far too big, strong, and ==messianic== for voluntary diminish ment. The choice for this ==superpower== is between ==enlightened== ==selfinterest== , with all its blind spots and failures, and raw coercion.

Trump is showing what raw coercion looks like. Rather than negotiate with Canada and Mexico, impose U.S. demands with tariffs; rather than strengthen NATO, undermine it and threaten a conflict with one of its smallest, most ==benign== member countries; rather than review aid programs for their ==efficacy== , shut them down, ==slander== the people who make them work, and shrug at the humanitarian catastrophe that follows. The deeper reason for the extinction event at USAID is Trump’s contempt for anything that looks like cooperation between the strong and the weak. “America First” is more ==imperialist== than isolationist, which is why William McKinley, not George Washington or John Quincy Adams, is Donald Trump’s new presidential hero. He’s using a techno-futurist billionaire to return America to the late 19th century, when the civil service was a patronage network and great-power doctrine held that “might makes right.” He’s ridding himself and the country of restraining codes— the rule of law at home, the rules-based order abroad—and replacing them with a simple test: “What’s in it for me?” He’s ==unilaterally== ==disarming== America of its soft power, making the United States no different from China, Russia, or Iran. This is why the ==gutting== of USAID has received propaganda assistance and glowing reviews from Beijing, Moscow, and Tehran.

==Transactional== logic has an obvious appeal. ==Dispensing== with the annoying ==niceties== of multilateral partnerships and foreign aid brings a kind of clarity to international relations, showing where the real muscle is, like ==a strip-down== before a wrestling match. Set loose, the U.S. might be strong enough to work its will on weaker friends and neighbors, or at least claim to do so. Trump’s threat of tariffs to intimidate Colombia into allowing ==deportation== flights to land there was like the assault on USAID—an easy demonstration project. His domination of the propaganda sphere allows him to convince the public of victories even where, as with Canada, there was never much of a dispute to begin with. If NATO dissolved while the U.S. grabbed Greenland, many Americans would regard it as a net win: We’d save money and gain a strategic chunk of the North Atlantic while freeing ourselves of an obligation whose benefit to us wasn’t entirely clear.

It isn’t obvious why funding the education of oppressed Burmese students serves our national interest. It’s easier to see the advantages of strongarming weak countries into giving in to our demands. If this creates ==resentment== , well, who said gratitude mattered between nations? Strength has its own attractive force. A sizable ==cohort== of Americans have made their peace with Trump, not because he tempered his cruelty and checked his abuses but because he is at the height of his power and is using it without restraint. This is called power worship. The Russian invasion of Ukraine won Vladimir Putin a certain admiration in countries of the global South, as well as among MAGA Americans, while Joe Biden’s appeals to democratic values seemed ==pallid== and hypocritical. The law of “might makes right” is the political norm in most countries. Trump needs no explaining in Nigeria or India.

Coercion also depends on the American people’s ==shortsightedness== and ==incuriosity== .Trump’s flood of executive orders and Musk’s assault on the federal government are intended to create such chaos that not even the insiders most affected understand what’s happening. An inattentive public might simply see a Washington melee—the disrupters against the bureaucrats. Short of going to war, if the U.S. starts behaving like the great powers of earlier centuries and the rival powers of our own, how many Americans will notice a difference in their own lives?

According to Rubio, the purpose of the aid pause is to weed out programs that don’t advance “core national interests.” Gawande compared the process to stopping a plane in midair and firing the crew in order to conduct a review of the airline industry. But the light of the ==bonfire== burning in Washington makes it easier to see how soft power actually works—how most aid programs do serve the national interest. Shutting down African health programs makes monitoring the recent outbreak of Ebola in Uganda, and preventing its spread from that region to the rest of the world, nearly impossible. In many countries, the end of aid opens the door wider to ==predatory== Chinese loans and propaganda. As one USAID official explained: “My job literally was countering China, providing development assistance in a much nicer, kinder, partnership way to local people who were being pressured and had their arms twisted.” When 70 Afghan students in central Asia, mostly women, had their scholarships to American universities suddenly suspended and in some cases their plane tickets canceled, the values of freedom and open inquiry lost a bit of their attractiveness. The American college administrator responsible for the students told me, “Young people who are sympathetic to the United States and share our best values are not only not being welcomed; they’re having the door slammed in their faces.”

Most Americans don’t want to believe that their government is taking life saving medicine away from sick people in Africa, or betraying Afghans who sacrificed for this country. They might disapprove of foreign aid, but they want starving children to be fed. This native ==generosity== explains why Trump and Musk have gone to such lengths to ==clog== the internet with falsehoods and hide the consequences of their cruelty. The only obstacle to ending American soft power isn’t Congress, the bureaucracy, or the courts, but public opinion.

One of the country’s most popular programs is the resettlement of refugees. For decades, ordinary American citizens have welcomed the world’s most ==persecuted== and desperate people—European Jews after World War II, Vietnamese after the fall of ==Saigon== , Afghans after the fall of Kabul. Refugees are in a separate category from most immigrants: After years of waiting and ==vetting== by U.S. and international agencies, they come here legally, with local sponsors. But Trump and his adviser Stephen Miller see them as no different from migrants crossing the southern border. The flurry of executive orders and memos has halted the processing of all refugees and ended funding for resettlement. The story has received little attention.

Here’s what the program’s shutdown means: I spoke with an Afghan special-forces captain who served alongside Americans— when Kabul was about to fall in 2021, he prevented armed Taliban at the airport from seizing U.S. weaponry, but he was left behind during the evacuation.

Arrested by the new regime, the captain was imprisoned for seven months and suffered regular and severe torture, including the ==amputation== of a ==testicle== . He managed to escape with his family to Pakistan in 2023 and was near the end of being processed as a refugee when Trump took office. He had heard Trump criticize the Biden administration for leaving military equipment behind in Afghanistan. Because he had worked to prevent that from happening, he told me, “that gave me a hope that the new administration would value my work and look at me as a valuable person, a person who is aligned with all the administration is hoping to achieve, and that would give a chance for my kids and family to be moved out safely.” Biden’s ==ineptitude== ==stranded== the captain once;

Trump’s ==coldheartedness== is doing it again.

A sense of loyalty and compassion isn’t ==extraneous== to American identity; it is at the core of national pride, and its betrayal exacts a cost that can’t be easily measured. The Biden administration created a program called Welcome Corps that allows ordinary Americans to act as resettlement agencies. (My wife and I participated in it.) In Pennsylvania, a retiree named Chuck Pugh formed a sponsor group to bring an Afghan family here, and the final medical exam was completed just before Inauguration Day. When resettlement was abruptly ended, Pugh found himself wondering, Who are we? I know what I want to think, but I’m just not sure. The sponsor group includes Pugh’s sister, Virginia Mirra. She and her husband are ==devout== Christians and ==ardent== Trump supporters. In early February, when I asked her how she felt about the suspension of the refugee program, she sounded surprised, and disappointed—she hadn’t heard the news. “I feel sad about that,” she said. “It does bother me. It’s starting to sink in. With these people in danger, I would wonder if there would be an exception made for them. How would we go about that?” Her husband frequently sends American-flag lapel pins to Trump, and I suggested that he write the president about the Afghan family. “I will talk to my husband tonight,” Mirra said. “And I will continue to pray that the Lord will protect them and bring them to this country by some means. I do believe in miracles.”

Vocabulary, phrases and sentences

Words Chinese Definition Phonetic Symbol
dismantle 拆除;拆卸;废除 /dɪsˈmæntl/
repurpose 将…用于新的目的;重新利用 /ˌriːˈpɜːrpəs/
roll them up 把它们卷起来 /rəʊl ðem ʌp/
be rife with corruption 充满腐败 /biː raɪf wɪð kəˈrʌpʃn/
polio 小儿麻痹症 /ˈpəʊlioʊ/
whiz 能手;专家 /wɪz/
seize 没收;查封 /siːz/
be placed on indefinite leave 被无限期停职 /biː pleɪst ɒn ɪnˈdefɪnət liːv/
pseudonym 笔名;假名 /ˈsjuːdənɪm/
authoritarian 独裁主义的;专制的 /ɔːˌθɒrəˈteəriən/
civil servant 公务员 /ˈsɪvl ˈsɜːvənt/
bare - bone 最低限度的 /ˈbeə bəʊn/
dismemberment 肢解;分割;瓜分 /dɪsˈmembəmənt/
veteran 老兵;老手;退伍军人 /ˈvetərən/
brutal 残忍的;野蛮的;冷酷的 /ˈbruːtl/
a curtain fall over the public information 对公众信息的掩盖 /ə ˈkɜːtn fɔːl ˈəʊvə ðə ˈpʌblɪk ˌɪnfəˈmeɪʃn/
outpour 倾泻;流出;流露 /ˈaʊtpɔː(r)/
distortion 扭曲;变形;失真;曲解 /dɪˈstɔːʃn/
outright 完全地;彻底地;公然地 /ˈaʊtraɪt/
falsehood 谎言;虚假;不实 /ˈfɔːlshʊd/
grant 奖学金 /ɡrɑːnt/
wrecking crew 破坏小组;拆除队 /ˈrekɪŋ kruː/
inclusion 包容 /ɪnˈkluːʒn/
genocide 种族灭绝;大屠杀 /ˈdʒenəsaɪd/
orthodoxy 正统观念;正统做法;正教 /ˈɔːθədɒksi/
terminology 术语;专门用语 /ˌtɜːmɪˈnɒlədʒi/
contest 争辩;质疑 /ˈkɒntest/ (动词)/ˈkɒntest/(名词)
champion 支持;捍卫 /ˈtʃæmpiən/(名词)/ˈtʃæmpiən/(动词)
executioner 刽子手;行刑者 /ˈeksɪkjuːʃənə(r)/
waiver 放弃;弃权;豁免 /ˈweɪvə(r)/
heedlessness 不注意;粗心大意 /ˈhiːdləsnəs/
wrecker 破坏者;肇事者;使船遇难的人 /ˈrekə(r)/
statutory 法定的;法规的;依照法令的 /ˈstætʃətri/
skeletal 骨骼的;骨瘦如柴的;梗概的 /ˈskelɪtl/
humanitarian 人道主义的;博爱的;慈善的 /hjuːˌmænɪˈteəriən/
envision 想象;设想;展望 /ɪnˈvɪʒn/
blitzkrieg 闪电战 /ˈblɪtskriːɡ/
bomber 轰炸机;投弹手 /ˈbɒmə(r)/
defenseless 无防御能力的;无助的 /dɪˈfensləs/
assault 攻击;袭击;突击 /əˈsɔːlt/
eviscerate 取出内脏;切除;彻底摧毁 /ɪˈvɪsəreɪt/
pluralism 多元主义;多元论;多元化 /ˈplʊərəlɪzəm/
postwar 战后的 /ˈpəʊstwɔː(r)/
coercion 强制;强迫;高压政治 /kəʊˈɜːʃn/
leviathan Leviathan 海中怪兽;庞然大物 /lɪˈvaɪəθən/
a fat target 一个容易攻击的目标 /ə ˈfæt ˈtɑːɡɪt/
wage 开展;发动;进行;工资 /ˈweɪdʒ/(动词)/ˈweɪdʒ/(名词)
counterinsurgency 反叛乱;平叛 /ˌkaʊntərɪnˈsɜːdʒənsi/
toasted the repressive 为镇压者干杯(这里意译就是支持镇压者) /ˈtəʊstɪd ðə rɪˈpresɪv/
shah (伊朗)国王 /ʃɑː/
antagonize 使对抗;使敌对;引起…的敌意 /ænˈtæɡənaɪz/
arrogance 傲慢;自大 /ˈærəɡəns/
bloat 使膨胀;使肿胀;肿胀;臃肿;膨胀 /ˈbləʊt/
chastened 受到惩罚后变得克制的; chastise(惩罚)的过去分词 /ˈtʃeɪsnd/
a plus - size Norway 一个大号挪威(形象说法,指左派幻想的像挪威那样温和的美国) /ə ˈplʌs saɪz ˈnɔːweɪ/
isolationist 孤立主义的 /ˌaɪsəˈleɪʃənɪst/
messianic 有救世主情结的;弥赛亚的 /ˌmesiˈænɪk/
superpower 超级大国 /ˈsuːpəpaʊə(r)/
enlightened 开明的;有见识的 /ɪnˈlaɪtnd/
selfinterest 自身利益 /ˈself ˈɪntrəst/
benign 良性的;和蔼的;温和的 /bɪˈnaɪn/
efficacy 功效;效力;效能 /ˈefɪkəsi/
slander 诽谤;诋毁 /ˈslændə(r)/
imperialist 帝国主义的 /ɪmˈpɪəriəlɪst/
unilaterally 单方面地 /ˌjuːnɪˈlætrəli/
disarm 解除武装;裁军;使无害 /dɪsˈɑːm/
gut 取出内脏;毁坏内部;勇气;胆量;直觉 /ˈɡʌt/
transactional 交易的;事务性的 /ˈtrænzækʃənl/
dispense 分配;分发;施予;执行;免除 /dɪˈspens/
nicety 细微之处;精确性;美好 /ˈnaɪsəti/
a strip - down 精简;缩减 /ə ˈstrɪp daʊn/
deportation 驱逐出境;放逐 /ˌdepɔːˈteɪʃn/
resentment 怨恨;愤恨 /rɪˈzentmənt/
cohort 一群人;一组;同生群 /ˈkəʊhɔːt/
pallid 苍白的;暗淡的;无生气的 /ˈpælɪd/
shortsightedness 近视;目光短浅 /ˈʃɔːtsaɪtɪdnəs/
incuriosity 无好奇心;不感兴趣 /ˌɪnkjʊəriˈɒsəti/
bonfire 篝火;营火 /ˈbɒnfaɪə(r)/
predatory 掠夺性的;食肉的;捕食性的 /ˈpredətri/
clog 堵塞;阻塞 /ˈklɒɡ/
persecuted 受迫害的;persecute(迫害)的过去分词 /ˈpɜːsɪkjuːtɪd/
Sigon 西贡(可能是特定名称) /ˈsaɪɡən/
vet 审查;检查;诊疗;兽医;老兵 /ˈvet/(动词)/ˈvet/(名词)
amputation 截肢;切断 /ˌæmpjuˈteɪʃn/
impetitude 急躁;鲁莽 /ɪmˈpetɪtjuːd/
strand 使搁浅;使滞留;线;股;缕 /ˈstrænd/
devout 虔诚的;笃信宗教的;热忱的 /dɪˈvaʊt/
ardent 热情的;热烈的;炽热的 /ˈɑːdənt/

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Ireland’s Contribution to English

Nearly everyone knows that countries such as the United Kingdom, the United States of America, Canada, Australia, and New Zealand are primarily English-speaking countries; that is, English is the mother tongue used in these countries. What is less well known is that English is also the mother ==tongue== in countries such as the Republic of Ireland (officially called Eire), Barbados, Jamaica, Trinidad, and Guyana. Among these latter few, the Irish have made contributions to the English language in both its ==lexicon== and literature which can ==be considered second to none== .

==Virtually== every aspect of English literature has been graced by the writings of the Irish. This fact is all the more amazing because Ireland is a relatively small country, with never more than four million people throughout its long history. Yet many great “English” writers were indeed born and often raised in Ireland, though many, too, immigrated to the United Kingdom at some point in their lives. Among these pillars of English literature were Jonathan Swift, William Butler Yeats, James Joyce, Samuel Beckett, Oscar Wilde, George Bernard Shaw, and Edmund Burke. Many other lesser-known figures have ==punctuated== English literature as well. These men’s contributions to the English language and to Western thought in general are ==immeasurable== . A review of two of these writers’ major works will reveal why.

Jonathan Swift (1667 -1745) by most reckoning is the best English-language satirist ever, and one of the world’s greatest as well. Born in Ireland of English parents, Swift went to school there through his bachelor’s degree (Trinity College, Dublin, capital of Ireland). Thereafter he frequently Traveled between England and Ireland, including years spent at Oxford College, where he earned his master’s degree. Swift wrote a great deal of poetry, but he is best regarded as a ==prose== ==satirist== . He wrote ==prolifically== both in Ireland and England, nearly constantly shuttling from one to the other. In Ireland he worked on Gulliver’s Travels, which he later had published in England in 1726. Already famous by that time, Swift would become ==immortalized== with this last great work. What child does not know the story of the brave sailor Gulliver as he travels through lands in which he is at turn both a giant and a ==midget== ? Yet most readers are not aware of Swift’s intent to satirize the political, academic, and religious leaders of his time. Read either way, Swift’s genius as a writer of English cannot be denied.

A giant of English Theater was George Bernard Shaw(1856 - 1950) . Born in Dublin, Shaw moved to England with his family when he was 20 and stayed there for most of the rest of his long life. His early fiction writing was so poor that he could not find a publisher. Only when he began to work as a ==playwright== did his ==fortunes== improve. Among the many, many plays for which Shaw is famous, perhaps his most lasting (though not his most critically acclaimed) is Pygmalion (1916), the story of a language teacher who attempts to” civilize” a young ==prostitute== by training her to speak correctly. If this story sounds familiar, it should: ==Pygmalion== was later filmed winning on Oscar for Shaw and later again transformed into the highly popular Broadway musical My Fair Lady (1956). A good story never dies: the original Pygmalion has since been updated in the hit movie Pretty woman (1990) starring Richard Gere and Julia Roberts. As with Shakespeare, many of Shaw’s plays are continually restaged or rewritten into new media because Shaw wrote on many themes which touch on the human condition, ==independent of time and space== .

Among the ==constellation== of Irish talents, perhaps Swift and Shaw are two among the more brilliant stars, but much more could be written of those mentioned above and many others. Though English literature written by the British suffices as an eternal and shining ==canon== of literature, it would be nonetheless ==dimmer== without the considerable talents of its Irish contributors

Vocabulary & Idioms

  • tongue——语言
  • lexicon——全部词汇
  • be second to none——无人出其右
  • virtually——几乎
  • punctuate——不时打断
  • immeasurable——不可估量的
  • prose——散文
  • immortalize——永垂不朽
  • midget——侏儒
  • playwright——剧作家
  • fortune——前途
  • prostitute——妓女
  • Pygmalion——《茶花女》
  • independent of time and space——独立于时间和空间
  • constellation——星座
  • canon——精品
  • dimmer——暗淡的

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使用for循环批量创建文件夹

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for i in {2..9}; do cp 0.01 0.0$i -r ; done

使用sed命令不打开文件而进行替换

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sed '3s/0.01/0.02/g' ICNAR

对第三行(3)出现的所有0.01(g,全局替换)进行替换(s表示替换操作),替换为0.02,只输出替换后的结果

sed ‘3/0.01/0.02/g’ INCAR > INCAR最后什么也没有

加上-i参数可以直接进行编辑

结合for循环和sed批量命名

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[storm@cachyos-x8664 ex03]$ for i in *; do sed -i "3s/0.05/$i/g" $i/INCAR ; done
[storm@cachyos-x8664 ex03]$ grep SIGMA */INCAR
0.01/INCAR:SIGMA = 0.01
0.02/INCAR:SIGMA = 0.02
0.03/INCAR:SIGMA = 0.03
0.04/INCAR:SIGMA = 0.04
0.05/INCAR:SIGMA = 0.05
0.06/INCAR:SIGMA = 0.06
0.07/INCAR:SIGMA = 0.07
0.08/INCAR:SIGMA = 0.08
0.09/INCAR:SIGMA = 0.09

使用双引号以读取变量的值

注意这里使用的是英文括号而不是花括号

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for i in $(seq 8 2 16); do cp 888/POSCAR ${i}${i}${i}/POSCAR; done

“提交任务的命令”

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yhbatch -p gsc -N 1 -J test job_sub 

找能量的命令

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grep  without OUTCAR | tail -n 1
grep ' without' OUTCAR | tail -n 1 # 本人常用的是这个
grep sigma OUTCAR | tail -n 1

提交任务,多个文件夹

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for i in *; do cd $i ; vasp1; cd $OLDPWD; done

alias vasp1=‘mpirun -n 8 vasp’

输出时间信息

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for i in *0; do echo -e  $i "\t" $(grep User $i/OUTCAR | awk '{print $4}'); done

绘图脚本

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import matplotlib.pyplot as plt
import numpy as np

x,y = np.loadtxt('data.dat', delimiter = ',',
usecols=(0,1), unpack=True)
plt.xlabel('ENCUT / eV')
plt.ylabel('Ttme / S')
plt.plot(x,y, 'rs-', linewidth=2.0)
plt.show()

在vim中进行替换

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: 10,30s/$/T T T/g

$表示每一行的末尾

提取能量(用制表符TAB进行分隔)

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for i in [0-9]*/; do
dir=${i%/}
energy=$(grep ' without' "$dir/OUTCAR" | tail -n 1 | awk '{print $7}')
printf "%s\t%s\n" "$dir" "$energy"
done > data

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John Doe

author.bio


author.job


Changchun, China