網(wǎng)上有很多關(guān)于pos機(jī)t1到t1結(jié)算,ABINIT結(jié)構(gòu)優(yōu)化和能帶計(jì)算教程的知識(shí)，也有很多人為大家解答關(guān)于pos機(jī)t1到t1結(jié)算的問題，今天pos機(jī)之家(m.afbey.com)為大家整理了關(guān)于這方面的知識(shí)，讓我們一起來(lái)看下吧!
本文目錄一覽：
pos機(jī)t1到t1結(jié)算
寫在教程前面：最近市場(chǎng)上很混亂，這里不直接點(diǎn)名，有兩家公司以各種低質(zhì)量教程并采取轉(zhuǎn)發(fā)朋友圈等低劣手段騙取用戶流量，往代算和線下培訓(xùn)引流，請(qǐng)廣大同學(xué)們提高警惕，辨別真?zhèn)?，以免上?dāng)受騙。做計(jì)算只看這里面介紹的平臺(tái)(第一性原理計(jì)算VASP零基礎(chǔ)教程)。
相比VASP和QE軟件，ABINIT軟件在網(wǎng)上的資料可謂少之又少，據(jù)我所知，只有一份很舊的臺(tái)灣教授寫的中文繁體字教程(該教程下載鏈接：http://lanzous.com/u/dft_family)。除此之外，唯一可參考的資料只有ABINIT官網(wǎng)教程(https://www.abinit.org)和官方論壇(https://forum.abinit.org)。今天給大家介紹如何用ABINIT軟件進(jìn)行結(jié)構(gòu)優(yōu)化和能帶計(jì)算。今天計(jì)算所用的例子是Si。
1、計(jì)算前的準(zhǔn)備：
VASP計(jì)算需要INCAR、POSCAR、KPOINTS、POTCAR文件，ABINIT計(jì)算需要*.in輸入文件，該文件包含了計(jì)算參數(shù)、原子坐標(biāo)信息、K點(diǎn)等信息；以及*.files文件，該文件包含了輸入文件名稱、輸出文件名稱、贗勢(shì)路徑等。
a) Si的結(jié)構(gòu)文件下載：
https://materialsproject.org/materials/mp-149
b) ABINIT輸入文件參數(shù)詳解：
https://docs.abinit.org/variables/
c) Si的贗勢(shì)下載(選擇的Si.GGA_PBE-JTH.xml)：
https://www.abinit.org/ATOMICDATA/014-si/index.html
d) ABINIT后處理軟件Abipy了解：
https://abinit.github.io/abipy/index.html
2、結(jié)構(gòu)優(yōu)化
假設(shè)你已經(jīng)新建好相應(yīng)文件夾，并把si.in、si.files、Si.GGA_PBE-JTH.xml和提交作業(yè)的腳本abinit.sh文件都準(zhǔn)備好了。這里僅僅展示輸入文件，不具體解釋參數(shù)含義，請(qǐng)自行閱讀官網(wǎng)介紹。收斂性測(cè)試另開教程講述。可以以這個(gè)作為模板，其它材料僅需要替換截?cái)嗄躤cut、k點(diǎn)ngkpt、贗勢(shì)、cell and system部分。
si.in
#### cell and system natom 2 ntypat 1 typat 1 1 znucl 14 xred 0.7500000000 0.7500000000 0.7500000000 0.5000000000 0.5000000000 0.5000000000 acell 1.0 1.0 1.0 rprim 0.0000000000 5.1679709341 5.1679709341 5.1679709341 0.0000000000 5.1679709341 5.1679709341 5.1679709341 0.0000000000### electronic ground statekptopt 1ngkpt 11 11 11nshiftk 1shiftk 0.0 0.0 0.0ecut 40.0pawecutdg 40.0nstep 50#tolrff 0.02toldfe 1.0d-7#occopt 3 tsmear 0.0001#nband 8#diemac 12.0#nsppol 2#spinat#0 0 1#0 0 1### XC#ixc 11### structural optimizationoptcell 2ionmov 2tolmxf 1.0d-06ntime 50ecutsm 0.5dilatmx 1.1### parallelizationautoparal 1#paral_kgb 1#npband 1#bandpp 1#npfft 1#npkpt 1### options for printingprtden 0 #otherwise _DEN file printed at each Broyden stepprteig 0prtwf 0
si.files
si.insi.outsiisiotmpSi.GGA_PBE-JTH.xml
abinit.sh
#!/bin/bashulimit -s unlimitedulimit -m unlimitedulimit -c unlimitedulimit -d unlimitedsource /home/gang/env/intel-2019.shsource /home/gang/env/impi-2019.shNP=12EXEC4=/home/gang/software/abinit-8.10.3/build/bin/abinitnohup mpirun -np $NP ${EXEC4} < si.files > log 2>&1 &
計(jì)算完成后，可以用Abipy查看優(yōu)化后的結(jié)構(gòu)(注意Number of relaxation steps performed: 8，如果等于輸入文件中的ntime，應(yīng)該檢查計(jì)算是否已經(jīng)達(dá)到收斂)，
abiopen.py sio_HIST.nc -p================================= File Info =================================Name: sio_HIST.ncDirectory: /home/gang/workdir/abinit/si-band/relaxSize: 6.15 kbAccess Time: Wed Dec 11 16:15:42 2019Modification Time: Wed Dec 11 16:14:14 2019Change Time: Wed Dec 11 16:14:14 2019============================= Initial Structure =============================Full Formula (Si2)Reduced Formula: Siabc : 3.867552 3.867552 3.867552angles: 60.000000 60.000000 60.000000Sites (2) # SP a b c cartesian_forces--- ---- ---- ---- ---- ----------------------------------------------------------- 0 Si 0.75 0.75 0.75 [ 1.25588503e-28 4.18628344e-29 -4.18628344e-29] eV ang^-1 1 Si 0.5 0.5 0.5 [-1.25588503e-28 -4.18628344e-29 4.18628344e-29] eV ang^-1Number of relaxation steps performed: 8============================== Final structure ==============================Full Formula (Si2)Reduced Formula: Siabc : 3.866526 3.866526 3.866526angles: 60.000000 60.000000 60.000000Sites (2) # SP a b c cartesian_forces--- ---- ---- ---- ---- ----------------------------------------------------------- 0 Si 0.75 0.75 0.75 [ 1.67495794e-28 -8.37478971e-29 -8.37478971e-29] eV ang^-1 1 Si 0.5 0.5 0.5 [-1.67495794e-28 8.37478971e-29 8.37478971e-29] eV ang^-1Volume change in percentage: -0.08%Percentage lattice parameter changes: a: -0.03%, b: -0.03%, c: -0%Stress tensor (Cartesian coordinates in GPa):[[-0.00015301 0. 0. ] [ 0. -0.00015301 0. ] [ 0. 0. -0.00015301]]Pressure: 0.000 [GPa]
3、能帶計(jì)算
進(jìn)行這一步之前請(qǐng)仔細(xì)閱讀介紹(https://docs.abinit.org/topics/ElecBandStructure/)，把上面優(yōu)化好的結(jié)構(gòu)替換掉si.in文件中對(duì)應(yīng)的部分。主要輸入文件內(nèi)容如下：
si.in
# Crystalline Si## Computation of the band structure.# First, a SCF density computation, then a non-SCF band structure calculation.ndtset 2#Dataset 1 : usual self-consistent calculationkptopt1 1 # Option for the automatic generation of k points, # taking into account the symmetrynshiftk1 1shiftk1 0.0 0.0 0.0ngkpt1 11 11 11prtden1 1 # Print the density, for use by dataset 2toldfe1 1.0d-7 # This value is way too large for most realistic studies of materials#Dataset 2 : the band structureiscf2 -2getden2 -1kptopt2 -4nband2 20ndivk2 10 10 10 10 # 10, 12 and 17 divisions of the 3 segments, delimited # by 4 points.kptbounds2 0.0 0.0 0.0 0.5 0.0 0.5 0.5 0.25 0.75 0.375 0.375 0.75 0.0 0.0 0.0tolwfr2 1.0d-12enunit2 1 # Will output the eigenenergies in eV#### cell and systemnatom 2ntypat 1typat 1 1znucl 14xred0.7500000000 0.7500000000 0.75000000000.5000000000 0.5000000000 0.5000000000acell 7.3066747348E+00 7.3066747348E+00 7.3066747348E+00rprim0.0000000000E+00 7.0710678119E-01 7.0710678119E-017.0710678119E-01 0.0000000000E+00 7.0710678119E-017.0710678119E-01 7.0710678119E-01 0.0000000000E+00### electronic ground state#kptopt 1#ngkpt 8 8 8#nshiftk 1#shiftk 0.0 0.0 0.0ecut 40.0pawecutdg 40.0nstep 50#tolrff 0.02#toldfe 1.0d-7#occopt 3 tsmear 0.0001#nband 8#diemac 12.0#nsppol 2#spinat#0 0 1#0 0 1### XC#ixc 11### structural optimization#optcell 2#ionmov 2#tolmxf 1.0d-06#ntime 50#ecutsm 0.5#dilatmx 1.1### parallelization#autoparal 1#paral_kgb 1#npband 1#bandpp 1#npfft 1#npkpt 1### options for printing#prtden 0 #otherwise _DEN file printed at each Broyden step#prteig 0#prtwf 0
si.files、abinit.sh、贗勢(shì)文件保持不變。
計(jì)算完成后，可以選擇用(/abinit-8.10.3/scripts/post_processing)目錄下的腳本處理：
ab_extended_scissors_guess.py bse_hexc ElectronPhononCoupling merge_gkk_nc.py plot_bs.py temperature-dependenceAbinitBandStructureMaker.py create_files.py get_irreps.py nonlop_dfpt_test posdopspectra.F90 wannier_bandstructure.pyabinit_eignc_to_bandstructure.py dynamic_pol.f matlab_data_analysis phondisp2abi.py Raman_spec.pyappa Elastic_debye.py merge_ddb_nc.py plot_bandstructure.py README
我們這里選擇用Abipy軟件處理，過程如下：
abiview.py ebands sio_DS2_GSR.nc --bxsf
處理完我們會(huì)得到sio_DS2_GSR.nc.agr文件，接下來(lái)用xmgrace繪圖軟件(http://plasma-gate.weizmann.ac.il/Grace/)直接繪圖即可(假設(shè)你已經(jīng)安裝了xmgrace)。
xmgrace sio_DS2_GSR.nc.agr
Si的能帶結(jié)構(gòu)如下所示：
和Materials Project網(wǎng)站VASP計(jì)算結(jié)果對(duì)比：
(來(lái)源：https://materialsproject.org/materials/mp-149/)
ABINIT軟件簡(jiǎn)介和安裝教程
歡迎加入DFT計(jì)算之家系列平臺(tái)交流
以上就是關(guān)于pos機(jī)t1到t1結(jié)算,ABINIT結(jié)構(gòu)優(yōu)化和能帶計(jì)算教程的知識(shí)，后面我們會(huì)繼續(xù)為大家整理關(guān)于pos機(jī)t1到t1結(jié)算的知識(shí)，希望能夠幫助到大家！
