* Bader charge analysis [#va4ae2b5] [[Henkelman Group:http://theory.cm.utexas.edu/henkelman/code/bader/]]が配布しているプログラムを利用してBader電荷の計算を行う。 ** グラフェン [#ed3f7d01] 以下ではノルム保存擬ポテンシャルC_pbe6TMを用いる。 *** SCF計算 [#be50a39b] 0 0 0 0 0 0 8.0000 20.0000 1 2 2 : GMAX, GMAXP, NTYP, NATM, NATM2 191 0 : number of space group, type of bravis lattice 4.655538364 4.655538364 20.000 90.0 90.0 120.0 : a,b,c,alpha,beta,gamma 24 24 1 1 1 1 : knx,kny,knz, k-point shift 0 0 : NCORD, NINV, : IWEI, IMDTYP, ITYP 0.6666666666 0.3333333333 0.0000000000 1 1 1 0.3333333333 0.6666666666 0.0000000000 1 1 1 6 0.1500 12.0107 1 1 0.d0 : TYPE 1IATOMN,ALFA,AMION,ILOC,IVAN 0 0 0 0 0 : ICOND 0-MD, 1-CONT.MD, 2-WAVE FN,, 3-WAVE FN CONT., iconstpw 0 1 : IPRE, IPRI 200 200 0 3600.00 0 : NMD1, NMD2, iter_last, CPUMAX,ifstop 3 1 : Simple=1,Broyd2=3,Blugel=6, 1:charge, 2:potential mix. 0 20 0.8 : starting mixing, kbxmix,alpha 0.60 0.50 0.60 0.70 1.00 : DTIM1, DTIM2, DTIM3, DTIM4, dtim_last 30.00 2 1 0.10D-08 1.d-06 : DTIO ,IMDALG, IEXPL, EDELTA -0.0010 0.10D+02 0 : WIDTH,FORCCR,ISTRESS ggapbe 1 : XCTYPE, nspin 1.00 3 : destm, n_stm 101 : NBZTYP 0-SF, 1-BK, 2-SC, 3-BCC, 4-FCC, 5-DIA, 6-HEX 0 0 0 : NKX, NKY, NKZ 0 0 0 : NKX2,NKY2,NKZ2 8 : NEG 1 : NEXTST(MB) 0 : 0; random numbers, 1; matrix diagon 2 0 0 0(MB) : imsd, i_2lm, i_sd2another, wksz for phase 0 : evaluation of eko difference.0 = no ,1 = yes 0 : npdosao 0 0.0 : SM_N, DOPPING #ref(http://www-cp.prec.eng.osaka-u.ac.jp/puki_state/my_image/gra1x1.png,nolink) *** 実空間の電荷密度 [#u873fbb8] icond=9として再計算して実空間の電荷密度nfchgt_r.dataを作成する。 *** Gaussian cube fileの作成 [#a3d3331c] /home/hamada/STATE/tools/ChargeUtil/chg2cubeを用いて電荷密度をGaussian cube形式に変換する。 $ chg2cube Enter the name of the STATE input file> your_input_file_name Enter the name of the charge density file> nfchgt_r.data Enter the prefix for output file(s)> charge reading nfchgt_r.data...done. # of data in nfchgt_r.data : 1 data #1 : ispin : 1 : ilevel: 1 Creating charge.cube...done. Program successfully ended *** Bader電荷の計算 [#i8ab8f23] $ bader charge.cube GRID BASED BADER ANALYSIS (Version 0.95a 02/26/16) OPEN ... charge.cube GAUSSIAN-STYLE INPUT FILE FFT-grid: 30 x 30 x 128 CLOSE ... charge.cube RUN TIME: 0.03 SECONDS CALCULATING BADER CHARGE DISTRIBUTION 0 10 25 50 75 100 PERCENT DONE: ********************** REFINING AUTOMATICALLY ITERATION: 1 EDGE POINTS: 23177 REASSIGNED POINTS: 969 ITERATION: 2 CHECKED POINTS: 9850 REASSIGNED POINTS: 0 RUN TIME: 0.15 SECONDS CALCULATING MINIMUM DISTANCES TO ATOMS 0 10 25 50 75 100 PERCENT DONE: ********************** RUN TIME: 0.01 SECONDS WRITING BADER ATOMIC CHARGES TO ACF.dat WRITING BADER VOLUME CHARGES TO BCF.dat NUMBER OF BADER MAXIMA FOUND: 6 SIGNIFICANT MAXIMA FOUND: 6 VACUUM CHARGE: 0.0205 NUMBER OF ELECTRONS: 8.00003 $ cat ACF.dat # X Y Z CHARGE MIN DIST ATOMIC VOL -------------------------------------------------------------------------------- 1 2.3277690 1.3439380 0.0000000 3.9020033 1.0751426 65.2790699 2 0.0000000 2.6878760 0.0000000 4.0774900 1.2120244 69.3785643 -------------------------------------------------------------------------------- VACUUM CHARGE: 0.0205 VACUUM VOLUME: 240.7492 NUMBER OF ELECTRONS: 8.0000 CHARGEに各原子の電荷が表示される。単位胞内の2つの炭素原子は等価なのに電荷に偏りが生じているのは、電荷密度のグリッドが粗いためと考えられる。 *** カットオフ依存性 [#g65fcc10] エネルギーカットオフを増加させて(電荷密度のグリッドを細かくして)電荷分布の収束性を調べる。 |gmaxp |CENTER: 20|CENTER: 30|CENTER: 40|CENTER: 50|CENTER: 60|CENTER: 70|CENTER: 80|CENTER: 90|CENTER: 100|h |grid-X|CENTER: 30|CENTER: 48|CENTER: 60|CENTER: 80|CENTER: 90|CENTER: 108|CENTER:120|CENTER:144|CENTER:150| |grid-Y|CENTER: 30|CENTER: 48|CENTER: 60|CENTER: 80|CENTER: 90|CENTER: 108|CENTER:120|CENTER:144|CENTER:150| |grid-Y|CENTER:128|CENTER:192|CENTER:256|CENTER:320|CENTER:384|CENTER: 450|CENTER:512|CENTER:576|CENTER:640| |炭素原子1の電荷|3.902|3.934|3.945|3.956|3.960|3.965|3.967|3.971|3.972| |炭素原子2の電荷|4.077|4.044|4.034|4.022|4.019|4.014|4.011|4.008|4.007| |電荷の偏り|0.175|0.110|0.088|0.066|0.059|0.049|0.044|0.037|0.035|