• data2molecule
  • data2POSCAR
  • DFT_deform

    data2molecule

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    import pandas as pd
    import numpy as np
    import os
    import time
    modelname="HemiCG"
    csvname=modelname+".csv"
    f = pd.read_csv(modelname+".data", header=None)
    str = [' atoms', ' bonds', ' angles', ' dihedrals', ' impropers', ' atom types', ' bond types', ' angle types',
           ' dihedral types', ' improper types', 'xlo xhi', 'ylo yhi', 'zlo zhi', 'Masses', 'Atoms', 'Bonds', 'Angles',
           'Dihedrals', 'Impropers']
    N = len(str)
    p = ' Impropers'
    row_id = np.zeros(N)

    for i in range(N):
        q = f[f[0].str.contains(str[i])].index.tolist()
        if len(q) == 1:
            row_id[i] = q[0]
    ## 筛选特定行 并 提取信息
    id_bo = int(row_id[15])
    id_an = int(row_id[16])
    id_di = int(row_id[17])
    id_im = int(row_id[18])
    ## 定义特定拓扑结构字符串并新建mol文件
    inistr = ["\t", "Coords", "\t", "Types", "\t", "Charges", "\t", "Bonds", "\t", "Angles", "\t", "Dihedrals", "\t",
              "Impropers", "\t"]
    strinsert = pd.DataFrame(inistr)
    mol = open('8_201.csv', 'w')
    info = ["#molecule file generated by python --JiahaoLi  " + time.strftime('%Y:%m:%d %H:%M:%S',
                                                                              time.localtime(int(time.time()))), "\t"];
    pd.DataFrame([info]).to_csv(csvname, mode='a', index=None, header=False)
    for i in range(4):
        f.iloc[int(row_id[i])].to_csv(csvname, mode='a', index=None, header=False)
    xyz = f.iloc[int(row_id[14]) + 1:id_bo]
    p = xyz[0].str.split(' ', expand=True)
    strinsert[0:3].to_csv(csvname, mode='a', index=None, header=False)

    tp = pd.merge(p.iloc[:, 0], p.iloc[:, 4:7], left_index=True, right_index=True)
    tp.to_csv(csvname, mode='a', index=None, header=False, sep=' ')
    strinsert[2:5].to_csv(csvname, mode='a', index=None, header=False)
    tp = pd.merge(p.iloc[:, 0], p.iloc[:, 2], left_index=True, right_index=True)
    tp.to_csv(csvname, mode='a', index=None, header=False, sep=' ')
    strinsert[4:7].to_csv(csvname, mode='a', index=None, header=False)
    tp = pd.merge(p.iloc[:, 0], p.iloc[:, 3], left_index=True, right_index=True)
    tp.to_csv(csvname, mode='a', index=None, header=False, sep=' ')
    ## 输出拓扑信息数目
    # mol.close()
    if id_bo == 0:
        mol.close()
    elif (id_bo != 0) & (id_an != 0) & (id_di != 0) & (id_im != 0):
        strinsert[6:9].to_csv(csvname, mode='a', header=False, index=None)
        p = f.iloc[id_bo + 1:id_an]
        p.to_csv(csvname, mode='a', index=None, header=False)
        strinsert[8:11].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_an + 1:id_di].to_csv(csvname, mode='a', index=None, header=False)
        strinsert[10:13].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_di + 1:id_im].to_csv(csvname, mode='a', index=None, header=False)
        strinsert[12::].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_im + 1::].to_csv(csvname, mode='a', index=None, header=False)

    elif (id_bo != 0) & (id_an != 0) & (id_di != 0) & (id_im == 0):
        strinsert[6:9].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_bo + 1:id_an].to_csv(csvname, mode='a', index=None, header=False)
        strinsert[8:11].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_an + 1:id_di].to_csv(csvname, mode='a', index=None, header=False)
        strinsert[10:13].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_di + 1::].to_csv(csvname, mode='a', index=None, header=False)

    elif (id_bo != 0) & (id_an != 0) & (id_di == 0) & (id_im != 0):
        strinsert[6:9].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_bo + 1:id_an].to_csv(csvname, mode='a', index=None, header=False)
        strinsert[8:11].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_an + 1:id_im].to_csv(csvname, mode='a', index=None, header=False)
        strinsert[12::].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_im + 1::].to_csv(csvname, mode='a', index=None, header=False)


    elif (id_bo != 0) & (id_an != 0) & (id_di == 0) & (id_im == 0):
        strinsert[6:9].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_bo + 1:id_an].to_csv(csvname, mode='a', index=None, header=False)
        strinsert[8:11].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_an + 1::].to_csv(csvname, mode='a', index=None, header=False)


    elif (id_bo != 0) & (id_an == 0) & (id_di != 0) & (id_im != 0):
        strinsert[6:9].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_bo + 1:id_di].to_csv(csvname, mode='a', index=None, header=False)
        strinsert[10:13].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_di + 1:id_im].to_csv(csvname, mode='a', index=None, header=False)
        strinsert[12::].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_im + 1::].to_csv(csvname, mode='a', index=None, header=False)

    elif (id_bo != 0) & (id_an == 0) & (id_di != 0) & (id_im == 0):
        strinsert[6:9].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_bo + 1:id_di].to_csv(csvname, mode='a', header=False, index=None)
        strinsert[10:13].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_di + 1::].to_csv(csvname, mode='a', index=None, header=False)

    elif (id_bo != 0) & (id_an == 0) & (id_di == 0) & (id_im != 0):
        strinsert[6:9].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_bo + 1:id_im].to_csv(csvname, mode='a', index=None, header=False)
        strinsert[12::].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_im + 1::].to_csv(csvname, mode='a', index=None, header=False)

    elif (id_bo != 0) & (id_an == 0) & (id_di == 0) & (id_im == 0):
        strinsert[6:9].to_csv(csvname, mode='a', header=False, index=None)
        f.iloc[id_bo + 1::].to_csv(csvname, mode='a', index=None, header=False)
    mol.close()
    os.rename(modelname+".csv", modelname+".mol")
    # m=f.iloc[id_bo:id_an]

    DFT计算材料变形

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#!/bin/sh
rm -r POSCAR
cp CONTCAR CONTCAR.$@
cp OSZICAR  OSZICAR.$@
mv CONTCAR POSCAR.$@
awk 'BEGIN{my_a = 0.01; my_b = 0}{
        if ((NR<=33&&NR>=10)||( NR<=102&&NR>=66 )||(NR<=110&&NR>=106)||(NR<=126&&NR>=112))  
	{
            my_b = $2 + my_a;
            if (my_b > 1)
                my_b = my_b - 1;
            printf("%.7f %.7f %.7f %s %s %s\n",$1, my_b,$3,$4,$5,$6);
        }    
        else print $0;
    }'  POSCAR.$@>POSCAR

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作者: 得意喵~