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fromciftoconfig
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fromciftoconfig
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#coding:utf-8
from numpy import *
from math import *
import urllib
import json
import os
import shutil
import time
def downloadjson(mid): # 下载json文件，得到字典
apiStem = "https://www.materialsproject.org/rest/v1/materials/%s/vasp/cif?API_KEY=**" % mid
print apiStem
c=urllib.urlopen(apiStem)
return json.loads(c.read())
def fromciftoconfig(mid, pseduo = 'NCPP-SOFT'):
dict = downloadjson(mid)
if dict["valid_response"] == False: return -1 # 如果response不存在， 直接返回
else:
rootdir = os.getcwd()
matdict = dict["response"]
numoftype = len(mid.split('-'))
middir = mid + "." + pseduo
createdir(middir)
j = 1
for i in range(len(matdict)):
sth = matdict[i]["cif"].split('\n')
if sth[15].split()[0] == '_cell_length_a': # 筛选出符合标准的
if len(sth[24].split()) == numoftype + 1: # 只算有特定原子的
id = matdict[i]["material_id"]
parentdir = os.getcwd()
createdir('%d.%s' % (j, id)) # 01 mp-250 something like that
j += 1
a = float(sth[15].split()[1])
b = float(sth[16].split()[1])
c = float(sth[17].split()[1])
alpha = float(sth[18].split()[1])
beta = float(sth[19].split()[1])
gamma = float(sth[20].split()[1])
ax, ay, az, bx, by, bz, cx, cy, cz = xandyandz(alpha, beta, gamma, a, b, c)
length = len(sth)
numofatom = length - 44 # 原子总数
prefix(numofatom, ax, ay, az, bx, by, bz, cx, cy, cz)
fwadd = open('atom.config', 'a')
repeatatomtype = []
for k in range(42, length - 2):
array = sth[k].split()
atomic = atomicnumber(array[0])
repeatatomtype.append(array[0])
x = float(array[3])
y = float(array[4])
z = float(array[5])
fwadd.write('\t%d\t%.12f\t%.12f\t%.12f 1 1 1\n' % (atomic, x, y, z))
time.sleep(0.1)
fwadd.close()
atomtype = list(set(repeatatomtype))
addpseduo(pseduo, atomtype)
addincar(atomtype, numofatom, a, b, c)
os.chdir(parentdir)
time.sleep(1)
os.chdir(rootdir)
return
def xandyandz(alpha, beta, gamma, a, b, c): # 对cif给出的构型进行计算得到晶格矢量
al = alpha * pi / 180
be = beta * pi / 180
ga = gamma * pi / 180
ax = a
ay = 0
az = 0
bx = b * cos(ga)
by = b * sin(ga)
bz = 0
cx = c * cos(be)
cy = c * ((cos(al) - cos(ga)*cos(be))/sin(ga))
cz = sqrt(c*c - cx*cx - cy*cy)
return ax, ay, az, bx, by, bz, cx, cy, cz
def atomicnumber(element): # atom.comfig中要用到原子序数
elements = {'H': 1, 'He': 2, 'Li': 3, 'Be': 4, 'B': 5, 'C': 6, \
'N': 7, 'O': 8, 'F': 9, 'Ne': 10, 'Na': 11, 'Mg': 12, 'Al': 13, \
'Si': 14, 'P': 15, 'S': 16, 'Cl': 17, 'Ar': 18, 'K': 19, 'Ca': 20, \
'Sc': 21, 'Ti': 22, 'V': 23, 'Cr': 24, 'Mn': 25, 'Fe': 26, 'Co': 27, \
'Ni': 28, 'Cu': 29, 'Zn': 30, 'Ga': 31, 'Ge': 32, 'As': 33, 'Se': 34, \
'Br': 35, 'Kr': 36, 'Rb': 37, 'Sr': 38, 'Y': 39, 'Zr': 40, 'Nb': 41, \
'Mo': 42, 'Tc': 43, 'Ru': 44, 'Rh': 45, 'Pd': 46, 'Ag': 47, 'Cd': 48, \
'In': 49, 'Sn': 50, 'Sb': 51, 'Te': 52, 'I': 53, 'Xe': 54, 'Cs': 55, \
'Ba': 56, 'Lu': 71, 'Hf': 72, 'Ta': 73, 'W': 74, 'Re': 75, 'Os': 76, \
'Ir': 77, 'Pt': 78, 'Au': 79, 'Hg': 80, 'Tl': 81, 'Pb': 82, 'Bi': 83, \
'Po': 84, 'At': 85, 'Rn': 86}
return elements[element]
def prefix(numofatom, ax, ay, az, bx, by, bz, cx, cy, cz): # 对每个atom.config写个抬头
fw = open('atom.config', 'w')
fw.write('\t%d\n' % numofatom)
fw.write("Lattice vector\n")
fw.write('\t%.10f\t%.10f\t%.10f\n' % (ax, ay, az))
fw.write('\t%.10f\t%.10f\t%.10f\n' % (bx, by, bz))
fw.write('\t%.10f\t%.10f\t%.10f\n' % (cx, cy, cz))
fw.write("Position, move_x, move_y, move_z\n")
fw.close()
def createdir(childir): # 在当前目录下创建指定名字文件夹并进入
currentdir = os.getcwd()
nextdir = os.path.join(currentdir, childir)
os.mkdir(nextdir)
os.chdir(nextdir)
def addpseduo(pseduo, atomtype): # 添加赝势文件
parentdir = '**'
listname = os.listdir(parentdir)
for i in range(len(listname)):
if listname[i] == pseduo:
dir = os.path.join(parentdir, listname[i])
atom = os.listdir(dir)
for j in range(len(atomtype)):
for k in range(len(atom)):
if atomtype[j] == atom[k]:
shutil.copy(os.path.join(dir, atomtype[j]), os.getcwd())
def addincar(atomtype, numofatom, lx, ly, lz): # 复制并修改etot.incar
incar = "**"
shutil.copy(incar, os.getcwd())
fw = open('etot.input', 'r+')
content = fw.readlines()
Xk, Yk, Zk = autokpoints(numofatom, lx, ly, lz)
content.insert(3, ' MP_N123 = %d %d %d 0 0 0\n' % (Xk, Yk, Zk))
number = 1
position = 5
for i in range(len(atomtype)):
content.insert(position, ' in.psp%d = %s\n' % (number, atomtype[i]))
number += 1
position += 1
fw = open('etot.input', 'w+')
fw.writelines(content)
fw.close()
def autokpoints(numofatom, lx, ly, lz):
numofkpoints = round(1000.0 / numofatom)
X = ly * lz
Y = lx * lz
Z = lx * ly
k = power(numofkpoints/(X * Y * Z), 1/3.0)
Xk = int(round(X * k))
Yk = int(round(Y * k))
Zk = int(round(Z * k))
return Xk, Yk, Zk