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pr-dire2cart.py
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pr-dire2cart.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#Convert direc coordiation to cartesian Writen By Qiang
#modified by nxu
#version 1.1
#时间 2018.4.25
#新增功能：自动根据所有原子的Z坐标，将原子分成若干层（差值小于1.5A），再提醒用户选择需要固定的原子层数（从底部原子开始固定）。
#对于本身为笛卡尔坐标的POSCAR ，转换功能无法使用，但是限制原子功能仍可以使用。
#用法：python dire2cart.py (自动完成POSCAR>CONTCAR的从分数坐标转为笛卡尔坐标) 或者 python dire2cart.py your_POSCAR
#新增用法: python dire2cart.py your_POSCAR any_character(任何字符) ，提醒用户选择需要固定的原子层数，完成原子的限制，默认转化为笛卡尔坐标
import sys
import os
print """
###################################
# #
#for VASP 5.2 or higher versions #
# #
###################################
"""
yuzhi = 1.5 #差值小于1.5A
if len(sys.argv) <= 1:
print(u"默认将POSCAR，CONTCAR由分数坐标转为笛卡尔坐标")
if not os.path.isfile("POSCAR"):
if not os.path.isfile("CONTCAR"):
print(u"Error,POSCAR，CONTCAR皆不存在！")
exit()
else:
script = sys.argv[0]
file_to_be_converted = "CONTCAR"
print u"正在完成CONTCAR的转换........"
else:
script = sys.argv[0]
file_to_be_converted = "POSCAR"
print u"正在完成CONTCAR的转换........"
else:
if len(sys.argv) == 2:
print(u"正在将你的文件%s由分数坐标转为笛卡尔坐标" %sys.argv[1])
else:
print(u"正在将你的文件%s由分数坐标转为笛卡尔坐标,接下来请输入你要固定的原子层数！" %sys.argv[1])
script, file_to_be_converted = sys.argv[:2]
file_read = open(file_to_be_converted, 'r')
line = file_read.readlines()
a1 = float(line[2].split()[0])
a2 = float(line[3].split()[0])
a3 = float(line[4].split()[0])
b1 = float(line[2].split()[1])
b2 = float(line[3].split()[1])
b3 = float(line[4].split()[1])
z1 = float(line[2].split()[2])
z2 = float(line[3].split()[2])
z3 = float(line[4].split()[2])
if len(sys.argv) >=3 and line[8][0] == 'c' or line[8][0] == 'C' or line[7][0] == 'C' or line[7][0] == 'c':
a2 = a3 = b1 = b3 = z1 = z2 = 0
a1 = b2 = z3 = 1
num_atoms = sum([int(x) for x in line[6].split()])
x_cartesian = []
y_cartesian = []
z_cartesian = []
tf = []
start_num = 9 # Default: With Selected T T T, coordination starts from line 9
def determinelayers(z_cartesian):
seq = sorted(z_cartesian)
min = seq[0]
layerscount = {}
sets = [min]
for j in range(len(seq)):
if abs(seq[j]-min) >= yuzhi:
min = seq[j]
sets.append(min)
for i in range(1,len(sets)+1):
layerscount[i] = []
for k in range(len(z_cartesian)):
if abs(z_cartesian[k]-sets[i-1]) <= yuzhi:
layerscount[i].append(k)
return layerscount
def convert():
for i in range(start_num, num_atoms + start_num):
x_cartesian.append(float(line[i].split()[0]) * a1 + float(line[i].split()[1]) * a2 + float(line[i].split()[2]) * a3)
y_cartesian.append(float(line[i].split()[0]) * b1 + float(line[i].split()[1]) * b2 + float(line[i].split()[2]) * b3)
z_cartesian.append(float(line[i].split()[0]) * z1 + float(line[i].split()[1]) * z2 + float(line[i].split()[2]) * z3)
if len(line[i].split()) > 3: # if T T T exist, there are more than 3 elements in the list line[i].split()
tf.append((line[i].split()[3]))
else:
tf.append(' ') # if there is no T T T, use space instead.
layerscount =determinelayers(z_cartesian)
#print layerscount
if len(sys.argv) >=3:
fixedlayer = int(input("Found %d layers, choose how many layers to be fixed." %len(layerscount)))
for i in range(1,len(layerscount)+1):
if i <= fixedlayer:
for j in layerscount[i]:
tf[j] = " F "
else:
for k in layerscount[i]:
tf[k] = " T "
file_out = open(file_to_be_converted+'_C', 'w')
for i in range(0,7):
file_out.write(line[i].rstrip() + '\n') # first 7 lines are kept the same
if len(sys.argv) >=3 and not 'S' in line[7]:
file_out.write('Selective\n')
if 'S' in line[7]:
file_out.write(line[7].rstrip()+ '\n') # if T T T exists, write the Selective line
file_out.write('Cartesian' + '\n') # Coordination system is Cartesian now.
for i in range(0,len(x_cartesian)):
file_out.write("\t%+-3.10f %+-3.10f %+-3.10f %s %s %s\n"
%(x_cartesian[i], y_cartesian[i], z_cartesian[i], tf[i], tf[i], tf[i]))
file_out.close()
print '-----------------------------------------------------\n'
print 'POSCAR with Cartesian Coordiations is named as %s_C\n' %(file_to_be_converted)
print '-----------------------------------------------------\n'
if line[7][0] == 'S' or line[7][0] == 's': # # With Selected T T T, coordination starts from line 9
start_num = 9
if line[8][0] == 'D' or line[8][0] == 'd':
print """
This POSCAR has Direct Coordinations, Conversion is starting....
"""
convert()
elif line[8][0] == 'C' or line[8][0] == 'c':
if len(sys.argv) >=3:
convert()
print u"发现是笛卡尔坐标，只用来限制原子!"
else:
print "This POSCAR has Cartesian Coordinations! Process is aborted!"
else :
print """
----------------------------------------------------
Pay Attetion! There is no TTT in coordinations part!
----------------------------------------------------
"""
start_num = 8 # without Selected, No T T T , coordination starts from line 8
if line[7][0] == 'D' or line[7][0] == 'd':
print """
This POSCAR has Direct Coordinations, Contersion starts....
"""
convert()
elif line[7][0] == 'C' or line[7][0] == 'c':
if len(sys.argv) >=3:
convert()
print u"发现是笛卡尔坐标，只用来限制原子!"
else:
print "This POSCAR has Cartesian Coordinations! Process is aborted!"
file_read.close()