POSCAR
我们以CsPbCl3结构为例，在Vesta中查看并选取需要固定的原子z坐标范围（0~0.16）。
结构对应的POSCAR，
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CsPbCl3
1.0
33.6300010681 0.0000000000 0.0000000000
0.0000000000 33.6300010681 0.0000000000
0.0000000000 0.0000000000 58.0250015259
Cl Cs Pb
576 216 180
Direct
0.000000000 0.083329998 0.094520003
0.000000000 0.083329998 0.191110000
0.000000000 0.083329998 0.287710011
0.000000000 0.083329998 0.384310007
0.000000000 0.083329998 0.480899990
0.083329998 0.000000000 0.094520003
...
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运行脚本
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import os
os.chdir(os.path.split(os.path.realpath(__file__))[0])
print('copyright by Zhaosheng Zhang (misaraty@163.com)\n' + 'last update: 2025-07-22\n')
# ======== Parameter Settings ========
zmin = 0.0 # Minimum fractional z-coordinate to fix
zmax = 0.16 # Maximum fractional z-coordinate to fix
input_path = "POSCAR"
output_path = "POSCAR_sd"
# ====================================
def normalise_frac(z):
"""Normalize a fractional coordinate to the range [0, 1)."""
while z < 0.0:
z += 1.0
while z >= 1.0:
z -= 1.0
return z
def process_poscar(lines, zmin, zmax):
"""
Process POSCAR assuming:
- No 'Selective Dynamics' present
- Line 7 is 'Direct'
- Coordinates start from line 8
"""
header = lines[:8]
natoms_list = list(map(int, header[6].split()))
total_atoms = sum(natoms_list)
coord_mode_idx = 7 # Line index of 'Direct'
coord_start_idx = 8 # Coordinates start from line 8 (index 8)
coord_end_idx = coord_start_idx + total_atoms
coords = lines[coord_start_idx:coord_end_idx]
processed = []
count_fixed = 0
for line in coords:
parts = line.strip().split()
if len(parts) < 3:
continue
try:
z = normalise_frac(float(parts[2]))
except ValueError:
continue
if zmin <= z <= zmax:
tag = ["F", "F", "F"]
count_fixed += 1
else:
tag = ["T", "T", "T"]
# Preserve original formatting
new_line = f"{' '.join(parts[:3])} {tag[0]} {tag[1]} {tag[2]}\n"
processed.append(new_line)
# Compose output lines
new_lines = header[:7]
new_lines.append("Selective Dynamics\n")
new_lines.append(lines[coord_mode_idx]) # 'Direct'
new_lines.extend(processed)
if coord_end_idx < len(lines):
new_lines.extend(lines[coord_end_idx:]) # Keep comments or blank lines
# Print stats
percent = 100.0 * count_fixed / total_atoms
print(f"✅ Process completed.")
print(f"Total atoms: {total_atoms}")
print(f"Fixed atoms: {count_fixed}")
print(f"Fixed fraction: {percent:.2f}%")
return new_lines
# === Main execution ===
with open(input_path, 'r') as f:
lines = f.readlines()
new_lines = process_poscar(lines, zmin, zmax)
with open(output_path, 'w') as f:
f.writelines(new_lines)
print(f"Modified POSCAR saved to: {output_path}")
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注意
运行前需要修改脚本中的zmin = 0.0和zmax = 0.16参数。
修改后POSCAR
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CsPbCl3
1.0
33.6300010681 0.0000000000 0.0000000000
0.0000000000 33.6300010681 0.0000000000
0.0000000000 0.0000000000 58.0250015259
Cl Cs Pb
576 216 180
Selective Dynamics
Direct
0.000000000 0.083329998 0.094520003 F F F
0.000000000 0.083329998 0.191110000 T T T
0.000000000 0.083329998 0.287710011 T T T
0.000000000 0.083329998 0.384310007 T T T
0.000000000 0.083329998 0.480899990 T T T
0.083329998 0.000000000 0.094520003 F F F
...
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