def modify_vasp_incar(cal_loc,
new_tags={},
remove_tags=[],
rename_old_incar=True):
"""
add new tags and remove obsolete tags in incar.
input arguments:
- cal_loc (str): the location of INCAR to be modified, <--required
- new_tags (dict): new tags to be added,
- remove_tags (list): incar tags that will be removed
- rename_old_incar (bool or str): if rename_old_incar is True, rename the old INCAR as INCAR_0, INCAR_1, INCAR_2, etc.
if rename_old_incar is False, the old INCAR will be overwritten by new INCAR.
if rename_old_incar is a string, rename the old INCAR as the string.
Default: True
return the valid INCAR dictionary if no modification is made.
"""
new_tags = {key.upper(): value for key, value in new_tags.items()}
remove_tags = [tag.upper() for tag in remove_tags]
new_incar_tag_name = new_tags.keys()
for tag in remove_tags:
if tag in new_incar_tag_name:
#import pprint
print("\n\n**directory: {}".format(cal_loc))
print("**new_tags:")
pprint.pprint(new_tags)
print("**remove_tags:")
pprint.pprint(remove_tags)
Error_info = "***You are gonna remove an INCAR tag {} via remove_tags.".format(
tag)
Error_info += "This contradicts the simultaneous attempt to set {} via new_tags**\n\n".format(
tag)
print(Error_info)
raise Exception("See the error information above.")
incar_dict = {}
with open(os.path.join(cal_loc, "INCAR"), "r") as incar_f:
lines = []
for line in incar_f:
pairs = line.strip().split("#")[0]
pairs = pairs.strip().split("!")[0]
if pairs.strip() == "":
continue
assert pairs.count(
"="
) == 1, "We ask you to set only one tag per line in INCAR, but there are more than one.\nwhere: {}\nline: {}".format(
cal_loc, line)
pairs = [tag_or_value.strip() for tag_or_value in pairs.split("=")]
incar_dict[pairs[0].upper()] = pairs[1]
incar_dict.update(new_tags)
for remove_tag in remove_tags:
if remove_tag in incar_dict.keys():
del incar_dict[remove_tag]
if new_tags == {} and remove_tags == []:
return incar_dict
if isinstance(rename_old_incar, bool):
if rename_old_incar:
rename_old_incar = find_next_name(cal_loc=cal_loc,
orig_name="INCAR")["next_name"]
decorated_os_rename(loc=cal_loc,
old_filename="INCAR",
new_filename=rename_old_incar)
#shutil.copyfile(os.path.join(cal_loc, "INCAR"), os.path.join(cal_loc, rename_old_incar))
elif isinstance(rename_old_incar, str):
decorated_os_rename(loc=cal_loc,
old_filename="INCAR",
new_filename=rename_old_incar)
#shutil.copyfile(os.path.join(cal_loc, "INCAR"), os.path.join(cal_loc, rename_old_incar))
else:
raise Exception(
"input argument rename_old_incar of modify_vasp_incar must be either bool or str."
)
with open(os.path.join(cal_loc, "INCAR"), "w") as incar_f:
for tag, value in sorted(incar_dict.items(),
key=lambda key_value_pair: key_value_pair[0]):
incar_f.write("{} = {}\n".format(tag, value))
def modify_vasp_incar0(cal_loc,
new_tags={},
comment_tags=[],
remove_tags=[],
rename_old_incar=True):
"""
add new tags and comment obsolete tags in incar.
input arguments:
- cal_loc (str): the location of INCAR to be modified, <--required
- new_tags (dict): new tags to be added,
- comment_tags (list): tags that will be obsolete by commenting them with "#"
- remove_tags (list): incar tags that will be removed
- rename_old_incar (bool or str): if rename_old_incar is True, rename the old INCAR as INCAR_0, INCAR_1, INCAR_2, etc.
if rename_old_incar is False, the old INCAR will be overwritten by new INCAR.
if rename_old_incar is a string, rename the old INCAR as the string.
Default: True
return the valid INCAR dictionary if no modification is made.
"""
new_tags = {key.upper(): value for key, value in new_tags.items()}
comment_tags = [tag.upper() for tag in comment_tags]
remove_tags = [tag.upper() for tag in remove_tags]
new_incar_tag_name = new_tags.keys()
for tag in comment_tags + remove_tags:
if tag in new_incar_tag_name:
#import pprint
print("\n\n**directory: {}".format(cal_loc))
print("**new_tags:")
pprint.pprint(new_tags)
print("**comment_tags:")
pprint.pprint(comment_tags)
print("**remove_tags:")
pprint.pprint(remove_tags)
Error_info = "***You are gonna comment of remove an INCAR tag {} via comment_tags/remove_tags.".format(
tag)
Error_info += "This contradicts the simultaneous attempt to set {} via new_tags**\n\n".format(
tag)
print(Error_info)
raise Exception("See the error information above.")
with open(os.path.join(cal_loc, "INCAR"), "r") as incar_f:
lines = []
for line in incar_f:
if line.strip() == "":
continue
pairs = line.strip().split("#")[0]
pairs = pairs.strip().split("!")[0]
#print(pairs, line)
if "#" in line:
comments = "#" + "#".join(line.strip().split("#")[1:])
elif "!" in line:
comments = "#" + "!".join(line.strip().split("!")[1:])
else:
comments = ""
for pair in [
pair.strip() for pair in pairs.split(";") if pair.strip()
]:
lines.append(pair)
if len(comments.strip()) > 1:
lines.append(comments)
incar = []
for line in lines:
if line.startswith("#"):
incar.append(line)
else:
#print(line)
key, value = line.split("=")
key = key.strip().upper()
value = value.strip()
if key in remove_tags:
continue
elif key in comment_tags:
incar.append("#" + line)
else:
incar.append([key, value])
valid_tag_ind_dict = {}
for line_ind, line in enumerate(incar):
if isinstance(line, list):
valid_tag_ind_dict[line[0]] = line_ind
for key, value in new_tags.items():
if key in valid_tag_ind_dict.keys():
incar[valid_tag_ind_dict[key]][1] = value
else:
incar.append([key, value])
#import pprint
#pprint.pprint(incar)
if new_tags == {} and comment_tags == [] and remove_tags == []:
return {item[0]: item[1] for item in incar if isinstance(item, list)}
if isinstance(rename_old_incar, bool):
if rename_old_incar:
rename_old_incar = find_next_name(cal_loc=cal_loc,
orig_name="INCAR")["next_name"]
decorated_os_rename(loc=cal_loc,
old_filename="INCAR",
new_filename=rename_old_incar)
#shutil.copyfile(os.path.join(cal_loc, "INCAR"), os.path.join(cal_loc, rename_old_incar))
elif isinstance(rename_old_incar, str):
decorated_os_rename(loc=cal_loc,
old_filename="INCAR",
new_filename=rename_old_incar)
#shutil.copyfile(os.path.join(cal_loc, "INCAR"), os.path.join(cal_loc, rename_old_incar))
else:
raise Exception(
"input argument rename_old_incar of modify_vasp_incar must be either bool or str."
)
with open(os.path.join(cal_loc, "INCAR"), "w") as incar_f:
for line in incar:
if isinstance(line, list):
incar_f.write("{} = {}\n".format(line[0], line[1]))
elif isinstance(line, str):
incar_f.write(line + "\n")
def modify_vasp_kpoints_for_2D(cal_loc,
kpoints_type,
denser_kpoints=1,
rename_old_kpoints=True,
tolerance=1.0e-5):
"""
modify KPOINTS at cal_loc.
input arguments:
- cal_loc (str): the location of the calculation.
- mode (str): 'MPRelaxSet', 'MPStaticSet', 'MPNonSCFSet_line', 'MPNonSCFSet_uniform', 'automatic'
- 'MPRelaxSet': pymatgen.io.vasp.sets.MPRelaxSet generates KPOINTS.
- 'MPStaticSet': pymatgen.io.vasp.sets.MPStaticSet generates KPOINTS.
- 'MPNonSCFSet_uniform': pymatgen.io.vasp.sets.MPNonSCFSet generates KPOINTS in the uniform mode for DOS
- 'MPNonSCFSet_line': pymatgen.io.vasp.sets.MPNonSCFSet generates KPOINTS in the line mode for band str
- 'automatic': This option indicates that KPOINTS is automatically generated
based on (gamma-centered) Monkhorst-Pack Scheme <--> 'MPRelaxSet', 'MPStaticSet'
- 'Line-mode': Since function Write_line_mode_KPOINTS can write KPOINTS for either 3D or 2D materials, file
KPOINTS remains unchanged.
- denser_kpoints (float): this tag is inactive at kpoints_type='MPNonSCFSet_uniform' or 'MPNonSCFSet_line'. Default: 1
- rename_old_kpoints (bool or str):
- if it is True, rename the old KPOINTS like KPOINTS_0, KPOINTS_1, KPINTS_2, ...
- if it is False, the old KPOINTS will be overwritten
- if it a string, the string is the new name of the old KPOINTS
Default: True
- tolerance (float): if abs(k_z) < tolerance for uniform and line modes,
we think this kpoint is valid; otherwise remove it.
Default: 1.0e-5
if old KPOINTS is saved, return the new name of the old KPOINTS.
"""
if kpoints_type.strip() not in [
"automatic", 'MPRelaxSet', 'MPStaticSet', 'MPNonSCFSet_line',
'MPNonSCFSet_uniform', "Line-mode"
]:
print(
"Error: for func modify_vasp_kpoints_for_2D, the input argument kpoints_tag must be on the those below:"
)
print(
"'MPRelaxSet', 'MPStaticSet', 'MPNonSCFSet_line', 'MPNonSCFSet_uniform', 'automatic'"
)
raise Exception("See above for the error information")
if kpoints_type == "Line-mode":
return True
with open(os.path.join(cal_loc, "KPOINTS"), "r") as f:
kpoints = [line.strip() for line in f if line.strip()]
if kpoints_type in ["automatic", 'MPRelaxSet', 'MPStaticSet']:
assert "gam" in kpoints[2].lower() or "mon" in kpoints[2].lower(
), "Error: fail to modify KPOINTS generated by pymatgen at {}".format(
cal_loc)
nk_list = [int(int(k) * denser_kpoints) for k in kpoints[3].split()]
if nk_list[2] != 1:
nk_list[2] = 1
kpoints[3] = "{} {} {}".format(*nk_list)
else:
assert "reci" in kpoints[2].lower(
), "Error: fail to modify KPOINTS generated by pymatgen in the uniform/line mode at {}".format(
cal_loc)
new_kpoints = []
for kpoint in kpoints[3:]:
k = kpoint.split()
k = [float(k[0]), float(k[1]), float(k[2]), int(k[3])]
if abs(k[2]) < tolerance:
new_kpoints.append(kpoint)
kpoints = kpoints[:3] + new_kpoints
kpoints[1] = str(len(new_kpoints))
if isinstance(rename_old_kpoints, bool):
if rename_old_kpoints:
new_name = find_next_name(cal_loc=cal_loc,
orig_name="KPOINTS")["next_name"]
shutil.move(os.path.join(cal_loc, "KPOINTS"),
os.path.join(cal_loc, new_name))
elif isinstance(rename_old_kpoints, str):
shutil.move(os.path.join(cal_loc, "KPOINTS"),
os.path.join(cal_loc, rename_old_kpoints))
else:
raise Exception(
"rename_old_kpoints must be either bool or str for func modify_vasp_kpoints_for_2D"
)
with open(os.path.join(cal_loc, "KPOINTS"), "w") as f:
for line in kpoints:
f.write(line + "\n")
if rename_old_kpoints == True:
return new_name
elif isinstance(rename_old_kpoints, str):
return rename_old_kpoints
def modify_vasp_kpoints_for_2D(self, rename_old_kpoints=True, tolerance=1.0e-5):
"""
modify KPOINTS properly for 2D structures.
support kpoints_type for KPOINTS modifications: 'MPRelaxSet', 'MPStaticSet', 'MPNonSCFSet_line', 'MPNonSCFSet_uniform', 'automatic'
- 'MPRelaxSet': pymatgen.io.vasp.sets.MPRelaxSet generates KPOINTS.
- 'MPStaticSet': pymatgen.io.vasp.sets.MPStaticSet generates KPOINTS.
- 'MPNonSCFSet_uniform': pymatgen.io.vasp.sets.MPNonSCFSet generates KPOINTS in the uniform mode for DOS
- 'MPNonSCFSet_line': pymatgen.io.vasp.sets.MPNonSCFSet generates KPOINTS in the line mode for band str
input arguments:
- rename_old_kpoints (bool or str):
- if it is True, rename the old KPOINTS like KPOINTS_0, KPOINTS_1, KPINTS_2, ...
- if it is False, the old KPOINTS will be overwritten
- if it a string, the string is the new name of the old KPOINTS
Default: True
- tolerance (float): if abs(k_z) < tolerance for uniform and line modes,
we think this kpoint is valid; otherwise remove it.
Default: 1.0e-5
if old KPOINTS is saved, return the new name of the old KPOINTS.
"""
kpoints_type = self.current_firework["kpoints_type"]
if kpoints_type.strip() not in ['MPRelaxSet', 'MPStaticSet', 'MPNonSCFSet_line', 'MPNonSCFSet_uniform']:
print("Error: for func modify_vasp_kpoints_for_2D, the input argument kpoints_tag must be on the those below:")
print("'MPRelaxSet', 'MPStaticSet', 'MPNonSCFSet_line', 'MPNonSCFSet_uniform'")
raise Exception("See above for the error information")
with open(os.path.join(self.cal_loc, "KPOINTS"), "r") as f:
kpoints = [line.strip() for line in f if line.strip()]
if kpoints_type in ['MPRelaxSet', 'MPStaticSet']:
assert "gam" in kpoints[2].lower() or "mon" in kpoints[2].lower(), "Error: fail to modify KPOINTS generated by pymatgen at {}".format(cal_loc)
nk_list = [int(k) for k in kpoints[3].split()]
if nk_list[2] != 1:
nk_list[2] = 1
kpoints[3] = "{} {} {}".format(*nk_list)
else:
assert "reci" in kpoints[2].lower(), "Error: fail to modify KPOINTS generated by pymatgen in the uniform/line mode at {}".format(cal_loc)
new_kpoints = []
for kpoint in kpoints[3:]:
k = kpoint.split()
k = [float(k[0]), float(k[1]), float(k[2]), int(k[3])]
if abs(k[2]) < tolerance:
new_kpoints.append(kpoint)
kpoints = kpoints[:3] + new_kpoints
kpoints[1] = str(len(new_kpoints))
if isinstance(rename_old_kpoints, bool):
if rename_old_kpoints:
new_name = find_next_name(cal_loc=self.cal_loc, orig_name="KPOINTS")["next_name"]
shutil.move(os.path.join(self.cal_loc, "KPOINTS"), os.path.join(self.cal_loc, new_name))
elif isinstance(rename_old_kpoints, str):
shutil.move(os.path.join(self.cal_loc, "KPOINTS"), os.path.join(self.cal_loc, rename_old_kpoints))
else:
raise Exception("rename_old_kpoints must be either bool or str for func modify_vasp_kpoints_for_2D")
with open(os.path.join(self.cal_loc, "KPOINTS"), "w") as f:
for line in kpoints:
f.write(line+"\n")
if rename_old_kpoints == True:
return new_name
elif isinstance(rename_old_kpoints, str):
return rename_old_kpoints
def modify_vasp_incar(cal_loc,
new_tags={},
comment_tags=[],
remove_tags=[],
rename_old_incar=True):
"""
add new tags and comment obsolete tags in incar.
input arguments:
- cal_loc (str): the location of INCAR to be modified, <--required
- new_tags (dict): new tags to be added,
- comment_tags (list): tags that will be obsolete by commenting them with "#"
- remove_tags (list): incar tags that will be removed
- rename_old_incar (bool or str): if rename_old_incar is True, rename the old INCAR as INCAR_0, INCAR_1, INCAR_2, etc.
if rename_old_incar is False, the old INCAR will be overwritten by new INCAR.
if rename_old_incar is a string, rename the old INCAR as the string.
Default: True
return the modified INCAR dictionary.
"""
new_tags = {key.upper(): value for key, value in new_tags.items()}
comment_tags = [tag.upper() for tag in comment_tags]
remove_tags = [tag.upper() for tag in remove_tags]
Valid_tags, Commented_tags = {}, {}
Ordered_tags = []
with open(os.path.join(cal_loc, "INCAR"), "r") as incar:
for line in incar:
items = [item.strip() for item in line.strip().split("=")]
if len(items) >= 2:
if items[0].startswith("#"):
tag = items[0].strip("#").upper().strip()
if tag in remove_tags:
continue
Commented_tags[tag] = items[1]
Ordered_tags.append(tag)
else:
tag = items[0].upper()
if tag in remove_tags:
continue
Valid_tags[items[0].upper()] = items[1]
Ordered_tags.append(tag)
for new_tag, value in new_tags.items():
Valid_tags[new_tag] = value
if new_tag not in Ordered_tags:
Ordered_tags.append(new_tag)
for comment_tag in comment_tags:
if comment_tag in Valid_tags.keys():
Commented_tags[comment_tag] = Valid_tags[comment_tag]
del Valid_tags[comment_tag]
if new_tags == {} and comment_tags == [] and remove_tags == []:
return Valid_tags
if isinstance(rename_old_incar, bool):
if rename_old_incar:
rename_old_incar = find_next_name(cal_loc=cal_loc,
orig_name="INCAR")["next_name"]
shutil.copyfile(os.path.join(cal_loc, "INCAR"),
os.path.join(cal_loc, rename_old_incar))
elif isinstance(rename_old_incar, str):
shutil.copyfile(os.path.join(cal_loc, "INCAR"),
os.path.join(cal_loc, rename_old_incar))
else:
raise Exception(
"input argument rename_old_incar of modify_vasp_incar must be either bool or str."
)
with open(os.path.join(cal_loc, "INCAR"), "w") as incar:
for tag in Ordered_tags:
if tag in Valid_tags.keys():
incar.write("{} = {}\n".format(tag, Valid_tags[tag]))
else:
incar.write("#{} = {}\n".format(tag, Commented_tags[tag]))