def copy_potcar(psp_dir, psp_uncompress, aci_name_map = {"USPP_GAA": "POT_GGA_US_PW91"}):
flag_copy = False
for potcar_path in psp_dir:
if not os.path.exists(potcar_path):
continue
file_str = os.listdir(potcar_path)
for file_i in file_str:
dst_path_name = parse_psp_name(file_i)
if not (dst_path_name or file_i in aci_name_map):
continue
if file_i in aci_name_map:
dst_path_name = aci_name_map[file_i]
psp_old = os.path.join(potcar_path, file_i)
psp_new = os.path.join(psp_uncompress, dst_path_name)
if os.path.isdir(psp_old):
if os.path.exists(psp_new):
warnings.warn("Potential({}) exists, and current potential will over write it.".format(psp_new))
shutil.rmtree(psp_new)
flag_copy = True
shutil.copytree(psp_old, psp_new)
else:
creat_folders(psp_new)
if file_i.endswith(".tar.gz") or file_i.endswith(".tgz"):
os.system("tar -zxvf " + psp_old + " -C " + psp_new)
flag_copy = True
elif file_i.endswith(".tar"):
os.system("tar -xvf " + psp_old + " -C " + psp_new)
flag_copy = True
else:
warnings.warn("Current file ({}) is not supported. The pseudopotential should be uncompressed \
or compressed file endi with .tar.gz or .tgz or .tar".format(file_i))
if not flag_copy:
warnings.warn("No supported pseudopotential was found in : {}.".format(", ".join(psp_dir)) + \
"The name rule ref. https://github.com/PhasesResearchLab/dfttk/blob/master/docs/Configuration.md")
return flag_copy
def config_atomate(path_to_store_config=".",
config_folder="config",
queue_script="vaspjob.pbs",
queue_type="pbs",
vasp_cmd_flag="vasp_std"):
"""
Configuration for atomate
Parameter
path_to_store_config: str (path-like)
The path to store the configuration files. Default: .
config_folder: str (path-like)
The path of config files. Default: config
queue_script: str (filename-like)
The submitting script for the queue system. Default: vaspjob.pbs
queue_type: str
Th type of queue system. Now, only support pbs. Default: pbs
vasp_cmd_flag: str
The flag of vasp_cmd to distinguish the vasp_cmd with other commands in the queue script
Return
None
"""
config_file = get_config_file(config_folder=config_folder,
queue_script=queue_script)
creat_folders(path_to_store_config + "/config")
creat_folders(path_to_store_config + "/logs")
if config_file[queue_script]:
#If the pbs file exists
param_dict = parse_queue_script(template=config_file[queue_script],
queue_type=queue_type,
vasp_cmd_flag=vasp_cmd_flag)
else:
param_dict = {}
param_dict["path_to_store_config"] = path_to_store_config
required_file = ["db.json", "my_launchpad.yaml"]
option_file = ["FW_config.yaml", "my_fworker.yaml", "my_qadapter.yaml"]
FileModule = {
"FW_config.yaml": "ConfigFW",
"my_fworker.yaml": "ConfigFworker",
"my_qadapter.yaml": "ConfigQadapter",
"db.json": "ConfigDb",
"my_launchpad.yaml": "ConfigLaunchFile"
}
files = required_file + option_file
for file in files:
if file in option_file:
eval(FileModule[file] + "(**param_dict).write_file()")
if config_file[file]:
update_configfile(
os.path.join(param_dict["path_to_store_config"],
"config/" + file), config_file[file])
#Add environment var
FW_CONFIG_FILE_VAL = os.path.join(path_to_store_config,
"config/FW_config.yaml")
add_path_var(force_override=True, FW_CONFIG_FILE=FW_CONFIG_FILE_VAL)
def handle_potcar_gz(psp_dir=None,
path_to_store_psp="psp_pymatgen",
aci=True,
vasp_cmd="vasp_std",
template="vaspjob.pbs",
queue_type="pbs"):
"""
Compress and move the pseudopotential to a specified path(path_to_store_psp)
(The compress is done by running "pmg config -p psp_dir path_to_store_psp" command)
Parameter
psp_dir: str (path-like)
The origial path containing psp. Both original and uncompressed are ok.
The name of the compressed file or the sub-folder containing psps must be in the following list
["potpaw_PBE", "POT_GGA_PAW_PBE","potpaw_PBE_52", "POT_GGA_PAW_PBE_52","potpaw_PBE_54", "POT_GGA_PAW_PBE_54",
"potpaw_PBE.52", "POT_GGA_PAW_PBE_52","potpaw_PBE.54", "POT_GGA_PAW_PBE_54","potpaw_LDA", "POT_LDA_PAW",
"potpaw_LDA.52", "POT_LDA_PAW_52","potpaw_LDA.54", "POT_LDA_PAW_54","potpaw_LDA_52", "POT_LDA_PAW_52",
"potpaw_LDA_54", "POT_LDA_PAW_54","potUSPP_LDA", "POT_LDA_US","potpaw_GGA", "POT_GGA_PAW_PW91",
"potUSPP_GGA", "POT_GGA_US_PW91"]
For more details, Ref:https://pymatgen.org/installation.html#potcar-setup
The example of the structure of the psp_dir:
e.g. psp_dir
├── potpaw_LDA.54.tar.gz
└── potpaw_PBE.54.tar.gz
or: psp_dir
├── potpaw_LDA_54
│ ├── Ac
│ ├── Ag
│ └── ...
├── potpaw_PBE_54
│ ├── Ac
│ ├── Ag
│ └── ...
└── ...
path_to_store_psp: str (path-like)
The destination to store the compressed psp. Default: psp_pymatgen
Return
None
"""
def copy_potcar(psp_dir,
psp_uncompress,
aci_name_map={"USPP_GAA": "POT_GGA_US_PW91"}):
flag_copy = False
for potcar_path in psp_dir:
if not os.path.exists(potcar_path):
continue
file_str = os.listdir(potcar_path)
for file_i in file_str:
dst_path_name = parse_psp_name(file_i)
if not (dst_path_name or file_i in aci_name_map):
continue
if file_i in aci_name_map:
dst_path_name = aci_name_map[file_i]
psp_old = os.path.join(potcar_path, file_i)
psp_new = os.path.join(psp_uncompress, dst_path_name)
if os.path.isdir(psp_old):
if os.path.exists(psp_new):
warnings.warn(
"Potential({}) exists, and current potential will over write it."
.format(psp_new))
shutil.rmtree(psp_new)
flag_copy = True
shutil.copytree(psp_old, psp_new)
else:
creat_folders(psp_new)
if file_i.endswith(".tar.gz") or file_i.endswith(".tgz"):
os.system("tar -zxvf " + psp_old + " -C " + psp_new)
flag_copy = True
elif file_i.endswith(".tar"):
os.system("tar -xvf " + psp_old + " -C " + psp_new)
flag_copy = True
else:
warnings.warn(
"Current file ({}) is not supported. The pseudopotential should be uncompressed \
or compressed file endi with .tar.gz or .tgz or .tar"
.format(file_i))
if not flag_copy:
warnings.warn("No supported pseudopotential was found in : {}.".format(", ".join(psp_dir)) + \
"The name rule ref. https://github.com/PhasesResearchLab/dfttk/blob/master/docs/Configuration.md")
return flag_copy
if not psp_dir:
psp_dir = ["pp", "pps", "psp", "potential", "pseudopotential"]
if isinstance(psp_dir, str):
psp_dir = []
aci_name_map = {"USPP_GAA": "POT_GGA_US_PW91"} #A typo in ACI cluster
psp_uncompress = get_abspath("./psp_uncompress")
creat_folders(psp_uncompress)
flag_aci = False
if aci:
#For ACI at PSU only
aci_pp_path = find_psppath_in_cluster(vasp_cmd=vasp_cmd,
psp_pathnames=psp_dir,
template=template,
queue_type=queue_type)
flag_aci = copy_potcar(aci_pp_path,
psp_uncompress,
aci_name_map=aci_name_map)
# file_str is not abspath, is relative path
flag_user = copy_potcar(psp_dir, psp_uncompress, aci_name_map=aci_name_map)
if not (flag_aci or flag_user):
raise FileNotFoundError(
"No pseudopotential was found, plese provide correct pseudopotential \
and use -psp parameter to point to correct position")
# config the POTCAR
os.system("pmg config -p " + psp_uncompress + " " + path_to_store_psp)
# Remove the uncompress folder
try:
shutil.rmtree(psp_uncompress)
except:
os.system("chmod +w " + os.path.join(psp_uncompress, "*/*"))
shutil.rmtree(psp_uncompress)