Merge pull request #96 from ZLI-afk/v1.2

V1.2.16

Author: kevinwenminion

apex/__init__.py

@@ -1,5 +1,5 @@
 import os
-__version__ = '1.2.15'
+__version__ = '1.2.17'
 LOCAL_PATH = os.getcwd()
 
 
@@ -27,9 +27,9 @@ def header():
     header_str += "  AAA           AAA   PPP           EEEEEEEEEE  XXX       XXX\n"
     header_str += "---------------------------------------------------------------\n"
     header_str += f"==>> Alloy Property EXplorer using simulations (v{__version__})\n"
-    header_str += "Please cite DOI: 10.48550/arXiv.2404.17330\n"
-    header_str += "Li et al, An extendable cloud-native alloy property explorer (2024).\n"
-    header_str += "See https://github.com/deepmodeling/APEX for more information.\n"
+    header_str += "Please cite DOI: 10.1038/s41524-025-01580-y\n"
+    header_str += "Li, Z., Wen, T., Zhang, Y. et al. APEX: an automated cloud-native material property explorer. npj Comput Mater 11, 88 (2025).\n"
+    header_str += "See https://doi.org/10.1038/s41524-025-01580-y for more information.\n"
     header_str += "---------------------------------------------------------------\n"
     header_str += "Checking input files..."
     print(header_str)

apex/core/calculator/ABACUS.py

@@ -159,9 +159,12 @@ def make_input_file(self, output_dir, task_type, task_param):
                     self.modify_input(incar, "calculation", "scf")
                 else:
                     raise RuntimeError("not supported calculation setting for ABACUS")
-
-            elif cal_type == "static":
+            elif cal_type == "static" and task_type != "phonon":
+                self.modify_input(incar, "calculation", "scf")
+            elif task_type == "phonon":
                 self.modify_input(incar, "calculation", "scf")
+                self.modify_input(incar, "cal_force", "1")
+                self.modify_input(incar, "cal_stress", "1")
 
             else:
                 raise RuntimeError("not supported calculation type for ABACUS")

apex/core/property/Interstitial.py

@@ -24,7 +24,6 @@
 
 upload_packages.append(__file__)
 
-PREDEFINED_LIST = ['bcc', 'fcc', 'hcp']
 TOL = 1e-5
 
 class Interstitial(Property):
@@ -41,6 +40,9 @@ def __init__(self, parameter, inter_param=None):
                 self.lattice_type = parameter["lattice_type"]
                 parameter["voronoi_param"] = parameter.get("voronoi_param", {})
                 self.voronoi_param = parameter["voronoi_param"]
+                parameter["special_list"] = parameter.get("special_list", ['bcc', 'fcc', 'hcp'])
+                self.special_list = parameter["special_list"]
+
             parameter["cal_type"] = parameter.get("cal_type", "relaxation")
             default_cal_setting = {
                 "relax_pos": True,
@@ -191,7 +193,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                 if not self.insert_ele:
                     self.insert_ele = [str(ii) for ii in set(ss.composition.elements)]
                 for ii in self.insert_ele:
-                    if self.structure_type in PREDEFINED_LIST:
+                    if self.structure_type in self.special_list:
                         # rotate and translate hcp structure to specific orientation for interstitial generation
                         if self.structure_type == 'hcp':
                             theta = -2 * np.pi / 3
@@ -278,7 +280,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                 os.chdir(self.path_to_work)
 
                 # create pre-defined special SIA structure for bcc fcc and hcp
-                if self.structure_type in PREDEFINED_LIST:
+                if self.structure_type in self.special_list:
                     self.task_list = []
                     if not os.path.isfile("task.000000/POSCAR"):
                         raise RuntimeError("need task.000000 structure as reference")

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="apex-flow",
-    version="1.2.15",
+    version="1.2.17",
     author="Zhuoyuan Li, Tongqi Wen",
     author_email="zhuoyli@outlook.com",
     description="Alloy Properties EXplorer using simulations",