Merge pull request #42 from ZLI-afk/v1.2

V1.2 to main

.github/workflows/mirror_gitee.yml

@@ -0,0 +1,13 @@
+name: Mirror to Gitee Repository
+
+on: [ push, delete, create ]
+
+# Ensures that only one mirror task will run at a time.
+concurrency:
+  group: git-mirror
+
+jobs:
+  git-mirror:
+    uses: deepmodeling/workflows/.github/workflows/mirror_gitee.yml@main
+    secrets:
+      SYNC_GITEE_PRIVATE_KEY: ${{ secrets.SYNC_GITEE_PRIVATE_KEY }}

apex/__init__.py

@@ -1,5 +1,5 @@
 import os
-__version__ = '1.2.0'
+__version__ = '1.2.9'
 LOCAL_PATH = os.getcwd()
 
 

apex/config.py

@@ -29,6 +29,8 @@ class Config:
     email: str = None
     password: str = None
     program_id: int = None
+    job_type: str = "container"
+    platform: str = "ali"
 
     # DispachterExecutor config
     dispatcher_config: dict = None
@@ -57,6 +59,7 @@ class Config:
     group_size: int = None
     pool_size: int = None
     upload_python_packages: list = field(default_factory=list)
+    exclude_upload_files: list = field(default_factory=list)
     lammps_image_name: str = None
     lammps_run_command: str = None
     vasp_image_name: str = None
@@ -108,8 +111,8 @@ def __post_init__(self):
                     "password": self.password,
                     "program_id": self.program_id,
                     "input_data": {
-                        "job_type": "container",
-                        "platform": "ali",
+                        "job_type": self.job_type,
+                        "platform": self.platform,
                         "scass_type": self.scass_type,
                     },
                 },
@@ -280,7 +283,7 @@ def get_executor(
             self,
             dispatcher_config: dict
     ) -> DispatcherExecutor:
-        if not (self.context_type or self.machine):
+        if not (self.context_type or self.machine or self.dispatcher_config):
             executor = None
         else:
             # get arguments for instantiation of the DispatcherExecutor

apex/core/calculator/ABACUS.py

@@ -148,6 +148,9 @@ def make_input_file(self, output_dir, task_type, task_param):
                 elif [relax_pos, relax_shape, relax_vol] == [False, True, True]:
                     self.modify_input(incar, "calculation", "cell-relax")
                     fix_atom = [True, True, True]
+                elif [relax_pos, relax_shape, relax_vol] == [True, False, True]:
+                    self.modify_input(incar, "calculation", "cell-relax")
+                    self.modify_input(incar, "fixed_axes", "shape")
                 elif [relax_pos, relax_shape, relax_vol] == [False, False, True]:
                     raise RuntimeError(
                         "relax volume but fix shape is not supported for ABACUS"

apex/core/calculator/Lammps.py

@@ -22,15 +22,15 @@
 upload_packages.append(__file__)
 
 # LAMMPS_INTER_TYPE = ['deepmd', 'eam_alloy', 'meam', 'eam_fs', 'meam_spline', 'snap', 'gap', 'rann', 'mace']
-
+MULTI_MODELS_INTER_TYPE = ["meam", "snap", "gap"]
 
 class Lammps(Task):
     def __init__(self, inter_parameter, path_to_poscar):
         self.inter = inter_parameter
         self.inter_type = inter_parameter["type"]
         self.type_map = inter_parameter["type_map"]
         self.in_lammps = inter_parameter.get("in_lammps", "auto")
-        if self.inter_type in ["meam", "snap"]:
+        if self.inter_type in MULTI_MODELS_INTER_TYPE:
             self.model = list(map(os.path.abspath, inter_parameter["model"]))
         else:
             self.model = os.path.abspath(inter_parameter["model"])
@@ -76,6 +76,16 @@ def set_model_param(self):
                 "param_type": self.type_map,
                 "deepmd_version": deepmd_version,
             }
+        elif self.inter_type == "gap":
+            model_name = list(map(os.path.basename, self.model))
+            self.model_param = {
+                "type": self.inter_type,
+                "model_name": model_name,
+                "param_type": self.type_map,
+                "init_string": self.inter.get("init_string", None),
+                "atomic_num_list": self.inter.get("atomic_num_list", None),
+                "deepmd_version": deepmd_version,
+            }
         else:
             model_name = os.path.basename(self.model)
             self.model_param = {
@@ -101,10 +111,10 @@ def symlink_force(self, target, link_name):
 
     def make_potential_files(self, output_dir):
         parent_dir = os.path.join(output_dir, "../../")
-        if self.inter_type in ["meam", "snap"]:
-            model_lib, model_file = map(os.path.basename, self.model[:2])
-            targets = [self.model[0], self.model[1]]
-            link_names = [model_lib, model_file]
+        if self.inter_type in MULTI_MODELS_INTER_TYPE:
+            model_file = map(os.path.basename, self.model)
+            targets = self.model
+            link_names = list(model_file)
         else:
             model_file = os.path.basename(self.model)
             targets = [self.model]
@@ -516,19 +526,19 @@ def _prepare_result_dict(self, atom_numbs, type_map_list, type_list, box, coord,
         return result_dict
 
     def forward_files(self, property_type="relaxation"):
-        if self.inter_type in ["meam", "snap"]:
+        if self.inter_type in MULTI_MODELS_INTER_TYPE:
             return ["conf.lmp", "in.lammps"] + list(map(os.path.basename, self.model))
         else:
             return ["conf.lmp", "in.lammps", os.path.basename(self.model)]
 
     def forward_common_files(self, property_type="relaxation"):
         if property_type not in ["eos"]:
-            if self.inter_type in ["meam", "snap"]:
+            if self.inter_type in MULTI_MODELS_INTER_TYPE:
                 return ["in.lammps"] + list(map(os.path.basename, self.model))
             else:
                 return ["in.lammps", os.path.basename(self.model)]
         else:
-            if self.inter_type in ["meam", "snap"]:
+            if self.inter_type in MULTI_MODELS_INTER_TYPE:
                 return list(map(os.path.basename, self.model))
             else:
                 return [os.path.basename(self.model)]

apex/core/calculator/VASP.py

@@ -78,8 +78,9 @@ def make_input_file(self, output_dir, task_type, task_param):
 
         # revise INCAR based on the INCAR provided in the "interaction"
         else:
+            approach = None
             if prop_type == "phonon":
-                approach = task_param.get("approach", "linear")
+                approach = task_param.get("approach")
                 logging.info(f"No specification of INCAR for {prop_type} calculation, will auto-generate")
                 if approach == "linear":
                     incar = incar_upper(Incar.from_str(
@@ -131,14 +132,15 @@ def make_input_file(self, output_dir, task_type, task_param):
                     )
                     incar["ISIF"] = isif
 
-            elif cal_type == "static":
+            elif cal_type == "static" and not approach == "linear":
                 nsw = 0
                 if not ("NSW" in incar and incar.get("NSW") == nsw):
                     logging.info(
                         "%s setting NSW to %d" % (self.make_input_file.__name__, nsw)
                     )
                     incar["NSW"] = nsw
-
+            elif cal_type == "static" and approach == "linear":
+                pass
             else:
                 raise RuntimeError("not supported calculation type for VASP")
 

apex/core/calculator/lib/abacus_utils.py

@@ -1,6 +1,6 @@
 #!/usr/bin/python3
 import logging
-import os, re
+import os, re, glob
 
 import dpdata
 import numpy as np
@@ -410,16 +410,23 @@ def final_stru(abacus_path):
             out_stru = bool(line.split()[1])
     logf = os.path.join(abacus_path, "OUT.%s/running_%s.log" % (suffix, calculation))
     if calculation in ["relax", "cell-relax"]:
-        if not out_stru:
+        if os.path.isfile(os.path.join(abacus_path, "OUT.%s/STRU_ION_D" % suffix)):
             return "OUT.%s/STRU_ION_D" % suffix
         else:
-            with open(logf) as f1:
-                lines = f1.readlines()
-            for i in range(1, len(lines)):
-                if lines[-i][36:41] == "istep":
-                    max_step = int(lines[-i].split()[-1])
-                    break
-            return "OUT.%s/STRU_ION%d_D" % (suffix, max_step)
+            # find the final name by STRU_ION*_D,
+            # for abacus version < v3.2.2, there has no STRU_ION_D file but has STRU_ION0_D STRU_ION1_D ... STRU_ION10_D ...
+            # so we need to find the last STRU_ION*_D file
+            stru_ions = glob.glob(
+                os.path.join(abacus_path, f"OUT.{suffix}/STRU_ION*_D")
+            )
+            if len(stru_ions) > 0:
+                # sort the file name by the number in the file name
+                stru_ions.sort(key=lambda x: int(x.split("_")[-2][3:]))
+                final_stru_ion = os.path.basename(stru_ions[-1])
+                return f"OUT.{suffix}/{final_stru_ion}"
+            else:
+                # if there has no STRU_ION_D, return the input STRU
+                return "STRU"
     elif calculation == "md":
         with open(logf) as f1:
             lines = f1.readlines()

apex/core/calculator/lib/lammps_utils.py

@@ -1,15 +1,14 @@
 #!/usr/bin/env python3
 
 import os
-import random
-import subprocess as sp
-import sys
+import re
 
 import dpdata
 from dpdata.periodic_table import Element
 from packaging.version import Version
 
 from apex.core.lib import util
+from apex.core.constants import PERIOD_ELEMENTS_BY_SYMBOL
 from dflow.python import upload_packages
 upload_packages.append(__file__)
 
@@ -153,11 +152,20 @@ def inter_snap(param):
 
 
 def inter_gap(param):
+    init_string = param["init_string"]
+    atomic_num_list = param["atomic_num_list"]
+    if init_string is None:
+        with open(param["model_name"][0], "r") as fp:
+            xml_contents = fp.read()
+        init_string = re.search(r'label="([^"]*)"', xml_contents).group(1)
+    if atomic_num_list is None:
+        atomic_num_list = [PERIOD_ELEMENTS_BY_SYMBOL.index(e) + 1 for e in param["param_type"]]
+
     ret = ""
     line = "pair_style      quip \n"
-    line += "pair_coeff      * * %s " % param["model_name"][0]
-    for ii in param["param_type"]:
-        line += ii + " "
+    line += f'pair_coeff      * * {param["model_name"][0]} "Potential xml_label={init_string}"  '
+    for ii in atomic_num_list:
+        line += str(ii) + " "
     line += "\n"
     ret += line
     return ret

apex/core/common_equi.py

@@ -85,9 +85,14 @@ def make_equi(confs, inter_param, relax_param):
                     sys.to("abacus/stru", stru)
                 else:
                     raise FileNotFoundError("No file %s" % stru)
+            if not os.path.exists(os.path.join(ii, POSCAR)):
+                sys = dpdata.System(stru, fmt="abacus/stru")
+                sys.to("vasp/poscar", os.path.join(ii, POSCAR))
 
             shutil.copyfile(stru, os.path.join(ii, "STRU.bk"))
             abacus_utils.modify_stru_path(stru, "pp_orb/", inter_param)
+            orig_poscar = poscar
+            orig_POSCAR = POSCAR
             poscar = os.path.abspath(stru)
             POSCAR = "STRU"
         if not os.path.exists(poscar):
@@ -105,6 +110,8 @@ def make_equi(confs, inter_param, relax_param):
         if os.path.isfile(POSCAR):
             os.remove(POSCAR)
         os.symlink(os.path.relpath(poscar), POSCAR)
+        if inter_param["type"] == "abacus":
+            os.symlink(os.path.relpath(orig_poscar), orig_POSCAR)
         os.chdir(cwd)
     task_dirs.sort()
     # generate task files
@@ -189,7 +196,11 @@ def post_equi(confs, inter_param):
         inter = make_calculator(inter_param, poscar)
         res = inter.compute(ii)
         contcar = os.path.join(ii, "CONTCAR")
-        ss = Structure.from_file(contcar)
+        try:
+            ss = Structure.from_file(contcar)
+        except FileNotFoundError:
+            logging.warning(f"No CONTCAR found in {ii}, skip")
+            continue
         st = StructureInfo(ss)
         struct_info_dict = {
             "space_group_symbol": st.space_group_symbol,

apex/core/constants.py

@@ -0,0 +1,14 @@
+PERIOD_ELEMENTS_BY_SYMBOL = [
+    "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne",
+    "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca",
+    "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn",
+    "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr",
+    "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn",
+    "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd",
+    "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb",
+    "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg",
+    "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th",
+    "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm",
+    "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Ds",
+    "Rg", "Cn", "Nh", "Fl", "Mc", "Lv", "Ts", "Og"
+]

apex/core/property/EOS.py

@@ -58,7 +58,7 @@ def __init__(self, parameter, inter_param=None):
     def make_confs(self, path_to_work, path_to_equi, refine=False):
         path_to_work = os.path.abspath(path_to_work)
         if os.path.exists(path_to_work):
-            logging.warning("%s already exists" % path_to_work)
+            logging.debug("%s already exists" % path_to_work)
         else:
             os.makedirs(path_to_work)
         path_to_equi = os.path.abspath(path_to_equi)
@@ -84,7 +84,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
         cwd = os.getcwd()
         task_list = []
         if self.reprod:
-            logging.info("eos reproduce starts")
+            print("eos reproduce starts")
             if "init_data_path" not in self.parameter:
                 raise RuntimeError("please provide the initial data path to reproduce")
             init_data_path = os.path.abspath(self.parameter["init_data_path"])
@@ -98,7 +98,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
 
         else:
             if refine:
-                logging.info("eos refine starts")
+                print("eos refine starts")
                 task_list = make_refine(
                     self.parameter["init_from_suffix"],
                     self.parameter["output_suffix"],
@@ -127,7 +127,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     )
 
             else:
-                logging.info(
+                print(
                     "gen eos from "
                     + str(self.vol_start)
                     + " to "
@@ -136,9 +136,9 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     + str(self.vol_step)
                 )
                 if self.vol_abs:
-                    logging.info("treat vol_start and vol_end as absolute volume")
+                    print("treat vol_start and vol_end as absolute volume")
                 else:
-                    logging.info("treat vol_start and vol_end as relative volume")
+                    print("treat vol_start and vol_end as relative volume")
 
                 if self.inter_param["type"] == "abacus":
                     equi_contcar = os.path.join(

apex/core/property/Elastic.py

@@ -33,7 +33,7 @@ def __init__(self, parameter, inter_param=None):
             self.shear_deform = parameter["shear_deform"]
             parameter.setdefault("conventional", False)
             self.conventional = parameter["conventional"]
-            parameter.setdefault("ieee", True)
+            parameter.setdefault("ieee", False)
             self.ieee = parameter["ieee"]
         parameter.setdefault("cal_type", "relaxation")
         self.cal_type = parameter["cal_type"]
@@ -55,7 +55,7 @@ def __init__(self, parameter, inter_param=None):
     def make_confs(self, path_to_work, path_to_equi, refine=False):
         path_to_work = os.path.abspath(path_to_work)
         if os.path.exists(path_to_work):
-            logging.warning("%s already exists" % path_to_work)
+            logging.debug("%s already exists" % path_to_work)
         else:
             os.makedirs(path_to_work)
         path_to_equi = os.path.abspath(path_to_equi)
@@ -96,7 +96,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
         os.chdir(cwd)
 
         if refine:
-            logging.info("elastic refine starts")
+            print("elastic refine starts")
             task_list = make_refine(
                 self.parameter["init_from_suffix"],
                 self.parameter["output_suffix"],