Merge pull request #83 from deepmodeling/devel-1.2.0

Devel 1.2.0

apex/__init__.py

@@ -1,5 +1,5 @@
 import os
-__version__ = '1.2.6'
+__version__ = '1.2.9'
 LOCAL_PATH = os.getcwd()
 
 

apex/config.py

@@ -59,6 +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

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

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/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"]

apex/core/property/Gamma.py

@@ -248,15 +248,15 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     task_list.append(output_task)
                     # print("# %03d generate " % ii, output_task)
 
-                    logging.info(f"# {count} generate {output_task}, with{len(obtained_slab.sites)} atoms")
+                    logging.info(f"# {count} generate {output_task}, with {len(obtained_slab.sites)} atoms")
 
                     # make confs
                     obtained_slab.to("POSCAR.tmp", "POSCAR")
                     vasp_utils.regulate_poscar("POSCAR.tmp", "POSCAR")
                     vasp_utils.sort_poscar("POSCAR", "POSCAR", ptypes)
                     if self.inter_param["type"] == "abacus":
                         abacus_utils.poscar2stru("POSCAR", self.inter_param, "STRU")
-                        os.remove("POSCAR")
+                        #os.remove("POSCAR")
                     # vasp.perturb_xz('POSCAR', 'POSCAR', self.pert_xz)
                     # record miller
                     dumpfn(self.plane_miller, "miller.json")
@@ -433,7 +433,7 @@ def __poscar_fix(self, poscar) -> None:
 
     def __stru_fix(self, stru) -> None:
         fix_dict = {"true": True, "false": False}
-        fix_xyz = [fix_dict[i] for i in self.addfix]
+        fix_xyz = [fix_dict[i] for i in self.add_fix]
         abacus_utils.stru_fix_atom(stru, fix_atom=fix_xyz)
 
     def __inLammpes_fix(self, inLammps) -> None:

apex/core/property/Interstitial.py

@@ -318,7 +318,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                         bcc_interstital_dict = {
                             'tetrahedral': {chl: [0.25, 0.5, 0]},
                             'octahedral': {chl: [0.5, 0.5, 0]},
-                            'crowdion': {chl: [0.25, 0.25, 0]},
+                            'crowdion': {chl: [0.25, 0.25, 0.25]},
                             '<111>dumbbell': {chl: [1 / 3, 1 / 3, 1 / 3],
                                               center: [2 / 3, 2 / 3, 2 / 3]},
                             '<110>dumbbell': {chl: [1 / 4, 3 / 4, 1 / 2],
@@ -408,7 +408,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                         output_task = os.path.join(self.path_to_work, "task.%06d" % ii)
                         os.chdir(output_task)
                         abacus_utils.poscar2stru("POSCAR", self.inter_param, "STRU")
-                        os.remove("POSCAR")
+                        #os.remove("POSCAR")
         os.chdir(cwd)
         return self.task_list
 

apex/core/property/Phonon.py

@@ -55,7 +55,7 @@ def __init__(self, parameter, inter_param=None):
                 self.BAND_POINTS = parameter["BAND_POINTS"]
                 parameter["BAND_CONNECTION"] = parameter.get('BAND_CONNECTION', True)
                 self.BAND_CONNECTION = parameter["BAND_CONNECTION"]
-            parameter["cal_type"] = parameter.get("cal_type", "relaxation")
+            parameter["cal_type"] = parameter.get("cal_type", "static")
             default_cal_setting = {
                 "relax_pos": True,
                 "relax_shape": False,
@@ -485,6 +485,12 @@ def phonopy_band_string_2_band_list(band_str: str, band_label: str = None):
         # return type -> list[list[dict[Any, Any]]]
         return band_list
 
+    @staticmethod
+    def check_same_copy(src, dst):
+        if os.path.samefile(src, dst):
+            return
+        shutil.copyfile(src, dst)
+
     def _compute_lower(self, output_file, all_tasks, all_res):
         cwd = Path.cwd()
         work_path = Path(output_file).parent.absolute()
@@ -497,10 +503,9 @@ def _compute_lower(self, output_file, all_tasks, all_res):
         if not self.reprod:
             os.chdir(work_path)
             if self.inter_param["type"] == 'abacus':
-                shutil.copyfile("task.000000/band.conf", "band.conf")
-                shutil.copyfile("task.000000/STRU.ori", "STRU")
-                shutil.copyfile("task.000000/phonopy_disp.yaml", "phonopy_disp.yaml")
-                os.system('phonopy -f task.0*/OUT.ABACUS/running_scf.log')
+                self.check_same_copy("task.000000/band.conf", "band.conf")
+                self.check_same_copy("task.000000/STRU.ori", "STRU")
+                self.check_same_copy("task.000000/phonopy_disp.yaml", "phonopy_disp.yaml")
                 os.system('phonopy -f task.0*/OUT.ABACUS/running_scf.log')
                 if os.path.exists("FORCE_SETS"):
                     print('FORCE_SETS is created')
@@ -510,9 +515,8 @@ def _compute_lower(self, output_file, all_tasks, all_res):
                 os.system('phonopy-bandplot --gnuplot band.yaml > band.dat')
 
             elif self.inter_param["type"] == 'vasp':
-                shutil.copyfile("task.000000/band.conf", "band.conf")
-                if not os.path.samefile("task.000000/POSCAR-unitcell", "POSCAR-unitcell"):
-                    shutil.copyfile("task.000000/POSCAR-unitcell", "POSCAR-unitcell")
+                self.check_same_copy("task.000000/band.conf", "band.conf")
+                self.check_same_copy("task.000000/POSCAR-unitcell", "POSCAR-unitcell")
 
                 if self.approach == "linear":
                     os.chdir(all_tasks[0])
@@ -528,8 +532,8 @@ def _compute_lower(self, output_file, all_tasks, all_res):
                     shutil.copyfile("band.dat", work_path/"band.dat")
 
                 elif self.approach == "displacement":
-                    shutil.copyfile("task.000000/band.conf", "band.conf")
-                    shutil.copyfile("task.000000/phonopy_disp.yaml", "phonopy_disp.yaml")
+                    self.check_same_copy("task.000000/band.conf", "band.conf")
+                    self.check_same_copy("task.000000/phonopy_disp.yaml", "phonopy_disp.yaml")
                     os.system('phonopy -f task.0*/vasprun.xml')
                     if os.path.exists("FORCE_SETS"):
                         print('FORCE_SETS is created')

apex/core/property/Surface.py

@@ -184,7 +184,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     vasp_utils.perturb_xz("POSCAR", "POSCAR", self.pert_xz)
                     if self.inter_param["type"] == "abacus":
                         abacus_utils.poscar2stru("POSCAR", self.inter_param, "STRU")
-                        os.remove("POSCAR")
+                        #os.remove("POSCAR")
                     # record miller
                     dumpfn(all_slabs[ii].miller_index, "miller.json")
 

apex/core/property/Vacancy.py

@@ -167,7 +167,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     dss[ii].to("POSCAR", "POSCAR")
                     if self.inter_param["type"] == "abacus":
                         abacus_utils.poscar2stru("POSCAR", self.inter_param, "STRU")
-                        os.remove("POSCAR")
+                        #os.remove("POSCAR")
                     # np.savetxt('supercell.out', self.supercell, fmt='%d')
                     dumpfn(self.supercell, "supercell.json")
         os.chdir(cwd)