Merge pull request #119 from deepmodeling/devel-1.3.0

Devel 1.3.0

Author: kevinwenminion

.gitignore

@@ -37,4 +37,4 @@ potential
 all_result.json
 
 # dflow debug folders generated by examples or local runs
-**/dflow_debug/
+**/dflow_debug/

apex/config.py

@@ -67,6 +67,10 @@ class Config:
     vasp_run_command: str = None
     abacus_image_name: str = None
     abacus_run_command: str = None
+    lammps_header_retry_attempts: int = 2
+    lammps_header_retry_delay: float = 5
+    lammps_transient_retry_attempts: int = 1
+    lammps_retry_group_size: int = None
 
     # common APEX config
     is_bohrium_dflow: bool = False
@@ -256,7 +260,11 @@ def basic_config_dict(self):
             "vasp_image_name": self.vasp_image_name,
             "vasp_run_command": self.vasp_run_command,
             "abacus_image_name": self.abacus_image_name,
-            "abacus_run_command": self.abacus_run_command
+            "abacus_run_command": self.abacus_run_command,
+            "lammps_header_retry_attempts": self.lammps_header_retry_attempts,
+            "lammps_header_retry_delay": self.lammps_header_retry_delay,
+            "lammps_transient_retry_attempts": self.lammps_transient_retry_attempts,
+            "lammps_retry_group_size": self.lammps_retry_group_size
         }
         return basic_config
 

apex/core/property/Gamma.py

@@ -36,6 +36,7 @@ def __init__(self, parameter, inter_param=None):
         self.reprod = parameter["reproduce"]
         if not self.reprod:
             if not ("init_from_suffix" in parameter and "output_suffix" in parameter):
+                parameter["cal_type"] = parameter.get("cal_type", "relaxation")
                 parameter["plane_miller"] = parameter.get("plane_miller", None)
                 self.plane_miller = parameter["plane_miller"]
                 parameter["slip_direction"] = parameter.get("slip_direction", None)
@@ -48,14 +49,18 @@ def __init__(self, parameter, inter_param=None):
                 self.supercell_size = parameter["supercell_size"]
                 parameter["vacuum_size"] = parameter.get("vacuum_size", 0)
                 self.vacuum_size = parameter["vacuum_size"]
-                parameter["add_fix"] = parameter.get(
-                    "add_fix", ["true", "true", "false"]
-                )  # standard method
+                if parameter["cal_type"] == "static" and "add_fix" not in parameter:
+                    parameter["add_fix"] = None
+                else:
+                    parameter["add_fix"] = parameter.get(
+                        "add_fix", ["true", "true", "false"]
+                    )  # standard method
                 self.add_fix = parameter["add_fix"]
                 parameter["n_steps"] = parameter.get("n_steps", 10)
                 self.n_steps = parameter["n_steps"]
                 self.atom_num = None
-            parameter["cal_type"] = parameter.get("cal_type", "relaxation")
+            else:
+                parameter["cal_type"] = parameter.get("cal_type", "relaxation")
             default_cal_setting = {
                 "relax_pos": True,
                 "relax_shape": False,
@@ -157,7 +162,18 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
 
                 equi_contcar = os.path.join(path_to_equi, CONTCAR)
                 if not os.path.exists(equi_contcar):
-                    raise RuntimeError("please do relaxation first")
+                    raise RuntimeError(
+                        "Gamma requires a baseline relaxation before PropsMake. "
+                        "For static gamma scans, run a static baseline relaxation "
+                        "with relax_pos=false, relax_shape=false, and relax_vol=false."
+                    )
+                equi_result = os.path.join(path_to_equi, "result.json")
+                if not os.path.exists(equi_result):
+                    raise RuntimeError(
+                        "Gamma post-processing requires relaxation/relax_task/result.json. "
+                        "Please provide a static baseline relaxation result before "
+                        "running gamma PropsMake."
+                    )
                 # print("we now only support gamma line calculation for BCC FCC and HCP metals")
                 # print(
                 #    f"supported slip systems are:\n{SlabSlipSystem.hint_string()}"
@@ -451,6 +467,8 @@ def __inLammpes_fix(self, inLammps) -> None:
         )
         with open(inLammps, "r") as fin1:
             contents = fin1.readlines()
+            lower_id = None
+            upper_id = None
             for ii in range(len(contents)):
                 upper = contents[ii].split()[:3] == ["variable", "N", "equal"]
                 lower = re.search("min_style       cg", contents[ii])
@@ -460,6 +478,13 @@ def __inLammpes_fix(self, inLammps) -> None:
                 elif upper:
                     upper_id = ii
                     # print(upper_id)
+            if lower_id is None or upper_id is None or lower_id >= upper_id:
+                raise RuntimeError(
+                    "Gamma add_fix was requested, but in.lammps does not contain "
+                    "a compatible minimization block to patch. For static gamma "
+                    "calculations set add_fix to null, or use a relaxation-style "
+                    "LAMMPS input with min_style cg and variable N equal markers."
+                )
             del contents[lower_id + 1:upper_id - 1]
             contents.insert(lower_id + 1, add_fix_str)
         with open(inLammps, "w") as fin2:

apex/core/property/Gruneisen.py

@@ -794,8 +794,8 @@ def _ensure_mesh_yaml(self, task_dir: str) -> None:
             raise FileNotFoundError(f"POSCAR not found in {task_dir}")
         os.chdir(task_dir)
         cell_file = "POSCAR-unitcell" if self.inter_param["type"] == "vasp" else "POSCAR"
-        command = (
-            'phonopy --nomeshsym --dim="%s %s %s" -c %s band.conf'
+        command = Phonon.phonopy_command(
+            '--nomeshsym --dim="%s %s %s" -c %s band.conf'
             % (self.supercell_size[0], self.supercell_size[1], self.supercell_size[2], cell_file)
         )
         subprocess.check_call(command, shell=True)
@@ -868,16 +868,16 @@ def _ensure_vasp_volume_outputs(
             cwd = os.getcwd()
             try:
                 os.chdir(helper_dir)
-                subprocess.check_call(
-                    Phonon.phonopy_setup_command(
+                Phonon.run_first_success(
+                    Phonon.phonopy_writefc_commands(
                         '--dim="%s %s %s" -c POSCAR-unitcell --writefc'
                         % (
                             self.supercell_size[0],
                             self.supercell_size[1],
                             self.supercell_size[2],
                         )
                     ),
-                    shell=True,
+                    required_file="FORCE_CONSTANTS",
                 )
             finally:
                 os.chdir(cwd)
@@ -888,8 +888,10 @@ def _ensure_vasp_volume_outputs(
             try:
                 os.chdir(helper_dir)
                 subprocess.check_call(
-                    'phonopy --dim="%s %s %s" -c POSCAR-unitcell band.conf'
-                    % (self.supercell_size[0], self.supercell_size[1], self.supercell_size[2]),
+                    Phonon.phonopy_command(
+                        '--dim="%s %s %s" -c POSCAR-unitcell band.conf'
+                        % (self.supercell_size[0], self.supercell_size[1], self.supercell_size[2])
+                    ),
                     shell=True,
                 )
                 self._write_band_dat()
@@ -954,14 +956,14 @@ def _ensure_abacus_volume_outputs(
                 # Pass phonopy_disp.yaml explicitly so phonopy reads the supercell from the yaml
                 # rather than falling into old-style POSCAR mode (which has no DIM).
                 if not os.path.isfile("FORCE_CONSTANTS"):
-                    subprocess.check_call(
-                        Phonon.phonopy_setup_command("phonopy_disp.yaml --writefc"),
-                        shell=True,
+                    Phonon.run_first_success(
+                        Phonon.phonopy_writefc_commands("phonopy_disp.yaml --writefc"),
+                        required_file="FORCE_CONSTANTS",
                     )
                 if not os.path.isfile("FORCE_CONSTANTS"):
                     raise FileNotFoundError(f"FORCE_CONSTANTS was not created in {helper_dir}")
                 if not os.path.isfile("mesh.yaml"):
-                    subprocess.check_call("phonopy band.conf", shell=True)
+                    subprocess.check_call(Phonon.phonopy_command("band.conf"), shell=True)
                     self._write_band_dat()
             finally:
                 os.chdir(cwd)
@@ -973,28 +975,7 @@ def _write_band_dat() -> None:
         if not os.path.isfile("band.yaml"):
             logging.warning("band.yaml was not created; skipping band.dat export")
             return
-        with open("band.dat", "w") as fp:
-            result = subprocess.run(
-                ["phonopy-bandplot", "--gnuplot", "band.yaml"],
-                stdout=fp,
-                stderr=subprocess.PIPE,
-                text=True,
-            )
-        if result.returncode == 0:
-            return
-        if os.path.isfile("band.dat") and os.path.getsize("band.dat") > 0:
-            logging.warning(
-                "phonopy-bandplot exited with code %s after writing band.dat; continuing. stderr: %s",
-                result.returncode,
-                result.stderr.strip(),
-            )
-            return
-        raise subprocess.CalledProcessError(
-            result.returncode,
-            ["phonopy-bandplot", "--gnuplot", "band.yaml"],
-            output=None,
-            stderr=result.stderr,
-        )
+        Phonon.write_band_dat()
 
     def _attach_abacus_reference_energies(
         self, task_infos: List[dict], task_result_map: Dict[str, str]

apex/core/property/Interstitial.py

@@ -294,6 +294,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     with open("task.000000/POSCAR", "r") as fin:
                         self.pos_line = fin.read().split("\n")
 
+                    chl = None
                     for idx, ii in enumerate(self.pos_line):
                         ss = ii.split()
                         if len(ss) > 3:
@@ -303,11 +304,19 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                                     and abs(0.14 / self.supercell[2] - float(ss[2])) < TOL
                             ):
                                 chl = idx
+                    if chl is None:
+                        raise RuntimeError(
+                            f"Could not locate the generated interstitial anchor site "
+                            f"for {self.structure_type} special interstitial generation. "
+                            "Check the relaxed structure, supercell, or set special_list=[] "
+                            "to use the Voronoi generator."
+                        )
                     shutil.rmtree("task.000000")
 
                     os.chdir(cwd)
                     # specify interstitial structures
                     if self.structure_type == 'bcc':
+                        center = None
                         for idx, ii in enumerate(self.pos_line):
                             ss = ii.split()
                             if len(ss) > 3:
@@ -317,6 +326,13 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                                         and abs(0.5 / self.supercell[2] - float(ss[2])) < TOL
                                 ):
                                     center = idx
+                        if center is None:
+                            raise RuntimeError(
+                                "Could not locate the BCC center atom required for "
+                                "special interstitial dumbbell generation. Check the "
+                                "relaxed structure/supercell or set special_list=[] "
+                                "to use the Voronoi generator."
+                            )
                         bcc_interstital_dict = {
                             'tetrahedral': {chl: [0.25, 0.5, 0]},
                             'octahedral': {chl: [0.5, 0.5, 0]},
@@ -331,6 +347,8 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                         total_task = self.__gen_tasks(bcc_interstital_dict)
 
                     elif self.structure_type == 'fcc':
+                        face = None
+                        corner = None
                         for idx, ii in enumerate(self.pos_line):
                             ss = ii.split()
                             if len(ss) > 3:
@@ -347,6 +365,13 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                                         and abs(1 / self.supercell[2] - float(ss[2])) < TOL
                                 ):
                                     corner = idx
+                        if face is None or corner is None:
+                            raise RuntimeError(
+                                "Could not locate the FCC face/corner atoms required "
+                                "for special interstitial generation. Check the relaxed "
+                                "structure/supercell or set special_list=[] to use the "
+                                "Voronoi generator."
+                            )
 
                         fcc_interstital_dict = {
                             'tetrahedral': {chl: [0.75, 0.25, 0.25]},
@@ -376,6 +401,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                         total_task = self.__gen_tasks(fcc_interstital_dict)
 
                     elif self.structure_type == 'hcp':
+                        center = None
                         for idx, ii in enumerate(self.pos_line):
                             ss = ii.split()
                             if len(ss) > 3:
@@ -385,6 +411,13 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                                         and abs(0.25 / self.supercell[2] - float(ss[2])) < TOL
                                 ):
                                     center = idx
+                        if center is None:
+                            raise RuntimeError(
+                                "Could not locate the HCP center atom required for "
+                                "special interstitial generation. Check the relaxed "
+                                "structure/supercell or set special_list=[] to use the "
+                                "Voronoi generator."
+                            )
                         hcp_interstital_dict = {
                             'O': {chl: [0, 0, 0.5]},
                             'BO': {chl: [0, 0, 0.25]},