Devel 1.2.0

.github/workflows/main.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.10"]
 
     steps:
     - uses: actions/checkout@master

README.md

@@ -413,6 +413,7 @@ Below are three examples (for detailed explanations of each parameter, please re
   | shear_deform | Float          | 0.01    | The deformation in other directions, default = 1e-2                                                                               |
   | conventional | Bool           | False   | Whether adopt conventional cell for deformation                                                                                   |
   | ieee         | Bool           | False   | Whether rotate relaxed structure into IEEE-standard format before deformation ([ref](https://ieeexplore.ieee.org/document/26560)) |
+  | modulus_type | String         | "voigt"   | Bulk and shear modulus average type (default: "voigt"). Choose from "voigt", "reuss" and "vrh"                                    |
 
 ##### 3.1.2.3. Surface
   | Key words | Data structure | Example | Description |

apex/__init__.py

@@ -1,5 +1,5 @@
 import os
-__version__ = '1.2.10'
+__version__ = '1.2.12'
 LOCAL_PATH = os.getcwd()
 
 

apex/core/calculator/Lammps.py

@@ -14,7 +14,8 @@
     inter_snap,
     inter_gap,
     inter_rann,
-    inter_mace
+    inter_mace,
+    inter_nep
 )
 from .Task import Task
 from dflow.python import upload_packages
@@ -55,6 +56,8 @@ def set_inter_type_func(self):
             self.inter_func = inter_rann
         elif self.inter_type == "mace":
             self.inter_func = inter_mace
+        elif self.inter_type == "nep":
+            self.inter_func = inter_nep
         else:
             self.inter_func = inter_eam_alloy
 

apex/core/calculator/__init__.py

@@ -8,4 +8,5 @@
     'gap',
     'rann',
     'mace',
+    'nep'
 ]

apex/core/calculator/lib/abacus_utils.py

@@ -4,7 +4,7 @@
 
 import dpdata
 import numpy as np
-from pymatgen.core.structure import Structure
+from pymatgen.core import Structure
 
 from . import abacus_scf
 from dflow.python import upload_packages

apex/core/calculator/lib/lammps_utils.py

@@ -138,6 +138,16 @@ def inter_mace(param):
     ret += line
     return ret
 
+def inter_nep(param):
+    ret = ""
+    line = "pair_style      nep \n"
+    line += "pair_coeff      * * %s " % param["model_name"][0]
+    for ii in param["param_type"]:
+        line += ii + " "
+    line += "\n"
+    ret += line
+    return ret
+
 
 def inter_snap(param):
     ret = ""

apex/core/common_equi.py

@@ -5,6 +5,7 @@
 import dpdata
 from monty.serialization import dumpfn
 from pymatgen.core.structure import Structure
+from pymatgen.analysis.structure_matcher import StructureMatcher
 from apex.core.calculator.lib import abacus_utils
 from apex.core.lib import crys
 from apex.core.calculator.calculator import make_calculator
@@ -14,7 +15,7 @@
 from apex.core.structure import StructureInfo
 from dflow.python import upload_packages
 upload_packages.append(__file__)
-lammps_task_type = ['deepmd', 'eam_alloy', 'meam', 'eam_fs', 'meam_spline', 'snap', 'gap', 'rann', 'mace']
+lammps_task_type = ['deepmd', 'eam_alloy', 'meam', 'eam_fs', 'meam_spline', 'snap', 'gap', 'rann', 'mace', 'nep']
 
 
 def make_equi(confs, inter_param, relax_param):
@@ -201,13 +202,23 @@ def post_equi(confs, inter_param):
         except FileNotFoundError:
             logging.warning(f"No CONTCAR found in {ii}, skip")
             continue
+        try:
+            init_ss = Structure.from_file(poscar)
+        except FileNotFoundError:
+            logging.warning(f"No POSCAR found in {ii}, skip")
+            continue
         st = StructureInfo(ss)
+        matcher = StructureMatcher()
+        is_match = matcher.fit(init_ss, ss)
+        if not is_match:
+            logging.warning(f"Structure mismatch after relaxation in {ii}")
         struct_info_dict = {
             "space_group_symbol": st.space_group_symbol,
             "space_group_number": st.space_group_number,
             "point_group_symbol": st.point_group_symbol,
             "crystal_system": st.crystal_system,
             "lattice_type": st.lattice_type,
+            "mismatch": not is_match,
         }
 
         dumpfn(struct_info_dict, os.path.join(ii, "structure.json"), indent=4)

apex/core/common_prop.py

@@ -1,7 +1,7 @@
 import glob
 import os
 from multiprocessing import Pool
-from monty.serialization import dumpfn
+from monty.serialization import dumpfn, loadfn
 
 from apex.core.calculator.calculator import make_calculator
 from apex.core.property.Elastic import Elastic
@@ -54,6 +54,12 @@ def make_property(confs, inter_param, property_list):
     conf_dirs.sort()
     for ii in conf_dirs:
         sepline(ch=ii, screen=True)
+        path_to_equi = os.path.join(ii, "relaxation", "relax_task")
+        try:
+            structure_dict = loadfn(os.path.join(path_to_equi, "structure.json"))
+        except FileNotFoundError:
+            structure_dict = {}
+        mismatch = structure_dict.get("mismatch", False)
         for jj in property_list:
             do_refine, suffix = handle_prop_suffix(jj)
             if not suffix:
@@ -63,8 +69,11 @@ def make_property(confs, inter_param, property_list):
             # determine the suffix: from scratch or refine
 
             property_type = jj["type"]
-            path_to_equi = os.path.join(ii, "relaxation", "relax_task")
             path_to_work = os.path.join(ii, property_type + "_" + suffix)
+            skip_mismatch = jj.get("skip_mismatch", False)
+            if mismatch and skip_mismatch:
+                print("Skip mismatched structure")
+                continue
 
             create_path(path_to_work)
 

apex/core/property/Elastic.py

@@ -35,6 +35,8 @@ def __init__(self, parameter, inter_param=None):
             self.conventional = parameter["conventional"]
             parameter.setdefault("ieee", False)
             self.ieee = parameter["ieee"]
+            parameter.setdefault("modulus_type", "voigt")
+            self.modulus_type = parameter["modulus_type"]
         parameter.setdefault("cal_type", "relaxation")
         self.cal_type = parameter["cal_type"]
         default_cal_setting = {
@@ -272,19 +274,27 @@ def _compute_lower(self, output_file, all_tasks, all_res):
             res_data["elastic_tensor"].append(c_ii)
             ptr_data += "\n"
 
-        BV = et.k_voigt / 1e4
-        GV = et.g_voigt / 1e4
+        if self.modulus_type == "voigt":
+            BV = et.k_voigt / 1e4
+            GV = et.g_voigt / 1e4
+        elif self.modulus_type == "reuss":
+            BV = et.k_reuss / 1e4
+            GV = et.g_reuss / 1e4
+        elif self.modulus_type == "vrh":
+            BV = et.k_vrh / 1e4
+            GV = et.g_vrh / 1e4
+
         EV = 9 * BV * GV / (3 * BV + GV)
         uV = 0.5 * (3 * BV - 2 * GV) / (3 * BV + GV)
 
-        res_data["BV"] = BV
-        res_data["GV"] = GV
-        res_data["EV"] = EV
-        res_data["uV"] = uV
-        ptr_data += "# Bulk   Modulus BV = %.2f GPa\n" % BV
-        ptr_data += "# Shear  Modulus GV = %.2f GPa\n" % GV
-        ptr_data += "# Youngs Modulus EV = %.2f GPa\n" % EV
-        ptr_data += "# Poission Ratio uV = %.2f\n " % uV
+        res_data["B"] = BV
+        res_data["G"] = GV
+        res_data["E"] = EV
+        res_data["u"] = uV
+        ptr_data += "# Bulk   Modulus B = %.2f GPa\n" % BV
+        ptr_data += "# Shear  Modulus G = %.2f GPa\n" % GV
+        ptr_data += "# Youngs Modulus E = %.2f GPa\n" % EV
+        ptr_data += "# Poission Ratio u = %.2f\n " % uV
 
         dumpfn(res_data, output_file, indent=4)
 

apex/op/property_ops.py

@@ -1,5 +1,6 @@
 import os, glob, pathlib, shutil, subprocess, logging
 from pathlib import Path
+from monty.serialization import loadfn
 from typing import List
 from dflow.python import (
     OP,
@@ -65,7 +66,23 @@ def execute(
         create_path(str(abs_path_to_prop))
         conf_path = abs_path_to_prop.parent
         prop_name = abs_path_to_prop.name
+
+        # break subworkflow if mismatch stop is set
         path_to_equi = conf_path / "relaxation" / "relax_task"
+        try:
+            structure_dict = loadfn(os.path.join(path_to_equi, "structure.json"))
+        except FileNotFoundError:
+            structure_dict = {}
+        mismatch = structure_dict.get("mismatch", False)
+        skip_mismatch = prop_param.get("skip_mismatch", False)
+        if mismatch and skip_mismatch:
+            print("Skipped due to mismatched relaxed structure")
+            return OPIO({
+                'output_work_path': abs_path_to_prop,
+                'task_names': [],
+                'njobs': 0,
+                'task_paths': []
+            })
 
         inter_param_prop = inter_param
         if "cal_setting" in prop_param and "overwrite_interaction" in prop_param["cal_setting"]:
@@ -141,6 +158,13 @@ def execute(self, op_in: OPIO) -> OPIO:
         task_names = op_in["task_names"]
         path_to_prop = op_in["path_to_prop"]
         inter_type = inter_param["type"]
+
+        if len(task_names) == 0:
+            print("Skip post property")
+            return OPIO({
+                'retrieve_path': []
+            })
+
         copy_dir_list_input = [path_to_prop.split('/')[0]]
         os.chdir(input_all)
         copy_dir_list = []

apex/reporter/property_report.py

@@ -131,17 +131,17 @@ def plotly_graph(res_data: dict, name: str, **kwargs):
         c44 = elastic_tensor[3][3]
         c55 = elastic_tensor[4][4]
         c66 = elastic_tensor[5][5]
-        BV = res_data['BV']
-        GV = res_data['GV']
-        EV = res_data['EV']
-        uV = res_data['uV']
+        BV = res_data['B']
+        GV = res_data['G']
+        EV = res_data['E']
+        uV = res_data['u']
 
         polar = go.Scatterpolar(
             name=name,
             r=[c11, c12, c13, c22, c23, c33,
                c44, c55, c66, BV, GV, EV, uV],
             theta=['C11', 'C12', 'C13', 'C22', 'C23', 'C33',
-                   'C44', 'C55', 'C66', 'BV', 'GV', 'EV', 'uV'],
+                   'C44', 'C55', 'C66', 'B', 'G', 'E', 'u'],
             fill='none'
         )
 
@@ -156,15 +156,15 @@ def plotly_graph(res_data: dict, name: str, **kwargs):
     def dash_table(res_data: dict, decimal: int = 3, **kwargs) -> dash_table.DataTable:
         ph = '-'
         et = res_data['elastic_tensor']
-        BV = res_data['BV']
-        GV = res_data['GV']
-        EV = res_data['EV']
-        uV = res_data['uV']
+        BV = res_data['B']
+        GV = res_data['G']
+        EV = res_data['E']
+        uV = res_data['u']
         null_t = [' '] * 6
-        BV_t = ['BV', BV, ph, ph, ph, ph]
-        GV_t = ['GV', GV, ph, ph, ph, ph]
-        EV_t = ['EV', EV, ph, ph, ph, ph]
-        uV_t = ['uV', uV, ph, ph, ph, ph]
+        BV_t = ['B', BV, ph, ph, ph, ph]
+        GV_t = ['G', GV, ph, ph, ph, ph]
+        EV_t = ['E', EV, ph, ph, ph, ph]
+        uV_t = ['u', uV, ph, ph, ph, ph]
         table_tensor = [et[0], et[1], et[2], et[3], et[4], et[5],
                         null_t, BV_t, GV_t, EV_t, uV_t]
 

examples/lammps_demo/global_bohrium.json

@@ -11,5 +11,5 @@
     "run_command":"lmp -in in.lammps",
     "batch_type": "Bohrium",
     "context_type": "Bohrium",
-    "scass_type":"c16_m62_1 * NVIDIA T4"
+    "scass_type":"1 * NVIDIA P100_16g"
 }

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="apex-flow",
-    version="1.2.10",
+    version="1.2.12",
     author="Zhuoyuan Li, Tongqi Wen",
     author_email="zhuoyli@outlook.com",
     description="Alloy Properties EXplorer using simulations",
@@ -34,7 +34,7 @@
         "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
         "Operating System :: OS Independent",
     ],
-    python_requires='>=3.8',
+    python_requires='>=3.10',
     entry_points={'console_scripts': [
          'apex = apex.__main__:main',
      ]}