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kevinwenminionkevinwenminion
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Merge pull request #89 from deepmodeling/devel-1.2.0
We added the option to specify the modulus approximation method (“voigt”, “reuss” or “vrh”) in the elasticity calculation workflow in 1.2.12.
2 parents 4d9cde0 + a6eb23d commit 95c4450

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+102
-33
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14 files changed

+102
-33
lines changed

‎.github/workflows/main.yml

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

‎README.md

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@@ -413,6 +413,7 @@ Below are three examples (for detailed explanations of each parameter, please re
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| shear_deform | Float | 0.01 | The deformation in other directions, default = 1e-2 |
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| conventional | Bool | False | Whether adopt conventional cell for deformation |
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| ieee | Bool | False | Whether rotate relaxed structure into IEEE-standard format before deformation ([ref](https://ieeexplore.ieee.org/document/26560)) |
416+
| modulus_type | String | "voigt" | Bulk and shear modulus average type (default: "voigt"). Choose from "voigt", "reuss" and "vrh" |
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##### 3.1.2.3. Surface
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| Key words | Data structure | Example | Description |

‎apex/__init__.py

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@@ -1,5 +1,5 @@
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import os
2-
__version__ = '1.2.10'
2+
__version__ = '1.2.12'
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LOCAL_PATH = os.getcwd()
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‎apex/core/calculator/Lammps.py

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,8 @@
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inter_snap,
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inter_gap,
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inter_rann,
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inter_mace
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inter_mace,
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inter_nep
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)
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from .Task import Task
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from dflow.python import upload_packages
@@ -55,6 +56,8 @@ def set_inter_type_func(self):
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self.inter_func = inter_rann
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elif self.inter_type == "mace":
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self.inter_func = inter_mace
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elif self.inter_type == "nep":
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self.inter_func = inter_nep
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else:
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self.inter_func = inter_eam_alloy
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‎apex/core/calculator/__init__.py

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Original file line numberDiff line numberDiff line change
@@ -8,4 +8,5 @@
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'gap',
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'rann',
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'mace',
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'nep'
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]

‎apex/core/calculator/lib/abacus_utils.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
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import dpdata
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import numpy as np
7-
from pymatgen.core.structure import Structure
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from pymatgen.core import Structure
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from . import abacus_scf
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from dflow.python import upload_packages

‎apex/core/calculator/lib/lammps_utils.py

Lines changed: 10 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -138,6 +138,16 @@ def inter_mace(param):
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ret += line
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return ret
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def inter_nep(param):
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ret = ""
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line = "pair_style nep \n"
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line += "pair_coeff * * %s " % param["model_name"][0]
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for ii in param["param_type"]:
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line += ii + " "
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line += "\n"
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ret += line
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return ret
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142152
def inter_snap(param):
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ret = ""

‎apex/core/common_equi.py

Lines changed: 12 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,7 @@
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import dpdata
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from monty.serialization import dumpfn
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from pymatgen.core.structure import Structure
8+
from pymatgen.analysis.structure_matcher import StructureMatcher
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from apex.core.calculator.lib import abacus_utils
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from apex.core.lib import crys
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from apex.core.calculator.calculator import make_calculator
@@ -14,7 +15,7 @@
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from apex.core.structure import StructureInfo
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from dflow.python import upload_packages
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upload_packages.append(__file__)
17-
lammps_task_type = ['deepmd', 'eam_alloy', 'meam', 'eam_fs', 'meam_spline', 'snap', 'gap', 'rann', 'mace']
18+
lammps_task_type = ['deepmd', 'eam_alloy', 'meam', 'eam_fs', 'meam_spline', 'snap', 'gap', 'rann', 'mace', 'nep']
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def make_equi(confs, inter_param, relax_param):
@@ -201,13 +202,23 @@ def post_equi(confs, inter_param):
201202
except FileNotFoundError:
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logging.warning(f"No CONTCAR found in {ii}, skip")
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continue
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try:
206+
init_ss = Structure.from_file(poscar)
207+
except FileNotFoundError:
208+
logging.warning(f"No POSCAR found in {ii}, skip")
209+
continue
204210
st = StructureInfo(ss)
211+
matcher = StructureMatcher()
212+
is_match = matcher.fit(init_ss, ss)
213+
if not is_match:
214+
logging.warning(f"Structure mismatch after relaxation in {ii}")
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struct_info_dict = {
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"space_group_symbol": st.space_group_symbol,
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"space_group_number": st.space_group_number,
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"point_group_symbol": st.point_group_symbol,
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"crystal_system": st.crystal_system,
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"lattice_type": st.lattice_type,
221+
"mismatch": not is_match,
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}
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dumpfn(struct_info_dict, os.path.join(ii, "structure.json"), indent=4)

‎apex/core/common_prop.py

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Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
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import glob
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import os
33
from multiprocessing import Pool
4-
from monty.serialization import dumpfn
4+
from monty.serialization import dumpfn, loadfn
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from apex.core.calculator.calculator import make_calculator
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from apex.core.property.Elastic import Elastic
@@ -54,6 +54,12 @@ def make_property(confs, inter_param, property_list):
5454
conf_dirs.sort()
5555
for ii in conf_dirs:
5656
sepline(ch=ii, screen=True)
57+
path_to_equi = os.path.join(ii, "relaxation", "relax_task")
58+
try:
59+
structure_dict = loadfn(os.path.join(path_to_equi, "structure.json"))
60+
except FileNotFoundError:
61+
structure_dict = {}
62+
mismatch = structure_dict.get("mismatch", False)
5763
for jj in property_list:
5864
do_refine, suffix = handle_prop_suffix(jj)
5965
if not suffix:
@@ -63,8 +69,11 @@ def make_property(confs, inter_param, property_list):
6369
# determine the suffix: from scratch or refine
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6571
property_type = jj["type"]
66-
path_to_equi = os.path.join(ii, "relaxation", "relax_task")
6772
path_to_work = os.path.join(ii, property_type + "_" + suffix)
73+
skip_mismatch = jj.get("skip_mismatch", False)
74+
if mismatch and skip_mismatch:
75+
print("Skip mismatched structure")
76+
continue
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6978
create_path(path_to_work)
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‎apex/core/property/Elastic.py

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@@ -35,6 +35,8 @@ def __init__(self, parameter, inter_param=None):
3535
self.conventional = parameter["conventional"]
3636
parameter.setdefault("ieee", False)
3737
self.ieee = parameter["ieee"]
38+
parameter.setdefault("modulus_type", "voigt")
39+
self.modulus_type = parameter["modulus_type"]
3840
parameter.setdefault("cal_type", "relaxation")
3941
self.cal_type = parameter["cal_type"]
4042
default_cal_setting = {
@@ -272,19 +274,27 @@ def _compute_lower(self, output_file, all_tasks, all_res):
272274
res_data["elastic_tensor"].append(c_ii)
273275
ptr_data += "\n"
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275-
BV = et.k_voigt / 1e4
276-
GV = et.g_voigt / 1e4
277+
if self.modulus_type == "voigt":
278+
BV = et.k_voigt / 1e4
279+
GV = et.g_voigt / 1e4
280+
elif self.modulus_type == "reuss":
281+
BV = et.k_reuss / 1e4
282+
GV = et.g_reuss / 1e4
283+
elif self.modulus_type == "vrh":
284+
BV = et.k_vrh / 1e4
285+
GV = et.g_vrh / 1e4
286+
277287
EV = 9 * BV * GV / (3 * BV + GV)
278288
uV = 0.5 * (3 * BV - 2 * GV) / (3 * BV + GV)
279289

280-
res_data["BV"] = BV
281-
res_data["GV"] = GV
282-
res_data["EV"] = EV
283-
res_data["uV"] = uV
284-
ptr_data += "# Bulk Modulus BV = %.2f GPa\n" % BV
285-
ptr_data += "# Shear Modulus GV = %.2f GPa\n" % GV
286-
ptr_data += "# Youngs Modulus EV = %.2f GPa\n" % EV
287-
ptr_data += "# Poission Ratio uV = %.2f\n " % uV
290+
res_data["B"] = BV
291+
res_data["G"] = GV
292+
res_data["E"] = EV
293+
res_data["u"] = uV
294+
ptr_data += "# Bulk Modulus B = %.2f GPa\n" % BV
295+
ptr_data += "# Shear Modulus G = %.2f GPa\n" % GV
296+
ptr_data += "# Youngs Modulus E = %.2f GPa\n" % EV
297+
ptr_data += "# Poission Ratio u = %.2f\n " % uV
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289299
dumpfn(res_data, output_file, indent=4)
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