From bbfbbe1754bada9114b74d60cd7de3d0b9a9b054 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Wed, 17 Apr 2024 17:45:26 +0800
Subject: [PATCH 01/35] fix: minor error

---
 apex/archive.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/apex/archive.py b/apex/archive.py
index ff175a4..5dbe507 100644
--- a/apex/archive.py
+++ b/apex/archive.py
@@ -199,7 +199,7 @@ def archive2db_from_json(config, json_file):
     if config.archive_key:
         data_id = config.archive_key
     else:
-        data_id = str(data_dict["work_path"])
+        data_id = data_dict['archive_key']
     data_dict['_id'] = data_id
 
     archive2db(config, data_dict, data_id)

From 6ed652228568b551657ffd06a83d0ecd83249b7c Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Wed, 17 Apr 2024 17:47:49 +0800
Subject: [PATCH 02/35] feat(elastic): support auto modification of input
 relaxed POSCAR-structure into IEEE-standard format before elastic deformation
 in Elastic.py

---
 apex/core/property/Elastic.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/apex/core/property/Elastic.py b/apex/core/property/Elastic.py
index 5d27ddf..a9b4d94 100644
--- a/apex/core/property/Elastic.py
+++ b/apex/core/property/Elastic.py
@@ -10,6 +10,9 @@
 from pymatgen.analysis.elasticity.strain import DeformedStructureSet, Strain
 from pymatgen.analysis.elasticity.stress import Stress
 from pymatgen.core.structure import Structure
+from pymatgen.core.tensors import Tensor
+from pymatgen.core.operations import SymmOp
+from pymatgen.core.lattice import Lattice
 from pymatgen.io.vasp import Incar, Kpoints
 
 from apex.core.calculator.lib import abacus_utils
@@ -32,6 +35,8 @@ 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)
+            self.ieee = parameter["ieee"]
         parameter.setdefault("cal_type", "relaxation")
         self.cal_type = parameter["cal_type"]
         default_cal_setting = {
@@ -141,6 +146,12 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                 ss = st.conventional_structure
                 ss.to(os.path.join(path_to_work, "POSCAR.conv"), "POSCAR")
 
+            # convert to IEEE-standard
+            if self.ieee:
+                rot = Tensor.get_ieee_rotation(ss)
+                op = SymmOp.from_rotation_and_translation(rot)
+                ss.apply_operation(op)
+
             dfm_ss = DeformedStructureSet(
                 ss,
                 symmetry=False,

From 13671ecee47ed895762c0bde268013043110cf1e Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Wed, 17 Apr 2024 17:53:13 +0800
Subject: [PATCH 03/35] feat(elastic): support auto modification of input
 relaxed POSCAR-structure into IEEE-standard format before elastic deformation
 in Elastic.py

---
 README.md | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index f03c670..fd892d0 100644
--- a/README.md
+++ b/README.md
@@ -252,11 +252,12 @@ Below are three examples (for detailed explanations of each parameter, please re
   | vol_abs | Bool | False | Whether to treat vol_start and vol_end as absolute volume, default = False |
 
 ##### 3.1.2.2. Elastic
-  | Key words    | Data structure | Example | Description                                        |
-  |:-------------|----------------|---------|----------------------------------------------------|
-  | norm_deform  | Float          | 0.01    | The deformation in xx, yy, zz, defaul = 1e-2       |
-  | shear_deform | Float          | 0.01    | The deformation in other directions, default = 1e-2 |
-  | conventional | Bool           | False   | Whether adopt conventional cell for deformation    |
+  | Key words    | Data structure | Example | Description                                                                                                                       |
+  |:-------------|----------------|---------|-----------------------------------------------------------------------------------------------------------------------------------|
+  | norm_deform  | Float          | 0.01    | The deformation in xx, yy, zz, defaul = 1e-2                                                                                      |
+  | shear_deform | Float          | 0.01    | The deformation in other directions, default = 1e-2                                                                               |
+  | conventional | Bool           | False   | Whether adopt conventional cell for deformation                                                                                   |
+  | ieee         | Bool           | True    | Whether rotate relaxed structure into IEEE-standard format before deformation ([ref](https://ieeexplore.ieee.org/document/26560)) |
 
 ##### 3.1.2.3. Surface
   | Key words | Data structure | Example | Description |

From fb25a9fcdd633d431c23d0f5022cfc36b4e3e1d8 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Wed, 17 Apr 2024 17:59:07 +0800
Subject: [PATCH 04/35] feat(elastic): support auto modification of input
 relaxed POSCAR-structure into IEEE-standard format before elastic deformation
 in Elastic.py

---
 apex/core/property/Elastic.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/apex/core/property/Elastic.py b/apex/core/property/Elastic.py
index a9b4d94..f0a524f 100644
--- a/apex/core/property/Elastic.py
+++ b/apex/core/property/Elastic.py
@@ -12,7 +12,6 @@
 from pymatgen.core.structure import Structure
 from pymatgen.core.tensors import Tensor
 from pymatgen.core.operations import SymmOp
-from pymatgen.core.lattice import Lattice
 from pymatgen.io.vasp import Incar, Kpoints
 
 from apex.core.calculator.lib import abacus_utils

From 74eeede5e6cdd6aa3d942f085a999f4c7fff193a Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Thu, 18 Apr 2024 13:35:38 +0800
Subject: [PATCH 05/35] test only

---
 apex/core/property/Elastic.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/apex/core/property/Elastic.py b/apex/core/property/Elastic.py
index f0a524f..de69bbd 100644
--- a/apex/core/property/Elastic.py
+++ b/apex/core/property/Elastic.py
@@ -4,7 +4,7 @@
 import re
 from shutil import copyfile
 
-import numpy as np
+import dpdata
 from monty.serialization import dumpfn, loadfn
 from pymatgen.analysis.elasticity.elastic import ElasticTensor
 from pymatgen.analysis.elasticity.strain import DeformedStructureSet, Strain
@@ -150,6 +150,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                 rot = Tensor.get_ieee_rotation(ss)
                 op = SymmOp.from_rotation_and_translation(rot)
                 ss.apply_operation(op)
+                ss.to(os.path.join(path_to_work, "POSCAR.ieee"), "POSCAR")
 
             dfm_ss = DeformedStructureSet(
                 ss,
@@ -177,9 +178,12 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                         os.remove(jj)
                 task_list.append(output_task)
                 dfm_ss.deformed_structures[ii].to("POSCAR", "POSCAR")
+                sys = dpdata.System("POSCAR", fmt='vasp/poscar')
+                os.remove("POSCAR")
+                sys.to("vasp/poscar", "poscar")
                 if self.inter_param["type"] == "abacus":
                     abacus_utils.poscar2stru("POSCAR", self.inter_param, "STRU")
-                    os.remove("POSCAR")
+                    #os.remove("POSCAR")
                 # record strain
                 df = Strain.from_deformation(dfm_ss.deformations[ii])
                 dumpfn(df.as_dict(), "strain.json", indent=4)

From d0c296727fde59c7442bebb74891b8fdf11931a5 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Thu, 18 Apr 2024 13:50:21 +0800
Subject: [PATCH 06/35] test only

---
 apex/core/property/Elastic.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/apex/core/property/Elastic.py b/apex/core/property/Elastic.py
index de69bbd..aa17511 100644
--- a/apex/core/property/Elastic.py
+++ b/apex/core/property/Elastic.py
@@ -179,8 +179,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                 task_list.append(output_task)
                 dfm_ss.deformed_structures[ii].to("POSCAR", "POSCAR")
                 sys = dpdata.System("POSCAR", fmt='vasp/poscar')
-                os.remove("POSCAR")
-                sys.to("vasp/poscar", "poscar")
+                sys.to("vasp/poscar", "POSCAR")
                 if self.inter_param["type"] == "abacus":
                     abacus_utils.poscar2stru("POSCAR", self.inter_param, "STRU")
                     #os.remove("POSCAR")

From cf2f43253f2b1e13a6016c76deb2766fdaf7f760 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Thu, 18 Apr 2024 16:33:15 +0800
Subject: [PATCH 07/35] undo test commit

---
 apex/core/property/Elastic.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/apex/core/property/Elastic.py b/apex/core/property/Elastic.py
index aa17511..ab55a24 100644
--- a/apex/core/property/Elastic.py
+++ b/apex/core/property/Elastic.py
@@ -178,8 +178,6 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                         os.remove(jj)
                 task_list.append(output_task)
                 dfm_ss.deformed_structures[ii].to("POSCAR", "POSCAR")
-                sys = dpdata.System("POSCAR", fmt='vasp/poscar')
-                sys.to("vasp/poscar", "POSCAR")
                 if self.inter_param["type"] == "abacus":
                     abacus_utils.poscar2stru("POSCAR", self.inter_param, "STRU")
                     #os.remove("POSCAR")

From 037ae1928c767db4ce96664d089f3b8d1c8101e2 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Sun, 21 Apr 2024 19:37:15 +0800
Subject: [PATCH 08/35] change: set default of ieee to be False in Elastic.py

---
 apex/core/property/Elastic.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/apex/core/property/Elastic.py b/apex/core/property/Elastic.py
index ab55a24..64364f0 100644
--- a/apex/core/property/Elastic.py
+++ b/apex/core/property/Elastic.py
@@ -34,7 +34,7 @@ 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"]

From 8250da4ecb63106311b8b2d65d619e1f6addcf55 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Mon, 22 Apr 2024 17:17:32 +0800
Subject: [PATCH 09/35] fix: unexpect termination of relaxation monitoring loop

---
 apex/flow.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/apex/flow.py b/apex/flow.py
index a19dcd5..ad264d3 100644
--- a/apex/flow.py
+++ b/apex/flow.py
@@ -77,7 +77,10 @@ def _monitor_relax(self):
             wf_status = self.workflow.query_status()
             if wf_status == 'Failed':
                 raise RuntimeError(f'Workflow failed (ID: {self.workflow.id}, UID: {self.workflow.uid})')
-            relax_post = step_info.get_step(name='relaxation-cal')[0]
+            try:
+                relax_post = step_info.get_step(name='relaxation-cal')[0]
+            except IndexError:
+                continue
             if relax_post['phase'] == 'Succeeded':
                 print(f'Relaxation finished (ID: {self.workflow.id}, UID: {self.workflow.uid})')
                 print('Retrieving completed tasks to local...')

From d0e2904067dd808aa46746c5b74cc284114f052c Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Mon, 22 Apr 2024 19:40:42 +0800
Subject: [PATCH 10/35] change: turn on default ieee translation

---
 apex/core/property/Elastic.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/apex/core/property/Elastic.py b/apex/core/property/Elastic.py
index 64364f0..b6bcd22 100644
--- a/apex/core/property/Elastic.py
+++ b/apex/core/property/Elastic.py
@@ -4,7 +4,6 @@
 import re
 from shutil import copyfile
 
-import dpdata
 from monty.serialization import dumpfn, loadfn
 from pymatgen.analysis.elasticity.elastic import ElasticTensor
 from pymatgen.analysis.elasticity.strain import DeformedStructureSet, Strain
@@ -34,7 +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", False)
+            parameter.setdefault("ieee", True)
             self.ieee = parameter["ieee"]
         parameter.setdefault("cal_type", "relaxation")
         self.cal_type = parameter["cal_type"]

From 0ca18b80576ddba5871980a869379551f4d9ca16 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Wed, 24 Apr 2024 16:33:30 +0800
Subject: [PATCH 11/35] feat(change): add `flow_name` to submit sub-mode for
 specification of workflow name; change default workflow name from flow type
 to workdir basename

---
 apex/config.py |  5 ++++-
 apex/flow.py   | 29 ++++++++++++++++++++++++++---
 apex/main.py   |  6 ++++++
 apex/submit.py | 10 ++++++++++
 4 files changed, 46 insertions(+), 4 deletions(-)

diff --git a/apex/config.py b/apex/config.py
index a9c15bb..21ba1cb 100644
--- a/apex/config.py
+++ b/apex/config.py
@@ -50,7 +50,7 @@ class Config:
     remote_password: str = None
     port: int = 22
 
-    # calculator config
+    # basic run config
     run_image_name: str = None
     run_command: str = None
     apex_image_name: str = "zhuoyli/apex_amd64"
@@ -63,8 +63,11 @@ class Config:
     vasp_run_command: str = None
     abacus_image_name: str = None
     abacus_run_command: str = None
+
+    # common APEX config
     is_bohrium_dflow: bool = False
     submit_only: bool = False
+    flow_name: str = None
 
     database_type: str = 'local'
     archive_method: str = 'sync'
diff --git a/apex/flow.py b/apex/flow.py
index ad264d3..1e502e6 100644
--- a/apex/flow.py
+++ b/apex/flow.py
@@ -69,6 +69,23 @@ def __init__(
         self.executor = executor
         self.upload_python_packages = upload_python_packages
 
+    @staticmethod
+    def regulate_name(name):
+        """
+        Adjusts the given workflow name to conform to RFC 1123 subdomain requirements.
+        It ensures the name is lowercase, contains only alphanumeric characters and hyphens,
+        and starts and ends with an alphanumeric character.
+        """
+        # lowercase the name
+        name = name.lower()
+        # substitute invalid characters with hyphens
+        name = re.sub(r'[^a-z0-9\-]', '-', name)
+        # make sure the name starts and ends with an alphanumeric character
+        name = re.sub(r'^[^a-z0-9]+', '', name)
+        name = re.sub(r'[^a-z0-9]+$', '', name)
+
+        return name
+
     def _monitor_relax(self):
         print('Waiting for relaxation result...')
         while True:
@@ -249,12 +266,14 @@ def submit_relax(
             download_path: Union[os.PathLike, str],
             relax_parameter: dict,
             submit_only: bool = False,
+            name: Optional[str] = None,
             labels: Optional[dict] = None
     ) -> str:
         self.upload_path = upload_path
         self.download_path = download_path
         self.relax_param = relax_parameter
-        self.workflow = Workflow(name='relaxation', labels=labels)
+        flow_name = name if name else self.regulate_name(os.path.basename(download_path))
+        self.workflow = Workflow(name=flow_name, labels=labels)
         relaxation = self._set_relax_flow(
             input_work_dir=upload_artifact(upload_path),
             relax_parameter=relax_parameter
@@ -275,12 +294,14 @@ def submit_props(
             download_path: Union[os.PathLike, str],
             props_parameter: dict,
             submit_only: bool = False,
+            name: Optional[str] = None,
             labels: Optional[dict] = None
     ) -> str:
         self.upload_path = upload_path
         self.download_path = download_path
         self.props_param = props_parameter
-        self.workflow = Workflow(name='property', labels=labels)
+        flow_name = name if name else self.regulate_name(os.path.basename(download_path))
+        self.workflow = Workflow(name=flow_name, labels=labels)
         subprops_list, subprops_key_list = self._set_props_flow(
             input_work_dir=upload_artifact(upload_path),
             props_parameter=props_parameter
@@ -302,13 +323,15 @@ def submit_joint(
             relax_parameter: dict,
             props_parameter: dict,
             submit_only: bool = False,
+            name: Optional[str] = None,
             labels: Optional[dict] = None
     ) -> str:
         self.upload_path = upload_path
         self.download_path = download_path
         self.relax_param = relax_parameter
         self.props_param = props_parameter
-        self.workflow = Workflow(name='joint', labels=labels)
+        flow_name = name if name else self.regulate_name(os.path.basename(download_path))
+        self.workflow = Workflow(name=flow_name, labels=labels)
         relaxation = self._set_relax_flow(
             input_work_dir=upload_artifact(upload_path),
             relax_parameter=self.relax_param
diff --git a/apex/main.py b/apex/main.py
index 55b8ade..8009127 100644
--- a/apex/main.py
+++ b/apex/main.py
@@ -76,6 +76,11 @@ def parse_args():
         choices=['relax', 'props', 'joint'],
         help="(Optional) Specify type of workflow to submit: (relax | props | joint)"
     )
+    parser_submit.add_argument(
+        "-n", "--name",
+        type=str, default=None,
+        help="(Optional) Specify name of the workflow",
+    )
 
     ##########################################
     # Do single step locally
@@ -526,6 +531,7 @@ def main():
             config_file=args.config,
             work_dirs=args.work,
             indicated_flow_type=args.flow,
+            flow_name=args.name,
             submit_only=args.submit_only,
             is_debug=args.debug
         )
diff --git a/apex/submit.py b/apex/submit.py
index ab2ebdb..0aa2a05 100644
--- a/apex/submit.py
+++ b/apex/submit.py
@@ -131,6 +131,7 @@ def submit(
         )
 
         flow_id = None
+        flow_name = wf_config.flow_name
         submit_only = wf_config.submit_only
         if flow_type == 'relax':
             flow_id = flow.submit_relax(
@@ -138,6 +139,7 @@ def submit(
                 download_path=work_dir,
                 relax_parameter=relax_param,
                 submit_only=submit_only,
+                name=flow_name,
                 labels=labels
             )
         elif flow_type == 'props':
@@ -146,6 +148,7 @@ def submit(
                 download_path=work_dir,
                 props_parameter=props_param,
                 submit_only=submit_only,
+                name=flow_name,
                 labels=labels
             )
         elif flow_type == 'joint':
@@ -155,6 +158,7 @@ def submit(
                 props_parameter=props_param,
                 relax_parameter=relax_param,
                 submit_only=submit_only,
+                name=flow_name,
                 labels=labels
             )
 
@@ -169,6 +173,7 @@ def submit_workflow(
     config_dict: dict,
     work_dirs: List[os.PathLike],
     indicated_flow_type: str,
+    flow_name: str = None,
     submit_only=False,
     is_debug=False,
     labels=None
@@ -188,6 +193,9 @@ def submit_workflow(
         config["debug_workdir"] = config_dict.get("debug_workdir", tmp_work_dir.name)
         s3_config["storage_client"] = None
 
+    if flow_name:
+        wf_config.flow_name = flow_name
+
     # judge basic flow info from user indicated parameter files
     (run_op, calculator, flow_type,
      relax_param, props_param) = judge_flow(parameter_dicts, indicated_flow_type)
@@ -269,6 +277,7 @@ def submit_from_args(
         config_file: os.PathLike,
         work_dirs,
         indicated_flow_type: str,
+        flow_name: str = None,
         submit_only=False,
         is_debug=False,
 ):
@@ -278,6 +287,7 @@ def submit_from_args(
         config_dict=load_config_file(config_file),
         work_dirs=work_dirs,
         indicated_flow_type=indicated_flow_type,
+        flow_name=flow_name,
         submit_only=submit_only,
         is_debug=is_debug,
     )

From 06996170588eb15f4194a709b98345e566f74c8e Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Wed, 24 Apr 2024 16:34:26 +0800
Subject: [PATCH 12/35] change: change default of `ieee` to False in Elastic.py

---
 apex/core/property/Elastic.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/apex/core/property/Elastic.py b/apex/core/property/Elastic.py
index b6bcd22..e0f63b4 100644
--- a/apex/core/property/Elastic.py
+++ b/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"]

From 37f793c83237a9cc36dade9408db2492a8b787ed Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Wed, 24 Apr 2024 16:44:10 +0800
Subject: [PATCH 13/35] Update README.md

---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index fd892d0..4863b39 100644
--- a/README.md
+++ b/README.md
@@ -109,7 +109,8 @@ The instructions regarding global configuration, [dflow](https://github.com/deep
   | group_size | Int | 1 | Number of tasks per parallel run group |
   | pool_size | Int | 1 | For multi tasks per parallel group, the pool size of multiprocessing pool to handle each task (1 for serial, -1 for infinity) |
   | upload_python_package | Optional[List] | None | Additional python packages required in the container |
-  | debug_pool_workers | Int | 1 | Pool size of parallel tasks running in the debug mode |
+  | debug_pool_workers | Int | 1 | Pool size of parallel tasks running in the debug mode | 
+  | flow_name | String | None | Specify name of workflow to be submitted (default: work path name) |
   | submit_only | Bool | False | Submit workflow only without automatic result retrieving |
 
 * **Dflow config**

From 0ec7455c1999510745fb298af0a94b2cbb1a10da Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Wed, 24 Apr 2024 16:51:43 +0800
Subject: [PATCH 14/35] change(minor): add `flow_type` to default `flow_name`

---
 apex/flow.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/apex/flow.py b/apex/flow.py
index 1e502e6..6d00180 100644
--- a/apex/flow.py
+++ b/apex/flow.py
@@ -273,6 +273,7 @@ def submit_relax(
         self.download_path = download_path
         self.relax_param = relax_parameter
         flow_name = name if name else self.regulate_name(os.path.basename(download_path))
+        flow_name += '-relax'
         self.workflow = Workflow(name=flow_name, labels=labels)
         relaxation = self._set_relax_flow(
             input_work_dir=upload_artifact(upload_path),
@@ -301,6 +302,7 @@ def submit_props(
         self.download_path = download_path
         self.props_param = props_parameter
         flow_name = name if name else self.regulate_name(os.path.basename(download_path))
+        flow_name += '-props'
         self.workflow = Workflow(name=flow_name, labels=labels)
         subprops_list, subprops_key_list = self._set_props_flow(
             input_work_dir=upload_artifact(upload_path),
@@ -331,6 +333,7 @@ def submit_joint(
         self.relax_param = relax_parameter
         self.props_param = props_parameter
         flow_name = name if name else self.regulate_name(os.path.basename(download_path))
+        flow_name += '-joint'
         self.workflow = Workflow(name=flow_name, labels=labels)
         relaxation = self._set_relax_flow(
             input_work_dir=upload_artifact(upload_path),

From be475c51f993000935ebd6abdab5d2fe617b4664 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Fri, 26 Apr 2024 13:25:23 +0800
Subject: [PATCH 15/35] change(minor): turn of defult `ieee` correction in
 Elastic.py

---
 apex/core/property/Elastic.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/apex/core/property/Elastic.py b/apex/core/property/Elastic.py
index e0f63b4..b6bcd22 100644
--- a/apex/core/property/Elastic.py
+++ b/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", False)
+            parameter.setdefault("ieee", True)
             self.ieee = parameter["ieee"]
         parameter.setdefault("cal_type", "relaxation")
         self.cal_type = parameter["cal_type"]

From d5106b463cbe28ad02a05b677ea208859b009e9e Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Sat, 27 Apr 2024 00:57:00 +0800
Subject: [PATCH 16/35] fix: reporter AttributeError by popping out
 `archive_key` from load dict from all_results.json in report.py

---
 apex/report.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/apex/report.py b/apex/report.py
index 79249d7..873beda 100644
--- a/apex/report.py
+++ b/apex/report.py
@@ -50,6 +50,7 @@ def report_local(input_path_list):
         data_dict = loadfn(kk)
         try:
             workdir_id = data_dict.pop('work_path')
+            _ = data_dict.pop('archive_key')
         except KeyError:
             logging.warning(msg=f'Invalid json for result archive, will skip: {kk}')
             continue

From 85415cf357daac8e1c7d0b957db91fd1869c88f2 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Sat, 27 Apr 2024 16:58:02 +0800
Subject: [PATCH 17/35] feat: simplify tmp upload dirs

---
 apex/utils.py | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/apex/utils.py b/apex/utils.py
index bf7fff2..7cf495a 100644
--- a/apex/utils.py
+++ b/apex/utils.py
@@ -42,13 +42,20 @@ def generate_random_string(length):
     return random_string
 
 
-def copy_all_other_files(src_dir, dst_dir, ignore_list=None) -> None:
+def copy_all_other_files(
+        src_dir,
+        dst_dir,
+        exclude_files=[],
+        include_dirs=[]
+) -> None:
     """
-    Copies all files from the source directory to the destination directory with some files excluded.
+    Copies all files from the source directory to the destination directory with some files excluded
+    and some directories included.
 
     :param src_dir: The path to the source directory.
     :param dst_dir: The path to the destination directory.
-    :ignore_list: files to be ignored.
+    :exclude_files: files to be ignored.
+    :include_dirs: directories to be included.
     """
     if not os.path.exists(src_dir):
         raise FileNotFoundError(f"Source directory {src_dir} does not exist.")
@@ -57,14 +64,12 @@ def copy_all_other_files(src_dir, dst_dir, ignore_list=None) -> None:
         os.makedirs(dst_dir)
 
     for item in os.listdir(src_dir):
-        if ignore_list and item in ignore_list:
-            continue
         src_path = os.path.join(src_dir, item)
         dst_path = os.path.join(dst_dir, item)
 
-        if os.path.isfile(src_path):
+        if os.path.isfile(src_path) and item not in exclude_files:
             shutil.copy2(src_path, dst_path)
-        elif os.path.isdir(src_path):
+        elif os.path.isdir(src_path) and item in include_dirs:
             shutil.copytree(src_path, dst_path)
 
 

From cdc0e2b096cd81cf7a42ff5d36421bd773b9fdb5 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Sat, 27 Apr 2024 17:00:13 +0800
Subject: [PATCH 18/35] feat: simplify tmp upload dirs

---
 apex/submit.py | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/apex/submit.py b/apex/submit.py
index 0aa2a05..27b5d50 100644
--- a/apex/submit.py
+++ b/apex/submit.py
@@ -41,6 +41,15 @@ def pack_upload_dir(
     os.chdir(work_dir)
     relax_confs = relax_param.get("structures", []) if relax_param else []
     prop_confs = prop_param.get("structures", []) if prop_param else []
+    relax_prefix = relax_param["interaction"].get("potcar_prefix", None) if relax_param else None
+    prop_prefix = prop_param["interaction"].get("potcar_prefix", None) if prop_param else None
+    include_dirs = set()
+    if relax_prefix:
+        relax_prefix_base = relax_prefix.split('/')[0]
+        include_dirs.add(relax_prefix_base)
+    if prop_prefix:
+        prop_prefix_base = prop_prefix.split('/')[0]
+        include_dirs.add(prop_prefix_base)
     confs = relax_confs + prop_confs
     assert len(confs) > 0, "No configuration path indicated!"
     conf_dirs = []
@@ -66,13 +75,11 @@ def pack_upload_dir(
                 backup_path(path_to_prop)
 
     """copy necessary files and directories into temp upload directory"""
-    # exclude 'all_result.json' from copy
-    conf_root_list = [conf.split('/')[0] for conf in conf_dirs]
-    conf_root_list = list(set(conf_root_list))
-    conf_root_list.sort()
-    ignore_copy_list = conf_root_list
-    ignore_copy_list.append("all_result.json")
-    copy_all_other_files(work_dir, upload_dir, ignore_list=ignore_copy_list)
+    copy_all_other_files(
+        work_dir, upload_dir,
+        exclude_files=["all_result.json"],
+        include_dirs=list(include_dirs)
+    )
     for ii in conf_dirs:
         build_conf_path = os.path.join(upload_dir, ii)
         os.makedirs(build_conf_path, exist_ok=True)

From 9d30174b591f41642977f44202b6e9cbfe468b85 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Sun, 28 Apr 2024 13:08:59 +0800
Subject: [PATCH 19/35] add nightly version tag

---
 apex/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/apex/__init__.py b/apex/__init__.py
index d810b1f..72faa07 100644
--- a/apex/__init__.py
+++ b/apex/__init__.py
@@ -1,5 +1,5 @@
 import os
-__version__ = '1.2.0'
+__version__ = '1.2.0.nightly-2024-04-28'
 LOCAL_PATH = os.getcwd()
 
 

From b33c8fc5ead80072ba6b101d9eb3e861ae5d3270 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Tue, 30 Apr 2024 13:28:10 +0800
Subject: [PATCH 20/35] add doi badge

---
 README.md        | 4 ++++
 apex/__init__.py | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 4863b39..49ab8ab 100644
--- a/README.md
+++ b/README.md
@@ -15,6 +15,10 @@
 * Add four additional **ML** pair styles (`snap`, `gap`, `rann` and `mace`) and an extra `meam-spline` in LAMMPS interation type support
 * Modify the single-step run command from `test` to `do` for improved clarity and consistencey
 
+## How to cite APEX
+If you use APEX in your research, please cite the following paper:
+[![](https://img.shields.io/badge/{doi}-{arXiv:2404.17330}-{blue}.svg)]({https://doi.org/10.48550/arXiv.2404.17330})
+
 ## Table of Contents
 
 - [APEX: Alloy Property EXplorer](#apex-alloy-property-explorer)
diff --git a/apex/__init__.py b/apex/__init__.py
index 72faa07..d810b1f 100644
--- a/apex/__init__.py
+++ b/apex/__init__.py
@@ -1,5 +1,5 @@
 import os
-__version__ = '1.2.0.nightly-2024-04-28'
+__version__ = '1.2.0'
 LOCAL_PATH = os.getcwd()
 
 

From 8826c09a14de6d2533f6e75922e5e64101ed93f1 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Tue, 30 Apr 2024 13:32:30 +0800
Subject: [PATCH 21/35] add doi badge

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 49ab8ab..3448fe6 100644
--- a/README.md
+++ b/README.md
@@ -17,7 +17,7 @@
 
 ## How to cite APEX
 If you use APEX in your research, please cite the following paper:
-[![](https://img.shields.io/badge/{doi}-{arXiv:2404.17330}-{blue}.svg)]({https://doi.org/10.48550/arXiv.2404.17330})
+[![](https://img.shields.io/badge/doi-arXiv:2404.17330-blue.svg)](https://doi.org/10.48550/arXiv.2404.17330)
 
 ## Table of Contents
 

From 16ff500b7c0c4a39d8cbcee795f81d3fb871760a Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Tue, 30 Apr 2024 13:37:36 +0800
Subject: [PATCH 22/35] add doi badge

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 3448fe6..aed60d4 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@
 # APEX: Alloy Property EXplorer
 
 [APEX](https://github.com/deepmodeling/APEX): Alloy Property EXplorer is a component of the [AI Square](https://aissquare.com/) project that involves the restructuring of the [DP-GEN](https://github.com/deepmodeling/dpgen) `auto_test` module to develop a versatile and extensible Python package for general alloy property calculations. This package enables users to conveniently establish a wide range of cloud-native property-test workflows by utilizing various computational approaches, including LAMMPS, VASP, ABACUS, and others.
-
+[![](https://img.shields.io/badge/release-1.2.0-blue.svg)](https://github.com/deepmodeling/APEX) [![](https://img.shields.io/badge/doi-arXiv:2404.17330-red.svg)](https://doi.org/10.48550/arXiv.2404.17330) 
 * Add a `retrieve` sub-command to allow results to be retrieved independently and manually for multiple properties (Remove `Distributor` and `Collector` OP)
 * Support common **dflow operations** with terminal commands
 * Incorporate results `archive` function to both local paths and NoSQL database ([MongoDB](https://www.mongodb.com/) and [DynamoDB](https://aws.amazon.com/cn/dynamodb/))

From 74a624c55448a6b334849b8f158f3e034d2b4984 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Tue, 30 Apr 2024 13:38:14 +0800
Subject: [PATCH 23/35] add doi badge

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index aed60d4..bbc3bb1 100644
--- a/README.md
+++ b/README.md
@@ -3,9 +3,9 @@
 </div>
 
 # APEX: Alloy Property EXplorer
-
-[APEX](https://github.com/deepmodeling/APEX): Alloy Property EXplorer is a component of the [AI Square](https://aissquare.com/) project that involves the restructuring of the [DP-GEN](https://github.com/deepmodeling/dpgen) `auto_test` module to develop a versatile and extensible Python package for general alloy property calculations. This package enables users to conveniently establish a wide range of cloud-native property-test workflows by utilizing various computational approaches, including LAMMPS, VASP, ABACUS, and others.
 [![](https://img.shields.io/badge/release-1.2.0-blue.svg)](https://github.com/deepmodeling/APEX) [![](https://img.shields.io/badge/doi-arXiv:2404.17330-red.svg)](https://doi.org/10.48550/arXiv.2404.17330) 
+[APEX](https://github.com/deepmodeling/APEX): Alloy Property EXplorer is a component of the [AI Square](https://aissquare.com/) project that involves the restructuring of the [DP-GEN](https://github.com/deepmodeling/dpgen) `auto_test` module to develop a versatile and extensible Python package for general alloy property calculations. This package enables users to conveniently establish a wide range of cloud-native property-test workflows by utilizing various computational approaches, including LAMMPS, VASP, ABACUS, and others.
+
 * Add a `retrieve` sub-command to allow results to be retrieved independently and manually for multiple properties (Remove `Distributor` and `Collector` OP)
 * Support common **dflow operations** with terminal commands
 * Incorporate results `archive` function to both local paths and NoSQL database ([MongoDB](https://www.mongodb.com/) and [DynamoDB](https://aws.amazon.com/cn/dynamodb/))

From af7dd4379637bd7bad143c651dbdbe1208997c65 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Tue, 30 Apr 2024 13:40:46 +0800
Subject: [PATCH 24/35] add doi badge

---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index bbc3bb1..1c48eee 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,7 @@
 
 # APEX: Alloy Property EXplorer
 [![](https://img.shields.io/badge/release-1.2.0-blue.svg)](https://github.com/deepmodeling/APEX) [![](https://img.shields.io/badge/doi-arXiv:2404.17330-red.svg)](https://doi.org/10.48550/arXiv.2404.17330) 
+
 [APEX](https://github.com/deepmodeling/APEX): Alloy Property EXplorer is a component of the [AI Square](https://aissquare.com/) project that involves the restructuring of the [DP-GEN](https://github.com/deepmodeling/dpgen) `auto_test` module to develop a versatile and extensible Python package for general alloy property calculations. This package enables users to conveniently establish a wide range of cloud-native property-test workflows by utilizing various computational approaches, including LAMMPS, VASP, ABACUS, and others.
 
 * Add a `retrieve` sub-command to allow results to be retrieved independently and manually for multiple properties (Remove `Distributor` and `Collector` OP)
@@ -17,7 +18,7 @@
 
 ## How to cite APEX
 If you use APEX in your research, please cite the following paper:
-[![](https://img.shields.io/badge/doi-arXiv:2404.17330-blue.svg)](https://doi.org/10.48550/arXiv.2404.17330)
+[arXiv:2404.17330](https://doi.org/10.48550/arXiv.2404.17330)
 
 ## Table of Contents
 

From f84068daf2f4befa1852d3e5df80cb569278e190 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Tue, 30 Apr 2024 16:35:28 +0800
Subject: [PATCH 25/35] add citation to header and README.md

---
 README.md        | 4 ++--
 apex/__init__.py | 4 ++++
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 1c48eee..6bb9102 100644
--- a/README.md
+++ b/README.md
@@ -17,8 +17,8 @@
 * Modify the single-step run command from `test` to `do` for improved clarity and consistencey
 
 ## How to cite APEX
-If you use APEX in your research, please cite the following paper:
-[arXiv:2404.17330](https://doi.org/10.48550/arXiv.2404.17330)
+If you use APEX in your future research, please cite the following paper for general purpose [![](https://img.shields.io/badge/doi-arXiv:2404.17330-red.svg)](https://doi.org/10.48550/arXiv.2404.17330) :
+> Z. Li, T. Wen, Y. Zhang, X. Liu, C. Zhang, A. S. L. S. Pattamatta, X. Gong, B. Ye, H.Wang, L. Zhang, D. J. Srolovitz, An extendable cloud- native alloy property explorer (2024). arXiv:2404.17330.
 
 ## Table of Contents
 
diff --git a/apex/__init__.py b/apex/__init__.py
index d810b1f..c0808e9 100644
--- a/apex/__init__.py
+++ b/apex/__init__.py
@@ -27,5 +27,9 @@ def header():
     header_str += "  AAA           AAA   PPP           EEEEEEEEEE  XXX       XXX\n"
     header_str += "---------------------------------------------------------------\n"
     header_str += f"==>> Alloy Property EXplorer using simulations (v{__version__})\n"
+    header_str += "Please read and cite: \n"
+    header_str += "Li et al, An extendable cloud- native alloy property explorer (2024). arXiv:2404.17330."
+    header_str += "See https://github.com/deepmodeling/APEX for more information.\n"
+    header_str += "---------------------------------------------------------------\n"
     header_str += "Checking input files..."
     print(header_str)

From 8c280fb913376bbafbe654d056540e8ab0b82540 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Tue, 30 Apr 2024 16:47:34 +0800
Subject: [PATCH 26/35] add citation to header and README.md

---
 README.md        | 7 +++++--
 apex/__init__.py | 4 ++--
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 6bb9102..6fca3fc 100644
--- a/README.md
+++ b/README.md
@@ -17,12 +17,15 @@
 * Modify the single-step run command from `test` to `do` for improved clarity and consistencey
 
 ## How to cite APEX
-If you use APEX in your future research, please cite the following paper for general purpose [![](https://img.shields.io/badge/doi-arXiv:2404.17330-red.svg)](https://doi.org/10.48550/arXiv.2404.17330) :
-> Z. Li, T. Wen, Y. Zhang, X. Liu, C. Zhang, A. S. L. S. Pattamatta, X. Gong, B. Ye, H.Wang, L. Zhang, D. J. Srolovitz, An extendable cloud- native alloy property explorer (2024). arXiv:2404.17330.
+If you use APEX in your future research, please cite the following paper for general purpose: 
+
+[![](https://img.shields.io/badge/doi-arXiv:2404.17330-red.svg)](https://doi.org/10.48550/arXiv.2404.17330)
+> Z. Li, T. Wen, Y. Zhang, X. Liu, C. Zhang, A. S. L. S. Pattamatta, X. Gong, B. Ye, H.Wang, L. Zhang, D. J. Srolovitz, An extendable cloud-native alloy property explorer (2024). arXiv:2404.17330.
 
 ## Table of Contents
 
 - [APEX: Alloy Property EXplorer](#apex-alloy-property-explorer)
+  - [How to cite APEX](#how-to-cite-apex)
   - [Table of Contents](#table-of-contents)
   - [1. Overview](#1-overview)
   - [2. Easy Install](#2-easy-install)
diff --git a/apex/__init__.py b/apex/__init__.py
index c0808e9..1487fd2 100644
--- a/apex/__init__.py
+++ b/apex/__init__.py
@@ -27,8 +27,8 @@ def header():
     header_str += "  AAA           AAA   PPP           EEEEEEEEEE  XXX       XXX\n"
     header_str += "---------------------------------------------------------------\n"
     header_str += f"==>> Alloy Property EXplorer using simulations (v{__version__})\n"
-    header_str += "Please read and cite: \n"
-    header_str += "Li et al, An extendable cloud- native alloy property explorer (2024). arXiv:2404.17330."
+    header_str += "Please cite DOI: 10.48550/arXiv.2404.17330\n"
+    header_str += "Li et al, An extendable cloud-native alloy property explorer (2024).\n"
     header_str += "See https://github.com/deepmodeling/APEX for more information.\n"
     header_str += "---------------------------------------------------------------\n"
     header_str += "Checking input files..."

From b5ade621e821e5f03c8a82ffe7226054f8357a6e Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Tue, 30 Apr 2024 16:48:30 +0800
Subject: [PATCH 27/35] add citation to header and README.md

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 6fca3fc..01593e6 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@
 </div>
 
 # APEX: Alloy Property EXplorer
-[![](https://img.shields.io/badge/release-1.2.0-blue.svg)](https://github.com/deepmodeling/APEX) [![](https://img.shields.io/badge/doi-arXiv:2404.17330-red.svg)](https://doi.org/10.48550/arXiv.2404.17330) 
+[![](https://img.shields.io/badge/release-1.2.0-blue.svg)](https://github.com/deepmodeling/APEX) [![](https://img.shields.io/badge/DOI-10.48550/arXiv.2404.17330-red.svg)](https://doi.org/10.48550/arXiv.2404.17330)
 
 [APEX](https://github.com/deepmodeling/APEX): Alloy Property EXplorer is a component of the [AI Square](https://aissquare.com/) project that involves the restructuring of the [DP-GEN](https://github.com/deepmodeling/dpgen) `auto_test` module to develop a versatile and extensible Python package for general alloy property calculations. This package enables users to conveniently establish a wide range of cloud-native property-test workflows by utilizing various computational approaches, including LAMMPS, VASP, ABACUS, and others.
 
@@ -19,7 +19,7 @@
 ## How to cite APEX
 If you use APEX in your future research, please cite the following paper for general purpose: 
 
-[![](https://img.shields.io/badge/doi-arXiv:2404.17330-red.svg)](https://doi.org/10.48550/arXiv.2404.17330)
+[![](https://img.shields.io/badge/DOI-10.48550/arXiv.2404.17330-red.svg)](https://doi.org/10.48550/arXiv.2404.17330)
 > Z. Li, T. Wen, Y. Zhang, X. Liu, C. Zhang, A. S. L. S. Pattamatta, X. Gong, B. Ye, H.Wang, L. Zhang, D. J. Srolovitz, An extendable cloud-native alloy property explorer (2024). arXiv:2404.17330.
 
 ## Table of Contents

From 480c6d6ab515db19c51ebce29c28c37e96cb45a9 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Tue, 30 Apr 2024 17:01:31 +0800
Subject: [PATCH 28/35] add citation to header and README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 01593e6..0b9a62f 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@
 </div>
 
 # APEX: Alloy Property EXplorer
-[![](https://img.shields.io/badge/release-1.2.0-blue.svg)](https://github.com/deepmodeling/APEX) [![](https://img.shields.io/badge/DOI-10.48550/arXiv.2404.17330-red.svg)](https://doi.org/10.48550/arXiv.2404.17330)
+[![](https://img.shields.io/badge/release-1.2.0-blue.svg)](https://github.com/deepmodeling/APEX)
 
 [APEX](https://github.com/deepmodeling/APEX): Alloy Property EXplorer is a component of the [AI Square](https://aissquare.com/) project that involves the restructuring of the [DP-GEN](https://github.com/deepmodeling/dpgen) `auto_test` module to develop a versatile and extensible Python package for general alloy property calculations. This package enables users to conveniently establish a wide range of cloud-native property-test workflows by utilizing various computational approaches, including LAMMPS, VASP, ABACUS, and others.
 

From 04d45e257b60ac268dea3b8f5372b7c92ef60d01 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Mon, 6 May 2024 12:04:20 +0800
Subject: [PATCH 29/35] add app link to header and README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 0b9a62f..a8895c4 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@
 </div>
 
 # APEX: Alloy Property EXplorer
-[![](https://img.shields.io/badge/release-1.2.0-blue.svg)](https://github.com/deepmodeling/APEX)
+[![](https://img.shields.io/badge/release-1.2.0-blue.svg)](https://github.com/deepmodeling/APEX) [![](https://img.shields.io/badge/APP-BohriumApp-orange.svg)](https://app.bohrium.dp.tech/apex/)
 
 [APEX](https://github.com/deepmodeling/APEX): Alloy Property EXplorer is a component of the [AI Square](https://aissquare.com/) project that involves the restructuring of the [DP-GEN](https://github.com/deepmodeling/dpgen) `auto_test` module to develop a versatile and extensible Python package for general alloy property calculations. This package enables users to conveniently establish a wide range of cloud-native property-test workflows by utilizing various computational approaches, including LAMMPS, VASP, ABACUS, and others.
 

From 1dc01136ebe23e9f5073dae14d8a7ab691698e8a Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Mon, 6 May 2024 15:36:06 +0800
Subject: [PATCH 30/35] add app link to header and README.md

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index a8895c4..66c0d08 100644
--- a/README.md
+++ b/README.md
@@ -7,6 +7,7 @@
 
 [APEX](https://github.com/deepmodeling/APEX): Alloy Property EXplorer is a component of the [AI Square](https://aissquare.com/) project that involves the restructuring of the [DP-GEN](https://github.com/deepmodeling/dpgen) `auto_test` module to develop a versatile and extensible Python package for general alloy property calculations. This package enables users to conveniently establish a wide range of cloud-native property-test workflows by utilizing various computational approaches, including LAMMPS, VASP, ABACUS, and others.
 
+## v1.2 Main Features Update
 * Add a `retrieve` sub-command to allow results to be retrieved independently and manually for multiple properties (Remove `Distributor` and `Collector` OP)
 * Support common **dflow operations** with terminal commands
 * Incorporate results `archive` function to both local paths and NoSQL database ([MongoDB](https://www.mongodb.com/) and [DynamoDB](https://aws.amazon.com/cn/dynamodb/))
@@ -25,6 +26,7 @@ If you use APEX in your future research, please cite the following paper for gen
 ## Table of Contents
 
 - [APEX: Alloy Property EXplorer](#apex-alloy-property-explorer)
+  - [v1.2 Main Features Update](#v12-main-features-update)
   - [How to cite APEX](#how-to-cite-apex)
   - [Table of Contents](#table-of-contents)
   - [1. Overview](#1-overview)

From 62c237014027b2f13b2abd194cf2dcaa4aac5b19 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Mon, 6 May 2024 15:48:01 +0800
Subject: [PATCH 31/35] add app link to header and README.md

---
 README.md | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 66c0d08..3c8b144 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@
 </div>
 
 # APEX: Alloy Property EXplorer
-[![](https://img.shields.io/badge/release-1.2.0-blue.svg)](https://github.com/deepmodeling/APEX) [![](https://img.shields.io/badge/APP-BohriumApp-orange.svg)](https://app.bohrium.dp.tech/apex/)
+[![](https://img.shields.io/badge/release-1.2.0-blue.svg)](https://github.com/deepmodeling/APEX)
 
 [APEX](https://github.com/deepmodeling/APEX): Alloy Property EXplorer is a component of the [AI Square](https://aissquare.com/) project that involves the restructuring of the [DP-GEN](https://github.com/deepmodeling/dpgen) `auto_test` module to develop a versatile and extensible Python package for general alloy property calculations. This package enables users to conveniently establish a wide range of cloud-native property-test workflows by utilizing various computational approaches, including LAMMPS, VASP, ABACUS, and others.
 
@@ -17,6 +17,10 @@
 * Add four additional **ML** pair styles (`snap`, `gap`, `rann` and `mace`) and an extra `meam-spline` in LAMMPS interation type support
 * Modify the single-step run command from `test` to `do` for improved clarity and consistencey
 
+## APEX Bohrium App
+[![](https://img.shields.io/badge/APP-BohriumApp-orange.svg)](https://app.bohrium.dp.tech/apex/)
+APEX also provides a web-based [Bohrium App](https://app.bohrium.dp.tech/apex/) for rapid and easy alloy property calculations without intensive JSON configuration (Notice: one will need a Bohrium account to access this service).
+
 ## How to cite APEX
 If you use APEX in your future research, please cite the following paper for general purpose: 
 

From 48fcc949c88892a7220556a0bf1b8ce2b41c79de Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Mon, 6 May 2024 15:50:37 +0800
Subject: [PATCH 32/35] add app link to header and README.md

---
 README.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 3c8b144..e18f6e8 100644
--- a/README.md
+++ b/README.md
@@ -19,12 +19,14 @@
 
 ## APEX Bohrium App
 [![](https://img.shields.io/badge/APP-BohriumApp-orange.svg)](https://app.bohrium.dp.tech/apex/)
+
 APEX also provides a web-based [Bohrium App](https://app.bohrium.dp.tech/apex/) for rapid and easy alloy property calculations without intensive JSON configuration (Notice: one will need a Bohrium account to access this service).
 
 ## How to cite APEX
+[![](https://img.shields.io/badge/DOI-10.48550/arXiv.2404.17330-red.svg)](https://doi.org/10.48550/arXiv.2404.17330)
+
 If you use APEX in your future research, please cite the following paper for general purpose: 
 
-[![](https://img.shields.io/badge/DOI-10.48550/arXiv.2404.17330-red.svg)](https://doi.org/10.48550/arXiv.2404.17330)
 > Z. Li, T. Wen, Y. Zhang, X. Liu, C. Zhang, A. S. L. S. Pattamatta, X. Gong, B. Ye, H.Wang, L. Zhang, D. J. Srolovitz, An extendable cloud-native alloy property explorer (2024). arXiv:2404.17330.
 
 ## Table of Contents

From fdfdca8affa23f9f70fc6114ad0afa25fe0cafb2 Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Mon, 6 May 2024 15:51:40 +0800
Subject: [PATCH 33/35] add app link to header and README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index e18f6e8..2cc3946 100644
--- a/README.md
+++ b/README.md
@@ -20,7 +20,7 @@
 ## APEX Bohrium App
 [![](https://img.shields.io/badge/APP-BohriumApp-orange.svg)](https://app.bohrium.dp.tech/apex/)
 
-APEX also provides a web-based [Bohrium App](https://app.bohrium.dp.tech/apex/) for rapid and easy alloy property calculations without intensive JSON configuration (Notice: one will need a Bohrium account to access this service).
+APEX also provides a web-based [Bohrium App](https://app.bohrium.dp.tech/apex/) for rapid and easy alloy property calculations without intensive JSON configuration (Note: one will need a Bohrium account to access this service).
 
 ## How to cite APEX
 [![](https://img.shields.io/badge/DOI-10.48550/arXiv.2404.17330-red.svg)](https://doi.org/10.48550/arXiv.2404.17330)

From 1ab7ddd1e5debc6a8b8c40e03b071e2c0869a89f Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Mon, 6 May 2024 16:29:34 +0800
Subject: [PATCH 34/35] update README.md

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 2cc3946..e049bd3 100644
--- a/README.md
+++ b/README.md
@@ -33,6 +33,7 @@ If you use APEX in your future research, please cite the following paper for gen
 
 - [APEX: Alloy Property EXplorer](#apex-alloy-property-explorer)
   - [v1.2 Main Features Update](#v12-main-features-update)
+  - [APEX Bohrium App](#apex-bohrium-app)
   - [How to cite APEX](#how-to-cite-apex)
   - [Table of Contents](#table-of-contents)
   - [1. Overview](#1-overview)

From 92b9ea6262953686c7b6f4a53953628d0637ef5b Mon Sep 17 00:00:00 2001
From: Zhuoyuan <75076820+ZLI-afk@users.noreply.github.com>
Date: Mon, 6 May 2024 17:26:49 +0800
Subject: [PATCH 35/35] update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index e049bd3..0f9001e 100644
--- a/README.md
+++ b/README.md
@@ -25,7 +25,7 @@ APEX also provides a web-based [Bohrium App](https://app.bohrium.dp.tech/apex/)
 ## How to cite APEX
 [![](https://img.shields.io/badge/DOI-10.48550/arXiv.2404.17330-red.svg)](https://doi.org/10.48550/arXiv.2404.17330)
 
-If you use APEX in your future research, please cite the following paper for general purpose: 
+If you use APEX in your research, please cite the following paper for general purpose: 
 
 > Z. Li, T. Wen, Y. Zhang, X. Liu, C. Zhang, A. S. L. S. Pattamatta, X. Gong, B. Ye, H.Wang, L. Zhang, D. J. Srolovitz, An extendable cloud-native alloy property explorer (2024). arXiv:2404.17330.