resolve conflicts

Author: felix5572

dpti/equi.py

@@ -131,7 +131,7 @@ def gen_equi_dump_settings(if_dump_avg_posi):
     return ret
 
 
-def gen_equi_ensemble_settings(ens):
+def gen_equi_ensemble_settings(ens, if_dump_avg_posi):
     # ens = equi_settings['ens']
     ret = ""
     if ens == "nvt":
@@ -156,6 +156,11 @@ def gen_equi_ensemble_settings(ens):
     ret += "velocity        all zero linear\n"
     ret += "# --------------------- RUN ------------------------------\n"
     ret += "run             ${NSTEPS}\n"
+    if if_dump_avg_posi:
+        ret += "undump           fp\n"
+        ret += "undump           1\n"
+        ret += "unfix            ap\n"
+        ret += "read_dump        dump.avgposi ${NSTEPS} x y z label x f_ap[1] label y f_ap[2] label z f_ap[3]\n"
     ret += "write_data      out.lmp\n"
     return ret
 
@@ -198,7 +203,9 @@ def gen_equi_lammps_input(
     )
     equi_thermo_settings = gen_equi_thermo_settings(timestep=timestep)
     equi_dump_settings = gen_equi_dump_settings(if_dump_avg_posi=if_dump_avg_posi)
-    equi_ensemble_settings = gen_equi_ensemble_settings(ens=ens)
+    equi_ensemble_settings = gen_equi_ensemble_settings(
+        ens=ens, if_dump_avg_posi=if_dump_avg_posi
+    )
 
     equi_lammps_input = (
         equi_header
@@ -355,7 +362,6 @@ def make_task(
     ens=None,
     temp=None,
     pres=None,
-    if_dump_avg_posi=None,
     npt_dir=None,
 ):
     equi_args = [
@@ -385,7 +391,6 @@ def make_task(
         ens=ens,
         temp=temp,
         pres=pres,
-        if_dump_avg_posi=if_dump_avg_posi,
         npt_dir=npt_dir,
     )
 
@@ -673,12 +678,6 @@ def add_subparsers(module_subparsers):
     parser_gen.add_argument(
         "-p", "--pressure", type=float, help="the pressure of the system"
     )
-    parser_gen.add_argument(
-        "-a",
-        "--avg-posi",
-        action="store_true",
-        help="dump the average position of atoms",
-    )
     parser_gen.add_argument(
         "-c", "--conf-npt", type=str, help="use conf computed from NPT simulation"
     )
@@ -728,7 +727,6 @@ def handle_gen(args):
         args.ensemble,
         args.temperature,
         args.pressure,
-        args.avg_posi,
         args.conf_npt,
     )
 

dpti/hti_liq.py

@@ -503,7 +503,9 @@ def compute_task(
     if "copies" in jdata:
         natoms *= np.prod(jdata["copies"])
     fe, fe_err, thermo_info = post_tasks(job, natoms)
-    print(f"hti_liq.compute_task: ideal gas fe = {fe:.68}eV, err = {fe_err[0]:.6f}eV, {fe_err[1]:.6f}eV per atom")
+    print(
+        f"hti_liq.compute_task: ideal gas fe = {fe:.68}eV, err = {fe_err[0]:.6f}eV, {fe_err[1]:.6f}eV per atom"
+    )
     _print_thermo_info(thermo_info)
 
     info = thermo_info.copy()

dpti/workflows/__init__.py

@@ -15,4 +15,4 @@
 
 # # dynamically import sub modules
 # for module_name in MODULES_TO_IMPORT:
-#     globals()[module_name] = _import_module(module_name)
+#     globals()[module_name] = _import_module(module_name)

dpti/workflows/flows/base_flow.py

@@ -1,29 +1,36 @@
-#%%
+# %%
 import os
-import json
-from typing import Dict, Any, List, Optional, Set
-import yaml
-from dataclasses import dataclass
-from abc import ABC, abstractmethod
-from prefect import flow, get_run_logger
-from prefect.artifacts import create_markdown_artifact
-from pydantic import BaseModel, Field, computed_field
-from functools import cached_property
-from typing import TypeVar, Protocol, Generic, Any, Optional, List, Union, AbstractSet, MutableMapping
 
 # from dependency_injector import containers, providers
 # from dependency_injector.wiring import Provide, inject
 import sys
 # sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../' '../', '../')))
+from abc import abstractmethod
+from dataclasses import dataclass
+from typing import (
+    Any,
+    Generic,
+    Protocol,
+    TypeVar,
+)
+
+from pydantic import BaseModel
+
+sys.path.insert(
+    0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../" "../", "../"))
+)
 # from dpti.workflows.service.service_container import WorkflowContainer, WorkflowServices
 from dpti.workflows.service.workflow_decorator import workflow_task_decorator
-from dpti.workflows.service.workflow_service_module import WorkflowServiceModule
-from dpti.workflows.service.workflow_service_module import WorkflowServices, BasicWorkflowServices
-
-from dpti.workflows.simulations.base import SettingsBase, FlowRuntimeContext, FlowMetaInfo, FlowProcedureControl
+from dpti.workflows.service.workflow_service_module import (
+    WorkflowServices,
+)
+from dpti.workflows.simulations.base import (
+    FlowMetaInfo,
+    FlowProcedureControl,
+    FlowRuntimeContext,
+)
 
-
-#%%
+# %%
 
 # WorkflowSettingsType = TypeVar('WorkflowSettingsType')
 
@@ -33,7 +40,6 @@
 #     flow_run_number: int
 
 
-
 # class WorkflowSettings(BaseModel):
 #     config_yaml: str
 #     flow_trigger_dir: str
@@ -67,33 +73,31 @@ class FlowTriggerInfo:
     flow_trigger_dir: str
 
 
-
 class workflow_context(BaseModel):
     flow_meta_info: FlowMetaInfo
     flow_trigger_info: FlowTriggerInfo
     # workflow_services: WorkflowServices  # Protocol 类型
     flow_procedure_control: FlowProcedureControl
-    
+
     # model_config = {
     #     "arbitrary_types_allowed": True  # 允许任意类型
     # }
-    
-# flow_params
 
 
+# flow_params
 
-DomainInputType = TypeVar('DomainInputType', bound=BaseModel)
 
+DomainInputType = TypeVar("DomainInputType", bound=BaseModel)
 
 
 class WorkflowSettingsModel(Protocol):
-    """需要满足的最小接口要求"""
+    """需要满足的最小接口要求."""
+
     flow_trigger_info: FlowTriggerInfo
     flow_procedure_control: FlowProcedureControl
     domain_input_raw: BaseModel
 
 
-
 class BaseWorkflow(Generic[DomainInputType]):
     workflow_services: WorkflowServices
     flow_trigger_dir: str
@@ -104,40 +108,38 @@ class BaseWorkflow(Generic[DomainInputType]):
     flow_run_number: int = 0
     # @inject
     # def __init__(self, workflow_services:WorkflowServices=Provide[WorkflowContainer.workflow_services]):
-        # """初始化工作流应用flow装饰器"""
-        # 应用flow装饰器
-        # self.workflow_services = workflow_services
-        
+    # """初始化工作流应用flow装饰器"""
+    # 应用flow装饰器
+    # self.workflow_services = workflow_services
+
     # def init_workflow_services(self, workflow_services:WorkflowServices):
     #     self.workflow_services = workflow_services
 
-        # self.flow_object = flow(
-        #     name=f"{self.__class__.__name__}Flow",
-        #     # flow_run_name=,
-        #     log_prints=True,
-        #     persist_result=True
-        # )(self.execute_flow)
-
-
-
+    # self.flow_object = flow(
+    #     name=f"{self.__class__.__name__}Flow",
+    #     # flow_run_name=,
+    #     log_prints=True,
+    #     persist_result=True
+    # )(self.execute_flow)
 
     # def __call__(self, flow_params: WorkflowSettingsModel) -> Any:
     #     """执行工作流"""
     #     r = self.execute_flow(flow_params=flow_params)
     #     return r
 
-
     @workflow_task_decorator
     def flow_start_check(self):
         flow_trigger_dir = self.flow_trigger_dir
         flow_run_number = self.flow_run_number
 
         # config_yaml = self.flow_params.domain_params.config_yaml
-        
+
         io_handler = self.workflow_services.io_handler
 
         self.check_if_flow_trigger_dir_exists()
-        produced_flow_running_dir = self.workflow_services.io_handler.setup_flow_running_dir()
+        produced_flow_running_dir = (
+            self.workflow_services.io_handler.setup_flow_running_dir()
+        )
         # io_handler.create_job_dir()
 
         return produced_flow_running_dir
@@ -151,23 +153,21 @@ def check_if_flow_trigger_dir_exists(self):
 
     # def check_if_config_yaml_exists(self, io_handler: IOHandler):
     #     pass
-        
+
     def execute_flow(self) -> Any:
-        """执行工作流"""
+        """执行工作流."""
         r = self._execute_impl()
         return r
-    
+
     @abstractmethod
     def _execute_impl(self) -> Any:
-        """执行工作流"""
+        """执行工作流."""
         pass
 
-
-
-
     # @abstractmethod
     # def _execute_impl(self, domain_input_raw: DomainInputRawType) -> Any:
     #     """执行工作流"""
     #     pass
 
-#%%
+
+# %%