NepTrainKit 2.0.6.dev27__tar.gz → 2.0.6.dev33__tar.gz

{neptrainkit-2.0.6.dev27 → neptrainkit-2.0.6.dev33}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: NepTrainKit
-Version: 2.0.6.dev27
+Version: 2.0.6.dev33
 Summary: NepTrainKit is a Python package for visualizing and manipulating training datasets for NEP.
 Author: Chen Cheng bing
 Author-email: Chen Cheng bing <1747193328@qq.com>

{neptrainkit-2.0.6.dev27 → neptrainkit-2.0.6.dev33}/src/NepTrainKit/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '2.0.6.dev27'
-__version_tuple__ = version_tuple = (2, 0, 6, 'dev27')
+__version__ = version = '2.0.6.dev33'
+__version_tuple__ = version_tuple = (2, 0, 6, 'dev33')

{neptrainkit-2.0.6.dev27 → neptrainkit-2.0.6.dev33}/src/NepTrainKit/core/canvas/pyqtgraph/canvas.py

@@ -282,8 +282,12 @@ class PyqtgraphCanvas(CanvasLayoutBase,GraphicsLayoutWidget, metaclass=CombinedM
                         y_range[0]=y_min
                     if y_max > y_range[1]:
                         y_range[1]=y_max
+            if plot.title!="descriptor":
 
-            view.setRange(xRange=x_range,yRange=y_range)
+                real_range=(min(x_range[0],y_range[0]),max(x_range[1],y_range[1]))
+                view.setRange(xRange=real_range,yRange=real_range)
+            else:
+                view.setRange(xRange=x_range,yRange=y_range)
 
     def pan(self, checked):
 

{neptrainkit-2.0.6.dev27 → neptrainkit-2.0.6.dev33}/src/NepTrainKit/core/canvas/vispy/canvas.py

@@ -16,12 +16,10 @@ from vispy import scene
 from vispy.app.backends import _pyside6
 from vispy.color import ColorArray
 from vispy.visuals.filters import MarkerPickingFilter
-
 from NepTrainKit import utils
 from NepTrainKit.core.canvas.base.canvas import VispyCanvasLayoutBase
 from NepTrainKit.core.io import NepTrainResultData
 from NepTrainKit.core.types import Brushes, Pens
-
 _pyside6
 vispy.use("PySide6", "gl2")
 
@@ -84,6 +82,7 @@ class ViewBoxWidget(scene.Widget):
         self.freeze()
 
 
+
     def convert_color(self, obj):
         if isinstance(obj, (QPen, QBrush)):
 
@@ -115,8 +114,8 @@ class ViewBoxWidget(scene.Widget):
         x = x[x > -10000]
         y = y[y > -10000]
         if x.size == 0:
-            x_range =None
-            y_range = None
+            x_range =[0,1]
+            y_range =[0,1]
 
         else:
 
@@ -134,9 +133,16 @@ class ViewBoxWidget(scene.Widget):
                 y_range[1] = y_max
         # self._view.camera.set_range( )
         #
+        if "descriptor"!=self.title:
+
+            real_range=(min(x_range[0],y_range[0]),max(x_range[1],y_range[1]))
+
+            self._view.camera.set_range( real_range,  real_range)
+        else:
+            self._view.camera.set_range( x_range,  y_range)
 
-        self._view.camera.set_range( x_range,  y_range)
     def set_current_point(self, x,y):
+
         if np.array(x).size == 0:
             if self.current_point is not None:
                 self.current_point.parent=None
@@ -174,6 +180,9 @@ class ViewBoxWidget(scene.Widget):
         if x.size != 0:
             self._scatter.set_data(np.vstack([x, y]).T, **kwargs)
             self.auto_range()
+        else:
+            self._scatter.set_data(np.empty((0, 3)), **kwargs)
+            self.auto_range()
         self.update_diagonal()
         return self._scatter
 
@@ -437,11 +446,10 @@ class VispyCanvas(VispyCanvasLayoutBase, scene.SceneCanvas, metaclass=CombinedMe
         self.nep_result_data.select_index.clear()
 
         for index,_dataset in enumerate(self.nep_result_data.dataset):
+
             plot=self.axes_list[index]
-            # if _dataset.x.size==0:
-            #
 
-            #     continue
+
             plot.title= _dataset.title
 
             plot.scatter(_dataset.x,_dataset.y,data=_dataset.structure_index,
@@ -450,6 +458,7 @@ class VispyCanvas(VispyCanvasLayoutBase, scene.SceneCanvas, metaclass=CombinedMe
 
                                       )
 
+            # continue
             if _dataset.group_array.num !=0:
                 #更新结构
                 if self.structure_index not in _dataset.group_array.now_data:
@@ -466,7 +475,6 @@ class VispyCanvas(VispyCanvasLayoutBase, scene.SceneCanvas, metaclass=CombinedMe
                 plot.text.text=text
                 plot.text.pos=pos
     def convert_pos(self,plot,pos):
-
         x_range = plot.xaxis.axis.domain  # x轴范围 [xmin, xmax]
         y_range = plot.yaxis.axis.domain # y轴范围 [ymin, ymax]
 

{neptrainkit-2.0.6.dev27 → neptrainkit-2.0.6.dev33}/src/NepTrainKit/core/io/nep.py

@@ -4,6 +4,9 @@
 # @Author  : 兵
 # @email    : 1747193328@qq.com
 import time
+
+from ase.stress import full_3x3_to_voigt_6_stress
+
 start=time.time()
 import os
 import traceback
@@ -17,6 +20,7 @@ from NepTrainKit.core import MessageManager, Structure, Config
 from NepTrainKit.core.calculator import NEPProcess
 
 
+
 from NepTrainKit.core.io.base import NepPlotData, StructureData
 
 
@@ -346,7 +350,7 @@ class NepTrainResultData(ResultData):
         """判断是否需要重新计算 NEP 数据。"""
 
 
-        output_files_exist = all([
+        output_files_exist = any([
             self.energy_out_path.exists(),
             self.force_out_path.exists(),
             self.stress_out_path.exists(),
@@ -424,7 +428,8 @@ class NepTrainResultData(ResultData):
             logger.debug(traceback.format_exc())
             virials_array = np.column_stack([virials, virials])
 
-        stress_array = virials_array * coefficient * 160.21766208  # 单位转换
+        stress_array = virials_array * coefficient  * 160.21766208  # 单位转换\
+
         stress_array = stress_array.astype(np.float32)
         if virials_array.size != 0:
             np.savetxt(self.virial_out_path, virials_array, fmt='%10.8f')

{neptrainkit-2.0.6.dev27 → neptrainkit-2.0.6.dev33}/src/NepTrainKit/core/pages/makedata.py

@@ -12,12 +12,9 @@ from PySide6.QtWidgets import QWidget, QGridLayout, QApplication
 from NepTrainKit.core import MessageManager
 from NepTrainKit.core.custom_widget import MakeWorkflowArea, CardGroup
 
-from NepTrainKit.core.views.cards import (MakeDataCard,CardGroup,CellScalingCard,ConsoleWidget,
-                                          SuperCellCard,PerturbCard,FilterDataCard,
-                                          MakeDataCardWidget,FPSFilterDataCard,VacancyDefectCard,
-card_info_dict
+from NepTrainKit.core.views.cards import   ConsoleWidget,card_info_dict
+
 
-                                          )
 from NepTrainKit.version import __version__
 from NepTrainKit import utils, module_path
 from ase.io import read as ase_read

{neptrainkit-2.0.6.dev27 → neptrainkit-2.0.6.dev33}/src/NepTrainKit/core/pages/show_nep.py

@@ -303,7 +303,7 @@ class ShowNepWidget(QWidget):
             return
 
         self.struct_index_spinbox.setMaximum(self.nep_result_data.num)
-        self.graph_widget.clear()
+        # self.graph_widget.clear()
 
         self.graph_widget.set_dataset(self.nep_result_data)
         self.nep_result_data.updateInfoSignal.connect(self.update_dataset_info)

{neptrainkit-2.0.6.dev27 → neptrainkit-2.0.6.dev33}/src/NepTrainKit/core/structure.py

@@ -6,11 +6,10 @@
 import json
 import os
 import re
-from itertools import product
+
 from copy import deepcopy
 import numpy as np
-from PySide6.QtCore import QThread
-from numpy.linalg import solve, norm
+
 
 from NepTrainKit import utils, module_path
 
@@ -132,15 +131,21 @@ class Structure():
     def per_atom_energy(self):
 
 
-        return self.additional_fields[ "energy"]/self.num_atoms
+        return self.additional_fields["energy"]/self.num_atoms
     @property
     def forces(self):
         return self.structure_info[self.force_label]
 
     @property
     def nep_virial(self):
-
-        vir=np.array(self.virial.split(" "),dtype=np.float32)
+        try:
+            vir=np.array(self.virial.split(" "),dtype=np.float32)
+        except:
+            #检查下有没有压强
+            try:
+                vir= np.array(self.stress.split(" "),dtype=np.float32)*self.volume*-1
+            except:
+                raise ValueError("No virial or stress data")
 
         return vir[[0,4,8,1,5,6]]/self.num_atoms
     @property
@@ -394,7 +399,7 @@ class Structure():
                     # 这里是为了后面的Config搜索做统一
                     key = "Config_type"
                     value=str(value)
-                if key.lower() in ("energy", "pbc","virial"):
+                if key.lower() in ("energy", "pbc","virial","stress"):
                     key=key.lower()
                 additional_fields[key] = value
                 # print(additional_fields)

{neptrainkit-2.0.6.dev27 → neptrainkit-2.0.6.dev33}/src/NepTrainKit/core/views/cards.py

@@ -55,9 +55,9 @@ def is_organic_cluster(symbols):
     if not has_carbon:
         return False
     # 可选：强制要求含氢（H）或其他有机元素
-    # organic_elements = {'H', 'O', 'N', 'S', 'P'}
-    # has_organic_elements = any(symbol in organic_elements for symbol in symbols)
-    # return has_carbon and has_organic_elements
+    organic_elements = {'H', 'O', 'N', 'S', 'P'}
+    has_organic_elements = any(symbol in organic_elements for symbol in symbols)
+    return has_carbon and has_organic_elements
     return True
 
 

{neptrainkit-2.0.6.dev27 → neptrainkit-2.0.6.dev33}/src/NepTrainKit/core/views/nep.py

@@ -53,7 +53,7 @@ class NepResultPlotWidget(QWidget):
 
     def clear(self):
         self.canvas.clear_axes()
-        self.last_figure_num=None
+        # self.last_figure_num=None
 
 
 
@@ -179,8 +179,10 @@ class NepResultPlotWidget(QWidget):
     def set_dataset(self,dataset):
 
         if self.last_figure_num !=len(dataset.dataset):
+
             self.canvas.init_axes(len(dataset.dataset))
             self.last_figure_num = len(dataset.dataset)
+
         self.canvas.set_nep_result_data(dataset)
         self.canvas.plot_nep_result()
 

{neptrainkit-2.0.6.dev27 → neptrainkit-2.0.6.dev33}/src/NepTrainKit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: NepTrainKit
-Version: 2.0.6.dev27
+Version: 2.0.6.dev33
 Summary: NepTrainKit is a Python package for visualizing and manipulating training datasets for NEP.
 Author: Chen Cheng bing
 Author-email: Chen Cheng bing <1747193328@qq.com>