from_file for gap/xyz

Author: felix5572

README.md

@@ -59,8 +59,9 @@ Now Class dpdata.MultiSystems Only support gap/quip xyz  format file.
 The following commands relating to `Class dpdata.MultiSystems` may be useful.
 ```python
 # load data
-# note that the prefix 'file_name=' and 'fmt=' can NOT be omitted
-xyz_multi_systems = dpdata.MultiSystems(file_name='xyz_unittest.xyz', fmt='gap/xyz')
+# note that in the second case the prefix 'file_name=' and 'fmt=' can NOT be omitted
+xyz_multi_systems = dpdata.MultiSystems.from_file('tests/xyz/xyz_unittest.xyz','gap/xyz')
+xyz_multi_systems = dpdata.MultiSystems(file_name='tests/syz/xyz_unittest.xyz', fmt='gap/xyz')
 
 # print the multi_system infomation
 print(xyz_multi_systems)

dpdata/system.py

@@ -905,7 +905,7 @@ def sort_atom_types(self):
 class MultiSystems:
     '''A set containing several systems.'''
 
-    def __init__(self, *systems, type_map=None,file_name=None, fmt=None):
+    def __init__(self, *systems,file_name=None, fmt=None,type_map=None):
         """
         Parameters
         ----------
@@ -914,9 +914,6 @@ def __init__(self, *systems, type_map=None,file_name=None, fmt=None):
         type_map : list of str
             Maps atom type to name
         """
-        if all(type(ii)==str for ii in systems) and len(systems)>0:
-            raise RuntimeError("the prefix 'file_name=' and 'fmt=' can not be omitted"
-                "for example MultiSystems(file_name='water.xyz', fmt='gap/xyz')" )
         self.systems = {}
         if type_map is not None:
             self.atom_names = type_map
@@ -956,6 +953,10 @@ def __add__(self, others) :
        elif isinstance(others, list):
           return self.__class__(self, *others)
        raise RuntimeError("Unspported data structure")
+    
+    @classmethod
+    def from_file(cls,file_name,fmt,type_map=None):
+        return cls(file_name=file_name, fmt=fmt,type_map=type_map)
 
     def get_nframes(self) :
         """Returns number of frames in all systems"""
@@ -1018,6 +1019,7 @@ def from_gap_xyz_file(self,filename):
             system=LabeledSystem(data=info_dict)
             self.append(system)
 
+
     def to_deepmd_raw(self, folder) :
         """
         Dump systems in deepmd raw format to `folder` for each system.

tests/test_gap_xyz.py

@@ -6,7 +6,7 @@
 
 class TestGapxyz(unittest.TestCase, CompLabeledSys):
     def setUp (self) :
-        self.multi_systems = dpdata.MultiSystems(file_name='xyz/xyz_unittest.xyz', fmt='gap/xyz')
+        self.multi_systems = dpdata.MultiSystems.from_file('xyz/xyz_unittest.xyz','gap/xyz')
         self.system_1 = self.multi_systems.systems['B1C9']
         self.system_2 = dpdata.LabeledSystem('xyz/B1C9', fmt='deepmd')
         self.places = 6