rename gap/xyz to quip/gap/xyz

Author: felix5572

README.md

@@ -51,17 +51,16 @@ The labels provided in the `OUTCAR`, i.e. energies, forces and virials (if any),
 
 The `System` or `LabeledSystem` can be constructed from the following file formats with the `format key` in the table passed to argument `fmt`:
 
-For `gap/quip xyz` files, single .xyz file may include many different configurations with different atom numbers and atom type.
+For `quip/gap xyz` files, single .xyz file may include many different configurations with different atom numbers and atom type.
 
 The Class `dpdata.MultiSystems`  can read data  this kind of file.
-Now Class dpdata.MultiSystems Only support gap/quip xyz  format file.
+Now Class dpdata.MultiSystems Only support quip/gap xyz  format file.
 
 The following commands relating to `Class dpdata.MultiSystems` may be useful.
 ```python
 # load data
-# 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')
+
+xyz_multi_systems = dpdata.MultiSystems.from_file('tests/xyz/xyz_unittest.xyz','quip/gap/xyz')
 
 # print the multi_system infomation
 print(xyz_multi_systems)
@@ -98,7 +97,7 @@ xyz_multi_systems.to_deepmd_raw('./my_deepmd_data/')
 | QE      | log    | False        | True    | LabeledSystem | 'qe/pw/scf'   |
 | QE      | log    | True         | False   | System        | 'qe/cp/traj'  |
 | QE      | log    | True         | True    | LabeledSystem | 'qe/cp/traj'  |
-|gap/quip|xyz|True|True|MultiSystems|'gap/xyz'|
+|quip/gap|xyz|True|True|MultiSystems|'quip/gap/xyz'|
 
 ## Access data
 These properties stored in `System` and `LabeledSystem` can be accessed by operator `[]` with the key of the property supplied, for example

dpdata/system.py

@@ -19,7 +19,7 @@
 from monty.json import MSONable
 from monty.serialization import loadfn,dumpfn
 from dpdata.periodic_table import Element
-from dpdata.xyz.gap_xyz import GapxyzSystems
+from dpdata.xyz.quip_gap_xyz import QuipGapxyzSystems
 
 class System (MSONable) :
     '''
@@ -905,7 +905,7 @@ def sort_atom_types(self):
 class MultiSystems:
     '''A set containing several systems.'''
 
-    def __init__(self, *systems,file_name=None, fmt=None,type_map=None):
+    def __init__(self, *systems,type_map=None):
         """
         Parameters
         ----------
@@ -920,15 +920,6 @@ def __init__(self, *systems,file_name=None, fmt=None,type_map=None):
         else:
             self.atom_names = []
         self.append(*systems)
-        if file_name is not None:
-            if fmt is None:
-                raise RuntimeError("must specify file format for file {}".format(file_name))
-            elif fmt == 'gap/xyz' or 'xyz':
-                self.from_gap_xyz_file(file_name)
-            else:
-                raise RuntimeError("unknown file format for file {} format {},now supported 'gap/xyz'".format(file_name, fmt))
-
-
 
     def __getitem__(self, key):
         """Returns proerty stored in System by key or by idx"""
@@ -955,8 +946,20 @@ def __add__(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 from_file(cls,file_name,fmt):
+        multi_systems = cls()
+        multi_systems.load_systems_from_file(file_name=file_name,fmt=fmt)
+        return multi_systems
+    
+    def load_systems_from_file(self, file_name=None, fmt=None):
+        if file_name is not None:
+            if fmt is None:
+                raise RuntimeError("must specify file format for file {}".format(file_name))
+            elif fmt == 'quip/gap/xyz' or 'xyz':
+                self.from_quip_gap_xyz_file(file_name)
+            else:
+                raise RuntimeError("unknown file format for file {} format {},now supported 'quip/gap/xyz'".format(file_name, fmt))
+
 
     def get_nframes(self) :
         """Returns number of frames in all systems"""
@@ -1012,10 +1015,10 @@ def check_atom_names(self, system):
             system.add_atom_names(new_in_self)
         system.sort_atom_names()
 
-    def from_gap_xyz_file(self,filename):
-        # gap_xyz_systems = GapxyzSystems(filename)
-        # print(next(gap_xyz_systems))
-        for info_dict in GapxyzSystems(filename):
+    def from_quip_gap_xyz_file(self,filename):
+        # quip_gap_xyz_systems = QuipGapxyzSystems(filename)
+        # print(next(quip_gap_xyz_systems))
+        for info_dict in QuipGapxyzSystems(filename):
             system=LabeledSystem(data=info_dict)
             self.append(system)
 

dpdata/xyz/gap_xyz.py renamed to dpdata/xyz/quip_gap_xyz.py

@@ -8,9 +8,9 @@
 import numpy as np
 from collections import OrderedDict
 import re 
-class GapxyzSystems(object):
+class QuipGapxyzSystems(object):
     """
-    deal with GapxyzFile 
+    deal with QuipGapxyzFile 
     """
     def __init__(self, file_name):
         self.file_object = open(file_name, 'r')

tests/test_gap_xyz.py renamed to tests/test_quip_gap_xyz.py

@@ -4,19 +4,19 @@
 from context import dpdata
 from comp_sys import CompLabeledSys
 
-class TestGapxyz(unittest.TestCase, CompLabeledSys):
+class TestQuipGapxyz(unittest.TestCase, CompLabeledSys):
     def setUp (self) :
-        self.multi_systems = dpdata.MultiSystems.from_file('xyz/xyz_unittest.xyz','gap/xyz')
+        self.multi_systems = dpdata.MultiSystems.from_file('xyz/xyz_unittest.xyz','quip/gap/xyz')
         self.system_1 = self.multi_systems.systems['B1C9']
         self.system_2 = dpdata.LabeledSystem('xyz/B1C9', fmt='deepmd')
         self.places = 6
         self.e_places = 6
         self.f_places = 6
         self.v_places = 4
 
-class TestGapxyz2(unittest.TestCase, CompLabeledSys):
+class TestQuipGapxyz2(unittest.TestCase, CompLabeledSys):
     def setUp (self) :
-        self.system_temp0 = dpdata.MultiSystems(file_name='xyz/xyz_unittest.xyz', fmt='gap/xyz')
+        self.system_temp0 = dpdata.MultiSystems.from_file(file_name='xyz/xyz_unittest.xyz', fmt='quip/gap/xyz')
         self.system_1 = self.system_temp0.systems['B5C7']
         self.system_temp1 = dpdata.LabeledSystem('xyz/B1C9', fmt='deepmd')
         self.system_temp2 = dpdata.LabeledSystem('xyz/B5C7', fmt='deepmd')