mlatom 2.0.0__tar.gz → 2.0.1__tar.gz

{MLatom-2.0.0/src/MLatom.egg-info → MLatom-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MLatom
-Version: 2.0.0
+Version: 2.0.1
 Summary: A Package for Atomistic Simulations with Machine Learning
 Home-page: http://mlatom.com
 Author: Pavlo O. Dral
@@ -112,7 +112,7 @@ Description: # Brief Introduction
         
         # About Program
         MLatom: a Package for Atomistic Simulations with Machine Learning    
-        Version 2.0  
+        Version 2.0.1
         http://mlatom.com/                             
                                                                                    
         Copyright (c) 2013-2021 Pavlo O. Dral                   
@@ -126,7 +126,7 @@ Description: # Brief Introduction
         
         1. Pavlo O. Dral, J. Comput. Chem. 2019, 40, 2339-2347             
         2. Pavlo O. Dral, Fuchun Ge, Bao-Xin Xue, Yi-Fan Hou, Max Pinheiro Jr, Jianxing Huang, Mario Barbatti, Top. Curr. Chem. 2021, 379, 27              
-        3. Pavlo O. Dral, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou, Max Pinheiro Jr, MLatom: A Package for Atomistic Simulations with Machine Learning, version 2.0, Xiamen University, Xiamen, China, 2013-2021.               
+        3. Pavlo O. Dral, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou, Max Pinheiro Jr, MLatom: A Package for Atomistic Simulations with Machine Learning, version 2.0.1, Xiamen University, Xiamen, China, 2013-2021.               
         
         
         # License

{MLatom-2.0.0 → MLatom-2.0.1}/README.md

@@ -104,7 +104,7 @@ MLatom also provides interfaces to some third-party software where extra ML mode
 
 # About Program
 MLatom: a Package for Atomistic Simulations with Machine Learning    
-Version 2.0  
+Version 2.0.1
 http://mlatom.com/                             
                                                                            
 Copyright (c) 2013-2021 Pavlo O. Dral                   
@@ -118,7 +118,7 @@ Cite as:
 
 1. Pavlo O. Dral, J. Comput. Chem. 2019, 40, 2339-2347             
 2. Pavlo O. Dral, Fuchun Ge, Bao-Xin Xue, Yi-Fan Hou, Max Pinheiro Jr, Jianxing Huang, Mario Barbatti, Top. Curr. Chem. 2021, 379, 27              
-3. Pavlo O. Dral, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou, Max Pinheiro Jr, MLatom: A Package for Atomistic Simulations with Machine Learning, version 2.0, Xiamen University, Xiamen, China, 2013-2021.               
+3. Pavlo O. Dral, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou, Max Pinheiro Jr, MLatom: A Package for Atomistic Simulations with Machine Learning, version 2.0.1, Xiamen University, Xiamen, China, 2013-2021.               
 
 
 # License

{MLatom-2.0.0 → MLatom-2.0.1}/setup.py

@@ -43,7 +43,7 @@ with open(os.path.join(here, 'README.md')) as f:
 
 setup(
     name = pkg_name,
-    version = "2.0.0",
+    version = "2.0.1",
     author = "Pavlo O. Dral",
     author_email = "admin@mlatom.com",
     license = 'CC BY-NC-ND 4.0',  # https://creativecommons.org/licenses/by-nc-nd/4.0/

{MLatom-2.0.0 → MLatom-2.0.1}/src/MLatom/MLatom.py

@@ -27,7 +27,7 @@
   !                                Cite as:                                   !
   ! Pavlo O. Dral, J. Comput. Chem. 2019, 40, 2339-2347                       !
   ! Pavlo O. Dral, Fuchun Ge, Bao-Xin Xue, Yi-Fan Hou, Max Pinheiro Jr,       !
-  ! Jianxing Huang, Mario Barbatti, submitted (check mlatom.com for updates)  !
+  ! Jianxing Huang, Mario Barbatti, Top. Curr. Chem. 2021, 379, 27
   !                                                                           !
   ! Pavlo O. Dral, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou, Max Pinheiro Jr,       !
   ! MLatom: A Package for Atomistic Simulations with Machine Learning         !

{MLatom-2.0.0 → MLatom-2.0.1}/src/MLatom/MLtasks.py

@@ -358,6 +358,7 @@ class MLtasksCls(object):
     def training(cls, locargs, setname=''):
         if args.MLprog.lower() in cls.mlatom_alias:
             mlatom_arg=addReplaceArg('estaccmlmodel','createmlmodel',locargs)
+            mlatom_arg=addReplaceArg('MLmodelOut','MLmodelOut=%s'%args.MLmodelOut, mlatom_arg)
 
             if args.XfileIn:
                 mlatom_arg=addReplaceArg('XfileIn','XfileIn=%s'% os.path.relpath(args.absXfileIn) ,mlatom_arg)
@@ -368,7 +369,14 @@ class MLtasksCls(object):
             if args.YgradXYZfile: 
                 mlatom_arg=addReplaceArg('ygradxyzfile','ygradxyzfile=%s'% os.path.relpath(args.absYgradXYZfile),mlatom_arg)
 
-            with open('%si%s.dat'%(cls.index_prefix, setname),'r')as f:
+            idx_dict={
+                'train': args.itrainin,
+                'subtrain': args.isubtrainin,
+                'validate': args.ivalidatein,
+                'test': args.itestin
+            }
+
+            with open(cls.index_prefix+idx_dict[setname],'r')as f:
                 ntrain=0
                 for line in f:
                     ntrain+=1
@@ -377,7 +385,7 @@ class MLtasksCls(object):
             mlatom_arg=addReplaceArg('Nvalidate','',mlatom_arg)
             mlatom_arg=addReplaceArg('Nsubtrain','',mlatom_arg)
             mlatom_arg=addReplaceArg('sampling','sampling=user-defined',mlatom_arg)
-            mlatom_arg=addReplaceArg('itrainin','itrainin=%si%s.dat'%(cls.index_prefix, setname),mlatom_arg)
+            mlatom_arg=addReplaceArg('itrainin','itrainin='+cls.index_prefix+idx_dict[setname],mlatom_arg)
             mlatom_arg=addReplaceArg('itestin','',mlatom_arg)
             mlatom_arg=addReplaceArg('ivalidatein','',mlatom_arg)
             mlatom_arg=addReplaceArg('isubtrainin','',mlatom_arg)
@@ -524,12 +532,21 @@ class MLtasksCls(object):
                 'validate':['subtrain','validate','subtrain'],
                 'test':['train','test','train']
             }
-            with open('%si%s.dat'%(cls.index_prefix, setdict[setname][0]),'r')as f:
+
+            idx_dict={
+                'train': args.itrainin,
+                'subtrain': args.isubtrainin,
+                'validate': args.ivalidatein,
+                'test': args.itestin
+            }
+
+            with open(cls.index_prefix+idx_dict[setdict[setname][0]],'r')as f:
                 ntrain=0
                 for line in f:
                     ntrain+=1
                 if setname=='train': ntrain=0
-            with open('%si%s.dat'%(cls.index_prefix, setname),'r')as f:
+                # MLatomF still check this number...
+            with open(cls.index_prefix+idx_dict[setname],'r')as f:
                 ntest=0
                 for line in f:
                     ntest+=1
@@ -538,8 +555,8 @@ class MLtasksCls(object):
             useargs=addReplaceArg('Ntrain','Ntrain=%s'% ntrain ,useargs)
             useargs=addReplaceArg('Ntest','Ntest=%s'%ntest,useargs)
             useargs=addReplaceArg('sampling','sampling=user-defined',useargs)
-            useargs=addReplaceArg('itrainin','itrainin=%si%s.dat'%(cls.index_prefix, setdict[setname][2]),useargs)
-            useargs=addReplaceArg('itestin','itestin=%si%s.dat'%(cls.index_prefix, setname),useargs)
+            useargs=addReplaceArg('itrainin','itrainin='+cls.index_prefix+idx_dict[setdict[setname][2]],useargs)
+            useargs=addReplaceArg('itestin','itestin='+cls.index_prefix+idx_dict[setname],useargs)
             useargs=addReplaceArg('mlmodelin','mlmodelin=%s'%args.mlmodelout,useargs)
             useargs=addReplaceArg('yestfile','',useargs)
             useargs=addReplaceArg('ygradXYZestfile','',useargs)

{MLatom-2.0.0 → MLatom-2.0.1/src/MLatom.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MLatom
-Version: 2.0.0
+Version: 2.0.1
 Summary: A Package for Atomistic Simulations with Machine Learning
 Home-page: http://mlatom.com
 Author: Pavlo O. Dral
@@ -112,7 +112,7 @@ Description: # Brief Introduction
         
         # About Program
         MLatom: a Package for Atomistic Simulations with Machine Learning    
-        Version 2.0  
+        Version 2.0.1
         http://mlatom.com/                             
                                                                                    
         Copyright (c) 2013-2021 Pavlo O. Dral                   
@@ -126,7 +126,7 @@ Description: # Brief Introduction
         
         1. Pavlo O. Dral, J. Comput. Chem. 2019, 40, 2339-2347             
         2. Pavlo O. Dral, Fuchun Ge, Bao-Xin Xue, Yi-Fan Hou, Max Pinheiro Jr, Jianxing Huang, Mario Barbatti, Top. Curr. Chem. 2021, 379, 27              
-        3. Pavlo O. Dral, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou, Max Pinheiro Jr, MLatom: A Package for Atomistic Simulations with Machine Learning, version 2.0, Xiamen University, Xiamen, China, 2013-2021.               
+        3. Pavlo O. Dral, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou, Max Pinheiro Jr, MLatom: A Package for Atomistic Simulations with Machine Learning, version 2.0.1, Xiamen University, Xiamen, China, 2013-2021.               
         
         
         # License