mlatom 2.0.0__py3-none-any.whl

MLatom/MLatom.py

@@ -0,0 +1,151 @@
+#!/usr/bin/env python3
+'''
+
+  !---------------------------------------------------------------------------!
+  !                                                                           !
+  !     MLatom: a Package for Atomistic Simulations with Machine Learning     !
+  !                               Version 2.0                                 !
+  !                           http://mlatom.com/                              !
+  !                                                                           !
+  !                  Copyright (c) 2013-2021 Pavlo O. Dral                    !
+  !                           http://dr-dral.com/                             !
+  !                                                                           !
+  ! All rights reserved. No part of MLatom may be used, published or          !
+  ! redistributed without written permission by Pavlo Dral.                   ! 
+  !                                                                           !
+  ! The above copyright notice and this permission notice shall be included   !
+  ! in all copies or substantial portions of the Software.                    !
+  !                                                                           !
+  ! The software is provided "as is", without warranty of any kind, express   !
+  ! or implied, including but not limited to the warranties of                !
+  ! merchantability, fitness for a particular purpose and noninfringement. In !
+  ! no event shall the authors or copyright holders be liable for any claim,  !
+  ! damages or other liability, whether in an action of contract, tort or     !
+  ! otherwise, arising from, out of or in connection with the software or the !
+  ! use or other dealings in the software.                                    !
+  !                                                                           !
+  !                                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)  !
+  !                                                                           !
+  ! 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                  !
+  !                                                                           !  
+  !---------------------------------------------------------------------------!
+
+'''
+
+import os, sys, subprocess, time, shutil, re, copy
+import sliceData, stopper
+import MLtasks, sliceData, stopper
+import interface_MLatomF
+import header
+from args_class import ArgsBase
+from doc import Doc
+
+class MLatomMainCls(object):
+    def __init__(self):
+        starttime = time.time()
+        
+        print(__doc__)
+        
+        print(' %s ' % ('='*78))
+        print(time.strftime(" MLatom started on %d.%m.%Y at %H:%M:%S", time.localtime()))
+        print('        with the following options:')
+        argsstr = '        '
+        for arg in sys.argv:
+            argsstr += arg + ' '
+        print(argsstr.rstrip())
+        if len(sys.argv[1:]) == 1:
+            if os.path.exists(sys.argv[1]):
+                print('\n        Input file content:')
+                print(' %s ' % ('_'*78))
+                with open(sys.argv[1], 'r') as finp:
+                    for line in finp:
+                        print(line.rstrip())
+                print(' %s ' % ('_'*78))
+        args = Args()
+        args.parse(sys.argv[1:])
+        print(' %s ' % ('='*78))
+        header.printHeader(args)
+        sys.stdout.flush()
+
+        # Set the number of threads
+        if args.nthreads:
+            os.environ["OMP_NUM_THREADS"] = str(args.nthreads)
+            os.environ["MKL_NUM_THREADS"] = str(args.nthreads)
+            os.environ["OMP_PROC_BIND"]   = 'true'
+        
+        # Perform requested task
+        if args.XYZ2X or args.sample or args.analyze:
+            interface_MLatomF.ifMLatomCls.run(args.args2pass)
+            pass
+        elif args.slice or args.sampleFromSlices or args.mergeSlices:
+            sliceData.sliceDataCls(argsSD = args.args2pass)
+        elif (args.useMLmodel    or args.createMLmodel or
+              args.estAccMLmodel or args.learningCurve or
+              args.MLNEA):
+            MLtasks.MLtasksCls(argsMLtasks = args.args2pass)
+        
+        endtime = time.time()
+        wallclock = endtime - starttime
+        print(' %s ' % ('='*78))
+        print(' Wall-clock time: %.2f s (%.2f min, %.2f hours)\n' % (wallclock, wallclock / 60.0, wallclock / 3600.0))
+        print(time.strftime(" MLatom terminated on %d.%m.%Y at %H:%M:%S", time.localtime()))
+        print(' %s ' % ('='*78))
+        sys.stdout.flush()
+
+class Args(ArgsBase):
+    def __init__(self):
+        super().__init__()
+        self.task_list = [
+            'XYZ2X', 'analyze', 'sample', 'sampleFromSlices', 'mergeSlices','slice',
+            'useMLmodel', 'createMLmodel', 'estAccMLmodel', 'learningCurve', 
+            'crossSection'
+        ]
+        self.add_default_dict_args(self.task_list, bool)
+        self.add_default_dict_args([
+            'useMLmodel', 'createMLmodel', 'estAccMLmodel', 'learningCurve','deltaLearn','selfCorrect','MLmodelType'
+            ],
+            bool
+        )
+        self.add_default_dict_args([
+            'MLprog'
+            ],
+            ''
+        )
+        self.add_default_dict_args([
+            'Yb', 'Yt', 'YestT', 'YestFile','XYZfile', 'XfileIn', 'Yfile', 'YgradXYZfile', 'absXfileIn', 'absXYZfile', 'absYfile', 'absYgradXYZfile', 'YgradXYZestFile', 'Ntrain', 'Nsubtrain', 'Nvalidate', 'Ntest', 'iTrainIn', 'iTestIn', 'iSubtrainIn', 'iValidateIn', 'sampling', 'MLmodelIn', 'MLmodelOut',
+            'molDescriptor', 'kernel'
+            ],
+            ''
+        )
+        self.add_dict_args({'MLmodelType': '', 'nthreads': None})
+        self.set_keyword_alias('crossSection', ['ML-NEA', 'ML_NEA', 'crossSection', 'cross-section', 'cross_section','MLNEA'])
+        self.args2pass = []
+
+    def parse(self, argsraw):
+        if len(argsraw) == 0:
+            Doc.printDoc({})
+            stopper.stopMLatom('At least one option should be provided')
+        elif len(argsraw) == 1:
+            if os.path.exists(argsraw[0]):
+                self.parse_input_file(argsraw[0])
+            else:
+                self.parse_input_content(argsraw[0])
+            self.args2pass = self.args_string_list(['', None])
+        elif len(argsraw) >= 2:
+            self.parse_input_content(argsraw)
+            self.args2pass = self.args_string_list(['', None])
+        self.checkArgs()
+
+    def checkArgs(self):
+        Ntasks = eval(' + '.join(map(lambda s: 'self.' + s, self.task_list)))
+        if Ntasks == 0:
+            Doc.printDoc({})
+            stopper.stopMLatom('At least one task should be requested')
+
+if __name__ == '__main__':
+    MLatomMainCls()