mlatom 2.0.2__tar.gz → 2.0.4__tar.gz

{MLatom-2.0.2/src/MLatom.egg-info → MLatom-2.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MLatom
-Version: 2.0.2
+Version: 2.0.4
 Summary: A Package for Atomistic Simulations with Machine Learning
 Home-page: http://mlatom.com
 Author: Pavlo O. Dral
@@ -122,7 +122,7 @@ 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 2.0.2
+Version 2.0.3
 http://mlatom.com/                             
                                                                            
 Copyright (c) 2013-2021 Pavlo O. Dral                   
@@ -136,7 +136,7 @@ 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 2.0.2, 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 2.0.3, Xiamen University, Xiamen, China, 2013-2021.               
 
 
 # License

{MLatom-2.0.2 → MLatom-2.0.4}/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 2.0.2
+Version 2.0.3
 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 2.0.2, 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 2.0.3, Xiamen University, Xiamen, China, 2013-2021.               
 
 
 # License

{MLatom-2.0.2 → MLatom-2.0.4}/setup.py

@@ -43,7 +43,7 @@ with open(os.path.join(here, 'README.md')) as f:
 
 setup(
     name = pkg_name,
-    version = "2.0.2",
+    version = "2.0.4",
     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/
@@ -54,7 +54,7 @@ setup(
     python_requires='>=3.7',
     packages = find_packages('src'),
     package_dir = {'' : 'src'},
-    scripts = ['mlatom', 'MLatomF'],
+    # scripts = ['mlatom', 'MLatomF'],
     package_data = {"": ['MLatomF', '*.json', 'cs.so']},
     classifiers = [
         "Programming Language :: Python :: 3",
@@ -64,9 +64,13 @@ setup(
         "Environment :: Console",
     ],
     install_requires = ['numpy', 'matplotlib'],
-    # entry_points = {
-    #     'console_scripts' : ['mlatom=MLatom.MLatom:MLatomMainCls']
-    # }
+    entry_points = {
+        'console_scripts' : ['mlatom-gui = MLatom.mlatom_gui:main',
+                             'mlatom_gui = MLatom.mlatom_gui:main',
+                             'mlatom = MLatom.shell_cmd:mlatom',
+                             # 'MLatom.py = MLatom.shell_cmd:mlatom',
+                             'MLatomF = MLatom.shell_cmd:MLatomF']
+    }
     # cmdclass = {
     #     "install_scripts": InstallScripts
     # }

MLatom-2.0.4/src/MLatom/LICENSE.CC-BY-NC-ND-4.0

@@ -0,0 +1,251 @@
+Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Public License
+
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{MLatom-2.0.2 → MLatom-2.0.4}/src/MLatom/ML_NEA.py

@@ -749,13 +749,13 @@ class GaussCalc(LinuxInterface):
         self.cd(orig_folder)
 
     def process_one_gauss_log(self, log_file: str) -> Tuple[List[float], List[float]]:
-        cmd = '''grep 'Excited State' %s | awk '{print $5}' > %s/SPC_E.TEMP''' % (log_file, self.temp_path)
+        cmd = '''grep -E 'Excited State +?[0-9]+' %s | awk '{print $5}' > %s/SPC_E.TEMP''' % (log_file, self.temp_path)
         err_code, _ = self.exec(cmd)
         E_file = os.path.join(self.temp_path, 'SPC_E.TEMP')
         if err_code != 0:
             err_print(f'extract E value from one gaussian log failed with error code: {err_code}')
 
-        cmd = '''grep 'Excited State' %s | awk '{print $9}' | sed s/f=//g > %s/SPC_f.TEMP''' % (log_file, self.temp_path)
+        cmd = '''grep -E 'Excited State +?[0-9]+' %s | awk '{print $9}' | sed s/f=//g > %s/SPC_f.TEMP''' % (log_file, self.temp_path)
         err_code, _ = self.exec(cmd)
         f_file = os.path.join(self.temp_path, 'SPC_f.TEMP')
         if err_code != 0:
@@ -795,8 +795,10 @@ class NewtonXCalc(LinuxInterface):
         self.cd(self.NX_path)
         self.change_geom(geom_path)
         self.run_dynamic(freq_path, atom_num, NEA_point)
+        eq_mole = Molecule()
+        eq_mole.read_xyz(geom_path)
+        self.multi_xyz.append(eq_mole)
         self.restore_multi_xyz(atom_num)
-        pass
 
     def change_geom(self, geom_path: str) -> None:
         # check whether trnasfer success (delete /dev/null and then check the output log)
@@ -823,11 +825,18 @@ class NewtonXCalc(LinuxInterface):
         with open(inp_name, 'w') as f:
             f.write(nx_inp)
         # err_code, out = self.exec(f'$NX/initcond.pl > NX-MD.log 2>&1')
-        err_code, out = self.exec('$NX/mk_qvector < initqp_input ; ' \
-                                  '$NX/weight < initqp_input &> weight.log ; ' \
-                                  '$NX/initqp < initqp_input &> initqp.log ')
-        if err_code != 0 or out != '':
-            err_print(f'Newton-X calculation failed!!!\nstatus code: {err_code} (0 stands for normal exit, none 0 stands for error)\noutput: {out}')
+        try:
+            err_code, out = self.exec('$NX/mk_qvector < initqp_input ; ' \
+                                      '$NX/weight < initqp_input &> weight.log ; ' \
+                                      '$NX/initqp < initqp_input &> initqp.log ')
+            if err_code != 0 or out != '':
+                err_print(f'Newton-X calculation failed!!!\nstatus code: {err_code} (0 stands for normal exit, none 0 stands for error)\noutput: {out}')
+        except:
+            os.system('$NX/mk_qvector < initqp_input ; ' \
+                      '$NX/weight < initqp_input &> weight.log ; ' \
+                      '$NX/initqp < initqp_input &> initqp.log ')
+            import time
+            time.sleep(0.01)
     
     def restore_multi_xyz(self, atom_num: int):
         with open('ini_qv') as f:
@@ -850,6 +859,7 @@ class NewtonXCalc(LinuxInterface):
             else:
                 err_print('processing ini_qv failed! exit!')
                 exit()
+        self.multi_xyz.append(mole)
     
     def _process_ini_qv_line(self, splited_line: List[str]) -> List[float]:
         xyz = map(lambda x: float(x.replace('D', 'e')), splited_line[0: 3])