mlatom 2.0.3__tar.gz → 2.0.5__tar.gz

{MLatom-2.0.3/src/MLatom.egg-info → MLatom-2.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MLatom
-Version: 2.0.3
+Version: 2.0.5
 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 2.0.3
+Version 2.0.5
 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 2.0.3, 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 2.0.5, Xiamen University, Xiamen, China, 2013-2021.               
 
 
 # License

{MLatom-2.0.3 → MLatom-2.0.5}/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 2.0.3
+Version 2.0.5
 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 2.0.3, 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 2.0.5, Xiamen University, Xiamen, China, 2013-2021.               
 
 
 # License

{MLatom-2.0.3 → MLatom-2.0.5}/setup.py

@@ -43,7 +43,7 @@ with open(os.path.join(here, 'README.md')) as f:
 
 setup(
     name = pkg_name,
-    version = "2.0.3",
+    version = "2.0.5",
     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-2.0.3 → MLatom-2.0.5}/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)
@@ -822,12 +824,9 @@ class NewtonXCalc(LinuxInterface):
                  ' nis = 1\n nfs = 2\n kvert = 1\n de = 100\n prog = 6.5\n iseed = 1234\n lvprt = 1\n/\n'
         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}')
+        os.system('$NX/mk_qvector < initqp_input')
+        os.system('$NX/weight     < initqp_input > weight.log')
+        os.system('$NX/initqp     < initqp_input > initqp.log')
     
     def restore_multi_xyz(self, atom_num: int):
         with open('ini_qv') as f:
@@ -850,6 +849,7 @@ 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])
@@ -2346,11 +2346,12 @@ class RecurPaperProcedure(ArgParser, LinuxInterface):
         self.delta_QC = 0.01
         self.delta_SPC = 0.3
         
-    def opt_freq_calc(self):
+    def opt_freq_calc(self, force_calc: bool=False):
         self.cd(self.work_path)
-        if self.exist_path(self.eq_init_xyz_name) and self.exist_path(self.nx_nea_geom_name):
-            self.opt_molecule.read_xyz(self.eq_init_xyz_name) 
-            return
+        if not force_calc:
+            if self.exist_path(self.eq_init_xyz_name) and self.exist_path(self.nx_nea_geom_name):
+                self.opt_molecule.read_xyz(self.eq_init_xyz_name) 
+                return
         if not EnvCheck.check_NX():
             exit()
         self.cd(self.work_path)
@@ -2362,28 +2363,37 @@ class RecurPaperProcedure(ArgParser, LinuxInterface):
             else:  # not exists opt-freq.com, raise error
                 err_print(f'not exists {self.gauss_opt_inp_name} or {self.gauss_opt_log_name}, exit')
                 exit()
+        else:
+            self.cp(self.gauss_opt_log_name, os.path.join(self.gauss.gauss_path, self.gauss_opt_log_name))
         # now exists opt-freq.log, extract opt.xyz & freq
-        self.opt_molecule = self.gauss.extract_xyz(
-            os.path.join(self.gauss.gauss_path, self.gauss_opt_log_name))
-        # self.opt_molecule.print_xyz(self.eq_xyz_name)  # no needed, don't pollute the working directory
+        if not force_calc:
+            self.opt_molecule = self.gauss.extract_xyz(
+                os.path.join(self.gauss.gauss_path, self.gauss_opt_log_name))
+            # self.opt_molecule.print_xyz(self.eq_xyz_name)  # no needed, don't pollute the working directory
 
     def NX_multi_xyz_calc(self):
-        self.cd(self.work_path)
-        if not self.exist_path(self.nx_nea_geom_name): # not exist multiple xyz.dat, need to calc it with NX
+        def NX_gen_ensemble():
+            if not EnvCheck.check_NX():
+                exit()
             self.cd(self.nx.NX_path)
             self.opt_molecule.print_xyz('opt.xyz')
             self.cp(os.path.join(self.gauss.gauss_path, self.gauss_opt_log_name),
                     os.path.join(self.nx.NX_path, 'opt.log'))
-            if not EnvCheck.check_NX():
-                exit()
             self.nx.invoke_NX('opt.xyz', 'opt.log', self.opt_molecule.atom_num, self.ML_point)
             self.multi_xyz = self.nx.multi_xyz
-        else:
-            # now exists xyz file, process this file and store it to self.multi_xyz_geom
+        
+        self.cd(self.work_path)
+        if self.exist_path(self.nx_nea_geom_name): # exists nea geom path
             self.multi_xyz = Molecule.read_multi_xyz(self.nx_nea_geom_name)
-            # self.ML_point = len(self.multi_xyz) - 1   # keep the MLpoint the same with ML-NEA (except the equibrium geom)
-            if len(self.multi_xyz) - 1 >= self.ML_point:
+            if len(self.multi_xyz) - 1 > self.ML_point:
                 self.multi_xyz = self.multi_xyz[:self.ML_point + 1]
+            elif len(self.multi_xyz) - 1 < self.ML_point:
+                orig_xyz = self.multi_xyz
+                self.opt_freq_calc(force_calc=True)
+                NX_gen_ensemble()
+                self.multi_xyz = orig_xyz + self.multi_xyz[len(orig_xyz): ]
+        else:  # not exists multiple nea geom data, need to calc it with NX
+            NX_gen_ensemble()
 
     def ML_NEA_calc_all(self):
         self.cd(self.cs_ML.ML_path)
@@ -2393,7 +2403,7 @@ class RecurPaperProcedure(ArgParser, LinuxInterface):
         # self.gauss.process_gaussian_log(self.gauss.all_log_path, self.max_state, pattern='', regex=False)
         ctl_adapter = CtlPartAdapter(self, CtlPartAdapter.paper_adapter)
         self.cs_ML.define_data_set(this=ctl_adapter, TD_point=self.TD_point, xyz_file=self.nx_nea_geom_name,
-                                   max_state=self.max_state, delta=0.01)
+                                   max_state=self.max_state, delta=self.delta_ML)
         self.cs_ML.ML_train_all()
         
     def ML_NEA_calc_iter(self):

{MLatom-2.0.3 → MLatom-2.0.5}/src/MLatom/README

@@ -1,5 +1,5 @@
 MLatom: a Package for Atomistic Simulations with Machine Learning
-Version 2.0.1
+Version 2.0.5
 http://mlatom.com/
 
 Copyright (c) 2013-2021 Pavlo O. Dral
@@ -15,7 +15,7 @@ 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 2.0.1, 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 2.0.5, Xiamen University, Xiamen, China, 2013-2021.
 
 In addition to above citations in the published work, the users have to cite the relevant literature for the MLatom features used. Examples of suggested citations are provided on http://mlatom.com/features page in form of web links and in the output of MLatom.