mlatom 3.17.0__tar.gz → 3.17.2__tar.gz

{mlatom-3.17.0/src/mlatom.egg-info → mlatom-3.17.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: mlatom
-Version: 3.17.0
+Version: 3.17.2
 Summary: A Package for AI-enhanced computational chemistry
 Home-page: http://mlatom.com
 Author: Pavlo O. Dral
@@ -18,7 +18,7 @@ License-File: LICENSE.txt
 # About Program
 MLatom: a Package for Atomistic Simulations with Machine Learning
 
-Version 3.17.0
+Version 3.17.2
 
 **Official website**: http://mlatom.com/    
 **Documentation**: http://mlatom.com/docs/                     
@@ -47,7 +47,7 @@ When this Software or its derivatives are used in scientific publications, it sh
 * Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Mario Barbatti, Olexandr Isayev, Cheng Wang, Bao-Xin Xue, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Lina Zhang, Shuang Zhang, Arif Ullah, Quanhao Zhang, Yanchi Ou. [MLatom 3: A Platform for Machine Learning-enhanced Computational Chemistry Simulations and Workflows](https://doi.org/10.1021/acs.jctc.3c01203).   *J. Chem. Theory Comput.* **2024**, *20*, 1193--1213.                                                                                               
 * Pavlo O. Dral, Fuchun Ge, Bao-Xin Xue, Yi-Fan Hou, Max Pinheiro Jr, Jianxing Huang, Mario Barbatti. [MLatom 2: An Integrative Platform for Atomistic Machine Learning](http://doi.org/10.1007/s41061-021-00339-5). *Top. Curr. Chem.* **2021**, *379*, 27.       
 * Pavlo O. Dral. [MLatom: A Program Package for Quantum Chemical Research Assisted by Machine Learning](http://dx.doi.org/10.1002/jcc.26004). *J. Comput. Chem.* **2019**, *40*, 2339--2347.                                                                                      
-* Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Bao-Xin Xue, Mikolaj Martyka, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Lina Zhang, Arif Ullah, Quanhao Zhang, Sebastian V. Pios, Yanchi Ou, Matheus O. Bispo, Vignesh B. Kumar, Xin-Yu Tong, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.17.0, Xiamen University, Xiamen, China, 2013-2024.
+* Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Bao-Xin Xue, Mikolaj Martyka, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Lina Zhang, Arif Ullah, Quanhao Zhang, Sebastian V. Pios, Yanchi Ou, Matheus O. Bispo, Vignesh B. Kumar, Xin-Yu Tong, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.17.2, Xiamen University, Xiamen, China, 2013-2024.
   [MLatom.com](http://mlatom.com).
                                                                       
 The citations for MLatom's interfaces and features shall be eventually

{mlatom-3.17.0 → mlatom-3.17.2}/README.md

@@ -1,7 +1,7 @@
 # About Program
 MLatom: a Package for Atomistic Simulations with Machine Learning
 
-Version 3.17.0
+Version 3.17.2
 
 **Official website**: http://mlatom.com/    
 **Documentation**: http://mlatom.com/docs/                     
@@ -30,7 +30,7 @@ When this Software or its derivatives are used in scientific publications, it sh
 * Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Mario Barbatti, Olexandr Isayev, Cheng Wang, Bao-Xin Xue, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Lina Zhang, Shuang Zhang, Arif Ullah, Quanhao Zhang, Yanchi Ou. [MLatom 3: A Platform for Machine Learning-enhanced Computational Chemistry Simulations and Workflows](https://doi.org/10.1021/acs.jctc.3c01203).   *J. Chem. Theory Comput.* **2024**, *20*, 1193--1213.                                                                                               
 * Pavlo O. Dral, Fuchun Ge, Bao-Xin Xue, Yi-Fan Hou, Max Pinheiro Jr, Jianxing Huang, Mario Barbatti. [MLatom 2: An Integrative Platform for Atomistic Machine Learning](http://doi.org/10.1007/s41061-021-00339-5). *Top. Curr. Chem.* **2021**, *379*, 27.       
 * Pavlo O. Dral. [MLatom: A Program Package for Quantum Chemical Research Assisted by Machine Learning](http://dx.doi.org/10.1002/jcc.26004). *J. Comput. Chem.* **2019**, *40*, 2339--2347.                                                                                      
-* Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Bao-Xin Xue, Mikolaj Martyka, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Lina Zhang, Arif Ullah, Quanhao Zhang, Sebastian V. Pios, Yanchi Ou, Matheus O. Bispo, Vignesh B. Kumar, Xin-Yu Tong, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.17.0, Xiamen University, Xiamen, China, 2013-2024.
+* Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Bao-Xin Xue, Mikolaj Martyka, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Lina Zhang, Arif Ullah, Quanhao Zhang, Sebastian V. Pios, Yanchi Ou, Matheus O. Bispo, Vignesh B. Kumar, Xin-Yu Tong, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.17.2, Xiamen University, Xiamen, China, 2013-2024.
   [MLatom.com](http://mlatom.com).
                                                                       
 The citations for MLatom's interfaces and features shall be eventually

{mlatom-3.17.0 → mlatom-3.17.2}/setup.py

@@ -43,7 +43,7 @@ with open(os.path.join(here, 'README.md')) as f:
 
 setup(
     name = pkg_name,
-    version = "3.17.0",
+    version = "3.17.2",
     author = "Pavlo O. Dral",
     author_email = "admin@mlatom.com",
     license = 'MIT (modified)',
@@ -68,7 +68,7 @@ setup(
     entry_points = {
         'console_scripts' : ['mlatom-gui = mlatom.mlatom_gui:main',
                              'mlatom_gui = mlatom.mlatom_gui:main',
-                             'mlatom = mlatom.shell_cmd:mlatom',
+                             'mlatom = mlatom.shell_cmd:mlatom_cmd_run',
                              # 'MLatom.py = MLatom.shell_cmd:mlatom',
                              'MLatomF = mlatom.shell_cmd:MLatomF']
     }

{mlatom-3.17.0 → mlatom-3.17.2}/src/mlatom/MLatom.py

@@ -4,7 +4,7 @@
   !---------------------------------------------------------------------------!
   !                                                                           !
   !     MLatom: a Package for Atomistic Simulations with Machine Learning     !
-  !                             MLatom 3.17.0                                 !
+  !                             MLatom 3.17.2                                 !
   !                                   @                                       !
   !                 Xiamen Atomistic Computing Suite (XACS)                   !
   !                                                                           !
@@ -38,7 +38,7 @@
   ! Sebastian V. Pios, Yanchi Ou, Matheus O. Bispo, Vignesh B. Kumar,         !
   ! Xin-Yu Tong,                                                              !
   ! MLatom: A Package for Atomistic Simulations with Machine Learning,        !
-  ! version 3.17.0, Xiamen University, Xiamen, China, 2013-2024.              !
+  ! version 3.17.2, Xiamen University, Xiamen, China, 2013-2024.              !
   !                                                                           !
   ! The citations for MLatom's interfaces and features shall be eventually    !
   ! included too. See header.py, ref.json and http://mlatom.com.              !
@@ -59,23 +59,24 @@ import os, sys, time
 # import header
 # from mlatom.MLtasks import CLItasks
 # from mlatom.args_class import mlatom_args
-import importlib.util
-# ~POD, 2025.03.23
-# the complicated import below is required to load the same instance of mlatom,
-# where this script is located.
-
-dir_path = os.path.dirname(os.path.abspath(__file__))
-path2init = os.path.join(dir_path, '__init__.py')
-dirname = os.path.basename(dir_path)
-spec = importlib.util.spec_from_file_location(dirname, path2init)
-mlatom_with_this_file = importlib.util.module_from_spec(spec)
-sys.modules[dirname] = mlatom_with_this_file
-spec.loader.exec_module(mlatom_with_this_file)
-header = mlatom_with_this_file.header
-CLItasks = mlatom_with_this_file.MLtasks.CLItasks
-mlatom_args = mlatom_with_this_file.args_class.mlatom_args
 
 def run(argv = []):
+    import importlib.util
+    # ~POD, 2025.03.23
+    # the complicated import below is required to load the same instance of mlatom,
+    # where this script is located.
+
+    dir_path = os.path.dirname(os.path.abspath(__file__))
+    path2init = os.path.join(dir_path, '__init__.py')
+    dirname = os.path.basename(dir_path)
+    spec = importlib.util.spec_from_file_location(dirname, path2init)
+    mlatom_with_this_file = importlib.util.module_from_spec(spec)
+    sys.modules[dirname] = mlatom_with_this_file
+    spec.loader.exec_module(mlatom_with_this_file)
+    header = mlatom_with_this_file.header
+    CLItasks = mlatom_with_this_file.MLtasks.CLItasks
+    mlatom_args = mlatom_with_this_file.args_class.mlatom_args
+    
     starttime = time.time()
     
     print(__doc__)

{mlatom-3.17.0 → mlatom-3.17.2}/src/mlatom/__init__.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
-from . import args_class, MLtasks, header, data, models, plot, simulations, stats, xyz, namd, constants, spectra
+from . import MLatom, args_class, MLtasks, header, data, models, plot, simulations, stats, xyz, namd, constants, spectra
+from .MLatom import run
 from .simulations import optimize_geometry, irc, freq, thermochemistry, md, generate_initial_conditions, vibrational_spectrum, md_parallel
 from .data import atom, molecule, molecular_database
 from .models import kreg, ani, msani

mlatom-3.17.2/src/mlatom/addons/uaiqm/uaiqm.py

@@ -0,0 +1,71 @@
+#!/usr/bin/env python3
+'''
+.. code-block::
+
+  !---------------------------------------------------------------------------! 
+  ! Add-on mock implementation for:                                           !
+  !                                                                           !
+  ! uaiqm: Universal and Updatable Artificial Intelligence-Enhanced           !
+  !        Quantum Mechanical Methods                                         ! 
+  ! Implementations by: Yuxinxin Chen and Pavlo O. Dral                       ! 
+  !---------------------------------------------------------------------------! 
+'''
+
+from ...model_cls import method_model
+
+class uaiqm(method_model):
+    """
+    The Universal and Updatable Artificial Intelligence-Quantum Mechanical methods.
+
+    Arguments:
+        method (str, optional): UAIQM method used. 
+        version (str, optional): The version of each UAIQM method. Default is the the newest.
+        uaiqm_kwargs (dictionary, optional): Keywords passed to calculation for each part in uaiqm.
+        selector (uaiqm selector, optional): If no customized selector is provided, default selection scheme will be used.
+        verbose (bool, optional): Whether to print information during automatic selection
+    
+    .. code-block:: python
+
+        # Initialize molecule
+        mol = ml.data.molecule()
+        mol.read_from_xyz_file(filename='ethanol.xyz')
+        # Run UAIQM calculation
+        uaiqm = ml.models.methods(method='uaiqm_odm2star@cc', version='newest')
+        uaiqm.predict(molecule=mol, calculate_energy=True, calculate_energy_gradients=True, calculate_hessian=True)
+        # Get energy, gradient, and prediction uncertainty of UAIQM method 
+        energy = mol.energy
+        gradient = mol.gradient
+
+    """
+    
+    supported_methods = ['uaiqm_optimal', 'uaiqm_nobaseline@dft', 'uaiqm_nobaseline@cc', 'uaiqm_odm2star@dft', 'uaiqm_odm2star@cc', 'uaiqm_gfn2xtbstar@dft', 'uaiqm_gfn2xtbstar@cc', 'uaiqm_wb97x631gp@cc', 'uaiqm_wb97xdef2tzvpp@cc']
+    
+    def __init__(
+        self, 
+        # <<< define methods <<<
+        method: str = 'uaiqm_gfn2xtbstar@cc', 
+        version: str = 'newest',
+        # <<< solvent - only support xtb based method now <<< 
+        solvent: str = None,
+        # <<< keywords for each componnet <<<
+        baseline_kwargs: dict = {},
+        dispersion_kwargs: dict = {},
+        # <<< set number of threads (default 1)<<<
+        nthreads: int = 1,
+        # <<< unused keyword <<<
+        selector = None,
+        # <<< verbose setting <<<
+        verbose: bool = False,
+        warning: bool = True,
+        # <<< file saving <<<
+        working_directory: str = None,
+        save_files_in_current_directory: bool = True
+        ):
+        
+        if self.is_method_supported(method=method):
+            raise ValueError(f'The requested method "{method}" is supported as an add-on in Aitomic, please refer to http://MLatom.com/aitomic for the instructions on how to obtain it.')
+        else:
+            self.raise_unsupported_method_error(method)
+    
+if __name__ == '__main__':
+    pass

mlatom-3.17.2/src/mlatom/shell_cmd.py

@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+import sys
+import os
+import time
+#from MLatom import run
+
+def mlatom_cmd_run(sleep=True):
+    import importlib.util
+    # ~POD, 2025.04.16
+    # the complicated import below is required to load the same instance of mlatom,
+    # which called this external script in the first place.
+    dir_path = os.path.dirname(os.path.abspath(__file__))
+    path2init = os.path.join(dir_path, '__init__.py')
+    dirname = os.path.basename(dir_path)
+    spec = importlib.util.spec_from_file_location(dirname, path2init)
+    mlatom4gaussian = importlib.util.module_from_spec(spec)
+    sys.modules[dirname] = mlatom4gaussian
+    spec.loader.exec_module(mlatom4gaussian)
+    mlatom4gaussian.run()
+    if sleep:
+        time.sleep(1)
+
+def MLatomF():
+    path = os.path.abspath(os.path.dirname(__file__))
+    os.system(f'{path}/MLatomF {" ".join(sys.argv[1:])}')
+    time.sleep(1)
+
+if __name__ == '__main__':
+    #run()
+    mlatom_cmd_run(sleep=False)

{mlatom-3.17.0 → mlatom-3.17.2/src/mlatom.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: mlatom
-Version: 3.17.0
+Version: 3.17.2
 Summary: A Package for AI-enhanced computational chemistry
 Home-page: http://mlatom.com
 Author: Pavlo O. Dral
@@ -18,7 +18,7 @@ License-File: LICENSE.txt
 # About Program
 MLatom: a Package for Atomistic Simulations with Machine Learning
 
-Version 3.17.0
+Version 3.17.2
 
 **Official website**: http://mlatom.com/    
 **Documentation**: http://mlatom.com/docs/                     
@@ -47,7 +47,7 @@ When this Software or its derivatives are used in scientific publications, it sh
 * Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Mario Barbatti, Olexandr Isayev, Cheng Wang, Bao-Xin Xue, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Lina Zhang, Shuang Zhang, Arif Ullah, Quanhao Zhang, Yanchi Ou. [MLatom 3: A Platform for Machine Learning-enhanced Computational Chemistry Simulations and Workflows](https://doi.org/10.1021/acs.jctc.3c01203).   *J. Chem. Theory Comput.* **2024**, *20*, 1193--1213.                                                                                               
 * Pavlo O. Dral, Fuchun Ge, Bao-Xin Xue, Yi-Fan Hou, Max Pinheiro Jr, Jianxing Huang, Mario Barbatti. [MLatom 2: An Integrative Platform for Atomistic Machine Learning](http://doi.org/10.1007/s41061-021-00339-5). *Top. Curr. Chem.* **2021**, *379*, 27.       
 * Pavlo O. Dral. [MLatom: A Program Package for Quantum Chemical Research Assisted by Machine Learning](http://dx.doi.org/10.1002/jcc.26004). *J. Comput. Chem.* **2019**, *40*, 2339--2347.                                                                                      
-* Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Bao-Xin Xue, Mikolaj Martyka, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Lina Zhang, Arif Ullah, Quanhao Zhang, Sebastian V. Pios, Yanchi Ou, Matheus O. Bispo, Vignesh B. Kumar, Xin-Yu Tong, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.17.0, Xiamen University, Xiamen, China, 2013-2024.
+* Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Bao-Xin Xue, Mikolaj Martyka, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Lina Zhang, Arif Ullah, Quanhao Zhang, Sebastian V. Pios, Yanchi Ou, Matheus O. Bispo, Vignesh B. Kumar, Xin-Yu Tong, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.17.2, Xiamen University, Xiamen, China, 2013-2024.
   [MLatom.com](http://mlatom.com).
                                                                       
 The citations for MLatom's interfaces and features shall be eventually

{mlatom-3.17.0 → mlatom-3.17.2}/src/mlatom.egg-info/SOURCES.txt

@@ -83,6 +83,8 @@ src/mlatom/MLatomF_src/strings.f90
 src/mlatom/MLatomF_src/timing.f90
 src/mlatom/MLatomF_src/types.f90
 src/mlatom/addons/__init__.py
+src/mlatom/addons/uaiqm/__init__.py
+src/mlatom/addons/uaiqm/uaiqm.py
 src/mlatom/aiqm1_model/__init__.py
 src/mlatom/aiqm1_model/aiqm1_cc_cv0.pt
 src/mlatom/aiqm1_model/aiqm1_cc_cv1.pt

{mlatom-3.17.0 → mlatom-3.17.2}/src/mlatom.egg-info/entry_points.txt

@@ -1,5 +1,5 @@
 [console_scripts]
 MLatomF = mlatom.shell_cmd:MLatomF
-mlatom = mlatom.shell_cmd:mlatom
+mlatom = mlatom.shell_cmd:mlatom_cmd_run
 mlatom-gui = mlatom.mlatom_gui:main
 mlatom_gui = mlatom.mlatom_gui:main

mlatom-3.17.0/src/mlatom/shell_cmd.py

@@ -1,17 +0,0 @@
-#!/usr/bin/env python
-import sys
-import os
-import time
-from MLatom import run
-
-def mlatom():
-    run()
-    time.sleep(1)
-
-def MLatomF():
-    path = os.path.abspath(os.path.dirname(__file__))
-    os.system(f'{path}/MLatomF {" ".join(sys.argv[1:])}')
-    time.sleep(1)
-
-if __name__ == '__main__':
-    run()