MultiOptPy 1.20.2__py3-none-any.whl

multioptpy/Wrapper/ieip_wrapper.py

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+
+
+import multioptpy.interface
+import multioptpy.ieip
+
+
+class IEIPJob:
+    """
+    Wrapper class to define and run an iEIP (reaction path search) job
+    from a Python script. This replaces ieipmain.py.
+    """
+    
+    def __init__(self, input_folder):
+        """
+        Initializes the iEIP job settings.
+        
+        Args:
+            input_folder (str): The input folder path.
+        """
+        
+        if not isinstance(input_folder, str):
+            raise TypeError("input_folder must be a string.")
+
+        self.input_args = [input_folder]
+
+        # Get default args using the modified ieipparser
+        parser = multioptpy.interface.init_parser()
+        self.args = multioptpy.interface.ieipparser(parser, self.input_args)
+        
+        self._ieip_instance = None
+
+    def set_option(self, key, value):
+        """Sets a single iEIP job option."""
+        if not hasattr(self.args, key):
+            print(f"Warning: Option '{key}' is not a default argparse argument.")
+        setattr(self.args, key, value)
+        print(f"Set option: {key} = {value}")
+
+    def set_options(self, **kwargs):
+        """Sets multiple iEIP job options using keyword arguments."""
+        print("Setting multiple job options...")
+        for key, value in kwargs.items():
+            self.set_option(key, value)
+
+    def run(self):
+        """Executes the iEIP job."""
+        print("\n--- Starting MultiOptPy iEIP Job ---")
+        print("Final Settings (args):")
+        for key, value in vars(self.args).items():
+            print(f"  {key}: {value}")
+        print("--------------------------------------")
+        
+        try:
+            self._ieip_instance = multioptpy.ieip.iEIP(self.args)
+            self._ieip_instance.run()
+            print("--- MultiOptPy Job Finished Successfully ---")
+        except Exception as e:
+            print(f"--- MultiOptPy Job FAILED ---")
+            print(f"An error occurred: {e}")
+            raise
+
+    def get_results(self):
+        """Retrieves the iEIP instance after the job has been run."""
+        if not self._ieip_instance:
+            print("Error: .run() must be called before get_results().")
+            return None
+        return self._ieip_instance
+
+# --- Example Usage ---
+if __name__ == "__main__":
+    print("=== Example: Defining an iEIP Job ===")
+    
+    # 1. Define the job
+    ieip_job = IEIPJob(input_folder="path/to/my_ieip_input")
+    
+    # 2. Configure the job
+    ieip_job.set_options(
+        usextb="GFN2-xTB",
+        NSTEP=50,
+        opt_method=["FIRE"]
+    )
+    
+    print("\n--- Job Configuration Complete ---")
+    print(f"Input folder: {ieip_job.args.INPUT}")
+    print(f"Method: {ieip_job.args.usextb}")
+
+    # 3. To run, uncomment:
+    # try:
+    #     ieip_job.run()
+    # except FileNotFoundError:
+    #     print("\nError: Input folder not found. Job skipped.")
+    # except Exception as e:
+    #     print(f"\nAn error occurred during job execution: {e}")

multioptpy/Wrapper/md_wrapper.py

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+
+import multioptpy.interface
+import multioptpy.moleculardynamics
+
+class MDJob:
+    """
+    Wrapper class to define and run a Molecular Dynamics (MD) job
+    from a Python script. This replaces mdmain.py.
+    """
+    
+    def __init__(self, input_file):
+        """
+        Initializes the MD job settings.
+        
+        Args:
+            input_file (str): The input psi4 file path.
+        """
+        
+        if not isinstance(input_file, str):
+            raise TypeError("input_file must be a string.")
+
+        self.input_args = [input_file]
+
+        # Get default args using the modified mdparser
+        parser = multioptpy.interface.init_parser()
+        self.args = multioptpy.interface.mdparser(parser, self.input_args)
+        
+        self._md_instance = None
+
+    def set_option(self, key, value):
+        """Sets a single MD job option."""
+        if not hasattr(self.args, key):
+            print(f"Warning: Option '{key}' is not a default argparse argument.")
+        setattr(self.args, key, value)
+        print(f"Set option: {key} = {value}")
+
+    def set_options(self, **kwargs):
+        """Sets multiple MD job options using keyword arguments."""
+        print("Setting multiple job options...")
+        for key, value in kwargs.items():
+            self.set_option(key, value)
+
+    def run(self):
+        """Executes the MD job."""
+        print("\n--- Starting MultiOptPy MD Job ---")
+        print("Final Settings (args):")
+        for key, value in vars(self.args).items():
+            print(f"  {key}: {value}")
+        print("----------------------------------")
+        
+        try:
+            self._md_instance = multioptpy.moleculardynamics.MD(self.args)
+            self._md_instance.run()
+            print("--- MultiOptPy Job Finished Successfully ---")
+        except Exception as e:
+            print(f"--- MultiOptPy Job FAILED ---")
+            print(f"An error occurred: {e}")
+            raise
+
+    def get_results(self):
+        """RetrieVes the MD instance after the job has been run."""
+        if not self._md_instance:
+            print("Error: .run() must be called before get_results().")
+            return None
+        return self._md_instance
+
+# --- Example Usage ---
+if __name__ == "__main__":
+    print("=== Example: Defining an MD Job ===")
+    
+    # 1. Define the job
+    md_job = MDJob(input_file="my_md_input.psi4")
+    
+    # 2. Configure the job
+    md_job.set_options(
+        usextb="GFN2-xTB",
+        NSTEP=1000,      # 1000 fs
+        temperature=300.0,
+        timestep=0.5     # 0.5 au
+    )
+    
+    print("\n--- Job Configuration Complete ---")
+    print(f"Input file: {md_job.args.INPUT}")
+    print(f"Timesteps: {md_job.args.NSTEP}")
+
+    # 3. To run, uncomment:
+    # try:
+    #     md_job.run()
+    # except FileNotFoundError:
+    #     print("\nError: Input file not found. Job skipped.")
+    # except Exception as e:
+    #     print(f"\nAn error occurred during job execution: {e}")

multioptpy/Wrapper/neb_wrapper.py

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+
+import multioptpy.interface
+import multioptpy.neb
+
+class NEBJob:
+    """
+    Wrapper class to define and run a Nudged Elastic Band (NEB) job
+    from a Python script. This replaces nebmain.py.
+    """
+    
+    def __init__(self, input_files):
+        """
+        Initializes the NEB job settings.
+        
+        Args:
+            input_files (list): 
+                A list of input file paths (e.g., ["reactant.xyz", "product.xyz"] 
+                or ["img1.xyz", "img2.xyz", ...]).
+        """
+        
+        if not isinstance(input_files, list) or len(input_files) == 0:
+            raise TypeError("input_files must be a non-empty list of strings.")
+
+        self.input_args = input_files
+
+        # Get default args using the modified nebparser
+        parser = multioptpy.interface.init_parser()
+        self.args = multioptpy.interface.nebparser(parser, self.input_args)
+        
+        self._neb_instance = None
+
+    def set_option(self, key, value):
+        """Sets a single NEB job option."""
+        if not hasattr(self.args, key):
+            print(f"Warning: Option '{key}' is not a default argparse argument.")
+        setattr(self.args, key, value)
+        print(f"Set option: {key} = {value}")
+
+    def set_options(self, **kwargs):
+        """Sets multiple NEB job options using keyword arguments."""
+        print("Setting multiple job options...")
+        for key, value in kwargs.items():
+            self.set_option(key, value)
+
+    def run(self):
+        """Executes the NEB job."""
+        print("\n--- Starting MultiOptPy NEB Job ---")
+        print("Final Settings (args):")
+        for key, value in vars(self.args).items():
+            print(f"  {key}: {value}")
+        print("-----------------------------------")
+        
+        try:
+            self._neb_instance = multioptpy.neb.NEB(self.args)
+            self._neb_instance.run()
+            print("--- MultiOptPy Job Finished Successfully ---")
+        except Exception as e:
+            print(f"--- MultiOptPy Job FAILED ---")
+            print(f"An error occurred: {e}")
+            raise
+
+    def get_results(self):
+        """Retrieves the NEB instance after the job has been run."""
+        if not self._neb_instance:
+            print("Error: .run() must be called before get_results().")
+            return None
+        return self._neb_instance
+
+# --- Example Usage ---
+if __name__ == "__main__":
+    print("=== Example: Defining a NEB Job ===")
+    
+    # 1. Define the job
+    neb_job = NEBJob(input_files=["reactant.xyz", "product.xyz"])
+    
+    # 2. Configure the job
+    neb_job.set_options(
+        usextb="GFN2-xTB",
+        NSTEP=100,
+        partition=8,      # 8 intermediate images
+        apply_CI_NEB=5    # Apply CI-NEB after 5 steps
+    )
+    
+    print("\n--- Job Configuration Complete ---")
+    print(f"Input files: {neb_job.args.INPUT}")
+    print(f"Images: {neb_job.args.partition}")
+
+    # 3. To run, uncomment:
+    # try:
+    #     neb_job.run()
+    # except FileNotFoundError:
+    #     print("\nError: Input file(s) not found. Job skipped.")
+    # except Exception as e:
+    #     print(f"\nAn error occurred during job execution: {e}")

multioptpy/Wrapper/optimize_wrapper.py

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+
+import multioptpy.interface
+import multioptpy.optimization
+
+class OptimizationJob:
+    """
+    A wrapper class to define and run a multioptpy optimization job
+    from a Python script. This replaces optmain.py.
+    """
+    
+    def __init__(self, input_file):
+        """
+        Initializes the optimization job settings.
+        (Omitted for brevity...)
+        """
+        if isinstance(input_file, str):
+            self.input_args = [input_file]
+        elif isinstance(input_file, list):
+            self.input_args = input_file
+        else:
+            raise TypeError("input_file must be a string or a list of strings.")
+        parser = multioptpy.interface.init_parser()
+        self.args = multioptpy.interface.optimizeparser(parser, self.input_args)
+        self._optimizer = None
+
+    def set_option(self, key, value):
+        """
+        Sets a single optimization job option.
+        (Omitted for brevity...)
+        """
+        if not hasattr(self.args, key):
+            print(f"Warning: Option '{key}' is not a default argparse argument.")
+        setattr(self.args, key, value)
+        print(f"Set option: {key} = {value}")
+
+    def set_options(self, **kwargs):
+        """
+        Sets multiple optimization job options using keyword arguments.
+        (Omitted for brevity...)
+        """
+        print("Setting multiple job options...")
+        for key, value in kwargs.items():
+            self.set_option(key, value)
+
+    def run(self):
+        """
+        Executes the optimization job.
+        (Omitted for brevity...)
+        """
+        print("\n--- Starting MultiOptPy Optimization Job ---")
+        print("Final Settings (args):")
+        for key, value in vars(self.args).items():
+            print(f"  {key}: {value}")
+        print("--------------------------------------------")
+        try:
+            self._optimizer = multioptpy.optimization.Optimize(self.args)
+            self._optimizer.run()
+            print("--- MultiOptPy Job Finished Successfully ---")
+        except Exception as e:
+            print(f"--- MultiOptPy Job FAILED ---")
+            print(f"An error occurred: {e}")
+            raise
+
+    def get_results(self):
+        """
+        Returns the internal optimizer instance after the job has run.
+        This instance contains the new file path methods.
+        """
+        if not self._optimizer:
+            print("Error: .run() must be called before get_results().")
+            return None
+        
+        # Return the instance itself, so we can call
+        # .get_result_file_path() on it
+        return self._optimizer
+

multioptpy/__init__.py

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+from . import interface
+from . import neb
+from . import ieip
+from . import moleculardynamics
+from . import optimization