<filename>popoff/fitting_code.py<gh_stars>0
import numpy as np
import os
import lammps
from popoff.collate_structures import collate_structural_data
import popoff.potentials as pot

class FitModel():
    """
    Class that collates all fitting information and runs the fitting process using PyMC3 and LAMMPS.
    """
    def __init__(self, potentials, lammps_data, cs_springs=None):
        """
        Initialise an instance for all information relating to the pysical and electronic structure needed for the Lammps input.
        
        Args:
            potentials (list(:obj:`BuckinghamPotential`)): BuckinghamPotential objects including labels (list(str)), atom_type_index (list(int)), a (obj), rho (obj), and c (obj). Each object is a BuckinghamParameter object.
            lammps_data (list(:obj:`LammpsData`)):  LammpsData objects containing atom_types (list(:obj:`AtomType`)), bond_types (list(:obj:`BondType`)), atoms (list(:obj:`Atom`)), bonds (list(:obj:`Bond`)), cell_lengths (list(float)), tilt_factor (list(float)), file_name (str), and expected_stress_tensors (np.array).
            cs_springs (dict): The key is the atom label (str) and the value the spring values (list(float)).
            
        Returns:
            None
        """  
        self.potentials = potentials
        self.lammps_data = lammps_data
        self.cs_springs = cs_springs

    @classmethod
    def collect_info(cls,params, structs, supercell=None):
        """
        Collects information from other classes relating to the potentials and lammps_data using params input information.
        
        Args:
            params (dict(dict)): Contains core_shell (bool), charges (float), masses (float), and cs_springs (list(float)) dictionaries where the keys are atom label (str). Also contains a potentials (list(float)) dictionary where the potentials keys are atom label pairs (str), example: 'Li-O'.
            structs (np.array): An array containing the list of structure numbers to fit to. Note: this starts from 0 not 1 so check your vasprun.xml numbering.
            supercell (list(int) (optional)): 3 integers defining the cell increase in x, y, and z for all structures. Default=None.
            
        Returns:
            :obj:`FitModel`: FitModel object containing potentials (list(:obj:`BuckinghamPotential`)), lammps_data (:obj:`LammpsData`), and cs_spring (dict).      
        """  
        lammps_data = collate_structural_data(params, structs, supercell)
        parameters = pot.buckingham_parameters(params['potentials'])
        potentials = pot.buckingham_potentials(params['potentials'], lammps_data[0].atom_types, parameters)
        if 'cs_springs' in params.keys():
            cs_springs =  params['cs_springs']
            return cls(potentials, lammps_data, cs_springs)
        else:
            return cls(potentials, lammps_data)
    
    def expected_forces(self):
        """
        Collates the expected forces on all atoms, in all structures to a flattened 2D array, where axis 0 is the list of atoms and axis 1 is the x,y,z forces.
        
        Args:
            None      
            
        Returns:
            np.array: 2D array of all atoms forces in all structures.
        """
        forces_data = []
        for structure in self.lammps_data:
            atom_forces = []
            for atoms in structure.atoms:
                atom_forces.append(atoms.forces)
            forces = np.stack(atom_forces, axis=0)
            core_mask = structure.core_mask()
            forces_data.append(forces[core_mask])
        expected_forces = np.concatenate(forces_data, axis=0)
        return expected_forces
    
    def expected_stresses(self):
        """
        Collates the expected stress tensors for each structure to a flattened 2D array, where each row contains the XX YY ZZ XY YZ XZ. Note this is vasp format which is different from lammps format. Lammps format will be converted to vasp format with :obj:`convert_stresses_to_vasp`.
        
        Args:
            None
            
        Returns:
            np.array: 2D array of the stress tensors in each structure.
        """
        stress_data = []
        for structure in self.lammps_data:
            stress_data.append(structure.expected_stress_tensors)
        expected_stresses = np.concatenate(stress_data, axis=0)
        return expected_stresses 
    
    def _set_charges(self, lmp):
        """
        Sets the charge on each atom in the structure by type for the specified Lammps system (changes for each iteration of the potential fit).
        
        Args:
            lmp (:obj:`lmp`): Lammps object with structure and specified commands implemented.
            
        Returns:
            None
        """
        for data in self.lammps_data:
            for atom_type in data.atom_types:
                lmp.command('set type %d charge %f' % (atom_type.atom_type_index, atom_type.charge))
    
    def _set_springs(self, lmp):
        """
        Sets the spring constant for the core-shell bonds for the specified Lammps system (changes for each iteration of the potential fit).
        
        Args:
            lmp (:obj:`lmp`): Lammps object with structure and specified commands implemented.
            
        Returns:
            None
        """
        for data in self.lammps_data:
            for bond_type in data.bond_types:
                    lmp.command(bond_type.bond_string())            
                    
    def _set_potentials(self, lmp):
        """
        Sets the potential for the specified Lammps system (changes for each iteration of the potential fit).
        
        Args:
            lmp (:obj:`lmp`): Lammps object with structure and specified commands implemented.
            
        Returns:
            None
        """
        for pot in self.potentials:
            lmp.command('{}'.format(pot.potential_string()))        
    
    def get_forces_and_stresses(self):
        """
        Runs a minimization (if core-shell atoms present) and zero step run for each instance and returns the forces and stress (pressure) tensors. If any core-shell atoms are present the output forces are masked, so only the forces acting on the rigid ion and core atoms are returned for direct comparison with the relating dft forces.
        
        Args:
            None
            
        Returns:
				np.array, np.array: x,y,z forces on each atom for each instance; stress tenosrs for each instance (each structure).
        """    
        instances = [lmp.initiate_lmp(self.cs_springs) for lmp in self.lammps_data]
        ip_forces = np.zeros(self.expected_forces().shape)
        structure_forces = []
        structure_stresses = []
        for ld, instance in zip(self.lammps_data, instances):
            self._set_potentials(instance)
            self._set_charges(instance)
            if self.cs_springs: #If coreshell do the minimisation otherwise do run(0) only
                self._set_springs(instance)
                instance.command('fix 1 cores setforce 0.0 0.0 0.0')
                instance.command('minimize 1e-25 1e-3 3000 10000')
                instance.command('unfix 1')
            instance.run(0)
            structure_forces.append(instance.system.forces[ld.core_mask()])
            structure_stresses.append(self.convert_stresses_to_vasp(instance))
        ip_forces = np.concatenate(structure_forces, axis=0)
        ip_stresses = np.concatenate(structure_stresses, axis=0)
        return ip_forces, ip_stresses      
     
    def convert_stresses_to_vasp(self, instance):
        """
        Extracts the stress tensors from the lammps object after MD has been run and converts them from bar to kBar, then swaps the last two columns to be in the same format as vasp stress tensors (XX YY ZZ XY YZ XZ).
        
        Args:
            instance (:obj:`lmp`): Lammps object after minimisation (if core-shell) and a zero step run.  
            
        Returns:
            np.array: stress tenosrs for the lammps instance (single structure).
        """
        ip_stresses = instance.thermo.computes['thermo_press'].vector / 1000
        ip_stresses[5], ip_stresses[4] = ip_stresses[4], ip_stresses[5]
        return ip_stresses
    
    def _charge_reset(self):
        """
        Resets charge (the working charge) to the formal charge for each atom type.
        
        Args:
            None
            
        Returns:
            None
        """
        for data in self.lammps_data:
            for at in data.atom_types:
                at.charge = at.formal_charge
       
    def _update_q_ratio(self, fitting_parameters):
        """
        Updates the charge ratio between a given core-shell pair. This is done by passing a factor dQ, which is added to the core charge and sutracted from the shell charge.
        
        Args:
            fitting_parameters (dict): The keys relate to the parameters being fitted, and the values are the corresponding values.
            
        Returns:
            None
        """
        for arg, value in fitting_parameters.items():
            if arg.startswith('dq_'):
                for data in self.lammps_data:
                    for at in data.atom_types:
                        if arg.endswith(at.element_type) and at.core_shell == 'core':
                            at.charge += value
                        if arg.endswith(at.element_type) and at.core_shell == 'shell':
                            at.charge -= value    
       
    def _update_springs(self, fitting_parameters):
        """
        Updates the spring constant for the given core-shell atom.
        
        Args:
            fitting_parameters (dict): The keys relate to the parameters being fitted, and the values are the corresponding values.
            
        Returns:
            None
        """
        for arg, value in fitting_parameters.items():
            for data in self.lammps_data:
                for bt in data.bond_types:
                    if bt.label == arg:
                        bt.spring_coeff_1 = value
                                             
    def _update_potentials(self, fitting_parameters):
        """
        Updates the buckingham potential for all parameters being fitted. If a specific parameter isn't updated, the current default value will be used and not varied.
        
        Args:
            fitting_parameters (dict): The keys relate to the parameters being fitted, and the values are the corresponding values.
            
        Returns:
            None
        """
        for arg, value in fitting_parameters.items():
            for pot in self.potentials:
                if arg == pot.a.label_string:
                    pot.a.value = value
                if arg == pot.rho.label_string:
                    pot.rho.value = value
                if arg == pot.c.label_string:
                    pot.c.value = value                                                
                            
    def _update_charge_scaling(self, fitting_parameters):
        """
        Updates the charge scaling for all atoms. This is done by passing a scaling factor between 0 and 1, which is multiplied by the charge. Example Li = +1 charge, with a scaling factor of 0.5 is 1*0.5, giving a scaled charge of 0.5.
        
        Args:
            fitting_parameters (dict): The keys relate to the parameters being fitted, and the values are the corresponding values.
            
        Returns:
            None
        """
        for arg, value in fitting_parameters.items():
            if arg == 'q_scaling':
                for data in self.lammps_data:
                    for at in data.atom_types:
                        at.charge *= value                      
                        
    def init_potential(self, values, args):
        """
        Takes a list of potential arguments and their corresponding values, resets the charges on the atoms, then applies a series of updates relating to the given arguements.
        
        Args:
            values (list(float)): Values relating to the fitting arguments passes in.
            args (list(str)): Keys relating to the fitting parameters for the system, such as charge, springs, and buckingham parameters.
            
        Returns:
            None
        """
        self._charge_reset()
        fitting_parameters = dict(zip(args, values))
        self._update_q_ratio(fitting_parameters)
        self._update_springs(fitting_parameters)
        self._update_potentials(fitting_parameters)        
        self._update_charge_scaling(fitting_parameters)                    
    
    def chi_squared_error(self, values, args):
        """
        Runs potential updates, and calculates a chi squared error between the dft and ip forces and stress tensors.
        
        Args:
            values (list(float)): Values relating to the fitting arguments passes in.
            args (list(str)): Keys relating to the fitting parameters for the system, such as charge, springs, and buckingham parameters.
            
        Returns:
            float: The chi squared error calculated between dft forces and the MD forces under the given potential and the DFT and MD stress tensors.
        """
        self.init_potential(values,args)
        ip_forces, ip_stresses = self.get_forces_and_stresses()
        force_diff = np.sum((self.expected_forces() - ip_forces)**2)/ self.expected_forces().size
        stress_diff = np.sum((self.expected_stresses() - ip_stresses)**2)/6
        return force_diff + (stress_diff*0.001)
    
    def get_lattice_params(self):
        """
        Runs a minimization (if core-shell atoms present) and a structure relaxation for each instance and returns the lammps instance.
        
        Args:
            None
            
        Returns:
            :obj:`lmp`: Lammps object with structure and specified commands implemented.
        """  
        instances = [lmp.initiate_lmp(self.cs_springs) for lmp in self.lammps_data]
        for ld, instance in zip(self.lammps_data, instances):
            self._set_potentials(instance)
            self._set_charges(instance)
            if self.cs_springs: #If coreshell do the minimisation otherwise do run(0) only
                self._set_springs(instance)
                instance.command('fix 1 cores setforce 0.0 0.0 0.0')
                instance.command('minimize 1e-25 1e-3 3000 10000')
                instance.command('unfix 1')
          
            instance.command('reset_timestep 0')
            instance.command('timestep 0.1')
            instance.command('fix 2 all box/relax aniso 1.0 vmax 0.0005')
            instance.command('min_style cg')
            instance.command('minimize 1e-25 1e-25 1000 5000')
            instance.command('unfix 2')
    
        return instances

    def reset_directories(self):
        """
        Removes any lammps files from the working directory.
        
        Args:
            None
            
        Returns:
            None
        """  
        os.system('rm lammps/coords*')

<filename>popoff/fitting_code.py<gh_stars>0
import numpy as np
import os
import lammps
from popoff.collate_structures import collate_structural_data
import popoff.potentials as pot

class FitModel():
    """
    Class that collates all fitting information and runs the fitting process using PyMC3 and LAMMPS.
    """
    def __init__(self, potentials, lammps_data, cs_springs=None):
        """
        Initialise an instance for all information relating to the pysical and electronic structure needed for the Lammps input.
        
        Args:
            potentials (list(:obj:`BuckinghamPotential`)): BuckinghamPotential objects including labels (list(str)), atom_type_index (list(int)), a (obj), rho (obj), and c (obj). Each object is a BuckinghamParameter object.
            lammps_data (list(:obj:`LammpsData`)):  LammpsData objects containing atom_types (list(:obj:`AtomType`)), bond_types (list(:obj:`BondType`)), atoms (list(:obj:`Atom`)), bonds (list(:obj:`Bond`)), cell_lengths (list(float)), tilt_factor (list(float)), file_name (str), and expected_stress_tensors (np.array).
            cs_springs (dict): The key is the atom label (str) and the value the spring values (list(float)).
            
        Returns:
            None
        """  
        self.potentials = potentials
        self.lammps_data = lammps_data
        self.cs_springs = cs_springs

    @classmethod
    def collect_info(cls,params, structs, supercell=None):
        """
        Collects information from other classes relating to the potentials and lammps_data using params input information.
        
        Args:
            params (dict(dict)): Contains core_shell (bool), charges (float), masses (float), and cs_springs (list(float)) dictionaries where the keys are atom label (str). Also contains a potentials (list(float)) dictionary where the potentials keys are atom label pairs (str), example: 'Li-O'.
            structs (np.array): An array containing the list of structure numbers to fit to. Note: this starts from 0 not 1 so check your vasprun.xml numbering.
            supercell (list(int) (optional)): 3 integers defining the cell increase in x, y, and z for all structures. Default=None.
            
        Returns:
            :obj:`FitModel`: FitModel object containing potentials (list(:obj:`BuckinghamPotential`)), lammps_data (:obj:`LammpsData`), and cs_spring (dict).      
        """  
        lammps_data = collate_structural_data(params, structs, supercell)
        parameters = pot.buckingham_parameters(params['potentials'])
        potentials = pot.buckingham_potentials(params['potentials'], lammps_data[0].atom_types, parameters)
        if 'cs_springs' in params.keys():
            cs_springs =  params['cs_springs']
            return cls(potentials, lammps_data, cs_springs)
        else:
            return cls(potentials, lammps_data)
    
    def expected_forces(self):
        """
        Collates the expected forces on all atoms, in all structures to a flattened 2D array, where axis 0 is the list of atoms and axis 1 is the x,y,z forces.
        
        Args:
            None      
            
        Returns:
            np.array: 2D array of all atoms forces in all structures.
        """
        forces_data = []
        for structure in self.lammps_data:
            atom_forces = []
            for atoms in structure.atoms:
                atom_forces.append(atoms.forces)
            forces = np.stack(atom_forces, axis=0)
            core_mask = structure.core_mask()
            forces_data.append(forces[core_mask])
        expected_forces = np.concatenate(forces_data, axis=0)
        return expected_forces
    
    def expected_stresses(self):
        """
        Collates the expected stress tensors for each structure to a flattened 2D array, where each row contains the XX YY ZZ XY YZ XZ. Note this is vasp format which is different from lammps format. Lammps format will be converted to vasp format with :obj:`convert_stresses_to_vasp`.
        
        Args:
            None
            
        Returns:
            np.array: 2D array of the stress tensors in each structure.
        """
        stress_data = []
        for structure in self.lammps_data:
            stress_data.append(structure.expected_stress_tensors)
        expected_stresses = np.concatenate(stress_data, axis=0)
        return expected_stresses 
    
    def _set_charges(self, lmp):
        """
        Sets the charge on each atom in the structure by type for the specified Lammps system (changes for each iteration of the potential fit).
        
        Args:
            lmp (:obj:`lmp`): Lammps object with structure and specified commands implemented.
            
        Returns:
            None
        """
        for data in self.lammps_data:
            for atom_type in data.atom_types:
                lmp.command('set type %d charge %f' % (atom_type.atom_type_index, atom_type.charge))
    
    def _set_springs(self, lmp):
        """
        Sets the spring constant for the core-shell bonds for the specified Lammps system (changes for each iteration of the potential fit).
        
        Args:
            lmp (:obj:`lmp`): Lammps object with structure and specified commands implemented.
            
        Returns:
            None
        """
        for data in self.lammps_data:
            for bond_type in data.bond_types:
                    lmp.command(bond_type.bond_string())            
                    
    def _set_potentials(self, lmp):
        """
        Sets the potential for the specified Lammps system (changes for each iteration of the potential fit).
        
        Args:
            lmp (:obj:`lmp`): Lammps object with structure and specified commands implemented.
            
        Returns:
            None
        """
        for pot in self.potentials:
            lmp.command('{}'.format(pot.potential_string()))        
    
    def get_forces_and_stresses(self):
        """
        Runs a minimization (if core-shell atoms present) and zero step run for each instance and returns the forces and stress (pressure) tensors. If any core-shell atoms are present the output forces are masked, so only the forces acting on the rigid ion and core atoms are returned for direct comparison with the relating dft forces.
        
        Args:
            None
            
        Returns:
				np.array, np.array: x,y,z forces on each atom for each instance; stress tenosrs for each instance (each structure).
        """    
        instances = [lmp.initiate_lmp(self.cs_springs) for lmp in self.lammps_data]
        ip_forces = np.zeros(self.expected_forces().shape)
        structure_forces = []
        structure_stresses = []
        for ld, instance in zip(self.lammps_data, instances):
            self._set_potentials(instance)
            self._set_charges(instance)
            if self.cs_springs: #If coreshell do the minimisation otherwise do run(0) only
                self._set_springs(instance)
                instance.command('fix 1 cores setforce 0.0 0.0 0.0')
                instance.command('minimize 1e-25 1e-3 3000 10000')
                instance.command('unfix 1')
            instance.run(0)
            structure_forces.append(instance.system.forces[ld.core_mask()])
            structure_stresses.append(self.convert_stresses_to_vasp(instance))
        ip_forces = np.concatenate(structure_forces, axis=0)
        ip_stresses = np.concatenate(structure_stresses, axis=0)
        return ip_forces, ip_stresses      
     
    def convert_stresses_to_vasp(self, instance):
        """
        Extracts the stress tensors from the lammps object after MD has been run and converts them from bar to kBar, then swaps the last two columns to be in the same format as vasp stress tensors (XX YY ZZ XY YZ XZ).
        
        Args:
            instance (:obj:`lmp`): Lammps object after minimisation (if core-shell) and a zero step run.  
            
        Returns:
            np.array: stress tenosrs for the lammps instance (single structure).
        """
        ip_stresses = instance.thermo.computes['thermo_press'].vector / 1000
        ip_stresses[5], ip_stresses[4] = ip_stresses[4], ip_stresses[5]
        return ip_stresses
    
    def _charge_reset(self):
        """
        Resets charge (the working charge) to the formal charge for each atom type.
        
        Args:
            None
            
        Returns:
            None
        """
        for data in self.lammps_data:
            for at in data.atom_types:
                at.charge = at.formal_charge
       
    def _update_q_ratio(self, fitting_parameters):
        """
        Updates the charge ratio between a given core-shell pair. This is done by passing a factor dQ, which is added to the core charge and sutracted from the shell charge.
        
        Args:
            fitting_parameters (dict): The keys relate to the parameters being fitted, and the values are the corresponding values.
            
        Returns:
            None
        """
        for arg, value in fitting_parameters.items():
            if arg.startswith('dq_'):
                for data in self.lammps_data:
                    for at in data.atom_types:
                        if arg.endswith(at.element_type) and at.core_shell == 'core':
                            at.charge += value
                        if arg.endswith(at.element_type) and at.core_shell == 'shell':
                            at.charge -= value    
       
    def _update_springs(self, fitting_parameters):
        """
        Updates the spring constant for the given core-shell atom.
        
        Args:
            fitting_parameters (dict): The keys relate to the parameters being fitted, and the values are the corresponding values.
            
        Returns:
            None
        """
        for arg, value in fitting_parameters.items():
            for data in self.lammps_data:
                for bt in data.bond_types:
                    if bt.label == arg:
                        bt.spring_coeff_1 = value
                                             
    def _update_potentials(self, fitting_parameters):
        """
        Updates the buckingham potential for all parameters being fitted. If a specific parameter isn't updated, the current default value will be used and not varied.
        
        Args:
            fitting_parameters (dict): The keys relate to the parameters being fitted, and the values are the corresponding values.
            
        Returns:
            None
        """
        for arg, value in fitting_parameters.items():
            for pot in self.potentials:
                if arg == pot.a.label_string:
                    pot.a.value = value
                if arg == pot.rho.label_string:
                    pot.rho.value = value
                if arg == pot.c.label_string:
                    pot.c.value = value                                                
                            
    def _update_charge_scaling(self, fitting_parameters):
        """
        Updates the charge scaling for all atoms. This is done by passing a scaling factor between 0 and 1, which is multiplied by the charge. Example Li = +1 charge, with a scaling factor of 0.5 is 1*0.5, giving a scaled charge of 0.5.
        
        Args:
            fitting_parameters (dict): The keys relate to the parameters being fitted, and the values are the corresponding values.
            
        Returns:
            None
        """
        for arg, value in fitting_parameters.items():
            if arg == 'q_scaling':
                for data in self.lammps_data:
                    for at in data.atom_types:
                        at.charge *= value                      
                        
    def init_potential(self, values, args):
        """
        Takes a list of potential arguments and their corresponding values, resets the charges on the atoms, then applies a series of updates relating to the given arguements.
        
        Args:
            values (list(float)): Values relating to the fitting arguments passes in.
            args (list(str)): Keys relating to the fitting parameters for the system, such as charge, springs, and buckingham parameters.
            
        Returns:
            None
        """
        self._charge_reset()
        fitting_parameters = dict(zip(args, values))
        self._update_q_ratio(fitting_parameters)
        self._update_springs(fitting_parameters)
        self._update_potentials(fitting_parameters)        
        self._update_charge_scaling(fitting_parameters)                    
    
    def chi_squared_error(self, values, args):
        """
        Runs potential updates, and calculates a chi squared error between the dft and ip forces and stress tensors.
        
        Args:
            values (list(float)): Values relating to the fitting arguments passes in.
            args (list(str)): Keys relating to the fitting parameters for the system, such as charge, springs, and buckingham parameters.
            
        Returns:
            float: The chi squared error calculated between dft forces and the MD forces under the given potential and the DFT and MD stress tensors.
        """
        self.init_potential(values,args)
        ip_forces, ip_stresses = self.get_forces_and_stresses()
        force_diff = np.sum((self.expected_forces() - ip_forces)**2)/ self.expected_forces().size
        stress_diff = np.sum((self.expected_stresses() - ip_stresses)**2)/6
        return force_diff + (stress_diff*0.001)
    
    def get_lattice_params(self):
        """
        Runs a minimization (if core-shell atoms present) and a structure relaxation for each instance and returns the lammps instance.
        
        Args:
            None
            
        Returns:
            :obj:`lmp`: Lammps object with structure and specified commands implemented.
        """  
        instances = [lmp.initiate_lmp(self.cs_springs) for lmp in self.lammps_data]
        for ld, instance in zip(self.lammps_data, instances):
            self._set_potentials(instance)
            self._set_charges(instance)
            if self.cs_springs: #If coreshell do the minimisation otherwise do run(0) only
                self._set_springs(instance)
                instance.command('fix 1 cores setforce 0.0 0.0 0.0')
                instance.command('minimize 1e-25 1e-3 3000 10000')
                instance.command('unfix 1')
          
            instance.command('reset_timestep 0')
            instance.command('timestep 0.1')
            instance.command('fix 2 all box/relax aniso 1.0 vmax 0.0005')
            instance.command('min_style cg')
            instance.command('minimize 1e-25 1e-25 1000 5000')
            instance.command('unfix 2')
    
        return instances

    def reset_directories(self):
        """
        Removes any lammps files from the working directory.
        
        Args:
            None
            
        Returns:
            None
        """  
        os.system('rm lammps/coords*')

Class that collates all fitting information and runs the fitting process using PyMC3 and LAMMPS. Initialise an instance for all information relating to the pysical and electronic structure needed for the Lammps input.                  Args:             potentials (list(:obj:`BuckinghamPotential`)): BuckinghamPotential objects including labels (list(str)), atom_type_index (list(int)), a (obj), rho (obj), and c (obj). Each object is a BuckinghamParameter object.             lammps_data (list(:obj:`LammpsData`)):  LammpsData objects containing atom_types (list(:obj:`AtomType`)), bond_types (list(:obj:`BondType`)), atoms (list(:obj:`Atom`)), bonds (list(:obj:`Bond`)), cell_lengths (list(float)), tilt_factor (list(float)), file_name (str), and expected_stress_tensors (np.array).             cs_springs (dict): The key is the atom label (str) and the value the spring values (list(float)).                      Returns:             None Collects information from other classes relating to the potentials and lammps_data using params input information.                  Args:             params (dict(dict)): Contains core_shell (bool), charges (float), masses (float), and cs_springs (list(float)) dictionaries where the keys are atom label (str). Also contains a potentials (list(float)) dictionary where the potentials keys are atom label pairs (str), example: 'Li-O'.             structs (np.array): An array containing the list of structure numbers to fit to. Note: this starts from 0 not 1 so check your vasprun.xml numbering.             supercell (list(int) (optional)): 3 integers defining the cell increase in x, y, and z for all structures. Default=None.                      Returns:             :obj:`FitModel`: FitModel object containing potentials (list(:obj:`BuckinghamPotential`)), lammps_data (:obj:`LammpsData`), and cs_spring (dict). Collates the expected forces on all atoms, in all structures to a flattened 2D array, where axis 0 is the list of atoms and axis 1 is the x,y,z forces.                  Args:             None                            Returns:             np.array: 2D array of all atoms forces in all structures. Collates the expected stress tensors for each structure to a flattened 2D array, where each row contains the XX YY ZZ XY YZ XZ. Note this is vasp format which is different from lammps format. Lammps format will be converted to vasp format with :obj:`convert_stresses_to_vasp`.                  Args:             None                      Returns:             np.array: 2D array of the stress tensors in each structure. Sets the charge on each atom in the structure by type for the specified Lammps system (changes for each iteration of the potential fit).                  Args:             lmp (:obj:`lmp`): Lammps object with structure and specified commands implemented.                      Returns:             None Sets the spring constant for the core-shell bonds for the specified Lammps system (changes for each iteration of the potential fit).                  Args:             lmp (:obj:`lmp`): Lammps object with structure and specified commands implemented.                      Returns:             None Sets the potential for the specified Lammps system (changes for each iteration of the potential fit).                  Args:             lmp (:obj:`lmp`): Lammps object with structure and specified commands implemented.                      Returns:             None Runs a minimization (if core-shell atoms present) and zero step run for each instance and returns the forces and stress (pressure) tensors. If any core-shell atoms are present the output forces are masked, so only the forces acting on the rigid ion and core atoms are returned for direct comparison with the relating dft forces.                  Args:             None                      Returns: 				np.array, np.array: x,y,z forces on each atom for each instance; stress tenosrs for each instance (each structure). #If coreshell do the minimisation otherwise do run(0) only Extracts the stress tensors from the lammps object after MD has been run and converts them from bar to kBar, then swaps the last two columns to be in the same format as vasp stress tensors (XX YY ZZ XY YZ XZ).                  Args:             instance (:obj:`lmp`): Lammps object after minimisation (if core-shell) and a zero step run.                        Returns:             np.array: stress tenosrs for the lammps instance (single structure). Resets charge (the working charge) to the formal charge for each atom type.                  Args:             None                      Returns:             None Updates the charge ratio between a given core-shell pair. This is done by passing a factor dQ, which is added to the core charge and sutracted from the shell charge.                  Args:             fitting_parameters (dict): The keys relate to the parameters being fitted, and the values are the corresponding values.                      Returns:             None Updates the spring constant for the given core-shell atom.                  Args:             fitting_parameters (dict): The keys relate to the parameters being fitted, and the values are the corresponding values.                      Returns:             None Updates the buckingham potential for all parameters being fitted. If a specific parameter isn't updated, the current default value will be used and not varied.                  Args:             fitting_parameters (dict): The keys relate to the parameters being fitted, and the values are the corresponding values.                      Returns:             None Updates the charge scaling for all atoms. This is done by passing a scaling factor between 0 and 1, which is multiplied by the charge. Example Li = +1 charge, with a scaling factor of 0.5 is 1*0.5, giving a scaled charge of 0.5.                  Args:             fitting_parameters (dict): The keys relate to the parameters being fitted, and the values are the corresponding values.                      Returns:             None Takes a list of potential arguments and their corresponding values, resets the charges on the atoms, then applies a series of updates relating to the given arguements.                  Args:             values (list(float)): Values relating to the fitting arguments passes in.             args (list(str)): Keys relating to the fitting parameters for the system, such as charge, springs, and buckingham parameters.                      Returns:             None Runs potential updates, and calculates a chi squared error between the dft and ip forces and stress tensors.                  Args:             values (list(float)): Values relating to the fitting arguments passes in.             args (list(str)): Keys relating to the fitting parameters for the system, such as charge, springs, and buckingham parameters.                      Returns:             float: The chi squared error calculated between dft forces and the MD forces under the given potential and the DFT and MD stress tensors. Runs a minimization (if core-shell atoms present) and a structure relaxation for each instance and returns the lammps instance.                  Args:             None                      Returns:             :obj:`lmp`: Lammps object with structure and specified commands implemented. #If coreshell do the minimisation otherwise do run(0) only Removes any lammps files from the working directory.                  Args:             None                      Returns:             None