├── .gitignore ├── README.md ├── environment-dev.yml ├── environment.yml ├── nanoparticle_optimization ├── __init__.py ├── forcefield.py ├── lib │ ├── __init__.py │ ├── chains │ │ ├── __init__.py │ │ └── alkane.py │ ├── moieties │ │ ├── CH2UA.py │ │ ├── CH3UA.py │ │ ├── CH4UA.py │ │ ├── MME.py │ │ ├── MMM.py │ │ └── __init__.py │ └── nanoparticles │ │ ├── AA_nano.py │ │ ├── CG_nano.py │ │ ├── __init__.py │ │ ├── bulk-silica-eq │ │ ├── README.md │ │ ├── data.SiO2_quench_10ps_reax.txt │ │ ├── data.silica_box.txt │ │ ├── ffield.reax │ │ ├── in.SiO2_melt_reax.txt │ │ └── in.SiO2_quench_10ps_reax.txt │ │ ├── bulk_silica.pdb │ │ ├── silica.py │ │ └── tnp.py ├── optimization.py ├── system.py ├── target.py └── utils │ ├── __init__.py │ ├── exceptions.py │ ├── matplotlibrc │ ├── parallel.py │ ├── target_data │ ├── np_alkane │ │ └── united_atom │ │ │ ├── ch2 │ │ │ ├── README.md │ │ │ ├── U_10nm_CH2-complete.txt │ │ │ ├── U_10nm_CH2-lr.txt │ │ │ ├── U_10nm_CH2_init.txt │ │ │ ├── U_10nm_CH2_revised.txt │ │ │ ├── U_10nm_CH2_well.txt │ │ │ ├── U_2nm_CH2-complete.txt │ │ │ ├── U_2nm_CH2-lr.txt │ │ │ ├── U_2nm_CH2_init.txt │ │ │ ├── U_2nm_CH2_revised.txt │ │ │ ├── U_2nm_CH2_well.txt │ │ │ ├── U_3nm_CH2-complete.txt │ │ │ ├── U_3nm_CH2-lr.txt │ │ │ ├── U_3nm_CH2_init.txt │ │ │ ├── U_3nm_CH2_revised.txt │ │ │ ├── U_3nm_CH2_well.txt │ │ │ ├── U_4nm_CH2-complete.txt │ │ │ ├── U_4nm_CH2-lr.txt │ │ │ ├── U_4nm_CH2_init.txt │ │ │ ├── U_4nm_CH2_revised.txt │ │ │ ├── U_4nm_CH2_well.txt │ │ │ ├── U_5nm_CH2-complete.txt │ │ │ ├── U_5nm_CH2-lr.txt │ │ │ ├── U_5nm_CH2_init.txt │ │ │ ├── U_5nm_CH2_revised.txt │ │ │ ├── U_5nm_CH2_trunc.txt │ │ │ ├── U_5nm_CH2_well.txt │ │ │ ├── U_6nm_CH2-complete.txt │ │ │ ├── U_6nm_CH2-lr.txt │ │ │ ├── U_6nm_CH2_init.txt │ │ │ ├── U_6nm_CH2_revised.txt │ │ │ ├── U_6nm_CH2_well.txt │ │ │ ├── U_7nm_CH2-complete.txt │ │ │ ├── U_7nm_CH2-lr.txt │ │ │ ├── U_7nm_CH2_init.txt │ │ │ ├── U_7nm_CH2_revised.txt │ │ │ ├── U_7nm_CH2_well.txt │ │ │ ├── U_8nm_CH2-complete.txt │ │ │ ├── U_8nm_CH2-lr.txt │ │ │ ├── U_8nm_CH2_init.txt │ │ │ ├── U_8nm_CH2_revised.txt │ │ │ ├── U_8nm_CH2_well.txt │ │ │ ├── U_9nm_CH2-complete.txt │ │ │ ├── U_9nm_CH2-lr.txt │ │ │ ├── U_9nm_CH2_init.txt │ │ │ ├── U_9nm_CH2_revised.txt │ │ │ ├── U_9nm_CH2_well.txt │ │ │ ├── gen-lr-data.py │ │ │ ├── gen-revised-data.py │ │ │ ├── pe_np_ch2_mpi-init.cpp │ │ │ ├── pe_np_ch2_mpi-lr.cpp │ │ │ └── pe_np_ch2_mpi-well.cpp │ │ │ └── ch3 │ │ │ ├── README.md │ │ │ ├── U_10nm_CH3-complete.txt │ │ │ ├── U_10nm_CH3-lr.txt │ │ │ ├── U_10nm_CH3_init.txt │ │ │ ├── U_10nm_CH3_revised.txt │ │ │ ├── U_10nm_CH3_well.txt │ │ │ ├── U_2nm_CH3-complete.txt │ │ │ ├── U_2nm_CH3-lr.txt │ │ │ ├── U_2nm_CH3_init.txt │ │ │ ├── U_2nm_CH3_revised.txt │ │ │ ├── U_2nm_CH3_well.txt │ │ │ ├── U_3nm_CH3-complete.txt │ │ │ ├── U_3nm_CH3-lr.txt │ │ │ ├── U_3nm_CH3_init.txt │ │ │ ├── U_3nm_CH3_revised.txt │ │ │ ├── U_3nm_CH3_well.txt │ │ │ ├── U_4nm_CH3-complete.txt │ │ │ ├── U_4nm_CH3-lr.txt │ │ │ ├── U_4nm_CH3_init.txt │ │ │ ├── U_4nm_CH3_revised.txt │ │ │ ├── U_4nm_CH3_well.txt │ │ │ ├── U_5nm_CH3-complete.txt │ │ │ ├── U_5nm_CH3-lr.txt │ │ │ ├── U_5nm_CH3_init.txt │ │ │ ├── U_5nm_CH3_revised.txt │ │ │ ├── U_5nm_CH3_well.txt │ │ │ ├── U_6nm_CH3-complete.txt │ │ │ ├── U_6nm_CH3-lr.txt │ │ │ ├── U_6nm_CH3_init.txt │ │ │ ├── U_6nm_CH3_revised.txt │ │ │ ├── U_6nm_CH3_well.txt │ │ │ ├── U_7nm_CH3-complete.txt │ │ │ ├── U_7nm_CH3-lr.txt │ │ │ ├── U_7nm_CH3_init.txt │ │ │ ├── U_7nm_CH3_revised.txt │ │ │ ├── U_7nm_CH3_well.txt │ │ │ ├── U_8nm_CH3-complete.txt │ │ │ ├── U_8nm_CH3-lr.txt │ │ │ ├── U_8nm_CH3_init.txt │ │ │ ├── U_8nm_CH3_revised.txt │ │ │ ├── U_8nm_CH3_well.txt │ │ │ ├── U_9nm_CH3-complete.txt │ │ │ ├── U_9nm_CH3-lr.txt │ │ │ ├── U_9nm_CH3_init.txt │ │ │ ├── U_9nm_CH3_revised.txt │ │ │ ├── U_9nm_CH3_well.txt │ │ │ ├── gen-lr-data.py │ │ │ ├── gen-revised-data.py │ │ │ ├── pe_np_ch3_mpi-init.cpp │ │ │ ├── pe_np_ch3_mpi-lr.cpp │ │ │ └── pe_np_ch3_mpi-well.cpp │ └── np_np │ │ ├── full │ │ ├── README.md │ │ ├── U_10nm.txt │ │ ├── U_25nm.txt │ │ ├── U_2nm.txt │ │ ├── U_3nm.txt │ │ ├── U_4nm.txt │ │ ├── U_5nm.txt │ │ ├── U_6nm.txt │ │ ├── U_7nm.txt │ │ ├── U_8nm.txt │ │ ├── U_9nm.txt │ │ └── pe_np_mpi.cpp │ │ ├── mixed_size │ │ ├── full │ │ │ ├── README.md │ │ │ ├── U_2nm-3nm.txt │ │ │ ├── U_2nm-4nm.txt │ │ │ ├── U_2nm-6nm.txt │ │ │ ├── U_2nm-8nm.txt │ │ │ ├── U_3nm-4nm.txt │ │ │ ├── U_3nm-6nm.txt │ │ │ ├── U_3nm-8nm.txt │ │ │ ├── U_4nm-6nm.txt │ │ │ ├── U_4nm-8nm.txt │ │ │ ├── U_6nm-8nm.txt │ │ │ └── pe_np_mpi_mixed.cpp │ │ └── truncated │ │ │ ├── README.md │ │ │ ├── U_2nm-3nm_truncated.txt │ │ │ ├── U_2nm-4nm_truncated.txt │ │ │ ├── U_2nm-6nm_truncated.txt │ │ │ ├── U_2nm-8nm_truncated.txt │ │ │ ├── U_3nm-4nm_truncated.txt │ │ │ ├── U_3nm-6nm_truncated.txt │ │ │ ├── U_3nm-8nm_truncated.txt │ │ │ ├── U_4nm-6nm_truncated.txt │ │ │ ├── U_4nm-8nm_truncated.txt │ │ │ └── U_6nm-8nm_truncated.txt │ │ └── truncated │ │ ├── README.md │ │ ├── U_10nm_truncated.txt │ │ ├── U_25nm_truncated.txt │ │ ├── U_2nm_truncated.txt │ │ ├── U_3nm_truncated.txt │ │ ├── U_4nm_truncated.txt │ │ ├── U_5nm_truncated.txt │ │ ├── U_6nm_truncated.txt │ │ ├── U_7nm_truncated.txt │ │ ├── U_8nm_truncated.txt │ │ └── U_9nm_truncated.txt │ └── testing.py ├── postBuild ├── setup.py └── tutorials ├── Example1-LJ-basic.ipynb ├── Example2-LJ-advanced.ipynb ├── Example3-Composite Nanoparticle.ipynb └── Example4-Nanoparticle.ipynb /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | *egg-info* 3 | *.pdf 4 | *.sh 5 | *.swp 6 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # NanoOpt: Deriving potentials for coarse-grained nanoparticles via potential-matching 2 | 3 | # Installation 4 | 5 | NanoOpt is centered around the [mBuild package](https://github.com/mosdef-hub/mbuild) which is easiest to install using the Anaconda package manager. The recommended installation instructions are as follows: 6 | 7 | #### NOTE 8 | 9 | For the version of mbuild used in this paper and study, use `environment.yml`. 10 | For a newer version of the packages with improved mBuild features, use `environment-dev.yml`. 11 | 12 | 1. Clone NanoOpt: 13 | ```sh 14 | git clone https://github.com/summeraz/nanoparticle_optimization 15 | cd nanoparticle_optimization 16 | ``` 17 | 18 | 2. Determine what version you want to use: 19 | Refer to the note above 20 | 21 | * If you want to emulate the study and paper: 22 | ``` 23 | git checkout bdaa8b8 24 | conda env create -f environment.yml 25 | conda activate nanoopt-binder 26 | pip install . 27 | ``` 28 | 29 | * If you want to use newer package versions 30 | ``` 31 | conda env create -f environment.yml 32 | conda activate nanoopt-binder 33 | pip install . 34 | ``` 35 | 36 | 37 | 38 | # Tutorials 39 | 40 | The `tutorials` directory contains several tutorials in the form of Jupyter notebooks that provide examples of the optimization code. 41 | These can be accessed online via Binder: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/mosdef-hub/nanoparticle_optimization/master) 42 | However, these are best run locally as several of the code blocks can take a considerable amount of time to run on Binder. 43 | -------------------------------------------------------------------------------- /environment-dev.yml: -------------------------------------------------------------------------------- 1 | name: nanoopt-binder 2 | 3 | channels: 4 | - conda-forge 5 | 6 | dependencies: 7 | - python>=3.5 8 | - numpy 9 | - scipy 10 | - numba 11 | - mbuild 12 | - py3dmol 13 | - nglview 14 | -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- 1 | name: nanoopt-binder 2 | 3 | channels: 4 | - conda-forge 5 | - defaults 6 | - mosdef 7 | - omnia 8 | 9 | dependencies: 10 | - python=3.5 11 | - numpy 12 | - scipy 13 | - numba 14 | - mbuild 15 | - nglview 16 | -------------------------------------------------------------------------------- /nanoparticle_optimization/__init__.py: -------------------------------------------------------------------------------- 1 | from nanoparticle_optimization.forcefield import * 2 | from nanoparticle_optimization.lib.nanoparticles.AA_nano import AA_nano 3 | from nanoparticle_optimization.lib.nanoparticles.CG_nano import CG_nano 4 | from nanoparticle_optimization.lib.nanoparticles.tnp import TNP 5 | from nanoparticle_optimization.optimization import Optimization 6 | from nanoparticle_optimization.system import System 7 | from nanoparticle_optimization.target import Target 8 | from nanoparticle_optimization.target import load as load_target 9 | from nanoparticle_optimization.utils.testing import run_all as test_all 10 | -------------------------------------------------------------------------------- /nanoparticle_optimization/lib/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mosdef-hub/nanoparticle_optimization/f0157fce30dd37d34b645a961b0125c76e108057/nanoparticle_optimization/lib/__init__.py -------------------------------------------------------------------------------- /nanoparticle_optimization/lib/chains/__init__.py: -------------------------------------------------------------------------------- 1 | from .alkane import Alkane 2 | -------------------------------------------------------------------------------- /nanoparticle_optimization/lib/chains/alkane.py: -------------------------------------------------------------------------------- 1 | from __future__ import division 2 | 3 | import mbuild as mb 4 | from nanoparticle_optimization.lib.moieties import CH2UA, CH3UA, MMM, MME 5 | 6 | 7 | class Alkane(mb.Compound): 8 | """An alkane chain 9 | 10 | Parameters 11 | ---------- 12 | chain_length 13 | fidelity : str 14 | The fidelity of the alkane model. Valid options are 'UA' for 15 | united-atom and 'CG' for a 3:1 coarse-grained mapping. 16 | cap_front 17 | cap_end 18 | """ 19 | def __init__(self, chain_length, fidelity, cap_front=True, cap_end=True): 20 | super(Alkane, self).__init__() 21 | 22 | if fidelity not in ['UA', 'CG']: 23 | raise Exception("`fidelity` must be either 'UA' or 'CG'.") 24 | if chain_length < 2: 25 | raise Exception("Chain length must be 2 or greater.") 26 | if fidelity == 'CG' and chain_length % 3 != 0: 27 | raise Exception("Chain length must be divisible by three for " 28 | "use with `fidelity`='CG'.") 29 | if fidelity == 'CG' and chain_length == 3: 30 | raise Exception("Chain length must be greater than 3 for " 31 | "use with `fidelity`='CG'.") 32 | 33 | if fidelity == 'UA': 34 | middle_bead = CH2UA() 35 | end_bead = CH3UA() 36 | if fidelity == 'CG': 37 | chain_length /= 3 38 | middle_bead = MMM() 39 | end_bead = MME() 40 | 41 | if not cap_front: 42 | chain_length += 1 43 | if not cap_end: 44 | chain_length += 1 45 | 46 | if chain_length > 2: 47 | chain = mb.Polymer(mb.clone(middle_bead), n=chain_length-2, 48 | port_labels=('up', 'down')) 49 | self.add(chain, 'chain') 50 | 51 | if cap_front: 52 | self.add(mb.clone(end_bead), 'front_cap') 53 | mb.force_overlap(self['front_cap'], self['front_cap']['up'], 54 | self['chain']['up']) 55 | else: 56 | # Hoist port label to `Alkane` level 57 | self.add(chain['up'], 'up', containment=False) 58 | 59 | if cap_end: 60 | self.add(mb.clone(end_bead), 'end_cap') 61 | mb.force_overlap(self['end_cap'], self['end_cap']['up'], 62 | self['chain']['down']) 63 | else: 64 | # Hoist port label to `Alkane` level 65 | self.add(chain['down'], 'down', containment=False) 66 | 67 | else: 68 | self.add(mb.clone(end_bead), 'front_cap') 69 | self.add(mb.clone(end_bead), 'end_cap') 70 | mb.force_overlap(self['end_cap'], self['end_cap']['up'], 71 | self['front_cap']['up']) 72 | -------------------------------------------------------------------------------- /nanoparticle_optimization/lib/moieties/CH2UA.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import mbuild as mb 3 | 4 | class CH2UA(mb.Compound): 5 | """ """ 6 | def __init__(self): 7 | super(CH2UA, self).__init__() 8 | self.add(mb.Particle(name='_CH2')) 9 | 10 | self.add(mb.Port(anchor=self[0], separation=0.075), 'up') 11 | 12 | self.add(mb.Port(anchor=self[0], orientation=[0, -1, 0], 13 | separation=0.075), 'down') 14 | -------------------------------------------------------------------------------- /nanoparticle_optimization/lib/moieties/CH3UA.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import mbuild as mb 3 | 4 | class CH3UA(mb.Compound): 5 | """ """ 6 | def __init__(self): 7 | super(CH3UA, self).__init__() 8 | self.add(mb.Particle(name='_CH3')) 9 | 10 | self.add(mb.Port(anchor=self[0], separation=0.075), 'up') 11 | -------------------------------------------------------------------------------- /nanoparticle_optimization/lib/moieties/CH4UA.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import mbuild as mb 3 | 4 | class CH4UA(mb.Compound): 5 | """ """ 6 | def __init__(self): 7 | super(CH4UA, self).__init__() 8 | self.add(mb.Particle(name='_CH4')) 9 | -------------------------------------------------------------------------------- /nanoparticle_optimization/lib/moieties/MME.py: -------------------------------------------------------------------------------- 1 | import mbuild as mb 2 | import numpy as np 3 | 4 | class MME(mb.Compound): 5 | """Coarse-grained alkane bead representing a CH2-CH2-CH3 group """ 6 | def __init__(self): 7 | super(MME, self).__init__() 8 | self.add(mb.Particle(name='_MME')) 9 | 10 | self.add(mb.Port(anchor=self[0], separation=0.18), 'up') 11 | -------------------------------------------------------------------------------- /nanoparticle_optimization/lib/moieties/MMM.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import mbuild as mb 3 | 4 | class MMM(mb.Compound): 5 | """Coarse-grained alkane bead containing a CH2-CH2-CH2 group""" 6 | def __init__(self): 7 | super(MMM, self).__init__() 8 | self.add(mb.Particle(name='_MMM')) 9 | 10 | self.add(mb.Port(anchor=self[0], separation=0.18), 'up') 11 | 12 | self.add(mb.Port(anchor=self[0], orientation=[0, -1, 0], 13 | separation=0.18), 'down') 14 | -------------------------------------------------------------------------------- /nanoparticle_optimization/lib/moieties/__init__.py: -------------------------------------------------------------------------------- 1 | from .CH2UA import CH2UA 2 | from .CH3UA import CH3UA 3 | from .CH4UA import CH4UA 4 | from .MME import MME 5 | from .MMM import MMM 6 | -------------------------------------------------------------------------------- /nanoparticle_optimization/lib/nanoparticles/AA_nano.py: -------------------------------------------------------------------------------- 1 | from __future__ import division 2 | 3 | import math 4 | 5 | import mbuild as mb 6 | import numpy as np 7 | from scipy.spatial import distance 8 | 9 | from .silica import Silica 10 | 11 | class AA_nano(mb.Compound): 12 | def __init__(self, radius=2.0, O_layer=False): 13 | """Initialize an AA_nano object. 14 | 15 | Args: 16 | radius (float): Radius of the nanoparticle 17 | """ 18 | super(AA_nano, self).__init__() 19 | 20 | single = Silica() 21 | 22 | O_buffer = 0.275 23 | # Replicate the bulk silica box if necessary 24 | # rep = math.ceil(((radius+O_buffer)/single.periodicity[0])*2.0) 25 | rep = math.ceil(((radius + O_buffer) / single.box.Lx) * 2.0 ) 26 | rep = int(rep) 27 | bulk = mb.recipes.TiledCompound(tile=single,n_tiles=np.array([rep,rep,rep]),name="bulk_silica") 28 | bulk_name = [] 29 | bulk_pos = [] 30 | for particle in bulk.particles(): 31 | bulk_name.append(particle.name) 32 | bulk_pos.append(particle.pos) 33 | bulk_center = [bulk.box.lengths[i]/2.0 for i in range(3)] 34 | dists = distance.cdist(bulk_pos,[bulk_center],'euclidean') 35 | types = {'1':'Si','2':'O'} 36 | if O_layer: 37 | shell_buffer = 0.5 38 | for i, dist in enumerate(dists): 39 | if types[bulk_name[i]] == 'Si' and dist <= radius and dist > radius - shell_buffer: 40 | particle = mb.Compound(name=types[bulk_name[i]], pos=bulk_pos[i]) 41 | self.add(particle, types[bulk_name[i]]+"_{}".format(i)) 42 | elif types[bulk_name[i]] == 'O' and dist <= radius + O_buffer and dist > radius - shell_buffer: 43 | particle = mb.Compound(name=types[bulk_name[i]], pos=bulk_pos[i]) 44 | self.add(particle, types[bulk_name[i]]+"_{}".format(i)) 45 | self.generate_bonds(name_a='Si', name_b='O', dmin=0.0, dmax=0.20419) 46 | components = self.bond_graph.connected_components() 47 | major_component = max(components, key=len) 48 | for atom in list(self.particles()): 49 | if atom not in major_component: 50 | dist = np.linalg.norm(atom.pos - bulk_center) 51 | if atom.name == 'O' and dist > radius: 52 | self.remove(atom) 53 | for i, dist in enumerate(dists): 54 | if dist <= radius - shell_buffer: 55 | particle = mb.Compound(name=types[bulk_name[i]], pos=bulk_pos[i]) 56 | self.add(particle, types[bulk_name[i]]+"_{}".format(i)) 57 | for bond in self.bonds(): 58 | self.remove_bond(bond) 59 | else: 60 | for i, dist in enumerate(dists): 61 | if dist <= radius: 62 | particle = mb.Compound(name=types[bulk_name[i]], pos=bulk_pos[i]) 63 | self.add(particle, types[bulk_name[i]]+"_{}".format(i)) 64 | 65 | if __name__ == "__main__": 66 | n = AA_nano(radius=9) 67 | n.save('AA-{}nm.mol2'.format(9)) 68 | -------------------------------------------------------------------------------- /nanoparticle_optimization/lib/nanoparticles/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mosdef-hub/nanoparticle_optimization/f0157fce30dd37d34b645a961b0125c76e108057/nanoparticle_optimization/lib/nanoparticles/__init__.py -------------------------------------------------------------------------------- /nanoparticle_optimization/lib/nanoparticles/bulk-silica-eq/README.md: -------------------------------------------------------------------------------- 1 | The scripts and files contains within this directory pertain to the equilbration of 2 | the amorphous silica bulk from which atomistic nanoparticles are carved. The contents 3 | of this directory are as follows: 4 | 5 | * **data.silica\_box.txt** - The initial box, a stoichiometric ratio of Si and O at 6 | a density of 2.2 g/mL. 7 | * **data.SiO2\_quench\_10ps\_reax.txt** - The final box. This is converted to PDB 8 | format for nanoparticle carving. 9 | * **ffield.reax** - Contains the ReaxFF parameters for silica, of Fogarty et al, used 10 | in box equilibration. 11 | * **in.SiO2\_melt\_reax.txt** - LAMMPS input script, melt the initial structure at 12 | a temperature of 10000K. 13 | * **in.SiO2\_quench\_10ps\_reax.txt** - LAMMPS input script, quench the melted silica 14 | to form an amorphous solid following the stepwise procedure of Litton and 15 | Garolfalini 16 | -------------------------------------------------------------------------------- /nanoparticle_optimization/lib/nanoparticles/bulk-silica-eq/in.SiO2_melt_reax.txt: -------------------------------------------------------------------------------- 1 | # Melting to 10000K following the procedure of Litton et al., J. App. Phys. 2001 2 | 3 | # Variable definitions 4 | variable t_amorph equal 10000 5 | variable t_lo equal 300 6 | variable seed equal 12345 7 | 8 | # Initialization 9 | units real 10 | boundary p p p 11 | atom_style full 12 | dimension 3 13 | processors * * * 14 | 15 | read_data data.silica_box.txt 16 | 17 | # Use the ReaxFF forcefield, parameters from Fogarty et al., JCP 2010 18 | pair_style reax/c NULL checkqeq yes 19 | pair_coeff * * ffield.reax Si O 20 | 21 | # Initial charge equilibration so our system doesn't blow up 22 | fix chrg all qeq/reax 1 0.0 10.0 1.0e-3 reax/c 23 | thermo 100 24 | run 1000 25 | 26 | # Energy minimization to make the system a bit happier 27 | minimize 1.0e-4 1.0e-6 1 10 28 | 29 | # Initialize velocities at room temp 30 | velocity all create ${t_lo} ${seed} dist gaussian 31 | 32 | reset_timestep 0 33 | 34 | neighbor 2.0 bin 35 | neigh_modify check yes 36 | 37 | timestep 0.1 38 | 39 | compute pe_eq all pe 40 | fix pe_log all ave/time 1 100 100 c_pe_eq file SiO2_eq_pe.txt 41 | 42 | # Run NVT at room temp for a bit longer to minimize energy 43 | fix integrator all nvt temp ${t_lo} ${t_lo} 100 44 | 45 | dump traj_eq all atom 100 SiO2_eq.lammpstrj 46 | 47 | restart 10000 restart.SiO2_box.* 48 | 49 | run 10000 50 | 51 | write_data data.silica_box_relaxed.txt 52 | 53 | unfix integrator 54 | undump traj_eq 55 | uncompute pe_eq 56 | unfix pe_log 57 | 58 | # Heat to 10000K 59 | timestep 0.5 60 | fix integrator all nvt temp ${t_lo} ${t_amorph} 100 61 | 62 | compute pe_melt all pe 63 | compute etot_melt all etotal 64 | compute t_melt all temp 65 | fix pe_log all ave/time 1 100 100 c_pe_melt c_etot_melt c_t_melt file SiO2_melt_pe.txt 66 | 67 | dump traj_eq all atom 500 SiO2_melt.lammpstrj 68 | 69 | run 40000 70 | 71 | write_restart restart.SiO2_10K_melt 72 | -------------------------------------------------------------------------------- /nanoparticle_optimization/lib/nanoparticles/bulk-silica-eq/in.SiO2_quench_10ps_reax.txt: -------------------------------------------------------------------------------- 1 | # Quench to 300K following the procedure of Litton et al., J. App. Phys. 2001 2 | variable qrate equal 10 3 | 4 | # Variable definitions 5 | variable t_amorph equal 10000 6 | variable t_lo equal 300 7 | variable seed equal 12345 8 | variable ts equal 0.5 9 | variable steptime equal ${qrate}*1000/${ts} 10 | 11 | # Initialization 12 | units real 13 | boundary p p p 14 | atom_style full 15 | dimension 3 16 | processors * * * 17 | 18 | read_restart restart.SiO2_10K_melt remap 19 | 20 | # Use the ReaxFF forcefield, parameters from Fogarty et al., JCP 2010 21 | pair_style reax/c NULL checkqeq yes 22 | pair_coeff * * ffield.reax Si O 23 | 24 | neighbor 2.0 bin 25 | neigh_modify check yes 26 | 27 | fix chrg all qeq/reax 1 0.0 10.0 1.0e-3 reax/c 28 | 29 | restart ${steptime} restart.SiO2_quench_${qrate}ps_reax.* 30 | 31 | thermo 100 32 | 33 | compute pe_quench all pe 34 | compute t_quench all temp 35 | fix pe_log all ave/time 1 100 100 c_pe_quench c_t_quench file SiO2_quench_${qrate}ps_pe.txt 36 | 37 | dump traj all xtc 100 SiO2_quench_${qrate}ps_reax.xtc 38 | 39 | timestep ${ts} 40 | 41 | # Cool at 8000K 42 | fix integrator all nvt temp 8000 8000 100 43 | run ${steptime} 44 | 45 | # Cool at 6000K 46 | unfix integrator 47 | fix integrator all nvt temp 6000 6000 100 48 | run ${steptime} 49 | 50 | # Cool at 4000K 51 | unfix integrator 52 | fix integrator all nvt temp 4000 4000 100 53 | run ${steptime} 54 | 55 | # Cool at 3000K 56 | unfix integrator 57 | fix integrator all nvt temp 3000 3000 100 58 | run ${steptime} 59 | 60 | # Cool at 2000K 61 | unfix integrator 62 | fix integrator all nvt temp 2000 2000 100 63 | run ${steptime} 64 | 65 | # Cool at 1000K 66 | unfix integrator 67 | fix integrator all nvt temp 1000 1000 100 68 | run ${steptime} 69 | 70 | # Cool at 300K 71 | unfix integrator 72 | fix integrator all nvt temp ${t_lo} ${t_lo} 100 73 | run ${steptime} 74 | 75 | write_data data.SiO2_quench_${qrate}ps_reax.txt 76 | -------------------------------------------------------------------------------- /nanoparticle_optimization/lib/nanoparticles/silica.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import mbuild as mb 3 | 4 | class Silica(mb.Compound): 5 | """An amorphous silica box, 2.2g/cm^3""" 6 | def __init__(self): 7 | super(Silica, self).__init__() 8 | 9 | mb.load('bulk_silica.pdb', compound=self, 10 | relative_to_module=self.__module__) 11 | self.box = mb.Box([5, 5, 5]) 12 | self.periodicity = [True, True, True] 13 | 14 | if __name__ == "__main__": 15 | s = Silica() 16 | -------------------------------------------------------------------------------- /nanoparticle_optimization/target.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | def load(filename): 4 | target_data = np.loadtxt(filename) 5 | try: 6 | target = Target(target_data[:,0], target_data[:,1], target_data[:,2]) 7 | except IndexError: 8 | target = Target(target_data[:,0], target_data[:,1]) 9 | return target 10 | 11 | class Target(object): 12 | def __init__(self, separations, potential, error=None): 13 | super(Target, self).__init__() 14 | 15 | self.separations = separations 16 | self.potential = potential 17 | if error is None: 18 | self.error = np.zeros(potential.shape[0]) 19 | else: 20 | self.error = error 21 | 22 | if __name__ == "__main__": 23 | pass 24 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mosdef-hub/nanoparticle_optimization/f0157fce30dd37d34b645a961b0125c76e108057/nanoparticle_optimization/utils/__init__.py -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/exceptions.py: -------------------------------------------------------------------------------- 1 | class BuildError(Exception): pass 2 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch2/README.md: -------------------------------------------------------------------------------- 1 | Target data for NP-alkane interactions was a bit tricky to collect as following the initial data collection it was found that additional data was needed in the region of the potential well and in the long-range region. Furthermore, the high error in the short range region did not result in a potential that monotonically decreased to the bottom of the well and monotonically increased afterward, due to slight fluctuations in the data. As a result, a function was applied to the data to ensure it satisfied that criteria. 2 | 3 | This led to the collection of several different sets of target data that were eventually combined into the final set (the files appended with "-complete"). Rather than removing these older files, everything is included in this directory. The following provides a brief description of the five files present for each radius: 4 | 5 | - U_Xnm_CH2_init.txt 6 | The initial target data collected (corresponding C++ file is pe_np_ch2_mpi-init.cpp) 7 | Pruned to remove the first 10 bins 8 | - U_?nm_CH2_well.txt 9 | U_?nm_CH2_init.txt + additional data collected in the 10 | short-range region (corresponding C++ file is pe_np_ch2_mpi-well.cpp) 11 | - U_?nm_CH2-lr.txt 12 | Data collected in the region of long range (corresponding C++ file is pe_np_ch2_mpi-lr.cpp) 13 | - U_?nm_CH2-revised.txt 14 | Combination of "-init" and "-well" data ensuring that points monotonically decrease to the bottom of the potential well and monotonically increase after. 15 | - U_?nm_CH2-complete.txt 16 | Combination of "-init", "-well", and "-lr" data ensuring that points monotonically decrease to the bottom of the potential well and monotonically increase after. 17 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch2/U_10nm_CH2-lr.txt: -------------------------------------------------------------------------------- 1 | 110.5 -0.0233421 0.00180326 2 | 111.5 -0.0167165 0.00163585 3 | 112.5 -0.012659 0.000904849 4 | 113.5 -0.0103817 0.000653499 5 | 114.5 -0.00827822 0.000513822 6 | 115.5 -0.00661444 0.000395722 7 | 116.5 -0.00534461 0.000196133 8 | 117.5 -0.00440583 0.000270297 9 | 118.5 -0.0037695 0.000222209 10 | 119.5 -0.00310788 0.000134578 11 | 120.5 -0.00259245 0.000158619 12 | 121.5 -0.00224884 0.000117814 13 | 122.5 -0.00195137 8.27441e-05 14 | 123.5 -0.0016791 7.79321e-05 15 | 124.5 -0.00147681 4.97555e-05 16 | 125.5 -0.00127709 4.99317e-05 17 | 126.5 -0.0011071 2.398e-05 18 | 127.5 -0.00100194 3.708e-05 19 | 128.5 -0.000896253 3.10631e-05 20 | 129.5 -0.000781018 2.75404e-05 21 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch2/U_10nm_CH2_init.txt: -------------------------------------------------------------------------------- 1 | 102.1 0.237458 1.53135 2 | 102.3 -0.0737818 1.27553 3 | 102.5 -0.228875 1.1185 4 | 102.7 -0.351593 0.941651 5 | 102.9 -0.522156 0.619116 6 | 103.1 -0.600399 0.311867 7 | 103.3 -0.617102 0.136448 8 | 103.5 -0.569894 0.101834 9 | 103.7 -0.510622 0.0856785 10 | 103.9 -0.453354 0.0822685 11 | 104.1 -0.398247 0.0711831 12 | 104.3 -0.356319 0.0607598 13 | 104.5 -0.312093 0.0494056 14 | 104.7 -0.275537 0.0433526 15 | 104.9 -0.241997 0.0364862 16 | 105.1 -0.21699 0.030411 17 | 105.3 -0.193565 0.025296 18 | 105.5 -0.17448 0.0225372 19 | 105.7 -0.155124 0.0198606 20 | 105.9 -0.139617 0.0161372 21 | 106.1 -0.125556 0.014259 22 | 106.3 -0.114125 0.0114385 23 | 106.5 -0.103162 0.01092 24 | 106.7 -0.0948429 0.00916496 25 | 106.9 -0.0855009 0.00774667 26 | 107.1 -0.0788491 0.00656802 27 | 107.3 -0.0719109 0.0057881 28 | 107.5 -0.0664752 0.00521168 29 | 107.7 -0.0608854 0.00474183 30 | 107.9 -0.0561718 0.00434068 31 | 108.1 -0.0521465 0.00376061 32 | 108.3 -0.0483562 0.0031525 33 | 108.5 -0.0447517 0.0028662 34 | 108.7 -0.0414144 0.0026605 35 | 108.9 -0.0385941 0.00239583 36 | 109.1 -0.0360841 0.00216427 37 | 109.3 -0.0337516 0.00191028 38 | 109.5 -0.0313776 0.00168386 39 | 109.7 -0.0295543 0.00146075 40 | 109.9 -0.0276037 0.00148547 41 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch2/U_10nm_CH2_revised.txt: -------------------------------------------------------------------------------- 1 | 1.024200000000000017e+02 -2.429870000000000085e-01 1.062489999999999934e+00 2 | 1.025799999999999983e+02 -2.900989999999999958e-01 1.060629999999999962e+00 3 | 1.026599999999999966e+02 -3.358400000000000274e-01 9.392519999999999758e-01 4 | 1.027000000000000028e+02 -3.515929999999999889e-01 9.416510000000000158e-01 5 | 1.027399999999999949e+02 -4.222420000000000062e-01 8.323270000000000390e-01 6 | 1.028199999999999932e+02 -4.971679999999999988e-01 6.280160000000000187e-01 7 | 1.029000000000000057e+02 -5.395100000000000451e-01 5.886010000000000408e-01 8 | 1.029800000000000040e+02 -5.729180000000000383e-01 4.330860000000000265e-01 9 | 1.030600000000000023e+02 -6.070480000000000320e-01 3.338860000000000161e-01 10 | 1.031400000000000006e+02 -6.145129999999999759e-01 2.698400000000000243e-01 11 | 1.032199999999999989e+02 -5.987240000000000339e-01 2.273429999999999895e-01 12 | 1.033799999999999955e+02 -5.949879999999999614e-01 1.158990000000000020e-01 13 | 1.034599999999999937e+02 -5.842929999999999513e-01 1.083940000000000042e-01 14 | 1.035000000000000000e+02 -5.698940000000000117e-01 1.018339999999999940e-01 15 | 1.035400000000000063e+02 -5.559039999999999537e-01 9.628369999999999984e-02 16 | 1.036200000000000045e+02 -5.418610000000000371e-01 9.045659999999999812e-02 17 | 1.037000000000000028e+02 -5.171980000000000466e-01 8.927169999999999550e-02 18 | 1.037800000000000011e+02 -4.928359999999999963e-01 8.796400000000000052e-02 19 | 1.038599999999999994e+02 -4.665900000000000047e-01 8.093820000000000181e-02 20 | 1.039000000000000057e+02 -4.533539999999999792e-01 8.226849999999999441e-02 21 | 1.039399999999999977e+02 -4.472360000000000224e-01 7.792949999999999877e-02 22 | 1.040999999999999943e+02 -3.982470000000000176e-01 7.118309999999999915e-02 23 | 1.042999999999999972e+02 -3.563189999999999968e-01 6.075980000000000270e-02 24 | 1.045000000000000000e+02 -3.120930000000000093e-01 4.940560000000000090e-02 25 | 1.047000000000000028e+02 -2.755369999999999764e-01 4.335259999999999808e-02 26 | 1.049000000000000057e+02 -2.419969999999999899e-01 3.648620000000000335e-02 27 | 1.050999999999999943e+02 -2.169899999999999884e-01 3.041100000000000053e-02 28 | 1.052999999999999972e+02 -1.935649999999999871e-01 2.529599999999999904e-02 29 | 1.055000000000000000e+02 -1.744799999999999962e-01 2.253720000000000029e-02 30 | 1.057000000000000028e+02 -1.551240000000000119e-01 1.986059999999999909e-02 31 | 1.059000000000000057e+02 -1.396169999999999911e-01 1.613720000000000085e-02 32 | 1.060999999999999943e+02 -1.255560000000000009e-01 1.425900000000000084e-02 33 | 1.062999999999999972e+02 -1.141250000000000042e-01 1.143850000000000075e-02 34 | 1.065000000000000000e+02 -1.031620000000000037e-01 1.091999999999999915e-02 35 | 1.067000000000000028e+02 -9.484289999999999388e-02 9.164959999999999773e-03 36 | 1.069000000000000057e+02 -8.550090000000000467e-02 7.746669999999999771e-03 37 | 1.070999999999999943e+02 -7.884910000000000529e-02 6.568019999999999935e-03 38 | 1.072999999999999972e+02 -7.191089999999999982e-02 5.788100000000000016e-03 39 | 1.075000000000000000e+02 -6.647519999999999818e-02 5.211679999999999785e-03 40 | 1.077000000000000028e+02 -6.088539999999999924e-02 4.741829999999999830e-03 41 | 1.079000000000000057e+02 -5.617180000000000090e-02 4.340680000000000406e-03 42 | 1.080999999999999943e+02 -5.214649999999999841e-02 3.760610000000000168e-03 43 | 1.082999999999999972e+02 -4.835620000000000196e-02 3.152499999999999920e-03 44 | 1.085000000000000000e+02 -4.475169999999999842e-02 2.866200000000000171e-03 45 | 1.087000000000000028e+02 -4.141439999999999705e-02 2.660500000000000104e-03 46 | 1.089000000000000057e+02 -3.859409999999999924e-02 2.395829999999999835e-03 47 | 1.090999999999999943e+02 -3.608410000000000090e-02 2.164269999999999822e-03 48 | 1.092999999999999972e+02 -3.375159999999999966e-02 1.910280000000000094e-03 49 | 1.095000000000000000e+02 -3.137759999999999855e-02 1.683859999999999914e-03 50 | 1.097000000000000028e+02 -2.955429999999999863e-02 1.460750000000000026e-03 51 | 1.099000000000000057e+02 -2.760369999999999838e-02 1.485470000000000020e-03 52 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch2/U_2nm_CH2-lr.txt: -------------------------------------------------------------------------------- 1 | 30.5 -0.0132324 0.0011819 2 | 31.5 -0.00911919 0.00108608 3 | 32.5 -0.00670546 0.00051998 4 | 33.5 -0.00525652 0.000527529 5 | 34.5 -0.00399923 0.000284555 6 | 35.5 -0.00307255 0.000189664 7 | 36.5 -0.00237461 0.000112881 8 | 37.5 -0.00188017 0.000152786 9 | 38.5 -0.00155801 0.000113256 10 | 39.5 -0.00124554 7.5032e-05 11 | 40.5 -0.000993135 6.68776e-05 12 | 41.5 -0.000837055 5.67255e-05 13 | 42.5 -0.00069744 4.39356e-05 14 | 43.5 -0.000584144 3.54079e-05 15 | 44.5 -0.000495287 2.30631e-05 16 | 45.5 -0.000412376 2.17556e-05 17 | 46.5 -0.000346566 7.41553e-06 18 | 47.5 -0.000303537 1.25188e-05 19 | 48.5 -0.000265533 1.02926e-05 20 | 49.5 -0.000223053 1.1331e-05 21 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch2/U_2nm_CH2_init.txt: -------------------------------------------------------------------------------- 1 | 22.3 0.217286 1.13536 2 | 22.5 -0.133466 0.85968 3 | 22.7 -0.317459 0.73511 4 | 22.9 -0.405985 0.595856 5 | 23.1 -0.46832 0.39685 6 | 23.3 -0.460135 0.219947 7 | 23.5 -0.443857 0.0963958 8 | 23.7 -0.398852 0.0628871 9 | 23.9 -0.351466 0.0501936 10 | 24.1 -0.305362 0.0457759 11 | 24.3 -0.267474 0.039563 12 | 24.5 -0.232831 0.0334971 13 | 24.7 -0.204031 0.029362 14 | 24.9 -0.178864 0.0240177 15 | 25.1 -0.156032 0.0185313 16 | 25.3 -0.138613 0.0162576 17 | 25.5 -0.122509 0.01388 18 | 25.7 -0.109017 0.0118966 19 | 25.9 -0.0969446 0.00977179 20 | 26.1 -0.0876199 0.00869415 21 | 26.3 -0.0774415 0.00734853 22 | 26.5 -0.0698373 0.00587977 23 | 26.7 -0.063115 0.00525031 24 | 26.9 -0.0572262 0.00453349 25 | 27.1 -0.0518983 0.0037444 26 | 27.3 -0.0470788 0.00351418 27 | 27.5 -0.0427833 0.00307117 28 | 27.7 -0.0388346 0.00274617 29 | 27.9 -0.0356913 0.00231681 30 | 28.1 -0.0327549 0.00209689 31 | 28.3 -0.0297977 0.00183781 32 | 28.5 -0.0275459 0.00160584 33 | 28.7 -0.025472 0.00147475 34 | 28.9 -0.0234132 0.00131307 35 | 29.1 -0.0216452 0.00117354 36 | 29.3 -0.020018 0.00109038 37 | 29.5 -0.0185535 0.000950344 38 | 29.7 -0.0172492 0.00083792 39 | 29.9 -0.0159281 0.000834568 40 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch2/U_2nm_CH2_revised.txt: -------------------------------------------------------------------------------- 1 | 2.257999999999999829e+01 -2.206359999999999988e-01 7.115540000000000198e-01 2 | 2.266000000000000014e+01 -3.154330000000000189e-01 7.062420000000000364e-01 3 | 2.269999999999999929e+01 -3.174589999999999912e-01 7.351100000000000412e-01 4 | 2.273999999999999844e+01 -3.573950000000000182e-01 6.728659999999999641e-01 5 | 2.282000000000000028e+01 -4.489119999999999777e-01 4.291139999999999954e-01 6 | 2.289999999999999858e+01 -4.541879999999999806e-01 4.541660000000000141e-01 7 | 2.298000000000000043e+01 -4.829559999999999964e-01 4.127430000000000265e-01 8 | 2.305999999999999872e+01 -4.619429999999999925e-01 4.386689999999999756e-01 9 | 2.321999999999999886e+01 -4.600299999999999945e-01 2.801250000000000129e-01 10 | 2.337999999999999901e+01 -4.622939999999999827e-01 1.329019999999999924e-01 11 | 2.346000000000000085e+01 -4.555060000000000220e-01 8.185660000000000158e-02 12 | 2.350000000000000000e+01 -4.438570000000000015e-01 9.639580000000000370e-02 13 | 2.353999999999999915e+01 -4.383460000000000134e-01 7.009289999999999965e-02 14 | 2.362000000000000099e+01 -4.161050000000000026e-01 6.607899999999999885e-02 15 | 2.369999999999999929e+01 -3.969779999999999975e-01 5.806010000000000337e-02 16 | 2.378000000000000114e+01 -3.786619999999999986e-01 5.518760000000000332e-02 17 | 2.385999999999999943e+01 -3.590329999999999910e-01 4.998289999999999678e-02 18 | 2.389999999999999858e+01 -3.514660000000000006e-01 5.019359999999999794e-02 19 | 2.394000000000000128e+01 -3.367240000000000233e-01 4.849749999999999894e-02 20 | 2.410000000000000142e+01 -3.053620000000000223e-01 4.577590000000000131e-02 21 | 2.430000000000000071e+01 -2.674739999999999895e-01 3.956300000000000094e-02 22 | 2.450000000000000000e+01 -2.328310000000000102e-01 3.349710000000000187e-02 23 | 2.469999999999999929e+01 -2.040309999999999901e-01 2.936199999999999921e-02 24 | 2.489999999999999858e+01 -1.788639999999999952e-01 2.401769999999999947e-02 25 | 2.510000000000000142e+01 -1.560320000000000040e-01 1.853130000000000055e-02 26 | 2.530000000000000071e+01 -1.386129999999999862e-01 1.625760000000000052e-02 27 | 2.550000000000000000e+01 -1.225090000000000068e-01 1.387999999999999998e-02 28 | 2.569999999999999929e+01 -1.090170000000000028e-01 1.189660000000000023e-02 29 | 2.589999999999999858e+01 -9.694460000000000577e-02 9.771790000000000684e-03 30 | 2.610000000000000142e+01 -8.761990000000000056e-02 8.694149999999999448e-03 31 | 2.630000000000000071e+01 -7.744149999999999645e-02 7.348529999999999819e-03 32 | 2.650000000000000000e+01 -6.983730000000000493e-02 5.879770000000000309e-03 33 | 2.669999999999999929e+01 -6.311500000000000443e-02 5.250310000000000220e-03 34 | 2.689999999999999858e+01 -5.722619999999999790e-02 4.533490000000000263e-03 35 | 2.710000000000000142e+01 -5.189830000000000138e-02 3.744400000000000159e-03 36 | 2.730000000000000071e+01 -4.707879999999999704e-02 3.514179999999999995e-03 37 | 2.750000000000000000e+01 -4.278330000000000327e-02 3.071169999999999803e-03 38 | 2.769999999999999929e+01 -3.883459999999999690e-02 2.746170000000000035e-03 39 | 2.789999999999999858e+01 -3.569130000000000219e-02 2.316809999999999876e-03 40 | 2.810000000000000142e+01 -3.275490000000000346e-02 2.096890000000000125e-03 41 | 2.830000000000000071e+01 -2.979769999999999988e-02 1.837810000000000051e-03 42 | 2.850000000000000000e+01 -2.754590000000000163e-02 1.605840000000000089e-03 43 | 2.869999999999999929e+01 -2.547200000000000158e-02 1.474749999999999932e-03 44 | 2.889999999999999858e+01 -2.341319999999999860e-02 1.313069999999999949e-03 45 | 2.910000000000000142e+01 -2.164519999999999986e-02 1.173540000000000043e-03 46 | 2.930000000000000071e+01 -2.001800000000000107e-02 1.090379999999999952e-03 47 | 2.950000000000000000e+01 -1.855350000000000055e-02 9.503439999999999934e-04 48 | 2.969999999999999929e+01 -1.724919999999999926e-02 8.379200000000000276e-04 49 | 2.989999999999999858e+01 -1.592810000000000059e-02 8.345680000000000502e-04 50 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch2/U_3nm_CH2-lr.txt: -------------------------------------------------------------------------------- 1 | 40.5 -0.0160926 0.00185858 2 | 41.5 -0.0117592 0.00133336 3 | 42.5 -0.00848715 0.000822329 4 | 43.5 -0.00681402 0.000594073 5 | 44.5 -0.00528035 0.000401174 6 | 45.5 -0.00416769 0.000329783 7 | 46.5 -0.0032291 0.000168181 8 | 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2.298180000000000014e-02 29 | 8.570000000000000284e+01 -1.515630000000000033e-01 1.895660000000000053e-02 30 | 8.590000000000000568e+01 -1.363620000000000110e-01 1.587500000000000022e-02 31 | 8.609999999999999432e+01 -1.226909999999999945e-01 1.315880000000000001e-02 32 | 8.629999999999999716e+01 -1.100180000000000047e-01 1.193280000000000035e-02 33 | 8.650000000000000000e+01 -1.023700000000000027e-01 1.040680000000000077e-02 34 | 8.670000000000000284e+01 -9.128039999999999765e-02 8.983019999999999547e-03 35 | 8.690000000000000568e+01 -8.349629999999999552e-02 8.016000000000000555e-03 36 | 8.709999999999999432e+01 -7.696010000000000351e-02 6.965029999999999659e-03 37 | 8.729999999999999716e+01 -7.027579999999999938e-02 5.867950000000000249e-03 38 | 8.750000000000000000e+01 -6.434940000000000104e-02 5.200240000000000071e-03 39 | 8.770000000000000284e+01 -5.921110000000000262e-02 4.747569999999999568e-03 40 | 8.790000000000000568e+01 -5.447520000000000140e-02 4.207680000000000101e-03 41 | 8.809999999999999432e+01 -5.056080000000000296e-02 3.615029999999999979e-03 42 | 8.829999999999999716e+01 -4.686309999999999781e-02 3.184139999999999800e-03 43 | 8.850000000000000000e+01 -4.315200000000000286e-02 2.939000000000000206e-03 44 | 8.870000000000000284e+01 -4.045460000000000028e-02 2.611979999999999857e-03 45 | 8.890000000000000568e+01 -3.737519999999999731e-02 2.379669999999999962e-03 46 | 8.909999999999999432e+01 -3.480119999999999741e-02 2.118749999999999974e-03 47 | 8.929999999999999716e+01 -3.267400000000000165e-02 1.983980000000000205e-03 48 | 8.950000000000000000e+01 -3.046659999999999993e-02 1.721290000000000103e-03 49 | 8.970000000000000284e+01 -2.842959999999999932e-02 1.439699999999999921e-03 50 | 8.990000000000000568e+01 -2.677500000000000019e-02 1.500990000000000006e-03 51 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch2/U_9nm_CH2-lr.txt: -------------------------------------------------------------------------------- 1 | 100.5 -0.0219962 0.0019257 2 | 101.5 -0.0158132 0.00165261 3 | 102.5 -0.0124328 0.000957113 4 | 103.5 -0.010199 0.000684234 5 | 104.5 -0.0080222 0.000518429 6 | 105.5 -0.0065713 0.000379002 7 | 106.5 -0.00517017 0.000235072 8 | 107.5 -0.00431005 0.000300341 9 | 108.5 -0.00362712 0.000202275 10 | 109.5 -0.0030292 0.000143836 11 | 110.5 -0.00251699 0.000138735 12 | 111.5 -0.00218721 0.000115454 13 | 112.5 -0.00187661 7.78745e-05 14 | 113.5 -0.00163151 7.39474e-05 15 | 114.5 -0.00143111 4.95769e-05 16 | 115.5 -0.00123636 4.53503e-05 17 | 116.5 -0.00106657 1.97308e-05 18 | 117.5 -0.000957791 3.24594e-05 19 | 118.5 -0.000855332 2.99513e-05 20 | 119.5 -0.000748897 2.5363e-05 21 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch2/U_9nm_CH2_init.txt: -------------------------------------------------------------------------------- 1 | 91.7 0.0106411 1.51054 2 | 91.9 -0.176041 1.34284 3 | 92.1 -0.317577 1.0522 4 | 92.3 -0.394662 0.98741 5 | 92.5 -0.414171 0.974004 6 | 92.7 -0.499227 0.706103 7 | 92.9 -0.598544 0.492234 8 | 93.1 -0.595095 0.280507 9 | 93.3 -0.567719 0.133101 10 | 93.5 -0.518704 0.0996855 11 | 93.7 -0.471183 0.0890639 12 | 93.9 -0.420687 0.0793465 13 | 94.1 -0.365839 0.0649407 14 | 94.3 -0.323564 0.0560801 15 | 94.5 -0.28581 0.0480356 16 | 94.7 -0.253571 0.0406592 17 | 94.9 -0.22566 0.0332669 18 | 95.1 -0.199817 0.0310762 19 | 95.3 -0.180263 0.0260676 20 | 95.5 -0.160733 0.0209615 21 | 95.7 -0.145254 0.0188668 22 | 95.9 -0.131023 0.0154355 23 | 96.1 -0.117474 0.0122593 24 | 96.3 -0.106972 0.0110766 25 | 96.5 -0.0975528 0.009598 26 | 96.7 -0.089164 0.00841176 27 | 96.9 -0.0812056 0.00706368 28 | 97.1 -0.0742285 0.0060161 29 | 97.3 -0.0686409 0.00565132 30 | 97.5 -0.0631633 0.00502392 31 | 97.7 -0.0582075 0.00433361 32 | 97.9 -0.0537201 0.00391711 33 | 98.1 -0.0497701 0.00345359 34 | 98.3 -0.046324 0.00317585 35 | 98.5 -0.0427117 0.00272613 36 | 98.7 -0.0397827 0.00240307 37 | 98.9 -0.0371687 0.00206991 38 | 99.1 -0.0348255 0.00206801 39 | 99.3 -0.0323579 0.00185423 40 | 99.5 -0.0303402 0.00165972 41 | 99.7 -0.0283219 0.00141532 42 | 99.9 -0.0266989 0.00129847 43 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch2/gen-lr-data.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | radii = np.arange(2, 11) 4 | 5 | for radius in radii: 6 | # Load the initial target data obtained 7 | initial_data = np.loadtxt('U_{:.0f}nm_CH2_init.txt'.format(radius)) 8 | 9 | # Load the additional data obtained around the well region 10 | all_data = np.loadtxt('U_{:.0f}nm_CH2_well.txt'.format(radius)) 11 | well_data = [] 12 | for point in all_data: 13 | if(point[1] not in initial_data[:,1] and \ 14 | point[2] not in initial_data[:,2]): 15 | well_data.append(point) 16 | well_data = np.array(well_data) 17 | well_data = well_data[::2] 18 | 19 | # Load the long-range target data obtained 20 | lr_data = np.loadtxt('U_{:.0f}nm_CH2-lr.txt'.format(radius)) 21 | 22 | revised_initial_data = [] 23 | for point in initial_data: 24 | if point not in well_data: 25 | revised_initial_data.append(point) 26 | revised_initial_data = np.array(revised_initial_data) 27 | 28 | total = np.vstack((lr_data, revised_initial_data, well_data)) 29 | total = total[np.argsort(total[:, 0])] 30 | 31 | # Include only monotonically decreasing points up to the bottom 32 | # of the well, and only monotonically increasing points after 33 | # the well 34 | argmin_U = np.argmin(total[:, 1]) 35 | after_well = total[:argmin_U] 36 | before_well = total[argmin_U:] 37 | before_well_monotonic = [before_well[0]] 38 | after_well_monotonic = [after_well[-1]] 39 | for i, point in enumerate(before_well[1:]): 40 | if point[1] < before_well_monotonic[-1][1]: 41 | continue 42 | before_well_monotonic.append(point) 43 | 44 | for i, point in enumerate(after_well[-2::-1]): 45 | if point[1] < after_well_monotonic[-1][1]: 46 | continue 47 | after_well_monotonic.append(point) 48 | after_well_monotonic.reverse() 49 | 50 | threshold = -0.2 51 | after_well_monotonic = np.array([val for val in after_well_monotonic 52 | if val[1] <= threshold]) 53 | before_well_monotonic = np.array(before_well_monotonic) 54 | 55 | total = np.vstack((after_well_monotonic, before_well_monotonic)) 56 | 57 | np.savetxt('U_{:.0f}nm_CH2-complete.txt'.format(radius), 58 | total[np.argsort(total[:,0])]) 59 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch2/gen-revised-data.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | #radii = np.arange(2, 11) 4 | radii = [9] 5 | 6 | for radius in radii: 7 | # Load the initial target data obtained 8 | initial_data = np.loadtxt('U_{:.0f}nm_CH2_init.txt'.format(radius)) 9 | 10 | # Load the additional data obtained around the well region 11 | all_data = np.loadtxt('U_{:.0f}nm_CH2_well.txt'.format(radius)) 12 | well_data = [] 13 | for point in all_data: 14 | if(point[1] not in initial_data[:,1] and \ 15 | point[2] not in initial_data[:,2]): 16 | well_data.append(point) 17 | well_data = np.array(well_data) 18 | well_data = well_data[::2] 19 | 20 | revised_initial_data = [] 21 | for point in initial_data: 22 | if point not in well_data: 23 | revised_initial_data.append(point) 24 | revised_initial_data = np.array(revised_initial_data) 25 | 26 | total = np.vstack((revised_initial_data, well_data)) 27 | total = total[np.argsort(total[:, 0])] 28 | 29 | # Include only monotonically decreasing points up to the bottom 30 | # of the well, and only monotonically increasing points after 31 | # the well 32 | argmin_U = np.argmin(total[:, 1]) 33 | after_well = total[:argmin_U] 34 | before_well = total[argmin_U:] 35 | before_well_monotonic = [before_well[0]] 36 | after_well_monotonic = [after_well[-1]] 37 | for i, point in enumerate(before_well[1:]): 38 | if point[1] < before_well_monotonic[-1][1]: 39 | continue 40 | before_well_monotonic.append(point) 41 | 42 | for i, point in enumerate(after_well[-2::-1]): 43 | if point[1] < after_well_monotonic[-1][1]: 44 | continue 45 | after_well_monotonic.append(point) 46 | after_well_monotonic.reverse() 47 | 48 | threshold = -0.2 49 | after_well_monotonic = np.array([val for val in after_well_monotonic 50 | if val[1] <= threshold]) 51 | before_well_monotonic = np.array(before_well_monotonic) 52 | 53 | total = np.vstack((after_well_monotonic, before_well_monotonic)) 54 | 55 | np.savetxt('U_{:.0f}nm_CH2_revised.txt'.format(radius), 56 | total[np.argsort(total[:,0])]) 57 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/README.md: -------------------------------------------------------------------------------- 1 | Target data for NP-alkane interactions was a bit tricky to collect as following the initial data collection it was found that additional data was needed in the region of the potential well and in the long-range region. Furthermore, the high error in the short range region did not result in a potential that monotonically decreased to the bottom of the well and monotonically increased afterward, due to slight fluctuations in the data. As a result, a function was applied to the data to ensure it satisfied that criteria. 2 | 3 | This led to the collection of several different sets of target data that were eventually combined into the final set (the files appended with "-complete"). Rather than removing these older files, everything is included in this directory. The following provides a brief description of the five files present for each radius: 4 | 5 | - U_Xnm_CH3_init.txt 6 | The initial target data collected (corresponding C++ file is pe_np_ch2_mpi-init.cpp) 7 | Pruned to remove the first 10 bins 8 | - U_?nm_CH3_well.txt 9 | U_?nm_CH3_init.txt + additional data collected in the 10 | short-range region (corresponding C++ file is pe_np_ch2_mpi-well.cpp) 11 | - U_?nm_CH3-lr.txt 12 | Data collected in the region of long range (corresponding C++ file is pe_np_ch2_mpi-lr.cpp) 13 | - U_?nm_CH3-revised.txt 14 | Combination of "-init" and "-well" data ensuring that points monotonically decrease to the bottom of the potential well and monotonically increase after. 15 | - U_?nm_CH3-complete.txt 16 | Combination of "-init", "-well", and "-lr" data ensuring that points monotonically decrease to the bottom of the potential well and monotonically increase after. 17 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_10nm_CH3-lr.txt: -------------------------------------------------------------------------------- 1 | 110.5 -0.0308439 0.00238437 2 | 111.5 -0.0220867 0.00216268 3 | 112.5 -0.016722 0.00119644 4 | 113.5 -0.0137156 0.000860749 5 | 114.5 -0.0109367 0.000678572 6 | 115.5 -0.00873802 0.000523205 7 | 116.5 -0.00706081 0.000259814 8 | 117.5 -0.00582026 0.000357516 9 | 118.5 -0.0049799 0.000293471 10 | 119.5 -0.0041057 0.000177939 11 | 120.5 -0.00342496 0.000209669 12 | 121.5 -0.00297094 0.00015571 13 | 122.5 -0.00257793 0.000109282 14 | 123.5 -0.00221831 0.000102904 15 | 124.5 -0.00195096 6.56841e-05 16 | 125.5 -0.00168712 6.60431e-05 17 | 126.5 -0.00146265 3.16918e-05 18 | 127.5 -0.00132363 4.89859e-05 19 | 128.5 -0.001184 4.10451e-05 20 | 129.5 -0.00103178 3.63883e-05 21 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_10nm_CH3_init.txt: -------------------------------------------------------------------------------- 1 | 102.1 0.189726 2.00162 2 | 102.3 -0.168258 1.74559 3 | 102.5 -0.403592 1.43845 4 | 102.7 -0.573993 1.18898 5 | 102.9 -0.74875 0.746874 6 | 103.1 -0.829943 0.369187 7 | 103.3 -0.842295 0.182886 8 | 103.5 -0.768878 0.141672 9 | 103.7 -0.684669 0.121576 10 | 103.9 -0.613469 0.109103 11 | 104.1 -0.538117 0.0963123 12 | 104.3 -0.472044 0.0779308 13 | 104.5 -0.416648 0.069886 14 | 104.7 -0.36456 0.0561266 15 | 104.9 -0.322744 0.0478308 16 | 105.1 -0.287869 0.0415115 17 | 105.3 -0.255893 0.0349124 18 | 105.5 -0.22853 0.0299523 19 | 105.7 -0.205093 0.0252423 20 | 105.9 -0.185976 0.0212629 21 | 106.1 -0.166729 0.0181029 22 | 106.3 -0.150804 0.0167162 23 | 106.5 -0.135798 0.0144621 24 | 106.7 -0.1245 0.0116757 25 | 106.9 -0.11351 0.0108601 26 | 107.1 -0.103207 0.00929439 27 | 107.3 -0.0956553 0.00747545 28 | 107.5 -0.087406 0.00659756 29 | 107.7 -0.0801918 0.00648939 30 | 107.9 -0.0739777 0.00553317 31 | 108.1 -0.0685481 0.0044534 32 | 108.3 -0.0635475 0.00419585 33 | 108.5 -0.0592647 0.0038984 34 | 108.7 -0.0548169 0.00355092 35 | 108.9 -0.0511027 0.00317397 36 | 109.1 -0.0476722 0.00275775 37 | 109.3 -0.0444219 0.00256337 38 | 109.5 -0.0414065 0.00241063 39 | 109.7 -0.0387999 0.00203207 40 | 109.9 -0.0365882 0.00180732 41 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_10nm_CH3_revised.txt: -------------------------------------------------------------------------------- 1 | 1.022600000000000051e+02 -2.068230000000000068e-01 1.618530000000000024e+00 2 | 1.023400000000000034e+02 -3.172519999999999785e-01 1.543500000000000094e+00 3 | 1.025000000000000000e+02 -4.087569999999999815e-01 1.495009999999999950e+00 4 | 1.026599999999999966e+02 -4.908770000000000078e-01 1.379459999999999908e+00 5 | 1.027000000000000028e+02 -5.739929999999999755e-01 1.188979999999999926e+00 6 | 1.027399999999999949e+02 -5.854080000000000394e-01 1.148740000000000094e+00 7 | 1.028199999999999932e+02 -6.784259999999999735e-01 9.905030000000000223e-01 8 | 1.029000000000000057e+02 -7.740259999999999918e-01 6.557190000000000518e-01 9 | 1.029800000000000040e+02 -8.165459999999999940e-01 5.715970000000000217e-01 10 | 1.030600000000000023e+02 -8.687310000000000310e-01 3.643589999999999884e-01 11 | 1.030999999999999943e+02 -8.299429999999999863e-01 3.691869999999999874e-01 12 | 1.032999999999999972e+02 -8.341060000000000141e-01 1.714610000000000023e-01 13 | 1.033799999999999955e+02 -8.193610000000000060e-01 1.521399999999999975e-01 14 | 1.034599999999999937e+02 -7.804410000000000514e-01 1.414279999999999982e-01 15 | 1.035000000000000000e+02 -7.688779999999999504e-01 1.416719999999999924e-01 16 | 1.035400000000000063e+02 -7.544140000000000290e-01 1.313449999999999895e-01 17 | 1.036200000000000045e+02 -7.164679999999999938e-01 1.243979999999999947e-01 18 | 1.037000000000000028e+02 -7.001169999999999893e-01 1.205429999999999974e-01 19 | 1.037800000000000011e+02 -6.562470000000000248e-01 1.177850000000000008e-01 20 | 1.038599999999999994e+02 -6.156880000000000130e-01 1.060180000000000011e-01 21 | 1.039000000000000057e+02 -6.134690000000000420e-01 1.091030000000000055e-01 22 | 1.039399999999999977e+02 -5.940809999999999702e-01 1.051939999999999958e-01 23 | 1.040999999999999943e+02 -5.381169999999999565e-01 9.631230000000000346e-02 24 | 1.042999999999999972e+02 -4.720440000000000191e-01 7.793079999999999452e-02 25 | 1.045000000000000000e+02 -4.166480000000000183e-01 6.988600000000000367e-02 26 | 1.047000000000000028e+02 -3.645599999999999952e-01 5.612659999999999871e-02 27 | 1.049000000000000057e+02 -3.227439999999999753e-01 4.783079999999999971e-02 28 | 1.050999999999999943e+02 -2.878689999999999860e-01 4.151149999999999979e-02 29 | 1.052999999999999972e+02 -2.558929999999999816e-01 3.491240000000000315e-02 30 | 1.055000000000000000e+02 -2.285300000000000109e-01 2.995230000000000115e-02 31 | 1.057000000000000028e+02 -2.050929999999999975e-01 2.524229999999999877e-02 32 | 1.059000000000000057e+02 -1.859760000000000024e-01 2.126290000000000124e-02 33 | 1.060999999999999943e+02 -1.667289999999999883e-01 1.810290000000000163e-02 34 | 1.062999999999999972e+02 -1.508039999999999936e-01 1.671620000000000050e-02 35 | 1.065000000000000000e+02 -1.357980000000000020e-01 1.446210000000000030e-02 36 | 1.067000000000000028e+02 -1.244999999999999996e-01 1.167570000000000066e-02 37 | 1.069000000000000057e+02 -1.135099999999999998e-01 1.086009999999999927e-02 38 | 1.070999999999999943e+02 -1.032069999999999932e-01 9.294389999999999596e-03 39 | 1.072999999999999972e+02 -9.565529999999999866e-02 7.475449999999999803e-03 40 | 1.075000000000000000e+02 -8.740599999999999759e-02 6.597559999999999709e-03 41 | 1.077000000000000028e+02 -8.019179999999999364e-02 6.489390000000000262e-03 42 | 1.079000000000000057e+02 -7.397769999999999346e-02 5.533169999999999582e-03 43 | 1.080999999999999943e+02 -6.854810000000000070e-02 4.453399999999999720e-03 44 | 1.082999999999999972e+02 -6.354750000000000676e-02 4.195850000000000100e-03 45 | 1.085000000000000000e+02 -5.926469999999999655e-02 3.898400000000000216e-03 46 | 1.087000000000000028e+02 -5.481690000000000174e-02 3.550919999999999944e-03 47 | 1.089000000000000057e+02 -5.110270000000000090e-02 3.173969999999999916e-03 48 | 1.090999999999999943e+02 -4.767219999999999791e-02 2.757749999999999785e-03 49 | 1.092999999999999972e+02 -4.442190000000000027e-02 2.563370000000000145e-03 50 | 1.095000000000000000e+02 -4.140649999999999886e-02 2.410629999999999978e-03 51 | 1.097000000000000028e+02 -3.879989999999999828e-02 2.032069999999999970e-03 52 | 1.099000000000000057e+02 -3.658820000000000128e-02 1.807320000000000064e-03 53 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_2nm_CH3-lr.txt: -------------------------------------------------------------------------------- 1 | 30.5 -0.0174853 0.0015586 2 | 31.5 -0.0120459 0.00143393 3 | 32.5 -0.00885828 0.000686723 4 | 33.5 -0.00694378 0.000696587 5 | 34.5 -0.00528317 0.000375468 6 | 35.5 -0.00405865 0.000250225 7 | 36.5 -0.00313656 0.000149021 8 | 37.5 -0.00248383 0.000201822 9 | 38.5 -0.00205839 0.0001497 10 | 39.5 -0.00164524 9.901e-05 11 | 40.5 -0.00131198 8.83692e-05 12 | 41.5 -0.00110581 7.49012e-05 13 | 42.5 -0.00092135 5.80391e-05 14 | 43.5 -0.000771627 4.67487e-05 15 | 44.5 -0.000654289 3.04513e-05 16 | 45.5 -0.000544756 2.87428e-05 17 | 46.5 -0.00045783 9.81718e-06 18 | 47.5 -0.000400995 1.65406e-05 19 | 48.5 -0.000350778 1.36019e-05 20 | 49.5 -0.000294658 1.49625e-05 21 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_2nm_CH3_init.txt: -------------------------------------------------------------------------------- 1 | 22.3 0.386321 1.74392 2 | 22.5 -0.210965 1.13335 3 | 22.7 -0.486177 0.973678 4 | 22.9 -0.668467 0.564432 5 | 23.1 -0.648944 0.547704 6 | 23.3 -0.659253 0.209973 7 | 23.5 -0.598572 0.107516 8 | 23.7 -0.531125 0.0823925 9 | 23.9 -0.46944 0.0717068 10 | 24.1 -0.403261 0.0620572 11 | 24.3 -0.354404 0.0535948 12 | 24.5 -0.311585 0.0420494 13 | 24.7 -0.270173 0.0378422 14 | 24.9 -0.236893 0.0320829 15 | 25.1 -0.209324 0.025397 16 | 25.3 -0.182981 0.0232259 17 | 25.5 -0.162392 0.0186702 18 | 25.7 -0.1435 0.0154928 19 | 25.9 -0.128518 0.0125717 20 | 26.1 -0.115148 0.0108688 21 | 26.3 -0.102806 0.00919086 22 | 26.5 -0.0919604 0.00797293 23 | 26.7 -0.0834827 0.00736137 24 | 26.9 -0.0754897 0.00594849 25 | 27.1 -0.0681122 0.00533539 26 | 27.3 -0.0621706 0.00440969 27 | 27.5 -0.0563574 0.00385151 28 | 27.7 -0.0513514 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39 | 39.9 -0.0260738 0.00175797 40 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_3nm_CH3_revised.txt: -------------------------------------------------------------------------------- 1 | 3.250000000000000000e+01 -3.090649999999999786e-01 1.346419999999999950e+00 2 | 3.257999999999999829e+01 -3.748460000000000125e-01 1.201140000000000096e+00 3 | 3.265999999999999659e+01 -6.128069999999999906e-01 7.331370000000000386e-01 4 | 3.274000000000000199e+01 -6.564410000000000522e-01 7.116510000000000336e-01 5 | 3.282000000000000028e+01 -7.260520000000000307e-01 5.837280000000000246e-01 6 | 3.297999999999999687e+01 -7.128060000000000507e-01 5.883500000000000396e-01 7 | 3.306000000000000227e+01 -7.692729999999999846e-01 3.027190000000000158e-01 8 | 3.310000000000000142e+01 -7.396740000000000537e-01 2.940519999999999801e-01 9 | 3.321999999999999886e+01 -7.108079999999999954e-01 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2.480399999999999792e-03 47 | 3.950000000000000000e+01 -3.016749999999999987e-02 2.168289999999999801e-03 48 | 3.970000000000000284e+01 -2.790629999999999847e-02 1.986939999999999974e-03 49 | 3.989999999999999858e+01 -2.607380000000000114e-02 1.757969999999999975e-03 50 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_4nm_CH3-lr.txt: -------------------------------------------------------------------------------- 1 | 50.5 -0.0245893 0.00283094 2 | 51.5 -0.017522 0.0017401 3 | 52.5 -0.0131999 0.00113896 4 | 53.5 -0.0103482 0.000797883 5 | 54.5 -0.00808138 0.000579861 6 | 55.5 -0.00648459 0.000375089 7 | 56.5 -0.00510131 0.000305086 8 | 57.5 -0.00421833 0.000265072 9 | 58.5 -0.00348843 0.000192429 10 | 59.5 -0.00286569 0.000146488 11 | 60.5 -0.00231984 0.000124575 12 | 61.5 -0.00199538 8.92219e-05 13 | 62.5 -0.00167996 7.61067e-05 14 | 63.5 -0.00143108 7.12942e-05 15 | 64.5 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0.0191839 20 | 46.1 -0.141638 0.0167523 21 | 46.3 -0.127097 0.0135715 22 | 46.5 -0.115524 0.0120156 23 | 46.7 -0.105726 0.0109256 24 | 46.9 -0.0949221 0.00906203 25 | 47.1 -0.087448 0.00826301 26 | 47.3 -0.0795983 0.00722342 27 | 47.5 -0.0726187 0.00605736 28 | 47.7 -0.067251 0.00532501 29 | 47.9 -0.0620231 0.00463786 30 | 48.1 -0.056769 0.00398392 31 | 48.3 -0.0526317 0.00364381 32 | 48.5 -0.0487122 0.00317321 33 | 48.7 -0.0450043 0.00284125 34 | 48.9 -0.0418234 0.00255939 35 | 49.1 -0.0387949 0.00221951 36 | 49.3 -0.0362307 0.00213883 37 | 49.5 -0.0337841 0.00180461 38 | 49.7 -0.0316926 0.00169129 39 | 49.9 -0.0294307 0.00146527 40 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_5nm_CH3-lr.txt: -------------------------------------------------------------------------------- 1 | 60.5 -0.0262498 0.00275623 2 | 61.5 -0.0189273 0.00177851 3 | 62.5 -0.0144033 0.00115384 4 | 63.5 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-0.783775 0.205876 8 | 53.5 -0.727486 0.138702 9 | 53.7 -0.650328 0.118774 10 | 53.9 -0.570947 0.102912 11 | 54.1 -0.507609 0.0935416 12 | 54.3 -0.447743 0.0803137 13 | 54.5 -0.387524 0.0690763 14 | 54.7 -0.339907 0.0574624 15 | 54.9 -0.303776 0.0461838 16 | 55.1 -0.264968 0.0378058 17 | 55.3 -0.237639 0.0323152 18 | 55.5 -0.212534 0.0265456 19 | 55.7 -0.190682 0.023075 20 | 55.9 -0.170251 0.0209889 21 | 56.1 -0.152833 0.0171141 22 | 56.3 -0.138234 0.0145262 23 | 56.5 -0.125868 0.0131952 24 | 56.7 -0.113826 0.0108898 25 | 56.9 -0.103631 0.00919312 26 | 57.1 -0.0944822 0.00841689 27 | 57.3 -0.0861784 0.00739881 28 | 57.5 -0.0795479 0.00644084 29 | 57.7 -0.0725485 0.00534939 30 | 57.9 -0.0664492 0.00512125 31 | 58.1 -0.0617067 0.0040985 32 | 58.3 -0.056956 0.00384455 33 | 58.5 -0.0524682 0.00354537 34 | 58.7 -0.0489268 0.00309474 35 | 58.9 -0.0454 0.00271316 36 | 59.1 -0.0422324 0.00237619 37 | 59.3 -0.0393155 0.00204743 38 | 59.5 -0.0366628 0.00206381 39 | 59.7 -0.0342721 0.00171837 40 | 59.9 -0.0318769 0.00153078 41 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_5nm_CH3_revised.txt: -------------------------------------------------------------------------------- 1 | 5.217999999999999972e+01 -2.079090000000000105e-01 1.857080000000000064e+00 2 | 5.242000000000000171e+01 -2.665879999999999916e-01 1.594710000000000072e+00 3 | 5.250000000000000000e+01 -4.110280000000000045e-01 1.481459999999999999e+00 4 | 5.265999999999999659e+01 -5.567419999999999591e-01 1.193729999999999958e+00 5 | 5.274000000000000199e+01 -4.949810000000000043e-01 1.306210000000000093e+00 6 | 5.282000000000000028e+01 -6.484100000000000419e-01 9.204170000000000407e-01 7 | 5.297999999999999687e+01 -7.131199999999999761e-01 7.263070000000000359e-01 8 | 5.306000000000000227e+01 -8.201779999999999626e-01 3.740689999999999849e-01 9 | 5.310000000000000142e+01 -7.944280000000000230e-01 3.949840000000000018e-01 10 | 5.321999999999999886e+01 -7.994050000000000322e-01 2.127890000000000059e-01 11 | 5.329999999999999716e+01 -7.928129999999999900e-01 1.811250000000000082e-01 12 | 5.338000000000000256e+01 -7.792000000000000037e-01 1.502429999999999877e-01 13 | 5.346000000000000085e+01 -7.456409999999999982e-01 1.370319999999999871e-01 14 | 5.350000000000000000e+01 -7.274859999999999660e-01 1.387019999999999920e-01 15 | 5.353999999999999915e+01 -7.063260000000000094e-01 1.245040000000000036e-01 16 | 5.361999999999999744e+01 -6.845240000000000213e-01 1.169349999999999973e-01 17 | 5.370000000000000284e+01 -6.501320000000000432e-01 1.106329999999999952e-01 18 | 5.378000000000000114e+01 -6.243119999999999781e-01 1.111790000000000000e-01 19 | 5.385999999999999943e+01 -5.893300000000000205e-01 1.064579999999999971e-01 20 | 5.389999999999999858e+01 -5.709469999999999823e-01 1.029120000000000035e-01 21 | 5.393999999999999773e+01 -5.546759999999999469e-01 9.366380000000000539e-02 22 | 5.410000000000000142e+01 -5.076089999999999769e-01 9.354160000000000252e-02 23 | 5.429999999999999716e+01 -4.477430000000000021e-01 8.031370000000000176e-02 24 | 5.450000000000000000e+01 -3.875239999999999796e-01 6.907629999999999326e-02 25 | 5.470000000000000284e+01 -3.399070000000000147e-01 5.746239999999999681e-02 26 | 5.489999999999999858e+01 -3.037759999999999905e-01 4.618379999999999708e-02 27 | 5.510000000000000142e+01 -2.649679999999999813e-01 3.780580000000000052e-02 28 | 5.529999999999999716e+01 -2.376389999999999891e-01 3.231520000000000226e-02 29 | 5.550000000000000000e+01 -2.125340000000000007e-01 2.654559999999999906e-02 30 | 5.570000000000000284e+01 -1.906819999999999904e-01 2.307499999999999829e-02 31 | 5.589999999999999858e+01 -1.702510000000000134e-01 2.098890000000000131e-02 32 | 5.610000000000000142e+01 -1.528329999999999966e-01 1.711410000000000015e-02 33 | 5.629999999999999716e+01 -1.382339999999999958e-01 1.452619999999999953e-02 34 | 5.650000000000000000e+01 -1.258680000000000077e-01 1.319520000000000068e-02 35 | 5.670000000000000284e+01 -1.138259999999999966e-01 1.088979999999999983e-02 36 | 5.689999999999999858e+01 -1.036310000000000009e-01 9.193120000000000805e-03 37 | 5.710000000000000142e+01 -9.448220000000000229e-02 8.416889999999999789e-03 38 | 5.729999999999999716e+01 -8.617840000000000222e-02 7.398809999999999588e-03 39 | 5.750000000000000000e+01 -7.954790000000000472e-02 6.440839999999999760e-03 40 | 5.770000000000000284e+01 -7.254850000000000187e-02 5.349389999999999874e-03 41 | 5.789999999999999858e+01 -6.644919999999999993e-02 5.121249999999999934e-03 42 | 5.810000000000000142e+01 -6.170670000000000321e-02 4.098499999999999713e-03 43 | 5.829999999999999716e+01 -5.695599999999999968e-02 3.844549999999999964e-03 44 | 5.850000000000000000e+01 -5.246819999999999956e-02 3.545369999999999945e-03 45 | 5.870000000000000284e+01 -4.892679999999999946e-02 3.094739999999999904e-03 46 | 5.889999999999999858e+01 -4.540000000000000285e-02 2.713160000000000051e-03 47 | 5.910000000000000142e+01 -4.223240000000000327e-02 2.376189999999999813e-03 48 | 5.929999999999999716e+01 -3.931550000000000322e-02 2.047429999999999823e-03 49 | 5.950000000000000000e+01 -3.666280000000000233e-02 2.063810000000000124e-03 50 | 5.970000000000000284e+01 -3.427209999999999979e-02 1.718370000000000097e-03 51 | 5.989999999999999858e+01 -3.187689999999999968e-02 1.530780000000000031e-03 52 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_6nm_CH3-lr.txt: -------------------------------------------------------------------------------- 1 | 70.5 -0.0271217 0.00245692 2 | 71.5 -0.0201819 0.00192259 3 | 72.5 -0.0150734 0.00119765 4 | 73.5 -0.0121712 0.000880468 5 | 74.5 -0.00953622 0.000580102 6 | 75.5 -0.00752477 0.000448035 7 | 76.5 -0.00602422 0.000201802 8 | 77.5 -0.00500055 0.000294411 9 | 78.5 -0.00422059 0.00024425 10 | 79.5 -0.00344588 0.000142043 11 | 80.5 -0.00286348 0.000168883 12 | 81.5 -0.00248655 0.00013117 13 | 82.5 -0.00212581 9.48522e-05 14 | 83.5 -0.0018095 9.14938e-05 15 | 84.5 -0.00159063 4.87768e-05 16 | 85.5 -0.00136055 4.80659e-05 17 | 86.5 -0.00115842 2.80508e-05 18 | 87.5 -0.0010506 3.89397e-05 19 | 88.5 -0.000931837 3.35326e-05 20 | 89.5 -0.000808866 2.66881e-05 21 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_6nm_CH3_init.txt: -------------------------------------------------------------------------------- 1 | 62.3 -0.214648 1.62395 2 | 62.5 -0.477937 1.32811 3 | 62.7 -0.558925 1.22215 4 | 62.9 -0.700374 0.837433 5 | 63.1 -0.743073 0.519216 6 | 63.3 -0.757467 0.207085 7 | 63.5 -0.690758 0.127928 8 | 63.7 -0.623449 0.107549 9 | 63.9 -0.544708 0.0893845 10 | 64.1 -0.487871 0.0793611 11 | 64.3 -0.42749 0.0714611 12 | 64.5 -0.367725 0.0603685 13 | 64.7 -0.335843 0.0495377 14 | 64.9 -0.292102 0.0392523 15 | 65.1 -0.259015 0.0351087 16 | 65.3 -0.232245 0.0296593 17 | 65.5 -0.207314 0.0239565 18 | 65.7 -0.184502 0.0204732 19 | 65.9 -0.16698 0.017626 20 | 66.1 -0.149889 0.0153233 21 | 66.3 -0.136185 0.0131883 22 | 66.5 -0.123509 0.012054 23 | 66.7 -0.112692 0.00993336 24 | 66.9 -0.102667 0.00868733 25 | 67.1 -0.0942016 0.00759126 26 | 67.3 -0.0861639 0.00641829 27 | 67.5 -0.079269 0.00592121 28 | 67.7 -0.0726079 0.00499194 29 | 67.9 -0.0673836 0.00452655 30 | 68.1 -0.0622284 0.00387595 31 | 68.3 -0.0573454 0.00351674 32 | 68.5 -0.0534597 0.00327949 33 | 68.7 -0.0495675 0.00274552 34 | 68.9 -0.0462241 0.00250004 35 | 69.1 -0.0428556 0.00221782 36 | 69.3 -0.0398631 0.00203971 37 | 69.5 -0.0374817 0.00189737 38 | 69.7 -0.0349699 0.00171158 39 | 69.9 -0.0327823 0.00150022 40 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_7nm_CH3-lr.txt: -------------------------------------------------------------------------------- 1 | 80.5 -0.0290208 0.00347166 2 | 81.5 -0.0204922 0.00182985 3 | 82.5 -0.0156701 0.00146383 4 | 83.5 -0.012507 0.000911495 5 | 84.5 -0.0100312 0.000607781 6 | 85.5 -0.00821637 0.000432255 7 | 86.5 -0.00645552 0.000370987 8 | 87.5 -0.00528004 0.000344884 9 | 88.5 -0.00445987 0.000234382 10 | 89.5 -0.00367232 0.00019998 11 | 90.5 -0.0030416 0.000191226 12 | 91.5 -0.00263451 0.000139339 13 | 92.5 -0.00227543 0.000114091 14 | 93.5 -0.00194136 8.99089e-05 15 | 94.5 -0.00169927 5.98315e-05 16 | 95.5 -0.00147681 6.55641e-05 17 | 96.5 -0.00126189 2.68172e-05 18 | 97.5 -0.00113645 4.40602e-05 19 | 98.5 -0.00101135 4.42475e-05 20 | 99.5 -0.000877261 3.11201e-05 21 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_7nm_CH3_init.txt: -------------------------------------------------------------------------------- 1 | 72.1 0.0478995 1.97673 2 | 72.3 -0.205668 1.77636 3 | 72.5 -0.413992 1.43004 4 | 72.7 -0.607528 1.08919 5 | 72.9 -0.776207 0.701155 6 | 73.1 -0.777911 0.541244 7 | 73.3 -0.782401 0.231662 8 | 73.5 -0.712664 0.143663 9 | 73.7 -0.642613 0.124827 10 | 73.9 -0.565082 0.11354 11 | 74.1 -0.491754 0.0938356 12 | 74.3 -0.435749 0.0836077 13 | 74.5 -0.386301 0.0641432 14 | 74.7 -0.337422 0.0581327 15 | 74.9 -0.299642 0.050445 16 | 75.1 -0.266501 0.0410087 17 | 75.3 -0.237908 0.0344621 18 | 75.5 -0.21343 0.0287071 19 | 75.7 -0.192297 0.0258601 20 | 75.9 -0.172905 0.0227398 21 | 76.1 -0.153795 0.0184342 22 | 76.3 -0.1392 0.0158518 23 | 76.5 -0.128396 0.0142086 24 | 76.7 -0.116301 0.0108947 25 | 76.9 -0.106931 0.0100774 26 | 77.1 -0.0965742 0.00924981 27 | 77.3 -0.0882874 0.00797635 28 | 77.5 -0.0815599 0.00721676 29 | 77.7 -0.0748128 0.00611532 30 | 77.9 -0.0692983 0.00558915 31 | 78.1 -0.0641861 0.00515113 32 | 78.3 -0.05931 0.00445508 33 | 78.5 -0.0549914 0.00403452 34 | 78.7 -0.0513969 0.00360211 35 | 78.9 -0.0478233 0.00315433 36 | 79.1 -0.0444025 0.00285899 37 | 79.3 -0.0414369 0.00263859 38 | 79.5 -0.0384192 0.00235161 39 | 79.7 -0.0360962 0.00211773 40 | 79.9 -0.0340314 0.00192291 41 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_8nm_CH3-lr.txt: -------------------------------------------------------------------------------- 1 | 90.5 -0.029296 0.00315282 2 | 91.5 -0.0213538 0.00195545 3 | 92.5 -0.0163035 0.00130611 4 | 93.5 -0.0131845 0.00122615 5 | 94.5 -0.0103707 0.000699076 6 | 95.5 -0.00832422 0.000432851 7 | 96.5 -0.00667067 0.000343613 8 | 97.5 -0.00554221 0.000384451 9 | 98.5 -0.00466917 0.000268238 10 | 99.5 -0.00384492 0.00018232 11 | 100.5 -0.00321165 0.000146922 12 | 101.5 -0.00278086 0.000154944 13 | 102.5 -0.00240989 0.000103247 14 | 103.5 -0.00206804 9.6112e-05 15 | 104.5 -0.00180959 6.38694e-05 16 | 105.5 -0.00156 6.53208e-05 17 | 106.5 -0.00134743 2.42825e-05 18 | 107.5 -0.00120905 4.83385e-05 19 | 108.5 -0.0010784 3.5711e-05 20 | 109.5 -0.000939851 3.24543e-05 21 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_8nm_CH3_init.txt: -------------------------------------------------------------------------------- 1 | 82.3 0.259792 2.07498 2 | 82.5 -0.116196 1.61184 3 | 82.7 -0.567813 1.0581 4 | 82.9 -0.66379 0.90483 5 | 83.1 -0.811454 0.49652 6 | 83.3 -0.816656 0.221858 7 | 83.5 -0.758673 0.159843 8 | 83.7 -0.687601 0.127019 9 | 83.9 -0.596953 0.112624 10 | 84.1 -0.533586 0.0981797 11 | 84.3 -0.467523 0.0784525 12 | 84.5 -0.410253 0.0671884 13 | 84.7 -0.360816 0.0570914 14 | 84.9 -0.321753 0.0500668 15 | 85.1 -0.279295 0.0387206 16 | 85.3 -0.253891 0.0346144 17 | 85.5 -0.222996 0.0293557 18 | 85.7 -0.201495 0.024809 19 | 85.9 -0.17993 0.0223171 20 | 86.1 -0.162739 0.0189181 21 | 86.3 -0.147079 0.0156656 22 | 86.5 -0.134239 0.0140263 23 | 86.7 -0.121577 0.0124534 24 | 86.9 -0.109232 0.00951196 25 | 87.1 -0.101166 0.00929388 26 | 87.3 -0.0925974 0.0082096 27 | 87.5 -0.0852204 0.00686042 28 | 87.7 -0.0782552 0.00674467 29 | 87.9 -0.0720873 0.00550157 30 | 88.1 -0.0667696 0.00481826 31 | 88.3 -0.0616165 0.00461677 32 | 88.5 -0.057376 0.00418436 33 | 88.7 -0.053021 0.00328364 34 | 88.9 -0.0494639 0.00308795 35 | 89.1 -0.0459619 0.00274957 36 | 89.3 -0.0429218 0.00253726 37 | 89.5 -0.0401299 0.0023493 38 | 89.7 -0.037535 0.00208664 39 | 89.9 -0.0352153 0.00187362 40 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_9nm_CH3-lr.txt: -------------------------------------------------------------------------------- 1 | 100.5 -0.0290556 0.00254237 2 | 101.5 -0.0208871 0.00218356 3 | 102.5 -0.0164241 0.00126514 4 | 103.5 -0.0134746 0.000905221 5 | 104.5 -0.0105978 0.000685085 6 | 105.5 -0.008681 0.00050105 7 | 106.5 -0.00683014 0.000310483 8 | 107.5 -0.00569379 0.000396859 9 | 108.5 -0.00479152 0.000267259 10 | 109.5 -0.00400176 0.000189896 11 | 110.5 -0.00332501 0.000183404 12 | 111.5 -0.00288954 0.000152586 13 | 112.5 -0.00247905 0.000102944 14 | 113.5 -0.00215531 9.76726e-05 15 | 114.5 -0.00189065 6.55633e-05 16 | 115.5 -0.0016333 5.98877e-05 17 | 116.5 -0.00140901 2.6073e-05 18 | 117.5 -0.00126529 4.29271e-05 19 | 118.5 -0.00112996 3.95676e-05 20 | 119.5 -0.000989343 3.3508e-05 21 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/U_9nm_CH3_init.txt: -------------------------------------------------------------------------------- 1 | 91.7 0.104065 2.19391 2 | 91.9 -0.204615 1.80904 3 | 92.1 -0.318266 1.6605 4 | 92.3 -0.556058 1.36653 5 | 92.5 -0.496938 1.50458 6 | 92.7 -0.695883 0.890048 7 | 92.9 -0.804464 0.626706 8 | 93.1 -0.838536 0.245248 9 | 93.3 -0.787449 0.162108 10 | 93.5 -0.70906 0.133275 11 | 93.7 -0.621692 0.125851 12 | 93.9 -0.553548 0.10682 13 | 94.1 -0.486241 0.0897901 14 | 94.3 -0.433214 0.0768835 15 | 94.5 -0.3834 0.0696766 16 | 94.7 -0.33374 0.0551029 17 | 94.9 -0.302466 0.0482485 18 | 95.1 -0.265467 0.0383536 19 | 95.3 -0.237261 0.0326497 20 | 95.5 -0.211196 0.0279549 21 | 95.7 -0.192791 0.0241108 22 | 95.9 -0.174603 0.0214977 23 | 96.1 -0.156057 0.017031 24 | 96.3 -0.141511 0.0154555 25 | 96.5 -0.127523 0.0128923 26 | 96.7 -0.11742 0.0111744 27 | 96.9 -0.10785 0.00992077 28 | 97.1 -0.0988899 0.00861216 29 | 97.3 -0.091049 0.00761915 30 | 97.5 -0.0831823 0.00637311 31 | 97.7 -0.07668 0.00593611 32 | 97.9 -0.0713713 0.00518258 33 | 98.1 -0.0656908 0.0043861 34 | 98.3 -0.0606737 0.00402534 35 | 98.5 -0.0567208 0.00350437 36 | 98.7 -0.0528348 0.00333204 37 | 98.9 -0.048927 0.00296421 38 | 99.1 -0.0457801 0.00259931 39 | 99.3 -0.0426649 0.00232037 40 | 99.5 -0.0400283 0.00221752 41 | 99.7 -0.0373887 0.00191498 42 | 99.9 -0.035147 0.001703 43 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/gen-lr-data.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | radii = np.arange(2, 11) 4 | 5 | for radius in radii: 6 | # Load the initial target data obtained 7 | initial_data = np.loadtxt('U_{:.0f}nm_CH3_init.txt'.format(radius)) 8 | 9 | # Load the additional data obtained around the well region 10 | all_data = np.loadtxt('U_{:.0f}nm_CH3_well.txt'.format(radius)) 11 | well_data = [] 12 | for point in all_data: 13 | if(point[1] not in initial_data[:,1] and \ 14 | point[2] not in initial_data[:,2]): 15 | well_data.append(point) 16 | well_data = np.array(well_data) 17 | well_data = well_data[::2] 18 | 19 | # Load the long-range target data obtained 20 | lr_data = np.loadtxt('U_{:.0f}nm_CH3-lr.txt'.format(radius)) 21 | 22 | revised_initial_data = [] 23 | for point in initial_data: 24 | if point not in well_data: 25 | revised_initial_data.append(point) 26 | revised_initial_data = np.array(revised_initial_data) 27 | 28 | total = np.vstack((lr_data, revised_initial_data, well_data)) 29 | total = total[np.argsort(total[:, 0])] 30 | 31 | # Include only monotonically decreasing points up to the bottom 32 | # of the well, and only monotonically increasing points after 33 | # the well 34 | argmin_U = np.argmin(total[:, 1]) 35 | after_well = total[:argmin_U] 36 | before_well = total[argmin_U:] 37 | before_well_monotonic = [before_well[0]] 38 | after_well_monotonic = [after_well[-1]] 39 | for i, point in enumerate(before_well[1:]): 40 | if point[1] < before_well_monotonic[-1][1]: 41 | continue 42 | before_well_monotonic.append(point) 43 | 44 | for i, point in enumerate(after_well[-2::-1]): 45 | if point[1] < after_well_monotonic[-1][1]: 46 | continue 47 | after_well_monotonic.append(point) 48 | after_well_monotonic.reverse() 49 | 50 | threshold = -0.2 51 | after_well_monotonic = np.array([val for val in after_well_monotonic 52 | if val[1] <= threshold]) 53 | before_well_monotonic = np.array(before_well_monotonic) 54 | 55 | total = np.vstack((after_well_monotonic, before_well_monotonic)) 56 | 57 | np.savetxt('U_{:.0f}nm_CH3-complete.txt'.format(radius), 58 | total[np.argsort(total[:,0])]) 59 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_alkane/united_atom/ch3/gen-revised-data.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | #radii = np.arange(2, 11) 4 | radii = [9] 5 | 6 | for radius in radii: 7 | # Load the initial target data obtained 8 | initial_data = np.loadtxt('U_{:.0f}nm_CH3_init.txt'.format(radius)) 9 | 10 | # Load the additional data obtained around the well region 11 | all_data = np.loadtxt('U_{:.0f}nm_CH3_well.txt'.format(radius)) 12 | well_data = [] 13 | for point in all_data: 14 | if(point[1] not in initial_data[:,1] and \ 15 | point[2] not in initial_data[:,2]): 16 | well_data.append(point) 17 | well_data = np.array(well_data) 18 | well_data = well_data[::2] 19 | 20 | revised_initial_data = [] 21 | for point in initial_data: 22 | if point not in well_data: 23 | revised_initial_data.append(point) 24 | revised_initial_data = np.array(revised_initial_data) 25 | 26 | total = np.vstack((revised_initial_data, well_data)) 27 | total = total[np.argsort(total[:, 0])] 28 | 29 | # Include only monotonically decreasing points up to the bottom 30 | # of the well, and only monotonically increasing points after 31 | # the well 32 | argmin_U = np.argmin(total[:, 1]) 33 | after_well = total[:argmin_U] 34 | before_well = total[argmin_U:] 35 | before_well_monotonic = [before_well[0]] 36 | after_well_monotonic = [after_well[-1]] 37 | for i, point in enumerate(before_well[1:]): 38 | if point[1] < before_well_monotonic[-1][1]: 39 | continue 40 | before_well_monotonic.append(point) 41 | 42 | for i, point in enumerate(after_well[-2::-1]): 43 | if point[1] < after_well_monotonic[-1][1]: 44 | continue 45 | after_well_monotonic.append(point) 46 | after_well_monotonic.reverse() 47 | 48 | threshold = -0.2 49 | after_well_monotonic = np.array([val for val in after_well_monotonic 50 | if val[1] <= threshold]) 51 | before_well_monotonic = np.array(before_well_monotonic) 52 | 53 | total = np.vstack((after_well_monotonic, before_well_monotonic)) 54 | 55 | np.savetxt('U_{:.0f}nm_CH3_revised.txt'.format(radius), 56 | total[np.argsort(total[:,0])]) 57 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/full/README.md: -------------------------------------------------------------------------------- 1 | This target data is the complete (non-zero) nanoparticle-nanoparticle interaction potential target data collected using the included C++ script. 2 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/full/U_10nm.txt: -------------------------------------------------------------------------------- 1 | 202.8 -114.153 9.28533 2 | 203.6 -87.0766 5.94763 3 | 204.4 -66.8988 4.531 4 | 205.2 -55.6483 2.51561 5 | 206 -47.7719 1.84847 6 | 206.8 -40.5246 1.93968 7 | 207.6 -34.845 1.63272 8 | 208.4 -31.1487 1.16501 9 | 209.2 -27.3124 0.815689 10 | 210 -24.0736 0.759867 11 | 210.8 -21.791 0.605548 12 | 211.6 -19.4152 0.525651 13 | 212.4 -17.7233 0.454731 14 | 213.2 -16.245 0.456609 15 | 214 -15.0619 0.388593 16 | 214.8 -13.5293 0.276232 17 | 215.6 -12.6242 0.257557 18 | 216.4 -11.595 0.211156 19 | 217.2 -10.7849 0.229703 20 | 218 -10.0404 0.221668 21 | 218.8 -9.51377 0.188133 22 | 219.6 -8.78817 0.135785 23 | 220.4 -8.27552 0.135077 24 | 221.2 -7.7482 0.184979 25 | 222 -7.32466 0.110472 26 | 222.8 -6.83936 0.114427 27 | 223.6 -6.43422 0.122651 28 | 224.4 -6.09436 0.0969946 29 | 225.2 -5.77319 0.0898172 30 | 226 -5.46602 0.0913462 31 | 226.8 -5.21033 0.0772921 32 | 227.6 -4.88205 0.0758067 33 | 228.4 -4.66202 0.0589209 34 | 229.2 -4.43941 0.0610602 35 | 230 -4.22902 0.0512269 36 | 230.8 -4.03189 0.0497775 37 | 231.6 -3.82844 0.0485896 38 | 232.4 -3.68875 0.0541453 39 | 233.2 -3.51581 0.0386387 40 | 234 -3.33849 0.0426963 41 | 234.8 -3.18471 0.0377551 42 | 235.6 -3.05316 0.044768 43 | 236.4 -2.92725 0.0397246 44 | 237.2 -2.82346 0.0310899 45 | 238 -2.71045 0.0278549 46 | 238.8 -2.59523 0.031475 47 | 239.6 -2.47128 0.0298193 48 | 240.4 -2.37047 0.0237052 49 | 241.2 -2.29028 0.022529 50 | 242 -2.2096 0.0267051 51 | 242.8 -2.12688 0.00273006 52 | 243.6 -2.036 0.0139915 53 | 244.4 -1.96486 0.0258947 54 | 245.2 -1.89168 0.0199052 55 | 246 -1.82904 0.0158672 56 | 246.8 -1.75703 0.0176862 57 | 247.6 -1.69912 0.0218649 58 | 248.4 -1.63268 0.0142978 59 | 249.2 -1.58129 0.0154418 60 | 250 -1.52097 0.0126909 61 | 250.8 -1.47667 0.0145249 62 | 251.6 -1.41599 0.00983898 63 | 252.4 -1.37795 0.0116401 64 | 253.2 -1.33806 0.0121669 65 | 254 -1.29009 0.0107064 66 | 254.8 -1.25416 0.0104931 67 | 255.6 -1.20212 0.00672164 68 | 256.4 -1.17276 0.00949061 69 | 257.2 -1.13265 0.0104871 70 | 258 -1.09738 0.0108518 71 | 258.8 -1.06918 0.00989565 72 | 259.6 -1.03242 0.00992416 73 | 260.4 -1.00522 0.00920799 74 | 261.2 -0.972587 0.00805071 75 | 262 -0.94358 0.00838659 76 | 262.8 -0.913666 0.00660818 77 | 263.6 -0.889893 0.00690178 78 | 264.4 -0.861821 0.00774652 79 | 265.2 -0.836888 0.00585673 80 | 266 -0.814208 0.00825481 81 | 266.8 -0.792188 0.0060175 82 | 267.6 -0.772446 0.00732762 83 | 268.4 -0.748027 0.00532619 84 | 269.2 -0.727732 0.00460601 85 | 270 -0.706188 0.00435153 86 | 270.8 -0.6896 0.00545936 87 | 271.6 -0.669028 0.00512296 88 | 272.4 -0.653634 0.00532499 89 | 273.2 -0.634732 0.00452697 90 | 274 -0.618148 0.00385749 91 | 274.8 -0.603749 0.00370689 92 | 275.6 -0.585114 0.00254241 93 | 276.4 -0.570178 0.00477513 94 | 277.2 -0.554662 0.00372157 95 | 278 -0.541808 0.00363839 96 | 278.8 -0.526269 0.00380552 97 | 279.6 -0.51369 0.00320989 98 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/full/U_25nm.txt: -------------------------------------------------------------------------------- 1 | 505 -155.083 2 | 508 -86.9485 3 | 511 -56.587 4 | 514 -39.8711 5 | 517 -29.5561 6 | 520 -22.6802 7 | 523 -17.8548 8 | 526 -14.3361 9 | 529 -11.6959 10 | 532 -9.66623 11 | 535 -8.07704 12 | 538 -6.81239 13 | 541 -5.7926 14 | 544 -4.96072 15 | 547 -4.27513 16 | 550 -3.70522 17 | 553 -3.22769 18 | 556 -2.82476 19 | 559 -2.48261 20 | 562 -2.1904 21 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/full/U_3nm.txt: -------------------------------------------------------------------------------- 1 | 61.25 -42.8984 2.30406 2 | 61.75 -34.8739 3.20476 3 | 62.25 -29.247 3.30003 4 | 62.75 -23.9932 2.46086 5 | 63.25 -19.962 1.67064 6 | 63.75 -16.5426 1.40383 7 | 64.25 -13.7813 0.997679 8 | 64.75 -11.8721 0.833381 9 | 65.25 -10.1133 0.63732 10 | 65.75 -8.83623 0.486418 11 | 66.25 -7.75105 0.435878 12 | 66.75 -6.88027 0.325952 13 | 67.25 -6.06722 0.312039 14 | 67.75 -5.41503 0.247506 15 | 68.25 -4.85479 0.205065 16 | 68.75 -4.39541 0.185443 17 | 69.25 -3.96646 0.167076 18 | 69.75 -3.58121 0.135867 19 | 70.25 -3.28848 0.123729 20 | 70.75 -2.99349 0.115527 21 | 71.25 -2.73583 0.10196 22 | 71.75 -2.51384 0.0815665 23 | 72.25 -2.31401 0.0731943 24 | 72.75 -2.12336 0.0714186 25 | 73.25 -1.98044 0.0655952 26 | 73.75 -1.82687 0.0514312 27 | 74.25 -1.70159 0.0474903 28 | 74.75 -1.57235 0.0402353 29 | 75.25 -1.46199 0.0390249 30 | 75.75 -1.36677 0.0362242 31 | 76.25 -1.27284 0.0347661 32 | 76.75 -1.19232 0.030058 33 | 77.25 -1.11202 0.0284619 34 | 77.75 -1.04212 0.0270559 35 | 78.25 -0.981786 0.0230982 36 | 78.75 -0.921657 0.021335 37 | 79.25 -0.867821 0.0196229 38 | 79.75 -0.815633 0.0180671 39 | 80.25 -0.768336 0.0173958 40 | 80.75 -0.722856 0.0147498 41 | 81.25 -0.680996 0.0131635 42 | 81.75 -0.645274 0.0129276 43 | 82.25 -0.608334 0.0127276 44 | 82.75 -0.580426 0.0109486 45 | 83.25 -0.54443 0.0101271 46 | 83.75 -0.518043 0.00962699 47 | 84.25 -0.492058 0.00946459 48 | 84.75 -0.464306 0.00732651 49 | 85.25 -0.444638 0.00793522 50 | 85.75 -0.422771 0.00750683 51 | 86.25 -0.400572 0.00685328 52 | 86.75 -0.381132 0.00661177 53 | 87.25 -0.363963 0.00658488 54 | 87.75 -0.345891 0.00586451 55 | 88.25 -0.330366 0.00543612 56 | 88.75 -0.314112 0.00425709 57 | 89.25 -0.300008 0.0051498 58 | 89.75 -0.286166 0.00527813 59 | 90.25 -0.273646 0.0042876 60 | 90.75 -0.261126 0.00413101 61 | 91.25 -0.25064 0.003692 62 | 91.75 -0.239517 0.00333155 63 | 92.25 -0.22861 0.00342274 64 | 92.75 -0.219487 0.0029657 65 | 93.25 -0.209689 0.00283201 66 | 93.75 -0.201262 0.00272906 67 | 94.25 -0.193009 0.00264845 68 | 94.75 -0.184552 0.002443 69 | 95.25 -0.177271 0.00242528 70 | 95.75 -0.169903 0.00225614 71 | 96.25 -0.163517 0.00216308 72 | 96.75 -0.156986 0.00217624 73 | 97.25 -0.15094 0.00177591 74 | 97.75 -0.145076 0.00190852 75 | 98.25 -0.139343 0.00194533 76 | 98.75 -0.133623 0.00157437 77 | 99.25 -0.128729 0.00177176 78 | 99.75 -0.124175 0.00144784 79 | 100.25 -0.119429 0.00143161 80 | 100.75 -0.114949 0.00142314 81 | 101.25 -0.110859 0.0011933 82 | 101.75 -0.10699 0.00130037 83 | 102.25 -0.10283 0.00126088 84 | 102.75 -0.0992797 0.00120814 85 | 103.25 -0.0954566 0.00106482 86 | 103.75 -0.0923268 0.00100691 87 | 104.25 -0.0890246 0.00120194 88 | 104.75 -0.0859734 0.000962834 89 | 105.25 -0.0829442 0.000878353 90 | 105.75 -0.0801651 0.000918826 91 | 106.25 -0.0773228 0.000916411 92 | 106.75 -0.0749133 0.000850157 93 | 107.25 -0.0722502 0.000720414 94 | 107.75 -0.0697851 0.000779088 95 | 108.25 -0.0676216 0.000685546 96 | 108.75 -0.065415 0.000759669 97 | 109.25 -0.0631737 0.00063868 98 | 109.75 -0.0612624 0.000563149 99 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/full/U_4nm.txt: -------------------------------------------------------------------------------- 1 | 81.25 -63.7192 1.47403 2 | 81.75 -52.9105 3.5519 3 | 82.25 -45.0043 3.02587 4 | 82.75 -36.4758 2.56322 5 | 83.25 -31.0653 2.14905 6 | 83.75 -26.0956 1.89008 7 | 84.25 -22.2027 1.30698 8 | 84.75 -18.9259 1.04872 9 | 85.25 -16.5358 0.851237 10 | 85.75 -14.3855 0.679706 11 | 86.25 -12.7905 0.537077 12 | 86.75 -11.2154 0.482222 13 | 87.25 -10.121 0.410002 14 | 87.75 -9.02802 0.332808 15 | 88.25 -8.19744 0.323789 16 | 88.75 -7.50096 0.276602 17 | 89.25 -6.77484 0.267672 18 | 89.75 -6.1653 0.202689 19 | 90.25 -5.67718 0.163256 20 | 90.75 -5.21677 0.170388 21 | 91.25 -4.82895 0.136321 22 | 91.75 -4.45274 0.125142 23 | 92.25 -4.09679 0.110782 24 | 92.75 -3.82573 0.0988164 25 | 93.25 -3.54777 0.0752384 26 | 93.75 -3.30375 0.0751441 27 | 94.25 -3.09596 0.0679549 28 | 94.75 -2.89544 0.0677353 29 | 95.25 -2.71469 0.0613618 30 | 95.75 -2.5386 0.055068 31 | 96.25 -2.38002 0.0428708 32 | 96.75 -2.24282 0.0490253 33 | 97.25 -2.11918 0.0413892 34 | 97.75 -1.98402 0.0428234 35 | 98.25 -1.88167 0.0386501 36 | 98.75 -1.77742 0.0346415 37 | 99.25 -1.68064 0.0284983 38 | 99.75 -1.58847 0.027763 39 | 100.25 -1.50888 0.0269151 40 | 100.75 -1.43139 0.0258829 41 | 101.25 -1.35968 0.0239553 42 | 101.75 -1.28655 0.0219682 43 | 102.25 -1.21931 0.0207381 44 | 102.75 -1.16484 0.0176577 45 | 103.25 -1.10761 0.0177627 46 | 103.75 -1.05562 0.0174374 47 | 104.25 -1.00547 0.0156135 48 | 104.75 -0.959991 0.0155713 49 | 105.25 -0.9116 0.0136401 50 | 105.75 -0.870958 0.0128675 51 | 106.25 -0.832693 0.012361 52 | 106.75 -0.795738 0.0121754 53 | 107.25 -0.763128 0.010904 54 | 107.75 -0.729515 0.00995412 55 | 108.25 -0.699223 0.00921861 56 | 108.75 -0.671063 0.00818568 57 | 109.25 -0.642059 0.00857235 58 | 109.75 -0.61583 0.00756944 59 | 110.25 -0.589989 0.00748246 60 | 110.75 -0.566886 0.00756518 61 | 111.25 -0.544559 0.00638838 62 | 111.75 -0.522108 0.00594421 63 | 112.25 -0.502811 0.00726734 64 | 112.75 -0.483383 0.00596874 65 | 113.25 -0.46515 0.00590849 66 | 113.75 -0.447769 0.00528944 67 | 114.25 -0.430811 0.00504888 68 | 114.75 -0.414325 0.00473447 69 | 115.25 -0.398483 0.00469796 70 | 115.75 -0.384169 0.00436569 71 | 116.25 -0.371182 0.00388979 72 | 116.75 -0.357297 0.00400752 73 | 117.25 -0.344381 0.00361547 74 | 117.75 -0.331999 0.00409658 75 | 118.25 -0.321083 0.00380964 76 | 118.75 -0.309983 0.00340248 77 | 119.25 -0.298971 0.0034952 78 | 119.75 -0.288222 0.00311569 79 | 120.25 -0.278912 0.00320993 80 | 120.75 -0.269571 0.00237885 81 | 121.25 -0.260827 0.00296561 82 | 121.75 -0.252359 0.00268935 83 | 122.25 -0.243728 0.00266006 84 | 122.75 -0.235461 0.0023374 85 | 123.25 -0.228461 0.00244984 86 | 123.75 -0.221076 0.00201257 87 | 124.25 -0.213344 0.00235994 88 | 124.75 -0.207275 0.00199436 89 | 125.25 -0.20072 0.00205562 90 | 125.75 -0.194212 0.00199689 91 | 126.25 -0.188335 0.00171086 92 | 126.75 -0.182345 0.00161824 93 | 127.25 -0.17693 0.00167695 94 | 127.75 -0.171523 0.00159315 95 | 128.25 -0.165988 0.00146952 96 | 128.75 -0.161546 0.00147301 97 | 129.25 -0.156439 0.00129471 98 | 129.75 -0.151878 0.00129845 99 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/full/U_5nm.txt: -------------------------------------------------------------------------------- 1 | 102.1 -62.5081 3.03683 2 | 102.7 -48.6341 3.259 3 | 103.3 -42.3305 3.0519 4 | 103.9 -33.1728 1.90128 5 | 104.5 -28.355 2.0391 6 | 105.1 -23.7916 1.39377 7 | 105.7 -19.742 1.10074 8 | 106.3 -17.5764 0.918702 9 | 106.9 -15.1465 0.686285 10 | 107.5 -13.4348 0.486599 11 | 108.1 -11.9781 0.428247 12 | 108.7 -10.7952 0.470596 13 | 109.3 -9.66583 0.352005 14 | 109.9 -8.78043 0.274444 15 | 110.5 -7.86053 0.241389 16 | 111.1 -7.31123 0.230352 17 | 111.7 -6.63426 0.182451 18 | 112.3 -6.0578 0.190098 19 | 112.9 -5.55837 0.128381 20 | 113.5 -5.13523 0.164794 21 | 114.1 -4.76064 0.117752 22 | 114.7 -4.41524 0.107337 23 | 115.3 -4.11893 0.0870201 24 | 115.9 -3.8106 0.0831277 25 | 116.5 -3.53527 0.0705317 26 | 117.1 -3.33836 0.0587706 27 | 117.7 -3.10698 0.0614668 28 | 118.3 -2.90865 0.0578531 29 | 118.9 -2.72035 0.047347 30 | 119.5 -2.57089 0.0444815 31 | 120.1 -2.41449 0.0408519 32 | 120.7 -2.26577 0.04522 33 | 121.3 -2.14337 0.0352556 34 | 121.9 -2.0219 0.0296745 35 | 122.5 -1.92082 0.0307575 36 | 123.1 -1.83008 0.0264879 37 | 123.7 -1.72272 0.0293654 38 | 124.3 -1.63417 0.0262848 39 | 124.9 -1.54484 0.0229363 40 | 125.5 -1.46859 0.0208089 41 | 126.1 -1.40263 0.0195925 42 | 126.7 -1.33391 0.025205 43 | 127.3 -1.26393 0.0171823 44 | 127.9 -1.20784 0.0178847 45 | 128.5 -1.15265 0.013779 46 | 129.1 -1.08939 0.0152415 47 | 129.7 -1.04183 0.0126092 48 | 130.3 -0.997744 0.0111509 49 | 130.9 -0.955162 0.0119077 50 | 131.5 -0.911499 0.0112822 51 | 132.1 -0.872666 0.0121083 52 | 132.7 -0.83521 0.0105026 53 | 133.3 -0.800654 0.00876494 54 | 133.9 -0.767256 0.00800637 55 | 134.5 -0.737568 0.00942939 56 | 135.1 -0.704053 0.00792882 57 | 135.7 -0.677911 0.00796669 58 | 136.3 -0.64888 0.00715799 59 | 136.9 -0.623803 0.00818746 60 | 137.5 -0.599712 0.00715937 61 | 138.1 -0.574699 0.00648632 62 | 138.7 -0.553514 0.00603467 63 | 139.3 -0.531081 0.00433123 64 | 139.9 -0.513739 0.00646104 65 | 140.5 -0.4925 0.0058115 66 | 141.1 -0.474865 0.00451876 67 | 141.7 -0.460048 0.00487711 68 | 142.3 -0.441599 0.00475167 69 | 142.9 -0.425268 0.00449929 70 | 143.5 -0.411145 0.00463136 71 | 144.1 -0.394772 0.00430623 72 | 144.7 -0.381086 0.00441076 73 | 145.3 -0.369653 0.00384795 74 | 145.9 -0.355402 0.00392334 75 | 146.5 -0.343503 0.00406601 76 | 147.1 -0.332331 0.00343629 77 | 147.7 -0.320249 0.00259801 78 | 148.3 -0.311106 0.003154 79 | 148.9 -0.300689 0.00270257 80 | 149.5 -0.290473 0.00309144 81 | 150.1 -0.281036 0.00271606 82 | 150.7 -0.270749 0.00278931 83 | 151.3 -0.26336 0.00246844 84 | 151.9 -0.25502 0.00213476 85 | 152.5 -0.246376 0.00190866 86 | 153.1 -0.238661 0.00201962 87 | 153.7 -0.231909 0.00199261 88 | 154.3 -0.223249 0.00183993 89 | 154.9 -0.217314 0.00208652 90 | 155.5 -0.210948 0.00228594 91 | 156.1 -0.204461 0.00189603 92 | 156.7 -0.198193 0.00190768 93 | 157.3 -0.191887 0.00150437 94 | 157.9 -0.186911 0.00173985 95 | 158.5 -0.18065 0.00148956 96 | 159.1 -0.17602 0.00127865 97 | 159.7 -0.169767 0.00132064 98 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/full/U_6nm.txt: -------------------------------------------------------------------------------- 1 | 121.5 -91.1764 1.44451 2 | 122.1 -76.0077 5.67324 3 | 122.7 -60.9923 4.289 4 | 123.3 -50.1028 3.70339 5 | 123.9 -41.8629 2.56565 6 | 124.5 -35.0462 1.94068 7 | 125.1 -29.5424 1.56108 8 | 125.7 -25.6683 1.14446 9 | 126.3 -22.4413 0.927691 10 | 126.9 -19.6401 0.664524 11 | 127.5 -17.3733 0.728876 12 | 128.1 -15.5706 0.519129 13 | 128.7 -13.9527 0.454557 14 | 129.3 -12.6896 0.42701 15 | 129.9 -11.5391 0.367144 16 | 130.5 -10.5236 0.331795 17 | 131.1 -9.58322 0.24389 18 | 131.7 -8.87405 0.242891 19 | 132.3 -8.14067 0.198162 20 | 132.9 -7.55717 0.158803 21 | 133.5 -6.95893 0.180199 22 | 134.1 -6.48396 0.145059 23 | 134.7 -6.03345 0.123174 24 | 135.3 -5.65386 0.114059 25 | 135.9 -5.27284 0.120415 26 | 136.5 -4.92281 0.0879209 27 | 137.1 -4.62638 0.0888285 28 | 137.7 -4.35199 0.0795786 29 | 138.3 -4.09816 0.0834074 30 | 138.9 -3.84887 0.0726167 31 | 139.5 -3.63838 0.0639228 32 | 140.1 -3.43626 0.0559263 33 | 140.7 -3.24714 0.0518274 34 | 141.3 -3.07488 0.0518565 35 | 141.9 -2.90438 0.0406428 36 | 142.5 -2.75356 0.0467373 37 | 143.1 -2.63096 0.0431874 38 | 143.7 -2.49417 0.0354595 39 | 144.3 -2.37698 0.0346444 40 | 144.9 -2.25376 0.0317318 41 | 145.5 -2.14973 0.0331287 42 | 146.1 -2.05045 0.0288321 43 | 146.7 -1.95583 0.0284663 44 | 147.3 -1.85786 0.0266449 45 | 147.9 -1.78168 0.0242375 46 | 148.5 -1.71206 0.0199365 47 | 149.1 -1.62918 0.0209157 48 | 149.7 -1.56794 0.0203432 49 | 150.3 -1.49373 0.0196706 50 | 150.9 -1.4346 0.0202526 51 | 151.5 -1.37388 0.0165842 52 | 152.1 -1.31717 0.0174109 53 | 152.7 -1.26388 0.015752 54 | 153.3 -1.21433 0.0140278 55 | 153.9 -1.16602 0.0145507 56 | 154.5 -1.12277 0.0130237 57 | 155.1 -1.07875 0.012393 58 | 155.7 -1.03749 0.0134835 59 | 156.3 -0.997369 0.0113371 60 | 156.9 -0.961808 0.0113408 61 | 157.5 -0.926183 0.0102077 62 | 158.1 -0.893008 0.0104415 63 | 158.7 -0.860355 0.00918334 64 | 159.3 -0.830854 0.00948209 65 | 159.9 -0.799939 0.00905305 66 | 160.5 -0.771027 0.0084117 67 | 161.1 -0.745296 0.00789684 68 | 161.7 -0.718206 0.00735366 69 | 162.3 -0.695791 0.00717753 70 | 162.9 -0.67151 0.0063232 71 | 163.5 -0.648578 0.00648386 72 | 164.1 -0.627545 0.00632593 73 | 164.7 -0.607138 0.00534869 74 | 165.3 -0.586248 0.00552896 75 | 165.9 -0.569739 0.00571119 76 | 166.5 -0.549558 0.00581552 77 | 167.1 -0.532888 0.00509733 78 | 167.7 -0.515778 0.00540455 79 | 168.3 -0.49918 0.00463831 80 | 168.9 -0.483724 0.00431223 81 | 169.5 -0.46894 0.00441121 82 | 170.1 -0.454143 0.00446054 83 | 170.7 -0.441023 0.00398862 84 | 171.3 -0.427733 0.00395575 85 | 171.9 -0.414456 0.00378905 86 | 172.5 -0.401999 0.00385508 87 | 173.1 -0.390582 0.00333228 88 | 173.7 -0.379286 0.00343665 89 | 174.3 -0.368398 0.00328253 90 | 174.9 -0.357311 0.00305199 91 | 175.5 -0.347442 0.00282172 92 | 176.1 -0.337924 0.00269568 93 | 176.7 -0.327645 0.00282993 94 | 177.3 -0.318657 0.00285085 95 | 177.9 -0.309913 0.00250997 96 | 178.5 -0.300561 0.00240131 97 | 179.1 -0.293224 0.00214693 98 | 179.7 -0.28552 0.00249481 99 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/full/U_7nm.txt: -------------------------------------------------------------------------------- 1 | 141.75 -99.2871 5.06449 2 | 142.45 -84.1408 7.63333 3 | 143.15 -64.7897 4.56616 4 | 143.85 -50.3936 2.00364 5 | 144.55 -41.7865 2.3038 6 | 145.25 -34.9511 2.12502 7 | 145.95 -29.9033 1.55022 8 | 146.65 -25.4229 1.03764 9 | 147.35 -22.5863 1.08236 10 | 148.05 -19.9462 0.616647 11 | 148.75 -17.5323 0.718381 12 | 149.45 -15.6613 0.572772 13 | 150.15 -14.0801 0.431291 14 | 150.85 -12.8386 0.411726 15 | 151.55 -11.5714 0.360603 16 | 152.25 -10.5019 0.29307 17 | 152.95 -9.67792 0.24402 18 | 153.65 -8.86946 0.283364 19 | 154.35 -8.15904 0.196352 20 | 155.05 -7.56106 0.185645 21 | 155.75 -7.01158 0.182029 22 | 156.45 -6.4937 0.152775 23 | 157.15 -6.04974 0.134722 24 | 157.85 -5.62103 0.121393 25 | 158.55 -5.2791 0.129237 26 | 159.25 -4.94285 0.0956939 27 | 159.95 -4.63486 0.102919 28 | 160.65 -4.35653 0.0826287 29 | 161.35 -4.09147 0.0830437 30 | 162.05 -3.84114 0.060484 31 | 162.75 -3.63698 0.0751777 32 | 163.45 -3.42745 0.0551635 33 | 164.15 -3.23694 0.0574505 34 | 164.85 -3.06793 0.0442297 35 | 165.55 -2.91669 0.0523551 36 | 166.25 -2.76929 0.0470807 37 | 166.95 -2.62273 0.0371937 38 | 167.65 -2.4853 0.0344181 39 | 168.35 -2.36572 0.0343306 40 | 169.05 -2.25658 0.037328 41 | 169.75 -2.16198 0.0348277 42 | 170.45 -2.05788 0.0281848 43 | 171.15 -1.95884 0.0265063 44 | 171.85 -1.86564 0.0231525 45 | 172.55 -1.78386 0.0263429 46 | 173.25 -1.70424 0.0228541 47 | 173.95 -1.63155 0.0214354 48 | 174.65 -1.55533 0.0189537 49 | 175.35 -1.49612 0.0189422 50 | 176.05 -1.42902 0.0196604 51 | 176.75 -1.3787 0.0161075 52 | 177.45 -1.31951 0.016949 53 | 178.15 -1.25967 0.0157164 54 | 178.85 -1.21913 0.0137595 55 | 179.55 -1.17278 0.0123509 56 | 180.25 -1.11964 0.0148266 57 | 180.95 -1.08003 0.013761 58 | 181.65 -1.03884 0.0119886 59 | 182.35 -0.997987 0.0108412 60 | 183.05 -0.960895 0.0105578 61 | 183.75 -0.923731 0.0103745 62 | 184.45 -0.893628 0.0102871 63 | 185.15 -0.857492 0.00939189 64 | 185.85 -0.826896 0.0078335 65 | 186.55 -0.800661 0.00866349 66 | 187.25 -0.772102 0.0079065 67 | 187.95 -0.746736 0.00790739 68 | 188.65 -0.717999 0.00673451 69 | 189.35 -0.695835 0.00643719 70 | 190.05 -0.673041 0.0061376 71 | 190.75 -0.649801 0.00650257 72 | 191.45 -0.62982 0.00454492 73 | 192.15 -0.607289 0.00599801 74 | 192.85 -0.589249 0.00596504 75 | 193.55 -0.566784 0.00429049 76 | 194.25 -0.550755 0.0054186 77 | 194.95 -0.532223 0.00474214 78 | 195.65 -0.513931 0.00511982 79 | 196.35 -0.498244 0.0043302 80 | 197.05 -0.483271 0.00470518 81 | 197.75 -0.47001 0.00417425 82 | 198.45 -0.4556 0.00372959 83 | 199.15 -0.440887 0.00423599 84 | 199.85 -0.428028 0.00379621 85 | 200.55 -0.414491 0.00377641 86 | 201.25 -0.402335 0.00327364 87 | 201.95 -0.390428 0.0034515 88 | 202.65 -0.380951 0.00308341 89 | 203.35 -0.367901 0.00342594 90 | 204.05 -0.357943 0.0029609 91 | 204.75 -0.346726 0.00310722 92 | 205.45 -0.336807 0.00279047 93 | 206.15 -0.327687 0.00314406 94 | 206.85 -0.319048 0.00271748 95 | 207.55 -0.310334 0.00254867 96 | 208.25 -0.301251 0.00245196 97 | 208.95 -0.292376 0.00282612 98 | 209.65 -0.284926 0.00246831 99 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/full/U_8nm.txt: -------------------------------------------------------------------------------- 1 | 162.45 -93.0946 6.33811 2 | 163.15 -76.8997 4.73546 3 | 163.85 -63.3264 4.55488 4 | 164.55 -49.905 3.07151 5 | 165.25 -41.7861 2.36659 6 | 165.95 -35.8218 1.66104 7 | 166.65 -30.7157 1.21293 8 | 167.35 -27.1486 1.07768 9 | 168.05 -24.0233 1.005 10 | 168.75 -21.2203 0.758193 11 | 169.45 -19.1927 0.635787 12 | 170.15 -17.0959 0.500492 13 | 170.85 -15.5359 0.480019 14 | 171.55 -14.1253 0.331109 15 | 172.25 -12.8725 0.276991 16 | 172.95 -11.8915 0.278555 17 | 173.65 -10.9399 0.284786 18 | 174.35 -10.1259 0.245935 19 | 175.05 -9.39972 0.202956 20 | 175.75 -8.67237 0.160555 21 | 176.45 -8.15587 0.164665 22 | 177.15 -7.72357 0.12271 23 | 177.85 -7.08661 0.135702 24 | 178.55 -6.59257 0.116253 25 | 179.25 -6.20224 0.0897935 26 | 179.95 -5.83777 0.112297 27 | 180.65 -5.51032 0.117535 28 | 181.35 -5.19843 0.0844067 29 | 182.05 -4.90185 0.0670849 30 | 182.75 -4.66783 0.0710439 31 | 183.45 -4.389 0.0743607 32 | 184.15 -4.17214 0.0750885 33 | 184.85 -3.96329 0.0648234 34 | 185.55 -3.74682 0.058841 35 | 186.25 -3.57334 0.0489045 36 | 186.95 -3.36227 0.0398489 37 | 187.65 -3.23472 0.0434825 38 | 188.35 -3.0733 0.0458755 39 | 189.05 -2.92653 0.038405 40 | 189.75 -2.80742 0.0402739 41 | 190.45 -2.69306 0.0362888 42 | 191.15 -2.5645 0.0299682 43 | 191.85 -2.4533 0.0300687 44 | 192.55 -2.34461 0.033489 45 | 193.25 -2.25397 0.0283951 46 | 193.95 -2.16069 0.0268476 47 | 194.65 -2.06729 0.0220529 48 | 195.35 -1.98823 0.0249919 49 | 196.05 -1.90694 0.0255198 50 | 196.75 -1.83329 0.0212024 51 | 197.45 -1.75826 0.0209444 52 | 198.15 -1.68974 0.0194734 53 | 198.85 -1.62956 0.0147883 54 | 199.55 -1.5773 0.0159066 55 | 200.25 -1.5081 0.0189071 56 | 200.95 -1.45626 0.0144544 57 | 201.65 -1.40301 0.0147671 58 | 202.35 -1.34709 0.0136492 59 | 203.05 -1.29871 0.0115693 60 | 203.75 -1.2514 0.0119645 61 | 204.45 -1.21164 0.0116663 62 | 205.15 -1.16768 0.010603 63 | 205.85 -1.12817 0.00892885 64 | 206.55 -1.09175 0.0129207 65 | 207.25 -1.0565 0.01113 66 | 207.95 -1.02265 0.00994767 67 | 208.65 -0.986338 0.00909607 68 | 209.35 -0.951427 0.00583256 69 | 210.05 -0.925974 0.00720135 70 | 210.75 -0.892646 0.00736812 71 | 211.45 -0.867958 0.00693064 72 | 212.15 -0.838554 0.0070722 73 | 212.85 -0.812243 0.00693266 74 | 213.55 -0.786993 0.00701236 75 | 214.25 -0.763398 0.00728383 76 | 214.95 -0.740847 0.00559175 77 | 215.65 -0.717714 0.00588751 78 | 216.35 -0.695406 0.0060173 79 | 217.05 -0.67525 0.00570934 80 | 217.75 -0.655271 0.00668346 81 | 218.45 -0.637672 0.0052563 82 | 219.15 -0.617638 0.00608848 83 | 219.85 -0.600383 0.00548595 84 | 220.55 -0.5833 0.00432011 85 | 221.25 -0.568094 0.00409806 86 | 221.95 -0.550892 0.00451195 87 | 222.65 -0.534372 0.00414516 88 | 223.35 -0.519521 0.0051315 89 | 224.05 -0.505117 0.00344716 90 | 224.75 -0.490519 0.00397311 91 | 225.45 -0.478306 0.00363366 92 | 226.15 -0.467193 0.00379244 93 | 226.85 -0.45493 0.00342405 94 | 227.55 -0.44298 0.00347771 95 | 228.25 -0.42994 0.00328824 96 | 228.95 -0.420926 0.00342048 97 | 229.65 -0.410362 0.00193948 98 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/full/U_9nm.txt: -------------------------------------------------------------------------------- 1 | 182 -118.891 6.40412 2 | 182.8 -98.3868 7.33257 3 | 183.6 -74.6837 6.15502 4 | 184.4 -60.3756 3.85789 5 | 185.2 -49.2566 3.14825 6 | 186 -41.5145 2.49122 7 | 186.8 -34.287 1.82836 8 | 187.6 -30.0971 1.33975 9 | 188.4 -26.4885 1.16487 10 | 189.2 -23.3461 0.816385 11 | 190 -20.733 0.780437 12 | 190.8 -18.5723 0.69879 13 | 191.6 -16.7738 0.473454 14 | 192.4 -15.1581 0.356105 15 | 193.2 -13.7623 0.366521 16 | 194 -12.6782 0.380878 17 | 194.8 -11.6842 0.282459 18 | 195.6 -10.7132 0.242859 19 | 196.4 -9.9334 0.221558 20 | 197.2 -9.15688 0.233139 21 | 198 -8.46507 0.158367 22 | 198.8 -7.99007 0.157337 23 | 199.6 -7.40124 0.106046 24 | 200.4 -6.90969 0.140064 25 | 201.2 -6.50266 0.148537 26 | 202 -6.08502 0.103389 27 | 202.8 -5.68872 0.102033 28 | 203.6 -5.33779 0.0955671 29 | 204.4 -5.05604 0.0884453 30 | 205.2 -4.78326 0.0898146 31 | 206 -4.54784 0.0767572 32 | 206.8 -4.25908 0.0646332 33 | 207.6 -4.07511 0.0624511 34 | 208.4 -3.85148 0.0614675 35 | 209.2 -3.63472 0.0566478 36 | 210 -3.47846 0.0526702 37 | 210.8 -3.31357 0.0426098 38 | 211.6 -3.12614 0.0416856 39 | 212.4 -2.98025 0.0465403 40 | 213.2 -2.87625 0.0378382 41 | 214 -2.71882 0.0300577 42 | 214.8 -2.60574 0.0298094 43 | 215.6 -2.47998 0.0354421 44 | 216.4 -2.37179 0.0320822 45 | 217.2 -2.28999 0.0287147 46 | 218 -2.19223 0.0233561 47 | 218.8 -2.08593 0.0244736 48 | 219.6 -2.00417 0.0252602 49 | 220.4 -1.91553 0.0212873 50 | 221.2 -1.84338 0.0189864 51 | 222 -1.77406 0.0218648 52 | 222.8 -1.70526 0.0217532 53 | 223.6 -1.64041 0.0178069 54 | 224.4 -1.56873 0.0207791 55 | 225.2 -1.5167 0.0132646 56 | 226 -1.4606 0.0168719 57 | 226.8 -1.40433 0.0158026 58 | 227.6 -1.35491 0.0159251 59 | 228.4 -1.30533 0.0133354 60 | 229.2 -1.25964 0.0133351 61 | 230 -1.21645 0.012908 62 | 230.8 -1.17232 0.011172 63 | 231.6 -1.12875 0.00974627 64 | 232.4 -1.08822 0.0107332 65 | 233.2 -1.05894 0.0104285 66 | 234 -1.01869 0.0102728 67 | 234.8 -0.98488 0.00962519 68 | 235.6 -0.951569 0.00838938 69 | 236.4 -0.920301 0.0081264 70 | 237.2 -0.890399 0.00855425 71 | 238 -0.864168 0.00840965 72 | 238.8 -0.835167 0.00888779 73 | 239.6 -0.807118 0.00621748 74 | 240.4 -0.783614 0.00590531 75 | 241.2 -0.758032 0.00606523 76 | 242 -0.736235 0.00610359 77 | 242.8 -0.712025 0.00593149 78 | 243.6 -0.693054 0.00652725 79 | 244.4 -0.670659 0.00569033 80 | 245.2 -0.650985 0.00595456 81 | 246 -0.630932 0.00567793 82 | 246.8 -0.612165 0.0054892 83 | 247.6 -0.596594 0.00431218 84 | 248.4 -0.580021 0.00475332 85 | 249.2 -0.563113 0.0050656 86 | 250 -0.546468 0.00473392 87 | 250.8 -0.530707 0.00449848 88 | 251.6 -0.51436 0.00405224 89 | 252.4 -0.501324 0.00475401 90 | 253.2 -0.488091 0.00367131 91 | 254 -0.474554 0.0035182 92 | 254.8 -0.45942 0.00358251 93 | 255.6 -0.450042 0.0032765 94 | 256.4 -0.437296 0.00268198 95 | 257.2 -0.424263 0.00322244 96 | 258 -0.412731 0.00337325 97 | 258.8 -0.401065 0.00257952 98 | 259.6 -0.392213 0.00289667 99 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/full/README.md: -------------------------------------------------------------------------------- 1 | This target data is the complete (non-zero) target data collected for mixed nanoparticle sizes using the included C++ script. 2 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/full/U_2nm-3nm.txt: -------------------------------------------------------------------------------- 1 | 51.25 -30.8691 3.52549 2 | 51.75 -29.5321 2.25375 3 | 52.25 -22.4216 1.94584 4 | 52.75 -18.1087 2.03841 5 | 53.25 -15.0996 1.60712 6 | 53.75 -12.2416 1.08963 7 | 54.25 -10.1375 0.796128 8 | 54.75 -8.2402 0.598099 9 | 55.25 -7.24786 0.552601 10 | 55.75 -6.19658 0.293926 11 | 56.25 -5.38012 0.323012 12 | 56.75 -4.66213 0.297807 13 | 57.25 -4.15542 0.229691 14 | 57.75 -3.68035 0.202844 15 | 58.25 -3.27459 0.1783 16 | 58.75 -2.92256 0.161945 17 | 59.25 -2.62598 0.120356 18 | 59.75 -2.36002 0.105938 19 | 60.25 -2.12791 0.0983944 20 | 60.75 -1.93409 0.0831198 21 | 61.25 -1.77796 0.074001 22 | 61.75 -1.60201 0.0578292 23 | 62.25 -1.4703 0.0595466 24 | 62.75 -1.34244 0.048426 25 | 63.25 -1.2339 0.0378842 26 | 63.75 -1.13369 0.0360263 27 | 64.25 -1.04444 0.0324139 28 | 64.75 -0.968023 0.0271689 29 | 65.25 -0.900809 0.0289948 30 | 65.75 -0.830066 0.0296577 31 | 66.25 -0.777575 0.0207236 32 | 66.75 -0.715958 0.0191881 33 | 67.25 -0.670093 0.0175753 34 | 67.75 -0.619589 0.0147094 35 | 68.25 -0.579992 0.0162822 36 | 68.75 -0.545483 0.0136497 37 | 69.25 -0.508413 0.0106441 38 | 69.75 -0.474964 0.0107433 39 | 70.25 -0.448234 0.0118793 40 | 70.75 -0.41827 0.00866045 41 | 71.25 -0.394167 0.0109507 42 | 71.75 -0.372777 0.00948131 43 | 72.25 -0.350384 0.00823363 44 | 72.75 -0.330029 0.00652243 45 | 73.25 -0.309244 0.00743224 46 | 73.75 -0.292931 0.00486825 47 | 74.25 -0.275917 0.0056545 48 | 74.75 -0.259376 0.00435369 49 | 75.25 -0.24832 0.00460834 50 | 75.75 -0.233425 0.00398854 51 | 76.25 -0.222529 0.00384328 52 | 76.75 -0.211376 0.00403603 53 | 77.25 -0.200439 0.00346304 54 | 77.75 -0.189083 0.00411986 55 | 78.25 -0.179952 0.00347873 56 | 78.75 -0.171895 0.00247743 57 | 79.25 -0.163142 0.00267944 58 | 79.75 -0.153971 0.0025573 59 | 80.25 -0.147014 0.00261228 60 | 80.75 -0.140954 0.00203143 61 | 81.25 -0.134137 0.00211798 62 | 81.75 -0.128006 0.00165201 63 | 82.25 -0.121282 0.00154117 64 | 82.75 -0.116099 0.00174582 65 | 83.25 -0.110682 0.00176086 66 | 83.75 -0.106299 0.00179404 67 | 84.25 -0.100981 0.00169476 68 | 84.75 -0.0968572 0.00156907 69 | 85.25 -0.0926655 0.00115621 70 | 85.75 -0.0886138 0.00129281 71 | 86.25 -0.084982 0.00122795 72 | 86.75 -0.0807002 0.00122243 73 | 87.25 -0.0777151 0.000957785 74 | 87.75 -0.0745552 0.00105074 75 | 88.25 -0.071479 0.00096792 76 | 88.75 -0.0682353 0.000949658 77 | 89.25 -0.0656844 0.000880381 78 | 89.75 -0.0629747 0.000937684 79 | 90.25 -0.060496 0.000695308 80 | 90.75 -0.0580993 0.000730826 81 | 91.25 -0.0560387 0.000694592 82 | 91.75 -0.053543 0.000623251 83 | 92.25 -0.0515988 0.000661029 84 | 92.75 -0.0495934 0.000721136 85 | 93.25 -0.0477977 0.000468497 86 | 93.75 -0.045666 0.000588012 87 | 94.25 -0.0441063 0.000487862 88 | 94.75 -0.0425754 0.000442745 89 | 95.25 -0.041122 0.000436194 90 | 95.75 -0.0394499 0.000531907 91 | 96.25 -0.0381233 0.000417324 92 | 96.75 -0.0369569 0.000412604 93 | 97.25 -0.035432 0.000393437 94 | 97.75 -0.0342061 0.000403513 95 | 98.25 -0.0329074 0.000299024 96 | 98.75 -0.0318167 0.000319438 97 | 99.25 -0.0307323 0.000287938 98 | 99.75 -0.0295914 0.000316564 99 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/full/U_2nm-4nm.txt: -------------------------------------------------------------------------------- 1 | 61.25 -34.9981 2.49886 2 | 61.75 -30.5966 3.50187 3 | 62.25 -26.5867 2.97071 4 | 62.75 -21.1316 2.0832 5 | 63.25 -18.2833 1.6554 6 | 63.75 -14.4892 0.994433 7 | 64.25 -12.001 0.770669 8 | 64.75 -10.2254 0.646205 9 | 65.25 -8.97095 0.674234 10 | 65.75 -7.63113 0.440094 11 | 66.25 -6.61451 0.370638 12 | 66.75 -5.83643 0.317094 13 | 67.25 -5.16283 0.266513 14 | 67.75 -4.55357 0.248808 15 | 68.25 -4.08313 0.170974 16 | 68.75 -3.63539 0.185084 17 | 69.25 -3.31278 0.116272 18 | 69.75 -3.02066 0.121857 19 | 70.25 -2.71134 0.0892472 20 | 70.75 -2.45482 0.0988125 21 | 71.25 -2.25561 0.0820303 22 | 71.75 -2.05621 0.064971 23 | 72.25 -1.88806 0.0672844 24 | 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104.25 -0.0667629 0.000698148 88 | 104.75 -0.0641389 0.000725773 89 | 105.25 -0.0620051 0.000757131 90 | 105.75 -0.0598425 0.000685555 91 | 106.25 -0.0577209 0.0006213 92 | 106.75 -0.0558227 0.000641175 93 | 107.25 -0.0539831 0.000489245 94 | 107.75 -0.0521007 0.000578837 95 | 108.25 -0.0501787 0.000468155 96 | 108.75 -0.0486556 0.000509008 97 | 109.25 -0.0469916 0.00046985 98 | 109.75 -0.0454653 0.000453721 99 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/full/U_2nm-6nm.txt: -------------------------------------------------------------------------------- 1 | 81.25 -47.1018 3.31184 2 | 81.75 -35.4988 2.69383 3 | 82.25 -29.3433 2.21097 4 | 82.75 -25.2924 1.98879 5 | 83.25 -21.01 1.72601 6 | 83.75 -17.1803 1.00063 7 | 84.25 -14.1902 0.805645 8 | 84.75 -12.0806 0.652516 9 | 85.25 -10.6992 0.699259 10 | 85.75 -9.30965 0.486822 11 | 86.25 -8.09602 0.389131 12 | 86.75 -7.13251 0.358881 13 | 87.25 -6.36824 0.320071 14 | 87.75 -5.66295 0.22496 15 | 88.25 -5.152 0.176839 16 | 88.75 -4.58017 0.174664 17 | 89.25 -4.14211 0.1572 18 | 89.75 -3.78626 0.120897 19 | 90.25 -3.43845 0.102917 20 | 90.75 -3.12881 0.100288 21 | 91.25 -2.86811 0.082728 22 | 91.75 -2.65135 0.0842084 23 | 92.25 -2.43866 0.0683253 24 | 92.75 -2.23697 0.0669361 25 | 93.25 -2.09124 0.0540085 26 | 93.75 -1.945 0.0472791 27 | 94.25 -1.79042 0.0472093 28 | 94.75 -1.66668 0.0358378 29 | 95.25 -1.56547 0.030772 30 | 95.75 -1.4468 0.0333028 31 | 96.25 -1.3717 0.0345653 32 | 96.75 -1.28266 0.0305473 33 | 97.25 -1.19278 0.0261912 34 | 97.75 -1.11722 0.0205232 35 | 98.25 -1.05338 0.0195812 36 | 98.75 -0.996025 0.0198243 37 | 99.25 -0.933733 0.0204069 38 | 99.75 -0.880576 0.0164414 39 | 100.25 -0.832285 0.0160332 40 | 100.75 -0.787407 0.0139484 41 | 101.25 -0.747262 0.011693 42 | 101.75 -0.703149 0.0123407 43 | 102.25 -0.666724 0.0121805 44 | 102.75 -0.634078 0.0108259 45 | 103.25 -0.601449 0.00951885 46 | 103.75 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0.00175906 77 | 119.25 -0.150429 0.00182132 78 | 119.75 -0.14491 0.00158856 79 | 120.25 -0.139959 0.00174239 80 | 120.75 -0.135126 0.00153249 81 | 121.25 -0.130135 0.00162022 82 | 121.75 -0.125422 0.00145594 83 | 122.25 -0.121816 0.00135984 84 | 122.75 -0.117071 0.00120694 85 | 123.25 -0.11362 0.00117528 86 | 123.75 -0.109255 0.000919883 87 | 124.25 -0.106011 0.00101685 88 | 124.75 -0.102305 0.0010781 89 | 125.25 -0.0990123 0.000952689 90 | 125.75 -0.0956942 0.000907185 91 | 126.25 -0.0924573 0.000898419 92 | 126.75 -0.0897421 0.000919565 93 | 127.25 -0.0867191 0.000900878 94 | 127.75 -0.0841574 0.000667547 95 | 128.25 -0.0814011 0.000787304 96 | 128.75 -0.078605 0.000835258 97 | 129.25 -0.0762297 0.000741244 98 | 129.75 -0.0739735 0.000609401 99 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/full/U_2nm-8nm.txt: -------------------------------------------------------------------------------- 1 | 101.5 -41.8179 3.02137 2 | 102.1 -36.3034 2.65307 3 | 102.7 -28.868 3.16837 4 | 103.3 -22.2411 1.66203 5 | 103.9 -18.1678 1.57478 6 | 104.5 -15.0182 1.09567 7 | 105.1 -12.5874 0.870654 8 | 105.7 -10.3246 0.494322 9 | 106.3 -9.10732 0.577058 10 | 106.9 -7.69626 0.313881 11 | 107.5 -6.81834 0.293313 12 | 108.1 -6.02594 0.269627 13 | 108.7 -5.2479 0.181374 14 | 109.3 -4.63129 0.184397 15 | 109.9 -4.19758 0.127487 16 | 110.5 -3.77054 0.142393 17 | 111.1 -3.41432 0.106808 18 | 111.7 -3.04933 0.0918256 19 | 112.3 -2.80951 0.0946354 20 | 112.9 -2.5595 0.0752819 21 | 113.5 -2.31838 0.0611013 22 | 114.1 -2.13329 0.058827 23 | 114.7 -1.9633 0.0667349 24 | 115.3 -1.82285 0.0510316 25 | 115.9 -1.67344 0.043474 26 | 116.5 -1.55864 0.0376955 27 | 117.1 -1.43344 0.0332881 28 | 117.7 -1.33568 0.0329345 29 | 118.3 -1.24354 0.0264177 30 | 118.9 -1.16775 0.0237227 31 | 119.5 -1.08271 0.0206592 32 | 120.1 -1.00999 0.01949 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0.00635752 56 | 99.25 -0.437617 0.00467585 57 | 99.75 -0.417488 0.00538982 58 | 100.25 -0.398856 0.00630799 59 | 100.75 -0.38044 0.00529622 60 | 101.25 -0.366937 0.00382398 61 | 101.75 -0.351022 0.00412199 62 | 102.25 -0.3375 0.00462258 63 | 102.75 -0.323455 0.00370332 64 | 103.25 -0.309903 0.00377224 65 | 103.75 -0.297564 0.00365195 66 | 104.25 -0.285897 0.0034668 67 | 104.75 -0.274423 0.00352226 68 | 105.25 -0.26352 0.00357114 69 | 105.75 -0.253789 0.00287742 70 | 106.25 -0.244434 0.00305255 71 | 106.75 -0.234663 0.00325537 72 | 107.25 -0.226947 0.00294272 73 | 107.75 -0.217713 0.00237781 74 | 108.25 -0.209875 0.00253343 75 | 108.75 -0.202178 0.00203723 76 | 109.25 -0.194897 0.00213276 77 | 109.75 -0.187529 0.0022544 78 | 110.25 -0.181188 0.00203668 79 | 110.75 -0.174883 0.0022447 80 | 111.25 -0.168895 0.00199458 81 | 111.75 -0.162609 0.00164153 82 | 112.25 -0.157039 0.00193791 83 | 112.75 -0.151833 0.00149113 84 | 113.25 -0.146258 0.00158503 85 | 113.75 -0.141432 0.00179949 86 | 114.25 -0.137068 0.00153904 87 | 114.75 -0.133 0.00143167 88 | 115.25 -0.128072 0.00136183 89 | 115.75 -0.124458 0.00130614 90 | 116.25 -0.119634 0.00109513 91 | 116.75 -0.116158 0.00126642 92 | 117.25 -0.112377 0.00112008 93 | 117.75 -0.108795 0.00107608 94 | 118.25 -0.105102 0.0011055 95 | 118.75 -0.102259 0.000887192 96 | 119.25 -0.0989288 0.000925919 97 | 119.75 -0.095724 0.00086182 98 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/full/U_3nm-6nm.txt: -------------------------------------------------------------------------------- 1 | 91.5 -54.6187 3.5242 2 | 92.1 -43.8162 4.0855 3 | 92.7 -35.9978 1.93239 4 | 93.3 -28.7634 2.03061 5 | 93.9 -24.1341 1.45611 6 | 94.5 -19.8226 1.22046 7 | 95.1 -16.7174 1.04785 8 | 95.7 -14.0909 0.791776 9 | 96.3 -12.2003 0.637427 10 | 96.9 -10.6866 0.457677 11 | 97.5 -9.34297 0.355358 12 | 98.1 -8.42198 0.328236 13 | 98.7 -7.45562 0.280062 14 | 99.3 -6.69891 0.265468 15 | 99.9 -5.97057 0.229781 16 | 100.5 -5.38376 0.157357 17 | 101.1 -4.93997 0.162605 18 | 101.7 -4.45103 0.147127 19 | 102.3 -4.06358 0.121952 20 | 102.9 -3.72982 0.117507 21 | 103.5 -3.4237 0.101867 22 | 104.1 -3.15085 0.0807907 23 | 104.7 -2.91155 0.0700878 24 | 105.3 -2.68839 0.0683712 25 | 105.9 -2.49739 0.05248 26 | 106.5 -2.33003 0.053894 27 | 107.1 -2.16346 0.0477612 28 | 107.7 -2.02057 0.0422359 29 | 108.3 -1.88413 0.0386894 30 | 108.9 -1.77055 0.0357357 31 | 109.5 -1.64561 0.0296009 32 | 110.1 -1.54454 0.028311 33 | 110.7 -1.45338 0.0297897 34 | 111.3 -1.36635 0.0282766 35 | 111.9 -1.27988 0.0214148 36 | 112.5 -1.20963 0.0189144 37 | 113.1 -1.14547 0.0224492 38 | 113.7 -1.07931 0.0190321 39 | 114.3 -1.01255 0.0181836 40 | 114.9 -0.966292 0.0164799 41 | 115.5 -0.910209 0.0153094 42 | 116.1 -0.861831 0.0131305 43 | 116.7 -0.821549 0.0150968 44 | 117.3 -0.778455 0.0123446 45 | 117.9 -0.733703 0.0115949 46 | 118.5 -0.702475 0.00974115 47 | 119.1 -0.665876 0.0107341 48 | 119.7 -0.632926 0.00987439 49 | 120.3 -0.604065 0.00851985 50 | 120.9 -0.577517 0.00934608 51 | 121.5 -0.547119 0.00806536 52 | 122.1 -0.523528 0.00764439 53 | 122.7 -0.50139 0.00769405 54 | 123.3 -0.478994 0.00685548 55 | 123.9 -0.455363 0.00682057 56 | 124.5 -0.43621 0.00579627 57 | 125.1 -0.416514 0.00580106 58 | 125.7 -0.398773 0.00471832 59 | 126.3 -0.382747 0.00464855 60 | 126.9 -0.365658 0.00402324 61 | 127.5 -0.351604 0.00489995 62 | 128.1 -0.336546 0.00471584 63 | 128.7 -0.323973 0.00536747 64 | 129.3 -0.309859 0.00340467 65 | 129.9 -0.29724 0.00355709 66 | 130.5 -0.285513 0.00289893 67 | 131.1 -0.274606 0.00321003 68 | 131.7 -0.263792 0.00304618 69 | 132.3 -0.254561 0.00323789 70 | 132.9 -0.243101 0.00290517 71 | 133.5 -0.235459 0.00261359 72 | 134.1 -0.226597 0.00204302 73 | 134.7 -0.217928 0.00273073 74 | 135.3 -0.20924 0.00200413 75 | 135.9 -0.202777 0.00207272 76 | 136.5 -0.195009 0.00194113 77 | 137.1 -0.187875 0.0020433 78 | 137.7 -0.181431 0.00188943 79 | 138.3 -0.175025 0.00207732 80 | 138.9 -0.168482 0.0015792 81 | 139.5 -0.16259 0.00172445 82 | 140.1 -0.157036 0.0016904 83 | 140.7 -0.151642 0.00151447 84 | 141.3 -0.146584 0.0013541 85 | 141.9 -0.141751 0.00159777 86 | 142.5 -0.136726 0.00154912 87 | 143.1 -0.132142 0.00139786 88 | 143.7 -0.128512 0.00118761 89 | 144.3 -0.12358 0.00126545 90 | 144.9 -0.119948 0.00117136 91 | 145.5 -0.116067 0.00123074 92 | 146.1 -0.11196 0.00125543 93 | 146.7 -0.108775 0.00102812 94 | 147.3 -0.105172 0.000967967 95 | 147.9 -0.101866 0.000820672 96 | 148.5 -0.0987697 0.000883578 97 | 149.1 -0.0956309 0.00074992 98 | 149.7 -0.0928449 0.000817746 99 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/full/U_3nm-8nm.txt: -------------------------------------------------------------------------------- 1 | 111.5 -63.1267 1.29347 2 | 112.1 -50.7951 4.3181 3 | 112.7 -41.9566 3.23805 4 | 113.3 -34.1996 3.08065 5 | 113.9 -27.5015 1.95917 6 | 114.5 -22.7526 1.26693 7 | 115.1 -19.414 1.14016 8 | 115.7 -16.4392 0.779979 9 | 116.3 -14.2897 0.718349 10 | 116.9 -12.301 0.621833 11 | 117.5 -10.8909 0.440617 12 | 118.1 -9.69838 0.373954 13 | 118.7 -8.68128 0.332826 14 | 119.3 -7.66976 0.25752 15 | 119.9 -6.98938 0.236812 16 | 120.5 -6.35483 0.232165 17 | 121.1 -5.77867 0.164911 18 | 121.7 -5.27546 0.157271 19 | 122.3 -4.80221 0.138006 20 | 122.9 -4.44362 0.146014 21 | 123.5 -4.09386 0.10621 22 | 124.1 -3.75052 0.101445 23 | 124.7 -3.47323 0.0785652 24 | 125.3 -3.22536 0.0723935 25 | 125.9 -3.00068 0.0691541 26 | 126.5 -2.7989 0.0630422 27 | 127.1 -2.61721 0.0611499 28 | 127.7 -2.43642 0.0500896 29 | 128.3 -2.28345 0.0437542 30 | 128.9 -2.14691 0.0456906 31 | 129.5 -2.0173 0.0407659 32 | 130.1 -1.89154 0.0305448 33 | 130.7 -1.78612 0.0386881 34 | 131.3 -1.68342 0.0330242 35 | 131.9 -1.58349 0.0310653 36 | 132.5 -1.50252 0.0244852 37 | 133.1 -1.4138 0.0237822 38 | 133.7 -1.33832 0.0239633 39 | 134.3 -1.27002 0.0186492 40 | 134.9 -1.19845 0.018108 41 | 135.5 -1.14177 0.0190037 42 | 136.1 -1.0805 0.0157772 43 | 136.7 -1.03471 0.016659 44 | 137.3 -0.978991 0.0178481 45 | 137.9 -0.93053 0.0128461 46 | 138.5 -0.881763 0.0124991 47 | 139.1 -0.843072 0.0125405 48 | 139.7 -0.803433 0.0115975 49 | 140.3 -0.768634 0.0115305 50 | 140.9 -0.733817 0.012416 51 | 141.5 -0.703317 0.00903421 52 | 142.1 -0.667967 0.00834107 53 | 142.7 -0.642056 0.00747329 54 | 143.3 -0.615646 0.00703066 55 | 143.9 -0.588003 0.00855114 56 | 144.5 -0.563769 0.00653338 57 | 145.1 -0.538314 0.00683968 58 | 145.7 -0.517975 0.00770395 59 | 146.3 -0.497481 0.00604115 60 | 146.9 -0.475535 0.00588882 61 | 147.5 -0.456949 0.00546328 62 | 148.1 -0.439874 0.00582731 63 | 148.7 -0.423293 0.00552263 64 | 149.3 -0.406223 0.00465774 65 | 149.9 -0.3902 0.00401432 66 | 150.5 -0.377005 0.0043652 67 | 151.1 -0.361513 0.0042621 68 | 151.7 -0.348645 0.00458404 69 | 152.3 -0.335389 0.0036767 70 | 152.9 -0.324072 0.00376616 71 | 153.5 -0.312021 0.00382025 72 | 154.1 -0.300676 0.00360422 73 | 154.7 -0.290591 0.00318755 74 | 155.3 -0.280101 0.00304859 75 | 155.9 -0.269759 0.0029526 76 | 156.5 -0.260145 0.00260995 77 | 157.1 -0.251585 0.00252166 78 | 157.7 -0.243549 0.00234598 79 | 158.3 -0.234821 0.00244171 80 | 158.9 -0.22696 0.00232035 81 | 159.5 -0.219581 0.00233576 82 | 160.1 -0.21296 0.00193737 83 | 160.7 -0.204848 0.00168035 84 | 161.3 -0.198799 0.0019611 85 | 161.9 -0.19269 0.00184372 86 | 162.5 -0.186301 0.00164745 87 | 163.1 -0.180625 0.00151854 88 | 163.7 -0.174503 0.00158745 89 | 164.3 -0.169138 0.00153267 90 | 164.9 -0.163704 0.00148901 91 | 165.5 -0.159004 0.00147288 92 | 166.1 -0.154525 0.00151412 93 | 166.7 -0.149629 0.0012323 94 | 167.3 -0.144983 0.00134865 95 | 167.9 -0.140496 0.00142687 96 | 168.5 -0.136768 0.00123122 97 | 169.1 -0.132419 0.00103404 98 | 169.7 -0.128896 0.00128976 99 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/full/U_4nm-6nm.txt: -------------------------------------------------------------------------------- 1 | 101.5 -67.5217 2.3827 2 | 102.1 -58.5224 4.29225 3 | 102.7 -47.923 3.58412 4 | 103.3 -37.9813 2.18855 5 | 103.9 -31.361 2.1147 6 | 104.5 -26.1299 1.29477 7 | 105.1 -22.1253 1.10621 8 | 105.7 -18.7926 0.90301 9 | 106.3 -16.2948 0.651738 10 | 106.9 -14.452 0.721244 11 | 107.5 -12.7076 0.567425 12 | 108.1 -11.1637 0.4245 13 | 108.7 -10.1294 0.303659 14 | 109.3 -8.99629 0.260183 15 | 109.9 -8.14982 0.264914 16 | 110.5 -7.40885 0.226872 17 | 111.1 -6.74373 0.195286 18 | 111.7 -6.19199 0.162419 19 | 112.3 -5.65428 0.157778 20 | 112.9 -5.19217 0.130565 21 | 113.5 -4.81229 0.116603 22 | 114.1 -4.43005 0.104332 23 | 114.7 -4.07891 0.0943742 24 | 115.3 -3.79179 0.0824621 25 | 115.9 -3.54579 0.0924212 26 | 116.5 -3.30059 0.0796501 27 | 117.1 -3.0926 0.0663348 28 | 117.7 -2.8806 0.0568454 29 | 118.3 -2.69924 0.0473635 30 | 118.9 -2.52722 0.0412802 31 | 119.5 -2.37107 0.0408176 32 | 120.1 -2.23512 0.0395873 33 | 120.7 -2.11199 0.0364262 34 | 121.3 -1.98755 0.0328427 35 | 121.9 -1.88028 0.0344653 36 | 122.5 -1.78049 0.0272924 37 | 123.1 -1.6817 0.0253844 38 | 123.7 -1.59139 0.0244329 39 | 124.3 -1.51096 0.0243681 40 | 124.9 -1.42721 0.0198196 41 | 125.5 -1.35634 0.0208098 42 | 126.1 -1.28675 0.0178155 43 | 126.7 -1.22608 0.0166937 44 | 127.3 -1.16689 0.0176287 45 | 127.9 -1.11334 0.0191824 46 | 128.5 -1.05733 0.0141206 47 | 129.1 -1.00714 0.0154373 48 | 129.7 -0.963581 0.0157059 49 | 130.3 -0.918626 0.0134203 50 | 130.9 -0.878624 0.0108361 51 | 131.5 -0.838485 0.0117627 52 | 132.1 -0.804591 0.00996344 53 | 132.7 -0.769815 0.0103729 54 | 133.3 -0.733632 0.00895512 55 | 133.9 -0.704468 0.00771225 56 | 134.5 -0.672746 0.00927341 57 | 135.1 -0.647206 0.00800638 58 | 135.7 -0.620905 0.0079567 59 | 136.3 -0.594949 0.00711844 60 | 136.9 -0.572046 0.00638859 61 | 137.5 -0.54926 0.00533562 62 | 138.1 -0.525416 0.00638876 63 | 138.7 -0.505408 0.0052046 64 | 139.3 -0.487582 0.00560899 65 | 139.9 -0.469131 0.00560579 66 | 140.5 -0.451276 0.00597036 67 | 141.1 -0.434734 0.00592535 68 | 141.7 -0.418254 0.00505058 69 | 142.3 -0.402549 0.0040039 70 | 142.9 -0.388047 0.00458878 71 | 143.5 -0.373959 0.00353978 72 | 144.1 -0.361212 0.00355709 73 | 144.7 -0.347817 0.00402267 74 | 145.3 -0.335916 0.00298815 75 | 145.9 -0.325113 0.00324422 76 | 146.5 -0.312925 0.00316012 77 | 147.1 -0.302661 0.00325253 78 | 147.7 -0.292632 0.00288525 79 | 148.3 -0.282867 0.00288993 80 | 148.9 -0.273397 0.00275206 81 | 149.5 -0.263875 0.00259779 82 | 150.1 -0.255836 0.00278641 83 | 150.7 -0.247604 0.00244796 84 | 151.3 -0.239385 0.00243078 85 | 151.9 -0.230957 0.00211601 86 | 152.5 -0.224257 0.00225039 87 | 153.1 -0.217768 0.002148 88 | 153.7 -0.21145 0.00188827 89 | 154.3 -0.203484 0.00191926 90 | 154.9 -0.197044 0.00200366 91 | 155.5 -0.191241 0.00164902 92 | 156.1 -0.185831 0.0017435 93 | 156.7 -0.178971 0.00112671 94 | 157.3 -0.174536 0.00132837 95 | 157.9 -0.169263 0.00146457 96 | 158.5 -0.164308 0.00153844 97 | 159.1 -0.159112 0.00126919 98 | 159.7 -0.154834 0.00141078 99 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/full/U_4nm-8nm.txt: -------------------------------------------------------------------------------- 1 | 122.1 -68.7116 6.68961 2 | 122.7 -54.3612 5.00367 3 | 123.3 -45.3698 2.88602 4 | 123.9 -36.4611 2.50796 5 | 124.5 -30.9661 2.00575 6 | 125.1 -25.8423 1.38623 7 | 125.7 -21.85 1.32914 8 | 126.3 -19.2049 0.930738 9 | 126.9 -16.9911 0.829879 10 | 127.5 -14.8797 0.562097 11 | 128.1 -13.1861 0.41225 12 | 128.7 -11.9403 0.434947 13 | 129.3 -10.7345 0.374069 14 | 129.9 -9.76967 0.257614 15 | 130.5 -8.80245 0.288322 16 | 131.1 -8.08289 0.272689 17 | 131.7 -7.37512 0.204959 18 | 132.3 -6.81158 0.189468 19 | 132.9 -6.28374 0.155046 20 | 133.5 -5.81078 0.155599 21 | 134.1 -5.35276 0.119376 22 | 134.7 -4.98662 0.114461 23 | 135.3 -4.68668 0.121084 24 | 135.9 -4.37106 0.088613 25 | 136.5 -4.07025 0.0850688 26 | 137.1 -3.81648 0.098302 27 | 137.7 -3.57319 0.0706453 28 | 138.3 -3.34344 0.0580716 29 | 138.9 -3.14917 0.0490374 30 | 139.5 -2.95002 0.0563586 31 | 140.1 -2.79707 0.0611048 32 | 140.7 -2.63586 0.0427001 33 | 141.3 -2.50214 0.0450744 34 | 141.9 -2.36065 0.0344341 35 | 142.5 -2.22479 0.0392441 36 | 143.1 -2.11938 0.0381954 37 | 143.7 -2.02188 0.0353122 38 | 144.3 -1.9134 0.036054 39 | 144.9 -1.81529 0.0295432 40 | 145.5 -1.72718 0.0288308 41 | 146.1 -1.63996 0.0271033 42 | 146.7 -1.56203 0.0226518 43 | 147.3 -1.49255 0.0191932 44 | 147.9 -1.4331 0.0211939 45 | 148.5 -1.36373 0.0181546 46 | 149.1 -1.30025 0.0184955 47 | 149.7 -1.24339 0.0164321 48 | 150.3 -1.18589 0.0152799 49 | 150.9 -1.13962 0.0175706 50 | 151.5 -1.08924 0.0137767 51 | 152.1 -1.04506 0.0136948 52 | 152.7 -1.00165 0.0126869 53 | 153.3 -0.96453 0.014133 54 | 153.9 -0.924632 0.0113739 55 | 154.5 -0.887516 0.0105131 56 | 155.1 -0.851657 0.011627 57 | 155.7 -0.817586 0.00753454 58 | 156.3 -0.785639 0.00915411 59 | 156.9 -0.757759 0.00908292 60 | 157.5 -0.72735 0.00880801 61 | 158.1 -0.701011 0.00833764 62 | 158.7 -0.672451 0.00748777 63 | 159.3 -0.648395 0.00727835 64 | 159.9 -0.625459 0.00694381 65 | 160.5 -0.604424 0.00650099 66 | 161.1 -0.583394 0.00646957 67 | 161.7 -0.563415 0.00572952 68 | 162.3 -0.541995 0.00586996 69 | 162.9 -0.522973 0.00581039 70 | 163.5 -0.50532 0.00546559 71 | 164.1 -0.488211 0.00580984 72 | 164.7 -0.47237 0.00526325 73 | 165.3 -0.456611 0.00455536 74 | 165.9 -0.440898 0.0042108 75 | 166.5 -0.424978 0.00441225 76 | 167.1 -0.412042 0.00375996 77 | 167.7 -0.398621 0.00389831 78 | 168.3 -0.386435 0.00343577 79 | 168.9 -0.374581 0.00359352 80 | 169.5 -0.36307 0.00345709 81 | 170.1 -0.351083 0.00369318 82 | 170.7 -0.340483 0.00302183 83 | 171.3 -0.330455 0.00296022 84 | 171.9 -0.319634 0.00287012 85 | 172.5 -0.30947 0.00270981 86 | 173.1 -0.300927 0.00243751 87 | 173.7 -0.292096 0.00274156 88 | 174.3 -0.282839 0.00261275 89 | 174.9 -0.274961 0.00250657 90 | 175.5 -0.266786 0.00231036 91 | 176.1 -0.259155 0.00207211 92 | 176.7 -0.251248 0.00223032 93 | 177.3 -0.243983 0.0019659 94 | 177.9 -0.237061 0.00209848 95 | 178.5 -0.230479 0.00178173 96 | 179.1 -0.224104 0.00158433 97 | 179.7 -0.218225 0.00168251 98 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/full/U_6nm-8nm.txt: -------------------------------------------------------------------------------- 1 | 141.75 -101.766 4.88927 2 | 142.45 -80.4196 7.68996 3 | 143.15 -62.9322 5.59875 4 | 143.85 -50.9678 4.07236 5 | 144.55 -41.9341 2.7233 6 | 145.25 -34.2539 1.91262 7 | 145.95 -29.1858 1.44067 8 | 146.65 -24.8732 1.14419 9 | 147.35 -21.735 0.646411 10 | 148.05 -19.1064 0.731903 11 | 148.75 -17.2505 0.578214 12 | 149.45 -15.3362 0.561145 13 | 150.15 -13.7083 0.436069 14 | 150.85 -12.352 0.367696 15 | 151.55 -11.3054 0.34574 16 | 152.25 -10.1801 0.262781 17 | 152.95 -9.38494 0.2101 18 | 153.65 -8.58393 0.257577 19 | 154.35 -7.88697 0.192513 20 | 155.05 -7.24264 0.183907 21 | 155.75 -6.73825 0.157696 22 | 156.45 -6.28594 0.134944 23 | 157.15 -5.79483 0.142651 24 | 157.85 -5.4593 0.109252 25 | 158.55 -5.09687 0.105555 26 | 159.25 -4.76078 0.0895952 27 | 159.95 -4.4517 0.0821751 28 | 160.65 -4.18523 0.0835654 29 | 161.35 -3.95574 0.0757468 30 | 162.05 -3.70823 0.0623293 31 | 162.75 -3.51039 0.0627118 32 | 163.45 -3.30244 0.0546953 33 | 164.15 -3.1198 0.0579545 34 | 164.85 -2.95826 0.0481453 35 | 165.55 -2.80524 0.0458107 36 | 166.25 -2.67572 0.0410957 37 | 166.95 -2.51533 0.0358767 38 | 167.65 -2.40237 0.0409449 39 | 168.35 -2.28422 0.0371218 40 | 169.05 -2.16644 0.0288645 41 | 169.75 -2.07641 0.0324382 42 | 170.45 -1.96906 0.0282616 43 | 171.15 -1.87725 0.0260124 44 | 171.85 -1.78458 0.023307 45 | 172.55 -1.71569 0.0236298 46 | 173.25 -1.64022 0.0203228 47 | 173.95 -1.57137 0.0212855 48 | 174.65 -1.49631 0.0187536 49 | 175.35 -1.43637 0.0166552 50 | 176.05 -1.37405 0.0174292 51 | 176.75 -1.31845 0.017447 52 | 177.45 -1.26763 0.0173411 53 | 178.15 -1.21473 0.0141125 54 | 178.85 -1.16437 0.0131805 55 | 179.55 -1.1197 0.0124084 56 | 180.25 -1.07333 0.0140211 57 | 180.95 -1.03598 0.0122249 58 | 181.65 -0.998793 0.0109136 59 | 182.35 -0.954974 0.0105849 60 | 183.05 -0.920176 0.00916176 61 | 183.75 -0.886923 0.00935824 62 | 184.45 -0.851371 0.0080572 63 | 185.15 -0.822616 0.00942548 64 | 185.85 -0.795164 0.00852039 65 | 186.55 -0.766239 0.00868641 66 | 187.25 -0.738777 0.008713 67 | 187.95 -0.713689 0.00769706 68 | 188.65 -0.68723 0.00709135 69 | 189.35 -0.665237 0.00612227 70 | 190.05 -0.642925 0.00684505 71 | 190.75 -0.62003 0.00661384 72 | 191.45 -0.601652 0.00526824 73 | 192.15 -0.580263 0.00613708 74 | 192.85 -0.562965 0.00558121 75 | 193.55 -0.5447 0.00407792 76 | 194.25 -0.525729 0.00456551 77 | 194.95 -0.508436 0.00449745 78 | 195.65 -0.491766 0.00432614 79 | 196.35 -0.477263 0.00460184 80 | 197.05 -0.461489 0.00489547 81 | 197.75 -0.448573 0.00432092 82 | 198.45 -0.434828 0.00381071 83 | 199.15 -0.42102 0.00393245 84 | 199.85 -0.40844 0.00346662 85 | 200.55 -0.3956 0.00386751 86 | 201.25 -0.384074 0.00343258 87 | 201.95 -0.373014 0.00349886 88 | 202.65 -0.361955 0.0029451 89 | 203.35 -0.351298 0.00286469 90 | 204.05 -0.340703 0.00302716 91 | 204.75 -0.331394 0.00308499 92 | 205.45 -0.321692 0.00252343 93 | 206.15 -0.312856 0.00249568 94 | 206.85 -0.305321 0.00257522 95 | 207.55 -0.296611 0.00257584 96 | 208.25 -0.287556 0.00225736 97 | 208.95 -0.279023 0.00249797 98 | 209.65 -0.272477 0.0017488 99 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/truncated/README.md: -------------------------------------------------------------------------------- 1 | This target data differs from the "full" target data, as values for nanoparticle-nanoparticle separations below d + 0.40323nm x 0.8 are excluded, where d is the nanoparticle diameter and 0.40323 is the diameter of silica. 2 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/truncated/U_2nm-3nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 53.25 -15.0996 1.60712 2 | 53.75 -12.2416 1.08963 3 | 54.25 -10.1375 0.796128 4 | 54.75 -8.2402 0.598099 5 | 55.25 -7.24786 0.552601 6 | 55.75 -6.19658 0.293926 7 | 56.25 -5.38012 0.323012 8 | 56.75 -4.66213 0.297807 9 | 57.25 -4.15542 0.229691 10 | 57.75 -3.68035 0.202844 11 | 58.25 -3.27459 0.1783 12 | 58.75 -2.92256 0.161945 13 | 59.25 -2.62598 0.120356 14 | 59.75 -2.36002 0.105938 15 | 60.25 -2.12791 0.0983944 16 | 60.75 -1.93409 0.0831198 17 | 61.25 -1.77796 0.074001 18 | 61.75 -1.60201 0.0578292 19 | 62.25 -1.4703 0.0595466 20 | 62.75 -1.34244 0.048426 21 | 63.25 -1.2339 0.0378842 22 | 63.75 -1.13369 0.0360263 23 | 64.25 -1.04444 0.0324139 24 | 64.75 -0.968023 0.0271689 25 | 65.25 -0.900809 0.0289948 26 | 65.75 -0.830066 0.0296577 27 | 66.25 -0.777575 0.0207236 28 | 66.75 -0.715958 0.0191881 29 | 67.25 -0.670093 0.0175753 30 | 67.75 -0.619589 0.0147094 31 | 68.25 -0.579992 0.0162822 32 | 68.75 -0.545483 0.0136497 33 | 69.25 -0.508413 0.0106441 34 | 69.75 -0.474964 0.0107433 35 | 70.25 -0.448234 0.0118793 36 | 70.75 -0.41827 0.00866045 37 | 71.25 -0.394167 0.0109507 38 | 71.75 -0.372777 0.00948131 39 | 72.25 -0.350384 0.00823363 40 | 72.75 -0.330029 0.00652243 41 | 73.25 -0.309244 0.00743224 42 | 73.75 -0.292931 0.00486825 43 | 74.25 -0.275917 0.0056545 44 | 74.75 -0.259376 0.00435369 45 | 75.25 -0.24832 0.00460834 46 | 75.75 -0.233425 0.00398854 47 | 76.25 -0.222529 0.00384328 48 | 76.75 -0.211376 0.00403603 49 | 77.25 -0.200439 0.00346304 50 | 77.75 -0.189083 0.00411986 51 | 78.25 -0.179952 0.00347873 52 | 78.75 -0.171895 0.00247743 53 | 79.25 -0.163142 0.00267944 54 | 79.75 -0.153971 0.0025573 55 | 80.25 -0.147014 0.00261228 56 | 80.75 -0.140954 0.00203143 57 | 81.25 -0.134137 0.00211798 58 | 81.75 -0.128006 0.00165201 59 | 82.25 -0.121282 0.00154117 60 | 82.75 -0.116099 0.00174582 61 | 83.25 -0.110682 0.00176086 62 | 83.75 -0.106299 0.00179404 63 | 84.25 -0.100981 0.00169476 64 | 84.75 -0.0968572 0.00156907 65 | 85.25 -0.0926655 0.00115621 66 | 85.75 -0.0886138 0.00129281 67 | 86.25 -0.084982 0.00122795 68 | 86.75 -0.0807002 0.00122243 69 | 87.25 -0.0777151 0.000957785 70 | 87.75 -0.0745552 0.00105074 71 | 88.25 -0.071479 0.00096792 72 | 88.75 -0.0682353 0.000949658 73 | 89.25 -0.0656844 0.000880381 74 | 89.75 -0.0629747 0.000937684 75 | 90.25 -0.060496 0.000695308 76 | 90.75 -0.0580993 0.000730826 77 | 91.25 -0.0560387 0.000694592 78 | 91.75 -0.053543 0.000623251 79 | 92.25 -0.0515988 0.000661029 80 | 92.75 -0.0495934 0.000721136 81 | 93.25 -0.0477977 0.000468497 82 | 93.75 -0.045666 0.000588012 83 | 94.25 -0.0441063 0.000487862 84 | 94.75 -0.0425754 0.000442745 85 | 95.25 -0.041122 0.000436194 86 | 95.75 -0.0394499 0.000531907 87 | 96.25 -0.0381233 0.000417324 88 | 96.75 -0.0369569 0.000412604 89 | 97.25 -0.035432 0.000393437 90 | 97.75 -0.0342061 0.000403513 91 | 98.25 -0.0329074 0.000299024 92 | 98.75 -0.0318167 0.000319438 93 | 99.25 -0.0307323 0.000287938 94 | 99.75 -0.0295914 0.000316564 95 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/truncated/U_2nm-4nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 63.25 -18.2833 1.6554 2 | 63.75 -14.4892 0.994433 3 | 64.25 -12.001 0.770669 4 | 64.75 -10.2254 0.646205 5 | 65.25 -8.97095 0.674234 6 | 65.75 -7.63113 0.440094 7 | 66.25 -6.61451 0.370638 8 | 66.75 -5.83643 0.317094 9 | 67.25 -5.16283 0.266513 10 | 67.75 -4.55357 0.248808 11 | 68.25 -4.08313 0.170974 12 | 68.75 -3.63539 0.185084 13 | 69.25 -3.31278 0.116272 14 | 69.75 -3.02066 0.121857 15 | 70.25 -2.71134 0.0892472 16 | 70.75 -2.45482 0.0988125 17 | 71.25 -2.25561 0.0820303 18 | 71.75 -2.05621 0.064971 19 | 72.25 -1.88806 0.0672844 20 | 72.75 -1.7259 0.0556512 21 | 73.25 -1.60854 0.0469749 22 | 73.75 -1.47563 0.0382794 23 | 74.25 -1.37068 0.0342924 24 | 74.75 -1.27054 0.0330532 25 | 75.25 -1.17731 0.031383 26 | 75.75 -1.09663 0.0254802 27 | 76.25 -1.01572 0.0234824 28 | 76.75 -0.951532 0.0202252 29 | 77.25 -0.886406 0.0220312 30 | 77.75 -0.832229 0.017044 31 | 78.25 -0.776111 0.0183723 32 | 78.75 -0.72913 0.0151669 33 | 79.25 -0.68312 0.0155942 34 | 79.75 -0.642621 0.0146 35 | 80.25 -0.601222 0.0104639 36 | 80.75 -0.569593 0.0119022 37 | 81.25 -0.538052 0.0113757 38 | 81.75 -0.507001 0.0114165 39 | 82.25 -0.478369 0.00859941 40 | 82.75 -0.450661 0.00880511 41 | 83.25 -0.425879 0.00742135 42 | 83.75 -0.402231 0.00792097 43 | 84.25 -0.382271 0.00571585 44 | 84.75 -0.362274 0.00588917 45 | 85.25 -0.345269 0.00611537 46 | 85.75 -0.325715 0.00580136 47 | 86.25 -0.310495 0.00533631 48 | 86.75 -0.293695 0.00444203 49 | 87.25 -0.280801 0.00466137 50 | 87.75 -0.265239 0.00501851 51 | 88.25 -0.253958 0.0036853 52 | 88.75 -0.242779 0.00393512 53 | 89.25 -0.229784 0.00458047 54 | 89.75 -0.219728 0.003674 55 | 90.25 -0.209642 0.00306641 56 | 90.75 -0.20071 0.00319706 57 | 91.25 -0.191056 0.00288232 58 | 91.75 -0.182459 0.00292392 59 | 92.25 -0.174276 0.0027641 60 | 92.75 -0.167619 0.00257939 61 | 93.25 -0.159113 0.00195117 62 | 93.75 -0.152909 0.00201693 63 | 94.25 -0.147043 0.00232219 64 | 94.75 -0.140134 0.0017716 65 | 95.25 -0.135026 0.00176031 66 | 95.75 -0.129428 0.00158135 67 | 96.25 -0.124397 0.00136504 68 | 96.75 -0.118993 0.00155111 69 | 97.25 -0.113977 0.00158597 70 | 97.75 -0.109894 0.00138192 71 | 98.25 -0.104963 0.00136326 72 | 98.75 -0.100931 0.00142411 73 | 99.25 -0.0971379 0.00124703 74 | 99.75 -0.0932532 0.00124562 75 | 100.25 -0.0897662 0.00119918 76 | 100.75 -0.086973 0.00120566 77 | 101.25 -0.0831901 0.00088469 78 | 101.75 -0.0801603 0.000933886 79 | 102.25 -0.0773128 0.00100698 80 | 102.75 -0.0744621 0.000931902 81 | 103.25 -0.0718311 0.00083714 82 | 103.75 -0.069217 0.000816228 83 | 104.25 -0.0667629 0.000698148 84 | 104.75 -0.0641389 0.000725773 85 | 105.25 -0.0620051 0.000757131 86 | 105.75 -0.0598425 0.000685555 87 | 106.25 -0.0577209 0.0006213 88 | 106.75 -0.0558227 0.000641175 89 | 107.25 -0.0539831 0.000489245 90 | 107.75 -0.0521007 0.000578837 91 | 108.25 -0.0501787 0.000468155 92 | 108.75 -0.0486556 0.000509008 93 | 109.25 -0.0469916 0.00046985 94 | 109.75 -0.0454653 0.000453721 95 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/truncated/U_2nm-6nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 83.25 -21.01 1.72601 2 | 83.75 -17.1803 1.00063 3 | 84.25 -14.1902 0.805645 4 | 84.75 -12.0806 0.652516 5 | 85.25 -10.6992 0.699259 6 | 85.75 -9.30965 0.486822 7 | 86.25 -8.09602 0.389131 8 | 86.75 -7.13251 0.358881 9 | 87.25 -6.36824 0.320071 10 | 87.75 -5.66295 0.22496 11 | 88.25 -5.152 0.176839 12 | 88.75 -4.58017 0.174664 13 | 89.25 -4.14211 0.1572 14 | 89.75 -3.78626 0.120897 15 | 90.25 -3.43845 0.102917 16 | 90.75 -3.12881 0.100288 17 | 91.25 -2.86811 0.082728 18 | 91.75 -2.65135 0.0842084 19 | 92.25 -2.43866 0.0683253 20 | 92.75 -2.23697 0.0669361 21 | 93.25 -2.09124 0.0540085 22 | 93.75 -1.945 0.0472791 23 | 94.25 -1.79042 0.0472093 24 | 94.75 -1.66668 0.0358378 25 | 95.25 -1.56547 0.030772 26 | 95.75 -1.4468 0.0333028 27 | 96.25 -1.3717 0.0345653 28 | 96.75 -1.28266 0.0305473 29 | 97.25 -1.19278 0.0261912 30 | 97.75 -1.11722 0.0205232 31 | 98.25 -1.05338 0.0195812 32 | 98.75 -0.996025 0.0198243 33 | 99.25 -0.933733 0.0204069 34 | 99.75 -0.880576 0.0164414 35 | 100.25 -0.832285 0.0160332 36 | 100.75 -0.787407 0.0139484 37 | 101.25 -0.747262 0.011693 38 | 101.75 -0.703149 0.0123407 39 | 102.25 -0.666724 0.0121805 40 | 102.75 -0.634078 0.0108259 41 | 103.25 -0.601449 0.00951885 42 | 103.75 -0.571277 0.00996647 43 | 104.25 -0.542666 0.00795475 44 | 104.75 -0.516364 0.00806588 45 | 105.25 -0.487794 0.00656897 46 | 105.75 -0.465982 0.00683156 47 | 106.25 -0.447444 0.00668252 48 | 106.75 -0.42295 0.00537535 49 | 107.25 -0.403284 0.00631297 50 | 107.75 -0.383864 0.00559566 51 | 108.25 -0.369034 0.00570972 52 | 108.75 -0.352255 0.0050534 53 | 109.25 -0.336719 0.00489993 54 | 109.75 -0.321155 0.00411282 55 | 110.25 -0.307587 0.00434731 56 | 110.75 -0.295475 0.00412746 57 | 111.25 -0.282309 0.00401421 58 | 111.75 -0.271545 0.00366358 59 | 112.25 -0.260426 0.00330132 60 | 112.75 -0.249716 0.00389923 61 | 113.25 -0.239092 0.00344208 62 | 113.75 -0.230409 0.00299508 63 | 114.25 -0.220587 0.00227432 64 | 114.75 -0.212024 0.00253893 65 | 115.25 -0.20362 0.00286524 66 | 115.75 -0.19579 0.00232083 67 | 116.25 -0.188975 0.00210881 68 | 116.75 -0.181375 0.00240156 69 | 117.25 -0.174203 0.00183769 70 | 117.75 -0.16795 0.00179541 71 | 118.25 -0.161886 0.00160076 72 | 118.75 -0.155641 0.00175906 73 | 119.25 -0.150429 0.00182132 74 | 119.75 -0.14491 0.00158856 75 | 120.25 -0.139959 0.00174239 76 | 120.75 -0.135126 0.00153249 77 | 121.25 -0.130135 0.00162022 78 | 121.75 -0.125422 0.00145594 79 | 122.25 -0.121816 0.00135984 80 | 122.75 -0.117071 0.00120694 81 | 123.25 -0.11362 0.00117528 82 | 123.75 -0.109255 0.000919883 83 | 124.25 -0.106011 0.00101685 84 | 124.75 -0.102305 0.0010781 85 | 125.25 -0.0990123 0.000952689 86 | 125.75 -0.0956942 0.000907185 87 | 126.25 -0.0924573 0.000898419 88 | 126.75 -0.0897421 0.000919565 89 | 127.25 -0.0867191 0.000900878 90 | 127.75 -0.0841574 0.000667547 91 | 128.25 -0.0814011 0.000787304 92 | 128.75 -0.078605 0.000835258 93 | 129.25 -0.0762297 0.000741244 94 | 129.75 -0.0739735 0.000609401 95 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/truncated/U_2nm-8nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 103.3 -22.2411 1.66203 2 | 103.9 -18.1678 1.57478 3 | 104.5 -15.0182 1.09567 4 | 105.1 -12.5874 0.870654 5 | 105.7 -10.3246 0.494322 6 | 106.3 -9.10732 0.577058 7 | 106.9 -7.69626 0.313881 8 | 107.5 -6.81834 0.293313 9 | 108.1 -6.02594 0.269627 10 | 108.7 -5.2479 0.181374 11 | 109.3 -4.63129 0.184397 12 | 109.9 -4.19758 0.127487 13 | 110.5 -3.77054 0.142393 14 | 111.1 -3.41432 0.106808 15 | 111.7 -3.04933 0.0918256 16 | 112.3 -2.80951 0.0946354 17 | 112.9 -2.5595 0.0752819 18 | 113.5 -2.31838 0.0611013 19 | 114.1 -2.13329 0.058827 20 | 114.7 -1.9633 0.0667349 21 | 115.3 -1.82285 0.0510316 22 | 115.9 -1.67344 0.043474 23 | 116.5 -1.55864 0.0376955 24 | 117.1 -1.43344 0.0332881 25 | 117.7 -1.33568 0.0329345 26 | 118.3 -1.24354 0.0264177 27 | 118.9 -1.16775 0.0237227 28 | 119.5 -1.08271 0.0206592 29 | 120.1 -1.00999 0.01949 30 | 120.7 -0.946736 0.0219185 31 | 121.3 -0.888526 0.018712 32 | 121.9 -0.830435 0.0158692 33 | 122.5 -0.785575 0.0159563 34 | 123.1 -0.735576 0.0144369 35 | 123.7 -0.697748 0.0106273 36 | 124.3 -0.653821 0.0139069 37 | 124.9 -0.619668 0.0102404 38 | 125.5 -0.584638 0.0113967 39 | 126.1 -0.551667 0.00942925 40 | 126.7 -0.524291 0.00993929 41 | 127.3 -0.495856 0.00766528 42 | 127.9 -0.469264 0.00764884 43 | 128.5 -0.446989 0.00730051 44 | 129.1 -0.421632 0.00656612 45 | 129.7 -0.401131 0.00583198 46 | 130.3 -0.382489 0.00693727 47 | 130.9 -0.36506 0.00535988 48 | 131.5 -0.345005 0.00419845 49 | 132.1 -0.328262 0.00551101 50 | 132.7 -0.315289 0.00484744 51 | 133.3 -0.299621 0.00446135 52 | 133.9 -0.285314 0.0037915 53 | 134.5 -0.272117 0.00328802 54 | 135.1 -0.261637 0.00405455 55 | 135.7 -0.249345 0.00293253 56 | 136.3 -0.238371 0.00297374 57 | 136.9 -0.228068 0.00262232 58 | 137.5 -0.217964 0.00273307 59 | 138.1 -0.209409 0.00314007 60 | 138.7 -0.20173 0.00247025 61 | 139.3 -0.192212 0.00236287 62 | 139.9 -0.183891 0.0019979 63 | 140.5 -0.176104 0.00181672 64 | 141.1 -0.16977 0.00219236 65 | 141.7 -0.163234 0.00176254 66 | 142.3 -0.157238 0.00191891 67 | 142.9 -0.150475 0.00176786 68 | 143.5 -0.144256 0.00128155 69 | 144.1 -0.139742 0.00143226 70 | 144.7 -0.133943 0.00150681 71 | 145.3 -0.128859 0.00156754 72 | 145.9 -0.124158 0.00138696 73 | 146.5 -0.119547 0.00141667 74 | 147.1 -0.114964 0.00138523 75 | 147.7 -0.11097 0.00122233 76 | 148.3 -0.106843 0.00120778 77 | 148.9 -0.103253 0.00137549 78 | 149.5 -0.0996438 0.0010592 79 | 150.1 -0.0958394 0.00117235 80 | 150.7 -0.092638 0.000871025 81 | 151.3 -0.0896633 0.000895606 82 | 151.9 -0.0863429 0.000865504 83 | 152.5 -0.0836239 0.000770021 84 | 153.1 -0.080782 0.000793864 85 | 153.7 -0.0780428 0.00079601 86 | 154.3 -0.0753385 0.000717617 87 | 154.9 -0.0729484 0.000672949 88 | 155.5 -0.0703159 0.000709356 89 | 156.1 -0.0682776 0.00087893 90 | 156.7 -0.0663315 0.000634143 91 | 157.3 -0.0641738 0.000584415 92 | 157.9 -0.0619275 0.000618222 93 | 158.5 -0.0597959 0.000478689 94 | 159.1 -0.0581034 0.000499806 95 | 159.7 -0.0563526 0.000533545 96 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/truncated/U_3nm-4nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 73.25 -24.1998 2.09409 2 | 73.75 -20.0888 1.34502 3 | 74.25 -17.1978 1.11873 4 | 74.75 -14.7879 0.946444 5 | 75.25 -12.8646 0.801757 6 | 75.75 -11.1783 0.628469 7 | 76.25 -9.73246 0.417907 8 | 76.75 -8.70156 0.383631 9 | 77.25 -7.75246 0.386927 10 | 77.75 -6.94697 0.223391 11 | 78.25 -6.28325 0.232555 12 | 78.75 -5.62952 0.252993 13 | 79.25 -5.12112 0.176351 14 | 79.75 -4.66072 0.141647 15 | 80.25 -4.26925 0.132045 16 | 80.75 -3.90434 0.126478 17 | 81.25 -3.61331 0.0859617 18 | 81.75 -3.30267 0.0910177 19 | 82.25 -3.05534 0.085399 20 | 82.75 -2.83399 0.0654181 21 | 83.25 -2.63676 0.0696302 22 | 83.75 -2.42945 0.0534415 23 | 84.25 -2.25864 0.0589718 24 | 84.75 -2.10699 0.0527763 25 | 85.25 -1.97887 0.0465134 26 | 85.75 -1.85474 0.040048 27 | 86.25 -1.72977 0.0417267 28 | 86.75 -1.62071 0.03352 29 | 87.25 -1.51834 0.0358065 30 | 87.75 -1.42837 0.0309161 31 | 88.25 -1.34795 0.0286445 32 | 88.75 -1.27579 0.0277091 33 | 89.25 -1.19722 0.0237488 34 | 89.75 -1.12486 0.0222782 35 | 90.25 -1.06793 0.0192867 36 | 90.75 -1.01237 0.0184614 37 | 91.25 -0.956924 0.017792 38 | 91.75 -0.903036 0.0149698 39 | 92.25 -0.851582 0.0145689 40 | 92.75 -0.811917 0.01333 41 | 93.25 -0.768084 0.0110372 42 | 93.75 -0.731332 0.0121734 43 | 94.25 -0.695326 0.00984991 44 | 94.75 -0.66309 0.0115151 45 | 95.25 -0.630433 0.00951538 46 | 95.75 -0.601182 0.00981176 47 | 96.25 -0.577948 0.00800415 48 | 96.75 -0.549584 0.00778792 49 | 97.25 -0.521331 0.00831691 50 | 97.75 -0.499088 0.00748472 51 | 98.25 -0.475238 0.00770642 52 | 98.75 -0.456296 0.00635752 53 | 99.25 -0.437617 0.00467585 54 | 99.75 -0.417488 0.00538982 55 | 100.25 -0.398856 0.00630799 56 | 100.75 -0.38044 0.00529622 57 | 101.25 -0.366937 0.00382398 58 | 101.75 -0.351022 0.00412199 59 | 102.25 -0.3375 0.00462258 60 | 102.75 -0.323455 0.00370332 61 | 103.25 -0.309903 0.00377224 62 | 103.75 -0.297564 0.00365195 63 | 104.25 -0.285897 0.0034668 64 | 104.75 -0.274423 0.00352226 65 | 105.25 -0.26352 0.00357114 66 | 105.75 -0.253789 0.00287742 67 | 106.25 -0.244434 0.00305255 68 | 106.75 -0.234663 0.00325537 69 | 107.25 -0.226947 0.00294272 70 | 107.75 -0.217713 0.00237781 71 | 108.25 -0.209875 0.00253343 72 | 108.75 -0.202178 0.00203723 73 | 109.25 -0.194897 0.00213276 74 | 109.75 -0.187529 0.0022544 75 | 110.25 -0.181188 0.00203668 76 | 110.75 -0.174883 0.0022447 77 | 111.25 -0.168895 0.00199458 78 | 111.75 -0.162609 0.00164153 79 | 112.25 -0.157039 0.00193791 80 | 112.75 -0.151833 0.00149113 81 | 113.25 -0.146258 0.00158503 82 | 113.75 -0.141432 0.00179949 83 | 114.25 -0.137068 0.00153904 84 | 114.75 -0.133 0.00143167 85 | 115.25 -0.128072 0.00136183 86 | 115.75 -0.124458 0.00130614 87 | 116.25 -0.119634 0.00109513 88 | 116.75 -0.116158 0.00126642 89 | 117.25 -0.112377 0.00112008 90 | 117.75 -0.108795 0.00107608 91 | 118.25 -0.105102 0.0011055 92 | 118.75 -0.102259 0.000887192 93 | 119.25 -0.0989288 0.000925919 94 | 119.75 -0.095724 0.00086182 95 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/truncated/U_3nm-6nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 93.3 -28.7634 2.03061 2 | 93.9 -24.1341 1.45611 3 | 94.5 -19.8226 1.22046 4 | 95.1 -16.7174 1.04785 5 | 95.7 -14.0909 0.791776 6 | 96.3 -12.2003 0.637427 7 | 96.9 -10.6866 0.457677 8 | 97.5 -9.34297 0.355358 9 | 98.1 -8.42198 0.328236 10 | 98.7 -7.45562 0.280062 11 | 99.3 -6.69891 0.265468 12 | 99.9 -5.97057 0.229781 13 | 100.5 -5.38376 0.157357 14 | 101.1 -4.93997 0.162605 15 | 101.7 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0.0016904 80 | 140.7 -0.151642 0.00151447 81 | 141.3 -0.146584 0.0013541 82 | 141.9 -0.141751 0.00159777 83 | 142.5 -0.136726 0.00154912 84 | 143.1 -0.132142 0.00139786 85 | 143.7 -0.128512 0.00118761 86 | 144.3 -0.12358 0.00126545 87 | 144.9 -0.119948 0.00117136 88 | 145.5 -0.116067 0.00123074 89 | 146.1 -0.11196 0.00125543 90 | 146.7 -0.108775 0.00102812 91 | 147.3 -0.105172 0.000967967 92 | 147.9 -0.101866 0.000820672 93 | 148.5 -0.0987697 0.000883578 94 | 149.1 -0.0956309 0.00074992 95 | 149.7 -0.0928449 0.000817746 96 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/truncated/U_3nm-8nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 113.3 -34.1996 3.08065 2 | 113.9 -27.5015 1.95917 3 | 114.5 -22.7526 1.26693 4 | 115.1 -19.414 1.14016 5 | 115.7 -16.4392 0.779979 6 | 116.3 -14.2897 0.718349 7 | 116.9 -12.301 0.621833 8 | 117.5 -10.8909 0.440617 9 | 118.1 -9.69838 0.373954 10 | 118.7 -8.68128 0.332826 11 | 119.3 -7.66976 0.25752 12 | 119.9 -6.98938 0.236812 13 | 120.5 -6.35483 0.232165 14 | 121.1 -5.77867 0.164911 15 | 121.7 -5.27546 0.157271 16 | 122.3 -4.80221 0.138006 17 | 122.9 -4.44362 0.146014 18 | 123.5 -4.09386 0.10621 19 | 124.1 -3.75052 0.101445 20 | 124.7 -3.47323 0.0785652 21 | 125.3 -3.22536 0.0723935 22 | 125.9 -3.00068 0.0691541 23 | 126.5 -2.7989 0.0630422 24 | 127.1 -2.61721 0.0611499 25 | 127.7 -2.43642 0.0500896 26 | 128.3 -2.28345 0.0437542 27 | 128.9 -2.14691 0.0456906 28 | 129.5 -2.0173 0.0407659 29 | 130.1 -1.89154 0.0305448 30 | 130.7 -1.78612 0.0386881 31 | 131.3 -1.68342 0.0330242 32 | 131.9 -1.58349 0.0310653 33 | 132.5 -1.50252 0.0244852 34 | 133.1 -1.4138 0.0237822 35 | 133.7 -1.33832 0.0239633 36 | 134.3 -1.27002 0.0186492 37 | 134.9 -1.19845 0.018108 38 | 135.5 -1.14177 0.0190037 39 | 136.1 -1.0805 0.0157772 40 | 136.7 -1.03471 0.016659 41 | 137.3 -0.978991 0.0178481 42 | 137.9 -0.93053 0.0128461 43 | 138.5 -0.881763 0.0124991 44 | 139.1 -0.843072 0.0125405 45 | 139.7 -0.803433 0.0115975 46 | 140.3 -0.768634 0.0115305 47 | 140.9 -0.733817 0.012416 48 | 141.5 -0.703317 0.00903421 49 | 142.1 -0.667967 0.00834107 50 | 142.7 -0.642056 0.00747329 51 | 143.3 -0.615646 0.00703066 52 | 143.9 -0.588003 0.00855114 53 | 144.5 -0.563769 0.00653338 54 | 145.1 -0.538314 0.00683968 55 | 145.7 -0.517975 0.00770395 56 | 146.3 -0.497481 0.00604115 57 | 146.9 -0.475535 0.00588882 58 | 147.5 -0.456949 0.00546328 59 | 148.1 -0.439874 0.00582731 60 | 148.7 -0.423293 0.00552263 61 | 149.3 -0.406223 0.00465774 62 | 149.9 -0.3902 0.00401432 63 | 150.5 -0.377005 0.0043652 64 | 151.1 -0.361513 0.0042621 65 | 151.7 -0.348645 0.00458404 66 | 152.3 -0.335389 0.0036767 67 | 152.9 -0.324072 0.00376616 68 | 153.5 -0.312021 0.00382025 69 | 154.1 -0.300676 0.00360422 70 | 154.7 -0.290591 0.00318755 71 | 155.3 -0.280101 0.00304859 72 | 155.9 -0.269759 0.0029526 73 | 156.5 -0.260145 0.00260995 74 | 157.1 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2.1147 3 | 104.5 -26.1299 1.29477 4 | 105.1 -22.1253 1.10621 5 | 105.7 -18.7926 0.90301 6 | 106.3 -16.2948 0.651738 7 | 106.9 -14.452 0.721244 8 | 107.5 -12.7076 0.567425 9 | 108.1 -11.1637 0.4245 10 | 108.7 -10.1294 0.303659 11 | 109.3 -8.99629 0.260183 12 | 109.9 -8.14982 0.264914 13 | 110.5 -7.40885 0.226872 14 | 111.1 -6.74373 0.195286 15 | 111.7 -6.19199 0.162419 16 | 112.3 -5.65428 0.157778 17 | 112.9 -5.19217 0.130565 18 | 113.5 -4.81229 0.116603 19 | 114.1 -4.43005 0.104332 20 | 114.7 -4.07891 0.0943742 21 | 115.3 -3.79179 0.0824621 22 | 115.9 -3.54579 0.0924212 23 | 116.5 -3.30059 0.0796501 24 | 117.1 -3.0926 0.0663348 25 | 117.7 -2.8806 0.0568454 26 | 118.3 -2.69924 0.0473635 27 | 118.9 -2.52722 0.0412802 28 | 119.5 -2.37107 0.0408176 29 | 120.1 -2.23512 0.0395873 30 | 120.7 -2.11199 0.0364262 31 | 121.3 -1.98755 0.0328427 32 | 121.9 -1.88028 0.0344653 33 | 122.5 -1.78049 0.0272924 34 | 123.1 -1.6817 0.0253844 35 | 123.7 -1.59139 0.0244329 36 | 124.3 -1.51096 0.0243681 37 | 124.9 -1.42721 0.0198196 38 | 125.5 -1.35634 0.0208098 39 | 126.1 -1.28675 0.0178155 40 | 126.7 -1.22608 0.0166937 41 | 127.3 -1.16689 0.0176287 42 | 127.9 -1.11334 0.0191824 43 | 128.5 -1.05733 0.0141206 44 | 129.1 -1.00714 0.0154373 45 | 129.7 -0.963581 0.0157059 46 | 130.3 -0.918626 0.0134203 47 | 130.9 -0.878624 0.0108361 48 | 131.5 -0.838485 0.0117627 49 | 132.1 -0.804591 0.00996344 50 | 132.7 -0.769815 0.0103729 51 | 133.3 -0.733632 0.00895512 52 | 133.9 -0.704468 0.00771225 53 | 134.5 -0.672746 0.00927341 54 | 135.1 -0.647206 0.00800638 55 | 135.7 -0.620905 0.0079567 56 | 136.3 -0.594949 0.00711844 57 | 136.9 -0.572046 0.00638859 58 | 137.5 -0.54926 0.00533562 59 | 138.1 -0.525416 0.00638876 60 | 138.7 -0.505408 0.0052046 61 | 139.3 -0.487582 0.00560899 62 | 139.9 -0.469131 0.00560579 63 | 140.5 -0.451276 0.00597036 64 | 141.1 -0.434734 0.00592535 65 | 141.7 -0.418254 0.00505058 66 | 142.3 -0.402549 0.0040039 67 | 142.9 -0.388047 0.00458878 68 | 143.5 -0.373959 0.00353978 69 | 144.1 -0.361212 0.00355709 70 | 144.7 -0.347817 0.00402267 71 | 145.3 -0.335916 0.00298815 72 | 145.9 -0.325113 0.00324422 73 | 146.5 -0.312925 0.00316012 74 | 147.1 -0.302661 0.00325253 75 | 147.7 -0.292632 0.00288525 76 | 148.3 -0.282867 0.00288993 77 | 148.9 -0.273397 0.00275206 78 | 149.5 -0.263875 0.00259779 79 | 150.1 -0.255836 0.00278641 80 | 150.7 -0.247604 0.00244796 81 | 151.3 -0.239385 0.00243078 82 | 151.9 -0.230957 0.00211601 83 | 152.5 -0.224257 0.00225039 84 | 153.1 -0.217768 0.002148 85 | 153.7 -0.21145 0.00188827 86 | 154.3 -0.203484 0.00191926 87 | 154.9 -0.197044 0.00200366 88 | 155.5 -0.191241 0.00164902 89 | 156.1 -0.185831 0.0017435 90 | 156.7 -0.178971 0.00112671 91 | 157.3 -0.174536 0.00132837 92 | 157.9 -0.169263 0.00146457 93 | 158.5 -0.164308 0.00153844 94 | 159.1 -0.159112 0.00126919 95 | 159.7 -0.154834 0.00141078 96 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/truncated/U_4nm-8nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 123.3 -45.3698 2.88602 2 | 123.9 -36.4611 2.50796 3 | 124.5 -30.9661 2.00575 4 | 125.1 -25.8423 1.38623 5 | 125.7 -21.85 1.32914 6 | 126.3 -19.2049 0.930738 7 | 126.9 -16.9911 0.829879 8 | 127.5 -14.8797 0.562097 9 | 128.1 -13.1861 0.41225 10 | 128.7 -11.9403 0.434947 11 | 129.3 -10.7345 0.374069 12 | 129.9 -9.76967 0.257614 13 | 130.5 -8.80245 0.288322 14 | 131.1 -8.08289 0.272689 15 | 131.7 -7.37512 0.204959 16 | 132.3 -6.81158 0.189468 17 | 132.9 -6.28374 0.155046 18 | 133.5 -5.81078 0.155599 19 | 134.1 -5.35276 0.119376 20 | 134.7 -4.98662 0.114461 21 | 135.3 -4.68668 0.121084 22 | 135.9 -4.37106 0.088613 23 | 136.5 -4.07025 0.0850688 24 | 137.1 -3.81648 0.098302 25 | 137.7 -3.57319 0.0706453 26 | 138.3 -3.34344 0.0580716 27 | 138.9 -3.14917 0.0490374 28 | 139.5 -2.95002 0.0563586 29 | 140.1 -2.79707 0.0611048 30 | 140.7 -2.63586 0.0427001 31 | 141.3 -2.50214 0.0450744 32 | 141.9 -2.36065 0.0344341 33 | 142.5 -2.22479 0.0392441 34 | 143.1 -2.11938 0.0381954 35 | 143.7 -2.02188 0.0353122 36 | 144.3 -1.9134 0.036054 37 | 144.9 -1.81529 0.0295432 38 | 145.5 -1.72718 0.0288308 39 | 146.1 -1.63996 0.0271033 40 | 146.7 -1.56203 0.0226518 41 | 147.3 -1.49255 0.0191932 42 | 147.9 -1.4331 0.0211939 43 | 148.5 -1.36373 0.0181546 44 | 149.1 -1.30025 0.0184955 45 | 149.7 -1.24339 0.0164321 46 | 150.3 -1.18589 0.0152799 47 | 150.9 -1.13962 0.0175706 48 | 151.5 -1.08924 0.0137767 49 | 152.1 -1.04506 0.0136948 50 | 152.7 -1.00165 0.0126869 51 | 153.3 -0.96453 0.014133 52 | 153.9 -0.924632 0.0113739 53 | 154.5 -0.887516 0.0105131 54 | 155.1 -0.851657 0.011627 55 | 155.7 -0.817586 0.00753454 56 | 156.3 -0.785639 0.00915411 57 | 156.9 -0.757759 0.00908292 58 | 157.5 -0.72735 0.00880801 59 | 158.1 -0.701011 0.00833764 60 | 158.7 -0.672451 0.00748777 61 | 159.3 -0.648395 0.00727835 62 | 159.9 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0.00178173 94 | 179.1 -0.224104 0.00158433 95 | 179.7 -0.218225 0.00168251 96 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/mixed_size/truncated/U_6nm-8nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 143.85 -50.9678 4.07236 2 | 144.55 -41.9341 2.7233 3 | 145.25 -34.2539 1.91262 4 | 145.95 -29.1858 1.44067 5 | 146.65 -24.8732 1.14419 6 | 147.35 -21.735 0.646411 7 | 148.05 -19.1064 0.731903 8 | 148.75 -17.2505 0.578214 9 | 149.45 -15.3362 0.561145 10 | 150.15 -13.7083 0.436069 11 | 150.85 -12.352 0.367696 12 | 151.55 -11.3054 0.34574 13 | 152.25 -10.1801 0.262781 14 | 152.95 -9.38494 0.2101 15 | 153.65 -8.58393 0.257577 16 | 154.35 -7.88697 0.192513 17 | 155.05 -7.24264 0.183907 18 | 155.75 -6.73825 0.157696 19 | 156.45 -6.28594 0.134944 20 | 157.15 -5.79483 0.142651 21 | 157.85 -5.4593 0.109252 22 | 158.55 -5.09687 0.105555 23 | 159.25 -4.76078 0.0895952 24 | 159.95 -4.4517 0.0821751 25 | 160.65 -4.18523 0.0835654 26 | 161.35 -3.95574 0.0757468 27 | 162.05 -3.70823 0.0623293 28 | 162.75 -3.51039 0.0627118 29 | 163.45 -3.30244 0.0546953 30 | 164.15 -3.1198 0.0579545 31 | 164.85 -2.95826 0.0481453 32 | 165.55 -2.80524 0.0458107 33 | 166.25 -2.67572 0.0410957 34 | 166.95 -2.51533 0.0358767 35 | 167.65 -2.40237 0.0409449 36 | 168.35 -2.28422 0.0371218 37 | 169.05 -2.16644 0.0288645 38 | 169.75 -2.07641 0.0324382 39 | 170.45 -1.96906 0.0282616 40 | 171.15 -1.87725 0.0260124 41 | 171.85 -1.78458 0.023307 42 | 172.55 -1.71569 0.0236298 43 | 173.25 -1.64022 0.0203228 44 | 173.95 -1.57137 0.0212855 45 | 174.65 -1.49631 0.0187536 46 | 175.35 -1.43637 0.0166552 47 | 176.05 -1.37405 0.0174292 48 | 176.75 -1.31845 0.017447 49 | 177.45 -1.26763 0.0173411 50 | 178.15 -1.21473 0.0141125 51 | 178.85 -1.16437 0.0131805 52 | 179.55 -1.1197 0.0124084 53 | 180.25 -1.07333 0.0140211 54 | 180.95 -1.03598 0.0122249 55 | 181.65 -0.998793 0.0109136 56 | 182.35 -0.954974 0.0105849 57 | 183.05 -0.920176 0.00916176 58 | 183.75 -0.886923 0.00935824 59 | 184.45 -0.851371 0.0080572 60 | 185.15 -0.822616 0.00942548 61 | 185.85 -0.795164 0.00852039 62 | 186.55 -0.766239 0.00868641 63 | 187.25 -0.738777 0.008713 64 | 187.95 -0.713689 0.00769706 65 | 188.65 -0.68723 0.00709135 66 | 189.35 -0.665237 0.00612227 67 | 190.05 -0.642925 0.00684505 68 | 190.75 -0.62003 0.00661384 69 | 191.45 -0.601652 0.00526824 70 | 192.15 -0.580263 0.00613708 71 | 192.85 -0.562965 0.00558121 72 | 193.55 -0.5447 0.00407792 73 | 194.25 -0.525729 0.00456551 74 | 194.95 -0.508436 0.00449745 75 | 195.65 -0.491766 0.00432614 76 | 196.35 -0.477263 0.00460184 77 | 197.05 -0.461489 0.00489547 78 | 197.75 -0.448573 0.00432092 79 | 198.45 -0.434828 0.00381071 80 | 199.15 -0.42102 0.00393245 81 | 199.85 -0.40844 0.00346662 82 | 200.55 -0.3956 0.00386751 83 | 201.25 -0.384074 0.00343258 84 | 201.95 -0.373014 0.00349886 85 | 202.65 -0.361955 0.0029451 86 | 203.35 -0.351298 0.00286469 87 | 204.05 -0.340703 0.00302716 88 | 204.75 -0.331394 0.00308499 89 | 205.45 -0.321692 0.00252343 90 | 206.15 -0.312856 0.00249568 91 | 206.85 -0.305321 0.00257522 92 | 207.55 -0.296611 0.00257584 93 | 208.25 -0.287556 0.00225736 94 | 208.95 -0.279023 0.00249797 95 | 209.65 -0.272477 0.0017488 96 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/truncated/README.md: -------------------------------------------------------------------------------- 1 | This target data differs from the "full" target data, as values for nanoparticle-nanoparticle separations below d + 0.40323nm x 0.8 are excluded, where d is the nanoparticle diameter and 0.40323 is the diameter of silica. 2 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/truncated/U_10nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 203.6 -87.0766 5.94763 2 | 204.4 -66.8988 4.531 3 | 205.2 -55.6483 2.51561 4 | 206 -47.7719 1.84847 5 | 206.8 -40.5246 1.93968 6 | 207.6 -34.845 1.63272 7 | 208.4 -31.1487 1.16501 8 | 209.2 -27.3124 0.815689 9 | 210 -24.0736 0.759867 10 | 210.8 -21.791 0.605548 11 | 211.6 -19.4152 0.525651 12 | 212.4 -17.7233 0.454731 13 | 213.2 -16.245 0.456609 14 | 214 -15.0619 0.388593 15 | 214.8 -13.5293 0.276232 16 | 215.6 -12.6242 0.257557 17 | 216.4 -11.595 0.211156 18 | 217.2 -10.7849 0.229703 19 | 218 -10.0404 0.221668 20 | 218.8 -9.51377 0.188133 21 | 219.6 -8.78817 0.135785 22 | 220.4 -8.27552 0.135077 23 | 221.2 -7.7482 0.184979 24 | 222 -7.32466 0.110472 25 | 222.8 -6.83936 0.114427 26 | 223.6 -6.43422 0.122651 27 | 224.4 -6.09436 0.0969946 28 | 225.2 -5.77319 0.0898172 29 | 226 -5.46602 0.0913462 30 | 226.8 -5.21033 0.0772921 31 | 227.6 -4.88205 0.0758067 32 | 228.4 -4.66202 0.0589209 33 | 229.2 -4.43941 0.0610602 34 | 230 -4.22902 0.0512269 35 | 230.8 -4.03189 0.0497775 36 | 231.6 -3.82844 0.0485896 37 | 232.4 -3.68875 0.0541453 38 | 233.2 -3.51581 0.0386387 39 | 234 -3.33849 0.0426963 40 | 234.8 -3.18471 0.0377551 41 | 235.6 -3.05316 0.044768 42 | 236.4 -2.92725 0.0397246 43 | 237.2 -2.82346 0.0310899 44 | 238 -2.71045 0.0278549 45 | 238.8 -2.59523 0.031475 46 | 239.6 -2.47128 0.0298193 47 | 240.4 -2.37047 0.0237052 48 | 241.2 -2.29028 0.022529 49 | 242 -2.2096 0.0267051 50 | 242.8 -2.12688 0.00273006 51 | 243.6 -2.036 0.0139915 52 | 244.4 -1.96486 0.0258947 53 | 245.2 -1.89168 0.0199052 54 | 246 -1.82904 0.0158672 55 | 246.8 -1.75703 0.0176862 56 | 247.6 -1.69912 0.0218649 57 | 248.4 -1.63268 0.0142978 58 | 249.2 -1.58129 0.0154418 59 | 250 -1.52097 0.0126909 60 | 250.8 -1.47667 0.0145249 61 | 251.6 -1.41599 0.00983898 62 | 252.4 -1.37795 0.0116401 63 | 253.2 -1.33806 0.0121669 64 | 254 -1.29009 0.0107064 65 | 254.8 -1.25416 0.0104931 66 | 255.6 -1.20212 0.00672164 67 | 256.4 -1.17276 0.00949061 68 | 257.2 -1.13265 0.0104871 69 | 258 -1.09738 0.0108518 70 | 258.8 -1.06918 0.00989565 71 | 259.6 -1.03242 0.00992416 72 | 260.4 -1.00522 0.00920799 73 | 261.2 -0.972587 0.00805071 74 | 262 -0.94358 0.00838659 75 | 262.8 -0.913666 0.00660818 76 | 263.6 -0.889893 0.00690178 77 | 264.4 -0.861821 0.00774652 78 | 265.2 -0.836888 0.00585673 79 | 266 -0.814208 0.00825481 80 | 266.8 -0.792188 0.0060175 81 | 267.6 -0.772446 0.00732762 82 | 268.4 -0.748027 0.00532619 83 | 269.2 -0.727732 0.00460601 84 | 270 -0.706188 0.00435153 85 | 270.8 -0.6896 0.00545936 86 | 271.6 -0.669028 0.00512296 87 | 272.4 -0.653634 0.00532499 88 | 273.2 -0.634732 0.00452697 89 | 274 -0.618148 0.00385749 90 | 274.8 -0.603749 0.00370689 91 | 275.6 -0.585114 0.00254241 92 | 276.4 -0.570178 0.00477513 93 | 277.2 -0.554662 0.00372157 94 | 278 -0.541808 0.00363839 95 | 278.8 -0.526269 0.00380552 96 | 279.6 -0.51369 0.00320989 97 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/truncated/U_25nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 505 -155.083 2 | 508 -86.9485 3 | 511 -56.587 4 | 514 -39.8711 5 | 517 -29.5561 6 | 520 -22.6802 7 | 523 -17.8548 8 | 526 -14.3361 9 | 529 -11.6959 10 | 532 -9.66623 11 | 535 -8.07704 12 | 538 -6.81239 13 | 541 -5.7926 14 | 544 -4.96072 15 | 547 -4.27513 16 | 550 -3.70522 17 | 553 -3.22769 18 | 556 -2.82476 19 | 559 -2.48261 20 | 562 -2.1904 21 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/truncated/U_3nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 63.25 -19.962 1.67064 2 | 63.75 -16.5426 1.40383 3 | 64.25 -13.7813 0.997679 4 | 64.75 -11.8721 0.833381 5 | 65.25 -10.1133 0.63732 6 | 65.75 -8.83623 0.486418 7 | 66.25 -7.75105 0.435878 8 | 66.75 -6.88027 0.325952 9 | 67.25 -6.06722 0.312039 10 | 67.75 -5.41503 0.247506 11 | 68.25 -4.85479 0.205065 12 | 68.75 -4.39541 0.185443 13 | 69.25 -3.96646 0.167076 14 | 69.75 -3.58121 0.135867 15 | 70.25 -3.28848 0.123729 16 | 70.75 -2.99349 0.115527 17 | 71.25 -2.73583 0.10196 18 | 71.75 -2.51384 0.0815665 19 | 72.25 -2.31401 0.0731943 20 | 72.75 -2.12336 0.0714186 21 | 73.25 -1.98044 0.0655952 22 | 73.75 -1.82687 0.0514312 23 | 74.25 -1.70159 0.0474903 24 | 74.75 -1.57235 0.0402353 25 | 75.25 -1.46199 0.0390249 26 | 75.75 -1.36677 0.0362242 27 | 76.25 -1.27284 0.0347661 28 | 76.75 -1.19232 0.030058 29 | 77.25 -1.11202 0.0284619 30 | 77.75 -1.04212 0.0270559 31 | 78.25 -0.981786 0.0230982 32 | 78.75 -0.921657 0.021335 33 | 79.25 -0.867821 0.0196229 34 | 79.75 -0.815633 0.0180671 35 | 80.25 -0.768336 0.0173958 36 | 80.75 -0.722856 0.0147498 37 | 81.25 -0.680996 0.0131635 38 | 81.75 -0.645274 0.0129276 39 | 82.25 -0.608334 0.0127276 40 | 82.75 -0.580426 0.0109486 41 | 83.25 -0.54443 0.0101271 42 | 83.75 -0.518043 0.00962699 43 | 84.25 -0.492058 0.00946459 44 | 84.75 -0.464306 0.00732651 45 | 85.25 -0.444638 0.00793522 46 | 85.75 -0.422771 0.00750683 47 | 86.25 -0.400572 0.00685328 48 | 86.75 -0.381132 0.00661177 49 | 87.25 -0.363963 0.00658488 50 | 87.75 -0.345891 0.00586451 51 | 88.25 -0.330366 0.00543612 52 | 88.75 -0.314112 0.00425709 53 | 89.25 -0.300008 0.0051498 54 | 89.75 -0.286166 0.00527813 55 | 90.25 -0.273646 0.0042876 56 | 90.75 -0.261126 0.00413101 57 | 91.25 -0.25064 0.003692 58 | 91.75 -0.239517 0.00333155 59 | 92.25 -0.22861 0.00342274 60 | 92.75 -0.219487 0.0029657 61 | 93.25 -0.209689 0.00283201 62 | 93.75 -0.201262 0.00272906 63 | 94.25 -0.193009 0.00264845 64 | 94.75 -0.184552 0.002443 65 | 95.25 -0.177271 0.00242528 66 | 95.75 -0.169903 0.00225614 67 | 96.25 -0.163517 0.00216308 68 | 96.75 -0.156986 0.00217624 69 | 97.25 -0.15094 0.00177591 70 | 97.75 -0.145076 0.00190852 71 | 98.25 -0.139343 0.00194533 72 | 98.75 -0.133623 0.00157437 73 | 99.25 -0.128729 0.00177176 74 | 99.75 -0.124175 0.00144784 75 | 100.25 -0.119429 0.00143161 76 | 100.75 -0.114949 0.00142314 77 | 101.25 -0.110859 0.0011933 78 | 101.75 -0.10699 0.00130037 79 | 102.25 -0.10283 0.00126088 80 | 102.75 -0.0992797 0.00120814 81 | 103.25 -0.0954566 0.00106482 82 | 103.75 -0.0923268 0.00100691 83 | 104.25 -0.0890246 0.00120194 84 | 104.75 -0.0859734 0.000962834 85 | 105.25 -0.0829442 0.000878353 86 | 105.75 -0.0801651 0.000918826 87 | 106.25 -0.0773228 0.000916411 88 | 106.75 -0.0749133 0.000850157 89 | 107.25 -0.0722502 0.000720414 90 | 107.75 -0.0697851 0.000779088 91 | 108.25 -0.0676216 0.000685546 92 | 108.75 -0.065415 0.000759669 93 | 109.25 -0.0631737 0.00063868 94 | 109.75 -0.0612624 0.000563149 95 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/truncated/U_4nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 83.25 -31.0653 2.14905 2 | 83.75 -26.0956 1.89008 3 | 84.25 -22.2027 1.30698 4 | 84.75 -18.9259 1.04872 5 | 85.25 -16.5358 0.851237 6 | 85.75 -14.3855 0.679706 7 | 86.25 -12.7905 0.537077 8 | 86.75 -11.2154 0.482222 9 | 87.25 -10.121 0.410002 10 | 87.75 -9.02802 0.332808 11 | 88.25 -8.19744 0.323789 12 | 88.75 -7.50096 0.276602 13 | 89.25 -6.77484 0.267672 14 | 89.75 -6.1653 0.202689 15 | 90.25 -5.67718 0.163256 16 | 90.75 -5.21677 0.170388 17 | 91.25 -4.82895 0.136321 18 | 91.75 -4.45274 0.125142 19 | 92.25 -4.09679 0.110782 20 | 92.75 -3.82573 0.0988164 21 | 93.25 -3.54777 0.0752384 22 | 93.75 -3.30375 0.0751441 23 | 94.25 -3.09596 0.0679549 24 | 94.75 -2.89544 0.0677353 25 | 95.25 -2.71469 0.0613618 26 | 95.75 -2.5386 0.055068 27 | 96.25 -2.38002 0.0428708 28 | 96.75 -2.24282 0.0490253 29 | 97.25 -2.11918 0.0413892 30 | 97.75 -1.98402 0.0428234 31 | 98.25 -1.88167 0.0386501 32 | 98.75 -1.77742 0.0346415 33 | 99.25 -1.68064 0.0284983 34 | 99.75 -1.58847 0.027763 35 | 100.25 -1.50888 0.0269151 36 | 100.75 -1.43139 0.0258829 37 | 101.25 -1.35968 0.0239553 38 | 101.75 -1.28655 0.0219682 39 | 102.25 -1.21931 0.0207381 40 | 102.75 -1.16484 0.0176577 41 | 103.25 -1.10761 0.0177627 42 | 103.75 -1.05562 0.0174374 43 | 104.25 -1.00547 0.0156135 44 | 104.75 -0.959991 0.0155713 45 | 105.25 -0.9116 0.0136401 46 | 105.75 -0.870958 0.0128675 47 | 106.25 -0.832693 0.012361 48 | 106.75 -0.795738 0.0121754 49 | 107.25 -0.763128 0.010904 50 | 107.75 -0.729515 0.00995412 51 | 108.25 -0.699223 0.00921861 52 | 108.75 -0.671063 0.00818568 53 | 109.25 -0.642059 0.00857235 54 | 109.75 -0.61583 0.00756944 55 | 110.25 -0.589989 0.00748246 56 | 110.75 -0.566886 0.00756518 57 | 111.25 -0.544559 0.00638838 58 | 111.75 -0.522108 0.00594421 59 | 112.25 -0.502811 0.00726734 60 | 112.75 -0.483383 0.00596874 61 | 113.25 -0.46515 0.00590849 62 | 113.75 -0.447769 0.00528944 63 | 114.25 -0.430811 0.00504888 64 | 114.75 -0.414325 0.00473447 65 | 115.25 -0.398483 0.00469796 66 | 115.75 -0.384169 0.00436569 67 | 116.25 -0.371182 0.00388979 68 | 116.75 -0.357297 0.00400752 69 | 117.25 -0.344381 0.00361547 70 | 117.75 -0.331999 0.00409658 71 | 118.25 -0.321083 0.00380964 72 | 118.75 -0.309983 0.00340248 73 | 119.25 -0.298971 0.0034952 74 | 119.75 -0.288222 0.00311569 75 | 120.25 -0.278912 0.00320993 76 | 120.75 -0.269571 0.00237885 77 | 121.25 -0.260827 0.00296561 78 | 121.75 -0.252359 0.00268935 79 | 122.25 -0.243728 0.00266006 80 | 122.75 -0.235461 0.0023374 81 | 123.25 -0.228461 0.00244984 82 | 123.75 -0.221076 0.00201257 83 | 124.25 -0.213344 0.00235994 84 | 124.75 -0.207275 0.00199436 85 | 125.25 -0.20072 0.00205562 86 | 125.75 -0.194212 0.00199689 87 | 126.25 -0.188335 0.00171086 88 | 126.75 -0.182345 0.00161824 89 | 127.25 -0.17693 0.00167695 90 | 127.75 -0.171523 0.00159315 91 | 128.25 -0.165988 0.00146952 92 | 128.75 -0.161546 0.00147301 93 | 129.25 -0.156439 0.00129471 94 | 129.75 -0.151878 0.00129845 95 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/truncated/U_5nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 103.3 -42.3305 3.0519 2 | 103.9 -33.1728 1.90128 3 | 104.5 -28.355 2.0391 4 | 105.1 -23.7916 1.39377 5 | 105.7 -19.742 1.10074 6 | 106.3 -17.5764 0.918702 7 | 106.9 -15.1465 0.686285 8 | 107.5 -13.4348 0.486599 9 | 108.1 -11.9781 0.428247 10 | 108.7 -10.7952 0.470596 11 | 109.3 -9.66583 0.352005 12 | 109.9 -8.78043 0.274444 13 | 110.5 -7.86053 0.241389 14 | 111.1 -7.31123 0.230352 15 | 111.7 -6.63426 0.182451 16 | 112.3 -6.0578 0.190098 17 | 112.9 -5.55837 0.128381 18 | 113.5 -5.13523 0.164794 19 | 114.1 -4.76064 0.117752 20 | 114.7 -4.41524 0.107337 21 | 115.3 -4.11893 0.0870201 22 | 115.9 -3.8106 0.0831277 23 | 116.5 -3.53527 0.0705317 24 | 117.1 -3.33836 0.0587706 25 | 117.7 -3.10698 0.0614668 26 | 118.3 -2.90865 0.0578531 27 | 118.9 -2.72035 0.047347 28 | 119.5 -2.57089 0.0444815 29 | 120.1 -2.41449 0.0408519 30 | 120.7 -2.26577 0.04522 31 | 121.3 -2.14337 0.0352556 32 | 121.9 -2.0219 0.0296745 33 | 122.5 -1.92082 0.0307575 34 | 123.1 -1.83008 0.0264879 35 | 123.7 -1.72272 0.0293654 36 | 124.3 -1.63417 0.0262848 37 | 124.9 -1.54484 0.0229363 38 | 125.5 -1.46859 0.0208089 39 | 126.1 -1.40263 0.0195925 40 | 126.7 -1.33391 0.025205 41 | 127.3 -1.26393 0.0171823 42 | 127.9 -1.20784 0.0178847 43 | 128.5 -1.15265 0.013779 44 | 129.1 -1.08939 0.0152415 45 | 129.7 -1.04183 0.0126092 46 | 130.3 -0.997744 0.0111509 47 | 130.9 -0.955162 0.0119077 48 | 131.5 -0.911499 0.0112822 49 | 132.1 -0.872666 0.0121083 50 | 132.7 -0.83521 0.0105026 51 | 133.3 -0.800654 0.00876494 52 | 133.9 -0.767256 0.00800637 53 | 134.5 -0.737568 0.00942939 54 | 135.1 -0.704053 0.00792882 55 | 135.7 -0.677911 0.00796669 56 | 136.3 -0.64888 0.00715799 57 | 136.9 -0.623803 0.00818746 58 | 137.5 -0.599712 0.00715937 59 | 138.1 -0.574699 0.00648632 60 | 138.7 -0.553514 0.00603467 61 | 139.3 -0.531081 0.00433123 62 | 139.9 -0.513739 0.00646104 63 | 140.5 -0.4925 0.0058115 64 | 141.1 -0.474865 0.00451876 65 | 141.7 -0.460048 0.00487711 66 | 142.3 -0.441599 0.00475167 67 | 142.9 -0.425268 0.00449929 68 | 143.5 -0.411145 0.00463136 69 | 144.1 -0.394772 0.00430623 70 | 144.7 -0.381086 0.00441076 71 | 145.3 -0.369653 0.00384795 72 | 145.9 -0.355402 0.00392334 73 | 146.5 -0.343503 0.00406601 74 | 147.1 -0.332331 0.00343629 75 | 147.7 -0.320249 0.00259801 76 | 148.3 -0.311106 0.003154 77 | 148.9 -0.300689 0.00270257 78 | 149.5 -0.290473 0.00309144 79 | 150.1 -0.281036 0.00271606 80 | 150.7 -0.270749 0.00278931 81 | 151.3 -0.26336 0.00246844 82 | 151.9 -0.25502 0.00213476 83 | 152.5 -0.246376 0.00190866 84 | 153.1 -0.238661 0.00201962 85 | 153.7 -0.231909 0.00199261 86 | 154.3 -0.223249 0.00183993 87 | 154.9 -0.217314 0.00208652 88 | 155.5 -0.210948 0.00228594 89 | 156.1 -0.204461 0.00189603 90 | 156.7 -0.198193 0.00190768 91 | 157.3 -0.191887 0.00150437 92 | 157.9 -0.186911 0.00173985 93 | 158.5 -0.18065 0.00148956 94 | 159.1 -0.17602 0.00127865 95 | 159.7 -0.169767 0.00132064 96 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/truncated/U_6nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 123.3 -50.1028 3.70339 2 | 123.9 -41.8629 2.56565 3 | 124.5 -35.0462 1.94068 4 | 125.1 -29.5424 1.56108 5 | 125.7 -25.6683 1.14446 6 | 126.3 -22.4413 0.927691 7 | 126.9 -19.6401 0.664524 8 | 127.5 -17.3733 0.728876 9 | 128.1 -15.5706 0.519129 10 | 128.7 -13.9527 0.454557 11 | 129.3 -12.6896 0.42701 12 | 129.9 -11.5391 0.367144 13 | 130.5 -10.5236 0.331795 14 | 131.1 -9.58322 0.24389 15 | 131.7 -8.87405 0.242891 16 | 132.3 -8.14067 0.198162 17 | 132.9 -7.55717 0.158803 18 | 133.5 -6.95893 0.180199 19 | 134.1 -6.48396 0.145059 20 | 134.7 -6.03345 0.123174 21 | 135.3 -5.65386 0.114059 22 | 135.9 -5.27284 0.120415 23 | 136.5 -4.92281 0.0879209 24 | 137.1 -4.62638 0.0888285 25 | 137.7 -4.35199 0.0795786 26 | 138.3 -4.09816 0.0834074 27 | 138.9 -3.84887 0.0726167 28 | 139.5 -3.63838 0.0639228 29 | 140.1 -3.43626 0.0559263 30 | 140.7 -3.24714 0.0518274 31 | 141.3 -3.07488 0.0518565 32 | 141.9 -2.90438 0.0406428 33 | 142.5 -2.75356 0.0467373 34 | 143.1 -2.63096 0.0431874 35 | 143.7 -2.49417 0.0354595 36 | 144.3 -2.37698 0.0346444 37 | 144.9 -2.25376 0.0317318 38 | 145.5 -2.14973 0.0331287 39 | 146.1 -2.05045 0.0288321 40 | 146.7 -1.95583 0.0284663 41 | 147.3 -1.85786 0.0266449 42 | 147.9 -1.78168 0.0242375 43 | 148.5 -1.71206 0.0199365 44 | 149.1 -1.62918 0.0209157 45 | 149.7 -1.56794 0.0203432 46 | 150.3 -1.49373 0.0196706 47 | 150.9 -1.4346 0.0202526 48 | 151.5 -1.37388 0.0165842 49 | 152.1 -1.31717 0.0174109 50 | 152.7 -1.26388 0.015752 51 | 153.3 -1.21433 0.0140278 52 | 153.9 -1.16602 0.0145507 53 | 154.5 -1.12277 0.0130237 54 | 155.1 -1.07875 0.012393 55 | 155.7 -1.03749 0.0134835 56 | 156.3 -0.997369 0.0113371 57 | 156.9 -0.961808 0.0113408 58 | 157.5 -0.926183 0.0102077 59 | 158.1 -0.893008 0.0104415 60 | 158.7 -0.860355 0.00918334 61 | 159.3 -0.830854 0.00948209 62 | 159.9 -0.799939 0.00905305 63 | 160.5 -0.771027 0.0084117 64 | 161.1 -0.745296 0.00789684 65 | 161.7 -0.718206 0.00735366 66 | 162.3 -0.695791 0.00717753 67 | 162.9 -0.67151 0.0063232 68 | 163.5 -0.648578 0.00648386 69 | 164.1 -0.627545 0.00632593 70 | 164.7 -0.607138 0.00534869 71 | 165.3 -0.586248 0.00552896 72 | 165.9 -0.569739 0.00571119 73 | 166.5 -0.549558 0.00581552 74 | 167.1 -0.532888 0.00509733 75 | 167.7 -0.515778 0.00540455 76 | 168.3 -0.49918 0.00463831 77 | 168.9 -0.483724 0.00431223 78 | 169.5 -0.46894 0.00441121 79 | 170.1 -0.454143 0.00446054 80 | 170.7 -0.441023 0.00398862 81 | 171.3 -0.427733 0.00395575 82 | 171.9 -0.414456 0.00378905 83 | 172.5 -0.401999 0.00385508 84 | 173.1 -0.390582 0.00333228 85 | 173.7 -0.379286 0.00343665 86 | 174.3 -0.368398 0.00328253 87 | 174.9 -0.357311 0.00305199 88 | 175.5 -0.347442 0.00282172 89 | 176.1 -0.337924 0.00269568 90 | 176.7 -0.327645 0.00282993 91 | 177.3 -0.318657 0.00285085 92 | 177.9 -0.309913 0.00250997 93 | 178.5 -0.300561 0.00240131 94 | 179.1 -0.293224 0.00214693 95 | 179.7 -0.28552 0.00249481 96 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/truncated/U_7nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 143.85 -50.3936 2.00364 2 | 144.55 -41.7865 2.3038 3 | 145.25 -34.9511 2.12502 4 | 145.95 -29.9033 1.55022 5 | 146.65 -25.4229 1.03764 6 | 147.35 -22.5863 1.08236 7 | 148.05 -19.9462 0.616647 8 | 148.75 -17.5323 0.718381 9 | 149.45 -15.6613 0.572772 10 | 150.15 -14.0801 0.431291 11 | 150.85 -12.8386 0.411726 12 | 151.55 -11.5714 0.360603 13 | 152.25 -10.5019 0.29307 14 | 152.95 -9.67792 0.24402 15 | 153.65 -8.86946 0.283364 16 | 154.35 -8.15904 0.196352 17 | 155.05 -7.56106 0.185645 18 | 155.75 -7.01158 0.182029 19 | 156.45 -6.4937 0.152775 20 | 157.15 -6.04974 0.134722 21 | 157.85 -5.62103 0.121393 22 | 158.55 -5.2791 0.129237 23 | 159.25 -4.94285 0.0956939 24 | 159.95 -4.63486 0.102919 25 | 160.65 -4.35653 0.0826287 26 | 161.35 -4.09147 0.0830437 27 | 162.05 -3.84114 0.060484 28 | 162.75 -3.63698 0.0751777 29 | 163.45 -3.42745 0.0551635 30 | 164.15 -3.23694 0.0574505 31 | 164.85 -3.06793 0.0442297 32 | 165.55 -2.91669 0.0523551 33 | 166.25 -2.76929 0.0470807 34 | 166.95 -2.62273 0.0371937 35 | 167.65 -2.4853 0.0344181 36 | 168.35 -2.36572 0.0343306 37 | 169.05 -2.25658 0.037328 38 | 169.75 -2.16198 0.0348277 39 | 170.45 -2.05788 0.0281848 40 | 171.15 -1.95884 0.0265063 41 | 171.85 -1.86564 0.0231525 42 | 172.55 -1.78386 0.0263429 43 | 173.25 -1.70424 0.0228541 44 | 173.95 -1.63155 0.0214354 45 | 174.65 -1.55533 0.0189537 46 | 175.35 -1.49612 0.0189422 47 | 176.05 -1.42902 0.0196604 48 | 176.75 -1.3787 0.0161075 49 | 177.45 -1.31951 0.016949 50 | 178.15 -1.25967 0.0157164 51 | 178.85 -1.21913 0.0137595 52 | 179.55 -1.17278 0.0123509 53 | 180.25 -1.11964 0.0148266 54 | 180.95 -1.08003 0.013761 55 | 181.65 -1.03884 0.0119886 56 | 182.35 -0.997987 0.0108412 57 | 183.05 -0.960895 0.0105578 58 | 183.75 -0.923731 0.0103745 59 | 184.45 -0.893628 0.0102871 60 | 185.15 -0.857492 0.00939189 61 | 185.85 -0.826896 0.0078335 62 | 186.55 -0.800661 0.00866349 63 | 187.25 -0.772102 0.0079065 64 | 187.95 -0.746736 0.00790739 65 | 188.65 -0.717999 0.00673451 66 | 189.35 -0.695835 0.00643719 67 | 190.05 -0.673041 0.0061376 68 | 190.75 -0.649801 0.00650257 69 | 191.45 -0.62982 0.00454492 70 | 192.15 -0.607289 0.00599801 71 | 192.85 -0.589249 0.00596504 72 | 193.55 -0.566784 0.00429049 73 | 194.25 -0.550755 0.0054186 74 | 194.95 -0.532223 0.00474214 75 | 195.65 -0.513931 0.00511982 76 | 196.35 -0.498244 0.0043302 77 | 197.05 -0.483271 0.00470518 78 | 197.75 -0.47001 0.00417425 79 | 198.45 -0.4556 0.00372959 80 | 199.15 -0.440887 0.00423599 81 | 199.85 -0.428028 0.00379621 82 | 200.55 -0.414491 0.00377641 83 | 201.25 -0.402335 0.00327364 84 | 201.95 -0.390428 0.0034515 85 | 202.65 -0.380951 0.00308341 86 | 203.35 -0.367901 0.00342594 87 | 204.05 -0.357943 0.0029609 88 | 204.75 -0.346726 0.00310722 89 | 205.45 -0.336807 0.00279047 90 | 206.15 -0.327687 0.00314406 91 | 206.85 -0.319048 0.00271748 92 | 207.55 -0.310334 0.00254867 93 | 208.25 -0.301251 0.00245196 94 | 208.95 -0.292376 0.00282612 95 | 209.65 -0.284926 0.00246831 96 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/truncated/U_8nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 163.85 -63.3264 4.55488 2 | 164.55 -49.905 3.07151 3 | 165.25 -41.7861 2.36659 4 | 165.95 -35.8218 1.66104 5 | 166.65 -30.7157 1.21293 6 | 167.35 -27.1486 1.07768 7 | 168.05 -24.0233 1.005 8 | 168.75 -21.2203 0.758193 9 | 169.45 -19.1927 0.635787 10 | 170.15 -17.0959 0.500492 11 | 170.85 -15.5359 0.480019 12 | 171.55 -14.1253 0.331109 13 | 172.25 -12.8725 0.276991 14 | 172.95 -11.8915 0.278555 15 | 173.65 -10.9399 0.284786 16 | 174.35 -10.1259 0.245935 17 | 175.05 -9.39972 0.202956 18 | 175.75 -8.67237 0.160555 19 | 176.45 -8.15587 0.164665 20 | 177.15 -7.72357 0.12271 21 | 177.85 -7.08661 0.135702 22 | 178.55 -6.59257 0.116253 23 | 179.25 -6.20224 0.0897935 24 | 179.95 -5.83777 0.112297 25 | 180.65 -5.51032 0.117535 26 | 181.35 -5.19843 0.0844067 27 | 182.05 -4.90185 0.0670849 28 | 182.75 -4.66783 0.0710439 29 | 183.45 -4.389 0.0743607 30 | 184.15 -4.17214 0.0750885 31 | 184.85 -3.96329 0.0648234 32 | 185.55 -3.74682 0.058841 33 | 186.25 -3.57334 0.0489045 34 | 186.95 -3.36227 0.0398489 35 | 187.65 -3.23472 0.0434825 36 | 188.35 -3.0733 0.0458755 37 | 189.05 -2.92653 0.038405 38 | 189.75 -2.80742 0.0402739 39 | 190.45 -2.69306 0.0362888 40 | 191.15 -2.5645 0.0299682 41 | 191.85 -2.4533 0.0300687 42 | 192.55 -2.34461 0.033489 43 | 193.25 -2.25397 0.0283951 44 | 193.95 -2.16069 0.0268476 45 | 194.65 -2.06729 0.0220529 46 | 195.35 -1.98823 0.0249919 47 | 196.05 -1.90694 0.0255198 48 | 196.75 -1.83329 0.0212024 49 | 197.45 -1.75826 0.0209444 50 | 198.15 -1.68974 0.0194734 51 | 198.85 -1.62956 0.0147883 52 | 199.55 -1.5773 0.0159066 53 | 200.25 -1.5081 0.0189071 54 | 200.95 -1.45626 0.0144544 55 | 201.65 -1.40301 0.0147671 56 | 202.35 -1.34709 0.0136492 57 | 203.05 -1.29871 0.0115693 58 | 203.75 -1.2514 0.0119645 59 | 204.45 -1.21164 0.0116663 60 | 205.15 -1.16768 0.010603 61 | 205.85 -1.12817 0.00892885 62 | 206.55 -1.09175 0.0129207 63 | 207.25 -1.0565 0.01113 64 | 207.95 -1.02265 0.00994767 65 | 208.65 -0.986338 0.00909607 66 | 209.35 -0.951427 0.00583256 67 | 210.05 -0.925974 0.00720135 68 | 210.75 -0.892646 0.00736812 69 | 211.45 -0.867958 0.00693064 70 | 212.15 -0.838554 0.0070722 71 | 212.85 -0.812243 0.00693266 72 | 213.55 -0.786993 0.00701236 73 | 214.25 -0.763398 0.00728383 74 | 214.95 -0.740847 0.00559175 75 | 215.65 -0.717714 0.00588751 76 | 216.35 -0.695406 0.0060173 77 | 217.05 -0.67525 0.00570934 78 | 217.75 -0.655271 0.00668346 79 | 218.45 -0.637672 0.0052563 80 | 219.15 -0.617638 0.00608848 81 | 219.85 -0.600383 0.00548595 82 | 220.55 -0.5833 0.00432011 83 | 221.25 -0.568094 0.00409806 84 | 221.95 -0.550892 0.00451195 85 | 222.65 -0.534372 0.00414516 86 | 223.35 -0.519521 0.0051315 87 | 224.05 -0.505117 0.00344716 88 | 224.75 -0.490519 0.00397311 89 | 225.45 -0.478306 0.00363366 90 | 226.15 -0.467193 0.00379244 91 | 226.85 -0.45493 0.00342405 92 | 227.55 -0.44298 0.00347771 93 | 228.25 -0.42994 0.00328824 94 | 228.95 -0.420926 0.00342048 95 | 229.65 -0.410362 0.00193948 96 | -------------------------------------------------------------------------------- /nanoparticle_optimization/utils/target_data/np_np/truncated/U_9nm_truncated.txt: -------------------------------------------------------------------------------- 1 | 183.6 -74.6837 6.15502 2 | 184.4 -60.3756 3.85789 3 | 185.2 -49.2566 3.14825 4 | 186 -41.5145 2.49122 5 | 186.8 -34.287 1.82836 6 | 187.6 -30.0971 1.33975 7 | 188.4 -26.4885 1.16487 8 | 189.2 -23.3461 0.816385 9 | 190 -20.733 0.780437 10 | 190.8 -18.5723 0.69879 11 | 191.6 -16.7738 0.473454 12 | 192.4 -15.1581 0.356105 13 | 193.2 -13.7623 0.366521 14 | 194 -12.6782 0.380878 15 | 194.8 -11.6842 0.282459 16 | 195.6 -10.7132 0.242859 17 | 196.4 -9.9334 0.221558 18 | 197.2 -9.15688 0.233139 19 | 198 -8.46507 0.158367 20 | 198.8 -7.99007 0.157337 21 | 199.6 -7.40124 0.106046 22 | 200.4 -6.90969 0.140064 23 | 201.2 -6.50266 0.148537 24 | 202 -6.08502 0.103389 25 | 202.8 -5.68872 0.102033 26 | 203.6 -5.33779 0.0955671 27 | 204.4 -5.05604 0.0884453 28 | 205.2 -4.78326 0.0898146 29 | 206 -4.54784 0.0767572 30 | 206.8 -4.25908 0.0646332 31 | 207.6 -4.07511 0.0624511 32 | 208.4 -3.85148 0.0614675 33 | 209.2 -3.63472 0.0566478 34 | 210 -3.47846 0.0526702 35 | 210.8 -3.31357 0.0426098 36 | 211.6 -3.12614 0.0416856 37 | 212.4 -2.98025 0.0465403 38 | 213.2 -2.87625 0.0378382 39 | 214 -2.71882 0.0300577 40 | 214.8 -2.60574 0.0298094 41 | 215.6 -2.47998 0.0354421 42 | 216.4 -2.37179 0.0320822 43 | 217.2 -2.28999 0.0287147 44 | 218 -2.19223 0.0233561 45 | 218.8 -2.08593 0.0244736 46 | 219.6 -2.00417 0.0252602 47 | 220.4 -1.91553 0.0212873 48 | 221.2 -1.84338 0.0189864 49 | 222 -1.77406 0.0218648 50 | 222.8 -1.70526 0.0217532 51 | 223.6 -1.64041 0.0178069 52 | 224.4 -1.56873 0.0207791 53 | 225.2 -1.5167 0.0132646 54 | 226 -1.4606 0.0168719 55 | 226.8 -1.40433 0.0158026 56 | 227.6 -1.35491 0.0159251 57 | 228.4 -1.30533 0.0133354 58 | 229.2 -1.25964 0.0133351 59 | 230 -1.21645 0.012908 60 | 230.8 -1.17232 0.011172 61 | 231.6 -1.12875 0.00974627 62 | 232.4 -1.08822 0.0107332 63 | 233.2 -1.05894 0.0104285 64 | 234 -1.01869 0.0102728 65 | 234.8 -0.98488 0.00962519 66 | 235.6 -0.951569 0.00838938 67 | 236.4 -0.920301 0.0081264 68 | 237.2 -0.890399 0.00855425 69 | 238 -0.864168 0.00840965 70 | 238.8 -0.835167 0.00888779 71 | 239.6 -0.807118 0.00621748 72 | 240.4 -0.783614 0.00590531 73 | 241.2 -0.758032 0.00606523 74 | 242 -0.736235 0.00610359 75 | 242.8 -0.712025 0.00593149 76 | 243.6 -0.693054 0.00652725 77 | 244.4 -0.670659 0.00569033 78 | 245.2 -0.650985 0.00595456 79 | 246 -0.630932 0.00567793 80 | 246.8 -0.612165 0.0054892 81 | 247.6 -0.596594 0.00431218 82 | 248.4 -0.580021 0.00475332 83 | 249.2 -0.563113 0.0050656 84 | 250 -0.546468 0.00473392 85 | 250.8 -0.530707 0.00449848 86 | 251.6 -0.51436 0.00405224 87 | 252.4 -0.501324 0.00475401 88 | 253.2 -0.488091 0.00367131 89 | 254 -0.474554 0.0035182 90 | 254.8 -0.45942 0.00358251 91 | 255.6 -0.450042 0.0032765 92 | 256.4 -0.437296 0.00268198 93 | 257.2 -0.424263 0.00322244 94 | 258 -0.412731 0.00337325 95 | 258.8 -0.401065 0.00257952 96 | 259.6 -0.392213 0.00289667 97 | -------------------------------------------------------------------------------- /postBuild: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | mkdir src 4 | cd src 5 | 6 | git clone https://github.com/mosdef-hub/mbuild.git 7 | cd mbuild 8 | pip install . 9 | cd .. 10 | 11 | git clone https://github.com/mosdef-hub/nanoparticle_optimization.git 12 | cd nanoparticle_optimization 13 | pip install . 14 | cd .. 15 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup, find_packages 2 | 3 | setup( 4 | name="nanoparticle_optimization", 5 | version="0.1.0", 6 | long_description=__doc__, 7 | packages=find_packages(), 8 | include_package_data=True, 9 | install_requires=[ 10 | 'numba', 11 | 'mbuild', 12 | 'matplotlib', 13 | ], 14 | zip_safe=False, 15 | ) 16 | --------------------------------------------------------------------------------