Merge pull request #3 from jjmaldonis/master

started adding pieces of the functionality

examples/Au18/structopt.in.json

@@ -57,10 +57,11 @@
     },
     "mutations": {
         "options": [
-            "lattice_alteration",
-            "lattice_alteration_group",
-            "rotation_geo",
-            "rotation"
+            "move_atoms",
+            "swap_positions",
+            "swap_species",
+            "rotate_atoms",
+            "rotate_cluster"
         ]
     },
     "fingerprinters": {

examples/Au18/structopt_load_xyz.in.json

@@ -0,0 +1,96 @@
+{
+    "globals":
+    {
+        "USE_MPI4PY": true
+    },
+    "generators": {
+        "structure_type": "cluster",
+        "initializers": [
+            {
+                "number_of_individuals": 5,
+                "data": {
+                    "filenames": [
+                        "/home/jmaldonis/StructOpt_modular/examples/Au18/structure1.xyz",
+                        "/home/jmaldonis/StructOpt_modular/examples/Au18/structure2.xyz",
+                        "/home/jmaldonis/StructOpt_modular/examples/Au18/structure3.xyz",
+                        "/home/jmaldonis/StructOpt_modular/examples/Au18/structure4.xyz",
+                        "/home/jmaldonis/StructOpt_modular/examples/Au18/structure5.xyz"
+                    ]
+                }
+            }
+        ]
+    },
+    "fitnesses":
+    {
+        "modules": [
+            "LAMMPS",
+            "FEMSIM"
+        ],
+        "weights": [
+            1.0,
+            1.0
+        ],
+        "FEMSIM": {
+            "parameter_filename": "/home/maldonis/USIT/StructOpt/StructOpt/fitness/FEMSIM/femsim-hrmc/parameters/femsim.in",
+            "vk_data_filename": "/home/maldonis/USIT/StructOpt/StructOpt/fitness/FEMSIM/femsim-hrmc/data/fem_exp_Zr50Cu35Al15_t3.txt",
+            "xsize": 28.2842712474619,
+            "ysize": 28.2842712474619,
+            "zsize": 28.2842712474619,
+            "Q": 0.0305,
+            "nphi": 1,
+            "npsi": 40,
+            "ntheta": 20,
+            "thickness_scaling_factor": 28.6378
+        },
+        "LAMMPS":{
+            "keep_files": true, 
+            "min_style": "cg\nmin_modify line quadratic", 
+            "minimize": "1e-8 1e-8 5000 10000", 
+            "pair_style": "eam", 
+            "parallel": true, 
+            "potential_file": "/home/jmaldonis/StructOpt/examples/Au18/Au_u3.eam", 
+            "thermo_steps": 1000
+        }
+    },
+    "relaxations":
+    {
+        "modules": [
+            "LAMMPS"
+        ],
+        "LAMMPS":{
+            "keep_files": true, 
+            "min_style": "cg\nmin_modify line quadratic", 
+            "minimize": "1e-8 1e-8 5000 10000", 
+            "pair_style": "eam", 
+            "parallel": true, 
+            "potential_file": "/home/jmaldonis/StructOpt/examples/Au18/Au_u3.eam", 
+            "thermo_steps": 1000
+        }
+    },
+    "mutations": {
+        "options": [
+            "move_atoms",
+            "swap_positions",
+            "swap_species",
+            "rotate_atoms",
+            "rotate_cluster"
+        ]
+    },
+    "fingerprinters": {
+        "options": []
+    },
+
+    "crossovers": {
+        "options": ["do_nothing"]
+    },
+    "predators": {
+        "options": ["do_nothing"]
+    },
+    "selections": {
+        "options": ["do_nothing"]
+    },
+
+    "fileio": {},
+    "postprocessing": {},
+    "tools": {}
+}

examples/Au18/structure1.xyz

@@ -0,0 +1,6 @@
+4
+10.0 10.0 10.0
+Zr 1.0 1.0 1.0
+Zr 2.0 2.0 2.0
+Zr 3.0 3.0 3.0
+Zr 4.0 4.0 4.0

examples/Au18/structure2.xyz

@@ -0,0 +1,6 @@
+4
+10.0 10.0 10.0
+Zr 1.0 1.0 1.0
+Zr 2.0 2.0 2.0
+Zr 3.0 3.0 3.0
+Zr 4.0 4.0 4.0

examples/Au18/structure3.xyz

@@ -0,0 +1,6 @@
+4
+10.0 10.0 10.0
+Zr 1.0 1.0 1.0
+Zr 2.0 2.0 2.0
+Zr 3.0 3.0 3.0
+Zr 4.0 4.0 4.0

examples/Au18/structure4.xyz

@@ -0,0 +1,6 @@
+4
+10.0 10.0 10.0
+Zr 1.0 1.0 1.0
+Zr 2.0 2.0 2.0
+Zr 3.0 3.0 3.0
+Zr 4.0 4.0 4.0

examples/Au18/structure5.xyz

@@ -0,0 +1,6 @@
+4
+10.0 10.0 10.0
+Zr 1.0 1.0 1.0
+Zr 2.0 2.0 2.0
+Zr 3.0 3.0 3.0
+Zr 4.0 4.0 4.0

structopt/__init__.py

@@ -1,8 +1,10 @@
 import time
 import logging
+import os
 
 from . import fileio
-from optimizer import Optimizer
+from .optimizer import Optimizer
+from . import common
 
 def setup(parameter_file):
     parameters = fileio.parameters.read(parameter_file)
@@ -40,6 +42,9 @@ def setup(parameter_file):
     if logging_level <= logging.DEBUG:
         debug_logger = fileio.logger_utils.initialize_logger(filename='{}-by-rank-debug.log'.format(parameters.globals.loggername), name="by-rank-debug", level=logging_level)
 
+    if not os.path.exists(parameters.globals.output_filename):
+        os.mkdir(parameters.globals.output_filename)
+
     # Set defaults for parameters and globally scope them
     parameters = fileio.parameters.set_default(parameters)
     globals()["parameters"] = parameters

structopt/clean.sh

@@ -0,0 +1,57 @@
+rm cluster/*.pyc
+rm cluster/individual/*.pyc
+rm cluster/population/*.pyc
+rm common/*.pyc
+rm common/individual/*.pyc
+rm common/individual/fingerprinters/*.pyc
+rm common/individual/fitnesses/*.pyc
+rm common/individual/generators/*.pyc
+rm common/individual/mutations/*.pyc
+rm common/individual/relaxations/*.pyc
+rm common/population/*.pyc
+rm common/population/crossovers/*.pyc
+rm common/population/fitnesses/*.pyc
+rm common/population/predators/*.pyc
+rm common/population/relaxations/*.pyc
+rm common/population/selections/*.pyc
+rm crystal/*.pyc
+rm crystal/individual/*.pyc
+rm crystal/population/*.pyc
+rm defect/*.pyc
+rm defect/individual/*.pyc
+rm defect/population/*.pyc
+rm fileio/*.pyc
+rm postprocessing/*.pyc
+rm surface/*.pyc
+rm surface/individual/*.pyc
+rm surface/population/*.pyc
+rm tools/*.pyc
+
+rm -rf cluster/__pycache__
+rm -rf cluster/individual/pycache__
+rm -rf cluster/population/pycache__
+rm -rf common/pycache__
+rm -rf common/individual/pycache__
+rm -rf common/individual/fingerprinters/pycache__
+rm -rf common/individual/fitnesses/pycache__
+rm -rf common/individual/generators/pycache__
+rm -rf common/individual/mutations/pycache__
+rm -rf common/individual/relaxations/pycache__
+rm -rf common/population/pycache__
+rm -rf common/population/crossovers/pycache__
+rm -rf common/population/fitnesses/pycache__
+rm -rf common/population/predators/pycache__
+rm -rf common/population/relaxations/pycache__
+rm -rf common/population/selections/pycache__
+rm -rf crystal/pycache__
+rm -rf crystal/individual/pycache__
+rm -rf crystal/population/pycache__
+rm -rf defect/pycache__
+rm -rf defect/individual/pycache__
+rm -rf defect/population/pycache__
+rm -rf fileio/pycache__
+rm -rf postprocessing/pycache__
+rm -rf surface/pycache__
+rm -rf surface/individual/pycache__
+rm -rf surface/population/pycache__
+rm -rf tools/pycache__

structopt/cluster/__init__.py

@@ -2,5 +2,7 @@
 
 
 class Cluster(Individual):
-    """A stucture containing a cluster of atoms."""
+    """ A stucture containing a non-periodic cluster of atoms. Relaxation algorithms such as LAMMPS and VASP require
+        a periodic structure, so when run though these types of algorithms, the cluster is embedded in a larger box.
+    """
 

structopt/common/__init__.py

@@ -0,0 +1 @@
+from . import individual, population

structopt/common/individual/__init__.py

@@ -2,14 +2,19 @@
 import random
 import ase
 from importlib import import_module
+import numpy as np
 
 import structopt
+from . import relaxations, fitnesses, mutations, fingerprinters, mutations
 
 
 class Individual(ase.Atoms):
     """An abstract base class for a structure."""
 
-    def __init__(self, **kwargs):
+    def __init__(self, index=None, **kwargs):
+        self._kwargs = kwargs  # Store the parameters necessary for initializing for making a copy of self
+        self.index = index
+
         cls_name = self.__class__.__name__.lower()
         # Load in the appropriate functionality
         fingerprinters = import_module('structopt.{cls_name}.individual.fingerprinters'.format(cls_name=cls_name))
@@ -23,22 +28,40 @@ def __init__(self, **kwargs):
         self.relaxations = relaxations.Relaxations()
 
         # Initialize the ase.Atoms structure
+        super().__init__()
         generators = import_module('structopt.{cls_name}.individual.generators'.format(cls_name=cls_name))
         generators.generate(self, **kwargs)
 
+
     def mutate(self):
         self.mutations.select_mutation()
         return self.mutations.mutate(self)
 
+
     def relax(self):
         return self.relaxations.relax(self)
 
+
     def fitness(self):
         return self.fitnesses.fitness(self)
 
+
     def fingerprint(self):
         return self.fingerprinters.fingerprint(self)
 
-    def __repr__(self):
-        return "<{cls} object at {loc}>".format(cls=self.__class__.__name__, loc=hex(id(self)))
+
+    def get_atom_indices_within_distance_of_atom(self, atom_index, distance):
+        dists = self.get_distances(atom_index, slice(None, None, None))
+        return np.where(dists < distance)
+
+    def get_nearest_atom_indices(self, atom_index, count):
+        dists = self.get_distances(atom_index, slice(None, None, None))[0]
+        return np.argsort(dists)[:count]
+
+    def copy(self):
+        new = self.__class__()
+        new.index = self.index  # TODO
+        new.extend(self)
+        return new
+
 

structopt/common/individual/generators/__init__.py

@@ -1,15 +1,41 @@
 import functools
+import numpy as np
 
 import structopt
 from structopt.common.individual import Individual
+from .read_xyz import read_xyz
 
-
-def generate(individual, *args, **kwargs):
+def generate(individual, **kwargs):
     """ Uses the relevant parameters from structopt to intialize the input Individual by modifying it in-place.
 
         Args:
             individual (Individual): an Individual that is uninitialized
-            *args, **kwargs: arguments for either ase.Atoms or a different generator function
+            **kwargs: keyword arguments for either ase.Atoms or a different generator function
     """
+    if 'filenames' in kwargs:
+        filename = kwargs['filenames'][individual.index]
+        atoms = read_xyz(filename)
+        individual.extend(atoms)
+        #individual.set_atomic_numbers(atoms.get_atomic_numbers())
+        #individual.set_charges(atoms.get_charges())
+        #individual.set_chemical_symbols(atoms.get_chemical_symbols())
+        #individual.set_initial_magnetic_moments(atoms.get_initial_magnetic_moments())
+        #individual.set_masses(atoms.get_masses())
+        #individual.set_momenta(atoms.get_momenta())
+        #individual.set_positions(atoms.get_positions())
+        #individual.set_scaled_positions(atoms.get_scaled_positions())
+        #individual.set_tags(atoms.get_tags())
+        #individual.set_velocities(atoms.get_velocities())
+
+        individual.set_pbc(True)
+        with open(filename) as of:
+            of.readline()  # number of atoms
+            sizes = of.readline()  # comment == box size
+            sizes = sizes.split()[:3]
+            sizes = [float(x) for x in sizes]
+            cell = np.identity(3)
+            np.fill_diagonal(cell, sizes)
+            individual.set_cell(cell)
+
     return None
 

structopt/common/individual/generators/read_xyz.py

@@ -0,0 +1,4 @@
+import structopt.fileio
+
+def read_xyz(filename):
+    return structopt.fileio.read_xyz(filename)