engine.py

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""" Engine base class from which all ForceBalance MD engines are derived. """

import abc
import os
import subprocess
import shutil
import numpy as np
import time
from collections import OrderedDict
import tarfile
import forcebalance
from forcebalance.nifty import *
from forcebalance.finite_difference import fdwrap_G, fdwrap_H, f1d2p, f12d3p
from forcebalance.optimizer import Counter
from forcebalance.output import getLogger
logger = getLogger(__name__)

class Engine(forcebalance.BaseClass):

    """
    Base class for all engines.

    1. Introduction
    
    In ForceBalance an Engine represents a molecular dynamics code
    and the calculations that may be carried out with that code.

    2. Purpose

    Previously system calls to MD software have been made by the
    Target.  Duplication of code was occurring, because different
    Targets were carrying out the same type of calculation.

    3. Also
    
    Target objects should contain Engine objects, because OpenMM
    Engine objects need to be initialized at the start of a
    calculation.

    """

    def __init__(self, name="engine", **kwargs):
        self.valkwd += ['mol', 'coords', 'name', 'target', 'pbc', 'FF', 'nonbonded_method', 'nonbonded_cutoff']
        kwargs = {i:j for i,j in kwargs.items() if j is not None and i in self.valkwd} 
        super(Engine, self).__init__(kwargs)
        self.name = name
        if 'verbose' in kwargs:
            self.verbose = verbose
        else:
            self.verbose = False
        
        if 'target' in kwargs:
            self.target = kwargs['target']
            self.root = self.target.root
            self.srcdir = os.path.join(self.root, self.target.tgtdir)
            self.tempdir = os.path.join(self.root, self.target.tempdir)
        else:
            warn_once("Running without a target, using current directory.")
            self.root = os.getcwd()
            self.srcdir = self.root
            self.tempdir = self.root
        if 'FF' in kwargs:
            self.FF = kwargs['FF']
        if hasattr(self,'target') and not hasattr(self,'FF'):
            self.FF = self.target.FF
        #============================================#
        #| Initialization consists of three stages: |#
        #| 1) Setting up options                    |#
        #| 2) Reading the source directory          |#
        #| 3) Preparing the temp directory          |#
        #============================================#
        
        self.setopts(**kwargs)
        cwd = os.getcwd()
        
        os.chdir(self.srcdir)
        self.readsrc(**kwargs)
        
        os.chdir(self.tempdir)
        self.prepare(**kwargs)
        os.chdir(cwd)
        
        if self.verbose:
            printcool_dictionary(OrderedDict([(i, self.__dict__[i]) for i in sorted(self.__dict__.keys())]), title="Attributes for engine %s" % self.__class__.__name__)
        return

    def setopts(self, **kwargs):
        return

    def readsrc(self, **kwargs):
        return

    def prepare(self, **kwargs):
        return