How to use the forcebalance.nifty._exec function in forcebalance

self.logger.debug("Verify nifty matrix manipulations perform as expected\n")
        ##matrix manipulations
        X=flat(X)
        self.assertEqual(X.shape, (6,))
        X=row(X)
        self.assertEqual(X.shape, (1,6))
        X=col(X)
        self.assertEqual(X.shape, (6,1))

        self.logger.debug("Running some test processes using nifty._exec()\n")
        ##_exec
        self.assertEqual(type(_exec("")),list)
        self.assertEqual(_exec("echo test")[0],"test")
        _exec("touch .test")
        self.assertTrue(os.path.isfile(".test"))
        _exec("rm .test")
        self.assertFalse(os.path.isfile(".test"))
        self.assertRaises(Exception, _exec, "exit 255")

def get_monomer_properties(print_stuff=0):
    # Multiply a quantity in nm to convert to a0
    nm_to_a0 = 1./0.05291772108
    # Multiply a quantity in e*a0 to convert to Debye
    ea0_to_debye = 0.393430307
    os.system("rm -rf *.log \#*")
    _exec(["./grompp"], print_command=False)
    _exec(["./mdrun"], outfnm="mdrun.txt", print_command=False)
    _exec("./trjconv -f traj.trr -o confout.gro -ndec 6".split(), stdin="0\n", print_command=False)
    x = []
    q = []
    for line in open("confout.gro").readlines():
        sline = line.split()
        if len(sline) >= 6 and isfloat(sline[3]) and isfloat(sline[4]) and isfloat(sline[5]):
            x.append([float(i) for i in sline[3:6]])
    for line in open("charges.log").readlines():
        sline = line.split()
        if 'AtomNr' in line:
            q.append(float(sline[5]))
    mode = 0
    a = []
    for line in open("mdrun.txt").readlines():
        if mode == 1:
            sline = line.split()
            if len(sline) == 3:

def get_monomer_properties(print_stuff=0):
    # Multiply a quantity in nm to convert to a0
    nm_to_a0 = 1./0.05291772108
    # Multiply a quantity in e*a0 to convert to Debye
    ea0_to_debye = 0.393430307
    os.system("rm -rf *.log \#*")
    _exec(["./grompp"], print_command=False)
    _exec(["./mdrun"], outfnm="mdrun.txt", print_command=False)
    _exec("./trjconv -f traj.trr -o confout.gro -ndec 6".split(), stdin="0\n", print_command=False)
    x = []
    q = []
    for line in open("confout.gro").readlines():
        sline = line.split()
        if len(sline) >= 6 and isfloat(sline[3]) and isfloat(sline[4]) and isfloat(sline[5]):
            x.append([float(i) for i in sline[3:6]])
    for line in open("charges.log").readlines():
        sline = line.split()
        if 'AtomNr' in line:
            q.append(float(sline[5]))
    mode = 0
    a = []
    for line in open("mdrun.txt").readlines():
        if mode == 1:

    @param[in] mvals Mathematical parameter values
    @param[in] FF ForceBalance force field object
    @return E A numpy array of energies in kilojoules per mole

    """
    # Part of the command line argument to TINKER.
    basename = xyz[:-4]
    xin = "%s" % xyz + ("" if tky == None else " -k %s" % tky)
    xain = "%s.arc" % basename + ("" if tky == None else " -k %s" % tky)
    
    # Print the force field file from the ForceBalance object, with modified parameters.
    FF.make(mvals)
    
    # Execute TINKER.
    cmdstr = "./analyze %s" % xain
    oanl = _exec(cmdstr,stdin="E",print_command=verbose,print_to_screen=verbose)

    # Read potential energy from file.
    E = []
    for line in oanl:
        if 'Total Potential Energy : ' in line:
            E.append(float(line.split()[4]))
    E = np.array(E) * 4.184
    if dipole:
        # If desired, read dipole from file.
        D = []
        for line in oanl:
            if 'Dipole X,Y,Z-Components :' in line:
                D.append([float(line.split()[i]) for i in range(-3,0)])
        D = np.array(D)
        # Return a Nx4 array with energies in the first column and dipole in columns 2-4.
        answer = np.hstack((E.reshape(-1,1), D.reshape(-1,3)))

def callamber(self, command, stdin=None, print_to_screen=False, print_command=False, **kwargs):

        """ Call AMBER; prepend amberhome to calling the appropriate ambertools program. """

        csplit = command.split()
        # Sometimes the engine changes dirs and the inpcrd/prmtop go missing, so we link it.
        # Prepend the AMBER path to the program call.
        prog = os.path.join(self.amberhome, "bin", csplit[0])
        csplit[0] = prog
        # No need to catch exceptions since failed AMBER calculations will return nonzero exit status.
        o = _exec(' '.join(csplit), stdin=stdin, print_to_screen=print_to_screen, print_command=print_command, rbytes=1024, **kwargs)
        return o

        @param[in] AHess Switch to turn on analytic Hessian
        @return Answer Contribution to the objective function
        
        """

        Answer = {}

        Results = {}
        Points = []  # These are the phase points for which data exists.
        BPoints = [] # These are the phase points for which we are doing MBAR for the condensed phase.
        mBPoints = [] # These are the phase points for which we are doing MBAR for the monomers.
        mPoints = [] # These are the phase points to use for enthalpy of vaporization; if we're scanning pressure then set hvap_wt for higher pressures to zero.
        tt = 0
        for label, PT in zip(self.Labels, self.PhasePoints):
            if os.path.exists('./%s/npt_result.p.bz2' % label):
                _exec('bunzip2 ./%s/npt_result.p.bz2' % label)
            elif os.path.exists('./%s/npt_result.p' % label): pass
            else:
                logger.warning('In %s :\n' % os.getcwd())
                logger.warning('The file ./%s/npt_result.p.bz2 does not exist so we cannot unzip it\n' % label)
            if os.path.exists('./%s/npt_result.p' % label):
                logger.info('Reading information from ./%s/npt_result.p\n' % label)
                Points.append(PT)
                Results[tt] = lp_load(open('./%s/npt_result.p' % label))
                if 'hvap' in self.RefData and PT[0] not in [i[0] for i in mPoints]:
                    mPoints.append(PT)
                if 'mbar' in self.RefData and PT in self.RefData['mbar'] and self.RefData['mbar'][PT]:
                    BPoints.append(PT)
                    if 'hvap' in self.RefData and PT[0] not in [i[0] for i in mBPoints]:
                        mBPoints.append(PT)
                tt += 1
            else:

def drive_msms(xyz, radii, density):
    with open(os.path.join('msms_input.p'),'w') as f: lp_dump((xyz, radii, density),f)
    _exec("CallMSMS.py", print_to_screen=False, print_command=False)
    return lp_load(open('msms_output.p'))

str(pt.idnr)), os.getcwd())
            
            # Dump the force field to a pickle file
            lp_dump((self.FF, mvals, self.OptionDict, AGrad), 'forcebalance.p')
                
            # Run the simulation chain for point.        
            cmdstr = ("%s python md_chain.py " % self.mdpfx +
                      " ".join(self.quantities) + " " +
                      "--engine %s " % self.engname +
                      "--length %d " % self.n_sim_chain + 
                      "--name %s " % self.simpfx +
                      "--temperature %f " % pt.temperature +
                      "--pressure %f " % pt.pressure +
                      "--nequil %d " % self.eq_steps +
                      "--nsteps %d " % self.md_steps)
            _exec(cmdstr, copy_stderr=True, outfnm='md_chain.out')
        
            os.chdir('..')

def nvt_simulation(self, temperature):
        """ Submit a NVT simulation to the Work Queue. """
        wq = getWorkQueue()
        if not os.path.exists('nvt_result.p'):
            link_dir_contents(os.path.join(self.root,self.rundir),os.getcwd())
            cmdstr = '%s python nvt.py %s %.3f' % (self.nptpfx, self.engname, temperature)
            if wq is None:
                logger.info("Running condensed phase simulation locally.\n")
                logger.info("You may tail -f %s/nvt.out in another terminal window\n" % os.getcwd())
                _exec(cmdstr, copy_stderr=True, outfnm='nvt.out')
            else:
                if hasattr(self, 'mol2'):
                    if hasattr(self, 'FF'):
                        mol2_send = list(set(self.mol2).difference(set(self.FF.fnms)))
                    else:
                        mol2_send = self.mol2
                else:
                    mol2_send = []
                queue_up(wq, command = cmdstr+' > nvt.out 2>&1 ',
                         input_files = self.nvtfiles + self.scripts + mol2_send + ['forcebalance.p'],
                         output_files = ['nvt_result.p', 'nvt.out'] + self.extra_output, tgt=self)