#! /usr/bin/env python
import random
import math

#-------------------------------Constants-----------------------------------
DEFAULT_MONTE_CARLO_STEPS = 100
DEFAULT_OUTPUT_PATH = '.'
DEFAULT_MDSTEPS = 10000
DEFAULT_BOUNDARY_CONDITIONS = "Vacuum"
DEFAULT_OUTPUT_FREQ = 10000
DEFAULT_PHYSICAL_TEMP = 300

EXECUTABLE = "ProtoMol"

#-----------------------------Global Data-------------------------------------
pdb_file = ""
psf_file = ""
par_file = ""
xyz_file_name = ""
dcd_file_name = ""
boundary_conditions = DEFAULT_BOUNDARY_CONDITIONS
monte_carlo_steps = DEFAULT_MONTE_CARLO_STEPS
md_steps = DEFAULT_MDSTEPS
output_freq = DEFAULT_OUTPUT_FREQ
output_path = DEFAULT_OUTPUT_PATH

replica_list = []

#------------------------Initialize random generator---------------------------- 
random.seed()


#-------------------------Global functions---------------------------------
#Function to parse the file name from a string holding its location.
def parse_file_name(file_name):
	split_name = file_name.split('/')
	return split_name[len(split_name)-1]


#Function to parse the file name and leave out its extension.
def remove_trailing_dots(file_name):
	split_name = file_name.split('.')
	return split_name[0]


#-------------------------Define Replica Object---------------------------------
class Replica(object):
	def __init__(self, id, temp):
		self.id	= id
		self.temp = temp
		self.exchgd_replica_id = -1
		self.potential_energy = None
		self.prev_temp = None
		self.exch_steps = []
		self.running = 0
		self.last_seen_step = -1

	def __str__(self):
		return "Replica %d at temp %f" % (self.id, self.temp)


#Function to generate a config file to send to workqueue. It returns the generated config file name.
def generate_config(output_path, pdb_file, psf_file, par_file, monte_carlo_step, md_steps, output_freq, replica_obj, generate_xyz = False, generate_dcd = False):

	#initialize the config file name based on the replica id.
	cfg_file_name = "%s/%s/%s/%d/%d-%d.cfg" % ( output_path, "simfiles", "config", replica_obj.id, replica_obj.id, monte_carlo_step)	
	cfg_file_stream = open(cfg_file_name, "w")

	#initialize string that will hold the config file values
	write_str = ""

	#Parse supplied files so only actual file name is passed, not full path of the file name
	input_pdb = "%s.%d-%d.pdb" % (remove_trailing_dots(parse_file_name(pdb_file)), replica_obj.id, monte_carlo_step)
	parsed_psf_file = parse_file_name(psf_file)
	parsed_par_file = parse_file_name(par_file)

	#Start writing the config file parameters and values
	write_str += "randomtype 1\n" 
	write_str += "numsteps %d\n" % md_steps
	write_str += "outputfreq %d\n" % output_freq

	write_str += "posfile %s\n" % input_pdb
	write_str += "psffile %s\n" % parsed_psf_file
	write_str += "parfile %s\n" % parsed_par_file
	
	if monte_carlo_step > 0:
		write_str += "velfile %s.%d-%d.vel\n" % (remove_trailing_dots(parse_file_name(pdb_file)), replica_obj.id, monte_carlo_step)

	write_str += "dofinPDBPosFile true\n" 
	write_str += "finPDBPosFile %s.%d-%d.pdb\n" % (remove_trailing_dots(parse_file_name(pdb_file)), replica_obj.id, monte_carlo_step+1)
	write_str += "finXYZVelFile %s.%d-%d.vel\n" % (remove_trailing_dots(parse_file_name(pdb_file)), replica_obj.id, monte_carlo_step+1)

	write_str += "temperature %f\n" % replica_obj.temp
	write_str += "boundaryConditions %s\n" % boundary_conditions
	write_str += "cellManager Cubic\n"
	write_str += "cellsize 69\n"

	if generate_xyz:
		write_str += "XYZPosFile %d.xyz\n" % replica_obj.id
		write_str += "XYZPosFileOutputFreq %d\n" % md_steps 
	if generate_dcd:
		write_str += "DCDFile %d.dcd\n" % replica_obj.id
		write_str += "DCDFileOutputFreq %d\n" % output_freq

	write_str += "allEnergiesFile %d.eng\n" % replica_obj.id
	write_str += "allEnergiesFileOutputFreq %d\n" % output_freq
	
	write_str += "seed %d\n" % random.randint(1, 1000000)
	write_str += "shake on\n"

	write_str += "integrator {\n"
	write_str += "level 0 langevinImpulse {\n"
	write_str += "temperature %f\n" % replica_obj.temp
	write_str += "gamma 5\n"
	write_str += "timestep 2\n"
	write_str += "force bond\n"
	write_str += "force angle\n"
	write_str += "force dihedral\n"
	write_str += "force improper\n"
	write_str += "force LennardJones Coulomb\n"
	write_str += " -switchingFunction C2 -switchingFunction C1 -algorithm NonbondedCutoff\n"
	write_str += "   -switchon          10\n"
	write_str += "   -cutoff            12\n"
	write_str += "   -cutoff            12\n"
	write_str += "   -cutoff            12\n"
	write_str += "}\n}"

	#Write to the config file
	cfg_file_stream.write(write_str)
	
	return cfg_file_name


#Function that to perform metropolis criteria check for two replicas.
def metropolis( u_i, u_j, t_i, t_j ):
    # Metropolis for replica i with potential energy u_i, temp t_i
    #            and replica j with potential energy u_j, temp t_j
	K_b = 0.001987191 #Constants.boltzmann()
	deltaE = (1 / (K_b * t_i) - 1/ (K_b * t_j) ) - (u_j - u_i)

	if( deltaE < 0 ):
		return True
		
	acceptProb = math.exp(-deltaE)
	randNum = random.random()

	if( randNum < acceptProb ):
		return True
	else:
		return False
