Dice Player Translation, Initial work on Dice Processes

This commit adds the functions responsible for creating Dice inputs and calling dice it self, the original functions were removed from the Dice.py file and added to SetGlobals' Internal and Dice classes

Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>

DPpack/Dice.py

@@ -9,13 +9,6 @@ from DPpack.PTable import *
 from DPpack.SetGlobals import *
 from DPpack.Misc import *
 
-
-dice_end_flag = "End of simulation"		## The normal end flag
-dice_flag_line = -2    					## must be in the line before the last
-umaAng3_to_gcm3 = 1.6605				## Conversion between uma/Ang3 to g/cm3
-
-max_seed = 4294967295					## Maximum allowed value for a seed (numpy)
-
 #######################################  functions  ######################################
 
 def make_inputs(cycle, proc):

DPpack/MolHandling.py

@@ -25,7 +25,7 @@ class System:
 		self.molecule = []
 		self.nmols = []
 
-	def add_type(self,nmols, m):
+	def add_type(self, nmols, m):
 		
 		self.molecule.append(m)
 		self.nmols.append(nmols)
@@ -189,21 +189,30 @@ class System:
 
 class Molecule:
 
-	def __init__(self):
+	def __init__(self, molname):
+
+		self.molname = molname
 
 		self.atom = []					# Lista de instancias de Atom
 		self.position = None			# Array Numpy
 		self.energy = None				# Array Numpy
 		self.gradient = None			# Array Numpy
 		self.hessian = None				# Array Numpy
+
 		self.total_mass = 0
 		self.com = None
+		self.ghost_atoms = [] # Stores the index of the ghost atoms in the atoms array
+		self.lp_atoms = []
 
 	def add_atom(self, a):
 
 		self.atom.append(a)			# Inserção de um novo atomo
 		self.total_mass += a.mass
 
+		if (a.na == ghost_number):
+
+			self.ghost_atoms.append(self.atom.index(a))
+
 		self.center_of_mass()
 
 	def center_of_mass(self):

DPpack/SetGlobals.py

@@ -3,10 +3,23 @@ import shutil
 import textwrap
 import types
 
+from numpy.core.fromnumeric import partition
+
 from DPpack.MolHandling import *
 from DPpack.PTable import *
 from DPpack.Misc import *
 
+from numpy import random
+import subprocess
+
+
+dice_end_flag = "End of simulation"		## The normal end flag
+dice_flag_line = -2    					## must be in the line before the last
+umaAng3_to_gcm3 = 1.6605				## Conversion between uma/Ang3 to g/cm3
+
+max_seed = 4294967295					## Maximum allowed value for a seed (numpy)
+
+
 class Internal:
 
 	def __init__(self, infile, outfile):
@@ -38,7 +51,7 @@ class Internal:
 
 		## Dice:
 		self.combrule = None
-		self.randominit = None
+		self.randominit = True
 
 	def read_keywords(self):
 
@@ -60,8 +73,17 @@ class Internal:
 			if key in self.player_keywords and len(value) != 0:  ##  'value' is not empty!
 				
 				if key == 'qmprog' and value[0].lower() in ("g03", "g09", "g16", "molcas"):
+					
 					setattr(self.player, key, value[0].lower())
 
+					if self.player.qmprog in ("g03","g09","g16"):
+
+						self.gaussian.qmprog = self.player.qmprog
+
+					# if self.player.qmprog == "molcas":
+
+					# 	pass
+				
 				elif key == 'opt' and value[0].lower() in ("yes", "no", "ts"):
 					setattr(self.player, key, value[0].lower())
 				
@@ -208,7 +230,6 @@ class Internal:
 			
 			# #### End
 
-		
 	def check_keywords(self):
 		
 		min_steps = 20000
@@ -388,12 +409,14 @@ class Internal:
 		for i in range(ntypes):
 
 			line += 1
-			nsites = ljfile.pop(0).split()[0]
+			nsites, molname = ljfile.pop(0).split()[:2]
+
 			if not nsites.isdigit():
 				sys.exit("Error: expected an integer in line {} of file {}".format(line, self.dice.ljname))
 			
 			nsites = int(nsites)
-			self.system.add_type(nsites,Molecule())
+
+			self.system.add_type(nsites, Molecule(molname))
 
 			for j in range(nsites):
 
@@ -466,7 +489,6 @@ class Internal:
 			if _var in locals() or _var in globals():
 				exec(f'del {_var}')
 
-	
 	def print_potential(self):
 		
 		formatstr = "{:<3d} {:>3d}  {:>10.5f} {:>10.5f} {:>10.5f}  {:>10.6f} {:>9.5f} {:>7.4f} {:>9.4f}\n"
@@ -575,7 +597,6 @@ class Internal:
 			else:
 				sys.exit("Error: cannot find formchk executable")
 
-
 	def calculate_step(self):
 		
 		invhessian = linalg.inv(self.system.molecule[0].hessian)
@@ -634,7 +655,7 @@ class Internal:
 
 			pass
 
-	### I still have to talk with Herbet about 
+	### I still have to talk with Herbet about this function
 	def populate_asec_vdw(self, cycle):
 			
 		asec_charges = []  	# (rx, ry, rz, chg)
@@ -647,11 +668,11 @@ class Internal:
 		
 		norm_factor = nconfigs * self.player.nprocs
 		
-		nsitesref = len(self.system.molecule[0]) + len(ghost_atoms) + len(lp_atoms)
+		nsitesref = len(self.system.molecule[0].atom) + len(self.system.molecule[0].ghost_atoms) + len(self.system.molecule[0].lp_atoms)
 		
 		nsites_total = self.dice.nmol[0] * nsitesref
 		for i in range(1, len(self.dice.nmol)):
-			nsites_total += self.dice.nmol[i] * len(self.system.molecule[i])
+			nsites_total += self.dice.nmol[i] * len(self.system.molecule[i].atom)
 		
 		thickness = []
 		picked_mols = []
@@ -691,7 +712,7 @@ class Internal:
 					for mol in range(nmols):  ## Run over molecules of each type
 					
 						new_molecule = []
-						for site in range(len(self.system.molecule[types].atoms)):  ## Run over sites of each molecule
+						for site in range(len(self.system.molecule[types].atom)):  ## Run over sites of each molecule
 						
 							new_molecule.append({})
 							line = xyzfile.pop(0).split()
@@ -771,6 +792,333 @@ class Internal:
 		
 		return asec_charges
 
+	## Dice related Upper fuctions
+
+	def print_last_config(self, cycle, proc):
+			
+		step_dir = "step{:02d}".format(cycle)
+		proc_dir = "p{:02d}".format(proc)
+		path = step_dir + os.sep + proc_dir
+		file = path + os.sep + self.dice.outname + ".xyz"
+		if not os.path.isfile(file):
+			sys.exit("Error: cannot find the xyz file {}".format(file))
+		try:
+			with open(file) as fh:
+				xyzfile = fh.readlines()
+		except:
+			sys.exit("Error: cannot open file {}".format(file))
+		
+		nsites = len(self.system.molecule[0].atom) * self.dice.nmol[0]	
+		for i in range(1, len(self.dice.nmol)):
+			nsites += self.dice.nmol[i] * len(self.system.molecule[i].atom)
+		
+		nsites += 2  ## To include the comment line and the number of atoms (xyz file format)
+		
+		nsites *= -1  ## Become an index to count from the end of xyzfile (list)
+		xyzfile = xyzfile[nsites :]  ## Take the last configuration
+		
+		
+		file = self.dice.outname + ".xyz.last-" + proc_dir
+		fh = open(file, "w")
+		for line in xyzfile:
+			fh.write(line)
+
+	def new_density(self, proc):
+		
+		file = self.dice.outname + ".xyz.last-" + "p{:02d}".format(proc)
+		if not os.path.isfile(file):
+			sys.exit("Error: cannot find the xyz file {} in main directory".format(file))
+		try:
+			with open(file) as fh:
+				xyzfile = fh.readlines()
+		except:
+			sys.exit("Error: cannot open file {}".format(file))
+		
+		box = xyzfile[1].split()
+		volume = float(box[-3]) * float(box[-2]) * float(box[-1])
+		
+		total_mass = 0
+		for i in range(len(self.system.molecule)):
+			
+			total_mass += self.system.molecule[i].total_mass * self.dice.nmol[i]
+		
+		density = (total_mass / volume) * umaAng3_to_gcm3
+		
+		return density
+
+	def simulation_process(self, cycle, proc):
+		
+		try:
+			self.dice.make_proc_dir(cycle, proc)
+			self.make_inputs(cycle, proc)
+			self.dice.run_dice(cycle, proc, self.outfile)
+		except Exception as err:
+			sys.exit(err)
+		
+	def make_inputs(self, cycle, proc):
+		
+		step_dir = "step{:02d}".format(cycle)
+		proc_dir = "p{:02d}".format(proc)
+		path = step_dir + os.sep + proc_dir
+		
+		num = time.time()					##  Take the decimal places 7 to 12 of the 
+		num = (num - int(num)) * 1e6		##  time in seconds as a floating point
+		num = int((num - int(num)) * 1e6)	##  to make an integer in the range 1-1e6
+		random.seed( (os.getpid() * num) % (max_seed + 1) )
+
+		if self.randominit == False or self.player.cyc > 1:
+			xyzfile = self.dice.outname + ".xyz.last-" + "p{:02d}".format(proc)
+			self.make_init_file(path, xyzfile)
+		
+		if len(self.dice.nstep) == 2:  ## Means NVT simulation
+			
+			self.make_nvt_ter(path)
+			self.make_nvt_eq(path)
+			
+		elif len(self.dice.nstep) == 3:  ## Means NPT simulation
+			
+			if self.randominit:
+				self.make_nvt_ter(path)
+			else:
+				self.dens = self.new_density(proc)
+			
+			self.make_npt_ter(path)
+			self.make_npt_eq(path)
+		
+		else:
+			sys.exit("Error: bad number of entries for 'nstep'")
+		
+		self.make_potential(path)
+
+	def make_nvt_ter(self,path):
+		
+		file = path + os.sep + "NVT.ter"
+		try:
+			fh = open(file, "w")
+		except:
+			sys.exit("Error: cannot open file {}".format(file))
+		
+		fh.write("title = {} - NVT Thermalization\n".format(self.dice.title))
+		fh.write("ncores = {}\n".format(self.dice.ncores))
+		fh.write("ljname = {}\n".format(self.dice.ljname))
+		fh.write("outname = {}\n".format(self.dice.outname))
+		
+		string = " ".join(str(x) for x in self.dice.nmol)
+		fh.write("nmol = {}\n".format(string))
+		
+		fh.write("dens = {}\n".format(self.dice.dens))
+		fh.write("temp = {}\n".format(self.dice.temp))
+		
+		if self.randominit:
+			fh.write("init = yes\n")
+			fh.write("nstep = {}\n".format(self.dice.nstep[0]))
+		else:
+			fh.write("init = yesreadxyz\n")
+			fh.write("nstep = {}\n".format(self.player.altsteps))
+		
+		fh.write("vstep = 0\n")
+		fh.write("mstop = 1\n")
+		fh.write("accum = no\n")
+		fh.write("iprint = 1\n")
+		fh.write("isave = 0\n")
+		fh.write("irdf = 0\n")
+		
+		seed = int(1e6 * random.random())
+		fh.write("seed = {}\n".format(seed))
+		fh.write("upbuf = {}".format(self.dice.upbuf))
+
+		
+		fh.close()
+
+	def make_nvt_eq(self, path):
+		
+		file = path + os.sep + "NVT.eq" 	
+		try:
+			fh = open(file, "w")
+		except:
+			sys.exit("Error: cannot open file {}".format(file))
+		
+		fh.write("title = {} - NVT Production\n".format(self.dice.title))
+		fh.write("ncores = {}\n".format(self.dice.ncores))
+		fh.write("ljname = {}\n".format(self.dice.ljname))
+		fh.write("outname = {}\n".format(self.dice.outname))
+		
+		string = " ".join(str(x) for x in self.dice.nmol)
+		fh.write("nmol = {}\n".format(string))
+		
+		fh.write("dens = {}\n".format(self.dice.dens))
+		fh.write("temp = {}\n".format(self.dice.temp))
+		fh.write("init = no\n")
+		fh.write("nstep = {}\n".format(self.dice.nstep[1]))
+		fh.write("vstep = 0\n")
+		fh.write("mstop = 1\n")
+		fh.write("accum = no\n")
+		fh.write("iprint = 1\n")
+		fh.write("isave = {}\n".format(self.isave))
+		fh.write("irdf = {}\n".format(10 * self.player.nprocs))
+		
+		seed = int(1e6 * random.random())
+		fh.write("seed = {}\n".format(seed))
+		
+		fh.close()
+
+	def make_npt_ter(self,path):
+		
+		file = path + os.sep + "NPT.ter"
+		try:
+			fh = open(file, "w")
+		except:
+			sys.exit("Error: cannot open file {}".format(file))
+		
+		fh.write("title = {} - NPT Thermalization\n".format(self.dice.title))
+		fh.write("ncores = {}\n".format(self.dice.ncores))
+		fh.write("ljname = {}\n".format(self.dice.ljname))
+		fh.write("outname = {}\n".format(self.dice.outname))
+		
+		string = " ".join(str(x) for x in self.dice.nmol)
+		fh.write("nmol = {}\n".format(string))
+		
+		fh.write("press = {}\n".format(self.dice.press))
+		fh.write("temp = {}\n".format(self.dice.temp))
+		
+		if self.dice.randominit == True:
+			fh.write("init = no\n")   ## Because there will be a previous NVT simulation
+			fh.write("vstep = {}\n".format(int(self.dice.nstep[1] / 5)))
+		else:
+			fh.write("init = yesreadxyz\n")
+			fh.write("dens = {:<8.4f}\n".format(self.dice.dens))
+			fh.write("vstep = {}\n".format(int(self.player.altsteps / 5)))
+		
+		fh.write("nstep = 5\n")
+		fh.write("mstop = 1\n")
+		fh.write("accum = no\n")
+		fh.write("iprint = 1\n")
+		fh.write("isave = 0\n")
+		fh.write("irdf = 0\n")
+		
+		seed = int(1e6 * random.random())
+		fh.write("seed = {}\n".format(seed))
+		
+		fh.close()
+
+	def make_npt_eq(self, path):
+		
+		file = path + os.sep + "NPT.eq"
+		try:
+			fh = open(file, "w")
+		except:
+			sys.exit("Error: cannot open file {}".format(file))
+		
+		fh.write("title = {} - NPT Production\n".format(self.dice.title))
+		fh.write("ncores = {}\n".format(self.dice.ncores))
+		fh.write("ljname = {}\n".format(self.dice.ljname))
+		fh.write("outname = {}\n".format(self.dice.outname))
+		
+		string = " ".join(str(x) for x in self.dice.nmol)
+		fh.write("nmol = {}\n".format(string))
+		
+		fh.write("press = {}\n".format(self.dice.press))
+		fh.write("temp = {}\n".format(self.dice.temp))
+		
+		fh.write("nstep = 5\n")
+		
+		fh.write("vstep = {}\n".format(int(self.dice.nstep[2] / 5)))
+		fh.write("init = no\n")
+		fh.write("mstop = 1\n")
+		fh.write("accum = no\n")
+		fh.write("iprint = 1\n")
+		fh.write("isave = {}\n".format(self.dice.isave))
+		fh.write("irdf = {}\n".format(10 * self.player.nprocs))
+		
+		seed = int(1e6 * random.random())
+		fh.write("seed = {}\n".format(seed))
+		
+		fh.close()
+
+	def make_init_file(self, path, file):
+		
+		if not os.path.isfile(file):
+			sys.exit("Error: cannot find the xyz file {} in main directory".format(file))
+		try:
+			with open(file) as fh:
+				xyzfile = fh.readlines()
+		except:
+			sys.exit("Error: cannot open file {}".format(file))
+		
+		nsites_mm = 0
+		for i in range(1, len(self.dice.nmol)):
+			nsites_mm += self.dice.nmol[i] * len(self.system.molecule[i].atom)
+		
+		nsites_mm *= -1  ## Become an index to count from the end of xyzfile (list)
+		xyzfile = xyzfile[nsites_mm :]  ## Only the MM atoms of the last configuration remains
+		
+		file = path + os.sep + self.dice.outname + ".xy"
+		
+		try:
+			fh = open(file, "w")
+		except:
+			sys.exit("Error: cannot open file {}".format(file))
+		
+		for atom in self.system.molecule[0].atom:
+			fh.write("{:>10.6f}  {:>10.6f}  {:>10.6f}\n".format(atom.rx, atom.ry, atom.rz))
+		
+		for i in self.system.molecule[0].ghost_atoms:
+			with self.system.molecule[0].atom[i] as ghost:
+				fh.write("{:>10.6f}  {:>10.6f}  {:>10.6f}\n".format(ghost.rx, ghost.ry, ghost.rz))
+		
+		for i in self.system.molecule[0].lp_atoms:
+			with self.system.molecule[0].atom[i] as lp:
+				fh.write("{:>10.6f}  {:>10.6f}  {:>10.6f}\n".format(lp.rx, lp.ry, lp.rz))
+		
+		for line in xyzfile:
+			atom = line.split()
+			rx = float(atom[1])
+			ry = float(atom[2])
+			rz = float(atom[3])
+			fh.write("{:>10.5f}  {:>10.5f}  {:>10.5f}\n".format(rx, ry, rz))
+		
+		fh.write("$end")
+		
+		fh.close()
+
+	def make_potential(self, path):
+		
+		fstr = "{:<3d} {:>3d}  {:>10.5f} {:>10.5f} {:>10.5f}  {:>10.6f} {:>9.5f} {:>7.4f}\n"
+		
+		file = path + os.sep + self.dice.ljname
+		try:
+			fh = open(file, "w")
+		except:
+			sys.exit("Error: cannot open file {}".format(file))
+		
+		fh.write("{}\n".format(self.dice.combrule))
+		fh.write("{}\n".format(len(self.dice.nmol)))
+		
+		nsites_qm = len(self.system.molecule[0].atom) + len(self.system.molecule[0].ghost_atoms) + len(self.system.molecule[0].lp_atoms)
+		
+		## Print the sites of the QM molecule
+		fh.write("{} {}\n".format(nsites_qm, self.system.molecule[0].molname))
+		for atom in self.system.molecule[0].atom:
+			fh.write(fstr.format(atom.lbl, atom.na, atom.rx, atom.ry, atom.rz, 
+													atom.chg, atom.eps, atom.sig))
+		
+		ghost_label = self.system.molecule[0].atom[-1].lbl + 1
+		for i in self.system.molecule[0].ghost_atoms:
+			fh.write(fstr.format(ghost_label, ghost_number, self.system.molecule[0].atom[i].rx, self.system.molecule[0].atom[i].ry, 
+															self.system.molecule[0].atom[i].rz, self.system.molecule[0].atom[i].chg, 0, 0))
+		
+		ghost_label += 1
+		for lp in self.system.molecule[0].lp_atoms:
+			fh.write(fstr.format(ghost_label, ghost_number, lp['rx'], lp['ry'], lp['rz'], 
+																			lp['chg'], 0, 0))
+		
+		## Print the sites of the other molecules
+		for mol in self.system.molecule[1:]:
+			fh.write("{} {}\n".format(len(mol.atom), mol.molname))
+			for atom in mol.atom:
+				fh.write(fstr.format(atom.lbl, atom.na, atom.rx, atom.ry, 
+										atom.rz, atom.chg, atom.eps, atom.sig))
+
 	class Player:
 
 		def __init__(self):
@@ -799,6 +1147,7 @@ class Internal:
 			self.progname = "dice"
 			self.path = None
 
+			self.init = "yes"
 			self.temp = 300.0
 			self.press = 1.0
 			self.isave = 1000         # ASEC construction will take this into account
@@ -814,7 +1163,162 @@ class Internal:
 			self.nstep = []    # 2 or 3 integer values related to 2 or 3 simulations
 								# (NVT th + NVT eq) or (NVT th + NPT th + NPT eq).
 								# This will control the 'nstep' keyword of Dice
+			self.upbuf = 360
 
+		def make_proc_dir(self, cycle, proc):
+			
+			step_dir = "step{:02d}".format(cycle)
+			proc_dir = "p{:02d}".format(proc)
+			path = step_dir + os.sep + proc_dir
+			try:
+				os.makedirs(path)
+			except:
+				sys.exit("Error: cannot make directory {}".format(path))
+			
+			return
+
+		def run_dice(self, cycle, proc, fh):
+			
+			step_dir = "step{:02d}".format(cycle)
+			proc_dir = "p{:02d}".format(proc)
+
+			try:
+				fh.write("Simulation process {} initiated with pid {}\n".format(step_dir+'/'+proc_dir, os.getpid()))
+				fh.flush()
+			except Exception as err:
+				print("I/O error({0}): {1}".format(err))
+
+			path = step_dir + os.sep + proc_dir
+			working_dir = os.getcwd()
+			os.chdir(path)
+			
+			if len(self.nstep) == 2:  ## Means NVT simulation
+				
+				## NVT thermalization
+				string = "(from " + ("random" if self.randominit else "previous") + " configuration)"
+				fh.write("p{:02d}> NVT thermalization initiated {} on {}\n".format(proc, string, 
+																					date_time()))
+				
+				infh = open("NVT.ter")
+				outfh = open("NVT.ter.out", "w")
+				
+				exit_status = subprocess.call(self.progname, stdin=infh, stdout=outfh)
+				infh.close()
+				outfh.close()
+				
+				if os.getppid() == 1:	## Parent process is dead
+					sys.exit()
+				
+				if exit_status != 0:
+					sys.exit("Dice process p{:02d} did not exit properly".format(proc))
+				else:
+					outfh = open("NVT.ter.out")          ## Open again to seek the normal end flag
+					flag = outfh.readlines()[dice_flag_line].strip()
+					outfh.close()
+					if flag != dice_end_flag:
+						sys.exit("Dice process p{:02d} did not exit properly".format(proc))
+				
+				## NVT production
+				fh.write("p{:02d}> NVT production initiated on {}\n".format(proc, date_time()))
+				
+				infh = open("NVT.eq")
+				outfh = open("NVT.eq.out", "w")
+				
+				exit_status = subprocess.call(self.progname, stdin=infh, stdout=outfh)
+				infh.close()
+				outfh.close()
+				
+				if os.getppid() == 1:	## Parent process is dead
+					sys.exit()
+				
+				if exit_status != 0:
+					sys.exit("Dice process p{:02d} did not exit properly".format(proc))
+				else:
+					outfh = open("NVT.eq.out")           ## Open again to seek the normal end flag
+					flag = outfh.readlines()[dice_flag_line].strip()
+					outfh.close()
+					if flag != dice_end_flag:
+						sys.exit("Dice process p{:02d} did not exit properly".format(proc))
+				
+				fh.write("p{:02d}> ----- NVT production finished on {}\n".format(proc, 
+																					date_time()))
+			
+			elif len(self.nstep) == 3:  ## Means NPT simulation
+				
+				## NVT thermalization if randominit
+				if self.randominit:
+					string = "(from random configuration)"
+					fh.write("p{:02d}> NVT thermalization initiated {} on {}\n".format(proc, 
+																			string, date_time()))
+					infh = open("NVT.ter")
+					outfh = open("NVT.ter.out", "w")
+					
+					exit_status = subprocess.call(self.progname, stdin=infh, stdout=outfh)
+					infh.close()
+					outfh.close()
+					
+					if os.getppid() == 1:	## Parent process is dead
+						sys.exit()
+				
+					if exit_status != 0:
+						sys.exit("Dice process p{:02d} did not exit properly".format(proc))
+					else:
+						outfh = open("NVT.ter.out")      ## Open again to seek the normal end flag
+						flag = outfh.readlines()[dice_flag_line].strip()
+						outfh.close()
+						if flag != dice_end_flag:
+							sys.exit("Dice process p{:02d} did not exit properly".format(proc))
+				
+				## NPT thermalization
+				string = (" (from previous configuration) " if not self.randominit else " ")
+				fh.write("p{:02d}> NPT thermalization initiated{}on {}\n".format(proc, string, 
+																					date_time()))
+				fh.flush()
+				infh = open("NPT.ter")
+				outfh = open("NPT.ter.out", "w")
+				
+				exit_status = subprocess.call(self.progname, stdin=infh, stdout=outfh)
+				infh.close()
+				outfh.close()
+				
+				if os.getppid() == 1:	## Parent process is dead
+					sys.exit()
+				
+				if exit_status != 0:
+					sys.exit("Dice process p{:02d} did not exit properly".format(proc))
+				else:
+					outfh = open("NPT.ter.out")          ## Open again to seek the normal end flag
+					flag = outfh.readlines()[dice_flag_line].strip()
+					outfh.close()
+					if flag != dice_end_flag:
+						sys.exit("Dice process p{:02d} did not exit properly".format(proc))
+				
+				## NPT production
+				fh.write("p{:02d}> NPT production initiated on {}\n".format(proc, date_time()))
+				
+				infh = open("NPT.eq")
+				outfh = open("NPT.eq.out", "w")
+				
+				exit_status = subprocess.call(self.progname, stdin=infh, stdout=outfh)
+				infh.close()
+				outfh.close()
+				
+				if os.getppid() == 1:	## Parent process is dead
+					sys.exit()
+				
+				if exit_status != 0:
+					sys.exit("Dice process p{:02d} did not exit properly".format(proc))
+				else:
+					outfh = open("NPT.eq.out")           ## Open again to seek the normal end flag
+					flag = outfh.readlines()[dice_flag_line].strip()
+					outfh.close()
+					if flag != dice_end_flag:
+						sys.exit("Dice process p{:02d} did not exit properly".format(proc))
+				
+				fh.write("p{:02d}> ----- NPT production finished on {}\n".format(proc, 
+																					date_time()))
+				
+			os.chdir(working_dir)
 
 	class Gaussian:
 

control.in

@@ -2,20 +2,21 @@
 initcyc = 1
 maxcyc = 3
 opt = NO
-nprocs = 2
+nprocs = 4
-qmprog = g09
+qmprog = g16
 lps = no
 ghosts = no
 altsteps = 20000
 
 # dice
-ncores = 1
+ncores = 3
 nmol = 1 100
 dens = 0.75
 nstep = 40000 60000 50000
 isave = 1000
 ljname = phb.pot
 outname = phb
+init = yes
 
 # Gaussian
 level = MP2/aug-cc-pVTZ

diceplayer.py

@@ -96,7 +96,7 @@ if __name__ == '__main__':
 
 	for i in range(len(internal.system.molecule)):
 		
-		internal.outfile.write("\nMolecule type {}:\n\n".format(i + 1))
+		internal.outfile.write("\nMolecule type {} - {}:\n\n".format(i + 1, internal.system.molecule[i].molname))
 		internal.system.molecule[i].print_mol_info(internal.outfile)
 		internal.outfile.write("    Translating and rotating molecule to standard orientation...")
 		internal.system.molecule[i].standard_orientation()
@@ -120,82 +120,83 @@ if __name__ == '__main__':
 		except EnvironmentError as err:
 			sys.exit(err)
 
-	# internal.outfile.write("\nStarting the iterative process.\n")
+	internal.outfile.write("\nStarting the iterative process.\n")
 	
-	# ## Initial position (in Bohr)
+	## Initial position (in Bohr)
-	# position = internal.system.molecule[0].read_position()
+	position = internal.system.molecule[0].read_position()
 	
-	# ## If restarting, read the last gradient and hessian
+	## If restarting, read the last gradient and hessian
-	# if internal.player.cyc > 1:
+	if internal.player.cyc > 1:
-	# 	if internal.player.qmprog in ("g03", "g09", "g16"):
+		if internal.player.qmprog in ("g03", "g09", "g16"):
-	# 		Gaussian.read_forces("grad_hessian.dat")
+			Gaussian.read_forces("grad_hessian.dat")
-	# 		Gaussian.read_hessian_fchk("grad_hessian.dat")
+			Gaussian.read_hessian_fchk("grad_hessian.dat")
 	
-	# 	#if player['qmprog'] == "molcas":
+		#if player['qmprog'] == "molcas":
-	# 		#Molcas.read_forces("grad_hessian.dat")
+			#Molcas.read_forces("grad_hessian.dat")
-	# 		#Molcas.read_hessian("grad_hessian.dat")
+			#Molcas.read_hessian("grad_hessian.dat")
+	
+	###
+	###  Start the iterative process
+	###
+	
+	for cycle in range(internal.player.cyc, internal.player.cyc + internal.player.maxcyc):
+	
+		internal.outfile.write("\n" + 90 * "-" + "\n")
+		internal.outfile.write("{} Step # {}\n".format(40 * " ", cycle))
+		internal.outfile.write(90 * "-" + "\n\n")
+		internal.outfile.flush()
+	
+		make_step_dir(cycle)
+	
+		if internal.player.altsteps == 0 or internal.player.cyc == 1:
+			internal.dice.randominit = True
+		else:
+			internal.dice.randominit = False
 	
 		####
-	####  Start the iterative process
+		####  Start block of parallel simulations
 		####
 		
-# 	for cycle in range(internal.player.cyc, internal.player.cyc + internal.player.maxcyc):
+		procs = []
+		sentinels = []
+		for proc in range(1, internal.player.nprocs + 1):
 		
-# 		internal.outfile.write("\n" + 90 * "-" + "\n")
+			p = Process(target=internal.simulation_process, args=(cycle, proc))
-# 		internal.outfile.write("{} Step # {}\n".format(40 * " ", cycle))
+			p.start()
-# 		internal.outfile.write(90 * "-" + "\n\n")
+			procs.append(p)
+			sentinels.append(p.sentinel)
 			
-# 		make_step_dir(cycle)
+		while procs:
+			finished = connection.wait(sentinels)
+			for proc_sentinel in finished:
+				i = sentinels.index(proc_sentinel)
+				status = procs[i].exitcode
+				procs.pop(i)
+				sentinels.pop(i)
+				if status != 0:
+					for p in procs:
+						p.terminate()
+					sys.exit(status)
 
-# 		if internal.player.altsteps == 0 or cycle == 1:
+		for proc in range(1, internal.player.nprocs + 1):
-# 			internal.dice.randominit = True
+			internal.print_last_config(cycle, proc)
-# 		else:
-# 			internal.dice.randominit = False
 		
-# 		####
+		####
-# 		####  Start block of parallel simulations
+		####  End of parallel simulations block
-# 		####
+		####	
 		
-# 		procs = []
+		# ## Make ASEC
-# 		sentinels = []
+		# internal.outfile.write("\nBuilding the ASEC and vdW meanfields... ")
-# 		for proc in range(1, internal.player.nprocs + 1):
+		# asec_charges = internal.populate_asec_vdw(cycle)
 		
-# 			p = Process(target=Dice.simulation_process, args=(cycle, proc, internal.outfile))
+		# ## After ASEC is built, compress files bigger than 1MB
-# 			p.start()
+		# for proc in range(1, internal.player.nprocs + 1):
-# 			procs.append(p)
+		# 	path = "step{:02d}".format(cycle) + os.sep + "p{:02d}".format(proc)
-# 			sentinels.append(p.sentinel)
+		# 	compress_files_1mb(path)
 		
-# 		while procs:
+		####
-# 			finished = connection.wait(sentinels)
+		####  Start QM calculation
-# 			for proc_sentinel in finished:
+		####
-# 				i = sentinels.index(proc_sentinel)
-# 				status = procs[i].exitcode
-# 				procs.pop(i)
-# 				sentinels.pop(i)
-# 				if status != 0:
-# 					for p in procs:
-# 						p.terminate()
-# 					sys.exit(status)
-		
-# 		for proc in range(1, internal.player.nprocs + 1):
-# 			Dice.print_last_config(cycle, proc)
-		
-# 		####
-# 		####  End of parallel simulations block
-# 		####	
-		
-# 		## Make ASEC
-# 		internal.outfile.write("\nBuilding the ASEC and vdW meanfields... ")
-# 		asec_charges = internal.populate_asec_vdw(cycle)
-		
-# 		## After ASEC is built, compress files bigger than 1MB
-# 		for proc in range(1, internal.player.nprocs + 1):
-# 			path = "step{:02d}".format(cycle) + os.sep + "p{:02d}".format(proc)
-# 			compress_files_1mb(path)
-		
-# 		####
-# 		####  Start QM calculation
-# 		####
 		
 # 		make_qm_dir(cycle)
 		

phb.pot

@@ -32,7 +32,7 @@
  7   1  -5.315819   1.136106   0.744794   0.20528900  0.0300  2.4200
  7   1  -3.338131  -2.250367  -1.102310   0.18436700  0.0300  2.4200
  7   1  -1.163740  -1.117915  -0.893805   0.16038200  0.0300  2.4200
-16
+16 PLACEHOLDER
  1   6   0.672026  -2.823446   0.002631  -0.11500000  0.0700  3.5500
  1   6   2.072026  -2.823446   0.002631  -0.11500000  0.0700  3.5500
  1   6   2.768235  -1.617645   0.002633  -0.11500000  0.0700  3.5500

run.log

@@ -2,10 +2,10 @@
 #############               Welcome to DICEPLAYER version 1.0                #############
 ##########################################################################################
 
-Your python version is 3.8.12 (default, Oct  7 2021, 05:40:48) 
+Your python version is 3.6.9 (default, Jan 26 2021, 15:33:00) 
-[GCC 11.1.0]
+[GCC 8.4.0]
 
-Program started on Sunday, 24 Oct 2021 at 00:46:13
+Program started on Friday, 05 Nov 2021 at 04:36:09
 
 Environment variables:
 OMP_STACKSIZE = Not set
@@ -21,9 +21,9 @@ ghosts = no
 lps = no
 maxcyc = 3
 maxstep = 0.3
-nprocs = 2
+nprocs = 4
 opt = no
-qmprog = g09
+qmprog = g16
 readhessian = no
 switchcyc = 3
 tol_factor = 1.2
@@ -35,9 +35,10 @@ vdwforces = no
 
 combrule = *
 dens = 0.75
+init = yes
 isave = 1000
 ljname = phb.pot
-ncores = 1
+ncores = 3
 nmol = 1 100
 nstep = 40000 60000 50000
 outname = phb
@@ -45,6 +46,7 @@ press = 1.0
 progname = dice
 temp = 300.0
 title = Diceplayer run
+upbuf = 360
 
 ------------------------------------------------------------------------------------------
                          GAUSSIAN variables being used in this run:
@@ -53,9 +55,15 @@ title = Diceplayer run
 chgmult = 0 1
 level = MP2/aug-cc-pVTZ
 pop = chelpg
-qmprog = g09
+qmprog = g16
 
 
+==========================================================================================
+
+Program dice found at /usr/local/bin/dice
+Program g16 found at /usr/local/g16/g16
+Program formchk found at /usr/local/g16/formchk
+
 ==========================================================================================
                     Potential parameters from file phb.pot:
 ------------------------------------------------------------------------------------------
@@ -123,7 +131,7 @@ Lbl  AN       X          Y          Z         Charge    Epsilon   Sigma     Mass
 
 ==========================================================================================
 
-Molecule type 1:
+Molecule type 1 - PHENOL:
 
     Center of mass = (    -0.0000 ,     0.0000 ,     0.0000 )
     Moments of inertia =  3.144054E+02  2.801666E+03  3.027366E+03
@@ -149,7 +157,7 @@ Molecule type 1:
     Dipole moment = (    9.8432 ,    0.6168 ,    0.8120 )     Total =    9.8959 Debye
 
 
-Molecule type 2:
+Molecule type 2 - PLACEHOLDER:
 
     Center of mass = (     1.6067 ,    -1.0929 ,     0.0026 )
     Moments of inertia =  1.205279E+02  2.859254E+02  4.033761E+02
@@ -166,12 +174,65 @@ Molecule type 2:
     New values:
     Center of mass = (     0.0000 ,    -0.0000 ,     0.0000 )
     Moments of inertia =  1.205279E+02  2.859254E+02  4.033761E+02
-    Major principal axis = (   1.000000 ,  -0.000000 ,   0.000000 )
+    Major principal axis = (  -1.000000 ,   0.000000 ,   0.000000 )
-    Inter principal axis = (   0.000000 ,   1.000000 ,  -0.000000 )
+    Inter principal axis = (   0.000000 ,   1.000000 ,   0.000000 )
-    Minor principal axis = (  -0.000000 ,   0.000000 ,   1.000000 )
+    Minor principal axis = (   0.000000 ,   0.000000 ,   1.000000 )
     Characteristic lengths = (   5.67 ,   5.13 ,   1.51 )
     Total mass =   112.20 au
     Total charge =  -0.0000 e
     Dipole moment = (    1.7575 ,    1.5369 ,   -0.0000 )     Total =    2.3347 Debye
 
 ==========================================================================================
+
+Starting the iterative process.
+
+------------------------------------------------------------------------------------------
+                                         Step # 1
+------------------------------------------------------------------------------------------
+
+Simulation process step01/p01 initiated with pid 7039
+Simulation process step01/p02 initiated with pid 7040
+Simulation process step01/p03 initiated with pid 7041
+Simulation process step01/p04 initiated with pid 7042
+p03> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 04:36:09
+p03> NPT thermalization initiated on 05 Nov 2021 at 04:42:40
+p01> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 04:36:09
+p01> NPT thermalization initiated on 05 Nov 2021 at 04:42:40
+p04> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 04:36:09
+p04> NPT thermalization initiated on 05 Nov 2021 at 04:42:52
+p02> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 04:36:09
+p02> NPT thermalization initiated on 05 Nov 2021 at 04:42:54
+
+------------------------------------------------------------------------------------------
+                                         Step # 2
+------------------------------------------------------------------------------------------
+
+Simulation process step02/p01 initiated with pid 7127
+Simulation process step02/p02 initiated with pid 7128
+Simulation process step02/p03 initiated with pid 7129
+Simulation process step02/p04 initiated with pid 7130
+p02> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 05:04:04
+p02> NPT thermalization initiated on 05 Nov 2021 at 05:10:41
+p01> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 05:04:04
+p01> NPT thermalization initiated on 05 Nov 2021 at 05:10:49
+p03> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 05:04:04
+p03> NPT thermalization initiated on 05 Nov 2021 at 05:10:51
+p04> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 05:04:04
+p04> NPT thermalization initiated on 05 Nov 2021 at 05:10:57
+
+------------------------------------------------------------------------------------------
+                                         Step # 3
+------------------------------------------------------------------------------------------
+
+Simulation process step03/p01 initiated with pid 7182
+Simulation process step03/p02 initiated with pid 7183
+Simulation process step03/p03 initiated with pid 7184
+Simulation process step03/p04 initiated with pid 7185
+p04> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 05:32:04
+p04> NPT thermalization initiated on 05 Nov 2021 at 05:38:40
+p01> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 05:32:04
+p01> NPT thermalization initiated on 05 Nov 2021 at 05:38:46
+p03> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 05:32:04
+p03> NPT thermalization initiated on 05 Nov 2021 at 05:38:51
+p02> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 05:32:04
+p02> NPT thermalization initiated on 05 Nov 2021 at 05:38:51

run.log.backup

@@ -2,10 +2,10 @@
 #############               Welcome to DICEPLAYER version 1.0                #############
 ##########################################################################################
 
-Your python version is 3.8.12 (default, Oct  7 2021, 05:40:48) 
+Your python version is 3.6.9 (default, Jan 26 2021, 15:33:00) 
-[GCC 11.1.0]
+[GCC 8.4.0]
 
-Program started on Sunday, 24 Oct 2021 at 00:44:02
+Program started on Friday, 05 Nov 2021 at 04:35:58
 
 Environment variables:
 OMP_STACKSIZE = Not set
@@ -21,9 +21,9 @@ ghosts = no
 lps = no
 maxcyc = 3
 maxstep = 0.3
-nprocs = 2
+nprocs = 4
 opt = no
-qmprog = g09
+qmprog = g16
 readhessian = no
 switchcyc = 3
 tol_factor = 1.2
@@ -35,9 +35,10 @@ vdwforces = no
 
 combrule = *
 dens = 0.75
+init = yes
 isave = 1000
 ljname = phb.pot
-ncores = 1
+ncores = 3
 nmol = 1 100
 nstep = 40000 60000 50000
 outname = phb
@@ -45,6 +46,7 @@ press = 1.0
 progname = dice
 temp = 300.0
 title = Diceplayer run
+upbuf = 360
 
 ------------------------------------------------------------------------------------------
                          GAUSSIAN variables being used in this run:
@@ -53,9 +55,15 @@ title = Diceplayer run
 chgmult = 0 1
 level = MP2/aug-cc-pVTZ
 pop = chelpg
-qmprog = g09
+qmprog = g16
 
 
+==========================================================================================
+
+Program dice found at /usr/local/bin/dice
+Program g16 found at /usr/local/g16/g16
+Program formchk found at /usr/local/g16/formchk
+
 ==========================================================================================
                     Potential parameters from file phb.pot:
 ------------------------------------------------------------------------------------------
@@ -123,7 +131,7 @@ Lbl  AN       X          Y          Z         Charge    Epsilon   Sigma     Mass
 
 ==========================================================================================
 
-Molecule type 1:
+Molecule type 1 - PHENOL:
 
     Center of mass = (    -0.0000 ,     0.0000 ,     0.0000 )
     Moments of inertia =  3.144054E+02  2.801666E+03  3.027366E+03
@@ -138,18 +146,18 @@ Molecule type 1:
     Translating and rotating molecule to standard orientation... Done
 
     New values:
-    Center of mass = (    -0.0000 ,     0.0000 ,     0.0000 )
+    Center of mass = (    -0.0000 ,    -0.0000 ,    -0.0000 )
     Moments of inertia =  3.144054E+02  2.801666E+03  3.027366E+03
     Major principal axis = (   1.000000 ,   0.000000 ,   0.000000 )
     Inter principal axis = (  -0.000000 ,   1.000000 ,  -0.000000 )
-    Minor principal axis = (  -0.000000 ,   0.000000 ,   1.000000 )
+    Minor principal axis = (   0.000000 ,   0.000000 ,   1.000000 )
     Characteristic lengths = (  11.97 ,   5.27 ,   2.99 )
     Total mass =   226.28 au
     Total charge =  -0.0000 e
     Dipole moment = (    9.8432 ,    0.6168 ,    0.8120 )     Total =    9.8959 Debye
 
 
-Molecule type 2:
+Molecule type 2 - PLACEHOLDER:
 
     Center of mass = (     1.6067 ,    -1.0929 ,     0.0026 )
     Moments of inertia =  1.205279E+02  2.859254E+02  4.033761E+02
@@ -164,14 +172,21 @@ Molecule type 2:
     Translating and rotating molecule to standard orientation... Done
 
     New values:
-    Center of mass = (     1.6067 ,    -1.0929 ,     0.0026 )
+    Center of mass = (     0.0000 ,    -0.0000 ,     0.0000 )
-    Moments of inertia =  1.561638E+02  6.739391E+02  8.270247E+02
+    Moments of inertia =  1.205279E+02  2.859254E+02  4.033761E+02
-    Major principal axis = (   0.899747 ,  -0.436411 ,   0.000541 )
+    Major principal axis = (  -1.000000 ,   0.000000 ,   0.000000 )
-    Inter principal axis = (   0.436411 ,   0.899747 ,  -0.001219 )
+    Inter principal axis = (   0.000000 ,   1.000000 ,   0.000000 )
-    Minor principal axis = (   0.000045 ,   0.001333 ,   0.999999 )
+    Minor principal axis = (   0.000000 ,   0.000000 ,   1.000000 )
-    Characteristic lengths = (   5.67 ,   5.05 ,   1.51 )
+    Characteristic lengths = (   5.67 ,   5.13 ,   1.51 )
     Total mass =   112.20 au
     Total charge =  -0.0000 e
-    Dipole moment = (    1.8148 ,    1.4689 ,   -0.0016 )     Total =    2.3347 Debye
+    Dipole moment = (    1.7575 ,    1.5369 ,   -0.0000 )     Total =    2.3347 Debye
 
 ==========================================================================================
+
+Starting the iterative process.
+
+------------------------------------------------------------------------------------------
+                                         Step # 1
+------------------------------------------------------------------------------------------
+