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>
This commit is contained in:
@@ -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):
|
||||
|
||||
@@ -60,7 +73,16 @@ 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
|
||||
@@ -388,13 +409,15 @@ 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):
|
||||
|
||||
line += 1
|
||||
@@ -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:
|
||||
|
||||
|
||||
Reference in New Issue
Block a user