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Dice Processes

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This commit creates and fixes the Dice process: NVT.ter, NPT.ter, NPT.eq

Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
This commit is contained in:
Vitor Hideyoshi
2021-11-26 13:14:59 +00:00
parent 0d877e3dce
commit 49d509029f
17 changed files with 272 additions and 5805 deletions
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527
DPpack/Dice.py
View File

@@ -1,527 +0,0 @@
import sys, os, time
import subprocess
from copy import deepcopy
from numpy import random
from DPpack.PTable import *
from DPpack.SetGlobals import *
from DPpack.Misc import *
####################################### functions ######################################
def make_inputs(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 not dice['randominit']:
xyzfile = dice['outname'] + ".xyz.last-" + "p{:02d}".format(proc)
make_init_file(path, xyzfile)
if len(dice['nstep']) == 2: ## Means NVT simulation
make_nvt_ter(path)
make_nvt_eq(path)
elif len(dice['nstep']) == 3: ## Means NPT simulation
if dice['randominit']:
make_nvt_ter(path)
else:
dice['dens'] = new_density(proc)
make_npt_ter(path)
make_npt_eq(path)
else:
sys.exit("Error: bad number of entries for 'nstep'")
make_potential(path)
return
def make_nvt_ter(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(dice['title']))
fh.write("ncores = {}\n".format(dice['ncores']))
fh.write("ljname = {}\n".format(dice['ljname']))
fh.write("outname = {}\n".format(dice['outname']))
string = " ".join(str(x) for x in dice['nmol'])
fh.write("nmol = {}\n".format(string))
fh.write("dens = {}\n".format(dice['dens']))
fh.write("temp = {}\n".format(dice['temp']))
if dice['randominit']:
fh.write("init = yes\n")
fh.write("nstep = {}\n".format(dice['nstep'][0]))
else:
fh.write("init = yesreadxyz\n")
fh.write("nstep = {}\n".format(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.close()
return
def make_nvt_eq(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(dice['title']))
fh.write("ncores = {}\n".format(dice['ncores']))
fh.write("ljname = {}\n".format(dice['ljname']))
fh.write("outname = {}\n".format(dice['outname']))
string = " ".join(str(x) for x in dice['nmol'])
fh.write("nmol = {}\n".format(string))
fh.write("dens = {}\n".format(dice['dens']))
fh.write("temp = {}\n".format(dice['temp']))
fh.write("init = no\n")
fh.write("nstep = {}\n".format(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(dice['isave']))
fh.write("irdf = {}\n".format(10 * player['nprocs']))
seed = int(1e6 * random.random())
fh.write("seed = {}\n".format(seed))
fh.close()
return
def make_npt_ter(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(dice['title']))
fh.write("ncores = {}\n".format(dice['ncores']))
fh.write("ljname = {}\n".format(dice['ljname']))
fh.write("outname = {}\n".format(dice['outname']))
string = " ".join(str(x) for x in dice['nmol'])
fh.write("nmol = {}\n".format(string))
fh.write("press = {}\n".format(dice['press']))
fh.write("temp = {}\n".format(dice['temp']))
if dice['randominit']:
fh.write("init = no\n") ## Because there will be a previous NVT simulation
fh.write("vstep = {}\n".format(int(dice['nstep'][1] / 5)))
else:
fh.write("init = yesreadxyz\n")
fh.write("dens = {:<8.4f}\n".format(dice['dens']))
fh.write("vstep = {}\n".format(int(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()
return
def make_npt_eq(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(dice['title']))
fh.write("ncores = {}\n".format(dice['ncores']))
fh.write("ljname = {}\n".format(dice['ljname']))
fh.write("outname = {}\n".format(dice['outname']))
string = " ".join(str(x) for x in dice['nmol'])
fh.write("nmol = {}\n".format(string))
fh.write("press = {}\n".format(dice['press']))
fh.write("temp = {}\n".format(dice['temp']))
fh.write("nstep = 5\n")
fh.write("vstep = {}\n".format(int(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(dice['isave']))
fh.write("irdf = {}\n".format(10 * player['nprocs']))
seed = int(1e6 * random.random())
fh.write("seed = {}\n".format(seed))
fh.close()
return
def make_init_file(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(dice['nmol'])):
nsites_mm += dice['nmol'][i] * len(molecules[i])
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 + dice['outname'] + ".xy"
try:
fh = open(file, "w")
except:
sys.exit("Error: cannot open file {}".format(file))
for atom in molecules[0]:
fh.write("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(atom['rx'], atom['ry'],
atom['rz']))
for ghost in ghost_atoms:
fh.write("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(ghost['rx'], ghost['ry'],
ghost['rz']))
for lps in lp_atoms:
fh.write("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(lps['rx'], lps['ry'],
lps['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()
return
def make_potential(path):
fstr = "{:<3d} {:>3d} {:>10.5f} {:>10.5f} {:>10.5f} {:>10.6f} {:>9.5f} {:>7.4f}\n"
file = path + os.sep + dice['ljname']
try:
fh = open(file, "w")
except:
sys.exit("Error: cannot open file {}".format(file))
fh.write("{}\n".format(dice['combrule']))
fh.write("{}\n".format(len(dice['nmol'])))
nsites_qm = len(molecules[0]) + len(ghost_atoms) + len(lp_atoms)
## Print the sites of the QM molecule
fh.write("{}\n".format(nsites_qm))
for atom in molecules[0]:
fh.write(fstr.format(atom['lbl'], atom['na'], atom['rx'], atom['ry'], atom['rz'],
atom['chg'], atom['eps'], atom['sig']))
ghost_label = molecules[0][-1]['lbl'] + 1
for ghost in ghost_atoms:
fh.write(fstr.format(ghost_label, ghost_number, ghost['rx'], ghost['ry'],
ghost['rz'], ghost['chg'], 0, 0))
ghost_label += 1
for lp in 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 molecules[1:]:
fh.write("{}\n".format(len(mol)))
for atom in mol:
fh.write(fstr.format(atom['lbl'], atom['na'], atom['rx'], atom['ry'],
atom['rz'], atom['chg'], atom['eps'], atom['sig']))
return
def make_proc_dir(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(cycle, proc, fh):
step_dir = "step{:02d}".format(cycle)
proc_dir = "p{:02d}".format(proc)
path = step_dir + os.sep + proc_dir
working_dir = os.getcwd()
os.chdir(path)
fh.write("Simulation process {} initiated with pid {}\n".format(proc_dir, os.getpid()))
if len(dice['nstep']) == 2: ## Means NVT simulation
## NVT thermalization
string = "(from " + ("random" if dice['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(dice['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(dice['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(dice['nstep']) == 3: ## Means NPT simulation
## NVT thermalization if randominit
if dice['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(dice['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 dice['randominit'] else " ")
fh.write("p{:02d}> NPT thermalization initiated{}on {}\n".format(proc, string,
date_time()))
infh = open("NPT.ter")
outfh = open("NPT.ter.out", "w")
exit_status = subprocess.call(dice['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(dice['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)
return
def print_last_config(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 + 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(molecules[0]) + len(ghost_atoms) + len(lp_atoms) ) * dice['nmol'][0]
for i in range(1, len(dice['nmol'])):
nsites += dice['nmol'][i] * len(molecules[i])
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 = dice['outname'] + ".xyz.last-" + proc_dir
fh = open(file, "w")
for line in xyzfile:
fh.write(line)
fh.close()
return
def new_density(proc):
file = 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(molecules)):
mol_mass = 0
for atom in molecules[i]:
mol_mass += atom['mass']
total_mass += mol_mass * dice['nmol'][i]
density = (total_mass / volume) * umaAng3_to_gcm3
return density
def simulation_process(cycle, proc, logfh):
try:
make_proc_dir(cycle, proc)
make_inputs(cycle, proc)
run_dice(cycle, proc, logfh)
except Exception as err:
sys.exit(err)
return

40
DPpack/Misc.py
View File

@@ -1,4 +1,5 @@
import os, sys, time
from posixpath import sep
import shutil, gzip
####################################### functions ######################################
@@ -33,31 +34,34 @@ def compress_files_1mb(path):
return
def make_simulation_dir():
sim_dir = "simfiles"
if os.path.exists(sim_dir):
sys.exit("Error: a file or a directory {} already exists, move or delete de simfiles directory to continue.".format(sim_dir))
try:
os.makedirs(sim_dir)
except:
sys.exit("Error: cannot make directory {}".format(sim_dir))
def make_step_dir(cycle):
sim_dir = "simfiles"
step_dir = "step{:02d}".format(cycle)
if os.path.exists(step_dir):
path = sim_dir + os.sep + step_dir
if os.path.exists(path):
sys.exit("Error: a file or directory {} already exists".format(step_dir))
try:
os.makedirs(step_dir)
except:
sys.exit("Error: cannot make directory {}".format(step_dir))
return
def make_qm_dir(cycle):
step_dir = "step{:02d}".format(cycle)
path = step_dir + os.sep + "qm"
try:
os.makedirs(path)
except:
sys.exit("Error: cannot make directory {}".format(path))
return
sys.exit("Error: cannot make directory {}".format(step_dir))
def make_qm_dir(cycle):
sim_dir = "simfiles"
step_dir = "step{:02d}".format(cycle)
path = sim_dir + os.sep + step_dir + os.sep + "qm"
try:
os.makedirs(path)
except:
sys.exit("Error: cannot make directory {}".format(path))

6
DPpack/MolHandling.py
View File

@@ -375,16 +375,22 @@ class Molecule:
evals, evecs = self.principal_axes()
if round(linalg.det(evecs)) == -1:
evecs[0,2] *= -1
evecs[1,2] *= -1
evecs[2,2] *= -1
if round(linalg.det(evecs)) != 1:
sys.exit("Error: could not make a rotation matrix while adopting the standard orientation")
rot_matrix = evecs.T
for atom in self.atom:
position = np.array([ atom.rx, atom.ry, atom.rz ])
new_position = np.matmul(rot_matrix, position.T).T
atom.rx = new_position[0]
atom.ry = new_position[1]
atom.rz = new_position[2]

162
DPpack/SetGlobals.py
View File

@@ -1,3 +1,4 @@
import setproctitle
import os, sys
import shutil
import textwrap
@@ -19,11 +20,11 @@ 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):
self.cyc = 1
self.infile = infile
self.outfile = outfile
@@ -51,7 +52,6 @@ class Internal:
## Dice:
self.combrule = None
self.randominit = True
def read_keywords(self):
@@ -126,6 +126,10 @@ class Internal:
elif key in ('ljname', 'outname', 'progname'):
setattr(self.dice, key, value[0])
elif key == 'randominit':
if value in ('always','first'):
setattr(self.dice,key,value)
elif key in ('ncores', 'isave'):
err = "Error: expected a positive integer for keyword {} in file {}".format(key, self.infile)
@@ -414,6 +418,9 @@ class Internal:
if not nsites.isdigit():
sys.exit("Error: expected an integer in line {} of file {}".format(line, self.dice.ljname))
if molname is None:
sys.exit("Error: expected a molecule name in line {} of file {}".format(line, self.dice.ljname))
nsites = int(nsites)
self.system.add_type(nsites, Molecule(molname))
@@ -679,7 +686,8 @@ class Internal:
for proc in range(1, self.player.nprocs + 1): ## Run over folders
path = "step{:02d}".format(cycle) + os.sep + "p{:02d}".format(proc)
simdir = "simfiles"
path = simdir + os.sep + "step{:02d}".format(cycle) + os.sep + "p{:02d}".format(proc)
file = path + os.sep + self.dice.outname + ".xyz"
if not os.path.isfile(file):
sys.exit("Error: cannot find file {}".format(file))
@@ -795,10 +803,11 @@ class Internal:
## Dice related Upper fuctions
def print_last_config(self, cycle, proc):
sim_dir = "simfiles"
step_dir = "step{:02d}".format(cycle)
proc_dir = "p{:02d}".format(proc)
path = step_dir + os.sep + proc_dir
path = sim_dir + os.sep + 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))
@@ -818,14 +827,18 @@ class Internal:
xyzfile = xyzfile[nsites :] ## Take the last configuration
file = self.dice.outname + ".xyz.last-" + proc_dir
file = path + os.sep + "last.xyz"
fh = open(file, "w")
for line in xyzfile:
fh.write(line)
def new_density(self, proc):
def new_density(self, cycle, proc):
file = self.dice.outname + ".xyz.last-" + "p{:02d}".format(proc)
sim_dir = "simfiles"
step_dir = "step{:02d}".format(cycle-1)
proc_dir = "p{:02d}".format(proc)
path = sim_dir + os.sep + step_dir + os.sep + proc_dir
file = path + os.sep + "last.xyz"
if not os.path.isfile(file):
sys.exit("Error: cannot find the xyz file {} in main directory".format(file))
try:
@@ -847,6 +860,8 @@ class Internal:
return density
def simulation_process(self, cycle, proc):
setproctitle.setproctitle("diceplayer-step{:0d}-p{:0d}".format(cycle,proc))
try:
self.dice.make_proc_dir(cycle, proc)
@@ -857,40 +872,49 @@ class Internal:
def make_inputs(self, cycle, proc):
sim_dir = "simfiles"
step_dir = "step{:02d}".format(cycle)
proc_dir = "p{:02d}".format(proc)
path = step_dir + os.sep + proc_dir
path = sim_dir + os.sep + 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)
if self.dice.randominit == 'first' and cycle > 1:
step_dir = "step{:02d}".format(cycle-1)
last_path = sim_dir + os.sep + step_dir + os.sep + proc_dir
xyzfile = last_path + os.sep + "last.xyz"
self.make_init_file(path, xyzfile)
if len(self.dice.nstep) == 2: ## Means NVT simulation
self.make_nvt_ter(path)
self.make_nvt_ter(cycle, path)
self.make_nvt_eq(path)
elif len(self.dice.nstep) == 3: ## Means NPT simulation
if self.randominit:
self.make_nvt_ter(path)
if self.dice.randominit == 'first' and cycle > 1:
self.dens = self.new_density(cycle, proc)
else:
self.dens = self.new_density(proc)
self.make_nvt_ter(cycle, path)
self.make_npt_ter(path)
self.make_npt_ter(cycle, 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):
# if (self.dice.randominit == 'first' and cycle > 1):
# last_path = sim_dir + os.sep + "step{:02d}".format(cycle-1) + os.sep + proc_dir
# shutil.copyfile(last_path + os.sep + "phb.dat", path + os.sep + "phb.dat")
def make_nvt_ter(self,cycle, path):
file = path + os.sep + "NVT.ter"
try:
@@ -909,12 +933,12 @@ class Internal:
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:
if self.dice.randominit == 'first' and cycle > 1:
fh.write("init = yesreadxyz\n")
fh.write("nstep = {}\n".format(self.player.altsteps))
else:
fh.write("init = yes\n")
fh.write("nstep = {}\n".format(self.dice.nstep[0]))
fh.write("vstep = 0\n")
fh.write("mstop = 1\n")
@@ -962,7 +986,7 @@ class Internal:
fh.close()
def make_npt_ter(self,path):
def make_npt_ter(self, cycle, path):
file = path + os.sep + "NPT.ter"
try:
@@ -981,13 +1005,14 @@ class Internal:
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:
if self.dice.randominit == 'first' and cycle > 1:
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)))
else:
fh.write("init = no\n") ## Because there will be a previous NVT simulation
fh.write("vstep = {}\n".format(int(self.dice.nstep[1] / 5)))
fh.write("nstep = 5\n")
fh.write("mstop = 1\n")
@@ -1055,27 +1080,27 @@ class Internal:
file = path + os.sep + self.dice.outname + ".xy"
try:
fh = open(file, "w")
fh = open(file, "w", 1)
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].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 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("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(rx, ry, rz))
fh.write("$end")
@@ -1137,7 +1162,7 @@ class Internal:
self.tol_factor = 1.2
self.qmprog = "g16"
self.cyc = 1
self.initcyc = 1
class Dice:
@@ -1147,7 +1172,8 @@ class Internal:
self.progname = "dice"
self.path = None
self.init = "yes"
self.randominit = 'first'
self.temp = 300.0
self.press = 1.0
self.isave = 1000 # ASEC construction will take this into account
@@ -1167,42 +1193,51 @@ class Internal:
def make_proc_dir(self, cycle, proc):
sim_dir = "simfiles"
step_dir = "step{:02d}".format(cycle)
proc_dir = "p{:02d}".format(proc)
path = step_dir + os.sep + proc_dir
path = sim_dir + os.sep + 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):
sim_dir = "simfiles"
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()
fh.write("Simulation process {} initiated with pid {}\n".format(sim_dir + os.sep + step_dir + os.sep + proc_dir, os.getpid()))
except Exception as err:
print("I/O error({0}): {1}".format(err))
path = step_dir + os.sep + proc_dir
path = sim_dir + os.sep + step_dir + os.sep + proc_dir
working_dir = os.getcwd()
os.chdir(path)
if len(self.nstep) == 2: ## Means NVT simulation
if self.randominit == 'no' or (self.randominit == 'first' and cycle > 1):
string_tmp = 'previous'
else:
string_tmp = 'random'
## NVT thermalization
string = "(from " + ("random" if self.randominit else "previous") + " configuration)"
fh.write("p{:02d}> NVT thermalization initiated {} on {}\n".format(proc, string,
string = "(from " + string_tmp + " configuration)"
fh.write("p{:02d}> NVT thermalization finished {} 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)
if shutil.which("bash") != None:
exit_status = subprocess.call(["bash","-c","exec -a dice-step{}-p{} {} < {} > {}".format(cycle, proc, self.progname, infh.name, outfh.name)])
else:
exit_status = subprocess.call(self.progname, stin=infh.name, stout=outfh.name)
infh.close()
outfh.close()
@@ -1224,7 +1259,11 @@ class Internal:
infh = open("NVT.eq")
outfh = open("NVT.eq.out", "w")
exit_status = subprocess.call(self.progname, stdin=infh, stdout=outfh)
if shutil.which("bash") != None:
exit_status = subprocess.call(["bash","-c","exec -a dice-step{}-p{} {} < {} > {}".format(cycle, proc, self.progname, infh.name, outfh.name)])
else:
exit_status = subprocess.call(self.progname, stin=infh.name, stout=outfh.name)
infh.close()
outfh.close()
@@ -1246,14 +1285,18 @@ class Internal:
elif len(self.nstep) == 3: ## Means NPT simulation
## NVT thermalization if randominit
if self.randominit:
if self.randominit == 'always' or (self.randominit == 'first' and cycle == 1):
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)
if shutil.which("bash") != None:
exit_status = subprocess.call(["bash","-c","exec -a dice-step{}-p{} {} < {} > {}".format(cycle, proc, self.progname, infh.name, outfh.name)])
else:
exit_status = subprocess.call(self.progname, stin=infh.name, stout=outfh.name)
infh.close()
outfh.close()
@@ -1270,14 +1313,21 @@ class Internal:
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,
if not self.randominit == 'always' or (self.randominit == 'first' and cycle == 1):
string = " (from previous configuration) "
else:
string = " "
fh.write("p{:02d}> NPT thermalization finished {} 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)
if shutil.which("bash") != None:
exit_status = subprocess.call(["bash","-c","exec -a dice-step{}-p{} {} < {} > {}".format(cycle, proc, self.progname, infh.name, outfh.name)])
else:
exit_status = subprocess.call(self.progname, stin=infh.name, stout=outfh.name)
infh.close()
outfh.close()
@@ -1299,7 +1349,11 @@ class Internal:
infh = open("NPT.eq")
outfh = open("NPT.eq.out", "w")
exit_status = subprocess.call(self.progname, stdin=infh, stdout=outfh)
if shutil.which("bash") != None:
exit_status = subprocess.call(["bash","-c","exec -a dice-step{}-p{} {} < {} > {}".format(cycle, proc, self.progname, infh.name, outfh.name)])
else:
exit_status = subprocess.call(self.progname, stin=infh.name, stout=outfh.name)
infh.close()
outfh.close()