Vitor Hideyoshi
0d877e3dce
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>
528 lines
14 KiB
Python
528 lines
14 KiB
Python
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
|
|
|
|
|
|
|