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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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.control.in.swp
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DPpack/Dice.py
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@@ -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

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

6
DPpack/MolHandling.py
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@@ -375,16 +375,22 @@ class Molecule:
evals, evecs = self.principal_axes() evals, evecs = self.principal_axes()
if round(linalg.det(evecs)) == -1: if round(linalg.det(evecs)) == -1:
evecs[0,2] *= -1 evecs[0,2] *= -1
evecs[1,2] *= -1 evecs[1,2] *= -1
evecs[2,2] *= -1 evecs[2,2] *= -1
if round(linalg.det(evecs)) != 1: if round(linalg.det(evecs)) != 1:
sys.exit("Error: could not make a rotation matrix while adopting the standard orientation") sys.exit("Error: could not make a rotation matrix while adopting the standard orientation")
rot_matrix = evecs.T rot_matrix = evecs.T
for atom in self.atom: for atom in self.atom:
position = np.array([ atom.rx, atom.ry, atom.rz ]) position = np.array([ atom.rx, atom.ry, atom.rz ])
new_position = np.matmul(rot_matrix, position.T).T new_position = np.matmul(rot_matrix, position.T).T
atom.rx = new_position[0] atom.rx = new_position[0]
atom.ry = new_position[1] atom.ry = new_position[1]
atom.rz = new_position[2] atom.rz = new_position[2]

158
DPpack/SetGlobals.py
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@@ -1,3 +1,4 @@
import setproctitle
import os, sys import os, sys
import shutil import shutil
import textwrap 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) max_seed = 4294967295 ## Maximum allowed value for a seed (numpy)
class Internal: class Internal:
def __init__(self, infile, outfile): def __init__(self, infile, outfile):
self.cyc = 1
self.infile = infile self.infile = infile
self.outfile = outfile self.outfile = outfile
@@ -51,7 +52,6 @@ class Internal:
## Dice: ## Dice:
self.combrule = None self.combrule = None
self.randominit = True
def read_keywords(self): def read_keywords(self):
@@ -127,6 +127,10 @@ class Internal:
elif key in ('ljname', 'outname', 'progname'): elif key in ('ljname', 'outname', 'progname'):
setattr(self.dice, key, value[0]) setattr(self.dice, key, value[0])
elif key == 'randominit':
if value in ('always','first'):
setattr(self.dice,key,value)
elif key in ('ncores', 'isave'): elif key in ('ncores', 'isave'):
err = "Error: expected a positive integer for keyword {} in file {}".format(key, self.infile) err = "Error: expected a positive integer for keyword {} in file {}".format(key, self.infile)
if not value[0].isdigit(): if not value[0].isdigit():
@@ -414,6 +418,9 @@ class Internal:
if not nsites.isdigit(): if not nsites.isdigit():
sys.exit("Error: expected an integer in line {} of file {}".format(line, self.dice.ljname)) 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) nsites = int(nsites)
self.system.add_type(nsites, Molecule(molname)) 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 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" file = path + os.sep + self.dice.outname + ".xyz"
if not os.path.isfile(file): if not os.path.isfile(file):
sys.exit("Error: cannot find file {}".format(file)) sys.exit("Error: cannot find file {}".format(file))
@@ -796,9 +804,10 @@ class Internal:
def print_last_config(self, cycle, proc): def print_last_config(self, cycle, proc):
sim_dir = "simfiles"
step_dir = "step{:02d}".format(cycle) step_dir = "step{:02d}".format(cycle)
proc_dir = "p{:02d}".format(proc) 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" file = path + os.sep + self.dice.outname + ".xyz"
if not os.path.isfile(file): if not os.path.isfile(file):
sys.exit("Error: cannot find the xyz file {}".format(file)) sys.exit("Error: cannot find the xyz file {}".format(file))
@@ -818,14 +827,18 @@ class Internal:
xyzfile = xyzfile[nsites :] ## Take the last configuration 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") fh = open(file, "w")
for line in xyzfile: for line in xyzfile:
fh.write(line) 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): if not os.path.isfile(file):
sys.exit("Error: cannot find the xyz file {} in main directory".format(file)) sys.exit("Error: cannot find the xyz file {} in main directory".format(file))
try: try:
@@ -848,6 +861,8 @@ class Internal:
def simulation_process(self, cycle, proc): def simulation_process(self, cycle, proc):
setproctitle.setproctitle("diceplayer-step{:0d}-p{:0d}".format(cycle,proc))
try: try:
self.dice.make_proc_dir(cycle, proc) self.dice.make_proc_dir(cycle, proc)
self.make_inputs(cycle, proc) self.make_inputs(cycle, proc)
@@ -857,32 +872,35 @@ class Internal:
def make_inputs(self, cycle, proc): def make_inputs(self, cycle, proc):
sim_dir = "simfiles"
step_dir = "step{:02d}".format(cycle) step_dir = "step{:02d}".format(cycle)
proc_dir = "p{:02d}".format(proc) 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 = time.time() ## Take the decimal places 7 to 12 of the
num = (num - int(num)) * 1e6 ## time in seconds as a floating point 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 num = int((num - int(num)) * 1e6) ## to make an integer in the range 1-1e6
random.seed( (os.getpid() * num) % (max_seed + 1) ) random.seed( (os.getpid() * num) % (max_seed + 1) )
if self.randominit == False or self.player.cyc > 1: if self.dice.randominit == 'first' and cycle > 1:
xyzfile = self.dice.outname + ".xyz.last-" + "p{:02d}".format(proc) 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) self.make_init_file(path, xyzfile)
if len(self.dice.nstep) == 2: ## Means NVT simulation 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) self.make_nvt_eq(path)
elif len(self.dice.nstep) == 3: ## Means NPT simulation elif len(self.dice.nstep) == 3: ## Means NPT simulation
if self.randominit: if self.dice.randominit == 'first' and cycle > 1:
self.make_nvt_ter(path) self.dens = self.new_density(cycle, proc)
else: 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) self.make_npt_eq(path)
else: else:
@@ -890,7 +908,13 @@ class Internal:
self.make_potential(path) 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" file = path + os.sep + "NVT.ter"
try: try:
@@ -909,12 +933,12 @@ class Internal:
fh.write("dens = {}\n".format(self.dice.dens)) fh.write("dens = {}\n".format(self.dice.dens))
fh.write("temp = {}\n".format(self.dice.temp)) fh.write("temp = {}\n".format(self.dice.temp))
if self.randominit: if self.dice.randominit == 'first' and cycle > 1:
fh.write("init = yes\n")
fh.write("nstep = {}\n".format(self.dice.nstep[0]))
else:
fh.write("init = yesreadxyz\n") fh.write("init = yesreadxyz\n")
fh.write("nstep = {}\n".format(self.player.altsteps)) 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("vstep = 0\n")
fh.write("mstop = 1\n") fh.write("mstop = 1\n")
@@ -962,7 +986,7 @@ class Internal:
fh.close() fh.close()
def make_npt_ter(self,path): def make_npt_ter(self, cycle, path):
file = path + os.sep + "NPT.ter" file = path + os.sep + "NPT.ter"
try: try:
@@ -981,13 +1005,14 @@ class Internal:
fh.write("press = {}\n".format(self.dice.press)) fh.write("press = {}\n".format(self.dice.press))
fh.write("temp = {}\n".format(self.dice.temp)) 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 if self.dice.randominit == 'first' and cycle > 1:
fh.write("vstep = {}\n".format(int(self.dice.nstep[1] / 5)))
else:
fh.write("init = yesreadxyz\n") fh.write("init = yesreadxyz\n")
fh.write("dens = {:<8.4f}\n".format(self.dice.dens)) fh.write("dens = {:<8.4f}\n".format(self.dice.dens))
fh.write("vstep = {}\n".format(int(self.player.altsteps / 5))) 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("nstep = 5\n")
fh.write("mstop = 1\n") fh.write("mstop = 1\n")
@@ -1055,27 +1080,27 @@ class Internal:
file = path + os.sep + self.dice.outname + ".xy" file = path + os.sep + self.dice.outname + ".xy"
try: try:
fh = open(file, "w") fh = open(file, "w", 1)
except: except:
sys.exit("Error: cannot open file {}".format(file)) sys.exit("Error: cannot open file {}".format(file))
for atom in self.system.molecule[0].atom: for atom in self.system.molecule[0].atom:
fh.write("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(atom.rx, atom.ry, atom.rz)) 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: # for i in self.system.molecule[0].ghost_atoms:
with self.system.molecule[0].atom[i] as ghost: # 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)) # 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: # for i in self.system.molecule[0].lp_atoms:
with self.system.molecule[0].atom[i] as lp: # 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)) # fh.write("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(lp.rx, lp.ry, lp.rz))
for line in xyzfile: for line in xyzfile:
atom = line.split() atom = line.split()
rx = float(atom[1]) rx = float(atom[1])
ry = float(atom[2]) ry = float(atom[2])
rz = float(atom[3]) 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("$end") fh.write("$end")
@@ -1137,7 +1162,7 @@ class Internal:
self.tol_factor = 1.2 self.tol_factor = 1.2
self.qmprog = "g16" self.qmprog = "g16"
self.cyc = 1 self.initcyc = 1
class Dice: class Dice:
@@ -1147,7 +1172,8 @@ class Internal:
self.progname = "dice" self.progname = "dice"
self.path = None self.path = None
self.init = "yes"
self.randominit = 'first'
self.temp = 300.0 self.temp = 300.0
self.press = 1.0 self.press = 1.0
self.isave = 1000 # ASEC construction will take this into account self.isave = 1000 # ASEC construction will take this into account
@@ -1167,42 +1193,51 @@ class Internal:
def make_proc_dir(self, cycle, proc): def make_proc_dir(self, cycle, proc):
sim_dir = "simfiles"
step_dir = "step{:02d}".format(cycle) step_dir = "step{:02d}".format(cycle)
proc_dir = "p{:02d}".format(proc) 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: try:
os.makedirs(path) os.makedirs(path)
except: except:
sys.exit("Error: cannot make directory {}".format(path)) sys.exit("Error: cannot make directory {}".format(path))
return
def run_dice(self, cycle, proc, fh): def run_dice(self, cycle, proc, fh):
sim_dir = "simfiles"
step_dir = "step{:02d}".format(cycle) step_dir = "step{:02d}".format(cycle)
proc_dir = "p{:02d}".format(proc) proc_dir = "p{:02d}".format(proc)
try: try:
fh.write("Simulation process {} initiated with pid {}\n".format(step_dir+'/'+proc_dir, os.getpid())) fh.write("Simulation process {} initiated with pid {}\n".format(sim_dir + os.sep + step_dir + os.sep + proc_dir, os.getpid()))
fh.flush()
except Exception as err: except Exception as err:
print("I/O error({0}): {1}".format(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() working_dir = os.getcwd()
os.chdir(path) os.chdir(path)
if len(self.nstep) == 2: ## Means NVT simulation 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 ## NVT thermalization
string = "(from " + ("random" if self.randominit else "previous") + " configuration)" string = "(from " + string_tmp + " configuration)"
fh.write("p{:02d}> NVT thermalization initiated {} on {}\n".format(proc, string, fh.write("p{:02d}> NVT thermalization finished {} on {}\n".format(proc, string,
date_time())) date_time()))
infh = open("NVT.ter") infh = open("NVT.ter")
outfh = open("NVT.ter.out", "w") 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() infh.close()
outfh.close() outfh.close()
@@ -1224,7 +1259,11 @@ class Internal:
infh = open("NVT.eq") infh = open("NVT.eq")
outfh = open("NVT.eq.out", "w") 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() infh.close()
outfh.close() outfh.close()
@@ -1246,14 +1285,18 @@ class Internal:
elif len(self.nstep) == 3: ## Means NPT simulation elif len(self.nstep) == 3: ## Means NPT simulation
## NVT thermalization if randominit ## NVT thermalization if randominit
if self.randominit: if self.randominit == 'always' or (self.randominit == 'first' and cycle == 1):
string = "(from random configuration)" string = "(from random configuration)"
fh.write("p{:02d}> NVT thermalization initiated {} on {}\n".format(proc, fh.write("p{:02d}> NVT thermalization initiated {} on {}\n".format(proc,
string, date_time())) string, date_time()))
infh = open("NVT.ter") infh = open("NVT.ter")
outfh = open("NVT.ter.out", "w") 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() infh.close()
outfh.close() outfh.close()
@@ -1270,14 +1313,21 @@ class Internal:
sys.exit("Dice process p{:02d} did not exit properly".format(proc)) sys.exit("Dice process p{:02d} did not exit properly".format(proc))
## NPT thermalization ## NPT thermalization
string = (" (from previous configuration) " if not self.randominit else " ") if not self.randominit == 'always' or (self.randominit == 'first' and cycle == 1):
fh.write("p{:02d}> NPT thermalization initiated{}on {}\n".format(proc, string, string = " (from previous configuration) "
else:
string = " "
fh.write("p{:02d}> NPT thermalization finished {} on {}\n".format(proc, string,
date_time())) date_time()))
fh.flush()
infh = open("NPT.ter") infh = open("NPT.ter")
outfh = open("NPT.ter.out", "w") 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() infh.close()
outfh.close() outfh.close()
@@ -1299,7 +1349,11 @@ class Internal:
infh = open("NPT.eq") infh = open("NPT.eq")
outfh = open("NPT.eq.out", "w") 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() infh.close()
outfh.close() outfh.close()

7
control.in
View File

@@ -1,5 +1,4 @@
# diceplayer # diceplayer
initcyc = 1
maxcyc = 3 maxcyc = 3
opt = NO opt = NO
nprocs = 4 nprocs = 4
@@ -10,13 +9,13 @@ altsteps = 20000
# dice # dice
ncores = 3 ncores = 3
nmol = 1 100 nmol = 1 50
dens = 0.75 dens = 0.75
nstep = 40000 60000 50000 nstep = 40000 60000 50000
isave = 1000 isave = 1000
ljname = phb.pot ljname = phb.ljc
outname = phb outname = phb
init = yes randominit = first
# Gaussian # Gaussian
level = MP2/aug-cc-pVTZ level = MP2/aug-cc-pVTZ

67
diceplayer.py
View File

@@ -1,11 +1,11 @@
#!/export/apps/python/361/bin/python3 #!/export/apps/python/361/bin/python3
import os, sys, time, signal import os, sys, time, signal
import setproctitle
import argparse import argparse
import shutil import shutil
from multiprocessing import Process, connection from multiprocessing import Process, connection
import DPpack.Dice as Dice
import DPpack.Gaussian as Gaussian import DPpack.Gaussian as Gaussian
from DPpack.PTable import * from DPpack.PTable import *
from DPpack.SetGlobals import * from DPpack.SetGlobals import *
@@ -17,6 +17,8 @@ if __name__ == '__main__':
#### Read and store the arguments passed to the program #### #### Read and store the arguments passed to the program ####
#### and set the usage and help messages #### #### and set the usage and help messages ####
setproctitle.setproctitle("diceplayer-current")
parser = argparse.ArgumentParser(prog='Diceplayer') parser = argparse.ArgumentParser(prog='Diceplayer')
parser.add_argument('--continue', dest='opt_continue' , default=False, action='store_true') parser.add_argument('--continue', dest='opt_continue' , default=False, action='store_true')
parser.add_argument('--version', action='version', version='%(prog)s 1.0') parser.add_argument('--version', action='version', version='%(prog)s 1.0')
@@ -37,21 +39,28 @@ if __name__ == '__main__':
outfile = open(args.outfile,'r') outfile = open(args.outfile,'r')
run_file = outfile.readlines() run_file = outfile.readlines()
control_sequence = ' Step # ' control_sequence = ' Step # '
sucessfull_sequence = '+----------------------------------------------------------------------------------------+'
for line in run_file: for line in run_file:
if control_sequence in line: if control_sequence in line:
cyc = int(line[-2]) + 1 cyc = int(line[-2])
if sucessfull_sequence in line:
cyc += 1
outfile.close() outfile.close()
os.rename(os.path.abspath(args.outfile),os.path.abspath(args.outfile)+".backup")
outfile = open(args.outfile,'w')
if os.path.isfile(args.outfile+".backup"):
os.remove(args.outfile+".backup")
if os.path.exists(args.outfile): os.rename(args.outfile,args.outfile+".backup")
os.rename(os.path.abspath(args.outfile),os.path.abspath(args.outfile)+".backup") outfile = open(args.outfile,'w',1)
outfile = open(args.outfile,'w')
elif os.path.exists(args.outfile):
os.rename(args.outfile, args.outfile+".backup")
outfile = open(args.outfile,'w',1)
else: else:
outfile = open(args.outfile,"w") outfile = open(args.outfile,"w",1)
except EnvironmentError as err: except EnvironmentError as err:
sys.exit(err) sys.exit(err)
@@ -71,7 +80,10 @@ if __name__ == '__main__':
internal.read_keywords() internal.read_keywords()
if args.opt_continue: if args.opt_continue:
internal.player.cyc = cyc try:
internal.player.initcyc = cyc
except:
sys.exit("Error: There is no sutable run.log file to continue the previous process")
internal.check_keywords() internal.check_keywords()
internal.print_keywords() internal.print_keywords()
@@ -106,17 +118,27 @@ if __name__ == '__main__':
internal.outfile.write(90 * "=") internal.outfile.write(90 * "=")
internal.outfile.write("\n") internal.outfile.write("\n")
if not args.opt_continue:
make_simulation_dir()
else:
simdir = "simfiles"
stepdir = "step{:02d}".format(internal.player.initcyc)
if os.path.exists(simdir+os.sep+stepdir):
shutil.rmtree(simdir+os.sep+stepdir)
#### Open the geoms.xyz file and prints the initial geometry if starting from zero #### Open the geoms.xyz file and prints the initial geometry if starting from zero
if internal.player.cyc == 1: if internal.player.initcyc == 1:
try: try:
geomsfh = open("geoms.xyz", "w", 1) path = "geoms.xyz"
geomsfh = open(path, "w", 1)
except EnvironmentError as err: except EnvironmentError as err:
sys.exit(err) sys.exit(err)
internal.system.print_geom(0, geomsfh) internal.system.print_geom(0, geomsfh)
else: else:
try: try:
geomsfh = open("geoms.xyz", "A", 1) path = "geoms.xyz"
geomsfh = open(path, "a", 1)
except EnvironmentError as err: except EnvironmentError as err:
sys.exit(err) sys.exit(err)
@@ -126,10 +148,10 @@ if __name__ == '__main__':
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.initcyc > 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")
@@ -139,20 +161,15 @@ if __name__ == '__main__':
### Start the iterative process ### Start the iterative process
### ###
for cycle in range(internal.player.cyc, internal.player.cyc + internal.player.maxcyc): internal.outfile.write("\n" + 90 * "-" + "\n")
for cycle in range(internal.player.initcyc, internal.player.initcyc + internal.player.maxcyc):
internal.outfile.write("\n" + 90 * "-" + "\n")
internal.outfile.write("{} Step # {}\n".format(40 * " ", cycle)) internal.outfile.write("{} Step # {}\n".format(40 * " ", cycle))
internal.outfile.write(90 * "-" + "\n\n") internal.outfile.write(90 * "-" + "\n\n")
internal.outfile.flush()
make_step_dir(cycle) make_step_dir(cycle)
if internal.player.altsteps == 0 or internal.player.cyc == 1:
internal.dice.randominit = True
else:
internal.dice.randominit = False
#### ####
#### Start block of parallel simulations #### Start block of parallel simulations
#### ####
@@ -181,6 +198,8 @@ if __name__ == '__main__':
for proc in range(1, internal.player.nprocs + 1): for proc in range(1, internal.player.nprocs + 1):
internal.print_last_config(cycle, proc) internal.print_last_config(cycle, proc)
internal.outfile.write("\n+" + 88 * "-" + "+\n")
#### ####
#### End of parallel simulations block #### End of parallel simulations block
#### ####

6
ghosts.in
View File

@@ -1,6 +0,0 @@
G 2 4 6 8 10 12 13 15 17 20
M 2 3 4 5 6 7 8 19 20 22
Z 23 25 26 27 28 29

4
lps.in
View File

@@ -1,4 +0,0 @@
1 12 13 14 109.5 0.95
2 9 10 11 50 1.2
#3 1 5 6
2 17 19 23

1602
new_cyclo.xyz
View File

File diff suppressed because it is too large Load Diff

1602
new_cyclo.xyz.new
View File

File diff suppressed because it is too large Load Diff

1782
new_cyclo.xyz.new2
View File

File diff suppressed because it is too large Load Diff

11
othercontrol.in
View File

@@ -1,11 +0,0 @@
initcyc = -4 pode?
maxcyc = 1
forces = yes
nprocs = 2
# dice
#nmol = aslkj 1 20 slkdfj
dens = 0.75
nsteps = 7000 2500 3876
isave = 1340
ljname = phb.pot

51
phb.pot
View File

@@ -1,51 +0,0 @@
*
2
31 PHENOL BLUE geom/chg MP2/aug-cc-pVTZ Charge MK LJ OPLSAA
1 6 -4.400337 0.665513 0.414312 -0.38759300 0.0700 3.5500
1 6 -4.499567 -0.672788 -0.153273 0.80400100 0.0700 3.5500
1 6 -3.256300 -1.289216 -0.613514 -0.33849100 0.0700 3.5500
1 6 -2.058491 -0.668069 -0.486739 -0.22078300 0.0700 3.5500
1 6 -1.971143 0.651479 0.105111 0.56352700 0.0700 3.5500
1 6 -3.206008 1.296843 0.497122 -0.14537200 0.0700 3.5500
2 8 -5.594533 -1.253085 -0.287655 -0.71446100 0.2100 2.9600
3 7 -0.874044 1.358704 0.276359 -0.72179200 0.1700 3.2500
4 6 0.387854 0.815120 0.144104 0.60712300 0.0700 3.5500
4 6 1.407755 1.658002 -0.332615 -0.29547600 0.0700 3.5500
4 6 0.759497 -0.468150 0.587914 -0.34666100 0.0700 3.5500
4 6 2.710211 1.215186 -0.461194 -0.29854600 0.0700 3.5500
4 6 2.073539 -0.898835 0.508310 -0.23428400 0.0700 3.5500
4 6 3.080760 -0.089365 -0.061116 0.29465100 0.0700 3.5500
5 7 4.372382 -0.539792 -0.201825 -0.19049700 0.1700 3.2500
6 6 5.419802 0.438244 -0.438362 -0.21318300 0.0660 3.5000
6 6 4.763609 -1.735216 0.522254 -0.22542000 0.0660 3.5000
7 1 6.366998 -0.085365 -0.519616 0.10984000 0.0300 2.5000
7 1 5.251961 0.966123 -1.374211 0.07714000 0.0300 2.5000
7 1 5.495169 1.174115 0.367485 0.12575800 0.0300 2.5000
7 1 4.158375 -2.584419 0.214461 0.08322900 0.0300 2.5000
7 1 5.796953 -1.962538 0.280411 0.11536100 0.0300 2.5000
7 1 4.674161 -1.617074 1.606614 0.12144000 0.0300 2.5000
7 1 0.028134 -1.095538 1.080074 0.17943400 0.0300 2.4200
7 1 2.318762 -1.865762 0.919126 0.17725000 0.0300 2.4200
7 1 3.451018 1.898797 -0.846692 0.19884400 0.0300 2.4200
7 1 1.147588 2.669090 -0.614979 0.17338800 0.0300 2.4200
7 1 -3.119300 2.296790 0.900595 0.15153400 0.0300 2.4200
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 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
1 6 2.068235 -0.405210 0.002635 -0.11500000 0.0700 3.5500
1 14 0.675894 -0.405219 0.002635 0.15000000 0.0700 3.5500
1 104 -0.024198 -1.617602 0.002633 -0.11500000 0.0700 3.5500
2 1 0.132026 -3.758753 0.002629 0.11500000 0.0300 2.4200
2 1 2.612026 -3.758753 0.002629 0.11500000 0.0300 2.4200
2 1 2.608235 0.530098 0.002636 0.11500000 0.0300 2.4200
2 1 -1.104198 -1.617602 0.002633 0.11500000 0.0300 2.4200
3 8 -0.004114 0.772571 0.002637 -0.58500000 0.1700 3.0700
3 1 0.619778 1.502200 0.002638 0.43500000 0.0000 0.0000
4 6 4.278235 -1.617645 0.002633 0.11500000 0.1700 3.8000
4 1 4.634902 -0.743994 0.507036 0.00000000 0.0000 0.0000
4 1 4.634902 -2.491297 0.507036 0.00000000 0.0000 0.0000
4 1 4.634902 -1.617645 -1.006173 0.00000000 0.0000 0.0000

108
run.log
View File

@@ -5,7 +5,7 @@
Your python version is 3.6.9 (default, Jan 26 2021, 15:33:00) Your python version is 3.6.9 (default, Jan 26 2021, 15:33:00)
[GCC 8.4.0] [GCC 8.4.0]
Program started on Friday, 05 Nov 2021 at 04:36:09 Program started on Saturday, 20 Nov 2021 at 14:52:20
Environment variables: Environment variables:
OMP_STACKSIZE = Not set OMP_STACKSIZE = Not set
@@ -15,9 +15,9 @@ OMP_STACKSIZE = Not set
------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------
altsteps = 20000 altsteps = 20000
cyc = 1
freq = no freq = no
ghosts = no ghosts = no
initcyc = 1
lps = no lps = no
maxcyc = 3 maxcyc = 3
maxstep = 0.3 maxstep = 0.3
@@ -35,15 +35,15 @@ vdwforces = no
combrule = * combrule = *
dens = 0.75 dens = 0.75
init = yes
isave = 1000 isave = 1000
ljname = phb.pot ljname = phb.ljc
ncores = 3 ncores = 3
nmol = 1 100 nmol = 1 50
nstep = 40000 60000 50000 nstep = 40000 60000 50000
outname = phb outname = phb
press = 1.0 press = 1.0
progname = dice progname = dice
randominit = first
temp = 300.0 temp = 300.0
title = Diceplayer run title = Diceplayer run
upbuf = 360 upbuf = 360
@@ -65,7 +65,7 @@ Program g16 found at /usr/local/g16/g16
Program formchk found at /usr/local/g16/formchk Program formchk found at /usr/local/g16/formchk
========================================================================================== ==========================================================================================
Potential parameters from file phb.pot: Potential parameters from file phb.ljc:
------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------
Combination rule: * Combination rule: *
@@ -131,7 +131,7 @@ Lbl AN X Y Z Charge Epsilon Sigma Mass
========================================================================================== ==========================================================================================
Molecule type 1 - PHENOL: Molecule type 1 - PHENOL_BLUE:
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 Moments of inertia = 3.144054E+02 2.801666E+03 3.027366E+03
@@ -190,49 +190,67 @@ Starting the iterative process.
Step # 1 Step # 1
------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------
Simulation process step01/p01 initiated with pid 7039 Simulation process simfiles/step01/p02 initiated with pid 15516
Simulation process step01/p02 initiated with pid 7040 p02> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 14:52:20
Simulation process step01/p03 initiated with pid 7041 Simulation process simfiles/step01/p01 initiated with pid 15515
Simulation process step01/p04 initiated with pid 7042 p01> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 14:52:20
p03> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 04:36:09 Simulation process simfiles/step01/p03 initiated with pid 15517
p03> NPT thermalization initiated on 05 Nov 2021 at 04:42:40 p03> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 14:52:20
p01> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 04:36:09 Simulation process simfiles/step01/p04 initiated with pid 15518
p01> NPT thermalization initiated on 05 Nov 2021 at 04:42:40 p04> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 14:52:20
p04> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 04:36:09 p03> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 14:54:12
p04> NPT thermalization initiated on 05 Nov 2021 at 04:42:52 p04> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 14:54:13
p02> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 04:36:09 p02> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 14:54:13
p02> NPT thermalization initiated on 05 Nov 2021 at 04:42:54 p01> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 14:54:13
p03> NPT production initiated on 20 Nov 2021 at 14:57:16
p02> NPT production initiated on 20 Nov 2021 at 14:57:19
p04> NPT production initiated on 20 Nov 2021 at 14:57:20
p01> NPT production initiated on 20 Nov 2021 at 14:57:21
p03> ----- NPT production finished on 20 Nov 2021 at 15:00:16
p02> ----- NPT production finished on 20 Nov 2021 at 15:00:21
p04> ----- NPT production finished on 20 Nov 2021 at 15:00:23
p01> ----- NPT production finished on 20 Nov 2021 at 15:00:27
------------------------------------------------------------------------------------------ +----------------------------------------------------------------------------------------+
Step # 2 Step # 2
------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------
Simulation process step02/p01 initiated with pid 7127 Simulation process simfiles/step02/p02 initiated with pid 15559
Simulation process step02/p02 initiated with pid 7128 p02> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:00:27
Simulation process step02/p03 initiated with pid 7129 Simulation process simfiles/step02/p01 initiated with pid 15558
Simulation process step02/p04 initiated with pid 7130 p01> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:00:27
p02> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 05:04:04 Simulation process simfiles/step02/p03 initiated with pid 15560
p02> NPT thermalization initiated on 05 Nov 2021 at 05:10:41 p03> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:00:27
p01> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 05:04:04 Simulation process simfiles/step02/p04 initiated with pid 15561
p01> NPT thermalization initiated on 05 Nov 2021 at 05:10:49 p04> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:00:27
p03> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 05:04:04 p03> NPT production initiated on 20 Nov 2021 at 15:01:30
p03> NPT thermalization initiated on 05 Nov 2021 at 05:10:51 p01> NPT production initiated on 20 Nov 2021 at 15:01:30
p04> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 05:04:04 p02> NPT production initiated on 20 Nov 2021 at 15:01:31
p04> NPT thermalization initiated on 05 Nov 2021 at 05:10:57 p04> NPT production initiated on 20 Nov 2021 at 15:01:31
p03> ----- NPT production finished on 20 Nov 2021 at 15:04:29
p02> ----- NPT production finished on 20 Nov 2021 at 15:04:33
p01> ----- NPT production finished on 20 Nov 2021 at 15:04:34
p04> ----- NPT production finished on 20 Nov 2021 at 15:04:37
------------------------------------------------------------------------------------------ +----------------------------------------------------------------------------------------+
Step # 3 Step # 3
------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------
Simulation process step03/p01 initiated with pid 7182 Simulation process simfiles/step03/p01 initiated with pid 15661
Simulation process step03/p02 initiated with pid 7183 p01> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:04:37
Simulation process step03/p03 initiated with pid 7184 Simulation process simfiles/step03/p02 initiated with pid 15662
Simulation process step03/p04 initiated with pid 7185 p02> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:04:37
p04> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 05:32:04 Simulation process simfiles/step03/p04 initiated with pid 15664
p04> NPT thermalization initiated on 05 Nov 2021 at 05:38:40 p04> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:04:37
p01> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 05:32:04 Simulation process simfiles/step03/p03 initiated with pid 15663
p01> NPT thermalization initiated on 05 Nov 2021 at 05:38:46 p03> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:04:37
p03> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 05:32:04 p03> NPT production initiated on 20 Nov 2021 at 15:05:41
p03> NPT thermalization initiated on 05 Nov 2021 at 05:38:51 p01> NPT production initiated on 20 Nov 2021 at 15:05:42
p02> NVT thermalization initiated (from random configuration) on 05 Nov 2021 at 05:32:04 p04> NPT production initiated on 20 Nov 2021 at 15:05:42
p02> NPT thermalization initiated on 05 Nov 2021 at 05:38:51 p02> NPT production initiated on 20 Nov 2021 at 15:05:44
p01> ----- NPT production finished on 20 Nov 2021 at 15:08:44
p03> ----- NPT production finished on 20 Nov 2021 at 15:08:45
p04> ----- NPT production finished on 20 Nov 2021 at 15:08:48
p02> ----- NPT production finished on 20 Nov 2021 at 15:08:51
+----------------------------------------------------------------------------------------+

32
run.log.backup
View File

@@ -5,7 +5,7 @@
Your python version is 3.6.9 (default, Jan 26 2021, 15:33:00) Your python version is 3.6.9 (default, Jan 26 2021, 15:33:00)
[GCC 8.4.0] [GCC 8.4.0]
Program started on Friday, 05 Nov 2021 at 04:35:58 Program started on Saturday, 20 Nov 2021 at 13:29:59
Environment variables: Environment variables:
OMP_STACKSIZE = Not set OMP_STACKSIZE = Not set
@@ -15,11 +15,11 @@ OMP_STACKSIZE = Not set
------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------
altsteps = 20000 altsteps = 20000
cyc = 1
freq = no freq = no
ghosts = no ghosts = no
initcyc = 1
lps = no lps = no
maxcyc = 3 maxcyc = 4
maxstep = 0.3 maxstep = 0.3
nprocs = 4 nprocs = 4
opt = no opt = no
@@ -35,15 +35,15 @@ vdwforces = no
combrule = * combrule = *
dens = 0.75 dens = 0.75
init = yes
isave = 1000 isave = 1000
ljname = phb.pot ljname = phb.ljc
ncores = 3 ncores = 3
nmol = 1 100 nmol = 1 50
nstep = 40000 60000 50000 nstep = 40000 60000 50000
outname = phb outname = phb
press = 1.0 press = 1.0
progname = dice progname = dice
randominit = first
temp = 300.0 temp = 300.0
title = Diceplayer run title = Diceplayer run
upbuf = 360 upbuf = 360
@@ -65,7 +65,7 @@ Program g16 found at /usr/local/g16/g16
Program formchk found at /usr/local/g16/formchk Program formchk found at /usr/local/g16/formchk
========================================================================================== ==========================================================================================
Potential parameters from file phb.pot: Potential parameters from file phb.ljc:
------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------
Combination rule: * Combination rule: *
@@ -131,7 +131,7 @@ Lbl AN X Y Z Charge Epsilon Sigma Mass
========================================================================================== ==========================================================================================
Molecule type 1 - PHENOL: Molecule type 1 - PHENOL_BLUE:
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 Moments of inertia = 3.144054E+02 2.801666E+03 3.027366E+03
@@ -190,3 +190,19 @@ Starting the iterative process.
Step # 1 Step # 1
------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------
Simulation process simfiles/step01/p01 initiated with pid 14014
p01> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 13:29:59
Simulation process simfiles/step01/p02 initiated with pid 14015
p02> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 13:29:59
Simulation process simfiles/step01/p03 initiated with pid 14016
p03> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 13:29:59
Simulation process simfiles/step01/p04 initiated with pid 14017
p04> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 13:29:59
p03> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 13:31:50
p01> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 13:31:51
p04> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 13:31:52
p02> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 13:31:52
p03> NPT production initiated on 20 Nov 2021 at 13:34:53
p02> NPT production initiated on 20 Nov 2021 at 13:34:57
p01> NPT production initiated on 20 Nov 2021 at 13:34:58
p04> NPT production initiated on 20 Nov 2021 at 13:35:00

64
test4.py
View File

@@ -1,64 +0,0 @@
#!/opt/local/bin/python3
import sys, math
from math import pi
import numpy as np
from numpy import linalg
from numpy.random import rand, random
from copy import deepcopy
from DPpack.MolHandling import *
from DPpack.PTable import *
natoms = input("# of atoms: ")
natoms = int(natoms)
file = input("xyz file: ")
molecules=[]
with open(file) as fh:
xyzfile = fh.readlines()
file += ".new"
file2 = file + "2"
fh = open(file, "w")
fh2 = open(file2, "w")
total_atoms = int(xyzfile.pop(0).split()[0])
fh.write("{}\n".format(total_atoms))
comment = xyzfile.pop(0)
fh.write("{}".format(comment))
nmols = round(total_atoms/natoms)
for i in range(nmols):
molecules.append([])
for j in range(natoms):
molecules[i].append({})
line = xyzfile.pop(0).split()
molecules[i][j]['na'] = int(line[0])
molecules[i][j]['rx'] = float(line[1])
molecules[i][j]['ry'] = float(line[2])
molecules[i][j]['rz'] = float(line[3])
molecules[i][j]['mass'] = atommass[molecules[0][j]['na']]
for atom in molecules[0]:
fh.write("{:>4s} {:>11.5f} {:>11.5f} {:>11.5f}\n".format(atomsymb[atom['na']],
atom['rx'], atom['ry'], atom['rz']))
fh2.write("{:>4s} {:>11.5f} {:>11.5f} {:>11.5f}\n".format(atomsymb[atom['na']],
atom['rx'], atom['ry'], atom['rz']))
for i in range(1, nmols):
fh2.write("{}\n".format(natoms))
fh2.write("{}".format(comment))
rmsd, projected_mol = rmsd_fit(molecules[i], molecules[0])
print("{:>9.5f}".format(rmsd))
for atom in projected_mol:
fh.write("{:>4s} {:>11.5f} {:>11.5f} {:>11.5f}\n".format(atomsymb[atom['na']],
atom['rx'], atom['ry'], atom['rz']))
fh2.write("{:>4s} {:>11.5f} {:>11.5f} {:>11.5f}\n".format(atomsymb[atom['na']],
atom['rx'], atom['ry'], atom['rz']))
fh.close()
fh2.close()