HideyoshiNakazone/DicePlayer
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Initial Translation of Gaussian Processes and Packaging of DicePlayer python module

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This commit adds the methods that were present in the Gaussian.py file into the SetGlobals.py file and packages the program into a diceplayer module so it can be ran using 'python3 -m diceplayer'

Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
This commit is contained in:
Vitor Hideyoshi
2021-12-03 21:28:27 +00:00
parent 49d509029f
commit 2a4e9eff0c
15 changed files with 1088 additions and 337 deletions
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4
control.in
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@@ -1,6 +1,6 @@
# diceplayer # diceplayer
maxcyc = 3 maxcyc = 3
opt = NO opt = YES
nprocs = 4 nprocs = 4
qmprog = g16 qmprog = g16
lps = no lps = no
@@ -11,7 +11,7 @@ altsteps = 20000
ncores = 3 ncores = 3
nmol = 1 50 nmol = 1 50
dens = 0.75 dens = 0.75
nstep = 40000 60000 50000 nstep = 4000 6000
isave = 1000 isave = 1000
ljname = phb.ljc ljname = phb.ljc
outname = phb outname = phb

527
diceplayer/DPpack/.Dice.py Normal file
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@@ -0,0 +1,527 @@
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

0
DPpack/.MolHandling.py → diceplayer/DPpack/.MolHandling.py
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0
DPpack/.SetGlobals.py → diceplayer/DPpack/.SetGlobals.py
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179
DPpack/Gaussian.py → diceplayer/DPpack/Gaussian.py
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@@ -148,7 +148,7 @@ def print_grad_hessian(cycle, cur_gradient, hessian):
return return
## Change the name to make_gaussian_input
def make_force_input(cycle, asec_charges): def make_force_input(cycle, asec_charges):
path = "step{:02d}".format(cycle) + os.sep + "qm" path = "step{:02d}".format(cycle) + os.sep + "qm"
@@ -241,92 +241,92 @@ def make_force_input(cycle, asec_charges):
def make_charge_input(cycle, asec_charges): # def make_charge_input(cycle, asec_charges):
path = "step{:02d}".format(cycle) + os.sep + "qm" # path = "step{:02d}".format(cycle) + os.sep + "qm"
file = path + os.sep + "asec2.gjf" # file = path + os.sep + "asec2.gjf"
try: # try:
fh = open(file, "w") # fh = open(file, "w")
except: # except:
sys.exit("Error: cannot open file {}".format(file)) # sys.exit("Error: cannot open file {}".format(file))
fh.write("%Chk=asec.chk\n") # fh.write("%Chk=asec.chk\n")
if gaussian['mem'] != None: # if gaussian['mem'] != None:
fh.write("%Mem={}MB\n".format(gaussian['mem'])) # fh.write("%Mem={}MB\n".format(gaussian['mem']))
fh.write("%Nprocs={}\n".format(player['nprocs'] * dice['ncores'])) # fh.write("%Nprocs={}\n".format(player['nprocs'] * dice['ncores']))
kword_line = "#P " + gaussian['chglevel'] + " " + gaussian['keywords'] + " Charge NoSymm" # kword_line = "#P " + gaussian['chglevel'] + " " + gaussian['keywords'] + " Charge NoSymm"
if player['opt'] != "no" or cycle > 1: # if player['opt'] != "no" or cycle > 1:
kword_line += " Guess=Read" # kword_line += " Guess=Read"
kword_line += " Pop={} Density=Current\n".format(gaussian['pop']) # kword_line += " Pop={} Density=Current\n".format(gaussian['pop'])
fh.write(textwrap.fill(kword_line, 90)) # fh.write(textwrap.fill(kword_line, 90))
fh.write("\n") # fh.write("\n")
fh.write("\nCharge calculation - Cycle number {}\n".format(cycle)) # fh.write("\nCharge calculation - Cycle number {}\n".format(cycle))
fh.write("\n") # fh.write("\n")
fh.write("{},{}\n".format(gaussian['chgmult'][0], gaussian['chgmult'][1])) # fh.write("{},{}\n".format(gaussian['chgmult'][0], gaussian['chgmult'][1]))
for atom in molecules[0]: # for atom in molecules[0]:
symbol = atomsymb[atom['na']] # symbol = atomsymb[atom['na']]
fh.write("{:<2s} {:>10.5f} {:>10.5f} {:>10.5f}\n".format(symbol, # fh.write("{:<2s} {:>10.5f} {:>10.5f} {:>10.5f}\n".format(symbol,
atom['rx'], atom['ry'], atom['rz'])) # atom['rx'], atom['ry'], atom['rz']))
if cycle >= player['switchcyc']: # if cycle >= player['switchcyc']:
for ghost in ghost_atoms: # for ghost in ghost_atoms:
fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format( # fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format(
ghost['rx'], ghost['ry'], ghost['rz'])) # ghost['rx'], ghost['ry'], ghost['rz']))
for lp in lp_atoms: # for lp in lp_atoms:
fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format( # fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format(
lp['rx'], lp['ry'], lp['rz'])) # lp['rx'], lp['ry'], lp['rz']))
fh.write("\n") # fh.write("\n")
## If gmiddle file was informed, write its contents in asec.gjf # ## If gmiddle file was informed, write its contents in asec.gjf
if gaussian['gmiddle'] != None: # if gaussian['gmiddle'] != None:
if not os.path.isfile(gaussian['gmiddle']): # if not os.path.isfile(gaussian['gmiddle']):
sys.exit("Error: cannot find file {} in main directory".format( # sys.exit("Error: cannot find file {} in main directory".format(
gaussian['gmiddle'])) # gaussian['gmiddle']))
try: # try:
with open(gaussian['gmiddle']) as gmiddlefile: # with open(gaussian['gmiddle']) as gmiddlefile:
gmiddle = gmiddlefile.readlines() # gmiddle = gmiddlefile.readlines()
except: # except:
sys.exit("Error: cannot open file {}".format(gaussian['gmiddle'])) # sys.exit("Error: cannot open file {}".format(gaussian['gmiddle']))
for line in gmiddle: # for line in gmiddle:
fh.write(line) # fh.write(line)
fh.write("\n") # fh.write("\n")
## Write the ASEC: # ## Write the ASEC:
for charge in asec_charges: # for charge in asec_charges:
fh.write("{:>10.5f} {:>10.5f} {:>10.5f} {:>11.8f}\n".format( # fh.write("{:>10.5f} {:>10.5f} {:>10.5f} {:>11.8f}\n".format(
charge['rx'], charge['ry'], charge['rz'], charge['chg'])) # charge['rx'], charge['ry'], charge['rz'], charge['chg']))
fh.write("\n") # fh.write("\n")
## If gbottom file was informed, write its contents in asec.gjf # ## If gbottom file was informed, write its contents in asec.gjf
if gaussian['gbottom'] != None: # if gaussian['gbottom'] != None:
if not os.path.isfile(gaussian['gbottom']): # if not os.path.isfile(gaussian['gbottom']):
sys.exit("Error: cannot find file {} in main directory".format( # sys.exit("Error: cannot find file {} in main directory".format(
gaussian['gbottom'])) # gaussian['gbottom']))
try: # try:
with open(gaussian['gbottom']) as gbottomfile: # with open(gaussian['gbottom']) as gbottomfile:
gbottom = gbottomfile.readlines() # gbottom = gbottomfile.readlines()
except: # except:
sys.exit("Error: cannot open file {}".format(gaussian['gbottom'])) # sys.exit("Error: cannot open file {}".format(gaussian['gbottom']))
for line in gbottom: # for line in gbottom:
fh.write(line) # fh.write(line)
fh.write("\n") # fh.write("\n")
fh.close() # fh.close()
return # return
@@ -371,50 +371,3 @@ def read_charges(file, fh):
fh.write("------------------------------------\n") fh.write("------------------------------------\n")
return return
def run_gaussian(cycle, type, fh):
path = "step{:02d}".format(cycle) + os.sep + "qm"
work_dir = os.getcwd()
os.chdir(path)
if type == "force":
infile = "asec.gjf"
elif type == "charge":
infile = "asec2.gjf"
fh.write("\nCalculation of {}s initiated with Gaussian on {}\n".format(type, date_time()))
exit_status = subprocess.call([player['qmprog'], infile])
if exit_status != 0:
sys.exit("Gaussian process did not exit properly")
fh.write("Calculation of {}s finished on {}\n".format(type, date_time()))
os.chdir(work_dir)
return
def run_formchk(cycle, fh):
path = "step{:02d}".format(cycle) + os.sep + "qm"
work_dir = os.getcwd()
os.chdir(path)
fh.write("Formatting the checkpoint file... ")
exit_status = subprocess.call(["formchk", "asec.chk"])
fh.write("Done\n")
os.chdir(work_dir)
return

0
DPpack/Misc.py → diceplayer/DPpack/Misc.py
View File

32
DPpack/MolHandling.py → diceplayer/DPpack/MolHandling.py
View File

@@ -8,8 +8,8 @@ from copy import deepcopy
import numpy as np import numpy as np
from numpy import linalg from numpy import linalg
from DPpack.Misc import * from diceplayer.DPpack.Misc import *
from DPpack.PTable import * from diceplayer.DPpack.PTable import *
env = ["OMP_STACKSIZE"] env = ["OMP_STACKSIZE"]
@@ -44,20 +44,6 @@ class System:
return distance return distance
def minimum_distance(self, index1, index2):
distances = []
for atom1 in self.molecule[index1]:
if atom1.na != ghost_number:
for atom2 in self.molecule[index2]:
if atom2.na != ghost_number:
dx = atom1.rx - atom2.rx
dy = atom1.ry - atom2.ry
dz = atom1.rz - atom2.rz
distances.append(math.sqrt(dx**2 + dy**2 + dz**2))
return min(distances)
def rmsd_fit(self, index_p, index_r): def rmsd_fit(self, index_p, index_r):
projecting_mol = self.molecule[index_p] projecting_mol = self.molecule[index_p]
@@ -434,6 +420,20 @@ class Molecule:
fh.write(" Dipole moment = ( {:>9.4f} , {:>9.4f} , {:>9.4f} ) Total = {:>9.4f} Debye\n\n".format( fh.write(" Dipole moment = ( {:>9.4f} , {:>9.4f} , {:>9.4f} ) Total = {:>9.4f} Debye\n\n".format(
chg_dip[1], chg_dip[2], chg_dip[3], chg_dip[4])) chg_dip[1], chg_dip[2], chg_dip[3], chg_dip[4]))
def minimum_distance(self, molec):
distances = []
for atom1 in self.atom:
if atom1.na != ghost_number:
for atom2 in molec.atom:
if atom2.na != ghost_number:
dx = atom1.rx - atom2.rx
dy = atom1.ry - atom2.ry
dz = atom1.rz - atom2.rz
distances.append(math.sqrt(dx**2 + dy**2 + dz**2))
return min(distances)
class Atom: class Atom:
def __init__(self, lbl,na,rx,ry,rz,chg,eps,sig): def __init__(self, lbl,na,rx,ry,rz,chg,eps,sig):

0
DPpack/Molcas.py → diceplayer/DPpack/Molcas.py
View File

0
DPpack/Optimization.py → diceplayer/DPpack/Optimization.py
View File

0
DPpack/PTable.py → diceplayer/DPpack/PTable.py
View File

417
DPpack/SetGlobals.py → diceplayer/DPpack/SetGlobals.py
View File

@@ -6,9 +6,9 @@ import types
from numpy.core.fromnumeric import partition from numpy.core.fromnumeric import partition
from DPpack.MolHandling import * from diceplayer.DPpack.MolHandling import *
from DPpack.PTable import * from diceplayer.DPpack.PTable import *
from DPpack.Misc import * from diceplayer.DPpack.Misc import *
from numpy import random from numpy import random
import subprocess import subprocess
@@ -129,7 +129,7 @@ class Internal:
elif key == 'randominit': elif key == 'randominit':
if value in ('always','first'): if value in ('always','first'):
setattr(self.dice,key,value) setattr(self.dice,key,value[0])
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)
@@ -207,7 +207,7 @@ class Internal:
sys.exit(err) sys.exit(err)
elif key == 'level': elif key == 'level':
setattr(self.gaussian, key, value) setattr(self.gaussian, key, value[0])
elif key in ('gmiddle', 'gbottom'): elif key in ('gmiddle', 'gbottom'):
setattr(self.gaussian, key, value[0]) setattr(self.gaussian, key, value[0])
@@ -665,8 +665,10 @@ class Internal:
### I still have to talk with Herbet about this function ### I still have to talk with Herbet about this function
def populate_asec_vdw(self, cycle): def populate_asec_vdw(self, cycle):
asec_charges = [] # (rx, ry, rz, chg) ## Both asec_charges and vdw_meanfield will utilize the Molecule() class and Atoms() with some None elements
vdw_meanfield = [] # (rx, ry, rz, eps, sig)
asec_charges = Molecule() # (lbl=None, na=None, rx, ry, rz, chg, eps=None, sig=None)
vdw_meanfield = Molecule() # (lbl=None, na=None, rx, ry, rz, chg=None, eps, sig)
if self.dice.nstep[-1] % self.dice.isave == 0: if self.dice.nstep[-1] % self.dice.isave == 0:
nconfigs = round(self.dice.nstep[-1] / self.dice.isave) nconfigs = round(self.dice.nstep[-1] / self.dice.isave)
@@ -719,24 +721,25 @@ class Internal:
for mol in range(nmols): ## Run over molecules of each type for mol in range(nmols): ## Run over molecules of each type
new_molecule = [] new_molecule = Molecule(self.system.molecule[type].molnale)
for site in range(len(self.system.molecule[types].atom)): ## Run over sites of each molecule for site in range(len(self.system.molecule[types].atom)): ## Run over sites of each molecule
new_molecule.append({}) new_molecule.append({})
line = xyzfile.pop(0).split() line = xyzfile.pop(0).split()
if line[0].title() != atomsymb[molecules[type][site]['na']].strip(): if line[0].title() != atomsymb[self.system.molecule[type].atom[site].na.strip()]:
sys.exit("Error reading file {}".format(file)) sys.exit("Error reading file {}".format(file))
new_molecule[site]['na'] = molecules[type][site]['na'] new_molecule.add_atom(Atom(self.system.molecule[type].atom[site].lbl,
new_molecule[site]['rx'] = float(line[1]) self.system.molecule[type].atom[site].na,
new_molecule[site]['ry'] = float(line[2]) self.system.molecule[type].atom[site].float(line[1]),
new_molecule[site]['rz'] = float(line[3]) self.system.molecule[type].atom[site].float(line[2]),
new_molecule[site]['chg'] = molecules[type][site]['chg'] self.system.molecule[type].atom[site].float(line[3]),
new_molecule[site]['eps'] = molecules[type][site]['eps'] self.system.molecule[type].atom[site].chg,
new_molecule[site]['sig'] = molecules[type][site]['sig'] self.system.molecule[type].atom[site].eps,
self.system.molecule[type].atom[site].sig))
dist = minimum_distance(molecules[0], new_molecule) dist = self.system.molecule[0].minimum_distance(new_molecule)
if dist < thickness[-1]: if dist < thickness[-1]:
mol_count += 1 mol_count += 1
for atom in new_molecule: for atom in new_molecule:
@@ -748,37 +751,37 @@ class Internal:
asec_charges[-1]['rz'] = atom['rz'] asec_charges[-1]['rz'] = atom['rz']
asec_charges[-1]['chg'] = atom['chg'] / norm_factor asec_charges[-1]['chg'] = atom['chg'] / norm_factor
if player['vdwforces'] == "yes": if self.player.vdwforces == "yes":
vdw_meanfield[-1]['rx'] = atom['rx'] vdw_meanfield[-1]['rx'] = atom['rx']
vdw_meanfield[-1]['ry'] = atom['ry'] vdw_meanfield[-1]['ry'] = atom['ry']
vdw_meanfield[-1]['rz'] = atom['rz'] vdw_meanfield[-1]['rz'] = atom['rz']
vdw_meanfield[-1]['eps'] = atom['eps'] vdw_meanfield[-1]['eps'] = atom['eps']
vdw_meanfield[-1]['sig'] = atom['sig'] vdw_meanfield[-1]['sig'] = atom['sig']
#### Read lines with ghosts or lps in molecules of type 0 (reference) # #### Read lines with ghosts or lps in molecules of type 0 (reference)
#### and, if dist < thickness, appends to asec # #### and, if dist < thickness, appends to asec
if type == 0: # if type == 0:
for ghost in ghost_atoms: # for ghost in ghost_atoms:
line = xyzfile.pop(0).split() # line = xyzfile.pop(0).split()
if line[0] != dice_ghost_label: # if line[0] != dice_ghost_label:
sys.exit("Error reading file {}".format(file)) # sys.exit("Error reading file {}".format(file))
if dist < thickness[-1]: # if dist < thickness[-1]:
asec_charges.append({}) # asec_charges.append({})
asec_charges[-1]['rx'] = float(line[1]) # asec_charges[-1]['rx'] = float(line[1])
asec_charges[-1]['ry'] = float(line[2]) # asec_charges[-1]['ry'] = float(line[2])
asec_charges[-1]['rz'] = float(line[3]) # asec_charges[-1]['rz'] = float(line[3])
asec_charges[-1]['chg'] = ghost['chg'] / norm_factor # asec_charges[-1]['chg'] = ghost['chg'] / norm_factor
for lp in lp_atoms: # for lp in lp_atoms:
line = xyzfile.pop(0).split() # line = xyzfile.pop(0).split()
if line[0] != dice_ghost_label: # if line[0] != dice_ghost_label:
sys.exit("Error reading file {}".format(file)) # sys.exit("Error reading file {}".format(file))
if dist < thickness[-1]: # if dist < thickness[-1]:
asec_charges.append({}) # asec_charges.append({})
asec_charges[-1]['rx'] = float(line[1]) # asec_charges[-1]['rx'] = float(line[1])
asec_charges[-1]['ry'] = float(line[2]) # asec_charges[-1]['ry'] = float(line[2])
asec_charges[-1]['rz'] = float(line[3]) # asec_charges[-1]['rz'] = float(line[3])
asec_charges[-1]['chg'] = lp['chg'] / norm_factor # asec_charges[-1]['chg'] = lp['chg'] / norm_factor
picked_mols.append(mol_count) picked_mols.append(mol_count)
@@ -865,12 +868,12 @@ class Internal:
try: try:
self.dice.make_proc_dir(cycle, proc) self.dice.make_proc_dir(cycle, proc)
self.make_inputs(cycle, proc) self.make_dice_inputs(cycle, proc)
self.dice.run_dice(cycle, proc, self.outfile) self.dice.run_dice(cycle, proc, self.outfile)
except Exception as err: except Exception as err:
sys.exit(err) sys.exit(err)
def make_inputs(self, cycle, proc): def make_dice_inputs(self, cycle, proc):
sim_dir = "simfiles" sim_dir = "simfiles"
step_dir = "step{:02d}".format(cycle) step_dir = "step{:02d}".format(cycle)
@@ -978,7 +981,7 @@ class Internal:
fh.write("mstop = 1\n") fh.write("mstop = 1\n")
fh.write("accum = no\n") fh.write("accum = no\n")
fh.write("iprint = 1\n") fh.write("iprint = 1\n")
fh.write("isave = {}\n".format(self.isave)) fh.write("isave = {}\n".format(self.dice.isave))
fh.write("irdf = {}\n".format(10 * self.player.nprocs)) fh.write("irdf = {}\n".format(10 * self.player.nprocs))
seed = int(1e6 * random.random()) seed = int(1e6 * random.random())
@@ -1144,6 +1147,286 @@ class Internal:
fh.write(fstr.format(atom.lbl, atom.na, atom.rx, atom.ry, fh.write(fstr.format(atom.lbl, atom.na, atom.rx, atom.ry,
atom.rz, atom.chg, atom.eps, atom.sig)) atom.rz, atom.chg, atom.eps, atom.sig))
# Gaussian related methods
def read_forces_fchk(self, file, fh):
forces = []
try:
with open(file) as tmpfh:
fchkfile = tmpfh.readlines()
except:
sys.exit("Error: cannot open file {}".format(file))
start = fchkfile.pop(0).strip()
while start.find("Cartesian Gradient") != 0: ## expression in begining of line
start = fchkfile.pop(0).strip()
degrees = 3 * len(self.system.molecule[0])
count = 0
while True:
values = fchkfile.pop(0).split()
forces.extend([ float(x) for x in values ])
count += len(values)
if count >= degrees:
forces = forces[:degrees]
break
gradient = np.array(forces)
fh.write("\nGradient read from file {}:\n".format(file))
fh.write("-----------------------------------------------------------------------\n"
"Center Atomic Forces (Hartree/Bohr)\n"
"Number Number X Y Z\n"
"-----------------------------------------------------------------------\n")
for i in range(len(self.system.molecule[0])):
fh.write(" {:>5d} {:>3d} {:>14.9f} {:>14.9f} {:>14.9f}\n".format(
i + 1, self.system.molecule[0][i]['na'], forces.pop(0), forces.pop(0), forces.pop(0)))
fh.write("-----------------------------------------------------------------------\n")
force_max = np.amax(np.absolute(gradient))
force_rms = np.sqrt(np.mean(np.square(gradient)))
fh.write(" Max Force = {:>14.9f} RMS Force = {:>14.9f}\n\n".format(
force_max, force_rms))
return gradient
def read_hessian_fchk(self, file):
force_const = []
try:
with open(file) as tmpfh:
fchkfile = tmpfh.readlines()
except:
sys.exit("Error: cannot open file {}".format(file))
start = fchkfile.pop(0).strip()
while start.find("Cartesian Force Constants") != 0:
start = fchkfile.pop(0).strip()
degrees = 3 * len(self.system.molecule[0])
last = round(degrees * (degrees + 1) / 2)
count = 0
while True:
values = fchkfile.pop(0).split()
force_const.extend([ float(x) for x in values ])
count += len(values)
if count >= last:
force_const = force_const[:last]
break
hessian = np.zeros((degrees, degrees))
for i in range(degrees):
for j in range(i + 1):
hessian[i,j] = force_const.pop(0)
hessian[j,i] = hessian[i,j]
return hessian
def read_hessian_log(self, file):
try:
with open(file) as tmpfh:
logfile = tmpfh.readlines()
except:
sys.exit("Error: cannot open file {}".format(file))
start = logfile.pop(0).strip()
while start.find("The second derivative matrix:") != 0:
start = logfile.pop(0).strip()
degrees = 3 * len(self.system.molecule[0])
hessian = np.zeros((degrees, degrees))
k = 0
while k < degrees:
logfile.pop(0)
for i in range(k, degrees):
values = logfile.pop(0).split()[1:]
for j in range(k, min(i + 1, k + 5)):
hessian[i,j] = float(values.pop(0))
hessian[j,i] = hessian[i,j]
k += 5
return hessian
def print_grad_hessian(self, cycle, cur_gradient, hessian):
try:
fh = open("grad_hessian.dat", "w")
except:
sys.exit("Error: cannot open file grad_hessian.dat")
fh.write("Optimization cycle: {}\n".format(cycle))
fh.write("Cartesian Gradient\n")
degrees = 3 * len(self.system.molecule[0])
for i in range(degrees):
fh.write(" {:>11.8g}".format(cur_gradient[i]))
if (i + 1) % 5 == 0 or i == degrees - 1:
fh.write("\n")
fh.write("Cartesian Force Constants\n")
last = degrees * (degrees + 1) / 2
count = 0
for i in range(degrees):
for j in range(i + 1):
count += 1
fh.write(" {:>11.8g}".format(hessian[i,j]))
if count % 5 == 0 or count == last:
fh.write("\n")
fh.close()
return
## Change the name to make_gaussian_input
def make_gaussian_input(self, cycle, asec_charges=None):
simdir="simfiles"
stepdir="step{:02d}".format(cycle)
path = simdir + os.sep + stepdir + os.sep + "qm"
file = path + os.sep + "asec.gjf"
try:
fh = open(file, "w")
except:
sys.exit("Error: cannot open file {}".format(file))
fh.write("%Chk=asec.chk\n")
if self.gaussian.mem != None:
fh.write("%Mem={}MB\n".format(self.gaussian.mem))
fh.write("%Nprocs={}\n".format(self.player.nprocs * self.dice.ncores))
kword_line = "#P " + str(self.gaussian.level)
if self.gaussian.keywords != None:
kword_line += " " + self.gaussian.keywords
if self.player.opt == 'yes':
kword_line += " Force"
# kword_line += " Charge"
kword_line += " NoSymm"
kword_line += " Pop={} Density=Current".format(self.gaussian.pop)
if cycle > 1:
kword_line += " Guess=Read"
fh.write(textwrap.fill(kword_line, 90))
fh.write("\n")
fh.write("\nForce calculation - Cycle number {}\n".format(cycle))
fh.write("\n")
fh.write("{},{}\n".format(self.gaussian.chgmult[0], self.gaussian.chgmult[1]))
for atom in self.system.molecule[0].atom:
symbol = atomsymb[atom.na]
fh.write("{:<2s} {:>10.5f} {:>10.5f} {:>10.5f}\n".format(symbol,
atom.rx, atom.ry, atom.rz))
# ## If also performing charge fit in the same calculation
# if cycle >= self.player.switchcyc:
# for ghost in ghost_atoms:
# fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format(
# ghost['rx'], ghost['ry'], ghost['rz']))
# for lp in lp_atoms:
# fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format(
# lp['rx'], lp['ry'], lp['rz']))
# fh.write("\n")
## If gmiddle file was informed, write its contents in asec.gjf
# if self.gaussian.gmiddle != None:
# if not os.path.isfile(self.gaussian.gmiddle):
# sys.exit("Error: cannot find file {} in main directory".format(
# self.gaussian.gmiddle))
# try:
# with open(self.gaussian.gmiddle) as gmiddlefile:
# gmiddle = gmiddlefile.readlines()
# except:
# sys.exit("Error: cannot open file {}".format(self.gaussian.gmiddle))
# for line in gmiddle:
# fh.write(line)
# fh.write("\n")
# ## Write the ASEC:
# for charge in asec_charges:
# fh.write("{:>10.5f} {:>10.5f} {:>10.5f} {:>11.8f}\n".format(
# charge['rx'], charge['ry'], charge['rz'], charge['chg']))
fh.write("\n")
# ## If gbottom file was informed, write its contents in asec.gjf
# if self.gaussian.gbottom != None:
# if not os.path.isfile(self.gaussian.gbottom):
# sys.exit("Error: cannot find file {} in main directory".format(
# self.gaussian.gbottom))
# try:
# with open(self.gaussian.gbottom) as gbottomfile:
# gbottom = gbottomfile.readlines()
# except:
# sys.exit("Error: cannot open file {}".format(self.gaussian.gbottom))
# for line in gbottom:
# fh.write(line)
# fh.write("\n")
# fh.close()
def read_charges(self, file, fh):
try:
with open(file) as tmpfh:
glogfile = tmpfh.readlines()
except:
sys.exit("Error: cannot open file {}".format(file))
start = glogfile.pop(0).strip()
while start != "Fitting point charges to electrostatic potential":
start = glogfile.pop(0).strip()
glogfile = glogfile[3:] ## Consume 3 more lines
fh.write("\nAtomic charges:\n")
fh.write("------------------------------------\n")
for atom in self.system.molecule[0].atom:
line = glogfile.pop(0).split()
atom_str = line[1]
charge = float(line[2])
atom.chg = charge
fh.write(" {:<2s} {:>10.6f}\n".format(atom_str, charge))
# if self.gaussian.pop == "chelpg":
# for ghost in ghost_atoms:
# line = glogfile.pop(0).split()
# atom_str = line[1]
# charge = float(line[2])
# ghost['chg'] = charge
# fh.write(" {:<2s} {:>10.6f}\n".format(atom_str, charge))
# for lp in lp_atoms:
# line = glogfile.pop(0).split()
# atom_str = line[1]
# charge = float(line[2])
# lp['chg'] = charge
# fh.write(" {:<2s} {:>10.6f}\n".format(atom_str, charge))
fh.write("------------------------------------\n")
class Player: class Player:
def __init__(self): def __init__(self):
@@ -1389,6 +1672,52 @@ class Internal:
self.pop = "chelpg" self.pop = "chelpg"
self.level = None self.level = None
def run_gaussian(self, cycle, type, fh):
simdir="simfiles"
stepdir="step{:02d}".format(cycle)
path = simdir + os.sep + stepdir + os.sep + "qm"
work_dir = os.getcwd()
os.chdir(path)
# if type == "force":
# infile = "asec.gjf"
# elif type == "charge":
# infile = "asec2.gjf"
infile = "asec.gjf"
fh.write("\nCalculation of {}s initiated with Gaussian on {}\n".format(type, date_time()))
if shutil.which("bash") != None:
exit_status = subprocess.call(["bash","-c","exec -a {}-step{} {} {}".format(self.qmprog, cycle, self.qmprog, infile)])
else:
exit_status = subprocess.call([self.qmprog, infile])
if exit_status != 0:
sys.exit("Gaussian process did not exit properly")
fh.write("Calculation of {}s finished on {}\n".format(type, date_time()))
os.chdir(work_dir)
def run_formchk(self, cycle, fh):
simdir="simfiles"
stepdir="step{:02d}".format(cycle)
path = simdir + os.sep + stepdir + os.sep + "qm"
work_dir = os.getcwd()
os.chdir(path)
fh.write("Formatting the checkpoint file... ")
exit_status = subprocess.call(["formchk", "asec.chk"])
fh.write("Done\n")
os.chdir(work_dir)
# class Molcas: # class Molcas:
# def __init(self): # def __init(self):

0
DPpack/__init__.py → diceplayer/DPpack/__init__.py
View File

92
diceplayer.py → diceplayer/__main__.py
View File

@@ -1,4 +1,4 @@
#!/export/apps/python/361/bin/python3 #!/usr/bin/python3
import os, sys, time, signal import os, sys, time, signal
import setproctitle import setproctitle
@@ -6,19 +6,18 @@ import argparse
import shutil import shutil
from multiprocessing import Process, connection from multiprocessing import Process, connection
import DPpack.Gaussian as Gaussian from diceplayer.DPpack.PTable import *
from DPpack.PTable import * from diceplayer.DPpack.SetGlobals import *
from DPpack.SetGlobals import * from diceplayer.DPpack.MolHandling import *
from DPpack.MolHandling import * from diceplayer.DPpack.Misc import *
from DPpack.Misc import *
_version = 'dev'
setproctitle.setproctitle("diceplayer-{}".format(_version))
if __name__ == '__main__': 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')
@@ -200,11 +199,11 @@ if __name__ == '__main__':
internal.outfile.write("\n+" + 88 * "-" + "+\n") internal.outfile.write("\n+" + 88 * "-" + "+\n")
#### ###
#### End of parallel simulations block ### End of parallel simulations block
#### ###
# ## Make ASEC ## Make ASEC
# internal.outfile.write("\nBuilding the ASEC and vdW meanfields... ") # internal.outfile.write("\nBuilding the ASEC and vdW meanfields... ")
# asec_charges = internal.populate_asec_vdw(cycle) # asec_charges = internal.populate_asec_vdw(cycle)
@@ -213,31 +212,26 @@ if __name__ == '__main__':
# path = "step{:02d}".format(cycle) + os.sep + "p{:02d}".format(proc) # path = "step{:02d}".format(cycle) + os.sep + "p{:02d}".format(proc)
# compress_files_1mb(path) # compress_files_1mb(path)
####
#### Start QM calculation
####
# make_qm_dir(cycle)
# if internal.player.opt == "yes":
### ###
# ## Gaussian block ### Start QM calculation
### ###
# if internal.player.qmprog in ("g03", "g09", "g16"):
# if cycle > 1: make_qm_dir(cycle)
# src = "step{:02d}".format(cycle - 1) + os.sep + "qm" + os.sep + "asec.chk"
# dst = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.chk"
# shutil.copyfile(src, dst)
# Gaussian.make_force_input(cycle, asec_charges) if internal.player.qmprog in ("g03", "g09", "g16"):
# Gaussian.run_gaussian(cycle, "force", internal.outfile)
# Gaussian.run_formchk(cycle, internal.outfile) if cycle > 1:
src = "simfiles" + os.sep + "step{:02d}".format(cycle - 1) + os.sep + "qm" + os.sep + "asec.chk"
dst = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.chk"
shutil.copyfile(src, dst)
internal.make_gaussian_input(cycle)
internal.gaussian.run_gaussian(cycle, "force", internal.outfile)
# internal.gaussian.run_formchk(cycle, internal.outfile)
# ## Read the gradient # ## Read the gradient
# file = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.fchk" # file = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.fchk"
# gradient = Gaussian.read_forces(file, internal.outfile) # gradient = internal.read_forces(file, internal.outfile)
# if len(cur_gradient) > 0: # if len(cur_gradient) > 0:
# old_gradient = cur_gradient # old_gradient = cur_gradient
# cur_gradient = gradient # cur_gradient = gradient
@@ -247,9 +241,9 @@ if __name__ == '__main__':
# if internal.player.readhessian == "yes": # if internal.player.readhessian == "yes":
# file = "grad_hessian.dat" # file = "grad_hessian.dat"
# internal.outfile.write("\nReading the hessian matrix from file {}\n".format(file)) # internal.outfile.write("\nReading the hessian matrix from file {}\n".format(file))
# hessian = Gaussian.read_hessian_fchk(file) # hessian = internal.read_hessian_fchk(file)
# else: # else:
# file = "step01" + os.sep + "qm" + os.sep + "asec.fchk" # file = "simfiles" + os.sep + "step01" + os.sep + "qm" + os.sep + "asec.fchk"
# internal.outfile.write("\nReading the hessian matrix from file {}\n".format(file)) # internal.outfile.write("\nReading the hessian matrix from file {}\n".format(file))
# hessian = internal.gaussian.read_hessian(file) # hessian = internal.gaussian.read_hessian(file)
@@ -272,15 +266,15 @@ if __name__ == '__main__':
# ## If needed, calculate the charges # ## If needed, calculate the charges
# if cycle < internal.player.switchcyc: # if cycle < internal.player.switchcyc:
# internal.gaussian.make_charge_input(cycle, asec_charges) # # internal.gaussian.make_charge_input(cycle, asec_charges)
# internal.gaussian.run_gaussian(cycle, "charge", internal.outfile) # internal.gaussian.run_gaussian(cycle, "charge", internal.outfile)
# ## Read the new charges and update molecules[0] # ## Read the new charges and update molecules[0]
# if cycle < internal.player.switchcyc: # if cycle < internal.player.switchcyc:
# file = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec2.log" # file = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec2.log"
# internal.gaussian.read_charges(file, internal.outfile) # internal.gaussian.read_charges(file, internal.outfile)
# else: # else:
# file = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.log" # file = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.log"
# internal.gaussian.read_charges(file, internal.outfile) # internal.gaussian.read_charges(file, internal.outfile)
# ## Print new info for molecule[0] # ## Print new info for molecule[0]
@@ -316,15 +310,15 @@ if __name__ == '__main__':
# if internal.player.qmprog in ("g03", "g09", "g16"): # if internal.player.qmprog in ("g03", "g09", "g16"):
# if cycle > 1: # if cycle > 1:
# src = "step{:02d}".format(cycle - 1) + os.sep + "qm" + os.sep + "asec.chk" # src = "simfiles" + os.sep + "step{:02d}".format(cycle - 1) + os.sep + "qm" + os.sep + "asec.chk"
# dst = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.chk" # dst = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.chk"
# shutil.copyfile(src, dst) # shutil.copyfile(src, dst)
# Gaussian.make_charge_input(cycle, asec_charges) # # internal.gaussian.make_charge_input(cycle, asec_charges)
# Gaussian.run_gaussian(cycle, "charge", internal.outfile) # internal.gaussian.run_gaussian(cycle, "charge", internal.outfile)
# file = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec2.log" # file = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec2.log"
# Gaussian.read_charges(file) # internal.read_charges(file)
# ## Print new info for molecule[0] # ## Print new info for molecule[0]
# internal.outfile.write("\nNew values for molecule type 1:\n\n") # internal.outfile.write("\nNew values for molecule type 1:\n\n")
@@ -338,11 +332,11 @@ if __name__ == '__main__':
# #### End of the iterative process # #### End of the iterative process
# #### # ####
# ## imprimir ultimas mensagens, criar um arquivo de potencial para ser usado em eventual # # ## imprimir ultimas mensagens, criar um arquivo de potencial para ser usado em eventual
# ## continuacao, fechar arquivos (geoms.xyz, run.log, ...) # # ## continuacao, fechar arquivos (geoms.xyz, run.log, ...)
# internal.outfile.write("\nDiceplayer finished normally!\n") # # internal.outfile.write("\nDiceplayer finished normally!\n")
# internal.outfile.close() # # internal.outfile.close()
# #### # # ####
# #### End of the program # # #### End of the program
# #### # # ####

110
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 Saturday, 20 Nov 2021 at 14:52:20 Program started on Friday, 03 Dec 2021 at 21:20:24
Environment variables: Environment variables:
OMP_STACKSIZE = Not set OMP_STACKSIZE = Not set
@@ -22,7 +22,7 @@ lps = no
maxcyc = 3 maxcyc = 3
maxstep = 0.3 maxstep = 0.3
nprocs = 4 nprocs = 4
opt = no opt = yes
qmprog = g16 qmprog = g16
readhessian = no readhessian = no
switchcyc = 3 switchcyc = 3
@@ -39,7 +39,7 @@ isave = 1000
ljname = phb.ljc ljname = phb.ljc
ncores = 3 ncores = 3
nmol = 1 50 nmol = 1 50
nstep = 40000 60000 50000 nstep = 20000 20000
outname = phb outname = phb
press = 1.0 press = 1.0
progname = dice progname = dice
@@ -115,8 +115,8 @@ Lbl AN X Y Z Charge Epsilon Sigma Mass
1 6 2.07203 -2.82345 0.00263 -0.115000 0.07000 3.5500 12.0110 1 6 2.07203 -2.82345 0.00263 -0.115000 0.07000 3.5500 12.0110
1 6 2.76823 -1.61764 0.00263 -0.115000 0.07000 3.5500 12.0110 1 6 2.76823 -1.61764 0.00263 -0.115000 0.07000 3.5500 12.0110
1 6 2.06824 -0.40521 0.00264 -0.115000 0.07000 3.5500 12.0110 1 6 2.06824 -0.40521 0.00264 -0.115000 0.07000 3.5500 12.0110
1 14 0.67589 -0.40522 0.00264 0.150000 0.07000 3.5500 28.0860 1 6 0.67589 -0.40522 0.00264 0.150000 0.07000 3.5500 12.0110
1 104 -0.02420 -1.61760 0.00263 -0.115000 0.07000 3.5500 0.0000 1 6 -0.02420 -1.61760 0.00263 -0.115000 0.07000 3.5500 12.0110
2 1 0.13203 -3.75875 0.00263 0.115000 0.03000 2.4200 1.0079 2 1 0.13203 -3.75875 0.00263 0.115000 0.03000 2.4200 1.0079
2 1 2.61203 -3.75875 0.00263 0.115000 0.03000 2.4200 1.0079 2 1 2.61203 -3.75875 0.00263 0.115000 0.03000 2.4200 1.0079
2 1 2.60824 0.53010 0.00264 0.115000 0.03000 2.4200 1.0079 2 1 2.60824 0.53010 0.00264 0.115000 0.03000 2.4200 1.0079
@@ -159,13 +159,13 @@ Molecule type 1 - PHENOL_BLUE:
Molecule type 2 - PLACEHOLDER: Molecule type 2 - PLACEHOLDER:
Center of mass = ( 1.6067 , -1.0929 , 0.0026 ) Center of mass = ( 1.5639 , -1.2534 , 0.0026 )
Moments of inertia = 1.205279E+02 2.859254E+02 4.033761E+02 Moments of inertia = 1.394830E+02 2.777126E+02 4.141185E+02
Major principal axis = ( 0.795913 , -0.605411 , -0.000001 ) Major principal axis = ( 0.865900 , -0.500217 , -0.000001 )
Inter principal axis = ( 0.605411 , 0.795913 , 0.000001 ) Inter principal axis = ( 0.500217 , 0.865900 , 0.000001 )
Minor principal axis = ( 0.000000 , -0.000002 , 1.000000 ) Minor principal axis = ( 0.000000 , -0.000002 , 1.000000 )
Characteristic lengths = ( 5.74 , 5.26 , 1.51 ) Characteristic lengths = ( 5.74 , 5.26 , 1.51 )
Total mass = 112.20 au Total mass = 108.14 au
Total charge = -0.0000 e Total charge = -0.0000 e
Dipole moment = ( 2.3293 , 0.1593 , -0.0000 ) Total = 2.3347 Debye Dipole moment = ( 2.3293 , 0.1593 , -0.0000 ) Total = 2.3347 Debye
@@ -173,14 +173,14 @@ Molecule type 2 - PLACEHOLDER:
New values: New values:
Center of mass = ( 0.0000 , -0.0000 , 0.0000 ) Center of mass = ( 0.0000 , -0.0000 , 0.0000 )
Moments of inertia = 1.205279E+02 2.859254E+02 4.033761E+02 Moments of inertia = 1.394830E+02 2.777126E+02 4.141185E+02
Major principal axis = ( -1.000000 , 0.000000 , 0.000000 ) Major principal axis = ( 1.000000 , -0.000000 , -0.000000 )
Inter principal axis = ( 0.000000 , 1.000000 , 0.000000 ) Inter principal axis = ( 0.000000 , 1.000000 , 0.000000 )
Minor principal axis = ( 0.000000 , 0.000000 , 1.000000 ) Minor principal axis = ( 0.000000 , -0.000000 , 1.000000 )
Characteristic lengths = ( 5.67 , 5.13 , 1.51 ) Characteristic lengths = ( 5.65 , 4.95 , 1.51 )
Total mass = 112.20 au Total mass = 108.14 au
Total charge = -0.0000 e Total charge = -0.0000 e
Dipole moment = ( 1.7575 , 1.5369 , -0.0000 ) Total = 2.3347 Debye Dipole moment = ( 1.9373 , 1.3031 , -0.0000 ) Total = 2.3347 Debye
========================================================================================== ==========================================================================================
@@ -190,67 +190,23 @@ Starting the iterative process.
Step # 1 Step # 1
------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------
Simulation process simfiles/step01/p02 initiated with pid 15516 Simulation process simfiles/step01/p01 initiated with pid 8024
p02> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 14:52:20 p01> NVT thermalization finished (from random configuration) on 03 Dec 2021 at 21:20:24
Simulation process simfiles/step01/p01 initiated with pid 15515 Simulation process simfiles/step01/p03 initiated with pid 8026
p01> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 14:52:20 p03> NVT thermalization finished (from random configuration) on 03 Dec 2021 at 21:20:24
Simulation process simfiles/step01/p03 initiated with pid 15517 Simulation process simfiles/step01/p02 initiated with pid 8025
p03> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 14:52:20 p02> NVT thermalization finished (from random configuration) on 03 Dec 2021 at 21:20:24
Simulation process simfiles/step01/p04 initiated with pid 15518 Simulation process simfiles/step01/p04 initiated with pid 8027
p04> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 14:52:20 p04> NVT thermalization finished (from random configuration) on 03 Dec 2021 at 21:20:24
p03> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 14:54:12 p02> NVT production initiated on 03 Dec 2021 at 21:21:22
p04> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 14:54:13 p04> NVT production initiated on 03 Dec 2021 at 21:21:23
p02> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 14:54:13 p03> NVT production initiated on 03 Dec 2021 at 21:21:23
p01> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 14:54:13 p01> NVT production initiated on 03 Dec 2021 at 21:21:27
p03> NPT production initiated on 20 Nov 2021 at 14:57:16 p03> ----- NVT production finished on 03 Dec 2021 at 21:22:35
p02> NPT production initiated on 20 Nov 2021 at 14:57:19 p04> ----- NVT production finished on 03 Dec 2021 at 21:22:36
p04> NPT production initiated on 20 Nov 2021 at 14:57:20 p02> ----- NVT production finished on 03 Dec 2021 at 21:22:36
p01> NPT production initiated on 20 Nov 2021 at 14:57:21 p01> ----- NVT production finished on 03 Dec 2021 at 21:22:39
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
------------------------------------------------------------------------------------------
Simulation process simfiles/step02/p02 initiated with pid 15559 Calculation of forces initiated with Gaussian on 03 Dec 2021 at 21:22:39
p02> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:00:27
Simulation process simfiles/step02/p01 initiated with pid 15558
p01> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:00:27
Simulation process simfiles/step02/p03 initiated with pid 15560
p03> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:00:27
Simulation process simfiles/step02/p04 initiated with pid 15561
p04> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:00:27
p03> NPT production initiated on 20 Nov 2021 at 15:01:30
p01> NPT production initiated on 20 Nov 2021 at 15:01:30
p02> NPT production initiated on 20 Nov 2021 at 15:01:31
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
------------------------------------------------------------------------------------------
Simulation process simfiles/step03/p01 initiated with pid 15661
p01> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:04:37
Simulation process simfiles/step03/p02 initiated with pid 15662
p02> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:04:37
Simulation process simfiles/step03/p04 initiated with pid 15664
p04> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:04:37
Simulation process simfiles/step03/p03 initiated with pid 15663
p03> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:04:37
p03> NPT production initiated on 20 Nov 2021 at 15:05:41
p01> NPT production initiated on 20 Nov 2021 at 15:05:42
p04> NPT production initiated on 20 Nov 2021 at 15:05:42
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
+----------------------------------------------------------------------------------------+

58
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 Saturday, 20 Nov 2021 at 13:29:59 Program started on Friday, 03 Dec 2021 at 21:18:49
Environment variables: Environment variables:
OMP_STACKSIZE = Not set OMP_STACKSIZE = Not set
@@ -19,10 +19,10 @@ freq = no
ghosts = no ghosts = no
initcyc = 1 initcyc = 1
lps = no lps = no
maxcyc = 4 maxcyc = 3
maxstep = 0.3 maxstep = 0.3
nprocs = 4 nprocs = 4
opt = no opt = yes
qmprog = g16 qmprog = g16
readhessian = no readhessian = no
switchcyc = 3 switchcyc = 3
@@ -39,7 +39,7 @@ isave = 1000
ljname = phb.ljc ljname = phb.ljc
ncores = 3 ncores = 3
nmol = 1 50 nmol = 1 50
nstep = 40000 60000 50000 nstep = 20000 20000
outname = phb outname = phb
press = 1.0 press = 1.0
progname = dice progname = dice
@@ -115,8 +115,8 @@ Lbl AN X Y Z Charge Epsilon Sigma Mass
1 6 2.07203 -2.82345 0.00263 -0.115000 0.07000 3.5500 12.0110 1 6 2.07203 -2.82345 0.00263 -0.115000 0.07000 3.5500 12.0110
1 6 2.76823 -1.61764 0.00263 -0.115000 0.07000 3.5500 12.0110 1 6 2.76823 -1.61764 0.00263 -0.115000 0.07000 3.5500 12.0110
1 6 2.06824 -0.40521 0.00264 -0.115000 0.07000 3.5500 12.0110 1 6 2.06824 -0.40521 0.00264 -0.115000 0.07000 3.5500 12.0110
1 14 0.67589 -0.40522 0.00264 0.150000 0.07000 3.5500 28.0860 1 6 0.67589 -0.40522 0.00264 0.150000 0.07000 3.5500 12.0110
1 104 -0.02420 -1.61760 0.00263 -0.115000 0.07000 3.5500 0.0000 1 6 -0.02420 -1.61760 0.00263 -0.115000 0.07000 3.5500 12.0110
2 1 0.13203 -3.75875 0.00263 0.115000 0.03000 2.4200 1.0079 2 1 0.13203 -3.75875 0.00263 0.115000 0.03000 2.4200 1.0079
2 1 2.61203 -3.75875 0.00263 0.115000 0.03000 2.4200 1.0079 2 1 2.61203 -3.75875 0.00263 0.115000 0.03000 2.4200 1.0079
2 1 2.60824 0.53010 0.00264 0.115000 0.03000 2.4200 1.0079 2 1 2.60824 0.53010 0.00264 0.115000 0.03000 2.4200 1.0079
@@ -159,13 +159,13 @@ Molecule type 1 - PHENOL_BLUE:
Molecule type 2 - PLACEHOLDER: Molecule type 2 - PLACEHOLDER:
Center of mass = ( 1.6067 , -1.0929 , 0.0026 ) Center of mass = ( 1.5639 , -1.2534 , 0.0026 )
Moments of inertia = 1.205279E+02 2.859254E+02 4.033761E+02 Moments of inertia = 1.394830E+02 2.777126E+02 4.141185E+02
Major principal axis = ( 0.795913 , -0.605411 , -0.000001 ) Major principal axis = ( 0.865900 , -0.500217 , -0.000001 )
Inter principal axis = ( 0.605411 , 0.795913 , 0.000001 ) Inter principal axis = ( 0.500217 , 0.865900 , 0.000001 )
Minor principal axis = ( 0.000000 , -0.000002 , 1.000000 ) Minor principal axis = ( 0.000000 , -0.000002 , 1.000000 )
Characteristic lengths = ( 5.74 , 5.26 , 1.51 ) Characteristic lengths = ( 5.74 , 5.26 , 1.51 )
Total mass = 112.20 au Total mass = 108.14 au
Total charge = -0.0000 e Total charge = -0.0000 e
Dipole moment = ( 2.3293 , 0.1593 , -0.0000 ) Total = 2.3347 Debye Dipole moment = ( 2.3293 , 0.1593 , -0.0000 ) Total = 2.3347 Debye
@@ -173,14 +173,14 @@ Molecule type 2 - PLACEHOLDER:
New values: New values:
Center of mass = ( 0.0000 , -0.0000 , 0.0000 ) Center of mass = ( 0.0000 , -0.0000 , 0.0000 )
Moments of inertia = 1.205279E+02 2.859254E+02 4.033761E+02 Moments of inertia = 1.394830E+02 2.777126E+02 4.141185E+02
Major principal axis = ( -1.000000 , 0.000000 , 0.000000 ) Major principal axis = ( 1.000000 , -0.000000 , -0.000000 )
Inter principal axis = ( 0.000000 , 1.000000 , 0.000000 ) Inter principal axis = ( 0.000000 , 1.000000 , 0.000000 )
Minor principal axis = ( 0.000000 , 0.000000 , 1.000000 ) Minor principal axis = ( 0.000000 , -0.000000 , 1.000000 )
Characteristic lengths = ( 5.67 , 5.13 , 1.51 ) Characteristic lengths = ( 5.65 , 4.95 , 1.51 )
Total mass = 112.20 au Total mass = 108.14 au
Total charge = -0.0000 e Total charge = -0.0000 e
Dipole moment = ( 1.7575 , 1.5369 , -0.0000 ) Total = 2.3347 Debye Dipole moment = ( 1.9373 , 1.3031 , -0.0000 ) Total = 2.3347 Debye
========================================================================================== ==========================================================================================
@@ -190,19 +190,11 @@ Starting the iterative process.
Step # 1 Step # 1
------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------
Simulation process simfiles/step01/p01 initiated with pid 14014 Simulation process simfiles/step01/p01 initiated with pid 7513
p01> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 13:29:59 p01> NVT thermalization finished (from random configuration) on 03 Dec 2021 at 21:18:49
Simulation process simfiles/step01/p02 initiated with pid 14015 Simulation process simfiles/step01/p02 initiated with pid 7514
p02> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 13:29:59 p02> NVT thermalization finished (from random configuration) on 03 Dec 2021 at 21:18:49
Simulation process simfiles/step01/p03 initiated with pid 14016 Simulation process simfiles/step01/p03 initiated with pid 7515
p03> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 13:29:59 p03> NVT thermalization finished (from random configuration) on 03 Dec 2021 at 21:18:49
Simulation process simfiles/step01/p04 initiated with pid 14017 Simulation process simfiles/step01/p04 initiated with pid 7516
p04> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 13:29:59 p04> NVT thermalization finished (from random configuration) on 03 Dec 2021 at 21:18:49
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