def gaussion_workers(chem_model, val):
while True:
simulation_time = time.time()
task = comm.recv(source=0, tag=MPI.ANY_TAG, status=status)
tag = status.Get_tag()
if tag == START:
state = task[0]
m = task[1]
all_posible = chem_kn_simulation(chem_model, state, val, m)
generate_smile = predict_smile(all_posible, val)
new_compound = make_input_smile(generate_smile)
score = []
kao = []
try:
m = Chem.MolFromSmiles(str(new_compound[0]))
except:
m = None
#if m!=None and len(task[i])<=81:
if m != None:
try:
logp = Descriptors.MolLogP(m)
except:
logp = -1000
SA_score = -sascorer.calculateScore(
MolFromSmiles(new_compound[0]))
cycle_list = nx.cycle_basis(
nx.Graph(
rdmolops.GetAdjacencyMatrix(
MolFromSmiles(new_compound[0]))))
if len(cycle_list) == 0:
cycle_length = 0
else:
cycle_length = max([len(j) for j in cycle_list])
if cycle_length <= 6:
cycle_length = 0
else:
cycle_length = cycle_length - 6
cycle_score = -cycle_length
#print cycle_score
#print SA_score
#print logp
SA_score_norm = (SA_score - SA_mean) / SA_std
logp_norm = (logp - logP_mean) / logP_std
cycle_score_norm = (cycle_score - cycle_mean) / cycle_std
score_one = SA_score_norm + logp_norm + cycle_score_norm
score.append(score_one)
else:
score.append(-1000)
score.append(new_compound[0])
score.append(rank)
comm.send(score, dest=0, tag=DONE)
simulation_fi_time = time.time() - simulation_time
print "simulation_fi_time:", simulation_fi_time
if tag == EXIT:
MPI.Abort(MPI.COMM_WORLD)
comm.send(None, dest=0, tag=EXIT)
def __init__(self, npxyz, xyzL, xyz_orig, ncxyz):
#initialise MPI and CPL
self.comm = MPI.COMM_WORLD
self.CPL = CPL()
self.CFD_COMM = self.CPL.init(CPL.CFD_REALM)
self.nprocs_realm = self.CFD_COMM.Get_size()
# Parameters of the cpu topology (cartesian grid)
self.npxyz = np.array(npxyz, order='F', dtype=np.int32)
self.NProcs = np.product(npxyz)
self.xyzL = np.array(xyzL, order='F', dtype=np.float64)
self.xyz_orig = np.array(xyz_orig, order='F', dtype=np.float64)
self.ncxyz = np.array(ncxyz, order='F', dtype=np.int32)
if (self.nprocs_realm != self.NProcs):
print("Non-coherent number of processes in CFD ",
self.nprocs_realm, " no equal to ", self.npxyz[0], " X ",
self.npxyz[1], " X ", self.npxyz[2])
MPI.Abort(errorcode=1)
#Setup coupled simulation
self.cart_comm = self.CFD_COMM.Create_cart(
[self.npxyz[0], self.npxyz[1], self.npxyz[2]])
self.CPL.setup_cfd(self.cart_comm, self.xyzL, self.xyz_orig,
self.ncxyz)
#Get limits of overlap region
self.olap_limits = self.CPL.get_olap_limits()
self.portion = self.CPL.my_proc_portion(self.olap_limits)
[self.ncxl, self.ncyl, self.nczl] = self.CPL.get_no_cells(self.portion)
self.dx = self.CPL.get("xl_cfd") / float(self.CPL.get("ncx"))
self.dy = self.CPL.get("yl_cfd") / float(self.CPL.get("ncy"))
self.dz = self.CPL.get("zl_cfd") / float(self.CPL.get("ncz"))
self.ioverlap = (self.CPL.get("icmax_olap") -
self.CPL.get("icmin_olap") + 1)
self.joverlap = (self.CPL.get("jcmax_olap") -
self.CPL.get("jcmin_olap") + 1)
self.koverlap = (self.CPL.get("kcmax_olap") -
self.CPL.get("kcmin_olap") + 1)
self.xoverlap = self.ioverlap * self.dx
self.yoverlap = self.joverlap * self.dy
self.zoverlap = self.koverlap * self.dz
def gaussion_workers(chem_model, val, gau_parallel, charge_check,
output_file_name, lock):
while True:
simulation_time = time.time()
task = comm.recv(source=0, tag=MPI.ANY_TAG, status=status)
tag = status.Get_tag()
#print('rank_tag:',rank, tag)
if tag == START:
state = task[0]
m = task[1]
ind = task[2]
new_compound = task[3]
print "new compound:", new_compound
score = []
kao = []
intensity = -1000000
deen = 1000000
gap = 1000000
mol_weight = 0
SA_score = 10
wavenum = -1000
logP = 0
dp = len(state)
nmr_wasser = -1
intensity_list = []
wl_list = []
standard_valence_list = [
0, 1, 0, 1, 2, 3, 4, 3, 2, 1, 0, 1, 2, 3, 4, 3, 2, 1, 0, 1, 2
]
try:
m = Chem.MolFromSmiles(
Chem.MolToSmiles(Chem.MolFromSmiles(str(new_compound[0])),
True))
mol_weight = Descriptors.MolWt(m)
logP = Crippen.MolLogP(m)
#SA_score = sascorer.calculateScore(m)
#print 'prev add Hs'
m_H = Chem.AddHs(m)
#print Chem.MolToSmiles(m_H)
standard_valence_list = [
0, 1, 0, 1, 2, 3, 4, 3, 2, 1, 0, 1, 2, 3, 4, 3, 2, 1, 0, 1,
2
]
ccheck = True
if charge_check:
for atom in m_H.GetAtoms():
#print standard_valence_list[atom.GetAtomicNum()], atom.GetExplicitValence()
if standard_valence_list[atom.GetAtomicNum(
)] != atom.GetExplicitValence():
ccheck = False
break
if not ccheck:
m = None
except:
m = None
if m != None:
H_count = 0
C_count = 0
for atom in m.GetAtoms():
H_count = H_count + atom.GetTotalNumHs(
includeNeighbors=False)
if atom.GetSymbol() == 'C':
C_count = C_count + 1
if H_count > target_outdic['nmr'][0].count(
'H') or C_count > target_outdic['nmr'][0].count('C'):
nmr_wasser = -1
print(str(new_compound[0]), 'rejected', H_count, C_count)
else:
print(str(new_compound[0]), 'accepeted', H_count, C_count)
try:
stable = transfersdf(str(new_compound[0]), ind)
except:
stable = -1
print('warning: unstable')
if stable == 1.0:
cd_path = os.getcwd()
try:
SDFinput = 'CheckMolopt' + str(ind) + '.sdf'
calc_sdf = GaussianDFTRun('B3LYP', '3-21G*',
gau_parallel, 'nmr',
SDFinput, 0)
outdic = calc_sdf.run_gaussian()
nmr_wasser = get_wasserstein_dist(
outdic, target_outdic)
print ind, '|', nmr_wasser, '|', new_compound[
0], '|', outdic['nmr']
if os.path.isfile('CheckMol' + str(ind) + '.sdf'):
shutil.move('CheckMol' + str(ind) + '.',
'dft_result')
if os.path.isfile('CheckMolopt' + str(ind) +
'.sdf'):
shutil.move('CheckMolopt' + str(ind) + '.sdf',
'dft_result')
except:
os.chdir(cd_path)
if os.path.isfile('CheckMolopt' + str(ind) +
'.sdf'):
os.remove('CheckMolopt' + str(ind) + '.sdf')
if os.path.isfile('CheckMol' + str(ind) + '.sdf'):
os.remove('CheckMol' + str(ind) + '.sdf')
else:
wavelength = None
if os.path.isfile('CheckMolopt' + str(ind) + '.sdf'):
os.remove('CheckMolopt' + str(ind) + '.sdf')
if os.path.isfile('CheckMol' + str(ind) + '.sdf'):
os.remove('CheckMol' + str(ind) + '.sdf')
score.append(wavenum)
score.append(new_compound[0])
score.append(rank)
score.append(intensity)
score.append(deen)
score.append(gap)
score.append(wl_list)
score.append(intensity_list)
score.append(ind)
score.append(mol_weight)
score.append(logP)
score.append(SA_score)
score.append(dp)
score.append(nmr_wasser)
comm.send(score, dest=0, tag=DONE)
simulation_fi_time = time.time() - simulation_time
###print("simulation_fi_time:",simulation_fi_time)
if tag == EXIT:
MPI.Abort(MPI.COMM_WORLD)
comm.send([-1000, '', 0, 0, 0, 0, [], [], ind, 0, 0, 0, 0],
dest=0,
tag=EXIT)
NPx = 3
NPy = 3
NPz = 3
NProcs = NPx * NPy * NPz
# Parameters of the mesh topology (cartesian grid)
ncxyz = np.array([18, 18, 18], order='F', dtype=np.int32)
xyzL = np.array([10.0, 10.0, 10.0], order='F', dtype=np.float64)
xyz_orig = np.array([0.0, 0.0, 0.0], order='F', dtype=np.float64)
# Create communicators and check that number of processors is consistent
realm_comm = CPL.create_comm(CPL.CFD_REALM)
nprocs_realm = realm_comm.Get_size()
if (nprocs_realm != NProcs):
print "ERROR: Non-coherent number of processors."
MPI.Abort(errorcode=1)
cart_comm = realm_comm.Create_cart([NPx, NPy, NPz])
CPL.cfd_init2(nsteps, dt, cart_comm, xyzL, xyz_orig, ncxyz, 1.0)
ols = CPL.get_olap_limits()
my_coords = cart_comm.Get_coords(cart_comm.Get_rank())
my_coords = np.array(my_coords, order='F', dtype=np.int32)
"""
#if (True):
# print str(cart_comm.Get_rank())+" "+ "mycoords: " + str(my_coords)+ "extents:" + str(extents)+ " "+str(nsteps)+ str(dt)+ str(cart_comm)+ \
# str(icoords)+ str(xyzL)+ str(ncxyz)+\
# str(1.0)+ str(ijkcmax)+ str(ijkcmin)+ str(iTmin)+ str(iTmax)\
# +str(jTmin)+ str(jTmax)+ str(kTmin)+ str(kTmax)
def gaussion_workers(chem_model, val):
while True:
simulation_time = time.time()
task = comm.recv(source=0, tag=MPI.ANY_TAG, status=status)
tag = status.Get_tag()
if tag == START:
state = task[0]
m = task[1]
ind = task[2]
all_posible = chem_kn_simulation(chem_model, state, val, m)
generate_smile = predict_smile(all_posible, val)
new_compound = make_input_smile(generate_smile)
score = []
kao = []
try:
m = Chem.MolFromSmiles(str(new_compound[0]))
except:
m = None
#if m!=None and len(task[i])<=81:
if m != None:
stable = tansfersdf(str(new_compound[0]), ind)
if stable == 1.0:
try:
SDFinput = 'CheckMolopt' + str(ind) + '.sdf'
calc_sdf = GaussianDFTRun('B3LYP', '6-31G', 1,
'uv homolumo', SDFinput, 0)
outdic = calc_sdf.run_gaussian()
wavelength = outdic['uv'][0]
#gap=outdic['gap'][0]
#lumo=outdic['gap'][1]
except:
wavelength = None
else:
wavelength = None
if wavelength != None and wavelength != []:
wavenum = wavelength[0]
gap = outdic['gap'][0]
lumo = outdic['gap'][1]
else:
wavenum = -1000
gap = -1000
lumo = -1000
else:
wavenum = -1000
gap = -1000
lumo = -1000
#score.append(wavenum)
score.append(gap)
score.append(lumo)
score.append(new_compound[0])
score.append(rank)
comm.send(score, dest=0, tag=DONE)
simulation_fi_time = time.time() - simulation_time
print "simulation_fi_time:", simulation_fi_time
if tag == EXIT:
MPI.Abort(MPI.COMM_WORLD)
comm.send(None, dest=0, tag=EXIT)
def gaussion_workers(chem_model, val, gau_parallel, charge_check):
while True:
simulation_time = time.time()
task = comm.recv(source=0, tag=MPI.ANY_TAG, status=status)
tag = status.Get_tag()
if tag == START:
state = task[0]
m = task[1]
ind = task[2]
all_posible = chem_kn_simulation(chem_model, state, val, m)
generate_smile = predict_smile(all_posible, val)
new_compound = make_input_smile(generate_smile)
score = []
kao = []
intensity = -1000000
deen = 1000000
gap = 1000000
mol_weight = 0
SA_score = 10
logP = 0
dp = len(state)
intensity_list = []
wl_list = []
standard_valence_list = [
0, 1, 0, 1, 2, 3, 4, 3, 2, 1, 0, 1, 2, 3, 4, 3, 2, 1, 0, 1, 2
]
s1_wavenum = -1000
s1_strength = 0
s1_wavelength = None
s1_wl_list = []
s1_str_list = []
try:
m = Chem.MolFromSmiles(str(new_compound[0]))
mol_weight = Descriptors.MolWt(m)
logP = Crippen.MolLogP(m)
SA_score = sascorer.calculateScore(m)
#print 'prev add Hs'
m_H = Chem.AddHs(m)
#print Chem.MolToSmiles(m_H)
standard_valence_list = [
0, 1, 0, 1, 2, 3, 4, 3, 2, 1, 0, 1, 2, 3, 4, 3, 2, 1, 0, 1,
2
]
ccheck = True
if charge_check:
for atom in m_H.GetAtoms():
#print standard_valence_list[atom.GetAtomicNum()], atom.GetExplicitValence()
if standard_valence_list[atom.GetAtomicNum(
)] != atom.GetExplicitValence():
ccheck = False
break
if not ccheck:
#print 'charge checked: not'
m = None
#print 'charge checked'
#if charge_check(m_H, standard_valence_list):
# print('charge_check: OK')
#else:
# m = None
except:
m = None
#if m!=None and len(task[i])<=81:
if m != None:
try:
stable = tansfersdf(str(new_compound[0]), ind)
except:
stable = -1
if stable == 1.0:
cd_path = os.getcwd()
try:
SDFinput = 'CheckMolopt' + str(ind) + '.sdf'
#wavelength=GauTDDFT_ForDFT('B3LYP', '3-21G*', 1, 'CheckMolopt'+str(ind)+'.sdf')
#STO3G
calc_sdf = GaussianDFTRun(
'B3LYP', '3-21G*', gau_parallel,
'OPT fluor energy deen uv homolumo', SDFinput, 0)
outdic = calc_sdf.run_gaussian()
wavelength = outdic['uv'][0]
s1_wavelength = outdic[
'S1 Wavelength and Oscillator strengths'][0]
print('ind', ind, 'wavelength', wavelength)
if os.path.isfile('CheckMol' + str(ind) + '.sdf'):
shutil.move('CheckMol' + str(ind) + '.sdf',
'dft_result')
if os.path.isfile('CheckMolopt' + str(ind) + '.sdf'):
shutil.move('CheckMolopt' + str(ind) + '.sdf',
'dft_result')
#if os.path.isfile('CheckMolopt'+str(ind)+'.com'):
# shutil.move('CheckMolopt'+str(ind)+'.com', 'dft_result')
#if os.path.isfile('CheckMolopt'+str(ind)+'.log'):
# shutil.move('CheckMolopt'+str(ind)+'.log', 'dft_result')
#if os.path.isfile('CheckMolopt'+str(ind)+'.chk'):
# os.remove('CheckMolopt'+str(ind)+'.chk')
except:
os.chdir(cd_path)
wavelength = None
if os.path.isfile('CheckMolopt' + str(ind) + '.sdf'):
os.remove('CheckMolopt' + str(ind) + '.sdf')
if os.path.isfile('CheckMol' + str(ind) + '.sdf'):
os.remove('CheckMol' + str(ind) + '.sdf')
else:
wavelength = None
if os.path.isfile('CheckMolopt' + str(ind) + '.sdf'):
os.remove('CheckMolopt' + str(ind) + '.sdf')
if os.path.isfile('CheckMol' + str(ind) + '.sdf'):
os.remove('CheckMol' + str(ind) + '.sdf')
if wavelength != None and wavelength != []:
wavenum = wavelength[0]
intensity = outdic['uv'][1][0]
deen = outdic['deen']
gap = outdic['gap']
wl_list = outdic['uv'][0]
intensity_list = outdic['uv'][1]
else:
wavenum = -1000
if s1_wavelength != None and s1_wavelength != []:
s1_wavenum = s1_wavelength[0]
s1_strength = outdic[
'S1 Wavelength and Oscillator strengths'][1][0]
s1_wl_list = outdic[
'S1 Wavelength and Oscillator strengths'][0]
s1_str_list = outdic[
'S1 Wavelength and Oscillator strengths'][1]
else:
s1_wavenum = -1000
else:
wavenum = -1000
score.append(wavenum)
score.append(new_compound[0])
score.append(rank)
score.append(intensity)
score.append(deen)
score.append(gap)
score.append(wl_list)
score.append(intensity_list)
score.append(ind)
score.append(mol_weight)
score.append(logP)
score.append(SA_score)
score.append(dp)
score.append(s1_wavenum) #flour
score.append(s1_strength)
score.append(s1_wl_list)
score.append(s1_str_list)
comm.send(score, dest=0, tag=DONE)
simulation_fi_time = time.time() - simulation_time
print("simulation_fi_time:", simulation_fi_time)
if tag == EXIT:
MPI.Abort(MPI.COMM_WORLD)
comm.send(
[-1000, '', 0, 0, 0, 0, [], [], ind, 0, 0, 0, 0, -1000, 0, [], []],
dest=0,
tag=EXIT)
def CFD(xyzL=[1.5E-003, 1.5E-003, 2.50E-003],
g=9.81,
ncxyz=[8, 8, 8],
npxyz=[1, 1, 1],
Nsteps=101):
#initialise MPI and CPL
comm = MPI.COMM_WORLD
CPL = CPL()
MD_COMM = CPL.init(CPL.CFD_REALM)
nprocs_realm = MD_COMM.Get_size()
## Parameters of the cpu topology (cartesian grid)
npxyz = np.array(npxyz, order='F', dtype=np.int32)
NProcs = np.product(npxyz)
xyzL = np.array(xyz, order='F', dtype=np.float64)
xyz_orig = np.array([0.0, 0.0, 0.0], order='F', dtype=np.float64)
ncxyz = np.array(ncxyz, order='F', dtype=np.int32)
if (nprocs_realm != NProcs):
print("Non-coherent number of processes in MD ", nprocs_realm,
" no equal to ", npxyz[0], " X ", npxyz[1], " X ", npxyz[2])
MPI.Abort(errorcode=1)
#Setup coupled simulation
cart_comm = MD_COMM.Create_cart([npxyz[0], npxyz[1], npxyz[2]])
CPL.setup_cfd(cart_comm, xyzL, xyz_orig, ncxyz)
#Get constraint region
cnst_limits = CPL.get_cnst_limits()
cnst_portion = CPL.my_proc_portion(cnst_limits)
[cnst_ncxl, cnst_ncyl, cnst_nczl] = CPL.get_no_cells(cnst_portion)
#Get overlap region
olap_limits = CPL.get_olap_limits()
BC_limits = np.array([
olap_limits[0], olap_limits[1], olap_limits[2], olap_limits[3],
olap_limits[4], olap_limits[5]
],
dtype=np.int32)
BC_portion = CPL.my_proc_portion(BC_limits)
[BC_ncxl, BC_ncyl, BC_nczl] = CPL.get_no_cells(BC_portion)
#Allocate send and recv arrays
recv_array = np.zeros((4, BC_ncxl, BC_ncyl, BC_nczl),
order='F',
dtype=np.float64)
send_array = np.zeros((9, cnst_ncxl, cnst_ncyl, cnst_nczl),
order='F',
dtype=np.float64)
for time in range(Nsteps):
# send data to update
send_array[2, :, :, :] = -5.9490638385009208e-08 * g # * mi
CPL.send(send_array, cnst_portion)
# recv data and plot
recv_array, ierr = CPL.recv(recv_array, BC_portion)
print(time)
CPL.finalize()
MPI.Finalize()
len_lists_to_send = 5000
# DISTANCE LISTS
if rank == 0:
# RUN PROGRAM
distance_list = load(distance_list_path)
shuffle(distance_list)
shuffle(distance_list)
dists = []
last_list = None
for x in itertools.permutations(distance_list):
dists.append(x)
list_length = len(dists)
if list_length >= len_lists_to_send:
if last_list == dists:
print ERROR_MESSAGE
MPI.Abort()
d = comm.recv(source=2, tag=1)
if d:
total_sent += list_length
comm.send([dists, (rank, name)], dest=2, tag=2)
p_2 = '[SENDING JOB TO ' + \
str(d[0])+' ON '+str(d[1])+'] '
p_3 = '[t_sent ' + str(total_sent) + '] '
last_list = dists
dists = []
p_4 = '[list_len was ' + \
str(list_length)+'| now : '+str(len(dists))+']'
print p_1 + p_2 + p_3 + p_4
else:
print p_1 + '[NO ONE TO SEND TO]'
# SHUTDOWN PROGRAM
