def run_orcajob(e, jobdetails, info):
jobtype = 'orca'
# info = inputs.load_json(e)
smi = info["FILTERED"][0]["SMI"]
pname = inputs.get_name_file(e)
print("%s : SMILES: %s" % (pname, smi))
#print len(info['conformers'])
if jobtype in info:
print "no"
print ("%s: there are %s %s conformers" % (pname, jobtype, len(info[jobtype])))
return -1
calc_orca = []
inpname = inputs.get_name_file(e) +'.inp'
bestconf = inputs.get_bestconf(e, info)
if None == bestconf:
print("%s: there are not %s mopac conformers" % (pname))
return False
mols = {}
mols['inchikey'] = info['inchikey']
mols['coords'] = info["FILTERED"][0]['mopac'][bestconf]['coords']
mols['charge'] = 0.0
inputs.create_input(e,'config.json','.inp', mols)
outfile = 'zindo.out'
#
# implement Signal catcher
#
handler = functools.partial(early_dead, outfile, e, info)
signal.signal(signal.SIGINT, handler)
signal.signal(signal.SIGTERM, handler)
callorca.run_orca(inpname)
calc = {}
if isfile(join(inputs.get_outpath(e),outfile)):
try:
print inputs.get_outpath(e)
calc = orcaloader.load_calc_list(inputs.get_outpath(e))
print calc
except:
info['lock']= 'ready'
info["FILTERED"][0][jobtype]= 'fail'
inputs.store_json(e,info)
return True
info["FILTERED"][0][jobtype] = calc
# readey may be gone of there is jobtype
info['lock']= 'ready'
inputs.store_json(e,info)
return True
def early_dead(outfile, e, info, signum, stack):
pname = inputs.get_name(e)
print(" \n %s:Dead signal %s\n" % (pname, signum))
info['lock'] = 'no'
inputs.store_json(e,info)
print("\n %s exit NOW \n" % pname)
sys.exit()
def early_dead(outfile, e, info, signum, stack):
pname = inputs.get_name(e)
print(" \n %s:Dead signal %s\n" % (pname, signum))
info['lock'] = 'no'
try:
calc = loader.load_calc_list(inputs.get_outpath(e), outfile)
info["FILTERED"][0]['nwchem'] = calc
except:
# it fails but just move on
print("%s: ed failed to parse a nwchemout" % pname)
info["FILTERED"][0]['nwchem'] = 'fail'
finally:
inputs.store_json(e, info)
print("\n %s exit NOW \n" % pname)
sys.exit()
def run_nwchemjob(e):
info = inputs.load_json(e)
smi = info["smiles"]
pname = inputs.get_name(e)
print("%s : SMILES: %s" % (pname, smi))
if 'mopac' in info:
print("%s: there are %s mopac conformers" %
(pname, len(info['mopac'])))
else:
print("%s: there are not %s mopac conformers" % (pname))
return False
if 'nwchem' in info:
print("%s: there are %s nwchem conformers" %
(pname, len(info['nwchem'])))
return True
calc_mop = []
for cc in range(len(info['conformers'])):
mols = {}
mols['inchikey'] = info['inchikey']
mols['coords'] = info['mopac'][cc]['coords']
mols['charge'] = 0.0
#print mols
print("%s: Processing CONF %s" % (pname, cc))
fname = '_CONF_' + str(cc)
inputs.create_input(e, 'config_nw.json', fname + '.nw', mols)
inpname = inputs.get_name_file(e) + fname + '.nw'
copyfile(inpname, 'nwchem')
callnw.run_nwchem('nwchem')
outfile = 'nwchem.out'
if isfile(outfile):
calc = loader.load_calc_list(inputs.get_outpath(e), 'nwchem.out')
calc_mop.append(calc)
info['nwchem'] = calc_mop
inputs.store_json(e, info)
def run_nwchemjob_best(e, job):
info = inputs.load_json(e)
smi = info["smiles"]
pname = inputs.get_name(e)
print("%s : SMILES: %s" % (pname, smi))
bestconf = inputs.get_bestconf(e)
if None == bestconf:
print("%s: there are not %s mopac conformers" % (pname))
return False
mols = {}
mols['inchikey'] = info['inchikey']
mols['coords'] = info['mopac'][bestconf]['coords']
mols['charge'] = 0.0
inputs.create_input(e,'config_nw.json','.nw', mols)
inpname = inputs.get_name_file(e) +'.nw'
copyfile(inpname, 'nwchem.nw')
print job
callnwbg.run_nwchem('nwchem', job)
outfile = 'nwchem.out'
calc_mop = []
if isfile(outfile):
calc = loader.load_calc_list(inputs.get_outpath(e), 'nwchem.out')
calc_mop.append(calc)
info['nwchem'] = calc_mop
info['lock']= 'ready'
inputs.store_json(e,info)
return True
def run_nwchemjob_best(e, job):
info = inputs.load_json(e)
smi = info["FILTERED"][0]["SMI"]
pname = inputs.get_name(e)
print("%s : SMILES: %s" % (pname, smi))
need_restart = False
outfile = join(inputs.get_outpath(e),'nwchem.out')
print outfile
calc = {}
if isfile(outfile):
try:
calc = loader.load_calc_list(inputs.get_outpath(e), 'nwchem.out')
except:
# it fails but just move on
info["FILTERED"][0]['nwchem'] = 'fail'
info['lock']= 'ready'
inputs.store_json(e,info)
return True
# calc_mop.append(calc)
# info['nwchem'] = calc_mop
else:
info['lock']= 'no'
inputs.store_json(e,info)
return True
if calc['optdone'] == True:
info['lock']= 'ready'
else:
info['lock']= 'no'
info["FILTERED"][0]['nwchem'] = calc
inputs.store_json(e,info)
return True
def run_nwchemjob_best(e, job, info):
# info = inputs.load_json(e)
smi = info["FILTERED"][0]["SMI"]
pname = inputs.get_name_file(e)
print("%s : SMILES: %s" % (pname, smi))
need_restart = False
outfile = 'nwchem.out'
print outfile
# if isfile(outfile):
# prevcalc = loader.load_calc_list(inputs.get_outpath(e), outfile, 'opt')
# optdone = prevcalc['optdone']
# if prevcalc['optdone'] == True:
# inputs.put_lock(e,'ready')
# return False
# elif prevcalc['optdone'] == False:
# need_restart = True
# rename_w_num(outfile)
# else:
# print ('%s: WARNING did something did not go further' % pname)
# return False
try:
if 'optdone' in info["FILTERED"][0]['nwchem']:
if info["FILTERED"][0]['nwchem']['optdone'] == True:
inputs.put_lock(e, 'ready', info)
return True
# else:
elif info["FILTERED"][0]['nwchem']['optdone'] == False:
need_restart = True
elif info["FILTERED"][0]['nwchem']['optdone'] == None:
need_restart = False
if isfile(outfile):
rename_w_num(outfile)
# elif info['nwchem']['optdone'] == False:
# need_restart = True
# if isfile(outfile):
# rename_w_num(outfile)
# else:
# print ('%s: WARNING did something did not go further' % pname)
# return False
except:
print("%s: no nwchem optdone info" % pname)
mols = {}
inpname = inputs.get_name_file(e) + '.nw'
if need_restart:
if isfile(inpname):
rename_w_num(inpname)
#we could restar with mols from prevcalc
mols['inchikey'] = info['inchikey']
mols['charge'] = 0.0
mols['coords'] = info["FILTERED"][0]['nwchem']['coords']
inputs.create_input(e, 'config_nwres.json', '.nw', mols)
else:
bestconf = inputs.get_bestconf(e, info)
if None == bestconf:
print("%s: there are not best mopac conformers" % (pname))
return False
# mols = {}
mols['inchikey'] = info['inchikey']
mols['coords'] = info["FILTERED"][0]['mopac'][bestconf]['coords']
mols['charge'] = 0.0
inputs.create_input(e, 'config_nw.json', '.nw', mols)
copyfile(inpname, 'nwchem.nw')
outfile = 'nwchem.out'
print outfile
#
# implement Signal catcher
#
handler = functools.partial(early_dead, outfile, e, info)
signal.signal(signal.SIGINT, handler)
signal.signal(signal.SIGTERM, handler)
# Do calculation
callnwbg.run_nwchem_sub('nwchem', job)
##debug print ("callnwbg My PID is: %s \n" % getpid())
##debug time.sleep(4000)
# calc_mop = []
calc = {}
if isfile(join(inputs.get_outpath(e), outfile)):
try:
calc = loader.load_calc_list(inputs.get_outpath(e), outfile)
except:
# it fails but just move on
info['lock'] = 'ready'
info["FILTERED"][0]['nwchem'] = 'fail'
inputs.store_json(e, info)
return True
# calc_mop.append(calc)
# info['nwchem'] = calc_mop
else:
info['lock'] = 'no'
inputs.store_json(e, info)
return True
if calc['optdone'] == True:
info['lock'] = 'ready'
else:
info['lock'] = 'no'
info["FILTERED"][0]['nwchem'] = calc
inputs.store_json(e, info)
return True
def run_nwchemjob_best(e):
info = inputs.load_json(e)
smi = info["smiles"]
pname = inputs.get_name(e)
print("%s : SMILES: %s" % (pname, smi))
need_restart = False
outfile = 'nwchem.out'
# if isfile(outfile):
# prevcalc = loader.load_calc_list(inputs.get_outpath(e), outfile, 'opt')
# optdone = prevcalc['optdone']
# if prevcalc['optdone'] == True:
# inputs.put_lock(e,'ready')
# return False
# elif prevcalc['optdone'] == False:
# need_restart = True
# rename_w_num(outfile)
# else:
# print ('%s: WARNING did something did not go further' % pname)
# return False
try:
if 'optdone' in info['nwchem']:
if info['nwchem']['optdone'] == True:
inputs.put_lock(e, 'ready')
return True
elif info['nwchem']['optdone'] == False:
need_restart = True
if isfile(outfile):
rename_w_num(outfile)
else:
print('%s: WARNING did something did not go further' % pname)
return False
except:
print("%s no nwcheminfo" % pname)
mols = {}
inpname = inputs.get_name_file(e) + '.nw'
if need_restart:
if isfile(inpname):
rename_w_num(inpname)
#we could restar with mols from prevcalc
mols['inchikey'] = info['inchikey']
mols['charge'] = 0.0
mols['coords'] = info['nwchem']['coords']
inputs.create_input(e, 'config_nwres.json', '.nw', mols)
else:
bestconf = inputs.get_bestconf(e)
if None == bestconf:
print("%s: there are not %s mopac conformers" % (pname))
return False
# mols = {}
mols['inchikey'] = info['inchikey']
mols['coords'] = info['mopac'][bestconf]['coords']
mols['charge'] = 0.0
inputs.create_input(e, 'config_nw.json', '.nw', mols)
copyfile(inpname, 'nwchem.nw')
callnw.run_nwchem('nwchem')
# calc_mop = []
calc = {}
if isfile(outfile):
try:
calc = loader.load_calc_list(inputs.get_outpath(e), 'nwchem.out')
except:
# it fails but just move on
info['lock'] = 'ready'
info['nwchem'] = 'fail'
inputs.store_json(e, info)
return True
# calc_mop.append(calc)
#info['nwchem'] = calc_mop
if calc['optdone'] == True:
# info['nwchem'] = calc_mop
info['lock'] = 'ready'
else:
info['lock'] = 'no'
info['nwchem'] = calc
inputs.store_json(e, info)
return True