def main():
M = Molecule(argv[1])
tempfnm = argv[3] if len(argv) >= 4 else None
if tempfnm != None:
M.add_quantum(tempfnm)
print M.Data.keys()
M.write(argv[2])
def main():
M = Molecule(argv[1])
tempfnm = argv[3] if len(argv) >= 4 else None
if tempfnm != None:
M.add_quantum(tempfnm)
print M.Data.keys()
M.write(argv[2])
def do_quantum(wq_port):
M = Molecule('shots.gro')
M.add_quantum('../settings/qchem.in')
# Special hack to add TIP3P waters.
if os.path.exists('waters.gro'):
print("Found waters.gro, loading as external waters and adding SPC charges.")
Mext = Molecule('waters.gro')
Q = col([-0.82 if (i%3==0) else 0.41 for i in range(Mext.na)])
Qext = [np.hstack((xyz, Q)) for xyz in Mext.xyzs]
M.qm_extchgs = Qext
# End special hack.
digits = len(str(len(M)-1))
formstr = '\"%%0%ii\"' % digits
def read_quantum():
Result = None
os.chdir('calcs')
for i in range(M.ns):
dnm = eval(formstr % i)
print("\rNow in directory %i" % i, end=' ')
if os.path.exists(dnm):
os.chdir(dnm)
if os.path.exists('qchem.out'):
Output = Molecule('qchem.out')
if os.path.exists('plot.esp'):
ESP = Molecule('plot.esp')
#print ESP.Data.keys()
Output.qm_espxyzs = list(ESP.qm_espxyzs)
Output.qm_espvals = list(ESP.qm_espvals)
#Output += Molecule('plot.esp')
if Result == None:
Result = Output
else:
Result += Output
else:
raise Exception("The output file %s doesn't exist." % os.path.abspath('qchem.out'))
os.chdir('..')
else:
raise Exception("The subdirectory %s doesn't exist." % os.path.abspath(dnm))
os.chdir('..')
return Result
def run_quantum():
ESP = create_esp_surfaces(M)
work_queue.set_debug_flag('all')
wq = work_queue.WorkQueue(wq_port, exclusive=False, shutdown=False)
wq.specify_name('forcebalance')
os.makedirs('calcs')
os.chdir('calcs')
for i in range(M.ns):
dnm = eval(formstr % i)
os.makedirs(dnm)
os.chdir(dnm)
M.edit_qcrems({'igdesp':len(ESP[i])})
M.write("qchem.in", select=i)
ESPBohr = np.array(ESP[i]) / bohr2ang
np.savetxt('ESPGrid',ESPBohr)
print("Queueing up job", dnm)
queue_up(wq, command = 'qchem40 qchem.in qchem.out',
input_files = ["qchem.in", "ESPGrid"],
output_files = ["qchem.out", "plot.esp", "efield.dat"], verbose=False)
os.chdir('..')
for i in range(M.ns):
wq_wait(wq)
os.chdir('..')
if os.path.exists('calcs'):
print("calcs directory exists. Reading calculation results.")
Result = read_quantum()
else:
print("calcs directory doesn't exist. Setting up and running calculations.")
run_quantum()
print("Now reading calculation results.")
Result = read_quantum()
print("Writing results to qdata.txt.")
Result.write('qdata.txt')
return Result