def anneal(atoms, bonds, angles, dihedrals, params, name=''):
run_name = utils.unique_filename('lammps/', 'anneal_'+name, '.data')
write_data_file(atoms, bonds, angles, dihedrals, params, run_name)
run_anneal(run_name)
jsub.wait(run_name)
tail = subprocess.Popen('tail lammps/'+run_name+'.xyz -n '+str(len(atoms)), shell=True, stdout=subprocess.PIPE).communicate()[0]
if 'No such file or directory' in tail:
raise Exception('Anneal '+run_name+' failed')
for i,line in enumerate(tail.splitlines()):
atoms[i].x, atoms[i].y, atoms[i].z = [float(s) for s in line.split()[1:]]
return atoms
def anneal(atoms, bonds, angles, dihedrals, params, name=""):
run_name = utils.unique_filename("lammps/", "anneal_" + name, ".data")
write_data_file(atoms, bonds, angles, dihedrals, params, run_name)
run_anneal(run_name)
jsub.wait(run_name)
tail = subprocess.Popen(
"tail lammps/" + run_name + ".xyz -n " + str(len(atoms)), shell=True, stdout=subprocess.PIPE
).communicate()[0]
if "No such file or directory" in tail:
raise Exception("Anneal " + run_name + " failed")
for i, line in enumerate(tail.splitlines()):
atoms[i].x, atoms[i].y, atoms[i].z = [float(s) for s in line.split()[1:]]
return atoms
def chelpg(atoms, theory, queue='batch', chkfile_run_name=None, name=''):
run_name = utils.unique_filename('gaussian/', 'chelpg_'+name+'_'+theory[:8].translate( string.maketrans('/(),*', '_____') ), '.log')
if chkfile_run_name:
shutil.copyfile('gaussian/'+chkfile_run_name+'.chk', 'gaussian/'+run_name+'.chk')
job(atoms, theory, queue, run_name, 'Pop=CHelpG')
jsub.wait(run_name)
try:
charges = parse_chelpg('gaussian/'+run_name+'.log')
except: #sometimes file is not written yet
time.sleep(10)
charges = parse_chelpg('gaussian/'+run_name+'.log')
if charges:
for i,charge in enumerate(charges):
atoms[i].charge = charge
return charges
def scan_modredundant(starting_atoms, basis, run_name_base, modredundant_section, param_starts, param_ends, n_steps):
ranges = [param_ends[i]-param_starts[i] for i in range(len(param_ends))]
increments = [r/n_steps for r in ranges]
params = [p for p in param_starts]
for step in xrange(n_steps):
run_name = run_name_base+str(step)
if step==0:
job(starting_atoms, basis, 'batch', run_name, 'Opt=(CalcFC,ModRedundant)', procs=1, extra_section=modredundant_section % tuple(params) )
else:
old_run_name = run_name_base+str(step-1)
atoms = parse_atoms('gaussian/'+old_run_name+'.log', check_convergence=False)[1]
shutil.copy('gaussian/'+old_run_name+'.chk', 'gaussian/'+run_name+'.chk')
job(atoms, basis, 'batch', run_name, 'Opt=(CalcFC,ModRedundant) Guess=Read', procs=1, extra_section=modredundant_section % tuple(params) )
jsub.wait(run_name)
for i in range(len(params)):
params[i] += increments[i]
if len(columns)==3:
charges.append( float(columns[2]) )
return charges
def minimize(atoms, theory, queue='batch', name='', restrained=None, async=False): #blocks until done
run_name = utils.unique_filename('gaussian/', 'min_'+name+'_'+theory[:8].translate( string.maketrans('/(),*', '_____') ), '.inp')
if not restrained:
job(atoms, theory, queue, run_name, 'Opt=CalcFC') #SCRF(Solvent=n-Hexane)
else:
dihedral = restrained
job(atoms, theory, queue, run_name, 'Opt=(ModRedundant,Loose,CalcFC)', extra_section='D %d %d %d %d F'%tuple([a.index for a in dihedral.atoms]))
if async:
return run_name
else:
jsub.wait(run_name)
energy, coords = parse_coords('gaussian/'+run_name+'.log')
if coords:
for i,xyz in enumerate(coords):
atoms[i].x, atoms[i].y, atoms[i].z = xyz
return run_name, energy
def chelpg(atoms, theory, queue='batch', chkfile_run_name=None, name=''):
run_name = utils.unique_filename('gaussian/', 'chelpg_'+name+'_'+theory[:8].translate( string.maketrans('/(),*', '_____') ), '.log')
if chkfile_run_name:
shutil.copyfile('gaussian/'+chkfile_run_name+'.chk', 'gaussian/'+run_name+'.chk')
job(atoms, theory, queue, run_name, 'Pop=CHelpG')
jsub.wait(run_name)
try:
charges = parse_chelpg('gaussian/'+run_name+'.log')
except: #sometimes file is not written yet
