def get_zr_range(st, thickness, zr):
red_thick = thickness/np.linalg.norm(st.rprimd[2])
# z_range = [z2 - thickness, z2]
zr_range = [zr - red_thick, zr]
printlog('zr_range is ', zr_range)
return zr_range
def suf_en(cl1, cl2, silent=0):
"""Calculate surface energy
cl1 - supercell with surface
cl2 - comensurate bulk supercell
the area is determined from r[0] and r[1];- i.e they lie in surface
"""
st1 = cl1.end
st2 = cl2.end
# pm = st1.convert2pymatgen(oxidation = {'Y':'Y3+', 'Ba':'Ba2+', 'Co':'Co2.25+', 'O':'O2-'})
A = np.linalg.norm(np.cross(st1.rprimd[0], st1.rprimd[1]))
# print(A)
if st1.natom % st2.natom > 0:
printlog(
'Warning! non-stoichiometric slab, check system sizes: natom1 = ',
st1.natom, 'natom2 = ', st2.natom, st1.natom / st2.natom)
mul = st1.natom / st2.natom
gamma = (cl1.e0 - cl2.e0 * mul) / 2 / A * header.eV_A_to_J_m
if not silent:
print('Surface energy = {:3.2f} J/m2 | {:} | {:} '.format(
gamma, cl1.id, cl2.id))
return gamma
def gunzip_file(filename):
printlog('unzipping file', filename)
with open(filename.replace('.gz', ''), 'wb') as f_out:
with gzip.open(filename, 'rb') as f_in:
shutil.copyfileobj(f_in, f_out)
return
def file_exists_on_server(file, addr):
file = file.replace('\\', '/') # make sure is POSIX
printlog('Checking existence of file', file, 'on server', addr)
exist = run_on_server(' ls ' + file, addr)
# if header.ssh_object:
# exist = header.ssh_object.fexists(file)
# else:
# exist = runBash('ssh '+addr+' ls '+file)
if 'No such file' in exist:
exist = ''
else:
exist = 'file exists'
if exist:
res = True
else:
res = False
printlog('File exist? ', res)
return res
def set_potential(self, znucl, arg=''):
# print arg
if not arg:
arg = header.PATH2POTENTIALS + '/' + invert(znucl)
printlog('Attention!, Default potentials is chosen from ',
header.PATH2POTENTIALS,
'for',
invert(znucl),
imp='Y')
if type(arg) not in (str, ):
# sys.exit("\nset_potential error\n")
raise RuntimeError
if znucl in self.potdir:
if arg == self.potdir[znucl]:
print_and_log(
"Warning! You already have the same potential for " +
str(znucl) + " element\n")
# print type(self.potdir)
self.potdir[znucl] = arg
self.history += "Potential for " + str(
znucl) + " was changed to " + arg + "\n"
print_and_log("Potential for " + str(znucl) + " was changed to " +
arg + "\n")
# self.update()
return
def write_occmatrix(occs, folder):
#create OCCMATRIX
makedir(folder)
printlog('I create OCCMATRIX in ', folder, imp='y')
filename = folder + '/OCCMATRIX'
with open(filename, 'w', newline='') as f:
numat = len(occs)
f.write(str(numat) + ' #num of atoms to be specified\n')
at_nums = occs.keys()
at_spin = [] # # 2 or 1
at_ltyp = [] # l - orbital type, 1 - s, 2 - d, 3 - f
for key in occs:
occ = occs[key]
if len(occ) == 10: # spin polarized, d orbital
at_spin.append(2)
at_ltyp.append(2)
else:
raise RuntimeError # please write by yourself for other cases
for i, l, s in zip(at_nums, at_spin, at_ltyp):
f.write(list2string([i + 1, l, s]) + ' #i, l, s\n')
# for sp in range(s):
f.write('spin 1\n')
for row in occs[i][0:len(occs[i]) // s]:
f.write(list2string(row) + '\n')
if s == 2:
f.write('spin 2\n')
for row in occs[i][len(occs[i]) // s:]:
f.write(list2string(row) + '\n')
f.write('\n')
return filename
def insert_atom(
st,
el,
i_void=None,
r_imp=1.6,
):
"""Simple Wrapper for inserting atoms """
r_impurity = r_imp
st_pores, sums, avds = determine_voids(st, r_impurity)
insert_positions = determine_unique_voids(st_pores, sums, avds)
printlog('To continue please choose *i_void* from the list above', imp='y')
if i_void == None:
sys.exit()
# st.name = st.name.split('+')[0]
xc = insert_positions[i_void]
st_new, i_add = st.add_atoms([xc], el, return_ins=True)
st_new.name += '+' + el + str(i_void)
st_new.des += ';Atom ' + el + ' added to ' + str(xc)
printlog(st.des, imp='y')
st_new.write_xyz()
st_new.magmom = [None]
return st_new, i_add
def printme(self):
for key in self.vasp_params:
if self.vasp_params[key] == None: continue
print_and_log( "{:30s} = {:s} ".format("s.vasp_params['"+key+"']", str(self.vasp_params[key]) ), imp = 'Y', end = '\n' )
printlog('ngkpt:', self.ngkpt, imp = 'Y')
printlog('POTDIR:', self.potdir, imp = 'Y', end = '\n' )
def vasp_step(v, msg, rm=0):
printlog('Calculating ' + msg + ' point!\n', imp='y')
copyfile(str(v) + '.POSCAR', 'POSCAR')
cl = vasp_run(3, msg, vasprun_command=vasprun_command)
copy_vasp_files(v)
if rm:
runBash('rm CHGCAR CHG WAVECAR')
return cl
def chgsum(cll, el, site, silent=1):
"""
calculate sum of Bader charges for particular atoms
"""
for cl in cll:
# print(cl.id, end = ' ')
try:
cl.chgsum[(el, site)] = 0
except:
pass
if not hasattr(cl, 'charges') or len(cl.charges) == 0:
cl.get_bader_ACF()
# determine_symmetry_positions(cl.end, el, silent = 0)
# print('')
try:
pos = determine_symmetry_positions(cll[0].end, el, silent=1)
except:
printlog('chgsum() Warning!', cll[0].id, 'is broken!')
return 0
for p in pos[site]:
''
for cl in cll:
if not hasattr(cl, 'chgsum'):
cl.chgsum = {}
cl.chgsum[(el, site)] = 0
cl.chgsum[(el, site)] += cl.charges[p]
# print('{:5.3f}'.format(cl.charges[p]), end = ' ')
# print('')
if not silent:
print('Sum of charges for ', el + str(site + 1), ':')
el_ind = cl.init.znucl.index(
invert(el)) # index of element in znucl and zval and nznucl
zval = cl.init.zval[el_ind] # number of electrons in chosen potential
for cl in cll:
cl.chgsum[(el, site)] /= len(pos[site])
chgsum = zval - cl.chgsum[(el, site)]
if cl == cll[0]:
chgsum_ref = chgsum
if not silent:
print('{:5.2f}({:4.2f})'.format(chgsum, chgsum_ref - chgsum), )
if not silent:
print('\n')
# print(cl.charges)
return chgsum
def setting_sshpass(cl):
if hasattr(cl , 'cluster'):
# print(cl.cluster)
# clust = header.CLUSTERS[cl.cluster]
if 'sshpass' in cl.cluster and cl.cluster['sshpass']:
printlog('setting sshpass to True', imp = '')
# sys.exit()
header.sshpass = cl.cluster['sshpass']
else:
header.sshpass = None
def makedir(path):
"""
*path* - path to some file
Make dirname(path) directory if it does not exist
"""
dirname = os.path.dirname(path)
if dirname and not os.path.exists(dirname):
os.makedirs(dirname)
printlog("Directory", dirname, " was created", imp = 'y')
return
def set_ngkpt(self,arg):
if not is_list_like(arg):
printlog("Error! set_ngkpt type error")
old = copy.copy(self.ngkpt)
self.ngkpt = copy.copy(arg)
self.kpoints_file = True
self.vasp_params['KSPACING'] = None
if old == arg:
print_and_log( "Warning! You did not change one of your parameters in new set", imp = 'y')
return
self.history += "ngkpt was changed from "+str(old)+" to "+str(arg) + " and KPOINTS file was swithed on\n"
return
def run_on_server(command, addr = None):
printlog('Running', command, 'on server ...')
command = command.replace('\\', '/') # make sure is POSIX
# sys.exit()
# print(header.sshpass)
# sys.exit()
if addr is None:
addr = header.cluster_address
if header.ssh_object:
# printlog('Using paramiko ...', imp = 'y')
# if 'ne' in header.warnings:
# sys.exit()
out = header.ssh_object.run(command, noerror = True, printout = 'ne' in header.warnings)
elif header.sshpass and header.sshpass == 'proxy':
com = 'ssh -tt sdv sshpass -f '+ header.path2pass +' ssh '+addr+' "'+command+'"'
# print(com)
# sys.exit()
out = runBash(com)
# print(out)
out = out.split('Connection to')[0] # remove last message Connection to ipaddress closed
# sys.exit()
elif header.sshpass:
com = 'sshpass -f '+header.path2pass+' ssh '+addr+' "'+command+'"'
# print(com)
# sys.exit()
out = runBash(com)
# sys.exit()
else:
bash_comm = 'ssh '+addr+' "'+command+'"'
# print(bash_comm)
# sys.exit()
out = runBash(bash_comm)
out = out.split('#')[-1].strip()
printlog(out)
# print(out)
# sys.exit()
return out
def update_var(st):
if st.natom != len(st.xred) != len(st.xcart) != len(st.typat) or len(
st.znucl) != max(st.typat):
printlog("Error! write_xyz: check your arrays.\n\n")
if st.xcart == [] or len(st.xcart) != len(st.xred):
printlog(
"Warining! write_xyz: len(xcart) != len(xred) making xcart from xred.\n"
)
st.xcart = xred2xcart(st.xred, st.rprimd)
#print xcart[1]
return st.rprimd, st.xcart, st.xred, st.typat, st.znucl, len(st.xred)
def vasp_run(n, des):
#allows to run vasp several times, here fireworks can be used
#n - number of attempts
#des - description of run
for i in range(n): # max three attempts
out = runBash(vasprun_command)
printlog(des, 'attempt', i, 'out is', out)
cl = CalculationVasp(output='OUTCAR')
out = cl.read_results(show='fo')
printlog('Results are', imp='y')
printlog(out, imp='y')
status = check(cl)
if status == 0:
break
else:
if os.path.exists('CONTCAR'):
copyfile('CONTCAR', 'POSCAR')
else:
printlog(
'No CONTCAR was found. No further attempts to run VASP',
imp='y')
break
return cl
def inherit_iset(ise_new,
ise_from,
varset,
override=False,
newblockfolder=None):
""" Create new set copying from existing and update some fields. If ise_from does not exist create new"""
ise_new = ise_new.strip()
ise_from = ise_from.strip()
if ise_from not in varset:
printlog("\nWarning! Set " + ise_from +
" does not exist. I return new empty set\n")
return InputSet(ise_new)
old = varset[ise_from]
for key in vasp_electronic_keys + vasp_ionic_keys + vasp_other_keys: #check if new keys was added
if key not in old.vasp_params:
old.vasp_params[key] = None
if override:
print_and_log("\nAttention! You have chosen to override set " +
ise_new + "\n")
elif ise_new in varset:
print_and_log(
"\nSet " + ise_new +
" already exists. I return it without changes. Be carefull not to spoil it\n"
)
return varset[ise_new]
new = copy.deepcopy(old)
new.ise = ise_new
new.compare_with = ise_from + " "
new.des = "no description for these set, see history"
new.conv = {}
print_and_log("New set " + ise_new + " was inherited from set " +
ise_from + "\n")
new.history = old.history + "\nSet " + ise_new + " was inherited from: " + ise_from + "\n"
if newblockfolder:
new.history += 'blockfolder changed from ' + new.blockfolder + ' to ' + newblockfolder + '\n'
new.blockfolder = newblockfolder
varset[ise_new] = new
return new
def form_en(sources, products, norm_el=None):
"""
Calculate formation energy of reaction.
sources, products - list of tuples (x, cl), where x is multiplier and cl is calculation
norm_el - which element to use for normalization
'all' - normalize by total number of atoms
'el' - normalize by this element
int - divide by this number
"""
El = []
Nzl = []
for ls in [sources, products]:
E = 0
Nz = {}
for x, cl in ls:
E += x * cl.e0
for i, z in enumerate(cl.end.znucl):
if z not in Nz:
Nz[z] = 0
Nz[z] += x * cl.end.nznucl[i]
El.append(E)
Nzl.append(Nz)
for z in Nzl[0]:
if abs(Nzl[0][z] - Nzl[1][z]) > 1e-5:
printlog('Error! Number of', invert(z),
'atoms in source and product are different!')
# norm = 1
if 'all' == norm_el:
norm = sum(Nzl[0].values())
elif type(norm_el) == str:
norm = Nzl[0][invert(norm_el)]
elif norm_el != None:
norm = norm_el
else:
norm = 1
print('Normalizing by ', norm_el, norm, 'atoms')
dE = (El[1] - El[0]) / norm
print('dE = {:4.2f} eV'.format(dE))
return dE
def makedir(path, renew_folder=False):
"""
*path* - path to some file
Make dirname(path) directory if it does not exist
"""
import shutil as S
dirname = os.path.dirname(path)
if renew_folder and os.path.exists(dirname): S.rmtree(path)
else: pass
if dirname and not os.path.exists(dirname):
os.makedirs(dirname)
printlog("Directory", dirname, " was created", imp = 'y')
return
def download(file, to_file):
# print(header.sshpass)
if header.ssh_object:
exist = file_exists_on_server(file, addr)
# try:
if exist:
printlog('Using paramiko: ssh_object.get(): from to ', file, to_file)
header.ssh_object.get(file, to_file )
out = ''
# except FileNotFoundError:
else:
out = 'error, file not found'
elif header.sshpass and header.sshpass == 'proxy':
# com = 'ssh sdv "sshpass -f ~/.ssh/p ssh ' + addr + ' \\"tar zcf - '+ file +'\\"" | tar zxf - '+to_file # does not work?
com = 'ssh sdv "sshpass -f ~/.ssh/p ssh ' + addr + ' \\"tar cf - '+ file +'\\"" > '+to_file
# print('sshpass',com)
# sys.exit()
out = runBash(com)
elif header.sshpass:
#com = 'rsync --rsh='+"'sshpass -f /home/aksenov/.ssh/p ssh' " +' -uaz '+addr+':'+file+ ' '+to_file
com = 'rsync --rsh='+"'sshpass -f "+header.path2pass+" ssh' " +' -uaz '+addr+':'+file+ ' '+to_file
out = runBash(com)
# print(addr)
# sys.exit()
else:
# print(addr,file,to_file)
out = runBash('rsync -uaz '+addr+':'+file+ ' '+to_file)
if 'error' in out:
res = out
else:
res = 'OK'
out = ''
printlog('Download result is ', res)
return out
def interface_en(cl, cl1, cl2, mul1=1, mul2=1, silent=0, n_intefaces=1):
"""
Calculate surface energy
cl - slab or cell with interface
cl1 - slab or cell with phase 1, usually substrate
cl2 - slab or cell with phase 2, usually film
mul1, mul2, - multiply cells
n_intefaces - number of similar interfaces in the system
Interface is assumed to be normal to R3!
"""
st = cl.end
st1 = cl1.end
st2 = cl2.end
natom = st.natom
natom1 = st1.natom
natom2 = st2.natom
A = np.linalg.norm(np.cross(st.rprimd[0], st.rprimd[1]))
A1 = np.linalg.norm(np.cross(st1.rprimd[0], st1.rprimd[1])) * mul1
A2 = np.linalg.norm(np.cross(st2.rprimd[0], st2.rprimd[1])) * mul2
print('Sets are {:} {:} {:}'.format(cl.id[1], cl1.id[1], cl2.id[1]))
print('Max forces are {:.1f} {:.1f} {:.1f} meV/A'.format(
cl.maxforce, cl1.maxforce, cl2.maxforce))
print('Surface areas: {:.1f} {:.1f} {:.1f} A^2'.format(A, A1, A2))
mul = natom / (natom1 * mul1 + natom2 * mul2
) # natom1 and natom2 should be scaled equally
# print(mul)
if natom != (natom1 * mul1 + natom2 * mul2) * mul:
printlog('Error! Number of atoms are different:', st.natom, st1.natom,
st2.natom)
diff = cl.e0 - (cl1.e0 * mul1 + cl2.e0 * mul2) * mul
gamma = diff / A * header.eV_A_to_J_m / n_intefaces # inteface
if not silent:
print('Interface energy = {:3.2f} J/m2 | {:3.2f} eV '.format(
gamma, diff))
return gamma
def setting_sshpass(cl=None, clust=None):
"""
Creates some variables for sshpass mode
cl (Caluculation) - object, should contain cluster dict, has higher priority
clust (dict) - cluster dicts
"""
if cl and hasattr(cl, 'cluster'):
clust = cl.cluster
# print(clust.get('sshpass'))
if clust and clust.get('sshpass') is True:
printlog('setting sshpass to True', imp='')
header.sshpass = clust['sshpass']
header.path2pass = clust.get('path2pass')
else:
header.sshpass = None
header.path2pass = None
def check_output(filename, check_string, load):
"""
Check if file exist and it is finished by search for check_string
"""
if filename and os.path.exists(filename):
out = grep_file(check_string, filename, reverse = True)
printlog('The grep result of',filename, 'is:', out)
# sys.exit()
if check_string in out or 'un' in load:
state = '4. Finished'
else:
state = '5. Broken outcar'
else:
state = '5. no OUTCAR'
return state
def cal_chg_diff(cl1, cl2, wcell, chg = 'CHGCAR'):
"""1. Calculate differences of charge densities
Works on local computer
wcell = 0 or 1 - which cell to use to show
chg (str) - which file to use
CHGCAR - the name as outcar
if not exist CHG is used
PARCHG - partial charge, the name without any additions
TO DO:
instead of paths to files, work with objects
d = d(cl1) - d(cl2)
d is calculated on server
"""
files = []
for cl in cl1, cl2:
if chg == 'CHGCAR':
file = cl.get_chg_file(nametype = 'asoutcar')
if not file:
printlog('No CHGCAR for cl',cl.id[0], 'trying CHG', imp = 'Y')
file = cl.get_chg_file('CHG', nametype = 'asoutcar')
elif chg == 'PARCHG':
file = cl.get_file('PARCHG')
files.append(file)
file1 = files[0]
file2 = files[1]
if file1 == None or file2 == None:
printlog('Error!, chg not found for one cl:', file1, file2)
working_dir = cl1.dir
dendiff_filename = working_dir + (chg+'_'+str(cl1.id[0])+'-'+str(cl2.id[0])).replace('.', '_')
printlog('Diff =', file1, '-', file2)
chgarith(file1, file2, '-', dendiff_filename, wcell)
printlog('Charge difference saved to', dendiff_filename, imp = 'Y')
return dendiff_filename
def wrapper_cp_on_server(file, to, new_filename = None):
"""
tries iterativly scratch and gz
"""
copy_to = to
copy_file = file
filename = os.path.basename(file)
if new_filename:
app = 'with new name '+new_filename
else:
app = ''
for s, gz in product([0,1], ['', '.gz']):
printlog('scratch, gz:', s, gz)
out = server_cp(copy_file+gz, to = to, gz = gz, scratch = s, new_filename = new_filename)
if out == '':
printlog('File', filename, 'was succesfully copied to',to, app, imp = 'y')
break
# else:
else:
printlog('Warning! File was not copied, probably it does not exist. Try using header.warnings = "neyY" for more details', imp = 'y')
return
def server_cp(copy_file, to, gz = True, scratch = False, new_filename = None):
if scratch:
if not header.PATH2ARCHIVE:
printlog('Warning! PATH2ARCHIVE is empty! Please put path archive in ~/simanrc.py or ./project_conf.py ')
copy_file = header.PATH2ARCHIVE + '/' + copy_file
else:
copy_file = header.project_path_cluster + '/' + copy_file
filename = os.path.basename(copy_file)
if new_filename is None:
new_filename = filename
if gz:
command = 'cp '+copy_file + ' ' + to +'/'+new_filename + '.gz ; gunzip -f '+ to+ '/'+new_filename+'.gz'
else:
command = 'cp '+copy_file + ' ' + to +'/'+new_filename
printlog('Running on server', command, imp = '')
if file_exists_on_server(copy_file, header.cluster_address):
out = run_on_server(command, addr = header.cluster_address)
printlog('Output of run_on_server', out, imp = '')
else:
out = 'error, file does not exist on server: '+copy_file
return out
def push_to_server(files = None, to = None, addr = None):
"""
if header.ssh_object then use paramiko
to (str) - path to remote folder !
"""
if not is_list_like(files):
files = [files]
to = to.replace('\\', '/') # make sure is POSIX
files_str = ' '.join(np.array(files ))
command = ' mkdir -p {:}'.format( to )
# print('asfsadfdsf', to)
printlog('push_to_server():', command, run_on_server(command, addr))
# sys.exit()
printlog('push_to_server(): uploading files ', files, 'to', addr, to)
if header.ssh_object:
for file in files:
# print(file, to)
header.ssh_object.put(file, to+'/'+os.path.basename(file) )
out = ''
elif header.sshpass and header.sshpass == 'proxy':
com = 'tar cf - '+ files_str + ' | ssh sdv "sshpass -f ~/.ssh/p ssh '+addr+' \\"cd '+header.cluster_home+' && tar xvf -\\"" '
# print(com)
# sys.exit()
out = runBash(com)
# print(out)
# sys.exit()
elif header.sshpass:
# if '@' not in addr:
# printlog('Error! Please provide address in the form user@address')
# l = addr.split('@')
# print(l)
# user = l[0]
# ad = l[1]
# com = 'rsync --rsh='+"'sshpass -f /home/aksenov/.ssh/p ssh' " +' -uaz '+files_str+ ' '+addr+':'+to
com = 'rsync --rsh='+"'sshpass -f "+header.path2pass+" ssh' " +' -uaz '+files_str+ ' '+addr+':'+to
# print(com)
# sys.exit()
out = runBash(com)
else:
out = runBash('rsync -uaz '+files_str+ ' '+addr+':'+to)
printlog(out)
return out
def insert_atom(
st,
el,
i_void=None,
i_void_list=None,
r_imp=1.6,
):
"""Simple Wrapper for inserting atoms
i_void (int) has higher priority than i_void_list
return st_new, i_add, sts_by_one
st_new - all positions are filled
i_add - the number of last inserted atom
sts_by_one - list of structures with only one inserted atom in all found positions
"""
r_impurity = r_imp
st_pores, sums, avds = determine_voids(st, r_impurity)
insert_positions = determine_unique_voids(st_pores, sums, avds)
printlog('To continue please choose *i_void* from the list above', imp='y')
# st.name = st.name.split('+')[0]
if i_void:
i_void_list = [i_void]
if i_void_list is None:
i_void_list = list(range(len(insert_positions)))
printlog('No i_void was provided, I insert all', imp='y')
st_new = st.copy()
sts_by_one = []
for i in i_void_list:
xc = insert_positions[i]
st_new, i_add = st_new.add_atoms([xc], el, return_ins=True)
st_one, _ = st.add_atoms([xc], el, return_ins=True)
st_one.name += '+' + el + str(i)
sts_by_one.append(st_one)
st_new.name += '+' + el + str(i)
st_new.des += ';Atom ' + el + ' added to ' + str(xc)
printlog(st.des, imp='y')
st_new.write_poscar()
st_new.magmom = [None]
return st_new, i_add, sts_by_one
def check(cl, exit=0):
# return 0 if ok, return 1 if failed
if hasattr(cl, 'e0'):
printlog('outcar is ok', imp='y')
out = 0
else:
printlog('outcar is broken ', imp='y')
out = 1
if exit:
printlog('exiting...', imp='y')
sys.exit()
return out
def metropolis(E1, E2, T=1):
"""
Metropolis algorithm
"""
decrease = False # energy reduction
# kb = 1.3806488*10**-23 / 1.6 * 10 **19
dE = E2 - E1
printlog("metropolis(): dE is ", dE)
if dE < -0.000001:
printlog("dE is ", dE, "Accept!")
decrease = True
elif 1 > math.exp(-dE / kb / T) > random():
printlog("Accepted due to the temperature; exponent is ",
math.exp(-dE / kb / T))
decrease = True
else:
printlog('Not accepted')
return decrease