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setup.py
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setup.py
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import yaml
from os import listdir,path,system,sys
from run_single_point import opt_type,str_parse,get_ats_from_xyz
base_dir = path.dirname(path.realpath(__file__)) + '/'
"""
setup.py usage:
python3 setup.py dfa=str clean=t/f at_dfa=str dfa_dir=str
dfa should either be a keyword in dict libxc_key (see below), or a
LibXC format string, like GGA_X_PW91,MGGA_C_RSCAN
This is the density functional approximation you want to use
Defaults to None if not specified
clean = boolean, only first character matters (t=True, f=False)
Defaults to True
xclib = LibXC or XCFun, sets library used to get XC DFA
Defaults to LibXC
at_dfa should be a directory name where wavefunction files are written to
Used to do dfa@at_dfta calculations
dfa_dir should be the name of the DFA directory if you don't want to use dfa as its name
Defaults to be same as dfa
examples : python3 setup.py dfa=LSDA clean=t
python3 setup.py dfa=GGA_X_PW91,GGA_C_PW91 xclib=LibXC
python3 setup.py dfa=PW91X,PW91C xclib=XCFun
"""
xcfun_key = {
'LSDA': '1.0*SLATERX, 1.0*PW92C', 'PBE': '1.0*PBEX, 1.0*PBEC',
'r2SCAN': '1.0*R2SCANX, 1.0*R2SCANC', 'SCAN': '1.0*SCANX, 1.0*SCANC',
'BLYP': '1.0*BECKEX, 1.0*LYPC'
}
libxc_key = {
'LSDA': 'LDA_X, LDA_C_PW', 'PBE': 'GGA_X_PBE, GGA_C_PBE',
'r2SCAN': 'MGGA_X_R2SCAN, MGGA_C_R2SCAN',
'SCAN': 'MGGA_X_SCAN, MGGA_C_SCAN',
'BLYP': 'GGA_X_B88, GGA_C_LYP',
'B3LYP': 'HYB_GGA_XC_B3LYP',
'LCwPBE': 'HYB_GGA_XC_LC_WPBE',
'M06-L': 'MGGA_X_M06_L, MGGA_C_M06_L',
'MN15-L': 'MGGA_X_MN15_L, MGGA_C_MN15_L',
}
# add eigenvalue level shifts here if you need them to stabilize convergence
lshiftd = { }
z_d = dict( H = 1, He = 2,
Li = 3, Be = 4, B = 5, C = 6, N = 7, O = 8, F = 9, Ne = 10,
Na = 11, Mg = 12, Al = 13, Si = 14, P = 15, S = 16, Cl = 17, Ar = 18,
K = 19, Ca = 20, Sc = 21, Ti = 22, V = 23, Cr = 24, Mn = 25, Fe = 26, Co = 27,
Ni = 28, Cu = 29, Zn = 30, Ga = 31, Ge = 32, As = 33, Se = 34, Br = 25, Kr = 36,
Rb = 37, Sr = 38, Y = 39, Zr = 40, Nb = 41, Mo = 42, Tc = 43, Ru = 44, Rh = 45,
Pd = 46, Ag = 47, Cd = 48, In = 49, Sn = 50, Sb = 51, Te = 52, I = 53, Xe = 54,
Pb = 82, Bi = 83 # I can't add all of them...
)
def setup(dfa,startclean=True,xclib='LibXC',wfdir = '',dfa_dir=None,inp_opts={}):
cmdict = yaml.load(open(base_dir+'BH76_chg_2s.yaml','r'), Loader=yaml.Loader)
if dfa_dir is not None:
wdir = base_dir + '{:}_BH76/'.format(dfa_dir)
else:
wdir = base_dir + '{:}_BH76/'.format(dfa)
if startclean and path.isdir(wdir):
system('rm -rf '+ wdir)
# specific options used universally
univ_opts = {
'gridsize': 9, 'symm': False, 'tol': 1.e-7, 'max_cycle': 500,
'verbose': 4, 'basis': 'aug-cc-pvqz'
}
for akey in inp_opts:
univ_opts[akey] = inp_opts[akey]
srcdir = base_dir + 'BH76_geometries/'
system('cp -r {:} {:}'.format(srcdir,wdir))
system('cp runjob.sh '+ wdir)
if dfa == 'HF':
system('mkdir {:}HF_WVFN'.format(wdir))
nscf_dft = False
if '@' in dfa:
nscf_dft = True
dfa,at_dfa = dfa.split('@')
univ_opts['max_cycle'] = 0
if path.isdir(wfdir) and len(listdir(wfdir)) > 0:
for asys in cmdict:
if asys == 'h' and at_dfa == 'HF':
# we use reduced density matrix for h, PySCF won't store the
# HF wavefunction file here. Dunno why
continue
cstr = 'cp {:}{:}/{:}_wvfn {:}{:}/wvfn'.format(base_dir,wfdir,\
asys,wdir,asys)
system(cstr)
else:
err_str = "I can't do {:}@{:} without {:} orbitals!".format(dfa,at_dfa,at_dfa)
raise SystemExit(err_str)
for asys in listdir(srcdir):
if asys[0] == '.':
continue
cdir = wdir + '/' + asys + '/'
#if dfa == 'HF':
# system('cp run_single_point_hf.py '+ cdir + 'run_single_point.py')
# univ_opts.pop('gridsize',None)
#else:
# system('cp run_single_point.py '+ cdir)
optstr = ''
for akey in univ_opts:
optstr += '{:} = {:}\n'.format(akey,univ_opts[akey])
optstr += 'charge = {:}\n'.format(cmdict[asys]['Charge'])
optstr += '2S = {:}\n'.format(cmdict[asys]['2S'])
if cmdict[asys]['R']:
optstr += 'restricted = True\n'
else:
optstr += 'restricted = False\n'
if dfa == 'HF':
optstr += 'xc = HF\n'
else:
xcstr = dfa
if xclib == 'XCFun':
if dfa in xcfun_key:
xcstr = xcfun_key[dfa]
elif xclib == 'LibXC':
if dfa in libxc_key:
xcstr = libxc_key[dfa]
else:
raise SystemExit('Unknown XC library '+xclib)
optstr += 'xc = {:}\n'.format(xcstr)
optstr += 'xc_lib = {:}\n'.format(xclib)
if asys in lshiftd:
optstr += 'levelshift = {:}\n'.format(lshiftd[asys])
optstr += 'xyz_fl = ./struc.xyz\n'# + cdir + 'struc.xyz\n'
strucfl = srcdir + '{:}/struc.xyz'.format(asys)
chem_comp = get_ats_from_xyz(strucfl)
#nats = len(chem_comp.keys())
"""
you can modify the basis you want to use here
if, for example, you want to use different bases for different atoms,
use the format
basis = atom 1 : basis 1 ; atom 2 : basis 2 ; ...
Example: H2O. To use STO-3G with H and cc-pVDZ with O, write
basis = H : STO-3G ; O : cc-pVDZ
spaces are ignored, use enough to be readable
"""
#basstr = 'aug-cc-pvqz'#'def2-QZVP'
#optstr += 'basis = {:}\n'.format(basis)
"""
For heavy atoms, an electronic core potential (ECP)/pseudopotential is
used by default when the atomic Z > 36 (Kr).
These aren't used in BH76 at all, but included here as an example
"""
ecpstr = ''
iat = 0
mz = -1
for anat in chem_comp:
if iat == 0:
cchar = ''
else:
cchar = '; '
if z_d[anat] > z_d['Kr']:
ecpstr += '{:}{:}: def2-qzvp'.format(cchar,anat)
iat += 1
if len(ecpstr) > 0:
optstr += 'ecp = {:}\n'.format(ecpstr)
optstr += 'logfile = ' + asys + '.txt\n'
if dfa == 'HF':
optstr += 'write_chkfl = True\n'
optstr += 'chkfl = ../HF_WVFN/{:}_wvfn\n'.format(asys)
if nscf_dft:
if asys == 'h' and at_dfa == 'HF':
optstr += 'init = HF DM\n'
else:
optstr += 'init = chkfl\n'
optstr += 'chkfl = ./wvfn'
inpfl = cdir + 'inp.txt'
with open(inpfl,'w+') as tfile:
tfile.write(optstr)
return
def parse_into_setup():
dfa = None
makeclean = True
xclib = 'LibXC'
wfdir = ''
dfa_dir = None
ioptd = {}
ioptl = []
for akey in opt_type:
for bkey in opt_type[akey]:
ioptl.append(bkey)
if len(sys.argv) < 2:
raise SystemExit('Need to specify density functional!')
else:
for astr in sys.argv[1:]:
key,val = astr.split('=')
lkey = key.lower()
if lkey == 'dfa':
dfa = val
elif lkey == 'clean':
if val.lower()[0] == 't':
makeclean = True
elif val.lower()[0] == 'f':
makeclean = False
else:
print('Keyword "clean" must be t/f!')
elif lkey == 'xclib':
xclib = val
elif lkey == 'at_dfa':
wfdir = val
elif lkey == 'dfa_dir':
dfa_dir = val
elif key in ioptl:
ioptd[key] = val
else:
print('Skipping unknown keyword {:}'.format(key))
setup(dfa,startclean=makeclean,xclib=xclib,wfdir=wfdir,dfa_dir=dfa_dir,\
inp_opts=ioptd)
return
if __name__ == "__main__":
#setup('LSDA@HF',startclean=True)
parse_into_setup()