import cubetools as ct
import sys
samp = ct.read_cube(open(sys.argv[1],'r'))
ct.freq_cutoff(samp,freq_cutoff=0.6)
ct.gaussian_averager(samp,sigma=6,nbr_dist=10,repeat=1)
ct.write_cube(samp,open("smoothed/"+sys.argv[1],"w"))
import cubetools
import copy
s1=cubetools.read_cube("qwalk_000.spin.dens.cube")
s2=cubetools.read_cube("../../../../undoped/PBE0/CHK/plots/qwalk_000.spin.dens.cube")
c1=cubetools.read_cube("qwalk_000.chg.dens.cube")
c2=cubetools.read_cube("../../../../undoped/PBE0/CHK/plots/qwalk_000.chg.dens.cube")
s1['data']-=s2['data'] #make 'up' the spin density
cubetools.write_cube(s1,"qwalk_000.spin_diff.dens.cube")
c1['data']-=c2['data'] #make 'up' the charge density
cubetools.write_cube(c1,"qwalk_000.chg_diff.dens.cube")
nup=66
ndown=66
'''
up=cubetools.read_cube("qwalk_000.plot_u.dens.cube")
down=cubetools.read_cube("qwalk_000.plot_d.dens.cube")
up=cubetools.normalize_abs(up)
down=cubetools.normalize_abs(down)
up['data']*=nup
down['data']*=ndown
up['data']-=down['data'] #make 'up' the spin density
cubetools.write_cube(up,"qwalk_000.spin.dens.cube")
up['data']+=2*down['data'] #make 'up' the charge density
cubetools.write_cube(up,"qwalk_000.chg.dens.cube")
'''
up=cubetools.read_cube("qwalk_000.plot_u.dens.cube")
down=cubetools.read_cube("qwalk_000.plot_d.dens.cube")
up_ct=cubetools.read_cube("qwalk_000.plot_u_ct.dens.cube")
down_ct=cubetools.read_cube("qwalk_000.plot_d_ct.dens.cube")
up=cubetools.normalize_abs(up)
down=cubetools.normalize_abs(down)
up_ct=cubetools.normalize_abs(up_ct)
down_ct=cubetools.normalize_abs(down_ct)
up['data']*=nup
down['data']*=ndown
up_ct['data']*=nup
down_ct['data']*=ndown
#Individual CT determinants
c_u_ct=copy.deepcopy(up_ct)
s_u_ct=copy.deepcopy(up_ct)
import cubetools
nup = 67
ndown = 66
import copy
#up=cubetools.read_cube("qwalk_000.plot_u.dens.cube")
#down=cubetools.read_cube("qwalk_000.plot_d.dens.cube")
#down=cubetools.read_cube("qwalk_000.plot_d_ex.dens.cube")
up = cubetools.read_cube("qwalk_110.plot_u.dens.cube")
down = cubetools.read_cube("qwalk_110.plot_d.dens.cube")
#down=cubetools.read_cube("qwalk_100.plot_d_ex.dens.cube")
up = cubetools.normalize_abs(up)
down = cubetools.normalize_abs(down)
up['data'] *= nup
down['data'] *= ndown
up['data'] -= down['data'] #make 'up' the spin density
cubetools.write_cube(up, "qwalk_110.spin.dens.cube")
up['data'] += 2 * down['data'] #make 'up' the charge density
cubetools.write_cube(up, "qwalk_110.chg.dens.cube")
def read_dir(froot,gosling='./gosling',read_cubes=False):
""" Reads a CRYSTAL + QWalk directory's data into a dictionary.
Current dictionary keys:
fmixing, kdens, excited_energy_err, ordering, total_energy_err,
excited_energy, ts, tole, total_energy, se_height, tolinteg,
supercell, mixing, kpoint, spinlock, dft_energy, a, c, broyden,
dft_moments, 1rdm, access_root, average, covariance
"""
############################################################################
# This first section should be edited to reflect naming conventions!
dftfile = froot+'.d12'
dftoutf = froot+'.d12.out'
# Start by taking only the real k-points, since I'm sure these are on solid
# ground, and have enough sample points. TODO generalize
realk1 = np.array([1,3,8,10,27,29,34,36]) - 1
realk2 = np.array([1,4,17,20,93,96,109,112]) - 1
oldrealk = np.array(['k0','k1','k2','k3','k4','k5','k6','k7'])
############################################################################
bres = {} # Data that is common to all k-points.
ress = {} # Dict of all k-point data in directory.
bres['access_root'] = os.getcwd() + '/' + froot
print("Working on",froot+"..." )
try:
with open(froot+'_metadata.json','r') as metaf:
metad = json.load(metaf)
try:
if metad['magnetic ordering'] != None:
bres['ordering'] = metad['magnetic ordering']
except KeyError: pass
try:
if metad['pressure'] != None:
bres['pressure'] = metad['pressure']
except KeyError: pass
try:
if metad['pressure'] != None:
bres['pressure'] = metad['pressure']
except KeyError: pass
except IOError:
print(" Didn't find any metadata")
print(" DFT params and results..." )
try:
dftdat = cio.read_cryinp(open(dftfile,'r'))
bres['a'] = dftdat['latparms'][0]
bres['c'] = dftdat['latparms'][1]
bres['se_height'] = dftdat['apos'][dftdat['atypes'].index(234)][-1]
for key in ['mixing','broyden','fmixing','tolinteg',
'kdens','spinlock','supercell','tole','basis']:
bres[key] = dftdat[key]
dftdat = cio.read_cryout(open(dftoutf,'r'))
bres['dft_energy'] = dftdat['dft_energy']
bres['dft_moments'] = dftdat['dft_moments']
except IOError:
print("There's no dft in this directory!")
return {}
# Determine k-point set and naming convention.
if os.path.isfile(froot+'_'+str(oldrealk[0])+'.sys'):
realk=oldrealk
print("Using old-style kpoint notation.")
elif os.path.isfile(froot+'_'+str(realk2[-1])+'.sys'):
realk=realk2
print("Using 6x6x6 kpoint notation.")
else:
realk=realk1
print("Using 4x4x4 kpoint notation.")
for rk in realk:
kroot = froot + '_' + str(rk)
print(" now DMC:",kroot+"..." )
try:
sysdat = qio.read_qfile(open(kroot+'.sys','r'))
dmcinp = qio.read_qfile(open(kroot+'.dmc','r'))
ress[rk] = bres.copy()
ress[rk]['kpoint'] = sysdat['system']['kpoint']
ress[rk]['ts'] = dmcinp['method']['timestep']
except IOError:
print(" (cannot find QMC input, skipping)")
continue
print(" energies..." )
try:
inpf = open(kroot+'.dmc.log','r')
egydat = qio.read_qenergy(inpf,gosling)
ress[rk]['dmc_energy'] = egydat['egy']
ress[rk]['dmc_energy_err'] = egydat['err']
except IOError:
print(" (cannot find ground state energy log file)")
try:
inpf = open(kroot+'.ogp.log','r')
ogpdat = qio.read_qenergy(inpf,gosling)
ress[rk]['dmc_excited_energy'] = ogpdat['egy']
ress[rk]['dmc_excited_energy_err'] = ogpdat['err']
except IOError:
print(" (cannot find excited state energy log file)")
if read_cubes:
print(" densities..." )
try:
inpf = open(kroot+'.dmc.up.cube','r')
upcube = ct.read_cube(inpf)
inpf = open(kroot+'.dmc.dn.cube','r')
dncube = ct.read_cube(inpf)
ress[rk]['updens'] = upcube
ress[rk]['dndens'] = dncube
except IOError:
print(" (cannot find electron density)")
except ValueError:
print(" (electron density is corrupted)")
print(" fluctuations..." )
try:
inpf = open(kroot+'.ppr.o','r')
fludat, fluerr = qio.read_number_dens(inpf)
if fludat is None:
print(" (Error in number fluctuation output, skipping)")
else:
avg, var, cov, avge, vare, cove = qio.moments(fludat,fluerr)
ress[rk]['average'] = avg
ress[rk]['covariance'] = cov
except IOError:
print(" (cannot find number fluctuation)")
print(" 1-RDM..." )
try:
inpf = open(kroot+'.ordm.o')
odmdat = qio.read_dm(inpf)
if odmdat is None:
print(" (Error in 1-RDM output, skipping)")
else:
ress[rk]['1rdm'] = odmdat
except IOError:
print(" (cannot find 1-RDM)")
print(" done." )
if ress == {}:
ress['dft-only'] = bres
return ress
def reader(fi): return ct.read_cube(open(fi,'r'),qwalk_patch=True) with mp.Pool(8) as pool:
import cubetools
f1 = cubetools.read_cube('test_mom.plot.orb7.cube')
f2 = cubetools.read_cube('test_mom.plot.orb10.cube')
f1 = cubetools.normalize_abs(f1)
f2 = cubetools.normalize_abs(f2)
f1['data'] -= f2['data']
cubetools.write_cube(f1, 'test_mom.plot.orbDiff.cube')
f1['data'] += 2 * f2['data']
cubetools.write_cube(f1, 'test_mom.plot.orbSum.cube')
def reader(fi):
return ct.read_cube(open(fi, 'r'), qwalk_patch=True)
import cubetools
nup = 14
ndown = 11
import copy
up = cubetools.read_cube("Cuvtz_r1.963925_c0_s3_B3LYP.plot_u.dens.cube")
down = cubetools.read_cube("Cuvtz_r1.963925_c0_s3_B3LYP.plot_d.dens.cube")
up = cubetools.normalize_abs(up)
down = cubetools.normalize_abs(down)
up['data'] *= nup
down['data'] *= ndown
up['data'] -= down['data'] #make 'up' the spin density
cubetools.write_cube(up, "spin3.dens.cube")
up['data'] += 2 * down['data'] #make 'up' the charge density
cubetools.write_cube(up, "chg3.dens.cube")
import cubetools
import copy
'''
s1=cubetools.read_cube("qwalk_000.spin.dens.cube")
s2=cubetools.read_cube("../../../../undoped/pbe0/col/plots/qwalk_000.spin.dens.cube")
c1=cubetools.read_cube("qwalk_000.chg.dens.cube")
c2=cubetools.read_cube("../../../../undoped/pbe0/col/plots/qwalk_000.chg.dens.cube")
s1['data']-=s2['data'] #make 'up' the spin density
cubetools.write_cube(s1,"qwalk_000.spin_diff.dens.cube")
c1['data']-=c2['data'] #make 'up' the charge density
cubetools.write_cube(c1,"qwalk_000.chg_diff.dens.cube")
'''
s1=cubetools.read_cube("qwalk_000.spin.dens.cube")
s2=cubetools.read_cube("../../CHK_ns/plots/qwalk_000.spin.dens.cube")
c1=cubetools.read_cube("qwalk_000.chg.dens.cube")
c2=cubetools.read_cube("../../CHK_ns/plots/qwalk_000.chg.dens.cube")
s1['data']-=s2['data'] #make 'up' the spin density
cubetools.write_cube(s1,"qwalk_000.spin_diff2.dens.cube")
c1['data']-=c2['data'] #make 'up' the charge density
cubetools.write_cube(c1,"qwalk_000.chg_diff2.dens.cube")
def read_dir(froot,gosling='./gosling',read_cubes=False):
""" Reads a CRYSTAL + QWalk directory's data into a dictionary.
Current dictionary keys:
fmixing, kdens, excited_energy_err, ordering, total_energy_err,
excited_energy, ts, tole, total_energy, se_height, tolinteg,
supercell, mixing, kpoint, spinlock, dft_energy, a, c, broyden,
dft_moments, 1rdm, access_root, average, covariance
"""
############################################################################
# This first section should be edited to reflect naming conventions!
dftfile = froot+'.d12'
dftoutf = froot+'.d12.out'
# Start by taking only the real k-points, since I'm sure these are on solid
# ground, and have enough sample points. TODO generalize
realk1 = np.array([1,3,8,10,27,29,34,36]) - 1
realk2 = np.array([1,4,17,20,93,96,109,112]) - 1
oldrealk = np.array(['k0','k1','k2','k3','k4','k5','k6','k7'])
############################################################################
bres = {} # Data that is common to all k-points.
ress = {} # Dict of all k-point data in directory.
bres['access_root'] = os.getcwd() + '/' + froot
print("Working on",froot+"..." )
try:
with open(froot+'_metadata.json','r') as metaf:
metad = json.load(metaf)
try:
if metad['magnetic ordering'] != None:
bres['ordering'] = metad['magnetic ordering']
except KeyError: pass
try:
if metad['pressure'] != None:
bres['pressure'] = metad['pressure']
except KeyError: pass
try:
if metad['pressure'] != None:
bres['pressure'] = metad['pressure']
except KeyError: pass
except IOError:
print(" Didn't find any metadata")
print(" DFT params and results..." )
try:
dftdat = cio.read_cryinp(open(dftfile,'r'))
bres['a'] = dftdat['latparms'][0]
bres['c'] = dftdat['latparms'][1]
bres['se_height'] = dftdat['apos'][dftdat['atypes'].index(234)][-1]
for key in ['mixing','broyden','fmixing','tolinteg',
'kdens','spinlock','supercell','tole','basis']:
bres[key] = dftdat[key]
dftdat = cio.read_cryout(open(dftoutf,'r'))
bres['dft_energy'] = dftdat['dft_energy']
bres['dft_moments'] = dftdat['dft_moments']
except IOError:
print("There's no dft in this directory!")
return {}
# Determine k-point set and naming convention.
if os.path.isfile(froot+'_'+str(oldrealk[0])+'.sys'):
realk=oldrealk
print("Using old-style kpoint notation.")
elif os.path.isfile(froot+'_'+str(realk2[-1])+'.sys'):
realk=realk2
print("Using 6x6x6 kpoint notation.")
else:
realk=realk1
print("Using 4x4x4 kpoint notation.")
for rk in realk:
kroot = froot + '_' + str(rk)
print(" now DMC:",kroot+"..." )
try:
sysdat = qio.read_qfile(open(kroot+'.sys','r'))
dmcinp = qio.read_qfile(open(kroot+'.dmc','r'))
ress[rk] = bres.copy()
ress[rk]['kpoint'] = sysdat['system']['kpoint']
ress[rk]['ts'] = dmcinp['method']['timestep']
except IOError:
print(" (cannot find QMC input, skipping)")
continue
print(" energies..." )
try:
inpf = open(kroot+'.dmc.log','r')
egydat = qio.read_qenergy(inpf,gosling)
ress[rk]['dmc_energy'] = egydat['egy']
ress[rk]['dmc_energy_err'] = egydat['err']
except IOError:
print(" (cannot find ground state energy log file)")
try:
inpf = open(kroot+'.ogp.log','r')
ogpdat = qio.read_qenergy(inpf,gosling)
ress[rk]['dmc_excited_energy'] = ogpdat['egy']
ress[rk]['dmc_excited_energy_err'] = ogpdat['err']
except IOError:
print(" (cannot find excited state energy log file)")
if read_cubes:
print(" densities..." )
try:
inpf = open(kroot+'.dmc.up.cube','r')
upcube = ct.read_cube(inpf)
inpf = open(kroot+'.dmc.dn.cube','r')
dncube = ct.read_cube(inpf)
ress[rk]['updens'] = upcube
ress[rk]['dndens'] = dncube
except IOError:
print(" (cannot find electron density)")
except ValueError:
print(" (electron density is corrupted)")
print(" fluctuations..." )
try:
inpf = open(kroot+'.ppr.o','r')
fludat, fluerr = qio.read_number_dens(inpf)
if fludat is None:
print(" (Error in number fluctuation output, skipping)")
else:
avg, var, cov, avge, vare, cove = qio.moments(fludat,fluerr)
ress[rk]['average'] = avg
ress[rk]['covariance'] = cov
except IOError:
print(" (cannot find number fluctuation)")
print(" 1-RDM..." )
try:
inpf = open(kroot+'.ordm.o')
odmdat = qio.read_dm(inpf)
if odmdat is None:
print(" (Error in 1-RDM output, skipping)")
else:
ress[rk]['1rdm'] = odmdat
except IOError:
print(" (cannot find 1-RDM)")
print(" done." )
if ress == {}:
ress['dft-only'] = bres
return ress
