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 read_dir_autogen(froot,gosling='./gosling',read_cubes=False):
""" Reads a CRYSTAL + QWalk directory's data into a dictionary, formats it
like how autogen would do. NOTE: this is *not* intended to read an
autogen-generated directory! This is for the purpose of joining an
autogen-generated database with another set of DMC data.
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 = list(map(str,np.array([1,3,8,10,27,29,34,36]) - 1))
realk2 = list(map(str,np.array([1,4,17,20,93,96,109,112]) - 1))
oldrealk = ['k0','k1','k2','k3','k4','k5','k6','k7']
############################################################################
res = {}
res['dft'] = {}
res['qmc'] = {}
res['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:
res['ordering'] = metad['magnetic ordering']
except KeyError: pass
try:
if metad['pressure'] != None:
res['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'))
res['a'] = dftdat['latparms'][-1]
res['c'] = dftdat['latparms'][1]
res['se_height'] = dftdat['apos'][dftdat['atypes'].index(234)][-1]
res['supercell'] = dftdat['supercell']
res['total_spin'] = dftdat['spinlock']
#res['initial_spin'] = dftdat['atomspin']
res['charge'] = 0
res['cif'] = "None"
res['control'] = {'id':froot}
for key in ['mixing','broyden','fmixing','tolinteg',
'kdens','tole','basis','initial_spin']:
res['dft'][key] = dftdat[key]
dftdat = cio.read_cryout(open(dftoutf,'r'))
res['dft']['energy'] = dftdat['dft_energy']
res['dft']['mag_moments'] = dftdat['dft_moments']
except IOError:
print("There's no dft in this directory!")
return res
# 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.")
dmc_ret = []
ppr_ret = []
for rk in realk:
entry = {}
entry['knum'] = int(rk.replace("k",""))
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'))
entry['kpoint'] = sysdat['system']['kpoint']
entry['timestep'] = dmcinp['method']['timestep']
entry['localization'] = "None"
entry['jastrow'] = "twobody"
entry['optimizer'] = "variance"
entry['excitations'] = "no"
except IOError:
print(" (cannot find QMC input, skipping)")
continue
print(" DMC results..." )
try:
os.system("{0} -json {1}.dmc.log > {1}.json".format(gosling,kroot))
dmc_entry = deepcopy(entry)
dmc_entry['results'] = json.load(open("{}.json".format(kroot)))
dmc_ret.append(dmc_entry)
except ValueError:
print(" (cannot find ground state energy log file)")
# I'm going to skip the optical gap information for now. Is this really
# taken care of in autogen yet?
#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)")
# I'm going to skip this for now since this is too large for the database
# generally.
#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(" Postprocessing results..." )
try:
inpf = open(kroot+'.ppr.o','r')
# TODO
# Apparently this directory is now missing, so you should fix this if
# needed.
#fludat = rn.read_number_dens_likejson(inpf)
if fludat is None:
print(" (Error in number fluctuation output, skipping)")
else:
ppr_entry = deepcopy(entry)
ppr_entry['results'] = {
'properties':{
'region_fluctuation':{
'fluctuation data': fludat}
}
}
ppr_ret.append(ppr_entry)
except IOError:
print(" (cannot find number fluctuation)")
# Going to skip for now, since it's not working for my format_autogen yet.
#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 len(dmc_ret) > 0:
res['qmc']['dmc'] = {}
res['qmc']['dmc']['results'] = dmc_ret
res['qmc']['dmc']['kpoint'] = sysdat['system']['kpoint']
res['qmc']['dmc']['timestep'] = dmcinp['method']['timestep']
res['qmc']['dmc']['localization'] = "None"
res['qmc']['dmc']['jastrow'] = "twobody"
res['qmc']['dmc']['optimizer'] = "variance"
res['qmc']['dmc']['nblock'] = -1
res['qmc']['dmc']['excitations'] = "no"
if len(ppr_ret) > 0:
res['qmc']['postprocess'] = {}
res['qmc']['postprocess']['results'] = ppr_ret
res['qmc']['postprocess']['kpoint'] = sysdat['system']['kpoint']
res['qmc']['postprocess']['timestep'] = dmcinp['method']['timestep']
res['qmc']['postprocess']['localization'] = "None"
res['qmc']['postprocess']['jastrow'] = "twobody"
res['qmc']['postprocess']['optimizer'] = "variance"
res['qmc']['postprocess']['excitations'] = "no"
res['qmc']['postprocess']['nblock'] = -1
return res
def read_dir_autogen(froot,gosling='./gosling',read_cubes=False):
""" Reads a CRYSTAL + QWalk directory's data into a dictionary, formats it
like how autogen would do. NOTE: this is *not* intended to read an
autogen-generated directory! This is for the purpose of joining an
autogen-generated database with another set of DMC data.
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 = list(map(str,np.array([1,3,8,10,27,29,34,36]) - 1))
realk2 = list(map(str,np.array([1,4,17,20,93,96,109,112]) - 1))
oldrealk = ['k0','k1','k2','k3','k4','k5','k6','k7']
############################################################################
res = {}
res['dft'] = {}
res['qmc'] = {}
res['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:
res['ordering'] = metad['magnetic ordering']
except KeyError: pass
try:
if metad['pressure'] != None:
res['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'))
res['a'] = dftdat['latparms'][-1]
res['c'] = dftdat['latparms'][1]
res['se_height'] = dftdat['apos'][dftdat['atypes'].index(234)][-1]
res['supercell'] = dftdat['supercell']
res['total_spin'] = dftdat['spinlock']
#res['initial_spin'] = dftdat['atomspin']
res['charge'] = 0
res['cif'] = "None"
res['control'] = {'id':froot}
for key in ['mixing','broyden','fmixing','tolinteg',
'kdens','tole','basis','initial_spin']:
res['dft'][key] = dftdat[key]
dftdat = cio.read_cryout(open(dftoutf,'r'))
res['dft']['energy'] = dftdat['dft_energy']
res['dft']['mag_moments'] = dftdat['dft_moments']
except IOError:
print("There's no dft in this directory!")
return res
# 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.")
dmc_ret = []
ppr_ret = []
for rk in realk:
entry = {}
entry['knum'] = int(rk.replace("k",""))
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'))
entry['kpoint'] = sysdat['system']['kpoint']
entry['timestep'] = dmcinp['method']['timestep']
entry['localization'] = "None"
entry['jastrow'] = "twobody"
entry['optimizer'] = "variance"
entry['excitations'] = "no"
except IOError:
print(" (cannot find QMC input, skipping)")
continue
print(" DMC results..." )
try:
os.system("{0} -json {1}.dmc.log > {1}.json".format(gosling,kroot))
dmc_entry = deepcopy(entry)
dmc_entry['results'] = json.load(open("{}.json".format(kroot)))
dmc_ret.append(dmc_entry)
except ValueError:
print(" (cannot find ground state energy log file)")
# I'm going to skip the optical gap information for now. Is this really
# taken care of in autogen yet?
#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)")
# I'm going to skip this for now since this is too large for the database
# generally.
#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(" Postprocessing results..." )
try:
inpf = open(kroot+'.ppr.o','r')
fludat = rn.read_number_dens_likejson(inpf)
if fludat is None:
print(" (Error in number fluctuation output, skipping)")
else:
ppr_entry = deepcopy(entry)
ppr_entry['results'] = {
'properties':{
'region_fluctuation':{
'fluctuation data': fludat}
}
}
ppr_ret.append(ppr_entry)
except IOError:
print(" (cannot find number fluctuation)")
# Going to skip for now, since it's not working for my format_autogen yet.
#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 len(dmc_ret) > 0:
res['qmc']['dmc'] = {}
res['qmc']['dmc']['results'] = dmc_ret
res['qmc']['dmc']['kpoint'] = sysdat['system']['kpoint']
res['qmc']['dmc']['timestep'] = dmcinp['method']['timestep']
res['qmc']['dmc']['localization'] = "None"
res['qmc']['dmc']['jastrow'] = "twobody"
res['qmc']['dmc']['optimizer'] = "variance"
res['qmc']['dmc']['nblock'] = -1
res['qmc']['dmc']['excitations'] = "no"
if len(ppr_ret) > 0:
res['qmc']['postprocess'] = {}
res['qmc']['postprocess']['results'] = ppr_ret
res['qmc']['postprocess']['kpoint'] = sysdat['system']['kpoint']
res['qmc']['postprocess']['timestep'] = dmcinp['method']['timestep']
res['qmc']['postprocess']['localization'] = "None"
res['qmc']['postprocess']['jastrow'] = "twobody"
res['qmc']['postprocess']['optimizer'] = "variance"
res['qmc']['postprocess']['excitations'] = "no"
res['qmc']['postprocess']['nblock'] = -1
return res
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
