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nexus: remove generate_only test override and modernize/clean examples

This commit is contained in:
Jaron Krogel 2018-06-06 10:53:31 -04:00
parent cd7ba065bb
commit 01b95d5595
10 changed files with 134 additions and 166 deletions
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45
nexus/examples/qmcpack/H2O/H2O.py
View File

@ -1,8 +1,9 @@
#! /usr/bin/env python
# H2O molecule with Quantum ESPRESSO orbitals
from nexus import settings,Job,run_project
from nexus import Structure,PhysicalSystem
from nexus import settings,job,run_project
from nexus import read_structure
from nexus import generate_physical_system
from nexus import generate_pwscf
from nexus import generate_pw2qmcpack
from nexus import generate_qmcpack,vmc,loop,linear,dmc
@ -11,12 +12,9 @@ from nexus import generate_qmcpack,vmc,loop,linear,dmc
settings(
pseudo_dir = '../pseudopotentials',
runs = 'runs',
results = 'results',
results = '',
sleep = 3,
#generate_only = False,
# Complicated setting only so examples can be run in test harness.
# For real runs, use the plain setting of 'generate_only' above.
generate_only = globals().get('override_generate_only_setting',False),
generate_only = 0,
status_only = 0,
machine = 'ws1',
)
@ -30,24 +28,23 @@ qmcpack = 'qmcpack'
dft_pps = ['O.BFD.upf','H.BFD.upf']
qmc_pps = ['O.BFD.xml','H.BFD.xml']
# Job Definitions (MPI Tasks, MP Threading, PBS Queue, Time, etc.)
scf_job = Job(app=pwscf,serial=True)
p2q_job = Job(app=pw2qmcpack,serial=True)
opt_job = Job(threads=4,app=qmcpack,serial=True)
dmc_job = Job(threads=4,app=qmcpack,serial=True)
# job Definitions (MPI Tasks, MP Threading, PBS Queue, Time, etc.)
scf_job = job(app=pwscf,serial=True)
p2q_job = job(app=pw2qmcpack,serial=True)
opt_job = job(threads=4,app=qmcpack,serial=True)
dmc_job = job(threads=4,app=qmcpack,serial=True)
# System To Be Simulated
structure = Structure()
structure.read_xyz('H2O.xyz')
structure = read_structure('H2O.xyz')
structure.bounding_box(
box = 'cubic',
scale = 1.5
)
structure.add_kmesh(
kgrid = (1,1,1),
kshift = (0,0,0)
)
H2O_molecule = PhysicalSystem(
kshift = (0,0,0),
)
H2O_molecule = generate_physical_system(
structure = structure,
net_charge = 0,
net_spin = 0,
@ -70,7 +67,7 @@ scf = generate_pwscf(
conv_thr = 1.0e-5,
mixing_beta = 0.7,
mixing_mode = 'local-TF',
degauss = 0.001
degauss = 0.001,
)
sims.append(scf)
@ -80,7 +77,7 @@ p2q = generate_pw2qmcpack(
path = '.',
job = p2q_job,
write_psir = False,
dependencies = (scf,'orbitals')
dependencies = (scf,'orbitals'),
)
sims.append(p2q)
@ -107,7 +104,7 @@ linopt1 = linear(
alloweddifference = 1e-4,
stepsize = 0.2,
stabilizerscale = 1.0,
nstabilizers = 3
nstabilizers = 3,
)
# QMC Optimization Parameters - Finer Sampling Set
@ -128,7 +125,7 @@ opt = generate_qmcpack(
('J2','bspline',8,4)],
calculations = [loop(max=4,qmc=linopt1),
loop(max=4,qmc=linopt2)],
dependencies = (p2q,'orbitals')
dependencies = (p2q,'orbitals'),
)
sims.append(opt)
@ -151,7 +148,7 @@ qmc = generate_qmcpack(
warmupsteps = 100,
blocks = 1,
timestep = 1.0,
usedrift = False
usedrift = False,
),
dmc(
minimumtargetwalkers = 128,
@ -160,10 +157,10 @@ qmc = generate_qmcpack(
timestep = 0.005,
steps = 10,
blocks = 200,
nonlocalmoves = True
nonlocalmoves = True,
)
],
dependencies = [(p2q,'orbitals'),(opt,'jastrow')]
dependencies = [(p2q,'orbitals'),(opt,'jastrow')],
)
sims.append(qmc)

84
nexus/examples/qmcpack/LiH/LiH.py
View File

@ -1,7 +1,7 @@
#! /usr/bin/env python
# LiH crystal with Quantum ESPRESSO orbitals
from nexus import settings,Job,run_project
from nexus import settings,job,run_project
from nexus import generate_physical_system
from nexus import generate_pwscf
from nexus import generate_pw2qmcpack
@ -13,11 +13,7 @@ settings(
runs = 'runs',
results = 'results',
sleep = 3,
#generate_only = False,
# Complicated setting only so examples can be run in test harness.
# For real runs, use the plain setting of 'generate_only' above.
generate_only = globals().get('override_generate_only_setting',False),
generate_only = 0,
status_only = 0,
machine = 'ws1',
)
@ -31,12 +27,12 @@ qmcpack = 'qmcpack'
dft_pps = ['Li.TN-DF.upf','H.TN-DF.upf']
qmc_pps = ['Li.pp.data','H.pp.data']
# Job Definitions (MPI Tasks, MP Threading, PBS Queue, Time, etc.)
scf_job = Job(app=pwscf,serial=True)
nscf_job = Job(app=pwscf,serial=True)
p2q_job = Job(app=pw2qmcpack,serial=True)
opt_job = Job(threads=4,app=qmcpack,serial=True)
dmc_job = Job(threads=4,app=qmcpack,serial=True)
# job Definitions (MPI Tasks, MP Threading, PBS Queue, Time, etc.)
scf_job = job(app=pwscf,serial=True)
nscf_job = job(app=pwscf,serial=True)
p2q_job = job(app=pw2qmcpack,serial=True)
opt_job = job(threads=4,app=qmcpack,serial=True)
dmc_job = job(threads=4,app=qmcpack,serial=True)
# System To Be Simulated
rocksalt_LiH = generate_physical_system(
@ -88,7 +84,7 @@ nscf = generate_pwscf(
ecutrho = 1800,
conv_thr = 1.0e-10,
mixing_beta = 0.7,
dependencies = (scf,'charge-density')
dependencies = (scf,'charge-density'),
)
sims.append(nscf)
@ -98,7 +94,7 @@ p2q = generate_pw2qmcpack(
path = '.',
job = p2q_job,
write_psir = False,
dependencies = (nscf,'orbitals')
dependencies = (nscf,'orbitals'),
)
sims.append(p2q)
@ -125,8 +121,8 @@ linopt1 = linear(
alloweddifference = 1e-4,
stepsize = 0.2,
stabilizerscale = 1.0,
nstabilizers = 3
)
nstabilizers = 3,
)
# QMC Optimization Parameters - Finer Sampling Set
linopt2 = linopt1.copy()
@ -146,19 +142,23 @@ opt = generate_qmcpack(
('J2','bspline',8)],
calculations = [loop(max=4,qmc=linopt1),
loop(max=4,qmc=linopt2)],
dependencies = (p2q,'orbitals')
dependencies = (p2q,'orbitals'),
)
pp = opt.input.get('pseudos')
pp.Li.format='casino'
pp.Li['l-local']='s'
pp.Li.nrule=2
pp.Li.lmax=2
pp.Li.cutoff=2.19
pp.H.format='casino'
pp.H['l-local']='s'
pp.H.nrule=2
pp.H.lmax=2
pp.H.cutoff=0.50
pp.Li.set(
format = 'casino',
l_local = 's',
nrule = 2,
lmax = 2,
cutoff = 2.19,
)
pp.H.set(
format = 'casino',
l_local = 's',
nrule = 2,
lmax = 2,
cutoff = 0.50,
)
sims.append(opt)
# QMC VMC/DMC With Optimized Jastrow Parameters
@ -180,7 +180,7 @@ qmc = generate_qmcpack(
warmupsteps = 100,
blocks = 1,
timestep = 1.0,
usedrift = False
usedrift = False,
),
dmc(
minimumtargetwalkers = 128,
@ -189,22 +189,26 @@ qmc = generate_qmcpack(
timestep = 0.005,
steps = 10,
blocks = 200,
nonlocalmoves = True
nonlocalmoves = True,
)
],
dependencies = [(p2q,'orbitals'),(opt,'jastrow')]
dependencies = [(p2q,'orbitals'),(opt,'jastrow')],
)
pp = qmc.input.get('pseudos')
pp.Li.format='casino'
pp.Li['l-local']='s'
pp.Li.nrule=2
pp.Li.lmax=2
pp.Li.cutoff=2.37
pp.H.format='casino'
pp.H['l-local']='s'
pp.H.nrule=2
pp.H.lmax=2
pp.H.cutoff=0.50
pp.Li.set(
format = 'casino',
l_local = 's',
nrule = 2,
lmax = 2,
cutoff = 2.37,
)
pp.H.set(
format = 'casino',
l_local = 's',
nrule = 2,
lmax = 2,
cutoff = 0.50,
)
sims.append(qmc)
run_project(sims)

30
nexus/examples/qmcpack/c20/c20.py
View File

@ -1,7 +1,8 @@
#! /usr/bin/env python
from nexus import settings,Job,run_project
from nexus import Structure,PhysicalSystem
from nexus import settings,job,run_project
from nexus import read_structure
from nexus import generate_physical_system
from nexus import generate_pwscf
from nexus import generate_pw2qmcpack
from nexus import generate_qmcpack
@ -12,22 +13,15 @@ from nexus import loop,linear,vmc,dmc
settings(
pseudo_dir = '../pseudopotentials',# directory with all pseudopotentials
sleep = 3, # check on runs every 'sleep' seconds
#generate_only = 0, # only make input files
# Complicated setting only so examples can be run in test harness.
# For real runs, use the plain setting of 'generate_only' above.
generate_only = globals().get('override_generate_only_setting',False),
generate_only = 0, # only make input files
status_only = 0, # only show status of runs
machine = 'ws16', # local machine is 16 core workstation
)
#generate the C20 physical system
# specify the xyz file
structure_file = 'c20.cage.xyz'
# make an empty structure object
structure = Structure()
# read in the xyz file
structure.read_xyz(structure_file)
structure = read_structure('c20.cage.xyz')
# place a bounding box around the structure
structure.bounding_box(
box = 'cubic', # cube shaped cell
@ -39,11 +33,11 @@ structure.add_kmesh(
kshift = (0,0,0) # and shift
)
# add electronic information
c20 = PhysicalSystem(
structure = structure, # C20 structure
c20 = generate_physical_system(
structure = structure, # C20 structure
net_charge = 0, # net charge in units of e
net_spin = 0, # net spin in units of e-spin
C = 4 # C has 4 valence electrons
C = 4, # C has 4 valence electrons
)
@ -55,7 +49,7 @@ scf = generate_pwscf(
# nexus inputs
identifier = 'scf', # identifier/file prefix
path = 'c20/scf', # directory for scf run
job = Job(cores=16), # run on 16 cores
job = job(cores=16), # run on 16 cores
pseudos = ['C.BFD.upf'], # pwscf PP file
system = c20, # run c20
# input format selector
@ -75,7 +69,7 @@ p2q = generate_pw2qmcpack(
# nexus inputs
identifier = 'p2q',
path = 'c20/nscf',
job = Job(cores=1),
job = job(cores=1),
# pw2qmcpack input parameters
write_psir = False,
# workflow dependencies
@ -89,7 +83,7 @@ opt = generate_qmcpack(
# nexus inputs
identifier = 'opt', # identifier/file prefix
path = 'c20/opt', # directory for opt run
job = Job(cores=16,app='qmcpack'),
job = job(cores=16,app='qmcpack'),
pseudos = ['C.BFD.xml'], # qmcpack PP file
system = c20, # run c20
# input format selector
@ -126,7 +120,7 @@ qmc = generate_qmcpack(
# nexus inputs
identifier = 'qmc', # identifier/file prefix
path = 'c20/qmc', # directory for dmc run
job = Job(cores=16,app='qmcpack'),
job = job(cores=16,app='qmcpack'),
pseudos = ['C.BFD.xml'], # qmcpack PP file
system = c20, # run c20
# input format selector

17
nexus/examples/qmcpack/diamond/diamond.py
View File

@ -1,6 +1,6 @@
#! /usr/bin/env python
from nexus import settings,Job,run_project
from nexus import settings,job,run_project
from nexus import generate_physical_system
from nexus import generate_pwscf
from nexus import generate_pw2qmcpack
@ -9,10 +9,7 @@ from nexus import generate_qmcpack,vmc
settings(
pseudo_dir = '../pseudopotentials',
status_only = 0,
#generate_only = False,
# Complicated setting only so examples can be run in test harness.
# For real runs, use the plain setting of 'generate_only' above.
generate_only = globals().get('override_generate_only_setting',False),
generate_only = 0,
sleep = 3,
machine = 'ws16'
)
@ -34,7 +31,7 @@ dia16 = generate_physical_system(
scf = generate_pwscf(
identifier = 'scf',
path = 'diamond/scf',
job = Job(cores=16,app='pw.x'),
job = job(cores=16,app='pw.x'),
input_type = 'generic',
calculation = 'scf',
input_dft = 'lda',
@ -49,15 +46,15 @@ scf = generate_pwscf(
conv = generate_pw2qmcpack(
identifier = 'conv',
path = 'diamond/scf',
job = Job(cores=1,app='pw2qmcpack.x'),
job = job(cores=1,app='pw2qmcpack.x'),
write_psir = False,
dependencies = (scf,'orbitals')
dependencies = (scf,'orbitals'),
)
qmc = generate_qmcpack(
identifier = 'vmc',
path = 'diamond/vmc',
job = Job(cores=16,threads=4,app='qmcpack'),
job = job(cores=16,threads=4,app='qmcpack'),
input_type = 'basic',
system = dia16,
pseudos = ['C.BFD.xml'],
@ -72,7 +69,7 @@ qmc = generate_qmcpack(
timestep = .4
)
],
dependencies = (conv,'orbitals')
dependencies = (conv,'orbitals'),
)
run_project(scf,conv,qmc)

9
nexus/examples/qmcpack/diamond/diamond_vacancy.py
View File

@ -5,16 +5,13 @@ from nexus import *
settings(
pseudo_dir = '../pseudopotentials',
status_only = 0,
#generate_only = False,
# Complicated setting only so examples can be run in test harness.
# For real runs, use the plain setting of 'generate_only' above.
generate_only = globals().get('override_generate_only_setting',False),
generate_only = 0,
sleep = 3,
machine = 'ws16'
)
relax_job = Job(cores=16,app='pw.x')
scf_job = Job(cores=16,app='pw.x')
relax_job = job(cores=16,app='pw.x')
scf_job = job(cores=16,app='pw.x')
dia16 = generate_physical_system(
structure = './d16vac.POSCAR',

40
nexus/examples/qmcpack/graphene/graphene.py
View File

@ -1,6 +1,6 @@
#! /usr/bin/env python
from nexus import settings,Job,run_project
from nexus import settings,job,run_project
from nexus import generate_physical_system
from nexus import generate_pwscf
from nexus import generate_pw2qmcpack
@ -12,16 +12,12 @@ from nexus import loop,linear,vmc,dmc
settings(
pseudo_dir = '../pseudopotentials',# directory with all pseudopotentials
sleep = 3, # check on runs every 'sleep' seconds
#generate_only = False,
# Complicated setting only so examples can be run in test harness.
# For real runs, use the plain setting of 'generate_only' above.
generate_only = globals().get('override_generate_only_setting',False),
generate_only = 0, # only make input files
status_only = 0, # only show status of runs
machine = 'ws16', # local machine is 16 core workstation
)
# generate the graphene physical system
graphene = generate_physical_system(
lattice = 'hexagonal', # hexagonal cell shape
@ -47,7 +43,7 @@ scf = generate_pwscf(
# nexus inputs
identifier = 'scf', # identifier/file prefix
path = 'graphene/scf', # directory for scf run
job = Job(cores=16), # run on 16 cores
job = job(cores=16), # run on 16 cores
pseudos = ['C.BFD.upf'], # pwscf PP file
system = graphene, # run graphene
# input format selector
@ -60,7 +56,7 @@ scf = generate_pwscf(
kgrid = (8,8,8), # MP grid of primitive cell
kshift = (1,1,1), # to converge charge density
wf_collect = False, # don't collect orbitals
use_folded = True # use primitive rep of graphene
use_folded = True, # use primitive rep of graphene
)
sims.append(scf)
@ -69,7 +65,7 @@ nscf_opt = generate_pwscf(
# nexus inputs
identifier = 'nscf', # identifier/file prefix
path = 'graphene/nscf_opt', # directory for nscf run
job = Job(cores=16), # run on 16 cores
job = job(cores=16), # run on 16 cores
pseudos = ['C.BFD.upf'], # pwscf PP file
system = graphene, # run graphene
# input format selector
@ -85,7 +81,7 @@ nscf_opt = generate_pwscf(
kgrid = (1,1,1), # single k-point for opt
kshift = (0,0,0), # gamma point
# workflow dependencies
dependencies = (scf,'charge_density')
dependencies = (scf,'charge_density'),
)
sims.append(nscf_opt)
@ -94,11 +90,11 @@ p2q_opt = generate_pw2qmcpack(
# nexus inputs
identifier = 'p2q',
path = 'graphene/nscf_opt',
job = Job(cores=1),
job = job(cores=1),
# pw2qmcpack input parameters
write_psir = False,
# workflow dependencies
dependencies = (nscf_opt,'orbitals')
dependencies = (nscf_opt,'orbitals'),
)
sims.append(p2q_opt)
@ -107,7 +103,7 @@ opt = generate_qmcpack(
# nexus inputs
identifier = 'opt', # identifier/file prefix
path = 'graphene/opt', # directory for opt run
job = Job(cores=16,app='qmcpack'),
job = job(cores=16,app='qmcpack'),
pseudos = ['C.BFD.xml'], # qmcpack PP file
system = graphene, # run graphene
# input format selector
@ -134,7 +130,7 @@ opt = generate_qmcpack(
)
],
# workflow dependencies
dependencies = (p2q_opt,'orbitals')
dependencies = (p2q_opt,'orbitals'),
)
sims.append(opt)
@ -144,7 +140,7 @@ nscf = generate_pwscf(
# nexus inputs
identifier = 'nscf', # identifier/file prefix
path = 'graphene/nscf', # directory for nscf run
job = Job(cores=16), # run on 16 cores
job = job(cores=16), # run on 16 cores
pseudos = ['C.BFD.upf'], # pwscf PP file
system = graphene, # run graphene
# input format selector
@ -158,7 +154,7 @@ nscf = generate_pwscf(
use_folded = True, # use primitive rep of graphene
wf_collect = True, # write out orbitals
# workflow dependencies
dependencies = (scf,'charge_density')
dependencies = (scf,'charge_density'),
)
sims.append(nscf)
@ -167,11 +163,11 @@ p2q = generate_pw2qmcpack(
# nexus inputs
identifier = 'p2q',
path = 'graphene/nscf',
job = Job(cores=1),
job = job(cores=1),
# pw2qmcpack input parameters
write_psir = False,
# workflow dependencies
dependencies = (nscf,'orbitals')
dependencies = (nscf,'orbitals'),
)
sims.append(p2q)
@ -180,7 +176,7 @@ qmc = generate_qmcpack(
# nexus inputs
identifier = 'qmc', # identifier/file prefix
path = 'graphene/qmc', # directory for dmc run
job = Job(cores=16,app='qmcpack'),
job = job(cores=16,app='qmcpack'),
pseudos = ['C.BFD.xml'], # qmcpack PP file
system = graphene, # run graphene
# input format selector
@ -207,16 +203,14 @@ qmc = generate_qmcpack(
],
# workflow dependencies
dependencies = [(p2q,'orbitals'),
(opt,'jastrow')]
(opt,'jastrow')],
)
# nexus monitors all runs
run_project(sims)
# print out the total energy
performed_runs = not settings.generate_only and not settings.status_only
if performed_runs:
@ -230,5 +224,3 @@ if performed_runs:
print ' {0} +/- {1} Ha'.format(le.mean,le.error)
#end if

27
nexus/examples/qmcpack/oxygen_dimer/oxygen_dimer.py
View File

@ -1,7 +1,7 @@
#! /usr/bin/env python
# import nexus functions
from nexus import settings,Job,get_machine,run_project
from nexus import settings,job,run_project
from nexus import generate_physical_system
from nexus import generate_pwscf
from nexus import generate_pw2qmcpack
@ -14,10 +14,7 @@ settings(
runs = '',
results = '',
status_only = 0,
#generate_only = False,
# Complicated setting only so examples can be run in test harness.
# For real runs, use the plain setting of 'generate_only' above.
generate_only = globals().get('override_generate_only_setting',False),
generate_only = 0,
sleep = 3,
machine = 'ws16',
)
@ -46,7 +43,7 @@ linopt1 = linear(
alloweddifference = 1e-4,
stepsize = 0.2,
stabilizerscale = 1.0,
nstabilizers = 3
nstabilizers = 3,
)
linopt2 = linopt1.copy()
@ -92,7 +89,7 @@ dimer = generate_physical_system(
Lbox = 15.0, # box size
units = 'A', # Angstrom units
net_spin = 2, # Nup-Ndown = 2
O = 6 # O has 6 val. electrons
O = 6, # pseudo O has 6 val. electrons
)
# describe scf run
@ -100,7 +97,7 @@ scf = generate_pwscf(
identifier = 'scf',
path = directory,
system = dimer,
job = Job(cores=16),
job = job(cores=16),
input_type = 'scf',
pseudos = ['O.BFD.upf'],
input_dft = 'lda',
@ -108,7 +105,7 @@ scf = generate_pwscf(
conv_thr = 1e-7,
mixing_beta = .7,
nosym = True,
wf_collect = True
wf_collect = True,
)
sims.append(scf)
@ -116,9 +113,9 @@ sims.append(scf)
p2q = generate_pw2qmcpack(
identifier = 'p2q',
path = directory,
job = Job(cores=1),
job = job(cores=1),
write_psir = False,
dependencies = (scf,'orbitals')
dependencies = (scf,'orbitals'),
)
sims.append(p2q)
@ -127,14 +124,14 @@ opt = generate_qmcpack(
identifier = 'opt',
path = directory,
system = dimer,
job = Job(cores=16,app='qmcpack'),
job = job(cores=16,app='qmcpack'),
input_type = 'basic',
pseudos = ['O.BFD.xml'],
bconds = 'nnn',
jastrows = [('J1','bspline',8,4.5), # 1 & 2 body Jastrows
('J2','pade',0.5,0.5)],
calculations = opt_calcs,
dependencies = (p2q,'orbitals')
dependencies = (p2q,'orbitals'),
)
sims.append(opt)
@ -143,14 +140,14 @@ qmc = generate_qmcpack(
identifier = 'qmc',
path = directory,
system = dimer,
job = Job(cores=16,app='qmcpack'),
job = job(cores=16,app='qmcpack'),
input_type = 'basic',
pseudos = ['O.BFD.xml'],
bconds = 'nnn',
jastrows = [],
calculations = qmc_calcs,
dependencies = [(p2q,'orbitals'),
(opt,'jastrow')]
(opt,'jastrow')],
)
sims.append(qmc)

37
nexus/examples/quantum_espresso/relax_Ge_T_vs_kpoints/relax_vs_kpoints_example.py
View File

@ -1,39 +1,27 @@
#! /usr/bin/env python
from nexus import settings
from nexus import Structure,PhysicalSystem
from nexus import generate_pwscf,Job
from nexus import generate_physical_system
from nexus import generate_pwscf,job
from nexus import run_project
# set global parameters of nexus
settings(
pseudo_dir = '../pseudopotentials',# directory with pseudopotentials
#generate_only = False,
# Complicated setting only so examples can be run in test harness.
# For real runs, use the plain setting of 'generate_only' above.
generate_only = globals().get('override_generate_only_setting',False),
generate_only = 0, # only write input files, T/F
status_only = 0, # only show run status, T/F
machine = 'ws16' # local machine is 16 core workstation
)
# describe the physical system
T_structure = Structure() # empty structure
T_structure.read_xyz('./Ge_T_16.xyz') # read in Ge T interstitial structure
T_structure.reset_axes([ # specify cell axes (in Angstrom)
[ 5.66, 5.66, 0. ],
[ 0. , 5.66, 5.66],
[ 5.66, 0. , 5.66]
])
T_system = PhysicalSystem( # make the physical system
structure = T_structure, # out of the T interstitial structure
Ge = 4 # pseudo-Ge has 4 valence electrons
T_system = generate_physical_system( # make the physical system
structure = './Ge_T_16.xyz', # out of the T interstitial structure
axes = [[ 5.66, 5.66, 0. ], # specify cell axes (in Angstrom)
[ 0. , 5.66, 5.66],
[ 5.66, 0. , 5.66]],
Ge = 4, # pseudo-Ge has 4 valence electrons
)
@ -44,7 +32,6 @@ supercell_kgrids = [(1,1,1), # 1 k-point
(6,6,6)] # 216 k-points
# describe the relaxation calculations
# and link them together into a simulation cascade
relaxations = [] # list of relax simulation objects
@ -53,7 +40,7 @@ for kgrid in supercell_kgrids: # loop over supercell kgrids
identifier = 'relax', # file prefix
# run directory
path = 'relax/kgrid_{0}{1}{2}'.format(*kgrid),
job = Job(cores=16), # will run with mpirun -np 16
job = job(cores=16), # will run with mpirun -np 16
input_type = 'relax', # this is a relax calculation
input_dft = 'pbe', # PBE functional
ecut = 50, # 50 Ry planewave cutoff
@ -61,7 +48,7 @@ for kgrid in supercell_kgrids: # loop over supercell kgrids
kgrid = kgrid, # supercell k-point grid
kshift = (1,1,1), # grid centered at supercell L point
pseudos = ['Ge.pbe-kjpaw.UPF'], # PBE pseudopotential
system = T_system # the interstitial system
system = T_system, # the interstitial system
)
# link together the simulation cascade
# current relax gets structure from previous
@ -72,12 +59,10 @@ for kgrid in supercell_kgrids: # loop over supercell kgrids
#end for
# perform the simulations
run_project(relaxations)
# analyze the results
performed_runs = not settings.generate_only and not settings.status_only
if performed_runs:

8
nexus/library/physical_system.py
View File

@ -662,10 +662,14 @@ def generate_physical_system(**kwargs):
if is_str:
if os.path.exists(s):
if 'elem' in kwargs:
kwargs['structure'] = read_structure(s,elem=kwargs['elem'])
s = read_structure(s,elem=kwargs['elem'])
else:
kwargs['structure'] = read_structure(s)
s = read_structure(s)
#end if
if 'axes' in kwargs:
s.reset_axes(kwargs['axes'])
#end if
kwargs['structure'] = s
else:
slow = s.lower()
format = None

3
nexus/library/qmcpack_input.py
View File

@ -2044,7 +2044,7 @@ class pseudopotential(QIxml):
#end class pseudopotential
class pseudo(QIxml):
attributes = ['elementtype','href','format','cutoff','lmax','nrule','l-local']
attributes = ['elementtype','href','format','cutoff','lmax','nrule','l_local']
elements = ['header','local','grid']
identifier = 'elementtype'
#end class pseudo
@ -2578,6 +2578,7 @@ Names.set_expanded_names(
pairtype = 'pairType',
printeloc = 'printEloc',
spindependent = 'spinDependent',
l_local = 'l-local',
)
for c in classes:
c.init_class()