def get_taito_configs():
scf_presub = '''
module purge
module load gcc
module load openmpi
module load openblas
module load hdf5-serial
'''
pmc_presub = '''
module purge
module load gcc
module load mkl
module load intelmpi
module load hdf5-par
module load fftw
module load boost
module load cmake
'''
qe = 'pw.x'
qe2 = 'qmcpack_taito_cpu_cpu_comp_SoA'
# 4 processes
scf = job(cores=4, minutes=30, user_env=False, presub=scf_presub, app=qe)
# 24 processes (1 node = 24 processors at taito)
#scf = job(nodes=1,hours=1,user_env=False,presub=scf_presub,app=qe)
vmc = job(cores=16,
minutes=10,
user_env + False,
presub=qmc_presub,
qpp=qe2)
jobs = {'scf': scf, 'vmc': vmc}
return jobs
def get_taito_configs():
scf_presub = '''
module purge
module load gcc
module load openmpi
module load openblas
module load hdf5-serial
'''
qmc_presub = '''
module purge
module load gcc
module load mkl
module load intelmpi
module load hdf5-par
module load fftw
module load boost
module load cmake
'''
qe = 'pw.x'
qe2 = 'qmcpack.x'
qe3 = 'pw2qmcpack.x'
# 4 processes
scf = job(cores=16, minutes=30, user_env=False, presub=scf_presub, app=qe)
# 24 processes (1 node = 24 processors at taito)
#scf = job(nodes=1,hours=1,user_env=False,presub=scf_presub,app=qe)
qmc = job(cores=16,
minutes=30,
threads=4,
user_env=False,
presurb=scf_presub,
app=qe2)
conv = job(cores=1, minutes=30, user_env=False, presub=scf_presub, app=qe3)
jobs = {'scf': scf, 'qmc': qmc, 'conv': conv}
return jobs
def get_puhti_configs():
# remember to load the modules used in compiling the code
# these are needed in running the code
scf_presub = '''
module load intel/19.0.4
module load hpcx-mpi/2.4.0
module load intel-mkl/2019.0.4
module load StdEnv
module load hdf5/1.10.4
'''
# what modules are needed for qmcpack
qmc_presub = '''
'''
# application that performs the calculations
qe_app='pw.x'
conv_app='pw2qmcpack.x'
qmc_app='qmcpack'
# csc queue
# https://docs.csc.fi/computing/running/batch-job-partitions/
csc_queue = 'small' # test, small, large, ...
# define jobs
# 4 processes for scf, 1 for conv, 20 for vmc, 20 for optim, 20 for dmc
scf = job(cores=4,minutes=10,user_env=False,presub=scf_presub,app=qe_app,queue=csc_queue)
conv = job(cores=1,minutes=10,user_env=False,presub=scf_presub,app=conv_app,queue=csc_queue)
vmc = job(cores=20,minutes=10,user_env=False,presub=qmc_presub,app=qmc_app,queue=csc_queue)
optim = job(cores=20,minutes=10,user_env=False,presub=qmc_presub,app=qmc_app,queue=csc_queue)
dmc = job(cores=20,minutes=20,user_env=False,presub=qmc_presub,app=qmc_app,queue=csc_queue)
# 40 processes (1 node = 40 processors at Puhti)
#scf = job(nodes=1,hours=1,user_env=False,presub=scf_presub,app=qe,queue=csc_queue)
jobs = {'scf' : scf, 'conv': conv, 'vmc': vmc, 'optim': optim, 'dmc': dmc}
return jobs
def get_taito_configs():
scf_presub = '''
module purge
module load gcc
module load openmpi
module load openblas
module load hdf5-serial
'''
qe = 'pw.x'
# 4 processes
scf = job(cores=4, minutes=30, user_env=False, presub=scf_presub, app=qe)
# 24 processes (1 node = 24 processors at taito)
#scf = job(nodes=1,hours=1,user_env=False,presub=scf_presub,app=qe)
jobs = {'scf': scf}
return jobs
# allow max of one job at a time (lab only)
vesta = get_machine('vesta')
vesta.queue_size = 1
# locations of pwscf, pw2qmcpack and qmcpack executables
pwscf = '/soft/applications/qmcpack/Binaries/pw.x'
pw2qmcpack = '/soft/applications/qmcpack/Binaries/pw2qmcpack.x'
qmcpack = '/soft/applications/qmcpack/Binaries/qmcpack'
# run directory and pseudopotentials
directory = 'bcc-beryllium' # directory to perform runs
dft_pps = ['Be.ncpp'] # pwscf pseudopotentials
qmc_pps = ['Be.xml'] # qmcpack pseudopotentials
# job details
dft_job = job(cores=16, hours=2, queue="qmcpack", app=pwscf)
p2q_job = job(cores=1, hours=2, queue="qmcpack", app=pw2qmcpack)
qmc_job = job(nodes=32, hours=2, threads=16, queue="qmcpack", app=qmcpack)
# specify k-point grids
kgrids = [(2, 2, 2), (3, 3, 3)]
sims = []
first = True
for kgrid in kgrids:
ks = '{0}{1}{2}'.format(*kgrid)
# create conventional cell tiled from primitive one
bcc_Be = generate_physical_system(lattice='cubic',
cell='primitive',
centering='I',
axes = '''1.785 1.785 0.000
0.000 1.785 1.785
1.785 0.000 1.785''',
elem_pos = '''
C 0.0000 0.0000 0.0000
C 0.8925 0.8925 0.8925
''',
kgrid = (1,1,1),
kshift = (0,0,0),
C = 4,
)
scf = generate_pyscf(
identifier = 'scf', # log output goes to scf.out
path = 'diamond_pp_dft_gamma', # directory to run in
job = job(serial=True,threads=16),# pyscf must run w/o mpi
template = './dft_template.py', # pyscf template file
system = system,
cell = obj( # used to make Cell() inputs
basis = 'bfd-vdz',
ecp = 'bfd',
drop_exponent = 0.1,
verbose = 5,
),
save_qmc = True, # save wfn data for qmcpack
)
c4q = generate_convert4qmc(
identifier = 'c4q',
path = 'diamond_pp_dft_gamma',
job = job(cores=1),
from nexus import settings,job,run_project
from nexus import generate_physical_system
from nexus import generate_pwscf
from nexus import generate_pw2qmcpack
from nexus import generate_qmcpack,vmc
settings(
pseudo_dir = './pseudopotentials',
status_only = 0,
generate_only = 1,
sleep = .3,
machine = 'oic5'
)
if settings.machine=='ws16':
scf_job = job(cores=16,app='pw.x')
conv_job = job(cores=1,app='pw2qmcpack.x')
qmc_job = job(cores=16,threads=4,app='qmcpack')
elif settings.machine=='oic5':
pwscf_modules = '''
module ()
{
eval `/opt/modules/3.1.6/bin/modulecmd bash $*`
}
module purge
module load mpi/openmpi-1.4.5-pgi
module load PGI/2013-64bit
module load composerxe/2013.5.192
module load hdf5/1.8.8-pgi-parallel
'''
qmcpack_modules = '''
# allow max of one job at a time (lab only)
vesta = get_machine('vesta')
vesta.queue_size = 1
# locations of pwscf, pw2qmcpack and qmcpack executables
pwscf = '/soft/applications/qmcpack/Binaries/pw.x'
pw2qmcpack = '/soft/applications/qmcpack/Binaries/pw2qmcpack.x'
qmcpack = '/soft/applications/qmcpack/Binaries/qmcpack_comp'
# run directory and pseudopotentials
directory = 'bcc-beryllium' # directory to perform runs
dft_pps = ['Be.ncpp'] # pwscf pseudopotentials
qmc_pps = ['Be.xml'] # qmcpack pseudopotentials
# job details
dft_job = job(cores=16, minutes=10, queue="qmcpack", app=pwscf)
p2q_job = job(cores=1, minutes=10, queue="qmcpack", app=pw2qmcpack)
qmc_job = job(nodes=32, minutes=10, threads=16, queue="qmcpack", app=qmcpack)
# specify k-point grids
kgrids = [(2, 2, 2), (3, 3, 3)]
sims = []
first = True
for kgrid in kgrids:
ks = '{0}{1}{2}'.format(*kgrid)
# create conventional cell tiled from primitive one
bcc_Be = generate_physical_system(lattice='cubic',
cell='primitive',
centering='I',
1.785 0.000 1.785''',
elem_pos = '''
C 0.0000 0.0000 0.0000
C 0.8925 0.8925 0.8925
''',
tiling = (2,1,1),
kgrid = (1,1,1),
kshift = (0,0,0),
C = 4,
)
system.change_units('B') # currently a bug in pyscf with A units
scf = generate_pyscf(
identifier = 'scf', # log output goes to scf.out
path = 'diamond/scf', # directory to run in
job = job(serial=True,threads=16),# pyscf must run w/o mpi
template = './scf_template.py', # pyscf template file
system = system,
cell = obj( # used to make Cell() inputs
basis = 'bfd-vdz',
ecp = 'bfd',
drop_exponent = 0.1,
verbose = 5,
),
save_qmc = True, # save wfn data for qmcpack
)
c4q = generate_convert4qmc(
identifier = 'c4q',
path = 'diamond/scf',
job = job(cores=1),
from nexus import generate_quantum_package
# note: you must source the QP config file before running this script
# source /your/path/to/quantum_package.rc
settings(
results = '',
status_only = 0,
generate_only = 0,
sleep = 3,
machine = 'ws12',
qprc = \
'/home/j1k/apps/quantum_package/qp2-2.0.0-beta/quantum_package.rc',
)
scf_job = job(cores=12, threads=12)
system = generate_physical_system(structure='H2O.xyz', )
scf = generate_quantum_package(
identifier='hf', # log output goes to hf.out
path='h2o_ae_hf', # directory to run in
job=scf_job,
system=system,
prefix='h2o', # create/use h2o.ezfio
run_type='scf', # qprun scf h2o.ezfio
ao_basis='cc-pvtz', # use cc-pvtz basis
)
run_project()
from nexus import generate_physical_system
from nexus import generate_quantum_package
# note: you must source the QP config file before running this script
# source /home/ubuntu/apps/qp2/quantum_package.rc
settings(
results='',
status_only=0,
generate_only=0,
sleep=3,
machine='ws16',
qprc='/home/ubuntu/apps/qp2/quantum_package.rc',
)
scf_job = job(cores=16, threads=16)
system = generate_physical_system(structure='H2O.xyz', )
scf = generate_quantum_package(
identifier='hf', # log output goes to hf.out
path='h2o_ae_hf', # directory to run in
job=scf_job,
system=system,
prefix='h2o', # create/use h2o.ezfio
run_type='scf', # qprun scf h2o.ezfio
ao_basis='cc-pvtz', # use cc-pvtz basis
)
run_project()
settings(
pseudo_dir='./pseudopotentials',
results='',
status_only=0,
generate_only=0,
sleep=3,
machine='ws16',
#machine = 'eos',
#account = 'mat151',
)
on_desktop = settings.machine == 'ws16'
on_cluster = settings.machine == 'eos'
if on_desktop:
scf_job = job(cores=16, app='pw.x')
conv_job = job(cores=1, app='pw2qmcpack.x')
qmc_job = job(cores=1) # fake/placeholder job
elif on_cluster:
scf_job = job(nodes=1) # fake/placeholder job
conv_job = job(nodes=1) # fake/placeholder job
modules = '''
source $MODULESHOME/init/bash
if (echo $LOADEDMODULES | grep -q pgi)
then
module unload PrgEnv-pgi
fi
if (echo $LOADEDMODULES | grep -q gnu)
then
module unload PrgEnv-gnu
fi
[ 0. , 1.785, 1.785],
[ 1.785, 0. , 1.785]],
elem = ['C','C'],
pos = [[ 0. , 0. , 0. ],
[ 0.8925, 0.8925, 0.8925]],
use_prim = True, # Use SeeK-path library to identify prim cell
tiling = [3,1,3], # Tile the cell
kgrid = (1,1,1),
kshift = (0,0,0), # Assumes we study transitions from Gamma. For non-gamma tilings, use kshift appropriately
C = 4
)
scf = generate_pwscf(
identifier = 'scf',
path = 'scf',
job = job(cores=16,app='pw.x'),
input_type = 'generic',
calculation = 'scf',
nspin = 2,
input_dft = 'lda',
ecutwfc = 200,
conv_thr = 1e-8,
nosym = False,
wf_collect = False,
system = dia,
kgrid = (4,4,4),
kshift = (0,0,0),
tot_magnetization = 0,
pseudos = ['C.BFD.upf'],
)
generate_only = 0,
status_only = 0,
machine = 'ws1',
)
# Executables (Indicate Path If Needed)
pwscf = 'pw.x'
pw2qmcpack = 'pw2qmcpack.x'
qmcpack = 'qmcpack'
# Pseudopotentials
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)
# System To Be Simulated
rocksalt_LiH = generate_physical_system(
lattice = 'cubic',
cell = 'primitive',
centering = 'F',
atoms = ('Li','H'),
basis = [[0.0,0.0,0.0],
[0.5,0.5,0.5]],
basis_vectors = 'conventional',
constants = 7.1,
0.000 1.785 1.785
1.785 0.000 1.785''',
elem_pos='''
C 0.0000 0.0000 0.0000
C 0.8925 0.8925 0.8925
''',
tiling=[[1, -1, 1], [1, 1, -1], [-1, 1, 1]],
kgrid=(1, 1, 1),
kshift=(0, 0, 0),
C=4,
)
scf = generate_pwscf(
identifier='scf',
path='diamond/scf',
job=job(cores=16, app='pw.x'),
input_type='generic',
calculation='scf',
input_dft='lda',
ecutwfc=200,
conv_thr=1e-8,
system=system,
pseudos=['C.BFD.upf'],
kgrid=(4, 4, 4),
kshift=(0, 0, 0),
)
nscf = generate_pwscf(
identifier='nscf',
path='diamond/nscf',
job=job(cores=16, app='pw.x'),
# allow max of one job at a time (lab only)
vesta = get_machine('vesta')
vesta.queue_size = 1
# locations of pwscf, pw2qmcpack and qmcpack executables
pwscf = '/soft/applications/qmcpack/Binaries/pw.x'
pw2qmcpack = '/soft/applications/qmcpack/Binaries/pw2qmcpack.x'
qmcpack = '/soft/applications/qmcpack/Binaries/qmcpack'
# run directory and pseudopotentials
directory = 'graphene' # directory to perform runs
dft_pps = ['C.BFD.upf'] # pwscf pseudopotentials
qmc_pps = ['C.BFD.xml'] # qmcpack pseudopotentials
# job details
dft_job = job(nodes=1, minutes=20, queue="qmcpack", app=pwscf)
p2q_job = job(cores=1, minutes=20, queue="qmcpack", app=pw2qmcpack)
qmc_job = job(nodes=32, minutes=20, threads=16, queue="qmcpack", app=qmcpack)
# create 2 atom sheet of graphene
graphene = generate_physical_system(
axes=[[9.30501148, 0.00000000, 0.0000000],
[-4.6525058, 8.05837632, 0.0000000],
[0.00000000, 0.00000000, 15.0000000]],
elem=['C', 'C', 'C', 'C', 'C', 'C', 'C', 'C'],
pos=[[0.00000000, 0.00000000, 7.50000000],
[2.32625287, 1.34306272, 7.50000000],
[4.65250574, 0.00000000, 7.50000000],
[6.97875861, 1.34306272, 7.50000000],
[-2.32625290, 4.02918816, 7.50000000],
[-0.00000003, 5.37225088, 7.50000000],
generate_only=0,
sleep=3,
machine='oic5')
# vasp job information
modules = '''
module ()
{
eval `/opt/modules/3.1.6/bin/modulecmd bash $*`
}
module purge
module load composerxe/2011.10.319
module load mpi/openmpi-1.4.5-intel
'''
vasp = '/home/j1k/apps/vasp/vasp53/5.3.3/vasp.oic_opt'
vjob = job(nodes=2, hours=2, presub=modules, user_env=False, app=vasp)
# vasp inputs used by all runs
shared_inputs = obj(
encut=550,
ediff=1e-8,
algo='Normal',
nelm=400,
nwrite=2,
prec='Accurate',
ismear=-5,
lwave=False,
lcharg=False,
lreal='.FALSE.',
nbands=200,
ispin=2,
machine='ws16')
dia16 = generate_physical_system(units='A',
axes=[[1.785, 1.785, 0.], [0., 1.785, 1.785],
[1.785, 0., 1.785]],
elem=['C', 'C'],
pos=[[0., 0., 0.], [0.8925, 0.8925, 0.8925]],
tiling=(2, 2, 2),
kgrid=(1, 1, 1),
kshift=(0, 0, 0),
C=4)
scf = generate_pwscf(
identifier='scf',
path='diamond/scf',
job=job(cores=12, app='pw.x'),
input_type='generic',
calculation='scf',
input_dft='lda',
ecutwfc=200,
conv_thr=1e-8,
nosym=True,
wf_collect=True,
system=dia16,
pseudos=['C.BFD.upf'],
)
conv = generate_pw2qmcpack(
identifier='conv',
path='diamond/scf',
job=job(cores=1, app='pw2qmcpack.x'),
supercell_kgrids = [
(1, 1, 1), # 1 k-point
(2, 2, 2), # 8 k-points
(4, 4, 4), # 64 k-points
(6, 6, 6)
] # 216 k-points
# describe the relaxation calculations
# and link them together into a simulation cascade
relaxations = [] # list of relax simulation objects
for kgrid in supercell_kgrids: # loop over supercell kgrids
relax = generate_pwscf( # make each relax simulation
identifier='relax', # file prefix
# run directory
path='relax/kgrid_{0}{1}{2}'.format(*kgrid),
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
conv_thr=1e-6, # convergence threshold
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
)
# link together the simulation cascade
# current relax gets structure from previous
if len(relaxations) > 0: # if it exists
relax.depends(relaxations[-1], 'structure')
#end if
relaxations.append(relax) # add relax simulation to the list
'''
system = generate_physical_system(
structure = 'geom.xyz',
Be = 2, # Zeff=7 for ccECP
H = 1,
net_spin = 0, # 2S
net_charge = 0,
)
sims = []
# perform Hartree-Fock
scf = generate_pyscf(
identifier = 'scf', # log output goes to scf.out
path = 'scf', # directory to run in
job = job(serial=True, nodes=4, queue='debug', hours=0.5, constraint='knl', presub=scf_presub),
#job = job(serial=True, nodes=1, threads=4, presub=scf_presub),
template = 'scf_guess/scf_template.py', # pyscf template file
system = system,
mole = obj( # used to make Mole() inputs
verbose = 4,
#symmetry = 'D2h',
),
save_qmc = True, # save wfn data for qmcpack
)
sims.append(scf)
#### convert orbitals to QMCPACK format
c4q = generate_convert4qmc(
identifier = 'c4q',
path = 'scf',
#Standardized Primitive cell -- run rest of the calculations on this cell
dia2_structure = get_primitive_cell(structure=dia.structure)['structure']
dia2_kpath = get_kpath(structure=dia2_structure)
#get_band_tiling and get_kpath require "SeeK-path" python3 libraries
dia2 = generate_physical_system(
structure=dia2_structure,
kgrid=(4, 4, 4),
kshift=(0, 0, 0),
C=4,
)
scf = generate_pwscf(
identifier='scf',
path='diamond/scf',
job=job(nodes=1, app='pw.x', hours=1),
input_type='generic',
calculation='scf',
nspin=2,
input_dft='lda',
ecutwfc=200,
conv_thr=1e-8,
nosym=True,
wf_collect=True,
system=dia2,
tot_magnetization=0,
pseudos=['C.BFD.upf'],
)
#K-path of the standardized primitive cell
dia2_structure.clear_kpoints()
dia2_kpts = generate_physical_system(
[ 0. , 1.785, 1.785],
[ 1.785, 0. , 1.785]],
elem = ['C','C'],
pos = [[ 0. , 0. , 0. ],
[ 0.8925, 0.8925, 0.8925]],
use_prim = True, # Use SeeK-path library to identify prim cell
tiling = [3,1,3], # Tile the cell
kgrid = (1,1,1),
kshift = (0,0,0), # Assumes we study transitions from Gamma. For non-gamma tilings, use kshift appropriately
C = 4
)
scf = generate_pwscf(
identifier = 'scf',
path = 'scf',
job = job(cores=16,app='pw.x'),
input_type = 'generic',
calculation = 'scf',
nspin = 2,
input_dft = 'lda',
ecutwfc = 200,
conv_thr = 1e-8,
nosym = False,
wf_collect = False,
system = dia,
kgrid = (4,4,4),
kshift = (0,0,0),
tot_magnetization = 0,
pseudos = ['C.BFD.upf'],
)
units = 'A', # in Angstrom
atoms = ('C','C'), # C primitive atoms
basis = [[ 0 , 0 , 0], # basis vectors
[2./3,1./3, 0]],
tiling = (2,2,1), # tiling of primitive cell
kgrid = (1,1,1), # Monkhorst-Pack grid
kshift = (.5,.5,.5), # and shift
C = 4 # C has 4 valence electrons
)
# scf run produces charge density
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
pseudos = ['C.BFD.upf'], # pwscf PP file
system = graphene, # run graphene
# input format selector
input_type = 'scf', # scf, nscf, relax, or generic
# pwscf input parameters
input_dft = 'lda', # dft functional
ecut = 150 , # planewave energy cutoff (Ry)
conv_thr = 1e-6, # scf convergence threshold (Ry)
mixing_beta = .7, # charge mixing factor
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
)
#! /usr/bin/env python
from nexus import settings,job,run_project,obj
from nexus import generate_physical_system
from nexus import generate_pyscf
settings(
results = '',
sleep = 3,
machine = 'ws16',
)
system = generate_physical_system(
structure = 'H2O.xyz',
)
scf = generate_pyscf(
identifier = 'scf', # log output goes to scf.out
path = 'h2o_ae_hf', # directory to run in
job = job(serial=True), # pyscf must run serially
template = './scf_template.py', # pyscf template file
system = system,
mole = obj( # used to make Mole() inputs
basis = 'ccpvtz',
symmetry = True,
),
)
run_project()
# Nexus settings
settings(
pseudo_dir='./pseudopotentials',
runs='',
results='',
status_only=0,
generate_only=0,
sleep=3,
#machine = 'ws4',
machine='vesta',
account='QMCPACK-Training',
)
# specify job details
if settings.machine.startswith('ws'): # running on workstation
dftjob = job(cores=4, app='pw.x')
p2qjob = job(cores=1, app='pw2qmcpack.x')
qmcjob = job(cores=4, app='qmcpack')
else: # running on Vesta
appdir = '/soft/applications/qmcpack/Binaries/'
dftjob = job(nodes=4,
threads=1,
hours=1,
queue='qmcpack',
app=appdir + 'pw.x')
p2qjob = job(cores=1,
threads=1,
hours=1,
queue='qmcpack',
app=appdir + 'pw2qmcpack.x')
qmcjob = job(nodes=32,
from nexus import generate_qmcpack
# note: you must source the QP config file before running this script
# source /home/ubuntu/apps/qp2/quantum_package.rc
settings(
results = '',
status_only = 0,
generate_only = 0,
sleep = 3,
machine = 'ws16',
qprc = '/home/ubuntu/apps/qp2/quantum_package.rc',
)
# define run details
qp_job = job(cores=16,threads=16)
c4q_job = job(cores=1)
qmc_job = job(cores=16,threads=16)
# read in structure for oxygen dimer
dimer = generate_physical_system(
structure = './O2.xyz',
net_spin = 2,
)
# path, job, system details are shared across runs
qp_shared = dict(
path = 'O_dimer/selci',
job = qp_job,
system = dimer,
prefix = 'fci', # single shared ezfio
from nexus import settings,job,run_project,obj
from nexus import generate_physical_system
from nexus import generate_gamess
settings(
pseudo_dir = './pseudopotentials',
results = '',
status_only = 0,
generate_only = 0,
sleep = 3,
machine = 'ws16',
ericfmt = '/your/path/to/ericfmt.dat'
)
gms_job = job(cores=16,app='gamess.x')
h2o = generate_physical_system(
# full atomic/electronic structure
elem = ['O','H','H'],
pos = [[0.000000, 0.000000, 0.000000],
[0.000000,-0.757160, 0.586260],
[0.000000, 0.757160, 0.586260]],
units = 'A', # Angstroms
net_spin = 0, # multiplicity=1, nup-ndown=0
O = 6, # Zeff=6 for BFD ECP
H = 1, # Zeff=1 for BFD ECP
# C2v symmetry structure
folded_elem = ['O','H'],
folded_pos = [[0.000000, 0.000000, 0.000000],
[0.000000, 0.757160, 0.586260]],
system = generate_physical_system(
units='A',
elem_pos='''
C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.10850000
H 1.04510382 0.00000000 -0.36950000
H -0.52255191 0.90508646 -0.36950000
H -0.52255191 -0.90508646 -0.36950000
''',
)
scf = generate_pyscf(
identifier='scf',
path='rhf',
job=job(serial=True),
template='./scf_template.py',
system=system,
mole=obj(basis='sto-3g', ),
checkpoint=True,
)
p2a = generate_pyscf_to_afqmc(
identifier='p2a',
path='rhf',
job=job(serial=True),
cholesky_threshold=1e-5,
verbose=True,
dependencies=(scf, 'wavefunction'),
)
#get_band_tiling requires "SeeK-path" python3 libraries
dia2 = generate_physical_system(
structure=dia2_structure,
kgrid=(1, 1, 1),
kshift=(
0, 0, 0
), # Assumes we study transitions from Gamma. For non-gamma tilings, use kshift appropriately
tiling=[3, 1, 3],
C=4,
)
scf = generate_pwscf(
identifier='scf',
path='diamond/scf',
job=job(nodes=1, app='pw.x', hours=1),
input_type='generic',
calculation='scf',
nspin=2,
input_dft='lda',
ecutwfc=200,
conv_thr=1e-8,
nosym=True,
wf_collect=True,
system=dia2,
tot_magnetization=0,
pseudos=['C.BFD.upf'],
)
nscf = generate_pwscf(
identifier='nscf',
from nexus import generate_pyscf
from nexus import generate_convert4qmc
from nexus import generate_qmcpack
settings(
results='',
sleep=3,
machine='ws16',
)
system = generate_physical_system(structure='H2O.xyz', )
scf = generate_pyscf(
identifier='scf', # log output goes to scf.out
path='h2o_ae_hf', # directory to run in
job=job(serial=True), # pyscf must run serially
template='./scf_template.py', # pyscf template file
system=system,
mole=obj( # used to make Mole() inputs
verbose=5,
basis='ccpvtz',
symmetry=True,
),
save_qmc=True, # save wfn data for qmcpack
)
c4q = generate_convert4qmc(
identifier='c4q',
path='h2o_ae_hf',
job=job(cores=1),
no_jastrow=True,
