#! /usr/bin/env python
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]],
)
#! /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()
#! /usr/bin/env python
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',
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
#! /usr/bin/env python3
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,loop,linear,vmc
settings(
pseudo_dir = './pseudopotentials',
results = '',
runs = 'diamond_runs',
status_only = 0,
generate_only = 0,
sleep = 3,
machine = 'ws16'
)
#Input structure
dia = 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]],
use_prim = True, # Use SeeK-path library to identify prim cell
tiling = [3,1,3], # Tile the cell
kgrid = (1,1,1),
import numpy as np
import os
from nexus import settings, Job, run_project, obj
from nexus import Structure, PhysicalSystem
from nexus import generate_physical_system
from nexus import generate_pwscf
from nexus import generate_pw2qmcpack, read_structure
from nexus import generate_qmcpack, vmc, loop, linear, dmc
from structure import optimal_tilematrix
# General Settings (Directories For I/O, Machine Type, etc.)
settings(pseudo_dir='../pseudopotentials',
runs='runs',
results='results',
sleep=5,
generate_only=0,
status_only=1,
machine='cades',
account='qmc')
#CHANGE_HERE_ONLY#
######################################################################
########################## Change here only ##########################`
#STRUCTURE
prim = read_structure('POSCAR')
prim.frozen = None
ph = generate_physical_system(structure=prim.copy(),
Li=1,
def apply_machine_settings(machine, run_dir, account='', nk=1, **kwargs):
""" apply default machines settings for hydrogen simulations
return a dictionary of jobs for ['dft','p2q','opt','dmc']
Args:
machine (str): one of ['golub','titan','ws4','ws8',...]. 'ws' stands for workstation.
run_dir (str): directory to run the jobs in.
account (str,optional): default is to depend on the machine's default in nexus.
nk (int,optional): the npool option in pw.x, default is 1 because it always runs. For large number of kpoints, set nk to be as large as possible for speed.
kwargs (dict): extra keyword arguments to be passed to nexus.settings.
Returns:
dict: jobs, a dictionary of nexus.obj objects for ['dft','p2q','opt','dmc'], each can be passed to create nexus.Job objects using Job(**jobs['dft']), for example.
"""
if (machine not in ['golub', 'titan', 'eos', 'bluewaters_xe'
]) and (not machine.startswith('ws')):
raise NotImplementedError('cannot handle machine=%s yet' % machine)
# end if
from nexus import settings, obj
if machine == 'titan':
account = 'mat158'
pseudo_dir = '/ccs/home/yyang173/scratch/hsolid/pseudo'
vdw_table = '/ccs/home/yyang173/scratch/hsolid/vdw/vdW_kernel_table'
qedir = '~/soft/espresso-5.3.0/bin'
ccdir = '~/soft/qmcpack-espresso-5.3.0/bin'
qmcdir = '~/soft/kylin_qmcpack'
elif machine == 'eos':
account = 'mat158'
pseudo_dir = '/ccs/home/yyang173/scratch/hsolid/pseudo'
vdw_table = '/ccs/home/yyang173/scratch/hsolid/vdw/vdW_kernel_table'
qedir = '~/soft/espresso-5.3.0/bin'
ccdir = '~/soft/qmcpack-espresso-5.3.0/bin'
qmcdir = '~/soft/intel_kylin_qmcpack'
elif machine == 'bluewaters_xe':
pseudo_dir = '/u/sciteam/yang5/scratch/hsolid/pseudo'
vdw_table = '/u/sciteam/yang5/scratch/hsolid/vdw/vdW_kernel_table'
qedir = '~/soft/espresso-5.3.0/bin'
ccdir = '~/soft/qmcpack-espresso-5.3.0/bin'
qmcdir = '~/soft/kylin_qmcpack'
elif machine == 'golub':
pseudo_dir = '/home/yyang173/scratch/hsolid/pseudo'
vdw_table = '/home/yyang173/scratch/hsolid/vdw/vdW_kernel_table'
qedir = '/projects/physics/yyang/soft/espresso-5.3.0/bin'
ccdir = '/projects/physics/yyang/soft/qmcpack-espresso-5.3.0/bin'
qmcdir = '~/soft/kylin_qmcpack'
else: # workstation, defaults should do
pseudo_dir = '/home/yyang173/Desktop/hsolid/pseudo'
vdw_table = '/home/yyang173/Desktop/hsolid/vdw/vdW_kernel_table'
qedir = '~/soft/espresso-5.3.0/bin'
ccdir = '~/soft/qmcpack-espresso-5.3.0/bin'
qmcdir = '~/soft/kylin_qmcpack'
# end if
settings(runs=run_dir,
machine=machine,
account=account,
pseudo_dir=pseudo_dir,
vdw_table=vdw_table,
**kwargs)
pw_bin = os.path.join(qedir, 'pw.x')
cc_bin = os.path.join(ccdir, 'pw2qmcpack.x')
qmc_bin = os.path.join(qmcdir, "qmcpack_cpu_real")
tabc_bin = os.path.join(qmcdir, "qmcpack_cpu_comp")
# assign jobs
if machine == 'titan':
dft_job = obj(nodes=1,
minutes=10,
app_options="-nk %d" % nk,
app=pw_bin)
p2q_job = obj(nodes=1, serial=True, minutes=30, app=cc_bin)
opt_job = obj(nodes=4, threads=8, hours=2, app=qmc_bin)
dmc_job = obj(nodes=8, threads=8, hours=2, app=qmc_bin)
elif machine == 'eos':
dft_job = obj(nodes=1,
minutes=10,
app_options="-nk %d" % nk,
app=pw_bin)
p2q_job = obj(nodes=1, serial=True, minutes=30, app=cc_bin)
opt_job = obj(nodes=4, threads=8, hours=2, app=qmc_bin)
dmc_job = obj(nodes=8, threads=8, hours=2, app=qmc_bin)
elif machine == 'bluewaters_xe':
dft_job = obj(nodes=1,
minutes=10,
app_options="-nk %d" % nk,
app=pw_bin)
p2q_job = obj(nodes=1, serial=True, minutes=30, app=cc_bin)
opt_job = obj(nodes=4, threads=8, hours=2, app=qmc_bin)
dmc_job = obj(nodes=8, threads=8, hours=2, app=qmc_bin)
for job in [dft_job, p2q_job, opt_job, dmc_job]:
job['user_env'] = False # the -V option is deprecated
# end for
elif machine == 'golub':
dft_job = obj(nodes=1, hours=4, app=pw_bin, app_options='-nk %d' % nk)
p2q_job = obj(nodes=1, serial=True, minutes=30, app=cc_bin)
opt_job = obj(nodes=1, threads=8, hours=4, app=qmc_bin)
dmc_job = obj(nodes=1, threads=8, hours=4, app=qmc_bin)
else:
dft_job = obj(app_options='-nk %d' % nk, app=pw_bin)
p2q_job = obj(serial=True, app=cc_bin)
opt_job = obj(app=qmc_bin, threads=8)
dmc_job = obj(app=qmc_bin, threads=8)
# end if
tabc_job = dmc_job.copy()
tabc_job.app = tabc_bin
jobs = {
'dft': dft_job,
'p2q': p2q_job,
'opt': opt_job,
'dmc': dmc_job,
'tabc': tabc_job
}
return jobs
#! /usr/bin/env python3
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
from structure import *
'''
This nexus example shows a variety of ways that excitations can be specified.
'''
settings(
pseudo_dir = '../../pseudopotentials',
runs = './runs_excitation_alternatives'
status_only = 0,
generate_only = 0,
sleep = 3,
machine = 'ws16'
)
#Input structure
dia = 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]],
#! /usr/bin/env python
import numpy as np
# ======= setup machine and jobs =======
from nexus import settings,Job,obj
machine_settings = obj(
runs = 'grid', # default to 'runs'
generate_only = 0,
status_only = 0,
sleep = 1,
machine = 'ws1',
ericfmt = '/opt/intel14/gamess-2014R1/auxdata/ericfmt.dat'
)
settings(**machine_settings)
gms_job = Job(serial=True,app="rungms",cores=1)
# ======= structure =======
from nexus import generate_physical_system, Structure
from nexus import generate_gamess
CH = 1.0655 # ang
CN = 1.1538 # ang
basis = 'ccd'
# ======= simulations =======
'''
MODERN BASIS SET FAMILIES (CCN, PCN, MCP_NZP, IMCP) ARE INTENDED
FOR USE ONLY AS SPHERICAL HARMONIC BASIS SETS. PLEASE SET ISPHER=1
IN THE $CONTRL GROUP IN ORDER TO USE GBASIS=ACCT
'''
#! /usr/bin/env python
from nexus import settings
from nexus import Structure,PhysicalSystem
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 = 0, # only generate 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
def test_settings():
# test full imports
import os
from nexus import settings, Settings, obj
from nexus_base import nexus_core, nexus_core_defaults
from nexus_base import nexus_noncore, nexus_noncore_defaults
from nexus_base import nexus_core_noncore, nexus_core_noncore_defaults
from pseudopotential import Pseudopotentials
from basisset import BasisSets
from machines import Job, Workstation
from project_manager import ProjectManager
from gamess import Gamess
from pwscf import Pwscf
from quantum_package import QuantumPackage
testing.check_final_state()
tpath = testing.setup_unit_test_output_directory('settings',
'test_settings')
# divert logging function
divert_nexus()
def aux_defaults():
# check that Job and ProjectManager settings are at default values
assert (Job.machine is None)
assert (ProjectManager.machine is None)
# check that Gamess, Pwscf, and Quantum Package settings are at default values
assert (Gamess.ericfmt is None)
assert (Gamess.mcppath is None)
assert (Pwscf.vdw_table is None)
assert (QuantumPackage.qprc is None)
#end def aux_defaults
def check_settings_core_noncore():
nckeys_check = set([
'command_line', 'debug', 'dependent_modes', 'emulate',
'file_locations', 'generate_only', 'graph_sims', 'indent',
'load_images', 'local_directory', 'mode', 'modes', 'monitor',
'primary_modes', 'progress_tty', 'pseudo_dir', 'pseudopotentials',
'remote_directory', 'results', 'runs', 'skip_submit', 'sleep',
'stages', 'stages_set', 'status', 'status_modes', 'status_only',
'trace', 'verbose'
])
nnckeys_check = set(
['basis_dir', 'basissets', 'pseudo_dir', 'pseudopotentials'])
setkeys_check = set([
'command_line', 'basis_dir', 'basissets', 'debug',
'dependent_modes', 'emulate', 'file_locations', 'generate_only',
'graph_sims', 'indent', 'load_images', 'local_directory', 'mode',
'modes', 'monitor', 'primary_modes', 'progress_tty', 'pseudo_dir',
'pseudopotentials', 'remote_directory', 'results', 'runs',
'skip_submit', 'sleep', 'stages', 'stages_set', 'status',
'status_modes', 'status_only', 'trace', 'verbose'
])
setkeys_allowed = setkeys_check | Settings.allowed_vars
nckeys = set(nexus_core.keys())
nnckeys = set(nexus_noncore.keys())
setkeys = set(settings.keys())
assert (nckeys == nckeys_check)
assert (nnckeys == nnckeys_check)
assert (setkeys >= setkeys_check)
assert (setkeys <= setkeys_allowed)
pairs = [(settings, nexus_core), (settings, nexus_noncore),
(nexus_core, nexus_noncore)]
for o1, o2 in pairs:
shared_keys = set(o1.keys()) & set(o2.keys())
for k in shared_keys:
v1 = o1[k]
v2 = o2[k]
if isinstance(v1, obj):
assert (object_eq(v1, v2))
else:
assert (value_eq(v1, v2))
#end if
#end for
#end for
#end check_settings_core_noncore
def check_empty_settings():
settings(command_line=False, )
settings.command_line = True
nexus_core.command_line = True
check_settings_core_noncore()
# nexus core sets basic run stages and Pseudopotentials object
assert (nexus_core.stages_set == set(
nexus_core_defaults.primary_modes))
assert (isinstance(nexus_core.pseudopotentials, Pseudopotentials))
assert (len(nexus_core.pseudopotentials) == 0)
nexus_core.stages_set = set()
nexus_core.stages = []
nexus_core.pseudopotentials = None
assert (object_eq(nexus_core, nexus_core_defaults))
# nexus noncore sets Pseudopotentials and BasisSets objects
assert (isinstance(nexus_noncore.pseudopotentials, Pseudopotentials))
assert (len(nexus_noncore.pseudopotentials) == 0)
assert (isinstance(nexus_noncore.basissets, BasisSets))
assert (len(nexus_noncore.basissets) == 0)
nnc_defaults = obj(nexus_noncore_defaults, nexus_core_noncore_defaults)
nexus_noncore.pseudopotentials = None
nexus_noncore.basissets = None
assert (object_eq(nexus_noncore, nnc_defaults))
# other settings objects should be at default also
aux_defaults()
#end def_check_empty_settings
# check that core settings are at default values
assert (object_eq(nexus_core, nexus_core_defaults))
assert (object_eq(nexus_noncore, nexus_noncore_defaults))
assert (object_eq(nexus_core_noncore, nexus_core_noncore_defaults))
aux_defaults()
# core settings remain almost at default with empty settings
check_empty_settings()
# check that a few basic user settings are applied appropriately
cwd = os.getcwd()
os.chdir(tpath)
dft_pseudos = ['Ni.opt.upf', 'O.opt.upf']
qmc_pseudos = ['Ni.opt.xml', 'O.opt.xml']
pseudos = dft_pseudos + qmc_pseudos
pseudo_path = './pseudopotentials'
if not os.path.exists(pseudo_path):
os.makedirs(pseudo_path)
for file in pseudos:
filepath = os.path.join(pseudo_path, file)
if not os.path.exists(filepath):
open(filepath, 'w').close()
#end if
#end for
#end if
settings(
pseudo_dir=pseudo_path,
status_only=0,
generate_only=1,
machine='ws16',
command_line=False,
)
check_settings_core_noncore()
assert (nexus_core.status_only == 0)
assert (nexus_core.generate_only == 1)
assert (nexus_core.pseudo_dir == './pseudopotentials')
assert (len(nexus_core.pseudopotentials) == 4)
assert (set(nexus_core.pseudopotentials.keys()) == set(pseudos))
assert (settings.machine == 'ws16')
assert (Job.machine == 'ws16')
assert (isinstance(ProjectManager.machine, Workstation))
assert (ProjectManager.machine.name == 'ws16')
os.chdir(cwd)
# check that a new empty settings works following basic
check_empty_settings()
# restore logging function
restore_nexus()
#! /usr/bin/env python3
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, dmc
from machine_configs import get_puhti_configs
from optim_params import *
settings(
pseudo_dir='./pseudopotentials',
status_only=0,
generate_only=1,
sleep=3,
machine='',
account='',
)
jobs = get_puhti_configs()
# The 4 commented lines below are as before in the vmc diamond case (Problem 3)
#dia16 = generate_physical_system()
#scf = generate_pwscf()
#conv = generate_pw2qmcpack()
#qmc = generate_qmcpack()
# Look into the needed imports and other settings when modifying your workflow scritps
# this loads some optimization parameters from optim_params
optims = getOptims()
from nexus import generate_pwscf
from nexus import generate_projwfc
from nexus import generate_pw2qmcpack
from nexus import generate_qmcpack
from nexus import vmc
from structure import *
from qmcpack_input import dm1b
from qmcpack_input import sposet
settings(
pseudo_dir = '../../pseudopotentials',
runs = 'runs_spin',
results = '',
status_only = 0,
generate_only = 0,
skip_submit = 0,
sleep = 3,
machine = 'ws4'
)
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 = (1,1,1),
C = 4
#! /usr/bin/env python
from nexus import settings,job,run_project
from nexus import read_structure,get_machine
from nexus import generate_physical_system
from nexus import generate_pwscf
b = '\n'+40*'='+'\n'
settings(
pseudo_dir = './pseudopotentials',
machine = 'ws16'
#machine = 'titan',
#account = 'XYZ123',
)
if settings.machine=='ws16':
scf_job = job(cores=16,app='pw.x')
elif settings.machine=='titan':
titan = get_machine('titan')
titan.queue_size = 2
scf_job = job(nodes=1,hours=1,app='pw.x')
else:
print 'no jobs for machine!'
#end if
s = read_structure('d16bulk.POSCAR')
s.remove([[0.8925,0.8925,0.8925]])
print b+'structure w/ vacancy\n',s
s.write('d16vac.xsf')
#! /usr/bin/env python
import numpy as np
# ======= setup machine and jobs =======
from nexus import settings, Job, obj
machine_settings = obj(
runs='grid', # default to 'runs'
generate_only=0,
status_only=0,
sleep=1,
machine='ws1',
ericfmt='/opt/intel14/gamess-2014R1/auxdata/ericfmt.dat')
settings(**machine_settings)
gms_job = Job(serial=True, app="rungms", cores=1)
# ======= structure =======
from nexus import generate_physical_system, Structure
from nexus import generate_gamess
CH = 1.0655 # ang
CN = 1.1538 # ang
basis = 'ccd'
# ======= simulations =======
'''
MODERN BASIS SET FAMILIES (CCN, PCN, MCP_NZP, IMCP) ARE INTENDED
FOR USE ONLY AS SPHERICAL HARMONIC BASIS SETS. PLEASE SET ISPHER=1
IN THE $CONTRL GROUP IN ORDER TO USE GBASIS=ACCT
'''
rhf_runs = []
#! /usr/bin/env python
from nexus import settings
settings(
generate_only = True, # only write input files, do not run
sleep = 3, # check on jobs every 3 seconds
pseudo_dir = './pseudopotentials', # path to PP file collection
machine = 'node8' # local machine is an 8 core workstation
)
settings(
status_only = True, # only write job status, do not run
generate_only = True, # only write input files, do not run
sleep = 3, # check on jobs every 3 seconds
pseudo_dir = './pseudopotentials', # path to PP file collection
local_directory = './' # base path for runs and results
runs = 'runs', # runs directory
results = 'results', # results directory
machine = 'titan', # local machine is Titan
account = 'MAT123', # allocation account on Titan
machine_info = dict(
oic5 = dict(
local_directory = '/home/your_id',
),
kraken = dict(
local_directory = '/nics/b/home/your_id'
)
#! /usr/bin/env python
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
settings(
pseudo_dir = '../../pseudopotentials',
results = '',
sleep = 3,
machine = 'ws16',
)
system = generate_physical_system(
units = 'A',
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
''',
tiling = [[ 1, -1, 1],
[ 1, 1, -1],
[-1, 1, 1]],
kgrid = (1,1,1),
kshift = (0,0,0),
C = 4,
)
#! /usr/bin/env python3
from nexus import settings,job,run_project,obj
from nexus import generate_physical_system
from nexus import generate_pyscf
from nexus import generate_convert4qmc
from nexus import generate_qmcpack,loop,linear,vmc,dmc
settings(
pseudo_dir = '/global/homes/h/haihan/Research/BeH2/instability/QZqmcT/001/pseudo',
results = '.',
runs = 'runs',
status_only = 0,
generate_only = 0,
sleep = 10, # In seconds
machine = 'cori', # Use lowercase letters
account = 'm2113', # QMCPACK
user = '******'
)
scf_presub = '''
export HDF5_USE_FILE_LOCKING=FALSE
module unload cray-libsci
module load cray-hdf5
#module load python/3.7-anaconda-2019.10
source activate myenv
module list
'''
system = generate_physical_system(
structure = 'geom.xyz',
#! /usr/bin/env python
# LiH crystal with Quantum ESPRESSO orbitals
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,loop,linear,dmc
# General Settings (Directories For I/O, Machine Type, etc.)
settings(
pseudo_dir = 'pseudopotentials',
runs = 'runs',
results = 'results',
sleep = 3,
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)
#! /usr/bin/env python
from nexus import settings,ProjectManager,Job
from nexus import Structure,PhysicalSystem
from nexus import loop,linear,vmc,dmc
from qmcpack_calculations import basic_qmc
#general settings for nexus
settings(
pseudo_dir = './pseudopotentials',# directory with all pseudopotentials
sleep = 3, # check on runs every 'sleep' seconds
generate_only = 0, # only make input files
status_only = 0, # only show status of runs
machine = 'node16', # 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)
# place a bounding box around the structure
structure.bounding_box(
box = 'cubic', # cube shaped cell
scale = 1.5 # 50% extra space
)
#! /usr/bin/env python
from nexus import settings, ProjectManager, Job
from nexus import Structure, PhysicalSystem
from nexus import loop, linear, vmc, dmc
from qmcpack_calculations import basic_qmc
#general settings for nexus
settings(
pseudo_dir='./pseudopotentials', # directory with all pseudopotentials
sleep=3, # check on runs every 'sleep' seconds
generate_only=0, # only make input files
status_only=0, # only show status of runs
machine='node16', # 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)
# place a bounding box around the structure
structure.bounding_box(
box='cubic', # cube shaped cell
scale=1.5 # 50% extra space
)
# make it a gamma point cell
structure.add_kmesh(
kgrid=(1, 1, 1), # Monkhorst-Pack grid
#! /usr/bin/env python
# imports from nexus and numpy
from numpy import arange, loadtxt
from nexus import settings, job, run_project, obj
from nexus import generate_physical_system
from nexus import generate_vasp
from nexus import graph_sims
# nexus settings
settings(pseudo_dir='./pseudopotentials',
results='',
status_only=0,
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
#! /usr/bin/env python3
# import Nexus functions
from nexus import settings, job, get_machine, run_project
from nexus import generate_physical_system
from nexus import generate_pwscf, generate_pw2qmcpack
from nexus import generate_qmcpack, loop, linear, vmc, dmc
# 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=32,
threads=1,
queue='qmcpack',
#! /usr/bin/env python
from nexus import settings
from nexus import Structure, PhysicalSystem
from nexus import generate_pwscf, Job
from nexus import ProjectManager
# set global parameters of nexus
settings(
pseudo_dir='./pseudopotentials', # directory with pseudopotentials
generate_only=0, # only generate input files, T/F
status_only=0, # only show run status, T/F
machine='node16' # 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
)
# specify MP k-point grids for successive relaxations
supercell_kgrids = [
(1, 1, 1), # 1 k-point
#! /usr/bin/env python3
from nexus import settings, job, run_project
from nexus import generate_physical_system
from nexus import generate_quantum_package
from nexus import generate_convert4qmc
from nexus import generate_cusp_correction
from nexus import generate_qmcpack
# 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='ws16',
qprc='/your/path/to/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
#! /usr/bin/env python
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=0,
sleep=3,
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(
skip_submit=True,
identifier='scf',
path='diamond/scf',
job=job(cores=16, app='pw.x'),
input_type='generic',
calculation='scf',
#! /usr/bin/env python
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
from nexus import loop, linear, vmc, dmc
# general settings for nexus
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),
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
cell='primitive', # primitive cell
centering='P', # primitive basis centering
constants=(2.462, 10.0), # a,c constants
units='A', # in Angstrom
atoms=('C', 'C'), # C primitive atoms
basis=[
[0, 0, 0], # basis vectors
#! /usr/bin/env python
from nexus import settings, job, 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 /your/path/to/quantum_package.rc
settings(
results = '',
status_only = 0,
generate_only = 0,
sleep = 3,
machine = 'ws16',
qprc = \
'/home/j1k/apps/quantum_package/qp2-2.0.0-beta/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
from nexus import settings, job, run_project
from nexus import generate_physical_system
from nexus import generate_quantum_package
from nexus import generate_convert4qmc
from nexus import generate_cusp_correction
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',
)
scf_job = job(cores=16, threads=16)
c4q_job = job(cores=1)
qmc_job = job(cores=16, threads=16)
system = generate_physical_system(structure='H2O.xyz', )
# perform Hartree-Fock
scf = generate_quantum_package(
identifier='hf', # log output goes to hf.out
path='H2O/hf', # directory to run in
# import nexus functions
from nexus import settings,Job,get_machine,run_project
from nexus import generate_physical_system
from nexus import generate_pwscf
from nexus import generate_pw2qmcpack
from nexus import generate_qmcpack
from nexus import loop,linear,vmc,dmc
# nexus settings
settings(
pseudo_dir = '../pseudopotentials',
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),
sleep = 3,
machine = 'ws16',
)
# specify optimization parameters
linopt1 = linear(
energy = 0.0,
unreweightedvariance = 1.0,
reweightedvariance = 0.0,
timestep = 0.4,
samples = 5120, # opt w/ 5120 samples
warmupsteps = 50,
#! /usr/bin/env python
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 = 0,
sleep = 3,
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(
#! /usr/bin/env python
from nexus import settings
from nexus import Structure, PhysicalSystem
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),
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
)
