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,