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Merge pull request #7 from anbenali/kgasperich/nexus-rmg-pptype
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Kgasperich/nexus rmg pptype
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@anbenali
anbenali authored Sep 28, 2023
2 parents 3c00702 + 2473e3e commit b9ff973
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225 changes: 225 additions & 0 deletions nexus/examples/rmg/02_diamond_scf_nscf_optJ123_dmc/Diamond_full.py
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#! /usr/bin/env python3

import os
cores = os.cpu_count() // 2

# Paths to executables. *** EDIT ME ***
rmg_bin="rmg-cpu"
qmc_bin="qmcpack_complex"

# Import Nexus stuff
from nexus import settings,job,run_project,obj
from nexus import generate_physical_system
from nexus import ppset
from nexus import generate_qmcpack
from nexus import generate_rmg

# machine settings
settings(
pseudo_dir = '../../qmcpack/pseudopotentials', # Pseudopotential directory
generate_only = 0, # only write input files, T/F
results = '', # Don't store results separately
sleep = 5, # Workflow polling frequency (sec)
machine = 'ws'+str(cores), # Executing on simple workstation
account = 'PSFMat_2',
)

scf_job = job(cores=cores, app=rmg_bin) # How to run RMG
opt_job = job(cores=cores, app=qmc_bin)


ppset(
label = 'BFD',
qmcpack = ['C.BFD.xml'],
rmg = ['C.BFD.xml'],

)

for struct in ['Diamond']:
primcell = generate_physical_system(
units = 'A',
structure = 'diamond',
cell = 'prim',
symm_kgrid=True,
C=4,
)
#Number of Supercells
tiled = primcell.structure.tile_opt(2)


scf=generate_rmg(
path = 'RMG/scf',
system = primcell,
virtual_frac = 1.0,
wf_grid_spacing = 0.15,
# nexus inputs
identifier = 'scf',
job = job(cores=1,app='rmg-cpu'),
pseudos = 'BFD',
input_type = 'generic',
# control options
calculation_mode = 'Quench Electrons',
compressed_infile = False,
compressed_outfile = False,
description = 'diamond',
energy_convergence_criterion = 1.0e-09,
max_scf_steps = 100,
#start_mode = 'Restart From File',
write_data_period = 10,
# cell parameter options
atomic_coordinate_type = 'Cell Relative',
kpoint_is_shift = (0,0,0),
kpoint_mesh = (3,2,1),
potential_grid_refinement = 2,
# pseudopotential related options
localize_localpp = False,
localize_projectors = False,
# kohn sham solver options
kohn_sham_mucycles = 3,
kohn_sham_solver = 'davidson',
# orbital occupation options
occupations_type = 'Fixed',
# charge density mixing options
charge_density_mixing = 0.5,
charge_mixing_type = 'Broyden',
potential_acceleration_constant_step = 1.0,
# diagonalization options
subdiag_driver = 'lapack',
exchange_correlation_type = 'pbe',
# miscellaneous options
kpoint_distribution = 1,
#qmcpack output
write_qmcpack_restart = True,
)
opt1=1
#Creating a 3x3x3 twist grid with a 2 Supercell
for grid in range(3,4):
supercell = generate_physical_system(
structure = tiled.copy(),
kgrid = (grid,grid,grid),
kshift = (1,1,1),
symm_kgrid = True,
C = 4,
)

nscf = generate_rmg(
path = 'RMG/nscf-'+str(grid)+'x'+str(grid)+'x'+str(grid),
system = supercell,
virtual_frac = 1.0,
wf_grid_spacing = 0.15,
# nexus inputs
identifier = 'nscf',
job = job(cores=1,app='rmg-cpu'),
pseudos = 'BFD',
input_type = 'generic',
# control options
calculation_mode = 'NSCF',
compressed_infile = False,
compressed_outfile = False,
description = 'diamond',
# cell parameter options
atomic_coordinate_type = 'Cell Relative',
kohn_sham_mucycles = 3,
kohn_sham_solver = 'davidson',
# diagonalization options
subdiag_driver = 'lapack',
exchange_correlation_type = 'pbe',
# miscellaneous options
kpoint_distribution = 1,
kpoint_is_shift = (1,1,1),
#Kpoint_mesh needs to have a negative number!!!!!
kpoint_mesh = (-3,2,1),
#qmcpack output
write_qmcpack_restart = True,
dependencies = (scf,'wavefunctions'),
)


if(opt1==1):
optJ12 = generate_qmcpack(
#block = True,
identifier = 'opt',
path = 'RMG/optJ12', # Run directory
job = opt_job,
input_type = 'basic',
system = supercell, # System to calculate
pseudos = 'BFD',
twistnum = 0,
meshfactor = 1.0, # you choose this and hybrid params
J1 = True, # Add a 1-body B-spline Jastrow
J2 = True, # Add a 2-body B-spline Jastrow
#J1_rcut = 6.842691799768850,
qmc = 'opt', # Do a wavefunction optimization
minmethod = 'oneshift', # Optimization algorithm (assumes energy minimization)
init_cycles = 2, # First 4 iterations allow large parameter changes
cycles = 5, # 8 subsequent iterations with smaller parameter changes
warmupsteps = 8, # First 8 steps are not recorded
blocks = 100, # Number of blocks to write in the .scalar.dat file
timestep = 0.1, # MC step size (nothing to do with time for VMC)
init_minwalkers = 0.01, # Smaller values -> bigger parameter change
minwalkers = 0.5, #
samples = 80000, # VMC samples per iteration
use_nonlocalpp_deriv = False,
dependencies = (nscf,'orbitals'),
)


optJ123 = generate_qmcpack(
#block = True,
identifier = 'opt',
path = 'RMG/optJ123', # Run directory
job = opt_job,
input_type = 'basic',
system = supercell, # System to calculate
twistnum = 0,
J3 = True, # Add a 2-body B-spline Jastrow
J3_rcut = 3.00, # Cutoff for J3
pseudos = 'BFD',
qmc = 'opt', # Do a wavefunction optimization
minmethod = 'oneshift', # Optimization algorithm (assumes energy minimization)
init_cycles = 2, # First 4 iterations allow large parameter changes
init_minwalkers = 0.01, # Smaller value -> bigger parameter change
cycles = 5, # Subsequent iterations with smaller parameter changes
minwalkers = 0.5, # Larger value -> smaller parameter change
warmupsteps = 4, # First steps are not recorded
blocks = 100, # Number of blocks to write in the .scalar.dat file
timestep = 0.1, # MC step size (nothing to do with time for VMC)
samples = 160000, # VMC samples per iteration
use_nonlocalpp_deriv = False, # Don't include nonlocal pseudo derivatives in optimization (this is nice to have for deep semicore states but expensive!)
dependencies = [(nscf,'orbitals'),
(optJ12, 'jastrow')],
)
opt1=2

# run DMC with 1,2 and 3 Body Jastrow function
qmc = generate_qmcpack(
#block = True,
identifier = 'dmc',
path = 'RMG/dmc-'+str(grid)+'x'+str(grid)+'x'+str(grid), # Run directory
job = job(cores=cores), # Submit with the number of cores available
system = supercell, # System to calculate
pseudos = 'BFD',
jastrows = [],
qmc = 'dmc', # dmc run
vmc_samples = 16000, # Number of Samples (selected from a VMC step)
vmc_warmupsteps = 100, # Number of Equilibration steps
warmupsteps = 100, # Number of Equilibration steps
vmc_blocks = 20, # Number of VMC blocks (To generate the DMC samples)
vmc_steps = 20, # Number of VMC steps (To generate DMC samples)
vmc_timestep = 0.1, # VMC Timestep (To Generate DMC samples)
timestep = 0.01, # DMC timestep
steps = 40, # start with small number for large timesteps [autocorrelation]
blocks = 1000, # Number of DMC blocks
nonlocalmoves = 'v3',
dependencies = [(nscf,'orbitals'),
(optJ123, 'jastrow')],
)


run_project()






4 changes: 2 additions & 2 deletions nexus/lib/qmcpack.py
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Expand Up @@ -44,6 +44,7 @@
from developer import unavailable
from nexus_base import nexus_core
from copy import deepcopy
from rmg import Rmg
try:
import h5py
except:
Expand Down Expand Up @@ -174,7 +175,7 @@ def incorporate_result(self,result_name,result,sim):
input = self.input
system = self.system
if result_name=='orbitals':
if isinstance(sim,Pw2qmcpack):
if isinstance(sim,(Pw2qmcpack,Rmg)):

h5file = result.h5file

Expand Down Expand Up @@ -273,7 +274,6 @@ def incorporate_result(self,result_name,result,sim):
#end if
#end if
qs.wavefunction = newwfn

else:
self.error('incorporating orbitals from '+sim.__class__.__name__+' has not been implemented')
#end if
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59 changes: 55 additions & 4 deletions nexus/lib/rmg.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,12 @@
##################################################################


import os
from simulation import Simulation
from generic import obj
from rmg_input import RmgInput,generate_rmg_input
from rmg_analyzer import RmgAnalyzer
from execute import execute



Expand All @@ -15,24 +18,72 @@ class Rmg(Simulation):
generic_identifier = 'rmg'
application = 'rmg-cpu'
application_properties = set(['serial','mpi'])
application_results = set([''])
application_results = set(['orbitals','wavefunctions'])


def __init__(self,**sim_args):
sync_from_scf = sim_args.pop('sync_from_scf',True)
Simulation.__init__(self,**sim_args)
self.sync_from_scf = False
#calc = self.input.ontrol.get('calculation_mode',None)
if self.input.calculation_mode=='NSCF':
self.sync_from_scf = sync_from_scf
#end if
#end def __init__




def check_result(self,result_name,sim):
calculating_result = False
input =self.input
if result_name=='orbitals':
conv_requested = self.input.write_qmcpack_restart
calculating_result = conv_requested
if result_name=='wavefunctions' :
calculating_result = True
return calculating_result
#end def check_result


def get_result(self,result_name,sim):
result = None
self.error('Ability to get result '+result_name+' has not been implemented.')
result = obj()
input = self.input
outdir = 'Waves'
result.locdir = self.locdir
result.outdir = os.path.join(self.locdir,outdir)
if result_name=='orbitals':
h5file = 'wave.out.h5'
result.h5file = os.path.join(self.locdir,outdir,h5file)
if result_name=='wavefunctions':
result.location = os.path.join(self.locdir,outdir,'wave.out')
#self.error('Ability to get result '+result_name+' has not been implemented.')
return result
#end def get_result


def incorporate_result(self,result_name,result,sim):
self.error('ability to incorporate result '+result_name+' has not been implemented')
#self.error('ability to incorporate result '+result_name+' has not been implemented')
if result_name=='wavefunctions':
res_path = os.path.abspath(result.locdir)
loc_path = os.path.abspath(self.locdir)
if res_path==loc_path:
None # don't need to do anything if in same directory
elif self.sync_from_scf: # rsync output into nscf dir
outdir = os.path.join(self.locdir,'Waves')
#outdir = os.path.join(self.locdir,c.outdir)
command = 'rsync -av {0}/* {1}/'.format(result.outdir,outdir)
if not os.path.exists(outdir):
os.makedirs(outdir)
#end if
sync_record = os.path.join(outdir,'nexus_sync_record')
if not os.path.exists(sync_record):
execute(command)
f = open(sync_record,'w')
f.write('\n')
f.close()
#end if
#end if
#end def incorporate_result


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