def h2_pyscf_equil_test():
jobs = []
xyz = open('structures/h2_equil.xyz', 'r')
xyz.readline() # Remove headers.
xyz.readline()
scfman = PySCFManager(name='scf',
path='test_h2eq_py',
writer=PySCFWriter({
'spin': 0,
'xyz': xyz.read()
}),
runner=PySCFRunnerPBS(queue='secondary',
nn=1,
np=16,
walltime='0:01:00'))
jobs.append(scfman)
var = QWalkManager(name='var',
path=scfman.path,
writer=VarianceWriter(),
reader=VarianceReader(),
runner=RunnerPBS(nn=1,
np=16,
queue='secondary',
walltime='0:05:00'),
trialfunc=SlaterJastrow(scfman, kpoint=0))
jobs.append(var)
lin = QWalkManager(name='linear',
path=scfman.path,
writer=LinearWriter(),
reader=LinearReader(),
runner=RunnerPBS(nn=1,
np=16,
queue='secondary',
walltime='0:10:00'),
trialfunc=SlaterJastrow(slatman=scfman,
jastman=var,
kpoint=0))
jobs.append(lin)
dmc = QWalkManager(name='dmc',
path=scfman.path,
writer=DMCWriter(),
reader=DMCReader(),
runner=RunnerPBS(
nn=1,
np=16,
queue='secondary',
walltime='0:10:00',
),
trialfunc=SlaterJastrow(slatman=scfman, jastman=lin))
jobs.append(dmc)
return jobs
def h2_test_local():
''' Simple test that checks PySCF using PySCFRunnerLocal.'''
# Most basic possible job.
eqwriter=PySCFWriter({'xyz':h2})
eqman=PySCFManager(
name='scf',
path='h2equil',
writer=eqwriter,
runner=PySCFRunnerLocal()
)
return [eqman]
def h2_test_PBS():
''' Simple tests that check PySCF and queue interaction.'''
# Change some options and run with PBS.
stwriter=PySCFWriter({
'xyz':h2stretch,
'method':'UKS',
'dm_generator':dm_set_spins([1,-1],[]),
})
stman=PySCFManager(
name='scf',
path='h2stretch',
writer=stwriter,
runner=PySCFRunnerPBS(nn=1,walltime='0:05:00',np=16,queue='secondary'),
)
return [stman]
sys.path.append('..')
# # Generating a PySCF input.
#
# One of the simplest uses of autogen is to generate input files in succinct ways and have an object store the options for posterity.
# ### The `PySCFWriter` object
# The PySCFWriter writes input files and stores the input parameters within itself.
# In[ ]:
from autopyscf import PySCFWriter
pyscf_writer = PySCFWriter()
pyscf_writer.__dict__
# ### Importing a structure.
# The only required input (without a default) is the structure definition.
# For molecules, this means specifying the xyz coordinates of the atoms.
# In[ ]:
# A hydrogen molecule.
h2='\n'.join([
'H 0.0 0.0 0.0 ',
'H 0.74 0.0 0.0 '
])
# ### Manager for hydrogen DFT run.
# The job of this manager is to give you DFT results for the hydrogen molecule.
# It has three "subordinates" at its disposal: the writer, the reader, and the runner from the last three notebooks.
#
# First, lets set these elementary parts up.
# In[ ]:
from autopyscf import PySCFWriter, PySCFReader
from autorunner import PySCFRunnerLocal
h2 = '\n'.join(['H 0.0 0.0 0.0 ', 'H 0.74 0.0 0.0 '])
# The three components we've seen already:
pyscf_writer = PySCFWriter({'xyz': h2, 'method': 'RKS', 'dft': 'pbe,pbe'})
pyscf_reader = PySCFReader()
pyscf_runner = PySCFRunnerLocal()
# The manger needs to know what space it has to work.
# This is the `path` arguement.
# Data will be stored on disk at this location.
#
# The manager also needs to have a `name`.
# All filenames are generated based on the `name` you give it.
# You can have multiple managers with the same `path` so long as they have different `name`.
# In[ ]:
from pyscfmanager import PySCFManager
pyscf_manager = PySCFManager(path='04-scratch',
from autorunner import PySCFRunnerLocal, RunnerLocal
from trialfunc import SlaterJastrow
from variance import VarianceWriter, VarianceReader
from pyscfmanager import PySCFManager
from qwalkmanager import QWalkManager
path = '00-scratch'
# A hydrogen molecule.
h2 = '\n'.join(['H 0.0 0.0 0.0 ', 'H 0.74 0.0 0.0 '])
# Input parameters for SCF calculation.
pyscf_writer = PySCFWriter({
'xyz': h2,
'dft': 'pbe,pbe',
'spin': 0,
'dm_generator': dm_set_spins([1, -1], []),
'pyscf_path': sys.path
})
vmc_writer = VarianceWriter()
# Manage the PySCF job.
scfmanager = PySCFManager(name='h2_pbe',
path=path,
writer=pyscf_writer,
runner=PySCFRunnerLocal())
# Manage the VMC job.
voptmanager = QWalkManager(name='h2_vopt',
path=path,