def nexus_tile(axes0, pos0, tmat):
""" tile a single species of particles from primitive to supercell
for multiple species, tile one species at a time, then concatenate.
Args:
axes0 (np.array): primitive lattice vectors
pos0 (np.array): primitive atomic positions
tmat (np.array): tile matrix
Return:
(np.array, np.array): axes, pos in supercell
"""
from nexus import Structure
s0 = Structure(axes=axes0, pos=pos0, elem=['H'] * len(pos0), units='B')
s1 = s0.tile(tmat)
return s1.axes, s1.pos
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
kshift=(0, 0, 0) # and shift
)
# add electronic information
c20 = PhysicalSystem(
structure=structure, # C20 structure
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
(2, 2, 2), # 8 k-points
pwscf = 'pw.x'
pw2qmcpack = 'pw2qmcpack.x'
qmcpack = 'qmcpack'
# Pseudopotentials
dft_pps = ['O.BFD.upf','H.BFD.upf']
qmc_pps = ['O.BFD.xml','H.BFD.xml']
# Job Definitions (MPI Tasks, MP Threading, PBS Queue, Time, etc.)
scf_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
structure = Structure()
structure.read_xyz('H2O.xyz')
structure.bounding_box(
box = 'cubic',
scale = 1.5
)
structure.add_kmesh(
kgrid = (1,1,1),
kshift = (0,0,0)
)
H2O_molecule = PhysicalSystem(
structure = structure,
net_charge = 0,
net_spin = 0,
O = 6,
H = 1,
#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
kshift = (0,0,0) # and shift
)
# add electronic information
c20 = PhysicalSystem(
structure = structure, # C20 structure
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
Ge = 4 # pseudo-Ge has 4 valence electrons
)
# specify MP k-point grids for successive relaxations
# ======= 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 = []
x = np.linspace(-1.5, 1.5, 32)
z = np.linspace(-1.0, 2.0, 32)
for i in range(len(x)):
for j in range(len(z)):
myid = "x%2.5f_z%2.5f" % (x[i], z[j])
struct = Structure(elem=['H', 'C', 'N'],
pos=[[x[i], 0, z[j]], [0, 0, -CH],
[0, 0, -(CH + CN)]],
units='A')
system = generate_physical_system(structure=struct,
net_charge=0,
net_spin=0)
rhf_inputs = obj(
identifier=myid + 'rhf',
scftyp='rhf',
gbasis=basis,
ispher=1,
runtyp='energy',
coord='unique',
system=system,
dirscf=True, # use ram for speed
job=gms_job,
)
