def b3lyp_prototype(cls, i_bs=0):
#
calc_b3lyp = CP2K() # cp2k object
calc_b3lyp.working_directory = './'
# pycp2k objects: hierarchy
CP2K_INPUT = calc_b3lyp.CP2K_INPUT # CP2K_INPUT is what we need
FORCE_EVAL = CP2K_INPUT.FORCE_EVAL_add()
FORCE_EVAL.Method = 'QUICKSTEP'
SUBSYS = FORCE_EVAL.SUBSYS
DFT = FORCE_EVAL.DFT
XC = DFT.XC
SCF = DFT.SCF
####################################################################################################################
# GLOBAL #
# FORCE EVAL #
set_global(CP2K_INPUT)
## SUBSYS ##
set_unperiodic_cell(SUBSYS, abc=cls.my_abc)
set_nonperiodic_poisson(DFT)
set_topology(SUBSYS, xyz_file_name=cls.xyz_file_name)
center_coordinates(SUBSYS)
## END SUBSYS ##
## DFT ##
set_dft(DFT,
potential_file_name=cls.potential_file_name,
basis_set_file_name=cls.basis_set_file_name)
set_cutoff(DFT, cutoff=cls.cutoff, rel_cutoff=cls.rel_cutoff, ngrids=5)
# set_scf(DFT, eps_scf=cls.eps_scf_dft[i_bs], max_scf=1000, scf_guess='RESTART')
# <-- even if no actual wfn saved, will not collapse, but start with ATOMIC guess
# add_ot(SCF, stepsize=0.04)
#
# add_outer_scf(OUTER_SCF)
# set_pbe(XC) # we start with pbe
# set_pbe0(XC) no pbe0 in the beginning
set_qs(DFT,
eps_default=1.0E-10, # should be 4 order of magnitude lower w.r.t. diag
eps_pgf_orb=np.sqrt(1.0E-20)) # --||-- 1E-20 helps to avoid in b3lyp
## END DFT ##
#
################################################################################################################
# todo probably let it converge with OT method
# change calculations to a diagonalization
add_diagonalization(SCF)
# add_smear(SCF_) # uses final T.
add_mixing(SCF) # add or not?
add_mos(SCF, added_mos=1000)
# plot h**o/lumo
# set_pbe0(XC_) # we want G0W0@PBE0. no pbe0 in the beginning
print_mo_cubes(DFT.PRINT, nhomo=10, nlumo=10) # all HOMOs are typicall plotted
set_scf(DFT, eps_scf=1E-6, max_scf=100) # I want it to end asap if not converged
# add G0W0!
add_b3lyp(XC)
return calc_b3lyp
def __init__(self, start=None, stop: Union[dict, str] = None, atoms: ase.Atoms = None, template_file: str = None,
tolerance: float = 0.002, cwd: str = './', project_name: str = 'optimization'):
"""
Constructor for the cutoff optimizer class
Parameters
----------
start : dict
Starting values to use in the analysis for the cutoff, rel_cutoff and ngrid optimization
stop : Union[dict, str]
Stop value to use in the analysis. If a float, the cutoff values will be taken between start and top, if
the string auto is given, an automatic optimization method is implemented to find the optimal cutoff.
template_file : str
A cp2k input file to be read in as a template and modified during the analysis
Note that you need not add the cutoff, rel cutoff, and monkhorst parameters need not be set here as they
will be added at the appropriate stage of the analysis.
atoms : ase.Atoms
Ase atoms object on which the analysis should be performed. We ask for an ase atoms object over a
coordinate file in order to avoid issues arising from file readers. If this is left empty, it is
assumed that the cell is defined in the cp2k input file
tolerance : float
The delta value at which the cutoff should be considered converged.
cwd : str
Directory in which the analysis should run and files should be stored.
project_name : str
Name of the project.
"""
if start is None:
start = {'Cutoff': 100, 'Ngrids': 5, 'Rel_cutoff': 60}
if stop is None:
stop = {'Cutoff': 1500, 'Ngrids': 8, 'Rel_cutoff': 120}
self.start = start
self.stop = stop
self.atoms = atoms
self.template_file = template_file
self.tolerance = tolerance
self.cwd = cwd
self.project_name = project_name
self.calculator = CP2K()
self.calculator.project_name = self.project_name
self.calculator.working_directory = self.cwd
self.calculator.parse(self.template_file)
self.force_eval = self.calculator.CP2K_INPUT.FORCE_EVAL_list[0]
self.force_eval.PRINT.FORCES.Section_parameters = "ON"
self.m_grid = self.force_eval.DFT.MGRID
self.loop_range = {}
self.force_array = {'Cutoff': [], 'Ngrids': [], 'Rel_cutoff': []}
self.energy_array = {'Cutoff': [], 'Ngrids': [], 'Rel_cutoff': []}
self.optimized_cutoff: float
self.optimized_rel_cutoff: float
self.optimized_n_grids: float
# Run checks
if type(stop) is str:
self._temp_operation_check()
if template_file is None:
print("You must give adequate calculator parameters")
sys.exit(1)
def energy_cp2k(self):
"""Quick routine to calculate total energy using CP2K
"""
from pycp2k import CP2K
calc = CP2K()
calc.working_directory = self.input.dict['working_directory']
# Determine if using less than max_processers would be better
if (int(self.input.dict['atoms_per_process']) != 0):
natoms = len(self.config.atom)
processes = natoms / float(self.input.dict['atoms_per_process'])
if (processes <= 1.0):
processes = 1
printx("atoms_per_process may be set too high for system size")
printx("Number of Atoms = " + str(natoms))
elif (processes > int(self.input.dict['max_mpi_processes'])):
processes = int(self.input.dict['max_mpi_processes'])
else:
processes = int(processes)
else:
processes = int(self.input.dict['max_mpi_processes'])
calc.mpi_n_processes = processes
self.config.atom.set_calculator(calc)
# load in cp2k options
execfile(self.input.dict['cp2k_input'])
calc.project_name = self.config.file_name
calc.write_input_file()
# If we only want the input file written, then we stop here
if (self.exetype == 'write'):
energy_per_area = 2.0e10
return energy_per_area
# if print_debug is true, we run energy calc without "try" to
# allow for better error message passing
if (self.input.dict['print_debug'] != 'False'):
calc.run()
else:
try:
calc.run()
except Exception as err:
printx('error occured in the energy calculation.')
energy_per_area = 1.0e10
return energy_per_area
# Read in the output file to find the final energy.
with open(calc.output_path, "r") as fin:
regex = re.compile(" ENERGY\| Total FORCE_EVAL \( QS \)"
" energy \(a\.u\.\):\s+(.+)\n")
for line in fin:
match = regex.match(line)
if match:
printx("Final energy: {}".format(match.groups()[0]))
energy = match.groups()[0]
area = self.config.atom.cell[0, 0] * self.config.atom.cell[1, 1]
if (self.input.dict['print_debug'] != 'False'):
printx('Area used for energy ' + self.config.file_name + 'is' +
str(area))
energy_per_area = float(energy) / area
return energy_per_area
def createDefaultCp2kCalcObj(**kwargs):
kwargs = {k.lower(): v for k, v in kwargs.items()}
outDir = kwargs.get("outdir", None)
projName = kwargs.get("projname", None)
outObj = CP2K()
outObj.working_directory = os.path.abspath(os.getcwd())
outObj.project_name = "cp2k_file"
#Shortcutrs for below
cp2kInput = outObj.CP2K_INPUT
globSect = cp2kInput.GLOBAL
forceEval = cp2kInput.FORCE_EVAL_add(
) #Generally the main section (at least for a SPE calc). Can be given more than once hence the add
subSys = forceEval.SUBSYS
dft = forceEval.DFT
#Defining tons of params here
globSect.Run_type = "ENERGY"
globSect.Print_level = "MEDIUM"
forceEval.Method = "Quickstep"
forceEval.PRINT.FORCES.Section_parameters = "On"
dft.Basis_set_file_name = "BASIS_SET"
dft.Potential_file_name = "GTH_POTENTIALS"
dft.QS.Eps_default = "1.0E-10"
dft.MGRID.Ngrids = "4"
dft.MGRID.Cutoff = "[eV] 5000"
dft.MGRID.Rel_cutoff = "[eV] 50000"
dft.XC.XC_FUNCTIONAL.Section_parameters = "PBE"
dft.KPOINTS.Scheme = "MONKHORST-PACK 1 1 1"
dft.SCF.Scf_guess = "ATOMIC"
dft.SCF.Eps_scf = "1.0E-7"
dft.SCF.Max_scf = "300"
dft.SCF.Added_mos = "4"
dft.SCF.DIAGONALIZATION.Section_parameters = "ON"
dft.SCF.DIAGONALIZATION.Algorithm = "Standard"
dft.SCF.MIXING.Section_parameters = "T"
dft.SCF.MIXING.Method = "BROYDEN_MIXING"
dft.SCF.MIXING.Alpha = "0.4"
dft.SCF.MIXING.Nbroyden = "8"
dft.SCF.SMEAR.Section_parameters = "ON"
dft.SCF.SMEAR.Method = "FERMI_DIRAC"
dft.SCF.SMEAR.Electronic_temperature = "[K] 157.9"
modCp2kObjBasedOnDict(outObj, kwargs)
return outObj
def test_repeated_keywords(self):
"""Ensures that repeatable keywords are correctly handled.
"""
# Test that input parser correctly reads repeated keywords
calc = CP2K()
calc.parse("./repeated_keywords/template.in")
force_eval = calc.CP2K_INPUT.FORCE_EVAL_list[0]
basis_files = force_eval.DFT.Basis_set_file_name
self.assertEqual(len(basis_files), 2)
# Test that non-repeatable keywords are replaced instead of repeated
periodic = force_eval.SUBSYS.CELL.Periodic
self.assertEqual(periodic, "XYZ")
def dft_prototype(cls, i_bs=0):
# creates CP2K object from scratch. Note that gw prototype takes dft_prototype as a starting point
calc_dft = CP2K() # cp2k object
calc_dft.working_directory = './'
# pycp2k objects: hierarchy
CP2K_INPUT = calc_dft.CP2K_INPUT # CP2K_INPUT is what we need
FORCE_EVAL = CP2K_INPUT.FORCE_EVAL_add()
FORCE_EVAL.Method = 'QUICKSTEP'
SUBSYS = FORCE_EVAL.SUBSYS
DFT = FORCE_EVAL.DFT
XC = DFT.XC
SCF = DFT.SCF
####################################################################################################################
# GLOBAL #
# FORCE EVAL #
set_global(CP2K_INPUT)
## SUBSYS ##
set_unperiodic_cell(SUBSYS, abc=cls.my_abc)
set_nonperiodic_poisson(DFT)
set_topology(SUBSYS, xyz_file_name=cls.xyz_file_name)
center_coordinates(SUBSYS)
## END SUBSYS ##
## DFT ##
set_dft(DFT,
potential_file_name=cls.potential_file_name,
basis_set_file_name=cls.basis_set_file_name)
set_cutoff(DFT, cutoff=cls.cutoff, rel_cutoff=cls.rel_cutoff, ngrids=5)
set_scf(DFT,
eps_scf=cls.eps_scf_dft[i_bs],
max_scf=1000,
scf_guess='RESTART')
# <-- even if no actual wfn saved, will not collapse, but start with ATOMIC guess
add_ot(SCF, stepsize=0.04)
#
# add_outer_scf(OUTER_SCF)
set_pbe(XC) # we start with pbe
# set_pbe0(XC) no pbe0 in the beginning
set_qs(
DFT,
eps_default=1.0E-10, # ad hoc
eps_pgf_orb=np.sqrt(1.0E-10)) # ad hoc
## END DFT ##
return calc_dft
def main():
# main settings
# todo: has to be inherited from the sh file:
sim = 'sim' # simulation folder name
database_folder = 'db'
# todo: this must be inherited
bh5670 = 'bh5670' # the outermost folder in the scratch where all other data are put
# todo yaml or predict
my_offset = 15 # from the molecule to a vacuum. 15-20 is recommended!
cutoff = 500
rel_cutoff = 50
basis_set_file_name = 'BASIS_CC_AUG_RI_NEW' # RI5, 2-5 cc, all aug-cc, RIFIT-all
my_basis_sets = [
'aug-cc-pVDZ', 'aug-cc-pVTZ', 'aug-cc-pVQZ', 'aug-cc-pV5Z'
]
my_ri_basis_sets = [
'aug-cc-pVDZ-RIFIT', 'aug-cc-pVTZ-RIFIT', 'aug-cc-pVQZ-RIFIT',
'aug-cc-pV5Z-RIFIT'
]
debug = True
# end: main settings
dummy_run = False # does not invoke cp2k if true
# parser begin
parser = argparse.ArgumentParser(description='rank and num of cpus')
parser.add_argument('-rank') # array job number
parser.add_argument(
'-num_cpus') # number of cpus you request for every array job
args = parser.parse_args()
# parser end
# parsing input
threads = int(args.num_cpus) - 1 # cpus used to compute
rank = '{:0>6}'.format(
args.rank) # transform rank from '1' to '000001' format
prefix_xyz_file_name = 'dsgdb9nsd'
xyz_file_name = f'{prefix_xyz_file_name}_{rank}.xyz'
xyz_file_location = f'{prefix_xyz_file_name}/{xyz_file_name}'
sim_folder_scratch = f'/scratch/{bh5670}/{sim}/{rank}'
sim_folder_home = f'{sim}/{rank}' # sim folder at home exists. you create later {rank} folder
if not os.path.exists(sim_folder_scratch):
os.mkdir(sim_folder_scratch)
else:
rmtree(sim_folder_scratch
) # leftovers from previous simulations will be removed
os.mkdir(sim_folder_scratch) # and the new folder will be created
# xyz object created, normal xyz file is created at scratch
my_xyz_file_obj = XYZ.from_file(
xyz_file_location) # object created using the file from home
xyz_at_scratch = sim_folder_scratch + '/' + xyz_file_name #
my_xyz_file_obj.write(xyz_at_scratch) # writes a normal xyz (into scratch)
# my molecule object is created. It will serve as a DB record
my_new_mol = Cp2kOutput(rank)
# rel_cutoff: 40; cutoff: 300; abc = 10
my_abc = str(my_xyz_file_obj.compute_box_size(offset=my_offset))[1:-2]
# GLOBAL SETTINGS
#
## base settings ##
my_potential_file_name = 'POTENTIAL'
my_potential = 'ALL'
my_project_name = "this_is_template"
# my_ri_aux_basis_set = 'RI-5Z' # often fails
organic_elements = [
'H', 'C', 'N', 'O', 'F', 'P', 'S', 'Cl', 'Br', 'B', 'I'
]
my_elements = organic_elements
inp_file_name = 'test_2345.inp'
my_vdw_parameters_file = 'dftd3.dat'
activate_vdw = False
activate_outer_scf = False
wf_corr_num_proc = 1 # 16 in the ref paper; -1 to use all
########################################### CREATE TEMPLATE FOR TWO RUNS ###########################################
calc = CP2K()
calc.working_directory = './'
calc.project_name = 'artem_gw_project'
calc.mpi_n_processes = 1
# pycp2k objects
CP2K_INPUT = calc.CP2K_INPUT
FORCE_EVAL = CP2K_INPUT.FORCE_EVAL_add()
FORCE_EVAL.Method = 'QUICKSTEP'
SUBSYS = FORCE_EVAL.SUBSYS
DFT = FORCE_EVAL.DFT
XC = DFT.XC
SCF = DFT.SCF
OUTER_SCF = DFT.SCF.OUTER_SCF
####################################################################################################################
# GLOBAL #
# FORCE EVAL #
set_global(CP2K_INPUT, project_name=my_project_name)
## SUBSYS ##
set_unperiodic_cell(SUBSYS, abc=my_abc)
set_nonperiodic_poisson(DFT)
set_topology(SUBSYS, xyz_file_name=xyz_file_name)
center_coordinates(SUBSYS)
## END SUBSYS ##
## DFT ##
set_dft(DFT,
potential_file_name=my_potential_file_name,
basis_set_file_name=basis_set_file_name)
set_cutoff(DFT, cutoff=cutoff, rel_cutoff=rel_cutoff, ngrids=5)
set_scf(DFT, eps_scf=1.0E-9, max_scf=500, scf_guess='ATOMIC')
add_ot(SCF, stepsize=0.05)
#
# add_outer_scf(OUTER_SCF)
set_pbe(XC) # we start with pbe
# set_pbe0(XC) no pbe0 in the beginning
set_qs(DFT, eps_default=1.0E-10, eps_pgf_orb=np.sqrt(1.0E-10))
# print_mo(DFT.PRINT)
if activate_vdw:
add_vdw(XC, vdw_parameters_file=my_vdw_parameters_file)
## END DFT ##
######################################## END: CREATE TEMPLATE ##########################################################
######################################## BEGIN: RUN CP2K TWO TIMES #####################################################
suffix = ['2', '3', '4'] # cardinal numbers of the database
# begin: input_from_yaml
# cp2k_exe_path = '/home/artem/soft/cp2k/cp2k-7.1/exe/local/cp2k.popt'
cp2k_exe_path = '/home/ws/bh5670/cp2k/cp2k-7.1/exe/local/cp2k.popt'
my_run_type = 'mpi'
for i_bs, suffix in enumerate(suffix):
# bs
calc_ = deepcopy(calc)
#
CP2K_INPUT_ = calc_.CP2K_INPUT
FORCE_EVAL_ = CP2K_INPUT_.FORCE_EVAL_list[0]
SUBSYS_ = FORCE_EVAL_.SUBSYS
DFT_ = FORCE_EVAL_.DFT
XC_ = DFT_.XC
SCF_ = DFT_.SCF
OUTER_SCF_ = DFT_.SCF.OUTER_SCF
#
set_global(CP2K_INPUT_, project_name=suffix)
add_elements(SUBSYS_,
elements=my_elements,
basis=my_basis_sets[i_bs],
aux_basis=my_ri_basis_sets[i_bs],
pot=my_potential)
# bs
output_file = f'out_{suffix}.out'
ot_file_name = 'OT_' + f'{suffix}_' + inp_file_name
diag_file_name = 'DIAG_' + f'{suffix}_' + inp_file_name
# end: input
if i_bs != 0:
set_scf(DFT_, eps_scf=1.0E-8, max_scf=500, scf_guess='RESTART'
) # TZ,QZ will start from RESTART of the DZ,QZ
try:
copy(sim_folder_scratch + '/' + f'{int(suffix)-1}-RESTART.wfn',
sim_folder_scratch + '/' + f'{suffix}-RESTART.wfn')
print('copied restart file 2->3 or 3->4')
except:
print('not succesfull copy of the restart file')
elif i_bs == 0:
set_scf(DFT_, eps_scf=1.0E-8, max_scf=500,
scf_guess='ATOMIC') # DZ with ATOMIC guess
# OT run to converge quickly
calc_.write_input_file(sim_folder_scratch + '/' + ot_file_name)
# first run
print(f"Running PBE with OT (basis set = {suffix})...")
if not dummy_run:
cp2k_run(input_file=ot_file_name,
xyz_file=xyz_file_name,
run_type=my_run_type,
np=threads,
output_file=f'out_ot_{suffix}.out',
cp2k_executable=cp2k_exe_path,
execution_directory=sim_folder_scratch)
# end: first run
print(f"I have finished cp2k with OT (basis set = {suffix})")
# DIAGONALIZATION RUN to reliably compute H**O and then GW
# remove the OT method
remove_ot(SCF_)
# change calculations to a diagonalization
add_diagonalization(SCF_)
# add_smear(SCF_) # uses final T.
add_mixing(SCF_) # add or not?
add_mos(SCF_, added_mos=1000)
# plot h**o/lumo
#set_pbe0(XC_) # we want G0W0@PBE0. no pbe0 in the beginning
print_mo_cubes(DFT_.PRINT, nhomo=10,
nlumo=10) # all HOMOs are typicall plotted
set_scf(DFT_, eps_scf=1E-6, max_scf=200)
# add G0W0!
add_gw_ver_0(XC_,
ev_sc_iter=1,
wf_corr_num_proc=wf_corr_num_proc,
rpa_num_quad_points=100,
max_memory_wf=4000,
max_memory_hf=500,
corr_occ=1,
corr_virt=1) # GW!
# it is important to keep WF memory smaller than HF memory, otherwise, it crashes
calc_.write_input_file(sim_folder_scratch + '/' + diag_file_name)
# second run
print(f"Running G0W0 with DIAG (basis set = {suffix})...")
my_out_file2 = f'out_diag_{suffix}.out'
if not dummy_run:
cp2k_run(input_file=diag_file_name,
xyz_file=xyz_file_name,
output_file=my_out_file2,
run_type=my_run_type,
np=threads,
cp2k_executable=cp2k_exe_path,
execution_directory=sim_folder_scratch)
print(f"I have finished cp2k with DIAG (basis set = {suffix})")
# extract h**o/lumo and gw h**o/lumo from the cp2k output file:
path_to_out2_file = sim_folder_scratch + '/' + my_out_file2
# extract from the output
try:
num_orb = extract_number_of_independent_orbital_function(
path_to_out2_file)
print(
f'basis set = {suffix}, number of independent orbital functions: {num_orb}'
)
except:
print('number of orbatals was not extracted')
num_orb = 'not extracted'
try:
homos, lumos = [], []
homos, lumos = return_homo_lumo(path_to_out2_file)
print(f'basis set = {suffix} ', 'h**o = ',
homos[-1] * eV_to_Hartree(), ' eV')
print(f'basis set = {suffix} ', 'lumo = ',
lumos[0] * eV_to_Hartree(), ' eV')
h**o = homos[-1] * eV_to_Hartree()
lumo = lumos[0] * eV_to_Hartree()
except:
print(f'H**o/Lumo were not extracted')
h**o = 'not extracted'
lumo = 'not extracted'
try:
gw_occ, gw_vir, homo_, lumo_ = return_gw_energies(
path_to_out2_file)
if isinstance(h**o, str) and isinstance(lumo, str):
h**o = homo_
lumo = lumo_
print(f'basis set = {suffix} ', 'h**o = ', h**o, ' eV')
print(f'basis set = {suffix} ', 'lumo = ', lumo, ' eV')
print(f'basis set = {suffix} ', 'gw h**o = ', gw_occ, ' eV')
print(f'basis set = {suffix} ', 'gw lumo = ', gw_vir, ' eV')
except:
print("GW energies were not extracted")
gw_occ = 'not extracted'
gw_vir = 'not extracted'
del calc_
# put computed data into the molecule object
my_new_mol.add_energies(int(suffix), h**o, lumo, gw_occ, gw_vir)
my_new_mol.add_num_orbitals(int(suffix), num_orb)
my_new_mol.extrapolate_energy()
db_record = my_new_mol.yield_dict(
) # this dict will be written into yaml. it will be a record in the global library
#
print("\nI am done\n")
print('saving to DB...')
with open(f'{database_folder}/DB_{rank}.yaml', 'w') as stream:
yaml.safe_dump(db_record, stream)
print(f"saved to {database_folder}/DB_{rank}.yaml")
print('I will remove the content the sim folder')
# Clean up before leave
status = my_new_mol.status()
if status == 'all_extracted': # all quantities are extracted
if debug:
print(
f'status: {status}, but debug is on ==> will move {sim_folder_scratch} to {sim_folder_home}'
)
copytree(sim_folder_scratch,
sim_folder_home) # will rewrite the folder
else:
print(f'status: {status} ==> will remove {sim_folder_scratch}')
try_to_remove_folder(sim_folder_scratch)
else:
print(f'status: {status} ==> will copy failed sim folder from scratch')
#if not os.path.exists(sim_folder_home):
#os.mkdir(sim_folder_home) # will overwrite if exists
copytree(sim_folder_scratch,
sim_folder_home) # will rewrite the folder
print(f"I have copied {sim_folder_scratch} to {sim_folder_home}")
try_to_remove_folder(sim_folder_scratch)
def main():
# My input_from_yaml #
# rel_cutoff: 40; cutoff: 300; abc = 10
my_abc = '10.0 10.0 10.0'
cutoff = 300
rel_cutoff = 40
# GLOBAL SETTINGS
threads = 121 # cpus used to compute
#
## base settings ##
#basis_set_base_path = '/home/artem/soft/cp2k/cp2k-7.1/data/'
basis_set_base_path = ''
# my_basis_set_file_name = basis_set_base_path + 'BASIS_RI_cc-TZ'G
#my_basis_set_file_name = basis_set_base_path + 'BASIS_def2_QZVP_RI_ALL'
basis_set_file_name = 'BASIS_CC_AUG_RI' # RI5, 2-5 cc, all aug-cc
my_vdw_parameters_file = basis_set_base_path + 'dftd3.dat'
#my_basis_set = 'def2-QZVP' # not used
# my_basis_sets = ['cc-pVDZ', 'cc-pVTZ', 'cc-pVQZ', 'cc-pV5Z']
my_basis_sets = [
'aug-cc-pVDZ', 'aug-cc-pVTZ', 'aug-cc-pVQZ', 'aug-cc-pV5Z'
]
# my_potential_file_name = basis_set_base_path + 'POTENTIAL'
my_potential_file_name = 'POTENTIAL'
my_potential = 'ALL'
my_project_name = "this_is_template"
my_xyz_file_name = 'H2O.xyz'
my_ri_aux_basis_set = 'RI-5Z' #
organic_elements = [
'H', 'C', 'N', 'O', 'F', 'P', 'S', 'Cl', 'Br', 'B', 'I'
]
my_elements = organic_elements
inp_file_name = 'test_2345.inp'
activate_vdw = False
activate_outer_scf = False
wf_corr_num_proc = 1 # 16 in the ref paper; -1 to use all
########################################### CREATE TEMPLATE FOR TWO RUNS ###########################################
calc = CP2K()
calc.working_directory = './'
calc.project_name = 'artem_gw_project'
calc.mpi_n_processes = 1
# pycp2k objects
CP2K_INPUT = calc.CP2K_INPUT
FORCE_EVAL = CP2K_INPUT.FORCE_EVAL_add()
FORCE_EVAL.Method = 'QUICKSTEP'
SUBSYS = FORCE_EVAL.SUBSYS
DFT = FORCE_EVAL.DFT
XC = DFT.XC
SCF = DFT.SCF
OUTER_SCF = DFT.SCF.OUTER_SCF
####################################################################################################################
# GLOBAL #
# FORCE EVAL #
set_global(CP2K_INPUT, project_name=my_project_name)
#set_force_eval(FORCE_EVAL)
## SUBSYS ##
set_unperiodic_cell(SUBSYS, abc=my_abc)
set_nonperiodic_poisson(DFT)
set_topology(SUBSYS, xyz_file_name=my_xyz_file_name)
# add_elements(SUBSYS,
# elements=elements,
# basis=my_basis_set,
# aux_basis=my_ri_aux_basis_set,
# pot=my_potential)
center_coordinates(SUBSYS)
## END SUBSYS ##
## DFT ##
set_dft(DFT,
potential_file_name=my_potential_file_name,
basis_set_file_name=basis_set_file_name)
set_cutoff(DFT, cutoff=cutoff, rel_cutoff=rel_cutoff, ngrids=5)
set_scf(DFT, eps_scf=1.0E-8, max_scf=500)
add_ot(SCF)
#
# add_outer_scf(OUTER_SCF)
set_pbe(XC) # we start with pbe
# set_pbe0(XC) no pbe0 in the beginning
set_qs(DFT, eps_default=1.0E-10, eps_pgf_orb=np.sqrt(1.0E-10))
# print_mo(DFT.PRINT)
if activate_vdw:
add_vdw(XC, vdw_parameters_file=my_vdw_parameters_file)
## END DFT ##
######################################## END: CREATE TEMPLATE ##########################################################
######################################## BEGIN: RUN CP2K TWO TIMES #####################################################
suffix = ['2', '3', '4', '5'] # of out folde
# begin: input_from_yaml
# cp2k_exe_path = '/home/artem/soft/cp2k/cp2k-7.1/exe/local/cp2k.popt'
cp2k_exe_path = '/home/ws/bh5670/cp2k/cp2k-7.1/exe/local/cp2k.popt'
run_folder = '2345_run_folder'
if not os.path.exists(run_folder):
os.mkdir(run_folder)
my_xyz_file_name = 'H2O.xyz'
my_run_type = 'mpi'
for i_bs, suffix in enumerate(suffix):
# bs
calc_ = deepcopy(calc)
#
CP2K_INPUT_ = calc_.CP2K_INPUT
FORCE_EVAL_ = CP2K_INPUT_.FORCE_EVAL_list[0]
SUBSYS_ = FORCE_EVAL_.SUBSYS
DFT_ = FORCE_EVAL_.DFT
XC_ = DFT_.XC
SCF_ = DFT_.SCF
OUTER_SCF_ = DFT_.SCF.OUTER_SCF
#
set_global(CP2K_INPUT_, project_name=suffix)
add_elements(SUBSYS_,
elements=my_elements,
basis=my_basis_sets[i_bs],
aux_basis=my_ri_aux_basis_set,
pot=my_potential)
# bs
output_file = f'out_{suffix}.out'
ot_file_name = 'OT_' + f'{suffix}_' + inp_file_name
diag_file_name = 'DIAG_' + f'{suffix}_' + inp_file_name
# end: input_from_yaml
# OT run to converge quickly
calc_.write_input_file(run_folder + '/' + ot_file_name)
# first run
print(f"Running PBE with OT (basis set = {suffix})...")
if True:
cp2k_run(input_file=ot_file_name,
xyz_file=my_xyz_file_name,
run_type=my_run_type,
np=threads,
output_file=f'out_ot_{suffix}.out',
cp2k_executable=cp2k_exe_path,
execution_directory=run_folder)
# end: first run
print(f"I have finished cp2k with OT (basis set = {suffix})")
# remove the OT method
remove_ot(SCF_)
# change calculations to a diagonalization
add_diagonalization(SCF_)
# add_smear(SCF) # add or not?
# add_mixing(SCF) # add or not?
# add_mos(SCF) # add or not?
# plot h**o/lumo
set_pbe0(XC_) # we want G-W0@PBE0. no pbe0 in the beginning
print_mo_cubes(DFT_.PRINT, nhomo=10,
nlumo=10) # all HOMOs are typicall plotted
set_scf(DFT_, eps_scf=1E-6)
# add G0W0!
add_gw_ver_0(
XC_,
ev_sc_iter=1,
wf_corr_num_proc=wf_corr_num_proc,
rpa_num_quad_points=100,
) # GW!
# DIAGONALIZATION RUN to reliably compute H**O and then GW
calc_.write_input_file(run_folder + '/' + diag_file_name)
# second run
print(f"Running G0W0 with DIAG (basis set = {suffix})...")
my_out_file2 = f'out_diag_{suffix}.out'
if True:
cp2k_run(input_file=diag_file_name,
xyz_file=my_xyz_file_name,
output_file=my_out_file2,
run_type=my_run_type,
np=threads,
cp2k_executable=cp2k_exe_path,
execution_directory=run_folder)
print(f"I have finished cp2k with DIAG (basis set = {suffix})")
# extract h**o/lumo and gw h**o/lumo from the cp2k output file:
path_to_out2_file = run_folder + '/' + my_out_file2
try:
homos, lumos = [], []
homos, lumos = return_homo_lumo(path_to_out2_file)
print('basis set = {suffix} ', 'h**o = ',
homos[-1] * eV_to_Hartree(), ' eV')
print('basis set = {suffix} ', 'lumo = ',
lumos[0] * eV_to_Hartree(), ' eV')
gw_occ, gw_vir = return_gw_energies(path_to_out2_file)
print('basis set = {suffix} ', 'gw h**o = ', gw_occ, ' eV')
print('basis set = {suffix} ', 'gw lumo = ', gw_vir, ' eV')
except:
print("H**O/LUMO and GW were not extracted")
print("\nI am done")
del calc_
def main():
# My input #
# rel_cutoff: 40; cutoff: 300; abc = 10
my_abc = '10.0 10.0 10.0'
cutoff = 300
rel_cutoff = 40
## base settings ##
basis_set_base_path = '/home/artem/soft/cp2k/cp2k-7.1/data/'
# my_basis_set_file_name = basis_set_base_path + 'BASIS_RI_cc-TZ'G
my_basis_set_file_name = basis_set_base_path + 'BASIS_def2_QZVP_RI_ALL'
my_vdw_parameters_file = basis_set_base_path + 'dftd3.dat'
my_basis_set = 'def2-QZVP'
my_potential_file_name = basis_set_base_path + 'POTENTIAL'
my_potential = 'ALL'
my_project_name = "methane_GW_PBE"
my_xyz_file_name = 'methane.xyz'
my_ri_aux_basis_set = 'RI-5Z' #
# organic_elements = ['H', 'C', 'N', 'O', 'F', 'P', 'S', 'Cl', 'Br', 'B', 'I']
# my_elements = ['H', 'O'] # for test
# my_element = ['H'] # for test
my_elements = ['H', 'C']
inp_file_name = 'GW_PBE_for_methane.inp'
activate_vdw = False
activate_outer_scf = False
activate_ot = False
activate_diagonalization = not activate_outer_scf
wf_corr_num_proc = 4 # 16 in the ref paper; -1 to use all
####################################################################################################################
calc = CP2K()
calc.working_directory = './'
calc.project_name = 'artem_gw_project'
calc.mpi_n_processes = 1
# pycp2k objects
CP2K_INPUT = calc.CP2K_INPUT
FORCE_EVAL = CP2K_INPUT.FORCE_EVAL_add()
FORCE_EVAL.Method = 'QUICKSTEP'
SUBSYS = FORCE_EVAL.SUBSYS
DFT = FORCE_EVAL.DFT
XC = DFT.XC
SCF = DFT.SCF
OUTER_SCF = DFT.SCF.OUTER_SCF
####################################################################################################################
# GLOBAL #
# FORCE EVAL #
set_global(CP2K_INPUT, project_name=my_project_name)
#set_force_eval(FORCE_EVAL)
## SUBSYS ##
set_unperiodic_cell(SUBSYS, abc=my_abc)
set_nonperiodic_poisson(DFT)
set_topology(SUBSYS, xyz_file_name=my_xyz_file_name)
add_elements(SUBSYS,
elements=my_elements,
basis=my_basis_set,
aux_basis=my_ri_aux_basis_set,
pot=my_potential)
center_coordinates(SUBSYS)
## END SUBSYS ##
## DFT ##
set_dft(DFT,
potential_file_name=my_potential_file_name,
basis_set_file_name=my_basis_set_file_name)
set_cutoff(DFT, cutoff=cutoff, rel_cutoff=rel_cutoff, ngrids=5)
set_scf(DFT, eps_scf=1.0E-10)
if activate_ot:
add_ot(SCF)
else:
add_diagonalization(SCF)
add_smear(SCF)
add_mixing(SCF)
add_mos(SCF)
#
add_outer_scf(OUTER_SCF)
set_pbe(XC) # alter: set_pb0, etc.
set_qs(DFT, eps_default=1.0E-15, eps_pgf_orb=1.0E-200)
add_gw_ver_0(XC) # GW!
print_mo_cubes(DFT.PRINT)
print_mo(DFT.PRINT)
if activate_vdw:
add_vdw(XC, vdw_parameters_file=my_vdw_parameters_file)
## END DFT ##
########################################################################################################################
calc.write_input_file(inp_file_name)
# calc.run()
print("I am done")
from pycp2k import CP2K
from ase.lattice.cubic import Diamond
from ase.visualize import view
#===============================================================================
# Create the Si lattice here
lattice = Diamond(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
symbol='Si',
latticeconstant=5.430697500,
size=(1, 1, 1))
# view(lattice)
#===============================================================================
# Setup directories and mpi
calc = CP2K()
calc.working_directory = "./"
calc.project_name = "si_bulk"
calc.mpi_n_processes = 2
#===============================================================================
# Create shortcuts for the most used subtrees of the input
CP2K_INPUT = calc.CP2K_INPUT
GLOBAL = CP2K_INPUT.GLOBAL
FORCE_EVAL = CP2K_INPUT.FORCE_EVAL_add()
SUBSYS = FORCE_EVAL.SUBSYS
DFT = FORCE_EVAL.DFT
SCF = DFT.SCF
#===============================================================================
# Fill input tree
def main():
general_sim_folder = 'sim'
database_file = 'db'
my_offset = 10 # from the molecule to a vacuum. 15-20 is recommended!
# it has to exist
dummy_run = False # does not invoke cp2k if true
# parser begin
parser = argparse.ArgumentParser(description='rank and num of cpus')
parser.add_argument('-rank') # array job number
parser.add_argument('-num_cpus') # number of cpus you request for every array job
args = parser.parse_args()
# parser end
# My input #
threads = args.num_cpus # cpus used to compute
rank = '{:0>6}'.format(args.rank)
original_xyz_file_name = f'dsgdb9nsd_{rank}.xyz'
db_xyz_file = f'dsgdb9nsd/{original_xyz_file_name}'
sim_folder = f'{general_sim_folder}/{rank}'
sim_folder_scratch = f'/scratch/bh5670/{rank}'
if not os.path.exists(sim_folder):
os.mkdir(sim_folder)
if not os.path.exists(sim_folder_scratch):
os.mkdir(sim_folder_scratch)
# use scratch
sim_folder = sim_folder_scratch
#
# xyz object, normal xyz file
my_xyz_file_obj = XYZ.from_file(db_xyz_file) # home
my_xyz_file_to_write = sim_folder + '/' + original_xyz_file_name # home
my_xyz_file_obj.write(my_xyz_file_to_write) # this written file will be called
my_xyz_file = original_xyz_file_name # just a name
# scratch
my_xyz_file_to_write_to_scratch = sim_folder_scratch + '/' + original_xyz_file_name
my_xyz_file_obj.write(my_xyz_file_to_write_to_scratch) # writes to scratch
# End: My input_from_yaml
# DB
my_new_mol = Cp2kOutput(rank)
# rel_cutoff: 40; cutoff: 300; abc = 10
my_abc = str(my_xyz_file_obj.compute_box_size(offset=my_offset))[1:-2]
print(my_abc)
cutoff = 300
rel_cutoff = 40
# GLOBAL SETTINGS
#
## base settings ##
#my_basis_set_file_name = basis_set_base_path + 'BASIS_def2_QZVP_RI_ALL'
basis_set_file_name = 'BASIS_CC_AUG_RI' # RI5, 2-5 cc, all aug-cc
my_vdw_parameters_file = 'dftd3.dat'
# my_basis_sets = ['cc-pVDZ', 'cc-pVTZ', 'cc-pVQZ', 'cc-pV5Z']
my_basis_sets = ['aug-cc-pVDZ', 'aug-cc-pVTZ', 'aug-cc-pVQZ', 'aug-cc-pV5Z']
# my_potential_file_name = basis_set_base_path + 'POTENTIAL'
my_potential_file_name = 'POTENTIAL'
my_potential = 'ALL'
my_project_name = "this_is_template"
my_ri_aux_basis_set = 'RI-5Z' #
organic_elements = ['H', 'C', 'N', 'O', 'F', 'P', 'S', 'Cl', 'Br', 'B', 'I']
my_elements = organic_elements
inp_file_name = 'test_2345.inp'
activate_vdw = False
activate_outer_scf = False
wf_corr_num_proc = 1 # 16 in the ref paper; -1 to use all
########################################### CREATE TEMPLATE FOR TWO RUNS ###########################################
calc = CP2K()
calc.working_directory = './'
calc.project_name = 'artem_gw_project'
calc.mpi_n_processes = 1
# pycp2k objects
CP2K_INPUT = calc.CP2K_INPUT
FORCE_EVAL = CP2K_INPUT.FORCE_EVAL_add()
FORCE_EVAL.Method = 'QUICKSTEP'
SUBSYS = FORCE_EVAL.SUBSYS
DFT = FORCE_EVAL.DFT
XC = DFT.XC
SCF = DFT.SCF
OUTER_SCF = DFT.SCF.OUTER_SCF
####################################################################################################################
# GLOBAL #
# FORCE EVAL #
set_global(CP2K_INPUT, project_name=my_project_name)
#set_force_eval(FORCE_EVAL)
## SUBSYS ##
set_unperiodic_cell(SUBSYS, abc=my_abc)
set_nonperiodic_poisson(DFT)
set_topology(SUBSYS, xyz_file_name=my_xyz_file)
# add_elements(SUBSYS,
# elements=elements,
# basis=my_basis_set,
# aux_basis=my_ri_aux_basis_set,
# pot=my_potential)
center_coordinates(SUBSYS)
## END SUBSYS ##
## DFT ##
set_dft(DFT,
potential_file_name=my_potential_file_name,
basis_set_file_name=basis_set_file_name)
set_cutoff(DFT, cutoff=cutoff, rel_cutoff=rel_cutoff, ngrids=5)
set_scf(DFT, eps_scf=1.0E-10, max_scf=500)
add_ot(SCF)
#
# add_outer_scf(OUTER_SCF)
set_pbe(XC) # we start with pbe
# set_pbe0(XC) no pbe0 in the beginning
set_qs(DFT,
eps_default=1.0E-10,
eps_pgf_orb=np.sqrt(1.0E-10))
# print_mo(DFT.PRINT)
if activate_vdw:
add_vdw(XC, vdw_parameters_file=my_vdw_parameters_file)
## END DFT ##
######################################## END: CREATE TEMPLATE ##########################################################
######################################## BEGIN: RUN CP2K TWO TIMES #####################################################
suffix = ['2', '3', '4'] # of out folde
# begin: input
# cp2k_exe_path = '/home/artem/soft/cp2k/cp2k-7.1/exe/local/cp2k.popt'
cp2k_exe_path = '/home/ws/bh5670/cp2k/cp2k-7.1/exe/local/cp2k.popt'
my_run_type = 'mpi'
for i_bs, suffix in enumerate(suffix):
# bs
calc_ = deepcopy(calc)
#
CP2K_INPUT_ = calc_.CP2K_INPUT
FORCE_EVAL_ = CP2K_INPUT_.FORCE_EVAL_list[0]
SUBSYS_ = FORCE_EVAL_.SUBSYS
DFT_ = FORCE_EVAL_.DFT
XC_ = DFT_.XC
SCF_ = DFT_.SCF
OUTER_SCF_ = DFT_.SCF.OUTER_SCF
#
set_global(CP2K_INPUT_, project_name=suffix)
add_elements(SUBSYS_,
elements=my_elements,
basis=my_basis_sets[i_bs],
aux_basis=my_ri_aux_basis_set,
pot=my_potential)
# bs
output_file = f'out_{suffix}.out'
ot_file_name = 'OT_' + f'{suffix}_' + inp_file_name
diag_file_name = 'DIAG_' + f'{suffix}_' + inp_file_name
# end: input
# OT run to converge quickly
calc_.write_input_file(sim_folder + '/' + ot_file_name)
# first run
print(f"Running PBE with OT (basis set = {suffix})...")
if not dummy_run:
cp2k_run(input_file=ot_file_name,
xyz_file=my_xyz_file,
run_type=my_run_type,
np=threads,
output_file=f'out_ot_{suffix}.out',
cp2k_executable=cp2k_exe_path,
execution_directory=sim_folder)
# end: first run
print(f"I have finished cp2k with OT (basis set = {suffix})")
# remove the OT method
remove_ot(SCF_)
# change calculations to a diagonalization
add_diagonalization(SCF_)
add_smear(SCF_) # add or not?
add_mixing(SCF_) # add or not?
add_mos(SCF_) # add or not?
# plot h**o/lumo
set_pbe0(XC_) # we want G-W0@PBE0. no pbe0 in the beginning
print_mo_cubes(DFT_.PRINT, nhomo=10, nlumo=10) # all HOMOs are typicall plotted
set_scf(DFT_, eps_scf=1E-6)
# add G0W0!
add_gw_ver_0(XC_,
ev_sc_iter=1,
wf_corr_num_proc=wf_corr_num_proc,
rpa_num_quad_points=100,
) # GW!
# DIAGONALIZATION RUN to reliably compute H**O and then GW
calc_.write_input_file(sim_folder + '/' + diag_file_name)
# second run
print(f"Running G0W0 with DIAG (basis set = {suffix})...")
my_out_file2 = f'out_diag_{suffix}.out'
if not dummy_run:
cp2k_run(input_file=diag_file_name,
xyz_file=my_xyz_file,
output_file=my_out_file2,
run_type=my_run_type,
np=threads,
cp2k_executable=cp2k_exe_path,
execution_directory=sim_folder)
print(f"I have finished cp2k with DIAG (basis set = {suffix})")
# extract h**o/lumo and gw h**o/lumo from the cp2k output file:
path_to_out2_file = sim_folder + '/' + my_out_file2
try:
num_orb = extract_number_of_independent_orbital_function(path_to_out2_file)
print(f'basis set = {suffix}, number of independent orbital functions: {num_orb}')
except:
print('number of orbatals was not extracted')
num_orb = 'not extracted'
try:
homos, lumos = [], []
homos, lumos = return_homo_lumo(path_to_out2_file)
print(f'basis set = {suffix} ', 'h**o = ', homos[-1]*eV_to_Hartree(), ' eV')
print(f'basis set = {suffix} ', 'lumo = ', lumos[0]*eV_to_Hartree(), ' eV')
h**o = homos[-1]*eV_to_Hartree()
lumo = lumos[0]*eV_to_Hartree()
except:
print(f'H**o/Lumo were not extracted')
h**o = 'not extracted'
lumo = 'not extracted'
try:
gw_occ, gw_vir, homo_, lumo_ = return_gw_energies(path_to_out2_file)
if isinstance(h**o, str) or isinstance(lumo, str):
h**o = homo_
lumo = lumo_
print(f'basis set = {suffix} ', 'h**o = ', h**o, ' eV')
print(f'basis set = {suffix} ', 'lumo = ', lumo, ' eV')
print(f'basis set = {suffix} ', 'gw h**o = ', gw_occ, ' eV')
print(f'basis set = {suffix} ', 'gw lumo = ', gw_vir, ' eV')
except:
print("GW energies were not extracted")
gw_occ = 'not extracted'
gw_vir = 'not extracted'
del calc_
#
my_new_mol.add_energies(int(suffix), h**o, lumo, gw_occ, gw_vir)
my_new_mol.add_num_orbitals(int(suffix), num_orb)
my_new_mol.extrapolate_energy()
db_record = my_new_mol.yield_dict()
#
print("\nI am done\n")
print('saving to DB...')
with open(f'{database_file}/DB_{rank}.yaml', 'w') as stream:
yaml.safe_dump(db_record, stream)
print(f"saved to DB_{rank}")
def _createNearBlankCP2KObject():
outObj = CP2K()
outObj.working_directory = os.path.abspath(os.getcwd())
outObj.project_name = "cp2k_file"
return outObj
def main():
# My input_from_yaml #
## base settings ##
basis_set_base_path = '/home/artem/soft/cp2k/cp2k-7.1/data/'
my_abc = '16.0 16.0 16.0'
# my_basis_set_file_name = basis_set_base_path + 'BASIS_RI_cc-TZ'G
my_basis_set_file_name = basis_set_base_path + 'BASIS_def2_QZVP_RI_ALL'
my_vdw_parameters_file = basis_set_base_path + 'dftd3.dat'
my_basis_set = 'def2-QZVP'
my_potential_file_name = basis_set_base_path + 'POTENTIAL'
my_potential = 'ALL'
my_project_name = "methane_GW_PBE"
my_xyz_file_name = 'methane.xyz'
my_ri_aux_basis_set = 'RI-5Z' #
# organic_elements = ['H', 'C', 'N', 'O', 'F', 'P', 'S', 'Cl', 'Br', 'B', 'I']
# elements = ['H', 'O'] # for test
# my_element = ['H'] # for test
my_elements = ['H', 'C']
activate_vdw = False
############################################# pycp2k ###############################################################
calc = CP2K()
calc.working_directory = './'
calc.project_name = 'artem_gw_project'
calc.mpi_n_processes = 1
# pycp2k objects
CP2K_INPUT = calc.CP2K_INPUT
FORCE_EVAL = CP2K_INPUT.FORCE_EVAL_add()
FORCE_EVAL.Method = 'QUICKSTEP'
SUBSYS = FORCE_EVAL.SUBSYS
DFT = FORCE_EVAL.DFT
XC = DFT.XC
SCF = DFT.SCF
################################################ mypycp2k ##########################################################
# GLOBAL #
# FORCE EVAL #
set_global(CP2K_INPUT, project_name=my_project_name)
#set_force_eval(FORCE_EVAL)
## SUBSYS ##
set_unperiodic_cell(SUBSYS, abc=my_abc)
set_nonperiodic_poisson(DFT)
set_topology(SUBSYS, xyz_file_name=my_xyz_file_name)
add_elements(SUBSYS,
elements=my_elements,
basis=my_basis_set,
aux_basis=my_ri_aux_basis_set,
pot=my_potential)
center_coordinates(SUBSYS)
## END SUBSYS ##
## DFT ##
set_dft(DFT,
potential_file_name=my_potential_file_name,
basis_set_file_name=my_basis_set_file_name)
set_cutoff(DFT, cutoff=900, rel_cutoff=100, ngrids=5)
set_scf(DFT, max_scf=1)
add_ot(SCF)
set_pbe(XC) # alter: set_pb0, etc.
set_qs(DFT,
eps_default=1.0E-15,
eps_pgf_orb=1.0E-200)
# add_gw_ver_0(XC) # GW!
#print_mo_cubes(DFT.PRINT)
#print_mo(DFT.PRINT)
if activate_vdw:
add_vdw(XC, vdw_parameters_file=my_vdw_parameters_file)
## END DFT ##
############################################### CHECK CONVERGENCE ######################################################
my_target_accuracy_eV = 1.E-3
if True:
my_abcs = [8, 10, 12, 14, 16]
my_cutoff = [100, 200, 300, 400, 500, 600, 700, 800, 900]
my_rel_cutoff = [20, 40, 60, 70, 80, 90, 100]
if False:
my_abcs = [6, 8, 10]
my_cutoff = [100, 200, 300]
my_rel_cutoff = [40, 50, 60]
print(f"Reference parameters are: \n "
f"cutoff = {calc.CP2K_INPUT.FORCE_EVAL_list[0].DFT.MGRID.Cutoff},\n "
f"rel_cut = {calc.CP2K_INPUT.FORCE_EVAL_list[0].DFT.MGRID.Rel_cutoff},\n "
f"abc = {calc.CP2K_INPUT.FORCE_EVAL_list[0].SUBSYS.CELL.Abc}\n")
# check abc (cell size) convergence
general_convergence(calc=copy.deepcopy(calc),
params=my_abcs,
func_to_accept_param=change_calc_abc,
target_accuracy_eV=my_target_accuracy_eV,
param_name='abc')
# check cutoff (absolute) convergence
general_convergence(calc=copy.deepcopy(calc),
params=my_cutoff,
func_to_accept_param=change_calc_cutoff,
target_accuracy_eV=my_target_accuracy_eV,
param_name='cutoff')
# check cutoff (relative) convergence
general_convergence(calc=copy.deepcopy(calc),
params=my_rel_cutoff,
func_to_accept_param=change_calc_rel_cutoff,
target_accuracy_eV=my_target_accuracy_eV,
param_name='rel_cutoff')
def main():
# My input #
# rel_cutoff: 40; cutoff: 300; abc = 10
my_abc = '10.0 10.0 10.0'
cutoff = 300
rel_cutoff = 40
## base settings ##
basis_set_base_path = '/home/artem/soft/cp2k/cp2k-7.1/data/'
# my_basis_set_file_name = basis_set_base_path + 'BASIS_RI_cc-TZ'G
my_basis_set_file_name = basis_set_base_path + 'BASIS_def2_QZVP_RI_ALL'
my_vdw_parameters_file = basis_set_base_path + 'dftd3.dat'
my_basis_set = 'def2-QZVP'
my_potential_file_name = basis_set_base_path + 'POTENTIAL'
my_potential = 'ALL'
my_project_name = "methane_GW_PBE"
my_xyz_file_name = 'methane.xyz'
my_ri_aux_basis_set = 'RI-5Z' #
# organic_elements = ['H', 'C', 'N', 'O', 'F', 'P', 'S', 'Cl', 'Br', 'B', 'I']
# my_elements = ['H', 'O'] # for test
# my_element = ['H'] # for test
my_elements = ['H', 'C']
inp_file_name = 'GW_PBE_for_methane.inp'
activate_vdw = False
activate_outer_scf = False
wf_corr_num_proc = 4 # 16 in the ref paper; -1 to use all
########################################### CREATE TEMPLATE FOR TWO RUNS ###########################################
calc = CP2K()
calc.working_directory = './'
calc.project_name = 'artem_gw_project'
calc.mpi_n_processes = 1
# pycp2k objects
CP2K_INPUT = calc.CP2K_INPUT
FORCE_EVAL = CP2K_INPUT.FORCE_EVAL_add()
FORCE_EVAL.Method = 'QUICKSTEP'
SUBSYS = FORCE_EVAL.SUBSYS
DFT = FORCE_EVAL.DFT
XC = DFT.XC
SCF = DFT.SCF
OUTER_SCF = DFT.SCF.OUTER_SCF
####################################################################################################################
# GLOBAL #
# FORCE EVAL #
set_global(CP2K_INPUT, project_name=my_project_name)
#set_force_eval(FORCE_EVAL)
## SUBSYS ##
set_unperiodic_cell(SUBSYS, abc=my_abc)
set_nonperiodic_poisson(DFT)
set_topology(SUBSYS, xyz_file_name=my_xyz_file_name)
add_elements(SUBSYS,
elements=my_elements,
basis=my_basis_set,
aux_basis=my_ri_aux_basis_set,
pot=my_potential)
center_coordinates(SUBSYS)
## END SUBSYS ##
## DFT ##
set_dft(DFT,
potential_file_name=my_potential_file_name,
basis_set_file_name=my_basis_set_file_name)
set_cutoff(DFT, cutoff=cutoff, rel_cutoff=rel_cutoff, ngrids=5)
set_scf(DFT, eps_scf=1.0E-10)
add_ot(SCF)
#
add_outer_scf(OUTER_SCF)
set_pbe(XC) # alter: set_pb0, etc.
set_qs(DFT, eps_default=1.0E-15, eps_pgf_orb=1.0E-200)
# add_gw_ver_0(XC) # GW!
print_mo_cubes(DFT.PRINT, nhomo=10,
nlumo=10) # all HOMOs are typicall plotted
# print_mo(DFT.PRINT)
if activate_vdw:
add_vdw(XC, vdw_parameters_file=my_vdw_parameters_file)
## END DFT ##
######################################## END: CREATE TEMPLATE ##########################################################
# begin: input
cp2k_exe_path = '/home/artem/soft/cp2k/cp2k-7.1/exe/local/cp2k.popt'
run_folder = 'my_run_folder'
output_file = 'out.out'
ot_file_name = 'OT_' + inp_file_name
diag_file_name = 'DIAG_' + inp_file_name
my_xyz_file_name = 'methane.xyz'
threads = 4
my_run_type = 'mpi'
# end: input
if not os.path.exists(run_folder):
os.mkdir(run_folder)
# OT run to converge quickly
calc.write_input_file(run_folder + '/' + ot_file_name)
# first run
print("Running cp2k with OT ...")
cp2k_run(input_file=ot_file_name,
xyz_file=my_xyz_file_name,
run_type=my_run_type,
np=threads,
output_file='out1.out',
cp2k_executable=cp2k_exe_path,
execution_directory=run_folder)
# end: first run
print("I have finished cp2k with OT")
# remove the OT method
remove_ot(SCF)
# change calculations to a diagonalization
add_diagonalization(SCF)
add_smear(SCF)
add_mixing(SCF)
add_mos(SCF)
# DIAGONALIZATION RUN to reliably compute H**O
calc.write_input_file(run_folder + '/' + diag_file_name)
# second run
print("Running cp2k with DIAG ...")
my_out_file2 = 'out2.out'
cp2k_run(input_file=diag_file_name,
xyz_file=my_xyz_file_name,
output_file=my_out_file2,
run_type=my_run_type,
np=threads,
cp2k_executable=cp2k_exe_path,
execution_directory=run_folder)
print("I have finished cp2k with DIAG")
homos, lumos = [], []
homos, lumos = return_homo_lumo(run_folder + '/' + my_out_file2)
print('h**o = ', homos[-1] * eV_to_Hartree(), ' eV')
print('lumo = ', lumos[0] * eV_to_Hartree(), ' eV')
print("\nI am done")