def my_cp2k_run(suf='2', ot_or_diag='ot'):
cp2k_run(input_file=my_inp_file(suf, ot_or_diag),
output_file=my_out_file(suf, ot_or_diag),
xyz_file=xyz_file_name,
run_type=my_run_type,
np=threads,
cp2k_executable=cp2k_exe_path,
execution_directory=sim_folder_scratch,
type_mpi=mpi)
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():
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}")
from cp2k_run.cp2k_run import cp2k_run
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()
parser = argparse.ArgumentParser(description='rank and num of cpus')
parser.add_argument('-rank')
parser.add_argument('-num_cpus')
args = parser.parse_args()
print(f'the following argument is passed: {args.rank}')
print('Now I will be doing cp2k...')
run_folder = f'{args.rank}' # will be created to copy there input_from_yaml file and run cp2k
if not os.path.exists(run_folder):
os.mkdir(run_folder)
cp2k_run(
cp2k_executable='cp2k.popt',
run_type='mpi',
np=args.num_cpus,
xyz_file='input_from_yaml.inp',
output_file=f'out_{args.rank}.out',
error_file=f'err_{args.rank}.err',
execution_directory=f'{args.rank}',
)
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")
def main():
scratch = os.environ['SCRATCH'] # SCRATCH has to be in the env var dict. Normally, it is.
# 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
parser.add_argument('-i') # input_from_yaml yaml file
args = parser.parse_args()
# parser end
# yaml file
yaml_file_name = args.i
with open(yaml_file_name) as stream:
input = yaml.load(stream=stream)
# end: yaml file
# todo: think over because it is imported twice
# end: run-or-check settings
debug = input['debug']
dummy_run = input['dummy_run']
# if not at cluster: test
# debug = True
# dummy_run = True
# end: if not at cluster
# folders names
sim = input['folder_names']['simulations']
db = input['folder_names']['database']
bh5670 = input['folder_names'][
'scratch'] # the outermost folder in the scratch folder where all other data are put
prefix_xyz_file_name = input['prefix_xyz_file_name']
my_offset = input['molecule_vacuum_offset']
try:
type_mpi = input['mpi']
except:
type_mpi = 'openmpi'
# parsing input_from_yaml
threads = int(args.num_cpus) # cpus used to compute. I do not subtract 1. This does not help
rank = '{:0>6}'.format(args.rank) # transform rank from '1' to '000001' format. This is not a general thing
xyz_file_name = f'{prefix_xyz_file_name}_{rank}.xyz'
xyz_file_location = f'{prefix_xyz_file_name}/{xyz_file_name}'
db_record_path = f'{db}/DB_{rank}.yaml' # file where the results will be saved todo: raeum es alles auf!
# check is the output exists
if os.path.exists(db_record_path):
print(f'The simulation results of mol. {rank} is already in the folder of reference')
exit()
# end: check if the output exists
if True: #not dummy_run:
sim_folder_scratch = f'{scratch}/{bh5670}/{sim}/{rank}'
else:
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
try:
my_xyz_file_obj = XYZ.from_file(xyz_file_location) # object created using the file from home
except: # test
my_xyz_file_obj = XYZ.from_file('H2O.xyz') # 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]
input['my_abc'] = my_abc
input['xyz_file_name'] = xyz_file_name
# misc
wf_corr_num_proc = 0 # 16 in the ref paper; -1 to use all
inp_file_name = 'test_2344.inp' # base file name
######################################## 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'
cp2k_exe_path = input['cp2k_exe_path']
my_run_type = 'mpi'
suffix = input['basis_set_suffix'] # todo: fix DZ --> 2, TZ --> 3, QZ --> 4
InputFactory.set_constants(input_from_yaml=input)
for i_bs, suffix in enumerate(suffix):
# start: ot dft
# I/O
output_file = f'out_{suffix}.out'
ot_file_name = 'OT_' + f'{suffix}_' + inp_file_name # for DFT (OT)
diag_file_name = 'DIAG_' + f'{suffix}_' + inp_file_name # for GW (DIAG)
# end: I/O
# OT dft simulation to converge quickly: create the simulation object
dft_ot_simulation = InputFactory.new_dft_ot(i_bs)
# OT dft: write input file
dft_ot_simulation.write_input_file(sim_folder_scratch + '/' + ot_file_name)
# OT dft run below ...
# ... but before, we copy the RESTART from the previous basis set (it exists unless for the smallest basis set)
if i_bs != 0:
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:
pass
#
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,
type_mpi=type_mpi)
# end: first run
print(f"I have finished cp2k with OT (basis set = {suffix})")
# DIAGONALIZATION RUN to reliably compute H**O and then GW
# gw: create the simulation object
gw_diag_simulations = InputFactory.new_gw(i_bs)
# gw: write the input file
gw_diag_simulations.write_input_file(sim_folder_scratch + '/' + diag_file_name)
# gw 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,
type_mpi=type_mpi)
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
# the method to extract?
# 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 orbitals 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 dft_ot_simulation, gw_diag_simulations
# 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() # level up?
db_record = my_new_mol.yield_dict() # this dict will be written into yaml. it will be a record in the global library
#
######################################## END: RUN CP2K TWO TIMES #######################################################
print("\nI am done\n")
if not dummy_run:
print('saving to DB...')
with open(f'{db}/DB_{rank}.yaml', 'w') as stream:
yaml.safe_dump(db_record, stream)
print(f"saved to {db}/DB_{rank}.yaml")
print('I will remove the content of 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, dirs_exist_ok=True) # 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
try:
copytree(sim_folder_scratch, sim_folder_home) # will rewrite the folder?
print(f"I have copied {sim_folder_scratch} to {sim_folder_home}")
except:
print(f"I could not copy {sim_folder_scratch} to {sim_folder_home}")
try_to_remove_folder(sim_folder_scratch)