def optimize_molecule(molecule, functional, length, dir):
molecule.save('mol_unopt_coord.xyz', overwrite='True')
with open('mol_unopt_coord.xyz', 'r') as fin:
data = fin.read().splitlines(True)
with open('mol_unopt_coord.xyz', 'w') as fout:
fout.writelines(data[2:])
molecule = molecule.to_parmed()
atom_list, mass_list, total_mass = info_molecule(molecule)
unique_atom_list = remove_duplicate(atom_list)
num_atoms = len(atom_list)
num_unique_atoms = len(unique_atom_list)
mySim = sim.SIM()
mySim.GLOBAL.RUN_TYPE = "GEO_OPT"
mySim.GLOBAL.PROJECT = "molecule_opt"
mySim.GLOBAL.PRINT_LEVEL = "LOW"
#FORCE EVAL SECTION
mySim.FORCE_EVAL.METHOD = 'QUICKSTEP'
mySim.FORCE_EVAL.SUBSYS.CELL.ABC = '{L} {L} {L}'.format(L=length)
mySim.FORCE_EVAL.SUBSYS.COORD.DEFAULT_KEYWORD = 'mol_unopt_coord.xyz'
mySim.FORCE_EVAL.SUBSYS.init_atoms(num_atoms)
for i in range(num_unique_atoms):
mySim.FORCE_EVAL.SUBSYS.KIND[
i + 1].SECTION_PARAMETERS = unique_atom_list[i]
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].BASIS_SET = basis_set(
unique_atom_list[i])
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].POTENTIAL = potential(
unique_atom_list[i], functional)
mySim.FORCE_EVAL.DFT.BASIS_SET_FILE_NAME = dir + 'BASIS_MOLOPT'
mySim.FORCE_EVAL.DFT.POTENTIAL_FILE_NAME = dir + 'GTH_POTENTIALS'
mySim.FORCE_EVAL.DFT.QS.EPS_DEFAULT = 1E-10
mySim.FORCE_EVAL.DFT.MGRID.CUTOFF = 400
mySim.FORCE_EVAL.DFT.MGRID.REL_CUTOFF = 40
mySim.FORCE_EVAL.DFT.MGRID.NGRIDS = 5
mySim.FORCE_EVAL.DFT.XC.XC_FUNCTIONAL.SECTION_PARAMETERS = functional
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.POTENTIAL_TYPE = 'PAIR_POTENTIAL'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.TYPE = 'DFTD3'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.PARAMETER_FILE_NAME = 'dftd3.dat'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.REFERENCE_FUNCTIONAL = functional
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.R_CUTOFF = 11
mySim.FORCE_EVAL.DFT.SCF.SCF_GUESS = 'ATOMIC'
mySim.FORCE_EVAL.DFT.SCF.MAX_SCF = 200
mySim.FORCE_EVAL.DFT.SCF.EPS_SCF = 1E-6
mySim.MOTION.GEO_OPT.TYPE = 'MINIMIZATION'
mySim.MOTION.GEO_OPT.OPTIMIZER = 'BFGS'
mySim.MOTION.GEO_OPT.MAX_ITER = 200
mySim.MOTION.GEO_OPT.MAX_DR = 1e-3
mySim.MOTION.CONSTRAINT.FIXED_ATOMS.LIST = '1'
mySim.write_changeLog(fn="mol_opt-changeLog.out")
mySim.write_errorLog()
mySim.write_inputFile(fn='mol_opt.inp')
import sys sys.setrecursionlimit(10000) from cssi_cp2k.classes import SIM as sim mySim = sim.SIM() mySim.GLOBAL.RUN_TYPE = "MD" mySim.GLOBAL.PROJECT = "iodine-liquid" mySim.GLOBAL.PRINT_LEVEL = "LOW" #FORCE EVAL SECTION mySim.FORCE_EVAL.METHOD='QUICKSTEP' mySim.FORCE_EVAL.STRESS_TENSOR='ANALYTICAL'; mySim.FORCE_EVAL.DFT.BASIS_SET_FILE_NAME='/home/siepmann/singh891/cp2k-6.1.0/data/BASIS_MOLOPT' mySim.FORCE_EVAL.DFT.POTENTIAL_FILE_NAME='/home/siepmann/singh891/cp2k-6.1.0/data/GTH_POTENTIALS' mySim.FORCE_EVAL.DFT.CHARGE=0 mySim.FORCE_EVAL.DFT.MULTIPLICITY=1 mySim.FORCE_EVAL.DFT.MGRID.CUTOFF=600 mySim.FORCE_EVAL.DFT.MGRID.REL_CUTOFF=60 mySim.FORCE_EVAL.DFT.MGRID.NGRIDS=4 mySim.FORCE_EVAL.DFT.QS.METHOD='GPW' mySim.FORCE_EVAL.DFT.QS.EPS_DEFAULT=1E-10 mySim.FORCE_EVAL.DFT.QS.EXTRAPOLATION='ASPC' mySim.FORCE_EVAL.DFT.POISSON.PERIODIC="XYZ" mySim.FORCE_EVAL.DFT.PRINT.E_DENSITY_CUBE.SECTION_PARAMETERS="OFF" mySim.FORCE_EVAL.DFT.SCF.SCF_GUESS='ATOMIC' mySim.FORCE_EVAL.DFT.SCF.MAX_SCF=30 mySim.FORCE_EVAL.DFT.SCF.EPS_SCF=1E-6
def optimize_molecule(molecule, functional, project_name, dire, temperature,
box_length, number_of_molecules, simulation_time, CUTOFF,
SCF_tolerence, basis_set, ensemble, timestep,
thermostat):
molecule.save('mol_unopt_coord.xyz', overwrite='True')
with open('mol_unopt_coord.xyz', 'r') as fin:
data = fin.read().splitlines(True)
with open('mol_unopt_coord.xyz', 'w') as fout:
fout.writelines(data[2:])
molecule = molecule.to_parmed()
atom_list, mass_list, total_mass = info_molecule(molecule)
unique_atom_list = remove_duplicate(atom_list)
unique_atom_list.sort()
num_atoms = len(atom_list)
num_unique_atoms = len(unique_atom_list)
mySim = sim.SIM()
#setting defaults
if basis_set[0] == None:
basis_set = basis_set * num_unique_atoms
if thermostat == None:
thermostat = 'NOSE'
if CUTOFF == None:
CUTOFF = 900
if SCF_tolerence == None:
SCF_tolerence = 1e-6
if ensemble == None:
ensemble = 'NVT'
mySim.GLOBAL.RUN_TYPE = "GEO_OPT"
mySim.GLOBAL.PROJECT = "molecule_opt"
mySim.GLOBAL.PRINT_LEVEL = "LOW"
#FORCE EVAL SECTION
mySim.FORCE_EVAL.METHOD = 'QUICKSTEP'
mySim.FORCE_EVAL.SUBSYS.CELL.ABC = '{L} {L} {L}'.format(L=2 * 10 *
box_length)
mySim.FORCE_EVAL.SUBSYS.COORD.DEFAULT_KEYWORD = 'mol_unopt_coord.xyz'
mySim.FORCE_EVAL.SUBSYS.init_atoms(num_atoms)
for i in range(num_unique_atoms):
mySim.FORCE_EVAL.SUBSYS.KIND[
i + 1].SECTION_PARAMETERS = unique_atom_list[i]
if basis_set[i] == None:
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].BASIS_SET = basis_set_setter(
unique_atom_list[i])
else:
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].BASIS_SET = basis_set[i]
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].POTENTIAL = potential(
unique_atom_list[i], functional)
mySim.FORCE_EVAL.DFT.BASIS_SET_FILE_NAME = dire + 'BASIS_MOLOPT'
mySim.FORCE_EVAL.DFT.POTENTIAL_FILE_NAME = dire + 'GTH_POTENTIALS'
mySim.FORCE_EVAL.DFT.QS.EPS_DEFAULT = 1E-10
mySim.FORCE_EVAL.DFT.MGRID.CUTOFF = CUTOFF
mySim.FORCE_EVAL.DFT.MGRID.REL_CUTOFF = 50
mySim.FORCE_EVAL.DFT.MGRID.NGRIDS = 5
mySim.FORCE_EVAL.DFT.XC.XC_FUNCTIONAL.SECTION_PARAMETERS = functional
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.POTENTIAL_TYPE = 'PAIR_POTENTIAL'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.TYPE = 'DFTD3'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.PARAMETER_FILE_NAME = 'dftd3.dat'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.REFERENCE_FUNCTIONAL = functional
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.R_CUTOFF = 11
mySim.FORCE_EVAL.DFT.SCF.SCF_GUESS = 'ATOMIC'
mySim.FORCE_EVAL.DFT.SCF.MAX_SCF = 200
mySim.FORCE_EVAL.DFT.SCF.EPS_SCF = SCF_tolerence
mySim.MOTION.GEO_OPT.TYPE = 'MINIMIZATION'
mySim.MOTION.GEO_OPT.OPTIMIZER = 'BFGS'
mySim.MOTION.GEO_OPT.MAX_ITER = 2
mySim.MOTION.GEO_OPT.MAX_DR = 1e-3
mySim.MOTION.CONSTRAINT.FIXED_ATOMS.LIST = '1'
mySim.write_changeLog(fn="mol_opt-changeLog.out")
mySim.write_errorLog()
mySim.write_inputFile(fn='mol_opt.inp')
def run_md_main(molecule, functional, project_name, dire, temperature,
box_length, number_of_molecules, simulation_time, CUTOFF,
SCF_tolerence, basis_set, ensemble, timestep, thermostat):
current_molecule = mb.clone(molecule)
current_molecule = current_molecule.to_parmed()
atom_list, mass_list, total_mass = info_molecule(current_molecule)
unique_atom_list = remove_duplicate(atom_list)
num_atoms = len(atom_list)
num_unique_atoms = len(unique_atom_list)
total_atoms = num_atoms * number_of_molecules
string = "tail -{} {}-pos-1.xyz > {}.xyz".format(total_atoms,
project_name + "pre",
project_name)
subprocess.call(string, shell=True)
if basis_set[0] == None:
basis_set = basis_set * num_unique_atoms
if thermostat == None:
thermostat = 'NOSE'
if CUTOFF == None:
CUTOFF = 900
if SCF_tolerence == None:
SCF_tolerence = 1e-6
if ensemble == None:
ensemble = 'NVT'
#we need to decide time_step
if timestep == None:
lightest = min(mass_list)
if lightest < 1.5:
time_step = 0.5
elif (lightest >= 1.5) and (lightest < 40):
time_step = 1
if lightest >= 40:
time_step = 1.5
steps = round(simulation_time * 1000 / time_step)
mySim = sim.SIM()
mySim.GLOBAL.RUN_TYPE = "MD"
mySim.GLOBAL.PROJECT = project_name
mySim.GLOBAL.PRINT_LEVEL = "LOW"
#FORCE EVAL SECTION
mySim.FORCE_EVAL.METHOD = 'QUICKSTEP'
mySim.FORCE_EVAL.STRESS_TENSOR = 'ANALYTICAL'
mySim.FORCE_EVAL.DFT.BASIS_SET_FILE_NAME = dire + 'BASIS_MOLOPT'
mySim.FORCE_EVAL.DFT.POTENTIAL_FILE_NAME = dire + 'GTH_POTENTIALS'
mySim.FORCE_EVAL.DFT.CHARGE = 0
mySim.FORCE_EVAL.DFT.MULTIPLICITY = 1
mySim.FORCE_EVAL.DFT.MGRID.CUTOFF = CUTOFF
mySim.FORCE_EVAL.DFT.MGRID.REL_CUTOFF = 50
mySim.FORCE_EVAL.DFT.MGRID.NGRIDS = 4
mySim.FORCE_EVAL.DFT.QS.METHOD = 'GPW'
mySim.FORCE_EVAL.DFT.QS.EPS_DEFAULT = 1E-8
mySim.FORCE_EVAL.DFT.QS.EXTRAPOLATION = 'ASPC'
mySim.FORCE_EVAL.DFT.POISSON.PERIODIC = "XYZ"
mySim.FORCE_EVAL.DFT.PRINT.E_DENSITY_CUBE.SECTION_PARAMETERS = "OFF"
mySim.FORCE_EVAL.DFT.SCF.SCF_GUESS = 'ATOMIC'
mySim.FORCE_EVAL.DFT.SCF.MAX_SCF = 2
mySim.FORCE_EVAL.DFT.SCF.EPS_SCF = SCF_tolerence
mySim.FORCE_EVAL.DFT.SCF.OT.SECTION_PARAMETERS = ".TRUE."
mySim.FORCE_EVAL.DFT.SCF.OT.PRECONDITIONER = "FULL_SINGLE_INVERSE"
mySim.FORCE_EVAL.DFT.SCF.OT.MINIMIZER = "DIIS"
mySim.FORCE_EVAL.DFT.SCF.OUTER_SCF.SECTION_PARAMETERS = '.TRUE.'
mySim.FORCE_EVAL.DFT.SCF.OUTER_SCF.MAX_SCF = 2
mySim.FORCE_EVAL.DFT.SCF.OUTER_SCF.EPS_SCF = 1e-6
mySim.FORCE_EVAL.DFT.SCF.PRINT.RESTART.SECTION_PARAMETERS = 'OFF'
mySim.FORCE_EVAL.DFT.SCF.PRINT.DM_RESTART_WRITE = '.TRUE.'
mySim.FORCE_EVAL.DFT.XC.XC_FUNCTIONAL.SECTION_PARAMETERS = functional
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.POTENTIAL_TYPE = 'PAIR_POTENTIAL'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.TYPE = 'DFTD3'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.PARAMETER_FILE_NAME = 'dftd3.dat'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.REFERENCE_FUNCTIONAL = functional
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.R_CUTOFF = 11
mySim.FORCE_EVAL.SUBSYS.COORD.DEFAULT_KEYWORD = project_name + ".xyz"
mySim.FORCE_EVAL.SUBSYS.init_atoms(num_atoms)
for i in range(num_unique_atoms):
mySim.FORCE_EVAL.SUBSYS.KIND[
i + 1].SECTION_PARAMETERS = unique_atom_list[i]
if basis_set[i] == None:
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].BASIS_SET = basis_set_setter(
unique_atom_list[i])
else:
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].BASIS_SET = basis_set[i]
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].POTENTIAL = potential(
unique_atom_list[i], functional)
mySim.FORCE_EVAL.SUBSYS.CELL.ABC = '{L} {L} {L}'.format(L=10 * box_length)
#MOTION SECTION
mySim.MOTION.GEO_OPT.OPTIMIZER = 'BFGS'
mySim.MOTION.GEO_OPT.MAX_ITER = 100
mySim.MOTION.GEO_OPT.MAX_DR = 0.003
mySim.MOTION.MD.ENSEMBLE = ensemble
mySim.MOTION.MD.STEPS = steps
mySim.MOTION.MD.TIMESTEP = time_step
mySim.MOTION.MD.TEMPERATURE = temperature
mySim.MOTION.MD.THERMOSTAT.TYPE = thermostat
mySim.MOTION.MD.THERMOSTAT.REGION = "MASSIVE"
mySim.MOTION.MD.THERMOSTAT.NOSE.LENGTH = 3
mySim.MOTION.MD.THERMOSTAT.NOSE.YOSHIDA = 3
mySim.MOTION.MD.THERMOSTAT.NOSE.TIMECON = 1000.0
mySim.MOTION.MD.THERMOSTAT.NOSE.MTS = 2
#mySim.MOTION.MD.PRINT.ENERGY.EACH.MD = 20
#mySim.MOTION.MD.PRINT.PROGRAM_RUN_INFO.EACH.MD = 20
#mySim.MOTION.MD.AVERAGES.SECTION_PARAMETERS= ".falbmbjse."
mySim.MOTION.PRINT.STRESS.SECTION_PARAMETERS = 'OFF'
mySim.MOTION.PRINT.TRAJECTORY.EACH.MD = 1
mySim.MOTION.PRINT.VELOCITIES.SECTION_PARAMETERS = 'OFF'
mySim.MOTION.PRINT.FORCES.SECTION_PARAMETERS = "OFF"
mySim.MOTION.PRINT.RESTART_HISTORY.SECTION_PARAMETERS = "ON"
mySim.MOTION.PRINT.RESTART_HISTORY.EACH.MD = 500
mySim.MOTION.PRINT.RESTART.SECTION_PARAMETERS = "ON"
mySim.MOTION.PRINT.RESTART.BACKUP_COPIES = 3
mySim.MOTION.PRINT.RESTART.EACH.MD = 1
mySim.write_changeLog(fn="md-main-changeLog.out")
mySim.write_errorLog()
mySim.write_inputFile(fn='md-main.inp')
def run_md_pre(molecule, functional, project_name, dire, temperature,
box_length, number_of_molecules, simulation_time, CUTOFF,
SCF_tolerence, basis_set, ensemble, timestep, thermostat,
table):
current_molecule = mb.clone(molecule)
molecule_pmd = mb.clone(current_molecule)
molecule_pmd = molecule_pmd.to_parmed()
atom_list, mass_list, total_mass = info_molecule(molecule_pmd)
unique_atom_list = remove_duplicate(atom_list)
num_atoms = len(atom_list)
num_unique_atoms = len(unique_atom_list)
unique_atom_list.sort()
box = mb.Box(lengths=[box_length, box_length, box_length])
current_molecule.xyz = table
print(number_of_molecules)
box_of_molecule = mb.fill_box(compound=current_molecule,
n_compounds=number_of_molecules,
box=box)
filename = project_name + ".xyz"
box_of_molecule.save(filename, overwrite=True)
with open(project_name + ".xyz", 'r') as fin:
data = fin.read().splitlines(True)
with open(project_name + ".xyz", 'w') as fout:
fout.writelines(data[2:])
if basis_set[0] == None:
basis_set = basis_set * num_unique_atoms
if thermostat == None:
thermostat = 'NOSE'
if CUTOFF == None:
CUTOFF = 900
if SCF_tolerence == None:
SCF_tolerence = 1e-6
if ensemble == None:
ensemble = 'NVT'
mySim = sim.SIM()
mySim.GLOBAL.RUN_TYPE = "MD"
mySim.GLOBAL.PROJECT = project_name + "pre"
mySim.GLOBAL.PRINT_LEVEL = "LOW"
#FORCE EVAL SECTION
mySim.FORCE_EVAL.METHOD = 'QUICKSTEP'
mySim.FORCE_EVAL.STRESS_TENSOR = 'ANALYTICAL'
mySim.FORCE_EVAL.DFT.BASIS_SET_FILE_NAME = dire + 'BASIS_MOLOPT'
mySim.FORCE_EVAL.DFT.POTENTIAL_FILE_NAME = dire + 'GTH_POTENTIALS'
mySim.FORCE_EVAL.DFT.CHARGE = 0
mySim.FORCE_EVAL.DFT.MULTIPLICITY = 1
mySim.FORCE_EVAL.DFT.MGRID.CUTOFF = CUTOFF
mySim.FORCE_EVAL.DFT.MGRID.REL_CUTOFF = 50
mySim.FORCE_EVAL.DFT.MGRID.NGRIDS = 4
mySim.FORCE_EVAL.DFT.QS.METHOD = 'GPW'
mySim.FORCE_EVAL.DFT.QS.EPS_DEFAULT = 1E-8
mySim.FORCE_EVAL.DFT.QS.EXTRAPOLATION = 'ASPC'
mySim.FORCE_EVAL.DFT.POISSON.PERIODIC = "XYZ"
mySim.FORCE_EVAL.DFT.PRINT.E_DENSITY_CUBE.SECTION_PARAMETERS = "OFF"
mySim.FORCE_EVAL.DFT.SCF.SCF_GUESS = 'ATOMIC'
mySim.FORCE_EVAL.DFT.SCF.MAX_SCF = 2
mySim.FORCE_EVAL.DFT.SCF.EPS_SCF = SCF_tolerence
mySim.FORCE_EVAL.DFT.SCF.OT.SECTION_PARAMETERS = ".TRUE."
mySim.FORCE_EVAL.DFT.SCF.OT.PRECONDITIONER = "FULL_SINGLE_INVERSE"
mySim.FORCE_EVAL.DFT.SCF.OT.MINIMIZER = "DIIS"
mySim.FORCE_EVAL.DFT.SCF.OUTER_SCF.SECTION_PARAMETERS = '.TRUE.'
mySim.FORCE_EVAL.DFT.SCF.OUTER_SCF.MAX_SCF = 10
mySim.FORCE_EVAL.DFT.SCF.OUTER_SCF.EPS_SCF = 1e-6
mySim.FORCE_EVAL.DFT.SCF.PRINT.RESTART.SECTION_PARAMETERS = 'OFF'
mySim.FORCE_EVAL.DFT.SCF.PRINT.DM_RESTART_WRITE = '.TRUE.'
mySim.FORCE_EVAL.DFT.XC.XC_FUNCTIONAL.SECTION_PARAMETERS = functional
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.POTENTIAL_TYPE = 'PAIR_POTENTIAL'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.TYPE = 'DFTD3'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.PARAMETER_FILE_NAME = 'dftd3.dat'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.REFERENCE_FUNCTIONAL = functional
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.R_CUTOFF = 11
mySim.FORCE_EVAL.SUBSYS.COORD.DEFAULT_KEYWORD = project_name + ".xyz"
mySim.FORCE_EVAL.SUBSYS.init_atoms(num_atoms)
for i in range(num_unique_atoms):
mySim.FORCE_EVAL.SUBSYS.KIND[
i + 1].SECTION_PARAMETERS = unique_atom_list[i]
if basis_set[i] == None:
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].BASIS_SET = basis_set_setter(
unique_atom_list[i])
else:
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].BASIS_SET = basis_set[i]
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].POTENTIAL = potential(
unique_atom_list[i], functional)
mySim.FORCE_EVAL.SUBSYS.CELL.ABC = '{L} {L} {L}'.format(L=10 * box_length)
#MOTION SECTION
mySim.MOTION.GEO_OPT.OPTIMIZER = 'BFGS'
mySim.MOTION.GEO_OPT.MAX_ITER = 100
mySim.MOTION.GEO_OPT.MAX_DR = 0.003
mySim.MOTION.MD.ENSEMBLE = ensemble
mySim.MOTION.MD.STEPS = 1
mySim.MOTION.MD.TIMESTEP = 0.2
mySim.MOTION.MD.TEMPERATURE = temperature
mySim.MOTION.MD.THERMOSTAT.TYPE = thermostat
mySim.MOTION.MD.THERMOSTAT.REGION = "MASSIVE"
mySim.MOTION.MD.THERMOSTAT.NOSE.LENGTH = 3
mySim.MOTION.MD.THERMOSTAT.NOSE.YOSHIDA = 3
mySim.MOTION.MD.THERMOSTAT.NOSE.TIMECON = 1000.0
mySim.MOTION.MD.THERMOSTAT.NOSE.MTS = 2
#mySim.MOTION.MD.PRINT.ENERGY.EACH.MD = 20
#mySim.MOTION.MD.PRINT.PROGRAM_RUN_INFO.EACH.MD = 20
#mySim.MOTION.MD.AVERAGES.SECTION_PARAMETERS= ".falbmbjse."
mySim.MOTION.PRINT.STRESS.SECTION_PARAMETERS = 'OFF'
mySim.MOTION.PRINT.TRAJECTORY.EACH.MD = 1
mySim.MOTION.PRINT.VELOCITIES.SECTION_PARAMETERS = 'OFF'
mySim.MOTION.PRINT.FORCES.SECTION_PARAMETERS = "OFF"
mySim.MOTION.PRINT.RESTART_HISTORY.SECTION_PARAMETERS = "ON"
mySim.MOTION.PRINT.RESTART_HISTORY.EACH.MD = 500
mySim.MOTION.PRINT.RESTART.SECTION_PARAMETERS = "ON"
mySim.MOTION.PRINT.RESTART.BACKUP_COPIES = 3
mySim.MOTION.PRINT.RESTART.EACH.MD = 1
mySim.write_changeLog(fn="md-pre-changeLog.out")
mySim.write_errorLog()
mySim.write_inputFile(fn='md-pre.inp')
def single_molecule_opt_files(instance):
molecule = instance.molecule
functional = instance.functional
box = instance.box
cutoff = instance.cutoff
scf_tolerance = instance.scf_tolerance
basis_set = instance.basis_set
basis_set_filename = instance.basis_set_filename
potential_filename = instance.potential_filename
fixed_list = instance.fixed_list
periodicity = instance.periodicity
n_iter = instance.n_iter
input_filename = instance.input_filename
output_filename = instance.output_filename
name = molecule.name
filled_box = mb.packing.fill_box(molecule, 1, box)
mol_unopt_coord = name + "_unoptimized_coord.xyz"
#opt_inp_file=name+'_optimization_input.inp'
filled_box.save(mol_unopt_coord, overwrite='True')
with open(mol_unopt_coord, 'r') as fin:
data = fin.read().splitlines(True)
with open(mol_unopt_coord, 'w') as fout:
fout.writelines(data[2:]) #deleting first two lines
print('Initial structure saved as {}'.format(mol_unopt_coord))
molecule = molecule.to_parmed()
atom_list, mass_list = info_molecule(molecule)
unique_atom_list = remove_duplicate(atom_list)
unique_atom_list.sort()
num_atoms = len(atom_list)
num_unique_atoms = len(unique_atom_list)
mySim = sim.SIM()
#setting defaults
mySim.GLOBAL.RUN_TYPE = "GEO_OPT"
mySim.GLOBAL.PROJECT_NAME = name + "_opt"
mySim.GLOBAL.PRINT_LEVEL = "LOW"
#FORCE EVAL SECTION
mySim.FORCE_EVAL.METHOD = 'QUICKSTEP'
mySim.FORCE_EVAL.SUBSYS.CELL.ABC = '{a} {b} {c}'.format(
a=10 * box.lengths[0], b=10 * box.lengths[1], c=10 * box.lengths[2])
mySim.FORCE_EVAL.SUBSYS.CELL.ALPHA_BETA_GAMMA = '{a} {b} {c}'.format(
a=box.angles[0], b=box.angles[1], c=box.angles[2])
mySim.FORCE_EVAL.SUBSYS.CELL.PERIODIC = periodicity
mySim.FORCE_EVAL.SUBSYS.COORD.DEFAULT_KEYWORD = mol_unopt_coord
mySim.FORCE_EVAL.SUBSYS.init_atoms(num_atoms)
for i in range(num_unique_atoms):
mySim.FORCE_EVAL.SUBSYS.KIND[
i + 1].SECTION_PARAMETERS = unique_atom_list[i]
if basis_set == [None]:
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].BASIS_SET = basis_set_setter(
unique_atom_list[i])
else:
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].BASIS_SET = basis_set[
unique_atom_list[i]]
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].POTENTIAL = potential(
unique_atom_list[i], functional)
mySim.FORCE_EVAL.DFT.BASIS_SET_FILE_NAME = basis_set_filename
mySim.FORCE_EVAL.DFT.POTENTIAL_FILE_NAME = potential_filename
mySim.FORCE_EVAL.DFT.QS.EPS_DEFAULT = 1E-7
mySim.FORCE_EVAL.DFT.MGRID.CUTOFF = cutoff
mySim.FORCE_EVAL.DFT.MGRID.REL_CUTOFF = 50
mySim.FORCE_EVAL.DFT.MGRID.NGRIDS = 4
mySim.FORCE_EVAL.DFT.XC.XC_FUNCTIONAL.SECTION_PARAMETERS = functional
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.POTENTIAL_TYPE = 'PAIR_POTENTIAL'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.TYPE = 'DFTD3'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.PARAMETER_FILE_NAME = 'dftd3.dat'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.REFERENCE_FUNCTIONAL = functional
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.R_CUTOFF = 8
mySim.FORCE_EVAL.DFT.SCF.SCF_GUESS = 'ATOMIC'
mySim.FORCE_EVAL.DFT.SCF.MAX_SCF = 30
mySim.FORCE_EVAL.DFT.SCF.EPS_SCF = scf_tolerance
if periodicity == 'NONE':
mySim.FORCE_EVAL.DFT.POISSON.PERIODIC = 'NONE'
mySim.FORCE_EVAL.DFT.POISSON.POISSON_SOLVER = 'WAVELET'
print(
'The box should be cubic for non-periodic calculations and the box must be around 15 times the size of the molecule when periodicity is NONE'
)
if not is_cubic(box) and periodicity == 'NONE':
print(
'The box should be cubic for non-periodic calculations and the box must be around 15 times the size of the molecule'
)
mySim.MOTION.GEO_OPT.TYPE = 'MINIMIZATION'
mySim.MOTION.GEO_OPT.OPTIMIZER = 'BFGS'
mySim.MOTION.GEO_OPT.MAX_ITER = n_iter
mySim.MOTION.GEO_OPT.MAX_DR = 1e-3
mySim.MOTION.CONSTRAINT.FIXED_ATOMS.LIST = fixed_list
mySim.write_changeLog(fn="mol_opt-changeLog.out")
mySim.write_errorLog()
mySim.write_inputFile(fn=input_filename)
print('Molecule optimization file saved as {}'.format(input_filename))
def md_files(instance):
molecules = instance.molecules
functional = instance.functional
box = instance.box
cutoff = instance.cutoff
scf_tolerance = instance.scf_tolerance
basis_set = instance.basis_set
basis_set_filename = instance.basis_set_filename
potential_filename = instance.potential_filename
fixed_list = instance.fixed_list
periodicity = instance.periodicity
simulation_time = instance.simulation_time
time_step = instance.time_step
ensemble = instance.ensemble
project_name = instance.project_name
temperature = instance.temperature
pressure = instance.pressure
n_molecules = instance.n_molecules
thermostat = instance.thermostat
traj_type = instance.traj_type
traj_freq = instance.traj_freq
seed = instance.seed
input_filename = instance.input_filename
output_filename = instance.output_filename
filled_box = mb.packing.fill_box(compound=molecules,
n_compounds=n_molecules,
box=box)
initial_coord_file = project_name + ".xyz"
filled_box.save(initial_coord_file, overwrite='True')
with open(initial_coord_file, 'r') as fin:
data = fin.read().splitlines(True)
with open(initial_coord_file, 'w') as fout:
fout.writelines(data[2:]) #deleting first two lines
print('MD initial structure saved as {}'.format(initial_coord_file))
atom_list = []
mass_list = []
for i in range(len(molecules)):
current_molecule = mb.clone(molecules[i])
current_molecule_pmd = current_molecule.to_parmed()
x, y = info_molecule(current_molecule_pmd)
atom_list.extend(x)
mass_list.extend(y)
unique_atom_list = remove_duplicate(atom_list)
num_atoms = len(atom_list)
num_unique_atoms = len(unique_atom_list)
unique_atom_list.sort()
mySim = sim.SIM()
#setting defaults
n_steps = int(simulation_time / time_step)
mySim.GLOBAL.RUN_TYPE = "MD"
mySim.GLOBAL.PROJECT_NAME = project_name
mySim.GLOBAL.PRINT_LEVEL = "LOW"
mySim.GLOBAL.SEED = seed
#FORCE EVAL SECTION
mySim.FORCE_EVAL.METHOD = 'QUICKSTEP'
mySim.FORCE_EVAL.STRESS_TENSOR = 'ANALYTICAL'
mySim.FORCE_EVAL.DFT.BASIS_SET_FILE_NAME = basis_set_filename
mySim.FORCE_EVAL.DFT.POTENTIAL_FILE_NAME = potential_filename
mySim.FORCE_EVAL.DFT.CHARGE = 0
mySim.FORCE_EVAL.DFT.MULTIPLICITY = 1
mySim.FORCE_EVAL.DFT.MGRID.CUTOFF = cutoff
mySim.FORCE_EVAL.DFT.MGRID.REL_CUTOFF = 50
mySim.FORCE_EVAL.DFT.MGRID.NGRIDS = 4
mySim.FORCE_EVAL.DFT.QS.METHOD = 'GPW'
mySim.FORCE_EVAL.DFT.QS.EPS_DEFAULT = 1E-7
mySim.FORCE_EVAL.DFT.QS.EXTRAPOLATION = 'ASPC'
mySim.FORCE_EVAL.DFT.POISSON.PERIODIC = periodicity
mySim.FORCE_EVAL.DFT.PRINT.E_DENSITY_CUBE.SECTION_PARAMETERS = "OFF"
mySim.FORCE_EVAL.DFT.SCF.SCF_GUESS = 'ATOMIC'
mySim.FORCE_EVAL.DFT.SCF.MAX_SCF = 30
mySim.FORCE_EVAL.DFT.SCF.EPS_SCF = scf_tolerance
mySim.FORCE_EVAL.DFT.SCF.OT.SECTION_PARAMETERS = ".TRUE."
mySim.FORCE_EVAL.DFT.SCF.OT.PRECONDITIONER = "FULL_SINGLE_INVERSE"
mySim.FORCE_EVAL.DFT.SCF.OT.MINIMIZER = "DIIS"
mySim.FORCE_EVAL.DFT.SCF.OUTER_SCF.SECTION_PARAMETERS = '.TRUE.'
mySim.FORCE_EVAL.DFT.SCF.OUTER_SCF.MAX_SCF = 10
mySim.FORCE_EVAL.DFT.SCF.OUTER_SCF.EPS_SCF = 1e-6
mySim.FORCE_EVAL.DFT.SCF.PRINT.RESTART.SECTION_PARAMETERS = 'OFF'
mySim.FORCE_EVAL.DFT.SCF.PRINT.DM_RESTART_WRITE = '.TRUE.'
mySim.FORCE_EVAL.DFT.XC.XC_FUNCTIONAL.SECTION_PARAMETERS = functional
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.POTENTIAL_TYPE = 'PAIR_POTENTIAL'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.TYPE = 'DFTD3'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.PARAMETER_FILE_NAME = 'dftd3.dat'
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.REFERENCE_FUNCTIONAL = functional
mySim.FORCE_EVAL.DFT.XC.VDW_POTENTIAL.PAIR_POTENTIAL.R_CUTOFF = 8
mySim.FORCE_EVAL.SUBSYS.COORD.DEFAULT_KEYWORD = project_name + ".xyz"
mySim.FORCE_EVAL.SUBSYS.init_atoms(num_atoms)
for i in range(num_unique_atoms):
mySim.FORCE_EVAL.SUBSYS.KIND[
i + 1].SECTION_PARAMETERS = unique_atom_list[i]
if basis_set == [None]:
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].BASIS_SET = basis_set_setter(
unique_atom_list[i])
else:
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].BASIS_SET = basis_set[
unique_atom_list[i]]
mySim.FORCE_EVAL.SUBSYS.KIND[i + 1].POTENTIAL = potential(
unique_atom_list[i], functional)
mySim.FORCE_EVAL.SUBSYS.CELL.ABC = '{a} {b} {c}'.format(
a=10 * box.lengths[0], b=10 * box.lengths[1], c=10 * box.lengths[2])
mySim.FORCE_EVAL.SUBSYS.CELL.ALPHA_BETA_GAMMA = '{a} {b} {c}'.format(
a=box.angles[0], b=box.angles[1], c=box.angles[2])
#MOTION SECTION
mySim.MOTION.GEO_OPT.OPTIMIZER = 'BFGS'
mySim.MOTION.GEO_OPT.MAX_ITER = 100
mySim.MOTION.GEO_OPT.MAX_DR = 0.003
mySim.MOTION.MD.ENSEMBLE = ensemble
mySim.MOTION.MD.STEPS = n_steps
mySim.MOTION.MD.TIMESTEP = time_step
if temperature_ensemble(ensemble):
mySim.MOTION.MD.TEMPERATURE = temperature
mySim.MOTION.MD.THERMOSTAT.TYPE = thermostat
mySim.MOTION.MD.THERMOSTAT.REGION = "MASSIVE"
mySim.MOTION.MD.THERMOSTAT.NOSE.LENGTH = 5
mySim.MOTION.MD.THERMOSTAT.NOSE.YOSHIDA = 3
mySim.MOTION.MD.THERMOSTAT.NOSE.TIMECON = 1000.0
mySim.MOTION.MD.THERMOSTAT.NOSE.MTS = 2
if pressure_ensemble(ensemble):
mySim.MOTION.MD.BAROSTAT.PRESSURE = pressure
if pressure == None:
print('you need to define pressure')
if fixed_list is not None:
mySim.MOTION.CONSTRAINT.FIXED_ATOMS.LIST = fixed_list
mySim.MOTION.MD.THERMOSTAT.REGION = "GLOBAL"
if periodicity == 'NONE':
mySim.FORCE_EVAL.DFT.POISSON.PERIODIC = 'NONE'
mySim.FORCE_EVAL.DFT.POISSON.POISSON_SOLVER = 'WAVELET'
if not is_cubic(box) and periodicity == 'NONE':
print(
'The box should be cubic for non-periodic calculations and the box must be around 15 times the size of the molecule'
)
mySim.MOTION.PRINT.STRESS.SECTION_PARAMETERS = 'OFF'
mySim.MOTION.PRINT.TRAJECTORY.EACH.MD = traj_freq
mySim.MOTION.PRINT.TRAJECTORY.FORMAT = traj_type
mySim.MOTION.PRINT.VELOCITIES.SECTION_PARAMETERS = 'OFF'
mySim.MOTION.PRINT.FORCES.SECTION_PARAMETERS = "OFF"
mySim.MOTION.PRINT.RESTART_HISTORY.SECTION_PARAMETERS = "ON"
mySim.MOTION.PRINT.RESTART_HISTORY.EACH.MD = 500
mySim.MOTION.PRINT.RESTART.SECTION_PARAMETERS = "ON"
mySim.MOTION.PRINT.RESTART.BACKUP_COPIES = 3
mySim.MOTION.PRINT.RESTART.EACH.MD = 1
mySim.write_changeLog(fn="md-changeLog.out")
mySim.write_errorLog()
mySim.write_inputFile(fn=input_filename)
print('MD input file saved as {}'.format(input_filename))