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Merge pull request #5 from QuantumMisaka/neb-dimer
Neb-dimer workflow
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| Original file line number | Diff line number | Diff line change |
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| from ase import Atom, Atoms | ||
| from ase.io import Trajectory, read, write | ||
| from ase.mep import DimerControl, MinModeAtoms, MinModeTranslate | ||
| from ase.optimize import BFGS, FIRE | ||
| from ase.calculators.abacus import Abacus, AbacusProfile | ||
| import os, sys | ||
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||
| import numpy as np | ||
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| fmax = 0.05 | ||
| dimer_input_file = 'dimer_init.traj' | ||
| init_eigenmode_method = 'displacement' | ||
| displacement_input = 'displacement_vector.npy' | ||
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||
| # setting for calculator | ||
| mpi = 16 | ||
| omp = 4 | ||
| abacus = "abacus" | ||
| #lib_dir = "/lustre/home/2201110432/example/abacus" | ||
| lib_dir = "/home/james/example" | ||
| pseudo_dir = f"{lib_dir}/PP" | ||
| basis_dir = f"{lib_dir}/ORB" | ||
| pp = { | ||
| 'H':'H_ONCV_PBE-1.0.upf', | ||
| 'Au':'Au_ONCV_PBE-1.0.upf', | ||
| } | ||
| basis = { | ||
| 'H':'H_gga_6au_100Ry_2s1p.orb', | ||
| 'Au':'Au_gga_7au_100Ry_4s2p2d1f.orb', | ||
| } | ||
| kpts = [3, 1, 3] | ||
| parameters = { | ||
| 'calculation': 'scf', | ||
| 'nspin': 2, | ||
| 'xc': 'pbe', | ||
| 'ecutwfc': 100, | ||
| 'ks_solver': 'genelpa', | ||
| 'symmetry': 0, | ||
| 'vdw_method': 'd3_bj', | ||
| 'smearing_method': 'gaussian', | ||
| 'smearing_sigma': 0.001, | ||
| 'basis_type': 'lcao', | ||
| 'mixing_type': 'broyden', | ||
| 'scf_thr': 1e-6, | ||
| 'scf_nmax': 100, | ||
| 'kpts': kpts, | ||
| 'pp': pp, | ||
| 'basis': basis, | ||
| 'pseudo_dir': pseudo_dir, | ||
| 'basis_dir': basis_dir, | ||
| 'cal_force': 1, | ||
| 'cal_stress': 1, | ||
| 'out_stru': 1, | ||
| 'out_chg': 0, | ||
| 'out_mul': 0, | ||
| 'out_bandgap': 0, | ||
| 'efield_flag': 1, | ||
| 'dip_cor_flag': 1, | ||
| 'efield_dir': 1, | ||
| 'efield_pos_max': 0.7 | ||
| } | ||
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|
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| class AbacusDimer: | ||
| """Customize Dimer calculation by using ABACUS""" | ||
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| def __init__(self, init_Atoms, parameters, abacus='abacus', | ||
| mpi=1, omp=1, directory='DIMER', | ||
| traj_file='dimer.traj', | ||
| init_eigenmode_method='displacement', | ||
| displacement_vector: np.ndarray = None,): | ||
| """Initialize Dimer method by using ASE-ABACUS | ||
| init_Atoms (Atoms object): starting image, can be from every way including NEB result | ||
| parameters (dict): settings of abacus input parameters | ||
| abacus (str): Abacus executable file. Default: 'abacus' | ||
| directory (str): calculator directory name, for parallel calculation {directory}-rank{i} will be the directory name | ||
| mpi (int): number of MPI for abacus calculator | ||
| omp (int): number of OpenMP for abacus calculator | ||
| traj_file (str): trajectory file name for dimer calculation, when running dimer calculation, trajetory will be written to this file, default is 'dimer.traj' | ||
| init_eigenmode_method (str): dimer initial eigenmode method. Choose from 'displacement' and 'gauss'. | ||
| displacement_vector (np.ndarray): displacement vector for dimer initial eigenmode. Only used when init_eigenmode_method is 'displacement' | ||
| """ | ||
| self.init_Atoms = init_Atoms | ||
| self.parameters = parameters | ||
| self.abacus = abacus | ||
| self.mpi = mpi | ||
| self.omp = omp | ||
| self.directory = directory | ||
| self.traj_file = traj_file | ||
| self.init_eigenmode_method = init_eigenmode_method | ||
| self.displacement_vector = displacement_vector | ||
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| def set_calculator(self): | ||
| """Set Abacus calculators""" | ||
| os.environ['OMP_NUM_THREADS'] = f'{self.omp}' | ||
| profile = AbacusProfile( | ||
| argv=['mpirun', '-np', f'{self.mpi}', self.abacus]) | ||
| out_directory = self.directory | ||
| calc = Abacus(profile=profile, directory=out_directory, | ||
| **self.parameters) | ||
| return calc | ||
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| def set_d_mask_by_displacement(self): | ||
| """set mask by displacement""" | ||
| print("=== Set mask by displacement vector where displacement is [0,0,0] ===") | ||
| d_mask = self.displacement_vector != np.zeros(3) | ||
| d_mask = d_mask[:,0].tolist() | ||
| return d_mask | ||
|
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| def set_d_mask_by_constraint(self): | ||
| """set mask by constraint of Atoms""" | ||
| print("=== Set mask by constraint read from init Atoms ===") | ||
| dimer_init = self.init_Atoms | ||
| const_list = dimer_init._get_constraints()[0] | ||
| const_list = const_list.todict()['kwargs']['indices'] | ||
| d_mask = [True] * len(dimer_init) | ||
| for ind in const_list: | ||
| d_mask[ind] = False | ||
| return d_mask | ||
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| def run(self, fmax=0.05): | ||
| """run dimer calculation workflow""" | ||
| dimer_init = self.init_Atoms | ||
| dimer_init.calc = self.set_calculator() | ||
| dimer_traj = Trajectory(self.traj_file, 'w', dimer_init) | ||
| if self.init_eigenmode_method == "displacement": | ||
| # d_mask = self.set_d_mask_by_displacement() # not the best | ||
| d_mask = self.set_d_mask_by_constraint() | ||
| d_control = DimerControl(initial_eigenmode_method=self.init_eigenmode_method, | ||
| displacement_method="vector", | ||
| mask=d_mask) | ||
| d_atoms = MinModeAtoms(dimer_init, d_control) | ||
| d_atoms.displace(displacement_vector=self.displacement_vector) | ||
| elif self.init_eigenmode_method == "gauss": | ||
| # leave a way for random displacement | ||
| d_mask = self.set_d_mask_by_constraint() | ||
| d_control = DimerControl(initial_eigenmode_method=self.init_eigenmode_method, | ||
| mask=d_mask) | ||
| d_atoms = MinModeAtoms(dimer_init, d_control) | ||
| else: | ||
| raise ValueError("init_eigenmode_method must be displacement or gauss") | ||
| dimer_relax = MinModeTranslate(d_atoms, trajectory=dimer_traj) | ||
| dimer_relax.run(fmax=fmax) | ||
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| if __name__ == "__main__": | ||
| # running process | ||
| # read initial guessed neb chain | ||
| dimer_init = read(dimer_input_file) | ||
| displacement_vector = np.load(displacement_input) | ||
| dimer = AbacusDimer(dimer_init, parameters, abacus=abacus, | ||
| mpi=mpi, omp=omp, | ||
| init_eigenmode_method=init_eigenmode_method, | ||
| displacement_vector=displacement_vector) | ||
| dimer.run(fmax=fmax) |
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| #!/bin/bash | ||
| #SBATCH --nodes=1 | ||
| #SBATCH --ntasks-per-node=16 | ||
| #SBATCH --cpus-per-task=4 | ||
| #SBATCH -J DIMER-ABACUS | ||
| #SBATCH -o run_dimer.out | ||
| #SBATCH -e run_dimer.err | ||
| #SBATCH -p C064M0256G | ||
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| # JamesMisaka in 2023-11-14 | ||
| # workflow of ase-abacus-dimer method | ||
| # for one calculator, ntasks-per-node for mpi, cpus-per-task for openmp | ||
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| # in developer's PKU-WM2 server | ||
| source /lustre/home/2201110432/apps/miniconda3/etc/profile.d/conda.sh | ||
| conda activate gpaw-intel | ||
| module load abacus/3.4.2-icx | ||
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| # if one just done neb calculation | ||
| python neb2dimer.py neb.traj # or neb_latest.traj | ||
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| # Job state | ||
| echo $SLURM_JOB_ID > JobRun.state | ||
| echo "Start at $(date)" >> JobRun.state | ||
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| # just do dimer by run ! | ||
| # do check your ntasks(mpi) and cpu(omp) setting is right | ||
| python dimer_run.py | ||
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| echo "===== Dimer Calculation Done at $(date)! =====" | ||
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| # Job State | ||
| echo "End at $(date)" >> JobRun.state |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,9 @@ | ||
| #!/bin/bash | ||
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| # full workflow controling NEB and Dimer calculation | ||
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| NEB_JOBID=$(sbatch neb_submit.sh) | awk '{print $4}' # get the jobid of neb and submit neb job | ||
| echo "NEB_JOBID is ${NEB_JOBID}" | ||
| DIMER_JOBID=$(sbatch --dependency=afterok:${NEB_JOBID} dimer_submit.sh) | awk '{print $4}' # submit dimer job after neb job done | ||
| echo "Dimer Job Submitted and will be run after NEB job !" | ||
| echo "DIMER_JOBID is ${DIMER_JOBID}" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| import numpy as np | ||
| import sys | ||
| from ase.io import Trajectory, read, write | ||
| from ase.mep.neb import NEBTools | ||
|
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| def neb2dimer(neb_traj:list, n_max:int=0, out_traj='dimer_init.traj', out_vec='displacement_vector.npy', | ||
| step_before_TS:int=1, step_after_TS:int=1): | ||
| ''' | ||
| Transform neb chain to dimer init | ||
| ''' | ||
| # you should use the latest neb chain or other single neb chain | ||
| # but a full neb chain is permitted, in which the latest neb chain will be used | ||
| if n_max == 0: | ||
| print("=== n_max set to 0, get n_images by using NEBTools ===") | ||
| n_images = NEBTools(neb_traj)._guess_nimages() | ||
| elif (n_max >= 0) and (type(n_max) == int): | ||
| n_images = n_max + 2 | ||
| else: | ||
| raise ValueError("n_max must be a non-negative integer") | ||
| if len(neb_traj) < n_images: | ||
| raise ValueError(f"n_images ={n_images} is larger than the length of neb_traj ={len(neb_traj)}") | ||
| elif len(neb_traj) > n_images: | ||
| print(f"=== n_images ={n_images} is smaller than the length of neb_traj ={len(neb_traj)} ! Only the last {n_images} images are used ===") | ||
| # used neb_chain is the final traj | ||
| neb_chain = neb_traj[-n_images:] | ||
| # get TS information from NEB chain | ||
| barrier = NEBTools(neb_chain).get_barrier()[0] | ||
| fmax = NEBTools(neb_chain).get_fmax() | ||
| raw_barrier = max([image.get_potential_energy() for image in neb_chain]) | ||
| TS_info = [(ind, image) | ||
| for ind, image in enumerate(neb_chain) | ||
| if image.get_potential_energy() == raw_barrier][0] | ||
| print(f"=== Locate TS in {TS_info[0]} of 0-{n_images-1} images ===") | ||
| print(f"=== TS Barrier: {barrier:.4f} (eV) ===") | ||
| print(f"=== TS Fmax: {fmax:.4f} (eV/A) ===") | ||
| print(f"=== TS images is output as {out_traj} for dimer init ===") | ||
| # output TS of neb for dimer init | ||
| write(out_traj, TS_info[1], format='traj') | ||
| # output displancement vector by using the nearest two images of TS | ||
| ind_before_TS = TS_info[0] - step_before_TS | ||
| ind_after_TS = TS_info[0] + step_after_TS | ||
| img_before = neb_chain[ind_before_TS] | ||
| img_after = neb_chain[ind_after_TS] | ||
| print(f"=== Displacement vector is generated by position minus from {ind_after_TS} image to {ind_before_TS} image ===") | ||
| displacement_vector = (img_after.positions - img_before.positions) | ||
| print(f"=== Displacement vector is output as {out_vec} for dimer init ===") | ||
| np.save(out_vec,displacement_vector) | ||
| return | ||
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| if __name__ == "__main__": | ||
| msg = ''' | ||
| neb2dimer.py is to make dimer inputfile by using neb result | ||
| Usage: | ||
| python neb2dimer.py [traj_file] ([n_max]) | ||
| Notice that n_max = n_images - 2 | ||
| These sctipt will output two files: | ||
| dimer_init.traj: TS of neb chain for dimer init-structure | ||
| displacement_vector.npy: displacement vector of dimer init | ||
| ''' | ||
| if len(sys.argv) < 2: | ||
| print(msg) | ||
| elif len(sys.argv) == 2: | ||
| if sys.argv == "--help" or sys.argv == "-h": | ||
| print(msg) | ||
| else: | ||
| traj_file = sys.argv[1] | ||
| neb_traj = Trajectory(traj_file) | ||
| neb2dimer(neb_traj) | ||
| else: | ||
| traj_file = sys.argv[1] | ||
| n_max = int(sys.argv[2]) | ||
| neb_traj = Trajectory(traj_file) | ||
| neb2dimer(neb_traj, n_max) |
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