From b6575b0925fb8b0e592fb972df61870285e705e9 Mon Sep 17 00:00:00 2001 From: gustavor101 Date: Fri, 23 Feb 2024 17:53:45 -0600 Subject: [PATCH 1/2] Add Ase example in paper Add example --- cp2k-example/initial.xyz | 343 +++++++++++++++++++++++++++++++ cp2k-example/sim_pysages_cp2k.py | 224 ++++++++++++++++++++ cp2k-example/submit.sh | 19 ++ 3 files changed, 586 insertions(+) create mode 100644 cp2k-example/initial.xyz create mode 100644 cp2k-example/sim_pysages_cp2k.py create mode 100644 cp2k-example/submit.sh diff --git a/cp2k-example/initial.xyz b/cp2k-example/initial.xyz new file mode 100644 index 0000000..5e04a69 --- /dev/null +++ b/cp2k-example/initial.xyz @@ -0,0 +1,343 @@ +341 +Lattice="15.0 0.0 0.0 0.0 15.0 0.0 0.0 0.0 15.0" Properties=species:S:1:pos:R:3:masses:R:1:momenta:R:3:forces:R:3 Built=T with=T Packmol=T energy=-54715.660501572 stress="-0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0" free_energy=-54715.660501572 pbc="T T T" +H 1.47478389 9.52606311 8.42477608 1.00800000 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0.54299553 +Cl 8.67914461 7.99258607 6.12813373 35.45000000 -0.24540659 -1.08625813 1.02445448 -0.18016422 -0.20638684 0.61680365 diff --git a/cp2k-example/sim_pysages_cp2k.py b/cp2k-example/sim_pysages_cp2k.py new file mode 100644 index 0000000..e4475f4 --- /dev/null +++ b/cp2k-example/sim_pysages_cp2k.py @@ -0,0 +1,224 @@ +import numpy +import pysages +from pysages.methods import SpectralABF +from ase.md.velocitydistribution import MaxwellBoltzmannDistribution +from ase.md.langevin import Langevin +from ase.io.trajectory import Trajectory +from pysages.methods import CVRestraints +from pysages.colvars.coordinates import Distance +from ase import units +from ase import Atoms +import matplotlib.pyplot as plt +from ase.io import read, write +from ase.calculators.cp2k import CP2K +import pickle +import os + +# System parameters +T = 300 +dt = 0.5 * units.fs +friction = 0.05 +append = True + +class CVLogger: + def __init__(self, cv_file, log_period): + self.cv_file = cv_file + self.log_period = log_period + self.counter = 0 + + def save_cv(self, xi): + with open(self.cv_file, "a+", encoding="utf8") as f: + f.write(str(self.counter) + "\t") + f.write("\t".join(map(str, xi.flatten())) + "\n") + + def __call__(self, snapshot, state, timestep): + if self.counter >= self.log_period and self.counter % self.log_period == 0: + self.save_cv(state.xi) + + self.counter += 1 + +def simulation(T=T, dt=dt, friction=friction): + cp2k_inp = ''' +&FORCE_EVAL +&DFT + BASIS_SET_FILE_NAME BASIS_PBE + POTENTIAL_FILE_NAME PBE_POTENTIALS + &QS + METHOD GPW + EXTRAPOLATION PS + EXTRAPOLATION_ORDER 3 + EPS_DEFAULT 1.0E-10 + &END QS + &POISSON + PERIODIC XYZ + &END POISSON + &SCF + EPS_SCF 1.0E-6 + SCF_GUESS ATOMIC + MAX_SCF 50 + &OT T + MINIMIZER DIIS + PRECONDITIONER FULL_SINGLE_INVERSE + &END OT + &END SCF + &XC + &XC_FUNCTIONAL PBE + &END XC_FUNCTIONAL + &VDW_POTENTIAL + DISPERSION_FUNCTIONAL PAIR_POTENTIAL + &PAIR_POTENTIAL + TYPE DFTD3 + PARAMETER_FILE_NAME dftd3.dat + REFERENCE_FUNCTIONAL PBE + R_CUTOFF [angstrom] 16.0 + &END PAIR_POTENTIAL + &END VDW_POTENTIAL + &END XC + &LS_SCF + MAX_SCF 50 + &END LS_SCF +&END DFT +&SUBSYS + &KIND H + MASS 2.0 + BASIS_SET DZVP-MOLOPT-PBE-GTH-q1 + POTENTIAL GTH-PBE-q1 + &END KIND + &KIND O + BASIS_SET DZVP-MOLOPT-PBE-GTH-q6 + POTENTIAL GTH-PBE-q6 + &END KIND + &KIND Na + BASIS_SET DZVP-MOLOPT-PBE-GTH-q9 + POTENTIAL GTH-PBE-q9 + &END KIND + &KIND Cl + BASIS_SET DZVP-MOLOPT-PBE-GTH-q7 + POTENTIAL GTH-PBE-q7 + &END KIND +&END SUBSYS +&END FORCE_EVAL +''' + + if os.path.exists('md.traj'): + traj = Trajectory('md.traj') + atoms = traj[-1] + else: + atoms = read('initial.xyz') + + for atom in atoms: + new_masses = atoms.get_masses() + if atom.symbol == 'H': + new_masses[atom.index] = 2.014 + atoms.set_masses(masses=new_masses) + + calc = CP2K(basis_set_file=None, + potential_file=None, + basis_set=None, + pseudo_potential=None, + xc=None, + max_scf=None, + uks=None, + cutoff=300*units.Ry, + stress_tensor=False, + inp=cp2k_inp) + + atoms.set_calculator(calc) + # MaxwellBoltzmannDistribution(atoms, temperature_K=300) + + dyn = Langevin(atoms, + timestep=dt, + temperature_K=T, + friction=friction, + logfile='md.log') + + if os.path.exists('md.traj') and append: + traj = Trajectory('md.traj', 'a', atoms) + else: + traj = Trajectory('md.traj', 'w', atoms) + + dyn.attach(traj.write, interval=1) + + return dyn + +# functions for ploting and storing data +def plot_energy(result): + fig, ax = plt.subplots() + + ax.set_xlabel("CV") + ax.set_ylabel("Free energy $[\\epsilon]$") + + free_energy = numpy.asarray(result["free_energy"]) + free_energy = free_energy - free_energy.max() + x = numpy.asarray(result["mesh"]) + ax.plot(x, free_energy, color="teal") + + fig.savefig("energy.png") + +def plot_forces(result): + fig, ax = plt.subplots() + + ax.set_xlabel("CV") + ax.set_ylabel("Forces $[\\epsilon]$") + + forces = numpy.asarray(result["mean_force"]) + x = numpy.asarray(result["mesh"]) + ax.plot(x, forces, color="teal") + + fig.savefig("forces.png") + +def plot_histogram(result): + fig, ax = plt.subplots() + + ax.set_xlabel("CV") + ax.set_ylabel("Histogram $[\\epsilon]$") + + hist = numpy.asarray(result["histogram"]) / numpy.nanmax( + numpy.asarray(result["histogram"]) + ) + x = numpy.asarray(result["mesh"]) + ax.plot(x, hist, color="teal") + + fig.savefig("histogram.png") + +def save_energy_forces(result): + Energy = numpy.asarray(result["free_energy"]) + Forces = numpy.asarray(result["mean_force"]) + Grid = numpy.asarray(result["mesh"]) + hist = numpy.asarray(result["histogram"]) / numpy.nanmax( + numpy.asarray(result["histogram"]) + ) + numpy.savetxt("FES.csv", numpy.column_stack([Grid, Energy])) + numpy.savetxt("Forces.csv", numpy.column_stack([Grid, Forces])) + numpy.savetxt("Histogram.csv", numpy.column_stack([Grid, hist])) + +def main(): + + # Define CV grid and CV restraints + grid = pysages.Grid(lower=(2.8), upper=(3.3), shape=(20,), periodic=False) + restraint = CVRestraints(lower=(2.75), upper=(3.35), ku=(75), kl=(75)) + + # Define CV and spectral abf method + cvs = [Distance([[339],[340]]),] + method = SpectralABF(cvs, grid, restraints=restraint, N=250) + + # Setup CVlogger to print info about CV + stride = 1 + cv_file = "cv.dat" + callback = CVLogger(cv_file, stride) + + # Run the method and pickle the results + # with open('1/raw_result.pickle', 'rb') as f: + # state = pickle.load(f) + + state = pysages.run(method,simulation,10,callback) + with open('raw_result.pickle', 'wb') as f: + pickle.dump(state, f) + + result = pysages.analyze(state) + plot_energy(result) + plot_forces(result) + plot_histogram(result) + save_energy_forces(result) + +main() \ No newline at end of file diff --git a/cp2k-example/submit.sh b/cp2k-example/submit.sh new file mode 100644 index 0000000..4d37fe8 --- /dev/null +++ b/cp2k-example/submit.sh @@ -0,0 +1,19 @@ +#!/bin/bash +#SBATCH -J WI-10 +#SBATCH -A m1266 +#SBATCH -N 1 +#SBATCH -c 4 +#SBATCH -n 64 +#SBATCH -C cpu +#SBATCH -q debug +##SBATCH -p +#SBATCH --time 10 +#SBATCH -o Report-%j.out + +export CP2K_DATA_DIR=$CONDA_PREFIX/cp2k-data +export OMP_NUM_THREADS=2 +export ASE_CP2K_COMMAND="mpirun -np 64 $CONDA_PREFIX/bin/cp2k_shell.psmp" + +ulimit -s unlimited + +python sim.py \ No newline at end of file From 3a4e63c803cdf177707d99916634b98fcb9fe2f6 Mon Sep 17 00:00:00 2001 From: gustavor101 Date: Fri, 23 Feb 2024 18:05:00 -0600 Subject: [PATCH 2/2] Update submit.sh Fix filename --- cp2k-example/submit.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cp2k-example/submit.sh b/cp2k-example/submit.sh index 4d37fe8..80499da 100644 --- a/cp2k-example/submit.sh +++ b/cp2k-example/submit.sh @@ -16,4 +16,4 @@ export ASE_CP2K_COMMAND="mpirun -np 64 $CONDA_PREFIX/bin/cp2k_shell.psmp" ulimit -s unlimited -python sim.py \ No newline at end of file +python sim_pysages_cp2k.py