def test_qmmm_acn(): import numpy as np import ase.units as units from ase import Atoms from ase.calculators.acn import (ACN, m_me, r_cn, r_mec, sigma_me, sigma_c, sigma_n, epsilon_me, epsilon_c, epsilon_n) from ase.calculators.qmmm import SimpleQMMM, LJInteractionsGeneral, EIQMMM from ase.constraints import FixLinearTriatomic from ase.optimize import BFGS # From https://www.sciencedirect.com/science/article/pii/S0166128099002079 eref = 4.9 * units.kcal / units.mol dref = 3.368 aref = 79.1 sigma = np.array([sigma_me, sigma_c, sigma_n]) epsilon = np.array([epsilon_me, epsilon_c, epsilon_n]) inter = LJInteractionsGeneral(sigma, epsilon, sigma, epsilon, 3) for calc in [ACN(), SimpleQMMM([0, 1, 2], ACN(), ACN(), ACN()), SimpleQMMM([0, 1, 2], ACN(), ACN(), ACN(), vacuum=3.0), EIQMMM([0, 1, 2], ACN(), ACN(), inter), EIQMMM([0, 1, 2], ACN(), ACN(), inter, vacuum=3.0), EIQMMM([3, 4, 5], ACN(), ACN(), inter, vacuum=3.0)]: dimer = Atoms('CCNCCN', [(-r_mec, 0, 0), (0, 0, 0), (r_cn, 0, 0), (r_mec, 3.7, 0), (0, 3.7, 0), (-r_cn, 3.7, 0)]) masses = dimer.get_masses() masses[::3] = m_me dimer.set_masses(masses) dimer.calc = calc fixd = FixLinearTriatomic(triples=[(0, 1, 2), (3, 4, 5)]) dimer.set_constraint(fixd) opt = BFGS(dimer, maxstep=0.04, trajectory=calc.name + '.traj', logfile=calc.name + 'd.log') opt.run(0.001, steps=1000) e0 = dimer.get_potential_energy() d0 = dimer.get_distance(1, 4) a0 = dimer.get_angle(2, 1, 4) fmt = '{0:>25}: {1:.3f} {2:.3f} {3:.1f}' print(fmt.format(calc.name, -e0, d0, a0)) assert abs(e0 + eref) < 0.013 assert abs(d0 - dref) < 0.224 assert abs(a0 - aref) < 2.9 print(fmt.format('reference', eref, dref, aref))
def test_rattle(): i = LJInteractions({('O', 'O'): (epsilon0, sigma0)}) for calc in [ TIP3P(), SimpleQMMM([0, 1, 2], TIP3P(), TIP3P(), TIP3P()), EIQMMM([0, 1, 2], TIP3P(), TIP3P(), i) ]: dimer = s22('Water_dimer') for m in [0, 3]: dimer.set_angle(m + 1, m, m + 2, angleHOH) dimer.set_distance(m, m + 1, rOH, fix=0) dimer.set_distance(m, m + 2, rOH, fix=0) fixOH1 = [(3 * i, 3 * i + 1) for i in range(2)] fixOH2 = [(3 * i, 3 * i + 2) for i in range(2)] fixHH = [(3 * i + 1, 3 * i + 2) for i in range(2)] dimer.set_constraint(FixBondLengths(fixOH1 + fixOH2 + fixHH)) dimer.calc = calc e = dimer.get_potential_energy() md = VelocityVerlet(dimer, 8.0 * units.fs, trajectory=calc.name + '.traj', logfile=calc.name + '.log', loginterval=5) md.run(25) de = dimer.get_potential_energy() - e assert abs(de - -0.028) < 0.001
def test_rattle_linear(): """Test RATTLE and QM/MM for rigid linear acetonitrile.""" import numpy as np from ase import Atoms from ase.calculators.acn import (ACN, m_me, r_cn, r_mec, sigma_me, sigma_c, sigma_n, epsilon_me, epsilon_c, epsilon_n) from ase.calculators.qmmm import SimpleQMMM, EIQMMM, LJInteractionsGeneral from ase.md.verlet import VelocityVerlet from ase.constraints import FixLinearTriatomic import ase.units as units sigma = np.array([sigma_me, sigma_c, sigma_n]) epsilon = np.array([epsilon_me, epsilon_c, epsilon_n]) i = LJInteractionsGeneral(sigma, epsilon, sigma, epsilon, 3) for calc in [ ACN(), SimpleQMMM([0, 1, 2], ACN(), ACN(), ACN()), EIQMMM([0, 1, 2], ACN(), ACN(), i) ]: dimer = Atoms('CCNCCN', [(-r_mec, 0, 0), (0, 0, 0), (r_cn, 0, 0), (r_mec, 3.7, 0), (0, 3.7, 0), (-r_cn, 3.7, 0)]) masses = dimer.get_masses() masses[::3] = m_me dimer.set_masses(masses) fixd = FixLinearTriatomic(triples=[(0, 1, 2), (3, 4, 5)]) dimer.set_constraint(fixd) dimer.calc = calc d1 = dimer[:3].get_all_distances() d2 = dimer[3:].get_all_distances() e = dimer.get_potential_energy() md = VelocityVerlet(dimer, 2.0 * units.fs, trajectory=calc.name + '.traj', logfile=calc.name + '.log', loginterval=20) md.run(100) de = dimer.get_potential_energy() - e assert np.all(abs(dimer[:3].get_all_distances() - d1) < 1e-10) assert np.all(abs(dimer[3:].get_all_distances() - d2) < 1e-10) assert abs(de - -0.005) < 0.001
def test_orca_qmmm(): from ase.calculators.tip4p import TIP4P, epsilon0, sigma0 from ase.calculators.orca import ORCA from ase.calculators.qmmm import EIQMMM, LJInteractions from ase.data import s22 atoms = s22.create_s22_system('Water_dimer') qmcalc = ORCA(label='water', orcasimpleinput='BLYP def2-SVP') lj = LJInteractions({('O', 'O'): (epsilon0, sigma0)}) atoms.calc = EIQMMM(selection=[0, 1, 2], qmcalc=qmcalc, mmcalc=TIP4P(), interaction=lj, output='orca_qmmm.log') e = atoms.get_potential_energy() assert abs(e + 2077.45445852) < 1.0
def test_qmmm_tip4p(): from math import cos, sin, pi import numpy as np #import matplotlib.pyplot as plt import ase.units as units from ase import Atoms from ase.calculators.tip4p import TIP4P, epsilon0, sigma0, rOH, angleHOH from ase.calculators.qmmm import (SimpleQMMM, EIQMMM, LJInteractions, LJInteractionsGeneral) from ase.constraints import FixInternals from ase.optimize import BFGS r = rOH a = angleHOH * pi / 180 # From https://doi.org/10.1063/1.445869 eexp = 6.24 * units.kcal / units.mol dexp = 2.75 aexp = 46 D = np.linspace(2.5, 3.5, 30) i = LJInteractions({('O', 'O'): (epsilon0, sigma0)}) # General LJ interaction object sigma_mm = np.array([sigma0, 0, 0]) epsilon_mm = np.array([epsilon0, 0, 0]) sigma_qm = np.array([sigma0, 0, 0]) epsilon_qm = np.array([epsilon0, 0, 0]) ig = LJInteractionsGeneral(sigma_qm, epsilon_qm, sigma_mm, epsilon_mm, 3) for calc in [ TIP4P(), SimpleQMMM([0, 1, 2], TIP4P(), TIP4P(), TIP4P()), SimpleQMMM([0, 1, 2], TIP4P(), TIP4P(), TIP4P(), vacuum=3.0), EIQMMM([0, 1, 2], TIP4P(), TIP4P(), i), EIQMMM([3, 4, 5], TIP4P(), TIP4P(), i, vacuum=3.0), EIQMMM([0, 1, 2], TIP4P(), TIP4P(), i, vacuum=3.0), EIQMMM([0, 1, 2], TIP4P(), TIP4P(), ig), EIQMMM([3, 4, 5], TIP4P(), TIP4P(), ig, vacuum=3.0), EIQMMM([0, 1, 2], TIP4P(), TIP4P(), ig, vacuum=3.0) ]: dimer = Atoms('OH2OH2', [(0, 0, 0), (r * cos(a), 0, r * sin(a)), (r, 0, 0), (0, 0, 0), (r * cos(a / 2), r * sin(a / 2), 0), (r * cos(a / 2), -r * sin(a / 2), 0)]) dimer.calc = calc E = [] F = [] for d in D: dimer.positions[3:, 0] += d - dimer.positions[3, 0] E.append(dimer.get_potential_energy()) F.append(dimer.get_forces()) F = np.array(F) #plt.plot(D, E) F1 = np.polyval(np.polyder(np.polyfit(D, E, 7)), D) F2 = F[:, :3, 0].sum(1) error = abs(F1 - F2).max() assert error < 0.01 dimer.constraints = FixInternals(bonds=[(r, (0, 1)), (r, (0, 2)), (r, (3, 4)), (r, (3, 5))], angles=[(a, (2, 0, 1)), (a, (5, 3, 4))]) opt = BFGS(dimer, maxstep=0.04, trajectory=calc.name + '.traj', logfile=calc.name + 'd.log') opt.run(0.01) e0 = dimer.get_potential_energy() d0 = dimer.get_distance(0, 3) R = dimer.positions v1 = R[2] - R[3] v2 = R[3] - (R[5] + R[4]) / 2 a0 = np.arccos( np.dot(v1, v2) / (np.dot(v1, v1) * np.dot(v2, v2))**0.5) / np.pi * 180 fmt = '{0:>23}: {1:.3f} {2:.3f} {3:.3f} {4:.1f}' print(fmt.format(calc.name, -min(E), -e0, d0, a0)) assert abs(e0 + eexp) < 0.002 assert abs(d0 - dexp) < 0.006 assert abs(a0 - aexp) < 2.5 print(fmt.format('reference', 9.999, eexp, dexp, aexp))
from ase import Atoms from ase.calculators.acn import (ACN, m_me, r_cn, r_mec, sigma_me, sigma_c, sigma_n, epsilon_me, epsilon_c, epsilon_n) from ase.calculators.qmmm import SimpleQMMM, EIQMMM, LJInteractionsGeneral from ase.md.verlet import VelocityVerlet from ase.constraints import FixLinearTriatomic import ase.units as units sigma = np.array([sigma_me, sigma_c, sigma_n]) epsilon = np.array([epsilon_me, epsilon_c, epsilon_n]) i = LJInteractionsGeneral(sigma, epsilon, sigma, epsilon, 3) for calc in [ ACN(), SimpleQMMM([0, 1, 2], ACN(), ACN(), ACN()), EIQMMM([0, 1, 2], ACN(), ACN(), i) ]: dimer = Atoms('CCNCCN', [(-r_mec, 0, 0), (0, 0, 0), (r_cn, 0, 0), (r_mec, 3.7, 0), (0, 3.7, 0), (-r_cn, 3.7, 0)]) masses = dimer.get_masses() masses[::3] = m_me dimer.set_masses(masses) fixd = FixLinearTriatomic(triples=[(0, 1, 2), (3, 4, 5)]) dimer.set_constraint(fixd) dimer.calc = calc
D = np.linspace(2.5, 3.5, 30) i = LJInteractions({('O', 'O'): (epsilon0, sigma0)}) # General LJ interaction object sigma_mm = np.array([0, 0, sigma0]) epsilon_mm = np.array([0, 0, epsilon0]) sigma_qm = np.array([0, 0, sigma0]) epsilon_qm = np.array([0, 0, epsilon0]) ig = LJInteractionsGeneral(sigma_qm, epsilon_qm, sigma_mm, epsilon_mm, 3) for calc in [TIP3P(), SimpleQMMM([0, 1, 2], TIP3P(), TIP3P(), TIP3P()), SimpleQMMM([0, 1, 2], TIP3P(), TIP3P(), TIP3P(), vacuum=3.0), EIQMMM([0, 1, 2], TIP3P(), TIP3P(), i), EIQMMM([3, 4, 5], TIP3P(), TIP3P(), i, vacuum=3.0), EIQMMM([0, 1, 2], TIP3P(), TIP3P(), i, vacuum=3.0), EIQMMM([0, 1, 2], TIP3P(), TIP3P(), ig), EIQMMM([3, 4, 5], TIP3P(), TIP3P(), ig, vacuum=3.0), EIQMMM([0, 1, 2], TIP3P(), TIP3P(), ig, vacuum=3.0)]: dimer = Atoms('H2OH2O', [(r * cos(a), 0, r * sin(a)), (r, 0, 0), (0, 0, 0), (r * cos(a / 2), r * sin(a / 2), 0), (r * cos(a / 2), -r * sin(a / 2), 0), (0, 0, 0)]) dimer.calc = calc E = []
interaction = LJInteractions({('O', 'O'): (epsilon0, sigma0)}) for selection in [[0, 1, 2], [3, 4, 5]]: name = ''.join(str(i) for i in selection) dimer = Atoms('OH2OH2', [(0, 0, 0), (-r * cos(a / 2), r * sin(a / 2), 0), (-r * cos(a / 2), -r * sin(a / 2), 0), (0, 0, 0), (-r * cos(a), 0, r * sin(a)), (-r, 0, 0)]) dimer.positions[3:, 0] += 2.8 dimer.constraints = FixBondLengths([ ((selection[i] + 3) % 6, (selection[i - 1] + 3) % 6) for i in range(3) ]) dimer.calc = EIQMMM(selection, GPAW(txt=name + '.txt', h=0.16), TIP4P(), interaction, vacuum=4, embedding=Embedding(rc=0.2, rc2=20, width=1), output=name + '.out') opt = LBFGS(dimer, trajectory=name + '.traj') opt.run(0.02) monomer = dimer[selection] monomer.center(vacuum=4) monomer.calc = GPAW(txt=name + 'M.txt', h=0.16) opt = PreconLBFGS(monomer, precon=Exp(A=3), trajectory=name + 'M.traj') opt.run(0.02) e0 = monomer.get_potential_energy() be = dimer.get_potential_energy() - e0 d = dimer.get_distance(0, 3) print(name, be, d)
def test_qmmm(testdir): r = rOH a = angleHOH * pi / 180 # From https://doi.org/10.1063/1.445869 eexp = 6.50 * units.kcal / units.mol dexp = 2.74 aexp = 27 D = np.linspace(2.5, 3.5, 30) i = LJInteractions({('O', 'O'): (epsilon0, sigma0)}) # General LJ interaction object sigma_mm = np.array([0, 0, sigma0]) epsilon_mm = np.array([0, 0, epsilon0]) sigma_qm = np.array([0, 0, sigma0]) epsilon_qm = np.array([0, 0, epsilon0]) ig = LJInteractionsGeneral(sigma_qm, epsilon_qm, sigma_mm, epsilon_mm, 3) for calc in [ TIP3P(), SimpleQMMM([0, 1, 2], TIP3P(), TIP3P(), TIP3P()), SimpleQMMM([0, 1, 2], TIP3P(), TIP3P(), TIP3P(), vacuum=3.0), EIQMMM([0, 1, 2], TIP3P(), TIP3P(), i), EIQMMM([3, 4, 5], TIP3P(), TIP3P(), i, vacuum=3.0), EIQMMM([0, 1, 2], TIP3P(), TIP3P(), i, vacuum=3.0), EIQMMM([0, 1, 2], TIP3P(), TIP3P(), ig), EIQMMM([3, 4, 5], TIP3P(), TIP3P(), ig, vacuum=3.0), EIQMMM([0, 1, 2], TIP3P(), TIP3P(), ig, vacuum=3.0) ]: dimer = Atoms('H2OH2O', [(r * cos(a), 0, r * sin(a)), (r, 0, 0), (0, 0, 0), (r * cos(a / 2), r * sin(a / 2), 0), (r * cos(a / 2), -r * sin(a / 2), 0), (0, 0, 0)]) dimer.calc = calc E = [] F = [] for d in D: dimer.positions[3:, 0] += d - dimer.positions[5, 0] E.append(dimer.get_potential_energy()) F.append(dimer.get_forces()) F = np.array(F) F1 = np.polyval(np.polyder(np.polyfit(D, E, 7)), D) F2 = F[:, :3, 0].sum(1) error = abs(F1 - F2).max() assert error < 0.01 dimer.constraints = FixInternals(bonds=[(r, (0, 2)), (r, (1, 2)), (r, (3, 5)), (r, (4, 5))], angles_deg=[ (np.degrees(a), (0, 2, 1)), (np.degrees(a), (3, 5, 4)) ]) opt = GPMin(dimer, trajectory=calc.name + '.traj', logfile=calc.name + 'd.log') opt.run(0.01) e0 = dimer.get_potential_energy() d0 = dimer.get_distance(2, 5) R = dimer.positions v1 = R[1] - R[5] v2 = R[5] - (R[3] + R[4]) / 2 a0 = np.arccos( np.dot(v1, v2) / (np.dot(v1, v1) * np.dot(v2, v2))**0.5) / np.pi * 180 fmt = '{0:>20}: {1:.3f} {2:.3f} {3:.3f} {4:.1f}' print(fmt.format(calc.name, -min(E), -e0, d0, a0)) assert abs(e0 + eexp) < 0.002 assert abs(d0 - dexp) < 0.01 assert abs(a0 - aexp) < 4 print(fmt.format('reference', 9.999, eexp, dexp, aexp))
def test_turbomole_qmmm(): """Test the Turbomole calculator in simple QMMM and explicit interaction QMMM simulations.""" r = rOH a = angleHOH * pi / 180 D = np.linspace(2.5, 3.5, 30) interaction = LJInteractions({('O', 'O'): (epsilon0, sigma0)}) qm_par = {'esp fit': 'kollman', 'multiplicity': 1} for calc in [ TIP3P(), SimpleQMMM([0, 1, 2], Turbomole(**qm_par), TIP3P(), TIP3P()), SimpleQMMM([0, 1, 2], Turbomole(**qm_par), TIP3P(), TIP3P(), vacuum=3.0), EIQMMM([0, 1, 2], Turbomole(**qm_par), TIP3P(), interaction), EIQMMM([3, 4, 5], Turbomole(**qm_par), TIP3P(), interaction, vacuum=3.0), EIQMMM([0, 1, 2], Turbomole(**qm_par), TIP3P(), interaction, vacuum=3.0) ]: dimer = Atoms('H2OH2O', [(r * cos(a), 0, r * sin(a)), (r, 0, 0), (0, 0, 0), (r * cos(a / 2), r * sin(a / 2), 0), (r * cos(a / 2), -r * sin(a / 2), 0), (0, 0, 0)]) dimer.calc = calc E = [] F = [] for d in D: dimer.positions[3:, 0] += d - dimer.positions[5, 0] E.append(dimer.get_potential_energy()) F.append(dimer.get_forces()) F = np.array(F) F1 = np.polyval(np.polyder(np.polyfit(D, E, 7)), D) F2 = F[:, :3, 0].sum(1) error = abs(F1 - F2).max() assert error < 0.9 dimer.set_constraint( FixInternals(bonds=[(r, (0, 2)), (r, (1, 2)), (r, (3, 5)), (r, (4, 5))], angles_deg=[(angleHOH, (0, 2, 1)), (angleHOH, (3, 5, 4))])) opt = BFGS(dimer, trajectory=calc.name + '.traj', logfile=calc.name + 'd.log') opt.run(0.01) e0 = dimer.get_potential_energy() d0 = dimer.get_distance(2, 5) R = dimer.positions v1 = R[1] - R[5] v2 = R[5] - (R[3] + R[4]) / 2 a0 = np.arccos( np.dot(v1, v2) / (np.dot(v1, v1) * np.dot(v2, v2))**0.5) / np.pi * 180 fmt = '{0:>20}: {1:.3f} {2:.3f} {3:.3f} {4:.1f}' print(fmt.format(calc.name, -min(E), -e0, d0, a0))
import ase.units as units from ase.calculators.tip3p import TIP3P, epsilon0, sigma0, rOH, angleHOH from ase.calculators.qmmm import SimpleQMMM, EIQMMM, LJInteractions from ase.data.s22 import create_s22_system as s22 from ase.md.verlet import VelocityVerlet from ase.constraints import FixBondLengths i = LJInteractions({('O', 'O'): (epsilon0, sigma0)}) for calc in [ TIP3P(), SimpleQMMM([0, 1, 2], TIP3P(), TIP3P(), TIP3P()), EIQMMM([0, 1, 2], TIP3P(), TIP3P(), i) ]: dimer = s22('Water_dimer') for m in [0, 3]: dimer.set_angle(m + 1, m, m + 2, angleHOH) dimer.set_distance(m, m + 1, rOH, fix=0) dimer.set_distance(m, m + 2, rOH, fix=0) fixOH1 = [(3 * i, 3 * i + 1) for i in range(2)] fixOH2 = [(3 * i, 3 * i + 2) for i in range(2)] fixHH = [(3 * i + 1, 3 * i + 2) for i in range(2)] dimer.set_constraint(FixBondLengths(fixOH1 + fixOH2 + fixHH)) dimer.calc = calc e = dimer.get_potential_energy() md = VelocityVerlet(dimer, 2.0 * units.fs,
from __future__ import print_function from ase.data import s22 from ase.calculators.tip3p import TIP3P, epsilon0, sigma0 from ase.calculators.qmmm import EIQMMM, LJInteractions, Embedding from gpaw import GPAW # Create system atoms = s22.create_s22_system('Water_dimer') atoms.center(vacuum=4.0) # Make QM atoms selection of first water molecule: qm_idx = range(3) # Set up interaction & embedding object interaction = LJInteractions({('O', 'O'): (epsilon0, sigma0)}) embedding = Embedding(rc=0.02) # Short range analytical potential cutoff # Set up calculator atoms.calc = EIQMMM(qm_idx, GPAW(txt='qm.out'), TIP3P(), interaction, embedding=embedding, vacuum=None, # if None, QM cell = MM cell output='qmmm.log') print(atoms.get_potential_energy())
a = angleHOH * np.pi / 180 # From http://dx.doi.org/10.1063/1.445869 eexp = 6.24 * units.kcal / units.mol dexp = 2.75 aexp = 46 D = np.linspace(2.5, 3.5, 30) inter = LJInteractions({('O', 'O'): (epsilon0, sigma0)}) for calc in [ TIP4P(), SimpleQMMM([0, 1, 2], TIP4P(), TIP4P(), TIP4P()), SimpleQMMM([0, 1, 2], TIP4P(), TIP4P(), TIP4P(), vacuum=3.0), EIQMMM([0, 1, 2], TIP4P(), TIP4P(), inter), EIQMMM([0, 1, 2], TIP4P(), TIP4P(), inter, vacuum=3.0), EIQMMM([3, 4, 5], TIP4P(), TIP4P(), inter, vacuum=3.0) ]: dimer = Atoms('OH2OH2', [(0, 0, 0), (r * cos(a), 0, r * sin(a)), (r, 0, 0), (0, 0, 0), (r * cos(a / 2), r * sin(a / 2), 0), (r * cos(a / 2), -r * sin(a / 2), 0)]) dimer.calc = calc E = [] F = [] for d in D: dimer.positions[3:, 0] += d - dimer.positions[3, 0] E.append(dimer.get_potential_energy()) F.append(dimer.get_forces()) F = np.array(F)
r = rOH a = angleHOH * pi / 180 D = np.linspace(2.5, 3.5, 30) interaction = LJInteractions({('O', 'O'): (epsilon0, sigma0)}) qm_par = {'esp fit': 'kollman', 'multiplicity': 1} for calc in [ TIP3P(), SimpleQMMM([0, 1, 2], Turbomole(**qm_par), TIP3P(), TIP3P()), SimpleQMMM([0, 1, 2], Turbomole(**qm_par), TIP3P(), TIP3P(), vacuum=3.0), EIQMMM([0, 1, 2], Turbomole(**qm_par), TIP3P(), interaction), EIQMMM([3, 4, 5], Turbomole(**qm_par), TIP3P(), interaction, vacuum=3.0), EIQMMM([0, 1, 2], Turbomole(**qm_par), TIP3P(), interaction, vacuum=3.0) ]: dimer = Atoms('H2OH2O', [(r * cos(a), 0, r * sin(a)), (r, 0, 0), (0, 0, 0), (r * cos(a / 2), r * sin(a / 2), 0), (r * cos(a / 2), -r * sin(a / 2), 0), (0, 0, 0)]) dimer.calc = calc