giovanni borghi molecular dynamics: doing it by car · bornoppenheimer molecular dynamics...
TRANSCRIPT
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Molecular dynamics: doing it by Car....
… and Parrinello
Hands-on Shanghai, July 2013
Giovanni Borghi([email protected])
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BornOppenheimer molecular dynamics
CarParrinello molecular dynamics
● Ions are treated classically● Electrons are treated quantum mechanically● Ionic mass >>>> Electronic mass: ion dynamics is decoupled from
electron dynamics; i.e. ionic forces are determined by the groundstate electronic charge density for every ionic configuration
● Ions are treated classically● Electrons are treated quantum mechanically, but they are
assigned a “fake”, unphysical, kinetic energy● Ion dynamics and electron dynamics are more or less coupled,
depending on ionic and (fake) electronic mass values (the fake electronic mass is not necessarily the physical one)
Cheaper!
Relax electrons
Move ions
Move ions & electrons
Ions: heavy,but computationally
light
Electrons: light,but computationally
heavy
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CP trick: fake Langevin dynamics
Fake because electrons are quantum, they obey Schroedingerequation with a single time derivative, rather than a double one
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The CP suite on my laptop
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_CP.html
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_CPPP.html
Online input description
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Running CP!
CP postprocessing: CPPP!
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CPMD run: what to do in practice
Relax electronic wavefunction:(electron_dynamics='damp'
ion_dynamics='none')
If you want ions atequilibrium positions:
(electron_dynamics='damp'ion_dynamics='damp')
Perform MD run:(electron_dynamics='verlet'
ion_dynamics='verlet')
dt=XXX orthogonalization=
'Gram-Schmidt'
dt=XXX (larger number) orthogonalization='ortho' (default)
ion_velocities='from_input'('random', 'zero')
Now initial positions are set!
Now initial velocities are set!
Set some ATOMC_POSITIONS
electron_velocities='default'('zero')
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CP units: atomic units
27.211.. eV
2.418 … x 10-5 ps.
Unless differently specified!!
Temperature: 315770 oKelvin
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Let's look at some input files
Simple case: H2 molecule
H H
Ionic mass
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One first relaxes electronicdegrees of freedom:dt small+'ortho'
or dt large+'Gram-Schmidt'
Never use GramSchmidt in molecular (undamped) dynamics: it does not work!
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Then:larger dt, and 'ortho'
'ortho' is the defaultorthogonalization
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Ionic+electronic relaxation:structural optimization
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MD run, no damping,'verlet' dynamics
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CP units: atomic units
Ecutwfc ---> Ry (0.5 EH)
Unless differently specified!!
Ecutrho ---> Ry (0.5 EH)
Ionic mass ---> a.m.u (=1/12 of C12 mass, =1823 me)
In the input file:
In the output file:
ATOMIC_POSITIONS: (Bohr, angstrom, crystal)
Electronic eigenvalues ---> (eV), ion temperature (oK)
In 'prefix.evp':
Time---> picoseconds (ps)Ionic temperature (tempp) ---> oK
Tempw --->oK fnosep --->THz (3 THz=100 cm-1)
Units should be specified either in input/output files, or in the online input description
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What do we have as output?
iprint_stdout, iprint, isave
Prints in:'prefix'.pos (ion positions), 'prefix'.vel (ion velocities),
'prefix'.cel (cell parameters),'prefix'.evp (energies, potentials), 'prefix'.eig (electronic eigenvalues),
...
Prints instandard output:my_simulation.out
Saves quantitiesinside 'outdir':
'prefix'_$ndr.save
EVERY ... … STEPS
&control outdir='outdir', prefix='prefix', ndr=$ndr, ndw=$ndw restart_mode= 'from_scratch' ('restart','reset_counters')
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every iprint_output steps,we get a summary of
energy, positions,velocities, cell parameters
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Interesting file: 'prefix'.evp
nfi---> number of iterationsekinc---> electron fake kinetic energytemphc(oK)---> temperature due to “cell” kinetic energytempp(oK)---> temperature due to ionic displacements within the celletot---> dft total energy (without ionic and cell kinetic energy)enthal---> etot+external_pressure*volumeecons---> etot+kinetic_energy_due_to_ions_movingecont---> econs+ekinc+(thermostat_total_energy)tps(ps)---> time
…...
…...
…...
…...
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Hands on exercise 1: cp on H2
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Relax electronic wavefunction
Damped dynamicselectrons+ions
Undamped dynamics
Role of electronicfake mass
vsionic mass
Care in choosingdamping
andtime step
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Sample input files : H.erelax.start.in
&control calculation='cp', restart_mode='from_scratch', nstep=xxx, iprint=2, isave=20, dt=xxx, ndr=90, ndw=91, pseudo_dir='./pseudo/', outdir='./tmp/', / &system ibrav=0, nat=2, ntyp=1, nbnd=1, nspin=1, ecutwfc=30.0, ecutrho=120.0, /
&electrons electron_dynamics='xxx', electron_damping=xxx, startingwfc='random', ampre=0.01, emass=xxx, emass_cutoff=3., orthogonalization='xxx', / &ions ion_dynamics='none', ion_radius(1)=1.0, /ATOMIC_SPECIES H 1.00 H.pz-vbc.UPFATOMIC_POSITIONS angstromH -0.4 0. 0.H 0.4 0. 0.CELL_PARAMETERS angstrom20.0 0. 0.0.0 20.0 0.0.0 0. 20.
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Sample input files : H.erelax.restart.in
&control calculation='cp', restart_mode='restart', nstep=xxx, iprint=2, isave=40, dt=xxx, ndr=91, ndw=92, pseudo_dir='./pseudo/', outdir='./tmp/', etot_conv_thr=1.e-7, / &system ibrav=0, nat=2, ntyp=1, nbnd=1, nspin=1, ecutwfc=30.0, ecutrho=120.0, /
&electrons electron_dynamics='xxx', electron_damping=xxx ortho_max=100, emass=xxx, emass_cutoff=3., / &ions ion_dynamics='none', ion_radius(1)=1.0, /ATOMIC_SPECIES H 1.00 H.pz-vbc.UPFATOMIC_POSITIONS angstromH -0.4 0. 0.H 0.4 0. 0.CELL_PARAMETERS angstrom20.0 0. 0.0.0 20.0 0.0.0 0. 20.
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Sample input files : H.ionrelax.in
&control calculation='cp', restart_mode='restart', nstep=xxx, iprint=2, isave=20, dt=xxx, ndr=94, ndw=941, pseudo_dir='./pseudo/', outdir='./tmp/', ekin_conv_thr=xxx, etot_conv_thr=xxx, forc_conv_thr=xxx, / &system ibrav=0, nat=2, ntyp=1, nbnd=1, nspin=1, ecutwfc=30.0, ecutrho=120.0, /
&electrons electron_dynamics='xxx', electron_damping=0.001, ortho_max=100, emass=500, emass_cutoff=3., electron_velocities='zero', / &ions ion_dynamics='xxx', ion_velocities='zero', ion_radius(1)=1.0, ion_damping=0.01 /ATOMIC_SPECIES H 1.00 H.pz-vbc.UPFATOMIC_POSITIONS angstromH -0.4 0. 0.H 0.4 0. 0.CELL_PARAMETERS angstrom20.0 0. 0.0.0 20.0 0.0.0 0. 20.
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Sample input files : H.md.in
&control calculation='cp', restart_mode='reset_counters', nstep=100, iprint=1, isave=10, dt=8, ndr=92, ndw=932, pseudo_dir='./pseudo/', outdir='./tmp/', / &system ibrav=0, nat=2, ntyp=1, nbnd=1, nspin=1, ecutwfc=30.0, ecutrho=120.0, /
&electrons electron_dynamics='xxx', ortho_max=100, emass=500, emass_cutoff=3., / &ions ion_dynamics='xxx', ion_radius(1)=1.0 /ATOMIC_SPECIES H 1.00 H.pz-vbc.UPFATOMIC_POSITIONS angstromH -0.4 0. 0.H 0.4 0. 0.CELL_PARAMETERS angstrom20.0 0. 0.0.0 20.0 0.0.0 0. 20.
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Some plots:Adjusting the electronic damping for optimal convergence
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Some plots:Adjusting the ionic damping for optimal convergence
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Electron & ion mass: their role
300 vs 1823
1823
1 vs 1823
This is the true picture
emass=1ion mass=1823
What happens if we increase emass?
emass=300ion mass=1823
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A large electron mass 'drags' the ions
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Hands on exercise 2: silicon
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Relax electronic wavefunction
Undamped dynamicselectrons+ionsno thermostat
Undamped dynamicselectrons+ions
with thermostat
How a Nose thermostat works.Behavior of the different energy terms
in the output files of cp.
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Sample input files : Si.erelax.start.in
&control calculation='cp', restart_mode='from_scratch', nstep=xxx, iprint=20, isave=20, dt=xxx, ndr=90, ndw=91, pseudo_dir='./pseudo/', outdir='./tmp/', / &system ibrav=0, nat=xxx, ntyp=1, nbnd=xxx, nspin=1, ecutwfc=20.0, ecutrho=80.0, /
&electrons electron_dynamics='xxx', electron_damping=0.1, startingwfc='random', ampre=0.01, orthogonalization='xxx', emass=xxx, emass_cutoff=3., / &ions ion_dynamics='xxx', ion_radius(1)=1.0, /ATOMIC_SPECIES Si 28.0855 Si.pz-vbc.UPFATOMIC_POSITIONS angstrom….
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Sample input files : Si.erelax.restart.in
&control calculation='cp', restart_mode='restart', nstep=xxx, iprint=10, isave=50, dt=xxx, ndr=91, ndw=92, pseudo_dir='./pseudo/', outdir='./tmp/', etot_conv_thr=xxx / &system ibrav=0, nat=xxx, ntyp=1, nbnd=xxx, nspin=1, ecutwfc=20.0, ecutrho=80.0, /
&electrons electron_dynamics='xxx', electron_damping=xxx, emass=700., emass_cutoff=3., / &ions ion_dynamics='xxx', ion_radius(1)=1.0, /ATOMIC_SPECIES Si 28.0855 Si.pz-vbc.UPFATOMIC_POSITIONS angstrom
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Sample input files : Si.md.in
&control calculation='cp', restart_mode='reset_counters', nstep=4000, iprint=10, isave=100, dt=4.0, ndr=92, ndw=931, pseudo_dir='./pseudo/', outdir='./tmp/', / &system ibrav=0, nat=16, ntyp=1, nbnd=32, nspin=1, ecutwfc=20.0, ecutrho=80.0, /
&electrons electron_dynamics='xxx', ortho_max=100, emass=100., emass_cutoff=3., / &ions ion_dynamics='xxx', ion_radius(1)=1.0 /ATOMIC_SPECIES Si 28.0855 Si.pz-vbc.UPFATOMIC_POSITIONS angstrom
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Sample input files : Si.md_th.in
&control calculation='cp', restart_mode='reset_counters', nstep=6000, iprint=10, isave=100, dt=4.0, ndr=92, ndw=932, pseudo_dir='./pseudo/', outdir='./tmp/', / &system ibrav=0, nat=xxx, ntyp=1, nbnd=xxx, nspin=1, ecutwfc=20.0, ecutrho=80.0, /
&electrons electron_dynamics='xxx', ortho_max=100, emass=100., emass_cutoff=3., / &ions ion_dynamics='verlet', ion_temperature='nose', tempw=300, fnosep=xxx, ion_radius(1)=1.0, /ATOMIC_SPECIES Si 28.0855 Si.pz-vbc.UPF
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Some plots
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Etot, econs, econt (nothermostat)
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Econs, econt (nothermostat)
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Ekinc (nothermostat)
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Temperature (nothermostat)
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Temperature (thermostat)
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Etot, econs, econt (thermostat)
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Econsetot and temperature
Which is the proportionalitycoefficient?
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&INPUTPP prefix = 'cp' , fileout = 'postproc' , outdir = './tmp' , output = 'xsf' , ndr = 931 , lcharge = .false. , atomic_number(1)=1 , ldynamics = .true. , nframes = 200 ,/
cppp.x input file: movies
This produces a film .axsfthat you can open with
xcrysden