Giovanni Borghi

Moleculardynamics: ([email protected])
doingitbyCar....

andParrinello

Hands-on Shanghai, July 2013

 BornOppenheimermoleculardynamics
Ionsaretreatedclassically Relax electrons
Electronsaretreatedquantummechanically
Ionicmass>>>>Electronicmass:iondynamicsisdecoupledfrom
electrondynamics;i.e.ionicforcesaredeterminedbytheground
stateelectronicchargedensityforeveryionicconfiguration
Move ions

Ions: heavy, Electrons: light,

but computationally but computationally
light heavy

CarParrinellomoleculardynamics
Move
Ionsaretreatedclassically ions & electrons
Electronsaretreatedquantummechanically,buttheyare
assignedafake,unphysical,kineticenergy Cheaper!
Iondynamicsandelectrondynamicsaremoreorlesscoupled,
dependingonionicand(fake)electronicmassvalues(thefake
electronicmassisnotnecessarilythephysicalone)
CPtrick:fakeLangevin
dynamics
Fake because electrons are quantum, they obey Schroedinger
equation with a single time derivative, rather than a double one
 TheCPsuiteonmylaptop

Online input description

http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_CP.html
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_CPPP.html
 RunningCP!

CPpostprocessing:CPPP!
 CPMDrun:whattodoinpractice
Set some ATOMC_POSITIONS

dt=XXX
Relax electronic wavefunction: orthogonalization=
(electron_dynamics='damp' 'Gram-Schmidt'
ion_dynamics='none')

dt=XXX (larger number)

orthogonalization=
If you want ions at 'ortho' (default)
equilibrium positions:
(electron_dynamics='damp'
ion_dynamics='damp') Now initial positions are set!
ion_velocities='from_input'
('random', 'zero')
Perform MD run: electron_velocities='default'
(electron_dynamics='verlet' ('zero')
ion_dynamics='verlet') Now initial velocities are set!
 CPunits:atomicunits Unless differently
specified!!

2.418 x 10-5 ps.

27.211.. eV
o
Temperature: 315770 Kelvin
Let'slookatsomeinputfiles

Simple case: H2 molecule

Ionic mass

H H
 Onefirstrelaxeselectronic
degreesoffreedom:
dtsmall+'ortho'
ordtlarge+'Gram-Schmidt'

NeveruseGramSchmidtinmolecular
(undamped)dynamics:itdoesnotwork!
 Then:
largerdt,and'ortho'

'ortho'isthedefault
orthogonalization
Ionic+electronicrelaxation:
structuraloptimization
MDrun,nodamping,
'verlet'dynamics
 CPunits:atomicunits Unless differently
specified!!

In the input file:

Ecutwfc ---> Ry (0.5 EH) Ecutrho ---> Ry (0.5 EH)

Ionic mass ---> a.m.u (=1/12 of C12 mass, =1823 me)

ATOMIC_POSITIONS: (Bohr, angstrom, crystal)

Tempw --->oK fnosep --->THz (3 THz=100 cm-1)

In the output file:

Electronic eigenvalues ---> (eV), ion temperature (oK)
In 'prefix.evp':
Time---> picoseconds (ps)
Ionic temperature (tempp) ---> oK
Units should be specified either in input/output files, or in
the online input description
 Whatdowehaveasoutput?
&control
outdir='outdir',
prefix='prefix',
ndr=$ndr, ndw=$ndw
restart_mode= 'from_scratch'
('restart','reset_counters')

EVERY ... iprint_stdout, iprint, isave STEPS

Prints in Saves quantities

Prints in: inside 'outdir':
standard output:
'prefix'.pos (ion positions), 'prefix'_$ndr.save
my_simulation.out
'prefix'.vel (ion velocities),
'prefix'.cel (cell parameters),
'prefix'.evp (energies, potentials),
'prefix'.eig (electronic eigenvalues),
...
every iprint_output steps,
we get a summary of
energy, positions,
velocities, cell parameters
 Interestingfile:'prefix'.evp

nfi---> number of iterations

ekinc---> electron fake kinetic energy
temphc(oK)---> temperature due to cell kinetic energy
tempp(oK)---> temperature due to ionic displacements within the cell
etot---> dft total energy (without ionic and cell kinetic energy)
enthal---> etot+external_pressure*volume
econs---> etot+kinetic_energy_due_to_ions_moving
econt---> econs+ekinc+(thermostat_total_energy)
tps(ps)---> time
...

...

...

...
Handsonexercise1:cponH2
 Relax electronic wavefunction

Damped dynamics Undamped dynamics

electrons+ions

Care in choosing Role of electronic

damping fake mass
and vs
time step ionic mass
 Sampleinputfiles:H.erelax.start.in

&control &electrons
calculation='cp', electron_dynamics='xxx',
restart_mode='from_scratch', electron_damping=xxx,
nstep=xxx, iprint=2, isave=20, startingwfc='random', ampre=0.01,
dt=xxx, emass=xxx, emass_cutoff=3.,
ndr=90, ndw=91, orthogonalization='xxx',
pseudo_dir='./pseudo/', /
outdir='./tmp/', &ions
/ ion_dynamics='none',
&system ion_radius(1)=1.0,
ibrav=0, /
nat=2, ntyp=1, nbnd=1, nspin=1, ATOMIC_SPECIES
ecutwfc=30.0, ecutrho=120.0, H 1.00 H.pz-vbc.UPF
/ ATOMIC_POSITIONS angstrom
H -0.4 0. 0.
H 0.4 0. 0.
CELL_PARAMETERS angstrom
20.0 0. 0.
0.0 20.0 0.
0.0 0. 20.
 Sampleinputfiles:H.erelax.restart.in

&control &electrons
calculation='cp', electron_dynamics='xxx',
restart_mode='restart', electron_damping=xxx
nstep=xxx, iprint=2, isave=40, ortho_max=100,
dt=xxx, emass=xxx,
ndr=91, ndw=92, emass_cutoff=3.,
pseudo_dir='./pseudo/', /
outdir='./tmp/', &ions
etot_conv_thr=1.e-7, ion_dynamics='none',
/ ion_radius(1)=1.0,
&system /
ibrav=0, ATOMIC_SPECIES
nat=2, ntyp=1, nbnd=1, nspin=1, H 1.00 H.pz-vbc.UPF
ecutwfc=30.0, ecutrho=120.0, ATOMIC_POSITIONS angstrom
/ H -0.4 0. 0.
H 0.4 0. 0.
CELL_PARAMETERS angstrom
20.0 0. 0.
0.0 20.0 0.
0.0 0. 20.
 Sampleinputfiles:H.ionrelax.in
&electrons
electron_dynamics='xxx',
&control electron_damping=0.001,
calculation='cp', ortho_max=100,
restart_mode='restart', emass=500,
nstep=xxx, iprint=2, isave=20, emass_cutoff=3.,
dt=xxx, electron_velocities='zero',
ndr=94, ndw=941, /
pseudo_dir='./pseudo/', &ions
outdir='./tmp/', ion_dynamics='xxx',
ekin_conv_thr=xxx, ion_velocities='zero',
etot_conv_thr=xxx, ion_radius(1)=1.0,
forc_conv_thr=xxx, ion_damping=0.01
/ /
&system ATOMIC_SPECIES
ibrav=0, H 1.00 H.pz-vbc.UPF
nat=2, ntyp=1, nbnd=1, nspin=1, ATOMIC_POSITIONS angstrom
ecutwfc=30.0, ecutrho=120.0, H -0.4 0. 0.
/ H 0.4 0. 0.
CELL_PARAMETERS angstrom
20.0 0. 0.
0.0 20.0 0.
0.0 0. 20.
 Sampleinputfiles:H.md.in

&control &electrons
calculation='cp', electron_dynamics='xxx',
restart_mode='reset_counters', ortho_max=100,
nstep=100, iprint=1, isave=10, emass=500,
dt=8, emass_cutoff=3.,
ndr=92, ndw=932, /
pseudo_dir='./pseudo/', &ions
outdir='./tmp/', ion_dynamics='xxx',
/ ion_radius(1)=1.0
&system /
ibrav=0, ATOMIC_SPECIES
nat=2, ntyp=1, nbnd=1, nspin=1, H 1.00 H.pz-vbc.UPF
ecutwfc=30.0, ecutrho=120.0, ATOMIC_POSITIONS angstrom
/ H -0.4 0. 0.
H 0.4 0. 0.
CELL_PARAMETERS angstrom
20.0 0. 0.
0.0 20.0 0.
0.0 0. 20.
 Someplots:
Adjustingtheelectronicdampingforoptimalconvergence
 Someplots:
Adjustingtheionicdampingforoptimalconvergence
 Electron&ionmass:theirrole

1823

This is the true picture What happens if we increase emass?

emass=1 emass=300
ion mass=1823 ion mass=1823

1 vs 1823 300 vs 1823

Alargeelectronmass'drags'theions
Handsonexercise2:silicon
 Relax electronic wavefunction

Undamped dynamics Undamped dynamics

electrons+ions electrons+ions
no thermostat with thermostat

How a Nose thermostat works.

Behavior of the different energy terms
in the output files of cp.
 Sampleinputfiles:Si.erelax.start.in

&control &electrons
calculation='cp', electron_dynamics='xxx',
restart_mode='from_scratch', electron_damping=0.1,
nstep=xxx, iprint=20, isave=20, startingwfc='random', ampre=0.01,
dt=xxx, orthogonalization='xxx',
ndr=90, ndw=91, emass=xxx, emass_cutoff=3.,
pseudo_dir='./pseudo/', /
outdir='./tmp/', &ions
/ ion_dynamics='xxx',
&system ion_radius(1)=1.0,
ibrav=0, /
nat=xxx, ntyp=1, nbnd=xxx, nspin=1, ATOMIC_SPECIES
ecutwfc=20.0, ecutrho=80.0, Si 28.0855 Si.pz-vbc.UPF
/ ATOMIC_POSITIONS angstrom
.
 Sampleinputfiles:Si.erelax.restart.in

&control &electrons
calculation='cp', electron_dynamics='xxx',
restart_mode='restart', electron_damping=xxx,
nstep=xxx, iprint=10, isave=50, emass=700., emass_cutoff=3.,
dt=xxx, /
ndr=91, ndw=92, &ions
pseudo_dir='./pseudo/', ion_dynamics='xxx',
outdir='./tmp/', ion_radius(1)=1.0,
etot_conv_thr=xxx /
/ ATOMIC_SPECIES
&system Si 28.0855 Si.pz-vbc.UPF
ibrav=0, ATOMIC_POSITIONS angstrom
nat=xxx, ntyp=1, nbnd=xxx, nspin=1,
ecutwfc=20.0, ecutrho=80.0,
/
 Sampleinputfiles:Si.md.in

&control &electrons
calculation='cp', electron_dynamics='xxx',
restart_mode='reset_counters', ortho_max=100,
nstep=4000, iprint=10, isave=100, emass=100., emass_cutoff=3.,
dt=4.0, /
ndr=92, ndw=931, &ions
pseudo_dir='./pseudo/', ion_dynamics='xxx',
outdir='./tmp/', ion_radius(1)=1.0
/ /
&system ATOMIC_SPECIES
ibrav=0, Si 28.0855 Si.pz-vbc.UPF
nat=16, ntyp=1, nbnd=32, nspin=1, ATOMIC_POSITIONS angstrom
ecutwfc=20.0, ecutrho=80.0,
/
 Sampleinputfiles:Si.md_th.in

&control &electrons
calculation='cp', electron_dynamics='xxx',
restart_mode='reset_counters', ortho_max=100,
nstep=6000, iprint=10, isave=100, emass=100., emass_cutoff=3.,
dt=4.0, /
ndr=92, ndw=932, &ions
pseudo_dir='./pseudo/', ion_dynamics='verlet',
outdir='./tmp/', ion_temperature='nose',
/ tempw=300, fnosep=xxx,
&system ion_radius(1)=1.0,
ibrav=0, /
nat=xxx, ntyp=1, nbnd=xxx, nspin=1, ATOMIC_SPECIES
ecutwfc=20.0, ecutrho=80.0, Si 28.0855 Si.pz-vbc.UPF
/
Someplots
Etot,econs,econt(nothermostat)
Econs,econt(nothermostat)
Ekinc(nothermostat)
Temperature(nothermostat)
Temperature(thermostat)
Etot,econs,econt(thermostat)
Econsetotandtemperature

Which is the proportionality

coefficient?
cppp.xinputfile:movies

&INPUTPP
prefix = 'cp' ,
fileout = 'postproc' ,
outdir = './tmp' ,
output = 'xsf' ,
ndr = 931 ,
lcharge = .false. ,
atomic_number(1)=1 ,
ldynamics = .true. ,
nframes = 200 ,
/

This produces a film .axsf

that you can open with
xcrysden