forked from lijiext/lammps
updated documentation and examples for coreshell
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Hendrik Heenen
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@ -2573,7 +2573,7 @@ well.
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6.26 Adiabatic core/shell model :link(howto_26),h4
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The adiabatic core-shell model by "Mitchell and
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Finchham"_#MitchellFinchham is a simple method for adding
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Fincham"_#MitchellFincham is a simple method for adding
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polarizability to a system. In order to mimic the electron shell of
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an ion, a satellite particle is attached to it. This way the ions are
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split into a core and a shell where the latter is meant to react to
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@ -2667,13 +2667,16 @@ bond_coeff 1 63.014 0.0
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bond_coeff 2 25.724 0.0 :pre
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When running dynamics with the adiabatic core/shell model, the
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following issues should be considered. Since the relative motion of
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the core and shell particles corresponds to the polarization, typical
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thermostats can alter the polarization behaviour, meaning the shell
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will not react freely to its electrostatic environment. This is
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critical during the equilibration of the system. Therefore
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it's typically desirable to decouple the relative motion of the
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core/shell pair, which is an imaginary degree of freedom, from the
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following issues should be considered. The relative motion of
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the core and shell particles corresponds to the polarization,
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hereby an instantaneous relaxation of the shells is approximated
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and a fast core/shell spring frequency ensures a nearly constant
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internal kinetic energy during the simulation.
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Thermostats can alter this polarization behaviour, by scaling the
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internal kinetic energy, meaning the shell will not react freely to
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its electrostatic environment.
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Therefore it is typically desirable to decouple the relative motion of
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the core/shell pair, which is an imaginary degree of freedom, from the
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real physical system. To do that, the "compute
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temp/cs"_compute_temp_cs.html command can be used, in conjunction with
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any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix
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@ -2704,6 +2707,22 @@ fix thermostatequ all nve # integrator as needed f
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fix_modify thermoberendsen temp CSequ
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thermo_modify temp CSequ # output of center-of-mass derived temperature :pre
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The pressure for the core/shell system is computed via the regular
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LAMMPS convention by "treating the cores and shells as individual
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particles"_#MitchellFincham2. For the thermo output of the pressure
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as well as for the application of a barostat, it is necessary to
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use an additional "pressure"_compute_pressure compute based on the
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default "temperature"_compute_temp and specifying it as a second
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argument in "fix modify"_fix_modify.html and
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"thermo_modify"_thermo_modify.html resulting in:
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(...)
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compute CSequ all temp/cs cores shells
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compute thermo_press_lmp all pressure thermo_temp # pressure for individual particles
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thermo_modify temp CSequ press thermo_press_lmp # modify thermo to regular pressure
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fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4
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fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification for correct kinetic scalar :pre
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If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
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relative motion of the core and the shell should in theory be
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stable. However numerical fluctuation can introduce a small
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@ -2724,24 +2743,18 @@ temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
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velocity all create 1427 134 bias yes temp CSequ
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velocity all scale 1427 temp CSequ :pre
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It is important to note that the polarizability of the core/shell
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pairs is based on their relative motion. Therefore the choice of
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spring force and mass ratio need to ensure much faster relative motion
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of the 2 atoms within the core/shell pair than their center-of-mass
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velocity. This allow the shells to effectively react instantaneously
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to the electrostatic environment. This fast movement also limits the
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timestep size that can be used.
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To maintain the correct polarizability of the core/shell pairs, the
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kinetic energy of the internal motion shall remain nearly constant.
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Therefore the choice of spring force and mass ratio need to ensure
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much faster relative motion of the 2 atoms within the core/shell pair
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than their center-of-mass velocity. This allows the shells to
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effectively react instantaneously to the electrostatic environment and
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limits energy transfer to or from the core/shell oscillators.
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This fast movement also dictates the timestep that can be used.
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The primary literature of the adiabatic core/shell model suggests that
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the fast relative motion of the core/shell pairs only allows negligible
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energy transfer to the environment. Therefore it is not intended to
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decouple the core/shell degree of freedom from the physical system
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during production runs. In other words, the "compute
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temp/cs"_compute_temp_cs.html command should not be used during
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production runs and is only required during equilibration. This way one
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is consistent with literature (based on the code packages DL_POLY or
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GULP for instance).
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energy transfer to the environment.
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The mentioned energy transfer will typically lead to a small drift
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in total energy over time. This internal energy can be monitored
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using the "compute chunk/atom"_compute_chunk_atom.html and "compute
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@ -2761,14 +2774,20 @@ command, to use as input to the "compute
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chunk/atom"_compute_chunk_atom.html command to define the core/shell
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pairs as chunks.
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For example,
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For example if core/shell pairs are the only molecules:
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read_data NaCl_CS_x0.1_prop.data
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compute prop all property/atom molecule
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compute cs_chunk all chunk/atom c_prop
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compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
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fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre
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For example if core/shell pairs and other molecules are present:
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fix csinfo all property/atom i_CSID # property/atom command
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read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file
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compute prop all property/atom i_CSID
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compute cs_chunk all chunk/atom c_prop
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compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
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fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre
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(...) :pre
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The additional section in the date file would be formatted like this:
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@ -2890,9 +2909,13 @@ Phys, 79, 926 (1983).
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:link(Shinoda)
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[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
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:link(MitchellFinchham)
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[(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
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:link(MitchellFincham)
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[(Mitchell and Fincham)] Mitchell, Finchham, J Phys Condensed Matter,
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5, 1031-1038 (1993).
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:link(MitchellFincham2)
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[(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter,
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6, 393-404 (1994).
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:link(howto-Lamoureux)
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[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
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@ -40,7 +40,8 @@ thermo 50
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thermo_style custom step etotal pe ke temp press &
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epair evdwl ecoul elong ebond fnorm fmax vol
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compute CSequ all temp/cs cores shells
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compute CStemp all temp/cs cores shells
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compute thermo_press_lmp all pressure thermo_temp # press for correct kinetic scalar
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# output via chunk method
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@ -49,16 +50,18 @@ compute CSequ all temp/cs cores shells
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#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
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#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
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thermo_modify temp CSequ
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thermo_modify temp CStemp press thermo_press_lmp
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# velocity bias option
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velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
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velocity all scale 1427 temp CSequ
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velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CStemp
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velocity all scale 1427 temp CStemp
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# thermostating using the core/shell decoupling
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fix thermoberendsen all temp/berendsen 1427 1427 0.4
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fix nve all nve
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fix_modify thermoberendsen temp CSequ
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fix_modify thermoberendsen temp CStemp
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# 2 fmsec timestep
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@ -0,0 +1,86 @@
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# Testsystem for core-shell model compared to Mitchel and Finchham
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# Hendrik Heenen, June 2014
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# ------------------------ INITIALIZATION ----------------------------
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units metal
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dimension 3
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boundary p p p
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atom_style full
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# ----------------------- ATOM DEFINITION ----------------------------
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fix csinfo all property/atom i_CSID
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read_data data.coreshell fix csinfo NULL CS-Info
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group cores type 1 2
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group shells type 3 4
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neighbor 2.0 bin
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comm_modify vel yes
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# ------------------------ FORCE FIELDS ------------------------------
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kspace_style ewald 1.0e-6
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pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
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pair_coeff * * 0.0 1.000 0.00 0.00 0.00
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pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
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pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
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pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
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bond_style harmonic
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bond_coeff 1 63.014 0.0
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bond_coeff 2 25.724 0.0
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# ------------------------ Equilibration Run -------------------------------
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reset_timestep 0
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thermo 50
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thermo_style custom step etotal pe ke temp press &
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epair evdwl ecoul elong ebond fnorm fmax vol
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compute CStemp all temp/cs cores shells
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compute thermo_press_lmp all pressure thermo_temp # press for correct kinetic scalar
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# output via chunk method
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#compute prop all property/atom i_CSID
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#compute cs_chunk all chunk/atom c_prop
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#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
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#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
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thermo_modify temp CStemp press thermo_press_lmp
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# 2 fmsec timestep
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timestep 0.002
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# velocity bias option
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velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CStemp
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velocity all scale 1427 temp CStemp
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# thermostating using the core/shell decoupling
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fix thermoberendsen all temp/berendsen 1427 1427 0.4
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fix nve all nve
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fix_modify thermoberendsen temp CStemp
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run 500
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unfix thermoberendsen
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unfix nve
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fix npt_equ all npt temp 1427 1427 0.04 iso 0 0 0.4
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fix_modify npt_equ temp CStemp press thermo_press_lmp # pressure for correct kinetic scalar
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run 500
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unfix npt_equ
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# ------------------------ Dynamic Run -------------------------------
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fix npt_dyn all npt temp 1427 1427 0.04 iso 0 0 0.4
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fix_modify npt_dyn temp CStemp press thermo_press_lmp # pressure for correct kinetic scalar
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run 1000
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