clean up doc src
This commit is contained in:
Steve Plimpton
@ -4,7 +4,7 @@
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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:line
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6. How-to discussions :h3
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@ -522,7 +522,7 @@ H mass = 1.008
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O charge = -1.040
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H charge = 0.520
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r0 of OH bond = 0.9572
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theta of HOH angle = 104.52
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theta of HOH angle = 104.52
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OM distance = 0.15
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LJ epsilon of O-O = 0.1550
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LJ sigma of O-O = 3.1536
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@ -629,7 +629,7 @@ the SPC and SPC/E models.
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Wikipedia also has a nice article on "water
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models"_http://en.wikipedia.org/wiki/Water_model.
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:line
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:line
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6.10 Coupling LAMMPS to other codes :link(howto_10),h4
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@ -729,7 +729,7 @@ LAMMPS and half to the other code and run both codes simultaneously
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before syncing them up periodically. Or it might instantiate multiple
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instances of LAMMPS to perform different calculations.
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:line
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:line
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6.11 Visualizing LAMMPS snapshots :link(howto_11),h4
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@ -832,7 +832,7 @@ rotation of [A], [B], and [C] and can be computed as follows:
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where A = | [A] | indicates the scalar length of [A]. The hat symbol (^)
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indicates the corresponding unit vector. {beta} and {gamma} are angles
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between the vectors described below. Note that by construction,
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between the vectors described below. Note that by construction,
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[a], [b], and [c] have strictly positive x, y, and z components, respectively.
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If it should happen that
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[A], [B], and [C] form a left-handed basis, then the above equations
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@ -841,17 +841,17 @@ to first apply an inversion. This can be achieved
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by interchanging two basis vectors or by changing the sign of one of them.
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For consistency, the same rotation/inversion applied to the basis vectors
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must also be applied to atom positions, velocities,
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must also be applied to atom positions, velocities,
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and any other vector quantities.
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This can be conveniently achieved by first converting to
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This can be conveniently achieved by first converting to
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fractional coordinates in the
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old basis and then converting to distance coordinates in the new basis.
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The transformation is given by the following equation:
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:c,image(Eqs/rotate.jpg)
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where {V} is the volume of the box, [X] is the original vector quantity and
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[x] is the vector in the LAMMPS basis.
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where {V} is the volume of the box, [X] is the original vector quantity and
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[x] is the vector in the LAMMPS basis.
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There is no requirement that a triclinic box be periodic in any
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dimension, though it typically should be in at least the 2nd dimension
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@ -938,17 +938,17 @@ defined above. The relationship between these 6 quantities
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(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) =
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(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
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:c,image(Eqs/box.jpg)
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:c,image(Eqs/box.jpg)
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The inverse relationship can be written as follows:
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:c,image(Eqs/box_inverse.jpg)
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:c,image(Eqs/box_inverse.jpg)
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The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed
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out or accessed by computes using the
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"thermo_style custom"_thermo_style.html keywords
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The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed
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out or accessed by computes using the
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"thermo_style custom"_thermo_style.html keywords
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{cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma},
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respectively.
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respectively.
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As discussed on the "dump"_dump.html command doc page, when the BOX
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BOUNDS for a snapshot is written to a dump file for a triclinic box,
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@ -2130,7 +2130,7 @@ but uses the Einstein formulation, analogous to the Einstein
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mean-square-displacement formulation for self-diffusivity. The
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time-integrated momentum fluxes play the role of Cartesian
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coordinates, whose mean-square displacement increases linearly
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with time at sufficiently long times.
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with time at sufficiently long times.
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:line
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@ -2510,8 +2510,8 @@ the electrostatic environment inducing polarizability.
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Technically, shells are attached to the cores by a spring force f =
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k*r where k is a parametrized spring constant and r is the distance
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between the core and the shell. The charges of the core and the shell
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add up to the ion charge, thus q(ion) = q(core) + q(shell). This
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setup introduces the ion polarizability (alpha) given by
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add up to the ion charge, thus q(ion) = q(core) + q(shell). This
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setup introduces the ion polarizability (alpha) given by
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alpha = q(shell)^2 / k. In a
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similar fashion the mass of the ion is distributed on the core and the
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shell with the core having the larger mass.
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@ -2526,7 +2526,7 @@ for NaCl, as found in examples/coreshell, has this format:
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432 atoms # core and shell atoms
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216 bonds # number of core/shell springs :pre
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4 atom types # 2 cores and 2 shells for Na and Cl
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4 atom types # 2 cores and 2 shells for Na and Cl
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2 bond types :pre
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0.0 24.09597 xlo xhi
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@ -2545,19 +2545,19 @@ Atoms :pre
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1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1
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2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1
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3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2
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4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2
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4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2
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(...) :pre
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Bonds # Bond topology for spring forces :pre
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1 2 1 2 # spring for core/shell pair 1
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2 2 3 4 # spring for core/shell pair 2
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2 2 3 4 # spring for core/shell pair 2
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(...) :pre
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Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
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defined between the shells. Coulombic interactions are defined
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between all cores and shells. If desired, additional bonds can be
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specified between cores.
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specified between cores.
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The "special_bonds"_special_bonds.html command should be used to
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turn-off the Coulombic interaction within core/shell pairs, since that
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@ -2620,7 +2620,7 @@ Note that to perform thermostatting using this definition of
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temperature, the "fix modify temp"_fix_modify.html command should be
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used to assign the compute to the thermostat fix. Likewise the
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"thermo_modify temp"_thermo_modify.html command can be used to make
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this temperature be output for the overall system.
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this temperature be output for the overall system.
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For the NaCl example, this can be done as follows:
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@ -2632,13 +2632,13 @@ 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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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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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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momentum to the system, which is noticable over long trajectories.
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Therefore it is recomendable to use the "fix
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momentum"_fix_momentum.html command in combination with "compute
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temp/cs"_compute_temp_cs.html when equilibrating the system to
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Therefore it is recomendable to use the "fix
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momentum"_fix_momentum.html command in combination with "compute
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temp/cs"_compute_temp_cs.html when equilibrating the system to
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prevent any drift.
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When intializing the velocities of a system with core/shell pairs, it
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@ -2661,17 +2661,17 @@ to the electrostatic environment. This fast movement also limits the
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timestep size 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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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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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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The mentioned energy transfer will typically lead to a a small drift
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in total energy over time. This internal energy can be monitored
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The mentioned energy transfer will typically lead to a 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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temp/chunk"_compute_temp_chunk.html commands. The internal kinetic
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energies of each core/shell pair can then be summed using the sum()
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@ -2702,14 +2702,14 @@ The additional section in the date file would be formatted like this:
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CS-Info # header of additional section :pre
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1 1 # column 1 = atom ID, column 2 = core/shell ID
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2 1
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3 2
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4 2
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5 3
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6 3
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7 4
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8 4
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1 1 # column 1 = atom ID, column 2 = core/shell ID
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2 1
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3 2
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4 2
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5 3
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6 3
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7 4
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8 4
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(...) :pre
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:line
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