initial commit. doc is in the works
This commit is contained in:
David Nicholson
@ -715,8 +715,10 @@ package"_Section_start.html#start_3.
|
||||
"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
|
||||
"nvk"_fix_nvk.html,
|
||||
"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
|
||||
"nvt/uef"_fix_nh_uef.html,
|
||||
"nph/eff"_fix_nh_eff.html,
|
||||
"npt/eff"_fix_nh_eff.html,
|
||||
"npt/uef"_fix_nh_uef.html,
|
||||
"nve/eff"_fix_nve_eff.html,
|
||||
"nvt/eff"_fix_nh_eff.html,
|
||||
"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
|
||||
@ -856,6 +858,7 @@ package"_Section_start.html#start_3.
|
||||
"meso/t/atom"_compute_meso_t_atom.html,
|
||||
"pe/tally"_compute_tally.html,
|
||||
"pe/mol/tally"_compute_tally.html,
|
||||
"pressure/uef"_compute_pressure_uef.html,
|
||||
"saed"_compute_saed.html,
|
||||
"smd/contact/radius"_compute_smd_contact_radius.html,
|
||||
"smd/damage"_compute_smd_damage.html,
|
||||
@ -884,6 +887,7 @@ package"_Section_start.html#start_3.
|
||||
"temp/deform/eff"_compute_temp_deform_eff.html,
|
||||
"temp/region/eff"_compute_temp_region_eff.html,
|
||||
"temp/rotate"_compute_temp_rotate.html,
|
||||
"temp/uef"_compute_temp_uef.html,
|
||||
"xrd"_compute_xrd.html :tb(c=6,ea=c)
|
||||
|
||||
:line
|
||||
|
||||
@ -150,6 +150,7 @@ Package, Description, Doc page, Example, Library
|
||||
"USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
|
||||
"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
|
||||
"USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
|
||||
"USER-UEF"_#USER-UEF, NEMD under extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
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"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
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||||
|
||||
:line
|
||||
@ -2770,6 +2771,33 @@ examples/USER/tally :ul
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||||
|
||||
:line
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||||
|
||||
UEF package :link(UEF),h4
|
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|
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[Contents:]
|
||||
|
||||
A fix style for the integration of the equations of motion under
|
||||
extensional flow with proper boundary conditions, as well
|
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as several supporting compute styles and an output option.
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|
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[Install or un-install:]
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|
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make yes-user-uef
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make machine :pre
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make no-user-uef
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make machine :pre
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|
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[Supporting info:]
|
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|
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src/USER-UEF: filenames -> commands
|
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"fix nvt/uef"_fix_nh_uef.html
|
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"compute pressure/uef"_compute_pressure_uef.html
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"compute temp/uef"_compute_temp_uef.html
|
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"dump cfg/uef"_dump_cfg_uef.html
|
||||
examples/uef :ul
|
||||
|
||||
:line
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||||
|
||||
USER-VTK package :link(USER-VTK),h4
|
||||
|
||||
[Contents:]
|
||||
|
||||
52
doc/src/compute_temp_uef.txt
Normal file
52
doc/src/compute_temp_uef.txt
Normal file
@ -0,0 +1,52 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
compute temp command :h3
|
||||
compute temp/kk command :h3
|
||||
|
||||
[Syntax:]
|
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|
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compute ID group-ID temp :pre
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||||
|
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ID, group-ID are documented in "compute"_compute.html command
|
||||
temp = style name of this compute command :ul
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||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all temp/uef
|
||||
|
||||
[Description:]
|
||||
|
||||
This command is used to compute the kinetic energy tensor in
|
||||
the correct reference frame when the USER-UEF package is used.
|
||||
It is not necessary to use this command to compute the scalar
|
||||
value of the temperature. A "compute temp"_compute_temp.html
|
||||
may be used for that purpose.
|
||||
|
||||
[Output info:]
|
||||
|
||||
Output information for this command can be found in the
|
||||
documentation for "compute temp"_compute_temp.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-UEF package. It is only enabled if
|
||||
LAMMPS was built with that package. See the
|
||||
"Making LAMMPS"_Section_start.html#start-3 section for more info.
|
||||
|
||||
|
||||
This command can only be used when "fix nvt/uef"_fix_nh_uef.html
|
||||
or "fix npt/uef"_fix_nh_uef.html is active.
|
||||
|
||||
[Related commands:]
|
||||
"compute temp"_compute_temp.html,
|
||||
"fix nvt/uef"_fix_nh_uef.html,
|
||||
"compute pressure/uef"_compute_pressure_uef.html
|
||||
|
||||
|
||||
[Default:] none
|
||||
715
doc/src/fix_nh_uef.txt
Normal file
715
doc/src/fix_nh_uef.txt
Normal file
@ -0,0 +1,715 @@
|
||||
<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix nvt/uef command :h3
|
||||
fix npt/uef command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID style_name erate eps_x eps_y temp Tstart Tstop Tdamp keyword value ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
style_name = {nvt/uef} or {npt/uef} :l
|
||||
Tstart, Tstop, and Tdamp are documented in the "fix_npt"_fix_nh.html command :l
|
||||
edot_x and edot_y are the strain rates in the x and y directions (1/(time units)) :l
|
||||
one or more keyword/value pairs may be appended :l
|
||||
keyword = {ext} or {strain} or {iso} or {x} or {y} or {z} or {tchain} or {pchain} or {tloop} or {ploop} or {mtk}
|
||||
{ext} value = {x} or {y} or {z} or {xy} or {yz} or {xz} = external dimensions
|
||||
This keyword sets the external dimensions used to calculate the scalar pressure
|
||||
{strain} values = e_x e_y = initial strain
|
||||
Use of this keyword is usually not necessary, but may be needed to resume a run with a data file.
|
||||
The {iso}, {x}, {y}, {z}, {tchain}, {pchain}, {tloop}, {ploop}, and {mtk} keywords are documented in the "fix_npt"_fix_nh.html command. :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix uniax_nvt all nvt/uef temp 400 400 100 erate 0.00001 -0.000005
|
||||
fix biax_nvt all nvt/uef temp 400 400 100 erate 0.000005 0.000005
|
||||
fix uniax_npt all npt/uef temp 400 400 300 iso 1 1 3000 erate 0.00001 -0.000005 ext yz
|
||||
fix biax_npt all npt/uef temp 400 400 100 erate 0.00001 -0.000005 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
||||
This fix is used to simulate non-equilibrium molecular dynamics (NEMD)
|
||||
under diagonal flow fields, including uniaxial and biaxial flow.
|
||||
Simulations under extensional flow may be carried out for an
|
||||
indefinite amount of time. It is an implementation of the boundary
|
||||
conditions from "(Dobson)"_#Dobson, and also uses numerical lattice reduction
|
||||
as was proposed by "(Hunt)"_#Hunt. The lattice reduction algorithm is from
|
||||
"(Semaev)"_Semaev. The package is intended for simulations of
|
||||
homogeneous flows, and integrates the SLLOD equations of motion,
|
||||
originally proposed by Hoover and Ladd (see "(Evans and Morriss)"_#Sllod).
|
||||
|
||||
NOTE: Due to an instability in the SLLOD equations under extension,
|
||||
"fix_momentum"_fix_momentum.html should be used to regularly reset the
|
||||
linear momentum.
|
||||
|
||||
The boundary conditions require a simulation box that does not have a
|
||||
consistent alignment relative to the applied flow field. Since LAMMPS
|
||||
utilizes an upper-triangular simulation box, it is not possible to express
|
||||
the evolving simulation box in the same coordinate system as the flow field.
|
||||
This fix keeps track of two coordinate systems: the flow frame, and the
|
||||
upper triangular LAMMPS frame. The coordinate systems are related to
|
||||
each other through the QR decomposition, as is illustrated in the image below.
|
||||
|
||||
image
|
||||
|
||||
During most molecular dynamics operations, the system is represented in the
|
||||
LAMMPS frame. Only when the positions and velocities are updated is the system
|
||||
rotated to the flow frame, and it is rotated back to the LAMMPS frame
|
||||
immediately afterwards. For this reason, all vector-valued quantities
|
||||
(except for the tensors from compute pressure/uef and compute temp/uef) will
|
||||
be computed in the LAMMPS frame. Rotationally invariant scalar quantities like
|
||||
the temperature and hydrostatic pressure, on the other hand, will be computed
|
||||
correctly. Additionally, the system is in the LAMMPS frame during all of the
|
||||
output steps, and therefore trajectory files made using the dump command
|
||||
will be in the LAMMPS frame unless the dump cfg/uef command is used.
|
||||
|
||||
:line
|
||||
|
||||
Temperature control is achieved with the default Nose-Hoover style
|
||||
thermostat documented in "fix_npt"_fix_nh.html. When this fix is active,
|
||||
only the peculiar velocity of each atom is stored, defined as the velocity
|
||||
relative to the streaming velocity. This is in contrast to
|
||||
"fix_nvt/sllod"_fix_nvt_sllod.html, which uses a lab-frame velocity, and
|
||||
removes the contribution from the streaming velocity in order to compute
|
||||
the temperature.
|
||||
|
||||
Pressure control is achieved using the default Nose-Hoover barostat documented
|
||||
in "fix_npt"_fix_npt.html. There are two ways to control the pressure using this
|
||||
fix. The first method involves using the {ext} keyword along with the {iso} pressure
|
||||
style. With this method, the pressure is controlled by scaling the simulation box
|
||||
isotropically to achieve the average pressure in the directions specified by {ext}.
|
||||
For example, if {ext xy} is used, the average pressure (Pxx+Pyy)/2 will be controlled.
|
||||
|
||||
This command will control the total hydrostatic pressure under uniaxial tension:
|
||||
|
||||
fix f1 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xyz :pre
|
||||
|
||||
This command will control the average stress in compression directions, which would
|
||||
correspond to free surfaces for fiber drawing, under uniaxial tension:
|
||||
|
||||
fix f2 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xy :pre
|
||||
|
||||
The second method for pressure control involves setting the normal stresses using
|
||||
the x, y , and/or z keywords. When using this method, the same pressure must be
|
||||
specified via {Pstart} and {Pstop} for all dimensions controlled. Any choice of
|
||||
pressure conditions that would cause LAMMPS to compute a deviatoric stress are not
|
||||
permissible and will result in an error. Additionally, all dimensions with
|
||||
controlled stress must have the same applied strain rate. The {ext} keyword must be
|
||||
set to the default value ({xyz}) when using this method.
|
||||
|
||||
For example, the following commands will work:
|
||||
|
||||
fix f3 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 y 1 1 5 erate -0.5 -0.5
|
||||
fix f4 all npt/uef temp 0.7 0.7 0.5 z 1 1 5 erate 0.5 0.5 :pre
|
||||
|
||||
The following commands will not work:
|
||||
|
||||
fix f5 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 1 1 5 erate -0.5 -0.5
|
||||
fix f6 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 2 2 5 erate 0.5 0.5 :pre
|
||||
|
||||
:line
|
||||
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Due to requirements of the boundary conditions, when the strain keyword
|
||||
is unset, or set to zero, the initial simulation box must be cubic and
|
||||
have style triclinic. If the box is initially of type ortho, use
|
||||
"change_box"_change_box.html before invoking the fix.
|
||||
|
||||
When this fix is applied, any orientation-dependent vector or
|
||||
tensor-valued quantities computed, except for the tensors from
|
||||
compute pressure/uef/compute temp/uef and coordinates from
|
||||
dump cfg/uef, will not be in the same coordinate system as
|
||||
the flow field.
|
||||
|
||||
:link(Dobson)
|
||||
[(Dobson)] Dobson, J Chem Phys, 141, 184103 (2014).
|
||||
|
||||
:link(Hunt)
|
||||
[(Hunt)] Hunt, Mol Simul, 42, 347 (2016).
|
||||
|
||||
:link(Semaev)
|
||||
[(Semaev)] Semaev, Cryptography and Lattices, 181 (2001).
|
||||
|
||||
:link(Sllod)
|
||||
[(Evans and Morriss)] Evans and Morriss, Phys Rev A, 30, 1528 (1984).
|
||||
|
||||
These commands perform time integration on Nose-Hoover style
|
||||
non-Hamiltonian equations of motion which are designed to generate
|
||||
positions and velocities sampled from the canonical (nvt),
|
||||
isothermal-isobaric (npt), and isenthalpic (nph) ensembles. This
|
||||
updates the position and velocity for atoms in the group each
|
||||
timestep.
|
||||
|
||||
The thermostatting and barostatting is achieved by adding some dynamic
|
||||
variables which are coupled to the particle velocities
|
||||
(thermostatting) and simulation domain dimensions (barostatting). In
|
||||
addition to basic thermostatting and barostatting, these fixes can
|
||||
also create a chain of thermostats coupled to the particle thermostat,
|
||||
and another chain of thermostats coupled to the barostat
|
||||
variables. The barostat can be coupled to the overall box volume, or
|
||||
to individual dimensions, including the {xy}, {xz} and {yz} tilt
|
||||
dimensions. The external pressure of the barostat can be specified as
|
||||
either a scalar pressure (isobaric ensemble) or as components of a
|
||||
symmetric stress tensor (constant stress ensemble). When used
|
||||
correctly, the time-averaged temperature and stress tensor of the
|
||||
particles will match the target values specified by Tstart/Tstop and
|
||||
Pstart/Pstop.
|
||||
|
||||
The equations of motion used are those of Shinoda et al in
|
||||
"(Shinoda)"_#nh-Shinoda, which combine the hydrostatic equations of
|
||||
Martyna, Tobias and Klein in "(Martyna)"_#nh-Martyna with the strain
|
||||
energy proposed by Parrinello and Rahman in
|
||||
"(Parrinello)"_#nh-Parrinello. The time integration schemes closely
|
||||
follow the time-reversible measure-preserving Verlet and rRESPA
|
||||
integrators derived by Tuckerman et al in "(Tuckerman)"_#nh-Tuckerman.
|
||||
|
||||
:line
|
||||
|
||||
The thermostat parameters for fix styles {nvt} and {npt} is specified
|
||||
using the {temp} keyword. Other thermostat-related keywords are
|
||||
{tchain}, {tloop} and {drag}, which are discussed below.
|
||||
|
||||
The thermostat is applied to only the translational degrees of freedom
|
||||
for the particles. The translational degrees of freedom can also have
|
||||
a bias velocity removed before thermostatting takes place; see the
|
||||
description below. The desired temperature at each timestep is a
|
||||
ramped value during the run from {Tstart} to {Tstop}. The {Tdamp}
|
||||
parameter is specified in time units and determines how rapidly the
|
||||
temperature is relaxed. For example, a value of 10.0 means to relax
|
||||
the temperature in a timespan of (roughly) 10 time units (e.g. tau or
|
||||
fmsec or psec - see the "units"_units.html command). The atoms in the
|
||||
fix group are the only ones whose velocities and positions are updated
|
||||
by the velocity/position update portion of the integration.
|
||||
|
||||
NOTE: A Nose-Hoover thermostat will not work well for arbitrary values
|
||||
of {Tdamp}. If {Tdamp} is too small, the temperature can fluctuate
|
||||
wildly; if it is too large, the temperature will take a very long time
|
||||
to equilibrate. A good choice for many models is a {Tdamp} of around
|
||||
100 timesteps. Note that this is NOT the same as 100 time units for
|
||||
most "units"_units.html settings.
|
||||
|
||||
:line
|
||||
|
||||
The barostat parameters for fix styles {npt} and {nph} is specified
|
||||
using one or more of the {iso}, {aniso}, {tri}, {x}, {y}, {z}, {xy},
|
||||
{xz}, {yz}, and {couple} keywords. These keywords give you the
|
||||
ability to specify all 6 components of an external stress tensor, and
|
||||
to couple various of these components together so that the dimensions
|
||||
they represent are varied together during a constant-pressure
|
||||
simulation.
|
||||
|
||||
Other barostat-related keywords are {pchain}, {mtk}, {ploop},
|
||||
{nreset}, {drag}, and {dilate}, which are discussed below.
|
||||
|
||||
Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
|
||||
Triclinic (non-orthogonal) simulation boxes have 6 adjustable
|
||||
dimensions (x,y,z,xy,xz,yz). The "create_box"_create_box.html, "read
|
||||
data"_read_data.html, and "read_restart"_read_restart.html commands
|
||||
specify whether the simulation box is orthogonal or non-orthogonal
|
||||
(triclinic) and explain the meaning of the xy,xz,yz tilt factors.
|
||||
|
||||
The target pressures for each of the 6 components of the stress tensor
|
||||
can be specified independently via the {x}, {y}, {z}, {xy}, {xz}, {yz}
|
||||
keywords, which correspond to the 6 simulation box dimensions. For
|
||||
each component, the external pressure or tensor component at each
|
||||
timestep is a ramped value during the run from {Pstart} to {Pstop}.
|
||||
If a target pressure is specified for a component, then the
|
||||
corresponding box dimension will change during a simulation. For
|
||||
example, if the {y} keyword is used, the y-box length will change. If
|
||||
the {xy} keyword is used, the xy tilt factor will change. A box
|
||||
dimension will not change if that component is not specified, although
|
||||
you have the option to change that dimension via the "fix
|
||||
deform"_fix_deform.html command.
|
||||
|
||||
Note that in order to use the {xy}, {xz}, or {yz} keywords, the
|
||||
simulation box must be triclinic, even if its initial tilt factors are
|
||||
0.0.
|
||||
|
||||
For all barostat keywords, the {Pdamp} parameter operates like the
|
||||
{Tdamp} parameter, determining the time scale on which pressure is
|
||||
relaxed. For example, a value of 10.0 means to relax the pressure in
|
||||
a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
|
||||
the "units"_units.html command).
|
||||
|
||||
NOTE: A Nose-Hoover barostat will not work well for arbitrary values
|
||||
of {Pdamp}. If {Pdamp} is too small, the pressure and volume can
|
||||
fluctuate wildly; if it is too large, the pressure will take a very
|
||||
long time to equilibrate. A good choice for many models is a {Pdamp}
|
||||
of around 1000 timesteps. However, note that {Pdamp} is specified in
|
||||
time units, and that timesteps are NOT the same as time units for most
|
||||
"units"_units.html settings.
|
||||
|
||||
Regardless of what atoms are in the fix group (the only atoms which
|
||||
are time integrated), a global pressure or stress tensor is computed
|
||||
for all atoms. Similarly, when the size of the simulation box is
|
||||
changed, all atoms are re-scaled to new positions, unless the keyword
|
||||
{dilate} is specified with a {dilate-group-ID} for a group that
|
||||
represents a subset of the atoms. This can be useful, for example, to
|
||||
leave the coordinates of atoms in a solid substrate unchanged and
|
||||
controlling the pressure of a surrounding fluid. This option should
|
||||
be used with care, since it can be unphysical to dilate some atoms and
|
||||
not others, because it can introduce large, instantaneous
|
||||
displacements between a pair of atoms (one dilated, one not) that are
|
||||
far from the dilation origin. Also note that for atoms not in the fix
|
||||
group, a separate time integration fix like "fix nve"_fix_nve.html or
|
||||
"fix nvt"_fix_nh.html can be used on them, independent of whether they
|
||||
are dilated or not.
|
||||
|
||||
:line
|
||||
|
||||
The {couple} keyword allows two or three of the diagonal components of
|
||||
the pressure tensor to be "coupled" together. The value specified
|
||||
with the keyword determines which are coupled. For example, {xz}
|
||||
means the {Pxx} and {Pzz} components of the stress tensor are coupled.
|
||||
{Xyz} means all 3 diagonal components are coupled. Coupling means two
|
||||
things: the instantaneous stress will be computed as an average of the
|
||||
corresponding diagonal components, and the coupled box dimensions will
|
||||
be changed together in lockstep, meaning coupled dimensions will be
|
||||
dilated or contracted by the same percentage every timestep. The
|
||||
{Pstart}, {Pstop}, {Pdamp} parameters for any coupled dimensions must
|
||||
be identical. {Couple xyz} can be used for a 2d simulation; the {z}
|
||||
dimension is simply ignored.
|
||||
|
||||
:line
|
||||
|
||||
The {iso}, {aniso}, and {tri} keywords are simply shortcuts that are
|
||||
equivalent to specifying several other keywords together.
|
||||
|
||||
The keyword {iso} means couple all 3 diagonal components together when
|
||||
pressure is computed (hydrostatic pressure), and dilate/contract the
|
||||
dimensions together. Using "iso Pstart Pstop Pdamp" is the same as
|
||||
specifying these 4 keywords:
|
||||
|
||||
x Pstart Pstop Pdamp
|
||||
y Pstart Pstop Pdamp
|
||||
z Pstart Pstop Pdamp
|
||||
couple xyz :pre
|
||||
|
||||
The keyword {aniso} means {x}, {y}, and {z} dimensions are controlled
|
||||
independently using the {Pxx}, {Pyy}, and {Pzz} components of the
|
||||
stress tensor as the driving forces, and the specified scalar external
|
||||
pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying
|
||||
these 4 keywords:
|
||||
|
||||
x Pstart Pstop Pdamp
|
||||
y Pstart Pstop Pdamp
|
||||
z Pstart Pstop Pdamp
|
||||
couple none :pre
|
||||
|
||||
The keyword {tri} means {x}, {y}, {z}, {xy}, {xz}, and {yz} dimensions
|
||||
are controlled independently using their individual stress components
|
||||
as the driving forces, and the specified scalar pressure as the
|
||||
external normal stress. Using "tri Pstart Pstop Pdamp" is the same as
|
||||
specifying these 7 keywords:
|
||||
|
||||
x Pstart Pstop Pdamp
|
||||
y Pstart Pstop Pdamp
|
||||
z Pstart Pstop Pdamp
|
||||
xy 0.0 0.0 Pdamp
|
||||
yz 0.0 0.0 Pdamp
|
||||
xz 0.0 0.0 Pdamp
|
||||
couple none :pre
|
||||
|
||||
:line
|
||||
|
||||
In some cases (e.g. for solids) the pressure (volume) and/or
|
||||
temperature of the system can oscillate undesirably when a Nose/Hoover
|
||||
barostat and thermostat is applied. The optional {drag} keyword will
|
||||
damp these oscillations, although it alters the Nose/Hoover equations.
|
||||
A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged.
|
||||
A non-zero value adds a drag term; the larger the value specified, the
|
||||
greater the damping effect. Performing a short run and monitoring the
|
||||
pressure and temperature is the best way to determine if the drag term
|
||||
is working. Typically a value between 0.2 to 2.0 is sufficient to
|
||||
damp oscillations after a few periods. Note that use of the drag
|
||||
keyword will interfere with energy conservation and will also change
|
||||
the distribution of positions and velocities so that they do not
|
||||
correspond to the nominal NVT, NPT, or NPH ensembles.
|
||||
|
||||
An alternative way to control initial oscillations is to use chain
|
||||
thermostats. The keyword {tchain} determines the number of thermostats
|
||||
in the particle thermostat. A value of 1 corresponds to the original
|
||||
Nose-Hoover thermostat. The keyword {pchain} specifies the number of
|
||||
thermostats in the chain thermostatting the barostat degrees of
|
||||
freedom. A value of 0 corresponds to no thermostatting of the
|
||||
barostat variables.
|
||||
|
||||
The {mtk} keyword controls whether or not the correction terms due to
|
||||
Martyna, Tuckerman, and Klein are included in the equations of motion
|
||||
"(Martyna)"_#nh-Martyna. Specifying {no} reproduces the original
|
||||
Hoover barostat, whose volume probability distribution function
|
||||
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence
|
||||
using {yes} is more correct, but in many cases the difference is
|
||||
negligible.
|
||||
|
||||
The keyword {tloop} can be used to improve the accuracy of integration
|
||||
scheme at little extra cost. The initial and final updates of the
|
||||
thermostat variables are broken up into {tloop} substeps, each of
|
||||
length {dt}/{tloop}. This corresponds to using a first-order
|
||||
Suzuki-Yoshida scheme "(Tuckerman)"_#nh-Tuckerman. The keyword {ploop}
|
||||
does the same thing for the barostat thermostat.
|
||||
|
||||
The keyword {nreset} controls how often the reference dimensions used
|
||||
to define the strain energy are reset. If this keyword is not used,
|
||||
or is given a value of zero, then the reference dimensions are set to
|
||||
those of the initial simulation domain and are never changed. If the
|
||||
simulation domain changes significantly during the simulation, then
|
||||
the final average pressure tensor will differ significantly from the
|
||||
specified values of the external stress tensor. A value of {nstep}
|
||||
means that every {nstep} timesteps, the reference dimensions are set
|
||||
to those of the current simulation domain.
|
||||
|
||||
The {scaleyz}, {scalexz}, and {scalexy} keywords control whether or
|
||||
not the corresponding tilt factors are scaled with the associated box
|
||||
dimensions when barostatting triclinic periodic cells. The default
|
||||
values {yes} will turn on scaling, which corresponds to adjusting the
|
||||
linear dimensions of the cell while preserving its shape. Choosing
|
||||
{no} ensures that the tilt factors are not scaled with the box
|
||||
dimensions. See below for restrictions and default values in different
|
||||
situations. In older versions of LAMMPS, scaling of tilt factors was
|
||||
not performed. The old behavior can be recovered by setting all three
|
||||
scale keywords to {no}.
|
||||
|
||||
The {flip} keyword allows the tilt factors for a triclinic box to
|
||||
exceed half the distance of the parallel box length, as discussed
|
||||
below. If the {flip} value is set to {yes}, the bound is enforced by
|
||||
flipping the box when it is exceeded. If the {flip} value is set to
|
||||
{no}, the tilt will continue to change without flipping. Note that if
|
||||
applied stress induces large deformations (e.g. in a liquid), this
|
||||
means the box shape can tilt dramatically and LAMMPS will run less
|
||||
efficiently, due to the large volume of communication needed to
|
||||
acquire ghost atoms around a processor's irregular-shaped sub-domain.
|
||||
For extreme values of tilt, LAMMPS may also lose atoms and generate an
|
||||
error.
|
||||
|
||||
The {fixedpoint} keyword specifies the fixed point for barostat volume
|
||||
changes. By default, it is the center of the box. Whatever point is
|
||||
chosen will not move during the simulation. For example, if the lower
|
||||
periodic boundaries pass through (0,0,0), and this point is provided
|
||||
to {fixedpoint}, then the lower periodic boundaries will remain at
|
||||
(0,0,0), while the upper periodic boundaries will move twice as
|
||||
far. In all cases, the particle trajectories are unaffected by the
|
||||
chosen value, except for a time-dependent constant translation of
|
||||
positions.
|
||||
|
||||
If the {update} keyword is used with the {dipole} value, then the
|
||||
orientation of the dipole moment of each particle is also updated
|
||||
during the time integration. This option should be used for models
|
||||
where a dipole moment is assigned to finite-size particles,
|
||||
e.g. spheroids via use of the "atom_style hybrid sphere
|
||||
dipole"_atom_style.html command.
|
||||
|
||||
The default dipole orientation integrator can be changed to the
|
||||
Dullweber-Leimkuhler-McLachlan integration scheme
|
||||
"(Dullweber)"_#nh-Dullweber when using {update} with the value
|
||||
{dipole/dlm}. This integrator is symplectic and time-reversible,
|
||||
giving better energy conservation and allows slightly longer timesteps
|
||||
at only a small additional computational cost.
|
||||
|
||||
:line
|
||||
|
||||
NOTE: Using a barostat coupled to tilt dimensions {xy}, {xz}, {yz} can
|
||||
sometimes result in arbitrarily large values of the tilt dimensions,
|
||||
i.e. a dramatically deformed simulation box. LAMMPS allows the tilt
|
||||
factors to grow a small amount beyond the normal limit of half the box
|
||||
length (0.6 times the box length), and then performs a box "flip" to
|
||||
an equivalent periodic cell. See the discussion of the {flip} keyword
|
||||
above, to allow this bound to be exceeded, if desired.
|
||||
|
||||
The flip operation is described in more detail in the doc page for
|
||||
"fix deform"_fix_deform.html. Both the barostat dynamics and the atom
|
||||
trajectories are unaffected by this operation. However, if a tilt
|
||||
factor is incremented by a large amount (1.5 times the box length) on
|
||||
a single timestep, LAMMPS can not accomodate this event and will
|
||||
terminate the simulation with an error. This error typically indicates
|
||||
that there is something badly wrong with how the simulation was
|
||||
constructed, such as specifying values of {Pstart} that are too far
|
||||
from the current stress value, or specifying a timestep that is too
|
||||
large. Triclinic barostatting should be used with care. This also is
|
||||
true for other barostat styles, although they tend to be more
|
||||
forgiving of insults. In particular, it is important to recognize that
|
||||
equilibrium liquids can not support a shear stress and that
|
||||
equilibrium solids can not support shear stresses that exceed the
|
||||
yield stress.
|
||||
|
||||
One exception to this rule is if the 1st dimension in the tilt factor
|
||||
(x for xy) is non-periodic. In that case, the limits on the tilt
|
||||
factor are not enforced, since flipping the box in that dimension does
|
||||
not change the atom positions due to non-periodicity. In this mode,
|
||||
if you tilt the system to extreme angles, the simulation will simply
|
||||
become inefficient due to the highly skewed simulation box.
|
||||
|
||||
NOTE: Unlike the "fix temp/berendsen"_fix_temp_berendsen.html command
|
||||
which performs thermostatting but NO time integration, these fixes
|
||||
perform thermostatting/barostatting AND time integration. Thus you
|
||||
should not use any other time integration fix, such as "fix
|
||||
nve"_fix_nve.html on atoms to which this fix is applied. Likewise,
|
||||
fix nvt and fix npt should not normally be used on atoms that also
|
||||
have their temperature controlled by another fix - e.g. by "fix
|
||||
langevin"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html
|
||||
commands.
|
||||
|
||||
See "this howto section"_Section_howto.html#howto_16 of the manual for
|
||||
a discussion of different ways to compute temperature and perform
|
||||
thermostatting and barostatting.
|
||||
|
||||
:line
|
||||
|
||||
These fixes compute a temperature and pressure each timestep. To do
|
||||
this, the fix creates its own computes of style "temp" and "pressure",
|
||||
as if one of these two sets of commands had been issued:
|
||||
|
||||
compute fix-ID_temp group-ID temp
|
||||
compute fix-ID_press group-ID pressure fix-ID_temp :pre
|
||||
|
||||
compute fix-ID_temp all temp
|
||||
compute fix-ID_press all pressure fix-ID_temp :pre
|
||||
|
||||
See the "compute temp"_compute_temp.html and "compute
|
||||
pressure"_compute_pressure.html commands for details. Note that the
|
||||
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
|
||||
+ underscore + "press". For fix nvt, the group for the new computes
|
||||
is the same as the fix group. For fix nph and fix npt, the group for
|
||||
the new computes is "all" since pressure is computed for the entire
|
||||
system.
|
||||
|
||||
Note that these are NOT the computes used by thermodynamic output (see
|
||||
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
|
||||
and {thermo_press}. This means you can change the attributes of this
|
||||
fix's temperature or pressure via the
|
||||
"compute_modify"_compute_modify.html command or print this temperature
|
||||
or pressure during thermodynamic output via the "thermo_style
|
||||
custom"_thermo_style.html command using the appropriate compute-ID.
|
||||
It also means that changing attributes of {thermo_temp} or
|
||||
{thermo_press} will have no effect on this fix.
|
||||
|
||||
Like other fixes that perform thermostatting, fix nvt and fix npt can
|
||||
be used with "compute commands"_compute.html that calculate a
|
||||
temperature after removing a "bias" from the atom velocities.
|
||||
E.g. removing the center-of-mass velocity from a group of atoms or
|
||||
only calculating temperature on the x-component of velocity or only
|
||||
calculating temperature for atoms in a geometric region. This is not
|
||||
done by default, but only if the "fix_modify"_fix_modify.html command
|
||||
is used to assign a temperature compute to this fix that includes such
|
||||
a bias term. See the doc pages for individual "compute
|
||||
commands"_compute.html to determine which ones include a bias. In
|
||||
this case, the thermostat works in the following manner: the current
|
||||
temperature is calculated taking the bias into account, bias is
|
||||
removed from each atom, thermostatting is performed on the remaining
|
||||
thermal degrees of freedom, and the bias is added back in.
|
||||
|
||||
:line
|
||||
|
||||
These fixes can be used with either the {verlet} or {respa}
|
||||
"integrators"_run_style.html. When using one of the barostat fixes
|
||||
with {respa}, LAMMPS uses an integrator constructed
|
||||
according to the following factorization of the Liouville propagator
|
||||
(for two rRESPA levels):
|
||||
|
||||
:c,image(Eqs/fix_nh1.jpg)
|
||||
|
||||
This factorization differs somewhat from that of Tuckerman et al, in
|
||||
that the barostat is only updated at the outermost rRESPA level,
|
||||
whereas Tuckerman's factorization requires splitting the pressure into
|
||||
pieces corresponding to the forces computed at each rRESPA level. In
|
||||
theory, the latter method will exhibit better numerical stability. In
|
||||
practice, because Pdamp is normally chosen to be a large multiple of
|
||||
the outermost rRESPA timestep, the barostat dynamics are not the
|
||||
limiting factor for numerical stability. Both factorizations are
|
||||
time-reversible and can be shown to preserve the phase space measure
|
||||
of the underlying non-Hamiltonian equations of motion.
|
||||
|
||||
NOTE: This implementation has been shown to conserve linear momentum
|
||||
up to machine precision under NVT dynamics. Under NPT dynamics,
|
||||
for a system with zero initial total linear momentum, the total
|
||||
momentum fluctuates close to zero. It may occasionally undergo brief
|
||||
excursions to non-negligible values, before returning close to zero.
|
||||
Over long simulations, this has the effect of causing the center-of-mass
|
||||
to undergo a slow random walk. This can be mitigated by resetting
|
||||
the momentum at infrequent intervals using the
|
||||
"fix momentum"_fix_momentum.html command.
|
||||
|
||||
:line
|
||||
|
||||
The fix npt and fix nph commands can be used with rigid bodies or
|
||||
mixtures of rigid bodies and non-rigid particles (e.g. solvent). But
|
||||
there are also "fix rigid/npt"_fix_rigid.html and "fix
|
||||
rigid/nph"_fix_rigid.html commands, which are typically a more natural
|
||||
choice. See the doc page for those commands for more discussion of
|
||||
the various ways to do this.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed in "Section 5"_Section_accelerate.html
|
||||
of the manual. The accelerated styles take the same arguments and
|
||||
should produce the same results, except for round-off and precision
|
||||
issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
|
||||
use the "suffix"_suffix.html command in your input script.
|
||||
|
||||
See "Section 5"_Section_accelerate.html of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
These fixes writes the state of all the thermostat and barostat
|
||||
variables to "binary restart files"_restart.html. See the
|
||||
"read_restart"_read_restart.html command for info on how to re-specify
|
||||
a fix in an input script that reads a restart file, so that the
|
||||
operation of the fix continues in an uninterrupted fashion.
|
||||
|
||||
The "fix_modify"_fix_modify.html {temp} and {press} options are
|
||||
supported by these fixes. You can use them to assign a
|
||||
"compute"_compute.html you have defined to this fix which will be used
|
||||
in its thermostatting or barostatting procedure, as described above.
|
||||
If you do this, note that the kinetic energy derived from the compute
|
||||
temperature should be consistent with the virial term computed using
|
||||
all atoms for the pressure. LAMMPS will warn you if you choose to
|
||||
compute temperature on a subset of atoms.
|
||||
|
||||
NOTE: If both the {temp} and {press} keywords are used in a single
|
||||
thermo_modify command (or in two separate commands), then the order in
|
||||
which the keywords are specified is important. Note that a "pressure
|
||||
compute"_compute_pressure.html defines its own temperature compute as
|
||||
an argument when it is specified. The {temp} keyword will override
|
||||
this (for the pressure compute being used by fix npt), but only if the
|
||||
{temp} keyword comes after the {press} keyword. If the {temp} keyword
|
||||
comes before the {press} keyword, then the new pressure compute
|
||||
specified by the {press} keyword will be unaffected by the {temp}
|
||||
setting.
|
||||
|
||||
The "fix_modify"_fix_modify.html {energy} option is supported by these
|
||||
fixes to add the energy change induced by Nose/Hoover thermostatting
|
||||
and barostatting to the system's potential energy as part of
|
||||
"thermodynamic output"_thermo_style.html.
|
||||
|
||||
These fixes compute a global scalar and a global vector of quantities,
|
||||
which can be accessed by various "output
|
||||
commands"_Section_howto.html#howto_15. The scalar value calculated by
|
||||
these fixes is "extensive"; the vector values are "intensive".
|
||||
|
||||
The scalar is the cumulative energy change due to the fix.
|
||||
|
||||
The vector stores internal Nose/Hoover thermostat and barostat
|
||||
variables. The number and meaning of the vector values depends on
|
||||
which fix is used and the settings for keywords {tchain} and {pchain},
|
||||
which specify the number of Nose/Hoover chains for the thermostat and
|
||||
barostat. If no thermostatting is done, then {tchain} is 0. If no
|
||||
barostatting is done, then {pchain} is 0. In the following list,
|
||||
"ndof" is 0, 1, 3, or 6, and is the number of degrees of freedom in
|
||||
the barostat. Its value is 0 if no barostat is used, else its value
|
||||
is 6 if any off-diagonal stress tensor component is barostatted, else
|
||||
its value is 1 if {couple xyz} is used or {couple xy} for a 2d
|
||||
simulation, otherwise its value is 3.
|
||||
|
||||
The order of values in the global vector and their meaning is as
|
||||
follows. The notation means there are tchain values for eta, followed
|
||||
by tchain for eta_dot, followed by ndof for omega, etc:
|
||||
|
||||
eta\[tchain\] = particle thermostat displacements (unitless)
|
||||
eta_dot\[tchain\] = particle thermostat velocities (1/time units)
|
||||
omega\[ndof\] = barostat displacements (unitless)
|
||||
omega_dot\[ndof\] = barostat velocities (1/time units)
|
||||
etap\[pchain\] = barostat thermostat displacements (unitless)
|
||||
etap_dot\[pchain\] = barostat thermostat velocities (1/time units)
|
||||
PE_eta\[tchain\] = potential energy of each particle thermostat displacement (energy units)
|
||||
KE_eta_dot\[tchain\] = kinetic energy of each particle thermostat velocity (energy units)
|
||||
PE_omega\[ndof\] = potential energy of each barostat displacement (energy units)
|
||||
KE_omega_dot\[ndof\] = kinetic energy of each barostat velocity (energy units)
|
||||
PE_etap\[pchain\] = potential energy of each barostat thermostat displacement (energy units)
|
||||
KE_etap_dot\[pchain\] = kinetic energy of each barostat thermostat velocity (energy units)
|
||||
PE_strain\[1\] = scalar strain energy (energy units) :ul
|
||||
|
||||
These fixes can ramp their external temperature and pressure over
|
||||
multiple runs, using the {start} and {stop} keywords of the
|
||||
"run"_run.html command. See the "run"_run.html command for details of
|
||||
how to do this.
|
||||
|
||||
These fixes are not invoked during "energy
|
||||
minimization"_minimize.html.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
{X}, {y}, {z} cannot be barostatted if the associated dimension is not
|
||||
periodic. {Xy}, {xz}, and {yz} can only be barostatted if the
|
||||
simulation domain is triclinic and the 2nd dimension in the keyword
|
||||
({y} dimension in {xy}) is periodic. {Z}, {xz}, and {yz}, cannot be
|
||||
barostatted for 2D simulations. The "create_box"_create_box.html,
|
||||
"read data"_read_data.html, and "read_restart"_read_restart.html
|
||||
commands specify whether the simulation box is orthogonal or
|
||||
non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz
|
||||
tilt factors.
|
||||
|
||||
For the {temp} keyword, the final Tstop cannot be 0.0 since it would
|
||||
make the external T = 0.0 at some timestep during the simulation which
|
||||
is not allowed in the Nose/Hoover formulation.
|
||||
|
||||
The {scaleyz yes} and {scalexz yes} keyword/value pairs can not be used
|
||||
for 2D simulations. {scaleyz yes}, {scalexz yes}, and {scalexy yes} options
|
||||
can only be used if the 2nd dimension in the keyword is periodic,
|
||||
and if the tilt factor is not coupled to the barostat via keywords
|
||||
{tri}, {yz}, {xz}, and {xy}.
|
||||
|
||||
These fixes can be used with dynamic groups as defined by the
|
||||
"group"_group.html command. Likewise they can be used with groups to
|
||||
which atoms are added or deleted over time, e.g. a deposition
|
||||
simulation. However, the conservation properties of the thermostat
|
||||
and barostat are defined for systems with a static set of atoms. You
|
||||
may observe odd behavior if the atoms in a group vary dramatically
|
||||
over time or the atom count becomes very small.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix nve"_fix_nve.html, "fix_modify"_fix_modify.html,
|
||||
"run_style"_run_style.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
|
||||
ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
|
||||
scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
|
||||
not coupled to barostat, otherwise no.
|
||||
|
||||
:line
|
||||
|
||||
:link(nh-Martyna)
|
||||
[(Martyna)] Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
|
||||
|
||||
:link(nh-Parrinello)
|
||||
[(Parrinello)] Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
|
||||
|
||||
:link(nh-Tuckerman)
|
||||
[(Tuckerman)] Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
|
||||
Martyna, J Phys A: Math Gen, 39, 5629 (2006).
|
||||
|
||||
:link(nh-Shinoda)
|
||||
[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
|
||||
|
||||
:link(nh-Dullweber)
|
||||
[(Dullweber)] Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107,
|
||||
5840 (1997).
|
||||
19
examples/USER/uef/README
Normal file
19
examples/USER/uef/README
Normal file
@ -0,0 +1,19 @@
|
||||
This directory contains two short example scripts for the USER-UEF
|
||||
package.
|
||||
|
||||
|
||||
nvt_uniaxial:
|
||||
A simulation of a WCA fluid under constant volume uniaxial strain
|
||||
with stretching in the z direction, compression in the x and y
|
||||
directions.The xx, yy and zz components of the pressure tensor are
|
||||
written to the log file. The simulation conditions are the same
|
||||
used in the paper by Thomas Hunt [http://arxiv.org/abs/1310.3905]
|
||||
and should yield an zz pressure near 5 and xx/yy pressures near 10.
|
||||
|
||||
npt_biaxial:
|
||||
A simulation of a WCA fluid under stress-controlled biaxial strain
|
||||
with stretching in the x and y directions, compression in the z
|
||||
direction. The zz stress is controlled using the ext keyword in fix
|
||||
npt/uef. The xx yy and zz components of the pressure tensor are
|
||||
written to the log file. The simulations conditions should yield
|
||||
xx/yy pressures near 5 and zz pressure near 10
|
||||
1022
examples/USER/uef/npt_biaxial/data.wca
Normal file
1022
examples/USER/uef/npt_biaxial/data.wca
Normal file
File diff suppressed because it is too large
Load Diff
31
examples/USER/uef/npt_biaxial/in.npt_biaxial
Normal file
31
examples/USER/uef/npt_biaxial/in.npt_biaxial
Normal file
@ -0,0 +1,31 @@
|
||||
# biaxial NPT deformation of WCA fluid
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
|
||||
pair_style lj/cut 1.122562
|
||||
read_data data.wca
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
change_box all triclinic
|
||||
|
||||
# these commads show the different methods that may be used to impose
|
||||
# a constant stress through isotropic or anisotropic coupling
|
||||
fix 1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z
|
||||
#fix 1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5 erate 0.5 0.5 ext xyz
|
||||
|
||||
fix 2 all momentum 100 linear 1 1 1
|
||||
|
||||
#dump 1 all atom 25 dump.lammpstrj
|
||||
|
||||
#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs
|
||||
|
||||
thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3]
|
||||
|
||||
thermo 50
|
||||
run 10000
|
||||
276
examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.1
Normal file
276
examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.1
Normal file
@ -0,0 +1,276 @@
|
||||
LAMMPS (30 Jul 2016)
|
||||
# biaxial NPT deformation of WCA fluid
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
|
||||
pair_style lj/cut 1.122562
|
||||
read_data data.wca
|
||||
orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
change_box all triclinic
|
||||
triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0)
|
||||
|
||||
# these commads show the different methods that may be used to impose
|
||||
# a constant stress through isotropic or anisotropic coupling
|
||||
fix 1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z
|
||||
#fix 1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5 erate 0.5 0.5 ext xyz
|
||||
|
||||
fix 2 all momentum 100 linear 1 1 1
|
||||
|
||||
#dump 1 all atom 25 dump.lammpstrj
|
||||
|
||||
#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs
|
||||
|
||||
thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3]
|
||||
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.62256
|
||||
ghost atom cutoff = 1.62256
|
||||
binsize = 0.811281 -> bins = 11 11 11
|
||||
Memory usage per processor = 2.40217 Mbytes
|
||||
Step 1_press[ 1_press[ 1_press[
|
||||
0 6.3937851 7.0436438 6.4461087
|
||||
50 7.9020345 7.303289 14.733929
|
||||
100 8.3214325 8.385843 13.166247
|
||||
150 5.7168419 5.6083988 9.7224198
|
||||
200 3.8875348 4.0840705 7.9912973
|
||||
250 4.2933724 4.2410519 7.7200953
|
||||
300 4.5452314 4.2434949 8.6709832
|
||||
350 5.446489 5.6166962 11.300536
|
||||
400 6.0682558 5.7787878 12.106852
|
||||
450 5.3884296 5.5066688 9.9100012
|
||||
500 4.8046418 4.7115986 9.9769201
|
||||
550 4.9043933 4.6240966 9.319336
|
||||
600 4.6843238 4.9571246 9.5325487
|
||||
650 5.1952989 5.195648 9.6187047
|
||||
700 5.4163364 5.2938289 10.136655
|
||||
750 5.6723178 5.0670261 11.415221
|
||||
800 5.9379901 5.6402916 10.815209
|
||||
850 5.0695389 5.3021432 10.742859
|
||||
900 4.6498962 4.7111912 9.8453523
|
||||
950 4.4811641 5.170132 9.421765
|
||||
1000 4.7501483 4.2420772 9.3510803
|
||||
1050 4.5973379 5.2046799 9.8632975
|
||||
1100 4.7879562 4.9051316 9.8658626
|
||||
1150 5.0528771 5.5048545 10.110913
|
||||
1200 4.9926563 5.2482081 9.9610863
|
||||
1250 4.8476232 4.8498859 9.5752989
|
||||
1300 5.2932038 5.0594534 10.869545
|
||||
1350 5.4720421 5.0830442 10.69386
|
||||
1400 4.8175566 4.9863651 10.041898
|
||||
1450 4.6307145 4.5615459 9.231299
|
||||
1500 5.0296259 4.5433558 8.7180513
|
||||
1550 4.8708444 5.1601014 10.256791
|
||||
1600 5.5098593 5.316773 10.224386
|
||||
1650 5.5055907 5.0516814 10.272037
|
||||
1700 4.6965552 5.2436628 9.8272905
|
||||
1750 5.0212307 4.740601 8.9738802
|
||||
1800 4.7756351 5.199734 9.9929449
|
||||
1850 4.7107092 5.177203 10.580427
|
||||
1900 5.0935608 4.5286844 9.3036832
|
||||
1950 4.8035855 4.894359 9.4423987
|
||||
2000 4.5643937 4.7480477 9.4384251
|
||||
2050 4.9314701 4.990414 10.151815
|
||||
2100 5.9828824 5.8188026 12.262691
|
||||
2150 5.5337303 5.4598468 10.136112
|
||||
2200 4.892172 4.8699674 9.1629905
|
||||
2250 4.5680591 4.5740533 9.5633545
|
||||
2300 5.0023535 4.3948659 8.9645774
|
||||
2350 5.2533056 4.9803884 10.255653
|
||||
2400 5.3330196 5.3888322 10.021617
|
||||
2450 5.2095527 4.8765336 10.135381
|
||||
2500 5.221153 5.2974568 10.2493
|
||||
2550 5.385331 5.0801192 10.490479
|
||||
2600 5.3274988 5.0253548 10.147587
|
||||
2650 4.718677 5.2710337 9.7549521
|
||||
2700 4.5811521 4.6083971 8.1923164
|
||||
2750 4.4743752 4.3319737 8.8690805
|
||||
2800 5.0215013 5.2262961 9.8627954
|
||||
2850 6.1005107 5.5994942 11.170661
|
||||
2900 5.9673524 5.362124 10.401699
|
||||
2950 5.5400849 5.7523993 10.292536
|
||||
3000 4.9202636 5.1210431 10.125839
|
||||
3050 4.5286487 5.3586164 9.8634322
|
||||
3100 4.5719961 5.1615414 9.8027972
|
||||
3150 5.4091919 4.8581943 9.96938
|
||||
3200 5.522125 5.3564838 9.7638407
|
||||
3250 4.9019062 5.2514758 9.2993079
|
||||
3300 5.2375918 5.1439012 9.4313575
|
||||
3350 4.750235 4.8692016 10.54193
|
||||
3400 5.5793211 5.4184157 11.021389
|
||||
3450 4.9022614 5.3166498 9.4629659
|
||||
3500 4.6348617 4.4650979 9.0665548
|
||||
3550 4.7922405 4.8961269 10.255446
|
||||
3600 4.8914457 5.1158894 9.4736084
|
||||
3650 5.062771 4.6725475 10.263484
|
||||
3700 5.4842823 5.7793971 10.342915
|
||||
3750 5.3136012 5.063065 10.398307
|
||||
3800 4.9372149 4.9270414 9.5304748
|
||||
3850 5.2144752 5.1716455 9.7575725
|
||||
3900 5.0892665 5.1697057 9.918052
|
||||
3950 5.1124507 5.354702 9.791366
|
||||
4000 5.1255084 5.1143653 10.913101
|
||||
4050 5.1891698 4.9913681 9.6871728
|
||||
4100 4.7663368 4.2435014 8.3815668
|
||||
4150 4.8060033 4.3415868 9.6553386
|
||||
4200 4.8548303 4.8006768 9.5995801
|
||||
4250 5.0976366 5.2683175 10.386444
|
||||
4300 5.8921937 5.5134696 10.788143
|
||||
4350 5.8323871 5.5255869 11.199128
|
||||
4400 5.2464655 5.0005905 10.311055
|
||||
4450 4.9264849 5.2499854 10.26702
|
||||
4500 4.4431895 4.536981 8.7489096
|
||||
4550 4.5180914 4.2080277 8.6525529
|
||||
4600 5.1782188 5.1224059 10.683341
|
||||
4650 5.4156233 4.8714464 10.473939
|
||||
4700 5.3107669 5.224614 10.569391
|
||||
4750 4.9538022 5.2509475 10.288918
|
||||
4800 4.6976945 4.8107142 9.8299772
|
||||
4850 5.1227936 5.0737571 10.440452
|
||||
4900 4.7580514 4.6375995 9.1971008
|
||||
4950 5.0647601 4.6470735 9.583131
|
||||
5000 5.196231 5.7531491 10.409807
|
||||
5050 5.6691323 5.7163652 12.335701
|
||||
5100 5.3603738 5.4887106 10.961712
|
||||
5150 4.455028 4.6494465 9.8096968
|
||||
5200 4.7596912 4.4804896 9.3762885
|
||||
5250 5.3144927 5.0113772 9.553101
|
||||
5300 5.3445266 4.8262035 9.1220802
|
||||
5350 5.1540657 5.5982676 10.765178
|
||||
5400 5.1773418 5.2684381 10.452351
|
||||
5450 4.8946859 5.3283747 9.8015564
|
||||
5500 5.2009608 4.7183522 9.4558009
|
||||
5550 5.4158589 5.5005458 10.539505
|
||||
5600 4.7196831 5.4181991 9.6439249
|
||||
5650 4.8333571 4.8601728 8.9350189
|
||||
5700 5.4395698 4.9730096 10.669681
|
||||
5750 5.2947443 5.6973259 10.020539
|
||||
5800 5.4391993 5.5255143 10.264969
|
||||
5850 4.9921388 5.2643827 10.217028
|
||||
5900 5.0048643 4.7952641 8.9718929
|
||||
5950 5.1843818 4.5987295 9.6858944
|
||||
6000 5.0343993 4.946933 9.7436708
|
||||
6050 4.6202714 5.3502658 10.752915
|
||||
6100 5.6914422 5.3621964 10.281827
|
||||
6150 5.1928763 5.9652686 10.923881
|
||||
6200 5.0030409 5.2013891 10.056308
|
||||
6250 4.9699876 5.2363753 9.9964211
|
||||
6300 4.9129606 4.4558458 9.0419952
|
||||
6350 4.6623958 4.4078264 8.528649
|
||||
6400 4.9811441 5.1183207 10.261751
|
||||
6450 5.3644017 5.5153937 10.401295
|
||||
6500 5.6674981 5.7427566 11.928777
|
||||
6550 5.1622364 5.3212928 10.067198
|
||||
6600 4.5954278 5.1645397 10.16724
|
||||
6650 4.9192712 5.0413326 9.95656
|
||||
6700 4.6179845 4.5656214 9.3798952
|
||||
6750 4.7287495 4.5071148 8.7890116
|
||||
6800 4.8600442 4.8083512 10.245595
|
||||
6850 5.0515531 5.1609272 10.553855
|
||||
6900 5.1159742 5.1359869 10.594699
|
||||
6950 4.8908884 5.0592418 9.5698704
|
||||
7000 4.7654136 4.7530776 8.9439321
|
||||
7050 4.779293 4.7534957 9.7244349
|
||||
7100 5.2265831 5.6869073 10.32717
|
||||
7150 5.4019177 5.15174 10.457567
|
||||
7200 4.9817102 5.0596098 10.337574
|
||||
7250 5.1836654 5.6065238 10.723108
|
||||
7300 4.2916569 4.457143 8.5419099
|
||||
7350 4.3906104 4.5439294 9.0805415
|
||||
7400 4.998572 5.3386063 10.491418
|
||||
7450 5.1109022 5.0506801 10.636116
|
||||
7500 5.0248381 5.019932 10.217023
|
||||
7550 5.0109265 5.1438717 9.9032426
|
||||
7600 4.6628614 4.6204146 8.9459669
|
||||
7650 4.8930717 5.0650009 10.049331
|
||||
7700 4.9373454 5.6265835 10.210644
|
||||
7750 5.5001067 5.3133253 10.667995
|
||||
7800 5.0816102 5.0125753 10.591986
|
||||
7850 4.9638046 5.1969015 9.9728333
|
||||
7900 4.8438207 4.9217213 8.9978809
|
||||
7950 4.7318805 4.6248537 8.6806596
|
||||
8000 5.2808543 5.2892613 10.932535
|
||||
8050 5.9609722 5.87087 10.47602
|
||||
8100 5.2190231 5.6693244 11.244536
|
||||
8150 5.3481127 5.2849903 10.222845
|
||||
8200 4.7833053 4.7404657 9.2034474
|
||||
8250 4.5461994 4.510467 10.294452
|
||||
8300 4.6025175 4.8332817 8.7967546
|
||||
8350 5.0389897 5.6642908 10.243402
|
||||
8400 4.8414338 4.8925143 9.3653631
|
||||
8450 5.5087429 4.7830361 10.831666
|
||||
8500 5.2678146 5.1697789 9.9105782
|
||||
8550 5.1211843 4.9097801 9.4165956
|
||||
8600 5.8239149 5.0821022 10.803261
|
||||
8650 5.3620154 5.5831747 11.16202
|
||||
8700 5.1625813 4.8791404 10.537681
|
||||
8750 4.5622461 5.0157549 10.013227
|
||||
8800 4.4051517 5.0224553 9.6364273
|
||||
8850 4.1711629 4.635617 8.5470244
|
||||
8900 4.7049907 5.2458435 10.100728
|
||||
8950 4.8568883 5.2360772 9.2306469
|
||||
9000 5.0091899 5.2203574 10.718541
|
||||
9050 5.1037824 4.9022451 10.24271
|
||||
9100 5.0789015 4.9331454 9.173614
|
||||
9150 5.3865455 5.3427553 11.40199
|
||||
9200 5.5089482 5.9423232 10.976063
|
||||
9250 5.1353552 5.0650262 10.040607
|
||||
9300 4.6761948 4.9155175 9.6413722
|
||||
9350 4.4780834 4.3934708 8.7049819
|
||||
9400 4.2561799 4.7906324 9.046134
|
||||
9450 5.6162819 5.2881846 9.9040868
|
||||
9500 5.7554547 5.6111262 10.23849
|
||||
9550 5.4230462 5.5656045 10.908006
|
||||
9600 5.5045685 4.9818892 9.8929535
|
||||
9650 5.0541481 5.0183351 9.5226021
|
||||
9700 4.9712829 5.2395398 9.9996693
|
||||
9750 5.0960017 5.4419775 10.914719
|
||||
9800 5.0790688 5.6378474 10.00789
|
||||
9850 4.9661747 5.114502 9.4585052
|
||||
9900 5.0133498 4.7456254 9.4572653
|
||||
9950 5.3318846 4.6643122 10.096292
|
||||
10000 5.2227687 4.8924305 9.5894615
|
||||
Loop time of 4.42114 on 1 procs for 10000 steps with 500 atoms
|
||||
|
||||
Performance: 977122.661 tau/day, 2261.858 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.72321 | 0.72321 | 0.72321 | 0.0 | 16.36
|
||||
Neigh | 2.6161 | 2.6161 | 2.6161 | 0.0 | 59.17
|
||||
Comm | 0.30217 | 0.30217 | 0.30217 | 0.0 | 6.83
|
||||
Output | 0.0034378 | 0.0034378 | 0.0034378 | 0.0 | 0.08
|
||||
Modify | 0.67004 | 0.67004 | 0.67004 | 0.0 | 15.16
|
||||
Other | | 0.1062 | | | 2.40
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 905 ave 905 max 905 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3340 ave 3340 max 3340 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3340
|
||||
Ave neighs/atom = 6.68
|
||||
Neighbor list builds = 4580
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:04
|
||||
276
examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.4
Normal file
276
examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.4
Normal file
@ -0,0 +1,276 @@
|
||||
LAMMPS (30 Jul 2016)
|
||||
# biaxial NPT deformation of WCA fluid
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
|
||||
pair_style lj/cut 1.122562
|
||||
read_data data.wca
|
||||
orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
change_box all triclinic
|
||||
triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0)
|
||||
|
||||
# these commads show the different methods that may be used to impose
|
||||
# a constant stress through isotropic or anisotropic coupling
|
||||
fix 1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z
|
||||
#fix 1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5 erate 0.5 0.5 ext xyz
|
||||
|
||||
fix 2 all momentum 100 linear 1 1 1
|
||||
|
||||
#dump 1 all atom 25 dump.lammpstrj
|
||||
|
||||
#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs
|
||||
|
||||
thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3]
|
||||
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.62256
|
||||
ghost atom cutoff = 1.62256
|
||||
binsize = 0.811281 -> bins = 11 11 11
|
||||
Memory usage per processor = 2.38201 Mbytes
|
||||
Step 1_press[ 1_press[ 1_press[
|
||||
0 6.3937851 7.0436438 6.4461087
|
||||
50 7.9020345 7.303289 14.733929
|
||||
100 8.3214325 8.385843 13.166247
|
||||
150 5.7168419 5.6083988 9.7224198
|
||||
200 3.8875348 4.0840705 7.9912973
|
||||
250 4.2933724 4.2410519 7.7200953
|
||||
300 4.5452314 4.2434949 8.6709832
|
||||
350 5.446489 5.6166962 11.300536
|
||||
400 6.0682558 5.7787878 12.106852
|
||||
450 5.3884296 5.5066688 9.9100012
|
||||
500 4.8046418 4.7115986 9.9769201
|
||||
550 4.9043933 4.6240966 9.319336
|
||||
600 4.6843238 4.9571246 9.5325487
|
||||
650 5.1952989 5.195648 9.6187047
|
||||
700 5.4163364 5.2938289 10.136655
|
||||
750 5.6723178 5.0670261 11.415221
|
||||
800 5.9379901 5.6402916 10.815209
|
||||
850 5.0695389 5.3021432 10.742859
|
||||
900 4.6498961 4.7111912 9.8453525
|
||||
950 4.4811637 5.170132 9.4217644
|
||||
1000 4.7501491 4.2420769 9.3510789
|
||||
1050 4.5973375 5.2046786 9.8633021
|
||||
1100 4.7879517 4.905134 9.8658575
|
||||
1150 5.0528775 5.5048673 10.110907
|
||||
1200 4.9926837 5.2482072 9.961051
|
||||
1250 4.8475661 4.8499052 9.5753719
|
||||
1300 5.2929874 5.0593404 10.869345
|
||||
1350 5.4722108 5.083063 10.693408
|
||||
1400 4.816304 4.9851244 10.041255
|
||||
1450 4.6280905 4.5646059 9.2298768
|
||||
1500 5.01985 4.5471327 8.721625
|
||||
1550 4.8741077 5.1549887 10.256565
|
||||
1600 5.4916921 5.3197646 10.281538
|
||||
1650 5.4772243 5.1837045 9.9982297
|
||||
1700 4.9419503 5.2869766 9.5825456
|
||||
1750 5.0000465 4.6358961 8.8873809
|
||||
1800 5.0008968 4.9755404 10.274347
|
||||
1850 5.3911106 5.0602442 10.252838
|
||||
1900 5.6306791 5.5982927 11.287727
|
||||
1950 5.0117663 4.9037147 9.9079668
|
||||
2000 4.9080829 4.8206128 9.2645313
|
||||
2050 4.7794302 4.5942332 9.22621
|
||||
2100 5.1197536 4.884078 9.9557557
|
||||
2150 5.5674448 4.9602998 10.825168
|
||||
2200 5.9993278 5.484917 11.201052
|
||||
2250 5.619781 5.2475017 10.382149
|
||||
2300 4.7213112 4.5460993 10.254176
|
||||
2350 4.4310098 4.6363048 8.2696199
|
||||
2400 4.2798177 4.1485611 8.2037599
|
||||
2450 5.0414399 5.2572888 10.126969
|
||||
2500 5.2807077 5.4633007 10.424033
|
||||
2550 5.4538601 5.3268172 10.06153
|
||||
2600 4.9750473 5.2268468 10.433373
|
||||
2650 4.8397032 5.2258654 9.8686538
|
||||
2700 4.8943282 4.7637421 9.8715146
|
||||
2750 4.8870682 4.7334316 9.2096451
|
||||
2800 4.7611053 4.9820018 9.0797655
|
||||
2850 4.826047 5.2478652 10.549013
|
||||
2900 5.5999506 5.0160442 9.6169413
|
||||
2950 5.6210454 5.1519961 10.23173
|
||||
3000 5.2132243 5.1449194 9.9778889
|
||||
3050 5.651798 5.5919186 10.772823
|
||||
3100 4.8453492 4.6559497 9.175617
|
||||
3150 4.359467 4.9901271 8.512659
|
||||
3200 4.5724772 4.8788065 9.2580198
|
||||
3250 5.3195893 5.6518901 10.562311
|
||||
3300 5.4571458 5.9778537 11.804991
|
||||
3350 5.1322763 5.280149 10.894715
|
||||
3400 4.9393514 4.9051844 9.3048468
|
||||
3450 4.6741698 4.6317669 9.4965959
|
||||
3500 4.8634066 4.9618835 8.926419
|
||||
3550 4.7096981 4.4196734 9.5607265
|
||||
3600 5.1871839 5.3427606 9.9467134
|
||||
3650 5.7619975 5.2486309 10.359674
|
||||
3700 5.2563068 5.4591612 10.360825
|
||||
3750 5.2492743 5.4861677 9.7648858
|
||||
3800 5.0335744 5.2240642 9.6668438
|
||||
3850 5.1003253 5.0865548 11.111281
|
||||
3900 5.2978019 5.2126205 10.581896
|
||||
3950 5.0067291 5.2645911 10.750446
|
||||
4000 4.6513682 4.7407991 9.3959165
|
||||
4050 4.1903728 4.4021987 8.8451881
|
||||
4100 5.0089655 4.4961608 9.7363416
|
||||
4150 5.1557684 5.6110293 10.804015
|
||||
4200 5.2607824 5.3663361 10.663617
|
||||
4250 5.0134036 5.1164765 9.3320261
|
||||
4300 4.2919496 4.6118896 9.2176556
|
||||
4350 4.9118467 4.9766595 9.8989104
|
||||
4400 5.7694762 5.2410849 10.660891
|
||||
4450 5.3793656 5.4714178 10.784611
|
||||
4500 5.187077 5.0952514 9.6404449
|
||||
4550 4.9522826 4.5959954 10.30975
|
||||
4600 4.9512246 5.0305627 10.295169
|
||||
4650 5.8017637 5.3485687 10.411051
|
||||
4700 5.2499784 4.8217382 10.077816
|
||||
4750 4.9961796 4.9148313 9.4660475
|
||||
4800 4.8958835 4.6546838 9.1730325
|
||||
4850 4.7408482 5.1862514 9.9399226
|
||||
4900 4.999383 4.9513486 9.5506941
|
||||
4950 5.0375134 4.63474 10.325618
|
||||
5000 5.0274884 5.391675 9.592851
|
||||
5050 5.3817822 5.5141892 11.43286
|
||||
5100 5.533224 5.1489534 10.56325
|
||||
5150 4.4884587 4.8979144 9.7439562
|
||||
5200 4.7352575 4.2854079 8.8328248
|
||||
5250 4.6347427 4.7579757 9.5316726
|
||||
5300 4.9765192 5.1378784 9.7376039
|
||||
5350 5.1899675 4.9469798 10.699202
|
||||
5400 5.0178189 5.47536 9.707559
|
||||
5450 4.9537295 5.1651951 9.7430567
|
||||
5500 4.8448459 4.6800231 9.297621
|
||||
5550 5.1703386 4.865903 10.090954
|
||||
5600 5.6293349 5.4332687 10.047955
|
||||
5650 5.2729245 6.180173 10.259202
|
||||
5700 5.1034054 5.2082315 10.031079
|
||||
5750 5.0982009 5.0158875 10.3517
|
||||
5800 4.8139573 4.8454398 10.001093
|
||||
5850 5.3237843 4.9860148 10.493724
|
||||
5900 4.421652 4.7147453 10.30137
|
||||
5950 5.3475173 4.8489279 9.7495241
|
||||
6000 5.013939 4.796874 9.7433063
|
||||
6050 5.1111778 5.2773346 10.245638
|
||||
6100 5.1484609 5.2230939 9.9800589
|
||||
6150 5.0101213 5.0702323 9.7021038
|
||||
6200 4.5881964 5.2635287 9.3903355
|
||||
6250 5.5340791 5.5956851 10.809705
|
||||
6300 5.3121762 5.3679934 9.4683653
|
||||
6350 5.072589 5.0111289 10.494452
|
||||
6400 5.3134876 5.3779245 11.439347
|
||||
6450 4.9930408 5.3215491 10.287925
|
||||
6500 4.6925854 4.4527123 9.3141266
|
||||
6550 4.5127115 4.5276223 9.2970101
|
||||
6600 4.6857945 5.0039986 9.8782575
|
||||
6650 5.4210348 4.6775837 10.404812
|
||||
6700 5.416291 5.1705872 10.935776
|
||||
6750 5.2396825 5.0306589 10.14922
|
||||
6800 5.3579349 4.9442072 10.510841
|
||||
6850 4.8287972 4.4930847 9.4697502
|
||||
6900 4.9688784 4.5977364 10.004321
|
||||
6950 4.7853293 4.5578984 9.0727469
|
||||
7000 5.0589506 4.9662362 11.04237
|
||||
7050 5.2657677 5.3989373 10.712811
|
||||
7100 5.5373555 5.6700228 10.099215
|
||||
7150 4.7085526 4.4207863 9.417028
|
||||
7200 4.7480934 4.8575585 9.970864
|
||||
7250 5.2732588 5.211703 9.8573725
|
||||
7300 5.0152654 5.5514349 11.104278
|
||||
7350 4.9255785 5.3533123 10.69476
|
||||
7400 5.1041241 5.0597338 9.5918592
|
||||
7450 4.7333067 4.584844 10.820426
|
||||
7500 4.9157751 5.0274623 10.706391
|
||||
7550 4.8231717 5.2251684 9.7721097
|
||||
7600 4.5115685 4.6809903 9.1230191
|
||||
7650 4.76928 5.0869557 9.2881957
|
||||
7700 5.1014383 5.4733369 9.9024386
|
||||
7750 5.7812792 5.6404429 10.895814
|
||||
7800 5.451651 5.4137204 10.471661
|
||||
7850 4.7982757 5.2043999 10.046712
|
||||
7900 4.4490306 4.546108 8.3934233
|
||||
7950 4.3147055 4.489834 8.8833017
|
||||
8000 5.0558378 5.1022203 11.21385
|
||||
8050 6.0715673 5.9289687 12.007167
|
||||
8100 5.4463621 5.8686057 9.7475724
|
||||
8150 4.6295786 4.5658519 8.9353979
|
||||
8200 4.4109788 4.4122705 8.8574801
|
||||
8250 4.9903375 5.2807872 10.024069
|
||||
8300 5.2930602 5.7480682 10.33242
|
||||
8350 5.6166755 5.3279586 10.761278
|
||||
8400 5.2344331 5.3991078 10.261601
|
||||
8450 4.9395736 4.8421048 10.544976
|
||||
8500 4.8692729 4.4538669 10.38133
|
||||
8550 4.7746965 4.5959252 10.413873
|
||||
8600 4.4344376 4.9176179 9.0368016
|
||||
8650 5.0230802 4.7795825 8.5121429
|
||||
8700 4.9279145 4.8844196 10.145405
|
||||
8750 5.343116 5.7462499 11.191805
|
||||
8800 5.4073851 5.1952022 9.6534892
|
||||
8850 5.6085471 5.1332845 10.28282
|
||||
8900 4.9077946 5.1446696 9.236557
|
||||
8950 4.9416647 5.2071136 10.106251
|
||||
9000 5.4201564 5.3733264 11.081109
|
||||
9050 5.9648951 5.5501112 12.621681
|
||||
9100 4.8947991 5.2187898 10.470022
|
||||
9150 4.48197 4.1036268 8.4201904
|
||||
9200 4.3946543 4.3973715 8.5340163
|
||||
9250 5.3021965 5.2717867 9.2560849
|
||||
9300 5.1768568 5.8272523 10.232503
|
||||
9350 5.7291082 5.7641611 11.622836
|
||||
9400 5.5971415 6.0957826 11.948662
|
||||
9450 4.6317008 4.8550521 9.7699372
|
||||
9500 4.3364192 4.4197985 8.8085022
|
||||
9550 4.4961662 4.5930997 9.6064493
|
||||
9600 4.901858 5.3789866 10.044551
|
||||
9650 5.2916208 4.9071387 9.9083075
|
||||
9700 4.8995154 4.78658 9.3871144
|
||||
9750 5.5045136 5.3070515 10.969147
|
||||
9800 5.2729372 6.0714054 11.027892
|
||||
9850 4.8794625 5.2788176 10.100819
|
||||
9900 4.6173961 4.6918339 9.2090718
|
||||
9950 4.7478539 4.6911854 8.6831286
|
||||
10000 4.9331146 5.3771408 11.489778
|
||||
Loop time of 2.62782 on 4 procs for 10000 steps with 500 atoms
|
||||
|
||||
Performance: 1643945.149 tau/day, 3805.429 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.29968 | 0.30667 | 0.31341 | 1.2 | 11.67
|
||||
Neigh | 1.0173 | 1.0395 | 1.0668 | 2.1 | 39.56
|
||||
Comm | 0.55804 | 0.59161 | 0.62132 | 3.5 | 22.51
|
||||
Output | 0.0028653 | 0.0035743 | 0.0056112 | 2.0 | 0.14
|
||||
Modify | 0.5692 | 0.5732 | 0.57625 | 0.4 | 21.81
|
||||
Other | | 0.1132 | | | 4.31
|
||||
|
||||
Nlocal: 125 ave 130 max 121 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Nghost: 452.25 ave 455 max 449 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Neighs: 837 ave 882 max 804 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 3348
|
||||
Ave neighs/atom = 6.696
|
||||
Neighbor list builds = 4598
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
1022
examples/USER/uef/nvt_uniaxial/data.wca
Normal file
1022
examples/USER/uef/nvt_uniaxial/data.wca
Normal file
File diff suppressed because it is too large
Load Diff
28
examples/USER/uef/nvt_uniaxial/in.nvt_uniaxial
Normal file
28
examples/USER/uef/nvt_uniaxial/in.nvt_uniaxial
Normal file
@ -0,0 +1,28 @@
|
||||
# uniaxial NVT deformation of WCA fluid
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
|
||||
pair_style lj/cut 1.122562
|
||||
read_data data.wca
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
change_box all triclinic
|
||||
|
||||
fix 1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5
|
||||
|
||||
fix 2 all momentum 100 linear 1 1 1
|
||||
|
||||
#dump 1 all atom 25 dump.lammpstrj
|
||||
|
||||
#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs
|
||||
|
||||
thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3]
|
||||
|
||||
thermo 50
|
||||
run 10000
|
||||
273
examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.1
Normal file
273
examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.1
Normal file
@ -0,0 +1,273 @@
|
||||
LAMMPS (30 Jul 2016)
|
||||
# uniaxial NVT deformation of WCA fluid
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
|
||||
pair_style lj/cut 1.122562
|
||||
read_data data.wca
|
||||
orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
change_box all triclinic
|
||||
triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0)
|
||||
|
||||
fix 1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5
|
||||
|
||||
fix 2 all momentum 100 linear 1 1 1
|
||||
|
||||
#dump 1 all atom 25 dump.lammpstrj
|
||||
|
||||
#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs
|
||||
|
||||
thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3]
|
||||
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.62256
|
||||
ghost atom cutoff = 1.62256
|
||||
binsize = 0.811281 -> bins = 11 11 11
|
||||
Memory usage per processor = 2.40217 Mbytes
|
||||
Step 1_press[ 1_press[ 1_press[
|
||||
0 6.3937851 7.0436438 6.4461087
|
||||
50 10.369902 10.999889 6.5437384
|
||||
100 12.411384 13.145871 7.8892802
|
||||
150 12.88182 12.114068 7.5155182
|
||||
200 10.375571 10.979773 6.5624056
|
||||
250 10.158901 10.251273 5.4525068
|
||||
300 10.011314 9.8371382 5.4031393
|
||||
350 9.4890008 9.7992108 5.054963
|
||||
400 9.1715116 9.2647886 4.9600208
|
||||
450 9.8495961 9.3353483 4.986786
|
||||
500 9.5903809 8.576173 4.8252116
|
||||
550 8.8057509 9.7152078 4.9089022
|
||||
600 8.9743682 10.031277 4.8924072
|
||||
650 10.233852 9.3059527 5.1977058
|
||||
700 9.2361906 9.6439971 5.0923763
|
||||
750 10.449751 9.5911465 5.2548714
|
||||
800 9.8366857 9.9873885 4.9456956
|
||||
850 10.266351 9.9620134 5.0602713
|
||||
900 9.6325813 9.3910946 5.1466624
|
||||
950 9.1911919 9.1519006 4.8275345
|
||||
1000 9.2871712 9.8508501 5.2674099
|
||||
1050 9.7052035 10.291793 5.160359
|
||||
1100 9.9425552 10.361827 5.5520484
|
||||
1150 10.377563 10.26588 5.5997436
|
||||
1200 9.6368269 10.354413 5.4137873
|
||||
1250 9.2071055 9.1706334 4.9800411
|
||||
1300 9.7140516 8.7257777 4.8536943
|
||||
1350 10.145983 9.8247797 4.8921813
|
||||
1400 9.1998975 9.6935675 5.2269871
|
||||
1450 9.4838136 8.9035726 4.6867121
|
||||
1500 9.066389 9.811658 4.8875316
|
||||
1550 10.007083 9.8946118 5.204609
|
||||
1600 9.722137 9.9291588 5.326712
|
||||
1650 9.7424614 9.6995966 5.3577819
|
||||
1700 9.7185135 9.5922931 5.385856
|
||||
1750 9.6368481 8.1414594 5.0046079
|
||||
1800 9.8065782 9.6798036 4.92473
|
||||
1850 9.0463737 10.024205 5.6495695
|
||||
1900 9.0774484 10.527582 5.0363426
|
||||
1950 9.1691461 10.049703 4.8517514
|
||||
2000 9.7619602 10.049532 5.2088038
|
||||
2050 9.9203348 9.8056395 5.7699852
|
||||
2100 9.1455665 9.5864018 5.1410542
|
||||
2150 8.8501135 9.7917307 5.141824
|
||||
2200 9.1433685 9.8168548 5.1742441
|
||||
2250 9.3248968 10.454532 5.5456356
|
||||
2300 10.210505 9.361499 5.0935226
|
||||
2350 9.5041186 9.598986 5.2451005
|
||||
2400 8.968896 9.2811921 4.7799868
|
||||
2450 9.8201159 10.133892 4.9981817
|
||||
2500 9.4421084 9.7875766 5.4124809
|
||||
2550 9.6410643 9.9148309 5.0603288
|
||||
2600 9.3810676 9.5346849 5.3233836
|
||||
2650 9.2340337 8.7233538 5.0361302
|
||||
2700 9.405597 9.7848488 4.7537042
|
||||
2750 9.9447412 9.2366502 4.9736459
|
||||
2800 10.189443 9.452684 5.624362
|
||||
2850 9.6680124 9.0941543 5.0101469
|
||||
2900 8.4350889 9.1595018 4.7706866
|
||||
2950 9.0056117 9.3498593 4.7655963
|
||||
3000 9.4795416 9.7400747 5.4705868
|
||||
3050 9.6605264 9.4558374 5.1240166
|
||||
3100 9.681451 9.7966554 5.3174458
|
||||
3150 9.7887528 9.7371194 4.9349103
|
||||
3200 9.9720054 9.5592538 5.2306417
|
||||
3250 10.185023 9.9436037 5.4127312
|
||||
3300 9.9670676 9.6069307 5.026261
|
||||
3350 9.0090411 9.5975249 4.8881019
|
||||
3400 9.6535707 9.748683 4.9933873
|
||||
3450 9.7774977 9.7570511 4.8512619
|
||||
3500 9.7250053 10.36386 5.4057249
|
||||
3550 9.567788 9.773413 5.3936671
|
||||
3600 9.2094148 9.0211247 5.2328675
|
||||
3650 9.3512098 9.73407 4.576624
|
||||
3700 9.159074 9.2611591 5.2996448
|
||||
3750 9.4772798 8.9792211 5.1007079
|
||||
3800 9.3898357 9.1150609 5.2126508
|
||||
3850 9.2466312 9.1460651 4.867472
|
||||
3900 9.9316993 9.3061137 5.1219265
|
||||
3950 9.2550913 9.780254 5.371885
|
||||
4000 10.005356 9.7328972 5.2535791
|
||||
4050 9.5228242 9.5134113 5.4181393
|
||||
4100 9.576808 10.082425 5.1272491
|
||||
4150 10.20265 9.6667058 5.529118
|
||||
4200 9.9443671 10.09427 5.6163734
|
||||
4250 9.4956875 9.9462818 5.0820085
|
||||
4300 10.350144 10.003702 5.1621505
|
||||
4350 10.119486 9.8691507 5.4913457
|
||||
4400 9.4991604 10.516185 5.2512264
|
||||
4450 9.0812854 9.2835603 5.1695714
|
||||
4500 9.7538478 8.5298834 4.5954607
|
||||
4550 9.8920394 9.3581299 5.202587
|
||||
4600 9.2694921 9.3338291 5.201958
|
||||
4650 10.925818 9.5062049 4.8694531
|
||||
4700 11.020014 10.130224 5.582409
|
||||
4750 9.5005142 9.3571561 5.456739
|
||||
4800 9.6670147 9.6628702 5.0451252
|
||||
4850 9.134147 9.1308788 4.7950594
|
||||
4900 9.7466206 8.6171443 4.8716275
|
||||
4950 9.0397505 9.1996036 5.2010502
|
||||
5000 9.6898652 9.8914655 5.3959279
|
||||
5050 10.06771 9.7523891 5.3690408
|
||||
5100 10.000963 9.6279379 5.4077384
|
||||
5150 9.8686159 10.179702 5.0686824
|
||||
5200 9.8866247 9.725152 5.4350049
|
||||
5250 9.2068346 10.214424 5.3187713
|
||||
5300 9.713992 9.8069045 5.496359
|
||||
5350 9.423852 9.364085 5.2144606
|
||||
5400 9.4350241 9.5584633 5.0339001
|
||||
5450 10.555124 10.784922 5.1938072
|
||||
5500 9.4147344 10.33187 5.4360602
|
||||
5550 9.8514653 9.6575827 5.4959779
|
||||
5600 9.3138107 9.6592624 4.941387
|
||||
5650 9.1224809 8.7112257 5.0435936
|
||||
5700 8.8289158 10.749686 4.8916132
|
||||
5750 9.7200279 10.030606 5.2033161
|
||||
5800 9.8439873 9.6289015 5.5131934
|
||||
5850 9.6257294 9.4128988 4.9196038
|
||||
5900 9.7490214 9.5776313 5.0301815
|
||||
5950 9.1430855 10.108944 5.1406243
|
||||
6000 9.3358644 9.5633737 4.9787073
|
||||
6050 9.4432774 8.9464304 5.1466052
|
||||
6100 8.8878373 9.5048946 4.9190238
|
||||
6150 9.6451898 9.2419823 5.0159841
|
||||
6200 9.5042173 8.9414307 5.2634247
|
||||
6250 9.0896505 9.7230651 5.3340322
|
||||
6300 8.8100599 8.8781352 5.4117914
|
||||
6350 9.3104601 9.0233294 5.3136432
|
||||
6400 9.368101 9.6387362 4.7833216
|
||||
6450 10.334343 9.8384149 5.3606204
|
||||
6500 9.8824036 10.022627 6.0857086
|
||||
6550 9.7034443 10.026765 5.17604
|
||||
6600 9.3757845 9.899268 5.2301359
|
||||
6650 10.540821 10.4343 5.5287065
|
||||
6700 9.6317649 9.8923579 5.6045768
|
||||
6750 9.5982772 10.07897 5.1221451
|
||||
6800 10.239883 10.189967 5.3167447
|
||||
6850 10.017271 9.7680902 5.229621
|
||||
6900 9.6200416 10.129301 5.1998759
|
||||
6950 9.0361417 8.923798 5.1652612
|
||||
7000 9.3153521 9.063054 4.6860773
|
||||
7050 8.6434091 9.0363436 4.7811975
|
||||
7100 9.4955395 9.3830541 5.022538
|
||||
7150 9.3392402 9.1847119 5.1544622
|
||||
7200 9.4676321 9.8370036 4.8854442
|
||||
7250 9.5115882 10.350324 4.9780525
|
||||
7300 9.6025583 9.6247917 5.473794
|
||||
7350 9.8919524 10.049446 4.9816931
|
||||
7400 9.6814319 9.9410894 5.265078
|
||||
7450 9.4130955 10.191436 5.2531256
|
||||
7500 9.8114668 8.8461635 5.0562894
|
||||
7550 10.321567 9.4730124 5.2043655
|
||||
7600 9.5059024 9.8330367 5.0749721
|
||||
7650 10.067084 10.606423 5.5598818
|
||||
7700 10.896159 10.084281 5.5159718
|
||||
7750 9.754306 10.162301 5.2475876
|
||||
7800 9.7278145 9.801009 5.0685504
|
||||
7850 9.8639905 10.323104 5.2458864
|
||||
7900 9.7246799 9.1377357 5.1841319
|
||||
7950 10.381792 9.6977533 5.0977386
|
||||
8000 9.7265224 9.2999829 4.7925571
|
||||
8050 9.5203288 9.3144956 4.7539211
|
||||
8100 9.6900973 9.6614063 5.304712
|
||||
8150 9.713677 9.9154149 4.8178575
|
||||
8200 9.4733597 9.8948632 5.036112
|
||||
8250 9.7783036 9.9554334 5.3355682
|
||||
8300 9.4034783 9.9156801 5.5539279
|
||||
8350 9.2984025 9.2013949 5.0753991
|
||||
8400 9.9299078 9.6166801 5.115776
|
||||
8450 9.526737 9.3312125 4.7800587
|
||||
8500 9.581956 10.065906 4.9756092
|
||||
8550 9.2767953 9.326006 5.3024978
|
||||
8600 9.799968 8.4660845 5.0199109
|
||||
8650 9.8985354 10.127852 4.9098064
|
||||
8700 8.7952691 10.521133 5.6840528
|
||||
8750 9.8299997 9.5588553 5.3085734
|
||||
8800 9.0811776 9.5704532 5.1684993
|
||||
8850 9.8303571 9.7618932 5.1251259
|
||||
8900 9.9238794 9.9654863 5.2999683
|
||||
8950 10.851304 9.9682289 5.4133763
|
||||
9000 9.5523794 9.1890766 5.1469144
|
||||
9050 9.7461948 8.9611236 4.9490826
|
||||
9100 10.138917 9.6757567 5.0473544
|
||||
9150 9.4869835 9.4786575 5.0142464
|
||||
9200 10.263518 10.079135 5.1493398
|
||||
9250 9.8691684 9.0908275 5.3221203
|
||||
9300 9.8586707 9.4177643 5.1525265
|
||||
9350 9.3375816 9.9167208 5.4846207
|
||||
9400 9.5603903 9.4813199 4.6237495
|
||||
9450 10.30892 9.5217736 5.6163214
|
||||
9500 9.327949 9.9831649 4.8923915
|
||||
9550 9.8421656 9.3202702 5.3352046
|
||||
9600 8.8543704 9.4556702 4.6430041
|
||||
9650 10.103399 9.2161072 4.8658062
|
||||
9700 9.507811 9.9647378 5.227369
|
||||
9750 9.4988096 8.9942893 5.2491418
|
||||
9800 9.8007958 9.234452 5.1740203
|
||||
9850 9.6029685 10.076042 5.023107
|
||||
9900 9.4035691 10.13782 5.2775777
|
||||
9950 9.6517135 10.355994 5.3035779
|
||||
10000 9.9157616 9.7741952 5.5269431
|
||||
Loop time of 4.303 on 1 procs for 10000 steps with 500 atoms
|
||||
|
||||
Performance: 1003950.961 tau/day, 2323.961 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.69667 | 0.69667 | 0.69667 | 0.0 | 16.19
|
||||
Neigh | 2.699 | 2.699 | 2.699 | 0.0 | 62.72
|
||||
Comm | 0.30701 | 0.30701 | 0.30701 | 0.0 | 7.13
|
||||
Output | 0.003968 | 0.003968 | 0.003968 | 0.0 | 0.09
|
||||
Modify | 0.49374 | 0.49374 | 0.49374 | 0.0 | 11.47
|
||||
Other | | 0.1026 | | | 2.38
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 908 ave 908 max 908 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3489 ave 3489 max 3489 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3489
|
||||
Ave neighs/atom = 6.978
|
||||
Neighbor list builds = 4567
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:04
|
||||
273
examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.4
Normal file
273
examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.4
Normal file
@ -0,0 +1,273 @@
|
||||
LAMMPS (30 Jul 2016)
|
||||
# uniaxial NVT deformation of WCA fluid
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
|
||||
pair_style lj/cut 1.122562
|
||||
read_data data.wca
|
||||
orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
reading velocities ...
|
||||
500 velocities
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
change_box all triclinic
|
||||
triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0)
|
||||
|
||||
fix 1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5
|
||||
|
||||
fix 2 all momentum 100 linear 1 1 1
|
||||
|
||||
#dump 1 all atom 25 dump.lammpstrj
|
||||
|
||||
#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs
|
||||
|
||||
thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3]
|
||||
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.62256
|
||||
ghost atom cutoff = 1.62256
|
||||
binsize = 0.811281 -> bins = 11 11 11
|
||||
Memory usage per processor = 2.38201 Mbytes
|
||||
Step 1_press[ 1_press[ 1_press[
|
||||
0 6.3937851 7.0436438 6.4461087
|
||||
50 10.369902 10.999889 6.5437384
|
||||
100 12.411384 13.145871 7.8892802
|
||||
150 12.88182 12.114068 7.5155182
|
||||
200 10.375571 10.979773 6.5624056
|
||||
250 10.158901 10.251273 5.4525068
|
||||
300 10.011314 9.8371382 5.4031393
|
||||
350 9.4890008 9.7992108 5.054963
|
||||
400 9.1715116 9.2647886 4.9600208
|
||||
450 9.8495961 9.3353483 4.986786
|
||||
500 9.5903809 8.576173 4.8252116
|
||||
550 8.8057509 9.7152078 4.9089022
|
||||
600 8.9743682 10.031277 4.8924072
|
||||
650 10.233852 9.3059527 5.1977058
|
||||
700 9.2361906 9.6439971 5.0923762
|
||||
750 10.449751 9.5911465 5.2548714
|
||||
800 9.8366858 9.9873885 4.9456956
|
||||
850 10.266351 9.9620134 5.0602713
|
||||
900 9.6325811 9.3910947 5.1466627
|
||||
950 9.1911905 9.1518997 4.8275335
|
||||
1000 9.2871725 9.8508561 5.2674079
|
||||
1050 9.7052018 10.291782 5.1603606
|
||||
1100 9.942582 10.361849 5.5520591
|
||||
1150 10.37757 10.265893 5.5997259
|
||||
1200 9.6367107 10.354442 5.4138733
|
||||
1250 9.2075329 9.1705 4.9806587
|
||||
1300 9.7125232 8.724748 4.852827
|
||||
1350 10.146185 9.8320894 4.8958299
|
||||
1400 9.1958247 9.7053023 5.2334931
|
||||
1450 9.4656613 8.9011194 4.7069541
|
||||
1500 9.0964228 9.8379154 4.8889701
|
||||
1550 10.074953 9.8121208 5.1614034
|
||||
1600 10.14322 9.7113028 5.0901612
|
||||
1650 9.9377801 9.8831912 5.2226793
|
||||
1700 9.4144883 8.5248477 4.9447402
|
||||
1750 9.0729219 9.612432 5.1999941
|
||||
1800 10.067363 9.8211216 5.1464764
|
||||
1850 9.3044429 8.9752352 5.0515339
|
||||
1900 9.4123739 9.1810527 5.3356061
|
||||
1950 9.3009721 10.013851 4.9527398
|
||||
2000 9.7741829 10.11286 5.3818321
|
||||
2050 9.6991106 9.7815812 5.1979016
|
||||
2100 9.2977435 9.4310005 5.0893893
|
||||
2150 10.325992 10.388415 4.9253076
|
||||
2200 10.193251 10.389764 5.4164579
|
||||
2250 9.9386988 9.63934 5.1685251
|
||||
2300 9.3128664 10.496199 5.423297
|
||||
2350 8.692096 9.761347 5.1356802
|
||||
2400 9.4532892 9.2946894 5.3127538
|
||||
2450 9.026436 8.8042728 4.9305279
|
||||
2500 8.9458518 9.6338731 5.1530972
|
||||
2550 8.9457961 9.7730997 5.1588
|
||||
2600 9.4313048 9.0489105 4.9937356
|
||||
2650 9.1625701 10.03039 4.9384831
|
||||
2700 10.135274 9.9106295 5.1582637
|
||||
2750 9.7419819 9.7329998 5.4813308
|
||||
2800 9.6793568 10.137218 4.9126985
|
||||
2850 9.8286116 9.8283148 5.2372177
|
||||
2900 9.2766894 9.5302835 5.1206658
|
||||
2950 9.6537203 9.8713609 5.2640351
|
||||
3000 9.704446 10.360629 5.2470236
|
||||
3050 9.289114 10.210593 4.9955164
|
||||
3100 9.5854695 9.0377602 5.0387963
|
||||
3150 9.4489179 9.0145734 4.9089788
|
||||
3200 8.9221328 8.8805863 4.7910012
|
||||
3250 8.9268792 8.6855592 4.7798689
|
||||
3300 9.5280088 9.6859376 5.1021255
|
||||
3350 9.7469167 9.7039449 5.3654161
|
||||
3400 10.163823 10.247303 5.3206912
|
||||
3450 10.328168 9.2596091 5.3903402
|
||||
3500 10.280033 10.087996 5.3980267
|
||||
3550 9.5278822 10.057563 4.9949376
|
||||
3600 9.3705739 9.9639827 5.1315405
|
||||
3650 10.003355 9.0323131 5.288539
|
||||
3700 9.5814093 9.742063 4.9937322
|
||||
3750 9.1121545 9.9600773 5.2621763
|
||||
3800 8.4753486 9.2930472 4.8939508
|
||||
3850 9.309286 9.0227214 4.9323125
|
||||
3900 9.0283302 10.048011 5.0801404
|
||||
3950 10.193343 10.279252 5.4390015
|
||||
4000 9.5170246 9.8575174 5.3284718
|
||||
4050 9.0306235 9.4210217 4.7042159
|
||||
4100 9.7801264 10.267131 4.8946632
|
||||
4150 10.161985 10.327002 5.3719225
|
||||
4200 10.242291 9.5148633 5.2938589
|
||||
4250 9.67955 10.025696 5.517063
|
||||
4300 9.0818798 9.655456 5.0976568
|
||||
4350 9.3181275 8.8534154 4.9252792
|
||||
4400 9.4111133 8.9481402 4.8338338
|
||||
4450 10.219905 10.0317 5.3278766
|
||||
4500 9.9718967 9.9808168 5.2294123
|
||||
4550 9.7194794 9.7613441 5.3369724
|
||||
4600 9.4826038 9.5426517 5.1951956
|
||||
4650 9.5794203 8.4729044 4.9375856
|
||||
4700 9.6409231 10.059765 4.9659309
|
||||
4750 9.0853564 9.6062246 5.1560466
|
||||
4800 9.5805015 10.26319 5.1395845
|
||||
4850 8.8662041 9.4757304 5.1729905
|
||||
4900 9.6230855 10.239009 5.1382048
|
||||
4950 10.401327 9.5494971 5.2688637
|
||||
5000 10.433047 9.9017863 5.4626886
|
||||
5050 10.318188 9.2998964 5.4707543
|
||||
5100 9.6958274 9.206341 5.0269859
|
||||
5150 9.5477552 10.099142 5.3760873
|
||||
5200 9.4904189 9.4403777 5.1638292
|
||||
5250 9.8421539 8.7828543 4.8612713
|
||||
5300 9.7354196 9.357113 4.9059656
|
||||
5350 9.9183987 9.4337973 5.2986167
|
||||
5400 10.045743 9.8399757 5.0930923
|
||||
5450 9.6414177 10.169944 5.3868716
|
||||
5500 10.035214 9.5316451 4.912222
|
||||
5550 9.16334 9.3853532 5.2319683
|
||||
5600 9.5075535 9.2548959 5.4425531
|
||||
5650 9.3854437 9.0700172 4.9845383
|
||||
5700 9.1868937 9.3061525 4.9155762
|
||||
5750 9.4785528 9.8271693 4.9974045
|
||||
5800 9.7809419 10.070618 5.3699816
|
||||
5850 10.791132 10.572676 5.3816834
|
||||
5900 10.091884 10.036391 5.7604455
|
||||
5950 9.4492785 8.9938163 4.9812227
|
||||
6000 9.2296463 10.334517 5.6374553
|
||||
6050 9.9339781 9.1097471 4.6847041
|
||||
6100 10.369857 9.261491 5.3354256
|
||||
6150 9.9444024 9.5330721 5.2413981
|
||||
6200 9.1507255 9.2108005 4.7010871
|
||||
6250 9.6093995 9.2275894 4.8659261
|
||||
6300 9.0300283 9.149341 4.9305141
|
||||
6350 9.6718904 9.5721387 4.9560051
|
||||
6400 9.615362 10.030978 4.8786582
|
||||
6450 10.343763 10.184481 5.2027613
|
||||
6500 9.3452563 9.7249417 5.2318842
|
||||
6550 9.9489414 10.373436 4.9258407
|
||||
6600 10.083741 10.87974 5.3665699
|
||||
6650 9.431476 9.7944015 5.4214407
|
||||
6700 9.3430129 10.032417 4.8538936
|
||||
6750 10.253341 9.5667637 5.3838115
|
||||
6800 8.9695591 9.888476 4.7973343
|
||||
6850 9.6952765 9.3339082 4.8432603
|
||||
6900 9.1038139 9.6295207 4.8572214
|
||||
6950 9.5374663 9.0498856 5.2316356
|
||||
7000 8.6844415 9.1416318 4.9513449
|
||||
7050 9.6271147 8.8341922 5.135948
|
||||
7100 9.3889214 9.6771129 5.1106028
|
||||
7150 9.4697432 9.9959141 4.8762717
|
||||
7200 9.9545962 9.5556848 5.2760968
|
||||
7250 10.153728 10.396722 5.4066282
|
||||
7300 9.5633599 9.8262997 5.5238788
|
||||
7350 10.476059 9.8526241 4.9928222
|
||||
7400 9.5848947 9.389115 5.1177333
|
||||
7450 9.3917853 9.8395056 5.5201002
|
||||
7500 9.2406374 9.4598141 4.9336365
|
||||
7550 9.1325284 9.0585 5.007436
|
||||
7600 9.5045307 9.5164648 4.8310378
|
||||
7650 9.5165952 9.5154581 5.3199138
|
||||
7700 9.1167042 9.3283907 4.9548988
|
||||
7750 9.5408306 10.191558 5.1889476
|
||||
7800 9.2362359 9.5066276 5.4139251
|
||||
7850 9.9533215 9.3418618 5.0073354
|
||||
7900 9.063471 9.2389687 5.1529568
|
||||
7950 9.6887619 9.3363144 5.0264365
|
||||
8000 10.244559 10.352116 5.3898068
|
||||
8050 10.522656 9.7844249 5.648648
|
||||
8100 10.456047 10.108097 5.234203
|
||||
8150 9.0497599 10.3333 5.5526068
|
||||
8200 9.1341912 9.7046196 4.7491692
|
||||
8250 9.3297032 9.2513325 4.9471519
|
||||
8300 9.9385635 9.8432553 4.9102209
|
||||
8350 9.506086 9.3628428 5.4489526
|
||||
8400 9.7575572 9.6628477 4.7835143
|
||||
8450 9.4234184 9.6901535 5.2506704
|
||||
8500 9.1019018 9.4713605 4.9996292
|
||||
8550 8.9668254 9.2297952 4.9015639
|
||||
8600 10.000082 9.852912 5.1235791
|
||||
8650 9.6677771 9.8825377 5.0888713
|
||||
8700 9.5220305 9.6140025 5.2621374
|
||||
8750 9.769165 9.1639605 4.942283
|
||||
8800 10.214712 9.0544214 5.0977658
|
||||
8850 10.050644 8.9450446 4.876467
|
||||
8900 9.7066878 9.8028705 5.1098917
|
||||
8950 9.8322209 9.5247394 5.1258681
|
||||
9000 10.116755 9.9220422 5.2801505
|
||||
9050 9.671068 9.448618 5.1789641
|
||||
9100 8.6872235 9.8346401 4.8940421
|
||||
9150 9.8181714 9.652061 4.9136383
|
||||
9200 9.5400873 9.9027439 5.3147415
|
||||
9250 9.2344784 9.9272383 5.397571
|
||||
9300 9.0207063 9.2498921 5.0643988
|
||||
9350 10.648665 9.0509298 5.0354353
|
||||
9400 9.7266263 9.5319347 5.4323366
|
||||
9450 9.5044169 9.7968623 5.2079039
|
||||
9500 9.0459316 9.6916313 5.1584987
|
||||
9550 9.1265901 10.045493 4.9476229
|
||||
9600 9.896449 9.509792 5.5305989
|
||||
9650 9.2957435 9.4288068 5.1885785
|
||||
9700 9.6000499 8.7187335 5.0900953
|
||||
9750 9.5997652 9.4810899 4.8707106
|
||||
9800 9.2198937 9.7067006 5.4461186
|
||||
9850 9.8794169 10.051937 5.0361319
|
||||
9900 9.9783069 9.9785092 5.2066807
|
||||
9950 9.0880268 9.5659803 5.3678011
|
||||
10000 9.6972182 9.9076171 5.1538951
|
||||
Loop time of 2.23728 on 4 procs for 10000 steps with 500 atoms
|
||||
|
||||
Performance: 1930919.704 tau/day, 4469.722 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.26111 | 0.26444 | 0.26854 | 0.5 | 11.82
|
||||
Neigh | 1.0268 | 1.037 | 1.0467 | 0.7 | 46.35
|
||||
Comm | 0.5321 | 0.55022 | 0.56515 | 1.6 | 24.59
|
||||
Output | 0.003746 | 0.0045477 | 0.006809 | 1.9 | 0.20
|
||||
Modify | 0.26509 | 0.26827 | 0.27182 | 0.5 | 11.99
|
||||
Other | | 0.1128 | | | 5.04
|
||||
|
||||
Nlocal: 125 ave 128 max 123 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 468.25 ave 470 max 467 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 869.75 ave 895 max 843 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 3479
|
||||
Ave neighs/atom = 6.958
|
||||
Neighbor list builds = 4555
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
@ -63,7 +63,7 @@ PACKUSER = user-atc user-awpmd user-cgdna user-cgsdk user-colvars \
|
||||
user-mgpt user-misc user-molfile \
|
||||
user-netcdf user-omp user-phonon user-qmmm user-qtb \
|
||||
user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
|
||||
user-vtk
|
||||
user-uef user-vtk
|
||||
|
||||
PACKLIB = compress gpu kim kokkos latte meam mpiio mscg poems \
|
||||
python reax voronoi \
|
||||
|
||||
198
src/USER-UEF/compute_pressure_uef.cpp
Normal file
198
src/USER-UEF/compute_pressure_uef.cpp
Normal file
@ -0,0 +1,198 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Contributing author: David Nicholson (MIT)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "mpi.h"
|
||||
#include "string.h"
|
||||
#include "stdlib.h"
|
||||
#include "compute_pressure_uef.h"
|
||||
#include "fix_nh_uef.h"
|
||||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "modify.h"
|
||||
#include "fix.h"
|
||||
#include "force.h"
|
||||
#include "pair.h"
|
||||
#include "bond.h"
|
||||
#include "angle.h"
|
||||
#include "dihedral.h"
|
||||
#include "improper.h"
|
||||
#include "kspace.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* Default values for the ext flags
|
||||
* ----------------------------------------------------------------------*/
|
||||
ComputePressureUef::ComputePressureUef(LAMMPS *lmp, int narg, char **arg) :
|
||||
ComputePressure(lmp, narg, arg)
|
||||
{
|
||||
ext_flags[0] = true;
|
||||
ext_flags[1] = true;
|
||||
ext_flags[2] = true;
|
||||
in_fix=false;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* Check for the uef fix
|
||||
* ----------------------------------------------------------------------*/
|
||||
void ComputePressureUef::init()
|
||||
{
|
||||
ComputePressure::init();
|
||||
// check to make sure the other uef fix is on
|
||||
// borrowed from Pieter's nvt/sllod code
|
||||
int i=0;
|
||||
for (i=0; i<modify->nfix; i++)
|
||||
{
|
||||
if (strcmp(modify->fix[i]->style,"nvt/uef")==0)
|
||||
break;
|
||||
if (strcmp(modify->fix[i]->style,"npt/uef")==0)
|
||||
break;
|
||||
}
|
||||
if (i==modify->nfix)
|
||||
error->all(FLERR,"Can't use compute pressure/uef without defining a fix nvt/npt/uef");
|
||||
ifix_uef=i;
|
||||
((FixNHUef*) modify->fix[ifix_uef])->get_ext_flags(ext_flags);
|
||||
|
||||
if (strcmp(temperature->style,"temp/uef") != 0)
|
||||
error->warning(FLERR,"The temperature used in compute pressure/ued is not of style temp/uef");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* Compute pressure in the directions i corresponding to ext_flag[i]=true
|
||||
* ----------------------------------------------------------------------*/
|
||||
double ComputePressureUef::compute_scalar()
|
||||
{
|
||||
|
||||
temperature->compute_scalar();
|
||||
// if all pressures are external the scalar is found as normal
|
||||
if (ext_flags[0] && ext_flags[1] && ext_flags[2])
|
||||
return ComputePressure::compute_scalar();
|
||||
|
||||
// otherwise compute the full tensor and average desired components
|
||||
compute_vector();
|
||||
addstep(update->ntimestep+1);
|
||||
|
||||
int k =0;
|
||||
scalar = 0;
|
||||
if (ext_flags[0])
|
||||
{
|
||||
scalar += vector[0];
|
||||
k++;
|
||||
}
|
||||
if (ext_flags[1])
|
||||
{
|
||||
scalar += vector[1];
|
||||
k++;
|
||||
}
|
||||
if (ext_flags[2])
|
||||
{
|
||||
scalar += vector[2];
|
||||
k++;
|
||||
}
|
||||
|
||||
scalar /= k;
|
||||
return scalar;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Compute the pressure tensor in the rotated coordinate system
|
||||
------------------------------------------------------------------------- */
|
||||
void ComputePressureUef::compute_vector()
|
||||
{
|
||||
invoked_vector = update->ntimestep;
|
||||
if (update->vflag_global != invoked_vector)
|
||||
error->all(FLERR,"Virial was not tallied on needed timestep");
|
||||
|
||||
if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag)
|
||||
error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for "
|
||||
"tensor components with kspace_style msm");
|
||||
|
||||
// invoke temperature if it hasn't been already
|
||||
|
||||
double *ke_tensor;
|
||||
if (keflag) {
|
||||
if (temperature->invoked_vector != update->ntimestep)
|
||||
temperature->compute_vector();
|
||||
ke_tensor = temperature->vector;
|
||||
}
|
||||
|
||||
if (dimension == 3) {
|
||||
inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
|
||||
virial_compute(6,3);
|
||||
if (in_fix)
|
||||
virial_rot(virial,rot);
|
||||
else
|
||||
{
|
||||
double r[3][3];
|
||||
( (FixNHUef*) modify->fix[ifix_uef])->get_rot(r);
|
||||
virial_rot(virial,r);
|
||||
}
|
||||
if (keflag) {
|
||||
for (int i = 0; i < 6; i++)
|
||||
vector[i] = (ke_tensor[i] + virial[i]) * inv_volume * nktv2p;
|
||||
} else
|
||||
for (int i = 0; i < 6; i++)
|
||||
vector[i] = virial[i] * inv_volume * nktv2p;
|
||||
} else {
|
||||
inv_volume = 1.0 / (domain->xprd * domain->yprd);
|
||||
virial_compute(4,2);
|
||||
if (keflag) {
|
||||
vector[0] = (ke_tensor[0] + virial[0]) * inv_volume * nktv2p;
|
||||
vector[1] = (ke_tensor[1] + virial[1]) * inv_volume * nktv2p;
|
||||
vector[3] = (ke_tensor[3] + virial[3]) * inv_volume * nktv2p;
|
||||
vector[2] = vector[4] = vector[5] = 0.0;
|
||||
} else {
|
||||
vector[0] = virial[0] * inv_volume * nktv2p;
|
||||
vector[1] = virial[1] * inv_volume * nktv2p;
|
||||
vector[3] = virial[3] * inv_volume * nktv2p;
|
||||
vector[2] = vector[4] = vector[5] = 0.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* get the current rotation matrix and store it
|
||||
------------------------------------------------------------------------- */
|
||||
void ComputePressureUef::update_rot()
|
||||
{
|
||||
( (FixNHUef*) modify->fix[ifix_uef])->get_rot(rot);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Transform the pressure tensor to the rotated coordinate system
|
||||
[P]rot = Q.[P].Q^t
|
||||
------------------------------------------------------------------------- */
|
||||
void ComputePressureUef::virial_rot(double *x, const double r[3][3])
|
||||
{
|
||||
|
||||
double t[3][3];
|
||||
// [00 10 20 ] [ 0 3 4 ] [00 01 02 ]
|
||||
// [01 11 21 ] [ 3 1 5 ] [10 11 12 ]
|
||||
// [02 12 22 ] [ 4 5 2 ] [20 21 22 ]
|
||||
for (int k = 0; k<3; ++k)
|
||||
{
|
||||
t[0][k] = x[0]*r[0][k] + x[3]*r[1][k] + x[4]*r[2][k];
|
||||
t[1][k] = x[3]*r[0][k] + x[1]*r[1][k] + x[5]*r[2][k];
|
||||
t[2][k] = x[4]*r[0][k] + x[5]*r[1][k] + x[2]*r[2][k];
|
||||
}
|
||||
x[0] = r[0][0]*t[0][0] + r[1][0]*t[1][0] + r[2][0]*t[2][0];
|
||||
x[3] = r[0][0]*t[0][1] + r[1][0]*t[1][1] + r[2][0]*t[2][1];
|
||||
x[4] = r[0][0]*t[0][2] + r[1][0]*t[1][2] + r[2][0]*t[2][2];
|
||||
x[1] = r[0][1]*t[0][1] + r[1][1]*t[1][1] + r[2][1]*t[2][1];
|
||||
x[5] = r[0][1]*t[0][2] + r[1][1]*t[1][2] + r[2][1]*t[2][2];
|
||||
x[2] = r[0][2]*t[0][2] + r[1][2]*t[1][2] + r[2][2]*t[2][2];
|
||||
}
|
||||
|
||||
66
src/USER-UEF/compute_pressure_uef.h
Normal file
66
src/USER-UEF/compute_pressure_uef.h
Normal file
@ -0,0 +1,66 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Contributing author: David Nicholson (MIT)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMPUTE_CLASS
|
||||
|
||||
ComputeStyle(pressure/uef,ComputePressureUef)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_COMPUTE_PRESSURE_UEF_H
|
||||
#define LMP_COMPUTE_PRESSURE_UEF_H
|
||||
|
||||
#include "compute_pressure.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ComputePressureUef : public ComputePressure {
|
||||
public:
|
||||
ComputePressureUef(class LAMMPS *, int, char **);
|
||||
virtual ~ComputePressureUef(){}
|
||||
virtual void init();
|
||||
virtual void compute_vector();
|
||||
virtual double compute_scalar();
|
||||
void update_rot();
|
||||
bool in_fix; //true if this compute is used in fix/nvt/npt
|
||||
|
||||
|
||||
protected:
|
||||
bool ext_flags[3]; // true if used in average output pressure
|
||||
void virial_rot(double*,const double[3][3]);
|
||||
int ifix_uef;
|
||||
double rot[3][3];
|
||||
};
|
||||
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
This class inherits most of the warnings from ComputePressure. The
|
||||
only additions are:
|
||||
|
||||
E: Can't use compute pressure/uef without defining a fix nvt/npt/uef
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
W: The temperature used in compute pressure/uef is not of style temp/uef
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
*/
|
||||
110
src/USER-UEF/compute_temp_uef.cpp
Normal file
110
src/USER-UEF/compute_temp_uef.cpp
Normal file
@ -0,0 +1,110 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Contributing author: David Nicholson (MIT)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "string.h"
|
||||
#include "stdlib.h"
|
||||
#include "compute_temp_uef.h"
|
||||
#include "fix_nh_uef.h"
|
||||
#include "update.h"
|
||||
#include "modify.h"
|
||||
#include "fix.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* Base constructor initialized to use rotation matrix
|
||||
* ----------------------------------------------------------------------*/
|
||||
ComputeTempUef::ComputeTempUef(LAMMPS *lmp, int narg, char **arg) :
|
||||
ComputeTemp(lmp, narg, arg)
|
||||
{
|
||||
rot_flag=true;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* Check for the uef fix
|
||||
* ----------------------------------------------------------------------*/
|
||||
void ComputeTempUef::init()
|
||||
{
|
||||
ComputeTemp::init();
|
||||
// check to make sure the other uef fix is on
|
||||
// borrowed from Pieter's nvt/sllod code
|
||||
int i=0;
|
||||
for (i=0; i<modify->nfix; i++)
|
||||
{
|
||||
if (strcmp(modify->fix[i]->style,"nvt/uef")==0)
|
||||
break;
|
||||
if (strcmp(modify->fix[i]->style,"npt/uef")==0)
|
||||
break;
|
||||
}
|
||||
if (i==modify->nfix)
|
||||
error->all(FLERR,"Can't use compute temp/uef without defining a fix nvt/npt/uef");
|
||||
ifix_uef=i;
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Compute the ke tensor in the proper coordinate system
|
||||
------------------------------------------------------------------------- */
|
||||
void ComputeTempUef::compute_vector()
|
||||
{
|
||||
ComputeTemp::compute_vector();
|
||||
if (rot_flag)
|
||||
{
|
||||
double rot[3][3];
|
||||
( (FixNHUef*) modify->fix[ifix_uef])->get_rot(rot);
|
||||
virial_rot(vector,rot);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* turn the rotation matrix on or off to properly account for the
|
||||
* coordinate system of the velocities
|
||||
------------------------------------------------------------------------- */
|
||||
void ComputeTempUef::yes_rot()
|
||||
{
|
||||
rot_flag =true;
|
||||
}
|
||||
void ComputeTempUef::no_rot()
|
||||
{
|
||||
rot_flag =false;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Transform the pressure tensor to the rotated coordinate system
|
||||
[P]rot = Q.[P].Q^t
|
||||
------------------------------------------------------------------------- */
|
||||
void ComputeTempUef::virial_rot(double *x, const double r[3][3])
|
||||
{
|
||||
|
||||
double t[3][3];
|
||||
// [00 10 20 ] [ 0 3 4 ] [00 01 02 ]
|
||||
// [01 11 21 ] [ 3 1 5 ] [10 11 12 ]
|
||||
// [02 12 22 ] [ 4 5 2 ] [20 21 22 ]
|
||||
for (int k = 0; k<3; ++k)
|
||||
{
|
||||
t[0][k] = x[0]*r[0][k] + x[3]*r[1][k] + x[4]*r[2][k];
|
||||
t[1][k] = x[3]*r[0][k] + x[1]*r[1][k] + x[5]*r[2][k];
|
||||
t[2][k] = x[4]*r[0][k] + x[5]*r[1][k] + x[2]*r[2][k];
|
||||
}
|
||||
x[0] = r[0][0]*t[0][0] + r[1][0]*t[1][0] + r[2][0]*t[2][0];
|
||||
x[3] = r[0][0]*t[0][1] + r[1][0]*t[1][1] + r[2][0]*t[2][1];
|
||||
x[4] = r[0][0]*t[0][2] + r[1][0]*t[1][2] + r[2][0]*t[2][2];
|
||||
x[1] = r[0][1]*t[0][1] + r[1][1]*t[1][1] + r[2][1]*t[2][1];
|
||||
x[5] = r[0][1]*t[0][2] + r[1][1]*t[1][2] + r[2][1]*t[2][2];
|
||||
x[2] = r[0][2]*t[0][2] + r[1][2]*t[1][2] + r[2][2]*t[2][2];
|
||||
}
|
||||
|
||||
60
src/USER-UEF/compute_temp_uef.h
Normal file
60
src/USER-UEF/compute_temp_uef.h
Normal file
@ -0,0 +1,60 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Contributing author: David Nicholson (MIT)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMPUTE_CLASS
|
||||
|
||||
ComputeStyle(temp/uef,ComputeTempUef)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_COMPUTE_TEMP_UEF_H
|
||||
#define LMP_COMPUTE_TEMP_UEF_H
|
||||
|
||||
#include "compute_temp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ComputeTempUef : public ComputeTemp {
|
||||
public:
|
||||
ComputeTempUef(class LAMMPS *, int, char **);
|
||||
virtual ~ComputeTempUef(){}
|
||||
virtual void init();
|
||||
virtual void compute_vector();
|
||||
void yes_rot();
|
||||
void no_rot();
|
||||
|
||||
|
||||
protected:
|
||||
bool rot_flag;
|
||||
void virial_rot(double*,const double[3][3]);
|
||||
int ifix_uef;
|
||||
};
|
||||
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
This class inherits most of the warnings from ComputePressure. The
|
||||
only addition is:
|
||||
|
||||
E: Can't use compute temp/uef without defining a fix nvt/npt/uef
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
*/
|
||||
113
src/USER-UEF/dump_cfg_uef.cpp
Normal file
113
src/USER-UEF/dump_cfg_uef.cpp
Normal file
@ -0,0 +1,113 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Contributing Author: David Nicholson (MIT)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
|
||||
#include <math.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "dump_cfg.h"
|
||||
#include "atom.h"
|
||||
#include "domain.h"
|
||||
#include "modify.h"
|
||||
#include "compute.h"
|
||||
#include "fix.h"
|
||||
#include "error.h"
|
||||
#include "dump_cfg_uef.h"
|
||||
#include "fix_nh_uef.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
enum{INT,DOUBLE,STRING,BIGINT}; // same as in DumpCustom
|
||||
|
||||
#define UNWRAPEXPAND 10.0
|
||||
#define ONEFIELD 32
|
||||
#define DELTA 1048576
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* base method is mostly fine, just need to find the FixNHUef
|
||||
* ----------------------------------------------------------------------*/
|
||||
void DumpCFGUef::init_style()
|
||||
{
|
||||
DumpCFG::init_style();
|
||||
|
||||
// check to make sure the other uef fix is on
|
||||
// borrowed from Pieter's nvt/sllod code
|
||||
int i=0;
|
||||
for (i=0; i<modify->nfix; i++)
|
||||
{
|
||||
if (strcmp(modify->fix[i]->style,"nvt/uef")==0)
|
||||
break;
|
||||
if (strcmp(modify->fix[i]->style,"npt/uef")==0)
|
||||
break;
|
||||
}
|
||||
if (i==modify->nfix)
|
||||
error->all(FLERR,"Can't use dump cfg/uef without defining a fix nvt/npt/uef");
|
||||
ifix_uef=i;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* this is really the only difference between the base class and this one.
|
||||
* since the output is in scaled coordinates, changing the simulation box
|
||||
* edges to the flow frame will put coordinates in the flow frame too.
|
||||
* ----------------------------------------------------------------------*/
|
||||
|
||||
void DumpCFGUef::write_header(bigint n)
|
||||
{
|
||||
// set scale factor used by AtomEye for CFG viz
|
||||
// default = 1.0
|
||||
// for peridynamics, set to pre-computed PD scale factor
|
||||
// so PD particles mimic C atoms
|
||||
// for unwrapped coords, set to UNWRAPEXPAND (10.0)
|
||||
// so molecules are not split across periodic box boundaries
|
||||
|
||||
double box[3][3],rot[3][3];
|
||||
((FixNHUef*) modify->fix[ifix_uef])->get_box(box);
|
||||
((FixNHUef*) modify->fix[ifix_uef])->get_rot(rot);
|
||||
// rot goes from "lab frame" to "upper triangular frame"
|
||||
// it's transpose takes the simulation box to the flow frame
|
||||
for (int i=0;i<3;i++)
|
||||
for(int j=i+1;j<3;j++)
|
||||
{
|
||||
double t=rot[i][j];
|
||||
rot[i][j]=rot[j][i];
|
||||
rot[j][i]=t;
|
||||
}
|
||||
mul_m2(rot,box);
|
||||
|
||||
|
||||
double scale = 1.0;
|
||||
if (atom->peri_flag) scale = atom->pdscale;
|
||||
else if (unwrapflag == 1) scale = UNWRAPEXPAND;
|
||||
|
||||
char str[64];
|
||||
sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT);
|
||||
fprintf(fp,str,n);
|
||||
fprintf(fp,"A = %g Angstrom (basic length-scale)\n",scale);
|
||||
// in box[][] columns are cell edges
|
||||
// in H0, rows are cell edges
|
||||
fprintf(fp,"H0(1,1) = %g A\n",box[0][0]);
|
||||
fprintf(fp,"H0(1,2) = %g A\n",box[1][0]);
|
||||
fprintf(fp,"H0(1,3) = %g A\n",box[2][0]);
|
||||
fprintf(fp,"H0(2,1) = %g A\n",box[0][1]);
|
||||
fprintf(fp,"H0(2,2) = %g A\n",box[1][1]);
|
||||
fprintf(fp,"H0(2,3) = %g A\n",box[2][1]);
|
||||
fprintf(fp,"H0(3,1) = %g A\n",box[0][2]);
|
||||
fprintf(fp,"H0(3,2) = %g A\n",box[1][2]);
|
||||
fprintf(fp,"H0(3,3) = %g A\n",box[2][2]);
|
||||
fprintf(fp,".NO_VELOCITY.\n");
|
||||
fprintf(fp,"entry_count = %d\n",nfield-2);
|
||||
for (int i = 0; i < nfield-5; i++)
|
||||
fprintf(fp,"auxiliary[%d] = %s\n",i,auxname[i]);
|
||||
}
|
||||
51
src/USER-UEF/dump_cfg_uef.h
Normal file
51
src/USER-UEF/dump_cfg_uef.h
Normal file
@ -0,0 +1,51 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Contributing Author: David Nicholson (MIT)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef DUMP_CLASS
|
||||
|
||||
DumpStyle(cfg/uef,DumpCFGUef)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_DUMP_CFG_UEF_H
|
||||
#define LMP_DUMP_CFG_UEF_H
|
||||
|
||||
#include "dump_cfg.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class DumpCFGUef : public DumpCFG {
|
||||
public:
|
||||
DumpCFGUef(LAMMPS *lmp, int narg, char **arg) :
|
||||
DumpCFG(lmp, narg, arg){}
|
||||
void init_style();
|
||||
void write_header(bigint);
|
||||
|
||||
protected:
|
||||
int ifix_uef;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Can't use dump cfg/uef without defining a fix nvt/npt/uef
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
*/
|
||||
846
src/USER-UEF/fix_nh_uef.cpp
Normal file
846
src/USER-UEF/fix_nh_uef.cpp
Normal file
@ -0,0 +1,846 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Contributing author: David Nicholson (MIT)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "string.h"
|
||||
#include "stdlib.h"
|
||||
#include "math.h"
|
||||
#include "fix_nh_uef.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "group.h"
|
||||
#include "comm.h"
|
||||
#include "irregular.h"
|
||||
#include "modify.h"
|
||||
#include "compute.h"
|
||||
#include "kspace.h"
|
||||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "output.h"
|
||||
#include "timer.h"
|
||||
#include "neighbor.h"
|
||||
#include "compute_pressure_uef.h"
|
||||
#include "compute_temp_uef.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
enum{ISO,ANISO,TRICLINIC};
|
||||
/* ----------------------------------------------------------------------
|
||||
Put all of the uef-only keywords at the back of arg and make narg smaller
|
||||
so FixNH::FixNH() only sees the keywords it knows. Save the numer of
|
||||
remaining keywords in rem.
|
||||
---------------------------------------------------------------------- */
|
||||
char ** FixNHUef::arg_kludge(int &narg, char **arg, int &rem)
|
||||
{
|
||||
int iarg = 3;
|
||||
bool flags[3]= {false,false,false};
|
||||
rem=0;
|
||||
char *tmp[3];
|
||||
while (iarg < narg)
|
||||
{
|
||||
if (strcmp(arg[iarg],"erate" ) == 0 && !flags[0])
|
||||
{
|
||||
tmp[0] = arg[iarg];
|
||||
tmp[1] = arg[iarg+1];
|
||||
tmp[2] = arg[iarg+2];
|
||||
for (int k=iarg+3; k<narg; k++)
|
||||
arg[k-3] = arg[k];
|
||||
arg[narg-1] = tmp[2];
|
||||
arg[narg-2] = tmp[1];
|
||||
arg[narg-3] = tmp[0];
|
||||
rem += 3;
|
||||
flags[0] = true;
|
||||
}
|
||||
else if (strcmp(arg[iarg],"strain" ) == 0 && !flags[1])
|
||||
{
|
||||
tmp[0] = arg[iarg];
|
||||
tmp[1] = arg[iarg+1];
|
||||
tmp[2] = arg[iarg+2];
|
||||
for (int k=iarg+3; k<narg; k++)
|
||||
arg[k-3] = arg[k];
|
||||
arg[narg-1] = tmp[2];
|
||||
arg[narg-2] = tmp[1];
|
||||
arg[narg-3] = tmp[0];
|
||||
rem += 3;
|
||||
flags[1] = true;
|
||||
}
|
||||
else if(strcmp(arg[iarg],"ext") == 0 && !flags[2])
|
||||
{
|
||||
tmp[0] = arg[iarg];
|
||||
tmp[1] = arg[iarg+1];
|
||||
for (int k=iarg+2; k<narg; k++)
|
||||
arg[k-2] = arg[k];
|
||||
arg[narg-1] = tmp[1];
|
||||
arg[narg-2] = tmp[0];
|
||||
rem += 2;
|
||||
flags[2] = true;
|
||||
}
|
||||
else
|
||||
iarg++;
|
||||
}
|
||||
narg -= rem;
|
||||
return arg;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* Parse the remaing keywords, do some error checking, and initalize
|
||||
* temp/pressure fixes
|
||||
---------------------------------------------------------------------- */
|
||||
FixNHUef::FixNHUef(LAMMPS *lmp, int narg, char **arg) :
|
||||
FixNH(lmp, narg, arg_kludge(narg,arg,rem))
|
||||
{
|
||||
|
||||
//initialization
|
||||
erate[0] = erate[1] = 0;
|
||||
//default values
|
||||
strain[0]=strain[1]= 0;
|
||||
ext_flags[0]=ext_flags[1]=ext_flags[2] = true;
|
||||
|
||||
// need to initialize these
|
||||
omega_dot[0]=omega_dot[1]=omega_dot[2]=0;
|
||||
|
||||
// parse remaining input
|
||||
bool erate_flag = false;
|
||||
int iarg = narg;
|
||||
narg += rem;
|
||||
while (iarg <narg)
|
||||
{
|
||||
if (strcmp(arg[iarg],"erate")==0) {
|
||||
if (iarg+3 > narg) error->all(FLERR,"Illegal fix nvt/npt/uef command");
|
||||
erate[0] = force->numeric(FLERR,arg[iarg+1]);
|
||||
erate[1] = force->numeric(FLERR,arg[iarg+2]);
|
||||
erate_flag = true;
|
||||
iarg += 3;
|
||||
}
|
||||
else if (strcmp(arg[iarg],"strain")==0) {
|
||||
if (iarg+3 > narg) error->all(FLERR,"Illegal fix nvt/npt/uef command");
|
||||
strain[0] = force->numeric(FLERR,arg[iarg+1]);
|
||||
strain[1] = force->numeric(FLERR,arg[iarg+2]);
|
||||
iarg += 3;
|
||||
}
|
||||
else if (strcmp(arg[iarg],"ext")==0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/uef command");
|
||||
if (strcmp(arg[iarg+1],"x")==0)
|
||||
ext_flags[1] = ext_flags[2] = false;
|
||||
else if (strcmp(arg[iarg+1],"y")==0)
|
||||
ext_flags[0] = ext_flags[2] = false;
|
||||
else if (strcmp(arg[iarg+1],"z")==0)
|
||||
ext_flags[0] = ext_flags[1] = false;
|
||||
else if (strcmp(arg[iarg+1],"xy")==0)
|
||||
ext_flags[2] = false;
|
||||
else if (strcmp(arg[iarg+1],"xz")==0)
|
||||
ext_flags[1] = false;
|
||||
else if (strcmp(arg[iarg+1],"yz")==0)
|
||||
ext_flags[0] = false;
|
||||
else if (strcmp(arg[iarg+1],"xyz")!=0)
|
||||
error->all(FLERR,"Illegal fix nvt/npt/uef command");
|
||||
|
||||
iarg += 2;
|
||||
}
|
||||
else
|
||||
error->all(FLERR,"Illegal fix nvt/npt/uef command");
|
||||
}
|
||||
if (!erate_flag)
|
||||
error->all(FLERR,"Keyword erate must be set for fix npt/npt/uef command");
|
||||
|
||||
if (mtchain_default_flag) mtchain=1;
|
||||
|
||||
if (!domain->triclinic)
|
||||
error->all(FLERR,"Simulation box must be triclinic for fix/nvt/npt/uef");
|
||||
|
||||
//check for conditions that impose a deviatoric stress
|
||||
if (pstyle == TRICLINIC)
|
||||
error->all(FLERR,"Only normal stresses can be controlled with fix/nvt/npt/uef");
|
||||
double erate_tmp[3];
|
||||
erate_tmp[0]=erate[0];
|
||||
erate_tmp[1]=erate[1];
|
||||
erate_tmp[2]=-erate[0]-erate[1];
|
||||
|
||||
if (pstyle == ANISO)
|
||||
{
|
||||
if (!(ext_flags[0] & ext_flags[1] & ext_flags[2]))
|
||||
error->all(FLERR,"The ext keyword may only be used with iso pressure control");
|
||||
for (int k=0;k<3;k++)
|
||||
for (int j=0;j<3;j++)
|
||||
if (p_flag[k] && p_flag[j])
|
||||
{
|
||||
double tol = 1e-6;
|
||||
if ( !nearly_equal(p_start[k],p_start[j],tol) || !nearly_equal(p_stop[k],p_stop[j],tol))
|
||||
error->all(FLERR,"All controlled stresses must have the same value in fix/nvt/npt/uef");
|
||||
if ( !nearly_equal(erate_tmp[k],erate_tmp[j],tol) || !nearly_equal(erate_tmp[k],erate_tmp[j],tol))
|
||||
error->all(FLERR,"Dimensions with controlled stresses must have same strain rate in fix/nvt/npt/uef");
|
||||
}
|
||||
}
|
||||
// conditions that produce a deviatoric stress have already
|
||||
// been eliminated.
|
||||
deviatoric_flag=0;
|
||||
|
||||
// need pre_exchange and irregular migration
|
||||
pre_exchange_flag = 1;
|
||||
irregular = new Irregular(lmp);
|
||||
|
||||
// flag that I change the box here (in case of nvt)
|
||||
box_change_shape = 1;
|
||||
|
||||
// initialize the UEFBox class which computes the box at each step
|
||||
uefbox = new UEF_utils::UEFBox();
|
||||
uefbox->set_strain(strain[0],strain[1]);
|
||||
|
||||
// reset fixedpoint to the stagnation point. I don't allow fixedpoint
|
||||
// to be set by the user.
|
||||
fixedpoint[0] = domain->boxlo[0];
|
||||
fixedpoint[1] = domain->boxlo[1];
|
||||
fixedpoint[2] = domain->boxlo[2];
|
||||
|
||||
// Create temp and pressure computes for uef
|
||||
int n = strlen(id) + 6;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,id);
|
||||
strcat(id_temp,"_temp");
|
||||
char **newarg = new char*[3];
|
||||
newarg[0] = id_temp;
|
||||
newarg[1] = (char *) "all";
|
||||
newarg[2] = (char *) "temp/uef";
|
||||
modify->add_compute(3,newarg);
|
||||
delete [] newarg;
|
||||
tcomputeflag = 1;
|
||||
n = strlen(id) + 7;
|
||||
id_press = new char[n];
|
||||
strcpy(id_press,id);
|
||||
strcat(id_press,"_press");
|
||||
newarg = new char*[4];
|
||||
newarg[0] = id_press;
|
||||
newarg[1] = (char *) "all";
|
||||
newarg[2] = (char *) "pressure/uef";
|
||||
newarg[3] = id_temp;
|
||||
modify->add_compute(4,newarg);
|
||||
delete [] newarg;
|
||||
pcomputeflag = 1;
|
||||
|
||||
nevery = 1;
|
||||
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* Erase the UEFBox object and get rid of the pressure compute if the nvt
|
||||
* version is being used. Everything else will be done in base destructor
|
||||
* ---------------------------------------------------------------------- */
|
||||
FixNHUef::~FixNHUef()
|
||||
{
|
||||
delete uefbox;
|
||||
if (pcomputeflag && !pstat_flag)
|
||||
{
|
||||
modify->delete_compute(id_press);
|
||||
delete [] id_press;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* Make the end_of_step() routine callable
|
||||
* ---------------------------------------------------------------------- */
|
||||
int FixNHUef::setmask()
|
||||
{
|
||||
int mask = FixNH::setmask();
|
||||
mask |= END_OF_STEP;
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* Run FixNH::init() and do more error checking. Set the pressure
|
||||
* pointer in the case that the nvt version is used
|
||||
* ---------------------------------------------------------------------- */
|
||||
void FixNHUef::init()
|
||||
{
|
||||
FixNH::init();
|
||||
|
||||
|
||||
// find conflict with fix/deform or other box chaging fixes
|
||||
for (int i=0; i < modify->nfix; i++)
|
||||
{
|
||||
if (strcmp(modify->fix[i]->id,id) != 0)
|
||||
if (modify->fix[i]->box_change_shape != 0)
|
||||
error->all(FLERR,"Can't use another fix which changes box shape with fix/nvt/npt/uef");
|
||||
}
|
||||
|
||||
|
||||
// this will make the pressure compute for nvt
|
||||
if (!pstat_flag)
|
||||
if (pcomputeflag)
|
||||
{
|
||||
int icomp = modify->find_compute(id_press);
|
||||
if (icomp<0)
|
||||
error->all(FLERR,"Pressure ID for fix/nvt/uef doesn't exist");
|
||||
pressure = modify->compute[icomp];
|
||||
|
||||
}
|
||||
if (strcmp(pressure->style,"pressure/uef") != 0)
|
||||
error->all(FLERR,"Using fix nvt/npt/uef without a compute pressure/uef");
|
||||
if (strcmp(temperature->style,"temp/uef") != 0)
|
||||
error->all(FLERR,"Using fix nvt/npt/uef without a compute temp/uef");
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* Run FixNH::setup() make sure the box is OK and set the rotation matrix
|
||||
* for the first step
|
||||
* ---------------------------------------------------------------------- */
|
||||
void FixNHUef::setup(int j)
|
||||
{
|
||||
double box[3][3];
|
||||
double vol = domain->xprd * domain->yprd * domain->zprd;
|
||||
uefbox->get_box(box,vol);
|
||||
double tol = 1e-4;
|
||||
// ensure the box is ok for uef
|
||||
bool isok = true;
|
||||
isok &= nearly_equal(domain->h[0],box[0][0],tol);
|
||||
isok &= nearly_equal(domain->h[1],box[1][1],tol);
|
||||
isok &= nearly_equal(domain->h[2],box[2][2],tol);
|
||||
isok &= nearly_equal(domain->xy,box[0][1],tol);
|
||||
isok &= nearly_equal(domain->yz,box[1][2],tol);
|
||||
isok &= nearly_equal(domain->xz,box[0][2],tol);
|
||||
if (!isok)
|
||||
error->all(FLERR,"Initial box is not close enough to the expected uef box");
|
||||
|
||||
uefbox->get_rot(rot);
|
||||
((ComputeTempUef*) temperature)->yes_rot();
|
||||
((ComputePressureUef*) pressure)->in_fix = true;
|
||||
((ComputePressureUef*) pressure)->update_rot();
|
||||
FixNH::setup(j);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* rotate -> initial integration step -> rotate back
|
||||
* ---------------------------------------------------------------------- */
|
||||
void FixNHUef::initial_integrate(int vflag)
|
||||
{
|
||||
inv_rotate_x(rot);
|
||||
inv_rotate_v(rot);
|
||||
inv_rotate_f(rot);
|
||||
((ComputeTempUef*) temperature)->no_rot();
|
||||
FixNH::initial_integrate(vflag);
|
||||
rotate_x(rot);
|
||||
rotate_v(rot);
|
||||
rotate_f(rot);
|
||||
((ComputeTempUef*) temperature)->yes_rot();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* rotate -> initial integration step -> rotate back (RESPA)
|
||||
* ---------------------------------------------------------------------- */
|
||||
void FixNHUef::initial_integrate_respa(int vflag, int ilevel, int iloop)
|
||||
{
|
||||
inv_rotate_x(rot);
|
||||
inv_rotate_v(rot);
|
||||
inv_rotate_f(rot);
|
||||
((ComputeTempUef*) temperature)->no_rot();
|
||||
FixNH::initial_integrate_respa(vflag,ilevel,iloop);
|
||||
rotate_x(rot);
|
||||
rotate_v(rot);
|
||||
rotate_f(rot);
|
||||
((ComputeTempUef*) temperature)->yes_rot();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* rotate -> final integration step -> rotate back
|
||||
* ---------------------------------------------------------------------- */
|
||||
void FixNHUef::final_integrate()
|
||||
{
|
||||
// update rot here since it must directly follow the virial calculation
|
||||
((ComputePressureUef*) pressure)->update_rot();
|
||||
inv_rotate_v(rot);
|
||||
inv_rotate_f(rot);
|
||||
((ComputeTempUef*) temperature)->no_rot();
|
||||
FixNH::final_integrate();
|
||||
rotate_v(rot);
|
||||
rotate_f(rot);
|
||||
((ComputeTempUef*) temperature)->yes_rot();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* at outer level: call this->final_integrate()
|
||||
* at other levels: rotate -> 2nd verlet step -> rotate back
|
||||
* ---------------------------------------------------------------------- */
|
||||
void FixNHUef::final_integrate_respa(int ilevel, int iloop)
|
||||
{
|
||||
// set timesteps by level
|
||||
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
|
||||
dthalf = 0.5 * step_respa[ilevel];
|
||||
// outermost level - update eta_dot and omega_dot, apply via final_integrate
|
||||
// all other levels - NVE update of v
|
||||
if (ilevel == nlevels_respa-1) final_integrate();
|
||||
else
|
||||
{
|
||||
inv_rotate_v(rot);
|
||||
inv_rotate_f(rot);
|
||||
nve_v();
|
||||
rotate_v(rot);
|
||||
rotate_f(rot);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
SLLOD velocity update in time-reversible (i think) increments
|
||||
v -> exp(-edot*dt/2)*v
|
||||
v -> v +f/m*dt
|
||||
v -> exp(-edot*dt/2)*v
|
||||
-----------------------------------------------------------------------*/
|
||||
void FixNHUef::nve_v()
|
||||
{
|
||||
double dtfm;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
double ex = erate[0]*dtf/2;
|
||||
double ey = erate[1]*dtf/2;
|
||||
double ez = -ex-ey;
|
||||
double e0 = exp(-ex);
|
||||
double e1 = exp(-ey);
|
||||
double e2 = exp(-ez);
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / rmass[i];
|
||||
v[i][0] *= e0;
|
||||
v[i][1] *= e1;
|
||||
v[i][2] *= e2;
|
||||
v[i][0] += dtfm*f[i][0];
|
||||
v[i][1] += dtfm*f[i][1];
|
||||
v[i][2] += dtfm*f[i][2];
|
||||
v[i][0] *= e0;
|
||||
v[i][1] *= e1;
|
||||
v[i][2] *= e2;
|
||||
}
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
v[i][0] *= e0;
|
||||
v[i][1] *= e1;
|
||||
v[i][2] *= e2;
|
||||
v[i][0] += dtfm*f[i][0];
|
||||
v[i][1] += dtfm*f[i][1];
|
||||
v[i][2] += dtfm*f[i][2];
|
||||
v[i][0] *= e0;
|
||||
v[i][1] *= e1;
|
||||
v[i][2] *= e2;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Don't actually move atoms in remap(), just change the box
|
||||
-----------------------------------------------------------------------*/
|
||||
void FixNHUef::remap()
|
||||
{
|
||||
double vol = domain->xprd * domain->yprd * domain->zprd;
|
||||
double domega = dto*(omega_dot[0]+omega_dot[1]+omega_dot[2])/3.;
|
||||
|
||||
// constant volume strain associated with barostat
|
||||
// box scaling
|
||||
double ex = dto*omega_dot[0]-domega;
|
||||
double ey = dto*omega_dot[1]-domega;
|
||||
uefbox->step_deform(ex,ey);
|
||||
strain[0] += ex;
|
||||
strain[1] += ey;
|
||||
|
||||
// volume change
|
||||
vol = vol*exp(3*domega);
|
||||
double box[3][3];
|
||||
uefbox->get_box(box,vol);
|
||||
domain->boxhi[0] = domain->boxlo[0]+box[0][0];
|
||||
domain->boxhi[1] = domain->boxlo[1]+box[1][1];
|
||||
domain->boxhi[2] = domain->boxlo[2]+box[2][2];
|
||||
domain->xy = box[0][1];
|
||||
domain->xz = box[0][2];
|
||||
domain->yz = box[1][2];
|
||||
domain->set_global_box();
|
||||
domain->set_local_box();
|
||||
uefbox->get_rot(rot);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
SLLOD position update in time-reversible (i think) increments
|
||||
x -> exp(edot*dt/2)*x
|
||||
x -> x + v*dt
|
||||
x -> exp(edot*dt/2)*x
|
||||
-----------------------------------------------------------------------*/
|
||||
void FixNHUef::nve_x()
|
||||
{
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
double ex = erate[0]*dtv;
|
||||
strain[0] += ex;
|
||||
double e0 = exp((ex+omega_dot[0]*dtv)/2);
|
||||
double ey = erate[1]*dtv;
|
||||
strain[1] += ey;
|
||||
double e1 = exp((ey+omega_dot[1]*dtv)/2.);
|
||||
double ez = -ex -ey;
|
||||
double e2 = exp((ez+omega_dot[2]*dtv)/2.);
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
// x update by full step only for atoms in group
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
x[i][0] *= e0;
|
||||
x[i][1] *= e1;
|
||||
x[i][2] *= e2;
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
x[i][0] *= e0;
|
||||
x[i][1] *= e1;
|
||||
x[i][2] *= e2;
|
||||
}
|
||||
}
|
||||
uefbox->step_deform(ex,ey);
|
||||
double box[3][3];
|
||||
double vol = domain->xprd * domain->yprd * domain->zprd;
|
||||
uefbox->get_box(box,vol);
|
||||
domain->boxhi[0] = domain->boxlo[0]+box[0][0];
|
||||
domain->boxhi[1] = domain->boxlo[1]+box[1][1];
|
||||
domain->boxhi[2] = domain->boxlo[2]+box[2][2];
|
||||
domain->xy = box[0][1];
|
||||
domain->xz = box[0][2];
|
||||
domain->yz = box[1][2];
|
||||
domain->set_global_box();
|
||||
domain->set_local_box();
|
||||
uefbox->get_rot(rot);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* Do the lattice reduction if necessary.
|
||||
-----------------------------------------------------------------------*/
|
||||
void FixNHUef::pre_exchange()
|
||||
{
|
||||
// only need to reset things if the lattice needs to be reduced
|
||||
if (uefbox->reduce())
|
||||
{
|
||||
// go to lab frame
|
||||
inv_rotate_x(rot);
|
||||
inv_rotate_v(rot);
|
||||
inv_rotate_f(rot);
|
||||
// get & set the new box and rotation matrix
|
||||
double vol = domain->xprd * domain->yprd * domain->zprd;
|
||||
double box[3][3];
|
||||
uefbox->get_box(box,vol);
|
||||
domain->boxhi[0] = domain->boxlo[0]+box[0][0];
|
||||
domain->boxhi[1] = domain->boxlo[1]+box[1][1];
|
||||
domain->boxhi[2] = domain->boxlo[2]+box[2][2];
|
||||
domain->xy = box[0][1];
|
||||
domain->xz = box[0][2];
|
||||
domain->yz = box[1][2];
|
||||
domain->set_global_box();
|
||||
domain->set_local_box();
|
||||
uefbox->get_rot(rot);
|
||||
|
||||
// rotate to the new upper triangular frame
|
||||
rotate_v(rot);
|
||||
rotate_x(rot);
|
||||
rotate_f(rot);
|
||||
|
||||
// put all atoms in the new box
|
||||
double **x = atom->x;
|
||||
imageint *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
for (int i=0; i<nlocal; i++) domain->remap(x[i],image[i]);
|
||||
|
||||
// move atoms to the right processors
|
||||
domain->x2lamda(atom->nlocal);
|
||||
irregular->migrate_atoms();
|
||||
domain->lamda2x(atom->nlocal);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* The following are routines to rotate between the lab and upper triangular
|
||||
* (UT) frames. For most of the time the simulation is in the UT frame.
|
||||
* To get to the lab frame, apply the inv_rotate_[..](rot) and to
|
||||
* get back to the UT frame apply rotate_[..](rot).
|
||||
*
|
||||
* Note: the rotate_x() functions also apply a shift to/from the fixedpoint
|
||||
* to make the integration a little simpler.
|
||||
* ---------------------------------------------------------------------- */
|
||||
void FixNHUef::rotate_x(double r[3][3])
|
||||
{
|
||||
double **x = atom->x;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
double xn[3];
|
||||
for (int i=0;i<nlocal;i++)
|
||||
{
|
||||
if (mask[i] & groupbit)
|
||||
{
|
||||
xn[0]=r[0][0]*x[i][0]+r[0][1]*x[i][1]+r[0][2]*x[i][2];
|
||||
xn[1]=r[1][0]*x[i][0]+r[1][1]*x[i][1]+r[1][2]*x[i][2];
|
||||
xn[2]=r[2][0]*x[i][0]+r[2][1]*x[i][1]+r[2][2]*x[i][2];
|
||||
x[i][0]=xn[0]+domain->boxlo[0];
|
||||
x[i][1]=xn[1]+domain->boxlo[1];
|
||||
x[i][2]=xn[2]+domain->boxlo[2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
void FixNHUef::inv_rotate_x(double r[3][3])
|
||||
{
|
||||
double **x = atom->x;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
double xn[3];
|
||||
for (int i=0;i<nlocal;i++)
|
||||
{
|
||||
if (mask[i] & groupbit)
|
||||
{
|
||||
x[i][0] -= domain->boxlo[0];
|
||||
x[i][1] -= domain->boxlo[1];
|
||||
x[i][2] -= domain->boxlo[2];
|
||||
xn[0]=r[0][0]*x[i][0]+r[1][0]*x[i][1]+r[2][0]*x[i][2];
|
||||
xn[1]=r[0][1]*x[i][0]+r[1][1]*x[i][1]+r[2][1]*x[i][2];
|
||||
xn[2]=r[0][2]*x[i][0]+r[1][2]*x[i][1]+r[2][2]*x[i][2];
|
||||
x[i][0]=xn[0];
|
||||
x[i][1]=xn[1];
|
||||
x[i][2]=xn[2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
void FixNHUef::rotate_v(double r[3][3])
|
||||
{
|
||||
double **v = atom->v;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
double vn[3];
|
||||
for (int i=0;i<nlocal;i++)
|
||||
{
|
||||
if (mask[i] & groupbit)
|
||||
{
|
||||
vn[0]=r[0][0]*v[i][0]+r[0][1]*v[i][1]+r[0][2]*v[i][2];
|
||||
vn[1]=r[1][0]*v[i][0]+r[1][1]*v[i][1]+r[1][2]*v[i][2];
|
||||
vn[2]=r[2][0]*v[i][0]+r[2][1]*v[i][1]+r[2][2]*v[i][2];
|
||||
v[i][0]=vn[0]; v[i][1]=vn[1]; v[i][2]=vn[2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
void FixNHUef::inv_rotate_v(double r[3][3])
|
||||
{
|
||||
double **v = atom->v;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
double vn[3];
|
||||
for (int i=0;i<nlocal;i++)
|
||||
{
|
||||
if (mask[i] & groupbit)
|
||||
{
|
||||
vn[0]=r[0][0]*v[i][0]+r[1][0]*v[i][1]+r[2][0]*v[i][2];
|
||||
vn[1]=r[0][1]*v[i][0]+r[1][1]*v[i][1]+r[2][1]*v[i][2];
|
||||
vn[2]=r[0][2]*v[i][0]+r[1][2]*v[i][1]+r[2][2]*v[i][2];
|
||||
v[i][0]=vn[0]; v[i][1]=vn[1]; v[i][2]=vn[2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
void FixNHUef::rotate_f(double r[3][3])
|
||||
{
|
||||
double **f = atom->f;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
double fn[3];
|
||||
for (int i=0;i<nlocal;i++)
|
||||
{
|
||||
if (mask[i] & groupbit)
|
||||
{
|
||||
fn[0]=r[0][0]*f[i][0]+r[0][1]*f[i][1]+r[0][2]*f[i][2];
|
||||
fn[1]=r[1][0]*f[i][0]+r[1][1]*f[i][1]+r[1][2]*f[i][2];
|
||||
fn[2]=r[2][0]*f[i][0]+r[2][1]*f[i][1]+r[2][2]*f[i][2];
|
||||
f[i][0]=fn[0]; f[i][1]=fn[1]; f[i][2]=fn[2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
void FixNHUef::inv_rotate_f(double r[3][3])
|
||||
{
|
||||
double **f = atom->f;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
double fn[3];
|
||||
for (int i=0;i<nlocal;i++)
|
||||
{
|
||||
if (mask[i] & groupbit)
|
||||
{
|
||||
fn[0]=r[0][0]*f[i][0]+r[1][0]*f[i][1]+r[2][0]*f[i][2];
|
||||
fn[1]=r[0][1]*f[i][0]+r[1][1]*f[i][1]+r[2][1]*f[i][2];
|
||||
fn[2]=r[0][2]*f[i][0]+r[1][2]*f[i][1]+r[2][2]*f[i][2];
|
||||
f[i][0]=fn[0]; f[i][1]=fn[1]; f[i][2]=fn[2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* Increase the size of the restart list to add in the strains
|
||||
* ---------------------------------------------------------------------- */
|
||||
int FixNHUef::size_restart_global()
|
||||
{
|
||||
return FixNH::size_restart_global() +2;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* Pack the strains after packing the default FixNH values
|
||||
* ---------------------------------------------------------------------- */
|
||||
int FixNHUef::pack_restart_data(double *list)
|
||||
{
|
||||
int n = FixNH::pack_restart_data(list);
|
||||
list[n++] = strain[0];
|
||||
list[n++] = strain[1];
|
||||
return n;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* read and set the strains after the default FixNH values
|
||||
* ---------------------------------------------------------------------- */
|
||||
void FixNHUef::restart(char *buf)
|
||||
{
|
||||
int n = size_restart_global();
|
||||
FixNH::restart(buf);
|
||||
double *list = (double *) buf;
|
||||
strain[0] = list[n-2];
|
||||
strain[1] = list[n-1];
|
||||
uefbox->set_strain(strain[0],strain[1]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* If the step writes a restart, reduce the box beforehand. This makes sure
|
||||
* the unique box shape can be found once the restart is read and that
|
||||
* all of the atoms lie within the box.
|
||||
* This may only be necessary for RESPA runs, but I'm leaving it in anyway.
|
||||
* ---------------------------------------------------------------------- */
|
||||
void FixNHUef::end_of_step()
|
||||
{
|
||||
if (update->ntimestep==output->next_restart)
|
||||
{
|
||||
pre_exchange();
|
||||
domain->x2lamda(atom->nlocal);
|
||||
domain->pbc();
|
||||
timer->stamp();
|
||||
comm->exchange();
|
||||
comm->borders();
|
||||
domain->lamda2x(atom->nlocal+atom->nghost);
|
||||
timer->stamp(Timer::COMM);
|
||||
neighbor->build();
|
||||
timer->stamp(Timer::NEIGH);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* reduce the simulation box after a run is complete. otherwise it won't
|
||||
* be possible to resume from a write_restart since the initialization of
|
||||
* the simulation box requires reduced simulation box
|
||||
* ---------------------------------------------------------------------- */
|
||||
void FixNHUef::post_run()
|
||||
{
|
||||
pre_exchange();
|
||||
domain->x2lamda(atom->nlocal);
|
||||
domain->pbc();
|
||||
timer->stamp();
|
||||
comm->exchange();
|
||||
comm->borders();
|
||||
domain->lamda2x(atom->nlocal+atom->nghost);
|
||||
timer->stamp(Timer::COMM);
|
||||
neighbor->build();
|
||||
timer->stamp(Timer::NEIGH);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* public read for rotation matrix
|
||||
* ---------------------------------------------------------------------- */
|
||||
void FixNHUef::get_rot(double r[3][3])
|
||||
{
|
||||
r[0][0] = rot[0][0];
|
||||
r[0][1] = rot[0][1];
|
||||
r[0][2] = rot[0][2];
|
||||
r[1][0] = rot[1][0];
|
||||
r[1][1] = rot[1][1];
|
||||
r[1][2] = rot[1][2];
|
||||
r[2][0] = rot[2][0];
|
||||
r[2][1] = rot[2][1];
|
||||
r[2][2] = rot[2][2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* public read for ext flags
|
||||
* ---------------------------------------------------------------------- */
|
||||
void FixNHUef::get_ext_flags(bool* e)
|
||||
{
|
||||
e[0] = ext_flags[0];
|
||||
e[1] = ext_flags[1];
|
||||
e[2] = ext_flags[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* public read for simulation box
|
||||
* ---------------------------------------------------------------------- */
|
||||
void FixNHUef::get_box(double b[3][3])
|
||||
{
|
||||
double box[3][3];
|
||||
double vol = domain->xprd * domain->yprd * domain->zprd;
|
||||
uefbox->get_box(box,vol);
|
||||
b[0][0] = box[0][0];
|
||||
b[0][1] = box[0][1];
|
||||
b[0][2] = box[0][2];
|
||||
b[1][0] = box[1][0];
|
||||
b[1][1] = box[1][1];
|
||||
b[1][2] = box[1][2];
|
||||
b[2][0] = box[2][0];
|
||||
b[2][1] = box[2][1];
|
||||
b[2][2] = box[2][2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
* comparing floats
|
||||
* it's imperfect, but should work provided no infinities
|
||||
* ---------------------------------------------------------------------- */
|
||||
bool FixNHUef::nearly_equal(double a, double b, double epsilon)
|
||||
{
|
||||
double absa = fabs(a);
|
||||
double absb = fabs(b);
|
||||
double diff = fabs(a-b);
|
||||
if (a == b) return true;
|
||||
else if ( (absa+absb) < epsilon)
|
||||
return diff < epsilon*epsilon;
|
||||
else
|
||||
return diff/(absa+absb) < epsilon;
|
||||
}
|
||||
125
src/USER-UEF/fix_nh_uef.h
Normal file
125
src/USER-UEF/fix_nh_uef.h
Normal file
@ -0,0 +1,125 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Contributing Author: David Nicholson (MIT)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
|
||||
#ifndef LMP_FIX_NH_UEF_H
|
||||
#define LMP_FIX_NH_UEF_H
|
||||
|
||||
#include "uef_utils.h"
|
||||
#include "fix_nh.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
class FixNHUef : public FixNH {
|
||||
public:
|
||||
FixNHUef(class LAMMPS *, int, char **);
|
||||
virtual ~FixNHUef();
|
||||
virtual int setmask();
|
||||
virtual void init();
|
||||
virtual void setup(int);
|
||||
virtual void pre_exchange();
|
||||
virtual int pack_restart_data(double*);
|
||||
virtual void restart(char *);
|
||||
virtual void end_of_step();
|
||||
virtual void initial_integrate(int);
|
||||
virtual void final_integrate();
|
||||
virtual void initial_integrate_respa(int, int, int);
|
||||
virtual void final_integrate_respa(int, int);
|
||||
virtual void post_run();
|
||||
void get_rot(double[3][3]);
|
||||
void get_ext_flags(bool*);
|
||||
void get_box(double[3][3]);
|
||||
|
||||
protected:
|
||||
virtual void remap();
|
||||
virtual int size_restart_global();
|
||||
virtual void nve_x();
|
||||
virtual void nve_v();
|
||||
char **arg_kludge(int&, char**, int&);
|
||||
void rotate_x(double [3][3]);
|
||||
void inv_rotate_x(double[3][3]);
|
||||
void rotate_v(double[3][3]);
|
||||
void inv_rotate_v(double[3][3]);
|
||||
void rotate_f(double[3][3]);
|
||||
void inv_rotate_f(double[3][3]);
|
||||
double strain[2],erate[2]; // strain/strain rate : [e_x, e_y]
|
||||
// always assume traceless e_z = -e_x-e_y
|
||||
|
||||
int rem; //this is for the narg kluge
|
||||
|
||||
UEF_utils::UEFBox *uefbox; // interface for the special simulation box
|
||||
|
||||
double rot[3][3]; // rotation matrix
|
||||
bool ext_flags[3]; // flags for external "free surfaces"
|
||||
bool nearly_equal(double,double,double);
|
||||
//bool rotate_output; // experimental feature. Too many issues for now
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
This is a base class for FixNH so it will inherit most of its error/warning messages along with the following:
|
||||
|
||||
E: Illegal fix nvt/npt/uef command
|
||||
|
||||
Self-explanatory
|
||||
|
||||
E: Keyword erate must be set for fix nvt/npt/uef command
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Simulation box must be triclinic for fix/nvt/npt/uef
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Only normal stresses can be controlled with fix/nvt/npt/uef
|
||||
|
||||
The keywords xy xz and yz cannot be used for pressure control
|
||||
|
||||
E: The ext keyword may only be used with iso pressure control
|
||||
|
||||
Self-explanatory
|
||||
|
||||
E: All controlled stresses must have the same value in fix/nvt/npt/uef
|
||||
|
||||
Stress control is only possible when the stress specified for each dimension is the same
|
||||
|
||||
E: Dimensions with controlled stresses must have same strain rate in fix/nvt/npt/uef
|
||||
|
||||
Stress-controlled dimensions with the same strain rate must have the same target stress.
|
||||
|
||||
E: Can't use another fix which changes box shape with fix/nvt/npt/uef
|
||||
|
||||
The fix npt/nvt/uef command must have full control over the box shape. You cannot use a simultaneous fix deform command, for example.
|
||||
|
||||
E: Pressure ID for fix/nvt/uef doesn't exist
|
||||
|
||||
The compute pressure introduced via fix_modify does not exist
|
||||
|
||||
E: Using fix nvt/npt/uef without a compute pressure/uef
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Using fix nvt/npt/uef without a compute temp/uef
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Initial box is not close enough to the expected uef box
|
||||
|
||||
The initial box does not correspond to the shape required by the value of the strain keyword. If the default strain value of zero was used, the initial box is not cubic.
|
||||
|
||||
*/
|
||||
33
src/USER-UEF/fix_npt_uef.cpp
Normal file
33
src/USER-UEF/fix_npt_uef.cpp
Normal file
@ -0,0 +1,33 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Contributing author: David Nicholson (MIT)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "string.h"
|
||||
#include "fix_npt_uef.h"
|
||||
#include "modify.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
|
||||
FixNPTUef::FixNPTUef(LAMMPS *lmp, int narg, char **arg) :
|
||||
FixNHUef(lmp, narg, arg)
|
||||
{
|
||||
if (!tstat_flag)
|
||||
error->all(FLERR,"Temperature control must be used with fix npt/uef");
|
||||
if (!pstat_flag)
|
||||
error->all(FLERR,"Pressure control must be used with fix npt/uef");
|
||||
|
||||
}
|
||||
50
src/USER-UEF/fix_npt_uef.h
Normal file
50
src/USER-UEF/fix_npt_uef.h
Normal file
@ -0,0 +1,50 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Contributing author: David Nicholson (MIT)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(npt/uef,FixNPTUef)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NPT_UEF_H
|
||||
#define LMP_FIX_NPT_UEF_H
|
||||
|
||||
#include "fix_nh_uef.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixNPTUef : public FixNHUef {
|
||||
public:
|
||||
FixNPTUef(class LAMMPS *, int, char **);
|
||||
~FixNPTUef() {}
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Temperature control must be used with fix npt uef
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Pressure control must be used with fix npt uef
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
*/
|
||||
35
src/USER-UEF/fix_nvt_uef.cpp
Normal file
35
src/USER-UEF/fix_nvt_uef.cpp
Normal file
@ -0,0 +1,35 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Contributing author: David Nicholson (MIT)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "string.h"
|
||||
#include "fix_nvt_uef.h"
|
||||
#include "modify.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
|
||||
FixNVTUef::FixNVTUef(LAMMPS *lmp, int narg, char **arg) :
|
||||
FixNHUef(lmp, narg, arg)
|
||||
{
|
||||
if (!tstat_flag)
|
||||
error->all(FLERR,"Temperature control must be used with fix nvt/uef");
|
||||
if (pstat_flag)
|
||||
error->all(FLERR,"Pressure control can't be used with fix nvt/uef");
|
||||
|
||||
}
|
||||
|
||||
|
||||
50
src/USER-UEF/fix_nvt_uef.h
Normal file
50
src/USER-UEF/fix_nvt_uef.h
Normal file
@ -0,0 +1,50 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Contributing author: David Nicholson (MIT)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(nvt/uef,FixNVTUef)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NVT_UEF_H
|
||||
#define LMP_FIX_NVT_UEF_H
|
||||
|
||||
#include "fix_nh_uef.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixNVTUef : public FixNHUef {
|
||||
public:
|
||||
FixNVTUef(class LAMMPS *, int, char **);
|
||||
~FixNVTUef(){}
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Temperature control must be used with fix npt uef
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Pressure control must be used with fix npt uef
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
*/
|
||||
365
src/USER-UEF/uef_utils.cpp
Normal file
365
src/USER-UEF/uef_utils.cpp
Normal file
@ -0,0 +1,365 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Contributing author: David Nicholson (MIT)
|
||||
-------------------------------------------------------------------------
|
||||
|
||||
This class contains functions to calculate the evolution of the periodic
|
||||
simulation box under elongational flow as described by Matthew Dobson
|
||||
in the arXiv preprint at http://arxiv.org/abs/1408.7078
|
||||
|
||||
Additionally, there are methods to do a lattice reduction to further
|
||||
reduce the simulation box using the method of Igor Semaev at
|
||||
http://link.springer.com/chapter/10.1007%2F3-540-44670-2_13
|
||||
*/
|
||||
#include <math.h>
|
||||
#include "uef_utils.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace UEF_utils;
|
||||
|
||||
UEFBox::UEFBox()
|
||||
{
|
||||
// initial box (also an inverse eigenvector matrix of automorphisms)
|
||||
double x = 0.327985277605681;
|
||||
double y = 0.591009048506103;
|
||||
double z = 0.736976229099578;
|
||||
l0[0][0]= z; l0[0][1]= y; l0[0][2]= x;
|
||||
l0[1][0]=-x; l0[1][1]= z; l0[1][2]=-y;
|
||||
l0[2][0]=-y; l0[2][1]= x; l0[2][2]= z;
|
||||
// spectra of the two automorpisms (log of eigenvalues)
|
||||
w1[0]=-1.177725211523360;
|
||||
w1[1]=-0.441448620566067;
|
||||
w1[2]= 1.619173832089425;
|
||||
w2[0]= w1[1];
|
||||
w2[1]= w1[2];
|
||||
w2[2]= w1[0];
|
||||
// initialize theta
|
||||
// strain = w1 * theta1 + w2 * theta2
|
||||
theta[0]=theta[1]=0;
|
||||
|
||||
|
||||
//set up the initial box l and change of basis matrix r
|
||||
for (int k=0;k<3;k++)
|
||||
for (int j=0;j<3;j++)
|
||||
{
|
||||
l[k][j] = l0[k][j];
|
||||
r[j][k]=(j==k);
|
||||
}
|
||||
|
||||
// get the initial rotation and upper triangular matrix
|
||||
rotation_matrix(rot, lrot ,l);
|
||||
|
||||
// this is just a way to calculate the automorphisms
|
||||
// themselves, which play a minor role in the calculations
|
||||
// it's overkill, but only called once
|
||||
double t1[3][3];
|
||||
double t1i[3][3];
|
||||
double t2[3][3];
|
||||
double t2i[3][3];
|
||||
double l0t[3][3];
|
||||
for (int k=0; k<3; ++k)
|
||||
for (int j=0; j<3; ++j)
|
||||
{
|
||||
t1[k][j] = exp(w1[k])*l0[k][j];
|
||||
t1i[k][j] = exp(-w1[k])*l0[k][j];
|
||||
t2[k][j] = exp(w2[k])*l0[k][j];
|
||||
t2i[k][j] = exp(-w2[k])*l0[k][j];
|
||||
l0t[k][j] = l0[j][k];
|
||||
}
|
||||
mul_m2(l0t,t1);
|
||||
mul_m2(l0t,t1i);
|
||||
mul_m2(l0t,t2);
|
||||
mul_m2(l0t,t2i);
|
||||
for (int k=0; k<3; ++k)
|
||||
for (int j=0; j<3; ++j)
|
||||
{
|
||||
a1[k][j] = round(t1[k][j]);
|
||||
a1i[k][j] = round(t1i[k][j]);
|
||||
a2[k][j] = round(t2[k][j]);
|
||||
a2i[k][j] = round(t2i[k][j]);
|
||||
}
|
||||
|
||||
// winv used to transform between
|
||||
// strain increments and theta increments
|
||||
winv[0][0] = w2[1];
|
||||
winv[0][1] = -w2[0];
|
||||
winv[1][0] = -w1[1];
|
||||
winv[1][1] = w1[0];
|
||||
double d = w1[0]*w2[1] - w2[0]*w1[1];
|
||||
for (int k=0;k<2;k++)
|
||||
for (int j=0;j<2;j++)
|
||||
winv[k][j] /= d;
|
||||
}
|
||||
|
||||
// get volume-correct r basis in: basis*cbrt(vol) = q*r
|
||||
void UEFBox::get_box(double x[3][3], double v)
|
||||
{
|
||||
v = cbrtf(v);
|
||||
for (int k=0;k<3;k++)
|
||||
for (int j=0;j<3;j++)
|
||||
x[k][j] = lrot[k][j]*v;
|
||||
}
|
||||
|
||||
// get rotation matrix q in: basis = q*r
|
||||
void UEFBox::get_rot(double x[3][3])
|
||||
{
|
||||
for (int k=0;k<3;k++)
|
||||
for (int j=0;j<3;j++)
|
||||
x[k][j]=rot[k][j];
|
||||
}
|
||||
|
||||
// diagonal, incompressible deformation
|
||||
void UEFBox::step_deform(const double ex, const double ey)
|
||||
{
|
||||
// increment theta values used in the reduction
|
||||
theta[0] +=winv[0][0]*ex + winv[0][1]*ey;
|
||||
theta[1] +=winv[1][0]*ex + winv[1][1]*ey;
|
||||
|
||||
// deformation of the box. reduce() needs to
|
||||
// be called regularly or calculation will become
|
||||
// unstable
|
||||
double eps[3];
|
||||
eps[0]=ex; eps[1] = ey; eps[2] = -ex-ey;
|
||||
for (int k=0;k<3;k++)
|
||||
{
|
||||
eps[k] = exp(eps[k]);
|
||||
l[k][0] = eps[k]*l[k][0];
|
||||
l[k][1] = eps[k]*l[k][1];
|
||||
l[k][2] = eps[k]*l[k][2];
|
||||
}
|
||||
rotation_matrix(rot,lrot, l);
|
||||
}
|
||||
// reuduce the current basis
|
||||
bool UEFBox::reduce()
|
||||
{
|
||||
// determine how many times to apply the automorphisms
|
||||
// and find new theta values
|
||||
int f1 = round(theta[0]);
|
||||
int f2 = round(theta[1]);
|
||||
theta[0] -= f1;
|
||||
theta[1] -= f2;
|
||||
|
||||
// store old change or basis matrix to determine if it
|
||||
// changes
|
||||
int r0[3][3];
|
||||
for (int k=0;k<3;k++)
|
||||
for (int j=0;j<3;j++)
|
||||
r0[k][j]=r[k][j];
|
||||
|
||||
// this modifies the old change basis matrix to
|
||||
// handle the case where the automorphism transforms
|
||||
// the box but the reduced basis doesn't change
|
||||
// (r0 should still equal r at the end)
|
||||
if (f1 > 0) for (int k=0;k<f1;k++) mul_m2 (a1,r0);
|
||||
if (f1 < 0) for (int k=0;k<-f1;k++) mul_m2 (a1i,r0);
|
||||
if (f2 > 0) for (int k=0;k<f2;k++) mul_m2 (a2,r0);
|
||||
if (f2 < 0) for (int k=0;k<-f2;k++) mul_m2 (a2i,r0);
|
||||
|
||||
// robust reduction to the box defined by Dobson
|
||||
for (int k=0;k<3;k++)
|
||||
{
|
||||
double eps = exp(theta[0]*w1[k]+theta[1]*w2[k]);
|
||||
l[k][0] = eps*l0[k][0];
|
||||
l[k][1] = eps*l0[k][1];
|
||||
l[k][2] = eps*l0[k][2];
|
||||
}
|
||||
// further reduce the box using greedy reduction and check
|
||||
// if it changed from the last step using the change of basis
|
||||
// matrices r and r0
|
||||
greedy(l,r);
|
||||
rotation_matrix(rot,lrot, l);
|
||||
return !mat_same(r,r0);
|
||||
}
|
||||
void UEFBox::set_strain(const double ex, const double ey)
|
||||
{
|
||||
theta[0] =winv[0][0]*ex + winv[0][1]*ey;
|
||||
theta[1] =winv[1][0]*ex + winv[1][1]*ey;
|
||||
theta[0] -= round(theta[0]);
|
||||
theta[1] -= round(theta[1]);
|
||||
|
||||
for (int k=0;k<3;k++)
|
||||
{
|
||||
double eps = exp(theta[0]*w1[k]+theta[1]*w2[k]);
|
||||
l[k][0] = eps*l0[k][0];
|
||||
l[k][1] = eps*l0[k][1];
|
||||
l[k][2] = eps*l0[k][2];
|
||||
}
|
||||
greedy(l,r);
|
||||
rotation_matrix(rot,lrot, l);
|
||||
}
|
||||
|
||||
// this is just qr reduction using householder reflections
|
||||
// m is input matrix, q is a rotation, r is upper triangular
|
||||
// q*m = r
|
||||
void rotation_matrix(double q[3][3], double r[3][3], const double m[3][3])
|
||||
{
|
||||
for (int k=0;k<3;k++)
|
||||
for (int j=0;j<3;j++)
|
||||
r[k][j] = m[k][j];
|
||||
|
||||
double a = -sqrt(col_prod(r,0,0))*r[0][0]/fabs(r[0][0]);
|
||||
double v[3];
|
||||
v[0] = r[0][0]-a;
|
||||
v[1] = r[1][0];
|
||||
v[2] = r[2][0];
|
||||
a = sqrt(v[0]*v[0]+v[1]*v[1]+v[2]*v[2]);
|
||||
v[0] /= a; v[1] /= a; v[2] /= a;
|
||||
double qt[3][3];
|
||||
for (int k=0;k<3;k++)
|
||||
for (int j=0;j<3;j++)
|
||||
{
|
||||
qt[k][j] = (k==j) - 2*v[k]*v[j];
|
||||
q[k][j]= qt[k][j];
|
||||
}
|
||||
mul_m2(qt,r);
|
||||
a = -sqrt(r[1][1]*r[1][1] + r[2][1]*r[2][1])*r[1][1]/fabs(r[1][1]);
|
||||
v[0] = 0;
|
||||
v[1] = r[1][1] - a;
|
||||
v[2] = r[2][1];
|
||||
a = sqrt(v[1]*v[1]+v[2]*v[2]);
|
||||
v[1] /= a;
|
||||
v[2] /= a;
|
||||
for (int k=0;k<3;k++)
|
||||
for (int j=0;j<3;j++)
|
||||
qt[k][j] = (k==j) - 2*v[k]*v[j];
|
||||
mul_m2(qt,r);
|
||||
mul_m2(qt,q);
|
||||
// this makes r have positive diagonals
|
||||
// q*m = r <==> (-q)*m = (-r) will hold row-wise
|
||||
if (r[0][0] < 0){ neg_row(q,0); neg_row(r,0); }
|
||||
if (r[1][1] < 0){ neg_row(q,1); neg_row(r,1); }
|
||||
if (r[2][2] < 0){ neg_row(q,2); neg_row(r,2); }
|
||||
}
|
||||
|
||||
|
||||
|
||||
//sort columns in order of increasing length
|
||||
void col_sort(double b[3][3],int r[3][3])
|
||||
{
|
||||
if (col_prod(b,0,0)>col_prod(b,1,1))
|
||||
{
|
||||
col_swap(b,0,1);
|
||||
col_swap(r,0,1);
|
||||
}
|
||||
if (col_prod(b,0,0)>col_prod(b,2,2))
|
||||
{
|
||||
col_swap(b,0,2);
|
||||
col_swap(r,0,2);
|
||||
}
|
||||
if (col_prod(b,1,1)>col_prod(b,2,2))
|
||||
{
|
||||
col_swap(b,1,2);
|
||||
col_swap(r,1,2);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// 1-2 reduction (Graham-Schmidt)
|
||||
void red12(double b[3][3],int r[3][3])
|
||||
{
|
||||
int y = round(col_prod(b,0,1)/col_prod(b,0,0));
|
||||
b[0][1] -= y*b[0][0];
|
||||
b[1][1] -= y*b[1][0];
|
||||
b[2][1] -= y*b[2][0];
|
||||
|
||||
r[0][1] -= y*r[0][0];
|
||||
r[1][1] -= y*r[1][0];
|
||||
r[2][1] -= y*r[2][0];
|
||||
if (col_prod(b,1,1) < col_prod(b,0,0))
|
||||
{
|
||||
col_swap(b,0,1);
|
||||
col_swap(r,0,1);
|
||||
red12(b,r);
|
||||
}
|
||||
}
|
||||
|
||||
// The Semaev condition for a 3-reduced basis
|
||||
void red3(double b[3][3], int r[3][3])
|
||||
{
|
||||
double b11 = col_prod(b,0,0);
|
||||
double b22 = col_prod(b,1,1);
|
||||
double b12 = col_prod(b,0,1);
|
||||
double b13 = col_prod(b,0,2);
|
||||
double b23 = col_prod(b,1,2);
|
||||
|
||||
double y2 =-(b23/b22-b12/b22*b13/b11)/(1-b12/b11*b12/b22);
|
||||
double y1 =-(b13/b11-b12/b11*b23/b22)/(1-b12/b11*b12/b22);
|
||||
|
||||
int x1=0;
|
||||
int x2=0;
|
||||
double min = col_prod(b,2,2);
|
||||
int x1v[2];
|
||||
int x2v[2];
|
||||
x1v[0] = floor(y1); x1v[1] = x1v[0]+1;
|
||||
x2v[0] = floor(y2); x2v[1] = x2v[0]+1;
|
||||
for (int k=0;k<2;k++)
|
||||
for (int j=0;j<2;j++)
|
||||
{
|
||||
double a[3];
|
||||
a[0] = b[0][2] + x1v[k]*b[0][0] + x2v[j]*b[0][1];
|
||||
a[1] = b[1][2] + x1v[k]*b[1][0] + x2v[j]*b[1][1];
|
||||
a[2] = b[2][2] + x1v[k]*b[2][0] + x2v[j]*b[2][1];
|
||||
double val=a[0]*a[0]+a[1]*a[1]+a[2]*a[2];
|
||||
if (val<min)
|
||||
{
|
||||
min = val;
|
||||
x1 = x1v[k];
|
||||
x2 = x2v[j];
|
||||
}
|
||||
}
|
||||
if (x1 || x2)
|
||||
{
|
||||
b[0][2] += x1*b[0][0] + x2*b[0][1];
|
||||
b[1][2] += x1*b[1][0] + x2*b[1][1];
|
||||
b[2][2] += x1*b[2][0] + x2*b[2][1];
|
||||
r[0][2] += x1*r[0][0] + x2*r[0][1];
|
||||
r[1][2] += x1*r[1][0] + x2*r[1][1];
|
||||
r[2][2] += x1*r[2][0] + x2*r[2][1];
|
||||
greedy_recurse(b,r); // note the recursion step is here
|
||||
}
|
||||
}
|
||||
|
||||
// the meat of the greedy reduction algorithm
|
||||
void greedy_recurse(double b[3][3], int r[3][3])
|
||||
{
|
||||
col_sort(b,r);
|
||||
red12(b,r);
|
||||
red3(b,r); // recursive caller
|
||||
}
|
||||
|
||||
// set r (change of basis) to be identity then reduce basis and make it unique
|
||||
void greedy(double b[3][3],int r[3][3])
|
||||
{
|
||||
r[0][1]=r[0][2]=r[1][0]=r[1][2]=r[2][0]=r[2][1]=0;
|
||||
r[0][0]=r[1][1]=r[2][2]=1;
|
||||
greedy_recurse(b,r);
|
||||
make_unique(b,r);
|
||||
}
|
||||
|
||||
// A reduced basis isn't unique. This procedure will make it
|
||||
// "more" unique. Degenerate cases are possible, but unlikely
|
||||
// with floating point math.
|
||||
void make_unique(double b[3][3], int r[3][3])
|
||||
{
|
||||
if (fabs(b[0][0]) < fabs(b[0][1]))
|
||||
{ col_swap(b,0,1); col_swap(r,0,1); }
|
||||
if (fabs(b[0][0]) < fabs(b[0][2]))
|
||||
{ col_swap(b,0,2); col_swap(r,0,2); }
|
||||
if (fabs(b[1][1]) < fabs(b[1][2]))
|
||||
{ col_swap(b,1,2); col_swap(r,1,2); }
|
||||
|
||||
if (b[0][0] < 0){ neg_col(b,0); neg_col(r,0); }
|
||||
if (b[1][1] < 0){ neg_col(b,1); neg_col(r,1); }
|
||||
if (det(b) < 0){ neg_col(b,2); neg_col(r,2); }
|
||||
}
|
||||
|
||||
139
src/USER-UEF/uef_utils.h
Normal file
139
src/USER-UEF/uef_utils.h
Normal file
@ -0,0 +1,139 @@
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Contributing author: David Nicholson (MIT)
|
||||
-------------------------------------------------------------------------
|
||||
|
||||
This class contains functions to calculate the evolution of the periodic
|
||||
simulation box under elongational flow as described by Matthew Dobson
|
||||
in the arXiv preprint at http://arxiv.org/abs/1408.7078
|
||||
|
||||
Additionally, there are methods to do a lattice reduction to further
|
||||
reduce the simulation box using the method of Igor Semaev at
|
||||
http://link.springer.com/chapter/10.1007%2F3-540-44670-2_13
|
||||
*/
|
||||
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
namespace UEF_utils {
|
||||
|
||||
class UEFBox
|
||||
{
|
||||
public:
|
||||
UEFBox();
|
||||
void set_strain(const double, const double);
|
||||
void step_deform(const double,const double);
|
||||
bool reduce();
|
||||
void get_box(double[3][3], double);
|
||||
void get_rot(double[3][3]);
|
||||
private:
|
||||
double l0[3][3]; // initial basis
|
||||
double w1[3],w2[3], winv[3][3]; // omega1 and omega2 (spectra of automorphisms)
|
||||
//double edot[3], delta[2];
|
||||
double theta[2];
|
||||
double l[3][3], rot[3][3], lrot[3][3];
|
||||
int r[3][3],a1[3][3],a2[3][3],a1i[3][3],a2i[3][3];
|
||||
};
|
||||
|
||||
|
||||
// lattice reduction routines
|
||||
void greedy(double[3][3],int[3][3]);
|
||||
void col_sort(double[3][3],int[3][3]);
|
||||
void red12(double[3][3],int[3][3]);
|
||||
void greedy_recurse(double[3][3],int[3][3]);
|
||||
void red3(double [3][3],int r[3][3]);
|
||||
void make_unique(double[3][3],int[3][3]);
|
||||
void rotation_matrix(double[3][3],double[3][3],const double [3][3]);
|
||||
|
||||
// A few utility functions for 3x3 arrays
|
||||
template<typename T>
|
||||
T col_prod(T x[3][3], int c1, int c2)
|
||||
{
|
||||
return x[0][c1]*x[0][c2]+x[1][c1]*x[1][c2]+x[2][c1]*x[2][c2];
|
||||
}
|
||||
|
||||
template<typename T>
|
||||
void col_swap(T x[3][3], int c1, int c2)
|
||||
{
|
||||
for (int k=0;k<3;k++)
|
||||
{
|
||||
T t = x[k][c2];
|
||||
x[k][c2]=x[k][c1];
|
||||
x[k][c1]=t;
|
||||
}
|
||||
}
|
||||
|
||||
template<typename T>
|
||||
void neg_col(T x[3][3], int c1)
|
||||
{
|
||||
x[0][c1] = -x[0][c1];
|
||||
x[1][c1] = -x[1][c1];
|
||||
x[2][c1] = -x[2][c1];
|
||||
}
|
||||
|
||||
template<typename T>
|
||||
void neg_row(T x[3][3], int c1)
|
||||
{
|
||||
x[c1][0] = -x[c1][0];
|
||||
x[c1][1] = -x[c1][1];
|
||||
x[c1][2] = -x[c1][2];
|
||||
}
|
||||
|
||||
template<typename T>
|
||||
T det(T x[3][3])
|
||||
{
|
||||
double val;
|
||||
val = x[0][0]*(x[1][1]*x[2][2] - x[1][2]*x[2][1]);
|
||||
val -= x[0][1]*(x[1][0]*x[2][2] - x[1][2]*x[2][0]);
|
||||
val += x[0][2]*(x[1][0]*x[2][1] - x[1][1]*x[2][0]);
|
||||
return val;
|
||||
}
|
||||
|
||||
template<typename T>
|
||||
bool mat_same(T x1[3][3], T x2[3][3])
|
||||
{
|
||||
bool v = true;
|
||||
for (int k=0;k<3;k++)
|
||||
for (int j=0;j<3;j++)
|
||||
v &= (x1[k][j]==x2[k][j]);
|
||||
return v;
|
||||
}
|
||||
|
||||
template<typename T>
|
||||
void mul_m1(T m1[3][3], const T m2[3][3])
|
||||
{
|
||||
T t[3][3];
|
||||
for (int k=0;k<3;k++)
|
||||
for (int j=0;j<3;j++)
|
||||
t[k][j]=m1[k][j];
|
||||
|
||||
for (int k=0;k<3;k++)
|
||||
for (int j=0;j<3;j++)
|
||||
m1[k][j] = t[k][0]*m2[0][j] + t[k][1]*m2[1][j] + t[k][2]*m2[2][j];
|
||||
}
|
||||
|
||||
template<typename T>
|
||||
void mul_m2(const T m1[3][3], T m2[3][3])
|
||||
{
|
||||
T t[3][3];
|
||||
for (int k=0;k<3;k++)
|
||||
for (int j=0;j<3;j++)
|
||||
t[k][j]=m2[k][j];
|
||||
|
||||
for (int k=0;k<3;k++)
|
||||
for (int j=0;j<3;j++)
|
||||
m2[k][j] = m1[k][0]*t[0][j] + m1[k][1]*t[1][j] + m1[k][2]*t[2][j];
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user