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merge fix sources and move into USER-MISC package. clean up docs

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Axel Kohlmeyer 2020-01-12 13:45:22 -05:00
parent ef4e061cb7
commit b6d86e3c91
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166
doc/src/fix_cauchy.txt → doc/src/fix_npt_cauchy.txt
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@ -49,9 +49,6 @@ keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {y
continue = {yes} or {no} = whether of not to continue from a previous run
{fixedpoint} values = x y z
x,y,z = perform barostat dilation/contraction around this point (distance units)
{update} value = {dipole} or {dipole/dlm}
dipole = update dipole orientation (only for sphere variants)
dipole/dlm = use DLM integrator to update dipole orientation (only for sphere variants) :pre
:ule
[Examples:]
@ -60,17 +57,16 @@ fix 1 water npt/cauchy temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
[Description:]
These commands perform time integration on Nose-Hoover style
This command performs 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.
positions and velocities sampled from the isothermal-isobaric (npt)
ensembles. This updates the position and velocity for atoms in the
group each timestep and the box dimensions.
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
addition to basic thermostatting and barostatting, this fix 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
@ -83,18 +79,18 @@ 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
"(Shinoda)"_#nc-Shinoda, which combine the hydrostatic equations of
Martyna, Tobias and Klein in "(Martyna)"_#nc-Martyna with the strain
energy proposed by Parrinello and Rahman in
"(Parrinello)"_#nh-Parrinello. The time integration schemes closely
"(Parrinello)"_#nc-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.
integrators derived by Tuckerman et al in "(Tuckerman)"_#nc-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 parameters are 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
@ -117,13 +113,12 @@ 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.
The barostat parameters are 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.
@ -263,7 +258,7 @@ 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
"(Martyna)"_#nc-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
@ -273,7 +268,7 @@ 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}
Suzuki-Yoshida scheme "(Tuckerman)"_#nc-Tuckerman. The keyword {ploop}
does the same thing for the barostat thermostat.
The keyword {nreset} controls how often the reference dimensions used
@ -319,20 +314,6 @@ 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
@ -367,11 +348,11 @@ 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
which performs thermostatting but NO time integration, this fix
performs 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
fix npt/cauchy 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.
@ -383,24 +364,15 @@ barostatting.
:line
These fixes compute a temperature and pressure each timestep. To do
this, the thermostat and barostat fixes create their own computes of
style "temp" and "pressure", as if one of these sets of commands had
been issued:
This fix 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 sets of commands had been issued:
For fix nvt:
compute fix-ID_temp group-ID temp
For fix npt and fix nph:
compute fix-ID_temp all temp
compute fix-ID_press all pressure fix-ID_temp :pre
For fix nvt, the group for the new temperature compute is the same as
the fix group. For fix npt and fix nph, the group for both the new
temperature and pressure compute is "all" since pressure is computed
for the entire system. In the case of fix nph, the temperature
compute is not used for thermostatting, but just for a kinetic-energy
contribution to the pressure. See the "compute
The group for both the new temperature and pressure compute is "all"
since pressure is computed for the entire system. 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".
@ -415,7 +387,7 @@ temperature or pressure during thermodynamic output via the
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
Like other fixes that perform thermostatting, fix npt/cauchy 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
@ -432,8 +404,8 @@ 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
This fix can be used with either the {verlet} or {respa}
"integrators"_run_style.html. When using this fix
with {respa}, LAMMPS uses an integrator constructed
according to the following factorization of the Liouville propagator
(for two rRESPA levels):
@ -451,59 +423,26 @@ 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
NOTE: 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 on the "Speed packages"_Speed_packages.html doc
page. 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 "Build
package"_Build_package.html doc page 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"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page 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
This fix 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
supported by this fix. 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
@ -522,14 +461,14 @@ 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
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix 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,
This fix computes a global scalar and a global vector of quantities,
which can be accessed by various "output commands"_Howto_output.html.
The scalar value calculated by these fixes is "extensive"; the vector
The scalar value calculated by this fix is "extensive"; the vector
values are "intensive".
The scalar is the cumulative energy change due to the fix.
@ -564,18 +503,21 @@ PE_etap\[pchain\] = potential energy of each barostat thermostat displacement (e
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
This fix can ramp its 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.
This fix is not invoked during "energy minimization"_minimize.html.
:line
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
{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
@ -604,7 +546,7 @@ the set values and the final true (Cauchy) stresses can be
considerable.
The {cauchystat} keyword modifies the barostat as per Miller et
al. (Miller)_"#nh-Miller" so that the Cauchy stress is controlled.
al. (Miller)_"#nc-Miller" so that the Cauchy stress is controlled.
{alpha} is the non-dimensional parameter, typically set to 0.001 or
0.01 that determines how aggresively the algorithm drives the system
towards the set Cauchy stresses. Larger values of {alpha} will modify
@ -629,8 +571,8 @@ related {alpha} and {continue} values). This restores the original
Parrinello-Rahman algorithm, but now with the correct simulation box
shape from the first fix.
These fixes can be used with dynamic groups as defined by the
"group"_group.html command. Likewise they can be used with groups to
This fix can be used with dynamic groups as defined by the
"group"_group.html command. Likewise it 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
@ -665,10 +607,6 @@ 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).
:link(nh-Miller)
[(Miller)] Miller, Tadmor, Gibson, Bernstein and Pavia, J Chem Phys,
144, 184107 (2016).

68
src/USER-CAUCHY/fix_npt_cauchy.cpp
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@ -1,68 +0,0 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include <cstring>
#include "fix_npt_cauchy.h"
#include "modify.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixNPTCauchy::FixNPTCauchy(LAMMPS *lmp, int narg, char **arg) :
FixCauchy(lmp, narg, arg)
{
if (!tstat_flag)
error->all(FLERR,"Temperature control must be used with fix npt/cauchy");
if (!pstat_flag)
error->all(FLERR,"Pressure control must be used with fix npt/cauchy");
// create a new compute temp style
// id = fix-ID + temp
// compute group = all since pressure is always global (group all)
// and thus its KE/temperature contribution should use group all
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";
modify->add_compute(3,newarg);
delete [] newarg;
tcomputeflag = 1;
// create a new compute pressure style
// id = fix-ID + press, compute group = all
// pass id_temp as 4th arg to pressure constructor
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";
newarg[3] = id_temp;
modify->add_compute(4,newarg);
delete [] newarg;
pcomputeflag = 1;
}

48
src/USER-CAUCHY/fix_npt_cauchy.h
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@ -1,48 +0,0 @@
/* -*- 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.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(npt/cauchy,FixNPTCauchy)
#else
#ifndef LMP_FIX_NPT_CAUCHY_H
#define LMP_FIX_NPT_CAUCHY_H
#include "fix_cauchy.h"
namespace LAMMPS_NS {
class FixNPTCauchy : public FixCauchy {
public:
FixNPTCauchy(class LAMMPS *, int, char **);
~FixNPTCauchy() {}
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Temperature control must be used with fix npt
Self-explanatory.
E: Pressure control must be used with fix npt
Self-explanatory.
*/

0
src/USER-CAUCHY/fix_cauchy.cpp → src/USER-MISC/fix_npt_cauchy.cpp
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0
src/USER-CAUCHY/fix_cauchy.h → src/USER-MISC/fix_npt_cauchy.h
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