ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Final polish of boxrelax. Updated documentation.

Browse Source
This commit is contained in:
Julien Guénolé
2017-08-16 20:01:16 +02:00
parent 6345e6b760
commit 0d901e8535
4 changed files with 83 additions and 38 deletions
Download Patch File Download Diff File Expand all files Collapse all files

76
doc/src/min_modify.txt
View File

@ -13,35 +13,45 @@ min_modify command :h3
min_modify keyword values ... :pre
one or more keyword/value pairs may be listed :ulb,l
keyword = {dmax} or {line} or {delaystep} or {dt_grow} or {dt_shrink}
or {alpha0} or {alpha_shrink} or {tmax} or {tmin} or {integrator}
keyword = {dmax} or {line}
or {integrator} or {tmax} or {tmin}
or {delaystep} or {dt_grow} or {dt_shrink} or {alpha0} or {alpha_shrink}
or {relaxbox} or {relaxbox_mod} or {relaxbox_rate} or {ptol}
or {halfstepback}
{dmax} value = max
max = maximum distance for line search to move (distance units)
{line} value = {backtrack} or {quadratic} or {forcezero}
backtrack,quadratic,forcezero = style of linesearch to use
{delaystep} value = steps
steps = number of steps for dynamics temporization, adaptglok only
{dtgrow} value = grow
grow = factor increasing the timestep, adaptglok only
{dtshrink} value = shrink
shrink = factor decreasing the timestep, adaptglok only
{alpha0} value = alpha
alpha = coefficient mixing velocities and forces, adaptglok only
{alphashrink} value = shrink
shrink = factor decreasing alpha, adaptglok only
{integrator} value = {eulerimplicit} or {eulerexplicit} or {verlet} or {leapfrog}
eulerimplicit,eulerexplicit,verlet,leapfrog = integration scheme (adaptglok)
{tmax} value = coef
coef = factor defining the maximum timestep, adaptglok only
coef = factor defining the maximum timestep (adaptglok)
{tmin} value = coef
coef = factor defining the minimum timestep, adaptglok only
{integrator} value = {eulerimplicit} or {eulerexplicit} or {verlet}
or {leapfrog}
eulerimplicit,eulerexplicit,verlet,leapfrog = integration scheme, adaptglok
{halfstepback} value = {yes} or {no}, adaptglok only :pre
coef = factor defining the minimum timestep (adaptglok)
{delaystep} value = steps
steps = number of steps for dynamics temporization (adaptglok)
{dtgrow} value = grow
grow = factor increasing the timestep (adaptglok)
{dtshrink} value = shrink
shrink = factor decreasing the timestep (adaptglok)
{alpha0} value = alpha
alpha = coefficient mixing velocities and forces (adaptglok)
{alphashrink} value = shrink
shrink = factor decreasing alpha (adaptglok)
{relaxbox} value = {no} or {iso} or {axial} or {x} or {y} or {z}
no = no changes in box dimension (default)
iso,aniso,x,y,z = type of box relaxation (adaptglok)
{relaxbox_mod} value = modulus
modulus = bulk modulus of the system, order of magnitude (adaptglok)
{relaxbox_rate} value = rate
rate = scaling factor to relax the box dimensions (adaptglok)
{halfstepback} value = {yes} or {no} (adaptglok) :pre
:ule
[Examples:]
min_modify dmax 0.2 :pre
min_modify dmax 0.2
min_modify integrator verlet tmax 0.4 relaxbox y relaxbox_mod 2e7 :pre
[Description:]
@ -85,21 +95,34 @@ that difference may be smaller than machine epsilon even if atoms
could move in the gradient direction to reduce forces further.
The style {adaptglok} has several parameters that can be tuned in order
to optimize the relaxation: {integrator}, {delaystep}, {dtgrow}, {dtshrink},
{alpha0}, {alphashrink}, {tmax} and {tmin}.
to optimize the relaxation: {integrator}, {tmax}, {tmin}, {delaystep}, {dtgrow}, {dtshrink},
{alpha0}, and {alphashrink}.
Different Newton {integrator} can be selected: explicit Euler,
semi-implicit Euler (= symplectic Euler), leapfrog, and velocity Verlet.
The parameters {tmax} and {tmin} define the maximum and minimum timestep
allowed during an adaptglok minimization. Those are not in time unit, but are
multiplication factor applied to the "timestep"_timestep.html. For example,
{tmax} = 2.0 means that the maximum value the timestep can reach is twice the
value defined by "timestep"_timestep.html.
multiplication factor applied to the "timestep"_timestep.html. Thus
{tmax} = 2.0 in metal "units"_units.html means that the maximum value
the timestep can reached during the relaxation is 2 ps (with the default
"timestep"_timestep.html value).
Note that even with the default parameters being chosen to be reliable in most
cases, adjusting "timestep"_timestep.html, {tmax} and {tmin} should be consider
to optimize the minimization, in particular for large/complex system.
For debugging purposes, it is possible to switch off the back step when
downhill with {halfstepback} = 0.
The style {adaptglok} performing a damped dynamics, it is not possible to use
"fix box/relax"_fix_box_relax.html to relax the simulation box.
Thus {adaptglok} implements a rudimentary box relaxation procedure that can be
controlled by the keywords {relaxbox}, {relaxbox_mod}, {relaxbox_rate}
and {ptol}.
Note that {relaxbox_mod} doesn't requires the exact value for the bulk modulus,
but rather the order of magnitude (in pressure "units"_units.html).
Ultimately, {relaxbox_mod} and {relaxbox_rate}
control how fast the relaxation of the box is performed: lower values will slow
down the box relaxation but improve the stability of the procedure.
[Restrictions:] none
[Related commands:]
@ -109,6 +132,7 @@ downhill with {halfstepback} = 0.
[Default:]
The option defaults are dmax = 0.1, line = quadratic,
integrator = eulerimplicit, delaystep = 20, dt_grow = 1.1, dt_shrink = 0.5,
alpha0 = 0.25, alpha_shrink = 0.99, tmax = 2.0, tmin = 0.02, adaptstep = yes
integrator = eulerimplicit, tmax = 2.0, tmin = 0.02,
delaystep = 20, dt_grow = 1.1, dt_shrink = 0.5, alpha0 = 0.25, alpha_shrink = 0.99,
relaxbox = no, relaxbox_mod = 1e6 and relaxbox_rate = 0.33, ptol = 0.1
and halfstepback = yes.

2
doc/src/min_style.txt
View File

@ -78,6 +78,8 @@ would normally use for dynamics simulations.
NOTE: The {quickmin}, {fire}, {adaptglok}, and {hftn} styles do not yet support the
use of the "fix box/relax"_fix_box_relax.html command or minimizations
involving the electron radius in "eFF"_pair_eff.html models.
The {adaptglok} style actually support box relaxation by the implementation of
a basic relaxation scheme, see "min_modify"_min_modify.html.
[Restrictions:] none

2
src/min.cpp
View File

@ -67,7 +67,7 @@ Min::Min(LAMMPS *lmp) : Pointers(lmp)
relaxbox_mod = 1000000;
relaxbox_rate = 0.33;
relaxbox_flag = 0;
ptol = 1e-5;
ptol = 0.1;
p_flag[0] = p_flag[1] = p_flag[2] = 0;
elist_global = elist_atom = NULL;

33
src/min_adaptglok.cpp
View File

@ -24,6 +24,8 @@
#include "modify.h"
#include "compute.h"
#include "domain.h"
#include "neighbor.h"
#include "comm.h"
using namespace LAMMPS_NS;
@ -46,8 +48,7 @@ void MinAdaptGlok::init()
if (tmax < tmin) error->all(FLERR,"tmax has to be larger than tmin");
if (dtgrow < 1.0) error->all(FLERR,"dtgrow has to be larger than 1.0");
if (dtshrink > 1.0) error->all(FLERR,"dtshrink has to be smaller than 1.0");
if (relaxbox_mod < 0.0)
error->all(FLERR,"relaxbox_mod has to be positif");
if (relaxbox_mod < 0.0) error->all(FLERR,"relaxbox_mod has to be positif");
// require periodicity in boxrelax dimensions
@ -65,9 +66,7 @@ void MinAdaptGlok::init()
last_negative = ntimestep_start = update->ntimestep;
if (relaxbox_flag){
int icompute = modify->find_compute("thermo_temp");
temperature = modify->compute[icompute];
icompute = modify->find_compute("thermo_press");
int icompute = modify->find_compute("thermo_press");
pressure = modify->compute[icompute];
}
}
@ -79,6 +78,24 @@ void MinAdaptGlok::setup_style()
double **v = atom->v;
int nlocal = atom->nlocal;
// print the parameters used within adaptglok into the log
const char *s1[] = {"eulerimplicit","verlet","leapfrog","eulerexplicit"};
const char *s2[] = {"no","yes"};
const char *s3[] = {"no","iso","aniso"};
if (comm->me == 0 && logfile) {
fprintf(logfile," Parameters for adaptglok: \n"
" dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin "
" integrator halfstepback relaxbox relaxbox_mod relaxbox_rate ptol \n"
" %4g %9i %6g %8g %6g %11g %4g %4g %13s %12s %8s %12g %13g %4g \n",
dmax, delaystep, dtgrow, dtshrink, alpha0, alphashrink, tmax, tmin,
s1[integrator], s2[halfstepback_flag], s3[relaxbox_flag], relaxbox_mod,
relaxbox_rate, ptol);
}
// initialize the velocities
for (int i = 0; i < nlocal; i++)
v[i][0] = v[i][1] = v[i][2] = 0.0;
}
@ -122,7 +139,7 @@ void MinAdaptGlok::relax_box()
// rescale simulation box and scale atom coords for all atoms
double **x = atom->x;
double epsilon;
double epsilon,disp;
double *current_pressure_v;
int *mask = atom->mask;
n = atom->nlocal + atom->nghost;
@ -144,7 +161,9 @@ void MinAdaptGlok::relax_box()
epsilon = pressure->scalar / relaxbox_mod;
for (int i = 0; i < 3; i++) {
if (relaxbox_flag == 2) epsilon = pressure->vector[i] / relaxbox_mod;
domain->boxhi[i] += p_flag[i] * domain->boxhi[i] * epsilon * relaxbox_rate;
disp = domain->boxhi[i] * epsilon * relaxbox_rate;
if (fabs(disp) > dmax) disp > 0.0 ? disp = dmax : disp = -1 * dmax;
domain->boxhi[i] += p_flag[i] * disp;
}
// reset global and local box to new size/shape