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Name change, add example

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This commit is contained in:
Gabriel Alkuino
2024-11-12 11:40:07 -05:00
committed by GitHub
parent 92d4bec1a3
commit 2bcd6d1f73
11 changed files with 357 additions and 855 deletions
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2
doc/src/Commands_fix.rst
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@ -58,6 +58,7 @@ OPT.
* :doc:`dt/reset (k) <fix_dt_reset>`
* :doc:`edpd/source <fix_dpd_source>`
* :doc:`efield (k) <fix_efield>`
* :doc:`efield/lepton <fix_efield_lepton>`
* :doc:`efield/tip4p <fix_efield>`
* :doc:`ehex <fix_ehex>`
* :doc:`electrode/conp (i) <fix_electrode>`
@ -69,7 +70,6 @@ OPT.
* :doc:`eos/cv <fix_eos_cv>`
* :doc:`eos/table <fix_eos_table>`
* :doc:`eos/table/rx (k) <fix_eos_table_rx>`
* :doc:`epot/lepton <fix_epot_lepton>`
* :doc:`evaporate <fix_evaporate>`
* :doc:`external <fix_external>`
* :doc:`ffl <fix_ffl>`

2
doc/src/fix.rst
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@ -237,6 +237,7 @@ accelerated styles exist.
* :doc:`dt/reset <fix_dt_reset>` - reset the timestep based on velocity, forces
* :doc:`edpd/source <fix_dpd_source>` - add heat source to eDPD simulations
* :doc:`efield <fix_efield>` - impose electric field on system
* :doc:`efield/lepton <fix_efield_lepton>` - impose electric field on system using a Lepton expression for the potential
* :doc:`efield/tip4p <fix_efield>` - impose electric field on system with TIP4P molecules
* :doc:`ehex <fix_ehex>` - enhanced heat exchange algorithm
* :doc:`electrode/conp <fix_electrode>` - impose electric potential
@ -248,7 +249,6 @@ accelerated styles exist.
* :doc:`eos/cv <fix_eos_cv>` - applies a mesoparticle equation of state to relate the particle internal energy to the particle internal temperature
* :doc:`eos/table <fix_eos_table>` - applies a tabulated mesoparticle equation of state to relate the particle internal energy to the particle internal temperature
* :doc:`eos/table/rx <fix_eos_table_rx>` - applies a tabulated mesoparticle equation of state to relate the concentration-dependent particle internal energy to the particle internal temperature
* :doc:`epot/lepton <fix_epot_lepton>` - apply electric potential on system using Lepton expression
* :doc:`evaporate <fix_evaporate>` - remove atoms from simulation periodically
* :doc:`external <fix_external>` - callback to an external driver program
* :doc:`ffl <fix_ffl>` - apply a Fast-Forward Langevin equation thermostat

8
doc/src/fix_efield.rst
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@ -45,8 +45,9 @@ Description
Add a force :math:`\vec{F} = q\vec{E}` to each charged atom in the group due to an
external electric field being applied to the system. If the system
contains point-dipoles, also add a torque on the dipoles due to the
external electric field.
contains point-dipoles, also add a torque :math:`\vec{T} = \vec{p} \times \vec{E}` on the dipoles due to the
external electric field. This fix does not compute the dipole force :math:`\vec{F} = (\vec{p} \cdot \nabla) \vec{E}`,
and the :doc:`fix efield/lepton <fix_efield_lepton>` command should be used instead.
.. versionadded:: 28Mar2023
@ -68,6 +69,7 @@ For point-dipoles, equal-style variables can be used, but atom-style
variables are not currently supported, since they imply a spatial
gradient in the electric field which means additional terms with
gradients of the field are required for the force and torque on dipoles.
The :doc:`fix efield/lepton <fix_efield_lepton>` command should be used instead.
Equal-style variables can specify formulas with various mathematical
functions, and include :doc:`thermo_style <thermo_style>` command
@ -229,7 +231,7 @@ Fix style *efield/tip4p* can only be used with tip4p pair styles.
Related commands
""""""""""""""""
:doc:`fix addforce <fix_addforce>`
:doc:`fix addforce <fix_addforce>`, :doc:`fix efield/lepton <fix_efield_lepton>`
Default
"""""""

281
doc/src/fix_epot_lepton.rst → doc/src/fix_efield_lepton.rst
View File

@ -1,138 +1,143 @@
.. index:: fix epot/lepton
fix epot/lepton command
=======================
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID epot/lepton V ...
* ID, group-ID are documented in the :doc:`fix <fix>` command
* style = *epot/lepton*
* V = electric potential (electric field * distance units)
* V must be a Lepton expression (see below)
* zero or more keyword/value pairs may be appended to args
* keyword = *region* or *step*
.. parsed-literal::
*region* value = region-ID
region-ID = ID of region atoms must be in to have effect
*step* value = h
h = step size for numerical differentiation (distance units)
Examples
""""""""
.. code-block:: LAMMPS
fix ex all epot/lepton "-E*x; E=1"
fix dexx all epot/lepton "-0.5*x^2" step 1
fix yukawa all epot/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A=1; B=1" step 1e-6
fix infp all epot/lepton "-abs(x)" step 1
variable th equal 2*PI*ramp(0,1)
fix erot all epot/lepton "-(x*cos(v_th)+y*sin(v_th))"
Description
"""""""""""
.. versionadded:: TBD
Add an electric potential :math:`V` that applies to a group of charged atoms a force :math:`\vec{F} = q \vec{E}`,
and to dipoles a force :math:`\vec{F} = (\vec{p} \cdot \nabla) \vec{E}` and torque :math:`\vec{T} = \vec{p} \times \vec{E}`,
where :math:`\vec{E} = - \nabla V`. The fix also evaluates the electrostatic energy (:math:`U_{q} = q V` and :math:`U_{p} = - \vec{p} \cdot \vec{E}`)
due to this potential when the :doc:`fix_modify energy yes <fix_modify>` command is specified (see below).
The `Lepton library <https://simtk.org/projects/lepton>`_, that the *epot/lepton* fix style interfaces with, evaluates
the expression string at run time to compute the energy, forces, and torques. It creates an analytical representation
of :math:`V` and :math:`\vec{E}`, while the gradient force is computed using a central difference scheme
.. math::
\vec{F} = \frac{|\vec{p}|}{2h} \left[ \vec{E}(\vec{x} + h \hat{p}) - \vec{E}(\vec{x} - h \hat{p}) \right] .
The Lepton expression must be either enclosed in quotes or must not contain any whitespace so that LAMMPS
recognizes it as a single keyword. More on valid Lepton expressions below. The final Lepton expression must
be a function of only :math:`x, y, z`, which refer to the current *unwrapped* coordinates of the atoms to ensure continuity.
Special care must be taken when using this fix with periodic boundary conditions or box-changing commands.
----------
.. include:: lepton_expression.rst
----------
If the *region* keyword is used, the atom must also be in the specified
geometric :doc:`region <region>` in order to be affected by the potential.
The *step* keyword is required when :doc:`atom_style dipole <atom_style>` is used and the electric field is non-uniform.
If you only want to apply a uniform electric field, the :doc:`fix efield <fix_efield>` command will be faster.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files
<restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the potential energy defined above to the global potential energy
of the system as part of :doc:`thermodynamic output <thermo_style>`.
The default setting for this fix is :doc:`fix_modify energy no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
fix to add the contribution due to the added ***forces*** on charges and dipoles
to both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute stress/atom
<compute_stress_atom>` commands. The former can be accessed by
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify virial no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
integrator the fix adding its forces. Default is the outermost level.
This fix computes a global scalar and a global 3-vector of forces,
which can be accessed by various :doc:`output commands <Howto_output>`.
The scalar is the potential energy discussed above.
The vector is the total force added to the group of atoms.
The scalar and vector values calculated by this fix are "extensive".
This fix cannot be used with the *start/stop* keywords of
the :doc:`run <run>` command.
The forces due to this fix are imposed during an energy minimization,
invoked by the :doc:`minimize <minimize>` command. You should not
specify force components with a variable that has time-dependence for
use with a minimizer, since the minimizer increments the timestep as
the iteration count during the minimization.
.. note::
If you want the electric potential energy to be included in the
total potential energy of the system (the quantity being minimized),
you MUST enable the :doc:`fix_modify <fix_modify>` *energy* option for this fix.
----------
Restrictions
""""""""""""
Fix style *epot/lepton* is part of the LEPTON package. It is only enabled if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`fix efield <fix_efield>`
Default
"""""""
none
.. index:: fix efield/lepton
fix efield/lepton command
=========================
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID efield/lepton V ...
* ID, group-ID are documented in the :doc:`fix <fix>` command
* style = *efield/lepton*
* V = electric potential (electric field * distance units)
* V must be a Lepton expression (see below)
* zero or more keyword/value pairs may be appended to args
* keyword = *region* or *step*
.. parsed-literal::
*region* value = region-ID
region-ID = ID of region atoms must be in to have effect
*step* value = h
h = step size for numerical differentiation (distance units)
Examples
""""""""
.. code-block:: LAMMPS
fix ex all efield/lepton "-E*x; E=1"
fix dexx all efield/lepton "-0.5*x^2" step 1
fix yukawa all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A=1; B=1" step 1e-6
fix infp all efield/lepton "-abs(x)" step 1
variable th equal 2*PI*ramp(0,1)
fix erot all efield/lepton "-(x*cos(v_th)+y*sin(v_th))"
Description
"""""""""""
.. versionadded:: TBD
Add an electric potential :math:`V` that applies to a group of charged atoms a force :math:`\vec{F} = q \vec{E}`,
and to dipoles a force :math:`\vec{F} = (\vec{p} \cdot \nabla) \vec{E}` and torque :math:`\vec{T} = \vec{p} \times \vec{E}`,
where :math:`\vec{E} = - \nabla V`. The fix also evaluates the electrostatic energy (:math:`U_{q} = q V` and :math:`U_{p} = - \vec{p} \cdot \vec{E}`)
due to this potential when the :doc:`fix_modify energy yes <fix_modify>` command is specified (see below).
.. note::
This command should be used instead of :doc:`fix efield <fix_efield>` if you want to impose a non-uniform electric field on a system with dipoles
since the latter does not include the dipole force term. If you only have charges or if the electric field gradient is negligible,
:doc:`fix efield <fix_efield>` should be used since it is faster.
The `Lepton library <https://simtk.org/projects/lepton>`_, that the *efield/lepton* fix style interfaces with, evaluates
the expression string at run time to compute the energy, forces, and torques. It creates an analytical representation
of :math:`V` and :math:`\vec{E}`, while the gradient force is computed using a central difference scheme
.. math::
\vec{F} = \frac{|\vec{p}|}{2h} \left[ \vec{E}(\vec{x} + h \hat{p}) - \vec{E}(\vec{x} - h \hat{p}) \right] .
The Lepton expression must be either enclosed in quotes or must not contain any whitespace so that LAMMPS
recognizes it as a single keyword. More on valid Lepton expressions below. The final Lepton expression must
be a function of only :math:`x, y, z`, which refer to the current *unwrapped* coordinates of the atoms to ensure continuity.
Special care must be taken when using this fix with periodic boundary conditions or box-changing commands.
----------
.. include:: lepton_expression.rst
----------
If the *region* keyword is used, the atom must also be in the specified
geometric :doc:`region <region>` in order to be affected by the potential.
The *step* keyword is required when :doc:`atom_style dipole <atom_style>` is used and the electric field is non-uniform.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files
<restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the potential energy defined above to the global potential energy
of the system as part of :doc:`thermodynamic output <thermo_style>`.
The default setting for this fix is :doc:`fix_modify energy no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
fix to add the contribution due to the added ***forces*** on charges and dipoles
to both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute stress/atom
<compute_stress_atom>` commands. The former can be accessed by
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify virial no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
integrator the fix adding its forces. Default is the outermost level.
This fix computes a global scalar and a global 3-vector of forces,
which can be accessed by various :doc:`output commands <Howto_output>`.
The scalar is the potential energy discussed above.
The vector is the total force added to the group of atoms.
The scalar and vector values calculated by this fix are "extensive".
This fix cannot be used with the *start/stop* keywords of
the :doc:`run <run>` command.
The forces due to this fix are imposed during an energy minimization,
invoked by the :doc:`minimize <minimize>` command. You should not
specify force components with a variable that has time-dependence for
use with a minimizer, since the minimizer increments the timestep as
the iteration count during the minimization.
.. note::
If you want the electric potential energy to be included in the
total potential energy of the system (the quantity being minimized),
you MUST enable the :doc:`fix_modify <fix_modify>` *energy* option for this fix.
----------
Restrictions
""""""""""""
Fix style *efield/lepton* is part of the LEPTON package. It is only enabled if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`fix efield <fix_efield>`
Default
"""""""
none

1
doc/utils/sphinx-config/false_positives.txt
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@ -1020,7 +1020,6 @@ eos
epair
epcc
epl
epot
Epp
Epq
eps

49
examples/LEPTON/in.efield-lepton Normal file
View File

@ -0,0 +1,49 @@
# Point dipoles in a 3d box with an external potential (ignoring dipolar interactions)
units lj
atom_style hybrid sphere dipole
dimension 3
boundary s s s
region box block -2 2 -2 2 -2 2
create_box 1 box
create_atoms 1 random 100 12345 NULL
# need both mass settings due to hybrid atom style
mass 1 1.0
set group all mass 1.0
set group all diameter 0.1
set group all dipole/random 98934 0.01
pair_style none
velocity all create 0.0 87287 mom yes rot yes
fix 1 all nve/sphere update dipole
###############################################################################################################
## Yukawa potential
#fix 2 all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A = 0.1; B = 5" step 1e-8
## Gradually increasing uniform field
#variable E equal ramp(0,1)
#fix 2 all efield/lepton "-v_E*(x+y+z)"
## Linear gradient field
fix 2 all efield/lepton "-1/6*x^3" step 1e-6
fix_modify 2 energy yes
###############################################################################################################
timestep 1e-3
compute erot all erotate/sphere
variable etotal equal "ke + c_erot + pe" # thermo etotal doesn't include erot
thermo_style custom step temp ke c_erot pe v_etotal
thermo 500
thermo_modify norm no
#dump 1 all custom 500 dump.dipole id x y z diameter mux muy muz fx fy fz tqx tqy tqz
run 10000

4
src/.gitignore vendored
View File

@ -95,8 +95,8 @@
/angle_lepton.h
/dihedral_lepton.cpp
/dihedral_lepton.h
/fix_epot_lepton.cpp
/fix_epot_lepton.h
/fix_efield_lepton.cpp
/fix_efield_lepton.h
/fix_wall_lepton.cpp
/fix_wall_lepton.h
/lepton_utils.cpp

495
src/LEPTON/fix_epot_lepton.cpp
View File

@ -1,495 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
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: Gabriel Alkuino (Syracuse University) - gsalkuin@syr.edu
Modified from fix_efield
------------------------------------------------------------------------- */
#include "fix_epot_lepton.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "input.h"
#include "modify.h"
#include "region.h"
#include "respa.h"
#include "update.h"
#include <array>
#include "Lepton.h"
#include "lepton_utils.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define EPSILON 1.0e-10
/* ---------------------------------------------------------------------- */
FixEpotLepton::FixEpotLepton(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), idregion(nullptr), region(nullptr)
{
if (domain->xperiodic || domain->yperiodic || domain->zperiodic) {
error->warning(FLERR, "Fix {} uses unwrapped coordinates", style);
}
if (narg < 4) utils::missing_cmd_args(FLERR, std::string("fix ") + style, error);
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
energy_global_flag = 1;
virial_global_flag = virial_peratom_flag = 1;
respa_level_support = 1;
ilevel_respa = 0;
// optional args
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg], "region") == 0) {
if (iarg + 2 > narg)
utils::missing_cmd_args(FLERR, std::string("fix ") + style + " region", error);
region = domain->get_region_by_id(arg[iarg + 1]);
if (!region) error->all(FLERR, "Region {} for fix {} does not exist", arg[iarg + 1], style);
idregion = utils::strdup(arg[iarg + 1]);
iarg += 2;
} else if (strcmp(arg[iarg], "step") == 0) {
if (iarg + 2 > narg)
utils::missing_cmd_args(FLERR, std::string("fix ") + style + "step", error);
h = utils::numeric(FLERR, arg[iarg+1], false, lmp);
iarg += 2;
} else {
error->all(FLERR, "Unknown keyword for fix {} command: {}", style, arg[iarg]);
}
}
// check validity of Lepton expression
// remove whitespace and quotes from expression string and then
// check if the expression can be parsed without error
expr = LeptonUtils::condense(arg[3]);
try {
auto parsed = Lepton::Parser::parse(LeptonUtils::substitute(expr, lmp));
auto phi = parsed.createCompiledExpression();
} catch (std::exception &e) {
error->all(FLERR, e.what());
}
force_flag = 0;
fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0;
}
/* ---------------------------------------------------------------------- */
FixEpotLepton::~FixEpotLepton()
{
delete[] idregion;
}
/* ---------------------------------------------------------------------- */
int FixEpotLepton::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixEpotLepton::init()
{
if (!atom->q_flag && !atom->mu_flag)
error->all(FLERR, "Fix {} requires atom attribute q or mu", style);
if (atom->mu_flag && !atom->torque_flag)
error->all(FLERR, "Dipoles must be finite-sized to rotate", style);
// set index and check validity of region
if (idregion) {
region = domain->get_region_by_id(idregion);
if (!region) error->all(FLERR, "Region {} for fix {} does not exist", idregion, style);
}
if (utils::strmatch(update->integrate_style, "^respa")) {
ilevel_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels - 1;
if (respa_level >= 0) ilevel_respa = MIN(respa_level, ilevel_respa);
}
// unit conversion factors and restrictions (see issue #1377)
char *unit_style = update->unit_style;
qe2f = force->qe2f;
mue2e = qe2f;
if (strcmp(unit_style, "electron") == 0 || strcmp(unit_style, "micro") == 0 || strcmp(unit_style, "nano") == 0) {
error->all(FLERR, "Fix {} does not support {} units", style, unit_style);
}
}
/* ---------------------------------------------------------------------- */
void FixEpotLepton::setup(int vflag)
{
if (utils::strmatch(update->integrate_style, "^respa")) {
auto respa = dynamic_cast<Respa *>(update->integrate);
respa->copy_flevel_f(ilevel_respa);
post_force_respa(vflag, ilevel_respa, 0);
respa->copy_f_flevel(ilevel_respa);
} else {
post_force(vflag);
}
}
/* ---------------------------------------------------------------------- */
void FixEpotLepton::min_setup(int vflag)
{
post_force(vflag);
}
/* ----------------------------------------------------------------------
Apply F = qE,
F = (mu . D) E,
T = mu x E
------------------------------------------------------------------------- */
void FixEpotLepton::post_force(int vflag)
{
double **f = atom->f;
double **x = atom->x;
int *mask = atom->mask;
imageint *image = atom->image;
int nlocal = atom->nlocal;
auto parsed = Lepton::Parser::parse(LeptonUtils::substitute(expr, lmp)).optimize();
Lepton::CompiledExpression phi;
auto dphi_x = parsed.differentiate("x").createCompiledExpression();
auto dphi_y = parsed.differentiate("y").createCompiledExpression();
auto dphi_z = parsed.differentiate("z").createCompiledExpression();
std::vector<Lepton::CompiledExpression*> dphis = {&dphi_x, &dphi_y, &dphi_z};
// check if reference to x, y, z exist
const std::array<std::string, 3> variableNames = {"x", "y", "z"};
std::array<bool, 3> phi_has_ref = {true, true, true};
if (atom->q_flag){
phi = parsed.createCompiledExpression();
for (size_t i = 0; i < 3; i++) {
try {
phi.getVariableReference(variableNames[i]);
}
catch (Lepton::Exception &) {
phi_has_ref[i] = false;
}
}
}
std::vector<std::array<bool, 3>> dphis_has_ref;
bool e_uniform = true;
for (auto &dphi : dphis) {
dphis_has_ref.push_back({false, false, false});
for (size_t i = 0; i < 3; i++) {
try {
(*dphi).getVariableReference(variableNames[i]);
dphis_has_ref.back()[i] = true;
e_uniform = false;
}
catch (Lepton::Exception &) {
// do nothing
}
}
}
if (!e_uniform && atom->mu_flag && h < 0) {
error->all(FLERR, "Fix {} requires keyword `step' for dipoles in a non-uniform electric field", style);
}
// virial setup
v_init(vflag);
// update region if necessary
if (region) region->prematch();
// fsum[0] = "potential energy" for added force
// fsum[123] = extra force added to atoms
fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0;
force_flag = 0;
double ex, ey, ez;
double fx, fy, fz;
double v[6], unwrap[3];
double xf, yf, zf, xb, yb, zb;
double exf, eyf, ezf, exb, eyb, ezb;
double tx, ty, tz;
double mu_norm, h_mu;
if (atom->q_flag && atom->mu_flag) {
double *q = atom->q;
double **mu = atom->mu;
double **t = atom->torque;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
domain->unmap(x[i], image[i], unwrap);
// evaluate e-field, used by q and mu
for (size_t j = 0; j < 3; j++) {
if (dphis_has_ref[j][0]) (*dphis[j]).getVariableReference("x") = unwrap[0];
if (dphis_has_ref[j][1]) (*dphis[j]).getVariableReference("y") = unwrap[1];
if (dphis_has_ref[j][2]) (*dphis[j]).getVariableReference("z") = unwrap[2];
}
ex = -dphi_x.evaluate();
ey = -dphi_y.evaluate();
ez = -dphi_z.evaluate();
if (phi_has_ref[0]) phi.getVariableReference("x") = unwrap[0];
if (phi_has_ref[1]) phi.getVariableReference("y") = unwrap[1];
if (phi_has_ref[2]) phi.getVariableReference("z") = unwrap[2];
// charges
// force = q E
fx = qe2f * q[i] * ex;
fy = qe2f * q[i] * ey;
fz = qe2f * q[i] * ez;
// potential energy = q phi
fsum[0] += qe2f * q[i] * phi.evaluate();
// dipoles
mu_norm = sqrt(mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2]);
if (mu_norm > EPSILON) {
// torque = mu cross E
t[i][0] += mue2e * (ez * mu[i][1] - ey * mu[i][2]);
t[i][1] += mue2e * (ex * mu[i][2] - ez * mu[i][0]);
t[i][2] += mue2e * (ey * mu[i][0] - ex * mu[i][1]);
// potential energy = - mu dot E
fsum[0] -= mue2e * (mu[i][0] * ex + mu[i][1] * ey + mu[i][2] * ez);
// force = (mu dot D) E
// using central difference method
h_mu = h / mu_norm;
xf = unwrap[0] + h_mu * mu[i][0];
yf = unwrap[1] + h_mu * mu[i][1];
zf = unwrap[2] + h_mu * mu[i][2];
for (size_t j = 0; j < 3; j++) {
if (dphis_has_ref[j][0]) (*dphis[j]).getVariableReference("x") = xf;
if (dphis_has_ref[j][1]) (*dphis[j]).getVariableReference("y") = yf;
if (dphis_has_ref[j][2]) (*dphis[j]).getVariableReference("z") = zf;
}
exf = -dphi_x.evaluate();
eyf = -dphi_y.evaluate();
ezf = -dphi_z.evaluate();
xb = unwrap[0] - h_mu * mu[i][0];
yb = unwrap[1] - h_mu * mu[i][1];
zb = unwrap[2] - h_mu * mu[i][2];
for (size_t j = 0; j < 3; j++) {
if (dphis_has_ref[j][0]) (*dphis[j]).getVariableReference("x") = xb;
if (dphis_has_ref[j][1]) (*dphis[j]).getVariableReference("y") = yb;
if (dphis_has_ref[j][2]) (*dphis[j]).getVariableReference("z") = zb;
}
exb = -dphi_x.evaluate();
eyb = -dphi_y.evaluate();
ezb = -dphi_z.evaluate();
fx += qe2f * (exf - exb) / 2.0 / h_mu;
fy += qe2f * (eyf - eyb) / 2.0 / h_mu;
fz += qe2f * (ezf - ezb) / 2.0 / h_mu;
}
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
fsum[1] += fx;
fsum[2] += fy;
fsum[3] += fz;
if (evflag) {
v[0] = fx * unwrap[0];
v[1] = fy * unwrap[1];
v[2] = fz * unwrap[2];
v[3] = fx * unwrap[1];
v[4] = fx * unwrap[2];
v[5] = fy * unwrap[2];
v_tally(i, v);
}
}
}
} else if (atom->q_flag && !atom->mu_flag) {
double *q = atom->q;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
domain->unmap(x[i], image[i], unwrap);
for (size_t j = 0; j < 3; j++) {
if (dphis_has_ref[j][0]) (*dphis[j]).getVariableReference("x") = unwrap[0];
if (dphis_has_ref[j][1]) (*dphis[j]).getVariableReference("y") = unwrap[1];
if (dphis_has_ref[j][2]) (*dphis[j]).getVariableReference("z") = unwrap[2];
}
ex = -dphi_x.evaluate();
ey = -dphi_y.evaluate();
ez = -dphi_z.evaluate();
if (phi_has_ref[0]) phi.getVariableReference("x") = unwrap[0];
if (phi_has_ref[1]) phi.getVariableReference("y") = unwrap[1];
if (phi_has_ref[2]) phi.getVariableReference("z") = unwrap[2];
// force = q E
fx = qe2f * q[i] * ex;
fy = qe2f * q[i] * ey;
fz = qe2f * q[i] * ez;
// potential energy = q phi
fsum[0] += qe2f * q[i] * phi.evaluate();
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
fsum[1] += fx;
fsum[2] += fy;
fsum[3] += fz;
if (evflag) {
v[0] = fx * unwrap[0];
v[1] = fy * unwrap[1];
v[2] = fz * unwrap[2];
v[3] = fx * unwrap[1];
v[4] = fx * unwrap[2];
v[5] = fy * unwrap[2];
v_tally(i, v);
}
}
}
} else if (!atom->q_flag && atom->mu_flag) {
double **mu = atom->mu;
double **t = atom->torque;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
mu_norm = sqrt(mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2]);
if (mu_norm > EPSILON) continue;
domain->unmap(x[i], image[i], unwrap);
for (size_t j = 0; j < 3; j++) {
if (dphis_has_ref[j][0]) (*dphis[j]).getVariableReference("x") = unwrap[0];
if (dphis_has_ref[j][1]) (*dphis[j]).getVariableReference("y") = unwrap[1];
if (dphis_has_ref[j][2]) (*dphis[j]).getVariableReference("z") = unwrap[2];
}
ex = -dphi_x.evaluate();
ey = -dphi_y.evaluate();
ez = -dphi_z.evaluate();
// torque = mu cross E
t[i][0] += mue2e * (ez * mu[i][1] - ey * mu[i][2]);
t[i][1] += mue2e * (ex * mu[i][2] - ez * mu[i][0]);
t[i][2] += mue2e * (ey * mu[i][0] - ex * mu[i][1]);
// potential energy = - mu dot E
fsum[0] -= mue2e * (mu[i][0] * ex + mu[i][1] * ey + mu[i][2] * ez);
// force = (mu dot D) E
// using central difference method
h_mu = h / sqrt(mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2]);
xf = unwrap[0] + h_mu * mu[i][0];
yf = unwrap[1] + h_mu * mu[i][1];
zf = unwrap[2] + h_mu * mu[i][2];
for (size_t j = 0; j < 3; j++) {
if (dphis_has_ref[j][0]) (*dphis[j]).getVariableReference("x") = xf;
if (dphis_has_ref[j][1]) (*dphis[j]).getVariableReference("y") = yf;
if (dphis_has_ref[j][2]) (*dphis[j]).getVariableReference("z") = zf;
}
exf = -dphi_x.evaluate();
eyf = -dphi_y.evaluate();
ezf = -dphi_z.evaluate();
xb = unwrap[0] - h_mu * mu[i][0];
yb = unwrap[1] - h_mu * mu[i][1];
zb = unwrap[2] - h_mu * mu[i][2];
for (size_t j = 0; j < 3; j++) {
if (dphis_has_ref[j][0]) (*dphis[j]).getVariableReference("x") = xb;
if (dphis_has_ref[j][1]) (*dphis[j]).getVariableReference("y") = yb;
if (dphis_has_ref[j][2]) (*dphis[j]).getVariableReference("z") = zb;
}
exb = -dphi_x.evaluate();
eyb = -dphi_y.evaluate();
ezb = -dphi_z.evaluate();
fx = qe2f * (exf - exb) / 2.0 / h_mu;
fy = qe2f * (eyf - eyb) / 2.0 / h_mu;
fz = qe2f * (ezf - ezb) / 2.0 / h_mu;
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
fsum[1] += fx;
fsum[2] += fy;
fsum[3] += fz;
if (evflag) {
v[0] = fx * unwrap[0];
v[1] = fy * unwrap[1];
v[2] = fz * unwrap[2];
v[3] = fx * unwrap[1];
v[4] = fx * unwrap[2];
v[5] = fy * unwrap[2];
v_tally(i, v);
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixEpotLepton::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixEpotLepton::min_post_force(int vflag)
{
post_force(vflag);
}
/* ----------------------------------------------------------------------
return energy added by fix
------------------------------------------------------------------------- */
double FixEpotLepton::compute_scalar()
{
if (force_flag == 0) {
MPI_Allreduce(fsum, fsum_all, 4, MPI_DOUBLE, MPI_SUM, world);
force_flag = 1;
}
return fsum_all[0];
}
/* ----------------------------------------------------------------------
return total extra force due to fix
------------------------------------------------------------------------- */
double FixEpotLepton::compute_vector(int n)
{
if (force_flag == 0) {
MPI_Allreduce(fsum, fsum_all, 4, MPI_DOUBLE, MPI_SUM, world);
force_flag = 1;
}
return fsum_all[n + 1];
}

60
src/LEPTON/fix_epot_lepton.h
View File

@ -1,60 +0,0 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
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: Gabriel Alkuino (Syracuse University) - gsalkuin@syr.edu
Modified from fix_efield
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
// clang-format off
FixStyle(epot/lepton,FixEpotLepton);
// clang-format on
#else
#ifndef LMP_FIX_EPOT_LEPTON_H
#define LMP_FIX_EPOT_LEPTON_H
#include "fix.h"
namespace LAMMPS_NS {
class FixEpotLepton : public Fix {
public:
FixEpotLepton(class LAMMPS *, int, char **);
~FixEpotLepton() override;
int setmask() override;
void init() override;
void setup(int) override;
void min_setup(int) override;
void post_force(int) override;
void post_force_respa(int, int, int) override;
void min_post_force(int) override;
double compute_scalar() override;
double compute_vector(int) override;
protected:
char *idregion;
class Region *region;
int ilevel_respa;
std::string expr;
int force_flag;
double h = -1.0;
double qe2f, mue2e;
double fsum[4], fsum_all[4];
};
} // namespace LAMMPS_NS
#endif
#endif

155
unittest/force-styles/tests/fix-timestep-epot_lepton.yaml → unittest/force-styles/tests/fix-timestep-efield_lepton.yaml
View File

@ -1,77 +1,78 @@
---
lammps_version: 27 Jun 2024
date_generated: Tue Sep 17 08:38:51 2024
epsilon: 2e-13
skip_tests:
prerequisites: ! |
atom full
fix efield
pre_commands: ! ""
post_commands: ! |
region half block 0 EDGE EDGE EDGE EDGE EDGE
fix move all nve
fix test solute epot/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A=1; B=1"
input_file: in.fourmol
natoms: 29
global_scalar: 1.6704454516566274
run_pos: ! |2
1 -2.7045174040786113e-01 2.4911873718363386e+00 -1.6695654631491835e-01
2 3.1004221019407835e-01 2.9612623619618166e+00 -8.5467074498303619e-01
3 -7.0398277208953364e-01 1.2305442007296870e+00 -6.2777337959095758e-01
4 -1.5818277418447926e+00 1.4837528245352911e+00 -1.2538808796681880e+00
5 -9.0729118448236790e-01 9.2661863916543652e-01 3.9958383542336978e-01
6 2.4837968642651539e-01 2.8318965710323424e-01 -1.2316675533799510e+00
7 3.4143233737928985e-01 -2.2652080889821399e-02 -2.5292246648830696e+00
8 1.1742106633496632e+00 -4.8857819177533296e-01 -6.3774855832878818e-01
9 1.3804619006746952e+00 -2.5282186304504617e-01 2.8361638661486044e-01
10 2.0510714422715428e+00 -1.4603992238436605e+00 -9.8323613298241641e-01
11 1.7878067664442001e+00 -1.9921902225913919e+00 -1.8890639278278800e+00
12 3.0062962291402449e+00 -4.9013271581056822e-01 -1.6231874104184338e+00
13 4.0515414154880354e+00 -8.9202039400328714e-01 -1.6400010189207204e+00
14 2.6066986955414859e+00 -4.1789289874186603e-01 -2.6634027530740045e+00
15 2.9695346087268195e+00 5.5422728642528218e-01 -1.2342046800948778e+00
16 2.6747089246970055e+00 -2.4124172919180635e+00 -2.3435358040545039e-02
17 2.2153515161424591e+00 -2.0897925974376559e+00 1.1963115055447653e+00
18 2.1369701703995672e+00 3.0158507413483879e+00 -3.5179348337128169e+00
19 1.5355837136075503e+00 2.6255292355356850e+00 -4.2353987779858899e+00
20 2.7727573005675157e+00 3.6923910449606199e+00 -3.9330842459130921e+00
21 4.9040128073216458e+00 -4.0752348172972228e+00 -3.6210314709902178e+00
22 4.3582355554441330e+00 -4.2126119427287785e+00 -4.4612844196314905e+00
23 5.7439382849308398e+00 -3.5821957939275575e+00 -3.8766361295936442e+00
24 2.0689243582420707e+00 3.1513346907257525e+00 3.1550389754825381e+00
25 1.3045351331495809e+00 3.2665125705836533e+00 2.5111855257438469e+00
26 2.5809237402711407e+00 4.0117602605482343e+00 3.2212060529090203e+00
27 -1.9611343130355228e+00 -4.3563411931353464e+00 2.1098293115521636e+00
28 -2.7473562684513140e+00 -4.0200819932378886e+00 1.5830052163433823e+00
29 -1.3126000191359133e+00 -3.5962518039481126e+00 2.2746342468736911e+00
run_vel: ! |2
1 8.1748902719248895e-03 1.6488825063890555e-02 4.7920575746796803e-03
2 5.4511084007743318e-03 5.2051261388670498e-03 -1.4434422725438370e-03
3 -8.2274804663814219e-03 -1.2934351097927732e-02 -4.0974640813287184e-03
4 -3.7810439919825625e-03 -6.5599673887508873e-03 -1.1281975069807595e-03
5 -1.1114610957297140e-02 -9.7941960094448405e-03 -2.8000606969231651e-03
6 -3.9614471141667384e-02 4.6885125158393097e-02 3.6916688468892268e-02
7 9.0823633550694307e-04 -1.0137209973964618e-02 -5.1576821598862101e-02
8 7.7662077312228937e-03 -3.3034358179113549e-03 3.4641870510036560e-02
9 1.9711566942801151e-03 3.6632927647716452e-03 1.5119486507285342e-02
10 2.9189761590759169e-02 -2.9234948386605512e-02 -1.5014329233453094e-02
11 -4.7800378310285741e-03 -3.7519133265433713e-03 -2.3499734597008941e-03
12 2.2651912734175032e-03 -3.4688766322378106e-04 -3.0617028612628929e-03
13 2.7541524307768692e-03 5.8168212242409026e-03 -7.9509320189794788e-04
14 3.5269195768251409e-03 -5.7943367272026312e-03 -3.9501557653067150e-03
15 -1.8489707819649144e-03 -5.8542853523402688e-03 6.2913780244787517e-03
16 1.8687298458400135e-02 -1.3267695591612149e-02 -4.5638131306342533e-02
17 -1.2902476276599238e-02 9.7586450769834993e-03 3.7292773489970149e-02
18 -8.0065797284243809e-04 -8.6270476160336701e-04 -1.4483040521307380e-03
19 1.2452390811276265e-03 -2.5061097157054544e-03 7.2998631050251199e-03
20 3.5930060220586732e-03 3.6938860299406654e-03 3.2322732694668697e-03
21 -1.4689220345082588e-03 -2.7352130061578030e-04 7.0581623990333337e-04
22 -7.0694199253619090e-03 -4.2577148926459460e-03 2.8079117595322244e-04
23 6.0446963119181341e-03 -1.4000131615895693e-03 2.5819754845648850e-03
24 3.1926367864219455e-04 -9.9445665025542493e-04 1.4999996888246658e-04
25 1.3789754587624503e-04 -4.4335894897561037e-03 -8.1808136628206090e-04
26 2.0485904035354775e-03 2.7813358632583834e-03 4.3245727149805969e-03
27 4.5604120337294426e-04 -1.0305523013893942e-03 2.1188058337867958e-04
28 -6.2544520861285771e-03 1.4127711177082084e-03 -1.8429821885090839e-03
29 6.4110631550796319e-04 3.1273432723457764e-03 3.7253671103666878e-03
...
---
lammps_version: 29 Aug 2024
tags: generated
date_generated: Tue Nov 12 08:53:18 2024
epsilon: 2e-13
skip_tests:
prerequisites: ! |
atom full
fix efield
pre_commands: ! ""
post_commands: ! |
region half block 0 EDGE EDGE EDGE EDGE EDGE
fix move all nve
fix test solute efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A=1; B=1"
input_file: in.fourmol
natoms: 29
global_scalar: 1.6704454516566274
run_pos: ! |2
1 -2.7045174040786113e-01 2.4911873718363386e+00 -1.6695654631491835e-01
2 3.1004221019407835e-01 2.9612623619618166e+00 -8.5467074498303619e-01
3 -7.0398277208953364e-01 1.2305442007296870e+00 -6.2777337959095758e-01
4 -1.5818277418447926e+00 1.4837528245352911e+00 -1.2538808796681880e+00
5 -9.0729118448236790e-01 9.2661863916543652e-01 3.9958383542336978e-01
6 2.4837968642651539e-01 2.8318965710323424e-01 -1.2316675533799510e+00
7 3.4143233737928985e-01 -2.2652080889821399e-02 -2.5292246648830696e+00
8 1.1742106633496632e+00 -4.8857819177533296e-01 -6.3774855832878818e-01
9 1.3804619006746952e+00 -2.5282186304504617e-01 2.8361638661486044e-01
10 2.0510714422715428e+00 -1.4603992238436605e+00 -9.8323613298241641e-01
11 1.7878067664442001e+00 -1.9921902225913919e+00 -1.8890639278278800e+00
12 3.0062962291402449e+00 -4.9013271581056822e-01 -1.6231874104184338e+00
13 4.0515414154880354e+00 -8.9202039400328714e-01 -1.6400010189207204e+00
14 2.6066986955414859e+00 -4.1789289874186603e-01 -2.6634027530740045e+00
15 2.9695346087268195e+00 5.5422728642528218e-01 -1.2342046800948778e+00
16 2.6747089246970055e+00 -2.4124172919180635e+00 -2.3435358040545039e-02
17 2.2153515161424591e+00 -2.0897925974376559e+00 1.1963115055447653e+00
18 2.1369701703995672e+00 3.0158507413483879e+00 -3.5179348337128169e+00
19 1.5355837136075503e+00 2.6255292355356850e+00 -4.2353987779858899e+00
20 2.7727573005675157e+00 3.6923910449606199e+00 -3.9330842459130921e+00
21 4.9040128073216458e+00 -4.0752348172972228e+00 -3.6210314709902178e+00
22 4.3582355554441330e+00 -4.2126119427287785e+00 -4.4612844196314905e+00
23 5.7439382849308398e+00 -3.5821957939275575e+00 -3.8766361295936442e+00
24 2.0689243582420707e+00 3.1513346907257525e+00 3.1550389754825381e+00
25 1.3045351331495809e+00 3.2665125705836533e+00 2.5111855257438469e+00
26 2.5809237402711407e+00 4.0117602605482343e+00 3.2212060529090203e+00
27 -1.9611343130355228e+00 -4.3563411931353464e+00 2.1098293115521636e+00
28 -2.7473562684513140e+00 -4.0200819932378886e+00 1.5830052163433823e+00
29 -1.3126000191359133e+00 -3.5962518039481126e+00 2.2746342468736911e+00
run_vel: ! |2
1 8.1748902719248895e-03 1.6488825063890555e-02 4.7920575746796803e-03
2 5.4511084007743318e-03 5.2051261388670498e-03 -1.4434422725438370e-03
3 -8.2274804663814219e-03 -1.2934351097927732e-02 -4.0974640813287184e-03
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...

155
unittest/force-styles/tests/fix-timestep-epot_lepton_region.yaml → unittest/force-styles/tests/fix-timestep-efield_lepton_region.yaml
View File

@ -1,77 +1,78 @@
---
lammps_version: 27 Jun 2024
date_generated: Tue Sep 17 08:42:57 2024
epsilon: 2e-13
skip_tests:
prerequisites: ! |
atom full
fix efield
pre_commands: ! ""
post_commands: ! |
region half block 0 EDGE EDGE EDGE EDGE EDGE
fix move all nve
fix test solute epot/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A=1; B=1" region half
input_file: in.fourmol
natoms: 29
global_scalar: 1.6224257709052041
run_pos: ! |2
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run_vel: ! |2
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...
---
lammps_version: 29 Aug 2024
tags: generated
date_generated: Tue Nov 12 08:53:32 2024
epsilon: 2e-13
skip_tests:
prerequisites: ! |
atom full
fix efield
pre_commands: ! ""
post_commands: ! |
region half block 0 EDGE EDGE EDGE EDGE EDGE
fix move all nve
fix test solute efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A=1; B=1" region half
input_file: in.fourmol
natoms: 29
global_scalar: 1.6224257709052041
run_pos: ! |2
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run_vel: ! |2
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...