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Remove even more whitespace

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This commit is contained in:
Gabriel Alkuino
2024-09-17 13:02:26 -04:00
committed by GitHub
parent bf492c108b
commit ae80dba958
2 changed files with 18 additions and 18 deletions
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26
doc/src/fix_epot_lepton.rst
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@ -42,21 +42,21 @@ 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).
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
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
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.
@ -98,9 +98,9 @@ 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.
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
@ -123,7 +123,7 @@ the iteration count during the minimization.
Restrictions
""""""""""""
Fix style *epot/lepton* is part of the LEPTON package. It is only enabled if LAMMPS was built with that package.
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.

10
src/LEPTON/fix_epot_lepton.cpp
View File

@ -76,7 +76,7 @@ FixEpotLepton::FixEpotLepton(LAMMPS *lmp, int narg, char **arg) :
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
@ -277,7 +277,7 @@ void FixEpotLepton::post_force(int vflag)
// 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];
@ -378,7 +378,7 @@ void FixEpotLepton::post_force(int vflag)
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;
@ -403,7 +403,7 @@ void FixEpotLepton::post_force(int vflag)
// 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];
@ -453,7 +453,7 @@ void FixEpotLepton::post_force(int vflag)
}
}
}
/* ---------------------------------------------------------------------- */
void FixEpotLepton::post_force_respa(int vflag, int ilevel, int /*iloop*/)