Remove even more whitespace
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@ -42,21 +42,21 @@ Description
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.. versionadded:: TBD
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.. versionadded:: TBD
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Add an electric potential :math:`V` that applies to a group of charged atoms a force :math:`\vec{F} = q \vec{E}`,
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Add an electric potential :math:`V` that applies to a group of charged atoms a force :math:`\vec{F} = q \vec{E}`,
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and to dipoles a force :math:`\vec{F} = (\vec{p} \cdot \nabla) \vec{E}` and torque :math:`\vec{T} = \vec{p} \times \vec{E}`,
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and to dipoles a force :math:`\vec{F} = (\vec{p} \cdot \nabla) \vec{E}` and torque :math:`\vec{T} = \vec{p} \times \vec{E}`,
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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}`)
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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}`)
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due to this potential when the :doc:`fix_modify energy yes <fix_modify>` command is specified (see below).
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due to this potential when the :doc:`fix_modify energy yes <fix_modify>` command is specified (see below).
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The `Lepton library <https://simtk.org/projects/lepton>`_, that the *epot/lepton* fix style interfaces with, evaluates
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The `Lepton library <https://simtk.org/projects/lepton>`_, that the *epot/lepton* fix style interfaces with, evaluates
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the expression string at run time to compute the energy, forces, and torques. It creates an analytical representation
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the expression string at run time to compute the energy, forces, and torques. It creates an analytical representation
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of :math:`V` and :math:`\vec{E}`, while the gradient force is computed using a central difference scheme
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of :math:`V` and :math:`\vec{E}`, while the gradient force is computed using a central difference scheme
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.. math::
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.. math::
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\vec{F} = \frac{|\vec{p}|}{2h} \left[ \vec{E}(\vec{x} + h \hat{p}) - \vec{E}(\vec{x} - h \hat{p}) \right] .
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\vec{F} = \frac{|\vec{p}|}{2h} \left[ \vec{E}(\vec{x} + h \hat{p}) - \vec{E}(\vec{x} - h \hat{p}) \right] .
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The Lepton expression must be either enclosed in quotes or must not contain any whitespace so that LAMMPS
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The Lepton expression must be either enclosed in quotes or must not contain any whitespace so that LAMMPS
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recognizes it as a single keyword. More on valid Lepton expressions below. The final Lepton expression must
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recognizes it as a single keyword. More on valid Lepton expressions below. The final Lepton expression must
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be a function of only :math:`x, y, z`, which refer to the current *unwrapped* coordinates of the atoms to ensure continuity.
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be a function of only :math:`x, y, z`, which refer to the current *unwrapped* coordinates of the atoms to ensure continuity.
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Special care must be taken when using this fix with periodic boundary conditions or box-changing commands.
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Special care must be taken when using this fix with periodic boundary conditions or box-changing commands.
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@ -98,9 +98,9 @@ fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
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integrator the fix adding its forces. Default is the outermost level.
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integrator the fix adding its forces. Default is the outermost level.
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This fix computes a global scalar and a global 3-vector of forces,
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This fix computes a global scalar and a global 3-vector of forces,
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which can be accessed by various :doc:`output commands <Howto_output>`.
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which can be accessed by various :doc:`output commands <Howto_output>`.
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The scalar is the potential energy discussed above.
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The scalar is the potential energy discussed above.
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The vector is the total force added to the group of atoms.
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The vector is the total force added to the group of atoms.
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The scalar and vector values calculated by this fix are "extensive".
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The scalar and vector values calculated by this fix are "extensive".
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This fix cannot be used with the *start/stop* keywords of
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This fix cannot be used with the *start/stop* keywords of
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@ -123,7 +123,7 @@ the iteration count during the minimization.
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Restrictions
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Restrictions
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""""""""""""
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""""""""""""
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Fix style *epot/lepton* is part of the LEPTON package. It is only enabled if LAMMPS was built with that package.
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Fix style *epot/lepton* is part of the LEPTON package. It is only enabled if LAMMPS was built with that package.
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See the :doc:`Build package <Build_package>` page for more info.
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See the :doc:`Build package <Build_package>` page for more info.
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@ -76,7 +76,7 @@ FixEpotLepton::FixEpotLepton(LAMMPS *lmp, int narg, char **arg) :
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error->all(FLERR, "Unknown keyword for fix {} command: {}", style, arg[iarg]);
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error->all(FLERR, "Unknown keyword for fix {} command: {}", style, arg[iarg]);
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}
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}
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}
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}
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// check validity of Lepton expression
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// check validity of Lepton expression
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// remove whitespace and quotes from expression string and then
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// remove whitespace and quotes from expression string and then
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// check if the expression can be parsed without error
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// check if the expression can be parsed without error
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@ -277,7 +277,7 @@ void FixEpotLepton::post_force(int vflag)
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// force = (mu dot D) E
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// force = (mu dot D) E
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// using central difference method
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// using central difference method
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h_mu = h / mu_norm;
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h_mu = h / mu_norm;
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xf = unwrap[0] + h_mu * mu[i][0];
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xf = unwrap[0] + h_mu * mu[i][0];
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yf = unwrap[1] + h_mu * mu[i][1];
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yf = unwrap[1] + h_mu * mu[i][1];
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zf = unwrap[2] + h_mu * mu[i][2];
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zf = unwrap[2] + h_mu * mu[i][2];
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@ -378,7 +378,7 @@ void FixEpotLepton::post_force(int vflag)
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for (int i = 0; i < nlocal; i++) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (mask[i] & groupbit) {
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if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
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if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
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mu_norm = sqrt(mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2]);
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mu_norm = sqrt(mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2]);
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if (mu_norm > EPSILON) continue;
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if (mu_norm > EPSILON) continue;
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@ -403,7 +403,7 @@ void FixEpotLepton::post_force(int vflag)
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// force = (mu dot D) E
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// force = (mu dot D) E
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// using central difference method
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// using central difference method
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h_mu = h / sqrt(mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2]);
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h_mu = h / sqrt(mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2]);
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xf = unwrap[0] + h_mu * mu[i][0];
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xf = unwrap[0] + h_mu * mu[i][0];
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yf = unwrap[1] + h_mu * mu[i][1];
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yf = unwrap[1] + h_mu * mu[i][1];
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zf = unwrap[2] + h_mu * mu[i][2];
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zf = unwrap[2] + h_mu * mu[i][2];
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@ -453,7 +453,7 @@ void FixEpotLepton::post_force(int vflag)
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}
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}
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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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void FixEpotLepton::post_force_respa(int vflag, int ilevel, int /*iloop*/)
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void FixEpotLepton::post_force_respa(int vflag, int ilevel, int /*iloop*/)
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