mirror of https://github.com/lammps/lammps.git
expand valid range of bond/angle style gaussian. update docs and tests.
This commit is contained in:
Axel Kohlmeyer
parent
23025316c9
commit
a098b16030
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@ -27,8 +27,10 @@ The *gaussian* angle style uses the potential:
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E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-2(\theta-\theta_{i})^2}{w_i^2}\right) \right)
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This analytical form is a suitable potential for obtaining
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mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano1>`
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This analytical form is a suitable potential for obtaining mesoscale
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effective force fields which can reproduce target atomistic
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distributions :ref:`(Milano) <Milano1>`.
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The following coefficients must be defined for each angle type via the
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:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
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the data file or restart files read by the :doc:`read_data <read_data>`
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@ -36,12 +38,12 @@ or :doc:`read_restart <read_restart>` commands:
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* :math:`T` temperature at which the potential was derived
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* :math:`n` (integer >=1)
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* :math:`A_1` (-)
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* :math:`w_1` (-)
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* :math:`A_1` (> 0, radians)
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* :math:`w_1` (> 0, radians)
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* :math:`\theta_1` (degrees)
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* ...
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* :math:`A_n` (-)
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* :math:`w_n` (-)
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* :math:`A_n` (> 0, radians)
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* :math:`w_n` (> 0, radians)
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* :math:`\theta_n` (degrees)
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@ -27,8 +27,9 @@ The *gaussian* bond style uses the potential:
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E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-2(r-r_{i})^2}{w_i^2}\right)\right)
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This analytical form is a suitable potential for obtaining
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mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano0>`
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This analytical form is a suitable potential for obtaining mesoscale
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effective force fields which can reproduce target atomistic
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distributions :ref:`(Milano) <Milano0>`
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The following coefficients must be defined for each bond type via the
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:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
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@ -37,21 +38,21 @@ or :doc:`read_restart <read_restart>` commands:
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* :math:`T` temperature at which the potential was derived
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* :math:`n` (integer >=1)
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* :math:`A_1` (-)
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* :math:`w_1` (-)
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* :math:`r_1` (length)
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* :math:`A_1` (> 0, distance)
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* :math:`w_1` (> 0, distance)
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* :math:`r_1` (>= 0, distance)
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* ...
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* :math:`A_n` (-)
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* :math:`w_n` (-)
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* :math:`r_n` (length)
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* :math:`A_n` (> 0, distance)
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* :math:`w_n` (> 0, distance)
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* :math:`r_n` (>= 0, distance)
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Restrictions
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""""""""""""
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This bond style can only be used if LAMMPS was built with the
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EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc
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page for more info.
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EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>`
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doc page for more info.
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Related commands
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""""""""""""""""
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@ -28,8 +28,8 @@
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using namespace LAMMPS_NS;
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using namespace MathConst;
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#define SMAL 0.001
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#define SMALL 1.0e-8
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static constexpr double SMALL = 0.001;
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static constexpr double SMALLG = 2.0e-308;
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/* ---------------------------------------------------------------------- */
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@ -112,7 +112,7 @@ void AngleGaussian::compute(int eflag, int vflag)
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if (c < -1.0) c = -1.0;
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s = sqrt(1.0 - c * c);
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if (s < SMAL) s = SMAL;
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if (s < SMALL) s = SMALL;
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s = 1.0 / s;
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// force & energy
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@ -123,13 +123,15 @@ void AngleGaussian::compute(int eflag, int vflag)
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for (int i = 0; i < nterms[type]; i++) {
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dtheta = theta - theta0[type][i];
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prefactor = (alpha[type][i] / (width[type][i] * sqrt(MY_PI2)));
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exponent = -2 * dtheta * dtheta / (width[type][i] * width[type][i]);
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exponent = -2.0 * dtheta * dtheta / (width[type][i] * width[type][i]);
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g_i = prefactor * exp(exponent);
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sum_g_i += g_i;
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sum_numerator += g_i * dtheta / (width[type][i] * width[type][i]);
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}
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if (sum_g_i < SMALL) sum_g_i = SMALL;
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// avoid overflow
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if (sum_g_i < sum_numerator * SMALLG) sum_g_i = sum_numerator * SMALLG;
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if (eflag) eangle = -(force->boltz * angle_temperature[type]) * log(sum_g_i);
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// I should check about the sign of this expression
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@ -198,14 +200,16 @@ void AngleGaussian::allocate()
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void AngleGaussian::coeff(int narg, char **arg)
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{
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if (narg < 6) error->all(FLERR, "Incorrect args for angle coefficients");
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if (narg < 6) utils::missing_cmd_args(FLERR, "angle_coeff", error);
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int ilo, ihi;
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utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error);
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double angle_temperature_one = utils::numeric(FLERR, arg[1], false, lmp);
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int n = utils::inumeric(FLERR, arg[2], false, lmp);
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if (narg != 3 * n + 3) error->all(FLERR, "Incorrect args for angle coefficients");
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if (n < 1) error->all(FLERR, "Invalid angle style gaussian value for n: {}", n);
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if (narg != 3 * n + 3) utils::missing_cmd_args(FLERR, "angle_coeff", error);
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if (!allocated) allocate();
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@ -223,7 +227,9 @@ void AngleGaussian::coeff(int narg, char **arg)
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theta0[i] = new double[n];
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for (int j = 0; j < n; j++) {
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alpha[i][j] = utils::numeric(FLERR, arg[3 + 3 * j], false, lmp);
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if (alpha[i][j] <= 0.0) error->all(FLERR, "Invalid value for A_{}: {}", j, alpha[i][j]);
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width[i][j] = utils::numeric(FLERR, arg[4 + 3 * j], false, lmp);
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if (width[i][j] <= 0.0) error->all(FLERR, "Invalid value for w_{}: {}", j, width[i][j]);
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theta0[i][j] = utils::numeric(FLERR, arg[5 + 3 * j], false, lmp) * MY_PI / 180.0;
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setflag[i] = 1;
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}
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@ -27,7 +27,7 @@
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using namespace LAMMPS_NS;
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using namespace MathConst;
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#define SMALL 1.0e-10
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static constexpr double SMALL = 2.0e-308;
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/* ---------------------------------------------------------------------- */
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@ -92,15 +92,16 @@ void BondGaussian::compute(int eflag, int vflag)
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for (int i = 0; i < nterms[type]; i++) {
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dr = r - r0[type][i];
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prefactor = (alpha[type][i] / (width[type][i] * sqrt(MY_PI2)));
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exponent = -2 * dr * dr / (width[type][i] * width[type][i]);
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exponent = -2.0 * dr * dr / (width[type][i] * width[type][i]);
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g_i = prefactor * exp(exponent);
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sum_g_i += g_i;
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sum_numerator += g_i * dr / (width[type][i] * width[type][i]);
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}
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// force & energy
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if (sum_g_i < SMALL) sum_g_i = SMALL;
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// avoid overflow
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if (sum_g_i < sum_numerator * SMALL) sum_g_i = sum_numerator * SMALL;
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// force & energy
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if (r > 0.0)
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fbond = -4.0 * (force->boltz * bond_temperature[type]) * (sum_numerator / sum_g_i) / r;
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else
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@ -153,14 +154,15 @@ void BondGaussian::allocate()
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void BondGaussian::coeff(int narg, char **arg)
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{
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if (narg < 6) error->all(FLERR, "Incorrect args for bond coefficients");
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if (narg < 6) utils::missing_cmd_args(FLERR, "bond_coeff", error);
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int ilo, ihi;
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utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
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double bond_temp_one = utils::numeric(FLERR, arg[1], false, lmp);
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int n = utils::inumeric(FLERR, arg[2], false, lmp);
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if (narg != 3 * n + 3) error->all(FLERR, "Incorrect args for bond coefficients");
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if (n < 1) error->all(FLERR, "Invalid bond style gaussian value for n: {}", n);
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if (narg != 3 * n + 3) utils::missing_cmd_args(FLERR, "bond_coeff", error);
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if (!allocated) allocate();
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@ -176,8 +178,11 @@ void BondGaussian::coeff(int narg, char **arg)
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r0[i] = new double[n];
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for (int j = 0; j < n; j++) {
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alpha[i][j] = utils::numeric(FLERR, arg[3 + 3 * j], false, lmp);
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if (alpha[i][j] <= 0.0) error->all(FLERR, "Invalid value for A_{}: {}", j, alpha[i][j]);
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width[i][j] = utils::numeric(FLERR, arg[4 + 3 * j], false, lmp);
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if (width[i][j] <= 0.0) error->all(FLERR, "Invalid value for w_{}: {}", j, width[i][j]);
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r0[i][j] = utils::numeric(FLERR, arg[5 + 3 * j], false, lmp);
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if (r0[i][j] <= 0.0) error->all(FLERR, "Invalid value for r0_{}: {}", j, r0[i][j]);
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setflag[i] = 1;
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}
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count++;
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@ -1,6 +1,7 @@
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---
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lammps_version: 17 Feb 2022
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date_generated: Fri Mar 18 22:17:50 2022
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lammps_version: 3 Nov 2022
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tags: generated
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date_generated: Mon Nov 21 21:52:14 2022
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epsilon: 1e-12
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skip_tests:
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prerequisites: ! |
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@ -19,70 +20,70 @@ bond_coeff: ! |
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equilibrium: 5 1.45 1.37 1.61 2.45 2.85
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extract: ! ""
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natoms: 29
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init_energy: 194.9780382216324
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init_stress: ! |-
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-2.4024989684355553e+01 -3.8521513996632500e+01 -1.0851224048428129e+01 1.2562604359180053e+01 1.3677283516797356e+01 4.3206731051245653e+00
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init_energy: 4638.6541482649545
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init_stress: ! |2-
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1.8359565872923367e+03 1.1685750963854580e+03 2.2772768476286187e+03 9.0129794950892881e+02 4.5431504423505157e+02 5.8087298633263757e+01
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init_forces: ! |2
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1 -1.7791337913398690e+00 -5.2745532425491986e+00 -1.9333096530222391e+00
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2 7.8999913149794128e-293 6.5010830500033665e-293 -9.2980646648301405e-293
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1 -2.6166538657523114e+02 -2.1914087860149658e+02 3.0394540432772982e+02
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2 2.5988625278389128e+02 2.1386632535894739e+02 -3.0587871398075208e+02
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3 2.4197086198752562e+01 -1.2911571268065043e+01 -1.2153319969868038e+01
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4 -3.5002110421521651e+00 9.8124800657318079e-01 -2.4834895420880554e+00
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5 -8.7934593181833831e-01 -1.3513167937313169e+00 4.4900533574430685e+00
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6 -1.9224405194016612e+01 1.9525383982308810e+01 1.1251608936919853e+01
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7 2.6580140740726381e-131 -1.3633763941647238e-130 -6.8018769495047054e-130
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8 1.4462104594211977e+00 -1.2568711136582216e+00 7.3991622652588918e-01
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9 1.2099652614352605e-300 1.3032068217192395e-300 5.3545155818429412e-300
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6 -3.1076039081690663e+01 8.0316024755627467e+01 3.1453576435533836e+02
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7 1.1851633887674051e+01 -6.0790640773318657e+01 -3.0328415541841849e+02
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8 -9.7268051920198786e+01 -1.0757818812527627e+02 -4.3610490313202450e+02
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9 9.8714262379619981e+01 1.0632131701161805e+02 4.3684481935855041e+02
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10 1.8282673669124623e+01 -6.7893037436650294e-01 1.0475143579619905e+01
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11 -9.5181855408160265e-01 -2.3577388099405021e+00 -3.8685744266264179e+00
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12 -1.1761121482537199e+01 -1.1840691118605761e+01 8.9587696830512531e+00
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13 3.9348879648968196e+00 -1.5566010373601853e+00 -7.3956496855403397e-02
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14 -1.5580348688551586e+00 3.1703943744370217e-01 -4.0404862787928506e+00
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15 -1.0483110905921594e-01 4.0280962447539723e+00 1.4354708657826634e+00
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16 -8.1019563183350432e+00 1.2376506087197068e+01 -1.2797826282089627e+01
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17 -9.6845722000297944e-125 6.7536031200741501e-125 2.5693469616608658e-124
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18 5.0042083741224387e-291 3.2014176819490257e-291 6.0624670892900674e-291
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19 -5.0042167517970120e-291 -3.2014265949545701e-291 -6.0624614384187022e-291
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20 8.3776745733654894e-297 8.9130055442585484e-297 -5.6508713648842736e-297
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21 5.0373663727594610e-296 1.1676684296048456e-296 8.1823232295641435e-296
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22 -5.1857245273845906e-296 -1.2567112623130275e-296 -8.1358238807042024e-296
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23 1.4835815462512912e-297 8.9042832708182009e-298 -4.6499348859940937e-298
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24 6.5124799547612842e-295 -1.0579059065054233e-295 5.4786730014873485e-295
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25 -6.5176382072810523e-295 1.0492453069148130e-295 -5.4792561056911984e-295
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26 5.1582525197680877e-298 8.6605995906103569e-298 5.8310420384964103e-299
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27 -1.5677247388593395e-295 -1.8232011058192963e-295 -3.8038051984576450e-296
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28 -3.2483754529644398e-299 1.3960035208884715e-299 -2.1978823514938368e-299
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29 1.5680495764046360e-295 1.8230615054672073e-295 3.8060030808091389e-296
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run_energy: 194.9688901668597
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run_stress: ! |-
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-2.4084235648269384e+01 -3.8596877573973650e+01 -1.0971337511117875e+01 1.2627485208541385e+01 1.3589007837800324e+01 4.4518443361436777e+00
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16 9.5774980977037984e+01 -6.0062791522626100e+01 -2.8838655412045694e+02
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17 -1.0387693729537303e+02 7.2439297609823171e+01 2.7558872783836733e+02
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18 -1.7290589161548496e+01 -1.3179016873564919e+02 5.1586854877010114e+02
|
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19 -2.6734331696703003e+02 -1.7103176128697325e+02 -3.2387856688053216e+02
|
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20 2.8463390612857853e+02 3.0282193002262244e+02 -1.9198998188956895e+02
|
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21 -1.3595471277589198e+02 -1.6879175531311859e+02 5.0125731248385966e+02
|
||||
22 -2.4366036541914886e+02 -5.9048783595141884e+01 -3.8227595956741493e+02
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23 3.7961507819504084e+02 2.2784053890826047e+02 -1.1898135291644472e+02
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||||
24 1.1246873070738241e+02 -4.4920523111996721e+02 2.6503426336875481e+02
|
||||
25 -3.4676635177604459e+02 5.5824357785083230e+01 -2.9151996318153743e+02
|
||||
26 2.3429762106866218e+02 3.9338087333488397e+02 2.6485699812782624e+01
|
||||
27 6.4413473322621542e+01 -4.9624245043025996e+02 1.7125457908457409e+02
|
||||
28 -3.5866433728099020e+02 1.5413756350253817e+02 -2.4267577083822729e+02
|
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29 2.9425086395836865e+02 3.4210488692772179e+02 7.1421191753653204e+01
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run_energy: 4618.705952125554
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run_stress: ! |2-
|
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1.8397902589595653e+03 1.1724487863122602e+03 2.2782759319716897e+03 9.0366417527896033e+02 4.5574598799336053e+02 5.9672689485998390e+01
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run_forces: ! |2
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1 -1.7800915383536471e+00 -5.2662174638478936e+00 -1.9311810441446928e+00
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2 9.1200716389742962e-293 7.5205784896271243e-293 -1.0695855329374170e-292
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||||
3 2.4188774318819682e+01 -1.2910730800434983e+01 -1.2139174094227805e+01
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||||
4 -3.4905807721708837e+00 9.7423802985974728e-01 -2.4827066691937869e+00
|
||||
5 -8.7826414385513407e-01 -1.3507945719900971e+00 4.4847167409249762e+00
|
||||
6 -1.9198711248640532e+01 1.9501343007070176e+01 1.1259539605043198e+01
|
||||
7 4.0781500460380220e-131 -2.0934766207882755e-130 -1.0411772151605081e-129
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||||
8 1.4035232720380466e+00 -1.2181526258990241e+00 7.2552718656771575e-01
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||||
9 1.4877356608185432e-300 1.5947265521745610e-300 6.5759628249586203e-300
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||||
10 1.8340705485218969e+01 -7.9602516938863732e-01 1.0533434146468263e+01
|
||||
11 -9.4713695434855716e-01 -2.3455928036230933e+00 -3.8477133980837270e+00
|
||||
12 -1.1753841378581289e+01 -1.1839528950721563e+01 8.9356024501072664e+00
|
||||
13 3.9289793641831325e+00 -1.5460483921060724e+00 -7.3078087497547045e-02
|
||||
14 -1.5515717239320088e+00 3.1019421574866657e-01 -4.0233193667488729e+00
|
||||
15 -1.1312732638809736e-01 4.0290637402465492e+00 1.4439547691915919e+00
|
||||
16 -8.1486573539896803e+00 1.2458251785086224e+01 -1.2885602238406578e+01
|
||||
17 -8.5522515805489358e-125 5.9749160301406998e-125 2.2702237597406565e-124
|
||||
18 2.5382954259673697e-291 1.6282298856292719e-291 3.0672317979786876e-291
|
||||
19 -2.5383561239391082e-291 -1.6282944740463789e-291 -3.0671910793881731e-291
|
||||
20 6.0697971738423079e-296 6.4588417107197222e-296 -4.0718590514496707e-296
|
||||
21 3.1636825215784415e-296 7.4502521705718285e-297 5.0914419661316058e-296
|
||||
22 -3.2413538119513539e-296 -7.9143971383319095e-297 -5.0672219270657353e-296
|
||||
23 7.7671290372912634e-298 4.6414496776008138e-298 -2.4220039065870281e-298
|
||||
24 1.1528889554480086e-295 -1.8584672369333140e-296 9.7061626349018667e-296
|
||||
25 -1.1544439355951613e-295 1.8323577266329387e-296 -9.7079719071127095e-296
|
||||
26 1.5549801471527681e-298 2.6109510300375245e-298 1.8092722108425850e-299
|
||||
27 -1.0502291554946705e-295 -1.2226612584790533e-295 -2.5738911540368265e-296
|
||||
28 -1.8342692926757559e-299 7.8715078988712594e-300 -1.2385711775450889e-299
|
||||
29 1.0504125824239381e-295 1.2225825434000646e-295 2.5751297252143716e-296
|
||||
1 -2.6123247146110606e+02 -2.1919307263372883e+02 3.0237555508171170e+02
|
||||
2 2.5946481985769248e+02 2.1395800468042034e+02 -3.0429922592566089e+02
|
||||
3 2.4104808395110172e+01 -1.2865854073142392e+01 -1.2083882913387207e+01
|
||||
4 -3.4905809559903060e+00 9.7423804418107429e-01 -2.4827069981835161e+00
|
||||
5 -8.7826407777385485e-01 -1.3507948021059526e+00 4.4847171151687837e+00
|
||||
6 -3.1019740486745086e+01 8.0315470917380424e+01 3.1385270827879697e+02
|
||||
7 1.1855512952124167e+01 -6.0859047439602143e+01 -3.0267942216207678e+02
|
||||
8 -9.7139239668224732e+01 -1.0689115264867354e+02 -4.3492337910287688e+02
|
||||
9 9.8566534070284817e+01 1.0565669621976006e+02 4.3567718006870649e+02
|
||||
10 1.8332862345492853e+01 -7.7546447474524260e-01 1.0479498854248916e+01
|
||||
11 -9.4713700870724160e-01 -2.3455930111707550e+00 -3.8477135785159731e+00
|
||||
12 -1.1753839309353248e+01 -1.1839526860590677e+01 8.9356008317611710e+00
|
||||
13 3.9289793641852362e+00 -1.5460483921084245e+00 -7.3078087496756511e-02
|
||||
14 -1.5515717239340792e+00 3.1019421574772799e-01 -4.0233193667504690e+00
|
||||
15 -1.1312732638930625e-01 4.0290637402491614e+00 1.4439547691937924e+00
|
||||
16 9.5584985328403420e+01 -6.0034377008082046e+01 -2.8814471939578698e+02
|
||||
17 -1.0371253029506924e+02 7.2457263526211193e+01 2.7530823253114755e+02
|
||||
18 -1.6734173006461219e+01 -1.3081888486925550e+02 5.1373496074962804e+02
|
||||
19 -2.6689091522155491e+02 -1.7109178558868115e+02 -3.2299073527643651e+02
|
||||
20 2.8362508822801612e+02 3.0191067045793665e+02 -1.9074422547319156e+02
|
||||
21 -1.3584009311603779e+02 -1.6741847021957338e+02 4.9993505971275158e+02
|
||||
22 -2.4342958636297089e+02 -5.9309435913166546e+01 -3.8123078015208006e+02
|
||||
23 3.7926967947900869e+02 2.2672790613273992e+02 -1.1870427956067151e+02
|
||||
24 1.1263526323552287e+02 -4.4826736307529882e+02 2.6440276469069875e+02
|
||||
25 -3.4626849198042515e+02 5.5368312528579615e+01 -2.9134479497708327e+02
|
||||
26 2.3363322874490228e+02 3.9289905054671920e+02 2.6942030286384533e+01
|
||||
27 6.4905554146281361e+01 -4.9580198077236491e+02 1.7016719858461872e+02
|
||||
28 -3.5803172302507875e+02 1.5409360889763499e+02 -2.4188045098816568e+02
|
||||
29 2.9312616887879739e+02 3.4170837187472995e+02 7.1713252403546960e+01
|
||||
...
|
||||
|
|
|
|||
Loading…
Reference in New Issue