mwlc angle potential

src/.gitignore

@@ -505,6 +505,8 @@
 /angle_harmonic.h
 /angle_mm3.cpp
 /angle_mm3.h
+/angle_mwlc.cpp
+/angle_mwlc.h
 /angle_quartic.cpp
 /angle_quartic.h
 /angle_spica.cpp

src/EXTRA-MOLECULE/angle_mwlc.cpp

@@ -0,0 +1,311 @@
+/* ----------------------------------------------------------------------
+   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: James D. Farrell (IoP CAS)
+   [ based on angle_cosine.cpp ]
+------------------------------------------------------------------------- */
+
+#include "angle_mwlc.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
+#include "math_const.h"
+#include "memory.h"
+#include "neighbor.h"
+
+#include <cmath>
+#include <cstring>
+
+using namespace LAMMPS_NS;
+using MathConst::MY_PI;
+
+/* ---------------------------------------------------------------------- */
+
+AngleMWLC::AngleMWLC(LAMMPS *_lmp) : Angle(_lmp)
+{
+  born_matrix_enable = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+AngleMWLC::~AngleMWLC()
+{
+  if (allocated && !copymode) {
+    memory->destroy(setflag);
+    memory->destroy(k1);
+    memory->destroy(k2);
+    memory->destroy(mu);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AngleMWLC::compute(int eflag, int vflag)
+{
+  int i1, i2, i3, n, type;
+  double delx1, dely1, delz1, delx2, dely2, delz2;
+  double eangle, f1[3], f3[3];
+  double rsq1, rsq2, r1, r2, c, a, a11, a12, a22;
+  double q, qm, Q;
+
+  eangle = 0.0;
+  ev_init(eflag, vflag);
+
+  double **x = atom->x;
+  double **f = atom->f;
+  int **anglelist = neighbor->anglelist;
+  int nanglelist = neighbor->nanglelist;
+  int nlocal = atom->nlocal;
+  int newton_bond = force->newton_bond;
+
+  for (n = 0; n < nanglelist; n++) {
+    i1 = anglelist[n][0];
+    i2 = anglelist[n][1];
+    i3 = anglelist[n][2];
+    type = anglelist[n][3];
+
+    // 1st bond
+
+    delx1 = x[i1][0] - x[i2][0];
+    dely1 = x[i1][1] - x[i2][1];
+    delz1 = x[i1][2] - x[i2][2];
+
+    rsq1 = delx1 * delx1 + dely1 * dely1 + delz1 * delz1;
+    r1 = sqrt(rsq1);
+
+    // 2nd bond
+
+    delx2 = x[i3][0] - x[i2][0];
+    dely2 = x[i3][1] - x[i2][1];
+    delz2 = x[i3][2] - x[i2][2];
+
+    rsq2 = delx2 * delx2 + dely2 * dely2 + delz2 * delz2;
+    r2 = sqrt(rsq2);
+
+    // c = cosine of angle
+
+    c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
+    c /= r1 * r2;
+    if (c > 1.0) c = 1.0;
+    if (c < -1.0) c = -1.0;
+
+    // force & energy
+
+    q = exp(-k1[type] * (1.0 + c));
+    qm = exp(-k2[type] * (1.0 + c) - mu[type]);
+    Q = q + qm;
+
+    if (eflag) eangle = -log(Q);
+
+    a = (k1[type] * q + k2[type] * qm) / Q;
+    a11 = a * c / rsq1;
+    a12 = -a / (r1 * r2);
+    a22 = a * c / rsq2;
+
+    f1[0] = a11 * delx1 + a12 * delx2;
+    f1[1] = a11 * dely1 + a12 * dely2;
+    f1[2] = a11 * delz1 + a12 * delz2;
+    f3[0] = a22 * delx2 + a12 * delx1;
+    f3[1] = a22 * dely2 + a12 * dely1;
+    f3[2] = a22 * delz2 + a12 * delz1;
+
+    // apply force to each of 3 atoms
+
+    if (newton_bond || i1 < nlocal) {
+      f[i1][0] += f1[0];
+      f[i1][1] += f1[1];
+      f[i1][2] += f1[2];
+    }
+
+    if (newton_bond || i2 < nlocal) {
+      f[i2][0] -= f1[0] + f3[0];
+      f[i2][1] -= f1[1] + f3[1];
+      f[i2][2] -= f1[2] + f3[2];
+    }
+
+    if (newton_bond || i3 < nlocal) {
+      f[i3][0] += f3[0];
+      f[i3][1] += f3[1];
+      f[i3][2] += f3[2];
+    }
+
+    if (evflag)
+      ev_tally(i1, i2, i3, nlocal, newton_bond, eangle, f1, f3, delx1, dely1, delz1, delx2, dely2,
+               delz2);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AngleMWLC::allocate()
+{
+  allocated = 1;
+  const int np1 = atom->nangletypes + 1;
+
+  memory->create(k1, np1, "angle:k1");
+  memory->create(k2, np1, "angle:k2");
+  memory->create(mu, np1, "angle:mu");
+  memory->create(setflag, np1, "angle:setflag");
+  for (int i = 1; i < np1; i++) setflag[i] = 0;
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one type
+------------------------------------------------------------------------- */
+
+void AngleMWLC::coeff(int narg, char **arg)
+{
+  if (narg != 4) error->all(FLERR, "Incorrect args for angle coefficients");
+  if (!allocated) allocate();
+
+  int ilo, ihi;
+  utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error);
+
+  double k1_one = utils::numeric(FLERR, arg[1], false, lmp);
+  double k2_one = utils::numeric(FLERR, arg[2], false, lmp);
+  double mu_one = utils::numeric(FLERR, arg[3], false, lmp);
+
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    k1[i] = k1_one;
+    k2[i] = k2_one;
+    mu[i] = mu_one;
+    setflag[i] = 1;
+    count++;
+  }
+
+  if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients");
+}
+
+/* ---------------------------------------------------------------------- */
+
+double AngleMWLC::equilibrium_angle(int /*i*/)
+{
+  return MY_PI;
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes out coeffs to restart file
+------------------------------------------------------------------------- */
+
+void AngleMWLC::write_restart(FILE *fp)
+{
+  fwrite(&k1[1], sizeof(double), atom->nangletypes, fp);
+  fwrite(&k2[1], sizeof(double), atom->nangletypes, fp);
+  fwrite(&mu[1], sizeof(double), atom->nangletypes, fp);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads coeffs from restart file, bcasts them
+------------------------------------------------------------------------- */
+
+void AngleMWLC::read_restart(FILE *fp)
+{
+  allocate();
+
+  if (comm->me == 0) {
+    utils::sfread(FLERR, &k1[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
+    utils::sfread(FLERR, &k2[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
+    utils::sfread(FLERR, &mu[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
+  }
+  MPI_Bcast(&k1[1], atom->nangletypes, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&k2[1], atom->nangletypes, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&mu[1], atom->nangletypes, MPI_DOUBLE, 0, world);
+
+  for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void AngleMWLC::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->nangletypes; i++) fprintf(fp, "%d %g %g %g\n", i, k1[i], k2[i], mu[i]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double AngleMWLC::single(int type, int i1, int i2, int i3)
+{
+  double **x = atom->x;
+
+  double delx1 = x[i1][0] - x[i2][0];
+  double dely1 = x[i1][1] - x[i2][1];
+  double delz1 = x[i1][2] - x[i2][2];
+  domain->minimum_image(delx1, dely1, delz1);
+  double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);
+
+  double delx2 = x[i3][0] - x[i2][0];
+  double dely2 = x[i3][1] - x[i2][1];
+  double delz2 = x[i3][2] - x[i2][2];
+  domain->minimum_image(delx2, dely2, delz2);
+  double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
+
+  double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
+  c /= r1 * r2;
+  if (c > 1.0) c = 1.0;
+  if (c < -1.0) c = -1.0;
+
+  double q = exp(-k1[type] * (1.0 + c));
+  double qm = exp(-k2[type] * (1.0 + c) - mu[type]);
+  return -log(q + qm);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AngleMWLC::born_matrix(int type, int i1, int i2, int i3, double &du, double &du2)
+{
+  double **x = atom->x;
+
+  double delx1 = x[i1][0] - x[i2][0];
+  double dely1 = x[i1][1] - x[i2][1];
+  double delz1 = x[i1][2] - x[i2][2];
+  domain->minimum_image(delx1, dely1, delz1);
+
+  double delx2 = x[i3][0] - x[i2][0];
+  double dely2 = x[i3][1] - x[i2][1];
+  double delz2 = x[i3][2] - x[i2][2];
+  domain->minimum_image(delx2, dely2, delz2);
+
+  double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
+  c /= sqrt((delx1 * delx1 + dely1 * dely1 + delz1 * delz1) *
+            (delx2 * delx2 + dely2 * dely2 + delz2 * delz2));
+  if (c > 1.0) c = 1.0;
+  if (c < -1.0) c = -1.0;
+
+  const double q = exp(-k1[type] * (1.0 + c));
+  const double qm = exp(-k2[type] * (1.0 + c) - mu[type]);
+  const double Q = q + qm;
+
+  du = (k1[type] * q + k2[type] * qm) / Q;
+  du2 = (k1[type] - k2[type]) / Q;
+  du2 *= -du2 * q * qm;
+}
+
+/* ----------------------------------------------------------------------
+   return ptr to internal members upon request
+------------------------------------------------------------------------ */
+
+void *AngleMWLC::extract(const char *str, int &dim)
+{
+  dim = 1;
+  if (strcmp(str, "k1") == 0) return (void *) k1;
+  if (strcmp(str, "k2") == 0) return (void *) k2;
+  if (strcmp(str, "mu") == 0) return (void *) mu;
+  return nullptr;
+}

src/EXTRA-MOLECULE/angle_mwlc.h

@@ -0,0 +1,52 @@
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+#ifdef ANGLE_CLASS
+// clang-format off
+AngleStyle(mwlc,AngleMWLC);
+// clang-format on
+#else
+
+#ifndef LMP_ANGLE_MWLC_H
+#define LMP_ANGLE_MWLC_H
+
+#include "angle.h"
+
+namespace LAMMPS_NS {
+
+    class AngleMWLC : public Angle {
+    public:
+        AngleMWLC(class LAMMPS *);
+        ~AngleMWLC() override;
+        void compute(int, int) override;
+        void coeff(int, char **) override;
+        double equilibrium_angle(int) override;
+        void write_restart(FILE *) override;
+        void read_restart(FILE *) override;
+        void write_data(FILE *) override;
+        double single(int, int, int, int) override;
+        void born_matrix(int type, int i1, int i2, int i3, double &du, double &du2) override;
+        void *extract(const char *, int &) override;
+
+    protected:
+        double *k1;
+        double *k2;
+        double *mu;
+
+        virtual void allocate();
+    };
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif