516 lines
19 KiB
C++
516 lines
19 KiB
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: Axel Kohlmeyer (Temple U)
|
|
Using parts of dihedral_table.cpp by Andrew Jewett (jewett.aij at gmail)
|
|
------------------------------------------------------------------------- */
|
|
|
|
#include "dihedral_lepton.h"
|
|
|
|
#include "atom.h"
|
|
#include "comm.h"
|
|
#include "domain.h"
|
|
#include "error.h"
|
|
#include "force.h"
|
|
#include "math_const.h"
|
|
#include "math_extra.h"
|
|
#include "memory.h"
|
|
#include "neighbor.h"
|
|
|
|
#include <cmath>
|
|
|
|
#include "Lepton.h"
|
|
#include "lepton_utils.h"
|
|
|
|
using namespace LAMMPS_NS;
|
|
using MathConst::DEG2RAD;
|
|
using MathConst::MY_2PI;
|
|
using MathConst::RAD2DEG;
|
|
using MathExtra::cross3;
|
|
using MathExtra::dot3;
|
|
using MathExtra::norm3;
|
|
|
|
static constexpr int g_dim = 3;
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
DihedralLepton::DihedralLepton(LAMMPS *_lmp) : Dihedral(_lmp), type2expression(nullptr)
|
|
{
|
|
writedata = 1;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
DihedralLepton::~DihedralLepton()
|
|
{
|
|
if (allocated) {
|
|
memory->destroy(setflag);
|
|
memory->destroy(type2expression);
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void DihedralLepton::compute(int eflag, int vflag)
|
|
{
|
|
ev_init(eflag, vflag);
|
|
ev_init(eflag, vflag);
|
|
if (evflag) {
|
|
if (eflag) {
|
|
if (force->newton_bond)
|
|
eval<1, 1, 1>();
|
|
else
|
|
eval<1, 1, 0>();
|
|
} else {
|
|
if (force->newton_bond)
|
|
eval<1, 0, 1>();
|
|
else
|
|
eval<1, 0, 0>();
|
|
}
|
|
} else {
|
|
if (force->newton_bond)
|
|
eval<0, 0, 1>();
|
|
else
|
|
eval<0, 0, 0>();
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
template <int EVFLAG, int EFLAG, int NEWTON_BOND> void DihedralLepton::eval()
|
|
{
|
|
std::vector<Lepton::CompiledExpression> dihedralforce;
|
|
std::vector<Lepton::CompiledExpression> dihedralpot;
|
|
try {
|
|
for (const auto &expr : expressions) {
|
|
auto parsed = Lepton::Parser::parse(LeptonUtils::substitute(expr, lmp));
|
|
dihedralforce.emplace_back(parsed.differentiate("phi").createCompiledExpression());
|
|
if (EFLAG) dihedralpot.emplace_back(parsed.createCompiledExpression());
|
|
}
|
|
} catch (std::exception &e) {
|
|
error->all(FLERR, e.what());
|
|
}
|
|
|
|
const double *const *const x = atom->x;
|
|
double *const *const f = atom->f;
|
|
const int *const *const dihedrallist = neighbor->dihedrallist;
|
|
const int ndihedrallist = neighbor->ndihedrallist;
|
|
const int nlocal = atom->nlocal;
|
|
|
|
// The dihedral angle "phi" is the angle between n123 and n234
|
|
// the planes defined by atoms i1,i2,i3, and i2,i3,i4.
|
|
//
|
|
// Definitions of vectors: vb12, vb23, vb34, perp12on23
|
|
// proj12on23, perp43on32, proj43on32
|
|
//
|
|
// Note: The positions of the 4 atoms are labeled x[i1], x[i2], x[i3], x[i4]
|
|
// (which are also vectors)
|
|
//
|
|
// proj12on23 proj34on23
|
|
// ---------> ----------->
|
|
// .
|
|
// .
|
|
// .
|
|
// x[i2] . x[i3]
|
|
// . __@----------vb23-------->@ . . . . .
|
|
// /|\ /| \ |
|
|
// | / \ |
|
|
// | / \ |
|
|
// perp12vs23 / \ |
|
|
// | / \ perp34vs23
|
|
// | vb12 \ |
|
|
// | / vb34 |
|
|
// | / \ |
|
|
// | / \ |
|
|
// | / \ |
|
|
// @ \ |
|
|
// _\| \|/
|
|
// x[i1] @
|
|
//
|
|
// x[i4]
|
|
//
|
|
|
|
double vb12[g_dim]; // displacement vector from atom i1 towards atom i2
|
|
// vb12[d] = x[i2][d] - x[i1][d] (for d=0,1,2)
|
|
double vb23[g_dim]; // displacement vector from atom i2 towards atom i3
|
|
// vb23[d] = x[i3][d] - x[i2][d] (for d=0,1,2)
|
|
double vb34[g_dim]; // displacement vector from atom i3 towards atom i4
|
|
// vb34[d] = x[i4][d] - x[i3][d] (for d=0,1,2)
|
|
|
|
// n123 & n234: These two unit vectors are normal to the planes
|
|
// defined by atoms 1,2,3 and 2,3,4.
|
|
double n123[g_dim]; //n123=vb23 x vb12 / |vb23 x vb12| ("x" is cross product)
|
|
double n234[g_dim]; //n234=vb23 x vb34 / |vb23 x vb34| ("x" is cross product)
|
|
|
|
double proj12on23[g_dim];
|
|
// proj12on23[d] = (vb23[d]/|vb23|) * dot3(vb12,vb23)/|vb12|*|vb23|
|
|
double proj34on23[g_dim];
|
|
// proj34on23[d] = (vb34[d]/|vb23|) * dot3(vb34,vb23)/|vb34|*|vb23|
|
|
double perp12on23[g_dim];
|
|
// perp12on23[d] = v12[d] - proj12on23[d]
|
|
double perp34on23[g_dim];
|
|
// perp34on23[d] = v34[d] - proj34on23[d]
|
|
|
|
double f1[3], f2[3], f3[3], f4[3];
|
|
|
|
for (int n = 0; n < ndihedrallist; n++) {
|
|
const int i1 = dihedrallist[n][0];
|
|
const int i2 = dihedrallist[n][1];
|
|
const int i3 = dihedrallist[n][2];
|
|
const int i4 = dihedrallist[n][3];
|
|
const int type = dihedrallist[n][4];
|
|
|
|
// ------ Step 1: Compute the dihedral angle "phi" ------
|
|
//
|
|
|
|
// get_phi() calculates the dihedral angle.
|
|
// This function also calculates the vectors:
|
|
// vb12, vb23, vb34, n123, and n234, which we will need later.
|
|
|
|
const double phi = get_phi(x[i1], x[i2], x[i3], x[i4], domain, vb12, vb23, vb34, n123, n234);
|
|
|
|
// ------ Step 2: Compute the gradient of phi with atomic position: ------
|
|
//
|
|
// Gradient variables:
|
|
//
|
|
// dphi_dx1, dphi_dx2, dphi_dx3, dphi_dx4 are the gradients of phi with
|
|
// respect to the atomic positions of atoms i1, i2, i3, i4, respectively.
|
|
// As an example, consider dphi_dx1. The d'th element is:
|
|
double dphi_dx1[g_dim]; // d phi
|
|
double dphi_dx2[g_dim]; // dphi_dx1[d] = ---------- (partial derivatives)
|
|
double dphi_dx3[g_dim]; // d x[i1][d]
|
|
double dphi_dx4[g_dim]; //where d=0,1,2 corresponds to x,y,z (if g_dim==3)
|
|
|
|
double dot123 = dot3(vb12, vb23);
|
|
double dot234 = dot3(vb23, vb34);
|
|
double L23sqr = dot3(vb23, vb23);
|
|
double L23 = sqrt(L23sqr); // (central bond length)
|
|
double inv_L23sqr = 0.0;
|
|
double inv_L23 = 0.0;
|
|
if (L23sqr != 0.0) {
|
|
inv_L23sqr = 1.0 / L23sqr;
|
|
inv_L23 = 1.0 / L23;
|
|
}
|
|
double neg_inv_L23 = -inv_L23;
|
|
double dot123_over_L23sqr = dot123 * inv_L23sqr;
|
|
double dot234_over_L23sqr = dot234 * inv_L23sqr;
|
|
|
|
for (int d = 0; d < g_dim; ++d) {
|
|
// See figure above for a visual definitions of these vectors:
|
|
proj12on23[d] = vb23[d] * dot123_over_L23sqr;
|
|
proj34on23[d] = vb23[d] * dot234_over_L23sqr;
|
|
perp12on23[d] = vb12[d] - proj12on23[d];
|
|
perp34on23[d] = vb34[d] - proj34on23[d];
|
|
}
|
|
|
|
// --- Compute the gradient vectors dphi/dx1 and dphi/dx4: ---
|
|
|
|
// These two gradients point in the direction of n123 and n234,
|
|
// and are scaled by the distances of atoms 1 and 4 from the central axis.
|
|
// Distance of atom 1 to central axis:
|
|
double perp12on23_len = sqrt(dot3(perp12on23, perp12on23));
|
|
// Distance of atom 4 to central axis:
|
|
double perp34on23_len = sqrt(dot3(perp34on23, perp34on23));
|
|
|
|
double inv_perp12on23 = 0.0;
|
|
if (perp12on23_len != 0.0) inv_perp12on23 = 1.0 / perp12on23_len;
|
|
double inv_perp34on23 = 0.0;
|
|
if (perp34on23_len != 0.0) inv_perp34on23 = 1.0 / perp34on23_len;
|
|
|
|
for (int d = 0; d < g_dim; ++d) {
|
|
dphi_dx1[d] = n123[d] * inv_perp12on23;
|
|
dphi_dx4[d] = n234[d] * inv_perp34on23;
|
|
}
|
|
|
|
// --- Compute the gradient vectors dphi/dx2 and dphi/dx3: ---
|
|
//
|
|
// This is more tricky because atoms 2 and 3 are shared by both planes
|
|
// 123 and 234 (the angle between which defines "phi"). Moving either
|
|
// one of these atoms effects both the 123 and 234 planes
|
|
// Both the 123 and 234 planes intersect with the plane perpendicular to the
|
|
// central bond axis (vb23). The two lines where these intersections occur
|
|
// will shift when you move either atom 2 or atom 3. The angle between
|
|
// these lines is the dihedral angle, phi. We can define four quantities:
|
|
// dphi123_dx2 is the change in "phi" due to the movement of the 123 plane
|
|
// ...as a result of moving atom 2.
|
|
// dphi234_dx2 is the change in "phi" due to the movement of the 234 plane
|
|
// ...as a result of moving atom 2.
|
|
// dphi123_dx3 is the change in "phi" due to the movement of the 123 plane
|
|
// ...as a result of moving atom 3.
|
|
// dphi234_dx3 is the change in "phi" due to the movement of the 234 plane
|
|
// ...as a result of moving atom 3.
|
|
|
|
double proj12on23_len = dot123 * inv_L23;
|
|
double proj34on23_len = dot234 * inv_L23;
|
|
// Interpretation:
|
|
//The magnitude of "proj12on23_len" is the length of the proj12on23 vector.
|
|
//The sign is positive if it points in the same direction as the central
|
|
//bond (vb23). Otherwise it is negative. The same goes for "proj34on23".
|
|
//(In the example figure in the comment above, both variables are positive.)
|
|
|
|
// The forumula used in the 8 lines below explained here:
|
|
// "supporting_information/doc/gradient_formula_explanation/"
|
|
double dphi123_dx2_coef = neg_inv_L23 * (L23 + proj12on23_len);
|
|
double dphi234_dx2_coef = inv_L23 * proj34on23_len;
|
|
|
|
double dphi234_dx3_coef = neg_inv_L23 * (L23 + proj34on23_len);
|
|
double dphi123_dx3_coef = inv_L23 * proj12on23_len;
|
|
|
|
for (int d = 0; d < g_dim; ++d) {
|
|
// Recall that the n123 and n234 plane normal vectors are proportional to
|
|
// the dphi/dx1 and dphi/dx2 gradients vectors
|
|
// It turns out we can save slightly more CPU cycles by expressing
|
|
// dphi/dx2 and dphi/dx3 as linear combinations of dphi/dx1 and dphi/dx2
|
|
// which we computed already (instead of n123 & n234).
|
|
dphi_dx2[d] = dphi123_dx2_coef * dphi_dx1[d] + dphi234_dx2_coef * dphi_dx4[d];
|
|
dphi_dx3[d] = dphi123_dx3_coef * dphi_dx1[d] + dphi234_dx3_coef * dphi_dx4[d];
|
|
}
|
|
|
|
const int idx = type2expression[type];
|
|
dihedralforce[idx].getVariableReference("phi") = phi;
|
|
double m_du_dphi = -dihedralforce[idx].evaluate();
|
|
|
|
// ----- Step 4: Calculate the force direction in real space -----
|
|
|
|
// chain rule:
|
|
// d U d U d phi
|
|
// -f = ----- = ----- * -----
|
|
// d x d phi d x
|
|
for (int d = 0; d < g_dim; ++d) {
|
|
f1[d] = m_du_dphi * dphi_dx1[d];
|
|
f2[d] = m_du_dphi * dphi_dx2[d];
|
|
f3[d] = m_du_dphi * dphi_dx3[d];
|
|
f4[d] = m_du_dphi * dphi_dx4[d];
|
|
}
|
|
|
|
// apply force to each of 4 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] += f2[0];
|
|
f[i2][1] += f2[1];
|
|
f[i2][2] += f2[2];
|
|
}
|
|
|
|
if (NEWTON_BOND || i3 < nlocal) {
|
|
f[i3][0] += f3[0];
|
|
f[i3][1] += f3[1];
|
|
f[i3][2] += f3[2];
|
|
}
|
|
|
|
if (NEWTON_BOND || i4 < nlocal) {
|
|
f[i4][0] += f4[0];
|
|
f[i4][1] += f4[1];
|
|
f[i4][2] += f4[2];
|
|
}
|
|
|
|
double edihedral = 0.0;
|
|
if (EFLAG) {
|
|
dihedralpot[idx].getVariableReference("phi") = phi;
|
|
edihedral = dihedralpot[idx].evaluate();
|
|
}
|
|
if (EVFLAG)
|
|
ev_tally(i1, i2, i3, i4, nlocal, NEWTON_BOND, edihedral, f1, f3, f4, -vb12[0], -vb12[1],
|
|
-vb12[2], vb23[0], vb23[1], vb23[2], vb34[0], vb34[1], vb34[2]);
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void DihedralLepton::allocate()
|
|
{
|
|
allocated = 1;
|
|
const int np1 = atom->ndihedraltypes + 1;
|
|
|
|
memory->create(type2expression, np1, "dihedral:type2expression");
|
|
memory->create(setflag, np1, "dihedral:setflag");
|
|
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
set coeffs for one or more types
|
|
------------------------------------------------------------------------- */
|
|
|
|
void DihedralLepton::coeff(int narg, char **arg)
|
|
{
|
|
if (narg != 2) error->all(FLERR, "Incorrect number of args for dihedral coefficients");
|
|
if (!allocated) allocate();
|
|
|
|
int ilo, ihi;
|
|
utils::bounds(FLERR, arg[0], 1, atom->ndihedraltypes, ilo, ihi, error);
|
|
|
|
// remove whitespace and quotes from expression string and then
|
|
// check if the expression can be parsed and evaluated without error
|
|
std::string exp_one = LeptonUtils::condense(arg[1]);
|
|
try {
|
|
auto parsed = Lepton::Parser::parse(LeptonUtils::substitute(exp_one, lmp));
|
|
auto dihedralpot = parsed.createCompiledExpression();
|
|
auto dihedralforce = parsed.differentiate("phi").createCompiledExpression();
|
|
dihedralpot.getVariableReference("phi") = 0.0;
|
|
dihedralforce.getVariableReference("phi") = 0.0;
|
|
dihedralforce.evaluate();
|
|
} catch (std::exception &e) {
|
|
error->all(FLERR, e.what());
|
|
}
|
|
|
|
std::size_t idx = 0;
|
|
for (const auto &exp : expressions) {
|
|
if (exp == exp_one) break;
|
|
++idx;
|
|
}
|
|
|
|
// if not found, add to list
|
|
if ((expressions.size() == 0) || (idx == expressions.size())) expressions.push_back(exp_one);
|
|
|
|
int count = 0;
|
|
for (int i = ilo; i <= ihi; i++) {
|
|
type2expression[i] = idx;
|
|
setflag[i] = 1;
|
|
count++;
|
|
}
|
|
|
|
if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients");
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
proc 0 writes out coeffs to restart file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void DihedralLepton::write_restart(FILE *fp)
|
|
{
|
|
fwrite(&type2expression[1], sizeof(int), atom->ndihedraltypes, fp);
|
|
|
|
int num = expressions.size();
|
|
int maxlen = 0;
|
|
for (const auto &exp : expressions) maxlen = MAX(maxlen, (int) exp.size());
|
|
++maxlen;
|
|
|
|
fwrite(&num, sizeof(int), 1, fp);
|
|
fwrite(&maxlen, sizeof(int), 1, fp);
|
|
for (const auto &exp : expressions) {
|
|
int n = exp.size() + 1;
|
|
fwrite(&n, sizeof(int), 1, fp);
|
|
fwrite(exp.c_str(), sizeof(char), n, fp);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
proc 0 reads coeffs from restart file, bcasts them
|
|
------------------------------------------------------------------------- */
|
|
|
|
void DihedralLepton::read_restart(FILE *fp)
|
|
{
|
|
allocate();
|
|
|
|
if (comm->me == 0) {
|
|
utils::sfread(FLERR, &type2expression[1], sizeof(int), atom->ndihedraltypes, fp, nullptr,
|
|
error);
|
|
}
|
|
MPI_Bcast(&type2expression[1], atom->ndihedraltypes, MPI_INT, 0, world);
|
|
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
|
|
|
|
int num, maxlen, len;
|
|
if (comm->me == 0) {
|
|
utils::sfread(FLERR, &num, sizeof(int), 1, fp, nullptr, error);
|
|
utils::sfread(FLERR, &maxlen, sizeof(int), 1, fp, nullptr, error);
|
|
}
|
|
MPI_Bcast(&num, 1, MPI_INT, 0, world);
|
|
MPI_Bcast(&maxlen, 1, MPI_INT, 0, world);
|
|
|
|
char *buf = new char[maxlen];
|
|
|
|
for (int i = 0; i < num; ++i) {
|
|
if (comm->me == 0) {
|
|
utils::sfread(FLERR, &len, sizeof(int), 1, fp, nullptr, error);
|
|
utils::sfread(FLERR, buf, sizeof(char), len, fp, nullptr, error);
|
|
}
|
|
MPI_Bcast(buf, maxlen, MPI_CHAR, 0, world);
|
|
expressions.emplace_back(buf);
|
|
}
|
|
|
|
delete[] buf;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
proc 0 writes to data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void DihedralLepton::write_data(FILE *fp)
|
|
{
|
|
for (int i = 1; i <= atom->ndihedraltypes; i++)
|
|
fprintf(fp, "%d %s\n", i, expressions[type2expression[i]].c_str());
|
|
}
|
|
|
|
// --------------------------------------------
|
|
// ------- Calculate the dihedral angle -------
|
|
// --------------------------------------------
|
|
|
|
double DihedralLepton::get_phi(double const *x1, //array holding x,y,z coords atom 1
|
|
double const *x2, // : : : : 2
|
|
double const *x3, // : : : : 3
|
|
double const *x4, // : : : : 4
|
|
Domain *domain, //<-periodic boundary information
|
|
// The following arrays are of doubles with g_dim elements.
|
|
// (g_dim is a constant known at compile time, usually 3).
|
|
// Their contents is calculated by this function.
|
|
// Space for these vectors must be allocated in advance.
|
|
// (This is not hidden internally because these vectors
|
|
// may be needed outside the function, later on.)
|
|
double *vb12, // will store x2-x1
|
|
double *vb23, // will store x3-x2
|
|
double *vb34, // will store x4-x3
|
|
double *n123, // will store normal to plane x1,x2,x3
|
|
double *n234) // will store normal to plane x2,x3,x4
|
|
const
|
|
{
|
|
for (int d = 0; d < g_dim; ++d) {
|
|
vb12[d] = x2[d] - x1[d]; // 1st bond
|
|
vb23[d] = x3[d] - x2[d]; // 2nd bond
|
|
vb34[d] = x4[d] - x3[d]; // 3rd bond
|
|
}
|
|
|
|
//Consider periodic boundary conditions:
|
|
domain->minimum_image(vb12[0], vb12[1], vb12[2]);
|
|
domain->minimum_image(vb23[0], vb23[1], vb23[2]);
|
|
domain->minimum_image(vb34[0], vb34[1], vb34[2]);
|
|
|
|
//--- Compute the normal to the planes formed by atoms 1,2,3 and 2,3,4 ---
|
|
|
|
cross3(vb23, vb12, n123); // <- n123=vb23 x vb12
|
|
cross3(vb23, vb34, n234); // <- n234=vb23 x vb34
|
|
|
|
norm3(n123);
|
|
norm3(n234);
|
|
|
|
double cos_phi = -dot3(n123, n234);
|
|
|
|
if (cos_phi > 1.0)
|
|
cos_phi = 1.0;
|
|
else if (cos_phi < -1.0)
|
|
cos_phi = -1.0;
|
|
|
|
double phi = acos(cos_phi);
|
|
|
|
if (dot3(n123, vb34) > 0.0) {
|
|
phi = -phi; //(Note: Negative dihedral angles are possible only in 3-D.)
|
|
phi += MY_2PI; //<- This ensures phi is always in the range 0 to 2*PI
|
|
}
|
|
return phi;
|
|
}
|